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Accurately predicting HFE is also recognized as one fundamental capability of molecular mechanics force field. Here, we present a systematic investigation on HFE calculations with AMOEBA polarizable force field at various parameterization and simulation conditions. The HFEs of seven small organic molecules have been obtained alchemically using the Bennett Acceptance Ratio method. We have compared two approaches to derive the atomic multipoles from quantum mechanical calculations: one directly from the new distributed multipole analysis and the other involving fitting to the electrostatic potential around the molecules. Wave functions solved at the MP2 level with four basis sets (6-311G*, 6-311++G(2d,2p), cc-pVTZ, and aug-cc-pVTZ) are used to derive the atomic multipoles. HFEs from all four basis sets show a reasonable agreement with experimental data (root mean square error 0.63 kcal/mol for aug-cc-pVTZ). We conclude that aug-cc-pVTZ gives the best performance when used with AMOEBA, and 6-311++G(2d,2p) is comparable but more efficient for larger systems. The results suggest that the inclusion of diffuse basis functions is important for capturing intermolecular interactions. The effect of long-range correction to van der Waals interaction on the hydration free energies is about 0.1 kcal/mol when the cutoff is 12Å, and increases linearly with the number of atoms in the solute/ligand. In addition, we also discussed the results from a hybrid approach that combines polarizable solute with fixed-charge water in the HFE calculation. © 2010 Wiley Periodicals, Inc. 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P.", "lastName": "Straatsma" }, { "creatorType": "author", "firstName": "H. J. C.", "lastName": "Berendsen" }, { "creatorType": "author", "firstName": "A. J.", "lastName": "Stam" } ], "abstractNote": "", "publicationTitle": "Molecular Physics: An International Journal at the Interface Between Chemistry and Physics", "publisher": "", "place": "", "date": "1986", "volume": "57", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "89", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1080/00268978600100071", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "0026-8976", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "Informaworld", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "7XTS32AG" ], "relations": {}, "dateAdded": "2011-07-22T09:02:30Z", "dateModified": "2011-07-22T09:02:30Z" } }, { "key": "DKKMXIQ2", "version": 1, "library": { "type": "group", "id": 50154, "name": "Wiesner Jiri", "links": { "alternate": { "href": "https://www.zotero.org/groups/wiesner_jiri", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/50154/items/DKKMXIQ2", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/wiesner_jiri/items/DKKMXIQ2", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/50154/items/TJBCTQ4G", "type": "application/json" } }, "meta": { "createdByUser": { "id": 457466, "username": "jiriwiesner", "name": "Jiri Wiesner", "links": { "alternate": { "href": "https://www.zotero.org/jiriwiesner", "type": "text/html" } } } }, "data": { "key": "DKKMXIQ2", "version": 1, "parentItem": "TJBCTQ4G", "itemType": "attachment", "linkMode": "imported_url", "title": "ACS Full Text Snapshot", "accessDate": "2011-07-21T21:47:43Z", "url": "http://pubs.acs.org/doi/full/10.1021/jp067741s", "note": "", "contentType": "text/html", "charset": "utf-8", "filename": "jp067741s.html", "md5": null, "mtime": 1311284894000, "tags": [], "relations": {}, "dateAdded": "2011-07-21T21:48:14Z", "dateModified": "2011-07-21T21:48:43Z" } }, { "key": "VTPRW69D", "version": 1, "library": { "type": "group", "id": 50154, "name": "Wiesner Jiri", "links": { "alternate": { "href": "https://www.zotero.org/groups/wiesner_jiri", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/50154/items/VTPRW69D", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/wiesner_jiri/items/VTPRW69D", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/50154/items/TJBCTQ4G", "type": "application/json" } }, "meta": { "createdByUser": { "id": 457466, "username": "jiriwiesner", "name": "Jiri Wiesner", "links": { "alternate": { "href": "https://www.zotero.org/jiriwiesner", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "VTPRW69D", "version": 1, "parentItem": "TJBCTQ4G", "itemType": "attachment", "linkMode": "imported_url", "title": "ACS Full Text PDF", "accessDate": "2011-07-21T21:47:42Z", "url": "http://pubs.acs.org/doi/pdf/10.1021/jp067741s", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Wang et al. - 2007 - Oxime-Induced Reactivation of Sarin-Inhibited AChE.pdf", "md5": "95f8cd0656612539d2a8208a0e917089", "mtime": 1311284894000, "tags": [], "relations": {}, "dateAdded": "2011-07-21T21:48:14Z", "dateModified": "2011-07-21T21:48:43Z" } }, { "key": "J3UHDTNR", "version": 1, "library": { "type": "group", "id": 50154, "name": "Wiesner Jiri", "links": { "alternate": { "href": "https://www.zotero.org/groups/wiesner_jiri", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/50154/items/J3UHDTNR", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/wiesner_jiri/items/J3UHDTNR", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/50154/items/TJBCTQ4G", "type": "application/json" } }, "meta": { "createdByUser": { "id": 457466, "username": "jiriwiesner", "name": "Jiri Wiesner", "links": { "alternate": { "href": "https://www.zotero.org/jiriwiesner", "type": "text/html" } } } }, "data": { "key": "J3UHDTNR", "version": 1, "parentItem": "TJBCTQ4G", "itemType": "attachment", "linkMode": "imported_url", "title": "Oxime-Induced Reactivation of Sarin-Inhibited AChE:  A Theoretical Mechanisms Study - The Journal of Physical Chemistry B (ACS Publications)", "accessDate": "2011-07-21T21:47:46Z", "url": "http://pubs.acs.org/doi/abs/10.1021/jp067741s", "note": "", "contentType": "text/html", "charset": "utf-8", "filename": "jp067741s.html", "md5": null, "mtime": 1311284894000, "tags": [], "relations": {}, "dateAdded": "2011-07-21T21:48:14Z", "dateModified": "2011-07-21T21:48:43Z" } }, { "key": "TJBCTQ4G", "version": 1, "library": { "type": "group", "id": 50154, "name": "Wiesner Jiri", "links": { "alternate": { "href": "https://www.zotero.org/groups/wiesner_jiri", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/50154/items/TJBCTQ4G", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/wiesner_jiri/items/TJBCTQ4G", "type": "text/html" } }, "meta": { "createdByUser": { "id": 457466, "username": "jiriwiesner", "name": "Jiri Wiesner", "links": { "alternate": { "href": "https://www.zotero.org/jiriwiesner", "type": "text/html" } } }, "creatorSummary": "Wang et al.", "parsedDate": "2007-03-01", "numChildren": 4 }, "data": { "key": "TJBCTQ4G", "version": 1, "itemType": "journalArticle", "title": "Oxime-Induced Reactivation of Sarin-Inhibited AChE:  A Theoretical Mechanisms Study", "creators": [ { "creatorType": "author", "firstName": "Jing", "lastName": "Wang" }, { "creatorType": "author", "firstName": "Jiande", "lastName": "Gu" }, { "creatorType": "author", "firstName": "Jerzy", "lastName": "Leszczynski" }, { "creatorType": "author", "firstName": "Mikolaj", "lastName": "Feliks" }, { "creatorType": "author", "firstName": "W. Andrzej", "lastName": "Sokalski" } ], "abstractNote": "Oximes (especially oximate anions) are used as potential reactivators of OP-inhibited AChE due to their unique α-effect nucleophilic reactivity. In the present study, by applying the DFT approach at the B3LYP/6-311G(d,p) level and the Møller−Plesset perturbation theory at the MP2/6-311G(d,p) level, the formoximate-induced reactivation patterns of the sarin-AChE adduct and the corresponding reaction mechanism have been investigated. The potential energy surface along the pathway of the reactivation reaction of sarin-inhibited AChE by oxime reveals that the reaction can occur quickly due to the relatively low energy barriers. A two-step process is a major pathway proposed for the studied reactivation reaction. Through the nucleophilic attack, the oximate first binds to the sarin-AChE adduct to form a relatively stable phosphorus complex. The regeneration of the serine takes place subsequently through an elimination step, which is expected to be competitive with the nucleophilic attacking process. The polarizable continuum model (PCM) has been applied to evaluate the solvate effects on the pathway. It is concluded that the reaction energy barriers are also low enough for the reaction to easily occur in solvent. The results derived from both the gas-phase model and the aqueous solvation model suggest that the studied oximate anion is an efficient antidote reagent for sarin-inhibited AChE.", "publicationTitle": "The Journal of Physical Chemistry B", "publisher": "", "place": "", "date": "March 01, 2007", "volume": "111", "issue": "9", "section": "", "partNumber": "", "partTitle": "", "pages": "2404-2408", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1021/jp067741s", "citationKey": "", "url": "http://dx.doi.org/10.1021/jp067741s", "accessDate": "2011-07-21T21:47:41Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "Oxime-Induced Reactivation of Sarin-Inhibited AChE", "language": "", "libraryCatalog": "ACS Publications", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "45B3GSAF" ], "relations": {}, "dateAdded": "2011-07-21T21:48:14Z", "dateModified": "2011-07-21T21:48:14Z" } }, { "key": "633WNNT7", "version": 1, "library": { "type": "group", "id": 50154, "name": "Wiesner Jiri", "links": { "alternate": { "href": "https://www.zotero.org/groups/wiesner_jiri", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/50154/items/633WNNT7", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/wiesner_jiri/items/633WNNT7", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/50154/items/TJBCTQ4G", "type": "application/json" } }, "meta": { "createdByUser": { "id": 457466, "username": "jiriwiesner", "name": "Jiri Wiesner", "links": { "alternate": { "href": "https://www.zotero.org/jiriwiesner", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "633WNNT7", "version": 1, "parentItem": "TJBCTQ4G", "itemType": "note", "note": "

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