{"id":"https://openalex.org/W2039680358","doi":"https://doi.org/10.1063/1.479860","title":"The alanine dipeptide free energy surface in solution","display_name":"The alanine dipeptide free energy surface in solution","publication_year":1999,"publication_date":"1999-09-22","ids":{"openalex":"https://openalex.org/W2039680358","doi":"https://doi.org/10.1063/1.479860","mag":"2039680358"},"language":"en","primary_location":{"id":"doi:10.1063/1.479860","doi":"https://doi.org/10.1063/1.479860","is_oa":false,"landing_page_url":"https://doi.org/10.1063/1.479860","pdf_url":null,"source":{"id":"https://openalex.org/S77047749","display_name":"The Journal of Chemical Physics","issn_l":"0021-9606","issn":["0021-9606","1089-7690","1520-9032"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-b","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310320257","host_organization_name":"American Institute of Physics","host_organization_lineage":["https://openalex.org/P4310320257"],"host_organization_lineage_names":["American Institute of Physics"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The Journal of Chemical Physics","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5091673051","display_name":"Paul E. Smith","orcid":"https://orcid.org/0000-0002-5565-3274","observed_orcids":["https://orcid.org/0000-0002-5565-3274"]},"institutions":[{"id":"https://openalex.org/I189590672","display_name":"Kansas State University","ror":"https://ror.org/05p1j8758","country_code":"US","type":"education","lineage":["https://openalex.org/I189590672"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Paul E. Smith","raw_affiliation_strings":["Department of Biochemistry, Kansas State University, Manhattan, Kansas 66506-3702"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Kansas State University, Manhattan, Kansas 66506-3702","institution_ids":["https://openalex.org/I189590672"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5091673051"],"corresponding_institution_ids":["https://openalex.org/I189590672"],"apc_list":{"value":3500,"currency":"USD","value_usd":3500},"apc_paid":null,"fwci":1.0337,"has_fulltext":false,"cited_by_count":130,"citation_normalized_percentile":{"value":0.7404681,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":99},"biblio":{"volume":"111","issue":"12","first_page":"5568","last_page":"5579"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9961000084877014,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9961000084877014,"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/T12044","display_name":"Advanced Physical and Chemical Molecular Interactions","score":0.002300000051036477,"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"}},{"id":"https://openalex.org/T10002","display_name":"Advanced Chemical Physics Studies","score":0.000699999975040555,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/alanine-dipeptide","display_name":"alanine dipeptide","score":1.0},{"id":"https://openalex.org/keywords/free-energy-landscape","display_name":"free energy landscape","score":0.9399999976158142},{"id":"https://openalex.org/keywords/solvation-models","display_name":"solvation models","score":0.7239999771118164},{"id":"https://openalex.org/keywords/explicit-solvent-model","display_name":"explicit solvent","score":0.7459999918937683},{"id":"https://openalex.org/keywords/tip3p-water-model","display_name":"TIP3P water model","score":0.6840000152587891},{"id":"https://openalex.org/keywords/helix-coil-transition","display_name":"helix-coil transition","score":0.8019999861717224},{"id":"https://openalex.org/keywords/polypeptide-chain-length","display_name":"polypeptide chain length","score":0.6549999713897705},{"id":"https://openalex.org/keywords/conformational-stability","display_name":"conformational stability","score":0.5799999833106995}],"concepts":[{"id":"https://openalex.org/C148093993","wikidata":"https://www.wikidata.org/wiki/Q739398","display_name":"Solvation","level":3,"score":0.8825050592422485},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.7880614995956421},{"id":"https://openalex.org/C2779138802","wikidata":"https://www.wikidata.org/wiki/Q418602","display_name":"Dipeptide","level":3,"score":0.7512595653533936},{"id":"https://openalex.org/C2779455329","wikidata":"https://www.wikidata.org/wiki/Q22908915","display_name":"Solvent models","level":4,"score":0.6719908118247986},{"id":"https://openalex.org/C75079739","wikidata":"https://www.wikidata.org/wiki/Q1571801","display_name":"Intramolecular force","level":2,"score":0.5984416604042053},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.5508584380149841},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.5403165817260742},{"id":"https://openalex.org/C64147673","wikidata":"https://www.wikidata.org/wiki/Q6007318","display_name":"Implicit solvation","level":4,"score":0.5034379363059998},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.4997687339782715},{"id":"https://openalex.org/C159467904","wikidata":"https://www.wikidata.org/wiki/Q2001702","display_name":"Chemical physics","level":1,"score":0.4496666193008423},{"id":"https://openalex.org/C132439834","wikidata":"https://www.wikidata.org/wiki/Q7559035","display_name":"Solvent effects","level":3,"score":0.44736480712890625},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.42385831475257874},{"id":"https://openalex.org/C99844830","wikidata":"https://www.wikidata.org/wiki/Q102441924","display_name":"Scaling","level":2,"score":0.4157339334487915},{"id":"https://openalex.org/C11072593","wikidata":"https://www.wikidata.org/wiki/Q3622068","display_name":"Accessible surface area","level":2,"score":0.4145182967185974},{"id":"https://openalex.org/C147789679","wikidata":"https://www.wikidata.org/wiki/Q11372","display_name":"Physical chemistry","level":1,"score":0.39855000376701355},{"id":"https://openalex.org/C2780471494","wikidata":"https://www.wikidata.org/wiki/Q146505","display_name":"Solvent","level":2,"score":0.3936651945114136},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.205147385597229},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.12911701202392578},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.12199869751930237},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.1137460470199585},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1063/1.479860","doi":"https://doi.org/10.1063/1.479860","is_oa":false,"landing_page_url":"https://doi.org/10.1063/1.479860","pdf_url":null,"source":{"id":"https://openalex.org/S77047749","display_name":"The Journal of Chemical Physics","issn_l":"0021-9606","issn":["0021-9606","1089-7690","1520-9032"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-b","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310320257","host_organization_name":"American Institute of Physics","host_organization_lineage":["https://openalex.org/P4310320257"],"host_organization_lineage_names":["American Institute of Physics"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The Journal of Chemical Physics","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":40,"referenced_works":["https://openalex.org/W1491642680","https://openalex.org/W1625910593","https://openalex.org/W1968673134","https://openalex.org/W1976499671","https://openalex.org/W1980381306","https://openalex.org/W1987615328","https://openalex.org/W1994941561","https://openalex.org/W1995938191","https://openalex.org/W1996886712","https://openalex.org/W1999479012","https://openalex.org/W2001611026","https://openalex.org/W2002957214","https://openalex.org/W2003984932","https://openalex.org/W2004151180","https://openalex.org/W2014237965","https://openalex.org/W2017370697","https://openalex.org/W2021000680","https://openalex.org/W2027408247","https://openalex.org/W2029325972","https://openalex.org/W2031504050","https://openalex.org/W2037274248","https://openalex.org/W2041090293","https://openalex.org/W2041902442","https://openalex.org/W2042744707","https://openalex.org/W2053096100","https://openalex.org/W2065965502","https://openalex.org/W2067299045","https://openalex.org/W2073623394","https://openalex.org/W2083863413","https://openalex.org/W2092144432","https://openalex.org/W2093595748","https://openalex.org/W2103734924","https://openalex.org/W2106140689","https://openalex.org/W2119773680","https://openalex.org/W2138132608","https://openalex.org/W2157081197","https://openalex.org/W2317136561","https://openalex.org/W2327367321","https://openalex.org/W2332674222","https://openalex.org/W4247951394"],"related_works":["https://openalex.org/W2021532988","https://openalex.org/W2956161633","https://openalex.org/W2095841883","https://openalex.org/W1982094285","https://openalex.org/W2011378420","https://openalex.org/W4255925422","https://openalex.org/W2033911044","https://openalex.org/W7099872049","https://openalex.org/W2763110045","https://openalex.org/W2032547472"],"abstract_inverted_index":{"Molecular":[0],"dynamics":[1],"(MD)":[2],"simulations":[3],"have":[4],"been":[5],"used":[6],"to":[7,88,139],"determine":[8],"the":[9,16,28,79,84,93,98,107,128,143],"two":[10],"dimensional":[11],"free":[12],"energy":[13],"surface":[14,126],"of":[15,34,42,57,142],"alanine":[17],"dipeptide":[18,23],"in":[19,73],"solution.":[20],"The":[21,123],"intramolecular":[22],"interactions":[24],"were":[25,36],"described":[26],"by":[27,49],"CHARMM22":[29],"force":[30],"field.":[31],"Three":[32],"models":[33,65,82],"solvation":[35,46,64],"considered;":[37],"(i)":[38],"a":[39],"simple":[40],"scaling":[41],"electrostatic":[43],"interactions,":[44],"(ii)":[45],"energies":[47],"determined":[48],"finite":[50],"difference":[51],"Poisson\u2013Boltzmann":[52],"calculations,":[53],"and":[54,114],"(iii)":[55],"inclusion":[56],"explicit":[58,94,124],"TIP3P":[59],"solvent":[60,95,125,144],"molecules.":[61],"All":[62],"three":[63],"produced":[66,127],"qualitatively":[67],"similar":[68],"effects,":[69],"but":[70],"differed":[71],"significantly":[72],"their":[74],"quantitative":[75],"values.":[76],"In":[77],"particular,":[78],"continuum":[80],"based":[81],"predicted":[83],"\u03b2":[85],"(extended)":[86],"conformation":[87],"be":[89],"most":[90],"stable,":[91],"whereas":[92],"model":[96],"favored":[97],"\u03b1R":[99],"(folded)":[100],"conformation.":[101],"Comparison":[102],"with":[103,131],"experimental":[104],"data":[105,138],"for":[106],"H\u2013N\u2013C\u03b1-H\u03b1":[108],"coupling":[109],"constant,":[110],"helix\u2013coil":[111],"transition":[112],"thermodynamics,":[113],"polypeptide":[115],"infinite":[116],"chain":[117],"length":[118],"characteristic":[119],"ratios":[120],"was":[121],"performed.":[122],"strongest":[129],"agreement":[130],"experiment,":[132],"although":[133],"there":[134],"is":[135],"no":[136],"unambiguous":[137],"support":[140],"any":[141],"models.":[145]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":8},{"year":2012,"cited_by_count":6}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-06-24T00:00:00"}