Quantum mechanical methods for enzyme kinetics.

This review discusses methods for the incorporation of quantum mechanical effects into enzyme kinetics simulations in which the enzyme is an explicit part of the model. We emphasize three aspects: (a) use of quantum mechanical electronic structure methods such as molecular orbital theory and density functional theory, usually in conjunction with molecular mechanics; (b) treating vibrational motions quantum mechanically, either in an instantaneous harmonic approximation, or by path integrals, or by a three-dimensional wave function coupled to classical nuclear motion; (c) incorporation of multidimensional tunneling approximations into reaction rate calculations.

[1]  Eugene P. Wigner,et al.  The transition state method , 1938 .

[2]  M. Polanyi,et al.  The Theory of Rate Processes , 1942, Nature.

[3]  R. Zwanzig.  High‐Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases , 1954 .

[4]  F. Young.  Biochemistry , 1955, The Indian Medical Gazette.

[5]  Rudolph A. Marcus,et al.  On the Theory of Oxidation‐Reduction Reactions Involving Electron Transfer. I , 1956 .

[6]  James C. Keck,et al.  Statistical investigation of dissociation cross-sections for diatoms , 1962 .

[7]  J. Pople,et al.  Approximate Self-Consistent Molecular Orbital Theory. I. Invariant Procedures , 1965 .

[8]  R. Feynman,et al.  Quantum Mechanics and Path Integrals , 1965 .

[9]  H. Johnston.  Gas Phase Reaction Rate Theory , 1966 .

[10]  D. Truhlar,et al.  Potential energy surfaces for atom transfer reactions involving hydrogens and halogens , 1971 .

[11]  Martin Karplus,et al.  Calculation of ground and excited state potential surfaces of conjugated molecules. I. Formulation and parametrization , 1972 .

[12]  James B. Anderson,et al.  Statistical theories of chemical reactions. Distributions in the transition region , 1973 .

[13]  W. Jencks,et al.  Binding energy, specificity, and enzymic catalysis: the circe effect. , 2006, Advances in enzymology and related areas of molecular biology.

[14]  M. Levitt,et al.  Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. , 1976, Journal of molecular biology.

[15]  Charles H. Bennett,et al.  Molecular Dynamics and Transition State Theory: The Simulation of Infrequent Events , 1977 .

[16]  M. Dewar,et al.  Ground States of Molecules. 38. The MNDO Method. Approximations and Parameters , 1977 .

[17]  R. Boyd.  Macroscopic and microscopic restrictions on chemical kinetics , 1977 .

[18]  David Chandler,et al.  Statistical mechanics of isomerization dynamics in liquids and the transition state approximation , 1978 .

[19]  John A. Montgomery,et al.  Trajectory analysis of a kinetic theory for isomerization dynamics in condensed phases , 1979 .

[20]  B. C. Garrett,et al.  Variational Transition State Theory , 1980 .

[21]  James T. Hynes,et al.  The stable states picture of chemical reactions. II. Rate constants for condensed and gas phase reaction models , 1980 .

[22]  Donald G. Truhlar,et al.  Improved treatment of threshold contributions in variational transition-state theory , 1980 .

[23]  Arieh Warshel,et al.  An empirical valence bond approach for comparing reactions in solutions and in enzymes , 1980 .

[24]  Combining transition state theory with quasiclassical trajectory calculations. Part 1.—Collinear collisions , 1981 .

[25]  A. Warshel,et al.  EMPIRICAL VALENCE BOND CALCULATIONS OF ENZYME CATALYSIS * , 1981, Annals of the New York Academy of Sciences.

[26]  P. Pechukas,et al.  TRANSITION STATE THEORY , 1981 .

[27]  John C. Tully,et al.  Molecular dynamics of infrequent events: Thermal desorption of xenon from a platinum surface , 1981 .

[28]  P. Pechukas.  Recent Developments in Transition State Theory , 1982 .

[29]  M Karplus,et al.  Dynamical theory of activated processes in globular proteins. , 1982, Proceedings of the National Academy of Sciences of the United States of America.

[30]  Arieh Warshel,et al.  Dynamics of reactions in polar solvents. Semiclassical trajectory studies of electron-transfer and proton-transfer reactions , 1982 .

[31]  B. C. Garrett,et al.  Current status of transition-state theory , 1983 .

[32]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[33]  B. C. Garrett,et al.  Test of variational transition state theory with a large‐curvature tunneling approximation against accurate quantal reaction probabilities and rate coefficients for three collinear reactions with large reaction‐path curvature: Cl+HCl, Cl+DCl, and Cl+MuCl , 1983 .

[34]  B. C. Garrett,et al.  Variational transition state theory and tunneling for a heavy–light–heavy reaction using an ab initio potential energy surface. 37Cl+H(D) 35Cl→H(D) 37Cl+35Cl , 1983 .

[35]  W. J. Stevens,et al.  Effective Potentials in Molecular Quantum Chemistry , 1984 .

[36]  Scott F. Smith,et al.  SN2 reaction profiles in the gas phase and aqueous solution , 1984 .

[37]  Car,et al.  Unified approach for molecular dynamics and density-functional theory. , 1985, Physical review letters.

[38]  Faraday Discuss , 1985 .

[39]  Eamonn F. Healy,et al.  Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model , 1985 .

[40]  U. Singh,et al.  A combined ab initio quantum mechanical and molecular mechanical method for carrying out simulations on complex molecular systems: Applications to the CH3Cl + Cl− exchange reaction and gas phase protonation of polyethers , 1986 .

[41]  D. C. Clary,et al.  The Theory of Chemical Reaction Dynamics , 1986 .

[42]  B. C. Garrett,et al.  Phenomenological manifestations of large-curvature tunneling in hydride-transfer reactions , 1986 .

[43]  D. Truhlar,et al.  Embedded-cluster model for the effect of phonons on hydrogen surface diffusion on copper , 1986 .

[44]  Arieh Warshel,et al.  Theoretical correlation of structure and energetics in the catalytic reaction of trypsin , 1986 .

[45]  Warren J. Hehre,et al.  AB INITIO Molecular Orbital Theory , 1986 .

[46]  Gillan.  Quantum simulation of hydrogen in metals. , 1988, Physical review letters.

[47]  Kent R. Wilson,et al.  Molecular dynamics of a model SN1 reaction in water , 1987 .

[48]  B. C. Garrett,et al.  Dynamical bottlenecks and semiclassical tunneling paths for chemical reactions , 1987 .

[49]  Parr,et al.  Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. , 1988, Physical review. B, Condensed matter.

[50]  W. L. Jorgensen,et al.  The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. , 1988, Journal of the American Chemical Society.

[51]  A. Becke,et al.  Density-functional exchange-energy approximation with correct asymptotic behavior. , 1988, Physical review. A, General physics.

[52]  S. Creighton,et al.  Simulation of free energy relationships and dynamics of SN2 reactions in aqueous solution , 1988 .

[53]  G. Voth,et al.  Rigorous formulation of quantum transition state theory and its dynamical corrections , 1989 .

[54]  Theoretical study of solvation effects on chemical reactions. A combined quantum chemical/Monte Carlo study of the Meyer-Schuster reaction mechanism in water , 1989 .

[55]  Imre G. Csizmadia,et al.  New theoretical concepts for understanding organic reactions , 1989 .

[56]  D. Truhlar,et al.  Dynamical Formulation of Transition State Theory: Variational Transition States and Semiclassical Tunneling , 1989 .

[57]  James J. P. Stewart,et al.  MOPAC: A semiempirical molecular orbital program , 1990, J. Comput. Aided Mol. Des..

[58]  J. Tully.  Molecular dynamics with electronic transitions , 1990 .

[59]  Mark A. Ratner,et al.  Validity of time-dependent self-consistent-field (TDSCF) approximations for unimolecular dynamics: A test for photodissociation of the Xe-HI cluster , 1990 .

[60]  M. Karplus,et al.  A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations , 1990 .

[61]  Bohdan Waszkowycz,et al.  A combined quantum mechanical/molecular mechanical model of the potential energy surface of ester hydrolysis by the enzyme phospholipase A2 , 1991 .

[62]  Arieh Warshel,et al.  Computer Modeling of Chemical Reactions in Enzymes and Solutions , 1991 .

[63]  R. Gerber,et al.  Mixed Quantum/Classical Molecular Dynamics Simulations of Chemical Reactions in Clusters and in Solids , 1991 .

[64]  T. Poulos,et al.  A metal‐mediated hydride shift mechanism for xylose isomerase based on the 1.6 Å Streptomycs rubiginosus structure with xylitol and D‐xylose , 1991, Proteins.

[65]  B. C. Garrett,et al.  The definition of reaction coordinates for reaction‐path dynamics , 1991 .

[66]  M Karplus,et al.  Computer simulation and analysis of the reaction pathway of triosephosphate isomerase. , 1991, Biochemistry.

[67]  D. Truhlar,et al.  Direct dynamics calculations with NDDO (neglect of diatomic differential overlap) molecular orbital theory with specific reaction parameters , 1991 .

[68]  I. H. Hillier,et al.  Combined quantum mechanical–molecular mechanical study of catalysis by the enzyme phospholipase A2: an investigation of the potential energy surface for amide hydrolysis , 1991 .

[69]  Arieh Warshel,et al.  Simulations of quantum mechanical corrections for rate constants of hydride-transfer reactions in enzymes and solutions , 1991 .

[70]  J. Janin,et al.  Protein engineering of xylose (glucose) isomerase from Actinoplanes missouriensis. 3. Changing metal specificity and the pH profile by site-directed mutagenesis. , 1992, Biochemistry.

[71]  J. Gao,et al.  A priori evaluation of aqueous polarization effects through Monte Carlo QM-MM simulations. , 1992, Science.

[72]  M. Karplus,et al.  Simulation analysis of triose phosphate isomerase: conformational transition and catalysis. , 1992, Faraday discussions.

[73]  Jiali Gao,et al.  Absolute free energy of solvation from Monte Carlo simulations using combined quantum and molecular mechanical potentials , 1992 .

[74]  G. Voth,et al.  Calculation of quantum activation free energies for proton transfer reactions in polar solvents , 1992 .

[75]  A. Warshel,et al.  Computer simulations of enzymatic reactions: examination of linear free-energy relationships and quantum-mechanical corrections in the initial proton-transfer step of carbonic anhydrase. , 1992, Faraday discussions.

[76]  B. C. Garrett,et al.  Centroid‐density quantum rate theory: Dynamical treatment of classical recrossing , 1993 .

[77]  B. C. Garrett,et al.  Centroid‐density quantum rate theory: Variational optimization of the dividing surface , 1993 .

[78]  Àngels González-Lafont,et al.  Direct dynamics calculation of the kinetic isotope effect for an organic hydrogen-transfer reaction, including corner-cutting tunneling in 21 dimensions , 1993 .

[79]  Arieh Warshel,et al.  Simulation of enzyme reactions using valence bond force fields and other hybrid quantum/classical approaches , 1993 .

[80]  V. Davidson,et al.  Deuterium kinetic isotope effect and stopped-flow kinetic studies of the quinoprotein methylamine dehydrogenase. , 1993, Biochemistry.

[81]  J. Klinman,et al.  Unmasking of hydrogen tunneling in the horse liver alcohol dehydrogenase reaction by site-directed mutagenesis. , 1993, Biochemistry.

[82]  J. Åqvist,et al.  Computer Simulation of the CO2/HCO3- Interconversion Step in Human Carbonic Anhydrase I , 1993 .

[83]  Jiali Gao,et al.  Potential of mean force for the isomerization of DMF in aqueous solution: a Monte Carlo QM/MM simulation study , 1993 .

[84]  Àngels González-Lafont,et al.  MORATE: a program for direct dynamics calculations of chemical reaction rates by semiempirical molecular orbital theory , 1993 .

[85]  Kenneth M. Merz,et al.  Calculation of solvation free energies using a density functional/molecular dynamics coupled potential , 1993 .

[86]  Arieh Warshel,et al.  A Quantized Classical Path Approach for Calculations of Quantum Mechanical Rate Constants , 1993 .

[87]  Donald G. Truhlar,et al.  Molecular modeling of the kinetic isotope effect for the [1,5]-sigmatropic rearrangement of cis-1,3-pentadiene , 1993 .

[88]  B. C. Garrett,et al.  Tunneling in the Presence of a Bath: A Generalized Transition State Theory Approach , 1994 .

[89]  György G. Ferenczy,et al.  Quantum mechanical computations on very large molecular systems: The local self‐consistent field method , 1994, J. Comput. Chem..

[90]  Dagmar Ringe,et al.  X-ray crystallographic structures of D-xylose isomerase-substrate complexes position the substrate and provide evidence for metal movement during catalysis. , 1994, Biochemistry.

[91]  Jiali Gao.  Monte Carlo Quantum Mechanical-Configuration Interaction and Molecular Mechanics Simulation of Solvent Effects on the n .fwdarw. .pi.* Blue Shift of Acetone , 1994 .

[92]  M. Frisch,et al.  Ab Initio Calculation of Vibrational Absorption and Circular Dichroism Spectra Using Density Functional Force Fields , 1994 .

[93]  S. Hammes-Schiffer,et al.  Proton transfer in solution: Molecular dynamics with quantum transitions , 1994 .

[94]  Jiali Gao,et al.  Computation of Intermolecular Interactions with a Combined Quantum Mechanical and Classical Approach , 1994 .

[95]  Karen N. Allen,et al.  Role of the divalent metal ion in sugar binding, ring opening, and isomerization by D-xylose isomerase: replacement of a catalytic metal by an amino acid. , 1994, Biochemistry.

[96]  G. Voth,et al.  The formulation of quantum statistical mechanics based on the Feynman path centroid density. V. Quantum instantaneous normal mode theory of liquids , 1994 .

[97]  Gregory K. Schenter,et al.  A variational centroid density procedure for the calculation of transmission coefficients for asymmetric barriers at low temperature , 1995 .

[98]  B. Brooks,et al.  HIV-1 Protease Cleavage Mechanism Elucidated with Molecular Dynamics Simulation , 1995 .

[99]  Jiali Gao,et al.  Transition Structure and Substituent Effects on Aqueous Acceleration of the Claisen Rearrangement , 1995 .

[100]  Feliu Maseras,et al.  IMOMM: A new integrated ab initio + molecular mechanics geometry optimization scheme of equilibrium structures and transition states , 1995, J. Comput. Chem..

[101]  Jiali Gao.  AN AUTOMATED PROCEDURE FOR SIMULATING CHEMICAL REACTIONS IN SOLUTION. APPLICATION TO THE DECARBOXYLATION OF 3-CARBOXYBENZISOXAZOLE IN WATER , 1995 .

[102]  Donald G. Truhlar,et al.  Parameterization of NDDO wavefunctions using genetic algorithms. An evolutionary approach to parameterizing potential energy surfaces and direct dynamics calculations for organic reactions , 1995 .

[103]  W. Richards,et al.  Insights into Chorismate Mutase Catalysis from a Combined QM/MM Simulation of the Enzyme Reaction , 1995 .

[104]  Alexander D. MacKerell,et al.  An all-atom empirical energy function for the simulation of nucleic acids , 1995 .

[105]  Makarov,et al.  Quantum transition-state theory below the crossover temperature. , 1995, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[106]  S. Hammes-Schiffer,et al.  Nonadiabatic transition state theory and multiple potential energy surface molecular dynamics of infrequent events , 1995 .

[107]  P. Kollman,et al.  A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .

[108]  P. Comba,et al.  Molecular Modeling and Dynamics of Bioinorganic Systems , 1995 .

[109]  J. Klinman,et al.  [14] Hydrogen tunneling in enzyme catalysis , 1995 .

[110]  H. Berendsen,et al.  CALCULATION OF THE PROTON-TRANSFER RATE USING DENSITY-MATRIX EVOLUTION AND MOLECULAR-DYNAMICS SIMULATIONS - INCLUSION OF THE PROTON EXCITED-STATES , 1995 .

[111]  A. Lambeir,et al.  Wild-type and mutant D-xylose isomerase from Actinoplanes missouriensis: metal-ion dissociation constants, kinetic parameters of deuterated and non-deuterated substrates and solvent-isotope effects. , 1995, The Biochemical journal.

[112]  W. Thiel,et al.  Hybrid Models for Combined Quantum Mechanical and Molecular Mechanical Approaches , 1996 .

[113]  D. York,et al.  Linear‐scaling semiempirical quantum calculations for macromolecules , 1996 .

[114]  Jiali Gao,et al.  Optimization of the Lennard‐Jones parameters for a combined ab initio quantum mechanical and molecular mechanical potential using the 3‐21G basis set , 1996 .

[115]  Arieh Warshel,et al.  How Important Are Quantum Mechanical Nuclear Motions in Enzyme Catalysis , 1996 .

[116]  S. L. Dixon,et al.  Semiempirical molecular orbital calculations with linear system size scaling , 1996 .

[117]  H. Berendsen,et al.  Approach to nonadiabatic transitions by density matrix evolution and molecular dynamics simulations , 1996 .

[118]  R. Wyatt,et al.  Dynamics of molecules and chemical reactions , 1996 .

[119]  Jean-Louis Rivail,et al.  Quantum chemical computations on parts of large molecules: the ab initio local self consistent field method , 1996 .

[120]  Jean-Louis Rivail,et al.  HYBRID CLASSICAL QUANTUM FORCE FIELD FOR MODELING VERY LARGE MOLECULES , 1996 .

[121]  Alexander D. MacKerell,et al.  Progress toward chemical accuracy in the computer simulation of condensed phase reactions. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[122]  J. A. McCammon,et al.  Quantum-Classical Molecular Dynamics Simulations of Proton Transfer Processes in Molecular Complexes and in Enzymes , 1996 .

[123]  Jiali Gao,et al.  Hybrid Quantum and Molecular Mechanical Simulations: An Alternative Avenue to Solvent Effects in Organic Chemistry , 1996 .

[124]  H Liu,et al.  A combined quantum/classical molecular dynamics study of the catalytic mechanism of HIV protease. , 1996, Journal of molecular biology.

[125]  D. Truhlar,et al.  Variational transition state theory without the minimum-energy path , 1997 .

[126]  Haiyan Liu,et al.  The reaction pathway of the isomerization of d‐xylose catalyzed by the enzyme d‐xylose isomerase: A theoretical study , 1997, Proteins.

[127]  D. Nguyen,et al.  Simulation of the enzyme reaction mechanism of malate dehydrogenase. , 1997, Biochemistry.

[128]  Jill E. Gready,et al.  Hybrid Quantum and Molecular Mechanical (QM/MM) Studies on the Pyruvate to l-Lactate Interconversion in l-Lactate Dehydrogenase , 1997 .

[129]  E. Neria,et al.  Molecular dynamics of an enzyme reaction: proton transfer in TIM , 1997 .

[130]  P. Nordlund,et al.  Energetics of nucleophile activation in a protein tyrosine phosphatase. , 1997, Journal of molecular biology.

[131]  A. Turner,et al.  Transition-state structural refinement with GRACE and CHARMM: Realistic modelling of lactate dehydrogenase using a combined quantum/classical method , 1997 .

[132]  Jiali Gao,et al.  Energy components of aqueous solution: Insight from hybrid QM/MM simulations using a polarizable solvent model , 1997, J. Comput. Chem..

[133]  G. Schürer,et al.  Semi-Empirical Mo Calculations on Enzyme Reaction Mechanisms , 1997 .

[134]  Gregory K. Schenter,et al.  Generalized path integral based quantum transition state theory , 1997 .

[135]  N. Burton,et al.  PREDICTION OF TRANSITION STATE STRUCTURE IN PROTEIN TYROSINE PHOSPHATASE CATALYSIS USING A HYBRID QM/MM POTENTIAL , 1997 .

[136]  Calculation of the geometry of a small protein using semiempirical methods , 1997 .

[137]  N. Burton,et al.  Catalytic Mechanism of the Enzyme Papain: Predictions with a Hybrid Quantum Mechanical/Molecular Mechanical Potential , 1997 .

[138]  Donald G. Truhlar,et al.  Importance of Quantum Effects for C−H Bond Activation Reactions , 1997 .

[139]  C. Dellago,et al.  Transition path sampling and the calculation of rate constants , 1998 .

[140]  J. C. Phillips,et al.  Quantum dynamics of the femtosecond photoisomerization of retinal in bacteriorhodopsin. , 1998, Faraday discussions.

[141]  Iris Antes,et al.  On the Treatment of Link Atoms in Hybrid Methods , 1998 .

[142]  P. Kollman,et al.  Combined ab initio and Free Energy Calculations To Study Reactions in Enzymes and Solution: Amide Hydrolysis in Trypsin and Aqueous Solution , 1998 .

[143]  C. Carter,et al.  Active Species for the Ground-State Complex of Cytidine Deaminase: A Linear-Scaling Quantum Mechanical Investigation , 1998 .

[144]  Gregory A. Voth,et al.  Multistate Empirical Valence Bond Model for Proton Transport in Water , 1998 .

[145]  J. Gready,et al.  Investigating Enzyme Reaction Mechanisms with Quantum Mechanical-Molecular Mechanical Plus Molecular Dynamics Calculations , 1998 .

[146]  Manuel F. Ruiz-López,et al.  MODELING OF PEPTIDE HYDROLYSIS BY THERMOLYSIN. A SEMIEMPIRICAL AND QM/MM STUDY , 1998 .

[147]  Christoph Dellago,et al.  Efficient transition path sampling: Application to Lennard-Jones cluster rearrangements , 1998 .

[148]  M. Field,et al.  A Generalized Hybrid Orbital (GHO) Method for the Treatment of Boundary Atoms in Combined QM/MM Calculations , 1998 .

[149]  Jiali Gao,et al.  Walden-Inversion-Enforced Transition-State Stabilization in a Protein Tyrosine Phosphatase , 1998 .

[150]  J. Rivail,et al.  The Local Self-Consistent Field Principles and Applications to Combined Quantum Mechanical-Molecular Mechanical Computations on Biomacromolecular Systems , 1998 .

[151]  The Geometry of Water in Liquid Water from Hybrid Ab Initio-Monte Carlo and Density Functional-Molecular Dynamics Simulations , 1998 .

[152]  M Hodoscek,et al.  Catalytic mechanism of aldose reductase studied by the combined potentials of quantum mechanics and molecular mechanics. , 1998, Biophysical chemistry.

[153]  D. Truhlar,et al.  TESTING THE ACCURACY OF PRACTICAL SEMICLASSICAL METHODS: VARIATIONAL TRANSITION STATE THEORY WITH OPTIMIZED MULTIDIMENSIONAL TUNNELING , 1998 .

[154]  CORRELATION OF CALCULATED ACTIVATION ENERGIES WITH EXPERIMENTAL RATE CONSTANTS FOR AN ENZYME CATALYZED AROMATIC HYDROXYLATION , 1998 .

[155]  Darrin M. York,et al.  Quantum Mechanical Treatment of Biological Macromolecules in Solution Using Linear-Scaling Electronic Structure Methods , 1998 .

[156]  Donald L Thompson,et al.  Modern Methods for Multidimensional Dynamics Computations in Chemistry , 1998 .

[157]  S. Hammes‐Schiffer.  Mixed Quantum/Classical Dynamics of Hydrogen Transfer Reactions , 1998 .

[158]  N. Burton,et al.  Prediction of the mechanisms of enzyme-catalysed reactions using hybrid quantum mechanical/molecular mechanical methods. , 1998, Faraday discussions.

[159]  Bernard R. Brooks,et al.  HIV-1 protease cleavage mechanism: A theoretical investigation based on classical MD simulation and reaction path calculations using a hybrid QM/MM potential , 1998 .

[160]  Sándor Suhai,et al.  Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties , 1998 .

[161]  Alexander D. MacKerell,et al.  All-atom empirical potential for molecular modeling and dynamics studies of proteins. , 1998, The journal of physical chemistry. B.

[162]  P. Kollman,et al.  Encyclopedia of computational chemistry , 1998 .

[163]  Y. Mo,et al.  Theoretical analysis of electronic delocalization , 1998 .

[164]  A Method of Hybrid Quantum-Classical Calculations for Large Organometallic-Metallobiochemical Systems: Applications to Iron Picket-Fence Porphyrin and Vitamin B12 , 1998 .

[165]  C. Cramer,et al.  Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics. , 1999, Chemical reviews.

[166]  Paul Tavan,et al.  A hybrid method for solutes in complex solvents: Density functional theory combined with empirical force fields , 1999 .

[167]  M. Sutcliffe,et al.  Enzymatic H-transfer requires vibration-driven extreme tunneling. , 1999, Biochemistry.

[168]  K. Merz,et al.  Combined Quantum Mechanical/Molecular Mechanical Methodologies Applied to Biomolecular Systems , 1999 .

[169]  Isotope Effects on the ATCase-Catalyzed Reaction , 1999 .

[170]  I. Tuñón,et al.  Analysis of a concerted mechanism in β-lactam enzymatic hydrolysis. A quantum mechanics/molecular mechanics study , 1999 .

[171]  A. Mulholland,et al.  Combined quantum mechanical and molecular mechanical reaction pathway calculation for aromatic hydroxylation by p-hydroxybenzoate-3-hydroxylase. , 1999, Journal of molecular graphics & modelling.

[172]  S. Hammes-Schiffer,et al.  Improvement of the Internal Consistency in Trajectory Surface Hopping , 1999 .

[173]  Transition States in the Reaction Catalyzed by Malate Dehydrogenase , 1999 .

[174]  W. Richards,et al.  Modelling the catalytic reaction in human aldose reductase , 1999, Proteins.

[175]  Vicent Moliner,et al.  Catalytic Mechanism of Dihydrofolate Reductase Enzyme. A Combined Quantum-Mechanical/Molecular-Mechanical Characterization of Transition State Structure for the Hydride Transfer Step , 1999 .

[176]  Modeling the Citrate Synthase Reaction: QM/MM and Small Model Calculations , 1999 .

[177]  Weitao Yang,et al.  A Linear-Scaling Quantum Mechanical Investigation of Cytidine Deaminase , 1999 .

[178]  D. Truhlar,et al.  Nonequilibrium Solvation Effects for a Polyatomic Reaction in Solution , 1999 .

[179]  Iris Antes,et al.  Adjusted Connection Atoms for Combined Quantum Mechanical and Molecular Mechanical Methods , 1999 .

[180]  Kenneth M. Merz,et al.  Solvent Dynamics and Mechanism of Proton Transfer in Human Carbonic Anhydrase II , 1999 .

[181]  Y. Mo,et al.  A simple electrostatic model for trisilylamine: Theoretical examinations of the n ->sigma* negative hyperconjugation, p pi -> d pi bonding, and stereoelectronic interaction , 1999 .

[182]  A Modification of Path Integral Quantum Transition State Theory for Asymmetric and Metastable Potentials , 1999 .

[183]  O. Tapia,et al.  Transition state structure invariance to model system size and calculation levels: a QM/MM study of the carboxylation step catalyzed by Rubisco , 1999 .

[184]  Tai-Sung Lee,et al.  A pseudobond approach to combining quantum mechanical and molecular mechanical methods , 1999 .

[185]  S Suhai,et al.  QM/MM study of the active site of free papain and of the NMA-papain complex. , 1999, Journal of biomolecular structure & dynamics.

[186]  Kenneth M. Merz,et al.  The Role of Polarization and Charge Transfer in the Solvation of Biomolecules , 1999 .

[187]  M. Blomberg,et al.  Density functional theory of biologically relevant metal centers. , 2003, Annual review of physical chemistry.

[188]  Charge transfer interactions in biology: A new view of the protein-water interface , 1999 .

[189]  Gregory A. Voth,et al.  The computer simulation of proton transport in water , 1999 .

[190]  M. Field,et al.  Is There a Covalent Intermediate in the Viral Neuraminidase Reaction? A Hybrid Potential Free-Energy Study , 1999 .

[191]  Christoph Dellago,et al.  On the calculation of reaction rate constants in the transition path ensemble , 1999 .

[192]  M. Field,et al.  A Hybrid Density Functional Theory/Molecular Mechanics Study of Nickel−Iron Hydrogenase: Investigation of the Active Site Redox States , 1999 .

[193]  Kenneth M. Merz,et al.  Rationalization of the enantioselectivity of subtilisin in DMF , 1999 .

[194]  Kenneth M. Merz,et al.  Divide and Conquer Interaction Energy Decomposition , 1999 .

[195]  D. Truhlar,et al.  Quantum Mechanical Dynamical Effects in an Enzyme-Catalyzed Proton Transfer Reaction , 1999 .

[196]  I. Tuñón,et al.  Modeling β‐lactam interactions in aqueous solution through combined quantum mechanics–molecular mechanics methods , 1999 .

[197]  Ian H. Williams,et al.  Transition-state structural refinement with GRACE and CHARMM: Flexible QM/MM modelling for lactate dehydrogenase , 1999 .

[198]  Modelling of Transition States in Condensed Phase Reactivity Studies , 1999 .

[199]  Adrian J. Mulholland,et al.  Ab initio QM/MM study of the citrate synthase mechanism. A low-barrier hydrogen bond is not involved , 2000 .

[200]  G. Schürer,et al.  The Mode of Action of Phospholipase A2: Semiempirical MO Calculations Including the Protein Environment , 2000 .

[201]  V. Luzhkov,et al.  Computer Simulation of Primary Kinetic Isotope Effects in the Proposed Rate-limiting Step of the Glyoxalase I Catalyzed Reaction* , 2000, The Journal of Biological Chemistry.

[202]  P. Agarwal,et al.  Combining Electronic Structure Methods with the Calculation of Hydrogen Vibrational Wavefunctions: Application to Hydride Transfer in Liver Alcohol Dehydrogenase , 2000 .

[203]  J. Vervoort,et al.  Modelling flavin and substrate substituent effects on the activation barrier and rate of oxygen transfer by p‐hydroxybenzoate hydroxylase , 2000, FEBS letters.

[204]  Modelling the enantioselectivity of subtilisin in water and organic solvents: insights from molecular dynamics and quantum mechanical/molecular mechanical studies , 2000 .

[205]  Martin J. Field,et al.  The generalized hybrid orbital method for combined quantum mechanical/molecular mechanical calculations: formulation and tests of the analytical derivatives , 2000 .

[206]  R. Friesner,et al.  Frozen orbital QM/MM methods for density functional theory , 2000 .

[207]  D. Truhlar,et al.  Quantum Dynamics of Hydride Transfer in Enzyme Catalysis , 2000 .

[208]  Martin J. Field,et al.  A Hybrid-Potential Free-Energy Study of the Isomerization Step of the Acetohydroxy Acid Isomeroreductase Reaction , 2000 .

[209]  S. P. Webb,et al.  Fourier grid Hamiltonian multiconfigurational self-consistent-field: A method to calculate multidimensional hydrogen vibrational wavefunctions , 2000 .

[210]  Alistair P. Rendell,et al.  Comparison of linear-scaling semiempirical methods and combined quantum mechanical/molecular mechanical methods applied to enzyme reactions , 2000 .

[211]  A. Warshel,et al.  Remarkable rate enhancement of orotidine 5'-monophosphate decarboxylase is due to transition-state stabilization rather than to ground-state destabilization. , 2000, Biochemistry.

[212]  Flexible QM/MM modelling embraces alternative mechanisms for lactate dehydrogenase , 2000 .

[213]  J. Rivail,et al.  Insights in the Peptide Hydrolysis Mechanism by Thermolysin: A Theoretical QM/MM study , 2000 .

[214]  Y. Mo,et al.  Ab initio QM/MM simulations with a molecular orbital‐valence bond (MOVB) method: application to an SN2 reaction in water , 2000 .

[215]  E. Lau,et al.  The importance of reactant positioning in enzyme catalysis: a hybrid quantum mechanics/molecular mechanics study of a haloalkane dehalogenase. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[216]  J. Bertrán,et al.  A QM/MM Study of the Conformational Equilibria in the Chorismate Mutase Active Site. The Role of the Enzymatic Deformation Energy Contribution , 2000 .

[217]  E. Pai,et al.  Electrostatic stress in catalysis: structure and mechanism of the enzyme orotidine monophosphate decarboxylase. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[218]  J. Mccammon,et al.  Quantum-dynamical picture of a multistep enzymatic process: reaction catalyzed by phospholipase A(2). , 2000, Biophysical journal.

[219]  P. Kollman,et al.  QM-FE Calculations of Aliphatic Hydrogen Abstraction in Citrate Synthase and in Solution: Reproduction of the Effect of Enzyme Catalysis and Demonstration that an Enolate Rather than an Enol Is Formed , 2000 .

[220]  Iñaki Tuñón,et al.  A quantum mechanics/molecular mechanics study of the acylation reaction of TEM1 β-lactamase and penicillanate , 2000 .

[221]  Sharon Hammes-Schiffer,et al.  Computational Studies of the Mechanism for Proton and Hydride Transfer in Liver Alcohol Dehydrogenase , 2000 .

[222]  Nathalie Reuter,et al.  Frontier Bonds in QM/MM Methods: A Comparison of Different Approaches , 2000 .

[223]  Peter A. Kollman,et al.  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 , 2000 .

[224]  Lars Ridder,et al.  A Quantum Mechanical/Molecular Mechanical Study of the Hydroxylation of Phenol and Halogenated Derivatives by Phenol Hydroxylase , 2000 .

[225]  Y. Mo,et al.  An ab initio molecular orbital-valence bond (MOVB) method for simulating chemical reactions in solution , 2000 .

[226]  Weitao Yang,et al.  How Is the Active Site of Enolase Organized To Catalyze Two Different Reaction Steps , 2000 .

[227]  Donald G. Truhlar,et al.  Multiconfiguration molecular mechanics algorithm for potential energy surfaces of chemical reactions , 2000 .

[228]  Alistair P. Rendell,et al.  Comparison of enzyme polarization of ligands and charge‐transfer effects for dihydrofolate reductase using point‐charge embedded ab initio quantum mechanical and linear‐scaling semiempirical quantum mechanical methods , 2000 .

[229]  Weitao Yang,et al.  Free energy calculation on enzyme reactions with an efficient iterative procedure to determine minimum energy paths on a combined ab initio QM/MM potential energy surface , 2000 .

[230]  Seogjoo J. Jang,et al.  A relationship between centroid dynamics and path integral quantum transition state theory , 2000 .

[231]  J. Gready,et al.  Combined Quantum and Molecular Mechanics (QM/MM) Study of the Ionization State of 8-Methylpterin Substrate Bound to Dihydrofolate Reductase , 2000 .

[232]  P. Kollman,et al.  QM and QM–FE simulations on reactions of relevance to enzyme catalysis: trypsin, catechol O-methyltransferase, β-lactamase and pseudouridine synthase , 2000 .

[233]  Richard J. Hall,et al.  Aspects of hybrid QM/MM calculations: The treatment of the QM/MM interface region and geometry optimization with an application to chorismate mutase , 2000 .

[234]  P. Kollman,et al.  Why Does Trypsin Cleave BPTI so Slowly , 2000 .

[235]  U. Rothlisberger,et al.  A comparative study of galactose oxidase and active site analogs based on QM/MM Car-Parrinello simulations , 2000, JBIC Journal of Biological Inorganic Chemistry.

[236]  P. Agarwal,et al.  Hybrid approach for including electronic and nuclear quantum effects in molecular dynamics simulations of hydrogen transfer reactions in enzymes , 2001 .

[237]  M. Tuckerman,et al.  Heavy-atom skeleton quantization and proton tunneling in "intermediate-barrier" hydrogen bonds. , 2001, Physical review letters.

[238]  P. Kollman,et al.  Elucidating the nature of enzyme catalysis utilizing a new twist on an old methodology: quantum mechanical-free energy calculations on chemical reactions in enzymes and in aqueous solution. , 2001, Accounts of chemical research.

[239]  A. Warshel,et al.  Circe Effect versus Enzyme Preorganization: What Can Be Learned from the Structure of the Most Proficient Enzyme? , 2001, Chembiochem : a European journal of chemical biology.

[240]  Donald G. Truhlar,et al.  Molecular Mechanics for Chemical Reactions: A Standard Strategy for Using Multiconfiguration Molecular Mechanics for Variational Transition State Theory with Optimized Multidimensional Tunneling , 2001 .

[241]  Quantum chemical study of ester aminolysis catalyzed by a single adenine: a reference reaction for the ribosomal peptide synthesis. , 2001, Journal of the American Chemical Society.

[242]  S. Schwartz,et al.  Internal Enzyme Motions as a Source of Catalytic Activity: Rate-Promoting Vibrations and Hydrogen Tunneling , 2001 .

[243]  M. Field,et al.  A hybrid potential reaction path and free energy study of the chorismate mutase reaction. , 2001, Journal of the American Chemical Society.

[244]  B. C. Garrett,et al.  Variational transition state theory evaluation of the rate constant for proton transfer in a polar solvent , 2001 .

[245]  D. Truhlar,et al.  Improved algorithm for corner-cutting tunneling calculations , 2001 .

[246]  Efthimios Kaxiras,et al.  A QM/MM Implementation of the Self-Consistent Charge Density Functional Tight Binding (SCC-DFTB) Method , 2001 .

[247]  Sally A. Hindle,et al.  Quantum mechanical/molecular mechanical methods and the study of kinetic isotope effects: modelling the covalent junction region and application to the enzyme xylose isomerase , 2001 .

[248]  W. Richards,et al.  Quantum mechanical/molecular mechanical study of three stationary points along the deacylation step of the catalytic mechanism of elastase , 2001 .

[249]  Kamaldeep K. Chohan,et al.  QM/MM studies show substantial tunneling for the hydrogen-transfer reaction in methylamine dehydrogenase. , 2001, Journal of the American Chemical Society.

[250]  Donald G. Truhlar,et al.  Quantum mechanical tunneling in methylamine dehydrogenase , 2001 .

[251]  B. C. Garrett,et al.  The role of collective solvent coordinates and nonequilibrium solvation in charge-transfer reactions , 2001 .

[252]  J. M. Lluch,et al.  A QM/MM study of the racemization of vinylglycolate catalyzed by mandelate racemase enzyme. , 2001, Journal of the American Chemical Society.

[253]  D. Truhlar,et al.  Displaced-points path integral method for including quantum effects in the Monte Carlo evaluation of free energies , 2001 .

[254]  Walter Thiel,et al.  Molecular dynamics study of oxygenation reactions catalysed by the enzyme p-hydroxybenzoate hydroxylase , 2001 .

[255]  D. Truhlar,et al.  Inclusion of Quantum Mechanical Vibrational Energy in Reactive Potentials of Mean Force , 2001 .

[256]  Donald G. Truhlar,et al.  Test of variational transition state theory with multidimensional tunneling contributions against an accurate full-dimensional rate constant calculation for a six-atom system , 2001 .

[257]  Joanna Trylska,et al.  Parameterization of the approximate valence bond (AVB) method to describe potential energy surface in the reaction catalyzed by HIV‐1 protease , 2001 .

[258]  M. Karplus,et al.  Triosephosphate isomerase: a theoretical comparison of alternative pathways. , 2001, Journal of the American Chemical Society.

[259]  D. Truhlar,et al.  The treatment of classically forbidden electronic transitions in semiclassical trajectory surface hopping calculations , 2001 .

[260]  P. Kollman,et al.  Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions. , 2001, Annual review of biophysics and biomolecular structure.

[261]  A. Mulholland.  The QM/MM Approach to Enzymatic Reactions , 2001 .

[262]  Y. Mo,et al.  New insight on the origin of the unusual acidity of Meldrum's acid from ab initio and combined QM/MM simulation study. , 2001, Journal of the American Chemical Society.

[263]  D. Truhlar,et al.  Canonical variational theory for enzyme kinetics with the protein mean force and multidimensional quantum mechanical tunneling dynamics. Theory and application to liver alcohol dehydrogenase , 2001 .

[264]  Arieh Warshel,et al.  Energetics and Dynamics of Enzymatic Reactions , 2001 .

[265]  L. Pratt.  Molecular theory of hydrophobic effects: "She is too mean to have her name repeated.". , 2001, Annual review of physical chemistry.

[266]  J. Åqvist.  Modelling of Proton Transfer Reactions in Enzymes , 2002 .

[267]  Chemical Shifts in Amino Acids, Peptides, and Proteins: From Quantum Chemistry to Drug Design , 2002 .

[268]  Ramkumar Rajamani,et al.  Combined QM/MM study of the opsin shift in bacteriorhodopsin , 2002, J. Comput. Chem..