Richard A. Friesner
Department of Chemistry
3000 Broadway, mail code 3110
New York , NY 10027

work : +1 212-854-7606
fax : +1 212-854-7454

Friesner Group

2000 - 2004 Publications


Golosov, Andrei A., Richard A. Friesner , and Philip Pechukas, Reduced Dynamics in Spin-Boson Models:  A Method for Both Slow and Fast Bath, J. Chem. Phys., 112, 5, 2095-2105 (2000).


Crystal, Joseph and Richard A. Friesner , Calculation of the Ionization Potentials and Electron Affinities of Bacteriochlorophyll and Bacteriopheophytin via Ab Initio Quantum Chemistry, J. Phys. Chem., 104, 11, 2362-2366, (2000).


Bridgewater B. M., Fillebeen T, Friesner RA, et al. A zinc thiolate species which mimics aspects of the chemistry of the Ada repair protein and matrix metalloproteinases: the synthesis, structure and reactivity of the tris(2-mercapto-1-phenylimidazolyl) hydroborato complex [Tm-Ph]ZnSPh, J Chem. Soc. Dalton (24): 4494-4496 (2000)     


Dunietz, Barry D., Michael D. Beachy, Yixiang Cao , Douglas A. Whittington, Stephen J. Lippard, and Richard A. Friesner , Large Scale ab Initio Quantum Chemical Calculation of the Intermediates in the Soluble Methane Monooxygenase Catalytic Cycle, J. Am. Chem. Soc., 122, 12, 2828-2839 (2000).


Eyrich, Volker A., Daron M. Standley, and Richard A. Friesner , Optimization in Computational Chemistry and Molecular Biology, C.A. Floudas and P.M. Pardalos, eds, pp 57-71, Kluwer Academic Publishers (2000).


Murphy, R.B., Y. Cao, M. Beachy, M.N. Ringnalda, and R.A. Friesner, Efficient pseudospectral methods for density functional calculations, J.  Chem. Phys., 112, 23, 10131-10141 (2000).


Murphy, R.B., D.M. Philipp, and R.A. Friesner, Frozen orbital QM/MM methods for density functional theory, Chem. Phys. Lett., 321, 113-120, (2000).


Bergquist, Catherine, Brian M. Bridgewater, C. Jeff Harlan, Jack R. Norton, Richard A. Friesner , and Gerard Parkin, Aqua, Alcohol, and Acetonitrile Adducts of Tris(perfluorophenyl) borane: Evaluation of Brnsted Acidity and Ligand Lability with Experimental and Computational Methods, J. Am. Chem. Soc., 122, 43, 10581-10590. (2000). 


Murphy, R.B., D.M. Philipp, and R.A. Friesner, A Mixed Quantum Mechanics/Molecular Mechanics (QM/MM) Method for Large-Scale Modeling of Chemistry in Protein Environments, J Comp. Chem., 21, 16, 1442-1457 (2000). 


Bergquist, Catherine, Hannah Storrie, Lawrence Koutcher, Brian M. Bridgewater, Richard A. Friesner , and Gerard Parkin, Factors Influencing the Thermodynamics of Zinc Alkoxide Formation by Alcoholysis of the Terminal Hydroxide Complex, [TpBut,Me]ZnOH: An Experimental and Theoretical Study Relevant to the Mechanism of Action of Liver Alcohol Dehydrogenase, J. Am. Chem. Soc., 122 (51), 12651 -12658, 2000.


Gherman, Benjamin F., Barry D. Dunietz, Douglas A. Whittington, Stephen J. Lippard, and Richard A. Friesner , Activation of the C-H Bond of Methane by Intermediate Q of Methane Monooxygenase:  A Theoretical Study, J. Am Chem. Soc., 123, 3836-3837, (2001).


Gherman, Benjamin F., Richard A. Friesner , Teh-Hwa Wong, Zhiyuan Min, Richard Bersohn, Photodissociation of acetaldehyde: the CH4 + CO channel, J. Chem. Phys., 114, 14, 6128-6133, (2001).


Zhang, Linda Yu, Emilio Gallicchio, Richard A. Friesner , and Ronald M. Levy, Solvent Models for Protein-Ligand Binding:  Comparison of Implicit Solvent Poisson and Surface Generalized Born Models with Explicit Solvent Simulations, J. Comput. Chem., 22, 6, 591-607 (2001).


Friesner, Richard A. and Barry D. Dunietz, Large Scale Ab Initio Quantum Chemical Calculations on Biological Systems, Accounts of Chemical Research, invited paper, 34, 351-358 (2001).


Kaminksi, George A., Richard A. Friesner , Julian Tirado-Rives, and William L. Jorgensen, Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides, J. Phys. Chem. B, 105, 28, 6474-6487 (2001).


Vargas, Rubicelia, Jorge Garza, Richard A. Friesner , Harry Stern , Benjamin P. Hay, and David A. Dixon ; Strength of the N-H···O=C and C-H···O=C Bonds in Formamide and N-Methylacetamide Dimers, J. Phys. Chem. A, 105(20); 4963-4968, (2001).


Shin, Jun Ho, Brian M. Bridgewater, David G. Churchill, Mu-Hyun Baik, Richard A. Friesner , and Gerard Parkin; An Experimental and Computational Analysis of the Formation of the Terminal Nitrido Complex (3-Cp*)2Mo(N)(N3) by Elimination of N2 from Cp*2Mo(N3)2: The Barrier to Elimination Is Strongly Influenced by the exo versus endo Configuration of the Azide Ligand, J. Am. Chem. Soc., 123(41); 10111-10112 (2001).


Zhou, Ruhong, Richard A. Friesner , Avijit Ghosh , Robert C. Rizzo, William L. Jorgensen, and R. M. Levy ; New Linear Interaction Method for Binding Affinity Calculations Using a Continuum Solvent Model, J. Phys. Chem. B; 105(42); 10388-10397 (2001).


Stern, Harry A., Frank Rittner, Bruce J. Berne, and Richard A. Friesner , Combined fluctuating charge and polarizable dipole models: Application to a five-site water potential function, J. Chem. Phys., 115, 2237 (2001).


Guallar, Victor, Benjamin F. Gherman, Stephen J. Lippard, and Richard A. Friesner , Quantum chemical studies of methane monooxygenase:  comparison with P450, Guest section:  Computational Bioinorganic Chemistry II, 236-242 (2001).


Guallar, Victor, Benjamin F. Gherman, William H. Miller, Stephen J. Lippard and Richard A. Friesner , Dynamics of Alkane Hydroxylation at the Non-Heme Diiron Center in Methane Monooxygenase, J. Am. Chem. Soc., 124, 3377-3384 (2001).


Baik, Mu-Hyun, Stephen J. Lippard, Richard A. Friesner , Theoretical Study on the Stability of N-Glycosyl Bonds: Why Does N7-Platination Not Promote Depurination? J. Am. Chem. Soc., 124, 4495-4503 (2001).


Standley, Daron M., Volker A. Eyrich, Yuling An , David L. Pincus, John R. Gunn and Richard A. Friesner , Protein Structure Prediction Using a Combination of Sequence-Based Alignment, Constrained Energy Minimization and Structure Alignment, Proteins: Structure, Function and Genetics, 45, S. 5, 133-139 (2001).


Baik, Mu-Hyun, Dongwhan Lee, Richard A. Friesner and Stephen J. Lippard, Theoretical Studies of Diiron(II) Complexes that Model Features of the Dioxygen-Activating Centers in Non-Heme Diiron Enzymes, Israel Journal of Chemistry, 41, 173-186 (2001).


Dunietz, Barry D.and Richard A. Friesner , Application and development of multiconfigurational localized perturbation theory, J. Chem. Phys., 115 (24): 11052-11067 (2001).


Crystal, Joseph, Linda Yu Zhang, Richard A. Friesner , and George Flynn, Computational Modeling for Scanning Tunneling Microscopy of Physisorbed Molecules via Ab Initio Quantum Chemistry, J. Phys. Chem. A, 106, 1802-1814 (2002).


Klicic, Jasna, J., Richard A. Friesner , Shi-Yi Liu, and Wayne C. Guida, Accurate Prediction of Acidity Constants in Aqueous Solution via Density Functional Theory and Self-Consistent Reaction Field Methods, J. Phys. Chem. A, 106, 1327-1335, (2002).


Margulis, Claudio J., Victor Guallar , Eunji Sim, Richard A. Friesner , and Bruce J. Berne, A New Semiempirical Approach to Study Ground and Excited States of Metal Complexes in Biological Systems, J. Phys. Chem. B, 106, 8038-8046 (2002).


An, Yuling, and Richard A. Friesner , A novel fold recognition method using composite predicted secondary structures, Proteins, Structure, Function and Genetics, 48, 2, 352-366, (2002).


Batista, Enrique and Richard A. Friesner , A Self-Consistent Charge-Embedding Methodology for ab Initio Quantum Chemical Cluster Modeling of Ionic Solids and Surfaces: Application to the (001) Surface of Hematite (a-Fe2O3). J. Phys. Chem. B,106(33); 8136-8141, (2002).


Eyrich, Volker A., Daron M. Standley, and Richard A. Friesner .  Richard A. Friesner, editor, I. Prigogine and Stuart A. Rice, series editors, Ab Initio Protein Structure Prediction Using a Size Dependent Tertiary Folding Potential, Computational Methods for Protein Folding (Advances in Chemical Physics, Vol. 120, 223-263), John Wiley and Sons, New York, NY, (2002).


Baik, Mu-Hyun and Richard A. Friesner , Computing redox potentials in solution: Density functional theory as a tool for rational design of redox agents, J. Phys. Chem. A, 106 (32): 7407-7412 (2002).


Jacobson, Matthew P., Richard A. Friesner , Zhexin Xiang and Barry Honig , On the Role of the Crystal Environment in Determining Protein Side-chain Conformations, J. Mol. Biol. 320 (3): 597-608 (2002).


Ambundo, Edna A., Richard A. Friesner , and Stephen J. Lippard, Reactions of Methane Monooxygenase Intermediate Q with Derivatized Methanes, J. Am. Chem. Soc., 124 (30): 8770-8771 (2002).


Hascall, Tony, Mu-Hyun Baik, Brian M. Bridgewater, Jun Ho Shin, David G. Churchill, Richard A. Friesner and Gerard F. Parkin 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) 22, 2644-2645 (2002).


Jacobson, Matthew P., George A. Kaminski, Richard A. Friesner and Chaya S. Rapp, Force Field Validation Using Protein Side Chain Prediction, J. Phys. Chem. B., 106 (44); 11673-11680 (2002).


Baik, Mu-Hyun, Joseph B. Crystal, and Richard A. Friesner , 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., 41, (23) 5926-5927 (2002).


Kaminski, George A., Harry A. Stern, B. J. Berne, Richard A. Friesner , Yixiang X. Cao, Robert B. Murphy, Ruhong Zhou , Thomas A. Halgren Development of a polarizable force field for proteins via ab initio quantum chemistry: First generation model and gas phase tests, J. Comput. Chem., 23, 16, 1515-1531 (2002).   


Andrec, Michael, Yuichi Harano, Matthew P. Jacobson Richard A. Friesner and Ronald M. Levy , Complete protein structure determination using backbone residual dipolar couplings and sidechain rotamer predication, J. of Structural and Functional Genomics, 2, 103-111, (2002). 


Baik, Mu-Hyun, Benjamin F. Gherman, Richard A. Friesner and Stephen J. Lippard, Hydroxylation of Methane by Non-Heme Diiron Enzymes:  Molecular Orbital Analysis of  the C-H Bond Activation by Reactive Intermediate Q, J. Am. Chem. Soc. 2002, 124, 14608-14615, (2002).


Kaminski, George A., Richard A. Friesner and Ruhong Zhou , A Computationally Inexpensive Modification of the Point Dipole Electrostatic Polarization Model for Molecular Simulations, J. Comput. Chem., 24, 3, 267-276, (2003).  


Zorman, Barry and Richard A. Friesner , Transitions in ZnS and CdSE Quantum Dots and Wavefunction Symmetry, J. Chem. Phys., 18, 13, 5937-5946 (2003).


Zhou, Zhiyong, Louis Brus , and Richard Friesner Electronic Structure and Luminescence of 1.1-and 1.4-nm Silicon Nanocrystals:  Oxide Shell versus Hydrogen Passivation, Nano Letters, 3, 2, 163-167 (2003).


Wirstam, Maria, Stephen J. Lippard, and Richard A. Friesner , Reversible Dioxygen Binding to Hemerythrin, , J. Am. Chem. Soc., 125, 13, 3980-3987 (2003).


Friesner, Richard A. Mu-Hyun Baik, Victor Guallar , Benjamin F. Gherman, Maria Wirstam , Robert B. Murphy and Stephen J. Lippard, How iron-containing proteins control dioxygen chemistry:  a detailed atomic level description via accurate quantum chemical and mixed quantum mechanics/molecular mechanics calculations, Coordination Chemistry Reviews, 238-239, 267-290 (2003).


Guallar, Victor, Mu-Hyun Baik , Stephen J. Lippard, and Richard A. Friesner , Peripheral heme substituents control the hydrogen-atom abstraction chemistry in cytochromes P450, Proc. Nat. Acad. Sci. USA, 100, 6998-7002 (2003).


Baik, Mu-Hyun, Martin Newcomb, Richard A. Friesner and Stephen J. Lippard, Mechanistic Studies on the Hydroxylation of Methane by Methane Monooxygenase,” Chemical Reviews, 103, 2385-2419 (2003).


Tang, Lihao, Elizabeth T. Papish, Graham P. Abramo, Jack R. Norton, Mu-Hyun Baik , Richard A. Friesner and Anthony Rappé, Kinetics and Thermodynamics of H• Transfer From (h5-C5R5)Cr(CO)3H to Methyl Methacrylate and Styrene, J. Am. Chem. Soc.125, 33, 10093-10102 (2003).   


Tang, Lihao, Elizabeth T. Papish, Graham P. Abramo, Jack R. Norton, Mu-Hyun Baik , Richard A. Friesner and Anthony Rappé, Additions and Corrections, J. Am. Chem. Soc., 8/31/06 to Kinetics and Thermodynamics of H• Transfer From (h5-C5R5)Cr(CO)3H to Methyl Methacrylate and Styrene, J. Am. Chem. Soc.125, 33, 10093-10102 (2003).   


Baik, Mu-Hyun, Richard A. Friesner and Stephen J. Lippard, "Theoretical Study of Cisplatin Binding to Purine Bases: Why Does Cisplatin Prefer Guanine over Adenine as Substrate?" J. Am. Chem. Soc., 125, 14082-14092 (2003).


Baik, Mu-Hyun; Friesner, Richard A.; Lippard, Stephen 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.  42, 8615-8617, (2003).


Zhou, Zhiyong, Richard A. Friesner , and Louis Brus, Electronic Structure of 1 to 2 nm Diameter Silicon Core/Shell Nanocrystals:  Surface Chemistry, Optical Spectra, Charge Transfer and Doping, J. Am. Chem. Soc., 125, 15599-15607 (2003). 


Kaminski, George A., Harry A. Stern, B. J. Berne, and Richard A. Friesner Development of an Accurate and Robust Polarizable Molecular Mechanics Force Field from Ab Initio Quantum Chemistry, J. Phys. Chem. A, 108, 621-627 (2004).


Guallar, Victor, Matt Jacobson, Ann McDermott and Richard A. Friesner , “Computational Modeling of the Catalytic Reaction in Triosephosphate Isomerase” J. Molec., Biol., 337, 227-239 (2004).  


Jacobson, Matthew P., David L. Pincus, Chaya S. Rapp, Tyler J. F. Day, Barry Honig , David E. Shaw, and Richard A. Friesner , A Hierarchical Approach to All-Atom Protein Loop Prediction, Prot. Struc. Func. Gen., 55, 2, 351-367 (2004).


Friesner, Richard A Friesner, Jay L. Banks, Robert B. Murphy, Thomas A. Halgren, Jasna J. Klicic, Daniel T. Mainz, Matthew P. Repasky, Eric H. Knoll, David E. Shaw, Mee Shelley, Jason K. Perry, Lynnette C. Sander, and Peter S. Shenkin, Glide: A New Approach for Rapid, Accurate Docking and Scoring.  I. Method and Assessment of Docking Accuracy, J. Med. Chem., 47, 7, 1739-1749 (2004).



Halgren, Thomas A., Robert B. Murphy,Richard A Friesner, Hege S. Beard, Leah L. Frye, W. Thomas Pollard, Jay L. Banks, Glide: A New Approach for Rapid,Accurate Docking and Scoring.  2.  Enrichment Factors in Database Screening, J. Med. Chem., 47, 7, 1750-1759 (2004).


Gherman, B.F., S.D. Goldberg, V.W. Cornish, R.A. Friesner, Mixed Quantum Mechanical/Molecular Mechanical (QM/MM) Study of the Deacylation Reaction in a Penicillin Binding Protein (PBP) Versus in a Class C β-Lactamase, J. Am. Chem. Soc., 126, 24, 7652-7664 (2004).


Yu, Zhiyun, Matthew P. Jacobson, Julia Josovitz. Chaya S. Rapp, and Richard A. Friesner, First-Shell Solvation of Ion Pairs:  Correction of Systematic Errors in Implicit Solvent Models, J. Phys. Chem., 108, 21, 6643-6654 (2004).


Li, Xin, Jacobson, RAF, High-Resolution Prediction of Protein Helix Positions and Orientations, Protein, Structure, Function and Bioinformatics, 55, 368-382 (2004).


Guallar, Victor and Richard A. Friesner , Cytochrome P450CAM Enzymatic Catalysis Cycle:  A Quantum Mechanics/Molecular Mechanics Study, J. Am. Chem. Soc., 126, 8501-8508 (2004). 


Gherman, Benjamin F., Mu-Hyun Baik, Stephen J. Lippard, and Richard A. Friesner , Dioxygen Activation in Methane Monooxygenase: A Theoretical Study, J. Am. Chem. Soc. 126, 2978-2990, (2004).


Zhou, Zhiyong, Michael Steigerwald, Mark Hybertsen, Louis Brus, and Richard A. Friesner , Electronic Structure of Tubular Aromatic Molecules derived from the Metallic (5,5) Armchair Single Wall Carbon Nanotube, J. Am. Chem. Soc., 126, 3597-3607 (2004).


Dukovic, Gordana, Brian E. White, Zhiyong Zhou, Feng Wang, Steffen Jockusch, Michael L. Steigerwald, Tony F. Heinz, Richard A. Freisner, Nicholas J. Turro and Louis E. Brus, Reversible Surface Oxidation and Efficient Lumnescence Quenching in Semiconductor Single-Wall Carbon Nanotubes, J. Am. Chem. Soc., 126 (46): 15269-15276, (2004).


Mu-Hyun Baik, Richard A. Friesner and Gerard Parkin, "Theoretical investigation of the metal-metal interaction in dimolybdenum complexes with bridging hydride and methyl ligands, Polyhedron, 23, 2879-2900, 2004.


Friesner, R.A. Combined quantum and molecular mechanics (QM/MM), Drug Discovery Today:  Technologies, 1, 3, 253-259 (2004).


Sarel J. Fleishman, Susan Harrington, Richard A. Friesner, Barry Honig and Nir Ben-Tal, An automatic Method for Prediction Transmembrane Protein Structures Using Cryo-EM and Evolutionary Data, Biophysical Journal, 87, 3448-3459, (2004).   


Kwang Taeg Rim, Thomas Müeller, Jeffrey P. Fitts, Kaveh Adib, Nicholas Camillone III, Richard M. Osgood, Enrique R. Batista, Richard A. Friesner, S. A. Joyce, and George W. Flynn, Scanning Tunneling Microscopy and Theoretical Study of Competitive Reactions in the Dissociative Chemisorption of CCl4 on Iron Oxide Surfaces, J. Phys. Chem. B;  108(43) 16753-16760 (2004).