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Publication Metadata only 1,3-bis(gamma-aminopropyl)tetramethyldisiloxane modified epoxy resins: curing and characterization(Elsevier, 1998) Department of Chemistry; Department of Chemistry; Yılgör, Emel; Yılgör, İskender; Researcher; Faculty Member; Department of Chemistry; College of Sciences; College of Sciences; 40527; 24181Incorporation of siloxane oligomers with reactive organofunctional terminal groups, such as amine, epoxy and carboxy, into the structure of epoxy networks, provides improvements in the fracture toughness, water absorption and surface properties of the resultant systems. 1,3-bis(gamma-aminopropyl) tetramethyldisiloxane (DSX) was used as a model curing agent and modifier in bis(4-aminocyclohexyl)methane (PACM-20) cured diglycidyl ether of bisphenol-A (DGEBA) based epoxy resins. Curing reactions followed by differential scanning calorimetry indicated faster reaction rates between DSX and DGEBA as compared with PACM-20 and DGEBA. Mechanical characterization of the modified products showed improvements in tensile and impact strengths as expected. Glass transition temperatures of these materials showed a decrease with an increase in DSX content.Publication Metadata only 3D coffee stains(Royal Soc Chemistry, 2017) N/A; N/A; Department of Electrical and Electronics Engineering; N/A; N/A; N/A; Department of Molecular Biology and Genetics; Department of Chemistry; Department of Chemistry; Department of Electrical and Electronics Engineering; Doğru-Yüksel, Itır Bakış; Söz, Çağla Koşak; Press, Daniel Aaron; Melikov, Rustamzhon; Begar, Efe; Çonkar, Deniz; Karalar, Elif Nur Fırat; Yılgör, Emel; Yılgör, İskender; Nizamoğlu, Sedat; PhD Student; PhD Student; Researcher; PhD Student; PhD Student; PhD Student; PhD Student; Faculty Member; Researcher; Faculty Member; Faculty Member; Department of Molecular Biology and Genetics; Department of Chemistry; Department of Electrical and Electronics Engineering; N/A; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); N/A; N/A; N/A; N/A; N/A; N/A; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Sciences; College of Sciences; College of Sciences; College of Engineering; N/A; N/A; N/A; N/A; N/A; N/A; 206349; N/A; 24181; 130295When a liquid droplet (e.g., coffee, wine, etc.) is splattered on a surface, the droplet dries in a ring-shaped stain. This widely observed pattern in everyday life occurs due to the phenomenon known as a coffee stain (or coffee ring) effect. While the droplet dries, the capillary flow moves and deposits the particles toward the pinned edges, which shows a 2D ring-like structure. Here we demonstrate the transition from a 2D to a 3D coffee stain that has a well-defined and hollow sphere-like structure, when the substrate surface is switched from hydrophilic to superhydrophobic. The 3D stain formation starts with the evaporation of the pinned aqueous colloidal droplet placed on a superhydrophobic surface that facilitates the particle flow towards the liquid-air interface. This leads to spherical skin formation and a cavity in the droplet. Afterwards the water loss in the cavity due to pervaporation leads to bubble nucleation and growth, until complete evaporation of the solvent. In addition to the superhydrophobicity of the surface, the concentration of the solution also has a significant effect on 3D coffee stain formation. Advantageously, 3D coffee stain formation in a pendant droplet configuration enables the construction of all-protein lasers by integrating silk fibroin with fluorescent proteins. No tools, components and/or human intervention are needed after the construction process is initiated; therefore, 3D coffee-stains hold promise for building self-assembled and functional 3D constructs and devices from colloidal solutions.Publication Metadata only 3D printed biodegradable polyurethaneurea elastomer recapitulates skeletal muscle structure and function(American Chemical Society (ACS), 2021) Gokyer, Seyda; Berber, Emine; Vrana, Engin; Orhan, Kaan; Abou Monsef, Yanad; Guvener, Orcun; Zinnuroglu, Murat; Oto, Cagdas; Huri, Pinar Yilgor; Department of Chemistry; Department of Chemistry; Yılgör, Emel; Yılgör, İskender; Researcher; Faculty Member; Department of Chemistry; College of Sciences; College of Sciences; N/A; 24181Effective skeletal muscle tissue engineering relies on control over the scaffold architecture for providing muscle cells with the required directionality, together with a mechanical property match with the surrounding tissue. Although recent advances in 3D printing fulfill the first requirement, the available synthetic polymers either are too rigid or show unfavorable surface and degradation profiles for the latter. In addition, natural polymers that are generally used as hydrogels lack the required mechanical stability to withstand the forces exerted during muscle contraction. Therefore, one of the most important challenges in the 3D printing of soft and elastic tissues such as skeletal muscle is the limitation of the availability of elastic, durable, and biodegradable biomaterials. Herein, we have synthesized novel, biocompatible and biodegradable, elastomeric, segmented polyurethane and polyurethaneurea (TPU) copolymers which are amenable for 3D printing and show high elasticity, low modulus, controlled biodegradability, and improved wettability, compared to conventional polycaprolactone (PCL) and PCL-based TPUs. The degradation profile of the 3D printed TPU scaffold was in line with the potential tissue integration and scaffold replacement process. Even though TPU attracts macrophages in 2D configuration, its 3D printed form showed limited activated macrophage adhesion and induced muscle-like structure formation by C2C12 mouse myoblasts in vitro, while resulting in a significant increase in muscle regeneration in vivo in a tibialis anterior defect in a rat model. Effective muscle regeneration was confirmed with immunohistochemical assessment as well as evaluation of electrical activity produced by regenerated muscle by EMG analysis and its force generation via a custom-made force transducer. Micro-CT evaluation also revealed production of more muscle-like structures in the case of implantation of cell-laden 3D printed scaffolds. These results demonstrate that matching the tissue properties for a given application via use of tailor-made polymers can substantially contribute to the regenerative outcomes of 3D printed tissue engineering scaffolds.Publication Metadata only 3D printed poly(lactic acid) scaffolds modified with chitosan and hydroxyapatite for bone repair applications(Elsevier, 2020) N/A; N/A; N/A; N/A; Department of Chemistry; Department of Chemical and Biological Engineering; Department of Chemistry; Nazeer, Muhammad Anwaar; Önder, Özgün Can; Sevgili, İlkem; Yılgör, Emel; Kavaklı, İbrahim Halil; Yılgör, İskender; PhD Student; PhD Student; PhD Student; Researcher; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; Department of Chemistry; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Sciences; College of Engineering; College of Sciences; N/A; N/A; N/A; N/A; 40319; 241813D printed poly(lactic acid) (PLA) scaffolds surface modified with chitosan (CS) and hydroxyapatite (HA) to produce a novel bioactive composite scaffold is reported. Excellent mechanical properties of PLA, the bioactivity of CS, and osteogenic characteristics of HA are combined to fabricate composite scaffolds using a simple desktop 3D printer. Scaffolds were characterized through attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy, scanning electron microscopy (SEM), energy dispersive X-ray (EDX) spectroscopy, X-ray diffraction (XRD) and water contact angle measurements before and after modification. Formic acid was used as a solvent to prepare stable CS/HA dispersions and was found to be a suitable solvent for producing PLA/CS/HA composites. Surface properties of modified scaffolds were superior in terms of hydrophilicity and bioactivity, which resulted in enhanced attachment and proliferation of human osteosarcoma cells in vitro compared to the unmodified PLA scaffolds.Publication Metadata only 3D printing of cytocompatible gelatin-cellulose-alginate blend hydrogels(Wiley-V C H Verlag Gmbh, 2020) Erkoc, Pelin; Uvak, Ileyna; Odeh, Yazan Nitham; Akdogan, Ozan; Odeh, Yazan Nitham; Akdogan, Ozan; N/A; Department of Chemistry; Department of Chemical and Biological Engineering; Nazeer, Muhammad Anwaar; Batool, Syeda Rubab; Kızılel, Seda; PhD Student; Researcher; Faculty Member; Department of Chemistry; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; College of Sciences; College of Engineering; N/A; N/A; 283763D bioprinting of hydrogels has gained great attention due to its potential to manufacture intricate and customized scaffolds that provide favored conditions for cell proliferation. Nevertheless, plain natural hydrogels can be easily disintegrated, and their mechanical strengths are usually insufficient for printing process. Hence, composite hydrogels are developed for 3D printing. This study aims to develop a hydrogel ink for extrusion-based 3D printing which is entirely composed of natural polymers, gelatin, alginate, and cellulose. Physicochemical interactions between the components of the intertwined gelatin-cellulose-alginate network are studied via altering copolymer ratios. The structure of the materials and porosity are assessed using infrared spectroscopy, swelling, and degradation experiments. The utility of this approach is examined with two different crosslinking strategies using glutaraldehyde or CaCl2. Multilayer cylindrical structures are successfully 3D printed, and their porous structure is confirmed by scanning electron microscopy and Brunauer-Emmett-Teller surface area analyses. Moreover, cytocompatibility of the hydrogel scaffolds is confirmed on fibroblast cells. The developed material is completely natural, biocompatible, economical, and the method is facile. Thus, this study is important for the development of advanced functional 3D hydrogels that have considerable potential for biomedical devices and artificial tissues.Publication Metadata only A coarse grained simulation study on the morphology of aba triblock copolymers(Elsevier, 2019) Onarana, Gülşah; Yurtsever, Mine; Department of Chemistry; Yılgör, İskender; Faculty Member; Department of Chemistry; College of Sciences; 24181The Dissipative Particle Dynamics (DPD) simulation technique was used to elucidate the composition-dependent equilibrium morphological behavior of three different symmetric ABA triblock copolymers, which were; poly(epsilon-caprolactone)-poly(dimethylsiloxane)-poly(epsilon-caprolactone) (PCL-PDMS-PCL), poly(epsilon-caprolactone)-poly(ethylene oxide)-poly(epsilon-caprolactone) (PCL-PEO-PCL) and poly(L-lactide)-poly(dimethylsiloxane)-poly(L-lactide) (PLLA-PDMS-PLLA). These polymers were chosen due to their biomedical and biotechnological importance. Polymeric A and B blocks were modeled as connected chain of beads with varying incompatibility. The impact of the block incompatibilities on the microphase separation as well as on the equilibrium phase behaviors were investigated at the mesoscopic scale. A detailed visual analysis of the DPD images and constructed phase diagram showed that quite different equilibrium morphologies were attainable by controlling the molecular weights of the blocks and the strength of the intermolecular interaction between them. More compatible A and B blocks underwent lamellar to cylindrical and cylindrical to spherical phase transitions at lower B block concentrations. Our results clearly showed that, Flory-Huggins interaction parameter (chi) and degree of polymerization (N) were the only control parameters, which determined the shape and size of the phase domains, as well as the extent of equilibrium nanophase separation. Our DPD simulated morphologies were compared with experimental images obtained by Atomic Force Microscopy (AFM).Publication Metadata only A coarse graining approach in molecular simulations: fuzzy potentials(Istanbul Technical University, 2003) Department of Chemistry; Department of Chemistry; Yurtsever, İsmail Ersin; Eşsiz, Şebnem; Faculty Member; Undergraduated Student; Department of Chemistry; College of Sciences; College of Sciences; 7129; 191615A new representation for interaction potential functions is presented. Unlike the orthodox approaches, the potential function is not a fixed function in terms of internuclear coordinates but a probabilistic one which contains information over a wide range of angular degrees of freedom. It is shown that such approaches can provide practical solutions for bulk systems of high density.Publication Metadata only A comparative study of the structure-property behavior of highly branched segmented poly(urethane urea) copolymers and their linear analogs(Elsevier Sci Ltd, 2005) Sheth, JP; Unal, S; Beyer, FL; Long, TE; Wilkes, GL; Department of Chemistry; Department of Chemistry; Yılgör, Emel; Yılgör, İskender; Researcher; Faculty Member; Department of Chemistry; College of Sciences; College of Sciences; N/A; 24181The solid-state structure-property behavior of highly branched segmented poly(urethane urea) (PUU) copolymers and their linear analog was investigated. A limited study of their solution theological behavior was also undertaken. The linear PUUs were synthesized by the two-step prepolymer method, whereas the oligomeric A(2) + B-3 methodology was utilized to synthesize the highly branched materials. The soft segments (SS) were either poly(tetramethylene oxide) (PTMO) or poly(propylene oxide) (PPO). All copolymers utilized in this study, with one exception, contained 28 wt% hard segment (HS) content. DMA, SAXS, and AFM studies indicated that the linear as well as the highly branched PUUs were microphase separated. The SS T-g of the highly branched PUUs was nearly identical to that of their respective linear analogs. However, the linear copolymers exhibited broader and less temperature sensitive rubbery plateaus, both attributed to one or both of two reasons. The first is better hydrogen bonding organization of the HS phase as well as greater HS lengths than in the highly branched analogs. The second parameter is that of a potentially higher chain entanglement for the linear systems relative to the branched analogs. Tapping-mode AFM phase images confirmed the microphase morphology indicated by SAXS and DMA. Ambient temperature strain-induced crystallization was observed in the PUU based on PTMO 2040 g/mol at a uniaxial strain of ca. 400%, irrespective of the chain architecture. Stress-strain, stress relaxation, and mechanical hysteresis of the highly branched copolymers were in general slightly poorer than that of their linear analogs. Ambient temperature solution viscosity of the highly branched materials in dimethyl formamide was substantially lower that that of the linear samples of nearly equal molecular weight.Publication Metadata only A comparative study on the effect of monodisperse Au and Ag nanoparticles on the performance of organic photovoltaic devices(Elsevier, 2021) Kacus, Hatice; Sevim, Melike; Biber, Mehmet; Baltakesmez, Ali; Aydogan, Sakir; Department of Chemistry; Metin, Önder; Faculty Member; Department of Chemistry; College of Sciences; 46962The monodisperse Au (similar to 5 nm) and Ag (similar to 3 nm) nanoparticles used in this study were obtained using surfactant-assistant solvothermal methods and characterized by XRD TEM and SEM. Then, these nanoparticles were embedded into the P3HT:PCBM photoactive layer at different ratios and the effects of the nanoparticles on the performance of the organic solar cells have been studied by varying the loading percent of the NPs in the range of 0.5-2 wt%. The best solar cell composition was determined to be 1 wt% for Au NPs and 0.5 wt% for Ag NPs. Optical absorption spectrum of P3HT:PCBM, P3HT:PCBM:AuNPs and P3HT:PCBM:AgNPs active layers were obtained using UV-visible spectroscopy. The J-V plots of ITO/PEDOT:PSS/P3HT:PCBM/LiF/Al solar cells having 1.10(-6) m(2) OSC area and with different Au NPs and Ag NPs loading ratios in the P3HT:PCBM were obtained under air mass (AM) 1.5G illumination. Open circuit voltage, short-circuit current density, fill factor, and power conversion efficiency of the OSC were calculated. The highest PCE values were obtained as 3.35% for Au NPs and as 3.50% for Ag NPs doped devices. This increase in PCEs was explained by a plasmonic effect that stems from the metallic NPs.Publication Metadata only A comprehensive study on the characteristic spectroscopic features of nitrogen doped graphene(Elsevier, 2019) Ogasawara, Hirohito; N/A; N/A; N/A; Department of Chemistry; Solati, Navid; Mobassem, Sonia; Kahraman, Abdullah; Kaya, Sarp; PhD Student; PhD Student; PhD Student; Faculty Member; Department of Chemistry; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Sciences; N/A; N/A; N/A; 116541Despite significant methodical improvements in the synthesis of N-doped graphene, there are still unsolved questions regarding the control of content and the configuration of nitrogen species in graphene honeycomb network. A cross-examination of X-ray photoelectron spectroscopy and Raman spectroscopy findings indicates that the nitrogen dopant amount is graphene thicknesses dependent, but the various nitrogen dopant coordination can be obtained on both double- and few-layer graphene. Characteristic defect features (D') appearing in Raman spectra upon N-doping is sensitive to nitrogen dopant coordination, graphitic-pyridinic/nitrilic species and therefore the doping level can be identified. Pyridinic and nitrilic nitrogen as primary species turn graphene to p-type semiconductor after a mild thermal treatment.Publication Metadata only A DFT study of polymerization mechanisms of indole(Elsevier Sci Ltd, 2002) Yurtsever, Mine; Department of Chemistry; Yurtsever, İsmail Ersin; Faculty Member; Department of Chemistry; College of Sciences; 7129Polymerization of unsubstituted indoles is studied by accurate density functional theory calculations. Relative stability of all possible dimers of indole is computed in order to understand the thermodynamics of polymerization. It is observed that 2-position is the most likely site to enhance polymerization. A selected set of trimers and tetramers which use a 2-position for linkages are generated to understand the further growth of polyindole. A study of local minima arising from different distributions of the torsional angles reveals that there are two equally probable conformations and the one with the torsional angle changing signs alternatively is slightly favored. The cyclic structures are also investigated and it is shown that it is possible to generate stable three- and four-membered cyclic structures. Finally, the structures of radical cations and intermediate states are fully optimized and the energetics of these metastable species are used to explain the competing mechanisms of radical-radical and radical-neutral pathways.Publication Metadata only A facile route for the preparation of silver nanoparticles-graphene oxide nanocomposites and their interactions with pyronin Y dye molecules(Elsevier, 2019) Senol, Ayse Merve; Onganer, Yavuz; Department of Chemistry; Metin, Önder; Faculty Member; Department of Chemistry; College of Sciences; 46962We report a facile synthesis of silver nanoparticles-graphene oxide (AgNPs-GO) nanocomposites and their interactions with Pyronin Y (PyY) molecules studied by UV-Vis absorption, steady-state and time-resolved fluorescence spectroscopy techniques in aqueous solution. With this aim, firstly, monodisperse AgNPs with two different sizes (4 and 6 nm) were synthesized by using a surfactant-assisted organic solution phase protocol comprising the consecutive thermal decomposition and reduction of silver (I) acetate. Secondly, AgNPs were anchored into GO nanoflakes via using liquid self-assembly method to prepare AgNPs-GO nanocomposites. The morphology and structure of both colloidal AgNPs and the AgNPs-GO nanocomposites were characterized by transmission electron microscopy (TEM), scanning electron microscopy (SEM), X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FT-IR) and absorption spectroscopy. Finally, AgNPs-GO nanocomposites were interacted with PyY molecules in aqueous solution and the photophysical properties of PyY were studied by UV-Vis absorption and fluorescence (steady-state and time-resolved) spectroscopy techniques. The spectroscopic results revealed that the photophysical properties of the dye were dramatically changed after its interaction with AgNPs-GO nanocomposites in aqueous solution.Publication Metadata only A facile synthesis of mesoporous graphitic carbon nitride supported palladium nanoparticles as highly effective and reusable catalysts for Stille coupling reactions under mild conditions(Royal Soc Chemistry, 2020) N/A; Department of Chemistry; N/A; Department of Chemistry; Department of Chemistry; Kalay, Erbay; Çetin, Sultan; Kölemen, Safacan; Metin, Önder; Researcher; PhD Student; Faculty Member; Faculty Member; Department of Chemistry; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); College of Sciences; Graduate School of Sciences and Engineering; College of Sciences; College of Sciences; 59456; N/A; 272051; 46962The development of a Stille coupling protocol that is operable under moderate conditions without using a base is highly required for the synthetic organic chemistry community, which requires an efficient nanocatalyst. In this respect, addressed herein is a facile one-pot synthesis of mesoporous graphitic carbon nitride (mpg-CN) supported Pd NPs, denoted as mpg-CN/Pd hereafter, and investigation of their catalytic activity in Stille cross-coupling reactions for the first time. It has been demonstrated that mpg-CN nanosheets can serve as not only a support material but also a stabilizer for the generation of 4.5 nm Pd NPs. The ecofriendly generated heterogeneous nanocatalyst was characterized by TEM, XRD, XPS, BET surface area and ICP-MS analysis. The mpg-CN/Pd nanocatalysts showed high activity in the Stille coupling reaction of a variety of electron-deficient and electron-rich aryl iodides/bromides and two different organostannanes with a wide substrate scope to afford the corresponding biaryls without using any bases and additional ligands under relatively mild conditions. The catalyst can be easily recovered from the reaction medium by centrifugation. It can be reused at least 5 times without any loss of activity.Publication Metadata only A facile synthesis of monodisperse cobalt–ruthenium alloy nanoparticles as catalysts for the dehydrogenation of morpholine borane and the hydrogenation of various organic compounds(Royal Soc Chemistry, 2022) Can, Hasan; Can, Sumeyra; Ebiri, Rustem; Department of Chemistry; Metin, Önder; Faculty Member; Department of Chemistry; College of Sciences; 46962Herein we report a novel wet-chemical protocol for the composition-controlled synthesis of monodisperse cobalt-ruthenium (CoRu) alloy NPs and their catalysis in the hydrolytic dehydrogenation of morpholine borane (MB) for chemical hydrogen storage and the hydrogenation of various organic compounds using MB as a hydrogen source. Monodisperse CoRu NPs with an average particle size of 1.7 +/- 0.6 nm at three different alloy compositions were prepared by the presented novel protocol that comprises the reduction of in situ formed ruthenium(iii) oleate complex with dicobalt octacarbonyl (Co-2(CO)(8)) in the presence of oleylamine (OAm). Next, as-synthesized CoRu alloy NPs were supported on carbon black (VC) and reduced graphene oxide (rGO) to study their catalysis in the dehydrogenation of MB and the transfer hydrogenation of various organic compouns bearing unsaturated functional groups (nitro, nitrile and carbonyl) using MB as a hydrogen source, respectively. VC-CoRu nanocatalysts exhibited a higher catalytic activity in hydrogen generation from the hydrolysis of MB with an initial turnover frequency (TOF) of 95 mol H-2*(mol (Co + Ru) min)(-1) while rGO-CoRu nanocatalysts showed better catalytic performance in the transfer hydrogenation reactions. All tested unsatured organic compounds (30 examples in total) are converted into corresponding hydrogenated products with the yields reaching up to 99% under mild conditions.Publication Open Access A high-performance metal-free hydrogen-evolution reaction electrocatalyst from bacterium derived carbon(Royal Society of Chemistry (RSC), 2015) Wei, Li; Karahan, Hüseyin Enis; Goh, Kunli; Jiang, Wenchao; Yu, Dingshan; Jiang, Rongrong; Chen, Yuan; Department of Chemistry; Birer, Özgür; Researcher; Department of Chemistry; College of SciencesWe report a sustainable approach to obtain carbon materials with nitrogen and phosphorus dual functionalities from a common bacterium strain (S. aureus) as a highly efficient hydrogen-evolution reaction (HER) catalyst. With mesoporous structure introduced by ZnCl2 salt and cathodic activation, it demonstrates an onset overpotential as low as 76 mV, a Tafel slope of 58.4 mV dec(-1) and a large normalized exchange current density of 1.72 x 10(-2) mA cm(-2), which are comparable to those of hitherto best metal-free and well-fabricated metallic HER catalystsPublication Metadata only A hydrogen peroxide responsive resorufin-based phototheranostic agent for selective treatment of cancer cells(Elsevier Sci Ltd, 2021) Department of Chemistry; Department of Chemistry; Almammadov, Toghrul; Kölemen, Safacan; Researcher; Faculty Member; Department of Chemistry; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Koç University Tüpraş Energy Center (KUTEM) / Koç Üniversitesi Tüpraş Enerji Merkezi (KÜTEM); Koç University Boron and Advanced Materials Application and Research Center (KUBAM) / Koç Üniversitesi Bor ve İleri Malzemeler Uygulama ve Araştırma Merkezi (KUBAM); College of Sciences; College of Sciences; N/A; 272051Enhanced selectivity towards cancer cells is one of the most essential features sought in new generation photodynamic therapy (PDT) agents in order to minimize the side effects on healthy cells and to improve the efficacy of the treatment. In this direction, one promising approach is to design activatable photosensitizers, which tend to stay in an OFF state and get activated only in cancer cells with tumor-associated stimuli. Based on this idea, herein we introduced a hydrogen peroxide (H2O2) activatable iodinated resorufin (RR-1) as a redshifted, water soluble and cancer cell selective photosensitizer. RR-1 exhibited high singlet oxygen quantum yield in aqueous solutions upon reacting with H2O2 and induced selective photocytotoxicity in colorectal (HCT116) and triple negative breast (MDA MB-231) cancer cells, which contain high level of reactive oxygen species (ROS). Additionally, fluorescence signal of the iodo-resorufin core was restored upon cleavage of the cage unit in these cancer cells. In contrast, very low photocytotoxicity and negligible fluorescence enhancement were observed in normal fibroblast (NIH-3T3) cells. RR-1 not only marks the first example of a H2O2 activatable resorufin-based photosensitizer but also represents the first ever resorufin-based theranostic agent. We anticipate that iodo-resorufin scaffold can be easily modified with different masking units towards realization of highly selective and efficient phototheranostic agents for treatment of various cancer cells.Publication Metadata only A leucine aminopeptidase activatable photosensitizer for cancer cell selective photodynamic therapy action(Elsevier Sci Ltd, 2021) N/A; N/A; N/A; Department of Chemistry; N/A; Department of Physics; Department of Chemistry; Department of Chemistry; Arslan, Büşra; Bilici, Kübra; Demirci, Gözde; Almammadov, Toghrul; Khan, Minahil; Sennaroğlu, Alphan; Acar, Havva Funda Yağcı; Kölemen, Safacan; Master Student; PhD Student; Master Student; Researcher; PhD Student; Faculty Member; Faculty Member; Faculty Member; Department of Physics; Department of Chemistry; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Koç University Boron and Advanced Materials Application and Research Center (KUBAM) / Koç Üniversitesi Bor ve İleri Malzemeler Uygulama ve Araştırma Merkezi (KUBAM); Koç University Tüpraş Energy Center (KUTEM) / Koç Üniversitesi Tüpraş Enerji Merkezi (KÜTEM); Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Sciences; Graduate School of Sciences and Engineering; College of Sciences; College of Sciences; College of Sciences; N/A; N/A; N/A; N/A; N/A; 23851; 178902; 272051Activity based photosensitizers (PS) continue to attract great attention as they enable selective photodynamic therapy action on cancer cells while sparing normal cells even under light irradiation. Sensitivity to specific enzymes that are differentially overexpressed in cancer cells is crucial in the design of activatable PSs. In this direction, we report here, for the first time, a leucine aminopeptidase (LAP) activatable PDT agent (HCL), which is a red-shifted, water soluble and photostable brominated hemicyanine derivative. HCL was activated by endogenous LAP enzyme selectively in A549 (lung) and HCT116 (colon) cancer cells containing high LAP levels and induced effective photocytotoxicity with negligible dark toxicity. Furthermore, the fluorescence of the parent bromo-hemicyanine core was restored upon LAP-based activation in cancer cells. On the other side, no remarkable phototoxicity or fluorescence turn-on was detected in healthy L929 cells. Thus, HCL serves as an effective and tumour associated LAP-sensitive phototheranostic agent. We believe different cancer-associated analytes can be utilized in combination with near-IR absorbing scaffolds in the scope of activatable PDT designs to enrich the tumour-selective PS arsenal.Publication Metadata only A metal nitride carbodiimide with a stuffed skutterudite-type structure: synthesis, crystal structure and ir spectra of (BA6N 5/6)2[NBN4][CN2]6(Walter de Gruyter, 2007) Reckeweg, Olaf; Disalvo, Francis J.; Department of Chemistry; Somer, Mehmet Suat; Faculty Member; Department of Chemistry; College of Sciences; 178882Coppery-red, transparent single crystals of (Ba6N 5/6)2[NbN4][CN2]6 [NbN4] [CN2]6 (Im3̄, no. 204, a = 1125.83(3) pm, Z = 2) are obtained by the reaction of Ba2N and ZnCN2 with the container walls of the arc-welded Nb ampoules at 1100 K. The title compound assumes a stuffed skutterudite-type structure in which edge-sharing (Ba6N5/6) octahedra form large voids which are occupied by either [NbN4] tetrahedra or by [N=C=N]2- units with symmetric C=N bond lengths of d = 121.8(6) pm but a bond angle deviating significantly from linearity (∠(N-C-N) = 175.3(9)°). The IR spectra corroborate this crystallographic result by the fact that all fundamental vibrations are visible in the IR spectrum [v1 = 1262 (symmetric stretching mode); v2 = 1957/2009 (antisymmetric stretching mode); v3 = 611/633/653 cm-1 (bending modes)], which is symmetry forbidden for [N=C=N]2- units having D∞h symmetry but expected for the C2v symmetry found in the title compound.Publication Metadata only A metal nitride carbodiimide with a stuffed skutterudite-type structure: synthesis, crystal structure and IR spectra of (Ba6N5/6) 2[NbN4][CN2] 6(Walter De Gruyter Gmbh, 2007) Reckeweg, Olaf; DiSalvo, Francis J.; Department of Chemistry; Somer, Mehmet Suat; Faculty Member; Department of Chemistry; College of Sciences; 178882Coppery-red, transparent single crystals of (Ba6N5/6)(2)[NbN4][CN2](6) (Im (3) over bar, no. 204, a = 1125.83(3) pm, Z = 2) are obtained by the reaction of Ba2N and ZnCN2 with the container walls of the arc-welded Nb ampoules at 1100 K. The title compound assumes a stuffed skutterudite-type structure in which edge-sharing (Ba6N5/6) Octahedra form large voids which are occupied by either [NbN4] tetrahedra or by [N=C=N](2-) units with symmetric C=N bond lengths of d = 121.8(6) pm but a bond angle deviating significantly from linearity (measured angle(N-C-N) = 175.3(9)degrees). The IR spectra corroborate this crystallographic result by the fact that all fundamental vibrations are visible in the IR spectrum [v(1) = 1262 (symmetric stretching mode); v(2) = 1957/2009 (antisymmetric stretching mode); v(3) = 611/633/653 cm(-1) (bending modes)], which is symmetry forbidden for [N=C=N](2-) units having D-infinity h symmetry but expected for the C-2v symmetry found in the title compound.Publication Metadata only A mixed basis with off-center Gaussian functions for the calculation of the potential energy surfaces for pi-stacking interactions: dimers of benzene and planar C-6(Springer, 2015) Department of Chemistry; Yurtsever, İsmail Ersin; Faculty Member; Department of Chemistry; College of Sciences; 7129A practical mixed basis set was developed to facilitate accurate calculations of potential energy surfaces for pi-stacking interactions. Correlation consistent basis sets (cc-PVXZ) were augmented by p-type Gaussian functions placed above and below the planes of C-6 moieties. Moller-Plesset (MP2, SCS-MP2) and coupled cluster [CCSD(T)] calculations show that such generated basis sets provide an accurate description of p-stacking systems with favorable computation times compared to the standard augmented basis sets. The addition of these off-center functions eliminates the linear dependence of the augmented basis sets, which is one of the most encountered numerical problems during calculation of the oligomers of polyaromatic hydrocarbons (PAH). In this work, we present a comparative study of the general characteristics of the potential energy surfaces for the parallel stacked and T-shape conformations of benzene and planar C6 clusters, using a combination of cc-PVXZ and our optimized functions. We discuss properties, such as the depth and curvature of the potential functions, short and long distance behavior, and the frictional forces between two model monomers.