No abstract is provided for this article.
Current "second-generation" force fields have been developed for use in Monte Carlo and molecular dynamics simulations for organic and biomolecular systems in solution. The performance of three such force fields, AMBER94, MMFF94, and OPLS-AA, is tested here through Monte Carlo (MC) statistical mechanics simulations for liquid butane, methanol, and N-methylacetamide (NMA). These liquids were chosen for their range of polarity and their representation of typical interactions found in proteins. From simulations at constant temperature and 1 atm pressure, the average errors in the computed densities and heats of vaporization are 3.8% and 5.1% with AMBER94 and 1.5% and 1.3% with OPLS-AA. With MMFF94, the computed densities and heats of vaporization for methanol and NMA are too low by 21−27%, while butane at −0.5 °C does not stop expanding during the simulation. A MC simulation using MMFF94 for butane with the density fixed at the experimental value yields a 32% error in the energy of vaporization. Analyses show that the optimal C−H and H−H nonbonded interactions with MMFF94 are too weak and occur at too large separations. Scaling of the MMFF94 parameter Ai, which is linearly related to the atomic radii, by 0.92 yields improved results for liquid butane.
ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTComputer-assisted mechanistic evaluation of organic reactions. 2. Perception of rings, aromaticity, and tautomersBarbara L. Roos-Kozel and William L. JorgensenCite this: J. Chem. Inf. Comput. Sci. 1981, 21, 2, 101–111Publication Date (Print):May 1, 1981Publication History Published online1 May 2002Published inissue 1 May 1981https://pubs.acs.org/doi/10.1021/ci00030a010https://doi.org/10.1021/ci00030a010research-articleACS PublicationsRequest reuse permissionsArticle Views179Altmetric-Citations20LEARN 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
ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTComputer-assisted mechanistic evaluation of organic reactions. 12. pKa predictions for organic compounds in Me2SOAlan J. Gushurst and William L. JorgensenCite this: J. Org. Chem. 1986, 51, 18, 3513–3522Publication Date (Print):September 1, 1986Publication History Published online1 May 2002Published inissue 1 September 1986https://doi.org/10.1021/jo00368a023RIGHTS & PERMISSIONSArticle Views268Altmetric-Citations22LEARN 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 InReddit PDF (1 MB) Get e-Alerts Get e-Alerts
No abstract is provided for this article.
Monte Carlo simulations have been used to determine changes in free energies of solvation for the rearrangement of chorismate to prephenate in water and methanol. Structures and partial charges from the ab initio RHF/6-31G* calculations of Wiest and Houk were used for the pseudodiequatorial and pseudodiaxial conformers of chorismate and for the transition structure. Free energy perturbation calculations yielded the differences in free energies of solvation for the three structures. The calculations reproduce the observed 100-fold rate increase in water over methanol. The origin of the rate difference is traced solely to an enhanced population of the pseudodiaxial conformer in water, which arises largely from a unique water molecule acting as a double hydrogen bond donor to the C4 hydroxyl group and the side-chain carboxylate. A Monte Carlo simulation was also carried out for the transition structure bound to E. coli chorismate mutase in order to characterize the key interactions in the active site. Consistent with earlier computational results for the Claisen rearrangement of allyl vinyl ether and inferences from crystal structures, the Monte Carlo simulations reveal two hydrogen bonds to the enolic oxygen in the transition structure for both the uncatalyzed reaction in water and the enzyme-catalyzed rearrangement.
Monte Carlo statistical mechanics simulations have been carried out for liquid tetrahydrofuran (THF) with and without pseudorotation at 1 atm and 25 °C. The intermolecular potential functions consisted of Lennard-Jones and Coulomb terms in the TIPS format reported previously for ethers. Pseudorotation of the ring was described using the generalized coordinates defined by Cremer and Pople, viz., the puckering amplitude and the phase angle of the ring. The corresponding intramolecular potential function was derived from molecular mechanics (MM2) calculations. Compared to the gas phase, the rings tend to be more flat and the population of the C2 twist geometry is slightly higher in liquid THF. However, pseudorotation has negligible effect on the calculated intermolecular structure and thermodynamic properties. The computed density, heat of vaporization, and heat capacity are in good agreement with experiment. The results are also compared with those from previous simulations of acyclic ethers. The present study provides the foundation for investigations of the solvating ability of THF.
Orbital theory provides a powerful tool for rationalizing and understanding many phenomena in chemistry. In most introductory chemistry courses, students are introduced to atomic and molecular orbitals in the form of two-dimensional drawings. In this work, we describe a general method for producing 3D printing files of orbital models that can be employed with most popular software packages for performing electronic structure calculations and molecular visualization. Methods for producing both solid and mesh orbitals are provided, including pointers for producing a model that is both informative and structurally sound. Finally, numerous examples of various systems of interest in physical organic chemistry are provided in the .stl format for 3D printing, as well as a fully illustrated tutorial for the process.
ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMonte Carlo Results for the Effect of Solvation on the Anomeric Equilibrium for 2-MethoxytetrahydropyranWilliam L. Jorgensen, Patricia I. Morales de Tirado, and Daniel L. SeveranceCite this: J. Am. Chem. Soc. 1994, 116, 5, 2199–2200Publication Date (Print):March 1, 1994Publication History Published online1 May 2002Published inissue 1 March 1994https://pubs.acs.org/doi/10.1021/ja00084a092https://doi.org/10.1021/ja00084a092research-articleACS PublicationsRequest reuse permissionsArticle Views120Altmetric-Citations47LEARN 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 (2)»Supporting Information Supporting Information Get e-Alerts
