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Sample records for crystal structures spectroscopic

  1. Crystal structure and spectroscopic elucidation of 3-phenylpyridinium hydrogensquarate.

    PubMed

    Koleva, Bojidarka B; Kolev, Tsonko; Tsanev, Tsanko; Kotov, Stefan; Mayer-Figge, Heike; Spiteller, Michael; Sheldrick, William S

    2010-01-01

    The novel 3-phenylpyridinium hydrogensquarate (1) has been synthesized and its structure and properties are elucidated spectroscopically, thermally and structurally, using single crystal X-ray diffraction, linear-polarized solid-state IR-spectroscopy, UV-spectroscopy, TGA, DSC, DTA and ESI MS. Quantum chemical calculations were used to obtain the electronic structure, vibrational data and electronic spectrum. 3-Phenylpyridinium hydrogensquarate, crystallizes in the space group P-1 and the ions in the unit cell are joined into layers by intermolecular NH...O=C((Sq)) bonds with bond lengths of 2.625 and 2.626 A, respectively. Hydrogentartarates form dimers by strong O=COH...OCO interactions (2.499 A). PMID:19931483

  2. N-methylcodeinium iodide—Crystal structure and spectroscopic elucidation

    NASA Astrophysics Data System (ADS)

    Seidel, R. W.; Bakalska, B. R.; Kolev, T.; Vassilev, D.; Mayer-Figge, H.; Spiteller, M.; Sheldrick, W. S.; Koleva, B. B.

    2009-07-01

    The correlation between the structure and the spectroscopic properties of N-methylcodeinium iodide ( 1) has been studied, using the methods of single crystal X-ray diffraction, IR-LD spectroscopy of oriented samples as a suspension in nematic liquid crystals, UV-vis spectroscopy and 1H and 13C NMR spectroscopy. HPLC tandem mass spectrometry (HPLC ESI MS/MS) and thermal methods were also employed. Quantum chemical calculations have been performed with a view to obtaining the electronic structure and vibrational properties of the title compound. Compound ( 1) crystallizes in the space group P2 12 12 1 and its cations and anions are joined by moderate intermolecular OH…I - interaction of length 3.442 Å. The codeine molecule exhibits the classical T-shape for opiates. A dihedral angle value of 86.4(5)° between the A/B/C and D/E planes is obtained. Rings A and B are effectively coplanar with an interplanar angle of 3.6(3)°.

  3. Micro-spectroscopic mapping: revealing internal structures of zircon crystals

    NASA Astrophysics Data System (ADS)

    Nasdala, L.; Reiners, P. W.; Hanchar, J. M.

    2003-04-01

    Natural zircon crystals typically deviate from perfect crystallinity and ideal chemical composition. If non-ideality features are not homogeneously distributed within a crystal but show a heterogeneity pattern, this is referred to as its "internal structure". Internal structures of zircon are mostly first caused by the heterogeneous incorporation of trace elements during crystal growth. Over time, these primary patterns may become more complex after being overprinted by radioactive self-irradiation and heterogeneous alteration or recrystallization. Internal structures may provide valuable information about the origin and post-growth history of zircon crystals. Further, they need to be recognized for sound microprobe dating, for instance to avoid biased results when straddling zones of different age. Revealing internal structures has thus become an important tool in zircon research. It is mostly done by means of backscattered electrons or cathodoluminescence imaging. These two techniques are advantageous over optical microscopy in the cross-polarized mode as the volume resolution is better and simple polished mounts instead of doubly-sided sections are needed. A disadvantage, however, is that the impact of electron beam during analysis causes local structural changes. Quantitative studies of the real structure of zircon samples, such as determination of the degree of the radiation damage, is therefore tainted with potential uncertainty when being done after electron probe analysis. As an alternative, we present images of internal zircon structures generated through visible laser excitation and mapping of the Raman and photoluminescence light. Due to the time-consuming mapping procedure, such images will perhaps not be routinely used. For detailed studies, however, they may provide most valuable information. Photoluminescence maps provide, for instance, information on both the distribution of rare earth elements (band integrals) and the short-range order (band

  4. Spectroscopic, thermal and structural studies on manganous malate crystals

    SciTech Connect

    Thomas, J. Lincy, A. Mahalakshmi, V.; Saban, K. V.

    2013-01-15

    Prismatic crystals of manganous malate have been prepared by controlled ionic diffusion in hydrosilica gel. The structure was elucidated using single crystal X-ray diffraction. The crystals are orthorhombic with space group Pbca. Vibrations of the functional groups were identified by the FTIR spectrum. Thermogravimetric and differential thermal analyses (TG-DTA) were carried out to explore the thermal decomposition pattern of the material. Structural information derived from FTIR and TG-DTA studies is in conformity with the single crystal XRD data.

  5. 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.

  6. Crystal structure and spectroscopic investigations of an organic monophosphate

    SciTech Connect

    Dhaouadi, H.; Marouani, H. Rzaigui, M.; Madani, A.

    2008-12-01

    Single crystals of (p-ClC{sub 6}H{sub 4}NH{sub 3})H{sub 2}PO{sub 4} are synthesized in water by interaction of H{sub 3}PO{sub 4} and (p-ClC{sub 6}H{sub 4}NH{sub 2}). This compound crystallizes in the orthorhombic system with the Pbca space group. Its unit-cell parameters are a = 9.724(3), b = 7.861(1), c = 25.078(6) A, V = 1917.1(6) A{sup 3} and Z = 8. The crystal structure has been solved and refined to R = 0.039, using 4298 independent reflections. The atomic arrangement can be described by inorganic layers parallel to ab plane, between which the organic cations are located. This compound exhibits a reversible phase transition at 403 K. The electrical conductivity measurements show that the (p-ClC{sub 6}H{sub 4}NH{sub 3})H{sub 2}PO{sub 4} has a conductivity value which goes from {sigma} = 0.88 x 10{sup -6} {omega}{sup -1} cm{sup -1} at room temperature (293 K) to 3.31 x 10{sup -4} {omega}{sup -1} cm{sup -1} at 433 K. Its characterisation by TA, NMR and IR is reported too.

  7. Thiosaccharine disulfide: Synthesis, crystal structure, spectroscopic characterization and theoretical study

    NASA Astrophysics Data System (ADS)

    Ferullo, Ricardo M.; Granados, Alejandro; Lanterna, Anabel; Güida, Jorge A.; Piro, Oscar E.; Castellano, Eduardo E.; Dennehy, Mariana

    2013-01-01

    The title compound, (thiosaccharine disulfide), bis[1,1'dioxide-2,3-dihidro-1,2-benzoisothiazol]disulfide, (tsac)2 has been synthesized and fully characterized by UV-Visible, IR, Raman, 1H and 13C NMR spectroscopy elemental analysis and structural X-ray crystallography. A DFT theoretical study has been performed and good agreement between experimental and theoretical values of structural parameters and vibration frequencies have been achieved.

  8. 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.

  9. Crystal structure, stability and spectroscopic properties of methane and CO2 hydrates.

    PubMed

    Martos-Villa, Ruben; Francisco-Márquez, Misaela; Mata, M Pilar; Sainz-Díaz, C Ignacio

    2013-07-01

    Methane hydrates are highly present in sea-floors and in other planets and their moons. Hence, these compounds are of great interest for environment, global climate change, energy resources, and Cosmochemistry. The knowledge of stability and physical-chemical properties of methane hydrate crystal structure is important for evaluating some new green becoming technologies such as, strategies to produce natural gas from marine methane hydrates and simultaneously store CO2 as hydrates. However, some aspects related with their stability, spectroscopic and other chemical-physical properties of both hydrates are not well understood yet. The structure and stability of crystal structure of methane and CO2 hydrates have been investigated by means of calculations with empirical interatomic potentials and quantum-mechanical methods based on Hartree-Fock and Density Functional Theory (DFT) approximations. Molecular Dynamic simulations have been also performed exploring different configurations reproducing the experimental crystallographic properties. Spectroscopic properties have also been studied. Frequency shifts of the main vibration modes were observed upon the formation of these hydrates, confirming that vibration stretching peaks of C-H at 2915cm(-1) and 2905cm(-1) are due to methane in small and large cages, respectively. Similar effect is observed in the CO2 clathrates. The guest-host binding energy in these clathrates calculated with different methods are compared and discussed in terms of adequacy of empirical potentials and DFT methods for describing the interactions between gas guest and the host water cage, proving an exothermic nature of methane and CO2 hydrates formation process. PMID:23911993

  10. 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.

  11. 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

  12. 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.

  13. Structure-spectroscopic relationship of co-crystals between a rare chromone structure type of barakol and some organic acids

    NASA Astrophysics Data System (ADS)

    Chimsook, T.; Teerawatananond, T.; Ngamrojnavanich, N.; Chaichit, N.; Kongsaeree, P.; Muangsin, N.

    2013-12-01

    Barakol, extracted from Cassia siamea Lamk. having an anxiolytic property, consists of a rare chromone core structure, therefore, in this work we investigate relation between the X-ray crystallography and physical properties such as spectroscopic data and the intermolecular interactions of the keto-enol forms based on the CSD search, especially e.g. hydrogen bonding, π-π interactions, ionic interactions and acid-base interactions and clarifies their ambiguous spectroscopic properties. The 1:1 molecular complexes of barakol and carboxylic acid (phthalic acid and 3-hydroxybenzoic acid) were prepared and the X-ray crystallographic studies revealed that the barakol-phthalate complex exists in an ion-pair complex. The formation of barakol-phthalate ion-pair complex is stabilized by the complementary of ion-ion interactions, π-π interactions and hydrogen bonding. The barakol-3-hydroxybenzoic acid complex is a π-π molecular complex. The co-crystallization of barakol-3-hydroxybenzoic acid complex is solely stabilized by π-π interactions. The spectroscopic studies including IR, 1H NMR and 13C NMR are consistent with the results from the X-ray analysis. The 1H NMR spectrum of the barakol and phthalic acid complex in a mixture of CDCl3-CD3OD showed a dramatic spectral changes with downfield shifts of the ortho-protons of phthalic acid (ΔδH(ppm) = 0.37), and the proton resonances of barakol (ΔδH(ppm) = 0.31 for proton H3, 0.53 for proton H4, 0.57 for proton H6 and 0.33 for proton H9).

  14. Structural, Dielectric and Temperature Dependent Raman Spectroscopic Studies on Swift Heavy Ion Irradiated Tgs Crystals

    NASA Astrophysics Data System (ADS)

    Bajpai, P. K.; Shah, Deepak; Kumar, Ravi; Kumar, Ashok; Katiyar, R. S.

    2011-11-01

    Polar cleavage surface of tri-glycine sulphate (TGS) of important room temperature ferroelectric crystal irradiated with 100 MeV oxygen ion beam are characterized to understand the effect of irradiation on structural, dielectric and vibrational modes of the crystal. X-ray diffraction results show lattice parameters a and b in monoclinic unit cell decrease with increasing fluence, whereas parameter `c' increases. However, the irradiated crystal remains in monoclinic phase. Dielectric anomaly peak value associated with paraelectric—ferroelectric phase transition gets reduce with irradiation and Tc shift towards lower temperature. A comparison of the Raman spectra of unirradiated crystal with those irradiated in both paraelectric and ferroelectric phase reveals the molecular ion getting distorted as a result of irradiation.

  15. Accidental formation of Gd₄(SiO₄)₂OTe: crystal structure and spectroscopic properties.

    PubMed

    Daszkiewicz, Marek; Gulay, Lubomir D

    2015-07-01

    Designing new functional materials with increasingly complex compositions is of current interest in science and technology. Complex rare-earth-based chalcogenides have specific thermal, electrical, magnetic and optical properties. Tetragadolinium bis[tetraoxidosilicate(IV)] oxide telluride, Gd4(SiO4)2OTe, was obtained accidentally while studying the Gd2Te3-Cu2Te system. The crystal structure was determined by means of single-crystal X-ray diffraction. The compound crystallizes in the space group Pnma. Three symmetry-independent gadolinium sites were determined. The excitation and emission spectra were collected at room temperature and at 10 K. Gd4(SiO4)2OTe appears to be a promising optical material when doped with rare-earth ions. PMID:26146399

  16. 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.

  17. 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.

  18. Ion-pair complexes with strong near infrared absorbance: syntheses, crystal structures and spectroscopic properties.

    PubMed

    Pei, Wen-Bo; Wu, Jian-Sheng; Liu, Jian-Lan; Ren, Xiao-Ming; Shen, Lin-Jiang

    2010-01-01

    Three ion-pair complexes, [4-NH(2)-Py](2)[M(mnt)(2)] (4-NH(2)-Py(1+)=4-amino-pyridinium; mnt(2-)=maleonitriledithiolate; M=Pt (1), Pd (2) or Ni (3)), have been synthesized and characterized. In the crystal of 1, the strong H-bonding interaction was found from the protonated N-atom of pyridinium to the CN group of [Pt(mnt)(2)](2-) together with a weak Pt...H interaction between the anion and the cation. The crystals of 2 and 3 are isostructural with very similar lattice parameters and packing structures, which are distinct from the crystal of 1. Two kinds of strong H-bonding interactions are observed in the crystals of 2 and 3 between the CN groups of [M(mnt)(2)](2-) anion and the protonated N-atom of 4-NH(2)-Py(1+) cation as well as the CN groups of [M(mnt)(2)](2-) anion and the amino group of 4-NH(2)-Py(1+) cation. Complex 1 shows an intense near-IR absorbance in acetonitrile and solid state, such an absorption band is probably assigned to IPCT transition as well as a trace amount of [Pt(mnt)(2)](1-) species; complex 3 possesses a weak near-IR absorption band which can be attributed to the mixture of d-d transition in [Ni(mnt)(2)](2-) and IPCT transition as well as a trace amount of [Ni(mnt)(2)](1-) species. PMID:19897406

  19. 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.

  20. 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.

  1. 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.

  2. 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

  3. Synthesis, crystal structures and spectroscopic properties of triazine-based hydrazone derivatives; a comparative experimental-theoretical study.

    PubMed

    Arshad, Muhammad Nadeem; Bibi, Aisha; Mahmood, Tariq; Asiri, Abdullah M; Ayub, Khurshid

    2015-01-01

    We report here a comparative theoretical and experimental study of four triazine-based hydrazone derivatives. The hydrazones are synthesized by a three step process from commercially available benzil and thiosemicarbazide. The structures of all compounds were determined by using the UV-Vis., FT-IR, NMR (1H and 13C) spectroscopic techniques and finally confirmed unequivocally by single crystal X-ray diffraction analysis. Experimental geometric parameters and spectroscopic properties of the triazine based hydrazones are compared with those obtained from density functional theory (DFT) studies. The model developed here comprises of geometry optimization at B3LYP/6-31G (d, p) level of DFT. Optimized geometric parameters of all four compounds showed excellent correlations with the results obtained from X-ray diffraction studies. The vibrational spectra show nice correlations with the experimental IR spectra. Moreover, the simulated absorption spectra also agree well with experimental results (within 10-20 nm). The molecular electrostatic potential (MEP) mapped over the entire stabilized geometries of the compounds indicated their chemical reactivates. Furthermore, frontier molecular orbital (electronic properties) and first hyperpolarizability (nonlinear optical response) were also computed at the B3LYP/6-31G (d, p) level of theory. PMID:25854752

  4. Preparation, spectroscopic characterization and crystal structures of ferrocenylalkanediols and derived acetates

    NASA Astrophysics Data System (ADS)

    Lapić, Jasmina; Bilić, Josipa; Cetina, Mario; Djaković, Senka; Rapić, Vladimir

    2011-01-01

    ( meso, dl)-3-(Ferrocenylmethyl)pentane-2,4-diol ( 3) was synthesized by reduction of 3-(ferrocenylmethyl)pentane-2,4-dione ( 2) with LiAlH 4 in a good yield and corresponding monoacetate 4 and diacetate 5 were prepared. Newly prepared compounds are characterized by elemental analysis, IR and NMR spectroscopy and will be used as a substrate or standards for lipase mediated desymmetrization. The structures of 3-(ferrocenylmethyl)pentane-2,4-diol ( 3) and 2-(ferrocenylmethyl)propane-1,3-diol diacetate ( 8), which is derived from prochiral 2-(ferrocenylmethyl)propane-1,2-diol ( 6), were determined by X-ray crystal structure analysis. The conformation of the cyclopentadienyl rings is eclipsed in 3 and almost halfway between eclipsed and staggered in 8. One O-H⋯O hydrogen bond links the molecules of diol 3 into chains, while one weak C-H⋯π interaction self-assembles the molecules of diacetate 8 into dimers.

  5. Crystal structure, spectroscopic investigation and thermal properties of L-lysine p-toluenesulfonate

    NASA Astrophysics Data System (ADS)

    Wang, L.; Wang, D. H.; Zhang, G. H.; Xu, D.; Deng, W. X.

    2016-03-01

    A novel organic crystal was prepared from L-lysine (Lly) and p-toluenesulfonic acid (pTS), which was grown from an aqueous solution by slow cooling method. The crystal system and the lattice parameters have been confirmed by single crystal X-ray diffraction studies. The FT-IR, FT-Raman, 1H-NMR and 13C-NMR spectral of the crystal have been recorded and analyzed. The spectral analyses confirmed the presence of various functional groups and the molecular configurations in LLTS crystal. The UV-Vis-NIR transmittance spectrum has been carried out which shows the cutoff wavelength around 280 nm. The thermal properties of crystal have been evaluated from thermogravimetric (TG) and differential thermal analysis (DTA). The melting point of grown crystal is fairly high, at around 259 °C. The nonlinear optical (NLO) properties of LLTS crystal were demonstrated by powder SHG experiment and also by quantum chemical calculations. The powder SHG efficiency of LLTS crystal is relatively low and very different from theoretical calculation results.

  6. 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.

  7. Red to Near-Infrared Isoindole BODIPY Fluorophores: Synthesis, Crystal Structures, and Spectroscopic and Electrochemical Properties.

    PubMed

    Yu, Changjiang; Wu, Qinghua; Wang, Jun; Wei, Yun; Hao, Erhong; Jiao, Lijuan

    2016-05-01

    A series of high-performance fluorophores named isoindole boron dipyrromethenes (BODIPYs) containing either symmetrical or unsymmetrical alkyl substitution patterns on pyrrole rings were synthesized by an efficient process and were characterized by X-ray diffraction and spectroscopic and electrochemical analyses. Most of these dyes show strong, sharp absorption and bright fluorescence emission in the red to near-infrared (NIR) region (up to 805 nm in acetonitrile). Pyrrolic alkyl substitutions lead to increases in the HOMO and LUMO energy levels and an overall decrease in the energy band gaps of the dye. Among the 23 isoindole BODIPY dyes synthesized, solvent-dependent fluorescence emission and lifetime decay were only observed for those containing a 3-methyl substituent on the uncoordinated pyrrole ring, whereas little variation in the fluorescence intensity was observed for the rest of the dyes upon changing the polarity of the solvent. These resultant dyes can be further functionalized via the Knoevenagel condensation on the α-methyl substituent of the chromophore to install a variety of functionalities, including a dimethylamine group demonstrated in this work. This dimethylamine-functionalized isoindole BODIPY shows weak fluorescence at 805 nm in acetonitrile and a ratiometric "turn-on" NIR fluorescence response to decreasing pH. PMID:27031115

  8. 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

  9. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

    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, 1H and 13C NMR data, ELUMO-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 ELUMO-HOMO calculations suggest these compounds may have applications as organic semiconducting materials.

  11. 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. PMID:25128674

  12. Crystal and molecular structure and spectroscopic behavior of isotypic synthetic analogs of the oxalate minerals stepanovite and zhemchuzhnikovite

    NASA Astrophysics Data System (ADS)

    Piro, Oscar E.; Echeverría, Gustavo A.; González-Baró, Ana C.; Baran, Enrique J.

    2016-04-01

    The crystal structure of synthetic stepanovite, Na[Mg(H2O)6][Fe(C2O4)3]·3H2O, and zhemchuzhnikovite, Na[Mg(H2O)6][Al0.55Fe0.45(C2O4)3]·3H2O, has been determined by single-crystal X-ray diffraction methods. The compounds are isotypic to each other and to the previously reported Na[Mg(H2O)6][M(C2O4)3]·3H2O (M: Cr, Al). They crystallize in the trigonal P3 c1 space group with Z = 6 molecules per unit cell and (hexagonal axes) a = 17.0483(4), c = 12.4218(4) Å for the iron compound, and a = 16.8852(5), c = 12.5368(5) Å for the Al/Fe solid solution. Comparison of our crystallographic results with previous X-ray diffraction and chemical data of type stepanovite and zhemchuzhnikovite minerals provides compelling evidence that these natural materials possess the same crystal and molecular structure as their synthetic counterparts. It is shown that the originally reported unit cell for stepanovite represents a pronounced sub-cell and that the correct unit cell and space group are based on weak superstructure reflections. The infrared and Raman spectra of both synthetic analogs were also recorded and are briefly discussed.

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

    NASA Astrophysics Data System (ADS)

    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.

  14. Halogen bonding in the antibacterial 1,2,4-triazole-3-thione derivative - Spectroscopic properties, crystal structure and conformational analysis

    NASA Astrophysics Data System (ADS)

    Miroslaw, Barbara; Plech, Tomasz; Wujec, Monika

    2015-03-01

    The molecular structure of 4-(4-bromophenyl)-5-(3-chlorophenyl)-2,4-dihydro-3H-1,2,4-triazole-3-thione (TP-4) has been determined by the X-ray diffraction experiment and compared to the geometry calculated in the ground state by using HF and DFT methods. The compound crystallizes in the triclinic P-1 space group. To explain the observed rotational disorder of meta-chloro-substituted aromatic ring the conformational analysis was performed for TP-4 and the molecular energy profile has been obtained. The vibrational frequencies in the solid state were recorded and compared to the calculated in the ground state. The molecular electrostatic potential isosurfaces (MEPS) were calculated to confirm the role of halogen bonds in stabilizing the crystal structure.

  15. 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.

  16. 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.

  17. Synthesis, spectroscopic studies and crystal structure of ( E)-2-(2,4-dihydroxybenzylidene)thiosemicarbazone and ( E)-2-[(1 H-indol-3-yl)methylene]thiosemicarbazone

    NASA Astrophysics Data System (ADS)

    Yıldız, Mustafa; Ünver, Hüseyin; Erdener, Diğdem; Kiraz, Aşkın; İskeleli, Nazan Ocak

    2009-02-01

    Thiosemicarbazone Schiff bases ( 1 and 2) derived from 2,4-dihydroxybenzaldehyde, indoline-3-carbaldehyde and thiosemicarbazone have been synthesized and their structures were elucidated by elemental analysis, FT-IR, 1H NMR, 13C NMR and UV-visible spectroscopic techniques. The structures of compounds 1 and 2 have also been examined cyrstallographically. The title compounds 1 and 2 crystallize in the monoclinic space group C2/ c and triclinic space group P1¯, with unit cell parameters: a = 21.421(1) and 7.233(1), b = 4.131(1) and 11.166(1), c = 24.942(2) and 13.648(1) Å, V = 1856.1(2) and 1019.5(1) Å 3, D x = 1.512 and 1.422 g cm -3 and Z = 8 and 4, respectively.

  18. Synthesis, crystal structure, spectroscopic and density functional theory (DFT) study of N-[3-anthracen-9-yl-1-(4-bromo-phenyl)-allylidene]-N-benzenesulfonohydrazine.

    PubMed

    Arshad, Muhammad Nadeem; Asiri, Abdullah M; Alamry, Khalid A; Mahmood, Tariq; Gilani, Mazhar Amjad; Ayub, Khurshid; Birinji, Abdulhadi Salih

    2015-05-01

    N-[3-anthracen-9-yl-1-(4-bromo-phenyl)-allylidene]-N-benzenesulfonohydrazine has been synthesized and characterized by various spectroscopic techniques including FT-IR, UV-vis, (1)H-NMR, (13)C-NMR spectroscopy, and the structure was unequivocally confirmed by single crystal X-ray diffraction studies. The compound crystallized in monoclinic system with P21/n space group, and adopted cis-geometry around the azomethine CN double bond. The X-ray crystal structure revealed that the intermolecular packing was stabilized by C-H⋯O type hydrogen bonding interaction, whereas NH was not involved in hydrogen bonding due to steric hindrance. Absorption wavelength was studied by scanning UV-vis. absorption spectrum in different solvents to explore excited state stability of the molecule in polar solvent. Density functional theory calculations were performed at B3LYP/6-31G (d, p) level in order to compare the experimental results with the theoretical results. The simulated molecular electrostatic potential (MEP), Mulliken charges and NPA (natural population analysis) also confirmed the presence of specific intermolecular hydrogen bonding (C-H⋯O). In addition natural bond orbital (NBO) analysis (intra and inter molecular bonding and interaction among bonds), frontier molecular orbital analysis (electronic properties) and first hyperpolarizability analysis (nonlinear optical response) were simulated at B3LYP/6-31G (d, p) level of theory. PMID:25721652

  19. Synthesis, crystal structure, spectroscopic and density functional theory (DFT) study of N-[3-anthracen-9-yl-1-(4-bromo-phenyl)-allylidene]-N-benzenesulfonohydrazine

    NASA Astrophysics Data System (ADS)

    Arshad, Muhammad Nadeem; Asiri, Abdullah M.; Alamry, Khalid A.; Mahmood, Tariq; Gilani, Mazhar Amjad; Ayub, Khurshid; Birinji, Abdulhadi Salih

    2015-05-01

    N-[3-anthracen-9-yl-1-(4-bromo-phenyl)-allylidene]-N-benzenesulfonohydrazine has been synthesized and characterized by various spectroscopic techniques including FT-IR, UV-vis, 1H-NMR, 13C-NMR spectroscopy, and the structure was unequivocally confirmed by single crystal X-ray diffraction studies. The compound crystallized in monoclinic system with P21/n space group, and adopted cis-geometry around the azomethine Cdbnd N double bond. The X-ray crystal structure revealed that the intermolecular packing was stabilized by C-H⋯O type hydrogen bonding interaction, whereas NH was not involved in hydrogen bonding due to steric hindrance. Absorption wavelength was studied by scanning UV-vis. absorption spectrum in different solvents to explore excited state stability of the molecule in polar solvent. Density functional theory calculations were performed at B3LYP/6-31G (d, p) level in order to compare the experimental results with the theoretical results. The simulated molecular electrostatic potential (MEP), Mulliken charges and NPA (natural population analysis) also confirmed the presence of specific intermolecular hydrogen bonding (C-H⋯O). In addition natural bond orbital (NBO) analysis (intra and inter molecular bonding and interaction among bonds), frontier molecular orbital analysis (electronic properties) and first hyperpolarizability analysis (nonlinear optical response) were simulated at B3LYP/6-31G (d, p) level of theory.

  20. 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.

  1. 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.

  2. 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.

  3. One pot synthesis of biologically active pregnane derivatives, their single crystal structures, spectroscopic characterization and theoretical calculations

    NASA Astrophysics Data System (ADS)

    Sethi, Arun; Bhatia, Akriti; Bhatia, Gitika; Shrivastava, Atul; Prakash, Rohit

    2013-11-01

    One pot allylic oxidation of 3β-acetoxypregna-5,16-diene-20-one (2) and nucleophilic addition at C-16 position of 3β-hydroxypregna-5,16-diene-20-one (3) yielded 3β-acetoxypregna-5,16-diene-7,20-dione (4) and 3β-hydroxy-16α-(5'-hydroxypentyloxy)-pregn-5-ene-20-one (5) respectively in high yield. A detailed theoretical study supported by X-ray analysis of compounds 4 and 5 has been carried out. Conformational analysis of compounds 4 and 5 was done with the help of crystal structure, which crystallize out in orthorhombic form having P212121 space group. Structural characterization of compounds 4 and 5 was done with the aid of 1H, 13C NMR, IR, UV, ESI-MS and ESI-HRMS. The molecular geometries and vibrational frequencies for compounds 4 and 5 in the ground state were calculated using the Density functional theory (DFT) with 6-31G(d,p) basis set and compared with experimental data. 1H and 13C nuclear magnetic resonance magnetic shifts of 4 and 5 were calculated using GIAO method and compared with the experimental data. UV-Vis spectra of both the compounds were recorded and electronic properties such as HOMO-LUMO energies were calculated by time dependent TD-DFT approach. The compounds were screened for their anti-hyperlipidemic and anti-oxidant activity.

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

    PubMed

    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/cm(3). 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

  5. Crystal structure, spectroscopic characterization and density functional studies of (E)-1-((3-methoxyphenylimino)methyl)naphthalen-2-ol.

    PubMed

    Alpaslan, Gökhan; Macit, Mustafa

    2014-01-01

    The Schiff base compound (E)-1-((3-methoxyphenylimino)methyl)naphthalen-2-ol was synthesized from the reaction of 2-hydroxy-1-naphthaldehyde with 3-methoxyaniline. The structural properties of the compound has been characterized by using FT-IR, UV-vis and X-ray single-crystal methods. According to X-ray diffraction result, the title compound exists in the phenol-imine tautomeric form. The molecular geometry, vibrational frequencies of the compound in the ground state have been calculated using the density functional theory (DFT/B3LYP) method with the 6-311++G(d,p) basis set, and compared with the experimental data. The obtained results show that the optimized molecular geometry is well reproduce the crystal structure. The theoretical vibrational frequencies are in good agreement with the experimental values. The calculations of electronic absorption spectra of tautomeric forms of the compound were performed by using TD-DFT calculations both in the gas phase and ethanol solvent. To investigate the tautomeric stability, optimization calculations at the B3LYP/6-311++G(d,p) level were performed for the phenol-imine and keto-amine forms of the compound. According to calculated results, the OH form is more stable than NH form. In addition, molecular electrostatic potential (MEP), frontier molecular orbital analysis (HOMO-LUMO), thermodynamic and, non-linear optical (NLO) properties of the compound were investigated using same theoretical calculations. PMID:24280299

  6. 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

  7. Chloride derivatives of lanthanoid(III) ortho-oxidotungstates(VI) with the formula LnCl[WO4] (Ln=Gd-Lu): Syntheses, crystal structures and spectroscopic properties

    NASA Astrophysics Data System (ADS)

    Schustereit, Tanja; Schleid, Thomas; Höppe, Henning A.; Kazmierczak, Karolina; Hartenbach, Ingo

    2015-03-01

    The lanthanoid(III) chloride ortho-oxidotungstates(VI) with the formula LnCl[WO4] crystallize monoclinically in space group C2/m (a=1019-1032, b=721-733, c=682-689 pm and β=107-108°, Z=4) for Ln=Gd-Er and triclinically in space group P1¯ (a=593-596, b=719-721, c=684-686 pm, α=93-94, β≈103 and γ≈122°, Z=2) for Ln=Tm-Lu. The monoclinic structure contains crystallographically unique Ln3+ cations, which are surrounded by two Cl- and six O2- anions forming distorted trigonal dodecahedra. Their fusion via common edges leads to anionic layers ∞ 2 {[ LnCl2/2eO4/2eO2/1t ] 6 - }. The polyhedra around the Ln3+ cations in the triclinic crystal structure are also built up by two Cl-, but only five O2- anions to form distorted monocapped trigonal prisms. Their linkage through edges constitutes anionic strands ∞ 1 {[ LnCl2/2eO2/2eO3/1t ] 6 - } along [100]. The complex anionic entities of both LnCl[WO4] arrangements become interconnected by W6+ cations to complete the structures by generating discrete [WO4]2- tetrahedra. Since the title compounds emerge as pure phases according to X-ray powder diffractometry, spectroscopic measurements such as single crystal Raman as well as diffuse reflectance spectroscopy (DRS) were performed. Furthermore, GdCl[WO4] and LuCl[WO4] are suitable host materials for doping with Eu3+, which leads to materials with a red luminescence upon excitation with UV light for both structures. Moreover, TbCl[WO4] exhibits a Tb3+-typical yellow-green bulk luminescence upon UV excitation, which could be analyzed by luminescence spectroscopy.

  8. Crystal structure and spectroscopic study on photochromism of 1-phenyl-3-methyl-4-benzal-5-pyrazolone 4-ethylthiosemicarbazone

    NASA Astrophysics Data System (ADS)

    Peng, Bang-hua; Liu, Guang-fei; Liu, Lang; Jia, Dian-zeng; Yu, Kai-bei

    2004-04-01

    The crystal structure of the title compound 1-phenyl-3-methyl-4-benzal-5-pyrazolone 4-ethyl thiosemicarbazone (PMBP-ETSC), as determined by X-ray analysis, shows that the pyrazolone moiety stabilizes in the keto form and the molecule is found to be in three-dimensional arrangement in the unit cell linked by intermolecular hydrogen bonds. The important bands in IR spectra, as well as the main signals of the 1H NMR spectra are assigned. Meanwhile, the steady state, time-dependent fluorescence emission spectroscopy, the powder UV-Vis reflection spectroscopy of the solid product and theoretical chemistry calculations of reaction rate constant are also studied, the results of which show that PMBP-ETSC can perform photochromism.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. Crystal structure, spectroscopic studies and quantum mechanical calculations of 2-[((3-iodo-4-methyl)phenylimino)methyl]-5-nitrothiophene

    NASA Astrophysics Data System (ADS)

    Özdemir Tarı, Gonca; Gümüş, Sümeyye; Ağar, Erbil

    2015-04-01

    The title compound, 2-[((3-iodo-4-methyl)phenylimino)methyl]-5-nitrothiophene, C12H9O2N2I1S1, was synthesized and characterized by IR, UV-Vis and single-crystal X-ray diffraction technique. The molecular structure was optimized at the B3LYP, B3PW91 and PBEPBE levels of the density functional method (DFT) with the 6-311G+(d,p) basis set. Using the TD-DFT method, the electronic absorption spectra of the title compound was computed in both the gas phase and ethanol solvent. The harmonic vibrational frequencies of the title compound were calculated using the same methods with the 6-311G+(d,p) basis set. The calculated results were compared with the experimental determination results of the compound. The energetic behavior such as the total energy, atomic charges, dipole moment of the title compound in solvent media were examined using the B3LYP, B3PW91 and PBEPBE methods with the 6-311G+(d,p) basis set by applying the Onsager and the polarizable continuum model (PCM). The molecular orbitals (FMOs) analysis, the molecular electrostatic potential map (MEP) and the nonlinear optical properties (NLO) for the title compound were obtained with the same levels of theory. And then thermodynamic properties for the title compound were obtained using the same methods with the 6-311G(d,p) basis set.

  14. A new supramolecular compound of chrome(III): Synthesis, spectroscopic characterization, X-ray crystal structure, DFT, and solution studies

    NASA Astrophysics Data System (ADS)

    Eshtiagh-Hosseini, Hossein; Yousefi, Zakieh; Mirzaei, Masoud; Chen, Ya-Guang; Ali Beyramabadi, S.; Shokrollahi, Ardeshir; Aghaei, Roghayyeh

    2010-06-01

    A new supramolecular compound of Cr(III) atom was synthesized and characterized by using elemental analysis, FTIR spectroscopy, UV-vis, and single crystal X-ray diffraction method. The chemical formula and space group of the resulting compound is (2-apymH)[Cr(pydc) 2]·2H 2O ( 1) (pydc = 2,6-pyridinedicarboxylate, 2-apym = 2-aminopyrimidine) and P2 1/ c where the final R value is 0.0157 for 3896 reflections collected. The [Cr(pydc) 2] - anions and the (2-apymH) + moiety form a three-dimensional solid state structure by a variety of noncovalent interactions such as ion pairing and hydrogen bonds interactions. On the basis of crystallographic data, it can be seen that Cr(III) atom is six-coordinated by two (pydc) 2- groups. With respect to bond lengths and angles, it is observed that coordination sphere around Cr(III) atom is a distorted octahedral. Furthermore, DFT calculation and solution study have been completely performed on 1 where corresponding data showed that obtained results from DFT and solution studies have good agreement with X-ray crystallography results. The optimized geometry confirms that the C-O (bonded) bond length of (pydc) 2- ligand in its complex form has been increased compared with the free ligand. The evidence shows that C-O (bonded) is weakened upon formation of complex, while C dbnd O (free) converted to double bond. Anionic complex possesses 90 occupied molecular orbitals and 3 half-occupied ones (91-93). A comparison between the stoichiometry of the crystalline complex in pydcH 2-2-apym-Cr system and the results obtained from solution studies clearly revealed that the CrL 2QH is the most abundant species existing in aqueous solution possesses a stoichiometry similar to that of the complex which was obtained in the solid state.

  15. 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.

  16. 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

  17. 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.

  18. A linear S-bridged trinuclear cobalt(III) complex with 2-aminobenzenethiol: Synthesis, crystal structure, and spectroscopic characterization.

    PubMed

    Panja, Anangamohan; Moore, Curtis E; Eichhorn, David M

    2013-01-01

    Treatment of cobalt(II) perchlorate hexahydrate with 2 molar equiv. of 2-aminobenzenethiol (Habt) in acetonitrile afforded a tricationic tricobalt complex, [Co{Co(abt)3}2](ClO4)3·2CH3CN, by aerial oxidation. The molecular structure of the meso (ΔΛ) form of the complex was determined by X-ray crystallography. In the complex cation, the central Co is coordinated by six thiolate groups from two terminal fac(S)-[Co(abt)3] units in an octahedral geometry, forming a linear S-bridged tricobalt structure. PMID:24465064

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

    Violet crystals of {[Cu(pn)2]2[Pt(CN)4]}[Pt(CN)4]·2H2O (1, pn=1,2-diaminopropane) and blue crystals of [Cu(pn)Pt(CN)4]n·nH2O (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)2-Pt(CN)4-Cu(pn)2]2+ complex cation and discrete [Pt(CN)4]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)4]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/kB=-1.64 K.

  20. 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.

  1. 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

  2. Spectroscopic Analysis Of Insulating Crystal Fibers

    NASA Technical Reports Server (NTRS)

    Buoncristiani, A. M.; Inge, Addison T.; Byvik, C. E.

    1990-01-01

    New method provides rapid characterization of optical properties. Technique for determining optical properties of insulating single-crystal fibers developed and applied to sapphire, spinel, and YAIO crystalline host fibers doped with triply ionized titanium. Crystal fibers grown more rapidly and less expensively.

  3. 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.

  4. Comprehensive Spectroscopic Determination of the Crystal Field Splitting in an Erbium Single-Ion Magnet.

    PubMed

    Rechkemmer, Yvonne; Fischer, Julia E; Marx, Raphael; Dörfel, María; Neugebauer, Petr; Horvath, Sebastian; Gysler, Maren; Brock-Nannestad, Theis; Frey, Wolfgang; Reid, Michael F; van Slageren, Joris

    2015-10-14

    The electronic structure of a novel lanthanide-based single-ion magnet, {C(NH2)3}5[Er(CO3)4]·11H2O, was comprehensively studied by means of a large number of different spectroscopic techniques, including far-infrared, optical, and magnetic resonance spectroscopies. A thorough analysis, based on crystal field theory, allowed an unambiguous determination of all relevant free ion and crystal field parameters. We show that inclusion of methods sensitive to the nature of the lowest-energy states is essential to arrive at a correct description of the states that are most relevant for the static and dynamic magnetic properties. The spectroscopic investigations also allowed for a full understanding of the magnetic relaxation processes occurring in this system. Thus, the importance of spectroscopic studies for the improvement of single-molecule magnets is underlined. PMID:26394012

  5. 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.

  6. 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.

  7. Synthesis, spectroscopic characterization, crystal structure, DNA interaction study and invitro biological screenings of 4-(5-chloro-2-hydroxyphenylamino)-4-oxobut-2-enoic acid

    NASA Astrophysics Data System (ADS)

    Sirajuddin, Muhammad; Nooruddin; Ali, Saqib; McKee, Vickie; Khan, Shahan Zeb; Malook, Khan

    2015-01-01

    The titled compound, 4-(5-chloro-2-hydroxyphenylamino)-4-oxobut-2-enoic acid was synthesized and characterized by various techniques like elemental analyses, FT-IR, NMR (1H, and 13C) and single crystal X-ray structural analysis. The appearance of the OH peak of the carboxylic acid in the FT-IR and NMR spectra conform the formation of the compound. A good agreement was found between the calculated values of C, H, N and found values in elemental analysis that show the purity of the compound. Protons H2 and H3 are in cis conformation with each other as conformed both from 1H NMR as well as from single crystal X-ray analysis. The molecular structure of the title compound, C10H10NO3Cl, is stabilized by short intramolecular Osbnd H- - -O hydrogen bonds within the molecule. In the crystal structure, intermolecular Nsbnd H- - -O hydrogen bonds link molecules into zigzag chains resulting in a dendrimer like structure. The title compound was screened for biological activities like interaction with DNA, cytotoxicity, antitumor and antioxidant activities. DNA interaction study reveals that the binding mode of interaction of the compound with SS-DNA is intercalative as it results in hypochromism along with significant red shift of 5 nm. It was also found to be effective antioxidant of 2,2-diphenyl-1-picrylhydrazyl radical (DPPH) and show almost comparable antioxidant activity to that of the standard and known antioxidant, ascorbic acid, at higher concentration. The antitumor activity data of the compound shows that it can be used as potent antitumor agent.

  8. Synthesis, spectroscopic characterization, crystal structure, DNA interaction study and invitro biological screenings of 4-(5-chloro-2-hydroxyphenylamino)-4-oxobut-2-enoic acid.

    PubMed

    Sirajuddin, Muhammad; Nooruddin; Ali, Saqib; McKee, Vickie; Khan, Shahan Zeb; Malook, Khan

    2015-01-01

    The titled compound, 4-(5-chloro-2-hydroxyphenylamino)-4-oxobut-2-enoic acid was synthesized and characterized by various techniques like elemental analyses, FT-IR, NMR ((1)H, and (13)C) and single crystal X-ray structural analysis. The appearance of the OH peak of the carboxylic acid in the FT-IR and NMR spectra conform the formation of the compound. A good agreement was found between the calculated values of C, H, N and found values in elemental analysis that show the purity of the compound. Protons H2 and H3 are in cis conformation with each other as conformed both from (1)H NMR as well as from single crystal X-ray analysis. The molecular structure of the title compound, C₁₀H₁₀NO₃Cl, is stabilized by short intramolecular OH---O hydrogen bonds within the molecule. In the crystal structure, intermolecular NH---O hydrogen bonds link molecules into zigzag chains resulting in a dendrimer like structure. The title compound was screened for biological activities like interaction with DNA, cytotoxicity, antitumor and antioxidant activities. DNA interaction study reveals that the binding mode of interaction of the compound with SS-DNA is intercalative as it results in hypochromism along with significant red shift of 5 nm. It was also found to be effective antioxidant of 2,2-diphenyl-1-picrylhydrazyl radical (DPPH) and show almost comparable antioxidant activity to that of the standard and known antioxidant, ascorbic acid, at higher concentration. The antitumor activity data of the compound shows that it can be used as potent antitumor agent. PMID:25022495

  9. Functional and structural model for the molybdenum-pterin binding site in dimethyl sulfoxide reductase. Synthesis, crystal structure, and spectroscopic investigations of trichloro(quinonoid-N(8)H-6,7-dihydropterin)oxomolybdenum(IV)

    SciTech Connect

    Fischer, B.; Schmalle, H.; Dubler, E.

    1995-11-08

    Dimethyl sulfoxide is the substrate to the molybdenum-dependent enzyme dimethyl sulfoxide reductase, which is a member of the large group of molybdenum-containing non-nitrogenase redox enzymes. The active site of these enzymes is thought to possess a so-called molybdopterin, a hydrogenated pterin with an unusual side chain containing a dithiolene group. Up to now the enzyme reactivity was mostly attributed to molybdenum and to the coordination of these sulfur ligands in the side chain. The pterin moiety was not taken into account as playing an active part essential for the enzyme reaction. We demonstrated for the first time a possible coordination of a hydrogenated pterin to molybdenum with a complex of quinonoid-dihydro-L-biopterin bound to molybdenum in the oxidation state + IV. Now we report the synthesis, crystal structure, and spectroscopic data for trichloro-(quinonoid-N(8)H-6,7-dihydropterin)oxomolybdenum(IV), [MoOCl{sub 3}(H{sup +}-q-H{sub 2}Ptr)](1) (dihydropterin = H{sub 2}Ptr). Crystal data: a = 9.966(3) {angstrom}, b = 14.408(4) {angstrom}, c = 17.362(5) {angstrom}, V = 2493(2) {angstrom}{sup 3}, Z = 8, orthohombic, space group Pbca, R{sub 1} = 0.059 and wR{sub 2} = 0.0150. 1 is synthesized in a redox reaction between Mo(VI)O{sub 2}Cl{sub 2} and tetrahydropterin [H{sub 4}Ptr{center_dot}2HCl] and contains a cationic quinonoid dihydropterin coordinated via the N(5) and O(4) atoms to the molybdenum atom. The crystal structure of 1 containing the hydrogenated pterin exhibits an unusually short Mo-N(5) bond length of 2.013(3) {angstrom}, as compared to 2.324(6) {angstrom} for the corresponding bond in oxidized pterin. 1 is able to quantitatively reduce the substrate dimethyl sulfoxide to dimethyl sulfide under the strict exclusion of oxygen. This reaction can be monitored by {sup 13}C-NMR spectroscopy. A simplified in vivo reaction cycle for the enzyme center of DMSO reductase is proposed as a working hypothesis.

  10. 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.

  11. Synthesis, spectroscopic characterization, antimicrobial activity and crystal structure of [Ag2(C10H10N3O3S)2(C5H5N)3

    NASA Astrophysics Data System (ADS)

    Tailor, Sanjay M.; Patel, Urmila H.

    2015-05-01

    Silver complex of 4-Amino-N-(5-methyl-1,2-oxazol-3-yl)benzenesulfonamide (sulfamethoxazole) (SMX) has been synthesized and characterized by elemental analysis, infrared, UV and NMR spectroscopy. The title compound, [Ag2(C10H10N3O3S)2(C5H5N)3] crystallizes in the orthorhombic space group Pna21 with lattice parameters a = 17.9527(5), b = 8.6529(3), c = 25.1621(7) Å and Z = 4. The structure is solved by direct method and refined to a final R = 0.0567 for 6732 reflections with I ⩾ 2σ(I). The results of IR, 1H NMR and 13C NMR spectral data suggest the binding of silver atom to the sulfonamide ligand which is in agreement with the crystal structure determination. X-ray analysis revealed that in the title compound, one silver atom is surrounded by three N atoms and one Ag atom leading to a distorted tetrahedral geometry and another silver atom is surrounded by four N atoms and one Ag atom leading to a slightly distorted square pyramid geometry with Ag⋯Ag separation distance of 3.026 Å. The dihedral angle between phenyl and isoxazole ring is 85.7(4)°. In the crystal structure, the molecules are linked via Nsbnd H⋯O, Csbnd H⋯O intermolecular and Csbnd H⋯O intramolecular interactions. Silver complex of sulfamethoxazole has been studied by electrical and thermal analysis. Silver sulfamethoxazole presents different antibacterial behavior against Escherichia coli and Staphylococcus aureus strains.

  12. 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.

  13. 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.

  14. Isoxazole derivatives of alpha-pinene isomers: Synthesis, crystal structure, spectroscopic characterization (FT-IR/NMR/GC-MS) and DFT studies

    NASA Astrophysics Data System (ADS)

    Eryılmaz, Serpil; Gül, Melek; İnkaya, Ersin; Taş, Murat

    2016-03-01

    In this paper, the alpha-pinene isoxazole derivatives (3a-b-c, 4a-b) were synthesized via 1,3-dipolar cycloaddition and characterized with FT-IR, 1H NMR, 13C NMR and GC-MS. Isoxazole (C21H23NO) compound (4a) 6,6,7a,-trimethyl-3-(naphthalen-2-yl)-3a,4,5,6,7,7a-hexahydro-5,7-methanobenzo[d] was characterized by X-ray single crystal diffraction technique. The compound crystallizes in the monoclinic space group P 212121, with Z = 4. The molecular geometry of the compound was optimized by applying Density Functional Theory (DFT/B3LYP) method with 6-31G(d,p) and 6-311 + G(d,p) basis sets in the ground state and geometric parameters were compared with the X-ray analysis results of the structure. Results of the experimental FT-IR and NMR spectral analysis were examined in order to determine the compliance with vibrational frequencies, 1H NMR and 13C NMR chemical shifts values by using the Gauge-Independent Atomic Orbital (GIAO) method calculated over the optimized structure. Besides molecular electrostatic potential (MEP), frontier molecular orbitals (FMOs), some global reactivity descriptors, thermodynamic properties, non-linear optical (NLO) behaviour and Mulliken charge analysis of the (4a) compound were computed with the same method in gas phase, theoretically.

  15. Spectroscopic characterization of charge-transfer complexes of morpholine with chloranilic and picric acids in organic media: Crystal structure of bis(morpholinium 2,4,6-trinitrocyclohexanolate)

    NASA Astrophysics Data System (ADS)

    Refat, Moamen S.; El-Zayat, Lamia A.; Yeşilel, Okan Zafer

    2010-02-01

    Electron donor-acceptor interaction of morpholine (morp) with chloranilic acid (cla) and picric acid (pa) as π-acceptors was investigated spectrophotometrically and found to form stable charge-transfer (CT) complexes (n-π*) of [(Hmorp) 2(cla)] and [(Hmorp)(pa)] 2. The donor site involved in CT interaction is morpholine nitrogen. These complexes are easily synthesized from the reaction of morp with cla and pa within MeOH and CHCl 3 solvents, respectively. 1HNMR, IR, elemental analyses, and UV-vis techniques characterize the two morpholinium charge-transfer complexes. Benesi-Hildebrand and its modification methods were applied to the determination of association constant ( K), molar extinction coefficient ( ɛ). The X-ray crystal structure was carried out for the interpretation the predict structure of the [(Hmorp)(pa)] 2 complex.

  16. Crystal structure and IR spectroscopic study of (CN{sub 3}H{sub 6}){sub 2}[(UO{sub 2}){sub 2}(C{sub 2}O{sub 4})(CH{sub 3}COO){sub 4}

    SciTech Connect

    Serezhkina, L. B.; Peresypkina, E. V.; Neklyudova, N. A.; Virovets, A. V.; Serezhkin, V. N.

    2013-03-15

    Compound (CN{sub 3}H{sub 6}){sub 2}[(UO{sub 2}){sub 2}(C{sub 2}O{sub 4})(CH{sub 3}COO){sub 4}] is synthesized and characterized by IR spectroscopy and single-crystal X-ray diffraction [a = 8.5264(2) A, b = 13.8438(4) A, c = 10.7284(2) A, {beta} = 103.543(1) Degree-Sign , space group P2{sub 1}/n, Z = 2, and R = 0.0258]. The main structural units of the crystals are binuclear [(UO{sub 2}){sub 2}C{sub 2}O{sub 4}(CH{sub 3}COO){sub 4}]{sup 2-} groups, which belong to the A{sub 2}K{sup 02}B{sub 4}{sup 01} crystal chemical group of uranyl complexes (A = UO{sub 2}{sup 2+}, K{sup 02} = C{sub 2}O{sub 4}{sup 2-}, and B{sup 01} = CH{sub 3}COO{sup -}). The coordination polyhedron of the uranium atom is the UO{sub 8} hexagonal bipyramid with the oxygen atoms of the uranyl ion at the axial positions. Uranium-containing groups and guanidinium cations are connected by electrostatic interactions and by the hydrogen bond system, which involves hydrogen atoms of guanidinium cations and oxygen atoms of oxalate and acetate anions. The results of the spectroscopic study of the compound agree with the X-ray diffraction data.

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. Crystal structure, spectroscopic and thermal properties of [Zn(Lap)2(DMF)(H2O)] and isomorphous [M(Lap)2]n (M: Cd, Mn) complexes

    NASA Astrophysics Data System (ADS)

    Farfán, R. A.; Espíndola, J. A.; Gomez, M. I.; de Jiménez, M. C. L.; Piro, O. E.; Castellano, E. E.; Martínez, M. A.

    2015-05-01

    The solid state structure of the lapacholate (Lap-) complexes with Zn(II), Cd(II) and Mn(II) were determined by X-ray diffraction methods. [Zn(Lap)2(DMF)(H2O)] crystallizes in the triclinic space group P 1 bar with a = 10.5051(4), b = 12.8020(4), c = 13.0394(4) Å, α = 60.418(2), β = 83.904(2), γ = 86.206(2)°, and Z = 2 molecules per unit cell. The isomorphous complexes [M(Lap)2]n (M: Cd, Mn) crystallize in the tetragonal space group P43212 with a = b = 13.5770(6) Å, c = 14.5730(6) Å (Cd), and a = b = 13.3539(4), c = 14.7148(4) Å (Mn), and Z = 4. In [Zn(Lap)2(DMF)(H2O)] the Zn(II) ion is in a distorted octahedral environment coordinated to two different and nearly perpendicular Lap- molecules acting as bidentate ligands through their adjacent carbonyl and phenol oxygen atoms. The remaining two cis-coordination sites are occupied by water and DMF molecules. [M(Lap)2]n (M: Cd, Mn) isomorphous complexes are also octahedral and present a supra-molecular arrangement in the lattice. There is only one independent Lap- molecule that coordinates the metal through all three ligand binding sites, giving rise to a 3-D structure of [M(Lap)2]n complexes that extends throughout the crystal lattice. The lapachol binding to metal is also revealed by the IR spectra. In fact, the carbonyl Cdbnd O stretching frequency is appreciable red-shifted in the complexes as compared to uncoordinated lapachol ligand. As expected, the IR and UV-Vis spectra of the isomorphous pair of complexes closely resemble to each other. Up to above 300 °C there are significant differences in the TGA of the Zn complex when compared with the isomorphous pair: while the former shows the loss of the secondary ligands (water and DMF), the latter exhibits a plateau signaling the lesser labile character of the lapacholate ligand.

  4. 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

  5. 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.

  6. Synthesis, crystal structure, spectroscopic properties, DFT calculation and biological activity of 4-chloro-N-(2-(2-nitrophenyl)acetoxy)-N-phenylbenzamide

    NASA Astrophysics Data System (ADS)

    He, Dian; Yang, Zhu-Qing; Hou, Meng; Teng, Chong; Wang, Xiao-Hong

    2014-11-01

    4-Chloro-N-(2-(2-nitrophenyl)acetoxy)-N-phenylbenzamide was synthesized and characterized by 1H NMR, 13C NMR, MS, IR and X-ray diffraction methods. The structure-property relationship and the antitumor activity based on electrochemical measurements, density functional theory calculations (DFT) and methylthiazolyldiphenyl-tetrazolium bromide (MTT) assay were investigated. The crystal structure adopts monoclinic space group P21/n with the unit cell parameters of a = 12.4385(10) Å, b = 6.5036(5) Å, c = 24.7944(19) Å, β = 103.045(9)°, V = 1954.0(3) Å3, Z = 4, and stabilized by π-π conjugation and hydrogen bonding interactions. The observed results of the compound have been compared with theoretical results and it is found that the experimental data show good agreement with calculated values. And the compound had slightly better inhibition than suberoylanilide hydroxamic acid (SAHA) in NCI-H460 cell line as well as the nearly same as SAHA in MCF-7, HCT-116, PC-3, and A549 cell lines.

  7. 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.

  8. 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.

  9. 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

  10. Crystal structure, DFT, spectroscopic and biological activity evaluation of analgin complexes with Co(ii), Ni(ii) and Cu(ii).

    PubMed

    Mansour, Ahmed M

    2014-11-14

    Reaction of analgin (NaL) with Co(ii), Ni(ii) and Cu(ii) salts in ethanol affords complexes of the type [ML2], which were characterized by elemental analysis, FT IR, UV-Vis, EPR, TG/DTA, magnetic susceptibility and conductance measurements. The copper(ii) complex crystallizes in the orthorhombic Pbca space group. Analgin behaves as a mono-negatively tridentate ligand via pyrazolone O, sulfonate O and tertiary amino groups. The interaction of the tertiary nitrogen with M(n+) ions is the main factor which determines the stability of complexes as revealed from natural bond orbital analysis data, where the binding energy of [ML2] decreases with an increase in the bond length of the M-N bond. Time-dependent density functional theory calculations were applied in order to realize the electronic structures and to explain the related experimental observations. The anti-bacterial activity was studied on Staphylococcus aureus and Escherichia coli. Coordination of analgin to Ni(ii) and Cu(ii) leads to a significant increase in its antibacterial activity as compared with the Co(ii) complex. PMID:25231028

  11. Thermal, optical and spectroscopic characterizations of borate laser crystals

    SciTech Connect

    Chavoutier, M.; Jubera, V.; Veber, P.; Velazquez, M.; Viraphong, O.; Hejtmanek, J.; Decourt, R.; Debray, J.; Menaert, B.; Segonds, P.; Adamietz, F.; Rodriguez, V.; Manek-Hoenninger, I.; Fargues, A.; Descamps, D.; Garcia, A.

    2011-02-15

    The Yb-content Li{sub 6}Ln(BO{sub 3}){sub 3} (Ln: Gd, Y) solid solution has been investigated. Crystal growth has been successful for several compositions. A 22% molar content of ytterbium ions was determined by chemical analysis (ICP). Physical properties relevant to laser operation like mechanical hardness, thermal expansion and thermal conductivity were measured on single crystals. Optical measurements, including refractive index and low temperature spectroscopy, were also performed. Finally, the effect of the Y/Gd ratio is discussed. -- Graphical abstract: Several solid solutions of a rare earth borate were studied. The figure illustrates one of these single crystals obtained by Czochralski and shows thermal behaviour and absorption spectra at low temperature. Display Omitted Research highlights: {yields} We have grown by Czochralski method five Li{sub 6}Ln(BO{sub 3}){sub 3} (Ln=Y, Gd,Yb) single crystals. {yields} Chemical, physical and spectroscopic characteristics are reported. {yields} Data relevant to laser operation are listed.

  12. Tyrammonium 4-nitrophthalate dihydrate: structural and spectroscopic elucidation.

    PubMed

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

    2009-01-01

    Tyrammonium 4-nitrophthalate has been synthesized and its structural and spectroscopic properties elucidated by single-crystal X-ray diffraction, solid-state polarized IR-spectroscopy of oriented colloids in a nematic host, HPLC with tandem mass spectrometry (HPLC ESI-MSMS), and TGV and DSC methods. The compound crystallizes in the monoclinic P2(1)/c space group and its structure consists of a 3D network of molecules joined by intermolecular interactions with the participation of cations, anions and two solvent molecules. The tyrammonium cation adopts a T trans configuration with corresponding angles of phi (1) = 76.0(4) degrees, phi (2 )= 54.8(1) degrees and phi (3) = 63.4(1) degrees, respectively. In the 4-nitrophthalate anion, the COO(-) and COOH groups are turned off the plane of the benzene ring at angles of tau (1) = 88.1(5) degrees and tau (2)= 22.1(7) degrees, respectively. PMID:18188664

  13. 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.

  14. 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

  15. 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.

  16. 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.

  17. 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

  18. 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

  19. 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.

  20. Nanoscale Ice: Spectroscopic Ellipsometry of Epitaxially-Grown Crystals

    NASA Astrophysics Data System (ADS)

    Cumiskey, A.; Grippaldi, J.; Magee, N. B.

    2011-12-01

    A new laboratory technique has been developed to examine the surface characteristics and kinetics of ice crystals at the nanoscale. Uncertainties remain regarding the fundamental physics of nucleation and depositional growth in atmospheric ice crystals. These molecular-scale uncertainties propagate upward into modeling outcomes at all scales of atmospheric interest: particle models, cloud models, mesoscale models, and climate models. Molecular-scale growth mechanisms and kinetics have been mainly inferred from bulk and particle-scale experiments as well as crystal-growth theory. The precarious nature of the ice surface resisted the first generation of direct nanoscale probing technologies, but new in-situ techniques including ESEM, AFM, and ellipsometry promise to divulge a wealth of new knowledge. Spectroscopic ellipsometry measures changes in the polarization state of light as it reflects off the surface of a thin film. This non-destructive technique is capable of measuring layer thicknesses as small as a single monolayer (~1 Å) and up to thicknesses of ~10 μm. Other physical parameters including index of refraction and surface roughness are also accessible. At the TCNJ Cloud Physics Laboratory, a Horiba Scientific Auto-SE ellipsometer (440 - 1000 nm spectral range) has been adapted for in-situ measurements of ice crystals. The ice crystals are grown epitaxially on various horizontal substrates in a custom-built static diffusion chamber. The diffusion chamber is housed within a vacuum chamber and an optical path is provided from the ellipsometer light source to sample stage and back to the ellipsometer analyzer at 75° from normal. The diffusion chamber is cooled in two stages, with initial cooling accomplished with a fluid-chilled block and final chilling controlled by two independent thermoelectric cells. A wide range of temperatures, pressures, and saturation ratios are accessible: from 0°C to -30°C, 50mb to atmospheric pressure, and from subsaturated to

  1. Melt Structure and Properties: a Spectroscopic Perspective

    NASA Astrophysics Data System (ADS)

    Stebbins, J.

    2006-12-01

    Entropy, volume, and their P/T derivatives are at the heart of models of the thermodynamics of silicate melts and magmas. Quantitative characterization of glass structure is leading to important new insights into the links from "Microscopic to Macroscopic" that can at least guide interpretations of data and in some cases even have predictive power. A few recent examples will be discussed here. The often-large configurational components to heat capacities, thermal expansivities, and compressibilities of melts strongly indicate that structural changes with temperature and pressure are of key importance. At least some aspects of thermal increases in configurational (as opposed to vibrational) disorder are amenable to spectroscopic detection, either with in situ methods or on glasses with varying quench rates and thus varying fictive temperatures. In some systems, such changes are now clear, and can be shown to make significant contributions to properties. These include network cation coordination in systems such as borate liquids (BO4 to BO3 at higher T), and Al-Si disordering in aluminosilicates. In general, however, progress in this rich problem has only begun. It has long been suspected from thermodynamic analyses (and theoretical simulations) that configurational changes in melts play a key role in volume compression at high pressure, over and above that which can be expressed in "normal" equations of state or from those expected from bond compression and bending. Scattering and spectroscopic studies have revealed some of the important aspects of pressure-induced structural changes, but again we are just at the beginning of full understanding. For example, binary silicate glasses quenched from high-P melts clearly record some systematic increases in Si coordination, while aluminosilicates record systematic pressure and compositional (modifier cation field strength) effects on Al coordination in recovered samples with large, quenched-in density increases

  2. Synthesis, spectroscopic, X-ray crystal structure, biological and DNA interaction studies of organotin(IV) complexes of 2-(4-ethoxybenzylidene) butanoic acid.

    PubMed

    Tariq, Muhammad; Muhammad, Niaz; Ali, Saqib; Shirazi, Jafir Hussain; Tahir, Muhammad Nawaz; Khalid, Nasir

    2014-03-25

    Six organotin(IV) carboxylates of the type R2SnL2 [R=CH3 (1), n-C4H9 (2), n-C8H17 (3)] and R3SnL [R=CH3 (4), n-C4H9 (5), C6H5 (6), where L=2-(4-ethoxybenzylidene) butanoic acid, have been synthesized and characterized by elemental analysis, FT-IR and NMR ((1)H, (13)C). The complex (1) was also analyzed by single crystal X-ray analysis. The complexes were screened for antimicrobial, cytotoxic and anti-tumor activities. The results showed significant activity in each area of the activity with few exceptions. DNA interactions studies of ligand HL and representative complex 2 were investigated by UV-Visible absorption spectroscopy and viscosity measurements. The results showed that both ligand HL and complex 2 interact with SS-DNA via intercalation as well as minor groove binding. PMID:24322756

  3. 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.

  4. 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.

  5. Spectroscopic characterization of Er-doped KPb 2Cl 5 laser crystals

    NASA Astrophysics Data System (ADS)

    Jenkins, N. W.; Bowman, S. R.; O'Connor, S.; Searles, S. K.; Ganem, Joseph

    2003-06-01

    A discussion of the spectroscopic properties of the low-phonon energy laser host material potassium lead chloride, KPb 2Cl 5, doped with trivalent erbium is presented. In this paper we present room temperature spectroscopic measurements and subsequent analysis based on the Judd-Ofelt model. Additionally, Stark level energies of the Er 3+ ions in the crystal were determined from spectroscopic measurements performed at cryogenic temperatures.

  6. 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.

  7. 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.

  8. 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.

  9. Investigation of spectroscopic properties of LiNbO3:Ho3+ crystals

    NASA Astrophysics Data System (ADS)

    Demirkhanyan, Hasmik G.

    2016-01-01

    In this paper the Stark problem for Ho3+ ion (4f10 electronic configuration) in LiNbO3 crystal is solved. Main spectroscopic parameters induced by inter-Stark transitions are determined. Based on analysis of experimental and theoretical data of the main spectroscopic characteristics of LiNbO3:Ho3+ crystals, it's perceptiveness as a material for optical cooling devices is shown.

  10. Photonic Crystal Laser Accelerator Structures

    SciTech Connect

    Cowan, Benjamin M

    2003-05-21

    Photonic crystals have great potential for use as laser-driven accelerator structures. A photonic crystal is a dielectric structure arranged in a periodic geometry. Like a crystalline solid with its electronic band structure, the modes of a photonic crystal lie in a set of allowed photonic bands. Similarly, it is possible for a photonic crystal to exhibit one or more photonic band gaps, with frequencies in the gap unable to propagate in the crystal. Thus photonic crystals can confine an optical mode in an all-dielectric structure, eliminating the need for metals and their characteristic losses at optical frequencies. We discuss several geometries of photonic crystal accelerator structures. Photonic crystal fibers (PCFs) are optical fibers which can confine a speed-of-light optical mode in vacuum. Planar structures, both two- and three-dimensional, can also confine such a mode, and have the additional advantage that they can be manufactured using common microfabrication techniques such as those used for integrated circuits. This allows for a variety of possible materials, so that dielectrics with desirable optical and radiation-hardness properties can be chosen. We discuss examples of simulated photonic crystal structures to demonstrate the scaling laws and trade-offs involved, and touch on potential fabrication processes.

  11. 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.

  12. Raman spectroscopic studies of Nd0.75Sm0.25GaO3 single crystals

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

    Single crystals of Nd1-xSmxGaO3 (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-1.

  13. Crystal structure, spectroscopic, magnetic and electronic structure studies of a novel Cu(II) amino acid complex [Cu(L-arg)2(H2O)]2(P4O12)·8H2O

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

    Single crystals of a novel copper (II) complex with the amino acid L-arginine (L-arg) and cyclotetraphosphate, [Cu(L-arg)2(H2O)]2(P4O12)·8H2O, 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)2(H2O)]24+ cation and an uncoordinated cyclotetraphosphate counter-anion (P4O124-). 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 (TN) lower than 2 K. The values of paramagnetic Curie-Weiss temperature (θcw) and the exchange parameter (J/KB) emphasize the existence of an antiferromagnetic interaction between the neighboring copper ions.

  14. 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)

  15. 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.

  16. 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

  17. 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.

  18. Spectroscopic ellipsometry study of Cu2ZnSnSe4 bulk crystals

    NASA Astrophysics Data System (ADS)

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

    2014-08-01

    Using spectroscopic ellipsometry we investigated and analyzed the pseudo-optical constants of Cu2ZnSnSe4 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 E0, E1A, and E1B 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. Concerning inorganic crystal structure types.

    PubMed

    Bergerhoff; Berndt; Brandenburg; Degen

    1999-04-01

    All representatives of an inorganic crystal structure type can be found systematically in the new database SICS (Standardized Inorganic Crystal Structures). It is derived from the Inorganic Crystal Structure Database (ICSD) by selecting the best determination of each phase. In addition, each entry is given in a standardized description and complemented by searchable descriptors Delta, which give the difference between all structures of an isopointal set. Because of the large number of structures the full information on relationships present can only be found by means of the new database itself. Some examples are given here in printed form. The limitations and the possibilities of expansion of SICS in terms of the concept of 'structure types' are demonstrated. PMID:10927350

  20. Synthesis, crystal structure and vibrational spectroscopic analysis of tetrakis(5-amino-1-H-1,2,4-triazol-4-ium) decachlorodibismuthate(III):[C2H5N4]4Bi2Cl10

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

    Physico-chemical properties of a new organic bismuthate(III), [C2H5N4]4Bi2Cl10 are discussed on the basis of X-ray crystal structure investigation. This compound crystallizes in the monoclinic space group C2/c, with a = 16.3622(3), b = 12.7941(2), c = 14.8178(2) Å, β = 98.5660(10)°, V = 3067.35(8) Å3 and Z = 4. The crystal structure consists of discrete binuclear [Bi2Cl10]4- anions and 3-amino-1-H-1,2,4-triazolium cations. The crystal packing is governed by strong Nsbnd H⋯N and weak Nsbnd H⋯Cl hydrogen bonds and Π-Π stacking interactions to form three-dimensional network. The 13C CP-MAS NMR spectrum is in agreement with the X-ray structure. The infrared study confirms the presence of the organic cation [C2H5N4]+. The vibrational absorption bands were identified by infrared spectroscopy and DFT calculations allowed their attribution.

  1. 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.

  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. Crystal structure of triclopyr

    PubMed Central

    Cho, Seonghwa; Kim, Jineun; Jeon, Youngeun; Kim, Tae Ho

    2014-01-01

    In the title compound {systematic name: 2-[(3,5,6-tri­chloro­pyridin-2-yl)­oxy]acetic acid}, the herbicide triclopyr, C7H4Cl3NO3, the asymmetric unit comprises two independent mol­ecules in which the dihedral angles between the mean plane of the carb­oxy­lic acid group and the pyridyl ring plane are 79.3 (6) and 83.8 (5)°. In the crystal, pairs of inter­molecular O—H⋯O hydrogen bonds form dimers through an R 2 2(8) ring motif and are extended into chains along [100] by weak π–π inter­actions [ring centroid separations = 3.799 (4) and 3.810 (4) Å]. In addition, short inter­molecular Cl⋯Cl contacts [3.458 (2) Å] connect the chains, yielding a two-dimensional architecture extending parallel to (020). The crystal studied was found to be non-merohedrally twinned with the minor component being 0.175 (4). PMID:25309266

  4. Crystal structure of triclopyr.

    PubMed

    Cho, Seonghwa; Kim, Jineun; Jeon, Youngeun; Kim, Tae Ho

    2014-09-01

    In the title compound {systematic name: 2-[(3,5,6-tri-chloro-pyridin-2-yl)-oxy]acetic acid}, the herbicide triclopyr, C7H4Cl3NO3, the asymmetric unit comprises two independent mol-ecules in which the dihedral angles between the mean plane of the carb-oxy-lic acid group and the pyridyl ring plane are 79.3 (6) and 83.8 (5)°. In the crystal, pairs of inter-molecular O-H⋯O hydrogen bonds form dimers through an R 2 (2)(8) ring motif and are extended into chains along [100] by weak π-π inter-actions [ring centroid separations = 3.799 (4) and 3.810 (4) Å]. In addition, short inter-molecular Cl⋯Cl contacts [3.458 (2) Å] connect the chains, yielding a two-dimensional architecture extending parallel to (020). The crystal studied was found to be non-merohedrally twinned with the minor component being 0.175 (4). PMID:25309266

  5. The First Mammalian Aldehyde Oxidase Crystal Structure

    PubMed Central

    Coelho, Catarina; Mahro, Martin; Trincão, José; Carvalho, Alexandra T. P.; Ramos, Maria João; Terao, Mineko; Garattini, Enrico; Leimkühler, Silke; Romão, Maria João

    2012-01-01

    Aldehyde oxidases (AOXs) are homodimeric proteins belonging to the xanthine oxidase family of molybdenum-containing enzymes. Each 150-kDa monomer contains a FAD redox cofactor, two spectroscopically distinct [2Fe-2S] clusters, and a molybdenum cofactor located within the protein active site. AOXs are characterized by broad range substrate specificity, oxidizing different aldehydes and aromatic N-heterocycles. Despite increasing recognition of its role in the metabolism of drugs and xenobiotics, the physiological function of the protein is still largely unknown. We have crystallized and solved the crystal structure of mouse liver aldehyde oxidase 3 to 2.9 Å. This is the first mammalian AOX whose structure has been solved. The structure provides important insights into the protein active center and further evidence on the catalytic differences characterizing AOX and xanthine oxidoreductase. The mouse liver aldehyde oxidase 3 three-dimensional structure combined with kinetic, mutagenesis data, molecular docking, and molecular dynamics studies make a decisive contribution to understand the molecular basis of its rather broad substrate specificity. PMID:23019336

  6. Mono- and binuclear Pd(II) complexes with 2-(5,6-dimethyl-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidin-2-yl)-N-phenylhydrazinecarbothioamide: Synthesis, crystal structure and spectroscopic characterization

    NASA Astrophysics Data System (ADS)

    Repich, Hlib; Orysyk, Svitlana; Bon, Volodymyr; Savytskyi, Pavlo; Pekhnyo, Vasyl

    2015-12-01

    Two novel Pd2+ mononuclear [Pd(HL)PPh3Cl]·nDMF (1) (n = 1, 2) and binuclear [Pd2(L)2(PPh3)2]·SPPh3·3DMF (2) complexes have been synthesized by reaction of [Pd(PPh3)2Cl2] with 2-(5,6-dimethyl-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidin-2-yl)-N-phenylhydrazinecarbothioamide and characterized by single-crystal X-ray diffraction. Complex 1 has been additionally characterized by 1H NMR, IR and UV-Vis spectroscopy. For the complex 1, two crystalline polymorphic modifications have been found: monoclinic (1a) and more stable triclinic (1b) one, which crystal structure differs by different crystal packing and number of lattice solvent molecules. In both polymorphs, the ligand molecules are coordinated as monoanion in thiol tautomeric form with transferring of thiosemicarbazide proton to nitrogen atom of thienopyrimidine moiety. In the case of complex 2, additional deprotonation of thienopyrimidine nitrogen atom leads to coordination of the ligand as dianion. The crystal structure of 2 also contains one molecule of triphenylphosphine sulfide formed by side reaction. In both complexes "soft" phosphorus atoms of triphenylphosphine molecules are coordinated in trans-positions to more "hard" nitrogen atoms.

  7. 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.

  8. Crystal structure refinement with SHELXL

    PubMed Central

    Sheldrick, George M.

    2015-01-01

    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. PMID:25567568

  9. 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.

  10. Thermal, optical and spectroscopic characterizations of borate laser crystals

    NASA Astrophysics Data System (ADS)

    Chavoutier, M.; Jubera, V.; Veber, P.; Velazquez, M.; Viraphong, O.; Hejtmanek, J.; Decourt, R.; Debray, J.; Menaert, B.; Segonds, P.; Adamietz, F.; Rodriguez, V.; Manek-Hönninger, I.; Fargues, A.; Descamps, D.; Garcia, A.

    2011-02-01

    The Yb-content Li 6Ln(BO 3) 3 ( Ln: Gd, Y) solid solution has been investigated. Crystal growth has been successful for several compositions. A 22% molar content of ytterbium ions was determined by chemical analysis (ICP). Physical properties relevant to laser operation like mechanical hardness, thermal expansion and thermal conductivity were measured on single crystals. Optical measurements, including refractive index and low temperature spectroscopy, were also performed. Finally, the effect of the Y/Gd ratio is discussed.

  11. Crystal structure of pyrazoxyfen

    PubMed Central

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

    2015-01-01

    The title compound, C20H16Cl2N2O3 (systematic name: 2-{[4-(2,4-di­chloro­benzo­yl)-1,3-di­methyl­pyrazol-5-yl}­oxy}-1-phenyl­ethan-1-one), is the benzoyl­pyrazole herbicide pyrazoxyfen. The asymmetric unit comprises two independent mol­ecules, A and B, in which the pyrazole ring makes dihedral angles of 80.29 (10) and 61.70 (10)° and 87.60 (10) and 63.92 (8)°, respectively, with the di­chloro­phenyl and phenyl rings. In the crystal, C—H⋯O and C—H⋯N hydrogen bonds, and C—H⋯π and π–π [3.646 (2) Å] inter­actions link adjacent mol­ecules, forming a two-dimensional network parellel to (011). In addition, the networks are linked by weak inter­molecular C—Cl⋯π [3.356 (2), 3.950 (2), 3.250 (2) and 3.575 (2) Å] inter­actions, resulting in a three-dimensional architecture. PMID:26870483

  12. Crystal structure of pyrazoxyfen.

    PubMed

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

    2015-12-01

    The title compound, C20H16Cl2N2O3 (systematic name: 2-{[4-(2,4-di-chloro-benzo-yl)-1,3-di-methyl-pyrazol-5-yl}-oxy}-1-phenyl-ethan-1-one), is the benzoyl-pyrazole herbicide pyrazoxyfen. The asymmetric unit comprises two independent mol-ecules, A and B, in which the pyrazole ring makes dihedral angles of 80.29 (10) and 61.70 (10)° and 87.60 (10) and 63.92 (8)°, respectively, with the di-chloro-phenyl and phenyl rings. In the crystal, C-H⋯O and C-H⋯N hydrogen bonds, and C-H⋯π and π-π [3.646 (2) Å] inter-actions link adjacent mol-ecules, forming a two-dimensional network parellel to (011). In addition, the networks are linked by weak inter-molecular C-Cl⋯π [3.356 (2), 3.950 (2), 3.250 (2) and 3.575 (2) Å] inter-actions, resulting in a three-dimensional architecture. PMID:26870483

  13. Spectroscopic characteristics of GdVO4: Dy3+ crystal

    NASA Astrophysics Data System (ADS)

    Ning, Kaijie; He, Xiaoming; Zhang, Lianhan; Liu, Youchen; Yin, Jigang; Zhang, Peixing; Chen, Guangzhu; Wang, Xiangyong; Chen, Zhe; Shi, Chunjun; Hong, Jiaqi; Hang, Yin

    2014-11-01

    Room temperature optical absorption, emission spectrum of GdVO4: Dy3+ crystal grown by Czochralski (CZ) method were measured and analyzed. Spectral parameters were calculated in the framework of the Judd-Ofelt theory. The GdVO4: Dy3+ crystal showed two intense and relatively broad absorption bands in UV wavelength range centered at 390 and 453 nm and two prominent emission peaks located at blue 485 and yellow 575 nm. The corresponding absorption and emission cross sections were estimated and the luminescence decay curve was analyzed. Optical spectroscopy investigations indicate that GdVO4: Dy3+ crystal would be a promising blue and yellow solid state laser material.

  14. 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. PMID:23160484

  15. 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.

  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. [Calculation of spectroscopic properties of Tm:YVO4 crystals].

    PubMed

    Song, Feng; Guo, Hong-cang; Zhang, Wan-lin; Zhang, Chao-bo; Shang, Mei-ru; Zhang, Guang-yin

    2002-02-01

    Sigma and pi polarized absorption spectra of Tm:YVO4 crystal have been measured at room temperature. Considering the difference of the sigma and pi polarized absorption spectra and the changing of the refractive index with different wavelengths, we calculate the intensity parameters of Tm3+ in crystal YVO4 which are omega 2 = 1.9416 x 10(-20) (cm2), omega 4 = 0.1568 x 10(-20) (cm2), omega 6 = 0.3963 x 10(-20) (cm2) by Judd-Ofelt theory. The spectra characteristic parameters, such as radiative transition rates, luminescence branching ratio, total radiative lifetime and integral cross-section are also calculated. The results show that the spontaneous rate of the transition 1D2-->3F4 is much higher than that of the transition 1D2 to other levels. PMID:12940012

  18. 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.

  19. 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

  20. 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].

  1. Crystal structure, spectroscopic properties, and magnetic behavior of the fluoride-derivatized lanthanoid(III) ortho-oxomolybdates(VI) LnF[MoO 4] ( Ln=Sm-Tm)

    NASA Astrophysics Data System (ADS)

    Hartenbach, Ingo; Strobel, Sabine; Dorhout, Peter K.; Schleid, Thomas

    2008-10-01

    The fluoride-derivatized lanthanoid(III) ortho-oxomolybdates(VI) LnF[MoO 4] ( Ln=Sm-Tm) crystallize in the monoclinic space group P2 1/ c with four formula units per unit cell ( a=516-528 pm, b=1220-1248 pm, c=659-678 pm, β=112.5-113.1°). The structure contains one crystallographically unique Ln3+ cation surrounded by two fluoride and six oxide anions in a square antiprism (CN=8). The square antiprisms [ LnF 2O 6] are interconnected via three edges to form layers ∞2{[LnF2/2eO4/2eO2/1t]} parallel (010), which are cross-linked along [010] by Mo 6+ in tetrahedral oxygen coordination to form the three-dimensional crystal structure. The fluoride anions within this arrangement exhibit a twofold coordination of Ln3+ cations in the shape of a boomerang, which is connected to another F - anion to form planar [F 2Ln2] 4+ rhombuses. Magnetic measurements for GdF[MoO 4], TbF[MoO 4], and DyF[MoO 4] show Curie-Weiss behavior, despite the peculiar arrangement of the lanthanoid(III) cations in layers comparable with those of gray arsenic. Furthermore, Raman, infrared, and diffuse reflectance spectroscopy data for these compounds were recorded and interpreted.

  2. Combining sequence-based prediction methods and circular dichroism and infrared spectroscopic data to improve protein secondary structure determinations

    PubMed Central

    Lees, Jonathan G; Janes, Robert W

    2008-01-01

    Background A number of sequence-based methods exist for protein secondary structure prediction. Protein secondary structures can also be determined experimentally from circular dichroism, and infrared spectroscopic data using empirical analysis methods. It has been proposed that comparable accuracy can be obtained from sequence-based predictions as from these biophysical measurements. Here we have examined the secondary structure determination accuracies of sequence prediction methods with the empirically determined values from the spectroscopic data on datasets of proteins for which both crystal structures and spectroscopic data are available. Results In this study we show that the sequence prediction methods have accuracies nearly comparable to those of spectroscopic methods. However, we also demonstrate that combining the spectroscopic and sequences techniques produces significant overall improvements in secondary structure determinations. In addition, combining the extra information content available from synchrotron radiation circular dichroism data with sequence methods also shows improvements. Conclusion Combining sequence prediction with experimentally determined spectroscopic methods for protein secondary structure content significantly enhances the accuracy of the overall results obtained. PMID:18197968

  3. First outer-sphere 1,3-diethyl-2-thiobarbituric compounds [M(H2O)6](1,3-diethyl-2-thiobarbiturate)2·2H2O (M = Co2+, Ni2+): Crystal structure, spectroscopic and thermal properties

    NASA Astrophysics Data System (ADS)

    Golovnev, Nicolay N.; Molokeev, Maxim S.; Lesnikov, Maxim K.; Atuchin, Victor V.

    2016-06-01

    Two new d-element compounds, [Co(H2O)6](Detba)2·2H2O (1) and [Ni(H2O)6](Detba)2·2H2O (2) (HDetba - 1,3-diethyl-2-thiobarbituric acid) were synthesized and characterized by single-crystal and powder X-ray diffraction analysis, TG-DSC and FT-IR. Structural analysis revealed that (1) and (2) are discrete structures, in which M2+ ion (M = Co, Ni) is six-coordinated by water molecules and it forms an octahedron. The outer-sphere Detba- ions and H2O molecules participate in Osbnd H⋯(O/S) intermolecular hydrogen bonds which form the 2D layer. Thermal decomposition includes the stage of dehydration and the following stage of oxidation of Detba- with a release of CO2, SO2, H2O, NH3 and isocyanate gases.

  4. 2D x-ray imaging spectroscopic diagnostics using convex bent crystal

    NASA Astrophysics Data System (ADS)

    Papp, Daniel; Presura, Radu; Wallace, Matt; Largent, Billy; Haque, Showera; Arias, Angel; Khanal, Vijay; Ivanov, Vladimir

    2013-10-01

    A new 2-dimensional time-integrated x-ray spectroscopic diagnostics technique was developed to create multi-monochromatic images of high-energy density Al plasmas. 2-dimensional is an advanced spectroscopic tool, providing a way to determine the spatial dependence of plasma temperature and density (Te and ne) in hot plasmas. The new technique uses the strong source broadening of convex cylindrically bent KAP crystal spectrometers, which contains spatial information along the dispersive direction. The perpendicular direction is imaged using a slit. The spatial resolution of the method is improved by the deconvolution of the source broadened line profiles from the lineshapes (recorded by the convex crystal spectrometer) with lineshapes of minimum instrumental broadening. The latter spectra were recorded with a concave cylindrically bent KAP crystal spectrometer, based on the Johann geometry. Spectroscopic model of the plasma x-ray emission was developed using the PrismSPECT code. The identification of suitable spectral features allows deriving Te and ne from line intensities. We applied this model to get temperature and density distribution maps for wire array z-pinch plasmas. Work supported by the DOE/NNSA under grant DE-NA0001834 and Cooperative Agreement DE-FC52-06NA27616.

  5. 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.

  6. 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.

  7. Growth and Raman spectroscopic characterization of As 4S 4 (II) single crystals

    NASA Astrophysics Data System (ADS)

    Kyono, Atsushi

    2010-11-01

    As described by Kutoglu (1976 [16]), single crystals of As 4S 4 (II) phase have been grown using a new two-step synthesis that drastically increases the reproducibility that is attainable in synthetic experiments. First, through photo-induced phase transformation, pararealgar powder is prepared as a precursor instead of AsS melt. Then it is dissolved and recrystallized from CS 2 solvent. Results show that single crystals of the As 4S 4 (II) phase were obtained reproducibly through the dissolution-recrystallization process. Single crystals of As 4S 4 (II) obtained using this method were translucent and showed a uniform yellow-orange color. The crystal exhibits a platelet-like shape as a thin film with well-developed faces (0 1 0) and (0 1¯ 0). The grown crystals are as large as 0.50×0.50×0.01 mm. They were characterized using powder and single crystal X-ray diffraction techniques to confirm the phase identification and the lattice parameters. The As 4S 4 (II) phase crystallizes in monoclinic system with cell parameters a=11.202(4) Å, b=9.954(4) Å, c=7.142(4) Å, β=92.81(4)°, V=795.4(6) Å 3, which shows good agreement with the former value. Raman spectroscopic studies elucidated the behavior of the substance and the relation among phases of tetra-arsenic tetrasulfide.

  8. 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.

  9. 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. PMID:16608282

  10. 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.

  11. 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.

  12. 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.

  13. Spectroscopic Properties of Neodymium-Doped Yttrium Orthovanadate Single Crystals with High-Resolution Measurement

    NASA Astrophysics Data System (ADS)

    Sato, Yoichi; Taira, Takunori

    2002-10-01

    The absorption and fluorescence spectra of the neodymium-doped yttrium orthovanadate (Nd:YVO4) single crystal were investigated carefully. For the 808.8-nm absorption cross section, the published values varied between 18.4 and 25.6 × 10-20 cm2 for π-polarization. The authors evaluated this spectroscopic parameter with high resolution at 0.5 nm, and discovered 48.4 cm-1 at 808.8 nm even for the absorption of 1 at.% Nd3+-ion-doped YVO4 single crystal. This value is 1.3 times larger than the well-known value, and confirms that Nd:YVO4 is very suitable for microchip lasers, and that certain laser characteristics of Nd:YVO4 of previous works should be re-evaluated.

  14. 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.

  15. [NiFe] hydrogenases: structural and spectroscopic studies of the reaction mechanism.

    PubMed

    Ogata, Hideaki; Lubitz, Wolfgang; Higuchi, Yoshiki

    2009-10-01

    [NiFe] hydrogenases catalyze the reversible oxidation of dihydrogen. For this simple reaction the molecule has developed a complex catalytic mechanism, during which the enzyme passes through various redox states. The [NiFe] hydrogenase contains several metal centres, including the bimetallic Ni-Fe active site, iron-sulfur clusters and a Mg(2+) ion. The Ni-Fe active site is located in the inner part of the protein molecule, therefore a number of pathways are involved in the catalytic reaction route. These consist of an electron transfer pathway, a proton transfer pathway and a gas-access channel. Over the last 10-15 years we have been investigating the crystal structures of the [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F, which is a sulfate-reducing anaerobic bacterium. So far the crystal structures of the oxidized, H(2)-reduced and carbon monoxide inhibited states have been determined at high resolution and have revealed a rather unique structure of the hetero-bimetallic Ni-Fe active site. Furthermore, intensive spectroscopic studies have been performed on the enzyme. Based on the crystal structure, a water-soluble Ni-Ru complex has been synthesized as a functional model for the [NiFe] hydrogenases. The present review gives an overview of the catalytic reaction mechanism of the [NiFe] hydrogenases. PMID:19759926

  16. 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

  17. The spectroscopic properties of Yb3+ doped α-BBO crystal

    NASA Astrophysics Data System (ADS)

    Yu, Pingsheng; Su, Liangbi; Wu, Feng; Xu, Jun

    2012-05-01

    2.0 mol% (relative to Ba2+) Yb3+ doped α-BaB2O4 (α-BBO) crystal was obtained by the Czochralski method. The doped crystal structure was determined by means of an X-ray diffraction analysis. The absorption, near-infrared (NIR) luminescence spectra and fluorescence decay curve of Yb3+ doped α-BBO crystal were investigated. NIR emission under 940 nm and 980 nm LDs (laser diodes) excitation was observed in the Yb doped α-BBO crystal.

  18. 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. PMID:25828887

  19. The molecular structure of chloritoid: A mid-infrared and near-infrared spectroscopic study

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

    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.

  20. Crystal structure of prethrombin-1

    SciTech Connect

    Chen, Zhiwei; Pelc, Leslie A.; Di Cera, Enrico

    2010-11-15

    Prothrombin is the zymogen precursor of the clotting enzyme thrombin, which is generated by two sequential cleavages at R271 and R320 by the prothrombinase complex. The structure of prothrombin is currently unknown. Prethrombin-1 differs from prothrombin for the absence of 155 residues in the N-terminal domain and is composed of a single polypeptide chain containing fragment 2 (residues 156-271), A chain (residues 272-320), and B chain (residues 321-579). The X-ray crystal structure of prethrombin-1 solved at 2.2-{angstrom} resolution shows an overall conformation significantly different (rmsd = 3.6 {angstrom}) from that of its active form meizothrombin desF1 carrying a cleavage at R320. Fragment 2 is rotated around the y axis by 29{sup o} and makes only few contacts with the B chain. In the B chain, the oxyanion hole is disrupted due to absence of the I16-D194 ion pair and the Na{sup +} binding site and adjacent primary specificity pocket are highly perturbed. A remarkable feature of the structure is that the autolysis loop assumes a helical conformation enabling W148 and W215, located 17 {angstrom} apart in meizothrombin desF1, to come within 3.3 {angstrom} of each other and completely occlude access to the active site. These findings suggest that the zymogen form of thrombin possesses conformational plasticity comparable to that of the mature enzyme and have significant implications for the mechanism of prothrombin activation and the zymogen {yields} protease conversion in trypsin-like proteases.

  1. 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.

  2. Spectroscopic and structural elucidation of amino acid derivatives and small peptides: experimental and theoretical tools.

    PubMed

    Kolev, Tsonko; Spiteller, Michael; Koleva, Bojidarka

    2010-01-01

    This mini review deals with the modern aspects of the spectroscopy and structural elucidation of amino acid derivatives and small biologically active compounds. Free peptide bond rotation in these systems yields various conformers, which possess differing biological activities. Another phenomenon is the intermolecular or intramolecular stacking observed in aromatic small peptides. Specifically, the main aim is to illustrate the successful application of the "complex tool", consisting of a combination of the theoretical approximation methods with experimental linear polarized infrared (IR-LD) and/or Raman spectroscopy of oriented colloid suspensions in a nematic host. The possibilities and limitations of the approach for detailed vibrational assignment and structural elucidation of small peptides are discussed. Having in mind that physical and chemical properties of these systems can be precisely calculated by means of ab initio and DFT methods at Hartee-Fock, MP2 and B3LYP level of theory, varying basis sets, the results obtained allow a precise assignment of many vibrational bands to the corresponding normal modes, electronic structures and conformational state. The validity of the conclusions about the structure or vibrational properties of these systems have been supported, compared and/or additionally proved by the results from independent physical methods. In this respect (1)H and (13)C-NMR, single crystal X-ray diffraction, HPLC tandem mass spectrometry as well as thermal methods are all employed. A well ordered crystal must first be grown in order to determine the molecular structure by the absolute method of single crystal X-ray diffraction. Although the 3D structures of peptides have been determined over the past decades, peptide crystallization is still a major obstacle to X-ray diffraction work, the presence of chiral centre/s makes for this difficulty. For this reason the "complex tool" presented can be regarded as an alternative method for obtaining of

  3. Photonic Crystal Laser-Driven Accelerator Structures

    SciTech Connect

    Cowan, B.; /SLAC

    2005-09-19

    We discuss simulated photonic crystal structure designs for laser-driven particle acceleration, focusing on three-dimensional planar structures based on the so-called ''woodpile'' lattice. We demonstrate guiding of a speed-of-light accelerating mode by a defect in the photonic crystal lattice and discuss the properties of this mode. We also discuss particle beam dynamics in the structure, presenting a novel method for focusing the beam. In addition we describe some potential coupling methods for the structure.

  4. Crystal structure of benzimidazolium salicylate

    PubMed Central

    Amudha, M.; Kumar, P. Praveen; Chakkaravarthi, G.

    2015-01-01

    In the anion of the title mol­ecular salt, C7H7N2 +·C7H5O3 − (systematic name: 1H-benzimidazol-3-ium 2-hy­droxy­ben­zo­ate), there is an intra­molecular O—H⋯O hydrogen bond that generates an S(6) ring motif. The CO2 group makes a dihedral angle of 5.33 (15)° with its attached ring. In the crystal, the dihedral angle between the benzimidazolium ring and the anion benzene ring is 75.88 (5)°. Two cations bridge two anions via two pairs of N—H⋯O hydrogen bonds, enclosing an R 4 4(16) ring motif, forming a four-membered centrosymmetric arrangement. These units are linked via C—H⋯O hydrogen bonds, forming chains propagating along the b-axis direction. The chains are linked by C—H⋯π and π–π inter­actions [inter-centroid distances = 3.4156 (7) and 3.8196 (8) Å], forming a three-dimensional structure. PMID:26594483

  5. Crystal structure of a perfect carbyne

    SciTech Connect

    Belenkov, E. A. Mavrinsky, V. V.

    2008-01-15

    The crystal structure of a perfect carbyne is calculated by the molecular mechanics methods. It is established that the carbyne crystals should consist of polycumulene chains arranged in hexagonal bundles. The unit cell of the perfect carbyne crystal is trigonal and contains one carbon atom. The unit cell parameters are as follows: a = b = c = 0.3580 nm, {alpha} = {beta} = {gamma} = 118.5{sup o}, and space group P3m1. The perfect carbyne single crystals have a stable structure at room temperature if the length of their constituent chains is larger than 500 nm.

  6. 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).)

  7. 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. PMID:27123546

  8. NMR-spectroscopic analysis of mixtures: from structure to function

    PubMed Central

    Forseth, Ry R.; Schroeder, Frank C.

    2010-01-01

    NMR spectroscopy as a particularly information-rich method offers unique opportunities for improving the structural and functional characterization of metabolomes, which will be essential for advancing the understanding of many biological processes. Whereas traditionally NMR spectroscopy was mostly relegated to the characterization of pure compounds, the last few years have seen a surge of interest in using NMR spectroscopic techniques for characterizing complex metabolite mixtures. Development of new methods was motivated partly by the realization that using NMR for the analysis of metabolite mixtures can help identify otherwise inaccessible small molecules, for example compounds that are prone to chemical decomposition and thus cannot be isolated. Furthermore, comparative metabolomics and statistical analyses of NMR-spectra have proven highly effective at identifying novel and known metabolites that correlate with changes in genotype or phenotype. In this review, we provide an overview of the range of NMR spectroscopic techniques recently developed for characterizing metabolite mixtures, including methods used in discovery-oriented natural product chemistry, in the study of metabolite biosynthesis and function, or for comparative analyses of entire metabolomes. PMID:21071261

  9. 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.

  10. Crystal structures of MBP fusion proteins.

    PubMed

    Waugh, David S

    2016-03-01

    Although chaperone-assisted protein crystallization remains a comparatively rare undertaking, the number of crystal structures of polypeptides fused to maltose-binding protein (MBP) that have been deposited in the Protein Data Bank (PDB) has grown dramatically during the past decade. Altogether, 102 fusion protein structures were detected by Basic Local Alignment Search Tool (BLAST) analysis. Collectively, these structures comprise a range of sizes, space groups, and resolutions that are typical of the PDB as a whole. While most of these MBP fusion proteins were equipped with short inter-domain linkers to increase their rigidity, fusion proteins with long linkers have also been crystallized. In some cases, surface entropy reduction mutations in MBP appear to have facilitated the formation of crystals. A comparison of the structures of fused and unfused proteins, where both are available, reveals that MBP-mediated structural distortions are very rare. PMID:26682969

  11. 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

  12. Synthesis, crystal structure, spectroscopic analysis and computational study of (Z)-1-(2,4-dinitrophenyl)-2-((E)-3-(4-methoxyphenyl)-1-(thiophen-2-yl) allylidene) hydrazine by DFT and AIM approach

    NASA Astrophysics Data System (ADS)

    Singh, Ashok Kumar; Singh, Ravindra Kumar

    2015-06-01

    The title compound was synthesized and characterized by IR, 1H NMR, 13C NMR and single crystal X-ray diffraction studies. Quantum chemical calculations have been performed at DFT level of theory using B3LYP functional and 6-31G(d,p) as basis set. Potential energy distribution (PED) for the normal modes of vibrations was done using Gar2ped program. The time dependent density functional theory (TD-DFT) was used to find the various electronic transitions within molecule in two different solvent of varying polarity. Non linear optical (NLO) behavior of title compound was investigated in different solvents by the computed value of first hyperpolarizability (β0). A combined theoretical and experimental correlation of 1H and 13C NMR spectra are in good agreement. Stability of molecules as a result of hyper-conjugative interactions and electron delocalization were analyzed using NBO analysis. The HOMO and LUMO analysis is used to determine the charge transfer within the molecule. Intramolecular interactions were analyzed by AIM approach. The chemical reactivity descriptors were calculated to study the reactive sites within molecule.

  13. A dielectric spectroscopic study of the disperse structure of asphaltene solutions at high pressures

    SciTech Connect

    Syunyaev, R.Z.; Sh. Abid, R.

    1994-03-01

    The disperse structure of oil asphaltenes in benzene and toluene solutions at different temperatures and concentrations were studied at pressures up to 1.0 GPa. The polarity of the asphaltene molecules allows the dielectric spectroscopic method to be used. A sharp increase in the relaxation time and the sizes of the asphaltene aggregates, calculated according to the Debye model near the phase transition point, were found in the benzene solution. The pressure value corresponding to crystallization is much higher in the toluene solution, and only the border region can be investigated. An explanation of the pressure dependences of the relaxation times are presented. The activation energies and the coefficients of isothermal compressibility are calculated.

  14. Crystal structure prediction of rigid molecules.

    PubMed

    Elking, Dennis M; Fusti-Molnar, Laszlo; Nichols, Anthony

    2016-08-01

    A non-polarizable force field based on atomic multipoles fit to reproduce experimental crystal properties and ab initio gas-phase dimers is described. The Ewald method is used to calculate both long-range electrostatic and 1/r(6) dispersion energies of crystals. The dispersion energy of a crystal calculated by a cutoff method is shown to converge slowly to the exact Ewald result. A method for constraining space-group symmetry during unit-cell optimization is derived. Results for locally optimizing 4427 unit cells including volume, cell parameters, unit-cell r.m.s.d. and CPU timings are given for both flexible and rigid molecule optimization. An algorithm for randomly generating rigid molecule crystals is described. Using the correct experimentally determined space group, the average and maximum number of random crystals needed to find the correct experimental structure is given for 2440 rigid single component crystals. The force field energy rank of the correct experimental structure is presented for the same set of 2440 rigid single component crystals assuming the correct space group. A complete crystal prediction is performed for two rigid molecules by searching over the 32 most probable space groups. PMID:27484371

  15. 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

  16. 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.

  17. Liquid crystal light valve structures

    NASA Technical Reports Server (NTRS)

    Koda, N. J. (Inventor)

    1985-01-01

    An improved photosensor film and liquid crystal light valves embodying said film is provided. The photosensor film and liquid crystal light valve is characterized by a significant lower image retention time while maintaining acceptable photosensitivity. The photosensor film is produced by sputter depositing CdS onto an ITO substrate in an atmosphere of argon/H2S gas while maintaining the substrate at a temperature in the range of about 130 C to about 200 C and while introducing nitrogen gas into the system to the extent of not more than about 1% of plasma mixture. Following sputter deposition of the CdS, the film is annealed in an inert gas at temperatures ranging from about 300 C to about 425 C.

  18. 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.

  19. 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

  20. Pholcodine monohydrate: Crystal structure and polymorphism

    NASA Astrophysics Data System (ADS)

    Petruševski, Gjorgji; Zbačnik, Marija; Kajdžanoska, Marina; Ugarkovic, Sonja; Trimčeski, Vase; Kaitner, Branko; Jovanovski, Gligor; Makreski, Petre

    2013-07-01

    The first crystal structure elucidation of pholcodine monohydrate, an important antitussive active pharmaceutical ingredient is reported herein. The studied compound crystallizes in the orthorhombic system in the space group P212121. Each H2O molecule is shared by two pholcodine molecules via three strong hydrogen bonds. The detailed crystallization screening from several different organic solvents afforded single crystals with various quality, all exhibiting prism-to-needlelike micro morphology. The investigation of the obtained single crystals by means of several physico-chemical, solid-state instrumental techniques (FT-IR, DSC, TG/DTG and XRPD) proved that pholcodine monohydrate exists in a single crystalline modification, identical to the commercial form of the compound.

  1. 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. PMID:26529434

  2. Spectroscopic characterization of Ti-doped α-ZnAl2S4 spinel-type single crystals

    NASA Astrophysics Data System (ADS)

    Anghel, Sergiu; Boulon, Georges; Brenier, Alain; Fortin, Emery; Klokishner, Sophia; Koshchug, Dmitrii; Kulyuk, Leonid; Sushkevich, Konstantin

    2010-02-01

    The spectroscopic characteristics of the α-ZnAl2S4 wide bandgap semiconductor doped with Ti ions are investigated. It is shown, that the ZnAl2S4:Ti spinel-type crystals exhibit luminescence in the IR spectral range 0.8-1.4 µm. The observed spectroscopic characteristics are assigned to the emission bands arising from the ligand -Ti4+ charge transfer for octahedral sites of titanium that is in agreement with the experimental evidence for the absence of the EPR signal from Ti ions. A qualitative explanation of the experimental data is given.

  3. Spectroscopic characterization of Ti-doped α-ZnAl2S4 spinel-type single crystals.

    PubMed

    Anghel, Sergiu; Boulon, Georges; Brenier, Alain; Fortin, Emery; Klokishner, Sophia; Koshchug, Dmitrii; Kulyuk, Leonid; Sushkevich, Konstantin

    2010-02-10

    The spectroscopic characteristics of the α-ZnAl(2)S(4) wide bandgap semiconductor doped with Ti ions are investigated. It is shown, that the ZnAl(2)S(4):Ti spinel-type crystals exhibit luminescence in the IR spectral range 0.8-1.4 µm. The observed spectroscopic characteristics are assigned to the emission bands arising from the ligand -Ti(4+) charge transfer for octahedral sites of titanium that is in agreement with the experimental evidence for the absence of the EPR signal from Ti ions. A qualitative explanation of the experimental data is given. PMID:21386352

  4. 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.

  5. 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}.

  6. Structural complexity and configurational entropy of crystals.

    PubMed

    Krivovichev, Sergey V

    2016-04-01

    Using a statistical approach, it is demonstrated that the complexity of a crystal structure measured as the Shannon information per atom [Krivovichev (2012). Acta Cryst. A68, 393-398] represents a negative contribution to the configurational entropy of a crystalline solid. This conclusion is in full accordance with the general agreement that information and entropy are reciprocal variables. It also agrees well with the understanding that complex structures possess lower entropies relative to their simpler counterparts. The obtained equation is consistent with the Landauer principle and points out that the information encoded in a crystal structure has a physical nature. PMID:27048729

  7. Crystal structure of anagyrine perchlorate.

    PubMed

    Turgunov, Kambarali K; Rakhimov, Shukhrat B; Vinogradova, Valentina I; Tashkhodjaev, Bakhodir

    2015-05-01

    The title mol-ecular salt, C15H21N2O(+)·ClO4 (-), crystallizes with four cations (A, B, C and D) and four anions in the chiral unit cell (space group P21). The alkaloid was isolated from the aerial parts of Genista Hispanica collected in the Samarkand region of Uzbekistan. Each cation is protonated at the N atom that bridges the alkaloid rings C and D. In each cation, ring A is almost planar and ring B adops a sofa conformation with the methyl-ene group bridging to the C ring as the flap. Rings C and D adopt chair conformations with a cis ring junction in all four cations. In the crystal, A+B and C+D dimeric pairs linked by pairs of N-H⋯O hydrogen bonds are observed, which generate R 2 (2)(16) loops in each case. The dimers are consolidated by weak aromatic π-π stacking inter-actions between the A rings [centroid-centroid distances = 3.913 (3) and 3.915 (3) Å]. PMID:25995939

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

    PubMed

    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 250-1100nm. 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. PMID:25498813

  9. 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.

  10. Spectroscopic and structural elucidation of merocyanine dye 2,5-[1-metyl-4-[2-(4-hydroxyphenyl)ethenyl)]piridinium]-hexane tetraphenylborate aggregation processes.

    PubMed

    Koleva, Bojidarka B; Stoyanov, Stanimir; Kolev, Tsonko; Petkov, Ivan; Spiteller, Michael

    2008-12-01

    Structural and spectroscopic elucidation of merocyanine dye, 2,5-[1-metyl-4-[2-(4-hydroxyphenyl)ethenyl)]piridinium]-hexane tetraphenylborate, is performed in gas and condense phase by means of solution and solid-state conventional and linear-polarized IR-spectroscopy of oriented colloids in nematic liquid crystal suspension, UV-vis and fluorescence methods, HPLC MS/MS tandem and ESI mass spectrometry, (1)H, (13)C and (1)H-(1)H COSY NMR, TGV and DSC methods. Quantum chemical DFT calculations are performed for structural optimization and spectroscopic properties prediction. PMID:18400554

  11. Spectroscopic and structural elucidation of merocyanine dye 2,5-[1-metyl-4-[2-(4-hydroxyphenyl)ethenyl)]piridinium]-hexane tetraphenylborate. Aggregation processes

    NASA Astrophysics Data System (ADS)

    Koleva, Bojidarka B.; Stoyanov, Stanimir; Kolev, Tsonko; Petkov, Ivan; Spiteller, Michael

    2008-12-01

    Structural and spectroscopic elucidation of merocyanine dye, 2,5-[1-metyl-4-[2-(4-hydroxyphenyl)ethenyl)]piridinium]-hexane tetraphenylborate, is performed in gas and condense phase by means of solution and solid-state conventional and linear-polarized IR-spectroscopy of oriented colloids in nematic liquid crystal suspension, UV-vis and fluorescence methods, HPLC MS/MS tandem and ESI mass spectrometry, 1H, 13C and 1H- 1H COSY NMR, TGV and DSC methods. Quantum chemical DFT calculations are performed for structural optimization and spectroscopic properties prediction.

  12. Raman Spectroscopic Studies on L-histidine, aniline Doped Triglycine Sulphate Single Crystals

    NASA Astrophysics Data System (ADS)

    Benial, A. Milton Franklin; Ramakrishnan, V.; Parameswari, A.

    2015-02-01

    Single crystals of triglycine sulphate (TGS) doped with L-histidine and aniline were studied by Raman Spectroscopy. The structure and symmetry of molecules, the nature of bonding and the effect of crystalline field on molecular vibrations were studied for pure and doped TGS. The characteristic group frequencies were identified and analysed for H2SO4 and glycine. The skeletal motion, lattice vibrational peaks were observed in the low wavenumber region. The site symmetry effect and the correlation field effect were studied from the splitting of vibrational bands. The observed Raman shift towards higher wave number region reveals that the symmetry reduction in doped TGS crystals. The broadening of Raman spectral line showed that a decrease in the hardness value for the doped crystals. Comparative studies of the Raman Spectra of pure TGS and doped TGS were also carried out.

  13. An Integrated Ultrafast Scanning Calorimetric and Micro Raman Spectroscopic Investigation of Polymer Crystallization

    NASA Astrophysics Data System (ADS)

    Zhou, Dongshan; Wei, Lai; Jiang, Jing; Xue, Gi; Wang, Xiaoliang

    2014-03-01

    Ultrafast differential scanning calorimetry (UFDSC) with scanning rate up to 1,000,000 K/s has already been used to study the kinetics of crystallization and phase transition of some polymers and liquid crystal. Recently, we developed stage type UFDSC (ST-UFDSC) with comparable controlled heating and cooling rates. ST-UFDSC enables sample treatment and measurement integrated with microstructural characterization. As an example, we investigated the Raman spectroscopy of PET at different crystallization stage obtained by programed rapid cooling and heating processes. Although the Raman spectroscopy is not acquired during rapid heat treatments, the structure is assumed to remain by ultrafast quench below the glass transition temperature, when the Raman spectroscopy is collected. We expect that the combination technique can be also used to investigate dynamic relaxation behaviors of metastable states obtained by ultrafast heat treatments. This work has been supported by NNSFC (Nos. 21027006 and 21274059) and 973 program, No. 2012CB821500).

  14. 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

  15. 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

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

    USGS Publications Warehouse

    Evans, H.T., Jr.; 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

  17. 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.

  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. 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

  20. Crystal structure of levomepromazine maleate

    PubMed Central

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

    2016-01-01

    The asymmetric unit of the title salt, C19H25N2OS+·C4H3O4 − [systematic name: (S)-3-(2-meth­oxy­pheno­thia­zin-10-yl)-N,N,2-tri­methyl­propanaminium 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 meth­oxy substituent at the pheno­thia­zine ring system. The crystal components form a three-dimensional supra­molecular network via N—H⋯O, C—H⋯O and C—H⋯π inter­actions. A comparison of the conformations of the levomepromazine cations with those of the neutral mol­ecule and similar protonated mol­ecules reveals significant conformational flexibility of the pheno­thia­zine ring system and the substituent at the pheno­thia­zine N atom. PMID:27308001

  1. 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. PMID:26666777

  2. 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

  3. 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

  4. 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).

  5. Polariton effect on the IR spectroscopic properties of crystals with symmetric O·H·O hydrogen bonds

    NASA Astrophysics Data System (ADS)

    Barabash, A.; Gavrilko, T.; Krasnoholovets, V.; Puchkovskaya, G.

    1997-12-01

    We propose a new approach to the band shape formation in crystals with strong symmetric hydrogen bonds. Our consideration is based on the assumption that the interaction between the incident light applied to the crystal and polarized optical photons is stronger than that between molecular excitations and the photons. In this case the formation of polaritons takes place and hence molecular excitations begin to interact with the polaritons. As a result, a new kind of correction to the absorption coefficient caused by the beam of the spectroscopic instrument appears. The complete band shape of the OH stretching band is computed. A comparison with the available experimental data is carried out.

  6. A Raman spectroscopic and electrochemical study of the photoinduced crystallization of triethylenediamine triiodide upon a silver electrode

    NASA Astrophysics Data System (ADS)

    Ozek, Toru; Irish, Donald E.

    1991-02-01

    When a silver electrode, electrochemically coated with AgI, is immersed in an electrolyte containing NaI and the diprotonated form of 1,4-diazabicyclo 2.2.2 octane (abbreviated DABCO-H22+), and is bathed in 514.5 nm radiation from an argon ion laser through the objective of the microscope attachment of the DILOR Omars-89 Raman spectrophotometer, crystals form from the focal point. These are attributed to DABCO-h22+ 213-. Both spectroscopic and electrochemical experiments are described and interrelated. A mechanism for this photoinduced electrochemical crystal growth is presented.

  7. New pressure-induced phase transitions of L-threonine crystal: A Raman spectroscopic study

    NASA Astrophysics Data System (ADS)

    Holanda, R. O.; Lima, J. A.; Freire, P. T. C.; Melo, F. E. A.; Mendes Filho, J.; Polian, A.

    2015-07-01

    L-threonine crystal was studied by Raman spectroscopy under pressure in the spectral range from 50 to 3300 cm-1. The pressure range of a previous study has been extended from 4 to 27.0 GPa. Modifications in the whole spectrum give us evidence of three structural phase transitions undergone by this amino acid as well as two conformational change. The classification of the vibrational modes and the behavior of their frequencies as a function of the pressure are presented.

  8. 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.

  9. Synthesis, growth, crystal structure and characterization of a new organic NLO crystal: L-Lysine 4-nitrophenolate monohydrate (LLPNP)

    NASA Astrophysics Data System (ADS)

    Mahadevan, M.; Magesh, M.; Ramachandran, K.; Anandan, P.; Arivanandhan, M.; Hayakawa, Y.

    2014-09-01

    L-Lysine 4-nitrophenolate monohydrate (LLPNP) has been synthesized and grown by solution growth method at room temperature using deionised water as a solvent. The crystal structure of the materials was solved by single crystal X-ray diffraction analysis and it was found that the material has orthorhombic system. The crystallinity of the grown crystals was studied by the powder X-ray diffraction analysis. Molecular structure of the grown crystal was investigated by 1H NMR spectroscopy. The various functional groups of the sample were identified by Fourier transform infrared and Fourier transform-Raman spectroscopic analyses. Thermal stability of the grown crystal has been studied by Thermogravimetric and Differential thermal (TG&DTA) analysis. The optical absorption of the grown crystals has been ascertained by UV-Vis-NIR absorption studies. Second harmonic generation (SHG) efficiency of the material has been determined by Kurtz and Perry technique and the efficiency was found to be 4.45 and 1.4 times greater than that of standard KDP and urea samples, respectively.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. Spectroscopic, structural and theoretical investigation of bis(4-trimethylammoniumbenzoate) hydroiodide hydrate

    NASA Astrophysics Data System (ADS)

    Komasa, Anna; Katrusiak, Andrzej; Kaźmierczak, Michał; Dega-Szafran, Zofia; Szafran, Mirosław

    2015-02-01

    The structure of bis(4-trimethylammoniumbenzoate) hydroiodide hydrate 1 has been studied by X-ray diffraction, B3LYP/6-311G(d,p) calculations, FTIR, Raman and NMR spectroscopic techniques. The crystal is polar in monoclinic space group Cc. Two 4-trimethylammoniumbenzoate moieties are joined by a short and asymmetric hydrogen bond of 2.45(2) Å. Water molecules are gradually released from the structure, causing shifts in the position of iodine anions, which induces their disorder. The water molecule interacts with 4-trimethylammoniumbenzoate moiety and iodide anion via two O(3)-H(1)⋯O(1) and O(3)-H(2)⋯I(1) hydrogen bonds of lengths 2.70(3) and 3.51(1) Å. Hydrogen bonds in theoretically predicted structures of 2 and 3 (in vacuum), and 4, 5 (in DMSO) optimized by the B3LYP/6-311G(d,p) approach are slightly longer than in crystal 1. The FTIR spectrum of 1 shows a broad and intense absorption in the 1500-400 cm-1 region, typical of short hydrogen bonds assigned to the νas(OHO) + γ(OHO) vibrations. The correlations between the experimental 13C and 1H chemical shifts (δexp) of the investigated compound in DMSO and the GIAO/B3LYP/6-311G(d,p) magnetic isotropic shielding constants (σcalc) calculated by using the screening solvation model (COSMO) are linear, δexp = a + b σcalc, and they well reproduce the experimental chemical shifts.

  20. 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.

  1. Growth and spectroscopic characterization of Pb2+:CaF2 crystals

    NASA Astrophysics Data System (ADS)

    Nicoara, I.; Paraschiva, M.; Stef, M.; Stef, F.

    2012-08-01

    CaF2 crystals doped with various concentrations of PbF2 (0.4, 0.5, 1 and 2 mol%) were grown in vacuum, in a shaped graphite furnace using the vertical Bridgman method. The optical absorption spectra reveal the four characteristic UV absorption bands (labeled A, B, C and D) of the Pb2+ ions. As the PbF2 concentration increases, the structure of the bands become clearly visible, that is characteristic for the ns 2 ions in various hosts. High intensity emission bands in the near UV spectral region have been observed. The dependence on the Pb2+ concentration of the optical absorption and emission of the Pb2+:CaF2 crystals were not reported before.

  2. 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.

  3. Absorption enhancement in graphene photonic crystal structures.

    PubMed

    Khaleque, Abdul; Hattori, Haroldo T

    2016-04-10

    Graphene, a single layer of carbon atoms arranged in a honeycomb lattice, is attracting significant interest because of its potential applications in electronic and optoelectronic devices. Although graphene exhibits almost uniform absorption within a large wavelength range, its interaction with light is weak. In this paper, the enhancement of the optical absorption in graphene photonic crystal structures is studied: the structure is modified by introducing scatterers and mirrors. It is shown that the absorption of the graphene photonic crystal structure can be enhanced about four times (nearly 40%) with respect to initial reference absorption of 9.8%. The study can be a useful tool for investigating graphene physics in different optical settings. PMID:27139857

  4. Crystal structure of low-symmetry rondorfite

    SciTech Connect

    Rastsvetaeva, R. K. Zadov, A. E.; Chukanov, N. V.

    2008-03-15

    The crystal structure of an aluminum-rich variety of the mineral rondorfite with the composition Ca{sub 16}[Mg{sub 2}(Si{sub 7}Al)(O{sub 31}OH)]Cl{sub 4} from the skarns of the Verkhne-Chegemskoe plateau (the Kabardino-Balkarian Republic, the Northern Caucasus Region, Russia) was solved in the triclinic space group with the unit-cell parameters a = 15.100(2) A, b = 15.110(2) A, c = 15.092(2) A, {alpha} = 90.06(1) deg., {beta} = 90.01(1) deg., {gamma} = 89.93(1) deg., Z = 4, sp. gr. P1. The structural model consisting of 248 independent atoms was determined by the phase-correction method and refined to R = 3.8% with anisotropic displacement parameters based on all 7156 independent reflections with 7156 F > 3{sigma}(F). The crystal structure is based on pentamers consisting of four Si tetrahedra linked by the central Mg tetrahedron. The structure can formally be refined in the cubic space group (a = 15.105 A, sp. gr. Fd-bar 3, seven independent positions) with anisotropic displacement parameters to R = 2.74% based on 579 reflections with F > 3{sigma}(F) without accounting for more than 1000 observed reflections, which are inconsistent with the cubic symmetry of the crystal structure.

  5. Crystal structure of low-symmetry rondorfite

    SciTech Connect

    Rastsvetaeva, R. K.; Zadov, A. E.; Chukanov, N. V.

    2008-03-15

    The crystal structure of an aluminum-rich variety of the mineral rondorfite with the composition Ca{sub 16}[Mg{sub 2}(Si{sub 7}Al)(O{sub 31}OH)]Cl{sub 4} from the skarns of the Verkhne-Chegemskoe plateau (the Kabardino-Balkarian Republic, the Northern Caucasus Region, Russia) was solved in the triclinic space group with the unit-cell parameters a = 15.100(2) Angstrom-Sign , b = 15.110(2) Angstrom-Sign , c = 15.092(2) Angstrom-Sign , {alpha} = 90.06(1) Degree-Sign , {beta} = 90.01(1) Degree-Sign , {gamma} = 89.93(1) Degree-Sign , Z = 4, sp. gr. P1. The structural model consisting of 248 independent atoms was determined by the phase-correction method and refined to R = 3.8% with anisotropic displacement parameters based on all 7156 independent reflections with 7156 F > 3{sigma}(F). The crystal structure is based on pentamers consisting of four Si tetrahedra linked by the central Mg tetrahedron. The structure can formally be refined in the cubic space group (a = 15.105 Angstrom-Sign , sp. gr. Fd 3 bar , seven independent positions) with anisotropic displacement parameters to R = 2.74% based on 579 reflections with F > 3{sigma}(F) without accounting for more than 1000 observed reflections, which are inconsistent with the cubic symmetry of the crystal structure.

  6. Li2Ca2Si2O7: Structural, spectroscopic and computational studies on a sorosilicate

    NASA Astrophysics Data System (ADS)

    Kahlenberg, Volker; Brunello, Emanuele; Hejny, Clivia; Krüger, Hannes; Schmidmair, Daniela; Tribus, Martina; Többens, Daniel M.

    2015-05-01

    Synthesis experiments in the system Li2O-CaO-SiO2 resulted in the formation of single-crystals of Li2Ca2Si2O7. Structural investigations were based on single-crystal diffraction. At ambient conditions the compound has the following basic crystallographic data: hexagonal symmetry, space group P6122, a=5.0961(2) Å, c=41.264(2) Å, V=928.07(6) Å3, Z=6. Structure solution was performed using direct methods. The final least-squares refinement calculations converged at a residual of R(|F|)=0.0260. From a structural point the lithium calcium silicate belongs to the group of pyrosilicates containing [Si2O7]-groups. Additional lithium and calcium cations are incorporated between the silicate dimers and are coordinated by four and six nearest oxygen neighbours, respectively. Each [LiO4]-tetrahedron shares two common corners with directly neighboring tetrahedra forming zweier single-chains which are running parallel to <1 0 0> in z-levels defined by the presence of the 61[0 0 1]-screw axes. From the corner-sharing [LiO4]- and [SiO4]-moieties a three dimensional framework can be constructed. An interesting feature of this framework is the presence of an O[3]-type bridging oxygen linking three tetrahedra (one [LiO4]- and two [SiO4]-units). Structural similarities with other silicates are discussed in detail. The high-temperature behavior of the Si-O, Ca-O and Li-O bond distances in Li2Ca2Si2O7 was investigated by in-situ single-crystal X-ray diffraction in the range between 65 and 700 °C. From the evolution of the lattice parameters, the thermal expansion tensor αij has been determined. The structural characterization has been supplemented by micro-Raman spectroscopy. Interpretation of the spectroscopic data including the allocation of the bands to certain vibrational species has been aided by DFT-calculations.

  7. 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).

  8. 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

  9. 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

  10. Spectroscopic, thermal and mechanical studies on 4-methylanilinium p-toluenesulfonate - a new organic NLO single crystal.

    PubMed

    Shanmugam, G; Brahadeeswaran, S

    2012-09-01

    Bulk crystals of newly identified organic nonlinear optical material 4-methylanilinium p-toluenesulfonate (PMPT) were grown by slow evaporation solution growth method using ethanol as a solvent. It crystallizes in monoclinic system with a noncentrosymmetric space group P2(1). The formation of the title compound was confirmed through microanalysis, X-ray diffraction and density measurements. The proton positions and functional groups have been identified and confirmed through nuclear magnetic resonance and Fourier transform infrared spectrums respectively. Optical properties are determined by UV-Visible and photoluminescence spectroscopic studies to explore its efficacy towards device fabrications. Thermal studies exhibited that the newly obtained PMPT crystals are stable up to 199 °C. Its mechanical strength was studied by Vickers micro hardness studies. PMID:22634406

  11. Synthesis and Crystal Structure of Gold Nanobelts

    PubMed Central

    2015-01-01

    Gold nanobelts were synthesized by the reduction of tetrachloroauric acid with ascorbic acid in the presence of the surfactants cetyltrimethylammonium bromide and sodium dodecylsulfate. The resulting structures have rectangular cross sectional dimensions that are tens of nanometers and lengths that are tens to hundreds of micrometers. We find that the nanobelt yield and resulting structures are very sensitive to temperature which is likely due to the transition of the surfactant solution from wormlike micelles to spherical micelles. The nanobelt crystal structure contains a mixture of face centered cubic and hexagonally close packed lattice phases that can be isolated and examined individually due to the unique nanobelt size and shape. PMID:24803725

  12. 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

  13. Photonic crystal and photonic wire device structures

    NASA Astrophysics Data System (ADS)

    De La Rue, Richard; Sorel, Marc; Johnson, Nigel; Rahman, Faiz; Ironside, Charles; Cronin, Lee; Watson, Ian; Martin, Robert; Jin, Chongjun; Pottier, Pierre; Chong, Harold; Gnan, Marco; Jugessur, Aju; Camargo, Edilson; Erwin, Grant; Md Zain, Ahmad; Ntakis, Iraklis; Hobbs, Lois; Zhang, Hua; Armenise, Mario; Ciminelli, Caterina; Coquillat, Dominique

    2005-09-01

    Photonic devices that exploit photonic crystal (PhC) principles in a planar environment continue to provide a fertile field of research. 2D PhC based channel waveguides can provide both strong confinement and controlled dispersion behaviour. In conjunction with, for instance, various electro-optic, thermo-optic and other effects, a range of device functionality is accessible in very compact PhC channel-guide devices that offer the potential for high-density integration. Low enough propagation losses are now being obtained with photonic crystal channel-guide structures that their use in real applications has become plausible. Photonic wires (PhWs) can also provide strong confinement and low propagation losses. Bragg-gratings imposed on photonic wires can provide dispersion and frequency selection in device structures that are intrinsically simpler than 2D PhC channel guides--and can compete with them under realistic conditions.

  14. 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.

  15. 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.

  16. 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

  17. Synthesis, crystal structure and characterization of [C9H11N4] H2PO4

    NASA Astrophysics Data System (ADS)

    Chtourou, A.; Boujelbene, M.; Allouch, F.; Mhiri, T.

    2014-04-01

    Chemical preparation crystal structure and spectroscopic investigations are given for a new organic-cation dihydrogenomonophosphate (C9H11N4) H2PO4 in the solid state. This compound crystallizes in the monoclinic space group P 21 with the following unit cell parameters: a = 9.640 (5) Ǻ. b = 4.582 (5) Ǻ. c = 14.094 (5) Ǻ, β = 106.979 (5)°, Z = 2, V = 595.4 (7) Å3. Crystal structure was solved with a final R = 0.054 for 2077 independent reflections. The atomic arrangement can be described as inorganic layers of HPO4- anions between which are located the organic groups. Solid-state 13C and 31P MAS-NMR spectroscopies are in agreement with the X-ray structure. Ab initio calculations allow the attribution of the phosphorous and carbon signals to the independent crystallographic sites and to the various atoms of the organic groups.

  18. Observations on the crystal structures of lueshite

    NASA Astrophysics Data System (ADS)

    Mitchell, Roger H.; Burns, Peter C.; Knight, Kevin S.; Howard, Christopher J.; Chakhmouradian, Anton R.

    2014-06-01

    Laboratory powder XRD patterns of the perovskite-group mineral lueshite from the type locality (Lueshe, Kivu, DRC) and pure NaNbO3 demonstrate that lueshite does not adopt the same space group ( Pbma; #57) as the synthetic compound. The crystal structures of lueshite (2 samples) from Lueshe, Mont Saint-Hilaire (Quebec, Canada) and Sallanlatvi (Kola, Russia) have been determined by single-crystal CCD X-ray diffraction. These room temperature X-ray data for all single-crystal samples can be satisfactorily refined in the orthorhombic space group Pbnm (#62). Cell dimensions, atomic coordinates of the atoms, bond lengths and octahedron tilt angles are given for four crystals. Conventional neutron diffraction patterns for Lueshe lueshite recorded over the temperature range 11-1,000 K confirm that lueshite does not adopt space group Pbma within these temperatures. Neutron diffraction indicates no phase changes on cooling from room temperature to 11 K. None of these neutron diffraction data give satisfactorily refinements but suggest that this is the space group Pbnm. Time-of-flight neutron diffraction patterns for Lueshe lueshite recorded from room temperature to 700 °C demonstrate phase transitions above 550 °C from Cmcm through P4 /mbm to above 650 °C. Cell dimensions and atomic coordinates of the atoms are given for the three high-temperature phases. The room temperature to 400 °C structures cannot be satisfactorily resolved, and it is suggested that the lueshite at room temperature consists of domains of pinned metastable phases with orthorhombic and/or monoclinic structures. However, the sequence of high-temperature phase transitions observed is similar to those determined for synthetic NaTaO3, suggesting that the equilibrated room temperature structure of lueshite is orthorhombic Pbnm.

  19. Crystal Structures of New Ammonium 5-Aminotetrazolates

    PubMed Central

    Lampl, Martin; Salchner, Robert; Laus, Gerhard; Braun, Doris E.; Kahlenberg, Volker; Wurst, Klaus; Fuhrmann, Gerda; Schottenberger, Herwig; Huppertz, Hubert

    2015-01-01

    The crystal structures of three salts of anionic 5-aminotetrazole are described. The tetramethylammonium salt (P1‒) forms hydrogen-bonded ribbons of anions which accept weak C–H⋯N contacts from the cations. The cystamine salt (C2/c) shows wave-shaped ribbons of anions linked by hydrogen bonds to screw-shaped dications. The tetramethylguanidine salt (P21/c) exhibits layers of anions hydrogen-bonded to the cations. PMID:26753100

  20. 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

  1. 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.

  2. 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)

  3. 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.

  4. Crystal Structure of the Protealysin Precursor

    PubMed Central

    Demidyuk, Ilya V.; Gromova, Tania Yu.; Polyakov, Konstantin M.; Melik-Adamyan, William R.; Kuranova, Inna P.; Kostrov, Sergey V.

    2010-01-01

    Protealysin (PLN) belongs to the M4 family of peptidases that are commonly known as thermolysin-like proteases (TLPs). All TLPs are synthesized as precursors containing N-terminal propeptides. According to the primary structure of the N-terminal propeptides, the family is divided into two distinct groups. Representatives of the first group including thermolysin and all TLPs with known three-dimensional structures have long prosequences (∼200 amino acids). Enzymes of the second group, whose prototype is protealysin, have short (∼50 amino acids) propeptides. Here, we present the 1.8 Å crystal structure of PLN precursor (proPLN), which is the first three-dimensional structure of a TLP precursor. Whereas the structure of the catalytic domain of proPLN is similar overall to previously reported structures of mature TLPs, it has specific features, including the absence of calcium-binding sites, and different structures of the N-terminal region and substrate-binding site. PLN propeptide forms a separate domain in the precursor and likely acts as an inhibitor that blocks the substrate-binding site and fixes the “open” conformation of the active site, which is unfavorable for catalysis. Furthermore the conserved PPL motif identified in our previous studies directly interacts with the S′ subsites of the active center being a critical element of the propeptide-catalytic domain interface. Comparison of the primary structures of TLPs with short propeptides suggests that the specific features revealed in the proPLN crystal structure are typical for all protealysin-like enzymes. Thus, such proteins can be considered as a separate subfamily of TLPs. PMID:19915005

  5. High-Pressure Catalytic Reactions of C6 Hydrocarbons on PlatinumSingle-Crystals and nanoparticles: A Sum Frequency Generation VibrationalSpectroscopic and Kinetic Study

    SciTech Connect

    Bratlie, Kaitlin

    2007-12-19

    Catalytic reactions of cyclohexene, benzene, n-hexane, 2-methylpentane, 3-methylpentane, and 1-hexene on platinum catalysts were monitored in situ via sum frequency generation (SFG) vibrational spectroscopy and gas chromatography (GC). SFG is a surface specific vibrational spectroscopic tool capable of monitoring submonolayer coverages under reaction conditions without gas-phase interference. SFG was used to identify the surface intermediates present during catalytic processes on Pt(111) and Pt(100) single-crystals and on cubic and cuboctahedra Pt nanoparticles in the Torr pressure regime and at high temperatures (300K-450K). At low pressures (<10{sup -6} Torr), cyclohexene hydrogenated and dehydrogenates to form cyclohexyl (C{sub 6}H{sub 11}) and {pi}-allyl C{sub 6}H{sub 9}, respectively, on Pt(100). Increasing pressures to 1.5 Torr form cyclohexyl, {pi}-allyl C{sub 6}H{sub 9}, and 1,4-cyclohexadiene, illustrating the necessity to investigate catalytic reactions at high-pressures. Simultaneously, GC was used to acquire turnover rates that were correlated to reactive intermediates observed spectroscopically. Benzene hydrogenation on Pt(111) and Pt(100) illustrated structure sensitivity via both vibrational spectroscopy and kinetics. Both cyclohexane and cyclohexene were produced on Pt(111), while only cyclohexane was formed on Pt(100). Additionally, {pi}-allyl c-C{sub 6}H{sub 9} was found only on Pt(100), indicating that cyclohexene rapidly dehydrogenates on the (100) surface. The structure insensitive production of cyclohexane was found to exhibit a compensation effect and was analyzed using the selective energy transfer (SET) model. The SET model suggests that the Pt-H system donates energy to the E{sub 2u} mode of free benzene, which leads to catalysis. Linear C{sub 6} (n-hexane, 2-methylpentane, 3-methylpentane, and 1-hexene) hydrocarbons were also investigated in the presence and absence of excess hydrogen on Pt(100). Based on spectroscopic signatures

  6. Crystal structure of natural phaeosphaeride A.

    PubMed

    Abzianidze, Victoria V; Poluektova, Ekaterina V; Bolshakova, Ksenia P; Panikorovskii, Taras L; Bogachenkov, Alexander S; Berestetskiy, Alexander O

    2015-08-01

    The asymmetric unit of the title compound, C15H23NO5, contains two independent mol-ecules. Phaeosphaeride A contains two primary sections, an alkyl chain consisting of five C atoms and a cyclic system consisting of fused five- and six-membered rings with attached substituents. In the crystal, the mol-ecules form layered structures. Nearly planar sheets, parallel to the (001) plane, form bilayers of two-dimensional hydrogen-bonded networks with the hy-droxy groups located on the inter-ior of the bilayer sheets. The network is constructed primarily of four O-H⋯O hydrogen bonds, which form a zigzag pattern in the (001) plane. The butyl chains inter-digitate with the butyl chains on adjacent sheets. The crystal was twinned by a twofold rotation about the c axis, with refined major-minor occupancy fractions of 0.718 (6):0.282 (6). PMID:26396831

  7. Crystal structures and freezing of dipolar fluids.

    PubMed

    Groh, B; Dietrich, S

    2001-02-01

    We investigate the crystal structure of classical systems of spherical particles with an embedded point dipole at T=0. The ferroelectric ground state energy is calculated using generalizations of the Ewald summation technique. Due to the reduced symmetry compared to the nonpolar case the crystals are never strictly cubic. For the Stockmayer (i.e., Lennard-Jones plus dipolar) interaction three phases are found upon increasing the dipole moment: hexagonal, body-centered orthorhombic, and body-centered tetragonal. An even richer phase diagram arises for dipolar soft spheres with a purely repulsive inverse power law potential approximately r(-n). A crossover between qualitatively different sequences of phases occurs near the exponent n=12. The results are applicable to electro- and magnetorheological fluids. In addition to the exact ground state analysis we study freezing of the Stockmayer fluid by density-functional theory. PMID:11308482

  8. 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.

  9. 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.

  10. Insight into the secondary structure of chloramphenicol acetyltransferase type I — computer analysis and FT-IR spectroscopic characterization of the protein structure

    NASA Astrophysics Data System (ADS)

    Andreeva, A. E.; Karamancheva, I. R.

    2001-05-01

    The secondary structure of chloramphenicol O-acetyltransferase type I (CAT I) and an N-terminal deleted mutant has been studied by Fourier transform infrared spectroscopy. The analysis of the amide I band of different samples (KBr, hydrated films and buffer solution) by Fourier self-deconvolution followed by a curve fitting was performed. The spectroscopic data have been utilized to determine the α-helix and β-structure % contents, which depend strongly on the protein sample preparation. Furthermore, the secondary structure of the enzyme-inhibitor Crystal Violet complex was analyzed. The observed difference in the secondary structural contents suggests that some conformational changes of the enzyme are induced by the inhibitor after binding.