An Efficient Method to Evaluate Intermolecular Interaction Energies in Large Systems Using Overlapping Multicenter ONIOM and the Fragment Molecular Orbital Method.

We propose an approach based on the overlapping multicenter ONIOM to evaluate intermolecular interaction energies in large systems and demonstrate its accuracy on several representative systems in the complete basis set limit at the MP2 and CCSD(T) level of theory. In the application to the intermolecular interaction energy between insulin dimer and 4'-hydroxyacetanilide at the MP2/CBS level, we use the fragment molecular orbital method for the calculation of the entire complex assigned to the lowest layer in three-layer ONIOM. The developed method is shown to be efficient and accurate in the evaluation of the protein-ligand interaction energies.

[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.