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

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, Just Accepted Manuscript, . 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.

392. A Reflection on Paul von Ragué Schleyer.
Jorgensen, W. L.
J. Chem. Theory Comput. 2015, 11, 1. doi:10.1021/ct501095w.

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.

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.

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.

388. Molecular dynamics and Monte Carlo simulations for protein.ligand binding and inhibitor design.
Cole, D. J.; Tirado-Rives, J.; Jorgensen, W. L.
Biochimica et Biophysica Acta (BBA) - General Subjects 2014, In Press Article. doi:10.1016/j.bbagen.2014.08.018.

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.

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.

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.

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

Group picture

2013

Group picture

2009

Group 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!