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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 two-dimensional photoluminescent cadmium(ii) coordination polymer containing a new coordination mode of pyridine-2,3-dicarboxylate: synthesis, structure and molecular simulations for gas storage and separation applications(Elsevier, 2013) Semerci, Fatih; Yesilel, Okan Zafer; Soylu, Mustafa Serkan; Buyukgungor, Orhan; Department of Chemical and Biological Engineering; Keskin, Seda; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 40548A novel two-dimensional (2D) coordination polymer, [Cd(mu-pydc)(2-meim)](n) (1) (pydc = pyridine-2,3-dicarboxylate, 2-meim = 2-methylimidazole) was synthesized and characterized by spectral methods (FT-IR and photoluminescence), elemental analysis, thermal analysis (TG, DTG and DTA) and single crystal X-ray diffraction techniques. Complex 1 displays a 2D layer structure through the linkage of bridging carboxyl oxygen and pyridine nitrogen atoms of the pydc ligand. Each Cd(II) center exhibits a distorted octahedral coordination environment with four carboxylate oxygen atoms and two nitrogen atoms from the pydc and 2-meim ligands. In 1, the pydc ligand exhibits a new coordination mode. The distances of adjacent Cd(II) atoms are 3.679 and 7.742 angstrom. The 2D layers are further linked by C-H.. .pi and pi...pi stacking to construct a 3D supramolecular structure. In order to assess the potential of 1 in gas storage and gas separation applications, molecular simulations were performed. Furthermore, 1 exhibits blue photoluminescence in the solid state at room temperature.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 Metadata only An unusual 3D metal-organic framework, {[Ag-4(mu(4)-pzdc)(2)(mu-en)(2)]center dot H2O}(n): C-H center dot center dot center dot Ag, N-H center dot center dot center dot Ag and (O-H)center dot center dot center dot Ag interactions and an unprecedented coordination mode for pyrazine-2,3-dicarboxylate(Royal Society of Chemistry (RSC), 2012) Yesilel, Okan Zafer; Gunay, Gunes; Darcan, Cihan; Soylu, Mustafa Serkan; Ng, Seik Weng; Department of Chemical and Biological Engineering; Keskin, Seda; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 40548A novel three-dimensional (3D) metal-organic framework of silver(I)-pyrazine-2,3-dicarboxylate (pzdc) with ethylenediamine ligand (en), {[Ag-4(mu(4)-pzdc)2(mu-en)(2)]center dot H2O}(n) (1), was synthesized and structurally characterized by spectral methods (FT-IR and photoluminescence), elemental analysis, thermal analysis (TG, DTG, DTA) and single crystal X-ray diffraction techniques. X-ray crystallographic study of 1 revealed that the pzdc ligand adopts a new coordination mode. Four Ag(I) atoms with different coordination geometries are linked together with carboxylate groups to form 1D tetranuclear building block. The adjacent 1D blocks are connected through the en ligand to form a 2D layer structure, which is further connected to a 3D framework by argentophilic interaction (Ag1 center dot center dot center dot Ag2 -3.096 and Ag3 center dot center dot center dot Ag4 - 3.3070 angstrom). The complex exhibits C-H center dot center dot center dot Ag, N-H center dot center dot center dot Ag intermolecular multicenter heteroacceptor (IMH) hydrogen-bonding interactions between the Ag(I) ions and hydrogen atoms of the en ligand and (O-H)center dot center dot center dot Ag interaction of the pseudo-agostic (IPA) between the Ag(I) ion and hydrogen atoms of the water molecule. In order to assess the potential of 1 in gas storage applications, we performed atomically detailed simulations. Furthermore, 1 exhibits green and unusual yellow luminescence in the solid state at room temperature. Complex 1 has also good antimicrobial activity (36-63 mu g mL(-1)) on studied microorganisms.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 Construction of homo- and heterometallic-pyridine-2,3-dicarboxylate metallosupramolecular networks with structural diversity: 1D T5(2) water tape and unexpected coordination mode of pyridine-2,3-dicarboxylate(Royal Society of Chemistry (RSC), 2013) Semerci, Fatih; Yesilel, Okan Zafer; Darcan, Cihan; Tas, Murat; Dal, Hakan; Department of Chemical and Biological Engineering; Keskin, Seda; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 40548Five new homo and heterometallic Cu(II), Cd(II), Cu(II)-Ag(I), Cu(II)-Cd(II) supramolecular networks with pyridine-2,3-dicarboxylate (pydc), {[Cu(mu-pydc)(dmpen)(2)]}(n) (1), [Cu-2(mu-pydc)(2)(emim)(4)]center dot 2H(2)O (2), [Cd(mu-pydc)(emim)(2)](n) (3), [Cu(en)(2)(H2O)(2)][Ag-2(pydc)(2)(mu-en)]center dot 6H(2)O (4) and {[Cd(H2O)(4)Cu(mu-pydc)(2)]center dot 2H(2)O}(n) (5) have been synthesized and structurally characterized (en = ethylenediamine, dmpen = 1,3-diamino-2,2-dimethylpropane and emim = 2-ethyl-4-methyl-imidazole). Owing to diverse binding modes and conformations of the pydc ligand and the different diamine or imidazole-containing coligands, these complexes exhibit structural and dimensional diversity. Complex 1 exhibits a new unexpected coordination mode of pydc, which is known as a chelating ligand, leading to the formation of a 1D coordination polymer. Complex 2 is the first dinuclear copper(II)-pydc complex containing a dinuclear metalloligand. Complex 3 is a one dimensional coordination polymer and the Cd(II) ion is six-coordinated in a distorted octahedral geometry. Complex 4 is the first 3d-4d heterometallic complex and shows two different coordination behaviors of the ethylenediamine ligand: common chelate mode and rare bridging mode. The most striking feature of 4 is the existence of a infinite T5(2) water tape. Complex 5 is the first 3d-4d heteropolynuclear complex obtained from a polynuclear metalloligand. Neighboring metalloligand double-chains bind to Cd(II) ions to form a two dimensional (2D) layered structure. Complex 4 exhibits weak emission due to the quenching effect of Cu(II) ions. Complexes 3 and 5 exhibit rare green emission and blue photoluminesence, respectively. Atomically detailed simulations were used to assess the potential of complexes in gas storage and gas separation applications. The antimicrobial properties of the complexes were also investigated by the broth dilution method (MIC). Complexes 4 and 5 are determined to be highly effective for antimicrobial activity.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 Effect of methylation of ionic liquids on the gas separation performance of ionic liquid/metal-organic framework composites(Royal Society of Chemistry (RSC), 2018) Department of Chemical and Biological Engineering; Nozari, Vahid; 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; N/A; 40548; 59917; N/A1-N-Butyl-3-methylimidazolium hexafluorophosphate, [BMIM]ijPF6], and its methylated form, 1-N-butyl2,3-dimethylimidazolium hexafluorophosphate, [BMMIM]ijPF6], were incorporated into CuBTC to examine the effect of methylation of ionic liquids (ILs) on the gas separation performance of the corresponding IL/ metal–organic framework (MOF) composites. Spectroscopic analysis revealed that the interactions of the methylated ILs with CuBTC were weaker compared to those of its non-methylated counterpart. Gas uptake measurements illustrated that this difference in the interactions influences the gas separation performance of the composites. Accordingly, the CO2/N2: 15/85 and CH4/N2: 50/50 selectivities increased by 37% and 60% for [BMMIM]ijPF6]/CuBTC and 34% and 50% for [BMIM]ijPF6]/CuBTC, respectively, compared to the corresponding selectivities of pristine CuBTC at 1000 mbar. The results revealed another structural parameter controlling the performance of the IL/MOF composites, a novel type of material with rapidly expanding application areas.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.