skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Accelerated computation of free energy profile at ab initio quantum mechanical/molecular mechanical accuracy via a semi-empirical reference potential. II. Recalibrating semi-empirical parameters with force matching

Journal Article · · Physical Chemistry Chemical Physics. PCCP
DOI:https://doi.org/10.1039/c9cp02593f· OSTI ID:1802214
ORCiD logo [1];  [2];  [3];  [4]; ORCiD logo [2]; ORCiD logo [1]
  1. Department of Chemistry and Biochemistry; University of Oklahoma; Norman; USA
  2. State Key Laboratory of Precision Spectroscopy; School of Physics and Materials Science; East China Normal University; Shanghai 200062; China
  3. School of Chemistry; University of New South Wales; Sydney; Australia
  4. Department of Chemistry and Chemical Biology; Indiana University-Purdue University Indianapolis; Indianapolis; USA

An efficient and accurate reference potential simulation protocol is proposed for producingab initioquantum mechanical/molecular mechanical (AI-QM/MM) quality free energy profiles for chemical reactions in a solvent or macromolecular environment.

Research Organization:
Q-Chem, Inc., Pleasanton, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC)
DOE Contract Number:
SC0011297
OSTI ID:
1802214
Journal Information:
Physical Chemistry Chemical Physics. PCCP, Vol. 21, Issue 37; ISSN 1463-9076
Country of Publication:
United States
Language:
English

References (88)

Computer Simulations of Enzyme Catalysis: Methods, Progress, and Insights journal June 2003
Modelling enzyme reaction mechanisms, specificity and catalysis journal October 2005
QM/MM studies of enzymes journal April 2007
Free Energies of Chemical Reactions in Solution and in Enzymes with Ab Initio Quantum Mechanics/Molecular Mechanics Methods journal May 2008
QM/MM: what have we learned, where are we, and where do we go from here? journal July 2006
Catalytic Mechanism and Product Specificity of the Histone Lysine Methyltransferase SET7/9:  An ab Initio QM/MM-FE Study with Multiple Initial Structures journal January 2006
A Water-Mediated and Substrate-Assisted Catalytic Mechanism for Sulfolobus solfataricus DNA Polymerase IV journal April 2007
A Proton-Shuttle Reaction Mechanism for Histone Deacetylase 8 and the Catalytic Role of Metal Ions journal July 2010
Catalytic Mechanism of RNA Backbone Cleavage by Ribonuclease H from Quantum Mechanics/Molecular Mechanics Simulations journal June 2011
Characterization of the Reaction Path and Transition States for RNA Transphosphorylation Models from Theory and Experiment journal November 2011
Quantum Mechanical/Molecular Mechanical Free Energy Simulations of the Self-Cleavage Reaction in the Hepatitis Delta Virus Ribozyme journal January 2014
Exploring the Role of the Third Active Site Metal Ion in DNA Polymerase η with QM/MM Free Energy Simulations journal June 2018
Absolute free energy of solvation from Monte Carlo simulations using combined quantum and molecular mechanical potentials journal January 1992
Ab Initio Calculations of Free Energy Barriers for Chemical Reactions in Solution journal December 1995
Convergence of QM/MM free-energy perturbations based on molecular-mechanics or semiempirical simulations journal January 2012
Optimized Monte Carlo data analysis journal September 1989
Statistically optimal analysis of samples from multiple equilibrium states journal September 2008
Bridging the gap between thermodynamic integration and umbrella sampling provides a novel analysis method: “Umbrella integration” journal October 2005
A New Maximum Likelihood Approach for Free Energy Profile Construction from Molecular Simulations journal December 2012
Roadmaps through Free Energy Landscapes Calculated Using the Multidimensional vFEP Approach journal November 2013
High‐Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases journal August 1954
Quantum mechanics/molecular mechanics dual Hamiltonian free energy perturbation journal August 2013
Accelerated Computation of Free Energy Profile at ab Initio Quantum Mechanical/Molecular Mechanics Accuracy via a Semi-Empirical Reference Potential. I. Weighted Thermodynamics Perturbation journal October 2018
Reaction Path Force Matching: A New Strategy of Fitting Specific Reaction Parameters for Semiempirical Methods in Combined QM/MM Simulations journal June 2014
Multiscale Quantum Mechanics/Molecular Mechanics Simulations with Neural Networks journal September 2016
Internal force corrections with machine learning for quantum mechanics/molecular mechanics simulations journal October 2017
Molecular Dynamics Simulations with Quantum Mechanics/Molecular Mechanics and Adaptive Neural Networks journal February 2018
Use of Nonequilibrium Work Methods to Compute Free Energy Differences Between Molecular Mechanical and Quantum Mechanical Representations of Molecular Systems journal November 2015
Reversible multiple time scale molecular dynamics journal August 1992
Acceleration of Ab Initio QM/MM Calculations under Periodic Boundary Conditions by Multiscale and Multiple Time Step Approaches journal September 2014
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 journal January 2008
Accelerating QM/MM Free Energy Calculations:  Representing the Surroundings by an Updated Mean Charge Distribution journal May 2008
Improving Efficiency in SMD Simulations Through a Hybrid Differential Relaxation Algorithm journal October 2014
Escaping free-energy minima journal September 2002
Accurate Quantum Chemical Free Energies at Affordable Cost journal June 2019
Efficient Strategy for the Calculation of Solvation Free Energies in Water and Chloroform at the Quantum Mechanical/Molecular Mechanical Level journal October 2017
Optimization of parameters for semiempirical methods I. Method journal March 1989
Density-functional exchange-energy approximation with correct asymptotic behavior journal September 1988
A new mixing of Hartree–Fock and local density‐functional theories journal January 1993
Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density journal January 1988
Advances in molecular quantum chemistry contained in the Q-Chem 4 program package journal September 2014
A Subspace, Interior, and Conjugate Gradient Method for Large-Scale Bound-Constrained Minimization Problems journal January 1999
Optimization of quantum mechanical molecular mechanical partitioning schemes: Gaussian delocalization of molecular mechanical charges and the double link atom method journal December 2002
A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations journal July 1990
SN2 reaction profiles in the gas phase and aqueous solution journal May 1984
Theoretical examination of the SN2 reaction involving chloride ion and methyl chloride in the gas phase and aqueous solution journal January 1985
Energy profile for a nonconcerted SN2 reaction in solution journal May 1985
Steric Retardation of S N 2 Reactions in the Gas Phase and Solution journal July 2004
Identity SN2 Reactions X−+CH3X→XCH3+X− (X=F, Cl, Br, and I) in Vacuum and in Aqueous Solution: A Valence Bond Study journal September 2006
Interfacing ab Initio Quantum Mechanical Method with Classical Drude Osillator Polarizable Model for Molecular Dynamics Simulation of Chemical Reactions journal June 2008
A priori computation of a solvent-enhanced SN2 reaction profile in water: the Menshutkin reaction journal September 1991
A two-dimensional energy surface for a type II SN2 reaction in aqueous solution journal October 1993
The interface of electronic structure and dynamics for reactions in solution journal January 1998
Solvent Effects on Methyl Transfer Reactions. 1. The Menshutkin Reaction journal March 1999
The Menshutkin Reaction in the Gas Phase and in Aqueous Solution: A Valence Bond Study journal December 2007
On the Ratio of Zwitterion Form to Uncharged Form of Glycine at Equilibrium in Various Aqueous Media journal October 1982
Thermodynamic parameters of the activation of glycine zwitterion protonation reactions journal June 1984
Potential Energy Function for Intramolecular Proton Transfer Reaction of Glycine in Aqueous Solution journal January 1998
Origin of the Transition State on the Free Energy Surface:  Intramolecular Proton Transfer Reaction of Glycine in Aqueous Solution journal October 1998
Intramolecular Proton Transfer of Glycine in Aqueous Solution Using Quantum Mechanics−Molecular Mechanics Simulations journal November 1998
Nonequilibrium Solvation and the Quantum Kramers Problem:  Proton Transfer in Aqueous Glycine journal March 2001
Ab initio molecular dynamics study of glycine intramolecular proton transfer in water journal May 2005
Incremental Solvation of Nonionized and Zwitterionic Glycine journal October 2006
Crystal structures of the monofunctional chorismate mutase from Bacillus subtilis and its complex with a transition state analog. journal September 1993
The Monofunctional Chorismate Mutase from Bacillus subtilis journal July 1994
Is chorismate mutase a prototypic entropy trap? - Activation parameters for the Bacillus subtilis enzyme journal April 1996
Exploring the quantum mechanical/molecular mechanical replica path method: a pathway optimization of the chorismate to prephenate Claisen rearrangement catalyzed by chorismate mutase
  • Lee Woodcock, H.; Hodošček, Milan; Sherwood, Paul
  • Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta), Vol. 109, Issue 3 https://doi.org/10.1007/s00214-002-0421-3
journal April 2003
Analysis of chorismate mutase catalysis by QM/MM modelling of enzyme-catalysed and uncatalysed reactions journal January 2011
Enzymatic Minimum Free Energy Path Calculations Using Swarms of Trajectories journal August 2014
Comparison of simple potential functions for simulating liquid water journal July 1983
Development and testing of a general amber force field journal January 2004
ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB journal July 2015
Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems journal June 1993
A smooth particle mesh Ewald method journal November 1995
The implementation of a fast and accurate QM/MM potential method in Amber journal January 2008
An extensible interface for QM/MM molecular dynamics simulations with AMBER journal October 2013
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 journal July 2007
Long-range corrected hybrid density functionals with damped atom–atom dispersion corrections journal January 2008
ωB97X-V: A 10-parameter, range-separated hybrid, generalized gradient approximation density functional with nonlocal correlation, designed by a survival-of-the-fittest strategy journal January 2014
How Many Conformations Need To Be Sampled To Obtain Converged QM/MM Energies? The Curse of Exponential Averaging journal October 2017
Achieving fast convergence of ab initio free energy perturbation calculations with the adaptive force-matching method journal February 2012
Convergence of single-step free energy perturbation journal December 2016
Model for small-sample bias of free-energy calculations applied to Gaussian-distributed nonequilibrium work measurements journal November 2004
Host–Guest Relative Binding Affinities at Density-Functional Theory Level from Semiempirical Molecular Dynamics Simulations journal February 2019
String method in collective variables: Minimum free energy paths and isocommittor surfaces journal July 2006
Investigations of α-helix↔β-sheet transition pathways in a miniprotein using the finite-temperature string method journal May 2014
Adaptive Finite Temperature String Method in Collective Variables journal December 2017
Mapping Free Energy Pathways for ATP Hydrolysis in the E. coli ABC Transporter HlyB by the String Method journal October 2018