Simulations of the solvent structure for macromolecules. II. Structure of water solvating Na⁺‐B‐DNA at 300 K and a model for conformational transitions induced by solvent variations

The structure of water and its interaction energy with a fragment of B‐DNA composed of 12 base pairs and of the corresponding 24 sugar and 22 phosphate units and Na + ions (one at each phosphate group) are analyzed using Monte Carlo simulations. The sample of water molecules, at the simulated temperature of 300 K, is composed of 447 water molecules. The results are discussed either in terms of statistical analyses over the 2,000,000 simulated conformations (after equilibration) or with reference to an “average configuration.” Comparison is made to a simulation previously presented for the same system but without counterions. Isotherm at different relative humidity, hydration, and reactivity scales for different sites, the hydration number at each site, the structure of intraphosphate and interphosphate hydrogen‐bonded filaments of water are reported and discussed. The stabilization of the B‐conformation induced by the solvent with counterion (“ion‐induced compression effect”) is analyzed on the base of the above findings. A preliminary model to predict conformational transition in DNA is presented. The analyses reported are very detailed to allow refined interpretations of spectroscopic (infrared, Raman, and nmr) and scattering (x‐ray and neutron beam) data on DNA insolution.