Combined QM/MM and path integral simulations of kinetic isotope effects in the proton transfer reaction between nitroethane and acetate ion in water
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[1] A. Kresge. The Nitroalkane Anomaly , 1974 .
[2] Darrin M York,et al. An Efficient Linear-Scaling Ewald Method for Long-Range Electrostatic Interactions in Combined QM/MM Calculations. , 2005, Journal of chemical theory and computation.
[3] 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 .
[4] D. Ceperley. Path integrals in the theory of condensed helium , 1995 .
[5] Klein,et al. Staging: A sampling technique for the Monte Carlo evaluation of path integrals. , 1985, Physical review. B, Condensed matter.
[6] D. Chandler,et al. Free energies of electron transfer , 1992 .
[7] Bruce J. Berne,et al. On the Simulation of Quantum Systems: Path Integral Methods , 1986 .
[8] Seogjoo J. Jang,et al. A relationship between centroid dynamics and path integral quantum transition state theory , 2000 .
[9] K. Nam,et al. Transition State Stabilization and α-Amino Carbon Acidity in Alanine Racemase , 2006 .
[10] W. J. Boyle,et al. Acidities, Broensted coefficients, and transition state structures for 1-arylnitroalkanes , 1972 .
[11] F. Young. Biochemistry , 1955, The Indian Medical Gazette.
[12] K. Hinsen,et al. Potential of mean force and reaction rates for proton transfer in acetylacetone , 1997 .
[13] Gill Mj,et al. Quantum simulation of hydrogen in metals. , 1987 .
[14] Arieh Warshel,et al. A Quantized Classical Path Approach for Calculations of Quantum Mechanical Rate Constants , 1993 .
[15] D. York,et al. Solvent polarization and kinetic isotope effects in nitroethane deprotonation and implications to the nitroalkane oxidase reaction. , 2005, Journal of the American Chemical Society.
[16] R. Feynman,et al. Quantum Mechanics and Path Integrals , 1965 .
[17] J. Gao,et al. A priori evaluation of aqueous polarization effects through Monte Carlo QM-MM simulations. , 1992, Science.
[18] C. F. Bernasconi. The principle of nonperfect synchronization: more than a qualitative concept? , 1992 .
[19] Jiali Gao,et al. Hybrid Quantum and Molecular Mechanical Simulations: An Alternative Avenue to Solvent Effects in Organic Chemistry , 1996 .
[20] M. Karplus,et al. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .
[21] R. Swendsen,et al. THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method , 1992 .
[22] T. Darden,et al. Generalization of the Gaussian electrostatic model: extension to arbitrary angular momentum, distributed multipoles, and speedup with reciprocal space methods. , 2006, The Journal of chemical physics.
[23] M. Tuckerman,et al. Heavy-atom skeleton quantization and proton tunneling in "intermediate-barrier" hydrogen bonds. , 2001, Physical review letters.
[24] Arieh Warshel,et al. Simulations of quantum mechanical corrections for rate constants of hydride-transfer reactions in enzymes and solutions , 1991 .
[25] D. Truhlar,et al. Inclusion of Quantum Mechanical Vibrational Energy in Reactive Potentials of Mean Force , 2001 .
[26] M. Valley,et al. Reductive half-reaction of nitroalkane oxidase: effect of mutation of the active site aspartate to glutamate. , 2003, Biochemistry.
[27] Jiali Gao,et al. Implementation of the bisection sampling method in path integral simulations. , 2005, Journal of molecular graphics & modelling.
[28] Gillan. Quantum simulation of hydrogen in metals. , 1988, Physical review letters.
[29] Arieh Warshel,et al. Energetics and Dynamics of Enzymatic Reactions , 2001 .
[30] Peter G. Wolynes,et al. Exploiting the isomorphism between quantum theory and classical statistical mechanics of polyatomic fluids , 1981 .
[31] W. Saunders. Calculations of isotope effects in elimination reactions: new experimental criteria for tunneling in slow proton transfers , 1985 .
[32] Donald G Truhlar,et al. Modeling the kinetics of bimolecular reactions. , 2006, Chemical reviews.
[33] C. J. Murray,et al. Hydrogen tunneling in enzyme reactions. , 1989, Science.
[34] Donald G Truhlar,et al. Multidimensional tunneling, recrossing, and the transmission coefficient for enzymatic reactions. , 2006, Chemical reviews.
[35] J. Hynes,et al. Reactive modes in condensed phase reactions , 1981 .
[36] Jiali Gao,et al. An Integrated Path Integral and Free-Energy Perturbation-Umbrella Sampling Method for Computing Kinetic Isotope Effects of Chemical Reactions in Solution and in Enzymes. , 2007, Journal of chemical theory and computation.
[37] Jiali Gao,et al. Path Integral Simulations of Proton Transfer Reactions in Aqueous Solution Using Combined QM/MM Potentials. , 2006, Journal of chemical theory and computation.
[38] V. Schramm. Enzymatic transition state poise and transition state analogues. , 2003, Accounts of chemical research.
[39] G. Voth. A Feynman Path Integral Formulation of Quantum Mechanical Transition State Theory , 1993 .
[40] G. Voth,et al. Calculation of quantum activation free energies for proton transfer reactions in polar solvents , 1992 .
[41] Gregory K. Schenter,et al. A variational centroid density procedure for the calculation of transmission coefficients for asymmetric barriers at low temperature , 1995 .
[42] Makarov,et al. Quantum transition-state theory below the crossover temperature. , 1995, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.
[43] S. Hammes‐Schiffer. Quantum-classical simulation methods for hydrogen transfer in enzymes: a case study of dihydrofolate reductase. , 2004, Current opinion in structural biology.
[44] Arieh Warshel,et al. How Important Are Quantum Mechanical Nuclear Motions in Enzyme Catalysis , 1996 .
[45] B. C. Garrett,et al. Centroid‐density quantum rate theory: Variational optimization of the dividing surface , 1993 .
[46] Eamonn F. Healy,et al. Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model , 1985 .
[47] D. Truhlar,et al. Quantum mechanical methods for enzyme kinetics. , 2003, Annual review of physical chemistry.
[48] W. L. Jorgensen,et al. Comparison of simple potential functions for simulating liquid water , 1983 .
[49] C. Brooks. Computer simulation of liquids , 1989 .
[50] J. Bigeleisen. Statistical Mechanics of Isotopic Systems with Small Quantum Corrections. I. General Considerations and the Rule of the Geometric Mean , 1955 .
[51] G. Voth,et al. Rigorous formulation of quantum transition state theory and its dynamical corrections , 1989 .
[52] Gregory K. Schenter,et al. Generalized path integral based quantum transition state theory , 1997 .
[53] D. Ceperley,et al. Simulation of quantum many-body systems by path-integral methods , 1984 .
[54] M. Valley,et al. Comparison of enzymatic and non-enzymatic nitroethane anion formation: thermodynamics and contribution of tunneling. , 2004, Journal of the American Chemical Society.
[55] 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.
[56] W. Huskey. Isotope Effects in Chemistry and Biology , 2006 .