{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,17]],"date-time":"2025-10-17T13:24:08Z","timestamp":1760707448461},"reference-count":51,"publisher":"Wiley","issue":"11","license":[{"start":{"date-parts":[[2004,9,7]],"date-time":"2004-09-07T00:00:00Z","timestamp":1094515200000},"content-version":"vor","delay-in-days":3598,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J Comput Chem"],"published-print":{"date-parts":[[1994,11]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>A method using molecular mechanics to calculate internal energies and the generalized Born\/surface area (GB\/SA) method for calculating solvation free energy has been compared with the corresponding terms obtained from <jats:italic>ab initio<\/jats:italic> quantum chemical calculations in the gas phase and the free energy perturbation method implemented in Monte Carlo (MC) simulations to study conformational equilibria in solution. 1,2\u2010Ethanediol, 2\u2010hydroxybenzoic acid, the neutral and protonated histamine, were considered in aqueous solution as systems capable of intramolecular hydrogen bonding. The molecular mechanics method with all atom and united atom models, using the AMBER* force field and the parameterization as implemented in the MacroModel modeling package and the GB\/SA continuum solvation model, produces smaller separation in relative conformer free energies than does the <jats:italic>ab initio<\/jats:italic> + MC method in aqueous solution. The GB\/SA relative solvation free energies using the charges from the AMBER* force fields were consistently smaller than the values obtained in Monte Carlo simulations. Using the charge sets from the Monte Carlo simulations and considering solute geometries with torsional angles fixed at the optimized <jats:italic>ab initio<\/jats:italic> values, the relative solvation free energies remained underestimated by up to 30% as compared to the Monte Carlo values. The AMBER*\/\/GB\/SA predicted most stable conformer for the 1,2\u2010ethandiol system in aqueous solution is in contrast with the <jats:italic>ab initio<\/jats:italic> + MC finding and the available experimental results. For the histamine system predictions by only the united atom AMBER*\/\/GB\/SA model agree with those by ab initio + MC and with data derived from nuclear magnetic resonance (NMR) experiments. Differences in the two methods are considered mainly due to the application of torsional parameters and atomic charges developed in the AMBER* parameter set for monofunctional polar systems. New parameters seem to be needed for quantitative description of the in\u2010solution conformational equilibria for organic compounds with a possible intramolecular hydrogen bond. \u00a9 1994 by John Wiley &amp; Sons, Inc.<\/jats:p>","DOI":"10.1002\/jcc.540151105","type":"journal-article","created":{"date-parts":[[2005,1,2]],"date-time":"2005-01-02T00:57:39Z","timestamp":1104627459000},"page":"1228-1240","source":"Crossref","is-referenced-by-count":10,"title":["Comparison of the molecular mechanics + generalized Born\/surface area and the <i>ab initio<\/i> + Monte Carlo simulation methods in estimating conformational equilibria in aqueous solution"],"prefix":"10.1002","volume":"15","author":[{"given":"Peter I.","family":"Nagy","sequence":"first","affiliation":[]},{"given":"Joseph E.","family":"Bitar","sequence":"additional","affiliation":[]},{"given":"Douglas A.","family":"Smith","sequence":"additional","affiliation":[]}],"member":"311","published-online":{"date-parts":[[2004,9,7]]},"reference":[{"key":"e_1_2_1_2_2","doi-asserted-by":"crossref","unstructured":"(a) D. 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