Molecular forces, geometries, and frequencies by systematic molecular fragmentation including embedded charges.

The accuracy of energies, energy gradients, and hessians evaluated by systematic molecular fragmentation is examined for a wide range of neutral molecules, zwitterions, and ions. A protocol is established that may employ embedded charges in conjunction with fragmentation to provide accurate evaluation of minimum energy geometries and vibrational frequencies in an automated procedure.

[1]  Michael A Collins,et al.  Approximate ab initio energies by systematic molecular fragmentation. , 2005, The Journal of chemical physics.

[2]  Donald G Truhlar,et al.  Electrostatically Embedded Many-Body Expansion for Large Systems, with Applications to Water Clusters. , 2007, Journal of chemical theory and computation.

[3]  Shridhar R. Gadre,et al.  Appraisal of molecular tailoring approach for large clusters. , 2013, The Journal of chemical physics.

[4]  Shuhua Li,et al.  An efficient implementation of the generalized energy-based fragmentation approach for general large molecules. , 2010, The journal of physical chemistry. A.

[5]  Nan Jiang,et al.  Electrostatic field-adapted molecular fractionation with conjugated caps for energy calculations of charged biomolecules. , 2006, The Journal of chemical physics.

[6]  Jiali Gao,et al.  A molecular-orbital derived polarization potential for liquid water , 1998 .

[7]  Luca Frediani,et al.  The Dalton quantum chemistry program system , 2013, Wiley interdisciplinary reviews. Computational molecular science.

[8]  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..

[9]  Ryan P. A. Bettens,et al.  On the accurate reproduction of ab initio interaction energies between an enzyme and substrate , 2007 .

[10]  Frank Weinhold,et al.  Natural bond orbital analysis of near‐Hartree–Fock water dimer , 1983 .

[11]  X. Chen,et al.  Fractionation of peptide with disulfide bond for quantum mechanical calculation of interaction energy with molecules. , 2004, The Journal of chemical physics.

[12]  K. Wüthrich,et al.  Comparison of NMR and crystal structures highlights conformational isomerism in protein active sites , 2010, Acta crystallographica. Section F, Structural biology and crystallization communications.

[13]  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 .

[14]  M. A. Collins,et al.  Molecular electrostatic potentials by systematic molecular fragmentation. , 2013, The Journal of chemical physics.

[15]  F. Allen.  The Cambridge Structural Database: a quarter of a million crystal structures and rising. , 2002, Acta crystallographica. Section B, Structural science.

[16]  Donald G Truhlar,et al.  X-Pol Potential: An Electronic Structure-Based Force Field for Molecular Dynamics Simulation of a Solvated Protein in Water. , 2009, Journal of chemical theory and computation.

[17]  Nicholas J Mayhall,et al.  Molecules-in-Molecules: An Extrapolated Fragment-Based Approach for Accurate Calculations on Large Molecules and Materials. , 2011, Journal of chemical theory and computation.

[18]  Raghunath O. Ramabhadran,et al.  Theoretical Thermochemistry for Organic Molecules: Development of the Generalized Connectivity-Based Hierarchy. , 2011, Journal of chemical theory and computation.

[19]  Kazuo Kitaura,et al.  The importance of three-body terms in the fragment molecular orbital method. , 2004, The Journal of chemical physics.

[20]  Jiali Gao,et al.  Energy components of aqueous solution: Insight from hybrid QM/MM simulations using a polarizable solvent model , 1997, J. Comput. Chem..

[21]  Jiali Gao,et al.  The Design of a Next Generation Force Field: The X-POL Potential. , 2007, Journal of chemical theory and computation.

[22]  Thom Vreven,et al.  Geometry optimization with QM/MM, ONIOM, and other combined methods. I. Microiterations and constraints , 2003, J. Comput. Chem..

[23]  Michael A Collins,et al.  Accuracy and efficiency of electronic energies from systematic molecular fragmentation. , 2006, The Journal of chemical physics.

[24]  Spencer R Pruitt,et al.  Fragmentation methods: a route to accurate calculations on large systems. , 2012, Chemical reviews.

[25]  Mark S. Gordon,et al.  Accurate methods for large molecular systems. , 2009, The journal of physical chemistry. B.

[26]  Wei Li,et al.  Generalized energy-based fragmentation approach for computing the ground-state energies and properties of large molecules. , 2007, The journal of physical chemistry. A.

[27]  John M Herbert,et al.  A generalized many-body expansion and a unified view of fragment-based methods in electronic structure theory. , 2012, The Journal of chemical physics.

[28]  F. Weinhold,et al.  Natural population analysis , 1985 .

[29]  Ye Mei,et al.  A new quantum method for electrostatic solvation energy of protein. , 2006, The Journal of chemical physics.

[30]  Kazuo Kitaura,et al.  Multiconfiguration self-consistent-field theory based upon the fragment molecular orbital method. , 2005, The Journal of chemical physics.

[31]  Michael A. Collins,et al.  Accurate treatment of nonbonded interactions within systematic molecular fragmentation , 2009 .

[32]  Mark S Gordon,et al.  Systematic fragmentation method and the effective fragment potential: an efficient method for capturing molecular energies. , 2009, The journal of physical chemistry. A.

[33]  Wei Li,et al.  A localized molecular-orbital assembler approach for Hartree-Fock calculations of large molecules. , 2005, The Journal of chemical physics.

[34]  Michael A Collins,et al.  Systematic fragmentation of large molecules by annihilation. , 2012, Physical chemistry chemical physics : PCCP.

[35]  Mark S Gordon,et al.  The fragment molecular orbital and systematic molecular fragmentation methods applied to water clusters. , 2012, Physical chemistry chemical physics : PCCP.

[36]  W. Li,et al.  An improved localized molecular-orbital assembler approach for Hartree–Fock calculations of general large molecules , 2012 .

[37]  Anthony J. Stone,et al.  The Theory of Intermolecular Forces , 2013 .

[38]  John Z. H. Zhang,et al.  Molecular fractionation with conjugate caps for full quantum mechanical calculation of protein-molecule interaction energy , 2003 .

[39]  Wei Li,et al.  An efficient fragment-based approach for predicting the ground-state energies and structures of large molecules. , 2005, Journal of the American Chemical Society.

[40]  N. Hush,et al.  Density-functional geometry optimization of the 150,000-atom photosystem-I trimer. , 2006, The Journal of chemical physics.

[41]  Weitao Yang,et al.  A density‐matrix divide‐and‐conquer approach for electronic structure calculations of large molecules , 1995 .

[42]  Heather Netzloff,et al.  Ab initio energies of nonconducting crystals by systematic fragmentation. , 2007, The Journal of chemical physics.

[43]  Anthony J Stone,et al.  Distributed Multipole Analysis:  Stability for Large Basis Sets. , 2005, Journal of chemical theory and computation.

[44]  R. P. Bettens,et al.  Accurately reproducing ab initio electrostatic potentials with multipoles and fragmentation. , 2009, The journal of physical chemistry. A.

[45]  John F. Ouyang,et al.  Combined Fragmentation Method: A Simple Method for Fragmentation of Large Molecules. , 2012, Journal of chemical theory and computation.

[46]  Jiali Gao,et al.  Communication: variational many-body expansion: accounting for exchange repulsion, charge delocalization, and dispersion in the fragment-based explicit polarization method. , 2012, The Journal of chemical physics.

[47]  Ryan P A Bettens,et al.  A new algorithm for molecular fragmentation in quantum chemical calculations. , 2006, The journal of physical chemistry. A.

[48]  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.

[49]  V Ganesh,et al.  Molecular tailoring approach for geometry optimization of large molecules: energy evaluation and parallelization strategies. , 2006, The Journal of chemical physics.

[50]  Jiali Gao,et al.  Toward a Molecular Orbital Derived Empirical Potential for Liquid Simulations , 1997 .

[51]  Nicholas J Mayhall,et al.  Many-Overlapping-Body (MOB) Expansion: A Generalized Many Body Expansion for Nondisjoint Monomers in Molecular Fragmentation Calculations of Covalent Molecules. , 2012, Journal of chemical theory and computation.

[52]  John Z. H. Zhang,et al.  FULL AB INITIO COMPUTATION OF PROTEIN-WATER INTERACTION ENERGIES , 2004 .

[53]  Kazuo Kitaura,et al.  The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems , 2009 .

[54]  Wei Li,et al.  Geometry optimizations and vibrational spectra of large molecules from a generalized energy-based fragmentation approach. , 2008, The journal of physical chemistry. A.