Richard A. Friesner - Publications

Affiliations: 
Chemistry Columbia University, New York, NY 
Area:
Computational Chemistry
Website:
http://www.columbia.edu/cu/chemistry/fac-bios/friesner/group/index.html

290 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Weber JL, Vuong H, Devlaminck PA, Shee J, Lee J, Reichman DR, Friesner RA. A Localized-Orbital Energy Evaluation for Auxiliary-Field Quantum Monte Carlo. Journal of Chemical Theory and Computation. PMID 35507769 DOI: 10.1021/acs.jctc.2c00111  0.726
2022 Rudshteyn B, Weber JL, Coskun D, Devlaminck PA, Zhang S, Reichman DR, Shee J, Friesner RA. Calculation of Metallocene Ionization Potentials via Auxiliary Field Quantum Monte Carlo: Toward Benchmark Quantum Chemistry for Transition Metals. Journal of Chemical Theory and Computation. PMID 35377642 DOI: 10.1021/acs.jctc.1c01071  0.806
2021 Lu C, Wu C, Ghoreishi D, Chen W, Wang L, Damm W, Ross GA, Dahlgren MK, Russell E, Von Bargen CD, Abel R, Friesner RA, Harder ED. OPLS4: Improving Force Field Accuracy on Challenging Regimes of Chemical Space. Journal of Chemical Theory and Computation. PMID 34096718 DOI: 10.1021/acs.jctc.1c00302  0.513
2021 Miller EB, Murphy RB, Sindhikara D, Borrelli KW, Grisewood MJ, Ranalli F, Dixon SL, Jerome S, Boyles NA, Day T, Ghanakota P, Mondal S, Rafi SB, Troast DM, Abel R, ... Friesner RA, et al. Reliable and Accurate Solution to the Induced Fit Docking Problem for Protein-Ligand Binding. Journal of Chemical Theory and Computation. PMID 33779166 DOI: 10.1021/acs.jctc.1c00136  0.801
2020 Weber JL, Churchill EM, Jockusch S, Arthur EJ, Pun AB, Zhang S, Friesner RA, Campos LM, Reichman DR, Shee J. prediction of annihilators for triplet-triplet annihilation upconversion auxiliary-field quantum Monte Carlo. Chemical Science. 12: 1068-1079. PMID 34163873 DOI: 10.1039/d0sc03381b  0.737
2020 Zhou T, Tsybovsky Y, Gorman J, Rapp M, Cerutti G, Chuang GY, Katsamba PS, Sampson JM, Schön A, Bimela J, Boyington JC, Nazzari A, Olia AS, Shi W, Sastry M, ... ... Friesner RA, et al. Cryo-EM Structures of SARS-CoV-2 Spike without and with ACE2 Reveal a pH-Dependent Switch to Mediate Endosomal Positioning of Receptor-Binding Domains. Cell Host & Microbe. PMID 33271067 DOI: 10.1016/j.chom.2020.11.004  0.765
2020 Zhou T, Tsybovsky Y, Olia AS, Gorman J, Rapp MA, Cerutti G, Katsamba PS, Nazzari A, Schon A, Wang PD, Bimela J, Shi W, Teng IT, Zhang B, Boyington JC, ... ... Friesner RA, et al. A pH-dependent switch mediates conformational masking of SARS-CoV-2 spike. Biorxiv : the Preprint Server For Biology. PMID 32637958 DOI: 10.1101/2020.07.04.187989  0.761
2020 Kumar M, Shee J, Rudshteyn B, Reichman DR, Friesner RA, Miller CE, Francisco JS. Multiple Stable Isoprene-Ozone Complexes Reveal Complex Entrance Channel Dynamics in the Isoprene + Ozone Reaction. Journal of the American Chemical Society. PMID 32431151 DOI: 10.1021/Jacs.0C02360  0.788
2020 Rudshteyn B, Coskun D, Weber JL, Arthur EJ, Zhang S, Reichman DR, Friesner RA, Shee J. Predicting Ligand-Dissociation Energies of 3 Coordination Complexes with Auxiliary-Field Quantum Monte Carlo. Journal of Chemical Theory and Computation. PMID 32293882 DOI: 10.1021/Acs.Jctc.0C00070  0.805
2020 Li G, Rudshteyn B, Shee J, Weber JL, Coskun D, Bochevarov AD, Friesner RA. Accurate Quantum Chemical Calculation of Ionization Potentials: Validation of the DFT-LOC Approach via a Large Data Set Obtained from Experiment and Benchmark Quantum Chemical Calculations. Journal of Chemical Theory and Computation. PMID 32150400 DOI: 10.1021/Acs.Jctc.9B00875  0.799
2019 Shee J, Arthur EJ, Zhang S, Reichman DR, Friesner RA. Singlet-Triplet Energy Gaps of Organic Biradicals and Polyacenes with Auxiliary-Field Quantum Monte Carlo. Journal of Chemical Theory and Computation. PMID 31381324 DOI: 10.1021/Acs.Jctc.9B00534  0.746
2019 Shee J, Rudshteyn B, Arthur EJ, Zhang S, Reichman DR, Friesner RA. On Achieving High Accuracy in Quantum Chemical Calculations of 3d Transition Metal-containing Systems: A Comparison of Auxiliary-Field Quantum Monte Carlo with Coupled Cluster, Density Functional Theory, and Experiment for Diatomic Molecules. Journal of Chemical Theory and Computation. PMID 30883110 DOI: 10.1021/Acs.Jctc.9B00083  0.814
2019 Clark AJ, Negron C, Hauser K, Sun M, Wang L, Abel R, Friesner RA. Relative Binding Affinity Prediction of Charge-Changing Sequence Mutations with FEP in Protein-Protein Interfaces. Journal of Molecular Biology. PMID 30776430 DOI: 10.1016/J.Jmb.2019.02.003  0.8
2019 Roos K, Wu C, Damm W, Reboul M, Stevenson JM, Lu C, Dahlgren MK, Mondal S, Chen W, Wang L, Abel R, Friesner RA, Harder ED. OPLS3e: Extending Force Field Coverage for Drug-Like Small Molecules. Journal of Chemical Theory and Computation. PMID 30768902 DOI: 10.1021/Acs.Jctc.8B01026  0.576
2018 Abel R, Manas ES, Friesner RA, Farid RS, Wang L. Modeling the value of predictive affinity scoring in preclinical drug discovery. Current Opinion in Structural Biology. 52: 103-110. PMID 30321805 DOI: 10.1016/J.Sbi.2018.09.002  0.551
2018 Shee J, Arthur EJ, Zhang S, Reichman DR, Friesner RA. Phaseless Auxiliary-Field Quantum Monte Carlo on Graphical Processing Units. Journal of Chemical Theory and Computation. PMID 29897748 DOI: 10.1021/Acs.Jctc.8B00342  0.741
2017 Jacobson LD, Bochevarov AD, Watson MA, Hughes TF, Rinaldo D, Ehrlich S, Steinbrecher TB, Vaitheeswaran S, Philipp DM, Halls MD, Friesner RA. An automated transition state search and its application to diverse types of organic reactions. Journal of Chemical Theory and Computation. PMID 28957627 DOI: 10.1021/Acs.Jctc.7B00764  0.328
2017 Abel R, Wang L, Harder ED, Berne BJ, Friesner RA. Advancing Drug Discovery through Enhanced Free Energy Calculations. Accounts of Chemical Research. PMID 28677954 DOI: 10.1021/Acs.Accounts.7B00083  0.68
2017 Shee J, Zhang S, Reichman DR, Friesner RA. Chemical Transformations Approaching Chemical Accuracy via Correlated Sampling in Auxiliary-Field Quantum Monte Carlo. Journal of Chemical Theory and Computation. PMID 28481546 DOI: 10.1021/Acs.Jctc.7B00224  0.757
2017 Abel R, Wang L, Mobley DL, Friesner RA. A Critical Review of Validation, Blind Testing, and Real-World Use of Alchemical Protein-Ligand Binding Free Energy Calculations. Current Topics in Medicinal Chemistry. PMID 28413950 DOI: 10.2174/1568026617666170414142131  0.604
2017 Steinbrecher T, Abel R, Clark A, Friesner R. Perspective: Free energy perturbation calculations of the thermodynamics of protein side chain mutations. Journal of Molecular Biology. PMID 28279701 DOI: 10.1016/J.Jmb.2017.03.002  0.597
2017 Friesner RA, Jerome SV. Localized orbital corrections for density functional calculations on transition metal containing systems Coordination Chemistry Reviews. 344: 205-213. DOI: 10.1016/J.Ccr.2017.02.014  0.814
2016 Fechner U, de Graaf C, Torda AE, Güssregen S, Evers A, Matter H, Hessler G, Richmond NJ, Schmidtke P, Segler MHS, Waller MP, Pleik S, Shea JE, Levine Z, Mullen R, ... ... Friesner R, et al. 11th German Conference on Chemoinformatics (GCC 2015) : Fulda, Germany. 8-10 November 2015. Journal of Cheminformatics. 8: 18. PMID 29270804 DOI: 10.1186/S13321-016-0119-5  0.455
2016 Wang L, Deng Y, Wu Y, Kim B, LeBard DN, Wandschneider D, Beachy M, Friesner RA, Abel R. Accurate Modeling of Scaffold Hopping Transformations in Drug Discovery. Journal of Chemical Theory and Computation. PMID 27933808 DOI: 10.1021/Acs.Jctc.6B00991  0.694
2016 Clark AJ, Gindin T, Zhang B, Wang L, Abel R, Murret CS, Xu F, Bao A, Lu NJ, Zhou T, Kwong PD, Shapiro L, Honig B, Friesner RA. Free Energy Perturbation Calculation of Relative Binding Free energy between Broadly Neutralizing Antibodies and the gp120 Glycoprotein of HIV-1. Journal of Molecular Biology. PMID 27908641 DOI: 10.1016/J.Jmb.2016.11.021  0.742
2016 Abel R, Mondal S, Masse C, Greenwood J, Harriman G, Ashwell MA, Bhat S, Wester R, Frye L, Kapeller R, Friesner RA. Accelerating drug discovery through tight integration of expert molecular design and predictive scoring. Current Opinion in Structural Biology. 43: 38-44. PMID 27816785 DOI: 10.1016/J.Sbi.2016.10.007  0.564
2016 Clark AJ, Tiwary P, Borrelli K, Feng S, Miller EB, Abel R, Friesner RA, Berne BJ. Prediction of Protein-Ligand Binding Poses via a Combination of Induced Fit Docking and Metadynamics Simulations. Journal of Chemical Theory and Computation. PMID 27145262 DOI: 10.1021/Acs.Jctc.6B00201  0.677
2016 Murphy RB, Repasky MP, Greenwood JR, Tubert-Brohman I, Jerome S, Annabhimoju R, Boyles NA, Schmitz CD, Abel R, Farid R, Friesner RA. WScore: A flexible and accurate treatment of explicit water molecules in ligand-receptor docking. Journal of Medicinal Chemistry. PMID 27054459 DOI: 10.1021/Acs.Jmedchem.6B00131  0.809
2016 Cao Y, Hughes T, Giesen D, Halls MD, Goldberg A, Vadicherla TR, Sastry M, Patel B, Sherman W, Weisman AL, Friesner RA. Highly efficient implementation of pseudospectral time-dependent density-functional theory for the calculation of excitation energies of large molecules. Journal of Computational Chemistry. PMID 27013141 DOI: 10.1002/Jcc.24350  0.392
2016 Coskun D, Jerome SV, Friesner RA. Evaluation of the performance of the B3LYP, PBE0, and M06 DFT functionals, and DBLOC-corrected versions, in the calculation of redox potentials and spin splittings for transition metal containing systems. Journal of Chemical Theory and Computation. PMID 26808695 DOI: 10.1021/Acs.Jctc.5B00782  0.787
2016 Zhang J, Weisman AL, Saitta P, Friesner RA. Efficient simulation of large materials clusters using the jaguar quantum chemistry program: Parallelization and wavefunction initialization International Journal of Quantum Chemistry. 116: 357-368. DOI: 10.1002/Qua.25043  0.747
2015 Harder E, Damm W, Maple J, Wu C, Reboul M, Xiang JY, Wang L, Lupyan D, Dahlgren MK, Knight JL, Kaus JW, Cerutti D, Krilov G, Jorgensen WL, Abel R, ... Friesner RA, et al. OPLS3: a force field providing broad coverage of drug-like small molecules and proteins. Journal of Chemical Theory and Computation. PMID 26584231 DOI: 10.1021/Acs.Jctc.5B00864  0.667
2015 Steinbrecher TB, Dahlgren M, Cappel D, Lin T, Wang L, Krilov G, Abel R, Friesner R, Sherman W. Accurate Binding Free Energy Predictions in Fragment Optimization. Journal of Chemical Information and Modeling. PMID 26457994 DOI: 10.1021/Acs.Jcim.5B00538  0.6
2015 Jerome SV, Hughes TF, Friesner RA. Successful application of the DBLOC method to the hydroxylation of camphor by cytochrome p450. Protein Science : a Publication of the Protein Society. PMID 26441133 DOI: 10.1002/Pro.2819  0.817
2015 Wang L, Wu Y, Deng Y, Kim B, Pierce L, Krilov G, Lupyan D, Robinson S, Dahlgren MK, Greenwood J, Romero DL, Masse C, Knight JL, Steinbrecher T, Beuming T, ... ... Friesner RA, et al. 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. Journal of the American Chemical Society. 137: 2695-703. PMID 25625324 DOI: 10.1021/Ja512751Q  0.772
2015 Stafford KA, Trbovic N, Butterwick JA, Abel R, Friesner RA, Palmer AG. Conformational preferences underlying reduced activity of a thermophilic ribonuclease H. Journal of Molecular Biology. 427: 853-66. PMID 25550198 DOI: 10.1016/J.Jmb.2014.11.023  0.558
2015 Goldfeld DA, Murphy R, Kim B, Wang L, Beuming T, Abel R, Friesner RA. Docking and free energy perturbation studies of ligand binding in the kappa opioid receptor. The Journal of Physical Chemistry. B. 119: 824-35. PMID 25395044 DOI: 10.1021/Jp5053612  0.8
2015 Mondal J, Friesner R, Berne BJ. Role of Desolvation in Thermodynamics and Kinetics of Ligand Binding to a Protein Biophysical Journal. 108: 12a. DOI: 10.1016/J.Bpj.2014.11.093  0.544
2014 Knight JL, Krilov G, Borrelli KW, Williams J, Gunn JR, Clowes A, Cheng L, Friesner RA, Abel R. Leveraging Data Fusion Strategies in Multireceptor Lead Optimization MM/GBSA End-Point Methods. Journal of Chemical Theory and Computation. 10: 3207-20. PMID 26588291 DOI: 10.1021/Ct500189S  0.551
2014 Mondal J, Friesner RA, Berne BJ. Role of Desolvation in Thermodynamics and Kinetics of Ligand Binding to a Kinase. Journal of Chemical Theory and Computation. 10: 5696-5705. PMID 25516727 DOI: 10.1021/Ct500584N  0.541
2014 Weisman AL, DuBay KH, Willets KA, Friesner RA. A first-principles polarized Raman method for determining whether a uniform region of a sample is crystalline or isotropic. The Journal of Chemical Physics. 141: 224702. PMID 25494765 DOI: 10.1063/1.4903308  0.734
2014 Jerome SV, Hughes TF, Friesner RA. Accurate pKa prediction in first-row hexaaqua transition metal complexes using the B3LYP-DBLOC method. The Journal of Physical Chemistry. B. 118: 8008-16. PMID 24707985 DOI: 10.1021/Jp501086H  0.808
2014 Zhu K, Day T, Warshaviak D, Murrett C, Friesner R, Pearlman D. Antibody structure determination using a combination of homology modeling, energy-based refinement, and loop prediction. Proteins. 82: 1646-55. PMID 24619874 DOI: 10.1002/Prot.24551  0.342
2014 Zhang J, Steigerwald M, Brus L, Friesner RA. Covalent O-H bonds as electron traps in proton-rich rutile TiO2 nanoparticles. Nano Letters. 14: 1785-9. PMID 24611728 DOI: 10.1021/Nl404307N  0.321
2014 Knight JL, Krilov G, Borrelli KW, Williams J, Gunn JR, Clowes A, Cheng L, Friesner RA, Abel R. Leveraging data fusion strategies in multireceptor lead optimization MM/GBSA end-point methods Journal of Chemical Theory and Computation. 10: 3207-3220. DOI: 10.1021/ct500189s  0.444
2013 Robustelli P, Trbovic N, Friesner RA, Palmer AG. Conformational Dynamics of the Partially Disordered Yeast Transcription Factor GCN4. Journal of Chemical Theory and Computation. 9. PMID 24409105 DOI: 10.1021/Ct400654R  0.354
2013 Miller EB, Murrett CS, Zhu K, Zhao S, Goldfeld DA, Bylund JH, Friesner RA. Prediction of Long Loops with Embedded Secondary Structure using the Protein Local Optimization Program. Journal of Chemical Theory and Computation. 9: 1846-4864. PMID 23814507 DOI: 10.1021/Ct301083Q  0.803
2013 Friesner RA, Abel R, Goldfeld DA, Miller EB, Murrett CS. Computational methods for high resolution prediction and refinement of protein structures. Current Opinion in Structural Biology. 23: 177-84. PMID 23688933 DOI: 10.1016/J.Sbi.2013.01.010  0.805
2013 Goldfeld DA, Friesner RA. The protein local optimization program and G-protein-coupled receptors: loop restoration and applications to homology modeling. Methods in Enzymology. 522: 1-20. PMID 23374177 DOI: 10.1016/B978-0-12-407865-9.00001-7  0.777
2013 Zeiske T, Stafford KA, Friesner RA, Palmer AG. Starting-structure dependence of nanosecond timescale intersubstate transitions and reproducibility of MD-derived order parameters. Proteins. 81: 499-509. PMID 23161667 DOI: 10.1002/Prot.24209  0.357
2013 Goldfeld DA, Zhu K, Beuming T, Friesner RA. Loop prediction for a GPCR homology model: algorithms and results. Proteins. 81: 214-28. PMID 22965891 DOI: 10.1002/Prot.24178  0.793
2013 Bochevarov AD, Harder E, Hughes TF, Greenwood JR, Braden DA, Philipp DM, Rinaldo D, Halls MD, Zhang J, Friesner RA. Jaguar: A high-performance quantum chemistry software program with strengths in life and materials sciences International Journal of Quantum Chemistry. 113: 2110-2142. DOI: 10.1002/Qua.24481  0.37
2012 DuBay KH, Hall ML, Hughes TF, Wu C, Reichman DR, Friesner RA. Accurate Force Field Development for Modeling Conjugated Polymers. Journal of Chemical Theory and Computation. 8: 4556-4569. PMID 26605615 DOI: 10.1021/Ct300175W  0.789
2012 Hughes TF, Friesner RA. Development of Accurate DFT Methods for Computing Redox Potentials of Transition Metal Complexes: Results for Model Complexes and Application to Cytochrome P450. Journal of Chemical Theory and Computation. 8: 442-59. PMID 26596595 DOI: 10.1021/Ct2006693  0.372
2012 Shivakumar D, Harder E, Damm W, Friesner RA, Sherman W. Improving the Prediction of Absolute Solvation Free Energies Using the Next Generation OPLS Force Field. Journal of Chemical Theory and Computation. 8: 2553-8. PMID 26592101 DOI: 10.1021/Ct300203W  0.367
2012 Zhang J, Hughes TF, Steigerwald M, Brus L, Friesner RA. Realistic cluster modeling of electron transport and trapping in solvated TiO2 nanoparticles. Journal of the American Chemical Society. 134: 12028-42. PMID 22738308 DOI: 10.1021/Ja3013787  0.303
2012 Repasky MP, Murphy RB, Banks JL, Greenwood JR, Tubert-Brohman I, Bhat S, Friesner RA. 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. Journal of Computer-Aided Molecular Design. 26: 787-99. PMID 22576241 DOI: 10.1007/S10822-012-9575-9  0.313
2012 Heckel JC, Weisman AL, Schneebeli ST, Hall ML, Sherry LJ, Stranahan SM, DuBay KH, Friesner RA, Willets KA. Polarized Raman spectroscopy of oligothiophene crystals to determine unit cell orientation. The Journal of Physical Chemistry. A. 116: 6804-16. PMID 22571336 DOI: 10.1021/Jp304192V  0.773
2012 Hughes TF, Harvey JN, Friesner RA. A B3LYP-DBLOC empirical correction scheme for ligand removal enthalpies of transition metal complexes: parameterization against experimental and CCSD(T)-F12 heats of formation. Physical Chemistry Chemical Physics : Pccp. 14: 7724-38. PMID 22513477 DOI: 10.1039/C2Cp40220C  0.366
2012 Wang L, Berne BJ, Friesner RA. On achieving high accuracy and reliability in the calculation of relative protein-ligand binding affinities. Proceedings of the National Academy of Sciences of the United States of America. 109: 1937-42. PMID 22308365 DOI: 10.1073/Pnas.1114017109  0.592
2012 Goldfeld DA, Zhu K, Beuming T, Friesner RA. Successful prediction of the intra- and extracellular loops of four G-protein-coupled receptors (Proceedings of the National Academy of Sciences of the United States of America (2011) 108, 20 (8275-8280) 10.1073/pnas.1016951108) Proceedings of the National Academy of Sciences of the United States of America. 109: 9665. DOI: 10.1073/pnas.1207511109  0.747
2012 Wang L, Berne BJ, Friesner RA. Ligand binding to protein-binding pockets with wet and dry regions (Proceedings of the National Academy of Sciences (2011) 108, 4 (1326-1330) DOI: 10.1073/pnas.1016793108) Proceedings of the National Academy of Sciences of the United States of America. 109: 9220. DOI: 10.1073/pnas.1207504109  0.424
2012 Dubay KH, Hall ML, Hughes TF, Wu C, Reichman DR, Friesner RA. Accurate force field development for modeling conjugated polymers Journal of Chemical Theory and Computation. 8: 4556-4569. DOI: 10.1021/ct300175w  0.765
2011 Hughes TF, Friesner RA. Correcting Systematic Errors in DFT Spin-Splitting Energetics for Transition Metal Complexes. Journal of Chemical Theory and Computation. 7: 19-32. PMID 26606215 DOI: 10.1021/Ct100359X  0.38
2011 Li J, Schneebeli ST, Bylund J, Farid R, Friesner RA. IDSite: An accurate approach to predict P450-mediated drug metabolism. Journal of Chemical Theory and Computation. 7: 3829-3845. PMID 22247702 DOI: 10.1021/Ct200462Q  0.73
2011 Schneebeli ST, Bochevarov AD, Friesner RA. Parameterization of a B3LYP specific correction for non-covalent interactions and basis set superposition error on a gigantic dataset of CCSD(T) quality non-covalent interaction energies. Journal of Chemical Theory and Computation. 7: 658-668. PMID 22058661 DOI: 10.1021/Ct100651F  0.676
2011 Zhao S, Zhu K, Li J, Friesner RA. Progress in super long loop prediction. Proteins. 79: 2920-35. PMID 21905115 DOI: 10.1002/Prot.23129  0.675
2011 Li J, Abel R, Zhu K, Cao Y, Zhao S, Friesner RA. The VSGB 2.0 model: a next generation energy model for high resolution protein structure modeling. Proteins. 79: 2794-812. PMID 21905107 DOI: 10.1002/Prot.23106  0.751
2011 Wang L, Friesner RA, Berne BJ. Replica exchange with solute scaling: a more efficient version of replica exchange with solute tempering (REST2). The Journal of Physical Chemistry. B. 115: 9431-8. PMID 21714551 DOI: 10.1021/Jp204407D  0.518
2011 Hughes TF, Friesner RA. Systematic investigation of the catalytic cycle of a single site ruthenium oxygen evolving complex using density functional theory. The Journal of Physical Chemistry. B. 115: 9280-9. PMID 21678966 DOI: 10.1021/Jp2026576  0.403
2011 Bounos G, Ghosh S, Lee AK, Plunkett KN, DuBay KH, Bolinger JC, Zhang R, Friesner RA, Nuckolls C, Reichman DR, Barbara PF. Controlling chain conformation in conjugated polymers using defect inclusion strategies. Journal of the American Chemical Society. 133: 10155-60. PMID 21612291 DOI: 10.1021/Ja2006687  0.766
2011 Goldfeld DA, Zhu K, Beuming T, Friesner RA. Successful prediction of the intra- and extracellular loops of four G-protein-coupled receptors. Proceedings of the National Academy of Sciences of the United States of America. 108: 8275-80. PMID 21536915 DOI: 10.1073/Pnas.1016951108  0.794
2011 Bochevarov AD, Li J, Song WJ, Friesner RA, Lippard SJ. Insights into the different dioxygen activation pathways of methane and toluene monooxygenase hydroxylases. Journal of the American Chemical Society. 133: 7384-97. PMID 21517016 DOI: 10.1021/Ja110287Y  0.622
2011 Abel R, Salam NK, Shelley J, Farid R, Friesner RA, Sherman W. Contribution of explicit solvent effects to the binding affinity of small-molecule inhibitors in blood coagulation factor serine proteases. Chemmedchem. 6: 1049-66. PMID 21506273 DOI: 10.1002/Cmdc.201000533  0.573
2011 Schneebeli ST, Kamenetska M, Cheng Z, Skouta R, Friesner RA, Venkataraman L, Breslow R. Single-molecule conductance through multiple π-π-stacked benzene rings determined with direct electrode-to-benzene ring connections. Journal of the American Chemical Society. 133: 2136-9. PMID 21265533 DOI: 10.1021/Ja111320N  0.706
2011 Wang L, Berne BJ, Friesner RA. Ligand binding to protein-binding pockets with wet and dry regions. Proceedings of the National Academy of Sciences of the United States of America. 108: 1326-30. PMID 21205906 DOI: 10.1073/Pnas.1016793108  0.549
2011 Goldfeld DA, Zhu K, Beuming T, Friesner RA. Reply to Nikiforovich et al.: Restoration of the loop regions of G-protein-coupled receptors Proceedings of the National Academy of Sciences of the United States of America. 108: E342. DOI: 10.1073/Pnas.1108089108  0.785
2010 Hall ML, Zhang J, Bochevarov AD, Friesner RA. Continuous Localized Orbital Corrections to Density Functional Theory: B3LYP-CLOC. Journal of Chemical Theory and Computation. 6: 3647-3663. PMID 21286233 DOI: 10.1021/Ct100418N  0.569
2010 Bochevarov AD, Friesner RA, Lippard SJ. The prediction of Fe Mössbauer parameters by the density functional theory: a benchmark study. Journal of Chemical Theory and Computation. 6: 3735-3749. PMID 21258606 DOI: 10.1021/Ct100398M  0.47
2010 Abel R, Wang L, Friesner RA, Berne BJ. A displaced-solvent functional analysis of model hydrophobic enclosures. Journal of Chemical Theory and Computation. 6: 2924-2934. PMID 21135914 DOI: 10.1021/Ct100215C  0.694
2010 Wang L, Friesner RA, Berne BJ. Hydrophobic interactions in model enclosures from small to large length scales: non-additivity in explicit and implicit solvent models. Faraday Discussions. 146: 247-62; discussion 2. PMID 21043426 DOI: 10.1039/B925521B  0.548
2010 Wang L, Friesner RA, Berne BJ. Competition of electrostatic and hydrophobic interactions between small hydrophobes and model enclosures. The Journal of Physical Chemistry. B. 114: 7294-301. PMID 20443643 DOI: 10.1021/Jp100772W  0.525
2010 Watts KS, Dalal P, Murphy RB, Sherman W, Friesner RA, Shelley JC. ConfGen: a conformational search method for efficient generation of bioactive conformers. Journal of Chemical Information and Modeling. 50: 534-46. PMID 20373803 DOI: 10.1021/Ci100015J  0.367
2010 Young T, Hua L, Huang X, Abel R, Friesner R, Berne BJ. Dewetting transitions in protein cavities. Proteins. 78: 1856-69. PMID 20225258 DOI: 10.1002/Prot.22699  0.652
2010 Friesner R, Wertheimer R. Model for primary charge separation in reaction centers of photosynthetic bacteria. Proceedings of the National Academy of Sciences of the United States of America. 79: 2138-42. PMID 16593176 DOI: 10.1073/Pnas.79.6.2138  0.315
2009 Hall ML, Goldfeld DA, Bochevarov AD, Friesner RA. Localized orbital corrections for the calculation of barrier heights in density functional theory. Journal of Chemical Theory and Computation. 5: 2996-3009. PMID 20161583 DOI: 10.1021/Ct9003965  0.81
2009 Tian L, Friesner RA. QM/MM Simulation on P450 BM3 Enzyme Catalysis Mechanism. Journal of Chemical Theory and Computation. 5: 1421-1431. PMID 20046929 DOI: 10.1021/Ct900040N  0.515
2009 Wang L, Abel R, Friesner RA, Berne BJ. Thermodynamic properties of liquid water: an application of a nonparametric approach to computing the entropy of a neat fluid. Journal of Chemical Theory and Computation. 5: 1462-1473. PMID 19851475 DOI: 10.1021/Ct900078K  0.641
2009 Schneebeli ST, Hall ML, Breslow R, Friesner R. Quantitative DFT modeling of the enantiomeric excess for dioxirane-catalyzed epoxidations. Journal of the American Chemical Society. 131: 3965-73. PMID 19243187 DOI: 10.1021/Ja806951R  0.776
2009 Trbovic N, Cho JH, Abel R, Friesner RA, Rance M, Palmer AG. Protein side-chain dynamics and residual conformational entropy. Journal of the American Chemical Society. 131: 615-22. PMID 19105660 DOI: 10.1021/Ja806475K  0.552
2009 Blagojevic V, Chen YR, Steigerwald M, Brus L, Friesner RA. Quantum chemical investigation of cluster models for TiO 2 nanoparticles with water-derived ligand passivation: Studies of excess electron states and implications for charge transport in the Gratzel cell Journal of Physical Chemistry C. 113: 19806-19811. DOI: 10.1021/Jp905332Z  0.33
2009 Wang T, Friesner RA. Computational modeling of the electronic structure of Oligothiophenes with various side chains Journal of Physical Chemistry C. 113: 2553-2561. DOI: 10.1021/Jp807733E  0.334
2008 Goldfeld DA, Bochevarov AD, Friesner RA. Localized orbital corrections applied to thermochemical errors in density functional theory: The role of basis set and application to molecular reactions. The Journal of Chemical Physics. 129: 214105. PMID 19063542 DOI: 10.1063/1.3008062  0.776
2008 Rinaldo D, Tian L, Harvey JN, Friesner RA. Density functional localized orbital corrections for transition metals. The Journal of Chemical Physics. 129: 164108. PMID 19045248 DOI: 10.1063/1.2974101  0.537
2008 Felts AK, Gallicchio E, Chekmarev D, Paris KA, Friesner RA, Levy RM. Prediction of Protein Loop Conformations using the AGBNP Implicit Solvent Model and Torsion Angle Sampling. Journal of Chemical Theory and Computation. 4: 855-868. PMID 18787648 DOI: 10.1021/Ct800051K  0.407
2008 Knight JL, Zhou Z, Gallicchio E, Himmel DM, Friesner RA, Arnold E, Levy RM. Exploring structural variability in X-ray crystallographic models using protein local optimization by torsion-angle sampling. Acta Crystallographica. Section D, Biological Crystallography. 64: 383-96. PMID 18391405 DOI: 10.1107/S090744490800070X  0.356
2008 Ko C, Malick DK, Braden DA, Friesner RA, Martínez TJ. Pseudospectral time-dependent density functional theory. The Journal of Chemical Physics. 128: 104103. PMID 18345873 DOI: 10.1063/1.2834222  0.365
2008 Maragakis P, Lindorff-Larsen K, Eastwood MP, Dror RO, Klepeis JL, Arkin IT, Jensen MØ, Xu H, Trbovic N, Friesner RA, Iii AG, Shaw DE. Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins. The Journal of Physical Chemistry. B. 112: 6155-8. PMID 18311962 DOI: 10.1021/Jp077018H  0.338
2008 Sellers BD, Zhu K, Zhao S, Friesner RA, Jacobson MP. Toward better refinement of comparative models: predicting loops in inexact environments. Proteins. 72: 959-71. PMID 18300241 DOI: 10.1002/Prot.21990  0.678
2008 Abel R, Young T, Farid R, Berne BJ, Friesner RA. Role of the active-site solvent in the thermodynamics of factor Xa ligand binding. Journal of the American Chemical Society. 130: 2817-31. PMID 18266362 DOI: 10.1021/Ja0771033  0.67
2008 Bochevarov AD, Friesner RA. The densities produced by the density functional theory: comparison to full configuration interaction. The Journal of Chemical Physics. 128: 034102. PMID 18205483 DOI: 10.1063/1.2821123  0.319
2008 Trbovic N, Kim B, Friesner RA, Palmer AG. Structural analysis of protein dynamics by MD simulations and NMR spin-relaxation. Proteins. 71: 684-94. PMID 17975832 DOI: 10.1002/Prot.21750  0.545
2007 Zhu K, Shirts MR, Friesner RA, Jacobson MP. Multiscale Optimization of a Truncated Newton Minimization Algorithm and Application to Proteins and Protein-Ligand Complexes. Journal of Chemical Theory and Computation. 3: 640-8. PMID 26637042 DOI: 10.1021/Ct600129F  0.688
2007 Zhu K, Shirts MR, Friesner RA. 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. Journal of Chemical Theory and Computation. 3: 2108-19. PMID 26636204 DOI: 10.1021/Ct700166F  0.656
2007 Repasky MP, Shelley M, Friesner RA. Flexible ligand docking with Glide. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit 8.12. PMID 18428795 DOI: 10.1002/0471250953.Bi0812S18  0.319
2007 Zhou Z, Felts AK, Friesner RA, Levy RM. Comparative performance of several flexible docking programs and scoring functions: enrichment studies for a diverse set of pharmaceutically relevant targets. Journal of Chemical Information and Modeling. 47: 1599-608. PMID 17585856 DOI: 10.1021/Ci7000346  0.319
2007 Huang X, Hagen M, Kim B, Friesner RA, Zhou R, Berne BJ. Replica exchange with solute tempering: efficiency in large scale systems. The Journal of Physical Chemistry. B. 111: 5405-10. PMID 17439169 DOI: 10.1021/Jp068826W  0.71
2007 Rinaldo D, Philipp DM, Lippard SJ, Friesner RA. Intermediates in dioxygen activation by methane monooxygenase: a QM/MM study. Journal of the American Chemical Society. 129: 3135-47. PMID 17326634 DOI: 10.1021/Ja0654074  0.521
2007 Hagen M, Kim B, Liu P, Friesner RA, Berne BJ. Serial replica exchange. The Journal of Physical Chemistry. B. 111: 1416-23. PMID 17249714 DOI: 10.1021/Jp064479E  0.652
2007 Xiang Z, Steinbach PJ, Jacobson MP, Friesner RA, Honig B. Prediction of side-chain conformations on protein surfaces. Proteins. 66: 814-23. PMID 17206724 DOI: 10.1002/Prot.21099  0.671
2007 Young T, Abel R, Kim B, Berne BJ, Friesner RA. Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding. Proceedings of the National Academy of Sciences of the United States of America. 104: 808-13. PMID 17204562 DOI: 10.1073/Pnas.0610202104  0.73
2007 Li X, Jacobson MP, Zhu K, Zhao S, Friesner RA. Assignment of polar states for protein amino acid residues using an interaction cluster decomposition algorithm and its application to high resolution protein structure modeling. Proteins. 66: 824-37. PMID 17154422 DOI: 10.1002/Prot.21125  0.675
2007 Zhu K, Shirts MR, Friesner RA. 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 Journal of Chemical Theory and Computation. 3: 2108-2119. DOI: 10.1021/ct700166f  0.579
2007 Zhu K, Shirts MR, Friesner RA, Jacobson MP. Multiscale optimization of a truncated newton minimization algorithm and application to proteins and protein-ligand complexes Journal of Chemical Theory and Computation. 3: 640-648. DOI: 10.1021/ct600129f  0.68
2006 Dixon SL, Smondyrev AM, Knoll EH, Rao SN, Shaw DE, Friesner RA. PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results. Journal of Computer-Aided Molecular Design. 20: 647-71. PMID 17124629 DOI: 10.1007/S10822-006-9087-6  0.557
2006 Friesner RA, Murphy RB, Repasky MP, Frye LL, Greenwood JR, Halgren TA, Sanschagrin PC, Mainz DT. Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. Journal of Medicinal Chemistry. 49: 6177-96. PMID 17034125 DOI: 10.1021/Jm051256O  0.375
2006 Friesner RA, Knoll EH, Cao Y. A localized orbital analysis of the thermochemical errors in hybrid density functional theory: achieving chemical accuracy via a simple empirical correction scheme. The Journal of Chemical Physics. 125: 124107. PMID 17014166 DOI: 10.1063/1.2263795  0.644
2006 Knoll EH, Friesner RA. Localized orbital corrections for the calculation of ionization potentials and electron affinities in density functional theory. The Journal of Physical Chemistry. B. 110: 18787-802. PMID 16986869 DOI: 10.1021/Jp0619888  0.645
2006 Zhu K, Pincus DL, Zhao S, Friesner RA. Long loop prediction using the protein local optimization program. Proteins. 65: 438-52. PMID 16927380 DOI: 10.1002/Prot.21040  0.559
2006 Ravindranathan KP, Gallicchio E, Friesner RA, McDermott AE, Levy RM. Conformational equilibrium of cytochrome P450 BM-3 complexed with N-palmitoylglycine: a replica exchange molecular dynamics study. Journal of the American Chemical Society. 128: 5786-91. PMID 16637647 DOI: 10.1021/Ja058465I  0.587
2006 Guallar V, Jarzecki AA, Friesner RA, Spiro TG. Modeling of ligation-induced helix/loop displacements in myoglobin: toward an understanding of hemoglobin allostery. Journal of the American Chemical Society. 128: 5427-35. PMID 16620114 DOI: 10.1021/Ja057318H  0.357
2006 Sherman W, Day T, Jacobson MP, Friesner RA, Farid R. Novel procedure for modeling ligand/receptor induced fit effects. Journal of Medicinal Chemistry. 49: 534-53. PMID 16420040 DOI: 10.1021/Jm050540C  0.566
2006 Farid R, Day T, Friesner RA, Pearlstein RA. New insights about HERG blockade obtained from protein modeling, potential energy mapping, and docking studies. Bioorganic & Medicinal Chemistry. 14: 3160-73. PMID 16413785 DOI: 10.1016/J.Bmc.2005.12.032  0.334
2006 Yu Z, Jacobson MP, Friesner RA. What role do surfaces play in GB models? A new-generation of surface-generalized born model based on a novel gaussian surface for biomolecules. Journal of Computational Chemistry. 27: 72-89. PMID 16261581 DOI: 10.1002/Jcc.20307  0.635
2006 Friesner RA, Jordan KD, Reichman D. Tribute to Robert J. Silbey The Journal of Physical Chemistry B. 110: 18734-18734. DOI: 10.1021/Jp062035C  0.586
2005 Maple JR, Cao Y, Damm W, Halgren TA, Kaminski GA, Zhang LY, Friesner RA. A Polarizable Force Field and Continuum Solvation Methodology for Modeling of Protein-Ligand Interactions. Journal of Chemical Theory and Computation. 1: 694-715. PMID 26641692 DOI: 10.1021/Ct049855I  0.417
2005 Kaminski GA, Maple JR, Murphy RB, Braden DA, Friesner RA. Pseudospectral Local Second-Order Møller-Plesset Methods for Computation of Hydrogen Bonding Energies of Molecular Pairs. Journal of Chemical Theory and Computation. 1: 248-54. PMID 26641295 DOI: 10.1021/Ct049880O  0.407
2005 Harder E, Kim B, Friesner RA, Berne BJ. Efficient Simulation Method for Polarizable Protein Force Fields:  Application to the Simulation of BPTI in Liquid Water. Journal of Chemical Theory and Computation. 1: 169-80. PMID 26641127 DOI: 10.1021/Ct049914S  0.659
2005 Kim B, Young T, Harder E, Friesner RA, Berne BJ. Structure and dynamics of the solvation of bovine pancreatic trypsin inhibitor in explicit water: a comparative study of the effects of solvent and protein polarizability. The Journal of Physical Chemistry. B. 109: 16529-38. PMID 16853101 DOI: 10.1021/Jp051569V  0.627
2005 Friesner RA. Modeling Polarization in Proteins and Protein-ligand Complexes: Methods and Preliminary Results. Advances in Protein Chemistry. 72: 79-104. PMID 16581373 DOI: 10.1016/S0065-3233(05)72003-9  0.407
2005 Banks JL, Beard HS, Cao Y, Cho AE, Damm W, Farid R, Felts AK, Halgren TA, Mainz DT, Maple JR, Murphy R, Philipp DM, Repasky MP, Zhang LY, Berne BJ, ... Friesner RA, et al. Integrated Modeling Program, Applied Chemical Theory (IMPACT). Journal of Computational Chemistry. 26: 1752-80. PMID 16211539 DOI: 10.1002/Jcc.20292  0.538
2005 Jovanovic T, Farid R, Friesner RA, McDermott AE. Thermal equilibrium of high- and low-spin forms of cytochrome P450 BM-3: repositioning of the substrate? Journal of the American Chemical Society. 127: 13548-52. PMID 16190718 DOI: 10.1021/Ja0524604  0.59
2005 Liu P, Kim B, Friesner RA, Berne BJ. Replica exchange with solute tempering: a method for sampling biological systems in explicit water. Proceedings of the National Academy of Sciences of the United States of America. 102: 13749-54. PMID 16172406 DOI: 10.1073/Pnas.0506346102  0.634
2005 Chakrabarti R, Klibanov AM, Friesner RA. Sequence optimization and designability of enzyme active sites. Proceedings of the National Academy of Sciences of the United States of America. 102: 12035-40. PMID 16103370 DOI: 10.1073/Pnas.0505397102  0.325
2005 Chakrabarti R, Klibanov AM, Friesner RA. Computational prediction of native protein ligand-binding and enzyme active site sequences. Proceedings of the National Academy of Sciences of the United States of America. 102: 10153-8. PMID 15998733 DOI: 10.1073/Pnas.0504023102  0.352
2005 Cao Y, Beachy MD, Braden DA, Morrill L, Ringnalda MN, Friesner RA. Nuclear-magnetic-resonance shielding constants calculated by pseudospectral methods. The Journal of Chemical Physics. 122: 224116. PMID 15974660 DOI: 10.1063/1.1924598  0.357
2005 Friesner RA. Ab initio quantum chemistry: methodology and applications. Proceedings of the National Academy of Sciences of the United States of America. 102: 6648-53. PMID 15870212 DOI: 10.1073/Pnas.0408036102  0.349
2005 Cho AE, Guallar V, Berne BJ, Friesner R. Importance of accurate charges in molecular docking: quantum mechanical/molecular mechanical (QM/MM) approach. Journal of Computational Chemistry. 26: 915-31. PMID 15841474 DOI: 10.1002/Jcc.20222  0.559
2005 Cao Y, Friesner RA. Molecular (hyper)polarizabilities computed by pseudospectral methods. The Journal of Chemical Physics. 122: 104102. PMID 15836304 DOI: 10.1063/1.1855881  0.355
2005 Friesner RA, Guallar V. Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis. Annual Review of Physical Chemistry. 56: 389-427. PMID 15796706 DOI: 10.1146/Annurev.Physchem.55.091602.094410  0.351
2005 Gherman BF, Lippard SJ, Friesner RA. Substrate hydroxylation in methane monooxygenase: quantitative modeling via mixed quantum mechanics/molecular mechanics techniques. Journal of the American Chemical Society. 127: 1025-37. PMID 15656641 DOI: 10.1021/Ja049847B  0.772
2005 Zhou Z, Steigerwald ML, Friesner RA, Brus L, Hybertsen MS. Structural and chemical trends in doped silicon nanocrystals: First-principles calculations Physical Review B - Condensed Matter and Materials Physics. 71. DOI: 10.1103/Physrevb.71.245308  0.389
2005 Zhou Z, Steigerwald ML, Friesner RA, Brus L, Hybertsen MS. Dopant local bonding and electrical activity near Si(001)-oxide interfaces Journal of Applied Physics. 98. DOI: 10.1063/1.2071447  0.312
2005 Harder E, Kim B, Friesner RA, Berne BJ. Efficient simulation method for polarizable protein force fields: Application to the simulation of BPTI in liquid water Journal of Chemical Theory and Computation. 1: 169-180. DOI: 10.1021/ct049914s  0.571
2004 Friesner RA. Combined quantum and molecular mechanics (QM/MM). Drug Discovery Today. Technologies. 1: 253-60. PMID 24981493 DOI: 10.1016/J.Ddtec.2004.11.008  0.311
2004 Fleishman SJ, Harrington S, Friesner RA, Honig B, Ben-Tal N. An automatic method for predicting transmembrane protein structures using cryo-EM and evolutionary data. Biophysical Journal. 87: 3448-59. PMID 15339802 DOI: 10.1529/Biophysj.104.046417  0.558
2004 Guallar V, Friesner RA. Cytochrome P450CAM enzymatic catalysis cycle: a quantum mechanics/molecular mechanics study. Journal of the American Chemical Society. 126: 8501-8. PMID 15238007 DOI: 10.1021/Ja036123B  0.36
2004 Gherman BF, Goldberg SD, Cornish VW, Friesner RA. Mixed quantum mechanical/molecular mechanical (QM/MM) study of the deacylation reaction in a penicillin binding protein (PBP) versus in a class C beta-lactamase. Journal of the American Chemical Society. 126: 7652-64. PMID 15198613 DOI: 10.1021/Ja036879A  0.717
2004 Li X, Jacobson MP, Friesner RA. High-resolution prediction of protein helix positions and orientations. Proteins. 55: 368-82. PMID 15048828 DOI: 10.1002/Prot.20014  0.613
2004 Jacobson MP, Pincus DL, Rapp CS, Day TJ, Honig B, Shaw DE, Friesner RA. A hierarchical approach to all-atom protein loop prediction. Proteins. 55: 351-67. PMID 15048827 DOI: 10.1002/Prot.10613  0.705
2004 Halgren TA, Murphy RB, Friesner RA, Beard HS, Frye LL, Pollard WT, Banks JL. Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. Journal of Medicinal Chemistry. 47: 1750-9. PMID 15027866 DOI: 10.1021/Jm030644S  0.322
2004 Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT, Repasky MP, Knoll EH, Shelley M, Perry JK, Shaw DE, Francis P, Shenkin PS. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. Journal of Medicinal Chemistry. 47: 1739-49. PMID 15027865 DOI: 10.1021/Jm0306430  0.643
2004 Zhou Z, Steigerwald M, Hybertsen M, Brus L, Friesner RA. Electronic structure of tubular aromatic molecules derived from the metallic (5,5) armchair single wall carbon nanotube. Journal of the American Chemical Society. 126: 3597-607. PMID 15025489 DOI: 10.1021/Ja039294P  0.352
2004 Guallar V, Jacobson M, McDermott A, Friesner RA. Computational modeling of the catalytic reaction in triosephosphate isomerase. Journal of Molecular Biology. 337: 227-39. PMID 15001364 DOI: 10.1016/J.Jmb.2003.11.016  0.711
2004 Gherman BF, Baik MH, Lippard SJ, Friesner RA. Dioxygen activation in methane monooxygenase: a theoretical study. Journal of the American Chemical Society. 126: 2978-90. PMID 14995216 DOI: 10.1021/Ja036506+  0.786
2004 Yu Z, Jacobson MP, Josovitz J, Rapp CS, Friesner RA. First-shell solvation of ion pairs: Correction of systematic errors in implicit solvent models Journal of Physical Chemistry B. 108: 6643-6654. DOI: 10.1021/Jp037821L  0.677
2004 Rim KT, Müller T, Fitts JP, Adib K, Camillone N, Osgood RM, Batista ER, Friesner RA, Joyce SA, Flynn GW. Scanning tunneling microscopy and theoretical study of competitive reactions in the dissociative chemisorption of CCl 4 on iron oxide surfaces Journal of Physical Chemistry B. 108: 16753-16760. DOI: 10.1021/Jp030937X  0.542
2004 Kaminski GA, Stern HA, Berne BJ, Friesner RA. Development of an accurate and robust polarizable molecular mechanics force field from ab initio quantum chemistry Journal of Physical Chemistry A. 108: 621-627. DOI: 10.1021/Jp0301103  0.557
2004 Baik MH, Friesner RA, Parkin G. Theoretical investigation of the metal-metal interaction in dimolybdenum complexes with bridging hydride and methyl ligands Polyhedron. 23: 2879-2900. DOI: 10.1016/J.Poly.2004.08.004  0.543
2003 Baik MH, Friesner RA, Lippard SJ. cis-[Pt(NH3)2(L)]2+/+ (L = Cl, H2O, NH3) binding to purines and CO: does pi-back-donation play a role? Inorganic Chemistry. 42: 8615-7. PMID 14686835 DOI: 10.1021/Ic035022B  0.564
2003 Zhou Z, Friesner RA, Brus L. Electronic structure of 1 to 2 nm diameter silicon core/shell nanocrystals: surface chemistry, optical spectra, charge transfer, and doping. Journal of the American Chemical Society. 125: 15599-607. PMID 14664607 DOI: 10.1021/Ja036443V  0.319
2003 Baik MH, Friesner RA, Lippard SJ. Theoretical study of cisplatin binding to purine bases: why does cisplatin prefer guanine over adenine? Journal of the American Chemical Society. 125: 14082-92. PMID 14611245 DOI: 10.1021/Ja036960D  0.6
2003 Tang L, Papish ET, Abramo GP, Norton JR, Baik MH, Friesner RA, Rappé A. Kinetics and thermodynamics of H. transfer from (eta5-C5R5)Cr(CO)3H (R = Ph, Me, H) to methyl methacrylate and styrene. Journal of the American Chemical Society. 125: 10093-102. PMID 12914473 DOI: 10.1021/Ja034927L  0.498
2003 Baik MH, Newcomb M, Friesner RA, Lippard SJ. Mechanistic studies on the hydroxylation of methane by methane monooxygenase. Chemical Reviews. 103: 2385-419. PMID 12797835 DOI: 10.1021/Cr950244F  0.558
2003 Guallar V, Baik MH, Lippard SJ, Friesner RA. Peripheral heme substituents control the hydrogen-atom abstraction chemistry in cytochromes P450. Proceedings of the National Academy of Sciences of the United States of America. 100: 6998-7002. PMID 12771375 DOI: 10.1073/Pnas.0732000100  0.628
2003 Wirstam M, Lippard SJ, Friesner RA. Reversible dioxygen binding to hemerythrin. Journal of the American Chemical Society. 125: 3980-7. PMID 12656634 DOI: 10.1021/Ja017692R  0.516
2003 Kaminski GA, Friesner RA, Zhou R. A computationally inexpensive modification of the point dipole electrostatic polarization model for molecular simulations. Journal of Computational Chemistry. 24: 267-76. PMID 12548718 DOI: 10.1002/Jcc.10170  0.585
2003 Friesner RA, Baik MH, Gherman BF, Guallar V, Wirstam M, Murphy RB, Lippard SJ. How iron-containing proteins control dioxygen chemistry: A detailed atomic level description via accurate quantum chemical and mixed quantum mechanics/molecular mechanics calculations Coordination Chemistry Reviews. 238: 267-290. DOI: 10.1016/S0010-8545(02)00284-9  0.81
2002 Andrec M, Harano Y, Jacobson MP, Friesner RA, Levy RM. Complete protein structure determination using backbone residual dipolar couplings and sidechain rotamer prediction. Journal of Structural and Functional Genomics. 2: 103-11. PMID 12836667 DOI: 10.1023/A:1020435630054  0.603
2002 Hascall T, Baik MH, Bridgewater BM, Shin JH, Churchill DG, Friesner RA, Parkin G. A non-classical hydrogen bond in the molybdenum arene complex [eta 6-C6H5C6H3(Ph)OH]Mo(PMe3)3: evidence that hydrogen bonding facilitates oxidative addition of the O-H bond. Chemical Communications (Cambridge, England). 2644-5. PMID 12510278 DOI: 10.1039/B208678F  0.502
2002 Baik MH, Gherman BF, Friesner RA, Lippard SJ. Hydroxylation of methane by non-heme diiron enzymes: molecular orbital analysis of C-H bond activation by reactive intermediate Q. Journal of the American Chemical Society. 124: 14608-15. PMID 12465971 DOI: 10.1021/Ja026794U  0.787
2002 Baik MH, Crystal JB, Friesner RA. Ab initio quantum calculation of the diabatic coupling matrix elements for the self-exchange redox couples M(Cp)20/+ (M = Fe, Co; Cp = C5H5). Inorganic Chemistry. 41: 5926-7. PMID 12425612 DOI: 10.1021/Ic025895Q  0.526
2002 Kaminski GA, Stern HA, Berne BJ, Friesner RA, Cao YX, Murphy RB, Zhou R, Halgren TA. Development of a polarizable force field for proteins via ab initio quantum chemistry: first generation model and gas phase tests. Journal of Computational Chemistry. 23: 1515-31. PMID 12395421 DOI: 10.1002/Jcc.10125  0.684
2002 Ambundo EA, Friesner RA, Lippard SJ. Reactions of methane monooxygenase intermediate Q with derivatized methanes. Journal of the American Chemical Society. 124: 8770-1. PMID 12137510 DOI: 10.1021/Ja0265759  0.395
2002 An Y, Friesner RA. A novel fold recognition method using composite predicted secondary structures. Proteins. 48: 352-66. PMID 12112702 DOI: 10.1002/Prot.10145  0.525
2002 Jacobson MP, Friesner RA, Xiang Z, Honig B. On the role of the crystal environment in determining protein side-chain conformations. Journal of Molecular Biology. 320: 597-608. PMID 12096912 DOI: 10.1016/S0022-2836(02)00470-9  0.655
2002 Guallar V, Gherman BF, Lippard SJ, Friesner RA. Quantum chemical studies of methane monooxygenase: comparision with P450. Current Opinion in Chemical Biology. 6: 236-42. PMID 12039010 DOI: 10.1016/S1367-5931(02)00310-1  0.762
2002 Baik MH, Friesner RA, Lippard SJ. Theoretical study on the stability of N-glycosyl bonds: why does N7-platination not promote depurination? Journal of the American Chemical Society. 124: 4495-503. PMID 11960480 DOI: 10.1021/Ja017588+  0.611
2002 Guallar V, Gherman BF, Miller WH, Lippard SJ, Friesner RA. Dynamics of alkane hydroxylation at the non-heme diiron center in methane monooxygenase. Journal of the American Chemical Society. 124: 3377-84. PMID 11916423 DOI: 10.1021/Ja0167248  0.742
2002 Baik MH, Friesner RA. Computing redox potentials in solution: Density functional theory as a tool for rational design of redox agents Journal of Physical Chemistry A. 106: 7407-7412. DOI: 10.1021/Jp025853N  0.568
2002 Jacobson MP, Kaminski GA, Friesner RA, Rapp CS. Force field validation using protein side chain prediction Journal of Physical Chemistry B. 106: 11673-11680. DOI: 10.1021/Jp021564N  0.611
2002 Margulis CJ, Guallar V, Sim E, Friesner RA, Berne BJ. A new semiempirical approach to study ground and excited states of metal complexes in biological systems Journal of Physical Chemistry B. 106: 8038-8046. DOI: 10.1021/Jp020705I  0.566
2002 Batista ER, Friesner RA. 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 (α-Fe2O3) Journal of Physical Chemistry B. 106: 8136-8141. DOI: 10.1021/Jp020509B  0.572
2002 Crystal J, Zhang LY, Friesner RA, Flynn GW. Computational modeling for scanning tunneling microscopy of physisorbed molecules via ab initio quantum chemistry Journal of Physical Chemistry A. 106: 1802-1814. DOI: 10.1021/Jp012629+  0.325
2002 Klicić JJ, Friesner RA, Liu SY, Guida WC. Accurate prediction of acidity constants in aqueous solution via density functional theory and self-consistent reaction field methods Journal of Physical Chemistry A. 106: 1327-1335. DOI: 10.1021/Jp012533F  0.402
2002 Eyrich VA, Friesner RA, Standley DM. AB initio protein structure prediction using a size-dependent tertiary folding potential Advances in Chemical Physics. 120: 223-263.  0.778
2002 Hascall T, Baik MH, Bridgewater BM, Shin JH, Churchill DG, Friesner RA, Parkin G. A non-classical hydrogen bond in the molybdenum arene complex [η6-C6H5C6H3(Ph) OH]Mo(PMe3)3: Evidence that hydrogen bonding facilitates oxidative addition of the O-H bond Chemical Communications. 2644-2645.  0.432
2001 Standley DM, Eyrich VA, An Y, Pincus DL, Gunn JR, Friesner RA. Protein structure prediction using a combination of sequence-based alignment, constrained energy minimization, and structural alignment. Proteins. 133-9. PMID 11835490 DOI: 10.1002/Prot.10005  0.801
2001 Shin JH, Bridgewater BM, Churchill DG, Baik MH, Friesner RA, Parkin G. An experimental and computational analysis of the formation of the terminal nitrido complex (eta3-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. Journal of the American Chemical Society. 123: 10111-2. PMID 11592896 DOI: 10.1021/Ja011416V  0.491
2001 Gherman BF, Dunietz BD, Whittington DA, Lippard SJ, Friesner RA. Activation of the C-H bond of methane by intermediate Q of methane monooxygenase: a theoretical study. Journal of the American Chemical Society. 123: 3836-7. PMID 11457123 DOI: 10.1021/Ja0055108  0.768
2001 Friesner RA, Dunietz BD. Large-scale ab initio quantum chemical calculations on biological systems. Accounts of Chemical Research. 34: 351-8. PMID 11352713 DOI: 10.1021/Ar980111R  0.664
2001 Baik M, Lee D, Friesner RA, Lippard SJ. Theoretical studies of diiron(II) complexes that model features of the dioxygen-activating centers in non-heme diiron enzymes Israel Journal of Chemistry. 41: 173-186. DOI: 10.1560/8Yug-V7Ef-Vhhp-6Ug2  0.622
2001 Dunietz BD, Friesner RA. Application and development of multiconfigurational localized perturbation theory Journal of Chemical Physics. 115: 11052-11067. DOI: 10.1063/1.1418442  0.646
2001 Stern HA, Rittner F, Berne BJ, Friesner RA. Combined fluctuating charge and polarizable dipole models: Application to a five-site water potential function Journal of Chemical Physics. 115: 2237-2251. DOI: 10.1063/1.1376165  0.556
2001 Gherman BF, Friesner RA, Wong TH, Min Z, Bersohn R. Photodissociation of acetaldehyde: The CH4+CO channel Journal of Chemical Physics. 114: 6128-6133. DOI: 10.1063/1.1355983  0.728
2001 Zhou R, Friesner RA, Ghosh A, Rizzo RC, Jorgensen WL, Levy RM. New linear interaction method for binding affinity calculations using a continuum solvent model Journal of Physical Chemistry B. 105: 10388-10397. DOI: 10.1021/Jp011480Z  0.558
2001 Kaminski GA, Friesner RA, Tirado-Rives J, Jorgensen WL. Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides Journal of Physical Chemistry B. 105: 6474-6487. DOI: 10.1021/Jp003919D  0.527
2001 Vargas R, Garza J, Friesner RA, Stern H, Hay BP, Dixon DA. Strength of the N-H⋯O=C and C-H⋯O=C bonds in formamide and N-methylacetamide dimers Journal of Physical Chemistry A. 105: 4963-4968. DOI: 10.1021/Jp003888M  0.366
2001 Zhang LY, Gallicchio E, Friesner RA, Levy RM. Solvent models for protein-ligand binding: Comparison of implicit solvent poisson and surface generalized born models with explicit solvent simulations Journal of Computational Chemistry. 22: 591-607. DOI: 10.1002/Jcc.1031  0.382
2000 Murphy RB, Cao Y, Beachy MD, Ringnalda MN, Friesner RA. Efficient pseudospectral methods for density functional calculations Journal of Chemical Physics. 112: 10131-10141. DOI: 10.1063/1.481704  0.351
2000 Golosov AA, Friesner RA, Pechukas P. Reduced dynamics in spin-boson models: A method for both slow and fast bath Journal of Chemical Physics. 112: 2095-2105. DOI: 10.1063/1.480888  0.305
2000 Crystal J, Friesner RA. Calculation of the lonization potentials and electron affinities of bacteriochlorophyll and bacteriopheophytin via ab initio quantum chemistry Journal of Physical Chemistry A. 104: 2362-2366. DOI: 10.1021/Jp991318K  0.407
2000 Dunietz BD, Beachy MD, Cao Y, Whittington DA, Lippard SJ, Friesner RA. Large scale ab initio quantum chemical calculation of the intermediates in the soluble methane monooxygenase catalytic cycle Journal of the American Chemical Society. 122: 2828-2839. DOI: 10.1021/Ja9920967  0.651
2000 Murphy RB, Philipp DM, Friesner RA. Frozen orbital QM/MM methods for density functional theory Chemical Physics Letters. 321: 113-120. DOI: 10.1016/S0009-2614(00)00289-X  0.406
2000 Murphy RB, Philipp DM, Friesner RA. A Mixed Quantum Mechanics/Molecular Mechanics (QM/MM) Method for Large-Scale Modeling of Chemistry in Protein Environments Journal of Computational Chemistry. 21: 1442-1457. DOI: 10.1002/1096-987X(200012)21:16<1442::Aid-Jcc3>3.0.Co;2-O  0.358
1999 Eyrich VA, Standley DM, Friesner RA. Prediction of protein tertiary structure to low resolution: performance for a large and structurally diverse test set. Journal of Molecular Biology. 288: 725-42. PMID 10329175 DOI: 10.1006/Jmbi.1999.2702  0.802
1999 Rapp CS, Friesner RA. Prediction of loop geometries using a generalized born model of solvation effects. Proteins. 35: 173-83. PMID 10223290 DOI: 10.1002/(Sici)1097-0134(19990501)35:2<173::Aid-Prot4>3.0.Co;2-2  0.406
1999 Eyrich VA, Standley DM, Felts AK, Friesner RA. Protein tertiary structure prediction using a branch and bound algorithm. Proteins. 35: 41-57. PMID 10090285 DOI: 10.1002/(Sici)1097-0134(19990401)35:1<41::Aid-Prot5>3.0.Co;2-N  0.8
1999 Standley DM, Eyrich VA, Felts AK, Friesner RA, McDermott AE. A branch and bound algorithm for protein structure refinement from sparse NMR data sets Journal of Molecular Biology. 285: 1691-1710. PMID 9917406 DOI: 10.1006/Jmbi.1998.2372  0.813
1999 Banks JL, Kaminski GA, Zhou R, Mainz DT, Berne BJ, Friesner RA. Parametrizing a polarizable force field from ab initio data. I. The fluctuating point charge model The Journal of Chemical Physics. 110: 741-754. DOI: 10.1063/1.478043  0.65
1999 Dunietz BD, Murphy RB, Friesner RA. Calculation of atomization energies by a multiconfigurational localized perturbation theory - Application for closed shell cases Journal of Chemical Physics. 110: 1921-1930. DOI: 10.1063/1.477859  0.666
1999 Dunietz BD, Murphy RB, Friesner RA. Calculation of atomization energies by a multiconfigurational localized perturbation theory—Application for closed shell cases The Journal of Chemical Physics. 110: 1921-1930. DOI: 10.1063/1.477859  0.589
1999 Stern HA, Kaminski GA, Banks JL, Zhou R, Berne BJ, Friesner RA. Fluctuating charge, polarizable dipole, and combined models: Parameterization from ab initio quantum chemistry Journal of Physical Chemistry B. 103: 4730-4737. DOI: 10.1021/Jp984498R  0.664
1999 Klicić JJ, Friesner RA. 1,3-Dipolar Addition of Phenylazide to the Carbon-Carbon Double Bond: An ab Initio Study Journal of Physical Chemistry A. 103: 1276-1282. DOI: 10.1021/Jp9839403  0.408
1999 Friesner RA. Correlated ab initio electronic structure calculations for large molecules Journal of Physical Chemistry A. 103: XI-1928. DOI: 10.1021/Jp9825157  0.395
1999 Friedrichs M, Zhou R, Edinger SR, Friesner RA. Poisson-boltzmann analytical gradients for molecular modeling calculations Journal of Physical Chemistry B. 103: 3057-3061. DOI: 10.1021/Jp982513M  0.36
1999 Friedrichs M, Zhou R, Edinger SR, Friesner RA. Poisson−Boltzmann Analytical Gradients for Molecular Modeling Calculations The Journal of Physical Chemistry B. 103: 3057-3061. DOI: 10.1021/jp982513m  0.482
1999 Philipp DM, Friesner RA. Mixed ab initio QM/MM modeling using frozen orbitals and tests with alanine dipeptide and tetrapeptide Journal of Computational Chemistry. 20: 1468-1494. DOI: 10.1002/(Sici)1096-987X(19991115)20:14<1468::Aid-Jcc2>3.0.Co;2-0  0.393
1998 Zhang LY, Friesner RA. Ab initio calculation of electronic coupling in the photosynthetic reaction center. Proceedings of the National Academy of Sciences of the United States of America. 95: 13603-5. PMID 9811846 DOI: 10.1073/Pnas.95.23.13603  0.331
1998 Standley DM, Gunn JR, Friesner RA, McDermott AE. Tertiary structure prediction of mixed α/β proteins via energy minimization Proteins: Structure, Function and Genetics. 33: 240-252. PMID 9779791 DOI: 10.1002/(Sici)1097-0134(19981101)33:2<240::Aid-Prot8>3.0.Co;2-M  0.607
1998 Friesner RA, Beachy MD. Quantum mechanical calculations on biological systems. Current Opinion in Structural Biology. 8: 257-62. PMID 9631302 DOI: 10.1016/S0959-440X(98)80048-1  0.34
1998 Liu YP, Kim K, Berne BJ, Friesner RA, Rick SW. Constructing ab initio force fields for molecular dynamics simulations Journal of Chemical Physics. 108: 4739-4755. DOI: 10.1063/1.475886  0.553
1998 Murphy RB, Friesner RA. Accurate quantum chemical calculation of the relative energetics of C20 carbon clusters via localized multireference perturbation calculations Chemical Physics Letters. 288: 403-407. DOI: 10.1016/S0009-2614(98)00324-8  0.351
1998 Chasman D, Beachy MD, Wang L, Friesner RA. Parallel pseudospectral electronic structure: I. Hartree-Fock calculations Journal of Computational Chemistry. 19: 1017-1029. DOI: 10.1002/(Sici)1096-987X(19980715)19:9<1017::Aid-Jcc3>3.0.Co;2-T  0.319
1997 Zhang LY, Friesner RA, Murphy RB. Ab initio quantum chemical calculation of electron transfer matrix elements for large molecules Journal of Chemical Physics. 107: 450-459. DOI: 10.1063/1.474406  0.382
1997 Cortis CM, Rossky PJ, Friesner RA. A three-dimensional reduction of the Ornstein-Zernicke equation for molecular liquids Journal of Chemical Physics. 107: 6400-6414. DOI: 10.1063/1.474300  0.308
1997 Murphy RB, Pollard WT, Friesner RA. Pseudospectral localized generalized Mo/ller–Plesset methods with a generalized valence bond reference wave function: Theory and calculation of conformational energies The Journal of Chemical Physics. 106: 5073-5084. DOI: 10.1063/1.473553  0.42
1997 Edinger SR, Cortis C, Shenkin PS, Friesner RA. Solvation Free Energies of Peptides:  Comparison of Approximate Continuum Solvation Models with Accurate Solution of the Poisson−Boltzmann Equation The Journal of Physical Chemistry B. 101: 1190-1197. DOI: 10.1021/Jp962156K  0.337
1997 Kim K, Friesner RA. Hydrogen bonding between amino acid backbone and side chain analogues: A high-level ab initio study Journal of the American Chemical Society. 119: 12952-12961. DOI: 10.1021/Ja971836D  0.317
1997 Beachy MD, Chasman D, Murphy RB, Halgren TA, Friesner RA. Accurate ab initio quantum chemical determination of the relative energetics of peptide conformations and assessment of empirical force fields Journal of the American Chemical Society. 119: 5908-5920. DOI: 10.1021/Ja962310G  0.407
1997 Black S, Friesner R, Lu P, Osgood R. Ab initio calculation of molecule-surface binding: methyl halides on GaAs(110) surfaces Surface Science. 382: 154-169. DOI: 10.1016/S0039-6028(97)00119-2  0.407
1997 Mainz DT, Klicic JJ, Friesner RA, Langlois JM, Perry JK. Extension of the PS-GVB electronic structure code to transition metal complexes Journal of Computational Chemistry. 18: 1863-1874. DOI: 10.1002/(Sici)1096-987X(19971130)18:15<1863::Aid-Jcc3>3.0.Co;2-M  0.375
1997 Cortis CM, Friesner RA. Numerical solution of the Poisson-Boltzmann equation using tetrahedral finite-element meshes Journal of Computational Chemistry. 18: 1591-1608. DOI: 10.1002/(Sici)1096-987X(199710)18:13<1591::Aid-Jcc3>3.0.Co;2-M  0.31
1996 Cortis CM, Langlois J, Beachy MD, Friesner RA. Quantum mechanical geometry optimization in solution using a finite element continuum electrostatics method The Journal of Chemical Physics. 105: 5472-5484. DOI: 10.1063/1.472388  0.359
1996 Marten B, Kim K, Cortis C, Friesner RA, Murphy RB, Ringnalda MN, Sitkoff D, Honig B. New Model for Calculation of Solvation Free Energies:  Correction of Self-Consistent Reaction Field Continuum Dielectric Theory for Short-Range Hydrogen-Bonding Effects The Journal of Physical Chemistry. 100: 11775-11788. DOI: 10.1021/Jp953087X  0.573
1995 Murphy RB, Beachy MD, Friesner RA, Ringnalda MN. Pseudospectral localized Mo/ller–Plesset methods: Theory and calculation of conformational energies The Journal of Chemical Physics. 103: 1481-1490. DOI: 10.1063/1.469769  0.423
1995 Zhang LY, Friesner RA. Ab Initio Electronic Structure Calculation of the Redox Potentials of Bacteriochlorophyll and Bacteriopheophytin in Solution The Journal of Physical Chemistry. 99: 16479-16482. DOI: 10.1021/J100044A042  0.4
1995 Humphreys DD, Friesner RA, Berne BJ. Simulated annealing of a protein in a continuum solvent by multiple-time-step molecular dynamics Journal of Physical Chemistry. 99: 10674-10685. DOI: 10.1021/J100026A035  0.497
1995 Zorman B, Ramakrishna MV, Friesner RA. Quantum Confinement Effects in CdSe Quantum Dots The Journal of Physical Chemistry. 99: 7649-7653. DOI: 10.1021/J100019A052  0.321
1994 Monge A, Friesner RA, Honig B. An algorithm to generate low-resolution protein tertiary structures from knowledge of secondary structure. Proceedings of the National Academy of Sciences of the United States of America. 91: 5027-9. PMID 8197177 DOI: 10.1073/Pnas.91.11.5027  0.522
1994 Friesner RA. Comparison of theory and experiment for electron transfers in proteins: where's the beef? Structure (London, England : 1993). 2: 339-43. PMID 8081749 DOI: 10.1016/S0969-2126(00)00035-6  0.308
1994 Murphy RB, Friesner RA, Ringnalda MN, Goddard WA. Pseudospectral contracted configuration interaction from a generalized valence bond reference The Journal of Chemical Physics. 101: 2986-2994. DOI: 10.1063/1.467611  0.327
1994 Greeley BH, Russo TV, Mainz DT, Friesner RA, Langlois J, Goddard WA, Donnelly RE, Ringnalda MN. New pseudospectral algorithms for electronic structure calculations: Length scale separation and analytical two‐electron integral corrections The Journal of Chemical Physics. 101: 4028-4041. DOI: 10.1063/1.467520  0.796
1994 Pollard WT, Friesner RA. Solution of the Redfield equation for the dissipative quantum dynamics of multilevel systems The Journal of Chemical Physics. 100: 5054-5065. DOI: 10.1063/1.467222  0.307
1994 Webster F, Wang ET, Rossky PJ, Friesner RA. Stationary phase surface hopping for nonadiabatic dynamics: Two-state systems The Journal of Chemical Physics. 100: 4835-4847. DOI: 10.1063/1.467204  0.326
1994 Tannor DJ, Marten B, Murphy R, Friesner RA, Sitkoff D, Nicholls A, Honig B, Ringnalda M, Goddard WA. Accurate First Principles Calculation of Molecular Charge Distributions and Solvation Energies from Ab Initio Quantum Mechanics and Continuum Dielectric Theory Journal of the American Chemical Society. 116: 11875-11882. DOI: 10.1021/Ja00105A030  0.545
1994 Humphreys DD, Friesner RA, Berne BJ. A multiple-time-step Molecular Dynamics algorithm for macromolecules Journal of Physical Chemistry. 98: 6885-6892. DOI: 10.1021/J100078A035  0.512
1994 Gunn JR, Monge A, Friesner RA, Marshall CH. Hierarchical algorithm for computer modeling of protein tertiary structure: folding of myoglobin to 6.2 .ANG. resolution The Journal of Physical Chemistry. 98: 702-711. DOI: 10.1021/J100053A053  0.357
1993 Pollard WT, Friesner RA. Efficient Fock matrix diagonalization by a Krylov‐space method The Journal of Chemical Physics. 99: 6742-6750. DOI: 10.1063/1.465817  0.308
1993 Friesner RA, Bentley JA, Menou M, Leforestier C. Adiabatic pseudospectral methods for multidimensional vibrational potentials The Journal of Chemical Physics. 99: 324-335. DOI: 10.1063/1.465810  0.351
1993 Lee JG, Friesner RA. Atomic charges for large molecules derived from electrostatic potentials: fragment density matrix approach The Journal of Physical Chemistry. 97: 3515-3519. DOI: 10.1021/J100116A013  0.31
1992 Jean JM, Friesner RA, Fleming GR. Application of a multilevel Redfield theory to electron transfer in condensed phases The Journal of Chemical Physics. 96: 5827-5842. DOI: 10.1063/1.462858  0.343
1992 Thiem H, Wiedenfeld DJ, Lee J, Friesner RA. AMBER force field parameters for the trimethylanilinium cation Bioorganic & Medicinal Chemistry Letters. 2: 291-294. DOI: 10.1016/S0960-894X(01)80202-X  0.307
1991 Webster FJ, Schnitker J, Friedrichs MS, Friesner RA, Rossky PJ. Solvation dynamics of the hydrated electron: A nonadiabatic quantum simulation. Physical Review Letters. 66: 3172-3175. PMID 10043717 DOI: 10.1103/Physrevlett.66.3172  0.315
1991 Friesner RA. New methods for electronic structure calculations on large molecules. Annual Review of Physical Chemistry. 42: 341-67. PMID 1747190 DOI: 10.1146/Annurev.Pc.42.100191.002013  0.365
1991 Won Y, Lee J, Ringnalda MN, Friesner RA. Pseudospectral Hartree–Fock gradient calculations The Journal of Chemical Physics. 94: 8152-8157. DOI: 10.1063/1.460097  0.367
1991 Webster F, Rossky PJ, Friesner RA. Nonadiabatic processes in condensed matter: semi-classical theory and implementation Computer Physics Communications. 63: 494-522. DOI: 10.1016/0010-4655(91)90272-M  0.303
1990 Ringnalda MN, Belhadj M, Friesner RA. Pseudospectral Hartree–Fock theory: Applications and algorithmic improvements The Journal of Chemical Physics. 93: 3397-3407. DOI: 10.1063/1.458819  0.366
1990 Langlois J, Muller RP, Coley TR, Goddard WA, Ringnalda MN, Won Y, Friesner RA. Pseudospectral generalized valence‐bond calculations: Application to methylene, ethylene, and silylene The Journal of Chemical Physics. 92: 7488-7497. DOI: 10.1063/1.458184  0.371
1990 Ringnalda MN, Won Y, Friesner RA. Pseudospectral Hartree–Fock calculations on glycine The Journal of Chemical Physics. 92: 1163-1173. DOI: 10.1063/1.458178  0.351
1990 Byers JD, Parsons WS, Friesner RA, Webber SE. Efficient numerical simulations of the time dependence of electronic energy transfer in polymers. 2. Short-range transfer and Foerster trapping Macromolecules. 23: 4835-4844. DOI: 10.1021/Ma00224A012  0.3
1989 Won Y, Friesner RA, Johnson MR, Sessler JL. Exciton interactions in synthetic porphyrin dimers. Photosynthesis Research. 22: 201-10. PMID 24424810 DOI: 10.1007/Bf00048299  0.359
1988 Friesner RA. An automatic grid generation scheme for pseudospectral self-consistent field calculations on polyatomic molecules The Journal of Physical Chemistry. 92: 3091-3096. DOI: 10.1021/J100322A017  0.343
1987 Lagos RE, Friesner RA. Green functions for anisotropic tight-binding hamiltonians: Application to exciton migration and optical lineshape Journal of Physics C: Solid State Physics. 20: 4833-4843. DOI: 10.1088/0022-3719/20/29/018  0.301
1987 Friesner RA. Solution of the Hartree–Fock equations for polyatomic molecules by a pseudospectral method The Journal of Chemical Physics. 86: 3522-3531. DOI: 10.1063/1.451955  0.354
1986 Moiseyev N, Friesner RA, Wyatt RE. Natural expansion of vibrational wave functions: RRGM with residue algebra The Journal of Chemical Physics. 85: 331-336. DOI: 10.1063/1.451660  0.33
1986 Friesner RA. Solution of the Hartree–Fock equations by a pseudospectral method: Application to diatomic molecules The Journal of Chemical Physics. 85: 1462-1468. DOI: 10.1063/1.451237  0.308
1986 Jean JM, Friesner RA. An accurate and efficient decoupling approximation for temperature‐dependent multimode resonance Raman spectra The Journal of Chemical Physics. 85: 2353-2364. DOI: 10.1063/1.451089  0.316
1986 Won Y, Lagos R, Friesner R. Numerical tests of a generalized multilevel vibronic coupling formalism The Journal of Chemical Physics. 84: 6567-6574. DOI: 10.1063/1.450709  0.33
1984 Lagos RE, Friesner RA. Cluster generalization of the dynamical coherent-potential approximation: Application to exciton-phonon interactions in molecular crystals Physical Review B. 29: 3045-3056. DOI: 10.1103/Physrevb.29.3045  0.311
1984 Calef DF, Friesner R, Korzeniewski G, Laird B, Silbey R. Calculation of the Green's function from high- and low-density series expansions for disordered transport Physical Review A. 29: 2963-2965. DOI: 10.1103/Physreva.29.2963  0.507
1984 Lagos RE, Friesner RA. Calculation of optical line shapes for generalized multilevel vibronic systems The Journal of Chemical Physics. 81: 5899-5905. DOI: 10.1063/1.447590  0.307
1984 Friesner RA, Levy RM. An optimized harmonic reference system for the evaluation of discretized path integrals The Journal of Chemical Physics. 80: 4488-4495. DOI: 10.1063/1.447232  0.326
1984 Dismukes G, Frank HA, Friesner R, Sauer K. Electronic interactions between iron and the bound semiquinones in bacterial photosynthesis. EPR spectroscopy of oriented cells of Rhodopseudomonas viridis Biochimica Et Biophysica Acta (Bba) - Bioenergetics. 764: 253-271. DOI: 10.1016/0005-2728(84)90096-3  0.636
1983 Frank HA, Machnicki J, Friesner R. ENERGY TRANSFER BETWEEN THE PRIMARY DONOR BACTERIOCHLOROPHYLL AND CAROTENOIDS IN Rhodopseudomonas sphaeroides Photochemistry and Photobiology. 38: 451-455. DOI: 10.1111/J.1751-1097.1983.Tb03365.X  0.548
1983 Korzeniewski G, Friesner R, Silbey R. Localized excitation transport on substitutionally disordered lattices Journal of Statistical Physics. 31: 451-465. DOI: 10.1007/Bf01019493  0.487
1982 Friesner R. Green’s functions and optical line shapes of a general two‐level system in the strong electronic coupling limit The Journal of Chemical Physics. 76: 2129-2135. DOI: 10.1063/1.443308  0.301
1982 Friesner R, Silbey R. Calculation of the exciton green's function of a molecular crystal from a two-site dynamical coherent potential approximation Chemical Physics Letters. 93: 107-110. DOI: 10.1016/0009-2614(82)83674-9  0.523
1981 Nairn JA, Friesner R, Frank HA, Sauer K. A new approach to the theory of linear dichroism in partially ordered systems. Application to reaction centers and whole cells of photosynthetic bacteria. Biophysical Journal. 32: 733-53. PMID 7020787 DOI: 10.1016/S0006-3495(80)85013-2  0.752
1981 Friesner RA, Silbey R. Linear vibronic coupling in a general two level system The Journal of Chemical Physics. 75: 3925-3936. DOI: 10.1063/1.442549  0.527
1981 Friesner R, Silbey R. Absorption and circular dichroism line shapes of a molecular dimer in the strong electronic coupling limit The Journal of Chemical Physics. 75: 5630-5639. DOI: 10.1063/1.442002  0.523
1981 Friesner R, Silbey R. Exciton–phonon coupling in a dimer: An analytic approximation for eigenvalues and eigenvectors The Journal of Chemical Physics. 74: 1166-1174. DOI: 10.1063/1.441224  0.513
1981 Nairn JA, Friesner R, Sauer K. A general theory of the spectroscopic properties of partially ordered ensembles. II. Two‐vector problems The Journal of Chemical Physics. 74: 5398-5406. DOI: 10.1063/1.440942  0.69
1981 Friesner R, McCracken JL, Sauer K. Transient solutions of the bloch equations for inhomogeneously broadened lines Journal of Magnetic Resonance (1969). 43: 343-356. DOI: 10.1016/0022-2364(81)90047-0  0.653
1981 Friesner R, Silbey R. Effect of inhomogeneous broadening on the optical line shape of molecular aggregates Chemical Physics Letters. 84: 365-369. DOI: 10.1016/0009-2614(81)80365-X  0.479
1979 Friesner R, Dismukes GC, Sauer K. Development of electron spin polarization in photosynthetic electron transfer by the radical pair mechanism. Biophysical Journal. 25: 277-94. PMID 233573 DOI: 10.1016/S0006-3495(79)85291-1  0.525
1979 Frank HA, Bolt J, Friesner R, Sauer K. Magnetophotoselection of the triplet state of reaction centers from Rhodopseudomonas sphaeroides R-26. Biochimica Et Biophysica Acta. 547: 502-11. PMID 226130 DOI: 10.1016/0005-2728(79)90030-6  0.647
1979 Frank HA, Friesner R, Nairn JA, Dismukes GC, Sauer K. The orientation of the primary donor in bacterial photosynthesis. Biochimica Et Biophysica Acta. 547: 484-501. PMID 226129 DOI: 10.1016/0005-2728(79)90029-X  0.734
1979 Friesner R, Nairn JA, Sauer K. Direct calculation of the orientational distribution function of partially ordered ensembles from the EPR line shape The Journal of Chemical Physics. 71: 358-365. DOI: 10.1063/1.438078  0.679
1979 Dismukes C, McGuire A, Friesner R, Sauer K. Electron spin polarization from the photosynthetic light reaction: Photosystem I Reviews of Chemical Intermediates. 3: 59-88. DOI: 10.1007/Bf03052281  0.519
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