An Efficient Method to Evaluate Intermolecular Interaction Energies in Large Systems Using Overlapping Multicenter ONIOM and the Fragment Molecular Orbital Method.
暂无分享,去创建一个
Kenneth M Merz | Kazuo Kitaura | Dmitri G Fedorov | K. Merz | K. Kitaura | D. Fedorov | I. Nakanishi | N. Asada | Isao Nakanishi | Naoya Asada
[1] Lori A Burns,et al. Basis set convergence of the coupled-cluster correction, δ(MP2)(CCSD(T)): best practices for benchmarking non-covalent interactions and the attendant revision of the S22, NBC10, HBC6, and HSG databases. , 2011, The Journal of chemical physics.
[2] Pavel Hobza,et al. Comparative Study of Selected Wave Function and Density Functional Methods for Noncovalent Interaction Energy Calculations Using the Extended S22 Data Set. , 2010, Journal of chemical theory and computation.
[3] Sotiris S. Xantheas,et al. Cooperativity and Hydrogen Bonding Network in Water Clusters , 2000 .
[4] Kazuo Kitaura,et al. The importance of three-body terms in the fragment molecular orbital method. , 2004, The Journal of chemical physics.
[5] Jacob Kongsted,et al. Accurate predictions of nonpolar solvation free energies require explicit consideration of binding-site hydration. , 2011, Journal of the American Chemical Society.
[6] Xin Xu,et al. Exploring the Sodium Cation Location and Aluminum Distribution in ZSM-5: A Systematic Study by the Extended ONIOM (XO) Method , 2011 .
[7] S. F. Boys,et al. The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors , 1970 .
[8] Thomas A. Halgren,et al. Merck molecular force field. IV. conformational energies and geometries for MMFF94 , 1996 .
[9] T. N. Bhat,et al. The Protein Data Bank , 2000, Nucleic Acids Res..
[10] Kazuo Kitaura,et al. Exploring chemistry with the fragment molecular orbital method. , 2012, Physical chemistry chemical physics : PCCP.
[11] S. Iwata. Dispersion energy evaluated by using locally projected occupied and excited molecular orbitals for molecular interaction. , 2011, The Journal of chemical physics.
[12] Takeshi Ishikawa,et al. Theoretical study of the prion protein based on the fragment molecular orbital method , 2009, J. Comput. Chem..
[13] Kazuo Kitaura,et al. Binding of influenza A virus hemagglutinin to the sialoside receptor is not controlled by the homotropic allosteric effect. , 2010, The journal of physical chemistry. B.
[14] Kazumasa Honda,et al. Estimated MP2 and CCSD(T) interaction energies of n-alkane dimers at the basis set limit: comparison of the methods of Helgaker et al. and Feller. , 2006, The Journal of chemical physics.
[15] Joshua R. Smith,et al. Development of a 3-body:many-body integrated fragmentation method for weakly bound clusters and application to water clusters (H2O)(n = 3-10, 16, 17). , 2011, The Journal of chemical physics.
[16] E. Ciszak,et al. The structure of a complex of hexameric insulin and 4'-hydroxyacetanilide. , 1994, Proceedings of the National Academy of Sciences of the United States of America.
[17] Mark S Gordon,et al. Water-benzene interactions: an effective fragment potential and correlated quantum chemistry study. , 2009, The journal of physical chemistry. A.
[18] Edward F. Valeev,et al. Estimates of the Ab Initio Limit for π−π Interactions: The Benzene Dimer , 2002 .
[19] Stefan Grimme,et al. Accurate description of van der Waals complexes by density functional theory including empirical corrections , 2004, J. Comput. Chem..
[20] Mario Raimondi,et al. Modification of the Roothaan equations to exclude BSSE from molecular interaction calculations , 1996 .
[21] Kazuo Kitaura,et al. Molecular recognition mechanism of FK506 binding protein: An all‐electron fragment molecular orbital study , 2007, Proteins.
[22] Sotiris S. Xantheas,et al. Ab initio studies of cyclic water clusters (H2O)n, n=1–6. II. Analysis of many‐body interactions , 1994 .
[23] Gustavo E. Scuseria,et al. Linear Scaling Density Functional Calculations with Gaussian Orbitals , 1999 .
[24] Pavel Hobza,et al. S66: A Well-balanced Database of Benchmark Interaction Energies Relevant to Biomolecular Structures , 2011, Journal of chemical theory and computation.
[25] Mark S Gordon,et al. Benzene-pyridine interactions predicted by the effective fragment potential method. , 2011, The journal of physical chemistry. A.
[26] Yoshihiro Kawaoka,et al. Influenza viral hemagglutinin complicated shape is advantageous to its binding affinity for sialosaccharide receptor. , 2007, Biochemical and biophysical research communications.
[27] K. Morokuma,et al. ONIOM: A Multilayered Integrated MO + MM Method for Geometry Optimizations and Single Point Energy Predictions. A Test for Diels−Alder Reactions and Pt(P(t-Bu)3)2 + H2 Oxidative Addition , 1996 .
[28] B. Sumpter,et al. Density-functional approaches to noncovalent interactions: a comparison of dispersion corrections (DFT-D), exchange-hole dipole moment (XDM) theory, and specialized functionals. , 2011, The Journal of chemical physics.
[29] 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.
[30] Jens Antony,et al. Fully ab initio protein‐ligand interaction energies with dispersion corrected density functional theory , 2012, J. Comput. Chem..
[31] 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.
[32] Mark S. Gordon,et al. General atomic and molecular electronic structure system , 1993, J. Comput. Chem..
[33] K. Merz,et al. Further analysis and comparative study of intermolecular interactions using dimers from the S22 database. , 2009, The Journal of chemical physics.
[34] Hiroshi Nakatsuji,et al. A multicore QM/MM approach for the geometry optimization of chromophore aggregate in protein , 2009, J. Comput. Chem..
[35] S. Grimme. Improved second-order Møller–Plesset perturbation theory by separate scaling of parallel- and antiparallel-spin pair correlation energies , 2003 .
[36] Spencer R Pruitt,et al. Fragmentation methods: a route to accurate calculations on large systems. , 2012, Chemical reviews.
[37] Mark S. Gordon,et al. Electrostatic energy in the effective fragment potential method: Theory and application to benzene dimer , 2007, J. Comput. Chem..
[38] Brian W. Hopkins,et al. Multicentred QM/QM methods for overlapping model systems , 2005 .
[39] T. H. Dunning. Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen , 1989 .
[40] Masami Uebayasi,et al. Pair interaction molecular orbital method: an approximate computational method for molecular interactions , 1999 .
[41] Francesco Aquilante,et al. Calculation of protein-ligand interaction energies by a fragmentation approach combining high-level quantum chemistry with classical many-body effects. , 2009, The journal of physical chemistry. B.
[42] Mark S Gordon,et al. Effective fragment potential study of the interaction of DNA bases. , 2011, The journal of physical chemistry. A.
[43] K. Kitaura,et al. Fragment molecular orbital method: an approximate computational method for large molecules , 1999 .
[44] Ye Mei,et al. Electrostatic polarization makes a substantial contribution to the free energy of avidin-biotin binding. , 2010, Journal of the American Chemical Society.
[45] Daniel Svozil,et al. Reference MP2/CBS and CCSD(T) quantum-chemical calculations on stacked adenine dimers. Comparison with DFT-D, MP2.5, SCS(MI)-MP2, M06-2X, CBS(SCS-D) and force field descriptions. , 2010, Physical chemistry chemical physics : PCCP.
[46] Kaori Fukuzawa,et al. Counterpoise-corrected interaction energy analysis based on the fragment molecular orbital scheme , 2011 .
[47] 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.
[48] Brian W. Hopkins,et al. A multicentered approach to integrated QM/QM calculations. Applications to multiply hydrogen bonded systems , 2003, J. Comput. Chem..
[49] C David Sherrill,et al. Formal Estimation of Errors in Computed Absolute Interaction Energies of Protein-ligand Complexes. , 2011, Journal of chemical theory and computation.
[50] Kazuo Kitaura,et al. Extending the power of quantum chemistry to large systems with the fragment molecular orbital method. , 2007, The journal of physical chemistry. A.