Scholarly Publications - Chemistry

Permanent URI for this collectionhttps://hdl.handle.net/11693/115489

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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.
Open Access
2D 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
3-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).
Open Access
[5]Rotaxane and [5]pseudorotaxane based on cucurbit[6]uril and anchored to a meso-tetraphenyl porphyrin
(2006) Tuncel, D.; Cindir, N.; Koldemir, Ü.
Water soluble [5]rotaxane and [5]pseudorotaxane based on cucurbit[6]uril 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 [5]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 cucurbit[6]uril from [5]pseudorotaxane under basic conditions. © Springer 2006.
Open Access
A [5]Rotaxane-Based photosensitizer for photodynamic therapy
(WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim, 2019) Özkan, Melis; Keser, Yağmur; Hadi, Seyed Ehsan; Tuncel, Dönüş
A [5]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 [5]rotaxane (3.5 µm), a killing efficiency of 96 % is achieved, whereas in the dark the effect is recorded as only around 9 %.
Open Access
6p 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.
There 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.
Open Access
A dormant reagent reaction-diffusion method for the generation of Co-Fe Prussian Blue analogue periodic precipitate particle libraries
(Wiley-VCH GmbH, 2023-08-25) Tootoonchian, Pedram; Kwiczak-Yiğitbaşı, Joanna; Turab Ali Khan, Muhammad; Chalil Oglou, Ramadan; Holló, G.; Karadaş, Ferdi; Lagzi, I.; Baytekin, Bilge
Liesegang patterns that develop as a result of reaction-diffusion can simultaneously form products with slightly different sizes spatially separated in a single medium. We show here a reaction-diffusion method using a dormant reagent (citrate) for developing Liesegang patterns of cobalt hexacyanoferrate Prussian Blue analog (PBA) particle libraries. This method slows the precipitation reaction and produces different-sized particles in a gel medium at different locations. The gel-embedded particles are still catalytically active. Finally, the applicability of the new method to other PBAs and 2D systems is presented. The method proves promising for obtaining similar inorganic framework libraries with catalytic abilities. © 2023 The Authors. Chemistry - A European Journal published by Wiley-VCH GmbH.
Open Access
A perspective on plant robotics: from bioinspiration to hybrid systems
(IOP Publishing Ltd., 2022-11-25) Meder, F.; Baytekin, Bilge; Dottore, E. D.; Meroz, Y.; Tauber, F.; Walker, I.; Mazzolai, B.
As miscellaneous as the Plant Kingdom is, correspondingly diverse are the opportunities for taking inspiration from plants for innovations in science and engineering. Especially in robotics, properties like growth, adaptation to environments, ingenious materials, sustainability, and energy-effectiveness of plants provide an extremely rich source of inspiration to develop new technologies—and many of them are still in the beginning of being discovered. In the last decade, researchers have begun to reproduce complex plant functions leading to functionality that goes far beyond conventional robotics and this includes sustainability, resource saving, and eco-friendliness. This perspective drawn by specialists in different related disciplines provides a snapshot from the last decade of research in the field and draws conclusions on the current challenges, unanswered questions on plant functions, plant-inspired robots, bioinspired materials, and plant-hybrid systems looking ahead to the future of these research fields.
Open Access
AC electrowetting modulation of low-volatile liquids probed by XPS: dipolar vs ionic screening
(American Chemical Society, 2019) Aydoğan-Göktürk, Pınar; Ülgüt, Burak; Süzer, Şefik
X-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.
Open Access
Access to symmetrical and unsymmetrical cyclobutanes via template directed [2+2] photodimerization reactions of cinnamic acids
(Georg Thieme Verlag, 2023-08-16) Yağcı, Bilge Banu; Munir, Badar; Zorlu, Y.; Türkmen, Yunus Emre
In this work, we have developed a general and broadly applicable template-directed photochemical [2+2]-cycloaddition reaction which provides access to a wide range of symmetrical and unsymmetrical cyclobutane products. The use of 1,8-dihydroxynaphthalene as a covalent template paved the way for successful and highly selective photochemical homodimerization and heterodimerization reactions in the solid state between cinnamic acid derivatives. Notably, the method works equally well with aryl- and heteroaryl-containing substrates leading to the formation of β-truxinic acid analogues as single diastereomers and in high yields (up to 99%).
Open Access
Accurate 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.
Open Access
Acetaldehyde 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.
Open Access
Activatable 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.
Open Access
Adsorption 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.
Open Access
Air-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.
Open Access
All-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.
Copper 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.
Open Access
Amplified 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.
Open Access
Analyses 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.
Open Access
Analysis 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.
Open Access
Analysis 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.
Open Access
Analysis of electrochemical noise in NiCd batteries throughout their lifetime
(TUBITAK, 2018) Ülgüt, Burak
Electrochemical 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.