Hydration of Nucleic Acid Bases Studied Using Novel Atom-Atom Potential Functions

Abstract

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.

Physical Nature of Hydrogen Bond

“…The facts indicated above substantiate the application of a number of model electrostatic potentials proposed or described in works [3,[9][10][11][12][13][14][15][16]. Those potentials allow one to explain the thermodynamic and the majority of kinetic properties of water, as well as many other systems.…”

“…It is a soft potential, whose parameters can be changed due to the interaction with neighbor molecules. This is a very important circumstance, which cannot be taken into account in the majority of phenomenological model potentials [11][12][13][14][15][16]. Unlike the original Stillinger-David potential [9], its generalized variant (GSD) more adequately involves the behavior of screening functions, which describe the effects of electron shell overlapping.…”

“…The variation of the dipole moment under the action of a neighbor molecule is one of the simplest manifestations of many-particle effects in the system. To estimate the influence of the second molecule, let us calculate the ratio µ (12) O /µ O between the dipole moments of the oxygen atom in the pair approximation (µ (12) O , see work [3]) and in the isolated water molecule (µ O ). The calculated dependence of µ (12) O /µ O on the distance between the oxygen atoms in two neighbor molecules is depicted in Fig.…”

Molecular dynamics study of crystalline water ices

“…Interactions between O and H atoms of water molecules were described using the PM potential [25]. Within the limits of this modeling potential it is supposed that the water molecule is rigid with the fixed bond angle HOH equal to the Note.…”

Nature of the Frequency Shift of Hydrogen Valence Vibrations in Water Molecules

“…On the one hand, the hydrogen bond is assumed to have a quantum-mechanical origin associated with a substantial overlapping of electron shells in the water molecule [15]. On the other hand, the thermodynamic and transport properties of water can be described quite satisfactorily with the help of intermolecular potentials [2,9,[16][17][18][19][20][21][22][23]. The latter have the structure…”