A5053850265- Spectroscopy and Quantum Chemical Studies
- Advanced Chemical Physics Studies
- Protein Structure and Dynamics
- HIV/AIDS drug development and treatment
- Various Chemistry Research Topics
- Academic Writing and Publishing
- Computational Drug Discovery Methods
- HIV Research and Treatment
- Chemical Reaction Mechanisms
- Inorganic and Organometallic Chemistry
- Analytical Chemistry and Chromatography
- Thermodynamic properties of mixtures
- Free Radicals and Antioxidants
- Molecular spectroscopy and chirality
- Chemical Thermodynamics and Molecular Structure
- Macrophage Migration Inhibitory Factor
- DNA and Nucleic Acid Chemistry
- Phase Equilibria and Thermodynamics
- Biochemical and Molecular Research
- Organic Chemistry Cycloaddition Reactions
- Molecular Junctions and Nanostructures
- History and advancements in chemistry
- Chemical and Physical Properties in Aqueous Solutions
- Enzyme Structure and Function
- Pneumocystis jirovecii pneumonia detection and treatment
Yale University
2016-2025
University of New Haven
2014-2019
Yale Cancer Center
2014
University at Buffalo, State University of New York
2013
Center for Discovery
2012
Auburn University
2007-2010
Czech Academy of Sciences, Institute of Biotechnology
2010
National Cancer Institute
2003-2010
St. Elizabeth Healthcare
2010
University of California, Los Angeles
1997-2009
Classical Monte Carlo simulations have been carried out for liquid water in the NPT ensemble at 25 °C and 1 atm using six of simpler intermolecular potential functions dimer: Bernal–Fowler (BF), SPC, ST2, TIPS2, TIP3P, TIP4P. Comparisons are made with experimental thermodynamic structural data including recent neutron diffraction results Thiessen Narten. The computed densities energies reasonable accord experiment except original BF model, which yields an 18% overestimate density poor...
The parametrization and testing of the OPLS all-atom force field for organic molecules peptides are described. Parameters both torsional nonbonded energetics have been derived, while bond stretching angle bending parameters adopted mostly from AMBER field. were determined by fitting to rotational energy profiles obtained ab initio molecular orbital calculations at RHF/6-31G*//RHF/6-31G* level more than 50 ions. quality fits was high with average errors conformational energies less 0.2...
ADVERTISEMENT RETURN TO ISSUEPREVarticleNEXTThe OPLS [optimized potentials for liquid simulations] potential functions proteins, energy minimizations crystals of cyclic peptides and crambinWilliam L. Jorgensen Julian Tirado-RivesCite this: J. Am. Chem. Soc. 1988, 110, 6, 1657–1666Publication Date (Print):March 1, 1988Publication History Published online1 March 1988Published inissue 1 1988https://pubs.acs.org/doi/10.1021/ja00214a001https://doi.org/10.1021/ja00214a001research-articleACS...
We present results of improving the OPLS-AA force field for peptides by means refitting key Fourier torsional coefficients. The fitting technique combines using accurate ab initio data as target, choosing an efficient subspace whole potential-energy surface, and determining weights each points based on magnitudes gradient. average energy RMS deviation from LMP2/cc-pVTZ(-f)//HF/6-31G** is reduced ca. 40% 0.81 to 0.47 kcal/mol a result electrostatically uncharged dipeptides. Transferability...
The parametrization and validation of the OPLS3 force field for small molecules proteins are reported. Enhancements with respect to previous version (OPLS2.1) include addition off-atom charge sites represent halogen bonding aryl nitrogen lone pairs as well a complete refit peptide dihedral parameters better model native structure proteins. To adequately cover medicinal chemical space, employs over an order magnitude more reference data associated parameter types relative other commonly used...
ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOptimized intermolecular potential functions for liquid hydrocarbonsWilliam L. Jorgensen, Jeffry D. Madura, and Carol J. SwensonCite this: Am. Chem. Soc. 1984, 106, 22, 6638–6646Publication Date (Print):October 1, 1984Publication History Published online1 May 2002Published inissue 1 October 1984https://pubs.acs.org/doi/10.1021/ja00334a030https://doi.org/10.1021/ja00334a030research-articleACS PublicationsRequest reuse permissionsArticle...
The ability of simple potential functions to reproduce accurately the density liquid water from −37 100 °C at 1 10 000 atm has been further explored. result is five-site TIP5P model, which yields significantly improved results; average error in over 100° temperature range −37.5 62.5 only 0.006 g cm−3. Classical Monte Carlo statistical mechanics calculations have performed optimize parameters, especially position negative charges along lone-pair directions. Initial with 216 molecules NPT...
An overview is provided on the development and status of potential energy functions that are used in atomic-level statistical mechanics molecular dynamics simulations water organic biomolecular systems. Some topics considered form force fields, their parameterization performance, liquids, computation free energies hydration, universal extension for molecules, choice atomic charges. The discussion models covers some history, performance issues, special such as nuclear quantum effects.
Testing of the commonly used hybrid density functional B3LYP with 6-31G(d), 6-31G(d,p), and 6-31+G(d,p) basis sets has been carried out for 622 neutral, closed-shell organic compounds containing elements C, H, N, O. The focus is comparison computed experimental heats formation isomerization energies. In addition, effect an empirical dispersion correction term evaluated found to improve agreement data. For compounds, mean absolute errors (MAE) in are 3.1, 2.6, 2.7, 2.4 kcal/mol...
The accurate calculation of protein/nucleic acid-ligand interactions or condensed phase properties by force field-based methods require a precise description the energetics intermolecular interactions. Despite progress made in fields, small molecule parameterization remains an open problem due to magnitude chemical space; most critical issue is estimation balanced set atomic charges with ability reproduce experimental properties. LigParGen web server provides intuitive interface for...
ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTQuantum and statistical mechanical studies of liquids. 10. Transferable intermolecular potential functions for water, alcohols, ethers. Application to liquid waterWilliam L. JorgensenCite this: J. Am. Chem. Soc. 1981, 103, 2, 335–340Publication Date (Print):January 1, 1981Publication History Published online1 May 2002Published inissue 1 January 1981https://pubs.acs.org/doi/10.1021/ja00392a016https://doi.org/10.1021/ja00392a016research-articleACS...
Designing tight-binding ligands is a primary objective of small-molecule drug discovery. Over the past few decades, free-energy calculations have benefited from improved force fields and sampling algorithms, as well advent low-cost parallel computing. However, it has proven to be challenging reliably achieve level accuracy that would needed guide lead optimization (∼5× in binding affinity) for wide range protein targets. Not surprisingly, widespread commercial application simulations been...
ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOptimized intermolecular potential functions for liquid alcoholsWilliam L. JorgensenCite this: J. Phys. Chem. 1986, 90, 7, 1276–1284Publication Date (Print):March 1, 1986Publication History Published online1 May 2002Published inissue 1 March 1986https://pubs.acs.org/doi/10.1021/j100398a015https://doi.org/10.1021/j100398a015research-articleACS PublicationsRequest reuse permissionsArticle Views3757Altmetric-Citations1033LEARN ABOUT THESE...
ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAromatic-aromatic interactions: free energy profiles for the benzene dimer in water, chloroform, and liquid benzeneWilliam L. Jorgensen Daniel SeveranceCite this: J. Am. Chem. Soc. 1990, 112, 12, 4768–4774Publication Date (Print):June 1, 1990Publication History Published online1 May 2002Published inissue 1 June 1990https://pubs.acs.org/doi/10.1021/ja00168a022https://doi.org/10.1021/ja00168a022research-articleACS PublicationsRequest reuse...
Abstract A series of Monte Carlo simulations has been carried out to characterize the temperature and size dependence results for liquid water using TIP4P potential function. Five temperatures from -25 100°C four system sizes 64 512 molecules have studied. Comparisons are made with experimental thermodynamic structural data as well prior simulations.
The development and validation of new peptide dihedral parameters are reported for the OPLS-AA force field. High accuracy quantum chemical methods were used to scan φ, ψ, χ1, χ2 potential energy surfaces blocked dipeptides. New Fourier coefficients angle terms field fit these surfaces, utilizing a Boltzmann-weighted error function systematically examining effects weighting temperature. To prevent overfitting available data, minimal number residue-specific peptide-specific torsion developed....
Perturbation theory has been applied to calculate the relative free energies of hydration methanol and ethane in dilute soluton. It is demonstrated that only two or three Monte Carlo simulations using double-wide sampling are necessary obtain results with high precision. The small statistical uncertainty computed change energy good accord experimental thermodynamic data most encouraging for application procedure a wide range problems. Structural effects accompanying mutation water also...
The OPLS all-atom (AA) force field for organic and biomolecular systems has been expanded to include carbohydrates. Starting with reported nonbonded parameters of alcohols, ethers, diols, torsional were fit reproduce results from ab initio calculations on the hexopyranoses, α,β-d-glucopyranose, α,β-d-mannopyranose, α,β-d-galactopyranose, methyl α,β-d-glucopyranoside, α,β-d-mannopyranoside. In all, geometry optimizations carried out 144 conformers at restricted Hartree–Fock (RHF)/6–31G*...
ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFree energy calculations: a breakthrough for modeling organic chemistry in solutionWilliam L. JorgensenCite this: Acc. Chem. Res. 1989, 22, 5, 184–189Publication Date (Print):May 1, 1989Publication History Published online1 May 2002Published inissue 1 1989https://pubs.acs.org/doi/10.1021/ar00161a004https://doi.org/10.1021/ar00161a004research-articleACS PublicationsRequest reuse permissionsArticle Views2493Altmetric-Citations558LEARN ABOUT THESE...
Classical force-field parameters have been developed for amines primarily by fitting to experimental data pure liquids and hydrogen-bond strengths from gas-phase ab initio calculations. The resultant were used calculate relative free energies of hydration ammonia, methylamine, dimethylamine, trimethylamine using energy perturbation calculations in Monte Carlo simulations (MC/FEP). results including the fact that most favorable ΔGhyd occurs methylamine are excellent agreement with data,...
The quality of the 1.14*CM1A and 1.20*CM5 charge models was evaluated for calculations free energies hydration. For a set 426 neutral molecules, yield MADs 1.26 1.21 kcal/mol, respectively. charges, which can be readily obtained large systems, exhibit deviations only subset functional groups. results these cases were systematically improved using localized bond-charge corrections (LBCC) by offsetting adjustments are made to partial charges atoms in specified bond types. Only 19 LBCCs needed...
ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEnergy component analysis for dilute aqueous solutions of lithium(1+), sodium(1+), fluoride(1-), and chloride(1-) ionsJayaraman Chandrasekhar, David C. Spellmeyer, William L. JorgensenCite this: J. Am. Chem. Soc. 1984, 106, 4, 903–910Publication Date (Print):February 1, 1984Publication History Published online1 May 2002Published inissue 1 February 1984https://pubs.acs.org/doi/10.1021/ja00316a012https://doi.org/10.1021/ja00316a012research-articleACS...