ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAb initio study of structures and binding energies for anion-water complexesJiali. Gao, Debra S. Garner, and William L. JorgensenCite this: J. Am. Chem. Soc. 1986, 108, 16, 4784–4790Publication Date (Print):August 1, 1986Publication History Published online1 May 2002Published inissue 1 August 1986https://pubs.acs.org/doi/10.1021/ja00276a016https://doi.org/10.1021/ja00276a016research-articleACS PublicationsRequest reuse permissionsArticle Views385Altmetric-Citations121LEARN 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
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, and χ2 potential energy surfaces for blocked dipeptides. New Fourier coefficients for the dihedral angle terms of the OPLS-AA force field were fit to these surfaces, utilizing a Boltzmann-weighted error function and systematically examining the effects of weighting temperature. To prevent overfitting to the available data, a minimal number of new residue-specific and peptide-specific torsion terms were developed. Extensive experimental solution-phase and quantum chemical gas-phase benchmarks were used to assess the quality of the new parameters, named OPLS-AA/M, demonstrating significant improvement over previous OPLS-AA force fields. A Boltzmann weighting temperature of 2000 K was determined to be optimal for fitting the new Fourier coefficients for dihedral angle parameters. Conclusions are drawn from the results for best practices for developing new torsion parameters for protein force fields.
ADVERTISEMENT RETURN TO ISSUEPREVarticleNEXTThe OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambinWilliam L. Jorgensen and 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 March 1988https://pubs.acs.org/doi/10.1021/ja00214a001https://doi.org/10.1021/ja00214a001research-articleACS PublicationsCopyright © 1988 American Chemical SocietyRequest reuse permissionsArticle Views15043Altmetric-Citations4056LEARN 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
Testing of the commonly used hybrid density functional B3LYP with the 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 the elements C, H, N, and O. The focus is comparison of computed and experimental heats of formation and isomerization energies. In addition, the effect of an empirical dispersion correction term has been evaluated and found to improve agreement with the experimental data. For the 622 compounds, the mean absolute errors (MAE) in the heats of formation are 3.1, 2.6, 2.7, and 2.4 kcal/mol for B3LYP/6-31G(d), B3LYP/6-31G(d,p), B3LYP/6-31+G(d,p), and B3LYP/6-31+G(d,p) with the dispersion correction. A diverse set of 34 isomerizations highlights specific issues of general interest, such as performance on differences in steric effects, conjugation, and bonding. The corresponding MAEs for the isomerizations are 2.7, 2.4, 2.2, and 1.9 kcal/mol. Improvement is obtained for isomerizations of amines and alcohols when both polarization and diffuse functions are used, but the overstabilization of linear alkanes compared to branched isomers can be relieved only with the dispersion correction. Besides the insights on DFT methods, the study also aimed to quantify the gains in accuracy that can be achieved by replacing energetics from NDO-based semiempirical methods with DFT results. Since the MAEs obtained with the PDDG/PM3 method for the 622 heats of formation and 34 isomerizations are 2.8 and 2.3 kcal/mol, negligible advantage in accuracy for the B3LYP-based methods emerged in the absence of the dispersion corrections.
No abstract is provided for this article.
The representation of chlorine, bromine, and iodine in aryl halides has been modified in the OPLS-AA and OPLS/CM1A force fields in order to incorporate halogen bonding. The enhanced force fields, OPLS-AAx and OPLS/CM1Ax, have been tested in calculations on gas-phase complexes of halobenzenes with Lewis bases, and for free energies of hydration, densities, and heats of vaporization of halobenzenes. Comparisons with results of MP2/aug-cc-pVDZ(-PP) calculations for the complexes are included. Implementation in the MCPRO software also allowed computation of relative free energies of binding for a series of HIV reverse transcriptase inhibitors via Monte Carlo/free-energy perturbation calculations. The results support the notion that the activity of an unusually potent chloro analog likely benefits from halogen bonding with the carbonyl group of a proline residue.
Presented on April 30, 2013 from 11:00 am to 12:00 pm in the Klaus Advanced Computing Building, Room 1116E.
ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNetwork topology in simulated waterRobin J. Speedy, Jeffry D. Madura, and William L. JorgensenCite this: J. Phys. Chem. 1987, 91, 4, 909–913Publication Date (Print):February 1, 1987Publication History Published online1 May 2002Published inissue 1 February 1987https://pubs.acs.org/doi/10.1021/j100288a029https://doi.org/10.1021/j100288a029research-articleACS PublicationsRequest reuse permissionsArticle Views361Altmetric-Citations115LEARN 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 options Get e-Alerts
No abstract is provided for this article.
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