An automated approach for the parameterization of accurate intermolecular force‐fields: Pyridine as a case study
暂无分享,去创建一个
Ivo Cacelli | Antonella Cimoli | Paolo Roberto Livotto | Giacomo Prampolini | I. Cacelli | G. Prampolini | P. R. Livotto | A. Cimoli
[1] K. Berka,et al. On the reliability of the AMBER force field and its empirical dispersion contribution for the description of noncovalent complexes. , 2010, Chemphyschem : a European journal of chemical physics and physical chemistry.
[2] F. Diederich,et al. Interactions with aromatic rings in chemical and biological recognition. , 2003, Angewandte Chemie.
[3] Yan Zhao,et al. Density Functionals for Noncovalent Interaction Energies of Biological Importance. , 2007, Journal of chemical theory and computation.
[4] Jonathan M. Goodman,et al. Hydrogen Bonding and π-Stacking: How Reliable are Force Fields? A Critical Evaluation of Force Field Descriptions of Nonbonded Interactions , 2009, J. Chem. Inf. Model..
[5] Alexander D. MacKerell,et al. All‐atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data , 2000 .
[6] J. Šponer,et al. Nature of Nucleic Acid−Base Stacking: Nonempirical ab Initio and Empirical Potential Characterization of 10 Stacked Base Dimers. Comparison of Stacked and H-Bonded Base Pairs , 1996 .
[7] William L. Jorgensen,et al. OPLS all‐atom force field for carbohydrates , 1997 .
[8] H. R. Noori. on "Understanding molecular simulations" , 2013 .
[9] 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.
[10] C. Zannoni,et al. Can nematic transitions be predicted by atomistic simulations? A computational study of the odd-even effect. , 2004, Chemphyschem : a European journal of chemical physics and physical chemistry.
[11] I. Cacelli,et al. How the Odd-Even Effects on the Inter-Molecular Potentials Propagate to the Order Parameter in the 4-Cyano-4′n-Alkylbiphenyl Series , 2007 .
[12] Yang Song,et al. Developing ab initio quality force fields from condensed phase quantum-mechanics/molecular-mechanics calculations through the adaptive force matching method. , 2008, The Journal of chemical physics.
[13] J. Berg,et al. Molecular dynamics simulations of biomolecules , 2002, Nature Structural Biology.
[14] Pavel Hobza,et al. Potential Energy Surface for the Benzene Dimer. Results of ab Initio CCSD(T) Calculations Show Two Nearly Isoenergetic Structures: T-Shaped and Parallel-Displaced , 1996 .
[15] Christopher M Baker,et al. Modeling Aromatic Liquids: Toluene, Phenol, and Pyridine. , 2007, Journal of chemical theory and computation.
[16] 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.
[17] Liliana Wroblewska,et al. A theoretical and experimental 14N NMR study of association of pyridine , 2001 .
[18] Pavel Hobza,et al. Assessment of the MP2 method, along with several basis sets, for the computation of interaction energies of biologically relevant hydrogen bonded and dispersion bound complexes. , 2007, The journal of physical chemistry. A.
[19] G. Pálinkás,et al. Investigation of the Structure of Liquid Pyridine: a Molecular Dynamics Simulation, an RISM, and an X-ray Diffraction Study , 1996 .
[20] S. Wetmore,et al. Evidence for Stabilization of DNA/RNA-Protein Complexes Arising from Nucleobase-Amino Acid Stacking and T-Shaped Interactions. , 2009, Journal of chemical theory and computation.
[21] I. Cacelli,et al. Structure and dynamics of mesogens using intermolecular potentials derived from ab initio calculations , 2007 .
[22] Edward G Hohenstein,et al. Assessment of the Performance of the M05-2X and M06-2X Exchange-Correlation Functionals for Noncovalent Interactions in Biomolecules. , 2008, Journal of chemical theory and computation.
[23] Claudio Amovilli,et al. Calculation of the intermolecular energy of large molecules by a fragmentation scheme: Application to the 4-n-pentyl-4′- cyanobiphenyl (5CB) dimer , 2002 .
[24] Donald G. Truhlar,et al. Basis-set extrapolation , 1998 .
[25] W. L. Jorgensen,et al. Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids , 1996 .
[26] G. Prampolini,et al. Computational study through atomistic potentials of a partial bilayer liquid crystal: structure and dynamics , 2009 .
[27] B. Stryczek. The Microscopic friction tensor for spinning and tumbling motions in liquid pyridine , 1986 .
[28] G A Petsko,et al. Aromatic-aromatic interaction: a mechanism of protein structure stabilization. , 1985, Science.
[29] P. Kollman,et al. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .
[30] William A. Goddard,et al. The Hessian biased singular value decomposition method for optimization and analysis of force fields , 1996 .
[31] Bobby G. Sumpter,et al. Assessment of standard force field models against high‐quality ab initio potential curves for prototypes of π–π, CH/π, and SH/π interactions , 2009, J. Comput. Chem..
[32] T. Darden,et al. A smooth particle mesh Ewald method , 1995 .
[33] T. Darden,et al. Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .
[34] Jirí Cerný,et al. Scaled MP3 non-covalent interaction energies agree closely with accurate CCSD(T) benchmark data. , 2009, Chemphyschem : a European journal of chemical physics and physical chemistry.
[35] G. Prampolini,et al. Atomistic computer simulation and experimental study on the dynamics of the n-cyanobiphenyls mesogenic series. , 2008, Journal of Physical Chemistry B.
[36] 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 .
[37] Michael P. Allen,et al. Advances in the Computer Simulations of Liquid Crystals , 2000 .
[38] Michal Otyepka,et al. Large-scale compensation of errors in pairwise-additive empirical force fields: comparison of AMBER intermolecular terms with rigorous DFT-SAPT calculations. , 2010, Physical chemistry chemical physics : PCCP.
[39] William L. Jorgensen,et al. Aromatic-aromatic interactions: free energy profiles for the benzene dimer in water, chloroform, and liquid benzene , 1990 .
[40] I. Cacelli,et al. Computer simulation of solid and liquid benzene with an atomistic interaction potential derived from ab initio calculations. , 2004, Journal of the American Chemical Society.
[41] J. Šponer,et al. Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α/γ Conformers , 2007 .
[42] Samuel Krimm,et al. Potential energy functions: From consistent force fields to spectroscopically determined polarizable force fields , 2003, Biopolymers.
[43] 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..
[44] S. Tsuzuki,et al. Model chemistry calculations of thiophene dimer interactions: origin of pi-stacking. , 2002, Journal of the American Chemical Society.
[45] I. Cacelli,et al. Atomistic simulation of a nematogen using a force field derived from quantum chemical calculations. , 2005, The journal of physical chemistry. B.
[46] H. Eckerlebe,et al. Effect of the Onsager coefficient and internal relaxation modes on spinodal decomposition in the high molecular isotopic blend polystyrene/deutero‐polystyrene studied with small angle neutron scattering , 1996 .
[47] Claudio Zannoni,et al. Towards in silico liquid crystals. Realistic transition temperatures and physical properties for n-cyanobiphenyls via molecular dynamics simulations. , 2009, Chemphyschem : a European journal of chemical physics and physical chemistry.
[48] Christopher M. Care,et al. Computer simulation of liquid crystals , 2005 .
[49] Alexander D. MacKerell. Empirical force fields for biological macromolecules: Overview and issues , 2004, J. Comput. Chem..
[50] G. Prampolini,et al. Subdiffusive dynamics of a liquid crystal in the isotropic phase. , 2008, The Journal of chemical physics.
[51] I. Cacelli,et al. Liquid crystal properties of the n-alkyl-cyanobiphenyl series from atomistic simulations with ab initio derived force fields. , 2007, The journal of physical chemistry. B.
[52] Krzysztof Szalewicz,et al. Intermolecular potentials based on symmetry-adapted perturbation theory with dispersion energies from time-dependent density-functional calculations. , 2005, The Journal of chemical physics.
[53] D. Truhlar,et al. A new local density functional for main-group thermochemistry, transition metal bonding, thermochemical kinetics, and noncovalent interactions. , 2006, The Journal of chemical physics.
[54] Stefan Grimme,et al. Accurate description of van der Waals complexes by density functional theory including empirical corrections , 2004, J. Comput. Chem..
[55] A. Becke. Density-functional thermochemistry. III. The role of exact exchange , 1993 .
[56] M. Schütz,et al. Density-functional theory-symmetry-adapted intermolecular perturbation theory with density fitting: a new efficient method to study intermolecular interaction energies. , 2005, The Journal of chemical physics.
[57] William L. Jorgensen,et al. Development of an all-atom force field for heterocycles. Properties of liquid pyridine and diazenes , 1998 .
[58] Alexander D. MacKerell,et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. , 1998, The journal of physical chemistry. B.
[59] Ivo Cacelli,et al. Force‐field modeling through quantum mechanical calculations: Molecular dynamics simulations of a nematogenic molecule in its condensed phases , 2009, J. Comput. Chem..
[60] Junmei Wang,et al. Development and testing of a general amber force field , 2004, J. Comput. Chem..
[61] M. Karplus,et al. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .
[62] Richard L. Jaffe,et al. A quantum chemistry study of benzene dimer , 1996 .
[63] Cooperative changes in the chiroptical properties of DNA induced by methanol. , 1984, Biopolymers.
[64] Stephen Neidle,et al. Principles of nucleic acid structure , 2007 .
[66] S. Tsuzuki,et al. Origin of attraction and directionality of the pi/pi interaction: model chemistry calculations of benzene dimer interaction. , 2002, Journal of the American Chemical Society.
[67] H. Berendsen,et al. A consistent empirical potential for water–protein interactions , 1984 .
[68] T. Halgren. Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94 , 1996, J. Comput. Chem..
[69] H. Berendsen,et al. Molecular dynamics with coupling to an external bath , 1984 .
[70] Ivo Cacelli,et al. Parametrization and Validation of Intramolecular Force Fields Derived from DFT Calculations. , 2007, Journal of chemical theory and computation.
[71] Edward G Hohenstein,et al. An assessment of theoretical methods for nonbonded interactions: comparison to complete basis set limit coupled-cluster potential energy curves for the benzene dimer, the methane dimer, benzene-methane, and benzene-H2S. , 2009, The journal of physical chemistry. A.
[72] C. Sherrill,et al. Effects of heteroatoms on aromatic pi-pi interactions: benzene-pyridine and pyridine dimer. , 2009, The journal of physical chemistry. A.
[73] R. Zahradník,et al. The World of Non-Covalent Interactions: 2006 , 2006 .
[74] M. Holz,et al. EXPERIMENTAL STUDY OF DYNAMIC ISOTOPE EFFECTS IN MOLECULAR LIQUIDS : DETECTION OF TRANSLATION-ROTATION COUPLING , 1996 .
[75] Kurt Kremer,et al. Computer simulations for macromolecular science , 2003 .
[76] T. Aminabhavi,et al. Density, Viscosity, Refractive Index, and Speed of Sound in the Binary Mixtures of Tri-n-butylamine + Triethylamine, + Tetrahydrofuran, + Tetradecane, + Tetrachloroethylene, + Pyridine, or + Trichloroethylene at (298.15, 303.15, and 308.15) K , 2003 .
[77] Stefan Grimme,et al. Semiempirical GGA‐type density functional constructed with a long‐range dispersion correction , 2006, J. Comput. Chem..
[78] B. Mishra,et al. Stacking and spreading interaction in N-heteroaromatic systems. , 2010, The journal of physical chemistry. A.
[79] Stefan Grimme,et al. Van der Waals interactions in aromatic systems: structure and energetics of dimers and trimers of pyridine. , 2005, Chemphyschem : a European journal of chemical physics and physical chemistry.
[80] Chemical Detail Force Fields for Mesogenic Molecules. , 2009, Journal of chemical theory and computation.
[81] Christopher J. Woods,et al. Biomolecular simulation and modelling: status, progress and prospects , 2008, Journal of The Royal Society Interface.
[82] Masuhiro Mikami,et al. Effects of the higher electron correlation correction on the calculated intermolecular interaction energies of benzene and naphthalene dimers: comparison between MP2 and CCSD(T) calculations , 2000 .
[83] C David Sherrill,et al. An Assessment of Density Functional Methods for Potential Energy Curves of Nonbonded Interactions: The XYG3 and B97-D Approximations. , 2010, Journal of chemical theory and computation.