2008 publications citing ADF
First author: Zhang, Zhenkui, The electronic properties and electron affinity of the hydrogenated nanodiamonds with surface reconstructions, APPLIED SURFACE SCIENCE, 255, 2623, (2008)
Abstract: By means of ab initio density functional theory calculations, we investigated the influence of the surface reconstructions on the geometries, stability, electronic structures and the electron affinity of the hydrogenated nanodiamonds, which is achieved by the dehydrogenation from neighboring hydrogenated sites. Our results show that the modifications of the geometries can tune the HOMO-LUMO gaps. The spatial variation of the LUMOs depends rather on the C-H bond length than on the respective surface sites and the causes are analyzed. For the hydrogen coverage decreases within the range of the surface carbons remaining hydrogenated, the values of the negative electron affinity show lowering trend, and can be explained by the increase of the surface C-H dipoles. These results may provide meaningful suggestions for designing the nanoscale diamond-based optoelectronic and electron-emission devices.
First author: Fan, Hongjun, Understanding and Predicting Distorted T- versus Y-Geometries for Neutral Chromous Complexes Supported by a Sterically Encumbering beta-Diketiminate Ligand, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130, 17351, (2008)
Abstract: A series of three-coordinate Cr(II) complexes sharing the common molecular fragment “(nacnac)Cr” (nacnac = [ArNC((t)Bu)](2)CH, Ar = 2,6-(i)Pr(2)C(6)H(3)) were prepared via salt metathesis with the dimer [(nacnac)Cr(mu-Cl)](2). Single-crystal X-ray diffraction studies revealed that the complexes (nacnac)Cr(L) (L = CH(2)(t)BU, CH(3), CH(2)CH(3), SiH{2,4,6-Me(3)C(6)H(2)}(2), O{2,6-(i)Pr(2)C(6)H(3)}, N{CH(3)}(2)) represent a rare class of mononuclear, neutral chromium complexes with a three-coordinate high-spin chromous metal center. Depending on the nature of the third ligand, L(-), these complexes can adopt either distorted T-shaped or Y-shaped coordination geometries, Density functional theory calculations and molecular orbital analyses in combination with a detailed molecular fragment energy decomposition were used to establish an intuitive concept of the key electronic structure patterns that determine the coordination geometry of preference. The frontier orbitals of the (nacnac)Cr(II) fragment direct pi-donating ligands to adopt Y-shaped geometry, whereas ligands that are primarily sigma-donors prefer T-shaped coordination. The relationship between electronics at the metal center and coordination geometry was extended to include the putative neutral three-coordinate high-spin complexes of Sc(II) and Mn(II), which are predicted to both adopt Y-shaped geometry.
First author: Ess, Daniel H., Transition State Energy Decomposition Study of Acetate-Assisted and Internal Electrophilic Substitution C-H Bond Activation by (acac-O,O)(2)Ir(X) Complexes (X = CH3COO, OH), ORGANOMETALLICS, 27, 6440, (2008)
Abstract: Chelate-assisted and internal electrophilic substitution type transition states were studied using a DFT-based energy decomposition method. Interaction energies for benzene and methane C-H bond activation by (acac-O,O)(2)Ir(X) complexes (X = CH3COO and OH) were evaluated using the absolutely localized molecular orbital energy decomposition analysis (ALMO-EDA). A ratio of similar to 1.5:1 for forward to reverse charge-transfer between (acac-O,O)(2)Ir(X) and benzene or methane transition state fragments confirms “ambiphilic” bonding, the result of an interplay between the electrophilic iridium center and the internal base component. This analysis also revealed that polarization effects account for a significant amount of transition state stabilization. The energy penalty to deform reactants into their transition state geometry, distortion energy, was also used to understand the large activation energy difference between six-membered and four-membered acetate-assisted transition states and help explain why these complexes do not activate the methane C-H bond.
First author: Bonnington, Kevin J., Oxidative Addition of S-S Bonds to Dimethylplatinum(II) Complexes: Evidence for a Binuclear Mechanism, ORGANOMETALLICS, 27, 6521, (2008)
Abstract: Oxidative addition of the S-S bond of S(2)py(2) (py = 2-pyridyl) to [Pt2Me4(mu-SMe2)(2)] occurs with displacement of Me2S to give [PtMe2(kappa(2)-S,N-Spy)(2)], 1. Oxidative addition of S2Ar2 (Ar = 2-pyridyl or Ph) to [PtMe2(NN)], NN = 2,2′-bipyridine or 1,10-phenanthroline, gives initially the binuclear Pt(III) complexes [{PtMe2(kappa(1)-S-SAr)(NN)}(2)], which react further with S2Ar2 to give [PtMe2(kappa(1)-S-SAr)(2)(NN)] and then, when Ar = 2-pyridyl, to give an equilibrium with free NN and complex 1. Evidence is presented that the S-S Oxidative addition to [Pt2Me4(mu-SMe2)(2)] occurs by a concerted mechanism whereas the reactions with [PtMe2(NN)] to give the binuclear complexes [{PtMe2(kappa(1)-S-SAr)(NN)}(2)] occur by a polar nonconcerted mechanism, involving a loosely bonded dimer [PtMe2(NN)](2).
First author: Stoyanov, Stanislav R., Multifunctional metal-doped carbon nanocapsules, JOURNAL OF CHEMICAL PHYSICS, 129, 6521, (2008)
Abstract: We present an ab initio study of carbon fullerenes, such as C(20), C(36), C(56), C(60), and C(68), that are substitutionally doped with transition metals coordinated to several nitrogen atoms. These capsules with porphyrinlike metal sites have remarkable electronic and spin polarizations. Additional doping by boron increases their highest occupied molecular orbital-lowest unoccupied molecular orbital gap, stabilizes their electronic structure, and causes their ground states to have higher spin multiplicity, where the spin density is spread over the capsule. These capsules could be applied in molecular electronics, catalysis, light harvesting, and nanomechanics.
First author: Ghosh, Abhik, Mapping the d-d Excited-State Manifolds of Transition Metal beta-Diiminato-Imido Complexes. Comparison of Density Functional Theory and CASPT2 Energetics, JOURNAL OF PHYSICAL CHEMISTRY A, 112, 12792, (2008)
Abstract: Trigonal-planar, middle transition metal diiminato-imido complexes do not exhibit high-spin states, as might be naively expected on the basis of their low coordination numbers. Instead, the known Fe(III), Co(III), and Ni(III) complexes exhibit S = (3)/(2), S = 0, and S = (1)/(2), ground states, respectively. Kohn-Sham DFT calculations have provided a basic molecular orbital picture of these compounds as well as a qualitative rationale for the observed spin states. Reported herein are ab initio multiconfiguration second-order perturbation theory (CASPT2) calculations, which provide a relatively detailed picture of the d-d excited-state manifolds of these complexes. Thus, for a C-2v Fe-III(diiminato)(NPh) model complex, two near-degenerate states (B-4(2) and B-4(1)) compete as contenders for the ground state. Moreover, the high-spin sextet, two additional quartets and even a low-spin doublet all occur at <0.5 eV, relative to the ground state. For the Co(III) system, although CASPT2 reproduces an S = 0 ground state, as observed experimentally for a related complex, the calculations also predict two exceedingly low-energy triplet states; there are, however, no other particularly low-energy d-d excited states. In contrast to the Fe(III) and Co(III) cases, the Ni(III) complex has a clearly nondegenerate B-2(2) ground state. The CASPT2 energetics provide benchmarks against which we can evaluate the performance of several common DFT methods. Although none of the functionals examined perform entirely satisfactorily, the B3LYP hybrid functional provides the best overall spin-state energetics.
First author: Pierrefixe, Simon C. A. H., Aromaticity and Antiaromaticity in 4-, 6-, 8-, and 10-Membered Conjugated Hydrocarbon Rings, JOURNAL OF PHYSICAL CHEMISTRY A, 112, 12816, (2008)
Abstract: Recently, we presented a molecular orbital (MO) model of aromaticity that explains, in terms of simple orbital-overlap arguments, why benzene (C6H6) has a regular structure with delocalized double bonds whereas the geometry of 1,3-cyclobutadiene (C4H4) is distorted with localized double bonds. Here, we show that the same model and the same type of orbital-overlap arguments also account for the irregular and regular structures of 1,3,5,7-cyclooctatetraene (C8H8) and 1,3,5,7,9-cyclodecapentaene (C10H10), respectively. Our MO model is based on accurate Kohn-Sham DFr analyses of the bonding in C4H4, C6H6, C8H8, and C10H10 and how the bonding mechanism is affected if these molecules undergo geometrical deformations between regular, delocalized ring structures and distorted ones with localized double bonds. The propensity of the 7 electrons is always to localize the double bonds, against the delocalizing force of the a electrons. Importantly, we show that the pi electrons nevertheless determine the localization (in C4H4 and C8H8) or delocalization (in C6H6 and C10H10) of the double bonds.
First author: Groenhof, Andre R., Alkane Hydroxylation by Peroxy Acids: A Comparison with the Cytochrome P450 Hydroxylation, JOURNAL OF PHYSICAL CHEMISTRY A, 112, 12855, (2008)
Abstract: Alkane hydroxylation by peroxy acids proceeds by a synchronous nonconcerted peroxy oxygen insertion into the C-H bond according to density functional theory. A comparable reaction sequence, initiated by homolytic peroxy bond cleavage, can be formulated for the alkane hydroxylation by the cytochrome P450 hydroperoxoheme Compound 0. This hydroxylation reaction proceeds by a two-step process because the formed reactive intermediate, Compound II, is significantly stabilized.
First author: Gayatri, Gaddamanugu, Further Shortening of the C-C Single Bond in Substituted Tetrahedranyl Tetrahedrane Systems: An Energy Decomposition Analysis, JOURNAL OF PHYSICAL CHEMISTRY A, 112, 12919, (2008)
Abstract: The computational study explores the electronic fine tuning of the exocyclic C-C single bond length in tetrahedranyl tetrahedrane as a function of various substituents. The factors which determine the bond lengths and bond strengths are examined by using the EDA method.
First author: Alvarado-Soto, Leonor, Spin-orbit effects on the aromaticity of the Re3Cl9 and Re3Br9 clusters, CHEMICAL PHYSICS LETTERS, 467, 94, (2008)
Abstract: Here, we report density functional calculations of the electronic structure and nuclear independent chemical shift (NICS) values of the Re3Cl9 and Re3Br9 clusters including scalar and spin-orbit relativistic effects (ADF + ZORA + SO). Our calculations have shown that both the clusters exhibit aromaticity and that spin-orbit effects decreases aromaticity due to the fact that the 5d(3/2) spinors are mostly occupied and are more contracted than the scalar 5d orbitals.
First author: Bugarcic, Tijana, The Contrasting Chemistry and Cancer Cell Cytotoxicity of Bipyridine and Bipyridinediol Ruthenium(II) Arene Complexes, INORGANIC CHEMISTRY, 47, 11470, (2008)
Abstract: The synthesis and characterization of ruthenium(II) arene complexes [(eta(6)-arene)Ru(N,N)Cl](0/+), where N,N = 2,2′-bipyridine (bipy), 2,2′-bipyridine-3,3′-diol (bipy(OH)(2)) or deprotonated 2,2′-bipyridine-3,3′-diol (bipy(OH)O) as N,N-chelating ligand, arene = benzene (bz), indan (ind), biphenyl (bip), rho-terphenyl (rho-terp), tetrahydronaphthalene (thn), tetrahydroanthracene (tha) or dihydroanthracene (dha), are reported, including the X-ray crystal structures of [(eta(6)-tha)Ru(bipy)Cl][PF6] (1), [(eta(6)-tha)Ru(bipy(OH)O)Cl] (2) and [(eta(6)-ind)Ru(bipy(OH)(2))Cl][PF6] (8). Complexes 1 and 2 exibit CH (arene)/pi (bipy or bipy(OH)O) interactions. In the X-ray structure of protonated complex 8, the pyridine rings are twisted (by 17.31 degrees). In aqueous solution (pH = 2-10), only deprotonated (bipy(OH)0) forms are present. Hydrolysis of the complexes was relatively fast in aqueous solution (t1/2 = 4-15 min, 310 K). When the arene is biphenyl, initial aquation of the complexes is followed by partial arene loss. Complexes with arene = tha, thn, dha, ind and rho-terp, and deprotonated bipyridinediol (bipy(OH)O) as chelating ligands, exhibited significant cytotoxicity toward A2780 human ovarian and A549 human lung cancer cells. Complexes [(eta(6)-bip)Ru(bipy(OH)O)Cl] (7) and [(eta(6)-bz)Ru(bipy(OH)O)Cl] (5) exhibited moderate cytotoxicity toward A2780 cells, but were inactive toward A549 cells. These activity data can be contrasted with those of the parent bipyridine complex [(eta(6)-tha)Ru(bipy)Cl][PF6] (1) which is inactive toward both A2780 ovarian and A549 lung cell lines. DFT calculations suggested that hydroxylation and methylation of the bipy ligand have little effect on the charge on Ru. The active complex [(eta(6)-tha)Ru(bipy(OH)O)Cl] (2) binds strongly to 9-ethyl-guanine (9-EtG). The X-ray crystal structure of the adduct [(eta(6)-tha)Ru(bipy(OH)O)(9-EtG-N7)][PF6] shows intramolecular CH (arene)/pi (bipy(OH)O) interactions and DFT calculations suggested that these are more stable than arene/9-EtG pi-pi interactions. However [(eta(6)-ind)Ru(bipy(OH)(2))Cl][PF6] (8) and [(eta(6-)ind)Ru(bipy)Cl][PF6] (16) bind only weakly to DNA. DNA may therefore not be the major target for complexes studied here.
First author: Fan, Jing, Circular Dichroism of Trigonal Dihedral Chromium(III) Complexes: A Theoretical Study based on Open-Shell Time-Dependent Density Functional Theory, INORGANIC CHEMISTRY, 47, 11656, (2008)
Abstract: Spin-unrestricted time-dependent density functional theory has been applied to the electronic circular dichroism spectra of Cr(III) complexes with an open-shell ground state, that is, [Cr(L-L)(3)](n+) with L-L = en(ethylenediamine), acac(acetylacetonate), ox(oxalate), mal(malonate), and Thiox(dithiooxalate). The simulated CD spectra are analyzed in details and compared with experimental data, as well as previous calculations on similar Co(III) complexes where available. The theoretical results serve as a tool for elucidating the absolute configuration of similar complexes, by pointing to transitions for which the sign of the rotatory strength can be used as fingerprint for one particular configuration.
First author: Nikolakis, Vladimiros A., Vanadium(V) Compounds with the Bis-(hydroxylamino)-1,3,5-triazine Ligand, H(2)bihyat: Synthetic, Structural, and Physical Studies of [(V2O3)-O-V(bihyat)(2)] and of the Enhanced Hydrolytic Stability Species cis-[(VO2)-O-V(bihyat)](-), INORGANIC CHEMISTRY, 47, 11698, (2008)
Abstract: Reaction of the ligand 2,6-bis[hydroxy(methyl)amino]-4-morpholino-1,3,5-triazine (H(2)bihyat) with (NaVO3)-O-V in aqueous solution followed by addition of either Ph4PCl or C(NH2)(3)Cl, respectively, gave the mononuclear vanadium(V) compounds Ph4P[(VO2)-O-V(bihyat)] center dot 1.5H(2)O (1) and C(NH2)(3)[(VO2)-O-V(bihyat)] (2). Treatment of (VOSO4)-O-IV center dot 5H(2)O with the ligand H(2)bihyat in methyl alcohol under specific conditions gave the oxo-bridged dimer [(V2O2)-O-V(mu(2)-O)(bihyat)(2)] (3). The structures for 1 and 3 were determined by X-ray crystallography and indicate that these compounds have distorted square-pyramidal arrangement around vanadium. The ligand bihyat(2-) is bonded to vanadium atom in a tridentate fashion at the pyridine-like nitrogen atom and the two deprotonated hydroxylamino oxygen atoms. The high electron density of the triazine ring nitrogen atoms, which results from the resonative contribution of electrons of exocyclic nitrogen atoms (Scheme 4), leads to very strong V-N bonds. The cis-[(VO2)-O-V(bihyat)](-) species exhibits high hydrolytic stability in aqueous solution over a wide pH range, 3.3-11.0, as it was evidenced by H-1 and V-51 NMR spectroscopy and potentiometry. The high affinity of the H(2)bihyat ligand for the (VO2+)-O-V unit, its tridentate character, as well as its small size, paves the way for potential applications in medicine, analysis, and catalysis for the C(NH2)(3)[(VO2)-O-V(bihyat)] compound. The molecular structures, vibrational and electronic spectra, and the energetics of the metal-ligand interaction for compounds 1 and 3 have been studied by means of density functional calculations.
First author: Santi, Saverio, Tunable electronic coupling in iron-chromium mixed-valence ions of methylated Cp-indene ligands, JOURNAL OF ORGANOMETALLIC CHEMISTRY, 693, 3797, (2008)
Abstract: A series of heterobimetallic mu(6)-[(ferrocenyl) indene]-Cr(CO)(3) complexes differing for the position of the ferrocenyl group, 1-(ferrocenyl) indene and 2-(ferrocenyl) indene, and the degree of indene methylation (tetramethyl- and hexamethyl-) have been prepared and studied with the aim to stabilise the mono- and dications generated by chemical and electrochemical oxidation, and at same time to tune the metal-metal electronic coupling in the mixed- valence cations. The magnitude of electronic delocalisation and spin density in the cations have been monitored by means of optical techniques (UV-Vis, near-IR, mid-IR) and EPR spectroscopy. The results have been rationalised in the framework of Marcus-Hush theory and at quantum chemistry level by DFT and TD-DFT methods, establishing that a metal-to-metal electronic coupling occurs the magnitude of which depends on the degree of indene methylation.
First author: van Eis, Maurice J., Tricarbonylchromium complexes of [5]- and [6]metacyclophane: an experimental and theoretical study, TETRAHEDRON, 64, 11641, (2008)
Abstract: Tricarbonylchromium complexes of [5]- and [6]metacyclophane were prepared and the interaction between the Cr(CO)(3) tripod and the cyclophane fragment was evaluated by both an experimental and a theoretical Study. The tricarbonylchromium complex of [5]metacyclophane Could only be obtained in Solution and was characterized by its H-1 NMR spectrum. The tricarbonylchromium complex of [6]metacyclophane was isolated and an X-ray crystal structure was obtained, which reveals that no significant geometric changes Occur upon coordination of the severely distorted aromatic ring. Computations on the tricarbonylchromium complexes of m-xylene, [5]- and [6]metacyclophane furthermore demonstrate that the corresponding complexation energy is remarkably unaffected by the degree of distortion of the aromatic ring. Theoretical analyses of the above model systems as well as complexes of planar and artificially deformed benzene with Cr(CO)(3) Show that this is primarily the result of two counteracting effects: (I) a stabilization due to an increased back-donation from the metal center to the benzene and (ii) a destabilization clue to the increasing strain in the aromatic ring.
First author: Kan Yu-He, Theoretical Investigation on Electronic Spectra of Fullerene Polypyridyl Ruthenium(II) Complexes by Density Functional Theory, ACTA CHIMICA SINICA, 66, 2585, (2008)
Abstract: Theoretical investigation on two derivatives of [Ru(bpy)(n)-C-60](2+) (bpy: 2,2-bipyridine; n=2, 3) has been performed by density functional theory. At TZP level, the compositions of frontier orbitals have been calculated in order to discuss the influence on C-60 by metal and ligands. Taking into account solvent effects, the absorption spectra were investigated by time-dependent density functional theory (TDDFT) with LB94 and SAOP functional to correct local density approximation. The results show that inclusion of the solvent leads to important change of absorption spectra, and solvation induces a blue shift to some extent. The spectra calculated in the presence of the solvent are in good agreement with the experiment. Low energy transitions were found to originate mainly from the mixed transitions containing the metal, whereas the higher energy band arises from C-60 and ligand charge transfer transitions.
First author: Burkholder, Eric, Unusual hydrothermal synthesis of a heteroaromatic macrocyclic complex, POLYHEDRON,27, 3700, (2008)
Abstract: Hydrothermal treatment of 2,3-bis(2′,6″-bipyridyl)quinoxaline, molybdenum trioxide, cupric acetate and water unexpectedly forms the Cu(II) complex of a planar, macrocyclic 2-acyl-6,2′-bipyridyl dimer, imbedded within a copper benzotrizolate-octamolybtate matrix. X-ray crystallographic characterization of this material. and scalar relativistic ZORA DFT modeling of the complex dication are presented.
First author: Krapp, Andreas, Carbon Complexes as Electronically and Sterically Tunable Analogues of Carbon Monoxide in Coordination Chemistry, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130, 16646, (2008)
Abstract: Quantum chemical calculations at DFT (BP86) and ab initio levels (CCSD(T)) have been carried out for transition metal carbon complexes [MX(2)(PR(3))(2)(C)] with various combinations of M = Fe, Ru, Os, X = F, Cl, Br, I, and R = H, Me, Ph, Cyc. Calculations have also been performed for [RuCl(2)(PMe(3))(NHC)(C)] and [RuCl(2)(NHC)(2)(C)] where NHC = N-heterocyclic carbene and for [M(Por)(C)] (M = Fe, Ru, Os; Por = porphyrin). The properties of the carbon complexes as donor ligands were studied by calculating the geometries and bond dissociation energies of the Lewis acid-base adducts with the Lewis acids M(CO)5 (M = Cr, Mo, W), PdCl(2)SMe(2), BH(3), BCl(3), and Fe(2)(CO)(8). The latter species are compared to the analogous CO complexes. The nature of the donor-acceptor interactions between the Lewis acids LA and carbon complexes [TM]C-LA is compared to the bonding in OC-LA. The bonding analysis was carried out with charge- and energy-partitioning methods. The bond strength and the donor-acceptor properties of metal carbon complexes closely resemble those of CO, and thus carbon complexes may be considered as electronically tuneable analogues of carbon monoxide. Similar properties are also calculated for the porphyrin carbon complexes 10MC, which bind more strongly and are slightly stronger pi acceptors than the [(X(2)(R)(2)M(C)] species. The carbon complexes [(X(2)(R)(2)M(C)] are slightly weaker pi acceptors than CO, and thus they tend to have slightly weaker bonds than CO in group-6 donor-acceptor complexes. The calculations suggest that bond energies of carbon complexes as ligands with d(10) transition metals are larger than those of CO. The theoretical results let it seem possible that adducts with more than one carbon complex as ligands may be synthesized and that even homoleptic complexes may be prepared.
First author: Jiang, Xuan, Dendritic Molecular Switch: Chiral Folding and Helicity Inversion, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130, 16812, (2008)
Abstract: Appropriately designed chemical architectures can fold to adopt well-defined secondary structures without the need for structural motifs of biological origin. We have designed tris(N-salicylideneaniline)based hyperbranched molecules that spontaneously collapse to compact three-blade propeller geometry of either (P)- or (M)-handedness. For a homologous series of compounds, a direct correlation was established between the absolute screw sense, either (P)- or (M)-, of this helical folding and the absolute configuration, either (R)- or (S)-, of the chiral alcohol groups introducing local asymmetric bias to the conformationally restricted molecular backbone. (1)H NMR and CD spectroscopic studies provided significant insights into structural folding and unfolding of these chiral molecules in solution, which proceed via reversible assembly and disassembly of the G-symmetric hydrogen-bonding network. Notably, solvents profoundly influenced this dynamic process. A strong correlation between the solvent donor number (DN) or solvent basicity (SB) parameters and the change in the Cotton effects pointed toward specific O-H center dot center dot center dot solvent interactions that drive structural unfolding and eventual refolding to apparently opposite helicity. This unusual chirality inversion process could also be induced by installation of chemical protecting groups that simulate specific solvent-solute interactions. Removal of this covalent mimic of the solvent shell restored the original screw sense of the parent molecule, thus establishing the feasibility of covalently triggered helicity inversion as a new mode of operation for chiroptical molecular switches.
First author: Niehaus, T. A., Efficient evaluation of the Fourier transform over products of Slater-type orbitals on different centers, JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL, 41, 16812, (2008)
Abstract: Using the shift-operator technique, a compact formula for the Fourier transform of a product of two Slater-type orbitals located on different atomic centers is derived. The result is valid for arbitrary quantum numbers and was found to be numerically stable for a wide range of geometrical parameters and momenta. Details of the implementation are presented together with benchmark data for representative integrals. We also discuss the assets and drawbacks of alternative algorithms available and analyze the numerical efficiency of the new scheme.
First author: Kozyra, P., From Electron Density Flow Towards Activation: Benzene Interacting with Cu(I) and Ag(I) Sites in ZSM-5. DFT Modeling, CATALYSIS LETTERS, 126, 241, (2008)
Abstract: Cu(I) and Ag(I) sites in ZSM-5 and their interaction with adsorbed benzene are studied by DFT cluster modeling aided with NOCV analysis of charge transfer processes. The interplay between donation and back donation from the cation to the ad-molecule, reinforced by the framework environment correlates with benzene activation shown also by the red shift in calculated and measured IR frequencies. Copper sites have better activation ability due to its stronger interaction with the framework, serving as electron reservoir, and better match between d orbitals and pi orbitals of benzene.
First author: Gupta, Ujjwal, Effect of Charge and Composition on the Structural Fluxionality and Stability of Nine Atom Tin-Bismuth Zintl Analogues, INORGANIC CHEMISTRY, 47, 10953, (2008)
Abstract: Synergistic studies of bismuth doped tin clusters combining photoelectron spectra with first principles theoretical investigations establish that highly charged Zintl ions, observed in the condensed phase, can be stabilized as isolated gas phase clusters through atomic substitution that preserves the overall electron count but reduces the net charge and thereby avoids instability because of coulomb repulsion, Mass spectrometry studies reveal that Sn8Bi-, Sn7Bi2-, and Sn6Bi3- exhibit higher abundances than neighboring species, and photoelectron spectroscopy show that all of these heteroatomic gas phase Zintl analogues (GPZAs) have high adiabatic electron detachment energies. Sn6Bi3- is found to be a particularly stable cluster, having a large highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO) gap. Theoretical calculations demonstrate that the Sn6Bi3- cluster is isoelectronic with the well know Sn-9(-4) Zintl ion; however, the fluxionality reported for Sn-9(-4) is suppressed by substituting Sn atoms with Bi atoms. Thus, while the electronic stability of the clusters is dominated by electron count, the size and position of the atoms affects the dynamics of the cluster as well. Substitution with Bi enlarges the cage compared with Sn-9(-4) making it favorable for endohedral doping, findings which suggest that these cages may find use for building blocks of cluster assembled materials.
First author: Kowol, Christian R., An Electrochemical Study of Antineoplastic Gallium, Iron and Ruthenium Complexes with Redox Noninnocent alpha-N-Heterocyclic Chalcogensemicarbazones, INORGANIC CHEMISTRY, 47, 11032, (2008)
Abstract: The electrochemical properties of a series of alpha-N-heterocyclic chalcogensemicarbazones (HL), namely, thiosemicarbazones, selenosemicarbazones, and semicarbazones, and their gallium(III), iron(III), and ruthenium(Ill) complexes with the general formula [ML2][Y] (M = Ga, Fe or Ru; Y = PF6-, NO3-, or FeCl4-) were studied by cyclic voltammetry. The novel compounds were characterized by elemental analysis, a number of spectroscopic methods (NMR, UV-vis, IR), mass spectrometry and by X-ray crystallography. All complexes show several, mostly reversible, redox waves attributable to the reduction of the noninnocent chalcogensemicarbazone ligands at lower potentials (<-0.4 V vs NHE) than the metal-centered iron or ruthenium redox waves (>0 V vs NHE) in organic electrolyte solutions. The cyclic voltammograms of the gallium complexes display at least two consecutive reversible one-electron reduction waves. These reductions are shifted by similar to 0.6 V to lower potentials in the corresponding iron and ruthenium complexes. The electrochemical, chemical, and spectroscopic data indicate that the ligand-centered reduction takes place at the CH3C=N double bond. Quantum chemical calculations on the geometric and electronic structures of 2-acetylpyridine N-4,N-4-dimethylthiosemicarbazone (HLB), the corresponding metal complexes [Ga(L-B)(2)](+) and [FeII(L-B)(2)], and the one-electron reduction product for each of these species support the assignment of the reduction site and elucidate the observed order of the ligand-centered redox potentials, E-1/2([Fe-II(L)(2)]) < E-1/2(HL) < E-1/2([Ga(L)(2)](+)). The influence of water on the redox potentials of the complexes is reported and the physiological relevance of the electrochemical data for cytotoxicity as well as for ribonucleotide reductase inhibitory capacity are discussed.
First author: Klein, Axel, Halide Ligands-More Than Just sigma-Donors? A Structural and Spectroscopic Study of Homologous Organonickel Complexes, INORGANIC CHEMISTRY, 47, 11324, (2008)
Abstract: The isoleptic organonickel complexes [(bpy)Ni(Mes)X] (bpy = 2,2′-bipyridine; Mes = 2,4,6-trimethylphenyl; X = F, Cl, Br, or l, and for comparison X = OMe and SCN) have been investigated by multiple spectroscopic means. Their structures have been determined in part by single-crystal X-ray diffraction, the full series by extended X-ray absorption fine structure. The long-wavelength charge transfer absorptions (mainly metal-to-ligand charge transfer) obtain contributions from the mesityl coligand but are almost invariable upon variation of X. UV-vis spectroscopy allowed investigation of the solvolysis reaction [(bpy)Ni(Mes)X] + Solv reversible arrow [(bpy)Ni(Mes)(Solv)](+) + X-, which occurs very fast for X = I (k = 0.176(4) M-1 s(-1)) or Br but very slow for X = Cl (k = 5.18(5) x 10(-5) M-1 cm(-1)) or F. Quantum chemical (density functional theory) calculations on the geometry, electronic states, and electronic transitions (time-dependent density functional theory) are very helpful for detailed insight into the role the X coligands play in these complexes. The combination of methods reveals rather strong, highly covalent Ni-X bonds for all halide coligands but marginal pi-donation.
First author: Swart, Marcel, Accurate Spin-State Energies for Iron Complexes, JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 4, 2057, (2008)
Abstract: A critical assessment of the OPBE functional is made for its performance for the geometries and spin-states of iron complexes. In particular, we have examined its performance for the geometry of first-row transition-metal (di)halides (MnX(2), FeX(2), COX(2), NiX(2), CuX, X=[F, CI]), whose results were previously [J. Chem. Theory Comput 2006, 2, 1282] found to be representative for a much larger and more diverse set of 32 metal complexes. For investigating the performance for spin ground-states of iron complexes, we examined a number of small iron complexes (Fe(II)Cl(4)(2-), Fe(III)Cl(4)(1-), Fe(II)Cl(6)(4-), Fe(III)Cl(6)(3-), Fe(II)CN(6)(4-), Fe(III)CN(6)(3-), Fe(VI)O(4)(2-), Fe(III)(NH(3))(6)(3+)), benchmark systems (Fe(II)(H(2)O)(6)(2+), Fe(II)(NH(3))(6)(2+), Fe(II)(bpy)(3)(2+)), and several challenging iron complexes such as the Fe(II)(phen)(2)(NCS)(2) spin-crossover compound, the monopyridylmethylamine Fe(II)(amp)(2)Cl(2) and dipyridylmethylamine Fe(II)(dpa)(2)(2+), and the bis complex of Fe(III)-1,4,7-triazacyclononane (Fe(III)((9)aneN(3))(2)(3+). In all these cases OPBE gives excellent results.
First author: Shearer, Jason, Both Met(109) and Met(112) are utilized for Cu(II) coordination by the amyloidogenic fragment of the human prion protein at physiological pH, JOURNAL OF INORGANIC BIOCHEMISTRY, 102, 2103, (2008)
Abstract: The prion protein is a ubiquitous neuronal membrane protein. Misfolding of the prion protein has been implicated in transmissible spongiform encephalopathies (prion diseases). It has been demonstrated that the human prion protein (PrP) is capable of coordinating at least five Cu(II) ions under physiological conditions; four copper binding sites can be found in the octarepeat domain between residues 61 and 91, while another copper binding site can be found in the unstructured “amyloidogenic” domain between residues 91 and 126 PrP(91-126). Herein we expand upon a previous Study 1]. Shearer, P. Soh, Inorg. Chem. 46 (2007) 710-719] where we demonstrated that the physiologically relevant high affinity Cu(II) coordination site within PrP(91-126) is found between residues 106 and 114. It was shown that Cu(II) is contained within a square planar (N/O)(3)S Coordination environment with one His imidazole ligand (H(111)) and one Met thioether ligand (either M(109) or M(112)). The identity of the Met thioether ligand was not identified in that study. In this study we perform a detailed investigation of the Cu(II) coordination environment within the PrP fragment containing residues 106-114 (PrP(106-114)) involving optical, Xray absorption, EPR, and fluorescence spectroscopies in conjunction with electronic Structure calculations. By using derivatives of PrP(106-114) with systematic Met -> Ile “Mutations” we show that the Cu(II) coordination environment within PrP(106-114) is actually comprised of a mixture of two major species; one Cu(II)(N/O)(3)S center with the M(109) thioether coordinated to Cu(II) and another Cu(II)(N/O)(3)S center with the M(112) thioether coordinated to Cu(II). Furthermore, deletion of one or more Met residues from the primary sequence of Pi-P(106-114) both reduces the Cu(II) affinity of the peptide by two to seven fold. and renders the resulting Cu(II) metallopeptides redox inactive. The biological implications of these findings are discussed.
First author: Romann, T., In situ infrared spectroscopic characterization of a bismuth-ethanol interface,ELECTROCHIMICA ACTA, 53, 8166, (2008)
Abstract: The structure and composition of substances adsorbed to a Bi(001)electrode in ethanolic LiClO4 solution were studied by cyclic voltammetry. electrochemical impedance and infrared reflectance spectroscopic methods. An analysis of the results demonstrates that at negative surface charge densities, there are no chemisorbed particles at the bismuth-ethanol solution interface. In solutions containing dissolved oxygen, an insoluble surface compound was detected at positive surface charge densities (E > -0.38V vs. Ag vertical bar AgCl). In a behavior very different from that of the platinum-electrolyte interface, no ethanol oxidation products were detected on the Bi electrode. Absorption peaks measured in the infrared spectra are mainly caused by the variation of solvated perchlorate anion adsorption resulting from changes in surface charge density with the variation of the bismuth electrode’s potential.
First author: Pal, Shrinwantu, The role of H bonding and dipole-dipole interactions on the electrical polarizations and charge mobilities in linear arrays of urea, thiourea, and their derivatives, JOURNAL OF CHEMICAL PHYSICS, 129, 8166, (2008)
Abstract: Computational studies using density functional theory are carried out on linear chains of urea, N,N-‘-dimethyl urea and N,N,N-‘,N-‘-tetramethyl urea, and their sulfur analogs, viz., thiourea, N,N-‘-dimethyl thiourea and N,N,N-‘,N-‘-tetramethyl thiourea with varying chain length, to understand the effect of hydrogen bonding and dipolar interactions on the optoelectronic response properties of such linear aggregates. While molecules of urea, N,N-‘-dimethyl urea, and the corresponding sulfur analogs, thiourea, N,N-‘-dimethyl thiourea, are stabilized in linear chains by hydrogen bonding, the molecules of N,N,N-‘,N-‘-tetramethyl urea and N,N,N-‘,N-‘-tetramethyl thiourea in the linear chains are stabilized by purely dipolar interactions. To understand the contributions of electrostatic and polarization effects on such intermolecular interactions, we study the effect of an external electric field on the intermolecular interactions in these systems. We find that the strength of hydrogen bonding increases while that of dipolar interactions decreases with increase in external field strength. We account for such findings by decomposing the interaction terms into charge-transfer and electrostatic interaction terms. The effects of these interactions on the linear and nonlinear optical properties together with transport properties such as carrier mobilities are estimated to understand their suitability for device applications.
First author: Pietrzyk, Piotr, DFT Analysis of g and C-13 Hyperfine Coupling Tensors for Model Ni-I(CO)(n)L-m (n=1-4, L = H2O, OH-) Complexes Epitomizing Surface Nickel(I) Carbonyls, JOURNAL OF PHYSICAL CHEMISTRY A, 112, 12208, (2008)
Abstract: Relativistic calculations within the spin-orbit mean-field (SOMF) approximation, the zero-order regular approximation (ZORA), and the scalar relativistic method based on the Pauli Hamiltonian were performed for the prediction and interpretation of the electronic g tensor and C-13 hyperfine tensor for a set of model polycarbonyl nickel(I) complexes with aqua or hydroxy coligands. They exhibit extensive similarities with heterogeneous [Ni-I(CO)(n)]-surface complexes produced upon adsorption of carbon monoxide on Ni(I)- ions grafted on silica or inside the zeolite channels. Benchmark calculations showing the influence of the exchange-orrelation functional on the g tensor were carried out for well-defined nickel(l) complexes of known structure. On this basis, the SOMF-B3LYP scheme was chosen for calculations of the g tensor, and the obtained results were in satisfactory agreement with literature EPR data found for the [(NiCO)-C-I)(n)]/SiO2 system. The calculated g and A(C-13) tensors allowed polycarborryl complexes of various stereochemistries to be distinguished. The nature of the Delta(gii) shifts was assessed in terms of the molecular orbital contributions due to the magnetic-field-induced couplings and their structure sensitivity. The noncoincidence of g and C-13 hyperfine principal axes and their orientation with respect to the molecular framework was also examined. The ability of DFT calculations to follow consistently variations of the EPR parameters induced by stereochemical changes around the Ni(I) center provides an invaluable reference for the interpretation of experimental results.
First author: Ryeng, Hege, DFT at Its Best: Metal- versus Ligand-Centered Reduction in Nickel Hydroporphyrins,JOURNAL OF PHYSICAL CHEMISTRY B, 112, 15158, (2008)
Abstract: DFT calculations, using the PW91, OLYP, and B3LYP functionals, have provided some of the first estimates of the relative energies of the Ni(I) and Ni(II) ligand anion radical states of hydroporphyrin complexes. Although the three functionals chosen sometimes yield discordant results, the results of this study are essentially functional-independent. For isobacteriochlorin derivatives, our calculations predict that the Ni(I) state may be favored by 0.5 eV or more, relative to the ligand anion radical state. For other hydroporphyrins, however, electrochemical studies indicate a much finer balance, which may be tipped one way or the other, depending on the substituents. DFT calculations nicely capture these rather subtle substituent effects. In particular, our results support and extend Bruckner and co-workers’ finding (from electrochemical studies) that the most rigid, strongly ruffled nickel chlorins prefer to reduce on the macrocycle, whereas their more flexible congeners undergo metal-centered reduction.
First author: Fateeva, Alexandra, Synthesis and conformational studies of chiral meso-(alpha, beta-unsaturated)-porphyrins, TETRAHEDRON, 64, 10874, (2008)
Abstract: We describe a method to improve the yield and the kinetics of the difficult syntheses of alpha, beta-unsaturatecl porphyrins, which enabled us to obtain a new chiral porphyrin derived from (S)-(-)-perillaldehyde in a 6% yield. Variable temperature NMR experiments on the free base, the zinc(II) and the nickel(II) complexes showed that two distinct and consecutive dynamic processes linked with the meso substituents rotation occurred. These processes can be analyzed as an evolution of the conformer composition upon temperature change. Higher values are found for the free energies of rotation of the substituent (measured by variable temperature H-1 NMR) compared to those of other equivalent porphyrins like meso-tetraphenyl porphyrin or meso-tetracyclohexyl porphyrin.
First author: Koo, In Sun, Theoretical Study of P-31 NMR Chemical Shifts for Organophosphorus Esters, Their Anions and O,O-Dimethylthiophosphorate Anion with Metal Complexes, BULLETIN OF THE KOREAN CHEMICAL SOCIETY, 29, 2252, (2008)
Abstract: A initio and density functional theory (DFT) studies along with gauge-including atomic orbitals (GIAO) have been carried out on P-31 NMR chemical shifts for a series of organophosphorus esters, replacing (RO)P=O by (RS)P=O, (RO)P=S and (RS)P=S functionalities, and for O,O-dimethylthiophosphorate ion (PA(-)) complexed with metal ions (Ag+, Hg2+). A initio and DFT results are in good agreement with experimental P-31 NMR chemical shifts. It is shown that the major contribution of 31 P NMR chemical shifts derives from the total paramagnetic tensor and variation of d orbital population at P atom by d(pi)-p(pi) bond back-donation.
First author: Thomas, Kolle Ekaney, Copper beta-Octakis(trifluoromethyl)corroles: New Paradigms for Ligand Substituent Effects in Transition Metal Complexes, INORGANIC CHEMISTRY, 47, 10469, (2008)
Abstract: The reaction of copper beta-octabromo-meso-triarylcorrole derivatives with methyl 2,2-difluoro-2-(fluorosulfonyl)acetate has provided four beta-octakis(trifluoromethyl)corrole complexes, Cu[(CF3)(8)T(p-XP)C] (X = F, H, Me, OMe), in moderate yields. The new complexes present a conglomeration of remarkable substituent effects, both steric and electronic. DFT (OLYP/TZP) geometry optimization of Cu[(CF3)(8)TPC] (i.e., X = H) indicates a sterically hindered, strongly saddled geometry, with numerous short F center dot center dot center dot F nonbonded contacts of 2.5-2.9 angstrom and certain beta carbons displaced by over 1.5 angstrom relative to the mean corrole plane. The CF3 groups generally appear as quartets in the F-19 NMR spectra, with unexpectedly large (5)J(FF) coupling constants of about 14 Hz, apparently a manifestation of the highly crowded structure. The eight CF3 groups together exert a powerful influence on the redox potentials of the copper corrole core. Thus, the E-1/2ox of Cu[(CF3)(8)TPC](1.4 V vs saturated calomel electrode) is a full half of a volt above that of Cu(TPC) (0.9 V) and a quarter of a volt above that of Cu(Br8TPC) (1.14 V). Intriguingly, the beta CF3 groups also greatly intensify the influence of the meso aryl substituents on the redox potentials, relative to the other Cu[Y8T(p-XP)C] series, where Y = H, F, and Br. The Cu[(CF3)(8)T(p-XP)C] complexes also exhibit the most red-shifted optical spectra of any series of metallocorroles synthesized to date. Thus, between Cu(TPC) and Cu[(CF3)(8)T(p-MeO-P)C], the Soret maximum shifts by nearly 100 nm. The observed red-shifts are attributed in part to charge-transfer transitions of the Soret region and in part to the extreme nonplanar distortions.
First author: Chval, Zdenek, The trans effect in square-planar platinum(II) complexes – A density functional study,JOURNAL OF COMPUTATIONAL CHEMISTRY, 29, 2370, (2008)
Abstract: The mechanism of substitution water exchange reactions in square planar trans-Pt[(NH3)(2)T(H2O)](n+) complexes is studied (T=H2O, NH3, OH-, F-, Cl-, Br, H2S, CH3S-, SCN-, CN-, PH3, CO, CH3-, H-, C2H4). The trans effect is explained in terms of sigma-donation and pi-back-donation whose relative strengths are quantified by the changes of electron occupations of 5d platinum atomic orbitals. The a-donation strength is linearly correlated with the Pt-H2O (leaving ligand) bond length (trans influence). The kinetic trans effect strength correlates proportionally with the a-donation ability of the trans-ligand except the ligands with strong pi-back-donation ability that stabilizes transition state structure. The a-donation ability of the ligand is dependent on the sigma-donation strength of the ligand in the trans position. Therefore the trans effect caused by sigma-donation can be understood as a competition between the trans-ligands for the opportunity to donate electron density to the central Pt(II) atom. The influence of the trans effect on the reaction mechanism is also shown. For ligands with a very strong or-donation (e.g. CH3- and H-), the substitution proceeds by a dissociative interchange (I-d) mechanism. Ligands with strong pi-back donation ability (e.g. C2H4) stabilize the pentacoordinated intermediate and the substitution proceeds by a two step associative mechanism. For ligands with weak sigma-donation and pi-back-donation abilities, the highest activation barriers have to be overcome and substitutions can be described by an associative interchange (I-a) mechanism. The results are supported by the energy decomposition and the natural orbital analysis.
First author: Herrmann, Carmen, QM/MM vibrational mode tracking, JOURNAL OF COMPUTATIONAL CHEMISTRY, 29, 2460, (2008)
Abstract: Vibrational spectroscopy is a powerful tool to investigate the structure and dynamics of biomolecules. When small subsystems of large molecules such as active centers of enzymes are studied, quantum chemical calculations based on quantum mechanics/molecular mechanics (QM/MM) coupling schemes are a valuable means to interpret the spectra. The goal of this work is a methodological pilot study on how to selectively and thus efficiently extract certain vibrational information for extended molecular systems described by QM/MM methods. This is achieved by an extension of the mode tracking algorithm and a comparison with the partial Hessian diagonalization approach. After validating the methodology for the CO stretching vibration of 2-butanone and a delocalized CO stretch in acetylacetone, the stretching and bending modes of the CO ligand in CO myoglobin are tracked. Such systems represent an ideal application for mode tracking, because only a few strongly localized vibrations are sought for, while the large remainder of the molecule is of interest only as far as it affects these local vibrations. This influence is treated exactly by mode tracking.
First author: Ziegler, Tom, A revised electronic Hessian for approximate time-dependent density functional theory,JOURNAL OF CHEMICAL PHYSICS, 129, 2460, (2008)
Abstract: Time-dependent density functional theory (TD-DFT) at the generalized gradient level of approximation (GGA) has shown systematic errors in the calculated excitation energies. This is especially the case for energies representing electron transitions between two separated regions of space or between orbitals of different spatial extents. It will be shown that these limitations can be attributed to the electronic ground state Hessian G(GGA). Specifically, we shall demonstrate that the Hessian G(GGA) can be used to describe changes in energy due to small perturbations of the electron density (Delta rho), but it should not be applied to one-electron excitations involving the density rearrangement (Delta rho) of a full electron charge. This is in contrast to Hartree-Fock theory where G(HF) has a trust region that is accurate for both small perturbations and one-electron excitations. The large trust radius of G(HF) can be traced back to the complete cancellation of Coulomb and exchange terms in Hartree-Fock (HF) theory representing self-interaction (complete self-interaction cancellation, CSIC). On the other hand, it is shown that the small trust radius for G(GGA) can be attributed to the fact that CSIC is assumed for GGA in the derivation of G(GGA) although GGA (and many other approximate DFT schemes) exhibits incomplete self-interaction cancellation (ISIC). It is further shown that one can derive a new matrix G(R-DFT) with the same trust region as G(HF) by taking terms due to ISIC properly into account. Further, with TD-DFT based on G(R-DFT), energies for state-to-state transitions represented by a one-electron excitation (psi(i)->psi(a)) are approximately calculated as Delta E-ai. Here Delta E-ai is the energy difference between the ground state Kohn-Sham Slater determinant and the energy of a Kohn-Sham Slater determinant where psi(i) has been replaced by psi(a). We make use of the new Hessian in two numerical applications involving charge-transfer excitations. It is concluded that higher than second order response theory (involving ISIC terms) must be used in approximate TD-DFT, in order to describe charge-transfer excitations.
First author: Wodrich, Matthew D., Empirical Corrections to Density Functional Theory Highlight the Importance of Nonbonded Intramolecular Interactions in Alkanes, JOURNAL OF PHYSICAL CHEMISTRY A, 112, 11495, (2008)
Abstract: Energies of alkanes computed with many popular and even newer density functionals are flawed by systematic errors, which become considerable with larger molecules. The same energies, however, are well described by post-Hartree-Fock methods. Similar DFT shortcomings are well documented for cases involving descriptions of intermolecular van der Waals complexes. One solution to the density functional problem is the addition of an empirical correction term, which more accurately models the known R-6 dependence of van der Waals energies. Here, we present the first empirical correction to DFT parametrized to reproduce experimental energies associated with intramolecular interactions in alkanes. Our training set used only three reactions involving simple linear and branched alkanes and provides a remarkable improvement over conventional DFT methods and empirical corrections optimized for intermolecular interactions. In contrast to many standard density functionals, the intramolecular empirical correction correctly predicts the lowest energy alkane isomer in addition to performing satisfactorily for describing the interaction energies of intermolecular complexes.
First author: Petro, Benjamin J., Photoelectron spectroscopy of dithiolatodiironhexacarbonyl models for the active site of [Fe-Fe] hydrogenases: Insight into the reorganization energy of the “rotated” structure in the enzyme, JOURNAL OF MOLECULAR STRUCTURE, 890, 281, (2008)
Abstract: Synthetic analogs, mu-(RS)(2)Fe(2)(CO)(6), of the active site of [Fe-Fe] hydrogenases do not have the semi-bridged CO and “rotated” structure found in the enzyme. However, recent studies have shown that cations of dithiolatodiiron complexes adopt this rotated structure. This paper reports the use of photoelectron spectroscopy in combination with density functional theory calculations to show that two previously reported complexes: mu-(1,2-benzenedithiolato)Fe(2)(CO)(6) and mu-(1,3-propanedithiolato)Fe(2)(CO)(6) and two new complexes: mu-(2,3-pyridinodithiolato)Fe(2)(CO)(6), and mu-(norbornane-2-exo,3-exo-dithiolato)Fe(2)(CO)(6) favor the “rotated” structure in their corresponding cations. Furthermore, these methods provide a measure of the reorganization energy between the “rotated” and “unrotated” structures in the gas phase. The results provide insight on the entatic state of the dithiolatodiiron site in the enzyme, in which the protein controls the structure of the active site. This structure influences the redox energy and reorganization energy enabling fast electron transfer.
First author: Fee, James A., Toward a Chemical Mechanism of Proton Pumping by the B-Type Cytochrome c Oxidases: Application of Density Functional Theory to Cytochrome ba(3) of Thermus thermophilus, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130, 15002, (2008)
Abstract: A mechanism for proton pumping by the B-type cytochrome c oxidises is presented in which one proton is pumped in conjunction with the weakly exergonic, two-electron reduction of Fe-bound O-2 to the Fe-Cu bridging peroxodianion and three protons are pumped in conjunction with the highly exergonic, two-electron reduction of Fe(III)-O–O–Cu(II) to form water and the active oxidized enzyme, Fe(III)–OH,Cu(II). The scheme is based on the active-site structure of cytochrome ba(3) from Thermus thermophilus, which is considered to be both necessary and sufficient for coupled O-2 reduction and proton pumping when appropriate gates are in place (not included in the model). Fourteen detailed structures obtained from density functional theory (DFT) geometry optimization are presented that are reasonably thought to occur during the four-electron reduction of O-2. Each proton-pumping step takes place when a proton resides on the imidazole ring of I-His376 and the large active-site cluster has a net charge of +1 due to an uncompensated, positive charge formally associated with CUB. Four types of DFT were applied to determine the energy of each intermediate, and standard thermochemical approaches were used to obtain the reaction free energies for each step in the catalytic cycle. This application of DFT generally conforms with previously suggested criteria for a valid model (Siegbahn, P. E. M.; Blomberg, M. A. R. Chem. Rev. 2000, 100, 421-437) and shows how the chemistry of O-2 reduction in the heme a(3)-CUB dinuclear center can be harnessed to generate an electrochemical proton gradient across the lipid bilayer.
First author: Younker, Jarod M., Structural Analysis of the Mn(IV)/Fe(III) Cofactor of Chlamydia trachomatis Ribonucleotide Reductase by Extended X-ray Absorption Fine Structure Spectroscopy and Density Functional Theory Calculations, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130, 15022, (2008)
Abstract: The class Ic ribonucleotide reductase from Chlamydia trachomatis (Ct) uses a stable Mn(IV)/Fe(III) cofactor to initiate nucleotide reduction by a free-radical mechanism. Extended X-ray absorption fine structure (EXAFS) spectroscopy and density functional theory (DFT) calculations are used to postulate a structure for this cofactor. Fe and Mn K-edge EXAFS data yield an intermetallic distance of similar to 2.92 angstrom. The Mn data also suggest the presence of a short 1.74 angstrom Mn-O bond. These metrics are compared to the results of DFT calculations on 12 cofactor models derived from the crystal structure of the inactive Fe(2)(III/III) form of the protein. Models are differentiated by the protonation states of their bridging and terminal OH(X) ligands as well as the location of the Mn(IV) ion (site 1 or 2). The models that agree best with experimental observation feature a mu-1,3-carboxylate bridge (E120), terminal solvent (H(2)O/OH) to site 1, one mu-O bridge, and one mu-OH bridge. The site-placement of the metal ions cannot be discerned from the available data.
First author: Green, Jennifer C., Synthetic and Computational Studies of Thiocarbonyl/sigma-Organyl Coupling Reactions,ORGANOMETALLICS, 27, 5548, (2008)
Abstract: The reactions of a range of coordinatively unsaturated sigma-organyl thiocarbony] complexes with 1,4,7-trithiacyclononane ([9]aneS(3)) have been investigated, leading in some but not all cases to migratory insertive coupling of thiocarbonyl and sigma-organyl ligands. Thus, under ambient conditions, the reaction of [RuR-Cl(CS)(PPh(3))(2)] (R = C(CO(2)Me)=CHCO(2)Me, C(C C-CPh)=CHPh, C(6)H(5)) with [9]aneS(3) provides sigma-organyl complexes [RuR(CS)(PPh(3))([9]aneS(3))](+). On heating, the species [Ru(C(6)H(5))(CS)(PPh(3))[9]aneS(3))](+) converts to the thiobenzoyl complex [Ru(eta(2)-SCPh)(PPh(3))([9]aneS(3))](+). Similarly the silyl complex [RuCl(SiMe(2)OEt)-(CS)(PPh(3))(2)] with [9]aneS3 provides [Ru(SiMe(2)OEt)(CS)(PPh(3))([9]aneS(3))](+). However, the styryl and stilbenyl complexes [Ru(CR=CHPh)Cl(CS)(PPh(3))(2)] (R = H, Ph) under similar conditions provide dihapto thioacyl derivatives [Ru(eta(2)-SCCR=CHPh)(PPh(3))([9]aneS(3)](+). The osmium species [Os(CH=CHC(6)H(4)Me-4)Cl(CS)-(BTD)(PPh(3))(2)] (BTD = 2,1,3-benzothiadiazole), however, yields only the nonmigrated product [Os(CH=CHC(6)H(4)Me-4)(CS)(PPh(3))([9]aneS(3))](+). Migratory insertion is not induced by other sulfur donor ligands, e.g., CY(3)PCS(2)(Cy = cyclohexyl) and Na[S(2)CNMe(2)], which provide the complexes [Ru(CH=CH(2))(S(2)CPCy(3))-(CS)(PPh(3))(2)](+) and [Ru(CH=CHPh)(S(2)CNMe(2))(CS)(PPh(3))(2)], respectively. The reactivity of different ligands (R) toward thiocarbonyl migratory insertion in [Ru(R)(CS)(PPh(3))([9]aneS(3)](+) was analyzed through density functional theory. The calculated barriers agree qualitatively with experimental observations. In order to determine the electronic effect of substituents on the migrating ligand, a series of hypothetical systems with phenyl ligands varying only in the para-substituent was considered. A general trend that electron-releasing substituents on the migrating ligand promote reaction was observed. Through symmetry-adapted fragment orbital analysis, this phenomenon is determined to correlate well with the energy of the highest occupied,pi-orbital of the ligand.
First author: Jaszewski, Adrian R., Time-Dependent DFT Studies of Metal Core-Electron Excitations in Mn Complexes,JOURNAL OF PHYSICAL CHEMISTRY A, 112, 11223, (2008)
Abstract: Time-dependent density functional theory (TDDFT) has been applied to study core excitations from Is and 2p Mn orbitals in a series of manganese complexes with oxygen and nitrogen donor ligands. The effect of basis set and functional on the excitation energy was evaluated in detail for one complex, Mn(acaC)(2) center dot (H(2)O)(2). The results obtained for a range of compounds, namely, [Mn(Im)(6)]Cl(2), Mn(CH(3)COO)(2)center dot 4H(2)O, Mn(acaC)(3), Mn(SALADHP)(2) and [Mn(SALPN)O](2), show good consistency with the data from X-ray absorption spectroscopy (XAS), confirming the relation between the Mn K-edge energy and the oxidation state of the Mn atom. The energies predicted for 2p core excitations show a dependence on the metal oxidation state very similar to that determined experimentally by 1s2p resonant inelastic X-ray scattering (RIXS) studies for Mn(acac)(2)center dot(H(2)O)(2), Mn(acac)(3), and Mn(sal)(2)(bipy). The reliability of the K-edge energies obtained in the present study indicates that TDDFT can be used in determining the oxidation states of Mn atoms in different computational models of the manganese cluster of photosystem II (PSII).
First author: Takahata, Yuji, Inductive and resonance effects based on core-electron binding energy shift,INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 108, 2326, (2008)
Abstract: It was shown that core-electron binding energy shift (Delta CEBE) could be used as a criterion of inductive (and resonant) effect at each ring carbon atom of substituted cyclohexanes (and benzenes). CEBEs were calculated using density-functional theory with the scheme Delta E-KS (PW86-PW91)/TZP//HF/6-31G*. The inductive effect thus calculated correlate highly with the Taft inductive effect (sigma(1)). The inductive effect in a substituted benzene can be well approximated by that determined in a substituted cyclohexane. Resonant effect was defined as the difference between Delta CEBE of a substituted benzene and Delta CEBE of a substituted cyclohexane. The resonance effect thus defined at para atom in substituted benzenes correlates fairly well with Taft (experimental) resonance effect (sigma(R)), very highly with Taft (theoretical) resonance effect (sigma(R,) (theory)) of literature.
First author: Sarkar, Saikat, An attempt towards coordination supramolecularity from Mn(II), Ni(II) and Cd(II) with a new hexadentate [N4O2] symmetrical Schiff base ligand: Syntheses, crystal structures, electrical conductivity and optical properties, POLYHEDRON, 27, 3359, (2008)
Abstract: To explore the influence of non-covalent weak force interactions, mainly exerted by carboxylic groups, on the formation of supramolecular architectures of transition metal complexes and their electrical conduction processes, a new symmetrical [N4O2] hexadentate Schiff base ligand, 1,8-N-bis(3-carboxy)disalicylidene-3,6-diazaoctane-1,8-diamine, abbreviated to H(4)fsatrien, and its complexes of Ni(II), Cd(II) and Mn(II) have been synthesized using in situ condensation of the ligand components in the presence of metal ions. The complexes were structurally characterized by elemental analyses, IR, UV-Vis, NMR. ESR, molar conductivity and magnetic measurements. The crystal structures of all the complexes have been determined by a single crystal X-ray diffraction study. The 1-D, 2-D and 3-D networks of the complexes are formed by pi-pi stacking, C-H…pi interactions and mono or bifurcated H-bonding. The electronic structures of the complexes have been examined using the DFT method. Solid-state properties (e.g. electrical conductivity at different temperatures and optical properties) of the Ni(II) and Mn(II) complexes have also been studied and, depending on the temperature, the conductivity of the complexes is found to be insulating and semiconducting (intrinsic and extrinsic) in nature. The optical band gap (E-gd) of complexes (1) and (3) is found to be 2.57 and 2.30 eV, respectively.
First author: Huang, Deguang, Crystallographic, Electrochemical, and Electronic Structure Studies of the Mononuclear Complexes of Au(I)/(II)/(III) with [9]aneS(2)O ([9]aneS(2)O=1-oxa-4,7-dithiacyclononane), INORGANIC CHEMISTRY, 47, 9919, (2008)
Abstract: To explore the influence of non-covalent weak force interactions, mainly exerted by carboxylic groups, on the formation of supramolecular architectures of transition metal complexes and their electrical conduction processes, a new symmetrical [N4O2] hexadentate Schiff base ligand, 1,8-N-bis(3-carboxy)disalicylidene-3,6-diazaoctane-1,8-diamine, abbreviated to H(4)fsatrien, and its complexes of Ni(II), Cd(II) and Mn(II) have been synthesized using in situ condensation of the ligand components in the presence of metal ions. The complexes were structurally characterized by elemental analyses, IR, UV-Vis, NMR. ESR, molar conductivity and magnetic measurements. The crystal structures of all the complexes have been determined by a single crystal X-ray diffraction study. The 1-D, 2-D and 3-D networks of the complexes are formed by pi-pi stacking, C-H…pi interactions and mono or bifurcated H-bonding. The electronic structures of the complexes have been examined using the DFT method. Solid-state properties (e.g. electrical conductivity at different temperatures and optical properties) of the Ni(II) and Mn(II) complexes have also been studied and, depending on the temperature, the conductivity of the complexes is found to be insulating and semiconducting (intrinsic and extrinsic) in nature. The optical band gap (E-gd) of complexes (1) and (3) is found to be 2.57 and 2.30 eV, respectively.
First author: Jacobsen, Heiko, Computational Study of Iron Bis(dithiolene) Complexes: Redox Non-Innocent Ligands and Antiferromagnetic Coupling, INORGANIC CHEMISTRY, 47, 10037, (2008)
Abstract: The molecular and electronic structure of monomeric ([Fe(S2C2H2)(2)](z), [Fe(S2C2(C6H4-p-OCH3)(2))(2)](z)) and dimeric ([{Fe(S2C2H2)(2))(2)](z), iron bis(dithiolene) complexes, and of their phosphine adducts ([(PH3)Fe(S2C2H2)(2)](z), [(P(C6H5)(3))Fe(S2C2H2)(2)](z), [(PH3)Fe(S2C2(C6H4-p-OCH3)(2))(2)](z), carrying various charges (z = 0, 1 -, 2-), have been investigated by density functional theory (DFT). Net total spin polarization values S of zero, two, and four have been considered for all neutral model compounds and their dianions, whereas all monoanions have been examined with net total spin polarization values S of one, three, and five. The DFT calculations utilized the pure functional BP86, as well as the hybrid functionals B3LYP and B3LYP*. For the monomers, the calculations reveal the presence of redox non-innocent dithiolene ligands and antiferromagnetic coupling between the ligands and the metal center. For the dimers, complexes with antiferromagnetically coupled iron centers have been found to represent structures of low energy, if not lowest energy structures. The spin-coupling constant of [{Fe(S2C2H2)(2)}(2)](2-) is calculated as J = -230 cm(-1). On the basis of the computational results, a model for reversible, electrochemically controlled binding and release of phosphine ligands to iron bis(dithiolene) complexes is proposed. Only BP86 and B3LYP* results, but not those of B3LYP calculations, are in qualitative agreement with experimental findings. BP86 calculations provide the best quantitative match in comparison with the experiment.
First author: Hinderberger, Dariush, Coordination and binding geometry of methyl-coenzyme M in the red1m state of methyl-coenzyme M reductase, JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY, 13, 1275, (2008)
Abstract: Methane formation in methanogenic Archaea is catalyzed by methyl-coenzyme M reductase (MCR) and takes place via the reduction of methyl-coenzyme M (CH(3)-S-CoM) with coenzyme B (HS-CoB) to methane and the heterodisulfide CoM-S-S-CoB. MCR harbors the nickel porphyrinoid coenzyme F(430) as a prosthetic group, which has to be in the Ni(I) oxidation state for the enzyme to be active. To date no intermediates in the catalytic cycle of MCR(red1) (red for reduced Ni) have been identified. Here, we report a detailed characterization of MCR(red1m) (“m” for methyl-coenzyme M), which is the complex of MCRred1a (“a” for absence of substrate) with CH3-S-CoM. Using continuous-wave and pulse electron paramagnetic resonance spectroscopy in combination with selective isotope labeling ((13)C and (2)H) of CH(3)-S-CoM, it is shown that CH(3)-S-CoM binds in the active site of MCR such that its thioether sulfur is weakly coordinated to the Ni(I) of F(430). The complex is stable until the addition of the second substrate, HS-CoB. Results from EPR spectroscopy, along with quantum mechanical calculations, are used to characterize the electronic and geometric structure of this complex, which can be regarded as the first intermediate in the catalytic mechanism.
First author: Thomas, Reji, Charge density analysis of two proton transfer complexes: Understanding hydrogen bonding and determination of in-crystal dipole moments, JOURNAL OF CHEMICAL SCIENCES, 120, 613, (2008)
Abstract: An experimental charge density study has been carried out on proton-transfer complexes exhibiting nonlinear optical (NLO) properties-melaminium tartrate monohydrate and l-asparaginium picrate employing high-resolution X-ray diffraction at 100 K. Both the complexes crystallize in non-centric space group P2(1) and the structures exhibit interesting patterns of N-HaEuro broken vertical bar O and O-HaEuro broken vertical bar O hydrogen bonding. Experimental determination of the dipole moment (A mu) for the asymmetric unit reveals that for both the crystals, there is a large cooperative enhancement in the crystalline A mu arising essentially due to hydrogen bond mediated charge transfer between the melaminium ion and the l-tartrate in one case, between the l-asparaginium ion and the picrate in the other complex. We have additionally performed theoretical calculations at the density functional theory (DFT) level to understand the origin of enhancement of the dipole moments in the two systems.
First author: Santhanamoorthi, N., Electron Charge Transfer in Linear and Cyclic Structures of Polypeptides, JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 5, 2264, (2008)
Abstract: Density functional theory has been used to investigate the intramolecular charge transfer, hole and electron, in linear and cyclic structures of [L-Ala-L-Val (AV)](3) and [L-Val-L-Ala(VA)](3) based on the Tight binding Hamiltonian approach. The linear and cyclic structures of (AV)(3) and (VA)(3) have been optimized at B3LYP/6-311 G(d,p) level of theory. After the geometry optimization, the fragment calculations have been performed in order to calculate the values of the charge transfer integrals, spatial overlap integrals and site-energies involved in the transport of both positive and negative charges through the peptide bonds of polypeptide. The calculations show that the conductivity property in peptides varies considerably with conformations of linear or cyclic structures and intramolecular interactions like H-bonding.
First author: Ducere, Jean-Marie, Quantifying the Donor-Acceptor Properties of Carbon Monoxide and Its Carbo-mer Using ELF Analysis, ORGANOMETALLICS, 27, 5263, (2008)
Abstract: The coordinating properties to nickel of CO and its carbo-mer C3O are compared on the basis of computational studies of Ni(CO)(4) and Ni(C3O)(CO)(3). The Ni-C3O bond is predicted to be stronger than the corresponding Ni-CO bond. Electron localization function (ELF) and atoms-in-molecules (AIM) analyses are used to estimate the donation and back-donation contributions to the net charge transfer involved in the corresponding nickel complexes of CO and C3O. The sigma-donating and pi-accepting properties for C3O toward Ni(CO)(3) are slightly stronger than for its CO parent. In both cases, however, pi-back-donation is the major electron transfer process.
First author: Cossairt, Brandi M., Phosphaalkenes as Long-Lived Phosphorus Cluster Surface Functional Groups: Intramolecular P=C Addition to a Niobium-Supported P-7 Cage, INORGANIC CHEMISTRY, 47, 9363, (2008)
Abstract: The diniobium octaphosphorus complex (P-8)[Nb(OC[(2)Ad]Mes)(3)](2) (1) (Ad = adamantylidene, Mes = 2,4,6-Me3C6H2) contains a reactive niobium phosphinidene moiety that can be exploited for metathetical scission of the Nb=P bond. When 1 is treated with aryl ketones, loss of ONb(OC[(2)Ad]Mes)(3)(OEt2) (2) is observed along with concomitant formation of the corresponding phosphaalkene (RC6H4)(2)C=PP7Nb(OC[(2)Ad]Mes)(3) (3- R). Complexes 3-R rearrange to incorporate the (RC6H4)(2)C=P unit into the phosphorus cage, thereby generating a saturated organo-phosphorus cluster complexed to the niobium tris-enolate platform, (RC6H4)(2)CP8Nb(OC[(2)Ad]Mes)(3) (4-R). The structure of one such rearranged cluster 4-H, as determined by X-ray crystallography, is briefly discussed. An Eyring analysis of the first-order rearrangement of 3-H to 4-H gives activation parameters of Delta H-double dagger = 16.7 kcal/mol and Delta S-double dagger = -20.4 eu. A Hammett analysis of the phosphaalkene rearrangement, 3-R to 4-R, with substitution varying at the para positions of the aryl rings, reveals a linear relationship between the a values and the rearrangement rate constants. A concerted, asynchronous mechanism for the least-motion rearrangement of 3-H to 4-H is presented. When 1 is treated with alkyl ketones, similar loss of 2 and formation of the corresponding phosphaalkene is observed; however, the phosphaalkene complexes have considerably greater stability and are readily isolated.
First author: Llusar, Rosa, Trinuclear Mo3S7 Clusters Coordinated to Dithiolate or Diselenolate Ligands and Their Use in the Preparation of Magnetic Single Component Molecular Conductors, INORGANIC CHEMISTRY, 47, 9400, (2008)
Abstract: A general route for the preparation of a series of dianionic Mo3S7 cluster complexes bearing dithiolate or diselenolate ligands, namely, [Mo3S7L3](2-) (where L = tfd (bis(trifluoromethyl)-1,2-dithiolate) (4(2-)), bdt (1,2-benzenedithiolate) (5(2-)), dmid (1,3-dithia-2-one-4,5-dithiolate) (6(2-)), and dsit (1,3-dithia-2-thione-4,5-diselenolate) (7(2-))) is reported by direct reaction Of [Mo3S7Br6](2-) and (n-Bu)(2)Sn(dithiolate). The redox properties, molecular structure, and electronic structure (BP86/VTZP) of the 4(2-) to 7(2-) clusters have also been investigated. The HOMO orbital in all complexes is delocalized over the ligand and the Mo3S7 cluster core. Ligand contributions to the HOMO range from 61.67% for 4(2-) to 82.07% for 7(2-), which would allow fine-tuning of the electronic and magnetic properties. These dianionic clusters present small energy gaps between the HOMO and HOMO-1 orbitals (0.277-0.104 eV). Complexes 6(2-) and 7(2-) are oxidized to the neutral state to afford microcrystalline or amorphous fine powders that exhibit semiconducting behavior and present antiferromagnetic exchange interactions. These compounds are new examples of the still rare single-component conductors based on cluster magnetic units.
First author: Illa, Ona, Understanding the pi-facial diastereoselectivity in the addition of chiral diaminophosphino(silyl)carbenes to activated olefins, TETRAHEDRON-ASYMMETRY, 19, 2353, (2008)
Abstract: The synthesis of a new chiral diaminophosphino(silyl)carbene, based on the use of (R,R)-cyclotlexane-trans-1,2-diamine, is described. Its reaction with methyl acrylate afforded a cyclopropane derivative as a single diastereomer. The diastereoselectivity in the addition reactions between olefins and chiral carbenes derived from C-2-symmetric diamines has also been Studied by theoretical calculations, which establish that it has a steric origin; we report a rationale to predict the absolute configuration of the adducts.
First author: Shahbazian, Shant, A Computational Study on Some Viable Targets for Gas-Phase Synthesis of Metal Complexes of the Cyclic (B6C)(-2) and Their Bonding Pattern, JOURNAL OF PHYSICAL CHEMISTRY A, 112, 10365, (2008)
Abstract: In this account, a detailed computational study is conducted to verify the geometric, energetic, and electronic properties of the planar cyclic (B6C)(-2) (as the simplest carrier of hexacoordinate carbon) Within some metal complexes. The [M(B6C)]((-)) (M = Li, Na, K) and [M(B6C)] (M = Be, Mg, Ca) series are employed for this purpose. Relevant ab initio calculations at both DFT and post-HF levels vividly demonstrate that this dianion is stabilized considerably in the electric field generated by cations, whereas the geometrical and electronic properties of this ring remain almost intact in these complexes. The complementary topological analysis of charge densities confirms that cyclic (B6C)(-2) Within these complexes exhibits the same topological patterns as the naked dianion, thus confirming the presence of an unusual charge density distribution in this dianion. An electrostatic model is proposed that not only qualitatively but also quantitatively explains the observed computational trends in these complexes. This model successfully traces the polarization of the central carbon atom of the ring in the presence of a hard, multiply charged cation. To facilitate experimental detection, the photoelectron spectra of the [M(B6C)]((-)) (M = Li, Na, K) series are computed and the dominant features are extracted. Although considered species are not global minima on their potential energy hypersurfaces, their kinetic stabilities are verified and demonstrated unequivocally.
First author: Shamov, Grigory A., Theoretical study of the oxygen exchange in uranyl hydroxide. An old riddle solved?,JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130, 13735, (2008)
Abstract: A multistep mechanism for the experimentally observed oxygen exchange [Inorg. Chem. 1999, 38, 1456] of UO22+ cations in highly alkaline solutions is suggested and probed computationally. It involves an equilibrium between [UO2(OH)(4)](2-) and [UO2(OH)(5)](3-), followed by formation of the stable [UO3(OH)(3)center dot H2O](3-) intermediate that forms from [UO2(OH)(5)](3-) through intramolecular water elimination. The [UO3(OH)(3)H2O](3-) intermediate facilitates oxygen exchange through proton shuttling, retaining trans-uranyl structures throughout, without formation of the cis-uranyl intermediates proposed earliar. Alternative cis-uranyl pathways have been explored but were found to have activation energies that are too high. Relativistic density functional theory (DFT) has been applied to obtain geometries and vibrational frequencies of the different species (reactants, intermediates, transition states, products) and to calculate reaction paths. Two different relativistic methods were used: a scalar four-component all-electron relativistic method and the zeroeth-order regular approximation. Calculations were conducted for both gas phase and condensed phase, the latter treated using the COSMO continuum model. An activation energy of 12.5 kcal/mol is found in solution for the rate-determining step, the reaction of changing the four-coordinated uranyl hydroxide to the five-coordinated one. This compares favorably to the experimental value of 9.8 +/- 0.7 kcal/mol. Activation energies of 7.8 and 5.1 kcal/mol are found for the hydrogen transfer between equatorial and axial oxygens through a water molecule in [UO3(OH)(3) center dot H2O](3-) in the gas phase and condensed phase, respectively. Contrary to previously proposed mechanisms that resulted in high activation barriers, we find energies that are low enough to facilitate the reaction at room temperature. For the activation energies, two approximate DFT methods, B3LYP and PBE, are compared. The differences in activation energies are only about 1-2 kcal/mol for these methods.
First author: Qian, Gang, Band Gap Tunable, Donor-Acceptor-Donor Charge-Transfer Heteroquinoid-Based Chromophores: Near Infrared Photoluminescence and Electroluminescence, CHEMISTRY OF MATERIALS, 20, 6208, (2008)
Abstract: A series of D-pi-A-pi-D type of near-infrared (NIR) fluorescent compounds based on benzobis(thia diazole) and its selenium analogues were synthesized and fully characterized by H-1 and C-13 NMR, high-resolution mass spectrometry, and elemental analysis. The absorption fluorescence, and electrochemical properties were also studied. Photoluminescence of these chromophores ranges from 900 to 1600 nm and their band gaps are between 1.19 and 0.56 eV. Replacing the sulfur by selenium can lead to a red shift for emission and reduce the band gaps further. Interestingly, compound 1 exhibits aggregation-induced emission enhancement effect in the solid state. All-organic light-emitting diodes based on M1 and M2 were made and exclusive NIR emissions above 1 mu m with external quantum efficiency of 0.05% and maximum radiance of 60 mW Sr-1 m(-2) were observed. The longest electroluminesence wavelength reaches 1115 nm.
First author: Wagner, Frank R., Direct space decomposition of ELI-D: Interplay of charge density and pair-volume function for different bonding situations, JOURNAL OF PHYSICAL CHEMISTRY A, 112, 9814, (2008)
Abstract: The topological features, i.e., gradients and curvatures of the same-spin electron pair restricted electron localizability indicator (ELI-D) in position space are analyzed in terms of those of the electron density and the pair-volume function. The analysis of the topology of these constituent functions and their interplay on ELI-D attractor formation for a number of molecules representing chemically different bonding situations allows distinguishing between different chemical bonding scenarios on a quantum mechanical basis without the recourse to orbitals. The occurrence of the Laplacian of the electron density in the expression for the Laplacian of ELI-D allows us to establish a physical link between electron localizability and electron pairing as displayed by ELI-D and the role of Laplacian of the density in this context.
First author: Yan, Li-Kai, Theoretical study on the considerable second-order nonlinear optical properties of naphthylimido-substituted hexamolybdates, JOURNAL OF PHYSICAL CHEMISTRY A, 112, 9919, (2008)
Abstract: The static first hyperpolarizabilities and origin of nonlinear optical (NLO) properties of [(2-methylnaphthyl)imido]hexamolybdates derivatives have been investigated by density functional theory (DFT). The [(2-methylnaphthyl)imido]hexamolybdate has considerable large first hyperpolarizability, 6.780 x 10(-30) esu, and it is larger than that of [(2,6-dimethylphenyl)arylimido]hexamolybdate due to the double aromatic rings in the naphthylimido ligand. The naphthylimido ligand acts as an electron-donor and the polyanion acts as an electron-acceptor. The substituent position on the naphthylimido is a key factor to determine the first hyperpolarizability of (naphthylimido)hexamolybdate derivatives. The derivative, which the iodine atom locates on the para nitrogen on the naphthylimido ligand, has the largest beta(0) value among the iodine-substituted derivatives. It suggests that the iodine atom is quasi linear with nitrogen and Mo, which is bonded to the nitrogen atom, could generate a large static electronic field and give the large contribution to NLO response. The introducing of electron-donors significantly enhances the first hyperpolarizabilities of (naphthylimido)hexamolybdates comparing with the electron-acceptors as the electron-donating ability is significantly enhanced when the electron-donor is attached to the naphthylimido segment. The present investigation provides important insight into NLO properties of (arylimido)molybdate derivatives.
First author: Marashdeh, Ali, Density functional theory study of the TiH2 interaction with a NaAlH4 cluster, JOURNAL OF PHYSICAL CHEMISTRY C, 112, 15759, (2008)
Abstract: To understand the role of titanium in catalyzing the de/rehydrogenation reactions in NaAlH4, it is necessary to determine the composition and structure of the catalytically active species that IS (are) formed during ball milling and de/rehydrogenation reactions. One of the species that is thought to be catalytically active is TiH2. We have performed a density functional theory study of TiH2 interacting with a NaAlH4 cluster. First, a TiH2 molecule was adsorbed on the (001) surface of NaAlH4 in different sites. Next, the TiH2 molecule or its Ti atom was moved inside the cluster either by exchanging the whole TiH2 molecule with Na or Al or by exchanging only the Ti atom with Na or Al and leaving the two hydrogen atoms on the. surface together with the exchanged atom. Our calculations suggest that, when restricting the possible outcomes to adsorption, TiH2 adsorbs on the surface above a Na site, pushing the Na atom subsurface. However, exchanging the whole TiH2 unit with the subsurface displaced Na atom is favorable compared to leaving the TIH, on the surface. All other investigated exchanges were found to be less stable than TiH2 adsorbed on the surface. The results are consistent with a zipper model that we recently proposed.
First author: Fox, Brian J., Solution behavior and structural properties of Cu(I) complexes featuring m-terphenyl isocyanides, INORGANIC CHEMISTRY, 47, 9010, (2008)
Abstract: The synthesis of the m-terphenyl isocyanide ligand CNArMes2 (Mes = 2,4,6-Me3C6H2) is described. Isocyanide CNArMes2 readily functions as a sterically encumbering supporting unit for several Cu(I) halide and pseudo halide fragments, fostering in some cases rare structural motifs. Combination of equimolar quantities of CNArMes2 and CuX (X = Cl, Br and I) in tetrahydrofuran (THF) solution results in the formation of the bridging halide complexes (mu-X)(2)[Cu(THF)(CNArMes2)](2). Addition of CNArMes2 to cuprous chloride in a 2:1 molar ratio generates the complex ClCu(CNArMes2)(2) in a straightforward manner. Single-crystal X-ray diffraction has revealed ClCu(CNArMes2)(2) to exist as a three-coordinate monomer in the solid state. As determined by solution H-1 NMR and FTIR spectroscopic studies, monomer ClCu(CNArMes2)(2) resists tight binding of a third CNArMes2 unit, resulting in rapid isocyanide exchange. Contrastingly, addition of 3 equiv of CNArMes2 to cuprous iodide readily affords the tris-isocyanide species, ICu(CNArMes2)(3), as determined by X-ray diffraction. Similar coordination behavior is observed in the tris-isocyanide salt [(THF)Cu(CNArMes2)(3)]OTf (OTf = O3SCF3), which is generated upon treatment of (C6H6)[Cu(OTf)](2) with 6 equiv of CNArMes2 in THF. The disparate coordination behavior of the [CuCl] fragment relative to both [Cul] and [CuOTf] is rationalized in terms of structure and Lewis acidity of the Cu-containing fragments. The putative triflate species [Cu(CNArMes2)(3)]OTf itself serves as a good Lewis acid and is found to weakly bind C6H6 in an eta(1)-C manner in the solid-state. Density Functional Theory is used to describe the bonding and energetics of the eta(1)-C Cu-C6H6 interaction.
First author: Fan, Jing, On the origin of circular dichroism in trigonal dihedral d(6) complexes of bidentate ligands containing only sigma-orbitals. A qualitative model based on a density functional theory study of Lambda-[Co(en)(3)](3+),CHIRALITY, 20, 938, (2008)
Abstract: Time-dependent density functional theory (TD-DFT) in conjunction with qualitative molecular orbital theory is employed to interpret the circular dichroism (CD) spectrum of Lambda-[Co(en)(3)](3+). The simulated spectrum based on TD-DFT is compared in details with the experimental data. Emphasis is put on a qualitative understanding of the origin of optical activity in a-bonded trigonal dihedral complexes with bidentate ligands in general. Rotatory strengths associated with the CD bands of both d-d transitions and ligand-to-metal charge transfer (LMCT) are interpreted based on the metal-ligand sigma-interactions. These interactions are in turn analyzed in terms of symmetry unique overlaps between metal d- and symmetry ligand-orbitals as well as the dependence of these overlaps on geometrical parameters of the complex.
First author: Bencini, Alessandro, Some considerations on the proper use of computational tools in transition metal chemistry, INORGANICA CHIMICA ACTA, 361, 3820, (2008)
Abstract: The current understanding of transition metal chemistry is reviewed placing the attention at the applications and applicability of computational quantum chemistry to the calculation and prediction of spectroscopic properties of transition metal complexes and molecular magnets.
First author: Dragonetti, Claudia, The role of 5-R-1, 10-phenanthroline (R = CH(3), NO(2)) on the emission properties and second-order NLO response of cationic Ir(III) organometallic chromophores, INORGANICA CHIMICA ACTA, 361, 4070, (2008)
Abstract: [Ir(cyclometallated 4,5-diphenyl-2-methyl-thiazole)(2)(5-R-1, 10-phenanthroline)][PF(6)] (R = CH(3), NO(2)) complexes were prepared and fully characterized, the structure of the complex with 5-CH(3)-1, 10-phenanthroline being also determined by X-ray diffraction. The emission properties of both complexes have been investigated and their second-order nonlinear optical (NLO) response has been determined experimentally by the EFISH technique and found to be similar but slightly lower than that of related [Ir(ppy)(2)(5-R-1, 10-phenanthroline)][PF(6)] (ppy = cyclometallated 2-phenylpyridine), characterized by one of the highest second-order NLO response ever reported for a metal complex. In the complexes, SOS/TDDFT calculations show that the large and negative sign of the measured hyperpolarizability is mainly due to the significant contribution of rather intense MLCT transitions involving the phenanthroline as acceptor ligand.
First author: Conradie, Jeanet, Bonding in Low-Coordinate Environments: Electronic Structure of Distorted Square-Planar Iron-imido Complexes With Pincer-Type Ligands, JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 4, 1576, (2008)
Abstract: Low-coordinate architectures sustain unusual chemistry for middle and late transition metals, of which imido complexes are an excellent example. Recent DFT studies have uncovered a number of unusual features in the bonding in trigonal-planar and pseudotetrahedral imido complexes. Herein, we have extended these studies to a unique, distorted square-planar iron-imido complex with a pincer-type pyridine-2,6-diimine (PDI) supporting ligand. DFT calculations indicate that the iron center in the formally Fe(II) complex Fe(PDI)(NPh) is better described as intermediate-spin Fe(III), antiferromagnetically coupled to a b(2)-symmetry PDI pi-anion radical. A comparative analysis of the major classes of low-coordinate imido complexes has uncovered a certain similarity between Fe(PDI)(NPh) and a trigonal-planar Fe(III)-nacnac-imido complex. Both ligand architectures afford a total of four energetically accessible d orbitals, resulting in intermediate-spin Fe(III) centers.
First author: Marshall, Delmar, Computational studies of CO and CO+: Density functional theory and time-dependent density functional theory, JOURNAL OF QUANTITATIVE SPECTROSCOPY & RADIATIVE TRANSFER, 109, 2546, (2008)
Abstract: Potential energy curves, equilibrium interatomic distances, term energies and harmonic vibration frequencies for the 16 lowest states of neutral carbon monoxide and the six lowest states of singly ionized carbon monoxide are Calculated by density functional theory (DFT) and linear-response time-dependent density functional (LR-TDDFF) theory. The results are compared with experimental data. The two theories, DFT and LR-TDDFT, are described briefly.
First author: Kong, Xiaojian, PARTICULAR MECHANISMS ON INSERTION OF ETHYLENE INTO Zr-H BOND OF Cp2ZrH2: A DFT STUDY, JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY, 7, 933, (2008)
Abstract: The mechanistic study on the insertion of ethylene into the Zr-H bond of Cp2ZrH2 to give Cp2Zr(H)(CH2CH3) is performed with the aid of density functional theory calculations. Two possible insertion pathways are proposed. One is the side-insertion and the other is the central-insertion. The rate-determining step is the ethylene insertion in the former path and formation of the adduct in the latter path. Our results of calculations predicted that the central-insertion path is preferred kinetically over the side-insertion path. Two types of Zr center dot center dot center dot H-C agostic interactions having different stabilities are described.
First author: Lyubimova, Olga, The nature of the metal-nitric oxide bond in the [M(CN)(5)(NO)](q) (M = Cr, Mn, Fe, Ru, Os, and Co) and trans-[Ru(NH3)(4)L(NO)](q) (L = pyrazine, pyridine, N-2, H2O, Cl-, CN-, NO2-) complexes: A bond-energy decomposition analysis, JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 865, 28, (2008)
Abstract: A bond-energy decomposition analysis (EDA) has been carried out to investigate the nature of the M-NO bonding in the pentacyanonitrosyl [Cr(CN)(5)(NO)](4), [Mn(CN)(5)(NO)](3-), [M(CN)(5)(NO)](2-) (M = Fe, Ru, Os), [Co(CN)(5)(NO)](3-) complexes and in the trans-nitrosyltetraammineruthenium [Ru(NH3)(4)L(NO)](q) (L = pyrazine, pyridine, N-2, H2O (q = 3); and L = Cl, CN, NO2- (q = 2)) complexes. For the pentacyanonitrosyl complexes of Fe, Ru, and Os three fragmentation models have been considered: {M(CN)(5)}(3-)center dot center dot center dot{NO}(+), {M(CN)(5)}(2-)center dot center dot center dot{NO}(0), and {M(CN)(5)}(-)center dot center dot center dot{NO}(-). The results of the EDA show that the linear M-NO bonds are predominantly covalent with a significant (similar to 70%) contribution of pi orbital interaction between unpaired electrons on the d(pi) and pi(center dot)(NO0) orbitals. EDA results point to the correlation between M-NO and M-L binding interactions in the trans-[Ru(NH3)(4)L(NO)](q) complexes.
First author: Li, Qinning, A TD-DFT study on dissociative loss of the axial and equatorial carbonyl for HCo(CO)(4),JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 865, 88, (2008)
Abstract: In this work we explore two probably competitive photodissociation pathways for the loss of an axial and equatorial carbonyl ligand in HCo(CO)(4) by means of TD-DFT calculations with the ADF program. The potential energy profiles for several low-lying singlet and triplet states along the two dissociation pathways are investigated upon vertical transitions. The calculations suggest that the equatorial homolysis of carbonyl plays an important role in the photodissociation processes. Accordingly, DFT studies on the ground state structure of HCo(CO)(3) reveal that for each dissociation channel there is a stable singlet state, corresponding to C(3v) and C(s) symmetry, respectively. Subsequently, a small energy barrier of 6.0 kJ/mol is found for isomerization of HCo(CO)(3) from the C(3v) conformation to the C(s) one. In addition, the absorption spectra of HCo(CO)(4) in the UV/vis region by the TD-DFT method are compared with the available experimental and theoretical results. The calculated spectrum positions of the starting absorption and the most intense absorption are in good agreement with the experimental observation.
First author: Garcia-Fernandez, P., Pseudo-Jahn-Teller origin of the low barrier hydrogen bond in N2H7+, JOURNAL OF CHEMICAL PHYSICS, 129, 88, (2008)
Abstract: The microscopic origin and quantum effects of the low barrier hydrogen bond (LBHB) in the proton-bound ammonia dimer cation N2H7+ were studied by means of ab initio and density-functional theory (DFT) methods. These results were analyzed in the framework of vibronic theory and compared to those obtained for the Zundel cation H5O2+. All geometry optimizations carried out using wavefunction-based methods [Hartree-Fock, second and fourth order Moller-Plesset theory (MP2 and MP4), and quadratic configuration interaction with singles and doubles excitations (QCISD)] lead to an asymmetrical H3N-H+center dot center dot center dot NH3 conformation (C-3v symmetry) with a small energy barrier (1.26 kcal/mol in MP4 and QCISD calculations) between both equivalent minima. The value of this barrier is underestimated in DFT calculations particularly at the local density approximation level where geometry optimization leads to a symmetric H3N center dot center dot center dot H+center dot center dot center dot NH3 structure (D-3d point group). The instability of the symmetric D3d structure is shown to originate from the pseudo-Jahn-Teller mixing of the electronic 1(A1g) ground state with five low lying excited states of A(2u) symmetry through the asymmetric alpha(2u) vibrational mode. A molecular orbital study of the pseudo-Jahn-Teller coupling has allowed us to discuss the origin of the proton displacement and the LBHB formation in terms of the polarization of the NH3 molecules and the transfer of electronic charge between the proton and the NH3 units (rebonding). The parallel study of the H5O2+ cation, which presents a symmetric single-well structure, allows us to analyze why these similar molecules behave differently with respect to proton transfer. From the vibronic analysis, a unified view of the Rudle-Pimentel three-center four-electron and charge transfer models of LBHBs is given. Finally, the large difference in the N-N distance in the D-3d and C-3v configurations of N2H7+ indicates a large anharmonic coupling between alpha(2u)-alpha(1g) modes along the proton-transfer dynamics. This issue was explored by solving numerically the vibrational Schrodinger equation corresponding to the bidimensional E[Q(alpha(2u)), Q(alpha(1g))] energy surface calculated at the MP4/6-311++G** level of theory.
First author: Domin, Dominik, Breathing orbital valence bond method in diffusion Monte Carlo: C-H bond dissociation of acetylene, JOURNAL OF PHYSICAL CHEMISTRY A, 112, 8964, (2008)
Abstract: This study explores the use of breathing orbital valence bond (BOVB) trial wave functions for diffusion Monte Carlo (DMC). The approach is applied to the computation of the carbon-hydrogen (C-H) bond dissociation energy (BDE) of acetylene. DMC with BOVB trial wave functions yields a C-H BDE of 132.4 +/- 0.9 kcal/mol, which is in excellent accord with the recommended experimental value of 132.8 +/- 0.7 kcal/mol. These values are to be compared with DMC results obtained with single determinant trial wave functions, using Hartree-Fock orbitals (137.5 +/- 0.5 kcal/mol) and local spin density (LDA) Kohn-Sham orbitals (135.6 +/- 0.5 kcal/mol).
First author: Tomono, H., Binding between endohedral Na atoms in Si clathrate I; a first principles study, JOURNAL OF PHYSICS-CONDENSED MATTER, 20, 8964, (2008)
Abstract: We investigate the binding nature of the endohedral sodium atoms with the density functional theory methods, presuming that the clathrate I consists of a sheaf of one-dimensional connections of Na@Si-24 cages interleaved in three perpendicular directions. Each sodium atom loses 30% of the 3s(1) charge to the frame, forming an ionic bond with the cage atoms; the rest of the electron contributes to the covalent bond between the nearest Na atoms. The presumption is proved to be valid; the configuration of the two Na atoms in the nearest Si-24 cages is more stable by 0.189 eV than that in the Si-20 and Si-24 cages. The energy of the beads of the two distorted Na atoms is more stable by 0.104 eV than that of the two infinitely separated Na atoms. The covalent bond explains both the preferential occupancies in the Si-24 cages and the low anisotropic displacement parameters of the endohedral atoms in the Si-24 cages in the [100] directions of the clathrate I.
First author: Groysman, Stanislav, A biomimetic approach to oxidized sites in the xanthine oxidoreductase family: Synthesis and stereochemistry of tungsten(VI) analogue complexes, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130, 12794, (2008)
Abstract: Two series of square pyramidal (SP) monodithiolene complexes, [(MO3-nSn)-O-VI(bdt)](2-) and their silylated derivatives [(MO2-nSn)-O-VI(OSiR3)(bdt)](-) (n = 0, M = Mo or W; n = 1, 2, M = W), synthesized in this and previous work, constitute the basic molecules in a biomimetic approach to structural analogues of the oxidized sites in the xanthine oxidoreductase enzyme family. Benzene-1,2-dithiolate (bdt) simulates native pyranopterindithiolene chelation in the basal plane, tungsten instead of the native metal molybdenum was employed in sulfido complexes to avoid autoreduction, and silylation models protonation. The complexes [MO3(bdt)](2-) and [MO2(OSiR3)(bdt)](-) represent inactive sites, while [MO2S(bdt)](2-) and [MOS(OSiR3)(bdt)](-), with basal sulfido and silyloxo ligands, are the first analogues of the catalytic sites. Also prepared were [MOS2(bdt)](2-) and [MS2(OSiR3)(bdt)](-), with basal sulfido and silyloxo ligands. Complexes are described by angular parameters which reveal occasional distortions from idealized SP toward a trigonal bipyramidal (TBP) structure arising from crystal packing forces in crystalline Et4N+ salts. Miminized energy structures from DFT calculations are uniformly SP and reproduce experimental structures. For example, the correct structure is predicted for [WO2S(bdt)](2-), whose basal and apical sulfido diastereomers are potentially interconvertible through a low-lying TBP transition state for pseudorotation. The lowest energy tautomer of the protonated form is calculated to be [WOS(OH)(bdt)](-), with basal sulfido and hydroxo ligands. Computational and experimental structures indicate that protein sites adopt intrinsic coordination geometries rather than those dictated by protein structure and environment.
First author: Bento, A. Patricia, Nucleophilicity and leaving-group ability in frontside and backside S(N)2 reactions,JOURNAL OF ORGANIC CHEMISTRY, 73, 7290, (2008)
Abstract: Nucleophilic substitution is ubiquitous in chemistry and well studied. Nucleophilicity and leaving-group ability have been related to various reactant properties, such as electronegativity, size, polarizability, and others. Yet, the state-of-the-art is to some extent still phenomenological. Here, we try to arrive at a straightforward, causal relationship between the reactants’ electronic structure and their S(N)2 reactivity. To this end. we have explored the potential energy surfaces of the backside as well as frontside S(N)2 reactions of X- + CHA(3)Y with X, Y = F, Cl, Br, and I, using relativistic density functional theory (DFT) at ZORA-OLYP/TZ2P. These explorations provide us with a consistent overview of trends, over a wide range of reactivities and pathways, which were analyzed using the activation strain model of chemical reactivity. A clear picture emerges from these analyses: nucleophilicity is determined by the electron-donor capability of the nucleophile (i.e., energy and shape of the X- np atomic orbital), and leaving-group ability derives directly from carbon-leaving group (C – Y) bond strength.
First author: Hu, Shao-Wen, Theoretical mechanism study of UF6 hydrolysis in the gas phase, JOURNAL OF PHYSICAL CHEMISTRY A, 112, 8877, (2008)
Abstract: The mechanism of the gas-phase reaction UF6 + H2O -> UOF4 + 2HF is explored using relativistic density functional theory calculations. Initially, H2O coordinates with UF6 to form a 1: 1 complex UF6 center dot H2O. Over an activation energy barrier of about 19 kcal/mol, H2O transfers a H atom to a nearby ligand F, resulting in UF5OH + HF. The eliminated HF or another H2O molecule may form a hydrogen bond with UF5OH. Starting from UF5OH, the second HF elimination results in UOF4. If UF5OH is in the isolated form, UF5OH -> UOF4 + HF takes place over a barrier of 24 kcal/mol. If UF5OH is hydrogen-bonded with H2O or HF, the conversion barrier is less than 10 kcal/mol. Once formed, the unstable UOF4 tends to associate with additional ligands and hydrogen-bonding donors. The calculated binding energies indicate the significance of such interactions, which may have profound impact on further HF eliminating reactions. The IR spectra features can be used to indicate the formation and interaction type of the intermediates and products.
First author: Osorio, E. A., Single-molecule transport in three-terminal devices, JOURNAL OF PHYSICS-CONDENSED MATTER, 20, 8877, (2008)
Abstract: Transport through single molecules has been studied using different test beds. In this paper we focus on three-terminal devices in which a molecule bridges the gap between two gold electrodes and a third electrode-the gate-is able to modulate the conduction properties of the junction. Depending on the electronic coupling, Gamma, between the molecule and the gold electrodes, different transport regimes can be distinguished. We show measurements on junctions incorporating different single-molecule systems which demonstrate the distinction between these regimes, as well as the experimental limitations in controlling the exact value of Gamma.
First author: Bart, Suzanne C., Carbon dioxide activation with sterically pressured mid- and high-valent uranium complexes, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130, 12536, (2008)
Abstract: Sterically pressured mid- to high-valent uranium complexes with an aryloxide substituted triazacyclononane ligand scaffold, [(((R)ArO)(3)tacn)(3-)], were studied for carbon dioxide activation and transformation chemistry. The high valent uranium(V) imido species [(((R)ArO)(3)tacn)U(NR)] (R = (t)Bu, R’ = 2,4,6-trimethylphenyl (2-(t)Bu); R = Ad, R’ = 2,4,6-trimethylphenyl (2-Ad); R = (t)Bu, R’ = phenyl (3-(t)Bu)) were synthesized and spectroscopically characterized. X-ray crystallography of the tert-butyl mesityl imido derivative, 2-(t)Bu, reveals coordination of a bent imido fragment with a relatively long U-N bond distance of 2.05 angstrom. The mesityl imido complexes reacted with carbon dioxide, readily extruding free isocyanate to produce uranium(V) terminal oxo species, [ (((R)ArO)(3)tacn)U(O)] (R = (t)Bu (4-(t)Bu), Ad (4-Ad)), presumably through multiple bond metathesis via a uranium(V) carbimate intermediate. Using the smaller phenyl imido fragment in 3-(t)Bu slowed isocyanate loss, allowing the uranium(V) carbimate intermediate to undergo a second metathesis reaction, ultimately producing the diphenyl ureate derivative, [(((tBu)ArO)(3)tacn)U(NPh(2))CO] (5-(t)Bu). Single crystal X-ray diffraction studies were carried out on both uranium(V) terminal oxo complexes and revealed short U-O bonds (1.85 angstrom) indicative of a formal U O triple bond. The electronic structure of the oxo U(V) complexes was investigated by electronic absorption and EPR spectroscopies as well as SQUID magnetization and DFT studies, which indicated that their electronic properties are highly unusual. To obtain insight into the reactivity Of CO(2) With U-N bonds, the reaction of the uranium(IV) amide species, [(((R)ArO)(3)tacn)U(NHMes)] (R = (t)Bu (6-(t)Bu), Ad (6-Ad) with carbon dioxide was investigated. These reactions produced the uranium(IV) carbamate complexes, [(((R)ArO)(3)tacn)U(CO(2)NHMes)] (R = (t)Bu (7-(t)Bu), Ad (7-Ad)), resulting from insertion of carbon dioxide into U-N(amide) bonds. The molecular structures of the synthesized uranium carbamate complexes highlight the different reactivities due to the steric pressure introduced by the alkyl derivatized tris(aryloxide) triazacyclononane ligand. The sterically open tert-butyl derivative creates a monodentate eta(1)-O bound carbamate species, while the sterically more bulky adamantyl-substituted compound forces a bidentate kappa(2)-O,O coordination mode of the carbamate ligand.
First author: Fukushima, Akinori, Theoretical study of the hydrogen adsorption on AlB nanowire, JOURNAL OF POWER SOURCES, 184, 60, (2008)
Abstract: We studied AlB nanowires as hydrogen storage materials based on density functional theory and Rigged QED theory. In this paper, we focused on the adsorption energy and the electronic structure of models. AlB nanowire models are compared with an Al nanowire model and AlB2 crystal structure in terms of density of states, electron density, kinetic energy density, tension density and stress tensor density. These results revealed AlB nanowires do not have the conductivity, while the Al nanowire and AlB2 bulk have it. It was also shown that the stabilization energies of AlB nanowires for the hydrogen adsorption are larger than that of Al nanowire. Adsorped hydrogens are more stable in the AlB nanowires than the Al nanowire.
First author: Seth, Michael, Application of magnetically perturbed time-dependent density functional theory to magnetic circular dichroism. III. Temperature-dependent magnetic circular dichroism induced by spin-orbit coupling, JOURNAL OF CHEMICAL PHYSICS, 129, 60, (2008)
Abstract: A methodology for calculating the temperature-dependent magnetic circular dichroism (MCD) of open-shell molecules with time-dependent density functional theory (TDDFT) is described. The equations for the MCD of an open-shell molecule including spin-orbit coupling in the low- and high-temperature limits are reviewed. Two effects lead to the temperature-dependent MCD: the breaking of degeneracies and the perturbation of transition dipoles by spin-orbit coupling. The equations necessary to evaluate the required terms using TDDFT-derived quantities are presented. The performance of the formalism is demonstrated through application to the MCD of several molecules. The spectra of these molecules have differing properties with respect to bandwidth, temperature dependence of the MCD, and relative magnitude of the temperature-dependent and temperature-independent components of the MCD. The important features of the experimental spectra are reproduced by the calculations.
First author: Liu, Yan-Chun, Theoretical study on a novel series of fullerene-containing organometallics Fe(eta(5)-C55X5)(2) (X = CH, N, B) and their large third-order Nonlinear optical properties, JOURNAL OF PHYSICAL CHEMISTRY A, 112, 8086, (2008)
Abstract: Geometry structures, electronic spectra, and third-order nonlinear optical (NLO) properties of Fe(eta(5)-C55X5)2 (X = CH, N, B) have first been investigated by time-dependent density functional theory. We analyzed the intramolecular interactions between ferrocene and the C-50 moiety. The calculated electronic absorption spectrum indicates that the short wavelength transitions are ascribed to the C-50 moiety mixed charge transfer transition of ferrocene itself, while the low energy excitation transitions are ascribed to the unique charge transfer transition from ferrocene to C-50 moiety in these systems. The third-order polarizability gamma values based on sum of states (SOS) method show that this class of ferrocene/fullerene hybrid molecule possesses a remarkably large third-order NLO response, especially for Fe(eta(5)-C55B5)(2) with the static third-order polarizability (gamma(av)) computed to be -10410 x 10(-36) esu and the intrinsic second hypepolarizability to be 0.250. Thus, these complexes have the potential to be used for excellent third-order nonlinear optical materials. Analysis of the major contributions to the gamma(av) value suggest that the charge transfer from ferrocene to C-50 moiety along the z-axis (through Fe atom and the centers of two hybrid fullerenes) play the key role in the NLO response. Furthermore, boron substitution is an effective way of enhancing the optical nonlinearity compared to CH and N substitution, owing to smaller energy gap and better Conjugation through the whole molecule.
First author: Kukovec, Boris-Marko, Pseudopolymorphism in nickel(II) complexes with 6-methylpicolinate. Synthesis, structural, spectroscopic, thermal, and Density Functional Theory studies, CRYSTAL GROWTH & DESIGN, 8, 3465, (2008)
Abstract: The reaction between 6-methylpicolinic acid (6-MepicH) and nickel(II) nitrate hexahydrate afforded a new octahedral complex containing two bidentate ligands and two water molecules in cis positions, which crystallized in two pseudopolymorphs, [Ni(6-Mepic)(2)(H2O)(2)]center dot 2H(2)O (1) with cocrystallized water molecules from water solution and [Ni(6-Mepic)(2)(H2O)(2)] (2) without cocrystallized water. In 1, two molecules of nickel(II) complex are assembled in centrosymmetric dimers by three hydrogen bonds, which form a two-dimensional network by means of water molecules. These layers interact through pi center dot center dot center dot pi stacking arrangements between pyridine rings in the third dimension. In 2, centrosymmetric dimers held together by hydrogen bonds form two parallel chains and assemble in a three-dimensional network by pi center dot center dot center dot pi stacking. Density functional theory (DFT) calculations (ADF) performed on model dimers showed the major role of the O-H center dot center dot center dot O hydrogen bonds in establishing the whole network, without requiring large distortions from the individual molecules. Raman and IR spectroscopy studies allowed a detailed comparison of the two species being addressed, and DFT calculations contributed to the assignment of several bands. Thermogravimetric experiments showed the successive loss of water molecules from 1, starting from the cocrystallized and continuing with the coordinated ones; in 2, the process started at the second stage.
First author: Rodriguez-Fortea, Antonio, Hydration of hydrogentungstate anions at different pH conditions: A Car-Parrinello molecular dynamics study, INORGANIC CHEMISTRY, 47, 7745, (2008)
Abstract: Standard density functional theory calculations with a continuous model of solvation as well as Car-Parrinello molecular dynamics simulations with explicit solvent molecules are carried out to analyze the effect of the pH of the solution on the coordination sphere of the W-VI ion. Both methodologies agree in predicting an expansion of the coordination sphere of the W-VI ion upon a decrease in the pH. Continuous solvation models, however, are unable to predict as stable some structural isomers of a hydrated hydrogentungstate anion and tungstic acid.
First author: Chavain, Natascha, Investigation of the redox behavior of ferroquine, a new antimalarial, MOLECULAR PHARMACEUTICS, 5, 710, (2008)
Abstract: Ferroquine (FQ or SR97193) is a unique ferrocene antimalarial drug candidate which just entered phase IIb clinical trials in autumn 2007. FQ is able to overcome the chloroquine (CQ) resistance problem, an important limit to the control of Plasmodium falciparum, the principal causative agent of malaria. However, as for other therapeutic agents such as chloroquine (CQ) and artemisin, its mechanism of action remains partially unknown. Most investigations have so far focused on comparing the activity of FQ to that of CQ in order to understand how the ferrocene core contributes to a stronger antiplasmodial activity. Studies have already shown that the ferrocene altered the shape, volume, lipophilicity, basicity and also electronic profile of the parent molecule and, hence, its pharmacodynamic behavior. However, few investigations have been undertaken to probe the real contribution of redox properties of the ferrocene (iron(II))/ferricinium (iron(III)) system in FQ as reported in this article. In our experimental and theoretical approach, we considered the redox profile of the ferrocene core of FQ in the specific conditions (acidic and oxidizing) of the parasitic digestive vacuole as a possible discriminating property from CQ in the antimalarial activity.
First author: Aldegunde, J., Hyperfine energy levels of alkali-metal dimers: Ground-state polar molecules in electric and magnetic fields, PHYSICAL REVIEW A, 78, 710, (2008)
Abstract: We investigate the energy levels of heteronuclear alkali-metal dimers in levels correlating with the lowest rotational level of the ground electronic state, which are important in efforts to produce ground-state ultracold molecules. We use density-functional theory to calculate nuclear quadrupole and magnetic coupling constants for KRb and RbCs and explore the hyperfine structure in the presence of electric and magnetic fields. For nonrotating states, the zero-field splittings are dominated by the electron-mediated part of the nuclear spin-spin coupling. They are a few kilohertz for KRb isotopologs and a few tens of kilohertz for RbCs isotopologs.
First author: Jones, Travis E., First-principles study of the mode-1 fracture of Fe-TiX interfaces (X = C, N), PHYSICAL REVIEW B, 78, 710, (2008)
Abstract: We compare the evolution of the charge density in mode-1 fracture with that in uniaxial separation of two model systems: coherent Fe-TiC and Fe-TiN interfaces. These charge densities were calculated using both band structure and cluster codes. The topology of charge density in the cluster calculations converged with that of the bulk within two coordination spheres. Furthermore, we found that the topology of initial and final states is independent of the applied strain. However, the topological evolution is strain dependent. While we observed one topological catastrophe in Fe-TiC, independent of strain, we saw two separate catastrophes under uniaxial separation of Fe-TiN and only one under mode-1 fracture. This behavior suggests that there is some kinetic control mediating fracture in these iron-ceramic interfaces.
First author: Gora, A., Mechanism of hydrogen abstraction by O- species in oxidative dehydrogenation of early alkanes: Propane, ethane and methane. Model theoretical DFT study, POLISH JOURNAL OF CHEMISTRY, 82, 1779, (2008)
Abstract: In this work we present simple mechanistic study on the effect of the interaction between early alkanes (methane, ethane and propane) with an O- species, postulated as reactive defect site on surfaces of many catalysts. The subject is focused on mechanisms of preliminary hydrogen abstraction by O- ion radical and prospective succeeding processes. The model for DFT calculations built of an alkane molecule and O- species is used for minimum energy pathway calculations along distinct reaction coordinate defined as a distance between oxygen and attacked atom. Our results show that O- and alkanes form stable preliminary complexes but only for methane the first hydrogen abstraction has meaningful energy barrier. Stability of the complex between formed hydroxyl and alkyl radical is also substantial but only for ethane and propane it determines different routes to stable intermediate products of ODH: alcohol precursors or appropriate alkenes. Formation of negatively charged precursors of corresponding alcohols is energetically or kinetically unfavourable and is of minor importance. The number and character of ODH products for propane may strongly vary depending on reaction conditions, what makes the catalysis for its oxidation highly sensitive to surface properties.
First author: Zalucka, J., Cu+, Ag+ and Na+ cationic sites in ZSM-5 interacting with benzene: DFT modeling, POLISH JOURNAL OF CHEMISTRY, 82, 1801, (2008)
Abstract: The present work concerns the activation of benzene by Cu+, Ag+ and Na+ ions in zeolites. DFT cluster calculations have been carried out to obtain geometric structure and electronic properties of the cluster models of the three systems to analyze differences and their impact on the activation of adsorbed benzene. Natural Orbitals for Chemical Valence (NOCV) has been used to estimate components of differential electron density: donation and back-donation. Zeolite framework is shown to enhance the latter and to influence strongly benzene activation for Cu+ and Ag+ sites.
First author: Wang, Xiaojing, Quantum chemical molecular dynamical investigation of alkyl nitrite photo-dissociated on copper surfaces, APPLIED SURFACE SCIENCE, 254, 6991, (2008)
Abstract: An accelerated quantum chemical molecular dynamical code “Colors-Excite” was used to investigate the photolysis of alkyl nitrites series, RONO (R=CH(3) and C(CH(3))(3)) on copper surfaces. Our calculations showed that the photo-dissociated processes are associated with the alkyl substituents of RONO when adsorbed on copper surfaces. For R=CH(3), a two-step photolysis reaction occurred, yielding diverse intermediate products including RO radical, NO, and HNO, consistent with those reported in gas phase. While for R=C(CH(3))(3), only one-step photolysis reaction occurred and gave intermediate products of RO radical and NO. Consequently, pure RO species were achieved to adsorb on metal surfaces by removing the NO species in photolysis reaction. The detailed photo-dissociated behaviors of RONO on copper surfaces with different alkyl substituents which are uncovered by the present simulation can be extended to explain the diverse dissociative mechanism experimentally observed. The quantum chemical molecular dynamical code “Colors-Excite” is proved to be highly applicable to the photo-dissociations on metal surfaces.
First author: Takahata, Yuji, Accurate calculation of N1s and C1s core electron binding energies of substituted pyridines. Correlation with basicity and with Hammett substituent constants, JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 863, 33, (2008)
Abstract: Substituent shifts of the energetics of four related ionization processes of pyridines and benzoic acids (Fig. I) were investigated. The first process is core-electron ionization of gas-phase pyridines (Fig. 1A), while the second concerns gas-phase acid-base reaction between a substituted pyridine and a Conjugated acid (Fig. 1B), and the third and fourth processes are the acid dissociation of substituted benzoic acids in aqueous solution (Fig. 1C and in vacuum (Fig. 1D), respectively. Core-electron binding energies for the first process Were Calculated using density-functional theory with the scheme Delta E-KS (PW86x-PW91c/TZP+C-ret)//HF/6-31G*. Average absolute deviation of calculated core electron binding energy shifts at N atom in Substituted pyridines from experiment was 0.08 eV. The shift at N coincides highly with that at a ring carbon atom. The four shifts corresponding to the four processes shown in Figs. 1A-D correlate strongly with one another. with numerical values fairly close to each other when expressed in unit of electron volts.
First author: Orian, Laura, Linkage isomerism of nitriles in rhodium half-sandwich metallacycles, ORGANOMETALLICS,27, 4028, (2008)
Abstract: A systematic analysis of the linkage isomerism of nitriles in half’sandwichfive-membered rhodacycles is presented for 15 nitriles of the general formula RCN. The hitherto elusive transition states connecting the two isomers have been located using advanced DFT methods.
First author: Lastra, Juan Maria Garcia, Orbital-free effective embedding potential at nuclear cusps, JOURNAL OF CHEMICAL PHYSICS, 129, 4028, (2008)
Abstract: A strategy to construct approximants to the kinetic-energy-functional dependent component (v(t)[rho(A),rho(B)](r)) of the effective potential in one-electron equations for orbitals embedded in a frozen-density environment [Eqs. (20) and (21) in Wesolowski and Warshel, J. Phys. Chem. 97, (1993) 8050] is proposed. In order to improve the local behavior of the orbital-free effective embedding potential near nuclei in the environment, the exact behavior of v(t)[rho(A),rho(B)](r) at rho(A)-> 0 and integral rho(B)dr=2 is taken into account. As a result, the properties depending on the quality of this potential are invariably improved compared to the ones obtained using conventional approximants which violated the considered exact condition. The approximants obtained following the proposed strategy and especially the simplest one constructed in this work are nondecomposable, i.e., cannot be used to obtain the analytic expression for the functional of the total kinetic energy.
First author: Hagemann, Hans, LiSc(BH4)(4): A novel salt of Li+ and discrete Sc(BH4)(4)(-) complex anions, JOURNAL OF PHYSICAL CHEMISTRY A, 112, 7551, (2008)
Abstract: LiSc(BH4)(4) has been prepared by ball milling of LiBH4 and ScCl3. Vibrational spectroscopy indicates the presence of discrete Sc(BH4)(4)(-) ions. DFT calculations of this isolated complex ion confirm that it is a stable complex, and the calculated vibrational spectra agree well with the experimental ones. The four BH4- groups are oriented with a tilted plane of three hydrogen atoms directed to the central Sc ion, resulting in a global 8 + 4 coordination. The crystal structure obtained by high-resolution synchrotron powder diffraction reveals a tetragonal unit cell with a = 6.076 angstrom and c = 12.034 angstrom (space group P-42c). The local structure of the Sc(BH4)(4)(-) complex is refined as a distorted form of the theoretical structure. The Li ions are found to be disordered along the z axis.
First author: Long, Juan, Stable geometric and electronic structures of gold-coated nanoparticles M@Au-12 (M=5d transition metals, from Hf to Hg): I-h or O-h?, JOURNAL OF PHYSICAL CHEMISTRY C, 112, 12646, (2008)
Abstract: The geometric and electronic structures of 5d transition metal “impurities” Hf to Hg encapsulated in icosahedral and cuboctahedral Au-12 cages have been investigated theoretically. The best density functional results of the small molecules Au-12, AuH, AuCl, and AuCu were obtained for the geometric structures with X alpha, and for the electronic energies of those frozen structures with VBP. The same procedure was then applied to the clusters. At the zeroth order regular relativistic approximation ZORA, both at the spin-averaged scalar and at the spin – orbit-split spinor levels, the cuboctahedral clusters tend to be more stable than their icosahedral isomers, except for W@Au-12. The neutral clusters have electronic closed shells only for I-h and O-h W@Au-12 and for O-h Hg@Au-12. The embedding energy of M into Au-12 is less attractive for the later transition metal atoms M.
First author: Gainsford, Graeme J., Density functional theory calculations of novel Rh(I) diphosphinite catalysts,POLYHEDRON, 27, 2529, (2008)
Abstract: Novel Rh(I) diphosphinite catalysts [Rh((R,R)-3,4-(bis(O-diphenylphosphino)-1,2,5,6-tetra-O-methyl-chiro-ino sitol)]+ ([Rh-CANDYPHOS]+) and [Rh((R,R)-3,4-(bis(O-diphenylphosphino)-1,2,5,6-tetra-O-ethyl-chiro-inos itol)]+ ([Rh-EtCP]+) have been prepared utilizing naturally-occurring resources. Potential energy surfaces for the catalyzed asymmetric hydrogenation of the prochiral enamides methyl-(Z)-alpha-acetamido cinnamate, methyl-(Z)-alpha-acetamido cinnamic acid and dimethyl itaconate have been surveyed using density function theory (DFF) methods. Key transition states were identified from previous [Rh((R,R)-DUPHOS)]+ studies for the two diastereoisomeric manifolds [1,2]. Transition state energies were found starting from models based on (1) the X-ray structure of the active complex (CANDY-PHOS)(n(4)(Z,Z)-cyclo-octa-1,5-diene)-rhodium(I) tetrafluoroborate CHCl3 solvate [3] and (2) models in which the complex (without substrate) started with C2 molecular symmetry. The difficulties encountered in calculations of the transition state energies of large cations are outlined and limitations noted. Transition state enthalpy values are compared with the observed experimental free energy differences results and previous studies [1,2]. The predictive aspects of the calculations appear to be limited with the starting models playing an important part in the absolute value of the final energies.
First author: Christoffers, Jens, A europium(II) complex with bis-pyridino-18-crown-6, POLYHEDRON, 27, 2688, (2008)
Abstract: A new Eu(II) complex, bis(perchlorato)(bis-pyridino-18-crown)europium(II), has been obtained in the crystalline form by electrolytic reduction. The metal ion is 10-coordinated and its surrounding consists of four macrocycle O atoms, two N ones and four O atoms from perchlorate anions. The compound shows a very broad absorption band, starting gently from 600 nm towards the UV region, and two weak luminescence bands with maxima at 430 and 500 nm. The performed density functional theory (DFT) calculations have shown that the absorption results from mixed f-d, f-s and charge transfer transitions. The possible mechanism of luminescence is also discussed.
First author: Fux, Samuel, Analysis of electron density distributions from subsystem density functional theory applied to coordination bonds, CHEMICAL PHYSICS LETTERS, 461, 353, (2008)
Abstract: We investigate the electron density topologies from a subsystem approach to density-functional theory (DFT) for subsystems connected by coordination bonds in comparison to Kohn-Sham-DFT reference calculations. Reasonable results can be obtained for weak dative bonds as in H3N center dot center dot center dot BH3 or for bonds with a rather ionic character as in TiCl4. Problems occur for dominant covalent bonding contributions. The subsystem approach shows serious deficiencies in cases of fragments with opposite charge. We show how this problem can be overcome by introduction of a long-distance correction to the embedding potential as recently proposed [C. R. Jacob, S. M. Beyhan, L. Visscher, J. Chem. Phys. 126 ( 2007) 234116].
First author: Harmer, Jeffrey, A nickel hydride complex in the active site of methyl-coenzyme M reductase: Implications for the catalytic cycle, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130, 10907, (2008)
Abstract: Methanogenic archaea utilize a specific pathway in their metabolism, converting C, substrates (i.e., CO(2)) or acetate to methane and thereby providing energy for the cell. Methyl-coenzyme M reductase (MCR) catalyzes the key step in the process, namely methyl-coenzyme M (CH3-S-COM) plus coenzyme B (HS-CoB) to methane and CoM-S-S-CoB. The active site of MCR contains the nickel porphinoid F(430). We report here on the coordinated ligands of the two paramagnetic MCR(red2) states, induced when HS-CoM (a reversible competitive inhibitor) and the second substrate HS-CoB or its analogue CH(3)-S-CoB are added to the enzyme in the active MCR(red1) state (Ni(I)F(430)). Continuous wave and pulse EPR spectroscopy are used to show that the MCR(red2a) state exhibits a very large proton hyperfine interaction with principal values A((1)H) = [-43,-42,-5] MHz and thus represents formally a Ni(III)F(430) hydride complex formed by oxidative addition to Nil. In view of the known ability of nickel hydrides to activate methane, and the growing body of evidence for the involvement of MCR in “reverse” methanogenesis (anaerobic oxidation of methane), we believe that the nickel hydride complex reported here could play a key role in helping to understand both the mechanism of “reverse” and “forward” methanogenesis.
First author: Singh, Priti, Redox properties of ruthenium nitrosyl porphyrin complexes with different axial ligation: Structural, spectroelectrochemical (IR, UV-visible, and EPR), and theoretical studies, INORGANIC CHEMISTRY, 47, 7106, (2008)
Abstract: Experimental and computational results for different ruthenium nitrosyl porphyrin complexes [(Por)Ru(NO)(X)](n+)(where Por(2-) = tetraphenylporphyrin dianion (TPP2-) or octaethylporphyrin dianion (OEP2-) and X = H2O (n = 1, 2, 3) or pyridine, 4-cyanopyridine, or 4-NN-dimethylaminopyridine (n = 1, 0)) are reported with respect to their electron-transfer behavior. The structure of [(TPP)Ru(NO)(H2O)]BF4 is established as an {MNO}(6) species with an almost-linear RuNO arrangement at 178.1(3)degrees. The compound [(Por)Ru(NO)(H2O)]BF4 undergoes two reversible one-electron oxidation processes. Spectroelectrochemical measurements (IR, UV-vis-NIR, and EPR) indicate that the first oxidation occurs on the porphyrin ring, as evident from the appearance of diagnostic porphyrin radical-anion vibrational bands (1530 cm(-1) for OEP center dot- and 1290 cm(-1) for TPP center dot-), from the small shift of similar to 20 cm(-1) for v(NO) and from the EPR signal at g(iso) approximate to 2.00. The second oxidation, which was found to be electrochemically reversible for the OEP compound, shows a 55 cm(-1) shift in v(NO), suggesting a partially metal-centered process. The compounds [(Por)Ru(NO)(X)]BF4, where X = pyridines, undergo a reversible one-electron reduction. The site of the reduction was determined by spectroelectrochemical studies to be NO-centered with a ca. -300 cm(-1) shift in v(NO). The EPR response of the NO center dot complexes was essentially unaffected by the variation in the substituted pyridines X. DFT calculations support the interpretation of the experimental results because the HOMO of [(TPP)Ru(NO)(X)](+), where X = H2O or pyridines, was calculated to be centered at the porphyrin pi system, whereas the LUMO of [(TPP)Ru(NO)(X)](+) has about 50% pi*(NO) character. This confirms that the (first) oxidation of [(Por)Ru(NO)(H2O)](+) occurs on the porphyrin ring wheras the reduction of [(Por)Ru(NO)(X)](+) is largely NO-centered with the metal remaining in the low-spin ruthenium(II) state throughout. The 4% pyridine contribution to the LUMO of [(TPP)Ru(NO)(py)](+) is correlated with the stability of the reduced form as opposed to that of the aqua complex.
First author: Long Juan, A DFT study of 5d transition metal impurities encapsulated in the icosahedral and cuboctahedral Ag-12 cages, ACTA CHIMICA SINICA, 66, 1771, (2008)
Abstract: The geometrical and electronic structures of 5d transition metal (TM) impurities encapsulated in the icosahedral and cuboctahedral Ag-12 cages have been investigated systematically by a relativistic density functional theory method. Calculated results show that the M-Ag bond lengths depend on two factors: the sum of atomic radii and the cluster’s electronic structure. The binding energy of M@Ag-12 varies with the embedding energy of M into Ag-12 cage and with the distortion energy of the originally empty Ag-12 cage upon embedding the M atom. The clusters with bonding HOMO are more stable than those with anti-bonding HOMO. It was found that the icosahedral clusters were not always more stable than their cuboctahedral isomers, while the cuboctahedral clusters of Hf@Ag-12, Ir@Ag-12, Au@Ag-12 and Hg@Ag-12 were more stable than their icosahedral isomers.
First author: Ye, Wei-Ping, Synthesis and characterization of titanium complexes bearing two beta-enaminoketonato ligands with electron-withdrawing groups and their behavior in ethylene polymerization, ORGANOMETALLICS, 27, 3642, (2008)
Abstract: A series of new titanium complexes with two asymmetric bidentate beta-enaminoketonato (N,O) ligands (4b-t), [RN=CCF3)CHC(t-BU)O](2)TiCl2 (4b, R = -C6H4F(o); 4c, R = -C6H4F(m);4d, R = -C6H4F(p); 4e, R = – C6H3F2(2,3); 4f, R = -C6H3F2(2,4); 4g, R = -C6H3F2(2,5); 4h, R = -C6H3F2(2,6); 4i, R = -C6H3F2(3,4); 4j, R = -C6H3F2(3,5); 4k, R = -C6H2F3(2,3,4); 4l, R = -C6H2F3(3,4,5); 4m, R = -C6H4CF3(o); 4n, R =-C6H4CF3(m); 4o, R = -C6H4CF3(p); 4p, R = -C6H4Cl(p); 4q, R = -C6H4I(p); 4r, R = -C6H4NO2(P); 4s, R = -CH2C6H5; 4t, R = -C6H11), have been synthesized and characterized. X-ray crystal structures suggest that complexes 4a-d, 4j, and 4m all adopt a distorted octahedral geometry around the titanium centers. Two chlorine atoms in complexes 4a-d and 4j are in cis-configuration, while those of complex 4m are trans. NMR spectra and X-ray structure analyses reveal that the conformational isomers of some complexes, such as 4b, in which the two beta-enaminoketonato ligands bear asymmetrical N-phenyl rings, exist both in solution and in solid state. With modified methylaluminoxane (MMAO) as a cocatalyst, complexes 4b-1 and 4n-q are highly active toward ethylene polymerization and produce high molecular weight polyethylenes. The catalytic activities are significantly enhanced by introducing electron-withdrawing groups (EWG), such as fluorine and chlorine atom(s) or the trifluoromethyl group, into suitable positions on the N-aryl rings. The titanium complex 4m is inactive toward ethylene polymerization due to the trans-configuration of the two chlorine atoms. In addition, the titanium complexes display low catalytic activity for ethylene polymerization only if the N-substituents are not aromatic.
First author: Perekalin, Dmitry S., New approach to the photochemically controlled crown ethers: (Tetramethylcyclobutadiene)cobalt complexes with benzo-15-crown-5 and dibenzo-18-crown-6, ORGANOMETALLICS,27, 3654, (2008)
Abstract: The photochemical substitution of benzene in [Cb*CO(C6H6)(+) (Cb* = C4Me4) with benzo-15-crown-5 (1) gives the corresponding pi-complex [Cb*Co(eta(6)-C6H4(OCH2CH2OCH2CH2)(2)O)](+) (2). A similar reaction with dibenzo-18-crown-6 (3) produces cation [Cb*Co(eta(6)-C6H4(OCH2CH2OCH2CH2O)(2)C6H4)](+) (4). Arene exchange is reversible, and both 1 and 3 can be regenerated by irradiation of 2 and 4 with excess benzene. The reaction of [Cb*CO(C6H6)](+) with 0.5 equiv of 3 gives dinuclear complex [trans-Cb*Co(mu-eta(6),eta(6)-C6H4(OCH2CH2OCH2CH2O)(2)C6H4)CoCb*](2+) (5). The structures of cations 4 and 5 were confirmed by X-ray diffraction. The electrochemical behavior of complexes prepared was studied. The sodium-binding ability of cobalt complexes 2, 4, and 5 (determined by NMR titration; K-a = 2500, 800, and 50, respectively) was found to be much smaller than that of the free crown ethers 1 and 3 (K-a = 200 000 and 5 000 000). DFT calculations suggest that this decrease is mainly due to electrostatic repulsion of Co+ and Na+ centers.
First author: Kahlal, Samia, Correlation between density functional studies and experimental data of three new 19-electron metal sandwich complexes containing amido, ester, and thioester cyclopentadienyl substituents, ORGANOMETALLICS,27, 3693, (2008)
Abstract: Three 18-electron complexes of the type [CpFeII(eta(6)-C6Me6)](+) containing an amido, an ester, and a thioester group directly attached to the Cp ring were synthesized and reduced to Fe-I 19-electron complexes. These new 19- electron stable complexes were characterized by UV/vis spectroscopy, showing significant differences in the obtained spectra. In order to better understand the structural and optical properties of the three 19-electron complexes (eta(5)-C5H4CONHR)Fe-I(eta(6)-C6Me6), (eta(5)-C5H4COOR)Fe-I(eta(6)- C6Me6), and (eta(5)-C5H4COSR)Fe(eta(6)-C6Me6), we have carried out DFT calculations on these compounds, as well as on their diamagnetic 18-electron cations [(eta(5)-CpCONHR)Fe-II(eta(6)-C6Me6)] [PF6], [(eta(5)-CpCOOR)Fe-II(eta(6)- C6Me6)][PF6], and [(eta(5)-CpCOSR)Fe-II(eta(6)-C6Me6)][PF6] for the sake of comparison. Full geometry optimizations under C, symmetry have been carried out on the six complexes, and their optical transitions have been computed on the optimized geometries at the time-dependent DFT (TD-DFT) level. The comparison of the data obtained for the three 19-electron complexes gives us significant information about the influence of the functionalized cyclopentadienyl ring on the electronic structure.
First author: Bloem, Robbert, Simulation of vibrational energy transfer in two-dimensional infrared spectroscopy of amide I and amide II modes in solution, JOURNAL OF CHEMICAL PHYSICS, 129, 3693, (2008)
Abstract: Population transfer between vibrational eigenstates is important for many phenomena in chemistry. In solution, this transfer is induced by fluctuations in molecular conformation as well as in the surrounding solvent. We develop a joint electrostatic density functional theory map that allows us to connect the mixing of and thereby the relaxation between the amide I and amide II modes of the peptide building block N-methyl acetamide. This map enables us to extract a fluctuating vibrational Hamiltonian from molecular dynamics trajectories. The linear absorption spectrum, population transfer, and two-dimensional infrared spectra are then obtained from this Hamiltonian by numerical integration of the Schrodinger equation. We show that the amide I/amide II cross peaks in two-dimensional infrared spectra in principle allow one to follow the vibrational population transfer between these two modes. Our simulations of N-methyl acetamide in heavy water predict an efficient relaxation between the two modes with a time scale of 790 fs. This accounts for most of the relaxation of the amide I band in peptides, which has been observed to take place on a time scale of 450 fs in N-methyl acetamide. We therefore conclude that in polypeptides, energy transfer to the amide II mode offers the main relaxation channel for the amide I vibration.
First author: Michalak, Artur, Bond multiplicity in transition-metal complexes: Applications of two-electron valence indices,JOURNAL OF PHYSICAL CHEMISTRY A, 112, 7256, (2008)
Abstract: In the present study the applicability of the bond multiplicities from the Nalewajski and Mrozek valence indices was demonstrated for a variety of transition metal-based systems. The Nalewajski-Mrozek valence indices and bond multiplicity indices have been implemented in the Amsterdam Density Functional program. Selected examples comprise the carbonyl complexes (selected tetra- and hexacarbonyls, binary monocarbonyls of the first-row transition metals), phosphines, the ligands’ trans-influence, as well as multiple metal-ligand and metal-metal bonds. The results show that the calculated bond multiplicity indices correspond well to experimental predictions based on bond lengths and vibrational frequencies for all discussed classes of complexes. Almost perfect linear correlation between the bond indices and vibrational frequencies was observed for carbonyls and the oxo complexes; the calculated bond multiplicity reproduces the accepted order for the trans-influence of different ligands, rationalizes unusually low vibrational freqencies in the [OsO3N](-) complex compared to other nitrido complexes, explains the geometrical asymmetry in the MoO3 solid, and confirms the multiple character of the metal-metal bond in the [Re2Cl8](2-) complex. Thus, the Nalewajski and Mrozek method can be successfully used as a supplementary analysis tool for electronic structure for studies involving transition metal complexes.
First author: Ess, Daniel H., Theory of 1,3-dipolar cycloadditions: Distortion/interaction and frontier molecular orbital models, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130, 10187, (2008)
Abstract: Quantum chemical calculations of activation barriers and reaction energies for 1,3-dipolar cycloadditions by the high-accuracy CBS-QB3 method reveal previously unrecognized quantitative trends in activation barriers. The distortion/interaction model of reactivity explains why (1) there is a monotonic decrease of similar to 6 kcal/mol in the activation energy along the series oxides, imine, and ylide for the diazonium, nitrilium, and azomethine betaine classes of 1,3-dipoles; (2) nitrilium and azomethine betaines with the same trio of atoms have almost identical cycloaddition barrier heights; (3) barrier heights for the cycloadditions of a given 1,3-dipole with ethylene and acetylene have the same activation energies (mean absolute deviation of 0.6 kcal/mol) in spite of very different reaction thermodynamics (Delta Delta H-rxn range = 14-43 kcal/mol) and frontier molecular orbital (FMO) energy gaps. The energy to distort the 1,3-dipole and dipolarophile to the transition state geometry, rather than FMO interactions or reaction thermodynamics, controls reactivity for cycloadditions of 1,3-dipoles with alkenes or alkynes. A distortion/interaction energy analysis was also carried out on the transition states for the cycloadditions of diazonium dipoles with a set of substituted alkenes (CH2CHX, X = OMe, Me, CO2Me, Cl, CN) and reveals that FMO interaction energies between the 1,3-dipole and the dipolarophile differentiate reactivity when transition state distortion energies are nearly constant.
First author: Berthet, Jean-Claude, Sterically congested uranyl complexes with seven-coordination of the UO2 unit: the peculiar ligation mode of nitrate in [UO2(NO3)(2)(Rbtp)] complexes, INORGANIC CHEMISTRY, 47, 6850, (2008)
Abstract: Addition of 1 or 2 molar equiv of Rbtp [Rbtp = 2,6-bis(5,6-dialkyl-1,2,4-triazin-3-yl)pyridine; R = Me, Pr-n to UO2(OTf)(2) in anhydrous acetonitrile gave the neutral compounds [UO2(OTf)2(Rbtp)] [R = Me (1), nPr (2)] and the cationic complexes [UO2(Rbtp)(2)][OTf](2) [R = Me (3), Pr-n (4)], respectively. No equilibrium between the mono and bis(Rbtp) complexes or between [UO2(RbtP)(2)][OTf](2) and free Rbtp in acetonitrile was detected by NMR spectroscopy. The crystal structures of 1 and 3 resemble those of their terpyridine analogues, and 3 is another example of a uranyl complex with the uranium atom in the unusual rhombohedral environment. In the presence of 1 molar equiv of Rbtp in acetonitrile, UO2(NO3)(2) was in equilibrium with [UO2(NO3)(2)(Rbtp)] and the formation of the bis adduct was not observed, even with an excess of Rbtp. The X-ray crystal structures Of [UO2(NO3)(2)(Rbtp)] [R = Me (5), Prn (6)] reveal a particular coordination geometry with seven coordinating atoms around the UO2 fragment. The large steric crowding in the equatorial girdle forces the bidentate nitrate ligands to be almost perpendicular to the mean equatorial plane, inducing bending of the UO2 fragment. The dinuclear oxo compound [U(CyMe(4)btbP)(2)(mu-O)UO2(NO3)(3)][OTf] (7), which was obtained fortuitously from a 1:21 mixture of U(OTf)(4), CyMe(4)btbp, and UO2(NO3)(2) [CyMe(4)btbp = 6,6′-bis-(3,3,6,6-tetramethyl-cyclohexane-1,2,4-triazin-3-yl)-2,2′-bipyr idine] is a very rare example of a mixed valence complex involving covalently bound U-IV and U-VI ions; its crystal structure also exhibits a seven coordinate uranyl moiety, with one bidentate nitrate group almost parallel to the UO2 fragment. The distinct structural features of [UO2(k(2)-NO3)(2)(Mebtp)], with its high coordination number and a noticeable bending of the UO2 fragment, and of [UO2(K-2-NO3)(k(1)-NO3)(terpy)], which displays a classical geometry, were analyzed by Density Functional Theory, considering the bonding energy components and the molecular orbitals involved in the interaction between the uranyl, nitrate, and Mebtp or terpy moieties. The unusual geometry of the Mebtp derivative with the seven coordinating atoms around the U02 fragment was found very stable. In both the Mebtp and terpy complexes, the origin of the interaction appears to be primarily steric (Pauli repulsion and electrostatic); this term represents 62-63% of the total bonding energy while the orbital term contributes to about 37-38%.
First author: Reber, Arthur C., From SiO molecules to silicates in circumstellar space: Atomic structures, growth patterns, and optical signatures of SinOm clusters, ACS NANO, 2, 1729, (2008)
Abstract: SiO is the dominant silicon bearing molecule in the circumstellar medium; however, it agglomerates to form oxygen-rich silicates. Here we present a synergistic effort combining experiments in beams with theoretical investigations to examine mechanisms for this oxygen enrichment. The oxygen enrichment may proceed via two processes, namely, (1) chemically driven compositional separation in (SiO),, motifs resulting in oxygen-rich and silicon-rich or pure silicon regions, and (2) reaction between SinOm clusters leading to oxygen richer and poorer fragments. While SiO2 molecules are emitted in selected chemical reactions, they readily oxidize larger SinOn clusters in exothermic reactions and are not likely to agglomerate into larger (SiO2)(n) motifs. Theoretically calculated optical absorption and infrared spectra of SinOm clusters exhibit features observed in the extended red emissions and blue luminescence from interstellar medium, indicating that the SinOm fragments could be contributing to these spectra.
First author: Barone, Giampaolo, Intercalation of daunomycin into stacked DNA base pairs. DFT study of an anticancer drug, JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 26, 115, (2008)
Abstract: We have computationally studied the intercalation of the antitumor drug daunomycin into six stacks of Watson-Crick DNA base pairs (i.e., AT-AT, AT-TA, GC-AT, CG-TA, GC-GC GC-CG) using density functional theory (DFF). The proton affinity of the DNA intercalator daunomycin in water was computed to be 159.2 kcal/mol at BP86/TZ2P, which is in line with the experimental observation that daunomycin is protonated under physiological conditions. The intercalation interaction of protonated daunomycin with two stacked DNA base pairs was studied through a hybrid approach in which intercalation is treated at LDA/TZP while the molecular structure of daunomycin and hydrogen-bonded Watson-Crick pairs is computed at BP86/TZ2P. We find that the affinity of the drug for the six considered base pair dimers decreases in the order AT-AT > AT-TA > GC-AT > GC-TA > GC-CG > GC-GC, in excellent agreement with experimental data on the thermodynamics of the interaction between daunomycin and synthetic polynucleotides in aqueous solution. Our analyses show that the overall stability of the intercalation complexes comes mainly from pi-pi stacking but an important contribution to the computed and experimentally observed sequence specificity comes from hydrogen bonding between daunomycin and hetero atoms in the minor groove of AT base pairs.
First author: Mitoraj, Mariusz, Applications of natural orbitals for chemical valence in a description of bonding in conjugated molecules, JOURNAL OF MOLECULAR MODELING, 14, 681, (2008)
Abstract: Natural orbitals for chemical valence (NOCV) were used to describe bonding in conjugated pi-electron molecules. The ‘single’ C-C bond in trans-1,3-butadiene, 1,3-butadiene-1,1,4,4-tetra-carboxilic acid, 1,3,5,7-octatetraene, and 11-cis-retinal was characterized. In the NOCV framework, the formation of the sigma-bond appears as the sum of two complementary charge transfer processes from each vinyl fragment to the bond region, and partially to the other fragment. The formation of the pi-component of the bond is described by two pairs of NOCV representing the transfer of charge density from the neighboring ‘double’ C-C bonds. The NOCV eigenvalues and the related fragment-fragment bond multiplicities were used as quantitative measures of the sigma- and pi- contributions. The sigma-component of the ‘single’ C-C bonds appears to be practically constant in the systems analyzed, whereas the pi-contributions increase from butadiene (ca. 7.5%) to retinal (ca. 14%).
First author: Liao, Meng-Sheng, STRUCTURE AND PROPERTIES OF PERFLUOROALKYLATED PHTHALOCYANINES: A THEORETICAL STUDY, JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY, 7, 541, (2008)
Abstract: Density functional theory (DFT) calculations are performed on a series of peripherally substituted free-base and fluorinated zinc phthalocyanines, namely FnPcM (M = 2H, Zn; n = 16, 32, 48, 64). F16PcM, F32PcM, and F48PcM all prefer a planar skeletal structure of the metallomacrocycle core. In the case of F64Pc, F64PcZn remains planar but F64PcH2 is domed. The occurrence of a dome distortion appears to be related, at least in part, to the orientation of the isopropyl – C3F7 substituents as well as to the intermolecular (packing) interactions. The trends in the calculated results of the Pc2–M2+ binding energy, polarizabilities, and electron excitation energies in H16PcM, F16PcM, and F64PcM are in agreement with the experimental observations, as are the geometrical features. It is further confirmed that the simpler F32PcM or F48PcM mimic the basic electronic properties of F64PcM.
First author: Liao, Meng-Sheng, ASSESSMENT OF SOME RECENTLY DEVELOPED DENSITY FUNCTIONALS FOR CALCULATIONS ON IRON PORPHYRINS, JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY, 7, 615, (2008)
Abstract: The behaviors of several recently developed density functionals (M05, M05-2x, M06, M06-2x, M06-L, KT1, KT2) in describing the spin-state energetics of iron porphyrins [ FeP, FeP(Cl), FeP(THF)(2), FeTpivPP] have been investigated, where KT1 and KT2 are pure GGA (generalized gradient approximation) functionals; M06-L is a meta-GGA functional that contains the kinetic-energy density tau[= Sigma(del phi(i))(2)]; M05, M05-2x, M06, and M06-2x are hybrid meta-GGA functionals that include both the kinetic-energy density and Hartree-Fock exchange. The results reveal that KT1 and KT2 are biased toward lower-spin states and so fail to give the correct ground state for the high-spin systems, but KT2 shows a significant improvement over KT1. M05, M05-2x, M06, and M06-2x yield results which are in qualitative agreement with the experimental findings for FeP(Cl) and FeP(THF)(2), but their relative energies for the high-spin states are actually underestimated greatly. Among the various functionals tested here, only M06-L is able to provide a satisfactory description of the energetics of FeP, FeP(Cl), and FeP(THF)(2), for which the ground-state multiplicities are surely known. FeTpivPP is predicted to be high spin by the M06-L functional, in agreement with the early experimental magnetic measurement, but different from the previous results (and conclusion) obtained with other various functionals.
First author: Bridgeman, Adam J., Detecting delocalization, NEW JOURNAL OF CHEMISTRY, 32, 1359, (2008)
Abstract: As the bonding in many compounds can be adequantely described using localized, two-centre two-electron bonds. the electronic Structure Of Molecules where such a description is inadequate is often chemically very interesting. Three-centre bond orders provide a useful tool for detecting the presence and analyzing the importance Of multicentre and hypervalent effects. To depict the resulting chemical structures, a graphical device is introduced which constructs the chemical connections ab initio from the electronic Structure. The three-centre, two-electron bonding in a set of electron-deficient boranes and the three-centre, four-electron bonding in a set of electron-rich Xenon fluorides has been analyzed and the approach has been used to test for the Occurrence and importance of pseudo-aromatic, closed-loops in polyoxometalates.
First author: Garcia-Lastra, J. M., Microscopic origin of the different colors displayed by MgAl2O4 : Cr3+ and emerald,PHYSICAL REVIEW B, 78, 1359, (2008)
Abstract: The difference in color between emerald (Be3Si6Al2O18:Cr3+, green) and the Cr3+-doped spinel MgAl2O4 (red) is striking, considering that in both systems color is due to CrO69- complexes with a close local symmetry (D-3 and the D-3d, respectively) and that the measured Cr3+-O2- distance is practically the same (1.98 +/- 0.01 and 1.97 +/- 0.01 angstrom, respectively). By means of density-functional calculations it is shown that. this surprising difference can reasonably be explained once the electric field, E-R, which all lattice ions lying outside the CrO69- complex exert on localized electrons, is taken into consideration. The origin of the different shape of E-R in the two host lattices is analyzed in detail. It is shown that E-R raises (decreases) the 2p(O) levels for Be3Si6Al2O18:Cr3+ (MgAl2O4:Cr3+) along the trigonal axis thus favoring a decrease (increase) of 10Dq. The present work demonstrates the key role played by E-R (not considered in the traditional ligand field theory) for understanding the differences exhibited by the same complex embedded in host lattices which do not have the same crystal structure. Some remarks on the color of Cr2O3 pure compound are also reported.
First author: Trueba, A., Nature of the Fe4/2 center in KTaO3: A density functional theory study, PHYSICAL REVIEW B,78, 1359, (2008)
Abstract: This work is aimed at clearing out the nature of the axial Fe4/2 center detected by electron-paramagnetic resonance in iron-doped KTaO3 for which two different models have been put forward. While some authors ascribe such a center to a Fe+ impurity at a K+ site, although suffering an off-center motion along < 001 > directions, other groups propose that the Fe4/2 center involves a Fe5+ ion at a Ta5+ site, which later also undergoes an off-center shift along a principal direction of the KTaO3 lattice. Seeking to clarify this puzzling situation, the possible off-center shift of both Fe5+ and Fe+ impurities in KTaO3 is explored in this work by means of density functional calculations. As a salient feature it is shown that there is a huge barrier that prevents the motion of Fe5+ against one of the closest O2- anions. The case of Fe+ at a K+ site is more complex as the energy difference (10Dq) between the lower-lying e(g) (similar to x(2)-y(2),3z(2)-r(2)) and t(2g) (similar to xy,xz,yz) O-h levels is found to be equal to only -0.038 eV, and thus several states as a function of the displacement coordinate Z(Fe) have to be explored in order to determine what is the actual ground state and the associated equilibrium coordinate Z(Fe)(0). The ground state is found to correspond to the b(1)(x(2)-y(2))(1) a(1)(3z(2)-r(2))(2) b(2)(xy)(2) e(xz,yz)(2) C-4 upsilon configuration with spin S=3/2 and Z(Fe)(0)=90 pm, thus involving a significant off-center motion from the K+ site, which is found to be accompanied by a small ligand relaxation. As a salient feature this ground state is different from that derived constraining Fe+ at the K+ site. The present calculations also reproduce the experimental feature g(perpendicular to)-g(0)>g(parallel to)-g(0) observed for the Fe4/2 center. An analysis of first-excited states at equilibrium allows one to understand this fingerprint in a simple way.
First author: Trueba, A., Influence of internal electric fields on bonding and properties of impurities in insulators: Mn2+ in LiBaF3 and normal perovskites, PHYSICAL REVIEW B, 78, 1359, (2008)
Abstract: Although in LiBaF3:Mn2+ the impurity replaces Li+ thus forming octahedral MnF64- units the experimental hyperfine and anisotropic superhyperfine constants and the energies of d-d optical transitions do not fit into the pattern observed for Mn2+-doped normal perovskite lattices. Seeking to look into this relevant issue first-principles calculations in the framework of the density-functional theory have been carried out for MnF64- complexes embedded in both KMgF3 and LiBaF3 host lattices which display normal and inverted perovskite structures respectively. The present calculations lead to a value of the equilibrium Mn2+-F- distance, R-I, which is the same for both host lattices within 0.015 angstrom. Despite this fact and in agreement with experimental data the calculated values of both the anisotropic superhyperfine constant, A(p), and the cubic-field splitting parameter, 10Dq, for LiBaF3:Mn2+ are found to be higher than those for KMgF3:Mn2+ while Racah parameters are a bit higher for the latter case. All these results, and also the 3% reduction undergone by the hyperfine constant on passing from KMgF3:Mn2+ to LiBaF3:Mn2+ are shown to be connected with a parallel increase in the covalency. These surprising results, which cannot be ascribed to a different R-I value, are shown to arise from. the internal electric field, E-R, due to all lattice ions lying outside the MnF64- complex. Although, according to symmetry, E-R is null at Mn2+ site this is shown to be not true in the neighborhood of ligands for the LiBaF3 host lattice. The quite different shape of E-R in normal and inverted perovskite lattices is shown to be already understood considering only the first two shells surrounding the MnF64- complex. The present results demonstrate that the traditional ligand field theory fails to understand the changes undergone by optical and magnetic parameters of a complex when a host lattice is replaced by another one which is not isomorphous. The relevance of present conclusions for understanding the color of Cr3+-based gemstones is also underlined.
First author: Zhao, Yan, Improved description of nuclear magnetic resonance chemical shielding constants using the M06-L meta-generalized-gradient-approximation density functional, JOURNAL OF PHYSICAL CHEMISTRY A, 112, 6794, (2008)
Abstract: The performance of the M06-L density functional has been tested for four databases of NMR isotropic chemical shielding constants. Comparison with the B3LYP, BLYP, HCTH, KT1, KT2, LSDA, OPBE, OLYP, PBE, TPSS, and VSXC functionals shows that M06-L has improved performance for calculating NMR chemical shielding constants, especially for highly correlated systems. We also found that VSXC and M06-L have encouraging accuracy for calculating C-13 chemical shielding constants, and both functionals perform very well for the chemical shielding constants in the o-benzyne molecule.
First author: Nicu, Valentin Paul, Effects of complex formation on vibrational circular dichroism spectra, JOURNAL OF PHYSICAL CHEMISTRY A, 112, 6978, (2008)
Abstract: The determination of absolute configurations of chiral compounds using VCD is performed by comparing measured vibrational circular dichroism (VCD) spectra with calculated spectra. The process is based on two facts: the two enantiomers have rotational strengths of opposite sign, and the absolute configuration of the molecule used in the calculation is known. However, calculations on isolated molecules very often predict VCD intensities of very different magnitude or even different signs compared to the spectra measured in solution. Therefore, we have carefully analyzed what type of changes are induced by complexation of a solvent molecule to a solute. In the theoretical example of benzoyl-benzoic acid (in a particular chiral conformation) hydrogen bonded to the achiral NH3, we distinguish six cases, ranging from no or very small changes in the rotational strengths of solute modes (case A) to changes of sign of rotational strengths (case B), changes in magnitude (case Q, nonzero rotational strengths for modes of the achiral solvent (“transfer of chirality”, case D), large frequency shifts accompanied by giant enhancements of the IR and VCD intensities of modes involved in hydrogen bonding (case E), and emergence of new peaks (case F). In this work, all of these situations will be discussed and their origin will be elucidated. On the basis of our analysis, we advocate that codes for VCD rotational strength calculation should output for each mode i the angle xi(i) between the electric and magnetic transition dipole moments because only “robust modes” with xi far from 90 degrees should be used for the determination of the absolute configuration.
First author: Aikens, Christine M., From discrete electronic states to plasmons: TDDFT optical absorption properties of Ag(n) (n = 10, 20, 35, 56, 84, 120) tetrahedral clusters, JOURNAL OF PHYSICAL CHEMISTRY C, 112, 11272, (2008)
Abstract: Time-dependent density functional theory calculations are employed to calculate the optical absorption spectra of silver tetrahedral Ag(n) (n = 10, 20, 35, 56, 84, 120) clusters with emphasis on neutral and ion clusters that correspond to shell closings. For the Ag(20) cluster, the convergence properties of the spectra with respect to basis set and density functional are examined, and the most accurate results are found to be in good agreement with experimental data. The Ag(n) spectra evolve from molecular-like to plasmon-like with increasing n, and from this we are able to extrapolate the plasmon energy and width to the large particle limit, leading to results that are in excellent agreement with continuum electrodynamics results. The results show that for the selected tetrahedral clusters, the plasmon width does not increase with decreasing cluster size as is commonly found (or assumed) for typical cluster shape distributions.
First author: Ramirez-Tagle, Rodrigo, Electronic structure and molecular properties of the [Mo6X8L6](2-); X = Cl, Br, I; L = F, Cl, Br, I clusters, CHEMICAL PHYSICS LETTERS, 460, 438, (2008)
Abstract: Relativistic TDDFT calculations including spin orbit interactions via the ZORA approximation and solvent effects were carried out on the [Mo6X8L6](2) X = Cl, Br, I; L = F, Cl, Br, I clusters. These calculations indicate that the closely spaced lowest excited states are largely centered on the cubic [Mo6X8](4+) core. Thus, our calculations and the electronic similarities with the strongly luminescent [Mo6Cl8Cl6](2), [Mo6Br8Br6](2) and [Mo6I8I6](2) clusters, suggest that the clusters [Mo6Cl8F6](2), [Mo6Br8F6](2), [Mo6I8F6](2), [Mo6I8Cl6](2) and [Mo6I8Br6](2) studied here might be also luminescent. The calculated bond energies and reactivity indexes indicate that the most labile clusters are those with axial iodide ligands.
First author: Kim, Jong Chan, Reaction mechanisms of dissociative chemisorption of HI, I-2, and CH3I on a magic cluster Al-13(-), JOURNAL OF COMPUTATIONAL CHEMISTRY, 29, 1626, (2008)
Abstract: We have investigated the transition-state structures and reaction mechanisms for the dissociative chemisorption reactions of HI, I-2, and CH3I on the magic cluster Al-13(-). The HI, I-2, and CH3I molecules approach Al-13(-) with an end-on orientation rather than a side-on orientation because of the more effective orbital overlap in the end-on orientation. The reactions of Al-13(-) with HI and I-2 would produce Al13HI- and Al13I2-, respectively, because of large exothermic energy changes and relatively small activation energies. The reaction of Al-13(-) with CH3I is unlikely to take place because of the low mobility of CH3 on Al-13(-) and the high activation barrier for the S(N)2-type reaction. The dissociative chemisorption reactions are preferred thermodynamically to the abstractive chemisorption reactions.
First author: Radius, Udo, Bonding of imidazol-2-ylidene ligands in nickel complexes, ORGANOMETALLICS, 27, 3410, (2008)
Abstract: The bonding of imidazol-2-ylidenes (H(2)Im) in a series of nickel complexes with seemingly different complex fragment group electronegativities, i.e., [Ni(H(2)Im)(3)], [Ni(H(2)Im)(2)], [Ni(H(2)Im)(CO)], [Ni(H(2)Im)-(CO)(2)], and [Ni(H(2)Im)(CO)(3)], was analyzed. This series provides theoretical evidence that the bonding of imidazol-2-ylidene ligands to metal-complex fragments strongly depends on the nature of the ligand environment of the metal complex. An analysis of a series of isostructural complexes D-2h- and D-2d-M(H(2)Im)(2) with different metals (M = Ni, Pd, Pt) reveals that the bonding also strongly depends on the metal used in the complex.
First author: Piro, Nicholas A., P(2) addition to terminal phosphide M P triple bonds: A rational synthesis of cyclo-P(3) complexes, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130, 9524, (2008)
Abstract: The diphosphaazide complex (Mes*NPP)Nb(N[Np]Ar)(3) (Mes* = 2,4,6-tri-tert-butylphenyl, Np = neopentyl, Ar = 3,5-Me(2)C(6)H(3)), 1, has previously been reported to lose the P(2) unit upon gentle heating, to form (Mes*N)Nb(N[Np]Ar)(3), 2. The first-order activation parameters for this process have been estimated here using an Eyring analysis to have the values Delta H(double dagger) = 19.6(2) kcal/mol and Delta S(double dagger) = -14.2(5) eu. The eliminated P2 unit can be transferred to the terminal phosphide complexes P M(N[(i)Pr]Ar)(3), 3-M (M = Mo, W), and [P Nb(N[Np]Ar)(3)](-), 3-Nb, to give the cyclo-P(3) complexes (P3)M(N[(i)Pr]Ar)3 and [(P3)Nb(N[Np]Ar)(3)](-). These reactions represent the formal addition of a PP triple bond across a M P triple bond and are the first efficient transfers of the P2 unit to substrates present in stoichiometric quantities. The related complex (OC)(5)W(lMes*NPP)Nb(N[Np]Ar)(3), 1-W(CO)(5), was used to transfer the (P(2))W(CO)(5) unit in an analogous manner to the substrates 3-M (M = Mo, W, Nb) as well as to [(OC)(5)WP=-Nb(N[Np]Ar)(3)](-). The rate constants for the fragmentation of 1 and 1 -W(CO)5 were unchanged in the presence of the terminal phosphide 3-Mo, supporting the hypothesis that molecular P2 and (P2)W(CO)5, respectively, are reactive intermediates. In a reaction related to the combination of P P and M P triple bonds, the phosphaalkyne AdC P (Ad = 1-adamantyl) was observed to react with 3-Mo to generate the cyclo-CP(2) complex (AdCP(2))Mo(N[(i)Pr]Ar)(3). Reactions of the electrophiles Ph(3)SnCl, Mes*NPCI, and AdC(O)CI with the anionic, nucleophilic complexes [(OC)(5)W(P(3))Nb(N[Np]Ar)(3)](-) and [{(OC)(5)W}(2)(P(3))Nb(N[Np]Ar)(3)](-) yielded coordinated eta(2)-triphosphirene ligands. The Mes*NPW(CO)(5) group of one such product engages in a fluxional ring-migration process, according to NMR spectroscopic data. The structures of (OC)(5)W(P(3))W(N[(i)Pr]Ar)(3), [(Et(2)O)Na][{(OC)(5)W}(2)-(P(3))Nb(N[Np]Ar)(3)], (AdCP(2))Mo(N[(i)Pr]Ar)(3), (OC)(5)W(Ph(3)SnP(3))Nb(N[Np]Ar)(3), Mes*NP(W(CO)(5))P(3)Nb(N[Np]Ar)(3), and {(OC)5W}(2)AdC(O)P(3)Nb(N[Np]Ar)(3), as determined by X-ray crystallography, are discussed in detail.
First author: Pelmenschikov, Vladimir, Ligand-bound S=1/2 FeMo-cofactor of nitrogenase: Hyperfine interaction analysis and implication for the central ligand X identity, INORGANIC CHEMISTRY, 47, 6162, (2008)
Abstract: Broken symmetry density functional theory (BS-DFT) has been used to address the hyperfine parameters of the single atom ligand X, proposed to be coordinated by six iron ions in the center of the paramagnetic FeMo-cofactor (FeMoco) of nitrogenase. Using the X = N alternative, we recently found that any hyperfine signal from X would be small (calculated A(iso)(X = N-14) = 0.3 MHz) due to both structural and electronic symmetry properties of the [Mo-7Fe-9S-X] FeMoco core in its resting S = 3/2 state. Here, we extend our BS-DFT approach to the 2e(-) reduced S = 1/2 FeMoco state. Alternative substrates coordinated to this FeMoco state effectively perturb the electronic and/or structural symmetry properties of the cofactor. Using an example of an allyl alcohol (H2C=CH-CH2-OH) product ligand, we consider three different binding modes at single iron site and three different BS-DFT spin state structures and show that this binding would enhance the key hyperfine signal A(iso)(X) by at least 1 order of magnitude (3.8 <= A(iso)(X = N-14) <= 14.7 MHz), and this result should not depend strongly on the exact identity of X (nitrogen, carbon, or oxygen). The interstitial atom, when the nucleus has a nonzero magnetic moment, should therefore be observable by ESR methods for some ligand-bound FeMoco states. In addition, our results illustrate structural details and likely spin-coupling patterns for models for early intermediates in the catalytic cycle.
First author: Cozzolino, Anthony F., Valence electronic structure of benzo-2,1,3-chalcogenadiazoles studied by photoelectron spectroscopy and density functional theory, INORGANIC CHEMISTRY, 47, 6220, (2008)
Abstract: The He I photoelectron spectra of benzo-2,1,3-thia-, selena-, and telluradiazole were measured, and the observed ionization bands were assigned by comparison with the results of DFT calculations. Whereas the B3LYP exchange-correlation functional provided orbital energies that permitted a preliminary assignment by application of Koopman’s theorem, a more-accurate interpretation was established by calculation of the vertical ionization energies with the PW91 functional and analysis of the correlation of energy levels along the homologous series. This strategy clarified earlier disagreements in the assignment of the spectrum of benzo-2,1,3-thiadiazole.
First author: Gueell, Mireia, Importance of the basis set for the spin-state energetics of iron complexes, JOURNAL OF PHYSICAL CHEMISTRY A, 112, 6384, (2008)
Abstract: We have performed a systematic investigation of the influence of the basis set on relative spin-state energies for a number of iron compounds. In principle, with an infinitely large basis set, both Slater-type orbital (STO) and Gaussian-type orbital (GTO) series should converge to the same final answer, which is indeed what we observe for both vertical and relaxed spin-state splittings. However, we see throughout the paper that the STO basis sets give consistent and rapidly converging results, while the convergence with respect to the basis set size is much slower for the GTO basis sets. For example, the large GTO basis sets that give good results for the vertical spin-state splittings of compounds 1-3 (6-311+G**, Ahlrichs VTZ2D2P) fail for the relaxed spin-state splittings of compound 4 (where 1 is Fe-(PyPepS)(2) (PyPepSH(2) = N-(2-mercaptophenyl)-2-pyridinecarboxamide), 2 is Fe(tsalen)Cl (tsalen = N,N’-ethylenebis-(thiosalicylideneiminato)), 3 is Fe(N(CH2-o-C6H4S)(3))(1-Me-imidazole), and 4 is FeFHOH). Very demanding GTO basis sets like Dunning’s correlation-consistent (cc-pVTZ, cc-pVQZ) basis sets are needed to achieve good results for these relaxed spin states. The use of popular (Pople-type) GTO, effective core potentials basis set (ECPB), or mixed ECPB(Fe):GTO(rest) basis sets is shown to lead to substantial deviations (2-10 kcal/mol, 14-24 kcal/mol for 3-21G), in particular for the high spin states that are typically placed at too low energy. Moreover, the use of an effective core potential in the ECPB basis sets results in spin-state splittings that are systematically different from the STO-GTO results.
First author: Pistonesi, Carolina, A DFT study of H adsorption on Pt(111) and Pt-Ru(111) surfaces, APPLIED SURFACE SCIENCE, 254, 5827, (2008)
Abstract: In this work a comparative analysis between different Pt-Ru(111) surface models and pure Pt(111) surface is presented. Some aspects of the electronic structure of the surfaces and hydrogen adsorption are analysed based on density functional theory calculations. The hydrogen adsorption energy is significantly reduced when Ru is present on the surface. The substitution of Pt atoms by Ru atoms reinforce the Pt-H bond while the metal-metal bond is strongly modified, making the system less stable.
First author: Filipuzzi, Serena, Weak eta(2)-olefin bonding in palladium and platinum allyl cationic complexes containing chiral monodentate ligands with alpha-phenyl methyl amine side chains, ORGANOMETALLICS, 27, 2949, (2008)
Abstract: Detailed NMR studies on a series of Pd and Pt allyl complexes containing phosphoramidite ligands with NCH(CH3)Ph side chains are reported. When a coordination position becomes available, e.g., via abstraction of a chloride ligand, one double bond of the phenyl group of the side chain complexes to the metal, affording an eta(2)-olefin structure. These allyl complexes exhibit a number of dynamic processes, and these have been elucidated via low-temperature NMR studies combined with 2D NOESY methods. DFT calculations confirm the ability of the amine side chain to coordinate to the metal almost without distortion, leading to a weak eta(2)-arene-Pd bonding interaction (similar to 13 kcal mol(-1)). The latter result is supported by the NMR studies.
First author: Lu, Tsai-Te, Anionic Roussin’s red esters (RREs) syn-/anti-[Fe(mu-SEt)(NO)(2)](2)(-): the critical role of thiolate ligands in regulating the transformation of RREs into dinitrosyl iron complexes and the anionic RREs, INORGANIC CHEMISTRY, 47, 6040, (2008)
Abstract: The anionic syn-/anti-(Fe(mu-SEt)(NO)(2)](2)(-) (2a) were synthesized and characterized by IR, UV-vis, EPR, and X-ray diffraction. The geometry of the [Fe(mu-S)(2)Fe] core is rearranged in going from [{Fe(NO)(2)}(9)-{Fe(NO)(2)}(9)] Roussin’s red ester [Fe(mu-SEt)(NO)(2)](2) (1a) (Fe center dot center dot center dot Fe distance of 2.7080(5) angstrom) to the [(Fe(NO)(2)}(9)-{Fe(NO)(2)}(10)] complex 2a (Fe center dot center dot center dot Fe distance of 2.8413(6) angstrom) to minimize the degree of Fe center dot center dot center dot Fe interaction to stabilize complex 2a. On the basis of X-ray absorption (Fe K- and L-edge), EPR and SQUID, complex 2a is best described as the anionic [{Fe(NO)(2)}(9)-{Fe(NO)(2)}(10)] Roussin’s red ester with the fully delocalized mixed-valence core. The complete bridgedthiolate cleavage yielded DNIC [(EtS)(2)Fe(NO)(2)](-) (3a) in the reaction of 2 equiv of [EtS](-) and complex la, whereas reaction of 2 equiv of [(t)BuS](-) with [Fe(mu-S(t)Bu)(NO)(2)](2) (1b) gave DNIC [((t)BuS)(2)Fe(NO)(2)](-) (3b) and the anionic Roussin’s red ester [Fe(mu-S(t)Bu)(NO)(2)](2)(-) (2b) through bridged-thiolate cleavage in combination with reduction. In contrast to the inertness of DNIC 3b toward complex 1b, nucleophile DNIC 3a induces the reduction of complex la to produce the anionic Roussin’s red ester 2a. Interestingly, dissolution of complex 3a in MeOH at 298 K finally led to the formation of a mixture of complexes 2a and 3a, in contrast to the dynamic equilibrium of complexes 3b and 1b observed in dissolution of complex 3b in MeOH. These results illustrate the aspect of how the steric structures of nucleophiles ([EtS](-) vs [(t)BuS](-) and [(EtS)(2)Fe(NO)(2)](-) vs [(tBuS)(2)Fe(NO)(2)](-)) function to determine the reaction products.
First author: Yan, Likai, On the origin of alternating bond distortions and the emergence of chirality in polyoxometalate anions, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130, 8223, (2008)
Abstract: Alternating short and long bond length (ABL) distortions observed within the ring structures of molecular metal oxide anions or polyoxometalates (POMs) are reminiscent of the cooperative linear ABL distortions in perovskite do metal oxides. We show herein that these distortions have a common origin: a pseudo Jahn-Teller (PJT) vibronic instability. Four POM structural types with different MnOn ring sizes are investigated herein using density functional theoretical methods: Lindqvist [M6O19](q-) (n = 4), Keggin alpha-[XM12O40](q-) (n = 6), Wells-Dawson alpha-[X2M18O62](q-) (n = 8), and Preyssler [(Na)P5W30O110](14-) (n = 10), where M = Mo-VI and W-VI and X = Si-IV, Ge-IV, P-V,P- As-v, S-VI, and Se-VI. Chirality is induced within the latter three structural types by the ABL ring distortions. The calculations confirm the PJT vibronic origin of the ABL distortions with good agreement between calculated geometries and published single-crystal X-ray diffraction data. Both theory and experiment show that the vibronic interaction and distortion magnitude increase for (1) molybdates relative to that of tungstates, (2) larger MnOn ring sizes, (3) increases in negative charge of the internalized fragments (O2- or XO4 (q-)), and (4) d(0) versus d(n) metal oxidation states. The PJT vibronic coupling model explains these observations in terms of the energy gap between Kohn-Sham frontier molecular orbitals (MOs) concomitant with the propensity for metal-oxygen.7-bonding within the MnOn rings. The frontier MOs for the undistorted nuclear configurations are largely nonbonding pi-O-p (occupied) and pi-M-d (unoccupied) in character, where smaller HOMO-LUMO (H-L) gap energies lead to greater metai-oxygen pi-orbital mixing under the influence of the nuclear distortion. A reduction in pi-bond order decreases the distortion in mixed-valence POMs. Of the tungstates examined, only the Preyssler anion shows pronounced ABL ring distortions, which derive from its large ring size and concomitant small H-L gap.
First author: Seldenthuis, Johannes S., Vibrational excitations in weakly coupled single-molecule junctions: A computational analysis, ACS NANO, 2, 1445, (2008)
Abstract: In bulk systems, molecules are routinely identified by their vibrational spectrum using Raman or infrared spectroscopy. In recent years, vibrational excitation lines have been observed in low-temperature conductance measurements on single-molecule junctions, and they can provide a similar means of identification. We present a method to efficiently calculate these excitation lines in weakly coupled, gateable single-molecule junctions, using a combination of ab initio density functional theory and rate equations. Our method takes transitions from excited to excited vibrational state into account by evaluating the Franck-Condon factors for an arbitrary number of vibrational quanta and is therefore able to predict qualitatively different behavior from calculations limited to transitions from ground state to excited vibrational state. We find that the vibrational spectrum is sensitive to the molecular contact geometry and the charge state, and that it is generally necessary to take more than one vibrational quantum into account. Quantitative comparison to previously reported measurements on pi-conjugated molecules reveals that our method is able to characterize the vibrational excitations and can be used to identify single molecules in a junction. The method is computationally feasible on commodity hardware.
First author: Garcia-Lastra, J. M., On the application of the bond transferability postulate to transition-metal complexes: Study of FeF63- and FeOF54- centers in KMgF3, APPLIED MAGNETIC RESONANCE, 34, 149, (2008)
Abstract: The equilibrium geometry of the C-4 nu FeOF54- center in KMgF3 has been explored by means of density functional theory calculations. Particular attention has been paid to the changes of electronic density on passing from the O-h FeF63- center in KMgF3 to FeOF54-, as well as to the variations undergone by the isotropic superhyperfine constant of axial A(s)(F-ax) and equatorial A(s)(F-eq) fluorine nuclei placed from Fe3+ at distances R-ax and R-eq, respectively. As a salient feature it is found for FeOF54- that, even if R-eq = R-ax, A(s)(F-eq) is significantly higher than A(s)(F-ax) thus pointing out that such quantities depend not only on the Fe3+-F- distance of the corresponding bond. Accordingly the obtained equilibrium distances R-ax = 0.2178 nm and R-eq = 0.2055 nm are not reproduced by any model based on the bond transferability. A slight off-center 0.018 nm displacement of Fe3+ towards O2- is derived through the present calculations which reproduce reasonably well the experimental ratio A(s)(F-eq)/A(s)(F-ax) = 2.3.
First author: Janicki, Rafal, Complexes of Yb3+ with EDTA and CDTA – Molecular and electronic structure, EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, 34, 3075, (2008)
Abstract: Two Yb3+ compounds, [C(NH2)(3)](2)[Yb(EDTA)(H2O)(2)]ClO4 center dot 6H(2)O and [C(NH2)(3)][Yb(CDTA)(H2O)(2)]center dot 4H(2)O, where EDTA is the ethylene diaminetetraacetate anion and CDTA is the trans-1,2-diaminecyclohexane-N,N,N’,N’-tetraacetate anion, were obtained and their crystal structures and spectroscopic properties were determined. In both compounds, the coordination geometries of the eight-coordinate Yb3+ ion are very similar. In each case, the inner sphere of the metal ion consists of four carboxyl oxygen atoms, two nitrogen atoms and two water molecules. The complexes were characterized by UV/Vis/NIR absorption at different temperatures and IR spectroscopy. The spectroscopic results revealed high sensitivity of the electronic 4f(13) configuration upon minor changes in the coordination geometry around the Yb3+ ion. These data also demonstrate that species present in solutions of Yb3+-EDTA are similar to those found in the crystal, whereas in solutions of Yb3+-CDTA an equilibrium between at least two different forms exists. For the Yb3+-EDTA complex in solution and in the crystalline state, a charge-transfer transition was detected. Theoretical calculations revealed its complicated (Yb -> ligand and ligand Yb) character.
First author: Mutseneck, Elena V., Cationic triple-decker complexes with a bridging 4-borataborepine ligand: Synthesis, structure, and bonding, EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, 34, 3320, (2008)
Abstract: Cationic 30VE triple-decker complexes [Cp*Ru(mu-eta(7):eta(7)-C(5)B(2)Me(6)H)ML](+) [ML = CO(C(4)Me(4)) (3a), RuCp* (4a), Rh(cod) (7a), and lr(cod) (8a)] with a bridging hexamethyl-4-borataborepine ligand were obtained by electrophilic stacking of the sandwich compound Cp*Ru(eta(7)-C(5)B(2)Me(6)H) (2a) with [ML](+) complex fragments. The reaction of the phenyl-substituted derivative Cp*Ru(eta(7)-7-PhC(5)B(2)Me(5)H) (2b) with [(C(4)Me(4))Co(MeCN)(3)](+) selectively affords the triple-decker complex [Cp*Ru(mu-eta(7)-7-PhC(5)B(2)Me(5)H)CO(C(4)Me(4))](+) (3b), whereas a similar reaction with [Cp*RuCl](4)/TIBF(4) produces a 1:3 mixture of cations, the triple-decker [Cp*Ru(mu-eta(7)-7-PhC(5)B(2)Me(5)H)RuCp*](+)(4b) and the arene-coordinated Cp*Ru(mu-eta(6):eta(7)-7-PhC(5)B(2)Me(5)H)RuCp*](+) (5). Stacking of [Cp*Ru(eta(7)-7-PhCH(2)C(5)B(2)Me(5)H) (2c) with [CpRu(MeCN)(3)](+) selectively gives the triple-decker complex [Cp*Ru(mu-eta(7)-7-PhCH(2)C(5)B(2)Me(5)H)RuCP](+) (6c). The dinuclear cations 3-8 were isolated as deep-colored air-stable salts with [BF(4)](-) or [PF(6)](-) anions in moderate to high yields. Structures of 3bPF(6), 4aBF(4), 7aBF(4), and 8aBF(4) were confirmed by X-ray diffraction studies. Energy decomposition analysis of complexes CpRu(ring) and [CpRu(ring)RuCp](+) (ring = Cp, C(5)BH(6), C(5)B(2)H(7)) revealed that the insertion of BH units makes the bonding between [ring](-) and [RuCp](+) more covalent. According to Mulliken population analysis, weakening of pi-donation and strengthening of delta-back donation occur in the same order. The electrostatic character of the bond and the contribution of sigma-donation to the covalent bonding are higher in the case of bifacially bonded rings. The b oron- containing triple-decker complexes are considerably more stable than the cyclopentadienyl analog.
First author: Verstraelen, T., ZEOBUILDER: A GUI toolkit for the construction of complex molecular structures on the nanoscale with building blocks, JOURNAL OF CHEMICAL INFORMATION AND MODELING, 48, 1530, (2008)
Abstract: In this paper, a new graphical toolkit, ZEOBUILDER, is presented for the construction of the most complex zeolite structures based on building blocks. Molecular simulations starting from these model structures give novel insights in the synthesis mechanisms of micro- and mesoporous materials. ZEOBUILDER is presented as an open-source code with easy plug-in facilities. This architecture offers an ideal platform for further development of new features. Another specific aspect in the architecture of ZEOBUILDER is the data structure with multiple reference frames in which molecules and molecular building blocks are placed and which are hierarchically ordered. The main properties of ZEOBUILDER are the feasibility for constructing complex structures, extensibility, and transferability. The application field of ZEOBUILDER is not limited to zeolite science but easily extended to the construction of other complex (bio)molecular systems. ZEOBUILDER is a unique user-friendly GUI toolkit with advanced plug-ins allowing the construction of the most complex molecular structures, which can be used as input for all ab initio and molecular mechanics program packages.
First author: Sartorel, Andrea, H2O2 activation by heteropolyacids with defect structures: the case of gamma-[(XO4)W10O32](n-) (X = Si, Ge, n=8; X = P, n=7), JOURNAL OF PHYSICAL ORGANIC CHEMISTRY, 21, 596, (2008)
Abstract: DFT calculations including relativistic and solvent effects have been carried out for elucidating geometries and energies of tetra-protonated, site-defective, polyoxotungstates with general formula gamma-(XO4)W10O32](n-) [X = Si, Ge, n-8; X=P, n=7). Converging spectroscopic and computational evidence point to a unique role played by the lacunary structure, and allow to address the electronic and structural factors dictating the protonation sites and equilibria of these complexes, as well as their impact on H2O2 activation. In all cases, the evolution of the four terminal W – O functions, bordering the site defect on the polyoxotungstate surface, towards a bis-aquo, bis-oxo structure is preferred over the formation of four terminal hydroxo ligands. Substitution of these W – OH2 functions with peroxo ligands and their involvement in the oxygen transfer to an alkene acceptor is also supported by DFT calculations.
First author: Mananes, A., Half-metallic finite zigzag single-walled carbon nanotubes from first principles, PHYSICAL REVIEW B, 78, 596, (2008)
Abstract: Density-functional calculations predict half-metallicity in zigzag single-walled carbon nanotubes of finite length with the two ends saturated with hydrogen. We have analyzed the change of the alpha- and beta-spin electronic gaps under the influence of an electric field applied along the nanotube axis. The half-metallic behavior, in which the electronic gap is zero for one spin flavor and nonzero for the other, is obtained for a critical electric field of 3.0/w V/angstrom, where w is the length of the nanotube. This critical field is the same as that predicted for graphene nanoribbons. By a detailed analysis of the spin structure of the ground state, we show the relevance of the edge states, electronic states spatially localized at the carbon atoms of the nanotube boundaries, on the on-set of half-metallicity, and on the magnetic properties of the finite semiconducting zigzag nanotubes.
First author: Caramori, Giovanni F., Analysis of the metal-ligand bonds in [Mo(X)(NH(2))(3)] (X = P, N, PO, and NO), [Mo(CO)(5)(NO)](+), and [Mo(CO)(5)(PO)](+), THEORETICAL CHEMISTRY ACCOUNTS, 120, 351, (2008)
Abstract: Quantum chemical calculations at the DFT level have been carried out for model complexes [Mo(P)(NH(2))(3)] (1), [Mo(N)(NH(2))(3)] (2), [Mo(PO)(NH(2))(3)] (3), [Mo(NO)(NH(2))(3)] (4), [Mo(CO)(5)(PO)](+) (5), and [Mo(CO)(5)(NO)](+) (6). The equilibrium geometries and the vibration frequencies are in good agreement with experimental and previous theoretical results. The nature of the Mo-PO, Mo-NO, Mo-PO(+), Mo-NO(+), Mo-P, and Mo-N bond has been investigated by means of the AIM, NBO and EDA methods. The NBO and EDA data complement each other in the interpretation of the interatomic interactions while the numerical AIM results must be interpreted with caution. The terminal Mo-P and Mo-N bonds in 1 and 2 are clearly electron-sharing triple bonds. The terminal Mo-PO and Mo-NO bonds in 3 and 4 have also three bonding contributions from a sigma and a degenerate pi orbital where the sigma components are more polarized toward the ligand end and the pi orbitals are more polarized toward the metal end than in 1 and 2. The EDA calculations show that the pi bonding contributions to the Mo-PO and Mo-NO bonds in 3 and 4 are much more important than the sigma contributions while sigma and pi bonding have nearly equal strength in the terminal Mo-P and Mo-N bonds in 1 and 2. The total (NH(2))(3)Mo-PO binding interactions are stronger than for (NH(2))(3)Mo-P which is in agreement with the shorter Mo-PO bond. The calculated bond orders suggest that there are only (NH(2))(3)Mo-PO and (NH(2))(3)Mo-NO double bonds which comes from the larger polarization of the sigma and pi contributions but a closer inspection of the bonding shows that these bonds should also be considered as electron-sharing triple bonds. The bonding situation in the positively charged complexes [(CO)(5)Mo-(PO)](+) and [(CO)(5)Mo-(NO)](+) is best described in terms of (CO)(5)Mo -> XO(+) donation and (CO)(5)Mo <- XO(+) backdonation (X = P, N) using the Dewar-Chatt-Duncanson model. The latter bonds are stronger and have a larger pi character than the Mo-CO bonds.
First author: Amati, Mario, Competition between Bailar and Ray-Dutt paths in conformational interconversion of tris-chelated complexes: a DFT study, THEORETICAL CHEMISTRY ACCOUNTS, 120, 447, (2008)
Abstract: Tris-chelated complexes of aluminum with alpha-isopropenyltropolonate and alpha-isopropyltropolonate ligands can be considered prototypical complexes for the study of internal rearrangements through prismatic transient structures. Such isomerization paths, known as Bailar and Ray-Dutt twists, have been suggested for these compounds on the basis of dynamic NMR study, but modern computational methodologies have never been applied to corroborate this finding. In this paper, we report a computational investigation about the internal isomerization processes of the mentioned complexes. Both the Bailar and Ray-Dutt twists have been found as possible reaction paths. The prismatic structures along each reaction path have been described as transition structures rather than intermediate and have been computationally characterized. A comparison between experimental and computational kinetic data has been performed.
First author: Dalach, P., Enhanced hydrogen uptake and the electronic structure of lithium-doped metal-organic frameworks, JOURNAL OF PHYSICAL CHEMISTRY C, 112, 9278, (2008)
Abstract: Metal-organic framework (MOF) materials show potential for gas separation and storage, and as hosts for highly selective catalyst molecules. Density functional theory (DFT) is applied to periodic band structures and to selected clusters representative of the cornerpost and strut environments of two MOFs to characterize the electronic environment. Binding sites and the binding energies of H-2 are calculated with and without the presence of a Li dopant. It is found that Li enhances the H-2 binding energies, both on the linking strut ring structures and for sites near cornerpost oxygen. MP2 correlation studies of the basic H-2-Li-bipyridine interaction are carried out to explore effects of correlation beyond DFT. Contrary to previous model assumptions, we find that Li associates strongly with the cornerposts and less so with aromatic rings.
First author: Schinzel, Sandra, Evaluation of the carbene hydride mechanism in the carbon-carbon bond formation process of alkane metathesis through a DFT study, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130, 7984, (2008)
Abstract: Olefin metathesis on a silica supported tantalumhydridocarbene complex, the key carbon-carbon making process in alkane metathesis, requires a large number of elementary steps in contrast to the known olefin metathesis pathway, which corresponds to successive [2 + 2]-cycloaddition and cycloreversion steps. The direct pathway is forbidden because it requires the formation of a high energy reaction intermediates, an olefin adduct of trigonal bipyramid (TBP) geometry, where the carbene is trans to an hydride ligand. Extra low-energy steps are therefore necessary to connect the reactants to products, the key being a turnstile interconversion at the metal lacyclobutane intermediates.
First author: Groenewold, Gary S., Infrared spectroscopy of dioxouranium(V) complexes with solvent molecules: Effect of reduction, CHEMPHYSCHEM, 9, 1278, (2008)
Abstract: UO(2)(+)-solvent complexes having the general formula [UO(2)-(ROH)](+) (R=H, CH(3) C(2)H(5), and n-C(3)H(7)) are formed using electrospray ionization and stored in a Fourier transform ion cyclotron resonance mass spectrometer, where they are isolated by mass-to-charge ratio, and then photofragmented using a free-electron loser scanning through the 10 mu m region of the infrared spectrum. Asymmetric O=U=O stretching frequencies (v) are measured over a very small range [from similar to 953cm(-1) for H(2)O to similar to 944 cm(-1) for n-propanol (n-PrOH)] for all four complexes, indicating that the nature of the alkyl group does not greatly affect the metal centre. The v(3) values generally decrease with increasing nucleophilicity of the solvent, except for the methanol (MeOH)-containing complex, which has a measured v(3) value equal to that of the n-PrOH-containing complex. The v, frequency values for these U(V) complexes are about 20 cm(-1) lower than those measured for isoelectronic U(VI) ion-pair species containing analogous alkoxides. v(3) values for the U(V) complexes are comparable to those for the anionic [UO(2)(NO(3))(3)](-) complex, and 40-70 cm(-1) lower than previously reported values for ligated uranyl(VI) dication complexes. The lower frequency is attributed to weakening of the O=U=O bonds by repulsion related to reduction of the U metal centre, which increases electron density in the antibonding pi* orbitals of the uranyl moiety. Computational modelling of the v(3) frequencies using the B3LYP and PBE functionals is in good agreement with the IRMPD measurements, in that the calculated values fall in a very small range and are within a few cm(-1) of measurements. The values generated using the LDA functional are slightly higher and substantially overestimate the trends. Subtleties in the trend in v(3) frequencies for the H(2)O-MeOH-EtOH-n-PrOH series are not reproduced by the calculations, specifically for the MeOH complex, which has a lower than expected value.
First author: Wang, Dongqi, Why do C-1-symmetric ansa-zirconocene catalysts produce lower molecular weight polymer’s for ethylene/propylene copolymerization than for ethylene/propylene homopolymerization?, ORGANOMETALLICS, 27, 2861, (2008)
Abstract: We have carried out a combined QM/MM study to rationalize the factors that can affect the performance of C-1-symmetric ansa-zirconocene catalysts that contain bridged cyclopentadienyl (Cp) and fluorenyl (Flu) ligands in olefin homo- and copolymerization. Two growing chains with different beta-C (tertiary or secondary) and two olefins (propene and ethylene) have been used for this purpose. Our calculations indicate that chain transfer has a higher barrier than chain propagation in EE (ethylene homopolymerization), PP (propylene homopolymerization), and PE (propylene complexation to a metal with a propyl chain) systems. However, the two processes are competitive in EP (ethylene complexation to a metal with a 2-methylpropyl chain) system. Substituents on the carbon in a C-H link weaken the C-H bond. This in turn determines the order EP < EE < PP < PE for the heat of reaction of the beta-hydrogen transfer process, giving rise to the chain termination, where the process with the most negative reaction heat is the more thermodynamically favorable. It is further argued that the barriers for the termination process must follow the same order of EP < EE < PP < PE. For the insertion process the barrier increases with the number of substituents on the olefin and the C-beta atom of the growing chain as PP > PE similar to EP > EE. The different propensity of the four systems for termination and propagation results in the higher barrier of termination for EE, PP, and PE, whereas the barriers are similar for EP. Our analysis explains why ethylene/propylene homopolymerization affords high molecular weight polymers, whereas ethylene/propylene copolymerization affords low molecular weight polymers.
First author: Seth, Michael, Application of magnetically perturbed time-dependent density functional theory to magnetic circular dichroism. II. Calculation of A terms, JOURNAL OF CHEMICAL PHYSICS, 128, 2861, (2008)
Abstract: The magnetically perturbed time-dependent density functional theory is used to derive equations for the magnetic circular dichroism (MCD) of degenerate transitions of closed shell molecules. The MCD of this type of transition can be divided into two contributions. The dominant contribution is usually that from A terms that arise because of the breaking of the degeneracy of the excited state in the presence of the magnetic field. The second contribution comes from B terms that arise because of the perturbation of the transition dipole by the magnetic field. The formalism is applied to ten tetrahedral d(0) transition metal oxy- and thioanions. The MCD parameters of these systems are reproduced quite well by the calculations. Simulated spectra derived from the calculated parameters are in good agreement with the observed spectra.
First author: Chang, Yu-Chang, Crystal engineering for pi-pi stacking via interaction between electron-rich and electron-deficient heteroaromatics, JOURNAL OF ORGANIC CHEMISTRY, 73, 4608, (2008)
Abstract: New dipolar compounds containing alternating electron-rich thieno[3,2-b]thiophene units and electron deficient units have been synthesized. Compounds with 5-pyrimidinyl (compound 2) or benzothiazole (compound 5) as the electron-deficient unit were structurally characterized by the single-crystal X-ray diffraction method. The arrangement of the molecules is found to be one-dimensional slipped-pi-stack for 2. That of 5 is of slipped-pi-stack, albeit with a tilt angle between neighboring pi-stacks. The pi-pi interfacial distances of the molecules in the crystal lattice are 3.47 and 3.59 angstrom for 2 and 5, respectively. On the basis of the crystal structure, compound 2, with negligible pi-pi slip along the short axis of the molecules, has a calculated electronic coupling value (0.153 eV) twice as large as that of the largest coupling of pentacene. Accordingly, the theoretically estimated hole mobility (mu(+)) for 2 (2.32 cm(2) s(-1) V(-1)) compares favorably with that of pentacene (1.93-5.43 cm(2) s(-1) V(-1)), despite of the larger reorganization energy for hole transport in 2. The symmetric intrastack S center dot center dot center dot C contacts found between the thieno[3,2-b]thiophene and pyrimidinyl units explain the unique features of the crystal structure of 2 and the resulting large electronic coupling.
First author: Smolentsev, Grigory, Three-dimensional local structure of photoexcited cu diimine complex refined by quantitative XANES analysis, JOURNAL OF PHYSICAL CHEMISTRY A, 112, 5363, (2008)
Abstract: The structural details of [Cu(dMP)(2)](+) (dmp = 2,9-dimethyl- 1,10-phenanthroline) at its metal-to-ligand charge-transfer (MLCT) excited-state in acetonitrile were extracted using quantitative analysis of Cu K-edge X-ray adsorption near edge structure (XANES). The study combines two techniques: fitting experimental XANES spectra with a multidimensional interpolation approximation, and calculating theoretical XANES spectra with molecular potentials beyond the muffin-tin approximation. The results of the study show that the best fit of the experimental XANES data must include a solvent molecule binding to the Cu with a short Cu-N distance of 2.00 angstrom. This confirms that the formation of an exciplex is responsible for the excited-state quenching in coordinating solvents, such as acetonitrile. Moreover, the calculations suggest that the formation of this exciplex state is accompanied by significant rocking distortions of the dmp ligands resulting in a 108 degrees angle between the N(solvent)-Cu bond and the C-2 symmetry axis of the dmp ligand. This combined approach allows us to extract molecular configurations that would otherwise be missed in a conventional qualitative XANES analysis.
First author: Tonzani, Stefano, Electronic excitations and spectra in single-stranded DNA, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130, 7607, (2008)
Abstract: Using density functional theory and molecular dynamics simulations, we show that delocalized states extending over three bases can be directly excited in single-stranded poly(A) DNA. The results are in semiquantitative agreement with recent experimental results for the delocalization length of these states in single- and double-stranded DNA. The structures used in these molecular dynamics calculations are validated by comparing calculated circular dichroic spectra for d(A)(2) and d(A)(4) with experiment. These spectra, which arise from highly stacked structures, are in good agreement with experiment, suggesting that the short delocalization in ssDNA arises in spite of strong stacking.
First author: Guan, Wei, Reversible redox-switchable second-order optical nonlinearity in polyoxometalate: A quantum chemical study of [PW11O39(ReN)](n-) (n=3-7), INORGANIC CHEMISTRY, 47, 5245, (2008)
Abstract: In this paper, the relationship between the reversible redox properties and the second-order nonlinear optical (NLO) responses for the title series of complexes has been systematically investigated by using the time-dependent density functional theory (TDDFT) method combined with the sum-over-states (SOS) formalism. The results reveal that the successive reduction processes of five PW11ReN redox states should be PW(11)Rev(VII) (1) -> PW11ReVI (2) -> PW11ReV (3) -> PW(11)Re(V)1e (4) -> PW(11)Re(V)2e (5). Furthermore, their electrochemical properties have been reproduced successfully. It is noteworthy that the second-order NLO behaviors can be switched by reversible redox for the present studied complexes. Full oxidation constitutes a convenient way to switch off the second-order polarizability (system 1). The incorporation of extra electrons causes significant enhancement in the second-order NLO activity, especially for the third reduced state (system 4), whose static second-order polarizability (beta(vec)) is about 144 times larger than that of fully oxidized 1. The characteristic of the charge-transfer transition corresponding to the dominant contributions to the beta(vec) values indicates that metal-centered redox processes influence the intramolecular donor or acceptor character. Therefore, these kinds of complexes with the facile and reversible redox states could become excellent switchable NLO materials.
First author: Zaleski-Ejgierd, Patryk, Structure and bonding of the MCN molecules, M=Cu, Ag, Au, Rg, JOURNAL OF CHEMICAL PHYSICS, 128, 5245, (2008)
Abstract: High-precision calculations are reported for the title series with M=Cu, Ag, Au, using CCSD(T) with the latest pseudopotentials and basis sets up to cc-pVQZ. The bond lengths for M=Cu, Ag, Au agree with experiment within better than 1 pm. The role of deep-core excitations is studied. The second-order spin-orbit effects are evaluated at the density functional theory level, including M=Rg. A qualitative bonding analysis suggests multiple M-C bonding. The calculated vibrational frequencies are expected to be more accurate than the available experimental estimates. The M-C bond lengths obey Cu < Rg < Au < Ag.
First author: Li, Qiaohong, Direct metal-metal interaction contributions to quadratic hyperpolarizability: A study on dirhenium complexes, JOURNAL OF PHYSICAL CHEMISTRY A, 112, 4965, (2008)
Abstract: We present a comparative study of the metal-metal interaction effect on the static quadratic hyperpolarizabilities of two typical dinuclear rhenium clusters. The electronic structures, excitation spectra, dipolar moments, static polarizabilities, and quadratic hyperpolarizabilities of the two complexes with direct metal-metal interactions have been computed and analyzed with the use of high-level DFT/TDDFT methods. The geometries and the first intense excitations agree with the relevant reported measurements. The orbital decomposition scheme (J. Phys. Chem. A 2006, 110, 1014-1021) has been applied to analyze the relationship between the electronic structures and nonlinear optical (NLO) properties of these two complexes. We propose an unprecedented NLO response mechanism featuring the contribution of the direct metal-metal interaction transition process in these dinuclear rhenium complexes. This contribution positively enhances the quadratic hyperpolarizability and relates to the intensity of the metal-metal interactions of the complexes. The results are helpful to the development of NLO chromophores in polynuclear metal clusters through the molecular design technique.
First author: Fan, Jing, On the origin of circular dichroism in trigonal dihedral cobalt (III) complexes of unsaturated bidentate Ligands, INORGANIC CHEMISTRY, 47, 4762, (2008)
Abstract: The circular dichroism spectra of the complexes Co(acac)(3), [CO(ox)(3)](3-), [Co(mal)(3)](3-), and (Co(Thiox)(3)](3-) with acac = acetylacetonate, ox = oxalate, mal = malonate, Thiox = dithioxalate, have been investigated computationally employing time-dependent density functional theory. A detailed comparison of the experimental and theoretical results is made. Rotatory strengths associated with typical electronic transitions in the complexes containing unsaturated ligands are interpreted within a qualitative framework in terms of transition moments for excitations within a single ligand.
First author: Bridgeman, Adam J., Modeling the vibronic spectra of transition metal complexes: The ligand-field spectrum of [PtCl(4)](2-), INORGANIC CHEMISTRY, 47, 4817, (2008)
Abstract: A framework for calculating the intensity distribution and vibrational fine structure in the polarized ligand-field spectrum of transition metal complexes using the Herzberg-Teller approach is introduced and used to model the spectrum of the [PtCl(4)](2-) ion. The model uses geometries, vibrational frequencies, and transition moments generated using density functional calculations on the ground and excited states, which arise from spin-allowed reorganization of the d electrons. The model predicts the whole spectral trace, including the polarization, the difference in the frequency of the electronic origin, the band maximum and the vertical transition energy, and the temperature dependence of the band intensities and the frequencies of the band maxima. Excitation to the (1)A(2g) state is accompanied by a vibrational progression in the breathing mode of the excited state, as observed experimentally. Excitation to both the (1)B(1g) and (1)E(g) states is accompanied by a loss of planarity and extended vibrational progressions in two modes, and the resulting spectra are inherently of low resolution.
First author: Pantazis, Dimitrios A., All-electron scalar relativistic basis sets for third-row transition metal atoms, JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 4, 908, (2008)
Abstract: A family of segmented all-electron relativistically contracted (SARC) basis sets for the elements Hf-Hg is constructed for use in conjunction with the Douglas-Kroll-Hess (DKH) and zeroth-order regular approximation (ZORA) scalar relativistic Hamiltonians. The SARC basis sets are loosely contracted and thus offer computational advantages compared to generally contracted relativistic basis sets, while their sufficiently small size allows them to be used in place of effective core potentials (ECPs) for routine studies of molecules. Practical assessments of the SARC basis sets in DFT calculations of atomic (ionization energies) as well as molecular properties (geometries and bond dissociation energies for MHn complexes) confirm that the basis sets yield accurate and reliable results, providing a balanced description of core and valence electron densities. CCSD(T) calculations on a series of gold diatomic compounds also demonstrate the applicability of the basis sets to correlated methods. The SARC basis sets will be of most utility in calculating molecular properties for which the core electrons cannot be neglected, such as studies of electron paramagnetic resonance, Mossbauer and X-ray absorption spectra, and topological analysis of electron densities.
First author: van Zeist, Willem-Jan, Reaction coordinates and the transition-vector approximation to the IRC, JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 4, 920, (2008)
Abstract: The appearance of a reaction profile or potential energy surface (PES) associated with the reaction path (defined as the path of steepest descent from the saddle point) depends on the choice of reaction coordinate onto which the intrinsic reaction coordinate is projected. This provides one with the freedom, but also the problem, of choosing the optimal perspective (i.e., the optimal reaction coordinate) for revealing what is essential for understanding the reaction. Here, we address this issue by analyzing a number of different reaction coordinates for the same set of model reactions, namely, prototypical oxidative addition reactions of C-X bonds to palladium. We show how different choices affect the appearance of the PES, and we discuss which qualities make a particular reaction coordinate most suitable for comparing and analyzing the reactions. Furthermore, we show how the transition vector (i.e., the normal mode associated with a negative force constant that leads from the saddle point to the steepest descent paths) can serve as a useful and computationally much more efficient approximation (designated TV-IRC) for full IRC computations, in the decisive region around the transition state.
First author: Bento, A. Patricia, E2 and S(N)2 reactions of X- + CH3CH2X (X = F, Cl); an ab initio and DFT benchmark study, JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 4, 929, (2008)
Abstract: We have computed consistent benchmark potential energy surfaces (PESs) for the anti-E2, syn-E2, and S(N)2 pathways of X- + CH3CH2X with X = F and Cl. This benchmark has been used to evaluate the performance of 31 popular density functionals, covering local-density approximation, generalized gradient approximation (GGA), meta-GGA, and hybrid density-functional theory (DFT). The ab initio benchmark has been obtained by exploring the PESs using a hierarchical series of ab initio methods [up to CCSD(T)] in combination with a hierarchical series of Gaussian-type basis sets (up to aug-cc-pVQZ). Our best CCSD(T) estimates show that the overall barriers for the various pathways increase in the order anti-E2 (X = F) < S(N)2 (X = F) < SN2 (X = Cl) similar to syn-E2 (X = F) < anti-E2 (X = Cl) < syn-E2 (X = Cl). Thus, anti-E2 dominates for F- + CH3CH2F, and S(N)2 dominates for Cl- + CH3CH2Cl, while syn-E2 is in all cases the least favorable pathway. Best overall agreement with our ab initio benchmark is obtained by representatives from each of the three categories of functionals, GGA, meta-GGA, and hybrid DFT, with mean absolute errors in, for example, central barriers of 4.3 (OPBE), 2.2 (M06-L), and 2.0 kcal/mol (M06), respectively. Importantly, the hybrid functional BHandH and the meta-GGA M06-L yield incorrect trends and qualitative features of the PESs (in particular, an erroneous preference for S(N)2 over the anti-E2 in the case of F- + CH3CH2F) even though they are among the best functionals as measured by their small mean absolute errors of 3.3 and 2.2 kcal/mol in reaction barriers. OLYP and B3LYP have somewhat higher mean absolute errors in central barriers (5.6 and 4.8 kcal/mol, respectively), but the error distribution is somewhat more uniform, and as a consequence, the correct trends are reproduced.
First author: Bermudez, V. M., Energy-level alignment in the adsorption of phosphonyl reagents on gamma-Al2O3,SURFACE SCIENCE, 602, 1938, (2008)
Abstract: Density functional theory is applied to the computation of the adsorption energy (Delta E-ads) for a series of molecules on gamma-Al2O3. Three different cluster models are used to represent the gamma-Al2O3 surface. The molecules of interest all contain a phosphonyl (P=O) functional group and adsorb via formation of a donor bond between the O atom and a threefold-coordinated tetrahedral Al [Al(T-d)] surface site. The highest occupied molecular orbital (HOMO) of the free molecule is, in all cases, composed largely of non-bonding orbitals on the O atom of the P=O group. The empty “dangling orbital” on the coordinatively-unsaturated Al(T-d) site constitutes a surface state. A linear relationship is found between Delta E-ads, and the difference between the orbital energies of the molecular HOMO (epsilon(H)) and the surface state (epsilon(S)). Trends in Delta E-ads, for different molecules can then be understood in terms of variations in epsilon(H). Likewise, differences in Delta E-ads, for various cluster models can be explained by considering the differences in the predicted epsilon(S) values. A further evaluation of the cluster models is presented by comparing results for the physisorption of H2O or CO with those obtained from two-dimensionally-periodic slab models. When differences in epsilon(H) and epsilon(S) are accounted for, the various models and computational procedures are seen to yield essentially equivalent results for adsorption of the molecules considered. These results are thought to constitute a useful conceptual tool for rationalizing Delta E-ads values for different molecules and cluster models.
First author: Oezbolat, Aysel, Isolation of the first Li/halogen phosphinidenoid transition-metal complex, DALTON TRANSACTIONS, 602, 2674, (2008)
Abstract: Isolation and characterisation of the first Li/halogen phosphinidenoid transition-metal complex as well as low-temperature solution NMR, MAS-NMR experiments, DFT structures and calculated NMR chemical shifts are reported.
First author: Valencia, Ramon, Understanding the stabilization of metal carbide endohedral fullerenes M2C2@C-82 and related systems, JOURNAL OF PHYSICAL CHEMISTRY A, 112, 4550, (2008)
Abstract: We analyze the electronic structure of carbide endohedral metallofullerenes of the type Sc2C2@C-82 and study the possibility of rotation of the encapsulated Sc2C2 moiety in the interior of the cage. Moreover, we rationalize the higher abundance of M2C2@C-82 (M = Sc, Y) in which the metal-carbide cluster is encapsulated in the C-3 nu-C-82:8 carbon cage with respect to other carbides of the same family on the basis of the formal transfer of four electrons from the cluster to the cage and sizeable (LUMO-3)-(LUMO-2) gap in the empty cages. This rule also applies to all those endohedral metallofullerenes in which the encapsulated cluster transfers four electrons to the carbon cage as, for example, the reduced [M@C-82](-) systems (M = group 3 or lanthanide metal ion).
First author: Lam, Cianh P., Structural and spectroscopic characterization of a charge-separated uranium benzophenone ketyl radical complex, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130, 6567, (2008)
Abstract: The reaction of [(((t-Bu)ArO)(3)tacn)U(III) (1) with 4,4′-di-tert-butylbenzophenone affords a unique isolable U(IV) ketyl radical species [(((t-Bu)ArO)(3)tacn)U(IV)(OC center dot(t-Bu) Ph(2))] (2) supported by XRD data, magnetization measurements, and DFT calculations. Isolation and full characterization of the corresponding diphenyl methoxide complex [(((t-Bu)ArO)(3)tacn)U(IV)(OCH(t-Bu)Ph(2))] (3) is also presented. The one-electron reduction of benzophenone by [(((Ad)ArO)(3)tacn)U(III)] (4) leads to a purple U(IV) ketyl radical intermediate [(((Ad)ArO)(3)-tacn)U(IV)(OC center dot Ph(2))] (5). This species is highly reactive, and attempts at isolation were unsuccessful and resulted in methoxide complex [(((Ad)ArO)(3)tacn)U(IV)(OCHPh2)] (6) from H abstraction and dinuclear para-coupled complex [(((Ad)ArO)(3)tacn)U(IV)(OCPhPh-CPh(2)O)U(IV)(((Ad)ArO)(3)tacn)] (7).
First author: Soldatova, Alexandra V., Photophysical behavior of open-shell first-row transition-metal octabutoxynaphthalocyanines: CoNc(OBu)(8) and CuNc(OBu)(8) as case studies, INORGANIC CHEMISTRY, 47, 4275, (2008)
Abstract: Ultrafast photodynamics and density functional theory/time-dependent density functional theory (DFT/TDDFT) results for complexes of Co and Cu with 5,9,14,18,23,27,32,36-octabutoxynaphthalocyanine [CoNc(OBu)(8) and CuNc(OBu)(8)] are reported. As a basis for this work, details concerning the syntheses of these complexes and the corresponding Zn complex (used as a reference) are given. Transient absorption spectrometry with femtosecond time resolution combined with a detailed DFT/TDDFT analysis has been employed to construct a complete picture of the excited-state dynamics after Q-band excitation of the Co and Cu complexes and to gain an understanding of the relationship between the nature of the metal center and the excited-state lifetime. The Co complex was shown to return to its ground state via two competing channels: a T-2(1)(pi, pi*) state that decayed with a lifetime of 1 ps and a low-lying (2)(d, d) state that repopulated the ground-state surface with a lifetime of 15 ps. CuNc (OBu)(8) showed ground-state repopulation from the T-2(1)(pi, pi*) state via a lower-lying ligand-to-metal charge-transfer (LMCT) state that was completed within a few nanoseconds. The photophysical behavior of the cobalt and copper complexes was compared to that previously reported for the nickel analog in an effort to highlight the effect of the central metal on the nature and rates of the deactivation pathways. The results described in this work provide basic knowledge that is relevant to the use of these compounds as photothermal sensitizers in cancer therapy.
First author: Lord, Richard L., Why does cyanide pretend to be a weak field ligand in [Cr(CN)(5)](3-)?, INORGANIC CHEMISTRY, 47, 4413, (2008)
Abstract: Chemical reasoning based on ligand-field theory suggests that homoleptic cyano complexes should exhibit low-spin configurations, particularly when the coordination sphere is nearly saturated. Recently, the well-known chromium hexacyano complex anion [Cr(CN)(6)](4-) was shown to lose cyanide to afford [Cr(CN)(5)](3-) in the absence of coordinating cations. Furthermore, (NEt4)(3)[Cr(CN)(5)] was found to be in a high-spin (S = 2) ground state, which challenges the common notion that cyanide is a strong field ligand and should always enforce low-spin configurations. Using density functional theory coupled to a continuum solvation model, we examined both the instability of the hexacyanochromate(II) anion and the relative energies of the different spin states of the pentacyanochromate(II) anion. By making direct comparisons to the analogous Fell complex, we found that cyanide electronically behaves as a strong-field ligand for both metals because the orbital interaction is energetically more favorable in the low-spin configuration than in the corresponding high-spin configuration. The Coulombic repulsion between the anionic cyanide ligands, however, dominates the overall energetics and ultimately gives preference to the high-spin complex, where the ligand-ligand separation is larger. Our calculations highlight that for a quantitative understanding of spin-state energetic ordering in a transition metal complex, ligand-ligand electrostatic interactions must be taken into account in. addition to classical ligand-field arguments based on M-L orbital interaction energies.
First author: Ogini, Francis O., An investigation of the formation of 1,3,5-heterosubstituted benzene rings by cyclo-condensation of acetyl-substituted organometallic complexes, JOURNAL OF ORGANOMETALLIC CHEMISTRY, 693, 1957, (2008)
Abstract: The cyclocondensation of acetylferrocene and acetylcymantrene catalyzed by SiCl(4) in ethanol yields a mixture of 1,3,5-trisubstituted benzenes and the intermediate 3,1-disubstituted (E)-2-buten-1-ones, including all the homo- and heterometallic species, which were separated and quantified by HPLC. The relative yields of these species are determined by the different ability of the organometallic groups to stabilize the cationic intermediates that participate in the reaction mechanism, which is measurable as the basicity of the starting materials. The X-ray crystal structures of 1-cymantrenyl-3,5-diferrocenylbenzene and (E)-3-cymantrenyl-1-ferrocenyl-2-buten-1-one are described within this report.
First author: Kadantsev, Eugene S., Implementation of a density functional theory-based method for the calculation of the hyperfine A-tensor in periodic systems with the use of numerical and slater type atomic orbitals: Application to paramagnetic defects, JOURNAL OF PHYSICAL CHEMISTRY A, 112, 4521, (2008)
Abstract: The A-tensor parameterizes the “hyperfine” interaction of an “effective” electronic spin with the magnetic field due to the nuclear spin as monitored in an electron paramagnetic resonance (EPR) experiment. In this account, we describe an implementation for the calculation of the A-tensor in systems with translational invariance based on the Kohn-Sham form of density functional theory (KS DFT). The method is implemented in the periodic program BAND, where the Bloch states are expanded in the basis of numerical and Slater-type atomic orbitals (NAOs/STOs). This basis is well-suited for the accurate representation of the electron density near the nuclei, a prerequisite for the calculation of highly accurate hyperfine parameters. Our implementation does not rely on the frozen core approximation tacitly assumed in the pseudopotential schemes. The implementation is validated by performing calculations on the A-tensor for small atoms and molecules within the supercell approach as well as for paramagnetic defects in solids. In particular, we consider the A-tensor of “normal” and “anomalous” muonium defects in diamond and of the hydrogen cyanide anion radical HCN- in a KCl host crystal lattice.
First author: Osuna, Silvia, Chemical reactivity of D-3h C-78 (Metallo)fullerene: Regioselectivity changes induced by Sc3N encapsulation, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130, 6206, (2008)
Abstract: We report here for the first time a full comparison of the exohedral reactivity of a given fullerene and its parent trinitride template endohedral metallofullerene. In particular, we study the thermodynamics and kinetics for the Diels-Alder [4 + 2] cycloaddition between 1,3-butadiene and free D-3h’-C-78 fullerene and between butadiene and the corresponding endohedral D-3h-Sc3N @ C-78 derivative. The reaction is studied for all nonequivalent bonds, in both the free and the endohedral fullerenes, at the BP86/TZP//BP86/DZP level. The change in exohedral reactivity and regioselectivity when a metal cluster is encapsulated inside the cage is profound. Consequently, the Diels-Alder reaction over the free fullerene and the endohedral derivative leads to totally different cycloadducts. This is caused by the metal nitride situated inside the fullerene cage that reduces the reactivity of the free fullerene and favors the reaction over different bonds.
First author: Alberola, Antonio, Synthesis and molecular and electronic structures of a series of Mo3CoSe4 cluster complexes with three different metal electron populations, INORGANIC CHEMISTRY, 47, 3661, (2008)
Abstract: The synthesis, crystal structure, and magnetic properties of [Mo-3(CoCO)Se-4(dmpe)(3)Cl-3] (1), [Mo-3(CoCl)Se-4(dmpe)(3)C-3] (2), and [Mo-3(CoCl)Se-4(dmpe)(3)Cl-3](TCNQ) ([2](TCNQ)) (dmpe = 1,2-bis(dimethylphosphanyl)ethane; TCNQ = 7,7,8,8-tetracyanoquinomethane) cubane-type complexes with 16, 15, and 14 metal electrons, respectively, are reported. These compounds complete the series of cobalt-containing Mo(3)CoQ(4) (Q = S, Se) cubane-type complexes, which allows a complete analysis of the consequences of replacing the inner chalcogen and the metal electron count on the structural, magnetic, and electrochemical properties. The experimental evidence is theoretically supported and rationalized on the basis of density-functional theory calculations. For the 15-metal electron [Mo-3(COCl)Se-4(dmpe)(3)Cl-3] complex with S = 1/2, both electron paramagnetic resonance and theoretical studies give support to a spin density mainly located on the heteroatom. The nature of the highest occupied molecular orbital upon chalcogen exchange within the Mo(3)CoQ(4) (Q = S, Se) series remains essentially unchanged, whereas the nature of the ligand attached to Cc (Cl or CO) results in a different ordering of the molecular orbital scheme. This behavior is explained by the absence of backdonation between an occupied d orbital of Co to an empty pi* Cl orbital, to yield frontier orbitals that differ from those of previous models.
First author: Donzello, Maria Pia, Tetra-2,3-pyrazinoporphyrazines with externally appended pyridine rings. 5. Synthesis, physicochemical and theoretical studies of a novel pentanuclear palladium(II) complex and related mononuclear species,INORGANIC CHEMISTRY, 47, 3903, (2008)
Abstract: New palladium(II) complexes of the free-base tetrakis[2,3-(5,6-di-2-pyridylpyrazino)porphyrazine], [Py(8)TPyzPzH(2)], have been prepared and their physicochemical properties examined. The investigated compounds are the pentanuclear species [(PdCl2)(4)Py(8)TPyzPzPd], the monopalladated complex [Py(8)TPyzPzPd], and its corresponding octaiodide salt [(2-Mepy)(8)TPyzPzPd)(I)(8). All three Pd-II complexes have a common central pyrazinoporphyrazine core and differ only at the periphery of the macrocycle, where the simple dipyridinopyrazine fragments present in [Py(8)TPyzPzPd] bear four PdCl2 units coordinated at the pyridine N atoms in the pentanuclear complex, [(PdCl2)(4)Py(8)TPyzPzPd), or carry pyridine-N(CH3)(+) moieties in the iodide of the octacation [(2-Mepy)(8)TPyzPzPd](8+). The structural features of the pentanuclear complex [(PdCl2)(4)Py(8)TPyzPzPd], partly supported by X-ray data and solution H-1 NMR spectra of the [(CN)(2)Py(2)PyzPdCl(2)] precursor, were elucidated through one- and two-dimensional H-1 NMR spectra in solution and density functional theory (DFT) calculations. Structural information on the monopalladated complex [Py(8)TPyzPzPd] was also obtained from DFT calculations. It was found that in the complex [(PdCl2)(4)Py(8)TPyzPzPd] the peripheral PdCl2 units adopt a py-py coordination mode and the generated N2PdCl2 moieties are directed nearly perpendicular to the plane of the pyrazinoporphyrazine ring, strictly recalling the arrangement found for the palladated precursor [(CN)(2)Py(2)PyzPdCl(2)]. NMR and DFT results consistently indicate that of the four structural isomers predictable for [(PdCl2)(4)Py(8)TPyzPzPd], one having all four N2PdCl2 moieties pointing on the same side of the macrocyclic framework (i.e., isomer 4:0, plus the 3:1 and the 2:2-cis and 2:2-trans isomers), the 4:0 isomer (C-4v symmetry) is the predominant form present. According to cyclic voltammetry and spectroelectrochemical results in pyridine, dimethyl sulfoxide (DMSO), and dimethylformamide (DMF), the monopalladated complex [Py(8)TPyzPzPd] undergoes four reversible or quasi-reversible one-electron ligand-centered reductions, similar to the behavior also observed for the pentanuclear complex [(PdCl2)(4)Py(8)TPyzPzPd], which shows an additional reduction peak attributable to the presence of PdCl2, Owing to the electron-withdrawing properties of the PdCl2 units, the pentanuclear complex is easier to reduce than the mononuclear complex [Py(8)TPyzPzPd], some related [Py(8)TPyzPzM] complexes, and their porphyrin or porphyrazine analogues, so much so that the corresponding monoanion radical is generated at potentials close to 0.0 V vs SCE in DMSO or DMF In turn, the monoanion of [(2-Mepy)(8)TPyzPzPd](I)(8) is also extremely easy to generate electrochemically. Indeed, because of the eight positively charged N-CH3+ groups in this complex the first reduction occurs at potentials close to +0.10 V in DMSO or DMF The redox behavior of the mono- and pentapalladated complexes has been rationalized on the basis of a detailed DFT analysis of their gound-state electronic structure.
First author: Quintal, Susana, Synthesis and properties of new trinuclear Mo(II) complexes containing imidazole and benzimidazole ferrocene units, INORGANICA CHIMICA ACTA, 361, 1584, (2008)
Abstract: The reaction of FcCOC1 (Fc = (C5H5) Fe(C5H4)) with benzimidazole or imidazole in 1: 1 ratio gives the ferrocenyl derivatives FcCO(benzim) (L1) or FcCO(im) (L2), respectively. Two molecules of L1 or L2 can replace two nitrile ligands in [Mo(eta(3)-C3H5)( CO)(2)(CH3CN)(2)Br] or [Mo(eta(3)-C5H5O)(CO)(2)(CH3CN)(2)Br] leading to the new trinuclear complexes [Mo(eta(3)-C3H5)(CO)(2)(L)(2)Br] (C1 for L = L1; C3 for L = L2) and [Mo(eta(3)-C5H5O)(CO)(2)(L)(2)Br] (C-2 for L = L1; C4 for L = L2) with L1 and L2 acting as N-monodentade ligands. L1, L2 and C2 were characterized by X-ray diffraction studies. [Mo(eta(3)-C5H5O)(CO) 2(L1)(2)Br] was shown to be a trinuclear species, with the two L1 molecules occupying one equatorial and one axial position in the coordination sphere of Mo(II). Cyclic voltammetric studies were performed for the two ligands L1 and L2, as well as for their molybdenum complexes, and kinetic and thermodynamic data for the corresponding redox processes obtained. In agreement with the nature of the frontier orbitals obtained from DFT calculations, L1 and L2 exhibit one oxidation process at the Fe(II) center, while C1, C3, and C4 display another oxidation wave at lower potentials, associated with the oxidation of Mo(II).
First author: Zurek, Eva, Experimental and theoretical investigations of the thermodynamic stability of Ba-C-60 and K-C-60 compound clusters, ACS NANO, 2, 1000, (2008)
Abstract: A novel experimental set-up was used to study superstable (magic) Ba-C-60 and K-C-60 compound clusters. The most stable systems observed cannot be rationalized by simple electronic or by geometrical shell filling arguments. Annealing the clusters past the temperature necessary for the fragmentation of the initial metastable clusters formed at the source reveals information about their thermodynamic stability. Higher temperatures yield larger species, suggesting that similar experiments may be used to rationally produce nanoscale clusters with highly desirable properties. Density functional calculations reveal ionic (K, Ba) and covalent (Ba) bonding between C-60 and the metal atoms. The entropic contribution to the Gibbs free energy is shown to be essential in determining absolute and relative cluster stabilities. In particular, we demonstrate that at higher temperatures the entropy favors the formation of larger clusters. A simple criterion which may be used to determine the absolute and relative stabilities of general multicomponent clusters is proposed.
First author: Zhang, Yi-Quan, Density functional theory studies of the magnetostructural correlations in the cyano-bridged Mo2Ni and Mo2Ni3 systems, EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, 2, 2199, (2008)
Abstract: A theoretical density functional study of the magnetostructural correlations in a series of cyano-bridged MoNi systems is presented. Our calculations by two approaches with several local density approximations (LDAs) and generalized gradient approximations (GGAs) show that: (1) the influence of the next-nearest-neighbor MoMo interactions on the MoNi interactions can be omitted; (2) the MoNi interactions strengthen with an increase in the Ni-N-brid-C-brid angle in the range 135 degrees to 175 degrees for all the functionals; (3) increasing the number of exchange coupling interactions from one to two will decrease the ferromagnetic MoNi interactions, but the influence of further increasing the number of exchange coupling interactions from two to three or four on the MoNi interactions is very small, because the peripheral units do not surround the same central metal ion in the MoNi systems that we investigated. Kahn’s theory was used to interpret the above results.
First author: Aquilante, Francesco, Cholesky decomposition-based multiconfiguration second-order perturbation theory (CD-CASPT2): Application to the spin-state energetics of Co-III(diiminato)(NPh), JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 4, 694, (2008)
Abstract: The electronic structure and low-lying electronic states of a Co-III(diiminato)(NPh) complex have been studied using mulficonfigurational wave function theory (CASSCF/CASPT2) The results have been compared to those obtained with density functional theory. The best agreement with ab initio results is obtained with a modified B3LYP functional containing a reduced amount (15%) of Hartree-Fock exchange. A relativistic basis set with 869 functions has been employed in the most extensive ab initio calculations, where a Cholesky decomposition technique was used to overcome problems arising from the large size of the two-electron integral matrix. It is shown that this approximation reproduces results obtained with the full integral set to a high accuracy, thus opening the possibility to use this approach to perform multiconfigurational wave-function-based quantum chemistry on much larger systems relative to what has been possible until now.
First author: Mihaylov, Tzvetan, DFT-based molecular modeling and vibrational study of the La(III) complex of 3,3 ‘-(benzylidene)bis(4-hydroxycoumarin), JOURNAL OF MOLECULAR MODELING, 14, 353, (2008)
Abstract: Molecular modeling of the La(III) complex of 3,3′-(benzylidene)bis(4-hydroxycoumarin) (PhDC) was performed using density functional theory (DFT) methods at B3LYP/6-31G(d) and BP86/TZP levels. Both Stuttgart-Dresden effective core potential and ZORA approximation were applied to the La(III) center. The electron density distribution and the nucleophilic centers of the deprotonated ligand PhDC2- in a solvent environment were estimated on the basis of Hirshfeld atomic charges, electrostatic potential values at the nuclei, and Nalewajski-Mrozek bond orders. In accordance with the empirical formula La(PhDC)(OH)(H2O), a chain structure of the complex was simulated by means of two types of molecular fragment: (1) two La(III) cations bound to one PhDC2- ligand, and (2) two PhDC2- ligands bound to one La(III) cation. Different orientations of PhDC2-, OH- and H2O ligands in the La(III) complexes were investigated using 20 possible [La(PhDC2-)(2)(OH)(H2O)](2-) fragments. Energy calculations predicted that the prism-like structure based on “tail-head” cis-LML2 type binding and stabilized via HO…HOH intramolecular hydrogen bonds is the most probable structure for the La(III) complex. The calculated vibrational spectrum of the lowest energy La(III) model fragment is in very good agreement with the experimental IR spectrum of the complex, supporting the suggested ligand binding mode to La(III) in a chain structure, namely, every PhDC2- interacts with two La(III) cations through both carbonylic and both hydroxylic oxygens, and every La(III) cation binds four oxygen atoms of two different PhDC2-.
First author: Muniz, Jesus, Theoretical study of the novel sandwich compound [Au3Cl3Tr2](2+), JOURNAL OF MOLECULAR MODELING, 14, 417, (2008)
Abstract: A theoretical study of a sandwich compound with a metal monolayer sheet between two aromatic ligands is presented. A full geometry optimization of the [Au3Cl3Tr2](2+) (1) compound, which is a triangular gold(I) monolayer sheet capped by chlorines and bounded to two cycloheptatrienyl (Tr) ligands was carried out using perturbation theory at the MP2 computational level and DFT. Compound (1) is in agreement with the 18-electron rule, the bonding nature in the complex may be interpreted from the donation interaction coming from the Tr rings to the Au array, and from the back-donation from the latter to the former. NICS calculations show a strong aromatic character in the gold monolayer sheet and Tr ligands; calculations done with HOMA, also report the same aromatic behavior on the cycloheptatrienyl fragments giving us an insight on the stability of (1). The Au -Au bond lengths indicate that an intramolecular aurophilic interaction among the Au(I) cations plays an important role in the bonding of the central metal sheet.
First author: Stoyanov, Stanislav R., Theoretical modeling of zeolite nanoparticle surface acidity for heavy oil upgrading,JOURNAL OF PHYSICAL CHEMISTRY C, 112, 6794, (2008)
Abstract: We performed periodic density functional theory (DFT) and quantum-mechanics/molecular mechanics (QM/MM) investigations of the surface acidity of zeolite nanoparticles derived from natural minerals that can be used for bitumen upgrading; in particular, in the process combining bitumen precracking with impurities removal that we recently reported. Bitumen molecules are large and cannot enter zeolite pores. These mainly adsorb on the outer surface of zeolite nanoparticles, which can be optimized for efficient bitumen upgrading and impurities removal. Two chabazite slab models obtained by (003) and (00) cuts that have four and two surface OH groups per unit cell, respectively, are used for the periodic DFT modeling of nanoparticle surfaces. The first model is also treated by using the QM/MM method. Bitumen molecules are represented by probing bases such as ammonia, pyridine, and 2,6-dimethylpyridine that are commonly used for experimental acidity characterization. Analysis of the model acidity characteristics, such as deprotonation energies, aluminum substitution energies, OH stretching frequencies. and Fukui functions produces very good correlations. For the deprotonated chabazite, the electrophilic Fukui functions predict the most stable Bronsted site. Our results suggest that the most reactive chabazite sites are O1 and O3. The three bases investigated become fully protonated upon adsorption to the chabazite Bronsted sites. The molecular orbital spatial distributions obtained by using the periodic and QM/MM methods are very similar, which indicates good correlations between the two modeling methods. The results of our zeolite acidity calculations are in good agreement with experimental data and other computational studies available. Our findings can be useful for the further modeling and rational design of catalytic zeolite nanoparticles for heavy oil upgrading.
First author: Takagi, Shigeyuki, Electron transfer from hydrogen molecule to Au(111) during dissociative adsorption: A first-principles study, JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN, 77, 6794, (2008)
Abstract: We investigate the electron transfer from a dissociatively adsorbed H-2 molecule to a Au(111) surface using the first-principles methods. A fractional electron transfers from a molecule to a substrate, and potential energy increases during the process. The initial energy increase coincides with that of the isolated, separated, and positively charged H-2 molecule calculated by the real-space density functional method. The barrier formation is due to the destabilization of the molecule induced by the electron transfer. The electronegativity difference between the adsorbate and the substrate determines the direction of the electron transfer.
First author: Johansson, Mikael P., 2D-3D transition of gold cluster anions resolved, PHYSICAL REVIEW A, 77, 6794, (2008)
Abstract: Small gold cluster anions Au-n(-) are known for their unusual two-dimensional (2D) structures, giving rise to properties very different from those of bulk gold. Previous experiments and calculations disagree about the number of gold atoms n(c) where the transition to 3D structures occurs. We combine trapped ion electron diffraction and state of the art electronic structure calculations to resolve this puzzle and establish n(c)=12. It is shown that theoretical studies using traditional generalized gradient functionals are heavily biased towards 2D structures. For a correct prediction of the 2D-3D crossover point it is crucial to use density functionals yielding accurate jellium surface energies, such as the Tao-Perdew-Staroverov-Scuseria (TPSS) functional or the Perdew-Burke-Emzerhof functional modified for solids (PBEsol). Further, spin-orbit effects have to be included, and large, flexible basis sets employed. This combined theoretical-experimental approach is promising for larger gold and other metal clusters.
First author: Zhao, Yan, The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals, THEORETICAL CHEMISTRY ACCOUNTS, 120, 215, (2008)
Abstract: We present two new hybrid meta exchange-correlation functionals, called M06 and M06-2X. The M06 functional is parametrized including both transition metals and nonmetals, whereas the M06-2X functional is a high-nonlocality functional with double the amount of nonlocal exchange (2X), and it is parametrized only for nonmetals. The functionals, along with the previously published M06-L local functional and the M06-HF full-Hartree-Fock functionals, constitute the M06 suite of complementary functionals. We assess these four functionals by comparing their performance to that of 12 other functionals and Hartree-Fock theory for 403 energetic data in 29 diverse databases, including ten databases for thermochemistry, four databases for kinetics, eight databases for noncovalent interactions, three databases for transition metal bonding, one database for metal atom excitation energies, and three databases for molecular excitation energies. We also illustrate the performance of these 17 methods for three databases containing 40 bond lengths and for databases containing 38 vibrational frequencies and 15 vibrational zero point energies. We recommend the M06-2X functional for applications involving main-group thermochemistry, kinetics, noncovalent interactions, and electronic excitation energies to valence and Rydberg states. We recommend the M06 functional for application in organometallic and inorganometallic chemistry and for noncovalent interactions.
First author: Krapp, Andreas, The strength of the sigma-, pi- and delta-bonds in Re2Cl82-, THEORETICAL CHEMISTRY ACCOUNTS, 120, 313, (2008)
Abstract: The geometry of Re2Cl82- has been optimized for the eclipsed (D-4h) equilibrium conformation and for the staggered (D-4d) conformation at BP86/TZ2P. The nature of the Re-Re bond which has a formal bond order four has been studied with an energy decomposition analysis (EDA). The EDA investigation indicates that the contribution of the b(2)(delta(xy)) orbitals to the Re-Re bond in the (1)A(1g)(delta(2)delta*(0)) ground state is negligibly small. The vertical excitation of one and two electrons from the bonding delta orbital into the anti-bonding delta* orbitals yielding the singly and doubly excited states (1)A(1g)(delta(1)delta*(1)) and (1)A(1g)(delta(0)delta*(2)) gives a destabilization of 17.5 and 36.1 kcal/mol, respectively, which is nearly the same as the total excitation energies. The preference for the D-4h geometry with eclipsing Re-Cl bonds is explained in terms of hyperconjugation rather than delta bonding. This is supported by the calculation of the triply bonded Re2Cl8 which also has an eclipsed energy minimum structure. The calculations also suggest that the Re-Re triple bond in Re2Cl8 is stronger than the Re-Re quadruple bond in Re2Cl82-. A negligible contribution of the delta orbital to the metal-metal bond strength is also calculated for Os2Cl8 which is isoelectronic with Re2Cl82-.
First author: Jacob, Christoph R., Software news and update a flexible implementation of frozen-density embedding for use in multilevel Simulations, JOURNAL OF COMPUTATIONAL CHEMISTRY, 29, 1011, (2008)
Abstract: A new implementation of frozen-density embedding (FDE) in the Amsterdam Density Functional (ADF) program package is presented. FDE is based on a subsystem formulation of density-functional theory (DFT), in which a large system is assembled from an arbitrary number of subsystems, which are coupled by an effective embedding potential. The new implementation allows both an optimization of all subsystems as a linear-scaling alternative to a conventional DFT treatment, the calculation of one active fragment in the presence of a frozen environment, and intermediate setups, in which individual subsystems are fully optimized, partially optimized, or completely frozen. It is shown how this flexible setup can facilitate the application of FDE in multilevel simulations.
First author: Notter, Francois-Paul, A theoretical study of the excited states of AmO2n+, n=1,2,3, JOURNAL OF CHEMICAL PHYSICS, 128, 1011, (2008)
Abstract: The ground and excited states of the AmO2+, AmO22+, and AmO23+ ions have been studied using the four-component configuration interaction singles doubles, spin-orbit complete active space self-consistent field, and spin-orbit complete active space-order perturbation theory methods. The roles of scalar relativistic effects and spin-orbit coupling are analyzed; results with different methods are carefully compared by a precise analysis of the wave functions. A molecular spinor diagram is used in relation to the four-component calculations while a ligand field model is used for the two-step method. States with the same number of electrons in the four nonbonding orbitals are in very good agreement with the two methods while ligand field and charge transfer states do not have the same excitation energies.
First author: Cifuentes, Marie P., Coordinating tectons: Bipyridyl terminated allenylidene complexes,ORGANOMETALLICS, 27, 1716, (2008)
Abstract: A series of complexes with T-conjugated carbon chains terminated by bipyridyl moieties has been prepared. These allenylidene complexes were derived from 9-hydroxy-9-ethynyl-4,5-diazafluorene, the preparation of which is reported; the new allenylidene complexes are highly colored with the cumulated carbon chain terminating in a bipyridyl unit providing a site for further coordination. The synthesis, characterization, and X-ray structure determination of tratis-[MCl(P boolean AND P)(2)=C=C=(4,5-diazafluoren-9-yl)]PF6 (M = Ru, P boolean AND P = bis(diphenylphosphino)methane (dppm), 1,2-bis(diphenylphosphino)ethane (dppe), 1,2-bis(dimethylphosphino)ethane (dmpe); M = Os, P boolean AND P = dppm) are described. The effect of the variation in metal and ligand on electronic and electrochemical characteristics of these complexes has been investigated by using UV-vis, solution electrochemistry, and a combination of these techniques in spectroelectrochemical experiments. DFT calculations have been performed on trans-[RuCl (P boolean AND P)(2) =C=C=(4,5-diazafluoren-9-yl)](q) (P boolean AND P = dppm, bis(dimethylphosphino)methane (dmpm); q = -1, 0, +1, +2) and subsequently solvent-corrected calculations with use of COSMO were also undertaken to examine the nature of electronic transitions in various oxidation states.
First author: Zhu, Hongjuan, Influence of cis and trans ligands in platinum(II) complexes on the ability of the platinum center to activate C-H bonds. A density functional theory study, ORGANOMETALLICS, 27, 1743, (2008)
Abstract: We have studied the influence of different ligands X (X = F, Cl, Br, I, NO2, and CN) on the C-H bond activation of CH4 in trans-PtCl2X(CH4)(-), 1, and trans-PtCl2X(CH4)(-), 2, where X is either trans (1) or cis (2) to methane. For I with X in the trans position, the trans-PtCl2X- fragment interacts with CH4 through the overlap between the empty d(sigma)-based. orbital 2a(1) pointing along the Pt-X direction and sigma(CH) on CH4. An interaction also takes place between an occupied d(sigma)-based orbital 1b(I) and the empty sigma*CH orbital on CH4, where the d(pi) metal orbital is positioned perpendicular to the PtCl2X- plane. The d(sigma) metal orbital contribution in 2a(1), is antibonding with respect to sigma(x) on X, whereas d(pi) in 1b(1), is antibonding with respect to pi(x). Through the series F, Cl, Br, 1, NO2, and CN, the energies of sigma(x) and pi(x) increase. This is mostly an electronegativity effect. The increase in energy causes an increase in the contribution from sigma(x), and pi(x) to 2a(1) and 1b(1), respectively. As a consequence, the bonding overlaps<sigma(ch vertical=”” bar)2a(1))=”” and=”” <sigma*(ch)vertical=”” bar=”” 1b(1))=”” will=”” diminish,=”” as=”” only=”” the=”” d-component=”” in=”” 2a(1)=”” 1b(1)=”” contributes=”” to=”” overlap.=”” a=”” result=”” of=”” decreasing=”” bonding=”” overlaps,=”” pt-ch4=”” bond=”” strength=”” decline.=”” it=”” is=”” thus=”” shown=”” that=”” experimentally=”” established=”” order=”” trans-labilizing=”” power=”” for=”” series=”” ligands=”” x=”” studied=”” here,=”” f=”” <=”” cl=”” br=”” 1=”” no2=”” cn,=”” can=”” be=”” related=”” orbital=”” energies=”” sigma(x)=”” pi(x)=”” electronegativity=”” elements=”” are=”” involved=”” these=”” orbitals.=”” labilization=”” c-h=”” activation=”” transition=”” state=”” even=”” larger=”” than=”” adduct=”” 1,=”” leading=”” an=”” increase=”” barrier=”” along=”” i=”” cn.=”” 2=”” with=”” cis=”” position,=”” solvation=”” has=”” largest=”” influence=”” on=”” trends=”” both=”” state.=”” however=”” barriers=”” quite=”” similar=”” different=”” x.<=”” p=””>
First author: Destro, Riccardo, Physicochemical properties of zwitterionic L- and DL-alanine crystals from their experimental and theoretical charge densities, JOURNAL OF PHYSICAL CHEMISTRY B, 112, 5163, (2008)
Abstract: The total experimental electron density distributions p(r) of zwitterionic L- and DL-alanine crystals, as derived from extensive sets of X-ray diffracted intensities collected at 23 and 19 K, are compared to gain an insight into the different physical properties of the two related chiral compounds in the solid state and to explore the extent of the p(r) transferability. Relevant parameters that characterize the two crystal forms are obtained, showing differences and similarities in terms of (i) geometric descriptors, (ii) topological indexes, (iii) molecular electrostatic potential (D(r) distributions, (iv) atomic volumes and charges, (v) molecular electric moments, and (vi) electrostatic interaction energies. To assess the relative stability of the racemate with respect to the pure enantiomer, the crystal lattice energies, as obtained through DFT fully periodic calculations, are also discussed and compared with the experimental sublimation enthalpies after correction for the proton-transfer energies. In-crystal group charges, evaluated with the quantum theory of atoms in molecules, are found to be transferable between the racemic and the pure enantiomer, at variance with group volumes. Similarly, molecular first and third moments are not strictly transferable and indicate that for the zwitterionic alanine molecule the molecular charge distribution in the DL-crystal is more polarized in the c direction by about 10%. By contrast, quantitative agreement is observed for second and fourth moments. Significant differences arise from (1) the crystal packing of the dipole vectors, which are aligned in an antiparallel fashion in the L-crystal, to be compared with a parallel alignment in the racemate, due the polar space group Pna2(1) of the latter, (2) the strongly attractive electrostatic energy of a homochiral pair in the L-crystal, which is opposed to the corresponding heterochiral pair in the DL-crystal form. The difference between these E-es values amounts to 135-150 kJ mol(-1). Despite this, the two crystal forms are predicted as equally thermodynamically favored by the theoretical P-B3LYP estimates of the crystal lattice energies. Finally, the necessity of an upgrading of the dispersion and exchange-repulsion terms currently adopted within the experimental charge density approach to intermolecular interactions is recognized and discussed.
First author: Loh, Andrea S., Adsorption and reaction of 1-epoxy-3-butene on Pt(111): Implications for heterogeneous catalysis of unsaturated oxygenates, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130, 5507, (2008)
Abstract: High-resolution electron energy loss spectroscopy (HREELS), temperature-programmed desorption (TPD), and density functional theory (DFT) calculations were used to study the adsorption and reaction of 1-epoxy-3-butene (EpB) on Pt(111). These investigations were conducted to help elucidate mechanisms for improving olefin hydrogenation selectivity in reactions of unsaturated oxygenates. EpB dosed to Pt(111) at 91 K adsorbs molecularly on the surface through the vinyl group with apparent rehybridization to a di-sigma-bound state. By 233 K, however, EpB undergoes epoxide ring opening to form an aldehyde intermediate, which further decomposes upon heating to yield gas phase products CO, H-2, and propylene. Comparison of the HREELS and TPD data to experiments performed with 2-butenal (crotonaldehyde) shows that EpB and 2-butenal decompose through related pathways. However, the EpB-derived aldehyde intermediate clearly has a unique structure, features of which have been elucidated by DFT calculations. In conjunction with previous surface science studies of EpB chemistry, these results can help explain selectivity trends for reactions of EpB on Pt catalysts and bimetallic PtAg catalysts, with indications that the enhanced olefin hydrogenation selectivity of PtAg catalysts likely originates from a bifunctional effect.
First author: Liddle, Stephen T., Synthesis and structural characterisation of an yttrium-alkyl-alkylidene, CHEMICAL COMMUNICATIONS, 130, 1747, (2008)
Abstract: The first structurally authenticated yttrium-alkyl-alkylidene is reported; structural, spectroscopic, and theoretical analyses show that whilst the yttrium-alkylidene bond is short, it possesses a bond order less than one and is comparable to the Y-C(alkyl) single bond within the same molecule.
First author: Bridgeman, Adam J., On the origin of paramagnetism in planar nickel(II) complexes, DALTON TRANSACTIONS, 130, 1989, (2008)
Abstract: The general rule that in Ni(II) d(8) chemistry, tetrahedral (or nearly tetrahedral) complexes have temperature dependent magnetic moments which are usually larger than the spin-only value whilst square planar complexes are diamagnetic is broken for certain Ni[P(Bu-t)(2)(O)NR](2) complexes. These have planar coordination for various alkyl groups but have the spectral and paramagnetic properties normally associated with tetrahedral systems. In contract to previous studies, density functional calculations show the unusual adoption of a high-spin rather than low-spin arrangement in the planar systems is due to the strong pi bonding of the amide group and the preference for a planar coordination is due to greater separation between the bulky nitrogen and phosphorus substituents.
First author: Han, Wen-Ge, Structural model studies for the peroxo intermediate P and the reaction pathway from P -> Q of methane monooxygenase using broken-symmetry density functional calculations, INORGANIC CHEMISTRY, 47, 2975, (2008)
Abstract: Several structural models for the active site of the peroxo intermediate state “P” of the hydroxylase component of soluble methane monooxygenase (MMOH) have been studied, using two DFT functionals OPBE and PW91 with broken-symmetry methodology and the conductor-like screening (COSMO) solvation model. These active site models have different O-2 binding modes to the diiron center, such as the mu-eta(2),eta(2), trans-mu-1,2 and cis-mu-1,2 conformations. The calculated properties, including optimized geometries, electronic energies, Fe net spin populations, and Mossbauer isomer shift and quadrupole splitting values, have been reported and compared with available experimental results. The high-spin antiferromagnetically (AF) coupled Fe3+ sites are correctly predicted by both OPBE and PW91 methods for all active site models. Our data analysis and comparisons favor a cis-mu-1,2 structure (model cis-mu-1,2a shown in Figure 9) likely to represent the active site of MMOH-P. Feasible structural changes from MMOH-P to another intermediate state MMOH-Q are also proposed, where the carboxylate group of Glu243 side chain has to open up from the mono-oxygen bridging position, and the dissociations of the terminal H2O ligand from Fe1 and of the oxygen atom in the carboxylate group of Glu144 from Fe2 are also necessary for the O-2 binding mode changes from cis to trans. The O-O bond is proposed to break in the trans-conformation and forms two mu-oxo bridges in MMOH-Q. The terminal H2O molecule and the Glu144 side chain then rebind with Fe1 and Fe2, respectively, in Q.
First author: Cavigliasso, German, Electronic structure and metal-metal interactions in trinuclear face-shared [M3X12](3-) (M = Mo, W; X = F, Cl, Br, I) systems, INORGANIC CHEMISTRY, 47, 3072, (2008)
Abstract: The molecular and electronic structures of trinuclear face-shared [M3X12](3-) species of Mo (X = F, Cl, Br, I) and W (X = Cl), containing linear chains of metal atoms, have been investigated using density functional theory. The possibility of variations in structure and bonding has been explored by considering both symmetric (D-3d) and unsymmetric (C-3v) forms, the latter having one long and one short metal-metal distance. Analysis of the bonding in the structurally characterized [Mo(3)l(12)](3-) trimer reveals that the metal-metal interaction qualitatively corresponds to a two-electron three-center sigma bond between the Mo atoms and, consequently, a formal Mo-Mo bond order of 0.5. However, the calculated spin densities suggest that the electrons in the metal-metal a bond are not fully decoupled and therefore participate in the antiferromagnetic interactions of the metal cluster. Although the same observation applies to [Mo3X12](3-) (X = Br, Cl, F) and [W3Cl12](3-), both the spin densities and shorter distances between the metal atoms indicate that the metal-metal interaction is stronger in these systems. The broken-symmetry approach combined with spin projection has been used to determine the energy of the low-lying spin multiplets arising from the magnetic coupling between the metal centers. Either the symmetric and unsymmetric S = 3/2 state is predicted to be the ground state for all five systems. For [MO3X12](3-) (X = Cl, Br, I), the symmetric form is more stable but the unsymmetric structure, where two metal centers are involved in a metal-metal triple bond while the third center is decoupled, lies close in energy and is thermally accessible. Consequently, at room temperature, interconversion between the two energetically equivalent configurations of the unsymmetric form should result in an averaged structure that is symmetric. This prediction is consistent with the reported structure Of [Mo(3)l(12)](3-), which, although symmetric, indicates significant movement of the central Mo atom toward the terminal Mo atoms on either side. In contrast, unsymmetric structures with a triple bond between two metal centers are predicted for [Mo3F2](3-) and [W3C12](3-), as the symmetric structure lies too high in energy to be thermally accessible.
First author: Boccia, A., Symmetry breaking effect in the ferrocene electronic structure by hydrocarbon-monosubstitution: An experimental and theoretical study, JOURNAL OF CHEMICAL PHYSICS, 128, 3072, (2008)
Abstract: We present here the results of a synchrotron radiation-excited UV-photoemission investigation and density functional theory calculations on a structurally related series of organometallic free molecules: ethylferrocene (EtFC), vinylferrocene (VFC), and ethynylferrocene (EFC). This series exemplifies the electronic interactions operating when the C-C substituent group of an aromatic ring is bound to the substrate surface atoms, from a single C-C bond to the double and triple C-C bond pi systems which are still able to preserve substrate-molecule conjugation. A detailed assignment of the gas phase valence photoelectron spectra is discussed, providing new data on the electronic structure of EtFC and EFC and offering a partial reinterpretation of previous assignments on VFC. The broken symmetry of ferrocene caused by the monosubstitution has notable effects on the removal of the molecular orbital (MO) degeneracy which is found to be especially remarkable for the ferrocenelike e(1)’ MOs. This effect is ascribed to the interaction between the aromatic cyclopentadyenyl ring and the substituent through sigma/pi hyperconjugation and pi-conjugation mechanisms depending on the nature of the hydrocarbon moiety and its conformational geometry. The vertical ionization energy values of the highest occupied MO for the alkylferrocene and ferrocene free molecules linearly correlate with the redox potential in acetonitrile for ferrocene and the corresponding hybrids obtained by covalently anchoring the free molecule on silicon.
First author: Jacob, Christoph R., A subsystem density-functional theory approach for the quantum chemical treatment of proteins, JOURNAL OF CHEMICAL PHYSICS, 128, 3072, (2008)
Abstract: We present an extension of the frozen-density embedding (FDE) scheme within density-functional theory [T. A. Wesolowski and A. Warshel, J. Phys. Chem. 97, 8050 (1993)] that can be applied to subsystems connected by covalent bonds, as well as a practical implementation of such an extended FDE scheme. We show how the proposed scheme can be employed for quantum chemical calculations of proteins by treating each constituting amino acid as a separate subsystem. To assess the accuracy of the extended FDE scheme, we present calculations for several dipeptides and for the protein ubiquitin.
First author: Grozema, Ferdinand C., Effect of structural dynamics on charge transfer in DNA hairpins, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130, 5157, (2008)
Abstract: We present a theoretical study of the positive charge transfer in stilbene-linked DNA hairpins containing only AT base pairs using a tight-binding model that includes a description of structural fluctuations. The parameters are the charge transfer integral between neighboring units and the site energies. Fluctuations in these parameters were studied by a combination of molecular dynamics simulations of the structural dynamics and density functional theory calculations of charge transfer integrals and orbital energies. The fluctuations in both parameters were found to be substantial and to occur on subpicosecond time scales. Tight-binding calculations of the dynamics of charge transfer show that for short DNA hairpins (<4 base pairs) the charge moves by a single-step superexchange mechanism with a relatively strong distance dependence. For longer hairpins, a crossover to a fluctuation-assisted incoherent mechanism was found. Analysis of the charge distribution during the charge transfer process indicates that for longer bridges substantial charge density builds up on the bridge, but this charge density is mostly confined to the adenine next to the hole donor. This is caused by the electrostatic interaction between the hole on the AT bridge and the negative charge on the hole donor. We conclude both that the relatively strong distance dependence for short bridges is mostly due to this electrostatic interaction and that structural fluctuations play a critical role in the charge transfer, especially for longer bridge lengths.
First author: Swart, Marcel, QUILD: QUantum-regions interconnected by local descriptions, JOURNAL OF COMPUTATIONAL CHEMISTRY, 29, 724, (2008)
Abstract: A new program for multilevel (QM/QM and/or QM/MM) approaches is presented that is able to combine different computational descriptions for different regions in a transparent and flexible manner. This program, designated QUILD (for QUantum-regions Interconnected by Local Descriptions), uses adapted delocalized coordinates (Int J Quantum Chem 2006, 106, 2536) for efficient geometry optimizations of equilibrium and transition-state structures, where both weak and strong coordinates may be present. The Amsterdam Density Functional (ADF) program is used for providing density functional theory and MM energies and gradients, while an interface to the ORCA program is available for including RHF, MP2, or semiempirical descriptions. The QUILD optimization setup reduces the number of geometry steps needed for the Baker test-set of 30 organic molecules by similar to 30% and for a weakly-bound test-set of 18 molecules by similar to 75% compared with the old-style optimizer in ADF, i.e., a speedup of roughly a factor four. We report two examples of using geometry optimizations with numerical gradients, for spin-orbit relativistic ZORA and for excited-state geometries. Finally, we show examples of its multilevel capabilities for a number of systems, including the multilevel boundary region of amino acid residues, an S(N)2 reaction in the gas-phase and in solvent, and a DNA duplex.
First author: O’Boyle, Noel M., cclib: A library for package-independent computational chemistry algorithms, JOURNAL OF COMPUTATIONAL CHEMISTRY, 29, 839, (2008)
Abstract: There are now a wide variety of packages for electronic structure calculations, each of which differs in the algorithms implemented and the output format. Many computational chemistry algorithms are only available to users of a particular package despite being generally applicable to the results of calculations by any package. Here we present cclib, a platform for the development of package-independent computational chemistry algorithms. Files from several versions of multiple electronic structure packages are automatically detected, parsed, and the extracted information converted to a standard internal representation. A number of population analysis algorithms have been implemented as a proof of principle. In addition, cclib is currently used as an input filter for two GUI applications that analyze output files: PyMOlyze and GaussSum.
First author: Garcia-Lastra, J. M., Pressure effects on CrCl63- embedded in cubic Cs2NaMCl6 (M=SC, Y) lattices: Study through periodic and cluster calculations, JOURNAL OF CHEMICAL PHYSICS, 128, 839, (2008)
Abstract: The structural, elastic, vibrational, and optical properties of cubic elpasolites Cs2NaMCl6 (M = Sc, Y) containing CrCl63- complexes have been investigated by means of both periodic and cluster calculations as a function of pressure in the framework of density functional theory. Aside from calculating the host lattice bulk modulus B-H and the local modulus B-1 associated with the CrCl63-, complex particular attention is paid to the pressure dependence of Huang-Rhys factors, S, and S, (related to local a(1g) and e(g) modes), and the Stokes shift associated with the first electronic excited state T-4(2g) (t(2g) (2)e(g)) of CrCl63-. The present calculations provide a big difference between B-H = 231 kbars and B-1 = 676 kbars derived for Cs2NaScCl6:Cr3+ at zero pressure which plays a key role for a right interpretation of pressure effects on vibration frequencies and optical parameters due to CrCl63-. The significant decrease of Huang-Rhys factors, S, and S, due to the pressure observed experimentally is well accounted for by the present work which supports that partial derivative S-a/partial derivative P is determined by the Gruneisen constant gamma(a) of the a(1g) local mode (whose frequency is v(a)) and the dependence of 10Dq on the metal-ligand distance. At the same time, the present results point out that the Stokes shift would be little pressure dependent in the range of 0-50 kbars. Accordingly the Ham effect in the T-4(2g) (t(2g) (2)eg) state of CrCl63- in the cubic elpasolites would also happen for a pressure up to 50 kbars but the spin-orbit constant would increase with respect to that at zero pressure. From the analysis carried out in this work it is also concluded that the figures dvIdP=0.55 cm(-1)/kbar and dS(a)/dP=-7.2 x 10(-3) kbar(-1) extracted from the complex emission band of Cs2NaScC16:Cr3+ are hardly compatible. This fact underlines the usefulness of ab initio calculations for helping in the analysis of complex experimental findings. Finally, as the CrCl63- unit is found to be to a good extent elastically decoupled from the rest of the elpasolite lattice, a model is shown to lead to an approximate relation between the pressure derivative of the local modulus and the Gruneisen constant y, 0 2008 American Institute of Physics.
First author: Morales, Giovanni, Theoretical comparison of ketene dimerization in the gas and liquid phase, JOURNAL OF PHYSICAL CHEMISTRY A, 112, 3192, (2008)
Abstract: We present the first theoretical comparison between ketene dimerization in gas phase and ketene dimerization in solution. Density functional theory (DFT) calculations on the ketene dimerization were carried out considering the following product dimers: diketene (d-I), 1,3-cyclobutanedione (d-II), 2,4-dimethylene-1,3-dioxetane (d-III), and 2-methyleneoxetan-3-one (d-IV). All structures were optimized at the PW86x+PBEc/DZP level of theory. Based on these geometries, a total of 58 meta and hybrid functionals were used to evaluate the heat of dimerization. The MPW1K functional was found to fit the experimental data best and subsequently used in the final analyses for all energy calculations. It was found on both kinetic and thermodynamic grounds that only d-I and d-II are formed during ketene dimerization in gas phase and solution. In gas phase, d-I is favored over d-II by 2 kcal/mol. However, the dimerization barrier for d-I is I kcal/mol higher than for d-II. Solvation makes dimerization more favorable. On the enthalpic surface this is due to a favorable interaction between the dimer dipole moment and solvent molecules. The dimer is stabilized further on the Gibbs energy surface by an increase of the dimerization entropy in solution compared to gas phase. The species d-I remains the most stable dimer in solution by I kcal/mol. Kinetically, the dimerization barriers for the relevant species d-I and d-II are cut in half by solvation, due to both favorable dimer-dipole/solvent interactions (Delta H-double dagger, Delta G(double dagger)) and an increase in the activation entropies (AY). While the dimerization barrier for d-II is lowest for the gas phase and toluene, the barrier for d-I formation becomes lowest for the more polar solvent acetone by 1 kcal/mol as d-I dimerization has the most polar transition state.
First author: Shearer, Jason, Probing variable amine/amide ligation in (NiN2S2)-N-II complexes using sulfur K-Edge and nickel L-edge X-ray absorption spectroscopies: Implications for the active site of nickel superoxide dismutase,INORGANIC CHEMISTRY, 47, 2649, (2008)
Abstract: Nickel superoxide dismutase (NiSOD) is a recently discovered metalloenzyme that catalyzes the disproportionation of O-2(center dot-) into O-2 and H2O2. In its reduced state, the mononuclear Ni-II ion is ligated by two cis-cysteinate sulfurs, an amine nitrogen (from the protein N-terminus), and an amide nitrogen (from the peptide backbone). Unlike many small molecule and metal lopeptide-based NiN2S2 complexes, S-based oxygenation is not observed in NiSOID. Herein we explore the spectroscopic properties of a series of three (NiN2S2)-N-II complexes (bisamine-ligated (bmmpdmed)Ni-II, amine/amide-ligated (Ni-II(BEAAM))(-), and bisamide-ligated (Ni-II(emi))(2-)) with varying amine/amide ligation to determine the origin of the dioxygen stability of NiSOD. Ni L-edge X-ray absorption spectroscopy (XAS) demonstrates that there is a progression in ligand-field strength with (bmmp-dmed)Ni-II having the weakest ligand field and (NiII(emi))(2-)) having the strongest ligand field. Furthermore, these Ni L-edge XAS studies also show that all three complexes are highly covalent with (Nill(BEEAM))- having the highest degree of metal-ligand covalency of the three compounds studied. S K-edge XAS also shows a high degree of Ni-S covalency in all three complexes. The electronic structures of the three complexes were probed using both hybrid-DFT and multiconfigurational SORCI calculations. These calculations demonstrate that the nucleophilic Ni(3d)/S(pi)* HOMO of these NiN2S2 complexes progressively decreases in energy as the amide-nitrogens are replaced with amine nitrogens. This decrease in energy of the HOMO deactivates the Ni-center toward O-2 reactivity. Thus, the Ni-S bond is protected from S-based oxygenation explaining the enhanced stability of the NiSOD active-site toward oxygenation by dioxygen.
First author: Jacobsen, Heiko, Hydrogen and dihydrogen bonding of transition metal hydrides, CHEMICAL PHYSICS,345, 95, (2008)
Abstract: Intermolecular interactions between a prototypical transition metal hydride WH(CO)(2)NO(PH3)(2) and a small proton donor H2O have been studied using DFT methodology. The hydride, nitrosyl and carbonyl ligand have been considered as site of protonation. Further, DFT-D calculations in which empirical corrections for the dispersion energy are included, have been carried out. A variety of pure and hybrid density functionals (BP86, PW91, PBE, BLYP, OLYP, B3LYP, B1PW91, PBE0, X3LYP) have been considered, and our calculations indicate the PBE functional and its hybrid variation are well suited for the calculation of transition metal hydride hydrogen and dihydrogen bonding. Dispersive interactions make up for a sizeable portion of the intermolecular interaction, and amount to 20-30% of the bond energy and to 30-40% of the bond enthalpy. An energy decomposition analysis reveals that the H center dot center dot center dot H bond of transition metal hydrides contains both covalent and electrostatic contributions.
First author: Ketterer, Nicole A., pi(radical)-pi(radical) bonding interactions generated by halogen oxidation of zirconium(IV) redox-active ligand complexes, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130, 4364, (2008)
Abstract: The new complex, [Zr(pda)(2)](n) (1, pda(2-) = N,N(‘)-bis(neo-pentyl)-ortho-phenylenediamide, n = 1 or 2), prepared by the reaction of 2 equiv of pdaLi(2) with ZrCl(4), reacts rapidly with halogen oxidants to afford the new product ZrX(2)(disq)(2) (3, X = Cl, Br, I; disq(-) = NAr-bis(neo-pentyl)-ortho-diiminosemiquinonate) in which each redox-active ligand has been oxidized by one electron. The oxidation products 3a-c have been structurally characterized and display an unusual parallel stacked arrangement of the disq(-) ligands in the solid state, with a separation of similar to 3 angstrom. Density functional calculations show a bonding-type interaction between the SOMOs of the disq- ligands to form a unique HOMO while the antiboncling linear combination forms a unique LUMO. This orbital configuration leads to a closed-shell-singlet ground-state electron configuration (S = 0). Temperature-dependent magnetism measurements indicate a low-lying triplet excited state at similar to 750 cm(-1). In solution, 3a-c show strong disq(-)-based absorption bands that are invariant across the halide series. Taken together these spectroscopic measurements provide experimental values for the one- and two-electron energies that characterize the pi-stacked bonding interaction between the two disqligands.
First author: Bencharif, Mustapha, Electron-sponge behavior, reactivity and electronic structures of cobalt-centered cubic Co9Te6(CO)(8) clusters, EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, 130, 1959, (2008)
Abstract: Extended investigations of the reaction sequence [Cp’ Nb-2(Te-2)H]/CH3Li/[Co-2(CO)(8)] (Cp’ = tBUC(5)H(4)) led to the identification of Li-n[3] {3 = [Co9Te6(CO)(8)]; n = 1, 2} salts through their transformation with [PPN]Cl into [PPN](n)[3] (PPN = Ph3PNPPh,). These compounds form in the solid state columnar ([PPN][3]) or undulated 2D ([PPN](2)[3]) supramolecular networks. Electrochemical studies of [Cp* Nb-2(CO)(2)][3] (Cp* = C5Me5) or [Na(THF)(6)][3] revealed the presence of the redox couples [3](-)/[3](2-)/[3](3-)/[3](4-)/[3](5-) regardless of the nature of the cation, whereas in the anodic part oxidative degradation of the cluster takes place. This behavior is in agreement with the observation that [3](-) containing salts form with PPh3AuCl or dppe decomposition products like [(PPh3)(2)Au][CoCl3PPh3] or [Co(CO)(2)dppe](2)(mu-Te). A neutral cluster comprising the CO@Co-8(mu(4)-Te)(6) core formed in the reaction of [CP* Nb-2(CO)(2)][Co11Te7(CO)(10)] with PPh3AuCl, which gave [Co9Te6(CO)(4)(PPh3)(4)] (4) after oxidative cluster degradation and CO substitution. 4 was characterized by Xray crystallography. DFT calculations carried out on all members of the [3](n) (n = +1 to -5) family and on related species indicate that there is no significant Jahn-Teller distortion (and therefore no connectivity change) for any of the considered electron counts. Magnetic investigations on [PPN][3] show that the ground state of [3](-) is a spin triplet with spins interacting antiferromagnetically in a 1D space.
First author: Holland, Jason P., Synthesis, radiolabelling and confocal fluorescence microscopy of styrene-derivatised bis(thiosemicarbazonato)zinc and -copper complexes, EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, 130, 1985, (2008)
Abstract: The synthesis of zinc(II) and copper(II) complexes of an unsymmetrical bis(thiosemicarbazonato) ligand containing a reactive styrene group are reported. The compounds have been characterised by a range of techniques including reverse-phase HPLC, cyclic voltammetry, NMR, UV/Vis, electron paramagnetic resonance and fluorescence emission spectroscopy. Time-dependent density functional theory calculations have been used to assign the electronic absorption spectrum of [Zn(II)ATSM] and probe the nature of the fluorescent excited state. Electrochemistry experiments show that the copper(II) complex undergoes quasi-reversible one-electron reduction at biologically accessible potentials and is within the range proposed for the complex to be hypoxia-selective. The copper-64 radiolabelled complex has been prepared in aqueous solution and characterised by reverse-phase radio-HPLC. Cellular uptake in HeLa cells has been observed using confocal fluorescence microscopy.
First author: Wahlin, Pernilla, An investigation of the accuracy of different DFT functionals on the water exchange reaction in hydrated uranyl(VI) in the ground state and the first excited state, JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 4, 569, (2008)
Abstract: We discuss the accuracy of density functional theory (DFT) in the gas phase for the water-exchange reactions in the uranyl(VI) aqua ion taking place both in the electronic ground state and in the first excited state (the luminescent (3)Delta(g) state). The geometries of the reactant and intermediates have been optimized using DFT and the B3LYP functional, with a restricted closed-shell formalism for the electronic ground state and either an unrestricted open-shell formalism or the time-dependent DFT method for the (3)Delta(g) state. The relative energies have been computed with wave-function-based methods such as Moller-Plesset second-order perturbation theory, or a minimal multireference perturbative calculation (minimal CASPT2); coupled-cluster method (CCSD(T)); DFT with B3LYP, BLYP, and BHLYP correlation and exchange functionals; and the hybrid DFT-multireference configuration interaction method. The results obtained with second-order perturbative methods are in excellent agreement with those obtained with the CCSD(T) method. However, DFT methods overestimate the energies of low coordination numbers, yielding to too high and too low reaction energies for the associative and dissociative reactions, respectively. Part of the errors appears to be associated with the amount of Hartree-Fock exchange used in the functional; for the dissociative intermediate in the ground state, the pure DFT functionals underestimate the reaction energy by 20 kJ/mol relative to wave-function-based methods, and when the amount of HF exchange is increased to 20% (B3LYP) and to 50% (BHLYP), the error is decreased to 13 and 4 kJ/mol, respectively.
First author: Kolesnikov, V. I., Quantum-Chemical Investigation of the Effect of Grain-Boundary Segregation on Wear Resistance of Steel, JOURNAL OF FRICTION AND WEAR, 29, 99, (2008)
Abstract: Quantum-chemical calculations of polyatomic clusters modeling the grain boundaries in the surface layer of steel are presented. Along with iron atoms, the clusters contain atoms of doping and impurity elements yielded to the boundary due to grain-boundary segregation. The effect of the chemical composition of segregants on the bond strength between the grains and, ultimately, on the wear resistance of steel is investigated. It is shown that the bond strength of segregated atoms with iron atoms in the surface layer of a metal is a substantial factor affecting the wear resistance.
First author: Ramirez-Tagle, Rodrigo, The luminescent [Mo6X8(NCS)(6)](2-) ( X = Cl, Br, I) clusters?: A computational study based on time-dependent density functional theory including spin-orbit and solvent-polarity effects, CHEMICAL PHYSICS LETTERS, 455, 38, (2008)
Abstract: Relativistic time-dependent density functional (TDDFT) calculations including spin-orbit interactions via the zero order regular approximation (ZORA) and solvent effects were carried out on the [Mo6X8(NCS)(6)](2-) cluster. These calculations indicate that the lowest energy electronic transitions of the LMCT type are similar to those observed in the strongly luminescent 24 electron hexanuclear rhenium chalcogenide clusters. The absorption maximum in all the solvents tends to shift to longer wavelengths as the face-capping halide ligand becomes heavier. Thus our calculations predict that the [Mo6X8(NCS)(6)](2-) clusters could be luminescent showing an intensity dependence with respect to both, the nature of the face-capping ligand and the solvent polarity.
First author: Garcia-Fernandez, P., Local symmetry change in BaF2 : Mn2+ at similar to 50 K: Microscopic insight,JOURNAL OF CHEMICAL PHYSICS, 128, 38, (2008)
Abstract: The microscopic origin of the abrupt cubic-tetrahedral symmetry change associated with the local a(2u) vibrational mode observed by electron paramagnetic resonance in BaF2:Mn2+ at similar to 50 K is explored by means of density functional theory calculations. It is found that while the a(2u) vibrational frequencies calculated for MnF86- in CaF2 (168 cm(-1)) and SrF2 (132 cm(-1)) are real, in the case of BaF2:Mn2+, the adiabatic potential curve along this mode exhibits a double well with a small barrier of 50 cm(-1). Although the ground and first excited vibrational states are localized around the energy minima, the rest of the excited states resemble those of a harmonic oscillator centered at Q(a(2u)) = 0. Moreover, only the inclusion of the anharmonic coupling between a(2u) and t(1u) modes allows one to understand the T-d-O-h transition temperature. It is shown that both the unusually high Mn2+-F- distance in BaF2:Mn2+ and the pseudo-Jahn-Teller interaction of the t(2g)(xy; xz; yz) antibonding orbital with filled t(1u) orbitals favor the a(2u) instability. The calculated a(2u) force constant for different electronic states supports this conclusion.
First author: Bulo, Rosa E., NMR solvent shifts of acetonitrile from frozen density embedding calculations, JOURNAL OF PHYSICAL CHEMISTRY A, 112, 2640, (2008)
Abstract: We present a density functional theory (DFT) study of solvent effects on nuclear magnetic shielding parameters. As a test example we have focused on the sensitive nitrogen shift of acetonitrile immersed in a selected set of solvents, namely water, chloroform, and cyclohexane. To include the effect of the solvent environment in an accurate and efficient manner, we employed the frozen-density embedding (FDE) scheme. We have included up to 500 solvent molecules in the NMR computations and obtained the cluster geometries from a large set of conformations generated with molecular dynamics. For small solute-solvent clusters comparison of the FDE results with conventional supermolecular DFT calculations shows close agreement. For the large solute-solvent clusters the solvent shift values are compared with experimental data and with values obtained using continuum solvent models. For the water -> cyclohexane shift the obtained Value is in very good agreement with experiments. For the water -> chloroform NMR solvent shift the classical force field used in the molecular dynamics simulations is found to introduce an error. This error can be largely avoided by using geometries taken from Car-Parrinello molecular dynamics simulations.
First author: Alam, Todd M., A solid-state NMR, X-ray diffraction, and ab initio investigation into the structures of novel tantalum oxyfluoride clusters, CHEMISTRY OF MATERIALS, 20, 2205, (2008)
Abstract: A series of tantalum oxyfluoride materials containing the [Ta4F16O4](4-) and [Ta8F24O12](8-) anion clusters have been synthesized and characterized using X-ray diffraction (XRD) and solid-state nuclear magnetic resonance (SSNMR) spectroscopy. The structure of both tantalum oxyfluoride materials display octahedrally bonded tantalum atoms with bridging oxygen and terminal fluoride atoms. The [Ta4F16O4](4-) cluster is an eight-membered ring, whereas the [Ta8F24O12](8-) cluster forms a cagelike structure. Solid-state dynamics of these clusters were explored by monitoring the impact of temperature on the one-dimensional (ID) F-19 magic angle spinning (MAS) NMR, C-13 cross-polarization (CP) MAS NMR, and two-dimensional (2D) double quantum (DQ) F-19 MAS NMR spectra. The DQ F-19 NMR correlation experiments allowed the through space connectivity between the different resolved fluorine environments to be determined, thus aiding in the spectral assignment and structural refinement of these materials. Ab initio F-19 NMR chemical shift calculations were used to assist in the interpretation of the F-19 NMR spectra. The influence of scalar relativistic and Ta-F spin-orbit coupling on the F-19 NMR shielding calculation arising from bonding to tantalum atoms, is also addressed.
First author: Huang, Deguang, Electronic structure of the mononuclear Ag(II) complex [Ag([18]aneS(4)O(2))](2+) ([18]aneS(4)O(2)=1,10-dioxa-4,7,13,16-tetrathiacyclooctadecane), CHEMICAL COMMUNICATIONS, 20, 1305, (2008)
Abstract: The structure of [Ag([18]aneS(4)O(2))](PF6)(2)center dot CH2Cl2 shows a highly unusual and unexpected boat conformation for the macrocycle with square-planar S-4-Coordination at the formal Ag(II) centre and the two ether O-centres lying on the same side of the S-4 plane; the SOMO in [Ag([18]aneS(4)O(2))](2+) possesses 22.7% Ag 4d(xy) character, as determined by multi-frequency EPR spectroscopy and supported by DFT calculations.
First author: Per, Manolo C., Electron-nucleus cusp correction and forces in quantum Monte Carlo, JOURNAL OF CHEMICAL PHYSICS, 128, 1305, (2008)
Abstract: A simple method is presented which ensures the electron-nucleus cusp condition is satisfied by the Slater-Jastrow wavefunctions commonly employed in quantum Monte Carlo simulations. The method is applied in variational energy calculations of the neon atom and a selection of molecules using both Gaussian and Slater basis sets. In addition, we discuss the relationship between the electron-nucleus cusps and the variance of forces, and investigate the sensitivity of forces to the quality of the cusps for various diatomic molecules.
First author: von Eschwege, Karel G., A DFT perspective on the structures and electronic spectra of the orange and blue isomers of photochromic dithizonatophenylmercury(II), JOURNAL OF PHYSICAL CHEMISTRY A, 112, 2211, (2008)
Abstract: The molecular structure and electronic spectra of the orange and blue isomers of the photochromic compound dithizonatophenylmercury(H) were theoretically studied utilizing density functional (DFT) methods. Computed structural results are in agreement with previously reported X-ray crystal data of the orange resting state. The herewith newly proposed geometrical structure of the blue photoexcited state is favored by more than 35 kJ center dot mol(-1) relative to the historically hypothesized geometry of the blue isomeric form. The key difference lies in the position of the backbone amine proton, being situated on the N4 position in the newly proposed structure, rather than on the N2 position as in the previously hypothesized geometry. Time dependent density functional theory as implemented in the Amsterdam Density Functional (ADF) and Gaussian 03 (G03) program systems yielded excitation energies for the blue isomer exhibiting bathochromic shifts, as observed in the experimentally determined UV/visible spectrum. B3LYP calculated excitation energies and oscillator strengths gave the best approximation of the experimentally observed electronic spectra of both isomers.
First author: Bickelhaupt, F. Matthias, Role of s-p orbital mixing in the bonding and properties of second-period diatomic molecules, JOURNAL OF PHYSICAL CHEMISTRY A, 112, 2437, (2008)
Abstract: Qualitative molecular orbital theory is widely used as a conceptual tool to understand chemical bonding. Symmetry-allowed orbital mixing between atomic or fragment orbitals of different energies can greatly complicate such qualitative interpretations of chemical bonding. We use high-level Amsterdam Density Functional calculations to examine the issue of whether orbital mixing for some familiar second-row homonuclear and heteronuclear diatomic molecules results in net bonding or antibonding character for a given molecular orbital. Our results support the use of slopes of molecular orbital energy versus bond distance plots (designated radial orbital-energy slope: ROS) as the most useful criterion for making this determination. Calculated atomic charges and frontier orbital properties of these molecules allow their acid-base chemistry, including their reactivities as ligands in coordination chemistry, to be better understood within the context of the Klopman interpretation of hard and soft acid-base theory. Such an approach can be extended to any molecular species.
First author: Xiong, Zhenhai, Electrostatic and covalent contributions in the coordination bonds of transition metal complexes, JOURNAL OF PHYSICAL CHEMISTRY A, 112, 2469, (2008)
Abstract: To develop a molecular mechanics force field for modeling complexes of transition metals and organic ligands, the electrostatic and covalent contributions in the coordination bonds were investigated using quantum mechanical density functional theory and model complexes of glyoxal diimine and the 2+ cations of the first row transition metals. The VDD and Hirshfeld charges are found to be closely correlated with the extent of the electron transfer between the ligands and the cations. Assuming the electrostatic contribution can be represented by the atomic partial charges, the covalent contributions in the coordination bonds are estimated to be in a range of 54-92% for the systems calculated. A simple force field was parametrized to validate the partial charge representation.
First author: Adhikari, Debashis, Structural, spectroscopic, and theoretical elucidation of a redox-active pincer-type ancillary applied in catalysis, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130, 3676, (2008)
Abstract: Pincer-type ligands are believed to be very robust scaffolds that can support multifarious functionalities as well as highly reactive metal motifs applied in organometallic chemistry, especially in the realm of catalysis. In this paper, we describe the redox and, therefore, noninnocent behavior of a PNP (PNP- = N[2-P(CHMe2)(2)-4-methylphenyl](2)) pincer ancillary bound to nickel. A combination of structural, spectroscopic, and theoretical techniques suggests that this type of framework can house an electron hole when coordinated to Ni(II).
First author: Mazzone, Gloria, Mechanistic aspects of the reaction of Th(+) and Th(2+) with water in the gas phase,INORGANIC CHEMISTRY, 47, 2083, (2008)
Abstract: Density functional theory calculations were performed to study the gas-phase reaction of Th(+) and Th(2+) with water. An in-depth analysis of the reaction pathways leading to different reaction products is presented. The obtained results are compared to experimental data and to the previously studied reactions of U cations with water.
First author: Satpati, Priyadarshi, Stabilization of an all-metal antiaromatic molecule (Al4Li4) using BH and C as caps,INORGANIC CHEMISTRY, 47, 2098, (2008)
Abstract: It has been reported by Pati et al. (J Am. Chem. Soc. 2005, 127, 3496) that coordination with a transition metal can stabilize the “antiaromatic”, all-metal compound Al4Li4. Here, we report that it can also be stabilized by capping with a main group element like C and its isoelectronic species BH. Our calculations of binding energy, nuclear independent chemical shift, energy decomposition analysis, and molecular orbital analysis support the capping-induced stability, reduction of bond length alternation, and increase of aromaticity of these BH/C-capped Al4Li4 systems. The interaction between p(x) and p(y) orbitals of BH/C and the HOMO and LUMO of Al4Li4 is responsible for the stabilization. Our calculations suggest that capping can introduce fluxionality at room temperature.
First author: McDonough, James E., Thermodynamic, kinetic, and computational study of heavier chalcogen (S, Se, and Te) terminal multiple bonds to molybdenum, carbon, and phosphorus, INORGANIC CHEMISTRY, 47, 2133, (2008)
Abstract: Enthalpies of chalcogen atom transfer to Mo(N[t-Bu]Ar)(3), where Ar = 3,5-C(6)H(3)Me(2), and to IPr (defined as bis-(2,6-isopropylphenyl)imidazol-2-ylidene) have been measured by solution calorimetry leading to bond energy estimates (kcal/mol) for EMo(N[t-Bu]Ar)(3) (E = S, 115; Se, 87; Te, 64) and EIPr (E = S, 102; Se, 77; Te, 53). The enthalpy of S-atom transfer to PMo(N[t-Bu]Ar)(3) generating SPMo(N[t-Bu]Ar)(3) has been measured, yielding a value of only 78 kcal/mol. The kinetics of combination of Mo(N[t-Bu]Ar)(3) with SMo(N[t-Bu]Ar)(3) yielding (mu-S)[Mo(N[t-Bu]Ar)(3)](2) have been studied, and yield activation parameters Delta H double dagger = 4.7 +/- 1 kcal/mol and Delta S double dagger = -33 +/- 5 eu. Equilibrium studies for the same reaction yielded thermochemical parameters Delta H degrees = -18.6 +/- 3.2 kcal/mol and Delta S degrees = -56.2 +/- 10.5 eu. The large negative entropy of formation of (mu-S)[Mo(N[t-Bu]Ar)(3)](2) is interpreted in terms of the crowded molecular structure of this complex as revealed by X-ray crystallography. The crystal structure of Te-atom transfer agent TePCy(3) is also reported. Quantum chemical calculations were used to make bond energy predictions as well as to probe terminal chalcogen bonding in terms of an energy partitioning analysis.
First author: Albrett, Amelia M., Corrole as a binucleating ligand: Preparation, molecular structure and density functional theory study of diboron corroles, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130, 2888, (2008)
Abstract: The reactions of BF3 center dot OEt2 with four triaryl corroles (H3Cor) give the complexes [(B2OF2)(Cor)]- in which the corrole acts as a binucleating ligand. The new complexes were fully characterized, including an X-ray crystal structure of the triphenylcorrole complex. Density functional theory calculations support the observation that the boron atoms coordinate in two dipyrromethene sites in a cisoid geometry on one face of the macrocycle rather than in the alternative dipyrromethene/bipyrrole sites. The UV-visible spectra are insensitive to the corrole substituents, consistent with the lack of low-lying orbitals associated with the coordinated boron atoms.
First author: Jardillier, N., One-electron quantum capping potential for hybrid QM/MM studies of silicate molecules and solids, CHEMICAL PHYSICS LETTERS, 454, 65, (2008)
Abstract: A one-electron quantum capping potential (QCP) for replacing the oxygen atom in silicate-type systems is developed. It is used to border the quantum region in a hybrid quantum mechanics/molecular mechanics (QM/MM) study. Its parametrization has been verified comparing the structures and atomic populations of silicate molecules with those provided by full QM calculations. The method has also been tested for the structure and (29) Si NMR shieldings of a mazzite cluster bordered with oxygen QCPs.
First author: Cerpa, Erick, Pentadienyl complexes of alkali metals: Structure and bonding, ORGANOMETALLICS, 27, 827, (2008)
Abstract: A systematic density functional study of the structure and bonding in the alkali-metal pentadienyl complexes C5H7E (E = Li-Cs) and their analogues derived from the 2,4-dimethylpentadienyl ligand is performed. The bonding in these structures has been analyzed in some detail with reference to molecular orbital analysis, and energy partition analysis, obtained by density functional calculations. An energy decomposition analysis indicates that the electrostatic interaction is the main factor to be considered in the stabilization of the gas-phase complexes we have studied. The stability of the U-shaped minimum energy structure decreases (the potential energy surface becomes more shallow) as the metal atom gets larger. We trace this behavior to a weakening of the metal-ligand binding due to the increasing diffuseness of the metal p orbitals on going down group 1. A significant pyramidalization at the terminal carbons in the coordinate U-shaped structure correlates with the strength of the metal-ligand binding. Initial results for the structural preferences of the complexes in solution for the lithium pentadienyl complex are examined in view of contrary experimental data. There still remains plenty of work to be done in modeling metal complexes in solution, and we suggest a way forward.
First author: Bordoni, Silvia, Diastereoselective synthesis of new rhodium-based amphiphilic polyol-Cp systems,ORGANOMETALLICS, 27, 945, (2008)
Abstract: The cyclopentadienide nucleophilic ring opening on the cyclopentene oxide affords diastereoselectively an efficient entry to a new polyalcoholic (1,2,4)-C(5)H(2)[CH CH(2))(3)CHOH](3) propeller-like, hybrid ligand CP(OOO). The diastereoselective rhodium complexation gives rise almost quantitatively to a new class of racemic CP(OOO)Rh(L,L) (L,L = nbd, cod, C(2)H(4), CO) complexes. Thermal treatment gives predominantly the air-stable CP(OOO)Rh(nbd) rac-4a (73.5%), having S(P) planar chirality, as determined by X-ray diffraction studies. It has also been possible to isolate its stable atropisomer rac-4c (20.5%), while the minor kinetic isomer rac-4b, showing opposite planar chirality (similar to 10%), has been identified by NOESY NMR experiments. The high solubility in water and benzene, evidencing the amphiphilic character, has been measured by the n-octanol/water partition coefficient. The intermolecular H-binding, due to the hydroxy groups, plays a crucial role in selecting the rhodium coordination in the reaction mixture, whereas in the solid, it determines the supramolecular organization. DFT calculations in vacuo are in agreement with the spectroscopically identified structures.
First author: Michalak, Artur, Bond orbitals from chemical valence theory, JOURNAL OF PHYSICAL CHEMISTRY A, 112, 1933, (2008)
Abstract: Two sets of orbitals are derived, directly connected to the Nalewajski-Mrozek valence and bond-multiplicity indices: Localized Orbitals from the Bond-Multiplicity Operator (LOBO) and the Natural Orbitals for Chemical Valence (NOCV). LOBO are defined as the eigenvectors of the bond-multiplicity operator. The expectation value of this operator is the corresponding bond index. Thus, the approach presented here allows for a discussion of localized orbitals and bond multiplicity within one common framework of chemical valence theory. Another set of orbitals discussed in the present work, NOCV, are defined as eigenvectors of the overall chemical valence operator. This set of orbitals can be especially useful for a description of bonding in transition metal complexes, as it allows for separation of the deformation density contributions originating from the ligand -> metal donation and metal -> ligand back-donation.
First author: Lyon, Jonathan T., Infrared spectra and electronic structures of agostic uranium methylidene molecules,INORGANIC CHEMISTRY, 47, 1435, (2008)
Abstract: Through reactions of laser-ablated uranium atoms with methylene halides CH2XY (XY = F-2, FCl, and Cl-2), a series of new actinide methylidene molecules CH2=UF2, CH2=UFCl, and CH2=UCl2 are formed as the major products. The identification of these complexes has been accomplished via matrix infrared spectra, isotopic substitution, and relativistic density functional calculations of the vibrational frequencies and infrared intensities. Density functional calculations using the generalized gradient approach (PW91) show that these CH2=UXY methylidene complexes prefer highly distorted agostic structures rather than the ethylene-like symmetric structures. The calculated agostic angles (angle H-C-U) are around 89 degrees for all the three uranium complexes, and the predicted vibrational modes and isotopic shifts agree well with experimental values. Electronic structure calculations reveal that these U(IV) molecules all have strong C=U double bonds in the triplet ground states with 5f(2) configurations. The calculated bond lengths and bond energies indicate that the C=U double bonds are slightly weaker in the fluoride species than in the chloride species because of the radial contraction of the U (6d) orbitals by the inductive effect of the fluorine substituent. The agostic uranium methylidene complexes are compared with analogous transition metal and thorium complexes, which reveal interesting differences in their chemistries.
First author: Tonzetich, Zachary J., A tungsten(VI) nitride having a W-2(mu-N)(2) core, INORGANIC CHEMISTRY, 47, 1560, (2008)
Abstract: The tungsten nitrido species, [W(mu-N)(CH(2-)t-Bu)(OAr)(2)](2) (Ar = 2,6-diisopropylphenyl), has been prepared in a reaction between the alkylidyne species, W(C-t-Bu)(CH2-t-Bu)(OAr)(2), and organonitriles. The dimeric nature of the nitride was established in the solid state through an X-ray study and in solution through a combination of N-15 NMR spectroscopy and vibrational spectroscopy. Reaction of the nitride with trimethylsilyl trifluoromethanesulfonate afforded the monomeric trimethylsilyl imido species, W(NSiMe3)(CH2-t-Bu)(OAr)(2)(OSO2CF3), which was also characterized crystallographically. The W2N2 core can be reduced by one electron electrochemically or in bulk with metallocenes to afford the radical anion, {n-Bu4N}{W(mu-N)(CH2-t-Bu)(OAr)(2)](2)}. Density functional theory calculations suggest that the lowest-energy allowable transition in [W(mu-N)(CH2-t-Bu)(OAr)(2)](2) is from a highest occupied molecular orbital consisting largely of ligand-based lone pairs into what is largely a metal-based lowest unoccupied molecular orbital.
First author: Han, Wen-Ge, Structural model studies for the high-valent intermediate Q of methane monooxygenase from broken-symmetry density functional calculations, INORGANICA CHIMICA ACTA, 361, 973, (2008)
Abstract: Mossbauer isomer shift parameters have been obtained for both density functional theory ( DFT) OPBE and OLYP functionals by linear regressions between the measured isomer shifts and calculated electron densities at Fe nuclei for a number of Fe-2+,Fe- 2.5+ and Fe-2.5+,Fe- 3+,Fe- 3.5+,Fe- 4+ complexes grouped separately. The calculated isomer shifts and quadrupole splittings on the sample Fe complexes from OPBE and OLYP functionals are similar to those of PW91 calculations [ J. Comput. Chem. 27 ( 2006) 1292], however the. t parameters from the linear regressions differ between PW91 and OPBE, OLYP. Four models for the active site structure of intermediate Q of the hydroxylase component of soluble methane monooxygenase ( MMOH) have been studied, using three DFT functionals OPBE, OLYP, and PW91, incorporated with broken-symmetry methodology and the conductor-like screening ( COSMO) solvation model. The calculated properties, including optimized geometries, electronic energies, pK(a)’s, Fe net spin populations, and Mossbauer isomer shifts and quadrupole splittings, have been reported and compared with available experimental values. The high-spin antiferromagnetically ( AF) coupled Fe 4+ sites are correctly predicted by OPBE and OLYP methods for all active site models. PW91 potential overestimates the Fe – ligand covalencies for some of the models because of spin crossover. Our calculations and data analysis support the structure ( our current model II shown in Fig. 8) proposed by Friesner and Lippard’s group [ J. Am. Chem. Soc. 123 ( 2001) 3836 – 3837], which contains an Fe4+( mu- O)(2)Fe4+ center, one axial water which also H- bonds to both side chains of Glu243 and Glu114, and one bidentate carboxylate group from the side chain of Glu144, which is likely to represent the active site of MMOH-Q. A new model structure ( model IV shown in Fig. 9), which has a terminal hydroxo and a protonated His147 which is dissociated from a nearby Fe, is more asymmetric in its Fe( mu-O)(2) Fe diamond core, and is another very good candidate for intermediate Q.
First author: Boysen, Ryan B., Development of palladium L-edge X-ray absorption spectroscopy and its application for chloropalladium complexes, INORGANICA CHIMICA ACTA, 361, 1047, (2008)
Abstract: X-ray absorption spectroscopy (XAS) is a synchrotron-based experimental technique that provides information about geometric and electronic structures of transition metal complexes. Combination of metal L-edge and ligand K-edge XAS has the potential to de. ne the complete experimental ground state electronic structures for metal complexes with unoccupied d manifolds. We developed a quantitative treatment for Pd L-edge spectroscopy on the basis of the well-established chlorine K-edge XAS for a series of chloropalladium complexes that are pre-catalysts in various organic transformations. We found that Pd-Cl bonds are highly covalent, such as 24 +/- 2%, 34 +/- 3%, and 48 +/- 4% chloride 3p character for each Pd-Cl bond in [PdCl4](2-), [PdCl6](2-), and PdCl2, respectively. Pd(2p -> 4d) transition dipole integrals of 20.8 (SSRL)/16.9 (ALS) eV and 14.1 (SSRL)/11.9 (ALS) eV were determined using various combinations of L-edges for Pd(II) and Pd(IV), respectively. Application of metal-ligand covalency and transition dipole integrals were demonstrated for the example of bridging chloride ligands in PdCl2. Our work lays the foundation for extending the quantitative treatment to other catalytically important ligands, such as phosphine, phosphite, olefin, amine, and alkyl in order to correlate the electronic structures of palladium complexes with their catalytic activity.
First author: Getty, Kendra, Assignment of pre-edge features in the RuK-edge X-ray absorption spectra of organometallic ruthenium complexes, INORGANICA CHIMICA ACTA, 361, 1059, (2008)
Abstract: The nature of the lowest energy bound-state transition in the Ru K-edge X-ray absorption spectra for a series of Grubbs-type ruthenium complexes was investigated. The pre-edge feature was unambiguously assigned as resulting from formally electric dipole forbidden Ru 4d <- 1s transitions. The intensities of these transitions are extremely sensitive to the ligand environment and the symmetry of the metal centre. In centrosymmetric complexes the pre-edge is very weak since it is limited by the weak electric quadrupole intensity mechanism. By contrast, upon breaking centrosymmetry, Ru 5p-4d mixing allows for introduction of electric dipole allowed character resulting in a dramatic increase in the pre-edge intensity. The information content of this approach is explored as it relates to complexes of importance in olefin metathesis and its relevance as a tool for the study of reactive intermediates.
First author: Cranswick, Matthew A., Metal-sulfur d pi-p pi buffering of the oxidations of metal-thiolate complexes: Photoelectron spectroscopy of (eta(5)-C5H5)Fe(CO)(2)SR (SR = SCH3, (SBu)-Bu-t) and (eta(5)-C5H5)Re(NO)(PR3)SCH3 (PR3 = (PPr3)-Pr-i, PPh3), INORGANICA CHIMICA ACTA, 361, 1122, (2008)
Abstract: The metal-sulfur bonding present in the transition metal-thiolate complexes CpFe(CO)(2)SCH3, CpFe(CO)(2)(SBu)-Bu-t, CpRe(NO)((PPr3)-Pr-i)SCH3, and CpRe(NO)(PPh3)SCH3 (Cp = eta(5)-C5H5) is investigated via gas-phase valence photoelectron spectroscopy. For all four complexes a strong d pi-p pi interaction exists between a filled predominantly metal d orbital of the [CpML2](+) fragment and the purely sulfur 3p pi lone pair of the thiolate. This interaction results in the highest occupied molecular orbital having substantial M-S pi* antibonding character. In the case of CpFe(CO)(2)SCH3, the first (lowest energy) ionization is from the Fe-S pi* orbital, the next two ionizations are from predominantly metal d orbitals, and the fourth ionization is from the Fe-S pi orbital. The pure sulfur p pi lone pair of the thiolate fragment is less stable than the filled metal d orbitals of the [CpFe(CO)(2)](+) fragment, resulting in a Fe-S pi* combination that is higher in sulfur character than the Fe-S pi combination. Interestingly, substitution of a tert-butyl group for the methyl group on the thiolate causes little shift in the first ionization, in contrast to the shift observed for related thiols. This is a consequence of the delocalization and electronic buffering provided by the Fe-S d pi-p pi interaction. For CpRe(NO)((PPr3)-Pr-i)SCH3 and CpRe(NO)(PPh3)SCH3, the strong acceptor ability of the nitrosyl ligand rotates the metal orbitals for optimum backbonding to the nitrosyl, and the thiolate rotates along with these orbitals to a different preferred orientation from that of the Fe complexes. The initial ionization is again the M-S pi* combination with mostly sulfur character, but now has considerable mixing among several of the valence orbitals. Because of the high sulfur character in the HOMO, ligand substitution on the metal also has a small effect on the ionization energy in comparison to the shifts observed for similar substitutions in other molecules. These experiments show that, contrary to the traditional interpretation of oxidation of metal complexes, removal of an electron from these metal-thiolate complexes is not well represented by an increase in the formal oxidation state of the metal, nor by simple oxidation of the sulfur, but instead is a variable mix of metal and sulfur content in the highest occupied orbital.
First author: Lee, Sonny C., Toward an expanded oxygen atom transfer reactivity scale: Computational investigation of the energetics of oxo transfer reaction couples, INORGANICA CHIMICA ACTA, 361, 1166, (2008)
Abstract: The computational prediction of gas phase enthalpy (neutral substrates) and aqueous free energy (anion substrates) changes has been evaluated for the oxygen atom transfer reaction X + 1/2O(2) -> XO. Several density functionals (SVWN, BP86, B3LYP) at double- and triple-zeta levels were surveyed, along with one composite ab initio method (G3(MP2)). Results are presented for extensive main group test sets for which experimental thermochemistry is available. In addition, several minimal reaction couples of the type [(MOL2)-O-IV]/[(MO2L2)-O-VI] (M = Mo, W) have been examined. Overall, the results suggest a computational approach to the energetics of oxo transfer is feasible, potentially affording an expanded oxo transfer reactivity scale.
First author: Guerra, Celia Fonseca, Watson-Crick base pairs with thiocarbonyl groups: How sulfur changes the hydrogen bonds in DNA, CENTRAL EUROPEAN JOURNAL OF CHEMISTRY, 6, 15, (2008)
Abstract: We have theoretically analyzed mimics of Watson-Crick AT and GC base pairs in which N-H center dot center dot center dot O hydrogen bonds are replaced by N-H center dot center dot center dot S, using the generalized gradient approximation (GGA) of density functional theory at BP86/TZ2P level. The general effect of the above substitutions is an elongation and a slight weakening of the hydrogen bonds that hold together the base pairs. However, the precise effects depend on how many, and in particular, on which hydrogen bonds AT and GC are substituted.. Another purpose of this work is to clarify the relative importance of electrostatic attraction versus orbital interaction in the hydrogen bonds involved in the mimics, using a quantitative bond energy decomposition scheme. At variance with widespread believe, the orbital interaction component in these hydrogen bonds is found to contribute more than 40% of the attractive interactions and is thus of the same order of magnitude as the electrostatic component, which provides the remaining attraction.
First author: Durivage, Jason C., The electronic structure and bonding of the first p-block paddlewheel complex, Bi-2(trifluoroacetate)(4), and comparison to d-block transition metal paddlewheel complexes: A photoelectron and density functional theory study, JOURNAL OF CLUSTER SCIENCE, 19, 275, (2008)
Abstract: The photoelectron spectrum and a density functional computational analysis of the first p-block paddlewheel complex, Bi-2(tfa)(4), where tfa = (O2CCF3)(-), are reported. The photoelectron spectrum of Bi-2(tfa)(4) contains an ionization band between the region of metal-based ionizations and the region of overlapping ligand ionizations that is not seen in the photoelectron spectra of d-block paddlewheel complexes. This additional ionization arises from an a(1g) symmetry combination of the tfa ligand orbitals that is directed for sigma bonding with the metals, and the unusual energy of this ionization follows from the different interaction of this orbital with the valence s and p orbitals of Bi compared to the valence d orbitals of transition metals. There is significant mixing between the Bi-Bi sigma bond and this a(1g) M-L sigma orbital. This observation led to a re-examination of the ionization differences between Mo-2(tfa)(4) and W-2(tfa)(4), where the metal-metal sigma and pi ionizations are overlapping for the Mo-2 molecule but a separate and sharp sigma ionization is observed for the W-2 molecule. The coalescing of the sigma and pi bond ionizations of Mo-2(tfa)(4) is due to greater ligand orbital character in the Mo-Mo sigma bond (similar to 7%) versus the W-W sigma bond (similar to 1%).
First author: Alvarez-Thon, Luis, Ground state of octahedral platinum hexafluoride, PHYSICAL REVIEW A, 77, 275, (2008)
Abstract: All previously published nonrelativistic and scalar relativistic electronic structure calculations of platinum hexafluoride predict a paramagnetic distorted octahedral molecule with a triplet ground state. The four-component spin-free method also predicts a distorted octahedral molecule with longest axial Pt-F bond due to the Jahn-Teller effect. However, four-component Dirac molecular Hartree-Fock and density-functional theory (DFT) and the two-component zeroth-order regular approach (ZORA) including spin-orbit interaction calculations predict a diamagnetic octahedral molecule with a closed-shell ground state, which is in accordance with the observation of the (19)F and (195)Pt high-resolution nuclear magnetic resonance spectra and its undisturbed ir and Raman spectra of PtF(6). The excitation energies involving the d-d transitions are well calculated by performing time-dependent DFT calculations using the two-component ZORA method. Thus, its octahedral molecular structure with a closed-shell ground state is stabilized by the effect of a spin-orbit interaction.
First author: Bakken, Vebjorn, Atomistic and electronic structure of bimetallic cobalt/rhenium clusters from density functional theory calculations, JOURNAL OF CHEMICAL PHYSICS, 128, 275, (2008)
Abstract: We have carried out computational density functional investigations of CoIReJ (J=0,1,2; I+J = 14) metal atom clusters. Through thorough optimization of geometry, spin polarization, and electronic configuration, the most stable structures for each cluster have been identified. While the global minima are found to be well defined and energetically well separated from other local minima, the study reveals a plethora of different structures and symmetries only moderately higher in energy. A key point of interest is the effect of doping the cobalt clusters with rhenium. Aside from significant structural reorganizations, rhenium is found to stabilize the clusters and couple down the spin. Furthermore, the most stable clusters comprise highly coordinated rhenium and, in the case of Co12Re2, Re-Re bonding. Our results are compared to earlier experimental and computational data.
First author: Carvalho, Alexandra T. P., Mechanism of thioredoxin-catalyzed disulfide reduction. Activation of the buried thiol and role of the variable active-site residues, JOURNAL OF PHYSICAL CHEMISTRY B, 112, 2511, (2008)
Abstract: Thioredoxins (Trx) are enzymes with a characteristic CXYC active-site motif that catalyze the reduction of disulfide bonds in other proteins. We have theoretically explored this reaction mechanism, both in the gas phase and in water, using density functional theory. The mechanism of disulfide reduction involves two consecutive thiol-disulfide exchange reactions, that is, nucleophilic substitutions at sulfur (S(N)2@S): first, by one Trx cysteine-thiolate group (Cys-32) at a sulfur atom of the disulfide substrate and, second, by the other Trx cysteine-thiolate group (the buried thiol of Cys-35) at the sulfur atom of the first Trx cysteine; We have investigated the intrinsic nature of such S(N)2@S substitution using the simple CH3S- + CH3SSCH3 model and how it is affected by solvation in aqueous solution. Next, we have examined how the behavior of the elementary S(N)2@S steps changes in the more realistic enzyme-substrate model CGPC + CH3SSCH3, which contains the active-site of Trx. In all model reactions, solvation turns the hypervalent trisulfide anion (i.e., the S(N)2@S transition species) from a stable complex into a transition state. Importantly, our analyses suggest that the deprotonation of the buried thiol (which is required before the latter can enter into the second S(N)2@S step) is done by the leaving group evolving from the first S(N)2@S step. Finally, molecular dynamics (MD) simulations, in the gas phase and in water, of CGPC, CGGC, and the corresponding wild-type Trx and P34G Trx show that the activity of the thioredoxin active-site motif (CXYC) is determined not only by the structural rigidity associated with the particular variable residues (XY) but also by the number of amide N-H groups. The latter are involved in the stabilization of the Cys-32 thiolate and thus affect the acidity and nucleophilicity of this residue.
First author: Chong, Daesung, [Re(eta(5)-C5H5)(CO)(3)](+) family of 17-electron compounds: Monomer/dimer equilibria and other reactions, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130, 2692, (2008)
Abstract: The anodic electrochemical oxidations of ReCP(CO)(3) (1, Cp = eta(5)-C5H5), Re(eta(5)-C5H4NH2)(CO)(3) (2), and ReCp*(CO)(3) (3, Cp* = eta(5)-C5Me5), have been studied in CH2Cl2 containing [NBU4][TFAB] (TFAB = [B(C6F5)(4)](-)) as supporting electrolyte. One-electron oxidations were observed with E-1/2 = 1.16, 0.79, and 0.91 V vs ferrocene for 1-3, respectively. In each case, rapid dimerization of the radical cation gave the dimer dication, [Re2Cp2 gamma(CO)(6)](2+) (where Cp-gamma represents a generic cyclopentadienyl ligand), which may be itself reduced cathodically back to the original 18-electron neutral complex ReCp gamma(CO)(3). DFT calculations show that the SOMO of 1(+) is highly Re-based and hybridized to point away from the metal, thereby facilitating the dimerization process and other reactions of the Re(II) center. The dinners, isolated in all three cases, have long metal-metal bonds that are unsupported by bridging ligands, the bond lengths being calculated as 3.229 angstrom for [Re2Cp2(CO)(6)](2+) (1(2)(2+)) and measured as 3.1097 angstrom for [Re-2(C5H4NH2)(2)(CO)(6)](2+) (2(2)(2+)) by X-ray crystallography on [Re-2(C5H4NH2)(2)(CO)(6)][TFAB](2). The monomer/dimer equilibrium constants are between K-dim = 10(5) M-1 and 10(7) M-1 for these systems, so that partial dissociation of the dimers gives a modest amount of the corresponding monomer that is free to undergo radical cation reactions. The radical 1(+) slowly abstracts a chlorine atom from dichloromethane to give the 18-electron complex [ReCp(CO)(3)Cl](+) as a side product. The radical cation 1(+) acts as a powerful one-electron oxidant capable of effectively driving outer-sphere electron-transfer reactions with reagents having potentials of up to 0.9 V vs ferrocene.
First author: Moore, Lucas R., Sterically demanding, sulfonated, triarylphosphines: Application to palladium-catalyzed cross-coupling, steric and electronic properties, and coordination chemistry, ORGANOMETALLICS, 27, 576, (2008)
Abstract: Tri(2,4-dimethyl-5-sulfonatophenyl)phosphine trisodium (TXPTS center dot Na-3) and tri(4-methoxy-2-methyl-5-sulfonatophenyl)phosphine trisodium (TMAPTS center dot Na-3) both provide more active catalysts for Suzuki and Sonogashira couplings of aryl bromides in aqueous solvents than tri(3-sulfonatophenyl)phosphine trisodium (TPPTS center dot Na-3). In the Heck coupling, TXPTS center dot Na-3 provides the most effective catalyst system. Cone angles determined from DFT-optimized structures show that both TXPTS center dot Na-3 (206) and TMAPTS center dot Na-3 (208) are significantly larger than TPPTS center dot Na-3 (165). The identity of the counterion had a significant effect on the calculated cone angles for these ligands. The electronic properties of these ligands determined by the CO stretching frequencies of trans-RhL2(Cl)CO complexes were identical, although calculated electronic parameters suggest subtle differences between these ligands. Similar to TPPTS center dot Na-3, both TXPTS center dot Na-3 and TMAPTS center dot Na-3 react with Pd(OAc)(2) in aqueous solvents to give LnPd0 complexes and the corresponding phosphine oxide. The reduction of palladium(II) by TXPTS center dot Na-3 is significantly slower than is seen with TMAPTS center dot Na-3 or TPPTS center dot Na-3 at room temperature. Evidence of palladacycle complexes derived from TXPTS center dot Na-3 and TMAPTS center dot Na-3 by activation of an ortho-methyl substituent was also observed in ligand coordination studies and under catalytic reaction conditions.
First author: Neugebauer, Johannes, Photophysical properties of natural light-harvesting complexes studied by subsystem density functional theory, JOURNAL OF PHYSICAL CHEMISTRY B, 112, 2207, (2008)
Abstract: In this study, we investigate the excited states and absorption spectra of a natural light-harvesting system by means of subsystem density functional theory. In systems of this type, both specific interactions of the pigments with surrounding protein side chains as well as excitation energy transfer (EET) couplings resulting from the aggregation behavior of the chromophores modify the photophysical properties of the individual pigment molecules. It is shown that the recently proposed approximate scheme (J. Chem. Phys. 2007, 126, 134116) for coupled excitations within a subsystem approach to time-dependent DFT is capable of describing both effects in a consistent manner, and is efficient enough to study even the large assemblies of chromophores occurring in the light-harvesting complex 2 (LH2) of the purple bacterium Rhodopseudomonas acidophila. A way to extract phenomenological coupling constants as used in model calculations on EET rates is outlined. The resulting EET coupling constants and spectral properties are in reasonable agreement with the available reference data. Possible problems related to the effective exchange-correlation kernel are discussed.
First author: Han, Young-Kyu, Toward an accurate self-interaction binding energy of magic cluster TiAu4, BULLETIN OF THE KOREAN CHEMICAL SOCIETY, 29, 305, (2008)
Abstract: We performed coupled-cluster calculations to determine the intermolecular interaction energy between two TiAu4 clusters. Our ab initio calculations predict that the binding energy is 2.89 eV, which is somewhat larger than the known binding energy of 2.0 eV for TiH4-TiH4. The intermolecular binding energy is relatively high, despite TiAu4 having all the attributes of a magic cluster. The favorable orbital interaction between occupied Au(6s) and unoccupied Ti(3d) orbitals leads to the strong dimeric interaction for TiAu4-TiAu4.
First author: Furet, Eric, On the sensitivity of f electrons to their chemical environment, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130, 2180, (2008)
Abstract: Density functional calculations have been carried out on three families of lanthanide complexes of D-3 or C-4 symmetry, namely [Ln((HO)-O-2)(9)](3+), [Ln(DPA)(3)](3-), and [Ln(DOTAM)](3+) (Ln = Y, La, Lu; DPA = pyridine-2,6-dicarboxylate; DOTAM = 1,4,7,10-tetracarbamoylmethyl-1,4,7,10-tetraazacyclododecane), to get some insights concerning the sensitivity of 4f electrons to the surrounding ligands. We show that the electron density accumulations found within 0.7 angstrom of the metal center, that precisely give the opposite image of the coordination sphere as they are located trans with respect to the Ln-ligand bonds, are almost exclusively due the f electrons. This polarization of the 4f electrons in lanthanides complexes has therefore to be considered as a general feature that plays a crucial role in some experimentally observed phenomenons such as the dependency of quadratic hyperpolarizability to the number of f electrons in [Ln(DPA)(3)](3-) complexes that we have evidenced.
First author: Irfan, Ahmad, Explaining the HOMO and LUMO distribution on individual ligands in mer-Alq3 and its “CH”/N substituted derivatives, JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 850, 79, (2008)
Abstract: HOMO and LUMO (FMOs) play important role in the optical properties of meridianal isomer of tris(8-hydroxyquinolino)aluminum (mer-Alq3) and its derivatives. The frontier molecular orbitals (FMOs) also play a vital role in the process of charge transport. It is urgent to find the reason of FMO distribution pattern among the ligands. The structures of mer-Alq3 and its “CH”/N substituted derivatives have been optimized at the B3LYP/6-31G* level. Energy decomposition analysis has been performed at the B3LYP/DZP level. The results of energy-partitioning analysis of ground states are discussed. It has been explained that HOMOs are on A-ligands due to weaker electrostatic interaction energy between L-a-AlLbLc fragments while LUMOs are on B-ligands due to weaker orbital interaction energy between L-b-AlLaLc fragments.
First author: Colombo, Maria Carola, Copper binding sites in the C-terminal domain of mouse prion protein: A hybrid (QM/MM) molecular dynamics study, PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 70, 1084, (2008)
Abstract: We present a hybrid QM/MM Car-Parrinello molecular dynamics study of the copper-loaded C-terminal domain of the mouse prion protein. By means of a statistical analysis of copper coordination in known protein structures, we localized the protein regions with the highest propensity for copper ion binding. The identified candidate structures were subsequently refined via QM/MM simulations. Their EPR characteristics were computed to make contact with the experimental data and to probe the sensitivity to structural and chemical changes. Overall best agreement with the experimental EPR data (Van Doorslaer et al., J Phys Chem B 2001; 105: 1631-1639) and the information currently available in the literature is observed for a binding site involving H187. Moreover, a reinterpretation of the experimental proton hyperfine couplings was possible in the light of the present computational findings.
First author: Mayer, A., A charge-dipole model for the static polarizability of nanostructures including aliphatic, olephinic, and aromatic systems, JOURNAL OF PHYSICAL CHEMISTRY A, 112, 1277, (2008)
Abstract: We present an electrostatic interaction model for the calculation of the static electronic polarization of hydrocarbons. In previous work, models have often been presented for one single type of hydrocarbons. Here, we discuss the different requirements for a model to describe aliphatic, olephinic, and aromatic systems. The model is based on the representation of the carbon and hydrogen atoms by induced electric charges and dipoles, where the actual values of the charges and dipoles are those that minimize the electrochemical energy of the molecule. The electrostatic interactions are described in terms of normalized propagators, which improves both the consistency and the numerical stability of the technique. For the calibration of our model, we sought at reproducing the molecular polarizabilities obtained by current density functional theory for a set of 48 reference structures. We propose parameters for each type of hydrocarbon, which provide an excellent agreement with the reference data (relative error on the mean molecular polarizabilities of 0.5, 1.4, and 1.9% for alkanes, alkenes, and aromatic molecules, respectively). We also propose parameters based on the local environment of each atom, which are better suited for the description of more complex molecules. We finally study the polarizability of fullerenes and small hydrogen-terminated (5,5) carbon nanotubes.
First author: Pantazis, Dimitrios A., A re-evaluation of the two-step spin crossover in the trinuclear cation [Co-3(dipyridylamido)(4)Cl-2], DALTON TRANSACTIONS, 112, 608, (2008)
Abstract: Density functional theory is used to explore the electronic states involved in the remarkable two-step spin crossover (S = 0 -> S = 1 -> S = 2) in the cationic extended metal atom chain [Co-3(dpa)(4)Cl-2](+) (dpa = the anion of 2-dipyridylamine) (R. Clerac, F A. Cotton, K. R. Dunbar, T. Lu, C. A. Murillo and X. Wang, J. Am. Chem. Soc., 2000, 122, 2272). The calculations are consistent with a model in which all three spin states share one common feature-a vacancy in the d(xy) orbital on the central cobalt atom which is stabilised by pi donation from four amide groups. As a result, all three can be considered to contain a Co2+-Co3+-Co2+ chain. The singlet and triplet states arise from antiferromagnetic and ferromagnetic coupling, respectively, between the unpaired electron in this d(xy) orbital and another localised entirely on the terminal cobalt centres (the antisymmetric combination of Co d(z)2). The singlet-triplet transition does not, therefore, populate any additional antibonding orbitals, and as a result the structure is almost invariant around the characteristic temperature of the singlet triplet transition. In the most stable quintet, in contrast, the symmetry of the Co-Co-Co chain is broken, giving rise to a localised high-spin CO(II) centre (S = 3/2), ferromagnetically coupled to a Co(III)-Co(II) dimer (S = 1/2). The structural changes associated with this transition are apparent in the X-ray data in subtle changes in both Co-N and Co-Cl bond lengths, although their magnitude is damped by the relatively low population (18%) of the quintet even at 300 K.
First author: Gonzalez-Baro, Ana C., Crystal structures, theoretical calculations, spectroscopic and electrochemical properties of Cr(III) complexes with dipicolinic acid and 1,10-phenantroline, POLYHEDRON, 27, 502, (2008)
Abstract: The crystal structures of compounds Na[Cr(dipic)(2)]center dot 2H(2)O (1) and [Cr(dipic)(phen)Cl]center dot 1/2H(2)O (2), dipic = dipicolinate, phen = 1,10-phenantroline, were determined. In both complexes, Cr(III) is in a distorted octahedral environment. In complex (1), the metal is coordinated to two nearly perpendicular dipic anions acting as tridentate ligands through one oxygen of each carboxylate group and the pyridinic nitrogen atom. In complex (2), Cr(III) ion is similarly coordinated to a dipic anion, defining a ligand equatorial plane. The phen molecule bridges the remaining equatorial coordination site and one of the axial positions through its N-atoms. The other axial position is occupied by a chloride ion.The optimized geometries of both compounds and their corresponding harmonic vibrational frequencies were calculated using methods of density functional theory. The infrared, Raman and electronic spectra of the complexes were recorded. Assignments of the most characteristic bands are reported and discussed. Their electrochemical properties were also investigated. Both compounds exhibit similar redox behavior; they undergo two main reduction processes involving the metal center and the dipicolinato ligand. No Cr(III) oxidation processes were found.
First author: Shamov, Grigory A., The role of peripheral alkyl substituents: A theoretical study of substituted and unsubstituted uranyl isoamethyrin complexes, INORGANIC CHEMISTRY, 47, 805, (2008)
Abstract: Relativistic density functional theory has been applied to the uranyl(VI) and uranyl(V) complexes of unsubstituted (1) and dodeca-alkyl-substituted (2) isoamethyrin (hexaphyrin(1.0.1.0.0.0)). The experimentally observed bent conformation in the uranyl(VI) complex of 2 (Sessler, J. L. et al. Angew. Chem., Int. Ed. 2001, 40, 591) is reproduced accurately by the calculations. It is entirely due to the external alkyl substitutents; the unsubstituted complexes of 1 are planar. Complex geometry and stability are seen to be the result of two competing factors; aromatic stabilization favors a planar conformation of the macrocycle whereas the bending affords a much better fit between the cavity and the uranyl cation. The uranyl(VI) complex of 2 is more stable than that of 1 as a result; the trend is reversed for the larger uranyl(V) cation. An energy decomposition analysis shows that the differences between U-VI and U-V originate in the different capabilities of these cations for covalent and/or polarization interactions with the ligands rather than in sterical factors.
First author: Di Censo, Davide, Synthesis, characterization, and DFT/TD-DFT calculations of highly phosphorescent blue light-emitting anionic iridium complexes, INORGANIC CHEMISTRY, 47, 980, (2008)
Abstract: Highly phosphorescent blue-light-emitting anionic iridium complexes (C4H9)(4)N[lr(2-phenylpyridine)(2)(CN)(2) (1), (C4H9)(4)N[Ir(2-phenyl-4-dimethylaminopyridine)(2)(CN)(2)] (2), (C4H9)(4)N[Ir(2-(2,4-difluorophenyl)-pyridine)2(CN)(2)] (3), (C4H9)(4)N[Ir(2-(2,4-difluorophenyl)-4-dimethylaminopyddine)2(CN)(2)] (4), and (C4H9)4N[lr(2-(3,5-difluorophenyl)-4-dimethylaminopyddine)2(CN)21 (5) were synthesized and characterized using NMR, UV-vis absorption, and emission spectroscopy and electrochemical methods. In these complexes color and quantum yield tuning aspects are demonstrated by modulating the ligands with substituting donor and acceptor groups on both the pyridine and phenyl moieties of 2-phenylpyridine. Complexes 1-5 display intense photoluminescence maxima in the blue region of the visible spectrum and exhibit very high phosphorescence quantum yields, in the range of 50-80%, with excited-state lifetimes of 1-4 mu s in acetonitrile solution at 298 K. DFT and time dependent-DFT calculations were performed on the ground and excited states of the investigated complexes to provide insight into the structural, electronic, and optical properties of these systems.
First author: de Hoog, Paul, Influence of the copper coordination geometry on the DNA cleavage activity of Clip-Phen complexes studied by DFT, EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, 47, 612, (2008)
Abstract: Six different Cu(Chp-Phen)(2+/+) complexes, with or without a coordinating chloride ligand, have been investigated by DFT calculations to evaluate the influence of the length and functional substituents of the bridge linking the two phenanthroline units on the DNA cleavage activity. The changes of the structural and energetic profiles imposed by the bridge of these complexes have been analyzed by comparison with the well studied nuclease active agent Cu(phen)(2)(2+/+). The present studies show that the bridge length of these complexes is critical for the consequent geometry, and both the strain and ligand binding energies. Upon reduction (needed for the DNA cleavage activity), the geometry of Cu(phen)(2) changes drastically. The behavior of the complexes with a 4- or 5-carbon bridge resembles the behavior of Cu(phen)(2)(2+/+). However, the geometries of the complexes with two- or three-carbon bridges are markedly different from the one of unbridged Cu(phen)(2)(+), as a result of constraints enforced by the short bridge. The results suggest that the cleaving activities of these bis-phenanthroline complexes are influenced by the different ligand environment geometries imposed by the bridge, and not by the change of the redox properties. It appears that the influence of the different bridges on the redox properties of the complexes is minor.
First author: van Bochove, Marc A., Nucleophilic substitution at C, Si and P: How solvation affects the shape of reaction profiles, EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, 47, 649, (2008)
Abstract: We have studied how solvation affects the shape of potential energy surfaces (PES) of archetypal nucleophilic substitution reactions at carbon (S(N)2@C), silicon (S(N)2@Si) and phosphorus (S(N)2@P), using the generalized gradient approximation (GGA) of density functional theory (DFT) at OLYP/TZ2P. Our model systems cover nucleophilic substitution, in water and in the gas phase, at carbon in X- + CH3Y (S(N)2@C), at silicon in X- + SiH3Y (S(N)2@Si), at tricoordinate phosphorus in X- + PR2Y (S(N)2@P3), and at tetraccordinate phosphorus in X- + POR2Y (S(N)2@P4) with substituents R = H, F, Cl, CH3, OCH3. In the gas phase, particular types of S(N)2 reactions are characterized by different shapes of reaction profiles, such as single-, double- and triple-well PESs. The main effect of solvation is to turn the PESs of the S(N)2@C but also of S(N)2@Si and S(N)2@P into unimodal reaction profiles which lead from the reactants via one single barrier to the products. The results are discussed in terms of differential solvation of reactants and transition states. We also address the question how the relative heights of reaction barriers are affected by solvation.
First author: Rahemi, H., Theoretical studies of the tetrachlorocuprate(II) anion: ADF geometry optimization, and calculation of the PES, EPR parameters, and vibrational frequencies, JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY, 7, 53, (2008)
Abstract: PES as functions of the trans-angle (theta) and the dihedral angle (epsilon) for optimized bond length is calculated. It is found that the most unstrained stable conformation of the CuCl42- is D-2d at theta = 129.45 degrees and epsilon = 90.0 degrees. Calculated EPR g values change smoothly and in a logarithmic manner in the experimental range. The g(33) value varies from 2.1287 (D-4h) to 2.2836 (T-d), and g(11) = g(22) from 2.035 to 2.1001. The Cu hyper. ne values of the D-4h are A(11) = -196.455 and A(22) = A(33) = -17.533. At the most stable D-2d conformation, the values are A(11) = -177.606 and A(22) = A(33) = 2.6266, all in the 10(-4) cm(-1) unit.The variation of EPR g values with molecular charge in the range of -2.0 to -2.8 were studied, and it was found that by increasing molecular charge, both components of g values are increased. For the D-2d conformation with molecular charge of -2.6, g perpendicular to = 2.085 (expt. = 2.094) and g parallel to = 2.243 (expt. = 2.238). For the D-4h conformation, calculated g parallel to values with increasing molecular charge improved, but g perpendicular to values deviated increasingly from experimental values. Frequencies are also calculated in the range of D-2d to D-4h.
First author: Keita, Bineta, A new class of efficient electrocatalysts for the reduction of protons into hydrogen based on the [Mo2O2S2](2+) building block, JOURNAL OF PHYSICAL CHEMISTRY C, 112, 1109, (2008)
Abstract: Oxothiomolybdenum wheels represent a new family of efficient electrocatalysts for the reduction of protons into hydrogen. The present study focuses on the complex [Mo8S8O8(OH)(8)(Ox)](2-) (1) as a lithium salt (Ox(2-) = oxalate), which exhibits an electrocatalytic reduction wave of protons in the presence of perchloric acid at about – 1.00 V versus SCE in DMF. Efficiency of this new electrocatalyst was evidenced by cyclic voltammetry and coulometry. DFT calculations were reported and bring about data of the protonated state of the catalyst, the first step of the postulated mechanism in the catalytic reaction. Other weak acids such as p-toluenesulfonic acid, trifluoroacetic acid, and acetic acid in DMF were tested and found to be efficient for the reduction of protons. The complex [Mo12S12O12(OH)(12)(Trim)](3-) (2) behaves also as an electrocatalyst, functioning at a very low overpotential. Finally, the biomimetic behaviors of this new class of efficient electrocatalysts for hydrogen production mimic those of hydrogenases and compare favorably with their performances.
First author: Nunzi, Francesca, Theoretical investigations of the effects of J-aggregation on the linear and nonlinear optical properties of E-4-(4-dimethylaminostyryl)-1-methylpyridinium [DAMS(+)], JOURNAL OF PHYSICAL CHEMISTRY C, 112, 1213, (2008)
Abstract: J-type aggregation of organic chromophores into inorganic host matrixes provides a useful route toward materials showing strong second-order nonlinear optical (NLO) response. The increased NLO response of J-aggregates is related to the peculiar arrangement of the NLO-phores into the host matrix, which produces the appearance of a narrow and intense band in the material electronic absorption spectrum, red-shifted with respect to the main absorption band of the isolated NLO-phore. A theoretical investigation, based on DFT, TDDFT, and ZINDO calculations on the relationship between the structural features of various [DAMS(+)] ([DAMS(+)] = E-4-(4-dimethylaminostyryl)-1-methylpyridinium) dimeric or oligomeric aggregates and their linear and nonlinear optical properties shows that the appearance of a new red-shifted absorption band, typical of J-aggregation, is associated with interchromophoric transitions of charge-transfer character, due to the splitting of HOMO and LUMO levels. The intensity of this latter band increases by increasing the number of NLO-phores in a model of oligomeric arrangement of J-aggregates. The calculated quadratic hyperpolarizabilities for the mostly responsive J-type trimeric aggregates of [DAMS(+)] are found to largely exceed that of three isolated NLO-phores, confirming a cooperative NLO strong contribution due to J-aggregation. Finally, our DFT and TDDFT calculations on eclipsed or with opposite dipole dimeric H-aggregates of [DAMS(+)] show a splitting of HOMO and LUMO levels, which gives place to interchromophoric transitions of charge-transfer character but blue-shifted, as observed experimentally.
First author: Van Zeist, Willem-Jan, Software news and update PyFrag – Streamlining your reaction path analysis,JOURNAL OF COMPUTATIONAL CHEMISTRY, 29, 312, (2008)
Abstract: The PyFrag program (released as PyFrag2007.01) is a “wrap-around” for the Amsterdam Density Functional (ADF) package and facilitates the extension of the fragment analysis method implemented in ADF along an entire potential energy surface. The purpose is to make analyses of reaction paths and other (in principle also multidimensional) potential energy surfaces more transparent and user-friendly. PyFrag also automates the analysis of reaction paths in terms of the extended activation strain model of chemical reactivity.
First author: Slepkov, Vladimir, Halogen-chalcogen interactions in [Mo3X7Y7](3-) clusters (X = S, Se, Te; Y=Cl, Br, I),JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 849, 112, (2008)
Abstract: The nature of halogen-chalcogen bonds in [Mo3X7Y7](3-) (X = S, Se, Te; Y = Cl, Br, I) clusters is studied using DFT quantum chemical calculations and the topological AIM theory. Comparison of the [Mo3X7Y7](3-) and [Mo3X7Y](3+) electron densities at (3, -1) critical points and the calculated formation energies of the clusters shows that the bonds result from a joint effect of shared halogen-chalcogen interactions and electrostatic halogen-halogen repulsion and can be considered as an example of supramolecular interactions.
First author: Kiewisch, Karin, Topological analysis of electron densities from Kohn-Sham and subsystem density functional theory, JOURNAL OF CHEMICAL PHYSICS, 128, 112, (2008)
Abstract: In this study, we compare the electron densities for a set of hydrogen-bonded complexes obtained with either conventional Kohn-Sham density functional theory (DFT) calculations or with the frozen-density embedding (FDE) method, which is a subsystem approach to DFT. For a detailed analysis of the differences between these two methods, we compare the topology of the electron densities obtained from Kohn-Sham DFT and FDE in terms of deformation densities, bond critical points, and the negative Laplacian of the electron density. Different kinetic-energy functionals as needed for the frozen-density embedding method are tested and compared to a purely electrostatic embedding. It is shown that FDE is able to reproduce the characteristics of the density in the bonding region even in systems such as the F-H-F(-) molecule, which contains one of the strongest hydrogen bonds. Basis functions on the frozen system are usually required to accurately reproduce the electron densities of supermolecular calculations. However, it is shown here that it is in general sufficient to provide just a few basis functions in the boundary region between the two subsystems so that the use of the full supermolecular basis set can be avoided. It also turns out that electron-density deformations upon bonding predicted by FDE lack directionality with currently available functionals for the nonadditive kinetic-energy contribution.
First author: Blake, Alexander J., Probing the mechanism of carbon-hydrogen bond activation by photochemically generated hydridotris(pyrazolyl)borato carbonyl rhodium complexes: New experimental and theoretical investigations,ORGANOMETALLICS, 27, 189, (2008)
Abstract: Fast time-resolved infrared (TRIR) experiments and density functional (DFT) calculations have been used to elucidate the complete reaction mechanism between alkanes and photolytically activated hydridotris(pyrazoly-1-yl)boratodicarbonylrhodium. TRIR spectra were obtained after photolysis of Rh(TP4-tBu-3,5-Me)(CO)(2) in n-heptane, n-decane, and cyclohexane and of Rh(Tp(3,5-Me))(CO)(2) in n-heptane and cyclohexane. Initial photolysis produces a coordinatively unsaturated, 16-electron monocarbonyl species that vibrationally relaxes to an intermediate with v(CO) of 1971 cm(-1) in n-heptane solution (species A). DFT calculations on Rh(Tp(3,5-Me))(CO)-RH (RH = C2H6, C6H12) suggest that A is the triplet state of a five-coordinate, square-pyramidal Rh(k(3) -Tp(3,5-Me))(CO)-RH, in which the alkane is weakly bound. Within the first 2 ns, a new transient grew in at 1993 cm(-1) (species B). The calculations show that the observed species B is the singlet state of a four-coordinate Rh(K-2-Tp(3,5-Me))(CO)(RH), in which the alkane is strongly bound and one pyrazolyl ring is rotated, decoordinating one N. The transient due to B grew at the same rate as A partially decayed. However, A did not decay completely, but persisted in equilibrium with B throughout the time up to 2500 ps. The v(CO) bands due to A and B decayed at the same rate as a band at 2026 cm(-1) grew in (tau ca. 29 ns, n-heptane). The latter band can be readily assigned to the final alkyl hydride products, Rh(K-3-Tp(4-tBu-3,5-Me))(CO)R(H) and Rh(K-3-Tp(3,5-Me))(CO)R(H) (species D). The experimental data do not allow the elucidation of which of the two alkane complexes, A or B, is C-H activating, or whether both of the complexes react to form the final product. The calculations suggest that a third intermediate (species Q is the C-H activating species, that is, the final product D is formed from C and not directly from either A or B. Species C is nominally a five-coordinate, square-pyramidal Rh(K-21/2-T-p3,T-5-Me)(CO)(RH) complex with a strongly bound alkane and one pyrazolyl partially decoordinated, but occupying the apical position of the square pyramid. Intermediate C is unobserved, as the calculations predict it possesses the same CO stretching frequency as the parent dicarbonyl. The unobserved species is predicted to lie on the reaction path between A and B and to be in rapid equilibrium with the four-coordinate species B.
First author: Koh, Sharon E., Modeling electron and hole transport in fluoroarene-oligothiopene semiconductors: Investigation of geometric and electronic structure properties, ADVANCED FUNCTIONAL MATERIALS, 18, 332, (2008)
Abstract: A theoretical study using density functional theory is undertaken to gain insight into how the structural, electronic, and electron-transfer characteristics of three Fluoroarene-oligothiophene semiconductors influence the preferred transport of electrons versus holes in field-effect transistor applications. The intermolecular electronic coupling interactions are analyzed through both a simplified energy-splitting in dimer (ESID) model and as a function of the entire dimer Hamiltonian in order to understand the impact of site energy differences; our results indicate that these differences are generally negligible for the series and, hence, use of the ESID model is valid. In addition, we also investigate the reduction and oxidation processes to understand the magnitudes of the intramolecular reorganization energy for the charge-hopping process and expected barrier heights for electron and hole injection into these materials. From the electronic coupling and intramolecular reorganization energies, estimates of the nearest-neighbor electron-transfer hopping rate constant for electrons are obtained. The ionization energetics suggest favored electron injection for the system with perfluoroarene groups at the end of the thiophene core, in agreement with experiments. The combined analyses of the electron-transfer properties and ionization processes suggest possible ambipolar behavior for these materials under favorable device conditions.
First author: Groenewold, Gary S., Infrared spectroscopy of discrete uranyl anion complexes, JOURNAL OF PHYSICAL CHEMISTRY A, 112, 508, (2008)
Abstract: The Free-Electron Laser for Infrared Experiments (FELIX) was used to study the wavelength-resolved multiple photon photodissociation of discrete, gas-phase uranyl (UO22+) complexes containing a single anionic ligand (A), with or without ligated solvent molecules (S). The uranyl antisymmetric and symmetric stretching frequencies were measured for complexes with general formula [UO(2)A(S)(n)](+), where A was hydroxide, methoxide, or acetate; S was water, ammonia, acetone, or acetonitrile; and n = 0-3. The values for the antisymmetric stretching frequency for uranyl ligated with only an anion ([UO(2)A](+)) were as low or lower than measurements for [UO2](2+) ligated with as many as five strong neutral donor ligands and are comparable to solution-phase values. This result was surprising because initial DFT calculations predicted values that were 30-40 cm(-1) higher, consistent with intuition but not with the data. Modification of the basis sets and use of alternative functionals improved computational accuracy for the methoxide and acetate complexes, but calculated values for the hydroxide were greater than the measurement regardless of the computational method used. Attachment of a neutral donor ligand S to [UO(2)A](+) produced [UO(2)AS](+), which produced only very modest changes to the uranyl antisymmetric stretch frequency, and did not universally shift the frequency to lower values. DFT calculations for [UO(2)AS](+) were in accord with trends in the data and showed that attachment of the solvent was accommodated by weakening of the U-anion bond as well as the uranyl. When uranyl frequencies were compared. for [UO(2)AS](+) species having different solvent neutrals, values decreased with increasing neutral nucleophilicity.
First author: Belpassi, Leonardo, The chemical bond between Au(I) and the noble gases. Comparative study of NgAuF and NgAu(+) (Ng = Ar, Kr, Xe) by density functional and coupled cluster methods, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130, 1048, (2008)
Abstract: The nature of the chemical bond between gold and the noble gases in the simplest prototype of Au(I) complexes (NgAuF and NgAu(+), where Ng = Ar, Kr, Xe), has been theoretically investigated by state of art all-electron fully relativistic DC-CCSD(T) and DFT calculations with extended basis sets. The main properties of the molecules, including dipole moments and polarizabilities, have been computed and a detailed study of the electron density changes upon formation of the Ng-Au bond has been made. The Ar-Au dissociation energy is found to be nearly the same in both Argon compounds. It almost doubles along the NgAuF series and nearly triples in the corresponding NgAu+ series. The formation of the Ng-Au(I) bonds is accompanied by a large and very complex charge redistribution pattern which not only affects the outer valence region but reaches deep into the core-electron region. The charge transfer from the noble gas to Au taking place in the NgAu+ systems is largely reduced in the fluorides but the Ng-Au chemical bond in the latter systems is found to be tighter near the equilibrium distance. The density difference analysis shows, for all three noble gases, a qualitatively identical nature of the Ng-Au bond, characterized by the pronounced charge accumulation in the middle of the Ng-Au internuclear region which is typical of a covalent bond. This bonding density accumulation is more pronounced in the fluorides, where the Au-F bond is found to become more ionic, while the overall density deformation is more evident and less localized in the NgAu+ systems. Accurate density difference maps and charge-transfer curves help explain very subtle features of the chemistry of Au(l), including its peculiar preference for tight linear bicordination.
First author: Norton, Joseph E., Theoretical characterization of titanyl phthalocyanine as a p-type organic semiconductor: Short intermolecular pi-pi interactions yield large electronic couplings and hole transport bandwidths, JOURNAL OF CHEMICAL PHYSICS, 128, 1048, (2008)
Abstract: The charge-transport properties of the triclinic phase II crystal of titanyl phthalocyanine (alpha-TiOPc) are explored within both a hopping and bandlike regime. Electronic coupling elements in convex- and concave-type dimers are calculated using density functional theory, and the relationship between molecular structure and crystal packing structure in model dimer configurations is considered. Hole transport bandwidths derived from crystal structure dimers are compared to those obtained from electronic band structure calculations; very good agreement between the two approaches is found. The calculations predict large hole bandwidths, on the order of 0.4 eV, and correspondingly very low hole reorganization energies.
First author: Lees, Nicholas S., ENDOR characterization of a synthetic diiron hydrazido complex as a model for nitrogenase intermediates, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130, 546, (2008)
Abstract: Molybdenum-dependent nitrogenase binds and reduces N-2 at the [Fe-7, Mo, S-9, X, homocitrate] iron-molybdenum cofactor (FeMo-co). Kinetic and spectroscopic studies of nitrogenase variants indicate that a single Fe-S face is the most likely binding site. Recently, substantial progress has been made in determining the structures of nitrogenase intermediates formed during alkyne and N-2 reduction through use of ENDOR spectroscopy. However, constraints derived from ENDOR studies of biomimetic complexes with known structure would powerfully contribute in turning experimentally derived ENDOR parameters into structures for species bound to FeMo-co during N-2 reduction. The first report of a paramagnetic Fe-S compound that binds reduced forms of N-2 involved Fe complexes stabilized by a bulky beta-diketiminate ligand (Vela, J.; Stoian, S.; Flaschenriem, C. J.; Munck, E.; Holland, P. L. J. Am. Chem. Soc. 2004, 126, 4522-4523). Treatment of a sulfidodiiron(II) complex with phenylhydrazine gave an isolable mixed-valence Fe-II-Fe-III complex with a bridging phenylhydrazido (PhNNH2) ligand, and this species now has been characterized by ENDOR spectroscopy. Using both N-15, H-2 labeled and unlabeled forms of the hydrazido ligand, the hyperfine and quadrupole parameters of the -N-NH2 moiety have been derived by a procedure that incorporates the (near-) mirror symmetry of the complex and involves a strategy which combines experiment with semiempirical and DFT computations. The results support the use of DFT computations in identifying nitrogenous species bound to FeMo-co of nitrogenase turnover intermediates and indicate that N-14 quadrupole parameters from nitrogenase intermediates will provide a strong indication of the nature of the bound nitrogenous species. Comparison of the large N-14 hyperfine couplings measured here with that of a hydrazine-derived species bound to FeMo-co of a trapped nitrogenase intermediate suggests that the ion(s) are not high spin and/or that the spin coupling coefficients of the coordinating cofactor iron ion(s) in the intermediate are exceptionally small.
First author: Mayer, A., An electrostatic interaction model for frequency-dependent polarizability: methodology and applications to hydrocarbons and fullerenes, NANOTECHNOLOGY, 19, 546, (2008)
Abstract: We present an electrostatic interaction model for the calculation of frequency-dependent electronic polarizability. The model is based on the representation of atoms by an induced electric charge and a dipole moment. The extension of the charge-dipole model to the interaction with oscillating electric fields requires us to account for the kinetics of the free moving charges and of the atomic dipoles. This step is achieved by first relating the oscillations of the atomic charges to the currents that flow through the atomic bonds. Adopting a classical description of this system of charges and dipoles, the time evolution of these quantities is determined from the principle that the action be minimized. As an application of this model, we compute the frequency-dependent molecular polarizability of hydrocarbons with different hybridization. We propose parameters for each chemical group, which provide an excellent agreement with reference data provided by current-density-functional theory. We finally study the frequency-dependent molecular polarizability of fullerenes ranging from C(60) to C(1500).
First author: Sherman, David M., Surface complexation of U(VI) on goethite (alpha-FeOOH), GEOCHIMICA ET COSMOCHIMICA ACTA, 72, 298, (2008)
Abstract: Sorption of U(VI) to goethite is a fundamental control on the mobility of uranium in soil and groundwater. Here, we investigated the sorption of U on goethite using EXAFS spectroscopy, batch sorption experiments and DFT calculations of the energetics and structures of possible surface complexes. Based on EXAFS spectra, it has previously been proposed that U(VI), as the uranyl cation UO22+, sorbs to Fe oxide hydroxide phases by forming a bidentate edge-sharing (E2) surface complex, >Fe(OH)(2)UO2(H2O)(n). Here, we argue that this complex alone cannot account for the sorption capacity of goethite (alpha-FeOOH). Moreover, we show that all of the EXAFS signal attributed to the E2 complex can be accounted for by multiple scattering. We propose that the dominant surface complex in CO2-free systems is a bidentate corner-sharing (C2) complex, (>FeOH)(2)UO2(H2O)(3) which can form on the dominant {101} surface. However, in the presence Of CO2, we find an enhancement Of UO2 sorption at low pH and attribute this to a (>FeO)CO2UO2 ternary complex. With increasing pH, U(VI) desorbs by the formation of aqueous carbonate and hydroxyl complexes. However, this desorption is preceded by the formation of a second ternary surface complex (>FeOH)(2)UO2CO3. The three proposed surface complexes, (>FeOH)(2)UO2(H2O)(3), >FeOCO2UO2, and (>FeOH)(2)UO2CO3 are consistent with EXAFS spectra. Using these complexes, we developed a surface complexation model for U on goethite with a 1-pK model for surface protonation, an extended Stern model for surface electrostatics and inclusion of all known UO2-OH-CO3 aqueous complexes in the current thermodynamic database. The model gives an excellent fit to our sorption experiments done in both ambient and reduced CO2 environments at surface loadings of 0.02-2.0 wt% U.
First author: Roger, Mathieu, Uranium and lanthanide complexes with the 2-mercapto benzothiazolate ligand: Evidence for a specific covalent binding site in the differentiation of isostructural lanthanide(III) and actinide(III) compounds,ORGANOMETALLICS, 27, 33, (2008)
Abstract: Treatment Of [U(CP*)(2)Cl-2] with KSBT in THF gave [U(CP*)(2)(SBT)(2)], which exhibits the usual bent sandwich configuration in the solid state with the two SBT ligands adopting the bidentate ligation mode. The monocyclopentadienyl compound [U(Cp*)(SBT)(3)] was synthesized by reaction of [U(Cp*)(BH4)(3)] with KSBT in THF, and its reduction with potassium amalgam in the presence of 18-crown-6 afforded the corresponding anionic complex [K(18-crown-6)(THF)(2)][U(Cp*)(SBT)(3)]. The lanthanide analogues [K(THF)(2)Ln(Cp*)(SBT)(3)] were obtained by treating [Ln(BH4)(3)(THF)(3)] with KSBT and KCp*; isomorphous crystals of [K(15-crown-5)(2)] [Ln(Cp*)(SBT)(3)] center dot THF [Ln = La, Ce, Nd] were formed upon addition of 15-crown-5. Comparison of the crystal structures of the pentagonal bipyramidal complexes [M(Cp*)(SBT)(3)](-) reveals that the M-N-ax distances are shorter than the M-N-eq distances, whatever the metal, the phenomenon being enhanced in the U(III) compound versus the Ln(III) analogues. The structural data obtained by relativistic density functional theory (DFT) calculations reproduce experimental trends. Electronic population and molecular orbital analyses show that the structural differences in the series of [M(Cp*)(SBT)(3)]- anions are related to the uranium 5f orbital-ligand mixing, which is greater than the lanthanide 4f orbital-ligand mixing. Moreover, the consideration of the corresponding bond orders and the analysis of the bonding energy bring to light a strong and specific interaction between the uranium and apical nitrogen atoms.
First author: Gaunt, Andrew J., Experimental and theoretical comparison of actinide and lanthanide bonding in M[N(EPR2)(2)](3) complexes (M = U, Pu, La, Ce; E = S, Se, Te; R = Ph, iPr, H), INORGANIC CHEMISTRY, 47, 29, (2008)
Abstract: Treatment of M[N(SiMe3)213 (M = J, Pu (An); La, Ce (Ln)) with NH(EPPh2)(2) and NH(EP/Pr-2)(2) (E = S, Se), afforded the neutral complexes M[N(EPR2)(2)](3) (R = Ph, Pr). Tellurium donor complexes were synthesized by treatment of MI3(SOl)(4) (M = U, Pu; sol = py and M La, Ce; sol = thf) with Na(tmeda)[N(TePiPr(2))(2)]. The complexes have been structurally and spectroscopically characterized with concomitant computational modeling through density functional theory (DFT) calculations. The An-E bond lengths are shorter than the Ln-E bond lengths for metal ions of similar ionic radii, consistent with an increase in covalent interactions in the actinide bonding relative to the lanthanide bonding. In addition, the magnitude of the differences in the bonding is slightly greater with increasing softness of the chalcogen donor atom. The DFT calculations for the model systems correlate well with experimentally determined metrical parameters. They indicate that the enhanced covalency in the WE bond as group 16 is descended arises mostly from increased metal d-orbital participation. Conversely, an increase in f-orbital participation is responsible for the enhancement of covalency in An-E bonds compared to Ln-E bonds. The fundamental and practical importance of such studies of the role of the valence d and f orbitals in the bonding of the f elements is emphasized.
First author: Hernandez-Molina, Rita, Heterometallic cuboidal clusters M3M ‘ Q(4) (M = Mo, W; M ‘= Sn, Pb, As, Sb; Q = S, Se): From coordination compounds to supramolecular adducts, INORGANIC CHEMISTRY, 47, 306, (2008)
Abstract: Reactions of the incomplete cuboidal clusters [M(3)Q(4)(acaC)(3)(PY)(3)](+) (M = Mo, W; Q = S, Se) with group 14 and 15 metal complexes with the S(2)p(0) electronic configuration (AsPh3, SbPh3, SbCl3, Sbl(3), Pbl(3)(-), SnCl3-) led to heterometal incorporation with the formation of cuboidal clusters of the type [M-3(EX3)Q(4)(acac)(3)(py)(3)](n+) (n = 0 for Sn, Pb; n = 1 for As, Sb), whose structures were determined by X-ray diffraction. The cuboidal clusters can be described as complexes of the cluster tridentate ligand [M(3)Q(4)(acac)(3)(PY)(3)](+) (mu(2)-chalcogen atoms as donors) with the EX3, where the E atom attains a distorted octahedral coordination. Analysis based on the bond distances E-Q gives the following sequence of affinity: As < Sb; Pb < Sn approximate to Sb; SbPh3 < Sbl(3) approximate to SbCl3; W3S4 < W3Se4. Interaction energies at the gas phase between [W(3)Q(4)(acac)(3)(py)(3)](+) (Q = S, Se) and SbX3 (X = 1, Ph) were computed at the DFT level (BP86/TZP). The magnitude of the interaction depends strongly on the substituents at Sb, and the replacement of iodine by the phenyl group decreases the interaction energy from -9.21 to -2.70 kcal/mol and from -12.73 to -3.85 kcal/mol for the W3SbS4 and W3SbSe4 cores, respectively.
First author: Matsuo, Shuji, X-ray absorption spectroscopic study on polymerization of aqueous aluminate by DV-X alpha molecular-orbital method, ADVANCES IN QUANTUM CHEMISTRY, VOL 54: DV-X ALPHA FOR INDUSTRIAL-ACADEMIC COOPERATION, 54, 193, (2008)
Abstract: Chemical species produced in the process of structural transition from aqueous aluminate to crystalline aluminum hydroxide (gibbsite) in 1.0M aqueous solution and their ratios are examined by the curve fitting for the experimental Al K-edge XANES spectra using the calculated XANES curves derived from the results of the discrete variational (DV)-X alpha molecular-orbital calculations and theoretical continuum curves as a baseline. The structural transform proceeds in order of: (I) decomposition of network structure of aluminate due to hydrolysis, (II) polymerization of hydrate ions, (III) precipitation of Al(OH)(3), and (IV) crystallization due to dehydration. The curve fittings for experimental XANES spectra corresponding to process (I)-(IV) during the transition are converged by [Al(OH)(4)](-) and [Al(OH)(4)(H2O)(2)](-) models for process (I), by [Al(OH)(4)](-), [Al(OH)(4)(H2O)(2)](-), and [Al(H2O)(6)](3+) models for process (II), by [Al(OH)(4)(H2O)(2)](-), [Al(H2O)(6)](3+), and gibbsite models for process (III), and by [Al(H2O)(6)](3+) and gibbsite models for process (IV).
First author: Cadenbach, Thomas, Methylgallium as a terminal ligand in [(Cp*Ga)(4)Rh(GaCH3)](+), ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 47, 3438, (2008)
Abstract: Chemical species produced in the process of structural transition from aqueous aluminate to crystalline aluminum hydroxide (gibbsite) in 1.0M aqueous solution and their ratios are examined by the curve fitting for the experimental Al K-edge XANES spectra using the calculated XANES curves derived from the results of the discrete variational (DV)-X alpha molecular-orbital calculations and theoretical continuum curves as a baseline. The structural transform proceeds in order of: (I) decomposition of network structure of aluminate due to hydrolysis, (II) polymerization of hydrate ions, (III) precipitation of Al(OH)(3), and (IV) crystallization due to dehydration. The curve fittings for experimental XANES spectra corresponding to process (I)-(IV) during the transition are converged by [Al(OH)(4)](-) and [Al(OH)(4)(H2O)(2)](-) models for process (I), by [Al(OH)(4)](-), [Al(OH)(4)(H2O)(2)](-), and [Al(H2O)(6)](3+) models for process (II), by [Al(OH)(4)(H2O)(2)](-), [Al(H2O)(6)](3+), and gibbsite models for process (III), and by [Al(H2O)(6)](3+) and gibbsite models for process (IV).
First author: Zhang, Yun, The low basicity of phosphabenzenes: First examples of protonation, alkylation, and silylation reactions, ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 47, 3801, (2008)
Abstract: Chemical species produced in the process of structural transition from aqueous aluminate to crystalline aluminum hydroxide (gibbsite) in 1.0M aqueous solution and their ratios are examined by the curve fitting for the experimental Al K-edge XANES spectra using the calculated XANES curves derived from the results of the discrete variational (DV)-X alpha molecular-orbital calculations and theoretical continuum curves as a baseline. The structural transform proceeds in order of: (I) decomposition of network structure of aluminate due to hydrolysis, (II) polymerization of hydrate ions, (III) precipitation of Al(OH)(3), and (IV) crystallization due to dehydration. The curve fittings for experimental XANES spectra corresponding to process (I)-(IV) during the transition are converged by [Al(OH)(4)](-) and [Al(OH)(4)(H2O)(2)](-) models for process (I), by [Al(OH)(4)](-), [Al(OH)(4)(H2O)(2)](-), and [Al(H2O)(6)](3+) models for process (II), by [Al(OH)(4)(H2O)(2)](-), [Al(H2O)(6)](3+), and gibbsite models for process (III), and by [Al(H2O)(6)](3+) and gibbsite models for process (IV).
First author: Noor, Awal, Metal-metal distances at the limit: A coordination compound with an ultrashort chromium-chromium bond, ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 47, 7246, (2008)
Abstract: Chemical species produced in the process of structural transition from aqueous aluminate to crystalline aluminum hydroxide (gibbsite) in 1.0M aqueous solution and their ratios are examined by the curve fitting for the experimental Al K-edge XANES spectra using the calculated XANES curves derived from the results of the discrete variational (DV)-X alpha molecular-orbital calculations and theoretical continuum curves as a baseline. The structural transform proceeds in order of: (I) decomposition of network structure of aluminate due to hydrolysis, (II) polymerization of hydrate ions, (III) precipitation of Al(OH)(3), and (IV) crystallization due to dehydration. The curve fittings for experimental XANES spectra corresponding to process (I)-(IV) during the transition are converged by [Al(OH)(4)](-) and [Al(OH)(4)(H2O)(2)](-) models for process (I), by [Al(OH)(4)](-), [Al(OH)(4)(H2O)(2)](-), and [Al(H2O)(6)](3+) models for process (II), by [Al(OH)(4)(H2O)(2)](-), [Al(H2O)(6)](3+), and gibbsite models for process (III), and by [Al(H2O)(6)](3+) and gibbsite models for process (IV).
First author: Hamon, Paul, Dramatic Remote Substitutent Effects on the Electronic Spin State of Bis(scorpionate) Iron(II) Complexes, ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 47, 8687, (2008)
Abstract: Chemical species produced in the process of structural transition from aqueous aluminate to crystalline aluminum hydroxide (gibbsite) in 1.0M aqueous solution and their ratios are examined by the curve fitting for the experimental Al K-edge XANES spectra using the calculated XANES curves derived from the results of the discrete variational (DV)-X alpha molecular-orbital calculations and theoretical continuum curves as a baseline. The structural transform proceeds in order of: (I) decomposition of network structure of aluminate due to hydrolysis, (II) polymerization of hydrate ions, (III) precipitation of Al(OH)(3), and (IV) crystallization due to dehydration. The curve fittings for experimental XANES spectra corresponding to process (I)-(IV) during the transition are converged by [Al(OH)(4)](-) and [Al(OH)(4)(H2O)(2)](-) models for process (I), by [Al(OH)(4)](-), [Al(OH)(4)(H2O)(2)](-), and [Al(H2O)(6)](3+) models for process (II), by [Al(OH)(4)(H2O)(2)](-), [Al(H2O)(6)](3+), and gibbsite models for process (III), and by [Al(H2O)(6)](3+) and gibbsite models for process (IV).
First author: Pierrefixe, Simon C. A. H., Aromaticity in Heterocyclic and inorganic benzene analogues, AUSTRALIAN JOURNAL OF CHEMISTRY, 61, 209, (2008)
Abstract: Recently, we presented a molecular orbital (MO) model of aromaticity that explains, in terms of simple orbital- overlap arguments, why benzene (C6H6) has a regular structure with delocalized double bonds. Here, we show that the same model and the same type of orbital- overlap arguments also account for heterocyclic and inorganic benzene analogues, such as s- triazine (C3N3H3), hexazine (N-6), borazine (B3N3H6), boroxine (B3O3H3), hexasilabenzene (Si6H6), and hexaphosphabenzene (P-6). Our MO model is based on accurate Kohn – Sham density- functional theory (DFT) analyses of the bonding in the seven model systems, and how the bonding mechanism is affected if these molecules undergo geometrical deformations between regular, delocalized ring structures and distorted ones with localized double bonds. It turns out that also in the heterocyclic and inorganic benzene analogues, the propensity of the p electrons is always to localize the double bonds, against the delocalizing force of the s electrons. The latter in general prevails, yielding the regular, delocalized ring structures. Interestingly, we find one exception to this rule: N-6.
First author: Wu, Guohua, State-resolved UV photofragmentation spectrum of the metal dication complex [Zn(pyridine)(4)](2+), CHEMICAL COMMUNICATIONS, 61, 4153, (2008)
Abstract: A combined theoretical and experimental study of electronic transitions in the complex [Zn(pyridine)(4)](2+) provides the first example of a state-resolved electronic spectrum to be recorded for a dication complex in the gas phase.
First author: Lin, Cheng-Lan, Electrochemical oxidation of double-stranded polybisnorbornenes containing linearly aligned ferrocene linkers, CHEMICAL COMMUNICATIONS, 61, 4484, (2008)
Abstract: Seventy percent of the ferrocene moieties in double-stranded polybisnorbornenes containing linearly aligned ferrocene linkers are oxidised and each of the neighbouring monomeric units in these polymers may strongly interact with each other; the oxidised form of 3c has been shown to be antiferromagnetic.
First author: Sierra, Miguel A., Computational and experimental tools in solving some mechanistic problems in the chemistry of Fischer carbene complexes, CHEMICAL COMMUNICATIONS, 61, 4671, (2008)
Abstract: Well-established bonding situations of organometallic complexes and extensive applications in synthesis have been achieved during the past 25 years. In contrast, very little attention has been devoted to the intimate understanding of their reaction mechanisms. In this feature article, we show how the combined use of experimental and computational tools can be used to explore some reaction mechanisms of Fischer-type carbene complexes. The results obtained clearly demonstrate the usefulness of these combined tools to unravel the intimacies of different thermal and photochemical transformations, not only to explain already known processes but to predict new reactivity involving these fascinating complexes.
First author: Pierrefixe, Simon C. A. H., Hypervalent silicon versus carbon: Ball-in-a-box model, CHEMISTRY-A EUROPEAN JOURNAL, 14, 819, (2008)
Abstract: Why is silicon hypervalent and carbon not? Or why is [Cl-CH(3)-Cl](-) labile with a tendency to localize one of its axial C-Cl bonds and to largely break the other one, while the isostructural and isoelectronic [Cl-SiH(3)-Cl](-) forms a stable pentavalent species with a delocalized structure featuring two equivalent Si-Cl bonds? Various hypotheses have been developed over the years focusing on electronic and steric factors. Here, we present the so-called ball-in-a-box model, which tackles hypervalence from a new perspective. This model reveals the key role of steric factors and provides a simple way of understanding the above phenomena in terms of different atom sizes. Our bonding analyses are supported by computation experiments in which we probe, among other things, the shape of the S(N)2 potential-energy surface of Cl(-) attacking a carbon atom in the series of substrates CH(3)Cl, (center dot)CH(2)Cl, (center dot center dot)CHCl, and (center dot center dot center dot)CCl. Our findings for ClCH(3)Cl(-) and ClSiH(3)Cl(-) are generalized to other Group 14 central atoms (Ge, Sn, and Ph) and axial substituents (F).
First author: Douglas, Thomas M., Intramolecular alkyl phosphine dehydrogenation in cationic rhodium complexes of tris(cyclopentylphosphine), CHEMISTRY-A EUROPEAN JOURNAL, 14, 1004, (2008)
Abstract: [Rh(nbd)(PCYp(3))(2)][BAr4F] (1) [nbd = norbornadiene, Ar-F = C6H3(CF3)(2), PCYP3 = tris(cyclopentylphosphine)] spontaneously undergoes dehydrogenation of each PCYP3 ligand in CH2Cl2 solution to form an equilibrium mixture of cis-[Rh{PCYp(2)(eta(2)-C5H7)}(2)][BAr4F] (2a) and trans-[Rh{PCYp(2)(eta(2)-C5H7)}(2)][BAr4F](2b), which have hybrid phosphine-alkene ligands. In this reaction nbd acts as a sequential acceptor of hydrogen to eventually give norbornane. Complex 2b is distorted in the solid-state away from square planar. DFT calculations have been used to rationalise this distortion. Addition of H-2 to 2a/b hydrogenates the phosphine-alkene ligand and forms the bisdihydrogen/dihydride complex [Rh(PCYp(3))(2)(H)(2)(eta(2)-H-2)(2)] [BAr4F] (5) which has been identified spectroscopically. Addition of the hydrogen acceptor tert-butylethene (tbe) to 5 eventually regenerates 2a/b, passing through an intermediate which has undergone dehydrogenation of only one PCYp(3) ligand, which can be trapped by addition of MeCN to form trans-[Rh{PCYp(2)(eta(2)-C5H7)}(PCYp(3))(NCMe)][BAr4F] (6). Dehydrogenation of a PCYp(3) ligand also occurs on addition of Na[BAr4F] to [RhCl(nbd)(PCyp(3))] in presence of arene (benzene, fluorobenzene) to give [Rh(eta(6)-C6H5X){PCYp(2)(eta(2)-C5H7)}][BAr4F] (7: X = F, 8: X = H). The related complex [Rh(nbd){PCYp(2)(eta(2)-C5H7)}][BAr4F] 9 is also reported. Rapid (approximate to 5 minutes) acceptorless dehydrogenation occurs on treatment of [RhCl(dppe)(PCyp(3))] with Na[BAr4F] to give [Rh(dppe){PCyp(2)(eta(2)-C5H7)}][BAr4F] (10), which reacts with H, to afford the dihydride/dihydrogen complex [Rh(dppe)(PCyp(3))(H)(2)(eta(2)-H-2)][BAr4F] (11). Competition experiments using the new mixed alkyl phosphine ligand PCy2(CYP) show that [RhCl(nbd){PCy2(CyP)}] undergoes dehydrogenation exclusively at the cyclopentyl group to give [Rh(eta(6)-C6H5X){PCy2(eta(2)-C5H7)}][BAr4F] (17: X = F, 18: X = H). The underlying reasons behind this preference have been probed using DFT calculations. All the complexes have been characterised by multinuclear NMR spectroscopy, and for 2a/b, 4, 6, 7, 8, 9 and 17 also by single crystal X-ray diffraction.
First author: Couzijn, Erik P. A., Fused tricyclic phosphiranes – Analysis of phosphorus chemical shieldings, CHEMISTRY-A EUROPEAN JOURNAL, 14, 1499, (2008)
Abstract: 1,2-Addition of transient W(CO)(5)-complexed phosphinidenes exo to hexamethyl Dewar benzene affords the novel 3-phosphatricyclo[3.2.0.0(2,4)]hept-6-ene complexes. The fused tricyclic phosphiranes are obtained as both the Z and the thermally less stable E isomers, the P-31 NMR chemical shifts of which differ by about 60 ppm. A computational investigation shows that the phosphorus pyramidalization and the presence of the gamma double bond are responsible for this effect. ne semiquantitative results contribute to a more systematic understanding of the structural influences on P-31 chemical shieldings. The congested double bond of the Z isomer can be epoxidized with m-chloroperbenzoic acid (MCPBA) to afford a fused tetracyclic P,O bis-adduct.
First author: Stenson, Philip A., Molecular and electronic structures of one-electron oxidized Ni(II)-(dithiosalicylidenediamine) complexes: Ni(III)-thiolate versus Ni(II)-thiyl radical states, CHEMISTRY-A EUROPEAN JOURNAL, 14, 2564, (2008)
Abstract: The dithiosalicylidenediamine Ni(II) complexes [Ni(L)] (R=tBu, R’= CH(2)C(CH(3))(2)CH(2) 1, R’= C(6)H(4) 2; R=H, R’=CH(2)C(CH(3))(2)CH(2) 3, R’= C(6)H(4) 4) have been prepared by transmetallation of the tetrahedral complexes [Zn(L)] (R=tBu, R’=CH(2)C-(CH(3))(2)CH(2) 7, R’=C(6)H(4) 8; R=H, R’= CH(2)C(CH(3))(2)CH(2) 9, R’= C(6)H(4) 10) formed by condensation of 2,4-di-R-thiosalicylaldehyde with diamines H,N-R’-NH(2) in the presence of Zn(II) salts. The diamagnetic mononuclear complexes [Ni(L)] show a distorted square-planar N(2)S(2) coordination environment and have been characterized by (1)H- and (13)C NMR and UV/Vis spectroscopies and by single-crystal X-ray crystallography. Cyclic voltammetry and coulombic measurements have established that complexes I and 2, incorporating tBu functionalities on the thiophenolate ligands, undergo reversible one-electron oxidation processes, whereas the analogous redox processes for plexes 3 and 4 are not reversible. The one-electron oxidized species, 1(+) and 2(+), can be generated quantitatively either electrochemically or chemically with 70% HClO(4). EPR and UV/Vis spectroscopic studies and supporting DFT calculations suggest that the SOMOs of 1(+) and 2(+) possess thiyl radical character, whereas those of 1(py)(2)(+) and 2(py)(2)(+) possess formal Ni(III) centers. Species 2(+) dimerizes at low temperature, and an X-ray crystallographic determination of the dimer [(2)(2)]-(ClO(4))(2).2CH(2)Cl(2) confirms that this dimerization involves the formation of a S-S bond (S center dot center dot center dot S = 2.202(5) angstrom).
First author: Gourlaouen, Christophe, Understanding lead chemistry from topological insights: The transition between holo- and hemidirected structures within the [Pb(CO)(n)](2+) model series, CHEMISTRY-A EUROPEAN JOURNAL, 14, 2730, (2008)
Abstract: In this Contribution, we focus to the currently unknown [Pb(CO)(n)](2+) model series (n=1 to 10), a set of compounds which allows us to investigate in-depth the holo- and hemidirectional character that lead complexes can exhibit. By means of DFT computations performed using either relativistic four- component formalisms coupled to all-electron basis sets for [Pb(CO)](2+), [Pb(OC)](2+) and [Pb(CO)(2)](2+), or scalar relativistic pseudopotentials for higher n values, the structure and the energetics of these species are investigated. The results are complemented by Constrained Space Orbital Variations (CSOV) and Electron Localization Function (ELF) comprehensive analyses in order to get better insights into the poorly documented chemical fundamentals of the Pb2+ cation. Whereas the discrimination between holo- and hemidirected structures is usually done according to the geometry, we here provide a quantitative indicator grounded on (P)V(Pb), the mean charge density of the valence monosynaptic V(Pb) ELFic basin associated to the metal cation. Free-enthalpy relying discussions show, moreover, that those gas-phase complexes having n = 7, 8 or 9 may be experimentally instable and should dissociate into [Pb(CO)(6)](2+) and a number of CO ligands. According to second-order differences in energy, it is anticipated that the n = 3 or 6 structures should be the most probable structures in the gas phase. Gathering all data from the present theoretical study allows us to propose some concepts that the versatile structural chemistry of Pb2+ complexes could rely on.
First author: Tonner, Ralf, Divalent carbon(0) chemistry, part 1: Parent compounds, CHEMISTRY-A EUROPEAN JOURNAL, 14, 3260, (2008)
Abstract: Quantum-chemical calculations with DFT (BP86) and ab initio methods [MP2, SCS-MP2, CCSD(T)] have been carried out for the molecules C(PH3)(2) (1), C(PMe3)(2) (2), C-(PPh3)(2) (3), C(PPh3)(CO) (4), C(CO)(2) (5), C(NHCH)2 (6), C(NHCMe)(2) (7) (Me2N)(2)C = C = C(NMe2)(2) (8), and NHC (9), where NHC = N-heterocyclic carbene and NHCMe=N-methyl-substituted NHC. The electronic structure in 1-9 was analyzed with charge- and energy-partitioning methods. The results show that the bonding situations in L2C compounds 1-8 can be interpreted in terms of donor-acceptor interactions between closed-shell ligands L and a carbon atom which has two lone-pair orbitals L -> C <- L. This holds particularly for the carbodiphosphoranes 1-3 where L=PR3, which therefore are classified as divalent carbon(0) compounds. The NBO analysis suggests that the best Lewis structures for the carbodicarbenes 6 and 7 where L is a NHC ligand have C = C = C double bonds as in the tetraaminoallene 8. However, the Lewis structures of 6-8, in which two lone-pair orbitals at the central carbon atom are enforced, have only a slightly higher residual density. Visual inspection of the frontier orbitals of the latter species reveals their pronounced lone-pair character, which suggests that even the quasi-linear tetraaminoallene 8 is a “masked” divalent carbon(0) compound. This explains the very shallow bending potential of 8. The same conclusion is drawn for phosphoranylketene 4 and for carbon suboxide (5), which according to the bonding analysis have hidden double-lone-pair character. The AIM analysis and the EDA calculations support the assignment of carbodiphosphoranes as divalent carbon(0) compounds, while NHC 9 is characterized as a divalent carbon(II) compound. The L -> C(D-1) donor-acceptor bonds are roughly twice as strong as the respective L -> BH3 bond.
First author: Tonner, Ralf, Divalent carbon(0) chemistry, part 2: Protonation and complexes with main group and transition metal lewis acids, CHEMISTRY-A EUROPEAN JOURNAL, 14, 3273, (2008)
Abstract: Quantum-chemical calculations with DFT (BP86) and ab initio methods (MP2, SCS-MP2) were carried out for protonated and diprotonated compounds N-H+ and N-(H+)(2) and for the complexes N-BH3, N-(BH3)(2), NCO2, N-(CO2)(2), N-W(CO)(5), N-Ni(CO)(3) and N-Ni(CO)(2) where N = C(PH3)(2) (1), C(PMe3)(2) (2), C(PPh3)(2) (3), C(PPh3)(CO) (4), C(CO)(2) (5), C(NHCH)(2) (6), C(NHCMe)(2) (7) (Me2N)(2)C = C = C(NMe2)(2) (8) and NHC (9) (NHCH=N-heterocyclic carbene, NHCMe=N-substituted N-heterocyclic carbene). Compounds 1-4 and 6-9 are very strong electron donors, and this is manifested in calculated protonation energies that reach values of up to 300 k cal mol(-1) for 7 and in very high bond strengths of the donor-acceptor complexes. The electronic structure of the compounds was analyzed with charge- and energy-partitioning methods. The calculations show that the experimentally known compounds 2-5 and 8 chemically behave like molecules L2C which have two L-C donor-acceptor bonds and a carbon atom with two electron lone pairs. The behavior is not directly obvious when the linear structures of carbon suboxide and tetraaminoallenes are considered. They only come to the fore on reaction with strong electron-pair acceptors. The calculations predict that single and double protonation of 5 and 8 take place at the central carbon atom, where the negative charge increases upon subsequent protonation. The hitherto experimentally unknown carbodicarbenes 6 and 7 are predicted to be even stronger Lewis bases than the carbodiphosphoranes 1-3.
First author: Petrie, Simon, Structural, magnetic coupling and oxidation state trends in models of the CaMn4 cluster in photosystem II, CHEMISTRY-A EUROPEAN JOURNAL, 14, 5482, (2008)
Abstract: Density functional theory calculations are reported on a set of isomeric structures I, II and III that share the structural formula [CaMn4C9H10N2O16](q+)center dot(H2O)(3) (q = -1, 01 1: 2 3). Species I has a skeletal structure, which has been previously identified as a close match to the ligated CaMn4 cluster in Photosystem II, as characterized in the most recent 3.0 angstrom crystal structure. Structures II and III are rearrangements of I, which largely retain that model’s bridging ligand framework, but feature metal atom positions broadly consistent with, respectively, the earlier 3.5 and 3.2 angstrom crystal structures for the Photosystem II water-oxidising complex (WOC). Our study explores the influence of the cluster charge state (and hence S state) on several important properties of the model structures; including the relative energies of the three models, their interconversion, trends in the individual Mn oxidation states, preferred hydration sites and favoured modes of magnetic coupling between the manganese atoms. We find that, for several of the explored cluster charge states, modest differences in the bridging-ligand geometry exert a powerful influence over the individual manganese oxidation states, but throughout these states the robustness of the tetrahedron formed by the Ca and three of the Mn atoms remains a significant feature and contrasts with the positional flexibility of the fourth Mn atom. Although structure I is lowest in energy for most S states, the energy differences between structures for a given S state are not large. Overall, structure II provides a better match for the EXAFS derived metal-metal distance parameters for the earlier S states (S-0 to S-2), but not for S-3 in which a significant structural change is observed experimentally. In this S state structure III provides a closer fit. The implications of these results, for the possible action of the WOC, are discussed.
First author: Zhang, Junyong, Effects of geometric isomerism and anions on the kinetics and mechanism of the stepwise formation of long-range DNA interstrand cross-links by dinuclear platinum antitumor complexes, CHEMISTRY-A EUROPEAN JOURNAL, 14, 6391, (2008)
Abstract: Reported herein is a detailed study of the kinetics and mechanism of formation of a 1,4-GG interstrand cross-link by the dinuclear platinum anticancer compound [N-15][{cis-PtCl(NH3)(2)}(2){mu-NH2(CH2)(6)NH2}](2+) (1,1/c,c (1)). The reaction of [N-15]1 with 5′-{d(ATATGTACATAT)(2)) (I) has been studied by [H-1, N-15] HSQC NMR spectroscopy in the presence of different concentrations of phosphate. In contrast with the geometric trans isomer (1,1/t,t), there was no evidence for an electrostatic preassociation of 1,1/c,c with the polyanionic DNA surface, and the pseudo-first-order rate constant for the aquation of [N-15]1 was actually slightly higher (rather than lower) than that in the absence of DNA. When phosphate is absent, the overall rate of formation of the cross-link is quite similar for the two geometric isomers, occurring slightly faster for 1,1/t,t. A major difference in the DNA binding pathways is the observation of phosphate-bound intermediates only in the case of 1,1/c,c. 15 mM phosphate causes a dramatic slowing in the overall rate of formation of DNA interstrand crosslinks due to both the slow formation and slow closure of the phosphatebound monofunctional adduct. A comparison of the molecular models of the bifunctional adducts of the two isomers shows that helical distortion is minimal and globally the structures of the 1,4 interstrand cross-links are quite similar. The effect of carrier ligand was investigated by similar studies of the ethylenediamine derivative [N-15]1-en. A pK(a) value of 5.43 was determined for the [N-15]1,1/c,c-en diaquated species. The rate of reaction of [N-15]1-en with duplex I is similar to that of 1,1/c,c and the overall conformation of the final adduct appears to be similar. The significance of these results to the development of “second-generation” polynuclear platinum clinical candidates based on the 1,1/c,c chelate (dach) series is discussed.
First author: Pierrefixe, Simon C. A. H., Hypervalent versus nonhypervalent carbon in noble-gas complexes,CHEMISTRY-A EUROPEAN JOURNAL, 14, 6901, (2008)
Abstract: Silicon in [Cl-SiH(3)-Cl] is hypervalent, whereas carbon in [Cl-CH(3)-Cl] is not. We have recently shown how this can be understood in terms of the ball-in-a-box model. according to which silicon fits perfectly into the box that is constituted by the five substituents, whereas carbon is too small and, in a sense, “drops to the bottom” of the box. But how does carbon acquire hypervalency in the isostructural and isoelectronic not) le gas (Ng)/methyl cation complexes [Ng-CH(3)-Ng](+) (Ng = He and Ne), which feature a delocalized D(3)-symmetric Structure with two equivalent C-Ng bonds? From Ng=Ar onwards, the [Ng-CH(3)-Ng](+) complex again acquired a propensity to localize one of its axial C-Ng bonds and to largely break the other one, and this propensity increases ill the order Ng = Ar < Kr < Xe < Rn. The behavior of the helium and neon complexes violates the ball-in-a-box principle. Why does this happen? The purpose of this stuck, is to answer these questions and to understand why carbon can become truly hypervalent under certain conditions. To this end, we have Carefully analyzed the structure and bonding in NgCH(3)Ng(+) and, for comparison. CH(3)Ng(+), NgHNg(+), and NgH(+). It appears that, at variance with [Cl-CH(3)-Cl](-), the carbon atom in [Ng-CH(3)-Ng](+) call no longer be considered as a ball in a box of the five substituents.
First author: Loison, Claire, Microsolvation effects on the optical properties of crystal violet, CHEMISTRY-A EUROPEAN JOURNAL, 14, 7351, (2008)
Abstract: We present a joint experimental and theoretical study of the photoabsorption and photodissociation behavior of crystal violet, that is, the tris[p-(dimethylamino)phenyl]methylcation. The photodissociation spectra of isolated and microsolvated crystal violet have been measured. A single band is observed for the bare cation. This is in good agreement with calculated vibronic absorption spectrum based on time-dependent density functional theory calculations. The interaction of crystal violet with a single water molecule shifts and broadens the photodissociation spectrum, so that is approaches the spectrum obtained in solution. theoretical calculations of the structure of the complex suggest that the shift in the absorption spectrum originates from a water molecule bonding with the central carbon atom of crystal violet.
First author: Gonzalez, Emmanuel, Models of the ox1 State of Methyleoenzyme M Reductase: Where are the Electrons?,CHEMISTRY-A EUROPEAN JOURNAL, 14, 9981, (2008)
Abstract: The nature of the nickel center in the ox I form of methylcoenzyme M reductase (MCRoxl), the enzyme that catalyzes the last step of biological methanogenesis, has long been controversial. A recent pulse electron paramagnetic resonance (EPR) study suggested a Ni-III-thiolate, or equivalently it high-spin Ni-II thiyl radical, description. The MCRoxl hyper-fine parameters are best interpreted in terms of a Ni d(x2-y2) SOMO, although a pure d(x2-y2) SOMO does not explain the fact that about 7% of the spin-density resides on the sulfur. The key goals of this DFT (PW91) study were to judge whether the Ni-III-thiolate description is chemically sensible and, if so, to provide a detailed molecular orbital (MO) description of MCRoxl. An Ni-III-thio-late description was indeed found to be reasonable and was obtained as the ground state for symmetrized (C-s) oxaporphyrin-, pyriporphyrin-, and isoporphyrin-based model complexes, as well as for a more realistic, biomimetic model. The model calculations yielded a number of insights, key among which are the following: 1) Although the SOMO topology may be viewed as d(x2-y2)-like, this MO also has a substantial amount of metal d(z2) character, allowing it to overlap with a thiolate sigma lone pair, which would otherwise be orthogonal. In one case (isoporphyrin), we were able to exploit the symmetry of the molecule to independently optimize the (d(x2-y2))(1) and (d(z2))(1) Ni-III states, which turned out to be very close in energy. 3)The near-degeneracy of these two states provides an elegant explanation for the tendency of these two orbitals to hybridize. Admixture of Substantial d(z2) character into the d(x2-y2)-type SOMO of our most realistic model of MCRoxl results in a small but distinct spin population of about 0.04 on the sulfur, apparently nicely confirming the conclusions derived from the pulse EPR study. Other pure functionals also confirm this picture, although the hybrid functional B3LYP yields a spin-density profile that is clearly at odds with the EPR study.
First author: Taehtinen, Petri, Computational NMR Spectroscopy of Organoarsenicals and the Natural Polyarsenic Compound Arsenicin A, CHEMISTRY-A EUROPEAN JOURNAL, 14, 10445, (2008)
Abstract: The (1)H and (13)C NMR chemical shifts and Coupling constants of a series of organoarsenic compounds were calculated with DFT methods and compared with available experimental Spectra. We show that non-relativistic methods Successfully model the NMR spectra of these Molecules; relativistic spin-orbit effects are small but appreciable for (13)C shifts, and their inclusion is beneficial. Application of the same methods of calculation to the intriguing natural polyarsenic compound arsenicin A allowed several viable alternative structures to be ruled out and thereby confirmed the previously suggested adamantane-like structure of arsenicin A. These results not only reinforce the known predictive power of DFT NMR calculations, but also open the way for the investigation of other naturally occurring molecules with unusual structures outside the scope of empirical methods.
First author: Hahn, F. Ekkehardt, pi-Bonding in Complexes of Benzannulated Biscarbenes, -germylenes, and -stannylenes: An Experimental and Theoretical Study, CHEMISTRY-A EUROPEAN JOURNAL, 14, 10716, (2008)
Abstract: Benzannulated bisstannylenes, exhibiting a CH(2)C(CH(3))(2)CH(2) linking unit and CH(2)tBu (1) or CH(2)CH(2)CH(2)NMe(2) (2) N-substituents, and their molybdenum tetacarbonyl complexes 3 and 4 have been prepared. The complexes 3 and 4 exhibit remarkably short Mo-E bond lengths compared to the related biscarbene and bisgermylene complexes. The experimentally determined bonding parameters of the molybdenum bisstannylene complexes are discussed based on DFT calculations.
First author: Bento, A. Patricia, Frontside versus Backside S(N)2 Substitution at Group 14 Atoms: Origin of Reaction Barriers and Reasons for Their Absence, CHEMISTRY-AN ASIAN JOURNAL, 3, 1783, (2008)
Abstract: We have theoretically studied the gas-phase nucleophilic substitution at group-14 atoms (S(N)2@A) in the model reactions of Cl- + AH(3)Cl (A = C, Si, Ge, Sri, and Pb) using relativistic density functional theory (DFT) at ZORA-OLYP/TZ2P. Firstly, we wish to explore and understand how the reaction coordinate zeta, and potential energy surfaces (PES) along zeta, vary as the center of nucleophilic attack changes from carbon to the heavier group-14 atoms. Secondly, a comparison between the more common backside reaction (S(N)2-b) and the frontside pathway (S(N)2-f) is performed. The S(N)2-b reaction is found to have a central barrier for A = C, but none for the other group-14 atoms, A = Si-Pb. Relativistic effects destabilize reactant complexes and transition species by up to 10 kcal mol(-1) (for S(N)2-f@Pb), but they do not change relative heights of barriers. We also address the nature of the transformation in the frontside S(N)2-f reactions in terms of turnstile rotation versus Berry-pseudorotation mechanism.
First author: Yang, Jenny Y., Hangman Salen Platforms Containing Dibenzofuran Scaffolds, CHEMSUSCHEM, 1, 941, (2008)
Abstract: The synthesis of salen ligands bearing two rigid dibenzofuran spacers functionalized with carboxylic acid and benzoic acid groups completes a series of “Hangman” ligands with the acid functionalities differentially extended across the molecular cleft. Stopped-flow studies show that a high-valent metal oxo intermediate is produced at Hangman platforms when H2O2 is employed as a primary oxidant. The activity of this oxo species in promoting the disproportionation of hydrogen peroxide and olefin epoxidations is discussed in the context of the distance between the acid group and the metal center. The chemistry of the Hangman oxo complexes described here provides a roadmap for water-splitting chemistry.
First author: Xiao Hai, Benchmark calculations on the atomization enthalpy, geometry and vibrational frequencies of UF6 with relativistic DFT methods, CHINESE JOURNAL OF STRUCTURAL CHEMISTRY, 27, 967, (2008)
Abstract: Benchmark calculations on the molar atomization enthalpy, geometry, and vibrational frequencies of uranium hexafluoride (UF6) have been performed by using relativistic density functional theory (DFT) with various levels of relativistic effects, different types of basis sets, and exchange-correlation functionals. Scalar relativistic effects are shown to be critical for the structural properties. The spin-orbit coupling effects are important for the calculated energies, but are much less important for other calculated ground-state properties of closed-shell UF6. We conclude through systematic investigations that ZORA- and RECP-based relativistic DFT methods are both appropriate for incorporating relativistic effects. Comparisons of different types of basis sets (Slater, Gaussian, and plane-wave types) and various levels of theoretical approximation of the exchange-correlation functionals were also made.
First author: Zheng, Ling-Ling, Engineering delocalizing pi electronic [Cu-3(II)(mu(3)-OH)(mu-pz)(3)](2+) species into organometallic frameworks by Ag-pi coordination, CRYSTENGCOMM, 10, 1467, (2008)
Abstract: Reactions of [Cu-3(II)(mu(3)-OH)(mu-pz)(3)](2+)-containing precursor [{Cu-3(mu(3)-OH)(mu-pz)(3)(Hpz)(3)}(2) (mu(6)-SO4)](NO3)(2)center dot MeCN center dot MeOH center dot 1.5H(2)O (1) with silver salts under mild conditions generate two novel Cu(II)-Ag(I) organometallic solids involving the 4-position C atom of pz(-) ligand bonded to the Ag centers, [Ag(Hpz)(2)](2)[{Ag-2(Hpz)(2)(NO3)(2)}{Cu-6(OH)(2)(pz)(6)(Hpz)(6)(SO4)}( 2)](NO3)(6)center dot 4H(2)O (2) and [{Ag(H2O)(2)}{Cu-3(OH)(pz)(3)(Hpz)(3)(H2O)(ClO4)(3)}](n) (3). 1 has a 1D coordination chain structure constructed with hexanuclear cluster units and mu-nitrate bridges. A pair of [Cu-3(II)(mu(3)-OH)(mu-pz)(3)(Hpz)(3)](2+) units bridged by one mu(3)-SO42- group constitutes the hexanuclear cluster. 2 contains 0D organometallic Ag2Cu12 cluster cations formed by a pair of [{Cu-3(OH)(pz)(3)(Hpz)(3)}(2)(mu(4)-SO4)](2+) cluster units and one neutral Ag-2(Hpz)(2)(NO3)(2) unit via Ag-pi(pz(-)) and Ag-O(NO3-) coordination, [Ag(Hpz)(2)](+) cations and nitrate anions as well as lattice water molecules. 3 contains 1D neutral organometallic chains constructed with anionic [Cu-3(OH)(pz)(3)(Hpz)(3)(H2O)(ClO4)(3)](-) cluster units and cationic [Ag(H2O)(2)](+) units via Ag-pi(pz(-)) coordination. MO calculations based on the {[Cu-3(OH)(pz)(3)(Hpz)(3)]-[Ag(H2O)(2)]-[Cu-3(OH)(pz)(3)(Hpz)(3)]}(5+) cation model with the related X-ray geometry were carried out. The Mayer bond orders of the Ag-C are calculated to be 0.249 and 0.275, showing that the Ag(I)-eta(1)-C orbital interactions are significantly attractive. A Bader analysis of the electron density further shows the presence of a (3,-1) bond-critical point linking the Ag(I) and C atoms and 1.366/1.378 angstrom away from Ag(I), which further confirms the existence of Ag(I)-C bonding between the fragments. The magnetic properties of 1-3 were also studied.
First author: Hnyk, Drahomir, The gas-phase structure of 1-selena-closo-dodecaborane(11), 1-SeB11H11, determined by the concerted use of electron diffraction and computational methods, DALTON TRANSACTIONS, 10, 96, (2008)
Abstract: The molecular structure of 1-selena-closo-dodecaborane(11), 1-SeB11H11, has been determined by the concerted use of quantum chemical calculations and gas-phase electron diffraction. The structure has C-5v symmetry and is distorted from a regular icosahedron mainly through the expansion of the pentagon of boron atoms adjacent to selenium, with r(a3,1)(B-B) = 192.2(2) pm. The Se-B bond length is extremely well determined [r(a3,1)(Se-B) = 212.9(2) pm] and this is re. ected by a pronounced peak in the radial-distribution curve. The accuracy of the experimental structure, as well as that calculated at the MP2/ 962(d) level, has been gauged by comparison of the B-11 chemical shifts (calculated at two different gauge-including atomic orbitals (GIAO) levels) with experimental NMR values. The inclusion of electron correlation in the magnetic property calculations (GIAO-MP2) gave superior results to those carried out using GIAO-Hartree-Fock.
First author: Christian, Gemma, Investigating CN- cleavage by three-coordinate M[N(R)Ar](3) complexes, DALTON TRANSACTIONS, 10, 338, (2008)
Abstract: Three-coordinate Mo[N(Bu-t)Ar](3) binds cyanide to form the intermediate [Ar(Bu-t)N](3)Mo-CN-Mo[N(Bu-t)Ar](3) but, unlike its N-2 analogue which spontaneously cleaves dinitrogen, the C-N bond remains intact. DFT calculations on the model [NH2](3)Mo/CN- system show that while the overall reaction is significantly exothermic, the final cleavage step is endothermic by at least 90 kJ mol(-1), accounting for why C-N bond cleavage is not observed experimentally. The situation is improved for the [H2N](3)W/CN- system where the intermediate and products are closer in energy but not enough for CN- cleavage to be facile at room temperature. Additional calculations were undertaken on the mixed-metal [H2N](3)Re+/CN-/W[NH2](3) and [H2N](3)Re+/CN-/Ta[NH2](3)(-) systems in which the metals ions were chosen to maximise the stability of the products on the basis of an earlier bond energy study. Although the reaction energetics for the [H2N](3)Re+/CN-/W[NH2](3) system are more favourable than those for the [H2N](3)W/CN- system, the final C-N cleavage step is still endothermic by 32 kJ mol(-1) when symmetry constraints are relaxed. The resistance of these systems to C-N cleavage was examined by a bond decomposition analysis of [H2N]M-L-1 L-2-M[NH2](3) intermediates for L-1 L-2 = N-2, CO and CN- which showed that backbonding from the metal into the L-1 = L-2 pi* orbitals is significantly less for CN- than for N-2 or CO due to the negative charge on CN- which results in a large energy gap between the metal d(pi) and the pi* orbitals of CN-. This, combined with the very strong M-CN- sigma interaction which stabilises the CN- intermediate, makes C-N bond cleavage in these systems unfavourable even though the C N triple bond is not as strong as the bond in N-2 or CO.
First author: Cavigliasso, German, A computational study of the electronic structure, bonding, and spectral properties of tripodal tetraamine Co(III) carbonate complexes, DALTON TRANSACTIONS, 10, 2433, (2008)
Abstract: Density functional calculations have been carried out on the experimentally characterized Co( III) [Co(N(4))(O(2)CO)](+) carbonate complexes containing a tripodal tetraamine ligand (N(4) = tpa, Metpa, Me(2)tpa, Me(3)tpa, pmea, pmap, tepa) and also the model [Co(NH(3))(4)(O(2)CO)](+) system. Calculations on the model species, performed using both gas-phase and solvent-corrected procedures, have revealed that the inclusion of a condensed-phase environment is necessary to obtain generally satisfactory results for the structural and bonding properties in these systems. Using the solvent-corrected approach, the observed trends in structural parameters for the metal-ligand bonds, (59)Co chemical shifts, and changes in visible absorption wavelengths have been satisfactorily reproduced for the [ Co( N4)( O2CO)]+ complexes. A time-dependent density functional analysis of the electronic excitations indicates that the overall composition and character of the relevant (d-d) transitions remain similar throughout the series, indicating that the changes in the Co-N interactions, associated with the structural variations occurring as the N-donor ligand identity and size change, appear most likely responsible for the particular spectroscopic features displayed by these species. These observations are further supported by molecular orbital and energy decomposition analyses. The results from the present calculations confirm recent findings that the inclusion of a treatment for solvent effects plays a critical role in the computational modelling of coordination complexes involving mixed ( anionic and neutral) ligands.
First author: Orto, Peter J., Cluster carbonyls of the [Re(6)(mu(3)-Se)(8)](2+) core: synthesis, structural characterization, and computational analysis, DALTON TRANSACTIONS, 10, 4247, (2008)
Abstract: The reactions of the previously reported cluster complexes [Re(6)(mu(3)-Se)(8)(PEt(3))(5)I] I, trans-[Re(6)(mu(3)-Se)(8)(PEt(3))(4)I(2)], and cis-[Re(6)(mu(3)-Se)(8)(PEt(3))(4)I(2)] with the [Re(6)(mu(3)-Se)(8)](2+) core with CO in the presence of AgSbF(6) afforded the corresponding cluster carbonyls [Re(6)(mu(3)-Se)(8)(PEt(3))(5)(CO)][SbF(6)](2) (1), trans-[Re(6)(mu(3)-Se)(8)(PEt(3))(4)(CO)(2)][SbF(6)](2) (2), and cis-[Re(6)(mu(3)-Se)(8)(PEt(3))(4)(CO)(2)][SbF(6)](2) (3). Infrared spectroscopy indicated weakening of the bond in CO, suggesting the existence of backbonding between the cluster core and the CO ligand(s). Electrochemical studies focusing on the reversible, one-electron oxidation of the cluster core revealed a large increase in the oxidation potential upon going from the acetonitrile derivatives to their carbonyl analogs, consistent with the depleted electron density of the cluster core upon CO ligation. Disparities between the IR spectra and oxidation potential between 2 and 3 indicate that electronic differences exist between sites trans and cis to the location of a ligand of interest. The active role played by the Se atoms in influencing the cluster-to-CO bonding interactions is suggested through this result and density functional (DF) computational analysis. The computations indicate that molecular orbitals near the HOMO account for backbonding interactions with a high percentage of participation of Se orbitals.
First author: Clough, Christopher R., 6-coordinate tungsten(VI) tris-n-isopropylanilide complexes: products of terminal oxo and nitrido transformations effected by main group electrophiles, DALTON TRANSACTIONS, 10, 4458, (2008)
Abstract: The nitridotungsten(VI) complex NW(N[i-Pr]Ar)3 (1-N, Ar = 3,5-Me(2)C(6)H(3)) reacts with ( CF3C(O))(2)O followed by ClSiMe(3) to give the isolable tri. uoroacetylimido-chloride complex 1-(NC(O)CF(3)) Cl, with oxalyl chloride to give cyanate-dichloride 1-( OCN)(Cl)(2), and with PCl(5) to give trichlorophosphinimide-dichloride 1-(NPCl3)(Cl)(2). The oxo-chloride complex 1-(O)Cl, obtained from 1-N upon treatment with pivaloyl chloride, reacts with PCl(5) to give trichloride 1-(Cl)(3). Synthetic and structural details are reported for the new tungsten trisanilide derivatives.
First author: Albrett, Amelia M., DFT survey of monoboron and diboron corroles: regio- and stereochemical preferences for a constrained, low- symmetry macrocycle, DALTON TRANSACTIONS, 10, 4464, (2008)
Abstract: The structures of a number of mono- and diboron corrole complexes have been optimized using DFT methods in order to establish regio- and stereochemical preferences for bonding of one or two boron atoms to the corrole macrocycle. The formulations of the complexes were suggested either from preliminary experimental results ( to be reported elsewhere) or by analogy with related diboron porphyrin compounds. The computational results suggest for the monoboron corroles BF2(H(2)corrole) and BPhH(H(2)corrole) that the regioisomer in which the boron is bound to a dipyrromethene site adjacent to the bipyrrole is preferred over the other possible regioisomers in which boron coordinates either in the bipyrrole or in the dipyrromethene site opposite the bipyrrole. In the N-substituted corrole complexes there are only two possiblities and, for each complex, the regioisomer with boron in the dipyrromethene site adjacent to the bipyrrole is lower in energy. For all four monoboron complexes the stereoisomers in which boron and both its substituents are displaced out of the mean N-4 plane are more stable than the boron in-plane stereoisomers. These regio- and stereochemical preferences are rationalised by an analysis of the deformations to the corrole macrocycle and the geometry at the boron atoms. The lowest energy structures in all cases correspond to the least strained con. gurations. In addition, all four complexes show significant BF center dot center dot center dot HN hydrogen bonding and BH center dot center dot center dot HN dihydrogen bonding interactions, which are maximised in the lowest energy con. gurations for each structure, indicating that these are important additional stabilising interactions. Three different regioisomers, each with cisoid or transoid stereochemistry were optimised for the diboron complex PhBOB( corrole) which contains a bridging BOB group. The dipyrromethene/ dipyrromethene isomer is more stable than either of the dipyrromethene/ bipyrrole isomers and cisoid stereochemistry is preferred over transoid. This contrasts with porphyrin complexes containing BOB groups for which both stereochemical possibilities are observed, and reflects the contracted size of the corrole macrocycle. Three further diboron corroles were investigated, the diboranyl cation [B-2(corrole)](+) and its one- and two-electron reduced derivatives B-2(corrole) and [B-2(corrole)](-). These calculations were undertaken to determine whether the site of reduction of [B-2(corrole)](+) is likely to be the diboron moiety or the macrocycle. The B-B bond lengths do not shorten upon reduction and an analysis of the molecular orbitals of each species indicates that reduction will be most likely to occur at the macrocycle, offering a potential route to an example of the two-electron reduced corrole ligand, an analogue of the 20-electron isophlorin ligand observed in the corresponding reduced porphyrin complex B-2( porphine).
First author: Lemonnier, Jean-Francois, Tuning the thermodynamic stability of oxothiomolybdenum wheels: crystal structures, studies in solution and DFT calculations, DALTON TRANSACTIONS, 10, 4565, (2008)
Abstract: The complexes [Mo12O12S12(OH)(12)(Muco)](2-) (Muco(2-) = muconate, C6H4O42-) and [Mo12O12S12(OH)(12)(TMT)](2-) (TMT2- = tetramethylterephthalate, C12H12O42-) have been obtained from the condensation of the [Mo2O2S2](2+) building block in the presence of Muco(2-) and TMT2-, respectively. Both compounds were structurally characterized, revealing host-guest architectures with one or two encapsulated water molecules. H-1 NMR spectra in DMSO and D2O showed that both complexes had an average symmetry higher than that in the solid state, due to changes in the distribution of encapsulated water molecules. The relative stabilities in water of the seven complexes encapsulating various di- or tricarboxylate guests, either rigid or non-rigid, have been determined. The stability scale obtained for the dianionic complexes is interpreted in relation with the rigidity or flexibility of the guests. A DFT study demonstrates that additional stabilization arises from the presence of inner hydrogen bonds involving 1, 2 or 3 water molecules, which even permit the extension of the H-bonds network to the first solvation sphere of the anion. DFT calculations were carried out on all investigated complexes as isolated or solvated anions and provide the sequence of the bond energies between the host and the guests, which is compared to the experimental data.
First author: McClintock, Lisa F., The donor ability of the chelated carbonate ligand: protonation and metallation of [(L)Co(O(2)CO)](+) complexes in aqueous solution, DALTON TRANSACTIONS, 10, 4984, (2008)
Abstract: The syntheses and X-ray structures of [Co(Me-tpa) O(2)COZnCl(3)], [Co(pmea)O(2)COZnCl(3)]center dot H(2)O [Co(trpyn)O(2)COZn(OH(2))(4)OCO(2)Co(trpyn)](ZnCl(4))(2)center dot H(2)O, [Co(trpyn)(O(2)COH)]ZnCl(4)center dot 3H(2)O and [Co(trpyn)(O(2)CO)]ClO(4) are reported (Me-tpa = [(6-methyl-2-pyridyl)methyl]bis(2-pyridylmethyl)amine, pmea = bis(2-pyridylmethyl)-2-(2-pyridylethyl)amine, trpyn = tris(2-(1-pyrazolyl) ethyl) amine). The chelated bicarbonate complex [Co(trpyn)(O(2)COH)] ZnCl(4)center dot 3H(2)O is isolated as a crystalline solid from an acidic solution of the parent carbonate [Co(trpyn)(O(2)CO)]ClO(4), and X-ray structural analysis shows that lengthening of the C=O(exo) bond and shortening of the C-O(endo) bond accompanies protonation. The bimetallic complex [Co(Me-tpa) O(2)COZnCl(3)] results from the unexpected coordination of ZnCl(3)(-) to the exo O atom of a chelated carbonate ligand. This complex is obtained from both acidic and neutral solutions in which [Zn(2+)] = 1.0 M, while the structurally similar complex [Co(pmea)O(2)COZnCl(3)]center dot H(2)O is isolated from an analogous neutral solution. The trimetallic complex [Co(trpyn)O(2)COZn(OH(2)) (4)OCO(2)Co(trpyn)]( ZnCl(4))(2)center dot H(2)O crystallises on prolonged standing of [Co(trpyn)(O(2)CO)]ClO(4) in a neutral solution having [Zn(2+)] = 1.0 M. The Zn-O bond lengths in all three complexes are indicative of bonds of significant strength. DFT calculations show that the nature of the bonding interaction between the Co(III) ion and the endo O atoms of the carbonate ligand remain essentially unaffected by coordination of Zn(2+) to the exo O atom. They also show that such coordination of Zn(2+) decreases the C-O(exo) bond order.
First author: Romo, Susanna, Influence of polyoxometalate ligands on the nature of high-valent transition metal nitrido species. A theoretical analysis of experimentally known and unprecedented compounds, DALTON TRANSACTIONS, 10, 5166, (2008)
Abstract: The electronic structure of group 6-8 transition metal (TM) nitrido derivatives [PW11O39{(TMN)-N-VI}](4-) is studied computationally and the potential reactivity of the polyoxoanions is discussed. The observed electrophilic reactivity for the Ru-VI nitrido derivative is rationalized from frontier molecular orbital analysis. When we move to the left or down in the periodic table (TM = Os, Tc, Re, Mo andW) the electrophilic character of the polyoxometalate decreases or the cluster should be better regarded as a nucleophile. The DFT analysis of the redox properties suggests that the still unknown high-valent (MnN)-N-VI and (FeN)-N-VI units could be stabilized by the porphyrin-like ligand [PW11O39](7-) and their electronic structure indicates that these anions should have a high potential reactivity towards nucleophiles.
First author: Maity, Amarendra N., A tetranuclear organorhenium(I) complex of the 2,3,5,6-tetrafluoro-7,7,8,8-tetracyano-p-quinodimethane radical anion, TCNQF4(center dot-), DALTON TRANSACTIONS, 10, 5749, (2008)
Abstract: The radical complex {(mu(4)-TCNQF(4))[Re(CO)(3)(bpy)](4)}(PF(6))(3), as prepared and isolated from the reaction between TCNQF4 and [Re(CO)(3)(bpy)(MeOH)](PF(6)), was studied electrochemically and by IR vibrational spectroscopy, UV-Vis-NIR absorption spectroscopy, and by EPR at 9.5, 190 and 285 GHz. The isotropic g factor of 2.0058, the detectable g anisotropy, and the 185,187Re EPR hyperfine coupling of 0.95 mT for four equivalent metal nuclei support predominant, but not exclusive, spin localisation at the bridging ligand. Nitrile and metal carbonyl stretching frequencies as well as the typically structured near infrared absorption band lend further support to (TCNQF4(center dot-))(Re(I))(4) as the most appropriate oxidation state formulation. In comparison to the non-radical complex {(m4-TCNQ)[Re(CO)(3)(bpy)](4)}(PF(6))(4) an X-ray structure analysis of {(mu(4)-TCNQF(4))[Re(CO)(3)(bpy)](4)}(PF(6))(3) shows a marginally more twisted (ReNCCCNRe)(C(6)X(4))(ReNCCCNRe) configuration and a different up/down arrangement of the [Re(CO)(3)(bpy)](+) groups. This first isolation, electrochemical, structural and spectroscopic characterisation of a discrete tetranuclear radical complex of a TCNQ-type ligand suggests a link between the stability of such materials and the rather small structural changes on ligand-based electron transfer.
First author: Laidlaw, William Michael, Solvent dependence of the g-anisotropy in the ESR of cyanide-bridged mixed-valence complexes, DALTON TRANSACTIONS, 10, 6257, (2008)
Abstract: The low temperature (similar to 5 K) X-band ESR spectra are reported of the cyanide-bridged mixed-valence complexes [(OC)(5)Cr(mu-CN)M(NH3)(5)]X-2 (M = Ru, Os; X = PF6-) in frozen matrices formed from nitromethane, acetonitrile and dimethylformamide with toluene. The anisotropy (g(parallel to) – g(perpendicular to)) is greater for the ruthenium than for the osmium complex. It is positive in all cases and is strongly dependent on the hydrogen-bonding interaction between the solvent matrix and the metal-ammine fragment, decreasing in the order nitromethane > acetonitrile > dimethylformamide. The axial ligand field parameter, Delta, is quite insensitive to the ammine metal (M) and is mainly determined by the solvent matrix. Density functional calculations, together with a simplified MO model, show that: (a) The value of Delta is dominated by the interaction between the filled cyanide pi-orbitals and the ammine-metal d(xz,yz) orbitals, (b) Delta decreases with increasing solvent donicity because the resulting positive shift of the d-orbital energies reduces this interaction, (c) the insensitivity of Delta to the ammine-metal arises because an increase in the energy mismatch between the cyanide pi-orbitals and the d-orbitals in osmium compound is offset by an increase in the 5d resonance integrals relative to those in the 4d shell. Semi-quantitative values are obtained for the pi and pi* resonance integrals. We point out that g(parallel to) determines that portion of the ammine-metal spin population that interacts with the cyanide bridge, and should therefore be correlated with the degree of metal-metal charge transfer in low-spin d(6)-d(5) intervalence compounds. X-band ESR spectra of the polycrystalline powders (M = Ru, Os; X = CF3SO3-) are rhombic with similar axial and rhombic ligand field parameters. The rhombicity is interpreted as resulting from asymmetric cation-anion hydrogen-bonding that is apparent in the crystal structures of these isomorphous compounds.
First author: Gabuda, S. P., Zero Field NMR of BiFeO3, FERROELECTRICS, 368, 369, (2008)
Abstract: The zero-field 209Bi NMR of bismuth ferrite, BiFeO3 is studied at 4.2 K. The complicated multicomponent spectrum is related to a combination of the Zeeman interaction of 209Bi nuclei with the local magnetic field, and of the quadrupolar coupling with spatially modulated electric field gradients (EFG) in the antiferromagnetic/ferroelectric phase of BiFeO3. The sinusoidal-wave modulation of the EFG is characterized by the variation of the 209Bi quadrupole interaction from 300 to 350 MHz. The microscopic mechanism of coupling between the ferroelectric and magnetic order parameters is studied using the density functional theory (DFT) calculations.
First author: Poleshchuk, O. K., Quadrupole coupling constants and isomeric Mossbauer shifts for halogen-containing gold, platinum, niobium, tantalum and antimony compounds, HYPERFINE INTERACTIONS, 181, 27, (2008)
Abstract: We have analyzed by means of Density functional theory calculations the nuclear quadrupole coupling constants of a range of gold, antimony, platinum, niobium and tantalum compounds. The geometrical parameters and halogen nuclear quadrupole coupling constants obtained by these calculations substantially corresponded to the data of microwave and nuclear quadrupole resonance spectroscopy. An analysis of the quality of the calculations that employ pseudo-potentials and all-electron basis sets for the halogen compounds was carried out. The zero order regular approximation (ZORA) method is shown to be a viable alternative for the calculation of halogen coupling constants in molecules. In addition, the ZORA model, in contrast to the pseudo-potential model, leads to realistic values of all metal nuclear quadrupole coupling constants. From Klopman’s approach, it follows that the relationship between the electrostatic bonding and covalent depends on the nature of the central atom. The results on Mossbauer chemical shifts are also in a good agreement with the coordination number of the central atom.
First author: Grozema, Ferdinand C., Mechanism of charge transport in self-organizing organic materials,INTERNATIONAL REVIEWS IN PHYSICAL CHEMISTRY, 27, 87, (2008)
Abstract: Currently there is great interest in the use of organic materials as the active component in opto-electronic devices such as field-effect transistors, light-emitting diodes, solar cells and in nanoscale molecular electronics. Device performance is to a large extent determined by the mobility of charge carriers, which strongly depends on material morphology. Therefore, a fundamental understanding of the relation between the mechanism of charge transport and chemical composition and supramolecular organization of the active organic material is essential for improvement of device performance. Self-assembling materials are of specific interest, since they have the potential to form well defined structures in which molecular ordering facilitates efficient charge transport. This review gives an overview of theoretical models that can be used to describe the mobility of charge carriers, including band theory for structurally ordered materials, tight-binding models for weakly disordered systems and hopping models for localized charges in strongly disordered materials. It is discussed how the charge transport parameters needed in these models; i.e. charge transfer integrals, site energies and reorganization energies, can be obtained from quantum chemical calculations. Illustrative examples of application of the theoretical methods to charge transport in self-assembling materials are discussed: columns of discotic molecules, stacks of oligo(phenylene-vinylene) molecules and strands of DNA base pairs. It is argued that the mobility of charge carriers along stacks of triphenylene and oligo(phenylene-vinylene) molecules can be significantly enhanced by improvement of molecular organization. According to calculations, the mobility of charge carriers along DNA strands is strongly limited by the large charge induced structural reorganization of the nucleobases and the surrounding water.
First author: Liao, Meng-Sheng, Electronic structure, absorption spectra, and hyperpolarisabilities of some novel push-pull zinc porphyrins. A DFT/TDDFT study, MOLECULAR PHYSICS, 106, 147, (2008)
Abstract: DFT/TDDFT calculations have been performed on some novel push-pull zinc porphyrins (denoted ZnPor 1, ZnPor 2, and ZnPor 3). This theoretical work aims to investigate the electronic structure, absorption spectra, and hyperpolarisabilities of these molecules. To examine the effects of the peripheral substituents on the molecular properties, zinc porphine (ZnP) and zinc tetraphenylporphine (ZnTPP) were also included in the study. The orbital energy level patterns of the substituted zinc porphyrins are indeed rather different from those of ZnP and ZnTPP. The peripheral substitution breaks the molecular D-4h symmetry of the porphyrin, thereby leading to the splitting of the absorption Q band. On the other hand, the B band in the spectra may not arise only from a single excited state; instead, it could be made up of several states that are close in energy. The calculated hyperpolarisabilities (beta(vec)) increase strongly from ZnPor 1 to ZnPor 2 to ZnPor3. The latter two molecules were predicted to have a large beta(vec) value and thus may have potential application in the development of nonlinear optical (NLO) materials.
First author: Zhang, Yunguang, A relativistic density functional study of gaseous uranium tetrahalides, MOLECULAR PHYSICS, 106, 1907, (2008)
Abstract: The molecular structures and vibrational frequencies of gaseous UX4 (X = F, Cl, Br and I) molecules have been investigated using generalized gradient approximation (GGA) functions (BP, BLYP, PBE and RPBE) with triplezeta polarized (TZP) basis set. Scalar relativistic effects are introduced via the zeroth-order regular approximation (ZORA) approach to the Dirac equation in the present study. Of the methods examined here the RPBE has the best performance in terms of the errors compared with experiment and reference for the vibrational frequencies. The bond dissociation energies (BDE) for U-X bonds in the UX4 were obtained using the RPBE method, and are in good agreement with experimental values. In addition, satisfactory calculated entropies of UX4 have also been obtained at temperatures ranging from 600 to 1200K in 50 steps using the same method.
First author: Costa, Paulo Jorge, Photoinduced bond cleavage in CH3ReO3: excited state dynamics, NEW JOURNAL OF CHEMISTRY, 32, 1904, (2008)
Abstract: The rhenium-methyl bond cleavage in CH3ReO3 has been investigated by means of quantum chemical calculations of the one-D potential energy surfaces (PES) associated to the low-lying singlet and triplet excited states of the molecule. The quantum dynamics is studied by wave packet propagations on the b (1)A(1) absorbing state coupled non-adiabatically to the low-lying a E-1 state. The spin-orbit states and spin-orbit couplings are evaluated according to the zeroth-order regular approximation (ZORA). The spin-orbit coupling between the a E-1 state and the a (3)A(1) dissociative state controls the radical formation (CH3)-C-center dot + (ReO3)-Re-center dot, which occurs in 400 fs.
First author: Siboulet, Bertrand, What can quantum chemistry tell us about Pa(v) hydration and hydrolysis?, NEW JOURNAL OF CHEMISTRY, 32, 2080, (2008)
Abstract: Published liquid – liquid extraction studies of Pa(v) were interpreted with aqueous mono-, di- and trications. B3LYP DFT is applied here to such cations surrounded by two explicit hydration layers: Linear or tetrahedral geometries are found for the Pa(v) aquo ions. PaO2+ is similar to the other AnO(2)(+) cations, but has strong apical bonds, resulting from the highly negative O-yl charge, which decreases along the An(v) series. This explains the instability of PaO2+ in water, and the differences with the heavier An(v). PaO2+ diprotonates to give Pa(OH)(2)(3+) and can further dihydrolyse to give Td-Pa(OH)4+, which might very well be the most stable Pa(v) monocation. PaOOH2+ is confirmed to be the Pa(v) aqueous dication invoked in the literature for pH <= 1.4 +/- 0.7. PaO3+ is confirmed in sulfate solution, with a bond length close to 180 pm. Pa(OH)(2)(3+) cannot be excluded in other conditions. The strong influence of the solvent was not fully taken into account in most previous theoretical studies that focused only on bare or partially solvated PaO2+. Toraishi et al. have studied hydrated Pa(v) and our work confirms this study and its qualitative interpretation. The new tetrahedral Pa(OH)(4)(+) geometry that is shown here to be important opens the field to further quantum chemical studies of Pa(v) and other f-elements. As a test for the two-shell model approach for Pa(v), fluoride coordination to Pa(v) is studied and compared with published EXAFS data: an excellent fit is obtained with the well-established species PaF72-, but most other stoichiometries tested are precluded.
First author: De Groot, Matheus T., Redox transitions of chromium, manganese, iron, cobalt and nickel protoporphyrins in aqueous solution, PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 10, 1023, (2008)
Abstract: The electrochemical redox behavior of immobilized chromium, manganese, iron, cobalt, and nickel protoporphyrins IX has been investigated over the pH 0-14 range. In the investigated potential domain the metalloporphyrins were observed in four different oxidation states (M-I, M-II, M-III and M-IV). The metalloporphyrins differ in the potentials at which the redox transitions occur, but the observed pH dependence of the redox transitions was similar for the different metalloporphyrins and revealed that the M-II/M-III and M-III/M-IV transitions were accompanied by a hydroxide transfer at high pH. The fact that the metalloporphyrins are immobilized on graphite does not seem to have a large influence on their redox behavior, as can be deduced from the comparable behavior of immobilized metalloporphyrins on gold and of watersoluble metalloporphyrins in solution. We also performed density functional theory (DFT) calculations on the metalloporphyrins in different oxidation states. The geometries and spin states predicted by these calculations agree well with experimentally determined values; the calculations were also able to predict the electrochemical potentials of the [M-II]/[M-III-OH] redox transition to within about 300 mV.
First author: Kwiatkowski, J. J., Simulating charge transport in tris(8-hydroxyquinoline) aluminium (Alq3), PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 10, 1852, (2008)
Abstract: We present a model of charge transport in organic solids which explicitly considers the packing and electronic structure of individual molecules. We simulate the time-of-flight mobility measurement in crystalline and disordered films of tris(8-hydroxyquinoline) aluminium (Alq3). The morphology of disordered Alq3 is modelled on a molecular scale, and density functional theory is used to determine the electronic couplings between molecules. Without any fitting parameters we predict electron mobilities in the crystalline and disordered phases of similar to 1 and similar to 10(-4) cm(2) V-1 s(-1), respectively. In good agreement with experiment we find that electron mobilities are two orders of magnitude greater than those of holes. We explain this difference in terms of the spatial extent of the frontier orbitals. Our results suggest that charge transport in disordered Alq3 is dominated by a few highly conducting pathways.
First author: Laimgruber, S., The ketene intermediate in the photochemistry of ortho-nitrobenzaldehyde, PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 10, 3872, (2008)
Abstract: The first intermediate of the photochemical transformation of ortho-nitrobenzaldehyde to ortho-nitrosobenzoic acid in acetonitrile solvent has been characterized by femtosecond spectroscopy and time-dependent density functional theory (TDDFT) calculations. Femtosecond stimulated Raman spectroscopy (FSRS) indicates that this intermediate adopts a ketene structure. This assignment is supported by the TDDFT results. A kinetic analysis of FSRS and transient absorption data points to two channels for the formation of the ketene. For the predominating first channel the formation takes 0.4 ps. For the second channel it is much slower and takes 220 ps. We assign the first channel to a reaction via an excited singlet state. The second one might involve a triplet state.
First author: Rooms, John F., Mercury-fluorine interactions: a matrix isolation investigation of Hg center dot center dot center dot F(2), HgF(2) and HgF(4) in argon matrices, PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 10, 4594, (2008)
Abstract: HgF(2) and Hg have been trapped in dilute F(2)/Ar and neat F(2) matrices, subjected to UV-Vis and vac-UV photolysis and annealing, with the products identified by FTIR, UV-Vis-NIR and Hg L(3)-edge XAFS spectroscopic techniques. Whilst there was no convincing evidence for the formation of HgF(4) under our argon matrix isolation conditions, a new Hg center dot center dot center dot F(2) complex was identified and subsequent photolysis yielded HgF2 very cleanly. Hg L(3)-edge EXAFS has provided the first experimental value of 1.94(2) angstrom for the Hg-F bond length in HgF(2), which is in excellent agreement with the computational values incorporating relativistic effects.
First author: Gomes, Andre Severo Pereira, Calculation of local excitations in large systems by embedding wave-function theory in density-functional theory, PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 10, 5353, (2008)
Abstract: We present a simple and efficient embedding scheme for the wave-function based calculation of the energies of local excitations in large systems. By introducing an embedding potential obtained from density-functional theory (DFT) it is possible to describe the effiect of an environment on local excitations of an embedded system in wave-function theory (WFT) calculations of the excitation energies. We outline the implementation of such a WFT-in-DFT embedding procedure employing the ADF, Dalton and DIRAC codes, where the embedded subsystem is treated with coupled cluster methods. We then evaluate this procedure in the calculation of the solvatochromic shift of acetone in water and of the f – f spectrum of NpO(2)(2+) embedded in a Cs(2)UO(2)Cl(4) crystal and find that our scheme does effiectively incorporate the environment effect in both cases. A particularly interesting finding is that with our embedding scheme we can model the equatorial Cl(-) ligands in NpO(2)Cl(4)(2-) quite accurately, compared to a fully wavefunction-based calculation, and this opens up the possibility of modeling the interaction of different ligands to actinyl species with relatively high accuracy but at a much reduced computational cost.
First author: Wawrzyniak, Piotr K., Protein-induced geometric constraints and charge transfer in bacteriochlorophyll-histidine complexes in LH2, PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 10, 6971, (2008)
Abstract: Bacteriochlorophyll-histidine complexes are ubiquitous in nature and are essential structural motifs supporting the conversion of solar energy into chemically useful compounds in a wide range of photosynthesis processes. A systematic density functional theory study of the NMR chemical shifts for histidine and for bacteriochlorophyll-a-histidine complexes in the light-harvesting complex II (LH2) is performed using the BLYP functional in combination with the 6-311++ G(d, p) basis set. The computed chemical shift patterns are consistent with available experimental data for positive and neutral(tau) (N(tau) protonated) crystalline histidines. The results for the bacteriochlorophyll-a-histidine complexes in LH2 provide evidence that the protein environment is stabilizing the histidine close to the Mg ion, thereby inducing a large charge transfer of similar to 0.5 electronic equivalent. Due to this protein-induced geometric constraint, the Mg-coordinated histidine in LH2 appears to be in a frustrated state very different from the formal neutral(pi) (N(pi) protonated) form. This finding could be important for the understanding of basic functional mechanisms involved in tuning the electronic properties and exciton coupling in LH2.
First author: Gomes, Thiago C. F., COMPUTATIONAL IMPLEMENTATION OF THE MODEL CHARGE-CHARGE FLUX-DIPOLE FLUX FOR CALCULATION AND ANALYSIS OF INFRARED INTENSITIES, QUIMICA NOVA, 31, 1750, (2008)
Abstract: The first computational implementation that automates the procedures involved in the calculation of infrared intensities using the charge-charge flux-dipole flux model is presented. The atomic charges and dipoles from the Quantum Theory of Atoms in Molecules (QTAIM) model was programmed for Morphy98, Gaussian98 and Gaussian03 programs outputs, but for the ChelpG parameters only the Gaussian programs are supported. Results of illustrative but new calculations for the water, ammonia and methane molecules at the MP2/6-311++G(3d,3p) theoretical level, using the ChelpG and QTAIM/Morphy charges and dipoles are presented. These results showed excellent agreement with analytical results obtained directly at the MP2/6-311++G(3d,3p) level of theory.
First author: Conradie, Marrigje M., Methyl Iodide Oxidative Addition to Rhodium(I) Complexes: a DFT and NMR Study of [Rh(FcCOCHCOCF(3))(CO)(PPh3)] and the Rhodium (III) Reaction Products, SOUTH AFRICAN JOURNAL OF CHEMISTRY-SUID-AFRIKAANSE TYDSKRIF VIR CHEMIE, 61, 102, (2008)
Abstract: A theoretical (DFT) study of the equilibrium geometry of the possible reaction products of the oxidative addition reaction [Rh(FcCOCHCOCF(3))(CO)(PPh3)] + CH3I (Fc = ferrocenyl), consistent with experimental observations, revealed that the first alkyl product results from trans addition to Rh-I. Isomerization via an acyl intermediate leads to a second octahedral alkyl product with the PPh3 group and the iodide above and below the square plane. Theoretical computations also revealed that the thermodynamic acyl product adopts a square-pyramidal geometry with the COCH3 group in the apical position.
First author: Jalkanen, K. J., Role of hydration in determining the structure and vibrational spectra of L-alanine and N-acetyl L-alanine N ‘-methylamide in aqueous solution: a combined theoretical and experimental approach, THEORETICAL CHEMISTRY ACCOUNTS, 119, 191, (2008)
Abstract: In this work we have utilized recent density functional theory Born-Oppenheimer molecular dynamics simulations to determine the first principles locations of the water molecules in the first solvation shell which are responsible for stabilizing the zwitterionic structure of L-alanine. Previous works have used chemical intuition or classical molecular dynamics simulations to position the water molecules. In addition, a complete shell of water molecules was not previously used, only the water molecules which were thought to be strongly interacting (H-bonded) with the zwitterionic species. In a previous work by Tajkhorshid et al. (J Phys Chem B 102:5899) the L-alanine zwitterion was stabilized by 4 water molecules, and a subsequent work by Frimand et al. (Chem Phys 255:165) the number was increased to 9 water molecules. Here we found that 20 water molecules are necessary to fully encapsulate the zwitterionic species when the molecule is embedded within a droplet of water, while 11 water molecules are necessary to encapsulate the polar region with the methyl group exposed to the surface, where it migrates during the MD simulation. Here we present our vibrational absorption, vibrational circular dichroism and Raman and Raman optical activity simulations, which we compare to the previous simulations and experimental results. In addition, we report new VA, VCD, Raman and ROA measurements for L-alanine in aqueous solution with the latest commercially available FTIR VA/VCD instrument (Biotools, Jupiter, FL, USA) and Raman/ROA instrument (Biotools). The signal to noise of the spectra of L-alanine measured with these new instruments is significantly better than the previously reported spectra. Finally we reinvestigate the causes for the stability of the P(pi) structure of the alanine dipeptide, also called N-acetyl-L-alanine N’-methylamide, in aqueous solution. Previously we utilized the B3LYP/6-31G* + Onsager continuum level of theory to investigate the stability of the NALANMA4WC Han et al. (J Phys Chem B 102:2587) Here we use the B3PW91 and B3LYP hybrid exchange correlation functionals, the aug-cc-pVDZ basis set and the PCM and CPCM (COSMO) continuum solvent models, in addition to the Onsager and no continuum solvent model. Here by the comparison of the VA, VCD, Raman and ROA spectra we can confirm the stability of the NALANMA4WC due to the strong hydrogen bonding between the four water molecules and the peptide polar groups. Hence we advocate the use of explicit water molecules and continuum solvent treatment for all future spectral simulations of amino acids, peptides and proteins in aqueous solution, as even the structure (conformer) present cannot always be found without this level of theory.
First author: Nicu, Valentin Paul, A vibrational circular dichroism implementation within a Slater-type-orbital based density functional framework and its application to hexa- and hepta-helicenes, THEORETICAL CHEMISTRY ACCOUNTS, 119, 245, (2008)
Abstract: We describe the implementation of the rotational strengths for vibrational circular dichroism (VCD) in the Slater-type orbital based Amsterdam Density Functional (ADF) package. We show that our implementation, which makes use of analytical derivative techniques and London atomic orbitals, yields origin independent rotational strengths. The basis set dependence in the particular case of Slater-type basis functions is also discussed. It turns out that the triple zeta STO basis sets with one set of polarization functions (TZP) are adequate for VCD calculations. The origin- dependence of the atomic axial tensors is checked by a distributed origin gauge implementation. The distributed and common origin gauge implementations yield virtually identical atomic axial tensors with the Slater-type basis sets employed here, proving that our implementation yields origin independent rotational strengths. We verify the implementation for a set of benchmark molecules, for which the dependence of the VCD spectra on the particular choice of the exchange-correlation functional is studied. The pure functionals BP86 and OLYP show a particularly good performance. Then, we apply this approach to study the VCD spectra of hexa- and hepta- helicenes. In particular we focus on relationships between the sign of the rotational strengths of the two helicenes.
First author: Leboschka, Markus, Dimerization of the 2-(Methylselenomethyl)benzimidazole-silver(I) Cation Involving a Ag-I-Ag-I Interaction, ZEITSCHRIFT FUR ANORGANISCHE UND ALLGEMEINE CHEMIE, 634, 2343, (2008)
Abstract: Reacting the bidentate ligand 2-(methylselenomethyl)-1H-benzimidazole (msb) with AgBF4 in CH3CN did not produce the expected [Ag-2(msb)(2)] ion with two five-membered chelate rings but the dimeric [Ag-2(msb)(2)](2), isolated and crystallized from acetonitrile/methanol as {[Ag(msb)(CH3CN)](2)}(BF4)(2) with six-membered chelate rings Ag-Ag-Se-C-C-N involving a Ag-Ag bond of 3.156(1) angstrom distance. DFT calculations reproduce the observed molecular structure of the dication.