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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. 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.

  20. 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.

  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

    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.

  19. 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

  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. 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

  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. 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.

  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. 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

  14. 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.

  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

    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.

  19. 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

  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. 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.

  11. 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.

  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. 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

  15. 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.

  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. 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.

  15. 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.

  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. 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

  5. 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

  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.

  11. Crystal structure of plant photosystem I

    NASA Astrophysics Data System (ADS)

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

    2003-12-01

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

  12. Flowing crystals: nonequilibrium structure of foam.

    PubMed

    Garstecki, Piotr; Whitesides, George M

    2006-07-14

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

  13. Spectroscopic and structural elucidation of alanyl-containing dipeptides and their hydrogensquarates

    NASA Astrophysics Data System (ADS)

    Koleva, Bojidarka B.; Kolev, Tsonko M.; Spiteller, Michael

    2008-04-01

    The hydrogensquarates of alanyl-containing dipeptides glycylalanine ( H-Gly-Ala-OH) and alanylalanine ( H-Ala-Ala-OH) are characterized structurally by means of quantum chemical ab initio calculations, solid-state linear-dichroic infrared (IR-LD) spectroscopy, 1H and 13C NMR data, ESI-MS, HPLC-MS/MS, TGV and DSC methods. The structures consist in positive charged peptide moiety and negative hydrogensquarate anion (HSq -), stabilizing by strong intermolecular hydrogen bonds. The theoretical and IR-LD spectroscopic data are compared with corresponding ones of zwitterion dipeptides with a view to understanding the structural and conformational changes as well as the IR-spectroscopic ones as a result of hydrogensquarates formation. The strong overlapped and complicated IR-spectroscopic bands typical for hydrogensquarates in solid-state are assigned supporting with the presented vibrational analysis of the dipeptides and of the hydrogensqauarate anion.

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

    NASA Astrophysics Data System (ADS)

    Jeragh, Bakir; El-Asmy, Ahmed A.

    2014-08-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  17. Structural investigation of the potassium vanadomolybdate crystal

    SciTech Connect

    Mucha, D.; Olszewski, P.K.; Napruszewska, B.

    1999-08-01

    Potassium vanadomolybdate KVMoO{sub 6} crystallizes in the orthorhombic system (space group Pnma, a = 10.3478(1) {angstrom}, b = 3.6967(1) {angstrom}, c = 13.3769(2) {angstrom}, Z = 4). With an X-ray powder diffraction technique, its structure was solved and refined by direct and Rietveld methods, respectively (R{sub F} = 3.33, R{sub 1} = 4.70, R{sub wp} = 12.44). The crystals are isostructural with PbV{sub 2}O{sub 6}. Octahedra of two types build chains parallel to the b direction; there is disorder in the octahedra described by different occupation numbers of V and Mo atoms: 0.721(4) and 0.279(4), respectively. Potassium atoms occupy the space between the octahedra chains. They play a decisive role, due to the large ionic radius, in generating both KVMoO{sub 6} and pseudobrannerite, K{sub x}V{sub x}Mo{sub 2{minus}x}O{sub 6} (0.76 {le} x {le} 0.82) structures, contrary to other alkali-metal vanadomolybdates of the brannerite structure type. The melting point of KVMoO{sub 6} was detected at 480 C using the DTA method.

  18. Crystal structure of a DNA catalyst.

    PubMed

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

    2016-01-14

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

  19. Temperature dependent spin structures in Hexaferrite crystal

    NASA Astrophysics Data System (ADS)

    Chao, Y. C.; Lin, J. G.; Chun, S. H.; Kim, K. H.

    2016-01-01

    In this work, the Hexaferrite Ba0.5Sr1.5Zn2Fe12O22 (BSZFO) is studied due to its interesting characteristics of long-wavelength spin structure. Ferromagnetic resonance (FMR) is used to probe the magnetic states of BSZFO single crystal and its temperature dependence behavior is analyzed by decomposing the multiple lines of FMR spectra into various phases. Distinguished phase transition is observed at 110 K for one line, which is assigned to the ferro(ferri)-magnetic transition from non-collinear to collinear spin state.

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

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

    Single crystals of Zn4(OH)2[(UO2)(PO4)2(OH)2(H2O)] (UZnP), Cs[(UO2)(HPO4)NO3] (UCsP), and In3[(UO2)2(PO4)4OH(H2O)6].2H2O (UInP) were obtained from hydrothermal reactions and have been structurally and chemically characterized. UZnP crystallizes in space group Pbcn, a=8.8817(7), b=6.6109(5), c=19.569(1) Å; UCsP crystallizes in P-1, a=7.015(2), b=7.441(1), c=9.393(2) Å, α=72.974(2), β=74.261(2), γ=79.498(2); and UInP crystallizes in P-1, a=7.9856(5), b=9.159(1), c=9.2398(6) Å α=101.289(1), β=114.642(1), γ=99.203(2). The U6+ cations are present as (UO2)2+ uranyl ions coordinated by five O atoms to give pentagonal bipyramids. The structural unit in UZnP is a finite cluster containing a uranyl pentagonal bipyramid that shares corners with two phosphate tetrahedra. The structural unit in UCsP is composed of uranyl pentagonal bipyramids with one chelating nitrate group that are linked into chains by three bridging hydrogen phosphate tetrahedra. In UInP, the structural unit contains pairs of edge-sharing uranyl pentagonal bipyramids with two chelating phosphate tetrahedra that are linked into chains through two bridging phosphate tetrahedra. Indium octahedra link these uranyl phosphate chains into a 3-dimensional framework. All three compounds exhibit unique structural units that deviate from the typical layered structures observed in uranyl phosphate solid-state chemistry.

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

    PubMed

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

    2009-12-01

    The novel chloride salt of 1-butyl-4-[2-(4-hydroxyphenyl)ethenyl)]pyridine (1), has been synthesized as the tetrahydrate and its structure and properties elucidated in detail spectroscopically, thermally and structurally, using single crystal X-ray diffraction, linear-polarized solid-state IR-spectroscopy, UV-spectroscopy and mass spectrometry. Quantum chemical calculations were performed with a view to supporting and explaining the experimental structural and spectroscopic data. The compound (1) crystallizes in triclinic P1 space group and its unit cell contains two independent 1-butyl-4-[2-(3,5-dimethoxy4-hydroxyphenyl)ethenyl)]pyridinium] cations, differing with respect to the butyl chain torsion angle for which values of 80.0(9) degrees and 173.6(3) degrees are observed. The cations and anions are joined into infinite layers, formed by two different dimers and including solvent molecules. Hydrogen bonds OH...OH(2) (2.814 A), HOH...O(CH(3)) (2.960 A), OH...Cl (2.967 A), HOH...Cl(-) (3.034, 3.188, 3.161 and 3.062 A) and HOH...OH(2) (2.772 A) are observed. For first time in the literature, we are reporting the crystal structure of the dye with the syring-fragment in the molecule. The spectroscopic properties of the novel compound are compared and with those of the corresponding quinoide form (2). Both the forms (1) and (2) are characterized by 21 and 140 nm solvatochromic effects depending of the type of the solvent. The UV-spectroscopic data in solution confirm the formation of classical H-aggregates in polar protic solvent mixture. PMID:19833548

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

    NASA Astrophysics Data System (ADS)

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

    2009-12-01

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

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

    PubMed

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

    2016-02-28

    The HOC(O)O radical is a product of the reaction of HOCO radicals with oxygen atoms. The present study provides theoretical prediction of critical spectroscopic features of this radical that should aid in its experimental characterization. Energies, structures, rotational constants, and harmonic frequencies are presented for the ground and two low-lying excited electronic states of HOC(O)O. The energies for the Ã(2)A(″)←X̃(2)A(') and B̃(2)A(')←X̃(2)A(') electronic transitions are reported. The band origin of the B̃←X̃ transition of HOC(O)O is predicted to occur in the near infrared region of the spectrum at around 1.5 eV and it is suggested to be the most promising one for observing this radical spectroscopically. The structural and spectroscopic similarities between HOC(O)O and the isoelectronic radical FC(O)O are discussed. The abundance of experimental data on the FC(O)O radical should guide the spectroscopic characterization of HOC(O)O and serve as a benchmark for the structural and spectroscopic parameters obtained from theory. PMID:26931701

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

    NASA Astrophysics Data System (ADS)

    Sun, Yi

    2001-10-01

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

  5. Crystal structure of yeast Sco1

    SciTech Connect

    Abajian, Carnie; Rosenzweig, Amy C.

    2010-03-05

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

  6. Crystal structure of mammalian acid sphingomyelinase.

    PubMed

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

    2016-01-01

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

  7. Crystal structure of mammalian acid sphingomyelinase

    PubMed Central

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

    2016-01-01

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

  8. Structure, thermodynamics, and crystallization of amorphous hafnia

    NASA Astrophysics Data System (ADS)

    Luo, Xuhui; Demkov, Alexander A.

    2015-09-01

    We investigate theoretically amorphous hafnia using the first principles melt and quench method. We identify two types of amorphous structures of hafnia. Type I and type II are related to tetragonal and monoclinic hafnia, respectively. We find type II structure to show stronger disorder than type I. Using the phonon density of states, we calculate the specific heat capacity for type II amorphous hafnia. Using the nudged elastic band method, we show that the averaged transition barrier between the type II amorphous hafnia and monoclinic phase is approximately 0.09 eV/HfO2. The crystallization temperature is estimated to be 421 K. The calculations suggest an explanation for the low thermal stability of amorphous hafnia.

  9. The Crystal Structure of Human Argonaute2

    SciTech Connect

    Schirle, Nicole T.; MacRae, Ian J.

    2012-07-18

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

  10. Crystal structure of human nicotinamide riboside kinase.

    PubMed

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

    2007-08-01

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

  11. Crystal Structure of Human Nicotinamide Riboside Kinase

    SciTech Connect

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

    2007-01-01

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

  12. The crystal structure of human Argonaute2.

    PubMed

    Schirle, Nicole T; MacRae, Ian J

    2012-05-25

    Argonaute proteins form the functional core of the RNA-induced silencing complexes that mediate RNA silencing in eukaryotes. The 2.3 angstrom resolution crystal structure of human Argonaute2 (Ago2) reveals a bilobed molecule with a central cleft for binding guide and target RNAs. Nucleotides 2 to 6 of a heterogeneous mixture of guide RNAs are positioned in an A-form conformation for base pairing with target messenger RNAs. Between nucleotides 6 and 7, there is a kink that may function in microRNA target recognition or release of sliced RNA products. Tandem tryptophan-binding pockets in the PIWI domain define a likely interaction surface for recruitment of glycine-tryptophan-182 (GW182) or other tryptophan-rich cofactors. These results will enable structure-based approaches for harnessing the untapped therapeutic potential of RNA silencing in humans. PMID:22539551

  13. Structure, thermodynamics, and crystallization of amorphous hafnia

    SciTech Connect

    Luo, Xuhui; Demkov, Alexander A.

    2015-09-28

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

  14. Structural studies of tubular discotic liquid crystals

    NASA Astrophysics Data System (ADS)

    Mindyuk, Oksana Yaroslavovna

    1999-11-01

    Discotic liquid crystals based on the rigid ring-shaped phenylacetylene macrocycle molecule (PAM) are of great interest due to their potential organization into supramolecular channels. We have used high resolution X-ray diffraction to study the structure of pure and doped PAM and to demonstrate that PAM forms a tubular columnar liquid crystal with an unexpected distortion and doubling of the underlying hexagonal lattice. We have doped PAM with different percentages of silver ions and determined that doping did not change peak positions on the powder diffraction data but significantly altered the intensity of the peaks. This implies that the silver ions were most likely intercalated within the channels formed by the PAM molecules, thus leaving the lattice parameters unaffected. We have also used grazing incidence X-ray diffraction and X-ray reflectivity to study Langmuir films of PAM. PAM adopts an "edge-on" molecular arrangement at the air-water interface. We will discuss the direct observation of the structural reorganization within macromolecular Langmuir films of disc-shaped ionophoric molecules arising from interactions with potassium and cesium ions in the subphase. The columnar order is disrupted by CsCl in the subphase and strongly enhanced by KCl in the subphase, thus effectively tailoring the structural properties of the Langmuir films for potential applications. We have also used X-ray reflectivity (XR) and grazing incidence x-ray diffraction (GID) to study Langmuir films of another macrocyclic ionophore: torand (tributyldodecahydrohexaazakekulene, "TBDK") molecules. TBDK is a rigid, triangular molecule; it has been investigated as a potential surface-active complexing agent. The system forms a stable monolayer at the air-water interface and exhibits two distinct structural phases at lower and higher pressures.

  15. Prediction of binary hard-sphere crystal structures.

    PubMed

    Filion, Laura; Dijkstra, Marjolein

    2009-04-01

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

  16. Crystal structure of bacterioferritin from Rhodobacter sphaeroides

    SciTech Connect

    Nam, Ki Hyun; Xu, Yongbin; Piao, Shunfu; Priyadarshi, Amit; Lee, Eun Hye; Kim, Hye-Yeon; Jeon, Young Ho; Ha, Nam-Chul; Hwang, Kwang Yeon

    2010-01-01

    Iron is essential for the survival of organisms, but either excess or deficient levels of iron induce oxidative stress, thereby causing cell damage. As a result, iron regulation is essential for proper cell growth and proliferation in most organisms. Bacterioferritin is a ferritin-like family protein that contains a heme molecule and a ferroxidase site at the di-iron center. This protein plays a primary role in intracellular iron storage for iron homeostasis, as well as in the maintenance of iron in a soluble and non-toxic form. Although several bacterioferritin structures have been determined, no structural studies have successfully elucidated the molecular function of the heme molecule and the ferroxidase center. Here, we report the crystal structure of bacterioferritin from Rhodobacter sphaeroides. This protein exists in a roughly spherical configuration via the assembly of 24 subunits. We describe the oligomeric arrangement, ferroxidase center and heme-binding site based on this structure. The protein contains a single iron-binding configuration in the ferroxidase center, which allows for the release of iron by His130 when the protein is in the intermediate state. The heme molecule in RsBfr is stabilized by shifting of the van der Waals interaction center between the porphyrin of the heme and Trp26. We anticipate that further structural analysis will provide a more complete understanding of the molecular mechanisms of members of the ferritin-like family.

  17. Structural Transitions in Cholesteric Liquid Crystal Droplets.

    PubMed

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

    2016-07-26

    Confinement of cholesteric liquid crystals (ChLC) into droplets leads to a delicate interplay between elasticity, chirality, and surface energy. In this work, we rely on a combination of theory and experiments to understand the rich morphological behavior that arises from that balance. More specifically, a systematic study of micrometer-sized ChLC droplets is presented as a function of chirality and surface energy (or anchoring). With increasing chirality, a continuous transition is observed from a twisted bipolar structure to a radial spherical structure, all within a narrow range of chirality. During such a transition, a bent structure is predicted by simulations and confirmed by experimental observations. Simulations are also able to capture the dynamics of the quenching process observed in experiments. Consistent with published work, it is found that nanoparticles are attracted to defect regions on the surface of the droplets. For weak anchoring conditions at the nanoparticle surface, ChLC droplets adopt a morphology similar to that of the equilibrium helical phase observed for ChLCs in the bulk. As the anchoring strength increases, a planar bipolar structure arises, followed by a morphological transition to a bent structure. The influence of chirality and surface interactions are discussed in the context of the potential use of ChLC droplets as stimuli-responsive materials for reporting molecular adsorbates. PMID:27249186

  18. Crystal structures of low-symmetry cancrinite and cancrisilite varieties

    NASA Astrophysics Data System (ADS)

    Rastsvetaeva, R. K.; Pekov, I. V.; Chukanov, N. V.; Rozenberg, K. A.; Olysych, L. V.

    2007-09-01

    The high-sodium variety of cancrinite [Si6.3Al5.7O24][Na2(H2O)2][Na5.7(CO3)0.9(SO4)0.1(H2O)0.6] (Kovdor Massif, Kola Peninsula, Russia) and the calcium-containing variety of cancrisilite [Si6.6Al5.4O24][(Na1.2Ca0.4)(H2O)1.6][Na6(CO3)1.3(H2O)1.2] (Khibiny Massif, Kola Peninsula, Russia) are studied. The trigonal unit cell parameters of the crystal structures under investigation are as follows: a = 12.727(4) Å, c = 5.186(2) Å, and space group P3 for the former mineral and a = 12.607(4) Å, c = 5.111(1) Å, and space group P3 for the latter mineral. The reduced symmetry of the new varieties as compared to the symmetry of typical cancrinite and typical cancrisilite is associated with the specific features in the arrangement of the carbonate groups and water molecules in channels. This inference is confirmed by the IR spectroscopic data.

  19. Spectroscopic studies of anthracyclines: Structural characterization and in vitro tracking.

    PubMed

    Szafraniec, Ewelina; Majzner, Katarzyna; Farhane, Zeineb; Byrne, Hugh J; Lukawska, Malgorzata; Oszczapowicz, Irena; Chlopicki, Stefan; Baranska, Malgorzata

    2016-12-01

    A broad spectroscopic characterization, using ultraviolet-visible (UV-vis) and Fourier transform infrared absorption as well as Raman scattering, of two commonly used anthracyclines antibiotics (DOX) daunorubicin (DNR), their epimers (EDOX, EDNR) and ten selected analogs is presented. The paper serves as a comprehensive spectral library of UV-vis, IR and Raman spectra of anthracyclines in the solid state and in solution. The particular advantage of Raman spectroscopy for the measurement and analysis of individual antibiotics is demonstrated. Raman spectroscopy can be used to monitor the in vitro uptake and distribution of the drug in cells, using both 488nm and 785nm as source wavelengths, with submicrometer spatial resolution, although the cellular accumulation of the drug is different in each case. The high information content of Raman spectra allows studies of the drug-cell interactions, and so the method seems very suitable for monitoring drug uptake and mechanisms of interaction with cellular compartments at the subcellular level. PMID:27372511

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

    SciTech Connect

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

    2015-06-24

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

  1. Crystal structures of five 6-mercaptopurine derivatives.

    PubMed

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

    2016-03-01

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

  2. Crystal structure of strontium dinickel iron orthophosphate

    PubMed Central

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

    2015-01-01

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

  3. RETRACTED: Crystal growth and spectroscopic characterization of Aloevera amino acid added lithium sulfate monohydrate: A non-linear optical crystal

    NASA Astrophysics Data System (ADS)

    Manimekalai, R.; Antony Joseph, A.; Ramachandra Raja, C.

    2014-03-01

    This article has been retracted: please see Elsevier Policy on Article Withdrawal. This article has been retracted at the request of authors. According to the author we have reported Aloevera Amino Acid added Lithium sulphate monohydrate [AALSMH] crystal is a new nonlinear optical crystal. From the recorded high performance liquid chromatography spectrum, by matching the retention times with the known compounds, the amino acids present in our extract are identified as homocystine, isoleucine, serine, leucine and tyrosine. From the thin layer chromatography and colorimetric estimation techniques, presence of isoleucine was identified and it was also confirmed by NMR spectrum. From the above studies, we came to conclude that AALSMH is new nonlinear optical crystal. After further investigation, lattice parameter values of AALSMH are coinciding with lithium sulphate. Therefore we have decided to withdraw our paper. Sorry for the inconvenience and time spent.

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

    PubMed

    Balachandar, R K; Kalainathan, S

    2013-12-01

    Organic nonlinear optical (NLO) crystal 2-chloro-N-[4-(dimethylamino)benzylidene]aniline (2Cl4DBA) was synthesized and grown by restricted slow evaporation technique at room temperature using acetone as solvent with good degree of transparency. The lattice parameters were determined and found to be noncentrosymmetric orthorhombic system by single crystal X-ray diffraction. The crystalline nature of the synthesized material was recorded by the powder X-ray diffraction pattern. Molecular structure of the grown crystal was investigated by (1)H and (13)C NMR and functional groups were identified by FTIR spectrum analysis. The optical absorbance of the grown crystal was ascertained by recording UV-Visible spectrum. Thermal and physiochemical stability of the grown material was investigated by TG/DTA analysis. SHG efficiency was determined by Kurtz-Perry Powder SHG technique and found to be 4.2 and 1.54 times greater that of standard KDP and urea crystals respectively. PMID:23933550

  5. Modeling Polymorphic Molecular Crystals with Electronic Structure Theory.

    PubMed

    Beran, Gregory J O

    2016-05-11

    Interest in molecular crystals has grown thanks to their relevance to pharmaceuticals, organic semiconductor materials, foods, and many other applications. Electronic structure methods have become an increasingly important tool for modeling molecular crystals and polymorphism. This article reviews electronic structure techniques used to model molecular crystals, including periodic density functional theory, periodic second-order Møller-Plesset perturbation theory, fragment-based electronic structure methods, and diffusion Monte Carlo. It also discusses the use of these models for predicting a variety of crystal properties that are relevant to the study of polymorphism, including lattice energies, structures, crystal structure prediction, polymorphism, phase diagrams, vibrational spectroscopies, and nuclear magnetic resonance spectroscopy. Finally, tools for analyzing crystal structures and intermolecular interactions are briefly discussed. PMID:27008426

  6. Crystal structures of the human adiponectin receptors.

    PubMed

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

    2015-04-16

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

  7. Crystal structure of natural phaeosphaeride A

    PubMed Central

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

    2015-01-01

    The asymmetric unit of the title compound, C15H23NO5, contains two independent mol­ecules. 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 mol­ecules form layered structures. Nearly planar sheets, parallel to the (001) plane, form bilayers of two-dimensional hydrogen-bonded networks with the hy­droxy groups located on the inter­ior 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 inter­digitate 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

  8. Crystal Structures of Respiratory Pathogen Neuraminidases

    SciTech Connect

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

    2009-01-01

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

  9. Crystal Structure of the VS ribozyme

    PubMed Central

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

    2015-01-01

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

  10. Crystal structure of oligoacenes under high pressure

    SciTech Connect

    Oehzelt, M.; Aichholzer, A.; Resel, R.; Heimel, G.; Venuti, E.; Della Valle, R. G.

    2006-09-01

    We report crystal structures of anthracene, tetracene, and pentacene under pressure. Energy dispersive x-ray diffraction experiments up to 9 GPa were performed. Quasiharmonic lattice dynamics calculations are compared to the experimental results and show excellent agreement. The results are discussed with particular emphasis on the pressure dependence of the unit cell dimensions and the rearrangement of the molecules. The high pressure data also allow an analysis of the equation of state of these substances as a function of molecular length. We report the bulk modulus of tetracene and pentacene (B{sub 0}=9.0 and 9.6 GPa, respectively) and its pressure derivative (B{sub 0}{sup '}=7.9 and 6.4, respectively). We find that the unit-cell volume and bulk modulus at ambient pressure follow a linear relationship with the molecular length.

  11. Exploring structural phase transitions of ion crystals

    PubMed Central

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

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

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

    ERIC Educational Resources Information Center

    Hong, Y. S.; And Others

    1980-01-01

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

  15. Crystal structure of human GDF11.

    PubMed

    Padyana, Anil K; Vaidialingam, Bhamini; Hayes, David B; Gupta, Priyanka; Franti, Michael; Farrow, Neil A

    2016-03-01

    Members of the TGF-β family of proteins are believed to play critical roles in cellular signaling processes such as those involved in muscle differentiation. The extent to which individual family members have been characterized and linked to biological function varies greatly. The role of myostatin, also known as growth differentiation factor 8 (GDF8), as an inhibitor of muscle differentiation is well understood through genetic linkages. In contrast, the role of growth differentiation factor 11 (GDF11) is much less well understood. In humans, the mature forms of GDF11 and myostatin are over 94% identical. In order to understand the role that the small differences in sequence may play in the differential signaling of these molecules, the crystal structure of GDF11 was determined to a resolution of 1.50 Å. A comparison of the GDF11 structure with those of other family members reveals that the canonical TGF-β domain fold is conserved. A detailed structural comparison of GDF11 and myostatin shows that several of the differences between these proteins are likely to be localized at interfaces that are critical for the interaction with downstream receptors and inhibitors. PMID:26919518

  16. Crystal Structure of Amylomaltase from Corynebacterium glutamicum.

    PubMed

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

    2016-07-20

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

  17. The Crystal Structure of Triuranyl Diphosphate Tetrahydrate

    NASA Astrophysics Data System (ADS)

    Locock, Andrew J.; Burns, Peter C.

    2002-01-01

    The hydrated neutral uranyl phosphate, (UO2)3(PO4)2(H2O)4, was synthesized by hydrothermal methods. Intensity data were collected using MoKα radiation and a CCD-based area detector. The crystal structure was solved by direct methods and refined by full-matrix least-squares techniques to agreement indices wR2=0.116 for all data, and R1=0.040, calculated for the 2764 unique observed reflections (∣Fo∣≥4σF). The compound is orthorhombic, space group Pnma, Z=4, a=7.063(1) Å, b=17.022(3) Å, c=13.172(3) Å, V=1583.5(5) Å3. The structure consists of sheets of phosphate tetrahedra and uranyl pentagonal bipyramids, with composition [(UO2)(PO4)]- and the uranophane sheet anion topology. The sheets are connected by a uranyl pentagonal bipyramid in the interlayer that shares corners with a phosphate tetrahedron on each of two adjacent sheets, resulting in an open framework with isolated H2O groups in the larger cavities of the structure.

  18. Crystal structure of human nicotinic acid phosphoribosyltransferase.

    PubMed

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

    2015-01-01

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

  19. Crystal structure of human nicotinic acid phosphoribosyltransferase

    PubMed Central

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

    2015-01-01

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

  20. Crystal Structure of Homo Sapiens Kynureninase†

    PubMed Central

    Lima, Santiago; Kristoforov, Roman; Momany, Cory; Phillips, Robert S.

    2008-01-01

    Kynureninase is a member of a large family of catalytically diverse but structurally homologous pyridoxal-5′-phosphate dependent enzymes known as the aspartate aminotransferase superfamily or α-family. The Homo sapiens and other eukaryotic constitutive kynureninases preferentially catalyze the hydrolytic cleavage of 3-hydroxy-L-kynurenine to produce 3-hydroxyanthranilate and L-alanine, while L-kynurenine is the substrate of many prokaryotic inducible kynureninases. The human enzyme was cloned with an N-terminal hexahistidine tag, expressed, and purified from a bacterial expression system using Ni-metal ion affinity chromatography. Kinetic characterization of the recombinant enzyme reveals classic Michaelis-Menten behavior, with a Km= 28.3 ± 1.9 μM, and a specific activity of 1.75 μmol min-1 mg-1 for 3-hydroxy-DL-kynurenine. Crystals of recombinant kynureninase were obtained that diffracted to 2.0 Å, and the atomic structure of the PLP-bound holoenzyme was solved by molecular replacement using the Pseudomonas fluorescens kynureninase structure (PDB accession 1qz9) as the phasing model. A structural superposition with the P. fluorescens kynureninase revealed that these two structures resemble the “open” and “closed” conformations of aspartate aminotransferase. The comparison illustrates the dynamic nature of these proteins’ small domains and reveals a role for Arg-434 similar to that in other AAT α-family members. Docking of 3-hydroxy-L-kynurenine into the human kynureninase active site suggests that Asn-333 and His-102 are involved in substrate binding and molecular discrimination between inducible and constitutive kynureninase substrates. PMID:17300176

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

    PubMed

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

    2009-12-24

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

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

    PubMed

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

    2015-11-10

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

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

    PubMed

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

    2011-02-21

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

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

    SciTech Connect

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

    2005-11-15

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

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

    NASA Astrophysics Data System (ADS)

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

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

  6. Spectroscopic properties of Carcinus aestuarii hemocyanin and its structural subunits

    NASA Astrophysics Data System (ADS)

    Dolashka-Angelova, Pavlina; Hristova, Rumiyana; Stoeva, Stanka; Voelter, Wolfgang

    1999-12-01

    Hemocyanin (Hc) of Carcinus aestuarii contains three major and one minor electrophoretically separable polypeptide chains which were purified by fast protein liquid chromatography (FPLC) ion exchange chromatography. N-terminal amino acid sequences of four structural subunits (SSs) from C. aestuarii were compared with known N-terminal sequences from other arthropodan hemocyanins. The conformational changes, induced by various treatments, were monitored by far UV, CD and fluorescence spectroscopy. The critical temperatures for the structural subunits, Tc, determined by fluorescence spectroscopy, are in the region of 52-59°C and coincide with the melting temperatures, Tm (49-55°C), determined by CD spectroscopy. The free energy of stabilization in water, Δ GDH 2O , toward guanidinium hydrochloride is about 1.3 times higher for the dodecameric Hc as compared to the isolated subunits and about one time higher for Ca1, comparing with other SSs. The studies reveal that the conformational stability of the native dodecamer towards various denaturants (temperature and guanidinium hydrochloride) indicate that the quaternary structure is stabilized by oligomerization between structural subunits, and the possibility of a structural role of the sugar mojeties cannot be excluded.

  7. Structure dependent hydrogen induced etching features of graphene crystals

    NASA Astrophysics Data System (ADS)

    Thangaraja, Amutha; Shinde, Sachin M.; Kalita, Golap; Papon, Remi; Sharma, Subash; Vishwakarma, Riteshkumar; Sharma, Kamal P.; Tanemura, Masaki

    2015-06-01

    H2 induced etching of graphene is of significant interest to understand graphene growth process as well as to fabricate nanoribbons and various other structures. Here, we demonstrate the structure dependent H2 induced etching behavior of graphene crystals. We synthesized graphene crystals on electro-polished Cu foil by an atmospheric pressure chemical vapor deposition process, where some of the crystals showed hexagonal shaped snowflake-dendritic morphology. Significant differences in H2 induced etching behavior were observed for the snowflake-dendritic and regular graphene crystals by annealing in a gas mixture of H2 and Ar. The regular graphene crystals were etched anisotropically creating hexagonal holes with pronounced edges, while etching of all the dendritic crystals occurred from the branches of lobs creating symmetrical fractal structures. The etching behavior provides important clue of graphene nucleation and growth as well as their selective etching to fabricate well-defined structures for nanoelectronics.

  8. Conformational polymorphs of isobutyl-6-amino-5-cyano-2-methyl-4-phenyl-4H-pyran-3-carboxylate: spectroscopic, structural and DFT approach.

    PubMed

    Prasad, A Aditya; Kumar, C Udhaya; Prakasam, B Arul; Meenakshisundaram, S P

    2016-06-01

    The crystal structure of a new crystalline phase, polymorph (II) of isobutyl-6-amino-5-cyano-2-methyl-4-phenyl-4H-pyran-3-carboxylate, was accurately determined by single-crystal X-ray diffraction analysis providing a clean identification of polymorphic forms. Comparison with a known phase, referred to as polymorph (I), reveals the type of supramolecular assembly. Inter- and intramolecular hydrogen-bonding interactions exhibit various supramolecular architectures in crystal packing and these variations confirm well the polymorphism in isobutyl-6-amino-5-cyano-2-methyl-4-phenyl-4H-pyran-3-carboxylate (IAPC) crystal structure. Crystal cohesion is achieved by N-H...N, N-H...O and C-H...H-C interactions, responsible for the formation and strengthening of the supramolecular assembly. The objective of this investigation is to study crystalline forms which can offer enhanced physicochemical properties, and also to recognize the molecular orientations between such forms. The conformational polymorphs of IAPC were compared spectroscopically by FT-IR and FT-Raman. The bulk phases were studied by X-ray powder diffraction patterns. External morphology was investigated using scanning electron microscopic images. The molecular interactions were quantified using Hirshfeld surface and fingerprint analysis. Density functional theory (DFT) computations were used to optimize the structure. The optimized structure is further subjected to an analysis of Mulliken population, natural population and electrostatic potential. PMID:27240761

  9. Optical spectroscopic properties of active nano-crystal doped transparent glass composites

    NASA Astrophysics Data System (ADS)

    Myint, Thandar

    Cr4+ and some Cr3+ ions doped tunable laser media operate in optical telecommunication bands. The tunability of some Cr 3+ doped media cover the telecom O,E,S,C and L bands while Er doped glass, widely used in optical amplifiers, covers only C bands. If the telecom utilizes Cr doped materials as the amplified media in fiber lasers and amplifiers, it can revolutionize the optical communications. But making Cr doped crystal in fiber form is difficult and expensive while the glass is the best material to make the fiber form. One solution to solve this problem is to synthesize the glass composites which have the good mechanical properties of glasses and perfect optical properties of bulk single crystals. In this thesis, synthesis and optical properties of chromium doped transparent glass-ceramics with the chemical composition similar to Cunyite(Cr4+:Ca2GeO 4) laser crystal are presented. Broadband structureless fluorescence and high quantum efficiency of new glass-ceramic make it the promising medium for fiber lasers and amplifiers. One barrier in synthesizing the glass ceramics is controlling the size of the nanocrystals inside the glass matrix. Since the glass composite is a two-phase (glass and crystal phase) system, the size of nano-crystals must be small to reduce the scattering and consequently produce the transparent sample. In order to produce smaller nano-crystals inside the glass matrix, porous glass with pore size of 4nm is also investigated. The optical properties of synthesized porous-glass show the crystal having a few lattice parameters in size can be grown inside the pore network.

  10. Crystal structures of five 6-mercaptopurine derivatives

    PubMed Central

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

    2016-01-01

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

  11. Crystal structure of a Trypanosoma brucei metacaspase

    PubMed Central

    McLuskey, Karen; Rudolf, Jana; Proto, William R.; Isaacs, Neil W.; Coombs, Graham H.; Moss, Catherine X.; Mottram, Jeremy C.

    2012-01-01

    Metacaspases are distantly related caspase-family cysteine peptidases implicated in programmed cell death in plants and lower eukaryotes. They differ significantly from caspases because they are calcium-activated, arginine-specific peptidases that do not require processing or dimerization for activity. To elucidate the basis of these differences and to determine the impact they might have on the control of cell death pathways in lower eukaryotes, the previously undescribed crystal structure of a metacaspase, an inactive mutant of metacaspase 2 (MCA2) from Trypanosoma brucei, has been determined to a resolution of 1.4 Å. The structure comprises a core caspase fold, but with an unusual eight-stranded β-sheet that stabilizes the protein as a monomer. Essential aspartic acid residues, in the predicted S1 binding pocket, delineate the arginine-specific substrate specificity. In addition, MCA2 possesses an unusual N terminus, which encircles the protein and traverses the catalytic dyad, with Y31 acting as a gatekeeper residue. The calcium-binding site is defined by samarium coordinated by four aspartic acid residues, whereas calcium binding itself induces an allosteric conformational change that could stabilize the active site in a fashion analogous to subunit processing in caspases. Collectively, these data give insights into the mechanistic basis of substrate specificity and mode of activation of MCA2 and provide a detailed framework for understanding the role of metacaspases in cell death pathways of lower eukaryotes. PMID:22529389

  12. Crystal Structure of Human Kynurenine Aminotransferase ll*

    SciTech Connect

    Han,Q.; Robinson, H.; Li, J.

    2008-01-01

    Human kynurenine aminotransferase II (hKAT-II) efficiently catalyzes the transamination of knunrenine to kynurenic acid (KYNA). KYNA is the only known endogenous antagonist of N-methyl-d-aspartate (NMDA) receptors and is also an antagonist of 7-nicotinic acetylcholine receptors. Abnormal concentrations of brain KYNA have been implicated in the pathogenesis and development of several neurological and psychiatric diseases in humans. Consequently, enzymes involved in the production of brain KYNA have been considered potential regulatory targets. In this article, we report a 2.16 Angstroms crystal structure of hKAT-II and a 1.95 Angstroms structure of its complex with kynurenine. The protein architecture of hKAT-II reveals that it belongs to the fold-type I pyridoxal 5-phosphate (PLP)-dependent enzymes. In comparison with all subclasses of fold-type I-PLP-dependent enzymes, we propose that hKAT-II represents a novel subclass in the fold-type I enzymes because of the unique folding of its first 65 N-terminal residues. This study provides a molecular basis for future effort in maintaining physiological concentrations of KYNA through molecular and biochemical regulation of hKAT-II.

  13. X-ray, spectroscopic and semiempirical investigation of the structure of lasalocid 6-bromohexyl ester and its complexes with alkali metal cations

    NASA Astrophysics Data System (ADS)

    Huczyński, Adam; Ratajczak-Sitarz, Małgorzata; Katrusiak, Andrzej; Brzezinski, Bogumil

    2011-07-01

    The ionophoric antibiotic lasalocid acid has been converted to a novel 6-bromohexyl ester (LASBR) and its structure has been determined in the crystal by X-ray diffraction and in solution by NMR and FT-IR methods. In the crystal two symmetry-independent LASBR molecules are present. The structure of LASBR in solution is slightly different because the strongest intramolecular C(1) dbnd O⋯H sbnd (3)O hydrogen bond in the pseudo-aromatic ring becomes partially broken and a new hydrogen bond between O(4)H and carbonyl group C(13) dbnd O is formed. LASBR forms complexes with Li +, Na + and K + cations of exclusively 1:1 stoichiometry. The structures of complexes have been studied and visualized using semi-empirical calculation based on results of spectrometric and spectroscopic investigation. It is demonstrated that in contrast to lasalocid acid the novel ester forms preferential complexes with Li + cation.

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

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

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

    PubMed

    Rödström, Karin E J; Lindkvist-Petersson, Karin

    2016-01-01

    Structure determination of superantigens and the complexes they form with immune receptors have over the years provided insight in their modes of action. This technique requires growing large and highly ordered crystals of the superantigen or receptor-superantigen complex, followed by exposure to X-ray radiation and data collection. Here, we describe methods for crystallizing superantigens and superantigen-receptor complexes using the vapor diffusion technique, how the crystals may be optimized, and lastly data collection and structure determination. PMID:26676036

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

    NASA Astrophysics Data System (ADS)

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

    2013-10-01

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

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

    PubMed

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

    2013-10-01

    Good quality and bulk single crystals of Pyrrolidinium p-Hydroxybenzoate (PYPHB), a newly identified nonlinear optical material, were grown for the first time. It crystallizes in monoclinic system with an acentric space group Cc. The molecular structure including carbon, proton positions and functional groups has been confirmed through nuclear magnetic resonance and Fourier transform infrared spectra. Its transmission window has been observed for UV-VIS-NIR region along with its theoretical limit. The photoluminescence behavior has been observed by exciting the crystal at 310 nm. The principal refractive indices and second order NLO coefficient of PYPHB are determined by Mach-Zehnder interferometer and Maker-Fringe experiments respectively. The coherence length and phase-matchablility of PYPHB crystals are measured to explore its efficacy towards device fabrications. The dipole moment, polarizability and molecular orbital energy of an isolated PYPHB molecule have also been calculated theoretically and the results are found to corroborate the experimental values. PMID:23792235

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  19. Undergraduates Improve upon Published Crystal Structure in Class Assignment

    ERIC Educational Resources Information Center

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

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2008-11-01

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

  1. Piezoelectric spectroscopic studies of Zn1-x-yBexMnymixed crystals

    NASA Astrophysics Data System (ADS)

    Zakrzewski, J.; Malinski, M.; Strzałkowski, K.; Firszt, F.; Legowski, S.; Meczynska, H.

    2008-02-01

    This paper presents results of experimental and theoretical piezoelectric studies of a group of mixed crystals of the type Zn1 - x - yBexMnySe. The fittings of theoretical to experimental amplitude and phase piezoelectric spectra were performed in a modified Jackson and Amer model. The influence of the surface treatment such as grinding, polishing and etching on the PZE spectra is analysed in the model of surface defects applied for the interpretation of the spectra for energies of photons below the energy gap of the crystal.

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

    SciTech Connect

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

    2014-02-28

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

  3. Three-Dimensional Photonic Crystal Laser-Driven Accelerator Structures

    SciTech Connect

    Cowan, B.; /SLAC

    2006-09-07

    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 describe guiding of a speed-of-light accelerating mode by a defect in the photonic crystal lattice and discuss the properties of this mode, including particle beam dynamics and potential coupling methods for the structure. We also discuss possible materials and power sources for this structure and their effects on performance parameters, as well as possible manufacturing techniques and the required tolerances. In addition we describe the computational technique and possible improvements in numerical modeling that would aid development of photonic crystal structures.

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

    ERIC Educational Resources Information Center

    Cady, Susan G.

    1997-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-07-01

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

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

    PubMed

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

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

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

    PubMed Central

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

    2016-01-01

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

  9. Spectroscopic elucidation of chemical structure of plasma-polymerized pyridine

    SciTech Connect

    Hozumi, K.; Kitamura, K.; Hashimoto, H.; Hamaoka, T.; Fujisawa, H.; Ishizawa, T.

    1983-05-01

    Chemical structure of the plasma-polymerized pyridine film produced on a glass reactor wall by means of the plasma technique in which the pyridine vapor was electronically excited by high-frequency power under a reduced pressure was elucidated. The polymer was highly hydrophilic and was soluble to some of the polar organic solvents so that nitrogen-containing polar functional groups were predicted to participate in the chemical structure of the polymer molecules. /sup 1/H-NMR, /sup 13/CNMR, and IR spectroscopies, high-resolution mass spectral data, and number-average molecular weight determination with some aid of microelemental analysis revealed the presence of various functional groups such as imine, nitrile, amine, pyridine ring, its N-oxide, and even amide. The oxygen atoms involved in the last two groups were supposedly introduced by contact with ambient air after the plasma process. The hydrophilic nature of the polymer which was essential for preparing reverse osmosis membrane was therefore due to the overall hydration effect of these polar functional groups.

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

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

  11. Structural, Magnetic and Spectroscopic Studies of Thin Manganite Films

    NASA Astrophysics Data System (ADS)

    Tyson, T. A.

    2003-03-01

    Starting from early experiments [1], evidence has been found for a close coupling of strain and the magnetotransport properties of manganite films. The characteristic feature found is that the metal to insulator transition temperature (TMI) is suppressed in very thin films [2]. In addition, studies show that the magnetic transition temperature (Tc) and TMI decouple in ultrathin films [3]. Systematic magnetization studies reveal that strain induces strong magnetic anisotropy [4]. Theoretical work also points to the sensitivity of Tc to biaxial strain [5]. Most studies have focused on single bulk properties. In order to understand the correlations between strain and the transport and magnetic properties we have examined the structure of films on multiple length scales. The local structure of films have been studies by x-ray absorption spectroscopy. The long -range structure has been studied by high-resolution x-ray diffraction and the microstructure has been studied by AFM measurements. These measurements are correlated with bulk magnetization and transport studies. Insight is gained on the evolution of lattice strain and Jahn-Teller distortions with thickness. Direct evidence is found for the arrest of charge ordering with strain and the existence of strain induced insulating regions of films. The magnetic ordering and transport properties as a function of strain as compared with bandstructure calculations. This work is supported by NSF Career Grant DMR-9733862 and DMR-0209243. Collaborators: Q. Qian, M. Deleon (NJIT), C. Dubourdiu (CNRS), J. Bai (ORNL), W. Prellier, A. Biswas, R. L. Greene (U. Maryland) [1] S. Jin et al., Appl. Phys. Lett. 67, 557 (1995). [2] (a) J. Z. Sun et al. Appl. Phys. Lett. 74, 3017 (1999). (b) F. S. Razi et al., Appl. Phys. Lett 76, 155 (2000) [3] J. Aarts et al., Appl. Phys. Lett. 72, 2975 (1998). (b) R. A. Rao et al., J. Appl. Phys. 85, 4794 (1999). [4] (a) X. W. Wu et al., Phys. Rev. B 61, 501 (2000). (b) J. O'Donnell et al., Appl. Phys

  12. Theoretical spectroscopic studies on chemical and electronic structures of arginylglycine.

    PubMed

    Li, Hongbao; Li, Leilei; Jiang, Jun; Lin, Zijing; Luo, Yi

    2015-10-14

    The energy differences between canonical and zwitterionic isomers of arginylglycine (ArgGly) at the CCSD/aug-cc-pVDZ level are too small (less than 1 kcal mol(-1)) to determine the dominant form in the gas phase from the energetic point of view. First-principles simulations have been performed for near-edge X-ray absorption fine-structure (NEXAFS) spectra and X-ray photoelectron spectra (XPS) at C, N and O K-edges, as well as for infrared (IR) spectra of neutral ArgGly. Noticeable spectral differences were found which enable the unambiguous identification of different neutral groups. We thus demonstrate X-ray spectroscopy as a powerful technique to study the conformation dependent chemical and electronic properties of neutral ArgGly. PMID:26266331

  13. Microstructure and Crystal Structure in TAGS Compositions

    SciTech Connect

    Thompson, A. J.; Sharp, J; Rawn, Claudia J

    2009-01-01

    GeTe, a small bandgap semiconductor that has native p-type defects due to Ge vacancies, is an important constituent in the thermoelectric material known as TAGS. TAGS is an acronym for alloys of GeTe with AgSbTe{sub 2}, and compositions are normally designated as TAGS-x, where x is the fraction of GeTe. TAGS-85 is the most important with regard to applications, and there is also commercial interest in TAGS-80. The crystal structure of GeTe{sub 1+{delta}} has a composition-dependent phase transformation at a temperature ranging from 430 C ({delta} = 0) to {approx}400 C ({delta} = 0.02). The high-temperature form is cubic. The low-temperature form is rhombohedral for {delta} < 0.01, as is the case for good thermoelectric performance. Addition of AgSbTe{sub 2} shifts the phase transformation to lower temperatures, and one of the goals of this work is a systematic study of the dependence of transformation temperature on the parameter x. We present results on phase transformations and associated instabilities in TAGS compositions in the range of 70 at.% to 85 at.% GeTe.

  14. Crystal structure of tolyl­fluanid

    PubMed Central

    Cho, Seonghwa; Kim, Jineun; Kang, Gihaeng; Kim, Tae Ho

    2014-01-01

    The title compound, C10H13Cl2FN2O2S2 {systematic name: N-[(di­chloro­fluoro­methyl)­sulfanyl]-N′,N′-dimethyl-N-p-tolyl­sulfamide}, is a well known fungicide. The dihedral angle between the mean plane of the di­methyl­amino group and that of the benzene ring is 32.3 (3)°. One Cl atom and one F atom of the di­chloro­fluoro­methyl­thio group are disordered over two sets of sites with an occupancy ratio of 0.605 (9):0.395 (9). In the crystal structure, two C—H⋯Cl hydrogen bonds link adjacent mol­ecules, forming dimers with R 2 2(14) loops. C—H⋯O hydrogen bonds link pairs of dimers into chains along the b-axis direction. These chains are joined by an additional C—H⋯O contact, generating a sheet in the ab plane. PMID:25484703

  15. Crystal structure of Clostridium difficile toxin A.

    PubMed

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

    2016-01-01

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

  16. Crystal structure of Clostridium difficile toxin A

    PubMed Central

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

    2016-01-01

    Clostridium difficile infection is the leading cause of hospital-acquired diarrhoea and pseudomembranous colitis. Disease is mediated by the actions of two toxins, TcdA and TcdB, which cause the diarrhoea, as well as inflammation and necrosis within the colon1,2. The toxins are large (308 and 270 kDa, respectively), homologous (47% amino acid identity) glucosyltransferases that target small GTPases within the host3,4. The multidomain toxins enter cells by receptor-mediated endocytosis and, upon exposure to the low pH of the endosome, insert into and deliver two enzymatic domains across the membrane. Eukaryotic inositol-hexakisphosphate (InsP6) binds an autoprocessing domain to activate a proteolysis event that releases the N-terminal glucosyltransferase domain into the cytosol. Here, we report the crystal structure of a 1,832-amino-acid fragment of TcdA (TcdA1832), which reveals a requirement for zinc in the mechanism of toxin autoprocessing and an extended delivery domain that serves as a scaffold for the hydrophobic α-helices involved in pH-dependent pore formation. A surface loop of the delivery domain whose sequence is strictly conserved among all large clostridial toxins is shown to be functionally important, and is highlighted for future efforts in the development of vaccines and novel therapeutics. PMID:27512603

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

    PubMed

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

    2015-02-25

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

  18. Spectroscopic and Crystal Field Consequences of Fluoride Binding by [Yb⋅DTMA]3+ in Aqueous Solution

    PubMed Central

    Blackburn, Octavia A.; Chilton, Nicholas F.; Keller, Katharina; Tait, Claudia E.; Myers, William K.; McInnes, Eric J. L.; Kenwright, Alan M.; Beer, Paul D.; Timmel, Christiane R.

    2015-01-01

    Abstract Yb⋅DTMA forms a ternary complex with fluoride in aqueous solution by displacement of a bound solvent molecule from the lanthanide ion. [Yb⋅DTMA⋅F]2+ and [Yb⋅DTMA⋅OH2]3+ are in slow exchange on the relevant NMR timescale (<2000 s−1), and profound differences are observed in their respective NMR and EPR spectra of these species. The observed differences can be explained by drastic modification of the ligand field states due to the fluoride binding. This changes the magnetic anisotropy of the YbIII ground state from easy‐axis to easy‐plane type, and this change is easily detected in the observed magnetic anisotropy despite thermal population of more than just the ground state. The spectroscopic consequences of such drastic changes to the ligand field represent important new opportunities in developing fluoride‐responsive complexes and contrast agents. PMID:27478267

  19. Spectroscopic and Crystal Field Consequences of Fluoride Binding by [Yb⋅DTMA]3+ in Aqueous Solution

    PubMed Central

    Blackburn, Octavia A; Chilton, Nicholas F; Keller, Katharina; Tait, Claudia E; Myers, William K; McInnes, Eric J L; Kenwright, Alan M; Beer, Paul D; Timmel, Christiane R; Faulkner, Stephen

    2015-01-01

    Yb⋅DTMA forms a ternary complex with fluoride in aqueous solution by displacement of a bound solvent molecule from the lanthanide ion. [Yb⋅DTMA⋅F]2+ and [Yb⋅DTMA⋅OH2]3+ are in slow exchange on the relevant NMR timescale (<2000 s−1), and profound differences are observed in their respective NMR and EPR spectra of these species. The observed differences can be explained by drastic modification of the ligand field states due to the fluoride binding. This changes the magnetic anisotropy of the YbIII ground state from easy-axis to easy-plane type, and this change is easily detected in the observed magnetic anisotropy despite thermal population of more than just the ground state. The spectroscopic consequences of such drastic changes to the ligand field represent important new opportunities in developing fluoride-responsive complexes and contrast agents. PMID:26223970

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

    PubMed

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

    2016-01-01

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

  1. Site-Specific Spectroscopic Reporters of the Local Electric Field, Hydration, Structure, and Dynamics of Biomolecules

    PubMed Central

    Waegele, Matthias M.; Culik, Robert M.; Gai, Feng

    2011-01-01

    Elucidating the underlying molecular mechanisms of protein folding and function is a very exciting and active research area, but poses significant challenges. This is due in part to the fact that existing experimental techniques are incapable of capturing snapshots along the ‘reaction coordinate’ in question with both sufficient spatial and temporal resolutions. In this regard, recent years have seen increased interests and efforts in development and employment of site-specific probes to enhance the structural sensitivity of spectroscopic techniques in conformational and dynamical studies of biological molecules. In particular, the spectroscopic and chemical properties of nitriles, thiocyanates, and azides render these groups attractive for the interrogation of complex biochemical constructs and processes. Here, we review their signatures in vibrational, fluorescence and NMR spectra and their utility in the context of elucidating chemical structure and dynamics of protein and DNA molecules. PMID:22003429

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

    NASA Astrophysics Data System (ADS)

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

    2013-05-01

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

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

    PubMed

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

    2013-05-01

    Single crystal of bis mercury ferric chloride tetra thiocyanate [Hg2FeCl3(SCN)4; (MFCTC)] was grown from ethanol-water (3:1) mixed solvent using slow evaporation solvent technique (SEST) for the first time. The cell parameters of the grown crystal were confirmed by single crystal XRD. The coordination of transition metal ions with the SCN ligand is well-identified using FT-IR spectral analysis. The chemical composition of MFCTC was confirmed using CHNS elemental test. The ESR spectral profile of MFCTC was recorded from 298 K to 110K, which strongly suggests the incorporation of Fe(3+) ion and its environment with respect to SCN ligand. The HPLC chromatogram of MFCTC highlights the purity of the compound. The UV-Vis-NIR studies revealed the ultra violet cut-off wavelength of MFCTC in ethanol as 338 nm. The dielectric constant and dielectric loss of the sample were studied as a function of frequency and temperature. The TGA-DTA and DSC thermal analysis show that the sample is thermally stable up to 234.31 °C, which is comparatively far better than the thermal stability of Hg3CdCl2(SCN)6; (171.3 °C) and other metal-organic coordination complex crystals such as CdHg(SCN)4 (198.5 °C), Hg(N2H4CS)4Mn(SCN)4 (199.06 °C) and Hg(N2H4CS)4Zn(SCN)4 (185 °C). The SHG conversion efficiency of MFCTC is found to be higher than KDP. PMID:23501934

  4. Raman spectroscopic study of cation disorder in poly- and single crystals of the nickel aluminate spinel

    NASA Astrophysics Data System (ADS)

    Laguna-Bercero, M. A.; Sanjuán, M. L.; Merino, R. I.

    2007-05-01

    The Raman spectrum of NiAl2O4 inverse spinel has been studied in quenched polycrystalline pellets produced by solid-state reaction and in single crystals grown by the floating zone method. The lattice parameters and inversion degrees were determined by x-ray diffraction. Polarization measurements in single crystals allow mode symmetry assignment. Then, a correlation is established between the bands observed in polycrystalline samples and those of single crystals. Both kinds of sample present more bands than the five expected (A1g+Eg+3T2g) in a cubic Fd3m spinel. This multiplicity is attributed to the almost fully inverted cation distribution in NiAl2O4, with inversion parameter xap0.9. The multiplicity of the high-frequency A1g band, in particular, is attributed to the different possible configurations of Ni2+ and Al3+ cations occupying the three octahedral sites close to a given oxygen ion. A strong downshift of the Eg mode frequency, as compared to the normal spinel MgAl2O4, is attributed to the longer bonding distance between oxygen and octahedral cations in inverse II-III spinels. Due to the small range of variation of x upon thermal treatment in NiAl2O4, no significant differences were found between the spectra of samples quenched at different temperatures, from 800 to 1200 °C.

  5. Novel photonic crystal cavities and related structures.

    SciTech Connect

    Luk, Ting Shan

    2007-11-01

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

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

    PubMed

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

    2015-08-24

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

  7. Photonic crystal structures with tunable structure color as colorimetric sensors.

    PubMed

    Wang, Hui; Zhang, Ke-Qin

    2013-01-01

    Colorimetric sensing, which transduces environmental changes into visible color changes, provides a simple yet powerful detection mechanism that is well-suited to the development of low-cost and low-power sensors. A new approach in colorimetric sensing exploits the structural color of photonic crystals (PCs) to create environmentally-influenced color-changeable materials. PCs are composed of periodic dielectrics or metallo-dielectric nanostructures that affect the propagation of electromagnetic waves (EM) by defining the allowed and forbidden photonic bands. Simultaneously, an amazing variety of naturally occurring biological systems exhibit iridescent color due to the presence of PC structures throughout multi-dimensional space. In particular, some kinds of the structural colors in living organisms can be reversibly changed in reaction to external stimuli. Based on the lessons learned from natural photonic structures, some specific examples of PCs-based colorimetric sensors are presented in detail to demonstrate their unprecedented potential in practical applications, such as the detections of temperature, pH, ionic species, solvents, vapor, humidity, pressure and biomolecules. The combination of the nanofabrication technique, useful design methodologies inspired by biological systems and colorimetric sensing will lead to substantial developments in low-cost, miniaturized and widely deployable optical sensors. PMID:23539027

  8. Photonic Crystal Structures with Tunable Structure Color as Colorimetric Sensors

    PubMed Central

    Wang, Hui; Zhang, Ke-Qin

    2013-01-01

    Colorimetric sensing, which transduces environmental changes into visible color changes, provides a simple yet powerful detection mechanism that is well-suited to the development of low-cost and low-power sensors. A new approach in colorimetric sensing exploits the structural color of photonic crystals (PCs) to create environmentally-influenced color-changeable materials. PCs are composed of periodic dielectrics or metallo-dielectric nanostructures that affect the propagation of electromagnetic waves (EM) by defining the allowed and forbidden photonic bands. Simultaneously, an amazing variety of naturally occurring biological systems exhibit iridescent color due to the presence of PC structures throughout multi-dimensional space. In particular, some kinds of the structural colors in living organisms can be reversibly changed in reaction to external stimuli. Based on the lessons learned from natural photonic structures, some specific examples of PCs-based colorimetric sensors are presented in detail to demonstrate their unprecedented potential in practical applications, such as the detections of temperature, pH, ionic species, solvents, vapor, humidity, pressure and biomolecules. The combination of the nanofabrication technique, useful design methodologies inspired by biological systems and colorimetric sensing will lead to substantial developments in low-cost, miniaturized and widely deployable optical sensors. PMID:23539027

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

    PubMed Central

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

    2012-01-01

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

  10. Structural and Thermoelectric Properties of Tungsten Diselenide Crystals

    NASA Astrophysics Data System (ADS)

    Patel, K. K.; Patel, K. D.; Patel, Mayur; Patel, C. A.; Pathak, V. M.; Srivastava, R.

    2011-12-01

    Crystals of Tungsten diselenide (WSe2) have been grown by direct vapour transport (DVT) technique using micro processor controlled dual zone horizontal furnace. The chemical composition and structure of grown crystals were confirmed using energy dispersive analysis of X-ray (EDAX) and X-ray diffraction (XRD). In the present investigation thermoelectric power measurements (TEP) have been carried out on the grown crystals. Different electrical transport parameters of semiconductors have been determined and discussed in the paper.

  11. Structural, spectral and mechanical studies of bimetallic crystal: cadmium manganese thiocyanate single crystals

    NASA Astrophysics Data System (ADS)

    Manikandan, M.; Vijaya Prasath, G.; Bhagavannarayan, G.; Vijayan, N.; Mahalingam, T.; Ravi, G.

    2012-09-01

    A nonlinear optical bimetallic thiocyanate complex crystal, cadmium manganese thiocyanate (CMTC) has been successfully synthesized. The growth of single crystals of cadmium manganese thiocyanate has been accomplished from aqueous solution using slow evaporation method. The presence of manganese and cadmium in the synthesized material was confirmed through energy dispersive spectrum (EDS) analysis. Structural analysis was carried out using powder X-ray diffractometer (PXRD) and crystalline perfection of the grown crystals was ascertained by high-resolution X-ray diffraction (HRXRD) analysis. Fourier transform infrared (FTIR) spectrum was taken to confirm the functional groups. The transmittance spectrum of the crystal in the UV-visible region has been recorded and the cutoff wavelength has been determined. The dielectric measurements for the crystals were performed for various frequencies and temperatures. The mechanical properties were evaluated by Vickers microhardness testing, which reveals hardness and stiffness constant of the crystals.

  12. Optical phonon modes and crystal structure of NaLaF4 single crystals

    NASA Astrophysics Data System (ADS)

    Lage, Márcio Martins; Matinaga, Franklin Massami; Gesland, Jean-Yves; Moreira, Roberto Luiz

    2006-03-01

    Polarized Raman scattering and infrared reflectivity measurements have been used to investigate the crystal structure of Czochralski-grown NaLaF4 single crystals. The phonon symmetries, the simultaneous presence of polar modes in the infrared and Raman spectra, as well as the observation of piezoelectric resonance, helped us to identify the P6 group as the correct one for this crystal. This material belongs to a family of sodium lanthanide tetrafluorides (NaLnF4) crystals, whose photoluminescence efficiency is comparable to LiYF4. Therefore, NaLaF4 crystals may be important in the development of diode pumped up-conversion solid-state lasers. The number and behavior of the observed optical phonon modes were analyzed in terms of group theory predictions for the group symmetry found. A few anomalies in the phonon characteristics are discussed in terms of cationic disorder in the crystal lattice.

  13. Thermal, spectroscopic and laser properties of Nd3+ in gadolinium scandium gallium garnet crystal produced by optical floating zone method

    NASA Astrophysics Data System (ADS)

    Tian, Li; Wang, Shuxian; Wu, Kui; Wang, Baolin; Yu, Haohai; Zhang, Huaijin; Cai, Huaqiang; Huang, Hui

    2013-12-01

    A neodymium-doped gadolinium scandium gallium garnet (Nd:GSGG) single crystal with dimensions of Φ 5 × 20 mm2 has been grown by means of optical floating zone (OFZ). X-ray powder diffraction (XRPD) result shows that the as-grown Nd:GSGG crystal possesses a cubic structure with space group Ia3d and a cell parameter of a = 1.2561 nm. Effective elemental segregation coefficients of the Nd:GSGG as-grown crystal were calculated by using X-ray fluorescence (XRF). The thermal properties of the Nd:GSGG crystal were systematically studied by measuring the specific heat, thermal expansion and thermal diffusion coefficient, and the thermal conductivity of this crystal was calculated. The absorption and luminescence spectra of Nd:GSGG were measured at room temperature (RT). By using the Judd-Ofelt (J-O) theory, the theoretical radiative lifetime was calculated and compared with the experimental result. Continuous wave (CW) laser performance was achieved with the Nd:GSGG at the wavelength of 1062 nm when it was pumped by a laser diode (LD). A maximum output power of 0.792 W at 1062 nm was obtained with a slope efficiency of 11.89% under a pump power of 7.36 W, and an optical-optical conversion efficiency of 11.72%.

  14. Application of Spectroscopic Methods for Structural Analysis of Chitin and Chitosan

    PubMed Central

    Kumirska, Jolanta; Czerwicka, Małgorzata; Kaczyński, Zbigniew; Bychowska, Anna; Brzozowski, Krzysztof; Thöming, Jorg; Stepnowski, Piotr

    2010-01-01

    Chitin, the second most important natural polymer in the world, and its N-deacetylated derivative chitosan, have been identified as versatile biopolymers for a broad range of applications in medicine, agriculture and the food industry. Two of the main reasons for this are firstly the unique chemical, physicochemical and biological properties of chitin and chitosan, and secondly the unlimited supply of raw materials for their production. These polymers exhibit widely differing physicochemical properties depending on the chitin source and the conditions of chitosan production. The presence of reactive functional groups as well as the polysaccharide nature of these biopolymers enables them to undergo diverse chemical modifications. A complete chemical and physicochemical characterization of chitin, chitosan and their derivatives is not possible without using spectroscopic techniques. This review focuses on the application of spectroscopic methods for the structural analysis of these compounds. PMID:20559489

  15. Evaluation of the photodegradation of crystal violet upon light exposure by mass spectrometric and spectroscopic methods.

    PubMed

    Weyermann, Céline; Kirsch, Dieter; Vera, César Costa; Spengler, Bernhard

    2009-03-01

    Crystal violet is a very common dye in ballpoint ink. Recent research suggests that the degradation of triarylmethane dyes gives an indication of the age of a ballpoint pen entry on a document. The main problem for the quantitative evaluation of the degradation is that it is highly dependent on the exposure to light. Moreover additional factors, such as additives and substrate play an important role in this process. The aim of this work is to compare the degradation pathways of the pure dye in water and ethanol upon exposure to xenon light by UV/VIS spectrophotometry and laser desorption ionization. Significant differences have been observed in the products and the kinetics of the degradation. N-demethylation, an expected decomposition process, was found to take place only in aqueous solution and kinetics calculations showed that the degradation occurred 2.5 times faster in ethanol compared to water. The degradation of crystal violet in inks from four ballpoint pens on paper was also studied for entries made over 2-3 years. It was observed that degradation reactions were quenched by the presence of another dye due to competitive absorption. It was also observed that the thickness of a stroke (concentration of ink) influenced the degradation process. In the absence of light only one ballpoint pen showed slight degradation. A better understanding of the influence of the paper, ink composition, and storage conditions is necessary to interpret correctly the age of an ink based on the degradation of dyes. PMID:19220655

  16. Structural and mechanical studies of cadmium manganese thiocyanate crystal

    NASA Astrophysics Data System (ADS)

    Manikandan, M. R.; Vijayaprasath, G.; babu, G. Anandha; Bhagavannarayan, G.; Vijayan, N.; Ravi, G.

    2012-06-01

    Single crystals of cadmium manganese thiocyanate (CMTC) have been synthesized successfully and grown by slow evaporation method. The structural perfection of the grown crystals has been analyzed by High resolution X-ray diffraction (HRXRD), which shows the crystalline perfection of the grown crystal is quite good. Optical behavior was assessed by UV-Vis analysis and found that no absorption in the UV visible region and it may be useful for second harmonic applications. The mechanical hardness of the grown crystals was studied and Vicker's microhardness, Stiffness constant was calculated.

  17. Hydroflux synthesis and crystal structure of new lanthanide tungstate oxyhydroxides

    NASA Astrophysics Data System (ADS)

    Latshaw, Allison M.; Smith, Mark D.; Chance, W. Michael; zur Loye, Hans-Conrad

    2015-04-01

    Single crystals of Na5Ln(OH)6WO4 where Ln = Er, Tm, and Yb were grown out of a NaOH hydroflux. The crystals were characterized by single crystal X-ray diffraction and were found to crystallize in the monoclinic space group I2/a. The lattice parameter ranges for the three structures are a = 11.2024(7) Å-11.2412(6) Å, b = 16.1850(10) Å-16.2220(10) Å, and c = 11.9913(7) Å-12.0323(7) Å while the β angle range is 101.999(2)°-102.025(2)°.

  18. Spectroscopic, optical, thermal, antimicrobial and density functional theory studies of 4-aminopyridinium 4-hydroxy benzoate hydrate crystal

    NASA Astrophysics Data System (ADS)

    Karthiga Devi, P.; Venkatachalam, K.; Poonkothai, M.

    2016-09-01

    The organic crystal 4-aminopyridinium 4-hydroxy benzoate hydrate was grown using slow evaporation method. Various characterization techniques such as single crystal X-ray diffraction, powder X-ray diffraction, FTIR, UV-visible-NIR spectroscopy and thermal analysis (TG-DSC) were employed to assay the structure and properties of the grown crystal. The antimicrobial evaluation of 4-aminopyridinium 4-hydroxy benzoate hydrate crystal was also performed against some bacteria and fungi. The minimum inhibitory concentration (MIC) values of 4-aminopyridinium 4-hydroxy benzoate hydrate were determined for bacterial and fungal strains. The assessment of optimized structure of the molecule and vibrational frequencies were done using DFT/B3LYP method with 6-31 G (d, p) basis set. The stability of the molecule, hyperconjugative interactions, delocalization of charges and intermolecular hydrogen bond were studied by applying natural bond orbital (NBO) analysis. TD-DFT method employing polarizable continuum model (PCM) was used to examine the electronic absorption spectrum. Evaluation of molecular electrostatic potential (MEP), Mulliken population charges and nonlinear optical (NLO) properties were also carried out. In addition, from the optimized geometry, frontier molecular orbitals analysis was executed.

  19. Spectroscopic study of red-light-emitting centers in K2Al2B2O7: Fe single crystals

    NASA Astrophysics Data System (ADS)

    Ogorodnikov, I. N.; Pustovarov, V. A.; Yakovlev, S. A.; Isaenko, L. I.

    2013-04-01

    We report on spectroscopic study of red-light-emitting centers in K2Al2B2O7 (KABO) single crystals containing ca. 2 ppm of Fe3+. Owing to the low Fe3+-concentration, KABO does not show noticeable absorption due to Fe3+d-d-transitions in the visible spectral region, but it exhibits the charge-transfer (CT) UV-absorption bands O-Fe at 4.7, 5.7 and 6.5 eV. The red photoluminescence at 1.675 eV (FWHM = 0.173 eV) is due to intracenter 4T1 (4G) → 6A1 (6S) transitions in Fe3+ ions. Because of partial overlapping of the fundamental absorption edge of the crystal, where mobile excitons are created, and a broad CT absorption band at 6.5 eV, the most intensive red emission occurs at 7 K upon excitation in the excitonic energy region. The presence of two nonequivalent Al2O7 clusters in KABO lattice provides two different types of red-light-emitting centers in the form of Fe3+ ion occupied the Al3+ tetrahedral site. Superposition of their luminescence bands determines both the spectrum and temperature dependence of red emission in KABO at T = 7-80 K: two bands with the ratio of intensities of ca. 2:1 are 20 meV-shifted relative to each other; two-stage thermal quenching obeys the Mott law with ET = 9 and 20 meV.

  20. Crystal structures of alkylperoxo and anhydride intermediates in an intradiol ring-cleaving dioxygenase

    PubMed Central

    Knoot, Cory J.; Purpero, Vincent M.; Lipscomb, John D.

    2015-01-01

    Intradiol aromatic ring-cleaving dioxygenases use an active site, nonheme Fe3+ to activate O2 and catecholic substrates for reaction. The inability of Fe3+ to directly bind O2 presents a mechanistic conundrum. The reaction mechanism of protocatechuate 3,4-dioxygenase is investigated here using the alternative substrate 4-fluorocatechol. This substrate is found to slow the reaction at several steps throughout the mechanistic cycle, allowing the intermediates to be detected in solution studies. When the reaction was initiated in an enzyme crystal, it was found to halt at one of two intermediates depending on the pH of the surrounding solution. The X-ray crystal structure of the intermediate at pH 6.5 revealed the key alkylperoxo-Fe3+ species, and the anhydride-Fe3+ intermediate was found for a crystal reacted at pH 8.5. Intermediates of these types have not been structurally characterized for intradiol dioxygenases, and they validate four decades of spectroscopic, kinetic, and computational studies. In contrast to our similar in crystallo crystallographic studies of an Fe2+-containing extradiol dioxygenase, no evidence for a superoxo or peroxo intermediate preceding the alkylperoxo was found. This observation and the lack of spectroscopic evidence for an Fe2+ intermediate that could bind O2 are consistent with concerted formation of the alkylperoxo followed by Criegee rearrangement to yield the anhydride and ultimately ring-opened product. Structural comparison of the alkylperoxo intermediates from the intra- and extradiol dioxygenases provides a rationale for site specificity of ring cleavage. PMID:25548185

  1. A Spectroscopic Study of Hydra I: The Possible Progenitor of the Eastern Banded Structure

    NASA Astrophysics Data System (ADS)

    Kimmig, Brian; Hargis, Jonathan R.; Willman, Beth; Caldwell, Nelson; Strader, Jay; Walker, Matthew G.

    2015-01-01

    We present initial results of an MMT/Hectochelle spectroscopic study of the Hydra I spatial overdensity located along the Eastern Banded Structure (EBS) stellar stream. The extended double-lobed structure and strength of the overdensity suggest that Hydra I may be the stream's progenitor and undergoing active disruption. With its distance of only ~10 kpc, Hydra I presents a unique opportunity to study the disruption of a star cluster or dwarf galaxy. In past work, SDSS/SEGUE velocities revealed Hydra I to be a kinematically cold structure. However, the small number of candidate members and the significant SEGUE velocity uncertainties (~10 - 15 km/s) precludes testing the nature of Hydra I. To better understand its chemo-dynamic properties, we have begun a spectroscopic survey of the Hydra I/EBS region in order to (i) obtain a robust, velocity-based selection of candidate member stars, (ii) use precise velocities to measure the velocity dispersion, (iii) study the spatial distribution of spectroscopic members, and (iv) measure its proper motion. At present, we have surveyed a ~3 deg x ~3 deg region, which encompasses the entire ~4 sq. deg spatial extent of Hydra I. We have obtained a total of 1354 spectra in this region, with RV uncertainties smaller than ~5 km/s at magnitudes brighter than g~21.6. This work presents our confirmation of Hydra I as a cold halo structure, as well as a more detailed analysis of the membership and spatial/velocity structure of Hydra I.

  2. Spectroscopic detection and state preparation of a single praseodymium ion in a crystal.

    PubMed

    Utikal, T; Eichhammer, E; Petersen, L; Renn, A; Götzinger, S; Sandoghdar, V

    2014-01-01

    The narrow optical transitions and long spin coherence times of rare earth ions in crystals make them desirable for a number of applications ranging from solid-state spectroscopy and laser physics to quantum information processing. However, investigations of these features have not been possible at the single-ion level. Here we show that the combination of cryogenic high-resolution laser spectroscopy with optical microscopy allows one to spectrally select individual praseodymium ions in yttrium orthosilicate. Furthermore, this spectral selectivity makes it possible to resolve neighbouring ions with a spatial precision of the order of 10 nm. In addition to elaborating on the essential experimental steps for achieving this long-sought goal, we demonstrate state preparation and read out of the three ground-state hyperfine levels, which are known to have lifetimes of the order of hundred seconds. PMID:24722142

  3. The photoacoustic spectroscopic investigations of the surface preparation of ZnSe crystals

    NASA Astrophysics Data System (ADS)

    Chrobak, Ł.; Maliński, M.; Zakrzewski, J.; Strzałkowski, K.

    2009-11-01

    This paper presents results of the photoacoustic (PA) spectral studies of a series of ZnSe crystals with differently prepared surfaces. All samples exhibited the surface absorption connected with defects states located on their surfaces. The quality of the surface preparation is expressed by the surface absorption coefficient spectra of the samples times the thickness of a damaged layer. In this paper both theoretical and experimental photoacoustic amplitude and phase spectra as also the corresponding computed surface and volume optical absorption coefficient spectra of the samples with differently prepared surfaces are presented and discussed. This is the first attempt of the quantitative evaluation of the surface quality of the samples from the photoacoustic experimental spectra.

  4. Spectroscopic investigation of the Cr to Tm energy transfer in Yttrium Aluminum Garnet (YAG) crystals

    NASA Technical Reports Server (NTRS)

    Dibartolo, B.

    1988-01-01

    New and interesting schemes have recently been considered for the efficient operation of solid-state ionic laser systems. Often the available data on these systems were obtained only because they seemed directly related to the laser performance and provide no insight into the physical processes. A more systematic approach is desirable, where more attention is devoted to the elementary basic processes and to the nature of the mechanisms at work. It is with this aim that we have undertaken the present study. Yttrium Aluminum Garnet (Y4Al5O12), called YAG, has two desirable properties as host for rare earth impurities: (1) trivalent rare earth ions can replace the yttrium without any charge compensation problem, and (2) YAG crystals have high cutoff energies. The results of measurements and calculations indicate that the Cr(3+) ion in YAG can be used to sensitize efficiently the Tm(3+) ion.

  5. Woodpile Structure Fabrication for Photonic Crystal Laser Acceleration

    SciTech Connect

    McGuinness, C.; Colby, E.; England, R. J.; Noble, R. J.; Sears, C. M.; Siemann, R.; Spencer, J.; Waltz, D.; Byer, R. L.; Plettner, T.; Cowan, B. M.

    2009-01-22

    We describe initial steps at fabricating a dielectric photonic bandgap accelerator structure designed to operate at near IR frequencies. Such a structure operating at these frequencies requires extremely small, sub-micron sized features, forcing one to use lithographic means for fabrication. A process based upon lithographic equipment at the Stanford Nanofabrication Facility has been developed and a four layer test structure has been fabricated. Unexpected problems with the final etch step, and corresponding modifications to the process flow addressing these problems, are described. Spectroscopic measurements of the structure have been taken and are compared to simulations.

  6. Woodpile Structure Fabrication for Photonic Crystal Laser Acceleration

    SciTech Connect

    McGuinness, C.; Byer, R.L.; Colby, E.; Cowan, B.M.; England, R.J.; Noble, R.J.; Plettner, T.; Sears, C.M.; Siemann, R.; Spencer, J.; Waltz, D.; /SLAC

    2010-06-30

    We describe initial steps at fabricating a dielectric photonic bandgap accelerator structure designed to operate at near IR frequencies. Such a structure operating at these frequencies requires extremely small, sub-micron sized features, forcing one to use lithographic means for fabrication. A process based upon lithographic equipment at the Stanford Nanofabrication Facility has been developed and a four layer test structure has been fabricated. Unexpected problems with the final etch step, and corresponding modifications to the process flow addressing these problems, are described. Spectroscopic measurements of the structure have been taken and are compared to simulations.

  7. Sculpting narrowband Fano resonances inherent in the large-area mid-infrared photonic crystal microresonators for spectroscopic imaging

    PubMed Central

    Liu, Jui-Nung; Schulmerich, Matthew V.; Bhargava, Rohit; Cunningham, Brian T.

    2014-01-01

    Fourier transform infrared (FT-IR) imaging spectrometers are almost universally used to record microspectroscopic imaging data in the mid-infrared (mid-IR) spectral region. While the commercial standard, interferometry necessitates collection of large spectral regions, requires a large data handling overhead for microscopic imaging and is slow. Here we demonstrate an approach for mid-IR spectroscopic imaging at selected discrete wavelengths using narrowband resonant filtering of a broadband thermal source, enabled by high-performance guided-mode Fano resonances in one-layer, large-area mid-IR photonic crystals on a glass substrate. The microresonant devices enable discrete frequency IR (DF-IR), in which a limited number of wavelengths that are of interest are recorded using a mechanically robust instrument. This considerably simplifies instrumentation as well as overhead of data acquisition, storage and analysis for large format imaging with array detectors. To demonstrate the approach, we perform DF-IR spectral imaging of a polymer USAF resolution target and human tissue in the C−H stretching region (2600−3300 cm−1). DF-IR spectroscopy and imaging can be generalized to other IR spectral regions and can serve as an analytical tool for environmental and biomedical applications. PMID:25089433

  8. Sculpting narrowband Fano resonances inherent in the large-area mid-infrared photonic crystal microresonators for spectroscopic imaging.

    PubMed

    Liu, Jui-Nung; Schulmerich, Matthew V; Bhargava, Rohit; Cunningham, Brian T

    2014-07-28

    Fourier transform infrared (FT-IR) imaging spectrometers are almost universally used to record microspectroscopic imaging data in the mid-infrared (mid-IR) spectral region. While the commercial standard, interferometry necessitates collection of large spectral regions, requires a large data handling overhead for microscopic imaging and is slow. Here we demonstrate an approach for mid-IR spectroscopic imaging at selected discrete wavelengths using narrowband resonant filtering of a broadband thermal source, enabled by high-performance guided-mode Fano resonances in one-layer, large-area mid-IR photonic crystals on a glass substrate. The microresonant devices enable discrete frequency IR (DF-IR), in which a limited number of wavelengths that are of interest are recorded using a mechanically robust instrument. This considerably simplifies instrumentation as well as overhead of data acquisition, storage and analysis for large format imaging with array detectors. To demonstrate the approach, we perform DF-IR spectral imaging of a polymer USAF resolution target and human tissue in the C-H stretching region (2600-3300 cm(-1)). DF-IR spectroscopy and imaging can be generalized to other IR spectral regions and can serve as an analytical tool for environmental and biomedical applications. PMID:25089433

  9. Errors in Crystal structure of HINT from Helicobacter pylori

    PubMed Central

    Maize, Kimberly M.

    2016-01-01

    Inaccuracies in the article, Crystal structure of HINT from Helicobacter pylori by Tarique et al. [(2016) Acta Cryst. F72, 42–48] are presented, and a brief history of HINT nomenclature is discussed. PMID:27050269

  10. Determination of channeling perspectives for complex crystal structures

    SciTech Connect

    Allen, W.R.

    1993-03-01

    Specification of the atomic arrangement for axes and planes of high symmetry is essential for crystal alignment using Rutherford backscattering and for studies of the lattice location of impurities in single crystals. By rotation of an inscribed orthogonal coordinate system, a visual image for a given perspective of a crystal structure can be specified. Knowledge of the atomic arrangement permits qualitative channeling perspectives to be visualized and calculation of continuum potentials for channeling. Channeling angular-yield profiles can then be analytically modeled and, subsequently, shadowing by host atoms of positions within the unit cell predicted. Software to calculate transformed atom positions for a channeling perspective in a single crystal are described and illustrated for the spinel crystal structure.

  11. Crystal Structure and Crystal Chemistry of Some Common REE Minerals and Nanpingite

    NASA Astrophysics Data System (ADS)

    Ni, Yunxiang

    1995-01-01

    Part I. Crystal structure and crystal chemistry of fluorocarbonate minerals. The crystal structure of bastnasite-(Ce) have been solved in P-62c and refined to R = 0.018. The structure is composed of (001) (CeF) layers interspersed with (CO_3) layers in a 1:1 ratio. The Ce atom is coordinated in rm CeO_6F_3 polyhedra. The atomic arrangement of synchysite-(Ce) has been solved and refined to R = 0.036 with a monoclinic space group C2/c. It possesses a (001) layer structure, with layers of (Ca) and (CeF) separated by layers of carbonate groups. The layers stack in a manner analogous to C2/c muscovite. Polytypism similar to the micas may exist in synchysite. The crystal structures of cordylite-(Ce) have been solved in P6 _3/mmc and refined to R = 0.023. The structure and chemical formula are different from those deduced by Oftedal. The formula is rm MBaCe_2(CO _3)_4F, where M is rm Na^+, Ca^{2+}_{1/2 }+ O_{1/2}, or any solution. The presence of (NaF) layer in the structure is the key difference from the Oftedal's structure. This redefinition of the chemical formula and crystal structure of cordylite will be proposed to IMA-CNMMN. Part II. Crystal structure and crystal chemistry of monazite-xenotime series. Monazite is monoclinic, P2 _1/n, and xenotime is isostructural with zircon (I4_1/amd). Both atomic arrangements are based on (001) chains of intervening phosphate tetrahedra and RE polyhedra, with a REO_8 polyhedron in xenotime that accommodates HRE (Tb - Lu) and a REO_9 polyhedron in monazite that preferentially incorporates LRE (La - Gd). As the structure "transforms" from xenotime to monazite, the crystallographic properties are comparable along the (001) chains, with structural adjustments of 2.2 A along (010) to accommodate the different size RE atoms. Part III. Crystal structure of nanpingite-2M _2, the Cs end-member of muscovite. The crystal structure of nanpingite has been refined to R = 0.058. Compared to K^+ in muscovite, the largest interlayer Cs^+ in

  12. Crystal structure of a methimazole-based ionic liquid.

    PubMed

    Gaitor, Jamie C; Zayas, Manuel Sanchez; Myrthil, Darrel J; White, Frankie; Hendrich, Jeffrey M; Sykora, Richard E; O'Brien, Richard A; Reilly, John T; Mirjafari, Arsalan

    2015-12-01

    The structure of 1-methyl-2-(prop-2-en-1-ylsulfan-yl)-1H-imidazol-3-ium bromide, C7H11N2S(+)·Br(-), has monoclinic (P21/c) symmetry. In the crystal, the components are linked by N-H⋯Br and C-H⋯Br hydrogen bonds. The crystal structure of the title compound undeniably proves that methimazole reacts through the thione tautomer, rather than the thiol tautomer in this system. PMID:26870468

  13. Raman spectroscopic investigation of polycrystalline structures of CVD-grown graphene by isotope labeling

    NASA Astrophysics Data System (ADS)

    Wang, Shengnan; Suzuki, Satoru; Hibino, Hiroki

    2014-10-01

    Topological defects, such as point defects, dislocations and grain boundaries, have a dramatic influence on the chemical and physical properties of large-scale graphene grown by chemical vapor deposition (CVD) method. Here we demonstrate the Raman visualization of polycrystalline structures in an isotopically modified CVD graphene. By means of the reversible reaction of methane on a copper catalyst, the etching of 12C-lattice and surface deposition of 13C-atoms occur in CVD graphene by sequentially introducing hydrogen and isotopic methane after standard growth of graphene with full monolayer coverage. Spatial Raman spectroscopic mapping on labeled graphene reveals pronounced network-like 13C-rich regions, which are further identified to exist along the grain boundaries of graphene by low-energy electron microscopy. The structural defects inside the graphene grains are also targeted in the isotope labeling process. Our work opens a new way to investigate multiple grain structures in CVD graphene with a simple spectroscopic technique.Topological defects, such as point defects, dislocations and grain boundaries, have a dramatic influence on the chemical and physical properties of large-scale graphene grown by chemical vapor deposition (CVD) method. Here we demonstrate the Raman visualization of polycrystalline structures in an isotopically modified CVD graphene. By means of the reversible reaction of methane on a copper catalyst, the etching of 12C-lattice and surface deposition of 13C-atoms occur in CVD graphene by sequentially introducing hydrogen and isotopic methane after standard growth of graphene with full monolayer coverage. Spatial Raman spectroscopic mapping on labeled graphene reveals pronounced network-like 13C-rich regions, which are further identified to exist along the grain boundaries of graphene by low-energy electron microscopy. The structural defects inside the graphene grains are also targeted in the isotope labeling process. Our work opens a new

  14. The Crystal and Molecular Structure of Dianhydrogossypol

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Dianhydrogossypol (4,4'-dihydroxy-5,5'-diisopropyl-7,7'-dimethyl-bis(3H-naphtho[1,8-bc]furan-3-one)) was made by refluxing gossypol in m-xylene. Proton NMR confirmed that complete conversion was achieved over several hours. Single crystals were obtained by slow evaporation of the product from dichl...

  15. Allophycocyanin and phycocyanin crystal structures reveal facets of phycobilisome assembly.

    PubMed

    Marx, Ailie; Adir, Noam

    2013-03-01

    X-ray crystal structures of the isolated phycobiliprotein components of the phycobilisome have provided high resolution details to the description of this light harvesting complex at different levels of complexity and detail. The linker-independent assembly of trimers into hexamers in crystal lattices of previously determined structures has been observed in almost all of the phycocyanin (PC) and allophycocyanin (APC) structures available in the Protein Data Bank. In this paper we describe the X-ray crystal structures of PC and APC from Synechococcus elongatus sp. PCC 7942, PC from Synechocystis sp. PCC 6803 and PC from Thermosynechococcus vulcanus crystallized in the presence of urea. All five structures are highly similar to other PC and APC structures on the levels of subunits, monomers and trimers. The Synechococcus APC forms a unique loose hexamer that may show the structural requirements for core assembly and rod attachment. While the Synechococcus PC assembles into the canonical hexamer, it does not further assemble into rods. Unlike most PC structures, the Synechocystis PC fails to form hexamers. Addition of low concentrations of urea to T. vulcanus PC inhibits this proteins propensity to form hexamers, resulting in a crystal lattice composed of trimers. The molecular source of these differences in assembly and their relevance to the phycobilisome structure is discussed. PMID:23201474

  16. Ferroelectric InMnO3: Growth of single crystals, structure and high-temperature phase transitions

    NASA Astrophysics Data System (ADS)

    Bekheet, Maged F.; Svoboda, Ingrid; Liu, Na; Bayarjargal, Lkhamsuren; Irran, Elisabeth; Dietz, Christian; Stark, Robert W.; Riedel, Ralf; Gurlo, Aleksander

    2016-09-01

    To understand the origin of the ferroelectricity in InMnO3, single crystals with average size of 1 mm were grown in PbF2 flux at 950 °C. The results of single crystal X-ray diffraction, second harmonic generation and piezoresponse force microscopy studies of high-quality InMnO3 single crystals reveal that the room-temperature state in this material is ferroelectric with P63cm symmetry. The polar InMnO3 specimen undergoes a reversible phase transition from non-centrosymmetric P63cm structure to a centrosymmetric P63/mmc structure at 700 °C as confirmed by the in situ high-temperature Raman spectroscopic and synchrotron X-ray diffraction experiments.

  17. Membrane protein structures without crystals, by single particle electron cryomicroscopy

    PubMed Central

    Vinothkumar, Kutti R

    2015-01-01

    It is an exciting period in membrane protein structural biology with a number of medically important protein structures determined at a rapid pace. However, two major hurdles still remain in the structural biology of membrane proteins. One is the inability to obtain large amounts of protein for crystallization and the other is the failure to get well-diffracting crystals. With single particle electron cryomicroscopy, both these problems can be overcome and high-resolution structures of membrane proteins and other labile protein complexes can be obtained with very little protein and without the need for crystals. In this review, I highlight recent advances in electron microscopy, detectors and software, which have allowed determination of medium to high-resolution structures of membrane proteins and complexes that have been difficult to study by other structural biological techniques. PMID:26435463

  18. Quantitative crystal structure descriptors from multiplicative congruential generators.

    PubMed

    Hornfeck, Wolfgang

    2012-03-01

    Special types of number-theoretic relations, termed multiplicative congruential generators (MCGs), exhibit an intrinsic sublattice structure. This has considerable implications within the crystallographic realm, namely for the coordinate description of crystal structures for which MCGs allow for a concise way of encoding the numerical structural information. Thus, a conceptual framework is established, with some focus on layered superstructures, which proposes the use of MCGs as a tool for the quantitative description of crystal structures. The multiplicative congruential method eventually affords an algorithmic generation of three-dimensional crystal structures with a near-uniform distribution of atoms, whereas a linearization procedure facilitates their combinatorial enumeration and classification. The outlook for homometric structures and dual-space crystallography is given. Some generalizations and extensions are formulated in addition, revealing the connections of MCGs with geometric algebra, discrete dynamical systems (iterative maps), as well as certain quasicrystal approximants. PMID:22338652

  19. Comparison of spectroscopic properties of Tm and Ho in YAG and YLF crystals

    NASA Technical Reports Server (NTRS)

    Armagan, G.; Buoncristiani, A. M.; Inge, A. T.; Di Bartolo, B.

    1991-01-01

    The paper compares the cross-relaxation, energy transfer and loss processes in Tm- and Ho-doped YAG and YLF as a function of temperature, Tm concentration, and excitation power. Significant differences in the behavior of Tm and Tm,Ho in YAG and YLF crystals were found. The cross-relaxation rates of Tm(6 pct) are faster in YLF (about 5 microsec) than YAG (about 10 microsec). The energy transfer rates between Tm and Ho are faster in YLF than YAG. The time it takes for the maximum intensity of 1.7-micron emission to drop 10 percent is 25 microsec for YLF:Tm(6 pct),Ho(0.6 pct) and 65 microsec YAG:Tm(6 pct),Ho(0.5 pct). The losses occurring with increasing pump power for 2.1-micron emission of the above samples are 30 percent less in YLF than YAG. These qualitative differences point to YLF as a valuable 2-micron laser host material.

  20. Distinct circular dichroism spectroscopic signatures of polyproline II and unordered secondary structures: Applications in secondary structure analyses

    PubMed Central

    Lopes, Jose L S; Miles, Andrew J; Whitmore, Lee; Wallace, B A

    2014-01-01

    Circular dichroism (CD) spectroscopy is a valuable method for defining canonical secondary structure contents of proteins based on empirically-defined spectroscopic signatures derived from proteins with known three-dimensional structures. Many proteins identified as being “Intrinsically Disordered Proteins” have a significant amount of their structure that is neither sheet, helix, nor turn; this type of structure is often classified by CD as “other”, “random coil”, “unordered”, or “disordered”. However the “other” category can also include polyproline II (PPII)-type structures, whose spectral properties have not been well-distinguished from those of unordered structures. In this study, synchrotron radiation circular dichroism spectroscopy was used to investigate the spectral properties of collagen and polyproline, which both contain PPII-type structures. Their native spectra were compared as representatives of PPII structures. In addition, their spectra before and after treatment with various conditions to produce unfolded or denatured structures were also compared, with the aim of defining the differences between CD spectra of PPII and disordered structures. We conclude that the spectral features of collagen are more appropriate than those of polyproline for use as the representative spectrum for PPII structures present in typical amino acid-containing proteins, and that the single most characteristic spectroscopic feature distinguishing a PPII structure from a disordered structure is the presence of a positive peak around 220nm in the former but not in the latter. These spectra are now available for inclusion in new reference data sets used for CD analyses of the secondary structures of soluble proteins. PMID:25262612

  1. Structural and biochemical characterization of engineered tissue using FTIR spectroscopic imaging: melanoma progression as an example

    NASA Astrophysics Data System (ADS)

    Bhargava, Rohit; Kong, Rong

    2008-02-01

    Engineered tissue represents a convenient path to providing models for imaging and disease progression. The use of these models or phantoms is becoming increasingly prevalent. While structural characterization of these systems is well-documented, a combination of biochemical and structural knowledge is often helpful. Fourier transform infrared (FTIR) spectroscopic imaging is a rapidly emerging technique that combines the molecular selectivity of spectroscopy with the spatial specificity of optical microscopy. Here, we report on the application of FTIR spectroscopic for analysis of a melanoma model in engineered skin. We first characterize the biochemical properties, consistency and spectral changes in different layers of growing skin. Results provide simple indices for monitoring tissue consistency and reproducibility as a function of time. Second, we introduce malignant melanocytes to simulate tumor formation and growth. Both cellular changes associated with tumor formation and growth can be observed. FTIR images indicate holistic chemical changes during the tumor growth, allowing for the development of automated pathology protocols. FTIR imaging being non-destructive, further, samples remain entirely compatible with downstream tissue processing or staining. We specifically examined the correlation of structural changes, molecular content and reproducibility of the model systems. The development of analysis, integrating spectroscopy, imaging and computation will allow for quality control and standardization of both the structural and biochemical properties of tissue phantoms.

  2. Laser Spectroscopic and Theoretical Studies of the Structures and Encapsulation Motifs of Functional Molecules

    SciTech Connect

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

    2015-02-01

    Extensive laser spectroscopic and theoretical studies have been recently carried out with the aim to reveal the structure and dynamics of encapsulation complexes in the gas phase. The characteristics of the encapsulation complexes are governed by the fact that (i) most of the host molecules are flexible and (ii) the complexes form high dimensional structures by using weak non-covalent interactions. These characteristics result in the possibility of the coexistence of many conformers in close energetic proximity. The combination of supersonic jet/laser spectroscopy and high level quantum chemical calculations is essential in tackling these challenging problems. In this report we describe our recent studies on the structures and dynamics of the encapsulation complexes formed by calix[4]arene (C4A), dibenzo-18-crown-6-ether (DB18C6), and benzo-18-crown-6-ether (B18C6) "hosts" interacting with N2, acetylene, water, and ammonia "guest" molecules. The gaseous host-guest complexes are generated under jet-cooled conditions. We apply various laser spectroscopic methods to obtain the conformer- and isomer-specified electronic and IR spectra. The experimental results are complemented with quantum chemical calculations ranging from density functional theory to high level first principles calculations at the MP2 and CCSD(T) levels of theory. We discuss the possible conformations of the bare host molecules, the structural changes they undergo upon complexation, and the key interactions that are responsible in stabilizing the specific complexes

  3. Laser spectroscopic and theoretical studies of the structures and encapsulation motifs of functional molecules

    SciTech Connect

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

    2015-01-22

    Extensive laser spectroscopic and theoretical studies have been recently carried out with the aim to reveal the structure and dynamics of encapsulation complexes in the gas phase. The characteristics of the encapsulation complexes are governed by the fact that (i) most of the host molecules are flexible and (ii) the complexes form high dimensional structures by using weak non-covalent interactions. These characteristics result in the possibility of the coexistence of many conformers in close energetic proximity. The combination of supersonic jet/laser spectroscopy and high level quantum chemical calculations is essential in tackling these challenging problems. In this report we describe our recent studies on the structures and dynamics of the encapsulation complexes formed by calix[4]arene (C4A), dibenzo-18-crown-6-ether (DB18C6), and benzo-18-crown-6-ether (B18C6) 'hosts' interacting with N{sub 2}, acetylene, water, and ammonia 'guest' molecules. The gaseous host-guest complexes are generated under jet-cooled conditions. We apply various laser spectroscopic methods to obtain the conformer- and isomer-specified electronic and IR spectra. The experimental results are complemented with quantum chemical calculations ranging from density functional theory to high level first principles calculations at the MP2 and CCSD(T) levels of theory. We discuss the possible conformations of the bare host molecules, the structural changes they undergo upon complexation, and the key interactions that are responsible in stabilizing the specific complexes.

  4. Pigment-protein architecture in the light-harvesting antenna complexes of purple bacteria: does the crystal structure reflect the native pigment-protein arrangement?

    PubMed

    Leupold, D; Voigt, B; Beenken, W; Stiel, H

    2000-09-01

    Structural analysis of crystallized peripheral (LH2) and core antenna complexes (LH1) of purple bacteria has revealed circular aggregates of high rotational symmetry (C8, C9 and C16, respectively). Quantum-chemical calculations indicate that in particular the waterwheel-like arrangements of pigments should show characteristic structure-sensitive spectroscopic behavior in the near infrared absorption region. Laser-spectroscopic data obtained with non-crystallized, isolated LH2 of Rhodospirillum molischianum are in line with a highly symmetric (C8) circular aggregate, but deviations have been found for LH2 of Rhodobacter sphaeroides and Rhodopseudomonas acidophila. For both the latter, C-shaped incomplete circular aggregates (as seen only recently in electron micrographs of crystallized LH1-reaction center complexes) may be a suitable preliminary model. PMID:11034303

  5. Study of InGaAs based MODFET structures using variable angle spectroscopic ellipsometry

    NASA Technical Reports Server (NTRS)

    Alterovitz, S. A.; Sieg, R. M.; Yao, H. D.; Snyder, P. G.; Woollam, J. A.; Pamulapati, J.; Bhattacharya, P. K.; Sekula-Moise, P. A.

    1991-01-01

    Variable angle spectroscopic ellipsometry was used to estimate the thicknesses of all layers within the optical penetration depth of InGaAs based MODFET structures. Strained and unstrained InGaAs channels were made by MBE on InP substrates and by MOCVD on GaAs substrates. In most cases, ellipsometrically determined thicknesses were within 10 percent of the growth calibration results. The MBE made InGaAs strained layers showed large strain effects, indicating a probable shift in the critical points of their dielectric function toward the InP lattice matched concentration.

  6. Access to a Cu(II)-O-Cu(II) motif: spectroscopic properties, solution structure, and reactivity.

    PubMed

    Haack, Peter; Kärgel, Anne; Greco, Claudio; Dokic, Jadranka; Braun, Beatrice; Pfaff, Florian F; Mebs, Stefan; Ray, Kallol; Limberg, Christian

    2013-10-30

    We report a complex with a rare Cu(II)-O-Cu(II) structural motif that is stable at room temperature, which allows its in-depth characterization by a variety of spectroscopic methods. Interest in such compounds is fueled by the recent discovery that a Cu(II)-O-Cu(II) species on the surface of Cu-ZSM-5 is capable of oxidizing methane to methanol, and this in turn ties into mechanistic discussions on the methane oxidation at the dicopper site within the particulate methane monooxygenase. For the synthesis of our Cu2O complex we have developed a novel, neutral ligand system, FurNeu, exhibiting two N-(N',N'-dimethylaminoethyl)(2-pyridylmethyl)amino binding pockets connected by a dibenzofuran spacer. The reaction of FurNeu with CuCl yielded [FurNeu](Cu2(μ-Cl))(CuCl2), 1, demonstrating the geometric potential of the ligand to stabilize Cu-X-Cu moieties. A Cu(I) precursor with weakly coordinating anions was chosen in the next step, namely [Cu(NCCH3)4]OTf, which led to the formation of [FurNeu](Cu(NCCH3))2(OTf)2, 3. Treatment of 3 with O2 or PhIO led to identical green solutions, whose UV-vis spectra were markedly different from the one displayed by [FurNeu](Cu)2(OTf)4, 4, prepared independently from FurNeu and Cu(OTf)2. Further investigations including PhIO consumption experiments, NMR and UV-vis spectroscopy, HR-ESI mass spectrometry, and protonation studies led to the identification of the green product as [FurNeu](Cu2(μ-O))(OTf)2, 5. DOSY NMR spectroscopy confirmed its monomeric character. Over longer periods of time 5 decomposes to give [Cu(picoloyl)2], formed through an oxidative N-dealkylation reaction followed by further oxidation of the ligand. Due to its slow decomposition reaction, all attempts to crystallize 5 failed. However, its structure in solution could be determined by EXAFS analysis in combination with DFT calculations, which revealed a Cu-O-Cu angle that amounts to 105.17°. Moreover, TDDFT calculations helped to rationalize the UV-vis absorptions of 5

  7. Access to a CuII–O–CuII Motif: Spectroscopic Properties, Solution Structure, and Reactivity

    PubMed Central

    Haack, Peter; Kärgel, Anne; Greco, Claudio; Dokic, Jadranka; Braun, Beatrice; Pfaff, Florian F.; Mebs, Stefan; Ray, Kallol; Limberg, Christian

    2013-01-01

    We report a complex with a rare CuII–O–CuII structural motif that is stable at room temperature, which allows its in-depth characterization by a variety of spectroscopic methods. Interest in such compounds is fueled by the recent discovery that a CuII–O–CuII species on the surface of Cu-ZSM-5 is capable of oxidizing methane to methanol and this in turn ties into mechanistic discussions on the methane oxidation at the dicopper site within the particulate methane monooxygenase. For the synthesis of our Cu2O complex we have developed a novel, neutral ligand system, FurNeu, exhibiting two N-(N',N'-dimethylaminoethyl)(2-pyridylmethyl)amino binding pockets connected by a dibenzofuran spacer. The reaction of FurNeu with CuCl yielded [FurNeu](Cu2(μ-Cl))(CuCl2), 1, demonstrating the geometric potential of the ligand to stabilize Cu–X–Cu moieties. A CuI precursor with weakly coordinating anions was chosen in the next step, namely [Cu(NCCH3)4]OTf, which led to the formation of [FurNeu](Cu(NCCH3))2(OTf)2, 3. Treatment of 3 with O2 or PhIO led to identical green solutions, whose UV/Vis spectra were markedly different from the one displayed by [FurNeu](Cu)2(OTf)4, 4, prepared independently from FurNeu and Cu(OTf)2. Further investigations including PhIO consumption experiments, NMR and UV/Vis spectroscopy, HR-ESI mass spectrometry and protonation studies led to the identification of the green product as [FurNeu](Cu2(μ-O))(OTf)2, 5. DOSY NMR spectroscopy confirmed its monomeric character. Over longer periods of time 5 decomposes to give [Cu(picoloyl)2], formed through an oxidative N-dealkylation reaction followed by further oxidation of the ligand. Due to its slow decomposition reaction all attempts to crystallize 5 failed. However, its structure in solution could be determined by EXAFS analysis in combination with DFT calculations, which revealed a Cu–O–Cu angle that amounts to 105.17°. Moreover, TDDFT calculations helped to rationalize the UV/Vis absorptions

  8. Crystal structure of CmlI, the arylamine oxygenase from the chloramphenicol biosynthetic pathway.

    PubMed

    Knoot, Cory J; Kovaleva, Elena G; Lipscomb, John D

    2016-09-01

    The diiron cluster-containing oxygenase CmlI catalyzes the conversion of the aromatic amine precursor of chloramphenicol to the nitroaromatic moiety of the active antibiotic. The X-ray crystal structures of the fully active, N-terminally truncated CmlIΔ33 in the chemically reduced Fe(2+)/Fe(2+) state and a cis μ-1,2(η (1):η (1))-peroxo complex are presented. These structures allow comparison with the homologous arylamine oxygenase AurF as well as other types of diiron cluster-containing oxygenases. The structural model of CmlIΔ33 crystallized at pH 6.8 lacks the oxo-bridge apparent from the enzyme optical spectrum in solution at higher pH. In its place, residue E236 forms a μ-1,3(η (1):η (2)) bridge between the irons in both models. This orientation of E236 stabilizes a helical region near the cluster which closes the active site to substrate binding in contrast to the open site found for AurF. A very similar closed structure was observed for the inactive dimanganese form of AurF. The observation of this same structure in different arylamine oxygenases may indicate that there are two structural states that are involved in regulation of the catalytic cycle. Both the structural studies and single crystal optical spectra indicate that the observed cis μ-1,2(η (1):η (1))-peroxo complex differs from the μ-η (1):η (2)-peroxo proposed from spectroscopic studies of a reactive intermediate formed in solution by addition of O2 to diferrous CmlI. It is proposed that the structural changes required to open the active site also drive conversion of the µ-1,2-peroxo species to the reactive form. PMID:27229511

  9. Predicting inclusion behaviour and framework structures in organic crystals.

    PubMed

    Cruz-Cabeza, Aurora J; Day, Graeme M; Jones, William

    2009-12-01

    We have used well-established computational methods to generate and explore the crystal structure landscapes of four organic molecules of well-known inclusion behaviour. Using these methods, we are able to generate both close-packed crystal structures and high-energy open frameworks containing voids of molecular dimensions. Some of these high-energy open frameworks correspond to real structures observed experimentally when the appropriate guest molecules are present during crystallisation. We propose a combination of crystal structure prediction methodologies with structure rankings based on relative lattice energy and solvent-accessible volume as a way of selecting likely inclusion frameworks completely ab initio. This methodology can be used as part of a rational strategy in the design of inclusion compounds, and also for the anticipation of inclusion behaviour in organic molecules. PMID:19876969

  10. Crystal structure of the co-crystal butyl­paraben–isonicotinamide (1/1)

    PubMed Central

    Bhardwaj, Rajni M.; Yang, Huaiyu; Florence, Alastair J.

    2016-01-01

    The title 1:1 co-crystal, C11H14O3·C6H6N2O [systematic name: butyl 4-hy­droxy­benzoate–isonicotinamide (1/1)], crystallizes with one mol­ecule of butyl­paraben (BPN) and one mol­ecule of isonicotinamide (ISN) in the asymmetric unit. In the crystal, BPN and ISN mol­ecules form hydrogen-bonded (O—H⋯N and N—H⋯O) dimers of paired BPN and ISN mol­ecules. These dimers are further connected to each other via N—H⋯O=C hydrogen bonds, creating ribbons in [011] which further stack along the a axis to form a layered structure with short C⋯C contacts of 3.285 (3) Å. Packing inter­actions within the crystal structure were assessed using PIXEL calculations. PMID:26870584

  11. Growth, characterization, and crystal structure of a new chalcone derivative single crystal

    NASA Astrophysics Data System (ADS)

    Shettigar, Venkataraya; Dharmaprakash, S. M.

    2006-09-01

    A new organic nonlinear optical (NLO) chalcone derivative viz.1- ( 4- methoxyphenyl )-3- (3,4 - dimethoxy phenyl ) - 2 - propene-1-one, has been synthesized by Claisen-Schmidt condensation method. The synthesized compound was purified by repeated recrystallization process. To confirm the identity of the synthesized compound, FTIR spectra was recorded and various functional groups present were identified. NMR spectra were recorded for structural identity and purity confirmation of the synthesized compound. Good quality single crystals were grown by solvent evaporation and slow cooling technique using acetone as solvent. The grown crystals were characterized by UV-Visible , differential thermal analysis and linear refractive index measurement. The hardness of the crystal was determined using Vicker's indentation method. The single crystal structure analysis of the crystal was performed and it is found that the crystal belongs to monoclinic system with space group P2 I. The powder second harmonic generation(SHG)frequency conversion efficiency of the crystal was determined using Nd: YAG laser(λ = 1064nm)and it is 15 times that of Urea.

  12. Spectroscopic and structural study of the newly synthesized heteroligand complex of copper with creatinine and urea

    NASA Astrophysics Data System (ADS)

    Gangopadhyay, Debraj; Singh, Sachin Kumar; Sharma, Poornima; Mishra, Hirdyesh; Unnikrishnan, V. K.; Singh, Bachcha; Singh, Ranjan K.

    2016-02-01

    Study of copper complex of creatinine and urea is very important in life science and medicine. In this paper, spectroscopic and structural study of a newly synthesized heteroligand complex of copper with creatinine and urea has been discussed. Structural studies have been carried out using DFT calculations and spectroscopic analyses were carried out by FT-IR, Raman, UV-vis absorption and fluorescence techniques. The copper complex of creatinine and the heteroligand complex were found to have much increased water solubility as compared to pure creatinine. The analysis of FT-IR and Raman spectra helps to understand the coordination properties of the two ligands and to determine the probable structure of the heteroligand complex. The LIBS spectra of the heteroligand complex reveal that the complex is free from other metal impurities. UV-visible absorption spectra and the fluorescence emission spectra of the aqueous solution of Cu-Crn-urea heteroligand complex at different solute concentrations have been analyzed and the complex is found to be rigid and stable in its monomeric form at very low concentrations.

  13. DFT calculations on spectroscopic and structural properties of a NLO chromophore

    NASA Astrophysics Data System (ADS)

    Altürk, Sümeyye; Avci, Davut; Tamer, Ömer; Atalay, Yusuf

    2016-03-01

    The molecular geometry optimization, vibrational frequencies and gauge including atomic orbital (GIAO) 1H and 13C NMR chemical shift values of 2-(1'-(4'''-Methoxyphenyl)-5'-(thien-2″-yl)pyrrol-2'-yl)-1,3-benzothiazole as potential nonlinear optical (NLO) material were calculated using density functional theory (DFT) HSEh1PBE method with 6-311G(d,p) basis set. The best of our knowledge, this study have not been reported to date. Additionally, a detailed vibrational study was performed on the basis of potential energy distribution (PED) using VEDA program. It is noteworthy that NMR chemical shifts are quite useful for understanding the relationship between the molecular structure and electronic properties of molecules. The computed IR and NMR spectra were used to determine the types of the experimental bands observed. Predicted values of structural and spectroscopic parameters of the chromophore were compared with each other so as to display the effects of the different substituents on the spectroscopic and structural properties. Obtained data showed that there is an agreement between the predicted and experimental data.

  14. Raman spectroscopic investigation of polycrystalline structures of CVD-grown graphene by isotope labeling.

    PubMed

    Wang, Shengnan; Suzuki, Satoru; Hibino, Hiroki

    2014-11-21

    Topological defects, such as point defects, dislocations and grain boundaries, have a dramatic influence on the chemical and physical properties of large-scale graphene grown by chemical vapor deposition (CVD) method. Here we demonstrate the Raman visualization of polycrystalline structures in an isotopically modified CVD graphene. By means of the reversible reaction of methane on a copper catalyst, the etching of (12)C-lattice and surface deposition of (13)C-atoms occur in CVD graphene by sequentially introducing hydrogen and isotopic methane after standard growth of graphene with full monolayer coverage. Spatial Raman spectroscopic mapping on labeled graphene reveals pronounced network-like (13)C-rich regions, which are further identified to exist along the grain boundaries of graphene by low-energy electron microscopy. The structural defects inside the graphene grains are also targeted in the isotope labeling process. Our work opens a new way to investigate multiple grain structures in CVD graphene with a simple spectroscopic technique. PMID:25303722

  15. Microsolvation of 2-thiouracil: molecular structure and spectroscopic parameters of the thiouracil-water complex.

    PubMed

    Puzzarini, Cristina; Biczysko, Malgorzata

    2015-05-28

    State-of-the-art quantum-chemical computations have been employed to accurately determine the equilibrium structure and interaction energy of the 2-thiouracil-water complex, thus extending available reference data for biomolecule solvation patterns. The coupled-cluster level of theory in conjunction with a triple-ζ basis set has been considered together with extrapolation to the basis set limit, performed by employing second-order Møller-Plesset perturbation theory, and inclusion of core-correlation and diffuse-function corrections. On the basis of the comparison of experiment and theory for 2-thiouracil [ Puzzarini et al. Phys. Chem. Chem. Phys. 2013 , 15 , 16965 - 16975 ], structural changes due to water complexation have been pointed out. Molecular and spectroscopic properties of the 2-thiouracil-water complex have then been studied by means of the composite computational approach introduced for the molecular structure evaluation. Among the results achieved, we mention the accurate determination of the molecular dipole moment and of the spectroscopic parameters required for predicting the rotational spectrum. PMID:25474644

  16. Evolution of molecular crystal optical phonons near structural phase transitions

    NASA Astrophysics Data System (ADS)

    Michki, Nigel; Niessen, Katherine; Xu, Mengyang; Markelz, Andrea

    Molecular crystals are increasingly important photonic and electronic materials. For example organic semiconductors are lightweight compared to inorganic semiconductors and have inexpensive scale up processing with roll to roll printing. However their implementation is limited by their environmental sensitivity, in part arising from the weak intermolecular interactions of the crystal. These weak interactions result in optical phonons in the terahertz frequency range. We examine the evolution of intermolecular interactions near structural phase transitions by measuring the optical phonons as a function of temperature and crystal orientation using terahertz time-domain spectroscopy. The measured orientation dependence of the resonances provides an additional constraint for comparison of the observed spectra with the density functional calculations, enabling us to follow specific phonon modes. We observe crystal reorganization near 350 K for oxalic acid as it transforms from dihydrate to anhydrous form. We also report the first THz spectra for the molecular crystal fructose through its melting point.

  17. Synthesis and spectroscopic characterization of dicyanamido-Cu(II) complexes. Part 2 : Crystal structure of the complexes of tris[2-(2-pyridylethyl)]amine, tris(2-pyridylmethyl)amine and 1,4-bis[2-(2-pyridylethyl)]piperazine

    NASA Astrophysics Data System (ADS)

    Mautner, Franz A.; Soileau, Jesse B.; Bankole, Paul K.; Gallo, August A.; Massoud, Salah S.

    2008-10-01

    Two classes of novel dicyanamido (dca)-Cu(II) complexes were synthesized with a variety of tetradentate tripod amines, tridentate amines and diazacycloalkanes with pyridyl arms of different alkyl lengths and with tetra-aza macrocycles with different cavity sizes; the mononuclear, Cu(L)(dca)]ClO 4 (L = tepa ( 1), TPA ( 2), pzdepy ( 4), hpzpy 2 ( 5), cyclen ( 7), cyclam ( 8), tacp ( 9)) or Cu(L)(dca)ClO 4 (L = MeDPA ( 10), Mepea ( 11)) and the dinuclear, [Cu 2(L') 2(dca)](ClO 4) 3 (L' = pmap ( 3), pzpy 2 ( 6)). The isolated complexes were structurally characterized by electronic and IR spectroscopy as well as by X-ray. Single crystal X-ray diffraction analysis of the complexes [Cu(tepa)(dca)]ClO 4 ( 1), [Cu(TPA)(dca)]ClO 4 ( 2) and [Cu(pzdepy)(dca)]ClO 4 ( 4) reveal their monomeric penta-coordinate nature with the isolated [Cu(L)(dca)] + cations and ClO4- counter ions. All the complexes with the exception of 2 adapt distorted square pyramidal geometry while the coordination polyhedron around the copper center in 2 may be described as a distorted trigonal bipyramidal stereochemistry. The visible spectra of the complexes in aqueous solutions or in methanol are in complete agreement with the assigned X-ray geometry around the Cu(II) centers.

  18. Datamining protein structure databanks for crystallization patterns of proteins.

    PubMed

    Valafar, Homayoun; Prestegard, James H; Valafar, Faramarz

    2002-12-01

    A study of 345 protein structures selected among 1,500 structures determined by nuclear magnetic resonance (NMR) methods, revealed useful correlations between crystallization properties and several parameters for the studied proteins. NMR methods of structure determination do not require the growth of protein crystals, and hence allow comparison of properties of proteins that have or have not been the subject of crystallographic approaches. One- and two-dimensional statistical analyses of the data confirmed a hypothesized relation between the size of the molecule and its crystallization potential. Furthermore, two-dimensional Bayesian analysis revealed a significant relationship between relative ratio of different secondary structures and the likelihood of success for crystallization trials. The most immediate result is an apparent correlation of crystallization potential with protein size. Further analysis of the data revealed a relationship between the unstructured fraction of proteins and the success of its crystallization. Utilization of Bayesian analysis on the latter correlation resulted in a prediction performance of about 64%, whereas a two-dimensional Bayesian analysis succeeded with a performance of about 75%. PMID:12594078

  19. Crystal structure of benzobi-cyclon.

    PubMed

    Kang, Gihaeng; Kim, Jineun; Lim, Hansu; Kim, Tae Ho

    2015-12-01

    In the title compound, C22H19ClO4S2 [systematic name: 3-(2-chloro-4-mesylbenzo-yl)-4-(phenyl-sulfan-yl)bi-cyclo-[3.2.1]oct-3-en-2-one], which is an unclassified herbicide, the dihedral angle between the plane of the phenyl and chloro-benzene rings is 19.9 (2)°. In the crystal, C-H⋯O hydrogen bonds link adjacent mol-ecules, generating two-dimensional networks extending parellel to (011). PMID:26870484

  20. Optical and structural properties of chalcone NLO single crystals

    NASA Astrophysics Data System (ADS)

    Rajesh Kumar, P. C.; Ravindrachary, V.; Janardhana, K.; Manjunath, H. R.; Karegouda, Prakash; Crasta, Vincent; Sridhar, M. A.

    2011-11-01

    Organic compound (E)-1-(4-methoxyphenyl)-3-(2,3,5-trichlorophenyl)prop-2-en-1-one [MPTCPP] with molecular formula C 16H 11Cl 3O 2 was synthesized using Claisen-Schmidt condensation reaction method. 1H NMR spectra was recorded to identify the various functional groups present in the compound and confirm the chemical structure. The single crystals were grown using slow evaporation solution growth technique. The UV-Visible spectrum study reveals that the crystal is transparent in the entire visible region and the absorption is observed at 364 nm. The Kurtz powder second harmonic generation (SHG) test shows that the MPTCPP is NLO active and its SHG efficiency is three times that of urea. Single crystal XRD study shows that the compound crystallizes in the monoclinic system with a space group Cc. The corresponding lattice parameters of the crystal are a = 28.215(5) Å, b = 3.9740(4) Å, c = 16.178(3) Å and V = 1503.0(4) Å 3. The micro hardness test was carried out and the work hardening coefficient value ( n) of the crystal was found to be 1.48. This indicates that the crystal is hard and is suitable for device application. The thermal study reveals that the thermal stability of the crystal is good.

  1. Synthesis, structural, spectroscopic and thermal characteristics of disubstituted biphenyl derivative: Biphenyl-4,4‧-diacetic acid

    NASA Astrophysics Data System (ADS)

    Sienkiewicz-Gromiuk, Justyna; Głuchowska, Halina; Tarasiuk, Bogdan; Mazur, Liliana; Rzączyńska, Zofia

    2014-07-01

    A novel 4,4‧-disubstituted biphenyl derivative featuring two acetic acid side arms symmetrically attached to a biphenyl system, that is biphenyl-4,4‧-diacetic acid (H2bpda), has been successfully synthesized by means of the three-stage organic strategy. The synthesis product was characterized by elemental analysis, various spectroscopic techniques including FT-IR, Raman, 1H and 13C NMR as well as thermogravimetric and TG-FT-IR coupled measurements. The phase purity of material was verified on the basis of the X-ray powder diffraction. The studied compound crystallizes in the monoclinic P21/c space group with half of the molecule in the asymmetric unit. Structural studies indicate intermolecular Osbnd H⋯O hydrogen bonding between the carboxylic groups of the adjacent molecules of H2bpda. The occurrence of intermolecularly associated carboxylic groups can also be clearly seen in the vibrational spectra of the acid. On thermal analysis both in air and nitrogen an anhydrous compound demonstrates considerable thermal stability.

  2. Single-Crystal Structure of a Covalent Organic Framework

    SciTech Connect

    Zhang, YB; Su, J; Furukawa, H; Yun, YF; Gandara, F; Duong, A; Zou, XD; Yaghi, OM

    2013-11-06

    The crystal structure of a new covalent organic framework, termed COF-320, is determined by single-crystal 3D electron diffraction using the rotation electron diffraction (RED) method for data collection. The COF crystals are prepared by an imine condensation of tetra-(4-anilyl)methane and 4,4'-biphenyldialdehyde in 1,4-dioxane at 120 degrees C to produce a highly porous 9-fold interwoven diamond net. COF-320 exhibits permanent porosity with a Langmuir surface area of 2400 m(2)/g and a methane total uptake of 15.0 wt % (176 cm(3)/cm(3)) at 25 degrees C and 80 bar. The successful determination of the structure of COF-320 directly from single-crystal samples is an important advance in the development of COF chemistry.

  3. The different conformations and crystal structures of dihydroergocristine

    NASA Astrophysics Data System (ADS)

    Mönch, B.; Kraus, W.; Köppen, R.; Emmerling, F.

    2016-02-01

    The identification of different forms of dihydroergocristine (DHEC) was carried out by crystallization from different organic solvents. DHEC was identified as potential template for molecularly imprinted polymers (MIPs) for the epimeric specific analysis of ergot alkaloids (EAs) in food. DHEC was crystallized from different solvents in order to mimic the typical MIP synthesis conditions. Four new solvatomorphs of DHEC were obtained. All solvatomorphs contain a water molecule in the crystal structure, whereas three compounds contain an additional solvent molecule. Based on the conformation of DHEC a comparison with typical EA molecules was possible. The analysis showed that DHEC is a suitable template for MIPs for EAs.

  4. Crystal chemistry and Mössbauer spectroscopic analysis of clays around Riyadh for brick industry

    NASA Astrophysics Data System (ADS)

    Khalil, Mutasim I.

    2013-04-01

    A total of 30 clay samples were collected from the area around Riyadh city, Saudi Arabia. A complete chemical analysis was carried out using different techniques. X-ray diffraction studies showed that the clay samples were mainly of the smectite group with traces of the kaolinite one. The samples studied were classified as nontronite clay minerals. One of the clay fraction has been studied by Mössbauer spectroscopy as raw clay fraction and after being fired at 950-1,000 °C. The Mössbauer spectra showed accessory iron compounds in the form of hematite and goethite. The structural iron contents disintegrate on firing transforming into magnetic iron oxide and a paramagnetic small particles iron oxide.

  5. Crystal Structure of L-Histidinium 2-Nitrobenzoate

    PubMed Central

    Natarajan, Subramanian; Moovendaran, Kalimuthu; Kalyana Sundar, Jeyaperumal; Ravikumar, Krishnan

    2012-01-01

    A new nonlinear optical organic compound, namely, L-histidinium 2-nitrobenzoate (abbreviated as LH2NB (I); ([C6H10N3O2]+ [C7H4NO4]−)), was synthesized. The molecular structure of LH2NB (I) was elucidated using single crystal X-ray diffraction technique. The second harmonic generation (SHG) efficiency of this compound is about two times that of the standard potassium dihydrogen phosphate crystals. PMID:22536482

  6. Boron-oxygen polyanion in the crystal structure of tunellite

    USGS Publications Warehouse

    Clark, J.R.

    1963-01-01

    The crystal structure of tunellite, SrO??3B2O 3??4H2O, with infinite sheets of composition n[B6O9(OH)2]2-, has cations and water molecules in the spaces within the sheets. Adjacent sheets are held together by hydrogen bonding through the water molecules. The boron-oxygen polyanions provide the first example in hydrated borate crystals of one oxygen linked to three borons.

  7. Structure of ice crystallized from supercooled water

    PubMed Central

    Malkin, Tamsin L.; Murray, Benjamin J.; Brukhno, Andrey V.; Anwar, Jamshed; Salzmann, Christoph G.

    2012-01-01

    The freezing of water to ice is fundamentally important to fields as diverse as cloud formation to cryopreservation. At ambient conditions, ice is considered to exist in two crystalline forms: stable hexagonal ice and metastable cubic ice. Using X-ray diffraction data and Monte Carlo simulations, we show that ice that crystallizes homogeneously from supercooled water is neither of these phases. The resulting ice is disordered in one dimension and therefore possesses neither cubic nor hexagonal symmetry and is instead composed of randomly stacked layers of cubic and hexagonal sequences. We refer to this ice as stacking-disordered ice I. Stacking disorder and stacking faults have been reported earlier for metastable ice I, but only for ice crystallizing in mesopores and in samples recrystallized from high-pressure ice phases rather than in water droplets. Review of the literature reveals that almost all ice that has been identified as cubic ice in previous diffraction studies and generated in a variety of ways was most likely stacking-disordered ice I with varying degrees of stacking disorder. These findings highlight the need to reevaluate the physical and thermodynamic properties of this metastable ice as a function of the nature and extent of stacking disorder using well-characterized samples. PMID:22232652

  8. Effects of 5f-elements on electronic structures and spectroscopic properties of gold superatom model

    NASA Astrophysics Data System (ADS)

    Gao, Yang; Wang, Zhigang

    2016-08-01

    5f-elements encaged in a gold superatomic cluster are capable of giving rise to unique optical properties due to their hyperactive valence electrons and great radial components of 5f/6d orbitals. Herein, we review our first-principles studies on electronic structures and spectroscopic properties of a series of actinide-embedded gold superatomic clusters with different dimensions. The three-dimensional (3D) and two-dimensional (2D) superatom clusters possess the 18-electron configuration of 1S21P61D10 and 10-electron configuration of 1S21P41D4, respectively. Importantly, their electronic absorption spectra can also be effectively explained by the superatom orbitals. Specifically, the charge transfer (CT) transitions involved in surface-enhance Raman spectroscopy (SERS) spectra for 3D and 2D structures are both from the filled 1D orbitals, providing the enhancement factors of the order of ∼ 104 at 488 nm and ∼ 105 at 456 nm, respectively. This work implies that the superatomic orbital transitions involved in 5f-elements can not only lead to a remarkable spectroscopic performance, but also a new direction for optical design in the future. Project supported by the National Natural Science Foundation of China (Grant No. 11374004), the Science and Technology Development Program of Jilin Province, China (Grant No. 20150519021JH), the Fok Ying Tung Education Foundation, China (Grant No. 142001), and the Support from the High Performance Computing Center (HPCC) of Jilin University, China.

  9. Distorted tetrahedral nickel-nitrosyl complexes: spectroscopic characterization and electronic structure.

    PubMed

    Soma, Shoko; Van Stappen, Casey; Kiss, Mercedesz; Szilagyi, Robert K; Lehnert, Nicolai; Fujisawa, Kiyoshi

    2016-09-01

    The linear nickel-nitrosyl complex [Ni(NO)(L3)] supported by a highly hindered tridentate nitrogen-based ligand, hydrotris(3-tertiary butyl-5-isopropyl-1-pyrazolyl)borate (denoted as L3), was prepared by the reaction of the potassium salt of the ligand with the nickel-nitrosyl precursor [Ni(NO)(Br)(PPh 3 ) 2 ]. The obtained nitrosyl complexes as well as the corresponding chlorido complexes [Ni(NO)(Cl)(PPh 3 ) 2 ] and [Ni(Cl)(L3)] were characterized by X-ray crystallography and different spectroscopic methods including IR/far-IR, UV-Vis, NMR, and multi-edge X-ray absorption spectroscopy at the Ni K-, Ni L-, Cl K-, and P K-edges. For comparative electronic structure analysis we also performed DFT calculations to further elucidate the electronic structure of [Ni(NO)(L3)]. These results provide the nickel oxidation state and the character of the Ni-NO bond. The complex [Ni(NO)(L3)] is best described as [Ni (II) (NO (-) )(L3)], and the spectroscopic results indicate that the phosphane complexes have a similar [Ni (II) (NO (-) )(X)(PPh 3 ) 2 ] ground state. PMID:27350153

  10. Structures and Encapsulation Motifs of Functional Molecules probed by Laser Spectroscopic and Theoretical methods

    SciTech Connect

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

    2010-04-01

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

  11. Heterogeneous Crystallization on Pairs of Pre-Structured Seeds

    PubMed Central

    2016-01-01

    Studying the effects of small pre-structured seeds on the crystallization transition in an undercooled monodisperse Lennard-Jones fluid with transition interface path sampling combined with molecular dynamics simulations, we analyze the impact of the simultaneous presence of two seeds with various structures. In the presence of seeds with face- and body-centered cubic structures, we find that decreasing the seed-to-seed distance enhances the probability of the crystalline clusters formed on one of the seeds to grow beyond the critical size, thus, increasing the crystal nucleation rates. In contrast, when seeds have an icosahedral structure, the crystalline clusters form mostly in the bulk. The crystal nucleation rate, however, is also determined by the distance between the seeds with regular structure in which the lattice spacing is equal to the bulk lattice constant, pointing to a heterogeneous crystal nucleation that occurs away from the icosahedrally structured seeds. For slightly squeezed seeds, the effects of the presence of seeds with face- and body-centered cubic structures are reduced in comparison to the regular seeds, and we do not see any effect of the presence of the second seed for seeds with squeezed icosahedral structure. PMID:27479875

  12. Spectroscopic properties and structure refinement of Nd3+:(Y0.9La0.1)2O3 transparent ceramics

    NASA Astrophysics Data System (ADS)

    Lu, Qing; Yang, Qiuhong; Jiang, Cen; Lu, Shenzhou; Yuan, Ye; Liu, Qiang; Lu, Bo

    2014-11-01

    (NdxY0.9-xLa0.1)2O3 (x = 0.01-0.04) transparent ceramics were fabricated by conventional solid state reaction processing. Spectroscopic properties and crystal structures were investigated. (Nd0.01Y0.89La0.1)2O3 ceramics display high transparency and dense structure with almost no pores. The highest transmittance reaches 80%. The absorption at LD wavelength 806 nm is high with broad full width at half maximum (FWHM) of about 6 nm. The strongest emission peak is centered at 1078 nm with broad FWHM of about 9 nm and the stimulated emission cross section is 4.97 × 10-20 cm2. The crystal structure was obtained via Rietveld refinement. It is found that (NdxY0.9-xLa0.1)2O3 crystallize in space group of Ia3bar, Z = 16. The lattice parameters and average bond lengths are increased with the increase of La2O3 and Nd2O3 contents.

  13. Crystal engineering with thioureas: A structure-based inquiry

    NASA Astrophysics Data System (ADS)

    Paisner, Kathryn A.

    2011-12-01

    Structural trends applicable to crystal engineering were studied in three classes of thiourea-based compounds. The aim of the study was to identify, predict, and ultimately design reliable single-molecule structural features, which could then be used to engineer crystals with desirable properties. In one class of compounds, this goal was achieved: N-alkyl and N-aryl derivatives of N,N'-bis(3-thioureidopropyl)piperazine adopted an identical conformation in the solid state, which resulted in near-identical crystal packing. A second class of closely related compounds, N-substituted tris(2-thioureidoethyl)amines, showed no such reliability in the solid state, likely because the parent structure lacked hydrogen-bonding functionalities sufficient to control intramolecular structure. In the third class of compounds that we studied, 1-benzoyl-3-(2-pyridyl)thioureas, substitution patterns were often predictive of molecular conformation; however, these intramolecular trends did not lead to recognizable crystal packing motifs. Nevertheless, certain physical properties observed in this last class of compounds---color, solubility, and often crystallinity---were conformer-specific, interestingly without any apparent relevance to crystal lattice structure. Solution-state and solid-state conformational trends in these 1-benzoyl-3-(2-pyridyl)thioureas have been documented, and speculations as to the source of color in one of the two observed conformations have been noted.

  14. Isolation, crystallization and crystal structure determination of bovine kidney Na(+),K(+)-ATPase.

    PubMed

    Gregersen, Jonas Lindholt; Mattle, Daniel; Fedosova, Natalya U; Nissen, Poul; Reinhard, Linda

    2016-04-01

    Na(+),K(+)-ATPase is responsible for the transport of Na(+) and K(+) across the plasma membrane in animal cells, thereby sustaining vital electrochemical gradients that energize channels and secondary transporters. The crystal structure of Na(+),K(+)-ATPase has previously been elucidated using the enzyme from native sources such as porcine kidney and shark rectal gland. Here, the isolation, crystallization and first structure determination of bovine kidney Na(+),K(+)-ATPase in a high-affinity E2-BeF3(-)-ouabain complex with bound magnesium are described. Crystals belonging to the orthorhombic space group C2221 with one molecule in the asymmetric unit exhibited anisotropic diffraction to a resolution of 3.7 Å with full completeness to a resolution of 4.2 Å. The structure was determined by molecular replacement, revealing unbiased electron-density features for bound BeF3(-), ouabain and Mg(2+) ions. PMID:27050261

  15. Spectroscopic properties of N- n-hexyltetrachlorophthalimide and supramolecular interactions in its crystals

    NASA Astrophysics Data System (ADS)

    Brycki, Bogumił; Kowalczyk, Iwona; Zieliński, Andrzej; Borowiak, Teresa; Wolska, Irena

    2008-02-01

    N- n-hexyltetrachlorophthalimide has been characterized by X-ray diffraction, FTIR, Raman and NMR spectroscopy. Also B3LYP and DFT calculations have been carried out. The optimized bond lengths, bond angles and torsion angles calculated by B3LYP/6-31G(d,p) approach have been compared with the X-ray data. The screening constants for 13C and 1H atoms have been calculated by the GIAO/B3LYP/6-31G(d,p) approach and analyzed. Linear correlations between the experimental 1H and 13C chemical shifts and the computed screening constants confirm the optimized geometry. The supramolecular structure is organized into hydrophilic and hydrophobic segments. The tetrachlorophthalimide moieties of the hydrophilic segments form infinite chains via halogen bonds C dbnd O⋯Cl. These bonds as well as weak intermolecular hydrogen bonds C sbnd H⋯O contribute to the parallel orientation of the chains and to the stabilization of their flat conformation. The intermolecular Cl⋯Cl interactions stabilize the organization of the hydrophilic segments.

  16. Synthesis and crystal structure determination of yttrium ultraphosphate YP{sub 5}O{sub 14}

    SciTech Connect

    Mbarek, A.; Graia, M. Chadeyron, G.; Zambon, D.; Bouaziz, J.; Fourati, M.

    2009-03-15

    The crystal structure of monoclinic YP{sub 5}O{sub 14} (space group C2/c, a=12.919(2) A, b=12.796(4) A, c=12.457(2) A, {beta}=91.30(1){sup o}, Z=8) has been refined from single-crystal X-ray diffraction data. Full-matrix least-squares refinement on F{sup 2} using 2249 independent reflections for 183 refinable parameters results in a final R value of 0.027 ({omega}R=0.069). The structure is isotypic with HoP{sub 5}O{sub 14}. This structure is built up from infinite layers of PO{sub 4} tetrahedra linked through isolated YO{sub 8} polyhedra. The three-dimensional cohesion of the framework results from Y-O-P bridges. This crystal structure refinement leads to the calculated X-ray diffraction powder pattern of this monoclinic polymorph, which has been the starting point of a thorough study of the solid-state synthesis of this ultraphosphate. This investigation further leads to a better outstanding of features observed during the synthesis of powdered samples. The thermal behavior of this ultraphosphate has been studied by DTA and TGA analyses. The infrared and Raman spectroscopic characterizations have been carried out on polycrystalline samples. The luminescence properties of the Eu{sup 3+} ion incorporated in the monoclinic C2/c polymorph of YP{sub 5}O{sub 14} as local structural probe show that in YP{sub 5}O{sub 14}: 5% Eu{sup 3+} sample, the Eu{sup 3+} ions are distributed over the two Y{sup 3+} crystallographic sites of C{sub 2} symmetry of this structure. - Graphical Abstract: The crystal structure of the monoclinic C2/c polymorph of YP{sub 5}O{sub 14} has been refined from single-crystal X-ray diffraction data. The luminescence properties of the Eu{sup 3+} ion incorporated in this matrix as local structural probe show that the Eu{sup 3+} ions are distributed over the two Y{sup 3+} crystallographic sites of C{sub 2} symmetry of this structure.

  17. Crystal structure of ammonia dihydrate II.

    PubMed

    Griffiths, Gareth I G; Fortes, A Dominic; Pickard, Chris J; Needs, R J

    2012-05-01

    We have used density-functional-theory (DFT) methods together with a structure searching algorithm to make an experimentally constrained prediction of the structure of ammonia dihydrate II (ADH-II). The DFT structure is in good agreement with neutron diffraction data and verifies the prediction. The structure consists of the same basic structural elements as ADH-I, with a modest alteration to the packing, but a considerable reduction in volume. The phase diagram of the known ADH and ammonia monohydrate + water-ice structures is calculated with the Perdew-Burke-Ernzerhof density functional, and the effects of a semi-empirical dispersion corrected functional are investigated. The results of our DFT calculations of the finite-pressure elastic constants of ADH-II are compared with the available experimental data for the elastic strain coefficients. PMID:22583254

  18. Theoretical Studies on the Electronic Structures and Properties of Complex Ceramic Crystals and Novel Materials

    SciTech Connect

    Ching, Wai-Yim

    2012-01-14

    This project is a continuation of a long program supported by the Office of Basic Energy Science in the Office of Science of DOE for many years. The final three-year continuation started on November 1, 2005 with additional 1 year extension to October 30, 2009. The project was then granted a two-year No Cost Extension which officially ended on October 30, 2011. This report covers the activities within this six year period with emphasis on the work completed within the last 3 years. A total of 44 papers with acknowledgement to this grant were published or submitted. The overall objectives of this project are as follows. These objectives have been evolved over the six year period: (1) To use the state-of-the-art computational methods to investigate the electronic structures of complex ceramics and other novel crystals. (2) To further investigate the defects, surfaces/interfaces and microstructures in complex materials using large scale modeling. (3) To extend the study on ceramic materials to more complex bioceramic crystals. (4) To initiate the study on soft condensed matters including water and biomolecules. (5) To focus on the spectroscopic studies of different materials especially on the ELNES and XANES spectral calculations and their applications related to experimental techniques. (6) To develop and refine computational methods to be effectively executed on DOE supercomputers. (7) To evaluate mechanical properties of different crystals and those containing defects and relate them to the fundamental electronic structures. (8) To promote and publicize the first-principles OLCAO method developed by the PI (under DOE support for many years) for applications to large complex material systems. (9) To train a new generation of graduate students and postdoctoral fellows in modern computational materials science and condensed matter physics. (10) To establish effective international and domestic collaborations with both experimentalists and theorists in materials

  19. Ytterbium- and neodymium-doped vanadate laser hose crystals having the apatite crystal structure

    DOEpatents

    Payne, Stephen A.; Kway, Wayne L.; DeLoach, Laura D.; Krupke, William F.; Chai, Bruce H. T.

    1994-01-01

    Yb.sup.3+ and Nd.sup.3+ doped Sr.sub.5 (VO.sub.4).sub.3 F crystals serve as useful infrared laser media that exhibit low thresholds of oscillation and high slope efficiencies, and can be grown with high optical quality. These laser media possess unusually high absorption and emission cross sections, which provide the crystals with the ability to generate greater gain for a given amount of pump power. Many related crystals such as Sr.sub.5 (VO.sub.4).sub.3 F crystals doped with other rare earths, transition metals, or actinides, as well as the many structural analogs of Sr.sub.5 (VO.sub.4).sub.3 F, where the Sr.sup.2+ and F.sup.- ions are replaced by related chemical species, have similar properties.

  20. Ytterbium- and neodymium-doped vanadate laser hose crystals having the apatite crystal structure

    DOEpatents

    Payne, S.A.; Kway, W.L.; DeLoach, L.D.; Krupke, W.F.; Chai, B.H.T.

    1994-08-23

    Yb[sup 3+] and Nd[sup 3+] doped Sr[sub 5](VO[sub 4])[sub 3]F crystals serve as useful infrared laser media that exhibit low thresholds of oscillation and high slope efficiencies, and can be grown with high optical quality. These laser media possess unusually high absorption and emission cross sections, which provide the crystals with the ability to generate greater gain for a given amount of pump power. Many related crystals such as Sr[sub 5](VO[sub 4])[sub 3]F crystals doped with other rare earths, transition metals, or actinides, as well as the many structural analogs of Sr[sub 5](VO[sub 4])[sub 3]F, where the Sr[sup 2+] and F[sup [minus

  1. Combined crystal structure prediction and high-pressure crystallization in rational pharmaceutical polymorph screening

    NASA Astrophysics Data System (ADS)

    Neumann, M. A.; van de Streek, J.; Fabbiani, F. P. A.; Hidber, P.; Grassmann, O.

    2015-07-01

    Organic molecules, such as pharmaceuticals, agro-chemicals and pigments, frequently form several crystal polymorphs with different physicochemical properties. Finding polymorphs has long been a purely experimental game of trial-and-error. Here we utilize in silico polymorph screening in combination with rationally planned crystallization experiments to study the polymorphism of the pharmaceutical compound Dalcetrapib, with 10 torsional degrees of freedom one of the most flexible molecules ever studied computationally. The experimental crystal polymorphs are found at the bottom of the calculated lattice energy landscape, and two predicted structures are identified as candidates for a missing, thermodynamically more stable polymorph. Pressure-dependent stability calculations suggested high pressure as a means to bring these polymorphs into existence. Subsequently, one of them could indeed be crystallized in the 0.02 to 0.50 GPa pressure range and was found to be metastable at ambient pressure, effectively derisking the appearance of a more stable polymorph during late-stage development of Dalcetrapib.

  2. Photonic crystal structures for efficent localization or extraction of light

    NASA Astrophysics Data System (ADS)

    Vuckovic, Jelena

    Three-dimensional (3D) photonic crystals offer the opportunity of light manipulation in all directions in space, but they are very difficult to fabricate. On the other hand, planar photonic crystals are much simpler to make, but they exhibit only a "quasi-3D" confinement, resulting from the combined action of 2D photonic crystal and internal reflection. The imperfect confinement in the third dimension produces some unwanted out-of-plane loss, which is usually a limiting factor in performance of these structures. This thesis proposes how to fully take advantage of the relatively simple fabrication of planar photonic crystals, by addressing a problem of loss-reduction. One of the greatest challenges in photonics is a construction of optical microcavities with small mode volumes and large quality factors, for efficient localization of light. Beside standard applications of these structures (such as lasers or filters), they can potentially be used for cavity QED experiments, or as building blocks for quantum networks. This work also presents the design and fabrication of optical microcavities based on planar photonic crystals, with mode volumes of the order of one half of cubic wavelength of light (measured in material) and with Q factors predicted to be even larger than 10 4. In addition to photonic crystals fabricated in semiconductors, we also address interesting properties of metallic photonic crystals and present our theoretical and experimental work on using them to improve the output of light emissive devices. Feature sizes of structures presented here are below those achievable by photolithography. Therefore, a high resolution lithography is necessary for their fabrication. The presently used e-beam writing techniques suffer from limitations in speed and wafer throughput, and they represent a huge obstacle to commercialization of photonic crystals. Our preliminary work on electron beam projection lithography, the technique that could provide us with the speed

  3. Spectroscopic characterization and molecular structure of 3,14-dimethyl-2,6,13,17-tetraazapentacyclo[16.4.0.1(2,17).1(6,13).0(7,12)]tetracosane.

    PubMed

    Moon, Dohyun; Hong, Yong Pyo; Choi, Jong Ha

    2016-09-01

    Constrained cyclam derivatives have been found to exhibit anti-HIV effects. The strength of binding to the CXCR4 receptor correlates with anti-HIV activity. The conformation of the macrocyclic compound is very important for co-receptor recognition. Therefore, knowledge of the conformation and crystal packing of macrocycles has become important in developing new highly effective anti-HIV drugs. Structural modifications of N-functionalized polyaza macrocyclic compounds have been achieved using various methods. A new synthesis affording single crystals of the title tetraazapentacyclo[16.4.0.1(2,17).1(6,13).0(7,12)]tetracosane macrocycle, C22H40N4, is reported. Formaldehyde reacts readily at room temperature with the tetraazatricyclo[16.4.0.0(2,17)]docosane precursor to yield a macropolycycle containing two five-membered rings. Characterization by elemental, spectroscopic and single-crystal X-ray diffraction analyses shows that the asymmetric unit contains half of a centrosymmetric molecule. The molecular structure shows a trans conformation for the two methylene bridges owing to molecular symmetry. The crystal structure is stabilized by intramolecular C-H...N hydrogen bonds. NMR and IR spectroscopic properties support the methylene-bridged macrocyclic structure. PMID:27585935

  4. Spectroscopic Survey Telescope design. III - Optical support structure and overall configuration

    NASA Astrophysics Data System (ADS)

    Ray, F. B.

    1990-07-01

    The Universities of Texas and Penn State are working together on an Arecibo-type optical telescope to be utilized in a semitransit mode for spectroscopic survey work. Its optics include a spherical primary mirror, a 2-element all-reflecting Gregorian spherical aberration corrector, and a series of optical fibers that will transmit light to a family of spectrographs. An optical support structure is being developed to permit position adjustment in azimuth only. During an azimuth position change, the instrument's entire weight is borne by steel rollers bearing on a circular crane rail of standard section, with support loads transmitted to the telescope base through pneumatic springs. Extensive application of various analytical procedures and computer-aided engineering tools has effectively allowed the detailed examination of several design iterations, thereby increasing the probability of success in the realized structure.

  5. Compact Couplers for Photonic Crystal Laser-Driven Accelerator Structures

    SciTech Connect

    Cowan, Benjamin; Lin, M.C.; Schwartz, Brian; Byer, Robert; McGuinness, Christopher; Colby, Eric; England, Robert; Noble, Robert; Spencer, James; /SLAC

    2012-07-02

    Photonic crystal waveguides are promising candidates for laser-driven accelerator structures because of their ability to confine a speed-of-light mode in an all-dielectric structure. Because of the difference between the group velocity of the waveguide mode and the particle bunch velocity, fields must be coupled into the accelerating waveguide at frequent intervals. Therefore efficient, compact couplers are critical to overall accelerator efficiency. We present designs and simulations of high-efficiency coupling to the accelerating mode in a three-dimensional photonic crystal waveguide from a waveguide adjoining it at 90{sup o}. We discuss details of the computation and the resulting transmission. We include some background on the accelerator structure and photonic crystal-based optical acceleration in general.

  6. Free-Standing Photonic Crystal Films with Gradient Structural Colors.

    PubMed

    Ding, Haibo; Liu, Cihui; Ye, Baofen; Fu, Fanfan; Wang, Huan; Zhao, Yuanjin; Gu, Zhongze

    2016-03-23

    Hydrogel colloidal crystal composite materials have a demonstrated value in responsive photonic crystals (PhCs) via controllable stimuli. Although they have been successfully exploited to generate a gradient of color distribution, the soft hydrogels have limitations in terms of stability and storage caused by dependence on environment. Here, we present a practical strategy to fabricate free-standing PhC films with a stable gradient of structural colors using binary polymer networks. A colloidal crystal hydrogel film was prepared for this purpose, with continuously varying photonic band gaps corresponding to the gradient of the press. Then, a second polymer network was used to lock the inside non-close-packed PhC structures and color distribution of the hydrogel film. It was demonstrated that our strategy could bring about a solution to the angle-dependent structural colors of the PhC films by coating the surface with special microstructures. PMID:26962967

  7. The high-resolution crystal structure of human LCAT.

    PubMed

    Piper, Derek E; Romanow, William G; Gunawardane, Ruwanthi N; Fordstrom, Preston; Masterman, Stephanie; Pan, Oscar; Thibault, Stephen T; Zhang, Richard; Meininger, David; Schwarz, Margrit; Wang, Zhulun; King, Chadwick; Zhou, Mingyue; Walker, Nigel P C

    2015-09-01

    LCAT is intimately involved in HDL maturation and is a key component of the reverse cholesterol transport (RCT) pathway which removes excess cholesterol molecules from the peripheral tissues to the liver for excretion. Patients with loss-of-function LCAT mutations exhibit low levels of HDL cholesterol and corneal opacity. Here we report the 2.65 Å crystal structure of the human LCAT protein. Crystallization required enzymatic removal of N-linked glycans and complex formation with a Fab fragment from a tool antibody. The crystal structure reveals that LCAT has an α/β hydrolase core with two additional subdomains that play important roles in LCAT function. Subdomain 1 contains the region of LCAT shown to be required for interfacial activation, while subdomain 2 contains the lid and amino acids that shape the substrate binding pocket. Mapping the naturally occurring mutations onto the structure provides insight into how they may affect LCAT enzymatic activity. PMID:26195816

  8. Modulated crystal structure of InMo4O6.

    PubMed

    Schultz, Peter; Simon, Arndt; Oeckler, Oliver

    2016-08-01

    The (3 + 1)-dimensional modulated crystal structure of the metal-rich cluster compound InMo4O6 was solved and refined from single-crystal data in the superspace group P4/mbm(00γ)00ss [q = 0, 0, 0.1536 (4); a = 9.6664 (9), c = 2.8645 (3) Å; R1(all) = 0.046, wR(all) = 0.076]. The crystal structure is closely related to the NaMo4O6 structure type. It is built from rods of Mo6 clusters condensed via trans edges. These form channels parallel to [001], in which In6 and In7 oligomers alternate. Weak diffuse planes parallel to (001)* interconnect the satellite reflections; they occur due to two-dimensional rod disorder of the In oligomer chains. PMID:27484384

  9. Conformational, electronic, and spectroscopic characterization of isophthalic acid (monomer and dimer structures) experimentally and by DFT

    NASA Astrophysics Data System (ADS)

    Bardak, F.; Karaca, C.; Bilgili, S.; Atac, A.; Mavis, T.; Asiri, A. M.; Karabacak, M.; Kose, E.

    2016-08-01

    Isophthalic acid (C6H4(CO2H)2) is a noteworthy organic compound widely used in coating and synthesis of resins and the production of commercially important polymers such as drink plastic bottles. The effects of isophthalic acid (IPA) on human health, toxicology, and biodegradability are the main focus of many researchers. Because structural and spectroscopic investigation of molecules provides a deep understanding of interactional behaviors of compounds, this study stands for exploring those features. Therefore, the spectroscopic, structural, electronic, and thermodynamical properties of IPA were thoroughly studied in this work experimentally using UV-Vis, 1H and 13C NMR, FT-IR, FT-Raman and theoretically via DFT and TD-DFT calculations. The UV-Vis absorption spectrum in water was taken in the region 200-400 nm. The NMR chemical shifts (1H and 13C) were recorded in DMSO solution. The infrared and Raman spectra of the solid IPA were recorded in the range of 4000-400 cm- 1 and 3500-50 cm- 1, respectively. DFT and TD-DFT calculations were performed at the level of B3LYP/6-311++G(d,p) in determination of geometrical structure, electronic structure analysis and normal mode. The 13C and 1H nuclear magnetic resonance (NMR) spectra were estimated by using the gauge-invariant atomic orbital (GIAO) method. The scaled quantum mechanics (SQM) method was used to determine the total energy distribution (TED) to assign the vibrational modes accurately. Weak interactions such as hydrogen bonding and Van der Walls were analyzed via reduced density gradient (RDG) analysis in monomeric and dimeric forms. Furthermore, the excitation energies, density of state (DOS) diagram, thermodynamical properties, molecular electro-static potential (MEP), and nonlinear optical (NLO) properties were obtained.

  10. Fourier transform infrared spectroscopic analysis of sperm chromatin structure and DNA stability.

    PubMed

    Oldenhof, H; Schütze, S; Wolkers, W F; Sieme, H

    2016-05-01

    Sperm chromatin structure and condensation determine accessibility for damage, and hence success of fertilization and development. The aim of this study was to reveal characteristic spectral features coinciding with abnormal sperm chromatin packing (i.e., DNA-protein interactions) and decreased fertility, using Fourier transform infrared spectroscopy. Chromatin structure in spermatozoa obtained from different stallions was investigated. Furthermore, spermatozoa were exposed to oxidative stress, or treated with thiol-oxidizing and disulfide-reducing agents, to alter chromatin structure and packing. Spectroscopic studies were corroborated with flow cytometric analyses using the DNA-intercalating fluorescent dye acridine orange. Decreased fertility of individuals correlated with increased abnormal sperm morphology and decreased stability toward induced DNA damage. Treatment with the disulfide reducing agent dithiothreitol resulted in increased sperm chromatin decondensation and DNA accessibility, similar as found for less mature epididymal spermatozoa. In situ infrared spectroscopic analysis revealed that characteristic bands arising from the DNA backbone (ν1230, ν1086, ν1051 cm(-1) ) changed in response to induced oxidative damage, water removal, and decondensation. This coincided with changes in the amide-I region (intensity at ν1620 vs. ν1640 cm(-1) ) denoting concomitant changes in protein secondary structure. Reduction in protein disulfide bonds resulted in a decreased value of the asymmetric to symmetric phosphate band intensity (ν1230/ν1086 cm(-1) ), suggesting that this band ratio is sensitive for the degree of chromatin condensation. Moreover, when analyzing spermatozoa from different individuals, it was found that the asymmetric/symmetric phosphate band ratio negatively correlated with the percentage of morphologically abnormal spermatozoa. PMID:26916383

  11. Conformational, electronic, and spectroscopic characterization of isophthalic acid (monomer and dimer structures) experimentally and by DFT.

    PubMed

    Bardak, F; Karaca, C; Bilgili, S; Atac, A; Mavis, T; Asiri, A M; Karabacak, M; Kose, E

    2016-08-01

    Isophthalic acid (C6H4(CO2H)2) is a noteworthy organic compound widely used in coating and synthesis of resins and the production of commercially important polymers such as drink plastic bottles. The effects of isophthalic acid (IPA) on human health, toxicology, and biodegradability are the main focus of many researchers. Because structural and spectroscopic investigation of molecules provides a deep understanding of interactional behaviors of compounds, this study stands for exploring those features. Therefore, the spectroscopic, structural, electronic, and thermodynamical properties of IPA were thoroughly studied in this work experimentally using UV-Vis, (1)H and (13)C NMR, FT-IR, FT-Raman and theoretically via DFT and TD-DFT calculations. The UV-Vis absorption spectrum in water was taken in the region 200-400nm. The NMR chemical shifts ((1)H and (13)C) were recorded in DMSO solution. The infrared and Raman spectra of the solid IPA were recorded in the range of 4000-400cm(-1) and 3500-50cm(-1), respectively. DFT and TD-DFT calculations were performed at the level of B3LYP/6-311++G(d,p) in determination of geometrical structure, electronic structure analysis and normal mode. The (13)C and (1)H nuclear magnetic resonance (NMR) spectra were estimated by using the gauge-invariant atomic orbital (GIAO) method. The scaled quantum mechanics (SQM) method was used to determine the total energy distribution (TED) to assign the vibrational modes accurately. Weak interactions such as hydrogen bonding and Van der Walls were analyzed via reduced density gradient (RDG) analysis in monomeric and dimeric forms. Furthermore, the excitation energies, density of state (DOS) diagram, thermodynamical properties, molecular electro-static potential (MEP), and nonlinear optical (NLO) properties were obtained. PMID:27107533

  12. Ultrasonic promoted synthesis of novel s-triazine-Schiff base derivatives; molecular structure, spectroscopic studies and their preliminary anti-proliferative activities

    NASA Astrophysics Data System (ADS)

    El-Faham, Ayman; Soliman, Saied M.; Ghabbour, Hazem A.; Elnakady, Yasser A.; Mohaya, Talal A.; Siddiqui, Mohammed R. H.; Albericio, Fernando

    2016-12-01

    Novel series of s-triazine-Schiff base derivatives were synthesized employing ultrasonic irradiation and characterized by NMR (1H and 13C), FT-IR, and elemental analysis. The use of ultrasonic irradiation has allowed the preparation of the target products with better yields in shorter reaction time and excellent purities compared to the conventional heating. X-ray single crystal diffraction experiments verified the molecular structure of four from the new prepared s-triaizne-Schiff base derivatives. The molecular structures of the studied compounds are computerized using DFT/B3LYP method. The effects of substituent at the triazine and phenyl ring on the electronic and spectroscopic properties of the studied compounds were also investigated. The natural atomic charges showed that pipridino-s-triazine derivatives are richer in electrons than those having morpholino derivatives. The anti-proliferative effects for the prepared compounds were tested against three different cancer cell lines.

  13. Crystal growth, structural, thermal and mechanical behavior of L-arginine 4-nitrophenolate 4-nitrophenol dihydrate (LAPP) single crystals

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

    Single crystals of L-arginine 4-nitrophenolate 4-nitrophenol dihydrate (LAPP) have been grown successfully from the solution of L-arginine and 4-nitrophenol. Slow evaporation of solvent technique was adopted to grow the bulk single crystals. Single crystal X-ray diffraction analysis confirms the grown crystal has monoclinic crystal system with space group of P21. Powder X-ray diffraction analysis shows the good crystalline nature. The crystalline perfection of the grown single crystals was analyzed by HRXRD by employing a multicrystal X-ray diffractometer. The functional groups were identified from proton NMR spectroscopic analysis. Linear and nonlinear optical properties were determined by UV-Vis spectrophotometer and Kurtz powder technique respectively. It is found that the grown crystal has no absorption in the green wavelength region and the SHG efficiency was found to be 2.66 times that of the standard KDP. The Thermal stability of the crystal was found by obtaining TG/DTA curve. The mechanical behavior of the grown crystal has been studied by Vicker's microhardness method.

  14. Synthesis, crystal structure, and in vitro and in silico molecular docking of novel acyl thiourea derivatives

    NASA Astrophysics Data System (ADS)

    Haribabu, Jebiti; Subhashree, Govindarajulu Rangabashyam; Saranya, Sivaraj; Gomathi, Kannayiram; Karvembu, Ramasamy; Gayathri, Dasararaju

    2015-08-01

    In the present study, a series of six biologically active substituted acyl thiourea compounds (1-6) has been synthesized from cyclohexanecarbonyl isothiocyanate and various primary amines (2-methyl aniline, aniline, 4-methoxy aniline, 4-ethoxy aniline, benzyl amine and 2-methoxy aniline). The synthesized compounds were characterized by elemental analyses, UV-Visible, FT-IR, 1H & 13C NMR and mass spectroscopic techniques. Three dimensional molecular structure of two compounds (1 and 5) was determined by single crystal X-ray crystallography. All the synthesized compounds show good anti-oxidant and anti-haemolytic activities. In silico molecular docking studies were performed to screen against DprE1 and HSP90 enzymes targeting tuberculosis and cancer respectively.

  15. The Crystal Structure of GXGD Membrane Protease FlaK

    SciTech Connect

    J Hu; Y Xue; S Lee; Y Ha

    2011-12-31

    The GXGD proteases are polytopic membrane proteins with catalytic activities against membrane-spanning substrates that require a pair of aspartyl residues. Representative members of the family include preflagellin peptidase, type 4 prepilin peptidase, presenilin and signal peptide peptidase. Many GXGD proteases are important in medicine. For example, type 4 prepilin peptidase may contribute to bacterial pathogenesis, and mutations in presenilin are associated with Alzheimer's disease. As yet, there is no atomic-resolution structure in this protease family. Here we report the crystal structure of FlaK, a preflagellin peptidase from Methanococcus maripaludis, solved at 3.6 {angstrom} resolution. The structure contains six transmembrane helices. The GXGD motif and a short transmembrane helix, helix 4, are positioned at the centre, surrounded by other transmembrane helices. The crystal structure indicates that the protease must undergo conformational changes to bring the GXGD motif and a second essential aspartyl residue from transmembrane helix 1 into close proximity for catalysis. A comparison of the crystal structure with models of presenilin derived from biochemical analysis reveals three common transmembrane segments that are similarly arranged around the active site. This observation reinforces the idea that the prokaryotic and human proteases are evolutionarily related. The crystal structure presented here provides a framework for understanding the mechanism of the GXGD proteases, and may facilitate the rational design of inhibitors that target specific members of the family.

  16. The crystal structure of GXGD membrane protease FlaK

    SciTech Connect

    Hu, Jian; Xue, Yi; Lee, Sangwon; Ha, Ya

    2011-09-20

    The GXGD proteases are polytopic membrane proteins with catalytic activities against membrane-spanning substrates that require a pair of aspartyl residues. Representative members of the family include preflagellin peptidase, type 4 prepilin peptidase, presenilin and signal peptide peptidase. Many GXGD proteases are important in medicine. For example, type 4 prepilin peptidase may contribute to bacterial pathogenesis, and mutations in presenilin are associated with Alzheimer's disease. As yet, there is no atomic-resolution structure in this protease family. Here we report the crystal structure of FlaK, a preflagellin peptidase from Methanococcus maripaludis, solved at 3.6 {angstrom} resolution. The structure contains six transmembrane helices. The GXGD motif and a short transmembrane helix, helix 4, are positioned at the centre, surrounded by other transmembrane helices. The crystal structure indicates that the protease must undergo conformational changes to bring the GXGD motif and a second essential aspartyl residue from transmembrane helix 1 into close proximity for catalysis. A comparison of the crystal structure with models of presenilin derived from biochemical analysis reveals three common transmembrane segments that are similarly arranged around the active site. This observation reinforces the idea that the prokaryotic and human proteases are evolutionarily related. The crystal structure presented here provides a framework for understanding the mechanism of the GXGD proteases, and may facilitate the rational design of inhibitors that target specific members of the family.

  17. Synthesis, Crystal structure, and Hirshfeld Surface Analysis of a New Mixed Ligand Copper(II) Complex.

    PubMed

    Shit, Shyamapada; Marschner, Christoph; Mitra, Samiran

    2016-01-01

    A new mixed ligand copper(II) complex, [Cu(2,4-pydc)(pic)(H(2)O)]∙H(2)O (1) (where 2,4-pydc = pyridine-2,4-dicarboxylate, pic = 2-picolylamine) has been synthesized and characterized by elemental analysis, FT-IR and UV-Vis spectroscopic and thermogravimetric methods. Single crystal X-ray diffraction analysis reveals that copper(II) atom in the title complex adopts distorted square pyramidal geometry. Structural characterization also reveals that interplay of O-H···O, N-H···O, C-H···O, and C-H···π interactions between lattice and coordinated water and ligands significantly contribute to the crystal packing leading to the formation and strengthening of three dimensional supramolecular assembly. Hirshfeld surface analysis employing 3D molecular surface contours and 2D fingerprint plots have been used to analyze intermolecular interactions present in the solid state of the crystal. PMID:26970797

  18. Constraints and restraints in crystal structure analysis

    PubMed Central

    Immirzi, Attilio

    2009-01-01

    The widely used restraint-based approach to structural analysis using diffraction data is critiqued. The convenience of using rigid constraints, through the use of internal coordinates, is discussed. PMID:22477768

  19. Ab initio modelling: Genesis of crystal structures

    NASA Astrophysics Data System (ADS)

    van de Walle, Axel

    2005-05-01

    Genetic algorithms prove useful to distil a complex quantum mechanical calculation of interatomic interactions down to its simplest mathematical expression. This makes it possible to predict the structure of new compounds from first principles.

  20. Crystal Structure of the Nipah Virus Phosphoprotein Tetramerization Domain

    PubMed Central

    Bruhn, Jessica F.; Barnett, Katherine C.; Bibby, Jaclyn; Thomas, Jens M. H.; Keegan, Ronan M.; Rigden, Daniel J.; Bornholdt, Zachary A.

    2014-01-01

    The Nipah virus phosphoprotein (P) is multimeric and tethers the viral polymerase to the nucleocapsid. We present the crystal structure of the multimerization domain of Nipah virus P: a long, parallel, tetrameric, coiled coil with a small, α-helical cap structure. Across the paramyxoviruses, these domains share little sequence identity yet are similar in length and structural organization, suggesting a common requirement for scaffolding or spatial organization of the functions of P in the virus life cycle. PMID:24155387

  1. Electronic structure of the CuBS2 crystal

    NASA Astrophysics Data System (ADS)

    Basalaev, Yu. M.; Gordienko, A. B.; Filippov, S. I.

    2012-09-01

    The band structure and spectra of the total and projected densities of states of a new crystal of the chalcopyrite family, namely, CuBS2, have been calculated in terms of the density functional theory. It has been found that the crystal is a pseudo-direct-band-gap semiconductor, and the best theoretical estimate of the optical band gap is 3.44 eV. The upper valence band of the CuBS2 crystal basically consists of the contributions from the p states of S atoms and the d states of Cu atoms. The crystal splitting is 0.2 eV. The bottom of the conduction band is basically formed by the sp states of boron and sulfur atoms with an admixture of the s states of copper atoms.

  2. Utilization of Protein Crystal Structures in Industry

    NASA Astrophysics Data System (ADS)

    Ishikawa, Kohki

    In industry, protein crystallography is used in mainly two technologies. One is structure-based drug design, and the other is structure-based enzyme engineering. Some successful cases together with recent advances are presented in this article. The cases include the development of an anti-influenza drug, and the introduction of engineered acid phosphatase to the manufacturing process of nucleotides used as umami seasoning.

  3. X-Ray crystal structure and molecular dynamics simulations of silver hake parvalbumin (Isoform B).

    PubMed Central

    Richardson, R. C.; King, N. M.; Harrington, D. J.; Sun, H.; Royer, W. E.; Nelson, D. J.

    2000-01-01

    Parvalbumins constitute a class of calcium-binding proteins characterized by the presence of several helix-loop-helix (EF-hand) motifs. In a previous study (Revett SP, King G, Shabanowitz J, Hunt DF, Hartman KL, Laue TM, Nelson DJ, 1997, Protein Sci 7:2397-2408), we presented the sequence of the major parvalbumin isoform from the silver hake (Merluccius bilinearis) and presented spectroscopic and structural information on the excised "EF-hand" portion of the protein. In this study, the X-ray crystal structure of the silver hake major parvalbumin has been determined to high resolution, in the frozen state, using the molecular replacement method with the carp parvalbumin structure as a starting model. The crystals are orthorhombic, space group C2221, with a = 75.7 A, b = 80.7 A, and c = 42.1 A. Data were collected from a single crystal grown in 15% glycerol, which served as a cryoprotectant for flash freezing at -188 degrees C. The structure refined to a conventional R-value of 21% (free R 25%) for observed reflections in the range 8 to 1.65 A [1 > 2sigma(I)]. The refined model includes an acetylated amino terminus, 108 residues (characteristic of a beta parvalbumin lineage), 2 calcium ions, and 114 water molecules per protein molecule. The resulting structure was used in molecular dynamics (MD) simulations focused primarily on the dynamics of the ligands coordinating the Ca2+ ions in the CD and EF sites. MD simulations were performed on both the fully Ca2+ loaded protein and on a Ca2+ deficient variant, with Ca2+ only in the CD site. There was substantial agreement between the MD and X-ray results in addressing the issue of mobility of key residues in the calcium-binding sites, especially with regard to the side chain of Ser55 in the CD site and Asp92 in the EF site. PMID:10739249

  4. A new potent calmodulin antagonist with arylalkylamine structure: crystallographic, spectroscopic and functional studies.

    PubMed

    Harmat, V; Böcskei, Z; Náray-Szabó, G; Bata, I; Csutor, A S; Hermecz, I; Arányi, P; Szabó, B; Liliom, K; Vértessy, B G; Ovádi, J

    2000-03-31

    An arylalkylamine-type calmodulin antagonist, N-(3, 3-diphenylpropyl)-N'-[1-R-(3, 4-bis-butoxyphenyl)ethyl]-propylene-diamine (AAA) is presented and its complexes with calmodulin are characterized in solution and in the crystal. Near-UV circular dichroism spectra show that AAA binds to calmodulin with 2:1 stoichiometry in a Ca(2+)-dependent manner. The crystal structure with 2:1 stoichiometry is determined to 2.64 A resolution. The binding of AAA causes domain closure of calmodulin similar to that obtained with trifluoperazine. Solution and crystal data indicate that each of the two AAA molecules anchors in the hydrophobic pockets of calmodulin, overlapping with two trifluoperazine sites, i.e. at a hydrophobic pocket and an interdomain site. The two AAA molecules also interact with each other by hydrophobic forces. A competition enzymatic assay has revealed that AAA inhibits calmodulin-activated phosphodiesterase activity at two orders of magnitude lower concentration than trifluoperazine. The apparent dissociation constant of AAA to calmodulin is 18 nM, which is commensurable with that of target peptides. On the basis of the crystal structure, we propose that the high-affinity binding is mainly due to a favorable entropy term, as the AAA molecule makes multiple contacts in its complex with calmodulin. PMID:10731425

  5. Crystal chemistry and structure refinement of five hydrated calcium borates

    USGS Publications Warehouse

    Clark, J.R.; Appleman, D.E.; Christ, C.L.

    1964-01-01

    The crystal structures of the five known members of the series Ca2B6O11??xH2O (x = 1, 5, 5, 7, 9, and 13) have been refined by full-matrix least-squares techniques, yielding bond distances and angles with standard errors of less than 0??01 A?? and 0??5??, respectively. The results illustrate the crystal chemical principles that govern the structures of hydrated borate compounds. The importance of hydrogen bonding in the ferroelectric transition of colemanite is confirmed by more accurate proton assignments. ?? 1964.

  6. Photonic crystals, light manipulation, and imaging in complex nematic structures

    NASA Astrophysics Data System (ADS)

    Ravnik, Miha; Å timulak, Mitja; Mur, Urban; Čančula, Miha; Čopar, Simon; Žumer, Slobodan

    2016-03-01

    Three selected approaches for manipulation of light by complex nematic colloidal and non-colloidal structures are presented using different own custom developed theoretical and modelling approaches. Photonic crystals bands of distorted cholesteric liquid crystal helix and of nematic colloidal opals are presented, also revealing distinct photonic modes and density of states. Light propagation along half-integer nematic disclinations is shown with changes in the light polarization of various winding numbers. As third, simulated light transmission polarization micrographs of nematic torons are shown, offering a new insight into the complex structure characterization. Finally, this work is a contribution towards using complex soft matter in optics and photonics for advanced light manipulation.

  7. Crystal Structure Effect on Electrical Properties of Ysz Ceramics

    NASA Astrophysics Data System (ADS)

    Zhang, Chunxia; Gong, Shengkai; Zhou, Chungen; Xu, Huibin

    YSZ samples were prepared by Plasma Spray (PS) and Electron Beam Physical Vapor Deposition (EB-PVD) respectively. Microstructure and morphology were observed by SEM and XRD. Grain size of PS-YSZ was non-uniform caused by the inclusion of nano particle by molten particle and column crystal structure was observed for EB-PVD-YSZ. The Arrhenius plots of two samples were graphed by analysis of the measurement results of AC impedance spectra. The conductive mechanisms for EB-PVD and PS YSZ were different due to the crystal structure.

  8. Structure of Scots pine defensin 1 by spectroscopic methods and computational modeling.

    PubMed

    Ermakova, Elena A; Faizullin, Dzhigangir A; Idiyatullin, Bulat Z; Khairutdinov, Bulat I; Mukhamedova, Liya N; Tarasova, Nadezhda B; Toporkova, Yana Y; Osipova, Elena V; Kovaleva, Valentina; Gogolev, Yuri V; Zuev, Yuriy F; Nesmelova, Irina V

    2016-03-01

    Defensins are part of the innate immune system in plants with activity against a broad range of pathogens, including bacteria, fungi and viruses. Several defensins from conifers, including Scots pine defensin 1 (Pinus sylvestris defensin 1, (PsDef1)) have shown a strong antifungal activity, however structural and physico-chemical properties of the family, needed for establishing the structure-dynamics-function relationships, remain poorly characterized. We use several spectroscopic and computational methods to characterize the structure, dynamics, and oligomeric state of PsDef1. The three-dimensional structure was modeled by comparative modeling using several programs (Geno3D, SWISS-MODEL, I-TASSER, Phyre(2), and FUGUE) and verified by circular dichroism (CD) and infrared (FTIR) spectroscopy. Furthermore, FTIR data indicates that the structure of PsDef1 is highly resistant to high temperatures. NMR diffusion experiments show that defensin exists in solution in the equilibrium between monomers and dimers. Four types of dimers were constructed using the HADDOCK program and compared to the known dimer structures of other plant defensins. Gaussian network model was used to characterize the internal dynamics of PsDef1 in monomer and dimer states. PsDef1 is a typical representative of P. sylvestris defensins and hence the results of this study are applicable to other members of the family. PMID:26687241

  9. Structure of self - assembled two-dimensional spherical crystals

    NASA Astrophysics Data System (ADS)

    Bausch, Andreas R.

    2004-03-01

    Dense spherical particles on a flat surface usually pack into a simple triangular lattice, similar to billiard balls at the start of a game. The minimum energy configuration for interacting particles on the curved surface of a sphere, however, presents special difficulties, as recognized already by J.J. Thomson. We describe experimental investigations of the structure of two-dimensional spherical crystals. The crystals, formed by beads self-assembled on water droplets in oil, serve as model systems for exploring very general theories about the minimum energy configurations of particles with arbitrary repulsive interactions on curved surfaces. Above a critical system size we find that crystals develop distinctive high-angle grain boundaries or "scars" not found in planar crystals. The number of excess defects in a scar is shown to grow linearly with the dimensionless system size. First experiments where the melting of the crystal structure was observable will be discussed. Dynamic triangulation methods allow the analysis of the dynamics of the defects. Possible modifications towards mechanically stabilized self assembly structures result in so called Colloidosomes, which are promising for many different encapsulation purposes.

  10. Photonics of liquid-crystal structures: A review

    SciTech Connect

    Palto, S. P. Blinov, L. M.; Barnik, M. I.; Lazarev, V. V.; Umanskii, B. A.; Shtykov, N. M.

    2011-07-15

    The original results of studies of the electro-optical and laser effects which have been performed at the Laboratory of Liquid Crystals of the Institute of Crystallography, Russian Academy of Sciences, over the last few years are reviewed. Cholesteric liquid crystals as vivid representatives of photonic structures and their behavior in an electric field are considered in detail. The formation of higher harmonics in the periodic distribution of the director field in a helical liquid crystal structure and, correspondingly, the new (anharmonic) mode of electro-optical effects are discussed. Another group of studies is devoted to bistable light switching by an electric field in chiral nematics. Polarization diffraction gratings controlled by an electric field are also considered. The results of studies devoted to microlasers on various photonic structures with cholesteric and nematic liquid crystals are considered in detail. Particular attention is given to the new regime: leaky-mode lasing. Designs of liquid crystal light amplifiers and their polarization, field, and spectral characteristics are considered in the last section.

  11. Crystal structures of two engineered thiol trypsins.

    PubMed

    McGrath, M E; Wilke, M E; Higaki, J N; Craik, C S; Fletterick, R J

    1989-11-28

    We have determined the three-dimensional structures of engineered rat trypsins which mimic the active sites of two classes of cysteine proteases. The catalytic serine was replaced with cysteine (S195C) to test the ability of sulfur to function as a nucleophile in a serine protease environment. This variant mimics the cysteine trypsin class of thiol proteases. An additional mutation of the active site aspartate to an asparagine (D102N) created the catalytic triad of the papain-type cysteine proteases. Rat trypsins S195C and D102N,S195C were solved to 2.5 and 2.0 A, respectively. The refined structures were analyzed to determine the structural basis for the 10(6)-fold loss of activity of trypsin S195C and the 10(8)-fold loss of activity of trypsin D102N,S195C, relative to rat trypsin. The active site thiols were found in a reduced state in contrast to the oxidized thiols found in previous thiol protease structures. These are the first reported structures of serine proteases with the catalytic centers of sulfhydryl proteases. Structure analysis revealed only subtle global changes in enzyme conformation. The substrate binding pocket is unaltered, and active site amino acid 102 forms hydrogen bonds to H57 and S214 as well as to the backbone amides of A56 and H57. In trypsin S195C, D102 is a hydrogen-bond acceptor for H57 which allows the other imidazole nitrogen to function as a base during catalysis. In trypsin D102N,S195C, the asparagine at position 102 is a hydrogen-bond donor to H57 which places a proton on the imidazole nitrogen proximal to the nucleophile. This tautomer of H57 is unable to act as a base in catalysis.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:2611228

  12. Formation of the structure of gold nanoclusters during crystallization

    SciTech Connect

    Gafner, Yu. Ya. Goloven'ko, Zh. V.; Gafner, S. L.

    2013-02-15

    The structure formation in gold nanoparticles 1.6-5.0 nm in diameter is studied by molecular dynamics simulation using a tight-binding potential. The simulation shows that the initial fcc phase in small Au clusters transforms into other structural modifications as temperature changes. As the cluster size increases, the transition temperature shifts toward the melting temperature of the cluster. The effect of various crystallization conditions on the formation of the internal structure of gold nanoclusters is studied in terms of microcanonical and canonical ensembles. The stability boundaries of various crystalline isomers are analyzed. The obtained dependences are compared with the corresponding data obtained for copper and nickel nanoparticles. The structure formation during crystallization is found to be characterized by a clear effect of the particle size on the stability of a certain isomer modification. Nickel and copper clusters are shown to exhibit common features in the formation of their structural properties, whereas gold clusters demonstrate much more complex behavior.

  13. CRYSTAL STRUCTURE ANALYSIS OF A PUTATIVE OXIDOREDUCTASE FROM KLEBSIELLA PNEUMONIAE

    SciTech Connect

    Baig, M.; Brown, A.; Eswaramoorthy, S.; Swaminathan, S.

    2009-01-01

    Klebsiella pneumoniae, a gram-negative enteric bacterium, is found in nosocomial infections which are acquired during hospital stays for about 10% of hospital patients in the United States. The crystal structure of a putative oxidoreductase from K. pneumoniae has been determined. The structural information of this K. pneumoniae protein was used to understand its function. Crystals of the putative oxidoreductase enzyme were obtained by the sitting drop vapor diffusion method using Polyethylene glycol (PEG) 3350, Bis-Tris buffer, pH 5.5 as precipitant. These crystals were used to collect X-ray data at beam line X12C of the National Synchrotron Light Source (NSLS) at Brookhaven National Laboratory (BNL). The crystal structure was determined using the SHELX program and refi ned with CNS 1.1. This protein, which is involved in the catalysis of an oxidation-reduction (redox) reaction, has an alpha/beta structure. It utilizes nicotinamide adenine dinucleotide phosphate (NADP) or nicotine adenine dinucleotide (NAD) to perform its function. This structure could be used to determine the active and co-factor binding sites of the protein, information that could help pharmaceutical companies in drug design and in determining the protein’s relationship to disease treatment such as that for pneumonia and other related pathologies.

  14. The crystal structure of aluminum doped β-rhombohedral boron

    NASA Astrophysics Data System (ADS)

    Bykova, Elena; Parakhonskiy, Gleb; Dubrovinskaia, Natalia; Chernyshov, Dmitry; Dubrovinsky, Leonid

    2012-10-01

    A crystal structure of aluminum doped β-rhombohedral boron was studied by single-crystal X-ray diffraction at 80 K. The crystals were synthesized using high-pressure high temperature technique at 3 GPa and 2100 K. The structure is based on three-dimensional framework made of B12 icosahedra with voids occupied by the B28-B-B28 units, it has the R-3m space group with a=10.9014(3), c=23.7225(7) Å lattice dimensions in hexagonal setting. Aluminum atoms are located in A1 and D special positions of the β-B structure with occupancies of 82.7(6)% and 11.3(4)%, respectively. Additional boron atoms are located near the D-site. Their possible distribution is discussed. Finally we have found two appropriate structural models whose refinement suggests two possible chemical compositions, AlB44.8(5) and AlB37.8(5), which are in a good agreement with the chemical analysis data obtained from EDX. The crystal structure of AlB44.8(5) is described in detail.

  15. Crystal structure of HINT from Helicobacter pylori.

    PubMed

    Tarique, K F; Devi, S; Abdul Rehman, S A; Gourinath, S

    2016-01-01

    Proteins belonging to the histidine triad (HIT) superfamily bind nucleotides and use the histidine triad motif to carry out dinucleotidyl hydrolase, nucleotidyltransferase and phosphoramidite hydrolase activities. Five different branches of this superfamily are known to exist. Defects in these proteins in humans are linked to many diseases such as ataxia, diseases of RNA metabolism and cell-cycle regulation, and various types of cancer. The histidine triad nucleotide protein (HINT) is nearly identical to proteins that have been classified as protein kinase C-interacting proteins (PKCIs), which also have the ability to bind and inhibit protein kinase C. The structure of HINT, which exists as a homodimer, is highly conserved from humans to bacteria and shares homology with the product of fragile histidine triad protein (FHit), a tumour suppressor gene of this superfamily. Here, the structure of HINT from Helicobacter pylori (HpHINT) in complex with AMP is reported at a resolution of 3 Å. The final model has R and Rfree values of 26 and 28%, respectively, with good electron density. Structural comparison with previously reported homologues and phylogenetic analysis shows H. pylori HINT to be the smallest among them, and suggests that it branched out separately during the course of evolution. Overall, this structure has contributed to a better understanding of this protein across the animal kingdom. PMID:26750483

  16. Crystal structure, matrix-isolation FTIR, and UV-induced conformational isomerization of 3-quinolinecarboxaldehyde.

    PubMed

    Kuş, Nihal; Henriques, Marta Sofia; Paixão, José António; Lapinski, Leszek; Fausto, Rui

    2014-09-25

    The crystal structure of 3-quinolinecarboxaldehyde (3QC) has been solved, and the compound has been shown to crystallize in the space group P21/c (monoclinic) with a = 6.306(4), b = 18.551(11), c = 6.999(4) Å, β = 106.111(13)°, and Z = 4. The crystals were found to exhibit pseudomerohedral twinning with a twin law corresponding to a two-fold rotation around the monoclinic (100) reciprocal lattice axis (or [4 0 1] in direct space). Individual molecules adopt the syn conformation in the crystal, with the oxygen atom of the aldehyde substituent directed toward the same side of the ring nitrogen atom. In the gas phase, the compound exists in two nearly isoenergetic conformers (syn and anti), which could be successfully trapped in solid argon at 10 K, and their infrared spectra are registered and interpreted. Upon in situ irradiation of matrix-isolated 3QC with UV light (λ > 315 nm), significant reduction of the population of the less stable anti conformer was observed, while that of the conformational ground state (syn conformer) increased, indicating occurrence of the anti → syn isomerization. Upon irradiation at higher energy (λ > 235 nm), the syn → anti reverse photoreaction was observed. Interpretation of the structural, spectroscopic, and photochemical experimental data received support from quantum chemical theoretical results obtained at both DFT/B3LYP (including TD-DFT investigation of excited states) and MP2 levels, using the 6-311++G(d,p) basis set. PMID:25144919

  17. Synthesis, molecular structure, spectroscopic and theoretical studies on E-2-ethoxy-4-[(4-ethoxyphenylimino)methyl]phenol

    NASA Astrophysics Data System (ADS)

    Zeyrek, Celal Tuğrul; Alpaslan, Gökhan; Alyar, Hamit; Yıldız, Mustafa; Dilek, Nefise; Ünver, Hüseyin

    2015-05-01

    Synthesis, crystallographic characterization, spectroscopic (FT-IR) and density functional modelling studies of a new Schiff base E-2-ethoxy-4-[(4-ethoxyphenylimino)methyl]phenol C17H19NO3 have been reported. The molecular structure obtained from X-ray single-crystal analysis of the investigated compound in the ground state has been compared using Hartree-Fock (HF) and density functional theory (DFT), B3LYP and B1B95 functional with the 6-311++G(d,p) basis set. In addition to the optimized geometrical structures, atomic charges, molecular electrostatic potential (MEP), natural bond orbital (NBO), nonlinear optical (NLO) effects and thermodynamic properties of the compound have been investigated by using DFT calculations. The electronic properties of the title compound in solvent media were also examined using the DFT calculations. The potential energy surface (PES) scans about important torsion angles are performed by using B3LYP/6-311++G (d,p) level of theoretical approximation for the compound. The experimental (FT-IR) and calculated vibrational frequencies (using DFT calculations) of the title compound have been compared. The predicted NLO properties of the compound which calculated by the B3LYP method with 6-31G(d), 6-31+G(d,p), 6-31++G(d,p), 6-311+G(d) and 6-311++G(d,p) basis sets are greater than ones urea. The standard thermodynamic functions were obtained for the title compound with the temperature ranging from 200 to 450 K.

  18. Determining complex crystal structures from high pressure single-crystal diffraction data collected on synchrotron sources

    NASA Astrophysics Data System (ADS)

    McMahon, M. I.; Loa, I.; Stinton, G. W.; Lundegaard, L. F.

    2013-08-01

    As part of a Long Term Project, single-crystal diffraction techniques have been developed for use at the high pressure beamlines ID09 and ID27 at the European Synchrotron Radiation Facility, and have been utilised to determine the crystal structures of various high pressure phases, including those with incommensurate structures, at both high and low temperatures. The same techniques have also been used to determine the structures of high pressure phases at the SRS, Diamond and Petra-III synchrotron sources. In this paper, we describe technical details of the methods developed, and describe some of the considerations necessary for planning experiments and collecting and processing the data. We then illustrate the quality of data that can be obtained, and the complexity of the structures that can be refined, using recent results obtained from complex high pressure phases of N2 and Ba.

  19. Crystallization of interleukin-18 for structure-based inhibitor design

    PubMed Central

    Krumm, Brian; Meng, Xiangzhi; Xiang, Yan; Deng, Junpeng

    2015-01-01

    Interleukin-18 (IL-18) is a pleiotropic pro-inflammatory cytokine belonging to the IL-1 superfamily. IL-18 plays an important role in host innate and acquired immune defense, with its activity being modulated in vivo by its naturally occurring antagonist IL-18 binding protein (IL-18BP). Recent crystal structures of human IL-18 (hIL-18) in complex with its antagonist or cognate receptor(s) have revealed a conserved binding interface on hIL-18 representing a promising drug target. An important step in this process is obtaining crystals of apo hIL-18 or hIL-18 in complex with small-molecule inhibitors, preferably under low ionic strength conditions. In this study, surface-entropy reduction (SER) and rational protein design were employed to facilitate the crystallization of hIL-18. The results provide an excellent platform for structure-based drug design. PMID:26057800

  20. Preparation, structural, and calorimetric characterization of bicomponent metallic photonic crystals

    NASA Astrophysics Data System (ADS)

    Kozlov, M. E.; Murthy, N. S.; Udod, I.; Khayrullin, I. I.; Baughman, R. H.; Zakhidov, A. A.

    2007-03-01

    We report preparation and characterization of novel bicomponent metal-based photonic crystals having submicron three-dimensional (3D) periodicity. Fabricated photonic crystals include SiO2 sphere lattices infiltrated interstitially with metals, carbon inverse lattices filled with metal or metal alloy spheres, Sb inverse lattices, and Sb inverse lattices filled with Bi spheres. Starting from a face centered SiO2 lattice template, these materials were obtained by sequences of either templating and template extraction or templating, template extraction, and retemplating. Surprising high fidelity was obtained for all templating and template extraction steps. Scanning electron microscopy (SEM), small angle X-ray scattering (SAXS) and differential scanning calorimetry (DSC) were used to characterize the structure and the effects of the structure on calorimetric properties. To the best of our knowledge, SAXS data on metallic photonic crystals were collected for first time.

  1. From molecular fragments to crystals: a UV Raman spectroscopic study on the mechanism of Fe-ZSM-5 synthesis.

    PubMed

    Fan, Fengtao; Sun, Keju; Feng, Zhaochi; Xia, Haian; Han, Bo; Lian, Yuxiang; Ying, Pinliang; Li, Can

    2009-01-01

    The nucleation process of iron-exchanged zeolite Fe-ZSM-5, from the assembly of distorted tetrahedrally coordinated iron species and silicate rings in the precursor to the final Fe-ZSM-5 crystals, as well as variations in the coordination environment of iron, were studied by UV resonance Raman spectroscopy and complementary techniques.The entire sequence of crystallization events of Fe-ZSM-5 was monitored by UV Raman spectroscopy in combination with HRTEM, UV/Vis spectroscopy, X-ray diffraction patterns, and periodic DFT calculations. Fe-ZSM-5 was synthesized by an organic-free method to avoid signal interference from the organic template in Raman spectra. Framework iron atoms with resonance Raman bands at 516, 1115, and 1165 cm(-1), and a Raman band at 1016 cm(-1) are detected for Fe-ZSM-5. In the early stage of Fe-ZSM-5 synthesis, the precursor contains iron atoms in distorted tetrahedral coordination and five- and six-membered silicate rings. Nucleation by aggregation of the precursor species was monitored by UV Raman spectroscopy based on the resonance Raman effect, and confirmed by periodic DFT calculations. Evolution of iron species on the surface and in the bulk phase was monitored by UV Raman spectroscopy with excitation at 244 and 325 nm, as well as HRTEM. Nucleation takes place first in the core of the amorphous particles, and crystalline nuclei with Fe-ZSM-5 structure are formed in the core by consuming the amorphous shell. Finally the amorphous particles are completely transformed into Fe-ZSM-5 crystals. PMID:19197930

  2. Can antimonide-based nanowires form wurtzite crystal structure?

    NASA Astrophysics Data System (ADS)

    Gorji Ghalamestani, Sepideh; Lehmann, Sebastian; Dick, Kimberly A.

    2016-01-01

    The epitaxial growth of antimonide-based nanowires has become an attractive subject due to their interesting properties required for various applications such as long-wavelength IR detectors. The studies conducted on antimonide-based nanowires indicate that they preferentially crystallize in the zinc blende (ZB) crystal structure rather than wurtzite (WZ), which is common in other III-V nanowire materials. Also, with the addition of small amounts of antimony to arsenide- and phosphide-based nanowires grown under conditions otherwise leading to WZ structure, the crystal structure of the resulting ternary nanowires favors the ZB phase. Therefore, the formation of antimonide-based nanowires with the WZ phase presents fundamental challenges and is yet to be explored, but is particularly interesting for understanding the nanowire crystal phase in general. In this study, we examine the formation of Au-seeded InSb and GaSb nanowires under various growth conditions using metalorganic vapor phase epitaxy. We address the possibility of forming other phases than ZB such as WZ and 4H in binary nanowires and demonstrate the controlled formation of WZ InSb nanowires. We further discuss the fundamental aspects of WZ growth in Au-seeded antimonide-based nanowires.The epitaxial growth of antimonide-based nanowires has become an attractive subject due to their interesting properties required for various applications such as long-wavelength IR detectors. The studies conducted on antimonide-based nanowires indicate that they preferentially crystallize in the zinc blende (ZB) crystal structure rather than wurtzite (WZ), which is common in other III-V nanowire materials. Also, with the addition of small amounts of antimony to arsenide- and phosphide-based nanowires grown under conditions otherwise leading to WZ structure, the crystal structure of the resulting ternary nanowires favors the ZB phase. Therefore, the formation of antimonide-based nanowires with the WZ phase presents

  3. Structure and spectroscopic studies of 2,3-diethoxycarbonyl-1-methylpyridinium nitrate

    NASA Astrophysics Data System (ADS)

    Barczyński, P.; Ratajczak-Sitarz, M.; Nowaczyk, Ł.; Katrusiak, A.; Dega-Szafran, Z.; Szafran, M.

    2013-03-01

    The structure of 2,3-diethoxycarbonyl-1-methylpyridinium nitrate (1) has been studied by X-ray diffraction, DFT calculations, FTIR, Raman and NMR spectra. The crystals are monoclinic, space group C2/c. Nitrate anion interacts electrostatically with the positively charged pyridinium nitrogen atom. In crystals the ethyl ester group at C(3) position (C(9)sbnd O(4)sbnd CH2sbnd CH3) is disordered in two orientations. The structures optimized by the B3LYP/6-311++G(d, p) 2 (in vacuum) and 3 (in CHCl3 solution) are similar to that in crystal 1. Linear correlations between the experimental 13C and 1H chemical shifts (δexp) of the investigated ester in CDCl3 and GIAO/B3LYP/6-311++G(d, p) magnetic isotropic shielding constants calculated by using the screening solvation model (COSMO), δexp = a + b · σcalc, are reported. The FTIR and Raman spectra of the solid compound are consistent with the X-ray structure.

  4. The Electronic Structure of Some Cyanohydrins-A Spectroscopically Under-Investigated Family of Compounds.

    PubMed

    Chrostowska, Anna; Darrigan, Clovis; Dargelos, Alain; Benidar, Abdessamad; Guillemin, Jean-Claude

    2015-12-01

    Cyanohydrins are usually formed by addition of hydrogen cyanide to aldehydes or ketones while the elimination of HCN from cyanohydrins is easily observed upon heating. The low thermal stability of these highly boiling compounds leads to difficult studies in the gas phase where partial or complete decomposition is usually observed. Consequently, the reported physicochemical properties of such compounds in the gas phase are still scarce. Keeping with this, four simple cyanohydrins, the glycolonitrile and methyl, vinyl and ethynyl derivatives, have been selected. These are possible candidates for the Interstellar Medium, where the corresponding aldehydes and HCN have been detected, and could have played an important role in prebiotic chemistry, as already proposed for some of them. Three well-suited spectroscopic techniques, namely, UV photoelectron, infrared, and Raman spectroscopies, in tandem with quantum calculations, have been chosen for the structure analysis. Photoelectron spectroscopy, successfully performed with gaseous compounds, provides the first comparative study on cyanohydrins in the gas phase. PMID:26361377

  5. Characterization of multilayer GaAs/AlGaAs transistor structures by variable angle spectroscopic ellipsometry

    NASA Technical Reports Server (NTRS)

    Merkel, Kenneth G.; Snyder, Paul G.; Woollam, John A.; Alterovitz, Samuel; Rai, A. K.

    1989-01-01

    Variable angle of incidence spectroscopic ellipsometry (VASE) has been implemented as a means of determining layer thickness, alloy composition, and growth quality of GaAs/AlGaAs samples composed of relatively thick layers as well as superlattices. The structures studied in this work contained GaAs/AlGaAs multilayers with a superlattice 'barrier' and were grown for later formation of modulation-doped field effect transistors (MODFETs). Sample modeling was performed by treating the superlattice as a bulk AlGaAs layer of unknown composition. Extremely good data fits were realized when five layer thicknesses and two alloy ratios were allowed to vary in a regression analysis. Room temperature excitonic effects associated with the e-hh(1), e-lh(1) and e-hh(2) transitions were observed in the VASE data.

  6. Gold nanoparticles assisted structural and spectroscopic modification in Er3+-doped zinc sodium tellurite glass

    NASA Astrophysics Data System (ADS)

    Awang, Asmahani; Ghoshal, S. K.; Sahar, M. R.; Arifin, R.

    2015-04-01

    Achieving enhanced spectroscopic properties of rare earth doped inorganic glasses by embedding metallic nanoparticles of controlled sizes is a challenging task. We report the gold (Au) NPs assisted modifications in structural and spectroscopic properties of melt-quench synthesized Er3+ doped zinc sodium tellurite glass. The growth of NPs is stimulated via time varying heat treatment at 300 °C. XRD patterns confirm the amorphous nature of glasses and TEM images manifest the growth of gold NPs with sizes between 6.1 and 10.7 nm. The heat treatment time dependent variations in physical properties are ascribed to the alteration in bonding of non-bridging oxygen ions. The UV-VIS-NIR spectra reveal six absorption peaks centered at 488, 523, 655, 800, 973 and 1533 nm corresponding to the transition from ground state of 4I15/2 to 4F7/2, 2H11/2, 4F9/2, 4I9/2,4I11/2, and 4I13/2 excited states of Er3+ ions, respectively. Surface plasmon resonance (SPR) bands are observed in the range of 618-632 nm. Judd-Ofelt analyses demonstrate a significant increase of spectroscopic quality factors (0.86-1.05) and branching ratio (0.62-92.38%). The up-conversion emission spectra of Er3+ exhibit three prominent peaks of reasonable green (502 nm), a moderate green (546 nm) and a strong red (629 nm). An enhancement in the red band luminescence intensity by a factor of 8.19 and 8.54 times are achieved for 2 and 4 h of heat treatments, respectively. This enhancement is attributed to the SPR effects of gold NPs producing an intense local field in the proximity of Er3+ ions and subsequent energy transfer between RE ions and NPs. The FTIR spectra display the presence of vibrational modes for ZnO4 bonds, Te-O bond in TeO3 (tp) and TeO4 (tbp) units and the hydroxyl groups. Excellent features of the results suggest that our method constitute a basis for tunable growth of gold NPs which is exceedingly useful for the optimization of optical and structural properties.

  7. A unified picture of the crystal structures of metals

    NASA Astrophysics Data System (ADS)

    Söderlind, Per; Eriksson, Olle; Johansson, Börje; Wills, J. M.; Boring, A. M.

    1995-04-01

    THE crystal structures of the light actinides have intrigued physicists and chemists for several decades1. Simple metals and transition metals have close-packed, high-symmetry structures, such as body-centred cubic, face-centred cubic and hexagonal close packing. In contrast, the structures of the light actinides are very loosely packed and of low symmetry-tetragonal, orthorhombic and monoclinic. To understand these differences, we have performed total-energy calculations, as a function of volume, for both high-and low-symmetry structures of a simple metal (aluminium), a non-magnetic transition metal (niobium), a ferromagnetic transition metal (iron) and a light actinide (uranium). We find that the crystal structure of all of these metals is determined by the balance between electrostatic (Madelung) interactions, which favour high symmetry, and a Peierls distortion of the crystal lattice, which favours low symmetry. We show that simple metals and transition metals can adopt low-symmetry structures on expansion of the lattice; and we predict that, conversely, the light actinides will undergo transitions to structures of higher symmetry on compression.

  8. Structural and optical properties of a new chalcone single crystal

    NASA Astrophysics Data System (ADS)

    Rajesh Kumar, P. C.; Ravindrachary, V.; Janardhana, K.; Poojary, Boja

    2012-09-01

    A new nonlinear optical material 1-(4-methylthiophenyl)-3-(4-methoxyphenyl)prop-2-en-1-one with molecular formula C17H16O2S was synthesized by using the Claisen-Schmidt condensation reaction method. The Various functional groups present in the compound were identified using recorded FT-IR spectrum. The crystal growth parameters have been studied using solubility test and acetone is found to be a very good solvent for the crystal growth at an ambient temperature. The transparent high quality single crystals up to a size of 26×2×2 mm3 were grown using the slow evaporation solution growth technique. UV-visible study was carried out and the spectrum reveals that the crystal is transparent in the entire visible region and absorptive in the UV region. The refractive index is determined using Brewster's angle method. The optical energy band gap of the material is measured using Tauc's plot and the direct method. The single crystal XRD of MMPP crystal shows the following cell parameters: a=5.9626(2) Å, b=15.3022(6) Å, c=16.0385(7) Å, α=β=γ=90°, volume=1463.37(10) Å3 with a space group of Pna21. The compound MMPP exhibits optical nonlinearity (NLO) and its second order NLO efficiency is 3.15 times to that of urea. The effect of functional groups OCH3 and SCH3 on the non-linearity as well as the structural property of the compound has been discussed. The crystal is thermally stable. High NLO efficiency, good thermal stability, good transparency and ability to grow as a high quality single crystal make this material very attractive for opto-electronic applications.

  9. Crystal structures of fusion proteins with large-affinity tags.

    PubMed

    Smyth, Douglas R; Mrozkiewicz, Marek K; McGrath, William J; Listwan, Pawel; Kobe, Bostjan

    2003-07-01

    The fusion of a protein of interest to a large-affinity tag, such as the maltose-binding protein (MBP), thioredoxin (TRX), or glutathione-S-transferase (GST), can be advantageous in terms of increased expression, enhanced solubility, protection from proteolysis, improved folding, and protein purification via affinity chromatography. Unfortunately, crystal growth is hindered by the conformational heterogeneity induced by the fusion tag, requiring that the tag is removed by a potentially problematic cleavage step. The first three crystal structures of fusion proteins with large-affinity tags have been reported recently. All three structures used a novel strategy to rigidly fuse the protein of interest to MBP via a short three- to five-amino acid spacer. This strategy has the potential to aid structure determination of proteins that present particular experimental challenges and are not conducive to more conventional crystallization strategies (e.g., membrane proteins). Structural genomics initiatives may also benefit from this approach as a way to crystallize problematic proteins of significant interest. PMID:12824478

  10. Redetermination of the crystal structure of NbF4.

    PubMed

    Bandemehr, Jascha; Conrad, Matthias; Kraus, Florian

    2016-08-01

    Single crystals of NbF4, niobium(IV) tetra-fluoride, were synthesized by disproportionation of Nb2F5 at 1273 K in a sealed niobium tube, extracted and studied by single-crystal X-ray diffraction. Previous reports on the crystal structure of NbF4 were based on X-ray powder diffraction data and the observed isotypicity to SnF4 [Gortsema & Didchenko (1965 ▸). Inorg. Chem. 4, 182-186; Schäfer et al. (1965 ▸). J. Less Common Met. 9, 95-104]. The data obtained from a single-crystal X-ray diffraction study meant the atomic coordinates could now be refined as well as their anisotropic displacement parameters, leading to a significant improvement of the structural model of NbF4. In the structure, the Nb atom is octahedron-like surrounded by six F atoms of which four are bridging to other NbF6 octa-hedra, leading to a layer structure extending parallel to the ab plane. PMID:27536416

  11. Redetermination of the crystal structure of NbF4

    PubMed Central

    Bandemehr, Jascha; Conrad, Matthias; Kraus, Florian

    2016-01-01

    Single crystals of NbF4, niobium(IV) tetra­fluoride, were synthesized by disproportionation of Nb2F5 at 1273 K in a sealed niobium tube, extracted and studied by single-crystal X-ray diffraction. Previous reports on the crystal structure of NbF4 were based on X-ray powder diffraction data and the observed isotypicity to SnF4 [Gortsema & Didchenko (1965 ▸). Inorg. Chem. 4, 182–186; Schäfer et al. (1965 ▸). J. Less Common Met. 9, 95–104]. The data obtained from a single-crystal X-ray diffraction study meant the atomic coordinates could now be refined as well as their anisotropic displacement parameters, leading to a significant improvement of the structural model of NbF4. In the structure, the Nb atom is octahedron-like surrounded by six F atoms of which four are bridging to other NbF6 octa­hedra, leading to a layer structure extending parallel to the ab plane. PMID:27536416

  12. Unusual Features of Crystal Structures of Some Simple Copper Compounds

    ERIC Educational Resources Information Center

    Douglas, Bodie

    2009-01-01

    Some simple copper compounds have unusual crystal structures. Cu[subscript 3]N is cubic with N atoms at centers of octahedra formed by 6 Cu atoms. Cu[subscript 2]O (cuprite) is also cubic; O atoms are in tetrahedra formed by 4 Cu atoms. These tetrahedra are linked by sharing vertices forming two independent networks without linkages between them.…

  13. Materials research at Stanford University. [composite materials, crystal structure, acoustics

    NASA Technical Reports Server (NTRS)

    1975-01-01

    Research activity related to the science of materials is described. The following areas are included: elastic and thermal properties of composite materials, acoustic waves and devices, amorphous materials, crystal structure, synthesis of metal-metal bonds, interactions of solids with solutions, electrochemistry, fatigue damage, superconductivity and molecular physics and phase transition kinetics.

  14. The diammoniate of diborane: Crystal structure and hydrogen release

    SciTech Connect

    Bowden, Mark E.; Heldebrant, David J.; Karkamkar, Abhijeet J.; Proffen, Thomas E.; Schenter, Gregory K.; Autrey, Thomas

    2010-10-12

    [(NH3)2BH2]+[BH4]- is formed from the room temperature decomposition of NH4+BH4-, via a NH3BH3 intermediate. Its crystal structure has been determined and contains disordered BH4- ions in 2 distinct sites. Hydrogen release is similar to that from NH3BH3 but with faster kinetics.

  15. Co-crystal formation based on structural matching.

    PubMed

    Zhou, Liping; Dodd, Stephanie; Capacci-Daniel, Christina; Garad, Sudhakar; Panicucci, Riccardo; Sethuraman, Vijay

    2016-06-10

    A co-crystal is defined as a single crystalline structure composed of two or more components with no proton transfer which are solid at room temperature. Our group has come up with the following rationale selection of co-formers for initial co-crystal screening: 1) selection of co-formers with the highest potential for hydrogen bonding with the API and 2) selection of co-formers with diversity of secondary structural characteristics. We demonstrate the feasibility of this technique with a Novartis drug candidate A. In the first tier, 20 co-formers were screened and two hits were identified. By examining the two co-formers, which worked from the first round, a second round of screening was undertaken with more focused chemical matter. Nineteen co-crystal formers closely related to the two hits in the first screen were screened in the second tier. From this screen five hits were identified. All the hits were compared for their physical and chemical stability and dissolution profile. Based on the comparison 4-aminobenzoic co-crystal was chosen for in-vivo comparison with the free form. The co-crystal had 12 times higher exposure than the free form thus overcoming the solubility limited exposure. PMID:26948852

  16. Analysis of voids in crystal structures: the methods of 'dual' crystal chemistry.

    PubMed

    Blatov, V A; Shevchenko, A P

    2003-01-01

    The theoretical basics of the analysis of voids in crystal structures by means of Voronoi-Dirichlet polyhedra (VDP) and of the graph theory are stated. Topological relations are considered between VDPs and atomic domains in a crystal field. These relations allow the separation of two non-intersecting topological subspaces in a crystal structure, whose connectednesses are defined by two finite 'reduced' graphs. The first, 'direct', subspace includes the atoms (VDP centres) and the network of interatomic bonds (VDP faces), the second, 'dual', one comprises the void centres (VDP vertices) and the system of channels (VDP edges) between them. Computer methods of geometrical-topological analysis of the 'dual' subspace are developed and implemented within the program package TOPOS. They are designed for automatically restoring the system of channels, visualizing and sizing voids and void conglomerates, dimensional analysis of continuous void systems, and comparative topological analysis of 'dual' subspaces for various substances. The methods of analysis of 'dual' and 'direct' subspaces are noted to differ from each other only in some details that allows the term 'dual' crystal chemistry to be introduced. The efficiency of the methods is shown with the analysis of compounds of different chemical nature: simple substances, ionic structures, superionic conductors, zeolites, clathrates, organic supramolecular complexes. PMID:12496460

  17. Crystal growth, structure analysis and characterisation of 2 - (1, 3 - dioxoisoindolin - 2 - yl) acetic acid single crystal

    SciTech Connect

    Sankari, R. Siva; Perumal, Rajesh Narayana

    2014-04-24

    Single crystal of dielectric material 2 - (1, 3 - dioxoisoindolin - 2 - yl) acetic acid has been grown by slow evaporation solution growth method. The grown crystal was harvested in 25 days. The crystal structure was analyzed by Single crystal X - ray diffraction. UV-vis-NIR analysis was performed to examine the optical property of the grown crystal. The thermal property of the grown crystal was studied by thermogravimetric analysis (TGA) and differential thermal analysis (DTA). The dielectric measurements were carried out and the dielectric constant was calculated and plotted at all frequencies.

  18. Crystal structure of SiB/sub 6/

    SciTech Connect

    Vlasse, M.; Slack, G.A.; Garbauskas, M.; Kasper, J.S.; Viala, J.C.

    1986-06-01

    The accurate and detailed structure of the compound SiB/sub 6/ has been determined by single-crystal X-ray diffraction. The final R value was 6.1% for 4225 reflections. The cell is orthorhombic with space group Pnnm and a = 14.397(7) A, b = 18.318(9) A, c = 9.911(7) A, and from the electron density appears to contain 43 silicon atoms and 238 boron atoms. The structure contains many features found in other structures of boron-rich phases, and obeys the crystal chemistry rules established for them. It contains interconnected icosahedra, icosihexahedra, as well as several isolated boron and silicon atoms. An unusual feature of this structure is the presence of icosihexahedra containing silicon atoms similar to those found previously in BeB/sub 3/.

  19. Domain Structures in Nematic Liquid Crystals on a Polycarbonate Surface

    PubMed Central

    Parshin, Alexander M.; Gunyakov, Vladimir A.; Zyryanov, Victor Y.; Shabanov, Vasily F.

    2013-01-01

    Alignment of nematic liquid crystals on polycarbonate films obtained with the use of solvents with different solvations is studied. Domain structures occurring during the growth on the polymer surface against the background of the initial thread-like or schlieren texture are demonstrated. It is established by optical methods that the domains are stable formations visualizing the polymer surface structures. In nematic droplets, the temperature-induced transition from the domain structure with two extinction bands to the structure with four bands is observed. This transition is shown to be caused by reorientation of the nematic director in the liquid crystal volume from the planar alignment to the homeotropic state with the pronounced radial configuration of nematic molecules on the surface. The observed textures are compared with different combinations of the volume LC orientations and the radial distribution of the director field and the disclination lines at the polycarbonate surface. PMID:23965955

  20. Domain structures in nematic liquid crystals on a polycarbonate surface.

    PubMed

    Parshin, Alexander M; Gunyakov, Vladimir A; Zyryanov, Victor Y; Shabanov, Vasily F

    2013-01-01

    Alignment of nematic liquid crystals on polycarbonate films obtained with the use of solvents with different solvations is studied. Domain structures occurring during the growth on the polymer surface against the background of the initial thread-like or schlieren texture are demonstrated. It is established by optical methods that the domains are stable formations visualizing the polymer surface structures. In nematic droplets, the temperature-induced transition from the domain structure with two extinction bands to the structure with four bands is observed. This transition is shown to be caused by reorientation of the nematic director in the liquid crystal volume from the planar alignment to the homeotropic state with the pronounced radial configuration of nematic molecules on the surface. The observed textures are compared with different combinations of the volume LC orientations and the radial distribution of the director field and the disclination lines at the polycarbonate surface. PMID:23965955

  1. Crystal Structure of the Bacillus subtilis Superoxide Dismutase

    SciTech Connect

    Liu, Ping; Ewis, H.E.; Huang, Y.-J; Lu, C.-D.; Tai, P.C.; Weber, Irene T.

    2008-06-01

    The sodA gene of Bacillus subtilis was expressed in Escherichia coli, purified and crystallized. The crystal structure of MnSOD was solved by molecular replacement with four dimers per asymmetric unit and refined to an R factor of 21.1% at 1.8 {angstrom} resolution. The dimer structure is very similar to that of the related enzyme from B. anthracis. Larger structural differences were observed with the human MnSOD, which has one less helix in the helical domain and a longer loop between two -strands and also showed differences in three amino acids at the intersubunit interface in the dimer compared with the two bacterial MnSODs. These structural differences can be exploited in the design of drugs that selectively target the Bacillus enzymes.

  2. Structural, spectroscopic, and computational studies of [2,2‧-bithiophene]-5-carboxylic acid

    NASA Astrophysics Data System (ADS)

    Einkauf, Jeffrey D.; Mathivathanan, Logesh; de Lill, Daniel T.

    2016-01-01

    The crystal structure of [2,2‧-bithiophene]-5-carboxylic acid was obtained from in-situ decarboxylation of [2,2‧-bithiophene]-5,5‧-dicarboxylic acid during solvothermal treatment. UV-Vis absorption and fluorescence spectroscopies were conducted in solution and solid-state on these two molecules as well as the precursor, 2,2‧-bithiophene. These molecules were modeled using DFT level of theory to explain the observed structural features and spectroscopy.

  3. VO{sub 2} (A): Reinvestigation of crystal structure, phase transition and crystal growth mechanisms

    SciTech Connect

    Rao Popuri, Srinivasa; Artemenko, Alla; Labrugere, Christine; Miclau, Marinela; Villesuzanne, Antoine; Pollet, Michaël

    2014-05-01

    Well crystallized VO{sub 2} (A) microrods were grown via a single step hydrothermal reaction in the presence of V{sub 2}O{sub 5} and oxalic acid. With the advantage of high crystalline samples, we propose P4/ncc as an appropriate space group at room temperature. From morphological studies, we found that the oriented attachment and layer by layer growth mechanisms are responsible for the formation of VO{sub 2} (A) micro rods. The structural and electronic transitions in VO{sub 2} (A) are strongly first order in nature, and a marked difference between the structural transition temperatures and electronic transitions temperature was evidenced. The reversible intra- (LTP-A to HTP-A) and irreversible inter- (HTP-A to VO{sub 2} (M1)) structural phase transformations were studied by in-situ powder X-ray diffraction. Attempts to increase the size of the VO{sub 2} (A) microrods are presented and the possible formation steps for the flower-like morphologies of VO{sub 2} (M1) are described. - Graphical abstract: Using a single step and template free hydrothermal synthesis, well crystallized VO{sub 2} (A) microrods were prepared and the P4/ncc space group was assigned to the room temperature crystal structure. Reversible and irreversible phase transitions among different VO{sub 2} polymorphs were identified and their progressive nature was highlighted. Attempts to increase the microrods size, involving layer by layer formation mechanisms, are presented. - Highlights: • Highly crystallized VO{sub 2} (A) microrods were grown via a single step hydrothermal process. • The P4/ncc space group was determined for VO{sub 2} (A) at room temperature. • The electronic structure and progressive nature of the structural phase transition were investigated. • A weak coupling between structural and electronic phase transitions was identified. • Different crystallite morphologies were discussed in relation with growth mechanisms.

  4. Synthesis, crystal structure, conformational analysis, nonlinear optical property and computational study of novel pregnane derivatives

    NASA Astrophysics Data System (ADS)

    Singh, Ranvijay Pratap; kant, Rajni; Singh, Kuldeep; Sharma, Sonia; Sethi, Arun

    2015-09-01

    The molecular structure and detailed spectroscopic analysis of some novel newly synthesized pregnane derivatives have been performed using experimental techniques like 1H, 13C NMR, NOESY, FT-IR, UV-visible spectroscopy, mass spectrometry, crystallography, as well as theoretical calculations. The structure and stereochemistry of 3β-benzoyloxy 16α-methoxy pregn-5-ene-20-one (3) has been confirmed by single crystal X-ray diffraction, which crystallized in orthorhombic form having P212121 space group with unit cell parameters a = 6.395(5) Å, b = 19.872(17) Å, c = 19.898(16) Å and Z = 4. Quantum chemical calculations have been performed by density functional theory (DFT) using B3LYP functional and 6-31G (d,p) basis set. The electronic properties such as frontier orbitals and band gap energies have been calculated using time dependent density functional theory (TD-DFT). The strength and nature of weak intramolecular interactions have been studied by AIM approach. The vibrational wavenumbers have been calculated using DFT method and assigned with the help of potential energy distribution (PED). Global and local reactivity descriptors have been computed to predict reactivity and reactive sites in the molecule. First hyperpolarizability values have been calculated to describe the nonlinear optical (NLO) property of the synthesized compounds. Molecular electrostatic potential (MEP) analysis has also been carried out.

  5. Minerals from Macedonia XXIII. Spectroscopic and structural characterization of schorl and beryl cyclosilicates.

    PubMed

    Makreski, Petre; Jovanovski, Gligor

    2009-08-01

    IR and Raman spectroscopy study on two collected cyclosilicate species: schorl (from tourmaline group), Na(Fe,Mg)(3)Al(6)(BO(3))(3)Si(6)O(18)(OH,F)(4) and beryl (Be,Mg,Fe)(3)Al(2)Si(6)O(18) were carried out. Although beryl is nominally anhydrous mineral, vibrational results strongly indicate that H(2)O molecules exist in the structural channels. The number of vibrational bands and their frequencies revealed the presence of H(2)O type II, in which C(2) symmetry axis of the water molecule is parallel to the structural channel (and to the c-axis of beryl). On the other hand, it was found that observed bands in the IR and Raman OH stretching region of the other tourmaline varieties appear as a result of the cation combinations involving dominant presence of Mg and Fe cations in the Y structural sites. The strong indication derived from the vibrational spectroscopic results that the studied mineral represents a schorl variety, coincide very well with the results obtained by powder X-ray diffraction and X-ray microprobe analysis. Both minerals show IR spectral similarities in the region below 1500 cm(-1), whereas the resemblance between the Raman spectra (1500-100 cm(-1)) is less expressed confirming that these spectra are more sensitive to compositional changes and to structural disorder. The identification of both minerals was additionally supported by studying the powder X-ray diffraction diagrams. PMID:18722809

  6. Reconstruction of explicit structural properties at the nanoscale via spectroscopic microscopy

    NASA Astrophysics Data System (ADS)

    Cherkezyan, Lusik; Zhang, Di; Subramanian, Hariharan; Taflove, Allen; Backman, Vadim

    2016-02-01

    The spectrum registered by a reflected-light bright-field spectroscopic microscope (SM) can quantify the microscopically indiscernible, deeply subdiffractional length scales within samples such as biological cells and tissues. Nevertheless, quantification of biological specimens via any optical measures most often reveals ambiguous information about the specific structural properties within the studied samples. Thus, optical quantification remains nonintuitive to users from the diverse fields of technique application. In this work, we demonstrate that the SM signal can be analyzed to reconstruct explicit physical measures of internal structure within label-free, weakly scattering samples: characteristic length scale and the amplitude of spatial refractive-index (RI) fluctuations. We present and validate the reconstruction algorithm via finite-difference time-domain solutions of Maxwell's equations on an example of exponential spatial correlation of RI. We apply the validated algorithm to experimentally measure structural properties within isolated cells from two genetic variants of HT29 colon cancer cell line as well as within a prostate tissue biopsy section. The presented methodology can lead to the development of novel biophotonics techniques that create two-dimensional maps of explicit structural properties within biomaterials: the characteristic size of macromolecular complexes and the variance of local mass density.

  7. Reconstruction of explicit structural properties at the nanoscale via spectroscopic microscopy.

    PubMed

    Cherkezyan, Lusik; Zhang, Di; Subramanian, Hariharan; Taflove, Allen; Backman, Vadim

    2016-02-01

    The spectrum registered by a reflected-light bright-field spectroscopic microscope (SM) can quantify the microscopically indiscernible, deeply subdiffractional length scales within samples such as biological cells and tissues. Nevertheless, quantification of biological specimens via any optical measures most often reveals ambiguous information about the specific structural properties within the studied samples. Thus, optical quantification remains nonintuitive to users from the diverse fields of technique application. In this work, we demonstrate that the SM signal can be analyzed to reconstruct explicit physical measures of internal structure within label-free, weakly scattering samples: characteristic length scale and the amplitude of spatial refractive-index (RI) fluctuations. We present and validate the reconstruction algorithm via finite-difference time-domain solutions of Maxwell's equations on an example of exponential spatial correlation of RI. We apply the validated algorithm to experimentally measure structural properties within isolated cells from two genetic variants of HT29 colon cancer cell line as well as within a prostate tissue biopsy section. The presented methodology can lead to the development of novel biophotonics techniques that create two-dimensional maps of explicit structural properties within biomaterials: the characteristic size of macromolecular complexes and the variance of local mass density. PMID:26886803

  8. Structural studies of E. coli ribosomes by spectroscopic techniques: A specialized review

    NASA Astrophysics Data System (ADS)

    Bonicontro, Adalberto; Risuleo, Gianfranco

    2005-12-01

    We present a review on our interdisciplinary line of research based on strategies of molecular biology and biophysics. These have been applied to the study of the prokaryotic ribosome of the bacterium Escherichia coli. Our investigations on this organelle have continued for more than a decade and we have adopted different spectroscopic biophysical techniques such as: dielectric and fluorescence spectroscopy as well as light scattering (photon correlation spectroscopy). Here we report studies on the whole 70S ribosomes and on the separated subunits 30S and 50S. Our results evidence intrinsic structural features of the subunits: the small shows a more "floppy" structure, while the large one appears to be more rigid. Also, an inner "kernel" formed by the RNA/protein association is found within the ribosome. This kernel is surrounded by a ribonucleoprotein complex more exposed to the solvent. Initial analyses were done on the so called Kaldtschmit-Wittmann ribosome: more recently we have extended the studies to the "tight couple" ribosome known for its better functional performance in vitro. Data evidence a phenomenological correlation between the differential biological activity and the intrinsic structural properties of the two-ribosome species. Finally, investigations were also conducted on particles treated at sub-denaturing temperatures and on ribosomes partially deproteinized by salt treatment (ribosomal cores). Results suggest that the thermal treatment and the selective removal of proteins cause analogous structural alterations.

  9. Single Crystal Structure Determination of Alumina to 1 Mbar

    NASA Astrophysics Data System (ADS)

    Dong, H.; Zhang, L.; Prakapenka, V.; Mao, H.

    2014-12-01

    Aluminum oxide (Al2O3) is an important ceramic material and a major oxide in the earth. Additionally, alumina is a widely used pressure standard in static high-pressure experiments (Cr3+-bearing corundum, ruby). The changes of its crystal structure with pressure (P) and temperature (T) are important for its applications and understanding its physical properties in the deep Earth. There have been numerous reports on the high P-T polymorphs of alumina. Previous theoretical calculations and experiments suggest that the crystal structure of Al2O3 evolves greatly at high P-T. In this study, we used the newly developed multigrain crystallography method combined with single-crystal x-ray diffraction analysis technique for the structure determination of alumina at high P-T to provide single-crystal structure refinement for high-pressure phases of Al2O3. Alumina powder was mixed with ~10% Pt and Ne was used as both pressure transmitting media and thermal insulating layers during laser-heating. Coarse-grained aggregates of Al2O3 were synthesized in a laser-heated diamond anvil cell. The structure change of Al2O3 was monitored by in situ x-ray diffraction at ~1 Mbar and 2700 K. The results allow us to distinguish the structural differences between the Rh2O3 (II) structure (space group Pbcn) and perovskite structure (space group Pbnm) for the first high-pressure phase of Al2O3. More detailed results will be discussed in the later work.

  10. Crystal structure of new AsS2 compound

    NASA Astrophysics Data System (ADS)

    Bolotina, N. B.; Brazhkin, V. V.; Dyuzheva, T. I.; Lityagina, L. M.; Kulikova, L. F.; Nikolaev, N. A.; Verin, I. A.

    2013-01-01

    AsS2 single crystals have been obtained for the first time from an As2S3 melt at pressures above 6 GPa and temperatures above 800 K in the As2S3 → AsS + AsS2 reaction. The monoclinic structure of the new high-pressure phase is solved by X-ray diffraction analysis and compared to the structure of high-pressure AsS phase, which was studied previously.

  11. Tailor-made force fields for crystal-structure prediction.

    PubMed

    Neumann, Marcus A

    2008-08-14

    A general procedure is presented to derive a complete set of force-field parameters for flexible molecules in the crystalline state on a case-by-case basis. The force-field parameters are fitted to the electrostatic potential as well as to accurate energies and forces generated by means of a hybrid method that combines solid-state density functional theory (DFT) calculations with an empirical van der Waals correction. All DFT calculations are carried out with the VASP program. The mathematical structure of the force field, the generation of reference data, the choice of the figure of merit, the optimization algorithm, and the parameter-refinement strategy are discussed in detail. The approach is applied to cyclohexane-1,4-dione, a small flexible ring. The tailor-made force field obtained for cyclohexane-1,4-dione is used to search for low-energy crystal packings in all 230 space groups with one molecule per asymmetric unit, and the most stable crystal structures are reoptimized in a second step with the hybrid method. The experimental crystal structure is found as the most stable predicted crystal structure both with the tailor-made force field and the hybrid method. The same methodology has also been applied successfully to the four compounds of the fourth CCDC blind test on crystal-structure prediction. For the five aforementioned compounds, the root-mean-square deviations between lattice energies calculated with the tailor-made force fields and the hybrid method range from 0.024 to 0.053 kcal/mol per atom around an average value of 0.034 kcal/mol per atom. PMID:18642947

  12. Structural evolution in the crystallization of rapid cooling silver melt

    SciTech Connect

    Tian, Z.A.; Dong, K.J.; Yu, A.B.

    2015-03-15

    The structural evolution in a rapid cooling process of silver melt has been investigated at different scales by adopting several analysis methods. The results testify Ostwald’s rule of stages and Frank conjecture upon icosahedron with many specific details. In particular, the cluster-scale analysis by a recent developed method called LSCA (the Largest Standard Cluster Analysis) clarified the complex structural evolution occurred in crystallization: different kinds of local clusters (such as ico-like (ico is the abbreviation of icosahedron), ico-bcc like (bcc, body-centred cubic), bcc, bcc-like structures) in turn have their maximal numbers as temperature decreases. And in a rather wide temperature range the icosahedral short-range order (ISRO) demonstrates a saturated stage (where the amount of ico-like structures keeps stable) that breeds metastable bcc clusters. As the precursor of crystallization, after reaching the maximal number bcc clusters finally decrease, resulting in the final solid being a mixture mainly composed of fcc/hcp (face-centred cubic and hexagonal-closed packed) clusters and to a less degree, bcc clusters. This detailed geometric picture for crystallization of liquid metal is believed to be useful to improve the fundamental understanding of liquid–solid phase transition. - Highlights: • A comprehensive structural analysis is conducted focusing on crystallization. • The involved atoms in our analysis are more than 90% for all samples concerned. • A series of distinct intermediate states are found in crystallization of silver melt. • A novelty icosahedron-saturated state breeds the metastable bcc state.

  13. Intermediate structures in radiation damaged titanite (CaTiSiO5): a Raman spectroscopic study.

    PubMed

    Zhang, Ming; Salje, Ekhard K H; Redfern, Simon A T; Bismayer, Ulrich; Groat, Lee A

    2013-03-20

    Effects of radiation damage and thermal annealing on the crystal structure of natural titanite (CaTiSiO(5)) were studied using Raman spectroscopy. The results show that well crystallized natural titanites generally have the P2(1)/a structure at the unit cell level, in contrast to the A2/a symmetry reported previously. Radiation caused by naturally incorporated impurities (such as U and Th) leads to structural damage and amorphization in titanite, as evidenced by a significant loss of band intensity, spectral broadening and frequency shifts. Additional bands (e.g. near 574 and 650 cm(-1)) occur in weakly or partially metamict titanite due to the formation of an intermediate phase (with the A2/a symmetry). Raman spectra of titanite thermal glasses showed features different from those of metamict titanite, especially in the Ti-O and Si-O stretching regions. The effect of thermal annealing is strongly affected by the initial degrees of damage that the sample experienced. Weakly damaged titanite samples showed that annealing leads to a structural recovery, and the spectral patterns of these recovered crystals are consistent with the P2(1)/a symmetry. Highly damaged titanite starts to recrystallize into an A2/a phase near 700-800 K, and additional structural modification occurs when annealed at 1300-1400 K, which involves significant change in broad Ti-O features. However, in terms of bandwidths, the metamict samples are far from fully recovered even on being annealed at 1300-1400 K. PMID:23407062

  14. Crystal Structure of Triosephosphate Isomerase from Trypanosoma cruzi in Hexane

    NASA Astrophysics Data System (ADS)

    Gao, Xiu-Gong; Maldonado, Ernesto; Perez-Montfort, Ruy; Garza-Ramos, Georgina; Tuena de Gomez-Puyou, Marietta; Gomez-Puyou, Armando; Rodriguez-Romero, Adela

    1999-08-01

    To gain insight into the mechanisms of enzyme catalysis in organic solvents, the x-ray structure of some monomeric enzymes in organic solvents was determined. However, it remained to be explored whether the structure of oligomeric proteins is also amenable to such analysis. The field acquired new perspectives when it was proposed that the x-ray structure of enzymes in nonaqueous media could reveal binding sites for organic solvents that in principle could represent the starting point for drug design. Here, a crystal of the dimeric enzyme triosephosphate isomerase from the pathogenic parasite Trypanosoma cruzi was soaked and diffracted in hexane and its structure solved at 2- angstrom resolution. Its overall structure and the dimer interface were not altered by hexane. However, there were differences in the orientation of the side chains of several amino acids, including that of the catalytic Glu-168 in one of the monomers. No hexane molecules were detected in the active site or in the dimer interface. However, three hexane molecules were identified on the surface of the protein at sites, which in the native crystal did not have water molecules. The number of water molecules in the hexane structure was higher than in the native crystal. Two hexanes localized at <4 angstrom from residues that form the dimer interface; they were in close proximity to a site that has been considered a potential target for drug design.

  15. On calculating the equilibrium structure of molecular crystals.

    SciTech Connect

    Mattsson, Ann Elisabet; Wixom, Ryan R.; Mattsson, Thomas Kjell Rene

    2010-03-01

    The difficulty of calculating the ambient properties of molecular crystals, such as the explosive PETN, has long hampered much needed computational investigations of these materials. One reason for the shortcomings is that the exchange-correlation functionals available for Density Functional Theory (DFT) based calculations do not correctly describe the weak intermolecular van der Waals' forces present in molecular crystals. However, this weak interaction also poses other challenges for the computational schemes used. We will discuss these issues in the context of calculations of lattice constants and structure of PETN with a number of different functionals, and also discuss if these limitations can be circumvented for studies at non-ambient conditions.

  16. Structural, magnetic and optical properties of two concomitant molecular crystals

    NASA Astrophysics Data System (ADS)

    Silva, Manuela Ramos; Milne, Bruce; Coutinho, Joana T.; Pereira, Laura C. J.; Martín-Ramos, Pablo; Pereira da Silva, Pedro S.; Martín-Gil, Jesús

    2016-03-01

    A new 1D complex has been prepared and characterized. X-ray single crystal structure confirms that the Cu(II) ions assemble in alternating chains with Cu … Cu distances of 2.5685(4) and 3.1760(4) Å. The temperature dependence of the magnetic susceptibility reveals an antiferromagnetic interaction between the paddle-wheel copper centers with an exchange of -300 cm-1. The exchange integral was also determined by quantum chemical ab-initio calculations, using polarised and unpolarised basis sets reproducing well the experimental value. The second harmonic generation efficiency of a concomitantly crystallized material was evaluated and was found to be comparable to urea.

  17. Solvent-controlled assembly of crystal structures: From centrosymmetric structure to noncentrosymmetric structure

    NASA Astrophysics Data System (ADS)

    Zhang, Le; Dang, Lilong; Luo, Feng; Feng, Xuefeng

    2016-02-01

    Reported here are two isomeric organic crystals and two HgI2-based coordination compounds by solvo(hydro)thermal method: [(TPTA)·H2O]n (1, Cc), [(TPTA)·H2O]n (2, Pbca), [Hg1.5I3(TPTA)0.5(CH3CN)·(H2O)0.5]n (3, P21) and [HgI2(TPTA)·H2O]n (4, P21/c) (TPTA = N,N‧,N″-tris(3-pyridyl)trimesic amide). Single crystal X-ray diffraction show that they afford noncentrosymmetric and centrosymmetric structures, respectively. Note that this kind of formations can be precisely controlled by changing the reaction solvent, thus indicating a facile method towards generating noncentrosymmetric structure.

  18. Can antimonide-based nanowires form wurtzite crystal structure?

    PubMed

    Gorji Ghalamestani, Sepideh; Lehmann, Sebastian; Dick, Kimberly A

    2016-02-01

    The epitaxial growth of antimonide-based nanowires has become an attractive subject due to their interesting properties required for various applications such as long-wavelength IR detectors. The studies conducted on antimonide-based nanowires indicate that they preferentially crystallize in the zinc blende (ZB) crystal structure rather than wurtzite (WZ), which is common in other III-V nanowire materials. Also, with the addition of small amounts of antimony to arsenide- and phosphide-based nanowires grown under conditions otherwise leading to WZ structure, the crystal structure of the resulting ternary nanowires favors the ZB phase. Therefore, the formation of antimonide-based nanowires with the WZ phase presents fundamental challenges and is yet to be explored, but is particularly interesting for understanding the nanowire crystal phase in general. In this study, we examine the formation of Au-seeded InSb and GaSb nanowires under various growth conditions using metalorganic vapor phase epitaxy. We address the possibility of forming other phases than ZB such as WZ and 4H in binary nanowires and demonstrate the controlled formation of WZ InSb nanowires. We further discuss the fundamental aspects of WZ growth in Au-seeded antimonide-based nanowires. PMID:26763161

  19. Projection structure of frog rhodopsin in two crystal forms.

    PubMed Central

    Schertler, G F; Hargrave, P A

    1995-01-01

    Rhodopsin is the G protein-coupled receptor that upon light activation triggers the visual transduction cascade. Rod cell outer segment disc membranes were isolated from dark-adapted frog retinas and were extracted with Tween detergents to obtain two-dimensional rhodopsin crystals for electron crystallography. When Tween 80 was used, tubular structures with a p2 lattice (a = 32 A, b = 83 A, gamma = 91 degrees) were formed. The use of a Tween 80/Tween 20 mixture favored the formation of larger p22(1)2(1) lattices (a = 40 A, b = 146 A, gamma = 90 degrees). Micrographs from frozen hydrated frog rhodopsin crystals were processed, and projection structures to 7-A resolution for the p22(1)2(1) form and to 6-A resolution for the p2 form were calculated. The maps of frog rhodopsin in both crystal forms are very similar to the 9-A map obtained previously for bovine rhodopsin and show that the arrangement of the helices is the same. In a tentative topographic model, helices 4, 6, and 7 are nearly perpendicular to the plane of the membrane. In the higher-resolution projection maps of frog rhodopsin, helix 5 looks more tilted than it appeared previously. The quality of the two frog rhodopsin crystals suggests that they would be suitable to obtain a three-dimensional structure in which all helices would be resolved. Images Fig. 1 Fig. 2 Fig. 6 PMID:8524807

  20. Spatially resolved analysis of short-range structure perturbations in a plastically bent molecular crystal

    NASA Astrophysics Data System (ADS)

    Panda, Manas K.; Ghosh, Soumyajit; Yasuda, Nobuhiro; Moriwaki, Taro; Mukherjee, Goutam Dev; Reddy, C. Malla; Naumov, Panče

    2015-01-01

    The exceptional mechanical flexibility observed with certain organic crystals defies the common perception of single crystals as brittle objects. Here, we describe the morphostructural consequences of plastic deformation in crystals of hexachlorobenzene that can be bent mechanically at multiple locations to 360° with retention of macroscopic integrity. This extraordinary plasticity proceeds by segregation of the bent section into flexible layers that slide on top of each other, thereby generating domains with slightly different lattice orientations. Microscopic, spectroscopic and diffraction analyses of the bent crystal showed that the preservation of crystal integrity when stress is applied on the (001) face requires sliding of layers by breaking and re-formation of halogen-halogen interactions. Application of stress on the (100) face, in the direction where π···π interactions dominate the packing, leads to immediate crystal disintegration. Within a broader perspective, this study highlights the yet unrecognized extraordinary malleability of molecular crystals with strongly anisotropic supramolecular interactions.