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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 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 Open Access Metallodielectric photonic crystals resonators(Society of Photo-optical Instrumentation Engineers (SPIE), 2003) Department of Physics; Serpengüzel, Ali; Faculty Member; Department of Physics; College of Sciences; 27855K-u band Fabry-Perot type resonances have been observed in the stop band of a metallodielectric photonic crystal by transmission measurements at microwave frequencies. The metallodielectric photonic crystal has a face centered cubic Bravais lattice structure with a lattice constant of 15 mm. Metallic spheres with 6.35 mm diameter are placed at the lattice sites. The metallodielectric photonic crystal displayed a directional bandgap with a lower band edge of 13.0 GHz, an upper band edge of 21.5 GHz, and a center frequency of 17.25 GHz, corresponding to a stop bandwidth center frequency ratio of 50%. The maximum rejection at the band center is 35 dB, corresponding to a 7 dB per unit cell rejection ratio. The Fabry-Perot type resonance in the k(u) band has a quality factor of 200, with a maximum transmission peak of -5 dB.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 Open Access Real- and Q-space travelling: multi-dimensional distribution maps of crystal-lattice strain (epsilon(044)) and tilt of suspended monolithic silicon nanowire structures(International Union of Crystallography, 2020) Dolabella, Simone; Frison, Ruggero; Chahine, Gilbert A.; Richter, Carsten; Schulli, Tobias U.; Taşdemir, Zuhal; Leblebici, Yusuf; Dommann, Alex; Neels, Antonia; Department of Mechanical Engineering; Alaca, Burhanettin Erdem; Faculty Member; Department of Mechanical Engineering; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); College of Engineering; 115108Silicon nanowire-based sensors find many applications in micro- and nano-electromechanical systems, thanks to their unique characteristics of flexibility and strength that emerge at the nanoscale. This work is the first study of this class of micro- and nano-fabricated silicon-based structures adopting the scanning X-ray diffraction microscopy technique for mapping the in-plane crystalline strain (epsilon(044)) and tilt of a device which includes pillars with suspended nanowires on a substrate. It is shown how the micro- and nanostructures of this new type of nanowire system are influenced by critical steps of the fabrication process, such as electron-beam lithography and deep reactive ion etching. X-ray analysis performed on the 044 reflection shows a very low level of lattice strain (<0.00025 Delta d/d) but a significant degree of lattice tilt (up to 0.214 degrees). This work imparts new insights into the crystal structure of micro- and nanomaterial-based sensors, and their relationship with critical steps of the fabrication process.Publication Open Access Refractive index-enhanced vortex lattices(Society of Photo-optical Instrumentation Engineers (SPIE), 2005) Oktel, Mehmet Özgür; Department of Physics; Müstecaplıoğlu, Özgür Esat; Faculty Member; Department of Physics; College of Sciences; 1674Light propagation through vortex matter in atomic Bose-Einstein condensates is examined. It is shown that vortex matter can be used as a photonic crystal by a refractive index enhancement scheme. Band structure of the vortex lattice is numerically calculated. Index enhanced vortex matter is shown to exhibit large refractive index contrast with the dilute thermal gas background in the vortex core. Depending on the depth of the index contrast full or directional photonic band gaps are found in the band structure. Experimental parameters required to generate band gaps in the visible region of the electromagnetic spectrum are calculated.Publication Open Access Syntheses, crystal structures, magnetic properties and vibrational spectra of nitridoborate-halide compounds Sr-2[BN2]Br and Eu-2[BN2]X (X = Br, I) with isolated [BN2](3-) units(Oldenbourg Verlag, 2011) Aydemir, Umut; Prots, Yurii; Schnelle, Walter; Akselrud, Lev; Hoehn, Peter; Department of Chemistry; Kokal, İlkin; Somer, Mehmet Suat; Master Student; Faculty Member; Department of Chemistry; College of Sciences; N/A; 178882The title compounds Sr-2[BN2]Br (1), Eu-2[BN2]Br (2) and Eu-2[BN2]I (3) were obtained from reactions of mixtures of Sr-3[BN2](2) and SrBr2 (1) and the binaries EuN, h-BN and EuX2 (X = Br, I) (2, 3), respectively. The crystal structure of Sr-2[BN2]Br was solved from X-ray powder diffraction data and those of the europium compounds from X-ray single crystal data. Sr-2[BN2]Br and Eu-2[BN2]Br are isotypic crystallizing in the rhombohedral space group R (3) over barm (No. 166, Pearson code: hR18; Z = 3; a = 4.11692(2) angstrom, c = 26.4611(2) angstrom (1); a = 4.0728(3) angstrom, c = 26.589(3) angstrom (2)). The crystal structures are built up by layers of condensed edge-sharing [B-N-B]@Eu-6 and [Br]@Eu-6 trigonal antiprisms, which are alternately stacked along [001] Eu-2[BN2]I - isotypic to Sr-2[BN2]I - crystallizes in the monoclinic space group P2(1)/m (No. 11, Pearson code: mP24; Z = 4; a = 10.2548(6) angstrom, b = 4.1587(3) angstrom, c = 13.1234(9) angstrom, beta = 91.215(4)degrees). The crystal structure is characterized by slightly puckered layers formed by condensed edge-sharing I@Eu-6 octahedra which are separated by isolated [BN2](3-) units. The bond lengths for the strictly linear [BN2](3-) anions in (1) and (2) are d(B-N) = 1.351(4) angstrom and 1.356(8) angstrom, respectively. In Eu-2[BN2]I two crystallograhically distinct [BN2](3-) anions are present with d(B1-N) = 1.32(4) angstrom, 1.37(4)angstrom and d(B2-N) = 1.30(4) angstrom, 1.34(4) angstrom, respectively. Their bond angles vary slightly: angle(N-B1-N) = 179(3)degrees and angle(N-B2-N) = 177(3)degrees. The magnetic susceptibility data of the europium compounds (2) and (3) indicate that the Eu ions are divalent with 4f(7) configuration. Vibrational spectra were measured and interpreted based on the D infinity(h) symmetry of the discrete linear [N-B-N](3-) moieties, considering the site symmetry reduction and the presence of two distinct [BN2](3-) groups in (3).