Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Article Citation - WoS: 5Citation - Scopus: 5Thickness-Dependent Piezoelecticity of Black Arsenic From Few-Layer To Monolayer(Elsevier, 2023) Akgenç Hanedar, Berna; Ersan, Fatih; Altalhi, Tariq; Yağmurcukardeş, Mehmet; Yakobson, BorisUltra-thin forms of black phosphorus (b-P) have been widely investigated due to its unique properties arising from the in-plane anisotropy in its crystal structure. Recently, two-dimensional (2D) forms of black arsenic (b-As) have also been added to the 2D family. In this study, the thickness-dependent structural, electronic, and piezoelectric properties of layered b-As are investigated by means of ab-initio calculations. The structural optimizations confirm the van der Waals type layered structure for both these structures. In addition, increasing the thickness is shown to result in the decreasing of the band gap arising from the confinement of electrons in the layers. In contrast to the case of b-P, it is revealed that a transition from indirect-to-direct band gap behavior can be found in b-As which can be important for optically identifying the single-layer structure. Moreover, the piezoelectric properties are investigated as a function of the number of layers. It is shown that while a single-layer of b-As does not exhibit piezoelectric features, even in the case of bilayer structures the piezoelectricity is created. Our results revealed the strong in-plane anisotropy in piezoelectric coefficients for the three-layer and thicker structures. We have shown that the out-of-plane piezoelectric properties can be achieved by non-centrosymmetric features in the out-of-plane direction in thicker structures of b-As.Article Citation - WoS: 6Citation - Scopus: 6Investigation of Interactions of Doxorubicin With Purine Nucleobases by Molecular Modeling(Springer, 2022) Akdeniz, Esra Şahin; Selçuki, CenkDoxorubicin, an anthracycline antibiotic with anti-tumor activity, is produced by the bacterium Streptomyces peucetius. The interactions between doxorubicin and genetic material and the details of the intercalation with DNA have been controversial issues. Thus, the interactions of doxorubicin with purine nucleobases were studied by quantum mechanical methods. Initially, conformer analyses of doxorubicin were performed with Spartan 08 software and 319 different conformers from 422 initial structures for doxorubicin were obtained. Geometry optimizations and frequency analyses were performed for each structure using density functional theory (DFT) at B3LYP/6-31G** level using Gaussian 09 software. The most stable 20 conformers of doxorubicin and tautomers of purine nucleobases were optimized again with ɷB97XD/6-31G** level and their interactions were also analyzed at the same level. The Discovery Studio 3.5 Visualizer was used to draw the initial and optimized structures of investigated geometries. The noncovalent interactions (NCIs) were visualized by calculating reduced density gradient (RDG) with Multiwfn program. The color-filled isosurfaces and RDG scatter maps of most stable interaction geometries were plotted by Visual Molecular Dynamics (VMD) software and Gnuplot 5.3 software, respectively. This study showed that adenine, guanine, and hypoxanthine nucleobases interact with doxorubicin by forming strong hydrogen bonds and π-π interactions. Considering the normal cellular conditions, the effect of solvent (water) on the interaction geometries were also analyzed and when compared to gas phase it was determined that the movements of the molecules were restricted and there was a minimal change between initial and optimized structures in the aqueous phase.