Yale University · Department of Chemistry

William L. Jorgensen Research Group

Five decades of contributions to computational chemistry and molecular design.

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 SN2 reactions in solution

1985
Free Energy

1st FEP calculation: CH3CH3 → CH3OH in water

1985–
Free Energy

FEP for reactions in solution (QM + MM), ΔGhyd, ion-pairing, pKas, 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 (MPro, 3CLPro) non-covalent, non-peptidic inhibitors

01 / 23  ·  1976–today
Prof. William L. Jorgensen
New Haven, Connecticut
News & Honors
2026 New paper

A faster force field, no loss in accuracy.

How readily a molecule dissolves in water versus an oily, nonpolar liquid affects where it ends up in the body — and how tightly a drug can bind its target. A new study computes these free energies of solvation for 101 organic molecules in both cyclohexane and water using Monte Carlo free-energy perturbation. The finding: the simpler united-atom OPLS model reproduces experiment just as accurately as the all-atom model (mean error ~0.5 kcal/mol), while running 5–10× faster.

Try the force field

Alkane conformer energies.

Put the 2026 united-atom OPLS model to work: enter an alkane — a chain, a branched skeleton, or a ring — and get the energy of every distinct conformer, from chair vs. twist-boat to anti vs. gauche.

Symposium attendees gathered on the steps of a courtyard at the Temple University Rome Campus
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.

Professor Jorgensen receiving the 2024 ACS Arthur C. Cope Award Arthur C. Cope Award medal
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.”

2021 Citation Laureate
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.

William L. Jorgensen at his Purdue laboratory in 1982, finalizing the Monte Carlo code that became BOSS
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.

Read the full history →

Festschrift cover — The Journal of Physical Chemistry B, Volume 119, Issue 3
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:

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 shield
Yale University
Department of Chemistry
Funding & Support
National Institutes of Health National Science Foundation National Institute of Allergy and Infectious Diseases DARPA National Foundation for Cancer Research Lupus Research Alliance