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  Photochemical reactions in biological systems: probing the effect of the environment by means of hybrid quantum chemistry/molecular mechanics simulations.

Boggio-Pasqua, M., Burmeister, C., Robb, M. A., & Groenhof, G. (2012). Photochemical reactions in biological systems: probing the effect of the environment by means of hybrid quantum chemistry/molecular mechanics simulations. Physical Chemistry Chemical Physics, 14(22), 7912-7928. doi:10.1039/C2CP23628A.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-000F-9BF7-5 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0027-C66E-4
Genre: Journal Article

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Boggio-Pasqua, M., Author
Burmeister, C.1, Author              
Robb, M. A., Author
Groenhof, G.1, Author              
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1Department of Theoretical and Computational Biophysics, MPI for biophysical chemistry, Max Planck Society, ou_578631              

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 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 in a protein complex. The initial step in such cases is normally the photoisomerization of a highly conjugated prosthetic group. To understand better the factors controlling the isomerization, we perform atomistic molecular dynamics simulations. In this perspective article we briefly review the key theoretical concepts of photochemical reactions and present a practical simulation scheme for simulating photochemical reactions in biomolecular systems. In our scheme, a multi-configurational quantum mechanical description is used to model the electronic rearrangement for those parts of the system that are involved in the photon absorption. For the remainder, typically consisting of the apo-protein and the solvent, a simple force field model is used. The interactions in the systems are thus computed within a hybrid quantum/classical framework. Forces are calculated on-the-fly, and a diabatic surface hopping procedure is used to model the excited-state decay. To demonstrate how this method is used we review our studies on photoactivation of the photoactive yellow protein, a bacterial photoreceptor. We will show what information can be obtained from the simulations, and, by comparing to recent experimental findings, what the limitations of our simulations are.

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Language(s): eng - English
 Dates: 2012-03-272012
 Publication Status: Published in print
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 Rev. Method: Peer
 Identifiers: DOI: 10.1039/C2CP23628A
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Title: Physical Chemistry Chemical Physics
Source Genre: Journal
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Pages: - Volume / Issue: 14 (22) Sequence Number: - Start / End Page: 7912 - 7928 Identifier: -