Computation of Hydration Free Energies Using the Multiple Environment Single System Quantum Mechanical/Molecular Mechanical Method.
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Andrew C Simmonett | Bernard R Brooks | Ye Mei | Benjamin T. Miller | John M Herbert | H Lee Woodcock | Benjamin T Miller | Gerhard König | Yihan Shao | Andrew C. Simmonett | Frank C Pickard | Frank C. Pickard | B. Brooks | J. Herbert | Y. Shao | H. Woodcock | Y. Mei | Gerhard König
[1] Gerhard König,et al. Non‐Boltzmann sampling and Bennett's acceptance ratio method: How to profit from bending the rules , 2011, J. Comput. Chem..
[2] Alexander D. MacKerell,et al. Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing , 2012, J. Chem. Inf. Model..
[3] Michael R. Shirts,et al. Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins , 2003 .
[4] M. Head‐Gordon,et al. Attenuated second-order Møller-Plesset perturbation theory: performance within the aug-cc-pVTZ basis. , 2013, Physical chemistry chemical physics : PCCP.
[5] A. Geoffrey Skillman,et al. SAMPL3: blinded prediction of host–guest binding affinities, hydration free energies, and trypsin inhibitors , 2012, Journal of Computer-Aided Molecular Design.
[6] P. Kollman,et al. An approach to computing electrostatic charges for molecules , 1984 .
[7] Jianpeng Ma,et al. CHARMM: The biomolecular simulation program , 2009, J. Comput. Chem..
[8] P. Pulay,et al. Efficient calculation of the energy of a molecule in an arbitrary electric field , 2009 .
[9] Bernard R. Brooks,et al. Interfacing Q‐Chem and CHARMM to perform QM/MM reaction path calculations , 2007, J. Comput. Chem..
[10] A. Becke,et al. Density-functional exchange-energy approximation with correct asymptotic behavior. , 1988, Physical review. A, General physics.
[11] Walter Thiel,et al. Exploiting QM/MM Capabilities in Geometry Optimization: A Microiterative Approach Using Electrostatic Embedding. , 2007, Journal of chemical theory and computation.
[12] Jerry M. Parks,et al. 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. , 2008, The Journal of chemical physics.
[13] V. Babin,et al. Development of a "First Principles" Water Potential with Flexible Monomers. II: Trimer Potential Energy Surface, Third Virial Coefficient, and Small Clusters. , 2014, Journal of chemical theory and computation.
[14] Arieh Ben-Naim,et al. Solvation thermodynamics of nonionic solutes , 1984 .
[15] D. Truhlar,et al. 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 , 2008 .
[16] C. Cramer,et al. A universal approach to solvation modeling. , 2008, Accounts of chemical research.
[17] V. Barone,et al. Toward reliable density functional methods without adjustable parameters: The PBE0 model , 1999 .
[18] Martin Head-Gordon,et al. Attenuating Away the Errors in Inter- and Intramolecular Interactions from Second-Order Møller-Plesset Calculations in the Small Aug-cc-pVDZ Basis Set. , 2012, The journal of physical chemistry letters.
[19] Yihan Shao,et al. Dual-basis second-order Moller-Plesset perturbation theory: A reduced-cost reference for correlation calculations. , 2006, The Journal of chemical physics.
[20] Martin Head-Gordon,et al. Approaching the Basis Set Limit in Density Functional Theory Calculations Using Dual Basis Sets without Diagonalization , 2004 .
[21] Parr,et al. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. , 1988, Physical review. B, Condensed matter.
[22] F. J. Luque,et al. On the performance of continuum solvation methods. A comment on "Universal approaches to solvation modeling". , 2009, Accounts of chemical research.
[23] Michael A. Collins,et al. Molecular Potential Energy Surfaces by Interpolation , 1994, International Conference on Computational Science.
[24] J. Herbert,et al. Rapid computation of intermolecular interactions in molecular and ionic clusters: self-consistent polarization plus symmetry-adapted perturbation theory. , 2012, Physical chemistry chemical physics : PCCP.
[25] Christopher J. Woods,et al. Compatibility of Quantum Chemical Methods and Empirical (MM) Water Models in Quantum Mechanics/Molecular Mechanics Liquid Water Simulations , 2010 .
[26] Bernard R. Brooks,et al. Computing the Free Energy along a Reaction Coordinate Using Rigid Body Dynamics , 2014, Journal of chemical theory and computation.
[27] J. Peter Guthrie,et al. SAMPL4, a blind challenge for computational solvation free energies: the compounds considered , 2014, Journal of Computer-Aided Molecular Design.
[28] W. L. Jorgensen,et al. Comparison of simple potential functions for simulating liquid water , 1983 .
[29] Jonathan W. Essex,et al. Extensive all-atom Monte Carlo sampling and QM/MM corrections in the SAMPL4 hydration free energy challenge , 2014, Journal of Computer-Aided Molecular Design.
[30] Gerhard König,et al. Multiscale Free Energy Simulations: An Efficient Method for Connecting Classical MD Simulations to QM or QM/MM Free Energies Using Non-Boltzmann Bennett Reweighting Schemes , 2014, Journal of chemical theory and computation.
[31] Andrew T. B. Gilbert,et al. Density functional triple jumping. , 2010, Physical chemistry chemical physics : PCCP.
[32] Peter Pulay,et al. Ultrafast Quantum Mechanics/Molecular Mechanics Monte Carlo simulations using generalized multipole polarizabilities , 2012 .
[33] Bernard R Brooks,et al. Correcting for the free energy costs of bond or angle constraints in molecular dynamics simulations. , 2015, Biochimica et biophysica acta.
[34] Marcelo A Martí,et al. Improving Efficiency in SMD Simulations Through a Hybrid Differential Relaxation Algorithm. , 2014, Journal of chemical theory and computation.
[35] Ye Mei,et al. Multiple Environment Single System Quantum Mechanical/Molecular Mechanical (MESS-QM/MM) Calculations. 1. Estimation of Polarization Energies , 2014, The journal of physical chemistry. A.
[36] M. Head‐Gordon,et al. Dual-basis analytic gradients. 1. Self-consistent field theory. , 2006, The journal of physical chemistry. A.
[37] Xin Xu,et al. A fast doubly hybrid density functional method close to chemical accuracy using a local opposite spin ansatz , 2011, Proceedings of the National Academy of Sciences.
[38] M. Head‐Gordon,et al. Long-range corrected hybrid density functionals with damped atom-atom dispersion corrections. , 2008, Physical chemistry chemical physics : PCCP.
[39] Donald G Truhlar,et al. Generalized Born Solvation Model SM12. , 2013, Journal of chemical theory and computation.
[40] Y. Sugita,et al. Multidimensional replica-exchange method for free-energy calculations , 2000, cond-mat/0009120.
[41] C. Cramer,et al. Universal solvation model based on solute electron density and on a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions. , 2009, The journal of physical chemistry. B.
[42] Yihan Shao,et al. Analytic Derivatives of Quartic-Scaling Doubly Hybrid XYGJ-OS Functional: Theory, Implementation, and Benchmark Comparison with M06-2X and MP2 Geometries for Nonbonded Compelexes. , 2013, Journal of chemical theory and computation.
[43] Peter Pulay,et al. Second-order Møller–Plesset calculations with dual basis sets , 2003 .
[44] Alexander D. MacKerell,et al. CHARMM general force field: A force field for drug‐like molecules compatible with the CHARMM all‐atom additive biological force fields , 2009, J. Comput. Chem..
[45] A. Tkatchenko,et al. Many-body van der Waals interactions in molecules and condensed matter , 2014, Journal of physics. Condensed matter : an Institute of Physics journal.
[46] Donald G Truhlar,et al. Charge Model 4 and Intramolecular Charge Polarization. , 2007, Journal of chemical theory and computation.
[47] David L Mobley,et al. Treating entropy and conformational changes in implicit solvent simulations of small molecules. , 2008, The journal of physical chemistry. B.
[48] Anthony Nicholls,et al. The SAMPL2 blind prediction challenge: introduction and overview , 2010, J. Comput. Aided Mol. Des..
[49] C. Cramer,et al. Self-Consistent Reaction Field Model for Aqueous and Nonaqueous Solutions Based on Accurate Polarized Partial Charges. , 2007, Journal of chemical theory and computation.
[50] Volodymyr Babin,et al. Development of a "First-Principles" Water Potential with Flexible Monomers. III. Liquid Phase Properties. , 2014, Journal of chemical theory and computation.
[51] P M Cullis,et al. Affinities of amino acid side chains for solvent water. , 1981, Biochemistry.
[52] Irwin D Kuntz,et al. Estimation of Absolute Free Energies of Hydration Using Continuum Methods: Accuracy of Partial Charge Models and Optimization of Nonpolar Contributions , 2022 .
[53] Volodymyr Babin,et al. Development of a "First Principles" Water Potential with Flexible Monomers: Dimer Potential Energy Surface, VRT Spectrum, and Second Virial Coefficient. , 2014, Journal of chemical theory and computation.
[54] P. Kollman,et al. Atomic charges derived from semiempirical methods , 1990 .
[55] A. Becke. A New Mixing of Hartree-Fock and Local Density-Functional Theories , 1993 .
[56] Ye Mei,et al. Predicting hydration free energies with a hybrid QM/MM approach: an evaluation of implicit and explicit solvation models in SAMPL4 , 2014, Journal of Computer-Aided Molecular Design.
[57] A. Becke. A multicenter numerical integration scheme for polyatomic molecules , 1988 .
[58] C. Breneman,et al. Determining atom‐centered monopoles from molecular electrostatic potentials. The need for high sampling density in formamide conformational analysis , 1990 .
[59] Y. M. Rhee,et al. Interpolated mechanics-molecular mechanics study of internal rotation dynamics of the chromophore unit in blue fluorescent protein and its variants. , 2012, The journal of physical chemistry. B.
[60] A. Tkatchenko,et al. Accurate and efficient method for many-body van der Waals interactions. , 2012, Physical review letters.
[61] Donald G. Truhlar,et al. 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 functionals and 12 other functionals , 2008 .
[62] J. Guthrie,et al. A blind challenge for computational solvation free energies: introduction and overview. , 2009, The journal of physical chemistry. B.
[63] J. Herbert,et al. Periodic boundary conditions for QM/MM calculations: Ewald summation for extended Gaussian basis sets. , 2013, The Journal of chemical physics.
[64] Matthew T. Geballe,et al. The SAMPL3 blind prediction challenge: transfer energy overview , 2012, Journal of Computer-Aided Molecular Design.
[65] T. P. Straatsma,et al. Treatment of rotational isomers in free energy evaluations. Analysis of the evaluation of free energy differences by molecular dynamics simulations of systems with rotational isomeric states , 1989 .
[66] Alán Aspuru-Guzik,et al. Advances in molecular quantum chemistry contained in the Q-Chem 4 program package , 2014, Molecular Physics.
[67] David L. Mobley,et al. Blind prediction of solvation free energies from the SAMPL4 challenge , 2014, Journal of Computer-Aided Molecular Design.