Welcome to the Jorgensen Lab

For the past thirty years, the Jorgensen Research Group has been at the forefront of computational chemistry and molecular design. Below is an outline of our progress:

1976-82QM studies of organic ions & ion-molecule complexes
1978- MC for liquids, OPLS force field development
1980- Solvent effects on conformational equilibria
1980-95Development of CAMEO for prediction of products of organic reactions
1983 TIP3P & TIP4P water models
1984 Free-energy profiles for SN2 reactions in solution
1985 1st FEP calculation: CH3CH3 --> CH3OH in water
1985- FEP for reactions in solution (QM + MM), ΔGhyd, ion-pairing, pKas, log P, hydrophobic effects, etc.
1988-96Molecular recognition/organic host-guest complexes
1989 Secondary electrostatic effects for G-C, A-T, etc.
1987- MD and MC for proteins, denaturation, folding, enzymatic rxns
1996- FEP/MC for protein-ligand binding
1997- Full QM/MM for organic & enzymatic reactions
2000- Structure-based drug design, ADME predictions
2001- Semiempirical molecular orbital method development
2003- FEP-guided design and synthesis of enzyme inhibitors

Newest Publications

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, Article ASAP, . doi:10.1021/ct300180w.

360. 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.

359. Targeting the von Hippel.Lindau 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.

358. Discovery of dimeric inhibitors by extension into the entrance channel of HIV-1 reverse transcriptase.
Ekkati, A. R.; Bollini, M.; Domaoai, R. A.; Spasov, K. A.; Anderson, K. S.; Jorgensen, W. L.
Bioorganic & Medicinal Chemistry Letters 2012, 22, 1565-1568. doi:10.1016/j.bmcl.2011.12.132.

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

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

355. Improving MM-GB/SA Scoring through the Application of the Variable Dielectric Model.
Ravindranathan, K.; Tirado-Rives, J.; Jorgensen, W. L.; Guimaraes, C. R. W.
J. Chem. Theory Comput. 2011, 7, 3859-3865. doi:10.1021/ct200565u.

354. On the Mechanism and Rate of Spontaneous Decomposition of Amino Acids.
Alexandrova, A. N.; Jorgensen, W. L.
J. Phys. Chem. B 2011, 115, 13624-13932. doi:10.1021/jp2081808.

For more details about the specifics of the research, please see the publications page and the research page.

Group picture

Award picture

At the 243rd National American Chemical Society meeting, in San Diego, CA, March 2012, Professor Jorgensen recieved the Joel Henry Hildebrand Award in Theoretical and Experimental Chemistry of Liquids. This award is sponsored by the Exxon Mobil Research and Engineering Company and was presented by Dr. Thomas F. Degnan, Jr. Manager, Breakthrough and Leads Generation, Exxon Mobil Research and Engineering Company. Congratulations Dr. Jorgensen!