Semi-empirical calculations including an empirical dispersive correction are used to calculate intermolecular interaction energies and structures for a large database containing 156 biologically relevant molecules (hydrogen-bonded DNA base pairs, interstrand base pairs, stacked base pairs and amino acid base pairs) for which MP2 and CCSD(T) complete basis set (CBS) limit estimates of the interaction energies are available. The dispersion corrected semi-empirical methods are parameterised against a small training set of 22 complexes having a range of biologically important non-covalent interactions. For the full molecule set (156 complexes), compared to the high-level ab initio database, the mean unsigned errors of the interaction energies at the corrected semi-empirical level are 1.1 (AM1-D) and 1.2 (PM3-D) kcal mol(-1), being a significant improvement over existing AM1 and PM3 methods (8.6 and 8.2 kcal mol(-1)). Importantly, the new semi-empirical methods are capable of describing the diverse range of biological interactions, most notably stacking interactions, which are poorly described by both current AM1 and PM3 methods and by many DFT functionals. The new methods require no more computer time than existing semi-empirical methods and therefore represent an important advance in the study of important biological interactions.

We describe the use of density functional theory (DFT-D) and semiempirical (AM1-D and PM3-D) methods having an added empirical dispersion correction, to treat noncovalent interactions between molecules involving sulfur atoms. The DFT-D method, with the BLYP and B3LYP functionals, was judged against a small-molecule database involving sulfur-π, S-H···S, and C-H···S interactions for which high-level MP2 or CCSD(T) estimates of the structures and binding or interaction energies are available. This database was also used to develop appropriate AM1-D and PM3-D parameters for sulfur. The DFT-D, AM1-D, and PM3-D methods were further assessed by calculating the structures and binding energies for a set of eight sulfur-containing base pairs, for which high-level ab initio data are available. The mean absolute deviations (MAD) for both sets of structures shown by the DFT-D methods are 0.04 Å for the intermolecular distances and less than 0.7 kcal mol(-)(1) for the binding and interaction energies. The corresponding values are 0.3 Å and 1.5 kcal mol(-)(1) for the semiempirical methods. For the complexes studied, the dispersion contributions to the overall binding and interaction energies are shown to be important, particularly for the complexes involving sulfur-π interactions.

High-level electronic structure calculations have been used to study the mechanism of hydrolysis of chlorine nitrate in neutral water clusters containing three to eight solvating water molecules. The calculations clarify some of the current uncertainties in the hydrolysis mechanism. As the size of the water cluster is increased, ClONO2 shows increasing ionization along the O2NO−Cl bond consistent with the proposed predissociation in which the electrophilicity of the chlorine atom is enhanced, thus making it more susceptible to nucleophilic attack from a surface water molecule. A species akin to the experimentally observed intermediate, H2OCl+ is found to be stable in a cluster containing eight water molecules. The hydrolysis products, ionized nitric (H3O+/NO3 -) and molecular hypochlorous (HOCl) acids, are found to be stable in two different types of structures, containing six and eight water molecules. For the water cluster containing six water molecules, which has a structure related to ordinary hexagonal ice, ClONO2 is hydrolyzed to yield H3O+/NO3 -/HOCl, with essentially no barrier. The calculations thus predict that hydrolysis of ClONO2 on PSC ice aerosols can proceed spontaneously in small neutral water clusters.

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