Influence of the environment on the infrared spectrum of alanine: An effective mode analysis
The vibrational spectrum of the alanine amino acid was computationally determined in the infrared range 1000–2000 cm−1, under various environments encompassing the gas, hydrated, and crystalline phases, by means of classical molecular dynamics trajectories, carried out with the Atomic Multipole Opti...
Gespeichert in:
Veröffentlicht in: | The Journal of chemical physics 2023-03, Vol.158 (9), p.094305-094305 |
---|---|
Hauptverfasser: | , , , , , |
Format: | Artikel |
Sprache: | eng |
Schlagworte: | |
Online-Zugang: | Volltext |
Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
container_end_page | 094305 |
---|---|
container_issue | 9 |
container_start_page | 094305 |
container_title | The Journal of chemical physics |
container_volume | 158 |
creator | Bowles, Jessica Jähnigen, Sascha Vuilleumier, Rodolphe Calvo, Florent Clavaguéra, Carine Agostini, Federica |
description | The vibrational spectrum of the alanine amino acid was computationally determined in the infrared range 1000–2000 cm−1, under various environments encompassing the gas, hydrated, and crystalline phases, by means of classical molecular dynamics trajectories, carried out with the Atomic Multipole Optimized Energetics for Biomolecular Simulation polarizable force field. An effective mode analysis was performed, in which the spectra are optimally decomposed into different absorption bands arising from well-defined internal modes. In the gas phase, this analysis allows us to unravel the significant differences between the spectra obtained for the neutral and zwitterionic forms of alanine. In condensed phases, the method provides invaluable insight into the molecular origins of the vibrational bands and further shows that peaks with similar positions can be traced to rather different molecular motions. |
doi_str_mv | 10.1063/5.0135608 |
format | Article |
fullrecord | <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_pubmed_primary_36889973</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>2785200651</sourcerecordid><originalsourceid>FETCH-LOGICAL-c418t-f758f9ef4b7089de6c63bc190d5ebd97fea8c095b3552b8f87dca67b8d6311033</originalsourceid><addsrcrecordid>eNp90E1LHTEYBeAgFr21LvoHJOCmLYx9M7n5cifSD0Hopt0VhkzyhkZmkmsyc8F_39F7tdBCV4Hk4eRwCHnL4IKB5B_FBTAuJOgDsmKgTaOkgUOyAmhZYyTIY_K61jsAYKpdH5FjLrU2RvEV-XmTwjBjckhzoNMvpJi2seQ0YppoTk9XMYViC3paN-imMo-P1g42xYSX9CpRDGF5iFukY_ZIbbLDQ431DXkV7FDxdH-ekB-fP32__trcfvtyc31127g101MTlNDBYFj3ainvUTrJe8cMeIG9Nyqg1Q6M6LkQba-DVt5ZqXrtJWcMOD8h73a5m5LvZ6xTN8bqcFgaYp5r1yotWgAp2ELP_6J3eS5L3ycFxkjOzaLe75QrudaCoduUONry0DHoHifvRLeffLFn-8S5H9G_yOeNF_BhB6qLk51iTi9mm8ufpG7jw__wv1__BixMlxQ</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2780996339</pqid></control><display><type>article</type><title>Influence of the environment on the infrared spectrum of alanine: An effective mode analysis</title><source>AIP Journals Complete</source><source>Alma/SFX Local Collection</source><creator>Bowles, Jessica ; Jähnigen, Sascha ; Vuilleumier, Rodolphe ; Calvo, Florent ; Clavaguéra, Carine ; Agostini, Federica</creator><creatorcontrib>Bowles, Jessica ; Jähnigen, Sascha ; Vuilleumier, Rodolphe ; Calvo, Florent ; Clavaguéra, Carine ; Agostini, Federica</creatorcontrib><description>The vibrational spectrum of the alanine amino acid was computationally determined in the infrared range 1000–2000 cm−1, under various environments encompassing the gas, hydrated, and crystalline phases, by means of classical molecular dynamics trajectories, carried out with the Atomic Multipole Optimized Energetics for Biomolecular Simulation polarizable force field. An effective mode analysis was performed, in which the spectra are optimally decomposed into different absorption bands arising from well-defined internal modes. In the gas phase, this analysis allows us to unravel the significant differences between the spectra obtained for the neutral and zwitterionic forms of alanine. In condensed phases, the method provides invaluable insight into the molecular origins of the vibrational bands and further shows that peaks with similar positions can be traced to rather different molecular motions.</description><identifier>ISSN: 0021-9606</identifier><identifier>EISSN: 1089-7690</identifier><identifier>DOI: 10.1063/5.0135608</identifier><identifier>PMID: 36889973</identifier><identifier>CODEN: JCPSA6</identifier><language>eng</language><publisher>United States: American Institute of Physics</publisher><subject>Absorption spectra ; Alanine ; Amino acids ; Infrared analysis ; Molecular dynamics ; Multipoles ; Physics ; Vapor phases ; Vibrational spectra</subject><ispartof>The Journal of chemical physics, 2023-03, Vol.158 (9), p.094305-094305</ispartof><rights>Author(s)</rights><rights>2023 Author(s). Published under an exclusive license by AIP Publishing.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c418t-f758f9ef4b7089de6c63bc190d5ebd97fea8c095b3552b8f87dca67b8d6311033</citedby><cites>FETCH-LOGICAL-c418t-f758f9ef4b7089de6c63bc190d5ebd97fea8c095b3552b8f87dca67b8d6311033</cites><orcidid>0000-0002-3621-3046 ; 0000-0001-6186-9955 ; 0000-0002-2480-3313 ; 0000-0003-2951-4964 ; 0000-0001-5531-2333 ; 0000-0001-5386-699X</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://pubs.aip.org/jcp/article-lookup/doi/10.1063/5.0135608$$EHTML$$P50$$Gscitation$$H</linktohtml><link.rule.ids>314,780,784,794,4509,27922,27923,76154</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/36889973$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Bowles, Jessica</creatorcontrib><creatorcontrib>Jähnigen, Sascha</creatorcontrib><creatorcontrib>Vuilleumier, Rodolphe</creatorcontrib><creatorcontrib>Calvo, Florent</creatorcontrib><creatorcontrib>Clavaguéra, Carine</creatorcontrib><creatorcontrib>Agostini, Federica</creatorcontrib><title>Influence of the environment on the infrared spectrum of alanine: An effective mode analysis</title><title>The Journal of chemical physics</title><addtitle>J Chem Phys</addtitle><description>The vibrational spectrum of the alanine amino acid was computationally determined in the infrared range 1000–2000 cm−1, under various environments encompassing the gas, hydrated, and crystalline phases, by means of classical molecular dynamics trajectories, carried out with the Atomic Multipole Optimized Energetics for Biomolecular Simulation polarizable force field. An effective mode analysis was performed, in which the spectra are optimally decomposed into different absorption bands arising from well-defined internal modes. In the gas phase, this analysis allows us to unravel the significant differences between the spectra obtained for the neutral and zwitterionic forms of alanine. In condensed phases, the method provides invaluable insight into the molecular origins of the vibrational bands and further shows that peaks with similar positions can be traced to rather different molecular motions.</description><subject>Absorption spectra</subject><subject>Alanine</subject><subject>Amino acids</subject><subject>Infrared analysis</subject><subject>Molecular dynamics</subject><subject>Multipoles</subject><subject>Physics</subject><subject>Vapor phases</subject><subject>Vibrational spectra</subject><issn>0021-9606</issn><issn>1089-7690</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2023</creationdate><recordtype>article</recordtype><recordid>eNp90E1LHTEYBeAgFr21LvoHJOCmLYx9M7n5cifSD0Hopt0VhkzyhkZmkmsyc8F_39F7tdBCV4Hk4eRwCHnL4IKB5B_FBTAuJOgDsmKgTaOkgUOyAmhZYyTIY_K61jsAYKpdH5FjLrU2RvEV-XmTwjBjckhzoNMvpJi2seQ0YppoTk9XMYViC3paN-imMo-P1g42xYSX9CpRDGF5iFukY_ZIbbLDQ431DXkV7FDxdH-ekB-fP32__trcfvtyc31127g101MTlNDBYFj3ainvUTrJe8cMeIG9Nyqg1Q6M6LkQba-DVt5ZqXrtJWcMOD8h73a5m5LvZ6xTN8bqcFgaYp5r1yotWgAp2ELP_6J3eS5L3ycFxkjOzaLe75QrudaCoduUONry0DHoHifvRLeffLFn-8S5H9G_yOeNF_BhB6qLk51iTi9mm8ufpG7jw__wv1__BixMlxQ</recordid><startdate>20230307</startdate><enddate>20230307</enddate><creator>Bowles, Jessica</creator><creator>Jähnigen, Sascha</creator><creator>Vuilleumier, Rodolphe</creator><creator>Calvo, Florent</creator><creator>Clavaguéra, Carine</creator><creator>Agostini, Federica</creator><general>American Institute of Physics</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>8FD</scope><scope>H8D</scope><scope>L7M</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-3621-3046</orcidid><orcidid>https://orcid.org/0000-0001-6186-9955</orcidid><orcidid>https://orcid.org/0000-0002-2480-3313</orcidid><orcidid>https://orcid.org/0000-0003-2951-4964</orcidid><orcidid>https://orcid.org/0000-0001-5531-2333</orcidid><orcidid>https://orcid.org/0000-0001-5386-699X</orcidid></search><sort><creationdate>20230307</creationdate><title>Influence of the environment on the infrared spectrum of alanine: An effective mode analysis</title><author>Bowles, Jessica ; Jähnigen, Sascha ; Vuilleumier, Rodolphe ; Calvo, Florent ; Clavaguéra, Carine ; Agostini, Federica</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c418t-f758f9ef4b7089de6c63bc190d5ebd97fea8c095b3552b8f87dca67b8d6311033</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><topic>Absorption spectra</topic><topic>Alanine</topic><topic>Amino acids</topic><topic>Infrared analysis</topic><topic>Molecular dynamics</topic><topic>Multipoles</topic><topic>Physics</topic><topic>Vapor phases</topic><topic>Vibrational spectra</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Bowles, Jessica</creatorcontrib><creatorcontrib>Jähnigen, Sascha</creatorcontrib><creatorcontrib>Vuilleumier, Rodolphe</creatorcontrib><creatorcontrib>Calvo, Florent</creatorcontrib><creatorcontrib>Clavaguéra, Carine</creatorcontrib><creatorcontrib>Agostini, Federica</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>Technology Research Database</collection><collection>Aerospace Database</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>MEDLINE - Academic</collection><jtitle>The Journal of chemical physics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Bowles, Jessica</au><au>Jähnigen, Sascha</au><au>Vuilleumier, Rodolphe</au><au>Calvo, Florent</au><au>Clavaguéra, Carine</au><au>Agostini, Federica</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Influence of the environment on the infrared spectrum of alanine: An effective mode analysis</atitle><jtitle>The Journal of chemical physics</jtitle><addtitle>J Chem Phys</addtitle><date>2023-03-07</date><risdate>2023</risdate><volume>158</volume><issue>9</issue><spage>094305</spage><epage>094305</epage><pages>094305-094305</pages><issn>0021-9606</issn><eissn>1089-7690</eissn><coden>JCPSA6</coden><abstract>The vibrational spectrum of the alanine amino acid was computationally determined in the infrared range 1000–2000 cm−1, under various environments encompassing the gas, hydrated, and crystalline phases, by means of classical molecular dynamics trajectories, carried out with the Atomic Multipole Optimized Energetics for Biomolecular Simulation polarizable force field. An effective mode analysis was performed, in which the spectra are optimally decomposed into different absorption bands arising from well-defined internal modes. In the gas phase, this analysis allows us to unravel the significant differences between the spectra obtained for the neutral and zwitterionic forms of alanine. In condensed phases, the method provides invaluable insight into the molecular origins of the vibrational bands and further shows that peaks with similar positions can be traced to rather different molecular motions.</abstract><cop>United States</cop><pub>American Institute of Physics</pub><pmid>36889973</pmid><doi>10.1063/5.0135608</doi><tpages>12</tpages><orcidid>https://orcid.org/0000-0002-3621-3046</orcidid><orcidid>https://orcid.org/0000-0001-6186-9955</orcidid><orcidid>https://orcid.org/0000-0002-2480-3313</orcidid><orcidid>https://orcid.org/0000-0003-2951-4964</orcidid><orcidid>https://orcid.org/0000-0001-5531-2333</orcidid><orcidid>https://orcid.org/0000-0001-5386-699X</orcidid><oa>free_for_read</oa></addata></record> |
fulltext | fulltext |
identifier | ISSN: 0021-9606 |
ispartof | The Journal of chemical physics, 2023-03, Vol.158 (9), p.094305-094305 |
issn | 0021-9606 1089-7690 |
language | eng |
recordid | cdi_pubmed_primary_36889973 |
source | AIP Journals Complete; Alma/SFX Local Collection |
subjects | Absorption spectra Alanine Amino acids Infrared analysis Molecular dynamics Multipoles Physics Vapor phases Vibrational spectra |
title | Influence of the environment on the infrared spectrum of alanine: An effective mode analysis |
url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-13T13%3A27%3A23IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_pubme&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Influence%20of%20the%20environment%20on%20the%20infrared%20spectrum%20of%20alanine:%20An%20effective%20mode%20analysis&rft.jtitle=The%20Journal%20of%20chemical%20physics&rft.au=Bowles,%20Jessica&rft.date=2023-03-07&rft.volume=158&rft.issue=9&rft.spage=094305&rft.epage=094305&rft.pages=094305-094305&rft.issn=0021-9606&rft.eissn=1089-7690&rft.coden=JCPSA6&rft_id=info:doi/10.1063/5.0135608&rft_dat=%3Cproquest_pubme%3E2785200651%3C/proquest_pubme%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2780996339&rft_id=info:pmid/36889973&rfr_iscdi=true |