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Publication Metadata only (Bis)phosphonic acid-functionalized poly(ethyleneimine)- poly(amido amine)s for selective in vitro transfection of osteosarcoma cells(Amer Chemical Soc, 2021) Güven, Melek Naz; Altuncu, Seçkin; Konca, Yeliz Utku; Avcı, Duygu; N/A; Department of Chemistry; Demirci, Gözde; Acar, Havva Funda Yağcı; Master Student; Faculty Member; Department of Chemistry; Graduate School of Sciences and Engineering; College of Sciences; N/A; 178902Osteosarcoma is aggressive bone cancer, whose treatment has not changed significantly for the past few decades. Although gene therapy methods have emerged as potential treatment routes, the need for efficient and nontoxic gene delivery systems targeting osteosarcoma cells remains a challenge. High-molecular-weight poly(ethyleneimine)s (PEIs) are used as universal transfection agents; however, they cause significant cytotoxicity. on the other hand, poly(amido amine)s (PAAs) are biocompatible, biodegradable polymers with promising transfection efficiency, which should be improved further. In this paper, we combined low-molecular-weight branched PEI (1800 Da) and PAA macromers functionalized with various amounts of (bis)phosphonic acid groups and pentanol (via 5-amino-1-pentanol (AP)). The (bis)phosphonic acid groups on these polymers (PAEIs) are intended to facilitate bone targeting. The molecular weights of the PAEI polymers were between 2600 and 8600 g/mol. Their cytotoxicities and green fluorescence protein (GFP) transfection efficiencies were tested on an osteosarcoma cell line (U-2 OS cells), which is challenging to transfect, and healthy muscle cells (C2C12). Both the cytotoxicity and transfection efficiency of PAEIs were affected by the phosphonic acid (via APA, 2-aminoethyl phosphonic acid) or bisphosphonic acid (via ALE, sodium alendronate) content of the polymers. PAEIs are more cytocompatible than both linear and branched 25 kDa PEI. ALE-containing PAEIs provided better transfection than APA-containing ones. The most efficient PAEI polymer, containing a 0.7:0.3 AP/ALE ratio, displayed a transfection efficiency that was five times higher than that of 25 kDa PEI with dramatically better cytocompatibility. This is comparable to FuGENE, but PAEI is more advantageous in selective transfection of the U-2 OS. This set of polymers may be promising candidates for targeted gene therapy of osteosarcoma.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 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 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 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 new antiaromatic compound: 1,4-biphenylenequinone synthesis and trapping reactions(American Chemical Society (ACS), 1997) Kılıç, Hamdullah; Balcı, Metin; Department of Chemistry; Yurtsever, İsmail Ersin; Faculty Member; Department of Chemistry; College of Sciences; 7129N/APublication Open Access A new class of porous materials for efficient CO2 separation: ionic liquid/graphene aerogel composites(Elsevier, 2021) Department of Chemical and Biological Engineering; N/A; Department of Chemistry; Zeeshan, Muhammad; Yalçın, Kaan; Keskin, Seda; Uzun, Alper; Öztuna, Feriha Eylül Saraç; Ünal, Uğur; PhD Student; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; Department of Chemistry; Koç University Tüpraş Energy Center (KUTEM) / Koç Üniversitesi Tüpraş Enerji Merkezi (KÜTEM); Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Graduate School of Sciences and Engineering; College of Engineering; College of Sciences; N/A; N/A; 40548; 59917; N/A; 42079Here, we report a new post-synthesis modification strategy for functionalizing reduced graphene aerogels (rGAs) towards an exceptional CO2 separation performance. 1-N-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]) was impregnated on a rGA, prepared by reducing GA at 700 degrees C, at various ionic liquid (IL) loadings of 5, 10, 30, and 50 wt%. The resulting composites were characterized in deep detail by X-ray photoelectron spectroscopy, X-ray diffraction, N-2 physical adsorption measurements, scanning electron microscopy, Fourier transform infrared and Raman spectroscopies, and thermogravimetric analysis. Results indicated the presence of interactions between the rGA surface and the anion of the IL, potentially improving the CO2 affinity. Volumetric gas adsorption measurements using these materials showed that the deposition of [BMIM][PF6] on rGA surface at an IL loading of 50 wt% boosts the CO2/CH4 selectivity by more than 20-times, exceeding an absolute value of 120, a remarkably higher CO2/CH4 selectivity compared to that of other functionalized materials under similar operating conditions. Tunability of both the IL structure and the surface characteristics of rGA offer a tremendous degree of flexibility for the rational design of these IL/rGA composites towards high performance in gas separation applications.