Directional Dependence of Hydrogen Bonds: a Density-based Energy Decomposition Analysis and Its Implications on Force Field Development.
暂无分享,去创建一个
Yingkai Zhang | Qin Wu | Zhenyu Lu | Nengjie Zhou | Yingkai Zhang | Qin Wu | Nengji Zhou | Zhenyu Lu
[1] T. Darden,et al. Simple Formulas for Improved Point-Charge Electrostatics in Classical Force Fields and Hybrid Quantum Mechanical/Molecular Mechanical Embedding. , 2008, International journal of quantum chemistry.
[2] W. Goddard,et al. Charge equilibration for molecular dynamics simulations , 1991 .
[3] Thomas A. Halgren,et al. The representation of van der Waals (vdW) interactions in molecular mechanics force fields: potential form, combination rules, and vdW parameters , 1992 .
[4] Qin Wu,et al. Empirical correction to density functional theory for van der Waals interactions , 2002 .
[5] Ad Bax,et al. An empirical backbone-backbone hydrogen-bonding potential in proteins and its applications to NMR structure refinement and validation. , 2004, Journal of the American Chemical Society.
[6] Hwanho Choi,et al. New angle‐dependent potential energy function for backbone–backbone hydrogen bond in protein–protein interactions , 2010, J. Comput. Chem..
[7] B. Thole. Molecular polarizabilities calculated with a modified dipole interaction , 1981 .
[8] A. Bondi. van der Waals Volumes and Radii , 1964 .
[9] Jean-Philip Piquemal,et al. Fragment-Localized Kohn-Sham Orbitals via a Singles Configuration-Interaction Procedure and Application to Local Properties and Intermolecular Energy Decomposition Analysis. , 2008, Journal of chemical theory and computation.
[10] Stefan Grimme,et al. Comparison of the performance of dispersion-corrected density functional theory for weak hydrogen bonds. , 2011, Physical chemistry chemical physics : PCCP.
[11] Mark S. Gordon,et al. Electrostatic energy in the effective fragment potential method: Theory and application to benzene dimer , 2007, J. Comput. Chem..
[12] Y. Mo,et al. Energy decomposition analysis of intermolecular interactions using a block-localized wave function approach , 2000 .
[13] 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.
[14] W. L. Jorgensen,et al. Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids , 1996 .
[15] Jirí Cerný,et al. Density functional theory augmented with an empirical dispersion term. Interaction energies and geometries of 80 noncovalent complexes compared with ab initio quantum mechanics calculations , 2007, J. Comput. Chem..
[16] C David Sherrill,et al. Oscillations in meta-generalized-gradient approximation potential energy surfaces for dispersion-bound complexes. , 2009, The Journal of chemical physics.
[17] P. Kollman,et al. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .
[18] Pengyu Y. Ren,et al. Consistent treatment of inter‐ and intramolecular polarization in molecular mechanics calculations , 2002, J. Comput. Chem..
[19] Sarah M. Tschampel,et al. TIP5P-Consistent Treatment of Electrostatics for Biomolecular Simulations. , 2007, Journal of chemical theory and computation.
[20] Pavel Hobza,et al. Stabilization and structure calculations for noncovalent interactions in extended molecular systems based on wave function and density functional theories. , 2010, Chemical reviews.
[21] 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.
[22] William H. Fink,et al. Frozen fragment reduced variational space analysis of hydrogen bonding interactions. Application to the water dimer , 1987 .
[23] D. Baker,et al. An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. , 2003, Journal of molecular biology.
[24] Norman L. Allinger,et al. Molecular mechanics. The MM3 force field for hydrocarbons. 1 , 1989 .
[25] S. F. Boys,et al. The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors , 1970 .
[26] Yuchun Lin,et al. Block-localized wavefunction (BLW) method at the density functional theory (DFT) level. , 2007, The journal of physical chemistry. A.
[27] M. Levitt,et al. Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. , 1976, Journal of molecular biology.
[28] Hwanho Choi,et al. Extended Morse function model for angle-dependent hydrogen bond in protein-protein interactions. , 2010, The journal of physical chemistry. B.
[29] Rustam Z. Khaliullin,et al. Unravelling the origin of intermolecular interactions using absolutely localized molecular orbitals. , 2007, The journal of physical chemistry. A.
[30] W. L. Jorgensen. The Many Roles of Computation in Drug Discovery , 2004, Science.
[31] Constantinos C. Pantelides,et al. Optimal Site Charge Models for Molecular Electrostatic Potentials , 2004 .
[32] 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..
[33] Cui Liu,et al. Development of a Polarizable Force Field Using Multiple Fluctuating Charges per Atom. , 2010, Journal of chemical theory and computation.
[34] Kazuo Kitaura,et al. A new energy decomposition scheme for molecular interactions within the Hartree‐Fock approximation , 1976 .
[35] D. Baker,et al. Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[36] Robert A. Wolkow,et al. Application of 25 density functionals to dispersion-bound homomolecular dimers , 2004 .
[37] T. P. Straatsma,et al. Free energy thermodynamic integrations in molecular dynamics simulations using a noniterative method to include electronic polarization , 1990 .
[38] Anthony J Stone,et al. Distributed Multipole Analysis: Stability for Large Basis Sets. , 2005, Journal of chemical theory and computation.
[39] Alexander D. MacKerell,et al. Determination of Electrostatic Parameters for a Polarizable Force Field Based on the Classical Drude Oscillator. , 2005, Journal of chemical theory and computation.
[40] Qin Wu,et al. A direct optimization method for calculating density functionals and exchange–correlation potentials from electron densities , 2003 .
[41] P. Kollman,et al. A well-behaved electrostatic potential-based method using charge restraints for deriving atomic char , 1993 .
[42] S. Grimme,et al. A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu. , 2010, The Journal of chemical physics.
[43] Donald G Truhlar,et al. Density functionals with broad applicability in chemistry. , 2008, Accounts of chemical research.
[44] J. Berg,et al. Molecular dynamics simulations of biomolecules , 2002, Nature Structural Biology.
[45] G. Hummer,et al. Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides. , 2009, The journal of physical chemistry. B.
[46] Clemence Corminboeuf,et al. Dispersion-corrected energy decomposition analysis for intermolecular interactions based on the BLW and dDXDM methods. , 2011, The journal of physical chemistry. A.
[47] Paul W Ayers,et al. Density-based energy decomposition analysis for intermolecular interactions with variationally determined intermediate state energies. , 2009, The Journal of chemical physics.
[48] Parr,et al. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. , 1988, Physical review. B, Condensed matter.
[49] Donald G Truhlar,et al. Including Charge Penetration Effects in Molecular Modeling. , 2010, Journal of chemical theory and computation.
[50] Steven J. Stuart,et al. Dynamical fluctuating charge force fields: Application to liquid water , 1994 .
[51] Mark S. Gordon,et al. Energy Decomposition Analyses for Many-Body Interaction and Applications to Water Complexes , 1996 .
[52] Stefan Grimme,et al. Semiempirical GGA‐type density functional constructed with a long‐range dispersion correction , 2006, J. Comput. Chem..
[53] David van der Spoel,et al. Molecular Dynamics Simulations of Water with Novel Shell-Model Potentials , 2001 .
[54] A. Becke. A multicenter numerical integration scheme for polyatomic molecules , 1988 .
[55] Francesc Illas,et al. Decomposition of the chemisorption bond by constrained variations: Order of the variations and construction of the variational spaces , 1992 .
[56] Haiyan Liu,et al. Refining the description of peptide backbone conformations improves protein simulations using the GROMOS 53A6 force field , 2009, J. Comput. Chem..
[57] Peter L. Freddolino,et al. Force field bias in protein folding simulations. , 2009, Biophysical journal.
[58] Artur Michalak,et al. A Combined Charge and Energy Decomposition Scheme for Bond Analysis. , 2009, Journal of chemical theory and computation.
[59] Ernest R. Davidson,et al. Energy partitioning of the self‐consistent field interaction energy of ScCO , 1989 .
[60] Weitao Yang,et al. Insights into Current Limitations of Density Functional Theory , 2008, Science.
[61] Mark S. Gordon,et al. The Effective Fragment Potential Method: A QM-Based MM Approach to Modeling Environmental Effects in Chemistry , 2001 .
[62] T. Voorhis,et al. Direct optimization method to study constrained systems within density-functional theory , 2005 .
[63] Jenn-Huei Lii,et al. The important role of lone-pairs in force field (MM4) calculations on hydrogen bonding in alcohols. , 2008, The journal of physical chemistry. A.
[64] Keiji Morokuma,et al. Molecular Orbital Studies of Hydrogen Bonds. III. C=O···H–O Hydrogen Bond in H2CO···H2O and H2CO···2H2O , 1971 .
[65] Michiel Sprik,et al. A polarizable model for water using distributed charge sites , 1988 .
[66] Hideaki Umeyama,et al. The origin of hydrogen bonding. An energy decomposition study , 1977 .
[67] C. Breneman,et al. Determining atom‐centered monopoles from molecular electrostatic potentials. The need for high sampling density in formamide conformational analysis , 1990 .
[68] Pengyu Y. Ren,et al. Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation , 2003 .
[69] I. Mayer,et al. Energy partitioning schemes. , 2006, Physical chemistry chemical physics : PCCP.
[70] P. Kollman,et al. Advancing beyond the atom‐centered model in additive and nonadditive molecular mechanics , 1997 .
[71] A. Garcia,et al. Microsecond simulations of the folding/unfolding thermodynamics of the Trp‐cage miniprotein , 2010, Proteins.
[72] A. Becke. Density-functional thermochemistry. III. The role of exact exchange , 1993 .
[73] Steven E Wheeler,et al. Integration Grid Errors for Meta-GGA-Predicted Reaction Energies: Origin of Grid Errors for the M06 Suite of Functionals. , 2010, Journal of chemical theory and computation.
[74] Alexander D. MacKerell,et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. , 1998, The journal of physical chemistry. B.
[75] Lori A Burns,et al. Assessment of the Performance of DFT and DFT-D Methods for Describing Distance Dependence of Hydrogen-Bonded Interactions. , 2011, Journal of chemical theory and computation.
[76] 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..
[77] Wilfred F van Gunsteren,et al. Biomolecular modeling: Goals, problems, perspectives. , 2006, Angewandte Chemie.
[78] Jean-Philip Piquemal,et al. Polarizable molecular dynamics simulation of Zn(II) in water using the AMOEBA force field. , 2010, Journal of Chemical Theory and Computation.
[79] M. V. Subbotin,et al. A quantum mechanical polarizable force field for biomolecular interactions , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[80] Pavel Hobza,et al. On the Structure and Geometry of Biomolecular Binding Motifs (Hydrogen-Bonding, Stacking, X-H···π): WFT and DFT Calculations. , 2010, Journal of chemical theory and computation.
[81] Xin Xu,et al. From The Cover: The X3LYP extended density functional for accurate descriptions of nonbond interactions, spin states, and thermochemical properties. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[82] Benoît Roux,et al. Modeling induced polarization with classical Drude oscillators: Theory and molecular dynamics simulation algorithm , 2003 .
[83] Yingkai Zhang,et al. Describing van der Waals interaction in diatomic molecules with generalized gradient approximations: The role of the exchange functional , 1997 .
[84] A. Becke,et al. Density-functional exchange-energy approximation with correct asymptotic behavior. , 1988, Physical review. A, General physics.
[85] David E. Bernholdt,et al. High performance computational chemistry: An overview of NWChem a distributed parallel application , 2000 .
[86] Margaret E. Johnson,et al. Current status of the AMOEBA polarizable force field. , 2010, The journal of physical chemistry. B.
[87] 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 .
[88] Wilfred F. van Gunsteren,et al. Development of a simple, self-consistent polarizable model for liquid water , 2003 .
[89] Weitao Yang,et al. A challenge for density functionals: Self-interaction error increases for systems with a noninteger number of electrons , 1998 .
[90] E. Vogt,et al. Semi-empirical atomic charges for use in computational chemistry of molecular sieves , 1998 .
[91] Alexander D. MacKerell,et al. Development of a polarizable intermolecular potential function (PIPF) for liquid amides and alkanes. , 2007, Journal of chemical theory and computation.
[92] Darrin M. York,et al. A chemical potential equalization method for molecular simulations , 1996 .
[93] J. Ponder,et al. Force fields for protein simulations. , 2003, Advances in protein chemistry.
[94] Jiali Gao,et al. Energy decomposition analysis based on a block-localized wavefunction and multistate density functional theory. , 2011, Physical chemistry chemical physics : PCCP.
[95] Patrick W. Fowler,et al. A model for the geometries of Van der Waals complexes , 1985 .
[96] Klaus Schulten,et al. Challenges in protein-folding simulations , 2010 .
[97] P. Kollman,et al. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? , 2000 .
[98] Jean-Philip Piquemal,et al. Gaussian Multipole Model (GMM). , 2010, Journal of chemical theory and computation.