{"id":"https://openalex.org/W2017370697","doi":"https://doi.org/10.1063/1.477819","title":"Calculation of conformational transitions and barriers in solvated systems: Application to the alanine dipeptide in water","display_name":"Calculation of conformational transitions and barriers in solvated systems: Application to the alanine dipeptide in water","publication_year":1999,"publication_date":"1999-01-22","ids":{"openalex":"https://openalex.org/W2017370697","doi":"https://doi.org/10.1063/1.477819","mag":"2017370697"},"language":"en","primary_location":{"id":"doi:10.1063/1.477819","doi":"https://doi.org/10.1063/1.477819","is_oa":false,"landing_page_url":"https://doi.org/10.1063/1.477819","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"},"parent_works":[],"lineage":["https://openalex.org/W2017370697"],"child_works_count":0,"type":"article","is_traditional":true,"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/A5068728134","display_name":"Joannis Apostolakis","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Joannis Apostolakis","raw_affiliation_strings":["Department of Biochemistry, University of Z\u00fcrich, Winterthurerstrasse 190, CH-8057\u200aZ\u00fcrich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, University of Z\u00fcrich, Winterthurerstrasse 190, CH-8057\u200aZ\u00fcrich, Switzerland","institution_ids":["https://openalex.org/I202697423"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030147129","display_name":"Philippe Ferrara","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Philippe Ferrara","raw_affiliation_strings":["Department of Biochemistry, University of Z\u00fcrich, Winterthurerstrasse 190, CH-8057\u200aZ\u00fcrich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, University of Z\u00fcrich, Winterthurerstrasse 190, CH-8057\u200aZ\u00fcrich, Switzerland","institution_ids":["https://openalex.org/I202697423"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035048768","display_name":"Amedeo Caflisch","orcid":"https://orcid.org/0000-0002-2317-6792","observed_orcids":["https://orcid.org/0000-0002-2317-6792"]},"institutions":[{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Amedeo Caflisch","raw_affiliation_strings":["Department of Biochemistry, University of Z\u00fcrich, Winterthurerstrasse 190, CH-8057\u200aZ\u00fcrich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, University of Z\u00fcrich, Winterthurerstrasse 190, CH-8057\u200aZ\u00fcrich, Switzerland","institution_ids":["https://openalex.org/I202697423"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I202697423"],"apc_list":{"value":3500,"currency":"USD","value_usd":3500},"apc_paid":null,"fwci":1.5323,"has_fulltext":false,"cited_by_count":217,"citation_normalized_percentile":{"value":0.81327376,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":93,"max":100},"biblio":{"volume":"110","issue":"4","first_page":"2099","last_page":"2108"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9682999849319458,"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":0.9682999849319458,"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":0.027400000020861626,"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":0.0017000000225380063,"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":0.9120000004768372},{"id":"https://openalex.org/keywords/conformational-change","display_name":"conformational change","score":0.8970000147819519},{"id":"https://openalex.org/keywords/free-energy-landscape","display_name":"free energy landscape","score":0.6309999823570251},{"id":"https://openalex.org/keywords/reaction-energy-barrier","display_name":"reaction barriers","score":0.7319999933242798},{"id":"https://openalex.org/keywords/solvation-effects","display_name":"solvation effects","score":0.6970000267028809},{"id":"https://openalex.org/keywords/potential-of-mean-force","display_name":"potential of mean force","score":0.8460000157356262},{"id":"https://openalex.org/keywords/reaction-coordinate","display_name":"reaction coordinate","score":0.5099999904632568},{"id":"https://openalex.org/keywords/targeted-molecular-dynamics","display_name":"targeted molecular dynamics","score":0.7710000276565552},{"id":"https://openalex.org/keywords/saddle-points","display_name":"saddle points","score":0.42500001192092896}],"concepts":[{"id":"https://openalex.org/C186633575","wikidata":"https://www.wikidata.org/wiki/Q845060","display_name":"Maxima and minima","level":2,"score":0.780992329120636},{"id":"https://openalex.org/C2779138802","wikidata":"https://www.wikidata.org/wiki/Q418602","display_name":"Dipeptide","level":3,"score":0.7384806871414185},{"id":"https://openalex.org/C109663097","wikidata":"https://www.wikidata.org/wiki/Q182453","display_name":"Adiabatic process","level":2,"score":0.6357548236846924},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.5545521974563599},{"id":"https://openalex.org/C84551667","wikidata":"https://www.wikidata.org/wiki/Q155640","display_name":"Potential energy","level":2,"score":0.5397025942802429},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.5197831988334656},{"id":"https://openalex.org/C119621388","wikidata":"https://www.wikidata.org/wiki/Q5377166","display_name":"Energy landscape","level":2,"score":0.5015869140625},{"id":"https://openalex.org/C10803110","wikidata":"https://www.wikidata.org/wiki/Q1341441","display_name":"Force field (fiction)","level":2,"score":0.4647260308265686},{"id":"https://openalex.org/C69308434","wikidata":"https://www.wikidata.org/wiki/Q5160266","display_name":"Conformational entropy","level":3,"score":0.436504989862442},{"id":"https://openalex.org/C14961307","wikidata":"https://www.wikidata.org/wiki/Q5377176","display_name":"Energy minimization","level":2,"score":0.4205317199230194},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3986453413963318},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.32169076800346375},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.3068450093269348},{"id":"https://openalex.org/C74650414","wikidata":"https://www.wikidata.org/wiki/Q11397","display_name":"Classical mechanics","level":1,"score":0.2828240692615509},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.2568047046661377},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.22012728452682495},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.21271201968193054},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.1390908658504486},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.11542865633964539},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1063/1.477819","doi":"https://doi.org/10.1063/1.477819","is_oa":false,"landing_page_url":"https://doi.org/10.1063/1.477819","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":[{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":25,"referenced_works":["https://openalex.org/W615417287","https://openalex.org/W1573009101","https://openalex.org/W1968184943","https://openalex.org/W1996886712","https://openalex.org/W2002957214","https://openalex.org/W2006869700","https://openalex.org/W2023472866","https://openalex.org/W2023634870","https://openalex.org/W2024487102","https://openalex.org/W2028231353","https://openalex.org/W2028702957","https://openalex.org/W2037050686","https://openalex.org/W2041090293","https://openalex.org/W2047730466","https://openalex.org/W2050863643","https://openalex.org/W2053096100","https://openalex.org/W2065101872","https://openalex.org/W2075502858","https://openalex.org/W2087223640","https://openalex.org/W2106140689","https://openalex.org/W2110043143","https://openalex.org/W2119773680","https://openalex.org/W2132465451","https://openalex.org/W2162166182","https://openalex.org/W2488677743"],"related_works":["https://openalex.org/W2010516507","https://openalex.org/W1970161521","https://openalex.org/W1968184943","https://openalex.org/W2045999460","https://openalex.org/W2020137114","https://openalex.org/W2011378420","https://openalex.org/W2074288620","https://openalex.org/W3023274239","https://openalex.org/W2323100538","https://openalex.org/W2119773680"],"abstract_inverted_index":{"Optimal":[0],"free":[1,20,268,292,334,364,371],"energy":[2,21,269,293,304,321,330,335,358,365,372],"paths":[3,83,94,98,171],"(OFEPs)":[4],"for":[5,44,58,134,233],"conformational":[6,108,235],"transitions":[7],"are":[8,29,41,56,118,123,129,142,184,256],"parallel":[9,30],"to":[10,25,31,80,196,200,212,230,287,312,369,374],"the":[11,19,32,36,54,59,82,92,96,102,105,113,127,135,149,152,155,160,176,179,182,190,194,202,205,214,218,222,234,244,264,267,272,279,291,295,300,302,306,314,317,320,324,328,332,340,344,347,350,353,356,363,370],"mean":[12,67,156],"force":[13,68],"at":[14,294],"every":[15],"nonstationary":[16],"point":[17],"of":[18,38,49,66,91,104,112,137,159,181,217,266,282,305,319,346,352,355],"landscape.":[22],"In":[23,51,151,204,275,299],"contrast":[24],"adiabatic":[26,97],"paths,":[27],"which":[28],"force,":[33],"OFEPs":[34,55,177],"include":[35],"effect":[37],"entropy":[39],"and":[40,71,126,178,316],"relevant":[42],"even":[43],"systems":[45],"with":[46,84,95,148,175,246,331,362],"diffusive":[47],"degrees":[48],"freedom.":[50],"this":[52],"study":[53],"computed":[57],"alanine":[60,114],"dipeptide":[61,115],"in":[62,99,116,140,251,323],"solution.":[63],"The":[64,89,110,169],"potential":[65,74],"is":[69,75,78,162,210,239,285,337],"calculated":[70,93,333],"an":[72,165],"effective":[73],"derived":[76],"that":[77,241,339],"used":[79,311],"obtain":[81],"a":[85,197,276],"minimization":[86],"based":[87],"algorithm.":[88],"comparison":[90],"vacuo":[100],"shows":[101],"influence":[103],"environment":[106],"on":[107,290],"transitions.":[109],"dynamics":[111,188],"water":[117,161],"more":[119,124],"complex,":[120],"since":[121],"there":[122],"minima":[125],"barriers":[128,183,322],"lower.":[130],"Two":[131],"simpler":[132],"methods":[133],"calculation":[136],"reaction":[138,248],"pathways":[139,255,284],"solution":[141],"evaluated":[143],"by":[144,164,225,242,263],"comparing":[145,327],"their":[146],"results":[147],"OFEPs.":[150],"first":[153,277],"method":[154],"electrostatic":[157],"field":[158],"approximated":[163],"analytical":[166],"continuum":[167],"model.":[168],"obtained":[170,219],"show":[172],"qualitative":[173],"agreement":[174],"height":[180,318,345],"similar.":[185],"Targeted":[186],"molecular":[187],"(TMD),":[189],"second":[191],"approach,":[192],"constrains":[193],"distance":[195],"target":[198],"conformation":[199],"accelerate":[201],"transition.":[203,236],"general":[206],"case,":[207],"however,":[208],"it":[209,238,336],"difficult":[211],"assess":[213],"physical":[215,280],"significance":[216,281],"paths.":[220],"Changing":[221],"initial":[223,273],"conditions":[224],"assigning":[226],"different":[227,231,247,254,283],"velocities":[228],"leads":[229],"solutions":[232],"Furthermore,":[237,349],"shown":[240,338],"performing":[243],"simulations":[245],"coordinates":[249],"or":[250],"opposite":[252],"directions":[253],"preferred.":[257],"This":[258],"result":[259],"can":[260],"be":[261],"explained":[262],"structure":[265],"landscape":[270],"around":[271],"conformations.":[274],"approximation":[278],"assumed":[286],"depend":[288],"mainly":[289],"highest":[296],"saddle":[297],"point.":[298],"literature":[301],"total":[303,329,357],"system":[307],"has":[308],"often":[309],"been":[310],"estimate":[313],"position":[315],"path.":[325],"By":[326],"former":[341],"largely":[342],"overestimates":[343],"barriers.":[348,366],"positions":[351],"maxima":[354],"do":[359],"not":[360],"coincide":[361],"Simple":[367],"approximations":[368],"lead":[373],"good":[375],"quantitative":[376],"agreement.":[377]},"counts_by_year":[{"year":2026,"cited_by_count":10},{"year":2025,"cited_by_count":13},{"year":2024,"cited_by_count":17},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":11},{"year":2013,"cited_by_count":7},{"year":2012,"cited_by_count":8}],"updated_date":"2026-11-10T11:39:43.021295","created_date":"2016-06-24T00:00:00"}