Literature DB >> 18956100

Free energies for biological electron transfer from QM/MM calculation: method, application and critical assessment.

Jochen Blumberger1.   

Abstract

Computer simulations of biological electron transfer reactions are reviewed with a focus on the calculation of reaction free energy (driving force) and reorganization free energy. Then a mixed quantum mechanical/molecular mechanical (QM/MM) approach is described which is designed for computation of these quantities for pure electron transfer reactions with large donor-acceptor separation distances. The method is applied to intra-protein electron transfer in Ru(bpy)(2)(im)His33 cytochrome c and the results compared to experimental data. Several modeling aspects which are important for successful calculation of free energies with QM/MM are discussed in detail.

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Year:  2008        PMID： 18956100     DOI： 10.1039/b807444e

Source DB:  PubMed          Journal:  Phys Chem Chem Phys        ISSN： 1463-9076            Impact factor:   3.676


  25 in total

1.  Calculating solution redox free energies with ab initio quantum mechanical/molecular mechanical minimum free energy path method.

Authors:  Xiancheng Zeng; Hao Hu; Xiangqian Hu; Weitao Yang
Journal:  J Chem Phys       Date:  2009-04-28       Impact factor: 3.488

Review 2.  A hybrid approach to simulation of electron transfer in complex molecular systems.

Authors:  Tomáš Kubař; Marcus Elstner
Journal:  J R Soc Interface       Date:  2013-07-24       Impact factor: 4.118

Review 3.  Biochemistry and theory of proton-coupled electron transfer.

Authors:  Agostino Migliore; Nicholas F Polizzi; Michael J Therien; David N Beratan
Journal:  Chem Rev       Date:  2014-04-01       Impact factor: 60.622

4.  Electron flow in multiheme bacterial cytochromes is a balancing act between heme electronic interaction and redox potentials.

Authors:  Marian Breuer; Kevin M Rosso; Jochen Blumberger
Journal:  Proc Natl Acad Sci U S A       Date:  2014-01-02       Impact factor: 11.205

5.  Computational evidence support the hypothesis of neuroglobin also acting as an electron transfer species.

Authors:  Licia Paltrinieri; Giulia Di Rocco; Gianantonio Battistuzzi; Marco Borsari; Marco Sola; Antonio Ranieri; Laura Zanetti-Polzi; Isabella Daidone; Carlo Augusto Bortolotti
Journal:  J Biol Inorg Chem       Date:  2017-04-04       Impact factor: 3.358

6.  2'-Deoxy-2'-fluoro-arabinonucleic acid: a valid alternative to DNA for biotechnological applications using charge transport.

Authors:  Ruijie D Teo; Elizabeth R Smithwick; Agostino Migliore
Journal:  Phys Chem Chem Phys       Date:  2019-10-24       Impact factor: 3.676

7.  On the Origins of the Linear Free Energy Relationships: Exploring the Nature of the Off-Diagonal Coupling Elements in S(N)2 Reactions.

Authors:  Edina Rosta; Arieh Warshel
Journal:  J Chem Theory Comput       Date:  2012-03-29       Impact factor: 6.006

8.  Mechanism of the Primary Charge Transfer Reaction in the Cytochrome bc1 Complex.

Authors:  Angela M Barragan; Klaus Schulten; Ilia A Solov'yov
Journal:  J Phys Chem B       Date:  2016-10-12       Impact factor: 2.991

9.  Fragment-based Quantum Mechanical/Molecular Mechanical Simulations of Thermodynamic and Kinetic Process of the Ru2+-Ru3+ Self-Exchange Electron Transfer.

Authors:  Xiancheng Zeng; Xiangqian Hu; Weitao Yang
Journal:  J Chem Theory Comput       Date:  2012-12-11       Impact factor: 6.006

10.  Quantum Mechanics/Molecular Mechanics Method Combined with Hybrid All-Atom and Coarse-Grained Model: Theory and Application on Redox Potential Calculations.

Authors:  Lin Shen; Weitao Yang
Journal:  J Chem Theory Comput       Date:  2016-03-15       Impact factor: 6.006
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