All publications 2000 - 2009

    2009

  • ''Computational Modeling of the Electronic Structure of Oligothiophenes with Various Side Chains,'' T. Wang and R.A. Friesner,
    J. Phys. Chem. C, 113, 6 (2009).
  • ''Editorial Overview,,'' Jeffrey Skolnick and Richard A. Friesner,
    Curr. Opin. Struct. Biol., 19, 117 (2009).
  • ''Localized orbital corrections for the barrier heights in density functional theory,'' M. L. Hall, D. A. Goldfeld, A. Bochevarov, and R. A. Friesner,
    J. Chem. Theory Comput., 5, 2996 (2009).
  • ''Protein Side-Chain Dynamics and Residual Conformational Entropy,'' N. Trbovic, J.-H. Cho, R. Abel, R. A. Friesner, M. Rance, A. G. Palmer, III,
    J. Am. Chem. Soc., 131, 615 (2009).
  • ''QM/MM Simulation on P450 BM3 Enzyme Catalysis Mechanism,'' Li Tian and Richard A. Friesner,
    Journal of Chemical Theory and Computation, 5, 1421 (2009).
  • ''Quantitative DFT Modeling of the Enantiomeric Excess for Dioxirane-Catalyzed Epoxidations,'' S. T. Schneebeli, M. L. Hall, R. Breslow, and R. Friesner,
    J. Am. Chem. Soc., 131, 3965 (2009).
  • ''Quantum Chemical Investigation of Cluster Models for TiO2 Nanoparticles with Water-Derived Ligand Passivation: Studies of Excess Electron States and Implications for Charge Transport in the Gratzel Cell,'' V. Blagojevic, Y.-R. Chen, M. Steigarwald, L. Brus, and R.A. Friesner,
    J. Phys. Chem. C, ASAP Article, (2009).
  • ''Thermodynamic Properties of Liquid Water: An Application of a Nonparametric Approach to Computing the Entropy of a Neat Fluid,'' L. Wang, R. Abel, R.A. Friesner, and B.J. Berne,
    J. Chem. Theo. Comput. , 5, 1462 (2009).

    2008

  • ''Density Functional Localized Orbital Corrections for Transition Metals,'' D. Rinaldo, L. Tian, J. N. Harvey, R. A. Friesner,
    J. Chem. Phys., 129, 164108 (2008).
  • ''Exploring structural variability in X-ray crystallographic models using protein local optimization by torsion-angle sampling,'' J. L. Knight, Z. Zhou, E. Gallicchio, D. M. Himmel, R. A. Friesner, E. Arnold, and R. M. Levy,
    Acta Crystallographica Sect. D, Biological Crystallography, 64, 383 (2008).
  • ''Localized orbital corrections applied to thermochemical errors in density functional theory: The role of basis set and the application to molecular reactions,'' D. A. Goldfeld, A. D. Bochevarov, and R. A. Friesner,
    J. Chem. Phys., 129, 214105 (2008).
  • ''Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins,'' P. Maragakis, K. Lindorff-larsen, M. P. Eastwood, R. O. Drorr, J. L. Klepeis, I. T. Arkin, M. O. Jensen, H. Xu, N. Trbovic, R. A. Friesner, A. G. Palmer III, and D. E. Shaw,
    J. Phys. Chem. B, 112, 6155 (2008).
  • ''Prediction of Protein Loop Conformations Using the AGBNP Implicit Solvent Model and Torsion Angle Sampling,'' A. K. Felts, E. Gallicchio, D. Chekmarev, K. A. Paris, R. A. Friesner and R. M. Levy,
    J. Chem. Theory Comput., 4, 855 (2008).
  • ''Pseudospectral time-dependent density functional theory,'' C. Ko, D. K. Malick, D. A. Braden, R. A. Friesner, and T. J. Martinez,
    J. Chem. Phys., 128, 104103 (2008).
  • ''Structural Analysis of Protein Dynamics by MD Simulations and NMR Spin Relaxation,'' N. Trbovic, B. Kim, R. A. Friesner, and A. G. Palmer, III,
    Proteins, Structure, Function, and Bioinformatics, 71, 684 (2008).
  • ''The densities produced by the density functional theory: Comparison to full configuration interaction,'' A. D. Bochevarov and R. A. Friesner,
    J. Chem. Phys., 128, 34102 (2008).
  • ''The Role of the Active-Site Solvent in the Thermodynamics of Factor Xa Ligand Binding,'' R. Abel, T. Young, R. Farid, B. J. Berne, and R. A. Friesner,
    J. Am. Chem. Soc., 130, 2817 (2008).
  • ''Towards better refinement of comparative models: Predicting loops in inexact environments,'' B. D. Sellers, K. Zhu, S. Zhao, R. A. Friesner, and M. P. Jacobson,
    Proteins, Structure, Function and Bioinformatics, 72, 959 (2008).

    2007

  • ''Assignment of polar states for protein amino acid residues using an interaction cluster decomposition algorithm and its application to high resolution protein structure modeling,'' X. Li, Matthew P. Jacobson, K. Zhu, S. Zhao, and R. A. Friesner,
    Prot. Struc. Func. Bioinfor., 66, 824 (2007).
  • ''Comparative Performance of Several Flexible Docking Programs and Scoring Functions: Enrichment Studies for a Diverse Set of Pharmaceutically Relevant Targets,'' Z. Zhou, A. K. Felts, R. A. Friesner, and R. M. Levy,
    J. Chem. Inf. Model., 47, 1599 (2007).
  • ''Improved Methods for Side Chain and Loop Predictions via the Protein Local Optimization Program: Variable Dielectric Model for Implicitly Improving the Treatment of Polarization Effects,'' K. Zhu and M. Shirts and R. A. Friesner,
    J. Chem. Theor. Comput., 3, 2108 (2007).
  • ''Intermediates in Dioxygen Activation by Methane Monooxygenase: A QM/MM Study,'' D. Rinaldo, D. M. Philipp, S. J. Lippard, and R. A. Friesner,
    J. Am. Chem. Soc., 129, 3135 (2007).
  • ''Motifs for molecular recognition exploiting hydrophobic enclosure in protein–ligand binding,'' T. Young, R. Abel, B. Kim, B. J. Berne, and R. A. Friesner,
    Proc. Nat. Acad. Sci., 104, 808 (2007).
  • ''Multiscale Optimization of a Truncated Newton Minimization Algorithm and Application to Proteins and Protein-Ligand Complexes,'' K. Zhu, M. R. Shirts, R. A. Friesner, and M. P. Jacobson,
    J. Chem. Theor. Comput., 3, 640 (2007).
  • ''Prediction of side-chain conformations on protein surfaces,'' Z. Xiang, P. J. Steinbach, M. P. Jacobson, R. A. Friesner, and B. Honig,
    Prot. Struc. Func. Bioinfor., 66, 814 (2007).
  • ''Replica Exchange with Solute Tempering: Efficiency in Large Scale Systems,'' X. Huang, M. Hagen, B. Kim, R. A. Friesner, R. Zhou, and B. J. Berne,
    J. Phys. Chem. B., 111, 5405 (2007).
  • ''Serial replica exchange,'' M. Hagen, B. Kim, P. Liu, Richard A. Friesner, and B. J. Berne,
    J. Phys. Chem. B., 111, 1416 (2007).

    2006

  • ''A Localized Orbital Analysis of the Thermochemical Errors in Hybrid Density Functional Theory: Achieving Chemical Accuracy via a Simple Empirical Correction Scheme,'' R. A. Friesner, E. H. Knoll, and Y. Cao,
    J. Chem. Phys., 125, 124107 (2006).
  • ''Conformational Equilibrium of Cytochrome P450 BM-3 Complexed with N-Palmitoylglycine: A Replica Exchange Molecular Dynamics Study,'' K. P. Ravindranathan, E. Gallicchio, R. A. Friesner, A. E. McDermott, and R. M. Levy,
    J. Am. Chem. Soc., 128, 5786 (2006).
  • ''Extra precision glide: Docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes,'' R. A. Friesner, R. B. Murphy, M. P. Repasky, L. L. Frye, J. R. Greenwood, T. A. Halgren, P. C. Sanschagrin, D. T. Mainz,
    J. Med. Chem., 49, 6177 (2006).
  • ''Kinetics and thermodynamics of H center dot transfer from (eta(5)-C5R5)Cr(CO)(3)H (R = Ph, Me, H) to methyl methacrylate and styrene,'' L. H. Tang, E. T. Papish, G. P. Abramo, J. R. Norton, M.-H. Baik, R. A. Friesner, and A. Rappe,
    J. Am. Chem. Soc., 128, 11314 (2006).
  • ''Localized Orbital Corrections for the Calculation of Ionization Potentials and Electron Affinities in Density Functional Theory,'' E. H. Knoll and R. A. Friesner,
    J. Phys. Chem. B, 110, 18787 (2006).
  • ''Long Loop Prediction Using the Protein Local Optimization Program,'' K. Zhu, D. L. Pincus, S. Zhao, and R. A. Friesner,
    Proteins, Structure, Function and Bioinformatics, 65, 438 (2006).
  • ''Modeling of Ligation-Induced Helix/Loop Displacements in Myoglobin: Toward an Understanding of Hemoglobin Allostery,'' V. Guallar, A. A. Jarzecki, R. A. Friesner, and T. G. Spiro,
    J. Am. Chem. Soc., 128, 5427 (2006).
  • ''Modeling polarization in proteins and protein-ligand complexes: Methods and preliminary results, Peptide Solvation and H-Bonds,'' R. A. Friesner,
    Advances in Protein Chemistry, 72, 79 (2006).
  • ''New insights about HERG blockade obtained from protein modeling, potential energy mapping, and docking studies,'' R. Farid, T. Day, R. A. Friesner, and R. A. Pearlstein,
    Bioorg. Med., Chem., 14, 3160 (2006).
  • ''Novel Procedure for Modeling Ligand/Receptor Induced fit Effects,'' W. Sherman, T. Day, M. P. Jacobson, R. A. Friesner, and R. Farid,
    J. Med. Chem., 49, 534 (2006).
  • ''PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and Preliminary results,'' S. L. Dixon, A. M. Smondyrev, E. H. Knoll, S. N. Rao, D. E. Shaw, and R. A. Friesner,
    J. Computer. Aided Mol. Des., 20, 647 (2006).
  • ''The Effect of Heme Environment on the Hydrogen Abstraction Reaction of Camphor in P450cam Catalysis: A QM/MM Study,'' A. Altun, V. Guallar, R. A. Friesner, S. Shaik, and W. Thiel,
    J. Am. Chem. Soc., 128, 3924 (2006).
  • ''Tribute to Robert J. Silbey,'' R. A. Friesner, K. D. Jordan, and D. R. Reichman,
    J. Phys. Chem. B., 110, 18734 (2006).
  • ''What role do surfaces play in GB models? A new-generation of surface-generalized Born model based on a novel Gaussian surface for biomolecules,'' Z. Yu, M. P. Jacobson, and R. A. Friesner,
    J. Comput. Chem., 27, 72 (2006).

    2005

  • ''Ab Initio Quantum Chemical and Mixed Quantum Mechanics/Molecular Mechanics (QM/MM) Methods for Studying Enzymatic Catalysis,'' R. A. Friesner and V. Guallar,
    Ann. Rev. Phys. Chem., 56, 389 (2005).
  • ''Ab Initio Quantum Chemistry: Methodology and Applications,'' R. A. Friesner,
    Proc. Nat. Acad. Sci. USA, 102, 6648 (2005).
  • ''A Polarizable Force Field and Continuum Solvation Methodology for Modeling of Protein-Ligand Interactions,'' J. R. Maple, Y. Cao, W. Damm, T. A. Halgren, G. A. Kaminski, L. Y. Zhang, and R. A. Friesner,
    J. Chem. Theory and Comput., 1, 694 (2005).
  • ''Computational prediction of native protein ligand-binding and enzyme active site sequences,'' R. Chakrabarti, A. M. Klibanov, and R. A. Friesner,
    Proc. Nat. Acad. Sci. USA, 102, 10153 (2005).
  • ''Dopant local bonding and electric activity near Si(100)-oxide Interfaces,'' Z. Zhou, M. L. Steigerwald, R. A. Friesner, L. Brus, and M. S. Hybertsen,
    J. App. Phys., 98, 76105 (2005).
  • ''Efficient simulation method for polarizable protein force fields: Application to the simulation of BPTI in liquid water,'' E. Harder, B. Kim, R. A. Friesner, and B. J. Berne,
    J. Chem. Theory and Comput., 1, 169 (2005).
  • ''Importance of Accurate Charges in Molecular Docking: Quantum Mechanical/Molecular Mechanical (QM/MM) Approach,'' A. E. Cho, V. Guallar, B. J. Berne, and Richard Friesner,
    J. Comp. Chem., 26, 915 (2005).
  • ''Integrated Modeling Program, Applied Chemical Theory (IMPACT),'' J. L. Banks, H. S. Beard, Y. Cao, A. E. Cho, W. Damm, R. Farid, A. K. Felts, T. A. Halgren, D. T. Mainz, J. R. Maple, R. Murphy, D. M. Philipp, M. P. Repasky, L. Y. Zhang, B. J. Berne, R. A. Friesner, E. Gallicchio and R. M. Levy,
    J. Comput. Chem., 26, 1752 (2005).
  • ''Molecular (hyper) polarizabilities computed by pseudospectral methods,'' Y. Cao and R. A. Friesner,
    J. Chem. Phys., 122, 104102 (2005).
  • ''Nuclear-magnetic-resonance shielding constants calculated by pseudospectral methods,'' Y. X. Cao, M. D. Beachy, D. A. Braden, L. Morrill, M. N. Ringnalda, and R. A. Friesner,
    J. Chem. Phys., 122, 224116 (2005).
  • ''Pseudospectral Local Second Order Mǿller-Plesset Methods for Computation of Hydrogen Bonding Energies of Molecular Pairs,'' G. A. Kaminski, J. Maple, R. B. Murphy, D. A. Braden, and R. A. Friesner,
    J. Chem. Theory and Comput., 1, 248 (2005).
  • ''Replica exchange with solute tempering: A method for sampling biological systems in explicit water,'' P. Liu, B. Kim, R. A. Friesner, and B. J. Berne,
    Proc. Nat. Acad. Sci. USA, 102, 13749 (2005).
  • ''Reply to Comment on “Strength of the N-H···O═C Bonds in Formamide and N-Methylacetamide Dimers,'' R. Vargas, J. Garza, R. A. Friesner, H. Stern, B. P. Hay, and D. A. Dixon,
    J. Phys. Chem. A, 109, 6991 (2005).
  • ''Sequence optimization and designability of enzyme active sites,'' R. Chakrabarti, A. M. Klibanov, and R. A. Friesner,
    Proc. Nat. Acad. Sci. USA, 102, 12035 (2005).
  • ''Structural and chemical trends in doped silicon nanocrystals: First-principles calculations,'' Z. Y. Zhou, M. L. Steigerwald, R. A. Friesner, L. Brus, M. S. Hybertsen,
    Phys. Rev. B, 71, 245308 (2005).
  • ''Structure & Dynamics of the Solvation of Bovine Pancreatic Trypsin Inhibitor in Explicit Water,'' B. Kim, T. Young, E. Harder, R. A. Friesner, and B. J. Berne,
    J. Phys. Chem. B, 109, 16529 (2005).
  • ''Substrate Hydroxylation in Methane Monooxygenase: Quantitative Modeling via Mixed Quantum Mechanics/Molecular Mechanics Techniques,'' B. F. Gherman, S. J. Lippard and R. A. Friesner,
    J. Am. Chem. Soc., 127, 1025 (2005).
  • ''Thermal Equilibrium of High- and Low- Spin Forms of Cytochrome P450 BM3: Repositioning of the Substrate?,'' T. Jovanovic, R. Farid, R. A. Friesner and A. E. McDermott,
    J. Am. Chem. Soc., 127, 13548 (2005).

    2004

  • ''A Hierarchical Approach to All-Atom Protein Loop Prediction,'' M. P. Jacobson, D. L. Pincus, C. S. Rapp, T. J. F. Day, B. Honig, D. E. Shaw, and R. A. Friesner,
    Prot. Struc. Func. Gen., 55, 351 (2004).
  • ''An automatic Method for Prediction Transmembrane Protein Structures Using Cryo-EM and Evolutionary Data,'' S. J. Fleishman, S. Harrington, R. A. Friesner, B. Honig and N. Ben-Tal,
    Biophys. J., 87, 3448 (2004).
  • ''Combined quantum and molecular mechanics (QM/MM),'' R. A. Friesner,
    Drug Discovery Today: Technologies, 1, 253 (2004).
  • ''Computational Modeling of the Catalytic Reaction in Triosephosphate Isomerase,'' V. Guallar, M. Jacobson, A. McDermott and R. A. Friesner,
    J. Mol. Biol., 337, 227 (2004).
  • ''Cytochrome P450CAM Enzymatic Catalysis Cycle: A Quantum Mechanics/Molecular Mechanics Study,'' V. Guallar and R. A. Friesner,
    J. Am. Chem. Soc., 126, 8501 (2004).
  • ''Development of an Accurate and Robust Polarizable Molecular Mechanics Force Field from Ab Initio Quantum Chemistry,'' G. A. Kaminski, H. A. Stern, B. J. Berne, and R. A. Friesner,
    J. Phys. Chem. A, 108, 621 (2004).
  • ''Dioxygen Activation in Methane Monooxygenase: A Theoretical Study,'' B. F. Gherman, M.-H. Baik, S. J. Lippard, and R. A. Friesner,
    J. Am. Chem. Soc., 126, 2978 (2004).
  • ''Electronic Structure of Tubular Aromatic Molecules derived from the Metallic (5,5) Armchair Single Wall Carbon Nanotube,'' Z. Zhou, M. Steigerwald, M. Hybertsen, L. Brus, and R. A. Friesner,
    J. Am. Chem. Soc., 126, 3597 (2004).
  • ''First-Shell Solvation of Ion Pairs: Correction of Systematic Errors in Implicit Solvent Models,'' Z. Yu, M. P. Jacobson, J. Josovitz, C. S. Rapp, and R. A. Friesner,
    J. Phys. Chem., 108, 6643 (2004).
  • ''Glide: A New Approach for Rapid,Accurate Docking and Scoring. 2. Enrichment Factors in Database Screening,'' T. A. Halgren, R. B. Murphy, R. A. Friesner, H. S. Beard, L. L. Frye, W. T. Pollard, and J. L. Banks,
    J. Med. Chem., 47, 1750 (2004).
  • ''Glide: A New Approach for Rapid, Accurate Docking and Scoring. I. Method and Assessment of Docking Accuracy,'' R. A. Friesner, J. L. Banks, R. B. Murphy, T. A. Halgren, J. J. Klicic, D. T. Mainz, Matthew P. Repasky, E. H. Knoll, D. E. Shaw, M. Shelley, J. K. Perry, L. C. Sander, and P. S. Shenkin,
    J. Med. Chem., 47, 1739 (2004).
  • ''High-Resolution Prediction of Protein Helix Positions and Orientations,'' X. Li, M. P. Jacobson, and R. A. Friesner,
    Protein, Structure, Function and Bioinformatics, 55, 368 (2004).
  • ''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,'' B. F. Gherman, S. D. Goldberg, V. W. Cornish, and R. A. Friesner,
    J. Am. Chem. Soc., 126, 7652 (2004).
  • ''Reversible Surface Oxidation and Efficient Lumnescence Quenching in Semiconductor Single-Wall Carbon Nanotubes,'' G. Dukovic, B. E. White, Z. Zhou, F. Wang, S. Jockusch, M. L. Steigerwald, T. F. Heinz, R. A. Freisner, N. J. Turro and L. E. Brus,
    J. Am. Chem. Soc., 126, 15269 (2004).
  • ''Scanning Tunneling Microscopy and Theoretical Study of Competitive Reactions in the Dissociative Chemisorption of CCl4 on Iron Oxide Surfaces,'' K. T. Rim, T. Müeller, J. P. Fitts, K. Adib, N. Camillone III, R. M. Osgood, E. R. Batista, R. A. Friesner, S. A. Joyce, and G. W. Flynn,
    J. Phys. Chem. B, 108, 16753 (2004).
  • ''Theoretical investigation of the metal-metal interaction in dimolybdenum complexes with bridging hydride and methyl ligands,'' M.-H. Baik, R. A. Friesner, and G. Parkin,
    Polyhedron, 23, 2879 (2004).

    2003

  • ''A Computationally Inexpensive Modification of the Point Dipole Electrostatic Polarization Model for Molecular Simulations,'' G. A. Kaminski, R. A. Friesner and R. Zhou,
    J. Comp. Chem., 24, 267 (2003).
  • ''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,'' L. Tang, E. T. Papish, G. P. Abramo, J. R. Norton, M.-H. Baik, R. A. Friesner, and A. Rappé,
    J. Am. Chem. Soc., 125, 10093 (2003).
  • ''cis-{Pt(NH3)2(L)}2+/+ (L = Cl, H2O, NH3) Binding to Purines and CO: Does p-Back-Donation Play a Role?,'' M.-H. Baik, R. A. Friesner, and S. J. Lippard,
    Inorg. Chem., 42, 8615 (2003).
  • ''Electronic Structure and Luminescence of 1.1-and 1.4-nm Silicon Nanocrystals: Oxide Shell versus Hydrogen Passivation,'' Z. Zhou, L. Brus, and R. Friesner,
    Nano Lett., 3, 163 (2003).
  • ''Electronic Structure of 1 to 2 nm Diameter Silicon Core/Shell Nanocrystals: Surface Chemistry, Optical Spectra, Charge Transfer and Doping,'' Z. Zhou, R. A. Friesner, and L. Brus,
    J. Am. Chem. Soc., 125, 15599 (2003).
  • ''How iron-containing proteins control dioxygen chemistry: a detailed atomic level description via accurate quantum chemical and mixed quantum mechanics/molecular mechanics calculations,'' R. A. Friesner, M.-H. Baik, V. Guallar, B. F. Gherman, M. Wirstam, R. B. Murphy and S. J. Lippard,
    Coordination Chemistry Reviews, 238, 267 (2003).
  • ''Mechanistic Studies on the Hydroxylation of Methane by Methane Monooxygenase,'' M.-H. Baik, M. Newcomb, R. A. Friesner and S. J. Lippard,
    Chemical Reviews, 103, 2385 (2003).
  • ''Peripheral heme substituents control the hydrogen-atom abstraction chemistry in cytochromes P450,'' V. Guallar, M.-H. Baik, S. J. Lippard, and R. A. Friesner,
    Proc. Nat. Acad. Sci. USA, 100, 6998 (2003).
  • ''Reversible Dioxygen Binding to Hemerythrin,'' M. Wirstam, S. J. Lippard, and R. A. Friesner,
    J. Am. Chem. Soc., 125, 3980 (2003).
  • ''Theoretical Study of Cisplatin Binding to Purine Bases: Why Does Cisplatin Prefer Guanine over Adenine as Substrate?,'' M.-H. Baik, R. A. Friesner and S. J. Lippard,
    J. Am. Chem. Soc., 125, 14082 (2003).
  • ''Transitions in ZnS and CdSE Quantum Dots and Wavefunction Symmetry,'' B. Zorman and R. A. Friesner,
    J. Chem. Phys., 18, 5937 (2003).

    2002

  • ''Ab Initio Protein Structure Prediction Using a Size Dependent Tertiary Folding Potential,'' V. A. Eyrich, D. M. Standley, and R. A. Friesner,
    Computational Methods for Protein Folding (Advances in Chemical Physics), 120, 223 Richard A. Friesner, editor, I. Prigogine and Stuart A. Rice, series editors, John Wiley and Sons, New York, NY (2002).
  • ''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),'' M.-H. Baik, J. B. Crystal, and R. A. Friesner,
    Inorg. Chem., 41, 5926 (2002).
  • ''Accurate Prediction of Acidity Constants in Aqueous Solution via Density Functional Theory and Self-Consistent Reaction Field Methods,'' J. Klicic, R. A. Friesner, S.-Y. Liu, and W. C. Guida,
    J. Phys. Chem. A, 106, 1327 (2002).
  • ''A New Semiempirical Approach to Study Ground and Excited States of Metal Complexes in Biological Systems,'' C. J. Margulis, V. Guallar, E.i Sim, R. A. Friesner, and B. J. Berne,
    J. Phys. Chem. B, 106, 8038 (2002).
  • ''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,'' T. Hascall, M.-H. Baik, B. M. Bridgewater, J. H. Shin, D. G. Churchill, R. A. Friesner and G. F. Parkin,
    Chemical Communications, (British Royal Society), 22, 264 (2002).
  • ''A novel fold recognition method using composite predicted secondary structures,'' Y. An and R. A. Friesner,
    Proteins, Structure, Function and Genetics, 48, 352 (2002).
  • ''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),'' E. Batista and R. A. Friesner,,
    J. Phys. Chem. B, 106, 8136 (2002).
  • ''Complete protein structure determination using backbone residual dipolar couplings and sidechain rotamer predication,'' M. Andrec, Y. Harano, M. P. Jacobson, R. A. Friesner, and R. M. Levy,
    J. of Struct. and Funct. Genomics, 2, 103 (2002).
  • ''Computational Modeling for Scanning Tunneling Microscopy of Physisorbed Molecules via Ab Initio Quantum Chemistry,'' J. Crystal, L. Y. Zhang, R. A. Friesner, and G. Flynn,
    J. Phys. Chem. A, 106, 1802 (2002).
  • ''Computing redox potentials in solution: Density functional theory as a tool for rational design of redox agents,'' M.-H. Baik and R. A. Friesner,
    J. Phys. Chem. A, 106, 7407 (2002).
  • ''Development of a polarizable force field for proteins via ab initio quantum chemistry: First generation model and gas phase tests,'' G. A. Kaminski, H. A. Stern, B. J. Berne, R. A. Friesner, Y. X. Cao, R. B. Murphy, R. Zhou, and T. A. Halgren,
    J. Comp. Chem., 23, 1515 (2002).
  • ''Force Field Validation Using Protein Side Chain Prediction,'' M. P. Jacobson, G. A. Kaminski, R. A. Friesner and C. S. Rapp,
    J. Phys. Chem. B, 106, 11673 (2002).
  • ''Hydroxylation of Methane by Non-Heme Diiron Enzymes: Molecular Orbital Analysis of the C-H Bond Activation by Reactive Intermediate Q,'' M.-H. Baik, B. F. Gherman, R. A. Friesner and S. J. Lippard,
    J. Am. Chem. Soc., 124, 14608 (2002).
  • ''On the Role of the Crystal Environment in Determining Protein Side-chain Conformations,'' M. P. Jacobson, R. A. Friesner, Z. Xiang and B. Honig,
    J. Mol. Biol., 320, 597 (2002).
  • ''Reactions of Methane Monooxygenase Intermediate Q with Derivatized Methanes,'' E. A. Ambundo, R. A. Friesner, and S. J. Lippard,
    J. Am. Chem. Soc., 124, 8770 (2002).

    2001

  • ''Activation of the C-H Bond of Methane by Intermediate Q of Methane Monooxygenase: A Theoretical Study,'' B. F. Gherman, B. D. Dunietz, D. A. Whittington, S. J. Lippard, and R. A. Friesner,
    J. Am. Chem. Soc., 123, 3836 (2001).
  • ''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. H. Shin, B. M. Bridgewater, D. G. Churchill, M.-H. Baik, R. A. Friesner, and G. Parkin,
    J. Am. Chem. Soc., 123, 10111 (2001).
  • ''Application and development of multiconfigurational localized perturbation theory,'' B. D. Dunietz, and R. A. Friesner,
    J. Chem. Phys., 115, 11052 (2001).
  • ''Combined fluctuating charge and polarizable dipole models: Application to a five-site water potential function,'' H. A. Stern, F. Rittner, B. J. Berne, and R. A. Friesner,
    J. Chem. Phys., 115, 2237 (2001).
  • ''Dynamics of Alkane Hydroxylation at the Non-Heme Diiron Center in Methane Monooxygenase,'' V. Guallar, B. F. Gherman, W. H. Miller, S. J. Lippard and R. A. Friesner,
    J. Am. Chem. Soc., 124, 3377 (2001).
  • ''Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides,'' G. A. Kaminksi, R. A. Friesner, J. Tirado-Rives, and W. L. Jorgensen,
    J. Phys. Chem. B, 105, 6474 (2001).
  • ''Large Scale Ab Initio Quantum Chemical Calculations on Biological Systems,'' R. A. Friesner and B. D. Dunietz,
    Accounts of Chemical Research, 34, 351 (2001).
  • ''New Linear Interaction Method for Binding Affinity Calculations Using a Continuum Solvent Model,'' R. Zhou, R. A. Friesner, A. Ghosh, R. C. Rizzo, W. L. Jorgensen, and R. M. Levy,
    J. Phys. Chem. B, 105, 10388 (2001).
  • ''Photodissociation of acetaldehyde: the CH4 + CO channel,'' B. F. Gherman, R. A. Friesner, T.-H. Wong, Z. Min, and R. Bersohn,
    J. Chem. Phys., 114, 6128 (2001).
  • ''Protein Structure Prediction Using a Combination of Sequence-Based Alignment, Constrained Energy Minimization and Structure Alignment,'' D. M. Standley, V. A. Eyrich, Y. An, D. L. Pincus, J. R. Gunn and R. A. Friesner,
    Proteins: Structure, Function and Genetics , 45, 133 (2001).
  • ''Quantum chemical studies of methane monooxygenase: comparison with P450, Guest section,'' V. Guallar, B. F. Gherman, S. J. Lippard, and R. A. Friesner,
    Computational Bioinorganic Chemistry II, 236 (2001).
  • ''Solvent Models for Protein-Ligand Binding: Comparison of Implicit Solvent Poisson and Surface Generalized Born Models with Explicit Solvent Simulations,'' L. Y. Zhang, E. Gallicchio, R. A. Friesner, and R. M. Levy,
    J. Comp. Chem., 22, 591 (2001).
  • ''Strength of the N-H···O=C and C-H···O=C Bonds in Formamide and N-Methylacetamide Dimers,'' R. Vargas, J. Garza, R. A. Friesner, H. Stern, B. P. Hay, and D. A. Dixon,
    J. Phys. Chem. A, 105, 4963 (2001).
  • ''Theoretical Studies of Diiron(II) Complexes that Model Features of the Dioxygen-Activating Centers in Non-Heme Diiron Enzymes,'' M.-H. Baik, L. Dongwhan, R. A. Friesner and S. J. Lippard,
    Isr. J. of Chem., 41, 173 (2001).
  • ''Theoretical Study on the Stability of N-Glycosyl Bonds: Why Does N7-Platination Not Promote Depurination?,'' M.-H. Baik, S. J. Lippard, and R. A. Friesner,
    J. Am.Chem.Soc., 124, 4495 (2001).

    2000

  • V. A. Eyrich, D. M. Standley, and R. A. Friesner,
    Optimization in Computational Chemistry and Molecular Biology, C.A. Floudas and P.M. Pardalos, eds, Kluwer Academic Publishers (2000).
  • ''A Mixed Quantum Mechanics/Molecular Mechanics (QM/MM) Method for Large-Scale Modeling of Chemistry in Protein Environments,'' R. B. Murphy, D. M. Philipp, and R. A. Friesner,
    J. Comp. Chem., 21, 1442 (2000).
  • ''Aqua, Alcohol, and Acetonitrile Adducts of Tris(perfluorophenyl) borane: Evaluation of Brönsted Acidity and Ligand Lability with Experimental and Computational methods,'' C. Bergquist, B. M. Bridgewater, C. J. Harlan, J. R. Norton, R. A. Friesner, and G. Parkin,
    J. Am. Chem. Soc., 122, 10581 (2000).
  • ''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,'' B. M. Bridgewater, T. Fillebeen, and R. A. Friesner,
    J Chem. Soc. Dalton, 24, 4494 (2000).
  • ''Calculation of the Ionization Potentials and Electron Affinities of Bacteriochlorophyll and Bacteriopheophytin via Ab Initio Quantum Chemistry,'' J. Crystal and R. A. Friesner,
    J. Phys. Chem., 104, 2362 (2000).
  • ''Efficient pseudospectral methods for density functional calculations,'' R. B. Murphy, Y. Cao, M. Beachy, M. N. Ringnalda, and R. A. Friesner,
    J. Chem. Phys., 112, 10131 (2000).
  • ''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,'' C. Bergquist, H. Storrie, L. Koutcher, B. M. Bridgewater, R. A. Friesner, and G. Parkin,
    J. Am. Chem. Soc., 122, 12651 (2000).
  • ''Frozen orbital QM/MM methods for density functional theory,'' R. B. Murphy, D. M. Philipp, and R. A. Friesner,
    Chem. Phys. Lett., 321, 113 (2000).
  • ''Large Scale ab Initio Quantum Chemical Calculation of the Intermediates in the Soluble Methane Monooxygenase,'' B. D. Dunietz, M. D. Beachy, Y. Cao, D. A. Whittington, S. J. Lippard, and R. A. Friesner,
    J. Am. Chem. Soc., 122, 2828 (2000).
  • ''Reduced Dynamics in Spin-Boson Models: A Method for Both Slow and Fast Bath,'' A. A. Golosov, R. A. Friesner, and P. Pechukas,
    J. Chem. Phys., 112, 2095 (2000).
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