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1. Structural and Energetic Predictions for Simple Hydrocarbons from the NDDO and CNDO Semiempirical Molecular Orbital Methods.
J. Am. Chem. Soc. 1970, 92, 749-753.
2. Charge Distribution Characteristics of Attractive Dominant Barriers.
Chem. Phys. Letts. 1970, 7, 483. doi:10.1016/0009-2614(70)80153-1.
3. Charge Density Analysis of Rotational Barriers.
J. Am. Chem. Soc. 1971, 93, 567-574.
4. Chemical Consequences of Orbital Interactions in Hydrocarbons Containing Unsaturatively Bridged Small Rings.
J. Am. Chem. Soc. 1973, 95, 6649-6654.
5. The Organic Chemist's Book of Orbitals.
6. Orbital Interactions in Molecules Containing Unsaturatively Bridged Cyclobutane and Bicyclobutane Rings.
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.
J. Am. Chem. Soc. 1975, 97, 3082-3090.
8. Computer-Assisted Synthetic Analysis. Synthetic Strategies Based on Appendages and the Use of Reconnective Transforms.
J. Am. Chem. Soc. 1976, 98, 189-203.
9. Computer-Assisted Synthetic Analysis. Generation of Synthetic Sequences Involving Sequential Functional Group Interchanges.
J. Am. Chem. Soc. 1976, 98, 203-209.
10. The Energetic Impact of Monohomoaromaticity.
J. Am. Chem. Soc. 1976, 98, 6784-6789.
11. The Behavior of Trishomocyclopropenyl Cations.
Tetrahedron Letters 1976, 3027. doi:10.1016/0040-4039(76)80061-5.
12. The Structure and Stability of Coates' Cations.
Tetrahedron Letters 1976, 3033. doi:10.1016/0040-4039(76)80062-7.
13. The Cyclic Structure of Monomeric Dilithioacetylene.
Tetrahedron Letters 1976, 3923. doi:10.1016/0040-4039(76)80183-9.
14. The Similarity of Solvent Effects on Carbocations.
J. Am. Chem. Soc. 1977, 99, 280-283.
15. The Influence of Increasing Solvation on the Relative Energies of Bisected and Bridged Ethyl Cations.
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.
J. Am. Chem. Soc. 1977, 99, 4272-4276.
17. Simple Prediction of Substituent Sensitivity for Carbocations.
J. Am. Chem. Soc. 1977, 99, 3840-3842.
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.
J. Org. Chem. 1978, 43, 491-497.
19. Proton Affinity Correlations for Alkyl Chlorides.
Chem. Phys. Letts. 1978, 53, 525. doi:10.1016/0009-2614(78)80061-X.
20. The Electronic Structure and Protonation of Alkyl Chlorides. .
J. Am. Chem. Soc. 1978, 100, 1049-1056.
21. Stereoelectronic Effects on the Protonation and Properties of 2-Norbornyl Chlorides.
J. Am. Chem. Soc. 1978, 100, 1511-1516.
22. Ab Initio Molecular Orbital Study of the Geometries, Properties and Protonation of Alkyl Chlorides.
J. Am. Chem. Soc. 1978, 100, 1057-1061.
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.
25. Ab Initio Molecular Orbital Study of the Geometries, Properties, and Protonation of Simple Organofluorides. .
J. Am. Chem. Soc. 1978, 100, 5278-5285.
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.
J. Org. Chem. 1979, 44, 737-740.
27. Monte Carlo Simulations of Liquid Hydrogen Fluoride.
J. Am. Chem. Soc. 1978, 100, 7824-7831.
28. Deriving Intermolecular Potential Functions for the Water Dimer from Ab Initio Calculations.
J. Am. Chem. Soc. 1979, 101, 2011-2016.
29. Minimal Basis Set Description of the Structure and Properties of Liquid Water.
J. Am. Chem. Soc. 1979, 101, 2016-2021.
30. Basis Set Dependence in Monte Carlo Simulations of Liquid Hydrogen Fluoride.
J. Chem. Phys. 1979, 70, 5888. doi:10.1063/1.437418.
31. Energy Partitioning Accompanying Fragmentation of Protonated Methanol.
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.
J. Chem. Phys. 1979, 71, 5034. doi:10.1063/1.438274.
33. The Structure and Properties of Liquid Methanol.
J. Am. Chem. Soc. 1980, 102, 543-549.
34. The Structure and Properties of Liquid Ammonia.
J. Am. Chem. Soc. 1980, 102, 3309-3315.
35. Monte Carlo Results for Hydrogen Bond Distributions in Liquid Water.
Chem. Phys. Lett. 1980, 70, 326. doi:10.1016/0009-2614(80)85344-9.
36. Computer Assisted Mechanistic Evaluation of Organic Reactions. l. Overview.
J. Org. Chem. 1980, 45, 2043-2051.
37. Transferable Intermolecular Potential Functions for Water, Alcohols, and Ethers. Application to Liquid Water.
J. Am. Chem. Soc. 1981, 103, 335-340.
38. Transferable Intermolecular Potential Functions. Application to Liquid Methanol Including Internal Rotation.
J. Am. Chem. Soc. 1981, 103, 341-345.
39. Simulation of Liquid Ethanol Including Internal Rotation.
J. Am. Chem. Soc. 1981, 103, 345-350.
40. Computer Assisted Mechanistic Evaluation of Organic Reactions, 2. Perception of Rings, Aromaticity, and Tautomers.
J. Chem. Info. Comp. Sci. 1981, 21, 101-111.
41. Ab Initio Studies of RO-...HOR' Complexes. Solvent Effects on the Relative Acidities of Water and Methanol.
J. Comp. Chem. 1981, 2, 7. doi:10.1002/jcc.540020103.
42. On the Existence of Homoaromaticity and Bicycloaromaticityin Carbanions.
J. Am. Chem. Soc. 1981, 103, 1372-1375.
43. Internal Rotation in Liquid 1,2-Dichloroethane and n-Butane.
J. Am. Chem. Soc. 1981, 103, 677-679.
44. Structures and Properties of Organic Liquids: n-Butane and 1,2-Dichloroethane and Their Conformational Equilibria.
J. Am. Chem. Soc. 1981, 103, 4393-4399.
45. Structures and Properties of Organic Liquids: n-Alkyl Ethers and Their Conformational Equilibria.
J. Am. Chem. Soc. 1981, 103, 3976-3985.
46. Sampling Efficiency in Monte Carlo Simulations of n-Butane in Dilute Solution.
J. Chem. Phys. 1981, 75, 1944. doi:10.1063/1.442219.
47. Pressure Dependence of the Structure and Properties of Liquid n-Butane.
J. Am. Chem. Soc. 1981, 103, 4721-4726.
48. PULSAR: A Personalized Microcomputer-Based System for Keyword Search and Retrieval of Literature Information.
J. Chem. Info. Comput. Sci. 1981, 21, 209-213.
49. Computer-Assisted Mechanistic Evaluation of Organic Reactions, 3. Ylid Chemistry and the Organometallic Chemistry of Li, Mg, and Lithium Cuprates.
J. Org. Chem. 1981, 46, 5284-5294.
50. Comment on Simulations of Liquid Ammonia Based on Quantum Mechanical Potential Functions.
J. Chem. Phys. 1981, 75, 2026. doi:10.1063/1.442239.
51. Pressure Dependence of Hydrogen Bonding in Liquid Methanol.
J. Am. Chem. Soc. 1982, 104, 373-378.
52. The Nature of Dilute Solutions of Sodium and Methoxide Ions in Methanol.
J. Am. Chem. Soc. 1982, 104, 4584-4591.
53. Pressure Dependence of the Mixing of Enantiomeric Liquids: 1,2-Dichloropropane.
J. Phys. Chem. 1982, 86, 2867-2873.
54. Ab Initio Study of Acid-Base Interactions. Proton, Lithium and Sodium Affinities of First and Second Row Bases.
J. Phys. Chem. 1982, 86, 3308-3318.
55. Fluoranthene: Synthesis and Biological Testing of Four Diol Epoxides.
J. Org. Chem. 1982, 47, 4873-4878.
56. Revised TIPS for Simulations of Liquid Water and Aqueous Solutions.
J. Chem. Phys. 1982, 77, 4156. doi:10.1063/1.444325.
57. Solvation and Conformation of Methanol in Water.
J. Am. Chem. Soc. 1983, 105, 1407-1413.
58. Monte Carlo Simulations of Liquid Tetrahydrofuran Including Pseudorotation.
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. Chem. Phys. 1982, 77, 5080. doi:10.1063/1.443682.
60. Convergence of Monte Carlo Simulations of Liquid Water in the NPT Ensemble.
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.
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.
J. Phys. Chem. 1983, 87, 1898-1902.
63. Computer-Assisted Mechanistic Evaluation of Organic Reactions. 4.Organosilicon Chemistry.
J. Org. Chem. 1983, 48, 1970-1979.
64. The Origin and Consequences of Alkene Pyramidalization in Ground and Triplet Excited States.
J. Am. Chem. Soc. 1983, 105, 5980-5988.
65. Comparison of Simple Potential Functions for Simulating Liquid Water.
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. Am. Chem. Soc. 1984, 106, 903-910.
67. Computer Assisted Analysis of Organic Reactions.
68. Computer Assisted Mechanistic Evaluation of Organic Reactions. 7. Six Electron Cycloadditions.
J. Org. Chem. 1983, 48, 3923-3941.
69. Theoretical Studies of Medium Effects on Conformational Equilibria.(Feature Article).
J. Phys. Chem. 1983, 87, 5304-5314.
70. An Improved Intermolecular Potential Function for Simulations of Liquid Hydrogen Fluoride.
Mol. Phys. 1984, 51, 119.
71. Torsional Effects in the Baeyer-Villiger Oxidation.
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.
J. Am. Chem. Soc. 1984, 106, 5104-5112.
73. General Treatment of Periselectivity.
J. Org. Chem. 1984, 49, 3001-3020.
74. SN2 Reaction Profiles in the Gas Phase and Aqueous Solution.
J. Am. Chem. Soc. 1984, 106, 3049-3050.
75. Optimized Intermolecular Potential Functions for Liquid Hydrocarbons.
J. Am. Chem. Soc. 1984, 106, 6638-6646.
76. Delta Plots - A New Way to Visualize Electronic Excitation.
J. Chem. Educ. 1985, 62, 298-301.
77. Theoretical Examination of the SN2 Reaction Involving Chloride Ion and Methyl Chloride in the Gas Phase and Aqueous Solution.
J. Am. Chem. Soc. 1985, 107, 154-163.
78. Optimized Intermolecular Potential Functions for Amides and Peptides.Structure and Properties of Liquid Amides.
J. Am. Chem. Soc. 1985, 107, 569-578.
79. Computer-Assisted Mechanistic Evaluation of Organic Reactions, 9. Reactions of Unsaturated Electrophiles Including Nucleophilic Aromatic Substitution.
J. Org. Chem. 1985, 50, 1056-1068.
80. Optimized Intermolecular Potential Functions for Amides and Peptides. Hydration of Amides.
J. Am. Chem. Soc. 1985, 107, 1489-1496.
81. Magnitude and Origin of the ß-Silicon Effect on Carbenium Ions.
J. Am. Chem. Soc. 1985, 107, 1496-1500.
82. Computer-Assisted Mechanistic Evaluation of Organic Reactions, 10. Stereochemistry.
J. Org. Chem. 1985, 50, 3174-3184.
83. Energy Profile for a Non-Concerted SN2 Reaction in Solution.
J. Am. Chem. Soc. 1985, 107, 2974-2975.
84. Monte Carlo Simulations of Alkanes in Water: Hydration Numbers and the Hydrophobic Effect.
J. Phys. Chem. 1985, 89, 3470-3473.
85. Computer-Assisted Mechanistic Evaluation of Organic Reactions, 11. Electrophilic Aromatic Substitution.
J. Org. Chem. 1985, 50, 4490-4498.
86. Monte Carlo Simulation of Differences in Free Energies of Hydration.
J. Chem. Phys. 1985, 83, 3050. doi:10.1063/1.449208.
87. Temperature and Size Dependence for Monte Carlo Simulations of TIP4P Water.
Mol. Phys. 1985, 56, 1381.
88. Monte Carlo Simulations of the Hydration of Ammonium and Carboxylate Ions.
J. Phys. Chem. 1986, 90, 2174-2182.
89. Optimized Intermolecular Potential Functions for Liquid Alcohols.
J. Phys. Chem. 1986, 90, 1276-1284.
90. Ab Initio and Monte Carlo Calculations for a Nucleophilic Addition Reaction in the Gas Phase and in Aqueous Solution.
J. Am. Chem. Soc. 1986, 108, 2517-2527.
91. Computer Simulations of Organic Reactions in Solution.
Ann. N. Y. Acad. Sci. 1986, 482, 198.
92. Computer-Assisted Mechanistic Evaluation of Organic Reactions, 12. pKa Predictions for Organic Compounds in DMSO.
J. Org. Chem. 1986, 51, 3513-3522.
93. Effect of Hydration on the Structure of an SN2 Transition State.
J. Phys. Chem. 1986, 90, 4651-4654.
94. Ab Initio Study of the Structures and Binding Energies of Anion-Water Complexes.
J. Am. Chem. Soc. 1986, 108, 4784-4790.
95. Intermolecular Potential Functions and Monte Carlo Simulations for Liquid Sulfur Compounds.
J. Phys. Chem. 1986, 90, 6379-6388.
96. Computer Simulation of Chemical and Biomolecular Systems.
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. Am. Chem. Soc. 1987, 109, 2349-2353.
98. Network Topology in Simulated Water.
J. Phys. Chem. 1987, 91, 909-913.
99. Energy Profiles for tert-Butyl Chloride Ion Pairs in Aqueous Solution.
J. Am. Chem. Soc. 1987, 109, 1891-1899.
100. Ab Initio Study of the Displacement Reactions of Chloride Ion with Formyl and Acetyl Chloride.
J. Am. Chem. Soc. 1987, 109, 3856-3861.
101. A General Treatment of Nucleophilic Chemistry.
J. Org. Chem. 1987, 52, 3724-3738.
102. Computational Investigations of Organic Reaction Mechanisms: Nucleophilic Reactions of Carbonyl Compounds.
ACS Symposium Ser. 1987, 353, 200.
103. A Priori Calculations of pKa's for Organic Compounds in Water. The pKa of Ethane.
J. Am. Chem. Soc. 1987, 109, 6857-6857.
104. Use of Statistical Perturbation Theory for Computing Solvent Effects on Molecular Conformation. Butane in Water.
J. Phys. Chem. 1987, 91, 6083-6085.
105. Energy Profiles for Organic Reactions in Solution.
Adv. Chem. Phys., Part II 1988, 70, 469.
106. The OPLS Force Field for Proteins. Energy Minimizations for Crystals of Cyclic Peptides and Crambin.
J. Am. Chem. Soc. 1988, 110, 1657-1666.
107. Monte Carlo Simulations of Liquid Acetonitrile with a Three-Site Model.
Molec. Phys. 1988, 63, 547.
108. Modeling Molecular Transformations in Solution.
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.
J. Org. Chem. 1988, 53, 3397-3408.
110. Computer-Assisted Mechanistic Evaluation of Organic Reactions. 15. Heterocycle Synthesis.
J. Org. Chem. 1988, 53, 2504-2520.
111. Cis/Trans Energy Difference for the Peptide Bond in the Gas Phase and Aqueous Solution.
J. Am. Chem. Soc. 1988, 110, 4212-4216.
112. Theoretical Examination of Hexanol-Water Interfaces.
J. Phys. Chem. 1988, 92, 5813-5822.
113. Efficient Computation of Absolute Free Energies of Binding by Computer Simulations. Application to the Methane Dimer in Water.
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.
Chem. Phys. 1989, 129, 193. doi:10.1016/0301-0104(89)80004-7.
115. Computer-Assisted Evaluation of Oxidation Reactions.
J. Org. Chem. 1989, 54, 2058-2085.
116. Ab Initio Investigation of the ß-Silicon Effect on Alkyland Cyclopropyl Carbenium Ions and Radicals.
J. Am. Chem. Soc. 1989, 111, 819-824.
117. Free Energies in Solution - The Aqua Vitae of Computer Simulations.
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. Am. Chem. Soc. 1989, 111, 2507-2516.
119. Variational Transition State for the Reaction of Cl2C: with Ethyleneand the Thermodynamics of Carbene Additions.
J. Am. Chem. Soc. 1989, 111, 1919-1920.
120. A Priori pKa Calculations and the Hydration of Organic Anions.
J. Am. Chem. Soc. 1989, 111, 4190-4197.
121. Structure and Binding for Rebek's Diacid in Chloroform. A Demure Host for Pyrazine.
J. Am. Chem. Soc. 1989, 111, 755-757.
122. Substituent Effects and Transition Structures for Diels-Alder Reactionsof Butadiene and Cyclopentadiene with Cyanoalkenes.
J. Am. Chem. Soc. 1989, 111, 9172-9176.
123. Molecular Dynamics Simulation of the Third Domain of Silver Pheasant Ovomucoid in Water.
Proceedings of the 1988 Nobel Symposium, Chem. Scripta 1989, 29A, 191.
124. Free Energy Calculations, A Breakthrough for Modeling Organic Chemistryin Solution.
Acc. Chem. Res. 1989, 22, 184-189.
125. Interactions Between Amides in Solution and the Thermodynamics of Weak Binding.
J. Am. Chem. Soc. 1989, 111, 3770-3771.
126. Molecular Dynamics of Proteins with the OPLS Potential Functions. Simulation of the Third Domain of Silver Pheasant Ovomucoid in Water.
J. Am. Chem. Soc. 1990, 112, 2773-2781.
127. Computer-Assisted Mechanistic Evaluation of Organic Reactions. 17. Free Radical Chain Reactions.
J. Org. Chem. 1990, 55, 9-27.
128. Relative Partition Coefficients for Organic Solutes from Fluid Simulations.
J. Phys. Chem. 1990, 94, 1683-1686.
129. Structure and Basicity of Silyl Ethers: A Crystallographic and Ab Initio Inquiry into the Mode of Silicon-Oxygen Interactions.
J. Am. Chem. Soc. 1990, 112, 697-703.
130. The Importance of Secondary Interactions in Triply Hydrogen-Bonded Complexes: Guanine-Cytosine vs. Uracil-Diaminopyridine.
J. Am. Chem. Soc. 1990, 112, 2008-2010.
131. Aromatic-Aromatic Interactions: Free Energy Profiles for the Benzene Dimer in Water, Chloroform, and Liquid Benzene.
J. Am. Chem. Soc. 1990, 112, 4768-4774.
132. Monte Carlo Simulations of Liquid Alkyl Ethers with the OPLS Potential Functions.
J. Comput. Chem. 1990, 11, 958. doi:10.1002/jcc.540110808.
133. Origin of the Strong Binding of Adenine to a Molecular Tweezer.
J. Am. Chem. Soc. 1990, 112, 7269-7278.
134. Computer Assisted Analysis of Reactions Involving Organic Free Radicals and Diradicals.
J. Chem. Info. Comput. Sci. 1990, 30, 458-466.
135. CAMEO: A Program for the Logical Prediction of the Products of Organic Reactions.
Pure Appl. Chem. 1990, 62, 1921.
136. OPLS Potential Functions for Nucleotide Bases. Relative Association Constants of Hydrogen-Bonded Base Pairs in Chloroform.
J. Am. Chem. Soc. 1991, 113, 2810-2819.
137. Monte Carlo Simulations of Liquid Acetic Acid and Methyl Acetate with the OPLS Potential Functions.
J. Phys. Chem. 1991, 95, 3315-3322.
138. Chemical Chameleons: Hydrogen Bonding with Imides and Lactams in Chloroform.
J. Am. Chem. Soc. 1991, 113, 209-216.
139. Molecular Dynamics Simulations of the Unfolding of an α-Helical Analog of Ribonuclease-A S-Peptide in Water.
140. Monte Carlo Simulations Yield Absolute Free Energies of Bindingfor Guanine-Cytosine and Adenine-Uracil Base Pairs in Chloroform.
Tetrahedron 1991, 47, 2491. doi:10.1016/S0040-4020(01)81783-X.
141. Computer-Assisted Mechanistic Evaluation of Organic Reactions. 18. Reductions with Hydrides.
J. Org. Chem. 1991, 56, 4718-4733.
142. Proton Affinities and Gas-phase Basicities of Alkyl and Silyl Ethers.
J. Org. Chem. 1991, 56, 6052-6059.
143. Computational Insights on Intermolecular Interactions and Bindingin Solution.
Chemtracts - Organic Chemistry 1991, 4, 91-119.
144. Computational Studies of FK506: Conformational Search and Molecular Dynamics Simulation in Water.
J. Am. Chem. Soc. 1991, 113, 9483-9493.
145. Solvent Effects on a Diels-Alder Reaction from Computer Simulations.
J. Am. Chem. Soc. 1991, 113, 7430-7432.
146. Rusting of the Lock and Key Model of Protein-Ligand Binding.
147. Computer-Assisted Mechanistic Analysis of Organic Reactions. 20. Ene and Retro-ene Chemistry.
J. Org. Chem. 1992, 57, 1904-1916.
148. Free Energy Profiles for Na+ Adsorption on a Metal Electrode.
J. Am. Chem. Soc. 1992, 114, 3220-3226.
149. Structure and Binding for Cyclophane-Arene Complexes in Water from Monte Carlo Simulations.
NATO ASI Series C 1992, 371, 383.
150. Enhanced View of Structure and Binding for Cyclophane-Arene Complexesthrough Joint Theoretical and Experimental Study.
J. Am. Chem. Soc. 1992, 114, 4003-4004.
151. Solvent Effects on the Barrier to Isomerization for a Tertiary Amide from Ab Initio and Monte Carlo Calculations.
J. Am. Chem. Soc. 1992, 114, 7535. doi:10.1021/ja00045a029.
152. Effects of Hydration on the Claisen Rearrangement of Allyl Vinyl Ether from Computer Simulations.
J. Am. Chem. Soc. 1992, 114, 10966.
153. Solvent Effects on the Diels-Alder Reaction of Methyl Vinyl Ketoneand Cyclopentadiene from Computer Simulations.
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.
J. Comp. Chem. 1993, 13, 195. doi:10.1002/jcc.540140207.
155. Monte Carlo Simulations of Pure Liquid Substituted Benzenes with OPLS Potential Functions.
J. Comp. Chem. 1993, 13, 206. doi:10.1002/jcc.540140208.
156. Modeling the Complexation of Substituted Benzenes by a Cyclophane Host in Water.
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.
J. Am. Chem. Soc. 1993, 115, 2936.
158. Molecular Dynamics Simulations of the Unfolding of Apomyoglobinin Water.
159. Supramolecular Chemistry. (Invited editorial.).
Proc. Nat. Acad. Sci., USA 1993, 90, 1635.
160. Urea: Potential Functions, log P, and Free Energy of Hydration.
Isr. J. Chem. 1993, 33, 323.
161. Limited Effects of Polarization for Cl-(H2O)nand Na+(H2O)n Clusters.
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.
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. Am. Chem. Soc. 1993, 115, 11590.
164. Computer Assisted Mechanistic Evaluation of Organic Reactions.22. The Generation and Use of Three-Dimensional Structures.
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.
J. Comp. Chem. 1993, 14, 1498. doi:10.1002/jcc.540141212.
166. Computational Investigations of Protein Denaturation: Apomyoglobinand Chaotrope-Arene Interactions.
Phil. Trans. Roy. Soc. London A 1993, 345, 87-96.
167. Mechanism for the Rotamase Activity of FK506 Binding Protein from Molecular Dynamics Simulations.
168. Quantification of Solvent Effects on the Acidities of Z and E Estersfrom Fluid Simulations.
J. Am. Chem. Soc. 1994, 116, 10630-10638.
169. Do Denaturants Interact with Aromatic Hydrocarbons in Water?.
J. Am. Chem. Soc. 1993, 115, 9271.
170. Enhanced Hydrogen Bonding of Water to Diels-Alder Transition States- Ab Initio Evidence.
J. Org. Chem. 1994, 59, 803-805.
171. Synthesis and Investigations of Enetetraynes.
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.
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.
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.
J. Org. Chem. 1994, 59, 762-772.
175. Investigation of Solvent Effects on Pericyclic Reactions by Computer Simulations.
Trans. Faraday Soc. 1994, 90, 1727-1732.
176. Monte Carlo Results for the Effect of Solvation on the Anomeric Equilibrium for 2-Methoxytetrahydropyran.
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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.
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184. A Comprehensive Study of the Rotational Profiles of Some Organic Systems by Ab Initio MO Theory, Forming a Basis for Peptide Torsional Parameters.
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186. Computer Assisted Mechanistic Evaluation of Organic Reactions,26. Diastereoselective Additions: Cram's Rule.
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187. The Energy Difference Between the Classical and the Nonclassical 2-Norbornyl Cation in Solution. A Combined Ab Initio - Monte Carlo Study.
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188. An Extended Linear Response Method for Determining Free Energies of Hydration.
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189. Free Energies of Hydration for Organic Molecules from Monte Carlo Simulations.
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.
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191. Dielectric Constants of Formamide and Dimethylformamide via Computer Simulations.
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192. Regioselective Synthesis of Allylic Alcohols Using the Mislow-Evans Rearrangement: A Theoretical Rationalization.
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193. The Importance of Polarization for Dipolar Solutes in Low-Dielectric Media: 1,2-Dichloroethane and Water in Cyclohexane.
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195. Molecular Recognition of Carbohydrates: Interaction of Diols with Acetate Ion.
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196. Monte Carlo vs. Molecular Dynamics for Conformational Sampling.
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197. The Origin of Self-Assembling Ternary Complex Stabilities and Template Ratios in Carceplex Formation.
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200. Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids.
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201. Performance of the AMBER94, MMFF94, and OPLS-AA Force Fields for Modeling Organic Liquids.
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202. Binding Affinities for Sulfonamide Inhibitors with Human Thrombinusing Monte Carlo Simulations with a Linear Response Method.
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203. Energetics of Cation-Olefin Addition in the Gas Phase and in Solution.
204. Free Energies of Solvation in Chloroform and Water from a Linear Response Approach.
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205. Approaches to Protein-Ligand Binding from Computer Simulations.
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206. Computational Binding Studies of Orthogonal Cyclosporin-Cyclophilin Pairs.
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207. Molecular Dynamics of the Unfolding of Barnase in Water and 8 M Aqueous Urea.
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208. The OPLS All-Atom Force Field for Carbohydrates.
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210. Monte Carlo Simulations for Proteins: Binding Affinities for Trypsin-Benzamidine Complexes via Free Energy Perturbations.
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211. Computational Investigations of Carbenium Ion Reactions Relevant to Sterol Biosynthesis.
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212. Elucidation of Transition Structures and Solvent Effects for Epoxidations by Dimethyldioxirane.
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213. Computational Approaches to Molecular Recognition.
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214. BOSS - Biochemical and Organic Simulation System.
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218. Temperature Dependence of TIP3P, SPC, and TIP4P Water from NPT Monte Carlo Simulations: Seeking a Temperature of Maximum Density.
219. Computation of Free Energy Changes in Solution.
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220. A QM/MM Method Based on CM1A Charges: Applications to Solvent Effects on Organic Equilibria and Reactions.
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221. Preorganized Metallomacrocycles: Improved Binding and Selectivity of Ammonia over Primary Amines.
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223. Monte Carlo Investigations of Selective Anion Complexation by a Bis(phenylurea)-p-tert-Butylcalixarene.
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225. Conformational Complexity of Succinic Acid and Its Monoanion in the Gas Phase and in Solution: Ab Initio Calculations and Monte Carlo Simulations.
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227. Ab Initio and Monte Carlo Study of Solvent Effects on a 1,3-Dipolar Cycloaddition.
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228. Prediction of Binding Affinities for TIBO Inhibitors of HIV-1 Reverse Transcriptase Using Monte Carlo Simulations in a Linear Response Method.
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229. Solvent as Catalyst - Computational Studies of Organic Chemistry in Solution.
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230. Computational Studies of Molecular Recognition from Alkane Dimers to Protein-Ligand Binding.
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231. Estimation of the Binding Affinities of FKBP12 Inhibitors Using a Linear Response Method.
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232. Computational Studies of the Molecular Recognition of Halide Anions by CalixAromatics.
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233. OPLS All-Atom Model for Amines: Resolution of the Amine Hydration Problem.
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234. Selective Anion Complexation by a Calixpyrrole Investigated by Monte Carlo Simulations.
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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.
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236. Perspective on "Equation of State Calculations by Fast Computing Machines".
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237. Developing a Dynamic Pharmacaphore Model for HIV-1 Integrase.
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238. Prediction of Properties from Simulations: Free Energies of Solvation in Hexadecane, Octanol, and Water.
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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.
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240. A five-site model liquid water and the reproduction of the density anomaly by rigid, non-polarizable models.
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241. Origin of the Inversion of the Acidity Order for Haloacetic Acidson Going from the Gas Phase to Solution.
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242. Prediction of Drug Solubility from Monte Carlo Simulations.
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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.
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244. Computational Binding Studies of Human pp60c-src SH2 Domain witha series of Nonpeptide, Phosphophenyl-Containing Ligands.
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245. Validation of a Model for the Complex of HIV-1 Reverse Transcriptasewith Sustiva through Computation of Resistance Profiles.
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246. Estimation of Binding Affinities for HEPT and Nevirapine Analogs with HIV-1Reverse Transcriptase via Monte Carlo Simulations.
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247. Diffusion constant of the TIP5P model liquid water.
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253. Estimation of Binding Affinities for Selective Thrombin Inhibitors via Monte Carlo Simulations.
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254. Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides.
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257. COX-2, Src SH2 Domain, HIV Reverse Transcriptase, and Thrombin:Computational Approaches to Drug Design.
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259. Antiviral Drug Design: Computational Analyses of the Effects of the L100I Mutation for HIV-RT on the binding of NNRTI's.
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266. Prediction of Activity for Non-nucleoside Inhibitors with HIV Reverse Transcriptase Based on Monte Carlo Simulations.
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267. PDDG/PM3 and PDDG/MNDO: Improved Semiempirical Methods.
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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.
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270. Investigation of Solvent Effects for the Claisen Rearrangement of Chorismate to Prephanate:Mechanistic Interpretation via Near Attack Conformations.
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272. Activity Predictions for Efavirenz Analogues with the K103N Mutant of HIV Reverse Transcriptase.
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273. Validation of a Model for the Complex of HIV-1 Reverse Transcriptase with the Novel Non-nucleoside Inhibitor TMC125.
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274. Analyses of Activuty for Factor Xa Inhibitors Based on Monte Carlo Simulations.
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275. Extension of the PDDG/PM3 and PDDG/MNDO Semiempirical Molecular Orbital Methods to Halogens.
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277. Steric Retardation of SN2 Reactions in the Gas Phase and Solution.
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278. Polypeptide Folding using Monte Carlo Sampling, Concerted Rotation, and Continum Solvation.
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279. General Model for Estimation of the Inhibition of Protein Kinasesusing Monte Carlo Simulations.
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280. Accuracy of Free Energies of Hydration from CM1 and CM3 Atomic Charges.
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281. HIV Reverse Transcriptase Variants: Molecular Modeling of Y181C,V106A, L100I, and K103N Mutations with Non-Nucleoside Inhibitors.
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282. The Many Roles of Computation in Drug Discovery.
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283. Free Energies of Hydration from a Generalized Born Model and an All-Atom Force Field.
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284. Energetic Preferences for α, β- versus β, γ-Unsaturation.
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285. Solvent Effects and Mechanism for a Nucleophilic Aromatic Substitution from QM/MM Simulations.
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286. Monte Carlo Backbone Sampling for Nucleic Acids using Concerted Rotations including Variable Bond Angles.
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287. Relationship between side chain structure and 14-helix stability of β3-peptides in water.
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288. Discovery of a Potent, Selective, and Efficacious Class of Reversible α-Ketoheterocycle Inhibitors of Fatty Acid Amide Hydrolase Effective as Analgesics.
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289. Macrophomate Synthase: QM/MM Simulations Address the Diels-Alder versus Michael-Aldol Reaction Mechanism.
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290. Potential energy functions for atomic-level simulations of water and organic and biomolecular systems.
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291. Molecular modeling of organic and biomolecular systems using BOSS and MCPRO.
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292. Extension of the PDDG/PM3 Semiempirical Molecular Orbital Method to Sulfur, Silicon, and Phosphorus.
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293. Influence of Inter- and Intramolecular Hydrogen Bonding on Kemp Decarboxylations from QM/MM Simulations.
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294. Effects of Arg90 Neutralization on the Enzyme-Catalyzed Rearrangement of Chorismate to Prephenate.
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295. Elucidation of Fatty Acid Amide Hydrolase Inhibition By Potent Alpha-Ketoheterocycle Derivatives From Monte Carlo Simulations.
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296. Assault on resistance: the use of computational chemistry in the development of anti-HIV drugs.
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297. NO-MNDO: Reintroduction of the Overlap Matrix into MNDO.
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298. Computer-aided design of non-nucleoside inhibitors of HIV-1 reverse transcriptase.
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299. Optimization of diarylamines as non-nucleoside inhibitors of HIV-1 reverse transcriptase.
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300. Solvent Effects on Organic Reactions from QM/MM Simulations.
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301. Cope Elimination: Elucidation of Solvent Effects from QM/MM Simulations.
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302. Medium Effects on the Decarboxylation of a Biotin Model in Pure and Mixed Solvents from QM/MM Simulations.
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303. Optimization of pyrimidinyl- and triazinyl-amines as non-nucleoside inhibitors of HIV-1 reverse transcriptase.
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304. Contribution of Conformer Focusing on the Uncertainty in Predicting Free Energies for Protein-Ligand Binding.
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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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.; Guimarães, 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.
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.
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, 118, 2820-2826. 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, 10, 2802-2812. doi:10.1021/ct500016d.
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.
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.
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.
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.
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.
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.
388. Molecular dynamics and Monte Carlo simulations for protein.ligand binding and inhibitor design.
Biochim. Biophys. Acta, Gen. Subj. 2015, 1850, 966-971. doi:10.1016/j.bbagen.2014.08.018.
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.
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.
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.
392. A Reflection on Paul von Ragué Schleyer.
J. Chem. Theory Comput. 2015, 11, 1. doi:10.1021/ct501095w.
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.
394. Autobiography of William L. Jorgensen: Scientific History and Recollections.
J. Phys. Chem. B 2015, 119, 624-632. doi:10.1021/jp510442j.
395. Group Members of William L. Jorgensen (1975-2014).
J. Phys. Chem. B 2015, 119, 633-634. doi:10.1021/jp5104406.
396. Abbreviated Curriculum Vitae of William L. Jorgensen.
J. Phys. Chem. B 2015, 119, 635-636. doi:10.1021/jp510441r.
397. Determination of partial molar volumes from free energy perturbation theory.
Phys. Chem. Chem. Phys. 2015, 17, 8407-8415. doi:10.1039/c4cp05304d.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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. STL files (zip, 50 MB).
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.
410. 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.
411. 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.
412. 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.
413. A Fluorescence Polarization Assay for Binding to Macrophage Migration Inhibitory Factor and Crystal Structures for Complexes of Two Potent Inhibitors.
J. Am. Chem. Soc. 2016, 138(27), 8630-8638. doi:10.1021/jacs.6b04910.
414. Performance of Protein-Ligand Force Fields for the Flavodoxin-Flavin Mononucleotide System.
J. Phys. Chem. Lett. 2016, 7(15), 3032-3036. doi:10.1021/acs.jpclett.6b01229.
415. Computer-aided discovery of anti-HIV agents.
Bioorg. Med. Chem. 2016, 24(20), 4768-4778. doi:10.1016/j.bmc.2016.07.039.
416. 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.
417. 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.
418. Improved treatment of nucleosides and nucleotides in the OPLS-AA force field.
Chem. Phys. Lett. 2017, 683, 276-280. doi:10.1016/j.cplett.2017.02.049.
419. 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.
420. Structural and Preclinical Studies of Computationally Designed Non-Nucleoside Reverse Transcriptase Inhibitors for Treating HIV infection.
Mol. Pharmacol. 2017, 91(4), 383-391. doi:10.1124/mol.116.107755.
421. 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.
422. 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.
423. Identification and Characterization of JAK2 Pseudokinase Domain Small Molecule Binders.
Puleo D. E.; Kucera K.; Hammarén 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.
424. 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.
425. 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.
426. 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.
427. 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.
428. 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. Advances and Insights for Small Molecule Inhibition of Macrophage Migration Inhibitory Factor..
J. Med. Chem. 2018, 61(18), 8104-8119. doi:10.1021/acs.jmedchem.8b00589.
430. 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. 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. 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. 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.
434. 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, Article ASAP. doi:10.1021/acs.jctc.9b00054.

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