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Mo SJ, Vreven T, Mennucci B, Morokuma K, Tomasi J. Theoretical study of the SN2 reaction of Cl−(H2O)+CH3Cl using our own N-layered integrated molecular orbital and molecular mechanics polarizable continuum model method (ONIOM, PCM). Theor Chem Acc 2004. [DOI: 10.1007/s00214-003-0519-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Kudo T, Akiba S, Kondo Y, Watanabe H, Morokuma K, Vreven T. Ab Initio Study of the Effect of Heteroatoms and Bulky Substituents on the Strain Energies of Cyclosilanes. Organometallics 2003. [DOI: 10.1021/om030534j] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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da Silva CO, Mennucci B, Vreven T. Combining Microsolvation and Polarizable Continuum Studies: New Insights in the Rotation Mechanism of Amides in Water. J Phys Chem A 2003. [DOI: 10.1021/jp0346918] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Vreven T, Morokuma K, Farkas O, Schlegel HB, Frisch MJ. Geometry optimization with QM/MM, ONIOM, and other combined methods. I. Microiterations and constraints. J Comput Chem 2003; 24:760-9. [PMID: 12666168 DOI: 10.1002/jcc.10156] [Citation(s) in RCA: 468] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Hybrid energy methods such as QM/MM and ONIOM, that combine different levels of theory into one calculation, have been very successful in describing large systems. Geometry optimization methods can take advantage of the partitioning of these calculations into a region treated at a quantum mechanical (QM) level of theory and the larger, remaining region treated by an inexpensive method such as molecular mechanics (MM). A series of microiterations can be employed to fully optimize the MM region for each optimization step in the QM region. Cartesian coordinates are used for the MM region and are chosen so that the internal coordinates of the QM region remain constant during the microiterations. The coordinates of the MM region are augmented to permit rigid body translation and rotation of the QM region. This is essential if any atoms in the MM region are constrained, but it also improves the efficiency of unconstrained optimizations. Because of the microiterations, special care is needed for the optimization step in the QM region so that the system remains in the same local valley during the course of the optimization. The optimization methodology with microiterations, constraints, and step-size control are illustrated by calculations on bacteriorhodopsin and other systems.
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Vreven T, Morokuma K. Investigation of the S 0 ?S 1 excitation in bacteriorhodopsin with the ONIOM(MO:MM) hybrid method. Theor Chem Acc 2003. [DOI: 10.1007/s00214-002-0418-y] [Citation(s) in RCA: 155] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Vreven T, Morokuma K. Prediction of the Dissociation Energy of Hexaphenylethane Using the ONIOM(MO:MO:MO) Method. J Phys Chem A 2002. [DOI: 10.1021/jp014588n] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Venturini A, Vreven T, Bernardi F, Olivucci M, Robb MA. Mechanism of Photodegradation of Polysilanes: A Relaxed Cross Section of the Conical Intersection Hyperline in 2-MethylTrisilane. Organometallics 2002. [DOI: 10.1021/om00010a069] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Torrent M, Vreven T, Musaev DG, Morokuma K, Farkas O, Schlegel HB. Effects of the protein environment on the structure and energetics of active sites of metalloenzymes. ONIOM study of methane monooxygenase and ribonucleotide reductase. J Am Chem Soc 2002; 124:192-3. [PMID: 11782169 DOI: 10.1021/ja016589z] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
As the first application of our recently developed ONIOM2(QM:MM) and ONIOM3(QM:QM:MM) codes to the metalloenzymes with a large number of protein residues, two members of the non-heme protein family, methane monooxygenause and ribonucleotide reductase, have been chosen. The "active-site + four alpha-helical fragments" model was adopted which includes about 1000 atoms from 62 residues around the Fe-centered spheres. Comparison of the active-site geometries of MMOH and R2 units optimized with this model with those obtained with the "active site only" (with only 39-46 atoms) model and the X-ray results clearly demonstrates the crucial role of the active site-protein interaction in the enzymatic activities.
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Vreven T, Mennucci B, da Silva CO, Morokuma K, Tomasi J. 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. J Chem Phys 2001. [DOI: 10.1063/1.1376127] [Citation(s) in RCA: 165] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Khoroshun DV, Musaev DG, Vreven T, Morokuma K. Theoretical Study on Bis(imino)pyridyl−Fe(II) Olefin Poly- and Oligomerization Catalysts. Dominance of Different Spin States in Propagation and β-Hydride Transfer Pathways. Organometallics 2001. [DOI: 10.1021/om010126k] [Citation(s) in RCA: 89] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Vreven T, Morokuma K. 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. J Chem Phys 2000. [DOI: 10.1063/1.1287059] [Citation(s) in RCA: 88] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Sanchez-Galvez A, Hunt P, Robb MA, Olivucci M, Vreven T, Schlegel HB. Ultrafast Radiationless Deactivation of Organic Dyes: Evidence for a Two-State Two-Mode Pathway in Polymethine Cyanines. J Am Chem Soc 2000. [DOI: 10.1021/ja993985x] [Citation(s) in RCA: 161] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Vreven T, Morokuma K. The accurate calculation and prediction of the bond dissociation energies in a series of hydrocarbons using the IMOMO (integrated molecular orbital+molecular orbital) methods. J Chem Phys 1999. [DOI: 10.1063/1.480227] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Blancafort L, Adam W, González D, Olivucci M, Vreven T, Robb MA. Theoretical Study of the 1,2 Rearrangement of Housane Radical Cations: Key Role of a Transient Cyclopentane-1,3-diyl Intermediate. J Am Chem Soc 1999. [DOI: 10.1021/ja991441p] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Garavelli M, Vreven T, Celani P, Bernardi F, Robb MA, Olivucci M. Photoisomerization Path for a Realistic Retinal Chromophore Model: The Nonatetraeniminium Cation. J Am Chem Soc 1998. [DOI: 10.1021/ja972695i] [Citation(s) in RCA: 126] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Garavelli M, Bernardi F, Olivucci M, Vreven T, Klein S, Celani P, Robb MA. Potential-energy surfaces for ultrafast photochemistry Static and dynamic aspects. Faraday Discuss 1998. [DOI: 10.1039/a802270d] [Citation(s) in RCA: 132] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Vreven T, Bernardi F, Garavelli M, Olivucci M, Robb MA, Schlegel HB. Ab Initio Photoisomerization Dynamics of a Simple Retinal Chromophore Model. J Am Chem Soc 1997. [DOI: 10.1021/ja9725763] [Citation(s) in RCA: 168] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Bearpark MJ, Bernardi F, Clifford S, Olivucci M, Robb MA, Vreven T. Cooperating Rings in cis-Stilbene Lead to an S0/S1 Conical Intersection. J Phys Chem A 1997. [DOI: 10.1021/jp961509c] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Bearpark MJ, Deumal M, Robb MA, Vreven T, Yamamoto N, Olivucci M, Bernardi F. Modeling Photochemical [4 + 4] Cycloadditions: Conical Intersections Located with CASSCF for Butadiene + Butadiene. J Am Chem Soc 1997. [DOI: 10.1021/ja962576n] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Bearpark MJ, Bernardi F, Clifford S, Olivucci M, Robb MA, Smith BR, Vreven T. The Azulene S1 State Decays via a Conical Intersection: A CASSCF Study with MMVB Dynamics. J Am Chem Soc 1996. [DOI: 10.1021/ja9514555] [Citation(s) in RCA: 133] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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