In July SCM attended the 2011 World Congress of the World Association of Theoretical and Computational Chemists (WATOC). This event was be held at the University of Santiago in Santiago de Compostela, Spain. At the end of this summer we also exhibited at the 14th International Density Functional Theory Conference to be held in Athens, Greece. As for our future plans, we will attend the Spring ACS conference in San Diego, and look for us at other conferences as well....
Some of the (over 1300) WATOC 2011 participants in Santiago de Compostella, Spain.
SCM was one of the major exhibitors and sponsors.
In May, 2011, The National Computing Infrastructure National Facility (NCI NF) of Australia and SCM, organized a web presentation for NCI facility users and others interested. Dr. Stan van Gisbergen and Dr. Matt Kundrat presented on behalf of SCM. This was our first large-scale "webinar" and we are encouraged by the results. We would like to give similar presentations in the future; if you are interested in participating in such a virtual seminar, please let us know.
Later in May, Dr. Kundrat traveled to the Emerald Isle to give a talk at the Complex and Adaptive Systems Laboratory (CASL) of the University College, Dublin. The following month Matt journeyed to the Midwestern United States to give talks at Illinois Institute of Technology, Northwestern University, The University of Michigan and Carnegie-Mellon University. Additionally, he made several stops for presentations at private companies and government labs in the US and in Europe.
Dye-sensitized solar cells (DSSCs) offer a promising means of harvesting the sun's energy, and the improvement of their efficiency has drawn the interest of theoretical chemists and physicists. In a 2011 issue of Physical Chemistry Chemical Physics, Abu Md Asaduzzaman and Georg Schreckenbach of The University of Manitoba, Winnipeg reported their results on the modeling of a prototype dye employed in such solar cells. They used ADF and other molecular modeling programs to investigate the I-/I3- redox reaction of a compound known as the "N3 dye".
Optimized structures of N3+I- (N3IRu and N3IOH) complexes
To conduct their study, Asaduzzaman and Schreckenbach carried out geometry optimization calculations of reactants, intermediates and products of the N3 dye reaction. The computed energies of these differing forms of the dye allowed them to model both the thermodynamics and the kinetics of the reaction. Key options in the molecular modeling programs which were used included relativistic spin-orbit coupling (with ZORA), Grimme's dispersion corrected functionals (DFT-D3), and solvent effects (with a continuum model). The researchers noted that proper solvation modeling was crucial to this study.
Among other things, the authors were able to support the conclusion that the step of the reaction in which the neutral dye is regenerated from its oxidized form is a major factor in limiting efficiency in solar cells comprised of such compounds. Hopefully the knowledge gained in studies such as this will be applied to development of ever increasingly efficient, newer generations of solar cells.
A. M. Asaduzzaman and G. Schreckenbach, Interactions of the N3 dye with the iodide redox shuttle: quantum chemical mechanistic studies of the dye regeneration in the dye-sensitized solar cell. Physical Chemistry Chemical Physics, 13, 15148 (2011).
"Superatomic" molecules and ions are fascinating species in which polyatomic clusters exhibit properties generally associated with single atoms. One of these such metal clusters, [Pt@Pb12]2-, has drawn the attention of Boris Le Guennic at Université Lyon and Jochen Autschbach at the University at Buffalo, due to its unique Nuclear Magnetic Resonance (NMR) properties. The researchers used the ADF program to compute shielding constants (a component of chemical shift) and spin-spin coupling constants for this superatomic ion, and compared their results to published experimental work. In doing so, they were able to explain the reasons behind the atypically large positive chemical shift calculated and observed in the 207Pb NMR. Their work is published in a special edition of the Canadian Journal of Chemistry dedicated to Professor Roderick E. Wasylishen.
Top: Structure and MO diagram of [Pt@Pb12]2-. Bottom: selected molecular orbitals, resembling p and g atomic orbitals in icosahedral space.
ADF's ability to carry out calculations with all electron basis sets (augmented with steep functions) is necessary for accurate NMR chemical shielding calculations. The ZORA method facilitates the proper modeling of the relativistic effects that are particularly prominent in heavy elements such as lead and platinum. The effects of spin-orbit coupling were significant, as expected for these heavy metals. The finite nucleus approximation, implemented in ADF by Autschbach et. al, was also seen to play an important role in modeling the coupling constants between these large nuclei.
B. Le Guennic, and J. Autschbach, [Pt@Pb12]2- - A challenging system for relativistic density functional theory calculations of 195Pt and 207Pb NMR parameters. Canadian Jourbnal of Chemistry, 89 (7), 814 (2011).
In a recent paper in ChemComm, researchers in Spain and the Netherlands have used a combination of ADF features to unravel the factors behind the fidelity in chemical, template-assisted primer extension. The analyses therein, based on state-of-the-art dispersion-corrected density functional theory (DFT), reveal key factors behind the intrinsic affinity of a DNA template-primer complex to select the correct nucleotide. They show that hydrogen bonds alone are not enough to achieve the correct preference for Watson-Crick pairs. This correct preference is only achieved after including solvent effects (partial desolvation). Stacking interactions, entropy effects and the helical structure imposed by the backbone are also crucial. Interestingly, the researchers also find what they dubbed the "nearest-neighbor effect": the nature of the terminal base in the primer strand has a non-negligible effect on the energetic preference of the template-primer complex for the correct incoming nucleotide. In other words, the precision of a particular DNA replication step fluctuates as a function of which nucleotide was incorporated in the previous cycle.
Above: A model complex of incoming nucleotide X' + template Y1'/Y2' strand + primer strand Z' in aqueous solution (see the text of the publication for details).
The features of ADF which made this study possible include the ability to treat simultaneously covalent and dispersion interactions (using Grimme's dispersion corrections) along with treatment of solvent effects (with COSMO).
J. Poater, M. Swart, C.Fonseca Guerra and F. M. Bickelhaupt, Selectivity in DNA replication. Interplay of steric shape, hydrogen bonds, n-stacking and solvent effects. Chemical Communications 47, 7326 (2011).
We always welcome suggestions for new ADF functionality that you would like to see included in a future release. Any questions or comments regarding this Newsletter, or other questions related to ADF, are also welcome and can be sent to info@scm.com. Feel free to contact us also in case you have some information that may be of interest to other ADF users, and that may be suitable material for a future Newsletter or news item on the SCM website.
These news items and more can be found in the news section of our website.
