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

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.

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.

423. Identification and Characterization of JAK2 Pseudokinase Domain Small Molecule Binders.
Puleo D. E.; Kucera K.; Hammar´┐Żn 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.

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.

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.

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.

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.

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, In Press, . doi:10.1016/j.cplett.2017.02.049.

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.

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.

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.

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.

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.

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.

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.

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!!!

2015


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.

2012


Group picture

Group Photo 2017


Group picture

Group Photo 2013