Simulations of the solvent structure for macromolecules. I. Solvation of B‐DNA double helix at T = 300 K

Monte Carlo simulations are reported for a system of 447 water molecules enclosing a B‐DNA double‐helix fragment with 12 base pairs and the corresponding sugar and phosphate units. From a detailed analysis on the interaction energies and probability distributions (at a simulated temperature of 300 K), the water molecules can be partitioned into clusters strongly interacting with (1) the phosphates, (2) the sugars, (3) the sugars and the bases, and (4) the base pairs. In addition, transgroove and interphosphate filament of hydrogen‐bonded water molecules have been detected. From simulations performed with variable numbers of water molecules, a theoretical isotherm has been obtained, with the characteristic sigmoidal shape, known from absorption–desorption experiments on related systems. The expected main features for the structure of water molecules solvating B‐DNA with Na + counterions are briefly discussed at the end of the paper.