Welcome to the Jorgensen Lab

For many 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
2009- Discovery of MIF antagonists and agonists
2011- Report of the most potent, non-toxic anti-HIV agents ever discovered
2013- Determination of X-ray crystal structures for protein-ligand complexes
2015- Report of the most potent, non-toxic inhibitors of human MIF ever discovered

William L. Jorgensen Festschrift

Festschrift Cover   The Journal of Physical Chemistry B
  January 22, 2015 , Volume 119, Issue 3 , Pages 621-1232.

  Festschrift Preface includes:
  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 .

Newest Publications

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, Article ASAP, . doi:10.1021/acs.jctc.6b00027.

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, Article ASAP, . doi:10.1021/acs.jpcb.6b00399.

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.

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).

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

Congratulations to Professor Jorgensen on being awarded the
2015 Tetrahedron Prize for Creativity in Bioorganic and Medicinal Chemistry!!!


Congratulations to Professor Jorgensen on recieving the
Joel Henry Hildebrand Award in Theoretical and Experimental Chemistry of Liquids!!!

Group picture

This award was 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.


Group picture

Group Photo 2013

Group picture

Group Photo 2009