Comparison of different computational methods for water structure optimisation
We have compared several computational techniques with the aim to compute the radial distribution function (RDF) as a good characterization of water structure. In particular, we have used molecular mechanic (AMBER99), semi-empirical (AM1, PM3, PM6) and ab initio (DFT) technique. It has been shown th...
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| Veröffentlicht in: | Acta Facultatis Pharmaceuticae Universitatis Comenianae 2012-01, Vol.59 (1), p.55-66 |
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| container_title | Acta Facultatis Pharmaceuticae Universitatis Comenianae |
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| creator | Staník, R. Ballo, P. Benkovský, I. |
| description | We have compared several computational techniques with the aim to compute the radial distribution function (RDF) as a good characterization of water structure. In particular, we have used molecular mechanic (AMBER99), semi-empirical (AM1, PM3, PM6) and ab initio (DFT) technique. It has been shown that molecular mechanic gives very poor results in the case of water RDF. Ab initio techniques which are in general accepted as very exact methods, in the case of water underestimate intermolecular interaction. Unexpectedly, the semi-empirical method with PM6 parameterisation gives the best results in comparison with RDF measured by X-ray scattering experiment.
Porovnali sme niekoľko výpočtových techník s cieľom získať radiálnu distribučnú funkciu (RDF), ktorá je vhodná na charakteristiku štruktúry vody. Menovite sme použili molekulovú mechaniku (AMBER99), semi-empirické (AM1, PM3, PM6) a ab initio (DFT) techniky. Ukázalo sa, že molekulová mechanika poskytuje veľmi slabé výsledky vzhľadom na RDF vody. Ab initio techniky, ktoré sú všeobecne akceptované ako veľmi presné metódy, v prípade vody podceňujú medzimolekulové interakcie. Prekvapujíco, semi-empirickám metóda s PM6 parametrizáciou poskytuje najlepšie výsledky v porovnaní s meraním RDF pomocou X-ray rozptylu. |
| doi_str_mv | 10.2478/v10219-012-0019-3 |
| format | Article |
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Porovnali sme niekoľko výpočtových techník s cieľom získať radiálnu distribučnú funkciu (RDF), ktorá je vhodná na charakteristiku štruktúry vody. Menovite sme použili molekulovú mechaniku (AMBER99), semi-empirické (AM1, PM3, PM6) a ab initio (DFT) techniky. Ukázalo sa, že molekulová mechanika poskytuje veľmi slabé výsledky vzhľadom na RDF vody. Ab initio techniky, ktoré sú všeobecne akceptované ako veľmi presné metódy, v prípade vody podceňujú medzimolekulové interakcie. Prekvapujíco, semi-empirickám metóda s PM6 parametrizáciou poskytuje najlepšie výsledky v porovnaní s meraním RDF pomocou X-ray rozptylu.</description><identifier>ISSN: 0301-2298</identifier><identifier>EISSN: 1338-6786</identifier><identifier>EISSN: 2453-6725</identifier><identifier>DOI: 10.2478/v10219-012-0019-3</identifier><language>eng</language><publisher>Bratislava: Versita</publisher><subject>Computational mathematics ; DFT ; Molecular structure ; Pharmaceutical sciences ; PM6 ; RDF ; Water ; water simulation</subject><ispartof>Acta Facultatis Pharmaceuticae Universitatis Comenianae, 2012-01, Vol.59 (1), p.55-66</ispartof><rights>Copyright Versita Jan 2012</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c2075-1a4cb5c8e6f57e440427fb29676bf5ebbe2699ba4de961731ee63738a46fe8403</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://www.proquest.com/docview/1321065893?pq-origsite=primo$$EHTML$$P50$$Gproquest$$Hfree_for_read</linktohtml><link.rule.ids>314,780,784,864,21388,21389,27924,27925,33530,33744,43659,43805,64385,64389,72469</link.rule.ids></links><search><creatorcontrib>Staník, R.</creatorcontrib><creatorcontrib>Ballo, P.</creatorcontrib><creatorcontrib>Benkovský, I.</creatorcontrib><title>Comparison of different computational methods for water structure optimisation</title><title>Acta Facultatis Pharmaceuticae Universitatis Comenianae</title><description>We have compared several computational techniques with the aim to compute the radial distribution function (RDF) as a good characterization of water structure. In particular, we have used molecular mechanic (AMBER99), semi-empirical (AM1, PM3, PM6) and ab initio (DFT) technique. It has been shown that molecular mechanic gives very poor results in the case of water RDF. Ab initio techniques which are in general accepted as very exact methods, in the case of water underestimate intermolecular interaction. Unexpectedly, the semi-empirical method with PM6 parameterisation gives the best results in comparison with RDF measured by X-ray scattering experiment.
Porovnali sme niekoľko výpočtových techník s cieľom získať radiálnu distribučnú funkciu (RDF), ktorá je vhodná na charakteristiku štruktúry vody. Menovite sme použili molekulovú mechaniku (AMBER99), semi-empirické (AM1, PM3, PM6) a ab initio (DFT) techniky. Ukázalo sa, že molekulová mechanika poskytuje veľmi slabé výsledky vzhľadom na RDF vody. Ab initio techniky, ktoré sú všeobecne akceptované ako veľmi presné metódy, v prípade vody podceňujú medzimolekulové interakcie. Prekvapujíco, semi-empirickám metóda s PM6 parametrizáciou poskytuje najlepšie výsledky v porovnaní s meraním RDF pomocou X-ray rozptylu.</description><subject>Computational mathematics</subject><subject>DFT</subject><subject>Molecular structure</subject><subject>Pharmaceutical sciences</subject><subject>PM6</subject><subject>RDF</subject><subject>Water</subject><subject>water simulation</subject><issn>0301-2298</issn><issn>1338-6786</issn><issn>2453-6725</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2012</creationdate><recordtype>article</recordtype><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><recordid>eNp1UEtLAzEQDqJgUX-AtwXPq3knexKtr0LxAbV4C9ntRFfbpiZZH__e1BXx4lxmGL7HzIfQPsGHlCt99EYwJVWJCS0xzgPbQAPCmC6l0nITDTDDpKS00ttoL8ZnnEtSKbgcoOuhX6xsaKNfFt4Vs9Y5CLBMRZP3XbKp9Us7LxaQnvwsFs6H4t0mCEVMoWtSF6Dwq9Qu2vgN3UVbzs4j7P30HXR_cT4ZXpXjm8vR8GRcNhQrURLLm1o0GqQTCjjHnCpX00oqWTsBdQ1UVlVt-QwqSRQjAJIppi2XDjTHbAcd9Lqr4F87iMk8-y7kS6MhjBIsha5YRpEe1QQfYwBnVqFd2PBpCDbr5EyfnMnJmXVyZs057jnvdp7_nMFj6D7z8MfgP-549ECEyAplr9DGBB-_lja8GKmYEuZuws3V2e2UTU-l0ewLwz2E9A</recordid><startdate>20120101</startdate><enddate>20120101</enddate><creator>Staník, R.</creator><creator>Ballo, P.</creator><creator>Benkovský, I.</creator><general>Versita</general><general>De Gruyter Poland</general><scope>BSCLL</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7X7</scope><scope>7XB</scope><scope>8AO</scope><scope>8C1</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BENPR</scope><scope>BYOGL</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>K9.</scope><scope>M0S</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope></search><sort><creationdate>20120101</creationdate><title>Comparison of different computational methods for water structure optimisation</title><author>Staník, R. ; Ballo, P. ; Benkovský, I.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c2075-1a4cb5c8e6f57e440427fb29676bf5ebbe2699ba4de961731ee63738a46fe8403</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2012</creationdate><topic>Computational mathematics</topic><topic>DFT</topic><topic>Molecular structure</topic><topic>Pharmaceutical sciences</topic><topic>PM6</topic><topic>RDF</topic><topic>Water</topic><topic>water simulation</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Staník, R.</creatorcontrib><creatorcontrib>Ballo, P.</creatorcontrib><creatorcontrib>Benkovský, I.</creatorcontrib><collection>Istex</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>ProQuest Central</collection><collection>East Europe, Central Europe Database</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><jtitle>Acta Facultatis Pharmaceuticae Universitatis Comenianae</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Staník, R.</au><au>Ballo, P.</au><au>Benkovský, I.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Comparison of different computational methods for water structure optimisation</atitle><jtitle>Acta Facultatis Pharmaceuticae Universitatis Comenianae</jtitle><date>2012-01-01</date><risdate>2012</risdate><volume>59</volume><issue>1</issue><spage>55</spage><epage>66</epage><pages>55-66</pages><issn>0301-2298</issn><eissn>1338-6786</eissn><eissn>2453-6725</eissn><abstract>We have compared several computational techniques with the aim to compute the radial distribution function (RDF) as a good characterization of water structure. In particular, we have used molecular mechanic (AMBER99), semi-empirical (AM1, PM3, PM6) and ab initio (DFT) technique. It has been shown that molecular mechanic gives very poor results in the case of water RDF. Ab initio techniques which are in general accepted as very exact methods, in the case of water underestimate intermolecular interaction. Unexpectedly, the semi-empirical method with PM6 parameterisation gives the best results in comparison with RDF measured by X-ray scattering experiment.
Porovnali sme niekoľko výpočtových techník s cieľom získať radiálnu distribučnú funkciu (RDF), ktorá je vhodná na charakteristiku štruktúry vody. Menovite sme použili molekulovú mechaniku (AMBER99), semi-empirické (AM1, PM3, PM6) a ab initio (DFT) techniky. Ukázalo sa, že molekulová mechanika poskytuje veľmi slabé výsledky vzhľadom na RDF vody. Ab initio techniky, ktoré sú všeobecne akceptované ako veľmi presné metódy, v prípade vody podceňujú medzimolekulové interakcie. Prekvapujíco, semi-empirickám metóda s PM6 parametrizáciou poskytuje najlepšie výsledky v porovnaní s meraním RDF pomocou X-ray rozptylu.</abstract><cop>Bratislava</cop><pub>Versita</pub><doi>10.2478/v10219-012-0019-3</doi><tpages>12</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Computational mathematics DFT Molecular structure Pharmaceutical sciences PM6 RDF Water water simulation |
| title | Comparison of different computational methods for water structure optimisation |
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