Ab initio SCF calculations with minimal STO-3G and extended 44-31G basis sets have been performed on the simple alkyl chlorides, HCl to t-BuCl, and their protonated analogs. MINDO/3 calculations are also reported for these species and a variety of cyclic and bicyclic chlorides. The much closer agreement with experiment for STO-3G proton affinities than for 44-31G values is in sharp contrast to the results for first-row bases. An excellent correlation is found between both the STO-3G and MINDO/3 proton affinities and the charge on the CIH fragment in RCIH+. For the acyclic chlorides, correlations of PA's with the polar substituent constant, σ*, and IP's are also reasonable. In addition, the calculated carbonium ion-HCl interaction energy for t-BuClH+ indicates that protonated tertiary chlorides are no more than marginally stable in the gas phase.
ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTQuantum and statistical mechanical studies of liquids. 2. Monte-Carlo simulations of liquid hydrogen fluorideWilliam L. JorgensenCite this: J. Am. Chem. Soc. 1978, 100, 25, 7824–7831Publication Date (Print):December 1, 1978Publication History Published online1 May 2002Published inissue 1 December 1978https://pubs.acs.org/doi/10.1021/ja00493a007https://doi.org/10.1021/ja00493a007research-articleACS PublicationsRequest reuse permissionsArticle Views232Altmetric-Citations62LEARN 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
The change in the relative acidities of the haloacetic acids on going from the gas phase to aqueous solution has been studied via ab initio calculations for the gas phase, the SCIPCM reaction field model for an aprotic polar solvent, and Monte Carlo statistical mechanics for aqueous solution. The relative gas phase acidities of acetic acid, the haloacetic acids and trifluoroacetic acid are well reproduced at the B3P86/6-311+G** and G2 levels of theory. The reaction field model reduced the relative acidities of fluoro- and bromoacetic acids to a value close to that found in aqueous solution, but it only reproduced half of the observed net effect of going from the gas phase to aqueous solution. Since the remainder of the solvent effect was probably due to hydrogen bonding, Monte Carlo calculations were carried out and they were in satisfactory accord with the aqueous solution pKa's.
ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMolecular dynamics simulations of the unfolding of an .alpha.-helical analog of ribonuclease A S-peptide in waterJulian Tirado-Rives and William L. JorgensenCite this: Biochemistry 1991, 30, 16, 3864–3871Publication Date (Print):April 23, 1991Publication History Published online1 May 2002Published inissue 23 April 1991https://doi.org/10.1021/bi00230a009RIGHTS & PERMISSIONSArticle Views497Altmetric-Citations191LEARN 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 (3 MB) Get e-Alerts Get e-Alerts
Monte Carlo simulation of liquid ammonia is reported. An initial potential function of the dimer was generated from minimal basis set calculations. The potential was uniformly scaled by a factor of 1.3 and the energy of the liquid was computed.(AIP)
Quantum and statistical mechanics have been used to determine energy profiles for the SN2 reaction of Cl- + CH3Cl in the gas phase, in aqueous solution, and in liquid DMF. The energy profile in the gas phase has the characteristic double-well form featuring unsymmetrical ion-dipole complexes as minima and a symmetrical transition state. Hydration causes the reaction surface to become almost unimodal and increases the barrier significantly. The reaction profile in DMF is intermediate between those for the gas phase and aqueous solution. The ion-dipole complexes are still free energy minima in DMF. Thus, the reaction in DMF involves initial formation of the complex before the rate-determining step. The computed results are shown to be in good accord with experimental free energies of activation. The same technique has been applied to the addition reaction of OH- + H2C = O in the gas phase and aqueous solution. Ab initio 6-31 + G* calculations indicate that the reaction proceeds essentially without activation in the gas phase. Hydration introduces a substantial energy barrier. The transition state in water has been located at a C-O separation of roughly 2 A. A key finding for both reactions is that the activation barriers induced by hydration result primarily from change in strengths rather than in numbers of solute-water hydrogen bonds along the reaction paths.
Plasma protein binding has a profound impact on the pharmacokinetic and pharmacodynamic properties of many drug candidates and is thus an integral component of drug discovery. Nevertheless, extant methods to examine small-molecule interactions with plasma protein have various limitations, thus creating a need for alternative methods. Herein we present a comprehensive and cross-validated in silico workflow for the prediction of small-molecule binding to Human Serum Albumin (HSA), the most ubiquitous plasma protein. This protocol reliably predicts small-molecule interactions with HSA, including a binding affinity calculation using multiple linear regression methods, binding site prediction using a naive-Bayes classifier, and a three-dimensional binding pose using induced fit docking. Furthermore, this workflow is implemented in a portable and automated format that can be downloaded and used by other end users, either as is or with customization.
Ab initio molecular orbital calculations have been carried out on over 50 model organic molecules and ions to provide the data necessary in the determination of torsional parameters for a force field involving polypeptides. The rotational energy profiles were obtained at the HF/6‐31G*//HF/6‐31G* level. The results were supported, in many cases, by full geometry optimizations and with consideration of correlation corrections at the MP2 level. With the exception of the dihedral angle being studied, all of the molecules were fully optimized with C 1 symmetry. © 1995 by John Wiley & Sons, Inc.
