When Water Plays an Active Role in Electronic Structure: Insights from First-Principles Molecular Dynamics Simulations of Biological Systems

In biological processes, the charge distribution is modified moving electrons and positive holes, mostly protons and metal ions, within hydrated macromolecular assemblies. These events are crucial to transfer the energy of chemical bonds into electric currents and ionic gradients, representing, respectively, energy flow and storage in cells. The modeling of the forces behind these processes is challenging, involving different space and time scales, ranging, at least, from confined electrons to macromolecules in the liquid water environment. Thanks to theoretical advances in first-principles computer simulations and to high performance computers, movements of electrons and transferable cations can be combined into robust and detailed dynamical models. This is also of great help in understanding the role of metal cofactors in important biological processes, like photosynthesis and oxidative stress. This chapter summarizes, through simple examples, statistical applications of density-functional theory, one of the most promising modeling techniques available for this level of description. Particular emphasis is devoted to bridge coarse grained models (built at whatever empirical level) with a refined description of the “reactive” portion of the system involving water molecules.