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 ß-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 ß-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.
doi:10.1021/ja00045a029.
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.
doi:10.1021/j100100a043.
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.
doi:10.1021/j100051a021.
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.
doi:10.1021/ja00152a025.
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 ß-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.; 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.
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,
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.
Cole, D. J.; Tirado-Rives, J.; Jorgensen, W. L.
Biochim. Biophys. Acta, Gen. Subj.
2015,
1850,
966-971.
doi:10.1016/j.bbagen.2014.08.018.
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.
Jorgensen, W. L.
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.
Jorgensen, W. L.
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.
Vilseck, J. Z.; Tirado-Rives, J.; Jorgensen, W. L.
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.
Cisneros, J. A.; Robertson, M. J.; Valhondo, M.; Jorgensen, W. L.
J. Am. Chem. Soc.
2016,
138(27),
8630-8638.
doi:10.1021/jacs.6b04910.
414.
Performance of Protein-Ligand Force Fields for the Flavodoxin-Flavin Mononucleotide System.
Robertson, M. J.; Tirado-Rives, J.; Jorgensen, W. L.
J. Phys. Chem. Lett.
2016,
7(15),
3032-3036.
doi:10.1021/acs.jpclett.6b01229.
415.
Computer-aided discovery of anti-HIV agents.
Jorgensen, W. L.
Bioorg. Med. Chem.
2016,
24(20),
4768-4778.
doi:10.1016/j.bmc.2016.07.039.
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.
Robertson, M. J.; Tirado-Rives, J.; Jorgensen, W. L.
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.
Kudalkar, S. N.; Beloor, J.; Chan, A. H.; Lee, W. -G.; Jorgensen, W. L.; Kumar, P; Anderson, K. S.;
Mol. Pharmacol.
2017,
91(4),
383-391.
doi:10.1124/mol.116.107755.
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..
Trivedi-Parmar, V.; Jorgensen, W.L.
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.
Novel Allosteric Covalent Inhibitors of Bifunctional Cryptosporidium hominis TS-DHFR from Parasitic Protozoa Identified by Virtual Screening..
Ruiz, V.; Czyzyk, D. J.; Valhondo, M.; Jorgensen, W. L.; Anderson, K. S.
Bioorg. Med. Chem. Lett.
2019,
29,
1413-1418. PMID: 30929953.
doi:10.1016/j.bmcl.2019.03.022.
434.
Computation of Protein-Ligand Binding Free Energies using Quantum Mechanical Bespoke Force Fields..
Cole, D.; Cabeza de Vaca, I.; Jorgensen, W.L.
Med. Chem. Commun.
2019,
10,
Advanced.
doi:10.1039/C9MD00017H.
435.
Development and Testing of the OPLS-AA/M Force Field for RNA..
Robertson, M. J.; Qian, Y.; Robinson, M. C.; Tirado-Rives, J.; Jorgensen, W.L.
J. Chem. Theory Comput
2019,
15,
2734-2742.
doi:10.1021/acs.jctc.9b00054.
436.
Robust FEP Protocols for Creating Molecules in Solution..
Cabeza de Vaca, I.; Zarzuela, R.; Tirado-Rives, J.; Jorgensen, W. L.
J. Chem. Theory Comput.
2019,
15,
3941-3948.
doi:10.1021/acs.jctc.9b00213.
437.
Structural and Pharmacological Evaluation of a Novel Non-nucleoside Reverse Transcriptase Inhibitor as a Promising Long Acting Nanoformulation for Treating HIV..
Kudalkar, S. N.; Ullah, I.; Bertoletti, N.; Mandl, H.; Cisneros, J. A.; Beloor, J.; Chan, A. H.; Saltzman, W. M.; Jorgensen, W. L.; Kumar, P.; Anderson, K. S.
Antiviral Res.
2019,
167,
110-116. PMID: 31034849.
doi:10.1016/j.antiviral.2019.04.010.
438.
In Vivo Anticryptosporidial Efficacy of a Prodrug Nanotherapy in a Mouse Model of Cryptosporidium Infection..
Ranjan, A.P.; Czyzyk, D.J.; Martinez-Traverso, G.; Valhondo, M.; Jorgensen, W.L; Vishwanatha, J.K.; Castellanos-Gonzalez, A.; Anderson, K.S.
Antimicrob. Agents Chemother.
2019,
00,
0000-0000. Submitted..
439.
Understanding the Structural Basis of Species Selective, Stereospecific Inhibition for Cryptosporidium and Human Thymidylate Synthase..
Czyzyk, D.J.; Valhondo, M.; Jorgensen, W. L.; Anderson, K.S.
FEBS Lett.
2019,
593,
2069-2078.
doi:10.1002/1873-3468.13474.
440.
QM/MM Calculations for the Cl- + CH3Cl SN2 Reaction in Water Using CM5 Charges and Density Functional Theory..
Tirado-Rives, J.; Jorgensen, W. L.
J. Phys. Chem. B
2019,
123,
5713-5717. Leo Radom Festschrift.
doi:10.1021/acs.jpca.9b04121.
441.
Molecular and Cellular Studies Evaluating a Potent 2-Cyanoindolizine Catechol Diether NNRTI Targeting Wildtype and Y181C Mutant HIV-1 Reverse Transcriptase .
Sasaki, T.; Gannam, Z. T. K.; Kudalkar, S. N.; Frey, K. M.; Lee, W.-G.; Spasov, K. A.; Jorgensen, W. L.; Anderson, K. S.
Bioorg. Med. Chem. Lett.
2019,
29,
2182-2188.
doi:10.1016/j.bmcl.2019.06.047.
442.
Structure Activity Relationship Towards the Design of Cryptosporidium Specific Thymidylate Synthase Inhibitors..
Czyzyk, D.; Valhondo, M.; Tirado-Rives, J.; Jorgensen, W. L.; Anderson, K. S.
Eur. J. Med. Chem.
2019,
183,
111673.
doi:10.1016/j.ejmech.2019.111673.
443.
Absolute Free Energy of Binding Calculations for Macrophage Migration Inhibitory Factor in Complex with a Drug-like Inhibitor..
Qian, Y.; Cabeza de Vaca, I.; Vilseck, J. Z.; Cole, D. J.; Tirado-Rives, J.; Jorgensen, W. L.
J. Phys. Chem. B
2019,
123,
8675-8685.
doi:10.1021/acs.jpcb.9b07588.
444.
Selective JAK2 Pseudokinase Ligands with a Diaminotriazole Core..
Liosi, M.-E.; Krimmer, S. G.; Newton, A. S.; Dawson, T. K.; Puleo, D. E.; Cutrona, K. J.; Schlessinger, J.; Jorgensen, W. L.
J. Med. Chem.
2020,
63,
5324-5340.
doi:10.1021/acs.jmedchem.0c00192.
445.
Structure-Guided Identification of DNMT3B Inhibitors..
Newton, A. S.; John C. Faver, J. C.; Micevic, G.; Muthusamy, V.; Kudalkar, S. N.; Bertoletti, N.; Anderson, K. S.; Bosenberg, M. W.; Jorgensen, W. L.
ACS Med. Chem. Lett.
2020,
11,
971-976. M. Botta Memorial Issue..
doi:10.1021/acsmedchemlett.0c00011.
446.
Metadynamics as a Post-Processing Method for Virtual Screening with Application to the Pseudokinase Domain of JAK2..
Cutrona, K. J.; Newton, A. S.; Krimmer, S. G.; Tirado-Rives, J.; Jorgensen, W. L.
J. Chem. Info. Model.
2020,
60,
4403-4415.
doi:10.1021/acs.jcim.0c00276.
447.
Targeting the TS dimer interface in bifunctional Cryptosporidium hominis TS-DHFR from parasitic protozoa: Virtual screening identifies novel TS allosteric inhibitors..
Ruiz, V. G.; Czyzyk, D. J.; Kumar, V. P.; Jorgensen, W. L.; Anderson, K. S.
Bioorg. Med. Chem. Lett.
2020,
30,
127292.
doi:10.1016/j.bmcl.2020.127292.
448.
Structural Investigation of 2-Naphthyl Phenyl Ether Inhibitors Bound to WT and Y181C Reverse Transcriptase Highlights Key Features of the NNRTI Binding Site..
Duong, V. N.; Ippolito, J. A.; Chan, A. H.; Lee, W.-G.; Spasov, K. S.; Jorgensen, W. L.; Anderson, K. S.
Protein Sci.
2020,
29,
1902-1910.
doi:10.1002/pro.3910.
449.
Explicit Representation of Cation-π Interactions in Force Fields with 1/r⁴ Non-bonded Terms..
Turupcu, A.; Tirado-Rives, J.; Jorgensen, W. L.
J. Chem. Theory Comput.
2020,
16,
7184-7194.
doi:10.1021/acs.jctc.0c00847.
450.
Identification of 14 Known Drugs as Inhibitors of the Main Protease of SARS-CoV-2..
Ghahremanpour, M.; Tirado-Rives, J.; Deshmukh, M.; Ippolito, J. A.; Zhang, C.-H.; Cabeza de Vaca, I.; Liosi, M.-E.; Anderson, K. S.; Jorgensen, W. L.
ACS Med. Chem. Lett.
2020,
11,
2526-2533.
doi:10.1021/acsmedchemlett.0c00521.
451.
Covalent Inhibition of Wild-Type HIV-1 Reverse Transcriptase Using a Fluorosulfate Warhead..
Ippolito, J. A.; Niu, H.; Bertoletti, N.; Carter, Z. J.; Jin, S.; Spasov, K. A.; Cisneros, J. A.; Valhondo, M.; Cutrona, K. J.; Anderson, K. S.; Jorgensen, W. L.
ACS Med. Chem. Lett.
2021,
12,
249-255.
doi:10.1021/acsmedchemlett.0c00612.
452.
Potent Noncovalent Inhibitors of the Main Protease of SARS-CoV2 from Molecular Sculpting of the Drug Perampanel Guided by Free Energy Perturbation Calculations..
Zhang, C-H.; Stone, E. A.; Deshmukh, M.; Ippolito, J. A.; Ghahremanpour, M. M.; Tirado-Rives, J.; Spasov, K. A.; Zhang, S.; Takeo, Y.; Kudalkar, S. N.; Liang, Z.; Isaacs, F.; Lindenbach, B.; Miller, S. J.; Anderson, K. S.; Jorgensen, W. L.
ACS Cent. Sci.
2021,
7,
467-475.
doi:10.1021/acscentsci.1c00039.
453.
Structure-guided Design of a Perampanel-derived Pharmacophore Targeting the SARS-CoV-2 Main Protease.
Deshmukh, M. G.; Ippolito, J. A.; Zhang, C.-H.; Stone, E. A.; Reilly, R. A.; Miller, S. J.; Jorgensen, W. L.; Anderson, K. S.;
Structure
2021,
29,
823-833.
doi:10.1016/j.str.2021.06.002.
454.
Indoloxytriazines as Binding Molecules for the JAK2 JH2 Pseudokinase Domain and its V617F Variant.
Newton, A. S.; Liosi, M.-E.; Henry, S. P.; Deiana, L.; Faver, J. C.; Krimmer, S. G.; Puleo, D. E.; Schlessinger, J.; Jorgensen, W. L.
Tetrahedron Lett.
2021,
153248.
doi:10.1016/j.tetlet.2021.153248.
455.
Optimization of Triarylpyridinone Inhibitors of the Main Protease of SARS-CoV-2 to Low-Nanomolar Antiviral Potency..
Zhang, C.-H.; Spasov, K. A.; Reilly, R. A.; Hollander, K. A.; Stone, E. A.; Ippolito, J. A.; Liosi, M.-E.; Deshmukh, M. G.; Tirado-Rives, J.; Zhang, S.; Liang, Z.; Miller, S. J.; Isaacs, F.; Lindenbach, B. D.; Anderson, K. S.; Jorgensen, W. L.
ACS Med. Chem. Lett.
2021,
12,
1325-1332.
doi:10.1021/acsmedchemlett.1c00326.
456.
Conversion of a False Virtual Screen Hit into Selective JAK2 JH2 Domain Binders Using Convergent Design Strategies..
Henry, S. P.; Liosi, M-E.; Ippolito, J. A.; Cutrona, K. J.; Krimmer, S. G.; Newton, A. S.; Schlessinger, J.; Jorgensen, W. L.
ACS Med. Chem. Lett.
2022,
12,
819-826.
doi:10.1021/acsmedchemlett.2c00051.
457.
Insights on JAK2 Modulation by Potent, Selective, and Cell-Permeable Pseudokinase-Domain Ligands..
Liosi, M.-E.; Ippolito, J. A.; Henry, S. P. Krimmer, S. G.; Newton, A. S.; Cutrona, K. J.; Olivarez, R. A.; Mohanty, J.; Schlessinger, J.; Jorgensen, W. L.
J. Med. Chem.
2022,
13,
819-826.
doi:10.1021/acs.jmedchem.2c00283.
458.
Refinement of the Optimized Potentials for Liquid Simulations Force Field for Thermodynamics and Dynamics of Liquid Alkanes..
Ghahremanpour, M. M.; Tirado-Rives, J.; Jorgensen, W. L.
J. Phys. Chem. B
2022,
126,
5896-5907.
doi:10.1021/acs.jpcb.2c03686.
459.
Covalent Modification of the JH2 Domain of Janus Kinase 2.
Henry, S. P.; Liosi, M-E.; Ippolito, J. A.; Menges, F.; Newton, A. S.; Schlessinger, J,; Jorgensen, W. L.
ACS Med. Chem. Lett.
2022,
13,
1819-1826.
doi:10.1021/acsmedchemlett.2c00414.
460.
Design, synthesis, and biological testing of biphenylmethyloxazole inhibitors targeting HIV-1 reverse transcriptase.
Carter, Z. J.; Hollander, K, A.; Spasov, K. A.; Anderson, K, S,; Jorgensen, W. L.
Bioorg. Med. Chem. Lett.
2023,
84,
129216.
doi:10.1016/j.bmcl.2023.129216.
461.
Progress on the Pharmacological Targeting of Janus Pseudokinases.
Henry, S. P.; Jorgensen, W. L.
J Med. Chem.
2023,
66,
10959-10990.
doi:10.1021/acs.jmedchem.3c00926.
462.
Computation of Absolute Binding Free Energies for Noncovalent Inhibitors with SARS-CoV-2 Main Protease.
Ghahremanpour, M. M.; Saar, A.; Tirado-Rives, J.; Jorgensen, W. L.
J. Chem. Inf. Model.
2023,
63,
5309-5318.
doi:10.1021/acs.jcim.3c00874.
463.
Exploring Novel HIV-1 Reverse Transcriptase Inhibitors with Drug Resistant Mutants: A Double Mutant Surprise.
Hollander, K,; Chan, A. H.; Frey, K. M.; Hunker, O.; Ippolito, J. A.; Spasov, K. A.; Yeh, Y. J.; Jorgensen, W. L.; Ho, Y.; Anderson, K. S.
Protein Sci.
2023,
32,
e4814.
doi:10.1002/pro.4814.
464.
Covalent and Noncovalent Strategies for Targeting Lys102 in HIV-1 Reverse Transcriptase.
Prucha, G. R.; Henry, S.; Hollander, K.; Carter, Z.; J.; Spasov, K. A.; Jorgensen, W. L.; Anderson, K, S.
Eur. J. Med. Chem.
2023,
262,
115984.
doi:10.1016/j.ejmech.2023.115894.
465.
Assessing Metadynamics and Docking for Absolute Binding Free Energy Calculations Using Severe Acute Respiratory Syndrome Coronavirus 2 Main Protease Inhibitors.
Saar, A.; Ghahremanpour, M. M.; Tirado-Rives, J.; Jorgensen, W. L.
J. Chem. Inf. Model.
2023,
63,
7210-7218.
doi:10.1021/acs.jcim.3c01453.
466.
A High-Throughput, High-Containment Human Primary Epithelial Airway Organ-on-Chip Platform for SARS-CoV-2 Therapeutic Screening.
Fisher, C. R.; Medie, F. M.; Luu, R. J.; Gaibler, R. B.; Mulhern, T. J.; Miller, C. R.; Zhang, C. J.; Rubio, L. D.; Marr, E. E.; Vijayakumar, V.; Gabriel, E. P; Lopez Quezada, L.; Zhang, C.-H.; Anderson, K. S. Jorgensen, W. L.; Alladina, J. W.;cMedoff, B. D.; Borenstein, J. T.; Gard, A. L.
Cells
2023,
12,
2639.
doi:10.3390/cells12222639.
467.
Ensemble Geometric Deep Learning of Aqueous Solubility.
Ghahremanpour, M. M.; Saar, A.; Tirado-Rives, J.; Jorgensen, W. L.
J. Chem. Inf. Model.
2023,
63,
7338-7349.
doi:10.1021/acs.jcim.3c01536.
468.
OPLS/2020 Force Field for Unsaturated Hydrocarbons, Alcohols, and Ethers.
Jorgensen, W. L.; Ghahremanpour, M. M.; Saar, A.; Tirado-Rives, J.
J. Phys. Chem. B
2023,
127,
250-262.
doi:10.1021/acs.jpcb.3c06602.
469.
Enthalpies and Entropies of Hydration From Monte Carlo Simulations..
Jorgensen, W. L.
Phys. Chem. Chem. Phys.
2024,
26,
8141-8147.
doi:10.1039/D4CP00297K.
470.
Proof-of-Concept Studies with a Computationally Designed Mpro Inhibitor as a Synergistic Combination Regimen Alternative to Paxlovid..
Papini, C.; Ullah, I.; Ranjan, A. P.; Zhang, S.'Wu, Q.; Spasov, K. A.; Zhang, C.; Mothes, W.; Crawford, J. M.; Lindenbach, B. D.; Uchil. P. D.; Kumar, P.; Jorgensen, W. L.; Anderson, K. S.
Proc. Nat. Acad. Sci. USA
2024,
121,
e2320713121.
doi:10.1073/pnas.2320713121.
471.
Prodrug nanotherapy demonstrates in vivo anticryptosporidial efficacy in a mouse model of chronic Cryptosporidium infection.
Ranjan, A. P.; Czyzyk, D. J.; Martinez-Traverso, G.; Sadiqova, A.; Valhondo, M.; Schaefer, D. A.; Spasov, K. A.; Jorgensen, W. L.; Vishwanatha, J. K.; Riggs, M. V.; Castellanos-Gonzalez, A.; Anderson, K. S.
RSC pharmaceutics
2024,
1,
963-975.
doi:10.1039/D4PM00093E.
472.
Monte Carlo simulations for free energies of hydration: Past to present.
Jorgensen, W. L.
J. Chem. Phys.
2024,
161,
064111.
doi:10.1063/5.0222659.
473.
The Beginnings of JCTC.
Jorgensen, W. L.
J. Chem. Theory Comput.
2024,
20,
7692-7693.
doi:10.1021/acs.jctc.4c01146.
474.
Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (Mpro) with Noncovalent Preclinical Candidate, Mpro61.
Kenneson, J. R.; Papini, C.; Tang, S.; Huynh,K.; Zhang, C-H.; Jorgensen, W. L.; Anderson, K. S.
ACS Bio & Med Chem Au
2025,
5,
215-226.
doi:10.1021/acsbiomedchemau.4c00109.
475.
Free Energies of Solvation in Benzene and Hexafluorobenzene: Is Explicit Polarization Needed?.
Jorgensen, W. L.; Tirado-Rives, J.
J. Phys. Chem. B
2025,
129,
6574-6583.
doi:10.1021/acs.jpcb.5c02405.
Dept of Chemistry, Yale University
New Haven, CT 06520-8107, USA
Phone: (203)432-6288
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