Materials Science and Engineering / Malzeme Bilimi ve Mühendisliği
Permanent URI for this collectionhttps://hdl.handle.net/11147/4719
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Article Citation - WoS: 15Citation - Scopus: 16Monitoring the Crystal Orientation of Black-Arsenic Via Vibrational Spectra(Royal Society of Chemistry, 2019) Kandemir, Ali; İyikanat, Fadıl; Şahin, HasanIn this study, the structural, mechanical, and vibrational properties of a recently discovered anisotropic ultra-thin material, black-arsenic (b-As), are investigated by using density functional theory. Direction dependent elastic constants such as in-plane stiffness, Young's modulus and Poisson's ratio of single-layer b-As are calculated and compared with those of the structural cousin black-phosphorus (b-P). The calculated Poisson's ratio of b-As for the zigzag direction is nearly 1, which is quite higher than that of b-P, 0.65. Besides, it is found that all the three elastic constants are highly anisotropic and their values in the zigzag direction are almost three times higher than that of the armchair direction. The mechanical strength of the material is also calculated and high-toughness is seen in both armchair and zigzag directions. It is revealed that the material is quite stiff against straining along the zigzag direction; in contrast, it is quite flexible along the armchair direction. Vibrational stability analysis shows that the material is stable up to 9% biaxially applied strain, and 12% and 45% uniaxially applied strain in the zigzag and armchair directions, respectively. Furthermore, the prominent Raman active peaks of the b-As structure show strong anisotropy in the strain dependent vibrational spectra and they can also be used for easy-determination of the crystal orientation of b-As from Raman measurements.Article Citation - WoS: 12Citation - Scopus: 13Predicted Polymorph Manipulation in an Exotic Double Perovskite Oxide(Royal Society of Chemistry, 2019) Su, He-Ping; Li, Shu-Fang; Han, Yifeng; Wu, Mei-Xia; Gui, Churen; Chang, Yanfen; Li, Man-Rong; Adem, UmutPredicted polymorph manipulation offers a cutting-edge route to design function-oriented materials in an exotic double perovskite-related oxide A(2)BB ' O-6 with small A-site cations. Herein, first-principles density functional theory calculations in light of the equation of state for solid, for the first time, was used to predict the Mg3TeO6 (R3)-to-perovskite (P2(1)/n) type phase transition in Mn3TeO6 at around 5 GPa, regardless of the deployment of magnetic interactions. The high-pressure synthesis and synchrotron diffraction crystal structure analysis corroborated experimentally the polymorph variation in Mn22+Mn2+Te6+O6, which was accompanied by a 13 K increase in the antiferromagnetic ordering temperature (37 K) in the high-pressure perovskite polymorph compared to that of the ambient-pressure R3 phase (24 K). The magnetodielectric coupling remains up to 50 K with the maximum being around the magnetic ordering temperature in the perovskite Mn3TeO6. Thus, the predicted polymorph manipulation here offers the possibility of discovering accelerated materials by inverse design in exotic perovskite oxides.Article Citation - WoS: 67Citation - Scopus: 66Bilayers of Janus Wsse: Monitoring the Stacking Type: Via the Vibrational Spectrum(Royal Society of Chemistry, 2018) Kandemir, Ali; Şahin, HasanMotivated by the recent successful synthesis of Janus type single layers of transition metal dichalcogenides, we investigate the stability, vibrational and electronic properties of the Janus single layer structure of WSSe and its bilayers by means of density functional theory. The structural and vibrational analysis show that the Janus single layer of WSSe forms a dynamically stable structure in the 2H phase. Owing to its non-centrosymmetric structure, the Janus WSSe single layer has two in-plane (E) and two out-of-plane (A) Raman active phonon modes. The eigen-frequencies of the prominent Raman active modes are calculated to be 277 (A) and 322 (E) cm-1. Similar to single layer WS2 and WSe2, Janus WSSe is a direct band gap semiconductor that has two electronically different faces. In addition, the possible bilayer stacking orders of the Janus WSSe single layers are investigated. It is found that there are 3 stacking types of bilayer Janus WSSe and each stacking type has distinctive Raman characteristics in its vibrational spectrum. Our results show that thanks to the vibrational characteristics, which stem from the distinctive interlayer interactions at different sides, the stability and stacking types of the bilayer of WSSe Janus structure can be monitored.Article Citation - WoS: 31Citation - Scopus: 33Enhanced Bactericidal and Photocatalytic Activities of Zno Nanostructures by Changing the Cooling Route(Royal Society of Chemistry, 2018) Horzum, Nesrin; Hilal, Mohamed Elhousseini; Işık, TuğbaWe report on a simple synthesis of ZnO nanowires by calcination of zinc acetate. The effect of calcination temperature and cooling route on the antibacterial and photocatalytic properties is demonstrated by varying the size and surface area of the nanowires. The decrease of the calcination temperature followed by a rapid cooling procedure leads to a smaller size and larger surface area of the nanowires. ZnO nanowires are found to be effective against the growth of E. coli at the microgram level. In addition, the photocatalytic activity of the synthesized ZnO nanowires is demonstrated by the successful degradation of the organic dye methylene blue.Article Citation - WoS: 55Citation - Scopus: 60Development of Molecularly Imprinted Polymers (mips) as a Solid Phase Extraction (spe) Sorbent for the Determination of Ibuprofen in Water(Royal Society of Chemistry, 2017) Ölçer, Yekta Arya; Demirkurt, Merve; Demir, Mustafa Muammer; Eroğlu, Ahmet EminIbuprofen is a well-known endocrine disrupter. In this study, highly selective molecularly imprinted polymers (MIPs) with different morphologies were synthesized via precipitation and bulk polymerization of methacrylic acid (MAA) and trimethylolpropane trimethacrylate (TRIM) in the presence of ibuprofen as a template. Non-imprinted polymers (NIPs) were also synthesized via the same procedure in the absence of ibuprofen. Spherical and monolithic MIPs were obtained using different experimental conditions, and the spherical MIP was shown to have better sorption towards ibuprofen. The optimum sample pH, sorbent amount, sample volume, and sorption time were determined to be 8.0, 25.0 mg, 10.0 mL, and 30.0 min, respectively. A methanol water mixture (MeOH:H2O, 80:20, pH 3.0) was employed as an eluent with >97% (±0.8, n = 3) desorption. The MIP demonstrated high selectivity towards ibuprofen in the presence of naproxen and ketoprofen. The validity of the proposed method was checked via spike recovery tests using drinking and tap water samples. The method worked efficiently for both water types, resulting in the recoveries of 97.2% (±0.3, n = 3) and 97.7% (±0.2, n = 3).Article Citation - WoS: 54Citation - Scopus: 53Nitrogen Doping for Facile and Effective Modification of Graphene Surfaces(Royal Society of Chemistry, 2017) Yanılmaz, Alper; Tomak, Aysel; Akbalı, Barış; Bacaksız, Cihan; Özçeri, Elif; Arı, Ozan; Senger, Ramazan Tuğrul; Selamet, Yusuf; Zareie, Hadi M.We report experimental and theoretical investigations of nitrogen doped graphene. A low-pressure Chemical Vapor Deposition (CVD) system was used to grow large-area graphene on copper foil, using ethylene as the carbon source. Nitrogen-doped graphene (N-graphene) was prepared by exposing the graphene transferred to different substrates to atomic nitrogen plasma. The effect of varying nitrogen flow rates on doping of graphene was investigated while keeping the power and time constant during the process. The N-graphene was characterized via Raman Spectroscopy, X-ray Photoelectron Spectroscopy (XPS), Scanning Tunneling Microscopy and Spectroscopy (STM and STS), and Fourier Transform Infrared spectroscopy (FTIR). Raman mapping of N-graphene was also performed to show homogeneity of nitrogen on the graphitic lattice. XPS results have revealed the presence of different nitrogen configurations in the graphitic lattice with similar doping concentrations. Density functional theory (DFT) based calculations showed that the periodic adsorption of N atoms predominantly occurs on top of the C atoms rather than through substitution of C in our N-graphene samples. Our results indicate a feasible procedure for producing N-graphene with homogenous and effective doping which would be valuable in electronic and optical applications.Article Citation - WoS: 33Citation - Scopus: 36Epr Studies of Intermolecular Interactions and Competitive Binding of Drugs in a Drug-Bsa Binding Model(Royal Society of Chemistry, 2016) Akdoğan, Yaşar; Emrullahoğlu, Mustafa; Tatlıdil, Diğdem; Üçüncü, Muhammed; Çakan Akdoğan, GülçinUnderstanding intermolecular interactions between drugs and proteins is very important in drug delivery studies. Here, we studied different binding interactions between salicylic acid and bovine serum albumin (BSA) using electron paramagnetic resonance (EPR) spectroscopy. Salicylic acid was labeled with a stable radical (spin label) in order to monitor its mobilized (free) or immobilized (bound to BSA) states. In addition to spin labeled salicylic acid (SL-salicylic acid), its derivatives including SL-benzoic acid, SL-phenol, SL-benzene, SL-cyclohexane and SL-hexane were synthesized to reveal the effects of various drug binding interactions. EPR results of these SL-molecules showed that hydrophobic interaction is the main driving force. Whereas each of the two functional groups (-COOH and -OH) on the benzene ring has a minute but detectable effect on the drug-protein complex formation. In order to investigate the effect of electrostatic interaction on drug binding, cationic BSA (cBSA) was synthesized, altering the negative net charge of BSA to positive. The salicylic acid loading capacity of cBSA is significantly higher compared to that of BSA, indicating the importance of electrostatic interaction in drug binding. Moreover, the competitive binding properties of salicylic acid, ibuprofen and aspirin to BSA were studied. The combined EPR results of SL-salicylic acid/ibuprofen and SL-ibuprofen/salicylic acid showed that ibuprofen is able to replace up to ∼83% of bound SL-salicylic acid, and salicylic acid can replace only ∼14% of the bound SL-ibuprofen. This indicates that ∼97% of all salicylic acid and ibuprofen binding sites are shared. On the other hand, aspirin replaces only ∼23% of bound SL-salicylic acid, and salicylic acid replaces ∼50% of bound SL-aspirin, indicating that ∼73% of all salicylic acid and aspirin binding sites are shared. These results show that EPR spectroscopy in combination with the spin labeling technique is a very powerful method to investigate drug binding dynamics in detail.Article Citation - WoS: 24Citation - Scopus: 27Physiological Concentrations of Albumin Favor Drug Binding(Royal Society of Chemistry, 2015) Tatlıdil, Diğdem; Üçüncü, Muhammed; Akdoğan, YaşarThe ability to track drug binding and release makes electron paramagnetic resonance (EPR) spectroscopy well suited for drug delivery studies. Using the continuous wave (cw) EPR technique to extract information about the dynamics of the spin labeled drugs we can simultaneously determine the bound and unbound drugs. Here, spin labeled salicylic acid (SLSA) binding to and release from bovine serum albumin (BSA) is investigated, as a model for drug-transport protein interaction. We studied SLSA-BSA binding in a wide concentration range and found that the stoichiometry of the drug-protein increases significantly when the physiological range of BSA concentration is reached. Our EPR results explicitly reveal that up to ∼7 SLSA can bind to one albumin at the physiological concentration, whereas at lower BSA concentrations (<0.125 mM) the SLSA-BSA stoichiometry is maximum 2. Moreover, we studied drug release and showed that the ratio of bound to unbound SLSA concentrations remains relatively stable during dialysis. This indicates that the binding equilibrium of SLSA is not altered through the process of dialysis. This study demonstrates that cw EPR spectroscopy in combination with spin labeled drugs is an effective technique for binding and release studies and stoichiometric analysis of drug-protein interactions.Article Citation - WoS: 45Citation - Scopus: 47Impedimetric Detection of Pathogenic Bacteria With Bacteriophages Using Gold Nanorod Deposited Graphite Electrodes(Royal Society of Chemistry, 2016) Moghtader, Farzaneh; Çongur, Gülşah; Zareie, Hadi M.; Erdem, Arzum; Pişkin, ErhanElectrochemical impedance spectroscopy (EIS) is applied for the detection of bacteria using bacteriophages as a bioprobe together with gold nanorods (GNRs). Escherichia coli-E. coli K12 was used as a model target bacteria and also for the propagation of its specific T4-phages. Gold nanorods (GNRs) were synthesized via a two-step protocol and characterized using different techniques. EIS measurements were conducted in an electrochemical cell consisting of a three electrode system. Single-use pencil graphite electrodes (PGE) were modified by the physical adsorption of GNRs to increase their interfacial conductivity and therefore sensitivity for impedimetric measurements. Therefore, interfacial charge-transfer resistance values (Rct) sharply decreased after GNRs deposition. Phages were adsorbed on these electrodes via a simple incubation protocol at room temperature, which resulted in an increase in Rct values, which was concluded to be as a result of nonconductive phage layers. These phage-carrying GNRs-PGEs were used for impedimetric detection of the target bacteria, E. coli. Significant increases at the Rct values were observed which were attributed to the insulation effects of the adsorbed bacterial layers. This increase was even more when the bacterial concentrations were higher. In the case of the non-target bacteria Staphylococcus aureus (S. aureus), conductivity noticeable decreases (due to nonspecific adsorption). However, in the case of E. coli, the Rct value increase is time dependent and reaches maximum in about 25-30 min, then decreases gradually as a result of bacterial lysis due to phage invasion on the electrode surfaces. In contrast, there were no time dependent changes with the non-target bacteria S. aureus (no infection and no lytic activity). It is concluded that the target bacteria could be detected using this very simple and inexpensive detection protocol with a minimum detection limit of 103 CFU mL-1 in approximately 100 μL bacterial suspension.Article Citation - WoS: 3Citation - Scopus: 3Gold Nanorod Encapsulated Bubbles(Royal Society of Chemistry, 2015) Tomak, Aysel; Zareie, Hadi M.A simple method has been described for synthesizing gold nanorods (GNRs) encapsulated bubbles in a controlled manner. The method involves the use of nitrogen gas in the seed-mediated synthesis method routinely used for synthesis of GNRs. Control over the morphology of the nanostructures was achieved by nitrogen gas flow. The synthesized structures were examined by UV-Vis Spectroscopy, Scanning Electron Microscopy (SEM) and Atomic Force Microscopy (AFM). New structures of this type could conceivably serve as plasmonic biosensors, nanodevices and photothermal theranostics with dual modality imaging functionality. © The Royal Society of Chemistry 2015.