Older Publications

 

2015

 

  • "OPLS3: a force field providing broad coverage of drug-like small molecules and proteins." E. Harder, W. Damm, J. Maple, C. Wu, M.Reboul, J. Yu Xiang, L. Wang, D.Lupyan, M. K. Dahlgren, J. L. Knight, J. W. Kaus, D. S. Cerutt, G. Krilov, W. L. Jorgensen, R. Abel, and R. A. Friesner, Journal of Chemical Ttheory and Computation, 12, 281-296 (2015).
  • ''Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field,'' L. Wang, Y. J. Wu, Y. Q. Deng, B. Kim, L. Pierce, G. Krilov, D. Lupyan, S. Robinson, M.K. Dahlgren, J. Greenwood, D.L. Romero, C. Masse, J.L. Knight, T. Steinbrecher, T. Beuming, W. Damm, E. Harder, W. Sherman,... W.L. Jorgensen, B.J. Berne, R.A. Friesner & R. Abel,
    Journal of the American Chemical Society, 137, 2695-2703 (2015).
  • "Accurate Binding Free Energy Predictions in Fragment Optimization." T. B. Steinbrecher, M. Dahlgren, D. Cappel, T. Lin, L. Wang, G. Krilov, R. Abel, R. Friesner, and W. Sherman, Journal of Chemical Information and Modeling, 55, 2411-2420.
  • ''Conformational Dynamics of the Partially Disordered Yeast Transcription Factor GCN4,'' P. Robustelli, N. Trbovic, R. A. Friesner & A. G. Palmer,
    Journal of Chemical Theory and Computation, 9, 5190-5200 (2015).

     

    2014

     

  • ''Accurate pK(a) Prediction in First-Row Hexaaqua Transition Metal Complexes Using the B3LYP-DBLOC Method,'' S.V. Jerome, T.F. Hughes & R.A. Friesner,
    Journal of Physical Chemistry B, 118, 8008-8016 (2014).
  • ''A first-principles polarized Raman method for determining whether a uniform region of a sample is crystalline or isotropic,'' A.L. Weisman, K.H. DuBay, K.A. Willets & R.A. Friesner,
    The Journal of Chemical Physics, 141, (2014).
  • ''Covalent O-H Bonds as Electron Traps in Proton-Rich Rutile TiO2 Nanoparticles,'' J. Zhang, M. Steigerwald, L. Brus & R.A. Friesner,
    Nano Letters, 14, 1785-1789 (2014).
  • ''Induced fit effects and water structure in modeling ligand binding to proteins: Conformational sampling, free energy perturbation molecular dynamics simulations, and kinetics of binding,'' R.A. Friesner,
    Abstracts of Papers of the American Chemical Society, 247, (2014).
  • ''Leveraging Data Fusion Strategies in Multireceptor Lead Optimization MM/GBSA End-Point Methods,'' J. L. Knight, G. Krilov, K. W. Borrelli, J. Williams, J. R. Gunn, A. Clowes, L. Cheng, R. A. Friesner & R. Abel,
    Journal of Chemical Theory and Computation, 10, 3207-3220 (2014).
  • ''Multicolor Live-Cell Chemical Imaging by Isotopically Edited Alkyne Vibrational Palette,'' Z. Chen, D. W. Paley, L. Wei, A. L. Weisman, R. A. Friesner, C. Nuckolls & W. Min,
    Journal of the American Chemical Society, 136, 8027-8033 (2014).
  • ''Role of Desolvation in Thermodynamics and Kinetics of Ligand Binding to a Kinase,'' J. Mondal, R.A. Friesner & B.J. Berne,
    Journal of Chemical Theory and Computation, 12, 5696-5705 (2014).
  • ''Water structure in protein active sites: Modeling localized water sites and their effect on protein-ligand binding free energies,'' R.A. Friesner,
    Abstracts of Papers of the American Chemical Society, 248, (2014).

     

    2013

    • ''Can't wait for crystallography? Novel methods for GPCR loop prediction and docking,'' D.A. Goldfeld & R.A. Friesner,
      Abstracts of Papers of the American Chemical Society, 245, (2013).
    • ''Computational methods for high resolution prediction and refinement of protein stuctures,'' R.A. Friesner, R. Abel, D.A. Goldfed, E.B. Miller and C. Murrett,
      Current Opinion in Structural Biology, 23, 177 (2013).
    • ''Conformational Dynamics of the Partially Disordered Yeast Transcription Factor GCN4,'' P. Robustelli, N. Trbovic, R.A. Friesner & A.G. Palmer,
      Journal of Chemical Theory and Computation, 9, 5190-5200 (2013).
    • ''Jaguar: A high-performance quantum chemistry software program with strengths in life and materials sciences,'' A. D. Bochevarov, E. Harder, T.F. Hughes, J.R. Greenwood, D.A. Braden, D.M. Philipp, D. Rinaldo, M.D. Halls, J. Zhang & R. A. Friesner,
      International Journal of Quantum Chemistry, 113, 2110-2142 (2013).
    • ''Loop prediction for a GPCR homology model: Algorithms and results.,'' D.A. Goldfeld, K. Zhu, T. Beuming. R.A. Friesner,
      Proteins, 81, 2, 214 (2013).
    • ''Non-covalent interactions and non-dynamic correlation: The new B3LYP-LOC-MM method accounts for both,'' A.D. Bochevarov & R.A. Friesner,
      Abstracts of Papers of the American Chemical Society, 245, (2013).
    • ''Prediction of Long Loops with Embedded Secondary Structure using the Protein Local Optimization Program,'' E.B. Miller, C.S. Murrett, K. Zhu, S. Zhao, D.A. Goldfeld, J.H. Bylund, R.A. Friesner,
      Journal of Chemical Theory and Computation, 9, 1846 (2013).
    • ''Starting-structure dependence of nanosecond timescale intersubstate transitions and reproducibility of MD-derived order parameters,'' T. Zeiske, K.A. Stafford, R.A. Friesner, A.G. Palmer, III ,
      Proteins, 81, 3, 499 (2013).
    • ''Theory and simulation. Editorial overview,'' R.A. Friesner, J. Skolnick,
      Current Opinion in Structural Biology, 23, 169 (2013).
    • ''The Protein Local Optimization Program and G-Protein-Coupled Receptors: Loop Restoration and Applications to Homology Modeling,'' D.A. Goldfeld & R.A. Friesner,
      G Protein Coupled Receptors: Modeling, Activation, Interactions and Virtual Screening, 522, 1-20 (2013).
    • ''Wscore: An empirical scoring function for protein-ligand binding which incorporates the water structure of the active site,'' R.A. Friesner,
      Abstracts of Papers of the American Chemical Society, 245, (2013).

      2012

       

    • ''A B3LYP-DBLOC empirical ligand removal enthalpies of transition metal complexes: parameterization against experimental and CCSD(T)-F12 heats of formation,'' T.F. Hughes, J.N. Harvey, R.A. Friesner,
      Phys. Chem. Chem. Phys., 14, 21, , 7724 (2012).
    • ''Accurate Force Field Development for Modeling Conjugated Polymers,'' K.H. DuBay, M.L. Hall, T.F. Hughes, C. Wu, D.R. Reichman, and R.A. Friesner,
      J. Chem. Theo. Comput., ASAP , TBD (2012).
    • ''Development of Accurate DFT Methods for Computing Redox Potentials of Transition Metal Complexes: Results for Model Complexes and Application to Cytochrome P450,'' T.F. Hughes and R.A. Friesner,
      J. Chemical Theory and Computation, 8, 442 (2012).
    • ''Docking performance of the glide program as evaluated on the Astex and DUD datasets: a complete set of glide SP results and selected results for a new scoring function integrating WaterMap and glide,'' M.P. Repasky, R.B. Robert B. Murphy, J.L. Bnaks, J.R. Greenwood, I. Tubert-Brohman, S. Bhat, R.A. Friesner,
      J. Comput. Aided Mol. Des., 26, 6, 787 (2012).
    • ''On achieving high accuracy and reliability in the calculation of relative protein-ligand binding affinities,'' L. Wang, B.J. Berne, and R.A. Friesner,
      Proc. Natl. Acad. Sci., 109, 6, 1937 (2012).
    • ''Polarized Raman Spectroscpy of Oligothiophene Crystals to Determine Unit Cell Orientation,'' J.C. Heckel, A.L. Weisman, S.T. Schneebeli, M.L. Hall, L.J. Sherry, S.M. Stranahan, K.H. DuBay, R.A. Friesner, K.A. Willets,
      J. Chem. Phys. A, 116, 25,, 6804 (2012).
    • ''Realistic Cluster Modeling of Electron Transport and Trapping in Solvated TiO2 Nanoparticles,'' J. Zhang, T.F. Hughes, M. Steigerwald, L. Brus, and R.A. Friesner,
      J. Am. Chem. Soc., 134, 29, 12028 (2012).
      PubMed ID: PMID: 22738308
    • ''Solvent Chemical Potential Mapping of Complex Surfaces,'' T. Young, B. Kim, R. Abel, R.A. Friesner, and B.J. Berne,
      TBD, In preparation, (2012).
    • ''Successful prediction of the intra- and extracellural loops of four G-protein-coupled receptors,'' D.A. Goldfeld, K. Zhu, T. Beuming, R.A. Friesner,
      PNAS, 108, 20, 8275 (2012).

       

      2011

       

    • ''Contribution of explicit solvent effects to the binding affinity of small-molecule inhibitors in blood coagulation factor serene proteases,'' R. Abel, N.K. Salam, J. Shelley, R. Farid, R.A. Friesner, and W. Sherman,
      Chem. Med. Chem., 6, 1049 (2011).
    • ''Controlling chain conformation in conjugated polymers using defect inclusion strategies,'' G. Bounos, S. Ghosh, A.K. Lee, K. Plunkett, K. DuBay, J.C. Bolinger, R. Zhang, C. Nuckolls, D. Reichman and P.F. Barbara,
      J. Am. Chem. Soc., 133, 10155 (2011).
    • ''IDSite: An Accurate Approach to Predict P450-Mediated Drug Metabolism,'' J. Li, S. Schneebeli, J. Bylund, R. Farid, and R.A. Friesner,
      J. Chem. Theo. Comput., 7, 3829 (2011).
      PubMed ID: PMC3254112 Available Aug 2012
    • ''Insights into the different dioxygen activation pathways of methane and toluene monooxygenase hydroxylases,'' A.D. Bochevarov, J. Li, W.J. Song, R.A. Friesner, and S.J. Lippard,
      J. Am. Chem. Soc., 133, 7384 (2011).
    • ''Ligand binding to protein-binding pockets with wet and dry regions,'' L. Wang, B.J. Berne, and R.A. Friesner,
      Proc. Natl. Acad. Sci., 108, 4, 1326 (2011).
      PubMed ID: PMC3029693
    • ''Parameterization of a B3LYP specific correction for dispersion interactions on a gigantic dataset of CCSD(T) quality non-covalent interaction energies,'' S.T. Schneebeli, A.D. Bochevarov, R. Friesner,
      J. Chem. Theory Comput., 7, 3, 658 (2011).
    • ''Progress in supper long loop prediction,'' S. Zhao, K. Zhu, J. Li, and R.A. Friesner,
      Proteins, 79, 2920 (2011).
    • ''Replica Exchange with Solute Scaling: A more efficient version of Replica Exchange with Solute Tempering (REST2),'' L. Wang, R.A. Friesner, and B.J. Berne,
      J. Chem. Phys. B, 115, 9431 (2011).
    • ''Single-molecule conductance through multiple π-π stacked benzene rings determined with direct electrode-to-benzene ring connections,'' S.T. Schneebeli, M. Kamenetska, Z. Cheng, R. Skouta, R. Friesner, L. Venkataraman, R. Breslow,
      J. Am. Chem. Soc., 133, 2136 (2011).
    • ''Successful preditciton of the intra - and extracellular loops of four G-protein-coupled receptors,'' D.A. Goldfeld, K. Zhu, T. Beuming, and R.A. Friesner,
      Proc. Natl. Acad. Sci., 108, 8275 (2011).
    • ''Systematic Investigation of the Catalytic Cycle of a Single Site Ruthenium Oxygen Evolving Complex Using Density Functional Theory,'' T.F. Hughes and R.A. Friesner,
      J. Phys. Chem. B, 1, 115, 9280 (2011).
    • ''Theory and simulation. Editorial overview,'' J. Skolnick and R.A. Friesner,
      Current Opinion in Structural Biology, 21, 147 (2011).
    • ''The VSGB 2.0 Model: A Next Generation Energy Model for High Resolution Protein Structure Modeling,'' J. Li, R. Abel, K. Zhu, Y. Cao, S. Zhao, and R.A. Friesner,
      Proteins, 79, 2794 (2011).

       

      2010

       

    • ''A Displaced-Solvent Functional Analysis of Model Hydrophobic Enclosures,'' R. Abel, L. Wang, R.A. Friesner, and B.J. Berne,
      J. Chem. Theo. Comput., 6, 2924 (2010).
    • ''Competition of Electrostatic and Hydrophobic Interactions Between Small Hydrophobes and Model Enclosures,'' L. Wang, R.A. Friesner, and B.J. Berne,
      J. Phys. Chem. B, 114, 21, 7294 (2010).
    • ''ConfGen: A Conformational Search Method for Efficient Generation of Bioactive Conformers,'' K.S. Watts, P. Dalal, R.B. Murphy, W. Sherman, R.A. Friesner, and J.C. Shelley,
      J. Chem. Inf. Model, 50, 4, 534 (2010).
    • ''Continuous Localized Orbital Corrections to Density Functional Theory: B3LYP - CLOC,'' M.L. Hall, J. Zhang, A.D. Bochevarov, R.A. Friesner,
      J. Chem. Theory Comput., 6, 3647 (2010).
    • ''Correcting Systematic Errors in DFT Spin-Splitting Energetics for Transition Metal Complexes,'' T. Hughes, and R.A. Friesner,
      J. Chem. Theo. Comput., 7, 19 (2010).
    • ''Dewetting Transitions in Protein Cavities,'' T. Young, L. Hua, X. Huang, R. Abel, R.A. Friesner, and B.J. Berne,
      Proteins, Structure, Function and Bioinformatics, 78, 8, 1856 (2010).
    • ''Hydrophobic Interactions in Model Enclosures from Small to Large Length Scales: Nonadditivity in Explicit and Implicit Solvent Models,'' L. Wang, R.A. Friesner, and B.J. Berne,
      J. Faraday Discussions, 146, 247 (2010).
    • ''The electrical properties of Biphenylenes,'' S. T. Schneebeli, M. Kamenetska, F. W. Foss Jr., H. Vazquez, R. Skouta, M. Hybertsen, L. Venkataraman, R. Breslow,
      Org. Lett., 12, 4114 (2010).

    2009

  • ''Computational Modeling of the Electronic Structure of Oligothiophenes with Various Side Chains,'' T. Wang and R.A. Friesner,
    J. Phys. Chem. C, 113, 2553 (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).
    PubMed ID: PMC2683258
  • ''QM/MM Simulation on P450 BM3 Enzyme Catalysis Mechanism,'' Li Tian and Richard A. Friesner,
    Journal of Chemical Theory and Computation, 5, 1421 (2009).
    PubMed ID: PMC2757081
  • ''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).
    PubMed ID: PMC2766528
  • ''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, 113, 19806 (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).
    PubMed ID: PMC2764996

    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).
    PubMed ID: PMC2673190
  • ''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).
    PubMed ID: PMC2533438
  • ''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).
    PubMed ID: PMC2750878
  • ''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).
    PubMed ID: PMC2761766
  • ''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).
    PubMed ID: PMC2764870

    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).
    PubMed ID: PMC2517126
  • ''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).
    PubMed ID: PMC2743384
  • ''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).
    PubMed ID: PMC2744475
  • ''Serial replica exchange,'' M. Hagen, B. Kim, P. Liu, Richard A. Friesner, and B. J. Berne,
    J. Phys. Chem. B., 111, 1416 (2007).
    PubMed ID: PMC2742604

    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).
  • ''Alpha2,3 and alpha2,6 N-linked sialic acids facilitate efficient binding and transduction by adeno-associated virus types 1 and 6.,'' Z. Wu, E. Miller, M. Agbandje-McKenna, & R.J. Samulski,
    J. Virol., 80, 9093 (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).
    PubMed ID: PMC2743414

    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).
    PubMed ID: PMC2742605
  • ''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).
    PubMed ID: PMC2742603
  • ''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).

    1999

  • ''1,3-Dipolar Addition of Phenylazide to the Carbon-Carbon Double Bond - An Ab Initio Study,'' J.J. Klicic, Jasna, and R.A. Friesner,
    J. Phys Chem, 103, 1276 (1999).
  • ''A Branch and Bound Algorithm for Protein Structure Refinement from Sparse NMR Data Sets,'' D. M. Standley, V.A. Eyrich, A.K. Felts, R.A. Friesner, and A.E. McDermott,
    J. Mol. Biol., 285, 1691 (1999).
  • ''Calculation of atomization energies by a multiconfigurational localized perturbation theory. Application for closed shell cases,'' B.D. Dunietz, R.B. Murhpy and R.A. Friesner,
    J. Chem. Phys., 110, 1921 (1999).
  • ''Correlated Ab Inito Electronic Structure Calculations for Large Molecules,'' R.A. Friesner, R.B. Murphy, M.D. Beachy, M.N. Ringnalda, W.T. Pollard, B.D. Dunietz, and Y. Cao,
    J. Phys. Chem. A, 103, 1913 (1999).
  • ''Efficient memory equation algorithm for reduced dynamics in spin-boson models,'' A. A. Golosov, R. A. Friesner and P. Pechukas,
    J. Chem. Phys., 110, 138 (1999).
  • ''Fluctuating Charge, Polarizable Dipole, and Combined Models: Parameterization from ab Inito Quantum Chemistry,'' H.A. Stern, G.A. Kaminski, J.L. Banks, R. Zhou, B.J. Berne, and R.A. Friesner,
    J. Phys. Chem. B, 103, 4730 (1999).
  • ''Mechanistic and Theoretical Analysis of the Oxidative Addition of H2 to the Six Coordinate Molybdenum and Tungsten Complexes, M(PMe3)4X2 (M = Mo, W;X = F, Cl, Br, l): An inverse Equilibrium Isotope Effect and an Unprecedented Halide Dependence,'' T. Hascall, D. Rabinovich, V.J. Murphy, M.D. Beachy, R.A. Friesner, and G. Parkin,
    J. Am. Chem. Soc., 121, 11402 (1999).
  • ''Mixed Ab Initio QM/MM Modeling Using Frozen Orbitals and Tests Mixed Ab Initio QM/MM Modeling Using Frozen Orbitals and Tests with Alanine Dipeptide and Tetrapeptide,'' D.M. Philipp, and R.A. Friesner,
    J. Comput. Chem., 20, 1468 (1999).
  • ''Parametrizing a polarizable force field from ab initio data. I: The fluctuating point charge model,'' J.L. Banks, G.A. Kaminski, R. Zhou, D. T. Mainz, B.J. Berne, and R.A. Friesner,
    J. Chem. Phys., 110, 741 (1999).
  • ''Poisson-Boltzmann Analytical Gradients for Molecular Modeling Calculations,'' M. Friedrichs, R. Zhou, S.R. Edinger, and R.A. Friesner,
    J. Phys. Chem. B, 103, 3057 (1999).
  • ''Prediction of Loop Geometries Using a Generalized Born Model of Solvation Effects,'' C. Sendrovic-Rapp, and R.A. Friesner,
    Proteins: Structure, Function and Genetics, 35, 173 (1999).
  • ''Prediction of Protein Tertiary Structure to Low Resolution: Performance for a Large and Structurally Diverse Test Set,'' V.A. Eyrich, D.M. Standley, and R.A. Friesner,
    J. Mol. Biol, 288, 725 (1999).
  • ''Protein Tertiary Structure Prediction Using a Branch and Bound Algorithm,'' V.A. Eyrich, D.M. Standley, A.K. Felts, and R.A. Friesner,
    Proteins: Structure, Function and Genetics, 35, 41 (1999).
  • ''Spin-spin model for two-level system/bath problems: a numerical study,'' A.A. Golosov, S.I. Tsonchev, P. Pechukas, and R.A. Friesner,
    J. Chem. Phys., 111, 9918 (1999).

    1998

  • ''Ab initio calculation of electronic coupling in the photosynthetic reaction center,'' L. Zhang, and R.A. Friesner,
    Proc. Natl. Acad. Sci., USA, 95, 13603 (1998).
  • ''Accurate Quantum Chemical Calculation of the Relative Energetics of C20 Carbon Clusters via Localized Multireference Perturbation Calculations,'' R.B. Murphy, and R.A. Friesner,
    Chem. Phys. Letts., 288, 403 (1998).
  • ''Constructing ab initio force fields for molecular dynamics simulations,'' Y.-P.Liu, K. Kim, B.J. Berne, R.A. Friesner, and S.W. Rick,
    J. Chem. Phys. , 108, 4739 (1998).
  • ''Efficient recursive implementation of the modified Broyden method and the direct inversion in the iterative subspace method: acceleration of self-consistent calculations,'' M. Kawata, C.M. Cortis, and R.A. Friesner,
    J. Chem. Phys., 108, 4426 (1998).
  • ''Generalized Born Model Based on a Surface Integral Formulation,'' A. Ghosh, C. Sendrovic-Rapp, and R.A. Friesner,
    J. Phys. Chem. B,, 102, 10983 (1998).
  • ''Parallel Pseudospectral Electronic Structure. I. Hartree-Fock Calculations,'' D. Chasman, M.D. Beachy, L. Wang, and R.A. Friesner,
    J. Comput. Chem, 19, 1017 (1998).
  • ''Parallel Pseudospectral Electronic Structure. II. Localized MØller-Plesset Calculations,'' M. Beachy, D. Chasman, R.A. Friesner, and R.B. Murphy,
    J. Comp. Chem., 19, 1030 (1998).
  • '' Pseudospectral Methods for Ab Initio Quantum Chemistry,'' R.A. Friesner, R.B. Murphy, and M.N. Ringnalda,
    Encyclopedia of Comp. Chem.,, 3, 2290 (1998).
  • ''Quantum mechanical calculations on biological systems,'' R.A. Friesner, and M. Beachy,
    Current Opinion in Structural Biology, 8, 257 (1998).
  • ''Tertiary Structure Prediction of Mixed alpha/beta Proteins via Energy Minimization,'' D. M. Standley, J. R. Gunn, R.A. Friesner, and A.E. McDermott,
    Proteins: Structure, Function and Genetics, 33, 240 (1998).

    1997

  • ''Ab Initio Calculation of Molecule-Surface Binding: Methyl Halides on GaAs (110) Surfaces,'' S. Black, S., R.A. Friesner, P. Lu, and R. Osgood,
    Surface Science, 382, 154 (1997).
  • ''Ab Initio quantum chemical calculation of electronic transfer matrix elements for large molecules,'' L. Zhang, R.A. Friesner, and Robert B. Murphy,
    J. Chem. Phys., 107, 450 (1997).
  • ''Accurate Ab Initio Quantum Chemical Determination of the Relative Energetics of Peptide Conformations and Assessment of Empirical Force Fields,'' M. Beachy, D. Chasman, R. Murphy, T. Halgren, and R.A. Friesner,
    J. Am. Chem. Soc.,, 119, 5908 (1997).
  • ''An Automatic 3D Finite Element Mesh Generation System for the Poisson-Boltzman Equation,'' C. Cortis, and R.A. Friesner,
    J. Comp. Chem., 18, 1570 (1997).
  • ''A three-dimensional reduction of the Ornstein-Zernicke equation for molecular liquids,'' C.M. Cortis, P.J. Rossky, and R.A. Friesner,
    J. Chem. Phys., 107, 6400 (1997).
  • ''Extension of the PS-GVB Electronic Structure Code to Transition Metal Complexes,'' D. Mainz, J. Klicic, R.A. Friesner, J.M. Langlois, and J.K. Perry,
    J. Comp. Chem., 18, 1863 (1997).
  • ''Hydrogen bonding between amino acid backbone and side chain analogues: A high level ab Initio study,'' K. Kim, and R.A. Friesner,
    J. Am. Chem. Soc., 119, 12952 (1997).
  • ''Numerical Solution of the Poisson-Boltzmann Equation Using Tetrahedral Finite-Element Meshes,'' C. Cortis, and R.A. Friesner,
    J. Comp. Chem., 18, 1591 (1997).
  • ''Pseudospectral localized generalized MØller-Plesset methods with a generalized valence bond reference wave function: Theory and calculation of conformational energies,'' R.B. Murphy, W.T. Pollard, and R.A. Friesner,
    J. Chem. Phys., 106, 5073 (1997).
  • ''Solvation Free Energies of Peptides: Comparision of Approximate Continuum Solvation Models with Accurate Solution of the Poisson-Boltzmann Equation,'' S.R. Edinger, C. Cortis, P.S. Shenkin, and R.A. Friesner,
    J. Phys. Chem., 101, 1190 (1997).

    1996

  • ''Computational Studies of Protein Folding,'' J.R. Gunn, and R.A. Friesner,
    Ann. Rev. Biophys. Biomol. Struct., 25, 315 (1996).
  • ''New Model for Calculation of Solvation Free Energies: Correction of Self-Consistent Reaction Field Continuum Dielectric Theory for Short Range Hydrogen Bonding Effects,'' B. Marten, K. Kim, C. Cortis, R.A. Friesner, R.B. Murphy, M.N. Ringnalda, D. Sitkoff, and B. Honig,
    J. Phys. Chem., 100, 11775 (1996).
  • ''Parallel Implementation of a Protein Structure Refinement Algorithm,'' J.R. Gunn, and R.A. Friesner,
    J. Comp. Chem., 17, 1217 (1996).
  • ''Quantum mechanical geometry optimization in solution using a finite element continuum electrostatics method,'' C. Cortis, J.M. Langlois, M. Beachy, and R.A. Friesner,
    J. Chem. Phys., 105, 5472 (1996).
  • ''Saturation of the second hyperpolarizability for polyacetylenes,'' D. Lu, B. Marten, M. Ringnalda, R.A. Friesner, and W.A. Goddard, III,
    Chem. Phys. Lett., 257, 224 (1996).
  • ''The Redfield Equation in Condensed Phase Quantum Dynamics,'' W.T. Pollard, A.K. Felts, and R.A. Friesner,
    Adv. Chem. Phys., XCIII, 77, New Methods in Computational Mechanics, eds. I. Prigogine and Stuart A. Rice, 471, 191272 (1996).

    1995

  • ''Ab initio predictions of large hyperpolarizability push-pull polymers: Julolidinyl-n-isoxazolone and julolidinyl-n-N,N’ -diethylthiobarbituric acids,'' D. Lu, B. Marten, Y. Cao, M. Ringnalda, R.A. Friesner, and W.A. Goddard, III,
    Chem. Phys. Lett., 242, 543 (1995).
  • ''Ab Initio Self-Consistent Reaction Field Calculation of the Redox Potentials of Bacteriochlorophyll and Bacteriopheophytin in Solution,'' L. Zhang, and R.A. Friesner,
    J. Phys. Chem., 99, 16479 (1995).
  • ''Adiabatic Pseudospectral Calculation of Four Atom Molecules: Application to Hydrogen Peroxide,'' J. Antikainen, R.A. Friesner, and C. Leforestier,
    J. Chem. Phys., 102, 1270 (1995).
  • ''Computer Modeling of Protein Folding: Conformational and Energetic Analysis of Reduced and Detailed Protein Models,'' A. Monge, E.J.P. Lathrop, J.R. Gunn, P.S. Shenkin, and R.A. Friesner,
    J. Mol. Biol., 247, 995 (1995).
  • ''Multilevel Redfield Treatment of Bridge-Mediated Electron Transfer: A Mechanism for Anomalous Distance Dependence,'' A. Felts, W.T. Pollard, and R.A. Friesner,
    J. Phys. Chem., 99, 2929 (1995).
  • ''Pseudospectral localized MØller-Plesset methods: Theory and calculation of conformational energies,'' R. B. Murphy, M. Beachy, M. Ringnalda, and R.A. Friesner,
    J. Chem. Phys., 103, 1481 (1995).
  • ''Quantum Confinement Effects in CdSe Quantum Dots,'' B. Zorman, M.V. Ramakrishna, and R.A. Friesner,
    J. Phys. Chem., 99, 7649 (1995).
  • ''Simulated Annealing of a Protein in a Continuum Solvent via Multiple Timescales Molecular Dynamics,'' D.D. Humphreys, R.A. Friesner, and B.J. Berne,
    J. Phys. Chem., 99, 10674 (1995).

    1994

  • ''Accurate Calculation of Charge Distributions and Solvation Energies with Ab Initio Quantum Mechanics and Dielectric Continuum Theory,'' D. Tannor, B. Marten, R. Murphy, M. Ringnalda, R.A. Friesner, A. Nicholls, , W.A. Goddard, III, and B. Honig,
    J. Am. Chem. Soc., 116, 11875 (1994).
  • ''A Generalized Direct Inversion in the Iterative Subspace Approach for Generalized Valence Bond Wavefunctions,'' R.P. Muller, J.M. Langlois, M.N. Ringnalda, R.A. Friesner, and W.Goddard, III,
    J. Chem. Phys., 100, 1226 (1994).
  • ''A Multiple Timescales Algorithm for Macromolecules,'' D.D. Humphreys, R.A. Friesner, and B.J. Berne,
    J. Phys. Chem., 98, 6885 (1994).
  • ''An Algorithm to Generate Low Resolution Protein Tertiary Structures from Secondary Structure Assignments,'' A. Monge, R.A. Friesner, and B. Honig,
    Proc. Nat. Acad. Sci., USA, 91, 5027 (1994).
  • ''Comparison of Theory and Experiment for Electron Transfers in Proteins: Where's the Beef,'' R.A. Friesner,
    Structure, 2, 339 (1994).
  • ''Hierarchical Algorithm for Computer Modeling of Protein Tertiary Structure; Folding of Myoglobin to 6.2 A Resolution,'' J. Gunn, A. Monge, R.A. Friesner, and C. Marshall,
    J. Phys. Chem., 98, 702 (1994).
  • ''Krylov Methods for the Incompressible Navier-Stokes Equations,'' W.S. Edwards, L.S. Tuckerman, R.A. Friesner, and D.C. Sorensen,
    J. Comp. Phys., 110, 82 (1994).
  • ''New Pseudospectral Algorithms for Electronic Structure Calculations: Length Scales and Two Electron Integral Corrections,'' B.H. Greeley, T. Russo, D. Mainz, R.A. Friesner, J.M. Langlois, W. Goddard, III, and M. Ringnalda,
    J. Chem. Phys., 101, 4028 (1994).
  • ''Pseudospectral Contracted Configuration Interaction from a Generalized Valence Bond Reference,'' R.B. Murphy, R.A. Friesner, M.N. Ringnalda, and W.A. Goddard, III,
    J. Chem. Phys., 101, 2986 (1994).
  • ''Simulation of Optical Spectra for Wild-Type and Mutant Reaction Centers of Rps. Sphaeroides,'' E. Lathrop, and R.A. Friesner,
    J. Phys. Chem., 99, 3056 (1994).
  • ''Solutions of the Redfield equation for the dissipative quantum dynamics of multilevel systems,'' W.T. Pollard, and R.A. Friesner,
    J. Chem. Phys., 100, 5054 (1994).
  • ''Stationary Phase Surface Hopping for Nonadiabatic Dynamics: Two State Systems,'' F. Webster, E. Wang, P. Rossky, and R.A. Friesner,
    J. Chem. Phys., 100, 4835 (1994).
  • ''Vibronic Mixing in the Strong Electronic Coupling Limit. Spectroscopic Effects of Forbidden Transitions,'' E. Lathrop, and R.A. Friesner,
    J. Phys. Chem., 98, 3050 (1994).

    1993

  • ''Adiabatic Pseudospectral Methods for Multidimensional Vibrational Potential Surfaces,'' R.A. Friesner, M. Minou, J. Bentley, and C. Leforestier,
    J. Chem. Phys., 99, 324 (1993).
  • ''An Adiabatic Pseudospectral Representation of Multidimensional Molecular Potentials in Numerical Grid Methods and Their Application to Schrodinger's Equation,'' C. Leforestier, and R.A. Friesner,
    Kluwer, Dordrecht, the Netherlands, C. Cerjan, ed., (1993).
  • ''Atomic Charges for Large Molecules Derived from Electrostatic Potentials; Fragment Density Matrix Approach,'' J.G. Lee, and R.A. Friesner,
    J. Phys. Chem., 97, 3515 (1993).
  • ''Krylov Space Methods for Fock Matrix Diagonalization,'' W.T. Pollard, and R.A. Friesner,
    J. Chem. Phys., 99, 6742 (1993).
  • ''Quantum Chemistry of Semiconductor Clusters,'' M.V. Ramakrishna, and R.A. Friesner,
    Israeli J. Chem., 33, 3 (1993).

    1992

  • ''Amber Force Field Parameters for the Trimethylanilium Cation,'' H.J. Thiem, D.J. Wiedenfeld, J.G. Lee, and R.A. Friesner,
    Bioorg. Med. Chem. Lett., 2, 291 (1992).
  • ''Application of a Multilevel Redfield Theory to Electron Transfer in Condensed Phases,'' J.M. Jean, G. Fleming, and R.A. Friesner,
    J. Chem. Phys., 96, 5827 (1992).
  • ''Effect of Charge Transfer States on the Zero Phonon Line of the Special Pair in the Bacterial Reaction Center, in The Photosynthetic Bacterial Reaction Center II,'' E. Lathrop, and R.A. Friesner,
    J. Breton and A. Vermeglio, eds., Plenum, NY (1992).
  • ''Hierarchical Methods for Polymer Simulations,'' L. Johnson, A. Monge, and R.A. Friesner,
    J. Chem. Phys., 97, 9355 (1992).
  • ''Prediction of Anomalous Red Shift in Semiconductor Clusters,'' M.V. Ramakrishna, and R.A. Friesner,
    J. Chem. Phys., 96, 873 (1992).

    1991

  • ''A Comparison of Different Propagation Schemes for the Time Dependent Schrodinger Equation,'' C. Leforestier, R.H. Bisseling, C. Cerjan, M.D. Fiet, R.A. Friesner, A. Guldberg, A. Hammerich, G. Jolicard, W. Karrlein, H.-D. Meyer, N. Lipkin, O. Roncero, and R. Kosloff,
    J. Comut. Phys., 94, 59 (1991).
  • ''Classical and Quantum Models of Activationless Reaction Dynamics, Ber. Bunsenges,'' J.M. Jean, G.R. Fleming, and R.A. Friesner,
    Ber. Bunsenges Phys. Chem., 95, 253 (1991).
  • ''Exciton Spectra of Semiconductor Clusters,'' M.V. Ramakrishna, and, R.A. Friesner,,
    Phys. Rev. Lett. , 67, 629 (1991).
  • ''Mobility Edge in Quantum Percolation: Fractal Character of Eigenfunctions and a Relation for the Correlation Dimension,'' D.E. Sigeti, X. Zhang, M.S. Friedrichs, and R.A. Friesner,
    Phys. Rev. B, 44, 614 (1991).
  • ''Nonadiabatic processes in condensed matter: semi-classical theory and implementation,'' F. Webster, P.J. Rossky, and R.A. Friesner,
    Computer Physics Communications (North Holland), 63, 494 (1991).
  • ''Pseudospectral Hartree-Fock gradient calculations,'' Y. Won, J.-G. Lee, M.N. Ringnalda, and R.A. Friesner,
    J. Chem. Phys., 94, 8152 (1991).
  • ''Quantum Confinement Effects in Semiconductor Clusters,'' M.V. Ramakrishna, and, R.A. Friesner,
    J. Chem. Phys., 95, 8309 (1991).
  • ''Scanning Electrochemical Microscopy: Theory and Application of the Transient (Chronoamperometric) SECM Response,'' A.J. Bard, G. Denuault, R.A. Friesner, B.C. Dornblaser, and L.S. Tuckerman,
    Analytical Chemistry, 63, 1282 (1991).
  • ''Solvation Dynamics of the Hydrated Electron: A Nonadiabatic Quantum Simulation,'' F. Webster, J. Schnitker, M. Friedrichs, R.A. Friesner, and P.J. Rossky,
    Phys. Rev. Lett., 66, 3172 (1991).

    1990

  • ''A new approach to electrochemical simulations based on eigenvalue – eigenvector solutions of the diffusion equation. Part II. Cyclic voltammetry and heterogeneous kinetics,'' T.C. Kavanaugh, M.S. Friedrichs, R.A. Friesner, and A.J. Bard,
    J. Electroanalytical Chemistry, 283, 1 (1990).
  • ''Efficient Numerical Simulations of the Time Dependence of Electronic Energy Transfer in Polymers. 2. Short-Range Transfer and Forster Trapping,'' J.D. Byers, W.S. Parsons, R.A. Friesner, and S.E. Webber,
    Macromolecules, 23, 4835 (1990).
  • ''Efficient Numerical Simulations of the Time Dependence of Electronic Energy Transfer In Polymers. 2. Short-Range Transfer and Forster Trapping,'' J.D. Byers, W.S. Parsons, R.A. Friesner, and S.E. Webber,
    Macromolecules, 23, 4835 (1990).
  • ''Pseudospectral generalized valence-bond calculations: Application to methylene, ethylene, and silylene,'' J.-M. Langlois, R.P. Muller, T.R. Coley, W.A. Goddard, III, M.N. Ringnalda, Y. Won, and R.A. Friesner,
    J. Chem. Phys., 92, 7488 (1990).
  • ''Pseudospectral Hartree-Fock calculations on glycine,'' M. Ringnalda, Y. Won, and R.A. Friesner,
    J. Chem. Phys., 92, 1163 (1990).
  • ''Pseudospectral Hartree-Fock Theory: Applications and Algorithmic Improvements,'' M.N. Ringnalda, M. Belhadj, and R.A. Friesner,
    J. Chem. Phys., 99, 3387 (1990).
  • ''Theoretical Analysis of Resonance Raman Spectra from the Blue Copper Protein Azurin,'' M. Belhadj, J.M. Jean, R.A. Friesner, J. Schoonover, and, W.H. Woodruff,
    J. Phys. Chem., 94, 2160 (1990).

    1989

  • ''A Method for Exponential Propagation of Large Systems of Stiff Nonlinear Differential Equations,'' R.A. Friesner, L.S. Tuckerman, B.C. Dornblaser, and T.A. Russo,
    J. Sci. Comp. , 4, 327 (1989).
  • ''An Automatic Grid Generation Scheme for Pseudospectral Self-Consistent Field Calculations on Polyatomic-Molecules,'' R.A. Friesner,
    J. Phys. Chem., 92, 3091 (1989).
  • ''A new approach to electrochemical simulations based on eigenvector-eigenvalue solutions of the diffusion equations: Part I. Potentiostatic boundary conditions,'' M.S. Friedrichs, R.A. Friesner and A.J. Bard,
    J. Electroanalytical Chemistr, 258, 243 (1989).
  • ''Photochemical Charge Separation in Photosynthetic Reaction Centers,'' R.A. Friesner, and Y. Won,
    Photochemistry and Photobiology, 50, 831 (1989).
  • ''Quantum Mechanical Study of the SEP Spectrum for HCN,'' J.A. Bentley, J.P. Brunet, R.E. Wyatt, C. Leforestier, and R.A. Friesner,
    Chem. Phys. Lett., 161, 393 (1989).
  • ''Spectroscopy and Electron Transfer Dynamics of the Photosynthetic Reaction Center,'' R.A. Friesner, and Y. Won,
    Biochimica et Biophysica Acta, 977, 99 (1989).

    1988

  • ''A-Priori Calculation of the Optical-Absorption Spectrum of the Hydrated Electron,'' J. Schnitker, K. Motakabbir, P.J. Rossky, and R.A. Friesner,
    Phys. Rev. Lett., 60, 456 (1988).
  • ''A Thermal-Expansion Model for the Special Pair of the Bacterial Reaction Center,'' Y.D. Won, and R.A. Friesner,
    Israeli J. Chem., 28, 67 (1988).
  • ''On the Viability of the Superexchange Mechanism in the Primary Charge Separation Step of Bacterial Photosynthesis,'' Y.D. Won, and R.A. Friesner,
    Biochimica et Biophysica Acta, 935, 9 (1988).
  • ''Simulation of Optical-Spectra from the Reaction Center of Rhodopseudomonas-Viridis,'' Won, Y., and R.A. Friesner,
    J. Phys. Chem., 92, 2208 (1988).
  • ''Theoretical-Studies of Photochemical Hole Burning in Photosynthetic Bacterial Reaction Centers,'' Won, Y., and R.A. Friesner,
    J. Phys. Chem., 92, 2214 (1988).
  • ''Theoretical study of the IR absorption spectrum of HCN,'' J.-P. Brunet, R.A. Friesner, R.E. Wyatt, and C. Leforestier,
    Chem. Phys. Lett., 153, 452 (1988).
  • ''Variable Quadratic Propagator for Quantum Monte-Carlo Simulations,'' P. Zhang, R.M. Levy, and R.A. Friesner,
    Chem. Phys. Lett., 144, 236 (1988).

    1987

  • ''Computational Approach to Large Quan Dynamic Problems,'' R.A. Friesner, J.-P. Brunet, R.E. Wyatt, and C. Leforestier,
    International Journal of High Performance Computing Applications, 1, 9 (1987).
  • ''Green-Functions for Anisotropic Tight-Binding Hamiltonians - Application to Exciton Migration and Optical Lineshape,'' R.E. Lagos, and R.A. Friesner,
    J. Phys. C: Solid State Phys., 20, 4833 (1987).
  • ''Simulation of Photochemical Hole-Burning Experiments on Photosynthetic Reaction Centers,'' Y.D. Won, and R.A. Friesner,
    Proc. Nat. Acad. Sci., 84, 5511 (1987).
  • ''Solution of the Hartree-Fock Equations for Polyatomic-Molecules by a Pseudospectral Method,'' R.A. Friesner,
    J. Chem. Phys., 86, 3522 (1987).
  • ''Solution of the Pauli Master Equation Via the Lanczos-Algorithm,,'' M,S. Friedrichs, and R.A. Friesner,
    Chem. Phys. Lett., 137, 285 (1987).

    1986

  • ''A Generalized Version of the Recursive Residue Generation Method for Vector Computers,'' R.A. Friesner, R.W. Wyatt, C. Hempel, and B. Criner,
    J. Comp. Phys., 64, 220 (1986).
  • ''An Accurate and Efficient Decoupling Approximation for Temperature-Dependent Multimode Resonance Raman-Spectra,'' J.M. Jean, and R.A. Friesner,
    J. Chem. Phys., 85, 2353 (1986).
  • ''Natural Expansion of Vibrational Wave-Functions - Rrgm with Residue Algebra,'' N. Moiseyev, R.A. Friesner, and R.E. Wyatt,
    J. Chem. Phys., 85, 331 (1986).
  • ''Numerical Tests of a Generalized Multilevel Vibronic Coupling Formalism,'' Y. Won, R. Lagos, and R.A. Friesner,
    J. Chem. Phys., 84, 6567 (1986).
  • ''Solution of the Hartree-Fock Equations by a Pseudospectral Method - Application to Diatomic-Molecules,'' R.A. Friesner,
    J. Chem. Phys., 85, 1462 (1986).

    1985

  • ''Calculation of Temperature-Dependent Multimode Resonance Raman Line-Shapes for Harmonic Potential Surfaces,'' R.A. Friesner, M. Pettitt, and J.M. Jean,
    J. Chem. Phys., 82, 2918 (1985).
  • ''Optical-Spectrum of Crystalline Anthracene - Comparison between Theory and Experiment,,'' R.E. Lago, and R.A. Friesner,
    Chem. Phys. Lett., 122, 98 (1985).
  • ''Quantum Statistical-Mechanics via the Recursive Residue Generation Method,'' R.A. Friesner, and R.E. Wyatt,
    J. Chem. Phys., 82, 1973 (1985).
  • ''Solution of Self-Consistent Field Electronic-Structure Equations by a Pseudospectral Method,'' R.A. Friesner,
    Chem. Phys. Lett., 116, 39 (1985).

    1984

  • ''An Optimized Harmonic Reference System for the Evaluation of Discretized Path-Integrals,'' R.A. Friesner and R.M. Levy,
    J. Chem. Phys., 80, 4488 (1984).
  • ''Calculation of Optical-Line Shapes for Generalized Multilevel Systems.,'' R.E. Lagos, and R.A. Friesner,
    J. Chem. Phys., 81, 5899 (1984).
  • ''Calculation of the Green’s function from high- and low-density series expansions for disordered transport,'' D.F. Calef, R. Friesner, G. Korzeniewski, B. Laird, and R. Silbey,
    Phys. Rev. A, 29, 2963 (1984).
  • ''Cluster Generalization of the Dynamical Coherent-Potential Approximation - Application to Exciton-Phonon Interactions in Molecular-Crystals.,'' R.E. Lagos, and R.A. Friesner,
    Phys. Rev. B, 29, 3045 (1984).
  • ''Electronic Interactions between Electron Transport Cofactors in Photosynthetic Membranes of Rhodopseudomonas Viridis,'' G.C. Dismukes, H.A. Frank, R.A. Friesner, and K. Sauer,
    Biochimica Et Biophysica Acta, 764, 253 (1984).
  • ''Quasi-Harmonic Method for Calculating Vibrational-Spectra from Classical Simulations on Multidimensional Anharmonic Potential Surfaces.,'' R.M. Levy, O.D. Rojas, R.A. Friesner,
    J. Phys. Chem., 88, 4233 (1984).
  • ''Vibronic Excitons in Crystalline Anthracene,'' R.E. Lagos, and R.A. Friesner,,
    J. Luminescence, 31, 618 (1984).

    1983

  • ''Cluster Generalizations of the Dynamical Coherent Potential Approximation.,'' R.E. Lagos, and R.A. Friesner,
    J. Opt. Soc. Am., 73, 1389 (1983).
  • ''Energy Transfer Between the Primary Donor Bacteriochlorophyll and Carotenoids in Rhodopseudomonas sphaeroides,'' H.A. Frank, J. Machnicki, and R. Friesner,
    Photochem. Photobiol., 38, 451 (1983).
  • ''Localized Excitation Transport on Substitutionally Disordered Lattices,'' G. Korzeniewski, R. Friesner, and R. Silbey,
    J. Statistical Phys., 31, 451 (1983).

    1982

  • ''Calculation of the Exciton Greens-Function of a Molecular-Crystal from a 2-Site Dynamical Coherent Potential Approximation.,'' R.A. Friesner, and R. Silbey,
    Chem. Phys. Lett., 93, 107 (1982).
  • ''Green-Functions and Optical-Line Shapes of a General 2-Level System in the Strong Electronic Coupling Limit.,'' R.A. Friesner,
    J. Chem. Phys., 76, 2129 (1982).
  • ''Model for primary charge separation in reaction centers of photosynthetic bacteria,'' R. Friesner, and R. Wertheimer,
    Proc. Nat. Acad. Sci., 79, 6, 2138 (1982).
    PubMed ID: PMCID: PMC346141

    1981

  • ''Absorption and Circular-Dichroism Line-Shapes of a Molecular in the Strong Electronic Coupling Limit,'' R. Friesner, and R. Silbey,
    J. Chem. Phys., 75, 5630 (1981).
  • '' A General-Theory of the Spectroscopic Properties of Partially Ordered Ensembles II. Two-Vector Problems,'' J.A. Nairn, R.A. Friesner, and K. Sauer,
    J. Chem. Phys., 74, 5398 (1981).
  • ''Effect of Inhomogeneous Broadening on the Optical-Line Shape of Molecular Aggregates,'' R.A. Friesner, and R. Silbey,
    Chem. Phys. Lett., 84, 365 (1981).
  • ''Exciton-Phonon Coupling in a Dimer - An Analytic Approximation for Eigenvalues and Eigenvectors,'' R. Friesner and K. Sauer,
    J. Chem. Phys., 74, 1166 (1981).
  • ''Linear Vibronic Coupling in a General 2 Level System,'' R.A. Friesner, and R. Silbey,
    J. Chem. Phys., 75, 3925 (1981).
  • ''Transient Solutions of the Bloch Equations for Inhomogeneously Broadened Lines,'' R.A. Friesner, J.L. Mccracken, and K. Sauer,
    J. Mag. Res., 43, 343 (1981).

    1980

  • ''A New Approach to the Theory of Linear Dichroism in Partially Ordered Systems - Application to Reaction Centers and Whole Cells of Photosynthetic Bacteria,'' J.A. Nairn, R. Friesner, H.A. Frank, and K. Sauer,
    Biophys. J., 32, 733 (1980).
  • ''Exciton interactions in synthetic porphyrin dimmers,'' Y. Won, R.A. Friesner, M.R. Johnson and J.L. Sessler,
    Photosynthesis Research, 22, 201 (1980).
  • ''General-Theory of the Spectroscopic Properties of Partially Ordered Ensembles .1. One Vector Problems,'' R.A. Friesner, J.A. Nairn, and K. Sauer,
    J. Chem. Phys., 72, 221 (1980).

    1979

  • ''Calculation of the Epr-Spectrum from Partially Ordered Ensembles Applied to a Photosynthetic System,'' R.A. Friesner, J.A. Nairn, K. Sauer,
    Biophys. J., 25, 148 (1979).
  • ''Development of Electron-Spin Polarization in Photosynthetic Electron-Transfer by the Radical Pair Mechanism,'' R.A. Friesner, G.C. Dismukes, and K. Sauer,
    Biophys. J., 25, 277 (1979).
    PubMed ID: PMC1328464
  • ''Direct Calculation of the Orientational Distribution Function of Partially Ordered Ensembles from the Epr Line-Shape,'' R. Friesner, J.A. Nairn, K. Sauer,
    J. Chem. Phys., 71, 358 (1979).
  • ''Magnetic-Properties of Electron-Transport Cofactors in Photosynthetic Membranes of Rhodopsuedomonas-Viridis,'' C. Dismukes, H. Frank, R.A. Friesner, et. al.,
    Biophys. J., 25, 54 (1979).
  • ''Magnetophotoselection of the Triplet-State of Reaction Centers from Rhodopseudomonas-Sphaeroides R-26,'' H.A. Frank, J. Bolt, R. Friesner, et. al.,
    Biochimica Et Biophysica Acta, 547, 502 (1979).
  • ''Orientation of the Primary Donor in Bacterial Photosynthesis,'' H.A. Frank, R. Friesner, J.A. Nairn, et. al.,
    Biochimica Et Biophysica Acta, 547, 484 (1979).
  • ''Orientation of the Primary Donor in Bacterial Photosynthesis,'' Frank, H.A., R. Friesner, J.A. Nairn, et. al.,
    Biophys. J., 25, 205 (1979).

    1977

  • ''Primary Light-Induced Events of Photosynthesis as Revealed by Anisotropic Electron-Spin Polarization .2. Radical Pair Theory of Membrane-Bound Radicals,'' C. Dismukes, R. Friesner, K. Sauer,
    Biophys. J., 17, 228 (1977).

    1974

  • ''Ferredoxin Circular Dichroism at 3600 cm-1,'' B. Hosein, R. Friesner, and G. Holzwarth,
    Biochimica Et Biophysica Acta, 368, 18 (1974).