Publications

483. Free Energies of Solvation in Cyclohexane and Water: United-Atom vs All-Atom. Jorgensen, W. L.; Tirado-Rives, J.. J. Chem. Theory Comput. 2026, 22, 7581-7593. doi:10.1021/acs.jctc.6c00989

482. Polycyclic Aromatic Hydrocarbons: Solvation, Solubility, and Hydrophobic Effects from Monte Carlo Simulations. Jorgensen, W. L.; Tirado-Rives, J.. J. Phys. Chem. B 2025, 129, 10467-10477. doi:10.1021/acs.jpcb.5c05354

481. Mechanistic basis for a novel dual-function Gag-Pol dimerizer potentiating CARD8 inflammasome activation and clearance of HIV-infected cells. Hollander, K.; Devarkar, S. C.; Tang, S.; Tiwari, R.; Ma, S.; Lee, W.; Denn, E. R.; Wang, Q.; Spasov, K. A.; Robbins, J. A.; Frey, K. M.; Jorgensen, W. L.; Xiong, Y.; Shan, L.; Anderson, K. S.. npj Drug Discov. 2025, 2, 22. doi:10.1038/s44386-025-00025-2

480. The need to implement FAIR principles in biomolecular simulations. Amaro, R. E.; et al., incl. Jorgensen, W. L.. Nat. Methods 2025, 22, 641-645. doi:10.1038/s41592-025-02635-0

479. Free Energies of Solvation in Benzene and Hexafluorobenzene: Is Explicit Polarization Needed?. Jorgensen, W. L.; Tirado-Rives, J. J. Phys. Chem. B 2025, 129, 6574-6583. doi:10.1021/acs.jpcb.5c02405

478. Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (Mpro) with Noncovalent Preclinical Candidate, Mpro61. Kenneson, J. R.; Papini, C.; Tang, S.; Huynh,K.; Zhang, C-H.; Jorgensen, W. L.; Anderson, K. S. ACS Bio & Med Chem Au 2025, 5, 215-226. doi:10.1021/acsbiomedchemau.4c00109

477. The Beginnings of JCTC. Jorgensen, W. L. J. Chem. Theory Comput 2024, 20, 7692-7693. doi:10.1021/acs.jctc.4c01146

476. Monte Carlo simulations for free energies of hydration: Past to present. Jorgensen, W. L. J. Chem. Phys 2024, 161, 064111. doi:10.1063/5.0222659

475. Prodrug nanotherapy demonstrates in vivo anticryptosporidial efficacy in a mouse model of chronic Cryptosporidium infection. Ranjan, A. P.; Czyzyk, D. J.; Martinez-Traverso, G.; Sadiqova, A.; Valhondo, M.; Schaefer, D. A.; Spasov, K. A.; Jorgensen, W. L.; Vishwanatha, J. K.; Riggs, M. V.; Castellanos-Gonzalez, A.; Anderson, K. S. RSC pharmaceutics 2024, 1, 963-975. doi:10.1039/D4PM00093E

474. Proof-of-Concept Studies with a Computationally Designed Mpro Inhibitor as a Synergistic Combination Regimen Alternative to Paxlovid. Papini, C.; Ullah, I.; Ranjan, A. P.; Zhang, S.'Wu, Q.; Spasov, K. A.; Zhang, C.; Mothes, W.; Crawford, J. M.; Lindenbach, B. D.; Uchil. P. D.; Kumar, P.; Jorgensen, W. L.; Anderson, K. S. Proc. Nat. Acad. Sci. USA 2024, 121, e2320713121. doi:10.1073/pnas.2320713121

473. Enthalpies and Entropies of Hydration From Monte Carlo Simulations. Jorgensen, W. L. Phys. Chem. Chem. Phys 2024, 26, 8141-8147. doi:10.1039/D4CP00297K

472. OPLS/2020 Force Field for Unsaturated Hydrocarbons, Alcohols, and Ethers. Jorgensen, W. L.; Ghahremanpour, M. M.; Saar, A.; Tirado-Rives, J. J. Phys. Chem. B 2024, 128, 250-262. doi:10.1021/acs.jpcb.3c06602

471. Ensemble Geometric Deep Learning of Aqueous Solubility. Ghahremanpour, M. M.; Saar, A.; Tirado-Rives, J.; Jorgensen, W. L. J. Chem. Inf. Model 2023, 63, 7338-7349. doi:10.1021/acs.jcim.3c01536

470. A High-Throughput, High-Containment Human Primary Epithelial Airway Organ-on-Chip Platform for SARS-CoV-2 Therapeutic Screening. Fisher, C. R.; Medie, F. M.; Luu, R. J.; Gaibler, R. B.; Mulhern, T. J.; Miller, C. R.; Zhang, C. J.; Rubio, L. D.; Marr, E. E.; Vijayakumar, V.; Gabriel, E. P; Lopez Quezada, L.; Zhang, C.-H.; Anderson, K. S. Jorgensen, W. L.; Alladina, J. W.;cMedoff, B. D.; Borenstein, J. T.; Gard, A. L. Cells 2023, 12, 2639. doi:10.3390/cells12222639

469. Assessing Metadynamics and Docking for Absolute Binding Free Energy Calculations Using Severe Acute Respiratory Syndrome Coronavirus 2 Main Protease Inhibitors. Saar, A.; Ghahremanpour, M. M.; Tirado-Rives, J.; Jorgensen, W. L. J. Chem. Inf. Model 2023, 63, 7210-7218. doi:10.1021/acs.jcim.3c01453

468. Covalent and Noncovalent Strategies for Targeting Lys102 in HIV-1 Reverse Transcriptase. Prucha, G. R.; Henry, S.; Hollander, K.; Carter, Z.; J.; Spasov, K. A.; Jorgensen, W. L.; Anderson, K, S. Eur. J. Med. Chem 2023, 262, 115984. doi:10.1016/j.ejmech.2023.115894

467. Exploring Novel HIV-1 Reverse Transcriptase Inhibitors with Drug Resistant Mutants: A Double Mutant Surprise. Hollander, K,; Chan, A. H.; Frey, K. M.; Hunker, O.; Ippolito, J. A.; Spasov, K. A.; Yeh, Y. J.; Jorgensen, W. L.; Ho, Y.; Anderson, K. S. Protein Sci 2023, 32, e4814. doi:10.1002/pro.4814

466. Computation of Absolute Binding Free Energies for Noncovalent Inhibitors with SARS-CoV-2 Main Protease. Ghahremanpour, M. M.; Saar, A.; Tirado-Rives, J.; Jorgensen, W. L. J. Chem. Inf. Model 2023, 63, 5309-5318. doi:10.1021/acs.jcim.3c00874

465. Progress on the Pharmacological Targeting of Janus Pseudokinases. Henry, S. P.; Jorgensen, W. L. J Med. Chem 2023, 66, 10959-10990. doi:10.1021/acs.jmedchem.3c00926

464. Design, synthesis, and biological testing of biphenylmethyloxazole inhibitors targeting HIV-1 reverse transcriptase. Carter, Z. J.; Hollander, K, A.; Spasov, K. A.; Anderson, K, S,; Jorgensen, W. L. Bioorg. Med. Chem. Lett 2023, 84, 129216. doi:10.1016/j.bmcl.2023.129216

463. Structural Studies and Structure Activity Relationships for Novel Computationally Designed Non-nucleoside Inhibitors and Their Interactions With HIV-1 Reverse Transcriptase. Frey, K. M.; Bertoletti, N.; Chan, A. H.; Ippolito, J. A.; Bollini, M.; Spasov, K. A.; Jorgensen, W. L.; Anderson, K. S.. Front. Mol. Biosci. 2022, 9, 805187. doi:10.3389/fmolb.2022.805187

462. Long-acting and extended-release implant and nanoformulations with a synergistic antiretroviral two-drug combination controls HIV-1 infection in a humanized mouse model. Beloor, J.; Kudalkar, S. N.; Buzzelli, G.; Yang, F.; Mandl, H. K.; Rajashekar, J. K.; Spasov, K. A.; Jorgensen, W. L.; Saltzman, W. M.; Anderson, K. S.; Kumar, P.. Bioeng. Transl. Med. 2022, 7, e10237. doi:10.1002/btm2.10237

461. Covalent Modification of the JH2 Domain of Janus Kinase 2. Henry, S. P.; Liosi, M-E.; Ippolito, J. A.; Menges, F.; Newton, A. S.; Schlessinger, J,; Jorgensen, W. L. ACS Med. Chem. Lett 2022, 13, 1819-1826. doi:10.1021/acsmedchemlett.2c00414

460. Refinement of the Optimized Potentials for Liquid Simulations Force Field for Thermodynamics and Dynamics of Liquid Alkanes. Ghahremanpour, M. M.; Tirado-Rives, J.; Jorgensen, W. L. J. Phys. Chem. B 2022, 126, 5896-5907. doi:10.1021/acs.jpcb.2c03686

459. Insights on JAK2 Modulation by Potent, Selective, and Cell-Permeable Pseudokinase-Domain Ligands. Liosi, M.-E.; Ippolito, J. A.; Henry, S. P. Krimmer, S. G.; Newton, A. S.; Cutrona, K. J.; Olivarez, R. A.; Mohanty, J.; Schlessinger, J.; Jorgensen, W. L. J. Med. Chem 2022, 13, 819-826. doi:10.1021/acs.jmedchem.2c00283

458. Conversion of a False Virtual Screen Hit into Selective JAK2 JH2 Domain Binders Using Convergent Design Strategies. Henry, S. P.; Liosi, M-E.; Ippolito, J. A.; Cutrona, K. J.; Krimmer, S. G.; Newton, A. S.; Schlessinger, J.; Jorgensen, W. L. ACS Med. Chem. Lett 2022, 12, 819-826. doi:10.1021/acsmedchemlett.2c00051

457. Optimization of Triarylpyridinone Inhibitors of the Main Protease of SARS-CoV-2 to Low-Nanomolar Antiviral Potency. Zhang, C.-H.; Spasov, K. A.; Reilly, R. A.; Hollander, K. A.; Stone, E. A.; Ippolito, J. A.; Liosi, M.-E.; Deshmukh, M. G.; Tirado-Rives, J.; Zhang, S.; Liang, Z.; Miller, S. J.; Isaacs, F.; Lindenbach, B. D.; Anderson, K. S.; Jorgensen, W. L. ACS Med. Chem. Lett 2021, 12, 1325-1332. doi:10.1021/acsmedchemlett.1c00326

456. Indoloxytriazines as Binding Molecules for the JAK2 JH2 Pseudokinase Domain and its V617F Variant. Newton, A. S.; Liosi, M.-E.; Henry, S. P.; Deiana, L.; Faver, J. C.; Krimmer, S. G.; Puleo, D. E.; Schlessinger, J.; Jorgensen, W. L. Tetrahedron Lett 2021, 153248. doi:10.1016/j.tetlet.2021.153248

455. Structure-guided Design of a Perampanel-derived Pharmacophore Targeting the SARS-CoV-2 Main Protease. Deshmukh, M. G.; Ippolito, J. A.; Zhang, C.-H.; Stone, E. A.; Reilly, R. A.; Miller, S. J.; Jorgensen, W. L.; Anderson, K. S.;. Structure 2021, 29, 823-833. doi:10.1016/j.str.2021.06.002

454. Potent Noncovalent Inhibitors of the Main Protease of SARS-CoV2 from Molecular Sculpting of the Drug Perampanel Guided by Free Energy Perturbation Calculations. Zhang, C-H.; Stone, E. A.; Deshmukh, M.; Ippolito, J. A.; Ghahremanpour, M. M.; Tirado-Rives, J.; Spasov, K. A.; Zhang, S.; Takeo, Y.; Kudalkar, S. N.; Liang, Z.; Isaacs, F.; Lindenbach, B.; Miller, S. J.; Anderson, K. S.; Jorgensen, W. L. ACS Cent. Sci 2021, 7, 467-475. doi:10.1021/acscentsci.1c00039

453. Covalent Inhibition of Wild-Type HIV-1 Reverse Transcriptase Using a Fluorosulfate Warhead. Ippolito, J. A.; Niu, H.; Bertoletti, N.; Carter, Z. J.; Jin, S.; Spasov, K. A.; Cisneros, J. A.; Valhondo, M.; Cutrona, K. J.; Anderson, K. S.; Jorgensen, W. L. ACS Med. Chem. Lett 2021, 12, 249-255. doi:10.1021/acsmedchemlett.0c00612

452. Identification of 14 Known Drugs as Inhibitors of the Main Protease of SARS-CoV-2. Ghahremanpour, M.; Tirado-Rives, J.; Deshmukh, M.; Ippolito, J. A.; Zhang, C.-H.; Cabeza de Vaca, I.; Liosi, M.-E.; Anderson, K. S.; Jorgensen, W. L. ACS Med. Chem. Lett 2020, 11, 2526-2533. doi:10.1021/acsmedchemlett.0c00521

451. Explicit Representation of Cation-π Interactions in Force Fields with 1/r⁴ Non-bonded Terms. Turupcu, A.; Tirado-Rives, J.; Jorgensen, W. L. J. Chem. Theory Comput 2020, 16, 7184-7194. doi:10.1021/acs.jctc.0c00847

450. Structural Investigation of 2-Naphthyl Phenyl Ether Inhibitors Bound to WT and Y181C Reverse Transcriptase Highlights Key Features of the NNRTI Binding Site. Duong, V. N.; Ippolito, J. A.; Chan, A. H.; Lee, W.-G.; Spasov, K. S.; Jorgensen, W. L.; Anderson, K. S. Protein Sci 2020, 29, 1902-1910. doi:10.1002/pro.3910

449. Targeting the TS dimer interface in bifunctional Cryptosporidium hominis TS-DHFR from parasitic protozoa: Virtual screening identifies novel TS allosteric inhibitors. Ruiz, V. G.; Czyzyk, D. J.; Kumar, V. P.; Jorgensen, W. L.; Anderson, K. S. Bioorg. Med. Chem. Lett 2020, 30, 127292. doi:10.1016/j.bmcl.2020.127292

448. Metadynamics as a Post-Processing Method for Virtual Screening with Application to the Pseudokinase Domain of JAK2. Cutrona, K. J.; Newton, A. S.; Krimmer, S. G.; Tirado-Rives, J.; Jorgensen, W. L. J. Chem. Info. Model 2020, 60, 4403-4415. doi:10.1021/acs.jcim.0c00276

447. Structure-Guided Identification of DNMT3B Inhibitors. Newton, A. S.; John C. Faver, J. C.; Micevic, G.; Muthusamy, V.; Kudalkar, S. N.; Bertoletti, N.; Anderson, K. S.; Bosenberg, M. W.; Jorgensen, W. L. ACS Med. Chem. Lett 2020, 11, 971-976. M. Botta Memorial Issue. doi:10.1021/acsmedchemlett.0c00011

446. Selective JAK2 Pseudokinase Ligands with a Diaminotriazole Core. Liosi, M.-E.; Krimmer, S. G.; Newton, A. S.; Dawson, T. K.; Puleo, D. E.; Cutrona, K. J.; Schlessinger, J.; Jorgensen, W. L. J. Med. Chem 2020, 63, 5324-5340. doi:10.1021/acs.jmedchem.0c00192

445. Absolute Free Energy of Binding Calculations for Macrophage Migration Inhibitory Factor in Complex with a Drug-like Inhibitor. Qian, Y.; Cabeza de Vaca, I.; Vilseck, J. Z.; Cole, D. J.; Tirado-Rives, J.; Jorgensen, W. L. J. Phys. Chem. B 2019, 123, 8675-8685. doi:10.1021/acs.jpcb.9b07588

444. Structure Activity Relationship Towards the Design of Cryptosporidium Specific Thymidylate Synthase Inhibitors. Czyzyk, D.; Valhondo, M.; Tirado-Rives, J.; Jorgensen, W. L.; Anderson, K. S. Eur. J. Med. Chem 2019, 183, 111673. doi:10.1016/j.ejmech.2019.111673

443. Molecular and Cellular Studies Evaluating a Potent 2-Cyanoindolizine Catechol Diether NNRTI Targeting Wildtype and Y181C Mutant HIV-1 Reverse Transcriptase. Sasaki, T.; Gannam, Z. T. K.; Kudalkar, S. N.; Frey, K. M.; Lee, W.-G.; Spasov, K. A.; Jorgensen, W. L.; Anderson, K. S. Bioorg. Med. Chem. Lett 2019, 29, 2182-2188. doi:10.1016/j.bmcl.2019.06.047

442. QM/MM Calculations for the Cl- + CH3Cl SN2 Reaction in Water Using CM5 Charges and Density Functional Theory. Tirado-Rives, J.; Jorgensen, W. L. J. Phys. Chem. B 2019, 123, 5713-5717. Leo Radom Festschrift. doi:10.1021/acs.jpca.9b04121

441. Understanding the Structural Basis of Species Selective, Stereospecific Inhibition for Cryptosporidium and Human Thymidylate Synthase. Czyzyk, D.J.; Valhondo, M.; Jorgensen, W. L.; Anderson, K.S. FEBS Lett 2019, 593, 2069-2078. doi:10.1002/1873-3468.13474

440. In Vivo Anticryptosporidial Efficacy of a Prodrug Nanotherapy in a Mouse Model of Cryptosporidium Infection. Ranjan, A.P.; Czyzyk, D.J.; Martinez-Traverso, G.; Valhondo, M.; Jorgensen, W.L; Vishwanatha, J.K.; Castellanos-Gonzalez, A.; Anderson, K.S. Antimicrob. Agents Chemother 2019, 00, 0000-0000. Submitted.

439. Structural and Pharmacological Evaluation of a Novel Non-nucleoside Reverse Transcriptase Inhibitor as a Promising Long Acting Nanoformulation for Treating HIV. Kudalkar, S. N.; Ullah, I.; Bertoletti, N.; Mandl, H.; Cisneros, J. A.; Beloor, J.; Chan, A. H.; Saltzman, W. M.; Jorgensen, W. L.; Kumar, P.; Anderson, K. S. Antiviral Res 2019, 167, 110-116. PMID: 31034849. doi:10.1016/j.antiviral.2019.04.010

438. Robust FEP Protocols for Creating Molecules in Solution. Cabeza de Vaca, I.; Zarzuela, R.; Tirado-Rives, J.; Jorgensen, W. L. J. Chem. Theory Comput 2019, 15, 3941-3948. doi:10.1021/acs.jctc.9b00213

437. Development and Testing of the OPLS-AA/M Force Field for RNA. Robertson, M. J.; Qian, Y.; Robinson, M. C.; Tirado-Rives, J.; Jorgensen, W.L. J. Chem. Theory Comput 2019, 15, 2734-2742. doi:10.1021/acs.jctc.9b00054

436. Computation of Protein-Ligand Binding Free Energies using Quantum Mechanical Bespoke Force Fields. Cole, D.; Cabeza de Vaca, I.; Jorgensen, W.L. Med. Chem. Commun 2019, 10, Advanced. doi:10.1039/C9MD00017H

435. Novel Allosteric Covalent Inhibitors of Bifunctional Cryptosporidium hominis TS-DHFR from Parasitic Protozoa Identified by Virtual Screening. Ruiz, V.; Czyzyk, D. J.; Valhondo, M.; Jorgensen, W. L.; Anderson, K. S. Bioorg. Med. Chem. Lett 2019, 29, 1413-1418. PMID: 30929953. doi:10.1016/j.bmcl.2019.03.022

434. Unbinding Dynamics of Non-Nucleoside Inhibitors from HIV-1 Reverse Transcriptase. Dodda, L. S.; Tirado-Rives, J.; Jorgensen, W.L. J. Phys. Chem. B 2019, 123(8), 1741-1748. doi:10.1021/acs.jpcb.8b10341

433. Molecular Dynamics Simulations of a Conformationally Mobile Peptide-Based Catalyst for Atroposelective Bromination. Yan, X. C.; Metrano, A. J.; Robertson, M. J.; Abascal, N. C.; Tirado-Rives, J.; Miller, S. J.; Jorgensen, W.L. ACS Catalysis 2018, 8(11), 9968-9979. doi:10.1021/acscatal.8b03563

432. Optimization of Pyrazoles as Phenol Surrogates to Yield Potent Inhibitors of Macrophage Migration Inhibitory Factor. Trivedi-Parmar, V.; Robertson, M. J.; Cisneros, J. A.; Krimmer, S. G.; Jorgensen, W.L. ChemMedChem 2018, 13(11), 1092-1097. doi:10.1002/cmdc.201800158

431. Advances and Insights for Small Molecule Inhibition of Macrophage Migration Inhibitory Factor. Trivedi-Parmar, V.; Jorgensen, W.L. J. Med. Chem 2018, 61(18), 8104-8119. doi:10.1021/acs.jmedchem.8b00589

430. Enhanced Monte Carlo Methods for Modeling Proteins Including Computation of Absolute Free Energies of Binding. Cabeza de Vaca, I.; Qian, Y.; VIlseck, J. Z.; Tirado-Rives, J.; Jorgensen, W.L. J. Chem. Theoty Comput 2018, 14(6), 3279-3288. doi:10.1021/acs.jctc.8b00031

429. Computationally-guided optimization of small-molecule inhibitors of the Aurora A kinase–TPX2 protein–protein interaction. Cole, D. J.; Janecek, M.; Stokes, J. E.; Rossmann, M.; Faver, J. C.; McKenzie, G. J.; Venkitaraman, A. R.; Hyvönen, M.; Spring, D. R.; Huggins, D. J.; Jorgensen, W. L.. Chem. Commun. 2017, 53, 9372-9375. doi:10.1039/c7cc05379g

428. From In Silico Hit to Long-Acting Late-Stage Preclinical Candidate to Combat HIV-1 Infection. Kudalkar, S.N.; Beloor, J.; Quijano, E.;Spasov, K.A., Lee, W-G.; Cisneros, J. A., Saltzman, W.M.; Kumar, P.; Jorgensen, W.L.; Anderson, K.S. Proc. Nat. Acad. Sci., USA 2017, 115(4), E802-E811. doi:10.1073/pnas.1717932115

427. Adding a Hydrogen Bond May Not Help: Naphthyridinone vs Quinoline Inhibitors of Macrophage Migration Inhibitory Factor. Dawson T. K.; Dziedzic, P.; Robertson, M.J.; Cisneros, J. A.,Krimmer, S.G.; Newton, A.S.;Tirado-Rives, J.; Jorgensen, W. L. ACS Med. Med. Chem. Lett 2017, 8(12), 1287-1291. doi:10.1021/acsmedchemlett.7b00384

426. Covalent inhibitors for eradication of drug-resistant HIV-1 reverse transcriptase: From design to protein crystallography. Chan A. H.; Lee W. G.; Spasov K. A.; Cisneros J. A. ; Kudalkar S. N.; Petrova Z. O.; Buckingham A. B.; Anderson K. S.; Jorgensen W. L. Proc. Nat. Acad. Sci., USA 2017, 114(36), 9725-9730. doi:10.1073/pnas.1711463114

425. Improved Description of Sulfur Charge Anisotropy in OPLS Force Fields: Model Development and Parameterization. Yan X. C.; Robertson, M. J.; Tirado-Rives, J.; Jorgensen, W. L. J. Phys. Chem. B 2017, 121 (27), 6626-6636. doi:10.1021/acs.jpcb.7b04233

424. Identification and Characterization of JAK2 Pseudokinase Domain Small Molecule Binders. Puleo D. E.; Kucera K.; Hammarn H. M.; Ungureanu D.; Newton A.S., Silvennoinen O.; Jorgensen, W. L.; Schlessinger,J. ACS Med. Med. Chem. Lett 2017, 8 (6), 618-621. doi:10.1021/acsmedchemlett.7b00153

423. JAK2 JH2 Fluorescence Polarization Assay and Crystal Structures for Complexes with Three Small Molecules. Newton A.S., Deiana L.; Puleo D. E.; Cisneros J. A.; Cutrona K. J.; Schlessinger,J.; Jorgensen, W. L. ACS Med. Med. Chem. Lett 2017, 8 (6), 614-617. doi:10.1021/acsmedchemlett.7b00154

422. LigParGen web server: An automatic OPLS-AA parameter generator for organic ligands. Dodda, L. S.; Cabeza de Vaca, I.; Tirado-Rives, J.; Jorgensen, W. L. Nuc. Acids Res 2017, W1, W331-W336. doi:10.1093/nar/gkx312

421. Structural and Preclinical Studies of Computationally Designed Non-Nucleoside Reverse Transcriptase Inhibitors for Treating HIV infection. Kudalkar, S. N.; Beloor, J.; Chan, A. H.; Lee, W. -G.; Jorgensen, W. L.; Kumar, P; Anderson, K. S.;. Mol. Pharmacol 2017, 91(4), 383-391. doi:10.1124/mol.116.107755

420. 1.14* CM1A-LBCC: Localized Bond-Charge Corrected CM1A Charges for Condensed-Phase Simulations. Dodda, L. S.; Vilseck, J. Z.; Tirado-Rives, J.; Jorgensen, W. L. J. Phys. Chem. B 2017, 121(15), 3684-3870. doi:10.1021/acs.jpcb.7b00272

419. Improved treatment of nucleosides and nucleotides in the OPLS-AA force field. Robertson, M. J.; Tirado-Rives, J.; Jorgensen, W. L. Chem. Phys. Lett 2017, 683, 276-280. doi:10.1016/j.cplett.2017.02.049

418. Systematic Study of Effects of Structural Modifications on the Aqueous Solubility of Drug-like Molecules. Cisneros, J. A.; Robertson, M. J.; Mercado, B. Q.; Jorgensen, W. L. ACS Med. Med. Chem. Lett 2017, 8(1), 124-127. doi:10.1021/acsmedchemlett.6b00451

417. Design, Conformation, and Crystallography of 2-Naphthyl Phenyl Ethers as Potent Anti-HIV Agents. Lee, W.-G.; Chan, A. H.; Spasov, K. A.; Anderson, K. S.; Jorgensen, W. L. ACS Med. Med. Chem. Lett 2016, 7(12), 1156-1160. doi:10.1021/acsmedchemlett.6b00390

416. Computer-aided discovery of anti-HIV agents. Jorgensen, W. L. Bioorg. Med. Chem 2016, 24(20), 4768-4778. doi:10.1016/j.bmc.2016.07.039

415. Performance of Protein-Ligand Force Fields for the Flavodoxin-Flavin Mononucleotide System. Robertson, M. J.; Tirado-Rives, J.; Jorgensen, W. L. J. Phys. Chem. Lett 2016, 7(15), 3032-3036. doi:10.1021/acs.jpclett.6b01229

414. A Fluorescence Polarization Assay for Binding to Macrophage Migration Inhibitory Factor and Crystal Structures for Complexes of Two Potent Inhibitors. Cisneros, J. A.; Robertson, M. J.; Valhondo, M.; Jorgensen, W. L. J. Am. Chem. Soc 2016, 138(27), 8630-8638. doi:10.1021/jacs.6b04910

413. Irregularities in enzyme assays: The case of macrophage migration inhibitory factor. Cisneros, J. A.; Robertson, M. J.; Valhondo, M.; Jorgensen, W. L. Bioorg. Med. Chem. Lett 2016, 26(12), 2764-2767. doi:10.1016/j.bmcl.2016.04.074

412. Biomolecular Force Field Parameterization via Atoms-in-Molecule Electron Density Partitioning. Cole, D. J.; Vilseck, J. Z.; Tirado-Rives, J.; Payne, M. C.; Jorgensen, W. L. J. Chem. Theory Comput 2016, 12(5), 2312-2323. doi:10.1021/acs.jctc.6b00027

411. Hydration Properties and Solvent Effects for All-Atom Solutes in Polarizable Coarse-Grained Water. Yan, X. C.; Tirado-Rives, J.; Jorgensen, W. L. J. Phys. Chem. B 2016, 120(33), 8102-8144. doi:10.1021/acs.jpcb.6b00399

410. Macrophage Migration Inhibitory Factor Is Detrimental in Pneumococcal Pneumonia and a Target for Therapeutic Immunomodulation. Weiser, J. N.; Roche, A. M.; Hergott, C. B.; LaRose, M. I.; Connolly, T.; Jorgensen, W. L.; et al.. J. Infect. Dis. 2015, 212, 1677-1682. doi:10.1093/infdis/jiv262

409. OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins. Harder, E.; Damm, W.; Maple, J.; Wu, C.; Reboul, M.; Xiang, J. Y.; Wang, L.; Lupyan, D.; Dahlgren, M. K.; Knight, J. L.; Kaus, J. W.; Cerutti, D. S.; Krilov, G.; Jorgensen, W. L.; Abel, R.; Friesner, R. A. J. Chem. Theory Comput 2015, 12, 281-296. doi:10.1021/acs.jctc.5b00864

408. Illustrating Concepts in Physical Organic Chemistry with 3D Printed Orbitals. Robertson, M. J.; Jorgensen, W. L. J. Chem. Educ 2015, 92, 2113-2116. doi:10.1021/acs.jchemed.5b00682

407. Potent Inhibitors Active against HIV Reverse Transcriptase with K101P, a Mutation Conferring Rilpivirine Resistance. Gray, W. T.; Frey, K. M.; Laskey, S. B.; Mislak, A. C.; Spasov, K. A.; Lee, W. G.; Bollini, M.; Siliciano, R. F.; Jorgensen, W. L.; Anderson, K. S. ACS Med. Chem. Lett 2015, 6, 1075-1079. doi:10.1021/acsmedchemlett.5b00254

406. Discovery and crystallography of bicyclic arylaminoazines as potent inhibitors of HIV-1 reverse transcriptase. Lee, W. G.; Frey, K. M.; Gallardo-Macias, R.; Spasov, K. A.; Chan, A. H.; Anderson, K. S.; Jorgensen, W. L. Bioorg. Med. Chem. Lett 2015, 25, 4824-4827. doi:10.1016/j.bmcl.2015.06.074

405. Application of a BOSS-Gaussian interface for QM/MM simulations of Henry and methyl transfer reactions. Vilseck, J. Z.; Kostal, J.; Tirado-Rives, J.; Jorgensen, W. L. J. Comput. Chem 2015, 36, 2064-2074. doi:10.1002/jcc.24045

404. Evaluation of CM5 Charges for Nonaqueous Condensed-Phase Modeling. Dodda, L. S.; Vilseck, J. Z.; Cutrona, K. J.; Jorgensen, W. L. J. Chem. Theory Comput 2015, 11, 4273-4282. doi:10.1021/acs.jctc.5b00414

403. Endothelial CD74 mediates macrophage migration inhibitory factor protection in hyperoxic lung injury. Sauler, M.; Zhang, Y.; Min, J. N.; Leng, L.; Shan, P.; Roberts, S.; Jorgensen, W. L.; Bucala, R.; Lee, P. J. FASEB J 2015, 29, 1940-1949. doi:10.1096/fj.14-260299

402. Improved Peptide and Protein Torsional Energetics with the OPLS-AA Force Field. Robertson, M. J.; Tirado-Rives, J.; Jorgensen, W. L. J. Chem. Theory Comput 2015, 11, 3499-3509. doi:10.1021/acs.jctc.5b00356

401. A nanotherapy strategy significantly enhances anticryptosporidial activity of an inhibitor of bifunctional thymidylate synthase-dihydrofolate reductase from Cryptosporidium. Mukerjee, A.; Iyidogan, P.; Castellanos-Gonzalez, A.; Cisneros, J. A.; Czyzyk, D.; Ranjan, A. P.; Jorgensen, W. L.; White Jr., A. C.; Vishwanatha, J. K.; Anderson, K. A. Bioorganic & Medicinal Chemistry Letters 2015, 25, 2065-2067. doi:10.1016/j.bmcl.2015.03.091

400. Structure-based Evaluation of Non-nucleoside Inhibitors with Improved Potency and Solubility that Target HIV Reverse Transcriptase Variants. Frey, K. M.; Puleo, D.; Spasov, K. A.; Bollini, M.; Jorgensen, W. L.; Anderson, K. S. J. Med. Chem 2015, 58, 2737-2745. doi:10.1021/jm501908a

399. Design, Synthesis, and Protein Crystallography of Biaryltriazoles as Potent Tautomerase Inhibitors of Macrophage Migration Inhibitory Factor. Dziedzic, P.; Cisneros, J. A.; Robertson, M. J.; Hare, A. A.; Danford, N. E.; Baxter, R. H. G.; Jorgensen, W. L. J. Am. Chem. Soc 2015, 137, 2996-3003. doi:10.1021/ja512112j

398. 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. Wang, L.; Wu, Y.; Deng, Y.; Kim, B.; Pierce, L.; Krilov, G.; Lupyan, D.; Robinson, S.; Dahlgren, M.; Greenwood, J.; Romero, D. L.; Masse, C.; Knight, J. L.; Steinbrecher, T.; Beuming, T.; Damm, W.; Harder, E.; Sherman, W.; Brewer, M.; Wester, R.; Murcko, M.; Frye, L.; Farid, R.; Lin, T.; Mobley, D. L.; Jorgensen, W. L.; Berne, B. J.; Friesner, R. A.; Abel, R. J. Am. Chem. Soc 2015, 137, 2695-2703. doi:10.1021/ja512751q

397. Determination of partial molar volumes from free energy perturbation theory. Vilseck, J. Z.; Tirado-Rives, J.; Jorgensen, W. L. Phys. Chem. Chem. Phys 2015, 17, 8407-8415. doi:10.1039/c4cp05304d

396. Abbreviated Curriculum Vitae of William L. Jorgensen. . J. Phys. Chem. B 2015, 119, 635-636. doi:10.1021/jp510441r

395. Group Members of William L. Jorgensen (1975-2014). . J. Phys. Chem. B 2015, 119, 633-634. doi:10.1021/jp5104406

394. Autobiography of William L. Jorgensen: Scientific History and Recollections. Jorgensen, W. L. J. Phys. Chem. B 2015, 119, 624-632. doi:10.1021/jp510442j

393. Tribute to William L. Jorgensen. Gao, J.; Orozco, M; Peishoff, C. E. J. Phys. Chem. B 2015, 119, 621-623. doi:10.1021/jp511519w

392. A Reflection on Paul von Ragué Schleyer. Jorgensen, W. L. J. Chem. Theory Comput 2015, 11, 1. doi:10.1021/ct501095w

391. The many faces of halogen bonding: a review of theoretical models and methods. Wolters, L. P.; Schyman, P.; Pavan, M. J.; Jorgensen, W. L.; Bickelhaupt, F. M.; Kozuch, S. WIREs Comput. Mol. Sci 2014, 4, 523-540. doi:10.1002/wcms.1189

390. Picomolar Inhibitors of HIV-1 Reverse Transcriptase: Design and Crystallography of Naphthyl Phenyl Ethers. Lee, W.G.; Frey, K. M.; Gallardo-Macias, R.; Spasov, K. A.; Bollini, M.; Anderson, K. S.; Jorgensen, W. L. ACS Med. Chem. Lett 2014, 5, 1259-1262. doi:10.1021/ml5003713

389. Crystallographic and Receptor Binding Characterization of Plasmodium falciparum Macrophage Migration Inhibitory Factor Complexed to Two Potent Inhibitors. Pantouris, G.; Rajasekaran, D.; Garcia, A. B.; Ruiz, V. G.; Leng, L.; Jorgensen, W. L.; Bucala, R.; Lolis, E. J. J. Med. Chem 2014, 57, 8652-8656. doi:10.1021/jm501168q

388. Molecular dynamics and Monte Carlo simulations for protein.ligand binding and inhibitor design. Cole, D. J.; Tirado-Rives, J.; Jorgensen, W. L. Biochim. Biophys. Acta, Gen. Subj 2015, 1850, 966-971. doi:10.1016/j.bbagen.2014.08.018

387. Structural studies provide clues for analog design of specific inhibitors of Cryptosporidium hominis thymidylate synthase.dihydrofolate reductase. Kumar, V. P.; Cisneros, J. A.; Frey, K. M.; Castellanos-Gonzalez, A.; Wang, Y.; Gangjee, A.; White, A. C. Jr.; Jorgensen, W. L.; Anderson, K. S. Bioorganic & Medicinal Chemistry Letters 2014, 24, 4158-4161. doi:10.1016/j.bmcl.2014.07.049

386. Biochemical Assays for the Discovery of TDP1 Inhibitors. Marchand, C.; Huang, S. N.; Dexheimer, T. S.; Lea, W. A.; Mott, B. T.; Chergui, A.; Naumova, A.; Stephen, A. G.; Rosenthal, A. S.; Rai, G.; Murai, J.; Gao, R.; Maloney, D. J.; Jadhav, A.; Jorgensen, W. L.; Simeonov, A.; Pommier, Y. Mol. Cancer Ther 2014, 13, 2116. doi:10.1158/1535-7163.MCT-13-0952

385. A mechanistic and structural investigation of modified derivatives of the diaryltriazine class of NNRTIs targeting HIV-1 reverse transcriptase. Mislak, A. C.; Frey, K. M.; Bollini, M.; Jorgensen, W. L.; Anderson, K. S. Biochimica et Biophysica Acta 2014, 1840, 2203-2211. doi:10.1016/j.bbagen.2014.04.001

384. Structure-Based Evaluation of C5 Derivatives in the Catechol Diether Series Targeting HIV-1 Reverse Transcriptase. Frey, K. M.; Gray, W. T.; Spasov, K. A.; Bollini, M.; Gallardo-Macias, R.; Jorgensen, W. L.; Anderson, K. S. Chemical Biology & Drug Design 2014, 83, 541-549. doi:10.1111/cbdd.12266

383. Illuminating HIV gp120-ligand recognition through computationally-driven optimization of antibody-recruiting molecules. Parker, C. G.; Dahlgren, M. K.; Tao, R. N.; Li, D. T.; Douglass, E. F. Jr.; Shoda, T.; Jawanda, N.; Spasov, K. A.; Lee, S.; Zhou, N.; Domaoal, R. A.; Sutton, R. E.; Anderson, K. S.; Krystal, M.; Jorgensen, W. L.; Spiegel, D. A. Chem. Sci 2014, 5, 2311-2317. doi:10.1039/C4SC00484A

382. Virtual screening reveals allosteric inhibitors of the Toxoplasma gondii thymidylate synthase.dihydrofolate reductase. Sharma, H.; Landau, M. J.; Sullivan, T. J.; Kumar, V. P.; Dahlgren, M. K.; Jorgensen, W. L.; Anderson, K. S. Bioorganic & Medicinal Chemistry Letters 2014, 24, 1232-1235. doi:10.1016/j.bmcl.2013.12.039

381. Evaluation of CM5 Charges for Condensed-Phase Modeling. Vilseck, J. Z.; Tirado-Rives, J.; Jorgensen, W. L. J. Chem. Theory Comput 2014, 10, 2802-2812. doi:10.1021/ct500016d

380. Cooperative Effects and Optimal Halogen Bonding Motifs for Self-Assembling Systems. Yan, X. C.; Schyman, P.; Jorgensen, W. L. J. Phys. Chem. A 2014, 118, 2820-2826. doi:10.1021/jp501553j

379. Enhanced Monte Carlo Sampling through Replica Exchange with Solute Tempering. Cole, D. J.; Tirado-Rives, J.; Jorgensen, W. L. J. Chem. Theory Comput 2014, 10, 565-571. doi:10.1021/ct400989x

378. Foundations of Biomolecular Modeling. Jorgensen, W. L. Cell 2013, 155, 1199-1202. doi:10.1016/j.cell.2013.11.023

377. Picomolar Inhibitors of HIV Reverse Transcriptase Featuring Bicyclic Replacement of a Cyanovinylphenyl Group. Lee, W. G.; Gallardo-Macias, R.; Frey, K. M.; Spasov, K. A.; Bollini, M.; Anderson, K. S.; Jorgensen, W. L. J. Am. Chem. Soc 2013, 135, 16705-16713. doi:10.1021/ja408917n

376. Optimization of diarylazines as anti-HIV agents with dramatically enhanced solubility. Bollini, M.; Cisneros, J. A.; Spasov, K. A.; Anderson, K. S.; Jorgensen, W. L. Bioorganic & Medicinal Chemistry Letters 2013, 23, 5213-5216. doi:10.1016/j.bmcl.2013.06.091

375. Extension into the entrance channel of HIV-1 reverse transcriptase-Crystallography and enhanced solubility. Bollini, M.; Frey, K. M.; Cisneros, J. A.; Spasov, K. A.; Das, K.; Bauman, J. D.; Arnold, E.; Anderson, K. S.; Jorgensen, W. L. Bioorganic & Medicinal Chemistry Letters 2013, 23, 5209-5212. doi:10.1016/j.bmcl.2013.06.093

374. Bifunctional Inhibition of HIV-1 Reverse Transcriptase: Mechanism and proof-of- concept as a novel therapeutic design strategy. Bailey, C.; Sullivan, T.; Iyidogan, P.; Tirado-Rives, J.; Chung, R.; Ruiz-Caro, J.; Mohamed, E.; Jorgensen, W. L.; Hunter, R.; Anderson, K. A. J. Med. Chem 2013, 56, 3959-3968. doi:10.1021/jm400160s

373. Limiting Cardiac Ischemia by Pharmacologic Augmentation of MIF-AMPK Signal Transduction. Wang, J.; Yan, X.; Yeung, E.; Gandavadi, S.; Hare, A. A.; Du, X.; Chen, Y.; Xiong, H.; Leng, L.; Young, L.; Jorgensen, W. L.; Li, J.; Bucala, R. Circulation 2013, 128, 225-236. doi:10.1161/CIRCULATIONAHA.112.000862

372. Polarized Protein-Specific Charges from Atoms-in-Molecule Electron Density Partitioning. Lee, L. P.; Cole, D. J.; Skylaris, C. K.; Jorgensen, W. L.; Payne, M. C. J. Chem. Theory Comput 2013, 9, 2981-2991. doi:10.1021/ct400279d

371. Small Molecular Modulation of Macrophage Migration Inhibitory Factor in the Hyperoxia-Induced Mouse Model of Bronchopulmonary Dysplasia. Sun, H.; Choo-Wing, R.; Fan, J.; Leng, L.; Hare, A. A.; Yu, S.; Jiang, D.; Noble, P.; Jorgensen, W. L.; Bucala, R.; Bhandari, V. Respiratory Res 2013, 14, 27. doi:10.1186/1465-9921-14-27

370. Characterization of Biaryl Torsional Energetics and its Treatment in OPLS All-Atom Force Fields. Dahlgren, M. K.; Schyman, P.; Tirado-Rives, J.; Jorgensen, W. L. J. Chem. Inf. Model 2013, 53, 1191-1199. doi:10.1021/ci4001597

369. Automated ligand- and structure-based protocol for in silico prediction of Human Serum Albumin binding. Hall, M. L.; Jorgensen, W. L.; Whitehead L. J. Chem. Inf. Model. 2013, 53, 907-922. doi:10.1021/ci3006098

368. Exploring Adsorption of Water and Ions on Carbon Surfaces using a Polarizable Force Field. Schyman, P.; Jorgensen, W. L. J. Phys. Chem. Lett 2013, 4, 468-474. doi:10.1021/jz302085c

367. Optimization of benzyloxazoles as non-nucleoside inhibitors of HIV 1 reverse transcriptase to enhance Y181C potency. Bollini, M.; Gallardo-Macias, R.; Spasov, K. A.; Tirado-Rives, J.; Anderson, K. S.; Jorgensen, W. L. Bioorg. Med. Chem. Lett 2013, 23, 1110-1113. doi:10.1016/j.bmcl.2012.11.115

366. Crystal Structures of HIV-1 Reverse Transcriptase with Picomolar Inhibitors Reveal Key Interactions for Drug Design. Frey, K. M.; Bollini, M.; Mislak, A. C.; Cisneros, J. A.; Gallardo-Macias, R.; Jorgensen, W. L.; Anderson, K. A. J. Am. Chem. Soc 2012, 134, 19501-19503. doi:10.1021/ja3092642

365. Virtual Screening and Optimization Yield Low-Nanomolar Inhibitors of the Tautomerase Activity of Plasmodium falciparum Macrophage Migration Inhibitory Factor. Dahlgren, M. K.; Garcia, A. B.; Hare, A. A.; Tirado-Rives, J.; Leng, L.; Bucala, R.; Jorgensen, W. L. J. Med. Chem 2012, 55, 10148-10159. doi:10.1021/jm301269s

364. Small Molecule Inhibitors of the Interaction between the E3 Ligase VHL and HIF1. Buckley, D. L.; Gustafson, J. L.; Van Molle, I.; Roth, A. G.; Tae, H. S.; Gareiss, P. C.; Jorgensen, W. L.; Ciulli, A.; Crews, C. M. Angew. Chem. Int. Ed 2012, 51, 11463-11467. doi:10.1002/anie.201206231

363. Challenges for Academic Drug Discovery. Jorgensen, W. L. Angew. Chem. Int. Ed. 2012, 51, 11680-11684. doi:10.1002/anie.201204625

362. Methyl Effects on Protein-Ligand Binding. Leung, C. S.; Leung, S. S. F.; Tirado-Rives, J.; Jorgensen, W. L. J. Med. Chem 2012, 55, 4489-4500. doi:10.1021/jm3003697

361. Treatment of Halogen Bonding in the OPLS-AA Force Field; Application to Potent Anti-HIV Agents. Jorgensen, W. L.; Schyman, P. J. Chem. Theory Comput 2012, 8, 3895-3901. doi:10.1021/ct300180w

360. Role of macrophage migration inhibitory factor in the regulatory T cell response of tumor-bearing mice. Choi, S.; Kim, H.-R.; Leng, L.; Kang, I.; Jorgensen, W. L.; Cho, C.-S.; Bucala, R.; Kim, W.-U. J. Immunol 2012, 189, 3905-3913. doi:10.4049/jimmunol.1102152

359. Discovery of dimeric inhibitors by extension into the entrance channel of HIV-1 reverse transcriptase. Ekkati, A. R.; Bollini, M.; Domaoal, R. A.; Spasov, K. A.; Anderson, K. A.; Jorgensen, W. L. Bioorg. Med. Chem. Lett 2012, 22, 1565-1568. doi:10.1016/j.bmcl.2011.12.132

358. Targeting the von Hippel-Landau E3 Ubiquitin Ligase using Small Molecules to Disrupt the VHL/HIF-1 Interaction. Buckley, D. L.; Van Molle, I.; Gareiss, P. C.; Tae, H. S.; Michel, J.; Noblin, D. J.; Jorgensen, W. L.; Ciulli, A.; Crews, C. M. J. Am. Chem. Soc 2012, 134, 4465-4468. doi:10.1021/ja209924v

357. Investigation of Solvent Effects on the Rate and Stereoselectivity of the Henry Reaction. Kostal, J.; Voutchkova, A. M.; Jorgensen, W. L. Org. Lett 2012, 14, 260-263. doi:10.1021/ol2030394

356. On the Mechanism and Rate of Spontaneous Decomposition of Amino Acids. Alexandrova, A.; Jorgensen, W. L. J. Phys. Chem. B 2011, 115, 13624-13632. doi:10.1021/jp2081808

355. Computationally-Guided Optimization of a Docking Hit to Yield Catechol Diethers as Potent Anti-HIV Agents. Bollini, M.; Domaoal, R. A.; Thakur, V. V.; Gallardo-Macias, R.; Spasov, K. A.; Anderson, K. A.; Jorgensen, W. L. J. Med. Chem 2011, 54, 8582-8591. doi:10.1021/jm201134m

354. Improving MM-GB/SA Scoring through the Application of the Variable Dielectric Model. Ravindranathan, K.; Tirado-Rives, J.; Jorgensen, W. L.; Guimares, C. R. W. J. Chem. Theory Comput 2011, 7, 3859-3866. doi:10.1021/ct200565u

353. Efficient Discovery of Potent Anti-HIV Agents Especially Targeting the Tyr181Cys Variant of HIV Reverse Transcriptase. Jorgensen, W. L., Bollini, M.; Thakur, V. V.; Domaoal, R. A.; Spasov, K. A.; Anderson, K. A. J. Am. Chem. Soc 2011, 133, 15686-15696. doi:10.1021/ja2058583

352. Benzisothiazolones as modulators of macrophage migration inhibitory factor. Jorgensen, W. L.; Trofimov, A.; Leng, L.; Hare, A. A.; Du, X. ; Bucala, R. Bioorg. Med. Chem. Lett 2011, 21, 4545-4549. doi:10.1016/j.bmcl.2011.05.127

351. Aryl Extensions of Thienopyrimidinones as Fibroblast Growth Factor Receptor 1 Kinase Inhibitors. Ekkati, A. R.; Mandiyan, V.; Ravindranathan, K. P.; Bae, J. H.; Schlessinger, J.; Jorgensen, W. L. Tetrahedron Lett 2011, 52, 2228-2231. doi:10.1016/j.tetlet.2010.12.081

350. Limiting Cardiac Ischemic Injury by Augmenting the MIF-AMPK Signaling Cascade with a Novel Class of MIF Receptor Agonists. Wang, J.; Yan,, X.; Yeung, E.; Gandavadi, S.; Hare, A. H.; Du, X.; Leng, L.; Jorgensen, W. L.; Li, J.; Bucala, R. Circulation 2010, 122, A15835.

349. Effects of Water Placement on Predictions of Binding Affinities for p38? MAP Kinase Inhibitors. Luccarelli, J.; Michel, J.; Tirado-Rives, J.; Jorgensen, W. L. J. Chem. Theory Comput 2010, 6, 3850-3856. doi:10.1021/ct100504h

348. Receptor agonists of macrophage migration inhibitory factor. Jorgensen, W. L.; Gandavadi, S.; Du, X.; Hare, A. A.; Trofimov, A.; Leng, L.; Bucala, R. Bioorg. Med. Chem. Lett 2010, 20, 7033-7036. doi:10.1016/j.bmcl.2010.09.118

347. Synthesis and Evaluation of Selected Key Methyl Ether Derivatives of Vancomycin Aglycon. Crane, C. M.; Pierce, J. G.; Leung, S. F.; Tirado-Rives, J.; Jorgensen, W. L.; Boger, D. L. J. Med. Chem 2010, 53, 7229-7235. doi:10.1021/jm100946e

346. E/Z Energetics for Molecular Modeling and Design. Terhorst, J. P.; Jorgensen, W. L. J. Chem. Theory Comput 2010, 6, 2762-2769. doi:10.1021/ct1004017

345. Drug Discovery: Pulled from a Protein's Embrace. Jorgensen, W. L. Nature 2010, 466, 42-43. doi:10.1038/466042a

344. Optimization of N-benzyl-benzoxazol-2-ones as receptor antagonists of macrophage migration inhibitory factor (MIF). Hare, A. A.; Leng, L.; Gandavadi, S.; Du, X.; Cournia, Z.; Bucala, R.; Jorgensen, W. L. Bioorg. Med. Chem. Lett 2010, 20, 5811-5814. doi:10.1016/j.bmcl.2010.07.129

343. A Remote Arene-Binding Site on Prostate Specific Membrane Antigen Revealed by Antibody-Recruiting Small Molecules. Zhang, A. X.; Murelli, R. P.; Barinka, C.; Michel, J.; Cocleaza, A.; Jorgensen, W. L.; Lubkowski, J.; Spiegel, D. A. J. Am. Chem. Soc 2010, 132, 12711-12716. doi:10.1021/ja104591m

342. Thorpe-Ingold Acceleration of Oxirane Formation is Mostly a Solvent Effect. Kostal, J.; Jorgensen, W. L. J. Am. Chem. Soc 2010, 132, 8766-8773. doi:10.1021/ja1023755

341. Exploring Solvent Effects upon the Menshutkin Reaction Using a Polarizable Force Field. Acevedo, O.; Jorgensen, W. L. J. Phys. Chem. B 2010, 114, 8425-8430. doi:10.1021/jp100765v

340. Quantum Mechanical/Molecular Mechanical Modeling Finds Diels-Alder Reactions Are Accelerated Less on the Surface of Water Than in Water. Thomas, L. L.; Tirado-Rives, J.; Jorgensen, W. L. J. Am. Chem. Soc 2010, 132, 3097-3104. doi:10.1021/ja909740y

339. Eastern Extension of Azoles as Non-Nucleoside Inhibitors of HIV-1 Reverse Transcriptase; Cyano Group Alternatives. Leung, C. S.; Zeevaart, J. G.; Domaoal, R. A.; Bollini, M.; Thakur, V. V.; Spasov, K. A.; Anderson, K. S.; Jorgensen, W. L. Bioorg. Med. Chem. Lett 2010, 20, 2485-2488. doi:10.1016/j.bmcl.2010.03.006

338. Discovery of Novel Fibroblast Growth Factor Receptor 1 Kinase Inhibitors by Structure-Based Virtual Screening. Ravindranathan, K. P.; Mandiyan, V.; Ekkati, A. R.; Bae, J. H.; Schlessinger, J.; Jorgensen, W. L. J. Med. Chem 2010, 53, 1662-1672. doi:10.1021/jm901386e

337. Advances in Quantum and Molecular Mechanical (QM/MM) Simulations for Organic and Enzymatic Reactions. Acevedo, O.; Jorgensen, W. L. Acc. Chem. Res 2010, 43, 142-151. doi:10.1021/ar900171c

336. Chemical Control over Immune Recognition: A Class of Antibody-Recruiting Small Molecules that Target Prostate Cancer. Murelli, R. P.; Zhang, A. X.; Michel, J.; Jorgensen, W. L.; Spiegel, D. A. J. Am. Chem. Soc 2009, 131, 17090-17092. doi:10.1021/ja906844e

335. Energetics of Displacing Water Molecules from Protein Binding Sites: Consequences for Ligand Optimization. Michel, J.; Tirado-Rives, J.; Jorgensen, W. L. J. Am. Chem. Soc 2009, 131, 15403-15411. doi:10.1021/ja906058w

334. Steric and Solvation Effects in Ionic S N 2 Reactions. Chen, X.; Regan, C. K.; Craig, S. L.; Krenske, E. H.; Houk, K. N.; Jorgensen, W. L.; Brauman, J. I. J. Am. Chem. Soc 2009, 131, 16162-16170. doi:10.1021/ja9053459

333. Prediction of the Water Content in Protein Binding Sites. Michel, J.; Tirado-Rives, J.; Jorgensen, W. L. J. Phys. Chem. B 2009, 113, 13337-13346. doi:10.1021/jp9047456

332. Vancomycin Analogs: Seeking Improved Binding of -Ala-Ala and -Ala-Lac Peptides by Side-Chain and Backbone Modifications. Leung, S. S. F.; Tirado-Rives, J.; Jorgensen, W. L. Bioorg. Med. Chem 2009, 17, 5874-5886. doi:10.1016/j.bmc.2009.07.006

331. Progress and Issues for Computationally-Guided Lead Discovery and Optimization. W. L. Jorgensen In. Drug Design: Structure and Ligand-Based Approaches 2009, pp..

330. In Silico Improvement of β 3 -Peptide Inhibitors of p53.bul.hDM2 and p53.bul.hDMX. Michel, J.; Harker, E. A.; Tirado-Rives, J.; Jorgensen, W. L.; Schepartz, A. J. Am. Chem. Soc 2009, 131, 6356-6357. doi:10.1021/ja901478e

329. Discovery of Wild-Type and Y181C Mutant Non-nucleoside HIV-1 Reverse Transcriptase Inhibitors Using Virtual Screening with Multiple Protein Structures. Nichols, S. E.; Domaoal, R. A.; Thakur, V. V.; Tirado-Rives, J.; Anderson, K. S.; Jorgensen, W. L. J. Chem. Inf. Model 2009, 49, 1272-1279. doi:10.1021/ci900068k

328. Vancomycin Resistance: Modeling Backbone Variants with -Ala-Ala and -Ala-Lac Peptides. Leung, S. S. F.; Tirado-Rives, J.; Jorgensen, W. L. Bioorg. Med. Chem. Lett 2009, 19, 1236-1239. doi:10.1016/j.bmcl.2008.12.072

327. Efficient Drug Lead Discovery and Optimization. Jorgensen, W. L. Acc. Chem. Res 2009, 42, 724-733. doi:10.1021/ar800236t

326. Novel Non-Active Site Inhibitor of Cryptosporidium Hominis TS-DHFR Identified by a Virtual Screen. Martucci, W. E.; Udier-Blagovic, M.; Atreya, C.; Babatunde, O.; Vargo, M. A.; Jorgensen, W. L.; Anderson, K. S. Bioorg. Med. Chem. Lett 2009, 19, 418-423. doi:10.1016/j.bmcl.2008.11.054

325. Discovery of Human Macrophage Migration Inhibitory Factor (MIF)-CD74 Antagonists via Virtual Screening. Cournia, Z.; Leng, L.; Gandavadi, S.; Du, X.; Bucala, R.; Jorgensen, W. L. J. Med. Chem 2009, 52, 416-424. doi:10.1021/jm801100v

324. Origin of the Activity Drop with the E50D Variant of Catalytic Antibody 34E4 for Kemp Elimination. Alexandrova, A. N; Jorgensen, W. L. J. Phys. Chem. B 2009, 113, 497-504. doi:10.1021/jp8076084

323. Exploiting Structural Analysis, In Silico Screening, and Serendipity to Identify Novel Inhibitors of Drug-Resistant Falciparum Malaria. Dasgupta, T.; Chitnumsub, P.; Kamchonwongpaisan, S.; Maneeruttanarungroj, C.; Nichols, S. E.; Lyons, T. M.; Tirado-Rives, J.; Jorgensen, W. L.; Yuthavong, Y.; Anderson, K. S. ACS Chem. Biol 2009, 4, 29-40. doi:10.1021/cb8002804

322. Catalytic Mechanism and Performance of Computationally Designed Enzymes for Kemp Elimination. Alexandrova, A. N.; Rothlisberger, D.; Baker, D.; Jorgensen, W. L. J. Am. Chem. Soc 2008, 130, 15907-15915. doi:10.1021/ja804040s

321. Optimization of Azoles as Anti-Human Immunodeficiency Virus Agents Guided by Free-Energy Calculations. Zeevaart, J. G.; Wang, L.; Thakur, V. V.; Leung, C. S.; Tirado-Rives, J.; Bailey, C. M.; Domaoal, R. A.; Anderson, K. S.; Jorgensen, W. L. J. Am. Chem. Soc 2008, 130, 9492-9499. doi:10.1021/ja8019214

320. Perspective on Free-Energy Perturbation Calculations for Chemical Equilibria. Jorgensen, W. L.; Thomas, L. L. J. Chem. Theory Comput 2008, 4, 869-876. doi:10.1021/ct800011m

319. Energetic Effects for Observed and Unobserved HIV-1 Reverse Transcriptase Mutations of Residues L100, V106, and Y181 in the Presence of Nevirapine and Efavirenz. Kroeger Smith, M. B.; Rader, L. H.; Franklin, A. M.; Taylor, E. V.; Smith, K. D.; Smith, R. H.; Tirado-Rives, J.; Jorgensen, W. L. Bioorg. Med. Chem. Lett 2008, 18, 969-972. doi:10.1016/j.bmcl.2007.12.033

318. Performance of B3LYP Density Functional Methods for a Large Set of Organic Molecules. Tirado-Rives, J.; Jorgensen, W. L. J. Chem. Theory Comput 2008, 4, 297-306. doi:10.1021/ct700248k

317. Optical Rotatory Dispersion of 2,3-Hexadiene and 2,3-Pentadiene. Wiberg, K. B.; Wang, Y.; Wilson, S. M.; Vaccaro, P. H.; Jorgensen, W.L.; Crawford, T. D.; Abrams, M. L.; Cheeseman, J. R.; Luderer, M. J. Phys. Chem. A 2008, 112, 2415-2422. doi:10.1021/jp076572o

316. Search for Non-Nucleoside Inhibitors of HIV-1 Reverse Transcriptase Using Chemical Similarity, Molecular Docking, and MM-GB/SA Scoring. Barreiro, G.; Guimaraes, C. R. W.; Tubert-Brohman, I.; Lyons, T. M.; Tirado-Rives, J.; Jorgensen, W. L. J. Chem. Inf. Model 2007, 47, 2416-2428. doi:10.1021/ci700271z

315. Polarization Effects for Hydrogen-Bonded Complexes of Substituted Phenols with Water and Chloride Ion. Jorgensen, W. L.; Jensen, K. P.; Alexandrova, A. N. J. Chem. Theory Comput 2007, 3, 1987-1992. doi:10.1021/ct7001754

314. From Docking False-Positive to Active Anti-HIV Agent. Barreiro, G.; Kim, J. T.; Guimaraes, C. R. W.; Bailey, C. M.; Domaoal, R. A.; Wang, L.; Anderson, K. S.; Jorgensen, W. L. J. Med. Chem 2007, 50, 5324-5329. doi:10.1021/jm070683u

313. Understanding Rate Accelerations for Diels-Alder Reactions in Solution Using Enhanced QM/MM Methodology. Acevedo, O.; Jorgensen, W. L. J. Chem. Theory Comput 2007, 3, 1412-1419. doi:10.1021/ct700078b

312. Elucidation of Rate Variations for a Diels-Alder Reaction in Ionic Liquids from QM/MM Simulations. Acevedo, O.; Jorgensen, W. L.; Evanseck, J. D. J. Chem. Theory Comput 2007, 3, 132-138. doi:10.1021/ct6002753

311. Computation of Accurate Activation Barriers for Methyl-Transfer Reactions of Sulfonium and Ammonium Salts in Aqueous Solution. Gunaydin, H.; Acevedo, O.; Jorgensen, W. L.; Houk, K. N. J. Chem. Theory Comput 2007, 3, 1028-1035. doi:10.1021/ct050318n

310. Why Urea Eliminates Ammonia Rather than Hydrolyzes in Aqueous Solution. Alexandrova, A. N.; Jorgensen, W. L. J. Phys. Chem. B 2007, 111, 720-730. doi:10.1021/jp066478s

309. FEP-Guided Selection of Bicyclic Heterocycles in Lead Optimization for Non-Nucleoside Inhibitors of HIV-1 Reverse Transcriptase. Kim, J. T.; Hamilton, A. D.; Bailey, C. M.; Domoal, R. A.; Wang, L; Anderson, K. S.; Jorgensen, W. L. J. Am. Chem. Soc 2006, 128, 15372-15373. doi:10.1021/ja066472g

308. Elucidation of Hydrolysis Mechanisms for Fatty Acid Amide Hydrolase and Its Lys142Ala Variant via QM/MM Simulations. Tubert-Brohman, I.; Acevedo, O.; Jorgensen, W. L. J. Am. Chem. Soc 2006, 128, 16904-16913. doi:10.1021/ja065863s

307. Halide, Ammonium, and Alkali Metal Ion Parameters for Modeling Aqueous Solutions. Jensen, K. P.; Jorgensen, W. L. J. Chem. Theory Comput 2006, 2, 1499-1509. doi:10.1021/ct600252r

306. Conformation of Alkanes in the Gas Phase and Pure Liquids. Thomas, L. L.; Christakis, T. J.; Jorgensen, W. L. J. Phys. Chem. B 2006, 110, 21198-21204. doi:10.1021/jp064811m

305. Comparison of SCC-DFTB and NDDO-Based Semiempirical Molecular Orbital Methods for Organic Molecules. Sattelmeyer, K. W.; Tirado-Rives, J.; Jorgensen, W. L. J. Phys. Chem. A 2006, 110, 13551-13559. doi:10.1021/jp064544k

304. Contribution of Conformer Focusing on the Uncertainty in Predicting Free Energies for Protein-Ligand Binding. Tirado-Rives, J.; Jorgensen, W. L. J. Med. Chem 2006, 49, 5880-5884. doi:10.1021/jm060763i

303. Optimization of pyrimidinyl- and triazinyl-amines as non-nucleoside inhibitors of HIV-1 reverse transcriptase. Thakur, V. V.; Kim, J. T.; Hamilton, A. D.; Bailey, C. M.; Domaoal, R. A.; Wang, L.; Anderson, K. S.; Jorgensen, W. L. Bioorg. Med. Chem. Lett 2006, 16, 5664-5667. doi:10.1016/j.bmcl.2006.08.037

302. Medium Effects on the Decarboxylation of a Biotin Model in Pure and Mixed Solvents from QM/MM Simulations. Acevedo, O.; Jorgensen, W. L. J. Org. Chem 2006, 71, 4896-4902. doi:10.1021/jo060533b

301. Cope Elimination: Elucidation of Solvent Effects from QM/MM Simulations. Acevedo, O.; Jorgensen, W. L. J. Am. Chem. Soc 2006, 128, 6141-6146. doi:10.1021/ja057523x

300. Solvent Effects on Organic Reactions from QM/MM Simulations. Acevedo, O.; Jorgensen, W. L. In. Annual Reports in Computational Chemistry 2006, pp. 263-278. doi:10.1016/s1574-1400(06)02014-7

299. Optimization of diarylamines as non-nucleoside inhibitors of HIV-1 reverse transcriptase. Ruiz-Caro, J.; Basavapathruni, A.; Kim, J. T.; Bailey, C. M.; Wang, L.; Anderson, K. S.; Hamilton, A. D.; Jorgensen, W. L. Bioorg. Med. Chem 2006, 16, 668-671. doi:10.1016/j.bmcl.2005.10.037

298. Computer-aided design of non-nucleoside inhibitors of HIV-1 reverse transcriptase. Jorgensen, W. L.; Ruiz-Caro, J.; Tirado-Rives, J.; Basavapathruni, A.; Anderson, K. S.; Hamilton, A. D. Bioorg. Med. Chem 2006, 16, 663-667. doi:10.1016/j.bmcl.2005.10.038

297. NO-MNDO: Reintroduction of the Overlap Matrix into MNDO. Sattelmeyer, K. W.; Tubert-Brohman, I.; Jorgensen, W. L. J. Chem. Theory. Comput 2006, 2, 413-419. doi:10.1021/ct050174c

296. Assault on resistance: the use of computational chemistry in the development of anti-HIV drugs. Smith, M. B. Kroeger; Smith, R. H., Jr.; Jorgensen, W. L. Curr. Pharm. Des 2006, 12, 1843-1856. doi:10.2174/138161206776873581

295. Elucidation of Fatty Acid Amide Hydrolase Inhibition By Potent Alpha-Ketoheterocycle Derivatives From Monte Carlo Simulations. Guimarães, C. R. W., Boger, D. L.; Jorgensen, W. L. J. Am. Chem. Soc 2005, 127, 17377-17384. doi:10.1021/ja055438j

294. Effects of Arg90 Neutralization on the Enzyme-Catalyzed Rearrangement of Chorismate to Prephenate. Guimarães, C. R. W.; Udier-Blagovic, M.; Tubert-Brohman, I.; Jorgensen, W. L. J. Chem. Theory Comput 2005, 1, 617-625. doi:10.1021/ct0500803

293. Influence of Inter- and Intramolecular Hydrogen Bonding on Kemp Decarboxylations from QM/MM Simulations. Acevedo, O.; Jorgensen, W. L. J. Am. Chem. Soc 2005, 127, 8829-8834. doi:10.1021/ja051793y

292. Extension of the PDDG/PM3 Semiempirical Molecular Orbital Method to Sulfur, Silicon, and Phosphorus. Tubert-Brohman, I.; Guimarães, C. R. W.; Jorgensen, W. L. J. Chem. Theory Comput 2005, 1, 817-823. doi:10.1021/ct0500287

291. Molecular modeling of organic and biomolecular systems using BOSS and MCPRO. Jorgensen, W. L.; Tirado-Rives, J. J. Comput. Chem 2005, 26, 1689-1700. doi:10.1002/jcc.20297

290. Potential energy functions for atomic-level simulations of water and organic and biomolecular systems. Jorgensen, W. L.; Tirado-Rives, J. Proc. Nat. Acad. Sci. USA 2005, 102, 6665-6670. doi:10.1073/pnas.0408037102

289. Macrophomate Synthase: QM/MM Simulations Address the Diels-Alder versus Michael-Aldol Reaction Mechanism. Guimarães, C. R. W ; Udier-Blagovic, M.; Jorgensen, W. L. J. Am. Chem. Soc 2005, 127, 3577-3588. doi:10.1021/ja043905b

288. Discovery of a Potent, Selective, and Efficacious Class of Reversible α-Ketoheterocycle Inhibitors of Fatty Acid Amide Hydrolase Effective as Analgesics. Boger, D. L.; Miyauchi, H.; Du, W.; Hardouin, C.; Fecik, R. A.; Cheng, H.; Hwang, I.; Hedrick, M. P.; Leung, D.; Acevedo, O.; Guimarães, C. R. W.; Jorgensen, W. L.; Cravatt, B. F. J. Med. Chem 2005, 48, 1849-1856. doi:10.1021/jm049614v

287. Relationship between side chain structure and 14-helix stability of β 3 -peptides in water. Kritzer, J. A.; Tirado-Rives, J.; Hart, S. A.; Lear, J. D.; Jorgensen, W.L.; Schepartz, A. J. Am. Chem. Soc 2005, 127, 167-178. doi:10.1021/ja0459375

286. Monte Carlo Backbone Sampling for Nucleic Acids using Concerted Rotations including Variable Bond Angles. Ulmschneider, J. P.; Jorgensen, W. L. J. Phys. Chem. B 2004, 108, 16883-16892. doi:10.1021/jp047796z

285. Solvent Effects and Mechanism for a Nucleophilic Aromatic Substitution from QM/MM Simulations. O. Acevedo, W. L. Jorgensen. Org. Lett 2004, 6, 281-2884. doi:10.1021/ol049121k

284. Energetic Preferences for α, β- versus β, γ-Unsaturation. Lee, P. S.; Du, W.; Boger, D. L.; Jorgensen, W. L. J. Org. Chem 2004, 69, 5448-5453. doi:10.1021/jo049363y

283. Free Energies of Hydration from a Generalized Born Model and an All-Atom Force Field. Jorgensen, W. L.; Ulmschneider, J. P.; Tirado-Rives, J. J. Phys. Chem. B 2004, 108, 16264-16270. doi:10.1021/jp0484579

282. The Many Roles of Computation in Drug Discovery. Jorgensen, W. L. Science 2004, 303, 1813-1818. doi:10.1126/science.1096361

281. HIV Reverse Transcriptase Variants: Molecular Modeling of Y181C,V106A, L100I, and K103N Mutations with Non-Nucleoside Inhibitors. Kroeger Smith, K.; Ruby, S.; Horouzhenko, S.; Buckingham, B.;Richardson, J.; Puleri, I.; Potts, E.; Jorgensen, W. L.; Arnold, E.; Zhang, W.; Hughes, S. H.; Michedja, C. J.; Smith, Jr., R. H. Drug Design and Discovery 2003, 18, 151-163. doi:10.1080/10559610390484203

280. Accuracy of Free Energies of Hydration from CM1 and CM3 Atomic Charges. Udier-Blagovic, M.; Morales de T., P.; Pearlman, S.A.; Jorgensen, W.L. J. Comput. Chem 2004, 25, 1322-1332. doi:10.1002/jcc.20059

279. General Model for Estimation of the Inhibition of Protein Kinasesusing Monte Carlo Simulations. Tominaga, Y. & Jorgensen, W.L. J. Med. Chem 2004, 47, 2534-2549. doi:10.1021/jm0304358

278. Polypeptide Folding using Monte Carlo Sampling, Concerted Rotation, and Continum Solvation. Ulmschneider, J.P.; Jorgensen, W.L. J. Am. Chem. Soc 2004, 126, 1849-1857. doi:10.1021/ja0378862

277. Steric Retardation of SN2 Reactions in the Gas Phase and Solution. Vayner, G.; Houk, K.N.; Jorgensen, W.L.; Brauman, J.I. J. Am. Chem. Soc 2004, 126, 9054-9058. doi:10.1021/ja049070m

276. Structural and Energetic Analyses for the Effects of the K103N Mutation of HIV-1 Reverse Transcriptase on Efavirenz Analogs. M.Udier-Blagovic; J. Tirado-Rives and W.L. Jorgensen. J. Med. Chem 2004, 47, 2389-2392. doi:10.1021/jm0303507

275. Extension of the PDDG/PM3 and PDDG/MNDO Semiempirical Molecular Orbital Methods to Halogens. I. Tubert-Brohman; C.R.W. Guimarães, M.P. Repasky & W.L. Jorgensen. J. Comput. Chem 2004, 25, 138-150. doi:10.1002/jcc.10356

274. Analyses of Activuty for Factor Xa Inhibitors Based on Monte Carlo Simulations. D. Ostrovsky; M. Udier-Blagovic and W.L. Jorgensen. J. Med. Chem 2003, 46, 5691-5699. doi:10.1021/jm030288d

273. Validation of a Model for the Complex of HIV-1 Reverse Transcriptase with the Novel Non-nucleoside Inhibitor TMC125. M. Udier-Blagovic, J. Tirado-Rives and W. L. Jorgensen. J. Am. Chem. Soc 2003, 125, 6016-6017. doi:10.1021/ja034308c

272. Activity Predictions for Efavirenz Analogues with the K103N Mutant of HIV Reverse Transcriptase. E.K. Watkins; M. Udier-Blagovic, J. Tirado-Rives, and W.L. Jorgensen. Bioorg. Med. Chem. Lett 2003, 13, 3337-3340. doi:10.1016/S0960-894X(03)00681-4

271. Contributions of Conformational Compression and Preferential Transition State Stabilization to the Rate Enhancement by Chorismate Mutase. C.R.W. Guimarães, M.P. Repasky, J. Chandrasekhar, J. Tirado-Rives, W.L. Jorgensen. J. Am. Chem. Soc 2003, 125, 6892-6899. doi:10.1021/ja021424r

270. Investigation of Solvent Effects for the Claisen Rearrangement of Chorismate to Prephanate:Mechanistic Interpretation via Near Attack Conformations. M.P. Repasky, C.R.W. Guimarães, J. Chandrasekhar, J. Tirado-Rives, and W.L. Jorgensen. J. Am. Chem. Soc 2003, 125, 6663-6672. doi:10.1021/ja021423z

269. Monte carlo backbone sampling for polypeptides with variable bond angles and dihedral angles using concerted totations and a gaussian bias. J. Ulmschnider and W.L. Jorgensen. J. Chem. Phys 2003, 118, 4261-4271. doi:10.1063/1.1542611

268. Molecular Modeling Calculations of HIV-1 Reverse Transcriptase Nonnucleoside Inhibitors: Correlation of Binding Energy with Biological Activity for Novel 2-Aryl-Substituted Benzimidazole Analogs. M.B. Kroeger Smith, B.M. Hose, A. Hawkins, J. Lipchock, R.C. Rizzo, J. Tirado-Rives, W. L. Jorgensen, C.J. Michejda, D.W. Farnsworth, and R.H., Jr. Smith. J. Med. Chem 2003, 46, 1940-1947. doi:10.1021/jm020271f

267. PDDG/PM3 and PDDG/MNDO: Improved Semiempirical Methods. M.P. Repasky, J. Chandrasekhar, and W.L. Jorgensen. J. Comput. Chem 2002, 23, 1601-1622. doi:10.1002/jcc.10162

266. Prediction of Activity for Non-nucleoside Inhibitors with HIV Reverse Transcriptase Based on Monte Carlo Simulations. R. C. Rizzo, M. Udier Blagovic, D.-P. Wang, E.K. Watkins, M.B. Kroeger Smith,R.H. Smith, Jr., J. Tirado-Rives, and W. L. Jorgensen. J. Med. Chem 2002, 45, 2970-2987. doi:10.1021/jm010580q

265. Estimation of Binding Affinities for Celecoxib Analogues with COX-2 via Monte Carlo - Extended Linear Response. S.S. Wesolowski and W.L. Jorgensen. Bioorg. Med. Chem. Lett 2002, 12, 267-270.

264. QM/MM Simulations of Cycloaddition Reactions in Water: Contribution of Enhanced Hydrogen Bonding at the Transition State to the Solvent Effects. J. Chandrasekhar, S. Shariffskul, and W.L. Jorgensen. J. Phys. Chem. B 2002, 106, 8078-8085. doi:10.1021/jp020326p

263. Three- versus four-coordinate phosphorus in the gas phase and in solution:Treacherous relative energies for Phosphine oxide and phosphinous acid. S.S. Wesolowski, N. R. Brinkmann, E. F. Valeev, H. F. Schaefer III,M. P. Repasky, and W. L. Jorgensen. J. Chem. Phys 2002, 116, 112-122. doi:10.1063/1.1418440

262. Prediction of Drug Solubility from Structure. W.L. Jorgensen and E. M. Duffy. Adv. Drug Delivery Reviews 2002, 54, 355-366.

261. Improved Semiempirical Heats of Formation through the Use of Bond and Group Equivalents. M. P. Repasky, J. Chandrasekhar, and W. L. Jorgensen. J. Comp. Chem 2002, 23, 498-510. doi:10.1002/jcc.10023

260. Quantum, intramolecular flexibility, and polarizability effects on the reproduction of the density anomaly of liquid water by simple potential functions. M. W. Mahoney and W. L. Jorgensen. J. Chem. Phys 2001, 115, 10758-10768. doi:10.1063/1.1418243

259. Antiviral Drug Design: Computational Analyses of the Effects of the L100I Mutation for HIV-RT on the binding of NNRTI's. D.-P Wang, R. C. Rizzo, J. Tirado-Rives, and W. L. Jorgensen. Bioorg. Med. Chem. Lett 2001, 11, 2799-2802. doi:10.1016/S0960-894X(01)00510-8

258. New Linear Interaction Method for Binding Affinity Calculations Using a Continum Solvent Model. R. Zhou, R. A. Friesner, A. Ghosh, R. C. Rizzo, W. L. Jorgensen and R. M. Levy. J. Phys. Chem. B 2001, 105, 10388-10397. doi:10.1021/jp011480z

257. COX-2, Src SH2 Domain, HIV Reverse Transcriptase, and Thrombin:Computational Approaches to Drug Design. W. L. Jorgensen, M.L.P. Price, D.J. Price, R.C. Rizzo, D. Wang, AC Pierce and J. Tirado-Rives In. Free Energy Calculations in Rational Drug Design 2001, pp. 299-316.

256. Perfluoroalkanes: Conformational Analysis and Liquid-State Properties from AB Initio and Monte Carlo Calculations. E. K. Watkins, and W. L. Jorgensen. J. Phys. Chem. A 2001, 105, 4118-4125. doi:10.1021/jp004071w

255. Protein Structure Based on NMR Data: An Enhanced Monte carlo Approach. A. C. Pierce, and W. L. Jorgensen. J. Biomol. NMR 2001, 00, 000-000.

254. Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides. G. Kaminski, R. A. Friesner, J. Tirado-Rives and W. L. Jorgensen. J. Phys. Chem. B 2001, 105, 6474-6487. doi:10.1021/jp003919d

253. Estimation of Binding Affinities for Selective Thrombin Inhibitors via Monte Carlo Simulations. A. C. Pierce, and W. L. Jorgensen. J. Med. Chem 2001, 44, 1043-1050. doi:10.1021/jm000405u

252. Improved Convergence of Binding Affinities with Free Energy Perturbation:Application to Nonpeptide Ligands with pp60 c-src SH2 Domain. D. L. Price, and W. L. Jorgensen. J. Comp. Aided Mol. Design 2001, 15, 681-695.

251. Gas-Phase and Liquid-State Properties of Esters, Nitriles, and Nitro Compounds with the OPLS-AA Force Field. M.L.P. Price, D. Ostrovsky, and W. L. Jorgensen. J. Comp. Chem 2001, 22, 1340-1352. doi:10.1002/jcc.1092

250. Efficient Exploration of Conformational Space Using the Stochastic Search Method: Application to -peptide Oligomers. J. Chandrasekhar, M. Saunders, and W. L. Jorgensen. J. Comp. Chem 2001, 22, 1646-1654. doi:10.1002/jcc.1120

249. Rationale for the Observed COX-2/COX-1 Selectivity of Celecoxib from Monte Carlo Simulations. M. L. P. Price, and W. L. Jorgensen. Biorg. Med. Chem. Lett 2001, 11, 1541-1544.

248. Rapid Estimation of Electronic Degrees of Freedom in Monte Carlo Calculations for Polarizable Models of Liquid Water. M. W. Mahoney and W. L. Jorgensen. J. Chem. Phys 2001, 114, 9337-9349. doi:10.1063/1.1370083

247. Diffusion constant of the TIP5P model liquid water. M. W. Mahoney, and W. L. Jorgensen. J. Chem. Phys 2001, 114, 363-366. doi:10.1063/1.1329346

246. Estimation of Binding Affinities for HEPT and Nevirapine Analogs with HIV-1Reverse Transcriptase via Monte Carlo Simulations. R. C. Rizzo, J. Tirado-Rives, and W. L. Jorgensen. J. Med. Chem 2001, 44, 145-154. doi:10.1021/jm000255n

245. Validation of a Model for the Complex of HIV-1 Reverse Transcriptasewith Sustiva through Computation of Resistance Profiles. R. C. Rizzo, De-Ping Wang, J. Tirado-Rives, and W. L. Jorgensen. J. Am. Chem. Soc 2000, 122, 12898-12900. doi:10.1021/ja003113r

244. Computational Binding Studies of Human pp60 c-src SH2 Domain witha series of Nonpeptide, Phosphophenyl-Containing Ligands. Daniel J. Price and W. L. Jorgensen. Biorg. Med. Chem. Lett 2000, 10, 2067-2070.

243. Analysis of Binding Affinities for Celecoxib Analogs with COX-1 and COX-2from Docking and Monte Carlo Simulations an Insight into COX-2/COX-1 Selectivity. M. L. Plount Price and W. L. Jorgensen. J. Am. Chem. Soc 2000, 122, 9455-9466. doi:10.1021/ja001018c

242. Prediction of Drug Solubility from Monte Carlo Simulations. W. L. Jorgensen and E. M. Duffy. Bioorg. Med. Chem. Lett 2000, 10, 1155-1158.

241. Origin of the Inversion of the Acidity Order for Haloacetic Acidson Going from the Gas Phase to Solution. K. B. Wiberg, S. Clifford, W. L. Jorgensen, and M. Frisch. J. Phys. Chem. A 2000, 104, 7625-7628. doi:10.1021/jp000944a

240. A five-site model liquid water and the reproduction of the density anomaly by rigid, non-polarizable models. M. W. Mahoney and W. L. Jorgensen. J. Chem. Phys 2000, 112, 8910-8922. doi:10.1063/1.481505

239. Monte Carlo Calculations on HIV-1 Reverse Transcriptase Complexed with the Nonnucleoside Inhibitor 8-Cl TIBO: Contribution of the L100I and Y181C Variants to Protein Stability and Biological Activity. M. B. Kroeger Smith, M. L. Lamb, J. Tirado-Rives, W. L. Jorgensen, C. J. Michejda, S. K. Ruby, and R. H. Smith, Jr. Protein Engin 2000, 13, 413-421.

238. Prediction of Properties from Simulations: Free Energies of Solvation in Hexadecane, Octanol, and Water. E. M. Duffy and W. L. Jorgensen. J. Am. Chem. Soc 2000, 122, 2878-2888. doi:10.1021/ja993663t

237. Developing a Dynamic Pharmacaphore Model for HIV-1 Integrase. H. A. Carlson, K. M. Masukawa, W. L. Jorgensen, R. D. Lins, J. M. Briggs, and J. A. McCammon. J. Med. Chem 2000, 43, 2100-2114. doi:10.1021/jm990322h

236. Perspective on "Equation of State Calculations by Fast Computing Machines". W. L. Jorgensen. Theor. Chem. Acc 2000, 103, 225-227. doi:10.1007/s002149900053

235. Host-Guest Chemistry of Rotaxanes and Catenanes: Application of a Polarizable All-Atom Force to Cyclobis(paraquat-p-phenylene) Complexes with Disubstituted Benzenes and Biphenyls. G. A. Kaminski and W. L. Jorgensen. Perkin Trans 1999, 2, 2365-2376.

234. Selective Anion Complexation by a Calix[4]pyrrole Investigated by Monte Carlo Simulations. W. P. van Hoorn and W. L. Jorgensen. J. Org. Chem 1999, 64, 7439-7444. doi:10.1021/jo9907437

233. OPLS All-Atom Model for Amines: Resolution of the Amine Hydration Problem. R. C. Rizzo and W. L. Jorgensen. J. Am. Chem. Soc 1999, 121, 4827-4836. doi:10.1021/ja984106u

232. Computational Studies of the Molecular Recognition of Halide Anions by Calix[4]Aromatics. N. A. McDonald, W. P. van Hoorn, E. M. Duffy, and W. L. Jorgensen. NATO ASI Ser., Ser. C 1999, 527, 147-156.

231. Estimation of the Binding Affinities of FKBP12 Inhibitors Using a Linear Response Method. M. L. Lamb, J. Tirado-Rives, and W. L. Jorgensen. Bioorg. Med. Chem 1999, 7, 851-860.

230. Computational Studies of Molecular Recognition from Alkane Dimers to Protein-Ligand Binding. W. L. Jorgensen, E. M. Duffy, J. W. Essex, D. L. Severance, J. F. Blake, N. A. McDonald, and J. Tirado-Rives In. Crystal Engineering 1999, pp. 113-125.

229. Solvent as Catalyst - Computational Studies of Organic Chemistry in Solution. D. Lim, C. Jenson, M. P. Repasky, and W. L. Jorgensen In. Transition State Modeling for Catalysis 1999, ACS Symposium Ser., Vol. 721, pp. 74-85.

228. Prediction of Binding Affinities for TIBO Inhibitors of HIV-1 Reverse Transcriptase Using Monte Carlo Simulations in a Linear Response Method. R. H. Smith, Jr., W. L. Jorgensen, J. Tirado-Rives, M. L. Lamb, P. A. Janssen, C. J. Michejda, and M. B. Kroeger Smith. J. Med. Chem 1998, 41, 5272-5286. doi:10.1021/jm9804174

227. Ab Initio and Monte Carlo Study of Solvent Effects on a 1,3-Dipolar Cycloaddition. M. P. Repasky and W. L. Jorgensen. J. Chem. Soc., Faraday Discuss 1998, 110, 379-389.

226. Development of an All-Atom Force Field for Heterocycles. Properties of Liquid Pyrrole, Furan, Diazoles, and Oxazoles. W. L. Jorgensen and N. A. McDonald. J. Phys. Chem. B 1998, 102, 8049-8059. doi:10.1021/jp981200o

225. Conformational Complexity of Succinic Acid and Its Monoanion in the Gas Phase and in Solution: Ab Initio Calculations and Monte Carlo Simulations. D. J. Price, J. D. Roberts, and W. L. Jorgensen. J. Am. Chem. Soc 1998, 120, 9672-9679. doi:10.1021/ja9812397

224. Investigations of Neurotrophic Inhibitors of FK506 Binding Protein via Monte Carlo Simulations. M. L. Lamb and W. L. Jorgensen. J. Med. Chem 1998, 41, 3928-3939. doi:10.1021/jm980062o

223. Monte Carlo Investigations of Selective Anion Complexation by a Bis(phenylurea)-p-tert-Butylcalix[4]arene. N. A. McDonald, E. M. Duffy, and W. L. Jorgensen. J. Am. Chem. Soc 1998, 120, 5104-5111. doi:10.1021/ja980140x

222. Ab Initio Calculations on Hydrogen-Bonded Complexes of Small Organic Molecules with Water. P. R. Rablen, J. W. Lockman, and W. L. Jorgensen. J. Phys. Chem. A 1998, 102, 3782-3797. doi:10.1021/jp980708o

221. Preorganized Metallomacrocycles: Improved Binding and Selectivity of Ammonia over Primary Amines. F. C. J. M. van Veggel, H. G. Noorlander-Bunt,W. L. Jorgensen and D. N. Reinhoudt. J. Org. Chem 1998, 63, 3554-3559. doi:10.1021/jo971943q

220. A QM/MM Method Based on CM1A Charges: Applications to Solvent Effects on Organic Equilibria and Reactions. G. A. Kaminski and W. L. Jorgensen. J. Phys. Chem. B 1998, 102, 1787-1796. doi:10.1021/jp980314x

219. Computation of Free Energy Changes in Solution. W. L. Jorgensen In. Encyclopedia of Computational Chemistry 1998, Vol. 2, pp. 1061-1070.

218. Temperature Dependence of TIP3P, SPC, and TIP4P Water from NPT Monte Carlo Simulations: Seeking a Temperature of Maximum Density. W. L. Jorgensen and C. Jenson. J. Comp. Chem 1998, 19, 1179-1186. doi:10.1002/(SICI)1096-987X(19980730)19:10<1179::AID-JCC6>3.0.CO;2-J

217. Monte Carlo Simulations of Liquids. W. L. Jorgensen In. Encyclopedia of Computational Chemistry 1998, Vol. 3, pp. 1754-1763.

216. OPLS Force Fields. W. L. Jorgensen In. Encyclopedia of Computational Chemistry 1998, Vol. 3, pp. 1986-1989.

215. ChemEdit - An Interactive Editor for Chemists. D. Lim and W. L. Jorgensen In. Encyclopedia of Computational Chemistry 1998, Vol. 5, pp. 3295-3302.

214. BOSS - Biochemical and Organic Simulation System. W. L. Jorgensen In. Encyclopedia of Computational Chemistry 1998, Vol. 5, pp. 3281-3285.

213. Computational Approaches to Molecular Recognition. M. L. Lamb and W. L. Jorgensen. Curr. Opinion Chem. Biol 1997, 1, 449-457.

212. Elucidation of Transition Structures and Solvent Effects for Epoxidations by Dimethyldioxirane. C. Jenson, J. Liu, K. N. Houk, and W. L. Jorgensen. J. Am. Chem. Soc 1997, 119, 12982-12983. doi:10.1021/ja971766a

211. Computational Investigations of Carbenium Ion Reactions Relevant to Sterol Biosynthesis. C. Jenson and W. L. Jorgensen. J. Am. Chem. Soc 1997, 119, 10846-10854. doi:10.1021/ja9714245

210. Monte Carlo Simulations for Proteins: Binding Affinities for Trypsin-Benzamidine Complexes via Free Energy Perturbations. J. W. Essex, D. L. Severance, J. Tirado-Rives, and W. L. Jorgensen. J. Phys. Chem 1997, 101, 9663-9669.

209. Development of an All-Atom Force Field for Heterocycles. Properties of Liquid Pyridine and Diazenes. W. L. Jorgensen and N. A. McDonald. J. Mol. Struct. (THEOCHEM) 1998, 424, 145-155. doi:10.1016/S0166-1280(97)00237-6

208. The OPLS All-Atom Force Field for Carbohydrates. W. Damm, A. Frontera, J. Tirado-Rives, and W. L. Jorgensen. J. Comp. Chem 1997, 18, 1955-1970. doi:10.1002/(SICI)1096-987X(199712)18:16<1955::AID-JCC1>3.0.CO;2-L

207. Molecular Dynamics of the Unfolding of Barnase in Water and 8 M Aqueous Urea. J. Tirado-Rives, M. Orozco, and W. L. Jorgensen. Biochemistry 1997, 36, 7313-7329. doi:10.1021/bi970096i

206. Computational Binding Studies of Orthogonal Cyclosporin-Cyclophilin Pairs. A. C. Pierce and W. L. Jorgensen. Angew. Chem 1997, 109, 1595-1598. 36, 1466-1469 ( 1997 ).

205. Approaches to Protein-Ligand Binding from Computer Simulations. W. L. Jorgensen, E. M. Duffy, J. W. Essex, D. L. Severance, J. F. Blake,D. K. Jones- Hertzog, M. L. Lamb, and J. Tirado-Rives. NATO ASI Ser., Ser. E 1997, 342, 21-34.

204. Free Energies of Solvation in Chloroform and Water from a Linear Response Approach. N. A. McDonald, H. A. Carlson, and W. L. Jorgensen. J. Phys. Org. Chem 1997, 10, 563-576.

203. Energetics of Cation-Olefin Addition in the Gas Phase and in Solution. C. Jenson and W. L. Jorgensen. Synlett 1997, 518-520. (E. J. Corey Issue).

202. Binding Affinities for Sulfonamide Inhibitors with Human Thrombinusing Monte Carlo Simulations with a Linear Response Method. D. K. Jones-Hertzog and W. L. Jorgensen. J. Med. Chem 1997, 40, 1539-1549. doi:10.1021/jm960684e

201. Performance of the AMBER94, MMFF94, and OPLS-AA Force Fields for Modeling Organic Liquids. G. Kaminski and W. L. Jorgensen. J. Phys. Chem 1996, 100, 18010-18013. doi:10.1021/jp9624257

200. Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids. W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives. J. Am. Chem. Soc 1996, 118, 11225-11236. doi:10.1021/ja9621760

199. Monte Carlo Investigations of Solvent Effects on the Chorismate to Prephenate Rearrangement. H. A. Carlson and W. L. Jorgensen. J. Am. Chem. Soc 1996, 118, 8475-8484. doi:10.1021/ja961500o

198. Viability of Molecular Modeling with Pentium-Based PC's. J. Tirado-Rives and W. L. Jorgensen. J. Comp. Chem 1996, 17, 1385-1386. doi:10.1002/(SICI)1096-987X(199608)17:11<1385::AID-JCC11>3.0.CO;2-M

197. The Origin of Self-Assembling Ternary Complex Stabilities and Template Ratios in Carceplex Formation. K. Nakamura, C. Sheu, A. E. Constable, K. N. Houk, J. C. Sherman, R.G. Chapman, and W. L. Jorgensen. J. Am. Chem. Soc 1997, 119, 4321-4322. doi:10.1021/ja9623065

196. Monte Carlo vs. Molecular Dynamics for Conformational Sampling. W. L. Jorgensen and J. Tirado-Rives. J. Phys. Chem 1996, 100, 14508-14513. doi:10.1021/jp960880x

195. Molecular Recognition of Carbohydrates: Interaction of Diols with Acetate Ion. W. L. Jorgensen, W. Damm, A. Frontera, and M. L. Lamb. NATO ASI Ser., Ser. C 1996, 485, 115-126.

194. SCRF/Monte Carlo Study of Solvent Effects on a Polar [2 + 2] Cycloaddition. D. Lim and W. L. Jorgensen. J. Phys. Chem 1996, 100, 17490-17500. doi:10.1021/jp962409+

193. The Importance of Polarization for Dipolar Solutes in Low-Dielectric Media: 1,2-Dichloroethane and Water in Cyclohexane. W. L. Jorgensen, N. A. McDonald, M. Selmi, and P. R. Rablen. J. Am. Chem. Soc 1995, 117, 11809-11810. doi:10.1021/ja00152a025

192. Regioselective Synthesis of Allylic Alcohols Using the Mislow-Evans Rearrangement: A Theoretical Rationalization. D. K. Jones-Hertzog and W. L. Jorgensen. J. Org. Chem 1995, 60, 6682-6683.

191. Dielectric Constants of Formamide and Dimethylformamide via Computer Simulations. J. W. Essex and W. L. Jorgensen. J. Phys. Chem 1995, 99, 17956-17962. doi:10.1021/j100051a021

190. Elucidation of Transition States and Solvent Effects for the Mislow-Evans Rearrangement of Allylic Sulfoxides. D. K. Jones-Hertzog and W. L. Jorgensen. J. Am. Chem. Soc 1995, 117, 9077-9078.

189. Free Energies of Hydration for Organic Molecules from Monte Carlo Simulations. W. L. Jorgensen and J. Tirado-Rives. Perspectives in Drug Discovery and Design 1995, 3, 123-138.

188. An Extended Linear Response Method for Determining Free Energies of Hydration. H. A. Carlson and W. L. Jorgensen. J. Phys. Chem 1995, 99, 10667-10673.

187. The Energy Difference Between the Classical and the Nonclassical 2-Norbornyl Cation in Solution. A Combined Ab Initio - Monte Carlo Study. P.R. Schreiner, D. L. Severance, W. L. Jorgensen, P. v.R. Schleyer, and H.F. Schaefer III. J. Am. Chem. Soc 1995, 117, 2663-2664.

186. Computer Assisted Mechanistic Evaluation of Organic Reactions,26. Diastereoselective Additions: Cram's Rule. J. M. Fleischer, A. J. Gushurst, and W. L. Jorgensen. J. Org. Chem 1995, 60, 490-498.

185. Investigations into the Stereochemistry of Steroid-Cyclophane Complexes via Monte Carlo Simulations. H. A. Carlson and W. L. Jorgensen. Tetrahedron (Symposium in Print) 1995, 51, 449-472. doi:10.1016/0040-4020(94)00908-D

184. A Comprehensive Study of the Rotational Profiles of Some Organic Systems by Ab Initio MO Theory, Forming a Basis for Peptide Torsional Parameters. D. S. Maxwell, J. Tirado-Rives, and W. L. Jorgensen. J. Comp. Chem 1995, 16, 984-1010. doi:10.1002/jcc.540160807

183. An Empirical Boundary Potential for Water Droplet Simulations. J. W. Essex and W. L. Jorgensen. J. Comp. Chem 1995, 16, 951-972. doi:10.1002/jcc.540160805

182. Generalized Alteration of Structure and Parameters (GASP); a New Method for Free Energy Perturbations in Systems Containing Flexible and/or Fixed Degrees of Freedom. D. L. Severance, J. W. Essex, and W. L. Jorgensen. J. Comp. Chem 1995, 16, 311-327. doi:10.1002/jcc.540160306

181. Free Energies of Hydration and Pure Liquid Properties of Hydrocarbons from the OPLS All-Atom Model. G. Kaminski, E. M. Duffy, T. Matsui, and W. L. Jorgensen. J. Phys. Chem 1994, 98, 13077-13081. doi:10.1021/j100100a043

180. Structure and Binding for Complexes of Rebek's Acridine Diacid with Pyrazine, Quinoxaline, and Pyridine from Monte Carlo Simulations withan All-Atom Force Field. E. M. Duffy and W. L. Jorgensen. J. Am. Chem. Soc 1994, 116, 6337-6343.

179. Effects of Hydration and Multiple Reactant Conformers on the Claisen Rearrangement of Allyl Vinyl Ether from Computer Simulations. D. L. Severance and W. L. Jorgensen. ACS Symposium Ser 1994, 568, 243-259.

178. Computer Assisted Mechanistic Evaluation of Organic Reactions, 25. Structure Diagram Positioning. H. E. Helson and W. L. Jorgensen. J. Chem. Info. Comput. Sci 1994, 34, 962-971.

177. Computer Assisted Mechanistic Evaluation of Organic Reactions,24. Carbene Chemistry. H. E. Helson and W. L. Jorgensen. J. Org. Chem 1994, 59, 3841-3856.

176. Monte Carlo Results for the Effect of Solvation on the Anomeric Equilibrium for 2-Methoxytetrahydropyran. W. L. Jorgensen, P. I. Morales de Tirado, and D. L. Severance. J. Am. Chem. Soc 1994, 116, 2199-2200.

175. Investigation of Solvent Effects on Pericyclic Reactions by Computer Simulations. W. L. Jorgensen, J. F. Blake, D. Lim, and D. L. Severance. Trans. Faraday Soc 1994, 90, 1727-1732.

174. Computer Assisted Mechanistic Evaluation of Organic Reactions.23. Dissolving Metal Reductions with Lithium in Liquid Ammonia Includingthe Birch Reduction. S. Sinclair and W. L. Jorgensen. J. Org. Chem 1994, 59, 762-772.

173. Solvent Effects on the Ring Opening of Cyclopropanones to Oxyallyls- A Combined Ab Initio and Monte Carlo Study. D. Lim, D. A. Hrovat, W. T. Borden, and W. L. Jorgensen. J. Am. Chem. Soc 1994, 116, 3494-3499.

172. Modeling Interactions with Benzene: Aryl-Aryl, Cation-π,and Chaotrope-π. W. L. Jorgensen, D. L. Severance, and E. M. Duffy In. in Computational Approaches in Supramolecular Chemistry 1994, pp. 161-173.

171. Synthesis and Investigations of Enetetraynes. D. Elbaum, T. B. Nguyen, W. L. Jorgensen, and S. L. Schreiber. Tetrahedron 1994, 50, 1503-1518. doi:10.1016/S0040-4020(01)80631-1

170. Enhanced Hydrogen Bonding of Water to Diels-Alder Transition States- Ab Initio Evidence. J. F. Blake, D. Lim, and W. L. Jorgensen. J. Org. Chem 1994, 59, 803-805.

169. Do Denaturants Interact with Aromatic Hydrocarbons in Water?. E. M. Duffy, P. J. Kowalczyk, and W. L. Jorgensen. J. Am. Chem. Soc 1993, 115, 9271.

168. Quantification of Solvent Effects on the Acidities of Z and E Estersfrom Fluid Simulations. J. D. Evanseck, K. N. Houk, J. M. Briggs, and W. L. Jorgensen. J. Am. Chem. Soc 1994, 116, 10630-10638.

167. Mechanism for the Rotamase Activity of FK506 Binding Protein from Molecular Dynamics Simulations. M. Orozco, J. Tirado-Rives, and W. L. Jorgensen. Biochemistry 1993, 32, 12864.

166. Computational Investigations of Protein Denaturation: Apomyoglobinand Chaotrope-Arene Interactions. W. L. Jorgensen, E. M. Duffy, and J.T irado-Rives. Phil. Trans. Roy. Soc. London A 1993, 345, 87-96.

165. Comparison of 6-31G* Based MST/SCRF and FEP Evaluations of the Free Energies of Hydration for Small Neutral Molecules. M. Orozco, W. L. Jorgensen, and F. J. Luque. J. Comp. Chem 1993, 14, 1498. doi:10.1002/jcc.540141212

164. Computer Assisted Mechanistic Evaluation of Organic Reactions.22. The Generation and Use of Three-Dimensional Structures. S. A. Gothe, H. E. Helson, I. Houdaverdis, I. Lagerstedt, S. Sinclair,and W. L. Jorgensen. J. Org. Chem 1993, 58, 5081.

163. Molecular Dynamics and Monte Carlo Simulations Favor the α-Helical Form for Alanine-based Peptides in Water. J. Tirado-Rives, D. S. Maxwell, and W. L. Jorgensen. J. Am. Chem. Soc 1993, 115, 11590.

162. Accuracy of Free Energies of Hydration for Organic Molecules from6-31G* Derived Partial Charges. H. A. Carlson, T. B. Nguyen, M. Orozco, and W. L. Jorgensen. J. Comp. Chem 1993, 14, 1240. doi:10.1002/jcc.540141013

161. Limited Effects of Polarization for Cl - (H 2 O)nand Na + (H 2 O)n Clusters. W. L. Jorgensen and D. L. Severance. J. Chem. Phys 1993, 99, 4233. doi:10.1063/1.466077

160. Urea: Potential Functions, log P, and Free Energy of Hydration. E. M. Duffy, D. L. Severance, and W. L. Jorgensen. Isr. J. Chem 1993, 33, 323.

159. Supramolecular Chemistry. (Invited editorial.). W. L. Jorgensen. Proc. Nat. Acad. Sci., USA 1993, 90, 1635.

158. Molecular Dynamics Simulations of the Unfolding of Apomyoglobinin Water. J. Tirado-Rives and W. L. Jorgensen. Biochemistry 1993, 32, 4175.

157. Ab Initio Study of Diels-Alder Reactions of Cyclopentadiene with Ethylene, Isoprene, Cyclopentadiene, Acrylonitrile, and Methyl Vinyl Ketone. W. L. Jorgensen, D. Lim, and J. F. Blake. J. Am. Chem. Soc 1993, 115, 2936. doi:10.1021/ja00060a048

156. Modeling the Complexation of Substituted Benzenes by a Cyclophane Host in Water. W. L. Jorgensen and T. B. Nguyen. Proc. Nat. Acad. Sci., USA 1993, 90, 1194. doi:10.1073/pnas.90.4.1194

155. Monte Carlo Simulations of Pure Liquid Substituted Benzenes with OPLS Potential Functions. W. L. Jorgensen, E. R. Laird, T. B. Nguyen, amd J. Tirado-Rives. J. Comp. Chem 1993, 13, 206. doi:10.1002/jcc.540140208

154. Monte Carlo Simulations of the Hydration of Substituted Benzenes with OPLS Potential Functions. W. L. Jorgensen and T. B. Nguyen. J. Comp. Chem 1993, 13, 195. doi:10.1002/jcc.540140207

153. Solvent Effects on the Diels-Alder Reaction of Methyl Vinyl Ketoneand Cyclopentadiene from Computer Simulations. W. L. Jorgensen, D. Lim, and J. F. Blake In. Elementary Reaction Steps in Heterogeneous Catalysis 1993, pp. 377-387.

152. Effects of Hydration on the Claisen Rearrangement of Allyl Vinyl Ether from Computer Simulations. D. L. Severance and W. L. Jorgensen. J. Am. Chem. Soc 1992, 114, 10966.

151. Solvent Effects on the Barrier to Isomerization for a Tertiary Amide from Ab Initio and Monte Carlo Calculations. E. M. Duffy, D. L. Severance, and W. L. Jorgensen. J. Am. Chem. Soc 1992, 114, 7535. doi:10.1021/ja00045a029

150. Enhanced View of Structure and Binding for Cyclophane-Arene Complexesthrough Joint Theoretical and Experimental Study. W. L. Jorgensen, T. B. Nguyen, E. M. Sanford, I. Chao, K. N. Houk,and F. Diederich. J. Am. Chem. Soc 1992, 114, 4003-4004. doi:10.1021/ja00036a074

149. Structure and Binding for Cyclophane-Arene Complexes in Water from Monte Carlo Simulations. W. L. Jorgensen and T. B. Nguyen. NATO ASI Series C 1992, 371, 383.

148. Free Energy Profiles for Na + Adsorption on a Metal Electrode. T. Matsui and W. L. Jorgensen. J. Am. Chem. Soc 1992, 114, 3220-3226. doi:10.1021/ja00035a009

147. Computer-Assisted Mechanistic Analysis of Organic Reactions. 20. Ene and Retro-ene Chemistry. G. D. Paderes and W. L. Jorgensen. J. Org. Chem 1992, 57, 1904-1916. doi:10.1021/jo00032a054

146. Rusting of the Lock and Key Model of Protein-Ligand Binding. W. L. Jorgensen. Science 1991, 254, 954-955. doi:10.1126/science.1719636

145. Solvent Effects on a Diels-Alder Reaction from Computer Simulations. J. F. Blake and W. L. Jorgensen. J. Am. Chem. Soc 1991, 113, 7430-7432. doi:10.1021/ja00019a055

144. Computational Studies of FK506: Conformational Search and Molecular Dynamics Simulation in Water. J. Pranata and W. L. Jorgensen. J. Am. Chem. Soc 1991, 113, 9483-9493. doi:10.1021/ja00025a010

143. Computational Insights on Intermolecular Interactions and Bindingin Solution. W. L. Jorgensen. Chemtracts - Organic Chemistry 1991, 4, 91-119.

142. Proton Affinities and Gas-phase Basicities of Alkyl and Silyl Ethers. J. F. Blake and W. L. Jorgensen. J. Org. Chem 1991, 56, 6052-6059. doi:10.1021/jo00021a018

141. Computer-Assisted Mechanistic Evaluation of Organic Reactions. 18. Reductions with Hydrides. G. D. Paderes, P. Metivier, and W. L. Jorgensen. J. Org. Chem 1991, 56, 4718-4733. doi:10.1021/jo00015a028

140. Monte Carlo Simulations Yield Absolute Free Energies of Bindingfor Guanine-Cytosine and Adenine-Uracil Base Pairs in Chloroform. J. Pranata and W. L. Jorgensen. Tetrahedron 1991, 47, 2491. doi:10.1016/S0040-4020(01)81783-X

139. Molecular Dynamics Simulations of the Unfolding of an α-Helical Analog of Ribonuclease-A S-Peptide in Water. J. Tirado-Rives and W. L. Jorgensen. Biochemistry 1991, 30, 3864-3861. doi:10.1021/bi00230a009

138. Chemical Chameleons: Hydrogen Bonding with Imides and Lactams in Chloroform. W. L. Jorgensen and D. L. Severance. J. Am. Chem. Soc 1991, 113, 209-216. doi:10.1021/ja00001a030

137. Monte Carlo Simulations of Liquid Acetic Acid and Methyl Acetate with the OPLS Potential Functions. J. M. Briggs, T. B. Nguyen, and W. L. Jorgensen. J. Phys. Chem 1991, 95, 3315-3322. doi:10.1021/j100161a065

136. OPLS Potential Functions for Nucleotide Bases. Relative Association Constants of Hydrogen-Bonded Base Pairs in Chloroform. J. Pranata, S. G. Wierschke, and W. L. Jorgensen. J. Am. Chem. Soc 1991, 113, 2810-2819. doi:10.1021/ja00008a002

135. CAMEO: A Program for the Logical Prediction of the Products of Organic Reactions. W. L. Jorgensen, E. R. Laird, A. J. Gushurst, J. M. Fleischer, S. A.Gothe, H. E. Helson, G. D. Paderes, and S. Sinclair. Pure Appl. Chem 1990, 62, 1921.

134. Computer Assisted Analysis of Reactions Involving Organic Free Radicals and Diradicals. E. R. Laird and W. L. Jorgensen. J. Chem. Info. Comput. Sci 1990, 30, 458-466. doi:10.1021/ci00068a018

133. Origin of the Strong Binding of Adenine to a Molecular Tweezer. J. F. Blake and W. L. Jorgensen. J. Am. Chem. Soc 1990, 112, 7269-7278. doi:10.1021/ja00176a029

132. Monte Carlo Simulations of Liquid Alkyl Ethers with the OPLS Potential Functions. J. M. Briggs, T. Matsui, and W. L. Jorgensen. J. Comput. Chem 1990, 11, 958. doi:10.1002/jcc.540110808

131. Aromatic-Aromatic Interactions: Free Energy Profiles for the Benzene Dimer in Water, Chloroform, and Liquid Benzene. W. L. Jorgensen and D. L. Severance. J. Am. Chem. Soc 1990, 112, 4768-4774. doi:10.1021/ja00168a022

130. The Importance of Secondary Interactions in Triply Hydrogen-Bonded Complexes: Guanine-Cytosine vs. Uracil-Diaminopyridine. W. L. Jorgensen and J. Pranata. J. Am. Chem. Soc 1990, 112, 2008-2010. doi:10.1021/ja00161a061

129. Structure and Basicity of Silyl Ethers: A Crystallographic and Ab Initio Inquiry into the Mode of Silicon-Oxygen Interactions. S. Shambayati, J. F. Blake, S. G. Wierschke, W. L. Jorgensen, and S.L. Schreiber. J. Am. Chem. Soc 1990, 112, 697-703. doi:10.1021/ja00158a031

128. Relative Partition Coefficients for Organic Solutes from Fluid Simulations. W. L. Jorgensen, J. M. Briggs, and M. L. Contreras. J. Phys. Chem 1990, 94, 1683-1686. doi:10.1021/j100367a084

127. Computer-Assisted Mechanistic Evaluation of Organic Reactions. 17. Free Radical Chain Reactions. E. R. Laird and W. L. Jorgensen. J. Org. Chem 1990, 55, 9-27. doi:10.1021/jo00288a005

126. Molecular Dynamics of Proteins with the OPLS Potential Functions. Simulation of the Third Domain of Silver Pheasant Ovomucoid in Water. J. Tirado-Rives and W. L. Jorgensen. J. Am. Chem. Soc 1990, 112, 2773-2781. doi:10.1021/ja00163a046

125. Interactions Between Amides in Solution and the Thermodynamics of Weak Binding. W. L. Jorgensen. J. Am. Chem. Soc 1989, 111, 3770-3771. doi:10.1021/ja00192a057

124. Free Energy Calculations: A Breakthrough for Modeling Organic Chemistry in Solution. W. L. Jorgensen. Acc. Chem. Res 1989, 22, 184-189. doi:10.1021/ar00161a004

123. Molecular Dynamics Simulation of the Third Domain of Silver Pheasant Ovomucoid in Water. W. L. Jorgensen and J. Tirado-Rives. Proceedings of the 1988 Nobel Symposium, Chem. Scripta 1989, 29A, 191.

122. Substituent Effects and Transition Structures for Diels-Alder Reactionsof Butadiene and Cyclopentadiene with Cyanoalkenes. K. N. Houk, R. J. Loncharich, J. F. Blake, and W. L. Jorgensen. J. Am. Chem. Soc 1989, 111, 9172-9176. doi:10.1021/ja00208a006

121. Structure and Binding for Rebek's Diacid in Chloroform. A Demure Host for Pyrazine. W. L. Jorgensen, S. Boudon, and T. B. Nguyen. J. Am. Chem. Soc 1989, 111, 755-757. doi:10.1021/ja00184a067

120. A Priori pKa Calculations and the Hydration of Organic Anions. W. L. Jorgensen and J. M. Briggs. J. Am. Chem. Soc 1989, 111, 4190-4197. doi:10.1021/ja00194a007

119. Variational Transition State for the Reaction of Cl2C: with Ethyleneand the Thermodynamics of Carbene Additions. J. F. Blake, S. G. Wierschke and W. L. Jorgensen. J. Am. Chem. Soc 1989, 111, 1919-1920. doi:10.1021/ja00187a078

118. Energetics and Hydration of the Constituent Ion Pairs of Tetramethylammonium Chloride. J. K. Buckner and W. L. Jorgensen. J. Am. Chem. Soc 1989, 111, 2507-2516. doi:10.1021/ja00189a023

117. Free Energies in Solution - The Aqua Vitae of Computer Simulations. W. L. Jorgensen In. Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications 1989, pp. 60.

116. Ab Initio Investigation of the -Silicon Effect on Alkyland Cyclopropyl Carbenium Ions and Radicals. M. R. Ibrahim and W. L. Jorgensen. J. Am. Chem. Soc 1989, 111, 819-824. doi:10.1021/ja00185a005

115. Computer-Assisted Evaluation of Oxidation Reactions. G. D. Paderes and W. L. Jorgensen. J. Org. Chem 1989, 54, 2058-2085. doi:10.1021/jo00270a014

114. Free Energy of TIP4P Water and the Free Energies of Hydration of CH4 and Cl- from Statistical Perturbation Theory. W. L. Jorgensen, J. F. Blake and J. K. Buckner. Chem. Phys 1989, 129, 193. doi:10.1016/0301-0104(89)80004-7

113. Efficient Computation of Absolute Free Energies of Binding by Computer Simulations. Application to the Methane Dimer in Water. W. L. Jorgensen, J. K. Buckner, S. Boudon and J. Tirado-Rives. J. Chem. Phys 1988, 89, 3742. doi:10.1063/1.454895

112. Theoretical Examination of Hexanol-Water Interfaces. J. Gao and W. L. Jorgensen. J. Phys. Chem 1988, 92, 5813-5822. doi:10.1021/j100331a053

111. Cis/Trans Energy Difference for the Peptide Bond in the Gas Phase and Aqueous Solution. W. L. Jorgensen and J. Gao. J. Am. Chem. Soc 1988, 110, 4212-4216. doi:10.1021/ja00221a020

110. Computer-Assisted Mechanistic Evaluation of Organic Reactions. 15. Heterocycle Synthesis. M. G. Bures and W. L. Jorgensen. J. Org. Chem 1988, 53, 2504-2520. doi:10.1021/jo00246a020

109. Computer-Assisted Mechanistic Evaluation of Organic Reactions, 14. Reactions of Sulfur and Phosphorus Ylides, Iminophosphoranes, and P=X-Activated Anions. A. J. Gushurst and W. L. Jorgensen. J. Org. Chem 1988, 53, 3397-3408. doi:10.1021/jo00250a001

108. Modeling Molecular Transformations in Solution. W. L. Jorgensen, J. K. Buckner, and J. Gao In. Chemical Reactivity in Liquids 1988, pp. 253-263.

107. Monte Carlo Simulations of Liquid Acetonitrile with a Three-Site Model. W. L. Jorgensen and J. M. Briggs. Molec. Phys 1988, 63, 547.

106. The OPLS Force Field for Proteins. Energy Minimizations for Crystals of Cyclic Peptides and Crambin. W. L. Jorgensen and J. Tirado-Rives. J. Am. Chem. Soc 1988, 110, 1657-1666. doi:10.1021/ja00214a001

105. Energy Profiles for Organic Reactions in Solution. W. L. Jorgensen. Adv. Chem. Phys., Part II 1988, 70, 469.

104. Use of Statistical Perturbation Theory for Computing Solvent Effects on Molecular Conformation. Butane in Water. W. L. Jorgensen and J. K. Buckner. J. Phys. Chem 1987, 91, 6083-6085. doi:10.1021/j100308a003

103. A Priori Calculations of pK a 's for Organic Compounds in Water. The pK a of Ethane. W. L. Jorgensen, J. M. Briggs, and J. Gao. J. Am. Chem. Soc 1987, 109, 6857-6857. doi:10.1021/ja00256a053

102. Computational Investigations of Organic Reaction Mechanisms: Nucleophilic Reactions of Carbonyl Compounds. W. L. Jorgensen, J. F. Blake, J. D. Madura, and S. G. Wierschke. ACS Symposium Ser 1987, 353, 200.

101. A General Treatment of Nucleophilic Chemistry. P. Metivier, A. J. Gushurst, and W. L. Jorgensen. J. Org. Chem 1987, 52, 3724-3738. doi:10.1021/jo00226a003

100. Ab Initio Study of the Displacement Reactions of Chloride Ion with Formyl and Acetyl Chloride. J. F. Blake and W. L. Jorgensen. J. Am. Chem. Soc 1987, 109, 3856-3861. doi:10.1021/ja00247a007

99. Energy Profiles for tert-Butyl Chloride Ion Pairs in Aqueous Solution. W. L. Jorgensen, J. K. Buckner, S. E. Huston, and P. J. Rossky. J. Am. Chem. Soc 1987, 109, 1891-1899. doi:10.1021/ja00241a001

98. Network Topology in Simulated Water. R. J. Speedy, J. D. Madura, and W. L. Jorgensen. J. Phys. Chem 1987, 91, 909-913. doi:10.1021/j100288a029

97. Ab Initio Study of the S N 2 Reactions of OH- and OOH-with CH 3 Cl. J. D. Evanseck, J. F. Blake, and W. L. Jorgensen. J. Am. Chem. Soc 1987, 109, 2349-2353. doi:10.1021/ja00242a018

96. Computer Simulation of Chemical and Biomolecular Systems. D. L. Beveridge and W. L. Jorgensen. Eds. Annals of the New York Academy of Sciences 1986, 482,.

95. Intermolecular Potential Functions and Monte Carlo Simulations for Liquid Sulfur Compounds. W. L. Jorgensen. J. Phys. Chem 1986, 90, 6379-6388. doi:10.1021/j100281a063

94. Ab Initio Study of the Structures and Binding Energies of Anion-Water Complexes. J. Gao, D. S. Garner, and W. L. Jorgensen. J. Am. Chem. Soc 1986, 108, 4784-4790. doi:10.1021/ja00276a016

93. Effect of Hydration on the Structure of an S N 2 Transition State. W. L. Jorgensen and J. K. Buckner. J. Phys. Chem 1986, 90, 4651-4654. doi:10.1021/j100410a037

92. Computer-Assisted Mechanistic Evaluation of Organic Reactions, 12. pK a Predictions for Organic Compounds in DMSO. A. J. Gushurst and W. L. Jorgensen. J. Org. Chem 1986, 51, 3513-3522. doi:10.1021/jo00368a023

91. Computer Simulations of Organic Reactions in Solution. W. L. Jorgensen, J. Chandrasekhar, J. K. Buckner, and J. D. Madura. Ann. N. Y. Acad. Sci 1986, 482, 198.

90. Ab Initio and Monte Carlo Calculations for a Nucleophilic Addition Reaction in the Gas Phase and in Aqueous Solution. J. D. Madura and W. L. Jorgensen. J. Am. Chem. Soc 1986, 108, 2517-2527. doi:10.1021/ja00270a005

89. Optimized Intermolecular Potential Functions for Liquid Alcohols. W. L. Jorgensen. J. Phys. Chem 1986, 90, 1276-1284. doi:10.1021/j100398a015

88. Monte Carlo Simulations of the Hydration of Ammonium and Carboxylate Ions. W. L. Jorgensen and J. Gao. J. Phys. Chem 1986, 90, 2174-2182. doi:10.1021/j100401a037

87. Temperature and Size Dependence for Monte Carlo Simulations of TIP4P Water. W. L. Jorgensen and J. D. Madura. Mol. Phys 1985, 56, 1381.

86. Monte Carlo Simulation of Differences in Free Energies of Hydration. W. L. Jorgensen and C. Ravimohan. J. Chem. Phys 1985, 83, 3050. doi:10.1063/1.449208

85. Computer-Assisted Mechanistic Evaluation of Organic Reactions, 11. Electrophilic Aromatic Substitution. M. G. Bures, B. L. Roos-Kozel, and W. L. Jorgensen. J. Org. Chem 1985, 50, 4490-4498. doi:10.1021/jo00223a015

84. Monte Carlo Simulations of Alkanes in Water: Hydration Numbers and the Hydrophobic Effect. W. L. Jorgensen, J. Gao, and C. Ravimohan. J. Phys. Chem 1985, 89, 3470-3473. doi:10.1021/j100262a010

83. Energy Profile for a Non-Concerted S N 2 Reaction in Solution. J. Chandrasekhar and W. L. Jorgensen. J. Am. Chem. Soc 1985, 107, 2974-2975. doi:10.1021/ja00296a024

82. Computer-Assisted Mechanistic Evaluation of Organic Reactions, 10. Stereochemistry. C. E. Peishoff and W. L. Jorgensen. J. Org. Chem 1985, 50, 3174-3184. doi:10.1021/jo00217a032

81. Magnitude and Origin of the -Silicon Effect on Carbenium Ions. S. G. Wierschke, J. Chandrasekhar, and W. L. Jorgensen. J. Am. Chem. Soc 1985, 107, 1496-1500. doi:10.1021/ja00292a008

80. Optimized Intermolecular Potential Functions for Amides and Peptides. Hydration of Amides. W. L. Jorgensen and C. J. Swenson. J. Am. Chem. Soc 1985, 107, 1489-1496. doi:10.1021/ja00292a007

79. Computer-Assisted Mechanistic Evaluation of Organic Reactions, 9. Reactions of Unsaturated Electrophiles Including Nucleophilic Aromatic Substitution. C. E. Peishoff and W. L. Jorgensen. J. Org. Chem 1985, 50, 1056-1068. doi:10.1021/jo00207a030

78. Optimized Intermolecular Potential Functions for Amides and Peptides.Structure and Properties of Liquid Amides. W. L. Jorgensen and C. J. Swenson. J. Am. Chem. Soc 1985, 107, 569-578. doi:10.1021/ja00289a008

77. Theoretical Examination of the SN2 Reaction Involving Chloride Ion and Methyl Chloride in the Gas Phase and Aqueous Solution. J. Chandrasekhar, S. F. Smith, and W. L. Jorgensen. J. Am. Chem. Soc 1985, 107, 154-163. doi:10.1021/ja00287a028

76. Delta Plots - A New Way to Visualize Electronic Excitation. H. Morrison, W. L. Jorgensen, B. Bigot, D. Severance, Y. Munoz-Sola,R. Strommen, and B. Pandey. J. Chem. Educ 1985, 62, 298-301. doi:10.1021/ed062p298

75. Optimized Intermolecular Potential Functions for Liquid Hydrocarbons. W. L. Jorgensen, J. D. Madura, and C. J. Swenson. J. Am. Chem. Soc 1984, 106, 6638-6646. doi:10.1021/ja00334a030

74. S N 2 Reaction Profiles in the Gas Phase and Aqueous Solution. J. Chandrasekhar, S. F. Smith, and W. L. Jorgensen. J. Am. Chem. Soc 1984, 106, 3049-3050. doi:10.1021/ja00322a059

73. General Treatment of Periselectivity. J. S. Burnier and W. L. Jorgensen. J. Org. Chem 1984, 49, 3001-3020. doi:10.1021/jo00190a029

72. Solvent Effects on the Relative Energies of Carbonium Ions. Solvationand Internal Rotation of the Allyl Cation in Liquid Hydrogen Fluoride. M. E. Cournoyer and W. L. Jorgensen. J. Am. Chem. Soc 1984, 106, 5104-5112. doi:10.1021/ja00330a012

71. Torsional Effects in the Baeyer-Villiger Oxidation. S. N. Suryawanshi, C. Swenson, W. L. Jorgensen, and P. L. Fuchs. Tetrahedron Letters 1984, 25, 1859. doi:10.1016/S0040-4039(01)90060-7

70. An Improved Intermolecular Potential Function for Simulations of Liquid Hydrogen Fluoride. M. E. Cournoyer and W. L. Jorgensen. Mol. Phys 1984, 51, 119.

69. Theoretical Studies of Medium Effects on Conformational Equilibria.(Feature Article). W. L. Jorgensen. J. Phys. Chem 1983, 87, 5304-5314. doi:10.1021/j150644a002

68. Computer Assisted Mechanistic Evaluation of Organic Reactions. 7. Six Electron Cycloadditions. J. A. Schmidt and W. L. Jorgensen. J. Org. Chem 1983, 48, 3923-3941. doi:10.1021/jo00170a010

67. Computer Assisted Analysis of Organic Reactions. W. L. Jorgensen. Kagaku 1983, 38, 483.

66. Energy Component Analysis for the Hydration of Li + , Na + , F - , and Cl -. J. Chandrasekhar, D. C. Spellmeyer, and W. L. Jorgensen. J. Am. Chem. Soc 1984, 106, 903-910. doi:10.1021/ja00316a012

65. Comparison of Simple Potential Functions for Simulating Liquid Water. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M.L. Klein. J. Chem. Phys 1983, 79, 926. doi:10.1063/1.445869

64. The Origin and Consequences of Alkene Pyramidalization in Ground and Triplet Excited States. K. N. Houk, N. G. Rondan, F. Brown, J. D. Madura, D. C. Spellmeyer,and W. L. Jorgensen. J. Am. Chem. Soc 1983, 105, 5980-5988. doi:10.1021/ja00357a004

63. Computer-Assisted Mechanistic Evaluation of Organic Reactions. 4.Organosilicon Chemistry. C. E. Peishoff and W. L. Jorgensen. J. Org. Chem 1983, 48, 1970-1979. doi:10.1021/jo00160a006

62. Ab Initio Study of the Structures and Binding Energies of Aluminum Monocation Complexes. S. F. Smith, J. Chandrasekhar and W. L. Jorgensen. J. Phys. Chem 1983, 87, 1898-1902. doi:10.1021/j100234a014

61. Monte Carlo Simulation of n-Butane in Water. Conformational Evidence for the Hydrophobic Effect. W. L. Jorgensen. J. Chem. Phys 1982, 77, 5757. doi:10.1063/1.443732

60. Convergence of Monte Carlo Simulations of Liquid Water in the NPT Ensemble. W. L. Jorgensen. Chem. Phys. Letts 1982, 92, 405. doi:10.1016/0009-2614(82)83437-4

59. The Nature of Dilute Solutions of Sodium Ion in Water, Methanol,and THF. J. Chandrasekhar and W. L. Jorgensen. J. Chem. Phys 1982, 77, 5080. doi:10.1063/1.443682

58. Monte Carlo Simulations of Liquid Tetrahydrofuran Including Pseudorotation. J. Chandrasekhar and W. L. Jorgensen. J. Chem. Phys 1982, 77, 5073. doi:10.1063/1.443681

57. Solvation and Conformation of Methanol in Water. W. L. Jorgensen and J. D. Madura. J. Am. Chem. Soc 1983, 105, 1407-1413. doi:10.1021/ja00344a001

56. Revised TIPS for Simulations of Liquid Water and Aqueous Solutions. W. L. Jorgensen. J. Chem. Phys 1982, 77, 4156. doi:10.1063/1.444325

55. Fluoranthene: Synthesis and Biological Testing of Four Diol Epoxides. W. H. Rastetter, R. B. Nachbar, S. Russo-Rodriguez, R. V. Wattley,W. G. Thilly, B. M. Andon, W. L. Jorgensen, and M. Ibrahim. J. Org. Chem 1982, 47, 4873-4878. doi:10.1021/jo00146a011

54. Ab Initio Study of Acid-Base Interactions. Proton, Lithium and Sodium Affinities of First and Second Row Bases. S. F. Smith, J. Chandrasekhar, and W. L. Jorgensen. J. Phys. Chem 1982, 86, 3308-3318. doi:10.1021/j100214a010

53. Pressure Dependence of the Mixing of Enantiomeric Liquids: 1,2-Dichloropropane. W. L. Jorgensen and B. Bigot. J. Phys. Chem 1982, 86, 2867-2873. doi:10.1021/j100212a013

52. The Nature of Dilute Solutions of Sodium and Methoxide Ions in Methanol. W. L. Jorgensen, B. Bigot, and J. Chandrasekhar. J. Am. Chem. Soc 1982, 104, 4584-4591. doi:10.1021/ja00381a013

51. Pressure Dependence of Hydrogen Bonding in Liquid Methanol. W. L. Jorgensen and M. Ibrahim. J. Am. Chem. Soc 1982, 104, 373-378. doi:10.1021/ja00366a001

50. Comment on Simulations of Liquid Ammonia Based on Quantum Mechanical Potential Functions. W. L. Jorgensen. J. Chem. Phys 1981, 75, 2026. doi:10.1063/1.442239

49. Computer-Assisted Mechanistic Evaluation of Organic Reactions, 3. Ylid Chemistry and the Organometallic Chemistry of Li, Mg, and Lithium Cuprates. T. D. Salatin, D. McLaughlin, and W. L. Jorgensen. J. Org. Chem 1981, 46, 5284-5294. doi:10.1021/jo00339a006

48. PULSAR: A Personalized Microcomputer-Based System for Keyword Search and Retrieval of Literature Information. S. F. Smith, W. L. Jorgensen, and P. L. Fuchs. J. Chem. Info. Comput. Sci 1981, 21, 209-213. doi:10.1021/ci00032a006

47. Pressure Dependence of the Structure and Properties of Liquid n-Butane. W. L. Jorgensen. J. Am. Chem. Soc 1981, 103, 4721-4726. doi:10.1021/ja00406a010

46. Sampling Efficiency in Monte Carlo Simulations of n-Butane in Dilute Solution. B. Bigot and W. L. Jorgensen. J. Chem. Phys 1981, 75, 1944. doi:10.1063/1.442219

45. Structures and Properties of Organic Liquids: n-Alkyl Ethers and Their Conformational Equilibria. W. L. Jorgensen and M. Ibrahim. J. Am. Chem. Soc 1981, 103, 3976-3985. doi:10.1021/ja00404a003

44. Structures and Properties of Organic Liquids: n-Butane and 1,2-Dichloroethane and Their Conformational Equilibria. W. L. Jorgensen, R. C. Binning, Jr., and B. Bigot. J. Am. Chem. Soc 1981, 103, 4393-4399. doi:10.1021/ja00405a018

43. Internal Rotation in Liquid 1,2-Dichloroethane and n-Butane. W. L. Jorgensen. J. Am. Chem. Soc 1981, 103, 677-679. doi:10.1021/ja00393a034

42. On the Existence of Homoaromaticity and Bicycloaromaticityin Carbanions. J. B. Grutzner and W. L. Jorgensen. J. Am. Chem. Soc 1981, 103, 1372-1375. doi:10.1021/ja00396a013

41. Ab Initio Studies of RO-...HOR' Complexes. Solvent Effects on the Relative Acidities of Water and Methanol. W. L. Jorgensen and M. Ibrahim. J. Comp. Chem 1981, 2, 7. doi:10.1002/jcc.540020103

40. Computer Assisted Mechanistic Evaluation of Organic Reactions, 2. Perception of Rings, Aromaticity, and Tautomers. B. L. Roos-Kozel and W. L. Jorgensen. J. Chem. Info. Comp. Sci 1981, 21, 101-111. doi:10.1021/ci00030a010

39. Simulation of Liquid Ethanol Including Internal Rotation. W. L. Jorgensen. J. Am. Chem. Soc 1981, 103, 345-350. doi:10.1021/ja00392a018

38. Transferable Intermolecular Potential Functions. Application to Liquid Methanol Including Internal Rotation. W. L. Jorgensen. J. Am. Chem. Soc 1981, 103, 341-345. doi:10.1021/ja00392a017

37. Transferable Intermolecular Potential Functions for Water, Alcohols, and Ethers. Application to Liquid Water. W. L. Jorgensen. J. Am. Chem. Soc 1981, 103, 335-340. doi:10.1021/ja00392a016

36. Computer Assisted Mechanistic Evaluation of Organic Reactions. l. Overview. T. D. Salatin and W. L. Jorgensen. J. Org. Chem 1980, 45, 2043-2051. doi:10.1021/jo01299a001

35. Monte Carlo Results for Hydrogen Bond Distributions in Liquid Water. W. L. Jorgensen. Chem. Phys. Lett 1980, 70, 326. doi:10.1016/0009-2614(80)85344-9

34. The Structure and Properties of Liquid Ammonia. W. L. Jorgensen and M. Ibrahim. J. Am. Chem. Soc 1980, 102, 3309-3315. doi:10.1021/ja00530a001

33. The Structure and Properties of Liquid Methanol. W. L. Jorgensen. J. Am. Chem. Soc 1980, 102, 543-549. doi:10.1021/ja00522a018

32. An Intermolecular Potential Function for the Methanol Dimer from Ab Initio Calculations. W. L. Jorgensen. J. Chem. Phys 1979, 71, 5034. doi:10.1063/1.438274

31. Energy Partitioning Accompanying Fragmentation of Protonated Methanol. R. J. Day, D. A. Krause, W. L. Jorgensen, and R. G. Cooks. Int. J. Mass Spectrom. Ion Phys 1979, 30, 83. doi:10.1016/0020-7381(79)80045-5

30. Basis Set Dependence in Monte Carlo Simulations of Liquid Hydrogen Fluoride. W. L. Jorgensen. J. Chem. Phys 1979, 70, 5888. doi:10.1063/1.437418

29. Minimal Basis Set Description of the Structure and Properties of Liquid Water. W. L. Jorgensen. J. Am. Chem. Soc 1979, 101, 2016-2021. doi:10.1021/ja00502a015

28. Deriving Intermolecular Potential Functions for the Water Dimer from Ab Initio Calculations. W. L. Jorgensen. J. Am. Chem. Soc 1979, 101, 2011-2016. doi:10.1021/ja00502a014

27. Monte Carlo Simulations of Liquid Hydrogen Fluoride. W. L. Jorgensen. J. Am. Chem. Soc 1978, 100, 7824-7831. doi:10.1021/ja00493a007

26. The Photoelectron Spectra of the 1,2,5,6-Tetramethyl-3,4,7,8-tetramethylene Derivatives of Tricyclo[3.3.0.0(2,6)]octane and Tricyclo[4.2.0.0(2,5)]octane. W. T. Borden, S. D. Young, D. C. Frost, N.P.C. Westwood, and W. L.Jorgensen. J. Org. Chem 1979, 44, 737-740. doi:10.1021/jo01319a016

25. Ab Initio Molecular Orbital Study of the Geometries, Properties, and Protonation of Simple Organofluorides.. W. L. Jorgensen and M. E. Cournoyer. J. Am. Chem. Soc 1978, 100, 5278-5285. doi:10.1021/ja00485a006

24. An Intermolecular Potential Function for the HF Dimer from Ab Initio 6-31G Computations.. W. L. Jorgensen and M. E. Cournoyer. J. Am. Chem. Soc 1978, 100, 4942-4945. doi:10.1021/ja00484a003

23. MINDO/3 Calculation of the Potential Energy Surface for C 3 H 5 + --> C 3 H 3 + + H 2 as Applied to Understanding Energy Partitioning Accompanying Fragmentation. D. A. Krause, R. J. Day, W. L. Jorgensen, and R. G. Cooks. Int. J. Mass Spectrom. Ion Phys 1978, 27, 227. doi:10.1016/0020-7381(78)80110-7

22. Ab Initio Molecular Orbital Study of the Geometries, Properties and Protonation of Alkyl Chlorides. W. L. Jorgensen. J. Am. Chem. Soc 1978, 100, 1057-1061. doi:10.1021/ja00472a006

21. Stereoelectronic Effects on the Protonation and Properties of 2-Norbornyl Chlorides. W. L. Jorgensen and J. E. Munroe. J. Am. Chem. Soc 1978, 100, 1511-1516. doi:10.1021/ja00473a031

20. The Electronic Structure and Protonation of Alkyl Chlorides.. W. L. Jorgensen. J. Am. Chem. Soc 1978, 100, 1049-1056. doi:10.1021/ja00472a005

19. Proton Affinity Correlations for Alkyl Chlorides. W. L. Jorgensen. Chem. Phys. Letts 1978, 53, 525. doi:10.1016/0009-2614(78)80061-X

18. Cycloaddition Reactions of 1,2,5,6-Tetramethyl-3,4,7,8-tetramethylenetricyclo[3.3.0.0(2,6)]octane. Evidence for Chemical Consequences of Orbital Interactions in Molecules Containing Unsaturatively 1,3-Bridged Cyclobutane Rings. W. T. Borden, A. Gold, and W. L. Jorgensen. J. Org. Chem 1978, 43, 491-497. doi:10.1021/jo00397a024

17. Simple Prediction of Substituent Sensitivity for Carbocations. W. L. Jorgensen. J. Am. Chem. Soc 1977, 99, 3840-3842. doi:10.1021/ja00453a055

16. The Importance of the Counter Ion. The Structures and Relative Energies of Homocubyl Cations and Ion Pairs. W. L. Jorgensen. J. Am. Chem. Soc 1977, 99, 4272-4276. doi:10.1021/ja00455a010

15. The Influence of Increasing Solvation on the Relative Energies of Bisected and Bridged Ethyl Cations. W. L. Jorgensen and J. E. Munroe. Tetrahedron Letters 1977, 581. doi:10.1016/S0040-4039(01)92699-1

14. The Similarity of Solvent Effects on Carbocations. W. L. Jorgensen. J. Am. Chem. Soc 1977, 99, 280-283. doi:10.1021/ja00443a067

13. The Cyclic Structure of Monomeric Dilithioacetylene. Y. Apeloig, P. v. R. Schleyer, J. S. Binkley, J. A. Pople, and W. L.Jorgensen. Tetrahedron Letters 1976, 3923. doi:10.1016/0040-4039(76)80183-9

12. The Structure and Stability of Coates' Cations. W. L. Jorgensen. Tetrahedron Letters 1976, 3033. doi:10.1016/0040-4039(76)80062-7

11. The Behavior of Trishomocyclopropenyl Cations. W. L. Jorgensen. Tetrahedron Letters 1976, 3027. doi:10.1016/0040-4039(76)80061-5

10. The Energetic Impact of Monohomoaromaticity. W. L. Jorgensen. J. Am. Chem. Soc 1976, 98, 6784-6789. doi:10.1021/ja00438a002

9. Computer-Assisted Synthetic Analysis. Generation of Synthetic Sequences Involving Sequential Functional Group Interchanges. E. J. Corey and W. L. Jorgensen. J. Am. Chem. Soc 1976, 98, 203-209. doi:10.1021/ja00417a031

8. Computer-Assisted Synthetic Analysis. Synthetic Strategies Based on Appendages and the Use of Reconnective Transforms. E. J. Corey and W. L. Jorgensen. J. Am. Chem. Soc 1976, 98, 189-203. doi:10.1021/ja00417a030

7. Chemical Consequences of Orbital Interactions. II. Ethylene and Butadiene Bridged Polycyclic Hydrocarbons Contain Three- and Four-Membered Rings. W. L. Jorgensen. J. Am. Chem. Soc 1975, 97, 3082-3090. doi:10.1021/ja00844a027

6. Orbital Interactions in Molecules Containing Unsaturatively Bridged Cyclobutane and Bicyclobutane Rings. W. L. Jorgensen and W. T. Borden. Tetrahedron Letters 1975, 223, 7. doi:10.1016/S0040-4039(00)71828-4

5. The Organic Chemist's Book of Orbitals. W. L. Jorgensen and L. Salem Academic Press, New York 1973 (In German, "Orbitale Organischer Molekule", Verlag Chemie. Weinheim/Bergstr., 1974.). 1973, (In German, "Orbitale Organischer Molekule", Verlag Chemie. Weinheim/Bergstr., 1974.).

4. Chemical Consequences of Orbital Interactions in Hydrocarbons Containing Unsaturatively Bridged Small Rings. W. L. Jorgensen and W. T. Borden. J. Am. Chem. Soc 1973, 95, 6649-6654. doi:10.1021/ja00801a021

3. Charge Density Analysis of Rotational Barriers. W. L. Jorgensen and L. C. Allen. J. Am. Chem. Soc 1971, 93, 567-574. doi:10.1021/ja00732a001

2. Charge Distribution Characteristics of Attractive Dominant Barriers. W. L. Jorgensen and L. C. Allen. Chem. Phys. Letts 1970, 7, 483. doi:10.1016/0009-2614(70)80153-1

1. Structural and Energetic Predictions for Simple Hydrocarbons from the NDDO and CNDO Semiempirical Molecular Orbital Methods. R. B. Davidson, W. L. Jorgensen, and L. C. Allen. J. Am. Chem. Soc 1970, 92, 749-753. doi:10.1021/ja00707a001

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