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Item Open Access[2+2] cycloadditions of sorbyl tosylate with imines/1-azadienes: a one-pot domino approach for α-alkylidene-β-lactams and their computational studies and antimicrobial evaluation(Wiley-Blackwell, 2018) Kumar, Y.; Bedi, P. M. S.; Singh, P.; Adeniyi, A. A.; Singh-Pillay, A.; Singh, P.; Bhargava, G.The manuscript describes a straightforward and atom-efficient method for the synthesis of α-alkylidene-β-lactams using sorbyl tosylate and imines/1-azadienes at high temperature (80 °C). The Density functional theory calculations have shown the prevalence of the first order kinetics in these [2+2] cycloadditions to produce mixture of 3-butadienyl-azetidin-2ones and 3-but-2-enylidene-azetidin-2-ones in good yields. The 3-but-2-enylidene-azetidin-2-ones have also shown antimicrobial activity against the E. coli, S. aureus, P. aeruginosa, B. cereus and B. subtilis. Item Open Access2D Network overtakes 3D for photocatalytic hydrogen evolution(Royal Society of Chemistry, 2022-07-18) Ahmad, Aliyu Aremu; Türkan Gamze Ulusoy, Ghobadi; Özbay, Ekmel; Karadaş, Ferdi; Ahmad, Aliyu Aremu; Türkan Gamze Ulusoy, Ghobadi; Özbay, Ekmel; Karadaş, Ferdi3-Dimensional (3D) cyanide coordination polymers, typically known as Prussian blue Analogues (PBAs), have received great attention in catalysis due to their stability, easily tuned metal sites, and porosity. However, their high crystallinities and relatively low number of surface-active sites significantly hamper their intrinsic catalytic activities. Herein, we report the utilization of a 2-dimensional (2D) layered cobalt tetracyanonickelate, [Co–Ni], for the reduction of protons to H2. Relying on its exposed facets, layered morphology, and abundant surface-active sites, [Co–Ni] can efficiently convert water and sunlight to H2 in the presence of a ruthenium photosensitizer (Ru PS) with an optimal evolution rate of 30 029 ± 590 μmol g−1 h−1, greatly exceeding that of 3D Co–Fe PBA [Co–Fe] and Co–Co PBA [Co–Co]. Furthermore, [Co–Ni] retains its structural integrity throughout a 6 hour photocatalytic cycle, which is confirmed by XPS, PXRD, and Infrared analysis. This recent work reveals the excellent morphologic properties that promote [Co–Ni] as an attractive catalyst for the hydrogen evolution reaction (HER). Item Open AccessRotaxane and pseudorotaxane based on cucurbituril and anchored to a meso-tetraphenyl porphyrin(2006) Tuncel, D.; Cindir, N.; Koldemir, Ü.Water soluble rotaxane and pseudorotaxane based on cucurbituril and anchored to a meso-tetraphenyl porphyrin have been synthesized and characterized by spectroscopic methods (1H-NMR, 13C-NMR and UV), and by elemental analysis, and mass spectrometry. The preliminary results of the pH-driven switching properties of rotaxane investigated through 1H-NMR spectroscopy are reported. These results were compared with those obtained from a model porphyrin, which was prepared by the de-threading cucurbituril from pseudorotaxane under basic conditions. © Springer 2006. Item Open AccessA Rotaxane-Based photosensitizer for photodynamic therapy(WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim, 2019) Özkan, Melis; Keser, Yağmur; Hadi, Seyed Ehsan; Tuncel, Dönüş; Özkan, Melis; Keser, Yağmur; Hadi, Seyed Ehsan; Tuncel, DönüşA rotaxane was synthesized through a catalytically self‐threading reaction in which CB6 serves as a macrocycle and acts as a catalyst for the 1,3‐dipolar cycloaddition reaction between the alkyne substituted porphyrin core and azide functionalized stopper groups by forming triazole. Application of this rotaxane as a photosensitizer in photodynamic therapy against cancer cells and in bacteria inactivation have also been demonstrated. This photosensitizer has an excellent water solubility and remains stable in biological media at physiological pH (7.4) for prolonged times. It has the ability to generate singlet oxygen efficiently; while it shows no dark cytotoxicity up to 300 µm to the MCF7 cancer cell line, it is photocytotoxic even at 2 µm and reduces the cell viability to around 70 % when exposed to white light. It also displays light‐triggered biocidal activity both against gram‐negative bacteria (Escherichia coli, E. coli) and gram‐positive bacteria (Bacillus subtilis). Upon white light irradiation for 1 min with a flux of 22 mW/cm2 of E. coli suspension incubated with rotaxane (3.5 µm), a killing efficiency of 96 % is achieved, whereas in the dark the effect is recorded as only around 9 %. Item Open Access6p valence relativistic effects in 5d photoemission spectrum of Pb atom and bonding properties of Pb-dimer using Dirac–Hartree–Fock formalism including many-body effects(AVS, 2022-06-22) Süzer, Şefik; Bagus, Paul S.; Süzer, ŞefikThere has been strong recent interest related to the large spin–orbit coupling in Pb monolayers on various properties of graphene and other 2D-materials. The underlying physical/chemical origin of the spin–orbit splitting has been discussed in terms of the valence 6p atomic level of the lead atom. Indeed, the photoelectron spectra of the Pb atom were the subject of investigations about 50 years ago in Dave Shirley’s laboratory at UC Berkeley. In a paper published in 1975, using He-I UV photoelectron spectroscopy, we reported an unexpected relative intensity ratio for the observed atomic Pb peaks (2P1/2 and 2P3/2) after removal of a 6p valence electron and attributed it to the large spin–orbit interaction in that level. In this contribution, we use the Dirac–Hartree–Fock formalism to reanalyze the complex spectral features reported five years later, for the 5d He-II UV photoelectron spectrum of atomic lead, to extract the 6p valence contribution, which turns out to be significant. Furthermore, we calculate the energy levels of the Pb-dimer at the experimental equilibrium geometry of the molecule to also find the significant contribution of the spin–orbit splitting of the atomic 6p levels in the composition of the valence molecular orbitals of the dimer. Such an approach can be extended to larger systems like monolayers containing lead or other heavy atoms, thus helping in designing 2D-materials with controlled and better targeted properties. Item Open AccessAC electrowetting modulation of low-volatile liquids probed by XPS: dipolar vs ionic screening(American Chemical Society, 2019) Aydoğan-Göktürk, Pınar; Ülgüt, Burak; Süzer, Şefik; Aydoğan-Göktürk, Pınar; Ülgüt, Burak; Süzer, ŞefikX-ray photoelectron spectroscopic (XPS) data have been recorded for a low-molecular-weight poly(ethylene glycol) microliter-sized sessile liquid drops sitting on a dielectric covered planar electrode while imposing a ±6 V square-wave actuation with varying frequencies between 10–1 and 105 Hz to tap into the information derivable from (AC) electrowetting. We show that this time-varying XPS spectra reveal two distinct behaviors of the device under investigation, below and above a critical frequency, measured as ∼70 Hz for the liquid poly(ethylene glycol) with a 600 Da molecular weight. Below the critical frequency, the liquid complies faithfully to the applied bias, as determined by the constant shift in the binding energy position of the XPS peaks representative of the liquid throughout its entire surface. The liquid completely screens the applied electrical field and the entire potential drop takes place at the liquid/dielectric interface. However, for frequencies above the critical value, the resistive component of the system dominates, resulting in the formation of equipotential surface contours, which are derived from the differences in the positions of the twinned O 1s peaks under AC application. This critical frequency is independent of the size of the liquid drop, and the amplitude of the excitation, but increases when ionic moieties are introduced. The XP spectra under AC actuation is also faithfully simulated using an equivalent circuit model consisting of only resistors and capacitors and using an electrical circuit simulation software. Moreover, a mimicking device is fabricated and its XP spectra are recorded using the Sn 3d peaks of the solder joints at different points on the circuit to confirm the reliability of the measured and simulated AC behaviors of the liquid. These new findings indicate that in contrast to direct current case, XPS measurements under variable frequency AC actuation reveal (through differences in the frequency response) information related to the chemical makeup of the liquid(s) and brings the laboratory-based XPS as a powerful complimentary arsenal to electrochemical analyses of liquids and their interfaces. Item Open AccessAccurate method for obtaining band gaps in conducting polymers using a DFT/hybrid approach(American Chemical Society, 1998) Salzner, U.; Pickup, P. G.; Poirier, R. A.; Lagowski, J. B.DFT calculations on a series of oligomers have been used to estimate band gaps, ionization potentials, electron affinities, and bandwidths for polyacetylene, polythiophene, polypyrrole, polythiazole, and a thiophene - thiazole copolymer. Using a slightly modified hybrid functional, we obtain band gaps within 0.1 eV of experimental solid-state values Calculated bond lengths and bond angles for the central ring of sexithiophene differ by less than 0.026 Å and 0.7° from those of the sexithiopnene crystal structure. IPs and EAs are overestimated by up to 0.77 eV compared to experimental bulk values. Extrapolated bandwidths agree reasonably well with bandwidths from band structure calculations. Item Open AccessAcetaldehyde partial oxidation on the Au (111) model catalyst surface: C-C bond activation and formation of methyl acetate as an oxidative coupling product(Elsevier, 2015) Karatok, M.; Vovk, E. I.; Shah, A. A.; Turksoy, A.; Ozensoy, E.Partial oxidation of acetaldehyde (CH3CHO) on the oxygen pre-covered Au(111) single crystal model catalyst was investigated via Temperature Programmed Desorption (TPD) and Temperature Programmed Reaction Spectroscopy (TPRS) techniques, where ozone (O3) was utilized as the oxygen delivery agent providing atomic oxygen to the reacting surface. We show that for low exposures of O3 and small surface oxygen coverages, two partial oxidation products namely, methyl acetate (CH3COOCH3) and acetic acid (CH3COOH) can be generated without the formation of significant quantities of carbon dioxide. The formation of methyl acetate as the oxidative coupling reaction product implies that oxygen pre-covered Au(111) single crystal model catalyst surface can activate C-C bonds. In addition to the generation of these products; indications of the polymerization of acetaldehyde on the gold surface were also observed as an additional reaction route competing with the partial and total oxidation pathways. The interplay between the partial oxidation, total oxidation and polymerization pathways reveals the complex catalytic chemistry associated with the interaction between the acetaldehyde and atomic oxygen on catalytic gold surfaces. Item Open AccessActivatable photosensitizers: agents for selective photodynamic therapy(Wiley-VCH Verlag, 2017) Li, X.; Kolemen, S.; Yoon, J.; Akkaya, E. U.Recent developments in the design of bifunctional and activatable photosensitizers rejuvenate the aging field of photodynamic sensitization and photodynamic therapy. While systematic studies have uncovered new dyes that can serve as potential photosensitizers, the most promising results have come from studies aimed at gaining precise control over the location and rate of cytotoxic singlet oxygen generation. As a consequence, higher selectivities and efficiencies in photodynamic treatment protocols are now within reach. This feature article highlights the variety of approaches that have been pursued to improve photodynamic therapy and to transform simple photosensitizers into smarter theranostic agents. Item Open AccessAdsorption behavior of radionuclides, 137Cs and 140Ba, onto solid humic acid(Springer, 2011) Çelebi, O.; Erten, Hasan N.In this research, the adsorption behaviors of two important fission product radionuclides (137Cs and 133Ba) onto sodium form of insolubilized humic acid (INaA) were investigated as a function of time, cation concentration and temperature, utilizing radiotracer method. The resulting data was fitted well to the Freundlich and Dubinin-Radushkevich (D-R) isotherms. Thermodynamic constants such as; free energy (ΔGads), enthalpy (ΔHads), entropy (ΔSads) of adsorption were determined. Temperature change didn't effect sorption processes significantly. Best fitting kinetic models were found for a better understanding of adsorption mechanisms. It was found that Ba2+ was adsorbed five times more than Cs+ onto structurally modified humic acid and kinetic studies indicated that adsorption behaviors of both ions obey the pseudo second order rate law. The effect of pH changes on adsorption was also examined and optimum pH range was found in the range of pH 6-8. FTIR and solid state carbon nmr (13CNMR) spectroscopic techniques were used to understand the structural changes during insolubilization process. Quantitative determination of adsorption sites was carried out using potentiometric titration method and the resulting data was treated by using appropriate Gran functions. Item Open AccessAir-stable n-channel diketopyrrolopyrrole-diketopyrrolopyrrole oligomers for high performance ambipolar organic transistors(American Chemical Society, 2016) Mukhopadhyay, T.; Puttaraju, B.; Senanayak, S. P.; Sadhanala, A.; Friend, R.; Faber, H. A.; Anthopoulos, T. D.; Salzner, U.; Meyer A.; Patil, S.n-channel organic semiconductors are prone to oxidation upon exposed to ambient conditions. Herein, we report design and synthesis of diketopyrrolopyrrole (DPP)-based oligomers for ambipolar organic thin-film transistors (OFETs) with excellent air and bias stability at ambient conditions. The cyclic voltammetry measurements reveal exceptional electrochemical stability during the redox cycle of oligomers. Structural properties including aggregation, crystallinity, and morphology in thin film were investigated by UV-visible spectroscopy, atomic force microscopy (AFM), thin-film X-ray diffraction (XRD), and grazing incidence small-angle X-ray scattering (GISAXS) measurements. AFM reveals morphological changes induced by different processing conditions whereas GISAXS measurements show an increase in the population of face-on oriented crystallites in films subjected to a combination of solvent and thermal treatments. These measurements also highlight the significance of chalcogen atom from sulfur to selenium on the photophysical, optical, electronic, and solid-state properties of DPP-DPP oligomers. Charge carrier mobilities of the oligomers were investigated by fabricating top-gate bottom-contact (TG-BC) thin-film transistors by annealing the thin films under various conditions. Combined solvent and thermal annealing of DPP-DPP oligomer thin films results in consistent electron mobilities as high as ∼0.2 cm2 V-1 s-1 with an on/off ratio exceeding 104. Field-effect behavior was retained for up to ∼4 weeks, which illustrates remarkable air and bias stability. This work paves the way toward the development of n-channel DPP-DPP-based oligomers exhibiting retention of field-effect behavior with superior stability at ambient conditions. Item Open AccessAll-solution-processed, oxidation-resistant copper nanowire networks for optoelectronic applications with year-long stability(American Chemical Society, 2020) Polat-Genlik, S.; Tigan, D.; Koçak, Yusuf; Ercan, Kerem Emre; Çiçek, Melih Ogeday; Tunca, S.; Koylan, S.; Coşkun, Ş.; Özensoy, Emrah; Ünalan, H. E.; Koçak, Yusuf; Ercan, Kerem Emre; Çiçek, Melih Ogeday; Özensoy, EmrahCopper nanowires (Cu NWs) hold promise as they possess equivalent intrinsic electrical conductivity and optical transparency to silver nanowires (Ag NWs) and cost substantially less. However, poor resistance to oxidation is the historical challenge that has prevented the large-scale industrial utilization of Cu NWs. Here, we use benzotriazole (BTA), an organic corrosion inhibitor, to passivate Cu NW networks. The stability of BTApassivated networks under various environmental conditions was monitored and compared to that of bare Cu NW control samples. BTA passivation greatly enhanced the stability of networks without deteriorating their optoelectronic performance. Moreover, to demonstrate their potential, BTA-passivated networks were successfully utilized in the fabrication of a flexible capacitive tactile sensor. This passivation strategy has a strong potential to pave the way for large-scale utilization of Cu NW networks in optoelectronic devices. Item Open AccessAmplified chemiluminescence signal for sensing fluoride ions(American Chemical Society, 2017) Turan, I. S.; Seven, O.; Ayan, S.; Akkaya, E. U.Bringing together the concepts of self-immolative linkers and chemiluminogen dioxetane modules, a chemiluminescence-based sensor for fluoride with signal amplification is presented. Signal amplification is obtained by triggering two chemiluminescence events for each reacting fluoride ion that in turn releases two fluoride ions for each ion. As expected, the chemiluminescence signal starts to rise following an induction period. In addition to the analytical potential, this chemical system is also of interest as a demonstration of positive feedback loop character. Item Open AccessAnalyses of products from autoclave reactions: Derivation of reaction parameters(1996) Demirel, B.; Paul J.This work presents energetics for high pressure hydroprocessing reactions derived from post analyses of liquid and gaseous products. Specifically, GC and GC/MS were used to follow the product distribution from the hydrocracking of methyldecalins over zeolite supported palladium and platinum catalysts as a function of temperature. Plain Arrhenius plots summarize key results and reveal possible connections in terms of 'activation energies' between hydrogen consumption and the amounts of different products. The total cycloalkane production and the consumption of hydrogen both show a simple temperature dependence with the same 'activation' energies. Methane production varies more rapidly with temperature but can still be described by a single exponential term. The final example, conversion to aromatics, displays a more complicated dependence with an accelerated yield at high temperature. This form of data analyses connects to a new routine for mass balance evaluations and it is now applied to model catalyst performance and to understand optimum reaction conditions. Other branches of this project include surface spectroscopic measurements of fresh, sulfided and used catalysts, characterization of partially hydrogenated naphthalenes and modeling of hydrogen activity at metal Sulfides. Item Open AccessAnalysis of charge transfer for in situ li intercalated carbon nanotubes(American Chemical Society, 2012) Rana, K.; Kucukayan-Dogu, G.; Sen, H. S.; Boothroyd, C.; Gulseren, O.; Bengu, E.Vertically aligned carbon nanotube (VA-CNT) arrays have been synthesized with lithium (Li) intercalation through an alcohol-catalyzed chemical vapor deposition technique by using a Li-containing catalyst. Scanning electron microscopy images display that synthesized carbon nanotubes (CNTs) are dense and vertically aligned. The effect of the Li-containing catalyst on VA-CNTs has been studied by using Raman spectroscopy, X-ray photoelectron spectroscopy (XPS), and electron energy loss spectroscopy (EELS). XPS results show the change in binding energy of Li 1s and C 1s peaks, which indicates that Li is inserted in VA-CNTs during growth. Analysis of Raman spectra reveals that the G-band profile of CNTs synthesized with the Li-containing catalyst is shifted, suggesting an electronic interaction between Li and neighboring C atoms of the CNTs. The EELS spectra of the C K edge and Li K edge from CNTs also confirmed that Li is inserted into CNTs during synthesis. We have performed ab inito calculations based on density functional theory for a further understanding of the structural and electronic properties of Li intercalated CNTs, especially addressing the controversial charge-transfer state between Li and C. Item Open AccessAnalysis of defects on BN nano-structures using high-resolution electron microscopy and density-functional calculations(2008) Bengu, E.; Marks, L. D.; Ovali, R. V.; Gulseren, O.Cubic boron nitride (c-BN) nucleation takes place on hexagonal boron nitride (h-BN) layers growing perpendicular to the substrate surface during thin film synthesis. Studies focused on the nucleation of the cubic phase suggest the possibility that transient phases and/or defects on these h-BN structures have a role in sp3-bonded cubic phase nucleation. In this study, we have investigated the nature, energetics, and structure of several possible defects on BN basal planes, including point defects, 4-, and 5-fold BN rings, that may possibly match the experimentally observed transient phase fine structure. TEM image observations are used to build approximate atomic models for the proposed structures, and DFT calculations are used to relax these structures while minimizing their respective total energies. These optimized atomic geometries are then used to simulate TEM images, which are compared to the experimentally observed structures. Data from DFT calculations and analysis of simulated images from the proposed atomic structures suggest that 4-fold BN rings are more likely to exist on the transient phase possibly leading to c-BN nucleation. © 2008 Elsevier B.V. All rights reserved. Item Open AccessAnalysis of electrochemical noise in NiCd batteries throughout their lifetime(TUBITAK, 2018) Ülgüt, Burak; Ülgüt, BurakElectrochemical noise measurements have been applied to electrochemical systems that show stochastic behavior. The standard area of study that benefits from this stochastic analysis is localized corrosion modes like pitting and crevice corrosion. Application of electrochemical noise measurements to battery systems, though rare, is recently becoming more popular. The present contribution first establishes a method of analyzing electrochemical voltage noise data for NiCd batteries, then follows four samples of batteries in terms of voltage noise throughout their lifetimes. The noises exhibited by battery systems are small, but finite. This noise is expected to be due to variations in the electrochemistry on the electrode surfaces of the battery. After careful analysis, the voltage noise behavior of NiCd batteries does not appear to show a statistically significant variation of electrochemical voltage noise throughout their lifetimes. Item Open AccessAnalysis of errors in zero-free-parameter modeling approach to predict the voltage of electrochemical energy storage systems under arbitrary load(Electrochemical Society, 2017) Ulgut, Burak; Uzundal, Can Berk; Özdemir, ElifIn a recently published article (J. Electrochem. Soc. 164 (2017) A1274-A1280), we described a new method to predict the voltage response of electrochemical energy storage systems during arbitrary load profiles. Our work shows that the impedance spectrum can be employed in the frequency domain in order to ultimately calculate the time domain behavior of the electrochemical energy storage system. The big advantage of this method is the fact that there are no free parameters and fits throughout. The present work deals with the sources of error in the above-mentioned prediction approach and looks for the effects of the various sources of error. The current analysis concludes that two big contributors to the overall error are the inaccuracies in the DC part of the prediction and the non-linearities that are not modeled by a linear impedance spectrum. Discussions are also made regarding ways to improve the performance of the modeling approach the most and where future work is going to be looking to improve. Item Open AccessAnalysis of Fe nanoparticles using XPS measurements under d.c. or pulsed-voltage bias(2010) Süzer, Şefik; Baer, D. R.; Engelhard, M. H.; Süzer, ŞefikThe impact of solution exposure on the charging properties of oxide coatings on Fe metal-core oxide-shell nanoparticles has been examined by sample biasing during XPS measurements. The Fe nanoparticles were suspended in relatively unreactive acetone and analyzed after particles containing solutions were deposited on SiO2/Si or Au substrates. The particle and substrate combinations were subjected to ±10V d.c. or ±5V a.c., biasing in the form of square wave (SQW) pulses. The samples experienced variable degrees of charging for which low-energy electrons at ∼1eV, 20 μA and low-energy Ar+ ions were used to minimize it. Application of d.c. bias and/or SQW pulses significantly influences the extent of charging, which is utilized to gather additional analytical information about the sample under investigation. This approach allows separation of otherwise overlapping peaks. Accordingly, the O1s peaks of the silicon oxide substrate, the iron oxide nanoparticles, and that of the casting solvent can be separated from each other. Similarly, the C1s peak belonging to the solvent can be separated from that of the adventitious carbon. The charging shifts of the iron nanoparticles are strongly influenced by the solvent to which the particles were exposed. Hence, acetone exhibited the largest shift, water the smallest, and methanol in between. Dynamical measurements performed by application of the voltage stress in the form of SQW pulses provides information about the time constants of the processes involved, which leads us to postulate that these charging properties we probe in these systems stem mainly from ionic movement(s). Item Open AccessAnalysis of polymers using evolved-gas and direct-pyrolysis techniques(Royal Society of Chemistry, 1994) Fares, M. M.; Yalcin, T.; Hacaloglu, J.; Gungor, A.; Süzer, Şefik; Süzer, ŞefikThermal analysis of polystyrene, poly(p-methylstyrene) and poly(α-methylstyrene) has been carried out using evolved-gas analysis by infrared and mass spectrometry, and direct-pyrolysis analysis by mass spectrometric techniques. Evolved-gas analysis, both by infrared and mass spectrometry, reveals features due mainly to the corresponding monomers or stable, volatile, and low relative molecular mass degradation products. In direct-pyrolysis mass spectrometry, however, primary decomposition products and heavier fragments such as dimers and trimers can also be detected. The ion-temperature profiles of the corresponding monomer ions reveal information about the thermal stability of the polymers.