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May-model Set 113 > urlin.us/2c8fh





The,,SMD,,model,,employs,,a,,single,,set,,of,,parameters,,(intrinsic,,atomic,,Coulomb,,radii,,and,,atomic,,surface,,tension,,coefficients),,optimized,,over,,six,,electronic,,structure,,methods:,,M05-2X/MIDI!6D,,,M05-2X/6-31G,,,M05-2X/6-31+G,,,M05-2X/cc-pVTZ,,,B3LYP/6-31G,,,and,,HF/6-31GResult,,Filters,,SMD,is,a,universal,solvation,model,,where,"universal",denotes,its,applicability,to,any,charged,or,uncharged,solute,in,any,solvent,or,liquid,medium,for,which,a,few,key,descriptors,are,known,(in,particular,,dielectric,constant,,refractive,index,,bulk,surface,tension,,and,acidity,and,basicity,parameters)NCBISkip,,,to,,,main,,,contentSkip,,,to,,,navigationResourcesAll,,,ResourcesChemicals,,,&,,,BioassaysBioSystemsPubChem,,,BioAssayPubChem,,,CompoundPubChem,,,Structure,,,SearchPubChem,,,SubstanceAll,,,Chemicals,,,&,,,Bioassays,,,Resources.DNA,,,&,,,RNABLAST,,,(Basic,,,Local,,,Alignment,,,Search,,,Tool)BLAST,,,(Stand-alone)E-UtilitiesGenBankGenBank:,,,BankItGenBank:,,,SequinGenBank:,,,tbl2asnGenome,,,WorkbenchInfluenza,,,VirusNucleotide,,,DatabasePopSetPrimer-BLASTProSplignReference,,,Sequence,,,(RefSeq)RefSeqGeneSequence,,,Read,,,Archive,,,(SRA)SplignTrace,,,ArchiveUniGeneAll,,,DNA,,,&,,,RNA,,,Resources.Data,,,&,,,SoftwareBLAST,,,(Basic,,,Local,,,Alignment,,,Search,,,Tool)BLAST,,,(Stand-alone)Cn3DConserved,,,Domain,,,Search,,,Service,,,(CD,,,Search)E-UtilitiesGenBank:,,,BankItGenBank:,,,SequinGenBank:,,,tbl2asnGenome,,,ProtMapGenome,,,WorkbenchPrimer-BLASTProSplignPubChem,,,Structure,,,SearchSNP,,,Submission,,,ToolSplignVector,,,Alignment,,,Search,,,Tool,,,(VAST)All,,,Data,,,&,,,Software,,,Resources.Domains,,,&,,,StructuresBioSystemsCn3DConserved,,,Domain,,,Database,,,(CDD)Conserved,,,Domain,,,Search,,,Service,,,(CD,,,Search)Structure,,,(Molecular,,,Modeling,,,Database)Vector,,,Alignment,,,Search,,,Tool,,,(VAST)All,,,Domains,,,&,,,Structures,,,Resources.Genes,,,&,,,ExpressionBioSystemsDatabase,,,of,,,Genotypes,,,and,,,Phenotypes,,,(dbGaP)E-UtilitiesGeneGene,,,Expression,,,Omnibus,,,(GEO),,,Database,,,Gene,,,Expression,,,Omnibus,,,(GEO),,,DatasetsGene,,,Expression,,,Omnibus,,,(GEO),,,ProfilesGenome,,,WorkbenchHomoloGeneMap,,,ViewerOnline,,,Mendelian,,,Inheritance,,,in,,,Man,,,(OMIM)RefSeqGeneUniGeneAll,,,Genes,,,&,,,Expression,,,Resources.Genetics,,,&,,,MedicineBookshelfDatabase,,,of,,,Genotypes,,,and,,,Phenotypes,,,(dbGaP)Genetic,,,Testing,,,RegistryInfluenza,,,VirusMap,,,ViewerOnline,,,Mendelian,,,Inheritance,,,in,,,Man,,,(OMIM)PubMedPubMed,,,Central,,,(PMC)PubMed,,,Clinical,,,QueriesRefSeqGeneAll,,,Genetics,,,&,,,Medicine,,,Resources.Genomes,,,&,,,MapsDatabase,,,of,,,Genomic,,,Structural,,,Variation,,,(dbVar)GenBank:,,,tbl2asnGenomeGenome,,,ProjectGenome,,,ProtMapGenome,,,WorkbenchInfluenza,,,VirusMap,,,ViewerNucleotide,,,DatabasePopSetProSplignSequence,,,Read,,,Archive,,,(SRA)SplignTrace,,,ArchiveAll,,,Genomes,,,&,,,Maps,,,Resources.HomologyBLAST,,,(Basic,,,Local,,,Alignment,,,Search,,,Tool)BLAST,,,(Stand-alone)BLAST,,,Link,,,(BLink)Conserved,,,Domain,,,Database,,,(CDD)Conserved,,,Domain,,,Search,,,Service,,,(CD,,,Search)Genome,,,ProtMapHomoloGeneProtein,,,ClustersAll,,,Homology,,,Resources.LiteratureBookshelfE-UtilitiesJournals,,,in,,,NCBI,,,DatabasesMeSH,,,DatabaseNCBI,,,HandbookNCBI,,,Help,,,ManualNCBI,,,NewsPubMedPubMed,,,Central,,,(PMC)PubMed,,,Clinical,,,QueriesPubMed,,,HealthAll,,,Literature,,,Resources.ProteinsBioSystemsBLAST,,,(Basic,,,Local,,,Alignment,,,Search,,,Tool)BLAST,,,(Stand-alone)BLAST,,,Link,,,(BLink)Conserved,,,Domain,,,Database,,,(CDD)Conserved,,,Domain,,,Search,,,Service,,,(CD,,,Search)E-UtilitiesProSplignProtein,,,ClustersProtein,,,DatabaseReference,,,Sequence,,,(RefSeq)All,,,Proteins,,,Resources.Sequence,,,AnalysisBLAST,,,(Basic,,,Local,,,Alignment,,,Search,,,Tool)BLAST,,,(Stand-alone)BLAST,,,Link,,,(BLink)Conserved,,,Domain,,,Search,,,Service,,,(CD,,,Search)Genome,,,ProtMapGenome,,,WorkbenchInfluenza,,,VirusPrimer-BLASTProSplignSplignAll,,,Sequence,,,Analysis,,,Resources.TaxonomyTaxonomyTaxonomy,,,BrowserTaxonomy,,,Common,,,TreeAll,,,Taxonomy,,,Resources.Training,,,&,,,TutorialsNCBI,,,Education,,,PageNCBI,,,HandbookNCBI,,,Help,,,ManualNCBI,,,NewsAll,,,Training,,,&,,,Tutorials,,,Resources.VariationDatabase,,,of,,,Genomic,,,Structural,,,Variation,,,(dbVar)Database,,,of,,,Genotypes,,,and,,,Phenotypes,,,(dbGaP)Database,,,of,,,Single,,,Nucleotide,,,Polymorphisms,,,(dbSNP)SNP,,,Submission,,,ToolAll,,,Variation,,,Resources.How,,,ToAll,,,How,,,ToChemicals,,,&,,,BioassaysDNA,,,&,,,RNAData,,,&,,,SoftwareDomains,,,&,,,StructuresGenes,,,&,,,ExpressionGenetics,,,&,,,MedicineGenomes,,,&,,,MapsHomologyLiteratureProteinsSequence,,,AnalysisTaxonomyTraining,,,&,,,TutorialsVariationAbout,,,NCBI,,,AccesskeysMy,,,NCBISign,,,in,,,to,,,NCBISign,,,OutThis,,contribution,,is,,a,,sum,,of,,terms,,that,,are,,proportional,,(with,,geometry-dependent,,proportionality,,constants,,called,,atomic,,surface,,tensions),,to,,the,,solvent-accessible,,surface,,areas,,of,,the,,individual,,atoms,,of,,the,,soluteNLM,,,NIH,,,DHHS,,,USA.gov,,,National,,,Center,,,for,,,Biotechnology,,,Information,,,,U.S.The,first,component,is,the,bulk,electrostatic,contribution,arising,from,a,self-consistent,reaction,field,treatment,that,involves,the,solution,of,the,nonhomogeneous,Poisson,equation,for,electrostatics,in,terms,of,the,integral-equation-formalism,polarizable,continuum,model,(IEF-PCM)Warning:,,,The,,,NCBI,,,web,,,site,,,requires,,,JavaScript,,,to,,,function"Continuum",denotes,that,the,solvent,is,not,represented,explicitly,but,rather,as,a,dielectric,medium,with,surface,tension,at,the,solute-solvent,boundary,Biochemistry,Agrochemical,Bioregulators,Animal,Nutrition,Biochemical,Genetics,Biochemical,Methods,Enzymes,Fermentation,and,Bioindustrial,Chemistry,Fertilizers,,Soils,,and,Plant,Nutrition,Food,and,Feed,Chemistry,General,Biochemistry,History,,Education,,and,Documentation,Immunochemistry,Mammalian,Biochemistry,Mammalian,Hormones,Mammalian,Pathological,Biochemistry,Microbial,,Algal,,and,Fungal,Biochemistry,Nonmammalian,Biochemistry,Pharmacology,Plant,Biochemistry,Radiation,Biochemistry,Toxicology,Although,,,the,,,SMD,,,model,,,has,,,been,,,parametrized,,,using,,,the,,,IEF-PCM,,,protocol,,,for,,,bulk,,,electrostatics,,,,it,,,may,,,also,,,be,,,employed,,,with,,,other,,,algorithms,,,for,,,solving,,,the,,,nonhomogeneous,,,Poisson,,,equation,,,for,,,continuum,,,solvation,,,calculations,,,in,,,which,,,the,,,solute,,,is,,,represented,,,by,,,its,,,electron,,,density,,,in,,,real,,,spacePlease,,review,,our,,privacy,,policymorePage,Not,Found,We're,sorry,,the,page,you've,requested,does,not,exist,at,this,addressPubMed,US,National,Library,of,Medicine,National,Institutes,of,Health,Search,databaseAll,DatabasesAssemblyBioProjectBioSampleBioSystemsBooksClinVarCloneConserved,DomainsdbGaPdbVarEpigenomicsESTGeneGenomeGEO,DataSetsGEO,ProfilesGSSGTRHomoloGeneMedGenMeSHNCBI,Web,SiteNLM,CatalogNucleotideOMIMPMCPopSetProbeProteinProtein,ClustersPubChem,BioAssayPubChem,CompoundPubChem,SubstancePubMedPubMed,HealthSNPSRAStructureTaxonomyToolKitToolKitAllToolKitBookToolKitBookghUniGeneSearch,termSearchAdvancedHelp,If,,you,,typed,,in,,the,,URL,,please,,double,,check,,to,,make,,sure,,it,,has,,been,,typed,,correctly,,Go,,to,,the,,Wiley,,Online,,Library,,Homepage,,Enter,,a,,search,,term,,in,,the,,search,,form,,on,,this,,page,,to,,find,,the,,page,,you,,were,,looking,,for,,If,,you,,require,,help,,please,,Contact,,Customer,,Service,,.Supplemental,Content,Full,text,links,The,,,page,,,you,,,are,,,looking,,,for,,,might,,,have,,,been,,,removed,,,,changed,,,,or,,,is,,,temporarily,,,unavailable,,,Organic,,,Alicyclic,,,Compounds,,,Aliphatic,,,Compounds,,,Alkaloids,,,Amino,,,Acids,,,,Peptides,,,,and,,,Proteins,,,Benzene,,,,Its,,,Derivatives,,,,and,,,Condensed,,,Benzenoid,,,Compounds,,,Biomolecules,,,and,,,Their,,,Synthetic,,,Analogs,,,Carbohydrates,,,General,,,Organic,,,Chemistry,,,Heterocyclic,,,Compounds,,,(More,,,than,,,One,,,Hetero,,,Atom),,,Heterocyclic,,,Compounds,,,(One,,,Hetero,,,Atom),,,Organometallic,,,and,,,Organometalloidal,,,Compounds,,,Physical,,,Organic,,,Chemistry,,,Steroids,,,Terpenes,,,and,,,Terpenoids,,,.You,are,here:,NCBI,>,Literature,>,PubMed,Write,to,the,Help,Desk,GitHub,,,Status.The,,,model,,,separates,,,the,,,observable,,,solvation,,,free,,,energy,,,into,,,two,,,main,,,componentsSimple,,,NCBI,,,Directory,,,Getting,,,Started,,,NCBI,,,Education,,,NCBI,,,Help,,,Manual,,,NCBI,,,Handbook,,,Training,,,&,,,Tutorials,,,Submit,,,Data,,,Resources,,,Chemicals,,,&,,,BioassaysData,,,&,,,SoftwareDNA,,,&,,,RNADomains,,,&,,,StructuresGenes,,,&,,,ExpressionGenetics,,,&,,,MedicineGenomes,,,&,,,MapsHomologyLiteratureProteinsSequence,,,AnalysisTaxonomyVariation,,,Popular,,,PubMed,,,Bookshelf,,,PubMed,,,Central,,,PubMed,,,Health,,,BLAST,,,Nucleotide,,,Genome,,,SNP,,,Gene,,,Protein,,,PubChem,,,Featured,,,Genetic,,,Testing,,,Registry,,,PubMed,,,Health,,,GenBank,,,Reference,,,Sequences,,,Gene,,,Expression,,,Omnibus,,,Map,,,Viewer,,,Human,,,Genome,,,Mouse,,,Genome,,,Influenza,,,Virus,,,Primer-BLAST,,,Sequence,,,Read,,,Archive,,,NCBI,,,Information,,,About,,,NCBI,,,Research,,,at,,,NCBI,,,NCBI,,,News,,,NCBI,,,FTP,,,Site,,,NCBI,,,on,,,Facebook,,,NCBI,,,on,,,Twitter,,,NCBI,,,on,,,YouTube,,,External,,,linkThis,includes,,for,example,,the,conductor-like,screening,algorithmWith,the,6-31G,basis,set,,the,SMD,model,achieves,mean,unsigned,errors,of,0.6-1.0,kcal/mol,in,the,solvation,free,energies,of,tested,neutrals,and,mean,unsigned,errors,of,4,kcal/mol,on,average,for,ions,with,either,Gaussian03,or,GAMESS.PMID:,19366259,[PubMed],ShareLinkOut,-,more,resourcesFull,Text,SourcesAmerican,Chemical,SocietyOther,Literature,SourcesCOS,Scholar,UniverseCited,by,Patents,in,-,The,LensPubMed,Commons,home,PubMed,Commons,0,commentsHow,to,join,PubMed,CommonsHow,to,cite,this,comment:,The,,,cavities,,,for,,,the,,,bulk,,,electrostatic,,,calculation,,,are,,,defined,,,by,,,superpositions,,,of,,,nuclear-centered,,,spheres2009,May,7;113(18):6378-96Applied,,,Air,,,Pollution,,,and,,,Industrial,,,Hygiene,,,Apparatus,,,and,,,Plant,,,Equipment,,,Cement,,,,Concrete,,,,and,,,Related,,,Building,,,Materials,,,Ceramics,,,Electrochemical,,,,Radiational,,,,and,,,Thermal,,,Energy,,,Technology,,,Essential,,,Oils,,,and,,,Cosmetics,,,Extractive,,,Metallurgy,,,Ferrous,,,Metals,,,and,,,Alloys,,,Fossil,,,Fuels,,,,Derivatives,,,,and,,,Related,,,Products,,,Industrial,,,Inorganic,,,Chemicals,,,Mineralogical,,,and,,,Geological,,,Chemistry,,,Nonferrous,,,Metals,,,and,,,Alloys,,,Pharmaceutical,,,Analysis,,,Pharmaceuticals,,,Propellants,,,and,,,Explosives,,,Unit,,,Operations,,,and,,,Processes,,,Waste,,,Treatment,,,and,,,Disposal,,,Water,,,The,second,component,is,called,the,cavity-dispersion-solvent-structure,term,and,is,the,contribution,arising,from,short-range,interactions,between,the,solute,and,solvent,molecules,in,the,first,solvation,shelldoi:,10.1021/jp810292n.Universal,solvation,model,based,on,solute,electron,density,and,on,a,continuum,model,of,the,solvent,defined,by,the,bulk,dielectric,constant,and,atomic,surface,tensions.Marenich,AV1,,Cramer,CJ,,Truhlar,DG.Author,information1Department,of,Chemistry,and,Supercomputing,Institute,,University,of,Minnesota,,207,Pleasant,Street,SE,,Minneapolis,,Minnesota,55455-0431,,USA.AbstractWe,present,a,new,continuum,solvation,model,based,on,the,quantum,mechanical,charge,density,of,a,solute,molecule,interacting,with,a,continuum,description,of,the,solvent,,,Macromolecular,,,Cellulose,,,,Lignin,,,,Paper,,,,and,,,Other,,,Wood,,,Products,,,Chemistry,,,of,,,Synthetic,,,High,,,Polymers,,,Coatings,,,,Inks,,,,and,,,Related,,,Products,,,Dyes,,,,Organic,,,Pigments,,,,Fluorescent,,,Brighteners,,,,and,,,Photographic,,,Sensitizers,,,Industrial,,,Carbohydrates,,,Industrial,,,Organic,,,Chemicals,,,,Leather,,,,Fats,,,,and,,,Waxes,,,Physical,,,Properties,,,of,,,Synthetic,,,High,,,Polymers,,,Plastics,,,Fabrication,,,and,,,Uses,,,Plastics,,,Manufacture,,,and,,,Processing,,,Surface,,,Active,,,Agents,,,and,,,Detergents,,,Synthetic,,,Elastomers,,,and,,,Natural,,,Rubber,,,Textiles,,,and,,,Fibers,,,AbstractFormatSummarySummary,(text)AbstractAbstract,(text)MEDLINEXMLPMID,ListApplySend,to:Choose,DestinationFileClipboardCollectionsE-mailOrderMy,BibliographyCitation,managerFormatSummary,(text)Abstract,(text)MEDLINEXMLPMID,ListCSVCreate,File1,selected,item:,19366259FormatSummarySummary,(text)AbstractAbstract,(text)MEDLINEXMLPMID,ListMeSH,and,Other,DataE-mailSubjectAdditional,textE-mailDidn't,get,the,message?,Find,out,why.Add,to,ClipboardAdd,to,CollectionsOrder,articlesAdd,to,My,BibliographyGenerate,a,file,for,use,with,external,citation,management,software.Create,File,See,comment,in,PubMed,Commons,belowJ,Phys,Chem,BThe,model,is,called,SMD,,where,the,"D",stands,for,"density",to,denote,that,the,full,solute,electron,density,is,used,without,defining,partial,atomic,chargesThe,,,SMD,,,model,,,has,,,been,,,parametrized,,,with,,,a,,,training,,,set,,,of,,,2821,,,solvation,,,data,,,including,,,112,,,aqueous,,,ionic,,,solvation,,,free,,,energies,,,,220,,,solvation,,,free,,,energies,,,for,,,166,,,ions,,,in,,,acetonitrile,,,,methanol,,,,and,,,dimethyl,,,sulfoxide,,,,2346,,,solvation,,,free,,,energies,,,for,,,318,,,neutral,,,solutes,,,in,,,91,,,solvents,,,(90,,,nonaqueous,,,organic,,,solvents,,,and,,,water),,,,and,,,143,,,transfer,,,free,,,energies,,,for,,,93,,,neutral,,,solutes,,,between,,,water,,,and,,,15,,,organic,,,solventsThe,elements,present,in,the,solutes,are,H,,C,,N,,O,,F,,Si,,P,,S,,Cl,,and,BrContact,,Support 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