Publications

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1970/92/i04/pdf/ja00707a001.pdf

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.

3. Charge Density Analysis of Rotational Barriers.
W. L. Jorgensen and L. C. Allen
J. Am. Chem. Soc. 1971, 93, 567-574.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1971/93/i03/pdf/ja00732a001.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1973/95/i20/pdf/ja00801a021.pdf

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.)

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.

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1975/97/i11/pdf/ja00844a027.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1976/98/i01/pdf/ja00417a030.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1976/98/i01/pdf/ja00417a031.pdf

10. The Energetic Impact of Monohomoaromaticity.
W. L. Jorgensen
J. Am. Chem. Soc. 1976, 98, 6784-6789.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1976/98/i22/pdf/ja00438a002.pdf

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

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

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.

14. The Similarity of Solvent Effects on Carbocations.
W. L. Jorgensen
J. Am. Chem. Soc. 1977, 99, 280-283.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1977/99/i01/pdf/ja00443a067.pdf

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.

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1977/99/i13/pdf/ja00455a010.pdf

17. Simple Prediction of Substituent Sensitivity for Carbocations.
W. L. Jorgensen
J. Am. Chem. Soc. 1977, 99, 3840-3842.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1977/99/i11/pdf/ja00453a055.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/joceah/1978/43/i03/pdf/jo00397a024.pdf

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

20. The Electronic Structure and Protonation of Alkyl Chlorides. .
W. L. Jorgensen
J. Am. Chem. Soc. 1978, 100, 1049-1056.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1978/100/i04/pdf/ja00472a005.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1978/100/i05/pdf/ja00473a031.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1978/100/i04/pdf/ja00472a006.pdf

23. MINDO/3 Calculation of the Potential Energy Surface for C3H5+--> C3H3++ H2 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.

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1978/100/i16/pdf/ja00484a003.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1978/100/i17/pdf/ja00485a006.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/joceah/1979/44/i05/pdf/jo01319a016.pdf

27. Monte Carlo Simulations of Liquid Hydrogen Fluoride.
W. L. Jorgensen
J. Am. Chem. Soc. 1978, 100, 7824-7831.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1978/100/i25/pdf/ja00493a007.pdf

28. Deriving Intermolecular Potential Functions for the Water Dimer from Ab Initio Calculations.
W. L. Jorgensen
J. Am. Chem. Soc. 1979, 101, 2011-2016.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1979/101/i08/pdf/ja00502a014.pdf

29. Minimal Basis Set Description of the Structure and Properties of Liquid Water.
W. L. Jorgensen
J. Am. Chem. Soc. 1979, 101, 2016-2021.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1979/101/i08/pdf/ja00502a015.pdf

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.

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.

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.

33. The Structure and Properties of Liquid Methanol.
W. L. Jorgensen
J. Am. Chem. Soc. 1980, 102, 543-549.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1980/102/i02/pdf/ja00522a018.pdf

34. The Structure and Properties of Liquid Ammonia.
W. L. Jorgensen and M. Ibrahim
J. Am. Chem. Soc. 1980, 102, 3309-3315.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1980/102/i10/pdf/ja00530a001.pdf

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.

36. Computer Assisted Mechanistic Evaluation of Organic Reactions. l. Overview.
T. D. Salatin and W. L. Jorgensen
J. Org. Chem. 1980, 45, 2043-2051.
http://pubs.acs.org/cgi-bin/sample.cgi/joceah/1980/45/i11/pdf/jo01299a001.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1981/103/i02/pdf/ja00392a016.pdf

38. Transferable Intermolecular Potential Functions. Application to Liquid Methanol Including Internal Rotation.
W. L. Jorgensen
J. Am. Chem. Soc. 1981, 103, 341-345.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1981/103/i02/pdf/ja00392a017.pdf

39. Simulation of Liquid Ethanol Including Internal Rotation.
W. L. Jorgensen
J. Am. Chem. Soc. 1981, 103, 345-350.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1981/103/i02/pdf/ja00392a018.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jcisd8/1981/21/i02/pdf/ci00030a010.pdf

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.

42. On the Existence of Homoaromaticity and Bicycloaromaticityin Carbanions.
J. B. Grutzner and W. L. Jorgensen
J. Am. Chem. Soc. 1981, 103, 1372-1375.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1981/103/i06/pdf/ja00396a013.pdf

43. Internal Rotation in Liquid 1,2-Dichloroethane and n-Butane.
W. L. Jorgensen
J. Am. Chem. Soc. 1981, 103, 677-679.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1981/103/i03/pdf/ja00393a034.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1981/103/i15/pdf/ja00405a018.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1981/103/i14/pdf/ja00404a003.pdf

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.

47. Pressure Dependence of the Structure and Properties of Liquid n-Butane.
W. L. Jorgensen
J. Am. Chem. Soc. 1981, 103, 4721-4726.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1981/103/i16/pdf/ja00406a010.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jcisd8/1981/21/i04/pdf/ci00032a006.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/joceah/1981/46/i26/pdf/jo00339a006.pdf

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.

51. Pressure Dependence of Hydrogen Bonding in Liquid Methanol.
W. L. Jorgensen and M. Ibrahim
J. Am. Chem. Soc. 1982, 104, 373-378.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1982/104/i02/pdf/ja00366a001.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1982/104/i17/pdf/ja00381a013.pdf

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.
http://pubs.acs.org/cgi-bin/archive.cgi/jpchax/1982/86/i15/pdf/j100212a013.pdf

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.
http://pubs.acs.org/cgi-bin/archive.cgi/jpchax/1982/86/i17/pdf/j100214a010.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/joceah/1982/47/i25/pdf/jo00146a011.pdf

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.

57. Solvation and Conformation of Methanol in Water.
W. L. Jorgensen and J. D. Madura
J. Am. Chem. Soc. 1983, 105, 1407-1413.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1983/105/i06/pdf/ja00344a001.pdf

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.

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.

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.

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.

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jpchax/1983/87/i11/pdf/j100234a014.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/joceah/1983/48/i12/pdf/jo00160a006.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1983/105/i19/pdf/ja00357a004.pdf

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.

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1984/106/i04/pdf/ja00316a012.pdf

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

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.
http://pubs.acs.org/cgi-bin/sample.cgi/joceah/1983/48/i22/pdf/jo00170a010.pdf

69. Theoretical Studies of Medium Effects on Conformational Equilibria.(Feature Article).
W. L. Jorgensen
J. Phys. Chem. 1983, 87, 5304-5314.
http://pubs.acs.org/cgi-bin/sample.cgi/jpchax/1983/87/i26/pdf/j150644a002.pdf

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

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.

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1984/106/i18/pdf/ja00330a012.pdf

73. General Treatment of Periselectivity.
J. S. Burnier and W. L. Jorgensen
J. Org. Chem. 1984, 49, 3001-3020.
http://pubs.acs.org/cgi-bin/sample.cgi/joceah/1984/49/i16/pdf/jo00190a029.pdf

74. SN2 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.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1984/106/i10/pdf/ja00322a059.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1984/106/i22/pdf/ja00334a030.pdf

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.
http://www.jce.divched.org/cgi-bin/JCE/jce-idx.pl?type=goto&volume=62&issue=4&page=298

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1985/107/i01/pdf/ja00287a028.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1985/107/i03/pdf/ja00289a008.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/joceah/1985/50/i07/pdf/jo00207a030.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1985/107/i06/pdf/ja00292a007.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1985/107/i06/pdf/ja00292a008.pdf

82. Computer-Assisted Mechanistic Evaluation of Organic Reactions, 10. Stereochemistry.
C. E. Peishoff and W. L. Jorgensen
J. Org. Chem. 1985, 50, 3174-3184.
http://pubs.acs.org/cgi-bin/sample.cgi/joceah/1985/50/i17/pdf/jo00217a032.pdf

83. Energy Profile for a Non-Concerted SN2 Reaction in Solution.
J. Chandrasekhar and W. L. Jorgensen
J. Am. Chem. Soc. 1985, 107, 2974-2975.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1985/107/i10/pdf/ja00296a024.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jpchax/1985/89/i16/pdf/j100262a010.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/joceah/1985/50/i23/pdf/jo00223a015.pdf

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.

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

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jpchax/1986/90/i10/pdf/j100401a037.pdf

89. Optimized Intermolecular Potential Functions for Liquid Alcohols.
W. L. Jorgensen
J. Phys. Chem. 1986, 90, 1276-1284.
http://pubs.acs.org/cgi-bin/sample.cgi/jpchax/1986/90/i07/pdf/j100398a015.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1986/108/i10/pdf/ja00270a005.pdf

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.

92. Computer-Assisted Mechanistic Evaluation of Organic Reactions, 12. pKa Predictions for Organic Compounds in DMSO.
A. J. Gushurst and W. L. Jorgensen
J. Org. Chem. 1986, 51, 3513-3522.
http://pubs.acs.org/cgi-bin/sample.cgi/joceah/1986/51/i18/pdf/jo00368a023.pdf

93. Effect of Hydration on the Structure of an SN2 Transition State.
W. L. Jorgensen and J. K. Buckner
J. Phys. Chem. 1986, 90, 4651-4654.
http://pubs.acs.org/cgi-bin/sample.cgi/jpchax/1986/90/i19/pdf/j100410a037.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1986/108/i16/pdf/ja00276a016.pdf

95. Intermolecular Potential Functions and Monte Carlo Simulations for Liquid Sulfur Compounds.
W. L. Jorgensen
J. Phys. Chem. 1986, 90, 6379-6388.
http://pubs.acs.org/cgi-bin/sample.cgi/jpchax/1986/90/i23/pdf/j100281a063.pdf

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, .

97. Ab Initio Study of the SN2 Reactions of OH- and OOH-with CH3Cl.
J. D. Evanseck, J. F. Blake, and W. L. Jorgensen
J. Am. Chem. Soc. 1987, 109, 2349-2353.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1987/109/i08/pdf/ja00242a018.pdf

98. Network Topology in Simulated Water.
R. J. Speedy, J. D. Madura, and W. L. Jorgensen
J. Phys. Chem. 1987, 91, 909-913.
http://pubs.acs.org/cgi-bin/sample.cgi/jpchax/1987/91/i04/pdf/j100288a029.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1987/109/i07/pdf/ja00241a001.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1987/109/i13/pdf/ja00247a007.pdf

101. A General Treatment of Nucleophilic Chemistry.
P. Metivier, A. J. Gushurst, and W. L. Jorgensen
J. Org. Chem. 1987, 52, 3724-3738.
http://pubs.acs.org/cgi-bin/sample.cgi/joceah/1987/52/i17/pdf/jo00226a003.pdf

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.

103. A Priori Calculations of pKa's for Organic Compounds in Water. The pKa of Ethane.
W. L. Jorgensen, J. M. Briggs, and J. Gao
J. Am. Chem. Soc. 1987, 109, 6857-6857.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1987/109/i22/pdf/ja00256a053.pdf

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.
http://pubs.acs.org/cgi-bin/archive.cgi/jpchax/1987/91/i24/pdf/j100308a003.pdf

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

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1988/110/i06/pdf/ja00214a001.pdf

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

108. Modeling Molecular Transformations in Solution.
W. L. Jorgensen, J. K. Buckner, and J. Gao
In Chemical Reactivity in Liquids M. Moreau and P. Turq (Eds.), Plenum Press: New York 1988, pp. 253-263.

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.
http://pubs.acs.org/cgi-bin/sample.cgi/joceah/1988/53/i15/pdf/jo00250a001.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/joceah/1988/53/i11/pdf/jo00246a020.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1988/110/i13/pdf/ja00221a020.pdf

112. Theoretical Examination of Hexanol-Water Interfaces.
J. Gao and W. L. Jorgensen
J. Phys. Chem. 1988, 92, 5813-5822.
http://pubs.acs.org/cgi-bin/sample.cgi/jpchax/1988/92/i20/pdf/j100331a053.pdf

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.

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.

115. Computer-Assisted Evaluation of Oxidation Reactions.
G. D. Paderes and W. L. Jorgensen
J. Org. Chem. 1989, 54, 2058-2085.
http://pubs.acs.org/cgi-bin/sample.cgi/joceah/1989/54/i09/pdf/jo00270a014.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1989/111/i03/pdf/ja00185a005.pdf

117. Free Energies in Solution - The Aqua Vitae of Computer Simulations.
W. L. Jorgensen
In Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications W. F. van Gunsteren and P. Weiner (Eds.), Escom Science Publishers: Leiden 1989, pp. 60.

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1989/111/i07/pdf/ja00189a023.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1989/111/i05/pdf/ja00187a078.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1989/111/i12/pdf/ja00194a007.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1989/111/i02/pdf/ja00184a067.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1989/111/i26/pdf/ja00208a006.pdf

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.

124. Free Energy Calculations, A Breakthrough for Modeling Organic Chemistryin Solution.
W. L. Jorgensen
Acc. Chem. Res. 1989, 22, 184-189.
http://pubs.acs.org/cgi-bin/sample.cgi/achre4/1989/22/i05/pdf/ar00161a004.pdf

125. Interactions Between Amides in Solution and the Thermodynamics of Weak Binding.
W. L. Jorgensen
J. Am. Chem. Soc. 1989, 111, 3770-3771.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1989/111/i10/pdf/ja00192a057.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1990/112/i07/pdf/ja00163a046.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/joceah/1990/55/i01/pdf/jo00288a005.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jpchax/1990/94/i04/pdf/j100367a084.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1990/112/i02/pdf/ja00158a031.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1990/112/i05/pdf/ja00161a061.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1990/112/i12/pdf/ja00168a022.pdf

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.

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1990/112/i20/pdf/ja00176a029.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jcisd8/1990/30/i04/pdf/ci00068a018.pdf

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.

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1991/113/i08/pdf/ja00008a002.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jpchax/1991/95/i08/pdf/j100161a065.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1991/113/i01/pdf/ja00001a030.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/bichaw/1991/30/i16/pdf/bi00230a009.pdf

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.

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.
http://pubs.acs.org/cgi-bin/sample.cgi/joceah/1991/56/i15/pdf/jo00015a028.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/joceah/1991/56/i21/pdf/jo00021a018.pdf

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

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1991/113/i25/pdf/ja00025a010.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1991/113/i19/pdf/ja00019a055.pdf

146. Rusting of the Lock and Key Model of Protein-Ligand Binding.
W. L. Jorgensen
Science 1991, 254, 954-955.
http://links.jstor.org/sici?sici=0036-8075%2819911115%293%3A254%3A5034%3C954%3AROTLAK%3E2.0.CO%3B2-T

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.
http://pubs.acs.org/cgi-bin/sample.cgi/joceah/1992/57/i06/pdf/jo00032a054.pdf

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1992/114/i09/pdf/ja00035a009.pdf

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.

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1992/114/i10/pdf/ja00036a074.pdf

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.

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.

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 R. W. Joynerand R. A. van Santen (Eds.), Kluwer Academic Publishers 1993, pp. 377-387.

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.

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.

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.

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.
http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/1993/115/i07/pdf/ja00060a048.pdf

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

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

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.

161. Limited Effects of Polarization for Cl-(H2O)nand Na+(H2O)n Clusters.
W. L. Jorgensen and D. L. Severance
J. Chem. Phys. 1993, 99, 4233. doi:10.1063/1.466077.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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 G. Wipff (Ed.), Kluwer Academic Publishers 1994, pp. 161-173.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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+.

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.

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.

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.

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.

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.

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.

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.

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.

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)

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.

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.

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).

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.

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.

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.

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.

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.

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.

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

214. BOSS - Biochemical and Organic Simulation System.
W. L. Jorgensen
In Encyclopedia of Computational Chemistry P. v.R. Schleyer (Ed.), Wiley: New York 1998, Vol. 5, pp. 3281-3285.

215. ChemEdit - An Interactive Editor for Chemists.
D. Lim and W. L. Jorgensen
In Encyclopedia of Computational Chemistry P. v.R. Schleyer (Ed.), Wiley: New York 1998, Vol. 5, pp. 3295-3302.

216. OPLS Force Fields.
W. L. Jorgensen
In Encyclopedia of Computational Chemistry P. v.R. Schleyer (Ed.), Wiley: New York 1998, Vol. 3, pp. 1986-1989.

217. Monte Carlo Simulations of Liquids.
W. L. Jorgensen
In Encyclopedia of Computational Chemistry P. v.R. Schleyer (Ed.), Wiley: New York 1998, Vol. 3, pp. 1754-1763.

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. (Allinger issue)

219. Computation of Free Energy Changes in Solution.
W. L. Jorgensen
In Encyclopedia of Computational Chemistry P. v.R. Schleyer (Ed.), Wiley: New York 1998, Vol. 2, pp. 1061-1070.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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 D. Truhlar and K. Morokuma (Eds.), 1999, ACS Symposium Ser., Vol. 721, pp. 74-85.

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 K. R. Seddon; M. Zaworotko (Eds.), Kluwer: Amsterdam 1999, pp. 113-125.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

244. Computational Binding Studies of Human pp60c-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.

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.

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.

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.

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.

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.

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.

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.

252. Improved Convergence of Binding Affinities with Free Energy Perturbation:Application to Nonpeptide Ligands with pp60c-src SH2 Domain.
D. L. Price, and W. L. Jorgensen
J. Comp. Aided Mol. Design. 2001, 15, 681-695.

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.

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.

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.

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.

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 M. R. Reddy and M. D. Elion (Eds.), Kluwer 2001, pp. 299-316.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

287. Relationship between side chain structure and 14-helix stability of β3-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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

300. Solvent Effects on Organic Reactions from QM/MM Simulations.
Acevedo, O.; Jorgensen, W. L.
In Annual Reports in Computational Chemistry Spellmeyer, D. (Eds.), Elsevier 2006, pp. 263-278.
http://www.elsevier.com/wps/find/bookdescription.cws_home/708361/description

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

330. In Silico Improvement of β3-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.

331. Progress and Issues for Computationally-Guided Lead Discovery and Optimization.
W. L. Jorgensen
In Drug Design: Structure and Ligand-Based Approaches K. Merz; C. Reynolds; D. Ringe (Eds.), Cambridge University Press: Cambridge, UK 2009, pp. .

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.

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.

334. Steric and Solvation Effects in Ionic SN2 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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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. Info. Model. 907-922, 2013, 53. doi:10.1021/ci3006098.

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.

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.

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..

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.

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.

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.

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.

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.

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

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.

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, ASAP, . doi:10.1021/jp501553j.

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