A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations

Keywords

MNDO, Molecular dynamics, Force field (fiction), Quantum, Ab initio

References

• Calculations of electrostatic properties in proteins. Analysis of contributions from induced protein dipoles.Daniel Van Belle, Ignace Couplet, Martine Prévost — 1987
• Quantum and statistical mechanical studies of liquids. 10. Transferable intermolecular potential functions for water, alcohols, and ethers. Application to liquid waterWilliam L. Jorgensen — 2002
• Ab initio methods in quantum chemistryKenneth P. Lawley — 1987
• Computational Aspects for Large Chemical SystemsE. Clementi — 1980
• Electronic Population Analysis on LCAO–MO Molecular Wave Functions. IRobert S. Mulliken — 1955
• The active site of papain. All-atom study of interactions with protein matrix and solvent.J.A.C. Rullmann, M.N. Bellido, P.Th. van Duijnen — 1989
• Methods of Electronic Structure TheoryHenry F. Schaefer — 1977
• Approximate molecular orbital theoryJohn A. Pople, David L. Beveridge — 1970
• Molecular dynamics of the A+BC reaction in rare gas solutionJohn P. Bergsma, Jeffrey R. Reimers, Kent R. Wilson — 1986
• Proteins: A Theoretical Perspective of Dynamics, Structure, and ThermodynamicsCharles L. Brooks, Martin Karplus, B. Montgomery Pettitt — 1988
• Microwave spectrum and structure of hydrogen bonded water dimerT. R. Dyke, J. S. Muenter — 1974
• Ab initio and Monte Carlo calculations for a nucleophilic addition reaction in the gas phase and in aqueous solutionJeffry D. Madura, William L. Jorgensen — 1986
• Ground States of Molecules. 38. The MNDO Method. Approximations and ParametersMichael J. S. Dewar, Walter Thiel — 1977
• Calculation of ground and excited state potential surfaces of conjugated molecules. I. Formulation and parametrizationA. Warshel, Martin Karplus — 1972
• Extensive theoretical studies of the hydrogen‐bonded complexes (H2O)2, (H2O)2H+, (HF)2, (HF)2H+, F2H−, and (NH3)2Michael J. Frisch, Janet E. Del Bene, J. Stephen Binkley — 1986
• The relationship between proximity and reactivity. An ab initio study of the flexibility of the OH.bul. + CH4 hydrogen abstraction transition state and a force-field model for the transition states of intramolecular hydrogen abstractionsAndrea E. Dorigo, K. N. Houk — 1988
• An electron–water pseudopotential for condensed phase simulationJürgen Schnitker, Peter J. Rossky — 1987
• Abinitio study of the hydrogen bonding interactions of formamide with water and methanolPaul G. Jasien, Walter J. Stevens — 1986
• The computer simulation of polar liquidsDavid J. Adams, Eveline M. Adams, Graham Hills — 1979
• Environmental effects on H-bond potentials: A SCRF MO CNDO/2 study of some model systems.O. Tapia, Fredy Sussman, E. Poulain — 1978

Cited by

• Etudes de systèmes organométalliques et biologiques par des méthodes hybrides mécanique quantique/mécanique moléculaireMarius Retegan — 2009
• Catalytic mechanism of aldose reductase studied by the combined potentials of quantum mechanics and molecular mechanics.K.A. Kovaly — 1998
• Computational methods in flavin research.幸司 舘野 — 1999
• QM/MM investigations of organic chemistry oriented questions.Thomas Schmidt, Alexander Paasche, Christoph Grebner — 2014
• A quantum mechanic/molecular mechanic study of the wild-type and N155S mutant HIV-1 integrase complexed with diketo acid.Joaquín Adsuar — 2008
• The implementation of a fast and accurate QM/MM potential method in AmberS.E. Kuehn — 2008
• Biomolecular simulation: historical picture and future perspectives.V.A. Fateev, I. V. Frolov, Albert Schwarz — 2008
• Characterization of purified New Delhi metallo-β-lactamase-1.Gene R. Laczniak, Ann‐Marie Kennedy — 2011
• Spectral shifts of the n → π* and π → π* transitions of uracil based on a modified form of solvent reorganization energy.Myoung soon Kim, 이가현 — 2012
• Development and application of ab initio QM/MM methods for mechanistic simulation of reactions in solution and in enzymes淑子 大久保, 至 叶内, 弘貴 大野 — 2009
• Quantum delocalization of protons in the hydrogen-bond network of an enzyme active siteR. L. Engelstad, Edward G. Lovell — 2014
• The systems-theoretical view of chemical conceptsMarkus Reiher — 2003
• Protein Conformational Landscapes and Catalysis. Influence of Active Site Conformations in the Reaction Catalyzed by L-Lactate DehydrogenaseCarmen Senabre Llabata — 2015
• Polarizable coarse‐grained models for molecular dynamics simulation of liquid cyclohexaneR. Ellner — 2015
• Embedded mean-field theory.洋光 椿 — 2015
• Excited states in large molecular systems through polarizable embedding.Michael Beigl — 2016
• Quantum Mechanical/Molecular Mechanical Analysis of the Catalytic Mechanism of Phosphoserine PhosphataseSalvador Rueda — 2018
• Solution and computational studies of kinetic isotope effects in flavoprotein and quinoprotein catalyzed substrate oxidations as probes of enzymic hydrogen tunneling and mechanismJaswir Basran, Laura Masgrau, MJ Sutcliffe — 2005
• A Quantum Chemical Approach to Reactions in BiomoleculesNathalie Reuter, Michel Loos, Géerald Monard — 1997
• Computational modeling of protein kinases: Molecular basis for inhibition and catalysisYingting Liu — 2010

Related papers

• An investigation of the relative stabilities of the isomers of CF2N2: Comparison of ab initio and MNDO calculationsChristopher Glidewell, Derek Higgins, Colin Thomson — 1987
• Comparative ab initio and semi-empirical study of hydrogen bonded complexes of NH3 and H2OE. Laura Coitiño, Oscar N. Ventura, Ramón M. Sosa — 1992
• Analysis of the gas‐phase addition of water to formaldehyde: A semiempirical and ab initio study of bifunctional catalysis by H2OOscar N. Ventura, E. Laura Coitiño, Agustı́ Lledós — 1992
• Secondary structure dependence of amyloid‐β(1–40) on simulation techniques and force field parametersMurat Caliskan, Sunay Y. Mandaci, Vladimir N. Uversky — 2021
• A Comparative Study of Two Different Force Fields on Structural and Thermodynamics Character of H1 Peptide via Molecular Dynamics SimulationsZanxia Cao, Jihua Wang — 2010
• Development and Optimization of a New Force Field for Flexible Aluminosilicates, Enabling Fast Molecular Dynamics Simulations on Parallel ArchitecturesAndrea Gabrieli, Marco Sant, Pierfranco Demontis — 2013
• Molecular dynamics simulations of an apoliprotein A-I derived peptide in explicit waterAthanassios Stavrakoudis — 2008
• Molecular dynamics simulations of a DMSO/water mixture using the AMBER force fieldSławomir Stachura, Chris J. Malajczuk, Ricardo L. Mancera — 2018
• The oximes of cyclopropenone, cyclopropanone and acetone and their O- and N-protonated forms. An ab initio and semiempirical quantum chemical studyAndré Otto — 1993