{"id":"https://openalex.org/W3003798005","doi":"https://doi.org/10.1002/jcc.26164","title":"Importance of model size in quantum mechanical studies of DNA intercalation","display_name":"Importance of model size in quantum mechanical studies of DNA intercalation","publication_year":2020,"publication_date":"2020-02-03","ids":{"openalex":"https://openalex.org/W3003798005","doi":"https://doi.org/10.1002/jcc.26164","mag":"3003798005","pmid":"https://pubmed.ncbi.nlm.nih.gov/32011009"},"language":"en","primary_location":{"id":"doi:10.1002/jcc.26164","doi":"https://doi.org/10.1002/jcc.26164","is_oa":false,"landing_page_url":"https://doi.org/10.1002/jcc.26164","pdf_url":null,"source":{"id":"https://openalex.org/S21117631","display_name":"Journal of Computational Chemistry","issn_l":"0192-8651","issn":["0192-8651","1096-987X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-b","jufo-1","medline","norway-1","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Chemistry","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.26434/chemrxiv.9936473","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5085714025","display_name":"Drew P. Harding","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]},{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Drew P. Harding","raw_affiliation_strings":["Center for Computational Quantum Chemistry, Department of Chemistry, University of Georgia, Athens, Georgia","Department of Chemistry Texas A&amp;M University College Station Texas"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Computational Quantum Chemistry, Department of Chemistry, University of Georgia, Athens, Georgia","institution_ids":["https://openalex.org/I165733156"]},{"raw_affiliation_string":"Department of Chemistry Texas A&amp;M University College Station Texas","institution_ids":["https://openalex.org/I91045830"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085517955","display_name":"Laura J. Kingsley","orcid":"https://orcid.org/0000-0002-5566-3974","observed_orcids":["https://orcid.org/0000-0002-5566-3974"]},"institutions":[{"id":"https://openalex.org/I127128434","display_name":"Genomics Institute of the Novartis Research Foundation","ror":"https://ror.org/017136v53","country_code":"US","type":"facility","lineage":["https://openalex.org/I127128434","https://openalex.org/I1283582996","https://openalex.org/I4210117619"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Laura J. Kingsley","raw_affiliation_strings":["Genomics Institute of the Novartis Research Foundation, San Diego, California"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genomics Institute of the Novartis Research Foundation, San Diego, California","institution_ids":["https://openalex.org/I127128434"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016539643","display_name":"Glen Spraggon","orcid":"https://orcid.org/0000-0001-7880-8454","observed_orcids":["https://orcid.org/0000-0001-7880-8454"]},"institutions":[{"id":"https://openalex.org/I127128434","display_name":"Genomics Institute of the Novartis Research Foundation","ror":"https://ror.org/017136v53","country_code":"US","type":"facility","lineage":["https://openalex.org/I127128434","https://openalex.org/I1283582996","https://openalex.org/I4210117619"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Glen Spraggon","raw_affiliation_strings":["Genomics Institute of the Novartis Research Foundation, San Diego, California"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genomics Institute of the Novartis Research Foundation, San Diego, California","institution_ids":["https://openalex.org/I127128434"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5007309417","display_name":"Steven E. Wheeler","orcid":"https://orcid.org/0000-0001-7824-6906","observed_orcids":["https://orcid.org/0000-0001-7824-6906"]},"institutions":[{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Steven E. Wheeler","raw_affiliation_strings":["Center for Computational Quantum Chemistry, Department of Chemistry, University of Georgia, Athens, Georgia"],"raw_orcid":"https://orcid.org/0000-0001-7824-6906","affiliations":[{"raw_affiliation_string":"Center for Computational Quantum Chemistry, Department of Chemistry, University of Georgia, Athens, Georgia","institution_ids":["https://openalex.org/I165733156"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5007309417"],"corresponding_institution_ids":["https://openalex.org/I165733156"],"apc_list":{"value":4300,"currency":"USD","value_usd":4300},"apc_paid":null,"fwci":0.4053,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.51226917,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":96},"biblio":{"volume":"41","issue":"12","first_page":"1175","last_page":"1184"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.8154000043869019,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.8154000043869019,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10002","display_name":"Advanced Chemical Physics Studies","score":0.13619999587535858,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.015599999576807022,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/dna-intercalation","display_name":"DNA intercalation","score":0.9980000257492065},{"id":"https://openalex.org/keywords/model-convergence","display_name":"model convergence","score":0.6069999933242798},{"id":"https://openalex.org/keywords/density-functional-theory-accuracy","display_name":"density functional accuracy","score":0.4659999907016754}],"concepts":[{"id":"https://openalex.org/C137824038","wikidata":"https://www.wikidata.org/wiki/Q175562","display_name":"Intercalation (chemistry)","level":2,"score":0.6766248941421509},{"id":"https://openalex.org/C512185932","wikidata":"https://www.wikidata.org/wiki/Q28745","display_name":"Nucleotide","level":3,"score":0.667592465877533},{"id":"https://openalex.org/C185581394","wikidata":"https://www.wikidata.org/wiki/Q145911","display_name":"Base pair","level":3,"score":0.6623636484146118},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.6332290768623352},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.5839248299598694},{"id":"https://openalex.org/C93282013","wikidata":"https://www.wikidata.org/wiki/Q420754","display_name":"Binding energy","level":2,"score":0.5523708462715149},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5152583122253418},{"id":"https://openalex.org/C61234307","wikidata":"https://www.wikidata.org/wiki/Q422960","display_name":"Nucleobase","level":3,"score":0.5082923769950867},{"id":"https://openalex.org/C159467904","wikidata":"https://www.wikidata.org/wiki/Q2001702","display_name":"Chemical physics","level":1,"score":0.3879593312740326},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.34780728816986084},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.32840830087661743},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.24266907572746277},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.1361512839794159},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.07454338669776917},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C179104552","wikidata":"https://www.wikidata.org/wiki/Q11165","display_name":"Inorganic chemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000077318","descriptor_name":"Density Functional Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1002/jcc.26164","doi":"https://doi.org/10.1002/jcc.26164","is_oa":false,"landing_page_url":"https://doi.org/10.1002/jcc.26164","pdf_url":null,"source":{"id":"https://openalex.org/S21117631","display_name":"Journal of Computational Chemistry","issn_l":"0192-8651","issn":["0192-8651","1096-987X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-b","jufo-1","medline","norway-1","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Chemistry","raw_type":"journal-article"},{"id":"doi:10.26434/chemrxiv.9936473","doi":"https://doi.org/10.26434/chemrxiv.9936473","is_oa":true,"landing_page_url":"https://doi.org/10.26434/chemrxiv.9936473","pdf_url":null,"source":{"id":"https://openalex.org/S4393918830","display_name":"ChemRxiv","issn_l":"2573-2293","issn":["2573-2293"],"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},{"id":"doi:10.26434/chemrxiv.9936473.v1","doi":"https://doi.org/10.26434/chemrxiv.9936473.v1","is_oa":true,"landing_page_url":"https://doi.org/10.26434/chemrxiv.9936473.v1","pdf_url":"https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744f9469df47af6f43419/original/importance-of-model-size-in-quantum-mechanical-studies-of-dna-intercalation.pdf","source":{"id":"https://openalex.org/S4393918830","display_name":"ChemRxiv","issn_l":"2573-2293","issn":["2573-2293"],"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},{"id":"pmid:32011009","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32011009","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of computational chemistry","raw_type":"Journal Article"},{"id":"pmh:oai:figshare.com:article/9936473","doi":null,"is_oa":true,"landing_page_url":"https://figshare.com/articles/Importance_of_Model_Size_in_Quantum_Mechanical_Studies_of_DNA_Intercalation/9936473","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.26434/chemrxiv.9936473","doi":"https://doi.org/10.26434/chemrxiv.9936473","is_oa":true,"landing_page_url":"https://doi.org/10.26434/chemrxiv.9936473","pdf_url":null,"source":{"id":"https://openalex.org/S4393918830","display_name":"ChemRxiv","issn_l":"2573-2293","issn":["2573-2293"],"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},"sustainable_development_goals":[],"sustainable_development_goals_aurora":[{"id":"https://metadata.un.org/sdg/7","score":0.7200000286102295,"display_name":"Affordable and clean energy"}],"study_designs":[],"awards":[{"id":"https://openalex.org/G7149749884","display_name":null,"funder_award_id":"CHE\u20101807328","funder_id":"https://openalex.org/F4320337393","funder_display_name":"Division of Chemistry"},{"id":"https://openalex.org/G975931649","display_name":"CAREER: Controlling Supramolecular Self-Assembly of Planar and Curved Polycyclic Aromatic Systems","funder_award_id":"1807328","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320308125","display_name":"Texas AgriLife Research","ror":"https://ror.org/01f5ytq51"},{"id":"https://openalex.org/F4320334074","display_name":"Georgia Advanced Computing Resource Center, University of Georgia","ror":null},{"id":"https://openalex.org/F4320334350","display_name":"High Performance Research Computing, Texas A and M University","ror":null},{"id":"https://openalex.org/F4320337393","display_name":"Division of Chemistry","ror":"https://ror.org/01ar8dr59"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":74,"referenced_works":["https://openalex.org/W28713913","https://openalex.org/W138835590","https://openalex.org/W208005321","https://openalex.org/W210528061","https://openalex.org/W628915318","https://openalex.org/W1514300426","https://openalex.org/W1554563779","https://openalex.org/W1584377288","https://openalex.org/W1936002140","https://openalex.org/W1967037562","https://openalex.org/W1968642986","https://openalex.org/W1969271683","https://openalex.org/W1970618622","https://openalex.org/W1981353016","https://openalex.org/W1984636774","https://openalex.org/W1988091937","https://openalex.org/W1988536922","https://openalex.org/W1993383767","https://openalex.org/W1994917514","https://openalex.org/W1999434027","https://openalex.org/W2001480785","https://openalex.org/W2002782616","https://openalex.org/W2003766833","https://openalex.org/W2006787354","https://openalex.org/W2018674598","https://openalex.org/W2033036967","https://openalex.org/W2034420686","https://openalex.org/W2039990656","https://openalex.org/W2040554029","https://openalex.org/W2044591029","https://openalex.org/W2060072337","https://openalex.org/W2062676340","https://openalex.org/W2064436859","https://openalex.org/W2069006374","https://openalex.org/W2075109239","https://openalex.org/W2076307566","https://openalex.org/W2076759130","https://openalex.org/W2078511427","https://openalex.org/W2082037815","https://openalex.org/W2087864238","https://openalex.org/W2092157292","https://openalex.org/W2093084777","https://openalex.org/W2096451055","https://openalex.org/W2096747776","https://openalex.org/W2107126659","https://openalex.org/W2111533830","https://openalex.org/W2116324490","https://openalex.org/W2120068428","https://openalex.org/W2130479394","https://openalex.org/W2131489964","https://openalex.org/W2135373957","https://openalex.org/W2143981217","https://openalex.org/W2144062946","https://openalex.org/W2149958087","https://openalex.org/W2150697053","https://openalex.org/W2161546495","https://openalex.org/W2169858698","https://openalex.org/W2317360768","https://openalex.org/W2331903636","https://openalex.org/W2342504566","https://openalex.org/W2344252179","https://openalex.org/W2395219955","https://openalex.org/W2400489255","https://openalex.org/W2501663698","https://openalex.org/W2570945763","https://openalex.org/W2739439285","https://openalex.org/W2903364247","https://openalex.org/W4213343138","https://openalex.org/W4231712746","https://openalex.org/W4241214627","https://openalex.org/W4252222576","https://openalex.org/W4253841416","https://openalex.org/W6602160113","https://openalex.org/W6724202202"],"related_works":["https://openalex.org/W2570945763","https://openalex.org/W2093084777","https://openalex.org/W2031633417","https://openalex.org/W1999434027","https://openalex.org/W2993159339","https://openalex.org/W7135230363","https://openalex.org/W2046703421","https://openalex.org/W2079460058","https://openalex.org/W2027626554","https://openalex.org/W2107126659"],"abstract_inverted_index":{"Abstract":[0],"The":[1,15,99],"convergence":[2],"of":[3],"DFT\u2010computed":[4],"interaction":[5,22,109],"energies":[6,23,110],"with":[7,68],"increasing":[8],"binding":[9,28,81,97],"site":[10,29,82],"model":[11],"size":[12],"was":[13],"assessed.":[14],"data":[16],"show":[17],"that":[18,39,57,63,72,84],"while":[19],"accurate":[20],"intercalator":[21],"can":[24,112],"be":[25,113],"derived":[26],"from":[27],"models":[30,83],"featuring":[31],"only":[32],"the":[33,43,76],"flanking":[34],"nucleotides":[35,54,90],"for":[36,55],"uncharged":[37],"intercalators":[38,56],"bind":[40,73],"parallel":[41],"to":[42,75,93,106,116],"DNA":[44,77],"base":[45,78],"pairs,":[46],"errors":[47],"remain":[48],"significant":[49],"even":[50],"when":[51],"including":[52],"distant":[53,69],"are":[58,91],"charged,":[59],"exhibit":[60],"groove\u2010binding":[61],"tails":[62],"engage":[64],"in":[65],"noncovalent":[66],"interactions":[67],"nucleotides,":[70],"or":[71],"perpendicular":[74],"pairs.":[79],"Consequently,":[80],"include":[85],"at":[86],"least":[87],"three":[88],"adjacent":[89],"required":[92],"consistently":[94],"predict":[95],"converged":[96],"energies.":[98],"computationally":[100],"inexpensive":[101],"HF\u20103c":[102],"method":[103],"is":[104],"shown":[105],"provide":[107],"reliable":[108],"and":[111],"routinely":[114],"applied":[115],"such":[117],"large":[118],"models.":[119]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2020-02-07T00:00:00"}
