Kevin E. Riley

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Interactions between amino acid side chains play a crucial role both within a folded protein and between the interacting protein molecules. Here we have selected a representative set of 24 of the 400 (20 × 20) possible interacting side chain pairs based on data from Atlas of Protein Side-Chain Interactions. For each pair, we obtained its most favorable(More)
In the past several years the MP2 method has been used extensively in studies of noncovalent interactions within biological systems such as proteins, DNA/RNA, and protein-ligand complexes. In this work we assess the performance that can be expected of this method, when paired with several different medium and extended basis sets, for the accurate(More)
MP2/aDZ Method S66 categories Dispersion subcategories H-bonds Dispersion Other A-A MP2/TZ 12.7 13.7 12.1 12.5 15.0 14.3 11.6 15.1 15.4 15.8 11.5 11.6 MP2/CBS 3.2 9.2 17.5 8.9 9.4 7.8 MP2C/CBS 11.3 12.4 14.3 10.6 6.3 19.7 SCS-MP2/CBS 12.5 19.0 15.4 13.1 21.2 30.9 SCS-MI-MP2/CBS 4.5 10.2 5.5 2.9 11.6 21.4 DW-MP2/CBS 3.7 10.8 6.2 2.4 12.1 23.2 MP3/CBS 3.6 9.0(More)
The reliable prediction of molecular properties is a vital task of computational chemistry. In recent years, density functional theory (DFT) has become a popular method for calculating molecular properties for a vast array of systems varying in size from small organic molecules to large biological compounds such as proteins. In this work we assess the(More)
Department of Chemistry, University of Puerto Rico, Rio Piedras, Puerto Rico 00931, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, 166 10 Prague, Czech Republic, Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius(More)
A positive π-hole is a region of positive electrostatic potential that is perpendicular to a portion of a molecular framework. It is the counterpart of a σ-hole, which is along the extension of a covalent bond to an atom. Both σ-holes and π-holes become more positive (a) in going from the lighter to the heavier atoms in a given Group of the periodic table,(More)
In recent years it has been recognized that, because of their unique properties, halogen bonds have tremendous potential in the development of new pharmaceutical compounds and materials. In this study we investigate the phenomenon of halogen bonding by carrying out ab initio calculations on the halomethane-formaldehyde complexes as well as the fluorine(More)
Halogen bonding is a unique type of noncovalent binding phenomenon in which a halogen atom interacts attractively with an electronegative atom such as oxygen or nitrogen. These types of interactions have been the subject of many recent investigations because of their potential in the development of new materials and pharmaceutical compounds. Recently, it(More)
This review summarises recent advances in quantum chemical calculations of base-stacking forces in nucleic acids. We explain in detail the very complex relationship between the gas-phase base-stacking energies, as revealed by quantum chemical (QM) calculations, and the highly variable roles of these interactions in nucleic acids. This issue is rarely(More)
Aromatic systems contain both σ- and π-electrons, which in turn constitute σ- and π-molecular orbitals (MOs). In discussing the properties of these systems, researchers typically refer to the highest occupied and lowest unoccupied MOs, which are π MOs. The characteristic properties of aromatic systems, such as their low ionization potentials and electron(More)