People
Last update: 21 June 2006

 

Thom Vreven

Thom Vreven

Email: thom@gaussian.com

Research Scientist II, Gaussian, Inc.
 Ph.D., King's College, London (U.K.), with Michael A. Robb
Postdoctoral work Emory University, Atlanta, with Keiji Morokuma

Contributions to Gaussian:
Extensions to ONIOM and molecular mechanics

  • Development and application of the ONIOM method.

    The ONIOM method in Gaussian allows the user to partition a chemical system into layers, which can then each be treated at a different computational level. The underlying idea is that the various parts of the system each play their own role in the process under investigation, and therefore require different accuracies. The result is that very accurate calculations can be carried out for a reasonable computational cost.

    ONIOM was first developed by Keiji Morokuma (Emory University , Atlanta). Over the last few years we have made extensions to the method, such as the inclusion of electronic embedding in QM/MM calculations. The ONIOM-PCM method was developed to take into account solvent effects (with Benedetta Mennucci, University of Pisa), and we have developed reliable QM/MM geometry optimization techniques and other ways to investigate potential energy surfaces (much with H. Bernhard Schlegel, Wayne State University, Detroit).

    We applied the ONIOM method to a large variety of chemical problems, such as enzyme reactions, photochemistry, catalysis, and the accurate calculation of bond dissociation energies.

  • Photochemistry

    My graduate work involved the very accurate (CASSCF) investigation of photochemical reactions of models for protonated Schiff bases, specifically the role of surface crossings. These chromophores can be found in the rhodopsin family of light sensitive proteins. Recently, using the ONIOM method, we have looked at the potential energy surfaces of larger (or complete) protonated Schiff base models, and investigated the effect of the protein environment in bacteriorhodopsin.

Investigation of the S0 -> S1 Excitation in Bacteriorhodopsin with the ONIOM(MO:MM) Hybrid Method

Geometry Optimization with QM/MM, ONIOM, and Other Combined Methods. I. Microiterations and Constraints

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

On the Application of the IMOMO (Integrated Molecular Orbital + Molecular Orbital) Method

Ab Initio Photoisomerization Dynamics of a Simple Retinal Chromophore Model

Publications:

Vreven, T., Morokuma, K., “Hybrid Methods: ONIOM(QM:MM) and QM/MM”, Annual Reports in Comp. Chem., 2 (2006) 37-53.

Vreven, T., Byun, K.S., Komaromi, I., Dapprich, S., Montgomery, J.A., Jr., Morokuma, K., Frisch, M.J., “Combining Quantum Mechanics Methods with Molecular Mechanics Methods in ONIOM”, Journal of Chemical Theory and Computation, 2 (2006) 815-826.

Vreven, T., Frisch, M.J., Kudin, K.N., Schlegel, H.B., Morokuma, K., “Geometry Optimization with QM/MM Methods II: Explicit Quadratic Coupling”, Molecular Physics, 104 (2006) 701-714.

Fermann, J.T., Moniz, T., Kiowski, O., McIntire, T.J., Auerbach, S.M., Vreven, T., Frisch, M.J., “Modeling Proton Transfer in Zeolites: Convergence Behavior of Embedded and Constrained Cluster Calculations”, Journal of Chemical Theory and Computation, 1 (2005) 1232-1239.

Li, J., Cross, J.B., Vreven, T., Meroueh, S.O., Mobashery, S., Schlegel H.B., “Lysine Carboxylation in Proteins: OXA-10 b -Lactamase”, Proteins, 61 (2005) 246-257.

Prabhakar, R., Vreven, T., Morokuma, K., Musaev D.G., “Elucidation of the Mechanism of Selenoprotein Glutathione Peroxidase (GPx)-Catalyzed Hydrogen Peroxide Reduction by Two Glutathione Molecules: A Density Functional Study” Biochemistry , 44 (2005) 11864-11871.

Cross, J.B., Vreven, T., Meroueh, S.O., Mobashery, S., Schlegel, H.B., "Computational Investigation of Irreversible Inactivation of the Zinc-Dependent Protease Carboxypeptidase A", J. Phys. Chem. B, 109 (2005) 4761.

da Silva, C.O., Mennucci, B., Vreven, T., "Density Functional Study of the Optical Rotation of Glucose in Aqueous Solution". J. Org. Chem. 69 (2004) 8161-8164.

Rega, N., Iyengar, S.S., Voth, G.A., Schlegel, H.B., Vreven, T., Frisch, M.J., "Hybrid ab-initio/empirical Molecular Dynamics: Combining the ONIOM Scheme with the Atom-centered Density Matrix Propagation (ADMP) Approach", J. Phys. Chem. B 108 (2004) 4210-4220.

Mo, S.J., 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. Accounts, 111 (2004) 154-161.

Vreven, T., Morokuma, K., "Investigation of the S0 -> S1 Excitation in Bacteriorhodopsin with the ONIOM(MO:MM) Hybrid Method" Theor. Chem. Accounts, 109 (2003) 125-132.

Vreven, T., Morokuma, K., Farkas, Ö., Schlegel, H.B., Frisch, M.J., "Geometry Optimization with QM/MM, ONIOM, and Other Combined Methods. I. Microiterations and Constraints" J. Comp. Chem., 24 (2003) 760-769.

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, 22 (2003) 4721-4724.

da Silva, C.O., Mennucci, B., Vreven, T., "Combining Microsolvation and Polarizable Continuum Studies: New Insights in the Rotation Mechanism of Amides in Water" J. Phys.Chem. A, 107 (2003) 6630-6637.

Vreven, T., Morokuma, K., "Prediction of the Dissociation Energy of Hexaphenylethane Using the ONIOM(MO:MO:MO) Method" J.Phys. Chem. A, 106 (2002) 6167-6170.

Torrent, M., Vreven, T., Musaev, D.G., Morokuma, K., Farkas, Ö., Schlegel, H.B., "Effects of the Protein Environment on the Structure and Energetics of Active Sites of Metalloenzymes. ONIOM Study of Methane Monooxygenase and Ribonucleotide Reductase" Journal of the American Chemical Society, 124 (2002) 192-193.

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. of Chem. Phys., 115 (2001) 62-72.

Morokuma, K, Musaev, DG, Vreven, T, Basch, H, Torrent, M, Khoroshun, DV "Model Studies of the Structures, Reactivities, and Reaction Mechanisms of Metalloenzymes" IBM Journal of Research and Development, 45 (2001) 367-395.

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 Beta-Hydride Transfer Pathways" Organometallics, 20 (2001) 2007-2026.

Vreven, T, Morokuma, K "The ONIOM (Our Own N-Layered Integrated Molecular Orbital + Molecular Mechanics) Method for the First Singlet Excited (S 1 ) State Photoisomerization Path of a Retinal Protonated Schiff Base" J. Chem. Phys., 113 (2000) 2969-2975.

Vreven, T, Morokuma, K "On the Application of the IMOMO (Integrated Molecular Orbital + Molecular Orbital) Method" J. Comp. Chem., 21 (2000) 1419-1432.

Bernardi, F, Olivucci, M, Robb, MA, Vreven, T, Soto, J "An Ab Initio Study of the Photochemical Decomposition of 3,3-Dimethyldiazirine" Journal of Organic Chemistry, 65 (2000) 7847-7857.

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" Journal of the American Chemical Society, 122 (2000) 2911-2924.

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., 111 (1999) 8799-8803.

Blancafort, L, Adam, W, Gonzalez, 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" Journal of the American Chemical Society, 121 (1999) 10583-10590.

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 Discussions, (1998) 51-70.

Garavelli, M, Vreven, T, Celani, P, Bernardi, F, Robb, MA, Olivucci, M "Photoisomerization Path for a Realistic Retinal Chromophore Model: The Nonatetraeniminium Cation" Journal of the American Chemical Society, 120 (1998) 1285-1288.

Vreven, T, Bernardi, F, Garavelli, M, Olivucci, M, Robb, MA, Schlegel, HB "Ab Initio Photoisomerization Dynamics of a Simple Retinal Chromophore Model" Journal of the American Chemical Society, 119 (1997) 12687-12688.

Bearpark, MJ, Bernardi, F, Clifford, S, Olivucci, M, Robb, MA, Vreven, T "Cooperating Rings in Cis-Stilbene Lead to an S-0/S-1 Conical Intersection" J. Phys.Chem. A, 101 (1997) 3841-3847.

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 Plus Butadiene" Journal of the American Chemical Society, 119 (1997) 709-718.

Bearpark, MJ, Bernardi, F, Clifford, S, Olivucci, M, Robb, MA, Vreven, T "18 Annulene: A Benzene-Like S0/S1 Conical Intersection Located with CASSCF+GVB" Molecular Physics, 89 (1996) 37-46.

Yamamoto, N, Vreven, T, Robb, MA, Frisch, MJ, Schlegel, HB "A Direct Derivative MC-SCF Procedure" Chem. Phys. Lett., 250 (1996) 373-378.

Bearpark, MJ, Bernardi, F, Clifford, S, Olivucci, M, Robb, MA, Smith, BR, Vreven, T "The Azulene S-1 State Decays Via a Conical Intersection: A CASSCF Study with MMVB Dynamics" Journal of the American Chemical Society, 118 (1996) 169-175.

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, 14 (1995) 4953-4956.