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Optimization of parameters for semiempirical methods I. Method
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journal
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March 1989 |
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A Proton-Shuttle Reaction Mechanism for Histone Deacetylase 8 and the Catalytic Role of Metal Ions
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journal
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July 2010 |
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Exploring the quantum mechanical/molecular mechanical replica path method: a pathway optimization of the chorismate to prephenate Claisen rearrangement catalyzed by chorismate mutase
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journal
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April 2003 |
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Reaction Path Force Matching: A New Strategy of Fitting Specific Reaction Parameters for Semiempirical Methods in Combined QM/MM Simulations
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journal
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June 2014 |
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Analysis of chorismate mutase catalysis by QM/MM modelling of enzyme-catalysed and uncatalysed reactions
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journal
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January 2011 |
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Bridging the gap between thermodynamic integration and umbrella sampling provides a novel analysis method: “Umbrella integration”
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journal
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October 2005 |
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High‐Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases
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journal
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August 1954 |
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Catalytic Mechanism of RNA Backbone Cleavage by Ribonuclease H from Quantum Mechanics/Molecular Mechanics Simulations
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journal
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June 2011 |
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A New Maximum Likelihood Approach for Free Energy Profile Construction from Molecular Simulations
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journal
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December 2012 |
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Intramolecular Proton Transfer of Glycine in Aqueous Solution Using Quantum Mechanics−Molecular Mechanics Simulations
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journal
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November 1998 |
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Use of Nonequilibrium Work Methods to Compute Free Energy Differences Between Molecular Mechanical and Quantum Mechanical Representations of Molecular Systems
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journal
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November 2015 |
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Internal force corrections with machine learning for quantum mechanics/molecular mechanics simulations
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journal
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October 2017 |
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Enzymatic Minimum Free Energy Path Calculations Using Swarms of Trajectories
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journal
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August 2014 |
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A smooth particle mesh Ewald method
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journal
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November 1995 |
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SN2 reaction profiles in the gas phase and aqueous solution
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journal
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May 1984 |
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Is chorismate mutase a prototypic entropy trap? - Activation parameters for the Bacillus subtilis enzyme
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journal
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April 1996 |
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Acceleration of Ab Initio QM/MM Calculations under Periodic Boundary Conditions by Multiscale and Multiple Time Step Approaches
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journal
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September 2014 |
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Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density
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journal
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January 1988 |
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Accurate Quantum Chemical Free Energies at Affordable Cost
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journal
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June 2019 |
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Convergence of QM/MM free-energy perturbations based on molecular-mechanics or semiempirical simulations
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journal
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January 2012 |
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Host–Guest Relative Binding Affinities at Density-Functional Theory Level from Semiempirical Molecular Dynamics Simulations
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journal
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February 2019 |
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Improving Efficiency in SMD Simulations Through a Hybrid Differential Relaxation Algorithm
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journal
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October 2014 |
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Optimization of quantum mechanical molecular mechanical partitioning schemes: Gaussian delocalization of molecular mechanical charges and the double link atom method
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journal
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December 2002 |
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Ab initio molecular dynamics study of glycine intramolecular proton transfer in water
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journal
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May 2005 |
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Energy profile for a nonconcerted SN2 reaction in solution
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journal
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May 1985 |
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An extensible interface for QM/MM molecular dynamics simulations with AMBER
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journal
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October 2013 |
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Advances in molecular quantum chemistry contained in the Q-Chem 4 program package
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journal
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September 2014 |
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Characterization of the Reaction Path and Transition States for RNA Transphosphorylation Models from Theory and Experiment
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journal
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November 2011 |
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Quantum Mechanical/Molecular Mechanical Free Energy Simulations of the Self-Cleavage Reaction in the Hepatitis Delta Virus Ribozyme
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journal
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January 2014 |
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Nonequilibrium Solvation and the Quantum Kramers Problem: Proton Transfer in Aqueous Glycine †
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journal
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March 2001 |
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Free Energies of Chemical Reactions in Solution and in Enzymes with Ab Initio Quantum Mechanics/Molecular Mechanics Methods
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journal
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May 2008 |
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QM/MM: what have we learned, where are we, and where do we go from here?
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journal
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July 2006 |
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Development and testing of a general amber force field
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journal
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January 2004 |
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Ab Initio Calculations of Free Energy Barriers for Chemical Reactions in Solution
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journal
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December 1995 |
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A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations
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journal
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July 1990 |
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ωB97X-V: A 10-parameter, range-separated hybrid, generalized gradient approximation density functional with nonlocal correlation, designed by a survival-of-the-fittest strategy
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journal
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January 2014 |
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Steric Retardation of S N 2 Reactions in the Gas Phase and Solution
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journal
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July 2004 |
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The influence of polarization functions on molecular orbital hydrogenation energies
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journal
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January 1973 |
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Investigations of α-helix↔β-sheet transition pathways in a miniprotein using the finite-temperature string method
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journal
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May 2014 |
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Computer Simulations of Enzyme Catalysis: Methods, Progress, and Insights
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journal
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June 2003 |
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Multiscale Quantum Mechanics/Molecular Mechanics Simulations with Neural Networks
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journal
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September 2016 |
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Optimized Monte Carlo data analysis
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journal
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September 1989 |
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The Monofunctional Chorismate Mutase from Bacillus subtilis
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journal
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July 1994 |
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Reversible multiple time scale molecular dynamics
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journal
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August 1992 |
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The implementation of a fast and accurate QM/MM potential method in Amber
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journal
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January 2008 |
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Identity SN2 Reactions X−+CH3X→XCH3+X− (X=F, Cl, Br, and I) in Vacuum and in Aqueous Solution: A Valence Bond Study
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journal
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September 2006 |
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Statistically optimal analysis of samples from multiple equilibrium states
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journal
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September 2008 |
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Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: Sequential sampling and optimization on the potential of mean force surface
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journal
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January 2008 |
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Incremental Solvation of Nonionized and Zwitterionic Glycine
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journal
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October 2006 |
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On the Ratio of Zwitterion Form to Uncharged Form of Glycine at Equilibrium in Various Aqueous Media
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journal
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October 1982 |
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Crystal structures of the monofunctional chorismate mutase from Bacillus subtilis and its complex with a transition state analog.
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journal
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September 1993 |
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Density-functional exchange-energy approximation with correct asymptotic behavior
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journal
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September 1988 |
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Molecular Dynamics Simulations with Quantum Mechanics/Molecular Mechanics and Adaptive Neural Networks
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journal
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February 2018 |
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Origin of the Transition State on the Free Energy Surface: Intramolecular Proton Transfer Reaction of Glycine in Aqueous Solution
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journal
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October 1998 |
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Exploring the Role of the Third Active Site Metal Ion in DNA Polymerase η with QM/MM Free Energy Simulations
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journal
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June 2018 |
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Model for small-sample bias of free-energy calculations applied to Gaussian-distributed nonequilibrium work measurements
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journal
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November 2004 |
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A two-dimensional energy surface for a type II SN2 reaction in aqueous solution
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journal
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October 1993 |
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Modelling enzyme reaction mechanisms, specificity and catalysis
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journal
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October 2005 |
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A new mixing of Hartree–Fock and local density‐functional theories
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journal
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January 1993 |
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The interface of electronic structure and dynamics for reactions in solution
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journal
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January 1998 |
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Escaping free-energy minima
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journal
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September 2002 |
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Mapping Free Energy Pathways for ATP Hydrolysis in the E. coli ABC Transporter HlyB by the String Method
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journal
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October 2018 |
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Thermodynamic parameters of the activation of glycine zwitterion protonation reactions
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journal
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June 1984 |
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A Water-Mediated and Substrate-Assisted Catalytic Mechanism for Sulfolobus solfataricus DNA Polymerase IV
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journal
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April 2007 |
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Theoretical examination of the SN2 reaction involving chloride ion and methyl chloride in the gas phase and aqueous solution
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journal
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January 1985 |
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Interfacing ab Initio Quantum Mechanical Method with Classical Drude Osillator Polarizable Model for Molecular Dynamics Simulation of Chemical Reactions
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journal
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June 2008 |
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A priori computation of a solvent-enhanced SN2 reaction profile in water: the Menshutkin reaction
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journal
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September 1991 |
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Potential Energy Function for Intramolecular Proton Transfer Reaction of Glycine in Aqueous Solution
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journal
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January 1998 |
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Roadmaps through Free Energy Landscapes Calculated Using the Multidimensional vFEP Approach
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journal
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November 2013 |
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The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals
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journal
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July 2007 |
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Adaptive Finite Temperature String Method in Collective Variables
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journal
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December 2017 |
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Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems
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journal
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June 1993 |
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The Menshutkin Reaction in the Gas Phase and in Aqueous Solution: A Valence Bond Study
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journal
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December 2007 |
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Long-range corrected hybrid density functionals with damped atom–atom dispersion corrections
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journal
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January 2008 |
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Quantum mechanics/molecular mechanics dual Hamiltonian free energy perturbation
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journal
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August 2013 |
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QM/MM studies of enzymes
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journal
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April 2007 |
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Absolute free energy of solvation from Monte Carlo simulations using combined quantum and molecular mechanical potentials
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journal
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January 1992 |
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A Subspace, Interior, and Conjugate Gradient Method for Large-Scale Bound-Constrained Minimization Problems
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journal
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January 1999 |
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String method in collective variables: Minimum free energy paths and isocommittor surfaces
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journal
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July 2006 |
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Catalytic Mechanism and Product Specificity of the Histone Lysine Methyltransferase SET7/9: An ab Initio QM/MM-FE Study with Multiple Initial Structures
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journal
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January 2006 |
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Comparison of simple potential functions for simulating liquid water
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journal
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July 1983 |
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Convergence of single-step free energy perturbation
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journal
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December 2016 |
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ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB
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journal
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July 2015 |
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How Many Conformations Need To Be Sampled To Obtain Converged QM/MM Energies? The Curse of Exponential Averaging
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journal
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October 2017 |
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Efficient Strategy for the Calculation of Solvation Free Energies in Water and Chloroform at the Quantum Mechanical/Molecular Mechanical Level
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journal
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October 2017 |
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Accelerating QM/MM Free Energy Calculations: Representing the Surroundings by an Updated Mean Charge Distribution
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journal
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May 2008 |
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Solvent Effects on Methyl Transfer Reactions. 1. The Menshutkin Reaction
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journal
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March 1999 |
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Accelerated Computation of Free Energy Profile at ab Initio Quantum Mechanical/Molecular Mechanics Accuracy via a Semi-Empirical Reference Potential. I. Weighted Thermodynamics Perturbation
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journal
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October 2018 |
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Achieving fast convergence of ab initio free energy perturbation calculations with the adaptive force-matching method
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journal
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February 2012 |