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Publication Metadata only A three-dimensional silver(I) framework assembled from 3,3′- thiodipropionate: synthesis, structure and molecular simulations for hydrogen gas adsorption(Pergamon-Elsevier Science Ltd, 2012) Arıcı, Mürsel; Yeşilel, Okan Zafer; Taş, Murat; Department of Chemical and Biological Engineering; Keskin, Seda; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 40548A novel three dimensional Ag(I)-3,3'-thiodipropionate metal organic framework, [Ag-2(mu(8)-tdp)](n) (1) (tdpH(2) = 3,3'-thiodipropionic acid), was synthesized and structurally characterized by FT-IR and photoluminescence spectroscopy, single crystal X-ray diffraction techniques and thermal analysis (TG, DTG and DTA). The compound crystallized in the monoclinic crystal system with the space group C2/c. The X-ray crystallographic study of 1 shows a short Ag center dot center dot center dot Ag contact with a distance of 3.022 angstrom. The most striking feature of 1 is that it exhibits a 3D porous framework with 1D infinite channels, and complex 1 exhibits strong fluorescent emission bands in the solid state at room temperature. Moreover, atomically detailed simulations were used to assess the potential of the complex for H-2 storage applications.Publication Metadata only A zinc(II) metal organic framework based on flexible o-phenylenediacetate and rigid 4,4′-azobis(pyridine) ligands: synthesis, crystal structure and hydrogen gas adsorption property(Pergamon-Elsevier Science Ltd, 2015) Gunay, Gunes; Yesilel, Okan Zafer; Erer, Hakan; Tabak, Ahmet; Department of Chemical and Biological Engineering; Keskin, Seda; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 40548A new three-dimensional (3D) metal organic framework, [Zn-2(mu(4)-o-pda)(2)(mu-abpy)](n) (1), has been synthesized by the hydrothermal reaction and characterized by FT-IR spectroscopy, elemental analysis, thermal analysis, X-ray powder diffraction, and single crystal X-ray diffraction techniques (o-H(2)pda = o-phenylenediacetic acid and abpy = 4,4'-azobis(pyridine)). Single crystal X-ray diffraction study reveals that complex 1 exhibits a binodal (3,7)-connected three-dimensional framework (3D) with the point symbol of (3.5(2))(3(2).4(4).5(7).6(7).7). Thermal analysis reveal that complex 1 is stable up to 300 degrees C. In order to investigate the potential of 1 in gas storage applications, we performed experiments and atomically detailed simulations to obtain H-2 adsorption isotherm at a pressure range of 0-1 atm at 77 K.Publication Open Access Case study of high-throughput drug screening and remote data collection for SARS-CoV-2 main protease by using serial femtosecond X-ray crystallography(Multidisciplinary Digital Publishing Institute (MDPI), 2021) Botha, Sabine; Ketawala, Gihan; Su, Zhen; Hayes, Brandon; Poitevin, Frederic; Batyuk, Alexander; Yoon, Chun Hong; Kupitz, Christopher; Durdağı, Serdar; Sierra, Raymond G.; Department of Molecular Biology and Genetics; Department of Chemical and Biological Engineering; Güven, Ömür; Gül, Mehmet; Ayan, Esra; Johnson, Jerome Austin; Çakılkaya, Barış; Karakadıoğlu, Gözde Usta; Ertem, Fatma Betül; Tokay, Nurettin; Yüksel, Büşra; Göcenler, Oktay; Büyükdağ, Cengizhan; Demirci, Hasan; PhD Student; Master Student; Undergraduate Student; Undergraduate Student; Faculty Member; Department of Molecular Biology and Genetics; Department of Chemical and Biological Engineering; Koç Üniversitesi İş Bankası Enfeksiyon Hastalıkları Uygulama ve Araştırma Merkezi (EHAM) / Koç University İşbank Center for Infectious Diseases (KU-IS CID); Graduate School of Sciences and Engineering; College of Sciences; N/A; N/A; N/A; N/A; N/A; N/A; N/A; N/A; N/A; N/A; N/A; 307350Since early 2020, COVID-19 has grown to affect the lives of billions globally. A worldwide investigation has been ongoing for characterizing the virus and also for finding an effective drug and developing vaccines. As time has been of the essence, a crucial part of this research has been drug repurposing; therefore, confirmation of in silico drug screening studies have been carried out for this purpose. Here we demonstrated the possibility of screening a variety of drugs efficiently by leveraging a high data collection rate of 120 images/second with the new low-noise, high dynamic range ePix10k2M Pixel Array Detector installed at the Macromolecular Femtosecond Crystallography (MFX) instrument at the Linac Coherent Light Source (LCLS). The X-ray Free-Electron Laser (XFEL) is used for remote high-throughput data collection for drug repurposing of the main protease (Mpro) of SARS-CoV-2 at ambient temperature with mitigated X-ray radiation damage. We obtained multiple structures soaked with nine drug candidate molecules in two crystal forms. Although our drug binding attempts failed, we successfully established a high-throughput Serial Femtosecond X-ray crystallographic (SFX) data collection protocol.Publication Metadata only Different dimensionality in Mn(II), Co(II) and Ni(II) aminoisophthalate metal-organic compounds: synthesis, characterization and gas adsorption properties(Pergamon-Elsevier Science Ltd, 2012) Gunay, Handan; Colak, Alper Tolga; Yesilel, Okan Zafer; Buyukgungor, Orhan; Department of Chemical and Biological Engineering; Keskin, Seda; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 40548Five new 5-aminoisophthalic acid (H(2)aip) complexes with Mn(II), Co(II) and Ni(II) ions, {[Mn-2(mu(3)-aip)(2)(bipy)(2)]center dot 2DMF center dot 2H(2)O)(n) (1), [Co(pmi)(H2O)(4)]center dot 2H(2)O (2), {[Ni(mu-aip)(H2O)(2)(en)]center dot 3H(2)O)(n) (3), [Ni(mu(3)-aip)(im)(H2O)(2)](n) (4) and [Ni(aip)(phen)(H2O)(3)]center dot 2H(2)O (5) (H(2)aip = 5-aminoisophthalic acid, bipy = 2,2'-bipyridine, pmi = 5-(pyridin-2-ylmethylamino)isophthalate, en = ethylenediamine, im = imidazole, phen = 1,10-phenanthroline) were synthesized at room temperature. The compounds were characterized by elemental analysis, magnetic and spectroscopic measurements (UV-Vis and FT-IR), single crystal X-ray diffraction techniques and thermal analysis (TG, DTG and DTA). Furthermore, in order to assess the potentials of the complexes in gas storage applications, we performed atomically detailed simulations. The single crystal X-ray diffraction study of 1 reveals a 2D coordination polymer. The 2D layers are extended into a 3D supramolecular network with 1D channel via interlayer pi center dot center dot center dot pi stacking interactions between bipy ligands. The voids of the channels are filled with guest water and DMF molecules. Schiff base complex 2 has been obtained from H(2)aip, pyridine-2-carboxaldehyde and CoCl(2 center dot)6H(2)O in a one-pot reaction. Compound 2 is a discrete mononuclear complex which crystallizes in the space group P2(1)/c. Complex 3 is a 1D coordination polymer and the Ni(II) ion is six-coordinated in a distorted octahedral geometry. In 3, aip exhibits a new coordination mode as a bis(monodentate) bridging ligand. Complexes 2 and 3 show 2D and 1D metal-water clusters between metal ions and water molecules, respectively. Complex 4 reveals a 2D coordination polymer that crystallizes in the space group P2(1)/c. Adjacent 2D layers are further extended into a 3D supramolecular network by hydrogen bonds and pi center dot center dot center dot pi interactions. The crystal analysis of 5 reveals that it is a mononuclear complex and the Ni(II) ion exhibits a distorted octahedral geometry.Publication Open Access Enhancing CO2/CH4 and CO2/N-2 separation performances of ZIF-8 by post-synthesis modification with [BMIM][SCN](Elsevier, 2018) Department of Chemical and Biological Engineering; Keskin, Seda; Uzun, Alper; Zeeshan, Muhammad; Faculty Member; PhD Student; Department of Chemical and Biological Engineering; 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; 40548; 59917; N/AIonic liquid (IL)-incorporated metal organic frameworks (MOFs) are promising materials for gas adsorption and separation processes. In this work, 1-n-butyl-3-methylimidazolium thiocyanate ([BMIM][ SCN]) was incorporated in a zeolitic imidazolate framework (ZIF-8) to examine the adsorption and separation of different gases. X-ray diffraction (XRD) and scanning electron microscopy (SEM) results confirmed that ZIF-8 retains its structural integrity in the IL-incorporated sample. The Brunauer-Emmett-Teller (BET) surface area and pore volume of the IL-incorporated sample decreased significantly indicating the IL confinement into the MOF. Results of thermogravimetric analysis (TGA) demonstrate changes in the decomposition temperatures of both bulk IL and pristine ZIF-8 when the IL was incorporated into the MOF pores. Fourier transform infrared (FTIR) spectroscopy was performed to confirm the presence of interactions and successful incorporation of IL into MOF. Gas adsorption isotherms of CO2, CH4, and N-2 were measured for pristine ZIF-8 and IL-incorporated ZIF-8. The uptake amounts for each gas decreased as compared to their values on pristine ZIF-8, however, the decrease in the CO2 uptake was less compared to CH4 and N-2. The IL-incorporated sample exhibited approximately 2.6-times higher ideal selectivity for CO2/CH4 and four-times higher ideal selectivity for CO2/N-2 at 1 mbar than their corresponding values for pristine ZIF-8. These results indicate that IL-MOF combinations offer a huge potential for gas separations.Publication Open Access Fast and selective adsorption of methylene blue from water using [BMIM][PF6]-incorporated UiO-66 and NH2-UiO-66(American Chemical Society (ACS), 2020) Department of Chemical and Biological Engineering; N/A; Kulak, Harun; Keskin, Seda; Uzun, Alper; Kavak, Safiyye; Polat, Hüsamettin Mert; Faculty Member; Department of Chemical and Biological Engineering; 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; N/A; 40548; 59917; N/A; N/AIncorporation of ionic liquids (ILs) into metal-organic frameworks (MOFs) offers a broad potential in various applications. However, their applications in wastewater treatment have remained unexplored. Here, we investigate their potential in wastewater treatment and demonstrate a new concept of IL incorporation in ligand-functionalized MOFs, introducing IL/FMOFs. The composites were prepared by incorporating 1-n-butyl-3-methylimidazolium hexafluorophosphate, [BMIM][PF6], into UiO-66 and NH2-UiO-66 and tested for the adsorption of methylene blue (MB) and methyl orange (MO) from aqueous solutions. Data showed that NH2-functionalization and [BMIM][PF6] incorporation improved MB removal performance of UiO-66 by 16- and 48-times, as the capacity increased from 84.8 to 144.7 mg g(-1) and 174.1 mg g(-1), respectively. When considering both modifications together, [BMIM][PF6]/NH2-UiO-66 was almost 300 times faster than that of UiO-66, and the capacity exceeded 200 mg g(-1). Data further suggested that IL incorporation almost doubled MB/MO selectivity because of the strong electrostatic interactions and hydrogen bonding between [PF6](-) and MB, and pi-pi interactions between the [BMIM](+) cation and MB molecules. These results are the first to demonstrate the prospect of combining ligand functionalization with IL incorporation for modifying MOFs, introducing IL/FMOF composites for fast and selective removal of pollutants from wastewater.Publication Metadata only Piperidine-based natural products targeting Type IV pili antivirulence: a computational approach(Elsevier, 2023) Ozcan, Aslihan; Akbulut, Berna Sariyar; Ozbek, Pemra; Department of Chemical and Biological Engineering; Keskin, Özlem; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 26605Type IV (T4) pilus is among the virulence factors with a key role in serious bacterial diseases. Specifically, in Neisseria meningitidis and Pseudomonas aeruginosa, it determines pathogenicity and causes infection. Here, a computational approach has been pursued to find piperidine-based inhibitor molecules against the elongation ATPase of T4 pili in these two selected pathogens. Using the modeled structures of the PilF and PilB ATPases of N. meningitidis and P. aeruginosa, virtual library screening via molecular docking has returned inhibitor molecule candidates. The dynamics of the best three binders have further been investigated in detail via molecular dy-namic simulations. Among these, ligands with COCONUT IDs CNP0030078 and CNP0051517 were found to have higher potential in the inhibition of ATPases based on molecular dynamic simulation analysis and biological activity information. The obtained results will guide future efforts in antivirulence drug development against T4 pili of N. meningitidis and P. aeruginosa.Publication Metadata only Radicalic cleavage pathway and DNA docking studies of novel chemotherapic platinum agent of 5,6-DI-2-ithienyl-2,3-dihydropyrazine(Pergamon-Elsevier Science Ltd, 2019) El Hag, Rabia; Abdusalam, Mohamed Musbah; Kayı, Hakan; Özalp-Yaman, Şeniz; Ayhan, Ceyda Açılan; Faculty Member; School of Medicine; 219658A new Pt(II) complex of the general formula ([PtCl2(L)]center dot H2O), where L is 5,6-di-2-thienyl-2,3-dihydropyrazine is synthesized as a potential antitumor agent and its structure is elucidated using a variety of physical and chemical procedures. DNA attaching ability of the complex is studied spectroscopically. UV and fluorometric titration, viscometric measurements and thermal decomposition studies agreed that two binding mode of actions, covalent and non-covalent bindings, are possible simultaneously. DNA helix cleavage studies clearly indicated OH center dot radical pathway in the presence of the reducing agent. Quantum mechanical calculations are carried out to call the minimum energy structures of the ligand and the complex, and to determine the FTIR, H-1 NMR and UV-Vis spectra using the density functional theory (DFT) at the B3LYP/LANL2DZ level of theory. Calculated geometrical parameters for the complex indicated a square-planar structure around the metallic center through the dithiopyridyl ring and two chlorine atoms. The minimum energy structure of the complex obtained from DFT conformational analysis is used in docking studies to investigate complex-DNA binding mechanisms. The complex interacts with DNA through three different mechanisms, namely, intercalation, covalent and electrostatic interaction. The most stable mode of interaction with lowest binding energy (-333.6 kcal/mol) was intercalation mode. Comparisons between theoretical and experimental findings are performed and a good agreement is obtained. (C) 2019 Elsevier Ltd. All rights reserved.