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Kıbrıs, Erman
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04.01. Department of Chemistry
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Scholarly Output
5
Articles
3
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2562/1202
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1
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1
WoS Citation Count
12
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11
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0
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2.40
Scopus Citations per Publication
2.20
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3
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2
| Journal | Count |
|---|---|
| Journal of Molecular Graphics & Modelling | 1 |
| Journal of Molecular Modeling | 1 |
| Talanta | 1 |
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5 results
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Article Citation - WoS: 6Citation - Scopus: 5Charmm Force Field Generation for a Cationic Thiophene Oligomer With Fftk(Springer, 2021) Kıbrıs, Erman; Elmacı Irmak, Nuran; Elmacı Irmak, Nuran; 04.01. Department of Chemistry; 04. Faculty of Science; 01. Izmir Institute of TechnologyIn 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: 6Citation - Scopus: 6A Novel 2-Aminophenalenone Fluorescent Probe Designed for Monitoring H2o2 for in Vitro and in Vivo Bioimaging(Elsevier, 2024) Saygılı, Ecem; Kıbrıs, Erman; Ersöz Gülseven, Esra; Kıbrıs, Erman; Çakan Akdoğan, Gülçin; Üçüncü, Muhammed; 04.01. Department of Chemistry; 04. Faculty of Science; 01. Izmir Institute of TechnologyA significant compound in living organisms, hydrogen peroxide (H2O2) plays a dual role as a signalling molecule in cellular communication and as a pivotal biomarker in assessing disease and oxidative stress. Thus, the detection of abnormal changes in H2O2 levels is essential to understanding its function and involvement in biological systems. The growing demand to meet the specific needs for applications, particularly in biological systems, has sharpened focus on highly sensitive, highly selective molecular sensors and, in turn, heightened interest in these diagnostic tools with innovative designs. In our study, 2-aminophenalenone (2-AP) was used for the first time as a fluorophore in a fluorescent probe. The 2-APB molecule obtained from the reaction of 2-AP with 4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl) benzyl chloroformate exhibited a highly selective and sensitive (i.e. 62 nM) detection profile for H2O2 compared with the other reactive oxygen species, anions, and metal cations. Moreover, offering naked-eye detection in aqueous solutions, 2-APB demonstrated excellent sensing performance, detection and real-time monitoring in relation to exogenous H2O2 in cells and endogenous H2O2 in zebrafish embryos. © 2024 Elsevier B.V.Article Molecular Dynamics Simulation of Ssdna and Cationic Polythiophene(Elsevier, 2023) Nalıncı Bardak, Nehir; Elmacı Irmak, Nuran; Kıbrıs, Erman; Kıbrıs, Erman; Demirci, Fethi Can; Elmacı Irmak, Nuran; 04.01. Department of Chemistry; 04. Faculty of Science; 01. Izmir Institute of TechnologyIn 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.Master Thesis Synthesis of Allyl Alcohols by Paladium-Catalyzed 1,3-Substitution Reactions of Alkenyl Epoxides With Organoborons(Izmir Institute of Technology, 2016) Kıbrıs, Erman; Kıbrıs, Erman; Artok, Levent; Artok, Levent; 04.01. Department of Chemistry; 04. Faculty of Science; 01. Izmir Institute of Technology1,3-Substitution reactions of allylic compounds having a good leaving group is a prominent method in Organic Chemistry for the synthesis of new allylic reagents with an exchanged functional group. These reactions usually require the use of metal catalysts and one of the most challenging aspects for these applications is the regio- and stereo-selectivity of the process for a wide range of substrate types. Other compounds such as vinyl epoxides are also acceptable for substitution reactions. An important advantage of using these reagents is that opening of the oxirane ring during the substitution process lead to the generation of a hydroxyl group and as a result affords allyl alcohols which are important intermediaries in organic syntheses. An example of regio-selective metal-catalyzed reactions of vinyl epoxides having a terminal alkenyl group with environmentally benign organoborons was reported in the literature. However, no such success could be achieved with vinyl epoxides with an internal alkenyl group. Therefore, within the context of this method internal vinyl epoxides were successfully subjected to 1,3-substitution reactions with organoborons which yielded arylated allyl alcohols in both a regio- and stereo-selective manner. The method is applicable under quite mild conditions where a palladium-AsPh3 combination is used to activate the process.Doctoral Thesis Molecular Modeling of Polyelectrolytes - Nucleotides / Nucleic Acids Interaction(01. Izmir Institute of Technology, 2022) Kıbrıs, Erman; Elmacı Irmak, Nuran; Elmacı Irmak, Nuran; 04.01. Department of Chemistry; 04. Faculty of Science; 01. Izmir Institute of TechnologyIn this thesis, poly- N, N, N-trimethyl-3-(4-methylthiophen-3-yl) oxy) propan-1-aminium force field parameters were generated via ffTK and CHARMM program to perform MD simulations. NBFIX parameters for the interactions of adenosine nucleotides and oligomer were also produced to improve simulations. The parameters were verified by comparing MM vs QM calculations, and simulated vs experimental UV/Vis spectra. Our results revealed that force field parameters obtained by CHARMM program can be applied successfully for the MD simulations of CPTs with different types of adenosine nucleotides (AMP, ADP, and ATP). Poly-(3-(2-((4-methylthiophen-3-yl) oxy) ethyl)-1-ethyl-4H-1λ4-imidazol-3-ium) and poly- N,N,N-trimethyl-6-((4-methylthiophen-3-yl) oxy) hexan-1-aminium are used for optical sensors, therefore parametrization and MD simulations for these compounds were performed to see the effect of nucleotides on the backbone structures of oligomers. Generally, increasing the phosphate group on nucleotides stretched out the backbone of structures, but the largest response was observed in the presence of ATP. The salt effect and temperature effect were also investigated on oligomer – nucleotide complexes. The increasing temperature shortened the backbone of the compounds, but not significant as experimentally. Addition of the monovalent or divalent cations do not affect linearity of oligomer structure in ATP medium for O3. However, O1 and O2 have a great respond to ATP with Mg2+, K+ and Ca2+ (most sensed) ions, O2 has almost no respond to ATP without these ions. Ca2+ is a key ion which regulates ATP production by mitochondria. O2 may take a part of a biosensor design to recognize ATP in the presence of Ca+2.