Perspective: Ab initio force field methods derived from quantum mechanics
暂无分享,去创建一个
[1] Nohad Gresh,et al. Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short‐range penetration correction up to quadrupoles , 2016, J. Comput. Chem..
[2] Mark S Gordon,et al. Effective fragment potential study of the interaction of DNA bases. , 2011, The journal of physical chemistry. A.
[3] G. Beran,et al. Spatially Homogeneous QM/MM for Systems of Interacting Molecules with on-the-Fly ab Initio Force-Field Parametrization. , 2010, Journal of chemical theory and computation.
[4] K. Kitaura,et al. Fragment molecular orbital method: an approximate computational method for large molecules , 1999 .
[5] Jean-Philip Piquemal,et al. GEM*: A Molecular Electronic Density-Based Force Field for Molecular Dynamics Simulations. , 2014, Journal of chemical theory and computation.
[6] William L. Jorgensen,et al. Optimized intermolecular potential functions for amides and peptides. Structure and properties of liquid amides , 1985 .
[7] N. Gresh,et al. Modeling copper(I) complexes: SIBFA molecular mechanics versus ab initio energetics and geometrical arrangements , 2002 .
[8] Ming-Jing Hwang,et al. Derivation of Class II Force Fields. 2. Derivation and Characterization of a Class II Force Field, CFF93, for the Alkyl Functional Group and Alkane Molecules , 1994 .
[9] Michael A Collins,et al. Approximate ab initio energies by systematic molecular fragmentation. , 2005, The Journal of chemical physics.
[10] Alexander D. MacKerell,et al. CHARMM fluctuating charge force field for proteins: II Protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model , 2004, J. Comput. Chem..
[11] P. Claverie,et al. Improvements of the continuum model. 1. Application to the calculation of the vaporization thermodynamic quantities of nonassociated liquids , 1988 .
[12] Jacopo Tomasi,et al. An Integrated Effective Fragment—Polarizable Continuum Approach to Solvation: Theory and Application to Glycine , 2002 .
[13] L. J. Schaad,et al. Deviations from Pairwise Additivity in Intermolecular Potentials , 1967 .
[14] P. Claverie,et al. Theoretical studies of molecular conformation. Derivation of an additive procedure for the computation of intramolecular interaction energies. Comparison withab initio SCF computations , 1984 .
[15] Mark S Gordon,et al. Charge transfer interaction in the effective fragment potential method. , 2006, The Journal of chemical physics.
[16] Nohad Gresh,et al. Toward a Separate Reproduction of the Contributions to the Hartree-Fock and DFT Intermolecular Interaction Energies by Polarizable Molecular Mechanics with the SIBFA Potential. , 2007, Journal of chemical theory and computation.
[17] M. Alderton,et al. Distributed multipole analysis , 2006 .
[18] C. Bannwarth,et al. A general intermolecular force field based on tight-binding quantum chemical calculations. , 2017, The Journal of chemical physics.
[19] M. Gordon,et al. Multipole Moments in the Effective Fragment Potential Method. , 2017, The journal of physical chemistry. A.
[20] Nohad Gresh,et al. Improved Formulas for the Calculation of the Electrostatic Contribution to the Intermolecular Interaction Energy from Multipolar Expansion of the Electronic Distribution. , 2003, The journal of physical chemistry. A.
[21] Pengyu Y. Ren,et al. Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation , 2003 .
[22] Nohad Gresh,et al. Interaction of neutral and zwitterionic glycine with Zn2+ in gas phase: ab initio and SIBFA molecular mechanics calculations , 2000 .
[23] Kazuo Kitaura,et al. The three-body fragment molecular orbital method for accurate calculations of large systems , 2006 .
[24] Jacopo Tomasi,et al. Approximate evaluations of the electrostatic free energy and internal energy changes in solution processes , 1982 .
[25] Arieh Warshel,et al. Polarizable Force Fields: History, Test Cases, and Prospects. , 2007, Journal of chemical theory and computation.
[26] Mark S Gordon,et al. Water-benzene interactions: an effective fragment potential and correlated quantum chemistry study. , 2009, The journal of physical chemistry. A.
[27] William H. Fink,et al. Frozen fragment reduced variational space analysis of hydrogen bonding interactions. Application to the water dimer , 1987 .
[28] A. Stone,et al. Ab Initio Atom-Atom Potentials Using CamCASP: Theory and Application to Many-Body Models for the Pyridine Dimer. , 2015, Journal of chemical theory and computation.
[29] Wei Zhang,et al. Strike a balance: Optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides , 2006, J. Comput. Chem..
[30] M. Karplus,et al. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .
[31] Kazuo Kitaura,et al. Energy Decomposition Analysis of Molecular Interactions , 1981 .
[32] Mark S Gordon,et al. Alanine: then there was water. , 2009, The journal of physical chemistry. B.
[33] Alexander D. MacKerell,et al. Development of CHARMM polarizable force field for nucleic acid bases based on the classical Drude oscillator model. , 2011, The journal of physical chemistry. B.
[34] Yonaton Heit,et al. Exploiting space‐group symmetry in fragment‐based molecular crystal calculations , 2014, J. Comput. Chem..
[35] I. Adamovic,et al. Dynamic polarizability, dispersion coefficient C6 and dispersion energy in the effective fragment potential method , 2005 .
[36] Spencer R Pruitt,et al. Efficient and accurate fragmentation methods. , 2014, Accounts of chemical research.
[37] N. Gresh,et al. Interactions within the alcohol dehydrogenase Zn(II)-metalloenzyme active site: Interplay between subvalence, electron correlation/dispersion, and charge transfer/induction effects , 2011 .
[38] Anthony J. Stone,et al. Distributed multipole analysis, or how to describe a molecular charge distribution , 1981 .
[39] Peter A. Kollman,et al. AMBER: Assisted model building with energy refinement. A general program for modeling molecules and their interactions , 1981 .
[40] Mark S. Gordon,et al. A combined discrete/continuum solvation model: Application to glycine , 2000 .
[41] Jan H. Jensen,et al. Intermolecular exchange-induction and charge transfer: Derivation of approximate formulas using nonorthogonal localized molecular orbitals , 2001 .
[42] Jan H. Jensen,et al. Continuum solvation of large molecules described by QM/MM: a semi-iterative implementation of the PCM/EFP interface , 2003 .
[43] C Z Wang,et al. Molecule intrinsic minimal basis sets. I. Exact resolution of ab initio optimized molecular orbitals in terms of deformed atomic minimal-basis orbitals. , 2004, The Journal of chemical physics.
[44] Mark S Gordon,et al. Solvent effects on the S(N)2 reaction: Application of the density functional theory-based effective fragment potential method. , 2005, The journal of physical chemistry. A.
[45] Nohad Gresh,et al. Representation of Zn(II) complexes in polarizable molecular mechanics. Further refinements of the electrostatic and short‐range contributions. Comparisons with parallel ab initio computations , 2005, J. Comput. Chem..
[46] Gregory J O Beran,et al. Approximating quantum many-body intermolecular interactions in molecular clusters using classical polarizable force fields. , 2009, The Journal of chemical physics.
[47] W. L. Jorgensen,et al. The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. , 1988, Journal of the American Chemical Society.
[48] Jesse G. McDaniel,et al. Physically-motivated force fields from symmetry-adapted perturbation theory. , 2013, The journal of physical chemistry. A.
[49] John Z. H. Zhang,et al. Molecular fractionation with conjugate caps for full quantum mechanical calculation of protein-molecule interaction energy , 2003 .
[50] K. Tang,et al. An improved simple model for the van der Waals potential based on universal damping functions for the dispersion coefficients , 1984 .
[51] Nohad Gresh,et al. Energetics of Zn2+ binding to a series of biologically relevant ligands: A molecular mechanics investigation grounded on ab initio self‐consistent field supermolecular computations , 1995, J. Comput. Chem..
[52] Nohad Gresh,et al. S/G-1: an ab initio force-field blending frozen Hermite Gaussian densities and distributed multipoles. Proof of concept and first applications to metal cations. , 2014, The journal of physical chemistry. A.
[53] Michael A Collins,et al. Accuracy and efficiency of electronic energies from systematic molecular fragmentation. , 2006, The Journal of chemical physics.
[54] Kaori Fukuzawa,et al. Fragment molecular orbital method: use of approximate electrostatic potential , 2002 .
[55] M. Gordon,et al. Charge transfer interaction using quasiatomic minimal-basis orbitals in the effective fragment potential method. , 2013, The Journal of chemical physics.
[56] 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.
[57] Jan H. Jensen,et al. Effective fragment molecular orbital method: a merger of the effective fragment potential and fragment molecular orbital methods. , 2010, The journal of physical chemistry. A.
[58] G. Beran,et al. Accurate Molecular Crystal Lattice Energies from a Fragment QM/MM Approach with On-the-Fly Ab Initio Force Field Parametrization. , 2011, Journal of chemical theory and computation.
[59] Mark S Gordon,et al. Benzene-pyridine interactions predicted by the effective fragment potential method. , 2011, The journal of physical chemistry. A.
[60] L. Slipchenko,et al. Accurate Prediction of Noncovalent Interaction Energies with the Effective Fragment Potential Method: Comparison of Energy Components to Symmetry-Adapted Perturbation Theory for the S22 Test Set. , 2012, Journal of chemical theory and computation.
[61] G. Beran. Modeling Polymorphic Molecular Crystals with Electronic Structure Theory. , 2016, Chemical reviews.
[62] T. Heine,et al. Extension of the Universal Force Field to Metal-Organic Frameworks. , 2014, Journal of chemical theory and computation.
[63] Norman L. Allinger,et al. Molecular mechanics. The MM3 force field for hydrocarbons. 1 , 1989 .
[64] M. Gordon,et al. The R(-7) Dispersion Interaction in the General Effective Fragment Potential Method. , 2014, Journal of chemical theory and computation.
[65] Lennart Nilsson,et al. Empirical energy functions for energy minimization and dynamics of nucleic acids , 1986 .
[66] Peter Politzer,et al. Chemical Applications of Atomic and Molecular Electrostatic Potentials: "Reactivity, Structure, Scattering, And Energetics Of Organic, Inorganic, And Biological Systems" , 2013 .
[67] Shridhar R. Gadre,et al. Ab initio quality one‐electron properties of large molecules: Development and testing of molecular tailoring approach , 2003, J. Comput. Chem..
[68] Spencer R Pruitt,et al. Fragmentation methods: a route to accurate calculations on large systems. , 2012, Chemical reviews.
[69] T. Darden,et al. Intermolecular electrostatic energies using density fitting. , 2005, The Journal of chemical physics.
[70] P. Kollman,et al. An all atom force field for simulations of proteins and nucleic acids , 1986, Journal of computational chemistry.
[71] Donald G Truhlar,et al. Incorporation of a QM/MM buffer zone in the variational double self-consistent field method. , 2008, The journal of physical chemistry. B.
[72] W. Goddard,et al. UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations , 1992 .
[73] M. Gordon,et al. Gradients of the polarization energy in the effective fragment potential method. , 2006, The Journal of chemical physics.
[74] S. Grimme. A General Quantum Mechanically Derived Force Field (QMDFF) for Molecules and Condensed Phase Simulations. , 2014, Journal of chemical theory and computation.
[75] Monica H Lamm,et al. Modeling styrene-styrene interactions. , 2006, The journal of physical chemistry. A.
[76] Mark S Gordon,et al. Ab initio investigation of the aqueous solvation of the nitrate ion. , 2015, Physical chemistry chemical physics : PCCP.
[77] Nohad Gresh,et al. Conformational properties of a model alanyl dipeptide and of alanine‐derived oligopeptides: Effects of solvation in water and in organic solvents—A combined SIBFA/continuum reaction field, ab initio self‐consistent field, and density functional theory investigation , 1998 .
[78] Benjamin Stamm,et al. Truncated Conjugate Gradient: An Optimal Strategy for the Analytical Evaluation of the Many-Body Polarization Energy and Forces in Molecular Simulations , 2016, Journal of chemical theory and computation.
[79] Mark S Gordon,et al. Analytic Gradients for the Effective Fragment Molecular Orbital Method. , 2016, Journal of chemical theory and computation.
[80] Charles L. Brooks,et al. CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations , 2004, J. Comput. Chem..
[81] Jesse G. McDaniel,et al. First-principles many-body force fields from the gas phase to liquid: a "universal" approach. , 2014, The journal of physical chemistry. B.
[82] P. N. Day,et al. A study of water clusters using the effective fragment potential and Monte Carlo simulated annealing , 2000 .
[83] G. Voth,et al. Multi-state Approach to Chemical Reactivity in Fragment Based Quantum Chemistry Calculations. , 2013, Journal of chemical theory and computation.
[84] G. Beran,et al. Predicting Organic Crystal Lattice Energies with Chemical Accuracy , 2010 .
[85] J. Tomasi,et al. Electrostatic interaction of a solute with a continuum. A direct utilizaion of AB initio molecular potentials for the prevision of solvent effects , 1981 .
[86] Mark S Gordon,et al. Modeling pi-pi interactions with the effective fragment potential method: the benzene dimer and substituents. , 2008, The journal of physical chemistry. A.
[87] Pengyu Y. Ren,et al. The Polarizable Atomic Multipole-based AMOEBA Force Field for Proteins. , 2013, Journal of chemical theory and computation.
[88] Ruhong Zhou,et al. Parametrizing a polarizable force field from ab initio data. I. The fluctuating point charge model , 1999 .
[89] P. Claverie,et al. The exact multicenter multipolar part of a molecular charge distribution and its simplified representations , 1988 .
[90] Ilya Kaliman,et al. LIBEFP: A new parallel implementation of the effective fragment potential method as a portable software library , 2013, J. Comput. Chem..
[91] Ryan P A Bettens,et al. Energy-Based Molecular Fragmentation Methods. , 2015, Chemical reviews.
[92] Jan H. Jensen,et al. Mapping Enzymatic Catalysis Using the Effective Fragment Molecular Orbital Method: Towards all ab initio Biochemistry , 2012, PloS one.
[93] T. Darden,et al. Towards a force field based on density fitting. , 2006, The Journal of chemical physics.
[94] T. Halgren,et al. Polarizable force fields. , 2001, Current opinion in structural biology.
[95] Nohad Gresh,et al. Intermolecular interactions: Elaboration on an additive procedure including an explicit charge-transfer contribution , 1986 .
[96] P. Fowler,et al. Long-range and overlap effects on collision-induced properties , 1992 .
[97] Guohui Li,et al. Advancement of polarizable force field and its use for molecular modeling and design. , 2015, Advances in experimental medicine and biology.
[98] S. Durell,et al. Specificity of acyl transfer from 2-mercaptobenzamide thioesters to the HIV-1 nucleocapsid protein. , 2007, Journal of the American Chemical Society.
[99] N. Gresh,et al. A molecular mechanics/continuum reaction field investigation of the interactions between polar amino acid side chains in water and organic solvents , 1995 .
[100] Nohad Gresh,et al. Model, Multiply Hydrogen-Bonded Water Oligomers (N = 3−20). How Closely Can a Separable, ab Initio-Grounded Molecular Mechanics Procedure Reproduce the Results of Supermolecule Quantum Chemical Computations? , 1997 .
[101] Y. Mo,et al. Energy decomposition analysis of intermolecular interactions using a block-localized wave function approach , 2000 .
[102] P. Claverie,et al. Computations of intermolecular interactions: Expansion of a charge-transfer energy contribution in the framework of an additive procedure. Applications to hydrogen-bonded systems , 1982 .
[103] 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.
[104] Alexandre Tkatchenko,et al. Two- and three-body interatomic dispersion energy contributions to binding in molecules and solids. , 2010, The Journal of chemical physics.
[105] Nohad Gresh,et al. Complexes of Pentahydrated Zn2+with Guanine, Adenine, and the Guanine−Cytosine and Adenine−Thymine Base Pairs. Structures and Energies Characterized by Polarizable Molecular Mechanics and ab Initio Calculations , 1999 .
[106] Ming-Jing Hwang,et al. Derivation of class II force fields. I. Methodology and quantum force field for the alkyl functional group and alkane molecules , 1994, J. Comput. Chem..
[107] M. Randic,et al. The theory of intermolecular forces in the region of small orbital overlap , 1965, Proceedings of the Royal Society of London. Series A. Mathematical and Physical Sciences.
[108] Yuri Alexeev,et al. Importance of Three-Body Interactions in Molecular Dynamics Simulations of Water Demonstrated with the Fragment Molecular Orbital Method. , 2016, Journal of chemical theory and computation.
[109] Jacopo Tomasi,et al. Electrostatic interaction of a solute with a continuum. Improved description of the cavity and of the surface cavity bound charge distribution. , 1987 .
[110] J. Herbert,et al. An efficient, fragment-based electronic structure method for molecular systems: self-consistent polarization with perturbative two-body exchange and dispersion. , 2011, The Journal of chemical physics.
[111] M. Gordon,et al. Dispersion Interactions in QM/EFP. , 2017, The journal of physical chemistry. A.
[112] Jirí Cerný,et al. Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs. , 2006, Physical chemistry chemical physics : PCCP.
[113] A. Stone,et al. Atom–atom potentials from ab initio calculations , 2007 .
[114] Kuang Yu,et al. Transferable next-generation force fields from simple liquids to complex materials. , 2015, Accounts of chemical research.
[115] M. Gordon,et al. Derivation and Implementation of the Gradient of the R(-7) Dispersion Interaction in the Effective Fragment Potential Method. , 2016, The journal of physical chemistry. A.
[116] Chris-Kriton Skylaris,et al. Energy decomposition analysis approaches and their evaluation on prototypical protein-drug interaction patterns. , 2015, Chemical Society Reviews.
[117] Emppu Salonen,et al. Polarizable force fields. , 2013, Methods in molecular biology.
[118] A. Stone,et al. Beyond Born-Mayer: Improved Models for Short-Range Repulsion in ab Initio Force Fields. , 2016, Journal of chemical theory and computation.
[119] U. Singh,et al. A NEW FORCE FIELD FOR MOLECULAR MECHANICAL SIMULATION OF NUCLEIC ACIDS AND PROTEINS , 1984 .
[120] Spencer R Pruitt,et al. Surface affinity of the hydronium ion: the effective fragment potential and umbrella sampling. , 2014, The journal of physical chemistry. B.
[121] Mark S Gordon,et al. Fully Integrated Effective Fragment Molecular Orbital Method. , 2013, Journal of chemical theory and computation.
[122] Mark S. Gordon,et al. Damping functions in the effective fragment potential method , 2009 .
[123] Eric D. Glendening,et al. Natural energy decomposition analysis: An energy partitioning procedure for molecular interactions with application to weak hydrogen bonding, strong ionic, and moderate donor–acceptor interactions , 1994 .
[124] Edward Teller,et al. Interaction of the van der Waals Type Between Three Atoms , 1943 .
[125] John Z H Zhang,et al. Theoretical method for full ab initio calculation of DNA/RNA-ligand interaction energy. , 2004, The Journal of chemical physics.
[126] Rustam Z. Khaliullin,et al. Unravelling the origin of intermolecular interactions using absolutely localized molecular orbitals. , 2007, The journal of physical chemistry. A.
[127] Shridhar R. Gadre,et al. Molecular Tailoring Approach for Simulation of Electrostatic Properties , 1994 .
[128] T. Darden,et al. Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .
[129] Norman L. Allinger,et al. Molecular mechanics. The MM3 force field for hydrocarbons. 3. The van der Waals' potentials and crystal data for aliphatic and aromatic hydrocarbons , 1989 .
[130] M. Gordon,et al. Methanol-water mixtures: a microsolvation study using the effective fragment potential method. , 2006, The journal of physical chemistry. A.
[131] Nohad Gresh,et al. Toward accurate solvation dynamics of lanthanides and actinides in water using polarizable force fields: from gas-phase energetics to hydration free energies , 2012, Theoretical Chemistry Accounts.
[132] Jacopo Tomasi,et al. Nonequilibrium solvation: An ab initio quantum‐mechanical method in the continuum cavity model approximation , 1993 .
[133] Jiali Gao,et al. The Design of a Next Generation Force Field: The X-POL Potential. , 2007, Journal of chemical theory and computation.
[134] Mark S. Gordon,et al. The Effective Fragment Potential Method: A QM-Based MM Approach to Modeling Environmental Effects in Chemistry , 2001 .
[135] M. Gordon,et al. Accurate first principles model potentials for intermolecular interactions. , 2013, Annual review of physical chemistry.
[136] Gregory J O Beran,et al. Practical quantum mechanics-based fragment methods for predicting molecular crystal properties. , 2012, Physical chemistry chemical physics : PCCP.
[137] Hui Li,et al. Energy decomposition analysis of covalent bonds and intermolecular interactions. , 2009, The Journal of chemical physics.
[138] Mark S. Gordon,et al. An effective fragment method for modeling solvent effects in quantum mechanical calculations , 1996 .
[139] Michael A. Collins,et al. Accurate treatment of nonbonded interactions within systematic molecular fragmentation , 2009 .
[140] Jacopo Tomasi,et al. Molecular Interactions in Solution: An Overview of Methods Based on Continuous Distributions of the Solvent , 1994 .
[141] Jan H. Jensen,et al. Modeling intermolecular exchange integrals between nonorthogonal molecular orbitals , 1996 .
[142] Norman L. Allinger,et al. Molecular mechanics. The MM3 force field for hydrocarbons. 2. Vibrational frequencies and thermodynamics , 1989 .
[143] G. Beran,et al. Accidental Degeneracy in Crystalline Aspirin: New Insights from High-Level ab Initio Calculations , 2012 .
[144] Paul S. Bagus,et al. A new analysis of charge transfer and polarization for ligand–metal bonding: Model studies of Al4CO and Al4NH3 , 1984 .
[145] Jenn-Huei Lii,et al. The MM3 force field for amides, polypeptides and proteins , 1991 .
[146] David J. Willock,et al. The relaxation of molecular crystal structures using a distributed multipole electrostatic model , 1995, J. Comput. Chem..
[147] M. Gordon,et al. The dispersion interaction between quantum mechanics and effective fragment potential molecules. , 2012, The Journal of chemical physics.
[148] Nohad Gresh,et al. Cation–ligand interactions: Reproduction of extended basis set Ab initio SCF computations by the SIBFA 2 additive procedure , 1985 .
[149] Darrin M. York,et al. The fast Fourier Poisson method for calculating Ewald sums , 1994 .
[150] Nohad Gresh,et al. Intermolecular interactions: Reproduction of the results of ab initio supermolecule computations by an additive procedure , 2009 .
[151] T. Darden,et al. A smooth particle mesh Ewald method , 1995 .
[152] G. Beran,et al. What Governs the Proton Ordering in Ice XV , 2013 .