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

Part of the Springer Series in Bio-/Neuroinformatics book series (SSBN, volume 1)

Abstract

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.

Keywords

Water Molecule Polarizable Continuum Model External Potential Ammonium Group Collective Variable 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  1. 1.Institute for Chemistry of Organo-Metallic CompoundsNational Research Council of ItalySesto fiorentino (Firenze)Italy

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