Welcome to the Jorgensen Lab

For the past thirty years, the Jorgensen Research Group has been at the forefront of computational chemistry. 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, 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- Polypeptide and nucleic acid folding

Newest publications

320. 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.

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

318. 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.

317. 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.

315. 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.

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

Group picture Julian Tirado-Rives Patricia Morales de Tirado Joseph Kim Laura Thomas Siegfried Leung Sara Nichols William L. Jorgensen Anastassia Alexandrova Birgit Albrecht Zoe Cournia Vinay Thakur Sunil Grandavadi John Terhorst Krishna Ravindranathan

Group picture

Happy Holidays from the Jorgensen Group!