Investigation of hydrogen bond interactions through the use of force fields and ab initio molecular dynamics simulations

Hydrogen bonds are ubiquitous in nature and play a fundamental role in many biological systems due to the abundance of water in cellular environments. As one of the stronger intermolecular interactions, the presence of hydrogen bonds alters many structural and dynamical properties of a molecular system at a very fundamental level. Here, we investigate many hydrogen bonding systems through the use of molecular dynamics simulations utilizing both empirical force fields as well as ab initio potentials derived from electronic structure calculations, to understand the changes in the structural and dynamical properties of different systems in the presence of water with atomistic resolution. We investigate the changes of solutes in the presence of water and vice versa by looking at structural and dynamical properties upon solvation of different solutes ranging from simple anions to proteins. In particular, the anions we consider are Cl−, O₂−, and dimethylphosphate. Next, we will look at the role hydrogen bonds and water plays in the formation of a proton gradient by bacteriorhodopsin. To conclude, we investigate the changes in dynamical properties of water resulting from contacts with the protein surface of barnase.