Molecular orbital theory of the hydrogen bond. XXIX. Water–thymine complexes

Hydration and stability of nucleic acid bases and base pairs

Empirical, quantum chemical calculations and molecular dynamics simulations of the role of a solvent on tautomerism of nucleic acid bases and structure and properties of nucleic acid base pairs are summarized. Attention was paid to microhydrated (by one and two water molecules) complexes, for which structures found by scanning of empirical potential surfaces were recalculated at a correlated ab initio level. Additionally, isolated as well as mono- and dihydrated H-bonded, T-shaped and stacked structures of all possible nucleic acid base pairs were studied at the same theoretical levels. We demonstrate the strong influence of a solvent on the tautomeric equilibrium between the tautomers of bases and on the spatial arrangement of the bases in a base pair. The results provide clear evidence that the prevalence of either the stacked or hydrogen-bonded structures of the base pairs in the solvent is not determined only by its bulk properties, but rather by specific hydrophilic interactions of the base pair with a small number of solvent molecules.

Vibrational and electronic excitations of H[sub 2]O on thymine films induced by low-energy electrons

We investigated vibrational and electronic excitations of 0.1-layer up to 2.4-layer film of H(2)O deposited on a 1.4-layer film of thymine condensed on Ar at a temperature of 18 K using high-resolution electron-energy loss (EEL) spectroscopy at the incident energy of 12 eV. The spectral contribution originating essentially from the H(2)O overlayer is obtained by separating the measured contribution from the underlying film of thymine, considering the electron beam attenuation in the H(2)O overlayer. The vibrational EEL spectrum of submonolayer amount of H(2)O on thymine, which excepts for small energy shift of the vibrational bands, is found to compare in intensity to that of the same amount of H(2)O deposited directly on the argon. The electronic energy-loss intensity near 8.6 eV, which is attributed to the excitation of (3,1)B(1) states of H(2)O in condensed phase, is observed to decrease by a factor of about 3 by the presence of the underlying film of thymine. This indicates that the corresponding cross section for excitation the (3,1)B(1) states of H(2)O by the electron impact is reduced significantly by the close proximity of the thymine molecules.

Elucidation of primary radiation damage in DNA through application of ab initio molecular orbital theory

This review summarizes the results of recent ab initio molecular orbital calculations performed on DNA constituents that attempt to further our understanding of the radiation-induced damage to DNA. The results reviewed include calculations performed on the four individual DNA bases, the base pairs in gas phase and modelled aqueous phase, the deoxyribose moiety, and a portion of the sugar-phosphate backbone. The emphasis is on the electron affinities and ionization potentials of the radical species calculated under various conditions (i.e. gas phase, aqueous phase, proton transfer, base stacking), as it has been shown that the initial ion radical distribution is largely a function of these two properties. Theoretical studies of the electronic excited states of the individual bases and radioprotection of the biomolecule by various thiol compounds are also reviewed. Finally, a summary is provided to allow for further elaboration of the current model for radiation damage to DNA and to show the present advantages and limitations of ab initio theory in the investigation of such processes.

Solvent bridging sites in A- and B-DNA helices

Nucleotide hydration is important for the understanding of the stability of and the transitions between the different helical conformations of DNA. We have used energy minimization and geometric criteria in order to look for possible sites for solvent which can bridge more than one polar or charged atomic group on a nucleotide. Such bridging sites between phosphate groups have been seen experimentally and used to explain the A to B transition. We show that these phosphate bridging sites occur at energy minima around A-DNA but do not occur around B-DNA. We also find that there are further low energy bridging sites which depend on sequence and which enable the more economical hydration of the A form.

Hydration of nucleic acid bases studied using novel atom-atom potential functions

New simple atom-atom potential functions for simulating behavior of nucleic acids and their fragments in aqueous solutions are suggested. These functions contains terms which are inversely proportional to the first (electrostatics), sixth (or tenth for the atoms, forming hydrogen bonds) and twelfth (repulsion of all the atoms) powers of interatomic distance. For the refinement of the potential function parameters calculations of ice lattice energy, potential energy and configuration of small clusters consisting of water and nucleic acid base molecules as well as Monte Carlo simulation of liquid water were performed. Calculations using new potential functions give rise to more linear hydrogen bonds between water and base molecules than using other potentials. Sites of preferential hydration of five nucleic bases - uracil, thymine, cytosine, guanine and adenine as well as of 6,6,9-trimethyladenine were found. In the most energetically favourable sites water molecular interacts with two adjacent hydrophilic centres of the base. Studies of interaction of the bases with several water molecules showed that water-water interactions play an important role in the arrangement of the nearest to the base water molecules. Hydrophilic centres are connected by "bridges" formed by hydrogen bonded water molecules. The results obtained are consistent with crystallographic and mass-spectrometric data.

Potential derived point charge model study of electrostatic interaction energies in some complexes of water with uracil, thymine, and cytosine

Potential derived (PD) point charges and segmental multipole moments are calculated for water, uracil, thymine, and cytosine using STO-3G quality wave functions. The PD point charges are used to estimate the electrostatic interaction energies for a series of complexes of water with these nucleic acid bases. It is shown here that the results obtained using simple PD charge model is very similar to those obtained from more elaborate segmental multipole moment analysis.