Mechanisms and Free Energies of Enzymatic Reactions

Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density

Lee, C., Yang, W., & Parr, R. G. (1988) · Physical Review B · doi:10.1103/physrevb.37.785 · Cited by 100,874

Density-functional exchange-energy approximation with correct asymptotic behavior

Becke, A. D. (1988) · Physical Review A · doi:10.1103/physreva.38.3098 · Cited by 53,711

Ab Initio Calculation of Vibrational Absorption and Circular Dichroism Spectra Using Density Functional Force Fields

Stephens, P. J., Devlin, F. J., Chabalowski, C. F., & Frisch, M. J. (1994) · The Journal of Physical Chemistry · doi:10.1021/j100096a001 · Cited by 23,248

A climbing image nudged elastic band method for finding saddle points and minimum energy paths

Henkelman, G., Uberuaga, B. P., & Jónsson, H. (2000) · The Journal of Chemical Physics · doi:10.1063/1.1329672 · Cited by 21,620

All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins

MacKerell, A. D., Bashford, D., Bellott, M., Dunbrack, R. L., Evanseck, J. D., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., et al. (1998) · The Journal of Physical Chemistry B · doi:10.1021/jp973084f · Cited by 14,311

Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model

Dewar, M. J. S., Zoebisch, E. G., Healy, E. F., & Stewart, J. J. P. (1985) · Journal of the American Chemical Society · doi:10.1021/ja00299a024 · Cited by 13,074

Density-functional theory of atoms and molecules

Patterson, J. D. (1989) · Annals of Nuclear Energy · doi:10.1016/0306-4549(89)90016-9 · Cited by 12,545

Density Functional Theory of Atoms and Molecules

Parr, R. G. (1980) · Horizons of Quantum Chemistry · doi:10.1007/978-94-009-9027-2_2 · Cited by 11,964

Unified Approach for Molecular Dynamics and Density-Functional Theory

Car, R., & Parrinello, M. (1985) · Physical Review Letters · doi:10.1103/physrevlett.55.2471 · Cited by 10,754

Ab initio molecular orbital theory

Hehre, W. J. (1976) · Accounts of Chemical Research · doi:10.1021/ar50107a003 · Cited by 7,930

Optimization of parameters for semiempirical methods I. Method

Stewart, J. J. P. (1989) · Journal of Computational Chemistry · doi:10.1002/jcc.540100208 · Cited by 7,633

Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling

Torrie, G. M., & Valleau, J. P. (1977) · Journal of Computational Physics · doi:10.1016/0021-9991(77)90121-8 · Cited by 6,091

Ground states of molecules. 38. The MNDO method. Approximations and parameters

Dewar, M. J. S., & Thiel, W. (1977) · Journal of the American Chemical Society · doi:10.1021/ja00457a004 · Cited by 5,128

Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme

Warshel, A., & Levitt, M. (1976) · Journal of Molecular Biology · doi:10.1016/0022-2836(76)90311-9 · Cited by 4,479

Design of Density Functionals by Combining the Method of Constraint Satisfaction with Parametrization for Thermochemistry, Thermochemical Kinetics, and Noncovalent Interactions

Zhao, Y., Schultz, N. E., & Truhlar, D. G. (2006) · Journal of Chemical Theory and Computation · doi:10.1021/ct0502763 · Cited by 3,743

Catalysis in chemistry and enzymology

Jencks, W. P. (1969) · Medical Entomology and Zoology · Cited by 3,217

High-Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases

Zwanzig, R. W. (1954) · The Journal of Chemical Physics · doi:10.1063/1.1740409 · Cited by 3,066

Density-functional thermochemistry. IV. A new dynamical correlation functional and implications for exact-exchange mixing

Becke, A. D. (1996) · The Journal of Chemical Physics · doi:10.1063/1.470829 · Cited by 2,769

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

Field, M. J., Bash, P. A., & Karplus, M. (1990) · Journal of Computational Chemistry · doi:10.1002/jcc.540110605 · Cited by 2,466

An Introduction to Statistical Thermodynamics

Hill, T. L., & Gillis, J. (1961) · Physics Today · doi:10.1063/1.3057470 · Cited by 2,207

Free energy calculations: Applications to chemical and biochemical phenomena

Kollman, P. (1993) · Chemical Reviews · doi:10.1021/cr00023a004 · Cited by 2,101

Force Fields for Protein Simulations

Ponder, J. W., & Case, D. A. (2003) · Advances in Protein Chemistry · doi:10.1016/s0065-3233(03)66002-x · Cited by 1,903

Structure and Mechanism in Protein Science

Fersht, A. (1998) · Cited by 1,882

IMOMM: A new integrated ab initio + molecular mechanics geometry optimization scheme of equilibrium structures and transition states

Maseras, F., & Morokuma, K. (1995) · Journal of Computational Chemistry · doi:10.1002/jcc.540160911 · Cited by 1,721

Design of Density Functionals That Are Broadly Accurate for Thermochemistry, Thermochemical Kinetics, and Nonbonded Interactions

Zhao, Y., & Truhlar, D. G. (2005) · The Journal of Physical Chemistry A · doi:10.1021/jp050536c · Cited by 1,708

Essentials of computational chemistry

Cramer, C. J. (2004) · Cited by 1,317

A Perspective on Enzyme Catalysis

Benkovic, S. J., & Hammes-Schiffer, S. (2003) · Science · doi:10.1126/science.1085515 · Cited by 1,262

How Enzymes Work: Analysis by Modern Rate Theory and Computer Simulations

Garcia-Viloca, M., Gao, J., Karplus, M., & Truhlar, D. G. (2004) · Science · doi:10.1126/science.1088172 · Cited by 1,171

Introduction to statistical thermodynamics

(1960) · Journal of the Franklin Institute · doi:10.1016/0016-0032(60)90133-2 · Cited by 1,145

Molecular Quantum Mechanics

(1959) · Physics Today · doi:10.1063/1.3060748 · Cited by 1,138

Computer Modeling of Chemical Reactions in Enzymes and Solutions

Warshel, A. (1991) · Medical Entomology and Zoology · Cited by 1,128

Modern methods and algorithms of quantum chemistry

Grotendorst, J. (2000) · Cited by 1,115

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

Singh, U. C., & Kollman, P. A. (1986) · Journal of Computational Chemistry · doi:10.1002/jcc.540070604 · Cited by 1,112

Transition path sampling and the calculation of rate constants

Dellago, C., Bolhuis, P. G., Csajka, F. S., & Chandler, D. (1998) · The Journal of Chemical Physics · doi:10.1063/1.475562 · Cited by 1,064

An empirical valence bond approach for comparing reactions in solutions and in enzymes

Warshel, A., & Weiss, R. M. (1980) · Journal of the American Chemical Society · doi:10.1021/ja00540a008 · Cited by 934

The Depth of Chemical Time and the Power of Enzymes as Catalysts

Wolfenden, R., & Snider, M. J. (2001) · Accounts of Chemical Research · doi:10.1021/ar000058i · Cited by 930

A Proficient Enzyme

Radzicka, A., & Wolfenden, R. (1995) · Science · doi:10.1126/science.7809611 · Cited by 896

Binding Energy, Specificity, and Enzymic Catalysis: The Circe Effect

Jencks, W. P. (1975) · Advances in Enzymology - and Related Areas of Molecular Biology · doi:10.1002/9780470122884.ch4 · Cited by 854

Simulation of enzyme reactions using valence bond force fields and other hybrid quantum/classical approaches

Åqvist, J., & Warshel, A. (1993) · Chemical Reviews · doi:10.1021/cr00023a010 · Cited by 823

Structure and mechanism

Oppenheimer, N. J., & James, T. L. (1989) · Academic Press eBooks · Cited by 820

Current status of transition-state theory

Truhlar, D. G., Hase, W. L., & Hynes, J. T. (1983) · The Journal of Physical Chemistry · doi:10.1021/j100238a003 · Cited by 820

Enzymatic Reaction Mechanisms

Walsh, C. T. (1978) · Cited by 803

Crystal Structure of Human Protein Tyrosine Phosphatase 1B

Barford, D., Flint, A. J., & Tonks, N. K. (1994) · Science · doi:10.1126/science.8128219 · Cited by 758

Q UANTUM M ECHANICAL M ETHODS FOR E NZYME K INETICS

Gao, J., & Truhlar, D. G. (2002) · Annual Review of Physical Chemistry · doi:10.1146/annurev.physchem.53.091301.150114 · Cited by 733

Monte Carlo simulation of differences in free energies of hydration

Jorgensen, W. L., & Ravimohan, C. (1985) · The Journal of Chemical Physics · doi:10.1063/1.449208 · Cited by 729

Loop and Subdomain Movements in the Mechanism of Escherichia coli Dihydrofolate Reductase: Crystallographic Evidence,

Sawaya, M. R., & Kraut, J. (1997) · Biochemistry · doi:10.1021/bi962337c · Cited by 660

Enzymatic cyclization of squalene and oxidosqualene to sterols and triterpenes

Abe, I., Rohmer, M., & Prestwich, G. D. (1993) · Chemical Reviews · doi:10.1021/cr00022a009 · Cited by 645

Ab initio molecular dynamics simulation of liquid water: Comparison of three gradient-corrected density functionals

Sprik, M., Hutter, J., & Parrinello, M. (1996) · The Journal of Chemical Physics · doi:10.1063/1.471957 · Cited by 607

A Priori Evaluation of Aqueous Polarization Effects through Monte Carlo QM-MM Simulations

Gao, J., & Xia, X. (1992) · Science · doi:10.1126/science.1411573 · Cited by 576

Hybrid Quantum and Molecular Mechanical Simulations: An Alternative Avenue to Solvent Effects in Organic Chemistry

Gao, J. (1996) · Accounts of Chemical Research · doi:10.1021/ar950140r · Cited by 517

Structure, Dynamics, and Catalytic Function of Dihydrofolate Reductase

Schnell, J. R., Dyson, H. J., & Wright, P. E. (2004) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.33.110502.133613 · Cited by 516

Enhanced sampling in molecular dynamics: use of the time-dependent Hartree approximation for a simulation of carbon monoxide diffusion through myoglobin

Elber, R., & Karplus, M. (1990) · Journal of the American Chemical Society · doi:10.1021/ja00181a020 · Cited by 512

Computer Simulations of Enzyme Catalysis: Methods, Progress, and Insights

Warshel, A. (2003) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.32.110601.141807 · Cited by 503

Computational Biochemistry and Biophysics

(2001) · CRC Press eBooks · doi:10.1201/9780203903827 · Cited by 492

Hydrogen Tunneling in Enzyme Reactions

Cha, Y., Murray, C. J., & Klinman, J. P. (1989) · Science · doi:10.1126/science.2646716 · Cited by 475

Crystallographic analysis of the catalytic mechanism of haloalkane dehalogenase

Verschueren, K. H. G., Seljée, F., Rozeboom, H. J., Kalk, K. H., & Dijkstra, B. W. (1993) · Nature · doi:10.1038/363693a0 · Cited by 467

Network of coupled promoting motions in enzyme catalysis

Agarwal, P. K., Billeter, S. R., Rajagopalan, P. T. R., Benkovic, S. J., & Hammes-Schiffer, S. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.052005999 · Cited by 460

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

Zhang, Y., Liu, H., & Yang, W. (2000) · The Journal of Chemical Physics · doi:10.1063/1.480503 · Cited by 455

Multistate Empirical Valence Bond Model for Proton Transport in Water

Schmitt, U. W., & Voth, G. A. (1998) · The Journal of Physical Chemistry B · doi:10.1021/jp9818131 · Cited by 445

The Absolute Rate of Reactions in Condensed Phases

Wynne-Jones, W. F. K., & Eyring, H. (1935) · The Journal of Chemical Physics · doi:10.1063/1.1749713 · Cited by 442

Enzymatic reaction mechanisms

Hofmann, E. (1980) · Trends in Biochemical Sciences · doi:10.1016/0968-0004(80)90242-x · Cited by 432

A method for determining reaction paths in large molecules: Application to myoglobin

Elber, R., & Karplus, M. (1987) · Chemical Physics Letters · doi:10.1016/0009-2614(87)80576-6 · Cited by 430

Transition States of Biochemical Processes

(1978) · Springer eBooks · doi:10.1007/978-1-4684-9978-0 · Cited by 418

Enzyme Mechanisms for Polycyclic Triterpene Formation

Wendt, K. U., Schulz, G. E., Corey, E. J., & Liu, D. R. (2000) · Angewandte Chemie International Edition · doi:10.1002/1521-3773(20000818)39:16<2812::aid-anie2812>3.0.co;2-# · Cited by 416

Theoretical examination of the SN2 reaction involving chloride ion and methyl chloride in the gas phase and aqueous solution

Chandrasekhar, J., Smith, S. F., & Jorgensen, W. L. (1985) · Journal of the American Chemical Society · doi:10.1021/ja00287a028 · Cited by 385

Perfection in enzyme catalysis: the energetics of triosephosphate isomerase

Knowles, J. R., & Albery, W. J. (1977) · Accounts of Chemical Research · doi:10.1021/ar50112a001 · Cited by 364

Efficient transition path sampling: Application to Lennard-Jones cluster rearrangements

Dellago, C., Bolhuis, P. G., & Chandler, D. (1998) · The Journal of Chemical Physics · doi:10.1063/1.476378 · Cited by 363

Energetics and Dynamics of Enzymatic Reactions

Villà, J., & Warshel, A. (2001) · The Journal of Physical Chemistry B · doi:10.1021/jp011048h · Cited by 357

Application of localized molecular orbitals to the solution of semiempirical self-consistent field equations

Stewart, J. J. P. (1996) · International Journal of Quantum Chemistry · doi:10.1002/(sici)1097-461x(1996)58:2<133::aid-qua2>3.0.co;2-z · Cited by 356

Multidimensional Tunneling, Recrossing, and the Transmission Coefficient for Enzymatic Reactions

Pu, J., Gao, J., & Truhlar, D. G. (2006) · Chemical Reviews · doi:10.1021/cr050308e · Cited by 348

Acyl‐CoA dehydrogenases: A mechanistic overview

Ghisla, S., & Thorpe, C. (2004) · European Journal of Biochemistry · doi:10.1046/j.1432-1033.2003.03946.x · Cited by 344

Liquid Water from First Principles: Investigation of Different Sampling Approaches

Kuo, I.-F. W., Mundy, C. J., McGrath, M. J., Siepmann, J. I., VandeVondele, J., Sprik, M., Hutter, J., Chen, B., Klein, M. L., Mohamed, F., et al. (2004) · The Journal of Physical Chemistry B · doi:10.1021/jp047788i · Cited by 338

Combined Quantum Mechanical/Molecular Mechanical Methodologies Applied to Biomolecular Systems

Monard, G., & Merz, K. M. (1999) · Accounts of Chemical Research · doi:10.1021/ar970218z · Cited by 336

A hybrid method for solutes in complex solvents: Density functional theory combined with empirical force fields

Eichinger, M., Tavan, P., Hutter, J., & Parrinello, M. (1999) · The Journal of Chemical Physics · doi:10.1063/1.479049 · Cited by 323

On the calculation of reaction rate constants in the transition path ensemble

Dellago, C., Bolhuis, P. G., & Chandler, D. (1999) · The Journal of Chemical Physics · doi:10.1063/1.478569 · Cited by 322

Protein Dynamics in Enzymatic Catalysis: Exploration of Dihydrofolate Reductase

Radkiewicz, J. L., & Brooks, C. L. (2000) · Journal of the American Chemical Society · doi:10.1021/ja9913838 · Cited by 312

Why Enzymes Are Proficient Catalysts: Beyond the Pauling Paradigm

Zhang, X., & Houk, K. N. (2005) · Accounts of Chemical Research · doi:10.1021/ar040257s · Cited by 304

Chemical Basis for Enzyme Catalysis

Bruice, T. C., & Benkovic, S. J. (2000) · Biochemistry · doi:10.1021/bi0003689 · Cited by 302

Direct dynamics calculations with NDDO (neglect of diatomic differential overlap) molecular orbital theory with specific reaction parameters

Gonzalez-Lafont, A., Truong, T. N., & Truhlar, D. G. (1991) · The Journal of Physical Chemistry · doi:10.1021/j100165a009 · Cited by 289

The Application of the Theory of Absolute Reacton Rates to Proteins.

Eyring, H., & Stearn, A. E. (1939) · Chemical Reviews · doi:10.1021/cr60078a005 · Cited by 270

SN2 reaction profiles in the gas phase and aqueous solution

Chandrasekhar, J., Smith, S. F., & Jorgensen, W. L. (1984) · Journal of the American Chemical Society · doi:10.1021/ja00322a059 · Cited by 265

The rate of hydrolysis of phosphomonoester dianions and the exceptional catalytic proficiencies of protein and inositol phosphatases

Lad, C., Williams, N. H., & Wolfenden, R. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0631607100 · Cited by 260

Dissecting the catalytic mechanism of protein-tyrosinephosphatases.

Zhang, Z. Y., Wang, Y., & Dixon, J. E. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.5.1624 · Cited by 260

The Incorporation of Quantum Effects in Enzyme Kinetics Modeling

Truhlar, D. G., Gao, J., Alhambra, C., Garcia-Viloca, M., Corchado, J., Sánchez, M. L., & Villà, J. (2002) · Accounts of Chemical Research · doi:10.1021/ar0100226 · Cited by 258

Backbone Dynamics in Dihydrofolate Reductase Complexes: Role of Loop Flexibility in the Catalytic Mechanism

Osborne, M. J., Schnell, J., Benkovic, S. J., Dyson, H. J., & Wright, P. E. (2001) · Biochemistry · doi:10.1021/bi010621k · Cited by 253

Dispersed Polaron Simulations of Electron Transfer in Photosynthetic Reaction Centers

Warshel, A., Chu, Z. T., & Parson, W. W. (1989) · Science · doi:10.1126/science.2675313 · Cited by 220

Sidechain torsional potentials and motion of amino acids in porteins: bovine pancreatic trypsin inhibitor.

Gelin, B. R., & Karplus, M. (1975) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.72.6.2002 · Cited by 214

Reaction-Path Energetics and Kinetics of the Hydride Transfer Reaction Catalyzed by Dihydrofolate Reductase

Garcia-Viloca, M., Truhlar, D. G., & Gao, J. (2003) · Biochemistry · doi:10.1021/bi034824f · Cited by 212

Structure of the triosephosphate isomerase-phosphoglycolohydroxamate complex: an analog of the intermediate on the reaction pathway

Davenport, R. C., Bash, P. A., Seaton, B. A., Karplus, M., Petsko, G. A., & Ringe, D. (1991) · Biochemistry · doi:10.1021/bi00238a002 · Cited by 210

Electrostatic stress in catalysis: Structure and mechanism of the enzyme orotidine monophosphate decarboxylase

Wu, N., Mo, Y., Gao, J., et al. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.050417797 · Cited by 208

Correlated motion and the effect of distal mutations in dihydrofolate reductase

Rod, T. H., Radkiewicz, J. L., & Brooks, C. L. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1230801100 · Cited by 207

Crystal structure of haloalkane dehalogenase: an enzyme to detoxify halogenated alkanes.

Franken, S. M., Rozeboom, H. J., Kalk, K. H., & Dijkstra, B. W. (1991) · The EMBO Journal · doi:10.1002/j.1460-2075.1991.tb07647.x · Cited by 204

Ab Initio Calculations of Free Energy Barriers for Chemical Reactions in Solution

Muller, R. P., & Warshel, A. (1995) · The Journal of Physical Chemistry · doi:10.1021/j100049a009 · Cited by 196

Alternative view of enzyme reactions.

Dewar, M. J., & Storch, D. M. (1985) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.82.8.2225 · Cited by 195

X-ray analysis of D-xylose isomerase at 1.9 A: native enzyme in complex with substrate and with a mechanism-designed inactivator.

Carrell, H. L., Glusker, J. P., Burger, V, Manfre, F., Tritsch, D., & Biellmann, J. F. (1989) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.86.12.4440 · Cited by 191

Tunneling and Coupled Motion in the Escherichia coli Dihydrofolate Reductase Catalysis

Sikorski, R. S., Wang, L., Markham, K. A., Rajagopalan, P. T. R., Benkovic, S. J., & Kohen, A. (2004) · Journal of the American Chemical Society · doi:10.1021/ja031683w · Cited by 191

Canonical Variational Theory for Enzyme Kinetics with the Protein Mean Force and Multidimensional Quantum Mechanical Tunneling Dynamics. Theory and Application to Liver Alcohol Dehydrogenase

Alhambra, C., Corchado, J., Sánchez, M. L., Garcia-Viloca, M., Gao, J., & Truhlar, D. G. (2001) · The Journal of Physical Chemistry B · doi:10.1021/jp0120312 · Cited by 189

THE CYCLIZATION OF SQUALENE IN CHOLESTEROL SYNTHESIS

Woodward, R. B., & Bloch, K. (1953) · Journal of the American Chemical Society · doi:10.1021/ja01104a535 · Cited by 187

Evidence for a Functional Role of the Dynamics of Glycine-121 of Escherichia coli Dihydrofolate Reductase Obtained from Kinetic Analysis of a Site-Directed Mutant

Cameron, C. E., & Benkovic, S. J. (1997) · Biochemistry · doi:10.1021/bi9716231 · Cited by 182

Transition State Dynamics and Relaxation Processes in Solutions: A Frontier of Physical Chemistry

Voth, G. A., & Hochstrasser, R. M. (1996) · The Journal of Physical Chemistry · doi:10.1021/jp960317e · Cited by 178

Understanding enzyme-catalyzed proton abstraction from carbon acids: details of stepwise mechanisms for .beta.-elimination reactions

Gerlt, J. A., & Gassman, P. G. (1992) · Journal of the American Chemical Society · doi:10.1021/ja00041a004 · Cited by 177

The crystal structure and mechanism of orotidine 5′-monophosphate decarboxylase

Appleby, T. C., Kinsland, C., Begley, T. P., & Ealick, S. E. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.259441296 · Cited by 162

Extremely Large Isotope Effects in the Soybean Lipoxygenase-Linoleic Acid Reaction

Glickman, M. H., Wiseman, J. S., & Klinman, J. P. (1994) · Journal of the American Chemical Society · doi:10.1021/ja00081a060 · Cited by 161

Dual-Level Reaction-Path Dynamics (the /// Approach to VTST with Semiclassical Tunneling). Application to OH + NH3 .fwdarw. H2O + NH2

Corchado, J. C., Espinosa-Garcia, J., Hu, W.-P., Rossi, I., & Truhlar, D. G. (1995) · The Journal of Physical Chemistry · doi:10.1021/j100002a037 · Cited by 159

Quantum mechanics simulation of protein dynamics on long timescale

Liu, H., Elstner, M., Kaxiras, E., Frauenheim, T., Hermans, J., & Yang, W. (2001) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.1114 · Cited by 150

Enzymes work by solvation substitution rather than by desolvation.

Warshel, A., Åqvist, J., & Creighton, S. (1989) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.86.15.5820 · Cited by 149

Apparent NAC Effect in Chorismate Mutase Reflects Electrostatic Transition State Stabilization

Štrajbl, M., Shurki, A., Kato, M., & Warshel, A. (2003) · Journal of the American Chemical Society · doi:10.1021/ja0356481 · Cited by 146

Remarkable Rate Enhancement of Orotidine 5‘-Monophosphate Decarboxylase Is Due to Transition-State Stabilization Rather Than to Ground-State Destabilization

Warshel, A., Štrajbl, M., Villà­-Freixa, J., & Florián, J. (2000) · Biochemistry · doi:10.1021/bi000987h · Cited by 140

Optimal alignment for enzymatic proton transfer: Structure of the Michaelis complex of triosephosphate isomerase at 1.2-Å resolution

Jogl, G., Rozovsky, S., McDermott, A. E., & Tong, L. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0233793100 · Cited by 140

An Ab Initio Molecular Orbital−Valence Bond (MOVB) Method for Simulating Chemical Reactions in Solution

Mo, Y., & Gao, J. (2000) · The Journal of Physical Chemistry A · doi:10.1021/jp994053i · Cited by 138

Insights into Chorismate Mutase Catalysis from a Combined QM/MM Simulation of the Enzyme Reaction

Lyne, P. D., Mulholland, A. J., & Richards, W. G. (1995) · Journal of the American Chemical Society · doi:10.1021/ja00150a037 · Cited by 135

Quantum Mechanical Dynamical Effects in an Enzyme-Catalyzed Proton Transfer Reaction

Alhambra, C., Gao, J., Corchado, J. C., Villà­-Freixa, J., & Truhlar, D. G. (1999) · Journal of the American Chemical Society · doi:10.1021/ja9831655 · Cited by 135

Ensemble‐averaged variational transition state theory with optimized multidimensional tunneling for enzyme kinetics and other condensed‐phase reactions

Truhlar, D. G., Gao, J., Garcia‐Viloca, M., Alhambra, C., Corchado, J. C., Sanchez, M. L., & Poulsen, T. D. (2004) · International Journal of Quantum Chemistry · doi:10.1002/qua.20205 · Cited by 132

Dynamics of a flexible loop in dihydrofolate reductase from Escherichia coli and its implication for catalysis

Falzone, C. J., Wright, P. E., & Benkovic, S. J. (1994) · Biochemistry · doi:10.1021/bi00168a007 · Cited by 129

A Carboxylate Oxygen of the Substrate Bridges the Magnesium Ions at the Active Site of Enolase: Structure of the Yeast Enzyme Complexed with the Equilibrium Mixture of 2-Phosphoglycerate and Phosphoenolpyruvate at 1.8 Å Resolution,

Larsen, T. M., Wedekind, J. E., Rayment, I., & Reed, G. H. (1996) · Biochemistry · doi:10.1021/bi952859c · Cited by 128

How Much Do Enzymes Really Gain by Restraining Their Reacting Fragments?

Shurki, A., Štrajbl, M., Villà­-Freixa, J., & Warshel, A. (2002) · Journal of the American Chemical Society · doi:10.1021/ja012230z · Cited by 127

Improving the QM/MM Description of Chemical Processes: A Dual Level Strategy To Explore the Potential Energy Surface in Very Large Systems

Martı́, S., Moliner, V., & Tuñón, I. (2005) · Journal of Chemical Theory and Computation · doi:10.1021/ct0501396 · Cited by 126

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

Kollman, P. A., Kuhn, B., Donini, O., Peräkylä, M., Stanton, R., & Bakowies, D. (2000) · Accounts of Chemical Research · doi:10.1021/ar000032r · Cited by 125

Conformational Changes in the Active Site Loops of Dihydrofolate Reductase during the Catalytic Cycle

Venkitakrishnan, R. P., Zaborowski, E., McElheny, D., Benkovic, S. J., Dyson, H. J., & Wright, P. E. (2004) · Biochemistry · doi:10.1021/bi048119y · Cited by 124

Effect of Mutation on Enzyme Motion in Dihydrofolate Reductase

Watney, J. B., Agarwal, P. K., & Hammes‐Schiffer, S. (2003) · Journal of the American Chemical Society · doi:10.1021/ja028487u · Cited by 123

Generalized transition state theory in terms of the potential of mean force

Schenter, G. K., Garrett, B. C., & Truhlar, D. G. (2003) · The Journal of Chemical Physics · doi:10.1063/1.1597477 · Cited by 119

X-ray Crystallographic Structures of D-Xylose Isomerase-Substrate Complexes Position the Substrate and Provide Evidence for Metal Movement during Catalysis

Lavie, A., Allen, K. N., Petsko, G. A., & Ringe, D. (1994) · Biochemistry · doi:10.1021/bi00184a016 · Cited by 116

NO rebinding to myoglobin: a reactive molecular dynamics study

Meuwly, M., Becker, O. M., Stote, R. H., & Karplus, M. (2002) · Biophysical Chemistry · doi:10.1016/s0301-4622(02)00093-5 · Cited by 116

Multiple-Steering QM−MM Calculation of the Free Energy Profile in Chorismate Mutase

Crespo, A., Marti, M. A., Estrin, D. A., & Roitberg, A. E. (2005) · Journal of the American Chemical Society · doi:10.1021/ja0452830 · Cited by 116

Small Temperature Dependence of the Kinetic Isotope Effect for the Hydride Transfer Reaction Catalyzed by Escherichia coli Dihydrofolate Reductase

Pu, J., Ma, S., Gao, J., et al. (2005) · The Journal of Physical Chemistry B · doi:10.1021/jp051184c · Cited by 116

Refined X-ray Structures of Haloalkane Dehalogenase at pH 6·2 and pH 8·2 and Implications for the Reaction Mechanism

Verschueren, K. H. G., Franken, S. M., Rozeboom, H. J., Kalk, K. H., & Dijkstra, B. W. (1993) · Journal of Molecular Biology · doi:10.1006/jmbi.1993.1436 · Cited by 113

Macrophomate Synthase: QM/MM Simulations Address the Diels−Alder versus Michael−Aldol Reaction Mechanism

Guimarães, C. R. W., Udier–Blagović, M., & Jorgensen, W. L. (2005) · Journal of the American Chemical Society · doi:10.1021/ja043905b · Cited by 111

Evidence for Environmentally Coupled Hydrogen Tunneling during Dihydrofolate Reductase Catalysis

Maglia, G., & Allemann, R. K. (2003) · Journal of the American Chemical Society · doi:10.1021/ja035692g · Cited by 106

Transition state stabilization and substrate strain in enzyme catalysis: ab initio QM/MM modelling of the chorismate mutase reaction

Ranaghan, K. E., Ridder, L., Szefczyk, B., Sokalski, W. A., Hermann, J. C., & Mulholland, A. J. (2004) · Organic & Biomolecular Chemistry · doi:10.1039/b313759g · Cited by 104

The Active Site and Enzyme Action

Koshland, D. E. (1960) · Advances in enzymology and related areas of molecular biology/Advances in enzymology and related subjects · doi:10.1002/9780470122679.ch2 · Cited by 103

Experiences of a Large-Scale Application of 1,2-Dichloroethane Degrading Microorganisms for Groundwater Treatment

Stucki, G., & Thüer, M. (1995) · Environmental Science & Technology · doi:10.1021/es00009a028 · Cited by 103

Activation of Orotidine 5‘-Monophosphate Decarboxylase by Phosphite Dianion: The Whole Substrate is the Sum of Two Parts

Amyes, T. L., Richard, J. P., & Tait, J. J. (2005) · Journal of the American Chemical Society · doi:10.1021/ja055493s · Cited by 102

Molecular dynamics of an enzyme reaction: proton transfer in TIM

Neria, E., & Kuplus, M. (1997) · Chemical Physics Letters · doi:10.1016/s0009-2614(97)00068-7 · Cited by 101

Walden-Inversion-Enforced Transition-State Stabilization in a Protein Tyrosine Phosphatase

Alhambra, C., Wu, L., Zhang, Z., & Gao, J. (1998) · Journal of the American Chemical Society · doi:10.1021/ja972578n · Cited by 98

Effects of Protein Glycosylation on Catalysis: Changes in Hydrogen Tunneling and Enthalpy of Activation in the Glucose Oxidase Reaction

Kohen, A., Jónsson, T., & Klinman, J. P. (1997) · Biochemistry · doi:10.1021/bi962492r · Cited by 97

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van der Vaart, A., & Merz, K. M. (1999) · Journal of the American Chemical Society · doi:10.1021/ja9912325 · Cited by 96

How Is the Active Site of Enolase Organized To Catalyze Two Different Reaction Steps?

Liu, H., Zhang, Y., & Yang, W. (2000) · Journal of the American Chemical Society · doi:10.1021/ja9936619 · Cited by 96

Three-Dimensional Structure of Butyryl-CoA Dehydrogenase from Megasphaera elsdenii

Djordjević, S., Pace, C. P., Stankovich, M. T., & Kim, J. J. (1995) · Biochemistry · doi:10.1021/bi00007a009 · Cited by 96

Hydride transfer catalyzed by xylose isomerase: Mechanism and quantum effects

Garcia‐Viloca, M., Alhambra, C., Truhlar, D. G., & Gao, J. (2002) · Journal of Computational Chemistry · doi:10.1002/jcc.10154 · Cited by 94

Solute Solvent Dynamics and Energetics in Enzyme Catalysis: The SN2 Reaction of Dehalogenase as a General Benchmark

Olsson, M. H. M., & Warshel, A. (2004) · Journal of the American Chemical Society · doi:10.1021/ja047151c · Cited by 91

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Byun, K., Mo, Y., & Gao, J. (2001) · Journal of the American Chemical Society · doi:10.1021/ja001369r · Cited by 91

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Morokuma, K. (2002) · Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences · doi:10.1098/rsta.2002.0993 · Cited by 90

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Röthlisberger, U., Carloni, P., Doclo, K., & Parrinello, M. (2000) · JBIC Journal of Biological Inorganic Chemistry · doi:10.1007/s007750050368 · Cited by 88

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Ridder, L., Rietjens, I. M. C. M., Vervoort, J. J. M., & Mulholland, A. J. (2002) · Journal of the American Chemical Society · doi:10.1021/ja0256360 · Cited by 82

Functional role of a mobile loop of Escherichia coli dihydrofolate reductase in transition-state stabilization

Li, L., Wright, P. E., Benkovic, S. J., & Falzone, C. J. (1992) · Biochemistry · doi:10.1021/bi00149a012 · Cited by 80

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Corey, E. J., Virgil, S. C., & Sarshar, S. (1991) · Journal of the American Chemical Society · doi:10.1021/ja00021a055 · Cited by 78

Catalytic Power and Transition-State Stabilization

Schowen, R. L. (1978) · Springer eBooks · doi:10.1007/978-1-4684-9978-0_2 · Cited by 76

Contribution of Phosphate Intrinsic Binding Energy to the Enzymatic Rate Acceleration for Triosephosphate Isomerase

Amyes, T. L., O’Donoghue, A. C., & Richard, J. P. (2001) · Journal of the American Chemical Society · doi:10.1021/ja016754a · Cited by 76

Ab initio simulations of water and water ions

Tuckerman, M. E., Laasonen, K. E., Sprik, M., & Parrinello, M. (1994) · Journal of Physics Condensed Matter · doi:10.1088/0953-8984/6/23a/010 · Cited by 75

Promoting Modes and Demoting Modes in Enzyme-Catalyzed Proton Transfer Reactions: A Study of Models and Realistic Systems

Cui, Q., & Karplus, M. (2002) · The Journal of Physical Chemistry B · doi:10.1021/jp0205057 · Cited by 74

Combined QM/MM Study of the Mechanism and Kinetic Isotope Effect of the Nucleophilic Substitution Reaction in Haloalkane Dehalogenase

Devi-Kesavan, L. S., & Gao, J. (2003) · Journal of the American Chemical Society · doi:10.1021/ja026955u · Cited by 70

Conformational Substates Modulate Hydride Transfer in Dihydrofolate Reductase

Thorpe, I. F., & Brooks, C. L. (2005) · Journal of the American Chemical Society · doi:10.1021/ja053558l · Cited by 70

Catalysis and Specificity in Enzymes: A Study of Triosephosphate Isomerase and Comparison with Methyl Glyoxal Synthase

Cui, Q., & Karplus, M. (2003) · Advances in protein chemistry · doi:10.1016/s0065-3233(03)66008-0 · Cited by 68

Analysis of the reaction mechanism and substrate specificity of haloalkane dehalogenases by sequential and structural comparisons

Damborský, J., & Koča, J. (1999) · Protein Engineering Design and Selection · doi:10.1093/protein/12.11.989 · Cited by 68

Solvent and Protein Effects on the Structure and Dynamics of the Rhodopsin Chromophore

Röhrig, U. F., Guidoni, L., & Röthlisberger, U. (2005) · ChemPhysChem · doi:10.1002/cphc.200500066 · Cited by 67

Toward Identification of Acid/Base Catalysts in the Active Site of Enolase: Comparison of the Properties of K345A, E168Q, and E211Q Variants

Poyner, R. R., Laughlin, L. T., Sowa, G., & Reed, G. H. (1996) · Biochemistry · doi:10.1021/bi952186y · Cited by 64

Molecular Recognition of the Substrate Diphosphate Group Governs Product Diversity in Trichodiene Synthase Mutants ,

Vedula, L. S., Rynkiewicz, M. J., Pyun, H., et al. (2005) · Biochemistry · doi:10.1021/bi050059o · Cited by 64

Preorganization and Reorganization as Related Factors in Enzyme Catalysis: The Chorismate Mutase Case

Martı́, S., Andrés, J., Moliner, V., Silla, E., Tuñón, I., & Bertrán, J. (2003) · Chemistry - A European Journal · doi:10.1002/chem.200390121 · Cited by 64

The importance of reactant positioning in enzyme catalysis: A hybrid quantum mechanics/molecular mechanics study of a haloalkane dehalogenase

Lau, E. Y., Kahn, K., Bash, P. A., & Bruice, T. C. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.18.9937 · Cited by 62

The Role of Collective Solvent Coordinates and Nonequilibrium Solvation in Charge-Transfer Reactions

Schenter, G. K., Garrett, B. C., & Truhlar, D. G. (2001) · The Journal of Physical Chemistry B · doi:10.1021/jp011981k · Cited by 62

Dynamics of an Enzymatic Substitution Reaction in Haloalkane Dehalogenase

Nam, K., Prat‐Resina, X., Garcia‐Viloca, M., Devi-Kesavan, L. S., & Gao, J. (2004) · Journal of the American Chemical Society · doi:10.1021/ja039093l · Cited by 62

Molecular Dynamics Simulations of Ground and Transition States for the SN2 Displacement of Cl- from 1,2-Dichloroethane at the Active Site of Xanthobacter autotrophicus Haloalkane Dehalogenase

Lightstone, F. C., Zheng, Y., & Bruice, T. C. (1998) · Journal of the American Chemical Society · doi:10.1021/ja980162j · Cited by 62

Calculation of the potential of mean force using molecular dynamics with linear constraints: An application to a conformational transition in a solvated dipeptide

Elber, R. (1990) · The Journal of Chemical Physics · doi:10.1063/1.458713 · Cited by 61

Conformational effects in enzyme catalysis: QM/MM free energy calculation of the ‘NAC’ contribution in chorismate mutase

Ranaghan, K. E., & Mulholland, A. J. (2004) · Chemical Communications · doi:10.1039/b402388a · Cited by 61

Strength of an Interloop Hydrogen Bond Determines the Kinetic Pathway in Catalysis byEscherichia coliDihydrofolate Reductase

Miller, G. P., & Benkovic, S. J. (1998) · Biochemistry · doi:10.1021/bi973065w · Cited by 60

Quantum mechanical tunneling in methylamine dehydrogenase

Alhambra, C., Sanchez, M. L., Corchado, J. C., Gao, J., & Truhlar, D. G. (2001) · Chemical Physics Letters · doi:10.1016/s0009-2614(01)00921-6 · Cited by 59

Structure, Mechanism, and Specificity of Protein-Tyrosine Phosphatases

Zhang, Z. (1997) · Current topics in cellular regulation · doi:10.1016/s0070-2137(97)80002-7 · Cited by 58

Design, Synthesis, and Characterization of a Potent Xylose Isomerase Inhibitor, D-Threonohydroxamic Acid, and High-Resolution X-ray Crystallographic Structure of the Enzyme-Inhibitor Complex

Allen, K. N., Lavie, A., Petsko, G. A., & Ringe, D. (1995) · Biochemistry · doi:10.1021/bi00011a032 · Cited by 58

A Molecular Modeling Study of the Catalytic Mechanism of Haloalkane Dehalogenase: 1. Quantum Chemical Study of the First Reaction Step

Damborský, J., Kutý, M., Němec, M., & Koča, J. (1997) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci960483j · Cited by 56

Reaction Mechanism of Chorismate Mutase Studied by the Combined Potentials of Quantum Mechanics and Molecular Mechanics

Lee, Y. S., Worthington, S. E., Krauß, M., & Brooks, B. R. (2002) · The Journal of Physical Chemistry B · doi:10.1021/jp0268718 · Cited by 53

Octahedral coordination at the high-affinity metal site in enolase: Crystallographic analysis of the MgII-enzyme complex from yeast at 1.9 .ANG. resolution

Wedekind, J. E., Reed, G. H., & Rayment, I. (1995) · Biochemistry · doi:10.1021/bi00013a022 · Cited by 50

Molecular Dynamics Simulations of Protein-Tyrosine Phosphatase 1B. II. Substrate-Enzyme Interactions and Dynamics

Peters, G. H. J., Frimurer, T. M., Andersen, J. N., & Olsen, O. H. (2000) · Biophysical Journal · doi:10.1016/s0006-3495(00)76768-3 · Cited by 48

Molecular Dynamics Simulations of Protein-Tyrosine Phosphatase 1B. I. Ligand-Induced Changes in the Protein Motions

Peters, G. H. J., Frimurer, T. M., Andersen, J. N., & Olsen, O. H. (1999) · Biophysical Journal · doi:10.1016/s0006-3495(99)76907-9 · Cited by 48

The Mechanism of Orotidine 5‘-Monophosphate Decarboxylase: Catalysis by Destabilization of the Substrate

Feng, W. Y., Austin, T. J., Chew, F., Gronert, S., & Wu, W. (2000) · Biochemistry · doi:10.1021/bi992553w · Cited by 48

Dynamic and Electrostatic Effects in Enzymatic Processes. An Analysis of the Nucleophilic Substitution Reaction in Haloalkane Dehalogenase

Soriano, A., Silla, E., Tuñón, I., & Ruiz‐López, M. F. (2005) · Journal of the American Chemical Society · doi:10.1021/ja046553h · Cited by 45

Structure, Protonation State and Dynamics of Catalase Compound II

Rovira, C. (2005) · ChemPhysChem · doi:10.1002/cphc.200400633 · Cited by 44

Non-enzymatic and enzymatic hydrolysis of alkyl halides: A haloalkane dehalogenation enzyme evolved to stabilize the gas-phase transition state of an S N 2 displacement reaction

Lightstone, F. C., Zheng, Y., Maulitz, A. H., & Bruice, T. C. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.16.8417 · Cited by 43

Chlorine Kinetic Isotope Effects on the Haloalkane Dehalogenase Reaction

Lewandowicz, A., Rudziński, J., Tronstad, L., Widersten, M., Ryberg, P., Matsson, O., & Paneth, P. (2001) · Journal of the American Chemical Society · doi:10.1021/ja003503d · Cited by 43

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Hur, S., Kahn, K., & Bruice, T. C. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.242721799 · Cited by 41

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Satoh, A. (2003) · The Journal of Biochemistry · doi:10.1093/jb/mvg143 · Cited by 40

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Lee, T., Chong, L. T., Chodera, J. D., & Kollman, P. A. (2001) · Journal of the American Chemical Society · doi:10.1021/ja011096f · Cited by 39

Erratum to: “Quantum mechanical tunneling in methylamine dehydrogenase” [Chem. Phys. Lett. 347 (2001) 512–518]

Alhambra, C., Sanchez, M. L., Corchado, J. C., Gao, J., & Truhlar, D. G. (2002) · Chemical Physics Letters · doi:10.1016/s0009-2614(02)00057-x · Cited by 38

Nonenzymatic and enzymatic hydrolysis of alkyl halides: A theoretical study of the S N 2 reactions of acetate and hydroxide ions with alkyl chlorides

Maulitz, A. H., Lightstone, F. C., Zheng, Y., & Bruice, T. C. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.13.6591 · Cited by 32

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Guimarães, C. R. W., Udier–Blagović, M., Tubert‐Brohman, I., & Jorgensen, W. L. (2005) · Journal of Chemical Theory and Computation · doi:10.1021/ct0500803 · Cited by 32

Solvent effects, reaction coordinates, and reorganization energies on nucleophilic substitution reactions in aqueous solution

Gao, J., Garcia‐Viloca, M., Poulsen, T. D., & Mo, Y. (2003) · Advances in physical organic chemistry · doi:10.1016/s0065-3160(03)38005-0 · Cited by 30

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Devi-Kesavan, L. S., Garcia‐Viloca, M., & Gao, J.-L. (2003) · Theoretical Chemistry Accounts · doi:10.1007/s00214-002-0419-x · Cited by 26

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Hart, J. C., Burton, N. A., Hillier, I. H., Harrison, M. J., & Jewsbury, P. J. (1997) · Chemical Communications · doi:10.1039/a702304i · Cited by 21

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Damborský, J., Bohac, M., Prokop, M., Kutý, M., & Koča, J. (1998) · Protein Engineering Design and Selection · doi:10.1093/protein/11.10.901 · Cited by 21

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Wang, M., Lu, Z., & Yang, W. (2004) · The Journal of Chemical Physics · doi:10.1063/1.1757437 · Cited by 17

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Chundawat, S. P. S., Beckham, G. T., Himmel, M. E., & Dale, B. E. (2011) · Annual Review of Chemical and Biomolecular Engineering · doi:10.1146/annurev-chembioeng-061010-114205 · Cited by 1,017

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Senn, H. M., & Thiel, W. (2006) · Topics in Current Chemistry · doi:10.1007/128_2006_084 · Cited by 428

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