# References¶

M. Swart and F.M. Bickelhaupt, Amsterdam, 2006.

M. Swart and F.M, Bickelhaupt, QUILD: QUantum-regions interconnected by local descriptions. Journal of Computational Chemistry 29, 724 (2008)

ADF2009.01, SCM, Theoretical Chemistry, Vrije Universiteit, Amsterdam, The Netherlands, http://www.scm.com E.J. Baerends, J. Autschbach, A. Bérces, F.M. Bickelhaupt, C. Bo, P.M. Boerrigter, L. Cavallo, D.P. Chong, L. Deng, R.M. Dickson, D.E. Ellis, M. van Faassen, L. Fan, T.H. Fischer, C. Fonseca Guerra, S.J.A. van Gisbergen, A.W. Götz, J.A. Groeneveld, O.V. Gritsenko, M. Grüning, F.E. Harris, P. van den Hoek, C.R. Jacob, H. Jacobsen, L. Jensen, G. van Kessel, F. Kootstra, M.V. Krykunov, E. van Lenthe, D.A. McCormack, A. Michalak, J. Neugebauer, V.P. Nicu, V.P. Osinga, S. Patchkovskii, P.H.T. Philipsen, D. Post, C.C. Pye, W. Ravenek, J.I. Rodríguez, P. Ros, P.R.T. Schipper, G. Schreckenbach, J.G. Snijders, M. Solà, M. Swart, D. Swerhone, G. te Velde, P. Vernooijs, L. Versluis, L. Visscher, O. Visser, F. Wang, T.A. Wesolowski, E.M. van Wezenbeek, G. Wiesenekker, S.K. Wolff, T.K. Woo, A.L. Yakovlev, and T. Ziegler

G. te Velde, F.M. Bickelhaupt, E.J. Baerends, C. Fonseca Guerra, S.J.A. van Gisbergen, J.G. Snijders and T. Ziegler, Chemistry with ADF. Journal of Computational Chemistry 22, 931 (2001)

W. Koch and M.C. Holthausen, A Chemist’s Guide to Density Functional Theory. Wiley-VCH: Weinheim, 2000.

R.G. Parr and W. Yang, Density functional theory of atoms and molecules. Oxford University Press: New York, 1989.

R. Dreizler and E. Gross, Density Functional Theory. Plenum Press: New York, 1995.

W.D. Cornell, P. Cieplak, C.I. Bayly, I.R. Gould, K.M. Merz, D.M. Ferguson, D.C. Spellmeyer, T. Fox, J.W. Caldwell and P.A. Kollman, A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules. Journal of the American Chemical Society 117, 5179 (1995)

T.K. Woo, P.E. Blöchl and T. Ziegler, Towards solvation simulations with a combined ab initio molecular dynamics and molecular mechanics approach. Journal of Molecular Structucture (THEOCHEM) 506, 313 (2000)

T.K. Woo, L. Cavallo, and T. Ziegler, Implementation of the IMOMM methodology for performing combined QM/MM molecular dynamics simulations and frequency calculations. Theoretical Chemistry Accounts 100, 307 (1998)

T.K. Woo, P.M. Margl, L. Deng, L. Cavallo, and T. Ziegler, Towards more realistic computational modeling of homogenous catalysis by density functional theory: combined QM/MM and ab initio molecular dynamics. Catalysis Today 50, 479 (1999)

T. Kamachi, and K. Yoshizawa, A Theoretical Study on the Mechanism of Camphor Hydroxylation by Compound I of Cytochrome P450. Journal of the American Chemical Society 125, 4652 (2003)

J.P.Perdew, A. Ruzsinszky, J.M. Tao, V.N. Staroverov, G.E. Scuseria and G.I. Csonka, Prescription for the design and selection of density functional approximations: More constraint satisfaction with fewer fits. Journal of Chemical Physics 123, 62201 (2005)

A. Rosa, G. Ricciardi, E.J. Baerends, Synergism of Porphyrin-Core Saddling and Twisting of meso-Aryl Substituents. Journal of Physical Chemistry A 110, 5180 (2006)

J.C. Schöneboom, H. Lin, N. Reuter, W. Thiel, S. Cohen, F. Ogliaro, S. Shaik, The Elusive Oxidant Species of Cytochrome P450 Enzymes: Characterization by Combined Quantum Mechanical/Molecular Mechanical (QM/MM) Calculations. Journal of the American Chemical Society 124, 8142 (2002)

M. Costas, X. Ribas, A. Poater, J.M. López Valbuena, R. Xifra, A. Company, M. Duran, M. Solà, A. Llobet, M. Corbella, M.A. Usón, J. Mahía, X. Solans, X.P. Shan and J. Benet-Buchholz, Article Copper(II) Hexaaza Macrocyclic Binuclear Complexes Obtained from the Reaction of Their Copper(I) Derivates and Molecular Dioxygen. Inorganic Chemistry 45, 3569 (2006)

X. Sala, E. Plantalech, I. Romero, M. Rodríguez, A. Llobet, A. Poater, M. Duran, M. Solà, S. Jansat, M. Gómez, T. Parella, H. Stoeckli-Evans and J. Benet-Buchholz, Atropisomeric Discrimination in New Ru

^{II}Complexes Containing the C_{2}-Symmetric Didentate Chiral Phenyl-1,2-bisoxazolinic Ligand. Chemistry: A European Journal 12, 2798 (2006)

A. Poater, S. Moradell, E. Pinilla, J. Poater, M. Solà, M.Á. Martínez and A. Llobet, A trinuclear Pt(II) compound with short Pt-Pt-Pt contacts. An analysis of the influence of pi-pi stacking interactions on the strength and length of the Pt-Pt bond. Dalton Transactions 2006, 1188 (2006)

N. Martín, M. Altable, S. Filippone, Á. Martín-Domenech, A. Poater and M. Solà, Regioselective Intramolecular Pauson-Khand Reactions of C60: An Electrochemical Study and Theoretical Underpinning. Chemistry: A European Journal 11, 2716 (2005)

J. Duran, A. Polo, J. Real, J. Benet-Buchholz, A. Poater and M. Solà, Stereodiscrimination in Phosphanylthiolato Nickel(II) Complexes. European Journal of Inorganic Chemistry 2003 4147 (2003)

N.C. Handy and A.J. Cohen, Left-right correlation energy. Molecular Physics 99, 403 (2001)

A.D. Becke, Density-functional exchange-energy approximation with correct asymptotic behavior. Physical Review A 38, 3098 (1988)

M. Swart, A.W. Ehlers and K. Lammertsma, Performance of the OPBE exchange-correlation functional. Molecular Physics 2004 102, 2467 (2004)

M. Swart and J.G. Snijders, Accuracy of geometries: influence of basis set, exchange.correlation potential, inclusion of core electrons, and relativistic corrections. Theoretical Chemistry Accounts 110, 34 (2003)

M. Swart, Metal-ligand bonding in metallocenes: Differentiation between spin state, electrostatic and covalent bonding. Inorganica Chimica Acta 360, 179 (2007)

M. Swart, A.R. Groenhof, A.W. Ehlers and K. Lammertsma, Validation of Exchange-Correlation Functionals for Spin States of Iron Complexes. Journal of Physical Chemistry A 108, 5479 (2004)

M. Swart, M. Solà and F.M. Bickelhaupt, Energy landscapes of nucleophilic substitution reactions: A comparison of density functional theory and coupled cluster methods. Journal of Computational Chemistry 28, 1551 (2007)

G.T. de Jong and F.M. Bickelhaupt, Oxidative Addition of the Chloromethane C-Cl Bond to Pd, an ab Initio Benchmark and DFT Validation Study. Journal of Chemical Theory and Computation 2, 322 (2006)

M. Grüning, O. Gritsenko and E.J. Baerends, Improved Description of Chemical Barriers with Generalized Gradient Approximations (GGAs) and Meta-GGAs. Journal of Physical Chemistry A 108, 4459 (2004)

T. van der Wijst, C. Fonseca Guerra, M. Swart and F.M. Bickelhaupt, Performance of various density functionals for the hydrogen bonds in DNA base pairs. Chemical Physics Letters 426, 415 (2006)

M. Swart, T. van der Wijst, C. Fonseca Guerra and F.M. Bickelhaupt, n-n stacking tackled with density functional theory. Journal of Molecular Modeling 13, 1245 (2007)

J.P. Perdew, Density-functional approximation for the correlation energy of the inhomogeneous electron gas. Physical Review B 33, 8822 (1986) Erratum: J.P. Perdew, Physical Review B 34, 7406 (1986)

C. Fonseca Guerra and F.M. Bickelhaupt, Charge Transfer and Environment Effects Responsible for Characteristics of DNA Base Pairing. Angewandte Chemie International Edition 38, 2942 (1999)

C. Fonseca Guerra and F.M. Bickelhaupt, Orbital Interactions in Strong and Weak Hydrogen Bonds are Essential for DNA Replication. Angewandte Chemie International Edition 41, 2092 (2002)

C. Fonseca Guerra, F.M. Bickelhaupt and E.J. Baerends, Orbital Interactions in Hydrogen Bonds Important for Cohesion in Molecular Crystals and Mismatched Pairs of DNA Bases. Crystal Growth Design 2, 239 (2002)

C. Fonseca Guerra, F.M. Bickelhaupt, J.G. Snijders and E.J. Baerends, The Nature of the Hydrogen Bond in DNA Base Pairs: The Role of Charge Transfer and Resonance Assistance. Chemistry - A European Journal 5, 3581 (1999)

C. Fonseca Guerra, F.M. Bickelhaupt, J.G. Snijders and E.J. Baerends, Hydrogen Bonding in DNA Base Pairs: Reconciliation of Theory and Experiment. Journal of the American Chemical Society 122, 4117 (2000)

T. Vreven and K. Morokuma, The ONIOM (our own N-layered integrated molecular orbital + molecular mechanics) method for the first singlet excited (S

_{1}) state photoisomerization path of a retinal protonated Schiff base. Journal of Chemical Physics 113, 2969 (2000)

M. Svensson, S. Humbel, R.D.J. Froese, T. Matsubara, S. Sieber and K. Morokuma, ONIOM: A Multilayered Integrated MO + MM Method for Geometry Optimizations and Single Point Energy Predictions. A Test for Diels.Alder Reactions and Pt(P(t-Bu)

_{3})_{2}+ H_{2}Oxidative Addition. Journal of Physical Chemistry 100, 19357 (1996)

M. Swart, AddRemove: A new link model for use in QM/MM studies. International Journal of Quantum Chemistry 91, 177 (2003)

M. Swart and F.M. Bickelhaupt, Optimization of strong and weak coordinates. International Journal of Quantum Chemistry 106, 2536 (2006)

J. Baker, A. Kessi and B. Delley, The generation and use of delocalized internal coordinates in geometry optimization. Journal of Chemical Physics 1996 105, 192 (1996)

P. Csaszar and P. Pulay, Geometry optimization by direct inversion in the iterative subspace. Journal of Molecular Structure 114, 31 (1984)

Ö. Farkas and H.B. Schlegel, Methods for optimizing large molecules. Part III. An improved algorithm for geometry optimization using direct inversion in the iterative subspace (GDIIS). Physical Chemistry Chemical Physics 4, 11 (2002)

D.L. Yeager, H.J.A. Jensen, P. Jørgensen, T.U. Helgaker, In Geometrical derivatives of energy surfaces and molecular properties. P. Jørgensen, and J. Simons, Eds.; Reidel Publishing: Dordrecht, 1986, p 229.

V. Bakken and T. Helgaker, The efficient optimization of molecular geometries using redundant internal coordinates. Journal of Chemical Physics 117, 9160 (2002)

J. Baker, Constrained optimization in delocalized internal coordinates. Journal of Computational Chemistry 18, 1079 (1997)

D. Unjaroen, M. swart, and W.R. Browne, Electrochemical Polymerization of Iron(III) Polypyridyl Complexes through C-C Coupling of Redox Non-innocent Phenolato Ligands. Inorganic Chemistry 56, 470 (2017)

ORCA. Note that the ORCA program is not provided within the ADF program package, and the user (or system administrator) has to download and install the program him/herself. At the time this manual was written the ORCA program was free of charge for academic groups.