메뉴 건너뛰기




Volumn 120, Issue 37, 2016, Pages 9913-9921

Exploring the Dependence of QM/MM Calculations of Enzyme Catalysis on the Size of the QM Region

Author keywords

[No Author keywords available]

Indexed keywords

CHARGE TRANSFER; CHEMICAL ACTIVATION; FREE ENERGY;

EID: 84988822547     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/acs.jpcb.6b07203     Document Type: Article
Times cited : (103)

References (56)
  • 1
    • 84925389025 scopus 로고    scopus 로고
    • Multiscale Modeling of Biological Functions: From Enzymes to Molecular Machines (Nobel Lecture)
    • Warshel, A. Multiscale Modeling of Biological Functions: From Enzymes to Molecular Machines (Nobel Lecture) Angew. Chem., Int. Ed. 2014, 53, 10020-10031 10.1002/anie.201403689
    • (2014) Angew. Chem., Int. Ed. , vol.53 , pp. 10020-10031
    • Warshel, A.1
  • 2
    • 60349127442 scopus 로고    scopus 로고
    • QM/MM Methods for Biomolecular Systems
    • Senn, H. M.; Thiel, W. QM/MM Methods for Biomolecular Systems Angew. Chem., Int. Ed. 2009, 48, 1198-1229 10.1002/anie.200802019
    • (2009) Angew. Chem., Int. Ed. , vol.48 , pp. 1198-1229
    • Senn, H.M.1    Thiel, W.2
  • 3
    • 27144494583 scopus 로고    scopus 로고
    • Modelling Enzyme Reaction Mechanisms, Specificity and Catalysis
    • Mulholland, A. J. Modelling Enzyme Reaction Mechanisms, Specificity and Catalysis Drug Discovery Today 2005, 10, 1393-1402 10.1016/S1359-6446(05)03611-1
    • (2005) Drug Discovery Today , vol.10 , pp. 1393-1402
    • Mulholland, A.J.1
  • 5
    • 21244497608 scopus 로고    scopus 로고
    • Ab Initio Quantum Chemical and Mixed Quantum Mechanics/Molecular Mechanics (QM/MM) Methods for Studying Enzymatic Catalysis
    • Friesner, R. A.; Guallar, V. Ab Initio Quantum Chemical and Mixed Quantum Mechanics/Molecular Mechanics (QM/MM) Methods for Studying Enzymatic Catalysis Annu. Rev. Phys. Chem. 2005, 56, 389-427 10.1146/annurev.physchem.55.091602.094410
    • (2005) Annu. Rev. Phys. Chem. , vol.56 , pp. 389-427
    • Friesner, R.A.1    Guallar, V.2
  • 7
    • 84988053595 scopus 로고
    • 3Cl + Cl- Exchange Reaction and Gas Phase Protonation of Polyethers
    • 3Cl + Cl- Exchange Reaction and Gas Phase Protonation of Polyethers J. Comput. Chem. 1986, 7, 718-730 10.1002/jcc.540070604
    • (1986) J. Comput. Chem. , vol.7 , pp. 718-730
    • Singh, U.C.1    Kollman, P.A.2
  • 9
    • 74849125160 scopus 로고    scopus 로고
    • The EVB as a Quantitative Tool for Formulating Simulations and Analyzing Biological and Chemical Reactions
    • Kamerlin, S. C. L.; Warshel, A. The EVB as a Quantitative Tool for Formulating Simulations and Analyzing Biological and Chemical Reactions Faraday Discuss. 2010, 145, 71-106 10.1039/B907354J
    • (2010) Faraday Discuss. , vol.145 , pp. 71-106
    • Kamerlin, S.C.L.1    Warshel, A.2
  • 10
    • 84886650408 scopus 로고    scopus 로고
    • Quantifying the Mechanism of Phosphate Monoester Hydrolysis in Aqueous Solution by Evaluating the Relevant Ab Initio QM/MM Free-Energy Surfaces
    • Plotnikov, N. V.; Prasad, B. R.; Chakrabarty, S.; Chu, Z. T.; Warshel, A. Quantifying the Mechanism of Phosphate Monoester Hydrolysis in Aqueous Solution by Evaluating the Relevant Ab Initio QM/MM Free-Energy Surfaces J. Phys. Chem. B 2013, 117, 12807-12819 10.1021/jp4020146
    • (2013) J. Phys. Chem. B , vol.117 , pp. 12807-12819
    • Plotnikov, N.V.1    Prasad, B.R.2    Chakrabarty, S.3    Chu, Z.T.4    Warshel, A.5
  • 11
    • 84937949194 scopus 로고    scopus 로고
    • Mediation of Donor-Acceptor Distance in an Enzymatic Methyl Transfer Reaction
    • Zhang, J.; Kulik, H. J.; Martinez, T. J.; Klinman, J. P. Mediation of Donor-Acceptor Distance in an Enzymatic Methyl Transfer Reaction Proc. Natl. Acad. Sci. U. S. A. 2015, 112, 7954-7959 10.1073/pnas.1506792112
    • (2015) Proc. Natl. Acad. Sci. U. S. A. , vol.112 , pp. 7954-7959
    • Zhang, J.1    Kulik, H.J.2    Martinez, T.J.3    Klinman, J.P.4
  • 14
    • 79961242697 scopus 로고    scopus 로고
    • The Quantum Chemical Cluster Approach for Modeling Enzyme Reactions
    • Siegbahn, P. E. M.; Himo, F. The Quantum Chemical Cluster Approach for Modeling Enzyme Reactions Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2011, 1, 323-336 10.1002/wcms.13
    • (2011) Wiley Interdiscip. Rev.: Comput. Mol. Sci. , vol.1 , pp. 323-336
    • Siegbahn, P.E.M.1    Himo, F.2
  • 15
    • 79952261796 scopus 로고    scopus 로고
    • Comparison of QM-Only and QM/MM Models for the Mechanism of Tyrosinase
    • Siegbahn, P. E. M.; Borowski, T. Comparison of QM-Only and QM/MM Models for the Mechanism of Tyrosinase Faraday Discuss. 2011, 148, 109-117 10.1039/C004378H
    • (2011) Faraday Discuss. , vol.148 , pp. 109-117
    • Siegbahn, P.E.M.1    Borowski, T.2
  • 16
    • 77949263093 scopus 로고    scopus 로고
    • Quantum Cluster Size and Solvent Polarity Effects on the Geometries and Mossbauer Properties of the Active Site Model for Ribonucleotide Reductase Intermediate X: A Density Functional Theory Study
    • Han, W. G.; Noodleman, L. Quantum Cluster Size and Solvent Polarity Effects on the Geometries and Mossbauer Properties of the Active Site Model for Ribonucleotide Reductase Intermediate X: A Density Functional Theory Study Theor. Chem. Acc. 2010, 125, 305-317 10.1007/s00214-009-0566-4
    • (2010) Theor. Chem. Acc. , vol.125 , pp. 305-317
    • Han, W.G.1    Noodleman, L.2
  • 17
    • 79955878968 scopus 로고    scopus 로고
    • Quantum Chemical Modeling of Enzymatic Reactions: The Case of Decarboxylation
    • Liao, R. Z.; Yu, J. G.; Himo, F. Quantum Chemical Modeling of Enzymatic Reactions: The Case of Decarboxylation J. Chem. Theory Comput. 2011, 7, 1494-1501 10.1021/ct200031t
    • (2011) J. Chem. Theory Comput. , vol.7 , pp. 1494-1501
    • Liao, R.Z.1    Yu, J.G.2    Himo, F.3
  • 18
    • 58149265260 scopus 로고    scopus 로고
    • Quantum Chemical Modeling of the Dehalogenation Reaction of Haloalcohol Dehalogenase
    • Hopmann, K. H.; Himo, F. Quantum Chemical Modeling of the Dehalogenation Reaction of Haloalcohol Dehalogenase J. Chem. Theory Comput. 2008, 4, 1129-1137 10.1021/ct8000443
    • (2008) J. Chem. Theory Comput. , vol.4 , pp. 1129-1137
    • Hopmann, K.H.1    Himo, F.2
  • 19
    • 18444364203 scopus 로고    scopus 로고
    • Methyl Transfer in Glycine N-Methyltransferase. A Theoretical Study
    • Velichkova, P.; Himo, F. Methyl Transfer in Glycine N-Methyltransferase. A Theoretical Study J. Phys. Chem. B 2005, 109, 8216-8219 10.1021/jp0443254
    • (2005) J. Phys. Chem. B , vol.109 , pp. 8216-8219
    • Velichkova, P.1    Himo, F.2
  • 20
    • 73049101676 scopus 로고    scopus 로고
    • The Reaction Mechanism of Phenylethanolamine N-Methyltransferase: A Density Functional Theory Study
    • Georgieva, P.; Wu, Q.; McLeish, M. J.; Himo, F. The Reaction Mechanism of Phenylethanolamine N-Methyltransferase: A Density Functional Theory Study Biochim. Biophys. Acta, Proteins Proteomics 2009, 1794, 1831-1837 10.1016/j.bbapap.2009.08.022
    • (2009) Biochim. Biophys. Acta, Proteins Proteomics , vol.1794 , pp. 1831-1837
    • Georgieva, P.1    Wu, Q.2    McLeish, M.J.3    Himo, F.4
  • 21
    • 77952400211 scopus 로고    scopus 로고
    • Quantum Chemical Modeling of Enzymatic Reactions: The Case of Histone Lysine Methyltransferase
    • Georgieva, P.; Himo, F. Quantum Chemical Modeling of Enzymatic Reactions: The Case of Histone Lysine Methyltransferase J. Comput. Chem. 2010, 31, 1707-1714 10.1002/jcc.21458
    • (2010) J. Comput. Chem. , vol.31 , pp. 1707-1714
    • Georgieva, P.1    Himo, F.2
  • 22
    • 84863698244 scopus 로고    scopus 로고
    • Convergence of Electronic Structure with the Size of the QM Region: Example of QM/MM NMR Shieldings
    • Flaig, D.; Beer, M.; Ochsenfeld, C. Convergence of Electronic Structure with the Size of the QM Region: Example of QM/MM NMR Shieldings J. Chem. Theory Comput. 2012, 8, 2260-2271 10.1021/ct300036s
    • (2012) J. Chem. Theory Comput. , vol.8 , pp. 2260-2271
    • Flaig, D.1    Beer, M.2    Ochsenfeld, C.3
  • 23
    • 84943455476 scopus 로고    scopus 로고
    • Converging Nuclear Magnetic Shielding Calculations with Respect to Basis and System Size in Protein Systems
    • Hartman, J. D.; Neubauer, T. J.; Caulkins, B. G.; Mueller, L. J.; Beran, G. J. Converging Nuclear Magnetic Shielding Calculations with Respect to Basis and System Size in Protein Systems J. Biomol. NMR 2015, 62, 327-340 10.1007/s10858-015-9947-2
    • (2015) J. Biomol. NMR , vol.62 , pp. 327-340
    • Hartman, J.D.1    Neubauer, T.J.2    Caulkins, B.G.3    Mueller, L.J.4    Beran, G.J.5
  • 24
    • 70350402094 scopus 로고    scopus 로고
    • A Convergence Study of QM/MM Isomerization Energies with the Selected Size of the QM Region for Peptidic Systems
    • Sumowski, C. V.; Ochsenfeld, C. A Convergence Study of QM/MM Isomerization Energies with the Selected Size of the QM Region for Peptidic Systems J. Phys. Chem. A 2009, 113, 11734-11741 10.1021/jp902876n
    • (2009) J. Phys. Chem. A , vol.113 , pp. 11734-11741
    • Sumowski, C.V.1    Ochsenfeld, C.2
  • 25
    • 84856432368 scopus 로고    scopus 로고
    • The Transition of Human Estrogen Sulfotransferase from Generalist to Specialist Using Directed Enzyme Evolution
    • Amar, D.; Berger, I.; Amara, N.; Tafa, G.; Meijler, M. M.; Aharoni, A. The Transition of Human Estrogen Sulfotransferase from Generalist to Specialist Using Directed Enzyme Evolution J. Mol. Biol. 2012, 416, 21-32 10.1016/j.jmb.2011.12.013
    • (2012) J. Mol. Biol. , vol.416 , pp. 21-32
    • Amar, D.1    Berger, I.2    Amara, N.3    Tafa, G.4    Meijler, M.M.5    Aharoni, A.6
  • 27
    • 79952607247 scopus 로고    scopus 로고
    • On the Convergence of QM/MM Energies
    • Hu, L.; Soderhjelm, P.; Ryde, U. On the Convergence of QM/MM Energies J. Chem. Theory Comput. 2011, 7, 761-777 10.1021/ct100530r
    • (2011) J. Chem. Theory Comput. , vol.7 , pp. 761-777
    • Hu, L.1    Soderhjelm, P.2    Ryde, U.3
  • 28
    • 84863696796 scopus 로고    scopus 로고
    • Comparison of QM-Only and QM/MM Models for the Mechanism of Tungsten-Dependent Acetylene Hydratase
    • Liao, R. Z.; Thiel, W. Comparison of QM-Only and QM/MM Models for the Mechanism of Tungsten-Dependent Acetylene Hydratase J. Chem. Theory Comput. 2012, 8, 3793-3803 10.1021/ct3000684
    • (2012) J. Chem. Theory Comput. , vol.8 , pp. 3793-3803
    • Liao, R.Z.1    Thiel, W.2
  • 29
    • 84865055429 scopus 로고    scopus 로고
    • A Meta-Analysis of the Val158met COMT Polymorphism and Violent Behavior in Schizophrenia
    • Singh, J. P.; Volavka, J.; Czobor, P.; Van Dorn, R. A. A Meta-Analysis of the Val158met COMT Polymorphism and Violent Behavior in Schizophrenia PLoS One 2012, 7, e43423 10.1371/journal.pone.0043423
    • (2012) PLoS One , vol.7 , pp. e43423
    • Singh, J.P.1    Volavka, J.2    Czobor, P.3    Van Dorn, R.A.4
  • 30
    • 84924064113 scopus 로고    scopus 로고
    • Empirical Valence Bond Simulations of the Hydride Transfer Step in the Monoamine Oxidase B Catalyzed Metabolism of Dopamine
    • Repič, M.; Vianello, R.; Purg, M.; Duarte, F.; Bauer, P.; Kamerlin, S. C. L.; Mavri, J. Empirical Valence Bond Simulations of the Hydride Transfer Step in the Monoamine Oxidase B Catalyzed Metabolism of Dopamine Proteins: Struct., Funct., Genet. 2014, 82, 3347-3355 10.1002/prot.24690
    • (2014) Proteins: Struct., Funct., Genet. , vol.82 , pp. 3347-3355
    • Repič, M.1    Vianello, R.2    Purg, M.3    Duarte, F.4    Bauer, P.5    Kamerlin, S.C.L.6    Mavri, J.7
  • 31
    • 84937642270 scopus 로고    scopus 로고
    • Methyltransferases Do Not Work by Compression, Cratic, or Desolvation Effects, but by Electrostatic Preorganization
    • Lameira, J.; Bora, R. P.; Chu, Z. T.; Warshel, A. Methyltransferases Do Not Work by Compression, Cratic, or Desolvation Effects, but by Electrostatic Preorganization Proteins: Struct., Funct., Genet. 2015, 83, 318-330 10.1002/prot.24717
    • (2015) Proteins: Struct., Funct., Genet. , vol.83 , pp. 318-330
    • Lameira, J.1    Bora, R.P.2    Chu, Z.T.3    Warshel, A.4
  • 32
    • 0032501378 scopus 로고    scopus 로고
    • Importance of Correlated Motions in Forming Highly Reactive near Attack Conformations in Catechol O-Methyltransferase
    • Lau, E. Y.; Bruice, T. C. Importance of Correlated Motions in Forming Highly Reactive near Attack Conformations in Catechol O-Methyltransferase J. Am. Chem. Soc. 1998, 120, 12387-12394 10.1021/ja9827447
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 12387-12394
    • Lau, E.Y.1    Bruice, T.C.2
  • 33
    • 0034701258 scopus 로고    scopus 로고
    • QM-FE and Molecular Dynamics Calculations on Catechol O-Methyltransferase: Free Energy of Activation in the Enzyme and in Aqueous Solution and Regioselectivity of the Enzyme-Catalyzed Reaction
    • Kuhn, B.; Kollman, P. A. QM-FE and Molecular Dynamics Calculations on Catechol O-Methyltransferase: Free Energy of Activation in the Enzyme and in Aqueous Solution and Regioselectivity of the Enzyme-Catalyzed Reaction J. Am. Chem. Soc. 2000, 122, 2586-2596 10.1021/ja992218v
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 2586-2596
    • Kuhn, B.1    Kollman, P.A.2
  • 34
    • 84961983443 scopus 로고    scopus 로고
    • Theoretical Modeling of Enzyme Catalytic Power: Analysis of ″cratic″ and Electrostatic Factors in Catechol O-Methyltransferase
    • Roca, M.; Marti, S.; Andres, J.; Moliner, V.; Tunon, I.; Bertran, J.; Williams, I. H. Theoretical Modeling of Enzyme Catalytic Power: Analysis of ″Cratic″ and Electrostatic Factors in Catechol O-Methyltransferase J. Am. Chem. Soc. 2003, 125, 7726-7737 10.1021/ja0299497
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 7726-7737
    • Roca, M.1    Marti, S.2    Andres, J.3    Moliner, V.4    Tunon, I.5    Bertran, J.6    Williams, I.H.7
  • 35
    • 33845563602 scopus 로고    scopus 로고
    • Catalysis in Glycine N-Methyltransferase: Testing the Electrostatic Stabilization and Compression Hypothesis
    • Soriano, A.; Castillo, R.; Christov, C.; Andres, J.; Moliner, V.; Tunon, I. Catalysis in Glycine N-Methyltransferase: Testing the Electrostatic Stabilization and Compression Hypothesis Biochemistry 2006, 45, 14917-14925 10.1021/bi061319k
    • (2006) Biochemistry , vol.45 , pp. 14917-14925
    • Soriano, A.1    Castillo, R.2    Christov, C.3    Andres, J.4    Moliner, V.5    Tunon, I.6
  • 36
    • 56849125410 scopus 로고    scopus 로고
    • QM/MM Simulations for Methyl Transfer in Solution and Catalysed by Comt: Ensemble-Averaging of Kinetic Isotope Effects
    • Kanaan, N.; Pernia, J. J. R.; Williams, I. H. QM/MM Simulations for Methyl Transfer in Solution and Catalysed by Comt: Ensemble-Averaging of Kinetic Isotope Effects Chem. Commun. 2008, 6114-6116 10.1039/b814212b
    • (2008) Chem. Commun. , pp. 6114-6116
    • Kanaan, N.1    Pernia, J.J.R.2    Williams, I.H.3
  • 37
    • 73349120806 scopus 로고    scopus 로고
    • Stewart Computational Chemistry: Colorado Springs, CO
    • Stewart, J. J. P. Mopac2009; Stewart Computational Chemistry: Colorado Springs, CO, 2008.
    • (2008) Mopac2009
    • Stewart, J.J.P.1
  • 38
    • 35448937584 scopus 로고    scopus 로고
    • Optimization of Parameters for Semiempirical Methods V: Modification of Nddo Approximations and Application to 70 Elements
    • Stewart, J. J. P. Optimization of Parameters for Semiempirical Methods V: Modification of Nddo Approximations and Application to 70 Elements J. Mol. Model. 2007, 13, 1173-1213 10.1007/s00894-007-0233-4
    • (2007) J. Mol. Model. , vol.13 , pp. 1173-1213
    • Stewart, J.J.P.1
  • 39
    • 0000728542 scopus 로고
    • Microscopic and Semimicroscopic Calculations of Electrostatic Energies in Proteins by the Polaris and Enzymix Programs
    • Lee, F. S.; Chu, Z. T.; Warshel, A. Microscopic and Semimicroscopic Calculations of Electrostatic Energies in Proteins by the Polaris and Enzymix Programs J. Comput. Chem. 1993, 14, 161-185 10.1002/jcc.540140205
    • (1993) J. Comput. Chem. , vol.14 , pp. 161-185
    • Lee, F.S.1    Chu, Z.T.2    Warshel, A.3
  • 40
    • 44649191697 scopus 로고    scopus 로고
    • Crystal Structures of Human 108V and 108M Catechol O-Methyltransferase
    • Rutherford, K.; Le Trong, I.; Stenkamp, R. E.; Parson, W. W. Crystal Structures of Human 108V and 108M Catechol O-Methyltransferase J. Mol. Biol. 2008, 380, 120-130 10.1016/j.jmb.2008.04.040
    • (2008) J. Mol. Biol. , vol.380 , pp. 120-130
    • Rutherford, K.1    Le Trong, I.2    Stenkamp, R.E.3    Parson, W.W.4
  • 41
    • 84986519238 scopus 로고
    • The Weighted Histogram Analysis Method for Free-Energy Calculations on Biomolecules 0.1. The Method
    • Kumar, S.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A.; Rosenberg, J. M. The Weighted Histogram Analysis Method for Free-Energy Calculations on Biomolecules 0.1. The Method J. Comput. Chem. 1992, 13, 1011-1021 10.1002/jcc.540130812
    • (1992) J. Comput. Chem. , vol.13 , pp. 1011-1021
    • Kumar, S.1    Bouzida, D.2    Swendsen, R.H.3    Kollman, P.A.4    Rosenberg, J.M.5
  • 42
    • 84902211292 scopus 로고    scopus 로고
    • An Effective Coarse-Grained Model for Biological Simulations: Recent Refinements and Validations
    • Vicatos, S.; Rychkova, A.; Mukherjee, S.; Warshel, A. An Effective Coarse-Grained Model for Biological Simulations: Recent Refinements and Validations Proteins: Struct., Funct., Genet. 2014, 82, 1168-1185 10.1002/prot.24482
    • (2014) Proteins: Struct., Funct., Genet. , vol.82 , pp. 1168-1185
    • Vicatos, S.1    Rychkova, A.2    Mukherjee, S.3    Warshel, A.4
  • 43
    • 0025005059 scopus 로고
    • Free Energy Relationships in Metalloenzyme-Catalyzed Reactions. Calculations of the Effects of Metal Ion Substitutions in Staphylococcal Nuclease
    • Åqvist, J.; Warshel, A. Free Energy Relationships in Metalloenzyme-Catalyzed Reactions. Calculations of the Effects of Metal Ion Substitutions in Staphylococcal Nuclease J. Am. Chem. Soc. 1990, 112, 2860-2868 10.1021/ja00164a003
    • (1990) J. Am. Chem. Soc. , vol.112 , pp. 2860-2868
    • Åqvist, J.1    Warshel, A.2
  • 44
    • 84958818299 scopus 로고    scopus 로고
    • Effects of Active-Site Modification and Quaternary Structure on the Regioselectivity of Catechol-O-Methyltransferase
    • Law, B. J.; Bennett, M. R.; Thompson, M. L.; Levy, C.; Shepherd, S. A.; Leys, D.; Micklefield, J. Effects of Active-Site Modification and Quaternary Structure on the Regioselectivity of Catechol-O-Methyltransferase Angew. Chem., Int. Ed. 2016, 55, 2683-2687 10.1002/anie.201508287
    • (2016) Angew. Chem., Int. Ed. , vol.55 , pp. 2683-2687
    • Law, B.J.1    Bennett, M.R.2    Thompson, M.L.3    Levy, C.4    Shepherd, S.A.5    Leys, D.6    Micklefield, J.7
  • 45
    • 0242681519 scopus 로고    scopus 로고
    • Ab Initio Frozen Density Functional Calculations of Proton Transfer Reactions in Solution
    • Wesolowski, T.; Muller, R. P.; Warshel, A. Ab Initio Frozen Density Functional Calculations of Proton Transfer Reactions in Solution J. Phys. Chem. 1996, 100, 15444-15449 10.1021/jp961068x
    • (1996) J. Phys. Chem. , vol.100 , pp. 15444-15449
    • Wesolowski, T.1    Muller, R.P.2    Warshel, A.3
  • 46
    • 0001325667 scopus 로고    scopus 로고
    • Constraining the Electron Densities in DFT Method as an Effective Way for Ab Initio Studies of Metal-Catalyzed Reactions
    • Hong, G.; Strajbl, M.; Wesolowski, T. A.; Warshel, A. Constraining the Electron Densities in DFT Method as an Effective Way for Ab Initio Studies of Metal-Catalyzed Reactions J. Comput. Chem. 2000, 21, 1554-1561 10.1002/1096-987X(200012)21:16<1554::AID-JCC12>3.0.CO;2-I
    • (2000) J. Comput. Chem. , vol.21 , pp. 1554-1561
    • Hong, G.1    Strajbl, M.2    Wesolowski, T.A.3    Warshel, A.4
  • 47
    • 0017100947 scopus 로고
    • Theoretical Studies of Enzymic Reactions - Dielectric, Electrostatic and Steric Stabilization of Carbonium-Ion in Reaction of Lysozyme
    • Warshel, A.; Levitt, M. Theoretical Studies of Enzymic Reactions-Dielectric, Electrostatic and Steric Stabilization of Carbonium-Ion in Reaction of Lysozyme J. Mol. Biol. 1976, 103, 227-249 10.1016/0022-2836(76)90311-9
    • (1976) J. Mol. Biol. , vol.103 , pp. 227-249
    • Warshel, A.1    Levitt, M.2
  • 48
    • 0001763714 scopus 로고    scopus 로고
    • Frontier Bonds in QM/MM Methods: A Comparison of Different Approaches
    • Reuter, N.; Dejaegere, A.; Maigret, B.; Karplus, M. Frontier Bonds in QM/MM Methods: A Comparison of Different Approaches J. Phys. Chem. A 2000, 104, 1720-1735 10.1021/jp9924124
    • (2000) J. Phys. Chem. A , vol.104 , pp. 1720-1735
    • Reuter, N.1    Dejaegere, A.2    Maigret, B.3    Karplus, M.4
  • 49
    • 0242391122 scopus 로고    scopus 로고
    • The Amide Bond: Pitfalls and Drawbacks of the Link Atom Scheme
    • Ferré, N.; Olivucci, M. The Amide Bond: Pitfalls and Drawbacks of the Link Atom Scheme J. Mol. Struct.: THEOCHEM 2003, 632, 71-82 10.1016/S0166-1280(03)00289-6
    • (2003) J. Mol. Struct.: THEOCHEM , vol.632 , pp. 71-82
    • Ferré, N.1    Olivucci, M.2
  • 50
    • 0030573150 scopus 로고    scopus 로고
    • Quantum Chemical Computations on Parts of Large Molecules: The Ab Initio Local Self Consistent Field Method
    • Assfeld, X.; Rivail, J.-L. Quantum Chemical Computations on Parts of Large Molecules: The Ab Initio Local Self Consistent Field Method Chem. Phys. Lett. 1996, 263, 100-106 10.1016/S0009-2614(96)01165-7
    • (1996) Chem. Phys. Lett. , vol.263 , pp. 100-106
    • Assfeld, X.1    Rivail, J.-L.2
  • 51
    • 0000411659 scopus 로고    scopus 로고
    • A Generalized Hybrid Orbital (GHO) Method for the Treatment of Boundary Atoms in Combined QM/MM Calculations
    • Gao, J.; Amara, P.; Alhambra, C.; Field, M. J. A Generalized Hybrid Orbital (GHO) Method for the Treatment of Boundary Atoms in Combined QM/MM Calculations J. Phys. Chem. A 1998, 102, 4714-4721 10.1021/jp9809890
    • (1998) J. Phys. Chem. A , vol.102 , pp. 4714-4721
    • Gao, J.1    Amara, P.2    Alhambra, C.3    Field, M.J.4
  • 52
    • 0000125682 scopus 로고    scopus 로고
    • Frozen Orbital QM/MM Methods for Density Functional Theory
    • Murphy, R. B.; Philipp, D. M.; Friesner, R. A. Frozen Orbital QM/MM Methods for Density Functional Theory Chem. Phys. Lett. 2000, 321, 113-120 10.1016/S0009-2614(00)00289-X
    • (2000) Chem. Phys. Lett. , vol.321 , pp. 113-120
    • Murphy, R.B.1    Philipp, D.M.2    Friesner, R.A.3
  • 53
    • 0001582558 scopus 로고    scopus 로고
    • A Pseudobond Approach to Combining Quantum Mechanical and Molecular Mechanical Methods
    • Zhang, Y.; Lee, T.-S.; Yang, W. A Pseudobond Approach to Combining Quantum Mechanical and Molecular Mechanical Methods J. Chem. Phys. 1999, 110, 46-54 10.1063/1.478083
    • (1999) J. Chem. Phys. , vol.110 , pp. 46-54
    • Zhang, Y.1    Lee, T.-S.2    Yang, W.3
  • 54
    • 24344484047 scopus 로고    scopus 로고
    • On Possible Pitfalls in Ab Initio Quantum Mechanics/Molecular Mechanics Minimization Approaches for Studies of Enzymatic Reactions
    • Klahn, M.; Braun-Sand, S.; Rosta, E.; Warshel, A. On Possible Pitfalls in Ab Initio Quantum Mechanics/Molecular Mechanics Minimization Approaches for Studies of Enzymatic Reactions J. Phys. Chem. B 2005, 109, 15645-15650 10.1021/jp0521757
    • (2005) J. Phys. Chem. B , vol.109 , pp. 15645-15650
    • Klahn, M.1    Braun-Sand, S.2    Rosta, E.3    Warshel, A.4
  • 56
    • 84971264954 scopus 로고    scopus 로고
    • Perspective: Defining and Quantifying the Role of Dynamics in Enzyme Catalysis
    • Warshel, A.; Bora, R. P. Perspective: Defining and Quantifying the Role of Dynamics in Enzyme Catalysis J. Chem. Phys. 2016, 144, 180901 10.1063/1.4947037
    • (2016) J. Chem. Phys. , vol.144 , pp. 180901
    • Warshel, A.1    Bora, R.P.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.