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Excited State Dynamics in Biomolecules

  1. Gerrit Groenhof1,
  2. Lars V. Schäfer1,
  3. Martial Boggio-Pasqua2,
  4. Michael A. Robb3

Published Online: 15 AUG 2009

DOI: 10.1002/3527600434.eap660

Encyclopedia of Applied Physics

Encyclopedia of Applied Physics

How to Cite

Groenhof, G., Schäfer, L. V., Boggio-Pasqua, M. and Robb, M. A. 2009. Excited State Dynamics in Biomolecules. Encyclopedia of Applied Physics. .

Author Information

  1. 1

    Max-Planck-Institute for Biophysical Chemistry, Department of Theoretical and Computational Biophysics, Göttingen, Germany

  2. 2

    IRSAMC, Université Paul Sabatier, Laboratoire de Chimie et Physique Quantiques, Toulouse, France

  3. 3

    Imperial College London, Department of Chemistry, London, SW7 2AZ, United Kingdom

Publication History

  1. Published Online: 15 AUG 2009

Abstract

Organisms have evolved a wide variety of mechanisms to utilize and respond to light. In many cases, the biological response is mediated by structural changes that follow photon absorption. These reactions typically occur at femto- to picosecond timescales. As the relevant time and spatial resolutions are notoriously hard to access experimentally, molecular dynamics (MD) simulations are the method of choice to study such ultrafast processes.

In the simulations, a multiconfigurational quantum mechanical (QM) description (CASSCF, CASPT2) is required to model the electronic rearrangement of those parts of the system that are involved in the absorption. For the remainder, typically consisting of the apoprotein and the solvent, a simple forcefield model (MM) suffices. QM/MM gradients have to be computed on-the-fly, and surface hopping procedures are needed to model the excited state decay. In this chapter, the computational framework underlying the atomistic simulation of photochemical events is reviewed and a few representative applications are discussed that demonstrate the validity of hybrid QM/MM approaches for photobiological reactions.

Keywords:

  • excited state dynamics;
  • force field;
  • molecular mechanics;
  • molecular dynamics;
  • molecular dynamics