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description=Computational chemistry at Yale — the Jorgensen group builds the simulation methods and force fields (BOSS, MCPRO, LigParGen, OPLS) behind modern drug design.;

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william l jorgensen research group yale university jorgensen lab research research from micromolar to picomolar free energy calculations predict which molecule to make next turning weak screening hits into drug strength inhibitors of hiv 1 reverse transcriptase and the sars cov 2 main protease explore research explore publications 484 papers and 24 patents newest first people alumni faculty and staff and everyone who trained here free energy history how free energy calculations began from the group s own records software software the code behind the calculations all software the group s tools the ligpargen web server the boss and mcpro monte carlo engines and the opls force fields most are free for academic use go to software prepare your molecule ligpargen new amber opls aa parameters by running boss for you programs boss the monte carlo engine the rest runs on opls aa m improved force field for proteins rna mcpro mc for proteins nucleic acids specialized tools conformer energies opls ua energies for alkane conformers pddg for mopac pddg pm3 pddg mndo for mopac6 news latest 2026 new paper squeezing liquids from 250 to 10 000 atm monte carlo densities of water and organic liquids match experiment to about 1 support for the lennard jones 12 6 potential read the news awards honors fifty years of service 2025 the rome symposium in photographs acs arthur c cope award 2024 achievement in organic chemistry clarivate citation laureate 2021 nobel class citation impact all news honors the full timeline of recognition contact yale university department of chemistry william l jorgensen research group five decades of contributions to computational chemistry and molecular design publications software tools an outline of our progress 1976 82 foundations qm studies of organic ions ion molecule complexes 1978 force fields mc for liquids opls force field development 1980 foundations solvent effects on conformational equilibria 1980 95 foundations development of cameo for prediction of products of organic reactions 1983 force fields tip3p tip4p water models 1984 free energy free energy profiles for s n 2 reactions in solution 1985 free energy 1st fep calculation ch 3 ch 3 ch 3 oh in water 1985 free energy fep for reactions in solution qm mm δg hyd ion pairing p k a s log p hydrophobic effects etc 1987 proteins md and mc for proteins denaturation folding enzymatic rxns 1988 96 free energy molecular recognition organic host guest complexes 1989 foundations secondary electrostatic effects for g c a t etc 1996 free energy fep mc for protein ligand binding 1997 free energy full qm mm for organic enzymatic reactions 2000 drug design structure based drug design adme predictions qikprop licensed by schrödinger tip5p reported 2001 foundations semiempirical molecular orbital method development 2003 drug design fep guided design and synthesis of enzyme inhibitors 2006 into industry mcpro licensed by schrödinger as mcpro the fep line introduced in 2015 carrying free energy perturbation into routine pharmaceutical use 2009 drug design discovery of mif antagonists and agonists 2011 drug design report of the most potent non toxic anti hiv agents 2013 drug design determination of x ray crystal structures for protein ligand complexes 2015 drug design report of the most potent non toxic inhibitors of human mif 2017 drug design discovery of selective binding molecules for the pseudokinase domain of jak2 2020 drug design fep guided design and synthesis of sars cov 2 main protease m pro 3cl pro non covalent non peptidic inhibitors 01 23 1976 today prof william l jorgensen new haven connecticut news honors 2026 new in ligpargen ligpargen now writes amber files ligpargen s opls aa parameters now come for amber too a prmtop topology its coordinates and a short minimization input alongside the files for gromacs openmm charmm namd lammps and the other programs the 2017 ligpargen paper planned amber output for its next update it is here now the prmtop carries opls s own rules the geometric mixing of lennard jones parameters written out pair by pair and 1 4 interactions at half strength so amber s programs openmm and acemd read it exactly it was checked with amber s own sander against gromacs and openmm on 16 molecules from amides and ions to a 137 atom chain the energies agree term by term within a few thousandths of a kcal mol try ligpargen 2025 fifty years of service celebrated in rome decoding chemical reactions celebrating bill jorgensen s half century of service brought colleagues collaborators and former students to the temple university rome campus on 26 27 september 2025 two days of talks spanning the field his work helped create speakers photographs video 2024 acs arthur c cope award congratulations to professor jorgensen on being awarded the 2024 acs arthur c cope award to recognize outstanding achievement in the field of organic chemistry the significance of which has become apparent within the five years preceding the year in which the award will be presented read the announcement from the american chemical society and from yale news 2021 clarivate citation laureate congratulations to professor jorgensen on being selected a 2021 citation laureate read the announcement from clarivate and from yale news click the image to watch the interview more news honors featured at the origin of free energy methods a 2025 history of the field in the journal of physical chemistry b traces the modern practice of alchemical free energy methods now central to structure based drug discovery through the group s landmark 1985 calculation drawing on archival letters and interviews from its own records the line runs forward too in 2006 schrödinger licensed the group s mcpro as mcpro and fep the binding affinity tool now used across the pharmaceutical industry was introduced in 2015 the dawn of alchemical free energy methods in biomolecular simulations macuglia d ciccotti g roux b j phys chem b 2025 129 12359 12389 monte carlo simulation of differences in free energies of hydration jorgensen w l ravimohan c j chem phys 1985 83 3050 3054 read the full history featured william l jorgensen festschrift the journal of physical chemistry b january 22 2015 volume 119 issue 3 pages 621 1232 view issue festschrift preface includes tribute to william l jorgensen gao j orozco m peishoff c e j phys chem b 2015 119 621 623 autobiography of william l jorgensen scientific history and recollections jorgensen w l j phys chem b 2015 119 624 632 group members of william l jorgensen 1975 2014 j phys chem b 2015 119 633 634 abbreviated curriculum vitae of william l jorgensen j phys chem b 2015 119 635 636 pictures the group the group through the years photos from 1980 to today with the faculty and staff of the group and the 162 graduates postdoctoral fellows and undergraduates who have trained in it yale university department of chemistry funding support contact w l jorgensen research group address department of chemistry yale university new haven ct 06520 8107 usa reach us phone 203 432 6288 send us a message resources software publications contact 2026 w l jorgensen research group yale university contact