{"doi":"10.1007/s00894-019-4080-x","title":"Molecular modeling and computational study of the chiral-dependent structures and properties of self-assembling diphenylalanine peptide nanotubes","abstract":null,"journal":"Journal of Molecular Modeling","year":2019,"id":588280,"datarank":0.8379000251164608,"base_score":3.5263605246161616,"endowment":3.5263605246161616,"self_citation_contribution":0.5289540786924243,"citation_network_contribution":0.3089459464240365,"self_endowment_contribution":0.5289540786924243,"citer_contribution":0.3089459464240365,"corpus_percentile":null,"corpus_rank":null,"citation_count":33,"citer_count":17,"citers_with_citation_signal":12,"citers_with_endowment":12,"datacite_reuse_total":1,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1504955,"name":"Pavel S. Zelenovskiy","orcid":null,"position":1,"is_corresponding":false},{"id":1504956,"name":"Alla S. Nuraeva","orcid":null,"position":2,"is_corresponding":false},{"id":1504888,"name":"Svitlana Kopyl","orcid":"0000-0003-3347-8628","position":3,"is_corresponding":false},{"id":1504957,"name":"Olga A. Zhulyabina","orcid":null,"position":4,"is_corresponding":false},{"id":1504958,"name":"Vsevolod A. Tverdislov","orcid":null,"position":5,"is_corresponding":false},{"id":1504884,"name":"Vladimir Bystrov","orcid":"0000-0003-1487-9469","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Molecular modeling and computational study of the chiral-dependent structures and properties of self-assembling diphenylalanine peptide nanotubes","abstract":"The structure and properties of diphenylalanine (FF) peptide nanotubes (PNT) based on phenylalanine were investigated by various molecular modeling methods. The main approach employed semi-empirical quantum-chemical methods (PM3 and AM1). Ab initio, density functional theory methods and molecular mechanical approaches were also used. Both model structures and structures extracted from experimental crystallographic databases obtained by X-ray methods were examined. A comparison of optimized model structures and structures obtained by natural self-assembly revealed important differences depending on chirality: D and L. In both the cases, the effect of chirality on the results of self-assembly of FF PNT was established: PNT based on the D-FF has large condensation energy E<sub>0</sub> in the transverse direction, and form thicker and shorter PNT bundles than those based on L-FF. A topological difference was established: model PNT were optimized into structures consisting of rings, while naturally self-assembled PNT consisted of helical turns. The latter nanotubes differed from the original L-FF and D-FF and formed helix structures of different chirality signs in accordance with the alternation rule of chirality due to macromolecule hierarchy. A topological transition between ring and helix turn PNT structures is discussed: self-assembled natural helix structures are favorable and their energy is lower by a value of the order of one to several eV.","is_dataset_classified":null,"base_score":3.5263605246161616,"endowment":3.5263605246161616,"datacite_reuse_total":1,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"31240406","pmcid":null,"openalex_id":"https://openalex.org/W2953620216","authors":[],"funders":[{"funder_name":"Russian Foundation for Basic Research","grant_id":"19-01-00519 А","title":null},{"funder_name":"Fundação para a Ciência e a Tecnologia, I.P.","grant_id":"UID/CTM/50011/2019","title":"CICECO-Aveiro Institute of Materials"},{"funder_name":"Fundação para a Ciência e a Tecnologia, I.P.","grant_id":"TUBITAK/0006/2014","title":"Phase transitions and ferroelectricity in self-assembled peptides nanotubes"},{"funder_name":"Fundação para a Ciência e a Tecnologia, I.P.","grant_id":"PTDC/QEQ-QAN/6373/2014","title":"Variable pressure solid-state NMR methods to study gas-surface interactions in nanoporous sorbent materials for industrial post/pre-combustion CO2 capture"},{"funder_name":"Fundação para a Ciência e a Tecnologia, I.P.","grant_id":"PTDC/CTM-CTM/31679/2017","title":"Development of novel piezoelectric materials based on nanostructured self-assembled peptides"}],"total_grants":5,"fwci":2.1479,"citation_percentile":0.86305,"influential_citations":0,"citation_trend":[{"year":2019,"count":2},{"year":2020,"count":9},{"year":2021,"count":7},{"year":2022,"count":7},{"year":2023,"count":1},{"year":2024,"count":4},{"year":2025,"count":1},{"year":2026,"count":2}],"oa_status":"closed","license":"Springer TDM","oa_locations":[{"url":"http://link.springer.com/content/pdf/10.1007/s00894-019-4080-x.pdf","host_type":"publisher"},{"url":"http://link.springer.com/article/10.1007/s00894-019-4080-x/fulltext.html","host_type":"publisher"},{"url":"https://doi.org/10.1007/s00894-019-4080-x","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/31240406","host_type":"repository"},{"url":"https://dx.doi.org/10.1007/s00894-019-4080-x","host_type":""}],"fields_of_study":["Supramolecular Self-Assembly in Materials","Polydiacetylene-based materials and applications","Chemical Synthesis and Analysis","02 engineering and technology","0210 nano-technology","01 natural sciences","0104 chemical sciences","Algorithms","Density Functional Theory","Dipeptides","Models, Molecular","Models, Theoretical","Molecular Conformation","Nanostructures","Nanotubes, Peptide","Phenylalanine"],"mesh_terms":["Density Functional Theory","Algorithms","Dipeptides","Models, Molecular","Models, Theoretical","Molecular Conformation","Phenylalanine","Nanotubes, Peptide","Nanostructures"],"keywords":["Chirality (physics)","Macromolecule","Helix (gastropod)","Ab initio","Self-assembly","Density functional theory","Materials science","Ab initio quantum chemistry methods","Computational chemistry","Crystallography","Topology (electrical circuits)","Chemical physics","Chemistry","Nanotechnology","Molecule","Physics","Quantum mechanics","Mathematics","Chiral symmetry","Organic chemistry","Molecular modeling","Topology","Molecular mechanics","Chirality","DFT","Semi-empirical methods","Peptide Nanotube","Diphenylalanine","Models, Molecular","Nanotubes, Peptide","Phenylalanine","Molecular Conformation","Dipeptides","Models, Theoretical","Algorithms","Nanostructures"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Affordable and clean energy"}],"linked_datasets":[{"doi":"10.5517/ccdc.csd.cc20702c","title":"CCDC 1853771: Experimental Crystal Structure Determination","publisher":"Cambridge Crystallographic Data Centre","resource_type":"Dataset"}],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-07-20T03:38:09.900644Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}