{"id":"https://openalex.org/W1994418194","doi":"https://doi.org/10.1016/s0006-3495(95)80023-8","title":"A free energy analysis of nucleic acid base stacking in aqueous solution","display_name":"A free energy analysis of nucleic acid base stacking in aqueous solution","publication_year":1995,"publication_date":"1995-10-01","ids":{"openalex":"https://openalex.org/W1994418194","doi":"https://doi.org/10.1016/s0006-3495(95)80023-8","mag":"1994418194","pmid":"https://pubmed.ncbi.nlm.nih.gov/8534823","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/1236383"},"language":"en","primary_location":{"id":"doi:10.1016/s0006-3495(95)80023-8","doi":"https://doi.org/10.1016/s0006-3495(95)80023-8","is_oa":true,"landing_page_url":"https://doi.org/10.1016/s0006-3495(95)80023-8","pdf_url":"https://doi.org/10.1016/s0006-3495(95)80023-8","source":{"id":"https://openalex.org/S98085912","display_name":"Biophysical Journal","issn_l":"0006-3495","issn":["0006-3495","1542-0086"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-a","jufo-2","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Biophysical Journal","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1016/s0006-3495(95)80023-8","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5064812602","display_name":"Richard A. Friedman","orcid":"https://orcid.org/0000-0002-5136-2998","observed_orcids":["https://orcid.org/0000-0002-5136-2998"]},"institutions":[{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"R.A. Friedman","raw_affiliation_strings":["Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA","institution_ids":["https://openalex.org/I78577930"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5036654109","display_name":"Barry H. Honig","orcid":"https://orcid.org/0000-0002-1835-1031","observed_orcids":["https://orcid.org/0000-0002-1835-1031","https://orcid.org/0000-0002-2480-6696"]},"institutions":[{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"B. Honig","raw_affiliation_strings":["Department of Biochemistry and Molecular Biophysics, Columbia University New York New York 10032 USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biophysics, Columbia University New York New York 10032 USA","institution_ids":["https://openalex.org/I78577930"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I78577930"],"apc_list":{"value":3000,"currency":"USD","value_usd":3000},"apc_paid":{"value":3000,"currency":"USD","value_usd":3000},"fwci":1.9713,"has_fulltext":false,"cited_by_count":236,"citation_normalized_percentile":{"value":0.87095463,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":93,"max":99},"biblio":{"volume":"69","issue":"4","first_page":"1528","last_page":"1535"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.9613999724388123,"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":0.9613999724388123,"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":0.016499999910593033,"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/T12274","display_name":"Electrostatics and Colloid Interactions","score":0.009700000286102295,"subfield":{"id":"https://openalex.org/subfields/1606","display_name":"Physical and Theoretical Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/electrostatic-interactions","display_name":"electrostatic interactions","score":0.9319999814033508},{"id":"https://openalex.org/keywords/hydrophobic-effect","display_name":"hydrophobic effect","score":0.7789999842643738},{"id":"https://openalex.org/keywords/van-der-waals-forces","display_name":"van der Waals interactions","score":0.949999988079071},{"id":"https://openalex.org/keywords/aqueous-solutions","display_name":"aqueous solutions","score":0.6439999938011169}],"concepts":[{"id":"https://openalex.org/C33347731","wikidata":"https://www.wikidata.org/wiki/Q285210","display_name":"Stacking","level":2,"score":0.8851516246795654},{"id":"https://openalex.org/C126061179","wikidata":"https://www.wikidata.org/wiki/Q189627","display_name":"van der Waals force","level":3,"score":0.8605968356132507},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.6935270428657532},{"id":"https://openalex.org/C184651966","wikidata":"https://www.wikidata.org/wiki/Q906356","display_name":"Aqueous solution","level":2,"score":0.6349509954452515},{"id":"https://openalex.org/C117626034","wikidata":"https://www.wikidata.org/wiki/Q26336","display_name":"Electrostatics","level":2,"score":0.5403227806091309},{"id":"https://openalex.org/C90260826","wikidata":"https://www.wikidata.org/wiki/Q899157","display_name":"Hydrophobic effect","level":2,"score":0.488369882106781},{"id":"https://openalex.org/C159467904","wikidata":"https://www.wikidata.org/wiki/Q2001702","display_name":"Chemical physics","level":1,"score":0.4869307279586792},{"id":"https://openalex.org/C87716614","wikidata":"https://www.wikidata.org/wiki/Q845744","display_name":"Static electricity","level":2,"score":0.46306082606315613},{"id":"https://openalex.org/C137277065","wikidata":"https://www.wikidata.org/wiki/Q2915446","display_name":"Non-covalent interactions","level":4,"score":0.45648691058158875},{"id":"https://openalex.org/C24107716","wikidata":"https://www.wikidata.org/wiki/Q123619","display_name":"Nucleic acid","level":2,"score":0.45359840989112854},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.4383698105812073},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.4146648049354553},{"id":"https://openalex.org/C112887158","wikidata":"https://www.wikidata.org/wiki/Q169324","display_name":"Hydrogen bond","level":3,"score":0.27166908979415894},{"id":"https://openalex.org/C147789679","wikidata":"https://www.wikidata.org/wiki/Q11372","display_name":"Physical chemistry","level":1,"score":0.17390212416648865},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.17067411541938782},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.161729633808136},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.07838514447212219},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.06441822648048401},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000225","descriptor_name":"Adenine","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D001482","descriptor_name":"Base Composition","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002151","descriptor_name":"Calorimetry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003596","descriptor_name":"Cytosine","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":"D004563","descriptor_name":"Electrochemistry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006147","descriptor_name":"Guanine","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D008433","descriptor_name":"Mathematics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009682","descriptor_name":"Magnetic Resonance Spectroscopy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013941","descriptor_name":"Thymine","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1016/s0006-3495(95)80023-8","doi":"https://doi.org/10.1016/s0006-3495(95)80023-8","is_oa":true,"landing_page_url":"https://doi.org/10.1016/s0006-3495(95)80023-8","pdf_url":"https://doi.org/10.1016/s0006-3495(95)80023-8","source":{"id":"https://openalex.org/S98085912","display_name":"Biophysical Journal","issn_l":"0006-3495","issn":["0006-3495","1542-0086"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-a","jufo-2","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Biophysical Journal","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:1236383","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1236383","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"Biophys J","raw_type":"Text"},{"id":"pmid:8534823","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/8534823","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":"Biophysical journal","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1016/s0006-3495(95)80023-8","doi":"https://doi.org/10.1016/s0006-3495(95)80023-8","is_oa":true,"landing_page_url":"https://doi.org/10.1016/s0006-3495(95)80023-8","pdf_url":"https://doi.org/10.1016/s0006-3495(95)80023-8","source":{"id":"https://openalex.org/S98085912","display_name":"Biophysical Journal","issn_l":"0006-3495","issn":["0006-3495","1542-0086"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-a","jufo-2","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Biophysical Journal","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G2675061549","display_name":"ELECTROSTATIC INTERACTIONS IN DNA","funder_award_id":"R01GM041371","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1994418194.pdf"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W187801720","https://openalex.org/W1494727421","https://openalex.org/W1597842671","https://openalex.org/W1966497102","https://openalex.org/W1997639796","https://openalex.org/W1999005083","https://openalex.org/W2000403363","https://openalex.org/W2008264122","https://openalex.org/W2012250751","https://openalex.org/W2025056997","https://openalex.org/W2037945309","https://openalex.org/W2039545730","https://openalex.org/W2053960685","https://openalex.org/W2055352191","https://openalex.org/W2062810119","https://openalex.org/W2068217205","https://openalex.org/W2076465236","https://openalex.org/W2077157973","https://openalex.org/W2080016546","https://openalex.org/W2083624153","https://openalex.org/W2084896972","https://openalex.org/W2087709543","https://openalex.org/W2092070327","https://openalex.org/W2106315897","https://openalex.org/W2148327043","https://openalex.org/W2153839211","https://openalex.org/W2158709145","https://openalex.org/W2159951367"],"related_works":["https://openalex.org/W2092422214","https://openalex.org/W1963877241","https://openalex.org/W1555823491","https://openalex.org/W2440663665","https://openalex.org/W2913123156","https://openalex.org/W1983373190","https://openalex.org/W2887087857","https://openalex.org/W2083763849","https://openalex.org/W1967664531","https://openalex.org/W2338235333"],"abstract_inverted_index":{"This":[0,75],"paper":[1],"reports":[2],"a":[3,56],"theoretical":[4],"study":[5],"of":[6,38,52,68,82,92,109,126],"the":[7,25,61,65,80,89,98,104,123],"free":[8,44,128],"energy":[9,129],"contributions":[10],"to":[11,72],"nucleic":[12],"acid":[13],"base":[14],"stacking":[15,127],"in":[16,60,97],"aqueous":[17],"solution.":[18],"Electrostatic":[19],"interactions":[20,42,70,113],"are":[21,33],"treated":[22,34],"by":[23,79,115],"using":[24],"finite":[26],"difference":[27],"Poisson-Boltzmann":[28],"method":[29],"and":[30,107],"nonpolar":[31],"effects":[32],"with":[35],"explicit":[36],"calculation":[37],"van":[39,110],"der":[40,111],"Waals":[41,112],"and/or":[43],"energy-surface":[45],"area":[46],"relationships.":[47],"Although":[48],"for":[49],"some":[50],"pairs":[51],"bases":[53],"there":[54],"is":[55,71,77],"favorable":[57,83],"Coulombic":[58],"interaction":[59],"stacked":[62,99],"conformation,":[63],"generally":[64],"net":[66],"effect":[67,106],"electrostatic":[69,85],"oppose":[73],"stacking.":[74,118],"result":[76],"caused":[78,114],"loss":[81],"base-solvent":[84],"interactions,":[86,102],"that":[87],"accompany":[88],"partial":[90],"removal":[91],"polar":[93],"atoms":[94],"from":[95],"water":[96],"conformation.":[100],"Nonpolar":[101],"involving":[103],"hydrophobic":[105],"enhancement":[108],"close-packing,":[116],"drive":[117],"The":[119],"calculations":[120],"qualitatively":[121],"reproduce":[122],"experimental":[124],"dependence":[125],"on":[130],"purine-pyrimidine":[131],"composition.":[132]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":10},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":10},{"year":2018,"cited_by_count":7},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":10},{"year":2014,"cited_by_count":8},{"year":2013,"cited_by_count":8},{"year":2012,"cited_by_count":10}],"updated_date":"2026-11-06T12:05:46.655746","created_date":"2016-06-24T00:00:00"}
