{"id":"https://openalex.org/W2151753618","doi":"https://doi.org/10.1002/jcc.20688","title":"Finding the transition state without initial guess: The growing string method for Newton trajectory to isomerization and enantiomerization reaction of alanine dipeptide and poly(15)alanine","display_name":"Finding the transition state without initial guess: The growing string method for Newton trajectory to isomerization and enantiomerization reaction of alanine dipeptide and poly(15)alanine","publication_year":2007,"publication_date":"2007-03-06","ids":{"openalex":"https://openalex.org/W2151753618","doi":"https://doi.org/10.1002/jcc.20688","mag":"2151753618","pmid":"https://pubmed.ncbi.nlm.nih.gov/17342714"},"language":"en","primary_location":{"id":"doi:10.1002/jcc.20688","is_oa":false,"landing_page_url":"https://doi.org/10.1002/jcc.20688","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,"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"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5059932944","display_name":"Wolfgang Quapp","orcid":"https://orcid.org/0000-0002-0366-1408"},"institutions":[{"id":"https://openalex.org/I926574661","display_name":"Leipzig University","ror":"https://ror.org/03s7gtk40","country_code":"DE","type":"education","lineage":["https://openalex.org/I926574661"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Wolfgang Quapp","raw_affiliation_strings":["Mathematical Institute, University of Leipzig, Augustus-Platz, D-04109 Leipzig, Germany. quapp@rz.uni-leipzig.de"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Mathematical Institute, University of Leipzig, Augustus-Platz, D-04109 Leipzig, Germany. quapp@rz.uni-leipzig.de","institution_ids":["https://openalex.org/I926574661"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5059932944"],"corresponding_institution_ids":["https://openalex.org/I926574661"],"apc_list":{"value":4840,"currency":"USD","value_usd":4840},"apc_paid":null,"fwci":1.538,"has_fulltext":false,"cited_by_count":33,"citation_normalized_percentile":{"value":0.81458733,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"28","issue":"11","first_page":"1834","last_page":"1847"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.9991999864578247,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.9991999864578247,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9980000257492065,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9972000122070312,"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/isomerization","display_name":"Isomerization","score":0.6657527089118958},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.6182327270507812},{"id":"https://openalex.org/keywords/transition-state","display_name":"Transition state","score":0.5827758312225342},{"id":"https://openalex.org/keywords/dipeptide","display_name":"Dipeptide","score":0.5758523941040039},{"id":"https://openalex.org/keywords/maxima-and-minima","display_name":"Maxima and minima","score":0.5162758231163025},{"id":"https://openalex.org/keywords/potential-energy-surface","display_name":"Potential energy surface","score":0.49033546447753906},{"id":"https://openalex.org/keywords/helix","display_name":"Helix (gastropod)","score":0.48692595958709717},{"id":"https://openalex.org/keywords/reaction-coordinate","display_name":"Reaction coordinate","score":0.4505855441093445},{"id":"https://openalex.org/keywords/string","display_name":"String (physics)","score":0.44006621837615967},{"id":"https://openalex.org/keywords/enantiomer","display_name":"Enantiomer","score":0.42055776715278625},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.4130042791366577},{"id":"https://openalex.org/keywords/curvilinear-coordinates","display_name":"Curvilinear coordinates","score":0.41272109746932983},{"id":"https://openalex.org/keywords/state","display_name":"State (computer science)","score":0.410064697265625},{"id":"https://openalex.org/keywords/crystallography","display_name":"Crystallography","score":0.3771964907646179},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.3269955515861511},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.2918877601623535},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.26843997836112976},{"id":"https://openalex.org/keywords/quantum-mechanics","display_name":"Quantum mechanics","score":0.20477339625358582},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.18824192881584167},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.15934333205223083},{"id":"https://openalex.org/keywords/mathematical-analysis","display_name":"Mathematical analysis","score":0.14319074153900146},{"id":"https://openalex.org/keywords/catalysis","display_name":"Catalysis","score":0.12984269857406616},{"id":"https://openalex.org/keywords/peptide","display_name":"Peptide","score":0.09187459945678711}],"concepts":[{"id":"https://openalex.org/C126661725","wikidata":"https://www.wikidata.org/wiki/Q903420","display_name":"Isomerization","level":3,"score":0.6657527089118958},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.6182327270507812},{"id":"https://openalex.org/C89031862","wikidata":"https://www.wikidata.org/wiki/Q906964","display_name":"Transition state","level":3,"score":0.5827758312225342},{"id":"https://openalex.org/C2779138802","wikidata":"https://www.wikidata.org/wiki/Q418602","display_name":"Dipeptide","level":3,"score":0.5758523941040039},{"id":"https://openalex.org/C186633575","wikidata":"https://www.wikidata.org/wiki/Q845060","display_name":"Maxima and minima","level":2,"score":0.5162758231163025},{"id":"https://openalex.org/C125277925","wikidata":"https://www.wikidata.org/wiki/Q2572687","display_name":"Potential energy surface","level":3,"score":0.49033546447753906},{"id":"https://openalex.org/C2778530040","wikidata":"https://www.wikidata.org/wiki/Q1937315","display_name":"Helix (gastropod)","level":3,"score":0.48692595958709717},{"id":"https://openalex.org/C18553476","wikidata":"https://www.wikidata.org/wiki/Q1076414","display_name":"Reaction coordinate","level":2,"score":0.4505855441093445},{"id":"https://openalex.org/C157486923","wikidata":"https://www.wikidata.org/wiki/Q1376436","display_name":"String (physics)","level":2,"score":0.44006621837615967},{"id":"https://openalex.org/C486523","wikidata":"https://www.wikidata.org/wiki/Q494483","display_name":"Enantiomer","level":2,"score":0.42055776715278625},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.4130042791366577},{"id":"https://openalex.org/C98343798","wikidata":"https://www.wikidata.org/wiki/Q1790208","display_name":"Curvilinear coordinates","level":2,"score":0.41272109746932983},{"id":"https://openalex.org/C48103436","wikidata":"https://www.wikidata.org/wiki/Q599031","display_name":"State (computer science)","level":2,"score":0.410064697265625},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.3771964907646179},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.3269955515861511},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.2918877601623535},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.26843997836112976},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.20477339625358582},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.18824192881584167},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.15934333205223083},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.14319074153900146},{"id":"https://openalex.org/C161790260","wikidata":"https://www.wikidata.org/wiki/Q82264","display_name":"Catalysis","level":2,"score":0.12984269857406616},{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.09187459945678711},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C2779965526","wikidata":"https://www.wikidata.org/wiki/Q308841","display_name":"Snail","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D004151","descriptor_name":"Dipeptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004151","descriptor_name":"Dipeptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004151","descriptor_name":"Dipeptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D007536","descriptor_name":"Isomerism","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007536","descriptor_name":"Isomerism","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007536","descriptor_name":"Isomerism","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D013237","descriptor_name":"Stereoisomerism","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013237","descriptor_name":"Stereoisomerism","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013237","descriptor_name":"Stereoisomerism","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1002/jcc.20688","is_oa":false,"landing_page_url":"https://doi.org/10.1002/jcc.20688","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,"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":"pmid:17342714","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17342714","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 computational chemistry","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Affordable and clean energy","score":0.8799999952316284,"id":"https://metadata.un.org/sdg/7"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":71,"referenced_works":["https://openalex.org/W1546896179","https://openalex.org/W1964836498","https://openalex.org/W1966293813","https://openalex.org/W1966577910","https://openalex.org/W1968429924","https://openalex.org/W1968674614","https://openalex.org/W1970334916","https://openalex.org/W1972685072","https://openalex.org/W1978842465","https://openalex.org/W1982497888","https://openalex.org/W1986614779","https://openalex.org/W1988675445","https://openalex.org/W1990198969","https://openalex.org/W1993018469","https://openalex.org/W1993045239","https://openalex.org/W1994834955","https://openalex.org/W1996636262","https://openalex.org/W1996765646","https://openalex.org/W1999009652","https://openalex.org/W2005865331","https://openalex.org/W2012379384","https://openalex.org/W2012383184","https://openalex.org/W2012947745","https://openalex.org/W2014606421","https://openalex.org/W2016926354","https://openalex.org/W2017284150","https://openalex.org/W2026215603","https://openalex.org/W2026232127","https://openalex.org/W2028344520","https://openalex.org/W2030177995","https://openalex.org/W2031430816","https://openalex.org/W2033197339","https://openalex.org/W2033396317","https://openalex.org/W2034278689","https://openalex.org/W2034357343","https://openalex.org/W2034478733","https://openalex.org/W2042588523","https://openalex.org/W2044846931","https://openalex.org/W2051434435","https://openalex.org/W2054453250","https://openalex.org/W2060075521","https://openalex.org/W2065248946","https://openalex.org/W2066084917","https://openalex.org/W2066549314","https://openalex.org/W2071075252","https://openalex.org/W2074101186","https://openalex.org/W2074274403","https://openalex.org/W2077340194","https://openalex.org/W2083232514","https://openalex.org/W2085053794","https://openalex.org/W2086849265","https://openalex.org/W2089981396","https://openalex.org/W2092123207","https://openalex.org/W2093330381","https://openalex.org/W2109455667","https://openalex.org/W2116582673","https://openalex.org/W2122946506","https://openalex.org/W2127040653","https://openalex.org/W2129055732","https://openalex.org/W2129206012","https://openalex.org/W2135173718","https://openalex.org/W2140992384","https://openalex.org/W2142506069","https://openalex.org/W2146346570","https://openalex.org/W2153579093","https://openalex.org/W2171755502","https://openalex.org/W2500587517","https://openalex.org/W3030345271","https://openalex.org/W3104575368","https://openalex.org/W3104767865","https://openalex.org/W4243372013"],"related_works":["https://openalex.org/W2076843374","https://openalex.org/W1499443070","https://openalex.org/W2053165901","https://openalex.org/W4224004747","https://openalex.org/W1980171958","https://openalex.org/W2359208223","https://openalex.org/W2070203645","https://openalex.org/W1993159871","https://openalex.org/W2032348035","https://openalex.org/W2031848957"],"abstract_inverted_index":{"We":[0],"report":[1],"a":[2,7,11,16,19,29,33,60,69,119,122,131],"new,":[3],"high-dimensional":[4],"application":[5,83],"of":[6,28,84,93,102,105,118,121,159,165,179,186],"method":[8,46,86],"for":[9],"finding":[10],"transition":[12,120],"state":[13],"(TS)":[14],"between":[15],"reactant":[17],"and":[18,112],"product":[20],"on":[21,59],"the":[22,26,44,79,85,91,94,103,115,135,140,145,152,166,171,177,183,187],"potential":[23],"energy":[24],"surface:":[25],"search":[27],"growing":[30,146],"string":[31,147],"along":[32,170],"reaction":[34,74],"path":[35],"defined":[36],"by":[37,68],"any":[38],"Newton":[39],"trajectory":[40],"in":[41,134],"combination":[42],"with":[43,151],"Berny":[45],"(Quapp,":[47],"J":[48],"Chem":[49],"Phys":[50],"(2005),":[51],"122,":[52],"174106;":[53],"we":[54],"have":[55],"provided":[56],"this":[57],"algorithm":[58],"web":[61],"page).":[62],"Two":[63],"given":[64],"minima":[65],"are":[66,168],"connected":[67],"one-dimensional,":[70],"but":[71],"usually":[72],"curvilinear":[73],"coordinate.":[75],"It":[76],"leads":[77],"to":[78,87,110],"TS":[80,92,116,172],"region.":[81],"The":[82,155],"alanine":[88],"dipeptide":[89],"finds":[90,114],"isomerisation":[95],"C(7":[96,106],"ax)":[97,107],"-->":[98],"C(5),":[99],"some":[100,160],"TSs":[101],"enantiomerisation":[104],"from":[108],"L-form":[109],"quasi-D-form,":[111],"it":[113],"region":[117],"partly":[123],"unfolded,":[124],"bent":[125],"structure":[126],"which":[127],"turns":[128],"back":[129],"into":[130],"mainly":[132],"alpha-helix":[133],"Ac(Ala)(15)NHMe":[136],"polyalanine":[137],"(all":[138],"at":[139,182],"quantum":[141],"mechanical":[142],"level":[143],"B3LYP/6-31G:":[144],"calculation":[148],"is":[149],"interfaced":[150],"Gaussian03":[153],"package).":[154],"formation":[156],"or":[157,162],"dissolvation":[158],"alpha-":[161],"3(10)-hydrogen":[163],"bonds":[164],"helix":[167],"discussed":[169],"pathway,":[173],"as":[174,176],"well":[175],"case":[178],"an":[180],"enantiomer":[181],"central":[184],"residue":[185],"helix.":[188]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":3},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}