The ONIOM method: its foundation and applications to metalloenzymes and photobiology

The ONIOM (our Own N‐layer Integrated molecular Orbital molecular Mechanics) method is one of the most popular, successful, and easily‐to‐implement hybrid quantum mechanics/molecular mechanics (QM/MM) methods to treat complex molecular systems. Hybrid QM/MM methods take advantage of the high accuracy of QM methods and the low computational cost of MM methods. One key feature of the ONIOM method is a simple linear extrapolation procedure, which allows the ONIOM method to be further extended to two‐layer ONIOM(QM1:QM2), three‐layer ONIOM(QM1:QM2:MM), and, in principle, any n‐layer n‐level‐of‐theory methods. Such hierarchical features of the ONIOM method are unique among the hybrid QM/MM methods. This review article provides an overview of the theoretical foundation and recent development of the ONIOM method. Some of its recent applications to metalloenzymes and photobiology will also be highlighted. Prospective ONIOM development for more realistic simulations on the complex systems will be discussed finally. © 2011 John Wiley & Sons, Ltd.

[1]  Ivan S Ufimtsev,et al.  Quantum Chemistry on Graphical Processing Units. 1. Strategies for Two-Electron Integral Evaluation. , 2008, Journal of chemical theory and computation.

[2]  Keiji Morokuma,et al.  The IMOMO method: Integration of different levels of molecular orbital approximations for geometry optimization of large systems: Test for n‐butane conformation and SN2 reaction: RCl+Cl− , 1996 .

[3]  Lucas Visscher,et al.  Toward a Practical Method for Adaptive QM/MM Simulations. , 2009, Journal of chemical theory and computation.

[4]  Takashi Otsuki,et al.  Crystal structure of human indoleamine 2,3-dioxygenase: catalytic mechanism of O2 incorporation by a heme-containing dioxygenase. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[5]  Sandeep Sharma,et al.  The density matrix renormalization group in quantum chemistry. , 2011, Annual review of physical chemistry.

[6]  Michel Dupuis,et al.  The ONIOM molecular dynamics method for biochemical applications : cytidine deaminase. , 2007 .

[7]  K. Morokuma,et al.  Determining Transition States in Bioinorganic Reactions , 2009 .

[8]  Arieh Warshel,et al.  A new paradigm for electrostatic catalysis of radical reactions in vitamin B12 enzymes , 2007, Proceedings of the National Academy of Sciences.

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

[10]  H. Werner,et al.  Chapter 4 On the Selection of Domains and Orbital Pairs in Local Correlation Treatments , 2006 .

[11]  K. Morokuma,et al.  ONIOM study on a missing piece in our understanding of heme chemistry: bacterial tryptophan 2,3-dioxygenase with dual oxidants. , 2010, Journal of the American Chemical Society.

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

[13]  Weitao Yang,et al.  Free energy calculation on enzyme reactions with an efficient iterative procedure to determine minimum energy paths on a combined ab initio QM/MM potential energy surface , 2000 .

[14]  U. Singh,et al.  A combined ab initio quantum mechanical and molecular mechanical method for carrying out simulations on complex molecular systems: Applications to the CH3Cl + Cl− exchange reaction and gas phase protonation of polyethers , 1986 .

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

[16]  A. Miyawaki,et al.  Primary Events of Photodynamics in Reversible Photoswitching Fluorescent Protein Dronpa , 2010 .

[17]  Sarah J. Thackray,et al.  Reassessment of the reaction mechanism in the heme dioxygenases. , 2009, Journal of the American Chemical Society.

[18]  Thom Vreven,et al.  The ONIOM (our own N-layered integrated molecular orbital + molecular mechanics) method for the first singlet excited (S1) state photoisomerization path of a retinal protonated Schiff base , 2000 .

[19]  R. Friesner,et al.  Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis. , 2005, Annual review of physical chemistry.

[20]  S. Iyengar,et al.  Combining quantum wavepacket ab initio molecular dynamics with QM/MM and QM/QM techniques: Implementation blending ONIOM and empirical valence bond theory. , 2008, The Journal of chemical physics.

[21]  K. Yoshizawa,et al.  Does Cob(II)alamin act as a conductor in coenzyme B12 dependent mutases? , 2007, Angewandte Chemie.

[22]  G. Chan,et al.  Chapter 7 The Density Matrix Renormalization Group in Quantum Chemistry , 2009 .

[23]  T. Holman,et al.  Structural and functional characterization of second-coordination sphere mutants of soybean lipoxygenase-1. , 2001, Biochemistry.

[24]  A. Laio,et al.  Escaping free-energy minima , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[25]  Brian W. Hopkins,et al.  A multicentered approach to integrated QM/QM calculations. Applications to multiply hydrogen bonded systems , 2003, J. Comput. Chem..

[26]  R. Mathies,et al.  Conical intersection dynamics of the primary photoisomerization event in vision , 2010, Nature.

[27]  M. Levitt,et al.  Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. , 1976, Journal of molecular biology.

[28]  K. Morokuma,et al.  Performance Evaluation of the Three-Layer ONIOM Method:  Case Study for a Zwitterionic Peptide. , 2006, Journal of chemical theory and computation.

[29]  K. Merz,et al.  Combined Quantum Mechanical/Molecular Mechanical Methodologies Applied to Biomolecular Systems , 1999 .

[30]  H. Senn,et al.  QM/MM Methods for Biological Systems , 2006 .

[31]  Keiji Morokuma,et al.  Mechanism of spectral tuning going from retinal in vacuo to bovine rhodopsin and its mutants: multireference ab initio quantum mechanics/molecular mechanics studies. , 2008, The journal of physical chemistry. B.

[32]  D. Truhlar,et al.  QM/MM: what have we learned, where are we, and where do we go from here? , 2007 .

[33]  K. Morokuma,et al.  A NEW ONIOM IMPLEMENTATION IN GAUSSIAN98. PART I. THE CALCULATION OF ENERGIES, GRADIENTS, VIBRATIONAL FREQUENCIES AND ELECTRIC FIELD DERIVATIVES , 1999 .

[34]  D. Truhlar,et al.  Combined Quantum Mechanical and Molecular Mechanical Methods for Calculating Potential Energy Surfaces: Tuned and Balanced Redistributed-Charge Algorithm. , 2010, Journal of chemical theory and computation.

[35]  Feliu Maseras,et al.  IMOMM: A new integrated ab initio + molecular mechanics geometry optimization scheme of equilibrium structures and transition states , 1995, J. Comput. Chem..

[36]  Kenneth M. Merz,et al.  Linear scaling molecular orbital calculations of biological systems using the semiempirical divide and conquer method , 2000, J. Comput. Chem..

[37]  J. Kussmann,et al.  Linear‐Scaling Methods in Quantum Chemistry , 2007 .

[38]  Hao Hu,et al.  Development and application of ab initio QM/MM methods for mechanistic simulation of reactions in solution and in enzymes. , 2009, Theochem.

[39]  T. Vreven,et al.  Searching for conical intersections of potential energy surfaces with the ONIOM method: application to previtamin D. , 2008, The journal of physical chemistry. A.

[40]  A. Miyawaki,et al.  Regulated Fast Nucleocytoplasmic Shuttling Observed by Reversible Protein Highlighting , 2004, Science.

[41]  Wilfred F van Gunsteren,et al.  Combined QM/MM Molecular Dynamics Study on a Condensed-Phase SN2 Reaction at Nitrogen:  The Effect of Explicitly Including Solvent Polarization. , 2007, Journal of chemical theory and computation.

[42]  Sergio Martí,et al.  Improving the QM/MM Description of Chemical Processes:  A Dual Level Strategy To Explore the Potential Energy Surface in Very Large Systems. , 2005, Journal of chemical theory and computation.

[43]  Hao Hu,et al.  Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods. , 2008, Annual review of physical chemistry.

[44]  Klaus Schulten,et al.  Photochemical reaction dynamics of the primary event of vision studied by means of a hybrid molecular simulation. , 2009, Biophysical journal.

[45]  F. Bernardi,et al.  A Computational Strategy for Organic Photochemistry , 2002 .

[46]  Sarah J. Thackray,et al.  Molecular insights into substrate recognition and catalysis by tryptophan 2,3-dioxygenase , 2007, Proceedings of the National Academy of Sciences.

[47]  Xiaosong Li,et al.  Geometry Optimization with Multilayer Methods Using Least-Squares Minimization. , 2010, Journal of chemical theory and computation.

[48]  K. Morokuma,et al.  Investigation of the S0S1 excitation in bacteriorhodopsin with the ONIOM(MO:MM) hybrid method , 2003 .

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

[50]  M. Elstner,et al.  Effect of polarization on the opsin shift in rhodopsins. 2. Empirical polarization models for proteins. , 2008, The journal of physical chemistry. B.

[51]  M. Martí,et al.  Evidence for a ferryl intermediate in a heme-based dioxygenase , 2009, Proceedings of the National Academy of Sciences.

[52]  Ruma Banerjee,et al.  Radical carbon skeleton rearrangements: catalysis by coenzyme B12-dependent mutases. , 2003, Chemical reviews.

[53]  Enrique R Batista,et al.  A Self-Consistent Space-Domain Decomposition Method for QM/MM Computations of Protein Electrostatic Potentials. , 2006, Journal of chemical theory and computation.

[54]  Iwao Ohmine,et al.  Proton Transfer in Bacteriorhodopsin: Structure, Excitation, IR Spectra, and Potential Energy Surface Analyses by an ab Initio QM/MM Method , 2000 .

[55]  Z Otwinowski,et al.  Crystal structure of soybean lipoxygenase L-1 at 1.4 A resolution. , 1996, Biochemistry.

[56]  Car,et al.  Unified approach for molecular dynamics and density-functional theory. , 1985, Physical review letters.

[57]  J. Stewart Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements , 2007, Journal of molecular modeling.

[58]  M. Karplus,et al.  A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations , 1990 .

[59]  Tomasz Borowski,et al.  Modeling enzymatic reactions involving transition metals. , 2006, Accounts of chemical research.

[60]  J. Tully Molecular dynamics with electronic transitions , 1990 .

[61]  Florian Weigend,et al.  Approximated electron repulsion integrals: Cholesky decomposition versus resolution of the identity methods. , 2009, The Journal of chemical physics.

[62]  M. Vincent,et al.  Computer simulation of zeolite structure and reactivity using embedded cluster methods , 1997 .

[63]  K. Morokuma,et al.  Modeling Enzymatic Reactions in Metalloenzymes and Photobiology by Quantum Mechanics (QM) and Quantum Mechanics/Molecular Mechanics (QM/MM) Calculations , 2010 .

[64]  Walter Thiel,et al.  Benchmark of Electronically Excited States for Semiempirical Methods: MNDO, AM1, PM3, OM1, OM2, OM3, INDO/S, and INDO/S2. , 2010, Journal of chemical theory and computation.

[65]  K. Morokuma,et al.  Insights into the (superoxo)Fe(III)Fe(III) intermediate and reaction mechanism of myo-inositol oxygenase: DFT and ONIOM(DFT:MM) study. , 2009, Journal of the American Chemical Society.

[66]  Ulf Ryde,et al.  How the Co-C bond is cleaved in coenzyme B12 enzymes: a theoretical study. , 2005, Journal of the American Chemical Society.

[67]  Helmut Grubmüller,et al.  Chromophore Protonation State Controls Photoswitching of the Fluoroprotein asFP595 , 2008, PLoS Comput. Biol..

[68]  Sason Shaik,et al.  Theoretical perspective on the structure and mechanism of cytochrome P450 enzymes. , 2005, Chemical reviews.

[69]  Satoshi Maeda,et al.  An Automated and Systematic Transition Structure Explorer in Large Flexible Molecular Systems Based on Combined Global Reaction Route Mapping and Microiteration Methods. , 2009, Journal of chemical theory and computation.

[70]  Thom Vreven,et al.  Implementation and Benchmark Tests of the DFTB Method and Its Application in the ONIOM Method , 2009 .

[71]  Carsten Krebs,et al.  Evidence for C-H cleavage by an iron-superoxide complex in the glycol cleavage reaction catalyzed by myo-inositol oxygenase. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

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

[73]  Thom Vreven,et al.  QM:QM electronic embedding using Mulliken atomic charges: energies and analytic gradients in an ONIOM framework. , 2008, The Journal of chemical physics.

[74]  A. Miyawaki,et al.  An optical marker based on the UV-induced green-to-red photoconversion of a fluorescent protein , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[75]  Nicholas J Mayhall,et al.  Charge Transfer Across ONIOM QM:QM Boundaries: The Impact of Model System Preparation. , 2010, Journal of chemical theory and computation.

[76]  K. Morokuma,et al.  DFT and ONIOM(DFT:MM) studies on Co-C bond cleavage and hydrogen transfer in B12-dependent methylmalonyl-CoA mutase. Stepwise or concerted mechanism? , 2009, Journal of the American Chemical Society.

[77]  Peng Tao,et al.  A toolkit to assist ONIOM calculations , 2010, J. Comput. Chem..

[78]  M. Frisch,et al.  Integrating steepest-descent reaction pathways for large molecules. , 2011, The Journal of chemical physics.

[79]  A. Warshel Computer simulations of enzyme catalysis: methods, progress, and insights. , 2003, Annual review of biophysics and biomolecular structure.

[80]  K. Morokuma,et al.  Computational insights into the mechanism of radical generation in B12-dependent methylmalonyl-CoA mutase. , 2006, Journal of the American Chemical Society.

[81]  G. Grisetti,et al.  Further Reading , 1984, IEEE Spectrum.

[82]  Competitive mechanistic pathways for green-to-red photoconversion in the fluorescent protein Kaede: a computational study. , 2010, The journal of physical chemistry. B.

[83]  Christian Eggeling,et al.  Structural basis for reversible photoswitching in Dronpa , 2007, Proceedings of the National Academy of Sciences.

[84]  Y. Sugita,et al.  Replica-exchange molecular dynamics method for protein folding , 1999 .

[85]  Guohui Li,et al.  Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes. , 2006, The journal of physical chemistry. B.

[86]  G. Voth,et al.  Hybrid Ab-Initio/Empirical Molecular Dynamics: Combining the ONIOM Scheme with the Atom-Centered Density Matrix Propagation (ADMP) Approach , 2004 .

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

[88]  Insights Arieh Warshel COMPUTER SIMULATIONS OF ENZYME CATALYSIS , 2003 .

[89]  D. Truhlar,et al.  Quantum mechanical methods for enzyme kinetics. , 2003, Annual review of physical chemistry.

[90]  K. Morokuma,et al.  Effects of the protein environment on the structure and energetics of active sites of metalloenzymes. ONIOM study of methane monooxygenase and ribonucleotide reductase. , 2002, Journal of the American Chemical Society.

[91]  Xin Li,et al.  A theoretical study on the nature of on- and off-states of reversibly photoswitching fluorescent protein Dronpa: absorption, emission, protonation, and Raman. , 2010, The journal of physical chemistry. B.

[92]  Klaus Schulten,et al.  Color tuning in rhodopsins: the mechanism for the spectral shift between bacteriorhodopsin and sensory rhodopsin II. , 2006, Journal of the American Chemical Society.

[93]  K. Morokuma,et al.  ONIOM as an efficient tool for calculating NMR chemical shielding constants in large molecules , 2000 .

[94]  Jasmine L. Gallaher,et al.  Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction , 2010, Science.

[95]  Teerakiat Kerdcharoen,et al.  ONIOM-XS: an extension of the ONIOM method for molecular simulation in condensed phase , 2002 .

[96]  G. Voth Coarse-Graining of Condensed Phase and Biomolecular Systems , 2008 .

[97]  M. Frisch,et al.  Link atom bond length effect in ONIOM excited state calculations. , 2010, The Journal of chemical physics.

[98]  V. Batista,et al.  Computational studies of the primary phototransduction event in visual rhodopsin. , 2006, Accounts of chemical research.

[99]  D. Truhlar,et al.  Self-Consistent Polarization of the Boundary in the Redistributed Charge and Dipole Scheme for Combined Quantum-Mechanical and Molecular-Mechanical Calculations. , 2007, Journal of chemical theory and computation.

[100]  Thom Vreven,et al.  Geometry optimization with QM/MM methods II: Explicit quadratic coupling , 2006 .

[101]  Jacopo Tomasi,et al.  The ONIOM-PCM method: Combining the hybrid molecular orbital method and the polarizable continuum model for solvation. Application to the geometry and properties of a merocyanine in solution , 2001 .

[102]  C. Krebs,et al.  myo-Inositol oxygenase: a radical new pathway for O(2) and C-H activation at a nonheme diiron cluster. , 2009, Dalton transactions.

[103]  K. Morokuma,et al.  Density functional theory study on a missing piece in understanding of heme chemistry: the reaction mechanism for indoleamine 2,3-dioxygenase and tryptophan 2,3-dioxygenase. , 2008, Journal of the American Chemical Society.

[104]  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 .

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

[106]  Thom Vreven,et al.  Matrix metalloproteinase 2 inhibition: combined quantum mechanics and molecular mechanics studies of the inhibition mechanism of (4-phenoxyphenylsulfonyl)methylthiirane and its oxirane analogue. , 2009, Biochemistry.

[107]  Thomas Frauenheim,et al.  Parameter Calibration of Transition-Metal Elements for the Spin-Polarized Self-Consistent-Charge Density-Functional Tight-Binding (DFTB) Method:  Sc, Ti, Fe, Co, and Ni. , 2007, Journal of chemical theory and computation.

[108]  M. Karplus,et al.  How Enzymes Work: Analysis by Modern Rate Theory and Computer Simulations , 2004, Science.

[109]  Keiji Morokuma,et al.  The IMOMO and IMONM methods for excited states. A study of the adiabatic S0 → T1,2 excitation energies of cyclic alkenes and enones , 1996 .

[110]  Donald G Truhlar,et al.  Redistributed charge and dipole schemes for combined quantum mechanical and molecular mechanical calculations. , 2005, The journal of physical chemistry. A.

[111]  A. Miyawaki,et al.  Light-dependent regulation of structural flexibility in a photochromic fluorescent protein , 2008, Proceedings of the National Academy of Sciences.

[112]  M. Davidson,et al.  Advances in fluorescent protein technology , 2011, Journal of Cell Science.

[113]  Y. Mo,et al.  New insight on the origin of the unusual acidity of Meldrum's acid from ab initio and combined QM/MM simulation study. , 2001, Journal of the American Chemical Society.

[114]  William L. Jorgensen,et al.  PDDG/PM3 and PDDG/MNDO: Improved semiempirical methods , 2002, J. Comput. Chem..

[115]  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 .

[116]  K. Morokuma,et al.  Protein Free Energy Corrections in ONIOM QM:MM Modeling: A Case Study for Isopenicillin N Synthase (IPNS). , 2011, Journal of chemical theory and computation.

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

[118]  K. Morokuma,et al.  Photochemistry of visual pigment in a G(q) protein-coupled receptor (GPCR)--insights from structural and spectral tuning studies on squid rhodopsin. , 2010, Chemistry.