Please use this identifier to cite or link to this item: https://hdl.handle.net/11147/11389
Title: CHARMM force field generation for a cationic thiophene oligomer with ffTK
Authors: Kıbrıs, Erman
Nalıncı Barbak, Nehir
Elmacı Irmak, Nuran
Keywords: Polyelectrolyte
Polythiophene
Molecular dynamics simulation
ffTK
Publisher: Springer
Abstract: In 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.
URI: https://doi.org/10.1007/s00894-020-04610-2
https://hdl.handle.net/11147/11389
ISSN: 1610-2940
0948-5023
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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