{"id":"https://openalex.org/W4323322050","doi":"https://doi.org/10.1021/acs.jcim.2c01525","title":"Estimating the Vertical Ionization Potential of Single-Stranded DNA Molecules","display_name":"Estimating the Vertical Ionization Potential of Single-Stranded DNA Molecules","publication_year":2023,"publication_date":"2023-03-06","ids":{"openalex":"https://openalex.org/W4323322050","doi":"https://doi.org/10.1021/acs.jcim.2c01525","pmid":"https://pubmed.ncbi.nlm.nih.gov/36877828"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.2c01525","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c01525","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://dipot.ulb.ac.be/dspace/bitstream/2013/360349/3/2023.02.27.530325v1.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5073330873","display_name":"Marianne Rooman","orcid":"https://orcid.org/0000-0002-3810-7802"},"institutions":[{"id":"https://openalex.org/I132053463","display_name":"Universit\u00e9 Libre de Bruxelles","ror":"https://ror.org/01r9htc13","country_code":"BE","type":"education","lineage":["https://openalex.org/I132053463"]}],"countries":["BE"],"is_corresponding":true,"raw_author_name":"Marianne Rooman","raw_affiliation_strings":["Computational Biology and Bioinformatics, Universit\u00e9 Libre de Bruxelles, 1050 Brussels, Belgium","Interuniversity Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium"],"affiliations":[{"raw_affiliation_string":"Computational Biology and Bioinformatics, Universit\u00e9 Libre de Bruxelles, 1050 Brussels, Belgium","institution_ids":["https://openalex.org/I132053463"]},{"raw_affiliation_string":"Interuniversity Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5085366265","display_name":"Fabrizio Pucci","orcid":"https://orcid.org/0000-0003-2916-022X"},"institutions":[{"id":"https://openalex.org/I132053463","display_name":"Universit\u00e9 Libre de Bruxelles","ror":"https://ror.org/01r9htc13","country_code":"BE","type":"education","lineage":["https://openalex.org/I132053463"]}],"countries":["BE"],"is_corresponding":true,"raw_author_name":"Fabrizio Pucci","raw_affiliation_strings":["Computational Biology and Bioinformatics, Universit\u00e9 Libre de Bruxelles, 1050 Brussels, Belgium","Interuniversity Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium"],"affiliations":[{"raw_affiliation_string":"Computational Biology and Bioinformatics, Universit\u00e9 Libre de Bruxelles, 1050 Brussels, Belgium","institution_ids":["https://openalex.org/I132053463"]},{"raw_affiliation_string":"Interuniversity Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5073330873","https://openalex.org/A5085366265"],"corresponding_institution_ids":["https://openalex.org/I132053463"],"apc_list":null,"apc_paid":null,"fwci":0.4568,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.65802883,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":98},"biblio":{"volume":"63","issue":"6","first_page":"1766","last_page":"1775"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":1.0,"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":1.0,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9995999932289124,"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/T10207","display_name":"Advanced biosensing and bioanalysis techniques","score":0.9994000196456909,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/nucleobase","display_name":"Nucleobase","score":0.9096086025238037},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.54807049036026},{"id":"https://openalex.org/keywords/basis-set","display_name":"Basis set","score":0.5232297778129578},{"id":"https://openalex.org/keywords/atomic-orbital","display_name":"Atomic orbital","score":0.4705500900745392},{"id":"https://openalex.org/keywords/ionization","display_name":"Ionization","score":0.4632799029350281},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.39341437816619873},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.38321608304977417},{"id":"https://openalex.org/keywords/density-functional-theory","display_name":"Density functional theory","score":0.28196388483047485},{"id":"https://openalex.org/keywords/ion","display_name":"Ion","score":0.20144051313400269},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.1698817014694214},{"id":"https://openalex.org/keywords/electron","display_name":"Electron","score":0.1305614709854126},{"id":"https://openalex.org/keywords/quantum-mechanics","display_name":"Quantum mechanics","score":0.09520244598388672},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.0718553364276886}],"concepts":[{"id":"https://openalex.org/C61234307","wikidata":"https://www.wikidata.org/wiki/Q422960","display_name":"Nucleobase","level":3,"score":0.9096086025238037},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.54807049036026},{"id":"https://openalex.org/C65956243","wikidata":"https://www.wikidata.org/wiki/Q2664086","display_name":"Basis set","level":3,"score":0.5232297778129578},{"id":"https://openalex.org/C189394030","wikidata":"https://www.wikidata.org/wiki/Q53860","display_name":"Atomic orbital","level":3,"score":0.4705500900745392},{"id":"https://openalex.org/C198291218","wikidata":"https://www.wikidata.org/wiki/Q190382","display_name":"Ionization","level":3,"score":0.4632799029350281},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.39341437816619873},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.38321608304977417},{"id":"https://openalex.org/C152365726","wikidata":"https://www.wikidata.org/wiki/Q1048589","display_name":"Density functional theory","level":2,"score":0.28196388483047485},{"id":"https://openalex.org/C145148216","wikidata":"https://www.wikidata.org/wiki/Q36496","display_name":"Ion","level":2,"score":0.20144051313400269},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.1698817014694214},{"id":"https://openalex.org/C147120987","wikidata":"https://www.wikidata.org/wiki/Q2225","display_name":"Electron","level":2,"score":0.1305614709854126},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.09520244598388672},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0718553364276886},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D004277","descriptor_name":"DNA, Single-Stranded","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004277","descriptor_name":"DNA, Single-Stranded","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004277","descriptor_name":"DNA, Single-Stranded","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.2c01525","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c01525","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:36877828","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36877828","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,"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 chemical information and modeling","raw_type":null},{"id":"pmh:oai:dipot.ulb.ac.be:2013/360349","is_oa":true,"landing_page_url":"http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/360349","pdf_url":"https://dipot.ulb.ac.be/dspace/bitstream/2013/360349/3/2023.02.27.530325v1.full.pdf","source":{"id":"https://openalex.org/S4306401063","display_name":"D\u00e9p\u00f4t institutionnel de l'Universit\u00e9 libre de Bruxelles (Universit\u00e9 Libre de Bruxelles)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I132053463","host_organization_name":"Universit\u00e9 Libre de Bruxelles","host_organization_lineage":["https://openalex.org/I132053463"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of chemical information and modeling, 63 (6","raw_type":"info:ulb-repo/semantics/openurl/article"}],"best_oa_location":{"id":"pmh:oai:dipot.ulb.ac.be:2013/360349","is_oa":true,"landing_page_url":"http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/360349","pdf_url":"https://dipot.ulb.ac.be/dspace/bitstream/2013/360349/3/2023.02.27.530325v1.full.pdf","source":{"id":"https://openalex.org/S4306401063","display_name":"D\u00e9p\u00f4t institutionnel de l'Universit\u00e9 libre de Bruxelles (Universit\u00e9 Libre de Bruxelles)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I132053463","host_organization_name":"Universit\u00e9 Libre de Bruxelles","host_organization_lineage":["https://openalex.org/I132053463"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of chemical information and modeling, 63 (6","raw_type":"info:ulb-repo/semantics/openurl/article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1329855610","display_name":null,"funder_award_id":"project","funder_id":"https://openalex.org/F4320321390","funder_display_name":"Fonds De La Recherche Scientifique - FNRS"}],"funders":[{"id":"https://openalex.org/F4320321390","display_name":"Fonds De La Recherche Scientifique - FNRS","ror":"https://ror.org/03q83t159"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4323322050.pdf"},"referenced_works_count":63,"referenced_works":["https://openalex.org/W22915921","https://openalex.org/W1583731466","https://openalex.org/W1662784304","https://openalex.org/W1965373089","https://openalex.org/W1980421351","https://openalex.org/W1980722147","https://openalex.org/W1982823228","https://openalex.org/W1995880669","https://openalex.org/W2000348939","https://openalex.org/W2001005515","https://openalex.org/W2001471795","https://openalex.org/W2009894611","https://openalex.org/W2016074545","https://openalex.org/W2017228637","https://openalex.org/W2017319917","https://openalex.org/W2027568006","https://openalex.org/W2031397281","https://openalex.org/W2034894609","https://openalex.org/W2037647371","https://openalex.org/W2038066877","https://openalex.org/W2039008283","https://openalex.org/W2041370687","https://openalex.org/W2043656093","https://openalex.org/W2044940178","https://openalex.org/W2046829847","https://openalex.org/W2051865375","https://openalex.org/W2058363175","https://openalex.org/W2062499566","https://openalex.org/W2073380384","https://openalex.org/W2083622242","https://openalex.org/W2084574399","https://openalex.org/W2085134918","https://openalex.org/W2090685881","https://openalex.org/W2094491807","https://openalex.org/W2094642658","https://openalex.org/W2094695040","https://openalex.org/W2095100262","https://openalex.org/W2099343472","https://openalex.org/W2107601759","https://openalex.org/W2133226965","https://openalex.org/W2135718797","https://openalex.org/W2136567909","https://openalex.org/W2142075099","https://openalex.org/W2145072946","https://openalex.org/W2150515211","https://openalex.org/W2154102250","https://openalex.org/W2154866190","https://openalex.org/W2157002105","https://openalex.org/W2169333028","https://openalex.org/W2312328902","https://openalex.org/W2419630360","https://openalex.org/W2620040559","https://openalex.org/W2790820083","https://openalex.org/W2804518991","https://openalex.org/W2886200373","https://openalex.org/W2947123473","https://openalex.org/W2954377403","https://openalex.org/W2981643175","https://openalex.org/W3023635524","https://openalex.org/W3045927897","https://openalex.org/W3129086358","https://openalex.org/W3166105599","https://openalex.org/W4225129690"],"related_works":["https://openalex.org/W2042148164","https://openalex.org/W4234581466","https://openalex.org/W2090335203","https://openalex.org/W2074615708","https://openalex.org/W1976608890","https://openalex.org/W4206001248","https://openalex.org/W2012718033","https://openalex.org/W2027961089","https://openalex.org/W3171656855","https://openalex.org/W2379092454"],"abstract_inverted_index":{"The":[0,118],"electronic":[1],"properties":[2],"of":[3,12,29,40,44,53,57,67,121,131,164,185,191,199],"DNA":[4,20,189,219],"molecules,":[5],"defined":[6],"by":[7,211],"the":[8,19,34,38,54,62,96,142,157,162,165,183,196,231],"sequence-dependent":[9],"ionization":[10,64],"potentials":[11,209],"nucleobases,":[13],"enable":[14],"long-range":[15],"charge":[16],"transport":[17],"along":[18],"stacks.":[21],"This":[22,152],"has":[23],"been":[24],"linked":[25],"to":[26,37,76,126,137,146,173],"a":[27,176],"range":[28],"key":[30],"physiological":[31],"processes":[32],"in":[33,72,141],"cells":[35],"and":[36,93,102,129,135,214],"triggering":[39],"nucleobase":[41,70,132],"substitutions,":[42],"some":[43],"which":[45,181],"may":[46],"cause":[47],"diseases.":[48],"To":[49,85],"gain":[50],"molecular-level":[51],"understanding":[52],"sequence":[55],"dependence":[56],"these":[58],"phenomena,":[59],"we":[60,88],"estimated":[61],"vertical":[63],"potential":[65],"(vIP)":[66],"all":[68,186],"possible":[69,187],"stacks":[71],"B-conformation,":[73],"containing":[74],"one":[75],"four":[77],"Gua,":[78],"Ade,":[79],"Thy,":[80],"Cyt,":[81],"or":[82],"methylated":[83],"Cyt.":[84],"do":[86],"this,":[87],"used":[89],"quantum":[90],"chemistry":[91],"calculations":[92],"more":[94],"precisely":[95],"second-order":[97],"M\u00f8ller-Plesset":[98],"perturbation":[99],"theory":[100,107],"(MP2)":[101],"three":[103],"double-hybrid":[104],"density":[105],"functional":[106],"methods,":[108],"combined":[109],"with":[110,149,156,207],"several":[111],"basis":[112,159],"sets":[113],"for":[114],"describing":[115],"atomic":[116],"orbitals.":[117],"calculated":[119,197],"vIP":[120,150,184,203],"single":[122],"nucleobases":[123],"were":[124,171],"compared":[125],"experimental":[127],"data":[128],"those":[130],"pairs,":[133],"triplets,":[134],"quadruplets,":[136],"observed":[138],"mutability":[139],"frequencies":[140],"human":[143],"genome,":[144],"reported":[145],"be":[147],"correlated":[148],"values.":[151],"comparison":[153],"selected":[154],"MP2":[155],"6-31G*":[158],"set":[160,174],"as":[161],"best":[163],"tested":[166],"calculation":[167],"levels.":[168],"These":[169],"results":[170],"exploited":[172],"up":[175],"recursive":[177],"model,":[178],"called":[179],"vIPer,":[180],"estimates":[182],"single-stranded":[188],"sequences":[190],"any":[192],"length":[193],"based":[194],"on":[195,230],"vIPs":[198],"overlapping":[200],"quadruplets.":[201],"vIPer's":[202],"values":[204],"correlate":[205],"well":[206],"oxidation":[208],"measured":[210],"cyclic":[212],"voltammetry":[213],"activities":[215],"obtained":[216],"through":[217],"photoinduced":[218],"cleavage":[220],"experiments,":[221],"further":[222],"validating":[223],"our":[224],"approach.":[225],"vIPer":[226],"is":[227],"freely":[228],"available":[229],"github.com/3BioCompBio/vIPer":[232],"repository.":[233]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
