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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 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.Publication Metadata only A new substrate for glutathione reductase: glutathione coated Ag2S quantum dots(Elsevier, 2019) N/A; N/A; N/A; Department of Chemistry; N/A; Aydemir, Duygu; Hashemkhani, Mahshid; Durmuşoğlu, Emek Göksu; Acar, Havva Funda Yağcı; Ulusu, Nuriye Nuray; PhD Student; PhD Student; PhD Student; Faculty Member; Faculty Member; Department of Chemistry; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Graduate School of Health Sciences; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Sciences; School of Medicine; N/A, N/A; N/A; 178902; 6807Glutathione (GSH), a key player in various cellular processes including detoxification, anti-oxidant defense system and cell proliferation is also a potentially good coating material for luminescent quantum dots. GSH is oxidized to oxidized glutathione (GSSG) under oxidative stress and then reduced back by glutathione reductase (GR) enzyme to maintain the balance of GSH/GSSG ratio. In this frame, GSH stabilized quantum dots (QDs) have never been evaluated as GR substrate. Here, GSH coated Ag2S QDs, luminescent in the medical window, were prepared and their GR activity were tested. We have shown by spectrophotometric methods that GSH-Ag2S acted as a substrate-analog for GR enzyme that had lower activity compared to the original substrate GSSG. These results provide a new perspective in the evaluation of QDs in medical applications, enzyme activity or level detection as well as possible means to study enzymes.Publication Open Access A new type of microphotoreactor with integrated optofluidic waveguide based on solid-air nanoporous aerogels(Royal Society of Chemistry (RSC), 2018) Jonas, Alexandr; Department of Chemistry; Department of Electrical and Electronics Engineering; Department of Physics; Özbakır, Yaprak; Erkey, Can; Kiraz, Alper; PhD Student; Faculty Member; Faculty Member; Department of Chemistry; Department of Electrical and Electronics Engineering; Department of Physics; College of Engineering; College of Sciences; N/A; 29633; 22542In this study, we developed a new type of microphotoreactor based on an optofluidic waveguide with aqueous liquid core fabricated inside a nanoporous aerogel. To this end, we synthesized a hydrophobic silica aerogel monolith with a density of 0.22 g cm(-3) and a low refractive index of 1.06 that-from the optical point of view-effectively behaves like solid air. Subsequently, we drilled an L-shaped channel within the monolith that confined both the aqueous core liquid and the guided light, the latter property arising due to total internal reflection of light from the liquid-aerogel interface. We characterized the efficiency of light guiding in liquid-filled channel and-using the light delivered by waveguiding-we carried out photochemical reactions in the channel filled with aqueous solutions of methylene blue dye. We demonstrated that methylene blue could be efficiently degraded in the optofluidic photoreactor, with conversion increasing with increasing power of the incident light. The presented optofluidic microphotoreactor represents a versatile platform employing light guiding concept of conventional optical fibres for performing photochemical reactions.Publication Metadata only A post-HF study on the interaction of iodine with small polyaromatic hydrocarbons(Springer, 2014) Sutay, Berkay; Yurtsever, Mine; Department of Chemistry; Yurtsever, İsmail Ersin; Faculty Member; Department of Chemistry; College of Sciences; 7129In this work, we present a theoretical study of the interaction between a diatomic iodine molecule with planar naphthalene and several other small polyaromatic hydrocarbons (PAHs). Our aim was to understand the general characteristics of the potential energy surface (PES) of this system; that is locating various local minima, finding the variation of PES around these optimum points by means of first principle calculations at MP2, SCS-MP2 and CCSD(T) levels of theory. Two basic orientations of the iodine molecule, i.e., parallel or perpendicular with respect to the naphthalene plane, are discussed. The PES of the former was investigated in detail, including the translation and rotation of I-2 (as a rigid rotor) along the naphtalene surface. It was concluded that, although the perpendicular conformations are usually 1 kcal mol(-1) more stable than the parallel conformation, this small difference does not exclude the presence of both conformations in the gas phase. Both structures were stable enough to hold more than 20 vibrational states. NBO analysis showed that the mutual polarization effects were greater for the perpendicular conformation. It was also observed that the I-2+naphtalene dimer interaction is almost twice of that of I-2+naphtalene, showing the long range character of the interaction.Publication Metadata only Acetylene-furan trimer formation at 0.37 K as a model for ultracold aggregation of non- and weakly polar molecules(Bilkent University, 2011) Metzelthin, Anja; Sánchez-García, Elsa; Schwaab, Gerhard; Thiel, Walter; Sander, Wolfram; Havenith, Martina; Department of Chemistry; Birer, Özgür; Researcher; Department of Chemistry; College of Sciences; N/AWe have studied the aggregation process of (C2H 2)⋯furan trimers at ultracold temperatures (0.37 K) in helium nanodroplets. Computational sampling of the potential energy surface using the multiple-minima-hypersurface (MMH) approach yielded seven possible minimum structures, optimized at the MP2 level of theory with the cc-pVTZ and 6-311++G(d,p) basis sets. Experimentally, we could assign five transitions in the IR spectrum of acetylene-furan aggregates in the acetylene C-H asym stretch region between 3240 and 3300 cm-1 to vibrational bands of the 2:1 acetylene-furan trimer. The transitions were assigned to three ring structures that all contain the T-shaped acetylene dimer as structural sub-motif. Two of the structures form a nonplanar ring involving a C-HAc⋯πFu bond, the third is a nearly planar ring containing a C-HAc⋯OFu bond. This assignment was corroborated by quantum mechanical/molecular dynamics (QM/MD) simulations mimicking in detail the aggregation process of precooled monomers. The simulations provided evidence for a transition from a higher level local minimum to the global minimum state over a small barrier during the aggregation process. The experimentally observed structures can be explained by a step-by-step aggregation of moieties pre-cooled to 0.37 K that are steered by intermediate and short-range electrostatic interactions. Thus, we are able to unravel a special aggregation mechanism which differs from aggregation of molecules with large dipole moments where this aggregation process is dominated by long range 1/r3 dipole-dipole interaction ("electrostatic steering"). This mechanism is expected to be a general mechanism in ultracold chemistry. Brrrr-cold! The aggregation process of (C2H 2)⋯furan trimers at ultracold temperatures (0.37 K) in helium nanodroplets is studied by a combination of computational and spectroscopic techniques. The results unravel a special aggregation mechanism for non- and weakly polar molecules, which is expected to be generally applicable in ultracold chemistry.Publication Open Access Activity-based photosensitizers with optimized triplet state characteristics toward cancer cell selective and image guided photodynamic therapy(American Chemical Society (ACS), 2022) Elmazoğlu, Zübeyir; Kepil, Dilay; Etienne, Thibaud; Marion, Antoine; Günbaş, Görkem; Department of Chemistry; Kılıç, Eda; 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); Graduate School of Sciences and Engineering; College of Sciences; N/A; N/A; 272051Activity-based theranostic photosensitizers are highly attractive in photodynarnic therapy as they offer enhanced therapeutic outcome on cancer cells with an imaging opportunity at the same time. However, photosensitizers (PS) cores that can be easily converted to activity-based photosensitizers (aPSs) are still quite limited in the literature. In this study, we modified the dicyanomethylene-4H-chromene (DCM) core with a heavy iodine atom to get two different PSs (DCMo-I, I-DCMo-Cl) that can be further converted to aPS after simple modifications. The effect of iodine positioning on singlet oxygen generation capacity was also evaluated through computational studies. DCMo-I showed better performance in solution experiments and further proved to be a promising phototheranostic scaffold via cell culture studies. Later, a cysteine (Cys) activatable PS based on the DCMo-I core (DCMo-I-Cys) was developed, which induced selective photocytotoxicity along with a fluorescence turn-on response in Cys rich cancer cells.Publication Metadata only Ae[Be2N2]: nitridoberyllates of the heavier alkaline-earth metals(Wiley-V C H Verlag Gmbh, 2004) Yaraşık, A; Akselrud, L; Leoni, S; Rosner, H; Schnelle, W; Kniep, R; Department of Chemistry; Somer, Mehmet Suat; Faculty Member; Department of Chemistry; College of Sciences; 178882N/A