JTHERGAS: Thermodynamic Estimation from 2D Graphical Representations of Molecules.
Identifieur interne : 000069 ( PubMed/Checkpoint ); précédent : 000068; suivant : 000070JTHERGAS: Thermodynamic Estimation from 2D Graphical Representations of Molecules.
Auteurs : Edward Blurock [France] ; V. Warth ; X. Grandmougin ; R. Bounaceur ; P A Glaude ; Frédérique Battin-Leclerc [France]Source :
- Energy (Oxford, England) [ 0360-5442 ] ; 2012.
Abstract
JTHERGAS is a versatile calculator (implemented in JAVA) to estimate thermodynamic information from two dimensional graphical representations of molecules and radicals involving covalent bonds based on the Benson additivity method. The versatility of JTHERGAS stems from its inherent philosophy that all the fundamental data used in the calculation should be visible, to see exactly where the final values came from, and modifiable, to account for new data that can appear in the literature. The main use of this method is within automatic combustion mechanism generation systems where fast estimation of a large number and variety of chemical species is needed. The implementation strategy is based on meta-atom definitions and substructure analysis allowing a highly extensible database without modification of the core algorithms. Several interfaces for the database and the calculations are provided from terminal line commands, to graphical interfaces to web-services. The first order estimation of thermodynamics is based summing up the contributions of each heavy atom bonding description. Second order corrections due to steric hindrance and ring strain are made. Automatic estimate of contributions due to internal, external and optical symmetries are also made. The thermodynamical data for radicals is calculated by taking the difference due to the lost of a hydrogen radical taking into account changes in symmetry, spin, rotations, vibrations and steric hindrances. The software is public domain and is based on standard libraries such as CDK and CML.
DOI: 10.1016/j.energy.2012.01.072
PubMed: 23761949
Affiliations:
- France
- Grand Est, Lorraine (région)
- Nancy
- Centre national de la recherche scientifique, Laboratoire réactions et génie des procédés, Université de Lorraine
Links toward previous steps (curation, corpus...)
Links to Exploration step
pubmed:23761949Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">JTHERGAS: Thermodynamic Estimation from 2D Graphical Representations of Molecules.</title>
<author><name sortKey="Blurock, Edward" sort="Blurock, Edward" uniqKey="Blurock E" first="Edward" last="Blurock">Edward Blurock</name>
<affiliation wicri:level="3"><nlm:affiliation>CNRS-LRGP, ENSIC, Nancy, France.</nlm:affiliation>
<country xml:lang="fr">France</country>
<wicri:regionArea>CNRS-LRGP, ENSIC, Nancy</wicri:regionArea>
<placeName><region type="region">Grand Est</region>
<region type="old region">Lorraine (région)</region>
<settlement type="city">Nancy</settlement>
</placeName>
</affiliation>
</author>
<author><name sortKey="Warth, V" sort="Warth, V" uniqKey="Warth V" first="V" last="Warth">V. Warth</name>
</author>
<author><name sortKey="Grandmougin, X" sort="Grandmougin, X" uniqKey="Grandmougin X" first="X" last="Grandmougin">X. Grandmougin</name>
</author>
<author><name sortKey="Bounaceur, R" sort="Bounaceur, R" uniqKey="Bounaceur R" first="R" last="Bounaceur">R. Bounaceur</name>
</author>
<author><name sortKey="Glaude, P A" sort="Glaude, P A" uniqKey="Glaude P" first="P A" last="Glaude">P A Glaude</name>
</author>
<author><name sortKey="Battin Leclerc, F" sort="Battin Leclerc, F" uniqKey="Battin Leclerc F" first="F" last="Battin-Leclerc">Frédérique Battin-Leclerc</name>
<affiliation><country>France</country>
<placeName><settlement type="city">Nancy</settlement>
<region type="region" nuts="2">Grand Est</region>
<region type="region" nuts="2">Lorraine (région)</region>
</placeName>
<orgName type="laboratoire" n="5">Laboratoire réactions et génie des procédés</orgName>
<orgName type="university">Université de Lorraine</orgName>
<orgName type="institution">Centre national de la recherche scientifique</orgName>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PubMed</idno>
<date when="2012">2012</date>
<idno type="doi">10.1016/j.energy.2012.01.072</idno>
<idno type="RBID">pubmed:23761949</idno>
<idno type="pmid">23761949</idno>
<idno type="wicri:Area/PubMed/Corpus">000067</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000067</idno>
<idno type="wicri:Area/PubMed/Curation">000067</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000067</idno>
<idno type="wicri:Area/PubMed/Checkpoint">000067</idno>
<idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">000067</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en">JTHERGAS: Thermodynamic Estimation from 2D Graphical Representations of Molecules.</title>
<author><name sortKey="Blurock, Edward" sort="Blurock, Edward" uniqKey="Blurock E" first="Edward" last="Blurock">Edward Blurock</name>
<affiliation wicri:level="3"><nlm:affiliation>CNRS-LRGP, ENSIC, Nancy, France.</nlm:affiliation>
<country xml:lang="fr">France</country>
<wicri:regionArea>CNRS-LRGP, ENSIC, Nancy</wicri:regionArea>
<placeName><region type="region">Grand Est</region>
<region type="old region">Lorraine (région)</region>
<settlement type="city">Nancy</settlement>
</placeName>
</affiliation>
</author>
<author><name sortKey="Warth, V" sort="Warth, V" uniqKey="Warth V" first="V" last="Warth">V. Warth</name>
</author>
<author><name sortKey="Grandmougin, X" sort="Grandmougin, X" uniqKey="Grandmougin X" first="X" last="Grandmougin">X. Grandmougin</name>
</author>
<author><name sortKey="Bounaceur, R" sort="Bounaceur, R" uniqKey="Bounaceur R" first="R" last="Bounaceur">R. Bounaceur</name>
</author>
<author><name sortKey="Glaude, P A" sort="Glaude, P A" uniqKey="Glaude P" first="P A" last="Glaude">P A Glaude</name>
</author>
<author><name sortKey="Battin Leclerc, F" sort="Battin Leclerc, F" uniqKey="Battin Leclerc F" first="F" last="Battin-Leclerc">Frédérique Battin-Leclerc</name>
<affiliation><country>France</country>
<placeName><settlement type="city">Nancy</settlement>
<region type="region" nuts="2">Grand Est</region>
<region type="region" nuts="2">Lorraine (région)</region>
</placeName>
<orgName type="laboratoire" n="5">Laboratoire réactions et génie des procédés</orgName>
<orgName type="university">Université de Lorraine</orgName>
<orgName type="institution">Centre national de la recherche scientifique</orgName>
</affiliation>
</author>
</analytic>
<series><title level="j">Energy (Oxford, England)</title>
<idno type="ISSN">0360-5442</idno>
<imprint><date when="2012" type="published">2012</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en">JTHERGAS is a versatile calculator (implemented in JAVA) to estimate thermodynamic information from two dimensional graphical representations of molecules and radicals involving covalent bonds based on the Benson additivity method. The versatility of JTHERGAS stems from its inherent philosophy that all the fundamental data used in the calculation should be visible, to see exactly where the final values came from, and modifiable, to account for new data that can appear in the literature. The main use of this method is within automatic combustion mechanism generation systems where fast estimation of a large number and variety of chemical species is needed. The implementation strategy is based on meta-atom definitions and substructure analysis allowing a highly extensible database without modification of the core algorithms. Several interfaces for the database and the calculations are provided from terminal line commands, to graphical interfaces to web-services. The first order estimation of thermodynamics is based summing up the contributions of each heavy atom bonding description. Second order corrections due to steric hindrance and ring strain are made. Automatic estimate of contributions due to internal, external and optical symmetries are also made. The thermodynamical data for radicals is calculated by taking the difference due to the lost of a hydrogen radical taking into account changes in symmetry, spin, rotations, vibrations and steric hindrances. The software is public domain and is based on standard libraries such as CDK and CML.</div>
</front>
</TEI>
<pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">23761949</PMID>
<DateCreated><Year>2013</Year>
<Month>6</Month>
<Day>13</Day>
</DateCreated>
<Article PubModel="Print"><Journal><ISSN IssnType="Print">0360-5442</ISSN>
<JournalIssue CitedMedium="Print"><Volume>43</Volume>
<Issue>1</Issue>
<PubDate><Year>2012</Year>
<Month>Jul</Month>
</PubDate>
</JournalIssue>
<Title>Energy (Oxford, England)</Title>
<ISOAbbreviation>Energy (Oxf)</ISOAbbreviation>
</Journal>
<ArticleTitle>JTHERGAS: Thermodynamic Estimation from 2D Graphical Representations of Molecules.</ArticleTitle>
<Pagination><MedlinePgn>161-171</MedlinePgn>
</Pagination>
<Abstract><AbstractText>JTHERGAS is a versatile calculator (implemented in JAVA) to estimate thermodynamic information from two dimensional graphical representations of molecules and radicals involving covalent bonds based on the Benson additivity method. The versatility of JTHERGAS stems from its inherent philosophy that all the fundamental data used in the calculation should be visible, to see exactly where the final values came from, and modifiable, to account for new data that can appear in the literature. The main use of this method is within automatic combustion mechanism generation systems where fast estimation of a large number and variety of chemical species is needed. The implementation strategy is based on meta-atom definitions and substructure analysis allowing a highly extensible database without modification of the core algorithms. Several interfaces for the database and the calculations are provided from terminal line commands, to graphical interfaces to web-services. The first order estimation of thermodynamics is based summing up the contributions of each heavy atom bonding description. Second order corrections due to steric hindrance and ring strain are made. Automatic estimate of contributions due to internal, external and optical symmetries are also made. The thermodynamical data for radicals is calculated by taking the difference due to the lost of a hydrogen radical taking into account changes in symmetry, spin, rotations, vibrations and steric hindrances. The software is public domain and is based on standard libraries such as CDK and CML.</AbstractText>
</Abstract>
<AuthorList><Author><LastName>Blurock</LastName>
<ForeName>Edward</ForeName>
<Initials>E</Initials>
<AffiliationInfo><Affiliation>CNRS-LRGP, ENSIC, Nancy, France.</Affiliation>
</AffiliationInfo>
</Author>
<Author><LastName>Warth</LastName>
<ForeName>V</ForeName>
<Initials>V</Initials>
</Author>
<Author><LastName>Grandmougin</LastName>
<ForeName>X</ForeName>
<Initials>X</Initials>
</Author>
<Author><LastName>Bounaceur</LastName>
<ForeName>R</ForeName>
<Initials>R</Initials>
</Author>
<Author><LastName>Glaude</LastName>
<ForeName>P A</ForeName>
<Initials>PA</Initials>
</Author>
<Author><LastName>Battin-Leclerc</LastName>
<ForeName>F</ForeName>
<Initials>F</Initials>
</Author>
</AuthorList>
<Language>ENG</Language>
<GrantList><Grant><GrantID>227669</GrantID>
<Agency>European Research Council</Agency>
<Country>International</Country>
</Grant>
</GrantList>
<PublicationTypeList><PublicationType UI="">JOURNAL ARTICLE</PublicationType>
</PublicationTypeList>
</Article>
<MedlineJournalInfo><MedlineTA>Energy (Oxf)</MedlineTA>
<NlmUniqueID>101607408</NlmUniqueID>
<ISSNLinking>0360-5442</ISSNLinking>
</MedlineJournalInfo>
<KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Benson rules</Keyword>
<Keyword MajorTopicYN="N">Thermodynamic estimation</Keyword>
<Keyword MajorTopicYN="N">automatic generation</Keyword>
<Keyword MajorTopicYN="N">enthalpy</Keyword>
<Keyword MajorTopicYN="N">entropy</Keyword>
<Keyword MajorTopicYN="N">heat capacity</Keyword>
</KeywordList>
</MedlineCitation>
<PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2013</Year>
<Month>6</Month>
<Day>14</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="pubmed"><Year>2013</Year>
<Month>6</Month>
<Day>14</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="medline"><Year>2013</Year>
<Month>6</Month>
<Day>14</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
</History>
<PublicationStatus>ppublish</PublicationStatus>
<ArticleIdList><ArticleId IdType="doi">10.1016/j.energy.2012.01.072</ArticleId>
<ArticleId IdType="pubmed">23761949</ArticleId>
<ArticleId IdType="pmc">PMC3677398</ArticleId>
<ArticleId IdType="mid">EMS53330</ArticleId>
</ArticleIdList>
<pmc-dir>nihms</pmc-dir>
</PubmedData>
</pubmed>
<affiliations><list><country><li>France</li>
</country>
<region><li>Grand Est</li>
<li>Lorraine (région)</li>
</region>
<settlement><li>Nancy</li>
</settlement>
<orgName><li>Centre national de la recherche scientifique</li>
<li>Laboratoire réactions et génie des procédés</li>
<li>Université de Lorraine</li>
</orgName>
</list>
<tree><noCountry><name sortKey="Bounaceur, R" sort="Bounaceur, R" uniqKey="Bounaceur R" first="R" last="Bounaceur">R. Bounaceur</name>
<name sortKey="Glaude, P A" sort="Glaude, P A" uniqKey="Glaude P" first="P A" last="Glaude">P A Glaude</name>
<name sortKey="Grandmougin, X" sort="Grandmougin, X" uniqKey="Grandmougin X" first="X" last="Grandmougin">X. Grandmougin</name>
<name sortKey="Warth, V" sort="Warth, V" uniqKey="Warth V" first="V" last="Warth">V. Warth</name>
</noCountry>
<country name="France"><region name="Grand Est"><name sortKey="Blurock, Edward" sort="Blurock, Edward" uniqKey="Blurock E" first="Edward" last="Blurock">Edward Blurock</name>
</region>
<name sortKey="Battin Leclerc, F" sort="Battin Leclerc, F" uniqKey="Battin Leclerc F" first="F" last="Battin-Leclerc">Frédérique Battin-Leclerc</name>
</country>
</tree>
</affiliations>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Wicri/Lorraine/explor/LrgpV1/Data/PubMed/Checkpoint
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000069 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/PubMed/Checkpoint/biblio.hfd -nk 000069 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Wicri/Lorraine |area= LrgpV1 |flux= PubMed |étape= Checkpoint |type= RBID |clé= pubmed:23761949 |texte= JTHERGAS: Thermodynamic Estimation from 2D Graphical Representations of Molecules. }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/PubMed/Checkpoint/RBID.i -Sk "pubmed:23761949" \ | HfdSelect -Kh $EXPLOR_AREA/Data/PubMed/Checkpoint/biblio.hfd \ | NlmPubMed2Wicri -a LrgpV1
![]() | This area was generated with Dilib version V0.6.32. | ![]() |