Statistical perturbation theory has been applied in Monte Carlo simulations to compute the free energy of TIP4P water and the absolute free energies of hydration of methane and chloride ion. The calculations entailed the mutation of a water molecule and of a chloride ion to methane and the subsequent disappearance of the methane in the presence of 216 TIP4P solvent molecules. The NPT ensemble was used at 25°C and 1 atm, so Gibbs free energies were obtained. The mutations to methane proceeded with high precision, while the removal of the methane yielded an uncertainty of about ±0.3 kcal/mol in ΔG. The accord with experimental results is good in all cases; in particular, the computed free energy of TIP4P water is −6.1±0.3 kcal/mol, while the experimental value is −6.3 kcal/mol. The present results demonstrate the utility of statistical perturbation theory for computing absolute free energies of solution and the quality of the underlying potential functions.
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ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTComputer-assisted mechanistic evaluation of organic reactions. 14. Reactions of sulfur and phosphorus ylides, iminophosphoranes, and P=X-activated anionsAlan J. Gushurst and William L. JorgensenCite this: J. Org. Chem. 1988, 53, 15, 3397–3408Publication Date (Print):July 1, 1988Publication History Published online1 May 2002Published inissue 1 July 1988https://pubs.acs.org/doi/10.1021/jo00250a001https://doi.org/10.1021/jo00250a001research-articleACS PublicationsRequest reuse permissionsArticle Views189Altmetric-Citations7LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTComputer-assisted mechanistic evaluation of organic reactions. 17. Free-radical chain reactionsEllen R. Laird and William L. JorgensenCite this: J. Org. Chem. 1990, 55, 1, 9–27Publication Date (Print):January 1, 1990Publication History Published online1 May 2002Published inissue 1 January 1990https://pubs.acs.org/doi/10.1021/jo00288a005https://doi.org/10.1021/jo00288a005research-articleACS PublicationsRequest reuse permissionsArticle Views388Altmetric-Citations56LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA priori calculations of pKa's for organic compounds in water. The pKa of ethaneWilliam L. Jorgensen, James M. Briggs, and Jiali GaoCite this: J. Am. Chem. Soc. 1987, 109, 22, 6857–6858Publication Date (Print):October 1, 1987Publication History Published online1 May 2002Published inissue 1 October 1987https://pubs.acs.org/doi/10.1021/ja00256a053https://doi.org/10.1021/ja00256a053research-articleACS PublicationsRequest reuse permissionsArticle Views837Altmetric-Citations100LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Since the late 1980s there have been striking advances, fueled by large increases in both industrial and NIH-funded academic research, that have revolutionized drug discovery. This period has seen the introduction of high-throughput screening (HTS), combinatorial chemistry, PC farms, Linux, SciFinder, structure-based design, virtual screening by docking, free-energy methods, absorption/distribution/metabolism/excretion (ADME) software, bioinformatics, routine biomolecular structure determination, structures for ion channels, G-protein-coupled receptors (GPCRs) and ribosomes, structure/activity relationships (SAR) obtained from nuclear magnetic resonance (SAR by NMR), fragment-based design, gene knockouts, proteomics, small interfering RNA (siRNA), and human genome sequences. The result is a much-accelerated progression from identification of biomolecular target to lead compound to clinical candidate. However, a serious concern is that the dramatic increase in drug discovery abilities and expenditures has not been paralleled by an increase in FDA approvals of new molecular entities. High demands for drug safety, broader and longer clinical trials, too much HTS, too little natural products research, and effective generic drugs for many once-pressing afflictions have all been suggested as contributors. Numerous corporate mergers and acquisitions may have also had adverse effects on productivity through distractions of reorganization and integration. Nevertheless, one should consider what the success would have been in the absence of the striking technical advances. Certainly, progress with some critical and challenging target classes such as kinases would have been greatly diminished, and the adverse impact on many cancer patients would have been profound.
The energetics of the Menshutkin reaction between triethylamine and ethyl iodide have been computed using B3LYP and MP2 with the LANL2DZ, LANL2DZd, SVP, MIDI!, 6-311G(d,p), and aug-cc-PVTZ basis sets. Small- and large-core energy-consistent relativistic pseudopotentials were employed. Solvent effect corrections were computed from QM/MM Monte Carlo simulations utilizing free-energy perturbation theory, PDDG/PM3, and both a nonpolarizable OPLS and polarizable OPLS-AAP force field. The B3LYP/MIDI! theory level provided the best DeltaG(++) values with a mean absolute error (MAE) of 4.9 kcal/mol from experiment in cyclohexane, CCl(4), THF, DMSO, acetonitrile, water, and methanol. However, the relative rates in cyclohexane, and to a certain extent CCl(4), were determined to be greatly underestimated when using the nonpolarizable OPLS force field. An overall reduction in the MAE to 3.1 kcal/mol using B3LYP/MIDI!/OPLS-AAP demonstrated the need for a fully polarizable force field when computing solvent effects for highly dipolar transition structures in low-dielectric media. The MAEs obtained with PDDG/PM3/OPLS and OPLS-AAP of 5.3 and 3.8 kcal/mol, respectively, provided comparable results to B3LYP at a fraction of the computational resources. The large rate accelerations observed in the reaction were correlated to an increased stabilization of the emerging charge separation at the transition state via favorable solute-solvent interactions.
Monte Carlo/free energy perturbation (MC/FEP) simulations were performed on a series of nonpeptide ligands of the human pp60c-src SH2 domain in order to calculate relative free energies of binding for each compound and to understand the structural requirements for high affinity binding. The amido compound, exhibiting the highest experimental affinity, takes advantage of an interaction with a previously unobserved structural water.
