Below are selected publications from all recent years; please check here to cite the use of Jaguar

• •  Galstyan, A.; Robertazzi, A.; Knapp, E.W., "Oxygen-Evolving Mn Cluster in Photosystem II: The Protonation Pattern and Oxidation State in the High-Resolution Crystal Structure," J. Am. Chem. Soc, 2012, 134, 7442–7449
• •  ö  Hughes, T. F.; Harvey, J. N.; Friesner, R. A., "A B3LYP-DBLOC empirical correction scheme for ligand removal enthalpies of transition metal complexes: parameterization against experimental and CCSD(T)-F12 heats of formation," Phys. Chem, 2012, 14, 7724-7738
• •  Lousada, M.C.; Johansson, A.J.; Brinck, T.; Jonsson, M., "Mechanism of H2O2 Decomposition on Transition Metal Oxide Surfaces," J. Phys. Chem. C., 2012, 116, 9533–9543
• •  Coletti, C.; Gonsalvi, L.; Guerriero, A.; Marvelli, L.; Peruzzini, M.; Reginato, G.; Re, N., "Electron-Poor Rhenium Allenylidenes and Their Reactivity toward Phosphines: A Combined Experimental and Theoretical Study," Organometallics., 2012, 31, 57–69
• •  ö  Lupyan, D.; Abramov, Y.A.; Sherman, W., "Close intramolecular sulfur–oxygen contacts: modified force field parameters for improved conformation generation," J. Comput. Aided Mol. Des., 2012, 26, 1195-1205
• •  Ghosh, K.; Sen, T., "(rac)-1,1'-binaphthyl-based simple receptors designed for fluorometric discrimination of maleic and fumaric acids," J. Phys. Chem. B, 2011, 115, 8597-608
• •  ö  Hughes, T.F.; Friesner, R.A., "Systematic investigation of the catalytic cycle of a single site ruthenium oxygen evolving complex using density functional theory," J. Phys. Chem. B, 2011, 115, 9280-9
• •  Klaić, L.; Trippier, P.C.; Mishra R. K.; Morimoto, R.I.; Silverman, R.B., "Remarkable Stereospecific Conjugate Additions to the Hsp90 Inhibitor Celastrol," J. Am. Chem. Soc., 2011, 133, 19634–19637
• •  Yu, T. H.; Sha, Y.; Liu, W.-G.; Merinov, B.V.; Shirvanian, P.; Goddard, W.A., "Mechanism for Degradation of Nafion in PEM Fuel Cells from Quantum Mechanics Calculations," J. Am. Chem. Soc., 2011, 133, 19857–19863
• •  Bryantsev, V.S.; Giordani, V.; Walker, W.; Blanco, M.; Zecevic, S.; Sasaki, K.; Uddin, J.; Addison, D.; Chase, G.V., "Predicting Solvent Stability in Aprotic Electrolyte –Air Batteries: Nucleophilic Substitution by the Superoxide Anion Radical (O₂^•–)," J. Phys. Chem. A, 2011, 115, 12399–12409
• •  Naredla, R. R.; Zheng, C.; Nilsson Lill, S.O.; Klumpp, D. A., "Charge Delocalization and Enhanced Acidity in Tricationic Superelectrophiles," J. Am. Chem. Soc., 2011, 133, 13169–13175
• •  Wang, T.; Brudvig, G.; Batista, V. S., "Characterization of Proton Coupled Electron Transfer in a Biomimetic Oxomanganese Complex: Evaluation of the DFT B3LYP Level of Theory," J. Chem. Theory Comput., 2010, 6, 755–760
• •  Georgiev, V.; Noack, H.; Borowski, T.; Blomberg, M.R.A.; Siegbahn, P.E.M., "DFT Study on the Catalytic Reactivity of a Functional Model Complex for Intradiol-Cleaving Dioxygenases," J. Phys. Chem. B, 2010, 114, 5878–5885
• •  King, H. D.; Meng, Z.; Deskus, J. A.; Sloan, C. P., Gao, Q.; Beno B.R.; Kozlowski, E.S.; LaPaglia, M.A.; Mattson, G.K.; Molski, T.F.; Taber, M.T.; Lodge, N.J.; Mattson, R.J.; Macor J.E., "Conformationally Restricted Homotryptamines. Part 7: 3-cis-(3-Aminocyclopentyl)indoles As Potent Selective Serotonin Reuptake Inhibitors," J. Med. Chem., 2010, 53, 7564–7572
• •  ö  Bochevarov, A.D.; Friesner, R.A.; Lippard, S.J., "Prediction of 57 Fe Mössbauer Parameters by Density Functional Theory: A Benchmark Study," J. Chem. Theory Comput., 2010, 6, 3735–3749
• •  Farber, E.; Herget, J.; Gascón, J. A.; Howell, A.R., "Unexpected Cleavage of 2-Azido-2-(hydroxymethyl)oxetanes: Conformation Determines Reaction Pathway? ," J. Org. Chem., 2010, 75, 7565–7572
• •  Kendrick, I.; Kumari, D.; Yakaboski, A.; Dimakis, D.; Smotkin, E.S., "Elucidating the Ionomer-Electrified Metal Interface," J. Am. Chem. Soc., 2010, 132, 17611–17616
• •  Gámiz-Hernández, A. P.; Galstyan, A. S.; Knapp, E., "Understanding Rubredoxin Redox Potentials: Role of H-Bonds on Model Complexes," J. Chem. Theory Comput., 2009, 5, 2898-2908
• •  ö  Wang T., Friesner R.A., "Computational modeling of the electronic structure of Oligothiophenes with various side chains," J. Phys. Chem. C, 2009, 113, 2553-2561
• •  ö  Schneebeli S.T., Hall M.L., Breslow R., Friesner R., "Quantitative DFT modeling of the enantiomeric excess for dioxirane-catalyzed epoxidations," J. Am. Chem. Soc., 2009, 131, 3965-3973
• •  Pipirou Z., Guallar V., Basran J., Metcalfe C.L., Murphy E.J., Bottrill A.R., Mistry S.C., Raven E.L., "Peroxide-dependent formation of a covalent link between Trp51 and the heme in cytochrome c peroxidase," Biochemistry, 2009, 48, 3593-3599
• •  ö  Tian L., Friesner R.A., "QM/MM simulation on P450 BM3 enzyme catalysis mechanism," J. Chem. Theory Comput., 2009, 5, 1421-1431
• •  Swiderek K., Panczakiewicz A., Bujacz A., Bujacz G., Paneth P., "Modeling of isotope effects on binding oxamate to lactic dehydrogenase," J. Phys. Chem. B, 2009, 113, 12782-12789
• •  ö  Wang, Y.; Haze, O.; Dinnocenzo, J. P.; Farid, S.; Farid, R. S.; Gould, I. R., "Bonded Exciplex Formation: Electronic and Stereoelectronic Effects," J. Phys. Chem. A, 2008, 112, 13088–13094
• •  ö  Ko, C.; Malick, D.K.; Braden, D.A.; Friesner, R.A.; Martínez, T.J., "Pseudospectral time-dependent density functional theory," J. Chem. Phys., 2008, 128, 104103-104111
• •  Berrios, C.; Cardenas-Jiron, G.; Marco, J.; Gutierrez, C.; Ureta-Zanartu, M., "Theoretical and Spectroscopic Study of Nickel(II) Porphyrin Derivatives," J. Phys. Chem. A, 2007, 111, 2706-2714
• •  Cheng, M.; Chenoweth, K.; Oxgaard, J.; vanDuin, A.; Goddard, W., "Single-Site Vanadyl Activation, Functionalization, and Reoxidation Reaction Mechanism for Propane Oxidative Dehydrogenation on the Cubic V4O10 Cluster," J. Phys. Chem. C, 2007, 111, 5115-5127
• •  Dede, M.; Drexler, M.; Fischer, H., "Heptahexaenylidene Complexes: Synthesis and Characterization of the First Complexes with an M=C=C=C=C=C=C=CR2 Moiety (M = Cr, W)," Organometallics, 2007, 26, 4294-4299
• •  Hagmayer, S.; Früh, A.; Haas, T.; Drexler, M.; Fischer, H., "Unprecedented Formation of Azulenylidene Ligands by Reaction of the Vinylidene Ligand in Arylvinylidene Pentacarbonyl Complexes of Chromium and Tungsten with Alkoxyacetylenes," Organometallics, 2007, 26, 3791-3801
• •  Hao, M.; Haq, O.; Muegge, I., "Torsion angle preference and energetics of small-molecule ligands bound to proteins," J. Chem. Inf. Model, 2007, 47, 2242-2252
• •  Jordan, B. J.; Pollier, M. A.; Miller, L. A.; Tiernan, C.; Clavier, G.; Audebert, P.; Rotello, V.M., "Redox-Modulated Recognition of Tetrazines Using Thioureas," Org. Lett., 2007, 9, 2835–2838
• •  Keith, J.; Behenna, D.C.; Mohr, J.T.; Ma, S.; Marinescu, S.C.; Oxgaard, J.; Stoltz, B.M., Goddard, W.A., "The inner-sphere process in the enantioselective Tsuji allylation reaction with (S)-t-Bu-phosphinooxazoline ligands," J. Am. Chem. Soc., 2007, 129, 11876-11877
• •  Pissarnitski, D.A.; Asberom, T.; Bara, T.A.; Buevich, A.V.; Clader, J.W.; Greenlee, W.J.; Guzik, H.S.; Josien, H.B.; Li, W.; McEwan, M.; McKittrick, B.A.; Nechuta, T.L.; Parker, E.M.; Sinning, L.; Smith, E.M.; Song, L.; Vaccaro, H.A.; Voigt, J.H.; Zhang, , "2,6-Disubstituted N-arylsulfonyl piperidines as gamma-secretase inhibitors," Bioorganic & Medicinal Chemistry Letters, 2007, 17, 57-62
• •  Quinn, J.; Foss, F.; Venkataraman, L.; Hybertsen, M.; Breslow, R., "Single-Molecule Junction Conductance through Diaminoacenes," J. Am. Chem. Soc., 2007, 129, 6714-6715
• •  Szczepanska, A.; Espartero, J.L.; Moreno-Vargas, A.J.; Carmona, A.T.; and Robina, I.; Remmert, S.; and Parish, C., "Synthesis and conformational analysis of novel trimeric maleimide cross-linking reagents," J. Org. Chem., 2007, 72, 6776-6785
• •  Venkataraman, L.; Park, Y.; Whalley, A.; Nuckolls, C.; Hybertsen, M.; Steigerwald, M., "Electronics and Chemistry: Varying Single-Molecule Junction Conductance Using Chemical Substituents," Nano Letters, 2007, 7, 502-506
• •  ö  Wang, Y.; Haze, O.; Dinnocenzo, J.P.; Farid, S.; Farid, R.S.; Gould, I.R., "Bonded Exciplexes. A New Concept in Photochemical Reactions," J. Org. Chem., 2007, 72, 6970-6981
• •  Blomberg, M.R.A.; Siegbahn, P.E.M., "Quantum chemistry applied to the mechanisms of transition metal containing enzymes -- cytochrome c oxidase, a particularly challenging case," J. Comput. Chem. , 2006, 27, 1373-1384
• •  Siegbahn, P.E.M.; Lundberg, M., "Hydroxide instead of bicarbonate in the structure of the oxygen evolving complex," J. Inorg. Biochem. , 2006, 100, 1035-1040
• •  ö  Rim, K.T.; Muller,T.; Fitts, J.P.; Adib, K.; Camillone, N.; Osgood, R.M.; Batista, E. R.; Friesner, R. A. ; Joyce, S. A.; Flynn, G. W., "Scanning tunneling microscopy and theoretical study of competitive reactions in the dissociative chemisorption of CCl4 on iron oxide surfaces," J. Phys. Chem. B., 2004, 108, 16753–16760
• •  ö  Dukovic, G.; White, B. E.; Zhou, Z. Y.; Wang, F.; Jockusch, S.; Steigerwald, M. L.; Heinz, T. F.; Friesner, R. A.; Turro, N. J.; Brus, L. E., "Reversible surface oxidation and efficient luminescence quenching in semiconductor single-wall carbon nanotubes," J. Am. Chem. Soc., 2004, 126, 15269–15276
• •  ö  Zhou, Z.; Steigerwald, M.; Hybertsen, M.; Brus, L.; Friesner, R. A., "Electronic Structure of Tubular Aromatic Molecules derived from the Metallic (5,5) Armchair Single Wall Carbon Nanotube," J. Am. Chem. Soc., 2004, 126, 3597–3607
• •  ö  Kaminski, G. A.; Stern, H. A.; Berne, B. J.; Friesner, R. A., "Development of an Accurate and Robust Polarizable Molecular Mechanics Force Field from Ab Initio Quantum Chemistry," J. Phys. Chem. A, 2004, 108, 621–627
• •  ö  Zhou, Z.; Friesner, R. A.; Brus, L., "Electronic Structure of 1 to 2 nm Diameter Silicon Core/Shell Nanocrystals: Surface Chemistry, Optical Spectra, Charge Transfer and Doping," J. Am. Chem. Soc., 2003, 125, 15599–15607
• •  ö  Baik, M.; Friesner, R. A.; Lippard, S. J., "cis-{Pt(NH3)2(L)}2+/+ (L = Cl, H2O, NH3) Binding to Purines and CO: Does p-Back-Donation Play a Role?," Inorg. Chem., 2003, 42, 8615–8617
• •  ö  Tang, L.; Papish, E. T.; Abramo, G. P.; Norton, J. R.; Baik, M.; Friesner, R. A.; Rappé, A., "Kinetics and Thermodynamics of H• Transfer From (h5-C5R5)Cr(CO)3H to Methyl Methacrylate and Styrene," J. Am. Chem. Soc., 2003, 125, 10093–10102
• •  ö  Zhou, Z.; Brus, L.; Friesner, R. A., "Electronic Structure and Luminescence of 1.1-and 1.4-nm Silicon Nanocrystals: Oxide Shell versus Hydrogen Passivation," Nano Letters, 2003, 3, 163–167
• •  ö  Kaminski, G. A.; Friesner, R. A.; Zhou, R., "A Computationally Inexpensive Modification of the Point Dipole Electrostatic Polarization Model for Molecular Simulations," J. Comput. Chem., 2003, 24, 267–276
• •  ö  Greenwood, J. R.; Begtrup, M., "Action of HCl on 3-hydroxypyrazolo(iso)quinolines to give 1-chloropyrazoles: evidence for an addition-elimination mechanism by ab initio calculations in gas phase and water," Theor. Chem. Acc., 2003, 109, 200–205
• •  Rivas-Silva, J.F.; Flores-Riveros, A.; Berrondo, M., "DFT study of 1-D Li6Gd(BO3)(3)," Int. J. Quantum Chem., 2003, 94, 105–112
• •  ö  Klicic, J. J. ; Friesner, R. A.; Liu, S. Y.; Guida, W. C., "Accurate prediction of acidity constants in aqueous solution via density functional theory and self-consistent reaction field methods," J. Phys. Chem. A, 2002, 106, 1327–1335
• •  ö  Guallar, V.; Gherman, B. F.; Miller, W. H.; Lippard, S. J.; Friesner, R.A., "Dynamics of alkane hydroxylation at the non-heme diiron center in methane monooxygenase," J. Am. Chem. Soc., 2002, 124, 3377–3384
• •  ö  Baik, M. H.; Friesner, R. A., "Computing redox potentials in solution: Density functional theory as a tool for rational design of redox agents," J. Phys. Chem. A, 2002, 106, 7407–7412
• •  ö  Crystal, J.; Zhang, L. Y.; Friesner, R. A.; Flynn, G., "Computational Modeling for Scanning Tunneling Microscopy of Physisorbed Molecules via Ab Initio Quantum Chemistry," J. Phys. Chem. A, 2002, 106, 1802–1814
• •  ö  Kaminski, G. A.; Stern, H. A.; Berne, B. J.; Friesner, R. A.; Cao, Y. X.; Murphy, R. B.; Zhou, R.; Halgren, T. A., "Development of a polarizable force field for proteins via ab initio quantum chemistry: First generation model and gas phase tests," J. Comput. Chem., 2002, 23, 1515–1531
• •  ö  Baik, M.; Crystal, J. B.; Friesner, R. A., "Ab Initio Quantum Calculation of the Diabatic Coupling Matrix Elemetns for the Self-Exchange Redox Couples M(Cp)2 0/+(M=Fe, Co; Cp=C5H5)," Inorg. Chem., 2002, 41, 5926–5927
• •  ö  Tony, H.; Baik, M.; Bridgewater, B. M.; Shin, J. H.; Churchill, D. G.; Friesner, R. A.; Parkin, G. F., "A non-classical hydrogen bond in the molybdenum arene complex [η6-C6H5C6H3(Ph)OH]Mo(PMe3)3: evidence that hydrogen bonding facilitates oxidative addition of the O–H bond," Chemical Communications, (British Royal Society), 2002, 22, 2644–2645
• •  ö  Gherman, B. F.; Dunietz, B. D.; Whittington, D. A.; Lippard, S. J.; Friesner, R. A., "Activation of the C-H bond of methane by intermediate Q of methane monoozygenase: A theoretical study," J. Am. Chem. Soc., 2001, 123, 3836–3837
• •  ö  Friesner, R. A.; Dunietz, B. D., "Large Scale Ab Initio Quantum Chemical Calculations on Biological Systems," Accounts of Chemical Research, 2001, 34, 351–358
• •  Yang, H.; Snee, P. T.; Kotz, K. T.; Payne, C. K.; Harris, C. B., "Femtosecond Infrared Study of the Dynamics of Solvation and Solvent Caging," J. Am. Chem. Soc., 2001, 123, 4204
• •  Snee, P. T.; Payne, C. K.; Kotz, K. T.; Yang, H.; Harris, C. B., "High Spin Reactivity Under Ambient Conditions: An Ultrafast UV-Pump IR-Probe Study," J. Am. Chem. Soc., 2001, 123, 2255–2264
• •  El Yazal, J.; Prendergast, F.G.; Shaw, D. E.; Pang, Y. P., "Protonation states of the chromophore of denatured green fluorescent proteins predicted by ab initio calculations," J. Am. Chem. Soc., 2000, 122, 11411–11415

• ö indicates papers (co)authored by Schrödinger scientist(s).