Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection

Permanent URI for this collectionhttps://hdl.handle.net/11147/7148

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Author: search.filters.author.Elmacı Irmak, Nuran

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  • Article
    Molecular Dynamics Simulation of Ssdna and Cationic Polythiophene
    (Elsevier, 2023) Nalıncı Bardak, Nehir; Kıbrıs, Erman; Demirci, Fethi Can; Elmacı Irmak, Nuran
    In this work, molecular dynamics simulations of complexes composed of single strand DNA (ssDNA) sequences and cationic oligothiophenes are performed to understand experimental findings and the sensing ability of polythiophene electrolytes toward ssDNA. The simulation results exhibit no significant structural effect for replacing the cationic amine moiety with imidazole derivative on the side group of the oligomer. Adding a homopurine strand elongates the oligomer backbone; on the contrary, mixing up the homopyrimidine strand causes compression. On the other hand, these ssDNAs do not notably affect the compactness of the oligomer backbones. The anion-cation interactions play an essential role in the structural and spectroscopic change of cationic polythiophenes (CPTs) upon complexation with ssDNAs. The red shift of CPTs in the UV-VIS spectra with the addition of homopurine strands might be explained by the strong anion-cation, weak pi -cation interactions, and high binding affinities. Nonpolar interactions (vdW and SA) and complex solvation energies dominate binding free energies. Hydrogen interaction analyses show that oligomers most likely approach the ssDNAs from their backbone upon complexation except for the duplex containing homopyrimidine strand and oligothiophene possessing imidazole derivative side chain.
  • Article
    Citation - WoS: 6
    Citation - Scopus: 5
    Charmm Force Field Generation for a Cationic Thiophene Oligomer With Fftk
    (Springer, 2021) Kıbrıs, Erman; Nalıncı Barbak, Nehir; Elmacı Irmak, Nuran
    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.
  • Article
    Citation - WoS: 18
    Citation - Scopus: 18
    A Computational Study on the Excited State Properties of a Cationic Cyanine Dye: Ttbc
    (Elsevier Ltd., 2011) Karaca, Sıla; Elmacı Irmak, Nuran; Elmacı, Nuran
    The ground and excited state behaviors of a biologically important mitochondria selective dye, 5,5',6,6'-tetrachloro-1,1',3,3'-tetraethyl-benzimidazolo carbocyanine (TTBC), were investigated in order to give useful information related to the enhancement of its electronic and optical properties. DFT and TDDFT levels of theory with different functionals and basis sets were used. The results obtained by using PBEPBE/6-31+G(d,p)/C-PCM are in good agreement with the experiments. The potential energy surface sections of TTBC were explored and the geometry optimized in the first excited state, S 1, to analyze the fluorescence spectrum of the dye. There are two distinct minima on the S 1 surface, one located near the ground state geometry and an energetically favorable twisted geometry, having a charge transfer character. The observation of similar ground and excited state dipoles as well as solvent-independent fluorescence and absorption wavelengths reveals that there is no competition between the two minima; the emission is dominantly coming from the more planar configuration.