Another Coarse Grain Model for Aqueous Solvation: WAT FOUR?

作者：Darre Leonardo; Machado Matias R; Dans Pablo D; Herrera Fernando E; Pantano Sergio^*

来源：Journal of Chemical Theory and Computation, 2010, 6(12): 3793-3807.

DOI：10.1021/ct100379f

Biological processes occur on space and time scales that are often unreachable for fully atomistic simulations. Therefore, simplified or coarse grain (CG) models for the theoretical study of these systems are frequently used. In this context, the accurate description of solvation properties remains an important and challenging field. In the present work, we report a new CG model based on the transient tetrahedral structures observed in pure water. Our representation lumps approximately 11 WATer molecules into FOUR tetrahedrally interconnected beads, hence the name WAT FOUR (WT4). Each bead carries a partial charge allowing the model to explicitly consider long-range electrostatics, generating its own dielectric permittivity and obviating the shortcomings of a uniform dielectric constant. We obtained a good representation of the aqueous environment for most biologically relevant temperature conditions in the range from 278 to 328 K. The model is applied to solvate simple CG electrolytes developed in this work (Na(+), K(+), and Cl(-)) and a recently published simplified representation of nucleic acids. In both cases, we obtained a good resemblance of experimental data and atomistic simulations. In particular, the solvation structure around DNA, partial charge neutralization by counterions, preference for sodium over potassium, and ion mediated minor groove narrowing as reported from X-ray crystallography are well reproduced by the present scheme. The set of parameters presented here opens the possibility of reaching the multimicroseconds time scale, including explicit solvation, ionic specificity, and long-range electrostatics, keeping nearly atomistic resolution with significantly reduced computational cost.

• 出版日期2010-12