Please use this identifier to cite or link to this item: https://hdl.handle.net/11147/11389
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dc.contributor.authorKıbrıs, Erman-
dc.contributor.authorNalıncı Barbak, Nehir-
dc.contributor.authorElmacı Irmak, Nuran-
dc.date.accessioned2021-11-06T09:48:28Z-
dc.date.available2021-11-06T09:48:28Z-
dc.date.issued2021-
dc.identifier.issn1610-2940-
dc.identifier.issn0948-5023-
dc.identifier.urihttps://doi.org/10.1007/s00894-020-04610-2-
dc.identifier.urihttps://hdl.handle.net/11147/11389-
dc.description.abstractIn the present work, CHARMM force field parameters are generated for a cationic oligomer of N, N, N-trimethyl-3-(4-methylthiophen-3-yl) oxy) propan-1-aminium) which has the potential for sensing biological molecules such as nucleic acids, nucleobases. We have used ffTK (force field tool kit) to obtain potential parameters. MD simulations are performed for 20-mer and its complexes with AMP and ATP. The simulation results are analyzed to see the number of phosphates in adenosine nucleotides effects on the structure of the backbone of oligomer. The UV-VIS calculations for the conformers which possess the most probable radius of gyration are carried out and compared to the experimental ones to validate the generated force field. Recent studies have shown that, biologically important anions (ATP, AMP, vb.) change the spectroscopic properties of cationic polythiophenes (CPT) in the solutions. This work aims to generate CHARMM compatible force field parameters for a CPT to explain experimental studies. The type of interactions will be investigated deeply to lead new biosensor studies by examining the formation and the structure of complexes that consist of a oligothiophene and biological molecules, ATP, AMP by molecular dynamic simulations.en_US
dc.description.sponsorshipThis work was supported by the Scientific and Technological Research Council of Turkey, TUBITAK, under the project numbers 119Z100.en_US
dc.language.isoenen_US
dc.publisherSpringeren_US
dc.relation.ispartofJournal of Molecular Modelingen_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.subjectPolyelectrolyteen_US
dc.subjectPolythiopheneen_US
dc.subjectMolecular dynamics simulationen_US
dc.subjectffTKen_US
dc.titleCHARMM force field generation for a cationic thiophene oligomer with ffTKen_US
dc.typeArticleen_US
dc.authorid0000-0002-9450-2436-
dc.departmentİzmir Institute of Technology. Chemistryen_US
dc.identifier.volume27en_US
dc.identifier.issue2en_US
dc.identifier.wosWOS:000608368300001en_US
dc.identifier.scopus2-s2.0-85098932478en_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.identifier.doi10.1007/s00894-020-04610-2-
dc.identifier.pmid33420831en_US
dc.authorwosidELMACI IRMAK, NURAN/B-6368-2012-
dc.identifier.wosqualityQ3-
dc.identifier.scopusqualityQ3-
item.grantfulltextopen-
item.openairetypeArticle-
item.languageiso639-1en-
item.cerifentitytypePublications-
item.fulltextWith Fulltext-
item.openairecristypehttp://purl.org/coar/resource_type/c_18cf-
crisitem.author.dept04.01. Department of Chemistry-
Appears in Collections:Chemistry / Kimya
PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
WoS İndeksli Yayınlar Koleksiyonu / WoS Indexed Publications Collection
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