First Principles Methods in Biology : From Continuum Models to Hybrid Ab initio Quantum Mechanics/Molecular Mechanics

First-principle (especially density functional theory)-based simulations are of paramount importance in studying biological reactivity and photophysics, as well as in the investigation of transition metal ions in biology and pharmacy. Either embedded in implicit (continuum models) or explicit molecular mechanics-based framework (the so-called quantum mechanics/molecular mechanics (QM/MM) methods), they are used to investigate problems, where the consideration of the electronic structure is indispensable. Here we briefly review some of the principles of these methods, with particular emphasis on hybrid Car–Parrinello/molecular mechanics, which has been developed by one of us (U.R). A brief survey of recent applications is also provided. We close this paper with a rather detailed discussion of continuum-based methodologies.