Literature DB >> 12868114

Exploring potential energy surfaces for chemical reactions: an overview of some practical methods.

H Bernhard Schlegel1.   

Abstract

Potential energy surfaces form a central concept in the application of electronic structure methods to the study of molecular structures, properties, and reactivities. Recent advances in tools for exploring potential energy surfaces are surveyed. Methods for geometry optimization of equilibrium structures, searching for transition states, following reaction paths and ab initio molecular dynamics are discussed. For geometry optimization, topics include methods for large molecules, QM/MM calculations, and simultaneous optimization of the wave function and the geometry. Path optimization methods and dynamics based techniques for transition state searching and reaction path following are outlined. Developments in the calculation of ab initio classical trajectories in the Born-Oppenheimer and Car-Parrinello approaches are described. Copyright 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1514-1527, 2003

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Year:  2003        PMID: 12868114     DOI: 10.1002/jcc.10231

Source DB:  PubMed          Journal:  J Comput Chem        ISSN: 0192-8651            Impact factor:   3.376


  11 in total

1.  Catalytic mechanism of human DNA polymerase lambda with Mg2+ and Mn2+ from ab initio quantum mechanical/molecular mechanical studies.

Authors:  G Andrés Cisneros; Lalith Perera; Miguel García-Díaz; Katarzyna Bebenek; Thomas A Kunkel; Lee G Pedersen
Journal:  DNA Repair (Amst)       Date:  2008-08-30

2.  Accelerating chemical reactions: exploring reactive free-energy surfaces using accelerated ab initio molecular dynamics.

Authors:  Levi C T Pierce; Phineus R L Markwick; J Andrew McCammon; Nikos L Doltsinis
Journal:  J Chem Phys       Date:  2011-05-07       Impact factor: 3.488

3.  Ambient-Potential Composite Ewald Method for ab Initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulation.

Authors:  Timothy J Giese; Darrin M York
Journal:  J Chem Theory Comput       Date:  2016-05-26       Impact factor: 6.006

4.  Quantum Chemical Calculations to Trace Back Reaction Paths for the Prediction of Reactants.

Authors:  Yosuke Sumiya; Yu Harabuchi; Yuuya Nagata; Satoshi Maeda
Journal:  JACS Au       Date:  2022-04-22

5.  Gauging the flexibility of the active site in soybean lipoxygenase-1 (SLO-1) through an atom-centered density matrix propagation (ADMP) treatment that facilitates the sampling of rare events.

Authors:  Prasad Phatak; Isaiah Sumner; Srinivasan S Iyengar
Journal:  J Phys Chem B       Date:  2012-08-17       Impact factor: 2.991

6.  Reaction mechanism of the epsilon subunit of E. coli DNA polymerase III: insights into active site metal coordination and catalytically significant residues.

Authors:  G Andrés Cisneros; Lalith Perera; Roel M Schaaper; Lars C Pedersen; Robert E London; Lee G Pedersen; Thomas A Darden
Journal:  J Am Chem Soc       Date:  2009-02-04       Impact factor: 15.419

7.  Free Radical Isomerizations in Acetylene Bromoboration Reaction.

Authors:  Hugo Semrád; Ctibor Mazal; Markéta Munzarová
Journal:  Molecules       Date:  2021-04-25       Impact factor: 4.411

8.  Multiple environment single system quantum mechanical/molecular mechanical (MESS-QM/MM) calculations. 1. Estimation of polarization energies.

Authors:  Alexander J Sodt; Ye Mei; Gerhard König; Peng Tao; Ryan P Steele; Bernard R Brooks; Yihan Shao
Journal:  J Phys Chem A       Date:  2014-10-30       Impact factor: 2.781

9.  The lipopolysaccharide from Capnocytophaga canimorsus reveals an unexpected role of the core-oligosaccharide in MD-2 binding.

Authors:  Simon Ittig; Buko Lindner; Marco Stenta; Pablo Manfredi; Evelina Zdorovenko; Yuriy A Knirel; Matteo dal Peraro; Guy R Cornelis; Ulrich Zähringer
Journal:  PLoS Pathog       Date:  2012-05-03       Impact factor: 6.823

10.  An Efficient and Accurate Formalism for the Treatment of Large Amplitude Intramolecular Motion.

Authors:  Guillaume Reinisch; Kenji Miki; Gérard L Vignoles; Bryan M Wong; Chris S Simmons
Journal:  J Chem Theory Comput       Date:  2012-06-12       Impact factor: 6.006

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