Browsing by Author "Karatas, D"

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    Modeling of molecular interaction between catechol and tyrosinase by DFT
    Polatoglu, I; Karatas, D
    In this study, the synthetic active site model of tyrosinase enzyme's (His(3))(CuOHCu)-O-center dot center dot-Cu-center dot center dot(His(3)) arrangement is constituted by applying the density functional theory (DFT) to reveal the enzymatic conversion of catechol in molecular basis. This is the first time the binding mechanisms of catechol in relation to the enzyme active site (met-tyrosinase) in a vacuum environment, explicit water, and solvent (ethanol, acetone)/water mixture have been studied using the DFT. The theoretical results are supported along with the experimental ones to clarify the structure-activity relationship in these models. As understood from the mechanisms, the initial H abstraction from catechol is the most probable rate-limiting step. The parameters that cause the copper region to become congested or comfortable for H abstraction, such as the ordered structure of water molecules, Cu-Cu distance, H-bond distance, orientation and conformation of histidine residues around the copper center, and electrostatic potential of the system, play a significant role in the catechol/met-tyrosinase interaction. (C) 2019 Elsevier B.V. All rights reserved.
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    Adsorption mechanism of HTAB-octanol mixture onto silica sensor by QCM-D and MD simulation
    Karatas, D; Can, MF; Karaguzel, C; Çelik, MS; Xu, ZH
    Adsorption of a mixture of cationic surfactant, Hexadecyl Trimetehyleammonium Bromide (HTAB) and octanol on silica surface has been studied at various surfactant and octanol concentrations by QCM-D (Quartz Crystal Microbalance with Dissipation monitoring) and Molecular Dynamics (MD) simulations. In the QCM-D studies, frequency, and dissipation values with HTAB alone gradually and significantly increased from -2 to -18 Hz and 0.18 x 10-6 to 1.2 x 10-6, respectively. However, addition of octanol to HTAB was shown to achieve better adsorption properties due to the co-adsorption effect. The frequency values with increasing octanol concentrations at constant HTAB concentration of 5 x 10-4 M raised them to -10 to -20 Hz with the favorable help of hydrophobic forces. Dissipation values, on the other hand, were significantly improved in the presence of alcohol due to chain length contribution. In addition, increase in contact angle values with increasing octanol concentration at constant HTAB concentration supports the QCM-D results. Experimental studies were then corroborated by Molecular Dynamics (MD) simulations to clarify morphological and structural properties of surfactant in the presence and absence of octanol. MD simulations demonstrated that interaction of HTAB with the silica surface is much more conducive due to the presence of octanol in the medium.
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    Demonstration of Interaction between Carbapenem Group Antibiotics and Different Immunosuppressant Drugs by Molecular Docking
    Karatas, D; Gonel, A; Koyuncu, I; Temiz, E; Egi, K; Durgun, M; Akmese, S; Caglayan, M
    Background It has been shown that drugs used parenterally cause errors in immunosuppressant concentrations measured by LC-MS / MS method. It is yet unknown whether this measurement error is due to drug-drug interaction or analytical interference.Objective The aim of this study is to investigate the possible interaction and inhibition concentrations of broad-spectrum antibiotics (ertapenem, meropenem, imipenem) with 4 different immunosuppressants (tacrolimus, sirolimus, everolimus, cyclosporine A) by molecular docking.Methods The docking results of ertapenem, meropenem, and imipenem-cilastatin drugs, which are frequently used in intensive care units and wards, were analyzed with the Autodock 4.2 program. Binding energy levels and inhibition concentrations were recorded.Results The highest binding energies of the most stable conformations, providing the best compatibility among the active ingredients, belong to cilastatin. The interaction energy of cilastatin with sirolimus in 320 conformations was calculated as -4.08 kcal/mol. Sirolimus interacted with ertapenem at -3.43, imipenem at -2.53, and meropenem at -3.84 kcal/mol. According to these values, the receptor, which is the most compatible host with all ligand molecules, is sirolimus. The least interaction energy value was calculated between cyclosporine and imipenem (-1.12 kcal / mol).Conclusion Concerning the most stable conformations of models docked with Autodock tools, it has been determined that carbapenems interact with immunosuppressants. Since the detected inhibition concentration levels can be seen in blood samples taken immediately after carbapenem injection, immunosuppressant measurement is recommended before the use of carbapenem in immunosuppressant monitoring of transplant patients.
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    Interfacial synergy of pre-lithiation silicon anodes and GNP/MnO2/S cathodes for lithium polysulfides in silicon-sulfur batteries studied via DFT
    Aslfattahi, N; Kiai, MS; Karatas, D; Baydogan, N; Samylingam, L; Kadirgama, K; Kok, CK
    The development of innovative electrodes with outstanding high-rate cycling performance for the next generation of sulfur-based batteries has emerged as a key area of research. This study presents a straightforward approach for designing silicon/graphene nanoplates as an anode material using a one-step hydrothermal process. Additionally, to reduce the shuttle effect, the GNP/MnO2/S cathode is investigated. In this study, MnO2 particles are grown in situ on the surface of the GNP. The pre-lithiation Si/GNP anode and the MnO2/GNP/S and GNP/S cathodes are evaluated at a current density of 1000 mA g-1. The findings reveal an impressive capacity retention of 1048 mA h g-1 after 200 cycles, indicating remarkable cycling performance for the cell with the pre-lithiation Si/GNP anode and the MnO2/GNP/S cathode. The capacity retention observed in thicker electrodes highlights the synergistic effect of the effective chemical absorption of lithium polysulfides by MnO2/GNP/S when used as sulfur hosts. Additionally, DFT calculations suggest that MnO2 has a significant tendency to adhere to the surface of polysulfides, aligning well with our findings regarding cycle performance, rate performance, and discharge capacity. The novel electrode configuration introduced in this study provides a novel pathway for the large-scale production of high-performance pre-lithiation Si-S batteries.
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    The Development and Experimental Analysis of Freestanding Single-Walled Carbon Nanotube/Sulfur Composite Cathode for the Next Generation of Sulfur-Based Batteries
    Kiai, MS; Aslfattahi, N; Karatas, D; Baydogan, N; Samylingam, L; Kadirgama, K; Kok, CK
    This work uses a solution-based and scalable method to provide a freestanding single-walled carbon nanotube (SWCNT)/S cathode in both Li-S and Na-S batteries. SWCNTs with high conductivity and surface area can enhance the cathode flexibility. The incorporation of oxygen and sulfur bonds can enhance active redox sites for chemical adsorption. Sulfur and oxygen effectively hinder the shuttle effect by improving chemical interactions between the polysulfides and the nonpolar carbon framework, leading to improved cyclability of Na-S and Li-S cells. The cycling stability plots of Na-S and Li-S batteries with freestanding SWCNT/S as a cathode are investigated for 150 cycles at a high current density of 1000 mA g-1. Both cells display a stable capacity behavior during cycling. The discharge capacity of the Li-S cell with the SWCNT/S cathode is retained at 978.2 mAh g-1 while the Na-S cell only shows the capacity retention of 769.4 mAh g-1 after 150 cycles. Coulombic efficiencies of approximate to 94% and 90% are observed for Li-S and Na-S cells respectively. Therefore, the SWCNT/S cathode in both Li-S and Na-S batteries hinders the polysulfide shuttle, providing high electrolyte diffusion, resulting in improved active material reutilization and minimized capacity fading. Freestanding SWCNT/S cathode can enhance cycling stability over long-term cycling and is proved to be a promising cathode in both Li-S and Na-S batteries.