Research Outputs

Permanent URI for this communityhttps://hdl.handle.net/20.500.14288/2

Browse

Filters

Advanced Search

Filter by

Settings

Indexed at: search.filters.indexed.ScopusSubject: search.filters.subject.Crystallography

Search Results

Now showing 1 - 10 of 30
  • Placeholder
    PublicationMetadata 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; 40548
    A 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.
  • Placeholder
    PublicationMetadata 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; 40548
    A 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.
  • Placeholder
    PublicationMetadata 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; 40548
    A 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.
  • Thumbnail Image
    PublicationOpen Access
    An advanced workflow for single-particle imaging with the limited data at an X-ray free-electron laser
    (International Union of Crystallography, 2020) Assalauova, Dameli; Kim, Young Yong; Bobkov, Sergey; Khubbutdinov, Ruslan; Rose, Max; Alvarez, Roberto; Andreasson, Jakob; Balaur, Eugeniu; Contreras, Alice; Gelisio, Luca; Hajdu, Janos; Hunter, Mark S.; Kurta, Ruslan P.; Li, Haoyuan; McFadden, Matthew; Nazari, Reza; Schwander, Peter; Teslyuk, Anton; Walter, Peter; Xavier, P. Lourdu; Yoon, Chun Hong; Zaare, Sahba; Ilyin, Viacheslav A.; Kirian, Richard A.; Hogue, Brenda G.; Aquila, Andrew; Vartanyants, Ivan A.; Department of Molecular Biology and Genetics; Demirci, Hasan; Faculty Member; Department of Molecular Biology and Genetics; College of Sciences; 307350
    An improved analysis for single-particle imaging (SPI) experiments, using the limited data, is presented here. Results are based on a study of bacteriophage PR772 performed at the Atomic, Molecular and Optical Science instrument at the Linac Coherent Light Source as part of the SPI initiative. Existing methods were modified to cope with the shortcomings of the experimental data: inaccessibility of information from half of the detector and a small fraction of single hits. The general SPI analysis workflow was upgraded with the expectation-maximization based classification of diffraction patterns and mode decomposition on the final virus-structure determination step. The presented processing pipeline allowed us to determine the 3D structure of bacteriophage PR772 without symmetry constraints with a spatial resolution of 6.9 nm. The obtained resolution was limited by the scattering intensity during the experiment and the relatively small number of single hits.
  • Placeholder
    PublicationMetadata 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; 40548
    A 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.
  • Thumbnail Image
    PublicationOpen 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; 307350
    Since 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.
  • Placeholder
    PublicationMetadata 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; 40548
    Five 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.
  • Placeholder
    PublicationMetadata only
    Crystal structure of 3R(S)-1 ' S(R)-2,2-dimethoxycarbonyl-3-(2 ',6 ',6 '-trimethyl-2 '-cyclohexen-1 '-yl)-2,3-dihydrofuran, C18H26O5
    (Walter De Gruyter Gmbh, 2002) Daut-Özdemir, Ayşe; Anaç, Olcay; Borrmann, Horst; Department of Chemistry; Somer, Mehmet Suat; Faculty Member; Department of Chemistry; College of Sciences; 178882
    N/A
  • Placeholder
    PublicationMetadata only
    Crystal structure of dicaesium hydrogenphosphide, Cs2[PH]
    (R Oldenbourg Verlag, 2001) von Schnering, Hans Georg; Peters, K.; Carrillo-Cabrera, Wilder; Grin, Y.; Department of Chemistry; Somer, Mehmet Suat; Faculty Member; Department of Chemistry; College of Sciences; 178882
    Cs2HP, orthorhombic, Pnma (No. 62), a = 8.626(2) Angstrom, b = 5.860(1) Angstrom, c = 10.759(2) Angstrom, V = 543.8 Angstrom (3), Z = 4, R-gt(F) = 0.058, wR(ref)(F-2) = 0.109, T = 293 K.
  • Placeholder
    PublicationMetadata only
    Crystal structure of dieuropium(II) dinitridoborate bromide, Eu-2[BN2]Br
    (De Gruyter, 2009) Hoehn, Peter; Prots, Yurii; N/A; Department of Chemistry; Kokal, İlkin; Somer, Mehmet Suat; Master Student; Faculty Member; Department of Chemistry; Graduate School of Sciences and Engineering; College of Sciences; N/A; 178882
    BBrEu2N2, trigonal, R (3) over barm (no. 166), a = 4.0728(3) angstrom, c = 26.589(3) angstrom, V = 382.0 angstrom(3), Z = 3, R-gt(F) = 0.029, wR(ref)(F-2) = 0.072, T = 293 K.