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An approach to the general extension of the OPLS all-atom (OPLS-AA) force field to heterocycles has been explored with testing for pyridine and the diazenes, pyridazine, pyrimidine, and pyrazine. For the non-bonded interactions, the partial atomic charges are obtained from fitting to the electrostatic potential surfaces from ab initio RHF/6–31G∗ calculations and standard OPLS values are used for the Lennard-Jones parameters. The harmonic bond-stretching and angle-bending parameters are largely adopted from the AMBER force field. The resultant OPLS-AA force field is shown to perform well for computing the structures of the heterocycles, heterocycle-water interaction energies, and thermodynamic properties of the four pure liquids. The latter quantities were computed from Monte Carlo statistical mechanics simulations; the average errors in computed densities and heats of vaporization are 0.8% and 2.7%. Free energies of hydration were also calculated for pyridine and pyrazine, and provided errors of under 1 kcal mol−1 in comparison to experimental data.
ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTInternal rotation in liquid 1,2-dichloroethane and n-butaneWilliam L. JorgensenCite this: J. Am. Chem. Soc. 1981, 103, 3, 677–679Publication Date (Print):February 1, 1981Publication History Published online1 May 2002Published inissue 1 February 1981https://pubs.acs.org/doi/10.1021/ja00393a034https://doi.org/10.1021/ja00393a034research-articleACS PublicationsRequest reuse permissionsArticle Views286Altmetric-Citations30LEARN 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
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ADVERTISEMENT RETURN TO ISSUEEditorialNEXTQSAR/QSPR and Proprietary DataWilliam L. JorgensenView Author Information Editor-in-ChiefCite this: J. Chem. Inf. Model. 2006, 46, 3, 937Publication Date (Web):May 22, 2006Publication History Published online22 May 2006Published inissue 1 May 2006https://pubs.acs.org/doi/10.1021/ci0680079https://doi.org/10.1021/ci0680079editorialACS PublicationsCopyright © 2006 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views3678Altmetric-Citations27LEARN 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 PDF (8 KB) Get e-AlertscloseSUBJECTS:Bioinformatics and computational biology,Drug discovery,Metabolism,Screening assays,Structure activity relationship Get e-Alerts
ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIntermolecular potential functions and Monte Carlo simulations for liquid sulfur compoundsWilliam L. JorgensenCite this: J. Phys. Chem. 1986, 90, 23, 6379–6388Publication Date (Print):November 1, 1986Publication History Published online1 May 2002Published inissue 1 November 1986https://pubs.acs.org/doi/10.1021/j100281a063https://doi.org/10.1021/j100281a063research-articleACS PublicationsRequest reuse permissionsArticle Views1103Altmetric-Citations129LEARN 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
Variations in hydrogen-bond strengths are investigated for complexes of nine para-substituted phenols (XPhOH) with a water molecule and chloride ion. Results from ab initio HF/6-311+G(d, p) and MP2/6-311+G(d, p)//HF/6-311+G(d, p) calculations are compared with those from the OPLS-AA and OPLS/CM1A force fields. In the OPLS-AA model, the partial charges on the hydroxyl group of phenol are not affected by the choice of para substituent, while the use of CM1A charges in the OPLS/CM1A approach does provide charge redistribution. The ab initio calculations reveal a 2.0-kcal/mol range in hydrogen-bond strengths for the XPhOH⋯OH(2) complexes in the order X = NO(2) > CN > CF(3) > Cl > F > H >OH >CH(3) > NH(2). The pattern is not well-reproduced with OPLS-AA, which also compresses the variation to 0.7 kcal/mol. However, the OPLS/CM1A results are in good accord with the ab initio findings for both the ordering and range, 2.3 kcal/mol. The hydrogen bonding is, of course, weaker with XPhOH as acceptor, the order for X is largely inverted, and the range is reduced to ca. 1.0 kcal/mol. The substituent effects are found to be much greater for the chloride ion complexes with a range of 11 kcal/mol. For quantitative treatment of such strong ion-molecule interactions the need for fully polarizable force fields is demonstrated.
Monte Carlo statistical mechanics simulations have been used to study the complexation of disubstituted benzenes by Diederich's octamethoxy tetraoxaparacyclophane host, 1. The calculations were carried out in the NPT ensemble at 25 °C and 1 atm in the presence of 768 water molecules. Relative free energies of binding were obtained for p-xylene, benzene, p-cresol, and hydroquinone from statistical perturbation theory. The computed preference of 2.8 ± 0.3 kcal/mol in DGb for binding p-xylene over hydroqinone compares well with the experimental result of 2.5 ± 0.3 kcal/mol. The computed results for benzene (2.0 ± 0.2 kcal/mol) and p-cresol (2.4 ± 0.2 kcal/mol) relative to p-xylene were predictions; however, the experimental data are now available and are lower by 1–2 kcal/mol. The computed structures for the complexes reveal interesting details. For example, hydroquinone protrudes somewhat from one side of the complex and participates in hydrogen bonds between one hydroxyl group and 1–2 water molecules and in an intracomplex hydrogen bond between the other hydroxyl group and ether oxygens. Benzene is predicted to be bound even more off-center, while p-cresol is centered and has an intracomplex hydrogen bond as in the case of hydroquinone.
Monte Carlo statistical mechanics simulations have been used to study the complexation of disubstituted benzenes by Diederich's octamethoxy tetraoxaparacyclophane host. Relative free energies of binding were obtained in water at 25 degrees C for benzene, p-xylene, p-cresol, p-dicyanobenzene, and hydroquinone from statistical perturbation theory. The computed results agree well with experimental data, including the binding affinity of benzene, which was determined after the calculations were completed. The computed structures for the complexes reveal details that are important for understanding the order of binding affinities. It is found that hydroquinone protrudes from one side of the complex and participates in hydrogen bonds between one hydroxyl group and two water molecules and in an intracomplex hydrogen bond between the other hydroxyl group and ether oxygens. The calculations also show a clear preference for binding p-cresol with the hydroxyl group hydrated rather than inside the host's cavity.
Optimized structures and relative energies for conformers of succinic acid and its monoanion in the gas phase were obtained using ab initio molecular orbital calculations at the MP2/6-311+G**//HF/6-31G* and MP2/6-311+G**//HF/6-31+G* levels, respectively. The lowest energy conformer for succinic acid, designated ZsgsZ, has a gauche conformation about the central C2−C3 bond; the lowest energy conformer with an E-acid group and an internal hydrogen bond is ca. 3 kcal/mol higher in energy. The lowest energy structure for the monoanion, Ecgs, does have the expected internal hydrogen bond and is 15 kcal/mol more stable than any alternative. The ab initio results were used to determine corresponding torsional-energy parameters in the OPLS all-atom force field. This allowed application of statistical perturbation theory in Monte Carlo simulations to explore the effect of hydration on the conformational equilibria. The diacid and monoanion were both computed to be ca. 80% gauche in water at 25 °C. These results are in excellent agreement with NMR data. Though the conformational results are consistent with the gauche effect, their true origin requires a detailed understanding of the potential internal hydrogen bonding and solvation. Thus, in contrast to the monoanion's striking gas-phase preference, neither the diacid nor monoanion are computed to populate E conformers in aqueous solution.
