William L. Jorgensen - Publications

Affiliations: 
Yale University, New Haven, CT 
Area:
computational chemistry and molecular design
Website:
http://zarbi.chem.yale.edu/

319 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
2020 Duong VN, Ippolito JA, Chan AH, Lee WG, Spasov KA, Jorgensen WL, Anderson KS. Structural Investigation of 2-Naphthyl Phenyl Ether Inhibitors Bound to WT and Y181C Reverse Transcriptase Highlights Key Features of the NNRTI Binding Site. Protein Science : a Publication of the Protein Society. PMID 32643196 DOI: 10.1002/Pro.3910  0.303
2020 Newton AS, Faver JC, Micevic G, Muthusamy V, Kudalkar SN, Bertoletti N, Anderson KS, Bosenberg MW, Jorgensen WL. Structure-Guided Identification of DNMT3B Inhibitors. Acs Medicinal Chemistry Letters. 11: 971-976. PMID 32435413 DOI: 10.1021/Acsmedchemlett.0C00011  0.307
2019 Qian Y, Cabeza de Vaca I, Vilseck JZ, Cole DJ, Tirado-Rives J, Jorgensen WL. Absolute Free Energy of Binding Calculations for Macrophage Migration Inhibitory Factor in Complex with a Druglike Inhibitor. The Journal of Physical Chemistry. B. PMID 31553604 DOI: 10.1021/Acs.Jpcb.9B07588  0.648
2019 Cole DJ, Cabeza de Vaca I, Jorgensen WL. Computation of protein-ligand binding free energies using quantum mechanical bespoke force fields. Medchemcomm. 10: 1116-1120. PMID 31391883 DOI: 10.1039/C9Md00017H  0.613
2019 Sasaki T, Gannam ZTK, Kudalkar SN, Frey KM, Lee WG, Spasov KA, Jorgensen WL, Anderson KS. Molecular and cellular studies evaluating a potent 2-cyanoindolizine catechol diether NNRTI targeting wildtype and Y181C mutant HIV-1 reverse transcriptase. Bioorganic & Medicinal Chemistry Letters. PMID 31281023 DOI: 10.1016/J.Bmcl.2019.06.047  0.346
2019 Tirado-Rives J, Jorgensen WL. QM/MM Calculations for the Cl + CHCl S2 Reaction in Water Using CM5 Charges and Density Functional Theory. The Journal of Physical Chemistry. A. PMID 31246023 DOI: 10.1021/Acs.Jpca.9B04121  0.343
2019 Cabeza de Vaca I, Zarzuela R, Tirado-Rives J, Jorgensen WL. Robust FEP Protocols for Creating Molecules in Solution. Journal of Chemical Theory and Computation. PMID 31185169 DOI: 10.1021/Acs.Jctc.9B00213  0.407
2019 Ruiz V, Czyzyk DJ, Valhondo M, Jorgensen WL, Anderson KS. Novel allosteric covalent inhibitors of bifunctional Cryptosporidium hominis TS-DHFR from parasitic protozoa identified by virtual screening. Bioorganic & Medicinal Chemistry Letters. PMID 30929953 DOI: 10.1016/J.Bmcl.2019.03.022  0.316
2019 Robertson MJ, Qian Y, Robinson MC, Tirado-Rives J, Jorgensen WL. Development and Testing of the OPLS-AA/M Force Field for RNA. Journal of Chemical Theory and Computation. PMID 30807148 DOI: 10.1021/Acs.Jctc.9B00054  0.555
2018 Yan XC, Metrano AJ, Robertson MJ, Abascal NC, Tirado-Rives J, Miller SJ, Jorgensen WL. Molecular Dynamics Simulations of a Conformationally Mobile Peptide-Based Catalyst for Atroposelective Bromination. Acs Catalysis. 8: 9968-9979. PMID 30687577 DOI: 10.1021/Acscatal.8B03563  0.563
2018 Dodda LS, Tirado-Rives J, Jorgensen WL. Unbinding Dynamics of Non-Nucleoside Inhibitors from HIV-1 Reverse Transcriptase. The Journal of Physical Chemistry. B. PMID 30571126 DOI: 10.1021/Acs.Jpcb.8B10341  0.327
2018 Cabeza de Vaca I, Qian Y, Vilseck JZ, Tirado-Rives J, Jorgensen WL. Enhanced Monte Carlo Methods for Modeling Proteins Including Computation of Absolute Free Energies of Binding. Journal of Chemical Theory and Computation. PMID 29708338 DOI: 10.1021/Acs.Jctc.8B00031  0.368
2018 Trivedi-Parmar V, Robertson MJ, Cisneros JA, Krimmer SG, Jorgensen WL. Optimization of Pyrazoles as Phenol Surrogates to Yield Potent Inhibitors of Macrophage Migration Inhibitory Factor. Chemmedchem. PMID 29575754 DOI: 10.1002/Cmdc.201800158  0.592
2018 Trivedi-Parmar V, Robertson MJ, Cisneros JA, Krimmer SG, Jorgensen WL. Front Cover: Optimization of Pyrazoles as Phenol Surrogates to Yield Potent Inhibitors of Macrophage Migration Inhibitory Factor (ChemMedChem 11/2018) Chemmedchem. 13: 1069-1069. DOI: 10.1002/Cmdc.201800277  0.539
2017 Robertson MJ, Tirado-Rives J, Jorgensen WL. Improved Treatment of Nucleosides and Nucleotides in the OPLS-AA Force Field. Chemical Physics Letters. 683: 276-280. PMID 29479109 DOI: 10.1016/J.Cplett.2017.02.049  0.562
2017 Dawson TK, Dziedzic P, Robertson MJ, Cisneros JA, Krimmer SG, Newton AS, Tirado-Rives J, Jorgensen WL. Adding a Hydrogen Bond May Not Help: Naphthyridinone vs Quinoline Inhibitors of Macrophage Migration Inhibitory Factor. Acs Medicinal Chemistry Letters. 8: 1287-1291. PMID 29259749 DOI: 10.1021/Acsmedchemlett.7B00384  0.582
2017 Cole DJ, Janecek M, Stokes JE, Rossmann M, Faver JC, McKenzie GJ, Venkitaraman AR, Hyvönen M, Spring DR, Huggins DJ, Jorgensen WL. Computationally-guided optimization of small-molecule inhibitors of the Aurora A kinase-TPX2 protein-protein interaction. Chemical Communications (Cambridge, England). PMID 28787041 DOI: 10.1039/C7Cc05379G  0.602
2017 Yan XC, Robertson MJ, Tirado-Rives J, Jorgensen WL. Improved Description of Sulfur Charge Anisotropy in OPLS Force Fields. Model Development and Parameterization. The Journal of Physical Chemistry. B. PMID 28627890 DOI: 10.1021/Acs.Jpcb.7B04233  0.603
2017 Dodda LS, Cabeza de Vaca I, Tirado-Rives J, Jorgensen WL. LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands. Nucleic Acids Research. PMID 28444340 DOI: 10.1093/Nar/Gkx312  0.33
2017 Dodda LS, Vilseck JZ, Tirado-Rives J, Jorgensen WL. Localized Bond Charge Corrected CM1A Charges for Condensed-Phase Simulations. The Journal of Physical Chemistry. B. PMID 28224794 DOI: 10.1021/Acs.Jpcb.7B00272  0.318
2017 Kudalkar SN, Beloor J, Chan AH, Lee WG, Jorgensen WL, Kumar P, Anderson KS. Structural and Preclinical Studies of Computationally-Designed Non-nucleoside Reverse Transcriptase Inhibitors for Treating HIV infection. Molecular Pharmacology. PMID 28167742 DOI: 10.1124/Mol.116.107755  0.307
2017 Cisneros JA, Robertson MJ, Mercado BQ, Jorgensen WL. Systematic Study of Effects of Structural Modifications on the Aqueous Solubility of Drug-like Molecules. Acs Medicinal Chemistry Letters. 8: 124-127. PMID 28105287 DOI: 10.1021/Acsmedchemlett.6B00451  0.59
2016 Lee WG, Chan AH, Spasov KA, Anderson KS, Jorgensen WL. Design, Conformation, and Crystallography of 2-Naphthyl Phenyl Ethers as Potent Anti-HIV Agents. Acs Medicinal Chemistry Letters. 7: 1156-1160. PMID 27994756 DOI: 10.1021/Acsmedchemlett.6B00390  0.308
2016 Jorgensen WL. Computer-aided discovery of anti-HIV agents. Bioorganic & Medicinal Chemistry. PMID 27485603 DOI: 10.1016/J.Bmc.2016.07.039  0.323
2016 Robertson MJ, Tirado-Rives J, Jorgensen WL. Performance of Protein-Ligand Force Fields for the Flavodoxin - Flavin Mononucleotide System. The Journal of Physical Chemistry Letters. PMID 27441982 DOI: 10.1021/Acs.Jpclett.6B01229  0.592
2016 Cisneros JA, Robertson MJ, Valhondo M, Jorgensen WL. A Fluorescence Polarization Assay for Binding to Macrophage Migration Inhibitory Factor and Crystal Structures for Complexes of Two Potent Inhibitors. Journal of the American Chemical Society. PMID 27299179 DOI: 10.1021/Jacs.6B04910  0.591
2016 Cisneros JA, Robertson MJ, Valhondo M, Jorgensen WL. Irregularities in enzyme assays: The case of macrophage migration inhibitory factor. Bioorganic & Medicinal Chemistry Letters. PMID 27156768 DOI: 10.1016/J.Bmcl.2016.04.074  0.556
2016 Cole DJ, Vilseck JZ, Tirado-Rives J, Payne MC, Jorgensen WL. Biomolecular Force Field Parameterization via Atoms-in-Molecule Electron Density Partitioning. Journal of Chemical Theory and Computation. PMID 27057643 DOI: 10.1021/Acs.Jctc.6B00027  0.704
2016 Yan XC, Tirado-Rives J, Jorgensen WL. Hydration Properties and Solvent Effects for All-Atom Solutes in Polarizable Coarse-Grained Water. The Journal of Physical Chemistry. B. PMID 26901452 DOI: 10.1021/Acs.Jpcb.6B00399  0.367
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, 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  0.528
2015 Dodda LS, Vilseck JZ, Cutrona KJ, Jorgensen WL. Evaluation of CM5 Charges for Nonaqueous Condensed-Phase Modeling. Journal of Chemical Theory and Computation. 11: 4273-82. PMID 26575922 DOI: 10.1021/Acs.Jctc.5B00414  0.336
2015 Gray WT, Frey KM, Laskey SB, Mislak AC, Spasov KA, Lee WG, Bollini M, Siliciano RF, Jorgensen WL, Anderson KS. Potent Inhibitors Active against HIV Reverse Transcriptase with K101P, a Mutation Conferring Rilpivirine Resistance. Acs Medicinal Chemistry Letters. 6: 1075-9. PMID 26487915 DOI: 10.1021/Acsmedchemlett.5B00254  0.308
2015 Vilseck JZ, Kostal J, Tirado-Rives J, Jorgensen WL. Application of a BOSS-Gaussian interface for QM/MM simulations of Henry and methyl transfer reactions. Journal of Computational Chemistry. 36: 2064-74. PMID 26311531 DOI: 10.1002/Jcc.24045  0.681
2015 Robertson MJ, Tirado-Rives J, Jorgensen WL. Improved Peptide and Protein Torsional Energetics with the OPLS-AA Force Field. Journal of Chemical Theory and Computation. 11: 3499-3509. PMID 26190950 DOI: 10.1021/Acs.Jctc.5B00356  0.518
2015 Lee WG, Frey KM, Gallardo-Macias R, Spasov KA, Chan AH, Anderson KS, Jorgensen WL. Discovery and crystallography of bicyclic arylaminoazines as potent inhibitors of HIV-1 reverse transcriptase. Bioorganic & Medicinal Chemistry Letters. 25: 4824-7. PMID 26166629 DOI: 10.1016/J.Bmcl.2015.06.074  0.778
2015 Frey KM, Puleo DE, Spasov KA, Bollini M, Jorgensen WL, Anderson KS. Structure-based evaluation of non-nucleoside inhibitors with improved potency and solubility that target HIV reverse transcriptase variants. Journal of Medicinal Chemistry. 58: 2737-45. PMID 25700160 DOI: 10.1021/Jm501908A  0.343
2015 Dziedzic P, Cisneros JA, Robertson MJ, Hare AA, Danford NE, Baxter RH, Jorgensen WL. Design, synthesis, and protein crystallography of biaryltriazoles as potent tautomerase inhibitors of macrophage migration inhibitory factor. Journal of the American Chemical Society. 137: 2996-3003. PMID 25697265 DOI: 10.1021/Ja512112J  0.786
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, ... ... Jorgensen WL, 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  0.647
2015 Vilseck JZ, Tirado-Rives J, Jorgensen WL. Determination of partial molar volumes from free energy perturbation theory. Physical Chemistry Chemical Physics : Pccp. 17: 8407-15. PMID 25589343 DOI: 10.1039/C4Cp05304D  0.381
2015 Cole DJ, Tirado-Rives J, Jorgensen WL. Molecular dynamics and Monte Carlo simulations for protein-ligand binding and inhibitor design. Biochimica Et Biophysica Acta. 1850: 966-71. PMID 25196360 DOI: 10.1016/J.Bbagen.2014.08.018  0.618
2015 Robertson MJ, Jorgensen WL. Illustrating Concepts in Physical Organic Chemistry with 3D Printed Orbitals Journal of Chemical Education. 92: 2113-2116. DOI: 10.1021/Acs.Jchemed.5B00682  0.554
2015 Lee WG, Frey KM, Gallardo-Macias R, Spasov KA, Chan AH, Anderson KS, Jorgensen WL. Discovery and crystallography of bicyclic arylaminoazines as potent inhibitors of HIV-1 reverse transcriptase Bioorganic and Medicinal Chemistry Letters. DOI: 10.1016/j.bmcl.2015.06.074  0.758
2014 Acevedo O, Jorgensen WL. Quantum and Molecular Mechanical (QM/MM) Monte Carlo Techniques for Modeling Condensed-Phase Reactions. Wiley Interdisciplinary Reviews. Computational Molecular Science. 4: 422-435. PMID 25431625 DOI: 10.1002/Wcms.1180  0.57
2014 Lee WG, Frey KM, Gallardo-Macias R, Spasov KA, Bollini M, Anderson KS, Jorgensen WL. Picomolar Inhibitors of HIV-1 Reverse Transcriptase: Design and Crystallography of Naphthyl Phenyl Ethers. Acs Medicinal Chemistry Letters. 5: 1259-62. PMID 25408842 DOI: 10.1021/Ml5003713  0.775
2014 Parker CG, Dahlgren MK, Tao RN, Li DT, Douglass EF, Shoda T, Jawanda N, Spasov KA, Lee S, Zhou N, Domaoal RA, Sutton RE, Anderson KS, Jorgensen WL, Krystal M, et al. Illuminating HIV gp120-Ligand Recognition through Computationally-Driven Optimization of Antibody-Recruiting Molecules. Chemical Science (Royal Society of Chemistry : 2010). 5: 2311-2317. PMID 25379167 DOI: 10.1039/C4Sc00484A  0.317
2014 Kumar VP, Cisneros JA, Frey KM, Castellanos-Gonzalez A, Wang Y, Gangjee A, White AC, Jorgensen WL, Anderson KS. Structural studies provide clues for analog design of specific inhibitors of Cryptosporidium hominis thymidylate synthase-dihydrofolate reductase. Bioorganic & Medicinal Chemistry Letters. 24: 4158-61. PMID 25127103 DOI: 10.1016/J.Bmcl.2014.07.049  0.31
2014 Vilseck JZ, Tirado-Rives J, Jorgensen WL. Evaluation of CM5 Charges for Condensed-Phase Modeling. Journal of Chemical Theory and Computation. 10: 2802-2812. PMID 25061445 DOI: 10.1021/Ct500016D  0.32
2014 Cole DJ, Tirado-Rives J, Jorgensen WL. Enhanced Monte Carlo Sampling through Replica Exchange with Solute Tempering. Journal of Chemical Theory and Computation. 10: 565-571. PMID 24803853 DOI: 10.1021/Ct400989X  0.645
2014 Mislak AC, Frey KM, Bollini M, Jorgensen WL, Anderson KS. A mechanistic and structural investigation of modified derivatives of the diaryltriazine class of NNRTIs targeting HIV-1 reverse transcriptase. Biochimica Et Biophysica Acta. 1840: 2203-11. PMID 24726448 DOI: 10.1016/J.Bbagen.2014.04.001  0.357
2014 Yan XC, Schyman P, Jorgensen WL. Cooperative effects and optimal halogen bonding motifs for self-assembling systems. The Journal of Physical Chemistry. A. 118: 2820-6. PMID 24678636 DOI: 10.1021/Jp501553J  0.701
2014 Frey KM, Gray WT, Spasov KA, Bollini M, Gallardo-Macias R, Jorgensen WL, Anderson KS. Structure-based evaluation of C5 derivatives in the catechol diether series targeting HIV-1 reverse transcriptase. Chemical Biology & Drug Design. 83: 541-9. PMID 24289305 DOI: 10.1111/Cbdd.12266  0.793
2014 Wolters LP, Schyman P, Pavan MJ, Jorgensen WL, Bickelhaupt FM, Kozuch S. The many faces of halogen bonding: A review of theoretical models and methods Wiley Interdisciplinary Reviews: Computational Molecular Science. 4: 523-540. DOI: 10.1002/Wcms.1189  0.702
2013 Lee WG, Gallardo-Macias R, Frey KM, Spasov KA, Bollini M, Anderson KS, Jorgensen WL. Picomolar inhibitors of HIV reverse transcriptase featuring bicyclic replacement of a cyanovinylphenyl group. Journal of the American Chemical Society. 135: 16705-13. PMID 24151856 DOI: 10.1021/Ja408917N  0.783
2013 Bollini M, Cisneros JA, Spasov KA, Anderson KS, Jorgensen WL. Optimization of diarylazines as anti-HIV agents with dramatically enhanced solubility. Bioorganic & Medicinal Chemistry Letters. 23: 5213-6. PMID 23937980 DOI: 10.1016/J.Bmcl.2013.06.091  0.312
2013 Lee LP, Cole DJ, Skylaris CK, Jorgensen WL, Payne MC. Polarized Protein-Specific Charges from Atoms-in-Molecule Electron Density Partitioning. Journal of Chemical Theory and Computation. 9: 2981-2991. PMID 23894231 DOI: 10.1021/Ct400279D  0.684
2013 Wang J, Tong C, Yan X, Yeung E, Gandavadi S, Hare AA, Du X, Chen Y, Xiong H, Ma C, Leng L, Young LH, Jorgensen WL, Li J, Bucala R. Limiting cardiac ischemic injury by pharmacological augmentation of macrophage migration inhibitory factor-AMP-activated protein kinase signal transduction. Circulation. 128: 225-36. PMID 23753877 DOI: 10.1161/Circulationaha.112.000862  0.677
2013 Dahlgren MK, Schyman P, Tirado-Rives J, Jorgensen WL. Characterization of biaryl torsional energetics and its treatment in OPLS all-atom force fields. Journal of Chemical Information and Modeling. 53: 1191-9. PMID 23621692 DOI: 10.1021/Ci4001597  0.699
2013 Sun H, Choo-Wing R, Fan J, Leng L, Syed MA, Hare AA, Jorgensen WL, Bucala R, Bhandari V. Small molecular modulation of macrophage migration inhibitory factor in the hyperoxia-induced mouse model of bronchopulmonary dysplasia. Respiratory Research. 14: 27. PMID 23448134 DOI: 10.1186/1465-9921-14-27  0.664
2013 Schyman P, Jorgensen WL. Exploring Adsorption of Water and Ions on Carbon Surfaces using a Polarizable Force Field. The Journal of Physical Chemistry Letters. 4: 468-474. PMID 23440601 DOI: 10.1021/Jz302085C  0.681
2013 Bollini M, Gallardo-Macias R, Spasov KA, Tirado-Rives J, Anderson KS, Jorgensen WL. Optimization of benzyloxazoles as non-nucleoside inhibitors of HIV-1 reverse transcriptase to enhance Y181C potency. Bioorganic & Medicinal Chemistry Letters. 23: 1110-3. PMID 23298809 DOI: 10.1016/J.Bmcl.2012.11.115  0.784
2012 Jorgensen WL, Schyman P. Treatment of Halogen Bonding in the OPLS-AA Force Field; Application to Potent Anti-HIV Agents. Journal of Chemical Theory and Computation. 8: 3895-3801. PMID 23329896 DOI: 10.1021/Ct300180W  0.736
2012 Frey KM, Bollini M, Mislak AC, Cisneros JA, Gallardo-Macias R, Jorgensen WL, Anderson KS. Crystal structures of HIV-1 reverse transcriptase with picomolar inhibitors reveal key interactions for drug design. Journal of the American Chemical Society. 134: 19501-3. PMID 23163887 DOI: 10.1021/Ja3092642  0.785
2012 Dahlgren MK, Garcia AB, Hare AA, Tirado-Rives J, Leng L, Bucala R, Jorgensen WL. Virtual screening and optimization yield low-nanomolar inhibitors of the tautomerase activity of Plasmodium falciparum macrophage migration inhibitory factor. Journal of Medicinal Chemistry. 55: 10148-59. PMID 23067344 DOI: 10.1021/Jm301269S  0.699
2012 Leung CS, Leung SS, Tirado-Rives J, Jorgensen WL. Methyl effects on protein-ligand binding. Journal of Medicinal Chemistry. 55: 4489-500. PMID 22500930 DOI: 10.1021/Jm3003697  0.73
2012 Buckley DL, Van Molle I, Gareiss PC, Tae HS, Michel J, Noblin DJ, Jorgensen WL, Ciulli A, Crews CM. Targeting the von Hippel-Lindau E3 ubiquitin ligase using small molecules to disrupt the VHL/HIF-1α interaction. Journal of the American Chemical Society. 134: 4465-8. PMID 22369643 DOI: 10.1021/Ja209924V  0.511
2012 Ekkati AR, Bollini M, Domaoal RA, Spasov KA, Anderson KS, Jorgensen WL. Discovery of dimeric inhibitors by extension into the entrance channel of HIV-1 reverse transcriptase. Bioorganic & Medicinal Chemistry Letters. 22: 1565-8. PMID 22269110 DOI: 10.1016/J.Bmcl.2011.12.132  0.302
2012 Kostal J, Voutchkova AM, Jorgensen WL. Investigation of solvent effects on the rate and stereoselectivity of the Henry reaction. Organic Letters. 14: 260-3. PMID 22168236 DOI: 10.1021/Ol2030394  0.658
2011 Bollini M, Domaoal RA, Thakur VV, Gallardo-Macias R, Spasov KA, Anderson KS, Jorgensen WL. Computationally-guided optimization of a docking hit to yield catechol diethers as potent anti-HIV agents. Journal of Medicinal Chemistry. 54: 8582-91. PMID 22081993 DOI: 10.1021/Jm201134M  0.796
2011 Alexandrova AN, Jorgensen WL. On the mechanism and rate of spontaneous decomposition of amino acids. The Journal of Physical Chemistry. B. 115: 13624-32. PMID 21995727 DOI: 10.1021/Jp2081808  0.606
2011 Jorgensen WL, Bollini M, Thakur VV, Domaoal RA, Spasov KA, Anderson KS. Efficient discovery of potent anti-HIV agents targeting the Tyr181Cys variant of HIV reverse transcriptase. Journal of the American Chemical Society. 133: 15686-96. PMID 21853995 DOI: 10.1021/Ja2058583  0.327
2011 Jorgensen WL, Trofimov A, Du X, Hare AA, Leng L, Bucala R. Benzisothiazolones as modulators of macrophage migration inhibitory factor. Bioorganic & Medicinal Chemistry Letters. 21: 4545-9. PMID 21719283 DOI: 10.1016/J.Bmcl.2011.05.127  0.697
2010 Luccarelli J, Michel J, Tirado-Rives J, Jorgensen WL. Effects of Water Placement on Predictions of Binding Affinities for p38α MAP Kinase Inhibitors. Journal of Chemical Theory and Computation. 6: 3850-3856. PMID 21278915 DOI: 10.1021/Ct100504H  0.561
2010 Jorgensen WL, Gandavadi S, Du X, Hare AA, Trofimov A, Leng L, Bucala R. Receptor agonists of macrophage migration inhibitory factor. Bioorganic & Medicinal Chemistry Letters. 20: 7033-6. PMID 20971005 DOI: 10.1016/J.Bmcl.2010.09.118  0.688
2010 Terhorst JP, Jorgensen WL. E/Z Energetics for Molecular Modeling and Design. Journal of Chemical Theory and Computation. 6: 2762-2769. PMID 20871784 DOI: 10.1021/Ct1004017  0.788
2010 Crane CM, Pierce JG, Leung SS, Tirado-Rives J, Jorgensen WL, Boger DL. Synthesis and evaluation of selected key methyl ether derivatives of vancomycin aglycon. Journal of Medicinal Chemistry. 53: 7229-35. PMID 20853900 DOI: 10.1021/Jm100946E  0.63
2010 Hare AA, Leng L, Gandavadi S, Du X, Cournia Z, Bucala R, Jorgensen WL. Optimization of N-benzyl-benzoxazol-2-ones as receptor antagonists of macrophage migration inhibitory factor (MIF). Bioorganic & Medicinal Chemistry Letters. 20: 5811-4. PMID 20728358 DOI: 10.1016/J.Bmcl.2010.07.129  0.692
2010 Zhang AX, Murelli RP, Barinka C, Michel J, Cocleaza A, Jorgensen WL, Lubkowski J, Spiegel DA. A remote arene-binding site on prostate specific membrane antigen revealed by antibody-recruiting small molecules. Journal of the American Chemical Society. 132: 12711-6. PMID 20726553 DOI: 10.1021/Ja104591M  0.492
2010 Acevedo O, Jorgensen WL. Exploring solvent effects upon the Menshutkin reaction using a polarizable force field. The Journal of Physical Chemistry. B. 114: 8425-30. PMID 20527873 DOI: 10.1021/Jp100765V  0.627
2010 Kostal J, Jorgensen WL. Thorpe-Ingold acceleration of oxirane formation is mostly a solvent effect. Journal of the American Chemical Society. 132: 8766-73. PMID 20524660 DOI: 10.1021/Ja1023755  0.662
2010 Leung CS, Zeevaart JG, Domaoal RA, Bollini M, Thakur VV, Spasov KA, Anderson KS, Jorgensen WL. Eastern extension of azoles as non-nucleoside inhibitors of HIV-1 reverse transcriptase; cyano group alternatives. Bioorganic & Medicinal Chemistry Letters. 20: 2485-8. PMID 20304641 DOI: 10.1016/J.Bmcl.2010.03.006  0.634
2010 Thomas LL, Tirado-Rives J, Jorgensen WL. Quantum mechanical/molecular mechanical modeling finds Diels-Alder reactions are accelerated less on the surface of water than in water. Journal of the American Chemical Society. 132: 3097-104. PMID 20148559 DOI: 10.1021/Ja909740Y  0.356
2010 Ravindranathan KP, Mandiyan V, Ekkati AR, Bae JH, Schlessinger J, Jorgensen WL. Discovery of novel fibroblast growth factor receptor 1 kinase inhibitors by structure-based virtual screening. Journal of Medicinal Chemistry. 53: 1662-72. PMID 20121196 DOI: 10.1021/Jm901386E  0.308
2010 Acevedo O, Jorgensen WL. Advances in quantum and molecular mechanical (QM/MM) simulations for organic and enzymatic reactions. Accounts of Chemical Research. 43: 142-51. PMID 19728702 DOI: 10.1021/Ar900171C  0.63
2010 LIM D, HROVAT DA, BORDEN WT, JORGENSEN WL. ChemInform Abstract: Solvent Effects on the Ring Opening of Cyclopropanones to Oxyallyls: A Combined ab initio and Monte Carlo Study. Cheminform. 25: no-no. DOI: 10.1002/chin.199434073  0.472
2009 Murelli RP, Zhang AX, Michel J, Jorgensen WL, Spiegel DA. Chemical control over immune recognition: a class of antibody-recruiting small molecules that target prostate cancer. Journal of the American Chemical Society. 131: 17090-2. PMID 19888723 DOI: 10.1021/Ja906844E  0.472
2009 Chen X, Regan CK, Craig SL, Krenske EH, Houk KN, Jorgensen WL, Brauman JI. Steric and solvation effects in ionic S(N)2 reactions. Journal of the American Chemical Society. 131: 16162-70. PMID 19842649 DOI: 10.1021/Ja9053459  0.329
2009 Michel J, Tirado-Rives J, Jorgensen WL. Energetics of displacing water molecules from protein binding sites: consequences for ligand optimization. Journal of the American Chemical Society. 131: 15403-11. PMID 19778066 DOI: 10.1021/Ja906058W  0.563
2009 Michel J, Tirado-Rives J, Jorgensen WL. Prediction of the water content in protein binding sites. The Journal of Physical Chemistry. B. 113: 13337-46. PMID 19754086 DOI: 10.1021/Jp9047456  0.559
2009 Leung SS, Tirado-Rives J, Jorgensen WL. Vancomycin analogs: Seeking improved binding of d-Ala-d-Ala and d-Ala-d-Lac peptides by side-chain and backbone modifications. Bioorganic & Medicinal Chemistry. 17: 5874-86. PMID 19620008 DOI: 10.1016/J.Bmc.2009.07.006  0.589
2009 Michel J, Harker EA, Tirado-Rives J, Jorgensen WL, Schepartz A. In Silico Improvement of beta3-peptide inhibitors of p53 x hDM2 and p53 x hDMX. Journal of the American Chemical Society. 131: 6356-7. PMID 19415930 DOI: 10.1021/Ja901478E  0.476
2009 Nichols SE, Domaoal RA, Thakur VV, Tirado-Rives J, Anderson KS, Jorgensen WL. Discovery of wild-type and Y181C mutant non-nucleoside HIV-1 reverse transcriptase inhibitors using virtual screening with multiple protein structures. Journal of Chemical Information and Modeling. 49: 1272-9. PMID 19374380 DOI: 10.1021/Ci900068K  0.664
2009 Jorgensen WL. Efficient drug lead discovery and optimization. Accounts of Chemical Research. 42: 724-33. PMID 19317443 DOI: 10.1021/Ar800236T  0.383
2009 Dasgupta T, Chitnumsub P, Kamchonwongpaisan S, Maneeruttanarungroj C, Nichols SE, Lyons TM, Tirado-Rives J, Jorgensen WL, Yuthavong Y, Anderson KS. Exploiting structural analysis, in silico screening, and serendipity to identify novel inhibitors of drug-resistant falciparum malaria. Acs Chemical Biology. 4: 29-40. PMID 19146480 DOI: 10.1021/Cb8002804  0.78
2009 Alexandrova AN, Jorgensen WL. Origin of the activity drop with the E50D variant of catalytic antibody 34E4 for Kemp elimination. The Journal of Physical Chemistry. B. 113: 497-504. PMID 19132861 DOI: 10.1021/Jp8076084  0.57
2009 Leung SS, Tirado-Rives J, Jorgensen WL. Vancomycin resistance: modeling backbone variants with D-Ala-D-Ala and D-Ala-D-Lac peptides. Bioorganic & Medicinal Chemistry Letters. 19: 1236-9. PMID 19128968 DOI: 10.1016/J.Bmcl.2008.12.072  0.571
2008 Tirado-Rives J, Jorgensen WL. Performance of B3LYP Density Functional Methods for a Large Set of Organic Molecules. Journal of Chemical Theory and Computation. 4: 297-306. PMID 26620661 DOI: 10.1021/Ct700248K  0.311
2008 Jorgensen WL, Thomas LL. Perspective on Free-Energy Perturbation Calculations for Chemical Equilibria. Journal of Chemical Theory and Computation. 4: 869-876. PMID 19936324 DOI: 10.1021/Ct800011M  0.371
2008 Alexandrova AN, Röthlisberger D, Baker D, Jorgensen WL. Catalytic mechanism and performance of computationally designed enzymes for Kemp elimination. Journal of the American Chemical Society. 130: 15907-15. PMID 18975945 DOI: 10.1021/Ja804040S  0.574
2008 Zeevaart JG, Wang L, Thakur VV, Leung CS, Tirado-Rives J, Bailey CM, Domaoal RA, Anderson KS, Jorgensen WL. Optimization of azoles as anti-human immunodeficiency virus agents guided by free-energy calculations. Journal of the American Chemical Society. 130: 9492-9. PMID 18588301 DOI: 10.1021/Ja8019214  0.637
2007 Acevedo O, Jorgensen WL. Understanding Rate Accelerations for Diels-Alder Reactions in Solution Using Enhanced QM/MM Methodology. Journal of Chemical Theory and Computation. 3: 1412-9. PMID 26633213 DOI: 10.1021/Ct700078B  0.631
2007 Gunaydin H, Acevedo O, Jorgensen WL, Houk KN. Computation of Accurate Activation Barriers for Methyl-Transfer Reactions of Sulfonium and Ammonium Salts in Aqueous Solution. Journal of Chemical Theory and Computation. 3: 1028-35. PMID 26627421 DOI: 10.1021/Ct050318N  0.632
2007 Acevedo O, Jorgensen WL, Evanseck JD. Elucidation of Rate Variations for a Diels-Alder Reaction in Ionic Liquids from QM/MM Simulations. Journal of Chemical Theory and Computation. 3: 132-8. PMID 26627159 DOI: 10.1021/Ct6002753  0.76
2007 Jorgensen WL, Jensen KP, Alexandrova AN. Polarization Effects for Hydrogen-Bonded Complexes of Substituted Phenols with Water and Chloride Ion. Journal of Chemical Theory and Computation. 3: 1987-1992. PMID 21132092 DOI: 10.1021/Ct7001754  0.579
2007 Barreiro G, Guimarães CR, Tubert-Brohman I, Lyons TM, Tirado-Rives J, Jorgensen WL. Search for non-nucleoside inhibitors of HIV-1 reverse transcriptase using chemical similarity, molecular docking, and MM-GB/SA scoring. Journal of Chemical Information and Modeling. 47: 2416-28. PMID 17949071 DOI: 10.1021/Ci700271Z  0.788
2007 Barreiro G, Kim JT, Guimarães CR, Bailey CM, Domaoal RA, Wang L, Anderson KS, Jorgensen WL. From docking false-positive to active anti-HIV agent. Journal of Medicinal Chemistry. 50: 5324-9. PMID 17918923 DOI: 10.1021/Jm070683U  0.308
2007 Alexandrova AN, Jorgensen WL. Why urea eliminates ammonia rather than hydrolyzes in aqueous solution. The Journal of Physical Chemistry. B. 111: 720-30. PMID 17249815 DOI: 10.1021/Jp066478S  0.619
2007 Acevedo O, Jorgensen WL. Understanding rate accelerations for Diels-Alder reactions in solution using enhanced QM/MM methodology Journal of Chemical Theory and Computation. 3: 1412-1419. DOI: 10.1021/ct700078b  0.504
2007 Acevedo O, Jorgensen WL, Evanseck JD. Elucidation of rate variations for a diels-alder reaction in ionic liquids from QM/MM simulations Journal of Chemical Theory and Computation. 3: 132-138. DOI: 10.1021/ct6002753  0.702
2007 Gunaydin H, Acevedo O, Jorgensen WL, Houk KN. Computation of accurate activation barriers for methyl-transfer reactions of sulfonium and ammonium salts in aqueous solution Journal of Chemical Theory and Computation. 3: 1028-1035. DOI: 10.1021/ct050318n  0.52
2006 Jensen KP, Jorgensen WL. Halide, Ammonium, and Alkali Metal Ion Parameters for Modeling Aqueous Solutions. Journal of Chemical Theory and Computation. 2: 1499-509. PMID 26627020 DOI: 10.1021/Ct600252R  0.338
2006 Sattelmeyer KW, Tubert-Brohman I, Jorgensen WL. NO-MNDO:  Reintroduction of the Overlap Matrix into MNDO. Journal of Chemical Theory and Computation. 2: 413-9. PMID 26626528 DOI: 10.1021/Ct050174C  0.786
2006 Tubert-Brohman I, Acevedo O, Jorgensen WL. Elucidation of hydrolysis mechanisms for fatty acid amide hydrolase and its Lys142Ala variant via QM/MM simulations. Journal of the American Chemical Society. 128: 16904-13. PMID 17177441 DOI: 10.1021/Ja065863S  0.792
2006 Sattelmeyer KW, Tirado-Rives J, Jorgensen WL. Comparison of SCC-DFTB and NDDO-based semiempirical molecular orbital methods for organic molecules. The Journal of Physical Chemistry. A. 110: 13551-9. PMID 17165882 DOI: 10.1021/Jp064544K  0.348
2006 Kim JT, Hamilton AD, Bailey CM, Domaoal RA, Domoal RA, Wang L, Anderson KS, Jorgensen WL. FEP-guided selection of bicyclic heterocycles in lead optimization for non-nucleoside inhibitors of HIV-1 reverse transcriptase. Journal of the American Chemical Society. 128: 15372-3. PMID 17131993 DOI: 10.1021/Ja066472G  0.349
2006 Thomas LL, Christakis TJ, Jorgensen WL. Conformation of alkanes in the gas phase and pure liquids. The Journal of Physical Chemistry. B. 110: 21198-204. PMID 17048945 DOI: 10.1021/Jp064811M  0.311
2006 Tirado-Rives J, Jorgensen WL. Contribution of conformer focusing to the uncertainty in predicting free energies for protein-ligand binding. Journal of Medicinal Chemistry. 49: 5880-4. PMID 17004703 DOI: 10.1021/Jm060763I  0.35
2006 Thakur VV, Kim JT, Hamilton AD, Bailey CM, Domaoal RA, Wang L, Anderson KS, Jorgensen WL. Optimization of pyrimidinyl- and triazinyl-amines as non-nucleoside inhibitors of HIV-1 reverse transcriptase. Bioorganic & Medicinal Chemistry Letters. 16: 5664-7. PMID 16931015 DOI: 10.1016/J.Bmcl.2006.08.037  0.317
2006 Acevedo O, Jorgensen WL. Medium effects on the decarboxylation of a biotin model in pure and mixed solvents from QM/MM simulations. The Journal of Organic Chemistry. 71: 4896-902. PMID 16776519 DOI: 10.1021/Jo060533B  0.63
2006 Acevedo O, Jorgensen WL. Cope elimination: elucidation of solvent effects from QM/MM simulations. Journal of the American Chemical Society. 128: 6141-6. PMID 16669683 DOI: 10.1021/Ja057523X  0.646
2006 Ruiz-Caro J, Basavapathruni A, Kim JT, Bailey CM, Wang L, Anderson KS, Hamilton AD, Jorgensen WL. Optimization of diarylamines as non-nucleoside inhibitors of HIV-1 reverse transcriptase. Bioorganic & Medicinal Chemistry Letters. 16: 668-71. PMID 16298131 DOI: 10.1016/J.Bmcl.2005.10.037  0.317
2006 Jorgensen WL, Ruiz-Caro J, Tirado-Rives J, Basavapathruni A, Anderson KS, Hamilton AD. Computer-aided design of non-nucleoside inhibitors of HIV-1 reverse transcriptase. Bioorganic & Medicinal Chemistry Letters. 16: 663-7. PMID 16263277 DOI: 10.1016/J.Bmcl.2005.10.038  0.339
2006 Acevedo O, Jorgensen WL. Chapter 14 Solvent Effects on Organic Reactions from QM/MM Simulations Annual Reports in Computational Chemistry. 2: 263-278. DOI: 10.1016/S1574-1400(06)02014-7  0.614
2005 Guimarães CR, Udier-Blagović M, Tubert-Brohman I, Jorgensen WL. Effects of Arg90 Neutralization on the Enzyme-Catalyzed Rearrangement of Chorismate to Prephenate. Journal of Chemical Theory and Computation. 1: 617-25. PMID 26641683 DOI: 10.1021/Ct0500803  0.79
2005 Tubert-Brohman I, Guimarães CR, Jorgensen WL. Extension of the PDDG/PM3 Semiempirical Molecular Orbital Method to Sulfur, Silicon, and Phosphorus. Journal of Chemical Theory and Computation. 1: 817-823. PMID 19011692 DOI: 10.1021/Ct0500287  0.768
2005 Guimarães CR, Boger DL, Jorgensen WL. Elucidation of fatty acid amide hydrolase inhibition by potent alpha-ketoheterocycle derivatives from Monte Carlo simulations. Journal of the American Chemical Society. 127: 17377-84. PMID 16332087 DOI: 10.1021/Ja055438J  0.519
2005 Acevedo O, Jorgensen WL. Influence of inter- and intramolecular hydrogen bonding on kemp decarboxylations from QM/MM simulations. Journal of the American Chemical Society. 127: 8829-34. PMID 15954791 DOI: 10.1021/Ja051793Y  0.64
2005 Jorgensen WL, Tirado-Rives J. Potential energy functions for atomic-level simulations of water and organic and biomolecular systems. Proceedings of the National Academy of Sciences of the United States of America. 102: 6665-70. PMID 15870211 DOI: 10.1073/Pnas.0408037102  0.351
2005 Boger DL, Miyauchi H, Du W, Hardouin C, Fecik RA, Cheng H, Hwang I, Hedrick MP, Leung D, Acevedo O, Guimarães CR, Jorgensen WL, Cravatt BF. Discovery of a potent, selective, and efficacious class of reversible alpha-ketoheterocycle inhibitors of fatty acid amide hydrolase effective as analgesics. Journal of Medicinal Chemistry. 48: 1849-56. PMID 15771430 DOI: 10.1021/Jm049614V  0.616
2005 Guimarães CR, Udier-Blagovi? M, Jorgensen WL. Macrophomate synthase: QM/MM simulations address the Diels-Alder versus Michael-Aldol reaction mechanism. Journal of the American Chemical Society. 127: 3577-88. PMID 15755179 DOI: 10.1021/Ja043905B  0.342
2004 Acevedo O, Jorgensen WL. Solvent effects and mechanism for a nucleophilic aromatic substitution from QM/MM simulations. Organic Letters. 6: 2881-4. PMID 15330638 DOI: 10.1021/Ol049121K  0.606
2004 Lee PS, Du W, Boger DL, Jorgensen WL. Energetic preferences for alpha,beta versus beta,gamma unsaturation. The Journal of Organic Chemistry. 69: 5448-53. PMID 15287795 DOI: 10.1021/Jo049363Y  0.433
2004 Vayner G, Houk KN, Jorgensen WL, Brauman JI. Steric retardation of SN2 reactions in the gas phase and solution. Journal of the American Chemical Society. 126: 9054-8. PMID 15264838 DOI: 10.1021/Ja049070M  0.378
2004 Udier-Blagovi? M, Morales De Tirado P, Pearlman SA, Jorgensen WL. Accuracy of free energies of hydration using CM1 and CM3 atomic charges. Journal of Computational Chemistry. 25: 1322-32. PMID 15185325 DOI: 10.1002/Jcc.20059  0.359
2004 Udier-Blagović M, Tirado-Rives J, Jorgensen WL. Structural and energetic analyses of the effects of the K103N mutation of HIV-1 reverse transcriptase on efavirenz analogues. Journal of Medicinal Chemistry. 47: 2389-92. PMID 15084137 DOI: 10.1021/Jm0303507  0.381
2004 Ulmschneider JP, Jorgensen WL. Polypeptide folding using Monte Carlo sampling, concerted rotation, and continuum solvation. Journal of the American Chemical Society. 126: 1849-57. PMID 14871118 DOI: 10.1021/Ja0378862  0.682
2004 Tubert-Brohman I, Guimarães CR, Repasky MP, Jorgensen WL. Extension of the PDDG/PM3 and PDDG/MNDO semiempirical molecular orbital methods to the halogens. Journal of Computational Chemistry. 25: 138-50. PMID 14635001 DOI: 10.1002/Jcc.10356  0.788
2004 Jorgensen WL, Ulmschneider JP, Tirado-Rives J. Free energies of hydration from a generalized born model and an all-atom force field Journal of Physical Chemistry B. 108: 16264-16270. DOI: 10.1021/Jp0484579  0.681
2004 Ulmschneider JP, Jorgensen WL. Monte Carlo backbone sampling for nucleic acids using concerted rotations including variable bond angles Journal of Physical Chemistry B. 108: 16883-16892. DOI: 10.1021/Jp047796Z  0.667
2003 Smith MB, Ruby S, Horouzhenko S, Buckingham B, Richardson J, Puleri I, Potts E, Jorgensen WL, Arnold E, Zhang W, Hughes SH, Michejda CJ, Smith RH. HIV-1 reverse transcriptase variants: molecular modeling of Y181C, V106A, L100I, and K103N mutations with nonnucleoside inhibitors using Monte Carlo simulations in combination with a linear response method. Drug Design and Discovery. 18: 151-63. PMID 15553926 DOI: 10.3109/10559610390484203  0.398
2003 Ostrovsky D, Udier-Blagović M, Jorgensen WL. Analyses of activity for factor Xa inhibitors based on Monte Carlo simulations. Journal of Medicinal Chemistry. 46: 5691-9. PMID 14667222 DOI: 10.1021/Jm030288D  0.653
2003 Udier-Blagović M, Watkins EK, Tirado-Rives J, Jorgensen WL. Activity predictions for efavirenz analogues with the K103N mutant of HIV reverse transcriptase. Bioorganic & Medicinal Chemistry Letters. 13: 3337-40. PMID 12951121 DOI: 10.1016/S0960-894X(03)00681-4  0.325
2003 Udier-Blagović M, Tirado-Rives J, Jorgensen WL. Validation of a model for the complex of HIV-1 reverse transcriptase with nonnucleoside inhibitor TMC125. Journal of the American Chemical Society. 125: 6016-7. PMID 12785806 DOI: 10.1021/Ja034308C  0.354
2003 Guimarães CR, Repasky MP, Chandrasekhar J, Tirado-Rives J, Jorgensen WL. Contributions of conformational compression and preferential transition state stabilization to the rate enhancement by chorismate mutase. Journal of the American Chemical Society. 125: 6892-9. PMID 12783541 DOI: 10.1021/Ja021424R  0.797
2003 Repasky MP, Guimarães CR, Chandrasekhar J, Tirado-Rives J, Jorgensen WL. Investigation of solvent effects for the Claisen rearrangement of chorismate to prephenate: mechanistic interpretation via near attack conformations. Journal of the American Chemical Society. 125: 6663-72. PMID 12769575 DOI: 10.1021/Ja021423Z  0.809
2003 Kroeger Smith MB, Hose BM, Hawkins A, Lipchock J, Farnsworth DW, Rizzo RC, Tirado-Rives J, Arnold E, Zhang W, Hughes SH, Jorgensen WL, Michejda CJ, Smith RH. Molecular modeling calculations of HIV-1 reverse transcriptase nonnucleoside inhibitors: correlation of binding energy with biological activity for novel 2-aryl-substituted benzimidazole analogues. Journal of Medicinal Chemistry. 46: 1940-7. PMID 12723956 DOI: 10.1021/Jm020271F  0.707
2003 Ulmschneider JP, Jorgensen WL. Monte Carlo backbone sampling for polypeptides with variable bond angles and dihedral angles using concerted rotations and a Gaussian bias Journal of Chemical Physics. 118: 4261-4271. DOI: 10.1063/1.1542611  0.685
2002 Repasky MP, Chandrasekhar J, Jorgensen WL. PDDG/PM3 and PDDG/MNDO: improved semiempirical methods. Journal of Computational Chemistry. 23: 1601-22. PMID 12395428 DOI: 10.1002/Jcc.10162  0.799
2002 Rizzo RC, Udier-Blagović M, Wang DP, Watkins EK, Kroeger Smith MB, Smith RH, Tirado-Rives J, Jorgensen WL. Prediction of activity for nonnucleoside inhibitors with HIV-1 reverse transcriptase based on Monte Carlo simulations. Journal of Medicinal Chemistry. 45: 2970-87. PMID 12086483 DOI: 10.1021/Jm010580Q  0.69
2002 Repasky MP, Chandrasekhar J, Jorgensen WL. Improved semiempirical heats of formation through the use of bond and group equivalents. Journal of Computational Chemistry. 23: 498-510. PMID 11908087 DOI: 10.1002/Jcc.10023  0.788
2002 Wesolowski SS, Jorgensen WL. Estimation of binding affinities for celecoxib analogues with COX-2 via Monte Carlo-extended linear response. Bioorganic & Medicinal Chemistry Letters. 12: 267-70. PMID 11814774 DOI: 10.1016/S0960-894X(01)00825-3  0.313
2002 Wesolowski SS, Brinkmann NR, Valeev EF, Schaefer HF, Repasky MP, Jorgensen WL. Three-versus four-coordinate phosphorus in the gas phase and in solution: Treacherous relative energies for phosphine oxide and phosphinous acid Journal of Chemical Physics. 116: 112-122. DOI: 10.1063/1.1418440  0.762
2002 Chandrasekhar J, Shariffskul S, Jorgensen WL. QM/MM Simulations for Diels−Alder Reactions in Water:  Contribution of Enhanced Hydrogen Bonding at the Transition State to the Solvent Effect† The Journal of Physical Chemistry B. 106: 8078-8085. DOI: 10.1021/Jp020326P  0.608
2001 Price DJ, Jorgensen WL. Improved convergence of binding affinities with free energy perturbation: application to nonpeptide ligands with pp60src SH2 domain. Journal of Computer-Aided Molecular Design. 15: 681-95. PMID 11718474 DOI: 10.1023/A:1012266200343  0.588
2001 Wang DP, Rizzo RC, Tirado-Rives J, Jorgensen WL. Antiviral drug design: computational analyses of the effects of the L100I mutation for HIV-RT on the binding of NNRTIs. Bioorganic & Medicinal Chemistry Letters. 11: 2799-802. PMID 11597403 DOI: 10.1016/S0960-894X(01)00510-8  0.685
2001 Price ML, Jorgensen WL. Rationale for the observed COX-2/COX-1 selectivity of celecoxib from Monte Carlo simulations. Bioorganic & Medicinal Chemistry Letters. 11: 1541-4. PMID 11412976 DOI: 10.1016/S0960-894X(00)00522-9  0.611
2001 Pierce AC, Jorgensen WL. Estimation of binding affinities for selective thrombin inhibitors via Monte Carlo simulations. Journal of Medicinal Chemistry. 44: 1043-50. PMID 11297451 DOI: 10.1021/Jm000405U  0.732
2001 Rizzo RC, Tirado-Rives J, Jorgensen WL. Estimation of binding affinities for HEPT and nevirapine analogues with HIV-1 reverse transcriptase via Monte Carlo simulations. Journal of Medicinal Chemistry. 44: 145-54. PMID 11170624 DOI: 10.1021/Jm000255N  0.706
2001 Mahoney MW, Jorgensen WL. Quantum, intramolecular flexibility, and polarizability effects on the reproduction of the density anomaly of liquid water by simple potential functions The Journal of Chemical Physics. 115: 10758-10768. DOI: 10.1063/1.1418243  0.61
2001 Mahoney MW, Jorgensen WL. Rapid estimation of electronic degrees of freedom in Monte Carlo calculations for polarizable models of liquid water The Journal of Chemical Physics. 114: 9337-9349. DOI: 10.1063/1.1370083  0.611
2001 Mahoney MW, Jorgensen WL. Diffusion constant of the TIP5P model of liquid water The Journal of Chemical Physics. 114: 363. DOI: 10.1063/1.1329346  0.571
2001 Watkins EK, Jorgensen WL. Perfluoroalkanes:  Conformational Analysis and Liquid-State Properties from ab Initio and Monte Carlo Calculations The Journal of Physical Chemistry A. 105: 4118-4125. DOI: 10.1021/Jp004071W  0.358
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  0.534
2001 Chandrasekhar J, Saunders M, Jorgensen WL. Efficient exploration of conformational space using the stochastic search method: application to ?-peptide oligomers Journal of Computational Chemistry. 22: 1646-1654. DOI: 10.1002/Jcc.1120  0.583
2001 Price MLP, Ostrovsky D, Jorgensen WL. Gas-phase and liquid-state properties of esters, nitriles, and nitro compounds with the OPLS-AA force field Journal of Computational Chemistry. 22: 1340-1352. DOI: 10.1002/Jcc.1092  0.585
2000 Price DJ, Jorgensen WL. Computational binding studies of human pp60c-src SH2 domain with a series of nonpeptide, phosphophenyl-containing ligands. Bioorganic & Medicinal Chemistry Letters. 10: 2067-70. PMID 10999472 DOI: 10.1016/S0960-894X(00)00401-7  0.564
2000 Smith MB, Lamb ML, Tirado-Rives J, Jorgensen WL, Michejda CJ, Ruby SK, Smith RH. Monte Carlo calculations on HIV-1 reverse transcriptase complexed with the non-nucleoside inhibitor 8-Cl TIBO: contribution of the L100I and Y181C variants to protein stability and biological activity. Protein Engineering. 13: 413-21. PMID 10877852 DOI: 10.1093/Protein/13.6.413  0.394
2000 Jorgensen WL, Duffy EM. Prediction of drug solubility from Monte Carlo simulations. Bioorganic & Medicinal Chemistry Letters. 10: 1155-8. PMID 10866370 DOI: 10.1016/S0960-894X(00)00172-4  0.34
2000 Carlson HA, Masukawa KM, Rubins K, Bushman FD, Jorgensen WL, Lins RD, Briggs JM, McCammon JA. Developing a dynamic pharmacophore model for HIV-1 integrase. Journal of Medicinal Chemistry. 43: 2100-14. PMID 10841789 DOI: 10.1021/Jm990322H  0.746
2000 Mahoney MW, Jorgensen WL. A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions The Journal of Chemical Physics. 112: 8910-8922. DOI: 10.1063/1.481505  0.602
2000 Duffy EM, Jorgensen WL. Prediction of properties from simulations: Free energies of solvation in hexadecane, octanol, and water Journal of the American Chemical Society. 122: 2878-2888. DOI: 10.1021/Ja993663T  0.369
2000 Rizzo RC, Wang DP, Tirado-Rives J, Jorgensen WL. Validation of a model for the complex of HIV-1 reverse transcriptase with sustiva through computation of resistance profiles [18] Journal of the American Chemical Society. 122: 12898-12900. DOI: 10.1021/Ja003113R  0.636
2000 Plount Price ML, Jorgensen WL. Analysis of Binding Affinities for Celecoxib Analogues with COX-1 and COX-2 from Combined Docking and Monte Carlo Simulations and Insight into the COX-2/COX-1 Selectivity Journal of the American Chemical Society. 122: 9455-9466. DOI: 10.1021/Ja001018C  0.382
1999 Lamb ML, Tirado-Rives J, Jorgensen WL. Estimation of the binding affinities of FKBP12 inhibitors using a linear response method. Bioorganic & Medicinal Chemistry. 7: 851-60. PMID 10400338 DOI: 10.1016/S0968-0896(99)00015-2  0.377
1999 Kaminski GA, Jorgensen WL. Host–guest chemistry of rotaxanes and catenanes: application of a polarizable all-atom force field to cyclobis(paraquat-p-phenylene) complexes with disubstituted benzenes and biphenyls† Journal of the Chemical Society-Perkin Transactions 1. 2365-2375. DOI: 10.1039/A905160K  0.345
1999 van Hoorn WP, Jorgensen WL. Selective Anion Complexation by a Calix[4]pyrrole Investigated by Monte Carlo Simulations The Journal of Organic Chemistry. 64: 7439-7444. DOI: 10.1021/Jo9907437  0.317
1999 Rizzo RC, Jorgensen WL. OPLS all-atom model for amines: Resolution of the amine hydration problem Journal of the American Chemical Society. 121: 4827-4836. DOI: 10.1021/Ja984106U  0.695
1998 Smith RH, Jorgensen WL, Tirado-Rives J, Lamb ML, Janssen PA, Michejda CJ, Kroeger Smith MB. Prediction of binding affinities for TIBO inhibitors of HIV-1 reverse transcriptase using Monte Carlo simulations in a linear response method. Journal of Medicinal Chemistry. 41: 5272-86. PMID 9857095 DOI: 10.1021/Jm9804174  0.384
1998 Lamb ML, Jorgensen WL. Investigations of neurotrophic inhibitors of FK506 binding protein via Monte Carlo simulations. Journal of Medicinal Chemistry. 41: 3928-39. PMID 9767630 DOI: 10.1021/Jm980062O  0.365
1998 McDonald NA, Jorgensen WL. Development of an All-Atom Force Field for Heterocycles. Properties of Liquid Pyrrole, Furan, Diazoles, and Oxazoles The Journal of Physical Chemistry B. 102: 8049-8059. DOI: 10.1021/Jp981200O  0.342
1998 Rablen PR, Lockman JW, Jorgensen WL. Ab Initio Study of Hydrogen-Bonded Complexes of Small Organic Molecules with Water The Journal of Physical Chemistry A. 102: 3782-3797. DOI: 10.1021/Jp980708O  0.382
1998 Kaminski GA, Jorgensen WL. A Quantum Mechanical and Molecular Mechanical Method Based on CM1A Charges:  Applications to Solvent Effects on Organic Equilibria and Reactions The Journal of Physical Chemistry B. 102: 1787-1796. DOI: 10.1021/Jp980314X  0.351
1998 Price DJ, Roberts JD, Jorgensen WL. Conformational complexity of succinic acid and its monoanion in the gas phase and in solution: Ab initio calculations and Monte Carlo simulations Journal of the American Chemical Society. 120: 9672-9679. DOI: 10.1021/Ja9812397  0.593
1998 McDonald NA, Duffy EM, Jorgensen WL. Monte Carlo investigations of selective anion complexation by a bis(phenylurea) p-tert-butylcalix[4]arene Journal of the American Chemical Society. 120: 5104-5111. DOI: 10.1021/Ja980140X  0.344
1998 Jorgensen WL, McDonald NA. Development of an all-atom force field for heterocycles. Properties of liquid pyridine and diazenes Journal of Molecular Structure: Theochem. 424: 145-155. DOI: 10.1016/S0166-1280(97)00237-6  0.373
1997 Tirado-Rives J, Orozco M, Jorgensen WL. Molecular dynamics simulations of the unfolding of barnase in water and 8 M aqueous urea. Biochemistry. 36: 7313-29. PMID 9200680 DOI: 10.1021/Bi970096I  0.373
1997 Jones-Hertzog DK, Jorgensen WL. Binding affinities for sulfonamide inhibitors with human thrombin using Monte Carlo simulations with a linear response method. Journal of Medicinal Chemistry. 40: 1539-49. PMID 9154975 DOI: 10.1021/Jm960684E  0.389
1997 Essex JW, Severance DL, Tirado-Rives J, Jorgensen WL. Monte Carlo Simulations for Proteins:  Binding Affinities for Trypsin−Benzamidine Complexes via Free-Energy Perturbations The Journal of Physical Chemistry B. 101: 9663-9669. DOI: 10.1021/Jp971990M  0.623
1997 Jenson C, Jorgensen WL. Computational Investigations of Carbenium Ion Reactions Relevant to Sterol Biosynthesis Journal of the American Chemical Society. 119: 10846-10854. DOI: 10.1021/Ja9714245  0.356
1997 Pierce AC, Jorgensen WL. Computational Binding Studies of Orthogonal Cyclosporin-Cyclophilin Pairs Angewandte Chemie International Edition in English. 36: 1466-1469. DOI: 10.1002/Anie.199714661  0.686
1997 Pierce AC, Jorgensen WL. Computergestützte Studien zur Bindung in orthogonalen Cyclosporin-Cyclophilin-Paaren Angewandte Chemie. 109: 1595-1598. DOI: 10.1002/Ange.19971091346  0.652
1997 McDonald NA, Carlson HA, Jorgensen WL. Free energies of solvation in chloroform and water from a linear response approach Journal of Physical Organic Chemistry. 10: 563-576. DOI: 10.1002/(Sici)1099-1395(199707)10:7<563::Aid-Poc912>3.0.Co;2-0  0.634
1996 Kaminski G, Jorgensen WL. Performance of the AMBER94, MMFF94, and OPLS-AA Force Fields for Modeling Organic Liquids The Journal of Physical Chemistry. 100: 18010-18013. DOI: 10.1021/Jp9624257  0.332
1996 Lim D, Jorgensen WL. SCRF/Monte Carlo Study of Solvent Effects on a Polar [2+2] Cycloaddition The Journal of Physical Chemistry. 100: 17490-17500. DOI: 10.1021/Jp962409+  0.369
1996 Jorgensen WL, Maxwell DS, Tirado-Rives, J. Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids Journal of the American Chemical Society. 118: 11225-11236. DOI: 10.1021/Ja9621760  0.634
1996 Carlson HA, Jorgensen WL. Monte Carlo investigations of solvent effects on the chorismate to prephenate rearrangement Journal of the American Chemical Society. 118: 8475-8484. DOI: 10.1021/Ja961500O  0.646
1995 Schreiner PR, Severance DL, Jorgensen WL, von Schleyer P, Schaefer HF. Energy Difference between the Classical and the Nonclassical 2-Norbornyl Cation in Solution. A Combined ab Initio-Monte Carlo Aqueous Solution Study Journal of the American Chemical Society. 117: 2663-2664. DOI: 10.1021/Ja00114A037  0.36
1995 Essex JW, Jorgensen WL. Dielectric constants of formamide and dimethylformamide via computer simulation The Journal of Physical Chemistry. 99: 17956-17962. DOI: 10.1021/J100051A021  0.552
1995 Carlson HA, Jorgensen WL. An Extended Linear Response Method for Determining Free Energies of Hydration The Journal of Physical Chemistry. 99: 10667-10673. DOI: 10.1021/J100026A034  0.577
1995 Carlson HA, Jorgensen WL. Investigations into the stereochemistry of cyclophane-steroid complexes via Monte Carlo simulations Tetrahedron. 51: 449-472. DOI: 10.1016/0040-4020(94)00908-D  0.63
1995 Jorgensen WL, Tirado-Rives J. Free energies of hydration for organic molecules from Monte Carlo simulations Perspectives in Drug Discovery and Design. 3: 123-138. DOI: 10.1007/Bf02174470  0.392
1995 Maxwell DS, Tirado-Rives J, Jorgensen WL. A comprehensive study of the rotational energy profiles of organic systems by ab initio MO theory, forming a basis for peptide torsional parameters Journal of Computational Chemistry. 16: 984-1010. DOI: 10.1002/Jcc.540160807  0.621
1995 Essex JW, Jorgensen WL. An empirical boundary potential for water droplet simulations Journal of Computational Chemistry. 16: 951-972. DOI: 10.1002/Jcc.540160805  0.588
1995 Severance DL, Essex JW, Jorgensen WL. Generalized alteration of structure and parameters: A new method for free-energy perturbations in systems containing flexible degrees of freedom Journal of Computational Chemistry. 16: 311-327. DOI: 10.1002/Jcc.540160306  0.569
1994 Jorgensen WL, Blake JF, Lim D, Severance DL. Investigation of solvent effects on pericyclic reactions by computer simulations Journal of the Chemical Society, Faraday Transactions. 90: 1727. DOI: 10.1039/Ft9949001727  0.366
1994 Helson HE, Jorgensen WL. Computer-Assisted Mechanistic Evaluation of Organic Reactions. 24. Carbene Chemistry The Journal of Organic Chemistry. 59: 3841-3856. DOI: 10.1021/Jo00093A017  0.301
1994 Blake JF, Lim D, Jorgensen WL. Enhanced Hydrogen Bonding of Water to Diels-Alder Transition States. Ab Initio Evidence The Journal of Organic Chemistry. 59: 803-805. DOI: 10.1021/Jo00083A021  0.357
1994 Sinclair S, Jorgensen WL. Computer Assisted Mechanistic Evaluation of Organic Reactions. 23. Dissolving Metal Reductions with Lithium in Liquid Ammonia Including the Birch Reduction The Journal of Organic Chemistry. 59: 762-772. DOI: 10.1021/Jo00083A017  0.319
1994 Evanseck JD, Houk KN, Briggs JM, Jorgensen WL. Quantification of Solvent Effects on the Acidities of Z and E Esters from Fluid Simulations Journal of the American Chemical Society. 116: 10630-10638. DOI: 10.1021/Ja00102A032  0.711
1994 Duffy EM, Jorgensen WL. Structure and Binding for Complexes of Rebek's Acridine Diacid with Pyrazine, Quinoxaline, and Pyridine from Monte Carlo Simulations with an All-Atom Force Field Journal of the American Chemical Society. 116: 6337-6343. DOI: 10.1021/Ja00093A038  0.303
1994 Lim D, Hrovat DA, Borden WT, Jorgensen WL. Solvent Effects on the Ring Opening of Cyclopropanones to Oxyallyls: A Combined ab Initio and Monte Carlo Study Journal of the American Chemical Society. 116: 3494-3499. DOI: 10.1021/Ja00087A040  0.533
1994 Jorgensen WL, Morales de Tirado PI, Severance DL. Monte Carlo Results for the Effect of Solvation on the Anomeric Equilibrium for 2-Methoxytetrahydropyran Journal of the American Chemical Society. 116: 2199-2200. DOI: 10.1021/Ja00084A092  0.311
1994 Kaminski G, Duffy EM, Matsui T, Jorgensen WL. Free Energies of Hydration and Pure Liquid Properties of Hydrocarbons from the OPLS All-Atom Model The Journal of Physical Chemistry. 98: 13077-13082. DOI: 10.1021/J100100A043  0.311
1993 Jorgensen WL, Nguyen TB. Modeling the complexation of substituted benzenes by a cyclophane host in water. Proceedings of the National Academy of Sciences of the United States of America. 90: 1194-200. PMID 11607365 DOI: 10.1073/Pnas.90.4.1194  0.367
1993 Tirado-Rives J, Jorgensen WL. Molecular dynamics simulations of the unfolding of apomyoglobin in water. Biochemistry. 32: 4175-84. PMID 8476847 DOI: 10.1021/Bi00067A004  0.312
1993 Orozco M, Tirado-Rives J, Jorgensen WL. Mechanism for the rotamase activity of FK506 binding protein from molecular dynamics simulations. Biochemistry. 32: 12864-74. PMID 8251509 DOI: 10.1021/Bi00210A040  0.328
1993 Jorgensen WL, Duffy EM, Tirado-Rives J. Computational investigations of protein denaturation : apomyoglobin and chaotrope-arene interactions Philosophical Transactions of the Royal Society A. 345: 87-96. DOI: 10.1098/Rsta.1993.0120  0.37
1993 Jorgensen WL, Severance DL. Limited effects of polarization for Cl−(H2O)n and Na+(H2O)n clusters The Journal of Chemical Physics. 99: 4233-4235. DOI: 10.1063/1.466077  0.303
1993 Tirado-Rives J, Maxwell DS, Jorgensen WL. Molecular dynamics and Monte Carlo simulations favor the a-helical form for alanine-based peptides in water Journal of the American Chemical Society. 115: 11590-11593. DOI: 10.1021/Ja00077A066  0.617
1993 Duffy EM, Kowalczyk PJ, Jorgensen WL. Do denaturants interact with aromatic hydrocarbons in water? Journal of the American Chemical Society. 115: 9271-9275. DOI: 10.1021/Ja00073A050  0.372
1993 Jorgensen WL, Lim D, Blake JF. Ab initio study of Diels-Alder reactions of cyclopentadiene with ethylene, isoprene, cyclopentadiene, acrylonitrile, and methyl vinyl ketone Journal of the American Chemical Society. 115: 2936-2942. DOI: 10.1021/Ja00060A048  0.326
1993 Orozco M, Jorgensen WL, Luque F. Comparison of 6-31G*-based MST/SCRF and FEP evaluations of the free energies of hydration for small neutral molecules Journal of Computational Chemistry. 14: 1498-1503. DOI: 10.1002/Jcc.540141212  0.362
1993 Carlson HA, Nguyen TB, Orozco M, Jorgensen WL. Accuracy of free energies of hydration for organic molecules from 6-31g*-derived partial charges Journal of Computational Chemistry. 14: 1240-1249. DOI: 10.1002/Jcc.540141013  0.618
1993 Jorgensen WL, Laird ER, Nguyen TB, Tirado-Rives J. Monte Carlo simulations of pure liquid substituted benzenes with OPLS potential functions Journal of Computational Chemistry. 14: 206-215. DOI: 10.1002/Jcc.540140208  0.351
1993 Jorgensen WL, Nguyen TB. Monte Carlo simulations of the hydration of substituted benzenes with OPLS potential functions Journal of Computational Chemistry. 14: 195-205. DOI: 10.1002/Jcc.540140207  0.391
1993 Duffy EM, Severance DL, Jorgensen WL. Urea: Potential Functions, logP, and Free Energy of Hydration Israel Journal of Chemistry. 33: 323-330. DOI: 10.1002/Ijch.199300039  0.381
1992 Duffy EM, Severance DL, Jorgensen WL. Solvent effects on the barrier to isomerization for a tertiary amide from ab initio and Monte Carlo calculations Journal of the American Chemical Society. 114: 7535-7542. DOI: 10.1021/Ja00045A029  0.345
1992 Matsui T, Jorgensen WL. Free energy profiles for sodium cation adsorption on a metal electrode Journal of the American Chemical Society. 114: 3220-3226. DOI: 10.1021/Ja00035A009  0.33
1991 Tirado-Rives J, Jorgensen WL. Molecular dynamics simulations of the unfolding of an alpha-helical analogue of ribonuclease A S-peptide in water. Biochemistry. 30: 3864-71. PMID 2018759 DOI: 10.1021/Bi00230A009  0.308
1991 Pranata J, Jorgensen WL. Computational studies on FK506: conformational search and molecular dynamics simulation in water Journal of the American Chemical Society. 113: 9483-9493. DOI: 10.1021/Ja00025A010  0.311
1991 Briggs JM, Nguyen TB, Jorgensen WL. Monte Carlo simulations of liquid acetic acid and methyl acetate with the OPLS potential functions The Journal of Physical Chemistry. 95: 3315-3322. DOI: 10.1021/J100161A065  0.565
1991 Pranata J, Jorgensen WL. Monte Carlo simulations yield absolute free energies of binding for guanine-cytosine and adenine-uracil base pairs in chloroform Tetrahedron. 47: 2491-2501. DOI: 10.1016/S0040-4020(01)81783-X  0.349
1990 Blake JF, Jorgensen WL. Origin of the strong binding of adenine to a molecular tweezer Journal of the American Chemical Society. 112: 7269-7278. DOI: 10.1021/Ja00176A029  0.352
1990 Jorgensen WL, Severance DL. Aromatic-aromatic interactions: free energy profiles for the benzene dimer in water, chloroform, and liquid benzene Journal of the American Chemical Society. 112: 4768-4774. DOI: 10.1021/Ja00168A022  0.343
1990 Jorgensen WL, Briggs JM, Contreras ML. Relative partition coefficients for organic solutes from fluid simulations The Journal of Physical Chemistry. 94: 1683-1686. DOI: 10.1021/J100367A084  0.598
1990 Briggs JM, Matsui T, Jorgensen WL. Monte Carlo simulations of liquid alkyl ethers with the OPLS potential functions Journal of Computational Chemistry. 11: 958-971. DOI: 10.1002/Jcc.540110808  0.613
1989 Jorgensen WL, Briggs JM. A priori pKa calculations and the hydration of organic anions Journal of the American Chemical Society. 111: 4190-4197. DOI: 10.1021/Ja00194A007  0.619
1989 Jorgensen WL. Free energy calculations: a breakthrough for modeling organic chemistry in solution Accounts of Chemical Research. 22: 184-189. DOI: 10.1021/Ar00161A004  0.317
1988 Jorgensen WL, Briggs JM. Monte carlo simulations of liquid acetonitrile with a three-site model Molecular Physics. 63: 547-558. DOI: 10.1080/00268978800100371  0.588
1988 Jorgensen WL, Buckner JK, Boudon S, Tirado‐Rives J. Efficient computation of absolute free energies of binding by computer simulations. Application to the methane dimer in water The Journal of Chemical Physics. 89: 3742-3746. DOI: 10.1063/1.454895  0.37
1988 Jorgensen WL, Gao J. Cis-trans energy difference for the peptide bond in the gas phase and in aqueous solution Journal of the American Chemical Society. 110: 4212-4216. DOI: 10.1021/Ja00221A020  0.518
1988 Gao J, Jorgensen WL. Theoretical examination of hexanol-water interfaces The Journal of Physical Chemistry. 92: 5813-5822. DOI: 10.1021/J100331A053  0.488
1988 Jorgensen WL, Gao J. Monte Carlo simulations of the hydration of ammonium and carboxylate ions [Erratum to document cited in CA104(22):194099Y] The Journal of Physical Chemistry. 92: 3692-3692. DOI: 10.1021/J100323A073  0.497
1988 JORGENSEN WL, BRIGGS JM, GAO J. ChemInform Abstract: A Priori Calculations of pKa′s for Organic Compounds in Water. The pKa of Ethane. Cheminform. 19. DOI: 10.1002/chin.198808060  0.522
1987 Jorgensen WL, Briggs JM, Gao J. A priori calculations of pKa's for organic compounds in water. The pKa of ethane Journal of the American Chemical Society. 109: 6857-6858. DOI: 10.1021/Ja00256A053  0.661
1987 Evanseck JD, Blake JF, Jorgensen WL. Ab initio study of the SN2 reactions of hydroxide and hydroperoxide with chloromethane Journal of the American Chemical Society. 109: 2349-2353. DOI: 10.1021/Ja00242A018  0.654
1987 Jorgensen WL, Buckner JK. Use of statistical perturbation theory for computing solvent effects on molecular conformation: butane in water The Journal of Physical Chemistry. 91: 6083-6085. DOI: 10.1021/J100308A003  0.31
1987 Speedy RJ, Madura JD, Jorgensen WL. Network topology in simulated water The Journal of Physical Chemistry. 91: 909-913. DOI: 10.1021/J100288A029  0.569
1987 EVANSECK JD, BLAKE JF, JORGENSEN WL. ChemInform Abstract: Ab initio Study of the SN2 Reactions of OH- and OOH- with CH3Cl Cheminform. 18. DOI: 10.1002/chin.198734106  0.591
1986 Jorgensen WL, Chandrasekhar J, Buckner JK, Madura JD. Computer simulations of organic reactions in solution. Annals of the New York Academy of Sciences. 482: 198-209. PMID 3471104 DOI: 10.1111/J.1749-6632.1986.Tb20951.X  0.696
1986 Gao J, Garner DS, Jorgensen WL. Ab initio study of structures and binding energies for anion-water complexes Journal of the American Chemical Society. 108: 4784-4790. DOI: 10.1021/Ja00276A016  0.59
1986 Madura JD, Jorgensen WL. Ab initio and Monte Carlo calculations for a nucleophilic addition reaction in the gas phase and in aqueous solution Journal of the American Chemical Society. 108: 2517-2527. DOI: 10.1021/Ja00270A005  0.62
1986 Jorgensen WL, Gao J. Monte Carlo simulations of the hydration of ammonium and carboxylate ions The Journal of Physical Chemistry. 90: 2174-2182. DOI: 10.1021/J100401A037  0.508
1986 Jorgensen WL. Optimized intermolecular potential functions for liquid alcohols The Journal of Physical Chemistry. 90: 1276-1284. DOI: 10.1021/J100398A015  0.338
1986 Jorgensen WL. Intermolecular potential functions and Monte Carlo simulations for liquid sulfur compounds The Journal of Physical Chemistry. 90: 6379-6388. DOI: 10.1021/J100281A063  0.311
1985 Jorgensen WL, Madura JD. Temperature and size dependence for monte carlo simulations of TIP4P water Molecular Physics. 56: 1381-1392. DOI: 10.1080/00268978500103111  0.562
1985 Jorgensen WL, Ravimohan C. Monte Carlo simulation of differences in free energies of hydration The Journal of Chemical Physics. 83: 3050-3054. DOI: 10.1063/1.449208  0.399
1985 Wierschke SG, Chandrasekhar J, Jorgensen WL. Magnitude and origin of the .beta.-silicon effect on carbenium ions Journal of the American Chemical Society. 107: 1496-1500. DOI: 10.1021/Ja00292A008  0.465
1985 Jorgensen WL, Gao J, Ravimohan C. Monte Carlo simulations of alkanes in water: hydration numbers and the hydrophobic effect The Journal of Physical Chemistry. 89: 3470-3473. DOI: 10.1021/J100262A010  0.526
1985 CHANDRASEKHAR J, JORGENSEN WL. ChemInform Abstract: ENERGY PROFILE FOR A NONCONCERTED SN2 REACTION IN SOLUTION Chemischer Informationsdienst. 16. DOI: 10.1002/chin.198542084  0.475
1985 Chandrasekhar J, Jorgensen WL. Energy profile for a nonconcerted SN2 reaction in solution Journal of the American Chemical Society. 107: 2974-2975. DOI: 10.1002/Chin.198542084  0.53
1985 WIERSCHKE SG, CHANDRASEKHAR J, JORGENSEN WL. ChemInform Abstract: MAGNITUDE AND ORIGIN OF THE β-SILICON EFFECT ON CARBENIUM IONS Chemischer Informationsdienst. 16. DOI: 10.1002/chin.198530065  0.404
1985 CHANDRASEKHAR J, SMITH SF, JORGENSEN WL. ChemInform Abstract: THEORETICAL EXAMINATION OF THE SN2 REACTION INVOLVING CHLORIDE ION AND METHYL CHLORIDE IN THE GAS PHASE AND AQUEOUS SOLUTION Chemischer Informationsdienst. 16. DOI: 10.1002/chin.198519097  0.458
1985 Chandrasekhar J, Smith SF, Jorgensen WL. Theoretical examination of the SN2 reaction involving chloride ion and methyl chloride in the gas phase and aqueous solution Journal of the American Chemical Society. 107: 154-163. DOI: 10.1002/Chin.198519097  0.516
1985 JORGENSEN WL, MADURA JD, SWENSON CJ. ChemInform Abstract: OPTIMIZED INTERMOLECULAR POTENTIAL FUNCTIONS FOR LIQUID HYDROCARBONS Chemischer Informationsdienst. 16. DOI: 10.1002/chin.198508061  0.486
1984 Cournoyer ME, Jorgensen WL. An improved intermolecular potential function for simulations of liquid hydrogen fluoride Molecular Physics. 51: 119-132. DOI: 10.1080/00268978400100081  0.347
1984 Jorgensen WL, Madura JD, Swenson CJ. Optimized intermolecular potential functions for liquid hydrocarbons Journal of the American Chemical Society. 106: 6638-6646. DOI: 10.1021/Ja00334A030  0.582
1984 Chandrasekhar J, Smith SF, Jorgensen WL. SN2 reaction profiles in the gas phase and aqueous solution Journal of the American Chemical Society. 106: 3049-3050. DOI: 10.1021/Ja00322A059  0.502
1984 Chandrasekhar J, Spellmeyer DC, Jorgensen WL. Energy component analysis for dilute aqueous solutions of lithium(1+), sodium(1+), fluoride(1-), and chloride(1-) ions Journal of the American Chemical Society. 106: 903-910. DOI: 10.1021/Ja00316A012  0.516
1984 Suryawanshi SN, Swenson CJ, Jorgensen WL, Fuchs PL. Torsional effects in the baeyer-villiger oxidation Tetrahedron Letters. 25: 1859-1862. DOI: 10.1016/S0040-4039(01)90060-7  0.448
1984 Cournoyer ME, Jorgensen WL. Solvent effects on the relative energies of carbonium ions. Solvation and internal rotation for the allyl cation in liquid hydrogen fluoride Journal of the American Chemical Society. 106: 5104-5112. DOI: 10.1002/Chin.198451135  0.323
1984 SURYAWANSHI SN, SWENSON CJ, JORGENSEN WL, FUCHS PL. ChemInform Abstract: BRUCEANTIN SUPPORT STUDIES. 7. TORSIONAL EFFECTS IN THE BAEYER-VILLIGER OXIDATION Chemischer Informationsdienst. 15. DOI: 10.1002/Chin.198435245  0.445
1984 CHANDRASEKHAR J, SMITH SF, JORGENSEN WL. ChemInform Abstract: SN2 REACTION PROFILES IN THE GAS PHASE AND AQUEOUS SOLUTION Chemischer Informationsdienst. 15. DOI: 10.1002/chin.198434086  0.443
1984 CHANDRASEKHAR J, SPELLMEYER DC, JORGENSEN WL. ChemInform Abstract: ENERGY COMPONENT ANALYSIS FOR DILUTE AQUEOUS SOLUTIONS OF LITHIUM(1+), SODIUM(1+), FLUORIDE(1-), AND CHLORIDE(1-) IONS Chemischer Informationsdienst. 15. DOI: 10.1002/chin.198420011  0.458
1983 Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. Comparison of simple potential functions for simulating liquid water The Journal of Chemical Physics. 79: 926-935. DOI: 10.1063/1.445869  0.695
1983 Jorgensen WL. Erratum: Monte Carlo simulation of n‐butane in water. Conformational evidence for the hydrophobic effect [J. Chem. Phys. 77, 5757 (1982)] The Journal of Chemical Physics. 78: 5846-5846. DOI: 10.1063/1.445502  0.313
1983 Jorgensen WL, Madura JD. Quantum and statistical mechanical studies of liquids. 25. Solvation and conformation of methanol in water Journal of the American Chemical Society. 105: 1407-1413. DOI: 10.1021/Ja00344A001  0.554
1983 Smith SF, Chandrasekhar J, Jorgensen WL. Ab initio study of the structures and binding energies of aluminum monocation complexes The Journal of Physical Chemistry. 87: 1898-1902. DOI: 10.1021/J100234A014  0.552
1983 Houk KN, Rondan NG, Brown FK, Jorgensen WL, Madura JD, Spellmeyer DC. Electronic origins and consequences of pyramidalization of asymmetric alkenes in ground and triplet excited states Journal of the American Chemical Society. 105: 5980-5988. DOI: 10.1002/Chin.198351060  0.506
1983 HOUK KN, RONDAN NG, BROWN FK, JORGENSEN WL, MADURA JD, SPELLMEYER DC. ChemInform Abstract: ELECTRONIC ORIGINS AND CONSEQUENCES OF PYRAMIDALIZATION OF ASYMMETRIC ALKENES IN GROUND AND TRIPLET EXCITED STATES Chemischer Informationsdienst. 14. DOI: 10.1002/chin.198351060  0.454
1983 JORGENSEN WL, MADURA JD. ChemInform Abstract: QUANTUM AND STATISTICAL MECHANICAL STUDIES OF LIQUIDS. 25. SOLVATION AND CONFORMATION OF METHANOL IN WATER Chemischer Informationsdienst. 14. DOI: 10.1002/chin.198338076  0.506
1983 CHANDRASEKHAR J, JORGENSEN WL. ChemInform Abstract: THE NATURE OF DILUTE SOLUTIONS OF SODIUM ION IN WATER, METHANOL, AND TETRAHYDROFURAN Chemischer Informationsdienst. 14. DOI: 10.1002/chin.198305068  0.442
1983 CHANDRASEKHAR J, JORGENSEN WL. ChemInform Abstract: MONTE CARLO SIMULATIONS OF LIQUID TETRAHYDROFURAN INCLUDING PSEUDOROTATION Chemischer Informationsdienst. 14. DOI: 10.1002/chin.198305067  0.468
1982 Jorgensen WL. Revised TIPS for simulations of liquid water and aqueous solutions The Journal of Chemical Physics. 77: 4156-4163. DOI: 10.1063/1.444325  0.339
1982 Jorgensen WL, Bigot B, Chandrasekhar J. Quantum and statistical mechanical studies of liquids. 21. The nature of dilute solutions of sodium and methoxide ions in methanol Journal of the American Chemical Society. 104: 4584-4591. DOI: 10.1021/Ja00381A013  0.498
1982 Smith SF, Chandrasekhar J, Jorgensen WL. Ab initio study of acid-base interactions. Proton, lithium, and sodium affinities of first- and second-row bases The Journal of Physical Chemistry. 86: 3308-3318. DOI: 10.1021/J100214A010  0.529
1982 Jorgensen WL. Convergence of Monte Carlo simulations of liquid water in the NPT ensemble Chemical Physics Letters. 92: 405-410. DOI: 10.1016/0009-2614(82)83437-4  0.301
1982 Jorgensen WL. Monte Carlo simulation of n‐butane in water. Conformational evidence for the hydrophobic effect The Journal of Chemical Physics. 77: 5757-5765. DOI: 10.1002/Chin.198308060  0.31
1982 Chandrasekhar J, Jorgensen WL. The nature of dilute solutions of sodium ion in water, methanol, and tetrahydrofuran The Journal of Chemical Physics. 77: 5080-5089. DOI: 10.1002/Chin.198305068  0.501
1982 Chandrasekhar J, Jorgensen WL. Monte Carlo simulations of liquid tetrahydrofuran including pseudorotation The Journal of Chemical Physics. 77: 5073-5079. DOI: 10.1002/Chin.198305067  0.524
1982 JORGENSEN WL, BIGOT B, CHANDRASEKHAR J. ChemInform Abstract: QUANTUM AND STATISTICAL MECHANICAL STUDIES OF LIQUIDS. 21. THE NATURE OF DILUTE SOLUTIONS OF SODIUM AND METHOXIDE IONS IN METHANOL Chemischer Informationsdienst. 13. DOI: 10.1002/chin.198247075  0.439
1981 Jorgensen WL. Comment on simulations of liquid ammonia based on quantum mechanical potential functions The Journal of Chemical Physics. 75: 2026-2027. DOI: 10.1063/1.442239  0.331
1981 Jorgensen WL. Quantum and statistical mechanical studies of liquids. 11. Transferable intermolecular potential functions. Application to liquid methanol including internal rotation Journal of the American Chemical Society. 103: 341-345. DOI: 10.1021/Ja00392A017  0.353
1981 Jorgensen WL. Quantum and statistical mechanical studies of liquids. 10. Transferable intermolecular potential functions for water, alcohols, and ethers. Application to liquid water Journal of the American Chemical Society. 103: 335-340. DOI: 10.1021/Ja00392A016  0.335
1981 Smith SF, Jorgensen WL, Fuchs PL. PULSAR: a personalized microcomputer-based system for keyword search and retrieval of literature information Journal of Chemical Information and Modeling. 21: 209-213. DOI: 10.1021/Ci00032A006  0.434
1981 Jorgensen WL, Ibrahim M. Ab initio studies of RO? ? HOR? complexes. Solvent effects on the relative acidities of water and methanol Journal of Computational Chemistry. 2: 7-11. DOI: 10.1002/Jcc.540020103  0.351
1980 Jorgensen W. Additions and Corrections - Deriving Intermolecular Potential Functions for the Water Dimer from Ab Initio Calculations Journal of the American Chemical Society. 102: 7619-7619. DOI: 10.1021/Ja00545A608  0.318
1980 Jorgensen WL, Ibrahim M. Structure and properties of liquid ammonia Journal of the American Chemical Society. 102: 3309-3315. DOI: 10.1021/Ja00530A001  0.388
1980 Jorgensen WL. Quantum and statistical mechanical studies of liquids. 7. Structure and properties of liquid methanol Journal of the American Chemical Society. 102: 543-549. DOI: 10.1021/Ja00522A018  0.342
1979 Jorgensen WL. Basis set dependence of the structure and properties of liquid hydrogen fluoride The Journal of Chemical Physics. 70: 5888-5897. DOI: 10.1063/1.437418  0.381
1979 Borden WT, Young SD, Frost DC, Westwood NPC, Jorgensen WL. Photoelectron spectra of the 1,2,5,6-tetramethyl-3,4,7,8-tetramethylene derivatives of tricyclo[3.3.0.02,6]octane and tricyclo[4.2.0.02,5]octane The Journal of Organic Chemistry. 44: 737-740. DOI: 10.1021/Jo01319A016  0.449
1979 Jorgensen WL. Quantum and statistical mechanical studies of liquids. 3. Deriving intermolecular potential functions for the water dimer from ab initio calculations Journal of the American Chemical Society. 101: 2011-2016. DOI: 10.1021/Ja00502A014  0.31
1979 Day R, Krause D, Jorgensen W, Cooks R. Energy partitioning accompanying fragmentation of protonated methanol International Journal of Mass Spectrometry and Ion Physics. 30: 83-92. DOI: 10.1016/0020-7381(79)80045-5  0.355
1979 Jorgensen WL. An intermolecular potential function for the methanol dimer from ab initio calculations The Journal of Chemical Physics. 71: 5034. DOI: 10.1002/Chin.198014073  0.305
1978 Borden WT, Gold A, Jorgensen WL. Cycloaddition reactions of 1,2,5,6-tetramethyl-3,4,7,8-tetramethylenetricyclo[3.3.0.02,6]octane. Evidence for chemical consequences of orbital interactions in molecules containing unsaturatively 1,3-bridged cyclobutane rings The Journal of Organic Chemistry. 43: 491-497. DOI: 10.1021/Jo00397A024  0.514
1978 Jorgensen WL, Cournoyer ME. Chemical consequences of orbital interactions. 14. Ab initio molecular orbital study of the geometries, properties, and protonation of simple organofluorides Journal of the American Chemical Society. 100: 1057-1061. DOI: 10.1021/Ja00472A006  0.304
1978 Krause D, Day R, Jorgensen W, Cooks R. MINDO/3 calculation of the potential energy surface for C3H5+ → C3H3+ + H2 as applied to understanding energy partitioning accompanying fragmentation International Journal of Mass Spectrometry and Ion Physics. 27: 227-237. DOI: 10.1016/0020-7381(78)80110-7  0.349
1978 Jorgensen WL. Proton affinity correlations for alkyl chlorides Chemical Physics Letters. 53: 525-529. DOI: 10.1016/0009-2614(78)80061-X  0.315
1978 Jorgensen WL. Chemical consequences of orbital interactions. 13. Ab initio molecular orbital study of the geometries, properties, and protonation of alkyl chlorides Journal of the American Chemical Society. 100: 1057-1061. DOI: 10.1002/Chin.197823065  0.317
1977 Jorgensen WL. Chemical consequences of orbital interactions. 8. The importance of the counterion. The relative energies of homocubyl cations and ion pairs Journal of the American Chemical Society. 99: 4272-4276. DOI: 10.1021/Ja00455A010  0.307
1977 Jorgensen WL, Munroe JE. The influence of increasing solvation on the relative energies of bisected and bridged ethyl cations Tetrahedron Letters. 18: 581-584. DOI: 10.1016/S0040-4039(01)92699-1  0.318
1976 Corey EJ, Jorgensen WL. Computer-assisted synthetic analysis. Generation of synthetic sequences involving sequential functional group interchanges Journal of the American Chemical Society. 98: 203-209. DOI: 10.1021/Ja00417A031  0.365
1976 Corey EJ, Jorgensen WL. Computer-assisted synthetic analysis. Synthetic strategies based on appendages and the use of reconnective transforms Journal of the American Chemical Society. 98: 189-203. DOI: 10.1021/Ja00417A030  0.359
1975 Jorgensen WL, Borden WT. Orbital interactions in molecules containing unsaturatively bridged cyclobutane and bicyclobutane rings Tetrahedron Letters. 16: 223-226. DOI: 10.1016/S0040-4039(00)71828-4  0.498
1973 Jorgensen WL, Borden WT. Chemical consequences of orbital interactions in hydrocarbons containing unsaturativety bridged small rings Journal of the American Chemical Society. 95: 6649-6654. DOI: 10.1021/Ja00801A021  0.498
1971 Allen LC, Jorgensen WL. Charge-density analysis of rotational barriers Journal of the American Chemical Society. 93: 567-574. DOI: 10.1021/Ja00732A001  0.489
1971 JORGENSEN WL, ALLEN LC. ChemInform Abstract: LADUNGSDICHTEANALYSE VON ROTATIONSBARRIEREN Chemischer Informationsdienst. Organische Chemie. 2: no-no. DOI: 10.1002/Chin.197117112  0.47
1970 Davidson RB, Jorgensen WL, Allen LC. Structural and energetic predictions for simple hydrocarbons from the NDDO [neglect of diatomic differential overlap] and CNDO [complete neglect of differential overlap] semiempirical molecular orbital methods Journal of the American Chemical Society. 92: 749-753. DOI: 10.1021/Ja00707A001  0.519
1970 Jorgensen WL, Allen LC. Charge distribution characteristics of attractive dominant barriers Chemical Physics Letters. 7: 483-485. DOI: 10.1016/0009-2614(70)80153-1  0.537
1970 DAVIDSON RB, JORGENSEN WL, ALLEN LC. ChemInform Abstract: STRUKTUR- UND ENERGIE-VORAUSBERECHNUNGEN FUER EINFACHE KOHLENWASSERSTOFFE DURCH NDDO- UND CNDO-HALBEMPIRISCHE MO-METHODEN Chemischer Informationsdienst. Organische Chemie. 1: no-no. DOI: 10.1002/Chin.197019049  0.527
Show low-probability matches.