Distribution of water hydrogens around adenine and cytosine during Car-Parrinello molecular dynamics simulation

Investigation of structure of nucleic acid bases (thymine, cytosine, guanine and adenine) surrounded by water shell using quantum-chemical calculations and Car-Parinello molecular dynamics revealed strong polarization of thymine, cytosine and guanine by polar environment. Structure of these molecules cannot be described by canonical chemical formulas due to significant contribution of zwitter-ionic resonant structures. Strong polarization of molecules in polar environment results in decrease of conformational flexibility of pyrimidine ring in thymine, cytosine and guanine and increase of flexibility of aromatic ring in adenine.

Results of simulation of nucleobase water solutions by Car- Parinello molecular dynamics method demonstrated that the most preferred way for interaction of water molecules with heterocycles of nucleic acid bases is the formation of mixed O-H…n/O-H…π hydrogen bonds where both lone pair of the nitrogen atoma and π-system of purine provides significant and comparable contributions into total energy of hydrogen bonding.

Presence of weak but numerous C-H…O hydrogen bonds in crystals and molecular complexes of hexaethynylhexamethoxy[6]pericyclyne results in formation of tubular structures which can be considered as supramolecular analogue of single walled carbon nanotubes. Energy of interactions between two macorocycles within such supramolecular nanotube is more than 20 kcal/mol. Small molecules like dichlromethane may be located inside nanotube due to halogen bonding to π-systems of triple bonds.

It was suggested a novel method for analysis of crystal structure of molecular crystals. Accurate calculations of energy of intermolecular interaction between molecules in crystal phase allow recognizing unambiguously preferred pattern of crystal packing. For example, in the case of crystal of derivative of phenanthroline it was revealed that molecules form strongly bonded stacked dimers which are organized in infinite columns due to weaker stacking interactions. Crystal structure may be presented as isotropic packing of such columns.

Localization of the lowest singlet excitations in three-decks paracyclophane

It was developed method for calculations of excitation indices and excitation charge transfer for time-dependent density functional theory.

This approach allows clear recognition of character of distribution of excitation within molecules.