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    Thom Vreven PhD

    AddressUniversity of Massachusetts Medical School
    364 Plantation Street, LRB
    Worcester MA 01605
    Phone508-856-2272
        Bibliographic 
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        1. Vreven T, Moal IH, Vangone A, Pierce BG, Kastritis PL, Torchala M, Chaleil R, Jiménez-García B, Bates PA, Fernandez-Recio J, Bonvin AM, Weng Z. Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2. J Mol Biol. 2015 Sep 25; 427(19):3031-41.
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        2. Pierce BG, Vreven T, Weng Z. Modeling T cell receptor recognition of CD1-lipid and MR1-metabolite complexes. BMC Bioinformatics. 2014; 15:319.
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        3. Zhang Z, Wang J, Schultz N, Zhang F, Parhad SS, Tu S, Vreven T, Zamore PD, Weng Z, Theurkauf WE. The HP1 homolog rhino anchors a nuclear complex that suppresses piRNA precursor splicing. Cell. 2014 Jun 5; 157(6):1353-63.
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        4. Pierce BG, Wiehe K, Hwang H, Kim BH, Vreven T, Weng Z. ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers. Bioinformatics. 2014 Jun 15; 30(12):1771-3.
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        5. Vreven T, Pierce BG, Hwang H, Weng Z. Performance of ZDOCK in CAPRI rounds 20-26. Proteins. 2013 Dec; 81(12):2175-82.
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        6. Lensink MF, Moal IH, Bates PA, Kastritis PL, Melquiond AS, Karaca E, Schmitz C, van Dijk M, Bonvin AM, Eisenstein M, Jiménez-García B, Grosdidier S, Solernou A, Pérez-Cano L, Pallara C, Fernández-Recio J, Xu J, Muthu P, Praneeth Kilambi K, Gray JJ, Grudinin S, Derevyanko G, Mitchell JC, Wieting J, Kanamori E, Tsuchiya Y, Murakami Y, Sarmiento J, Standley DM, Shirota M, Kinoshita K, Nakamura H, Chavent M, Ritchie DW, Park H, Ko J, Lee H, Seok C, Shen Y, Kozakov D, Vajda S, Kundrotas PJ, Vakser IA, Pierce BG, Hwang H, Vreven T, Weng Z, Buch I, Farkash E, Wolfson HJ, Zacharias M, Qin S, Zhou HX, Huang SY, Zou X, Wojdyla JA, Kleanthous C, Wodak SJ. Blind prediction of interfacial water positions in CAPRI. Proteins. 2014 Apr; 82(4):620-32.
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        7. Hwang H, Vreven T, Weng Z. Binding interface prediction by combining protein-protein docking results. Proteins. 2014 Jan; 82(1):57-66.
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        8. Moretti R, Fleishman SJ, Agius R, Torchala M, Bates PA, Kastritis PL, Rodrigues JP, Trellet M, Bonvin AM, Cui M, Rooman M, Gillis D, Dehouck Y, Moal I, Romero-Durana M, Perez-Cano L, Pallara C, Jimenez B, Fernandez-Recio J, Flores S, Pacella M, Praneeth Kilambi K, Gray JJ, Popov P, Grudinin S, Esquivel-Rodríguez J, Kihara D, Zhao N, Korkin D, Zhu X, Demerdash ON, Mitchell JC, Kanamori E, Tsuchiya Y, Nakamura H, Lee H, Park H, Seok C, Sarmiento J, Liang S, Teraguchi S, Standley DM, Shimoyama H, Terashi G, Takeda-Shitaka M, Iwadate M, Umeyama H, Beglov D, Hall DR, Kozakov D, Vajda S, Pierce BG, Hwang H, Vreven T, Weng Z, Huang Y, Li H, Yang X, Ji X, Liu S, Xiao Y, Zacharias M, Qin S, Zhou HX, Huang SY, Zou X, Velankar S, Janin J, Wodak SJ, Baker D. Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions. Proteins. 2013 Nov; 81(11):1980-7.
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        9. Vreven T, Hwang H, Pierce BG, Weng Z. Evaluating template-based and template-free protein-protein complex structure prediction. Brief Bioinform. 2014 Mar; 15(2):169-76.
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        10. Vreven T, Hwang H, Weng Z. Exploring angular distance in protein-protein docking algorithms. PLoS One. 2013; 8(2):e56645.
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        11. Zhang F, Wang J, Xu J, Zhang Z, Koppetsch BS, Schultz N, Vreven T, Meignin C, Davis I, Zamore PD, Weng Z, Theurkauf WE. UAP56 couples piRNA clusters to the perinuclear transposon silencing machinery. Cell. 2012 Nov 9; 151(4):871-84.
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        12. Vreven T, Thompson LM, Larkin SM, Kirker I, Bearpark MJ. Deconstructing the ONIOM Hessian: Investigating Method Combinations for Transition Structures. J Chem Theory Comput. 2012 Dec 11; 8(12):4907-14.
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        13. Vreven T, Hwang H, Pierce BG, Weng Z. Prediction of protein-protein binding free energies. Protein Sci. 2012 Mar; 21(3):396-404.
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        14. Fleishman SJ, Whitehead TA, Strauch EM, Corn JE, Qin S, Zhou HX, Mitchell JC, Demerdash ON, Takeda-Shitaka M, Terashi G, Moal IH, Li X, Bates PA, Zacharias M, Park H, Ko JS, Lee H, Seok C, Bourquard T, Bernauer J, Poupon A, Azé J, Soner S, Ovali SK, Ozbek P, Tal NB, Haliloglu T, Hwang H, Vreven T, Pierce BG, Weng Z, Pérez-Cano L, Pons C, Fernández-Recio J, Jiang F, Yang F, Gong X, Cao L, Xu X, Liu B, Wang P, Li C, Wang C, Robert CH, Guharoy M, Liu S, Huang Y, Li L, Guo D, Chen Y, Xiao Y, London N, Itzhaki Z, Schueler-Furman O, Inbar Y, Potapov V, Cohen M, Schreiber G, Tsuchiya Y, Kanamori E, Standley DM, Nakamura H, Kinoshita K, Driggers CM, Hall RG, Morgan JL, Hsu VL, Zhan J, Yang Y, Zhou Y, Kastritis PL, Bonvin AM, Zhang W, Camacho CJ, Kilambi KP, Sircar A, Gray JJ, Ohue M, Uchikoga N, Matsuzaki Y, Ishida T, Akiyama Y, Khashan R, Bush S, Fouches D, Tropsha A, Esquivel-Rodríguez J, Kihara D, Stranges PB, Jacak R, Kuhlman B, Huang SY, Zou X, Wodak SJ, Janin J, Baker D. Community-wide assessment of protein-interface modeling suggests improvements to design methodology. J Mol Biol. 2011 Nov 25; 414(2):289-302.
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        15. Vreven T, Hwang H, Weng Z. Integrating atom-based and residue-based scoring functions for protein-protein docking. Protein Sci. 2011 Sep; 20(9):1576-86.
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        16. Hwang H, Vreven T, Whitfield TW, Wiehe K, Weng Z. A machine learning approach for the prediction of protein surface loop flexibility. Proteins. 2011 Aug; 79(8):2467-74.
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        17. Caricato M, Vreven T, Trucks GW, Frisch MJ. J Chem Theory Comput. Oscillator Strengths in ONIOM Excited State Calculations. 2011; 1(7):180-7.
        18. Caricato M, Vreven T, Trucks GW, Frisch MJ. Oscillator Strengths in ONIOM Excited State Calculations. J Chem Theory Comput. 2011 Jan 11; 7(1):180-7.
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        19. Hwang H, Vreven T, Pierce BG, Hung JH, Weng Z. Performance of ZDOCK and ZRANK in CAPRI rounds 13-19. Proteins. 2010 Nov 15; 78(15):3104-10.
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        20. Hwang H, Vreven T, Janin J, Weng Z. Protein-protein docking benchmark version 4.0. Proteins. 2010 Nov 15; 78(15):3111-4.
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        21. Caricato M, Vreven T, Trucks GW, Frisch MJ. Link atom bond length effect in ONIOM excited state calculations. J Chem Phys. 2010 Aug 7; 133(5):054104.
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        22. Tao P, Fisher JF, Shi Q, Vreven T, Mobashery S, Schlegel HB. Matrix metalloproteinase 2 inhibition: combined quantum mechanics and molecular mechanics studies of the inhibition mechanism of (4-phenoxyphenylsulfonyl)methylthiirane and its oxirane analogue. Biochemistry. 2009 Oct 20; 48(41):9839-47.
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        23. Caricato M, Vreven T, Trucks GW, Frisch MJ, Wiberg KB. Using the ONIOM hybrid method to apply equation of motion CCSD to larger systems: benchmarking and comparison with time-dependent density functional theory, configuration interaction singles, and time-dependent Hartree-Fock. J Chem Phys. 2009 Oct 7; 131(13):134105.
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        24. Lundberg M, Kawatsu T, Vreven T, Frisch MJ, Morokuma K. Transition States in a Protein Environment - ONIOM QM:MM Modeling of Isopenicillin N Synthesis. J Chem Theory Comput. 2009 Jan 13; 5(1):222-34.
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        25. Zheng G, Lundberg M, Jakowski J, Vreven T, Frisch MJ, Morokuma K. Int J Quantum Chem. Implementation and Benchmark Tests of the DFTB method and Its Application in the ONIOM Method. 2009; 109:1841-54 .
        26. Lundberg M, Kawatu T, Vreven T, Frisch MJ, Morokuma K. J Chem Theory Comput. Transition States in the Protein Environment – ONIOM QM:MM Modeling of Isopenicillin N Synthesis. 2009; 5:222-34 .
        27. Frisch MJ, Scalmani G, Vreven T, Zheng G. Mol Phys. Analytic Second Derivatives for Semiempirical Models Based on MNDO. 2009; 107 :881-9.
        28. Larkin SM, Vreven T, Bearpark MJ, Morokuma K. Can J Chem. The Application of the ONIOM Hybrid Method to the Cycloaddition Reactions of Bromo Substituted 2(H)-Pyran-2-ones. 2009; 87:872-9.
        29. Hall KF, Vreven T, Frisch MJ, Bearpark MJ. Three-layer ONIOM studies of the dark state of rhodopsin: the protonation state of Glu181. J Mol Biol. 2008 Oct 31; 383(1):106-21.
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        30. Bearpark MJ, Larkin SM, Vreven T. Searching for conical intersections of potential energy surfaces with the ONIOM method: application to previtamin D. J Phys Chem A. 2008 Aug 7; 112(31):7286-95.
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        31. Hratchian HP, Parandekar PV, Raghavachari K, Frisch MJ, Vreven T. QM:QM electronic embedding using Mulliken atomic charges: energies and analytic gradients in an ONIOM framework. J Chem Phys. 2008 Jan 21; 128(3):034107.
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        32. Khoroshun DV, Musaev DG, Vreven T, Morokuma K. Organometallics. Theoretical Study on Bis(imino)pyridyl-Fe(II) Olefin Poly- and Oligomerization Catalysts. Dominance of Different Spin States in Propagation and ß-hydride Transfer Pathways. 2007; 20:2007-26.
        33. Bearpark MJ, Ogliaro F, Vreven T, Boggio-Pasqua M, Frisch MJ, Larkin SM, Morrison M, Robb MA. J Photochem Photobiol A. CASSCF Calculations for Photoinduced Processes in Large Molecules: Choosing when to use the RASSCF, ONIOM, and MMVB approximations. 2007; 190:207-27.
        34. Viswanathan U, Fermann JT, Toy LK, Auerbach SM, Vreven T, Frisch MJ. J Phys Chem C. Modeling Proton Jumps in HY Zeolite: Effects of Acid Site Heterogeneity. 2007; 111:18341-47 .
        35. Mori S, Vreven T, Morokuma K. Transition states of binap-rhodium(I)-catalyzed asymmetric hydrogenation: theoretical studies on the origin of the enantioselectivity. Chem Asian J. 2006 Sep 18; 1(3):391-403.
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        36. Morokuma K, Wang Q, Vreven T. Performance Evaluation of the Three-Layer ONIOM Method:? Case Study for a Zwitterionic Peptide. J Chem Theory Comput. 2006 Sep; 2(5):1317-24.
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        37. Prabhakar R, Vreven T, Frisch MJ, Morokuma K, Musaev DG. Is the protein surrounding the active site critical for hydrogen peroxide reduction by selenoprotein glutathione peroxidase? An ONIOM study. J Phys Chem B. 2006 Jul 13; 110(27):13608-13.
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        38. Vreven T, Byun KS, Komáromi I, Dapprich S, Montgomery JA, Morokuma K, Frisch MJ. Combining Quantum Mechanics Methods with Molecular Mechanics Methods in ONIOM. J Chem Theory Comput. 2006 May; 2(3):815-26.
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        39. Morokuma K, Wang Q, Vreven T. J Chem Theory Comput. Performance Evaluation of the Three-Layer ONIOM Method: Case Study for a Zwitterionic Peptide. 2006; 2:1317-24 .
        40. Vreven T, Byun KS, Komaromi I, Dapprich D, Montgomery Jr. JA, Morokuma K, Frisch MJ. J. Chem. Theory Comput. Combining Quantum Mechanics Methods with Molecular Mechanics Methods in ONIOM. 2006; 2:815-26.
        41. Vreven T, Frisch MJ, Kudin KN, Schlegel HB, Morokuma K. Mol Phys. Geometry Optimization with QM/MM Methods II. Explicit Quadratic Coupling. 2006; 104:701-14.
        42. Deng W, Vreven T, Frisch MJ, Wiberg KB. J Mol Struct (THEOCHEM). Application of the ONIOM Method to Enantioselective Deprotonation in the Presence of Spartein. 2006; 775 :93-9 .
        43. Fermann JT, Moniz T, Kiowski O, McIntire TJ, Auerbach SM, Vreven T, Frisch MJ. Modeling Proton Transfer in Zeolites:? Convergence Behavior of Embedded and Constrained Cluster Calculations. J Chem Theory Comput. 2005 Nov; 1(6):1232-9.
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        44. Li J, Cross JB, Vreven T, Meroueh SO, Mobashery S, Schlegel HB. Lysine carboxylation in proteins: OXA-10 beta-lactamase. Proteins. 2005 Nov 1; 61(2):246-57.
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        45. Prabhakar R, Vreven T, Morokuma K, Musaev DG. Elucidation of the mechanism of selenoprotein glutathione peroxidase (GPx)-catalyzed hydrogen peroxide reduction by two glutathione molecules: a density functional study. Biochemistry. 2005 Sep 6; 44(35):11864-71.
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        46. Cross JB, Vreven T, Meroueh SO, Mobashery S, Schlegel HB. Computational investigation of irreversible inactivation of the zinc-dependent protease carboxypeptidase A. J Phys Chem B. 2005 Mar 17; 109(10):4761-9.
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        47. Fermann JT, Moniz T, Kiowski O, McIntire TJ, Auerbach SM, Vreven T, Frisch MJ. J Chem Theory Comput. Modeling Proton Transfer in Zeolites: Convergence Behavior of Embedded and Constrained Cluster Calculations. 2005; 1:1232-9.
        48. da Silva CO, Mennucci B, Vreven T. Density functional study of the optical rotation of glucose in aqueous solution. J Org Chem. 2004 Nov 12; 69(23):8161-4.
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        49. Rega N, Iyengar SS, Voth GA, Schlegel HB, Vreven T, Frisch MJ. J Phys Chem B. Hybrid ab-initio/empirical Molecular Dynamics: Combining the ONIOM Scheme with the Atom-centered Density Matrix Propagation (ADMP) Approach. 2004; 108:4210-20.
        50. Mo SJ, Vreven T, Mennucci B, Morokuma K, Tomasi J. Theor Chem Acc. 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). 2004; 111:154-61.
        51. 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 Apr 30; 24(6):760-9.
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        52. Kudo T, Akiba S, Kondo Y, Watanabe H, Morokuma K, Vreven T. Organometallics. Ab initio Study of the Effect of Heteroatoms and Bulky Substituents on the Strain Energies of Cyclosilanes. 2003; 22:4721-4.
        53. Vreven T, Morokuma K. Theor Chem Acc. Investigation of the S0 ? S1 Excitation in Bacteriorhodopsin with the ONIOM(MO:MM) Hybrid Method. 2003; 109:125-32.
        54. da Silva CO, Mennucci B, Vreven T. J Phys Chem A. Combining Micro-solvation and Polarizable Continuum Studies: New Insights in the Rotation Mechanism of Amides in Water. 2003; 107:6630-7.
        55. 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 Jan 16; 124(2):192-3.
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        56. Vreven T, Morokuma K. J Phys Chem A. The Prediction of the Dissociation Energy of Hexaphenylethane Using the ONIOM(MO:MO:MO) Hybrid Method. 2002; 106:6167-70.
        57. Morokuma K, Musaev DG, Vreven T, Basch H, Torrent M, Khoroshun DV. IBM J Res & Dev. Model studies of the structures, rectivities, and reaction mechanisms of metalloenzymes. 2001; 45:367-95.
        58. Vreven T, Mennucci B, da Silva CO, Morokuma K, Tomasi J. J Chem Phys. 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; 115:62-72.
        59. Bernardi F, Olivucci M, Robb MA, Vreven T, Soto J. An ab initio study of the photochemical decomposition of 3, 3-dimethyldiazirine J Org Chem. 2000 Nov 17; 65(23):7847-57.
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        60. Sanchez-Galvez A, Hunt P, Robb MA, Olivucci M, Vreven T, Schlegel HB. J Am Chem Soc. Ultrafast Radiationless Deactivation of Organic Dyes: Evidence for a Two-State Two-Mode Pathway in Polymethine Cyanines. 2000; 122:2911-24.
        61. Vreven T, Morokuma K. J Chem Phys. 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; 113:2969-75.
        62. Vreven T, Morokuma K. J Comp Chem. On the Application of the IMOMO (Integrated Molecular Orbital + Molecular Orbital) Method. 2000; 21:1419-1432.
        63. Vreven T, Morokuma K. J Chem Phys. 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; 111:8799-803.
        64. Blancafort L, Adam W, Gonzalez D, Olivucci M, Vreven T, Robb MA. J Am Chem Soc. Theoretical Study of the 1,2 Rearrangement of Housane Radical Cations: Key Role of a Transient Cyclopentane-1,3-diyl Intermediate. 1999; 121:10583-90.
        65. Garavelli M, Bernardi F, Olivucci M, Vreven T, Klein S, Celani P, Robb MA. Faraday Discuss. Potential-energy Surfaces for Ultrafast Photochemistry: Static and Dynamic Aspects. 1998; 110:51-70.
        66. Garavelli M, Vreven T, Celani P, Bernardi F, Robb MA, Olivucci M. Photoisomerization Path for a Realistic Retinal Chromophore Model: The Nonatetraenimminium Cation. 1998; 120:1285-8.
        67. Bearpark MJ, Deumal M, Robb MA, Vreven T, Yamamoto N, Olivucci M, Bernardi F. J Am Chem Soc. Modelling Photochemical [4+4] Cycloadditions: Conical Intersections Located with CASSCF for Butadiene+Butadiene. 1997; 119:709-18.
        68. Bearpark MJ, Bernardi F, Olivucci M, Robb MA, Clifford S, Vreven T. J Phys Chem A. Cooperating Rings in cis-Stilbene lead to an S0/S1 Conical Intersection. 1997; 102:3841-7.
        69. Vreven T, Bernardi F, Garavelli M, Olivucci M, Robb MA, Schlegel HB . J Am Chem Soc. Ab Initio Photoisomerization Dynamics of a Simple Retinal Chromophore Model. 1997; 119:12687-8.
        70. Bearpark MJ, Bernardi F, Clifford S, Olivucci M, Robb MA, Smith BR, Vreven T. J Am Chem Soc. The Azulene S1 State Decays via a Conical Intersection: A CASSCF Study with MMVB Dynamics. 1996; 118:169-75.
        71. Yamamoto N, Vreven T, Robb MA, Frisch MJ, Schlegel HB. Chem Phys Lett. A Direct Derivative MC-SCF Procedure. 1996; 250:373-8.
        72. Bearpark MJ, Bernardi F, Clifford S, Olivucci M, Robb MA, Vreven T. Mol Phys. [18] Annulene: a Benzene-like S0/S1 Conical Intersection Located with CASSCF+GVB. 1996; 89:36-46.
        73. Venturini A, Vreven T, Bernardi F, Olivucci M, Robb MA. Organometallics. The Mechanism of Photodegradation of Polysilanes: A Relaxed Cross Section of the Conical Intersection Hyperline in 2-Methyl-Trisilane. 1995; 14:4953-6.
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