Science.gov

Sample records for crystal structures spectroscopic

  1. Synthesis, structural and spectroscopic investigations of nanostructured samarium oxalate crystals.

    PubMed

    Vimal, G; Mani, Kamal P; Biju, P R; Joseph, Cyriac; Unnikrishnan, N V; Ittyachen, M A

    2014-03-25

    Nanostructured samarium oxalate crystals were prepared via microwave assisted co-precipitation method. The crystal structure and morphology of the sample were analyzed using X-ray powder diffraction, Scanning electron microscopy and Transmission electron microscopy. The presence of functional groups is ascertained by Fourier transform infrared spectroscopy. Samarium oxalate nanocrystals of average size 20 nm were aggregated together to form nano-plate structure in sub-microrange. Detailed spectroscopic investigation of the prepared phosphor material was carried out by Judd-Ofelt analysis based on the UV-Visible-NIR absorption spectra and photoluminescence emission spectra. The analysis reveals that the transition from energy level (4)G5/2 to (6)H7/2 of Sm(3+) ion has maximum branching ratio and the corresponding orange emission can be used for display applications.

  2. One dimensional coordination polymers: Synthesis, crystal structures and spectroscopic properties

    NASA Astrophysics Data System (ADS)

    Karaağaç, Dursun; Kürkçüoğlu, Güneş Süheyla; Şenyel, Mustafa; Şahin, Onur

    2016-11-01

    Two new one dimensional (1D) cyanide complexes, namely [M(4-aepy)2(H2O)2][Pt(CN)4], (4-aepy = 4-(2-aminoethyl)pyridine M = Cu(II) (1) or Zn(II) (2)), have been synthesized and characterized by vibrational (FT-IR and Raman) spectroscopy, single crystal X-ray diffraction, thermal and elemental analyses techniques. The crystallographic analyses reveal that 1 and 2 are isomorphous and isostructural, and crystallize in the monoclinic system and C2 space group. The Pt(II) ions are coordinated by four cyanide-carbon atoms in the square-planar geometry and the [Pt(CN)4]2- ions act as a counter ion. The M(II) ions display an N4O2 coordination sphere with a distorted octahedral geometry, the nitrogen donors belonging to four molecules of the organic 4-aepy that act as unidentate ligands and two oxygen atoms from aqua ligands. The crystal structures of 1 and 2 are similar each other and linked via intermolecular hydrogen bonding, Pt⋯π interactions to form 3D supramolecular network. Vibration assignments of all the observed bands are given and the spectral features also supported to the crystal structures of the complexes.

  3. Synthesis, spectroscopic characterizations, crystal structures and DFT studies of nalidixic acid carbonyl hydrazones derivatives

    NASA Astrophysics Data System (ADS)

    Bergamini, F. R. G.; Ribeiro, M. A.; Lancellotti, M.; Machado, D.; Miranda, P. C. M. L.; Cuin, A.; Formiga, A. L. B.; Corbi, P. P.

    2016-09-01

    This article describes the synthesis and characterization of the 1-ethyl-7-methyl-4-oxo-1,4-dihydro-1,8-naphthyridine-3-carbohydrazide (hzd) and six carbonyl hydrazones derivatives of the nalidixic with 1H-pyrrol-2-ylmethylidene (hpyrr), 1H-imidazol-2-ylmethylidene (h2imi), pyridin-2-ylmethylidene (h2py), pyridin-3-ylmethylidene (h3py), pyridin-4-ylmethylidene(h4py) and (2-hydroxyphenyl)methylidene (hsali). The carbonyl hydrazones were characterized by elemental and ESI-QTOF-MS analyses, IR and detailed NMR spectroscopic measurements. The 2D NMR experiments allowed the unambiguous assignment of the hydrogen, carbon and nitrogen atoms, which have not been reported for nalidixic acid carbonyl hydrazone derivatives so far. Crystal structures of hzd and the new carbonyl hydrazones h2imi, hpyrr and h3py were determined by X-ray diffraction studies. Although the synthesis of hzd was reported decades ago, the hzd crystal structure have not been reported yet. Geometric optimizations of all the characterized structures were performed with the aid of DFT studies. Despite the fact that the hydrazones with 2-pyridine carboxylic acid (h2py) and salicyl aldehyde (hsali) were already reported by literature, a detailed spectroscopic study followed by DFT studies are also reported for such compounds in this manuscript. Antimicrobial studies of the compounds are also presented.

  4. Crystal structures and spectroscopic properties of ester amide and diamide of squaric acid with prolinamide

    NASA Astrophysics Data System (ADS)

    Kolev, Tsonko; Seidel, Rüdiger W.; Mayer-Figge, Heike; Spiteller, Michael; Sheldrick, William S.; Koleva, Bojidarka B.

    2009-04-01

    We report the synthesis, spectroscopic and structural elucidation of two prolinamide derivatives of squaric acid, i.e. prolinamide ester amide of squaric acid ethyl ester ( 1) and prolinamide diamide of squaric acid dihydrate ( 2). Both compounds crystallize in non-centrosymmetric space groups, monoclinic P2 1 ( 1) and orthorhombic P2 12 12 1 ( 2), respectively. For first time in the literature the crystal structure of homodiamide of amino acid amide of squaric acid is reported. The data for heterodiamides is also absent. Supramolecular zig-zag chains by hydrogen bonds of H 2N-C dbnd O⋯HNH (3.020 Å) and HNH⋯O dbnd C (Sq) (2.972 Å) types with the participation of amide and squaric acid (Sq) fragments, -C dbnd O-NH 2 and O dbnd C (Sq) are refined in ( 1). A helix supramolecular structure is formed in ( 2) by moderate intermolecular HNH⋯O dbnd C(NH 2) hydrogen bond with length of 2.947 Å. The two crystallographical non-equivalent water molecules stabilized the helix by interactions of types HOH⋯O dbnd C (Sq) (2.917 Å), HOH⋯O dbnd C(NH 2) (2.899 Å), H 2O⋯NH 2(C dbnd O) (2.972 Å), respectively. Optical and magnetic properties are investigated with a view to explain the correlation structure-properties of the newly synthesized molecules.

  5. Spectroscopic studies and crystal structure of (E)-N Prime -(2-hydroxy-3-methoxybenzylidene)isonicotinohydrazide

    SciTech Connect

    Ozay, H. Yildiz, M.; Unver, H.; Kiraz, A.

    2013-01-15

    The structure of compound has also been examined cyrstallographically. It crystallizes in the monoclinic space group P2{sub 1}/c with a = 7.673(1), b = 16.251(2), c = 10.874(1) A, {beta} = 110.42(1) Degree-Sign , V = 1270.7(3) A{sup 3}, D{sub x} = 1.418 g cm{sup -3}, R{sub 1} = 0.0349 and wR{sub 2} = 0.0935 [I > 2{sigma}(I)], respectively. The title compound has been synthesized from the reaction of isonicotinohydrazide with 2-hydroxy-3-methoxybenzaldehyde. It has been characterized by using elemental analysis, MS, IR, {sup 1}H NMR, {sup 13}C NMR and UV-Visible spectroscopic techniques.

  6. EuAu3Al2: Crystal and Electronic Structures and Spectroscopic, Magnetic, and Magnetocaloric Properties.

    PubMed

    Schmiegel, Jan-Patrick; Block, Theresa; Gerke, Birgit; Fickenscher, Thomas; Touzani, Rachid St; Fokwa, Boniface P T; Janka, Oliver

    2016-09-01

    The intermetallic compound EuAu3Al2 has been prepared by reaction of the elements in tantalum ampules. The structure was refined from single-crystal data, indicating that the title compound crystallizes in the orthorhombic crystal system (a = 1310.36(4), b = 547.87(1), c = 681.26(2) pm) with space group Pnma (wR2 = 0.0266, 1038 F(2) values, 35 parameters) and is isostructural to SrAu3Al2 (LT-SrZn5 type). Full ordering of the gold and aluminum atoms was observed. Theoretical calculations confirm that the title compound can be described as a polar intermetallic phase containing a polyanionic [Au3Al2](δ-) network featuring interconnected strands of edge-sharing [AlAu4] tetrahedra. Magnetic measurements and (151)Eu Mössbauer spectroscopic investigations confirmed the divalent character of the europium atoms. Ferromagnetic ordering below TC = 16.5(1) K was observed. Heat capacity measurements showed a λ-type anomaly at T = 15.7(1) K, in line with the ordering temperature from the susceptibility measurements. The magnetocaloric properties of EuAu3Al2 were determined, and a magnetic entropy of ΔSM = -4.8 J kg(-1) K(-1) for a field change of 0 to 50 kOe was determined. Band structure calculations found that the f-bands of Eu present at the Fermi level of non-spin-polarized calculations are responsible for the ferromagnetic ordering in this phase, whereas COHP chemical bonding coupled with Bader charge analysis confirmed the description of the structure as covalently bonded polyanionic [Au3Al2](δ-) network interacting ionically with Eu(δ+). PMID:27532875

  7. Spectroscopic manifestations of local crystal distortions in excited 4f states in crystals of huntite structure

    SciTech Connect

    Malakhovskii, A. V.; Gnatchenko, S. L.; Kachur, I. S.; Piryatinskaya, V. G.; Sukhachev, A. L.; Sokolov, A. E.; Strokova, A. Ya.; Kartashev, A. V.; Temerov, V. L.

    2013-01-15

    Optical absorption spectra of YbAl{sub 3}(BO{sub 3}){sub 4}, TmAl{sub 3}(BO{sub 3}){sub 4} and TbFe{sub 3}(BO{sub 3}){sub 4} trigonal crystals have been studied in temperature range 2-300 K. Temperature behavior of absorption lines parameters has shown, that during some f-f transitions the local environment of rare earth ions undergo distortions, which are absent in the ground state.

  8. Squaraines: crystal structures and spectroscopic analysis of hydrated and anhydrous forms of squaric acid-isoniazid species.

    PubMed

    dos Reis, Felipe D; Gatti, Isabela C; Garcia, Humberto C; de Oliveira, Vanessa E; de Oliveira, Luiz F C

    2014-12-11

    The crystal structures, synthesis procedure, thermal behavior, and spectroscopic properties of a new squaraine SqINH·H2O and its anhydrous arrangement are described. This squaraine is obtained through an acid-base reaction using squaric acid (H2Sq) and isoniazid (INH) as precursors. Both squaraines crystallize in the monoclinic system, but in different space groups: the hydrated and anhydrous arrangement crystallizes in the P2₁ and P2₁/c space group, respectively. The crystallographic data strongly suggest that the structures present an expressive increase in their electronic delocalization all over the molecular structure of both compounds, when compared with the reagents. The bond distances for both structures present an average value intermediate between a single and double character (1.463(3) Å for SqINH·H2O and 1.4959(3) Å for SqINH). The vibrational and electronic data also corroborate with this proposal, since the band shifts indicate that the conjugation over the system is increased, as indicated by the blue shift observed for the carbonyl stretching bands for both compounds. The presence of the water molecule is responsible for a decrease in fluorescence emission, as determined by the emission spectra recorded for both compounds.

  9. Synthesis, crystal structures and spectroscopic properties of cobalt(II) complexes with chelating sulfonylamidophosphate ligands

    NASA Astrophysics Data System (ADS)

    Znovjyak, Kateryna O.; Seredyuk, Maksym; Kusz, Joachim; Nowak, Maria; Moroz, Olesia V.; Sliva, Tetiana Yu; Amirkhanov, Vladimir M.

    2015-11-01

    Two new cobalt(II) complexes with general formula Co(L1)2Phen (1) and Co(L2)2Phen (2), in which HL1 = dimethyl phenylsulfonylphosphoramidate and HL2 = dimethyl tosylphosphoramidate, were prepared in one-step synthesis and characterized by IR, UV-VIS spectroscopy, TGA-DTA and elemental analysis. Moreover, the single crystal structures of 1 and 2 were determined by single crystal X-ray diffractometry. Complexes consist of mononuclear units comprising two L1-(or L2-) and phenanthroline ligands bidentatly linked to metal ion. The UV-VIS spectra of complexes in the solid state show broad asymmetric band at 530 nm attributed to the d-d transition of the metal ion. Comparing of these spectra with the absorption spectra in acetone, octahedral environment of the cobalt(II) ion in solution were considered. The structural similarity of 1 and 2 leads to a similar thermal decomposition profile.

  10. Crystal structure of a DNA containing the planar, phenoxazine-derived bi-functional spectroscopic probe Ç

    PubMed Central

    Edwards, Thomas E.; Cekan, Pavol; Reginsson, Gunnar W.; Shelke, Sandip A.; Ferré-D’Amaré, Adrian R.; Schiemann, Olav; Sigurdsson, Snorri Th.

    2011-01-01

    Previously, we developed the deoxycytosine analog Ç (C-spin) as a bi-functional spectroscopic probe for the study of nucleic acid structure and dynamics using electron paramagnetic resonance (EPR) and fluorescence spectroscopy. To understand the effect of Ç on nucleic acid structure, we undertook a detailed crystallographic analysis. A 1.7 Å resolution crystal structure of Ç within a decamer duplex A-form DNA confirmed that Ç forms a non-perturbing base pair with deoxyguanosine, as designed. In the context of double-stranded DNA Ç adopted a planar conformation. In contrast, a crystal structure of the free spin-labeled base ç displayed a ∼20° bend at the oxazine linkage. Density function theory calculations revealed that the bent and planar conformations are close in energy and exhibit the same frequency for bending. These results indicate a small degree of flexibility around the oxazine linkage, which may be a consequence of the antiaromaticity of a 16-π electron ring system. Within DNA, the amplitude of the bending motion is restricted, presumably due to base-stacking interactions. This structural analysis shows that the Ç forms a planar, structurally non-perturbing base pair with G indicating it can be used with high confidence in EPR- or fluorescence-based structural and dynamics studies. PMID:21252294

  11. 1D cyanide complexes with 2-pyridinemethanol: Synthesis, crystal structures and spectroscopic properties

    NASA Astrophysics Data System (ADS)

    Sayın, Elvan; Kürkçüoğlu, Güneş Süheyla; Yeşilel, Okan Zafer; Hökelek, Tuncer

    2015-12-01

    Two new one-dimensional coordination polymers, [Cu(hmpH)2Pd(μ-CN)2(CN)2]n (1) and [Cu(hmpH)2Pt(μ-CN)2(CN)2]n (2), (hmpH = 2-pyridinemethanol), have been synthesized and characterized by vibrational (FT-IR and Raman) spectroscopy, single crystal X-ray diffraction, thermal and elemental analyses techniques. Single crystal X-ray diffraction analysis indicates that complexes 1 and 2 are isomorphous and isostructural, and crystallize in the triclinic system and P-1 space group. The Pd(II) or Pt(II) ions are four coordinated with four cyanide-carbon atoms in a square planar geometry. Cu(II) ion displays a distorted octahedral coordination by two N-atoms and two O-atoms of hmpH ligands, two bridging cyanide groups. In one dimensional structure of the complexes, [M(CN)4]2- (M = Pd(II) or Pt(II)) anions and [Cu(hmpH)2]2+ cations are linked via bridging cyanide ligands. In the complexes, the presence of intramolecular C-H⋯M (M = Pd(II) or Pt(II)) interactions with distance values of 3.00-2.95 Å are established, respectively.

  12. A new heterometallic (Ni 2+ and Cr 3+) complex - Crystal structure and spectroscopic characterization

    NASA Astrophysics Data System (ADS)

    Jurić, Marijana; Planinić, Pavica; Žilić, Dijana; Rakvin, Boris; Prugovečki, Biserka; Matković-Čalogović, Dubravka

    2009-04-01

    A new heterometallic complex, of the composition [Ni(bpy) 3] 2[Cr(C 2O 4) 3]NO 3·10H 2O (bpy = 2,2'-bipyridine) ( 1), was synthesized and characterized by elemental and TG/DTA analyses, IR, UV/vis and EPR spectroscopy and by a single-crystal X-ray diffraction study. The compound crystallizes in the monoclinic P2 1/ c space group, with the unit cell parameters: a = 23.201(7), b = 13.562(4), c = 22.350(7) Å, β = 92.782(5)°, V = 7024(4) Å 3 and Z = 4. The molecular structure of 1 consists of two symmetry independent [Ni(bpy) 3] 2+ cations, one [Cr(C 2O 4) 3] 3- anion, one nitrate anion and 10 molecules of water. Due to the rigidity of the didentate ligands, both [Ni(bpy) 3] 2+ and [Cr(C 2O 4) 3] 3- ions possess a trigonally distorted octahedral geometry. Analysis of crystal packing revealed the existence of a specific type of supramolecular contact comprising four bipyridine ligands from two neighbouring [Ni(bpy) 3] 2+ units - a quadruple aryl embrace (QAE) contact. The electronic spectrum showed superposition of bands characteristic for both nickel(II) and chromium(III) six-coordinated ions. The X-band EPR spectra were recorded on a single crystal and on a powdered sample of 1 in the temperature range 300-5 K. From the obtained spectra, the spin-Hamiltonian parameters for Cr 3+ were deduced. Throughout the investigated temperature range, Ni 2+ was EPR silent.

  13. Synthesis, crystal structure, spectroscopic, thermal and dielectric properties of a novel semi-organic pentachloroantimonate (III)

    NASA Astrophysics Data System (ADS)

    Lahbib, Ikram; Rzaigui, Mohamed; Smirani, Wajda

    2016-09-01

    A new organic-inorganic hybrid material of formula (C10H15N2F)5(SbCl5)5.2H2O was synthesized and characterized by X-Ray diffraction analysis. It crystallizes in the monoclinic space group P21/c with the following unit cell parameters a = 15.819(4) Å, b = 17.685(3) Å, c = 30.529(4) Å, Z = 4 and V = 8540(3) Å3. The examination of the structure shows that the three-dimensional frameworks are produced by Nsbnd H⋯Cl, Nsbnd H⋯O, Csbnd H⋯Cl and Nsbnd H⋯F, Csbnd H⋯F hydrogen bonding and Cl⋯Cl interactions. IR, Raman and UV-Visible spectroscopies were also used to characterize this compound. In addition, the fluorescent properties of this compound have been investigated in the liquid state at room temperature. Differential scanning calorimetry (DSC) has revealed a structural phase transition of the order-disorder type around 370 K. Dielectric investigations revealed a step-wise change of the electric permittivity at Ttr characteristic of the crystal in the high-temperature phase. The evolution of dielectric constant as a function of temperature of the sample has been investigated in order to determine some related parameters. Measurements of AC conductivity as a function of frequency at different temperatures indicated a hopping conduction mechanism and/or reorientational motion.

  14. Spectroscopic studies, antimicrobial activities and crystal structures of N-(2-hydroxy-3-methoxybenzalidene)1-aminonaphthalene

    NASA Astrophysics Data System (ADS)

    Ünver, Hüseyin; Yıldız, Mustafa; Dülger, Başaran; Özgen, Özen; Kendi, Engin; Durlu, Tahsin Nuri

    2005-03-01

    Schiff base N-(2-hydroxy-3-methoxybenzalidene)1-aminonaphthalene has been synthesized from the reaction of 2-hydroxy-3-methoxybenzaldehyde with 1-aminonaphthalene. The compound were characterized by elemental analysis, FT-IR, 1H NMR, 13C NMR and UV-visible techniques. The UV-visible spectra of the Schiff base were studied in polar and nonpolar solvents in acidic and basic media. The structure of the compound has been examined cyrstallographically. There are two independent molecules in the asymmetric unit. It crystallizes in the monoclinic space group P21/c, with unit cell parameters: a=14, 602(2), b=5,800(1), c=16, 899(1) Å, V=1394.4(2) Å 3, Dx=1.321 g cm -3 and Z=4. The crystal structure was solved by direct methods and refined by full-matrix least squares to a find R=0.041 of for 1179 observed reflections. The title compound's antimicrobial activities also have been studied. The antimicrobial activities of the ligand has been screened in vitro against the organisms Escherichia coli ATCC 11230, Staphylococcus aureus ATCC 6538, Klebsiella pneumoniae UC57, Micrococcus luteus La 2971, Proteus vulgaris ATCC 8427, Pseudomonas aeruginosa ATCC 27853, Mycobacterium smegmatis CCM 2067, Bacillus cereus ATCC 7064 and Listeria monocytogenes ATCC 15313, the yeast cultures Candida albicans ATCC 10231, Kluyveromyces fragilis NRRL 2415, Rhodotorula rubra DSM 70403, Debaryomyces hansenii DSM 70238 and Hanseniaspora guilliermondii DSM 3432.

  15. Synthesis, spectroscopic characterization and crystal structure of novel NNNN-donor μ-bis(bidentate) tetraaza acyclic Schiff base ligands

    NASA Astrophysics Data System (ADS)

    Habibi, Mohammad Hossein; Shojaee, Elahe; Nichol, Gary S.

    2012-12-01

    Novel NNNN-donor μ-bis(bidentate) tetraaza acyclic Schiff base ligands with different substituents (CF3, N(CH3)2 or OH groups) were synthesized by the condensation reaction of triethylenetetramine with 4-substituted benzaldehydes. Triethylenetetramine tris(4-trifluoromethylbenzylidene) (TTFMB), triethylenetetramine tris(4-dimethylaminobenzylidene) (TTDMB) and triethylenetetramine tris(2,4-dihydroxybenzylidene) (TTDHB) were formed as N4 donor ligands. The formation of a five-membered imidazolidine ring from the ethylenediamine backbone as a spacer-cumbridging unit gives rise to a new type of imidazolidine ligand. The structure of the TTFMB and TTDMB were determined by single crystal X-ray crystallography. The synthesized ligands have been characterized on the basis of the results of cyclic voltammetry (CV) and spectroscopic studies viz. FT-IR spectroscopy (FT-IR), mass spectroscopy (MS) and UV-Vis spectroscopy (UV-Vis).

  16. Synthesis, spectroscopic characterization and crystal structure of novel NNNN-donor μ-bis(bidentate) tetraaza acyclic Schiff base ligands.

    PubMed

    Habibi, Mohammad Hossein; Shojaee, Elahe; Nichol, Gary S

    2012-12-01

    Novel NNNN-donor μ-bis(bidentate) tetraaza acyclic Schiff base ligands with different substituents (CF(3), N(CH(3))(2) or OH groups) were synthesized by the condensation reaction of triethylenetetramine with 4-substituted benzaldehydes. Triethylenetetramine tris(4-trifluoromethylbenzylidene) (TTFMB), triethylenetetramine tris(4-dimethylaminobenzylidene) (TTDMB) and triethylenetetramine tris(2,4-dihydroxybenzylidene) (TTDHB) were formed as N(4) donor ligands. The formation of a five-membered imidazolidine ring from the ethylenediamine backbone as a spacer-cumbridging unit gives rise to a new type of imidazolidine ligand. The structure of the TTFMB and TTDMB were determined by single crystal X-ray crystallography. The synthesized ligands have been characterized on the basis of the results of cyclic voltammetry (CV) and spectroscopic studies viz. FT-IR spectroscopy (FT-IR), mass spectroscopy (MS) and UV-Vis spectroscopy (UV-Vis).

  17. Crystal structure, complexation, spectroscopic characterization and antimicrobial evaluation of 3,4-dihydroxybenzylidene isonicotinyl-hydrazone

    NASA Astrophysics Data System (ADS)

    Jeragh, Bakir; Ali, Mayada S.; El-Asmy, Ahmed A.

    2015-06-01

    A single crystal of 3,4-dihydroxybenzylidene isonicotinylhydrazone, HBINH, has been grown and solved by X-ray crystallography. The VO2+, Zr4+, Co2+, Ni2+, Cu2+, Zn2+, Cd2+, Hg2+ and Pd2+ complexes of HBINH have been prepared and spectroscopically characterized. The data confirmed the formulae [Co(HBINH)(H2O)Cl]Cl·H2O, [Pd(HBINH)Cl2], [Zn(HBINH)2Cl2], [Cd(HBINH)(H2O)2Cl2]·1½H2O, [(VO)2(HBINH-3H)(OH)(H2O)], [Ni2(HBINH)(H2O)6Cl2]Cl2, [Cu2(HBINH-3H)(H2O)2(OAc)]·3H2O, [Zr2(HBINH-3H)Cl4]Cl, [Hg2(HBINH)Cl4] and the dimer {[Cu(HBINH)Cl]Cl}2. Most of the complexes have intense colors and high melting points and some are electrolytes in DMSO solution. The ligand behaves as a neutral bidentate in the Co(II), Cu(II), Pd(II), Zn(II) and Cd(II) complexes; dibasic tetradentate in [Ni2(HBINH)(H2O)6Cl2]Cl2 and tribasic tetradentate in [Cu2(HBINH-3H)(OAc)]·5H2O, [(VO)2(HBINH-3H)(OH)(H2O)] and [Zr2(HBINH-3H)Cl4]Cl by the loss of 3H+ due to the deprotonation of the two hydroxyl groups and the enolization of the amide (Odbnd CNH) group. A tetrahedral geometry was proposed for the Co(II), Cu(II), Zn(II) and Hg(II) complexes; square-planar for the Pd(II) complex; square-pyramid for the VO2+ complex and octahedral for the Ni(II) and Cd(II) complexes. The complexes [Cd(HBINH)(H2O)2Cl2]·1½H2O, [(VO)2(HBINH-3H)(OH)(H2O)] and [Cu2(HBINH-3H)-(H2O)2(OAc)]·3H2O have activities against Bacillus sp. M3010, Candida albicans, Escherichia coli, Staphylococcus aureus and Slamonella sp. PA393.

  18. Crystal structure, complexation, spectroscopic characterization and antimicrobial evaluation of 3,4-dihydroxybenzylidene isonicotinyl-hydrazone.

    PubMed

    Jeragh, Bakir; Ali, Mayada S; El-Asmy, Ahmed A

    2015-06-15

    A single crystal of 3,4-dihydroxybenzylidene isonicotinylhydrazone, HBINH, has been grown and solved by X-ray crystallography. The VO(2+), Zr(4+), Co(2+), Ni(2+), Cu(2+), Zn(2+), Cd(2+), Hg(2+) and Pd(2+) complexes of HBINH have been prepared and spectroscopically characterized. The data confirmed the formulae [Co(HBINH)(H2O)Cl]Cl·H2O, [Pd(HBINH)Cl2], [Zn(HBINH)2Cl2], [Cd(HBINH)(H2O)2Cl2]·1½H2O, [(VO)2(HBINH-3H)(OH)(H2O)], [Ni2(HBINH)(H2O)6Cl2]Cl2, [Cu2(HBINH-3H)(H2O)2(OAc)]·3H2O, [Zr2(HBINH-3H)Cl4]Cl, [Hg2(HBINH)Cl4] and the dimer {[Cu(HBINH)Cl]Cl}2. Most of the complexes have intense colors and high melting points and some are electrolytes in DMSO solution. The ligand behaves as a neutral bidentate in the Co(II), Cu(II), Pd(II), Zn(II) and Cd(II) complexes; dibasic tetradentate in [Ni2(HBINH)(H2O)6Cl2]Cl2 and tribasic tetradentate in [Cu2(HBINH-3H)(OAc)]·5H2O, [(VO)2(HBINH-3H)(OH)(H2O)] and [Zr2(HBINH-3H)Cl4]Cl by the loss of 3H(+) due to the deprotonation of the two hydroxyl groups and the enolization of the amide (OCNH) group. A tetrahedral geometry was proposed for the Co(II), Cu(II), Zn(II) and Hg(II) complexes; square-planar for the Pd(II) complex; square-pyramid for the VO(2+) complex and octahedral for the Ni(II) and Cd(II) complexes. The complexes [Cd(HBINH)(H2O)2Cl2]·1½H2O, [(VO)2(HBINH-3H)(OH)(H2O)] and [Cu2(HBINH-3H)-(H2O)2(OAc)]·3H2O have activities against Bacillus sp. M3010, Candida albicans, Escherichia coli, Staphylococcus aureus and Slamonella sp. PA393. PMID:25791887

  19. Syntheses, spectroscopic characterization, crystal structure and natural rubber vulcanization activity of new disulfides derived from sulfonyldithiocarbimates

    NASA Astrophysics Data System (ADS)

    Alves, Leandro de Carvalho; Rubinger, Mayura Marques Magalhães; Tavares, Eder do Couto; Janczak, Jan; Pacheco, Elen Beatriz Acordi Vasques; Visconte, Leila Lea Yuan; Oliveira, Marcelo Ribeiro Leite

    2013-09-01

    The compounds (Bu4N)2[(4-RC6H4SO2NCS2)2] [Bu4N = tetrabutylammonium cation; R = H (1), F (2), Cl (3) and Br (4)] and (Ph4P)2[(4-RC6H4SO2NCS2)2]ṡH2O [Ph4P = tetraphenylphosphonium cation and R = I (5)] were synthesized by the reaction of the potassium dithiocarbimates (4-RC6H4SO2NCS2K2ṡ2H2O) with I2 and Bu4NBr or Ph4PCl. The IR data were consistent with the formation of the dithiocarbimatodisulfides anions. The NMR spectra showed the expected signals for the cations and anions in a 2:1 proportion. The structures of compounds 1-5 were determined by the single crystal X-ray diffraction. The compounds 2, 3 and 4 are isostructural and crystallise in the centrosymmetric space group C2/c of the monoclinic system. Compound 1 crystallises in the monoclinic system in the space group of P21/n and the compound 5 crystallises in the centrosymmetric space group P-1 of the triclinic system. The complex anions of compounds 2, 3 and 4 exhibit similar conformations having twofold symmetry, while in 1 and 5 the anions exhibit C1 symmetry. The activity of the new compounds in the vulcanization of the natural rubber was evaluated and compared to the commercial accelerators ZDMC, TBBS and TMTD. These studies confirm that the sulfonyldithiocarbimato disulfides anions are new vulcanization accelerators, being slower than the commercial accelerators, but producing a greater degree of crosslinking, and scorch time values compatible with good processing safety for industrial applications. The mechanical properties, stress and tear resistances were determined and compared to those obtained with the commercial accelerators.

  20. Cobalt dipicolinate complexes with nicotinamide and isonicotinamide ligands: Syntheses, crystal structures, spectroscopic, thermal and voltammetric studies

    NASA Astrophysics Data System (ADS)

    Uçar, İbrahim; Bulut, Ahmet; Karadağ, Ahmet; Kazak, Canan

    2007-06-01

    Two new dipicolinate complexes of cobalt, [Co(dpc)(na)(H 2O) 2]·H 2O ( 1) and [Co(dpc)(ina)(H 2O) 2] ( 2) [dpc is dipicolinate or pyridine-2,6-dicarboxylate, na is nicotinamide and ina is isonicotinamide], have been prepared and characterized by thermal analysis, IR spectroscopy and X-ray diffraction techniques. The complex ( 1) crystallizes in triclinic system, whereas the complex ( 2) crystallizes in monoclinic system. The Co(II) ion in both complexes is bonded to dpc ligand through pyridine N atom together with one O atom of each carboxylate group, two aqua ligands and N pyridine atom of na ( 1) or ina ( 2), forming the distorted octahedral geometry. The complex molecules ( 1) and ( 2) are connected via N sbnd H⋯O and O sbnd H⋯O hydrogen bonds. The voltammetric behaviour of complexes ( 1) and ( 2) was also investigated in DMSO (dimethylsulfoxide) solution by cyclic voltammetry using n-Bu 4NClO 4 supporting electrolyte. The complexes exhibit only metal centered electroactivity in the potential ±1.25 V versus Ag/AgCl reference electrode.

  1. Amino-Functionalized Layered Crystalline Zirconium Phosphonates: Synthesis, Crystal Structure, and Spectroscopic Characterization.

    PubMed

    Taddei, Marco; Sassi, Paola; Costantino, Ferdinando; Vivani, Riccardo

    2016-06-20

    Two new layered zirconium phosphonates functionalized with amino groups were synthesized starting from aminomethylphosphonic acid in the presence of different mineralizers, and their structures were solved from powder X-ray diffraction data. Their topologies are unprecedented in zirconium phosphonate chemistry: the first, of formula ZrH[F3(O3PCH2NH2)], prepared in the presence of hydrofluoric acid, features uncommon ZrO2F4 units and a remarkable thermal stability; the second, of formula Zr2H2[(C2O4)3(O3PCH2NH2)2]·2H2O, prepared in the presence of oxalic acid, is based on ZrO7 units with oxalate anions coordinated to the metal atom, which were never observed before in any zirconium phosphonate. In addition, the structure of another compound based on (2-aminoethyl)phosphonic acid is reported, which was the object of a previously published study. This compound has layered α-type structure with -NH3(+) groups located in the interlayer space. All of the reported compounds were further characterized by means of vibrational spectroscopy, which provided important information on fine structural details that cannot be deduced from the powder X-ray diffraction data. PMID:27254781

  2. Crystal structure, spectroscopic characterization and antibacterial activities of a silver complex with sulfameter

    NASA Astrophysics Data System (ADS)

    Nakahata, Douglas H.; Lustri, Wilton R.; Cuin, Alexandre; Corbi, Pedro P.

    2016-12-01

    A silver complex with the sulfonamide sulfameter, also known as sulfamethoxydiazine (SMTR), was prepared and characterized. Chemical analyses were consistent with the [Ag(C11H11N4O3S)] composition (AgSMTR), while conductivity measurements in DMSO indicated a non-electrolyte behavior of the complex in this solvent. High-resolution ESI(+)-QTOF mass spectrometric experiments revealed the presence of the [Ag(C11H11N4O3S)+H]+ and [Ag2(C11H11N4O3S)2+H]+ species in solution. Infrared and NMR spectroscopies indicated coordination of the ligand to the metal by the nitrogen atoms of the sulfonamide group and of the pyrimidine ring. The structure of AgSMTR was solved by powder X-ray diffraction technique using the Rietveld method. The solved structure confirms the formation of a dimer, where each silver ion is coordinated by one of the nitrogen atoms of the pyrimidine ring, the nitrogen of the sulfonamide group and by an oxygen atom from the sulfonyl group. An argentophilic interaction of 2.901(1) Å is present in this dimeric structure. The AgSMTR complex was assayed over Gram-positive (Staphylococcus aureus) and Gram-negative (Pseudomonas aeruginosa and Escherichia coli) bacterial strains, and it was found that the compound is 8 times more active over the Gram-negative bacteria in DMSO solution, with MIC values in the micromolar range.

  3. Spectroscopic, thermal and single crystal structure investigations of 2-bromotrimesic acid and its trimethyl ester analogue

    NASA Astrophysics Data System (ADS)

    Münch, Alexander S.; Katzsch, Felix; Gruber, Tobias; Mertens, Florian O. R. L.

    2014-09-01

    Two analogues of the well investigated trimesic acid viz. the 2-bromobenzene-1,3,5-tricarboxylic acid 1 and their ester trimethyl 2-bromobenzene-1,3,5-tricarboxylate 2, have been synthesised and their X-ray structures were solved. Acid 1 crystallises as 1:1 inclusion compound with water in a layer structure. Like in the solid state structure of trimesic acid, we found strong Osbnd HṡṡṡO hydrogen bonds between one of the carboxyl groups and a neighbouring molecule to form a hydrogen bonding motif R22(8). Additionally, a water molecule and a second acid function of 1 are involved in further hydrogen bonding featuring the graph set R44(12) forming what might be called a water inserted dimer. As shown by TG-DSC measurements the water molecule in the 1:1 inclusion compound of 1 is engaged in two strong Osbnd HṡṡṡO hydrogen bonds, it escapes at a rather low temperature of 99 °C. Bromine monosubstitution at the benzene ring forces the third carboxylic acid out of the mean plane of the molecule, which disturbs the coplanar arrangement of the three COOH moieties. Thus, the typical “chicken-wire” network formation is hindered. In the trimethyl 2-bromobenzene-1,3,5-tricarboxylate (2), the formation of strong Osbnd HṡṡṡO hydrogen bonds is disabled by esterification of the acid functions. Nevertheless, the packing of 2 features solvent free molecular layers formed by BrṡṡṡO contacts and connected van der Waals interactions. These layers are linked to each other by inverse bifurcated hydrogen bonds in term weak Csbnd HṡṡṡO contacts. The results of the X-ray analysis could be confirmed by infrared spectroscopy.

  4. Crystal structures, spectroscopic and theoretical study of novel Schiff bases of 2-(methylthiomethyl)anilines.

    PubMed

    Olalekan, Temitope E; Adejoro, Isaiah A; VanBrecht, Bernardus; Watkins, Gareth M

    2015-03-15

    New Schiff bases derived from p-methoxysalicylaldehyde and 2-(methylthiomethyl)anilines (substituted with methyl, methoxy, nitro) were synthesized and characterized by elemental analyses, FT-IR, NMR, electronic spectra and quantum chemical calculations. X-ray crystallography of two compounds showed the solid structures are stabilized by intramolecular and intermolecular H-bonds. The effect of OH⋯N interaction between the phenolic hydrogen and imine nitrogen on the proton and carbon NMR shifts, and the role of CH⋯O and CH⋯S contacts are discussed. The bond lengths and angles, (1)H and (13)C NMR data, E(LUMO-HOMO), dipole moments and polarizability of the compounds were predicted by density functional theory, DFT (B3LYP/6-31G∗∗) method. The experimental geometric parameters and the NMR shifts were compared with the calculated values, which gave good correlations. The electronic effects of aryl ring substituents (methyl, methoxy and nitro) on the properties of the resulting compounds, such as the color, NMR shifts, electronic spectra and the calculated energy band gaps, dipole moments and polarizability are discussed. Increase in electron density shifted the phenolic proton resonance to lower fields. The methoxy-substituted compound has a small dipole moment and subsequent large polarizability value. Highest polarity was indicated by the nitro compound which also showed high polarizability due to its larger size. The energy gaps obtained from E(LUMO-HOMO) calculations suggest these compounds may have applications as organic semiconducting materials.

  5. Crystal structures, spectroscopic and theoretical study of novel Schiff bases of 2-(methylthiomethyl)anilines.

    PubMed

    Olalekan, Temitope E; Adejoro, Isaiah A; VanBrecht, Bernardus; Watkins, Gareth M

    2015-03-15

    New Schiff bases derived from p-methoxysalicylaldehyde and 2-(methylthiomethyl)anilines (substituted with methyl, methoxy, nitro) were synthesized and characterized by elemental analyses, FT-IR, NMR, electronic spectra and quantum chemical calculations. X-ray crystallography of two compounds showed the solid structures are stabilized by intramolecular and intermolecular H-bonds. The effect of OH⋯N interaction between the phenolic hydrogen and imine nitrogen on the proton and carbon NMR shifts, and the role of CH⋯O and CH⋯S contacts are discussed. The bond lengths and angles, (1)H and (13)C NMR data, E(LUMO-HOMO), dipole moments and polarizability of the compounds were predicted by density functional theory, DFT (B3LYP/6-31G∗∗) method. The experimental geometric parameters and the NMR shifts were compared with the calculated values, which gave good correlations. The electronic effects of aryl ring substituents (methyl, methoxy and nitro) on the properties of the resulting compounds, such as the color, NMR shifts, electronic spectra and the calculated energy band gaps, dipole moments and polarizability are discussed. Increase in electron density shifted the phenolic proton resonance to lower fields. The methoxy-substituted compound has a small dipole moment and subsequent large polarizability value. Highest polarity was indicated by the nitro compound which also showed high polarizability due to its larger size. The energy gaps obtained from E(LUMO-HOMO) calculations suggest these compounds may have applications as organic semiconducting materials. PMID:25576935

  6. Spectroscopic, crystal structural and electrochemical studies of zinc(II)-Schiff base complex obtained from 2,3-diaminobenzene and 2-hydroxy naphthaldehyde.

    PubMed

    Ouari, Kamel; Bendia, Sabrina; Weiss, Jean; Bailly, Corinne

    2015-01-25

    Mononuclear zinc(II) complex, [Zn(II)L], where L is a dianionic ligand, has been synthesized and characterized by elemental analysis, electronic, IR and NMR [(1)H, (13)C, DEPT, (1)H-(1)H COSY, ROESY, HSQC and HMBC] spectroscopic techniques. Structural analysis of the complex by single crystal X-ray crystallography shows the presence of a distorted square planar coordination geometry (NNOO) of the metal center. The crystal of the title complex C28H18N2O2Zn belongs to the orthorhombic system with space group Pmn21. Electrochemical behavior of the Zn(II)L complex has been investigated by cyclic voltammetry on glassy carbon and platinum electrodes in DMF at 100 mV/s scan rate.

  7. Crystal structure characterization as well as theoretical study of spectroscopic properties of novel Schiff bases containing pyrazole group.

    PubMed

    Guo, Jia; Ren, Tiegang; Zhang, Jinglai; Li, Guihui; Li, Weijie; Yang, Lirong

    2012-09-01

    A series of novel Schiff bases containing pyrazole group were synthesized using 1-aryl-3-methyl-4-benzoyl-5-pyrazolone and phenylenediamine as the starting materials. All as-synthesized Schiff bases were characterized by means of NMR, FT-IR, and MS; and the molecular geometries of two Schiff bases as typical examples were determined by means of single crystal X-ray diffraction. In the meantime, the ultraviolet-visible light absorption spectra and fluorescent spectra of various as-synthesized products were also measured. Moreover, the B3LYP/6-1G(d,p) method was used for the optimization of the ground state geometry of the Schiff bases; and the spectroscopic properties of the products were computed and compared with corresponding experimental data based on cc-pVTZ basis set of TD-B3LYP method. It has been found that all as-synthesized Schiff bases show a remarkable absorption peak in a wavelength range of 270-370 nm; and their maximum emission peaks are around 344 nm and 332 nm, respectively.

  8. 4-Hydroxy-N′-[(1E)-1-(4-methylphenyl)ethylidene]benzohydrazide: Synthesis, crystal structure, and spectroscopic studies

    SciTech Connect

    Dilek, N.; Güneş, B.; Gökçe, C.; Güp, R.

    2013-12-15

    The titled compound has been synthesized by reaction of 4′-methylacetophenon with 4-hydrox-ybenzohydrazide in presence of catalytic amount of glacial acetic acid. The compound is characterized by elemental analysis, IR, {sup 1}H NMR, {sup 13}C NMR and UV-visible spectra. The crystal structure was determined by X-ray diffraction method. Both X-ray data and NMR spectra indicate that the molecule exists in a trans configuration with respect to the C=N bond. The observation of strong ν(C=O) peak in IR spectra of the aroylhydrazone compound suggests that it is in keto form in solid state. X-ray diffraction results confirm this suggestion. In the crystal structure, there are N-H...O and O-H...O hydrogen bonds and weak C-H...π interaction.

  9. Synthesis, crystal structure, spectroscopic, fluorescent, thermal properties and EPR spectra of doped Cu2+ ions in [Cd(sac)2(H2O)2(meim)2] single crystal

    NASA Astrophysics Data System (ADS)

    Fidan, M.; Semerci, F.; Şahin, E.; Yeşilel, O. Z.; Tapramaz, R.; Şahin, Y.

    2013-06-01

    The crystal structures of the six-coordinate complexes [Cd(sac)2(H2O)2(meim)2] (complex 1) formed by reaction of 4-methylimidazole(meim) with [Cd(sac)2(H2O)4]·2H2O (saccharinate = sac), was synthesized and characterized by elemental analysis, infrared (IR) and electron paramagnetic resonance (EPR) spectroscopy, thermal analysis and X-ray single crystal diffraction. X-ray diffraction analysis revealed that complex 1 crystallized in the monoclinic crystal system with space group P21/c. The Cd(II) center was six-coordinated with four nitrogen atoms from two sac and two 4-meim ligands, two oxygen atoms from two aqua ligands. Spectral and thermal analysis data for complex 1 was in agreement with the crystal structures. In addition complex 1 displayed blue fluorescent emission in the solid state at room temperature. Single crystal EPR spectra at room temperature are resolved and have exhibited that two different Cu2+ complexes were located in different chemical environments which contained two magnetically nonequivalent Cu2+ sites. In low temperature EPR spectra down to 110 °C did show no considerable change. At higher temperatures, however, both thermo gravimetric analyses (TGA) and EPR spectra showed detectable changes around 140 °C; the causes and the mechanisms of changes are discussed.

  10. Synthesis, crystal structure, spectroscopic characterization and theoretical study of (2E)-N-phenyl-2-(pyridin-3-ylmethylidene)hydrazinecarboxamide

    NASA Astrophysics Data System (ADS)

    Soria-Martínez, R.; Mendoza-Meroño, R.; García-Granda, S.

    2016-02-01

    In this work, the experimental and theoretical study of new semicarbazone have been reported. The new semicarbazone was synthesized and characterized by FT-IR, FT-Raman and NMR, and the crystal structure was determined by X-ray single-crystal diffraction. The crystallographic asymmetric unit was optimized using DFT method and compared with the experimental data. The experimental FT-IR and FT-Raman have been compared with calculated vibrational frequencies, using B3LYP/6-311*G(d,p). The stability and charge delocalization were studied by natural bond orbital (NBO) analysis as well as the molecular electrostatic potential (MEP). The 1H and 13C chemical shifts values have been calculated by the GIAO method. Non covalent interactions analysis in real space was done, based on the electron density and its derivates, it provides a rich representation of VdW interactions, hydrogen bonds, and the inter and intramolecular steric repulsions.

  11. Synthesis, crystal structure, spectroscopic properties and potential anti-cancerous activities of four unsaturated bis-norcantharimides

    NASA Astrophysics Data System (ADS)

    Cheng, Shuang-Shuang; Shi, Yan; Ma, Xiao-Na; Xing, Dian-Xiang; Liu, Lian-Dong; Liu, Yun; Zhao, Yun-Xue; Sui, Qi-Cheng; Tan, Xue-Jie

    2016-07-01

    Four unsaturated norcantharimide (UNCI) dimers were synthesized and characterized by elemental analysis, ESI-QTOF-MS, FT/IR, UV-Vis, 1H and 13C NMR as well as single crystal X-ray diffraction. In addition, theoretical studies have been investigated to compare with the experimental findings. Introduction of various lengths of single bond link chains provides high conformational flexibility and thus unusual molecular and crystal structures for dimers. Two of the four dimers twist into helicate, but crystallize into centrosymmetric lattice; one adopts approximately centrosymmetric conformer, but packs into non-centrosymmetric polar space group (P21). Moreover, in vitro cytotoxic activities of four UNCI dimers and their corresponding saturated NCI dimers were evaluated. All four UNCI dimers are inactive and one NCI dimer shows modest cytotoxicity. These findings were compared with the relevant results in literature. It is found that the antitumor properties of UNCI/NCI dimers depend mainly on the length of link chains (the longer chain, the higher therapeutic efficacy) and have relationship with the double bond, which requires more experimental support.

  12. Layered solids based on second-sphere coordination interactions: synthesis, spectroscopic characterization, crystal structure and packing of two copper(II) naphthalene-2-sulfonates

    NASA Astrophysics Data System (ADS)

    Sharma, Raj Pal; Sharma, Rajni; Bala, Ritu; Rychlewska, Urszula; Warżajtis, Beata

    2005-03-01

    [Cu(H 2O) 6](C 10H 7SO 3) 21 was obtained from reaction of CuCO 3·Cu(OH) 2 and naphthalene-2-sulphonic acid in aqueous medium in 1:4 molar ratio. It crystallizes in the monoclinic space group P2 1/ n with a=7.0582(3) Å, b=6.2666(3) Å, and c=27.1420(10) Å, β=92.678(4)°, Z=2. The structure was determined from 1986 observed reflections and refined to R=0.033. When ethylenediamine was added to hexaaquacopper(II) naphthalene-2-sulfonate dissolved in water, [Cu(en) 2(H 2O) 2](C 10H 7SO 3) 22 was obtained which crystallizes in the triclinic space group P1¯ with a=7.1491(5) Å, b=7.1949(5) Å, and c=14.6500(10) Å, α=99.025(6)°, β=98.976(6)°, and γ=104.262(6)°, Z=1. The structure was determined from 2296 observed reflections and refined to R=0.0313. X-ray structure determination of 1 revealed an ionic structure consisting of [Cu(H 2O) 6] +2 and two naphthalene-2-sulfonate anions while that of 2 contains [Cu(en) 2(H 2O) 2] 2+ cation and two naphthalene-2-sulfonate anions. Characteristic for the studied crystals is the alternated-layer arrangement of complex cations and naphthalene-2-sulfonate anions, linked together via hydrogen bonding, and the presence of a particularly robust R22(8) hydrogen-bonding motif that joins the complex cation with two oxygen atoms of the same sulfonate group. Elemental analyses, IR, UV/vis spectroscopic studies are consistent with the structures revealed by X-ray structure determination.

  13. New organic single crystal of (benzylthio)acetic acid: Synthesis, crystal structure, spectroscopic (ATR-FTIR, 1H and 13C NMR) and thermal characterization

    NASA Astrophysics Data System (ADS)

    Sienkiewicz-Gromiuk, Justyna; Tarasiuk, Bogdan; Mazur, Liliana

    2016-04-01

    (Benzylthio)acetic acid (Hbta) was synthesized with 78% yield from benzyl chloride and thiourea as substrates. Well-shaped crystals of Hbta were grown by slow solvent evaporation technique from pure methanol. The compound was investigated by single-crystal X-ray and powder diffraction techniques and was also characterized by other analytical methods, like ATR-FTIR, 1H and 13C NMR and TG/DSC. The acid molecule adopts bent conformation in the solid state. The crystal structure of Hbta is stabilized by numerous intermolecular interactions, including O-H···O, C-H···O, C-H···S and C-H···π contacts. Thermal decomposition of the obtained material takes place above 150 °C.

  14. Synthesis, Crystal Structure, Spectroscopic Properties, and Interaction with Ct-DNA of Zn(II) with 2-Aminoethanethiol Hydrochloride Ligand

    PubMed Central

    Shu, Xu-gang; Wu, Chun-li; Li, Cui-jin; Zhang, Min; Wan, Ke; Wu, Xin

    2016-01-01

    The zinc(II) complex (C2H6NS)2Zn·ZnCl2 was synthesized with 2-aminoethanethiol hydrochloride and zinc sulfate heptahydrate as the raw materials in aqueous solution. The composition and structure of the complex were characterized by elemental analysis, infrared spectra, single crystal X-ray diffraction, and thermogravimetry. The crystal structure of the zinc(II) complex belongs to monoclinic system, space group P  21/n, with cell parameters of a = 0.84294(4), b = 0.83920(4), c = 1.65787(8) nm, Z = 2, and D = 2.041 g/cm3. In this paper, the interaction of complex with Ct-DNA was investigated by UV-visible and viscosimetric techniques. Upon addition of the complex, important changes were observed in the characteristic UV-Vis bands (hyperchromism) of calf thymus DNA and some changes in specific viscosity. The experimental results showed that the complex is bound to DNA intercalative (intercalation binding). PMID:26977140

  15. Synthesis, crystal structure investigation, spectroscopic characterizations and DFT computations on a novel 1-(2-chloro-4-phenylquinolin-3-yl)ethanone

    NASA Astrophysics Data System (ADS)

    Murugavel, S.; Stephen, C. S. Jacob Prasanna; Subashini, R.; Reddy, H. Raveendranatha; AnanthaKrishnan, Dhanabalan

    2016-10-01

    The title compound 1-(2-chloro-4-phenylquinolin-3-yl)ethanone (CPQE) was synthesised effectively by chlorination of 3-acetyl-4-phenylquinolin-2(1H)-one (APQ) using POCl3 reagent. Structural and vibrational spectroscopic studies were performed by utilizing single crystal X-ray diffraction, FTIR and NMR spectral analysis along with DFT method utilizing GAUSSIAN‧ 03 software. Veda program has been employed to perform a detailed interpretation of vibrational spectra. Mulliken population analyses on atomic charges, MEP, HOMO-LUMO, NBO, Global chemical reactivity descriptors and thermodynamic properties have been examined by (DFT/B3LYP) method with the 6-311G(d,p) basis set level.

  16. Crystal structures and spectroscopic properties of polycyano-polycadmate host clathrates including a CT complex guest of methylviologen dication and aromatic donor.

    PubMed

    Yoshikawa, Hirofumi; Nishikiori, Shin-ichi

    2005-09-21

    A series of polycyano-polycadmate (PCPC) host clathrates including a CT complex of methylviologen dication (MV2+) and an aromatic donor as a guest were synthesized, and their crystal structures and spectroscopic properties were investigated. The PCPC host has a framework structure built with Cd2+ ions as coordination centres and cyanides as bridging ligands. This framework host has negative charge and includes a cationic guest together with an ordinary neutral guest. MV2+, which is a strong acceptor, was included as a cationic guest and an aromatic compound, which works as a donor, was included as a neutral guest. Crystal structures of seven clathrates, whose neutral guests were o-cresol, m-cresol, p-cresol, 1-methylnaphthalene, 1,2,4-trimethoxybenzene, pyrrole and aniline, were determined by single crystal X-ray diffraction methods. In all cases MV2+ and the neutral guest formed a CT complex with a face to face stacking structure and were included as a CT complex guest. However, depending on each clathrate the ratio of aromatic donor to MV2+ was different and several variations were found in their PCPC host structures. The clathrates had their own colour depending on their neutral guest. The plot of the CT transition energies estimated from optical CT bands against the ionization potentials of the neutral guests satisfied a linear relationship predicted by Mulliken theory. However, the CT transition energies observed in the clathrates showed a shift to lower energy by ca. 0.6 eV compared with those observed in corresponding acetonitrile solutions. PMID:16127500

  17. Crystal structure and Mössbauer spectroscopic study of FeSnF6·6H2O

    NASA Astrophysics Data System (ADS)

    Denes, Georges; Mousser, Abdelhamid; Merazig, Hocine

    1994-12-01

    Large single crystals of FeSnF6·6H2O were grown when aqueous hydrofluoric solutions of SnF2 and FeF2 were allowed to evaporate in air. Tin-119 Mössbauer spectroscopy at ambient temperature shows a single line at slightly negative isomer shift relative to CaSnO3 at room temperature (δ=-0.380(6) mm/s, Δ=0). This is characteristic of tetravalent tin octahedrally coordinated by fluorine. The X-ray crystal structure shows that tin(IV) is coordinated by 6 fluorine atoms, and Fe(II) by 6 water molecules. Both sites show a slight distortion from octahedral symmetry: the six distances are equal (Sn-Fe=1.941(3) Å and Fe-O=2.112(3) Å), whereas there are two values of angles (Fe-Sn-F=90.4(1)° and 89.6(1)°; O-Fe-O=91.1(1)° and 88.9(1)°). The material is an ionic compound [SnF6]2-[Fe(H2O)6]2+.

  18. Synthesis, crystal structure, spectroscopic characterization and nonlinear optical properties of manganese (II) complex of picolinate: A combined experimental and computational study

    NASA Astrophysics Data System (ADS)

    Tamer, Ömer; Avcı, Davut; Atalay, Yusuf; Çoşut, Bünyemin; Zorlu, Yunus; Erkovan, Mustafa; Yerli, Yusuf

    2016-02-01

    A novel manganese (II) complex with picolinic acid (pyridine 2-carboxylic acid, Hpic), namely, [Mn(pic)2(H2O)2] was prepared and its crystal structure was fully characterized by using single crystal X-ray diffraction. Picolinate (pic) ligands were coordinated to the central manganese(II) ion as bidentate N,O-donors through the nitrogen atoms of pyridine rings and the oxygen atoms of carboxylate groups forming five-membered chelate rings. The spectroscopic characterization of Mn(II) complex was performed by the applications of FT-IR, Raman, UV-vis and EPR techniques. In order to support these studies, density functional theory (DFT) calculations were carried out by using B3LYP level. IR and Raman spectra were simulated at B3LYP level, and obtained results indicated that DFT calculations generally give compatible results to the experimental ones. The electronic structure of the Mn(II) complex was predicted using time dependent DFT (TD-DFT) method with polarizable continuum model (PCM). Molecular stability, hyperconjugative interactions, intramolecular charge transfer (ICT) and bond strength were investigated by applying natural bond orbital (NBO) analysis. Nonlinear optical properties of Mn(II) complex were investigated by the determining of molecular polarizability (α) and hyperpolarizability (β) parameters.

  19. CuNd{sub 2}Ge{sub 2}O{sub 8}: Crystal growth, crystal structure, and magnetic and spectroscopic properties

    SciTech Connect

    Campa, J.A.; Gutierrez-Puebla, E.; Monge, M.A.; Valero, R.C.; Mira, J.; Rivas, J.

    1995-12-01

    After crystals of CuNd{sub 2}Ge{sub 2}O{sub 8} are grown using CuO as self flux, the crystal structure is determined by single-crystal X-ray diffraction in the space group Cm (No. 8) to an R value of 5.1%. It is monoclinic, with a = 9.846(2){angstrom}, b=15.335(5) {angstrom}, c=8.336(1) {angstrom}, {beta}=148.48(2), V=657.9(5) {angstrom}{sub 3}, Z=4, and D{sub c}=6.31 g cm{sup -3}. CuNd{sub 2}Ge{sub 2}O{sub 8} shows a novel tridimensional structure type with chains of very distorted CuO{sub 6} octahedra, two kinds of coordinations for germanium (GeO{sub 5} trigonal bipyramids and rather regular GeO{sub 4} tetrahedra), and NdO{sub 8} triangulated dodecahedra. Above 100 K the reciprocal of the dc magnetic susceptibility of CuNd{sub 2}Ge{sub 2}O{sub 8} follows the Curie-Weiss law {chi}{sup -1} = 162(1)T+5971(93)g Oe/emu, with Weiss constant of spectra in the range 1000-100 cm{sup -1} are related to those of comparable species. The absorption spectrum at room temperature in the 350-7000 nm region is also given.

  20. Syntheses, crystal structures and spectroscopic properties of copper(II)-tetracyanometallate(II) complexes with nicotinamide and isonicotinamide ligands

    NASA Astrophysics Data System (ADS)

    Sayın, Elvan; Kürkçüoğlu, Güneş Süheyla; Yeşilel, Okan Zafer; Hökelek, Tuncer

    2015-09-01

    Four new one dimensional (1D) cyanide complexes, namely {[Cu(NH3)4(μ-na)][M‧(CN)4]}n and {[Cu(NH3)2(ina)2M‧(μ-CN)2(CN)2]}n (M‧(II) = Pd (1 and 3) or Pt (2 and 4), na:nicotinamide and ina:isonicotinamide) have been synthesized and characterized by elemental, spectral (FT-IR and Raman), and thermal (TG, DTG and DTA) analyses. The crystal structures of complexes 1-3 have been determined by single crystal X-ray diffraction technique. In complexes 1 and 2, na ligand is coordinated to the adjacent Cu(II) ions as a bridging ligand, giving rise to 1D linear cationic chain and the [M‧(CN)4]2- anionic complex acts as a counter ion. Complexes 3 and 4 are also 1D linear chain in which two cyanide ligands bridged neighboring M‧(II) and Cu(II) ions, while ina ligand is coordinated Cu(II) ion through nitrogen atom of pyridine ring. In the complexes, the Cu(II) ions adopt distorted octahedral geometries, while M‧(II) ions are four coordinated with four carbon atoms from cyanide ligands in square-planar geometries. The adjacent chains are further stacked through intermolecular hydrogen bond, Nsbnd Hṡṡṡπ, Csbnd H⋯M‧ and M‧⋯π interactions to form 3D supramolecular networks. Vibration assignments are given for all the observed bands. In addition, thermal stabilities of the compounds are also discussed.

  1. Spectroscopic characterization and biological activity of dihydrazone transition metal complexes: Crystal structure of 2,3-butanedione bis(isonicotinylhydrazone)

    NASA Astrophysics Data System (ADS)

    El-Sayed, Ahmed E. M.; Al-Fulaij, O. A.; Elaasar, A. A.; El-Defrawy, M. M.; El-Asmy, A. A.

    2015-01-01

    Metal complexes of the chloride, nitrate and acetate salts of Co(II), Ni(II) Cu(II), Zn(II), Cd(II) or Hg(II) with 2,3-butanedione bis(isonicotinylhydrazone) [BBINH] have been synthesized and structurally characterized. The crystal of BBINH was solved to crystallize as monoclinic system with space group of P121/c14. The formulae of the complexes were assigned based on the elemental analysis and mass spectra. The formation of BBINH complexes depend on the metal anion used. All complexes are nonelectrolytes except for the complexes 2, 3, 4 are (1:1) and 13 and 14 which are 1:2 electrolytes. BBINH behaves as a neutral tetradentate (N2O2) in the chloride complexes of Ni(II), Cu(II), Zn(II), Cd(II) and Hg(II). In [Co2(BBINH)(H2O)Cl3]ClṡH2O, BBINH has the same dentate but with the two Co(II) ions. In the acetate complexes, [Ni2(BBINH-2H)(H2O)2(OAc)2]ṡ3H2O and [Cu2(BBINH-2H)(OAc)2]ṡ5H2O, BBINH acts as a binegative tetradentate with the two metal ions. The ligand in the nitrate complexes acts as a neutral bidentate via the two hydrazone azomethine Cdbnd NHy; the nitrate ions are ionic in the Cd(II) and Zn(II) complexes and covalent in the Ni(II) complex. The data are supported by NMR (1H and 13C) spectra. The magnetic moments and electronic spectra of all complexes provide tetrahedral, square planar and/or octahedral structure. The decomposition of the complexes revealed the outer and inner solvents as well as the remaining residue based on TGA. The complexes have variable activities against some bacteria and fungi. The ligand is inactive against all tested organisms. The activity of Cd(II) and Hg(II) may be related to the geometry of the complexes.

  2. Growth, Structure, Thermal Properties and Spectroscopic Characteristics of Nd3+-Doped KGdP4O12 Crystal

    PubMed Central

    Sun, Tongqing; Zhang, Yu; Shan, Pai; Zhang, Zichang; Chen, Shaolin; Kong, Yongfa; Xu, Jingjun

    2014-01-01

    A single crystal of Nd3+-doped KGdP4O12 was successfully grown with the top-seeded solution growth and slow cooling (TSSG−SC) technique. It crystallizes in space group C2/c with cell parameters a = 7.812(2) Å, b = 12.307(3) Å, c = 10.474(2) Å, β = 110.84(3)° and Z = 4. The IR and Raman spectra also indicated that the phosphoric polyhedra of Nd:KGdP4O12 has a cyclic symmetry. The chemical composition of the crystal was analyzed and the distribution coefficient of Nd3+ was calculated. The crystal morphology of KGdP4O12 was identified using X-ray diffraction. The compound has good thermal stability to 920°C. Its specific heat and thermal conductivity were determined for potential applications. The spectral properties of Nd:KGdP4O12 indicates that it exhibits broad absorption and emission bands, which are attributed to low symmetry of the crystal. The broad absorption band around 798 nm has a full-width at half-maximum (FWHM) of 14.8 nm and is suitable for AlGaAs laser diode pumping. Moreover, 5 at% Nd3+-doped KGdP4O12 crystal has a long luminescence lifetime of 300 μs and a high quantum efficiency of 96%. PMID:24968165

  3. Crystal structure and X-ray photoemission spectroscopic study of A{sub 2}LaMO{sub 6} [A=Ba, Ca; M=Nb, Ta

    SciTech Connect

    Dutta, Alo; Saha, Sujoy; Sinha, T.P.

    2015-09-15

    The X-ray photoemission spectroscopic (XPS) study of the double perovskite oxides A{sub 2}LaMO{sub 6} [A=Ba, Ca; M=Nb, Ta] synthesized by the solid-state reaction technique has been carried out to investigate the nature of the chemical state of the constituent ions and the bonding between them. The Rietveld refinement of the X-ray diffraction patterns suggests the monoclinic crystal structure of all the materials at room temperature. The negative and positive chemical shifts of the core level XPS spectrum of O-1s and Nb-3d{sub 3/2}/Ta-4f{sub 5/2} respectively suggest the covalent bonding between Nb/Ta cations and O ion. The change of the bonding strength between the anion and the cations from one material to another has been analyzed. The vibrational property of the materials is investigated using the room temperature Raman spectra. A large covalency of Ta-based compound than Nb compound is confirmed from the relative shifting of the Raman modes of the materials. - Graphical abstract: Crystal structure of two perovskite oxides CLN and CLT is investigated. XPS study confirms the two different co-ordination environments of Ca and covalent bonding between B-site cations and O-ion. - Highlights: • Ordered perovskite structure obtained by Rietveld refinement of XRD patterns. • Study of nature of chemical bonding by X-ray photoemission spectroscopy. • Opposite chemical shift of d-states of Nb/Ta with respect to O. • Covalent bonding between d-states of Nb/Ta and O. • Relative Raman shifts of CLN and CLT substantiate the more covalent character of Ta than Nb.

  4. From the molecular structure to spectroscopic and material properties: computational investigation of a bent-core nematic liquid crystal.

    PubMed

    Greco, Cristina; Marini, Alberto; Frezza, Elisa; Ferrarini, Alberta

    2014-05-19

    We present a computational investigation of the nematic phase of the bent-core liquid crystal A131. We use an integrated approach that bridges density functional theory calculations of molecular geometry and torsional potentials to elastic properties through the molecular conformational and orientational distribution function. This unique capability to simultaneously access different length scales enables us to consistently describe molecular and material properties. We can reassign (13)C NMR chemical shifts and analyze the dependence of phase properties on molecular shape. Focusing on the elastic constants we can draw some general conclusions on the unconventional behavior of bent-core nematics and highlight the crucial role of a properly-bent shape.

  5. Single crystal growth of Yb doped NaGd(WO{sub 4}){sub 2} and structural and spectroscopic studies

    SciTech Connect

    Singh, S. G.; Singh, A. K.; Desai, D. G.; Tiwari, B.; Tyagi, M.

    2014-04-24

    High quality single crystals of NaGd(WO{sub 4}){sub 2} doped with 5 mol % Yb and oriented along <001> have been grown by the Czochralski technique in Ar atmosphere. The tetragonal space group I41/a accounts for all the reflections observed in the powder X-ray diffraction analysis. Polarized optical spectroscopy at room temperature revealed a direction dependence of absorption at different wavelength. As a novel uniaxial laser host for Yb{sup 3+}, NaGd(WO{sub 4}){sub 2} is characterized with respect to its transparency and band-edge. The emission spectrum of Yb{sup 3+} (excitation: 980-990 nm diode laser) was also recorded.

  6. Synthesis, crystal structure and spectroscopic properties of a supramolecular zinc(II) complex with N2O2 coordination sphere.

    PubMed

    Dong, Wen-Kui; Zhang, Li-Sha; Sun, Yin-Xia; Zhao, Meng-Meng; Li, Gang; Dong, Xiu-Yan

    2014-01-01

    A new hexa-coordinated zinc(II) complex, namely [ZnL(H2O)2]n, with N2O2 coordination sphere (H2L=4,4'-dibromo-6,6'-dichloro-2,2'-[ethylenedioxybis(nitrilomethylidyne)]diphenol) has been synthesized and structurally characterized by elemental analyses, IR, UV-vis spectra and TG-DTA analyses, etc. Crystallographic data are monoclinic, space group P2(1)/c, a=24.634(2)Å, b=10.144(1)Å, c=7.9351(6)Å, β=91.371(2)°, V=1982.4(3)Å(3), Dc=2.099 g/cm(3), Z=4. The zinc(II) complex exhibits a slightly distorted octahedral geometry with halogen-substituted Salen-type bisoxime forming the basal N2O2 coordination sphere and two oxygen atoms from two coordinated water molecules in the axial position. The hydrogen-bonding and π-π stacking interactions have stabilized the zinc(II) complex molecules to form a self-assembling infinite dual metal-water chain-like structure with the nearest Zn⋯Zn distance of 4.954(4)Å.

  7. Low-dimensional compounds containing cyanido groups. XXVIII. Crystal structure, spectroscopic and magnetic properties of two copper(II) tetracyanidoplatinate complexes with 1,2-diaminopropane

    SciTech Connect

    Vavra, Martin; Potočňák, Ivan; Dušek, Michal; Čižmár, Erik; Ozerov, Mykhaylo; Zvyagin, Sergei A.

    2015-05-15

    Violet crystals of ([Cu(pn){sub 2}]{sub 2}[Pt(CN){sub 4}])[Pt(CN){sub 4}]·2H{sub 2}O (1, pn=1,2-diaminopropane) and blue crystals of [Cu(pn)Pt(CN){sub 4}]{sub n}·nH{sub 2}O (2) were prepared under hydrothermal conditions and characterized using elemental analysis, IR and UV–vis spectroscopy and by X-ray crystal structure analysis. Different number of ν(C≡N) absorption bands of these two compounds reflects their different structures. An X-ray crystal structure analysis has shown that complex 1 is of ionic character and is formed from trinuclear [Cu(pn){sub 2}–Pt(CN){sub 4}–Cu(pn){sub 2}]{sup 2+} complex cation and discrete [Pt(CN){sub 4}]{sup 2–} anion together with two molecules of crystal water. On the other hand, complex 2 is of polymeric character and is formed by 2D networks of [Cu(pn)Pt(CN){sub 4}]{sub n} composition and completed by n molecules of crystal water. Magnetic measurements show the presence of a weak antiferromagnetic exchange interaction in complex 1 (Θ=–0.2 K), while the magnetic susceptibility of complex 2 is well described by the model of uniform S=1/2 spin chain with exchange interaction J/k{sub B}=–1.64 K. - Graphical abstract: Two complexes of different structural types from the system Cu(II) – 1,2–diaminopropane – [Pt(CN){sub 4}]{sup 2–} have been isolated. These were characterized by IR and UV–VIS spectroscopy, X–ray crystal structure analysis together with the magnetic measurements. On one hand ([Cu(pn){sub 2}]{sub 2}[Pt(CN){sub 4}])[Pt(CN){sub 4}]∙2H{sub 2}O is of ionic character and is formed from trinuclear complex cation and discrete anion together with two molecules of crystal water. On the other hand, [Cu(pn)Pt(CN){sub 4}]{sub n}∙nH{sub 2}O is of polymeric character and is formed by 2D networks of [Cu(pn)Pt(CN){sub 4}]{sub n} composition and completed by n molecules of crystal water. - Highlights: • Two complexes of different compositions from one system have been isolated. • First complex is of

  8. Crystal structure and spectroscopic study on photochromism of 1,3-diphenyl-4-(4‧-fluoro)benzal-5-pyrazolone N(4)-phenyl semicarba-zone

    NASA Astrophysics Data System (ADS)

    Chai, Hui; Liu, Guangfei; Liu, Lang; Jia, Dianzeng; Guo, Zaiping; Lang, Jianping

    2005-10-01

    A novel compound 1,3-diphenyl-4-(4'-fluoro)benzal-5-pyrazolone N(4)-phenyl semicarbazone (DP4FBP-PSC) has been synthesized. X-ray single crystal structure analysis shows that the compound has interlaced structure linked by intermolecular hydrogen bonds. The results of fluorescence emission spectroscopy, UV-Vis reflection spectroscopy and the reaction rate constant indicate that DP4FBP-PSC is photochromic material. Its photochromic mechanism was investigated by structure analysis.

  9. Synthesis, single crystal structure, spectroscopic characterization and molecular properties of (2E)-3-(2,6-dichlorophenyl)-1-(3,4-dimethoxyphenyl)prop-2-en-1-one

    NASA Astrophysics Data System (ADS)

    Chidan Kumar, C. S.; Quah, Ching Kheng; Balachandran, V.; Fun, Hoong-Kun; Asiri, A. M.; Chandraju, Siddegowda; Karabacak, Mehmet

    2016-07-01

    A novel (2E)-3-(2,6-dichlorophenyl)-1-(3,4-dimethoxyphenyl)prop-2-en-1-one (DCPDMP) compound has been synthesized and its single crystal has been grown by slow evaporation technique. The structure of the compound has been characterized by FT-IR, FT-Raman and single-crystal X-ray diffraction techniques. The optimized molecular structure, vibrational wavenumbers, corresponding vibrational assignments of the compound have been investigated by means of the density functional theory. The molecule crystallizes in triclinic system, space group P-1 with a = 7.6179 (7), b = 8.5023 (7), c = 12.1967 (10) Å, V = 764.39 (11) Å3 and two molecules in the unit cell. The crystal structure is primarily stabilized through intramolecular C-H … Cl and C-H … O hydrogen bonds and intermolecular C-H … O and weak C-H … π interactions. These inter- and intramolecular interactions are analyzed. Moreover, the molecular electrostatic potential surface of the molecule has been constructed. Global and local reactivity descriptors and dipole moment (μ), static polarizability (α), first order hyperpolarizability (β) and optical gap (ΔE) have been also calculated to study the nonlinear optical (NLO) property of the title compound.

  10. Synthesis, spectroscopic characterization and crystal structure of 5-bromo-1-(2-cyano-pyridin-4-yl)-1 H-indazole-3-carboxylic acid diethylamide

    NASA Astrophysics Data System (ADS)

    Anuradha, G.; Vasuki, G.; Surendrareddy, G.; Veerareddy, A.; Dubey, P. K.

    2014-07-01

    The title compound 5-bromo-1-(2-cyano-pyridin-4-yl)-1 H-indazole-3-carboxylic acid diethylamide, C18H16BrN5O, is prepared from 5-bromoindazole-3-carboxylic acid methylester. N 1-arylation is carried out with 4-chloro-2-cyanopyridine and the resulting product is converted to diethylamide by reacting with thionyl chloride and diethylamine. The structure is identified from its FT-IR, 1H NMR, 13C NMR spectroscopy, elemental analysis data and unambiguously confirmed by single crystal X-ray diffraction studies. There are two symmetry independent molecules in the asymmetric unit with no significant differences in bond lengths and angles. The title compound crystallizes in the triclinic system, space group , with a = 11.2330(2); b = 11.6130(2); c = 15.4710(3) Å, α = 92.515(1)°; β = 109.956(1)°; γ = 107.199(1)°; V = 1788.45(6)Å3 and z = 4. An intramolecular C-H…N hydrogen bond forms an S(6) ring motif in one of the unique molecules. In the crystal, two molecules are linked about a center of inversion by C-H…O hydrogen bonded dimers generating an R {2/2}(16) ring motif. The crystal packing is stabilized by C-H…N, C-H…O hydrogen bonds and π…π stacking interactions.

  11. Growth and spectroscopic properties of samarium oxalate single crystals

    NASA Astrophysics Data System (ADS)

    Vimal, G.; Mani, Kamal P.; Jose, Gijo; Biju, P. R.; Joseph, Cyriac; Unnikrishnan, N. V.; Ittyachen, M. A.

    2014-10-01

    Single crystals of samarium oxalate decahydrate were synthesized using single diffusion gel technique and the conditions influencing the size, shape and quality were optimized. Highly transparent crystals of size 3×2×1 mm3 with a well defined hexagonal morphology were grown during a time period of two weeks. X ray powder diffraction analysis revealed that the grown crystals crystallize in the monoclinic system with space group P21/c and the proposed chemical formula and linkage of water molecules were confirmed using thermogravimetric analysis. The various functional groups of the oxalate ligand and the water of crystallization were identified by Fourier transform infrared spectroscopy. Spectroscopic investigations such as electric dipole transition probability, magnetic dipole transition probability and branching ratios of all possible transitions from 4G5/2 level of Sm3+ ions were estimated from the absorption spectra using JO theory. The spectroscopic analysis suggested that the crystal has a strong and efficient orange red emission. This is confirmed from the photoluminescence spectrum with a wavelength peak at 595 nm and hence this promising emission can be effectively used for optical amplification.

  12. A crystallographic and spectroscopic study on the effect of X-ray radiation on the crystal structure of Melanocarpus albomyces laccase

    SciTech Connect

    Hakulinen, Nina . E-mail: nina.hakulinen@joensuu.fi; Kruus, Kristiina; Koivula, Anu; Rouvinen, Juha . E-mail: juha.rouvinen@joensuu.fi

    2006-12-01

    Laccases (p-diphenol dioxygen oxidoreductases) belong to the family of blue multicopper oxidases, which catalyse the four-electron reduction of dioxygen to water concomitantly through the oxidation of substrate molecules. Blue multicopper oxidases have four coppers, a copper (T1) forming a mononuclear site and a cluster of three coppers (T2, T3, and T3') forming a trinuclear site. Because X-rays are known to liberate electrons during data collection and may thus affect the oxidation state of metals, we have investigated the effect of X-ray radiation upon the crystal structure of a recombinant laccase from Melanocarpus albomyces through the use of crystallography and crystal absorption spectroscopy. Two data sets with different strategies, a low and a high-dose data set, were collected at synchrotron. We have observed earlier that the trinuclear site had an elongated electron density amidst coppers, suggesting dioxygen binding. The low-dose synchrotron structure showed similar elongated electron density, but the high-dose X-ray radiation removed the bulk of this density. Therefore, X-ray radiation could alter the active site of laccase from M. albomyces. Absorption spectra of the crystals (320, 420, and 590 nm) during X-ray radiation were measured at a home laboratory. Spectra clearly showed how that the band at 590 nm had vanished, resulting from the T1 copper being reduced, during the long X-ray measurements. The crystal colour changed from blue to colourless. Absorptions at 320 and 420 nm seemed to be rather permanent. The absorption at 320 nm is due to the T3 coppers and it is proposed that absorption at 420 nm is due to the T2 copper when dioxygen or a reaction intermediate is close to this copper.

  13. Synthesis and spectroscopic characterization of cobalt(III)-alkyl amine complexes showing surface affinity: Single crystal X-ray structure determinations

    NASA Astrophysics Data System (ADS)

    Anbalagan, K.; Maharaja Mahalakshmi, C.; Ganeshraja, A. S.

    2011-11-01

    Structurally integrated cobalt(III) complexes showing interesting surface affinity in the interfacial electron transfer reactions were synthesized by incorporating alkyl amines into the coordination sphere of cis-[Co III(en) 2(RNH 2)Cl]Cl 2; (where RNH 2 = MeNH 2 ( 1), EtNH 2 ( 2), Pr nNH 2 ( 3), Bu nNH 2 ( 4), Bu iNH 2 ( 5), Pen nNH 2 ( 6), Hex nNH 2 ( 7) and BzNH 2 ( 8)) through a modified synthetic route. Such complexes are playing important role as electron acceptors in the interfacial electron transfer reactions taking place between metal complex and nanosized semiconductor particles in energy conversion schemes. The complexes were characterized by spectral, 1H NMR and 13C NMR techniques, which indicate the 1,2-diamino ethane site angles are closely similar forming five membered gauche configuration. Single crystal X-ray refinements were made to explore the structures of five complexes ( 2)-( 5) and ( 7). The complexes under study crystallize either in monoclinic or orthorhombic structure and the space consists; ( 2) P2 1/ n, ( 3) P2 12 12 1, ( 4) Pbca, ( 5) P2 1 and (7) P2 1/ n. The Co(III) ion does not have an electronic preference, however, the structures reflect the conformational preference of RNH 2 ligand.

  14. Synthesis, spectroscopic, crystal structure and DNA binding of Ru(II) complexes with 2-hydroxy-benzoic acid [1-(4-hydroxy-6-methyl-2-oxo-2H-pyran-3-yl)-ethylidene]-hydrazide

    NASA Astrophysics Data System (ADS)

    Chitrapriya, Nataraj; Sathiya Kamatchi, Thangavel; Zeller, Matthias; Lee, Hyosun; Natarajan, Karuppannan

    2011-10-01

    Reactions of 2-hydroxy-benzoic acid [1-(4-hydroxy-6-methyl-2-oxo-2H-pyran-3-yl)-ethylidene]-hydrazide (H 2L) with [RuHCl(CO)(EPh 3) 3] (E = P or As) were carried out and the new complexes obtained were characterized by elemental analysis, electronic, IR, 1H NMR and 13C NMR spectroscopic techniques and single crystal X-ray diffraction studies. Complex ( 1) crystallizes in the monoclinic space group P2(1)/ c with unit cell dimensions a = 18.6236(17) Å, b = 12.8627(12) Å, c = 21.683(2) Å, α = 90.00, β = 114.626(2), γ = 90.00 V = 4721.8(8) Å, Z = 4. The crystal structure of the complex shows Ru(II) atom is six-coordinated, forming a slightly distorted octahedral geometry with two P atoms in axial positions, and three chelating donor atoms of the tridentate Schiff base ligand and one carbonyl group located in the equatorial plane. The molecular structure is stabilized by intramolecular O—H···N interactions. No intermolecular hydrogen bond was observed. The intramolecular hydrogen bond exists between the oxygen atom from salicylic acid moiety and nitrogen from the same moiety. A variety of solution studies were carried out for the determination of DNA binding mode of the complexes. The results suggest that both complexes bind to Herring sperm DNA via non intercalative mode.

  15. Synthesis, spectroscopic, crystal structure and DNA binding of Ru(II) complexes with 2-hydroxy-benzoic acid [1-(4-hydroxy-6-methyl-2-oxo-2H-pyran-3-yl)-ethylidene]-hydrazide.

    PubMed

    Chitrapriya, Nataraj; Kamatchi, Thangavel Sathiya; Zeller, Matthias; Lee, Hyosun; Natarajan, Karuppannan

    2011-10-15

    Reactions of 2-hydroxy-benzoic acid [1-(4-hydroxy-6-methyl-2-oxo-2H-pyran-3-yl)-ethylidene]-hydrazide (H(2)L) with [RuHCl(CO)(EPh(3))(3)] (E = P or As) were carried out and the new complexes obtained were characterized by elemental analysis, electronic, IR, (1)H NMR and (13)C NMR spectroscopic techniques and single crystal X-ray diffraction studies. Complex (1) crystallizes in the monoclinic space group P2(1)/c with unit cell dimensions a=18.6236(17) Å, b=12.8627(12) Å, c=21.683(2) Å, α=90.00, β=114.626(2), γ=90.00 V=4721.8(8) Å, Z=4. The crystal structure of the complex shows Ru(II) atom is six-coordinated, forming a slightly distorted octahedral geometry with two P atoms in axial positions, and three chelating donor atoms of the tridentate Schiff base ligand and one carbonyl group located in the equatorial plane. The molecular structure is stabilized by intramolecular O-H···N interactions. No intermolecular hydrogen bond was observed. The intramolecular hydrogen bond exists between the oxygen atom from salicylic acid moiety and nitrogen from the same moiety. A variety of solution studies were carried out for the determination of DNA binding mode of the complexes. The results suggest that both complexes bind to Herring sperm DNA via non intercalative mode. PMID:21763180

  16. Second sphere coordination in oxoanion binding: Synthesis, spectroscopic characterisation and crystal structures of trans-[bis(ethylenediamine)dinitrocobalt(III)] diclofenac and chlorate

    NASA Astrophysics Data System (ADS)

    Sharma, Rajni; Sharma, Raj Pal; Bala, Ritu; Kariuki, B. M.

    2007-01-01

    In the exploration of cationic cobaltammine [ trans-Co(en) 2(NO 2) 2] + as an anion receptor, binding with oxoanions diclofenac and chlorate ions has been investigated. Yellow crystals of [ trans-Co(en) 2(NO 2) 2]C 14H 10Cl 2NO 2. 2H 2O I, and [ trans-Co(en) 2(NO 2) 2]ClO 3II, have been obtained from a mixture of trans-[bis(ethylenediamine)dinitrocobalt(III)] nitrate solution with sodium diclofenac and sodium chlorate, respectively, in aqueous medium. The products were characterised by elemental analyses, IR, UV/vis, 1H and 13C NMR spectroscopy. Single crystal X-ray structure determinations revealed that electrostatic forces of attraction besides second sphere hydrogen bonding interactions stabilize the crystal lattice. Oxygen atoms of the halate and carboxylate group in diclofenac ions act as hydrogen bond acceptors thereby forming N sbnd H en⋯O bonds. The results show that [ trans-Co(en) 2(NO 2) 2] + is a promising anion receptor for the weakly coordinating halate and diclofenac ions in aqueous medium. Solubility measurements indicate that the affinity of cationic cobaltammine [ trans-Co(en) 2(NO 2) 2] + is greater for diclofenac than for the chlorate ion.

  17. Synthesis, crystal structure, and spectroscopic studies of organic-inorganic hybrid material: [C7H10NO]2BiBr5

    NASA Astrophysics Data System (ADS)

    Aloui, Z.; Ferretti, V.; Abid, S.; Lefebvre, F.; Rzaigui, M.; Ben Nasr, C.

    2016-08-01

    A novel organic-inorganic hybrid compound, 2-methoxyanilinium pentabromobismuthate(III), [C7H10NO]2BiBr5, was synthesized and its structure determined by means of single crystal X-ray diffraction studies at room temperature. The molecule crystallizes in the orthorhombic C2221 space group with cell parameters a = 11.8870(4), b = 23.4775(8), c = 8.1232(3) Å, V = 2267.0(1) Å3 and four molecules in the unit cell. The structure of the title compound is built up from one-dimensional [BiBr5]2n-n polyanionic zig-zag chains composed of deformed BiBr6 octahedra share Br(2) apex and 2-methoxyanilinium cations. The assignment of the vibrational bands was based on comparison with vibrational mode frequencies of homologous compounds. Theoretical calculations were performed using density functional theory (DFT) for studying the vibrational spectrum of the investigated molecule in its ground state. The 13C CP-MAS NMR spectrum is in agreement with the X-ray structure.

  18. Site-Directed Spectroscopic Probes of Actomyosin Structural Dynamics

    PubMed Central

    Thomas, David D.; Kast, David; Korman, Vicci L.

    2010-01-01

    Spectroscopy of myosin and actin has entered a golden age. High-resolution crystal structures of isolated actin and myosin have been used to construct detailed models for the dynamic actomyosin interactions that move muscle. Improved protein mutagenesis and expression technologies have facilitated site-directed labeling with fluorescent and spin probes. Spectroscopic instrumentation has achieved impressive advances in sensitivity and resolution. Here we highlight the contributions of site-directed spectroscopic probes to understanding the structural dynamics of myosin II and its actin complexes in solution and muscle fibers. We emphasize studies that probe directly the movements of structural elements within the myosin catalytic and light-chain domains, and changes in the dynamics of both actin and myosin due to their alternating strong and weak interactions in the ATPase cycle. A moving picture emerges in which single biochemical states produce multiple structural states, and transitions between states of order and dynamic disorder power the actomyosin engine. PMID:19416073

  19. Copper and cobalt coordination polymers based on isophthalate as bridging ligands and imidazole as capping ligands: Syntheses, crystal structures, spectroscopic characterization

    NASA Astrophysics Data System (ADS)

    Song, Jiang-Feng; Chen, Yan; Li, Zhi-Gang; Zhou, Rui-Sha; Xu, Xiao-Yu; Xu, Ji-Qing

    2007-10-01

    Two novel coordination polymers, {[Cu(ip)(Him) 2(DMF)]·H 2O} ( 1) and Co(ip)(Him) 2 ( 2), (ip = isophthalate, Him = imidazole) were prepared under hydrothermal conditions and their structures were determined by single-crystal X-ray diffraction. X-ray structural analysis reveals that 1-D zigzag metal-organic chains are connected to form a 3-D supramolecular framework in compounds 1 and 2 by hydrogen-bonding and π-π interaction or other intermolecular contacts. Infrared, UV-vis, and elemental analysis were performed to characterize the two compounds. The result of magnetic determination for compound 2 shows there exist antiferromagnetic interaction between magnetic centers.

  20. An unexpected cobalt(III) complex containing a Schiff base ligand: Synthesis, crystal structure, spectroscopic behavior, electrochemical property and SOD-like activity

    NASA Astrophysics Data System (ADS)

    Chai, Lan-Qin; Huang, Jiao-Jiao; Zhang, Hong-Song; Zhang, Yu-Li; Zhang, Jian-Yu; Li, Yao-Xin

    2014-10-01

    An unexpected mononuclear Co(III) complex, [Co(L2)2·(CH3COO)]·CH3OH (HL2 = 1-(2-{[(E)-3,5-dichloro-2-hydroxybenzylidene]amino}phenyl)ethanone oxime), has been synthesized via complexation of Co(II) acetate tetrahydrate with HL1 originally. The plausible reaction mechanism for the formation of quinazoline-type ligand was proposed. HL1 and its corresponding Co(III) complex were characterized by IR, as well as by elemental analysis and UV-vis spectroscopy. The crystal structure of the complex has been determined by single-crystal X-ray diffraction. Each complex links two other molecules into an infinite 1-D chain via intermolecular hydrogen bonding interactions. Moreover, the electrochemical properties of the cobalt(III) complex were studied by cyclic voltammetry and X-ray photoelectron spectrum (XPS). In addition, superoxide dismutase-like activities of HL1 and Co(III) complex were also investigated.

  1. Crystal structure, spectroscopic properties and DFT studies on copper (II) complex of bis{(E)-1-[(2-phenoxyphenylimino)methyl]naphthalene-2-ol}chloroform solvate

    NASA Astrophysics Data System (ADS)

    Macit, Mustafa; Alpaslan, Gökhan

    2014-08-01

    Copper (II) complex of the title Schiff base compound was synthesized from the reaction of 2-hydroxy-1-naphthaldehyde with 2-phenoxyaniline. The complex has been characterized by FT-IR, and X-ray single-crystal techniques. The molecular geometry, vibrational frequencies values of the compound in the ground state have been calculated using the density functional theory (DFT/B3LYP) method with the LANL2DZ basis set and compared with the experimental data. The calculated results show that the optimized geometry is compatible with the crystal structure and the theoretical vibrational frequencies are in good agreement with the experimental values. The energetic behavior of the compound in solvent media has been examined using B3LYP method with the LANL2DZ basis set by applying the polarizable continuum model (PCM). In addition, frontier molecular orbital analysis (HOMO-LUMO), natural bond orbital analysis (NBO) and non-linear optical (NLO) properties of the compound were investigated using same theoretical calculations.

  2. An unexpected cobalt(III) complex containing a Schiff base ligand: Synthesis, crystal structure, spectroscopic behavior, electrochemical property and SOD-like activity.

    PubMed

    Chai, Lan-Qin; Huang, Jiao-Jiao; Zhang, Hong-Song; Zhang, Yu-Li; Zhang, Jian-Yu; Li, Yao-Xin

    2014-10-15

    An unexpected mononuclear Co(III) complex, [Co(L2)2·(CH3COO)]·CH3OH (HL2=1-(2-{[(E)-3,5-dichloro-2-hydroxybenzylidene]amino}phenyl)ethanone oxime), has been synthesized via complexation of Co(II) acetate tetrahydrate with HL1 originally. The plausible reaction mechanism for the formation of quinazoline-type ligand was proposed. HL1 and its corresponding Co(III) complex were characterized by IR, as well as by elemental analysis and UV-vis spectroscopy. The crystal structure of the complex has been determined by single-crystal X-ray diffraction. Each complex links two other molecules into an infinite 1-D chain via intermolecular hydrogen bonding interactions. Moreover, the electrochemical properties of the cobalt(III) complex were studied by cyclic voltammetry and X-ray photoelectron spectrum (XPS). In addition, superoxide dismutase-like activities of HL1 and Co(III) complex were also investigated.

  3. Synthesis, crystal structure, and vibrational spectroscopic and UV-visible studies of Cs{sub 2}MnP{sub 2}O{sub 7}

    SciTech Connect

    Kaoua, Saida; Krimi, Saida; Pechev, Stanislav; Gravereau, Pierre; Chaminade, Jean-Pierre; Couzi, Michel; El Jazouli, Abdelaziz

    2013-02-15

    A new member of the A{sub 2}MP{sub 2}O{sub 7} diphosphate family, Cs{sub 2}MnP{sub 2}O{sub 7}, has been synthesized and structurally characterized. The crystal structure was determined by single crystal X-Ray diffraction. Cs{sub 2}MnP{sub 2}O{sub 7} crystallizes in the orthorhombic system, space group Pnma ( Music-Sharp-Sign 62), with the unit cell parameters a=16.3398(3), b=5.3872(1), c=9.8872(2) A, Z=4 and V=870.33(3) A{sup 3}. The structure parameters were refined to a final R{sub 1}/wR{sub 2}=0.0194/0.0441 for 1650 observed reflections. The 2D framework of Cs{sub 2}MnP{sub 2}O{sub 7} structure consists of P{sub 2}O{sub 7} and MnO{sub 5} units. The corner-shared MnO{sub 5} and P{sub 2}O{sub 7} units are alternately arranged along the b axis to form [(MnO)P{sub 2}O{sub 7}]{sub {infinity}} chains. These chains are interconnected by an oxygen atom to form sheets parallel to the (b, c) plane. The cesium atoms are located between the sheets in 9- and 10-fold coordinated sites. The infrared and Raman vibrational spectra have been investigated. A factor group analysis leads to the determination of internal modes of (P{sub 2}O{sub 7}) groups. UV-visible spectrum consists of weak bands, between 340 and 700 nm, assigned to the forbidden d-d transitions of Mn{sup 2+} ion, and of a strong band around 250 nm, attributed to the O--Mn charge transfer. - Graphical abstract: Structure of Cs{sub 2}MnP{sub 2}O{sub 7}: The 2D structure of Cs{sub 2}MnP{sub 2}O{sub 7} is built from P{sub 2}O{sub 7} diphosphate groups and MnO{sub 5} square pyramids which share corners and form [(MnO)P{sub 2}O{sub 7}]{sub {infinity}} chains along b axis. These chains are interconnected by an oxygen atom to form wavy (MnP{sub 2}O{sub 7}){sup 2-} sheets parallel to the (b, c) plane. The cesium ions are located between these sheets in the inter-layers space, in zigzag positions. Highlights: Black-Right-Pointing-Pointer A new diphosphate, Cs{sub 2}MnP{sub 2}O{sub 7}, has been synthesized and structurally

  4. Crystal structure, magnetic, thermal behavior, and spectroscopic studies of two new bimetallic hydrogenselenites: [Cu2-xNix (HSeO3)2Cl2.4H2O], (x = 0.62; 0.91)

    NASA Astrophysics Data System (ADS)

    Hentech, I.; Zehani, K.; Kabadou, A.; Ben Salah, A.; Loukil, M.; Bessais, L.

    2016-08-01

    Two new iso-structural bimetallic hydrogenselenites [Cu2-xNix(HSeO3)2Cl2.4H2O] (x = 0.62; 0.91) have been synthesized from solution and characterized by single-crystal and powder X-ray diffraction. They crystallized in the orthorhombic Pnma space group with the following lattice parameters: for Cu1.09Ni0.91(HSeO3)2Cl2.4H2O: a = 9.0931 (2) Å, b = 17.7717 (4) Å, c = 7.1620 (2) Å, Z = 4, and for Cu1.38Ni0.62(HSeO3)2Cl2.4H2O: a = 9.0931 (4) Å, b = 17.7467 (7) Å, c = 7.1717 (3) Å; Z = 4. The crystal structure of this compound consists by a three-dimensional framework, but it may be described as a bi-dimensional structure consisting of layers, parallel to the (010) plane formed by two types of (Cu/Ni) octahedral and (HSeO3)- trigonal pyramids. The magnetic measurement, thermal and spectroscopic studies were performed for these compounds. The magnetic results reveal the appearance of a weak ferromagnetic behavior at low temperature (Tc = 16 K for x = 0.91 and 18.8 K for x = 0.62). The DSC analysis enabled us to locate two endothermic peaks. The first peak can be attributed to a completely dehydration of the material, in this transformation, the compounds undergo a structural phase transition which can favor a non-centrosymmetric phase at high temperature confirmed by the thermodiffractograms measurement. The second peak for these samples is due to the ferro-paraelectric phase transition which can be explained by an order- disorder transition.

  5. Dimeric and polymeric mercury(II) complexes of 1-methyl-1,2,3,4-tetrazole-5-thiol: Synthesis, crystal structure, spectroscopic characterization, and thermal analyses

    NASA Astrophysics Data System (ADS)

    Taheriha, Mohammad; Ghadermazi, Mohammad; Amani, Vahid

    2016-03-01

    Two-dimensional coordination polymer of [Hg(μ3-mmtz)2]n (1) and centrosymmetric dinuclear complexes of {[H2en][Hg2(mmtz)4(μ-Br)2]} (2) and {[H2en][Hg2(mmtz)4(μ-I)2]} (3) (where Hmmtz is 1-methyl-1,2,3,4-tetrazole-5-thiol and en is ethylene diamine) were synthesized from the reaction of Hmmtz and en with HgCl2, HgBr2 and HgI2, respectively, in CH3OH. Complex 1 was also synthesized from the reaction of Hmmtz and en with HgX2 (X = OAc and SCN) in CH3OH. These three complexes were thoroughly characterized by elemental analysis (CHN), thermal gravimetric analysis (TGA), differential thermal analyses (DTA), infrared, UV-vis, 1H NMR, and luminescence spectroscopy, and their structures were determined by single-crystal X-ray diffraction.

  6. Cationic half-sandwich Ru(II) complexes containing (N,N)-bound Schiff-base ligands: Synthesis, crystal structure analysis and spectroscopic studies

    NASA Astrophysics Data System (ADS)

    Tao, Li; Miao, Qian; Tehrani, Alireza Azhdari; Hajiashrafi, Taraneh; Hu, Mao-Lin; Morsali, Ali

    2016-08-01

    Three Ru(II) half-sandwich complexes containing (N,N)-bound Schiff-base ligands, [(η6-C6H6) RuCl(L1)]PF6 (1) L1 = (E)-1-(6-methylpyridin-2-yl)-N-(p-tolyl)methanimine, [(η6-p-cymene)RuCl(L1)]PF6 (2) and [(η6-p-cymene)RuCl(L2)]PF6(3) L2 = (E)-1-(6-bromopyridin-2-yl)-N-(p-tolyl)methanimine, were synthesized, characterized and their supramolecular structures were analyzed. The crystal packing of these compounds was studied using geometrical analysis and Hirshfeld surface analysis. The fluorescence behavior of these compounds was also studied. TD-DFT calculations were carried out to better understand the fluorescence properties of complexes 1-3. These compounds could be promising for the design of organometallic dye systems.

  7. Spectroscopic study, antimicrobial activity and crystal structures of N-(2-hydroxy-5-nitrobenzalidene)4-aminomorpholine and N-(2-hydroxy-1-naphthylidene)4-aminomorpholine

    NASA Astrophysics Data System (ADS)

    Yıldız, Mustafa; Ünver, Hüseyin; Dülger, Başaran; Erdener, Diğdem; Ocak, Nazan; Erdönmez, Ahmet; Durlu, Tahsin Nuri

    2005-03-01

    Schiff bases N-(2-hydroxy-3-nitrobenzalidene)4-aminomorpholine ( 1) and N-(2-hydroxy-1-naphthylidene)4-aminomorpholine ( 2) were synthesized from the reaction of 4-aminomorpholine with 2-hydroxy-5-nitrobenzaldehyde and 2-hydroxy-1-naphthaldehyde. Compounds 1 and 2 were characterized by elemental analysis, IR, 1H NMR, 13C NMR and UV-Visible techniques. The UV-Visible spectra of the Schiff bases with OH group in ortho position to the imino group were studied in polar and nonpolar solvents in acidic and basic media. The structures of compounds 1 and 2 have been examined cyrstallographically, for two compounds exist as dominant form of enol-imines in both the solutions and solid state. The title compounds 1 and 2 crystallize in the monoclinic space group P2 1/ c and P2 1/ n with unit cell parameters: a=8.410(1) and 11.911(3), b=6.350(9) and 4.860(9), c=21.728(3) and 22.381(6) Å, β=90.190(1) and 95.6(2)°, V=1160.6(3) and 1289.5(5) Å 3, Dx=1.438 and 1.320 g cm -3, respectively. The crystal structures were solved by direct methods and refined by full-matrix least squares. The antimicrobial activities of compounds 1 and 2 have also been studied. The antimicrobial activities of the ligands have been screened in vitro against the organisms Escherichia coli ATCC 11230, Staphylococcus aureus ATCC 6538, Klebsiella pneumoniae UC57, Micrococcus luteus La 2971, Proteus vulgaris ATCC 8427, Pseudomonas aeruginosa ATCC 27853, Mycobacterium smegmatis CCM 2067, Bacillus cereus ATCC 7064, Listeria monocytogenes ATCC 15313, Candida albicans ATCC 10231, Kluyveromyces fragilis NRRL 2415, Rhodotorula rubra DSM 70403, Debaryomyces hansenii DSM 70238 and Hanseniaspora guilliermondii DSM 3432.

  8. Low-dimensional compounds containing cyano groups. XVII. Crystal structure, spectroscopic, thermal and magnetic properties of [Cu(bmen){sub 2}][Pt(CN){sub 4}] (bmen=N,N'-dimethylethylenediamine)

    SciTech Connect

    Potocnak, Ivan Vavra, Martin; Cizmar, Erik; Kajnakova, Marcela; Radvakova, Alena; Steinborn, Dirk; Zvyagin, Sergei A.; Wosnitza, Jochen; Feher, Alexander

    2009-01-15

    The synthesis, structural analysis, spectroscopic studies, susceptibility and specific-heat measurements of {l_brace}[Cu(bmen){sub 2}][Pt(CN){sub 4}]{r_brace}{sub n} (bmen=N,N'-dimethylethylenediamine) are presented. X-ray crystal-structure analysis revealed that the [Pt(CN){sub 4}]{sup 2-} building blocks are combined with [Cu(bmen){sub 2}]{sup 2+} units to form a chain-like structure along the a axis. The Cu(II) atoms are hexacoordinated by four nitrogen atoms in the equatorial plane belonging to two molecules of bidentate bmen ligands with average Cu-N distance of 2.043(18) A. The axial positions are occupied by two nitrogen atoms from bridging [Pt(CN){sub 4}]{sup 2-} anions at a longer axial Cu-N distance of 2.490(4) A. The compound is characterized by the presence of a weak antiferromagnetic exchange coupling J/k{sub B}=0.6 K. Despite the one-dimensional (1D) character of the structure, the analysis of the magnetic properties and specific heat at very low temperatures shows that [Cu(bmen){sub 2}][Pt(CN){sub 4}] behaves as a two-dimensional (2D) square-lattice Heisenberg magnet with weak interlayer coupling. - Graphical abstract: The synthesis, structural analysis, spectroscopic studies, susceptibility and specific-heat measurements of {l_brace}[Cu(bmen){sub 2}][Pt(CN){sub 4}]{r_brace}{sub n} (bmen=N,N'-dimethylethylenediamine) are presented. X-ray crystal-structure analysis revealed that the [Pt(CN){sub 4}]{sup 2-} building blocks are combined with [Cu(bmen){sub 2}]{sup 2+} units to form a chain-like structure. The compound is characterized by the presence of a weak antiferromagnetic exchange coupling J/k{sub B}=-0.6 K. Despite the one-dimensional character of the structure, the analysis of the magnetic properties and specific heat at very low temperatures shows that [Cu(bmen){sub 2}][Pt(CN){sub 4}] behaves as a two-dimensional square-lattice Heisenberg magnet with weak interlayer coupling.

  9. Synthesis, crystal structure, and spectroscopic and thermal properties of the polymeric compound catena-poly[[bis(2,4-dichlorobenzoato)zinc(II)]-μ-isonicotinamide].

    PubMed

    Homzová, Katarína; Györyová, Katarína; Koman, Marián; Melník, Milan; Juhászová, Žofia

    2015-09-01

    Zinc(II) carboxylates with O-, S- and N-donor ligands are interesting for their structural features, as well as for their antibacterial and antifungal activities. The one-dimensional zinc(II) coordination complex catena-poly[[bis(2,4-dichlorobenzoato-κO)zinc(II)]-μ-isonicotinamide-κ(2)N(1):O], [Zn(C7H3Cl2O2)2(C6H6N2O)]n, has been prepared and characterized by IR spectroscopy, single-crystal X-ray analysis and thermal analysis. The tetrahedral ZnO3N coordination about the Zn(II) cation is built up by the N atom of the pyridine ring, an O atom of the carbonyl group of the isonicotinamide ligand and two O atoms of two dichlorobenzoate ligands. Isonicotinamide serves as a bridge between tetrahedra, with a Zn···Zn distance of 8.8161 (7) Å. Additionally, π-π interactions between the planar benzene rings contribute to the stabilization of the extended structure. The structure is also stabilized by intermolecular hydrogen bonds between the amino and carboxylate groups of the ligands, forming a two-dimensional network. During thermal decomposition of the complex, isonicotinamide, dichlorobenzene and carbon dioxide were evolved. The final solid product of the thermal decomposition heated up to 1173 K was metallic zinc. PMID:26322615

  10. Synthesis, crystal structure, and spectroscopic and thermal properties of the polymeric compound catena-poly[[bis(2,4-dichlorobenzoato)zinc(II)]-μ-isonicotinamide].

    PubMed

    Homzová, Katarína; Györyová, Katarína; Koman, Marián; Melník, Milan; Juhászová, Žofia

    2015-09-01

    Zinc(II) carboxylates with O-, S- and N-donor ligands are interesting for their structural features, as well as for their antibacterial and antifungal activities. The one-dimensional zinc(II) coordination complex catena-poly[[bis(2,4-dichlorobenzoato-κO)zinc(II)]-μ-isonicotinamide-κ(2)N(1):O], [Zn(C7H3Cl2O2)2(C6H6N2O)]n, has been prepared and characterized by IR spectroscopy, single-crystal X-ray analysis and thermal analysis. The tetrahedral ZnO3N coordination about the Zn(II) cation is built up by the N atom of the pyridine ring, an O atom of the carbonyl group of the isonicotinamide ligand and two O atoms of two dichlorobenzoate ligands. Isonicotinamide serves as a bridge between tetrahedra, with a Zn···Zn distance of 8.8161 (7) Å. Additionally, π-π interactions between the planar benzene rings contribute to the stabilization of the extended structure. The structure is also stabilized by intermolecular hydrogen bonds between the amino and carboxylate groups of the ligands, forming a two-dimensional network. During thermal decomposition of the complex, isonicotinamide, dichlorobenzene and carbon dioxide were evolved. The final solid product of the thermal decomposition heated up to 1173 K was metallic zinc.

  11. Crystal structure and spectroscopic properties of a new oxyarsenate Li{sub 0.5}Ni{sub 0.25}TiOAsO{sub 4}

    SciTech Connect

    Chakir, M. . E-mail: fachakir@yahoo.fr; El Jazouli, A.; Chaminade, J.P.; Bouree, F.

    2007-07-03

    The new oxyarsenate Li{sub 0.5}Ni{sub 0.25}TiOAsO{sub 4} has been synthesized and studied by a combination of X-ray powder diffraction, neutrons powder diffraction and vibrational spectroscopy. Li{sub 0.5}Ni{sub 0.25}TiOAsO{sub 4} crystallizes in the monoclinic P2{sub 1}/c space group with the unit cell parameters: a = 6.5854(3) A, b = 7.4665(4) A, c = 7.4969(4) A, {beta} = 89.884(6){sup o}, V = 368.62(1) A{sup 3} and Z = 4. The structure has been determined at room temperature from neutrons diffraction by the Rietveld method analysis. It is formed by a 3D network of TiO{sub 6} octahedra and AsO{sub 4} tetrahedra sharing corners. Structural refinement shows a partial and a statistical occupancy of 2a and 2b sites by Li{sup +} and Ni{sup 2+} ions. TiO{sub 6} octahedra are linked together by corners and form infinite chains along c-axis. Raman and infrared studies confirm the existence of -Ti-O-Ti- chains. Diffuse reflectance spectrum indicates the presence of octahedrally coordinated Ni{sup 2+} ions.

  12. Three-dimensional Raman spectroscopic imaging of protein crystals deposited on a nanodroplet.

    PubMed

    Nitahara, Satoshi; Maeki, Masatoshi; Yamaguchi, Hiroshi; Yamashita, Kenichi; Miyazaki, Masaya; Maeda, Hideaki

    2012-12-21

    Confocal Raman spectroscopic imaging has been used to find the location of protein crystals deposited in a nanodroplet. The depth of the protein crystal has been clearly identified by comparing the three-dimensional Raman spectroscopic images of the protein with those of water. Additionally, the low concentration region around a growing protein crystal in the nanodroplet was visualized using two-dimensional Raman spectroscopic imaging.

  13. Spectroscopic Investigation of Ce(3+) Doped Fluoride Crystals

    NASA Technical Reports Server (NTRS)

    Reinhart, Donald H.; Armagan, Guzin; Marsh, Waverly; Barnes, James; Chai, B. H. T.

    1995-01-01

    Doping of the trivalent rare-earth cerium ion into fluoride crystals is of interest in producing turnable ultra-violet solid state lasers. These lasers are desirable for many applications in medicine, industry, and scientific research, including remote sensing. High absorption and stimulated emission cross sections of the dipole allowed 4f-5d transitions show promise in cerium as a laser ion in crystals. Several research groups have already reported the observation of stimulated emission of cerium in LiYF4, LiSrAlF6, and LiCaAlF6. However, the color center formation in the crystals due to the excited state absorption of ultra-violet pump light adds difficulty to achieving laser action. We have investigated the spectroscopic properties of cerium such as absorption and emission spectra, and lifetimes in four different fluoride crystals, including LiCaAlF6, LiSrAlF6, KyF4 and LiYF4. We have derived the polarized absorption and stimulated emission cross sections from transmission and fluorescence emission measurements for each of the host crystals. we have measured the lifetime of the lowest 5d level; moreover, investigated the temperature dependence of this lifetime and color center formation. Our results on absorption and stimulated emission cross sections for LiCaAlF6 and LiSrAlF6 are similar to the results already published.

  14. 3-D supramolecular architectures in the three new complexes constructed from mixed ligands: Syntheses, crystal structures, spectroscopic properties, XRPD and thermal study

    NASA Astrophysics Data System (ADS)

    Yang, Guo-Ping; Wang, Yao-Yu; Wang, Hong; Wang, Cui-Juan; Wen, Gui-Lin; Shi, Qi-Zhen; Peng, Shie-Ming

    2008-10-01

    Three new coordination polymers [Cu 2(bptc) (bpdap) 2]·4H 2O ( 1), {Zn 2(bptc)(bpe)(H 2O) 6} n ( 2) and {Co 2(bptc)(bpe)(H 2O) 8} n ( 3) [H 4bptc = 3,3',4,4'-biphenyltetracarboxylate acid, bpdap = N, N'-bis(2-pyridyl)-2,6-diaminopyridine, bpe = trans-1,2-bis(4-pyridyl)ethene] have been hydrothermally synthesized in different pH values and structurally characterized by single-crystal X-ray diffraction. The non-covalent interactions of hydrogen bond extend complexes 1, 2 and 3 into supramolecular architectures, where 1 exhibits a 3-D framework with 1-D open channels where the guest water molecules are located. Importantly, two kinds of chiral helical H-bonded chains appear in 1, and some types of H-bonded patterns exist in 1, 2 and 3. It is more remarkable that the building block bptc anion adopts versatile coordination modes in these complexes. The elemental analysis, IR spectra, XRPD and TG analysis are discussed for 1, 2 and 3. In addition, the fluorescence is also studied for 2 here.

  15. Synthesis, crystal structure and spectroscopic and electrochemical properties of bridged trisbenzoato copper-zinc heterobinuclear complex of 2,2‧-bipyridine

    NASA Astrophysics Data System (ADS)

    Koch, Angira; Kumar, Arvind; Singh, Suryabhan; Borthakur, Rosmita; Basumatary, Debajani; Lal, Ram A.; Shangpung, Sankey

    2015-03-01

    The synthesis of the heterobinuclear copper-zinc complex [CuZn(bz)3(bpy)2]ClO4 (bz = benzoate) from benzoic acid and bipyridine is described. Single crystal X-ray diffraction studies of the heterobinuclear complex reveals the geometry of the benzoato bridged Cu(II)-Zn(II) centre. The copper or zinc atom is pentacoordinate, with two oxygen atoms from bridging benzoato groups and two nitrogen atoms from one bipyridine forming an approximate plane and a bridging oxygen atom from a monodentate benzoate group. The Cu-Zn distance is 3.345 Å. The complex is normal paramagnetic having μeff value equal to 1.75 BM, ruling out the possibility of Cu-Cu interaction in the structural unit. The ESR spectrum of the complex in CH3CN at RT exhibit an isotropic four line spectrum centred at g = 2.142 and hyperfine coupling constants Aav = 63 × 10-4 cm-1, characteristic of a mononuclear square-pyramidal copper(II) complexes. At LNT, the complex shows an isotropic spectrum with g|| = 2.254 and g⊥ = 2.071 and A|| = 160 × 10-4 cm-1. The Hamiltonian parameters are characteristic of distorted square pyramidal geometry. Cyclic voltammetric studies of the complex have indicated quasi-reversible behaviour in acetonitrile solution.

  16. Complexes of cis-dioxomolybdenum(VI) and oxovanadium(IV) with a tridentate ONS donor ligand: synthesis, spectroscopic properties, X-ray crystal structure and catalytic activity.

    PubMed

    Fayed, Ahmed M; Elsayed, Shadia A; El-Hendawy, Ahmed M; Mostafa, Mohamed R

    2014-08-14

    New cis-dioxomolybdenum(VI) and oxovanadium(IV) complexes of the Schiff base, derived from S-methyl dithiocarbazate and 2,3-dihydroxybenzaldehyde (H2dhsm), have been synthesized. The complexes of the type cis-[MoO2(dhsm)] (1a), cis-[MoO2(dhsm)(D)] (1b-1d) [D=neutral monodentate ligand; EtOH, pyridine (py) or imidazole (imz)], [VO(dhsm)(NN)] (2a, 2b) [NN=2,2'-bipyridine (bipy) or 1,10-phenanthroline (phen)] and [VO(dhsm)] (2c) have been isolated, characterized by (1)H NMR, IR, UV-Vis and EPR spectral studies and investigated by cyclic voltammetry. The X-ray crystal structure of cis-[MoO2(dhsm)(EtOH)] (1b) has been determined and shows that the complex has a distorted octahedral geometry in which the H2dhsm behaves as a dianionic ONS tridentate ligand coordinating via phenoxide oxygen, hydrazinic nitrogen and thiolate sulfur. The oxomolybdenum(IV) complex [MoO(dhsm)] (1e) has obtained from dioxomolybdenum(VI) complex (1b) by oxo abstraction with PPh3. The reactivity of the complexes toward catalytic oxidation of alcohols in the presence of H2O2 and t-BuOOH as co-oxidants under solvent free conditions is reported. PMID:24747851

  17. Complexes of cis-dioxomolybdenum(VI) and oxovanadium(IV) with a tridentate ONS donor ligand: Synthesis, spectroscopic properties, X-ray crystal structure and catalytic activity

    NASA Astrophysics Data System (ADS)

    Fayed, Ahmed M.; Elsayed, Shadia A.; El-Hendawy, Ahmed M.; Mostafa, Mohamed R.

    2014-08-01

    New cis-dioxomolybdenum(VI) and oxovanadium(IV) complexes of the Schiff base, derived from S-methyl dithiocarbazate and 2,3-dihydroxybenzaldehyde (H2dhsm), have been synthesized. The complexes of the type cis-[MoO2(dhsm)] (1a), cis-[MoO2(dhsm)(D)] (1b-1d) [D = neutral monodentate ligand; EtOH, pyridine (py) or imidazole (imz)], [VO(dhsm)(Nsbnd N)] (2a, 2b) [Nsbnd N = 2,2‧-bipyridine (bipy) or 1,10-phenanthroline (phen)] and [VO(dhsm)] (2c) have been isolated, characterized by 1H NMR, IR, UV-Vis and EPR spectral studies and investigated by cyclic voltammetry. The X-ray crystal structure of cis-[MoO2(dhsm)(EtOH)] (1b) has been determined and shows that the complex has a distorted octahedral geometry in which the H2dhsm behaves as a dianionic ONS tridentate ligand coordinating via phenoxide oxygen, hydrazinic nitrogen and thiolate sulfur. The oxomolybdenum(IV) complex [MoO(dhsm)] (1e) has obtained from dioxomolybdenum(VI) complex (1b) by oxo abstraction with PPh3. The reactivity of the complexes toward catalytic oxidation of alcohols in the presence of H2O2 and t-BuOOH as co-oxidants under solvent free conditions is reported.

  18. Crystal structure and spectroscopic analysis of a new oxalate-bridged Mn(II) compound: catena-poly[guanidinium [[aqua-chlorido-manganese(II)]-μ2-oxalato-κ(4) O (1),O (2):O (1'),O (2')] monohydrate].

    PubMed

    Sehimi, Hiba; Chérif, Ichraf; Zid, Mohamed Faouzi

    2016-05-01

    As part of our studies on the synthesis and the characterization of oxalate-bridged compounds M-ox-M (ox = oxalate dianion and M = transition metal ion), we report the crystal structure of a new oxalate-bridged Mn(II) phase, {(CH6N3)[Mn(C2O4)Cl(H2O)]·H2O} n . In the compound, a succession of Mn(II) ions (situated on inversion centers) adopting a distorted octa-hedral coordination and bridged by oxalate ligands forms parallel zigzag chains running along the c axis. These chains are inter-connected through O-H⋯O hydrogen-bonding inter-actions to form anionic layers parallel to (010). Individual layers are held together via strong hydrogen bonds involving the guanidinium cations (N-H⋯O and N-H⋯Cl) and the disordered non-coordinating water mol-ecule (O-H⋯O and O-H⋯Cl), as well as by guanidinium π-π stacking. The structural data were confirmed by IR and UV-Visible spectroscopic analysis. PMID:27308028

  19. Study of a series of cobalt(II) sulfonamide complexes: Synthesis, spectroscopic characterization, and microbiological evaluation against M. tuberculosis. Crystal structure of [Co(sulfamethoxazole)2(H2O)2]·H2O

    NASA Astrophysics Data System (ADS)

    Mondelli, Melina; Pavan, Fernando; de Souza, Paula C.; Leite, Clarice Q.; Ellena, Javier; Nascimento, Otaciro R.; Facchin, Gianella; Torre, María H.

    2013-03-01

    Nowadays, the research for new and better antimicrobial compounds is an important field due to the increase of immunocompromised patients, the use of invasive medical procedures and extensive surgeries, among others, that can affect the incidence of infections. Another big problem associated is the occurrence of drug-resistant microbial strains that impels a ceaseless search for new antimicrobial agents. In this context, a series of heterocyclic-sulfonamide complexes with Co(II) was synthesized and characterized with the aim of obtaining new antimicrobial compounds. The structural characterization was performed using different spectroscopic methods (UV-Vis, IR, and EPR). In spite of the fact that the general stoichiometry for all the complexes was Co(sulfonamide)2·nH2O, the coordination atoms were different depending on the coordinated sulfonamide. The crystal structure of [Co(sulfamethoxazole)2(H2O)2]·H2O was obtained by X-ray diffraction showing that Co(II) is in a slightly tetragonal distorted octahedron where sulfamethoxazole molecules act as a head-to-tail bridges between two cobalt atoms, forming polymeric chains. Besides, the activity against Mycobacterium tuberculosis, one of the responsible for tuberculosis, and the cytotoxicity on J774A.1 macrophage cells were evaluated.

  20. Chelation, spectroscopic characterization, biological activity and crystal structure of 2,3-butanedione isonicotinylhydrazone: Determination of Zr4+ after flotation separation

    NASA Astrophysics Data System (ADS)

    Al-Fulaij, O. A.; Jeragh, B.; El-Sayed, A. E. M.; El-Defrawy, M. M.; El-Asmy, A. A.

    2015-02-01

    New metal complexes of Co(II), Ni(II) Cu(II), Zn(II), Cd(II), Pd(II) and Hg(II) with 2,3-butanedione isonicotinylhydrazone [BINH] have been prepared and investigated. Single crystal for BINH is grown and solved as orthorhombic with P 21 21 2 space group. The formula of the ligand was assigned based on the elemental analysis, mass spectra and conductivity measurements. The complexes assigned the formulae [M(BINH-H)Cl]ṡnH2O (Mdbnd Co(II), Ni(II), Cu(II), Zn(II); n = 0 or 1); [Hg(BINH-H)(H2O)2Cl]; [Cd(BINH)Cl2]ṡ2H2O and [Pd(BINH)Cl2]ṡH2O. All complexes are nonelectrolytes. BINH acts as a tridentate ligand in [M(BINH-H)Cl]ṡnH2O and [Hg(BINH-H)(H2O)2Cl] coordinating through Cdbnd Oketonic, Csbnd Oamedic and Cdbnd Nhy and as a neutral bidentate through Cdbnd Oketonic and Cdbnd Nhy in [Cd(BINH)Cl2]ṡ2H2O and [Pd(BINH)Cl2]ṡH2O; the pyridine nitrogen has no rule in coordination. The data are supported by NMR (1H and 13C) spectra. The magnetic moments and electronic spectra provide a tetrahedral structure for the Co(II), Ni(II), Cu(II), Zn(II) and Cd(II) complexes; square-planar for the Pd(II) complex and octahedral for the Hg(II) complex. The TGA of the complexes depicted the outer and inner water molecules as well as the final residue. The cobalt and cadmium complexes ended with the metal while the Cu(II), Zn(II) and Pd(II) complexes ended with complex species. [Hg(BINH-H)(H2O)2Cl] has no residue. The ligand is inactive against all tested organisms except for Bacillus thuringiensis. The Hg(II) complex is found more active than the other complexes. The flotation technique is found applicable for the separation of micro amount (10 ppm) of Zr4+ using 10 ppm of BINH and 1 × 10-5 mol L-1 of oleic acid at pH 6 with efficiency of 98% with no interferences.

  1. Growth and spectroscopic investigation of a new crystal for NLO applications: C10H20KN5O9

    NASA Astrophysics Data System (ADS)

    Hanumantharao, Redrothu; Kalainathan, S.

    2012-12-01

    Nonlinear optical crystals of Bis (L-glutamine) potassium nitrate (BGPN) were grown by slow evaporation technique at ambient temperature. Solubility and metastable zone width of BGPN in aqueous solution were determined. The grown crystal was characterized by single crystal XRD, Powder XRD, FT-IR 1H NMR, EDAX, mass and optical spectroscopic techniques. Single crystal XRD revealed that compound crystallizes in orthorhombic system with non-centrosymmetric space group P212121. The sharp peaks from powder XRD spectrum show the high crystallinity of the grown crystal. FT-IR confirms the presence of functional groups and molecular structure was confirmed by 1H NMR spectrum of the grown crystal. Molecular mass of BGPN sample has been verified by high resolution mass spectroscopic analysis. The presence of potassium in the compound and composition of grown crystals was confirmed on the basis of energy dispersive analysis of X-ray (EDAX). Thermal stability of the grown crystal was studied by TGA-DTA analysis. An optical UV-Vis-NIR spectrum for BGPN sample was recorded in the range of 190-1100 nm. Fluorescence studies shows material BGPN emits blue fluorescence. Second harmonic generation (SHG) studies have been performed by famous Kurtz powder technique with reference to standard potassium dihydrogen phosphate single crystals (KDP). It is found from this technique that SHG efficiency of BGPN is in comparison to that of standard KDP crystals.

  2. Growth and spectroscopic investigation of a new crystal for NLO applications: C₁₀H₂ ₀KN₅O₉.

    PubMed

    Hanumantharao, Redrothu; Kalainathan, S

    2012-12-01

    Nonlinear optical crystals of Bis (l-glutamine) potassium nitrate (BGPN) were grown by slow evaporation technique at ambient temperature. Solubility and metastable zone width of BGPN in aqueous solution were determined. The grown crystal was characterized by single crystal XRD, Powder XRD, FT-IR (1)H NMR, EDAX, mass and optical spectroscopic techniques. Single crystal XRD revealed that compound crystallizes in orthorhombic system with non-centrosymmetric space group P2(1)2(1)2(1). The sharp peaks from powder XRD spectrum show the high crystallinity of the grown crystal. FT-IR confirms the presence of functional groups and molecular structure was confirmed by (1)H NMR spectrum of the grown crystal. Molecular mass of BGPN sample has been verified by high resolution mass spectroscopic analysis. The presence of potassium in the compound and composition of grown crystals was confirmed on the basis of energy dispersive analysis of X-ray (EDAX). Thermal stability of the grown crystal was studied by TGA-DTA analysis. An optical UV-Vis-NIR spectrum for BGPN sample was recorded in the range of 190-1100 nm. Fluorescence studies shows material BGPN emits blue fluorescence. Second harmonic generation (SHG) studies have been performed by famous Kurtz powder technique with reference to standard potassium dihydrogen phosphate single crystals (KDP). It is found from this technique that SHG efficiency of BGPN is in comparison to that of standard KDP crystals. PMID:23063862

  3. Growth and spectroscopic investigation of a new crystal for NLO applications: C₁₀H₂ ₀KN₅O₉.

    PubMed

    Hanumantharao, Redrothu; Kalainathan, S

    2012-12-01

    Nonlinear optical crystals of Bis (l-glutamine) potassium nitrate (BGPN) were grown by slow evaporation technique at ambient temperature. Solubility and metastable zone width of BGPN in aqueous solution were determined. The grown crystal was characterized by single crystal XRD, Powder XRD, FT-IR (1)H NMR, EDAX, mass and optical spectroscopic techniques. Single crystal XRD revealed that compound crystallizes in orthorhombic system with non-centrosymmetric space group P2(1)2(1)2(1). The sharp peaks from powder XRD spectrum show the high crystallinity of the grown crystal. FT-IR confirms the presence of functional groups and molecular structure was confirmed by (1)H NMR spectrum of the grown crystal. Molecular mass of BGPN sample has been verified by high resolution mass spectroscopic analysis. The presence of potassium in the compound and composition of grown crystals was confirmed on the basis of energy dispersive analysis of X-ray (EDAX). Thermal stability of the grown crystal was studied by TGA-DTA analysis. An optical UV-Vis-NIR spectrum for BGPN sample was recorded in the range of 190-1100 nm. Fluorescence studies shows material BGPN emits blue fluorescence. Second harmonic generation (SHG) studies have been performed by famous Kurtz powder technique with reference to standard potassium dihydrogen phosphate single crystals (KDP). It is found from this technique that SHG efficiency of BGPN is in comparison to that of standard KDP crystals.

  4. Synthesis, spectroscopic properties, crystal structure and density functional studies of Cu(II) complex with 2-((dehydroabietylamine)methyl)-6-methoxyphenol

    NASA Astrophysics Data System (ADS)

    Liu, Bao-Yu; Liu, Zheng; Han, Guo-Cheng; Li, Yan-Hong

    2010-06-01

    The metal complex of CuL 2 (L = 2-((dehydroabietylamine)methyl)-6-methoxyphenol) has been synthesized and characterized by spectral method (IR), elemental analysis, thermal analysis (TG, DTG) and single crystal X-ray diffraction techniques. Molecular geometry from X-ray experiment of the title compound in the ground-state has been compared using the density functional method (B3LYP) with LANL2DZ basis set. UV-vis spectra has been measured and DFT calculations at B3LYP/LANL2DZ level of theory proved that the electronic spectra of CuL 2 was attributed to intra-complex electronic transitions as well as d- d electronic transitions. Besides, Mulliken charge analysis, natural bond orbitals (NBO), frontier molecular orbitals (FMO) were performed at B3LYP/LANL2DZ level of theory.

  5. Structural and spectroscopic studies of fluoroprotactinates.

    PubMed

    De Sio, Stéphanie M; Wilson, Richard E

    2014-02-01

    Seven protactinium(V) fluoride compounds have been synthesized, and their crystal structures and Raman spectra are reported. (NH4)2PaF7, K2PaF7, Rb2PaF7, and Cs2PaF7 were found to crystallize in the monoclinic space group P21/c for the ammonium compound and C2/c for the K(+)-, Rb(+)-, and Cs(+)-containing compounds, with nine-coordinate Pa forming infinite chains through fluorine bridges. Na3PaF8 crystallizes in the tetragonal space group I4/mmm with eight-coordinate Pa in tetragonal geometry, while tetramethylammonium fluoroprotactinate shows two different structures: (Me4N)2(H3O)PaF8, an eight-coordinate molecular compound crystallizing in the monoclinic space group C2/c, and (Me4N)PaF6, an eight-coordinate Pa compound forming infinite chains and crystallizing in the orthorhombic space group Pnnm. A comparison of solid- and solution-state Raman data indicates that the PaF8(-) anion could be the predominant Pa(V) complex in concentrated solutions of aqueous HF.

  6. Structural and spectroscopic studies of fluoroprotactinates.

    PubMed

    De Sio, Stéphanie M; Wilson, Richard E

    2014-02-01

    Seven protactinium(V) fluoride compounds have been synthesized, and their crystal structures and Raman spectra are reported. (NH4)2PaF7, K2PaF7, Rb2PaF7, and Cs2PaF7 were found to crystallize in the monoclinic space group P21/c for the ammonium compound and C2/c for the K(+)-, Rb(+)-, and Cs(+)-containing compounds, with nine-coordinate Pa forming infinite chains through fluorine bridges. Na3PaF8 crystallizes in the tetragonal space group I4/mmm with eight-coordinate Pa in tetragonal geometry, while tetramethylammonium fluoroprotactinate shows two different structures: (Me4N)2(H3O)PaF8, an eight-coordinate molecular compound crystallizing in the monoclinic space group C2/c, and (Me4N)PaF6, an eight-coordinate Pa compound forming infinite chains and crystallizing in the orthorhombic space group Pnnm. A comparison of solid- and solution-state Raman data indicates that the PaF8(-) anion could be the predominant Pa(V) complex in concentrated solutions of aqueous HF. PMID:24437929

  7. Synthesis, crystal structures, spectroscopic analysis and DFT calculations of 2-ethoxy-1-naphtaldehyde and (E)-N-((2-ethoxynaphthalen-1-yl)methylene)-3-methylaniline

    NASA Astrophysics Data System (ADS)

    Yıldırım, M. Hakkı; Yıldırım, Arzu Özek; Macit, Mustafa; Ağar, Ayşen Alaman; Paşaoğlu, Hümeyra; Soylu, M. Serkan

    2016-08-01

    (E)-N-((2-ethoxynaphthalen-1-yl)methylene)-3-methylaniline has been synthesized and characterized by using single-crystal X-ray diffraction, FT-IR, UV-Visible spectroscopy and computational methods. By using the same techniques, also for the first time, the 2-ethoxy-1-naphtaldehyde has been characterized. The molecular geometries, intra- and inter-molecular interactions of the compounds have been found by using X-ray crystallography. Characteristic infrared bands and the electronic bands have been discovered by experimental and theoretical IR and UV-Vis. spectroscopy. The geometry optimizations and the calculations of IR frequencies have been performed by using the Gaussian type orbitals at Gaussian 09W and the Slater type orbitals at ADF2009.01 software. In addition, the Fukui functions have been calculated to reveal active sites of the compounds. Furthermore, non-linear optical properties and thermodynamic correlation functions have been theoretically found for a further study of the titled compounds.

  8. Vaterite Crystals Contain Two Interspersed Crystal Structures

    NASA Astrophysics Data System (ADS)

    Kabalah-Amitai, Lee; Mayzel, Boaz; Kauffmann, Yaron; Fitch, Andrew N.; Bloch, Leonid; Gilbert, Pupa U. P. A.; Pokroy, Boaz

    2013-04-01

    Calcite, aragonite, and vaterite are the three anhydrous polymorphs of calcium carbonate, in order of decreasing thermodynamic stability. Although vaterite is not commonly found in geological settings, it is an important precursor in several carbonate-forming systems and can be found in biological settings. Because of difficulties in obtaining large, pure, single crystals, the crystal structure of vaterite has been elusive for almost a century. Using aberration-corrected high-resolution transmission electron microscopy, we found that vaterite is actually composed of at least two different crystallographic structures that coexist within a pseudo-single crystal. The major structure exhibits hexagonal symmetry; the minor structure, existing as nanodomains within the major matrix, is still unknown.

  9. Mononuclear copper (II) salicylate complexes with 1,2-dimethylimidazole and 2-methylimidazole: Synthesis, spectroscopic and crystal structure characterization and their superoxide scavenging activities

    NASA Astrophysics Data System (ADS)

    Abuhijleh, A. Latif

    2010-09-01

    The complexes cis-bis (1,2-dimethylimidazole) bis (salicylato) copper (II) ( 1) and tris (2-methylimidazole) (salicylato) copper (II) ( 2) have been prepared by the reaction of appropriate methylimidazole derivative with binuclear copper (II) aspirinate. Spectral and X-ray structural studies for complex 1 showed that the copper ion is coordinated in a cis arrangement to two imidazole nitrogen atoms and two carboxylate oxygen atoms from the salicylate mono-anion ligands. The second carboxylate oxygen atoms form weak axial interactions with the copper ion. Spectral, magnetic and analytical data for complex 2 showed that the copper ion is bonded to three 2-methylimidazole nitrogen atoms and one doubly deprotonated salicylate di-anion, which is chelated to Cu (II) ion through one of its carboxylate oxygen atoms and the deprotonated hydroxyl oxygen atom to form distorted square-pyramidal geometry having CuN 3O + O chromophore. The superoxide dismutase (SOD) mimetic activities (IC 50) of the complexes 1, 2 and the structurally known mixture complexes Cu (imidazole) n(salicylato) 2( 3) (where n = 2, 5 and 6) were determined using the xanthine-xanthine oxidase assay and compared with those reported for other copper (II) complexes with anti-inflammatory drugs. The results obtained indicated that complexes 1- 3 have high SOD-like activities, which may act as good mimics for native Cu, Zn-SOD enzyme.

  10. pH- and mol-ratio dependent formation of zinc(II) coordination polymers with iminodiacetic acid: Synthesis, spectroscopic, crystal structure and thermal studies

    SciTech Connect

    Ni Lubin; Zhang Ronghua; Liu Qiongxin; Xia Wensheng; Wang Hongxin; Zhou Zhaohui

    2009-10-15

    Three novel zinc coordination polymers (NH{sub 4}){sub n}[Zn(Hida)Cl{sub 2}]{sub n} (1), [Zn(ida)(H{sub 2}O){sub 2}]{sub n} (2), [Zn(Hida){sub 2}]{sub n}.4nH{sub 2}O (3) (H{sub 2}ida=iminodiacetic acid) and a monomeric complex [Zn(ida)(phen)(H{sub 2}O)].2H{sub 2}O (4) (phen=1,10-phenanthroline) have been synthesized and characterized by X-ray diffraction methods. 1 and 2 form one-dimensional (1-D) chain structures, whereas 3 exhibits a three-dimensional (3-D) diamondoid framework with an open channel. The mononuclear complex 4 is extended into a 3-D supramolecular architecture through hydrogen bonds and pi-pi stacking. Interestingly, cyclic nonplanar tetrameric water clusters are observed that encapsulated in the 3-D lattice of 4. Based on {sup 1}H and {sup 13}C NMR observations, there is obvious coordination of complex 2 in solution, while 1 and 3 decompose into free iminodiacetate ligand. Monomer [Zn(ida)(H{sub 2}O){sub 3}] (5) is considered as a possible discrete species from 2. These coordination polymers can serve as good molecular precursors for zinc oxide. - Text3: Reaction of zinc salt with iminodiacetic acid afforded three new coordination polymers 1-3 and a monomer 4, which is dependent on pH value and molar ratio of the reactants.

  11. Spectroscopic study of mixed oxide SAT 1- x:LA x perovskite crystals

    NASA Astrophysics Data System (ADS)

    Runka, T.; Łapsa, K.; Łapiński, A.; Aleksiyko, R.; Berkowski, M.; Drozdowski, M.

    2004-10-01

    Mixed perovskite crystals have been grown from multicomponent melts using the Czochralski method. The Raman, FT-IR and Brillouin investigations of perovskite (1- x)Sr(Al 0.5Ta 0.5)O 3: xLaAlO 3 crystals are reported. The measurements have been performed for several LA concentrations in the range 0.22≤ x≤0.36 at room temperature. The assignment of vibrational modes of IR and Raman spectra was proposed. The experimental results were correlated with structural data, obtained from X-ray diffraction study. The dependence of hypersonic velocity of transverse and longitudinal modes as a function of LA content was also determined. Spectroscopic investigations confirmed the disordered Al/Ta distribution, which increases with the increase of LA content.

  12. Inorganic Crystal Structure Database (ICSD)

    National Institute of Standards and Technology Data Gateway

    SRD 84 FIZ/NIST Inorganic Crystal Structure Database (ICSD) (PC database for purchase)   The Inorganic Crystal Structure Database (ICSD) is produced cooperatively by the Fachinformationszentrum Karlsruhe(FIZ) and the National Institute of Standards and Technology (NIST). The ICSD is a comprehensive collection of crystal structure data of inorganic compounds containing more than 140,000 entries and covering the literature from 1915 to the present.

  13. Crystal structure of propaquizafop

    PubMed Central

    Jeon, Youngeun; Kim, Jineun; Lee, Sangjin; Kim, Tae Ho

    2014-01-01

    The title compound, C22H22ClN3O5 {systematic name: 2-(propan-2-yl­idene­amino­oxy)ethyl (R)-2-[4-(6-chloro­quin­oxalin-2-yl­oxy)phen­oxy]propionate}, is a herbicide. The asymmetric unit comprises two independent mol­ecules in which the dihedral angles between the phenyl ring and the quinoxaline ring plane are 75.93 (7) and 82.77 (8)°. The crystal structure features C—H⋯O, C—H⋯N, and C—H⋯Cl hydrogen bonds, as well as weak π–π inter­actions [ring-centroid separation = 3.782 (2) and 3.5952 (19) Å], resulting in a three-dimensional architecture. PMID:25553037

  14. Crystal structure of methane oxidation enzyme determined

    SciTech Connect

    Baum, R.

    1994-01-10

    A team of chemists has determined to 2.2-[angstrom] resolution the crystal structure of the hydroxylase protein of methane monooxygenase, the enzyme system responsible for the biological oxidation of methane. The hydroxylase, at a molecular weight of 251,000 daltons, if by far the largest component of methane monooxygenase. Although the crystal structure of the hydroxylase did not reveal any startling surprises about the enzyme-many features of the hydroxylase had been inferred previously from modeling and spectroscopic studies -- obtaining it is a significant achievement. For one thing, the crystal structure unambiguously confirms aspects of the enzyme structure that been at least somewhat speculative. The three-dimensional structure of the enzyme, the chemist say, also provides important insight into biological methane oxidation, including how methane, a relatively inert gas, might diffuse to and bind near the active site of the enzyme. The structure points to particular amino acid residues that are likely to participate in catalysis, and clarifies the structure of the dinuclear iron core of the enzyme.

  15. Demonstration of Crystal Structure.

    ERIC Educational Resources Information Center

    Neville, Joseph P.

    1985-01-01

    Describes an experiment where equal parts of copper and aluminum are heated then cooled to show extremely large crystals. Suggestions are given for changing the orientation of crystals by varying cooling rates. Students are more receptive to concepts of microstructure after seeing this experiment. (DH)

  16. Crystal structure determination of Efavirenz

    NASA Astrophysics Data System (ADS)

    Popeneciu, Horea; Tripon, Carmen; Borodi, Gheorghe; Pop, Mihaela Maria; Dumitru, Ristoiu

    2015-12-01

    Needle-shaped single crystals of the title compound, C14H9ClF3NO2, were obtained from a co-crystallization experiment of Efavirenz with maleic acid in a (1:1) ratio, using methanol as solvent. Crystal structure determination at room temperature revealed a significant anisotropy of the lattice expansion compared to the previously reported low-temperature structure. In both low- and room temperature structures the cyclopropylethynyl fragment in one of the asymmetric unit molecules is disordered. While at low-temperature only one C atom exhibits positional disorder, at room temperature the disorder is present for two C atoms of the cyclopropane ring.

  17. Generation of crystal structures using known crystal structures as analogues

    PubMed Central

    Cole, Jason C.; Groom, Colin R.; Read, Murray G.; Giangreco, Ilenia; McCabe, Patrick; Reilly, Anthony M.; Shields, Gregory P.

    2016-01-01

    This analysis attempts to answer the question of whether similar molecules crystallize in a similar manner. An analysis of structures in the Cambridge Structural Database shows that the answer is yes – sometimes they do, particularly for single-component structures. However, one does need to define what we mean by similar in both cases. Building on this observation we then demonstrate how this correlation between shape similarity and packing similarity can be used to generate potential lattices for molecules with no known crystal structure. Simple intermolecular interaction potentials can be used to minimize these potential lattices. Finally we discuss the many limitations of this approach. PMID:27484374

  18. Spectroscopic ellipsometry study of Cu{sub 2}ZnSnSe{sub 4} bulk crystals

    SciTech Connect

    León, M. Lopez, N.; Merino, J. M.; Caballero, R.; Levcenko, S.; Gurieva, G.; Serna, R.; Bodnar, I. V.; Nateprov, A.; Guc, M.; Arushanov, E.; Schorr, S.; Perez-Rodriguez, A.

    2014-08-11

    Using spectroscopic ellipsometry we investigated and analyzed the pseudo-optical constants of Cu{sub 2}ZnSnSe{sub 4} bulk crystals, grown by the Bridgman method, over 0.8–4.5 eV photon energy range. The structures found in the spectra of the complex pseudodielectric functions were associated to E{sub 0}, E{sub 1A}, and E{sub 1B} interband transitions and were analyzed in frame of the Adachi's model. The interband transition parameters such as strength, threshold energy, and broadening were evaluated by using the simulated annealing algorithm. In addition, the pseudo-complex refractive index, extinction coefficient, absorption coefficient, and normal-incidence reflectivity were derived over 0.8–4.5 eV photon energy range.

  19. Catechol oxidase activity of a series of new dinuclear copper(II) complexes with 3,5-DTBC and TCC as substrates: syntheses, X-ray crystal structures, spectroscopic characterization of the adducts and kinetic studies.

    PubMed

    Banu, Kazi Sabnam; Chattopadhyay, Tanmay; Banerjee, Arpita; Bhattacharya, Santanu; Suresh, Eringathodi; Nethaji, Munirathinam; Zangrando, Ennio; Das, Debasis

    2008-08-18

    A series of dinuclear copper(II) complexes has been synthesized with the aim to investigate their applicability as potential structure and function models for the active site of catechol oxidase enzyme. They have been characterized by routine physicochemical techniques as well as by X-ray single-crystal structure analysis: [Cu 2(H 2L2 (2))(OH)(H 2O)(NO 3)](NO 3) 3.2H 2O ( 1), [Cu(HL1 (4))(H 2O)(NO 3)] 2(NO 3) 2.2H 2O ( 2), [Cu(L1 (1))(H 2O)(NO 3)] 2 ( 3), [Cu 2(L2 (3))(OH)(H 2O) 2](NO 3) 2, ( 4) and [Cu 2(L2 (1))(N 3) 3] ( 5) [L1 = 2-formyl-4-methyl-6R-iminomethyl-phenolato and L2 = 2,6-bis(R-iminomethyl)-4-methyl-phenolato; for L1 (1) and L2 (1), R = N-propylmorpholine; for L2 (2), R = N-ethylpiperazine; for L2 (3), R = N-ethylpyrrolidine, and for L1 (4), R = N-ethylmorpholine]. Dinuclear 1 and 4 possess two "end-off" compartmental ligands with exogenous mu-hydroxido and endogenous mu-phenoxido groups leading to intermetallic distances of 2.9794(15) and 2.9435(9) A, respectively; 2 and 3 are formed by two tridentate compartmental ligands where the copper centers are connected by endogenous phenoxido bridges with Cu-Cu separations of 3.0213(13) and 3.0152(15) A, respectively; 5 is built by an end-off compartmental ligand having exogenous mu-azido and endogenous mu-phenoxido groups with a Cu-Cu distance of 3.133(2) A (mean of two independent molecules). The catecholase activity of all of the complexes has been investigated in acetonitrile and methanol medium by UV-vis spectrophotometric study using 3,5-di- tert-butylcatechol (3,5-DTBC) and tetrachlorocatechol (TCC) as substrates. In acetonitrile medium, the conversion of 3,5-DTBC to 3,5-di- tert-butylbenzoquinone (3,5-DTBQ) catalyzed by 1- 5 is observed to proceed via the formation of two enzyme-substrate adducts, ES1 and ES2, detected spectroscopically for the first time. In methanol medium no such enzyme-substrate adduct has been detected, and the 3,5-DTBC to 3,5-DTBQ conversion is observed to be catalyzed by 1- 5

  20. Structural and spectroscopic studies of a model for catechol oxidase.

    PubMed

    Smith, Sarah J; Noble, Christopher J; Palmer, Randahl C; Hanson, Graeme R; Schenk, Gerhard; Gahan, Lawrence R; Riley, Mark J

    2008-05-01

    A binuclear copper complex, [Cu2(BPMP) (OAc)2][ClO4] x H2O, has been prepared using the binucleating ligand 2,6-bis[bis(pyridin-2-ylmethylamino)methyl]-4-methylphenol (H-BPMP). The X-ray crystal structure reveals the copper centers to have a five-coordinate square pyramidal geometry, with the acetate ligands bound terminally. The bridging phenolate occupies the apical position of the square-based pyramids and magnetic susceptibility, electron paramagnetic resonance (EPR) and variable-temperature variable-field magnetic circular dichroism (MCD) measurements indicate that the two centers are very weakly antiferromagnetically coupled (J = -0.6 cm(-1)). Simulation of the dipole-dipole-coupled EPR spectrum showed that in solution the Cu-O-Cu angle was increased from 126 degrees to 160 degrees and that the internuclear distance was larger than that observed crystallographically. The high-resolution spectroscopic information obtained has been correlated with a detailed ligand-field analysis to gain insight into the electronic structure of the complex. Symmetry arguments have been used to demonstrate that the sign of the MCD is characteristic of the tetragonally elongated environment. The complex also displays catecholase activity (k(cat) = 15 +/- 1.5 min(-1), K(M) = 6.4 +/- 1.8 mM), which is compared with other dicopper catechol oxidase models. PMID:18188615

  1. Study of spectroscopic and thermal characteristics of nonlinear optical molecular crystals based on 4-nitrophenol

    NASA Astrophysics Data System (ADS)

    Pavlovetc, I. M.; Fokina, M. I.

    2016-08-01

    The paper presents the results of study of spectroscopic and thermal characteristics of molecular co-crystals: 2-aminopyridine-4-nitrophenol-4-mtrophenolate (2AP4N) and 2,6- diaminopyridine-4-nitrophenol-4nitrophenolate (26DAP4N). Crystals were successfully grown by slow evaporation technique. Optical transparency in the region of 190-1100 was found to be suitable for applications with cut off wavelengths 420 and 430 nm respectively. Thermogravimetric and differential thermal analysis show good quality and thermal stability for studied crystals. Kurtz and Perry powder technique proves that the crystals are acentric and have significant nonlinear optical response.

  2. Synthesis, single crystal structure, spectroscopic characterization and molecular properties of (2E)-3-(2,6-dichlorophenyl)-1-(3,4-dimethoxyphenyl)prop-2-en-1-one

    NASA Astrophysics Data System (ADS)

    Chidan Kumar, C. S.; Quah, Ching Kheng; Balachandran, V.; Fun, Hoong-Kun; Asiri, A. M.; Chandraju, Siddegowda; Karabacak, Mehmet

    2016-07-01

    A novel (2E)-3-(2,6-dichlorophenyl)-1-(3,4-dimethoxyphenyl)prop-2-en-1-one (DCPDMP) compound has been synthesized and its single crystal has been grown by slow evaporation technique. The structure of the compound has been characterized by FT-IR, FT-Raman and single-crystal X-ray diffraction techniques. The optimized molecular structure, vibrational wavenumbers, corresponding vibrational assignments of the compound have been investigated by means of the density functional theory. The molecule crystallizes in triclinic system, space group P-1 with a = 7.6179 (7), b = 8.5023 (7), c = 12.1967 (10) Å, V = 764.39 (11) Å3 and two molecules in the unit cell. The crystal structure is primarily stabilized through intramolecular C-H … Cl and C-H … O hydrogen bonds and intermolecular C-H … O and weak C-H … π interactions. These inter- and intramolecular interactions are analyzed. Moreover, the molecular electrostatic potential surface of the molecule has been constructed. Global and local reactivity descriptors and dipole moment (μ), static polarizability (α), first order hyperpolarizability (β) and optical gap (ΔE) have been also calculated to study the nonlinear optical (NLO) property of the title compound.

  3. Spectroscopic and thermal characterizations of Yb:LaF3 single crystal

    NASA Astrophysics Data System (ADS)

    Hong, Jiaqi; Zhang, Lianhan; Hang, Yin; Xu, Min

    2016-10-01

    A Yb3+ doped LaF3 laser crystal was detailed investigated by both spectroscopic and thermal measurements. A peak absorption at 974 nm with FWHM broader than 60 nm makes the crystal suitable to InGaAs LDs. Fluorescence spectrum and calculated spectroscopic parameters show potential of Yb:LaF3 crystal to laser operations around 1009 nm. A relatively long fluorescence lifetime of 2.92 ms was detected for Yb3+:2F5/2 manifold. The thermal diffusivity and specific heat capacity in the range of 300-575 K were studied to calculate the thermal conductivity of Yb:LaF3. The results indicate that the Yb:LaF3 crystal is a good candidate for diode-pumped ∼1 μm solid-state laser applications.

  4. Crystal structure of cyproconazole

    PubMed Central

    Kang, Gihaeng; Kim, Jineun; Kwon, Eunjin; Kim, Tae Ho

    2015-01-01

    The title compound [systematic name: 2-(4-chloro­phen­yl)-3-cyclo­propyl-1-(1H-1,2,4-triazol-1-yl)butan-2-ol], C15H18ClN3O, is a conazole fungicide. The asymmetric unit comprises two enanti­omeric pairs (mol­ecules A and B) in which the dihedral angles between the chloro­phenyl and triazole rings are 46.54 (9) (mol­ecule A) and 67.03 (8)° (mol­ecule B). In the crystal, C—H⋯O, O—H⋯N and C—H⋯Cl hydrogen bonds and weak C—H⋯π inter­actions [3.473 (2) Å] link adjacent mol­ecules, forming columns along the a axis. PMID:26870467

  5. Crystal structure of flumioxazin

    PubMed Central

    Park, Hyunjin; Kim, Jineun; Kwon, Eunjin; Kim, Tae Ho

    2015-01-01

    The title compound {systematic name: 2-[7-fluoro-3,4-di­hydro-3-oxo-4-(prop-2-yn-1-yl)-2H-1,4-benzoxazin-6-yl]-4,5,6,7-tetra­hydro-1H-iso­indole-1,3(2H)-dione}, C19H15FN2O4, is a dicarboximide herbicide. The dihedral angle between the male­imide and benzene ring planes is 66.13 (5)°. In the crystal, C—H⋯O and C—H⋯F hydrogen bonds and weak C—H⋯π inter­actions [3.5601 (19) Å] link adjacent mol­ecules, forming two-dimensional networks extending parallel to the (110) plane. PMID:26594468

  6. Crystal structure determination of Efavirenz

    SciTech Connect

    Popeneciu, Horea Dumitru, Ristoiu; Tripon, Carmen Borodi, Gheorghe Pop, Mihaela Maria

    2015-12-23

    Needle-shaped single crystals of the title compound, C{sub 14}H{sub 9}ClF{sub 3}NO{sub 2}, were obtained from a co-crystallization experiment of Efavirenz with maleic acid in a (1:1) ratio, using methanol as solvent. Crystal structure determination at room temperature revealed a significant anisotropy of the lattice expansion compared to the previously reported low-temperature structure. In both low- and room temperature structures the cyclopropylethynyl fragment in one of the asymmetric unit molecules is disordered. While at low-temperature only one C atom exhibits positional disorder, at room temperature the disorder is present for two C atoms of the cyclopropane ring.

  7. Kramers-Kronig-consistent optical functions of anisotropic crystals: generalized spectroscopic ellipsometry on pentacene.

    PubMed

    Dressel, M; Gompf, B; Faltermeier, D; Tripathi, A K; Pflaum, J; Schubert, M

    2008-11-24

    The Kramers-Kronig relations between the real and imaginary parts of a response function are widely used in solid-state physics to evaluate the corresponding quantity if only one component is measured. They are among the most fundamental statements since only based on the analytical behavior and causal nature of the material response [Phys. Rev. 104, 1760-1770 (1956)]. Optical losses, for instance, can be obtained from the dispersion of the dielectric constant at all wavelengths, and vice versa [Handbook of optical constants of solids, Vol. 1, p. 35]. Although the general validity was never casted into doubt, it is a longstanding problem that Kramers-Kronig relations cannot simply be applied to anisotropic crystalline materials because contributions from different directions mix in a frequency-dependent way. Here we present a general method to identify frequency-independent principal polarizability directions for which the Kramers-Kronig relations are obeyed even in materials with lowest symmetry. Using generalized spectroscopic ellipsometry on a single crystal surface of triclinic pentacene, as an example, enables us to evaluate the complex dielectric constant and to compare it with band-structure calculations along the crystallographic directions. A general recipe is provided how to proceed from a macroscopic measurement on a low symmetry crystal plane to the microscopic dielectric properties of the unit cell, along whose axes the Kramers-Kronig relations hold.

  8. Crystal structure refinement with SHELXL

    SciTech Connect

    Sheldrick, George M.

    2015-01-01

    New features added to the refinement program SHELXL since 2008 are described and explained. The improvements in the crystal structure refinement program SHELXL have been closely coupled with the development and increasing importance of the CIF (Crystallographic Information Framework) format for validating and archiving crystal structures. An important simplification is that now only one file in CIF format (for convenience, referred to simply as ‘a CIF’) containing embedded reflection data and SHELXL instructions is needed for a complete structure archive; the program SHREDCIF can be used to extract the .hkl and .ins files required for further refinement with SHELXL. Recent developments in SHELXL facilitate refinement against neutron diffraction data, the treatment of H atoms, the determination of absolute structure, the input of partial structure factors and the refinement of twinned and disordered structures. SHELXL is available free to academics for the Windows, Linux and Mac OS X operating systems, and is particularly suitable for multiple-core processors.

  9. Spectroscopic studies of Yb3+-doped rare earth orthosilicate crystals

    NASA Astrophysics Data System (ADS)

    Campos, S.; Denoyer, A.; Jandl, S.; Viana, B.; Vivien, D.; Loiseau, P.; Ferrand, B.

    2004-06-01

    Infrared transmission and Raman scattering have been used to study Raman active phonons and crystal-field excitations in Yb3+-doped yttrium, lutetium and scandium orthosilicate crystals (Y2SiO5 (YSO), Lu2SiO5 (LSO) and Sc2SiO5 (SSO)), which belong to the same C2h6 crystallographic space group. Energy levels of the Yb3+ ion 2F5/2 manifold are presented. In the three hosts, Yb3+ ions experience high crystal field strength, particularly in Yb:SSO. Satellites in the infrared transmission spectra have been detected for the first time in the Yb3+-doped rare earth orthosilicates. They could be attributed to perturbed Yb3+ sites of the lattices or to magnetically coupled Yb3+ pairs.

  10. Crystal structure, spectroscopic investigations and quantum chemical calculation studies of (3aR,6S,7aR)-7a-bromo-6-methyl-2-[(4-methylphenyl)sulfonyl]-1,2,3,6,7,7a-hexahydro-3a,6-epoxyisoindole: A combined experimental and theoretical studies

    NASA Astrophysics Data System (ADS)

    Alaşalvar, Can; Demircan, Aydın; Koşar, Başak; Pekacar, Ali İhsan; Büyükgüngör, Orhan

    2016-11-01

    The crystal structure and spectroscopic properties of (3aR,6S,7aR)-7a-bromo-6-methyl-2-[(4-methylphenyl)sulfonyl]-1,2,3,6,7,7a-hexahydro-3a,6-epoxyisoindole were determined by X-ray diffraction, IR and 13CNMR and 1H NMR spectroscopy techniques. We investigate molecular and crystal structure of the new sulfonamide, which was derived from an environmental friendly cyclization reaction in water. This work allow to the development of a stereo-selective tandem allylamine isomerization/Diels Alder cyclo-addition sequence led to rapid assembly of complex nitrogen containing heterocycles. The molecular geometry from X-ray determination, vibrational frequencies and NMR shifts values of the title compound in the ground state have been calculated by using CAM-B3LYP and B3LYP methods with 6-311++G(d,p) basis sets. The calculated results show that the optimized geometry can well regenerate the crystal structure and theoretical vibrational frequencies and chemical shift data are in good agreement with experimental data. Besides, it is examined nonlinear optic properties, molecular electrostatic potential map and HOMO-LUMO orbitals of the molecule.

  11. Crystal chemistry and real structure of crystals

    NASA Astrophysics Data System (ADS)

    Bartl, H.; Bats, J. W.; Dyck, W.; Fuess, H.; Gregory, A.; Joswig, W.; Lottermoser, W.; Koerfer, M.; Mueller, R.; Schweiss, B. P.

    1984-03-01

    Elastic and inelastic scattering, X-ray diffraction and spectroscopy were combined to obtain a comprehensive picture of the properties of crystals. The electron density distribution allows one to verify the models of the theoretical chemistry. Systematic investigations of chemically similar anions (ClO3 and ClO4; S2O3, SO3 and SO4) show differences in bonding and reaction capability. The X-ray-neutron method applied to these anions shows maxima between 0.2 and 0.4 eXA to the power-3 in the bondings of the unbound electrons on S and D. For the SO3-group good agreement is found with theoretical calculations. The effect of the Mg (two times ionized) cation on the density is demonstrated on the water molecules of MgS2O3.6H2O and MgSO3.6H2O. Magnetic structure and magnetization density were investigated on CO3V2O8, Fe2SiO4 and Mn2SiO4 with polarized neutrons. The differences in magnetic moments of both cation states is also demonstrated for Fe2SiO4 with complementary Mossbauer measurements. Inelastic time of flight experiments allow predictions concerning the motion of the NH3-group in aniliniumbromide and of the water molecule in natural zeolites. The theoretical model to calculate the photon dispersion on CaSO4 shows good agreement with the measured dispersion curves.

  12. Crystal Structure of Bi

    SciTech Connect

    Borg, Stefan; Svensson, Goeran

    2001-02-15

    The room temperature structures of the two-layer Aurivillius phases Bi{sub 2.5}Me{sub 0.5}Nb{sub 2}O{sub 9} (Me=Na, K) have been refined with the Rietveld method from powder neutron diffraction data ({lambda}=1.470 {angstrom}). They consist of (Bi{sub 2}O{sub 2}){sup 2+} layers interleaved with perovskite (Bi{sub 0.5}Me{sub 0.5}Nb{sub 2}O{sub 7}){sup 2-} (Me=Na, K) slabs. The structures were refined in the orthorhombic space group A2{sub 1}am, Z=4, and the unit cell parameters of the two oxides are a= 5.4937(3), b=5.4571(4), c=24.9169(14) {angstrom} and a=5.5005(8), b=5.4958(8), c=25.2524(16) {angstrom}, respectively. The orthorhombic distortion increases with decreasing Me+ cation size in the perovskite layer (Bi/Me){sup 2+} site and the lone pair electrons from the Bi{sup 3+} cation are influencing the site distortion. This is in agreement with other two-layer Aurivillius phases and originates from bonding requirements depending on size and electronic environment.

  13. Growth and spectroscopic properties of Er,Yb : YCOB crystals

    NASA Astrophysics Data System (ADS)

    Yu, Young Moon; Jin Ju, Jung; Cha, Myoungsik

    2001-07-01

    High quality Yb 3+ and Er 3+ co-doped YCa 4O(BO 3) 3 crystals were grown by the Czochralski method. Phase relationships between Y 3+/Yb 3+/Er 3+ and Ca 2+/B 3+ in the vicinity of the stoichiometric composition of YCa 4O(BO 3) 3 were discussed. The calculated absorption and emission cross sections were estimated. Efficient energy transfer from the excited Yb 3+ to the Er 3+ leads to strong emissions in the wavelength range of 1510-1580 nm peaking at 1535 nm. Lifetime of Er- 4I 11/2 was measured to be 1.23 ms. The energy transfer efficiency of 97% for Er 0.02Yb 0.2Y 0.78Ca 4O(BO 3) 3 crystal was estimated from the reduced lifetimes of the Yb 3+- 2F 5/2 level.

  14. Low-dimensional compounds containing cyano groups. XIV. Crystal structure, spectroscopic, thermal and magnetic properties of [CuL {sub 2}][Pt(China){sub 4}] complexes (L=ethylenediamine or N,N-dimethylethylenediamine)

    SciTech Connect

    Potocnak, Ivan . E-mail: ivan.potocnak@upjs.sk; Vavra, Martin; Cizmar, Erik; Tibenska, Katarina; Orendacova, Alzbeta; Steinborn, Dirk; Wagner, Christoph; Dusek, Michal; Fejfarova, Karla; Schmidt, Harry; Muller, Thomas; Orendac, Martin; Feher, Alexander

    2006-07-15

    Violet crystals of [Cu(en){sub 2}][Pt(China){sub 4}] and blue crystals of [Cu(dmen){sub 2}][Pt(China){sub 4}] were crystallized from the water-methanol solution containing CuCl{sub 2}.2H{sub 2}O, ethylenediamine (en) or N,N-dimethylethylenediamine (dmen) and K{sub 2}[Pt(China){sub 4}].3H{sub 2}O. Both compounds were characterized using elemental analysis, infrared and UV-VIS spectroscopy, magnetic measurements, specific heat measurements and thermal analysis. X-ray structure analysis revealed chain-like structure in both compounds. The covalent chains are built of Cu(II) ions linked by [Pt(China){sub 4}]{sup 2-} anions in the [111] and [101] direction, respectively. The Cu(II) atoms are hexacoordinated by four nitrogen atoms in the equatorial plane from two molecules of bidentate ligands L with average Cu-N distance of 2.022(2) and 2.049(4) A, respectively. Axial positions are occupied by two nitrogen atoms from bridging [Pt(China){sub 4}]{sup 2-} anions at longer Cu-N distance of 2.537(2) and 2.600(5) A, respectively. Both materials are characterized by the presence of weak antiferromagnetic exchange coupling. Despite the one-dimensional (1D) character of the structure, the analysis of magnetic properties and specific heat at very low temperatures shows that [Cu(en){sub 2}][Pt(China){sub 4}] behaves as two-dimensional (2D) spatially anisotropic square lattice Heisenberg magnet, while more pronounced influence of interlayer coupling is observed in [Cu(dmen){sub 2}][Pt(China){sub 4}]. - Graphical abstract: Chain-like structure in [Cu(en){sub 2}][Pt(China){sub 4}] (R=H) and [Cu(dmen){sub 2}][Pt(China){sub 4}] (R=CH{sub 3}) compounds.

  15. A new series of bis(ene-1,2-dithiolato)tungsten(IV), -(V), -(VI) complexes as reaction centre models of tungsten enzymes: preparation, crystal structures and spectroscopic properties.

    PubMed

    Sugimoto, Hideki; Hatakeda, Kohei; Toyota, Kazuo; Tatemoto, Susumu; Kubo, Minoru; Ogura, Takashi; Itoh, Shinobu

    2013-03-01

    The carbomethoxy substituted dithiolene ligand (L(COOMe)) enabled us to develop a series of new bis(ene-1,2-dithiolato)tungsten complexes including W(IV)O, W(IV)(OSiBuPh(2)), W(VI)O(2), W(VI)O(OSiBuPh(2)) and W(VI)O(S) core structures. By using these tungsten complexes, a systematic study of the terminal monodentate ligand effects has been performed on the structural, spectroscopic properties and reactivity. The structure and spectroscopic properties of the tungsten complexes have also been compared to those of the molybdenum complexes coordinated by the same ligand to investigate the effects of the metal ion (W vs. Mo). X-ray crystallographic analyses of the tungsten(IV) complexes have revealed that the tungsten centres adopt a distorted square pyramidal geometry with a dithiolene ligand having an ene-1,2-dithiolate form. On the other hand, the dioxotungsten(VI) complex exhibits an octahedral structure consisting of the bidentate L(COOMe) and two oxo groups, in which π-delocalization was observed between the W(VI)O(2) and ene-1,2-dithiolate units. The tungsten(IV) and dioxotungsten(VI) complexes are isostructural with the molybdenum counter parts. DFT calculation study of the W(VI)O(S) complex has indicated that the W=S bond of 2.2 Å is close to the bond length between the tungsten centre and ambiguously assigned terminal monodentate atom in aldehyde oxidoreductase of the tungsten enzyme. Resonance Raman (rR) spectrum of the W(VI)O(S) complex has shown the two inequivalent L(COOMe) ligands with respect to their bonding interactions with the tungsten centre, reproducing the appearance of two ν(C=C) stretches in the rR spectrum of aldehyde oxidoreductase. Sulfur atom transfer reaction from the W(VI)O(S) complex to triphenylphosphines has also been studied kinetically to demonstrate that the tungsten complex has a lower reactivity by about one-order of magnitude, when compared with its molybdenum counterpart.

  16. Crystal structure of guggulsterone Z

    SciTech Connect

    Gupta, V. K. Bandhoria, P.; Gupta, B. D.; Gupta, K. K.

    2006-03-15

    The crystal structure of the title compound (4,17(20)-trans-pregnadiene-3,16-dione, C{sub 21}H{sub 28}O{sub 2}) has been determined by direct methods using single-crystal X-ray diffraction data. The compound crystallizes into the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1} with the unit cell parameters a = 7.908(2) A, b = 13.611(3) A, c = 16.309(4) A, and Z = 4. The structure has been refined to R = 0.058 for 3667 observed reflections. The bond distances and angles are in good agreement with guggulsterone E and other related steroid molecules. Ring A exists in the distorted sofa conformation, while rings B and C adopt the distorted chair conformation. Five-membered ring D is intermediate between the half-chair and envelope conformations. The A/B ring junction is quasi-trans, while ring systems B/C and C/D are trans fused about the C(8)-C(9) and C(13)-C(14) bonds, respectively. The steroid nucleus has a small twist, as shown by the C(19)-C(10)...C(13)-C(18) pseudo-torsion angle of 7.2{sup o}. The crystal structure is stabilized by intra-and intermolecular C-H...O hydrogen bonds.

  17. Spectroscopic study and structure of ( E)-2-[(2-chlorobenzylimino)methyl]methoxyphenol

    NASA Astrophysics Data System (ADS)

    Ünver, Hüseyin; Yıldız, Mustafa; Özay, Hava; Durlu, Tahsin Nuri

    2009-12-01

    ( E)-2-[(2-Chlorobenzylimino)methyl]methoxyphenol has been synthesized from the reaction of 2-hydroxy-3-methoxy-1-benzaldehyde( o-vanillin) with 2-chlorobenzylamine. The title compound has been characterized by using elemental analysis, FT-IR, 1H NMR, 13C NMR and UV-vis spectroscopic techniques. The crystal structure of the title compound has also been examined cyrstallographically. It crystallizes in the orthorhombic space group Pbca with unit cell parameters: a = 7.208(1) Å, b = 13.726(2) Å, c = 27.858(4) Å, V = 2756.0(1) Å 3, Dc = 1.18 g cm -3 and Z = 8. The crystal structure was solved by direct methods and refined by full-matrix least squares to a find R = 0.046 for 2773 observed reflections.

  18. Molten salt flux synthesis and crystal structure of a new open-framework uranyl phosphate Cs{sub 3}(UO{sub 2}){sub 2}(PO{sub 4})O{sub 2}: Spectroscopic characterization and cationic mobility studies

    SciTech Connect

    Yagoubi, S.; Renard, C.; Abraham, F.; Obbade, S.

    2013-04-15

    The reaction of triuranyl diphosphate tetrahydrate precursor (UO{sub 2}){sub 3}(PO{sub 4}){sub 2}(H{sub 2}O){sub 4} with a CsI flux at 750 °C yields a yellow single crystals of new compound Cs{sub 3}(UO{sub 2}){sub 2}(PO{sub 4})O{sub 2}. The crystal structure (monoclinic, space group C2/c, a=13.6261 (13) Å, b=8.1081(8) Å, c=12.3983(12) Å, β=114.61(12)°, V=1245.41(20) Å{sup 3} with Z=4) has been solved using direct methods and Fourier difference techniques. A full-matrix least-squares refinement on the basis of F{sup 2} yielded R1=0.028 and wR2=0.071 for 79 parameters and 1352 independent reflections with I≥2σ(I) collected on a BRUKER AXS diffractometer with MoKα radiation and a charge-coupled device detector. The crystal structure is built by two independent uranium atoms in square bipyramidal coordination, connected by two opposite corners to form infinite chains {sup 1}{sub ∞}[UO{sub 5}] and by one phosphorus atom in a tetrahedral environment PO{sub 4}. The two last entities {sup 1}{sub ∞}[UO{sub 5}] and PO{sub 4} are linked by sharing corners to form a three-dimensional structure presenting different types of channels occupied by Cs{sup +} alkaline cations. Their mobility within the tunnels were studied between 280 and 800 °C and compared with other tunneled uranyl minerals. The infrared spectrum shows a good agreement with the values inferred from the single crystal structure analysis of uranyl phosphate compound. - Graphical abstract: Arrhenius plot of the electrical conductivity of tunneled compounds Cs{sub 3}U{sub 2}PO{sub 10} and CsU{sub 2}Nb{sub 2}O{sub 11.5}. Highlights: ► The reaction of (UO{sub 2}){sub 3}(PO{sub 4}){sub 2}(H{sub 2}O){sub 4} in excess of molten CsI leads to single-crystals of new tunneled compound Cs{sub 3}(UO{sub 2}){sub 2}(PO{sub 4})O{sub 2}. ► Ionic conductivity measurements and crystal structure analysis indicate a strong connection of the Cs{sup +} cations to the tunnels. ► A low symmetry in Cs{sub 3}(UO{sub 2

  19. Hydrothermal synthesis, crystal structure, thermal behavior and spectroscopic and magnetic properties of two new organically templated fluoro-vanadyl-hydrogenarsenates: (R){sub 0.5}[(VO)(HAsO{sub 4})F] (R: Ethylenediammonium and piperazinium)

    SciTech Connect

    Berrocal, Teresa

    2008-04-15

    Two new fluoro-vanadyl-hydrogenarsenate compounds templated by ethylenediamine and piperazine with formula, (C{sub 2}N{sub 2}H{sub 10}){sub 0.5}[(VO)(HAsO{sub 4})F] (1) and (C{sub 4}N{sub 2}H{sub 12}){sub 0.5}[(VO)(HAsO{sub 4})F] (2), respectively, have been synthesized by using mild hydrothermal conditions under autogenous pressure. The crystal structures have been solved from single-crystal X-ray diffraction data. The phases crystallize in the P2{sub 1}/c monoclinic space group with the unit-cell parameters a=7.8634(4) A, b=7.7658(4) A, c=10.4195(6) A, {beta}=101.524(5){sup o} for compound (1) and a=6.301(1) A, b=10.244(1) A, c=10.248(1) A and {beta}=95.225(1){sup o} for compound (2). These phases exhibit a layered inorganic framework. In both cases, the structure is built from secondary building units (SBU) which are formed by [V{sub 2}O{sub 8}F{sub 2}] edge-shared dimeric vanadyl octahedra, connected by the vertices to two hydrogenarsenate tetrahedra. The repetition of this SBU unit originates sheets along the [1 0 0] direction. The ethylenediammonium and piperazinium cations are located inside the interlayer space. The limit of thermal stability for compounds (1) and (2) is, approximately, 250 and 230 deg. C, respectively. Near this temperature, both phases loose their organic cations and the fluoride anions. The diffuse reflectance spectra confirm the presence of vanadyl ions, in which the vanadium(IV) cations have a d{sup 1} electronic configuration in a slightly distorted octahedral environment. ESR spectra of both phases are isotropic with mean g-values of 1.93 and 1.96 for ethylendiamine and piperazine phases, respectively. Magnetic measurements for (1) and (2) indicate the existence of antiferromagnetic exchange couplings. - Graphical abstract: Polyhedral view of the layered crystal structure of (C{sub 2}H{sub 10}N{sub 2}){sub 0.5} [(VO)(HAsO{sub 4})F].

  20. Second sphere coordination complexes via hydrogen bonding: Synthesis, spectroscopic characterisation of [ trans-Co(en) 2Cl 2]CdX 4 (X=Br or I) and single crystal X-ray structure determination of [ trans-Co(en) 2Cl 2]CdBr 4

    NASA Astrophysics Data System (ADS)

    Sharma, Raj Pal; Sharma, Rajni; Bala, Ritu; Salas, Juan M.; Quiros, Miguel

    2006-08-01

    In an effort to explore [ trans-Co(en) 2Cl 2] + as anion receptor for tetrabromocadmate and tetraiodocadmate ion, green coloured single crystals of [ trans-Co(en) 2Cl 2]CdBr 4I and [ trans-Co(en) 2Cl 2]CdI 4II have been obtained by slowly mixing the separately dissolved trans-dichlorobis(ethylenediamine)cobalt(III) chloride with potassium tetrabromocadmate and tetraiodocadmate in aqueous medium in 2:1 molar ratio. The newly synthesized complex salt was characterized on the basis of elemental analysis and spectroscopic techniques (IR, UV/visible, 1H and 13C NMR). Single crystal X-ray structure determination of [ trans-Co(en) 2Cl 2] 2CdBr 4 revealed that it crystallizes in the orthorhombic space group Pbca with a=18.6201(10), b=12.0872(6), c=24.0877(12) Å, V=5421.3(5) Å 3, Z=8, R=0.0727. Supramolecular hydrogen bonding networks between ionic groups: bromide ions of tetrabromocadmate group and NH groups of coordinated ethylenediamine molecules, i.e. N-H⋯Br - interactions by second sphere coordination besides electrostatic forces of attraction have been observed. This suggests that [ trans-Co(en) 2Cl 2] + is a promising anion receptor for the tetrabromocadmate.

  1. Synthesis and spectroscopic characterization of Yb3+ in Ca1-XYbXF2+X crystals

    NASA Astrophysics Data System (ADS)

    Ito, M.; Goutaudier, C.; Guyot, Y.; Lebbou, K.; Fukuda, T.; Boulon, G.

    2004-11-01

    Ca1-XYbXF2+X crystals were grown by two different methods: simple melting under CF{4} atmosphere and laser heated pedestal growth (LHPG) method under Ar atmosphere. Spectroscopic characterization has been carried out to separate different crystallographic site in Ca1-XYbXF2+X crystals and to identify Stark's levels of Yb3+ transitions. Experimental decay time dependence of Yb3+ concentration was analyzed by using concentration gradient fiber in order to understand concentration quenching mechanisms. Energy transfer to unexpected rare earth impurities observed by up-conversion emission spectra in visible region under IR Yb3+ ion pumping seems to be an efficient process.

  2. Correction: Spectroscopic characteristics of the OSIRIS near-backscattering crystal analyser spectrometer on the ISIS pulsed neutron source.

    PubMed

    Telling, Mark T F; Campbell, Stuart I; Engberg, Dennis; Martín Y Marero, David; Andersen, Ken H

    2016-03-21

    Correction for 'Spectroscopic characteristics of the OSIRIS near-backscattering crystal analyser spectrometer on the ISIS pulsed neutron source' by Mark T. F. Telling et al., Phys. Chem. Chem. Phys., 2005, 7, 1255-1261.

  3. Crystal structure, magnetic, thermal behavior, and spectroscopic studies of two new bimetallic hydrogenselenites: [Cu2-xNix (HSeO3)2Cl2.4H2O], (x = 0.62; 0.91)

    NASA Astrophysics Data System (ADS)

    Hentech, I.; Zehani, K.; Kabadou, A.; Ben Salah, A.; Loukil, M.; Bessais, L.

    2016-08-01

    Two new iso-structural bimetallic hydrogenselenites [Cu2-xNix(HSeO3)2Cl2.4H2O] (x = 0.62; 0.91) have been synthesized from solution and characterized by single-crystal and powder X-ray diffraction. They crystallized in the orthorhombic Pnma space group with the following lattice parameters: for Cu1.09Ni0.91(HSeO3)2Cl2.4H2O: a = 9.0931 (2) Å, b = 17.7717 (4) Å, c = 7.1620 (2) Å, Z = 4, and for Cu1.38Ni0.62(HSeO3)2Cl2.4H2O: a = 9.0931 (4) Å, b = 17.7467 (7) Å, c = 7.1717 (3) Å; Z = 4. The crystal structure of this compound consists by a three-dimensional framework, but it may be described as a bi-dimensional structure consisting of layers, parallel to the (010) plane formed by two types of (Cu/Ni) octahedral and (HSeO3)- trigonal pyramids. The magnetic measurement, thermal and spectroscopic studies were performed for these compounds. The magnetic results reveal the appearance of a weak ferromagnetic behavior at low temperature (Tc = 16 K for x = 0.91 and 18.8 K for x = 0.62). The DSC analysis enabled us to locate two endothermic peaks. The first peak can be attributed to a completely dehydration of the material, in this transformation, the compounds undergo a structural phase transition which can favor a non-centrosymmetric phase at high temperature confirmed by the thermodiffractograms measurement. The second peak for these samples is due to the ferro-paraelectric phase transition which can be explained by an order- disorder transition.

  4. Syntheses, crystal structures and spectroscopic characterization of two new octahedral nickel(II) complexes of a Schiff base ligand derived from pyridoxal and 2-(pyrid-2-yl)ethylamine

    NASA Astrophysics Data System (ADS)

    Mandal, Senjuti; Modak, Ritwik; Sikdar, Yeasin; Naskar, Barnali; Goswami, Sanchita

    2014-09-01

    Two new coordination compounds based on ONN donor Schiff base ligand derived from pyridoxal and 2-(pyrid-2-yl)ethylamine, namely {[Ni(HL)(H2O)2](ClO4)2}∞ (1) and [Ni(HL)(H2O)(SCN)2] (2) have been synthesized and structurally characterized by single-crystal X-ray diffraction along with other physical techniques, including elemental analysis, IR spectra and UV-Vis studies. X-ray studies suggest that both 1 and 2 are mononuclear nickel(II) complexes and exhibit distorted octahedral geometry. In these compounds the pyridoxal based Schiff base ligand displays different coordination modes constructing various architectures.

  5. The crystal structure of waxes.

    PubMed

    Dorset, D L

    1995-12-01

    Quantitative electron crystallographic studies have been carried out on epitaxially oriented multi-component waxes. Intensities from two paraffin-based samples, an artificial six-component medium wax (equimolar distribution of chain lengths) and a petroleum-based wax (Gaussian distribution of chain lengths) have been used to determine their crystal structures. As found earlier for binary paraffin solid solutions, differences in molecular volume are compensated by longitudinal molecular shifts within individual lamellae. Nevertheless, each lamellar surface must remain flat enough, and with enough crystallographic order intact, to nucleate the next lamella, thus accounting for the observed long-range correlation in these crystals. Recrystallized beeswax also has a layer packing somewhat similar to the paraffin waxes. However, in this case, the lamellar order is 'frustrated' so that a certain amount of 'nematically' ordered material must be present, spanning the nascent lamellar interfaces. PMID:8554724

  6. Synthesis and spectroscopic characterization of magnesium oxalate nano-crystals.

    PubMed

    Lakshmi Reddy, S; Ravindra Reddy, T; Siva Reddy, G; Endo, Tamio; Frost, Ray L

    2014-04-01

    Synthesis of MgC92)O(4)⋅2H(2)O nano particles was carried out by thermal double decomposition of solutions of oxalic acid dihydrate (C(2)H(2)O(4)⋅2H(2)O) and Mg(OAc)(2)⋅(40H(2)O employing CATA-2R microwave reactor. Structural elucidation was carried out by employing X-ray diffraction (XRD), particle size and shape were studied by transmission electron microscopy (TEM) and nature of bonding was investigated by optical absorption and near-infrared (NIR) spectral studies. The powder resulting from this method is pure and possesses distorted rhombic octahedral structure. The synthesized nano rod is 80 nm in diameter and 549 nm in length.

  7. Structural, spectroscopic and DFT study of 4-methoxybenzohydrazide Schiff bases. A new series of polyfunctional ligands.

    PubMed

    Ferraresi-Curotto, Verónica; Echeverría, Gustavo A; Piro, Oscar E; Pis-Diez, Reinaldo; González-Baró, Ana C

    2015-02-25

    Five Schiff bases obtained from condensation of 4-methoxybenzohydrazide with related aldehydes, namely o-vanillin, vanillin, 5-bromovanillin, 5-chlorosalicylaldehyde and 5-bromosalicylaldehyde were prepared. A detailed structural and spectroscopic study is reported. The crystal structures of four members of the family were determined and compared with one another. The hydrazones obtained from 5-chlorosalicylaldehyde and 5-bromosalicylaldehyde resulted to be isomorphic to each other. The solid-state structures are stabilized by intra-molecular O-H⋯N interactions in salicylaldehyde derivatives between the O-H moiety from the aldehyde and the hydrazone nitrogen atom. All crystals are further stabilized by inter-molecular H-bonds mediated by the crystallization water molecule. A comparative analysis between experimental and theoretical results is presented. The conformational space was searched and geometries were optimized both in gas phase and including solvent effects. The structure is predicted for the compound for which the crystal structure was not determined. Infrared and electronic spectra were measured and assigned with the help of data obtained from computational methods based on the Density Functional Theory.

  8. Structural, spectroscopic and DFT study of 4-methoxybenzohydrazide Schiff bases. A new series of polyfunctional ligands.

    PubMed

    Ferraresi-Curotto, Verónica; Echeverría, Gustavo A; Piro, Oscar E; Pis-Diez, Reinaldo; González-Baró, Ana C

    2015-02-25

    Five Schiff bases obtained from condensation of 4-methoxybenzohydrazide with related aldehydes, namely o-vanillin, vanillin, 5-bromovanillin, 5-chlorosalicylaldehyde and 5-bromosalicylaldehyde were prepared. A detailed structural and spectroscopic study is reported. The crystal structures of four members of the family were determined and compared with one another. The hydrazones obtained from 5-chlorosalicylaldehyde and 5-bromosalicylaldehyde resulted to be isomorphic to each other. The solid-state structures are stabilized by intra-molecular O-H⋯N interactions in salicylaldehyde derivatives between the O-H moiety from the aldehyde and the hydrazone nitrogen atom. All crystals are further stabilized by inter-molecular H-bonds mediated by the crystallization water molecule. A comparative analysis between experimental and theoretical results is presented. The conformational space was searched and geometries were optimized both in gas phase and including solvent effects. The structure is predicted for the compound for which the crystal structure was not determined. Infrared and electronic spectra were measured and assigned with the help of data obtained from computational methods based on the Density Functional Theory. PMID:25255482

  9. Structural, spectroscopic and DFT study of 4-methoxybenzohydrazide Schiff bases. A new series of polyfunctional ligands

    NASA Astrophysics Data System (ADS)

    Ferraresi-Curotto, Verónica; Echeverría, Gustavo A.; Piro, Oscar E.; Pis-Diez, Reinaldo; González-Baró, Ana C.

    2015-02-01

    Five Schiff bases obtained from condensation of 4-methoxybenzohydrazide with related aldehydes, namely o-vanillin, vanillin, 5-bromovanillin, 5-chlorosalicylaldehyde and 5-bromosalicylaldehyde were prepared. A detailed structural and spectroscopic study is reported. The crystal structures of four members of the family were determined and compared with one another. The hydrazones obtained from 5-chlorosalicylaldehyde and 5-bromosalicylaldehyde resulted to be isomorphic to each other. The solid-state structures are stabilized by intra-molecular Osbnd H⋯N interactions in salicylaldehyde derivatives between the Osbnd H moiety from the aldehyde and the hydrazone nitrogen atom. All crystals are further stabilized by inter-molecular H-bonds mediated by the crystallization water molecule. A comparative analysis between experimental and theoretical results is presented. The conformational space was searched and geometries were optimized both in gas phase and including solvent effects. The structure is predicted for the compound for which the crystal structure was not determined. Infrared and electronic spectra were measured and assigned with the help of data obtained from computational methods based on the Density Functional Theory.

  10. Mild hydrothermal synthesis, crystal structure, thermal behaviour, spectroscopic and magnetic properties of (NH{sub 4}){sub 0.80}Li{sub 0.20}[Fe(AsO{sub 4})F

    SciTech Connect

    Berrocal, Teresa

    2011-10-15

    The (NH{sub 4}){sub 0.80}Li{sub 0.20}[Fe(AsO{sub 4})F] compound has been synthesized under mild hydrothermal conditions. The compound crystallize in the orthorhombic Pna2{sub 1} space group, with cell parameters a=13.352(9), b=6.7049(9), c=10.943(2) A and Z=8. The compound belongs to the KTiO(PO{sub 4}) structure type, with chains alternating FeO{sub 4}F{sub 2} octahedra and AsO{sub 4} tetrahedra, respectively, running along the 'a' and 'b' crystallographic axes. The diffuse reflectance spectrum in the visible region shows the forbidden electronic transitions characteristic of the Fe(III) d{sup 5}-high spin cation in slightly distorted octahedral geometry. The Moessbauer spectrum at room temperature is characteristic of iron (III) cations. The ESR spectra, carried out from room temperature to 200 K, remain isotropic with variation in temperature; the g-value being 1.99(1). Magnetic measurements indicate the predominance of strong antiferromagnetic interactions. - Graphical Abstract: Three-dimensional structure of (NH{sub 4}){sub 0.80}Li{sub 0.20}[Fe(AsO{sub 4})F], a fluoroarsenate containing lithium and ammonium in the structural cavities. Highlights: > (NH{sub 4}){sub 0.80}Li{sub 0.20}[Fe(AsO{sub 4})F] has been synthesized by mild hydrothermal technique. > The compound exhibits a three-dimensional structure. > Moessbauer spectrum indicates the existence of Fe(III) cations. > Visible spectroscopy confirms the hexacoordination of Fe(III). > Magnetic measurements indicate the existence of a global antiferromagnetic ordering.

  11. Crystalline perfection, spectroscopic investigations and transport properties of trisglycine zinc chloride NLO single crystal

    NASA Astrophysics Data System (ADS)

    Sugandhi, K.; Dinakaran, S.; Jose, M.; Uthrakumar, R.; Jeya Rejendran, A.; Bhagvannarayana, G.; Joseph, V.; Jerome Das, S.

    2010-09-01

    Bulk single crystals of trisglycine zinc chloride have been grown from aqueous solution by slow cooling technique. Single crystal and powder XRD analyses confirmed orthorhombic crystal structure with non-centrosymmetric space group Pbn2 1. High resolution X-ray diffraction results have established that the quality of the grown crystal is quite good for device fabrication. The crystal was characterized by FTIR and NMR spectral analyses. Optical absorption studies show that the material has very low absorption in the wavelength range 240-2000 nm. The analysis of absorption coefficient in the absorption region reveals a direct band gap of 4.21 eV. The crystal possesses remarkable thermal stability up to 229 °C. Photoconductivity studies of the grown crystal revealed the positive photoconducting nature. The grown crystal exhibited considerable hardness anisotropy with Vicker’s hardness tester. Dielectric constant and dielectric loss were calculated by varying frequencies at different temperatures.

  12. Structural, spectroscopic and theoretical study of novel ephedrinum salt

    NASA Astrophysics Data System (ADS)

    Ivanova, B.; Kolev, T.; Lamshöft, M.; Mayer-Figge, H.; Seidel, R.; Sheldrick, W. S.; Spiteller, M.

    2010-05-01

    Ephedrinum violurate dihydrate was synthesized, spectroscopically and structural elucidated. The data are compared with those of the free-base ephedrine hemihydrate. Discussion on the stable conformer of the ephedrinum cation is carried out. Quantum chemical calculations were performed for the theoretical elucidation of the conformational preference of the ephedrinum cation and its vibrational properties. The model systems neutral ephedrine hemihydrate ( 1) and violurate salt dihydrate ( 2) are elucidated.

  13. Nanoscale resolved infrared probing of crystal structure and of plasmon-phonon coupling.

    PubMed

    Huber, A; Ocelic, N; Taubner, T; Hillenbrand, R

    2006-04-01

    We show that slight variations of a crystal lattice cause significant spectral modifications of phonon-polariton resonant near-field interaction between polar semiconductor crystals and a scanning metal tip. Exploiting the effect for near-field imaging a SiC polytype boundary, we establish infrared mapping of crystal structure and crystal defects at 20 nm spatial resolution (lambda/500). By spectroscopic probing of doped SiC polytypes, we find that phonon-polariton resonant near-field interaction is also sensitive to electronic properties due to plasmon-phonon coupling in the crystals.

  14. Hydrothermal synthesis, crystal structure and spectroscopic and magnetic properties of (C{sub 2}H{sub 10}N{sub 2})[Mn{sub 2.09}Co{sub 0.91}(HPO{sub 3}){sub 4}

    SciTech Connect

    Fernandez-Armas, S.; Mesa, J.L.; Pizarro, J.L.; Pena, A.; Chapman, J.P.; Arriortua, M.I

    2004-09-01

    (C{sub 2}H{sub 10}N{sub 2})[Mn{sub 2.09}Co{sub 0.91}(HPO{sub 3}){sub 4}] has been synthesized using mild hydrothermal conditions under autogeneous pressure. The compound crystallizes in the triclinic P-1 space group. The unit-cell parameters are a = 5.4061(8), b = 5.4150(7), c = 14.136(2) A, {alpha} = 80.84(1), {beta} = 85.41(1), {gamma} = 60.00(1) and Z = 1. The compound shows a layered structure constructed from M{sub 3}O{sub 12} trimer units linked thorough the (HPO{sub 3}){sup 2-} phosphite oxoanions with the ethylenediammonium cations located between the sheets compensating the anionic charge of the inorganic framework. The IR and Raman spectra confirm the presence of the ethylenediammonium cation and phosphite anion. The diffuse reflectance spectrum is in accordance with the presence of Co(II) and Mn(II) high spin cations in slightly distorted octahedral symmetry. The calculated Dq and Racah parameters for the Co(II) cations are Dq = 710, B = 870 and C = 4100 cm{sup -1}. The magnetic measurements indicate the existence of antiferromagnetic interactions as the major interactions. Hysteresis observed at low temperature indicates a weak ferromagnetic component, due to a non-cancellation of spins, with coercitive field of 900 G and magnetization of 700 emu/mol.

  15. Checking nucleic acid crystal structures.

    PubMed

    Das, U; Chen, S; Fuxreiter, M; Vaguine, A A; Richelle, J; Berman, H M; Wodak, S J

    2001-06-01

    The program SFCHECK [Vaguine et al. (1999), Acta Cryst. D55, 191-205] is used to survey the quality of the structure-factor data and the agreement of those data with the atomic coordinates in 105 nucleic acid crystal structures for which structure-factor amplitudes have been deposited in the Nucleic Acid Database [NDB; Berman et al. (1992), Biophys. J. 63, 751-759]. Nucleic acid structures present a particular challenge for structure-quality evaluations. The majority of these structures, and DNA molecules in particular, have been solved by molecular replacement of the double-helical motif, whose high degree of symmetry can lead to problems in positioning the molecule in the unit cell. In this paper, the overall quality of each structure was evaluated using parameters such as the R factor, the correlation coefficient and various atomic error estimates. In addition, each structure is characterized by the average values of several local quality indicators, which include the atomic displacement, the density correlation, the B factor and the density index. The latter parameter measures the relative electron-density level at the atomic position. In order to assess the quality of the model in specific regions, the same local quality indicators are also surveyed for individual groups of atoms in each structure. Several of the global quality indicators are found to vary linearly with resolution and less than a dozen structures are found to exhibit values significantly different from the mean for these indicators, showing that the quality of the nucleic acid structures tends to be rather uniform. Analysis of the mutual dependence of the values of different local quality indicators, computed for individual residues and atom groups, reveals that these indicators essentially complement each other and are not redundant with the B factor. Using several of these indicators, it was found that the atomic coordinates of the nucleic acid bases tend to be better defined than those of

  16. Observation of Frenkel and charge transfer excitons in pentacene single crystals using spectroscopic generalized ellipsometry

    NASA Astrophysics Data System (ADS)

    Qi, Dongchen; Su, Haibin; Bastjan, M.; Jurchescu, O. D.; Palstra, T. M.; Wee, Andrew T. S.; Rübhausen, M.; Rusydi, A.

    2013-09-01

    We report on the emerging and admixture of Frenkel and charge transfer (CT) excitons near the absorption onset in pentacene single crystals. Using high energy-resolution spectroscopic generalized ellipsometry with in-plane polarization dependence, the excitonic nature of three lowest lying excitations is discussed. Their distinct polarization dependence strongly indicates the presence of both Frenkel and CT types of excitons near the excitation onset. In particular, the peculiar polarization behavior of the second excitation can only be rationalized by taking into account the inherent CT transition dipole moment. This observation has important implications for the pentacene-based optoelectronic devices.

  17. Septin crystallization for structural analysis.

    PubMed

    Valadares, N F; Garratt, R C

    2016-01-01

    Septins are filament-forming proteins found in many eukaryotes. Despite being important components of the cytoskeleton, only recently details of their macromolecular assemblies and crystal structures have started to appear in the literature. These are of fundamental importance to the understanding of cytoskeleton dynamics, membrane barrier formation, and bacterial caging, as well as essential cellular processes such as cell division, exocytosis, and vesicle trafficking. However, obtaining this data is frequently hindered by several experimental difficulties common to the majority of septin samples. Here we provide an overview of the current approaches to circumvent or minimize the experimental complications observed in septin crystallography focusing mainly, but not exclusively, on the choice of the septin construct and how to best prepare the sample itself. PMID:27473918

  18. Second sphere coordination in anion binding: Synthesis and spectroscopic characterisation of [ trans-Co(en) 2Cl 2]X (X=SCN or N 3). Single crystal X-ray structure determination and packing of [ trans-Co(en) 2Cl 2]N 3

    NASA Astrophysics Data System (ADS)

    Sharma, Raj Pal; Sharma, Rajni; Bala, Ritu; Venugopalan, Paloth

    2006-04-01

    In an effort to explore [ trans-Co(en) 2Cl 2] + as anion receptor for linear thiocyanate and azide ions, green coloured microcrystalline [ trans-Co(en) 2Cl 2]SCN I and single crystals of [ trans-Co(en) 2Cl 2]N 3II have been obtained by slowly mixing the separately dissolved trans-dichlorobis(ethylenediamine)cobalt(III) chloride with ammonium thiocyanate and sodium azide respectively in aqueous medium in 1:1 molar ratio. The newly synthesised complex salts were characterised on the basis of elemental analysis and spectroscopic techniques (IR, UV/vis, 1H and 13C NMR). Single crystal X-ray structure determination of II revealed that it crystallizes in the triclinic space group P 1 with a=6.293(1) Å, b=6.696(1) Å, c=7.116(1) Å, α=94.02(1)°, β=111.42(1)°, γ=99.86(1)°, V=272.13(7) Å 3, Z=1, R=0.0183. Supramolecular hydrogen bonding networks between ionic groups: nitrogen atoms of azide group and NH groups of coordinated ethylenediamine molecules, i.e. N-H⋯N - interactions by second sphere coordination besides electrostatic forces of attraction have been observed which probably exist in case of thiocyanate also. This suggests that [ trans-Co(en) 2Cl 2] + is a promising anion receptor for the linear ions SCN - and N 3-. The solubility product measurements indicate that the affinity of cationic cobaltammine [ trans-Co(en) 2Cl 2] + is greater for azide ion than thiocyanate ion.

  19. Synthesis and characterization of low-OH-fluor-chlorapatite: A single-crystal XRD and NMR spectroscopic study

    SciTech Connect

    McCubbin, Francis M; Mason, Harris E; Park, Hyunsoo; Phillips, Brian L; Parise, John B; Nekvasil, Hanna; Lindsley, Donald H

    2008-12-12

    Los-OH apatite of the compositional range Ca{sub 4.99-5.06}(PO{sub 4}){sub 2.98-3.00}F{sub 0.51-0.48}Cl{sub 0.38-0.36}OH{sub 0.14-0.12} was synthesized and characterized structurally by synchrotron-based single-crystal X-ray diffraction (XRD), and multiple nuclear magnetic resonance (NMR) spectroscopic techniques. the average structure is hexagonal with space group P6{sub 3}/m. The presence of scattering in the single-crystal diffraction data set, which is incommensurate within the average hexagonal structure, suggests the presence of localized short-range monoclinic domains. Complex lineshapes in the {sup 31}P and {sup 19}F MAS NMR spectra are also consistent with the presence of an incommensurate phase. No evidence was detected for splitting of the Ca2 site into two distinct sites (as had been previously reported for hexagonal ternary apatities). Structure refinement and {sup 19}F{l_brace}{sup 35}Cl{r_brace} TRAPDOR NMR experiments verified intercolumnal neighboring of F and Cl atoms (inter-column distance of 2.62 {angstrom}) within this low-OH{sup -} apatite suggesting that long-range neighboring of F and Cl within the apatite anion channels is feasible.

  20. Silver sulfadoxinate: Synthesis, structural and spectroscopic characterizations, and preliminary antibacterial assays in vitro

    NASA Astrophysics Data System (ADS)

    Zanvettor, Nina T.; Abbehausen, Camilla; Lustri, Wilton R.; Cuin, Alexandre; Masciocchi, Norberto; Corbi, Pedro P.

    2015-02-01

    The sulfa drug sulfadoxine (SFX) reacted with Ag+ ions in aqueous solution, affording a new silver(I) complex (AgSFX), which was fully characterized by chemical, spectroscopic and structural methods. Elemental, ESI-TOF mass spectrometric and thermal analyses of AgSFX suggested a [Ag(C12H13N4O2S)] empirical formula. Infrared spectroscopic measurements indicated ligand coordination to Ag(I) through the nitrogen atoms of the (deprotonated) sulfonamide group and by the pyrimidine ring, as well as through oxygen atom(s) of the sulfonamide group. These hypotheses were corroborated by 13C and 15N SS-NMR spectroscopy and by an unconventional structural characterization based on X-ray powder diffraction data. The latter showed that AgSFX crystallizes as centrosymmetric dimers with a strong Ag⋯Ag interaction of 2.7435(6) Å, induced by the presence of exo-bidentate N,N‧ bridging ligands and the formation of an eight-membered ring of [AgNCN]2 sequence, nearly planar. Participation of oxygen atoms of the sulfonamide residues generates in the crystal a 1D coordination polymer, likely responsible for its very limited solubility in all common solvents. Besides the analytical, spectroscopic and structural description, the antibacterial properties of AgSFX were assayed using disc diffusion methods against Escherichia coli and Pseudomonas aeruginosa (Gram-negative), and Staphylococcus aureus (Gram-positive) bacterial strains. The AgSFX complex showed to be active against Gram-positive and Gram-negative bacterial strains, being comparable to the activities of silver sulfadiazine.

  1. Synthesis, spectroscopic and structural perspective of new ferrocenyl amides

    NASA Astrophysics Data System (ADS)

    Etter, Martin; Nigar, Asifa; Ali, Naveed Zafar; Akhter, Zareen; Dinnebier, Robert E.

    2016-05-01

    Two new ferrocene derivatives with amide linkages were synthesized by the condensation of 4-ferrocenylaniline with n-alkyl acid chloride derivatives as pristine orange solids in good yields. FTIR and 1H/13C NMR studies have confirmed the basic structure of the molecules with the involvement of intermolecular H-bonding, which together with the ferrocene-like packing ensures the stability of the crystal structure. Crystal structures for both compounds were solved by Rietveld refinements of high resolution X-ray powder diffraction data. The XRD results show that both compounds crystallize in the monoclinic space group P21/c. The primary feature of the crystal structure is a double layer of ferrocenyl groups stretched out in the b-c -plane perpendicular to the a-axis, with packing of the ferrocenyl groups occurring in a manner similar to that of pure ferrocene. Despite the close structural similarity, both compounds differ in the optimized geometry of respective Ferrocene conformers. The Cp rings are eclipsed for one Ferrocene conformer and close to staggered for the other, owing to the low energy barrier for the rotation of a cyclopentadienyl ring relative to the rest of the molecule.

  2. Synthesis, crystal growth and spectroscopic investigation of novel metal organic crystal: β-Alanine cadmium bromide monohydrate (β-ACBM)

    NASA Astrophysics Data System (ADS)

    Renugadevi, R.; Kesavasamy, R.

    2014-07-01

    β-Alanine cadmium bromide monohydrate (β-ACBM), a new metal organic crystal has been grown from aqueous solution by slow evaporation technique. The grown crystals have been subjected to single crystal X-ray diffraction analysis to determine the crystal structure. The β-ACBM crystallized in monoclinic system with space group P21/c. The presence of protons and carbons in the β-alanine cadmium bromide monohydrate was confirmed by 1H and 13C nuclear magnetic resonance spectral analysis. The mode of vibration of different molecular groups present in β-ACBM was identified by FT-IR spectral analysis. Transparency of crystals in UV-Vis-NIR region has also been studied. The thermal characteristics of as-grown crystals were analyzed using thermo gravimetric and differential thermal analyses. The magnetic property of the grown crystal was investigated using Vibrating Sample Magnetometer (VSM) at ambient temperature. The mechanical stability of β-ACBM was evaluated by Vickers microhardness measurement.

  3. Crystal structure and spectroscopic analysis of a new oxalate-bridged MnII compound: catena-poly[guanidinium [[aqua­chlorido­manganese(II)]-μ2-oxalato-κ4 O 1,O 2:O 1′,O 2′] monohydrate

    PubMed Central

    Sehimi, Hiba; Chérif, Ichraf; Zid, Mohamed Faouzi

    2016-01-01

    As part of our studies on the synthesis and the characterization of oxalate-bridged compounds M–ox–M (ox = oxalate dianion and M = transition metal ion), we report the crystal structure of a new oxalate-bridged MnII phase, {(CH6N3)[Mn(C2O4)Cl(H2O)]·H2O}n. In the compound, a succession of MnII ions (situated on inversion centers) adopting a distorted octa­hedral coordination and bridged by oxalate ligands forms parallel zigzag chains running along the c axis. These chains are inter­connected through O—H⋯O hydrogen-bonding inter­actions to form anionic layers parallel to (010). Individual layers are held together via strong hydrogen bonds involving the guanidinium cations (N—H⋯O and N—H⋯Cl) and the disordered non-coordinating water mol­ecule (O—H⋯O and O—H⋯Cl), as well as by guanidinium π–π stacking. The structural data were confirmed by IR and UV–Visible spectroscopic analysis. PMID:27308028

  4. Spectroscopic survey telescope design. I - Primary mirror structure and support

    NASA Astrophysics Data System (ADS)

    Ray, F. B.; Krishnamachari, S. V.

    1988-09-01

    The present design for a spectroscopic survey telescope uses a spherical primary mirror whose figure requires that a secondary focus assembly be driven at the tracking rate in an attitude normal to the spherical focal surface, while the telescope, being tilted at a predetermined angular zenith distance, need only be 'set' (and clamped) occasionally in azimuth. The spherical primary mirror segments are configured to an identical radius-of-curvature and supported on a fully triangulated stainless steel space frame; a structural analysis using finite elements indicates that the expected static performance of both the individual segments and the overall space frame present reasonable goals for current engineering practice.

  5. Synthesis, electrochemistry, and spectroscopic properties of six-coordinate monooxomolybdenum(VI) complexes containing tridentate Schiff base and bidentate catecholate ligands. Crystal and molecular structure of (N-salicylidene-2-aminophenolato)(naphthalene-2,3-diolato)oxomolybdenum(VI)

    SciTech Connect

    Mondal, J.U.; Schultz, F.A.; Brennan, T.D.; Scheidt, W.R.

    1988-11-02

    Six-coordinate monooxomolybdenum(VI) complexes, MoO(cat)(Sap), where Sap/sup 2 -/ = the Schiff base dianion N-salicylidene-2-aminophenolate and cat/sup 2 -/ = catecholate Cat/sup 2 -/, naphthalene-2,3-diolate (Naphcat/sup 2 -/), or 3,5-di-tert-butylcatecholate (DTBcat/sup 2 -/), are prepared by reacting the Mo(VI) dimer. (MoO/sub 2/(Sap))/sub 2/, with the appropriate catechol. The products are characterized by cyclic voltammetry, mass spectrometry, and uv/vis, ir, and /sup 95/Mo NMR spectroscopy. The MoO(cat)(Sap) complexes represent the first examples of a mononuclear MoO/sup 4 +/ center with a coordination number of six. The crystal structure of the MoO-(Naphcat)(Sap) derivative is reported, confirming the six-coordinate, distorted octahedrla environment about Mo(VI). Bond angles in the coordination group deviate from the ideal value of 90/degrees/ as a consequence of the ligand bite constraints and because all four O-Mo-O angles involving the terminal oxo ligand are larger than the ideal 90/degrees/ value. MoO(cat)(Sap) complexes undergo reversible one-electronic reduction at -0.5 to -0.7 V versus Fc /sup +/0/ followed by irreversible one-electron reduction at -1.6 to -1.9 V. Reversible MoO/sup 4 +//MoO/sup 3 +/ electrochemistry is attributed to the fact that the Mo d/sub xy/orbital of MoO(cat)(Sap) can be singly occupied upon reduction to Mo(V) without unfavorable interaction with the four bonds in its equatorial plane. This contrasts with the irreversible electrochemical behavior of seven-coordinate MoO/sup 4 +/ complexes, which contain five such bonds. The /sup 95/Mo NMR chemical shift of MoO(Naphcat)(Sap) is +385 ppM versus external molybdate; this value is highly deshielded with respect to seven-coordinate MoO/sup 4 +/ and six-coordinate MoO/sub 2//sup 2 +/ complexes with O and N donors. 35 references, 4 figures, 5 tables.

  6. The molecular structure of chloritoid: a mid-infrared and near-infrared spectroscopic study.

    PubMed

    Li, Kuo; Liu, Qinfu; Cheng, Hongfei; Deng, Yutao; Frost, Ray L

    2015-06-15

    The mineral chloritoid collected from the argillite in the bottom of Yaopo Formation of Western Beijing was characterized by mid-infrared (MIR) and near-infrared (NIR) spectroscopy. The MIR spectra showed all fundamental vibrations including the hydroxyl units, basic aluminosilicate framework and the influence of iron on the chloritoid structure. The NIR spectrum of the chloritoid showed combination (ν+δ)OH bands with the fundamental stretching (ν) and bending (δ) vibrations. Based on the chemical component data and the analysis result from the MIR and NIR spectra, the crystal structure of chloritoid from western hills of Beijing, China, can be illustrated. Therefore, the application of the technique across the entire infrared region is expected to become more routine and extend its usefulness, and the reproducibility of measurement and richness of qualitative information should be simultaneously considered for proper selection of a spectroscopic method for the unit cell structural analysis.

  7. Crystal structure analysis of intermetallic compounds

    NASA Technical Reports Server (NTRS)

    Conner, R. A., Jr.; Downey, J. W.; Dwight, A. E.

    1968-01-01

    Study concerns crystal structures and lattice parameters for a number of new intermetallic compounds. Crystal structure data have been collected on equiatomic compounds, formed between an element of the Sc, Ti, V, or Cr group and an element of the Co or Ni group. The data, obtained by conventional methods, are presented in an easily usable tabular form.

  8. Spectroscopic refractive indices of monoclinic single crystal and ceramic Lutetium oxyorthosilicate (LSO) from 200 to 850 nm

    SciTech Connect

    Jellison Jr, Gerald Earle; Specht, Eliot D; Boatner, Lynn A; Singh, David J; Melcher, Charles L

    2012-01-01

    The four real values of the dielectric function tensor of the monoclinic crystal Lu2SiO5 or lutetium oxyorthosilicate (LSO) have been determined using generalized ellipsometry from 200 to 850 nm. The three principal values are fit to the Sellmeier model, and they indicate that the band gap of LSO is less than ~9 eV. The off-diagonal element 12 is non-zero over the entire spectrum, but it is very close to zero for wavelengths longer than ~400 nm, indicating that structurally monoclinic LSO is nearly optically orthorhombic in this wavelength region. The spectroscopic dielectric functions of three isotropic ceramic LSO samples are presented, which are consistent with the dielectric functions of single-crystal LSO when the effects of porosity are included. As a comparison, the dielectric functions are also determined using relativistic electronic structure and optical calculations based on the recently developed potential functional of Tran and Blaha (Phys. Rev. Lett. 102, 226401 (2009).)

  9. Crystal growth and spectroscopic properties of Er3+ ions doped CdF2 single crystals

    NASA Astrophysics Data System (ADS)

    Djellab, S.; Diaf, M.; Labbaci, K.; Guerbous, L.

    2014-04-01

    Single crystals of Er3+:CdF2 with good optical quality were grown by a Bridgman technique after purification of the starting materials. Absorption and emission spectra are recorded at room temperature. The Judd-Ofelt (JO) analysis was applied to obtain the three phenomenological intensity parameters and the transition strengths. These JO parameters are used to calculate the radiative transition probabilities, the radiation lifetimes and the branching ratios. The results obtained are in good agreement with those of other fluoride laser materials. We also carried out luminescence measurements for red and green emission. The studied host may offer infrared and visible laser emissions.

  10. Theoretical prediction of crystal structures of rubrene

    NASA Astrophysics Data System (ADS)

    Obata, Shigeaki; Miura, Toshiaki; Shimoi, Yukihiro

    2014-01-01

    We theoretically predict crystal structures and molecular arrangements for rubrene molecule using CONFLEX program and compare them with the experimental ones. The most, second-most, and fourth-most stable predicted crystal structures show good agreement with the triclinic, orthorhombic, and monoclinic polymorphs of rubrene, respectively. The change in molecular conformation is also predicted between crystalline and gas phases: the tetracene backbone takes flat conformation in crystalline phase as in the observed structure. Meanwhile, it is twisted in gas phase. The theoretical prediction method used in this work provides the successful results on the determination of the three kinds of crystal structures and molecular arrangements for rubrene molecule.

  11. Phenanthro[4,5-fgh]quinoxaline-Fused Subphthalocyanines: Synthesis, Structure, and Spectroscopic Characterization.

    PubMed

    Pan, Houhe; Liu, Wenbo; Wang, Chiming; Wang, Kang; Jiang, Jianzhuang

    2016-07-01

    A series of four phenanthro[4,5-fgh]quinoxaline-fused subphthalocyanine derivatives 0-3 containing zero, one, two, and three phenanthro[4,5-fgh]quinoxaline moieties, respectively, were isolated from the mixed cyclotrimerization reaction of 2,9-di-tert-butylphenanthro[4,5-fgh]quinoxaline-5,6-dicarbonitrile with 4,5-bis(2,6-diisopropylphenoxy)phthalonitrile and characterized by a series of spectroscopic methods including MALDI-TOF mass, (1) H NMR, electronic absorption, magnetic circular dichroism (MCD), and fluorescence spectroscopy. The molecular structures for the compounds 0 and 2 were clearly revealed on the basis of single-crystal X-ray diffraction analysis. Their electrochemical properties were also studied by cyclic voltammetry. In particular, theoretical calculations in combination with the electronic absorption and electrochemical analyses revealed the significant influence of the fused-phenanthro[4,5-fgh]quinoxaline units on the electronic structures.

  12. Spectroscopic and laser characterization of Yb,Tm:KLu(WO4)2 crystal

    NASA Astrophysics Data System (ADS)

    Loiko, P. A.; Serres, J. M.; Mateos, X.; Demesh, M. P.; Yasukevich, A. S.; Yumashev, K. V.; Petrov, V.; Griebner, U.; Aguiló, M.; Díaz, F.

    2016-01-01

    We report on a comprehensive spectroscopic and laser characterization of monoclinic Yb,Tm:KLu(WO4)2 crystals. Stimulated-emission cross-section spectra corresponding to the 3F4 → 3H6 transition of Tm3+ ions are determined. The radiative lifetime of the 3F4 state of Tm3+ ions is 0.82 ms. The maximum Yb3+ → Tm3+ energy transfer efficiency is 83.9% for 5 at.% Yb - 8 at.% Tm doping. The fractional heat loading for Yb,Tm:KLu(WO4)2 is 0.45 ± 0.05. Using a hemispherical cavity and 5 at.% Yb - 6 at.% Tm doped crystal, a maximum CW power of 227 mW is achieved at 1.983-2.011 μm with a maximum slope efficiency η = 14%. In the microchip laser set-up, the highest slope efficiency is 20% for a 5 at.% Yb- 8 at.% Tm doped crystal with a maximum output power of 201 mW at 1.99-2.007 μm. Operation of Yb,Tm:KLu(WO4)2 as a vibronic laser emitting at 2.081-2.093 μm is also demonstrated.

  13. Crystals in which some metal atoms are more equal than others: inequalities from crystal packing and their spectroscopic/magnetic consequences.

    PubMed

    Nippe, Michael; Wang, Jingfang; Bill, Eckhard; Hope, Håkon; Dalal, Naresh S; Berry, John F

    2010-10-13

    Crystal structures of the heterometallic compounds CrCrFe(dpa)(4)Cl(2) (1), CrCrMn(dpa)(4)Cl(2) (2), and MoMoMn(dpa)(4)Cl(2) (3) (dpa = 2,2'-dipyridylamide) show disorder in the metal atom positions such that the linear M(A)[quadruple bond]M(A)···M(B) array for a given molecule in the crystal is oriented in one of two opposing directions. Despite the fact that the direct coordination sphere of the metals in the two crystallographically independent orientations is identical, subtle differences in some metal-ligand bond distances are observed in 1 and 3 due to differences in the orientation of a solvent molecule of crystallization. The Fe(II) and Mn(II) ions serve as sensitive local spectroscopic probes that have been interrogated by Mössbauer spectroscopy and high-field EPR spectroscopy, respectively. The subtle differences in the two independent Fe and Mn sites in 1 and 3 unexpectedly give rise to unusually large differences in the measured Fe quadrupole splitting (ΔE(Q)) in 1 and Mn zero-field splitting (D) in 3. Variable-temperature/single-crystal EPR spectroscopy has allowed us to determine that the temperature-dependent D tensors in 3 are oriented along the metal-metal axis and that they show significantly different dynamic behavior with temperature. The differences in ΔE(Q) and D are reproduced by density functional calculations on truncated models for 1 and 3 that lack the quadruply bonded M(A)[quadruple bond]M(A) groups, though the magnitude of the calculated effect is not as large as that observed experimentally. We suggest that the large observed differences in ΔE(Q) and D for the individual sites could be due to the influence of the strong diamagnetic anisotropy of the quadruply bonded M[quadruple bond]M unit.

  14. Structural characterization of thin film photonic crystals

    SciTech Connect

    Subramania, G.; Biswas, R.; Constant, K.; Sigalas, M. M.; Ho, K. M.

    2001-06-15

    We quantitatively analyze the structure of thin film inverse-opal photonic crystals composed of ordered arrays of air pores in a background of titania. Ordering of the sphere template and introduction of the titania background were performed simultaneously in the thin film photonic crystals. Nondestructive optical measurements of backfilling with high refractive index liquids, angle-resolved reflectivity, and optical spectroscopy were combined with band-structure calculations. The analysis reveals a thin film photonic crystal structure with a very high filling fraction (92{endash}94%) of air and a substantial compression along the c axis ({similar_to}22{endash}25%).

  15. Pattern information extraction from crystal structures

    NASA Astrophysics Data System (ADS)

    Okuyan, Erhan; Güdükbay, Uğur; Gülseren, Oğuz

    2007-04-01

    Determining the crystal structure parameters of a material is an important issue in crystallography and material science. Knowing the crystal structure parameters helps in understanding the physical behavior of material. It can be difficult to obtain crystal parameters for complex structures, particularly those materials that show local symmetry as well as global symmetry. This work provides a tool that extracts crystal parameters such as primitive vectors, basis vectors and space groups from the atomic coordinates of crystal structures. A visualization tool for examining crystals is also provided. Accordingly, this work could help crystallographers, chemists and material scientists to analyze crystal structures efficiently. Program summaryTitle of program: BilKristal Catalogue identifier: ADYU_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYU_v1_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Licensing provisions: None Programming language used: C, C++, Microsoft .NET Framework 1.1 and OpenGL Libraries Computer: Personal Computers with Windows operating system Operating system: Windows XP Professional RAM: 20-60 MB No. of lines in distributed program, including test data, etc.:899 779 No. of bytes in distributed program, including test date, etc.:9 271 521 Distribution format:tar.gz External routines/libraries: Microsoft .NET Framework 1.1. For visualization tool, graphics card driver should also support OpenGL Nature of problem: Determining crystal structure parameters of a material is a quite important issue in crystallography. Knowing the crystal structure parameters helps to understand physical behavior of material. For complex structures, particularly, for materials which also contain local symmetry as well as global symmetry, obtaining crystal parameters can be quite hard. Solution method: The tool extracts crystal parameters such as primitive vectors, basis vectors and identify the space group from

  16. Growth and spectroscopic properties of Ca9Nd(VO4)7 single crystal

    NASA Astrophysics Data System (ADS)

    Demesh, M. P.; Yasukevich, A. S.; Kuleshov, N. V.; Kosmyna, M. B.; Mateychenko, P. V.; Nazarenko, B. P.; Shekhovtsov, A. N.; Kornienko, A. A.; Dunina, E. B.; Orlovich, V. A.; Khodasevich, I. A.; Paszkowicz, W.; Behrooz, A.

    2016-10-01

    Ca9Nd(VO4)7 single crystal was grown by the Czochralski method in inert atmosphere. The crystal structure and chemical composition were studied. Polarized absorption and luminescence spectra were investigated in details. It was found that the Ca9Nd(VO4)7 crystals belongs to self-activated laser materials with a weak concentration quenching of luminescence. Judd-Ofelt analysis was performed. The emission cross-sections spectra for 4F3/2 → 4I9/2, 4I11/2, 4I13/2 transitions were determined. For the first time Raman spectra of the Ca9Nd(VO4)7 single crystal were recorded and interpreted.

  17. Structural and spectroscopic characterization of mixed planetary ices.

    PubMed

    Plattner, Nuria; Lee, Myung Won; Meuwly, Markus

    2010-01-01

    Mixed ices play a central role in characterizing the origin, evolution, stability and chemistry of planetary ice surfaces. Examples include the polar areas of Mars, the crust of the Jupiter moon Europa, or atmospheres of planets and their satellites, particularly in the outer solar system. Atomistic simulations using accurate representations of the interaction potentials have recently shown to be suitable to quantitatively describe both, the mid- and the far-infrared spectrum of mixed H2O/CO amorphous ices. In this work, molecular dynamics simulations are used to investigate structural and spectroscopic properties of mixed and crystalline ices containing H2O, CO and CO2. Particular findings include: (a) the sensitivity of the water bending mode to the local environment of the water molecules which, together with structural insights from MD simulations, provides a detailed picture for the relationship between spectroscopy and structure; and (b) the sensitivity of the low-frequency spectrum to the structure of the mixed CO2/H2O ice. Specifically, for mixed H2O/CO2 ices with low water contents isolated water molecules are found which give rise to a band shifted by only 12 cm(-1) from the gas-phase value whereas for increasing water concentration (for a 1 : 1 mixture) the band progressively shifts to higher frequency because water clusters can form. More generally it is found that changes in the ice structure due to the presence of CO2 are larger compared to changes induced by the presence of CO and that this difference is reflected in the shape of the water bending vibration. Thus, the water bending vibration appears to be a suitable diagnostic for structural and chemical aspects of mixed ices. PMID:21302549

  18. Structures of cyano-biphenyl liquid crystals

    NASA Technical Reports Server (NTRS)

    Chu, Yuan-Chao; Tsang, Tung; Rahimzadeh, E.; Yin, L.

    1989-01-01

    The structures of p-alkyl- p'-cyano- bicyclohexanes, C(n)H(2n+1) (C6H10)(C6H10) CN (n-CCH), and p-alkyl- p'-cyano- biphenyls, C(n)H(2n+1) (C6H4)(C6H4) CN (n-CBP), were studied. It is convenient to use an x ray image intensification device to search for symmetric x ray diffraction patterns. Despite the similarities in molecular structures of these compounds, very different crystal structures were found. For the smectic phase of 2CCH, the structure is close to rhombohedral with threefold symmetry. In contrast, the structure is close to hexagonal close-packed with two molecules per unit cell for 4CCH. Since intermolecular forces may be quite weak for these liquid crystals systems, it appears that crystal structures change considerably when the alkyl chain length is slightly altered. Different structures were also found in the crystalline phase of n-CBP for n = 6 to 9. For n = 7 to 9, the structures are close to monclinic. The structures are reminiscent of the smectic-A liquid crystal structures with the linear molecules slightly tilted away from the c-axis. In contrast, the structure is quite different for n = 6 with the molecules nearly perpendicular to the c-axis.

  19. One-dimensional mercury(II) halide coordination polymers of 3,6-bis(2-pyridyl)-1,2,4,5-tetrazine ligand: Synthesis, crystal structure, spectroscopic and DFT studies

    NASA Astrophysics Data System (ADS)

    Saghatforoush, Lotfali; Khoshtarkib, Zeinab; Amani, Vahid; Bakhtiari, Akbar; Hakimi, Mohammad; Keypour, Hassan

    2016-01-01

    Three new coordination polymers, [Hg(μ-bptz)X2]n (X=Cl (1), Br (2)) and [Hg2(μ-bptz)(μ-I)2I2]n (3) (bptz=3,6-bis(2-pyridyl)-1,2,4,5-tetrazine) were synthesized. X-ray structural analysis indicated that compounds 1 and 2 are composed of one-dimensional (1D) linear chains while the compound 3 has 1D stair-stepped structure. The electronic band structure along with density of states (DOS) calculated by the DFT method indicates that compound 1 and 2 are direct band gap semiconductors; however, compound 3 is an indirect semiconductor. The linear optical properties of the compounds are also calculated by DFT method. According to the DFT calculations, the observed emission band of the compounds in solid state is due to electron transfer from an excited bptz-π* state (CBs) to the top of VBs. 1H NMR spectra of the compounds indicate that, in solution phase, the compounds don't decompose completely. Thermal stability of the compounds is studied using TG, DTA methods.

  20. From protein structure to function via single crystal optical spectroscopy

    PubMed Central

    Ronda, Luca; Bruno, Stefano; Bettati, Stefano; Storici, Paola; Mozzarelli, Andrea

    2015-01-01

    The more than 100,000 protein structures determined by X-ray crystallography provide a wealth of information for the characterization of biological processes at the molecular level. However, several crystallographic “artifacts,” including conformational selection, crystallization conditions and radiation damages, may affect the quality and the interpretation of the electron density maps, thus limiting the relevance of structure determinations. Moreover, for most of these structures, no functional data have been obtained in the crystalline state, thus posing serious questions on their validity in infereing protein mechanisms. In order to solve these issues, spectroscopic methods have been applied for the determination of equilibrium and kinetic properties of proteins in the crystalline state. These methods are UV-vis spectrophotometry, spectrofluorimetry, IR, EPR, Raman, and resonance Raman spectroscopy. Some of these approaches have been implemented with on-line instruments at X-ray synchrotron beamlines. Here, we provide an overview of investigations predominantly carried out in our laboratory by single crystal polarized absorption UV-vis microspectrophotometry, the most applied technique for the functional characterization of proteins in the crystalline state. Studies on hemoglobins, pyridoxal 5′-phosphate dependent enzymes and green fluorescent protein in the crystalline state have addressed key biological issues, leading to either straightforward structure-function correlations or limitations to structure-based mechanisms. PMID:25988179

  1. Crystal engineering: From design of crystal structures to fabrication of composite crystals

    NASA Astrophysics Data System (ADS)

    Luo, Tzy-Jiun Mark

    This thesis reports how to design and control co-crystal structures from a kinetic point of view, and demonstrates the control of crystal morphology through understanding the kinetics and crystal structures. In chapter one, the in-situ atomic force microscope (AFM) was utilized to investigate how side chain on a glycine 2,5-diketopiperazine (GLYDKP) backbone can affect the assembly of GLYDKP, and showed that methyl groups cause larger energy barrier for crystallization. Because the introduction of functional group on the side chain could inevitably slow down the assembly process, a different approach should be considered. Chapter two shows that formic acid at low concentration can accelerate the assembly process without incorporating into the crystal structure. Because formic acid only crystallizes with GLYDKP in concentrated solution, these results prove that co-crystallization is a better method for incorporating functionalized molecules into a solid than direct modification of molecule itself. Chapter three focuses on the rational design of GLYDKP cocrystals by utilizing the observation found in chapter two. Structure of GLYDKP and formic acid crystal was analyzed to search possible guest molecules for cocrystal studies. This method successfully identified eleven molecules that crystallize with GLYDKP, and proved that crystal structure can be controlled through weak interactions such as C-H•••O=C and C-H•••Cl interactions. Chapter four and chapter five explore the possibility of using self-assembled process to control morphology of crystals and surface epitaxy. Metal(II) bis(imidazolium 2,b-pyridinedicarboxylate) complexes were chosen and two morphologies associated with different metal ions were found: rhombohedral (Type I) and rectangular (Type II) crystals. In this study, an additive was found to change the morphology of crystal from type I to type II, and then methods of producing various shapes of composite crystals were also established. These

  2. Isomerism of Cyanomethanimine: Accurate Structural, Energetic, and Spectroscopic Characterization.

    PubMed

    Puzzarini, Cristina

    2015-11-25

    The structures, relative stabilities, and rotational and vibrational parameters of the Z-C-, E-C-, and N-cyanomethanimine isomers have been evaluated using state-of-the-art quantum-chemical approaches. Equilibrium geometries have been calculated by means of a composite scheme based on coupled-cluster calculations that accounts for the extrapolation to the complete basis set limit and core-correlation effects. The latter approach is proved to provide molecular structures with an accuracy of 0.001-0.002 Å and 0.05-0.1° for bond lengths and angles, respectively. Systematically extrapolated ab initio energies, accounting for electron correlation through coupled-cluster theory, including up to single, double, triple, and quadruple excitations, and corrected for core-electron correlation and anharmonic zero-point vibrational energy, have been used to accurately determine relative energies and the Z-E isomerization barrier with an accuracy of about 1 kJ/mol. Vibrational and rotational spectroscopic parameters have been investigated by means of hybrid schemes that allow us to obtain rotational constants accurate to about a few megahertz and vibrational frequencies with a mean absolute error of ∼1%. Where available, for all properties considered, a very good agreement with experimental data has been observed.

  3. Raman spectroscopic studies of Nd{sub 0.75}Sm{sub 0.25}GaO{sub 3} single crystals

    SciTech Connect

    Nithya, R. Ravindran, T. R.; Daniel, D. J.

    2015-06-24

    Single crystals of Nd{sub 1-x}Sm{sub x}GaO{sub 3} (x= 0 and 0.25) were grown by a four mirror IR image furnace using floating zone technique. The crystals are characterized by X-ray diffraction and Raman spectroscopic measurements. NGO adopts orthorhombic structure with Pbnm symmetry and samarium substituted compound also exhibited the same structure as that of the pristine compound without secondary phases. Polarized Raman spectra are measured at ambient temperature in a back scattering geometry. Spectra exhibit low intensity first-order Raman bands. In addition, several high intensity second-order Raman bands have been observed in the frequency range 2000 to 4000 cm{sup −1}.

  4. Influence of vapor transport equilibration on spectroscopic parameters of Er3+ in LiNbO3 crystals

    NASA Astrophysics Data System (ADS)

    Zhang, De-Long; Wang, Dun-Chun; Pun, E. Y. B.

    2005-05-01

    A number of X-, Y- and Z-cut Er(/Yb):LiNbO3 crystals with six different doping levels of rare earth ions were annealed at 1110 °C for 120 h using the vapor transport equilibration (VTE) technique. At room temperature, -polarized or unpolarized absorption spectra of these VTE-treated crystals and corresponding as-grown crystals were recorded in the wavelength range 280-1700 nm. The absorption characteristics of the VTE-treated crystals are summarized and compared with those of the as-grown crystals. The (Li+ + RE3+)/Nb5+(RE3+ = Er3+ or Er3+ + Yb3+) ratios in the VTE-treated Er(/Yb):LiNbO3 crystals were evaluated using the optical absorption edge or Raman linewidth of the 153 cm-1 E(TO) phonon. Based upon the measured spectral data, spectroscopic parameters of Er3+ ions in as-grown and VTE-treated crystals were calculated using the Judd-Ofelt (J-O) theory. The influences of Er3+ doping level, type of crystal cut and VTE treatment on the key spectroscopic parameters, including integrated absorption coefficient, oscillator strength, J-O parameters and radiative lifetimes of three dominant emission manifolds (4I13/2 (1530 nm), 4F9/2 (660 nm) and 4S3/2 (560 nm)), are discussed and summarized and compared with the results for as-grown crystals. The results for as-grown crystals are also compared with those reported previously. The present theoretical result concerning the VTE effect on the 1530 nm lifetime is in rough agreement with the experimental result reported previously.

  5. Synthesis, structure, spectroscopic and electrochemical properties of bis(histamine-saccharinate) copper(II) complex

    NASA Astrophysics Data System (ADS)

    Bulut, İclal; Uçar, İbrahim; Karabulut, Bünyamin; Bulut, Ahmet

    2007-05-01

    Crystal structure of [Cu(hsm) 2(sac) 2] (hsm is histamine and sac is saccharinate) complex has been determined by X-ray diffraction analyses and its magnetic environment has been identified by electron paramagnetic resonance (EPR) technique. The title complex crystallizes in the monoclinic system, space group P 21/ c with a = 7.4282(4), b = 22.5034(16), c = 8.3300(5) Å, β = 106.227(4)°, V = 1336.98(14) Å 3, and Z = 2. The structure consist of discrete [Cu(hsm) 2(sac) 2] molecules in which the copper ion is centrosymmetrically coordinated by two histamine ligands forming an equatorial plane [Cu-N hsm = 2.024(2) and Cu-N hsm = 2.0338(18) Å]. Two N atoms from the saccharinate ligands coordinate on the elongated axial positions with Cu-N sac being 2.609(5) Å. The complex is also characterized by spectroscopic (IR, UV/Vis) and thermal (TG, and TDA) methods. The cyclic voltammogram of the title complex investigated in DMSO (dimethylsulfoxide) solution exhibits only metal centred electroactivity in the potential range - 1.25-1.5 V versus Ag/AgCl reference electrode. The molecular orbital bond coefficients of Cu(II) ion in d 9 state is also calculated by using EPR and optical absorption parameters.

  6. Synthesis, structure, crystal growth and characterization of a novel semiorganic nonlinear optical L-proline lithium bromide monohydrate single crystal

    NASA Astrophysics Data System (ADS)

    Sathiskumar, S.; Balakrishnan, T.; Ramamurthi, K.; Thamotharan, S.

    2015-03-01

    L-Proline lithium bromide monohydrate (LPLBM), a promising semiorganic nonlinear optical material, was synthesized and single crystals of LPLBM were grown from solution by slow evaporation technique. Single crystal X-ray structure solution reveals that the grown crystal belongs to monoclinic system with space group P21. Presence of various functional groups was identified by FT-IR and FT-Raman spectral analyses. UV-Vis-NIR spectroscopic study shows that the LPLBM crystal possesses 90% of transmittance in the range of 250-1100 nm. Vickers microhardness values, the dielectric constant and dielectric loss of the LPLBM crystal were reported. Elemental analysis by energy dispersive X-ray analysis shows the presence of carbon, nitrogen, oxygen and bromine. The surface morphology of the crystal was investigated using scanning electron microscopic study. The thermal stability of the LPLBM crystal was studied from TGA and DSC analysis. Second harmonic generation efficiency of the LPLBM crystal measured by Kurtz and Perry powder technique using Nd:YAG laser is about 0.3 times that of urea.

  7. Crystallization and Structure Analysis of Membrane Proteins

    NASA Astrophysics Data System (ADS)

    Newman, Richard

    In recent years, there has been great progress in the determination of high-resolution three-dimensional (3D) structures of membrane proteins. The first major breakthrough came with the crystallization (1) and X-ray crystallography (2,3) of the bacterial photosynthetic reaction center (see refs. 4 and 5 for reviews). The structure of another, entirely different membrane protein, the bacterial outer membrane porin from Rhodobacter capsulatus, has now been determined by X-ray crystallography (6). Recent results by electron crystallography of two-dimensional (2D) crystals have been most encouraging. The high-resolution 3D structure of bacteriorhodopsin (7) plant light-harvesting complex (8) and projection maps of several other membrane proteins at similar resolutions (9-11) have been obtained by this technique. Electron crystallography seems particularly appropriate for membrane proteins that are prone to form 2D crystals, and it is hoped that many more structures will be determined in this way.

  8. Crystal structure of levomepromazine maleate.

    PubMed

    Gál, Gyula Tamás; May, Nóra Veronika; Bombicz, Petra

    2016-05-01

    The asymmetric unit of the title salt, C19H25N2OS(+)·C4H3O4 (-) [systematic name: (S)-3-(2-meth-oxy-pheno-thia-zin-10-yl)-N,N,2-tri-methyl-propanaminium hydrogen maleate], comprises two (S)-levomepromazine cations and two hydrogen maleate anions. The conformations of the two cations are similar. The major difference relates to the orientation of the meth-oxy substituent at the pheno-thia-zine ring system. The crystal components form a three-dimensional supra-molecular network via N-H⋯O, C-H⋯O and C-H⋯π inter-actions. A comparison of the conformations of the levomepromazine cations with those of the neutral mol-ecule and similar protonated mol-ecules reveals significant conformational flexibility of the pheno-thia-zine ring system and the substituent at the pheno-thia-zine N atom. PMID:27308001

  9. Synthesis, spectroscopic studies and crystal structure of the Schiff base ligand L derived from condensation of 2-thiophenecarboxaldehyde and 3,3'-diaminobenzidine and its complexes with Co(II), Ni(II), Cu(II), Cd(II) and Hg(II): Comparative DNA binding studies of L and its Co(II), Ni(II) and Cu(II) complexes

    NASA Astrophysics Data System (ADS)

    Shakir, Mohammad; Abbasi, Ambreen; Azam, Mohammad; Khan, Asad U.

    2011-09-01

    The Schiff base ligand, N,N'-bis-(2-thiophenecarboxaldimine)-3,3'-diaminobenzidine (L) obtained from condensation of 2-thiophenecarboxaldehyde and 3,3'-diaminobenzidine, was used to synthesize the complexes of type, [M 2L 2]Cl 4 [M = Co(II), Ni(II), Cu(II), Cd(II) and Hg(II)]. The newly synthesized ligand (L) was characterized on the basis of the results of elemental analysis, FT-IR, 1H NMR, 13C NMR, mass spectroscopic studies and single crystal X-ray crystallography. The characteristic resonance signals in 1H NMR and 13C NMR spectra indicated the presence of azomethine group as a result of condensation reaction. The stoichiometry, bonding and stereochemistries of complexes were ascertained on the basis of results of elemental analysis, magnetic susceptibility measurements, molar conductance and spectroscopic studies viz., FT-IR, 1H and 13C NMR, UV-vis and EPR. EPR, UV-vis and magnetic moment data revealed an octahedral geometry for complexes with distortion in Cu(II) complex and conductivity data show 1:2 electrolytic nature of complexes. Absoption and fluorescence spectroscopic studies supported that Schiff base ligand L and its Co(II), Ni(II) and Cu(II) complexes exhibited significant binding to calf thymus DNA. The complexes exhibited higher affinity to calf thymus DNA than the free Schiff base ligand L.

  10. Nucleation and structural growth of cluster crystals

    NASA Astrophysics Data System (ADS)

    Leitold, Christian; Dellago, Christoph

    2016-08-01

    We study the nucleation of crystalline cluster phases in the generalized exponential model with exponent n = 4. Due to the finite value of this pair potential for zero separation, at high densities the system forms cluster crystals with multiply occupied lattice sites. Here, we investigate the microscopic mechanisms that lead to the formation of cluster crystals from a supercooled liquid in the low-temperature region of the phase diagram. Using molecular dynamics and umbrella sampling, we calculate the free energy as a function of the size of the largest crystalline nucleus in the system, and compare our results with predictions from classical nucleation theory. Employing bond-order parameters based on a Voronoi tessellation to distinguish different crystal structures, we analyze the average composition of crystalline nuclei. We find that even for conditions where a multiply occupied fcc crystal is the thermodynamically stable phase, the nucleation into bcc cluster crystals is strongly preferred. Furthermore, we study the particle mobility in the supercooled liquid and in the cluster crystal. In the cluster crystal, the motion of individual particles is captured by a simple reaction-diffusion model introduced previously to model the kinetics of hydrogen bonds.

  11. Nucleation and structural growth of cluster crystals.

    PubMed

    Leitold, Christian; Dellago, Christoph

    2016-08-21

    We study the nucleation of crystalline cluster phases in the generalized exponential model with exponent n = 4. Due to the finite value of this pair potential for zero separation, at high densities the system forms cluster crystals with multiply occupied lattice sites. Here, we investigate the microscopic mechanisms that lead to the formation of cluster crystals from a supercooled liquid in the low-temperature region of the phase diagram. Using molecular dynamics and umbrella sampling, we calculate the free energy as a function of the size of the largest crystalline nucleus in the system, and compare our results with predictions from classical nucleation theory. Employing bond-order parameters based on a Voronoi tessellation to distinguish different crystal structures, we analyze the average composition of crystalline nuclei. We find that even for conditions where a multiply occupied fcc crystal is the thermodynamically stable phase, the nucleation into bcc cluster crystals is strongly preferred. Furthermore, we study the particle mobility in the supercooled liquid and in the cluster crystal. In the cluster crystal, the motion of individual particles is captured by a simple reaction-diffusion model introduced previously to model the kinetics of hydrogen bonds. PMID:27544116

  12. The crystal structure and crystal chemistry of fernandinite and corvusite

    USGS Publications Warehouse

    Evans, H.T.; Post, J.E.; Ross, D.R.; Nelen, J.A.

    1994-01-01

    Using type material of fernandinite from Minasragra, Peru, and corvusite from the Jack Claim, La Sal Mountains, Utah, the properties and crystal chemistry of these minerals have been determined by Rietveld analysis of the powder X-ray-diffraction patterns. The crystal structure of both species is isotypic with the V2O5 -type layer first found for ??-Ag0.68V2O5; it consists of chains of VO6 octahedra linked by opposite corners (parallel to b) condensed by edge-sharing to form the layer. The vanadium has average valence 4.8, and the resulting layer-charge is balanced by varying amounts of Ca, Na, and K in the interlayer region accompanied by labile water. This study has confirmed the validity of fernandinite as a unique mineral species. It is closely related to corvusite, from which it is distinguished on the basis of the dominant interlayer cation: Ca for fernandinite, Na for curvusite. -Authors

  13. Spectroscopic Signatures and Structural Motifs of Dopamine: a Computational Study

    NASA Astrophysics Data System (ADS)

    Srivastava, Santosh Kumar; Singh, Vipin Bahadur

    2016-06-01

    Dopamine (DA) is an essential neurotransmitter in the central nervous system and it plays integral role in numerous brain functions including behaviour, cognition, emotion, working memory and associated learning. In the present work the conformational landscapes of neutral and protonated dopamine have been investigated in the gas phase and in aqueous solution by MP2 and DFT (M06-2X, ωB97X-D, B3LYP and B3LYP-D3) methods. Twenty lowest energy structures of neutral DA were subjected to geometry optimization and the gauche conformer, GIa, was found to be the lowest gas phase structure at the each level of theory in agreement with the experimental rotational spectroscopy. All folded gauche conformers (GI) where lone electron pair of the NH2 group is directed towards the π system of the aromatic ring ( 'non up' ) are found more stable in the gas phase. While in aqueous solution, all those gauche conformers (GII) where lone electron pair of the NH2 group is directed opposite from the π system of the aromatic ring ('up' structures) are stabilized significantly.Nine lowest energy structures, protonated at the amino group, are optimized at the same MP2/aug-cc-pVDZ level of theory. In the most stable gauche structures, g-1 and g+1, mainly electrostatic cation - π interaction is further stabilized by significant dispersion forces as predicted by the substantial differences between the DFT and dispersion corrected DFT-D3 calculations. In aqueous environment the intra-molecular cation- π distance in g-1 and g+1 isomers, slightly increases compared to the gas phase and the magnitude of the cation- π interaction is reduced relative to the gas phase, because solvation of the cation decreases its interaction energy with the π face of aromatic system. The IR intensity of the bound N-H+ stretching mode provides characteristic 'IR spectroscopic signatures' which can reflect the strength of cation- π interaction energy. The CC2 lowest lying S1 ( 1ππ* ) excited state of neutral

  14. Crystal structure of potassium sodium tartrate trihydrate

    SciTech Connect

    Egorova, A. E. Ivanov, V. A.; Somov, N. V.; Portnov, V. N.; Chuprunov, E. V.

    2011-11-15

    Crystals of potassium sodium tartrate trihydrate (dl-KNaC{sub 4}H{sub 4}O{sub 6} {center_dot} 3H{sub 2}O) were obtained from an aqueous solution. The crystal shape was described. The atomic structure of the compound was determined and compared with the known structures of dl-KNaC{sub 4}H{sub 4}O{sub 6} {center_dot} 4H{sub 2}O and l-KNaC{sub 4}H{sub 4}O{sub 6} {center_dot} 4H{sub 2}O.

  15. Structural and spectroscopic characterisation of a heme peroxidase from sorghum.

    PubMed

    Nnamchi, Chukwudi I; Parkin, Gary; Efimov, Igor; Basran, Jaswir; Kwon, Hanna; Svistunenko, Dimitri A; Agirre, Jon; Okolo, Bartholomew N; Moneke, Anene; Nwanguma, Bennett C; Moody, Peter C E; Raven, Emma L

    2016-03-01

    A cationic class III peroxidase from Sorghum bicolor was purified to homogeneity. The enzyme contains a high-spin heme, as evidenced by UV-visible spectroscopy and EPR. Steady state oxidation of guaiacol was demonstrated and the enzyme was shown to have higher activity in the presence of calcium ions. A Fe(III)/Fe(II) reduction potential of -266 mV vs NHE was determined. Stopped-flow experiments with H2O2 showed formation of a typical peroxidase Compound I species, which converts to Compound II in the presence of calcium. A crystal structure of the enzyme is reported, the first for a sorghum peroxidase. The structure reveals an active site that is analogous to those for other class I heme peroxidase, and a substrate binding site (assigned as arising from binding of indole-3-acetic acid) at the γ-heme edge. Metal binding sites are observed in the structure on the distal (assigned as a Na(+) ion) and proximal (assigned as a Ca(2+)) sides of the heme, which is consistent with the Ca(2+)-dependence of the steady state and pre-steady state kinetics. It is probably the case that the structural integrity (and, thus, the catalytic activity) of the sorghum enzyme is dependent on metal ion incorporation at these positions.

  16. Spectroscopic characteristics of the OSIRIS near-backscattering crystal analyser spectrometer on the ISIS pulsed neutron source.

    PubMed

    Telling, Mark T F; Campbell, Stuart I; Engberg, Dennis; Marero, David Martín y; Andersen, Ken H

    2005-03-21

    The OSIRIS neutron instrument on the ISIS pulsed source now affords the option of high-resolution quasi-elastic and inelastic neutron spectroscopy. In this paper, the performance of OSIRIS is presented, with the spectroscopic characteristics of the instrument being discussed in terms of energy resolution, signal to background ratio and neutron count rate. Recent improvements to the spectrometer are described, in particular the effect of cooling the crystal analysers close to liquid helium temperature to enhance the sensitivity of the instrument. The performance of OSIRIS is also likened to back-scattering, crystal analyser spectrometers at other neutron sources.

  17. Crystal structure of canagliflozin hemihydrate

    PubMed Central

    Liu, Kai-Hang; Gu, Jian-Ming; Hu, Xiu-Rong; Tang, Gu-Ping

    2016-01-01

    There are two canagliflozin mol­ecules (A and B) and one water mol­ecule in the asymmetric unit of the title compound, C24H25FO5S·0.5H2O [systematic name: (2S,3R,4R,5S,6R)-2-(3-{[5-(4-fluoro­phen­yl)thio­phen-2-yl]meth­yl}-4-methylphen­yl)-6-(hy­droxy­meth­yl)-3,4,5,6-tetra­hydro-2H-pyran-3,4,5-triol hemihydrate]. The dihedral angles between the methyl­benzene and thio­phene rings are 115.7 (4) and 111.7 (4)°, while the dihedral angles between the fluoro­benzene and thio­phene rings are 24.2 (6) and 20.5 (9)° in mol­ecules A and B, respectively. The hydro­pyran ring exhibits a chair conformation in both canagliflozin mol­ecules. In the crystal, the canagliflozin mol­ecules and lattice water mol­ecules are connected via O—H⋯O hydrogen bonds into a three-dimensional supra­molecular architecture. PMID:27308030

  18. Crystal structure of canagliflozin hemihydrate.

    PubMed

    Liu, Kai-Hang; Gu, Jian-Ming; Hu, Xiu-Rong; Tang, Gu-Ping

    2016-05-01

    There are two canagliflozin mol-ecules (A and B) and one water mol-ecule in the asymmetric unit of the title compound, C24H25FO5S·0.5H2O [systematic name: (2S,3R,4R,5S,6R)-2-(3-{[5-(4-fluoro-phen-yl)thio-phen-2-yl]meth-yl}-4-methylphen-yl)-6-(hy-droxy-meth-yl)-3,4,5,6-tetra-hydro-2H-pyran-3,4,5-triol hemihydrate]. The dihedral angles between the methyl-benzene and thio-phene rings are 115.7 (4) and 111.7 (4)°, while the dihedral angles between the fluoro-benzene and thio-phene rings are 24.2 (6) and 20.5 (9)° in mol-ecules A and B, respectively. The hydro-pyran ring exhibits a chair conformation in both canagliflozin mol-ecules. In the crystal, the canagliflozin mol-ecules and lattice water mol-ecules are connected via O-H⋯O hydrogen bonds into a three-dimensional supra-molecular architecture. PMID:27308030

  19. Characterization of spectroscopic and laser properties of Pr3+ in Sr5(PO4)3F crystal

    NASA Astrophysics Data System (ADS)

    Sardar, Dhiraj K.; Castano, Francisco

    2002-02-01

    Spectroscopic and laser properties have been characterized for Pr3+ incorporated into Sr5(PO4)3F crystal belonging to the apatite structure family. The standard Judd-Ofelt analysis has been applied to the measured optical absorption intensities to determine the radiative decay rates, branching ratios, and emission cross sections of principal intermanifold transitions of Pr3+ from the 1D2 and 3P0 states to the lower-lying manifolds in the visible region. The measured room temperature fluorescence lifetimes of the 1D2→3H4 (594 nm) and 3P0→3F2 (625 nm) transition are 325 and 105 μs, respectively, while the Judd-Ofelt analysis predicts the radiative lifetimes for the 1D2 and 3P0 states to be 822 and 116 μs, respectively. The room temperature emission cross sections of the 1D2→3H4 and 3P0→3F2 intermanifold transitions have been also determined to be 0.54×10-20 and 4.15×10-20 cm2, respectively.

  20. Computing stoichiometric molecular composition from crystal structures

    PubMed Central

    Gražulis, Saulius; Merkys, Andrius; Vaitkus, Antanas; Okulič-Kazarinas, Mykolas

    2015-01-01

    Crystallographic investigations deliver high-accuracy information about positions of atoms in crystal unit cells. For chemists, however, the structure of a molecule is most often of interest. The structure must thus be reconstructed from crystallographic files using symmetry information and chemical properties of atoms. Most existing algorithms faithfully reconstruct separate molecules but not the overall stoichiometry of the complex present in a crystal. Here, an algorithm that can reconstruct stoichiometrically correct multimolecular ensembles is described. This algorithm uses only the crystal symmetry information for determining molecule numbers and their stoichiometric ratios. The algorithm can be used by chemists and crystallographers as a standalone implementation for investigating above-molecular ensembles or as a function implemented in graphical crystal analysis software. The greatest envisaged benefit of the algorithm, however, is for the users of large crystallographic and chemical databases, since it will permit database maintainers to generate stoichiometrically correct chemical representations of crystal structures automatically and to match them against chemical databases, enabling multidisciplinary searches across multiple databases. PMID:26089747

  1. Structure-property evolution during polymer crystallization

    NASA Astrophysics Data System (ADS)

    Arora, Deepak

    The main theme of this research is to understand the structure-property evolution during crystallization of a semicrystalline thermoplastic polymer. A combination of techniques including rheology, small angle light scattering, differential scanning calorimetry and optical microscopy are applied to follow the mechanical and optical properties along with crystallinity and the morphology. Isothermal crystallization experiments on isotactic poly-1-butene at early stages of spherulite growth provide quantitative information about nucleation density, volume fraction of spherulites and their crystallinity, and the mechanism of connecting into a sample spanning structure. Optical microscopy near the fluid-to-solid transition suggests that the transition, as determined by time-resolved mechanical spectroscopy, is not caused by packing/jamming of spherulites but by the formation of a percolating network structure. The effect of strain, Weissenberg number (We ) and specific mechanical work (w) on rate of crystallization (nucleation followed by growth) and on growth of anisotropy was studied for shear-induced crystallization of isotactic poly-1-butene. The samples were sheared for a finite strain at the beginning of the experiment and then crystallized without further flow (Janeschitz-Kriegl protocol). Strain requirements to attain steady state/leveling off of the rate of crystallization were found to be much larger than the strain needed to achieve steady state of flow. The large strain and We>1 criteria were also observed for morphological transition from spherulitic growth to oriented growth. An apparatus for small angle light scattering (SALS) and light transmission measurements under shear was built and tested at the University of Massachusetts Amherst. As a new development, the polarization direction can be rotated by a liquid crystal polarization rotator (LCPR) with a short response time of 20 ms. The experiments were controlled and analyzed with a LabVIEW(TM) based

  2. Crystal structure of Arabidopsis thaliana cytokinin dehydrogenase

    SciTech Connect

    Bae, Euiyoung; Bingman, Craig A.; Bitto, Eduard; Aceti, David J.; Phillips, Jr., George N.

    2008-08-13

    Since first discovered in Zea mays, cytokinin dehydrogenase (CKX) genes have been identified in many plants including rice and Arabidopsis thaliana, which possesses CKX homologues (AtCKX1-AtCKX7). So far, the three-dimensional structure of only Z. mays CKX (ZmCKX1) has been determined. The crystal structures of ZmCKX1 have been solved in the native state and in complex with reaction products and a slowly reacting substrate. The structures revealed four glycosylated asparagine residues and a histidine residue covalently linked to FAD. Combined with the structural information, recent biochemical analyses of ZmCKX1 concluded that the final products of the reaction, adenine and a side chain aldehyde, are formed by nonenzymatic hydrolytic cleavage of cytokinin imine products resulting directly from CKX catalysis. Here, we report the crystal structure of AtCKX7 (gene locus At5g21482.1, UniProt code Q9FUJ1).

  3. Thorium and uranium diphosphonates: Syntheses, structures, and spectroscopic properties

    SciTech Connect

    Adelani, Pius O.; Albrecht-Schmitt, Thomas E.

    2012-08-15

    Four new thorium and uranium diphosphonate compounds, [H{sub 3}O]{l_brace}Th{sub 2}[C{sub 6}H{sub 4}(PO{sub 3}){sub 2}]{sub 2}F{r_brace} (Thbbp-1), An{sub 2}{l_brace}(O{sub 3}PC{sub 6}H{sub 4}PO{sub 3}H){sub 2}[C{sub 6}H{sub 4}(PO{sub 3}H){sub 2}]{r_brace} [An=Th(IV), U(IV)] (Thbbp-2)/(U4bbp), and [(C{sub 2}H{sub 5})(CH{sub 3}){sub 3}N][(UO{sub 2}){sub 3}(O{sub 3}PC{sub 6}H{sub 4}PO{sub 3}H){sub 2}F(H{sub 2}O)] (U6bbp) have been synthesized hydrothermally using 1,4-benzenebisphosphonic acid as ligand. The crystal structures of these compounds were determined by single crystal X-ray diffraction. Thbbp-1 and Thbbp-2 contain seven-coordinate Th(IV) within ThO{sub 6}F and ThO{sub 7} units with capped trigonal prismatic and capped octahedral geometries, respectively. U4bbp is isotypic with Thbbp-2. The structure of U6bbp contains U(VI) is the common seven-coordinate pentagonal bipyramid. - Graphical abstract: Coordination polyhedra and luminescence properties in thorium and uranium compounds. Highlights: Black-Right-Pointing-Pointer Three-dimensional thorium and uranium complexes. Black-Right-Pointing-Pointer Conversion of U(VI) to U(IV) under hydrothermal condition. Black-Right-Pointing-Pointer Unusual seven-coordinate thorium complexes exhibiting capped octahedral and capped trigonal prismatic geometries.

  4. Crystal structure of the eukaryotic ribosome.

    PubMed

    Ben-Shem, Adam; Jenner, Lasse; Yusupova, Gulnara; Yusupov, Marat

    2010-11-26

    Crystal structures of prokaryotic ribosomes have described in detail the universally conserved core of the translation mechanism. However, many facets of the translation process in eukaryotes are not shared with prokaryotes. The crystal structure of the yeast 80S ribosome determined at 4.15 angstrom resolution reveals the higher complexity of eukaryotic ribosomes, which are 40% larger than their bacterial counterparts. Our model shows how eukaryote-specific elements considerably expand the network of interactions within the ribosome and provides insights into eukaryote-specific features of protein synthesis. Our crystals capture the ribosome in the ratcheted state, which is essential for translocation of mRNA and transfer RNA (tRNA), and in which the small ribosomal subunit has rotated with respect to the large subunit. We describe the conformational changes in both ribosomal subunits that are involved in ratcheting and their implications in coordination between the two associated subunits and in mRNA and tRNA translocation.

  5. Shear induced structures in crystallizing cocoa butter

    NASA Astrophysics Data System (ADS)

    Mazzanti, Gianfranco; Guthrie, Sarah E.; Sirota, Eric B.; Marangoni, Alejandro G.; Idziak, Stefan H. J.

    2004-03-01

    Cocoa butter is the main structural component of chocolate and many cosmetics. It crystallizes in several polymorphs, called phases I to VI. We used Synchrotron X-ray diffraction to study the effect of shear on its crystallization. A previously unreported phase (phase X) was found and a crystallization path through phase IV under shear was observed. Samples were crystallized under shear from the melt in temperature controlled Couette cells, at final crystallization temperatures of 17.5^oC, 20^oC and 22.5^oC in Beamline X10A of NSLS. The formation of phase X was observed at low shear rates (90 s-1) and low crystallization temperature (17.5^oC), but was absent at high shear (720 s-1) and high temperature (20^oC). The d-spacing and melting point suggest that this new phase is a mixture rich on two of the three major components of cocoa butter. We also found that, contrary to previous reports, the transition from phase II to phase V can happen through the intermediate phase IV, at high shear rates and temperature.

  6. Linking vegetation structure, function and physiology through spectroscopic remote sensing

    NASA Astrophysics Data System (ADS)

    Serbin, S.; Singh, A.; Couture, J. J.; Shiklomanov, A. N.; Rogers, A.; Desai, A. R.; Kruger, E. L.; Townsend, P. A.

    2015-12-01

    Terrestrial ecosystem process models require detailed information on ecosystem states and canopy properties to properly simulate the fluxes of carbon (C), water and energy from the land to the atmosphere and assess the vulnerability of ecosystems to perturbations. Current models fail to adequately capture the magnitude, spatial variation, and seasonality of terrestrial C uptake and storage, leading to significant uncertainties in the size and fate of the terrestrial C sink. By and large, these parameter and process uncertainties arise from inadequate spatial and temporal representation of plant traits, vegetation structure, and functioning. With increases in computational power and changes to model architecture and approaches, it is now possible for models to leverage detailed, data rich and spatially explicit descriptions of ecosystems to inform parameter distributions and trait tradeoffs. In this regard, spectroscopy and imaging spectroscopy data have been shown to be invaluable observational datasets to capture broad-scale spatial and, eventually, temporal dynamics in important vegetation properties. We illustrate the linkage of plant traits and spectral observations to supply key data constraints for model parameterization. These constraints can come either in the form of the raw spectroscopic data (reflectance, absorbtance) or physiological traits derived from spectroscopy. In this presentation we highlight our ongoing work to build ecological scaling relationships between critical vegetation characteristics and optical properties across diverse and complex canopies, including temperate broadleaf and conifer forests, Mediterranean vegetation, Arctic systems, and agriculture. We focus on work at the leaf, stand, and landscape scales, illustrating the importance of capturing the underlying variability in a range of parameters (including vertical variation within canopies) to enable more efficient scaling of traits related to functional diversity of ecosystems.

  7. Crystal structure of monobasic sodium tartrate monohydrate

    SciTech Connect

    Titaeva, E. K. Somov, N. V.; Portnov, V. N.; Titaev, D. N.

    2015-01-15

    Crystals of a new polymorphic modification of monobasic sodium tartrate monohydrate NaHC{sub 4}H{sub 4}O{sub 6} · H{sub 2}O have been grown in a metasilicate gel. Their atomic structure is solved by X-ray diffraction.

  8. Structure analysis on synthetic emerald crystals

    NASA Astrophysics Data System (ADS)

    Lee, Pei-Lun; Lee, Jiann-Shing; Huang, Eugene; Liao, Ju-Hsiou

    2013-05-01

    Single crystals of emerald synthesized by means of the flux method were adopted for crystallographic analyses. Emerald crystals with a wide range of Cr3+-doping content up to 3.16 wt% Cr2O3 were examined by X-ray single crystal diffraction refinement method. The crystal structures of the emerald crystals were refined to R 1 (all data) of 0.019-0.024 and w R 2 (all data) of 0.061-0.073. When Cr3+ substitutes for Al3+, the main adjustment takes place in the Al-octahedron and Be-tetrahedron. The effect of substitution of Cr3+ for Al3+ in the beryl structure results in progressively lengthening of the Al-O distance, while the length of the other bonds remains nearly unchanged. The substitution of Cr3+ for Al3+ may have caused the expansion of a axis, while keeping the c axis unchanged in the emerald lattice. As a consequence, the Al-O-Si and Al-O-Be bonding angles are found to decrease, while the angle of Si-O-Be increases as the Al-O distance increases during the Cr replacement.

  9. Dithizone and its oxidation products: a DFT, spectroscopic, and X-ray structural study.

    PubMed

    von Eschwege, Karel G; Conradie, Jeanet; Kuhn, Annemarie

    2011-12-29

    Air oxidation of ortho-fluorodithizone resulted in the first X-ray resolved structure of a disulfide of dithizone, validating the last outstanding X-ray structure in the oxidation of dithizone, H(2)Dz, which proceeds via the disulfide, (HDz)(2), to the deprotonated dehydrodithizone tetrazolium salt, Dz. Density functional theory calculations established the energetically favored tautomers along the entire pathway; in gas phase and in polar as well as nonpolar solvent environments. DFT calculations using the classic pure OLYP and PW91, or the newer B3LYP hybrid functional, as well as MP2 calculations, yielded the lowest energy structures in agreement with corresponding experimental X-ray crystallographic results. Atomic charge distribution patterns confirmed the cyclization reaction pathway and crystal packing of Dz. Time dependent DFT for the first time gave satisfactory explanation for the solvatochromic properties of dithizone, pointing to different tautomers that give rise to the observed orange color in methanol and green in dichloromethane. Concentratochromism of H(2)Dz was observed in methanol. Computed orbitals and oscillators are in close agreement with UV-visible spectroscopic experimental results.

  10. Dithizone and its oxidation products: a DFT, spectroscopic, and X-ray structural study.

    PubMed

    von Eschwege, Karel G; Conradie, Jeanet; Kuhn, Annemarie

    2011-12-29

    Air oxidation of ortho-fluorodithizone resulted in the first X-ray resolved structure of a disulfide of dithizone, validating the last outstanding X-ray structure in the oxidation of dithizone, H(2)Dz, which proceeds via the disulfide, (HDz)(2), to the deprotonated dehydrodithizone tetrazolium salt, Dz. Density functional theory calculations established the energetically favored tautomers along the entire pathway; in gas phase and in polar as well as nonpolar solvent environments. DFT calculations using the classic pure OLYP and PW91, or the newer B3LYP hybrid functional, as well as MP2 calculations, yielded the lowest energy structures in agreement with corresponding experimental X-ray crystallographic results. Atomic charge distribution patterns confirmed the cyclization reaction pathway and crystal packing of Dz. Time dependent DFT for the first time gave satisfactory explanation for the solvatochromic properties of dithizone, pointing to different tautomers that give rise to the observed orange color in methanol and green in dichloromethane. Concentratochromism of H(2)Dz was observed in methanol. Computed orbitals and oscillators are in close agreement with UV-visible spectroscopic experimental results. PMID:22103321

  11. Crystal structure of a plectonemic RNA supercoil

    SciTech Connect

    Stagno, Jason R.; Ma, Buyong; Li, Jess; Altieri, Amanda S.; Byrd, R. Andrew; Ji, Xinhua

    2012-12-14

    Genome packaging is an essential housekeeping process in virtually all organisms for proper storage and maintenance of genetic information. Although the extent and mechanisms of packaging vary, the process involves the formation of nucleic-acid superstructures. Crystal structures of DNA coiled coils indicate that their geometries can vary according to sequence and/or the presence of stabilizers such as proteins or small molecules. However, such superstructures have not been revealed for RNA. Here we report the crystal structure of an RNA supercoil, which displays one level higher molecular organization than previously reported structures of DNA coiled coils. In the presence of an RNA-binding protein, two interlocking RNA coiled coils of double-stranded RNA, a 'coil of coiled coils', form a plectonemic supercoil. Molecular dynamics simulations suggest that protein-RNA interaction is required for the stability of the supercoiled RNA. This study provides structural insight into higher order packaging mechanisms of nucleic acids.

  12. Crystal structure of zwitterionic bisimidazolium sulfonates

    NASA Astrophysics Data System (ADS)

    Kohmoto, Shigeo; Okuyama, Shinpei; Yokota, Nobuyuki; Takahashi, Masahiro; Kishikawa, Keiki; Masu, Hyuma; Azumaya, Isao

    2012-05-01

    Crystal structures of three zwitterionic bisimidazolium salts 1-3 in which imidazolium sulfonate moieties were connected with aromatic linkers, p-xylylene, 4,4'-dimethylenebiphenyl, and phenylene, respectively, were examined. The latter two were obtained as hydrates. An S-shaped molecular structure in which the sulfonate moiety was placed on the imidazolium ring was observed for 1. A helical array of hydrated water molecules was obtained for 2 while a linear array of hydrated water molecules was observed for 3.

  13. Crystal Structure of Human Enterovirus 71

    SciTech Connect

    Plevka, Pavel; Perera, Rushika; Cardosa, Jane; Kuhn, Richard J.; Rossmann, Michael G.

    2013-04-08

    Enterovirus 71 is a picornavirus associated with fatal neurological illness in infants and young children. Here, we report the crystal structure of enterovirus 71 and show that, unlike in other enteroviruses, the 'pocket factor,' a small molecule that stabilizes the virus, is partly exposed on the floor of the 'canyon.' Thus, the structure of antiviral compounds may require a hydrophilic head group designed to interact with residues at the entrance of the pocket.

  14. Spectroscopic and structural investigation of oxocarbon salts with tetraalkylammonium ions

    NASA Astrophysics Data System (ADS)

    Georgopoulos, Stéfanos L.; Garcia, Humberto C.; Edwards, Howell G. M.; Cappa de Oliveira, Luiz Fernando

    2016-03-01

    In this study the synthesis, vibrational spectra (infrared and Raman) and crystal structures of three oxocarbon compounds with tetra-alkyl ammonium counter cations, namely [N(C3H7)4](HC4O4) (1), [N(C4H9)4]2[(C4O4) (H2C4O4)2] (2) and [N(C2H5)4]2(C5O5)·5H2O (3), have been reported. The supramolecular arrangement for all compounds as shown by x-ray diffraction indicate that strong donor (D)-acceptor (A) hydrogen bonds D-H…A are present in the dimer formation with monohydrogen squarate anion HC4O4- (2.503 Å) and for the trimer with two squaric acid moieties (H2C4O4) and the squarate dianion C4O42- (2.500 Å), for compounds 1 and 2, respectively. In contrast, compound 3 was stabilized through only averagely strong hydrogen bonds (2.735 Å) between all five oxygen atoms of the croconate dianion with different water molecules of crystallization of the supramolecular system. The presence of bands in the Raman spectrum at 1793 and 1670 cm-1 for compounds 1 and 2 have been assigned to the ν(Cdbnd O), ν(Cdbnd C) + ν(Cdbnd O) modes, thus confirming the oxocarbon presence in the solid structure, as well as the bands at 1716 and 1601 cm-1 for compound 3, assigned to the ν(Cdbnd O) and ν(CO) + ν(CC) + δ(CCC) + δ(CO) coupled modes of the associated croconate dianion (C5O52-). An important Raman signal observed for all structures can be seen at ca. 2950 cm-1 which is associated with the ν(CH2) and ν(CH3) stretching modes from the tetraalkylammonium cations.

  15. Photonic Crystal Laser-Driven Accelerator Structures

    SciTech Connect

    Cowan, Benjamin M.

    2007-08-22

    Laser-driven acceleration holds great promise for significantly improving accelerating gradient. However, scaling the conventional process of structure-based acceleration in vacuum down to optical wavelengths requires a substantially different kind of structure. We require an optical waveguide that (1) is constructed out of dielectric materials, (2) has transverse size on the order of a wavelength, and (3) supports a mode with speed-of-light phase velocity in vacuum. Photonic crystals---structures whose electromagnetic properties are spatially periodic---can meet these requirements. We discuss simulated photonic crystal accelerator structures and describe their properties. We begin with a class of two-dimensional structures which serves to illustrate the design considerations and trade-offs involved. We then present a three-dimensional structure, and describe its performance in terms of accelerating gradient and efficiency. We discuss particle beam dynamics in this structure, demonstrating a method for keeping a beam confined to the waveguide. We also discuss material and fabrication considerations. Since accelerating gradient is limited by optical damage to the structure, the damage threshold of the dielectric is a critical parameter. We experimentally measure the damage threshold of silicon for picosecond pulses in the infrared, and determine that our structure is capable of sustaining an accelerating gradient of 300 MV/m at 1550 nm. Finally, we discuss possibilities for manufacturing these structures using common microfabrication techniques.

  16. Crystal structure refinement from electron diffraction data

    SciTech Connect

    Dudka, A. P. Avilov, A. S.; Lepeshov, G. G.

    2008-05-15

    A procedure of crystal structure refinement from electron diffraction data is described. The electron diffraction data on polycrystalline films are processed taking into account possible overlap of reflections and two-beam interaction. The diffraction from individual single crystals in an electron microscope equipped with a precession attachment is described using the Bloch-wave method, which takes into account multibeam scattering, and a special approach taking into consideration the specific features of the diffraction geometry in the precession technique. Investigations were performed on LiF, NaF, CaF{sub 2}, and Si crystals. A method for reducing experimental data, which allows joint electron and X-ray diffraction study, is proposed.

  17. Crystal structure of riboflavin synthase

    SciTech Connect

    Liao, D.-I.; Wawrzak, Z.; Calabrese, J.C.; Viitanen, P.V.; Jordan, D.B.

    2010-03-05

    Riboflavin synthase catalyzes the dismutation of two molecules of 6,7-dimethyl-8-(1'-D-ribityl)-lumazine to yield riboflavin and 4-ribitylamino-5-amino-2,6-dihydroxypyrimidine. The homotrimer of 23 kDa subunits has no cofactor requirements for catalysis. The enzyme is nonexistent in humans and is an attractive target for antimicrobial agents of organisms whose pathogenicity depends on their ability to biosynthesize riboflavin. The first three-dimensional structure of the enzyme was determined at 2.0 {angstrom} resolution using the multiwavelength anomalous diffraction (MAD) method on the Escherichia coli protein containing selenomethionine residues. The homotrimer consists of an asymmetric assembly of monomers, each of which comprises two similar {beta} barrels and a C-terminal {alpha} helix. The similar {beta} barrels within the monomer confirm a prediction of pseudo two-fold symmetry that is inferred from the sequence similarity between the two halves of the protein. The {beta} barrels closely resemble folds found in phthalate dioxygenase reductase and other flavoproteins. The three active sites of the trimer are proposed to lie between pairs of monomers in which residues conserved among species reside, including two Asp-His-Ser triads and dyads of Cys-Ser and His-Thr. The proposed active sites are located where FMN (an analog of riboflavin) is modeled from an overlay of the {beta} barrels of phthalate dioxygenase reductase and riboflavin synthase. In the trimer, one active site is formed, and the other two active sites are wide open and exposed to solvent. The nature of the trimer configuration suggests that only one active site can be formed and be catalytically competent at a time.

  18. Crystal-Field and Covalency Effects in Uranates: An X-ray Spectroscopic Study.

    PubMed

    Butorin, Sergei M; Kvashnina, Kristina O; Smith, Anna L; Popa, Karin; Martin, Philippe M

    2016-07-01

    The electronic structure of U(V) - and U(VI) -containing uranates NaUO3 and Pb3 UO6 was studied by using an advanced technique, namely X-ray absorption spectroscopy (XAS) in high-energy-resolution fluorescence-detection (HERFD) mode. Due to a significant reduction in core-hole lifetime broadening, the crystal-field splittings of the 5f shell were probed directly in HERFD-XAS spectra collected at the U 3d edge, which is not possible by using conventional XAS. In addition, the charge-transfer satellites that result from U 5f-O 2p hybridization were clearly resolved. The crystal-field parameters, 5f occupancy, and degree of covalency of the chemical bonding in these uranates were estimated by using the Anderson impurity model by calculating the U 3d HERFD-XAS, conventional XAS, core-to-core (U 4f-3d transitions) resonant inelastic X-ray scattering (RIXS), and U 4f X-ray photoelectron spectra. The crystal field was found to be strong in these systems and the 5f occupancy was determined to be 1.32 and 0.84 electrons in the ground state for NaUO3 and Pb3 UO6 , respectively, which indicates a significant covalent character for these compounds. PMID:27257782

  19. The Surface Structure of Ground Metal Crystals

    NASA Technical Reports Server (NTRS)

    Boas, W.; Schmid, E.

    1944-01-01

    The changes produced on metallic surfaces as a result of grinding and polishing are not as yet fully understood. Undoubtedly there is some more or less marked change in the crystal structure, at least, in the top layer. Hereby a diffusion of separated crystal particles may be involved, or, on plastic material, the formation of a layer in greatly deformed state, with possible recrystallization in certain conditions. Czochralski verified the existence of such a layer on tin micro-sections by successive observations of the texture after repeated etching; while Thomassen established, roentgenographically by means of the Debye-Scherrer method, the existence of diffused crystal fractions on the surface of ground and polished tin bars, which he had already observed after turning (on the lathe). (Thickness of this layer - 0.07 mm). Whether this layer borders direct on the undamaged base material or whether deformed intermediate layers form the transition, nothing is known. One observation ty Sachs and Shoji simply states that after the turning of an alpha-brass crystal the disturbance starting from the surface, penetrates fairly deep (approx. 1 mm) into the crystal (proof by recrystallization at 750 C).

  20. Persistent hydrogen bonding in polymorphic crystal structures.

    PubMed

    Galek, Peter T A; Fábián, László; Allen, Frank H

    2009-02-01

    The significance of hydrogen bonding and its variability in polymorphic crystal structures is explored using new automated structural analysis methods. The concept of a chemically equivalent hydrogen bond is defined, which may be identified in pairs of structures, revealing those types of bonds that may persist, or not, in moving from one polymorphic form to another. Their frequency and nature are investigated in 882 polymorphic structures from the Cambridge Structural Database. A new method to compare conformations of equivalent molecules is introduced and applied to derive distinct subsets of conformational and packing polymorphs. The roles of chemical functionality and hydrogen-bond geometry in persistent interactions are systematically explored. Detailed structural comparisons reveal a large majority of persistent hydrogen bonds that are energetically crucial to structural stability. PMID:19155561

  1. The crystal structure of methane phase III

    NASA Astrophysics Data System (ADS)

    Neumann, Marcus A.; Press, Werner; Nöldeke, Christian; Asmussen, Bernd; Prager, Michael; Ibberson, Richard M.

    2003-07-01

    Methane is the simplest organic molecule, and like many supposedly simple molecular materials it has a rich phase diagram. While crystal structures could be determined for two of the solid phases, that of the low temperature phase III remained unsolved. Using high-resolution neutron powder diffraction and a direct-space Monte Carlo simulated annealing approach, this fundamental structure has now finally been solved. It is orthorhombic with space group Cmca, and 16 molecules in the unit cell. The structure is closely related to that of phase II, yet is no subgroup of it.

  2. Spectroscopic, thermal and X-ray structural study of the antiparasitic and antiviral drug nitazoxanide

    NASA Astrophysics Data System (ADS)

    Bruno, Flavia P.; Caira, Mino R.; Monti, Gustavo A.; Kassuha, Diego E.; Sperandeo, Norma R.

    2010-12-01

    Nitazoxanide [2-(acetyloxy)- N-(5-nitro-2-thiazolyl)benzamide, NTZ] is a potent antiparasitic and antiviral agent recently approved. The anti-protozoal activity of NTZ is believed to be due to interference with the pyruvate:ferredoxin oxidoreductase (PFOR) enzyme dependent electron transfer reaction. As drug-enzyme interactions are governed by the three-dimensional stereochemistry of both participants, the crystal structure of NTZ was determined for the first time to identify the conformational preferences that may be related to biological activity. NTZ crystallizes as the carboxamide tautomer in the orthorhombic system, space group Pna2 1 with the following parameters at 100(2) K: a = 14.302(2) Å, b = 5.2800(8) Å, c = 33.183(5) Å, V = 2505.8(6) Å 3, Z = 8, D x = 1.629 g cm -3, R = 0.0319, wR2 = 0.0799 for 5121 reflections. In addition, the spectroscopic and thermal properties were determined and related to the molecular structure. The 13C CPMAS NMR spectra showed resolved signals for each carbon of NTZ, some signals being broad due to residual dipolar interaction with quadrupolar 14N nuclei. In particular, the resonance at about 127 ppm showed multiplicity, indicating more than one molecule in the asymmetric unit and this is consistent with the crystallographic data. The DSC and TG data revealed that NTZ shows a single DSC melting peak with extrapolated onset at 201 °C which is accompanied by a TG weight loss, indicating that NTZ melts with decomposition.

  3. Coagulation factor XII protease domain crystal structure

    PubMed Central

    Pathak, M; Wilmann, P; Awford, J; Li, C; Hamad, BK; Fischer, PM; Dreveny, I; Dekker, LV; Emsley, J

    2015-01-01

    Background Coagulation factor XII is a serine protease that is important for kinin generation and blood coagulation, cleaving the substrates plasma kallikrein and FXI. Objective To investigate FXII zymogen activation and substrate recognition by determining the crystal structure of the FXII protease domain. Methods and results A series of recombinant FXII protease constructs were characterized by measurement of cleavage of chromogenic peptide and plasma kallikrein protein substrates. This revealed that the FXII protease construct spanning the light chain has unexpectedly weak proteolytic activity compared to β-FXIIa, which has an additional nine amino acid remnant of the heavy chain present. Consistent with these data, the crystal structure of the light chain protease reveals a zymogen conformation for active site residues Gly193 and Ser195, where the oxyanion hole is absent. The Asp194 side chain salt bridge to Arg73 constitutes an atypical conformation of the 70-loop. In one crystal form, the S1 pocket loops are partially flexible, which is typical of a zymogen. In a second crystal form of the deglycosylated light chain, the S1 pocket loops are ordered, and a short α-helix in the 180-loop of the structure results in an enlarged and distorted S1 pocket with a buried conformation of Asp189, which is critical for P1 Arg substrate recognition. The FXII structures define patches of negative charge surrounding the active site cleft that may be critical for interactions with inhibitors and substrates. Conclusions These data provide the first structural basis for understanding FXII substrate recognition and zymogen activation. PMID:25604127

  4. Spectroscopic characterisation and crystal field calculations of varicoloured kyanites from Loliondo, Tanzania

    NASA Astrophysics Data System (ADS)

    Wildner, Manfred; Beran, Anton; Koller, Friedrich

    2013-04-01

    Orange, ochre-coloured, light green and dark blue varieties of kyanite, ideally Al2SiO5, from Loliondo, Tanzania, have been characterised by electron microprobe analysis and polarised infrared and optical absorption spectroscopy. All colour varieties show elevated Fe contents of 0.39 to 1.31 wt.% FeO, but Ti contents only in the range of the EMP detection limit. Orange and ochre-coloured crystals have Mn contents of 0.23 and 0.06 wt.% MnO, respectively, the dark blue kyanite contains 0.28 wt.% Cr2O3, while the light green sample is nearly free from transition metal cations other than Fe. Polarised infrared spectra reveal OH defect concentrations of 3 to 17 wt.ppm H2O with structural OH defects partially replacing the OB (O2) oxygen atoms. Polarised optical absorption spectra show that the colour of all four varieties is governed by crystal field d-d transitions of trivalent cations, i.e. Fe3+ (all samples), Mn3+ (orange and ochre) and Cr3+ (blue kyanite), replacing Al in sixfold coordinated triclinic sites of the kyanite structure. Intervalence charge transfer, the prevalent colour-inducing mechanism in `usual' (Cr-poor) blue kyanites, seems to play a very minor, if any, role in the present samples. Crystal field calculations in both a `classic' tetragonal and in the semiempirical Superposition Model approach, accompanied by distance- and angle-least-squares refinements, indicate that Fe3+ preferably occupies the Al4 site, Cr3+ prefers the Al1 and Al2 sites, and Mn3+ predominantly enters the Al1 site. In each case specific local relaxation effects were observed according to the crystal chemical preferences of these transition metal cations. Furthermore, the high values obtained in the calculations for the interelectronic repulsion parameter Racah B correspond to a high ionic contribution to Me3+-O bonding in the kyanite structure. In the particular case of the blue sample, band positions specifically related to the high Racah B value enable this `unusual' type of

  5. Measurement of ionic polarization of SrTiO3 single crystal by far-infrared spectroscopic ellipsometry

    NASA Astrophysics Data System (ADS)

    Kanehara, Kazuki; Hoshina, Takuya; Takeda, Hiroaki; Tsurumi, Takaaki

    2014-07-01

    We developed a far-infrared spectroscopic ellipsometer for measuring the complex permittivity of high-permittivity materials in the terahertz (THz) region and demonstrated the dielectric function of SrTiO3 single crystal at 0.75-21 THz. The responses of the Slater, Last, and O6 displacive modes, which are all optical phonon modes of SrTiO3 at room temperature, were clearly observed. The complex permittivity measured by the ellipsometer agreed with the permittivity simulated by a damped harmonic oscillator model. The far-infrared spectroscopic ellipsometry is useful to analyze the phonon modes of high-permittivity materials, which enable us to understand the contribution of the ionic polarizations to the low-frequency permittivity.

  6. Synthesis, structural characterization, Hirshfeld surface analysis and spectroscopic studies of cadmium (II) chloride complex with 4-hydroxy-1-methylpiperidine

    NASA Astrophysics Data System (ADS)

    Soudani, S.; Ferretti, V.; Jelsch, C.; Lefebvre, F.; Nasr, C. Ben

    2016-05-01

    The chemical preparation, crystal structure, Hirshfeld surface analysis and spectroscopic characterization of the novel cadmium (II) 4-hydroxy-1-methylpiperidine complex, Cd4Cl10(C6H14NO)2·2H2O, have been reported. The atomic arrangement can be described as built up by an anionic framework, formed by edge sharing CdCl6 and CdCl5O octahedral linear chains spreading along the a-axis. These chains are interconnected by water molecules via O-H⋯Cl and O-H⋯O hydrogen bonds to form layers parallel to (011) plane. The organic cations are inserted between layers through C-H⋯Cl hydrogen bonds. Investigation of intermolecular interactions and crystal packing via Hirshfeld surface analysis reveals that the HC⋯Cl and HC⋯HC intermolecular interactions are the most abundant contacts of the organic cation in the crystal packing. The statistical analysis of crystal contacts reveals the driving forces in the packing formation. The 13C and 15N CP-MAS NMR spectra are in agreement with the X-ray structure. The vibrational absorption bands were identified by infrared spectroscopy. DFT calculations allowed the attribution of the NMR peaks and of the IR bands.

  7. Spectroscopic ellipsometry study of novel nanostructured transparent conducting oxide structures

    NASA Astrophysics Data System (ADS)

    Khosroabadi, Akram A.; Norwood, R. A.

    2013-02-01

    Spectroscopic ellipsometry has been used to find the optical constants, including refractive index, extinction coefficient, thickness and volume fraction of nanostructured transparent conducting oxides including indium tin oxide (ITO) and indium zinc oxide (IZO). We observed sharp features in the ellipsometry data, with the spectral peaks and positions depending on the nanostructure dimensions and material. A superposition of Lorentzian oscillators and the effective medium approximation has been applied to determine the volume ratio of voids and nanopillars, thereby providing the effective optical constants.

  8. Novel Approach for Clustering Zeolite Crystal Structures.

    PubMed

    Lach-Hab, M; Yang, S; Vaisman, I I; Blaisten-Barojas, E

    2010-04-12

    Informatics approaches play an increasingly important role in the design of new materials. In this work we apply unsupervised statistical learning for identifying four framework-type attractors of zeolite crystals in which several of the zeolite framework types are grouped together. Zeolites belonging to these super-classes manifest important topological, chemical and physical similarities. The zeolites form clusters located around four core framework types: LTA, FAU, MFI and the combination of EDI, HEU, LTL and LAU. Clustering is performed in a 9-dimensional space of attributes that reflect topological, chemical and physical properties for each individual zeolite crystalline structure. The implemented machine learning approach relies on hierarchical top-down clustering approach and the expectation maximization method. The model is trained and tested on ten partially independent data sets from the FIZ/NIST Inorganic Crystal Structure Database.

  9. Crystal structure, spectroscopic, magnetic and electronic structure studies of a novel Cu(II) amino acid complex [Cu(L-arg){sub 2}(H{sub 2}O)]{sub 2}(P{sub 4}O{sub 12}){center_dot}8H{sub 2}O

    SciTech Connect

    Hemissi, H.; Nasri, M.; Abid, S.; Al-Deyab, S.S.; Dhahri, E.; Hlil, E.K.; Rzaigui, M.

    2012-12-15

    Single crystals of a novel copper (II) complex with the amino acid L-arginine (L-arg) and cyclotetraphosphate, [Cu(L-arg){sub 2}(H{sub 2}O)]{sub 2}(P{sub 4}O{sub 12}){center_dot}8H{sub 2}O, were prepared in aqueous solution and were characterized by X-ray diffraction, spectroscopy (diffuse reflectance, UV-vis and IR) and thermal analysis. Magnetic measurements and electronic structure calculations were also performed. Crystal structure determination reveals that this compound has a nonsymmetrical atomic arrangement, containing mainly a binuclear [Cu(L-arg){sub 2}(H{sub 2}O)]{sub 2}{sup 4+} cation and an uncoordinated cyclotetraphosphate counter-anion (P{sub 4}O{sub 12}{sup 4-}). The tetravalent cation contains two independent Cu(II) ions in two different chemical environments. This compound exhibits an antiferromagnetic (AFM) to paramagnetic (PM) phase transition at a temperature (T{sub N}) lower than 2 K. The values of paramagnetic Curie-Weiss temperature ({theta}{sub cw}) and the exchange parameter (J/K{sub B}) emphasize the existence of an antiferromagnetic interaction between the neighboring copper ions. - Graphical abstract: The atomic arrangement of [Cu(L-arg){sub 2}(H{sub 2}O)]{sub 2}(P{sub 4}O{sub 12}){center_dot}8H{sub 2}O is built up of corrugated 2D-supramolecular layers and 1D-supramolecular anionic chain constructed by [P{sub 4}O{sub 12}(H{sub 2}O){sub 6}]{sub n}{sup 4n-}. Highlights: Black-Right-Pointing-Pointer Crystal structure of unusual cationic binuclear complex of [Cu(L-arg){sub 2}(H{sub 2}O)]{sub 2}(P{sub 4}O{sub 12}){center_dot}8H{sub 2}O. Black-Right-Pointing-Pointer An anti-syn equatorial-apical carboxylate bridging mode of both copper (II) centers. Black-Right-Pointing-Pointer [Cu(L-arg){sub 2}(H{sub 2}O)]{sub 2}{sup 4+} are held together by extensive H-bonds into wave-like layer. Black-Right-Pointing-Pointer Magnetic measurements exhibit an antiferomagnetic interaction between Cu(II). Black-Right-Pointing-Pointer Electronic structure

  10. Crystal structure of an archaeal actin homolog.

    PubMed

    Roeben, Annette; Kofler, Christine; Nagy, István; Nickell, Stephan; Hartl, F Ulrich; Bracher, Andreas

    2006-04-21

    Prokaryotic homologs of the eukaryotic structural protein actin, such as MreB and ParM, have been implicated in determination of bacterial cell shape, and in the segregation of genomic and plasmid DNA. In contrast to these bacterial actin homologs, little is known about the archaeal counterparts. As a first step, we expressed a predicted actin homolog of the thermophilic archaeon Thermoplasma acidophilum, Ta0583, and determined its crystal structure at 2.1A resolution. Ta0583 is expressed as a soluble protein in T.acidophilum and is an active ATPase at physiological temperature. In vitro, Ta0583 forms sheets with spacings resembling the crystal lattice, indicating an inherent propensity to form filamentous structures. The fold of Ta0583 contains the core structure of actin and clearly belongs to the actin/Hsp70 superfamily of ATPases. Ta0583 is approximately equidistant from actin and MreB on the structural level, and combines features from both eubacterial actin homologs, MreB and ParM. The structure of Ta0583 co-crystallized with ADP indicates that the nucleotide binds at the interface between the subdomains of Ta0583 in a manner similar to that of actin. However, the conformation of the nucleotide observed in complex with Ta0583 clearly differs from that in complex with actin, but closely resembles the conformation of ParM-bound nucleotide. On the basis of sequence and structural homology, we suggest that Ta0583 derives from a ParM-like actin homolog that was once encoded by a plasmid and was transferred into a common ancestor of Thermoplasma and Ferroplasma. Intriguingly, both genera are characterized by the lack of a cell wall, and therefore Ta0583 could have a function in cellular organization.

  11. Predicting polymeric crystal structures by evolutionary algorithms

    NASA Astrophysics Data System (ADS)

    Zhu, Qiang; Sharma, Vinit; Oganov, Artem R.; Ramprasad, Ramamurthy

    2014-10-01

    The recently developed evolutionary algorithm USPEX proved to be a tool that enables accurate and reliable prediction of structures. Here we extend this method to predict the crystal structure of polymers by constrained evolutionary search, where each monomeric unit is treated as a building block with fixed connectivity. This greatly reduces the search space and allows the initial structure generation with different sequences and packings of these blocks. The new constrained evolutionary algorithm is successfully tested and validated on a diverse range of experimentally known polymers, namely, polyethylene, polyacetylene, poly(glycolic acid), poly(vinyl chloride), poly(oxymethylene), poly(phenylene oxide), and poly (p-phenylene sulfide). By fixing the orientation of polymeric chains, this method can be further extended to predict the structures of complex linear polymers, such as all polymorphs of poly(vinylidene fluoride), nylon-6 and cellulose. The excellent agreement between predicted crystal structures and experimentally known structures assures a major role of this approach in the efficient design of the future polymeric materials.

  12. Spectroscopic and laser properties of SrMoO4:Tm3+ crystal under 1700-nm laser diode pumping

    NASA Astrophysics Data System (ADS)

    Doroshenko, M. E.; Papashvili, A. G.; Dunaeva, E. E.; Ivleva, L. I.; Osiko, V. V.; Jelinkova, H.; Sulc, J.; Nemec, M.

    2016-10-01

    Spectroscopic and laser properties of Tm3+ ions under 1700 nm excitation in SrMoO4 crystal are investigated. Negligible effect of cross-relaxation process (3H4sbnd 3F4, 3H6sbnd 3F4) on population of 3F4 level for thulium concentrations up to 0.25 at.% was demonstrated. Efficient lasing with slope efficiency up to 18% and broadband (over 100 nm) tuning at room temperature under 1700 nm diode pumping were obtained.

  13. Solvate Structures and Computational/Spectroscopic Characterization of LiPF6 Electrolytes

    SciTech Connect

    Han, Sang D.; Yun, Sung-Hyun; Borodin, Oleg; Seo, D. M.; Sommer, Roger D.; Young, Victor G.; Henderson, Wesley A.

    2015-04-23

    Raman spectroscopy is a powerful method for identifying ion-ion interactions, but only if the vibrational band signature for the anion coordination modes can be accurately deciphered. The present study characterizes the PF6- anion P-F Raman symmetric stretching vibrational band for evaluating the PF6-...Li+ cation interactions within LiPF6 crystalline solvates to create a characterization tool for liquid electrolytes. To facilitate this, the crystal structures for two new solvates—(G3)1:LiPF6 and (DEC)2:LiPF6 with triglyme and diethyl carbonate, respectively—are reported. The information obtained from this analysis provides key guidance about the ionic association information which may be obtained from a Raman spectroscopic evaluation of electrolytes containing the LiPF6 salt and aprotic solvents. Of particular note is the overlap of the Raman bands for both solvent-separated ion pair (SSIP) and contact ion pair (CIP) coordination in which the PF6- anions are uncoordinated or coordinated to a single Li+ cation, respectively.

  14. Fourier Analysis and Structure Determination--Part III: X-ray Crystal Structure Analysis.

    ERIC Educational Resources Information Center

    Chesick, John P.

    1989-01-01

    Discussed is single crystal X-ray crystal structure analysis. A common link between the NMR imaging and the traditional X-ray crystal structure analysis is reported. Claims that comparisons aid in the understanding of both techniques. (MVL)

  15. Crystal growth and vibrational spectroscopic studies of the semiorganic non-linear optical crystal--bisthiourea magnesium sulphate.

    PubMed

    Krishnakumar, V; Ramachandraraja, C; Sundararajan, R S

    2007-09-01

    The semiorganic non-linear optical crystal bisthiourea magnesium sulphate (BTMS) was grown by slow evaporation technique using water as solvent. Vibrational spectra were recorded to determine the symmetries of molecular vibrations. The observed Raman and infrared bands were also assigned and discussed. The optical transmission spectral study was carried out to test the transmitting ability of the crystal in the visible range. The second harmonic generation test of BTMS revealed the non-linear nature of the crystal. The TGA/DTA curve was also recorded for the experimental crystal. PMID:17185029

  16. Determining crystal structures through crowdsourcing and coursework

    NASA Astrophysics Data System (ADS)

    2016-09-01

    We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality.

  17. Determining crystal structures through crowdsourcing and coursework.

    PubMed

    Horowitz, Scott; Koepnick, Brian; Martin, Raoul; Tymieniecki, Agnes; Winburn, Amanda A; Cooper, Seth; Flatten, Jeff; Rogawski, David S; Koropatkin, Nicole M; Hailu, Tsinatkeab T; Jain, Neha; Koldewey, Philipp; Ahlstrom, Logan S; Chapman, Matthew R; Sikkema, Andrew P; Skiba, Meredith A; Maloney, Finn P; Beinlich, Felix R M; Popović, Zoran; Baker, David; Khatib, Firas; Bardwell, James C A

    2016-09-16

    We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality.

  18. Determining crystal structures through crowdsourcing and coursework.

    PubMed

    Horowitz, Scott; Koepnick, Brian; Martin, Raoul; Tymieniecki, Agnes; Winburn, Amanda A; Cooper, Seth; Flatten, Jeff; Rogawski, David S; Koropatkin, Nicole M; Hailu, Tsinatkeab T; Jain, Neha; Koldewey, Philipp; Ahlstrom, Logan S; Chapman, Matthew R; Sikkema, Andrew P; Skiba, Meredith A; Maloney, Finn P; Beinlich, Felix R M; Popović, Zoran; Baker, David; Khatib, Firas; Bardwell, James C A

    2016-01-01

    We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality. PMID:27633552

  19. Determining crystal structures through crowdsourcing and coursework

    PubMed Central

    Horowitz, Scott; Koepnick, Brian; Martin, Raoul; Tymieniecki, Agnes; Winburn, Amanda A.; Cooper, Seth; Flatten, Jeff; Rogawski, David S.; Koropatkin, Nicole M.; Hailu, Tsinatkeab T.; Jain, Neha; Koldewey, Philipp; Ahlstrom, Logan S.; Chapman, Matthew R.; Sikkema, Andrew P.; Skiba, Meredith A.; Maloney, Finn P.; Beinlich, Felix R. M.; Caglar, Ahmet; Coral, Alan; Jensen, Alice Elizabeth; Lubow, Allen; Boitano, Amanda; Lisle, Amy Elizabeth; Maxwell, Andrew T.; Failer, Barb; Kaszubowski, Bartosz; Hrytsiv, Bohdan; Vincenzo, Brancaccio; de Melo Cruz, Breno Renan; McManus, Brian Joseph; Kestemont, Bruno; Vardeman, Carl; Comisky, Casey; Neilson, Catherine; Landers, Catherine R.; Ince, Christopher; Buske, Daniel Jon; Totonjian, Daniel; Copeland, David Marshall; Murray, David; Jagieła, Dawid; Janz, Dietmar; Wheeler, Douglas C.; Cali, Elie; Croze, Emmanuel; Rezae, Farah; Martin, Floyd Orville; Beecher, Gil; de Jong, Guido Alexander; Ykman, Guy; Feldmann, Harald; Chan, Hugo Paul Perez; Kovanecz, Istvan; Vasilchenko, Ivan; Connellan, James C.; Borman, Jami Lynne; Norrgard, Jane; Kanfer, Jebbie; Canfield, Jeffrey M.; Slone, Jesse David; Oh, Jimmy; Mitchell, Joanne; Bishop, John; Kroeger, John Douglas; Schinkler, Jonas; McLaughlin, Joseph; Brownlee, June M.; Bell, Justin; Fellbaum, Karl Willem; Harper, Kathleen; Abbey, Kirk J.; Isaksson, Lennart E.; Wei, Linda; Cummins, Lisa N.; Miller, Lori Anne; Bain, Lyn; Carpenter, Lynn; Desnouck, Maarten; Sharma, Manasa G.; Belcastro, Marcus; Szew, Martin; Szew, Martin; Britton, Matthew; Gaebel, Matthias; Power, Max; Cassidy, Michael; Pfützenreuter, Michael; Minett, Michele; Wesselingh, Michiel; Yi, Minjune; Cameron, Neil Haydn Tormey; Bolibruch, Nicholas I.; Benevides, Noah; Kathleen Kerr, Norah; Barlow, Nova; Crevits, Nykole Krystyne; Dunn, Paul; Roque, Paulo Sergio Silveira Belo Nascimento; Riber, Peter; Pikkanen, Petri; Shehzad, Raafay; Viosca, Randy; James Fraser, Robert; Leduc, Robert; Madala, Roman; Shnider, Scott; de Boisblanc, Sharon; Butkovich, Slava; Bliven, Spencer; Hettler, Stephen; Telehany, Stephen; Schwegmann, Steven A.; Parkes, Steven; Kleinfelter, Susan C.; Michael Holst, Sven; van der Laan, T. J. A.; Bausewein, Thomas; Simon, Vera; Pulley, Warwick; Hull, William; Kim, Annes Yukyung; Lawton, Alexis; Ruesch, Amanda; Sundar, Anjali; Lawrence, Anna-Lisa; Afrin, Antara; Maheshwer, Bhargavi; Turfe, Bilal; Huebner, Christian; Killeen, Courtney Elizabeth; Antebi-Lerrman, Dalia; Luan, Danny; Wolfe, Derek; Pham, Duc; Michewicz, Elaina; Hull, Elizabeth; Pardington, Emily; Galal, Galal Osama; Sun, Grace; Chen, Grace; Anderson, Halie E.; Chang, Jane; Hewlett, Jeffrey Thomas; Sterbenz, Jennifer; Lim, Jiho; Morof, Joshua; Lee, Junho; Inn, Juyoung Samuel; Hahm, Kaitlin; Roth, Kaitlin; Nair, Karun; Markin, Katherine; Schramm, Katie; Toni Eid, Kevin; Gam, Kristina; Murphy, Lisha; Yuan, Lucy; Kana, Lulia; Daboul, Lynn; Shammas, Mario Karam; Chason, Max; Sinan, Moaz; Andrew Tooley, Nicholas; Korakavi, Nisha; Comer, Patrick; Magur, Pragya; Savliwala, Quresh; Davison, Reid Michael; Sankaran, Roshun Rajiv; Lewe, Sam; Tamkus, Saule; Chen, Shirley; Harvey, Sho; Hwang, Sin Ye; Vatsia, Sohrab; Withrow, Stefan; Luther, Tahra K; Manett, Taylor; Johnson, Thomas James; Ryan Brash, Timothy; Kuhlman, Wyatt; Park, Yeonjung; Popović, Zoran; Baker, David; Khatib, Firas; Bardwell, James C. A.

    2016-01-01

    We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality. PMID:27633552

  20. Crystal structure of MboIIA methyltransferase.

    SciTech Connect

    Osipiuk, J.; Walsh, M. A.; Joachimiak, A.; Biosciences Division; Univ. of Gdansk; Medical Research Council France

    2003-09-15

    DNA methyltransferases (MTases) are sequence-specific enzymes which transfer a methyl group from S-adenosyl-L-methionine (AdoMet) to the amino group of either cytosine or adenine within a recognized DNA sequence. Methylation of a base in a specific DNA sequence protects DNA from nucleolytic cleavage by restriction enzymes recognizing the same DNA sequence. We have determined at 1.74 {angstrom} resolution the crystal structure of a {beta}-class DNA MTase MboIIA (M {center_dot} MboIIA) from the bacterium Moraxella bovis, the smallest DNA MTase determined to date. M {center_dot} MboIIA methylates the 3' adenine of the pentanucleotide sequence 5'-GAAGA-3'. The protein crystallizes with two molecules in the asymmetric unit which we propose to resemble the dimer when M {center_dot} MboIIA is not bound to DNA. The overall structure of the enzyme closely resembles that of M {center_dot} RsrI. However, the cofactor-binding pocket in M {center_dot} MboIIA forms a closed structure which is in contrast to the open-form structures of other known MTases.

  1. Crystal Structure of the 30S Ribosomal Subunit from Thermus Thermophilus. Purification, Crystallization and Structure Determination

    SciTech Connect

    Clemons, William M.; Brodersen, Ditlev E.; McCutcheonn, John P.; May, Joanna L.C.; Carter, Andrew P.; Morgan-Warren, Robert J.; Wimberly, Brian T.; Ramakrishnan, Venki

    2009-10-07

    We describe the crystallization and structure determination of the 30 S ribosomal subunit from Thermus thermophilus. Previous reports of crystals that diffracted to 10 {angstrom} resolution were used as a starting point to improve the quality of the diffraction. Eventually, ideas such as the addition of substrates or factors to eliminate conformational heterogeneity proved less important than attention to detail in yielding crystals that diffracted beyond 3 {angstrom} resolution. Despite improvements in technology and methodology in the last decade, the structure determination of the 30 S subunit presented some very challenging technical problems because of the size of the asymmetric unit, crystal variability and sensitivity to radiation damage. Some steps that were useful for determination of the atomic structure were: the use of anomalous scattering from the LIII edges of osmium and lutetium to obtain the necessary phasing signal; the use of tunable, third-generation synchrotron sources to obtain data of reasonable quality at high resolution; collection of derivative data precisely about a mirror plane to preserve small anomalous differences between Bijvoet mates despite extensive radiation damage and multi-crystal scaling; the pre-screening of crystals to ensure quality, isomorphism and the efficient use of scarce third-generation synchrotron time; pre-incubation of crystals in cobalt hexaammine to ensure isomorphism with other derivatives; and finally, the placement of proteins whose structures had been previously solved in isolation, in conjunction with biochemical data on protein-RNA interactions, to map out the architecture of the 30 S subunit prior to the construction of a detailed atomic-resolution model.

  2. Stress-induced crystal-to-crystal transformations in high-density polyethylene-layered silicate nano-composites: a spectroscopic study.

    PubMed

    Tzavalas, Spiros; Gregoriou, Vasilis G

    2005-09-01

    High-density polyethylene (HDPE)-clay nano-composites have been prepared using the melt intercalation technique. Organically modified montmorillonite at various loadings (0.5--7%) was used as a nano-additive. Fourier transform infrared spectroscopy (FT-IR) was utilized for the first time to monitor the stress-induced crystal-to-crystal transformations of the polyethylene matrix with respect to the clay loading as well as to the degree of mechanical strain. In addition, polarized infrared measurements revealed information on both the orientation and the stress-induced distortion of the crystals. It was concluded that the crystal-to-crystal transformations are hindered by the presence of the clay, which also prevented the crystals from orienting even at low clay loadings (1%). Finally, X-ray diffraction (XRD) and differential scanning calorimetry (DSC) measurements confirmed the presence of the stress-induced crystalline structures in agreement with the infrared measurements.

  3. Spectroscopic and structural study of some 2,5-hexanedione bis(salicyloylhydrazone) complexes: Crystal structures of its Ni(II) and Cu(II) complexes and N-(2,5-dimethyl-1H-pyrrol-1-yl)-2-hydroxy-benzamide

    NASA Astrophysics Data System (ADS)

    Jeragh, Bakir; El-Asmy, Ahmed A.

    2014-08-01

    The reaction between 2,5-hexanedione and salicylic acid hydrazide produced two compounds: 2,5-hexanedione bis(salicyloylhydrazone) [HDSH] (ethanol insoluble) and N-(2,5-dimethyl-1H-pyrrol-1-yl)-2-hydroxybenzamide [DPH] (ethanol soluble). HDSH formed complexes with Co(II), Ni(II), Cu(II), Zn(II), Cd(II), Hg(II) and Pd(II) which are characterized by elemental analyses, spectra (IR, 1H NMR, ESR and MS), thermal and magnetic measurements. The crystals of [Ni(HDSH-2H)(EtOH)(H2O)] and [Cu(HDSH-2H)] were solved having octahedral and square-planar geometries, respectively. The other complexes have the formulae [Co(HDSH-2H)(H2O)2], [Cu(HDSH-H)2], [Zn(HDSH-2H)(H2O)2], [Cd2(HDSH-4H)(H2O)4], [Cd2(HDSH-2H)(H2O)4Cl2]; [Hg(HDSH-2H)] and [Pd2(HDSH-4H)(H2O)4]. The obtained complexes are stable in air and non-hygroscopic. The magnetic moments and electronic spectra of the complexes provide different geometries. The ESR spectra support the mononuclear geometry for [Cu(HDSH-2H)] and [Cu(HDSH-H)2]. The thermal decomposition of the complexes revealed the coordinated waters as well as the end product which is in most cases the metal oxide. The crystal structure of N-(2,5-dimethyl-1H-pyrrol-1-yl)-2-hydroxybenzamide is solved by X-ray technique.

  4. Crystal structure prediction from first principles: The crystal structures of glycine

    NASA Astrophysics Data System (ADS)

    Lund, Albert M.; Pagola, Gabriel I.; Orendt, Anita M.; Ferraro, Marta B.; Facelli, Julio C.

    2015-04-01

    Here we present the results of our unbiased searches of glycine polymorphs obtained using the genetic algorithms search implemented in MGAC, modified genetic algorithm for crystals, coupled with the local optimization and energy evaluation provided by Quantum Espresso. We demonstrate that it is possible to predict the crystal structures of a biomedical molecule using solely first principles calculations. We were able to find all the ambient pressure stable glycine polymorphs, which are found in the same energetic ordering as observed experimentally and the agreement between the experimental and predicted structures is of such accuracy that the two are visually almost indistinguishable.

  5. Crystal Structure Prediction from First Principles: The Crystal Structures of Glycine

    PubMed Central

    Lund, Albert M.; Pagola, Gabriel I.; Orendt, Anita M.; Ferraro, Marta B.; Facelli, Julio C.

    2015-01-01

    Here we present the results of our unbiased searches of glycine polymorphs obtained using the Genetic Algorithms search implemented in Modified Genetic Algorithm for Crystals coupled with the local optimization and energy evaluation provided by Quantum Espresso. We demonstrate that it is possible to predict the crystal structures of a biomedical molecule using solely first principles calculations. We were able to find all the ambient pressure stable glycine polymorphs, which are found in the same energetic ordering as observed experimentally and the agreement between the experimental and predicted structures is of such accuracy that the two are visually almost indistinguishable. PMID:25843964

  6. Flowing crystals: nonequilibrium structure of foam.

    PubMed

    Garstecki, Piotr; Whitesides, George M

    2006-07-14

    Bubbles pushed through a quasi-two-dimensional channel self-organize into a variety of periodic lattices. The structures of these lattices correspond to local minima of the interfacial energy. The "flowing crystals" are long-lived metastable states, a small subset of possible local minima of confined quasi-two-dimensional foams [P. Garstecki and G. M. Whitesides, Phys. Rev. E 73, 031603 (2006)10.1103/PhysRevE.73.031603]. Experimental results suggest that the choice of the structures that we observe is dictated by the dynamic stability of the cyclic processes of their formation. Thus, the dynamic system that we report provides a unique example of nonequilibrium self-organization that results in structures that correspond to local minima of the relevant energy functional. PMID:16907453

  7. Crystal structure of plant photosystem I

    NASA Astrophysics Data System (ADS)

    Ben-Shem, Adam; Frolow, Felix; Nelson, Nathan

    2003-12-01

    Oxygenic photosynthesis is the principal producer of both oxygen and organic matter on Earth. The conversion of sunlight into chemical energy is driven by two multisubunit membrane protein complexes named photosystem I and II. We determined the crystal structure of the complete photosystem I (PSI) from a higher plant (Pisum sativum var. alaska) to 4.4Å resolution. Its intricate structure shows 12 core subunits, 4 different light-harvesting membrane proteins (LHCI) assembled in a half-moon shape on one side of the core, 45 transmembrane helices, 167 chlorophylls, 3 Fe-S clusters and 2 phylloquinones. About 20 chlorophylls are positioned in strategic locations in the cleft between LHCI and the core. This structure provides a framework for exploration not only of energy and electron transfer but also of the evolutionary forces that shaped the photosynthetic apparatus of terrestrial plants after the divergence of chloroplasts from marine cyanobacteria one billion years ago.

  8. Crystal structure of a DNA catalyst.

    PubMed

    Ponce-Salvatierra, Almudena; Wawrzyniak-Turek, Katarzyna; Steuerwald, Ulrich; Höbartner, Claudia; Pena, Vladimir

    2016-01-14

    Catalysis in biology is restricted to RNA (ribozymes) and protein enzymes, but synthetic biomolecular catalysts can also be made of DNA (deoxyribozymes) or synthetic genetic polymers. In vitro selection from synthetic random DNA libraries identified DNA catalysts for various chemical reactions beyond RNA backbone cleavage. DNA-catalysed reactions include RNA and DNA ligation in various topologies, hydrolytic cleavage and photorepair of DNA, as well as reactions of peptides and small molecules. In spite of comprehensive biochemical studies of DNA catalysts for two decades, fundamental mechanistic understanding of their function is lacking in the absence of three-dimensional models at atomic resolution. Early attempts to solve the crystal structure of an RNA-cleaving deoxyribozyme resulted in a catalytically irrelevant nucleic acid fold. Here we report the crystal structure of the RNA-ligating deoxyribozyme 9DB1 (ref. 14) at 2.8 Å resolution. The structure captures the ligation reaction in the post-catalytic state, revealing a compact folding unit stabilized by numerous tertiary interactions, and an unanticipated organization of the catalytic centre. Structure-guided mutagenesis provided insights into the basis for regioselectivity of the ligation reaction and allowed remarkable manipulation of substrate recognition and reaction rate. Moreover, the structure highlights how the specific properties of deoxyribose are reflected in the backbone conformation of the DNA catalyst, in support of its intricate three-dimensional organization. The structural principles underlying the catalytic ability of DNA elucidate differences and similarities in DNA versus RNA catalysts, which is relevant for comprehending the privileged position of folded RNA in the prebiotic world and in current organisms. PMID:26735012

  9. Crystal structure of a DNA catalyst.

    PubMed

    Ponce-Salvatierra, Almudena; Wawrzyniak-Turek, Katarzyna; Steuerwald, Ulrich; Höbartner, Claudia; Pena, Vladimir

    2016-01-14

    Catalysis in biology is restricted to RNA (ribozymes) and protein enzymes, but synthetic biomolecular catalysts can also be made of DNA (deoxyribozymes) or synthetic genetic polymers. In vitro selection from synthetic random DNA libraries identified DNA catalysts for various chemical reactions beyond RNA backbone cleavage. DNA-catalysed reactions include RNA and DNA ligation in various topologies, hydrolytic cleavage and photorepair of DNA, as well as reactions of peptides and small molecules. In spite of comprehensive biochemical studies of DNA catalysts for two decades, fundamental mechanistic understanding of their function is lacking in the absence of three-dimensional models at atomic resolution. Early attempts to solve the crystal structure of an RNA-cleaving deoxyribozyme resulted in a catalytically irrelevant nucleic acid fold. Here we report the crystal structure of the RNA-ligating deoxyribozyme 9DB1 (ref. 14) at 2.8 Å resolution. The structure captures the ligation reaction in the post-catalytic state, revealing a compact folding unit stabilized by numerous tertiary interactions, and an unanticipated organization of the catalytic centre. Structure-guided mutagenesis provided insights into the basis for regioselectivity of the ligation reaction and allowed remarkable manipulation of substrate recognition and reaction rate. Moreover, the structure highlights how the specific properties of deoxyribose are reflected in the backbone conformation of the DNA catalyst, in support of its intricate three-dimensional organization. The structural principles underlying the catalytic ability of DNA elucidate differences and similarities in DNA versus RNA catalysts, which is relevant for comprehending the privileged position of folded RNA in the prebiotic world and in current organisms.

  10. Spectroscopic studies of excitons in cuprous oxide: Natural crystals and synthetic thick films on magnesium oxide

    NASA Astrophysics Data System (ADS)

    Sun, Yi

    2001-10-01

    We observed exciton photoluminescence from Cu2O natural bulk crystals under two-photon excitation to the 1s, as well as to the 2s level, over a wide temperature range. The direct recombination emission, denoted as Xo, and a phonon- assisted, electric-dipole radiative transition involving G-12 longitudinal optical phonons, denoted as Xo- G-12 , were observed for 1s excitation. We have studied the angular (at 1.8K) and temperature (from 1.8K to 297K) dependence of the time integrated photoluminescence intensity of both emission features. For resonant pumping to the 1s level, the direct emission is strongly enhanced at low temperature. It is forward directed, however, with an angular width substantially larger than the divergence of the excitation beam; excitation to the 2s level (which subsequently decays into a 1s level) results in a more isotropic angular distribution of Xo emission. The lifetime of the Xo emission resulting from resonant excitation to the 1s level at 1.8K is ~2ns, shorter than the decay time of thermalized orthoexcitons. The results support the idea that resonant two-photon excitation to the 1s level results primarily in a quadrupole-orthoexciton-polariton formation. A theory involving the Green's function and coupled photon-exciton wave equations was developed to simulate the coherent polariton propagation. To study excitons in a spatially confined geometry, we developed an ex situ growth technique to obtain single-crystal like Cu2O thick films on MgO substrates. The optical absorption spectrum exhibits the exciton absorption series up to n = 5p at low temperature. 1s orthoexciton direct emission and phonon-assisted emission features were observed to split into three (on MgO (110)) and two (on MgO (111)) peaks. The distortion of film crystal structure and the effective Hamiltonian including a deformation potential were used to explain the energy level splitting and shift of the 1s orthoexcitons in Cu2O films. Cu2O dots and waveguides were also

  11. Synthesis, spectroscopic, structural characterization, electrochemical and antimicrobial activity studies of the Schiff base ligand and its transition metal complexes

    NASA Astrophysics Data System (ADS)

    Aslantaş, Mehmet; Kendi, Engin; Demir, Necmettin; Şabik, Ali E.; Tümer, Mehmet; Kertmen, Metin

    2009-10-01

    In this study, the Schiff base ligand trans-N,N'-bis[(2,4-dichlorophenyl) methylidene] cyclohexane-1,2-diamine (L) and its copper(II), nickel(II) and palladium(II) transition metal complexes were prepared and characterized by the analytical and spectroscopic methods. The 1H( 13C) NMR spectra of the ligand and its diamagnetic complexes were recorded in DMSO-d 6 solvent and obtained data confirm that the nitrogen atoms of the imine groups coordinated to the metal ions. Electrochemical properties of the ligand and its metal complexes were investigated in the DMF solvent at the 100 and 250 mV s -1 scan rates. The ligand and metal complexes showed both reversible and irreversible processes at these scan rates. The single crystal of the ligand (L) was obtained from MeOH solution, and its crystal structure was determined by X-ray diffraction. The C-H⋯Cl hydrogen bonding interactions in the molecule were seen which increase the stability of the crystal structure. The antimicrobial activity studies of the ligand and its metal complexes were carried out by using the various bacteria and fungi.

  12. Synthesis, spectroscopic and structural elucidation of 1-butyl-4-[2-(3,5-dimethoxy-4-hydroxyphenyl)ethenyl)]pyridinium chloride tetrahydrate

    NASA Astrophysics Data System (ADS)

    Koleva, B. B.; Kolev, T.; Lamshöft, M.; Mayer-Figge, H.; Sheldrick, W. S.; Spiteller, M.

    2009-12-01

    The novel chloride salt of 1-butyl-4-[2-(4-hydroxyphenyl)ethenyl)]pyridine ( 1), has been synthesized as the tetrahydrate and its structure and properties elucidated in detail spectroscopically, thermally and structurally, using single crystal X-ray diffraction, linear-polarized solid-state IR-spectroscopy, UV-spectroscopy and mass spectrometry. Quantum chemical calculations were performed with a view to supporting and explaining the experimental structural and spectroscopic data. The compound ( 1) crystallizes in triclinic P1¯ space group and its unit cell contains two independent 1-butyl-4-[2-(3,5-dimethoxy4-hydroxyphenyl)ethenyl)]pyridinium] cations, differing with respect to the butyl chain torsion angle for which values of 80.0(9)° and 173.6(3)° are observed. The cations and anions are joined into infinite layers, formed by two different dimers and including solvent molecules. Hydrogen bonds OH⋯OH 2 (2.814 Å), HOH⋯O(CH 3) (2.960 Å), OH⋯Cl (2.967 Å), HOH⋯Cl - (3.034, 3.188, 3.161 and 3.062 Å) and HOH⋯OH 2 (2.772 Å) are observed. For first time in the literature, we are reporting the crystal structure of the dye with the syring-fragment in the molecule. The spectroscopic properties of the novel compound are compared and with those of the corresponding quinoide form ( 2). Both the forms ( 1) and ( 2) are characterized by 21 and 140 nm solvatochromic effects depending of the type of the solvent. The UV-spectroscopic data in solution confirm the formation of classical H-aggregates in polar protic solvent mixture.

  13. Synthesis, structure, and spectroscopic characterization of three uranyl phosphates with unique structural units

    SciTech Connect

    Wylie, Ernest M.; Dawes, Colleen M.; Burns, Peter C.

    2012-12-15

    Single crystals of Zn{sub 4}(OH){sub 2}[(UO{sub 2})(PO{sub 4}){sub 2}(OH){sub 2}(H{sub 2}O)] (UZnP), Cs[(UO{sub 2})(HPO{sub 4})NO{sub 3}] (UCsP), and In{sub 3}[(UO{sub 2}){sub 2}(PO{sub 4}){sub 4}OH(H{sub 2}O){sub 6}].2H{sub 2}O (UInP) were obtained from hydrothermal reactions and have been structurally and chemically characterized. UZnP crystallizes in space group Pbcn, a=8.8817(7), b=6.6109(5), c=19.569(1) A; UCsP crystallizes in P-1, a=7.015(2), b=7.441(1), c=9.393(2) A, {alpha}=72.974(2), {beta}=74.261(2), {gamma}=79.498(2); and UInP crystallizes in P-1, a=7.9856(5), b=9.159(1), c=9.2398(6) A {alpha}=101.289(1), {beta}=114.642(1), {gamma}=99.203(2). The U{sup 6+} cations are present as (UO{sub 2}){sup 2+} uranyl ions coordinated by five O atoms to give pentagonal bipyramids. The structural unit in UZnP is a finite cluster containing a uranyl pentagonal bipyramid that shares corners with two phosphate tetrahedra. The structural unit in UCsP is composed of uranyl pentagonal bipyramids with one chelating nitrate group that are linked into chains by three bridging hydrogen phosphate tetrahedra. In UInP, the structural unit contains pairs of edge-sharing uranyl pentagonal bipyramids with two chelating phosphate tetrahedra that are linked into chains through two bridging phosphate tetrahedra. Indium octahedra link these uranyl phosphate chains into a 3-dimensional framework. All three compounds exhibit unique structural units that deviate from the typical layered structures observed in uranyl phosphate solid-state chemistry. - Graphical abstract: Three new uranyl phosphates with unique structural units are reported. Black-Small-Square Highlights: Black-Right-Pointing-Pointer Three new uranyl phosphates have been synthesized hydrothermally. Black-Right-Pointing-Pointer Single crystal analyses reveal unique structural units. Black-Right-Pointing-Pointer The dimensionality of these compounds deviate from typical U{sup 6+} layered structures.

  14. Engineering surface atomic structure of single-crystal cobalt (II) oxide nanorods for superior electrocatalysis

    PubMed Central

    Ling, Tao; Yan, Dong-Yang; Jiao, Yan; Wang, Hui; Zheng, Yao; Zheng, Xueli; Mao, Jing; Du, Xi-Wen; Hu, Zhenpeng; Jaroniec, Mietek; Qiao, Shi-Zhang

    2016-01-01

    Engineering the surface structure at the atomic level can be used to precisely and effectively manipulate the reactivity and durability of catalysts. Here we report tuning of the atomic structure of one-dimensional single-crystal cobalt (II) oxide (CoO) nanorods by creating oxygen vacancies on pyramidal nanofacets. These CoO nanorods exhibit superior catalytic activity and durability towards oxygen reduction/evolution reactions. The combined experimental studies, microscopic and spectroscopic characterization, and density functional theory calculations reveal that the origins of the electrochemical activity of single-crystal CoO nanorods are in the oxygen vacancies that can be readily created on the oxygen-terminated {111} nanofacets, which favourably affect the electronic structure of CoO, assuring a rapid charge transfer and optimal adsorption energies for intermediates of oxygen reduction/evolution reactions. These results show that the surface atomic structure engineering is important for the fabrication of efficient and durable electrocatalysts. PMID:27650485

  15. Engineering surface atomic structure of single-crystal cobalt (II) oxide nanorods for superior electrocatalysis.

    PubMed

    Ling, Tao; Yan, Dong-Yang; Jiao, Yan; Wang, Hui; Zheng, Yao; Zheng, Xueli; Mao, Jing; Du, Xi-Wen; Hu, Zhenpeng; Jaroniec, Mietek; Qiao, Shi-Zhang

    2016-09-21

    Engineering the surface structure at the atomic level can be used to precisely and effectively manipulate the reactivity and durability of catalysts. Here we report tuning of the atomic structure of one-dimensional single-crystal cobalt (II) oxide (CoO) nanorods by creating oxygen vacancies on pyramidal nanofacets. These CoO nanorods exhibit superior catalytic activity and durability towards oxygen reduction/evolution reactions. The combined experimental studies, microscopic and spectroscopic characterization, and density functional theory calculations reveal that the origins of the electrochemical activity of single-crystal CoO nanorods are in the oxygen vacancies that can be readily created on the oxygen-terminated {111} nanofacets, which favourably affect the electronic structure of CoO, assuring a rapid charge transfer and optimal adsorption energies for intermediates of oxygen reduction/evolution reactions. These results show that the surface atomic structure engineering is important for the fabrication of efficient and durable electrocatalysts.

  16. Engineering surface atomic structure of single-crystal cobalt (II) oxide nanorods for superior electrocatalysis.

    PubMed

    Ling, Tao; Yan, Dong-Yang; Jiao, Yan; Wang, Hui; Zheng, Yao; Zheng, Xueli; Mao, Jing; Du, Xi-Wen; Hu, Zhenpeng; Jaroniec, Mietek; Qiao, Shi-Zhang

    2016-01-01

    Engineering the surface structure at the atomic level can be used to precisely and effectively manipulate the reactivity and durability of catalysts. Here we report tuning of the atomic structure of one-dimensional single-crystal cobalt (II) oxide (CoO) nanorods by creating oxygen vacancies on pyramidal nanofacets. These CoO nanorods exhibit superior catalytic activity and durability towards oxygen reduction/evolution reactions. The combined experimental studies, microscopic and spectroscopic characterization, and density functional theory calculations reveal that the origins of the electrochemical activity of single-crystal CoO nanorods are in the oxygen vacancies that can be readily created on the oxygen-terminated {111} nanofacets, which favourably affect the electronic structure of CoO, assuring a rapid charge transfer and optimal adsorption energies for intermediates of oxygen reduction/evolution reactions. These results show that the surface atomic structure engineering is important for the fabrication of efficient and durable electrocatalysts. PMID:27650485

  17. Crystal structure of 2,2-dimethyl succinic acid.

    PubMed

    Ozcan, Yusuf; Osmanoğlu, Semsettin; Ide, Semra

    2003-08-01

    The title compound crystallizes triclinically in space group of P1. The C2-COOH and C3-COOH molecular groups are planar. The crystal structure is stabilized by the formation of intermolecular (O-HO) hydrogen bonds. PMID:12945684

  18. Structure and spectroscopic properties of low-lying states of the HOC(O)O radical.

    PubMed

    Linguerri, Roberto; Puzzarini, Cristina; Francisco, Joseph S

    2016-02-28

    The HOC(O)O radical is a product of the reaction of HOCO radicals with oxygen atoms. The present study provides theoretical prediction of critical spectroscopic features of this radical that should aid in its experimental characterization. Energies, structures, rotational constants, and harmonic frequencies are presented for the ground and two low-lying excited electronic states of HOC(O)O. The energies for the Ã(2)A″←X̃(2)A' and B̃(2)A'←X̃(2)A' electronic transitions are reported. The band origin of the B̃←X̃ transition of HOC(O)O is predicted to occur in the near infrared region of the spectrum at around 1.5 eV and it is suggested to be the most promising one for observing this radical spectroscopically. The structural and spectroscopic similarities between HOC(O)O and the isoelectronic radical FC(O)O are discussed. The abundance of experimental data on the FC(O)O radical should guide the spectroscopic characterization of HOC(O)O and serve as a benchmark for the structural and spectroscopic parameters obtained from theory.

  19. Synthesis, crystal growth, thermal and spectroscopic studies of acentric materials constructed from aminopyridines and 4-nitrophenol

    NASA Astrophysics Data System (ADS)

    Pavlovetc, Ilia M.; Draguta, Sergiu; Fokina, Maria I.; Timofeeva, Tatiana V.; Denisyuk, Igor Yu

    2016-03-01

    A series of single co-crystals of non-centrosymmetric complexes of different mono- and diaminopyridines, namely 4-aminopyridine, 3,4-diaminopyridine, 2-amino-6-methylpyridine, 2,6-diaminopyridine, 2-aminopyridine, with 4-nitrophenol were grown by slow evaporation technique from solution at constant temperature. Optical transparency in the region of 300-1100 nm was found to be suitable for nonlinear optical applications with cut off wavelengths at 420-474 nm for these co-crystals. Single crystal X-ray analysis confirms the non-centrosymmetric packing. Thermogravimetric and differential thermal analysis shows good thermal stability of the studied compounds with melting point at range 99-172 °C for different co-crystals. The second harmonic generation efficiency has been measured on single crystals by comparative SHG technique relative to KTP crystal. The nonlinear optical coefficient of the compounds was found to be up to 39 pm/V.

  20. Crystal structure of yeast Sco1

    SciTech Connect

    Abajian, Carnie; Rosenzweig, Amy C.

    2010-03-05

    The Sco family of proteins are involved in the assembly of the dinuclear CuA site in cytochrome c oxidase (COX), the terminal enzyme in aerobic respiration. These proteins, which are found in both eukaryotes and prokaryotes, are characterized by a conserved CXXXC sequence motif that binds copper ions and that has also been proposed to perform a thiol:disulfide oxidoreductase function. The crystal structures of Saccharomyces cerevisiae apo Sco1 (apo-ySco1) and Sco1 in the presence of copper ions (Cu-ySco1) were determined to 1.8- and 2.3-{angstrom} resolutions, respectively. Yeast Sco1 exhibits a thioredoxin-like fold, similar to that observed for human Sco1 and a homolog from Bacillus subtilis. The Cu-ySco1 structure, obtained by soaking apo-ySco1 crystals in copper ions, reveals an unexpected copper-binding site involving Cys181 and Cys216, cysteine residues present in ySco1 but not in other homologs. The conserved CXXXC cysteines, Cys148 and Cys152, can undergo redox chemistry in the crystal. An essential histidine residue, His239, is located on a highly flexible loop, denoted the Sco loop, and can adopt positions proximal to both pairs of cysteines. Interactions between ySco1 and its partner proteins yeast Cox17 and yeast COX2 are likely to occur via complementary electrostatic surfaces. This high-resolution model of a eukaryotic Sco protein provides new insight into Sco copper binding and function.

  1. Crystal Structure of Human DNA Methyltransferase 1.

    PubMed

    Zhang, Zhi-Min; Liu, Shuo; Lin, Krystal; Luo, Youfu; Perry, John Jefferson; Wang, Yinsheng; Song, Jikui

    2015-07-31

    DNMT1 (DNA methyltransferase 1) is responsible for propagating the DNA methylation patterns during DNA replication. DNMT1 contains, in addition to a C-terminal methyltransferase domain, a large N-terminal regulatory region that is composed of an RFTS (replication foci targeting sequence) domain, a CXXC zinc finger domain and a pair of BAH (bromo adjacent homology) domains. The regulatory domains of DNMT1 mediate a network of protein-protein and protein-DNA interactions to control the recruitment and enzymatic activity of DNMT1. Here we report the crystal structure of human DNMT1 with all the structural domains (hDNMT1, residues 351-1600) in complex with S-adenosyl-l-homocysteine at 2.62Å resolution. The RFTS domain directly associates with the methyltransferase domain, thereby inhibiting the substrate binding of hDNMT1. Through structural analysis, mutational, biochemical and enzymatic studies, we further identify that a linker sequence between the CXXC and BAH1 domains, aside from its role in the CXXC domain-mediated DNMT1 autoinhibition, serves as an important regulatory element in the RFTS domain-mediated autoinhibition. In comparison with the previously determined structure of mouse DNMT1, this study also reveals a number of distinct structural features that may underlie subtle functional diversity observed for the two orthologues. In addition, this structure provides a framework for understanding the functional consequence of disease-related hDNMT1 mutations.

  2. The crystal structure of vyuntspakhite: A redetermination

    NASA Astrophysics Data System (ADS)

    Yakubovich, O. V.; Steele, I. M.

    2009-09-01

    The crystal structure of the mineral vyuntspakhite (Y, TR)6{Al2(OH)3[H1.48Si1.88O7][SiO4][SiO3(OH)]}2( a = 5.7551(11) Å, b = 14.752(3) Å, c = 15.906(4) Å, β = 96.046(4)°, sp. gr. P21/ n, Z = 2), which had been established earlier in the pseudo-unit cell, is redetermined by X-ray diffraction ( R = 0.040, T = 100 K). The redetermination of the structure shows that pronounced pseudotranslation along the axis c' = c/3 is associated with the fact that Y( TR) atoms are related by a 1/3 translation along the [001] direction. Most of the hydrogen atoms are located. The crystal-chemical function of hydrogen bonds is analyzed. In the unit cell of vyuntspakhite, the cationic layers consisting of edge-sharing (Y, TR) eight-vertex polyhedra alternate along the b axis with mixed anionic layers composed of isolated Si tetrahedra (orthotetrahedra), Si2O7 double-tetrahedra (diortho) groups, Al five-vertex polyhedra, and Al2O8 double-tetrahedra groups linked by shared vertices and through hydrogen bonding.

  3. Fine crystal structure of porous corundum ceramics

    NASA Astrophysics Data System (ADS)

    Grigoriev, M. V.; Kulkov, S. N.

    2011-05-01

    The microstructure of corundum ceramics based on powders with a varying grain size has been investigated. Both commercial alumina powders and those fabricated by denitration of aluminum salts in a high-frequency discharge plasma were used. An increase in the plasma-chemical Al2O3 powder content in the sample was found to change the pore structure of the corundum ceramics from a high-porosity ceramic skeleton with a well-developed system of channel-forming pores to ceramics with isolated pores. The change in the pore structure was observed for 50% porosity and caused an increase in the level of crystal lattice microdistortions. An increase in the sintering temperature from 1200 to 1650°C is shown to be responsible for a two-fold increase in the average crystallite size and for annealing of lattice defects along grain boundaries.

  4. Crystal structure of mammalian acid sphingomyelinase

    PubMed Central

    Gorelik, Alexei; Illes, Katalin; Heinz, Leonhard X.; Superti-Furga, Giulio; Nagar, Bhushan

    2016-01-01

    Acid sphingomyelinase (ASMase, ASM, SMPD1) converts sphingomyelin into ceramide, modulating membrane properties and signal transduction. Inactivating mutations in ASMase cause Niemann–Pick disease, and its inhibition is also beneficial in models of depression and cancer. To gain a better understanding of this critical therapeutic target, we determined crystal structures of mammalian ASMase in various conformations. The catalytic domain adopts a calcineurin-like fold with two zinc ions and a hydrophobic track leading to the active site. Strikingly, the membrane interacting saposin domain assumes either a closed globular conformation independent from the catalytic domain, or an open conformation, which establishes an interface with the catalytic domain essential for activity. Structural mapping of Niemann–Pick mutations reveals that most of them likely destabilize the protein's fold. This study sheds light on the molecular mechanism of ASMase function, and provides a platform for the rational development of ASMase inhibitors and therapeutic use of recombinant ASMase. PMID:27435900

  5. Crystal structure of mammalian acid sphingomyelinase.

    PubMed

    Gorelik, Alexei; Illes, Katalin; Heinz, Leonhard X; Superti-Furga, Giulio; Nagar, Bhushan

    2016-01-01

    Acid sphingomyelinase (ASMase, ASM, SMPD1) converts sphingomyelin into ceramide, modulating membrane properties and signal transduction. Inactivating mutations in ASMase cause Niemann-Pick disease, and its inhibition is also beneficial in models of depression and cancer. To gain a better understanding of this critical therapeutic target, we determined crystal structures of mammalian ASMase in various conformations. The catalytic domain adopts a calcineurin-like fold with two zinc ions and a hydrophobic track leading to the active site. Strikingly, the membrane interacting saposin domain assumes either a closed globular conformation independent from the catalytic domain, or an open conformation, which establishes an interface with the catalytic domain essential for activity. Structural mapping of Niemann-Pick mutations reveals that most of them likely destabilize the protein's fold. This study sheds light on the molecular mechanism of ASMase function, and provides a platform for the rational development of ASMase inhibitors and therapeutic use of recombinant ASMase. PMID:27435900

  6. The Crystal Structure of Human Argonaute2

    SciTech Connect

    Schirle, Nicole T.; MacRae, Ian J.

    2012-07-18

    Argonaute proteins form the functional core of the RNA-induced silencing complexes that mediate RNA silencing in eukaryotes. The 2.3 angstrom resolution crystal structure of human Argonaute2 (Ago2) reveals a bilobed molecule with a central cleft for binding guide and target RNAs. Nucleotides 2 to 6 of a heterogeneous mixture of guide RNAs are positioned in an A-form conformation for base pairing with target messenger RNAs. Between nucleotides 6 and 7, there is a kink that may function in microRNA target recognition or release of sliced RNA products. Tandem tryptophan-binding pockets in the PIWI domain define a likely interaction surface for recruitment of glycine-tryptophan-182 (GW182) or other tryptophan-rich cofactors. These results will enable structure-based approaches for harnessing the untapped therapeutic potential of RNA silencing in humans.

  7. Structure, thermodynamics, and crystallization of amorphous hafnia

    SciTech Connect

    Luo, Xuhui; Demkov, Alexander A.

    2015-09-28

    We investigate theoretically amorphous hafnia using the first principles melt and quench method. We identify two types of amorphous structures of hafnia. Type I and type II are related to tetragonal and monoclinic hafnia, respectively. We find type II structure to show stronger disorder than type I. Using the phonon density of states, we calculate the specific heat capacity for type II amorphous hafnia. Using the nudged elastic band method, we show that the averaged transition barrier between the type II amorphous hafnia and monoclinic phase is approximately 0.09 eV/HfO{sub 2}. The crystallization temperature is estimated to be 421 K. The calculations suggest an explanation for the low thermal stability of amorphous hafnia.

  8. Crystal structure of human nicotinamide riboside kinase.

    PubMed

    Khan, Javed A; Xiang, Song; Tong, Liang

    2007-08-01

    Nicotinamide riboside kinase (NRK) has an important role in the biosynthesis of NAD(+) as well as the activation of tiazofurin and other NR analogs for anticancer therapy. NRK belongs to the deoxynucleoside kinase and nucleoside monophosphate (NMP) kinase superfamily, although the degree of sequence conservation is very low. We report here the crystal structures of human NRK1 in a binary complex with the reaction product nicotinamide mononucleotide (NMN) at 1.5 A resolution and in a ternary complex with ADP and tiazofurin at 2.7 A resolution. The active site is located in a groove between the central parallel beta sheet core and the LID and NMP-binding domains. The hydroxyl groups on the ribose of NR are recognized by Asp56 and Arg129, and Asp36 is the general base of the enzyme. Mutation of residues in the active site can abolish the catalytic activity of the enzyme, confirming the structural observations. PMID:17698003

  9. Crystal Structure of Human Nicotinamide Riboside Kinase

    SciTech Connect

    Khan,J.; Xiang, S.; Tong, L.

    2007-01-01

    Nicotinamide riboside kinase (NRK) has an important role in the biosynthesis of NAD{sup +} as well as the activation of tiazofurin and other NR analogs for anticancer therapy. NRK belongs to the deoxynucleoside kinase and nucleoside monophosphate (NMP) kinase superfamily, although the degree of sequence conservation is very low. We report here the crystal structures of human NRK1 in a binary complex with the reaction product nicotinamide mononucleotide (NMN) at 1.5 {angstrom} resolution and in a ternary complex with ADP and tiazofurin at 2.7 {angstrom} resolution. The active site is located in a groove between the central parallel {beta} sheet core and the LID and NMP-binding domains. The hydroxyl groups on the ribose of NR are recognized by Asp56 and Arg129, and Asp36 is the general base of the enzyme. Mutation of residues in the active site can abolish the catalytic activity of the enzyme, confirming the structural observations.

  10. Near Surface Structure of Organic Semiconductor Tetracene Single Crystal

    NASA Astrophysics Data System (ADS)

    Wakabayashi, Yusuke; Morisaki, Hazuki; Kimura, Tsuyoshi; Miwa, Kazumoto; Koretsune, Takashi; Takeya, Jun

    2014-03-01

    Electric conduction in organic crystals is highly anisotropic because of the anisotropic molecular orbitals. Crystal structure governs the transfer through the overlap integral among the highest occupied (or lowest unoccupied) molecular orbitals. In case of organic devices, the place where electrons conduct is the interface. Therefore, the surface structure of organic single crystals is relevant. Surface relaxation of the structure of rubrene single crystal was firstly observed by means of surface x-ray diffraction a few years ago. This time we performed similar measurement on tetracene single crystal, whose molecular shape has large similarity with rubrene while the crystal structure is very different. Tetracene single crystal was grown by the physical vapor transport method, and the surface x-ray diffraction experiments were performed at BL-3A and 4C of the Photon Factory, KEK, Japan. Obtained electron density profile shows a large structural deformation at the surface layer of tetracene.

  11. Prediction of binary hard-sphere crystal structures.

    PubMed

    Filion, Laura; Dijkstra, Marjolein

    2009-04-01

    We present a method based on a combination of a genetic algorithm and Monte Carlo simulations to predict close-packed crystal structures in hard-core systems. We employ this method to predict the binary crystal structures in a mixture of large and small hard spheres with various stoichiometries and diameter ratios between 0.4 and 0.84. In addition to known binary hard-sphere crystal structures similar to NaCl and AlB2, we predict additional crystal structures with the symmetry of CrB, gammaCuTi, alphaIrV, HgBr2, AuTe2, Ag2Se, and various structures for which an atomic analog was not found. In order to determine the crystal structures at infinite pressures, we calculate the maximum packing density as a function of size ratio for the crystal structures predicted by our GA using a simulated annealing approach. PMID:19518387

  12. Structural and spectroscopic investigations on deuteron glasses belonging to the potassium dihydrogen phosphate family

    SciTech Connect

    Choudhury, Rajul Ranjan Chitra, R.; Abraham, Geogy J.

    2015-06-24

    X-ray powder diffraction and Raman measurements were performed on the mixed crystals of deuterated potassium dihydrogen phosphate (DKDP) and deuterated ammonium dihydrogen phosphate (DADP) grown at our lab. These crystals are known to behave like deuteron glasses due to frustration between ferroelectric and antiferroelectric ordering. Both spectral as well as structural studies indicate that crystals belonging to the glassy regions of the crystal composition have stronger O-D-O hydrogen bonds as compared to those belong to the ferroelectric or antiferroelectric regions of the crystal composition.

  13. Structural Transitions in Cholesteric Liquid Crystal Droplets.

    PubMed

    Zhou, Ye; Bukusoglu, Emre; Martínez-González, José A; Rahimi, Mohammad; Roberts, Tyler F; Zhang, Rui; Wang, Xiaoguang; Abbott, Nicholas L; de Pablo, Juan J

    2016-07-26

    Confinement of cholesteric liquid crystals (ChLC) into droplets leads to a delicate interplay between elasticity, chirality, and surface energy. In this work, we rely on a combination of theory and experiments to understand the rich morphological behavior that arises from that balance. More specifically, a systematic study of micrometer-sized ChLC droplets is presented as a function of chirality and surface energy (or anchoring). With increasing chirality, a continuous transition is observed from a twisted bipolar structure to a radial spherical structure, all within a narrow range of chirality. During such a transition, a bent structure is predicted by simulations and confirmed by experimental observations. Simulations are also able to capture the dynamics of the quenching process observed in experiments. Consistent with published work, it is found that nanoparticles are attracted to defect regions on the surface of the droplets. For weak anchoring conditions at the nanoparticle surface, ChLC droplets adopt a morphology similar to that of the equilibrium helical phase observed for ChLCs in the bulk. As the anchoring strength increases, a planar bipolar structure arises, followed by a morphological transition to a bent structure. The influence of chirality and surface interactions are discussed in the context of the potential use of ChLC droplets as stimuli-responsive materials for reporting molecular adsorbates.

  14. Benzofuranyl Esters: Synthesis, Crystal Structure Determination, Antimicrobial and Antioxidant Activities.

    PubMed

    Kumar, C S Chidan; Then, Li Yee; Chia, Tze Shyang; Chandraju, Siddegowda; Win, Yip-Foo; Sulaiman, Shaida Fariza; Hashim, Nurul Shafiqah; Ooi, Kheng Leong; Quah, Ching Kheng; Fun, Hoong-Kun

    2015-09-11

    A series of five new 2-(1-benzofuran-2-yl)-2-oxoethyl 4-(un/substituted)benzoates 4(a-e), with the general formula of C₈H₅O(C=O)CH₂O(C=O)C₆H₄X, X = H, Cl, CH₃, OCH₃ or NO₂, was synthesized in high purity and good yield under mild conditions. The synthesized products 4(a-e) were characterized by FTIR, ¹H-, (13)C- and ¹H-(13)C HMQC NMR spectroscopic analysis and their 3D structures were confirmed by single-crystal X-ray diffraction studies. These compounds were screened for their antimicrobial and antioxidant activities. The tested compounds showed antimicrobial ability in the order of 4b < 4a < 4c < 4d < 4e and the highest potency with minimum inhibition concentration (MIC) value of 125 µg/mL was observed for 4e. The results of antioxidant activities revealed the highest activity for compound 4e (32.62% ± 1.34%) in diphenyl-2-picrylhydrazyl (DPPH) radical scavenging, 4d (31.01% ± 4.35%) in ferric reducing antioxidant power (FRAP) assay and 4a (27.11% ± 1.06%) in metal chelating (MC) activity.

  15. Synthesis, crystal growth and spectroscopic investigation of second order organic nonlinear optical single crystal: 2-chloro-N-[4-(dimethylamino)benzylidene]aniline.

    PubMed

    Balachandar, R K; Kalainathan, S

    2013-12-01

    Organic nonlinear optical (NLO) crystal 2-chloro-N-[4-(dimethylamino)benzylidene]aniline (2Cl4DBA) was synthesized and grown by restricted slow evaporation technique at room temperature using acetone as solvent with good degree of transparency. The lattice parameters were determined and found to be noncentrosymmetric orthorhombic system by single crystal X-ray diffraction. The crystalline nature of the synthesized material was recorded by the powder X-ray diffraction pattern. Molecular structure of the grown crystal was investigated by (1)H and (13)C NMR and functional groups were identified by FTIR spectrum analysis. The optical absorbance of the grown crystal was ascertained by recording UV-Visible spectrum. Thermal and physiochemical stability of the grown material was investigated by TG/DTA analysis. SHG efficiency was determined by Kurtz-Perry Powder SHG technique and found to be 4.2 and 1.54 times greater that of standard KDP and urea crystals respectively.

  16. Crystal structures of five 6-mercaptopurine derivatives.

    PubMed

    Gomes, Lígia R; Low, John Nicolson; Magalhães E Silva, Diogo; Cagide, Fernando; Borges, Fernanda

    2016-03-01

    The crystal structures of five 6-mercaptopurine derivatives, viz. 2-[(9-acetyl-9H-purin-6-yl)sulfan-yl]-1-(3-meth-oxy-phen-yl)ethan-1-one (1), C16H14N4O3S, 2-[(9-acetyl-9H-purin-6-yl)sulfan-yl]-1-(4-meth-oxy-phen-yl)ethan-1-one (2), C16H14N4O3S, 2-[(9-acetyl-9H-purin-6-yl)sulfan-yl]-1-(4-chloro-phen-yl)ethan-1-one (3), C15H11ClN4O2S, 2-[(9-acetyl-9H-purin-6-yl)sulfan-yl]-1-(4-bromo-phen-yl)ethan-1-one (4), C15H11BrN4O2S, and 1-(3-meth-oxy-phen-yl)-2-[(9H-purin-6-yl)sulfan-yl]ethan-1-one (5), C14H12N4O2S. Compounds (2), (3) and (4) are isomorphous and accordingly their mol-ecular and supra-molecular structures are similar. An analysis of the dihedral angles between the purine and exocyclic phenyl rings show that the mol-ecules of (1) and (5) are essentially planar but that in the case of the three isomorphous compounds (2), (3) and (4), these rings are twisted by a dihedral angle of approximately 38°. With the exception of (1) all mol-ecules are linked by weak C-H⋯O hydrogen bonds in their crystals. There is π-π stacking in all compounds. A Cambridge Structural Database search revealed the existence of 11 deposited compounds containing the 1-phenyl-2-sulfanyl-ethanone scaffold; of these, only eight have a cyclic ring as substituent, the majority of these being heterocycles. PMID:27006794

  17. Crystal structure of strontium dinickel iron orthophosphate

    PubMed Central

    Ouaatta, Said; Assani, Abderrazzak; Saadi, Mohamed; El Ammari, Lahcen

    2015-01-01

    The title compound, SrNi2Fe(PO4)3, synthesized by solid-state reaction, crystallizes in an ordered variant of the α-CrPO4 structure. In the asymmetric unit, two O atoms are in general positions, whereas all others atoms are in special positions of the space group Imma: the Sr cation and one P atom occupy the Wyckoff position 4e (mm2), Fe is on 4b (2/m), Ni and the other P atom are on 8g (2), one O atom is on 8h (m) and the other on 8i (m). The three-dimensional framework of the crystal structure is built up by [PO4] tetra­hedra, [FeO6] octa­hedra and [Ni2O10] dimers of edge-sharing octa­hedra, linked through common corners or edges. This structure comprises two types of layers stacked alternately along the [100] direction. The first layer is formed by edge-sharing octa­hedra ([Ni2O10] dimer) linked to [PO4] tetra­hedra via common edges while the second layer is built up from a strontium row followed by infinite chains of alternating [PO4] tetra­hedra and FeO6 octa­hedra sharing apices. The layers are held together through vertices of [PO4] tetra­hedra and [FeO6] octa­hedra, leading to the appearance of two types of tunnels parallel to the a- and b-axis directions in which the Sr cations are located. Each Sr cation is surrounded by eight O atoms. PMID:26594419

  18. On the structure of erythritol and L-threitol in the solid state: An infrared spectroscopic study

    NASA Astrophysics Data System (ADS)

    Jesus, A. J. Lopes; Redinha, J. S.

    2009-12-01

    FTIR spectra of crystalline erythritol and L-threitol were recorded between 4000 and 400 cm -1, at temperatures ranging from 298 K to 15 K. The most important bands were assigned by comparing the experimental and theoretical spectra. The latter were obtained from optimizations that started with the original crystal coordinates taken from the X-ray and neutron diffraction data, using the B3LYP/6-311++G(d, p) model chemistry. Spectra of the deuterated solids at 15 K were also used to help with the spectral assignments, particularly in the OH stretching region. The hydrogen bonding network of both isomers was the object of particular attention in the optimized conformations as well as in the crystalline solids. The possible existence of intramolecular hydrogen bonds in the optimized structures was checked by Atoms-In-Molecules (AIM) and Natural Bond Orbital (NBO) theories. A correlation between the spectroscopic results and the diffraction data was obtained.

  19. Growth and spectroscopic, thermodynamic and nonlinear optical studies of L-threonine phthalate crystal

    NASA Astrophysics Data System (ADS)

    Theras, J. Elberin Mary; Kalaivani, D.; Jayaraman, D.; Joseph, V.

    2015-10-01

    L-threonine phthalate (LTP) single crystal has been grown using a solution growth technique at room temperature. Single crystal X-ray diffraction analysis reveals that LTP crystallizes in monoclinic crystal system with space group C2/c. The optical absorption studies show that the crystal is transparent in the entire visible region with a cut-off wavelength 309 nm. The optical band gap is found to be 4.05 eV. The functional groups of the synthesized compound have been identified by FTIR spectral analysis. The functional groups present in the material were also confirmed by FT-RAMAN spectroscopy. Surface morphology and the presence of various elements were studied by SEM-EDAX analysis. The thermal stability of LTP single crystal has been analyzed by TGA/DTA studies. The thermodynamic parameters such as activation energy, entropy, enthalpy and Gibbs free energy were determined for the grown material using TG data and Coats-Redfern relation. Since the grown crystal is centrosymmetric, Z-Scan studies were carried out for analyzing the third order nonlinear optical property. The nonlinear absorption coefficient, nonlinear refractive index and susceptibility have been measured using Z-Scan technique.

  20. Crystal Structures of Respiratory Pathogen Neuraminidases

    SciTech Connect

    Hsiao, Y.; Parker, D; Ratner, A; Prince, A; Tong, L

    2009-01-01

    Currently there is pressing need to develop novel therapeutic agents for the treatment of infections by the human respiratory pathogens Pseudomonas aeruginosa and Streptococcus pneumoniae. The neuraminidases of these pathogens are important for host colonization in animal models of infection and are attractive targets for drug discovery. To aid in the development of inhibitors against these neuraminidases, we have determined the crystal structures of the P. aeruginosa enzyme NanPs and S. pneumoniae enzyme NanA at 1.6 and 1.7 {angstrom} resolution, respectively. In situ proteolysis with trypsin was essential for the crystallization of our recombinant NanA. The active site regions of the two enzymes are strikingly different. NanA contains a deep pocket that is similar to that in canonical neuraminidases, while the NanPs active site is much more open. The comparative studies suggest that NanPs may not be a classical neuraminidase, and may have distinct natural substrates and physiological functions. This work represents an important step in the development of drugs to prevent respiratory tract colonization by these two pathogens.

  1. Crystal structures of the human adiponectin receptors.

    PubMed

    Tanabe, Hiroaki; Fujii, Yoshifumi; Okada-Iwabu, Miki; Iwabu, Masato; Nakamura, Yoshihiro; Hosaka, Toshiaki; Motoyama, Kanna; Ikeda, Mariko; Wakiyama, Motoaki; Terada, Takaho; Ohsawa, Noboru; Hato, Masakatsu; Ogasawara, Satoshi; Hino, Tomoya; Murata, Takeshi; Iwata, So; Hirata, Kunio; Kawano, Yoshiaki; Yamamoto, Masaki; Kimura-Someya, Tomomi; Shirouzu, Mikako; Yamauchi, Toshimasa; Kadowaki, Takashi; Yokoyama, Shigeyuki

    2015-04-16

    Adiponectin stimulation of its receptors, AdipoR1 and AdipoR2, increases the activities of 5' AMP-activated protein kinase (AMPK) and peroxisome proliferator-activated receptor (PPAR), respectively, thereby contributing to healthy longevity as key anti-diabetic molecules. AdipoR1 and AdipoR2 were predicted to contain seven transmembrane helices with the opposite topology to G-protein-coupled receptors. Here we report the crystal structures of human AdipoR1 and AdipoR2 at 2.9 and 2.4 Å resolution, respectively, which represent a novel class of receptor structure. The seven-transmembrane helices, conformationally distinct from those of G-protein-coupled receptors, enclose a large cavity where three conserved histidine residues coordinate a zinc ion. The zinc-binding structure may have a role in the adiponectin-stimulated AMPK phosphorylation and UCP2 upregulation. Adiponectin may broadly interact with the extracellular face, rather than the carboxy-terminal tail, of the receptors. The present information will facilitate the understanding of novel structure-function relationships and the development and optimization of AdipoR agonists for the treatment of obesity-related diseases, such as type 2 diabetes. PMID:25855295

  2. The crystal structure Escherichia coli Spy.

    PubMed

    Kwon, Eunju; Kim, Dong Young; Gross, Carol A; Gross, John D; Kim, Kyeong Kyu

    2010-11-01

    Escherichia coli spheroplast protein y (EcSpy) is a small periplasmic protein that is homologous with CpxP, an inhibitor of the extracytoplasmic stress response. Stress conditions such as spheroplast formation induce the expression of Spy via the Cpx or the Bae two-component systems in E. coli, though the function of Spy is unknown. Here, we report the crystal structure of EcSpy, which reveals a long kinked hairpin-like structure of four α-helices that form an antiparallel dimer. The dimer contains a curved oval shape with a highly positively charged concave surface that may function as a ligand binding site. Sequence analysis reveals that Spy is highly conserved over the Enterobacteriaceae family. Notably, three conserved regions that contain identical residues and two LTxxQ motifs are placed at the horizontal end of the dimer structure, stabilizing the overall fold. CpxP also contains the conserved sequence motifs and has a predicted secondary structure similar to Spy, suggesting that Spy and CpxP likely share the same fold.

  3. Growth and spectroscopic characterization of Nd 3BWO 9 single crystal

    NASA Astrophysics Data System (ADS)

    Majchrowski, A.; Michalski, E.; Brenier, A.

    2003-01-01

    Pure and ytterbium-doped neodymium borotungstate (Nd 3BWO 9, and Nd 2.85Yb 0.15BWO 9, respectively) single crystals have been grown by means of high-temperature solution growth method from 15 mol% solution in PbO. The phase of both crystals was confirmed to be hexagonal with acentric space group P6 3. Absorption and luminescence spectra as well as decay time for 4F 3/2→ 4I 11/2 transition in neodymium borotungstate were measured and discussed. The obtained results show that Nd 3BWO 9 is suitable as high-neodymium-content laser crystal for microchip laser applications.

  4. Crystal Structure of the VS ribozyme

    PubMed Central

    Suslov, Nikolai B.; DasGupta, Saurja; Huang, Hao; Fuller, James R.; Lilley, David M.J.; Rice, Phoebe A.; Piccirilli, Joseph A.

    2015-01-01

    Varkud Satellite (VS) ribozyme mediates rolling circle replication of a plasmid found in the Neurospora mitochondria. We report crystal structures of this ribozyme at 3.1Å resolution, revealing an intertwined dimer formed by an exchange of substrate helices. Within each protomer, an arrangement of three-way helical junctions organizes seven helices into a global fold that creates a docking site for the substrate helix of the other protomer, resulting in the formation of two active sites in trans. This mode of RNA-RNA association resembles the process of domain swapping in proteins and has implications for RNA regulation and evolution. Within each active site, adenine and guanine nucleobases abut the scissile phosphate, poised to serve direct roles in catalysis. Similarities to the active sites of the hairpin and hammerhead ribozymes highlight the functional significance of active site features, underscore the ability of RNA to access functional architectures from distant regions of sequence space, and suggest convergent evolution. PMID:26414446

  5. Exploring structural phase transitions of ion crystals

    PubMed Central

    Yan, L. L.; Wan, W.; Chen, L.; Zhou, F.; Gong, S. J.; Tong, X.; Feng, M.

    2016-01-01

    Phase transitions have been a research focus in many-body physics over past decades. Cold ions, under strong Coulomb repulsion, provide a repealing paradigm of exploring phase transitions in stable confinement by electromagnetic field. We demonstrate various conformations of up to sixteen laser-cooled 40Ca+ ion crystals in a home-built surface-electrode trap, where besides the usually mentioned structural phase transition from the linear to the zigzag, two additional phase transitions to more complicated two-dimensional configurations are identified. The experimental observation agrees well with the numerical simulation. Heating due to micromotion of the ions is analysed by comparison of the numerical simulation with the experimental observation. Our investigation implies very rich and complicated many-body behaviour in the trapped-ion systems and provides effective mechanism for further exploring quantum phase transitions and quantum information processing with ultracold trapped ions. PMID:26865229

  6. Crystal structure of a snake venom cardiotoxin

    SciTech Connect

    Rees, B.; Samama, J.P.; Thierry, J.C.; Gilibert, M.; Fischer, J.; Schweitz, H.; Lazdunski, M.; Moras, D.

    1987-05-01

    Cardiotoxin V/sup II/4 from Naja mossambica crystallizes in space group P6/sub 1/ (a = b = 73.9 A; c = 59.0 A) with two molecules of toxin (molecular mass = 6715 Da) in the asymmetric unit. The structure was solved by using a combination of multiple isomorphous replacement and density modification methods. Model building and least-squares refinement led to an agreement factor of 27% for a data set to 3-A resolution prior to any inclusion of solvent molecules. The topology of the molecule is similar to that found in short and long snake neurotoxins, which block the nicotinic acetylcholine receptor. Major differences occur in the conformation of the central loop, resulting in a change in the concavity of the molecule. Hydrophobic residues are clustered in two distinct areas. The existence of stable dimeric entities in the crystalline state, with the formation of a six-stranded antiparallel ..beta.. sheet, may be functionally relevant.

  7. Infrared spectroscopic study of molecular hydrogen bonding in chiral smectic liquid crystals

    PubMed

    Jang; Park; Kim; Glaser; Clark

    2000-10-01

    We report the use of Fourier-transform infrared (IR) spectroscopy to probe intermolecular and intramolecular hydrogen bonding in thermotropic liquid-crystal phases. Infrared spectra of aligned smectic liquid crystal materials vs temperature, and of isotropic liquid-crystal mixtures vs concentration were measured in homologs both with and without hydrogen bonding. Hydrogen bonding significantly changes the direction and magnitude of the vibrational dipole transition moments, causing marked changes in the IR dichroic absorbance profiles of hydrogen-bonded molecular subfragments. A GAUSSIAN94 computation of the directions, magnitudes, and frequencies of the vibrational dipole moments of molecular subfragments shows good agreement with the experimental data. The results show that IR dichroism can be an effective probe of hydrogen bonding in liquid-crystal phases.

  8. Vibrational Spectroscopic Studies of Adsorbates on Metal and Silicon Single Crystal Surfaces.

    NASA Astrophysics Data System (ADS)

    Horn, Andrew B.

    Available from UMI in association with The British Library. The design of an experiment to investigate the surface chemistry of silicon, with specific application to the study of intermediates formed during the chemical vapour deposition of silicon from silane homologues was considered in a theoretical manner using classical optical techniques, and experimental verification of the ability to detect multilayers of physically adsorbed species was performed. Both reflection-absorption infrared spectroscopy and transmission infrared spectroscopy were investigated. Some of the steps involved in the cleaning of a silicon wafer were investigated. Chemical etching of the wafers was simulated using hydrofluoric acid solutions and hydrogen peroxide/sulphuric acid rinses and monitored using transmission infrared spectroscopy. Thermal annealing and argon ion sputter etching were investigated using transmission infrared spectroscopy, Auger electron spectroscopy and low energy electron diffraction. The adsorption of disilane, Si_{z}H_{rm e} on Si(100) was investigated at a variety of temperatures. Contamination was demonstrated to be significant in the passivation of the surface to a point where little reactivity could be observed at room temperature. Physical adsorption was seen to occur in a dynamic pressure of disilane at ca. 130K. The adsorption of disilane at temperatures ranging from 100K to 300K was investigated on Ru(0001). At low temperatures, disilane was seen to adsorb molecularly at 100K, with partial decomposition in the first layer. Annealing to higher temperatures and adsorption at 160K was seen to produce adsorbed SiH_{n } (n = 1-3), which desorbed above 270K. At room temperature, disilane adsorbed dissociatively to form an SiH species which formed a variety of structures at increasing coverage, evidenced by complex LEED patterns. At higher temperatures, the adsorbed silicon reacted with the ruthenium crystal to form a ruthenium silicide as an incommensurate

  9. Water Vapor Uptake of Ultrathin Films of Biologically Derived Nanocrystals: Quantitative Assessment with Quartz Crystal Microbalance and Spectroscopic Ellipsometry.

    PubMed

    Niinivaara, Elina; Faustini, Marco; Tammelin, Tekla; Kontturi, Eero

    2015-11-10

    Despite the relevance of water interactions, explicit analysis of vapor adsorption on biologically derived surfaces is often difficult. Here, a system was introduced to study the vapor uptake on a native polysaccharide surface; namely, cellulose nanocrystal (CNC) ultrathin films were examined with a quartz crystal microbalance with dissipation monitoring (QCM-D) and spectroscopic ellipsometry (SE). A significant mass uptake of water vapor by the CNC films was detected using the QCM-D upon increasing relative humidity. In addition, thickness changes proportional to changes in relative humidity were detected using SE. Quantitative analysis of the results attained indicated that in preference to being soaked by water at the point of hydration each individual CNC in the film became enveloped by a 1 nm thick layer of adsorbed water vapor, resulting in the detected thickness response. PMID:26461931

  10. Structures and spectroscopic properties of Ni(II) and Mn(II) complexes based on 5-(3‧, 5‧-dicarboxylphenyl) picolinic acid ligand

    NASA Astrophysics Data System (ADS)

    Ma, Qi; Song, Jin-Ping; Su, Feng; Guo, Jun-Mei; Guo, Yong; Dong, Chuan

    2016-05-01

    Two novel complexes including [Ni(Hdcppa)(H2O)4] (1) and {[Mn3(dcppa)2(H2O)6]·2H2O}n (2) have been synthesized and characterized by single crystal X-ray structure analysis and elemental analysis. Results show that 1 is a mononuclear nickel(II) compound with octahedron coordination geometry, while 2 is a stairs-like 2D layer structure consisting of the trinuclear MnII units linked through dcppa3-. Spectroscopic and electrochemical properties of the complexes 1-2 have also been studied in dimethyl sulfoxide solution at room temperature.

  11. Crystal Structure of Amylomaltase from Corynebacterium glutamicum.

    PubMed

    Joo, Seongjoon; Kim, Sangwoo; Seo, Hogyun; Kim, Kyung-Jin

    2016-07-20

    Amylomaltase is an essential enzyme in maltose utilization and maltodextrin metabolism, and it has been industrially used for the production of cyclodextrin and modification of starch. We determined the crystal structure of amylomaltase from Corynebacterium glutamicum (CgAM) at a resolution of 1.7 Å. Although CgAM forms a dimer without NaCl, it exists as a monomer in physiological concentration of NaCl. CgAM is composed of N- and C-terminal domains, which can be further divided into two and four subdomains, respectively. It exhibits a unique structural feature at the functionally unknown N-domain and also shows two striking differences at the C-domain compared to other amylomaltases. These differences at extended edge of the substrate-binding site might affect substrate specificity for large cyclodextrin formation. The bis-tris methane and sulfate molecules bound at the substrate-binding site of our current structure mimic the binding of the hydroxyl groups of glucose bound at subsites -1 and -2, respectively. PMID:27366969

  12. Some Lower Valence Vanadium Fluorides: Their Crystal Distortions, Domain Structures, Modulated Structures, Ferrimagnetism, and Composition Dependence.

    ERIC Educational Resources Information Center

    Hong, Y. S.; And Others

    1980-01-01

    Describes some contemporary concepts unique to the structure of advanced solids, i.e., their crystal distortions, domain structures, modulated structures, ferrimagnetism, and composition dependence. (Author/CS)

  13. Revisiting the blind tests in crystal structure prediction: accurate energy ranking of molecular crystals.

    PubMed

    Asmadi, Aldi; Neumann, Marcus A; Kendrick, John; Girard, Pascale; Perrin, Marc-Antoine; Leusen, Frank J J

    2009-12-24

    In the 2007 blind test of crystal structure prediction hosted by the Cambridge Crystallographic Data Centre (CCDC), a hybrid DFT/MM method correctly ranked each of the four experimental structures as having the lowest lattice energy of all the crystal structures predicted for each molecule. The work presented here further validates this hybrid method by optimizing the crystal structures (experimental and submitted) of the first three CCDC blind tests held in 1999, 2001, and 2004. Except for the crystal structures of compound IX, all structures were reminimized and ranked according to their lattice energies. The hybrid method computes the lattice energy of a crystal structure as the sum of the DFT total energy and a van der Waals (dispersion) energy correction. Considering all four blind tests, the crystal structure with the lowest lattice energy corresponds to the experimentally observed structure for 12 out of 14 molecules. Moreover, good geometrical agreement is observed between the structures determined by the hybrid method and those measured experimentally. In comparison with the correct submissions made by the blind test participants, all hybrid optimized crystal structures (apart from compound II) have the smallest calculated root mean squared deviations from the experimentally observed structures. It is predicted that a new polymorph of compound V exists under pressure.

  14. Revisiting the blind tests in crystal structure prediction: accurate energy ranking of molecular crystals.

    PubMed

    Asmadi, Aldi; Neumann, Marcus A; Kendrick, John; Girard, Pascale; Perrin, Marc-Antoine; Leusen, Frank J J

    2009-12-24

    In the 2007 blind test of crystal structure prediction hosted by the Cambridge Crystallographic Data Centre (CCDC), a hybrid DFT/MM method correctly ranked each of the four experimental structures as having the lowest lattice energy of all the crystal structures predicted for each molecule. The work presented here further validates this hybrid method by optimizing the crystal structures (experimental and submitted) of the first three CCDC blind tests held in 1999, 2001, and 2004. Except for the crystal structures of compound IX, all structures were reminimized and ranked according to their lattice energies. The hybrid method computes the lattice energy of a crystal structure as the sum of the DFT total energy and a van der Waals (dispersion) energy correction. Considering all four blind tests, the crystal structure with the lowest lattice energy corresponds to the experimentally observed structure for 12 out of 14 molecules. Moreover, good geometrical agreement is observed between the structures determined by the hybrid method and those measured experimentally. In comparison with the correct submissions made by the blind test participants, all hybrid optimized crystal structures (apart from compound II) have the smallest calculated root mean squared deviations from the experimentally observed structures. It is predicted that a new polymorph of compound V exists under pressure. PMID:19950907

  15. Structural, spectroscopic, and magnetic properties of Eu3+-doped GdVO4 nanocrystals synthesized by a hydrothermal method.

    PubMed

    Szczeszak, Agata; Grzyb, Tomasz; Śniadecki, Zbigniew; Andrzejewska, Nina; Lis, Stefan; Matczak, Michał; Nowaczyk, Grzegorz; Jurga, Stefan; Idzikowski, Bogdan

    2014-12-01

    New interesting aspects of the spectroscopic properties, magnetism, and method of synthesis of gadolinium orthovanadates doped with Eu(3+) ions are discussed. Gd(1-x)Eu(x)VO4 (x = 0, 0.05, 0.2) bifunctional luminescent materials with complex magnetic properties were synthesized by a microwave-assisted hydrothermal method. Products were formed in situ without previous precipitation. The crystal structures and morphologies of the obtained nanomaterials were analyzed by X-ray diffraction and transmission and scanning electron microscopy. Crystallographic data were analyzed using Rietveld refinement. The products obtained were nanocrystalline with average grain sizes of 70-80 nm. The qualitative and quantitative elemental composition as well as mapping of the nanocrystals was proved using energy-dispersive X-ray spectroscopy. The spectroscopic properties of red-emitting nanophosphors were characterized by their excitation and emission spectra and luminescence decays. Magnetic measurements were performed by means of vibrating sample magnetometry. GdVO4 and Gd0.8Eu0.2VO4 exhibited paramagnetic behavior with a weak influence of antiferromagnetic couplings between rare-earth ions. In the substituted sample, an additional magnetic contribution connected with the population of low-lying excited states of europium was observed. PMID:25383487

  16. Two new two-dimensional organically templated phosphite compounds: (C{sub 6}H{sub 16}N{sub 2}){sub 0.5}[M(HPO{sub 3})F], M=Fe(II) and Co(II): Solvothermal synthesis, crystal structures, thermal, spectroscopic, and magnetic properties

    SciTech Connect

    Fernandez-Armas, Sergio; Mesa, Jose L. . E-mail: qipmeruj@lg.ehu.es; Pizarro, Jose L.; Chung, U-Chan; Arriortua, Maria I.; Rojo, Teofilo . E-mail: qiproapt@lg.ehu.es

    2005-11-15

    The organically templated (C{sub 6}H{sub 16}N{sub 2}){sub 0.5}[M(HPO{sub 3})F] [M(II)=Fe (1) and Co (2)] compounds have been synthesized by using mild hydrothermal conditions under autogeneous pressure. The crystal structures have been determined from X-ray single-crystal diffraction data. The compounds are isostructural and crystallize in the C2/c monoclinic space group. The unit-cell parameters are a=5.607(1), b=21.276(4), c=11.652(1)A, {beta}=93.74(1) deg. for the iron phase and a=5.5822(7), b=21.325(3), c=11.4910(1)A, {beta}=93.464(9){sup o} for the cobalt compound with Z=4. The crystal structure of these compounds consists of [M(HPO{sub 3})F]{sup -} anionic sheets. The layers are constructed from chains which contain [M{sub 2}O{sub 6}F{sub 3}] dimeric units linked by fluoride ions. The trans-1,4-diaminocyclohexane cations are placed in the interlayer space. The IR and Raman spectra show the bands corresponding to the phosphite oxoanion and organic dication. The Dq and Racah (B and C) parameters have been calculated from the diffuse reflectance spectra in the visible region. Dq parameter is 790cm{sup -1} for compound (1). For phase (2) the Dq value is 725cm{sup -1} and B and C are 930 and 4100cm{sup -1}, respectively. The thermal evolution of the molar magnetic susceptibilities of these compounds show maxima at 20.0 and 6.0K for the iron(II) and cobalt(II) phases, respectively. These results indicate the existence of antiferromagnetic interactions in both compounds.

  17. Crystal structures of Bacillus subtilis Lon protease.

    PubMed

    Duman, Ramona E; Löwe, Jan

    2010-08-27

    Lon ATP-dependent proteases are key components of the protein quality control systems of bacterial cells and eukaryotic organelles. Eubacterial Lon proteases contain an N-terminal domain, an ATPase domain, and a protease domain, all in one polypeptide chain. The N-terminal domain is thought to be involved in substrate recognition, the ATPase domain in substrate unfolding and translocation into the protease chamber, and the protease domain in the hydrolysis of polypeptides into small peptide fragments. Like other AAA+ ATPases and self-compartmentalising proteases, Lon functions as an oligomeric complex, although the subunit stoichiometry is currently unclear. Here, we present crystal structures of truncated versions of Lon protease from Bacillus subtilis (BsLon), which reveal previously unknown architectural features of Lon complexes. Our analytical ultracentrifugation and electron microscopy show different oligomerisation of Lon proteases from two different bacterial species, Aquifex aeolicus and B. subtilis. The structure of BsLon-AP shows a hexameric complex consisting of a small part of the N-terminal domain, the ATPase, and protease domains. The structure shows the approximate arrangement of the three functional domains of Lon. It also reveals a resemblance between the architecture of Lon proteases and the bacterial proteasome-like protease HslUV. Our second structure, BsLon-N, represents the first 209 amino acids of the N-terminal domain of BsLon and consists of a globular domain, similar in structure to the E. coli Lon N-terminal domain, and an additional four-helix bundle, which is part of a predicted coiled-coil region. An unexpected dimeric interaction between BsLon-N monomers reveals the possibility that Lon complexes may be stabilised by coiled-coil interactions between neighbouring N-terminal domains. Together, BsLon-N and BsLon-AP are 36 amino acids short of offering a complete picture of a full-length Lon protease.

  18. Crystal structure of human nicotinic acid phosphoribosyltransferase.

    PubMed

    Marletta, Ada Serena; Massarotti, Alberto; Orsomando, Giuseppe; Magni, Giulio; Rizzi, Menico; Garavaglia, Silvia

    2015-01-01

    Nicotinic acid phosphoribosyltransferase (EC 2.4.2.11) (NaPRTase) is the rate-limiting enzyme in the three-step Preiss-Handler pathway for the biosynthesis of NAD. The enzyme catalyzes the conversion of nicotinic acid (Na) and 5-phosphoribosyl-1-pyrophosphate (PRPP) to nicotinic acid mononucleotide (NaMN) and pyrophosphate (PPi). Several studies have underlined the importance of NaPRTase for NAD homeostasis in mammals, but no crystallographic data are available for this enzyme from higher eukaryotes. Here, we report the crystal structure of human NaPRTase that was solved by molecular replacement at a resolution of 2.9 Å in its ligand-free form. Our structural data allow the assignment of human NaPRTase to the type II phosphoribosyltransferase subfamily and reveal that the enzyme consists of two domains and functions as a dimer with the active site located at the interface of the monomers. The substrate-binding mode was analyzed by molecular docking simulation and provides hints into the catalytic mechanism. Moreover, structural comparison of human NaPRTase with the other two human type II phosphoribosyltransferases involved in NAD biosynthesis, quinolinate phosphoribosyltransferase and nicotinamide phosphoribosyltransferase, reveals that while the three enzymes share a conserved overall structure, a few distinctive structural traits can be identified. In particular, we show that NaPRTase lacks a tunnel that, in nicotinamide phosphoribosiltransferase, represents the binding site of its potent and selective inhibitor FK866, currently used in clinical trials as an antitumoral agent. PMID:26042198

  19. Effect of substituents on redox, spectroscopic and structural properties of conjugated diaryltetrazines--a combined experimental and theoretical study.

    PubMed

    Kurach, Ewa; Djurado, David; Rimarčik, Jan; Kornet, Aleksandra; Wlostowski, Marek; Lukeš, Vladimir; Pécaut, Jacques; Zagorska, Malgorzata; Pron, Adam

    2011-02-21

    Two series of new soluble conjugated compounds containing tetrazine central ring have been synthesized. The three-ring compounds have been synthesized by the reaction of aryl cyanide (where aryl = thienyl, alkylthienyl, phenyl or pyridyl) with hydrazine followed by oxidation of the intermediate product with diethyl azodicarboxylate. The five-ring compounds have been prepared using two pathways: (i) reaction of 5-cyano-2,2'-bithiophene (or its alkyl derivative) with hydrazine; (ii) via Suzuki or Stille coupling of 3,6-bis(5-bromo-2-thienyl)-1,2,4,5-tetrazine with a stannyl or boronate derivative of alkylthiophene. UV-vis spectroscopic properties of the synthesized compounds are strongly dependent on the nature of the aryl group, the position of the solubilizing substituent and the length of the molecule, showing the highest bathochromic shift (λ(max) > 440 nm) for five-ring compounds with alkyl groups attached to C(α) carbon in the terminal thienyl ring. An excellent linear correlation has been found for spectroscopically determined and theoretically calculated (TD-B3LYP/6-31G*) excitation energies. With the exception of dipyridyl derivative, the calculated lowest unoccupied molecular orbital (LUMO) level of the investigated molecules changes within a narrow range (from -2.63 to -2.41 eV), in line with the electrochemical data, which show a reversible reduction process with the redox potential varying from -1.23 V to -1.33 V (vs. Fc/Fc(+)). The electrochemically determined positions of the LUMO levels are consistently lower by 0.9 to 1.2 eV with respect to the calculated ones. All molecules readily crystallize. Single crystal studies of 3,6-bis(2,2'-bithien-5-yl)-1,2,4,5-tetrazine show that it crystallizes in a P2(1)/c space group whose structural arrangement is not very favorable to the charge carriers flow within the crystal. Powder diffraction studies of other derivatives have shown that their structural organization is sensitive to the position of the

  20. Crystal and molecular structure of 2,4,4-trisubstituted 5-amino-4 H-imidazoles

    NASA Astrophysics Data System (ADS)

    Bellanato, J.; Avendaño, C.; Ramos, M. T.; Smith-Verdier, P.; Florencio, F.; Garcia-Blanco, S.

    Three 5-amino-4 H-imidazole derivatives 2(2-pyridyl) and 2-ethoxycarbonyl-4,4-pentamethylene-5-amino-and 2(2-pyridyl)-4,4-dimethyl-5(2-pyridylamino)4 H-imidazoles have been studied by i.r. and Raman spectroscopy. The crystal structure of one has been determined by X-ray diffraction. The tautomeric amino-imino equilibrium in different working conditions is also studied from spectroscopic data. The amino and the unconjugated imino forms are characterized.

  1. Spectral and structural studies of GdCOB and YCOB crystals

    NASA Astrophysics Data System (ADS)

    Lupei, Aurelia; Antic-Fidancev, E.; Aka, Gerard; Vivien, Daniel; Gheorghe, L.; Gheorghe, Cristian

    2004-10-01

    The structural data obtained from of high resolution optical spectroscopic investigations on Nd3+, Eu3+ and Yb3+ ions in rare earth calcium oxoborate crystals RCOB, mainly GdCOB and YCOB, but also EuCOB, are compared with those obtained from other studies such as X-ray diffraction or differential thermal analysis. The dependence of non-equivalent center intensities and on R3+ (dopants) ionic radii is in qualitative accord with X-ray diffraction data. The glassy like behavior of 4F3/2 Nd3+ emission under selective excitation, as well as the shift of one line of 5Do --> 7F1 Eu3+ emission are explained in terms of cationic structural disorder of RCOB crystals.

  2. NaCo(H2PO2)3: Crystal structure and physical study

    NASA Astrophysics Data System (ADS)

    El Bali, Brahim; Lachkar, Mohammed; Essehli, Rachid; Dusek, Michal; Rohlicek, Jan; Mircescu, Nicoleta; Haisch, Christoph

    2016-11-01

    NaCo(H2PO2)3 was synthesized in solution and its structure was studied by single-crystal X-ray diffraction. It crystallizes in the cubic space group P213 (#198), Z = 4, a = 9.2563(16) Å, V = 793.1(2) Å3. Final residual factors of the refined structure model R/Rw were 0.0367/0.0941. The cations Na+ and Co2+ are both octahedrally coordinated. [NaO6] and [CoO6] share edges to form channels propagating along [1,-1, -1] with the [H2PO2] pseudo-pyramids adjusted inside the channels to the above mentioned octahedra. The IR and Raman spectroscopic studies show the expected bands of the hypophosphite anion. NaCo(H2PO2)3 did not show any electrochemical activity under the electrochemical test conditions (2.4-4.5 V vs. Na/Na+).

  3. Spectroscopic, nonlinear optical and quantum chemical studies on Pyrrolidinium p-Hydroxybenzoate--a phase matchable organic NLO crystal.

    PubMed

    Shanmugam, G; Belsley, M S; Isakov, D; Gomes, E de Matos; Nehru, K; Brahadeeswaran, S

    2013-10-01

    Good quality and bulk single crystals of Pyrrolidinium p-Hydroxybenzoate (PYPHB), a newly identified nonlinear optical material, were grown for the first time. It crystallizes in monoclinic system with an acentric space group Cc. The molecular structure including carbon, proton positions and functional groups has been confirmed through nuclear magnetic resonance and Fourier transform infrared spectra. Its transmission window has been observed for UV-VIS-NIR region along with its theoretical limit. The photoluminescence behavior has been observed by exciting the crystal at 310 nm. The principal refractive indices and second order NLO coefficient of PYPHB are determined by Mach-Zehnder interferometer and Maker-Fringe experiments respectively. The coherence length and phase-matchablility of PYPHB crystals are measured to explore its efficacy towards device fabrications. The dipole moment, polarizability and molecular orbital energy of an isolated PYPHB molecule have also been calculated theoretically and the results are found to corroborate the experimental values.

  4. Structural and spectroscopic changes to natural nontronite induced by experimental impacts between 10 and 40 GPa

    NASA Astrophysics Data System (ADS)

    Friedlander, Lonia R.; Glotch, Timothy D.; Bish, David L.; Dyar, M. Darby; Sharp, Thomas G.; Sklute, Elizabeth C.; Michalski, Joseph R.

    2015-05-01

    Many phyllosilicate deposits remotely detected on Mars occur within bombarded terrains. Shock metamorphism from meteor impacts alters mineral structures, producing changed mineral spectra. Thus, impacts have likely affected the spectra of remotely sensed Martian phyllosilicates. We present spectral analysis results for a natural nontronite sample before and after laboratory-generated impacts over five peak pressures between 10 and 40 GPa. We conducted a suite of spectroscopic analyses to characterize the sample's impact-induced structural and spectral changes. Nontronite becomes increasingly disordered with increasing peak impact pressure. Every infrared spectroscopic technique used showed evidence of structural changes at shock pressures above ~25 GPa. Reflectance spectroscopy in the visible near-infrared region is primarily sensitive to the vibrations of metal-OH and interlayer H2O groups in the nontronite octahedral sheet. Midinfrared (MIR) spectroscopic techniques are sensitive to the vibrations of silicon and oxygen in the nontronite tetrahedral sheet. Because the tetrahedral and octahedral sheets of nontronite deform differently, impact-driven structural deformation may contribute to differences in phyllosilicate detection between remote sensing techniques sensitive to different parts of the nontronite structure. Observed spectroscopic changes also indicated that the sample's octahedral and tetrahedral sheets were structurally deformed but not completely dehydroxylated. This finding is an important distinction from previous studies of thermally altered phyllosilicates in which dehydroxylation follows dehydration in a stepwise progression preceding structural deformation. Impact alteration may thus complicate mineral-specific identifications based on the location of OH-group bands in remotely detected spectra. This is a key implication for Martian remote sensing arising from our results.

  5. Growth and Vibrational Spectroscopic Investigations of NLO Crystal Barium Thiourea Chloride

    NASA Astrophysics Data System (ADS)

    Kumari, M. Meena; Ravikumar, C.; Amalanathan, M.; Jayakumar, V. S.; Joe, I. Hubert

    2008-11-01

    The crystal of NLO interest, Barium thiourea chloride (BTC) has been crystallized and is subjected to FT-IR and NIR FT-Raman spectral studies along with the quantum chemical computations. The equilibrium geometry, first hyperpolarizability, various bonding features and vibrational wavenumbers have been calculated by B3LYP density functional theory (DFT) calculations at the LANL2DZ level. The predicted vibrational spectra are in fair agreement with the experiment. The broadening of NH2 stretching wavenumber indicates the intermolecular N-H…CI hydrogen bonding present in the molecule.

  6. Spectroscopic properties of erbium-doped yttria-stabilised zirconia crystals

    SciTech Connect

    Ryabochkina, P A; Sidorova, N V; Ushakov, S N; Lomonova, E E

    2014-02-28

    Yttria-stabilised zirconia crystals ZrO{sub 2} – Y{sub 2}O{sub 3} (6 mol %) – Er{sub 2}O{sub 3} (5.85 mol %) are grown by directional crystallisation in a cold container using direct RF melting. The spectral and luminescent properties of these crystals are studied in order to use them as active media of solid state lasers emitting in the wavelength range 1.5 – 1.7 μm. (active media)

  7. Crystallization and Structure Determination of Superantigens and Immune Receptor Complexes.

    PubMed

    Rödström, Karin E J; Lindkvist-Petersson, Karin

    2016-01-01

    Structure determination of superantigens and the complexes they form with immune receptors have over the years provided insight in their modes of action. This technique requires growing large and highly ordered crystals of the superantigen or receptor-superantigen complex, followed by exposure to X-ray radiation and data collection. Here, we describe methods for crystallizing superantigens and superantigen-receptor complexes using the vapor diffusion technique, how the crystals may be optimized, and lastly data collection and structure determination.

  8. Preparation of Low Band Gap Fibrillar Structures by Solvent Induced Crystallization

    NASA Astrophysics Data System (ADS)

    Wang, Hsin-Wei; Pentzer, Emily; Emerick, Todd; Russell, Thomas

    2014-03-01

    Solution-induced crystallization of the low band gap polymer poly[ N-9''-heptadecanyl-2,7-carbazole-alt-5,5-(4',7'-di-2-thienyl-2',1',3'-benzothiadiazole)] (PCDTBT) was shown to give fibril-like structures of 40-60 nm width and ~ 0.5 μm length. These structures, formed by heating and cooling PCDTBT in a marginal solvent, were characterized by AFM, TEM, GI-WAXS, and steady state absorption and emission spectroscopy. The width of the PCDTBT structures suggests that the polymer chains are oriented perpendicular to the fiber axis, while the observed undulated structures, as revealed by AFM, suggest that the nanostructures may be composed of smaller crystalline units, suggesting a crystal face-specific assembly. Surprisingly, no spectroscopic signatures in either absorption or emission were observed upon crystallization of PCDTBT, in sharp contrast to the well-known conjugated polymer poly(3-hexyl thiophene) (P3HT). The solution-based crystallization of PCDTBT offers insight into the self-assembly of conjugated polymers and a better understanding of their role in photovoltaic devices

  9. Single-Molecule Spectroscopic Investigations of RNA Structural Dynamics

    NASA Astrophysics Data System (ADS)

    Fiore, Julie L.; Nesbitt, David J.

    2007-03-01

    To function properly, catalytic RNAs (ribozymes) fold into specific three-dimensional shapes stabilized by multiple tertiary interactions. However, only limited information is available on the contributions of individual tertiary contacts to RNA conformational dynamics. The Tetrahymena ribozymes's P4--P6 domain forms a hinged, ``candy-cane'' structure with parallel helices clamped by two motifs, the GAAA tetraloop-tetraloop receptor and adenosine (A)-rich bulge--P4 helix interactions. Previously, we characterized RNA folding due to a tetraloop-receptor interaction. In this study, we employ time-resolved single-molecule FRET methods to probe A-rich bulge induced structural dynamics. Specifically, fluorescently labeled RNA constructs excited by a pulsed 532 nm laser are detected in the confocal region of an inverted microscope, with each photon sorted by arrival time, color and polarization. We resolve the kinetic dependence of A-rich bulge-P4 helix docking/undocking on cationic environment (e.g. Na^+ and Mg^2+ concentration.) At saturating [Mg^2+], the docked structure appears only weakly stabilized, while only 50% of the molecules exhibit efficient folding.

  10. Vibrational spectroscopic and structural investigations on fullerene: A DFT approach

    NASA Astrophysics Data System (ADS)

    Christy, P. Anto; Premkumar, S.; Asath, R. Mohamed; Mathavan, T.; Benial, A. Milton Franklin

    2016-05-01

    The molecular structure of fullerene (C60) molecule was optimized by the DFT/B3LYP method with 6-31G and 6-31G(d,p) basis sets using Gaussian 09 program. The vibrational frequencies were calculated for the optimized molecular structure of the molecule. The calculated vibrational frequencies confirm that the molecular structure of the molecule was located at the minimum energy potential energy surface. The calculated vibrational frequencies were assigned on the basis of functional group analysis and also confirmed using the GaussView 05 software. The frontier molecular orbitals analysis was carried out. The FMOs related molecular properties were predicted. The higher ionization potential, higher electron affinity, higher softness, lower band gap energy and lower hardness values were obtained, which confirm that the fullerene molecule has a higher molecular reactivity. The Mulliken atomic charge distribution of the molecule was also calculated. Hence, these results play an important role due to its potential applications as drug delivery devices.

  11. Spectroscopic investigations of the electronic structure of neptunyl ions.

    SciTech Connect

    Wilkerson, M. P.; Berg, J. M.; Dewey, H. J.

    2003-01-01

    Molecular electronic structures are innately sensitive to the geometric and chemical environments around the metal center of coordination compounds . However, the interrelationships between the electronic structures and molecular geometries of actinide species, which often contain more than one electron in the Sf valence shell, are quite complex due to the large numbers of possible electronic states and high densities of vibronically enabled transitions .1'2 Investigations of the optical signatures of simple, well-defined molecular systems should provide the most straightforward approach for unharnessing these fundamental relationships, and in particular, systems with a single electron in the valence Sf shell, such as the neptunyl ion (Np0 22+), should provide the most viable means for characte rizing actinide electronic structure. Furthermore, Sf orbital-occupied actinide systems exhibit not only visible and ultraviolet ligand-to-metal charge-transfer spectral bands, but also near-infrared Sf-Sf transitions resulting from promotion of a Sf electron to an orbital of primarily Sf character .

  12. Exfoliation and Raman Spectroscopic Fingerprint of Few-Layer NiPS3 Van der Waals Crystals

    PubMed Central

    Kuo, Cheng-Tai; Neumann, Michael; Balamurugan, Karuppannan; Park, Hyun Ju; Kang, Soonmin; Shiu, Hung Wei; Kang, Jin Hyoun; Hong, Byung Hee; Han, Moonsup; Noh, Tae Won; Park, Je-Geun

    2016-01-01

    The range of mechanically cleavable Van der Waals crystals covers materials with diverse physical and chemical properties. However, very few of these materials exhibit magnetism or magnetic order, and thus the provision of cleavable magnetic compounds would supply invaluable building blocks for the design of heterostructures assembled from Van der Waals crystals. Here we report the first successful isolation of monolayer and few-layer samples of the compound nickel phosphorus trisulfide (NiPS3) by mechanical exfoliation. This material belongs to the class of transition metal phosphorus trisulfides (MPS3), several of which exhibit antiferromagnetic order at low temperature, and which have not been reported in the form of ultrathin sheets so far. We establish layer numbers by optical bright field microscopy and atomic force microscopy, and perform a detailed Raman spectroscopic characterization of bilayer and thicker NiPS3 flakes. Raman spectral features are strong functions of excitation wavelength and sample thickness, highlighting the important role of interlayer coupling. Furthermore, our observations provide a spectral fingerprint for distinct layer numbers, allowing us to establish a sensitive and convenient means for layer number determination. PMID:26875451

  13. Exfoliation and Raman Spectroscopic Fingerprint of Few-Layer NiPS3 Van der Waals Crystals.

    PubMed

    Kuo, Cheng-Tai; Neumann, Michael; Balamurugan, Karuppannan; Park, Hyun Ju; Kang, Soonmin; Shiu, Hung Wei; Kang, Jin Hyoun; Hong, Byung Hee; Han, Moonsup; Noh, Tae Won; Park, Je-Geun

    2016-01-01

    The range of mechanically cleavable Van der Waals crystals covers materials with diverse physical and chemical properties. However, very few of these materials exhibit magnetism or magnetic order, and thus the provision of cleavable magnetic compounds would supply invaluable building blocks for the design of heterostructures assembled from Van der Waals crystals. Here we report the first successful isolation of monolayer and few-layer samples of the compound nickel phosphorus trisulfide (NiPS3) by mechanical exfoliation. This material belongs to the class of transition metal phosphorus trisulfides (MPS3), several of which exhibit antiferromagnetic order at low temperature, and which have not been reported in the form of ultrathin sheets so far. We establish layer numbers by optical bright field microscopy and atomic force microscopy, and perform a detailed Raman spectroscopic characterization of bilayer and thicker NiPS3 flakes. Raman spectral features are strong functions of excitation wavelength and sample thickness, highlighting the important role of interlayer coupling. Furthermore, our observations provide a spectral fingerprint for distinct layer numbers, allowing us to establish a sensitive and convenient means for layer number determination. PMID:26875451

  14. Exfoliation and Raman Spectroscopic Fingerprint of Few-Layer NiPS3 Van der Waals Crystals.

    PubMed

    Kuo, Cheng-Tai; Neumann, Michael; Balamurugan, Karuppannan; Park, Hyun Ju; Kang, Soonmin; Shiu, Hung Wei; Kang, Jin Hyoun; Hong, Byung Hee; Han, Moonsup; Noh, Tae Won; Park, Je-Geun

    2016-02-15

    The range of mechanically cleavable Van der Waals crystals covers materials with diverse physical and chemical properties. However, very few of these materials exhibit magnetism or magnetic order, and thus the provision of cleavable magnetic compounds would supply invaluable building blocks for the design of heterostructures assembled from Van der Waals crystals. Here we report the first successful isolation of monolayer and few-layer samples of the compound nickel phosphorus trisulfide (NiPS3) by mechanical exfoliation. This material belongs to the class of transition metal phosphorus trisulfides (MPS3), several of which exhibit antiferromagnetic order at low temperature, and which have not been reported in the form of ultrathin sheets so far. We establish layer numbers by optical bright field microscopy and atomic force microscopy, and perform a detailed Raman spectroscopic characterization of bilayer and thicker NiPS3 flakes. Raman spectral features are strong functions of excitation wavelength and sample thickness, highlighting the important role of interlayer coupling. Furthermore, our observations provide a spectral fingerprint for distinct layer numbers, allowing us to establish a sensitive and convenient means for layer number determination.

  15. Exfoliation and Raman Spectroscopic Fingerprint of Few-Layer NiPS3 Van der Waals Crystals

    NASA Astrophysics Data System (ADS)

    Kuo, Cheng-Tai; Neumann, Michael; Balamurugan, Karuppannan; Park, Hyun Ju; Kang, Soonmin; Shiu, Hung Wei; Kang, Jin Hyoun; Hong, Byung Hee; Han, Moonsup; Noh, Tae Won; Park, Je-Geun

    2016-02-01

    The range of mechanically cleavable Van der Waals crystals covers materials with diverse physical and chemical properties. However, very few of these materials exhibit magnetism or magnetic order, and thus the provision of cleavable magnetic compounds would supply invaluable building blocks for the design of heterostructures assembled from Van der Waals crystals. Here we report the first successful isolation of monolayer and few-layer samples of the compound nickel phosphorus trisulfide (NiPS3) by mechanical exfoliation. This material belongs to the class of transition metal phosphorus trisulfides (MPS3), several of which exhibit antiferromagnetic order at low temperature, and which have not been reported in the form of ultrathin sheets so far. We establish layer numbers by optical bright field microscopy and atomic force microscopy, and perform a detailed Raman spectroscopic characterization of bilayer and thicker NiPS3 flakes. Raman spectral features are strong functions of excitation wavelength and sample thickness, highlighting the important role of interlayer coupling. Furthermore, our observations provide a spectral fingerprint for distinct layer numbers, allowing us to establish a sensitive and convenient means for layer number determination.

  16. Undergraduates Improve upon Published Crystal Structure in Class Assignment

    ERIC Educational Resources Information Center

    Horowitz, Scott; Koldewey, Philipp; Bardwell, James C.

    2014-01-01

    Recently, 57 undergraduate students at the University of Michigan were assigned the task of solving a crystal structure, given only the electron density map of a 1.3 Å crystal structure from the electron density server, and the position of the N-terminal amino acid. To test their knowledge of amino acid chemistry, the students were not given the…

  17. Position sensitivity in 3"×3" Spectroscopic LaBr3:Ce Crystals

    NASA Astrophysics Data System (ADS)

    Blasi, N.; Giaz, A.; Boiano, C.; Brambilla, S.; Camera, F.; Million, B.; Riboldi, S.

    2015-06-01

    The position sensitivity of a thick, cylindrical and continuous 3" × 3" (7.62 cm × 7.62 cm) LaBr3:Ce crystal with diffusive surfaces was investigated. Nuclear physics basic research uses thick LaBr3:Ce crystals (> 3cm) to measure medium or high energy gamma rays (0.5 MeV < Eγ< 20 MeV). In the first measurement the PMT photocathode entrance window was covered by black absorber except for a small window 1 cm × 1cm wide. A complete scan of the detector over a 0.5 cm step grid was performed. The data show that even in a 3" thick LaBr3:Ce crystal with diffusive surfaces the position of the full energy peak centroid depends on the source position. The position of the full energy peak centroids are sufficient to identify the collimated gamma source position. The crystal was then coupled to four Position Sensitive Photomultipliers (PSPMT). We acquired the signals from the 256 segments of the four PSPMTs grouping them into 16 elements. An event by event analysis shows a positon resolution of the order of 2 cm.

  18. Predicting crystal structure by merging data mining with quantum mechanics.

    PubMed

    Fischer, Christopher C; Tibbetts, Kevin J; Morgan, Dane; Ceder, Gerbrand

    2006-08-01

    Modern methods of quantum mechanics have proved to be effective tools to understand and even predict materials properties. An essential element of the materials design process, relevant to both new materials and the optimization of existing ones, is knowing which crystal structures will form in an alloy system. Crystal structure can only be predicted effectively with quantum mechanics if an algorithm to direct the search through the large space of possible structures is found. We present a new approach to the prediction of structure that rigorously mines correlations embodied within experimental data and uses them to direct quantum mechanical techniques efficiently towards the stable crystal structure of materials.

  19. Isolation of brassicasterol, its synthetic prodrug-crystal structure, stereochemistry and theoretical studies

    NASA Astrophysics Data System (ADS)

    Sethi, Arun; Prakash, Rohit; Srivastava, Sangeeta; Amandeep; Bishnoi, Abha; Singh, Ranvijay Pratap

    2014-07-01

    In the present study brassicasterol (1), was isolated from the chloroform extract of the flowers of Allamanda violacea and identified with the help of different spectroscopic techniques like 1H, 13C, 2D NMR (1H-1H COSY), IR, UV and mass spectrometry. A novel prodrug was synthesized by carrying out esterification of brassicasterol (1) with the well known drug naproxen using Steglich esterification to give 3β-(2-(6-methoxynaphthalene-2yl) propionoxy) 24 methyl cholest-5, 22-dien (2). Compounds 2 was subjected to single crystal X-ray diffraction technique and crystallized out in monoclinic form having P21 space group and stabilized by CH-π interactions. Structure and stereochemistry of compound 2 was established with the help of modern spectroscopic techniques like 1H NMR, IR, UV, mass spectrometry as well as with single crystal X-ray diffraction. Molecular geometry and vibrational frequencies of compounds 1 and 2 were calculated by density functional method (DFT/B3LYP) using 6-31G (d, p) basis set, bond parameters and IR frequencies were correlated with the experimental data. 1H and 13C chemical shifts of compound 1 and 1H chemical shifts of compound 2 were calculated with GIAO method and correlated with experimental data. Hyperconjugative interactions were studied with the help of natural bond order analysis (NBO). Electronic properties of both the compounds such as HOMO-LUMO energies were measured with the help of time dependent DFT method.

  20. Use of Pom Pons to Illustrate Cubic Crystal Structures.

    ERIC Educational Resources Information Center

    Cady, Susan G.

    1997-01-01

    Describes a method that uses olefin pom pons to illustrate cubic crystal structure. Facilitates hands-on examination of different packing arrangements such as hexagonal close-packed and cubic close-packed structures. (JRH)

  1. Crystal structure at 1.5Å resolution of the PsbV2 cytochrome from the cyanobacterium Thermosynechococcus elongatus.

    PubMed

    Suga, Michihiro; Lai, Thanh-Lan; Sugiura, Miwa; Shen, Jian-Ren; Boussac, Alain

    2013-10-01

    PsbV2 is a c-type cytochrome present in a very low abundance in the thermophilic cyanobacterium Thermosynechococcus elongatus. We purified this cytochrome and solved its crystal structure at a resolution of 1.5Å. The protein existed as a dimer in the crystal, and has an overall structure similar to other c-type cytochromes like Cytc6 and Cytc550, for example. However, the 5th and 6th heme iron axial ligands were found to be His51 and Cys101, respectively, in contrast to the more common bis-His or His/Met ligands found in most cytochromes. Although a few other c-type cytochromes were suggested to have this axial coordination, this is the first crystal structure reported for a c-type heme with this unusual His/Cys axial coordination. Previous spectroscopic characterizations of PsbV2 are discussed in relation to its structural properties.

  2. Coordination Modes of Americium in the Am2(C2O4)3(H2O)6·4H2O Oxalate: Synthesis, Crystal Structure, Spectroscopic Characterizations and Comparison in the M2(C2O4)3(H2O)6·nH2O (M = Ln, An) Series.

    PubMed

    Tamain, C; Arab-Chapelet, B; Rivenet, M; Legoff, X F; Loubert, G; Grandjean, S; Abraham, F

    2016-01-01

    Americium oxalate single crystals, Am2(C2O4)3(H2O)6·4H2O, were prepared by in situ oxalic acid generation by slow hydrolysis of the diester. Their structure was determined by single-crystal X-ray diffraction and was solved by the direct methods and Fourier difference techniques. The structure (space group P21/c, a = 11.184(4) Å, b = 9.489(4) Å, c = 10.234(4) Å, β = 114.308(8)°, Z = 2) consists of layers formed by six-membered rings of actinide metals connected through oxalate ions. The americium atoms are nine-coordinated by six oxygen atoms from three bidentate oxalate ligands and three water molecules. The distances within the coordination sphere as well as infrared and Raman spectra of several isostructural lanthanide (Ce(III), Pr(III), Nd(III), Sm(III), Gd(III)) and actinide (Pu(III), Am(III)) oxalates were compared to evaluate the similarities and the differences between the two series. PMID:26675037

  3. Crystal structure of Clostridium difficile toxin A.

    PubMed

    Chumbler, Nicole M; Rutherford, Stacey A; Zhang, Zhifen; Farrow, Melissa A; Lisher, John P; Farquhar, Erik; Giedroc, David P; Spiller, Benjamin W; Melnyk, Roman A; Lacy, D Borden

    2016-01-01

    Clostridium difficile infection is the leading cause of hospital-acquired diarrhoea and pseudomembranous colitis. Disease is mediated by the actions of two toxins, TcdA and TcdB, which cause the diarrhoea, as well as inflammation and necrosis within the colon(1,2). The toxins are large (308 and 270 kDa, respectively), homologous (47% amino acid identity) glucosyltransferases that target small GTPases within the host(3,4). The multidomain toxins enter cells by receptor-mediated endocytosis and, upon exposure to the low pH of the endosome, insert into and deliver two enzymatic domains across the membrane. Eukaryotic inositol-hexakisphosphate (InsP6) binds an autoprocessing domain to activate a proteolysis event that releases the N-terminal glucosyltransferase domain into the cytosol. Here, we report the crystal structure of a 1,832-amino-acid fragment of TcdA (TcdA1832), which reveals a requirement for zinc in the mechanism of toxin autoprocessing and an extended delivery domain that serves as a scaffold for the hydrophobic α-helices involved in pH-dependent pore formation. A surface loop of the delivery domain whose sequence is strictly conserved among all large clostridial toxins is shown to be functionally important, and is highlighted for future efforts in the development of vaccines and novel therapeutics. PMID:27571750

  4. Crystal structure of Clostridium difficile toxin A

    PubMed Central

    Chumbler, Nicole M.; Rutherford, Stacey A.; Zhang, Zhifen; Farrow, Melissa A.; Lisher, John P.; Farquhar, Erik; Giedroc, David P.; Spiller, Benjamin W.; Melnyk, Roman A.; Lacy, D. Borden

    2016-01-01

    Clostridium difficile infection is the leading cause of hospital-acquired diarrhoea and pseudomembranous colitis. Disease is mediated by the actions of two toxins, TcdA and TcdB, which cause the diarrhoea, as well as inflammation and necrosis within the colon1,2. The toxins are large (308 and 270 kDa, respectively), homologous (47% amino acid identity) glucosyltransferases that target small GTPases within the host3,4. The multidomain toxins enter cells by receptor-mediated endocytosis and, upon exposure to the low pH of the endosome, insert into and deliver two enzymatic domains across the membrane. Eukaryotic inositol-hexakisphosphate (InsP6) binds an autoprocessing domain to activate a proteolysis event that releases the N-terminal glucosyltransferase domain into the cytosol. Here, we report the crystal structure of a 1,832-amino-acid fragment of TcdA (TcdA1832), which reveals a requirement for zinc in the mechanism of toxin autoprocessing and an extended delivery domain that serves as a scaffold for the hydrophobic α-helices involved in pH-dependent pore formation. A surface loop of the delivery domain whose sequence is strictly conserved among all large clostridial toxins is shown to be functionally important, and is highlighted for future efforts in the development of vaccines and novel therapeutics. PMID:27571750

  5. Structures and spectroscopic characterization of calcium chloride-nicotinamide, -isonicotinamide, -picolinamide and praseodymium bromide-nicotinamide complexes

    NASA Astrophysics Data System (ADS)

    Xue, Junhui; Jiang, Ye; Li, Weihong; Yang, Limin; Xu, Yizhuang; Zhao, Guozhong; Zhang, Gaohui; Bu, Xiaoxia; Liu, Kexin; Chen, Jia'er; Wu, Jinguang

    2015-02-01

    The coordination structures formed by calcium complexes with nicotinamide (na), isonicotinamide (ina) and picolinamide (pa) and praseodymium bromide-na are reported. The structures of CaCl2·(C6H6N2O)2·2H2O (Ca-na), CaCl2·(C6H6N2O)2·4H2O (Ca-ina), CaCl2·(C6H6N2O)2·5H2O (Ca-pa) and PrBr3·(C6H6N2O)2·6H2O (PrBr-na) in the solid state have been characterized by X-ray single crystal diffraction, FTIR, FIR, THz and Raman spectroscopies. Carbonyl oxygen of nicotinamide is coordinated to Ca2+, but it is O-monodentate (carbonyl oxygen) and N,O-bidentate ligand (pyridyl nitrogen and carbonyl oxygen) for Pr3+ to form a chain structure in PrBr-na. For isonicotinamide, only carbonyl oxygen atom is coordinated to Ca2+. Pyridyl nitrogen and carbonyl oxygen of picolinamide are coordinated to Ca2+ to form a five-membered ring structure. The crystal structure and spectroscopic results indicate the differences of the coordination of Ca and Pr ions, the changes of hydrogen bonds and conformation of the ligands induced by complexation. Unlike transition metal ions, Sr2+ or lanthanide ions, Ca2+ is inclined to coordinate to carbonyl oxygen atoms of the ligands.

  6. Structures and spectroscopic characterization of calcium chloride-nicotinamide, -isonicotinamide, -picolinamide and praseodymium bromide-nicotinamide complexes.

    PubMed

    Xue, Junhui; Jiang, Ye; Li, Weihong; Yang, Limin; Xu, Yizhuang; Zhao, Guozhong; Zhang, Gaohui; Bu, Xiaoxia; Liu, Kexin; Chen, Jia'er; Wu, Jinguang

    2015-02-25

    The coordination structures formed by calcium complexes with nicotinamide (na), isonicotinamide (ina) and picolinamide (pa) and praseodymium bromide-na are reported. The structures of CaCl2·(C6H6N2O)2·2H2O (Ca-na), CaCl2·(C6H6N2O)2·4H2O (Ca-ina), CaCl2·(C6H6N2O)2·5H2O (Ca-pa) and PrBr3·(C6H6N2O)2·6H2O (PrBr-na) in the solid state have been characterized by X-ray single crystal diffraction, FTIR, FIR, THz and Raman spectroscopies. Carbonyl oxygen of nicotinamide is coordinated to Ca(2+), but it is O-monodentate (carbonyl oxygen) and N,O-bidentate ligand (pyridyl nitrogen and carbonyl oxygen) for Pr(3+) to form a chain structure in PrBr-na. For isonicotinamide, only carbonyl oxygen atom is coordinated to Ca(2+). Pyridyl nitrogen and carbonyl oxygen of picolinamide are coordinated to Ca(2+) to form a five-membered ring structure. The crystal structure and spectroscopic results indicate the differences of the coordination of Ca and Pr ions, the changes of hydrogen bonds and conformation of the ligands induced by complexation. Unlike transition metal ions, Sr(2+) or lanthanide ions, Ca(2+) is inclined to coordinate to carbonyl oxygen atoms of the ligands.

  7. Structures and spectroscopic characterization of calcium chloride-nicotinamide, -isonicotinamide, -picolinamide and praseodymium bromide-nicotinamide complexes.

    PubMed

    Xue, Junhui; Jiang, Ye; Li, Weihong; Yang, Limin; Xu, Yizhuang; Zhao, Guozhong; Zhang, Gaohui; Bu, Xiaoxia; Liu, Kexin; Chen, Jia'er; Wu, Jinguang

    2015-02-25

    The coordination structures formed by calcium complexes with nicotinamide (na), isonicotinamide (ina) and picolinamide (pa) and praseodymium bromide-na are reported. The structures of CaCl2·(C6H6N2O)2·2H2O (Ca-na), CaCl2·(C6H6N2O)2·4H2O (Ca-ina), CaCl2·(C6H6N2O)2·5H2O (Ca-pa) and PrBr3·(C6H6N2O)2·6H2O (PrBr-na) in the solid state have been characterized by X-ray single crystal diffraction, FTIR, FIR, THz and Raman spectroscopies. Carbonyl oxygen of nicotinamide is coordinated to Ca(2+), but it is O-monodentate (carbonyl oxygen) and N,O-bidentate ligand (pyridyl nitrogen and carbonyl oxygen) for Pr(3+) to form a chain structure in PrBr-na. For isonicotinamide, only carbonyl oxygen atom is coordinated to Ca(2+). Pyridyl nitrogen and carbonyl oxygen of picolinamide are coordinated to Ca(2+) to form a five-membered ring structure. The crystal structure and spectroscopic results indicate the differences of the coordination of Ca and Pr ions, the changes of hydrogen bonds and conformation of the ligands induced by complexation. Unlike transition metal ions, Sr(2+) or lanthanide ions, Ca(2+) is inclined to coordinate to carbonyl oxygen atoms of the ligands. PMID:25280333

  8. Anisotropic domain structure of KTiOPO4 crystals

    NASA Astrophysics Data System (ADS)

    Urenski, P.; Lesnykh, M.; Rosenwaks, Y.; Rosenman, G.; Molotskii, M.

    2001-08-01

    Highly anisotropic ferroelectric domain structure is observed in KTiOPO4 (KTP) crystals reversed by low electric field. The applied Miller-Weinreich model for sidewise motion of domain walls indicates that this anisotropy results from the peculiarities of KTP crystal lattice. The domain nuclei of dozen nanometer size, imaged by atomic force microscopy method, demonstrate regular hexagonal forms. The orientation of domain walls of the elementary nuclei coincides with the orientation of the facets of macroscopic KTP crystals. The observed strong domain elongation along one principal crystal axis allows us to improve tailoring of ferroelectric domain engineered structures for nonlinear optical converters.

  9. Preparation of iridescent colloidal crystal coatings with variable structural colors.

    PubMed

    Cong, Hailin; Yu, Bing; Wang, Shaopeng; Qi, Limin; Wang, Jilei; Ma, Yurong

    2013-07-29

    Iridescent colloidal crystal coatings with variable structural colors were fabricated by incorporating carbon black nanoparticles (CB-NPs) into the voids of polystyrene (PS) colloidal crystals. The structural color of the colloid crystal coatings was not only greatly enhanced after the composition but also varied with observation angles. By changing the diameter of monodisperse PS colloids in the composites, colloidal crystal coatings with three primary colors for additive or subtractive combination were obtained. After incorporation of the PS/CB-NPs hybrid coatings into polydimethylsiloxane (PDMS) matrix, manmade opal jewelry with variable iridescent colors was made facilely. PMID:23938656

  10. Growth, spectroscopic and physicochemical properties of bis mercury ferric chloride tetra thiocyanate: A nonlinear optical crystal

    NASA Astrophysics Data System (ADS)

    Ramesh, V.; Shihabuddeen Syed, A.; Jagannathan, K.; Rajarajan, K.

    2013-05-01

    Single crystal of bis mercury ferric chloride tetra thiocyanate [Hg2FeCl3(SCN)4; (MFCTC)] was grown from ethanol-water (3:1) mixed solvent using slow evaporation solvent technique (SEST) for the first time. The cell parameters of the grown crystal were confirmed by single crystal XRD. The coordination of transition metal ions with the SCN ligand is well-identified using FT-IR spectral analysis. The chemical composition of MFCTC was confirmed using CHNS elemental test. The ESR spectral profile of MFCTC was recorded from 298 K to 110 K, which strongly suggests the incorporation of Fe3+ ion and its environment with respect to SCN ligand. The HPLC chromatogram of MFCTC highlights the purity of the compound. The UV-Vis-NIR studies revealed the ultra violet cut-off wavelength of MFCTC in ethanol as 338 nm. The dielectric constant and dielectric loss of the sample were studied as a function of frequency and temperature. The TGA-DTA and DSC thermal analysis show that the sample is thermally stable up to 234.31 °C, which is comparatively far better than the thermal stability of Hg3CdCl2(SCN)6; (171.3 °C) and other metal-organic coordination complex crystals such as CdHg(SCN)4 (198.5 °C), Hg(N2H4CS)4Mn(SCN)4 (199.06 °C) and Hg(N2H4CS)4Zn(SCN)4 (185 °C). The SHG conversion efficiency of MFCTC is found to be higher than KDP.

  11. Structures and Encapsulation Motifs of Functional Molecules Probed by Laser Spectroscopic and Theoretical Methods

    PubMed Central

    Kusaka, Ryoji; Inokuchi, Yoshiya; Xantheas, Sotiris S.; Ebata, Takayuki

    2010-01-01

    We report laser spectroscopic and computational studies of host/guest hydration interactions between functional molecules (hosts) and water (guest) in supersonic jets. The examined hosts include dibenzo-18-crown-6-ether (DB18C6), benzo-18-crown-6-ether (B18C6) and calix[4]arene (C4A). The gaseous complexes between the functional molecular hosts and water are generated under jet-cooled conditions. Various laser spectroscopic methods are applied for these species: the electronic spectra are observed by laser-induced fluorescence (LIF), mass-selected resonance enhanced multiphoton ionization (REMPI) and ultraviolet-ultraviolet hole-burning (UV-UV HB) spectroscopy, whereas the vibrational spectra for each individual species are observed by infrared-ultraviolet double resonance (IR-UV DR) spectroscopy. The obained results are analyzed by first principles electronic structure calculations. We discuss the conformations of the host molecules, the structures of the complexes, and key interactions forming the specific complexes. PMID:22319310

  12. Photonic crystal channel drop filters based on fractal structures

    NASA Astrophysics Data System (ADS)

    Dideban, Ali; Habibiyan, Hamidreza; Ghafoorifard, Hassan

    2014-09-01

    In this paper we introduce new configurations of channel drop filters based on two-dimensional photonic crystals. Structures consist of two photonic crystal waveguides and a fractal-shaped resonator between them. The effect of structural parameters on resonance frequency and drop efficiency is investigated. Calculations of band structure and propagation of electromagnetic field through devices are done by plane wave expansion (PWE) and finite difference time domain (FDTD) methods, respectively. In our designs more than 95% drop efficiency with quality factor of ~1150 is achievable at wavelength near 1540 nm, which in comparison with other photonic crystal resonator structures is a very satisfactory and acceptable result.

  13. Novel photonic crystal cavities and related structures.

    SciTech Connect

    Luk, Ting Shan

    2007-11-01

    The key accomplishment of this project is to achieve a much more in-depth understanding of the thermal emission physics of metallic photonic crystal through theoretical modeling and experimental measurements. An improved transfer matrix technique was developed to enable incorporation of complex dielectric function. Together with microscopic theory describing emitter radiative and non-radiative relaxation dynamics, a non-equilibrium thermal emission model is developed. Finally, experimental methodology was developed to measure absolute emissivity of photonic crystal at high temperatures with accuracy of +/-2%. Accurate emissivity measurements allow us to validate the procedure to treat the effect of the photonic crystal substrate.

  14. A Dominant Factor for Structural Classification of Protein Crystals.

    PubMed

    Qi, Fei; Fudo, Satoshi; Neya, Saburo; Hoshino, Tyuji

    2015-08-24

    With the increasing number of solved protein crystal structures, much information on protein shape and atom geometry has become available. It is of great interest to know the structural diversity for a single kind of protein. Our preliminary study suggested that multiple crystal structures of a single kind of protein can be classified into several groups from the viewpoint of structural similarity. In order to broadly examine this finding, cluster analysis was applied to the crystal structures of hemoglobin (Hb), myoglobin (Mb), human serum albumin (HSA), hen egg-white lysozyme (HEWL), and human immunodeficiency virus type 1 protease (HIV-1 PR), downloaded from the Protein Data Bank (PDB). As a result of classification by cluster analysis, 146 crystal structures of Hb were separated into five groups. The crystal structures of Mb (n = 284), HEWL (n = 336), HSA (n = 63), and HIV-1 PR (n = 488) were separated into six, five, three, and six groups, respectively. It was found that a major factor causing these structural separations is the space group of crystals and that crystallizing agents have an influence on the crystal structures. Amino acid mutation is a minor factor for the separation because no obvious point mutation making a specific cluster group was observed for the five kinds of proteins. In the classification of Hb and Mb, the species of protein source such as humans, rabbits, and mice is another significant factor. When the difference in amino sequence is large among species, the species of protein source is the primary factor causing cluster separation in the classification of crystal structures. PMID:26230289

  15. In vivo protein crystallization opens new routes in structural biology.

    PubMed

    Koopmann, Rudolf; Cupelli, Karolina; Redecke, Lars; Nass, Karol; Deponte, Daniel P; White, Thomas A; Stellato, Francesco; Rehders, Dirk; Liang, Mengning; Andreasson, Jakob; Aquila, Andrew; Bajt, Sasa; Barthelmess, Miriam; Barty, Anton; Bogan, Michael J; Bostedt, Christoph; Boutet, Sébastien; Bozek, John D; Caleman, Carl; Coppola, Nicola; Davidsson, Jan; Doak, R Bruce; Ekeberg, Tomas; Epp, Sascha W; Erk, Benjamin; Fleckenstein, Holger; Foucar, Lutz; Graafsma, Heinz; Gumprecht, Lars; Hajdu, Janos; Hampton, Christina Y; Hartmann, Andreas; Hartmann, Robert; Hauser, Günter; Hirsemann, Helmut; Holl, Peter; Hunter, Mark S; Kassemeyer, Stephan; Kirian, Richard A; Lomb, Lukas; Maia, Filipe R N C; Kimmel, Nils; Martin, Andrew V; Messerschmidt, Marc; Reich, Christian; Rolles, Daniel; Rudek, Benedikt; Rudenko, Artem; Schlichting, Ilme; Schulz, Joachim; Seibert, M Marvin; Shoeman, Robert L; Sierra, Raymond G; Soltau, Heike; Stern, Stephan; Strüder, Lothar; Timneanu, Nicusor; Ullrich, Joachim; Wang, Xiaoyu; Weidenspointner, Georg; Weierstall, Uwe; Williams, Garth J; Wunderer, Cornelia B; Fromme, Petra; Spence, John C H; Stehle, Thilo; Chapman, Henry N; Betzel, Christian; Duszenko, Michael

    2012-03-01

    Protein crystallization in cells has been observed several times in nature. However, owing to their small size these crystals have not yet been used for X-ray crystallographic analysis. We prepared nano-sized in vivo-grown crystals of Trypanosoma brucei enzymes and applied the emerging method of free-electron laser-based serial femtosecond crystallography to record interpretable diffraction data. This combined approach will open new opportunities in structural systems biology.

  16. In vivo protein crystallization opens new routes in structural biology

    PubMed Central

    Koopmann, Rudolf; Cupelli, Karolina; Redecke, Lars; Nass, Karol; DePonte, Daniel P; White, Thomas A; Stellato, Francesco; Rehders, Dirk; Liang, Mengning; Andreasson, Jakob; Aquila, Andrew; Bajt, Sasa; Barthelmess, Miriam; Barty, Anton; Bogan, Michael J; Bostedt, Christoph; Boutet, Sébastien; Bozek, John D; Caleman, Carl; Coppola, Nicola; Davidsson, Jan; Doak, R Bruce; Ekeberg, Tomas; Epp, Sascha W; Erk, Benjamin; Fleckenstein, Holger; Foucar, Lutz; Graafsma, Heinz; Gumprecht, Lars; Hajdu, Janos; Hampton, Christina Y; Hartmann, Andreas; Hartmann, Robert; Hauser, Günter; Hirsemann, Helmut; Holl, Peter; Hunter, Mark S; Kassemeyer, Stephan; Kirian, Richard A; Lomb, Lukas; Maia, Filipe R N C; Kimmel, Nils; Martin, Andrew V; Messerschmidt, Marc; Reich, Christian; Rolles, Daniel; Rudek, Benedikt; Rudenko, Artem; Schlichting, Ilme; Schulz, Joachim; Seibert, M Marvin; Shoeman, Robert L; Sierra, Raymond G; Soltau, Heike; Stern, Stephan; Strüder, Lothar; Timneanu, Nicusor; Ullrich, Joachim; Wang, Xiaoyu; Weidenspointner, Georg; Weierstall, Uwe; Williams, Garth J; Wunderer, Cornelia B; Fromme, Petra; Spence, John C H; Stehle, Thilo; Chapman, Henry N; Betzel, Christian; Duszenko, Michael

    2012-01-01

    Protein crystallization in cells has been observed several times in nature. However, owing to their small size these crystals have not yet been used for X-ray crystallographic analysis. We prepared nano-sized in vivo–grown crystals of Trypanosoma brucei enzymes and applied the emerging method of free-electron laser-based serial femtosecond crystallography to record interpretable diffraction data. This combined approach will open new opportunities in structural systems biology. PMID:22286384

  17. In vivo protein crystallization opens new routes in structural biology.

    PubMed

    Koopmann, Rudolf; Cupelli, Karolina; Redecke, Lars; Nass, Karol; Deponte, Daniel P; White, Thomas A; Stellato, Francesco; Rehders, Dirk; Liang, Mengning; Andreasson, Jakob; Aquila, Andrew; Bajt, Sasa; Barthelmess, Miriam; Barty, Anton; Bogan, Michael J; Bostedt, Christoph; Boutet, Sébastien; Bozek, John D; Caleman, Carl; Coppola, Nicola; Davidsson, Jan; Doak, R Bruce; Ekeberg, Tomas; Epp, Sascha W; Erk, Benjamin; Fleckenstein, Holger; Foucar, Lutz; Graafsma, Heinz; Gumprecht, Lars; Hajdu, Janos; Hampton, Christina Y; Hartmann, Andreas; Hartmann, Robert; Hauser, Günter; Hirsemann, Helmut; Holl, Peter; Hunter, Mark S; Kassemeyer, Stephan; Kirian, Richard A; Lomb, Lukas; Maia, Filipe R N C; Kimmel, Nils; Martin, Andrew V; Messerschmidt, Marc; Reich, Christian; Rolles, Daniel; Rudek, Benedikt; Rudenko, Artem; Schlichting, Ilme; Schulz, Joachim; Seibert, M Marvin; Shoeman, Robert L; Sierra, Raymond G; Soltau, Heike; Stern, Stephan; Strüder, Lothar; Timneanu, Nicusor; Ullrich, Joachim; Wang, Xiaoyu; Weidenspointner, Georg; Weierstall, Uwe; Williams, Garth J; Wunderer, Cornelia B; Fromme, Petra; Spence, John C H; Stehle, Thilo; Chapman, Henry N; Betzel, Christian; Duszenko, Michael

    2012-03-01

    Protein crystallization in cells has been observed several times in nature. However, owing to their small size these crystals have not yet been used for X-ray crystallographic analysis. We prepared nano-sized in vivo-grown crystals of Trypanosoma brucei enzymes and applied the emerging method of free-electron laser-based serial femtosecond crystallography to record interpretable diffraction data. This combined approach will open new opportunities in structural systems biology. PMID:22286384

  18. Photonic Crystal Structures with Tunable Structure Color as Colorimetric Sensors

    PubMed Central

    Wang, Hui; Zhang, Ke-Qin

    2013-01-01

    Colorimetric sensing, which transduces environmental changes into visible color changes, provides a simple yet powerful detection mechanism that is well-suited to the development of low-cost and low-power sensors. A new approach in colorimetric sensing exploits the structural color of photonic crystals (PCs) to create environmentally-influenced color-changeable materials. PCs are composed of periodic dielectrics or metallo-dielectric nanostructures that affect the propagation of electromagnetic waves (EM) by defining the allowed and forbidden photonic bands. Simultaneously, an amazing variety of naturally occurring biological systems exhibit iridescent color due to the presence of PC structures throughout multi-dimensional space. In particular, some kinds of the structural colors in living organisms can be reversibly changed in reaction to external stimuli. Based on the lessons learned from natural photonic structures, some specific examples of PCs-based colorimetric sensors are presented in detail to demonstrate their unprecedented potential in practical applications, such as the detections of temperature, pH, ionic species, solvents, vapor, humidity, pressure and biomolecules. The combination of the nanofabrication technique, useful design methodologies inspired by biological systems and colorimetric sensing will lead to substantial developments in low-cost, miniaturized and widely deployable optical sensors. PMID:23539027

  19. Thermal, spectroscopic and laser properties of Nd3+ in gadolinium scandium gallium garnet crystal produced by optical floating zone method

    NASA Astrophysics Data System (ADS)

    Tian, Li; Wang, Shuxian; Wu, Kui; Wang, Baolin; Yu, Haohai; Zhang, Huaijin; Cai, Huaqiang; Huang, Hui

    2013-12-01

    A neodymium-doped gadolinium scandium gallium garnet (Nd:GSGG) single crystal with dimensions of Φ 5 × 20 mm2 has been grown by means of optical floating zone (OFZ). X-ray powder diffraction (XRPD) result shows that the as-grown Nd:GSGG crystal possesses a cubic structure with space group Ia3d and a cell parameter of a = 1.2561 nm. Effective elemental segregation coefficients of the Nd:GSGG as-grown crystal were calculated by using X-ray fluorescence (XRF). The thermal properties of the Nd:GSGG crystal were systematically studied by measuring the specific heat, thermal expansion and thermal diffusion coefficient, and the thermal conductivity of this crystal was calculated. The absorption and luminescence spectra of Nd:GSGG were measured at room temperature (RT). By using the Judd-Ofelt (J-O) theory, the theoretical radiative lifetime was calculated and compared with the experimental result. Continuous wave (CW) laser performance was achieved with the Nd:GSGG at the wavelength of 1062 nm when it was pumped by a laser diode (LD). A maximum output power of 0.792 W at 1062 nm was obtained with a slope efficiency of 11.89% under a pump power of 7.36 W, and an optical-optical conversion efficiency of 11.72%.

  20. Isomorph invariance of the structure and dynamics of classical crystals

    NASA Astrophysics Data System (ADS)

    Albrechtsen, Dan E.; Olsen, Andreas E.; Pedersen, Ulf R.; Schrøder, Thomas B.; Dyre, Jeppe C.

    2014-09-01

    This paper shows by computer simulations that some crystalline systems have curves in their thermodynamic phase diagrams, so-called isomorphs, along which structure and dynamics in reduced units are invariant to a good approximation. The crystals are studied in a classical-mechanical framework, which is generally a good description except significantly below melting. The existence of isomorphs for crystals is validated by simulations of particles interacting via the Lennard-Jones pair potential arranged into a face-centered cubic (fcc) crystalline structure; the slow vacancy-jump dynamics of a defective fcc crystal is also shown to be isomorph invariant. In contrast, a NaCl crystal model does not exhibit isomorph invariances. Other systems simulated, though in less detail, are the Wahnström binary Lennard-Jones crystal with the MgZn2 Laves crystal structure, monatomic fcc crystals of particles interacting via the Buckingham pair potential and via a purely repulsive pair potential diverging at a finite separation, an ortho-terphenyl molecular model crystal, and SPC/E hexagonal ice. Except for NaCl and ice, the crystals simulated all have isomorphs. Based on previous simulations of liquid models, we conjecture that crystalline solids with isomorphs include most or all formed by atoms or molecules interacting via metallic or van der Waals forces, whereas covalently bonded or hydrogen-bonded crystals are not expected to have isomorphs; crystals of ions or dipolar molecules constitute a limiting case for which isomorphs are only expected when the Coulomb interactions are relatively weak. We briefly discuss the consequences of the findings for theories of melting and crystallization.

  1. Spectroscopic, optical, thermal, antimicrobial and density functional theory studies of 4-aminopyridinium 4-hydroxy benzoate hydrate crystal

    NASA Astrophysics Data System (ADS)

    Karthiga Devi, P.; Venkatachalam, K.; Poonkothai, M.

    2016-09-01

    The organic crystal 4-aminopyridinium 4-hydroxy benzoate hydrate was grown using slow evaporation method. Various characterization techniques such as single crystal X-ray diffraction, powder X-ray diffraction, FTIR, UV-visible-NIR spectroscopy and thermal analysis (TG-DSC) were employed to assay the structure and properties of the grown crystal. The antimicrobial evaluation of 4-aminopyridinium 4-hydroxy benzoate hydrate crystal was also performed against some bacteria and fungi. The minimum inhibitory concentration (MIC) values of 4-aminopyridinium 4-hydroxy benzoate hydrate were determined for bacterial and fungal strains. The assessment of optimized structure of the molecule and vibrational frequencies were done using DFT/B3LYP method with 6-31 G (d, p) basis set. The stability of the molecule, hyperconjugative interactions, delocalization of charges and intermolecular hydrogen bond were studied by applying natural bond orbital (NBO) analysis. TD-DFT method employing polarizable continuum model (PCM) was used to examine the electronic absorption spectrum. Evaluation of molecular electrostatic potential (MEP), Mulliken population charges and nonlinear optical (NLO) properties were also carried out. In addition, from the optimized geometry, frontier molecular orbitals analysis was executed.

  2. Application of Spectroscopic Methods for Structural Analysis of Chitin and Chitosan

    PubMed Central

    Kumirska, Jolanta; Czerwicka, Małgorzata; Kaczyński, Zbigniew; Bychowska, Anna; Brzozowski, Krzysztof; Thöming, Jorg; Stepnowski, Piotr

    2010-01-01

    Chitin, the second most important natural polymer in the world, and its N-deacetylated derivative chitosan, have been identified as versatile biopolymers for a broad range of applications in medicine, agriculture and the food industry. Two of the main reasons for this are firstly the unique chemical, physicochemical and biological properties of chitin and chitosan, and secondly the unlimited supply of raw materials for their production. These polymers exhibit widely differing physicochemical properties depending on the chitin source and the conditions of chitosan production. The presence of reactive functional groups as well as the polysaccharide nature of these biopolymers enables them to undergo diverse chemical modifications. A complete chemical and physicochemical characterization of chitin, chitosan and their derivatives is not possible without using spectroscopic techniques. This review focuses on the application of spectroscopic methods for the structural analysis of these compounds. PMID:20559489

  3. Spectroscopic study of red-light-emitting centers in K2Al2B2O7: Fe single crystals

    NASA Astrophysics Data System (ADS)

    Ogorodnikov, I. N.; Pustovarov, V. A.; Yakovlev, S. A.; Isaenko, L. I.

    2013-04-01

    We report on spectroscopic study of red-light-emitting centers in K2Al2B2O7 (KABO) single crystals containing ca. 2 ppm of Fe3+. Owing to the low Fe3+-concentration, KABO does not show noticeable absorption due to Fe3+d-d-transitions in the visible spectral region, but it exhibits the charge-transfer (CT) UV-absorption bands O-Fe at 4.7, 5.7 and 6.5 eV. The red photoluminescence at 1.675 eV (FWHM = 0.173 eV) is due to intracenter 4T1 (4G) → 6A1 (6S) transitions in Fe3+ ions. Because of partial overlapping of the fundamental absorption edge of the crystal, where mobile excitons are created, and a broad CT absorption band at 6.5 eV, the most intensive red emission occurs at 7 K upon excitation in the excitonic energy region. The presence of two nonequivalent Al2O7 clusters in KABO lattice provides two different types of red-light-emitting centers in the form of Fe3+ ion occupied the Al3+ tetrahedral site. Superposition of their luminescence bands determines both the spectrum and temperature dependence of red emission in KABO at T = 7-80 K: two bands with the ratio of intensities of ca. 2:1 are 20 meV-shifted relative to each other; two-stage thermal quenching obeys the Mott law with ET = 9 and 20 meV.

  4. Structural and mechanical studies of cadmium manganese thiocyanate crystal

    NASA Astrophysics Data System (ADS)

    Manikandan, M. R.; Vijayaprasath, G.; babu, G. Anandha; Bhagavannarayan, G.; Vijayan, N.; Ravi, G.

    2012-06-01

    Single crystals of cadmium manganese thiocyanate (CMTC) have been synthesized successfully and grown by slow evaporation method. The structural perfection of the grown crystals has been analyzed by High resolution X-ray diffraction (HRXRD), which shows the crystalline perfection of the grown crystal is quite good. Optical behavior was assessed by UV-Vis analysis and found that no absorption in the UV visible region and it may be useful for second harmonic applications. The mechanical hardness of the grown crystals was studied and Vicker's microhardness, Stiffness constant was calculated.

  5. Spectroscopic detection and state preparation of a single praseodymium ion in a crystal.

    PubMed

    Utikal, T; Eichhammer, E; Petersen, L; Renn, A; Götzinger, S; Sandoghdar, V

    2014-04-11

    The narrow optical transitions and long spin coherence times of rare earth ions in crystals make them desirable for a number of applications ranging from solid-state spectroscopy and laser physics to quantum information processing. However, investigations of these features have not been possible at the single-ion level. Here we show that the combination of cryogenic high-resolution laser spectroscopy with optical microscopy allows one to spectrally select individual praseodymium ions in yttrium orthosilicate. Furthermore, this spectral selectivity makes it possible to resolve neighbouring ions with a spatial precision of the order of 10 nm. In addition to elaborating on the essential experimental steps for achieving this long-sought goal, we demonstrate state preparation and read out of the three ground-state hyperfine levels, which are known to have lifetimes of the order of hundred seconds.

  6. Spectroscopic investigation of the Cr to Tm energy transfer in Yttrium Aluminum Garnet (YAG) crystals

    NASA Technical Reports Server (NTRS)

    Dibartolo, B.

    1988-01-01

    New and interesting schemes have recently been considered for the efficient operation of solid-state ionic laser systems. Often the available data on these systems were obtained only because they seemed directly related to the laser performance and provide no insight into the physical processes. A more systematic approach is desirable, where more attention is devoted to the elementary basic processes and to the nature of the mechanisms at work. It is with this aim that we have undertaken the present study. Yttrium Aluminum Garnet (Y4Al5O12), called YAG, has two desirable properties as host for rare earth impurities: (1) trivalent rare earth ions can replace the yttrium without any charge compensation problem, and (2) YAG crystals have high cutoff energies. The results of measurements and calculations indicate that the Cr(3+) ion in YAG can be used to sensitize efficiently the Tm(3+) ion.

  7. Spectroscopic detection and state preparation of a single praseodymium ion in a crystal.

    PubMed

    Utikal, T; Eichhammer, E; Petersen, L; Renn, A; Götzinger, S; Sandoghdar, V

    2014-01-01

    The narrow optical transitions and long spin coherence times of rare earth ions in crystals make them desirable for a number of applications ranging from solid-state spectroscopy and laser physics to quantum information processing. However, investigations of these features have not been possible at the single-ion level. Here we show that the combination of cryogenic high-resolution laser spectroscopy with optical microscopy allows one to spectrally select individual praseodymium ions in yttrium orthosilicate. Furthermore, this spectral selectivity makes it possible to resolve neighbouring ions with a spatial precision of the order of 10 nm. In addition to elaborating on the essential experimental steps for achieving this long-sought goal, we demonstrate state preparation and read out of the three ground-state hyperfine levels, which are known to have lifetimes of the order of hundred seconds. PMID:24722142

  8. Spectroscopic detection and state preparation of a single praseodymium ion in a crystal

    NASA Astrophysics Data System (ADS)

    Utikal, T.; Eichhammer, E.; Petersen, L.; Renn, A.; Götzinger, S.; Sandoghdar, V.

    2014-04-01

    The narrow optical transitions and long spin coherence times of rare earth ions in crystals make them desirable for a number of applications ranging from solid-state spectroscopy and laser physics to quantum information processing. However, investigations of these features have not been possible at the single-ion level. Here we show that the combination of cryogenic high-resolution laser spectroscopy with optical microscopy allows one to spectrally select individual praseodymium ions in yttrium orthosilicate. Furthermore, this spectral selectivity makes it possible to resolve neighbouring ions with a spatial precision of the order of 10 nm. In addition to elaborating on the essential experimental steps for achieving this long-sought goal, we demonstrate state preparation and read out of the three ground-state hyperfine levels, which are known to have lifetimes of the order of hundred seconds.

  9. Sculpting narrowband Fano resonances inherent in the large-area mid-infrared photonic crystal microresonators for spectroscopic imaging

    PubMed Central

    Liu, Jui-Nung; Schulmerich, Matthew V.; Bhargava, Rohit; Cunningham, Brian T.

    2014-01-01

    Fourier transform infrared (FT-IR) imaging spectrometers are almost universally used to record microspectroscopic imaging data in the mid-infrared (mid-IR) spectral region. While the commercial standard, interferometry necessitates collection of large spectral regions, requires a large data handling overhead for microscopic imaging and is slow. Here we demonstrate an approach for mid-IR spectroscopic imaging at selected discrete wavelengths using narrowband resonant filtering of a broadband thermal source, enabled by high-performance guided-mode Fano resonances in one-layer, large-area mid-IR photonic crystals on a glass substrate. The microresonant devices enable discrete frequency IR (DF-IR), in which a limited number of wavelengths that are of interest are recorded using a mechanically robust instrument. This considerably simplifies instrumentation as well as overhead of data acquisition, storage and analysis for large format imaging with array detectors. To demonstrate the approach, we perform DF-IR spectral imaging of a polymer USAF resolution target and human tissue in the C−H stretching region (2600−3300 cm−1). DF-IR spectroscopy and imaging can be generalized to other IR spectral regions and can serve as an analytical tool for environmental and biomedical applications. PMID:25089433

  10. Molecular structures and crystal packings of 2-styrylquinoxaline derivatives

    NASA Astrophysics Data System (ADS)

    Kuz'mina, L. G.; Sitin, A. G.; Gulakova, E. N.; Fedorova, O. A.; Lermontova, E. Kh.; Churakov, A. V.

    2012-01-01

    The crystal and molecular structures of 2-styrylquinoxaline derivatives with different substituents in the styryl fragment are determined. The degree of planarity of the molecules studied varies in a very wide range, from 1.7° to 33.5°. In the ethylene fragment, the double bond is essentially localized. The bicycle-pedal disordering of the ethylene fragment is found in the crystals of the methoxy and oxyacetyl derivatives of 2-styrylquinoxaline. None of the packings contains packing motifs favorable for the photocycloaddition (PCA) reaction with single crystal retention. The crystal packings of these compounds and that of 2-(4-methylstyryl)quinoxaline are characterized by a stacking motif of the head-to-head type, which eliminates the possibility of PCA taking place with single crystal retention but is suitable for this reaction in polycrystalline films. The crystal packing of 2-(3,4-dimethoxystyryl)quinoxaline does not contain elements with stacking interactions.

  11. Crystal structures of alkylperoxo and anhydride intermediates in an intradiol ring-cleaving dioxygenase

    PubMed Central

    Knoot, Cory J.; Purpero, Vincent M.; Lipscomb, John D.

    2015-01-01

    Intradiol aromatic ring-cleaving dioxygenases use an active site, nonheme Fe3+ to activate O2 and catecholic substrates for reaction. The inability of Fe3+ to directly bind O2 presents a mechanistic conundrum. The reaction mechanism of protocatechuate 3,4-dioxygenase is investigated here using the alternative substrate 4-fluorocatechol. This substrate is found to slow the reaction at several steps throughout the mechanistic cycle, allowing the intermediates to be detected in solution studies. When the reaction was initiated in an enzyme crystal, it was found to halt at one of two intermediates depending on the pH of the surrounding solution. The X-ray crystal structure of the intermediate at pH 6.5 revealed the key alkylperoxo-Fe3+ species, and the anhydride-Fe3+ intermediate was found for a crystal reacted at pH 8.5. Intermediates of these types have not been structurally characterized for intradiol dioxygenases, and they validate four decades of spectroscopic, kinetic, and computational studies. In contrast to our similar in crystallo crystallographic studies of an Fe2+-containing extradiol dioxygenase, no evidence for a superoxo or peroxo intermediate preceding the alkylperoxo was found. This observation and the lack of spectroscopic evidence for an Fe2+ intermediate that could bind O2 are consistent with concerted formation of the alkylperoxo followed by Criegee rearrangement to yield the anhydride and ultimately ring-opened product. Structural comparison of the alkylperoxo intermediates from the intra- and extradiol dioxygenases provides a rationale for site specificity of ring cleavage. PMID:25548185

  12. Woodpile Structure Fabrication for Photonic Crystal Laser Acceleration

    SciTech Connect

    McGuinness, C.; Colby, E.; England, R. J.; Noble, R. J.; Sears, C. M.; Siemann, R.; Spencer, J.; Waltz, D.; Byer, R. L.; Plettner, T.; Cowan, B. M.

    2009-01-22

    We describe initial steps at fabricating a dielectric photonic bandgap accelerator structure designed to operate at near IR frequencies. Such a structure operating at these frequencies requires extremely small, sub-micron sized features, forcing one to use lithographic means for fabrication. A process based upon lithographic equipment at the Stanford Nanofabrication Facility has been developed and a four layer test structure has been fabricated. Unexpected problems with the final etch step, and corresponding modifications to the process flow addressing these problems, are described. Spectroscopic measurements of the structure have been taken and are compared to simulations.

  13. Woodpile Structure Fabrication for Photonic Crystal Laser Acceleration

    SciTech Connect

    McGuinness, C.; Byer, R.L.; Colby, E.; Cowan, B.M.; England, R.J.; Noble, R.J.; Plettner, T.; Sears, C.M.; Siemann, R.; Spencer, J.; Waltz, D.; /SLAC

    2010-06-30

    We describe initial steps at fabricating a dielectric photonic bandgap accelerator structure designed to operate at near IR frequencies. Such a structure operating at these frequencies requires extremely small, sub-micron sized features, forcing one to use lithographic means for fabrication. A process based upon lithographic equipment at the Stanford Nanofabrication Facility has been developed and a four layer test structure has been fabricated. Unexpected problems with the final etch step, and corresponding modifications to the process flow addressing these problems, are described. Spectroscopic measurements of the structure have been taken and are compared to simulations.

  14. Crystal structure of a methimazole-based ionic liquid.

    PubMed

    Gaitor, Jamie C; Zayas, Manuel Sanchez; Myrthil, Darrel J; White, Frankie; Hendrich, Jeffrey M; Sykora, Richard E; O'Brien, Richard A; Reilly, John T; Mirjafari, Arsalan

    2015-12-01

    The structure of 1-methyl-2-(prop-2-en-1-ylsulfan-yl)-1H-imidazol-3-ium bromide, C7H11N2S(+)·Br(-), has monoclinic (P21/c) symmetry. In the crystal, the components are linked by N-H⋯Br and C-H⋯Br hydrogen bonds. The crystal structure of the title compound undeniably proves that methimazole reacts through the thione tautomer, rather than the thiol tautomer in this system. PMID:26870468

  15. Comparison of spectroscopic properties of Tm and Ho in YAG and YLF crystals

    NASA Technical Reports Server (NTRS)

    Armagan, G.; Buoncristiani, A. M.; Inge, A. T.; Di Bartolo, B.

    1991-01-01

    The paper compares the cross-relaxation, energy transfer and loss processes in Tm- and Ho-doped YAG and YLF as a function of temperature, Tm concentration, and excitation power. Significant differences in the behavior of Tm and Tm,Ho in YAG and YLF crystals were found. The cross-relaxation rates of Tm(6 pct) are faster in YLF (about 5 microsec) than YAG (about 10 microsec). The energy transfer rates between Tm and Ho are faster in YLF than YAG. The time it takes for the maximum intensity of 1.7-micron emission to drop 10 percent is 25 microsec for YLF:Tm(6 pct),Ho(0.6 pct) and 65 microsec YAG:Tm(6 pct),Ho(0.5 pct). The losses occurring with increasing pump power for 2.1-micron emission of the above samples are 30 percent less in YLF than YAG. These qualitative differences point to YLF as a valuable 2-micron laser host material.

  16. The Crystal and Molecular Structure of Dianhydrogossypol

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Dianhydrogossypol (4,4'-dihydroxy-5,5'-diisopropyl-7,7'-dimethyl-bis(3H-naphtho[1,8-bc]furan-3-one)) was made by refluxing gossypol in m-xylene. Proton NMR confirmed that complete conversion was achieved over several hours. Single crystals were obtained by slow evaporation of the product from dichl...

  17. Raman spectroscopic investigation of polycrystalline structures of CVD-grown graphene by isotope labeling

    NASA Astrophysics Data System (ADS)

    Wang, Shengnan; Suzuki, Satoru; Hibino, Hiroki

    2014-10-01

    Topological defects, such as point defects, dislocations and grain boundaries, have a dramatic influence on the chemical and physical properties of large-scale graphene grown by chemical vapor deposition (CVD) method. Here we demonstrate the Raman visualization of polycrystalline structures in an isotopically modified CVD graphene. By means of the reversible reaction of methane on a copper catalyst, the etching of 12C-lattice and surface deposition of 13C-atoms occur in CVD graphene by sequentially introducing hydrogen and isotopic methane after standard growth of graphene with full monolayer coverage. Spatial Raman spectroscopic mapping on labeled graphene reveals pronounced network-like 13C-rich regions, which are further identified to exist along the grain boundaries of graphene by low-energy electron microscopy. The structural defects inside the graphene grains are also targeted in the isotope labeling process. Our work opens a new way to investigate multiple grain structures in CVD graphene with a simple spectroscopic technique.Topological defects, such as point defects, dislocations and grain boundaries, have a dramatic influence on the chemical and physical properties of large-scale graphene grown by chemical vapor deposition (CVD) method. Here we demonstrate the Raman visualization of polycrystalline structures in an isotopically modified CVD graphene. By means of the reversible reaction of methane on a copper catalyst, the etching of 12C-lattice and surface deposition of 13C-atoms occur in CVD graphene by sequentially introducing hydrogen and isotopic methane after standard growth of graphene with full monolayer coverage. Spatial Raman spectroscopic mapping on labeled graphene reveals pronounced network-like 13C-rich regions, which are further identified to exist along the grain boundaries of graphene by low-energy electron microscopy. The structural defects inside the graphene grains are also targeted in the isotope labeling process. Our work opens a new

  18. Comparative study of crystallographic, spectroscopic, and laser properties of Tm3+ in NaT(WO4)2 (T=La, Gd, Y, and Lu) disordered single crystals

    NASA Astrophysics Data System (ADS)

    Cano-Torres, J. M.; Rico, M.; Han, X.; Serrano, M. D.; Cascales, C.; Zaldo, C.; Petrov, V.; Griebner, U.; Mateos, X.; Koopmann, P.; Kränkel, C.

    2011-11-01

    Tetragonal double tungstate single crystals with formula NaT(WO4)2 have been grown by the Czochralski (T = Gd, La, Y) or by the top-seeded solution growth (T = Lu) methods with Tm concentration between 8 × 1018 and 7.85 × 1020 cm-3. The spectroscopic properties of Tm3+ in these crystals are related with the peculiarities of their I4¯ crystalline structure. Sixty-five percent of La ions in NaLa(WO4)2 are in the 2d site, while in the other crystal hosts, the lanthanide occupies preferentially the 2b site (59% in T = Gd, 74% in T = Y, and 58% in T = Lu). As a consequence, the linewidths of spectral bands associated with the electronic transitions are significantly narrower in NaLa(WO4)2 than in the rest of the isostructural crystals considered. Polarized spectroscopic measurements at 5 K and at higher temperatures, along with energy level simulation of the 4f12 configuration using a single-electron Hamiltonian, including free-ion and crystal field interactions, allowed us to determine the irreducible representation and energy of Stark levels up to the 3P0 multiplet and thus to obtain realistic partition functions (Z) used for emission cross-section calculations. In particular, for the 3F4(u) → 3H6(l) laser transition at λ ≈ 2 μm, this provides: Zl/Zu = 1.436 (T = Gd), 1.464 (T = La), 1.448 (T = Y), and 1.471 (T = Lu). Radiative lifetimes calculated by the Judd-Ofelt and Füchtbauer-Ladenburg methods are in agreement and decrease in the following order T = Gd, La, Y, and Lu, however, nonradiative losses are stronger for T = Gd and La crystals; therefore, experimental lifetimes of 1D2, 1G4, 3H4, and 3F4 Tm3+ multiplets do not change too much with crystal host. For 4.68 at.% Tm:NaY(WO4)2 crystal continuous-wave laser operation is obtained with ≈42% of slope efficiency and a record (for this crystal class) tuning capability of λ = 1847-2069 nm. The broad bandwidths, ΔλFWHM > 20 nm, of the free-running laser emission are promising for ultrafast (fs) mode

  19. Ferroelectric InMnO3: Growth of single crystals, structure and high-temperature phase transitions

    NASA Astrophysics Data System (ADS)

    Bekheet, Maged F.; Svoboda, Ingrid; Liu, Na; Bayarjargal, Lkhamsuren; Irran, Elisabeth; Dietz, Christian; Stark, Robert W.; Riedel, Ralf; Gurlo, Aleksander

    2016-09-01

    To understand the origin of the ferroelectricity in InMnO3, single crystals with average size of 1 mm were grown in PbF2 flux at 950 °C. The results of single crystal X-ray diffraction, second harmonic generation and piezoresponse force microscopy studies of high-quality InMnO3 single crystals reveal that the room-temperature state in this material is ferroelectric with P63cm symmetry. The polar InMnO3 specimen undergoes a reversible phase transition from non-centrosymmetric P63cm structure to a centrosymmetric P63/mmc structure at 700 °C as confirmed by the in situ high-temperature Raman spectroscopic and synchrotron X-ray diffraction experiments.

  20. Crystal structure of ABPO5 and optical study of Pr3+ embedded in these compounds

    NASA Astrophysics Data System (ADS)

    Ben Ali, A.; Antic-Fidancev, E.; Viana, B.; Aschehoug, P.; Taibi, M.; Aride, J.; Boukhari, A.

    2001-10-01

    The crystal structure of borophosphates ABPO5 (A = alkaline earth or Pb) was resolved on a polycrystalline sample using the Rietveld method. The x-ray diffraction patterns data show that ABPO5 crystallize in a centrosymmetric space group P3121 and their structure is related to the borogermanates REBGeO5 with a stillwellite-type structure. Pr3+ ion was used as a local structural probe to corroborate the structural resolution results. Absorption and fluorescence spectra of A1-xPrxBP1-xGexO5 (A = alkaline earth or Pb; x = 0.05) have been investigated at different temperatures. At 9 K the 3H4 → 3P0 transition of trivalent praseodymium ion (4f2 configuration) is observed as a single line. This indicates a unique crystallographic site for the rare earth ion in these compounds replacing the divalent cation. Energy level schemes were deduced from the low-temperature spectroscopic measurements. Comparing the electronic level splittings of studied compounds with the already reported data on REBGeO5 doped with Pr3+ ion, it is possible to dispel the doubt existing about structural determination. Moreover, under 460 nm excitation, intense red emission of trivalent praseodymium is observed corresponding to 1D2 → 3H4 transition. The lifetime measurements of 1D2 level have been performed for all the title compounds.

  1. Membrane protein structures without crystals, by single particle electron cryomicroscopy

    PubMed Central

    Vinothkumar, Kutti R

    2015-01-01

    It is an exciting period in membrane protein structural biology with a number of medically important protein structures determined at a rapid pace. However, two major hurdles still remain in the structural biology of membrane proteins. One is the inability to obtain large amounts of protein for crystallization and the other is the failure to get well-diffracting crystals. With single particle electron cryomicroscopy, both these problems can be overcome and high-resolution structures of membrane proteins and other labile protein complexes can be obtained with very little protein and without the need for crystals. In this review, I highlight recent advances in electron microscopy, detectors and software, which have allowed determination of medium to high-resolution structures of membrane proteins and complexes that have been difficult to study by other structural biological techniques. PMID:26435463

  2. Crystal structure of actinide metals at high compression

    SciTech Connect

    Fast, L.; Soederlind, P.

    1995-08-01

    The crystal structures of some light actinide metals are studied theoretically as a function of applied pressure. The first principles electronic structure theory is formulated in the framework of density functional theory, with the gradient corrected local density approximation of the exchange-correlation functional. The light actinide metals are shown to be well described as itinerant (metallic) f-electron metals and generally, they display a crystal structure which have, in agreement with previous theoretical suggestions, increasing degree of symmetry and closed-packing upon compression. The theoretical calculations agree well with available experimental data. At very high compression, the theory predicts closed-packed structures such as the fcc or the hcp structures or the nearly closed-packed bcc structure for the light actinide metals. A simple canonical band picture is presented to explain in which particular closed-packed form these metals will crystallize at ultra-high pressure.

  3. Laser spectroscopic and theoretical studies of the structures and encapsulation motifs of functional molecules

    SciTech Connect

    Ebata, Takayuki; Kusaka, Ryoji; Xantheas, Sotiris S.

    2015-01-22

    Extensive laser spectroscopic and theoretical studies have been recently carried out with the aim to reveal the structure and dynamics of encapsulation complexes in the gas phase. The characteristics of the encapsulation complexes are governed by the fact that (i) most of the host molecules are flexible and (ii) the complexes form high dimensional structures by using weak non-covalent interactions. These characteristics result in the possibility of the coexistence of many conformers in close energetic proximity. The combination of supersonic jet/laser spectroscopy and high level quantum chemical calculations is essential in tackling these challenging problems. In this report we describe our recent studies on the structures and dynamics of the encapsulation complexes formed by calix[4]arene (C4A), dibenzo-18-crown-6-ether (DB18C6), and benzo-18-crown-6-ether (B18C6) 'hosts' interacting with N{sub 2}, acetylene, water, and ammonia 'guest' molecules. The gaseous host-guest complexes are generated under jet-cooled conditions. We apply various laser spectroscopic methods to obtain the conformer- and isomer-specified electronic and IR spectra. The experimental results are complemented with quantum chemical calculations ranging from density functional theory to high level first principles calculations at the MP2 and CCSD(T) levels of theory. We discuss the possible conformations of the bare host molecules, the structural changes they undergo upon complexation, and the key interactions that are responsible in stabilizing the specific complexes.

  4. Laser Spectroscopic and Theoretical Studies of the Structures and Encapsulation Motifs of Functional Molecules

    SciTech Connect

    Ebata, Takayuki; Kusaka, Ryoji; Xantheas, Sotiris S.

    2015-02-01

    Extensive laser spectroscopic and theoretical studies have been recently carried out with the aim to reveal the structure and dynamics of encapsulation complexes in the gas phase. The characteristics of the encapsulation complexes are governed by the fact that (i) most of the host molecules are flexible and (ii) the complexes form high dimensional structures by using weak non-covalent interactions. These characteristics result in the possibility of the coexistence of many conformers in close energetic proximity. The combination of supersonic jet/laser spectroscopy and high level quantum chemical calculations is essential in tackling these challenging problems. In this report we describe our recent studies on the structures and dynamics of the encapsulation complexes formed by calix[4]arene (C4A), dibenzo-18-crown-6-ether (DB18C6), and benzo-18-crown-6-ether (B18C6) "hosts" interacting with N2, acetylene, water, and ammonia "guest" molecules. The gaseous host-guest complexes are generated under jet-cooled conditions. We apply various laser spectroscopic methods to obtain the conformer- and isomer-specified electronic and IR spectra. The experimental results are complemented with quantum chemical calculations ranging from density functional theory to high level first principles calculations at the MP2 and CCSD(T) levels of theory. We discuss the possible conformations of the bare host molecules, the structural changes they undergo upon complexation, and the key interactions that are responsible in stabilizing the specific complexes

  5. Laser spectroscopic and theoretical studies of the structures and encapsulation motifs of functional molecules

    NASA Astrophysics Data System (ADS)

    Ebata, Takayuki; Kusaka, Ryoji; Xantheas, Sotiris S.

    2015-01-01

    Extensive laser spectroscopic and theoretical studies have been recently carried out with the aim to reveal the structure and dynamics of encapsulation complexes in the gas phase. The characteristics of the encapsulation complexes are governed by the fact that (i) most of the host molecules are flexible and (ii) the complexes form high dimensional structures by using weak non-covalent interactions. These characteristics result in the possibility of the coexistence of many conformers in close energetic proximity. The combination of supersonic jet/laser spectroscopy and high level quantum chemical calculations is essential in tackling these challenging problems. In this report we describe our recent studies on the structures and dynamics of the encapsulation complexes formed by calix[4]arene (C4A), dibenzo-18-crown-6-ether (DB18C6), and benzo-18-crown-6-ether (B18C6) "hosts" interacting with N2, acetylene, water, and ammonia "guest" molecules. The gaseous host-guest complexes are generated under jet-cooled conditions. We apply various laser spectroscopic methods to obtain the conformer- and isomer-specified electronic and IR spectra. The experimental results are complemented with quantum chemical calculations ranging from density functional theory to high level first principles calculations at the MP2 and CCSD(T) levels of theory. We discuss the possible conformations of the bare host molecules, the structural changes they undergo upon complexation, and the key interactions that are responsible in stabilizing the specific complexes.

  6. Distinct circular dichroism spectroscopic signatures of polyproline II and unordered secondary structures: Applications in secondary structure analyses

    PubMed Central

    Lopes, Jose L S; Miles, Andrew J; Whitmore, Lee; Wallace, B A

    2014-01-01

    Circular dichroism (CD) spectroscopy is a valuable method for defining canonical secondary structure contents of proteins based on empirically-defined spectroscopic signatures derived from proteins with known three-dimensional structures. Many proteins identified as being “Intrinsically Disordered Proteins” have a significant amount of their structure that is neither sheet, helix, nor turn; this type of structure is often classified by CD as “other”, “random coil”, “unordered”, or “disordered”. However the “other” category can also include polyproline II (PPII)-type structures, whose spectral properties have not been well-distinguished from those of unordered structures. In this study, synchrotron radiation circular dichroism spectroscopy was used to investigate the spectral properties of collagen and polyproline, which both contain PPII-type structures. Their native spectra were compared as representatives of PPII structures. In addition, their spectra before and after treatment with various conditions to produce unfolded or denatured structures were also compared, with the aim of defining the differences between CD spectra of PPII and disordered structures. We conclude that the spectral features of collagen are more appropriate than those of polyproline for use as the representative spectrum for PPII structures present in typical amino acid-containing proteins, and that the single most characteristic spectroscopic feature distinguishing a PPII structure from a disordered structure is the presence of a positive peak around 220nm in the former but not in the latter. These spectra are now available for inclusion in new reference data sets used for CD analyses of the secondary structures of soluble proteins. PMID:25262612

  7. Access to a CuII–O–CuII Motif: Spectroscopic Properties, Solution Structure, and Reactivity

    PubMed Central

    Haack, Peter; Kärgel, Anne; Greco, Claudio; Dokic, Jadranka; Braun, Beatrice; Pfaff, Florian F.; Mebs, Stefan; Ray, Kallol; Limberg, Christian

    2013-01-01

    We report a complex with a rare CuII–O–CuII structural motif that is stable at room temperature, which allows its in-depth characterization by a variety of spectroscopic methods. Interest in such compounds is fueled by the recent discovery that a CuII–O–CuII species on the surface of Cu-ZSM-5 is capable of oxidizing methane to methanol and this in turn ties into mechanistic discussions on the methane oxidation at the dicopper site within the particulate methane monooxygenase. For the synthesis of our Cu2O complex we have developed a novel, neutral ligand system, FurNeu, exhibiting two N-(N',N'-dimethylaminoethyl)(2-pyridylmethyl)amino binding pockets connected by a dibenzofuran spacer. The reaction of FurNeu with CuCl yielded [FurNeu](Cu2(μ-Cl))(CuCl2), 1, demonstrating the geometric potential of the ligand to stabilize Cu–X–Cu moieties. A CuI precursor with weakly coordinating anions was chosen in the next step, namely [Cu(NCCH3)4]OTf, which led to the formation of [FurNeu](Cu(NCCH3))2(OTf)2, 3. Treatment of 3 with O2 or PhIO led to identical green solutions, whose UV/Vis spectra were markedly different from the one displayed by [FurNeu](Cu)2(OTf)4, 4, prepared independently from FurNeu and Cu(OTf)2. Further investigations including PhIO consumption experiments, NMR and UV/Vis spectroscopy, HR-ESI mass spectrometry and protonation studies led to the identification of the green product as [FurNeu](Cu2(μ-O))(OTf)2, 5. DOSY NMR spectroscopy confirmed its monomeric character. Over longer periods of time 5 decomposes to give [Cu(picoloyl)2], formed through an oxidative N-dealkylation reaction followed by further oxidation of the ligand. Due to its slow decomposition reaction all attempts to crystallize 5 failed. However, its structure in solution could be determined by EXAFS analysis in combination with DFT calculations, which revealed a Cu–O–Cu angle that amounts to 105.17°. Moreover, TDDFT calculations helped to rationalize the UV/Vis absorptions

  8. Access to a Cu(II)-O-Cu(II) motif: spectroscopic properties, solution structure, and reactivity.

    PubMed

    Haack, Peter; Kärgel, Anne; Greco, Claudio; Dokic, Jadranka; Braun, Beatrice; Pfaff, Florian F; Mebs, Stefan; Ray, Kallol; Limberg, Christian

    2013-10-30

    We report a complex with a rare Cu(II)-O-Cu(II) structural motif that is stable at room temperature, which allows its in-depth characterization by a variety of spectroscopic methods. Interest in such compounds is fueled by the recent discovery that a Cu(II)-O-Cu(II) species on the surface of Cu-ZSM-5 is capable of oxidizing methane to methanol, and this in turn ties into mechanistic discussions on the methane oxidation at the dicopper site within the particulate methane monooxygenase. For the synthesis of our Cu2O complex we have developed a novel, neutral ligand system, FurNeu, exhibiting two N-(N',N'-dimethylaminoethyl)(2-pyridylmethyl)amino binding pockets connected by a dibenzofuran spacer. The reaction of FurNeu with CuCl yielded [FurNeu](Cu2(μ-Cl))(CuCl2), 1, demonstrating the geometric potential of the ligand to stabilize Cu-X-Cu moieties. A Cu(I) precursor with weakly coordinating anions was chosen in the next step, namely [Cu(NCCH3)4]OTf, which led to the formation of [FurNeu](Cu(NCCH3))2(OTf)2, 3. Treatment of 3 with O2 or PhIO led to identical green solutions, whose UV-vis spectra were markedly different from the one displayed by [FurNeu](Cu)2(OTf)4, 4, prepared independently from FurNeu and Cu(OTf)2. Further investigations including PhIO consumption experiments, NMR and UV-vis spectroscopy, HR-ESI mass spectrometry, and protonation studies led to the identification of the green product as [FurNeu](Cu2(μ-O))(OTf)2, 5. DOSY NMR spectroscopy confirmed its monomeric character. Over longer periods of time 5 decomposes to give [Cu(picoloyl)2], formed through an oxidative N-dealkylation reaction followed by further oxidation of the ligand. Due to its slow decomposition reaction, all attempts to crystallize 5 failed. However, its structure in solution could be determined by EXAFS analysis in combination with DFT calculations, which revealed a Cu-O-Cu angle that amounts to 105.17°. Moreover, TDDFT calculations helped to rationalize the UV-vis absorptions of 5

  9. Electronic and structural properties of molybdenum thin films as determined by real-time spectroscopic ellipsometry

    SciTech Connect

    Walker, J. D.; Khatri, H.; Ranjan, V.; Li Jian; Collins, R. W.; Marsillac, S.

    2009-04-06

    Real-time spectroscopic ellipsometry (RTSE) is shown to be an effective contactless probe of radio frequency magnetron sputtered molybdenum thin films used as the back electrode in chalcopyrite [Cu(In,Ga)Se{sub 2}] solar cells. A series of Mo thin films was sputtered onto soda-lime glass substrates at Ar pressures ranging from 4 to 20 mTorr. RTSE measurements reveal how Ar pressure affects the nucleation and growth mechanisms that influence the films' ultimate grain structure and properties. Determinations of the free electron relaxation times at optical frequencies reveal that higher pressures lead to a smaller average grain size and increased void volume fraction.

  10. Growth, characterization, and crystal structure of a new chalcone derivative single crystal

    NASA Astrophysics Data System (ADS)

    Shettigar, Venkataraya; Dharmaprakash, S. M.

    2006-09-01

    A new organic nonlinear optical (NLO) chalcone derivative viz.1- ( 4- methoxyphenyl )-3- (3,4 - dimethoxy phenyl ) - 2 - propene-1-one, has been synthesized by Claisen-Schmidt condensation method. The synthesized compound was purified by repeated recrystallization process. To confirm the identity of the synthesized compound, FTIR spectra was recorded and various functional groups present were identified. NMR spectra were recorded for structural identity and purity confirmation of the synthesized compound. Good quality single crystals were grown by solvent evaporation and slow cooling technique using acetone as solvent. The grown crystals were characterized by UV-Visible , differential thermal analysis and linear refractive index measurement. The hardness of the crystal was determined using Vicker's indentation method. The single crystal structure analysis of the crystal was performed and it is found that the crystal belongs to monoclinic system with space group P2 I. The powder second harmonic generation(SHG)frequency conversion efficiency of the crystal was determined using Nd: YAG laser(λ = 1064nm)and it is 15 times that of Urea.

  11. Crystal structure of the co-crystal butyl-paraben-isonicotinamide (1/1).

    PubMed

    Bhardwaj, Rajni M; Yang, Huaiyu; Florence, Alastair J

    2016-01-01

    The title 1:1 co-crystal, C11H14O3·C6H6N2O [systematic name: butyl 4-hy-droxy-benzoate-isonicotinamide (1/1)], crystallizes with one mol-ecule of butyl-paraben (BPN) and one mol-ecule of isonicotinamide (ISN) in the asymmetric unit. In the crystal, BPN and ISN mol-ecules form hydrogen-bonded (O-H⋯N and N-H⋯O) dimers of paired BPN and ISN mol-ecules. These dimers are further connected to each other via N-H⋯O=C hydrogen bonds, creating ribbons in [011] which further stack along the a axis to form a layered structure with short C⋯C contacts of 3.285 (3) Å. Packing inter-actions within the crystal structure were assessed using PIXEL calculations. PMID:26870584

  12. Crystal structure of the co-crystal butyl­paraben–isonicotinamide (1/1)

    PubMed Central

    Bhardwaj, Rajni M.; Yang, Huaiyu; Florence, Alastair J.

    2016-01-01

    The title 1:1 co-crystal, C11H14O3·C6H6N2O [systematic name: butyl 4-hy­droxy­benzoate–isonicotinamide (1/1)], crystallizes with one mol­ecule of butyl­paraben (BPN) and one mol­ecule of isonicotinamide (ISN) in the asymmetric unit. In the crystal, BPN and ISN mol­ecules form hydrogen-bonded (O—H⋯N and N—H⋯O) dimers of paired BPN and ISN mol­ecules. These dimers are further connected to each other via N—H⋯O=C hydrogen bonds, creating ribbons in [011] which further stack along the a axis to form a layered structure with short C⋯C contacts of 3.285 (3) Å. Packing inter­actions within the crystal structure were assessed using PIXEL calculations. PMID:26870584

  13. Crystal structure of the co-crystal butyl-paraben-isonicotinamide (1/1).

    PubMed

    Bhardwaj, Rajni M; Yang, Huaiyu; Florence, Alastair J

    2016-01-01

    The title 1:1 co-crystal, C11H14O3·C6H6N2O [systematic name: butyl 4-hy-droxy-benzoate-isonicotinamide (1/1)], crystallizes with one mol-ecule of butyl-paraben (BPN) and one mol-ecule of isonicotinamide (ISN) in the asymmetric unit. In the crystal, BPN and ISN mol-ecules form hydrogen-bonded (O-H⋯N and N-H⋯O) dimers of paired BPN and ISN mol-ecules. These dimers are further connected to each other via N-H⋯O=C hydrogen bonds, creating ribbons in [011] which further stack along the a axis to form a layered structure with short C⋯C contacts of 3.285 (3) Å. Packing inter-actions within the crystal structure were assessed using PIXEL calculations.

  14. Crystal structure of CmlI, the arylamine oxygenase from the chloramphenicol biosynthetic pathway.

    PubMed

    Knoot, Cory J; Kovaleva, Elena G; Lipscomb, John D

    2016-09-01

    The diiron cluster-containing oxygenase CmlI catalyzes the conversion of the aromatic amine precursor of chloramphenicol to the nitroaromatic moiety of the active antibiotic. The X-ray crystal structures of the fully active, N-terminally truncated CmlIΔ33 in the chemically reduced Fe(2+)/Fe(2+) state and a cis μ-1,2(η (1):η (1))-peroxo complex are presented. These structures allow comparison with the homologous arylamine oxygenase AurF as well as other types of diiron cluster-containing oxygenases. The structural model of CmlIΔ33 crystallized at pH 6.8 lacks the oxo-bridge apparent from the enzyme optical spectrum in solution at higher pH. In its place, residue E236 forms a μ-1,3(η (1):η (2)) bridge between the irons in both models. This orientation of E236 stabilizes a helical region near the cluster which closes the active site to substrate binding in contrast to the open site found for AurF. A very similar closed structure was observed for the inactive dimanganese form of AurF. The observation of this same structure in different arylamine oxygenases may indicate that there are two structural states that are involved in regulation of the catalytic cycle. Both the structural studies and single crystal optical spectra indicate that the observed cis μ-1,2(η (1):η (1))-peroxo complex differs from the μ-η (1):η (2)-peroxo proposed from spectroscopic studies of a reactive intermediate formed in solution by addition of O2 to diferrous CmlI. It is proposed that the structural changes required to open the active site also drive conversion of the µ-1,2-peroxo species to the reactive form. PMID:27229511

  15. Predicting inclusion behaviour and framework structures in organic crystals.

    PubMed

    Cruz-Cabeza, Aurora J; Day, Graeme M; Jones, William

    2009-12-01

    We have used well-established computational methods to generate and explore the crystal structure landscapes of four organic molecules of well-known inclusion behaviour. Using these methods, we are able to generate both close-packed crystal structures and high-energy open frameworks containing voids of molecular dimensions. Some of these high-energy open frameworks correspond to real structures observed experimentally when the appropriate guest molecules are present during crystallisation. We propose a combination of crystal structure prediction methodologies with structure rankings based on relative lattice energy and solvent-accessible volume as a way of selecting likely inclusion frameworks completely ab initio. This methodology can be used as part of a rational strategy in the design of inclusion compounds, and also for the anticipation of inclusion behaviour in organic molecules. PMID:19876969

  16. Evolution of molecular crystal optical phonons near structural phase transitions

    NASA Astrophysics Data System (ADS)

    Michki, Nigel; Niessen, Katherine; Xu, Mengyang; Markelz, Andrea

    Molecular crystals are increasingly important photonic and electronic materials. For example organic semiconductors are lightweight compared to inorganic semiconductors and have inexpensive scale up processing with roll to roll printing. However their implementation is limited by their environmental sensitivity, in part arising from the weak intermolecular interactions of the crystal. These weak interactions result in optical phonons in the terahertz frequency range. We examine the evolution of intermolecular interactions near structural phase transitions by measuring the optical phonons as a function of temperature and crystal orientation using terahertz time-domain spectroscopy. The measured orientation dependence of the resonances provides an additional constraint for comparison of the observed spectra with the density functional calculations, enabling us to follow specific phonon modes. We observe crystal reorganization near 350 K for oxalic acid as it transforms from dihydrate to anhydrous form. We also report the first THz spectra for the molecular crystal fructose through its melting point.

  17. Spectroscopic and structural study of the newly synthesized heteroligand complex of copper with creatinine and urea.

    PubMed

    Gangopadhyay, Debraj; Singh, Sachin Kumar; Sharma, Poornima; Mishra, Hirdyesh; Unnikrishnan, V K; Singh, Bachcha; Singh, Ranjan K

    2016-02-01

    Study of copper complex of creatinine and urea is very important in life science and medicine. In this paper, spectroscopic and structural study of a newly synthesized heteroligand complex of copper with creatinine and urea has been discussed. Structural studies have been carried out using DFT calculations and spectroscopic analyses were carried out by FT-IR, Raman, UV-vis absorption and fluorescence techniques. The copper complex of creatinine and the heteroligand complex were found to have much increased water solubility as compared to pure creatinine. The analysis of FT-IR and Raman spectra helps to understand the coordination properties of the two ligands and to determine the probable structure of the heteroligand complex. The LIBS spectra of the heteroligand complex reveal that the complex is free from other metal impurities. UV-visible absorption spectra and the fluorescence emission spectra of the aqueous solution of Cu-Crn-urea heteroligand complex at different solute concentrations have been analyzed and the complex is found to be rigid and stable in its monomeric form at very low concentrations.

  18. Spectroscopic and structural study of the newly synthesized heteroligand complex of copper with creatinine and urea

    NASA Astrophysics Data System (ADS)

    Gangopadhyay, Debraj; Singh, Sachin Kumar; Sharma, Poornima; Mishra, Hirdyesh; Unnikrishnan, V. K.; Singh, Bachcha; Singh, Ranjan K.

    2016-02-01

    Study of copper complex of creatinine and urea is very important in life science and medicine. In this paper, spectroscopic and structural study of a newly synthesized heteroligand complex of copper with creatinine and urea has been discussed. Structural studies have been carried out using DFT calculations and spectroscopic analyses were carried out by FT-IR, Raman, UV-vis absorption and fluorescence techniques. The copper complex of creatinine and the heteroligand complex were found to have much increased water solubility as compared to pure creatinine. The analysis of FT-IR and Raman spectra helps to understand the coordination properties of the two ligands and to determine the probable structure of the heteroligand complex. The LIBS spectra of the heteroligand complex reveal that the complex is free from other metal impurities. UV-visible absorption spectra and the fluorescence emission spectra of the aqueous solution of Cu-Crn-urea heteroligand complex at different solute concentrations have been analyzed and the complex is found to be rigid and stable in its monomeric form at very low concentrations.

  19. Raman spectroscopic investigation of polycrystalline structures of CVD-grown graphene by isotope labeling.

    PubMed

    Wang, Shengnan; Suzuki, Satoru; Hibino, Hiroki

    2014-11-21

    Topological defects, such as point defects, dislocations and grain boundaries, have a dramatic influence on the chemical and physical properties of large-scale graphene grown by chemical vapor deposition (CVD) method. Here we demonstrate the Raman visualization of polycrystalline structures in an isotopically modified CVD graphene. By means of the reversible reaction of methane on a copper catalyst, the etching of (12)C-lattice and surface deposition of (13)C-atoms occur in CVD graphene by sequentially introducing hydrogen and isotopic methane after standard growth of graphene with full monolayer coverage. Spatial Raman spectroscopic mapping on labeled graphene reveals pronounced network-like (13)C-rich regions, which are further identified to exist along the grain boundaries of graphene by low-energy electron microscopy. The structural defects inside the graphene grains are also targeted in the isotope labeling process. Our work opens a new way to investigate multiple grain structures in CVD graphene with a simple spectroscopic technique. PMID:25303722

  20. Crystal chemistry and Mössbauer spectroscopic analysis of clays around Riyadh for brick industry

    NASA Astrophysics Data System (ADS)

    Khalil, Mutasim I.

    2013-04-01

    A total of 30 clay samples were collected from the area around Riyadh city, Saudi Arabia. A complete chemical analysis was carried out using different techniques. X-ray diffraction studies showed that the clay samples were mainly of the smectite group with traces of the kaolinite one. The samples studied were classified as nontronite clay minerals. One of the clay fraction has been studied by Mössbauer spectroscopy as raw clay fraction and after being fired at 950-1,000 °C. The Mössbauer spectra showed accessory iron compounds in the form of hematite and goethite. The structural iron contents disintegrate on firing transforming into magnetic iron oxide and a paramagnetic small particles iron oxide.

  1. Optical and structural properties of chalcone NLO single crystals

    NASA Astrophysics Data System (ADS)

    Rajesh Kumar, P. C.; Ravindrachary, V.; Janardhana, K.; Manjunath, H. R.; Karegouda, Prakash; Crasta, Vincent; Sridhar, M. A.

    2011-11-01

    Organic compound (E)-1-(4-methoxyphenyl)-3-(2,3,5-trichlorophenyl)prop-2-en-1-one [MPTCPP] with molecular formula C 16H 11Cl 3O 2 was synthesized using Claisen-Schmidt condensation reaction method. 1H NMR spectra was recorded to identify the various functional groups present in the compound and confirm the chemical structure. The single crystals were grown using slow evaporation solution growth technique. The UV-Visible spectrum study reveals that the crystal is transparent in the entire visible region and the absorption is observed at 364 nm. The Kurtz powder second harmonic generation (SHG) test shows that the MPTCPP is NLO active and its SHG efficiency is three times that of urea. Single crystal XRD study shows that the compound crystallizes in the monoclinic system with a space group Cc. The corresponding lattice parameters of the crystal are a = 28.215(5) Å, b = 3.9740(4) Å, c = 16.178(3) Å and V = 1503.0(4) Å 3. The micro hardness test was carried out and the work hardening coefficient value ( n) of the crystal was found to be 1.48. This indicates that the crystal is hard and is suitable for device application. The thermal study reveals that the thermal stability of the crystal is good.

  2. Single-Crystal Structure of a Covalent Organic Framework

    SciTech Connect

    Zhang, YB; Su, J; Furukawa, H; Yun, YF; Gandara, F; Duong, A; Zou, XD; Yaghi, OM

    2013-11-06

    The crystal structure of a new covalent organic framework, termed COF-320, is determined by single-crystal 3D electron diffraction using the rotation electron diffraction (RED) method for data collection. The COF crystals are prepared by an imine condensation of tetra-(4-anilyl)methane and 4,4'-biphenyldialdehyde in 1,4-dioxane at 120 degrees C to produce a highly porous 9-fold interwoven diamond net. COF-320 exhibits permanent porosity with a Langmuir surface area of 2400 m(2)/g and a methane total uptake of 15.0 wt % (176 cm(3)/cm(3)) at 25 degrees C and 80 bar. The successful determination of the structure of COF-320 directly from single-crystal samples is an important advance in the development of COF chemistry.

  3. Structural, morphological and spectroscopic properties of Eu{sup 3+}-doped rare earth fluorides synthesized by the hydrothermalmethod

    SciTech Connect

    Grzyb, Tomasz; Runowski, Marcin; Szczeszak, Agata; Lis, Stefan

    2013-04-15

    Rare earth fluorides (REF{sub 3}, RE=Y, La, Gd or Yb) doped with 5% of Eu{sup 3+} ions were synthesized via the hydrothermal method and their physicochemical properties were compared. The synthesis was carried out in an aqueous medium at elevated pressure and temperature. The reaction was performed in situ, with use of NaBF{sub 4} as a source of fluoride ions. Structural and morphological properties of obtained nanophosphors were characterized with the use of powder X-ray diffraction (XRD), transmission electron microscopy (TEM) and Raman spectroscopy. Synthesized products were nanocrystalline with hexagonal or orthorhombic crystal structures. They showed different morphology, from nanoplates to nanorings, depending on the used REF{sub 3} fluoride as the host for the Eu{sup 3+} ions. The elemental composition was confirmed by the energy-dispersive X-ray spectroscopy (EDX) results. Spectroscopic properties were investigated by measuring the excitation and emission spectra. Also luminescence lifetimes were determined. The synthesized materials showed bright red luminescence, due to the presence of Eu{sup 3+} ions in their structure. - Graphical abstract: Luminescence spectra of the REF{sub 3}:Eu{sup 3+} (RE=Y, La, Gd and Yb) fluorides and their TEM images as background. Highlights: ► Nanocrystalline fluorides were synthesized using modified hydrothermal method. ► Structural and morphological properties of in situ prepared nanomaterials were studied. ► Luminescence properties of REF{sub 3}:Eu{sup 3+} (RE=Y, La, Gd, Yb) were compared and investigated.

  4. The different conformations and crystal structures of dihydroergocristine

    NASA Astrophysics Data System (ADS)

    Mönch, B.; Kraus, W.; Köppen, R.; Emmerling, F.

    2016-02-01

    The identification of different forms of dihydroergocristine (DHEC) was carried out by crystallization from different organic solvents. DHEC was identified as potential template for molecularly imprinted polymers (MIPs) for the epimeric specific analysis of ergot alkaloids (EAs) in food. DHEC was crystallized from different solvents in order to mimic the typical MIP synthesis conditions. Four new solvatomorphs of DHEC were obtained. All solvatomorphs contain a water molecule in the crystal structure, whereas three compounds contain an additional solvent molecule. Based on the conformation of DHEC a comparison with typical EA molecules was possible. The analysis showed that DHEC is a suitable template for MIPs for EAs.

  5. Observation and Analysis of Polymer Crystal Structures at the Stem Level. Implications Regarding Polymer Crystallization Processes.

    NASA Astrophysics Data System (ADS)

    Lotz, Bernard

    2003-03-01

    The building element of chain folded polymer crystals is the individual stem that spans the lamellar thickness. For chiral but racemic helical polymers such as polyolefins (e.g. isotactic and syndiotactic polypropylene and poly(1-butene)), stems can be right- or left-handed helices. These polymers can exist in various crystal polymorphs that are either "racemic" or "chiral" (made of both, or of only one helical hand). Upon crystallization, each stem has a conformational "choice", but must adapt to the crystal structure and, once crystallized, is characterized by a "conformational tag" (right or left hand). Various means exist to determine or observe helical hands in polyolefin lamellae: Atomic Force Microscopy on epitaxially crystallized samples, or, for the alpha phase of isotactic polypropylene, analysis of its specific lamellar branching. These observations and analyses indicate that the helical hand of stems is tightly determined by the substrate or growth face topography, i.e. indicate that the depositing stem probes and adapts to the surface structure prior to successful attachment. This "post-mortem" analysis of the crystal structure and stem chirality emphasizes the "sequential" nature of the growth process (successive attachment of individual stems). It is in line with early views on polymer crystallization. It is at variance with recently introduced models or scenarios that assume either some pre-ordering of the polymer melt as a result of spinodal decomposition and/or accretion of polymer chains in pseudo-crystalline bundles followed by (solid state) reorganization of the bundles to generate fully grown lamellae.

  6. Influence of vapor transport equilibration on spectroscopic properties of Er :LiNbO3 crystal heavily codoped with MgO

    NASA Astrophysics Data System (ADS)

    Zhang, De-Long; Wang, Dun-Chun; Pun, E. Y. B.

    2005-05-01

    Z-cut MgO heavily codoped (6mol%) Er(0.4mol%):LiNbO3 crystals were thermally treated at 1110 and 1120°C over 100, 120, and 220h using vapor transport equilibration (VTE) technique. Visible and infrared-absorption and x-ray powder diffraction have been used to characterize their spectral, spectroscopic, and crystalline phase characteristics in comparison with the as-grown crystal. The experimental results show that VTE treatment results in the reduction of background absorption and 4-5-nm blueshift of the optical-absorption edge, qualitatively showing that these crystals have been brought closer to stoichiometric composition. The VTE procedure also results in remarkable Er3+ absorption changes. These spectroscopic changes imply that the VTE treatment may result in the formation of ErNbO4 precipitates in all VTE crystals. In addition, the VTE treatment also results in substantial spectral changes with respect to OH - absorption. These OH - spectral changes are explained from the viewpoint of VTE-induced site-occupancy alterations of intrinsic and extrinsic defects. Based upon the measured absorption spectra, the influences of VTE treatment on the Er3+ spectroscopic parameters were studied by using the Judd-Ofelt (JO) theory. The theoretical results show that VTE treatment has a little influence on the branch ratio, and a substantial influence on JO parameters and electron transition probability because of the phase transformation with respect to Er3+. The VTE treatment results in the increase of the JO parameters by more than 50% and theoretical radiative lifetime by 50%-120%.

  7. Boron-oxygen polyanion in the crystal structure of tunellite

    USGS Publications Warehouse

    Clark, J.R.

    1963-01-01

    The crystal structure of tunellite, SrO??3B2O 3??4H2O, with infinite sheets of composition n[B6O9(OH)2]2-, has cations and water molecules in the spaces within the sheets. Adjacent sheets are held together by hydrogen bonding through the water molecules. The boron-oxygen polyanions provide the first example in hydrated borate crystals of one oxygen linked to three borons.

  8. Structure of ice crystallized from supercooled water

    PubMed Central

    Malkin, Tamsin L.; Murray, Benjamin J.; Brukhno, Andrey V.; Anwar, Jamshed; Salzmann, Christoph G.

    2012-01-01

    The freezing of water to ice is fundamentally important to fields as diverse as cloud formation to cryopreservation. At ambient conditions, ice is considered to exist in two crystalline forms: stable hexagonal ice and metastable cubic ice. Using X-ray diffraction data and Monte Carlo simulations, we show that ice that crystallizes homogeneously from supercooled water is neither of these phases. The resulting ice is disordered in one dimension and therefore possesses neither cubic nor hexagonal symmetry and is instead composed of randomly stacked layers of cubic and hexagonal sequences. We refer to this ice as stacking-disordered ice I. Stacking disorder and stacking faults have been reported earlier for metastable ice I, but only for ice crystallizing in mesopores and in samples recrystallized from high-pressure ice phases rather than in water droplets. Review of the literature reveals that almost all ice that has been identified as cubic ice in previous diffraction studies and generated in a variety of ways was most likely stacking-disordered ice I with varying degrees of stacking disorder. These findings highlight the need to reevaluate the physical and thermodynamic properties of this metastable ice as a function of the nature and extent of stacking disorder using well-characterized samples. PMID:22232652

  9. Spectroscopic properties and structure refinement of Nd3+:(Y0.9La0.1)2O3 transparent ceramics

    NASA Astrophysics Data System (ADS)

    Lu, Qing; Yang, Qiuhong; Jiang, Cen; Lu, Shenzhou; Yuan, Ye; Liu, Qiang; Lu, Bo

    2014-11-01

    (NdxY0.9-xLa0.1)2O3 (x = 0.01-0.04) transparent ceramics were fabricated by conventional solid state reaction processing. Spectroscopic properties and crystal structures were investigated. (Nd0.01Y0.89La0.1)2O3 ceramics display high transparency and dense structure with almost no pores. The highest transmittance reaches 80%. The absorption at LD wavelength 806 nm is high with broad full width at half maximum (FWHM) of about 6 nm. The strongest emission peak is centered at 1078 nm with broad FWHM of about 9 nm and the stimulated emission cross section is 4.97 × 10-20 cm2. The crystal structure was obtained via Rietveld refinement. It is found that (NdxY0.9-xLa0.1)2O3 crystallize in space group of Ia3bar, Z = 16. The lattice parameters and average bond lengths are increased with the increase of La2O3 and Nd2O3 contents.

  10. Effects of 5f-elements on electronic structures and spectroscopic properties of gold superatom model

    NASA Astrophysics Data System (ADS)

    Gao, Yang; Wang, Zhigang

    2016-08-01

    5f-elements encaged in a gold superatomic cluster are capable of giving rise to unique optical properties due to their hyperactive valence electrons and great radial components of 5f/6d orbitals. Herein, we review our first-principles studies on electronic structures and spectroscopic properties of a series of actinide-embedded gold superatomic clusters with different dimensions. The three-dimensional (3D) and two-dimensional (2D) superatom clusters possess the 18-electron configuration of 1S21P61D10 and 10-electron configuration of 1S21P41D4, respectively. Importantly, their electronic absorption spectra can also be effectively explained by the superatom orbitals. Specifically, the charge transfer (CT) transitions involved in surface-enhance Raman spectroscopy (SERS) spectra for 3D and 2D structures are both from the filled 1D orbitals, providing the enhancement factors of the order of ∼ 104 at 488 nm and ∼ 105 at 456 nm, respectively. This work implies that the superatomic orbital transitions involved in 5f-elements can not only lead to a remarkable spectroscopic performance, but also a new direction for optical design in the future. Project supported by the National Natural Science Foundation of China (Grant No. 11374004), the Science and Technology Development Program of Jilin Province, China (Grant No. 20150519021JH), the Fok Ying Tung Education Foundation, China (Grant No. 142001), and the Support from the High Performance Computing Center (HPCC) of Jilin University, China.

  11. Effects of 5f-elements on electronic structures and spectroscopic properties of gold superatom model

    NASA Astrophysics Data System (ADS)

    Gao, Yang; Wang, Zhigang

    2016-08-01

    5f-elements encaged in a gold superatomic cluster are capable of giving rise to unique optical properties due to their hyperactive valence electrons and great radial components of 5f/6d orbitals. Herein, we review our first-principles studies on electronic structures and spectroscopic properties of a series of actinide-embedded gold superatomic clusters with different dimensions. The three-dimensional (3D) and two-dimensional (2D) superatom clusters possess the 18-electron configuration of 1S21P61D10 and 10-electron configuration of 1S21P41D4, respectively. Importantly, their electronic absorption spectra can also be effectively explained by the superatom orbitals. Specifically, the charge transfer (CT) transitions involved in surface-enhance Raman spectroscopy (SERS) spectra for 3D and 2D structures are both from the filled 1D orbitals, providing the enhancement factors of the order of ˜ 104 at 488 nm and ˜ 105 at 456 nm, respectively. This work implies that the superatomic orbital transitions involved in 5f-elements can not only lead to a remarkable spectroscopic performance, but also a new direction for optical design in the future. Project supported by the National Natural Science Foundation of China (Grant No. 11374004), the Science and Technology Development Program of Jilin Province, China (Grant No. 20150519021JH), the Fok Ying Tung Education Foundation, China (Grant No. 142001), and the Support from the High Performance Computing Center (HPCC) of Jilin University, China.

  12. Heterogeneous Crystallization on Pairs of Pre-Structured Seeds.

    PubMed

    Jungblut, Swetlana; Dellago, Christoph

    2016-09-01

    Studying the effects of small pre-structured seeds on the crystallization transition in an undercooled monodisperse Lennard-Jones fluid with transition interface path sampling combined with molecular dynamics simulations, we analyze the impact of the simultaneous presence of two seeds with various structures. In the presence of seeds with face- and body-centered cubic structures, we find that decreasing the seed-to-seed distance enhances the probability of the crystalline clusters formed on one of the seeds to grow beyond the critical size, thus, increasing the crystal nucleation rates. In contrast, when seeds have an icosahedral structure, the crystalline clusters form mostly in the bulk. The crystal nucleation rate, however, is also determined by the distance between the seeds with regular structure in which the lattice spacing is equal to the bulk lattice constant, pointing to a heterogeneous crystal nucleation that occurs away from the icosahedrally structured seeds. For slightly squeezed seeds, the effects of the presence of seeds with face- and body-centered cubic structures are reduced in comparison to the regular seeds, and we do not see any effect of the presence of the second seed for seeds with squeezed icosahedral structure. PMID:27479875

  13. Heterogeneous Crystallization on Pairs of Pre-Structured Seeds

    PubMed Central

    2016-01-01

    Studying the effects of small pre-structured seeds on the crystallization transition in an undercooled monodisperse Lennard-Jones fluid with transition interface path sampling combined with molecular dynamics simulations, we analyze the impact of the simultaneous presence of two seeds with various structures. In the presence of seeds with face- and body-centered cubic structures, we find that decreasing the seed-to-seed distance enhances the probability of the crystalline clusters formed on one of the seeds to grow beyond the critical size, thus, increasing the crystal nucleation rates. In contrast, when seeds have an icosahedral structure, the crystalline clusters form mostly in the bulk. The crystal nucleation rate, however, is also determined by the distance between the seeds with regular structure in which the lattice spacing is equal to the bulk lattice constant, pointing to a heterogeneous crystal nucleation that occurs away from the icosahedrally structured seeds. For slightly squeezed seeds, the effects of the presence of seeds with face- and body-centered cubic structures are reduced in comparison to the regular seeds, and we do not see any effect of the presence of the second seed for seeds with squeezed icosahedral structure. PMID:27479875

  14. Crystal structure and characterization of a novel organic optical crystal: 2-Aminopyridinium trichloroacetate

    SciTech Connect

    Dhanaraj, P.V.; Rajesh, N.P.; Vinitha, G.; Bhagavannarayana, G.

    2011-05-15

    Research highlights: {yields} Good quality crystals of 2-aminopyridinium trichloroacetate were grown for first time. {yields} 2-Aminopyridinium trichloroacetate crystal belongs to monoclinic crystal system with space group P21/c. {yields} 2-Aminopyridinium trichloroacetate crystal exhibits third order nonlinear optical properties. {yields} 2-Aminopyridinium trichloroacetate is a low dielectric constant material. -- Abstract: 2-Aminopyridinium trichloroacetate, a novel organic optical material has been synthesized and crystals were grown from aqueous solution employing the technique of controlled evaporation. 2-Aminopyridinium trichloroacetate crystallizes in monoclinic system with space group P2{sub 1}/c and the lattice parameters are a = 8.598(5) A, b = 11.336(2) A, c = 11.023(2) A, {beta} = 102.83(1){sup o} and volume = 1047.5(3) A{sup 3}. High-resolution X-ray diffraction measurements were performed to analyze the structural perfection of the grown crystals. Thermal analysis shows a sharp endothermic peak at 124 {sup o}C due to melting reaction of 2-aminopyridinium trichloroacetate. UV-vis-NIR studies reveal that 2-aminopyridinium trichloroacetate has UV cutoff wavelength at 354 nm. Dielectric studies show that dielectric constant and dielectric loss decreases with increasing frequency and finally it becomes almost a constant at higher frequencies for all temperatures. The negative nonlinear optical parameters of 2-aminopyridinium trichloroacetate were derived by the Z-scan technique.

  15. Isolation, crystallization and crystal structure determination of bovine kidney Na(+),K(+)-ATPase.

    PubMed

    Gregersen, Jonas Lindholt; Mattle, Daniel; Fedosova, Natalya U; Nissen, Poul; Reinhard, Linda

    2016-04-01

    Na(+),K(+)-ATPase is responsible for the transport of Na(+) and K(+) across the plasma membrane in animal cells, thereby sustaining vital electrochemical gradients that energize channels and secondary transporters. The crystal structure of Na(+),K(+)-ATPase has previously been elucidated using the enzyme from native sources such as porcine kidney and shark rectal gland. Here, the isolation, crystallization and first structure determination of bovine kidney Na(+),K(+)-ATPase in a high-affinity E2-BeF3(-)-ouabain complex with bound magnesium are described. Crystals belonging to the orthorhombic space group C2221 with one molecule in the asymmetric unit exhibited anisotropic diffraction to a resolution of 3.7 Å with full completeness to a resolution of 4.2 Å. The structure was determined by molecular replacement, revealing unbiased electron-density features for bound BeF3(-), ouabain and Mg(2+) ions. PMID:27050261

  16. Structural effects of monovalent anions on polymorphic lysozyme crystals.

    PubMed

    Vaney, M C; Broutin, I; Retailleau, P; Douangamath, A; Lafont, S; Hamiaux, C; Prangé, T; Ducruix, A; Riès-Kautt, M

    2001-07-01

    Understanding direct salt effects on protein crystal polymorphism is addressed by comparing different crystal forms (triclinic, monoclinic, tetragonal and orthorhombic) for hen, turkey, bob white quail and human lysozymes. Four new structures of hen egg-white lysozyme are reported: crystals grown in the presence of NapTS diffracted to 1.85 A, of NaI to 1.6 A, of NaNO(3) to 1.45 A and of KSCN to 1.63 A. These new structures are compared with previously published structures in order to draw a mapping of the surface of different lysozymes interacting with monovalent anions, such as nitrate, chloride, iodide, bromide and thiocyanate. An analysis of the structural sites of these anions in the various lysozyme structures is presented. This study shows common anion sites whatever the crystal form and the chemical nature of anions, while others seem specific to a given geometry and a particular charge environment induced by the crystal packing.

  17. Synthesis and crystal structure determination of yttrium ultraphosphate YP{sub 5}O{sub 14}

    SciTech Connect

    Mbarek, A.; Graia, M. Chadeyron, G.; Zambon, D.; Bouaziz, J.; Fourati, M.

    2009-03-15

    The crystal structure of monoclinic YP{sub 5}O{sub 14} (space group C2/c, a=12.919(2) A, b=12.796(4) A, c=12.457(2) A, {beta}=91.30(1){sup o}, Z=8) has been refined from single-crystal X-ray diffraction data. Full-matrix least-squares refinement on F{sup 2} using 2249 independent reflections for 183 refinable parameters results in a final R value of 0.027 ({omega}R=0.069). The structure is isotypic with HoP{sub 5}O{sub 14}. This structure is built up from infinite layers of PO{sub 4} tetrahedra linked through isolated YO{sub 8} polyhedra. The three-dimensional cohesion of the framework results from Y-O-P bridges. This crystal structure refinement leads to the calculated X-ray diffraction powder pattern of this monoclinic polymorph, which has been the starting point of a thorough study of the solid-state synthesis of this ultraphosphate. This investigation further leads to a better outstanding of features observed during the synthesis of powdered samples. The thermal behavior of this ultraphosphate has been studied by DTA and TGA analyses. The infrared and Raman spectroscopic characterizations have been carried out on polycrystalline samples. The luminescence properties of the Eu{sup 3+} ion incorporated in the monoclinic C2/c polymorph of YP{sub 5}O{sub 14} as local structural probe show that in YP{sub 5}O{sub 14}: 5% Eu{sup 3+} sample, the Eu{sup 3+} ions are distributed over the two Y{sup 3+} crystallographic sites of C{sub 2} symmetry of this structure. - Graphical Abstract: The crystal structure of the monoclinic C2/c polymorph of YP{sub 5}O{sub 14} has been refined from single-crystal X-ray diffraction data. The luminescence properties of the Eu{sup 3+} ion incorporated in this matrix as local structural probe show that the Eu{sup 3+} ions are distributed over the two Y{sup 3+} crystallographic sites of C{sub 2} symmetry of this structure.

  18. Ytterbium- and neodymium-doped vanadate laser hose crystals having the apatite crystal structure

    DOEpatents

    Payne, S.A.; Kway, W.L.; DeLoach, L.D.; Krupke, W.F.; Chai, B.H.T.

    1994-08-23

    Yb[sup 3+] and Nd[sup 3+] doped Sr[sub 5](VO[sub 4])[sub 3]F crystals serve as useful infrared laser media that exhibit low thresholds of oscillation and high slope efficiencies, and can be grown with high optical quality. These laser media possess unusually high absorption and emission cross sections, which provide the crystals with the ability to generate greater gain for a given amount of pump power. Many related crystals such as Sr[sub 5](VO[sub 4])[sub 3]F crystals doped with other rare earths, transition metals, or actinides, as well as the many structural analogs of Sr[sub 5](VO[sub 4])[sub 3]F, where the Sr[sup 2+] and F[sup [minus

  19. Ytterbium- and neodymium-doped vanadate laser hose crystals having the apatite crystal structure

    DOEpatents

    Payne, Stephen A.; Kway, Wayne L.; DeLoach, Laura D.; Krupke, William F.; Chai, Bruce H. T.

    1994-01-01

    Yb.sup.3+ and Nd.sup.3+ doped Sr.sub.5 (VO.sub.4).sub.3 F crystals serve as useful infrared laser media that exhibit low thresholds of oscillation and high slope efficiencies, and can be grown with high optical quality. These laser media possess unusually high absorption and emission cross sections, which provide the crystals with the ability to generate greater gain for a given amount of pump power. Many related crystals such as Sr.sub.5 (VO.sub.4).sub.3 F crystals doped with other rare earths, transition metals, or actinides, as well as the many structural analogs of Sr.sub.5 (VO.sub.4).sub.3 F, where the Sr.sup.2+ and F.sup.- ions are replaced by related chemical species, have similar properties.

  20. Combined crystal structure prediction and high-pressure crystallization in rational pharmaceutical polymorph screening

    NASA Astrophysics Data System (ADS)

    Neumann, M. A.; van de Streek, J.; Fabbiani, F. P. A.; Hidber, P.; Grassmann, O.

    2015-07-01

    Organic molecules, such as pharmaceuticals, agro-chemicals and pigments, frequently form several crystal polymorphs with different physicochemical properties. Finding polymorphs has long been a purely experimental game of trial-and-error. Here we utilize in silico polymorph screening in combination with rationally planned crystallization experiments to study the polymorphism of the pharmaceutical compound Dalcetrapib, with 10 torsional degrees of freedom one of the most flexible molecules ever studied computationally. The experimental crystal polymorphs are found at the bottom of the calculated lattice energy landscape, and two predicted structures are identified as candidates for a missing, thermodynamically more stable polymorph. Pressure-dependent stability calculations suggested high pressure as a means to bring these polymorphs into existence. Subsequently, one of them could indeed be crystallized in the 0.02 to 0.50 GPa pressure range and was found to be metastable at ambient pressure, effectively derisking the appearance of a more stable polymorph during late-stage development of Dalcetrapib.

  1. Structural and spectroscopic characterization of 2,2‧-methylenedi-8-quinolinol dihydrochloride dihydrate

    NASA Astrophysics Data System (ADS)

    Zinczuk, J.; Piro, O. E.; Castellano, E. E.; Baran, E. J.

    2008-12-01

    The crystal structure of the title compound, a promising ligand for chelatoterapies in the treatment of Alzheimer's disease, has been determined by single crystal X-ray diffractometry. The compound crystallized in the monoclinic space group C2/c with Z = 4. The dimeric 8-quinolinol molecule is sited on a crystallographic twofold axis passing through the CH 2 carbon atom that links the symmetry related molecular halves, giving rise to a two-bladed propeller-like conformation. The 1H and 13C NMR as well as the FT-IR and Raman spectra of the compound were also recorded and are briefly discussed. Some comparisons with spectra of related species are made.

  2. Theoretical Studies on the Electronic Structures and Properties of Complex Ceramic Crystals and Novel Materials

    SciTech Connect

    Ching, Wai-Yim

    2012-01-14

    This project is a continuation of a long program supported by the Office of Basic Energy Science in the Office of Science of DOE for many years. The final three-year continuation started on November 1, 2005 with additional 1 year extension to October 30, 2009. The project was then granted a two-year No Cost Extension which officially ended on October 30, 2011. This report covers the activities within this six year period with emphasis on the work completed within the last 3 years. A total of 44 papers with acknowledgement to this grant were published or submitted. The overall objectives of this project are as follows. These objectives have been evolved over the six year period: (1) To use the state-of-the-art computational methods to investigate the electronic structures of complex ceramics and other novel crystals. (2) To further investigate the defects, surfaces/interfaces and microstructures in complex materials using large scale modeling. (3) To extend the study on ceramic materials to more complex bioceramic crystals. (4) To initiate the study on soft condensed matters including water and biomolecules. (5) To focus on the spectroscopic studies of different materials especially on the ELNES and XANES spectral calculations and their applications related to experimental techniques. (6) To develop and refine computational methods to be effectively executed on DOE supercomputers. (7) To evaluate mechanical properties of different crystals and those containing defects and relate them to the fundamental electronic structures. (8) To promote and publicize the first-principles OLCAO method developed by the PI (under DOE support for many years) for applications to large complex material systems. (9) To train a new generation of graduate students and postdoctoral fellows in modern computational materials science and condensed matter physics. (10) To establish effective international and domestic collaborations with both experimentalists and theorists in materials

  3. Spectroscopic characterization and molecular structure of 3,14-dimethyl-2,6,13,17-tetraazapentacyclo[16.4.0.1(2,17).1(6,13).0(7,12)]tetracosane.

    PubMed

    Moon, Dohyun; Hong, Yong Pyo; Choi, Jong Ha

    2016-09-01

    Constrained cyclam derivatives have been found to exhibit anti-HIV effects. The strength of binding to the CXCR4 receptor correlates with anti-HIV activity. The conformation of the macrocyclic compound is very important for co-receptor recognition. Therefore, knowledge of the conformation and crystal packing of macrocycles has become important in developing new highly effective anti-HIV drugs. Structural modifications of N-functionalized polyaza macrocyclic compounds have been achieved using various methods. A new synthesis affording single crystals of the title tetraazapentacyclo[16.4.0.1(2,17).1(6,13).0(7,12)]tetracosane macrocycle, C22H40N4, is reported. Formaldehyde reacts readily at room temperature with the tetraazatricyclo[16.4.0.0(2,17)]docosane precursor to yield a macropolycycle containing two five-membered rings. Characterization by elemental, spectroscopic and single-crystal X-ray diffraction analyses shows that the asymmetric unit contains half of a centrosymmetric molecule. The molecular structure shows a trans conformation for the two methylene bridges owing to molecular symmetry. The crystal structure is stabilized by intramolecular C-H...N hydrogen bonds. NMR and IR spectroscopic properties support the methylene-bridged macrocyclic structure. PMID:27585935

  4. General approach to the analysis of plasmonic structures using spectroscopic ellipsometry

    NASA Astrophysics Data System (ADS)

    Verre, R.; Modreanu, M.; Ualibek, O.; Fox, D.; Fleischer, K.; Smith, C.; Zhang, H.; Pemble, M.; McGilp, J. F.; Shvets, I. V.

    2013-06-01

    In this article a route to analyze the full optical response of plasmonic structures is developed. First, the simple case of an anisotropic thin plasmonic layer supported on a transparent substrate is analyzed by introducing a quantity named anisotropic surface excess function (ASEF). The spectral features are analyzed in terms of effective dielectric function, demonstrating a more direct relation with the plasmonic response of the layer. The formalism is then generalized using a transfer matrix method. The formalism developed is supported by experimental evidence obtained by measuring the response of anisotropic nanoparticle arrays grown at a glancing angle. The agreement between theory and experiment is clear, suggesting that SE can be conveniently employed to measure the spectroscopic response of plasmonic structures. It is also demonstrated that the figure of merit of the plasmonic resonance for refractive index sensing can be greatly improved, with optimized measurement configurations, using polarized spectroscopy.

  5. Spectroscopic Survey Telescope design. III - Optical support structure and overall configuration

    NASA Astrophysics Data System (ADS)

    Ray, F. B.

    1990-07-01

    The Universities of Texas and Penn State are working together on an Arecibo-type optical telescope to be utilized in a semitransit mode for spectroscopic survey work. Its optics include a spherical primary mirror, a 2-element all-reflecting Gregorian spherical aberration corrector, and a series of optical fibers that will transmit light to a family of spectrographs. An optical support structure is being developed to permit position adjustment in azimuth only. During an azimuth position change, the instrument's entire weight is borne by steel rollers bearing on a circular crane rail of standard section, with support loads transmitted to the telescope base through pneumatic springs. Extensive application of various analytical procedures and computer-aided engineering tools has effectively allowed the detailed examination of several design iterations, thereby increasing the probability of success in the realized structure.

  6. Crystal growth, structural, thermal and mechanical behavior of L-arginine 4-nitrophenolate 4-nitrophenol dihydrate (LAPP) single crystals

    NASA Astrophysics Data System (ADS)

    Mahadevan, M.; Ramachandran, K.; Anandan, P.; Arivanandhan, M.; Bhagavannarayana, G.; Hayakawa, Y.

    2014-12-01

    Single crystals of L-arginine 4-nitrophenolate 4-nitrophenol dihydrate (LAPP) have been grown successfully from the solution of L-arginine and 4-nitrophenol. Slow evaporation of solvent technique was adopted to grow the bulk single crystals. Single crystal X-ray diffraction analysis confirms the grown crystal has monoclinic crystal system with space group of P21. Powder X-ray diffraction analysis shows the good crystalline nature. The crystalline perfection of the grown single crystals was analyzed by HRXRD by employing a multicrystal X-ray diffractometer. The functional groups were identified from proton NMR spectroscopic analysis. Linear and nonlinear optical properties were determined by UV-Vis spectrophotometer and Kurtz powder technique respectively. It is found that the grown crystal has no absorption in the green wavelength region and the SHG efficiency was found to be 2.66 times that of the standard KDP. The Thermal stability of the crystal was found by obtaining TG/DTA curve. The mechanical behavior of the grown crystal has been studied by Vicker's microhardness method.

  7. Modulated crystal structure of InMo4O6.

    PubMed

    Schultz, Peter; Simon, Arndt; Oeckler, Oliver

    2016-08-01

    The (3 + 1)-dimensional modulated crystal structure of the metal-rich cluster compound InMo4O6 was solved and refined from single-crystal data in the superspace group P4/mbm(00γ)00ss [q = 0, 0, 0.1536 (4); a = 9.6664 (9), c = 2.8645 (3) Å; R1(all) = 0.046, wR(all) = 0.076]. The crystal structure is closely related to the NaMo4O6 structure type. It is built from rods of Mo6 clusters condensed via trans edges. These form channels parallel to [001], in which In6 and In7 oligomers alternate. Weak diffuse planes parallel to (001)* interconnect the satellite reflections; they occur due to two-dimensional rod disorder of the In oligomer chains. PMID:27484384

  8. The high-resolution crystal structure of human LCAT.

    PubMed

    Piper, Derek E; Romanow, William G; Gunawardane, Ruwanthi N; Fordstrom, Preston; Masterman, Stephanie; Pan, Oscar; Thibault, Stephen T; Zhang, Richard; Meininger, David; Schwarz, Margrit; Wang, Zhulun; King, Chadwick; Zhou, Mingyue; Walker, Nigel P C

    2015-09-01

    LCAT is intimately involved in HDL maturation and is a key component of the reverse cholesterol transport (RCT) pathway which removes excess cholesterol molecules from the peripheral tissues to the liver for excretion. Patients with loss-of-function LCAT mutations exhibit low levels of HDL cholesterol and corneal opacity. Here we report the 2.65 Å crystal structure of the human LCAT protein. Crystallization required enzymatic removal of N-linked glycans and complex formation with a Fab fragment from a tool antibody. The crystal structure reveals that LCAT has an α/β hydrolase core with two additional subdomains that play important roles in LCAT function. Subdomain 1 contains the region of LCAT shown to be required for interfacial activation, while subdomain 2 contains the lid and amino acids that shape the substrate binding pocket. Mapping the naturally occurring mutations onto the structure provides insight into how they may affect LCAT enzymatic activity. PMID:26195816

  9. Ultrasonic promoted synthesis of novel s-triazine-Schiff base derivatives; molecular structure, spectroscopic studies and their preliminary anti-proliferative activities

    NASA Astrophysics Data System (ADS)

    El-Faham, Ayman; Soliman, Saied M.; Ghabbour, Hazem A.; Elnakady, Yasser A.; Mohaya, Talal A.; Siddiqui, Mohammed R. H.; Albericio, Fernando

    2016-12-01

    Novel series of s-triazine-Schiff base derivatives were synthesized employing ultrasonic irradiation and characterized by NMR (1H and 13C), FT-IR, and elemental analysis. The use of ultrasonic irradiation has allowed the preparation of the target products with better yields in shorter reaction time and excellent purities compared to the conventional heating. X-ray single crystal diffraction experiments verified the molecular structure of four from the new prepared s-triaizne-Schiff base derivatives. The molecular structures of the studied compounds are computerized using DFT/B3LYP method. The effects of substituent at the triazine and phenyl ring on the electronic and spectroscopic properties of the studied compounds were also investigated. The natural atomic charges showed that pipridino-s-triazine derivatives are richer in electrons than those having morpholino derivatives. The anti-proliferative effects for the prepared compounds were tested against three different cancer cell lines.

  10. Conformational, electronic, and spectroscopic characterization of isophthalic acid (monomer and dimer structures) experimentally and by DFT

    NASA Astrophysics Data System (ADS)

    Bardak, F.; Karaca, C.; Bilgili, S.; Atac, A.; Mavis, T.; Asiri, A. M.; Karabacak, M.; Kose, E.

    2016-08-01

    Isophthalic acid (C6H4(CO2H)2) is a noteworthy organic compound widely used in coating and synthesis of resins and the production of commercially important polymers such as drink plastic bottles. The effects of isophthalic acid (IPA) on human health, toxicology, and biodegradability are the main focus of many researchers. Because structural and spectroscopic investigation of molecules provides a deep understanding of interactional behaviors of compounds, this study stands for exploring those features. Therefore, the spectroscopic, structural, electronic, and thermodynamical properties of IPA were thoroughly studied in this work experimentally using UV-Vis, 1H and 13C NMR, FT-IR, FT-Raman and theoretically via DFT and TD-DFT calculations. The UV-Vis absorption spectrum in water was taken in the region 200-400 nm. The NMR chemical shifts (1H and 13C) were recorded in DMSO solution. The infrared and Raman spectra of the solid IPA were recorded in the range of 4000-400 cm- 1 and 3500-50 cm- 1, respectively. DFT and TD-DFT calculations were performed at the level of B3LYP/6-311++G(d,p) in determination of geometrical structure, electronic structure analysis and normal mode. The 13C and 1H nuclear magnetic resonance (NMR) spectra were estimated by using the gauge-invariant atomic orbital (GIAO) method. The scaled quantum mechanics (SQM) method was used to determine the total energy distribution (TED) to assign the vibrational modes accurately. Weak interactions such as hydrogen bonding and Van der Walls were analyzed via reduced density gradient (RDG) analysis in monomeric and dimeric forms. Furthermore, the excitation energies, density of state (DOS) diagram, thermodynamical properties, molecular electro-static potential (MEP), and nonlinear optical (NLO) properties were obtained.

  11. Conformational, electronic, and spectroscopic characterization of isophthalic acid (monomer and dimer structures) experimentally and by DFT.

    PubMed

    Bardak, F; Karaca, C; Bilgili, S; Atac, A; Mavis, T; Asiri, A M; Karabacak, M; Kose, E

    2016-08-01

    Isophthalic acid (C6H4(CO2H)2) is a noteworthy organic compound widely used in coating and synthesis of resins and the production of commercially important polymers such as drink plastic bottles. The effects of isophthalic acid (IPA) on human health, toxicology, and biodegradability are the main focus of many researchers. Because structural and spectroscopic investigation of molecules provides a deep understanding of interactional behaviors of compounds, this study stands for exploring those features. Therefore, the spectroscopic, structural, electronic, and thermodynamical properties of IPA were thoroughly studied in this work experimentally using UV-Vis, (1)H and (13)C NMR, FT-IR, FT-Raman and theoretically via DFT and TD-DFT calculations. The UV-Vis absorption spectrum in water was taken in the region 200-400nm. The NMR chemical shifts ((1)H and (13)C) were recorded in DMSO solution. The infrared and Raman spectra of the solid IPA were recorded in the range of 4000-400cm(-1) and 3500-50cm(-1), respectively. DFT and TD-DFT calculations were performed at the level of B3LYP/6-311++G(d,p) in determination of geometrical structure, electronic structure analysis and normal mode. The (13)C and (1)H nuclear magnetic resonance (NMR) spectra were estimated by using the gauge-invariant atomic orbital (GIAO) method. The scaled quantum mechanics (SQM) method was used to determine the total energy distribution (TED) to assign the vibrational modes accurately. Weak interactions such as hydrogen bonding and Van der Walls were analyzed via reduced density gradient (RDG) analysis in monomeric and dimeric forms. Furthermore, the excitation energies, density of state (DOS) diagram, thermodynamical properties, molecular electro-static potential (MEP), and nonlinear optical (NLO) properties were obtained. PMID:27107533

  12. Microscopic characterization of defect structure in RDX crystals.

    PubMed

    Bouma, R H B; Duvalois, W; Van der Heijden, A E D M

    2013-12-01

    Three batches of the commercial energetic material RDX, as received from various production locations and differing in sensitivity towards shock initiation, have been characterized with different microscopic techniques in order to visualize the defect content in these crystals. The RDX crystals are embedded in an epoxy matrix and cross-sectioned. By a treatment of grinding and polishing of the crystals, the internal defect structure of a multitude of energetic crystals can be visualized using optical microscopy, scanning electron microscopy and confocal scanning laser microscopy. Earlier optical micrographs of the same crystals immersed in a refractive index matched liquid could visualize internal defects, only not in the required detail. The combination of different microscopic techniques allows for a better characterization of the internal defects, down to inclusions of approximately 0.5 μm in size. The defect structure can be correlated to the sensitivity towards a high-amplitude shock wave of the RDX crystals embedded in a polymer bonded explosive. The obtained experimental results comprise details on the size, type and quantity of the defects. These details should provide modellers with relevant and realistic information for modelling defects in energetic materials and their effect on the initiation and propagation of shock waves in PBX formulations.

  13. Synthesis, crystal structure, and in vitro and in silico molecular docking of novel acyl thiourea derivatives

    NASA Astrophysics Data System (ADS)

    Haribabu, Jebiti; Subhashree, Govindarajulu Rangabashyam; Saranya, Sivaraj; Gomathi, Kannayiram; Karvembu, Ramasamy; Gayathri, Dasararaju

    2015-08-01

    In the present study, a series of six biologically active substituted acyl thiourea compounds (1-6) has been synthesized from cyclohexanecarbonyl isothiocyanate and various primary amines (2-methyl aniline, aniline, 4-methoxy aniline, 4-ethoxy aniline, benzyl amine and 2-methoxy aniline). The synthesized compounds were characterized by elemental analyses, UV-Visible, FT-IR, 1H & 13C NMR and mass spectroscopic techniques. Three dimensional molecular structure of two compounds (1 and 5) was determined by single crystal X-ray crystallography. All the synthesized compounds show good anti-oxidant and anti-haemolytic activities. In silico molecular docking studies were performed to screen against DprE1 and HSP90 enzymes targeting tuberculosis and cancer respectively.

  14. Electronic structure of the CuBS2 crystal

    NASA Astrophysics Data System (ADS)

    Basalaev, Yu. M.; Gordienko, A. B.; Filippov, S. I.

    2012-09-01

    The band structure and spectra of the total and projected densities of states of a new crystal of the chalcopyrite family, namely, CuBS2, have been calculated in terms of the density functional theory. It has been found that the crystal is a pseudo-direct-band-gap semiconductor, and the best theoretical estimate of the optical band gap is 3.44 eV. The upper valence band of the CuBS2 crystal basically consists of the contributions from the p states of S atoms and the d states of Cu atoms. The crystal splitting is 0.2 eV. The bottom of the conduction band is basically formed by the sp states of boron and sulfur atoms with an admixture of the s states of copper atoms.

  15. The crystal structure of GXGD membrane protease FlaK

    SciTech Connect

    Hu, Jian; Xue, Yi; Lee, Sangwon; Ha, Ya

    2011-09-20

    The GXGD proteases are polytopic membrane proteins with catalytic activities against membrane-spanning substrates that require a pair of aspartyl residues. Representative members of the family include preflagellin peptidase, type 4 prepilin peptidase, presenilin and signal peptide peptidase. Many GXGD proteases are important in medicine. For example, type 4 prepilin peptidase may contribute to bacterial pathogenesis, and mutations in presenilin are associated with Alzheimer's disease. As yet, there is no atomic-resolution structure in this protease family. Here we report the crystal structure of FlaK, a preflagellin peptidase from Methanococcus maripaludis, solved at 3.6 {angstrom} resolution. The structure contains six transmembrane helices. The GXGD motif and a short transmembrane helix, helix 4, are positioned at the centre, surrounded by other transmembrane helices. The crystal structure indicates that the protease must undergo conformational changes to bring the GXGD motif and a second essential aspartyl residue from transmembrane helix 1 into close proximity for catalysis. A comparison of the crystal structure with models of presenilin derived from biochemical analysis reveals three common transmembrane segments that are similarly arranged around the active site. This observation reinforces the idea that the prokaryotic and human proteases are evolutionarily related. The crystal structure presented here provides a framework for understanding the mechanism of the GXGD proteases, and may facilitate the rational design of inhibitors that target specific members of the family.

  16. The Crystal Structure of GXGD Membrane Protease FlaK

    SciTech Connect

    J Hu; Y Xue; S Lee; Y Ha

    2011-12-31

    The GXGD proteases are polytopic membrane proteins with catalytic activities against membrane-spanning substrates that require a pair of aspartyl residues. Representative members of the family include preflagellin peptidase, type 4 prepilin peptidase, presenilin and signal peptide peptidase. Many GXGD proteases are important in medicine. For example, type 4 prepilin peptidase may contribute to bacterial pathogenesis, and mutations in presenilin are associated with Alzheimer's disease. As yet, there is no atomic-resolution structure in this protease family. Here we report the crystal structure of FlaK, a preflagellin peptidase from Methanococcus maripaludis, solved at 3.6 {angstrom} resolution. The structure contains six transmembrane helices. The GXGD motif and a short transmembrane helix, helix 4, are positioned at the centre, surrounded by other transmembrane helices. The crystal structure indicates that the protease must undergo conformational changes to bring the GXGD motif and a second essential aspartyl residue from transmembrane helix 1 into close proximity for catalysis. A comparison of the crystal structure with models of presenilin derived from biochemical analysis reveals three common transmembrane segments that are similarly arranged around the active site. This observation reinforces the idea that the prokaryotic and human proteases are evolutionarily related. The crystal structure presented here provides a framework for understanding the mechanism of the GXGD proteases, and may facilitate the rational design of inhibitors that target specific members of the family.

  17. Photonic crystals, light manipulation, and imaging in complex nematic structures

    NASA Astrophysics Data System (ADS)

    Ravnik, Miha; Å timulak, Mitja; Mur, Urban; Čančula, Miha; Čopar, Simon; Žumer, Slobodan

    2016-03-01

    Three selected approaches for manipulation of light by complex nematic colloidal and non-colloidal structures are presented using different own custom developed theoretical and modelling approaches. Photonic crystals bands of distorted cholesteric liquid crystal helix and of nematic colloidal opals are presented, also revealing distinct photonic modes and density of states. Light propagation along half-integer nematic disclinations is shown with changes in the light polarization of various winding numbers. As third, simulated light transmission polarization micrographs of nematic torons are shown, offering a new insight into the complex structure characterization. Finally, this work is a contribution towards using complex soft matter in optics and photonics for advanced light manipulation.

  18. Crystal chemistry and structure refinement of five hydrated calcium borates

    USGS Publications Warehouse

    Clark, J.R.; Appleman, D.E.; Christ, C.L.

    1964-01-01

    The crystal structures of the five known members of the series Ca2B6O11??xH2O (x = 1, 5, 5, 7, 9, and 13) have been refined by full-matrix least-squares techniques, yielding bond distances and angles with standard errors of less than 0??01 A?? and 0??5??, respectively. The results illustrate the crystal chemical principles that govern the structures of hydrated borate compounds. The importance of hydrogen bonding in the ferroelectric transition of colemanite is confirmed by more accurate proton assignments. ?? 1964.

  19. Utilization of Protein Crystal Structures in Industry

    NASA Astrophysics Data System (ADS)

    Ishikawa, Kohki

    In industry, protein crystallography is used in mainly two technologies. One is structure-based drug design, and the other is structure-based enzyme engineering. Some successful cases together with recent advances are presented in this article. The cases include the development of an anti-influenza drug, and the introduction of engineered acid phosphatase to the manufacturing process of nucleotides used as umami seasoning.

  20. Direct current electric field assembly of colloidal crystals displaying reversible structural color.

    PubMed

    Shah, Aayush A; Ganesan, Mahesh; Jocz, Jennifer; Solomon, Michael J

    2014-08-26

    We report the application of low-voltage direct current (dc) electric fields to self-assemble close-packed colloidal crystals in nonaqueous solvents from colloidal spheres that vary in size from as large as 1.2 μm to as small as 0.1 μm. The assemblies are created rapidly (∼2 min) from an initially low volume fraction colloidal particle suspension using a simple capacitor-like electric field device that applies a steady dc electric voltage. Confocal microscopy is used to observe the ordering that is produced by the assembly method. This spatial evidence for ordering is consistent with the 6-fold diffraction patterns identified by light scattering. Red, green, and blue structural color is observed for the ordered assemblies of colloids with diameters of 0.50, 0.40, and 0.29 μm, respectively, consistent with spectroscopic measurements of reflectance. The diffraction and spectrophotometry results were found to be consistent with the theoretical Bragg's scattering expected for closed-packed crystals. By switching the dc electric field from on to off, we demonstrate reversibility of the structural color response on times scales ∼60 s. The dc electric field assembly method therefore represents a simple method to produce reversible structural color in colloidal soft matter.

  1. Synthesis, crystal structure, crystal growth and physical properties of N,N-diethyl anilinium picrate

    NASA Astrophysics Data System (ADS)

    Subramaniyan @ Raja, R.; Anandha Babu, G.; Ramasamy, P.

    2011-11-01

    Crystalline substance of N,N-diethyl anilinium picrate (NNDEAP) has been synthesized and single crystals of NNDEAP were successfully grown for the first time by the slow evaporation solution growth technique at room temperature with dimensions 14×10×10 mm3. The formation of the new crystal has been confirmed by single crystal X-ray diffraction studies. The structural perfection of the grown crystal was analyzed by high resolution X-ray diffraction (HRXRD) measurements. The functional groups of NNDEAP have been identified by Fourier transform infrared spectral studies. Thermogravimetric analysis (TGA) and differential thermal analysis (DTA) have also been carried out and the thermal behavior of NNDEAP has been studied. The UV-vis-NIR studies have been carried out to identify the optical transmittance and the cut off wavelength of NNDEAP is identified. The dielectric loss and the dielectric constant as a function of frequency and temperature were measured for the grown crystal and the nature of variation of dielectric constant εr and dielectric losses (tan δ) were studied. Vicker's hardness test has been carried out on NNDEAP to measure the load dependent hardness. The laser induced surface damage threshold for the grown crystal was measured using Nd:YAG laser.

  2. Structure of self - assembled two-dimensional spherical crystals

    NASA Astrophysics Data System (ADS)

    Bausch, Andreas R.

    2004-03-01

    Dense spherical particles on a flat surface usually pack into a simple triangular lattice, similar to billiard balls at the start of a game. The minimum energy configuration for interacting particles on the curved surface of a sphere, however, presents special difficulties, as recognized already by J.J. Thomson. We describe experimental investigations of the structure of two-dimensional spherical crystals. The crystals, formed by beads self-assembled on water droplets in oil, serve as model systems for exploring very general theories about the minimum energy configurations of particles with arbitrary repulsive interactions on curved surfaces. Above a critical system size we find that crystals develop distinctive high-angle grain boundaries or "scars" not found in planar crystals. The number of excess defects in a scar is shown to grow linearly with the dimensionless system size. First experiments where the melting of the crystal structure was observable will be discussed. Dynamic triangulation methods allow the analysis of the dynamics of the defects. Possible modifications towards mechanically stabilized self assembly structures result in so called Colloidosomes, which are promising for many different encapsulation purposes.

  3. Photonics of liquid-crystal structures: A review

    SciTech Connect

    Palto, S. P. Blinov, L. M.; Barnik, M. I.; Lazarev, V. V.; Umanskii, B. A.; Shtykov, N. M.

    2011-07-15

    The original results of studies of the electro-optical and laser effects which have been performed at the Laboratory of Liquid Crystals of the Institute of Crystallography, Russian Academy of Sciences, over the last few years are reviewed. Cholesteric liquid crystals as vivid representatives of photonic structures and their behavior in an electric field are considered in detail. The formation of higher harmonics in the periodic distribution of the director field in a helical liquid crystal structure and, correspondingly, the new (anharmonic) mode of electro-optical effects are discussed. Another group of studies is devoted to bistable light switching by an electric field in chiral nematics. Polarization diffraction gratings controlled by an electric field are also considered. The results of studies devoted to microlasers on various photonic structures with cholesteric and nematic liquid crystals are considered in detail. Particular attention is given to the new regime: leaky-mode lasing. Designs of liquid crystal light amplifiers and their polarization, field, and spectral characteristics are considered in the last section.

  4. From molecular fragments to crystals: a UV Raman spectroscopic study on the mechanism of Fe-ZSM-5 synthesis.

    PubMed

    Fan, Fengtao; Sun, Keju; Feng, Zhaochi; Xia, Haian; Han, Bo; Lian, Yuxiang; Ying, Pinliang; Li, Can

    2009-01-01

    The nucleation process of iron-exchanged zeolite Fe-ZSM-5, from the assembly of distorted tetrahedrally coordinated iron species and silicate rings in the precursor to the final Fe-ZSM-5 crystals, as well as variations in the coordination environment of iron, were studied by UV resonance Raman spectroscopy and complementary techniques.The entire sequence of crystallization events of Fe-ZSM-5 was monitored by UV Raman spectroscopy in combination with HRTEM, UV/Vis spectroscopy, X-ray diffraction patterns, and periodic DFT calculations. Fe-ZSM-5 was synthesized by an organic-free method to avoid signal interference from the organic template in Raman spectra. Framework iron atoms with resonance Raman bands at 516, 1115, and 1165 cm(-1), and a Raman band at 1016 cm(-1) are detected for Fe-ZSM-5. In the early stage of Fe-ZSM-5 synthesis, the precursor contains iron atoms in distorted tetrahedral coordination and five- and six-membered silicate rings. Nucleation by aggregation of the precursor species was monitored by UV Raman spectroscopy based on the resonance Raman effect, and confirmed by periodic DFT calculations. Evolution of iron species on the surface and in the bulk phase was monitored by UV Raman spectroscopy with excitation at 244 and 325 nm, as well as HRTEM. Nucleation takes place first in the core of the amorphous particles, and crystalline nuclei with Fe-ZSM-5 structure are formed in the core by consuming the amorphous shell. Finally the amorphous particles are completely transformed into Fe-ZSM-5 crystals.

  5. Accurate molecular structure and spectroscopic properties for nucleobases: A combined computational - microwave investigation of 2-thiouracil as a case study

    PubMed Central

    Puzzarini, Cristina; Biczysko, Malgorzata; Barone, Vincenzo; Peña, Isabel; Cabezas, Carlos; Alonso, José L.

    2015-01-01

    The computational composite scheme purposely set up for accurately describing the electronic structure and spectroscopic properties of small biomolecules has been applied to the first study of the rotational spectrum of 2-thiouracil. The experimental investigation was made possible thanks to the combination of the laser ablation technique with Fourier Transform Microwave spectrometers. The joint experimental – computational study allowed us to determine accurate molecular structure and spectroscopic properties for the title molecule, but more important, it demonstrates a reliable approach for the accurate investigation of isolated small biomolecules. PMID:24002739

  6. CRYSTAL STRUCTURE ANALYSIS OF A PUTATIVE OXIDOREDUCTASE FROM KLEBSIELLA PNEUMONIAE

    SciTech Connect

    Baig, M.; Brown, A.; Eswaramoorthy, S.; Swaminathan, S.

    2009-01-01

    Klebsiella pneumoniae, a gram-negative enteric bacterium, is found in nosocomial infections which are acquired during hospital stays for about 10% of hospital patients in the United States. The crystal structure of a putative oxidoreductase from K. pneumoniae has been determined. The structural information of this K. pneumoniae protein was used to understand its function. Crystals of the putative oxidoreductase enzyme were obtained by the sitting drop vapor diffusion method using Polyethylene glycol (PEG) 3350, Bis-Tris buffer, pH 5.5 as precipitant. These crystals were used to collect X-ray data at beam line X12C of the National Synchrotron Light Source (NSLS) at Brookhaven National Laboratory (BNL). The crystal structure was determined using the SHELX program and refi ned with CNS 1.1. This protein, which is involved in the catalysis of an oxidation-reduction (redox) reaction, has an alpha/beta structure. It utilizes nicotinamide adenine dinucleotide phosphate (NADP) or nicotine adenine dinucleotide (NAD) to perform its function. This structure could be used to determine the active and co-factor binding sites of the protein, information that could help pharmaceutical companies in drug design and in determining the protein’s relationship to disease treatment such as that for pneumonia and other related pathologies.

  7. The crystal structure of samarosporin I at atomic resolution.

    PubMed

    Gessmann, Renate; Axford, Danny; Evans, Gwyndaf; Brückner, Hans; Petratos, Kyriacos

    2012-11-01

    The atomic resolution structures of samarosporin I have been determined at 100 and 293 K. This is the first crystal structure of a natural 15-residue peptaibol. The amino acid sequence in samarosporin I is identical to emerimicin IV and stilbellin I. Samarosporin is a peptide antibiotic produced by the ascomycetous fungus Samarospora rostrup and belongs to peptaibol subfamily 2. The structures at both temperatures are very similar to each other adopting mainly a 3₁₀-helical and a minor fraction of α-helical conformation. The helices are significantly bent and packed in an antiparallel fashion in the centered monoclinic lattice leaving among them an approximately 10-Å channel extending along the crystallographic twofold axis. Only two ordered water molecules per peptide molecule were located in the channel. Comparisons have been carried out with crystal structures of subfamily 2 16-residue peptaibols antiamoebin and cephaibols. The repercussion of the structural analysis of samarosporin on membrane function is discussed.

  8. Crystal structure, matrix-isolation FTIR, and UV-induced conformational isomerization of 3-quinolinecarboxaldehyde.

    PubMed

    Kuş, Nihal; Henriques, Marta Sofia; Paixão, José António; Lapinski, Leszek; Fausto, Rui

    2014-09-25

    The crystal structure of 3-quinolinecarboxaldehyde (3QC) has been solved, and the compound has been shown to crystallize in the space group P21/c (monoclinic) with a = 6.306(4), b = 18.551(11), c = 6.999(4) Å, β = 106.111(13)°, and Z = 4. The crystals were found to exhibit pseudomerohedral twinning with a twin law corresponding to a two-fold rotation around the monoclinic (100) reciprocal lattice axis (or [4 0 1] in direct space). Individual molecules adopt the syn conformation in the crystal, with the oxygen atom of the aldehyde substituent directed toward the same side of the ring nitrogen atom. In the gas phase, the compound exists in two nearly isoenergetic conformers (syn and anti), which could be successfully trapped in solid argon at 10 K, and their infrared spectra are registered and interpreted. Upon in situ irradiation of matrix-isolated 3QC with UV light (λ > 315 nm), significant reduction of the population of the less stable anti conformer was observed, while that of the conformational ground state (syn conformer) increased, indicating occurrence of the anti → syn isomerization. Upon irradiation at higher energy (λ > 235 nm), the syn → anti reverse photoreaction was observed. Interpretation of the structural, spectroscopic, and photochemical experimental data received support from quantum chemical theoretical results obtained at both DFT/B3LYP (including TD-DFT investigation of excited states) and MP2 levels, using the 6-311++G(d,p) basis set. PMID:25144919

  9. Structural and spectroscopic properties of an aliphatic boronic acid studied by combination of experimental and theoretical methods

    NASA Astrophysics Data System (ADS)

    Cyrański, Michał K.; Jezierska, Aneta; Klimentowska, Paulina; Panek, Jarosław J.; Żukowska, GraŻyna Z.; Sporzyński, Andrzej

    2008-03-01

    Boronic acids have emerged as one of the most useful class of organoboron molecules, with application in synthesis, catalysis, analytical chemistry, supramolecular chemistry, biology, and medicine. In this study, the structural and spectroscopic properties of n-butylboronic acid were investigated using experimental and theoretical approaches. X-ray crystallography method provided structural information on the studied compound in the solid state. Infrared and Raman spectroscopy served as tools for the data collection on vibrational modes of the analyzed system. Car-Parrinello molecular dynamics simulations in solid state were carried out at 100 and 293K to investigate an environmental and temperature influence on molecular properties of the n-butylboronic acid. Analysis of interatomic distances of atoms involved in the intermolecular hydrogen bond was performed to study the proton motion in the crystal. Subsequently, Fourier transform of autocorrelation functions of atomic velocities and dipole moment was applied to study the vibrational properties of the compound. In addition, the inclusion of quantum nature of proton motion was performed for O-H stretching vibrational mode by application of the envelope method for intermolecular hydrogen-bonded system. The second part of the computational study consists of simulations performed in vacuo. Monomeric and dimeric forms of the n-butylboronic acid were investigated using density functional theory and Møller-Plesset second-order perturbation method. The basis set superposition error was estimated. Finally, atoms in molecules (AIM) theory was applied to study electron density topology and properties of the intermolecular hydrogen bond. Successful reproduction of the molecular properties of the n-butylboronic acid by computational methodologies, presented in the manuscript, indicates the way for future studies of large boron-containing organic systems of importance in biology or materials science.

  10. Structural and spectroscopic properties of an aliphatic boronic acid studied by combination of experimental and theoretical methods.

    PubMed

    Cyrański, Michał K; Jezierska, Aneta; Klimentowska, Paulina; Panek, Jarosław J; Zukowska, Grazyna Z; Sporzyński, Andrzej

    2008-03-28

    Boronic acids have emerged as one of the most useful class of organoboron molecules, with application in synthesis, catalysis, analytical chemistry, supramolecular chemistry, biology, and medicine. In this study, the structural and spectroscopic properties of n-butylboronic acid were investigated using experimental and theoretical approaches. X-ray crystallography method provided structural information on the studied compound in the solid state. Infrared and Raman spectroscopy served as tools for the data collection on vibrational modes of the analyzed system. Car-Parrinello molecular dynamics simulations in solid state were carried out at 100 and 293 K to investigate an environmental and temperature influence on molecular properties of the n-butylboronic acid. Analysis of interatomic distances of atoms involved in the intermolecular hydrogen bond was performed to study the proton motion in the crystal. Subsequently, Fourier transform of autocorrelation functions of atomic velocities and dipole moment was applied to study the vibrational properties of the compound. In addition, the inclusion of quantum nature of proton motion was performed for O-H stretching vibrational mode by application of the envelope method for intermolecular hydrogen-bonded system. The second part of the computational study consists of simulations performed in vacuo. Monomeric and dimeric forms of the n-butylboronic acid were investigated using density functional theory and Moller-Plesset second-order perturbation method. The basis set superposition error was estimated. Finally, atoms in molecules (AIM) theory was applied to study electron density topology and properties of the intermolecular hydrogen bond. Successful reproduction of the molecular properties of the n-butylboronic acid by computational methodologies, presented in the manuscript, indicates the way for future studies of large boron-containing organic systems of importance in biology or materials science. PMID:18376948

  11. Crystal structure of HINT from Helicobacter pylori.

    PubMed

    Tarique, K F; Devi, S; Abdul Rehman, S A; Gourinath, S

    2016-01-01

    Proteins belonging to the histidine triad (HIT) superfamily bind nucleotides and use the histidine triad motif to carry out dinucleotidyl hydrolase, nucleotidyltransferase and phosphoramidite hydrolase activities. Five different branches of this superfamily are known to exist. Defects in these proteins in humans are linked to many diseases such as ataxia, diseases of RNA metabolism and cell-cycle regulation, and various types of cancer. The histidine triad nucleotide protein (HINT) is nearly identical to proteins that have been classified as protein kinase C-interacting proteins (PKCIs), which also have the ability to bind and inhibit protein kinase C. The structure of HINT, which exists as a homodimer, is highly conserved from humans to bacteria and shares homology with the product of fragile histidine triad protein (FHit), a tumour suppressor gene of this superfamily. Here, the structure of HINT from Helicobacter pylori (HpHINT) in complex with AMP is reported at a resolution of 3 Å. The final model has R and Rfree values of 26 and 28%, respectively, with good electron density. Structural comparison with previously reported homologues and phylogenetic analysis shows H. pylori HINT to be the smallest among them, and suggests that it branched out separately during the course of evolution. Overall, this structure has contributed to a better understanding of this protein across the animal kingdom. PMID:26750483

  12. Crystallization of interleukin-18 for structure-based inhibitor design

    PubMed Central

    Krumm, Brian; Meng, Xiangzhi; Xiang, Yan; Deng, Junpeng

    2015-01-01

    Interleukin-18 (IL-18) is a pleiotropic pro-inflammatory cytokine belonging to the IL-1 superfamily. IL-18 plays an important role in host innate and acquired immune defense, with its activity being modulated in vivo by its naturally occurring antagonist IL-18 binding protein (IL-18BP). Recent crystal structures of human IL-18 (hIL-18) in complex with its antagonist or cognate receptor(s) have revealed a conserved binding interface on hIL-18 representing a promising drug target. An important step in this process is obtaining crystals of apo hIL-18 or hIL-18 in complex with small-molecule inhibitors, preferably under low ionic strength conditions. In this study, surface-entropy reduction (SER) and rational protein design were employed to facilitate the crystallization of hIL-18. The results provide an excellent platform for structure-based drug design. PMID:26057800

  13. Use of ultra stable UNCG tetraloop hairpins to fold RNA structures: thermodynamic and spectroscopic applications.

    PubMed Central

    Molinaro, M; Tinoco, I

    1995-01-01

    RNA molecules of > 20 nucleotides have been the focus of numerous recent NMR structural studies. Several investigators have used the UNCG family of hairpins to ensure proper folding. We show that th UUCG hairpin has a minimum requirement of a two base-pair stem. Hairpins with a CG loop closing base pair and an initial 5'CG or 5'GC base pair have a melting temperature approximately 55 degrees C in 10 mM sodium phosphate. The high stability of even such small hairpins suggests that the hairpin can serve as a nucleation site for folding. For high resolution NMR work, the UNCG loop family (UACG in particular) provides excellent spectroscopic markers in one-dimensional exchangeable spectra, in two-dimensional COSY spectra and in NOESY spectra that clearly define it as forming a hairpin. This allows straightforward initiation of chemical shift assignments. PMID:7544890

  14. Structural and surface topography analysis of AlN single crystals grown on 6H-SiC substrates

    NASA Astrophysics Data System (ADS)

    Sumathi, R. R.; Barz, R. U.; Straubinger, T.; Gille, P.

    2012-12-01

    Bulk AlN single crystals (3 mm thick and 1 in. diameter) were hetero-epitaxially grown on (0001) 6H-SiC substrates by the sublimation method. Double-crystal x-ray diffraction and micro-Raman results confirm the good crystallinity as well as structural homogeneity of the grown crystals. The presence of low-angle grain boundaries was observed by x-ray diffraction rocking curve analysis and also supported by defect-selective etching analysis. The estimated defect density of the 3 mm thick crystals is about (5-8)×105 cm-2. 3D-microstructures with different morphology were observed on the as-grown crystal surfaces and were interpreted to be originated from screw dislocations. These screw dislocations are decorated by carbon impurities as evidenced by micro-Raman spectroscopic measurements. SiC incorporation in the grown crystals was found to be fairly low with 4 mol% at 2 mm distance from the interface and varies slightly between different sub-grains.

  15. Interleukin-22 and its crystal structure.

    PubMed

    Nagem, Ronaldo Alves Pinto; Ferreira Júnior, José Ribamar; Dumoutier, Laure; Renauld, Jean-Christophe; Polikarpov, Igor

    2006-01-01

    Interleukin-22 (IL-22) is a cytokine that regulates the production of acute phase proteins of the immunological response. On binding to its cognate receptor (IL-22R1), which is associated to the interleukin-10 receptor 2 (IL-10R2), IL-22 promotes activation of signal transducer and activator of transcription (STAT) pathway and several other cellular responses. A soluble receptor termed interleukin-22 binding protein (IL-22BP) is also able to bind to IL-22 as a natural protein antagonist, and probably provides systemic regulation of IL-22 activity. This inflammatory response system is analyzed here in terms of its molecular physiology and structural assembly. Three-dimensional (3D) model of IL-22 and structural basis of its interactions with the cognate receptors are discussed.

  16. Structural and optical properties of a new chalcone single crystal

    NASA Astrophysics Data System (ADS)

    Rajesh Kumar, P. C.; Ravindrachary, V.; Janardhana, K.; Poojary, Boja

    2012-09-01

    A new nonlinear optical material 1-(4-methylthiophenyl)-3-(4-methoxyphenyl)prop-2-en-1-one with molecular formula C17H16O2S was synthesized by using the Claisen-Schmidt condensation reaction method. The Various functional groups present in the compound were identified using recorded FT-IR spectrum. The crystal growth parameters have been studied using solubility test and acetone is found to be a very good solvent for the crystal growth at an ambient temperature. The transparent high quality single crystals up to a size of 26×2×2 mm3 were grown using the slow evaporation solution growth technique. UV-visible study was carried out and the spectrum reveals that the crystal is transparent in the entire visible region and absorptive in the UV region. The refractive index is determined using Brewster's angle method. The optical energy band gap of the material is measured using Tauc's plot and the direct method. The single crystal XRD of MMPP crystal shows the following cell parameters: a=5.9626(2) Å, b=15.3022(6) Å, c=16.0385(7) Å, α=β=γ=90°, volume=1463.37(10) Å3 with a space group of Pna21. The compound MMPP exhibits optical nonlinearity (NLO) and its second order NLO efficiency is 3.15 times to that of urea. The effect of functional groups OCH3 and SCH3 on the non-linearity as well as the structural property of the compound has been discussed. The crystal is thermally stable. High NLO efficiency, good thermal stability, good transparency and ability to grow as a high quality single crystal make this material very attractive for opto-electronic applications.

  17. Crystal growth, structure analysis and characterisation of 2 - (1, 3 - dioxoisoindolin - 2 - yl) acetic acid single crystal

    SciTech Connect

    Sankari, R. Siva; Perumal, Rajesh Narayana

    2014-04-24

    Single crystal of dielectric material 2 - (1, 3 - dioxoisoindolin - 2 - yl) acetic acid has been grown by slow evaporation solution growth method. The grown crystal was harvested in 25 days. The crystal structure was analyzed by Single crystal X - ray diffraction. UV-vis-NIR analysis was performed to examine the optical property of the grown crystal. The thermal property of the grown crystal was studied by thermogravimetric analysis (TGA) and differential thermal analysis (DTA). The dielectric measurements were carried out and the dielectric constant was calculated and plotted at all frequencies.

  18. Influence of the real-life structures in optical metrology using spectroscopic scatterometry analysis

    NASA Astrophysics Data System (ADS)

    Quintanilha, R.; Hazart, J.; Thony, P.; Henry, D.

    2005-08-01

    During the last five years scatterometry measurement using ellispometry and reflectometry has met a great interest in nano and microelectronics fab. Today, this technology of measurement is used to control lot production and has become mature for 1D-grating measurements. Nevertheless, some aspects of this method of measurement are always under research studies. This paper focuses on one of these aspects: the evaluation of the influence of the "real-life 1D-structure" (linewidth variations along the lines and line to line, roughness, defect inside the grating) on spectroscopic signatures and on scatterometry measurement methods. The measurements have been carried out on KLA-TENCOR ellispometer and on Nanometrics reflectometer in order to compare the two methods of measurement. The simulations have been done with MMFE (Modal Method of Fourier Expansion) software developed by LETI labs. To control defect characteristics and defect distributions, one wafer was printed using electron beam lithography. The aim is the evaluation of the impact of defects in the grating on the spectroscopic signatures and its influence on extracted geometrical parameters by fitting the experimental curves. Different deviations to real-life structures have been studied. First we focus on the influence of typical defects of lithography processes such as bridging and partial destruction of lines and on the influence of CD distribution values inside the grating. Then, we study the influence and the possibilities of measuring Line Edge Roughness (LER). For LER measurements different targets have been also exposed on e-beam tool. Simulations and experimental measurements have been carried out. All the results obtained have been compared with imaging standard tool: top down SEM measurement.

  19. Crystal structures and morphologies of fractionated milk fat in nanoemulsions.

    PubMed

    Truong, Tuyen; Morgan, Garry P; Bansal, Nidhi; Palmer, Martin; Bhandari, Bhesh

    2015-03-15

    The triacylglycerol (TAG) crystal structures and morphologies of fractionated milk lipids in nanoemulsions were investigated at 4°C. Droplet size (0.17 versus 1.20 μm), lipid composition (stearin versus olein) and cooling rate (1 versus 10°C min(-1)) had an influence on the structural properties. Five crystal polymorphs (α, β'1, β'2, β1, and β2) were formed with either triple and/or double chain length structures in the solid phases of the emulsified systems. X-ray scattering peak intensities were reduced with the nanoemulsion particles. The internal structure of TAG exhibited stacking of individual lamellar layers (3.8-4.2 nm). Various anisometric shapes of fat nanoparticles were formed due to a highly sharp curvature of the nano-size droplets. The shape of olein nanoparticles was more polyhedral compared to the stearin. TAG crystals arranged in a planar-layered organisation at the slower cooling rate. These differences imply that the nanometric confinement of oil droplets modifies the fat crystal habit.

  20. Unusual Features of Crystal Structures of Some Simple Copper Compounds

    ERIC Educational Resources Information Center

    Douglas, Bodie

    2009-01-01

    Some simple copper compounds have unusual crystal structures. Cu[subscript 3]N is cubic with N atoms at centers of octahedra formed by 6 Cu atoms. Cu[subscript 2]O (cuprite) is also cubic; O atoms are in tetrahedra formed by 4 Cu atoms. These tetrahedra are linked by sharing vertices forming two independent networks without linkages between them.…

  1. Redetermination of the crystal structure of NbF4.

    PubMed

    Bandemehr, Jascha; Conrad, Matthias; Kraus, Florian

    2016-08-01

    Single crystals of NbF4, niobium(IV) tetra-fluoride, were synthesized by disproportionation of Nb2F5 at 1273 K in a sealed niobium tube, extracted and studied by single-crystal X-ray diffraction. Previous reports on the crystal structure of NbF4 were based on X-ray powder diffraction data and the observed isotypicity to SnF4 [Gortsema & Didchenko (1965 ▸). Inorg. Chem. 4, 182-186; Schäfer et al. (1965 ▸). J. Less Common Met. 9, 95-104]. The data obtained from a single-crystal X-ray diffraction study meant the atomic coordinates could now be refined as well as their anisotropic displacement parameters, leading to a significant improvement of the structural model of NbF4. In the structure, the Nb atom is octahedron-like surrounded by six F atoms of which four are bridging to other NbF6 octa-hedra, leading to a layer structure extending parallel to the ab plane. PMID:27536416

  2. Redetermination of the crystal structure of NbF4

    PubMed Central

    Bandemehr, Jascha; Conrad, Matthias; Kraus, Florian

    2016-01-01

    Single crystals of NbF4, niobium(IV) tetra­fluoride, were synthesized by disproportionation of Nb2F5 at 1273 K in a sealed niobium tube, extracted and studied by single-crystal X-ray diffraction. Previous reports on the crystal structure of NbF4 were based on X-ray powder diffraction data and the observed isotypicity to SnF4 [Gortsema & Didchenko (1965 ▸). Inorg. Chem. 4, 182–186; Schäfer et al. (1965 ▸). J. Less Common Met. 9, 95–104]. The data obtained from a single-crystal X-ray diffraction study meant the atomic coordinates could now be refined as well as their anisotropic displacement parameters, leading to a significant improvement of the structural model of NbF4. In the structure, the Nb atom is octahedron-like surrounded by six F atoms of which four are bridging to other NbF6 octa­hedra, leading to a layer structure extending parallel to the ab plane. PMID:27536416

  3. Materials research at Stanford University. [composite materials, crystal structure, acoustics

    NASA Technical Reports Server (NTRS)

    1975-01-01

    Research activity related to the science of materials is described. The following areas are included: elastic and thermal properties of composite materials, acoustic waves and devices, amorphous materials, crystal structure, synthesis of metal-metal bonds, interactions of solids with solutions, electrochemistry, fatigue damage, superconductivity and molecular physics and phase transition kinetics.

  4. The diammoniate of diborane: Crystal structure and hydrogen release

    SciTech Connect

    Bowden, Mark E.; Heldebrant, David J.; Karkamkar, Abhijeet J.; Proffen, Thomas E.; Schenter, Gregory K.; Autrey, Thomas

    2010-10-12

    [(NH3)2BH2]+[BH4]- is formed from the room temperature decomposition of NH4+BH4-, via a NH3BH3 intermediate. Its crystal structure has been determined and contains disordered BH4- ions in 2 distinct sites. Hydrogen release is similar to that from NH3BH3 but with faster kinetics.

  5. Magnetic assembly of nonmagnetic particles into photonic crystal structures.

    PubMed

    He, Le; Hu, Yongxing; Kim, Hyoki; Ge, Jianping; Kwon, Sunghoon; Yin, Yadong

    2010-11-10

    We report the rapid formation of photonic crystal structures by assembly of uniform nonmagnetic colloidal particles in ferrofluids using external magnetic fields. Magnetic manipulation of nonmagnetic particles with size down to a few hundred nanometers, suitable building blocks for producing photonic crystals with band gaps located in the visible regime, has been difficult due to their weak magnetic dipole moment. Increasing the dipole moment of magnetic holes has been limited by the instability of ferrofluids toward aggregation at high concentration or under strong magnetic field. By taking advantage of the superior stability of highly surface-charged magnetite nanocrystal-based ferrofluids, in this paper we have been able to successfully assemble 185 nm nonmagnetic polymer beads into photonic crystal structures, from 1D chains to 3D assemblies as determined by the interplay of magnetic dipole force and packing force. In a strong magnetic field with large field gradient, 3D photonic crystals with high reflectance (83%) in the visible range can be rapidly produced within several minutes, making this general strategy promising for fast creation of large-area photonic crystals using nonmagnetic particles as building blocks.

  6. Analysis of voids in crystal structures: the methods of 'dual' crystal chemistry.

    PubMed

    Blatov, V A; Shevchenko, A P

    2003-01-01

    The theoretical basics of the analysis of voids in crystal structures by means of Voronoi-Dirichlet polyhedra (VDP) and of the graph theory are stated. Topological relations are considered between VDPs and atomic domains in a crystal field. These relations allow the separation of two non-intersecting topological subspaces in a crystal structure, whose connectednesses are defined by two finite 'reduced' graphs. The first, 'direct', subspace includes the atoms (VDP centres) and the network of interatomic bonds (VDP faces), the second, 'dual', one comprises the void centres (VDP vertices) and the system of channels (VDP edges) between them. Computer methods of geometrical-topological analysis of the 'dual' subspace are developed and implemented within the program package TOPOS. They are designed for automatically restoring the system of channels, visualizing and sizing voids and void conglomerates, dimensional analysis of continuous void systems, and comparative topological analysis of 'dual' subspaces for various substances. The methods of analysis of 'dual' and 'direct' subspaces are noted to differ from each other only in some details that allows the term 'dual' crystal chemistry to be introduced. The efficiency of the methods is shown with the analysis of compounds of different chemical nature: simple substances, ionic structures, superionic conductors, zeolites, clathrates, organic supramolecular complexes. PMID:12496460

  7. Comment on the paper: "Crystal growth and spectroscopic characterization of Aloevera amino acid added lithium sulfate monohydrate: a non-linear optical crystal".

    PubMed

    Srinivasan, Bikshandarkoil R

    2015-01-01

    The title paper (Manimekalai et al., 2014) reports a slow evaporation solution growth of a so called 'Aloevera amino acid added lithium sulfate monohydrate' (AALSMH) crystal. In this communication, many points of criticism, concerning the crystal growth, NMR spectrum and X-ray powder pattern of this so called AALSMH nonlinear optical crystal are highlighted.

  8. Spectroscopic properties of Bi2ZnOB2O6 single crystals doped with Pr3+ ions: Absorption and luminescence investigations

    NASA Astrophysics Data System (ADS)

    Kasprowicz, D.; Brik, M. G.; Jaroszewski, K.; Pedzinski, T.; Bursa, B.; Głuchowski, P.; Majchrowski, A.; Michalski, E.

    2015-09-01

    Nonlinear optical Bi2ZnOB2O6 single crystals doped with Pr3+ ions were grown using the Kyropoulos method. The absorption and luminescence properties of these new systems were investigated for the first time. The crystals are characterized by the large values of nonlinear optical coefficients. Effective luminescence of the Pr3+ ions makes this system an excellent candidate for the near-infrared (NIR) and/or ultraviolet (UV) to visible (VIS) laser converters. Based on the obtained experimental spectroscopic data, detailed analysis of the absorption and luminescence spectra was performed using the conventional Judd-Ofelt theory. Those transitions, which can be potentially used for laser applications of the Pr3+ ion, have been identified. In addition to the intensity parameters Ω2, Ω4, Ω6 the branching ratios and radiative lifetimes were estimated for all possible transitions in the studied spectral region.

  9. Spectroscopic and magnetic studies of erbium(III)-TEMPO complex as a potential single-molecule magnet: Interplay of the crystal-field and exchange coupling effects

    NASA Astrophysics Data System (ADS)

    Karbowiak, Mirosław; Rudowicz, Czesław; Nakamura, Takeshi; Murakami, Rina; Ishida, Takayuki

    2016-10-01

    Crystallographic, spectroscopic, and magnetic studies of three-center systems: lanthanoid-Ln3+ ions doubly-coordinated by TEMPO (2,2,6,6-tetramethylpiperidin-1-oxyl) radicals [Ln-TEMPO2] are reported. The temperature dependence of alternating-current magnetic susceptibility indicates the single-molecule-magnet behavior of Er-TEMPO2, exhibiting relatively slow magnetization relaxation. Well-resolved absorption spectra were obtained only for Er-TEMPO2. Other samples yielded spectra not amenable for meaningful interpretation. The crystal-field parameters (CFPs) determined from the measured Er3+-energy levels served as starting CFPs for fitting the direct-current magnetic susceptibility result. Compatibility of the so-determined and fine-tuned CFPs, and interplay between crystal-field-related effects and exchange-coupling effects are considered. Exchange couplings in Ln-TEMPO2 appear antiferromagnetic and unexpectedly large.

  10. VO{sub 2} (A): Reinvestigation of crystal structure, phase transition and crystal growth mechanisms

    SciTech Connect

    Rao Popuri, Srinivasa; Artemenko, Alla; Labrugere, Christine; Miclau, Marinela; Villesuzanne, Antoine; Pollet, Michaël

    2014-05-01

    Well crystallized VO{sub 2} (A) microrods were grown via a single step hydrothermal reaction in the presence of V{sub 2}O{sub 5} and oxalic acid. With the advantage of high crystalline samples, we propose P4/ncc as an appropriate space group at room temperature. From morphological studies, we found that the oriented attachment and layer by layer growth mechanisms are responsible for the formation of VO{sub 2} (A) micro rods. The structural and electronic transitions in VO{sub 2} (A) are strongly first order in nature, and a marked difference between the structural transition temperatures and electronic transitions temperature was evidenced. The reversible intra- (LTP-A to HTP-A) and irreversible inter- (HTP-A to VO{sub 2} (M1)) structural phase transformations were studied by in-situ powder X-ray diffraction. Attempts to increase the size of the VO{sub 2} (A) microrods are presented and the possible formation steps for the flower-like morphologies of VO{sub 2} (M1) are described. - Graphical abstract: Using a single step and template free hydrothermal synthesis, well crystallized VO{sub 2} (A) microrods were prepared and the P4/ncc space group was assigned to the room temperature crystal structure. Reversible and irreversible phase transitions among different VO{sub 2} polymorphs were identified and their progressive nature was highlighted. Attempts to increase the microrods size, involving layer by layer formation mechanisms, are presented. - Highlights: • Highly crystallized VO{sub 2} (A) microrods were grown via a single step hydrothermal process. • The P4/ncc space group was determined for VO{sub 2} (A) at room temperature. • The electronic structure and progressive nature of the structural phase transition were investigated. • A weak coupling between structural and electronic phase transitions was identified. • Different crystallite morphologies were discussed in relation with growth mechanisms.

  11. Crystal growth, spectral, structural and optical studies of π-conjugated stilbazolium crystal: 4-bromobenzaldehyde-4'-N'-methylstilbazolium tosylate.

    PubMed

    Krishna Kumar, M; Sudhahar, S; Bhagavannarayana, G; Mohan Kumar, R

    2014-05-01

    Nonlinear optical (NLO) organic compound, 4-bromobenzaldehyde-4'-N'-methylstilbazolium tosylate was synthesized by reflux method. The formation of molecular complex was confirmed from (1)H NMR, FT-IR and FT-Raman spectral analyses. The single crystals were grown by slow evaporation solution growth method and the crystal structure and atomic packing of grown crystal was identified. The morphology and growth axis of grown crystal were determined. The crystal perfection was analyzed using high resolution X-ray diffraction study on (001) plane. Thermal stability, decomposition stages and melting point of the grown crystal were analyzed. The optical absorption coefficient (α) and energy band gap (E(g)) of the crystal were determined using UV-visible absorption studies. Second harmonic generation efficiency of the grown crystal was examined by Kurtz powder method with different particle size using 1064 nm laser. Laser induced damage threshold study was carried out for the grown crystal using Nd:YAG laser. PMID:24531108

  12. Band structures in Sierpinski triangle fractal porous phononic crystals

    NASA Astrophysics Data System (ADS)

    Wang, Kai; Liu, Ying; Liang, Tianshu

    2016-10-01

    In this paper, the band structures in Sierpinski triangle fractal porous phononic crystals (FPPCs) are studied with the aim to clarify the effect of fractal hierarchy on the band structures. Firstly, one kind of FPPCs based on Sierpinski triangle routine is proposed. Then the influence of the porosity on the elastic wave dispersion in Sierpinski triangle FPPCs is investigated. The sensitivity of the band structures to the fractal hierarchy is discussed in detail. The results show that the increase of the hierarchy increases the sensitivity of ABG (Absolute band gap) central frequency to the porosity. But further increase of the fractal hierarchy weakens this sensitivity. On the same hierarchy, wider ABGs could be opened in Sierpinski equilateral triangle FPPC; whilst, a lower ABG could be opened at lower porosity in Sierpinski right-angled isosceles FPPCs. These results will provide a meaningful guidance in tuning band structures in porous phononic crystals by fractal design.

  13. Domain structures in nematic liquid crystals on a polycarbonate surface.

    PubMed

    Parshin, Alexander M; Gunyakov, Vladimir A; Zyryanov, Victor Y; Shabanov, Vasily F

    2013-01-01

    Alignment of nematic liquid crystals on polycarbonate films obtained with the use of solvents with different solvations is studied. Domain structures occurring during the growth on the polymer surface against the background of the initial thread-like or schlieren texture are demonstrated. It is established by optical methods that the domains are stable formations visualizing the polymer surface structures. In nematic droplets, the temperature-induced transition from the domain structure with two extinction bands to the structure with four bands is observed. This transition is shown to be caused by reorientation of the nematic director in the liquid crystal volume from the planar alignment to the homeotropic state with the pronounced radial configuration of nematic molecules on the surface. The observed textures are compared with different combinations of the volume LC orientations and the radial distribution of the director field and the disclination lines at the polycarbonate surface. PMID:23965955

  14. Crystal Structure of the Bacillus subtilis Superoxide Dismutase

    SciTech Connect

    Liu, Ping; Ewis, H.E.; Huang, Y.-J; Lu, C.-D.; Tai, P.C.; Weber, Irene T.

    2008-06-01

    The sodA gene of Bacillus subtilis was expressed in Escherichia coli, purified and crystallized. The crystal structure of MnSOD was solved by molecular replacement with four dimers per asymmetric unit and refined to an R factor of 21.1% at 1.8 {angstrom} resolution. The dimer structure is very similar to that of the related enzyme from B. anthracis. Larger structural differences were observed with the human MnSOD, which has one less helix in the helical domain and a longer loop between two -strands and also showed differences in three amino acids at the intersubunit interface in the dimer compared with the two bacterial MnSODs. These structural differences can be exploited in the design of drugs that selectively target the Bacillus enzymes.

  15. Crystal structure and stereochemistry study of 2-substituted benzoxazole derivatives.

    PubMed

    Mabied, Ahmed F; Shalaby, Elsayed M; Zayed, Hamdia A; El-Kholy, Esmat; Farag, Ibrahim S A; Ahmed, Naima A

    2014-01-01

    The structure of 2-[(4-chlorophenylazo) cyanomethyl] benzoxazole, C15H9ClN4O (I), has triclinic ([Formula: see text]) symmetry. The structure displays N-H ⋯ N hydrogen bonding. The structure of 2-[(arylidene) cyanomethyl] benzoxazoles, C17H10N2O3 (II), has triclinic ([Formula: see text]) symmetry. The structure displays C-H ⋯ N, C-H ⋯ C hydrogen bonding. In (I), the chlorophenyl and benzoxazole groups adopt a trans configuration with respect to the central cyanomethyle hydrazone moiety. Compound (II) crystallized with two molecules in the asymmetric unit shows cisoid conformation between cyano group and benzoxazole nitrogen, contrary to (I). In (II) the benzodioxole has an envelope conformation (the C17 atom is the flap atom). The molecular geometry obtained using molecular mechanics (MM) calculations has been discussed along with the results of single crystal analysis.

  16. Domain Structures in Nematic Liquid Crystals on a Polycarbonate Surface

    PubMed Central

    Parshin, Alexander M.; Gunyakov, Vladimir A.; Zyryanov, Victor Y.; Shabanov, Vasily F.

    2013-01-01

    Alignment of nematic liquid crystals on polycarbonate films obtained with the use of solvents with different solvations is studied. Domain structures occurring during the growth on the polymer surface against the background of the initial thread-like or schlieren texture are demonstrated. It is established by optical methods that the domains are stable formations visualizing the polymer surface structures. In nematic droplets, the temperature-induced transition from the domain structure with two extinction bands to the structure with four bands is observed. This transition is shown to be caused by reorientation of the nematic director in the liquid crystal volume from the planar alignment to the homeotropic state with the pronounced radial configuration of nematic molecules on the surface. The observed textures are compared with different combinations of the volume LC orientations and the radial distribution of the director field and the disclination lines at the polycarbonate surface. PMID:23965955

  17. Domain structures in nematic liquid crystals on a polycarbonate surface.

    PubMed

    Parshin, Alexander M; Gunyakov, Vladimir A; Zyryanov, Victor Y; Shabanov, Vasily F

    2013-01-01

    Alignment of nematic liquid crystals on polycarbonate films obtained with the use of solvents with different solvations is studied. Domain structures occurring during the growth on the polymer surface against the background of the initial thread-like or schlieren texture are demonstrated. It is established by optical methods that the domains are stable formations visualizing the polymer surface structures. In nematic droplets, the temperature-induced transition from the domain structure with two extinction bands to the structure with four bands is observed. This transition is shown to be caused by reorientation of the nematic director in the liquid crystal volume from the planar alignment to the homeotropic state with the pronounced radial configuration of nematic molecules on the surface. The observed textures are compared with different combinations of the volume LC orientations and the radial distribution of the director field and the disclination lines at the polycarbonate surface.

  18. Crystallization studies of lunar igneous rocks: crystal structure of synthetic armalcolite.

    PubMed

    Lind, M D; Housley, R M

    1972-02-01

    Crystals of armalcolite, Mg(0.5)Fe(0.5)Ti(2)O(5), up to several millimeters in length have been grown from a glass initially having the composition of lunar rock 10017. A single-crystal x-ray study has confirmed that the crystals are isomorphous with pseudobrookite and has shown that the cations are strongly ordered, with the Ti(4+) ions occupying the 8f sites and the Fe(2+) and Mg(2+) ions randomly distributed over the 4c sites. An examination of karrooite, MgTi(2)O(5), has revealed a similar distribution of Mg(2+) and Ti(4+) ions. A reexamination of earlier x-ray and Mössbauer data for pseudobrookite, Fe(2)TiO(5), has shown that it is more consistent with this type of ordering than with the inverse structure that has been generally assumed.

  19. Reconstruction of explicit structural properties at the nanoscale via spectroscopic microscopy.

    PubMed

    Cherkezyan, Lusik; Zhang, Di; Subramanian, Hariharan; Taflove, Allen; Backman, Vadim

    2016-02-01

    The spectrum registered by a reflected-light bright-field spectroscopic microscope (SM) can quantify the microscopically indiscernible, deeply subdiffractional length scales within samples such as biological cells and tissues. Nevertheless, quantification of biological specimens via any optical measures most often reveals ambiguous information about the specific structural properties within the studied samples. Thus, optical quantification remains nonintuitive to users from the diverse fields of technique application. In this work, we demonstrate that the SM signal can be analyzed to reconstruct explicit physical measures of internal structure within label-free, weakly scattering samples: characteristic length scale and the amplitude of spatial refractive-index (RI) fluctuations. We present and validate the reconstruction algorithm via finite-difference time-domain solutions of Maxwell's equations on an example of exponential spatial correlation of RI. We apply the validated algorithm to experimentally measure structural properties within isolated cells from two genetic variants of HT29 colon cancer cell line as well as within a prostate tissue biopsy section. The presented methodology can lead to the development of novel biophotonics techniques that create two-dimensional maps of explicit structural properties within biomaterials: the characteristic size of macromolecular complexes and the variance of local mass density. PMID:26886803

  20. Reconstruction of explicit structural properties at the nanoscale via spectroscopic microscopy

    NASA Astrophysics Data System (ADS)

    Cherkezyan, Lusik; Zhang, Di; Subramanian, Hariharan; Taflove, Allen; Backman, Vadim

    2016-02-01

    The spectrum registered by a reflected-light bright-field spectroscopic microscope (SM) can quantify the microscopically indiscernible, deeply subdiffractional length scales within samples such as biological cells and tissues. Nevertheless, quantification of biological specimens via any optical measures most often reveals ambiguous information about the specific structural properties within the studied samples. Thus, optical quantification remains nonintuitive to users from the diverse fields of technique application. In this work, we demonstrate that the SM signal can be analyzed to reconstruct explicit physical measures of internal structure within label-free, weakly scattering samples: characteristic length scale and the amplitude of spatial refractive-index (RI) fluctuations. We present and validate the reconstruction algorithm via finite-difference time-domain solutions of Maxwell's equations on an example of exponential spatial correlation of RI. We apply the validated algorithm to experimentally measure structural properties within isolated cells from two genetic variants of HT29 colon cancer cell line as well as within a prostate tissue biopsy section. The presented methodology can lead to the development of novel biophotonics techniques that create two-dimensional maps of explicit structural properties within biomaterials: the characteristic size of macromolecular complexes and the variance of local mass density.

  1. Minerals from Macedonia XXIII. Spectroscopic and structural characterization of schorl and beryl cyclosilicates.

    PubMed

    Makreski, Petre; Jovanovski, Gligor

    2009-08-01

    IR and Raman spectroscopy study on two collected cyclosilicate species: schorl (from tourmaline group), Na(Fe,Mg)(3)Al(6)(BO(3))(3)Si(6)O(18)(OH,F)(4) and beryl (Be,Mg,Fe)(3)Al(2)Si(6)O(18) were carried out. Although beryl is nominally anhydrous mineral, vibrational results strongly indicate that H(2)O molecules exist in the structural channels. The number of vibrational bands and their frequencies revealed the presence of H(2)O type II, in which C(2) symmetry axis of the water molecule is parallel to the structural channel (and to the c-axis of beryl). On the other hand, it was found that observed bands in the IR and Raman OH stretching region of the other tourmaline varieties appear as a result of the cation combinations involving dominant presence of Mg and Fe cations in the Y structural sites. The strong indication derived from the vibrational spectroscopic results that the studied mineral represents a schorl variety, coincide very well with the results obtained by powder X-ray diffraction and X-ray microprobe analysis. Both minerals show IR spectral similarities in the region below 1500 cm(-1), whereas the resemblance between the Raman spectra (1500-100 cm(-1)) is less expressed confirming that these spectra are more sensitive to compositional changes and to structural disorder. The identification of both minerals was additionally supported by studying the powder X-ray diffraction diagrams. PMID:18722809

  2. Infrared Spectroscopic Study For Structural Investigation Of Lithium Lead Silicate Glasses

    SciTech Connect

    Ahlawat, Navneet; Aghamkar, Praveen; Ahlawat, Neetu; Agarwal, Ashish; Monica

    2011-12-12

    Lithium lead silicate glasses with composition 30Li{sub 2}O{center_dot}(70-x)PbO{center_dot}xSiO{sub 2}(where, x = 10, 20, 30, 40, 50 mol %)(LPS glasses) were prepared by normal melt quench technique at 1373 K for half an hour in air to understand their structure. Compositional dependence of density, molar volume and glass transition temperature of these glasses indicates more compactness of the glass structure with increasing SiO{sub 2} content. Fourier transform infrared (FTIR) spectroscopic data obtained for these glasses was used to investigate the changes induced in the local structure of samples as the ratio between PbO and SiO{sub 2} content changes from 6.0 to 0.4. The observed absorption band around 450-510 cm{sup -1} in IR spectra of these glasses indicates the presence of network forming PbO{sub 4} tetrahedral units in glass structure. The increase in intensity with increasing SiO{sub 2} content (upto x = 30 mol %) suggests superposition of Pb-O and Si-O bond vibrations in absorption band around 450-510 cm{sup -1}. The values of optical basicity in these glasses were found to be dependent directly on PbO/SiO{sub 2} ratio.

  3. Minerals from Macedonia XXIII. Spectroscopic and structural characterization of schorl and beryl cyclosilicates.

    PubMed

    Makreski, Petre; Jovanovski, Gligor

    2009-08-01

    IR and Raman spectroscopy study on two collected cyclosilicate species: schorl (from tourmaline group), Na(Fe,Mg)(3)Al(6)(BO(3))(3)Si(6)O(18)(OH,F)(4) and beryl (Be,Mg,Fe)(3)Al(2)Si(6)O(18) were carried out. Although beryl is nominally anhydrous mineral, vibrational results strongly indicate that H(2)O molecules exist in the structural channels. The number of vibrational bands and their frequencies revealed the presence of H(2)O type II, in which C(2) symmetry axis of the water molecule is parallel to the structural channel (and to the c-axis of beryl). On the other hand, it was found that observed bands in the IR and Raman OH stretching region of the other tourmaline varieties appear as a result of the cation combinations involving dominant presence of Mg and Fe cations in the Y structural sites. The strong indication derived from the vibrational spectroscopic results that the studied mineral represents a schorl variety, coincide very well with the results obtained by powder X-ray diffraction and X-ray microprobe analysis. Both minerals show IR spectral similarities in the region below 1500 cm(-1), whereas the resemblance between the Raman spectra (1500-100 cm(-1)) is less expressed confirming that these spectra are more sensitive to compositional changes and to structural disorder. The identification of both minerals was additionally supported by studying the powder X-ray diffraction diagrams.

  4. Structural studies of E. coli ribosomes by spectroscopic techniques: A specialized review

    NASA Astrophysics Data System (ADS)

    Bonicontro, Adalberto; Risuleo, Gianfranco

    2005-12-01

    We present a review on our interdisciplinary line of research based on strategies of molecular biology and biophysics. These have been applied to the study of the prokaryotic ribosome of the bacterium Escherichia coli. Our investigations on this organelle have continued for more than a decade and we have adopted different spectroscopic biophysical techniques such as: dielectric and fluorescence spectroscopy as well as light scattering (photon correlation spectroscopy). Here we report studies on the whole 70S ribosomes and on the separated subunits 30S and 50S. Our results evidence intrinsic structural features of the subunits: the small shows a more "floppy" structure, while the large one appears to be more rigid. Also, an inner "kernel" formed by the RNA/protein association is found within the ribosome. This kernel is surrounded by a ribonucleoprotein complex more exposed to the solvent. Initial analyses were done on the so called Kaldtschmit-Wittmann ribosome: more recently we have extended the studies to the "tight couple" ribosome known for its better functional performance in vitro. Data evidence a phenomenological correlation between the differential biological activity and the intrinsic structural properties of the two-ribosome species. Finally, investigations were also conducted on particles treated at sub-denaturing temperatures and on ribosomes partially deproteinized by salt treatment (ribosomal cores). Results suggest that the thermal treatment and the selective removal of proteins cause analogous structural alterations.

  5. Serendibite, a Complicated, New, Inorganic Crystal Structure

    PubMed Central

    Buerger, Martin J.; Venkatakrishnan, V.

    1974-01-01

    Serendibite with very similar analyses is known from Ceylon and New York. The triclinic cell of symmetry P[unk] and volume 670.9 Å3 contains 2Ca1.64Mg2.64Fe0.27IIAl4.64B1.66Si3O20, with 14 metal atoms and 20 oxygen atoms in the asymmetric unit. It was solved by the “direct” method of transforming the ordinary three-dimensional Patterson function into an approximation of the electron density by using conjugate peaks and minimum functions, followed by successive Fourier syntheses and least-squares refinement to R = 7.1%. This new structure is composed of interrupted brucite-type layers which form an octahedral framework, and winged single chains of tetrahedra. The structure has units of similar, but not identical, geometry to those of the minerals sapphirine and aenigmatite, and these similar units are assembled in a different way. PMID:16592193

  6. Single Crystal Structure Determination of Alumina to 1 Mbar

    NASA Astrophysics Data System (ADS)

    Dong, H.; Zhang, L.; Prakapenka, V.; Mao, H.

    2014-12-01

    Aluminum oxide (Al2O3) is an important ceramic material and a major oxide in the earth. Additionally, alumina is a widely used pressure standard in static high-pressure experiments (Cr3+-bearing corundum, ruby). The changes of its crystal structure with pressure (P) and temperature (T) are important for its applications and understanding its physical properties in the deep Earth. There have been numerous reports on the high P-T polymorphs of alumina. Previous theoretical calculations and experiments suggest that the crystal structure of Al2O3 evolves greatly at high P-T. In this study, we used the newly developed multigrain crystallography method combined with single-crystal x-ray diffraction analysis technique for the structure determination of alumina at high P-T to provide single-crystal structure refinement for high-pressure phases of Al2O3. Alumina powder was mixed with ~10% Pt and Ne was used as both pressure transmitting media and thermal insulating layers during laser-heating. Coarse-grained aggregates of Al2O3 were synthesized in a laser-heated diamond anvil cell. The structure change of Al2O3 was monitored by in situ x-ray diffraction at ~1 Mbar and 2700 K. The results allow us to distinguish the structural differences between the Rh2O3 (II) structure (space group Pbcn) and perovskite structure (space group Pbnm) for the first high-pressure phase of Al2O3. More detailed results will be discussed in the later work.

  7. Crystal structure of new AsS2 compound

    NASA Astrophysics Data System (ADS)

    Bolotina, N. B.; Brazhkin, V. V.; Dyuzheva, T. I.; Lityagina, L. M.; Kulikova, L. F.; Nikolaev, N. A.; Verin, I. A.

    2013-01-01

    AsS2 single crystals have been obtained for the first time from an As2S3 melt at pressures above 6 GPa and temperatures above 800 K in the As2S3 → AsS + AsS2 reaction. The monoclinic structure of the new high-pressure phase is solved by X-ray diffraction analysis and compared to the structure of high-pressure AsS phase, which was studied previously.

  8. Structural evolution in the crystallization of rapid cooling silver melt

    SciTech Connect

    Tian, Z.A.; Dong, K.J.; Yu, A.B.

    2015-03-15

    The structural evolution in a rapid cooling process of silver melt has been investigated at different scales by adopting several analysis methods. The results testify Ostwald’s rule of stages and Frank conjecture upon icosahedron with many specific details. In particular, the cluster-scale analysis by a recent developed method called LSCA (the Largest Standard Cluster Analysis) clarified the complex structural evolution occurred in crystallization: different kinds of local clusters (such as ico-like (ico is the abbreviation of icosahedron), ico-bcc like (bcc, body-centred cubic), bcc, bcc-like structures) in turn have their maximal numbers as temperature decreases. And in a rather wide temperature range the icosahedral short-range order (ISRO) demonstrates a saturated stage (where the amount of ico-like structures keeps stable) that breeds metastable bcc clusters. As the precursor of crystallization, after reaching the maximal number bcc clusters finally decrease, resulting in the final solid being a mixture mainly composed of fcc/hcp (face-centred cubic and hexagonal-closed packed) clusters and to a less degree, bcc clusters. This detailed geometric picture for crystallization of liquid metal is believed to be useful to improve the fundamental understanding of liquid–solid phase transition. - Highlights: • A comprehensive structural analysis is conducted focusing on crystallization. • The involved atoms in our analysis are more than 90% for all samples concerned. • A series of distinct intermediate states are found in crystallization of silver melt. • A novelty icosahedron-saturated state breeds the metastable bcc state.

  9. Tailor-made force fields for crystal-structure prediction.

    PubMed

    Neumann, Marcus A

    2008-08-14

    A general procedure is presented to derive a complete set of force-field parameters for flexible molecules in the crystalline state on a case-by-case basis. The force-field parameters are fitted to the electrostatic potential as well as to accurate energies and forces generated by means of a hybrid method that combines solid-state density functional theory (DFT) calculations with an empirical van der Waals correction. All DFT calculations are carried out with the VASP program. The mathematical structure of the force field, the generation of reference data, the choice of the figure of merit, the optimization algorithm, and the parameter-refinement strategy are discussed in detail. The approach is applied to cyclohexane-1,4-dione, a small flexible ring. The tailor-made force field obtained for cyclohexane-1,4-dione is used to search for low-energy crystal packings in all 230 space groups with one molecule per asymmetric unit, and the most stable crystal structures are reoptimized in a second step with the hybrid method. The experimental crystal structure is found as the most stable predicted crystal structure both with the tailor-made force field and the hybrid method. The same methodology has also been applied successfully to the four compounds of the fourth CCDC blind test on crystal-structure prediction. For the five aforementioned compounds, the root-mean-square deviations between lattice energies calculated with the tailor-made force fields and the hybrid method range from 0.024 to 0.053 kcal/mol per atom around an average value of 0.034 kcal/mol per atom.

  10. Tailor-made force fields for crystal-structure prediction.

    PubMed

    Neumann, Marcus A

    2008-08-14

    A general procedure is presented to derive a complete set of force-field parameters for flexible molecules in the crystalline state on a case-by-case basis. The force-field parameters are fitted to the electrostatic potential as well as to accurate energies and forces generated by means of a hybrid method that combines solid-state density functional theory (DFT) calculations with an empirical van der Waals correction. All DFT calculations are carried out with the VASP program. The mathematical structure of the force field, the generation of reference data, the choice of the figure of merit, the optimization algorithm, and the parameter-refinement strategy are discussed in detail. The approach is applied to cyclohexane-1,4-dione, a small flexible ring. The tailor-made force field obtained for cyclohexane-1,4-dione is used to search for low-energy crystal packings in all 230 space groups with one molecule per asymmetric unit, and the most stable crystal structures are reoptimized in a second step with the hybrid method. The experimental crystal structure is found as the most stable predicted crystal structure both with the tailor-made force field and the hybrid method. The same methodology has also been applied successfully to the four compounds of the fourth CCDC blind test on crystal-structure prediction. For the five aforementioned compounds, the root-mean-square deviations between lattice energies calculated with the tailor-made force fields and the hybrid method range from 0.024 to 0.053 kcal/mol per atom around an average value of 0.034 kcal/mol per atom. PMID:18642947

  11. Thermodynamics of sublimation, crystal lattice energies, and crystal structures of racemates and enantiomers: (+)- and (+/-)-ibuprofen.

    PubMed

    Perlovich, German L; Kurkov, Sergey V; Hansen, Lars Kr; Bauer-Brandl, Annette

    2004-03-01

    Thermodynamic differences between ibuprofen (IBP) racemate and the (+)-enantiomer were studied by X-ray diffraction, thermoanalysis, and crystal energy calculations. The thermodynamic functions of sublimation (as a measure of crystal lattice energy) were obtained by the transpiration method. The sublimation enthalpies (DeltaH(sub)) of (+/-)-IBP and (+)-IBP are 115.8 +/- 0.6 and 107.4 +/- 0.5 kJ. mol(-1), respectively. Using the temperature dependency of the saturated vapor pressure, the relative fractions of enthalpy and entropy of the sublimation process were calculated, and the sublimation process for both the racemate and the enantiomer was found to be enthalpy driven (62%). Two different force fields, Mayo et al. (M) and Gavezzotti (G), were used for comparative analysis of crystal lattice energies. Both force fields revealed that the van der Waals term contributes more to the packing energy in (+)-IBP than in (+/-)-IBP. The hydrogen bonding energy, however, contributes at 29.7 and 32.3% to the total crystal lattice energy in (+)-IBP and (+/-)-IBP (M), respectively. Furthermore, different structure fragments of the IBP molecule were analyzed with respect to their contribution to nonbonded van der Waals interactions. The effect of the C-H distance on the van der Waals term of the crystal lattice energy was also studied.

  12. Crystal structure of 4-carbamoylpyridinium chloride.

    PubMed

    Fellows, Simon M; Prior, Timothy J

    2016-04-01

    The hydro-chloride salt of isonicotinamide, C6H7N2O(+)·Cl(-), has been synthesized from a dilute solution of hydro-chloric acid in aceto-nitrile. The compound displays monoclinic symmetry (space group C2/c) at 150 K, similar to the related hydro-chloride salt of nicotinamide. The asymmetric unit contains one protonated isonicotinamide mol-ecule and a chloride anion. An array of hydrogen-bonding inter-actions, including a peculiar bifurcated pyridinium-chloride inter-action, results in linear chains running almost perpendicularly in the [150] and [1-50] directions within the structure. A description of the hydrogen-bonding network and comparison with similar compounds are presented. PMID:27375858

  13. Crystal structure of 4-carbamoylpyridinium chloride

    PubMed Central

    Fellows, Simon M.; Prior, Timothy J.

    2016-01-01

    The hydro­chloride salt of isonicotinamide, C6H7N2O+·Cl−, has been synthesized from a dilute solution of hydro­chloric acid in aceto­nitrile. The compound displays monoclinic symmetry (space group C2/c) at 150 K, similar to the related hydro­chloride salt of nicotinamide. The asymmetric unit contains one protonated isonicotinamide mol­ecule and a chloride anion. An array of hydrogen-bonding inter­actions, including a peculiar bifurcated pyridinium–chloride inter­action, results in linear chains running almost perpendicularly in the [150] and [1-50] directions within the structure. A description of the hydrogen-bonding network and comparison with similar compounds are presented. PMID:27375858

  14. Crystal structures of Ziegler-Natta catalyst supports.

    PubMed

    Malizia, Federica; Fait, Anna; Cruciani, Giuseppe

    2011-12-01

    The crystal structures of three MgCl(2)·nEtOH complexes with n=1.5, 2.8, and 3.3 have been fully determined. Such complexes are the fundamental precursors for Ziegler-Natta polymerization catalysts used to produce polyolefins on a multimillion-ton scale worldwide. The ab initio structure solution showed that the structure of MgCl(2)·nEtOH complexes with n=1.5 and 2.8 are based on ribbons of metal-centered octahedra, whereas for n=3.3 this chainlike arrangement breaks into a threadlike structure of isolated octahedra linked by hydrogen bonds. A clear correlation between catalyst performance and the crystal structure of precursors has been found, and reveals the fundamental role of the latter in determining catalyst properties. The direct knowledge of building blocks in the precursor structures will help to develop more accurate models for activated catalysts. These models will not require the arbitrary and oversimplified assumption of locating the catalyst active sites on selected cut surfaces of the α-MgCl(2) crystal lattice. PMID:22052708

  15. On calculating the equilibrium structure of molecular crystals.

    SciTech Connect

    Mattsson, Ann Elisabet; Wixom, Ryan R.; Mattsson, Thomas Kjell Rene

    2010-03-01

    The difficulty of calculating the ambient properties of molecular crystals, such as the explosive PETN, has long hampered much needed computational investigations of these materials. One reason for the shortcomings is that the exchange-correlation functionals available for Density Functional Theory (DFT) based calculations do not correctly describe the weak intermolecular van der Waals' forces present in molecular crystals. However, this weak interaction also poses other challenges for the computational schemes used. We will discuss these issues in the context of calculations of lattice constants and structure of PETN with a number of different functionals, and also discuss if these limitations can be circumvented for studies at non-ambient conditions.

  16. Structural, magnetic and optical properties of two concomitant molecular crystals

    NASA Astrophysics Data System (ADS)

    Silva, Manuela Ramos; Milne, Bruce; Coutinho, Joana T.; Pereira, Laura C. J.; Martín-Ramos, Pablo; Pereira da Silva, Pedro S.; Martín-Gil, Jesús

    2016-03-01

    A new 1D complex has been prepared and characterized. X-ray single crystal structure confirms that the Cu(II) ions assemble in alternating chains with Cu … Cu distances of 2.5685(4) and 3.1760(4) Å. The temperature dependence of the magnetic susceptibility reveals an antiferromagnetic interaction between the paddle-wheel copper centers with an exchange of -300 cm-1. The exchange integral was also determined by quantum chemical ab-initio calculations, using polarised and unpolarised basis sets reproducing well the experimental value. The second harmonic generation efficiency of a concomitantly crystallized material was evaluated and was found to be comparable to urea.

  17. Modeling liquid crystal bilayer structures with minimal surfaces.

    PubMed

    Enlow, J D; Enlow, R L; McGrath, K M; Tate, M W

    2004-01-22

    This paper describes a new convenient and accurate method of calculating x-ray diffraction integrated intensities from detailed cubic bilayer structures. The method is employed to investigate the structure of a particular surfactant system (didodecyldimethylammonium bromide in a solution of oil and heavy water), for which single-crystal experimental data have recently been collected. The diffracted peak intensities correlate well with theoretical structures based on mathematical minimal surfaces. Optimized electron density profiles of the bilayer are presented, providing new insight into key features of the bilayer structure.

  18. Spectral studies of semicarbazones derived from 3- and 4-formylpyridine and 3- and 4-acetylpyridine: crystal and molecular structure of 3-formylpyridine semicarbazone

    NASA Astrophysics Data System (ADS)

    Beraldo, Heloisa; Nacif, Wanderlene F.; West, Douglas X.

    2001-08-01

    Semicarbazones derived from 3- and 4-formylpyridine (H3FoPyS, H4FoPyS) and 3- and 4-acetylpyridine (H3AcPyS, H4AcPyS) were prepared and studied spectroscopically. Complete NMR assignments for these semicarbazones were made using DEPT135, as well as HMQC and HMBC heteronuclear correlation techniques. The crystal and molecular structures of H3FoPyS were determined.

  19. Spectroscopic, thermal and cw dual-wavelength laser characteristics of Nd:LaF3 single crystal

    NASA Astrophysics Data System (ADS)

    Hong, Jiaqi; Zhang, Lianhan; Li, Jing; Wang, Zhaowei; He, Jingliang; Zhang, Peixiong; Wang, Yaqi; Hang, Yin

    2016-03-01

    A Nd-doped LaF3 crystal was grown by Czochralski method, and the rocking curves of (0 0 2) and (1 1 0) diffraction planes show good crystallinity quality of the as-grown crystal. Room-temperature fluorescence spectrum and transmittance spectrum of Nd:LaF3 crystal were investigated, both indicating probable dual-wavelength emissions at ∼1.04 μm and ∼1.06 μm. The thermal diffusivity and thermal conductivity of Nd:LaF3 crystal were detailed studied. Cw dual-wavelength laser operation of Nd:LaF3 single crystal at 1040 nm and around 1065 nm with LD pumping was demonstrated. A maximum output power of 302 mW was obtained with a slope efficiency of about 18.5% with respect to the pump power. The results of our study indicate the Nd:LaF3 crystal a promising laser crystal.

  20. Can antimonide-based nanowires form wurtzite crystal structure?

    PubMed

    Gorji Ghalamestani, Sepideh; Lehmann, Sebastian; Dick, Kimberly A

    2016-02-01

    The epitaxial growth of antimonide-based nanowires has become an attractive subject due to their interesting properties required for various applications such as long-wavelength IR detectors. The studies conducted on antimonide-based nanowires indicate that they preferentially crystallize in the zinc blende (ZB) crystal structure rather than wurtzite (WZ), which is common in other III-V nanowire materials. Also, with the addition of small amounts of antimony to arsenide- and phosphide-based nanowires grown under conditions otherwise leading to WZ structure, the crystal structure of the resulting ternary nanowires favors the ZB phase. Therefore, the formation of antimonide-based nanowires with the WZ phase presents fundamental challenges and is yet to be explored, but is particularly interesting for understanding the nanowire crystal phase in general. In this study, we examine the formation of Au-seeded InSb and GaSb nanowires under various growth conditions using metalorganic vapor phase epitaxy. We address the possibility of forming other phases than ZB such as WZ and 4H in binary nanowires and demonstrate the controlled formation of WZ InSb nanowires. We further discuss the fundamental aspects of WZ growth in Au-seeded antimonide-based nanowires. PMID:26763161

  1. Projection structure of frog rhodopsin in two crystal forms.

    PubMed Central

    Schertler, G F; Hargrave, P A

    1995-01-01

    Rhodopsin is the G protein-coupled receptor that upon light activation triggers the visual transduction cascade. Rod cell outer segment disc membranes were isolated from dark-adapted frog retinas and were extracted with Tween detergents to obtain two-dimensional rhodopsin crystals for electron crystallography. When Tween 80 was used, tubular structures with a p2 lattice (a = 32 A, b = 83 A, gamma = 91 degrees) were formed. The use of a Tween 80/Tween 20 mixture favored the formation of larger p22(1)2(1) lattices (a = 40 A, b = 146 A, gamma = 90 degrees). Micrographs from frozen hydrated frog rhodopsin crystals were processed, and projection structures to 7-A resolution for the p22(1)2(1) form and to 6-A resolution for the p2 form were calculated. The maps of frog rhodopsin in both crystal forms are very similar to the 9-A map obtained previously for bovine rhodopsin and show that the arrangement of the helices is the same. In a tentative topographic model, helices 4, 6, and 7 are nearly perpendicular to the plane of the membrane. In the higher-resolution projection maps of frog rhodopsin, helix 5 looks more tilted than it appeared previously. The quality of the two frog rhodopsin crystals suggests that they would be suitable to obtain a three-dimensional structure in which all helices would be resolved. Images Fig. 1 Fig. 2 Fig. 6 PMID:8524807

  2. Investigation of Bovine Serum Albumin (BSA) Attachment onto Self-Assembled Monolayers (SAMs) Using Combinatorial Quartz Crystal Microbalance with Dissipation (QCM-D) and Spectroscopic Ellipsometry (SE)

    PubMed Central

    Phan, Hanh T. M.; Bartelt-Hunt, Shannon; Rodenhausen, Keith B.; Schubert, Mathias; Bartz, Jason C.

    2015-01-01

    Understanding protein adsorption kinetics to surfaces is of importance for various environmental and biomedical applications. Adsorption of bovine serum albumin to various self-assembled monolayer surfaces including neutral and charged hydrophilic and hydrophobic surfaces was investigated using in-situ combinatorial quartz crystal microbalance with dissipation and spectroscopic ellipsometry. Adsorption of bovine serum albumin varied as a function of surface properties, bovine serum albumin concentration and pH value. Charged surfaces exhibited a greater quantity of bovine serum albumin adsorption, a larger bovine serum albumin layer thickness, and increased density of bovine serum albumin protein compared to neutral surfaces at neutral pH value. The quantity of adsorbed bovine serum albumin protein increased with increasing bovine serum albumin concentration. After equilibrium sorption was reached at pH 7.0, desorption of bovine serum albumin occurred when pH was lowered to 2.0, which is below the isoelectric point of bovine serum albumin. Our data provide further evidence that combinatorial quartz crystal microbalance with dissipation and spectroscopic ellipsometry is a sensitive analytical tool to evaluate attachment and detachment of adsorbed proteins in systems with environmental implications. PMID:26505481

  3. Structural characterization of C-S-H and C-A-S-H samples-Part II: Local environment investigated by spectroscopic analyses

    SciTech Connect

    Renaudin, Guillaume; Russias, Julie; Leroux, Fabrice; Cau-dit-Coumes, Celine; Frizon, Fabien

    2009-12-15

    Spectroscopic studies ({sup 1}H, {sup 23}Na and {sup 27}Al MAS NMR and Raman spectroscopy) have been used to characterize three series of C-S-H samples (0.8structural model allows to describe the C-S-H structure whatever the Ca/Si ratio and (2) the insertion of aluminum into the C-S-H structure led to the degradation of the crystallinity and to a systematic increase of the basal spacing of about 2 A regardless the Ca/(Si+Al) ratio (at a constant Al/Si ratio of 0.1). Spectroscopic investigations indicate that the main part of the Al atoms is readily incorporated into the interlayer region of the C-S-H structure. Al atoms are mainly inserted as four-fold coordinated aluminates in the dreierketten silicate chain (either in bridging or paired tetrahedra) at low Ca/Si ratio. Four-fold aluminates are progressively replaced by six-fold coordinated aluminates located into the interlayer region of the C-S-H structure and bonded to silicate chains. Investigation of the hydrogen bonding in C-S-H indicates that the main part of the hydrogen bonds is intra-main layer, and thus explains the low stacking cohesion of the C-S-H structure leading to its nanometric crystal size and the OD character of the tobermorite like structures. - Graphical abstract: The insertion of aluminum atoms into the C-S-H structure has been investigated by spectroscopic analyses ({sup 27}Al and {sup 1}H MAS NMR and Raman). The previously determined structural continuity, when increasing the C/S ratio from the C-S-H(I) type to the C-S-H(II) type, has been confirmed even in the presence of aluminum.

  4. Mononuclear anionic octahedral cobalt(III) complexes based on N-salicylidene-o-aminophenol and its derivatives: Synthetic, structural and spectroscopic studies

    NASA Astrophysics Data System (ADS)

    Alexopoulou, Konstantina I.; Zagoraiou, Eirini; Zafiropoulos, Theodoros F.; Raptopoulou, Catherine P.; Psycharis, Vassilis; Terzis, Aris; Perlepes, Spyros P.

    2015-02-01

    The reactions of Co(II) sources with N-salicylidene-o-aminophenol (H2saph), N-salicylidene-o-amino-4-methylphenol (H2saph-4Me) and N-salicylidene-o-amino-4-chlorophenol (H2saph-4Cl) were studied in MeOH. The new solid complexes (Bu4,SUP>n,/SUP> N) [CoIII(saph)2] (1), (Et3NH)[CoIII(saph-4Me)2]ṡMeOHṡMeCO2H (2ṡMeOHṡMeCO2H) and (Et3NH)[CoIII(saph-4Cl)2]ṡMeOHṡMeCO2H (3ṡMeOHṡMeCO2H) have been isolated and their structures determined by single-crystal, X-ray crystallography. The three compounds contain the mononuclear, low- spin octahedral anion [CoIIIL2 ] - (H2L = H2saph, H2saph-4Me, H2saph-4Cl), in which both L2- ligands act as tridentate chelating, meridional ONO donors. The crystal structures of 2ṡMeOHṡMeCO2H and 3ṡMeOHṡMeCO2H are built through H-bonding and π-π stacking interactions. The new complexes were characterized by elemental analyses and spectroscopic (IR, Raman, UV/VIS, 1H NMR) data. All data are discussed in terms of the nature of bonding and known structures.

  5. Structural, crystal structure, Hirshfeld surface analysis and physicochemical studies of a new chlorocadmate template by 1-(2-hydroxyethyl)piperazine

    NASA Astrophysics Data System (ADS)

    Soudani, S.; Jeanneau, E.; Jelsch, C.; Lefebvre, F.; Ben Nasr, C.

    2016-11-01

    The synthesis, crystal structure and spectroscopic characterization of a new chlorocadmate template by the 1-(2-hydroxyethyl)piperazine ligand are reported. In the atomic arrangement, the CdCl5O entities are deployed in corrugated rows along the a-axis at y = 1/4 and y = 3/4 to form layers parallel to the (a,b) plane. In these crystals, piperazinediium cations are in a chair conformation and are inserted between these layers through Nsbnd H⋯Cl, Csbnd H⋯Cl, Osbnd H⋯Cl and Nsbnd H⋯O hydrogen bonds to form infinite three-dimensional network. Investigation of intermolecular interactions and crystal packing via Hirshfeld surface analysis reveals that H⋯Cl and Csbnd H⋯Hsbnd C intermolecular interactions are the most abundant contacts of the organic cation in the crystal packing. The crystal contacts enrichments reveals that, the Cd++ … Cl- salt bridges, the Cd⋯O complexation and Osbnd H⋯Cl- and Nsbnd H⋯Cl-strong H-bonds are the driving forces in the packing formation. The presence of twelve independent chloride anions and four organic cation in the asymmetric unit allowed comparing their contact propensities. The 13C and 15N CP-MAS NMR spectra are in agreement with the X-ray structure. Additional characterization of this compound has also been performed by IR spectroscopy.

  6. Band structure and optical properties of diglycine nitrate crystal

    NASA Astrophysics Data System (ADS)

    Andriyevsky, Bohdan; Ciepluch-Trojanek, Wioleta; Romanyuk, Mykola; Patryn, Aleksy; Jaskólski, Marcin

    2005-07-01

    Experimental and theoretical investigations of the electron energy characteristics and optical spectra for diglycine nitrate crystal (DGN), (NH 2CH 2COOH) 2·HNO 3, in the paraelectric phase ( T=295 K) are presented. Spectral dispersion of light reflection R( E) have been measured in the range of 3-22 eV and the optical functions n( E) and k( E) have been calculated using Kramers-Kronig relations. First principal calculations of the electron energy characteristic and optical spectra of DGN crystal have been performed in the frame of density functional theory using CASTEP code (CAmbridge Serial Total Energy Package). Optical transitions forming the low-energy edge of fundamental absorption are associated with the nitrate groups NO 3. Peculiarities of the band structure and DOS projected onto glycine and NO 3 groups confirm the molecular character of DGN crystal.

  7. Crystal structure and density of helium to 232 kbar

    NASA Technical Reports Server (NTRS)

    Mao, H. K.; Wu, Y.; Jephcoat, A. P.; Hemley, R. J.; Bell, P. M.; Bassett, W. A.

    1988-01-01

    The properties of helium and hydrogen at high pressure are topics of great interest to the understanding of planetary interiors. These materials constitute 95 percent of the entire solar system. A technique was presented for the measurement of X-ray diffraction from single-crystals of low-Z condenses gases in a diamond-anvil cell at high pressure. The first such single-crystal X-ray diffraction measurements on solid hydrogen to 26.5 GPa were presented. The application of this technique to the problem of the crystal structure, equation of state, and phase diagram of solid helium is reported. Crucial for X-ray diffraction studies of these materials is the use of a synchrotron radiation source which provides high brillance, narrow collimation of the incident and diffracted X-ray beams to reduce the background noise, and energy-dispersive diffraction techniques with polychromatic (white) radiation, which provides high detection efficiency.

  8. Structure and melting behavior of classical bilayer crystals of dipoles

    SciTech Connect

    Lu Xin; Wu Changqin; Micheli, Andrea; Pupillo, Guido

    2008-07-01

    We study the structure and melting of a classical bilayer system of dipoles in a setup where the dipoles are oriented perpendicular to the planes of the layers and the density of dipoles is the same in each layer. Due to the anisotropic character of the dipole-dipole interactions, we find that the ground-state configuration is given by two hexagonal crystals positioned on top of each other, independent of the interlayer spacing and dipolar density. For large interlayer distances these crystals are independent, while in the opposite limit of small interlayer distances the system behaves as a two-dimensional crystal of paired dipoles. Within the harmonic approximation for the phonon excitations, the melting temperature of these crystalline configurations displays a nonmonotonic dependence on the interlayer distance, which is associated with a re-entrant melting behavior in the form of solid-liquid-solid-liquid transitions at fixed temperature.

  9. Chromophore-labelled, luminescent platinum complexes: syntheses, structures, and spectroscopic properties.

    PubMed

    Stacey, Oliver J; Ward, Benjamin D; Coles, Simon J; Horton, Peter N; Pope, Simon J A

    2016-06-21

    Ligands based upon 4-carboxamide-2-phenylquinoline derivatives have been synthesised with solubilising octyl hydrocarbon chains and tethered aromatic chromophores to give naphthyl (), anthracenyl () and pyrenyl () ligand variants, together with a non-chromophoric analogue () for comparison. (1)H NMR spectroscopic studies of the ligands showed that two non-interchangeable isomers exist for and while only one isomer exists for and . Supporting DFT calculations on suggest that the two isomers may be closely isoenergetic with a relatively high barrier to exchange of ca. 100 kJ mol(-1). These new ligands were cyclometalated with Pt(ii) to give complexes [Pt()(acac)] (acac = acetylacetonate). The spectroscopically characterised complexes were studied using multinuclear NMR spectroscopy including (195)Pt{(1)H} NMR studies which revealed δPtca. -2785 ppm for [Pt()(acac)]. X-ray crystallographic studies were undertaken on [Pt()(acac)] and [Pt()(acac)], each showing the weakly distorted square planar geometry at Pt(ii); the structure of [Pt()(acac)] showed evidence for intermolecular Pt-Pt interactions. The UV-vis. absorption studies show that the spectral profiles for [Pt()(acac)] are a composite of the organic chromophore centred bands and a broad (1)MLCT (5d → π*) band (ca. 440 nm) associated with the complex. Luminescence studies showed that complexes [Pt()(acac)] are dual emissive with fluorescence characteristic of the tethered fluorophore and long-lived phosphorescence attributed to (3)MLCT emission. In the case of the pyrenyl derivative, [Pt()(acac)], the close energetic matching of the (3)MLCT and (3)LCpyr excited states led to an elongation of the (3)MLCT emission lifetime (τ = 42 μs) under degassed solvent conditions, suggestive of energy transfer processes between the two states. PMID:27241625

  10. Synthesis, growth, structural, spectral, thermal, chemical etching, linear and nonlinear optical and mechanical studies of an organic single crystal 4-chloro 4-nitrostilbene (CONS): A potential NLO material

    NASA Astrophysics Data System (ADS)

    Dinakaran, Paul M.; Kalainathan, S.

    2013-07-01

    4-Chloro 4-nitrostilbene (CONS) a new organic nonlinear optical material has been synthesized. Employing slow evaporation method, good optical quality single crystals (dimensions up to 6 × 2 × 3 mm3) have been grown using ethyl methyl ketone (EMK) as a solvent. The grown crystals have been subjected to various characterizations such as single crystal X-ray diffraction, powder XRD, Fourier Transform Infrared spectroscopy (FTIR), proton NMR, solid UV absorption, SHG studies. Single crystal X-ray diffraction reveals that the crystal system belongs to monoclinic with noncentrosymmetric space group P21. The UV-Vis absorption spectrum has been recorded and found that the cut off wavelength is 380 nm. Functional groups and the structure of the title compound have been confirmed by FTIR and 1H NMR spectroscopic analyses respectively. Molecular mass of the CONS confirmed by the high resolution mass spectral analysis .The thermal behavior of the grown crystal has been studied by TG/DTA analysis and it shows the melting point is at 188.66 °C. Dislocations and growth pattern present in the grown crystal revealed by the etching study. The mechanical strength of the CONS crystal has been studied by Vicker's hardness measurement. The SHG efficiency of the grown crystal has been determined by Kurtz and Perry powder test which revealed that the CONS crystal (327 mV) has 15 times greater efficiency than that of KDP (21.7 mV).

  11. Resolving the structure of ionized helium in the intergalactic medium with the far ultraviolet spectroscopic explorer.

    PubMed

    Kriss, G A; Shull, J M; Oegerle, W; Zheng, W; Davidsen, A F; Songaila, A; Tumlinson, J; Cowie, L L; Deharveng, J M; Friedman, S D; Giroux, M L; Green, R F; Hutchings, J B; Jenkins, E B; Kruk, J W; Moos, H W; Morton, D C; Sembach, K R; Tripp, T M

    2001-08-10

    The neutral hydrogen (H I) and ionized helium (He II) absorption in the spectra of quasars are unique probes of structure in the early universe. We present Far-Ultraviolet Spectroscopic Explorer observations of the line of sight to the quasar HE2347-4342 in the 1000 to 1187 angstrom band at a resolving power of 15,000. We resolve the He II Lyman alpha (Lyalpha) absorption as a discrete forest of absorption lines in the redshift range 2.3 to 2.7. About 50 percent of these features have H I counterparts with column densities N(H I) > 10(12.3) per square centimeter that account for most of the observed opacity in He II Lyalpha. The He II to H I column density ratio ranges from 1 to >1000, with an average of approximately 80. Ratios of <100 are consistent with photoionization of the absorbing gas by a hard ionizing spectrum resulting from the integrated light of quasars, but ratios of >100 in many locations indicate additional contributions from starburst galaxies or heavily filtered quasar radiation. The presence of He II Lyalpha absorbers with no H I counterparts indicates that structure is present even in low-density regions, consistent with theoretical predictions of structure formation through gravitational instability.

  12. Molecular structure, spectroscopic assignments and other quantum chemical calculations of anticancer drugs - A review.

    PubMed

    Ghasemi, A S; Deilam, M; Sharifi-Rad, J; Ashrafi, F; Hoseini-Alfatemi, S M

    2015-01-01

    In many texts, both theoretical and experimental studies on molecular structure and spectroscopic assignments of anticancer medicines have been reported. Molecular geometry parameters have been experimentally obtained by x-ray structure determination method and optimized using computational chemistry method like density functional theory. In this review, we consider calculations based on density function theory at B3LYP/6-31G (d,p) and B3LYP/6-311++G (d,p) levels of theory. Based on optimized geometric parameters of the molecules, molecular structures (length of bonds, bond angles and torsion angles) and vibrational assignments have been obtained. Molecular stability and bond strength have been investigated by applying natural bond orbital (NBO) analysis. Other molecular properties such as mulliken population analysis, thermodynamic properties and polarizabitities of these drugs have been reported. Calculated energies of HOMO and LUMO show that charge transfer occurs in the molecular. Information about the size, shape, charge density distribution and site of molecular chemical reactivity has been obtained by mapping electron density isosurface of electrostatic and compared with experiment data. PMID:26638891

  13. Comparability of a three-dimensional structure in biopharmaceuticals using spectroscopic methods.

    PubMed

    Pérez Medina Martínez, Víctor; Abad-Javier, Mario E; Romero-Díaz, Alexis J; Villaseñor-Ortega, Francisco; Pérez, Néstor O; Flores-Ortiz, Luis F; Medina-Rivero, Emilio

    2014-01-01

    Protein structure depends on weak interactions and covalent bonds, like disulfide bridges, established according to the environmental conditions. Here, we present the validation of two spectroscopic methodologies for the measurement of free and unoxidized thiols, as an attribute of structural integrity, using 5,5'-dithionitrobenzoic acid (DTNB) and DyLight Maleimide (DLM) as derivatizing agents. These methods were used to compare Rituximab and Etanercept products from different manufacturers. Physicochemical comparability was demonstrated for Rituximab products as DTNB showed no statistical differences under native, denaturing, and denaturing-reducing conditions, with Student's t-test P values of 0.6233, 0.4022, and 0.1475, respectively. While for Etanercept products no statistical differences were observed under native (P = 0.0758) and denaturing conditions (P = 0.2450), denaturing-reducing conditions revealed cysteine contents of 98% and 101%, towards the theoretical value of 58, for the evaluated products from different Etanercept manufacturers. DLM supported equality between Rituximab products under native (P = 0.7499) and denaturing conditions (P = 0.8027), but showed statistical differences among Etanercept products under native conditions (P < 0.001). DLM suggested that Infinitam has fewer exposed thiols than Enbrel, although DTNB method, circular dichroism (CD), fluorescence (TCSPC), and activity (TNF α neutralization) showed no differences. Overall, this data revealed the capabilities and drawbacks of each thiol quantification technique and their correlation with protein structure.

  14. Comparability of a Three-Dimensional Structure in Biopharmaceuticals Using Spectroscopic Methods

    PubMed Central

    Abad-Javier, Mario E.; Romero-Díaz, Alexis J.; Villaseñor-Ortega, Francisco; Pérez, Néstor O.; Flores-Ortiz, Luis F.

    2014-01-01

    Protein structure depends on weak interactions and covalent bonds, like disulfide bridges, established according to the environmental conditions. Here, we present the validation of two spectroscopic methodologies for the measurement of free and unoxidized thiols, as an attribute of structural integrity, using 5,5′-dithionitrobenzoic acid (DTNB) and DyLight Maleimide (DLM) as derivatizing agents. These methods were used to compare Rituximab and Etanercept products from different manufacturers. Physicochemical comparability was demonstrated for Rituximab products as DTNB showed no statistical differences under native, denaturing, and denaturing-reducing conditions, with Student's t-test P values of 0.6233, 0.4022, and 0.1475, respectively. While for Etanercept products no statistical differences were observed under native (P = 0.0758) and denaturing conditions (P = 0.2450), denaturing-reducing conditions revealed cysteine contents of 98% and 101%, towards the theoretical value of 58, for the evaluated products from different Etanercept manufacturers. DLM supported equality between Rituximab products under native (P = 0.7499) and denaturing conditions (P = 0.8027), but showed statistical differences among Etanercept products under native conditions (P < 0.001). DLM suggested that Infinitam has fewer exposed thiols than Enbrel, although DTNB method, circular dichroism (CD), fluorescence (TCSPC), and activity (TNFα neutralization) showed no differences. Overall, this data revealed the capabilities and drawbacks of each thiol quantification technique and their correlation with protein structure. PMID:24963443

  15. Use of Pom Pons To Illustrate Cubic Crystal Structures

    NASA Astrophysics Data System (ADS)

    Cady, Susan G.

    1997-07-01

    In general chemistry classes, students are introduced to the ways in which atoms are arranged in cubic crystal structures. Transposing the textbook illustrations into three dimensional structures is difficult for some students. This transitions is easier if a three dimensional model is available for examination. Several 3D models are cited. A quick to assemble, inexpensive, colorful, and durable alternative to these models and styrofoam balls is the use of olefin pom pons. Different sized pom pons can be used to demonstrate how the atomic radius will vary when comparing the different types of cubic crystal unit cells. Being made of a coarse material, pom pons can be stacked to illustrate different packing arrangements such as hexagonal close-packed and cubic close-packed structures. Pom pons make great atoms.

  16. Crystal structure of Brinzolamide: a carbonic anhydrase inhibitor.

    PubMed

    Zheng, Huirong; Lou, Benyong

    2016-05-01

    In crystal structure of the title compound, C12H21N3O5S3 [systematic name: (R)-4-ethyl-amino-2-(3-meth-oxy-prop-yl)-3,4-di-hydro-2H-thieno[3,2-e][1,2]thia-zine-6-sulfonamide 1,1-dioxide], there exist three kinds of hydrogen-bonding inter-actions. The sulfonamide group is involved in hydrogen bonding with the secondary amine and the meth-oxy O atom, resulting in the formation of layers parallel to the bc plane. The layers are linked by an N-H⋯O hydrogen bond involving a sulfonamide O atom as acceptor and the secondary amine H atom as donor, which gives rise to the formation of a unique bilayer structure. The absolute structure of the mol-ecule in the crystal was determined by resonant scattering [Flack parameter = 0.01 (4)]. PMID:27308020

  17. First principles investigation of the structure of a bacteriochlorophyll crystal

    SciTech Connect

    Marchi, M. |; Hutter, J.; Parrinello, M.

    1996-08-21

    In this communication we present an ab initio study of the crystal of methyl bacteriophorbide (MeBPheo) a, a bacteriochlorophyll derivative, and high-precision structure of which is available. Our main purpose has been to investigate the viability of the technique toward complex molecular systems relevant to biologically important phenomena, in this particular case photosynthesis. Here we present the following results: First, we show that DFT is capable of calculating nuclear positions in excellent agreement with the experimental X-ray structure. Second, the calculated electronic density of the HOMO orbital reveals a {pi} type bond between rings I and III, consistent with the one-dimensional chain structure of the MeBPheo a molecules in the crystal. Finally, after performing the optimization of the molecular geometry with one electron in the LUMO state, we find localized bond length changes near the ring II of the MeBPheo a. 19 refs., 3 figs.

  18. Myelin structures formed by thermotropic smectic liquid crystals.

    PubMed

    Peddireddy, Karthik; Kumar, Pramoda; Thutupalli, Shashi; Herminghaus, Stephan; Bahr, Christian

    2013-12-17

    We report on transient structures, formed by thermotropic smectic-A liquid crystals, resembling the myelin figures of lyotropic lamellar liquid crystals. The thermotropic myelin structures form during the solubilization of a smectic-A droplet in an aqueous phase containing a cationic surfactant at concentrations above the critical micelle concentration. Similar to the lyotropic myelin figures, the thermotropic myelins appear in an optical microscope as flexible tubelike structures growing at the smectic/aqueous interface. Polarizing microscopy and confocal fluorescence microscopy show that the smectic layers are parallel to the tube surface and form a cylindrically bent arrangement around a central line defect in the tube. We study the growth behavior of this new type of myelins and discuss similarities to and differences from the classical lyotropic myelin figures.

  19. Thermally triggered solid-state single-crystal-to-single-crystal structural transformation accompanies property changes.

    PubMed

    Li, Quan-Quan; Ren, Chun-Yan; Huang, Yang-Yang; Li, Jian-Li; Liu, Ping; Liu, Bin; Liu, Yang; Wang, Yao-Yu

    2015-03-16

    The 1D complex [(CuL0.5H2O)⋅H2O]n (1) (H4L = 2,2'-bipyridine-3,3',6,6'-tetracarboxylic acid) undergoes an irreversible thermally triggered single-crystal-to-single-crystal (SCSC) transformation to produce the 3D anhydrous complex [CuL0.5]n (2). This SCSC structural transformation was confirmed by single-crystal X-ray diffraction analysis, thermogravimetric (TG) analysis, powder X-ray diffraction (PXRD) patterns, variable-temperature powder X-ray diffraction (VT-PXRD) patterns, and IR spectroscopy. Structural analyses reveal that in complex 2, though the initial 1D chain is still retained as in complex 1, accompanied with the Cu-bound H2O removed and new O(carboxyl)-Cu bond forming, the coordination geometries around the Cu(II) ions vary from a distorted trigonal bipyramid to a distorted square pyramid. With the drastic structural transition, significant property changes are observed. Magnetic analyses show prominent changes from antiferromagnetism to weak ferromagnetism due to the new formed Cu1-O-C-O-Cu4 bridge. The catalytic results demonstrate that, even though both solid-state materials present high catalytic activity for the synthesis of 2-imidazolines derivatives and can be reused, the activation temperature of complex 1 is higher than that of complex 2. In addition, a possible pathway for the SCSC structural transformations is proposed.

  20. Crystal structure of a symbiosis-related lectin from octocoral.

    PubMed

    Kita, Akiko; Jimbo, Mitsuru; Sakai, Ryuichi; Morimoto, Yukio; Miki, Kunio

    2015-09-01

    D-Galactose-binding lectin from the octocoral, Sinularia lochmodes (SLL-2), distributes densely on the cell surface of microalgae, Symbiodinium sp., an endosymbiotic dinoflagellate of the coral, and is also shown to be a chemical cue that transforms dinoflagellate into a non-motile (coccoid) symbiotic state. SLL-2 binds with high affinity to the Forssman antigen (N-acetylgalactosamine(GalNAc)α1-3GalNAcβ1-3Galα1-4Galβ1-4Glc-ceramide), and the presence of Forssman antigen-like sugar on the surface of Symbiodinium CS-156 cells was previously confirmed. Here we report the crystal structures of SLL-2 and its GalNAc complex as the first crystal structures of a lectin involved in the symbiosis between coral and dinoflagellate. N-Linked sugar chains and a galactose derivative binding site common to H-type lectins were observed in each monomer of the hexameric SLL-2 crystal structure. In addition, unique sugar-binding site-like regions were identified at the top and bottom of the hexameric SLL-2 structure. These structural features suggest a possible binding mode between SLL-2 and Forssman antigen-like pentasaccharide. PMID:26022515

  1. Crystal structure of a symbiosis-related lectin from octocoral.

    PubMed

    Kita, Akiko; Jimbo, Mitsuru; Sakai, Ryuichi; Morimoto, Yukio; Miki, Kunio

    2015-09-01

    D-Galactose-binding lectin from the octocoral, Sinularia lochmodes (SLL-2), distributes densely on the cell surface of microalgae, Symbiodinium sp., an endosymbiotic dinoflagellate of the coral, and is also shown to be a chemical cue that transforms dinoflagellate into a non-motile (coccoid) symbiotic state. SLL-2 binds with high affinity to the Forssman antigen (N-acetylgalactosamine(GalNAc)α1-3GalNAcβ1-3Galα1-4Galβ1-4Glc-ceramide), and the presence of Forssman antigen-like sugar on the surface of Symbiodinium CS-156 cells was previously confirmed. Here we report the crystal structures of SLL-2 and its GalNAc complex as the first crystal structures of a lectin involved in the symbiosis between coral and dinoflagellate. N-Linked sugar chains and a galactose derivative binding site common to H-type lectins were observed in each monomer of the hexameric SLL-2 crystal structure. In addition, unique sugar-binding site-like regions were identified at the top and bottom of the hexameric SLL-2 structure. These structural features suggest a possible binding mode between SLL-2 and Forssman antigen-like pentasaccharide.

  2. Rigidity analysis of protein biological assemblies and periodic crystal structures

    PubMed Central

    2013-01-01

    Background We initiate in silico rigidity-theoretical studies of biological assemblies and small crystals for protein structures. The goal is to determine if, and how, the interactions among neighboring cells and subchains affect the flexibility of a molecule in its crystallized state. We use experimental X-ray crystallography data from the Protein Data Bank (PDB). The analysis relies on an effcient graph-based algorithm. Computational experiments were performed using new protein rigidity analysis tools available in the new release of our KINARI-Web server http://kinari.cs.umass.edu. Results We provide two types of results: on biological assemblies and on crystals. We found that when only isolated subchains are considered, structural and functional information may be missed. Indeed, the rigidity of biological assemblies is sometimes dependent on the count and placement of hydrogen bonds and other interactions among the individual subchains of the biological unit. Similarly, the rigidity of small crystals may be affected by the interactions between atoms belonging to different unit cells. We have analyzed a dataset of approximately 300 proteins, from which we generated 982 crystals (some of which are biological assemblies). We identified two types of behaviors. (a) Some crystals and/or biological assemblies will aggregate into rigid bodies that span multiple unit cells/asymmetric units. Some of them create substantially larger rigid cluster in the crystal/biological assembly form, while in other cases, the aggregation has a smaller effect just at the interface between the units. (b) In other cases, the rigidity properties of the asymmetric units are retained, because the rigid bodies did not combine. We also identified two interesting cases where rigidity analysis may be correlated with the functional behavior of the protein. This type of information, identified here for the first time, depends critically on the ability to create crystals and biological assemblies

  3. Spectroscopic characterization and energy transfer process in cobalt and cobalt-iron co-doped ZnSe/ZnS crystals

    NASA Astrophysics Data System (ADS)

    Peppers, J.; Martyshkin, D. V.; Fedorov, V. V.; Mirov, S. B.

    2014-02-01

    Cobalt doped II-VI wide band semiconductors (e.g. ZnSe, ZnS, CdSe) are promising media for infrared (IR) laser applications. They could be utilized as effective passive Q-switches for cavities of Alexandrite as well as Nd and Er lasers operating over 0.7-0.8, 1.3-1.6, and ~2.8 μm spectral ranges. We report spectroscopic characterization of Co:ZnSe and Co:ZnS crystals. Absorption cross-sections were measured for 4A2(F) → 4T1(P), 4A2(F) → 4T1(F), and 4A2(F) → 4T2(F) transitions with maximum absorption at 768(726), 1615(1500), 2690(2740) nm for ZnSe(ZnS) crystals, respectively. The calculated absorption cross-sections of the above transitions were estimated to be 64(56)×1019, 7.5(7.8)×1019, and 0.52(0.49)×1019 cm2 for ZnSe(ZnS) crystal hosts. In addition to the above applications the cobalt ions could be utilized for excitation of Fe2+ ions via resonance energy transfer process. Tunable room temperature lasing of Fe 2+ doped binary and ternary chalcogenides has been successfully demonstrated over 3.5-6 μm spectral range. However, II-VI lasers based on Fe2+ active ions don't feature convenient commercially available pump sources (e.g. some Fe doped crystal hosts require pump wavelengths longer than 3 μm). Therefore, the process of energy transfer from Co2+ to Fe2+ ions could enable utilization of commercially available visible and near-infrared pump sources. We report a spectroscopic characterization of iron-cobalt co-doped ZnS and ZnSe crystals over 14-300K temperature range. Mid-IR laser oscillation at 3.9 μm(3.6 μm) via energy transfer in the Co:Fe:ZnSe (Co:Fe:ZnS) co-doped crystals was demonstrated under cobalt excitation at 4A2(F) → 4T1(P) (~0.7μm) and 4A2(F) → 4T1(F) (~1.56 μm) transitions.

  4. Structural engineering of three-dimensional phononic crystals

    NASA Astrophysics Data System (ADS)

    Delpero, Tommaso; Schoenwald, Stefan; Zemp, Armin; Bergamini, Andrea

    2016-02-01

    Artificially-structured materials are attracting the research interest of a growing community of scientists for the possibility to develop novel materials with advantageous properties that arise from the ability to tailor the propagation of elastic waves, and thus energy, through them. In this work, we propose a three-dimensional phononic crystal whose unit cell has been engineered to obtain a strong wave-attenuation band in the middle of the acoustic frequency range. The combination of its acoustic properties with the dimensions of the unit cell and its static mechanical properties makes it an interesting material for possibly several applications in civil and mechanical engineering, for instance as the core of an acoustically insulating sandwich panel. A sample of this crystal has been manufactured and experimentally tested with respect to its acoustic transmissibility. The performance of the phononic crystal core is remarkable both in terms of amplitude reduction in the transmissibility and width of the attenuation band. A parametric study has been finally conducted on selected geometrical parameters of the unit cell and on their effect on the macroscopic properties of the crystal. This work represents an application-oriented example of how the macroscopic properties of an artificially-structured material can be designed, according to specific needs, by a conventional engineering of its unit cell.

  5. Lattice dynamics of crystals having R2MX6 structure

    NASA Astrophysics Data System (ADS)

    Torres, D. I.; Freire, J. D.; Katiyar, R. S.

    1997-10-01

    The theory of lattice dynamics in the harmonic approximation using a rigid-ion model due to Born and Huang [Dynamical Theory of Crystal Lattices (Oxford University Press, New York, 1954)], is applied to ionic crystals of the R2MX6 type with antifluorite structure namely, K2SnCl6, K2PtBr6, Cs2SnBr6, and Rb2SnBr6 in the cubic phase. The model expresses the potential energy as the sum of long-range Coulomb interactions and repulsive short-range interactions between ions in the primitive cell. A function of axially symmetric type is used to approximate the short-range part, and the number of force constant parameters were reduced utilizing stability conditions in the manner described by Katiyar [J. Phys. C 3, 1087 (1970)]. The remaining constants were determined by a nonlinear least-squares analysis of some experimental frequencies at the critical point Γ. The long-range contributions were calculated using the Ewald transformation as described by Cowley [Acta Crystallogr. 15, 687 (1962)]. Phonon frequencies and the normal modes of vibrations at the zone center were obtained; of particular interest is the resulting lowest librational frequency for each crystal. We obtained excellent agreement between the calculated and the observed frequencies. The resulting effective charge parameters indicated that these crystals are partially ionic. In general, the results offered a better vision of the structural phase transition mechanism involving the rotational mode T1g.

  6. Structural and spectroscopic analyses of europium doped yttrium oxyfluoride powders prepared by combustion synthesis

    SciTech Connect

    Rakov, Nikifor; Guimarães, R. B.; Maciel, Glauco S.; Lozano B, W.

    2013-07-28

    A facile widely spread technique employed to produce low-cost high-yield oxide powders, combustion synthesis, was used to prepare yttrium oxyfluoride crystalline ceramic powders. The structure of the powders was analyzed by X-ray powder diffraction and Rietveld refinement. Samples heat treated at 700 °C had a predominance of vernier orthorhombic Y{sub 6}O{sub 5}F{sub 8} phase, while samples heat treated at 800 °C crystallized in stoichiometric rhombohedral YOF phase. The samples were doped with luminescent europium trivalent ions (Eu{sup 3+}) in different concentrations (1–15 wt.%) and Judd-Ofelt theory was used to probe the distortion from the inversion symmetry of the local crystal field and the degree of covalency between the rare-earth ion and the surrounding ligands. The luminescence lifetime was measured and the luminescence quantum efficiency (LQE) was estimated. We observed that Eu{sup 3+}:Y{sub 6}O{sub 5}F{sub 8} samples presented higher LQE in spite of the larger local crystal field anisotropy found for Eu{sup 3+}:YOF samples.

  7. Raman spectroscopic characterization of the core-rim structure in reaction bonded boron carbide ceramics

    SciTech Connect

    Jannotti, Phillip; Subhash, Ghatu; Zheng, James Q.; Halls, Virginia; Karandikar, Prashant G.; Salamone, S.; Aghajanian, Michael K.

    2015-01-26

    Raman spectroscopy was used to characterize the microstructure of reaction bonded boron carbide ceramics. Compositional and structural gradation in the silicon-doped boron carbide phase (rim), which develops around the parent boron carbide region (core) due to the reaction between silicon and boron carbide, was evaluated using changes in Raman peak position and intensity. Peak shifting and intensity variation from the core to the rim region was attributed to changes in the boron carbide crystal structure based on experimental Raman observations and ab initio calculations reported in literature. The results were consistent with compositional analysis determined by energy dispersive spectroscopy. The Raman analysis revealed the substitution of silicon atoms first into the linear 3-atom chain, and then into icosahedral units of the boron carbide structure. Thus, micro-Raman spectroscopy provided a non-destructive means of identifying the preferential positions of Si atoms in the boron carbide lattice.

  8. The Rapid Crystallization Strategy for Structure-Based Inhibitor Design

    NASA Astrophysics Data System (ADS)

    Bergfors, Terese

    RAPID (Rapid Approaches to Pathogen Inhibitor Discovery) is an integrated center for structural biology, computational chemistry, and medicinal chemistry at Uppsala University, Sweden. The main target of the structural biology section is Mycobacterium tuberculosis. Key concepts in the crystallization strategy include minimal screening and buffer optimization. Examples are presented showing how these concepts have been successful in RAPID projects. Three screening methods are used: vapor-diffusion, micro-batch, and microfluidics. Our experiences may be relevant for other small, academic laboratories involved in structure-based inhibitor design.

  9. Crystal structure of inactive form of Rab3B

    SciTech Connect

    Zhang, Wei; Shen, Yang; Jiao, Ronghong; Liu, Yanli; Deng, Lingfu; Qi, Chao

    2012-06-28

    Rab proteins are the largest family of ras-related GTPases in eukaryotic cells. They act as directional molecular switches at membrane trafficking, including vesicle budding, cargo sorting, transport, tethering, and fusion. Here, we generated and crystallized the Rab3B:GDP complex. The structure of the complex was solved to 1.9 {angstrom} resolution and the structural base comparison with other Rab3 members provides a structural basis for the GDP/GTP switch in controlling the activity of small GTPase. The comparison of charge distribution among the members of Rab3 also indicates their different roles in vesicular trafficking.

  10. Crystal structure of four-stranded Oxytricha telomeric DNA

    NASA Technical Reports Server (NTRS)

    Kang, C.; Zhang, X.; Ratliff, R.; Moyzis, R.; Rich, A.

    1992-01-01

    The sequence d(GGGGTTTTGGGG) from the 3' overhang of the Oxytricha telomere has been crystallized and its three-dimensional structure solved to 2.5 A resolution. The oligonucleotide forms hairpins, two of which join to make a four-stranded helical structure with the loops containing four thymine residues at either end. The guanine residues are held together by cyclic hydrogen bonding and an ion is located in the centre. The four guanine residues in each segment have a glycosyl conformation that alternates between anti and syn. There are two four-stranded molecules in the asymmetric unit showing that the structure has some intrinsic flexibility.

  11. A nearly on-axis spectroscopic system for simultaneously measuring UV-visible absorption and X-ray diffraction in the SPring-8 structural genomics beamline.

    PubMed

    Sakaguchi, Miyuki; Kimura, Tetsunari; Nishida, Takuma; Tosha, Takehiko; Sugimoto, Hiroshi; Yamaguchi, Yoshihiro; Yanagisawa, Sachiko; Ueno, Go; Murakami, Hironori; Ago, Hideo; Yamamoto, Masaki; Ogura, Takashi; Shiro, Yoshitsugu; Kubo, Minoru

    2016-01-01

    UV-visible absorption spectroscopy is useful for probing the electronic and structural changes of protein active sites, and thus the on-line combination of X-ray diffraction and spectroscopic analysis is increasingly being applied. Herein, a novel absorption spectrometer was developed at SPring-8 BL26B2 with a nearly on-axis geometry between the X-ray and optical axes. A small prism mirror was placed near the X-ray beamstop to pass the light only 2° off the X-ray beam, enabling spectroscopic analysis of the X-ray-exposed volume of a crystal during X-ray diffraction data collection. The spectrometer was applied to NO reductase, a heme enzyme that catalyzes NO reduction to N2O. Radiation damage to the heme was monitored in real time during X-ray irradiation by evaluating the absorption spectral changes. Moreover, NO binding to the heme was probed via caged NO photolysis with UV light, demonstrating the extended capability of the spectrometer for intermediate analysis.

  12. Crystal structure optimisation using an auxiliary equation of state

    SciTech Connect

    Jackson, Adam J.; Skelton, Jonathan M.; Hendon, Christopher H.; Butler, Keith T.; Walsh, Aron

    2015-11-14

    Standard procedures for local crystal-structure optimisation involve numerous energy and force calculations. It is common to calculate an energy–volume curve, fitting an equation of state around the equilibrium cell volume. This is a computationally intensive process, in particular, for low-symmetry crystal structures where each isochoric optimisation involves energy minimisation over many degrees of freedom. Such procedures can be prohibitive for non-local exchange-correlation functionals or other “beyond” density functional theory electronic structure techniques, particularly where analytical gradients are not available. We present a simple approach for efficient optimisation of crystal structures based on a known equation of state. The equilibrium volume can be predicted from one single-point calculation and refined with successive calculations if required. The approach is validated for PbS, PbTe, ZnS, and ZnTe using nine density functionals and applied to the quaternary semiconductor Cu{sub 2}ZnSnS{sub 4} and the magnetic metal-organic framework HKUST-1.

  13. Crystal structure optimisation using an auxiliary equation of state.

    PubMed

    Jackson, Adam J; Skelton, Jonathan M; Hendon, Christopher H; Butler, Keith T; Walsh, Aron

    2015-11-14

    Standard procedures for local crystal-structure optimisation involve numerous energy and force calculations. It is common to calculate an energy-volume curve, fitting an equation of state around the equilibrium cell volume. This is a computationally intensive process, in particular, for low-symmetry crystal structures where each isochoric optimisation involves energy minimisation over many degrees of freedom. Such procedures can be prohibitive for non-local exchange-correlation functionals or other "beyond" density functional theory electronic structure techniques, particularly where analytical gradients are not available. We present a simple approach for efficient optimisation of crystal structures based on a known equation of state. The equilibrium volume can be predicted from one single-point calculation and refined with successive calculations if required. The approach is validated for PbS, PbTe, ZnS, and ZnTe using nine density functionals and applied to the quaternary semiconductor Cu2ZnSnS4 and the magnetic metal-organic framework HKUST-1.

  14. Human hemoglobin structural and functional alterations and heme degradation upon interaction with benzene: A spectroscopic study

    NASA Astrophysics Data System (ADS)

    Hosseinzadeh, Reza; Moosavi-Movahedi, Ali Akbar

    2016-03-01

    Here, the effect of benzene on hemoglobin structure, stability and heme prosthetic group integrity was studied by different methods. These included UV-vis absorption spectrophotometry, normal and synchronous fluorescence techniques, and differential scanning calorimetry (DSC). Our results indicated that benzene has high hemolytic potential even at low concentrations. The UV-vis spectroscopic results demonstrated that benzene altered both the globin chain and the heme prosthetic group of hemoglobin increasing met- and deoxy-Hb, while decreasing oxy-Hb. However, with increasing benzene the concentration of all species decreased due to heme destruction. The spectrophotometric results show that benzene has a high potential for penetrating the hydrophobic pocket of hemoglobin. These results were consistent with the molecular docking simulation results of benzene-hHb. Aggregation and thermal denaturation studies show that the increased benzene concentration induced hemoglobin aggregation with a decrease in stability, which is consistent with the DSC results. Conventional fluorescence spectroscopy revealed that the heme degradation species were produced in the presence of benzene. The results of constant wavelength synchronous fluorescence spectroscopy (CWSFS) indicated that at least five heme-degraded species were produced. Together, our results indicated that benzene has adverse effects on hemoglobin structure and function, and heme degradation.

  15. A Spectroscopic Investigation on the Structural Evolution of Soy Based Polyurethane Foams

    NASA Astrophysics Data System (ADS)

    Puthanparambil, Deepa; Kimball, Casey; Hsu, Shaw L.

    2009-03-01

    Our current research deals with an economical and renewable soy based polyol for use in polyurethane foams. Infrared spectroscopic studies have revealed that the amount of polyurea segments formed and the kinetics of their formation in soy based polyurethane foam systems are considerably different from traditional systems employing ethylene oxide -- propylene oxide based polyols. The most crucial aspect of this research deals with the miscibility of water in the reactive mixtures involving extremely hydrophobic soy-based polyols. High Field Nuclear Magnetic Resonance Spectroscopy (NMR) with D2O as the probing agent was employed to determine the miscibility behavior at the molecular level. This technique was able to establish the structure and location of dispersed water, which can be extremely different based on the polyols used, thus affecting the morphology of the foam. The length and amount of polyureas directly impact the kinetics of the phase separation process to form the hard-segment rich domains and associated physical properties. The aggregation of these polyurea hard domains were characterized by the hydrogen bonds formed. This structural transformation as a function of reaction is also reflected in the segmental relaxation kinetics characterized by spin-spin diffusion, measured using a low field NMR instrument.

  16. Spectroscopic and structural studies of energetically efficient transport in nanocontacts to NiSi nanowires

    NASA Astrophysics Data System (ADS)

    Stein, A.; Farhat, I. A. H.; Lacevic, N.; Bazuhair, S. K.; Azhar, S. S.; Isakovic, A. F.

    Understanding correlations between mechanical, thermal, structural and electronic transport properties of different nanocontact geometries to nanowires, such as Au/Cu-NiSi-Si, remain one of the major goals of nanodevices reliability and scalability research. Aiming to clarify the failure modes and processes that affect the energy efficiency of transport and switching in constrained nanocontact geometries, such as end contacts, we conducted the structural, spectroscopic, and noise correlation studies. We show how the spatial (in)homogeneity at and in the near vicinity of the interface affects the transport performance of the nanojunctions. Mobile Ni clusters are identified at the nanojunction interface via Raman spectromicroscopy and their influence on charge transport is analyzed. We also show that the noise correlation spectra and micro-X-ray stress-strain studies in the nanojunctions are effictive tools in predicting the energy efficiency of the nanojunctions. A computational study of the interfacial properties of metal/Ni-Si via DFT and MD simulations is implemented. Work supported by Mubadala-SRC # 2011-KJ-2190. A part of the work done at BNL-CFN, supported by DOE. A part of the work done at Cornell Univ.CFN and CCMR, supported by the NSF.

  17. Quantitative spectroscopic diffuse optical tomography of the breast guided by imperfect a priori structural information

    NASA Astrophysics Data System (ADS)

    Boverman, Gregory; Miller, Eric L.; Li, Ang; Zhang, Quan; Chaves, Tina; Brooks, Dana H.; Boas, David A.

    2005-09-01

    Spectroscopic diffuse optical tomography (DOT) can directly image the concentrations of physiologically significant chromophores in the body. This information may be of importance in characterizing breast tumours and distinguishing them from benign structures. This paper studies the accuracy with which lesions can be characterized given a physiologically realistic situation in which the background architecture of the breast is heterogeneous yet highly structured. Specifically, in simulation studies, we assume that the breast is segmented into distinct glandular and adipose regions. Imaging with a high-resolution imaging modality, such as magnetic resonance imaging, in conjunction with a segmentation by a clinical expert, allows the glandular/adipose boundary to be determined. We then apply a two-step approach in which the background chromophore concentrations of each region are estimated in a nonlinear fashion, and a more localized lesion is subsequently estimated using a linear perturbational approach. In addition, we examine the consequences which errors in the breast segmentation have on estimating both the background and inhomogeneity chromophore concentrations.

  18. A NdIII enantiomeric pair: Synthesis, crystal structures and near-infrared luminescent properties

    NASA Astrophysics Data System (ADS)

    Li, Feng-Cai; Li, Xi-Li; Hu, Ming; Zhang, Xue-Li; Chen, Conghui; Zhu, Cancan

    2016-08-01

    Based on enantiopure bis-bidentate N-donor ligands (-)/(+)-2,5-bis(4,5-pinene- 2-pyridyl)pyrazine (LR/LS), a new pair of NdIII enantiomers with the formula Nd(dbm)3LR/S·2H2O (R-1 and S-1 being the isomers containing the LR and LS ligands, respectively, and dbm = dibenzoylmethanate) have been isolated and characterized by X-ray crystallography and spectroscopic methods. Notably, unlike our previously reported homodinuclear EuIII and DyIII complexes based on the identical ligands (LR and LS), the dinuclear NdIII congener have not been obtained by controlling the ligand-to-metal ratio as expected, the reason of which was elucidated in this work. The crystal structure analyses of R-1 and S-1 reveal that they are mononuclear NdIII complexes and crystallize in chiral space group P212121 of the orthorhombic system. Circular dichroic (CD) spectra confirmed their chiroptical activities and enantiomeric nature. The photoluminescence investigations showed that they display characteristic near-infrared (NIR) emissions of the NdIII ions with notable emitting lifetime value.

  19. Synthesis, crystal structure, and spectral studies of 10-(2-Benzothiazolylazo)-9-phenanthrol

    SciTech Connect

    Davydov, V. V.; Sokol, V. I.; Polyanskaya, N. A.; Linko, R. V. Ryabov, M. A.; Sergienko, V. S.

    2012-03-15

    10-(2-Benzothiazolylazo)-9-phenanthrol (L) is prepared by a reaction of 2-hydrazinobenzothiazol with 9,10-phenanthrenequinone. The crystal and molecular structure of the L{center_dot}CHCl{sub 3} solvate is determined by X-ray diffraction. The data of the X-ray diffraction study, as well as IR, {sup 1}H NMR, and electronic absorption spectra, indicate that in the crystal state and solutions the L molecule exists in the form of a quinohydrazone tautomer (b) (s-trans, cis) stabilized by the intramolecular N{sub 2}-HN{sub 2} Horizontal-Ellipsis O1 hydrogen bond. The 'mobile' H atom is located at the N2 atom of the azo group. The benzothiazolyl and phenanthrenequinone fragments are nearly coplanar. Spectroscopic criteria for the state of L in various media are determined based on the data of IR, {sup 1}H NMR, and electronic absorption spectroscopy and the results of the Pariser-Parr-Pople quantum-chemical calculations.

  20. Crystal structure of a novel red copper protein from Nitrosomonas europaea

    SciTech Connect

    Lieberman, R.L.; Arciero, D.M.; Hooper, A.B.; Rosenzweig, A.C.

    2010-03-08

    Nitrosocyanin (NC) is a mononuclear red copper protein isolated from the ammonia oxidizing bacterium Nitrosomonas europaea. Although NC exhibits some sequence homology to classic blue copper proteins, its spectroscopic and electrochemical properties are drastically different. The 1.65 {angstrom} resolution crystal structure of oxidized NC reveals an unprecedented trimer of single domain cupredoxins. Each copper center is partially covered by an unusual extended {beta}-hairpin structure from an adjacent monomer. The copper ion is coordinated by His 98, His 103, Cys 95, a single side chain oxygen of Glu 60, and a solvent molecule. In the 2.3 {angstrom} resolution structure of reduced NC, His 98 shifts away from the copper ion, and the solvent molecule is not observed. The arrangement of these ligands renders the coordination geometry of the NC red copper center distinct from that of blue copper centers. In particular, the red copper center has a higher coordination number and lacks the long Cu-S(Met) and short Cu-S(Cys) bond distances characteristic of blue copper. Moreover, the red copper center is square pyramidal whereas blue copper is typically distorted tetrahedral. Analysis of the NC structure provides insight into possible functions of this new type of biological copper center.