Literature DB >> 21639432

Conical intersections in solution: formulation, algorithm, and implementation with combined quantum mechanics/molecular mechanics method.

Ganglong Cui1, Weitao Yang.   

Abstract

The significance of conical intersections in photophysics, photochemistry, and photodissociation of polyatomic molecules in gas phase has been demonstrated by numerous experimental and theoretical studies. Optimization of conical intersections of small- and medium-size molecules in gas phase has currently become a routine optimization process, as it has been implemented in many electronic structure packages. However, optimization of conical intersections of small- and medium-size molecules in solution or macromolecules remains inefficient, even poorly defined, due to large number of degrees of freedom and costly evaluations of gradient difference and nonadiabatic coupling vectors. In this work, based on the sequential quantum mechanics and molecular mechanics (QM/MM) and QM/MM-minimum free energy path methods, we have designed two conical intersection optimization methods for small- and medium-size molecules in solution or macromolecules. The first one is sequential QM conical intersection optimization and MM minimization for potential energy surfaces; the second one is sequential QM conical intersection optimization and MM sampling for potential of mean force surfaces, i.e., free energy surfaces. In such methods, the region where electronic structures change remarkably is placed into the QM subsystem, while the rest of the system is placed into the MM subsystem; thus, dimensionalities of gradient difference and nonadiabatic coupling vectors are decreased due to the relatively small QM subsystem. Furthermore, in comparison with the concurrent optimization scheme, sequential QM conical intersection optimization and MM minimization or sampling reduce the number of evaluations of gradient difference and nonadiabatic coupling vectors because these vectors need to be calculated only when the QM subsystem moves, independent of the MM minimization or sampling. Taken together, costly evaluations of gradient difference and nonadiabatic coupling vectors in solution or macromolecules can be reduced significantly. Test optimizations of conical intersections of cyclopropanone and acetaldehyde in aqueous solution have been carried out successfully.
© 2011 American Institute of Physics

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Year:  2011        PMID: 21639432      PMCID: PMC3124537          DOI: 10.1063/1.3593390

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  57 in total

1.  Excited-state properties and environmental effects for protonated schiff bases: a theoretical study.

Authors:  Adélia J A Aquino; Mario Barbatti; Hans Lischka
Journal:  Chemphyschem       Date:  2006-10-13       Impact factor: 3.102

Review 2.  QM/MM studies of enzymes.

Authors:  Hans Martin Senn; Walter Thiel
Journal:  Curr Opin Chem Biol       Date:  2007-02-16       Impact factor: 8.822

Review 3.  Isomerization through conical intersections.

Authors:  Benjamin G Levine; Todd J Martínez
Journal:  Annu Rev Phys Chem       Date:  2007       Impact factor: 12.703

4.  Solvent effect on conical intersections in excited-state 9H-adenine: radiationless decay mechanism in polar solvent.

Authors:  Shohei Yamazaki; Shigeki Kato
Journal:  J Am Chem Soc       Date:  2007-02-14       Impact factor: 15.419

5.  Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: sequential sampling and optimization on the potential of mean force surface.

Authors:  Hao Hu; Zhenyu Lu; Jerry M Parks; Steven K Burger; Weitao Yang
Journal:  J Chem Phys       Date:  2008-01-21       Impact factor: 3.488

6.  Photodynamics in complex environments: ab initio multiple spawning quantum mechanical/molecular mechanical dynamics.

Authors:  Aaron M Virshup; Chutintorn Punwong; Taras V Pogorelov; Beth A Lindquist; Chaehyuk Ko; Todd J Martínez
Journal:  J Phys Chem B       Date:  2009-03-19       Impact factor: 2.991

Review 7.  P450 enzymes: their structure, reactivity, and selectivity-modeled by QM/MM calculations.

Authors:  Sason Shaik; Shimrit Cohen; Yong Wang; Hui Chen; Devesh Kumar; Walter Thiel
Journal:  Chem Rev       Date:  2010-02-10       Impact factor: 60.622

8.  Ab initio based surface-hopping dynamics study on ultrafast internal conversion in cyclopropanone.

Authors:  Ganglong Cui; Weihai Fang
Journal:  J Phys Chem A       Date:  2011-02-14       Impact factor: 2.781

9.  Development and application of ab initio QM/MM methods for mechanistic simulation of reactions in solution and in enzymes.

Authors:  Hao Hu; Weitao Yang
Journal:  Theochem       Date:  2009-03-30

10.  Location of Two Seams in the Proximity of the C2v ππ* Minimum Energy Path of Formaldehyde.

Authors:  Luca De Vico; Roland Lindh
Journal:  J Chem Theory Comput       Date:  2009-01-13       Impact factor: 6.006

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  1 in total

1.  Hybrid dynamics simulation engine for metalloproteins.

Authors:  Manuel Sparta; David Shirvanyants; Feng Ding; Nikolay V Dokholyan; Anastassia N Alexandrova
Journal:  Biophys J       Date:  2012-08-22       Impact factor: 4.033

  1 in total

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