XO: An extended ONIOM method for accurate and efficient modeling of large systems

Calculation of large complex systems remains to be a great challenge, where there is always a trade‐off between accuracy and efficiency. Recently, we proposed the extended our own n‐layered integrated molecular orbital (ONIOM) method (XO) (Guo, Wu, Xu, Chem. Phys. Lett. 2010, 498, 203) which surmounts some inherited limitations of the popular ONIOM method by introducing the inclusion‐exclusion principle used in the fragmentation methods. The present work sets up general guidelines for the construction of a good XO scheme. In particular, force‐error test is proposed to quantitatively validate the usefulness of an XO scheme, taking accuracy, efficiency and scalability all into account. Representative studies on zeolites, polypeptides and cyclodextrins have been carried out to demonstrate how to strive for high accuracy without sacrificing efficiency. As a natural extension, XO is applied to calculate the total energy, fully optimized geometry and vibrational spectra of the whole system, where ONIOM becomes inapplicable. © 2012 Wiley Periodicals, Inc.

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

[2]  Thom Vreven,et al.  Model studies of the structures, reacitivities, and reaction mechanisms of metalloenzymes , 2001, IBM J. Res. Dev..

[3]  Emanuel H. Rubensson,et al.  Hartree-Fock calculations with linearly scaling memory usage. , 2008, The Journal of chemical physics.

[4]  Kenneth M Merz,et al.  Divide-and-Conquer Hartree-Fock Calculations on Proteins. , 2010, Journal of chemical theory and computation.

[5]  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.

[6]  David A. Dixon,et al.  Annual reports in computational chemistry , 2007 .

[7]  Timothy A. Keiderling,et al.  Transfer of molecular property tensors in cartesian coordinates: A new algorithm for simulation of vibrational spectra , 1997 .

[8]  Robert Wieczorek,et al.  Comparison of fully optimized alpha- and 3(10)-helices with extended beta-strands. An ONIOM density functional theory study. , 2004, Journal of the American Chemical Society.

[9]  Lou Massa,et al.  Kernel energy method illustrated with peptides , 2005 .

[10]  Àngels González-Lafont,et al.  Testing electronic structure methods for describing intermolecular H · · · H interactions in supramolecular chemistry , 2004, J. Comput. Chem..

[11]  Gregory S. Tschumper,et al.  Efficient and Accurate Methods for the Geometry Optimization of Water Clusters: Application of Analytic Gradients for the Two-Body:Many-Body QM:QM Fragmentation Method to (H2O)n, n = 3-10. , 2011, Journal of chemical theory and computation.

[12]  Jumras Limtrakul,et al.  Mechanistic Investigation on 1,5- to 2,6-Dimethylnaphthalene Isomerization Catalyzed by Acidic β Zeolite: ONIOM Study with an M06-L Functional , 2009 .

[13]  Anuja P. Rahalkar,et al.  Enabling ab initio Hessian and frequency calculations of large molecules. , 2008, The Journal of chemical physics.

[14]  Adrian J Mulholland,et al.  Comparison of different quantum mechanical/molecular mechanics boundary treatments in the reaction of the hepatitis C virus NS3 protease with the NS5A/5B substrate. , 2007, The journal of physical chemistry. B.

[15]  Frédéric Thibault-Starzyk,et al.  Infrared Evidence of a Third Brønsted Site in Mordenites , 2004 .

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

[17]  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.

[18]  Markus Reiher,et al.  Analysis of the Cartesian Tensor Transfer Method for Calculating Vibrational Spectra of Polypeptides. , 2011, Journal of chemical theory and computation.

[19]  K. Morokuma,et al.  On the application of the IMOMO (integrated molecular orbital + molecular orbital) method , 2000 .

[20]  Wei Li,et al.  Fragmentation-based QM/MM simulations: length dependence of chain dynamics and hydrogen bonding of polyethylene oxide and polyethylene in aqueous solutions. , 2008, The journal of physical chemistry. B.

[21]  Darrin M. York,et al.  Multi-scale Quantum Models for Biocatalysis , 2009 .

[22]  Tai-Sung Lee,et al.  A pseudobond approach to combining quantum mechanical and molecular mechanical methods , 1999 .

[23]  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.

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

[25]  K. Kitaura,et al.  Fragment molecular orbital method: an approximate computational method for large molecules , 1999 .

[26]  Peeter Burk,et al.  Hybrid quantum chemical and density functional theory (ONIOM) study of the acid sites in zeolite ZSM-5 , 2004 .

[27]  Notker Rösch,et al.  Elastic Polarizable Environment Cluster Embedding Approach for Covalent Oxides and Zeolites Based on a Density Functional Method , 2003 .

[28]  Jan Řezáč,et al.  Multilevel Fragment-Based Approach (MFBA): A Novel Hybrid Computational Method for the Study of Large Molecules. , 2010, Journal of chemical theory and computation.

[29]  Christian Ochsenfeld,et al.  A convergence study of QM/MM isomerization energies with the selected size of the QM region for peptidic systems. , 2009, The journal of physical chemistry. A.

[30]  Yingkai Zhang,et al.  Improved pseudobonds for combined ab initio quantum mechanical/molecular mechanical methods. , 2005, The Journal of chemical physics.

[31]  Anan Wu,et al.  XO: An extended ONIOM method for accurate and efficient geometry optimization of large molecules , 2010 .

[32]  Giampaolo Barone,et al.  H-ZSM-5 modified zeolite : Quantum chemical models of acidic sites , 2007 .

[33]  L. Kantorovich,et al.  Partitioning scheme for density functional calculations of extended systems. , 2009, The Journal of chemical physics.

[34]  Marcus Lundberg,et al.  The ONIOM Method and its Applications to Enzymatic Reactions , 2009 .

[35]  Yang,et al.  Direct calculation of electron density in density-functional theory. , 1991, Physical review letters.

[36]  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 .

[37]  M. Field,et al.  A Generalized Hybrid Orbital (GHO) Method for the Treatment of Boundary Atoms in Combined QM/MM Calculations , 1998 .

[38]  Andrei L. Tchougréeff,et al.  Hybrid Methods of Molecular Modeling , 2008 .

[39]  Joshua A. Plumley,et al.  The importance of hydrogen bonding between the glutamine side chains to the formation of amyloid VQIVYK parallel beta-sheets: an ONIOM DFT/AM1 study. , 2010, Journal of the American Chemical Society.

[40]  Thom Vreven,et al.  Chapter 3 Hybrid Methods: ONIOM(QM:MM) and QM/MM , 2006 .

[41]  Martin Head-Gordon,et al.  Derivation and efficient implementation of the fast multipole method , 1994 .

[42]  Robert Wieczorek,et al.  H-Bonding Cooperativity and Energetics of α-Helix Formation of Five 17-Amino Acid Peptides , 2003 .

[43]  Yuriko Aoki,et al.  A theoretical synthesis of polymers by using uniform localization of molecular orbitals: Proposal of an elongation method , 1991 .

[44]  Xin Xu,et al.  DCMB that combines divide‐and‐conquer and mixed‐basis set methods for accurate geometry optimizations, total energies, and vibrational frequencies of large molecules , 2012, J. Comput. Chem..

[45]  Kazuo Kitaura,et al.  A combined effective fragment potential-fragment molecular orbital method. II. Analytic gradient and application to the geometry optimization of solvated tetraglycine and chignolin. , 2011, The Journal of chemical physics.

[46]  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 .

[47]  Keiji Morokuma,et al.  Case Studies of ONIOM(DFT:DFTB) and ONIOM(DFT:DFTB:MM) for Enzymes and Enzyme Mimics , 2010 .

[48]  Kenny B. Lipkowitz,et al.  Applications of Computational Chemistry to the Study of Cyclodextrins. , 1998, Chemical reviews.

[49]  Keiji Morokuma,et al.  ONIOM and Its Applications to Material Chemistry and Catalyses , 2003 .

[50]  Pär Söderhjelm,et al.  On the Convergence of QM/MM Energies. , 2011, Journal of chemical theory and computation.

[51]  Robert Wieczorek,et al.  The energetic and structural effects of single amino acid substitutions upon capped alpha-helical peptides containing 17 amino acid residues. An ONIOM DFT/AM1 study. , 2005, Journal of the American Chemical Society.

[52]  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.

[53]  Thom Vreven,et al.  The accurate calculation and prediction of the bond dissociation energies in a series of hydrocarbons using the IMOMO (integrated molecular orbital+molecular orbital) methods , 1999 .

[54]  P. Davoli,et al.  The crystal structure refinement of a natural mordenite , 1986 .

[55]  Walter Thiel,et al.  QM/MM methods for biomolecular systems. , 2009, Angewandte Chemie.

[56]  Thom Vreven,et al.  Getting the Most out of ONIOM: Guidelines and Pitfalls , 2010 .

[57]  Thom Vreven,et al.  Combining Quantum Mechanics Methods with Molecular Mechanics Methods in ONIOM. , 2006, Journal of chemical theory and computation.

[58]  K. Kitaura,et al.  Multilayer formulation of the fragment molecular orbital method (FMO). , 2005, The journal of physical chemistry. A.

[59]  Petr Kulhánek,et al.  Evaluating boundary dependent errors in QM/MM simulations. , 2009, The journal of physical chemistry. B.

[60]  Adrian J Mulholland,et al.  Testing high-level QM/MM methods for modeling enzyme reactions: acetyl-CoA deprotonation in citrate synthase. , 2010, The journal of physical chemistry. B.

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

[62]  Eric Schwegler,et al.  Linear scaling computation of the Hartree–Fock exchange matrix , 1996 .

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

[64]  D. Suárez,et al.  Thermochemical Fragment Energy Method for Biomolecules: Application to a Collagen Model Peptide. , 2009, Journal of chemical theory and computation.

[65]  Ranbir Singh,et al.  J. Mol. Struct. (Theochem) , 1996 .

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

[67]  Arieh Warshel,et al.  Multiscale modeling of biological functions. , 2011, Physical chemistry chemical physics : PCCP.

[68]  Yi Luo,et al.  An elongation method for first principle simulations of electronic structures and electron transport properties of finite nanostructures. , 2006, The Journal of chemical physics.

[69]  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.

[70]  Rahul V Pinjari,et al.  Theoretical studies on hydrogen bonding, NMR chemical shifts and electron density topography in alpha, beta and gamma-cyclodextrin conformers. , 2007, The journal of physical chemistry. A.

[71]  Djamaladdin G. Musaev,et al.  Real size of ligands, reactants and catalysts: Studies of structure, reactivity and selectivity by ONIOM and other hybrid computational approaches ☆ , 2010 .