Adenine-thymine molecular dynamics simulation. Conformation, hydration andmagnetic behaviour

In order to contribute to the knowledge of the properties of hydrogen bonds in macromolecular systems we performed molecular dynamics simulations of t he pair adenine-thymine base pair in SPC/E water. Interaction parameters of adenine and thymine atoms are those corresponding to the GROMOS force fiel d, except for atoms along the hydrogen bonds. In such cases the repulsion c oefficient of the van der Wals components of the potential were taken as tw ice the regular coefficients. Atomic partial charges were calculated with t he GAUSSIAN94 package including solvent effects. Simulations were done with the GROMOS86 simulation package working in the isothermal-isobaric ensembl e at 30 K and 1 atm. Two torsional angles were selected to describe the twi sting of the ring defined by the two hydrogen bonds and the atoms involved. The molecule was found to be mainly in two conformations, defined by the a bove-mentioned angles. Radial distribution functions of water oxygen atoms around different solute atoms suggest a non-polar behaviour but with little effect on the hydrogen bond network and the diffusion coefficient of bulk water. The adenine-thymine electrooptic and magnetic properties show slight changes during the overall run. (C) 1999 Elsevier Science B.V. All rights reserved.