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.

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

Fingerprinting redox and ligand states in haemprotein crystal structures using resonance Raman spectroscopy.

PubMed

Kekilli, Demet; Dworkowski, Florian S N; Pompidor, Guillaume; Fuchs, Martin R; Andrew, Colin R; Antonyuk, Svetlana; Strange, Richard W; Eady, Robert R; Hasnain, S Samar; Hough, Michael A

2014-05-01

It is crucial to assign the correct redox and ligand states to crystal structures of proteins with an active redox centre to gain valid functional information and prevent the misinterpretation of structures. Single-crystal spectroscopies, particularly when applied in situ at macromolecular crystallography beamlines, allow spectroscopic investigations of redox and ligand states and the identification of reaction intermediates in protein crystals during the collection of structural data. Single-crystal resonance Raman spectroscopy was carried out in combination with macromolecular crystallography on Swiss Light Source beamline X10SA using cytochrome c' from Alcaligenes xylosoxidans. This allowed the fingerprinting and validation of different redox and ligand states, identification of vibrational modes and identification of intermediates together with monitoring of radiation-induced changes. This combined approach provides a powerful tool to obtain complementary data and correctly assign the true oxidation and ligand state(s) in redox-protein crystals.

Synthesis, growth, structural, spectroscopic and optical studies of a semiorganic NLO crystal: zinc guanidinium phosphate.

PubMed

Suvitha, A; Murugakoothan, P

2012-02-01

The semi-organic nonlinear optical (NLO) crystal, zinc guanidinium phosphate (ZGuP) has been grown through synthesis between zinc sulphate, guanidine carbonate and orthophosphoric acid from its aqueous solution by slow solvent evaporation technique. Solubility of the synthesized material has been determined for various temperatures using water as solvent. The grown crystal has been characterized by powder X-ray diffraction to confirm the crystal structure. Investigation has been carried out to assign the vibrational frequencies of the grown crystals by Fourier transform infrared spectroscopy technique. (1)H and (13)C FT-NMR have been recorded to elucidate the molecular structure. The optical absorption study confirms the suitability of the crystal for device applications. The second harmonic generation (SHG) efficiency of ZGuP is found to be 1.825 times that of potassium dihydrogen phosphate (KDP). Thermal behavior of the grown crystals has been studied by thermogravimetric and differential thermal analysis. The mechanical properties of the grown crystals have been studied using Vickers microhardness tester. Copyright © 2011 Elsevier B.V. All rights reserved.

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

PubMed

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

2015-02-25

Five Schiff bases obtained from condensation of 4-methoxybenzohydrazide with related aldehydes, namely o-vanillin, vanillin, 5-bromovanillin, 5-chlorosalicylaldehyde and 5-bromosalicylaldehyde were prepared. A detailed structural and spectroscopic study is reported. The crystal structures of four members of the family were determined and compared with one another. The hydrazones obtained from 5-chlorosalicylaldehyde and 5-bromosalicylaldehyde resulted to be isomorphic to each other. The solid-state structures are stabilized by intra-molecular O-H⋯N interactions in salicylaldehyde derivatives between the O-H moiety from the aldehyde and the hydrazone nitrogen atom. All crystals are further stabilized by inter-molecular H-bonds mediated by the crystallization water molecule. A comparative analysis between experimental and theoretical results is presented. The conformational space was searched and geometries were optimized both in gas phase and including solvent effects. The structure is predicted for the compound for which the crystal structure was not determined. Infrared and electronic spectra were measured and assigned with the help of data obtained from computational methods based on the Density Functional Theory. Copyright © 2014 Elsevier B.V. All rights reserved.

Development of X-ray spectroscopic polarimetry with bent Si crystals and CFRP substrate

NASA Astrophysics Data System (ADS)

Iizuka, Ryo; Izumiya, Takanori; Tsuboi, Yohko

2016-07-01

The light from celestial objects includes four important quantities; images, time variation, energy spectrum, and polarization. In the field of X-ray astronomy, the capabilities of the former three have remarkably developed. On the other hand, the progress for the polarimetry is considerably delayed because of technical difficulties. In order to make a breakthrough in the field of X-ray polarimetry, we have developed a new type of optics for X-ray polarimetry. The system is collecting Bragg crystal with large area and very high sensitivity for the polarization dedicated to Fe-K lines. We adopt the 400 re ection of Si(100) crystals with high sensitivity for the polarization around Fe-K lines (6 7 keV), and bent the crystals with the wide X-ray band and high S/N ratio. Furthermore, to install small area of CCD to non-focal plane, it also has the spectroscopic capability with the better resolution than that of general X-ray CCD. Our previous development was to bent Si crystals to the cylindrical shape of circle and parabola with the DLC deposition. However, for the better optics for the X-ray polarimetry, the shape should be the paraboloid of revolution to collect X-rays with high S/N ratio. We searched for the method to bent the Si crystals to the shape of the paraboloid of revolution. We devised the method to mold the crystal and the CFRP substrate simultaneously pushed to the sophisticated foundation with the paraboloid of revolution. We developed the prototype of about 8 inch in radius of one-quater size. The crystals was also bent in the circumferential direction. Therefore, the image capability examined with optical parallel beam is 0.6 degree. In this thesis, we discussed the new design for X-ray spectroscopic polarimetry, the evaluation of image capability.

Effect of Partial Crystallization on the Structural and Luminescence Properties of Er3+-Doped Phosphate Glasses

PubMed Central

Lopez-Iscoa, Pablo; Salminen, Turkka; Hakkarainen, Teemu; Petit, Laeticia; Janner, Davide; Boetti, Nadia G.; Lastusaari, Mika; Pugliese, Diego; Paturi, Petriina; Milanese, Daniel

2017-01-01

Er-doped phosphate glass ceramics were fabricated by melt-quenching technique followed by a heat treatment. The effect of the crystallization on the structural and luminescence properties of phosphate glasses containing Al2O3, TiO2, and ZnO was investigated. The morphological and structural properties of the glass ceramics were characterized by Field Emission-Scanning Electron Microscopy (FE-SEM), X-ray Diffraction (XRD), and micro-Raman spectroscopy. Additionally, the luminescence spectra and the lifetime values were measured in order to study the influence of the crystallization on the spectroscopic properties of the glasses. The volume ratio between the crystal and the glassy phases increased along with the duration of the heat treatment. The crystallization of the glass ceramics was confirmed by the presence of sharp peaks in the XRD patterns and different crystal phases were identified depending on the glass composition. Sr(PO3)2 crystals were found to precipitate in all the investigated glasses. As evidenced by the spectroscopic properties, the site of the Er3+ ions was not strongly affected by the heat treatment except for the fully crystallized glass ceramic which does not contain Al2O3, TiO2, and ZnO. An increase of the lifetime was also observed after the heat treatment of this glass. Therefore, we suspect that the Er3+ ions are incorporated in the precipitated crystals only in this glass ceramic. PMID:28772833

Synthesis, structure, spectroscopic investigations, and computational studies of optically pure β-ketoamide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mtat, D.; Touati, R.; Guerfel, T., E-mail: taha-guerfel@yahoo.fr

2016-12-15

Chemical preparation, X-ray single crystal diffraction, IR and NMR spectroscopic investigations of a novel nonlinear optical organic compound (C{sub 17}H{sub 22}NO{sub 2}Cl) are described. The compound crystallizes in the orthorhombic system with the non-centrosymmetric sp. gr. P2{sub 1}2{sub 1}2{sub 1}. In the crystal structure, molecules are interconnected by N–H…O hydrogen bonds forming infinite chains along a axis. The Hirshfeld surface and associated fingerprint plots of the compound are presented to explore the nature of intermolecular interactions and their relative contributions in building the solid-state architecture. The molecular HOMO–LUMO compositions and their respective energy gaps are also drawn to explain themore » activity of the compound. The first hyperpolarizability β{sub tot} of the title compound is determined using DFT calculations. The optical properties are also investigated by UV–Vis absorption spectrum.« less

Thermal, spectroscopic, and ab initio structural characterization of carprofen polymorphs.

PubMed

Bruni, Giovanna; Gozzo, Fabia; Capsoni, Doretta; Bini, Marcella; Macchi, Piero; Simoncic, Petra; Berbenni, Vittorio; Milanese, Chiara; Girella, Alessandro; Ferrari, Stefania; Marini, Amedeo

2011-06-01

Commercial and recrystallized polycrystalline samples of carprofen, a nonsteroidal anti-inflammatory drug, were studied by thermal, spectroscopic, and structural techniques. Our investigations demonstrated that recrystallized sample, stable at room temperature (RT), is a single polymorphic form of carprofen (polymorph I) that undergoes an isostructural polymorphic transformation by heating (polymorph II). Polymorph II remains then metastable at ambient conditions. Commercial sample is instead a mixture of polymorphs I and II. The thermodynamic relationships between the two polymorphs were determined through the construction of an energy/temperature diagram. The ab initio structural determination performed on synchrotron X-Ray powder diffraction patterns recorded at RT on both polymorphs allowed us to elucidate, for the first time, their crystal structure. Both crystallize in the monoclinic space group type P2(1) /c, and the unit cell similarity index and the volumetric isostructurality index indicate that the temperature-induced polymorphic transformation I → II is isostructural. Polymorphs I and II are conformational polymorphs, sharing a very similar hydrogen bond network, but with different conformation of the propanoic skeleton, which produces two different packing. The small conformational change agrees with the low value of transition enthalpy obtained by differential scanning calorimetry measurements and the small internal energy computed with density functional methods. Copyright © 2011 Wiley-Liss, Inc.

Probing Zeolite Crystal Architecture and Structural Imperfections using Differently Sized Fluorescent Organic Probe Molecules.

PubMed

Hendriks, Frank C; Schmidt, Joel E; Rombouts, Jeroen A; Lammertsma, Koop; Bruijnincx, Pieter C A; Weckhuysen, Bert M

2017-05-05

A micro-spectroscopic method has been developed to probe the accessibility of zeolite crystals using a series of fluorescent 4-(4-diethylaminostyryl)-1-methylpyridinium iodide (DAMPI) probes of increasing molecular size. Staining large zeolite crystals with MFI (ZSM-5) topology and subsequent mapping of the resulting fluorescence using confocal fluorescence microscopy reveal differences in structural integrity: the 90° intergrowth sections of MFI crystals are prone to develop structural imperfections, which act as entrance routes for the probes into the zeolite crystal. Polarization-dependent measurements provide evidence for the probe molecule's alignment within the MFI zeolite pore system. The developed method was extended to BEA (Beta) crystals, showing that the previously observed hourglass pattern is a general feature of BEA crystals with this morphology. Furthermore, the probes can accurately identify at which crystal faces of BEA straight or sinusoidal pores open to the surface. The results show this method can spatially resolve the architecture-dependent internal pore structure of microporous materials, which is difficult to assess using other characterization techniques such as X-ray diffraction. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Single crystal X-ray diffraction, spectroscopic and mass spectrometric studies of furanocoumarin peucedanin.

PubMed

Bartnik, Magdalena; Arczewska, Marta; Hoser, Anna A; Mroczek, Tomasz; Kamiński, Daniel M; Głowniak, Kazimierz; Gagoś, Mariusz; Woźniak, Krzysztof

2014-01-01

The structure of peucedanin, isolated from Peucedanum tauricum Bieb. (Apiaceae), has been established using single crystal X-ray diffraction. This furanocoumarin isolated from the light petroleum extract of P. tauricum fruits was characterized by high resolution EI-MS, sATR-FTIR and 2D NMR spectroscopic techniques. The EI-MS showed the typical fragmentation pattern of methoxyfuranocoumarins. Extensive 1D (1H and 13C) as well as 2D NMR data enabled complete assignment of the carbon atoms in the peucedanin molecule. The FTIR data confirms intermolecular hydrogen bonding between peucedanin molecules in polar solvents. Peucedanin crystallises in the R-3 space group from the trigonal system with one molecule in the asymmetric part of the unit cell. The crystal lattice of peucedanin consists of the molecules arranged in separate columns. They are related by two fold screw axes and centres of symmetry. Interestingly, peucedanin columns form two channels per unit cell with a diameter of 7.5angstrom going through the crystal lattice in the Z-direction. These channels are filled with disordered water molecules, which are surrounded by hydrophobic methyl groups and are located exactly at the centres of the channels. The peucedanin molecules are stacked in a single column with the opposite orientation of the neighbouring molecules. These results could be interesting in further application of this molecule, for example in biological tests of its activity.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dutta, Alo, E-mail: alo_dutta@yahoo.com; Saha, Sujoy; Kumari, Premlata

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 strengthmore » 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.« less

Growth and spectroscopic properties of Sm3+:KY(WO4)2 crystal

NASA Astrophysics Data System (ADS)

Demesh, M. P.; Dernovich, O. P.; Gusakova, N. V.; Yasukevich, A. S.; Kornienko, A. A.; Dunina, E. B.; Fomicheva, L. A.; Pavlyuk, A. A.; Kuleshov, N. V.

2018-01-01

A Sm3+:KY(WO4)2 crystal was grown by the modified Czochralski technique. Polarized absorption and fluorescence spectra, as well as a fluorescence decay curve, were recorded at room temperature. Radiative properties such as emission probabilities, branching ratios and radiative lifetimes were investigated within the framework of the Judd-Ofelt theory as well as the theory of f-f transition intensities which takes into account the influence of the excited configurations. Emission cross section spectra were determined. 4G5/2 fluorescence decay was analyzed within the framework of the Inokuti-Hirayama model. The spectroscopic properties of Sm:KYW crystal were compared with those of other Sm3+-doped materials.

Spectroscopic characterisation of Er-doped LuVO4 single crystals

NASA Astrophysics Data System (ADS)

Lisiecki, R.; Dominiak-Dzik, G.; Solarz, P.; Strzęp, A.; Ryba-Romanowski, W.; Łukasiewicz, T.

2010-12-01

The LuVO4:Er single crystals were grown by the Czochralski technique. The crystal-field split energy levels of Er3+ ion were derived experimentally employing absorption and emission spectra measured at T=10 K. The Judd-Ofelt phenomenological method was used to estimate intensity parameters, radiative lifetimes and branching ratios of luminescence. The excited state dynamics of the LuVO4:Er systems was investigated and experimental lifetimes of emitting levels were measured. The emission cross section of the 4I13/2→4I15/2 transition in the infrared was calculated by the Füchtbauer-Ladenburg method. The gain cross section, estimated for several inverse-population parameters, allowed us to evaluate a potential laser activity of the LuVO4:Er system at 1.6 μm. Also, the potential range of the optical pumping was assessed based on absorption spectra achieved at the room temperature. The optical losses related to the green up-converted emission, encountered under the 978 nm excitation between 300 and 670 K were indicated and discussed. Spectroscopic peculiarities of the Er3+-doped LuVO4 crystal were discussed in relation to optical properties of the YVO4:Er and GdVO4:Er crystals. Taking into account the high quantum efficiency of the 4I13/2 level, and satisfactory absorption and emission features, the LuVO4:Er crystal can be considered as a promising active material for laser operation near 1.6 μm.

Selective detection of Cu2 + and Co2 + in aqueous media: Asymmetric chemosensors, crystal structure and spectroscopic studies

NASA Astrophysics Data System (ADS)

Dogaheh, Samira Gholizadeh; Khanmohammadi, Hamid; Carolina Sañudo, E.

2017-05-01

Two new azo-azomethine receptors, H2L1 and H2L2, containing hydrazine, naphthalene and different electron withdrawing groups, Cl and NO2, have been designed and synthesized for qualitative and quantitative detection of Cu2 + and Co2 + in aqueous media. The crystal structure of H2L1is reported. The H2L1was used as a chemosensor for selective detection of trace amount of Cu2 + in aqueous media. H2L2 was also applied to naked-eye distinction of Cu2 + and Co2 + from other transition metal ions in aqueous media. Detection limit of Cu2 + is 1.13 μM and 1.26 μM, in water, for H2L1 and H2L2, respectively, which are lower than the World Health Organization (WHO) recommended level. The binuclear Cu2 + and Co2 + complexes of the receptors have been also prepared and characterized using spectroscopic methods and MALDI-TOF mass analysis. Furthermore, the binding stoichiometry between the receptors upon the addition Cu2 + and Co2 + has been investigated using Job's plot. Moreover, the fluorescence emission spectra of the receptors and their metal complexes are also reported.

[Effect of annealing temperature on the crystallization and spectroscopic response of a small-molecule semiconductor doped in polymer film].

PubMed

Yin, Ming; Zhang, Xin-Ping; Liu, Hong-Mei

2012-11-01

The crystallization properties of the perylene (EPPTC) molecules doped in the solid film of the derivative of polyfluorene (F8BT) at different annealing temperatures, as well as the consequently induced spectroscopic response of the exciplex emission in the heterojunction structures, were studied in the present paper. Experimental results showed that the phase separation between the small and the polymer molecules in the blend film is enhanced with increasing the annealing temperature, which leads to the crystallization of the EPPTC molecules due to the strong pi-pi stacking. The size of the crystal phase increases with increasing the annealing temperature. However, this process weakens the mechanisms of the heterojunction configuration, thus, the total interfacial area between the small and the polymer molecules and the amount of exciplex are reduced significantly in the blend film. Meanwhile, the energy transfer from the polymer to the small molecules is also reduced. As a result, the emission from the exciplex becomes weaker with increasing the annealing temperature, whereas the stronger emission from the polymer molecules and from the crystal phase of the small molecules can be observed. These experimental results are very important for understanding and tailoring the organic heterojunction structures. Furthermore, this provides photophysics for improving the performance of photovoltaic or solar cell devices.

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

DOE PAGES

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

2014-12-29

Intradiol aromatic ring-cleaving dioxygenases use an active site, nonheme Fe 3+ to activate O 2 and catecholic substrates for reaction. The inability of Fe 3+ to directly bind O 2 presents a mechanistic conundrum. The reaction mechanism of protocatechuate 3,4-dioxygenase is investigated in this paper 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 surroundingmore » solution. The X-ray crystal structure of the intermediate at pH 6.5 revealed the key alkylperoxo-Fe 3+ species, and the anhydride-Fe 3+ 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 Fe 2+-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 Fe 2+ intermediate that could bind O 2 are consistent with concerted formation of the alkylperoxo followed by Criegee rearrangement to yield the anhydride and ultimately ring-opened product. Finally, structural comparison of the alkylperoxo intermediates from the intra- and extradiol dioxygenases provides a rationale for site specificity of ring cleavage.« less

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

PubMed

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

2016-03-21

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

Vibrational and structural investigation of SOUL protein single crystals by using micro-Raman spectroscopy

NASA Astrophysics Data System (ADS)

Rossi, Barbara; Giarola, Marco; Mariotto, Gino; Ambrosi, Emmanuele; Monaco, Hugo L.

2010-05-01

Protein SOUL is a new member of the recently discovered putative heme-binding protein family called SOUL/HEBP and, to date, no structural information exists for this protein. Here, micro-Raman spectroscopy is used to study the vibrational properties of single crystals obtained from recombinant protein SOUL by means of two different optimization routes. This spectroscopic approach offers the valuable advantage of the in-situ collection of experimental data from protein crystals, placed onto a hanging-drop plate, under the same conditions used to grow the crystals. By focusing on the regions of amides I and III bands, some secondary structure characteristic features have been recognized. Moreover, some side-chain marker bands were observed in the Raman spectra of SOUL crystals and the unambiguous assignment of these peaks inferred by comparing the experimental Raman spectra of pure amino acids and their Raman intensities computed using quantum chemical calculations. Our comparative analysis allows to get a deeper understanding of the side-chain environments and of the interactions involving these specific amino acids in the two different SOUL crystals.

Spectroscopic study of shock-induced decomposition in ammonium perchlorate single crystals.

PubMed

Gruzdkov, Y A; Winey, J M; Gupta, Y M

2008-05-01

Time-resolved Raman scattering measurements were performed on ammonium perchlorate (AP) single crystals under stepwise shock loading. For particular temperature and pressure conditions, the intensity of the Raman spectra in shocked AP decayed exponentially with time. This decay is attributed to shock-induced chemical decomposition in AP. A series of shock experiments, reaching peak stresses from 10-18 GPa, demonstrated that higher stresses inhibit decomposition while higher temperatures promote it. No orientation dependence was found when AP crystals were shocked normal to the (210) and (001) crystallographic planes. VISAR (velocity interferometer system for any reflector) particle velocity measurements and time-resolved optical extinction measurements carried out to verify these observations are consistent with the Raman data. The combined kinetic and spectroscopic results are consistent with a proton-transfer reaction as the first decomposition step in shocked AP.

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.

Growth and spectroscopic properties of Tm3+:NaBi(MoO4)2 single crystal

NASA Astrophysics Data System (ADS)

Gusakova, N. V.; Mudryi, A. V.; Demesh, M. P.; Yasukevich, A. S.; Pavlyuk, A. A.; Kornienko, A. A.; Dunina, E. B.; Khodasevich, I. A.; Orlovich, V. A.; Kuleshov, N. V.

2018-06-01

In this work we report the spectroscopic properties of Tm3+:NaBi(MoO4)2 crystals with the dopant concentrations of 0.7 at.% and 3 at.%. The energy levels of the Tm3+ in the NaBi(MoO4)2 host were determined from polarized optical absorption and photoluminescence spectra measured at 77.4 K. Radiative properties of the crystals were calculated in context of Judd-Ofelt theory. Raman spectra of the crystal were studied. The concentration dependences of emission decay times of 3H4 and 3F4 levels were analyzed. The potential of the crystal for building tunable and ultrafast pulse lasers is shown on the base of cross sections and gain coefficient in the range of 1.9 μm.

The first mammalian aldehyde oxidase crystal structure: insights into substrate specificity.

PubMed

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

2012-11-23

Aldehyde oxidases have pharmacological relevance, and AOX3 is the major drug-metabolizing enzyme in rodents. The crystal structure of mouse AOX3 with kinetics and molecular docking studies provides insights into its enzymatic characteristics. Differences in substrate and inhibitor specificities can be rationalized by comparing the AOX3 and xanthine oxidase structures. The first aldehyde oxidase structure represents a major advance for drug design and mechanistic studies. 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.

Spectroscopy and crystal structures of natural stereoisomers of neoclerodane diterpenoids from Teucrium yemense of Saudi medicinal plant

NASA Astrophysics Data System (ADS)

Nur-e-Alam, Mohammad; Kanthasamy, Gopikkaa; Yousaf, Muhammad; Alqahtani, Ali S.; Ghabbour, Hazem A.; Al-Rehaily, Adnan J.

2017-11-01

3-O-deacetylteugracilin (1) and teugracilin B (2), two natural stereoisomers, are isolated from Teucrium yemense (Defl). These two compounds are almost identical to each other, differing only at the C6 stereocenter. We now crystallise these two compounds and for the first time, determine the crystal structure through single crystal X-ray diffraction, and the stereochemistry for all positions using spectroscopic data. These techniques enable us to establish the difference between the two compounds. Careful interpretation of the results indicates that HRMS and 1 and 2D NMR spectroscopy, are in agreement with single crystal X-ray diffraction data.

Effects of scandium substitution on the crystal structure and luminescence properties of LuBO{sub 3}: Ce{sup 3+}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Yuntao, E-mail: caswyt@hotmail.com; Ren, Guohao, E-mail: rgh@mail.sic.ac.cn; Ding, Dongzhou

2012-10-15

The calcite phase of LuBO{sub 3} and ScBO{sub 3} polycrystalline powders were synthesized by solid state reaction method, and the Lu{sub 1-x}Sc{sub x}BO{sub 3}:Ce (x=0.2, 0.5, 0.7) single crystals were grown by the Czochralski method. A large composition deviation between the initial polycrystalline powders and final single crystal was confirmed by electron probe micro-analysis. Raman spectroscopy revealed that moderate lattice disorder was induced by scandium substitution. However, based on the single crystal X-ray study, we finally concluded that the crystal structure of lutetium scandium orthoborate still crystallized in the rhombohedral system belonging to R3{sup -}c. Furthermore, the relationship between themore » energies of the five 5d levels of Ce{sup 3+} and the crystalline environment was revealed. The total redshift, total crystal field splitting, and centroid shift of Lu{sub 1-x}Sc{sub x}BO{sub 3}:Ce{sup 3+} were calculated based on their VUV excitation spectra. The variations trend of these observed spectroscopic parameters was in accordance with the predicted ones. - Graphical abstract: The crystal structure of Lu{sub 1-x}Sc{sub x}BO{sub 3}:Ce is rhombohedral system with R3{sup -}c space group. The relationship between the energies of the five Ce{sup 3+} 5d levels and the crystalline environment is established. Highlights: Black-Right-Pointing-Pointer Moderate lattice disorder is induced by scandium doping. Black-Right-Pointing-Pointer The crystal structure of Lu{sub 1-x}Sc{sub x}BO{sub 3}:Ce is rhombohedral system with R3{sup -}c space group. Black-Right-Pointing-Pointer Relationship between energies of Ce{sup 3+} 5d levels and crystalline environment is established. Black-Right-Pointing-Pointer The spectroscopic parameters are experimentally and theoretically calculated.« less

pH-Dependent reversible crystal transformation of 1-carboxymethyl-1-methyl-pyrrolidinium bromides and their spectroscopic fingerprint

NASA Astrophysics Data System (ADS)

Tong, Ya-yan; Zhang, Heng; Chang, Liang-liang; Xuan, Xiao-peng

2018-03-01

In this work, two 1-carboxymethyl-1-methyl-pyrrolidinium bromides (N-methylpyrrolidine betaine hydrobromides) with the stoichiometry of betaine:hydrobromic acid as 1:1 and 2:1, denoted as CMPRHBr-I and CMPRHBr-II, respectively, were prepared and crystallographically determined. The large difference in these two structures is the type of hydrogen bonds, resulting in the different thermal stability. A strong Osbnd H ⋯ Br hydrogen bond was observed in CMPRHBr-I, whereas O ⋯ H ⋯ O hydrogen bond in CMPRHBr-II. Both these two crystals can mutually transform by changing the pH value of the aqueous solution. Vibrational spectroscopic studies shows that these two structures can be easily distinguished by the characteristic bands such as νCdbnd O stretching vibration and the D-type bands. Our studies indicate that it should be cautious of the structural change as this type of organic salts was purified and recrystallized.

Preparation, characterization and crystal structures of three salts of the quaterpyridine ligand

NASA Astrophysics Data System (ADS)

Ciesielski, Artur; Stefankiewicz, Artur R.; Patroniak, Violetta; Kubicki, Maciej

2009-07-01

As a result of a reaction between 6,6'''-dimethyl-2,2':6',2'':6'',2'''-quaterpyridine C 22H 18N 4 and lanthanide(III) salts, compounds, [C 22H 20N 4] 2+·2(CF 3SO 3) - ( 1) and [C 22H 20N 4] 2+·2(ClO 4) - ( 2), have been obtained. They were characterized by spectroscopic techniques (ESI-MS, NMR, IR), elemental analysis, and their formulae were confirmed on the basis of X-ray crystallography. It turned out that the perchlorate crystallizes as two solvates: with acetonitrile and disordered water molecules. These are the first structural characterization of a 6,6'″-dimethyl-2,2':6',2″:6″,2'″-quaterpyridinium dication. Due to the intramolecular hydrogen bond it adopts the previously unobserved cis/trans/cis conformation. In all three crystals the dications have C i symmetry, they occupy the special positions in their respective space groups. In the crystal structures the π-π stacking and weak hydrogen bonds add directionality to the dominating electrostatic interactions between cations and anions.

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

Raman spectroscopic investigations on natural samples from the Integrated Ocean Drilling Program (IODP) Expedition 311: indications for heterogeneous compositions in hydrate crystals.

PubMed

Schicks, J M; Ziemann, M A; Lu, H; Ripmeester, J A

2010-12-01

Natural gas hydrates usually are found in the form of structure I, encasing predominantly methane in the hydrate lattices as guest molecules, sometimes also minor amount of higher hydrocarbons, CO2 or H2S. Raman spectroscopy is an approved tool to determine the composition of the hydrate phase. Thus, in this study Raman spectroscopic analyses have been applied to hydrate samples obtained from Integrated Ocean Drilling Program (IODP) Expedition 311 in two different approaches: studying the samples randomly taken from the hydrate core, and--as a new application--mapping small areas on the surface of clear hydrate crystals. The results obtained imply that the gas composition of hydrate, in terms of relative concentrations of CH4 and H2S, is not homogeneous over a core or even within a crystal. The mapping method yielded results with very high lateral resolution, indicating the coexistence of different phases with the same structure but different compositions within a hydrate crystal. Copyright © 2010 Elsevier B.V. All rights reserved.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bratlie, Kaitlin

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 -6 Torr), cyclohexene hydrogenated and dehydrogenates to form cyclohexyl (C 6H 11) and π-allyl Cmore » 6H 9, respectively, on Pt(100). Increasing pressures to 1.5 Torr form cyclohexyl, π-allyl C 6H 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, π-allyl c-C 6H 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 2u mode of free benzene, which leads to catalysis. Linear C 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, mechanisms for catalytic isomerization and

Co2+-doped diopside: crystal structure and optical properties

NASA Astrophysics Data System (ADS)

Gori, C.; Tribaudino, M.; Mezzadri, F.; Skogby, H.; Hålenius, U.

2018-05-01

Synthetic clinopyroxenes along the CaMgSi2O6-CaCoSi2O6 join were investigated by a combined chemical-structural-spectroscopic approach. Single crystals were synthesized by flux growth methods, both from Ca-saturated and Ca-deficient starting compositions. Single crystal structure refinements show that the incorporation of Co2+ at the octahedrally coordinated cation sites of diopside, increases the unit-cell as well as the M1 and the M2 polyhedral volumes. Spectroscopic investigations (UV-VIS-NIR) of the Ca-rich samples reveal three main optical absorption bands, i.e. 4 T 1g → 4 T 2g( F), 4 T 1g → 4 A 2g( F) and 4 T 1g → 4 T 1g( P) as expected for Co2+ at a six-coordinated site. The bands arising from the 4 T 1g → 4 T 2g( F) and the 4 T 1g → 4 T 1g( P) electronic transitions, are each split into two components, due to the distortions of the M1 polyhedron from ideal Oh-symmetry. In spectra of both types, a band in the NIR range at ca 5000 cm-1 is caused by the 4 A 2g → 4 T 1g( F) electronic transition in Co2+ in a cubic field in the M2 site. Furthermore, an additional component to a band system at 14,000 cm-1, due to electronic transitions in Co2+ at the M2 site, is recorded in absorption spectra of Ca-deficient samples. No variations in Dq and Racah B parameters for Co2+ at the M1 site in response to compositional changes, were demonstrated, suggesting complete relaxation of the M1 polyhedron within the CaMgSi2O6-CaCoSi2O6 solid solution.

Co2+-doped diopside: crystal structure and optical properties

NASA Astrophysics Data System (ADS)

Gori, C.; Tribaudino, M.; Mezzadri, F.; Skogby, H.; Hålenius, U.

2017-12-01

Synthetic clinopyroxenes along the CaMgSi2O6-CaCoSi2O6 join were investigated by a combined chemical-structural-spectroscopic approach. Single crystals were synthesized by flux growth methods, both from Ca-saturated and Ca-deficient starting compositions. Single crystal structure refinements show that the incorporation of Co2+ at the octahedrally coordinated cation sites of diopside, increases the unit-cell as well as the M1 and the M2 polyhedral volumes. Spectroscopic investigations (UV-VIS-NIR) of the Ca-rich samples reveal three main optical absorption bands, i.e. 4 T 1g → 4 T 2g(F), 4 T 1g → 4 A 2g(F) and 4 T 1g → 4 T 1g(P) as expected for Co2+ at a six-coordinated site. The bands arising from the 4 T 1g → 4 T 2g(F) and the 4 T 1g → 4 T 1g(P) electronic transitions, are each split into two components, due to the distortions of the M1 polyhedron from ideal Oh-symmetry. In spectra of both types, a band in the NIR range at ca 5000 cm-1 is caused by the 4 A 2g → 4 T 1g(F) electronic transition in Co2+ in a cubic field in the M2 site. Furthermore, an additional component to a band system at 14,000 cm-1, due to electronic transitions in Co2+ at the M2 site, is recorded in absorption spectra of Ca-deficient samples. No variations in Dq and Racah B parameters for Co2+ at the M1 site in response to compositional changes, were demonstrated, suggesting complete relaxation of the M1 polyhedron within the CaMgSi2O6-CaCoSi2O6 solid solution.

Synthesis of polyimides from α,αʹ-bis(3-aminophenoxy)-p-xylene: Spectroscopic, single crystal XRD and thermal studies

NASA Astrophysics Data System (ADS)

Ashraf, Ahmad Raza; Akhter, Zareen; Simon, Leonardo C.; McKee, Vickie; Castel, Charles Dal

2018-05-01

The meta-catenated ether-based diamine monomer α,αʹ-bis(3-aminophenoxy)-p-xylene (3APX) was synthesized from dinitro precursor α,αʹ-bis(3-nitrophenoxy)-p-xylene (3NPX). FTIR, 1H and 13C NMR spectroscopic studies accompanied by elemental analysis were performed for structural elucidations of 3NPX and 3APX. The spatial orientations of 3APX were explored by single crystal X-ray diffraction analysis. Its crystal system was found to be monoclinic, adopting the space group P21/c. The synthesized diamine monomer (3APX) was used for preparation of new series of polyimides by reacting with three different dianhydrides (BTDA, ODPA, 6FDA). The relevant copolyimides were developed via incorporation of 4,4ʹ-methylenedianiline (MDA) in the backbone of afore-synthesized polyimides. The structures of polyimides and copolyimides were verified by FTIR and 1H NMR spectroscopic techniques. Their properties were evaluated by dynamic and isothermal TGA (nitrogen and air atmospheres) and WAXRD studies. Polyimides displayed significantly high thermal stability as their degradation started around 400 °C and it was improved further by execution of copolymerization strategy with MDA. The 5% weight loss temperature (T5) of polyimides under nitrogen atmosphere was in the range of 425-460 °C while for copolyimides it increased to 454-498 °C. Thermal decomposition in air was slower than nitrogen between 400 and 550 °C however it was accelerated above 550 °C. Isothermal TGA disclosed that copolyimides have the ability to endure elevated temperatures for extended period. WAXRD analysis showed the amorphous nature of polyimides and copolyimides.

Crystal structure and vibrational spectra of melaminium arsenate

NASA Astrophysics Data System (ADS)

Anbalagan, G.; Marchewka, M. K.; Pawlus, K.; Kanagathara, N.

2015-01-01

The crystals of the new melaminium arsenate (MAS) [C3H7N6+ṡH2AsO4-] were obtained by the slow evaporation of an aqueous solution at room temperature. Single crystal X-ray diffraction analysis reveals that the crystal belongs to triclinic system with centro symmetric space group P-1. The crystals are built up from single protonated melaminium residues and single dissociated arsenate H2AsO4- anions. The protonated melaminium ring is almost planar. A combination of ionic and donor-acceptor hydrogen-bond interactions linking together the melaminium and arsenate residues forms a three-dimensional network. Vibrational spectroscopic analysis is reported on the basis of FT-IR and FT-Raman spectra recorded at room temperature. Hydrogen bonded network present in the crystal gives notable vibrational effect. DSC has also been performed for the crystal shows no phase transition in the studied temperature range (113-293 K).

Quartz crystal microbalance with coupled spectroscopic ellipsometry-study of temperature-responsive polymer brush systems

NASA Astrophysics Data System (ADS)

Adam, Stefan; Koenig, Meike; Rodenhausen, Keith Brian; Eichhorn, Klaus-Jochen; Oertel, Ulrich; Schubert, Mathias; Stamm, Manfred; Uhlmann, Petra

2017-11-01

Using a combined setup of quartz crystal microbalance with dissipation monitoring together with spectroscopic ellipsometry, the thermo-responsive behavior of two different brush systems (poly(N-isopropyl acrylamide) and poly(2-oxazoline)s) was investigated and compared to the behavior of the free polymer in solution. Poly(2-oxazoline)s with three different hydrophilicities were prepared by changing the content of a hydrophilic comonomer. While both polymer types exhibit a sharp, discontinuous thermal transition in solution, in the brush state the transition gets broader in the case of poly(N-isopropyl acrylamide) and is transformed into a continuous transition for poly(2-oxazoline)s. The position of the transition in solution is influenced by the degree of hydrophilicity of the poly(2-oxazoline). The difference in areal mass detected by quartz crystal microbalance and by spectroscopic ellipsometry, has been attributed to the chain segment density profile of the polymer brushes. Applying this density profile information, for poly(N-isopropyl acrylamide) two different swelling stages could be identified, while for poly(2-oxazoline) the transition between a parabolic and more step-wise profile is found continuous. The different swelling characteristics were attributed to the different miscibility behavior types, with the brush state acting similar to a crosslinked system.

Spectroscopic ellipsometric studies of the dielectric function of Cd1-x-yMnxFeyTe single crystals

NASA Astrophysics Data System (ADS)

Hwang, Younghun; Kim, Hyekyeong; Um, Youngho; Park, Hyoyeol

2004-06-01

Cd1-x-yMnxFeyTe single crystals grown by the vertical Bridgman method have been studied by measuring the complex dielectric function using spectroscopic ellipsometry in the 1.5 5.5 eV photon energy range at room temperature. The CP energy parameters of the E0, E1, E1 + 1, and E2 structures were determined by fitting the second-derivative spectra (d2/d2) with a theoretical model, i.e., the standard critical point (SCP) line shapes. The E1, E1 + 1, and E2 energies decreased with increasing Fe composition y, which is due to the hybridization effect of the valence and conduction bands in Cd1-xMnxTe with Fe 3d levels.

Efficient green luminescence of terbium oxalate crystals: A case study with Judd-Ofelt theory and single crystal structure analysis and the effect of dehydration on luminescence

NASA Astrophysics Data System (ADS)

Alexander, Dinu; Joy, Monu; Thomas, Kukku; Sisira, S.; Biju, P. R.; Unnikrishnan, N. V.; Sudarsanakumar, C.; Ittyachen, M. A.; Joseph, Cyriac

2018-06-01

Design and synthesis of Lanthanide based metal organic framework is a frontier area of research owing to their structural diversity enabling specific applications. The luminescence properties of rare earths, tuned by the structural features of Ln-MOFs are investigated extensively. Rare earth oxalates which can be synthesized in a facile method, ensuring the structural features of MOFs with excellent photoluminescence characteristics deserves much attention. This work is the first time report on the single crystal structure and Judd-Ofelt (JO) theoretical analysis - their correlation with the intense and sharp green luminescence of Terbium oxalate crystals. The intense green luminescence observed for Terbium oxalate crystals for a wide range of excitation from DUV to visible region despite the luminescence limiting factors are discussed. The absence of concentration quenching and lifting up of forbidden nature of f-f transitions, allowing direct excitation of Terbium ions is analysed with the help of JO theory and single crystal structure analysis. The JO analysis predicted the asymmetry of Terbium sites, allowing the electric dipole transitions and from the JO intensity parameters, promising spectroscopic parameters - emission cross section, branching ratio, gain band width and gain coefficient of the material were calculated. The single crystal structure analysis revealed the asymmetry of Tb sites and structure of Terbium oxalate is formed by the hydrogen bonded stacking of overlapped six Terbium membered rings connected by the oxalate ligands. The molecularly thick layers thus formed on the crystal surface are imaged by the atomic force microscopy. The presence of water channels in the structure and the effect of lattice water molecules on the luminescence intensity are also investigated.

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.

Synthesis, spectroscopic, single crystal diffraction and potential nonlinear optical properties of novel pyrazoline derivatives: Interplay of experimental and computational analyses.

PubMed

Arshad, Muhammad Nadeem; Birinji, Abdulhadi Salih; Khalid, Muhammad; Asiri, Abdullah M; Al-Amry, Khalid A; Aqlan, Faisal M S; Braga, Ataualpa A C

2018-09-05

Pyrazoline are widely being studied due to their potential applications in chemical field. Herein, five pyrazolines compounds were synthesized and characterized spectroscopically using nuclear magnetic resonance techniques ( 1 H NMR & 13 C NMR) to determine the structures of molecules along-with UV-Visible and infrared (FT-IR) studies for additional spectroscopic support in characterization of entitle synthesized molecules. Unit cells, specific space groups, bond lengths, bond angles and hydrogen bonding interactions were determined by the x-ray diffraction studies. Further, computational study of compounds with B3LYP/6-311 + G(d,p) level were carried out to explore optimized geometry, spectroscopic data for FT-IR, frontier molecular orbitals (FMOs) and non-linear optical (NLO) parameters. While, UV-Vis spectral were performed by TD-DFT/B3LYP/6-311 + G(d,p) level. The experimental results of spectroscopic and single crystal studies were compared and found in good agreement with the computational. The global reactivity parameters have been calculated with the help of the energy of FMOs. The order for the total first and second order hyperpolarizabilities of 1-5 is found in the following orders: 1 > 4 > 3 > 5 > 2 and 1 > 4 > 5 > 2 > 3 respectively. Overall, greater NLO response than urea molecule prove that investigated molecules are excellent candidate for NLO applications. Copyright © 2018 Elsevier B.V. All rights reserved.

Structural, crystal structure, Hirshfeld surface analysis and physicochemical studies of a new chlorocadmate template by 1-(2-hydroxyethyl)piperazine

NASA Astrophysics Data System (ADS)

Soudani, S.; Jeanneau, E.; Jelsch, C.; Lefebvre, F.; Ben Nasr, C.

2016-11-01

The synthesis, crystal structure and spectroscopic characterization of a new chlorocadmate template by the 1-(2-hydroxyethyl)piperazine ligand are reported. In the atomic arrangement, the CdCl5O entities are deployed in corrugated rows along the a-axis at y = 1/4 and y = 3/4 to form layers parallel to the (a,b) plane. In these crystals, piperazinediium cations are in a chair conformation and are inserted between these layers through Nsbnd H⋯Cl, Csbnd H⋯Cl, Osbnd H⋯Cl and Nsbnd H⋯O hydrogen bonds to form infinite three-dimensional network. Investigation of intermolecular interactions and crystal packing via Hirshfeld surface analysis reveals that H⋯Cl and Csbnd H⋯Hsbnd C intermolecular interactions are the most abundant contacts of the organic cation in the crystal packing. The crystal contacts enrichments reveals that, the Cd++ … Cl- salt bridges, the Cd⋯O complexation and Osbnd H⋯Cl- and Nsbnd H⋯Cl-strong H-bonds are the driving forces in the packing formation. The presence of twelve independent chloride anions and four organic cation in the asymmetric unit allowed comparing their contact propensities. The 13C and 15N CP-MAS NMR spectra are in agreement with the X-ray structure. Additional characterization of this compound has also been performed by IR spectroscopy.

Synthesis, structural analysis, Hirshfeld surface, spectroscopic characterization and, in vitro, antioxidant activity of a novel organic cyclohexaphosphate

NASA Astrophysics Data System (ADS)

Fezai, Ramzi; Mezni, Ali; Rzaigui, Mohamed

2018-02-01

The new hybrid [4-Cl-2-(CH3)C6H3NH3]6P6O18·2H2O was synthesized under normal conditions of temperature and pressure. Single crystal X-ray diffraction study was used to identify its structure. It revealed that this organic cyclohexaphosphate crystallized in the P 1 bar triclinic space group with a = 10.41 (10) Å b = 10.94 (7) Å, c = 15.45 (10) Å, α = 77.37 (8), β = 89.75 (8)°, γ = 61.69 (7)°, V = 1501 (2) Å3 and Z = 1. In the crystal framework, the assembling of the three dimensional (3D) structure is formed by intermolecular hydrogen bonds and Van Der Waals interactions. A spectroscopic characterization was carried out to elucidate the structure (UV-Vis, FTIR, 31P MAS-NMR and fluorescent properties). The thermal stability was studied by TG-DTA diagrams under argon atmosphere. Furthermore, 3-D Hirshfeld surfaces in combination with 2-D fingerprint plots were carried out. This compound was also evaluated for its antioxidant activity; four tests were done, in vitro, 1,1-diphenyl-2-picrylhydrazyl (DPPH•), hydroxyl scavenging ability (OH•), ferric reducing power (FRP) and ferrous ion chelating (FIC) ability, using ascorbic acid as a control.

Systematic Comparison of Crystal and NMR Protein Structures Deposited in the Protein Data Bank

PubMed Central

Sikic, Kresimir; Tomic, Sanja; Carugo, Oliviero

2010-01-01

Nearly all the macromolecular three-dimensional structures deposited in Protein Data Bank were determined by either crystallographic (X-ray) or Nuclear Magnetic Resonance (NMR) spectroscopic methods. This paper reports a systematic comparison of the crystallographic and NMR results deposited in the files of the Protein Data Bank, in order to find out to which extent these information can be aggregated in bioinformatics. A non-redundant data set containing 109 NMR – X-ray structure pairs of nearly identical proteins was derived from the Protein Data Bank. A series of comparisons were performed by focusing the attention towards both global features and local details. It was observed that: (1) the RMDS values between NMR and crystal structures range from about 1.5 Å to about 2.5 Å; (2) the correlation between conformational deviations and residue type reveals that hydrophobic amino acids are more similar in crystal and NMR structures than hydrophilic amino acids; (3) the correlation between solvent accessibility of the residues and their conformational variability in solid state and in solution is relatively modest (correlation coefficient = 0.462); (4) beta strands on average match better between NMR and crystal structures than helices and loops; (5) conformational differences between loops are independent of crystal packing interactions in the solid state; (6) very seldom, side chains buried in the protein interior are observed to adopt different orientations in the solid state and in solution. PMID:21293729

Spectroscopic properties of heavily Ho3+-doped barium yttrium fluoride crystals

NASA Astrophysics Data System (ADS)

Ji, En-Cai; Liu, Qiang; Nie, Ming-Ming; Luo, Hui; Hu, Yu-Xi; Guan, Zhou-Guo; Gong, Ma-Li

2015-09-01

The 30 at.% Ho: BaY2F8 crystals were grown by the Czochralski method, and their spectroscopic properties are analyzed systematically by standard Judd-Ofelt theory. The Judd-Ofelt intensity parameters are estimated to be Ω2 = 6.74 × 10-20 cm2, Ω4 = 1.20 × 10-20 cm2, and Ω6 = 0.66 × 10-20 cm2, and the fluorescence branching ratios and radiative lifetimes for a series of excited state manifolds are also determined. The emission cross sections with our measured infrared luminescence spectra, especially important for 4.1 μm, are calculated to be about 4.37 × 10-21 cm2. The crystal quality is preliminarily tested through a mid-infrared laser emission experiment. Project supported by the National Natural Science Foundation of China (Grant No. 61275146), the Research Fund for the Doctoral Program of Higher Education of China (Grant No. 20120002110066), and the Special Program of the Co-construction with Beijing Municipal Government of China (Grant No. 20121000302).

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

Synthesis and crystal structure determination of yttrium ultraphosphate YP 5O 14

NASA Astrophysics Data System (ADS)

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

2009-03-01

The crystal structure of monoclinic YP 5O 14 (space group C2/ c, a=12.919(2) Å, b=12.796(4) Å, c=12.457(2) Å, β=91.30(1)°, Z=8) has been refined from single-crystal X-ray diffraction data. Full-matrix least-squares refinement on F2 using 2249 independent reflections for 183 refinable parameters results in a final R value of 0.027 ( ωR=0.069). The structure is isotypic with HoP 5O 14. This structure is built up from infinite layers of PO 4 tetrahedra linked through isolated YO 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 3+ ion incorporated in the monoclinic C2/ c polymorph of YP 5O 14 as local structural probe show that in YP 5O 14: 5% Eu 3+ sample, the Eu 3+ ions are distributed over the two Y 3+ crystallographic sites of C 2 symmetry of this structure.

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.

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.

Synthesis, characterization, crystal structure and quantum chemical investigations of three novel coumarin-benzenesulfonohydrazide derivatives

NASA Astrophysics Data System (ADS)

Chethan Prathap, K. N.; Lokanath, N. K.

2018-04-01

Coumarin derivatives are an important class of heterocyclic compounds due to their physical and biological properties. Coumarin derivatives have been identified with many significant electro-optical properties and biological activities. Three novel coumarin derivatives containing benzene sulfonohydrazide group were synthesized by condensation reaction. The synthesized compounds were characterized by various spectroscopic techniques (Mass, 1H/13C NMR and FTIR). Thermal and optical properties were investigated by thermogravimetric analysis (TGA), differential scanning calorimetry (DSC) and UV-Vis spectroscopic studies. Finally their structures were confirmed by single crystal X-ray diffraction (XRD) studies. The three compounds exhibit diverse intermolecular interactions, as observed by the crystal packing and Hirshfeld surface analysis. Further, their structures were optimized by density functional theory (DFT) calculations using B3LYP hybrid functionals with 6-311G+(d,p) level basis set. The Mulliken charge, molecular electrostatic potential (MEP), frontier molecular orbitals (HOMO-LUMO) were investigated. The experimentally determined parameters were compared with those calculated theoretically and they complement each other with a very good correlation. The transitions among the molecular orbitals were investigated using time-dependent density functional theory (TD-DFT) and the electronic absorption spectra obtained showed very good agreement with the experimentally measured UV-Vis spectra. Furthermore, non-linear optical (NLO) properties were investigated by calculating polarizabilities and hyperpolarizabilities. All three compounds exhibit significantly high hyperpolarizabilities compared to the reference material urea, which makes them potential candidates for NLO applications.

Structure-Dependent Spectroscopic Properties of Yb3+-Doped Phosphosilicate Glasses Modified by SiO₂.

PubMed

Wang, Ling; Zeng, Huidan; Yang, Bin; Ye, Feng; Chen, Jianding; Chen, Guorong; Smith, Andew T; Sun, Luyi

2017-02-28

Yb 3+ -doped phosphate glasses containing different amounts of SiO₂ were successfully synthesized by the conventional melt-quenching method. The influence mechanism of SiO₂ on the structural and spectroscopic properties was investigated systematically using the micro-Raman technique. It was worth noting that the glass with 26.7 mol % SiO₂ possessed the longest fluorescence lifetime (1.51 ms), the highest gain coefficient (1.10 ms·pm²), the maximum Stark splitting manifold of ²F 7/2 level (781 cm -1 ), and the largest scalar crystal-field N J and Yb 3+ asymmetry degree. Micro-Raman spectra revealed that introducing SiO₂ promoted the formation of P=O linkages, but broke the P=O linkages when the SiO₂ content was greater than 26.7 mol %. Based on the previous 29 Si MAS NMR experimental results, these findings further demonstrated that the formation of [SiO₆] may significantly affect the formation of P=O linkages, and thus influences the spectroscopic properties of the glass. These results indicate that phosphosilicate glasses may have potential applications as a Yb 3+ -doped gain medium for solid-state lasers and optical fiber amplifiers.

Comparative spectroscopic analysis of urinary calculi inhibition by Larrea Tridentata infusion and NDGA chemical extract

NASA Astrophysics Data System (ADS)

Manciu, Felicia

2012-10-01

In the present comparative spectroscopic study we try to understand calcium oxalate kidney stone formation as well as its inhibition by using a traditional medicine approach with Larrea Tridentata (LT) herbal extracts and nordihydroguaiaretic acid (NDGA), which is a chemical extract of the LT bush. The samples were synthesized without and with LT or NDGA using a simplified single diffusion gel growth technique. While the use of infusion from LT decreases the sizes of calcium oxalate crystals and also changes their structure from monohydrate for pure crystals to dihydrate for crystals grown with different amounts of inhibitor, both Raman and infrared absorption spectroscopic techniques, which are the methods of analysis employed in this work, reveal that NDGA is not responsible for the change in the morphology of calcium oxalate crystals and does not contribute significantly to the inhibition process. The presence of NDGA slightly affects the structure of the crystals by modifying the strength of the C-C bonds as seen in the Raman data. Also, the current infrared absorption results demonstrate the presence of NDGA in the samples through a vibrational line that corresponds to the double bond between carbon atoms of the ester group of NDGA.

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

PubMed

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

2012-09-01

A series of novel Schiff bases containing pyrazole group were synthesized using 1-aryl-3-methyl-4-benzoyl-5-pyrazolone and phenylenediamine as the starting materials. All as-synthesized Schiff bases were characterized by means of NMR, FT-IR, and MS; and the molecular geometries of two Schiff bases as typical examples were determined by means of single crystal X-ray diffraction. In the meantime, the ultraviolet-visible light absorption spectra and fluorescent spectra of various as-synthesized products were also measured. Moreover, the B3LYP/6-1G(d,p) method was used for the optimization of the ground state geometry of the Schiff bases; and the spectroscopic properties of the products were computed and compared with corresponding experimental data based on cc-pVTZ basis set of TD-B3LYP method. It has been found that all as-synthesized Schiff bases show a remarkable absorption peak in a wavelength range of 270-370 nm; and their maximum emission peaks are around 344 nm and 332 nm, respectively. Copyright © 2012 Elsevier B.V. All rights reserved.

Spectroscopic and neutron detection properties of rare earth and titanium doped LiAlO 2 single crystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dickens, Peter T.; Marcial, José; McCloy, John

In this study, LiAlO2 crystals doped with rare-earth elements and Ti were produced by the CZ method and spectroscopic and neutron detection properties were investigated. Photoluminescence revealed no clear luminescent activation of LiAlO2 by the rare-earth dopants though some interesting luminescence was observed from secondary phases within the crystal. Gamma-ray pulse height spectra collected using a 137Cs source exhibited only a Compton edge for the crystals. Neutron modeling using Monte Carlo N-Particle Transport Code revealed most neutrons used in the detection setup are thermalized, and while using natural lithium in the crystal growth, which contains 7.6 % 6Li, a 10more » mm Ø by 10 mm sample of LiAlO2 has a 70.7 % intrinsic thermal neutron capture efficiency. Furthermore, the pulse height spectra collected using a 241Am-Be neutron source demonstrated a distinct neutron peak.« less

Spectroscopic and neutron detection properties of rare earth and titanium doped LiAlO 2 single crystals

DOE PAGES

Dickens, Peter T.; Marcial, Jose; McCloy, John; ...

2017-05-17

In this study, LiAlO 2 crystals doped with rare-earth elements and Ti were produced by the CZ method and spectroscopic and neutron detection properties were investigated. Photoluminescence revealed no clear luminescent activation of LiAlO 2 by the rare-earth dopants though some interesting luminescence was observed from secondary phases within the crystal. Gamma-ray pulse height spectra collected using a 137Cs source exhibited only a Compton edge for the crystals. Neutron modeling using Monte Carlo N-Particle Transport Code revealed most neutrons used in the detection setup are thermalized, and while using natural lithium in the crystal growth, which contains 7.6% 6Li, amore » 10 mm Ø by 10 mm sample of LiAlO 2 has a 70.7% intrinsic thermal neutron capture efficiency. Furthermore, the pulse height spectra collected using a 241Am-Be neutron source demonstrated a distinct neutron peak.« less

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

PubMed

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

2014-12-10

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. Copyright © 2014 Elsevier B.V. All rights reserved.

Maintenance of supersaturation I: indomethacin crystal growth kinetic modeling using an online second-derivative ultraviolet spectroscopic method.

PubMed

Patel, Dhaval D; Joguparthi, Vijay; Wang, Zeren; Anderson, Bradley D

2011-07-01

Formulations that produce supersaturated solutions after their oral administration have received increased attention as a means to improve bioavailability of poorly water-soluble drugs. Although it is widely recognized that excipients can prolong supersaturation, the mechanisms by which these beneficial effects are realized are generally unknown. Difficulties in separately measuring the kinetics of nucleation and crystal growth have limited progress in understanding the mechanisms by which excipients contribute to the supersaturation maintenance. This paper describes the crystal growth kinetic modeling of indomethacin, a poorly water-soluble drug, from supersaturated aqueous suspensions using a newly developed, online second-derivative ultraviolet spectroscopic method. The apparent indomethacin equilibrium solubility after crystal growth at a high degree of supersaturation (S=6) was approximately 55% higher than the indomethacin equilibrium solubility determined prior to growth, which was attributed to the deposition of a higher energy indomethacin form on the seed crystals. The indomethacin crystal growth kinetics (S=6) was of first order. By comparing the mass transfer coefficients from indomethacin dissolution and crystal growth, it was shown that the indomethacin crystal growth kinetics at S=6 was bulk diffusion controlled. The change in indomethacin seed crystal size distribution before and after crystal growth was determined and modeled using a mass-balance relationship. Copyright © 2011 Wiley-Liss, Inc. and the American Pharmacists Association

Growth, structural, optical, mechanical and quantum chemical analysis of unidirectional grown bis(guanidinium) 5-sulfosalicylate (BGSSA) single crystal

NASA Astrophysics Data System (ADS)

Sreedevi, R.; Saravana Kumar, G.; Amarsingh Bhabu, K.; Balu, T.; Murugakoothan, P.; Rajasekaran, T. R.

2018-02-01

Bis(guanidinium) 5-sulfosalicylate single crystal was grown by using Sankaranarayanan-Ramasamy (SR) method from the solution of methanol and water in equimolar ratio. Good quality crystal with 50 mm length and 10 mm in diameter was grown. The grown crystal was subjected to single crystal X-ray diffraction analysis to confirm the crystal structure and it was found to be orthorhombic. UV-Vis-NIR spectroscopic study revealed that the SR method grown crystal had good optical transparency with wide optical band gap of 4.4 eV. The presence of the functional groups and modes of vibrations were identified by FTIR spectroscopy recorded in the range 4000-400 cm-1. The mechanical strength of the grown crystal was confirmed using Vickers microhardness tester by applying load from 25 g to 100 g. Density functional theory (DFT) method with B3LYP/6-31-G (d,p) level basis set was employed and hence the optimized molecular geometry, first order hyperpolarizability, dipole moment, thermodynamic functions, molecular electrostatic potential and frontier molecular orbital analysis of the grown BGSSA sample was computed and analysed.

Structural and spectroscopic studies of a rare non-oxido V(v) complex crystallized from aqueous solution

DOE PAGES

Leggett, Christina J.; Parker, Bernard F.; Teat, Simon J.; ...

2016-01-14

A “bare” V 5+ complex with glutaroimide-dioxime (H 3L), a ligand for uranium recovery from seawater, was synthesized from aqueous solution as Na[V(L) 2]2H 2O and the structure determined by x-ray diffraction. It is the first non-oxo V(v) complex that has been directly synthesized in and crystallized from aqueous solution.

Structural and spectroscopic studies of a rare non-oxido V(v) complex crystallized from aqueous solution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leggett, Christina J.; Parker, Bernard F.; Teat, Simon J.

A “bare” V 5+ complex with glutaroimide-dioxime (H 3L), a ligand for uranium recovery from seawater, was synthesized from aqueous solution as Na[V(L) 2]2H 2O and the structure determined by x-ray diffraction. It is the first non-oxo V(v) complex that has been directly synthesized in and crystallized from aqueous solution.

Studies on the syntheses, structural Characterization, antimicrobial of the CO-CRYSTAL 1,10-phenanthrolin-1-IUM(1,10-phenH+)-caffeine(caf)-hexafluorophosphate

NASA Astrophysics Data System (ADS)

El Hamdani, H.; El Amane, M.; Duhayon, C.

2018-03-01

Co-crystal of 1,10-phenanthrolin-1-ium-caffeine-hexafluorophosphate was synthesized, studied by FTIR, 1H, 13C NMR, DSC and X-ray structure and crystallized in the monoclinic space group C2/c. The unit cell parameters are a = 19.3761 (3), b = 17.9548 (3), c = 13.8074 (3) with β = 117.8132 (10). The final R value is 0.069 for 29,522 measured reflections. The co-crystal structure analysis indicate the 1,10-phenanthroline is protonated by one nitrogen atom and formed the 1,10-phenanthrolin-1-ium cation, which is stabilized by hydrogen bonds N+-H…Odbnd C interaction with carbonyl and imidazol ring in caffeine molecule. The intermolecular hydrogen bonds: Csbnd H...O, Csbnd H...N, Nsbnd H...O, Csbnd H...F and intramolecular hydrogen bond: C1sbnd H12...O14, together play a vital role in stabilizing the structure of co-crystal. The X-ray structural analysis confirm the assignments of the structure from infrared, 1H, 13C NMR, spectroscopic data DSC and molar conductivity analysis. The antimicrobial activity of the co-crystal was studied.

Crystal structure, spectroscopic study, photoluminescent properties and DFT calculations of the 2-guanidinobenzimidazolium dichloride and dibromide monohydrate salts

NASA Astrophysics Data System (ADS)

Hassen, S.; Chebbi, H.; Zid, M. F.; Arfaoui, Y.

2018-09-01

Two organic salts compounds C8H13Cl2N5O(1) and C8H13Br2N5O(2) were prepared by slow evaporation at room temperature and characterized through single-crystal X-ray diffraction, photoluminescence, IR and UV-Vis diffuse reflectance spectroscopy (UV/DRS) from which the optical properties were determined. The asymmetric unit of (1) and (2) consists of a discrete guanidinobenzimidazolium, two halide anions X- (X = Cl, Br) and one crystallization water molecule. The crystal structures of the two title salts are stabilized by Nsbnd H … X, Osbnd H … X, Nsbnd H⋯O and Csbnd H … X hydrogen bonds. Moreover, the protonated 2-guanidobenzimidazole shows a π-π interaction adding extra stability to the three-dimensional architecture. The ground state geometries of the two compounds were optimized using density functional theory (DFT) at the 6-311+G(2d, 2p) level of theory. In order to study the excited states, time-depending density functional theory calculations were performed on the optimized structures at the same level of theory. The calculated electronic absorption and infrared spectra were in good agreement with the experimental ones.

Growth, structural, optical and surface analysis of piperazinium tartrate: A NLO single crystal

NASA Astrophysics Data System (ADS)

Gupta, Apurva; Raseel Rahman M., K.; Nair, Lekha

2018-05-01

Single crystal of piperazinium tartrate (PPZT) was grown by the slow evaporation solution growth technique at room temperature. Crystallinity of grown crystal was examined by powder X-ray diffraction. High transparency and wide band gap were observed in the UV-Visible spectroscopic studies. Intense and broad emissions were observed in the blue region, as that is indicated by photoluminescence spectroscopy. The quality of the grown PPZT single crystals were analyzed by the etching studies using the water as the etchant.

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.

Synthesis, growth, structure and nonlinear optical properties of a semiorganic 2-carboxy pyridinium dihydrogen phosphate single crystal

NASA Astrophysics Data System (ADS)

Nagapandiselvi, P.; Baby, C.; Gopalakrishnan, R.

2015-09-01

A new semiorganic compound namely, 2-carboxy pyridinium dihydrogen phosphate (2CPDP) was synthesised and grown as single crystals by slow evaporation solution growth technique. Single crystal XRD showed that 2CPDP belongs to monoclinic crystal system with space group P21/n. The molecular structure was further confirmed by modern spectroscopic techniques like FT-NMR (1H, 13C &31P), FT-IR, UV-Vis-NIR and Fluorescence. The UV-Vis-NIR analysis revealed suitability of the crystal for nonlinear optical applications. The photo active nature of the material is established from fluorescence studies. TG-DSC analysis showed that 2CPDP was thermally stable up to 170 °C. The dependence of dielectric properties on frequency and temperature were also studied. Nonlinear optical absorption determined from open aperture Z-Scan analysis by employing picosecond Nd-YAG laser, revealed that 2CPDP can serve as a promising candidate for optical limiting applications.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Soudani, S.; Ferretti, V.; Jelsch, C.

The chemical preparation, crystal structure, Hirshfeld surface analysis and spectroscopic characterization of the novel cadmium (II) 4-hydroxy-1-methylpiperidine complex, Cd{sub 4}Cl{sub 10}(C{sub 6}H{sub 14}NO){sub 2}·2H{sub 2}O, have been reported. The atomic arrangement can be described as built up by an anionic framework, formed by edge sharing CdCl{sub 6} and CdCl{sub 5}O 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 revealsmore » that the H{sub C}⋯Cl and H{sub C}⋯H{sub C} 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 {sup 13}C and {sup 15}N 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.« less

Growth, structural, spectroscopic, thermal, dielectric and optical study of cobalt sulphide-doped ADP crystals

NASA Astrophysics Data System (ADS)

Kochuparampil, A. P.; Joshi, J. H.; Joshi, M. J.

2017-09-01

As ammonium dihydrogen phosphate (ADP) is a popular nonlinear optical crystal, to engineer its linear and nonlinear optical properties, the chalcogenide compound cobalt sulphide (CoS) was doped and the crystals were grown by the slow solvent evaporation method. To increase the solubility of CoS in water, its nanoparticles were synthesized by wet chemical technique using ethylene diamine as the capping agent followed by microwave irradiation. The nanoparticle sample exhibited finite solubility in water and was used to dope in ADP crystals. The powder XRD patterns showed the single phase nature of the doped crystals. The FTIR spectra confirmed the presence of various functional groups and EDAX gave the estimation of Co and S elements. The EPR spectroscopy also confirmed the presence of cobalt in the doped samples. TGA indicated slightly less thermal stability of the doped crystals compared to the pure ADP. The dielectric study was carried out at room temperature in the frequency range from 100Hz to 1MHz. Also, various linear optical parameters were evaluated for pure and doped crystals using UV-Vis spectroscopy. The second harmonic generation (SHG) efficiency of Nd:YAG laser was evaluated by the Kurtz and Parry method for the doped samples, it was found to be slightly lesser than that of the pure ADP crystals.

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

Structural and spectroscopic characterization, reactivity study and charge transfer analysis of the newly synthetized 2-(6-hydroxy-1-benzofuran-3-yl) acetic acid

NASA Astrophysics Data System (ADS)

Murthy, P. Krishna; Krishnaswamy, G.; Armaković, Stevan; Armaković, Sanja J.; Suchetan, P. A.; Desai, Nivedita R.; Suneetha, V.; SreenivasaRao, R.; Bhargavi, G.; Aruna Kumar, D. B.

2018-06-01

The title compound 2-(6-hydroxy-1-benzofuran-3-yl) acetic acid (abbreviated as HBFAA) has been synthetized and characterized by FT-IR, FT-Raman and NMR spectroscopic techniques. Solid state crystal structure of HBFAA has been determined by single crystal X-ray diffraction technique. The crystal structure features O-H⋯O and C-H⋯O intermolecular interactions resulting in a two dimensional supramolecular architecture. The presence of various intermolecular interactions is well supported by the Hirshfeld surface analysis. The molecular properties of HBFAA were performed by Density functional theory (DFT) using B3LYP/6-311G++(d,p) method at ground state in gas phase, compile these results with experimental values and shows mutual agreement. The vibrational spectral analysis were carried out using FT-IR and FT-Raman spectroscopic techniques and assignment of each vibrational wavenumber made on the basis of potential energy distribution (PED). And also frontier orbital analysis (FMOs), global reactivity descriptors, non-linear optical properties (NLO) and natural bond orbital analysis (NBO) of HBFAA were computed with same method. Efforts were made in order to understand global and local reactivity properties of title compound by calculations of MEP, ALIE, BDE and Fukui function surfaces in gas phase, together with thermodynamic properties. Molecular dynamics simulation and radial distribution functions were also used in order to understand the influence of water to the stability of title compound. Charge transfer between molecules of HBFAA has been investigated thanks to the combination of MD simulations and DFT calculations.

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.

Crystal structures of substrate-free and retinoic acid-bound cyanobacterial cytochrome P450 CYP120A1.

PubMed

Kühnel, Karin; Ke, Na; Cryle, Max J; Sligar, Stephen G; Schuler, Mary A; Schlichting, Ilme

2008-06-24

The crystal structures of substrate-free and all-trans-retinoic acid-bound CYP120A1 from Synechocystis sp. PCC 6803 were determined at 2.4 and 2.1 A resolution, respectively, representing the first structural characterization of a cyanobacterial P450. Features of CYP120A1 not observed in other P450 structures include an aromatic ladder flanking the channel leading to the active site and a triple-glycine motif within SRS5. Using spectroscopic methods, CYP120A1 is shown to bind 13-cis-retinoic acid, 9-cis-retinoic acid, and retinal with high affinity and dissociation constants of less than 1 microM. Metabolism of retinoic acid by CYP120A1 suggests that CYP120A1 hydroxylates a variety of retinoid derivatives in vivo. On the basis of the retinoic acid-bound CYP120A1 crystal structure, we propose that either carbon 2 or the methyl groups (C16 or C17) of the beta-ionone ring are modified by CYP120A1.

Solvate Structures and Computational/Spectroscopic Characterization of LiPF6 Electrolytes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Han, Sang D.; Yun, Sung-Hyun; Borodin, Oleg

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 ofmore » 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.« less

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

Polymer:Fullerene Bimolecular Crystals for Near-Infrared Spectroscopic Photodetectors.

PubMed

Tang, Zheng; Ma, Zaifei; Sánchez-Díaz, Antonio; Ullbrich, Sascha; Liu, Yuan; Siegmund, Bernhard; Mischok, Andreas; Leo, Karl; Campoy-Quiles, Mariano; Li, Weiwei; Vandewal, Koen

2017-09-01

Spectroscopic photodetection is a powerful tool in disciplines such as medical diagnosis, industrial process monitoring, or agriculture. However, its application in novel fields, including wearable and biointegrated electronics, is hampered by the use of bulky dispersive optics. Here, solution-processed organic donor-acceptor blends are employed in a resonant optical cavity device architecture for wavelength-tunable photodetection. While conventional photodetectors respond to above-gap excitation, the cavity device exploits weak subgap absorption of intermolecular charge-transfer states of the intercalating poly[2,5-bis(3-tetradecylthiophen-2-yl)thieno[3,2-b]thiophene] (PBTTT):[6,6]-phenyl-C61-butyric acid methyl ester (PCBM) bimolecular crystal. This enables a highly wavelength selective, near-infrared photoresponse with a spectral resolution down to 14 nm, as well as dark currents and detectivities comparable with commercial inorganic photodetectors. Based on this concept, a miniaturized spectrophotometer, comprising an array of narrowband cavity photodetectors, is fabricated by using a blade-coated PBTTT:PCBM thin film with a thickness gradient. As an application example, a measurement of the transmittance spectrum of water by this device is demonstrated. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structural and spectroscopic properties of the polar antiferromagnet N i2MnTe O6

NASA Astrophysics Data System (ADS)

Retuerto, Maria; Skiadopoulou, Stella; Borodavka, Fedir; Kadlec, Christelle; Kadlec, Filip; Prokleška, Jan; Deng, Zheng; Alonso, Jose A.; Fernandez-Diaz, Maria T.; Saouma, Felix O.; Jang, Joon I.; Legut, Dominik; Kamba, Stanislav; Greenblatt, Martha

2018-04-01

We present a structural and spectroscopic study of the compound N i2MnTe O6 , closely related to the polar antiferromagnet N i3Te O6 known to show a colossal magnetoelectric effect and pronounced elementary magnetoelectric excitations. We prepared single crystals and polycrystalline samples of N i2MnTe O6 showing the same polar structure as N i3Te O6 from room temperature down to 4 K with the R 3 space-group symmetry. Magnetic and dielectric measurements have indicated an antiferromagnetic phase transition at TN≈70 K , almost 20 K higher than that of N i3Te O6 . Extensive infrared, Raman, and terahertz spectroscopy experiments were employed for investigating lattice and spin excitations, revealing all phonons predicted by the factor group analysis. Terahertz spectra below TN reveal one new excitation, which is strongly influenced by external magnetic field, thus assigned to a magnon.

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.

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

NASA Astrophysics Data System (ADS)

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

2013-09-01

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

Use of Crystal Structure Informatics for Defining the Conformational Space Needed for Predicting Crystal Structures of Pharmaceutical Molecules.

PubMed

Iuzzolino, Luca; Reilly, Anthony M; McCabe, Patrick; Price, Sarah L

2017-10-10

Determining the range of conformations that a flexible pharmaceutical-like molecule could plausibly adopt in a crystal structure is a key to successful crystal structure prediction (CSP) studies. We aim to use conformational information from the crystal structures in the Cambridge Structural Database (CSD) to facilitate this task. The conformations produced by the CSD Conformer Generator are reduced in number by considering the underlying rotamer distributions, an analysis of changes in molecular shape, and a minimal number of molecular ab initio calculations. This method is tested for five pharmaceutical-like molecules where an extensive CSP study has already been performed. The CSD informatics-derived set of crystal structure searches generates almost all the low-energy crystal structures previously found, including all experimental structures. The workflow effectively combines information on individual torsion angles and then eliminates the combinations that are too high in energy to be found in the solid state, reducing the resources needed to cover the solid-state conformational space of a molecule. This provides insights into how the low-energy solid-state and isolated-molecule conformations are related to the properties of the individual flexible torsion angles.

Structure-Dependent Spectroscopic Properties of Yb3+-Doped Phosphosilicate Glasses Modified by SiO2

PubMed Central

Wang, Ling; Zeng, Huidan; Yang, Bin; Ye, Feng; Chen, Jianding; Chen, Guorong; Smith, Andew T.; Sun, Luyi

2017-01-01

Yb3+-doped phosphate glasses containing different amounts of SiO2 were successfully synthesized by the conventional melt-quenching method. The influence mechanism of SiO2 on the structural and spectroscopic properties was investigated systematically using the micro-Raman technique. It was worth noting that the glass with 26.7 mol % SiO2 possessed the longest fluorescence lifetime (1.51 ms), the highest gain coefficient (1.10 ms·pm2), the maximum Stark splitting manifold of 2F7/2 level (781 cm−1), and the largest scalar crystal-field NJ and Yb3+ asymmetry degree. Micro-Raman spectra revealed that introducing SiO2 promoted the formation of P=O linkages, but broke the P=O linkages when the SiO2 content was greater than 26.7 mol %. Based on the previous 29Si MAS NMR experimental results, these findings further demonstrated that the formation of [SiO6] may significantly affect the formation of P=O linkages, and thus influences the spectroscopic properties of the glass. These results indicate that phosphosilicate glasses may have potential applications as a Yb3+-doped gain medium for solid-state lasers and optical fiber amplifiers. PMID:28772601

Structural and spectroscopic investigation of glycinium oxalurate

NASA Astrophysics Data System (ADS)

Kavitha, T.; Pasupathi, G.; Marchewka, M. K.; Anbalagan, G.; Kanagathara, N.

2017-09-01

Glycinium oxalurate (GO) single crystals has been synthesized and grown by the slow solvent evaporation method at room temperature. Single crystal X-ray diffraction study confirms that GO crystal crystallizes in the monoclinic system with centrosymmetric space group P121/c1. The grown crystals are built up from single protonated glycinium residues and single dissociated oxalurate anions. A combination of ionic and donor-acceptor hydrogen-bond interactions linking together the glycine and oxaluric acid residues forms a three-dimensional network. Hydrogen bonded network present in the crystal gives notable vibrational effect. The molecular geometry, vibrational frequencies and intensity of the vibrational bands have been interpreted with the aid of structure optimization based on HF and density functional theory B3LYP methods with 6-311++G(d,p) basis set. Frontier molecular orbital energies and other related electronic properties are calculated. The natural bonding orbital (NBO) charges have been calculated and interpreted. The molecular electrostatic potential map has been constructed and discussed in detail.

A New Star-shaped Carbazole Derivative with Polyhedral Oligomeric Silsesquioxane Core: Crystal Structure and Unique Photoluminescence Property.

PubMed

Xu, Zixuan; Yu, Tianzhi; Zhao, Yuling; Zhang, Hui; Zhao, Guoyun; Li, Jianfeng; Chai, Lanqin

2016-01-01

A new inorganic–organic hybrid material based on polyhedral oligomeric silsesquioxane (POSS) capped with carbazolyl substituents, octakis[3-(carbazol-9-yl)propyldimethylsiloxy]-silsesquioxane (POSS-8Cz), was successfully synthesized and characterized. The X-ray crystal structure of POSS-8Cz were described. The photophysical properties of POSS-8Cz were investigated by using UV–vis,photoluminescence spectroscopic analysis. The hybrid material exhibits blue emission in the solution and the solid film.The morphology and thermal stablity properties were measured by X-ray diffraction (XRD) and TG-DTA analysis.

Crystal field analysis of the energy level structure of Cs2NaAlF6:Cr3+

NASA Astrophysics Data System (ADS)

Rudowicz, C.; Brik, M. G.; Avram, N. M.; Yeung, Y. Y.; Gnutek, P.

2006-06-01

An analysis of the energy level structure of Cr3+ ions in Cs2NaAlF6 crystal is performed using the exchange charge model (ECM) together with the crystal field analysis/microscopic spin Hamiltonian (CFA/MSH) computer package. Utilizing the crystal structure data, our approach enables modelling of the crystal field parameters (CFPs) and thus the energy level structure for Cr3+ ions at the two crystallographically inequivalent sites in Cs2NaAlF6. Using the ECM initial adjustment procedure, the CFPs are calculated in the crystallographic axis system centred at the Cr3+ ion at each site. Additionally the CFPs are also calculated using the superposition model (SPM). The ECM and SPM predicted CFP values match very well. Consideration of the symmetry aspects for the so-obtained CFP datasets reveals that the latter axis system matches the symmetry-adapted axis system related directly to the six Cr-F bonds well. Using the ECM predicted CFPs as an input for the CFA/MSH package, the complete energy level schemes are calculated for Cr3+ ions at the two sites. Comparison of the theoretical results with the experimental spectroscopic data yields satisfactory agreement. Our results confirm that the actual symmetry at both impurity sites I and II in the Cs2NaAlF6:Cr3+ system is trigonal D3d. The ECM predicted CFPs may be used as the initial (starting) parameters for simulations and fittings of the energy levels for Cr3+ ions in structurally similar hosts.

Integrative interactive visualization of crystal structure, band structure, and Brillouin zone

NASA Astrophysics Data System (ADS)

Hanson, Robert; Hinke, Ben; van Koevering, Matthew; Oses, Corey; Toher, Cormac; Hicks, David; Gossett, Eric; Plata Ramos, Jose; Curtarolo, Stefano; Aflow Collaboration

The AFLOW library is an open-access database for high throughput ab-initio calculations that serves as a resource for the dissemination of computational results in the area of materials science. Our project aims to create an interactive web-based visualization of any structure in the AFLOW database that has associate band structure data in a way that allows novel simultaneous exploration of the crystal structure, band structure, and Brillouin zone. Interactivity is obtained using two synchronized JSmol implementations, one for the crystal structure and one for the Brillouin zone, along with a D3-based band-structure diagram produced on the fly from data obtained from the AFLOW database. The current website portal (http://aflowlib.mems.duke.edu/users/jmolers/matt/website) allows interactive access and visualization of crystal structure, Brillouin zone and band structure for more than 55,000 inorganic crystal structures. This work was supported by the US Navy Office of Naval Research through a Broad Area Announcement administered by Duke University.

Structural variability of E. coli thioredoxin captured in the crystal structures of single-point mutants

PubMed Central

Noguera, Martín E.; Vazquez, Diego S.; Ferrer-Sueta, Gerardo; Agudelo, William A.; Howard, Eduardo; Rasia, Rodolfo M.; Manta, Bruno; Cousido-Siah, Alexandra; Mitschler, André; Podjarny, Alberto; Santos, Javier

2017-01-01

Thioredoxin is a ubiquitous small protein that catalyzes redox reactions of protein thiols. Additionally, thioredoxin from E. coli (EcTRX) is a widely-used model for structure-function studies. In a previous paper, we characterized several single-point mutants of the C-terminal helix (CTH) that alter global stability of EcTRX. However, spectroscopic signatures and enzymatic activity for some of these mutants were found essentially unaffected. A comprehensive structural characterization at the atomic level of these near-invariant mutants can provide detailed information about structural variability of EcTRX. We address this point through the determination of the crystal structures of four point-mutants, whose mutations occurs within or near the CTH, namely L94A, E101G, N106A and L107A. These structures are mostly unaffected compared with the wild-type variant. Notably, the E101G mutant presents a large region with two alternative traces for the backbone of the same chain. It represents a significant shift in backbone positions. Enzymatic activity measurements and conformational dynamics studies monitored by NMR and molecular dynamic simulations show that E101G mutation results in a small effect in the structural features of the protein. We hypothesize that these alternative conformations represent samples of the native-state ensemble of EcTRX, specifically the magnitude and location of conformational heterogeneity. PMID:28181556

Structural variability of E. coli thioredoxin captured in the crystal structures of single-point mutants

NASA Astrophysics Data System (ADS)

Noguera, Martín E.; Vazquez, Diego S.; Ferrer-Sueta, Gerardo; Agudelo, William A.; Howard, Eduardo; Rasia, Rodolfo M.; Manta, Bruno; Cousido-Siah, Alexandra; Mitschler, André; Podjarny, Alberto; Santos, Javier

2017-02-01

Thioredoxin is a ubiquitous small protein that catalyzes redox reactions of protein thiols. Additionally, thioredoxin from E. coli (EcTRX) is a widely-used model for structure-function studies. In a previous paper, we characterized several single-point mutants of the C-terminal helix (CTH) that alter global stability of EcTRX. However, spectroscopic signatures and enzymatic activity for some of these mutants were found essentially unaffected. A comprehensive structural characterization at the atomic level of these near-invariant mutants can provide detailed information about structural variability of EcTRX. We address this point through the determination of the crystal structures of four point-mutants, whose mutations occurs within or near the CTH, namely L94A, E101G, N106A and L107A. These structures are mostly unaffected compared with the wild-type variant. Notably, the E101G mutant presents a large region with two alternative traces for the backbone of the same chain. It represents a significant shift in backbone positions. Enzymatic activity measurements and conformational dynamics studies monitored by NMR and molecular dynamic simulations show that E101G mutation results in a small effect in the structural features of the protein. We hypothesize that these alternative conformations represent samples of the native-state ensemble of EcTRX, specifically the magnitude and location of conformational heterogeneity.

A soft X-ray spectroscopic perspective of electron localization and transport in tungsten doped bismuth vanadate single crystals.

PubMed

Jovic, Vedran; Rettie, Alexander J E; Singh, Vijay R; Zhou, Jianshi; Lamoureux, Bethany; Buddie Mullins, C; Bluhm, Hendrik; Laverock, Jude; Smith, Kevin E

2016-11-23

Doped BiVO 4 is a promising photoelectrochemical water splitting anode, whose activity is hampered by poor charge transport. Here we use a set of X-ray spectroscopic methods to probe the origin and nature of localized electron states in W:BiVO 4 . Furthermore, using the polarized nature of the X-rays, we probe variations in the electronic structure along the crystal axes. In this manner, we reveal aspects of the electronic structure related to electron localization and observations consistent with conductivity anisotropy between the ab-plane and c-axis. We verify that tungsten substitutes as W 6+ for V 5+ in BiVO 4 . This is shown to result in the presence of inter-band gap states related to electrons at V 4+ sites of e symmetry. The energetic position of the states in the band gap suggest that they are highly localized and may act as recombination centres. Polarization dependent X-ray absorption spectra reveal anisotropy in the electronic structure between the ab-plane and c-axis. Results show the superior hybridization between V 3d and O 2p states, higher V wavefunction overlap and broader conduction bands in the ab-plane than in the c-axis. These insights into the electronic structure are discussed in the context of existing experimental and theoretical reports regarding charge transport in BiVO 4 .

Spectroscopic analysis and efficient diode-pumped 1.9 μm Tm3+-doped β'-Gd2(MoO4)3 crystal laser.

PubMed

Tang, Jianfeng; Chen, Yujin; Lin, Yanfu; Gong, Xinghong; Huang, Jianhua; Luo, Zundu; Huang, Yidong

2011-07-04

Tm3+-doped β'-Gd2(MoO4)3 single crystal was grown by the Czochralski method. Spectroscopic analysis was carried out along different polarizations. End-pumped by a quasi-cw diode laser at 795 nm in a plano-concave cavity, an average laser output power of 58 mW around 1.9 μm was achieved in a 0.93-mm-thick crystal when the output coupler transmission was 7.1%. The absorbed pump threshold was 8 mW and the slope efficiency of the laser was 57%. This crystal has smooth and broad gain curve around 1.9 μm, which shows that it is also a potential gain medium for tunable and short pulse lasers.

Colour centres and nanostructures on the surface of laser crystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kulagin, N A

2012-11-30

This paper presents a study of structural and radiationinduced colour centres in the bulk and ordered nanostructures on the surface of doped laser crystals: sapphire, yttrium aluminium garnet and strontium titanate. The influence of thermal annealing, ionising radiation and plasma exposure on the spectroscopic properties of high-purity materials and crystals containing Ti, V and Cr impurities is examined. Colour centres resulting from changes in the electronic state of impurities and plasma-induced surface modification of the crystals are studied by optical, EPR and X-ray spectroscopies, scanning electron microscopy and atomic force microscopy. X-ray line valence shift measurements are used to assessmore » changes in the electronic state of some impurity and host ions in the bulk and on the surface of oxide crystals. Conditions are examined for the formation of one- and two-level arrays of ordered crystallites 10{sup -10} to 10{sup -7} m in size on the surface of crystals doped with irongroup and lanthanoid ions. The spectroscopic properties of the crystals are analysed using ab initio self-consistent field calculations for Me{sup n+} : [O{sup 2-}]{sub k} clusters. (interaction of laser radiation with matter. laser plasma)« less

Computed crystal energy landscapes for understanding and predicting organic crystal structures and polymorphism.

PubMed

Price, Sarah Sally L

2009-01-20

The phenomenon of polymorphism, the ability of a molecule to adopt more than one crystal structure, is a well-established property of crystalline solids. The possible variations in physical properties between polymorphs make the reliable reproduction of a crystalline form essential for all research using organic materials, as well as quality control in manufacture. Thus, the last two decades have seen both an increase in interest in polymorphism and the availability of the computer power needed to make the computational prediction of organic crystal structures a practical possibility. In the past decade, researchers have made considerable improvements in the theoretical basis for calculating the sets of structures that are within the energy range of possible polymorphism, called crystal energy landscapes. It is common to find that a molecule has a wide variety of ways of packing with lattice energy within a few kilojoules per mole of the most stable structure. However, as we develop methods to search for and characterize "all" solid forms, it is also now usual for polymorphs and solvates to be found. Thus, the computed crystal energy landscape reflects and to an increasing extent "predicts" the emerging complexity of the solid state observed for many organic molecules. This Account will discuss the ways in which the calculation of the crystal energy landscape of a molecule can be used as a complementary technique to solid form screening for polymorphs. Current methods can predict the known crystal structure, even under "blind test" conditions, but such successes are generally restricted to those structures that are the most stable over a wide range of thermodynamic conditions. The other low-energy structures can be alternative polymorphs, which have sometimes been found in later experimental studies. Examining the computed structures reveals the various compromises between close packing, hydrogen bonding, and pi-pi stacking that can result in energetically feasible

Spectroscopic and molecular docking studies on the interaction of human serum albumin with copper(II) complexes

NASA Astrophysics Data System (ADS)

Guhathakurta, Bhargab; Pradhan, Ankur Bikash; Das, Suman; Bandyopadhyay, Nirmalya; Lu, Liping; Zhu, Miaoli; Naskar, Jnan Prakash

2017-02-01

Two osazone based ligands, butane-2,3-dione bis(2‧-pyridylhydrazone) (BDBPH) and hexane-3,4-dione bis(2‧-pyridylhydrazone) (HDBPH), were synthesized out of the 2:1 M Schiff base condensation of 2-hydrazino pyridine respectively with 2,3-butanedione and 3,4-hexanedione. The X-ray crystal structures of both the ligands have been determined. The copper(II) complex of HDBPH has also been synthesized and structurally characterized. HDBPH and its copper(II) complex have thoroughly been characterized through various spectroscopic and analytical techniques. The X-ray crystal structure of the copper complex of HDBPH shows that it is a monomeric Cu(II) complex having 'N4O2' co-ordination chromophore. Interaction of human serum albumin (HSA) with these ligands and their monomeric copper(II) complexes have been studied by various spectroscopic means. The experimental findings show that the ligands as well as their copper complexes are good HSA binders. Molecular docking investigations have also been done to unravel the mode of binding of the species with HSA.

Mid-infrared fiber-coupled supercontinuum spectroscopic imaging using a tapered chalcogenide photonic crystal fiber

NASA Astrophysics Data System (ADS)

Rosenberg Petersen, Christian; Prtljaga, Nikola; Farries, Mark; Ward, Jon; Napier, Bruce; Lloyd, Gavin Rhys; Nallala, Jayakrupakar; Stone, Nick; Bang, Ole

2018-02-01

We present the first demonstration of mid-infrared spectroscopic imaging of human tissue using a fiber-coupled supercontinuum source spanning from 2-7.5 μm. The supercontinuum was generated in a tapered large mode area chalcogenide photonic crystal fiber in order to obtain broad bandwidth, high average power, and single-mode output for good imaging properties. Tissue imaging was demonstrated in transmission by raster scanning over a sub-mm region of paraffinized colon tissue on CaF2 substrate, and the signal was measured using a fiber-coupled grating spectrometer. This demonstration has shown that we can distinguish between epithelial and surrounding connective tissues within a paraffinized section of colon tissue by imaging at discrete wavelengths related to distinct chemical absorption features.

Crystal structure and infrared spectra of dicesium trans-tetraaquadichlorochromium(III) chloride

NASA Astrophysics Data System (ADS)

Neumann, E.; Stefov, V.; Šoptrajanov, B.; Engelen, B.; Lutz, H. D.

2004-12-01

The crystal structure of dicesium trans-tetraaquadichlorochromium(III) chloride Cs 2Cr IIICl 5·4H 2O with trans-[M IIIX 2(H 2O) 4] + complex ions (space group C2/c, Z=4, a=1915.3(4) pm, b=614.1(1) pm, c=1392.0(3) pm, and β=118.24(3)°, final R1=0.0246 for 2100 unique reflections) was redetermined by single-crystal X-ray diffraction studies. It was found to crystallize in a 2c super structure of the structure reported previously (Inorg. Chem. 20 (1981) 1566; Inorg. Chem. 36 (1997) 2248). The obtained structure data now agree with the results of infrared spectroscopic studies, which has been confirmed in this work, namely that there are two different hydrate H 2O molecules in the structure. Phase transitions, static or dynamic disorder of the hydrate H 2O molecules, and space group C2/m proposed in the literature were ruled out. The coordinates of the four hydrogen positions derived from the X-ray data have been improved via the O-H distances derived from the wave numbers of the OD stretching modes of matrix isolated HDO molecules (2426, 2323, and 2306 cm -1, 263 K) by using the νOD versus rO-H correlation curve reported in the literature (J. Mol. Struct. 404 (1997) 63). The νOD versus rH⋯Cl correlation curve reported by Mikenda (J. Mol. Struct. 147 (1986) 1) should be improved, especially for strong hydrogen bonds. The two hydrate H 2O molecules of the title compound are strongly distorted with a weak and a relatively strong O-H⋯Cl hydrogen bond each thus intramolecular coupling of the two OH stretching vibrations to coupled ones is largely reduced and, hence, the wavenumbers of the OH and OD stretching modes of the HDO molecules mainly resemble those of the H 2O and D 2O molecules. The strength of the hydrogen bonds is in accordance with the predictions of the competitive and synergetic effects. Chloro ligands are weaker hydrogen bond acceptor groups than chloride ions.

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

PubMed

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

2014-12-01

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

Spectroscopic ellipsometry study of Cu2ZnSnS4 bulk poly-crystals

NASA Astrophysics Data System (ADS)

Levcenko, S.; Hajdeu-Chicarosh, E.; Garcia-Llamas, E.; Caballero, R.; Serna, R.; Bodnar, I. V.; Victorov, I. A.; Guc, M.; Merino, J. M.; Pérez-Rodriguez, A.; Arushanov, E.; León, M.

2018-04-01

The linear optical properties of Cu2ZnSnS4 bulk poly-crystals have been investigated using spectroscopic ellipsometry in the range of 1.2-4.6 eV at room temperature. The characteristic features identified in the optical spectra are explained by using the Adachi analytical model for the interband transitions at the corresponding critical points in the Brillouin zone. The experimental data have been modeled over the entire spectral range taking into account the lowest E0 transition near the fundamental absorption edge and E1A and E1B higher energy interband transitions. In addition, the spectral dependences of the refractive index, extinction coefficient, absorption coefficient, and normal-incidence reflectivity values have been accurately determined and are provided since they are essential data for the design of Cu2ZnSnS4 based optoelectronic devices.

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.

High-speed prediction of crystal structures for organic molecules

NASA Astrophysics Data System (ADS)

Obata, Shigeaki; Goto, Hitoshi

2015-02-01

We developed a master-worker type parallel algorithm for allocating tasks of crystal structure optimizations to distributed compute nodes, in order to improve a performance of simulations for crystal structure predictions. The performance experiments were demonstrated on TUT-ADSIM supercomputer system (HITACHI HA8000-tc/HT210). The experimental results show that our parallel algorithm could achieve speed-ups of 214 and 179 times using 256 processor cores on crystal structure optimizations in predictions of crystal structures for 3-aza-bicyclo(3.3.1)nonane-2,4-dione and 2-diazo-3,5-cyclohexadiene-1-one, respectively. We expect that this parallel algorithm is always possible to reduce computational costs of any crystal structure predictions.

Spectroscopic characterizations of organic/inorganic nanocomposites

NASA Astrophysics Data System (ADS)

Govani, Jayesh R.

2009-12-01

In the present study, pure and 0.3 wt%, 0.4 wt%, as well as 0.5 wt% L-arginine doped potassium dihydrogen phosphate (KDP) crystals were grown using solution growth techniques and further subjected to infrared (IR) absorption and Raman studies for confirmation of chemical group functionalization for investigating the incorporation mechanism of the L-arginine organic material into the KDP crystal structure. Infrared spectroscopic analysis suggests that structural changes are occurring for the L-arginine molecule as a result of its interaction with the KPD crystal. Infrared spectroscopic technique confirms the disturbance of the N-H, C-H and C-N bonds of the amino acid, suggesting successful incorporation of L-arginine into the KDP crystals. Raman analysis also reveals modification of the N-H, C-H and C-N bonds of the amino acid, implying successful inclusion of L-arginine into the KDP crystals. With the help of Gaussian software, a prediction of possible incorporation mechanisms of the organic material was obtained from comparison of the simulated infrared and Raman vibrational spectra with the experimental results. Furthermore, we also studied the effect of L-arginine doping on the thermal stability of the grown KDP crystal by employing Thermo gravimetric analysis (TGA). TGA suggests that increasing the level of L-arginine doping speeds the decomposition process and it weakens the KDP crystal, which indicates successful doping of the KDP crystals with L-arginine amino acid. Urinary stones are one of the oldest and most widely spread diseases in humans, animals and birds. Many remedies have been employed through the ages for the treatment of urinary stones. Recent medicinal measures reflect the modern advances, which are based on surgical removal, percutaneous techniques and extracorporeal shock wave lithotripsy (ESWL). Although these procedures are valuable, they are quite expensive for most people. Furthermore, recurrence of these diseases is awfully frequent with

Spectroscopic and structural study of novel interaction product of pyrrolidine-2-thione with molecular iodine. Presumable mechanisms of oxidation

NASA Astrophysics Data System (ADS)

Chernov'yants, Margarita S.; Burykin, Igor V.; Starikova, Zoya A.; Tereznikov, Alexander Yu.; Kolesnikova, Tatiana S.

2013-09-01

Synthesis, spectroscopic and structural characterization of novel interaction product of pyrrolidine-2-thione with molecular iodine is reported. The ability of pyrrolidine-2-thione to form the outer-sphere charge-transfer complex C4H7NS·I2 with iodine molecule in dilute chloroform solution has been studied by UV/vis spectroscopy. Oxidative desulfurization promotes ring fusion of two pyrrolidine-2-thione molecules. The product of iodine induced oxidative desulfurization has been studied by X-ray diffraction method. The crystal structure of the reaction product is formed by 5-(2-thioxopyrrolidine-1-yl)-3,4-dihydro-2H-pyrrolium (C8H13N2S+) cations and pentaiodide anions I5-, which are linked by the intermolecular I⋯Hsbnd C and I⋯C close contacts. The angular pentaiodide anions can be considered as structures formed by coordination of two iodine molecules to the iodide ion (type 1) or by the coordination of iodine molecule to the triiodide ion (type 2).

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.

Synthesis, crystal structure, photoluminescence and electrochemical properties of a sandwiched Ni2Ce complex

NASA Astrophysics Data System (ADS)

Güngör, Seyit Ali; Kose, Muhammet

2017-12-01

In this study, a Ni2Ce complex [(NiL)2Ce(NO3)2](NO3) was synthesized and characterized by spectroscopic and analytical methods. The structure of the complex was determined by single crystal X-ray diffraction study. In the structure of the complex, a Ce(III) ion is sandwiched between the two NiL units, which are virtually parallel to each other. The Ce(III) center is 12-coordinate, surrounded by 12 oxygen atoms; four are from phenolic groups, four from methoxy groups, and four from two bidentate nitrate ligands. Hirshfeld surface analysis was used to evaluate the inter-molecular interactions within the crystal packing. The complex molecules are linked by H⋯ONO2 interactions. The largest contribution is H⋯O/O⋯H with 41.6% contribution and followed by H⋯H contacts with 39.1%. The complex showed an excitation band in the range of 510-580 nm. A band in the range of 520-580 nm observed in the emission spectrum almost completely overlapped. This suggests that the band in the emission spectrum of the complex is not the actual fluorescence emission and is assigned to the Rayleigh scattering band. Electrochemical and thermal behaviours of the complex were also investigated.

Cytotoxicity of copper(II)-complexes with some S-alkyl derivatives of thiosalicylic acid. Crystal structure of the binuclear copper(II)-complex with S-ethyl derivative of thiosalicylic acid

NASA Astrophysics Data System (ADS)

Nikolić, Miloš V.; Mijajlović, Marina Ž.; Jevtić, Verica V.; Ratković, Zoran R.; Novaković, Slađana B.; Bogdanović, Goran A.; Milovanović, Jelena; Arsenijević, Aleksandar; Stojanović, Bojana; Trifunović, Srećko R.; Radić, Gordana P.

2016-07-01

The spectroscopically predicted structure of the obtained copper(II)-complex with S-ethyl derivative of thiosalicylic acid was confirmed by X-ray structural study and compared to previously reported crystal structure of the Cu complex with S-methyl derivative. Single crystals suitable for X-ray measurements were obtained by slow crystallization from a water solution. Cytotoxic effects of S-alkyl (R = benzyl (L1), methyl (L2), ethyl (L3), propyl (L4) and butyl (L5)) derivatives of thiosalicylic acid and the corresponding binuclear copper(II)-complexes on murine colon carcinoma cell lines, CT26 and CT26.CL25 and human colon carcinoma cell line HCT-116 were reported here. The analysis of cancer cell viability showed that all the tested complexes had low cytotoxic effect on murine colon carcinoma cell lines, but several times higher cytotoxicity on normal human colon carcinoma cells.

Tungsten Incorporation into Gallium Oxide: Crystal Structure, Surface and Interface Chemistry, Thermal Stability and Interdiffusion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rubio, E. J.; Mates, T. E.; Manandhar, S.

Tungsten (W) incorporated gallium oxide (Ga2O3) (GWO) thin films were deposited by radio-frequency magnetron co-sputtering of W-metal and Ga2O3-ceramic targets. Films were produced by varying sputtering power applied to the W-target in order to achieve variable W-content (0-12 at%) into Ga2O3 while substrate temperature was kept constant at 500 °C. Chemical composition, chemical valence states, microstructure and crystal structure of as-deposited and annealed GWO films were evaluated as a function of W-content. The structural and chemical analyses indicate that the samples deposited without any W-incorporation are stoichiometric, nanocrystalline Ga2O3 films, which crystallize in β-phase monoclinic structure. While GWO films alsomore » crystallize in monoclinic β-Ga2O3 phase, W-incorporation induces surface amorphization as revealed by structural studies. The chemical valence state of Ga ions probed by X-ray photoelectron spectroscopic (XPS) analyses is characterized by the highest oxidation state i.e., Ga3+. No changes in Ga chemical state are noted for variable W-incorporation in the range of 0-12 at%. Rutherford backscattering spectrometry (RBS) analyses indicate the uniform distribution of W-content in the GWO films. However, XPS analyses indicate the formation of mixed valence states for W ions, which may be responsible for surface amorphization in GWO films. GWO films were stable up to 900 oC, at which point thermally induced secondary phase (W-oxide) formation was observed. A transition to mesoporous structure coupled with W interdiffusion occurs due to thermal annealing as derived from the chemical analyses at the GWO films’ surface as well as depth-profiling towards the GWO-Si interface. A model has been formulated to account for the mechanism of W-incorporation, thermal stability and interdiffusion via pore formation in GWO films.« less

Synthesis, crystal structure and optical properties of two new layered cadmium iodates: Cd(IO{sub 3})X (X=Cl, OH)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Bing-Ping, E-mail: ybp@fjirsm.ac.cn; Mao, Jiang-Gao

Systematic explorations of new compounds in the cadmium iodate system by hydrothermal reactions led to two layered iodates, namely, Cd(IO{sub 3})X (X=Cl, OH). Cd(IO{sub 3})Cl crystallizes in the orthorhombic space group Cmca (No. 64) whereas Cd(IO{sub 3})(OH) crystallizes in the orthorhombic space group Pnma (No. 62). Cd(IO{sub 3})Cl displays a unique double layered structure composed of {sup 1}{sub ∞}[Cd−O{sub 3}Cl]{sub n} chains. Cadmium octahedrons form a 1D chain along the a-axis through edge sharing, and such chains are further interconnected via IO{sub 3} groups to form a special double layer on (020) plane. Cd(IO{sub 3})(OH) also exhibits a layered structuremore » that is composed of cadmium cations, IO{sub 3} groups and hydroxyl ions. Within a layer, chains of CdO{sub 6} edge-shared octahedra are observed along the b-axis. And these chains are connected by IO{sub 3} groups into a layer parallel to the bc plane. Spectroscopic characterizations, elemental analysis, and thermogravimetric analysis for the reported two compounds are also presented. - Graphical abstract: Two new layered cadmium iodates Cd(IO{sub 3})X (X=Cl, OH) are reported. Cd(IO{sub 3})Cl features a unique double layered structure whereas Cd(IO{sub 3})(OH) displays an ordinary layered structure. - Highlights: • Two new layered cadmium iodates Cd(IO{sub 3})X (X=Cl, OH) are reported. • Cd(IO{sub 3})Cl features a unique double layered structure. • Cd(IO{sub 3})(OH) displays an ordinary layered structure. • The spectroscopic and thermal properties have been studied in detail.« less

Crystal structure, spectral, thermal and dielectric studies of a new zinc benzoate single crystal

NASA Astrophysics Data System (ADS)

Bijini, B. R.; Prasanna, S.; Deepa, M.; Nair, C. M. K.; Rajendra Babu, K.

2012-11-01

Single crystals of zinc benzoate with a novel structure were grown in gel media. Sodium metasilicate of gel density 1.04 g/cc at pH 6 was employed to yield transparent single crystals. The crystal structure of the compound was ascertained by single crystal X-ray diffractometry. It was noted that the crystal belongs to monoclinic system with space group P21/c with unit cell parameters a = 10.669(1) Å, b = 12.995(5) Å, c = 19.119(3) Å, and β = 94.926(3)°. The crystal was seen to possess a linear polymeric structure along b-axis; with no presence of coordinated or lattice water. CHN analysis established the stoichiometric composition of the crystal. The existence of functional groups present in the single crystal system was confirmed by FT-IR studies. The thermal characteristic of the sample was analysed by TGA-DTA techniques, and the sample was found to be thermally stable up to 280 °C. The kinetic and thermodynamic parameters were also determined. UV-Vis spectroscopy corroborated the transparency of the crystal and revealed the optical band gap to be 4 eV. Dielectric studies showed decrease in the dielectric constant of the sample with increase in frequency.

A nearly on-axis spectroscopic system for simultaneously measuring UV-visible absorption and X-ray diffraction in the SPring-8 structural genomics beamline.

PubMed

Sakaguchi, Miyuki; Kimura, Tetsunari; Nishida, Takuma; Tosha, Takehiko; Sugimoto, Hiroshi; Yamaguchi, Yoshihiro; Yanagisawa, Sachiko; Ueno, Go; Murakami, Hironori; Ago, Hideo; Yamamoto, Masaki; Ogura, Takashi; Shiro, Yoshitsugu; Kubo, Minoru

2016-01-01

UV-visible absorption spectroscopy is useful for probing the electronic and structural changes of protein active sites, and thus the on-line combination of X-ray diffraction and spectroscopic analysis is increasingly being applied. Herein, a novel absorption spectrometer was developed at SPring-8 BL26B2 with a nearly on-axis geometry between the X-ray and optical axes. A small prism mirror was placed near the X-ray beamstop to pass the light only 2° off the X-ray beam, enabling spectroscopic analysis of the X-ray-exposed volume of a crystal during X-ray diffraction data collection. The spectrometer was applied to NO reductase, a heme enzyme that catalyzes NO reduction to N2O. Radiation damage to the heme was monitored in real time during X-ray irradiation by evaluating the absorption spectral changes. Moreover, NO binding to the heme was probed via caged NO photolysis with UV light, demonstrating the extended capability of the spectrometer for intermediate analysis.

Spectroscopic ellipsometry in vacuum ultraviolet spectral area

NASA Astrophysics Data System (ADS)

Fuchs, Detlef

An ellipsometer is developed and built, which allows the direct spectroscopic evaluation of dielectric function of solid bodies in the energy area 5 to 35 eV. A linear polarized synchrotron radiation was used as light source. The Stokes parameters and the Mueller matrices were used for the mathematical modeling, which take into account the properties of the synchrotron light and the analyzer, which depend on the wavelength. The crystals of the semiconductor bindings GaAs, GaP, InP and ZnS were examined. Ellipsometric measurements and reflection spectra show a displacement of spectral structures towards lower photon energies after the storage.

Non-covalent interactions in 2-methylimidazolium copper(II) complex (MeImH)2[Cu(pfbz)4]: Synthesis, characterization, single crystal X-ray structure and packing analysis

NASA Astrophysics Data System (ADS)

Sharma, Raj Pal; Saini, Anju; Kumar, Santosh; Kumar, Jitendra; Sathishkumar, Ranganathan; Venugopalan, Paloth

2017-01-01

A new anionic copper(II) complex, (MeImH)2 [Cu(pfbz)4] (1) where, MeImH = 2-methylimidazolium and pfbz = pentafluorobenzoate has been isolated by reacting copper(II) sulfate pentahydrate, pentafluorobenzoic acid and 2-methylimidazole in ethanol: water mixture in 1:2:2 molar ratio. This complex 1 has been characterized by elemental analysis, thermogravimetric analysis, spectroscopic techniques (UV-Vis, FT-IR) and conductance measurements. The complex salt crystallizes in monoclinic crystal system with space group C2/c. Single crystal X-ray structure determination revealed the presence of discrete ions: [Cu(pfbz)4]2- anion and two 2-methylimidazolium cation (C4H7N2)+. The crystal lattice is stabilized by strong hydrogen bonding and F⋯F interactions between cationic-anionic and the anionic-anionic moieties respectively, besides π-π interactions.

Dual exposure, two-photon, conformal phasemask lithography for three dimensional silicon inverse woodpile photonic crystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shir, Daniel J.; Nelson, Erik C.; Chanda, Debashis

2010-01-01

The authors describe the fabrication and characterization of three dimensional silicon inverse woodpile photonic crystals. A dual exposure, two-photon, conformal phasemask technique is used to create high quality polymer woodpile structures over large areas with geometries that quantitatively match expectations based on optical simulations. Depositing silicon into these templates followed by the removal of the polymer results in silicon inverse woodpile photonic crystals for which calculations indicate a wide, complete photonic bandgap over a range of structural fill fractions. Spectroscopic measurements of normal incidence reflection from both the polymer and siliconphotonic crystals reveal good optical properties.

Crystal structure and conformational analysis of s-cis-(acetylacetonato)(ethylenediamine-N,N'-diacetato)-chromium(III): development of vibrationally optimized force field (VOFF).

PubMed

Choi, Jong-Ha; Niketić, Svetozar R; Djordjević, Ivana; Clegg, William; Harrington, Ross W

2012-05-01

The crystal structure of [Cr(edda)(acac)] (edda = ethylediamine-N,N'-diacetate; acac = acetylacetonato) has been determined by a single crystal X-ray diffraction study at 150 K. The chromium ion is in a distorted octahedral environment coordinated by two N and two O atoms of chelating edda and two O atoms of acac, resulting in s-cis configuration. The complex crystallizes in the space group P2(1)/c of the monoclinic system in a cell of dimensions a = 10.2588(9), b = 15.801(3), c = 8.7015(11) Å, β =101.201(9)° and Z = 4. The mean Cr-N(edda), Cr-O(edda) and Cr-O(acac) bond distances are 2.0829(14), 1.9678(11) and 1.9477(11) Å while the angles O-Cr-O of edda and O-Cr-O of acac are 171.47(5) and 92.72(5)°, respectively. The crystal structure is stabilized by N-H···O hydrogen bonds linking [Cr(edda)(acac)] molecules in distinct linear strands. The visible electronic and IR spectroscopic properties are also discussed. An improved, physically more realistic force field, Vibrationally Optimized Force Field (VOFF), capable of reproducing structural and vibrational properties of [Cr(edda)(acac)] was developed and its transferability demonstrated on selected chromium(III) complexes with similar ligands.

Compact & Ultra-High Resolution Terahertz Spectroscopic/Fingerprint System

DTIC Science & Technology

2011-05-11

successfully fusion - spliced with commercial silica fibers for the first time, which makes the whole MOPA system monolithic. Fig. 7 (a) shows the output...QPM-GaP crystals and the proposed THz crystal fiber converters for high power parametric THz source, THz waveguide modeling for high efficiency and...THz spectroscopic/fingerprinting system. We have achieved 0.212 mJ fiber laser pulses with transform-limited linewidth, bonded QPM-GaP crystals and

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.

Cadmium (II) macrocyclic Schiff-base complexes containing piperazine moiety: Synthesis, spectroscopic, X-ray structure, theoretical and antibacterial studies

NASA Astrophysics Data System (ADS)

Keypour, Hassan; Mahmoudabadi, Masoumeh; Shooshtari, Amir; Bayat, Mehdi; Mohsenzadeh, Fariba; Gable, Robert William

2018-03-01

The new Cd(II) macrocyclic Schiff-base complexes were prepared via the metal templated [1 + 1] cyclocondensation of 2,2'-(piperazine-1,4-diylbis (methylene))dianiline (A) and 2,6-pyridinedicarbaldehyde or 2,6-diacetylpyridine. The products were characterized by elemental analysis, mass spectrometry and spectroscopic methods such as: FT-IR, 1H and 13C-NMR, the crystal structure of [CdL1(ClO4)2](CH3CN) (1) complex was also obtained by single-crystal X-ray crystallography. The complexes were tested for in vitro antibacterial properties against some bacteria. The complexes had antibacterial properties and in some cases were active even more than standards. The geometries of the [CdLn (ClO4)2], (n = 1,2) complexes have been optimized at the BP86/def2-SVP level of theory. Also the nature of Cd←Ln (n = 1, 2) bonds in [CdLn (ClO4)2], (n = 1,2) complexes are studied with the help of NBO and Energy decomposition analysis (EDA). Results showed that the nature of metal-ligand bond in the complexes is slightly more electrostatic with a contribution of about 52% in total interaction energy.

Synthesis, growth, structural, spectroscopic and optical studies of a new semiorganic nonlinear optical crystal: L-valine hydrochloride.

PubMed

Kirubavathi, K; Selvaraju, K; Valluvan, R; Vijayan, N; Kumararaman, S

2008-04-01

Single crystals of a new semiorganic nonlinear optical (NLO) material, L-valine hydrochloride (LVHCl), having dimensions up to 20 mm x 6 mm x 4 mm have been grown by slow evaporation solution growth technique. Single crystal X-ray diffraction studies confirm that the grown crystal belongs to the monoclinic system. The functional groups presented in the crystal were confirmed by Fourier transform infrared (FTIR) technique. Optical transmission spectrum shows very low absorption in the entire visible region. Differential thermal and thermogravimetric analyses confirmed that the crystal is stable up to 211 degrees C. The powder second harmonic generation (SHG) efficiency of LVHCl is 1.7 times efficient as potassium dihydrogen phosphate (KDP).

Li{sub 2}Ca{sub 2}Si{sub 2}O{sub 7}: Structural, spectroscopic and computational studies on a sorosilicate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kahlenberg, Volker, E-mail: volker.kahlenberg@uibk.ac.at; Brunello, Emanuele; Hejny, Clivia

2015-05-15

Synthesis experiments in the system Li{sub 2}O–CaO–SiO{sub 2} resulted in the formation of single-crystals of Li{sub 2}Ca{sub 2}Si{sub 2}O{sub 7}. Structural investigations were based on single-crystal diffraction. At ambient conditions the compound has the following basic crystallographic data: hexagonal symmetry, space group P6{sub 1}22, a=5.0961(2) Å, c=41.264(2) Å, V=928.07(6) Å{sup 3}, 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 [Si{sub 2}O{sub 7}]-groups. Additional lithium and calcium cations are incorporated between the silicate dimers andmore » are coordinated by four and six nearest oxygen neighbours, respectively. Each [LiO{sub 4}]-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 6{sub 1}{sup [0} {sup 0} {sup 1]}-screw axes. From the corner-sharing [LiO{sub 4}]- and [SiO{sub 4}]-moieties a three dimensional framework can be constructed. An interesting feature of this framework is the presence of an O{sup [3]}-type bridging oxygen linking three tetrahedra (one [LiO{sub 4}]- and two [SiO{sub 4}]-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 Li{sub 2}Ca{sub 2}Si{sub 2}O{sub 7} was investigated by in{sub -}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 α{sub ij} 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

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.

Computational and spectroscopic studies of a new Schiff base 3-hydroxy-4-methoxybenzylidene(2-hydroxyphenyl)amine and molecular structure of its corresponding zwitterionic form.

PubMed

Habibi, Mohammad Hossein; Shojaee, Elahe; Ranjbar, Mahnaz; Memarian, Hamid Reza; Kanayama, Akihiko; Suzuki, Takayoshi

2013-03-15

Computational and spectroscopic properties of a novel Schiff base compound, 3-hydroxy-4-methoxybenzylidene(2-hydroxyphenyl)amine were studied. The crystal structures of the title compound and its corresponding zwitterionic form were analyzed by X-ray diffraction. The presence of N-H, C-O and C=N stretching vibrations in IR spectrum strongly suggest that the title compound has zwitterionic form in the solid state. Molecular geometry of the title compound in the ground state has been calculated using the density functional method (DFT) at B3LYP 6-31++G(d,p) basis set and was compared with the experimental data. The calculated results of the title compound show that the optimized geometry can well reproduce the crystal structure. The molecule shows absorption bands at 345 and 363 nm in EtOH. The shoulder-shaped bands at 415 nm can be assigned to n→π(*) transitions. The absorption band is observed at 285 nm in EtOH corresponds to the π→π(*) transitions. Copyright © 2012 Elsevier B.V. All rights reserved.

Vibrational spectroscopic studies of an organic non-linear optical crystal 8-hydroxyquinolinium picrate

NASA Astrophysics Data System (ADS)

Krishna Kumar, V.; Nagalakshmi, R.

2007-04-01

8-Hydroxyquinolinium picrate (8-HQP) was synthesized by the addition of equimolar quantities of 8-hydroxyquinoline (8-HQ) and picric acid (PA). Single crystals were grown from N, N dimethyl formamide (DMF) by restricted evaporation method at room temperature. The solubility of 8-HQP was determined in different solvents at various temperatures. The structural characterization of the grown crystals was carried out by X-ray diffraction. Vibrational modes were classified on the basis of group theoretical analysis and the spectral bands were compared with those of parent compounds in order to propose a tentative assignment by recording FT-IR, FT-Raman and polarized Raman spectra in different crystal orientations. The crystal possess lower cut-off at 230 nm and good transparency as confirmed by optical transmittance studies.

Morphological, spectroscopic and thermal studies of samarium chloride coordinated single crystal grown by slow evaporation method

NASA Astrophysics Data System (ADS)

Slathia, Goldy; Raina, Bindu; Gupta, Rashmi; Bamzai, K. K.

2018-05-01

The synthesis of samarium chloride coordinated single crystal was carried out at room temperature by slow evaporation method. The crystal possesses a well defined hexagonal morphology with six symmetrically equivalent growth sectors separated by growth boundaries. The theoretical morphology has been established by structural approach using Bravaise-Friedele-Donnaye-Harker (BFDH) law. Fourier transform infra red spectroscopy was carried in order to study the geometry and structure of the crystal. The detailed thermogravimetric analysis elucidates the thermal stability of the complex.

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.

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.

Likelihood-based modification of experimental crystal structure electron density maps

DOEpatents

Terwilliger, Thomas C [Sante Fe, NM

2005-04-16

A maximum-likelihood method for improves an electron density map of an experimental crystal structure. A likelihood of a set of structure factors {F.sub.h } is formed for the experimental crystal structure as (1) the likelihood of having obtained an observed set of structure factors {F.sub.h.sup.OBS } if structure factor set {F.sub.h } was correct, and (2) the likelihood that an electron density map resulting from {F.sub.h } is consistent with selected prior knowledge about the experimental crystal structure. The set of structure factors {F.sub.h } is then adjusted to maximize the likelihood of {F.sub.h } for the experimental crystal structure. An improved electron density map is constructed with the maximized structure factors.

Synthesis, crystal structures and Hirshfeld surface analyses of two new Salen type nickel/sodium heteronuclear complexes

NASA Astrophysics Data System (ADS)

Mahlooji, Niloofar; Behzad, Mahdi; Tarahhomi, Atekeh; Maroney, Michael; Rudbari, Hadi Amiri; Bruno, Giuseppe; Ghanbari, Bahram

2016-04-01

Two new heteronuclear Nickel(II)/Sodium(I) complexes of a side-off compartmental Schiff base ligand were synthesized and characterized by spectroscopic methods. Crystal structures of both of the complexes were also obtained. The Schiff base ligand was synthesized from the condensation of meso-1,2-diphenyl-1,2-ethylenediamine with 2-hydroxy-3-methoxybenzaldehyde. In both of the complexes the Ni(II) ion is coordinated to the inner N2O2 coordination sphere with square-planar geometry and the Na(I) ion is coordinated to the outer O2 O2‧ coordination sphere. In Complex (1) with general formula [Ni(L)Na(CH3OH)(ClO4)] the sodium ion is seven coordinated while in (2) with general formula [{Ni(L)Na(OH2)}2(μ-Ni(CN)4)] the sodium ion is six coordinated. Intermolecular interactions in two studied complexes were analyzed using 3D Hirshfeld surfaces and corresponding 2D fingerprint plots. This analysis showed that the H … H and C … H/H … C contacts for both structures (altogether 67.5% of total Hirshfeld surface area for (1) and 77.6% for (2)) and the O … H/H … O (24.2%) for (1) and the N … H/H … N (8.1%) contacts for (2) were the characteristic intermolecular contacts in the related crystal structures.

Band structures in fractal grading porous phononic crystals

NASA Astrophysics Data System (ADS)

Wang, Kai; Liu, Ying; Liang, Tianshu; Wang, Bin

2018-05-01

In this paper, a new grading porous structure is introduced based on a Sierpinski triangle routine, and wave propagation in this fractal grading porous phononic crystal is investigated. The influences of fractal hierarchy and porosity on the band structures in fractal graidng porous phononic crystals are clarified. Vibration modes of unit cell at absolute band gap edges are given to manifest formation mechanism of absolute band gaps. The results show that absolute band gaps are easy to form in fractal structures comparatively to the normal ones with the same porosity. Structures with higher fractal hierarchies benefit multiple wider absolute band gaps. This work provides useful guidance in design of fractal porous phononic crystals.

Construction of crystal structure prototype database: methods and applications.

PubMed

Su, Chuanxun; Lv, Jian; Li, Quan; Wang, Hui; Zhang, Lijun; Wang, Yanchao; Ma, Yanming

2017-04-26

Crystal structure prototype data have become a useful source of information for materials discovery in the fields of crystallography, chemistry, physics, and materials science. This work reports the development of a robust and efficient method for assessing the similarity of structures on the basis of their interatomic distances. Using this method, we proposed a simple and unambiguous definition of crystal structure prototype based on hierarchical clustering theory, and constructed the crystal structure prototype database (CSPD) by filtering the known crystallographic structures in a database. With similar method, a program structure prototype analysis package (SPAP) was developed to remove similar structures in CALYPSO prediction results and extract predicted low energy structures for a separate theoretical structure database. A series of statistics describing the distribution of crystal structure prototypes in the CSPD was compiled to provide an important insight for structure prediction and high-throughput calculations. Illustrative examples of the application of the proposed database are given, including the generation of initial structures for structure prediction and determination of the prototype structure in databases. These examples demonstrate the CSPD to be a generally applicable and useful tool for materials discovery.

Construction of crystal structure prototype database: methods and applications

NASA Astrophysics Data System (ADS)

Su, Chuanxun; Lv, Jian; Li, Quan; Wang, Hui; Zhang, Lijun; Wang, Yanchao; Ma, Yanming

2017-04-01

Crystal structure prototype data have become a useful source of information for materials discovery in the fields of crystallography, chemistry, physics, and materials science. This work reports the development of a robust and efficient method for assessing the similarity of structures on the basis of their interatomic distances. Using this method, we proposed a simple and unambiguous definition of crystal structure prototype based on hierarchical clustering theory, and constructed the crystal structure prototype database (CSPD) by filtering the known crystallographic structures in a database. With similar method, a program structure prototype analysis package (SPAP) was developed to remove similar structures in CALYPSO prediction results and extract predicted low energy structures for a separate theoretical structure database. A series of statistics describing the distribution of crystal structure prototypes in the CSPD was compiled to provide an important insight for structure prediction and high-throughput calculations. Illustrative examples of the application of the proposed database are given, including the generation of initial structures for structure prediction and determination of the prototype structure in databases. These examples demonstrate the CSPD to be a generally applicable and useful tool for materials discovery.

Crystal structure of low-symmetry rondorfite

NASA Astrophysics Data System (ADS)

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

2008-03-01

The crystal structure of an aluminum-rich variety of the mineral rondorfite with the composition Ca16[Mg2(Si7Al)(O31OH)]Cl4 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) Å, b = 15.110(2) Å, c = 15.092(2) Å, α = 90.06(1)°, β = 90.01(1)°, γ = 89.93(1)°, 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 > 3σ( 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 Å, sp. gr. Fd overline 3 , seven independent positions) with anisotropic displacement parameters to R = 2.74% based on 579 reflections with F > 3σ( F) without accounting for more than 1000 observed reflections, which are inconsistent with the cubic symmetry of the crystal structure.

Crystal structures of the GCaMP calcium sensor reveal the mechanism of fluorescence signal change and aid rational design.

PubMed

Akerboom, Jasper; Rivera, Jonathan D Vélez; Guilbe, María M Rodríguez; Malavé, Elisa C Alfaro; Hernandez, Hector H; Tian, Lin; Hires, S Andrew; Marvin, Jonathan S; Looger, Loren L; Schreiter, Eric R

2009-03-06

The genetically encoded calcium indicator GCaMP2 shows promise for neural network activity imaging, but is currently limited by low signal-to-noise ratio. We describe x-ray crystal structures as well as solution biophysical and spectroscopic characterization of GCaMP2 in the calcium-free dark state, and in two calcium-bound bright states: a monomeric form that dominates at intracellular concentrations observed during imaging experiments and an unexpected domain-swapped dimer with decreased fluorescence. This series of structures provides insight into the mechanism of Ca2+-induced fluorescence change. Upon calcium binding, the calmodulin (CaM) domain wraps around the M13 peptide, creating a new domain interface between CaM and the circularly permuted enhanced green fluorescent protein domain. Residues from CaM alter the chemical environment of the circularly permuted enhanced green fluorescent protein chromophore and, together with flexible inter-domain linkers, block solvent access to the chromophore. Guided by the crystal structures, we engineered a series of GCaMP2 point mutants to probe the mechanism of GCaMP2 function and characterized one mutant with significantly improved signal-to-noise. The mutation is located at a domain interface and its effect on sensor function could not have been predicted in the absence of structural data.

Crystal engineering of ibuprofen compounds: From molecule to crystal structure to morphology prediction by computational simulation and experimental study

NASA Astrophysics Data System (ADS)

Zhang, Min; Liang, Zuozhong; Wu, Fei; Chen, Jian-Feng; Xue, Chunyu; Zhao, Hong

2017-06-01

We selected the crystal structures of ibuprofen with seven common space groups (Cc, P21/c, P212121, P21, Pbca, Pna21, and Pbcn), which was generated from ibuprofen molecule by molecular simulation. The predicted crystal structures of ibuprofen with space group P21/c has the lowest total energy and the largest density, which is nearly indistinguishable with experimental result. In addition, the XRD patterns for predicted crystal structure are highly consistent with recrystallization from solvent of ibuprofen. That indicates that the simulation can accurately predict the crystal structure of ibuprofen from the molecule. Furthermore, based on this crystal structure, we predicted the crystal habit in vacuum using the attachment energy (AE) method and considered solvent effects in a systematic way using the modified attachment energy (MAE) model. The simulation can accurately construct a complete process from molecule to crystal structure to morphology prediction. Experimentally, we observed crystal morphologies in four different polarity solvents compounds (ethanol, acetonitrile, ethyl acetate, and toluene). We found that the aspect ratio decreases of crystal habits in this ibuprofen system were found to vary with increasing solvent relative polarity. Besides, the modified crystal morphologies are in good agreement with the observed experimental morphologies. Finally, this work may guide computer-aided design of the desirable crystal morphology.

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.

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

Crystal structure of minoxidil at low temperature and polymorph prediction.

PubMed

Martín-Islán, Africa P; Martín-Ramos, Daniel; Sainz-Díaz, C Ignacio

2008-02-01

An experimental and theoretical investigation on crystal forms of the popular and ubiquitous pharmaceutical Minoxidil is presented here. A new crystallization method is presented for Minoxidil (6-(1-piperidinyl)-2,4-pyrimidinediamide 3-oxide) in ethanol-poly(ethylene glycol), yielding crystals with good quality. The crystal structure is determined at low temperature, with a final R value of 0.035, corresponding to space group P2(1) (monoclinic) with cell dimensions a = 9.357(1) A, b = 8.231(1) A, c = 12.931(2) A, and beta = 90.353(4) degrees . Theoretical calculations of the molecular structure of Minoxidil are set forward using empirical force fields and quantum-mechanical methods. A theoretical prediction for Minoxidil crystal structure shows many possible polymorphs. The predicted crystal structures are compared with X-ray experimental data obtained in our laboratory, and the experimental crystal form is found to be one of the lowest energy polymorphs.

New investigations of the guanine trichloro cuprate(II) complex crystal

NASA Astrophysics Data System (ADS)

Fabijanić, Ivana; Matković-Čalogović, Dubravka; Pilepić, Viktor; Ivanišević, Irena; Mohaček-Grošev, Vlasta; Sanković, Krešimir

2017-01-01

Crystals of the guanine trichloro cuprate(II) complex, (HGua)2[Cu2Cl6]·2H2O (HGua = protonated guanine), were prepared and analysed by spectroscopic (IR, Raman) and computational methods. A new single-crystal X-ray diffraction analysis was conducted to obtain data with lower standard uncertainties than those in the previously published structure. Raman and IR spectroscopy and quantum-mechanical analysis gave us new insight into the vibrational states of the (HGua)2[Cu2Cl6]·2H2O crystal. The vibrational spectra of the crystal were assigned by performing a normal coordinate analysis for a free dimer with a centre of inversion as the only symmetry element. The stretching vibration observed at 279 cm-1 in the infrared spectrum corresponds to the N-Cu bond. The noncovalent interaction (NCI) plots and quantum theory of atoms in molecules (QTAIM) analysis of the electron density obtained from periodic DFT calculations elucidated the interactions that exist within the crystal structure. Closed-shell ionic attractions, as well as weak and medium strength hydrogen bonds, prevailed in the crystal packing.

Spectroscopic, single crystal X-ray, Hirshfeld, in vitro and in silico biological evaluation of a new series of potent thiazole nucleus integrated with pyrazoline scaffolds

NASA Astrophysics Data System (ADS)

Salian, Vinutha V.; Narayana, Badiadka; Sarojini, Balladka K.; Kumar, Madan S.; Nagananda, Govinahalli S.; Byrappa, Kullaiah; Kudva, Avinash K.

2017-03-01

In the present study, the spectroscopic characterization of a new series of substituted thiazole linked pyrazoline scaffolds 4a-l was performed. The formation of 4a-l from the intermediate 3-(4-chlorophenyl)-5-[4-(propan-2-yl)phenyl]-4,5-dihydro-1H-pyrazole-1-carbothioamide 2 and substituted 2-bromo-1-phenylethanone 3a-l was evidenced through the changes in FTIR, 1H NMR, 13C NMR, LCMS data. The X-ray diffraction studies revealed that compound 2 and 4g crystallized in monoclinic crystal system with P21/n space group. Compound 4j crystallized in triclinic system, P1¯ space group with Z = 4. The percentage of intermolecular contacts and distribution of electrostatic potential of molecular crystal structures was resolved by Hirshfeld surface analysis with 2D finger plots and electrostatic potential map. The newly synthesized derivatives were screened for their in vitro antioxidant and antimicrobial activity. The single crystal studies revealed that, for compounds 2, 4g and 4j the isopropyl phenyl ring is positioned at near right angle with the other rings. Due to the lack of planarity of bulkier group substituted to phenyl ring (ring B), all the synthesized molecules showed weak to moderate radical scavenging capacity owing to the destabilization of the radical formed during oxidation. Also, on performing molecular docking studies to explore the interactions of ligand with the target pyrimidine nucleoside hydrolase YbeK with bound ribose complex (PNH, PDB ID-3GHW), disclosed that active compounds emerged for in vitro studies also bound to PNH more efficiently. The compounds with polar group substitution interacted through hydrogen bonding while other molecules with non-covalent interactions.

Crystallographic, Spectroscopic, and Computational Analysis of a Flavin-C4a-Oxygen Adduct in Choline Oxidase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Orville, A.M.; Lountos, G. T.; Finnegan, S.

2009-02-03

Flavin C4a-OO(H) and C4a-OH adducts are critical intermediates proposed in many flavoenzyme reaction mechanisms, but they are rarely detected even by rapid transient kinetics methods. We observe a trapped flavin C4a-OH or C4a-OO(H) adduct by single-crystal spectroscopic methods and in the 1.86 {angstrom} resolution X-ray crystal structure of choline oxidase. The microspectrophotometry results show that the adduct forms rapidly in situ at 100 K upon exposure to X-rays. Density functional theory calculations establish the electronic structures for the flavin C4a-OH and C4a-OO(H) adducts and estimate the stabilization energy of several active site hydrogen bonds deduced from the crystal structure. Wemore » propose that the enzyme-bound FAD is reduced in the X-ray beam. The aerobic crystals then form either a C4a-OH or C4a-OO(H) adduct, but an insufficient proton inventory prevents their decay at cryogenic temperatures.« less

Crystallographic, Spectroscopic, and Computational Analysis of a Flavin C4a-Oxygen Adduct in Choline Oxidase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Orville, A.; Lountos, G; Finnegan, S

2009-01-01

Flavin C4a-OO(H) and C4a-OH adducts are critical intermediates proposed in many flavoenzyme reaction mechanisms, but they are rarely detected even by rapid transient kinetics methods. We observe a trapped flavin C4a-OH or C4a-OO(H) adduct by single-crystal spectroscopic methods and in the 1.86 {angstrom} resolution X-ray crystal structure of choline oxidase. The microspectrophotometry results show that the adduct forms rapidly in situ at 100 K upon exposure to X-rays. Density functional theory calculations establish the electronic structures for the flavin C4a-OH and C4a-OO(H) adducts and estimate the stabilization energy of several active site hydrogen bonds deduced from the crystal structure. Wemore » propose that the enzyme-bound FAD is reduced in the X-ray beam. The aerobic crystals then form either a C4a-OH or C4a-OO(H) adduct, but an insufficient proton inventory prevents their decay at cryogenic temperatures.« less

From molecule to solid: The prediction of organic crystal structures

NASA Astrophysics Data System (ADS)

Dzyabchenko, A. V.

2008-10-01

A method for predicting the structure of a molecular crystal based on the systematic search for a global potential energy minimum is considered. The method takes into account unequal occurrences of the structural classes of organic crystals and symmetry of the multidimensional configuration space. The programs of global minimization PMC, comparison of crystal structures CRYCOM, and approximation to the distributions of the electrostatic potentials of molecules FitMEP are presented as tools for numerically solving the problem. Examples of predicted structures substantiated experimentally and the experience of author’s participation in international tests of crystal structure prediction organized by the Cambridge Crystallographic Data Center (Cambridge, UK) are considered.

Structural Color Patterns by Electrohydrodynamic Jet Printed Photonic Crystals.

PubMed

Ding, Haibo; Zhu, Cun; Tian, Lei; Liu, Cihui; Fu, Guangbin; Shang, Luoran; Gu, Zhongze

2017-04-05

In this work, we demonstrate the fabrication of photonic crystal patterns with controllable morphologies and structural colors utilizing electrohydrodynamic jet (E-jet) printing with colloidal crystal inks. The final shape of photonic crystal units is controlled by the applied voltage signal and wettability of the substrate. Optical properties of the structural color patterns are tuned by the self-assembly of the silica nanoparticle building blocks. Using this direct printing technique, it is feasible to print customized functional patterns composed of photonic crystal dots or photonic crystal lines according to relevant printing mode and predesigned tracks. This is the first report for E-jet printing with colloidal crystal inks. Our results exhibit promising applications in displays, biosensors, and other functional devices.

Crystal Structure Prediction via Deep Learning.

PubMed

Ryan, Kevin; Lengyel, Jeff; Shatruk, Michael

2018-06-06

We demonstrate the application of deep neural networks as a machine-learning tool for the analysis of a large collection of crystallographic data contained in the crystal structure repositories. Using input data in the form of multi-perspective atomic fingerprints, which describe coordination topology around unique crystallographic sites, we show that the neural-network model can be trained to effectively distinguish chemical elements based on the topology of their crystallographic environment. The model also identifies structurally similar atomic sites in the entire dataset of ~50000 crystal structures, essentially uncovering trends that reflect the periodic table of elements. The trained model was used to analyze templates derived from the known binary and ternary crystal structures in order to predict the likelihood to form new compounds that could be generated by placing elements into these structural templates in combinatorial fashion. Statistical analysis of predictive performance of the neural-network model, which was applied to a test set of structures never seen by the model during training, indicates its ability to predict known elemental compositions with a high likelihood of success. In ~30% of cases, the known compositions were found among top-10 most likely candidates proposed by the model. These results suggest that the approach developed in this work can be used to effectively guide the synthetic efforts in the discovery of new materials, especially in the case of systems composed of 3 or more chemical elements.

Crystal Structure of Hydrazinium Iodide by Neutron Diffraction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Campbell, Eric V.; Wang, Xiaoping; Miller, Joel S.

The structure of hydrazinium iodide, [H 5N 2] +·I -, at 100 K has monoclinic (P2 1/n) symmetry from single crystal neutron diffraction with a = 7.4599(7) Å, b = 5.3185(6) Å, c = 10.1628(11) Å, β = 103.150(10)°, V = 392.64(7) Å 3, Z = 4. The refinement converged to R = 0.0575, wR 2 = 0.1602, S = 1.022. Data for the crystal structure was collected on the SNS TOPAZ single-crystal time-of-flight Laue diffractometer. The compound has a one-dimensional structure which displays N–H···N hydrogen bonding. Finally, accurate intra- and intermolecular N–H distances have been determined.

Crystal Structure of Hydrazinium Iodide by Neutron Diffraction

DOE PAGES

Campbell, Eric V.; Wang, Xiaoping; Miller, Joel S.

2017-10-31

The structure of hydrazinium iodide, [H 5N 2] +·I -, at 100 K has monoclinic (P2 1/n) symmetry from single crystal neutron diffraction with a = 7.4599(7) Å, b = 5.3185(6) Å, c = 10.1628(11) Å, β = 103.150(10)°, V = 392.64(7) Å 3, Z = 4. The refinement converged to R = 0.0575, wR 2 = 0.1602, S = 1.022. Data for the crystal structure was collected on the SNS TOPAZ single-crystal time-of-flight Laue diffractometer. The compound has a one-dimensional structure which displays N–H···N hydrogen bonding. Finally, accurate intra- and intermolecular N–H distances have been determined.

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.

Synthesis, crystal structure, spectroscopic characterization, docking simulation and density functional studies of 1-(3,4-dimethoxyphenyl) -3-(4-flurophenyl)-propan-1-one

NASA Astrophysics Data System (ADS)

Khamees, Hussien Ahmed; Jyothi, Mahima; Khanum, Shaukath Ara; Madegowda, Mahendra

2018-06-01

The compound 1-(3,4-dimethoxyphenyl)-3-(4-flurophenyl)-propan-1-one (DFPO) was synthesized by Claisen-Schmidt condensation reaction and the single crystals were obtained by slow evaporation method. Three-dimensional structure was confirmed by single crystal X-ray diffraction method and exhibiting the triclinic crystal system with space group P-1. The crystal structure is stabilized by Csbnd H⋯O intermolecular and weak interactions. Computed molecular geometry has been obtained by density functional theory (DFT) and compared with experimental results. The spectra of both FT-IR in the range (4000-400 cm-1) and FT- Raman (3500-50 cm-1) of DFPO were recorded experimentally and computed by (DFT) using B3LYP/6-311G (d,p) as basis sets. Intramolecular charge transfer has been scanned using natural bond orbital (NBO) analysis and revealed the various contribution of bonding and lone pair to the stabilization of molecule. Nonlinear optical activity (NLO) of the title compound has been determined by second harmonic generation (SHG) and computed using DFT method. Hyperpolarizability, HOMO-LUMO energy gap, hardness, softness electronegativity and others Global reactivity descriptors of DFPO has been calculated and revealed complete picture of chemical reactivity of DFPO. Hirshfeld surface analyses were applied to investigate the intermolecular interactions and revealed that more than two-thirds of the inter contacts are associated with O⋯H, C⋯H and H⋯H interactions. Docking studies of DFPO showed inhibition of Vascular endothelial growth Factor human receptor (VEGFR-2) signalling pathway, which indicates DFPO as anti-angiogenesis, that play pivotal role in cancer, so we suggest it for clinical studies to evaluate its potential to treat human cancers.

Crystal structures of carbonates up to Mbar pressures determined by single crystal synchrotron radiation diffraction

NASA Astrophysics Data System (ADS)

Merlini, M.

2013-12-01

The recent improvements at synchrotron beamlines, currently allow single crystal diffraction experiments at extreme pressures and temperatures [1,2] on very small single crystal domains. We successfully applied such technique to determine the crystal structure adopted by carbonates at mantle pressures. The knowledge of carbon-bearing phases is in fact fundamental for any quantitative modelling of global carbon cycle. The major technical difficulty arises after first order transitions or decomposition reactions, since original crystal (apx. 10x10x5 μm3) is transformed in much smaller crystalline domains often with random orientation. The use of 3D reciprocal space visualization software and the improved resolution of new generation flat panel detectors, however, allow both identification and integration of each single crystal domain, with suitable accuracy for ab-initio structure solution, performed with direct and charge-flipping methods and successive structure refinements. The results obtained on carbonates, indicate two major crystal-chemistry trends established at high pressures. The CO32- units, planar and parallel in ambient pressure calcite and dolomite structures, becomes non parallel in calcite- and dolomite-II and III phases, allowing more flexibility in the structures with possibility to accommodate strain arising from different cation sizes (Ca and Mg in particular). Dolomite-III is therefore also observed to be thermodynamically stable at lower mantle pressures and temperatures, differently from dolomite, which undergoes decomposition into pure end-members in upper mantle. At higher pressure, towards Mbar (lowermost mantle and D'' region) in agreement with theoretical calculations [3,4] and other experimental results [5], carbon coordination transform into 4-fold CO4 units, with different polymerisation in the structure depending on carbonate composition. The second important crystal chemistry feature detected is related to Fe2+ in Fe

Crystallization of dienelactone hydrolase in two space groups: structural changes caused by crystal packing

PubMed Central

Porter, Joanne L.; Carr, Paul D.; Collyer, Charles A.; Ollis, David L.

2014-01-01

Dienelactone hydrolase (DLH) is a monomeric protein with a simple α/β-hydrolase fold structure. It readily crystallizes in space group P212121 from either a phosphate or ammonium sulfate precipitation buffer. Here, the structure of DLH at 1.85 Å resolution crystallized in space group C2 with two molecules in the asymmetric unit is reported. When crystallized in space group P212121 DLH has either phosphates or sulfates bound to the protein in crucial locations, one of which is located in the active site, preventing substrate/inhibitor binding. Another is located on the surface of the enzyme coordinated by side chains from two different molecules. Crystallization in space group C2 from a sodium citrate buffer results in new crystallographic protein–protein interfaces. The protein backbone is highly similar, but new crystal contacts cause changes in side-chain orientations and in loop positioning. In regions not involved in crystal contacts, there is little change in backbone or side-chain configuration. The flexibility of surface loops and the adaptability of side chains are important factors enabling DLH to adapt and form different crystal lattices. PMID:25005082

A novel structure of gel grown strontium cyanurate crystal and its structural, optical, electrical characterization

NASA Astrophysics Data System (ADS)

Divya, R.; Nair, Lekshmi P.; Bijini, B. R.; Nair, C. M. K.; Gopakumar, N.; Babu, K. Rajendra

2017-12-01

Strontium cyanurate crystals with novel structure and unique optical property like mechanoluminescence have been grown by conventional gel method. Transparent crystals were obtained. The single crystal X-ray diffraction analysis reveals the exquisite structure of the grown crystal. The crystal is centrosymmetric and has a three dimensional polymeric structure. The powder X ray diffraction analysis confirms its crystalline nature. The functional groups present in the crystal were identified by Fourier transform infrared spectroscopy. Elemental analysis confirmed the composition of the complex. A study of thermal properties was done by thermo gravimetric analysis and differential thermal analysis. The optical properties like band gap, refractive index and extinction coefficient were evaluated from the UV visible spectral analysis. The etching study was done to reveal the dislocations in the crystal which in turn explains mechanoluminescence emission. The mechanoluminescence property exhibited by the crystal makes it suitable for stress sensing applications. Besides being a centrosymmetric crystal, it also exhibits NLO behavior. Dielectric properties were studied and theoretical calculations of Fermi energy, valence electron plasma energy, penn gap and polarisability have been done.

Crystal structure of enolase from Drosophila melanogaster.

PubMed

Sun, Congcong; Xu, Baokui; Liu, Xueyan; Zhang, Zhen; Su, Zhongliang

2017-04-01

Enolase is an important enzyme in glycolysis and various biological processes. Its dysfunction is closely associated with diseases. Here, the enolase from Drosophila melanogaster (DmENO) was purified and crystallized. A crystal of DmENO diffracted to 2.0 Å resolution and belonged to space group R32. The structure was solved by molecular replacement. Like most enolases, DmENO forms a homodimer with conserved residues in the dimer interface. DmENO possesses an open conformation in this structure and contains conserved elements for catalytic activity. This work provides a structural basis for further functional and evolutionary studies of enolase.

Structural, vibrational and thermal studies of a new nonlinear optical crystal tetrapropylammonium dihydrogenmonoarsenate bis arsenic acid.

PubMed

Dhouib, Ikram; Feki, Habib; Guionneau, Philippe; Mhiri, Tahar; Elaoud, Zakaria

2014-10-15

Single crystals of tetrapropylammonium dihydrogenmonoarsenate bis arsenic acid [CH3CH2CH2]4N (H2AsO4) (H3AsO4)2, a potential new nonlinear optical (NLO) material of interest were prepared by the slow evaporation technique and characterized by means of single-crystal X-ray diffraction, thermal analysis, FT-IR and Raman spectroscopy. The title compound belongs to the monoclinic space group Ia with the following unit cell dimensions: a=8.116(2) Ǻ, b=33.673(4) Ǻ, c=8.689(2) Ǻ, β=95.34(2)°. The structure consists of infinite parallel two-dimensional planes built of mutually [H2AsO4(-)] and [H3AsO4] tetrahedra connected by strong O-H⋯O hydrogen bonding giving birth to trimmers. The planes of inorganic groups are alternated with those of the organic cations. The geometry, first hyperpolarizability and harmonic vibrational wavenumbers were calculated by means of density functional theory DFT with the B3LYP/6-31G(d) level of theory. Good consistency was found between the calculated results and the experimental structure, IR, and Raman spectra. The detailed interpretation of the vibrational modes was carried out building on the proposed DFT calculations as primary source of assignment and by comparison with the spectroscopic studies of similar compounds. The first hyperpolarizability βtot of the title compound is about 14.6 times more than that of the reference crystal KDP, which may explain the importance of the compound under study. Copyright © 2014 Elsevier B.V. All rights reserved.

Correlation Between Structural, Spectroscopic, and Reactivity Properties Within a Series of Structurally Analogous Metastable Manganese(III)-Alkylperoxo Complexes

PubMed Central

Coggins, Michael K.; Martin-Diaconescu, Vlad; DeBeer, Serena; Kovacs, Julie A.

2013-01-01

Manganese–peroxos are proposed as key intermediates in a number of important biochemical and synthetic transformations. Our understanding of the structural, spectroscopic, and reactivity properties of these metastable species is limited, however, and correlations between these properties have yet to be established experimentally. Herein we report the crystallographic structures of a series of structurally related metastable Mn(III)–OOR compounds, and examine their spectroscopic and reactivity properties. The four reported Mn(III)–OOR compounds extend the number of known end-on Mn(III)–(η1-peroxos) to six. The ligand backbone is shown to alter the metal–ligand distances and modulate the electronic properties key to bonding and activation of the peroxo. The mechanism of thermal decay of these metastable species is examined via variable-temperature kinetics. Strong correlations between structural (O–O and Mn⋯Npy,quin distances), spectroscopic (E(πv*(O–O) → Mn CT band), νO–O), and kinetic (ΔH‡ and ΔS‡) parameters for these complexes provide compelling evidence for rate-limiting O–O bond cleavage. Products identified in the final reaction mixtures of Mn(III)–OOR decay are consistent with homolytic O–O bond scission. The N-heterocyclic amines and ligand backbone (Et vs Pr) are found to modulate structural and reactivity properties, and O–O bond activation is shown, both experimentally and theoretically, to track with metal ion Lewis acidity. The peroxo O–O bond is shown to gradually become more activated as the N-heterocyclic amines move closer to the metal ion causing a decrease in π-donation from the peroxo πv*(O–O) orbital. The reported work represents one of very few examples of experimentally verified relationships between structure and function. PMID:23432090

Correlation between structural, spectroscopic, and reactivity properties within a series of structurally analogous metastable manganese(III)-alkylperoxo complexes.

PubMed

Coggins, Michael K; Martin-Diaconescu, Vlad; DeBeer, Serena; Kovacs, Julie A

2013-03-20

Manganese-peroxos are proposed as key intermediates in a number of important biochemical and synthetic transformations. Our understanding of the structural, spectroscopic, and reactivity properties of these metastable species is limited, however, and correlations between these properties have yet to be established experimentally. Herein we report the crystallographic structures of a series of structurally related metastable Mn(III)-OOR compounds, and examine their spectroscopic and reactivity properties. The four reported Mn(III)-OOR compounds extend the number of known end-on Mn(III)-(η(1)-peroxos) to six. The ligand backbone is shown to alter the metal-ligand distances and modulate the electronic properties key to bonding and activation of the peroxo. The mechanism of thermal decay of these metastable species is examined via variable-temperature kinetics. Strong correlations between structural (O-O and Mn···N(py,quin) distances), spectroscopic (E(πv*(O-O) → Mn CT band), ν(O-O)), and kinetic (ΔH(‡) and ΔS(‡)) parameters for these complexes provide compelling evidence for rate-limiting O-O bond cleavage. Products identified in the final reaction mixtures of Mn(III)-OOR decay are consistent with homolytic O-O bond scission. The N-heterocyclic amines and ligand backbone (Et vs Pr) are found to modulate structural and reactivity properties, and O-O bond activation is shown, both experimentally and theoretically, to track with metal ion Lewis acidity. The peroxo O-O bond is shown to gradually become more activated as the N-heterocyclic amines move closer to the metal ion causing a decrease in π-donation from the peroxo πv*(O-O) orbital. The reported work represents one of very few examples of experimentally verified relationships between structure and function.

Crystal Structure and Antitumor Activity of the Novel Zwitterionic Complex of tri-n-Butyltin(IV) with 2-Thiobarbituric Acid

PubMed Central

Balas, Vasilios I.; Hadjikakou, Sotiris K.; Hadjiliadis, Nick; Kourkoumelis, Nikolaos; Light, Mark E.; Hursthouse, Mike; Metsios, Apostolos K.; Karkabounas, Spyros

2008-01-01

A novel tri-n-butyl(IV) derivative of 2-thiobarbituric acid (HTBA) of formula [(n-Bu)3Sn(TBA) H2O] (1) has been synthesized and characterized by elemental analysis and 119Sn-NMR and FT-IR spectroscopic techniques. The crystal structure of complex 1 has been determined by single crystal X-ray diffraction analysis at 120(2) K. The geometry around Sn(IV) is trigonal bipyramidal. Three n-butyl groups and one oxygen atom from a deprotonated 2-thiobarbituric ligand are bonded to the metal center. The geometry is completed with one oxygen from a water molecule. Compound 1 exhibits potent, in vitro, cytotoxicity against sarcoma cancer cells (mesenchymal tissue) from the Wistar rat, polycyclic aromatic hydrocarbons (PAH, benzo[a]pyrene) carcinogenesis. In addition, the inhibition caused by 1, in the rate of lipoxygenase (LOX) catalyzed oxidation reaction of linoleic acid to hyperoxolinoleic acid, has been also kinetically and theoretically studied. The results are compared to that of cisplatin. PMID:18401456

Physical and Structural Studies on the Cryo-cooling of Insulin Crystals

NASA Technical Reports Server (NTRS)

Lovelace, J.; Bellamy, H.; Snell, E. H.; Borgstahl, G.

2003-01-01

Reflection profiles were analyzed from microgravity-(mg) and earth-grown insulin crystals to measure mosaicity (h) and to reveal mosaic domain structure and composition. The effects of cryocooling on single and multi-domain crystals were compared. The effects of cryocooling on insulin structure were also re-examined. Microgravity crystals were larger, more homogeneous, and more perfect than earth crystals. Several mg crystals contained primarily a single mosaic domain with havg of 0.005deg. The earth crystals varied in quality and all contained multiple domains with havg of 0.031deg. Cryocooling caused a 43-fold increase in h for mg crystals (havg=0.217deg) and an %fold increase for earth crystals (havg=0.246deg). These results indicate that very well-ordered crystals are not completely protected from the stresses associated with cryocooling, especially when structural perturbations occur. However, there were differences in the reflection profiles. For multi-mosaic domain crystals, each domain individually broadened and separated from the other domains upon cryo-cooling. Cryo-cooling did not cause an increase in the number of domains. A crystal composed of a single domain retained this domain structure and the reflection profiles simply broadened. Therefore, an improved signal-to-noise ratio for each reflection was measured from cryo-cooled single domain crystals relative to cryo-cooled multi-domain crystals. This improved signal, along with the increase in crystal size, facilitated the measurement of the weaker high- resolution reflections. The observed broadening of reflection profiles indicates increased variation in unit cell dimensions which may be linked to cryo-cooling-associated structural changes and disorder.

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.

Optical properties of Mn 2+ in KCaF 3 single crystal

NASA Astrophysics Data System (ADS)

Mazurak, Z.; Ratuszna, A.; Daniel, Ph.

1999-02-01

It is known that the spectroscopic properties of 3d impurities in crystals are very sensitive to the environment of the ion and can be changed considerably by using different matrices. The crystal structure of KCaF 3 has been previously determined by the Rietveld profile method. At room temperature, KCa 1- xMn xF 3 ( x<0.1) crystallizes in monoclinic C2 h ( B2 1/ m) symmetry. The local geometries around Mn 2+ in this crystals, in their ground and excited states, are the primary properties that govern the spectroscopic behavior of these systems, which enjoy of fundamental and technological interest. The present work reports the absorption and luminescence spectra of the Mn 2+-doped KCaF 3 (fluoroperovskite). The luminescence spectra recorded over a range of temperatures are dominated by wide bands, corresponding to the 4T 1(G)→ 6A 1(G), Mn 2+ transition. The lifetime ( τ= f( T)) of the first excited state 4T 1(G) was measured as a function of temperature. The lifetime of the Mn 2+ emission, in this crystal have been found to be temperature independent ( τ<7 μs). The absorption and emission spectra of Mn 2+ (3d 5) in KCaF 3 are analyzed using a C4 crystal-field hamiltonian. The calculated energy levels are in good agreement with those obtained experimentally. The resulting crystal-field parameters Bnm are a good representation of the crystal-field interactions of Mn 2+ in KCaF 3.

The use of small-molecule structures to complement protein–ligand crystal structures in drug discovery

PubMed Central

Cole, Jason C.

2017-01-01

Many ligand-discovery stories tell of the use of structures of protein–ligand complexes, but the contribution of structural chemistry is such a core part of finding and improving ligands that it is often overlooked. More than 800 000 crystal structures are available to the community through the Cambridge Structural Database (CSD). Individually, these structures can be of tremendous value and the collection of crystal structures is even more helpful. This article provides examples of how small-molecule crystal structures have been used to complement those of protein–ligand complexes to address challenges ranging from affinity, selectivity and bioavailability though to solubility. PMID:28291759

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

PubMed

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

2015-09-11

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

Crystal Structures of the GCaMP Calcium Sensor Reveal the Mechanism of Fluorescence Signal Change and Aid Rational Design

DOE Office of Scientific and Technical Information (OSTI.GOV)

Akerboom, Jasper; Velez Rivera, Jonathan D.; Rodriguez Guilbe, María M.

The genetically encoded calcium indicator GCaMP2 shows promise for neural network activity imaging, but is currently limited by low signal-to-noise ratio. We describe x-ray crystal structures as well as solution biophysical and spectroscopic characterization of GCaMP2 in the calcium-free dark state, and in two calcium-bound bright states: a monomeric form that dominates at intracellular concentrations observed during imaging experiments and an unexpected domain-swapped dimer with decreased fluorescence. This series of structures provides insight into the mechanism of Ca{sup 2+}-induced fluorescence change. Upon calcium binding, the calmodulin (CaM) domain wraps around the M13 peptide, creating a new domain interface between CaMmore » and the circularly permuted enhanced green fluorescent protein domain. Residues from CaM alter the chemical environment of the circularly permuted enhanced green fluorescent protein chromophore and, together with flexible inter-domain linkers, block solvent access to the chromophore. Guided by the crystal structures, we engineered a series of GCaMP2 point mutants to probe the mechanism of GCaMP2 function and characterized one mutant with significantly improved signal-to-noise. The mutation is located at a domain interface and its effect on sensor function could not have been predicted in the absence of structural data.« less

The Cambridge Structural Database: a quarter of a million crystal structures and rising.

PubMed

Allen, Frank H

2002-06-01

The Cambridge Structural Database (CSD) now contains data for more than a quarter of a million small-molecule crystal structures. The information content of the CSD, together with methods for data acquisition, processing and validation, are summarized, with particular emphasis on the chemical information added by CSD editors. Nearly 80% of new structural data arrives electronically, mostly in CIF format, and the CCDC acts as the official crystal structure data depository for 51 major journals. The CCDC now maintains both a CIF archive (more than 73,000 CIFs dating from 1996), as well as the distributed binary CSD archive; the availability of data in both archives is discussed. A statistical survey of the CSD is also presented and projections concerning future accession rates indicate that the CSD will contain at least 500,000 crystal structures by the year 2010.

Single-Crystal Structure of a Covalent Organic Framework

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, YB; Su, J; Furukawa, H

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 anmore » important advance in the development of COF chemistry.« less

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.

Crystal structure, Hirshfeld surface analysis, quantum mechanical study and spectroscopic characterization of the non-centrosymmetric coordination compound bis(4-fluoroaniline)dichloridozincate

NASA Astrophysics Data System (ADS)

Ben Nasr, M.; Soudani, S.; Lefebvre, F.; Jelsch, C.; Ben Nasr, C.

2017-06-01

The Zn(II) complex with the monodentate ligand 4-fluoroaniline, ZnCl2(C6H4FNH2)2, has been prepared and characterized by single crystal X-ray diffraction, solid state nuclear magnetic resonance, infrared spectroscopy and differential scanning calorimetry. The Zn(II) ion is tetracoordinated by two nitrogen atoms of two monodentate 4-fluoroaniline ligands and two chlorine atoms. In the molecular arrangement, the ZnCl2(C6H4FNH2)2 entities are interconnected via Nsbnd H⋯Cl hydrogen bonds to form layers parallel to the (a, b) plane. The nature and proportion of contacts in the crystal packing were investigated through the Hirshfeld surfaces. The crystal is mainly maintained by electrostatic attractions Cl- … Hsbnd N and by extensive hydrophobic contacts as revealed by the Hirshfeld 2D fingerprint plots and statistical analysis. The13C and 19F CP-MAS NMR spectra are in agreement with the X-ray structure and confirm the phase purity of the crystalline sample. The vibrational absorption bands were identified by infrared spectroscopy. A calorimetric study shows that the title compound is stable until 262.5 °C.

Applications of the Cambridge Structural Database in organic chemistry and crystal chemistry.

PubMed

Allen, Frank H; Motherwell, W D Samuel

2002-06-01

The Cambridge Structural Database (CSD) and its associated software systems have formed the basis for more than 800 research applications in structural chemistry, crystallography and the life sciences. Relevant references, dating from the mid-1970s, and brief synopses of these papers are collected in a database, DBUse, which is freely available via the CCDC website. This database has been used to review research applications of the CSD in organic chemistry, including supramolecular applications, and in organic crystal chemistry. The review concentrates on applications that have been published since 1990 and covers a wide range of topics, including structure correlation, conformational analysis, hydrogen bonding and other intermolecular interactions, studies of crystal packing, extended structural motifs, crystal engineering and polymorphism, and crystal structure prediction. Applications of CSD information in studies of crystal structure precision, the determination of crystal structures from powder diffraction data, together with applications in chemical informatics, are also discussed.

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.

A comparative study of the spectroscopic properties of Mn4+ in the garnet Y2Mg3Ge3O12 and the commercial Mg28Ge7.55O32F15.04 phosphor

NASA Astrophysics Data System (ADS)

Srivastava, A. M.

2018-05-01

The spectroscopic properties of Mn4+ (3 d3) ions in the garnet Y2Mg3Ge3O12 and in the commercial Mg28Ge7.55O32F15.04 (MFG) phosphors are compared. We find that despite the differences in host crystal composition and crystal structures, the 4A2g→ 4T1g and 2Eg→4A2g optical transitions of the Mn4+ ion occur at similar energies. We provide some insights into the nature of chemical bonding that is responsible for the observed similarity in the spectroscopic data. Additionally, discussion is given to the site preference of the Mn4+ ion in the MFG host crystal.

Structural, spectroscopic and cytotoxicity studies of TbF3@CeF3 and TbF3@CeF3@SiO2 nanocrystals.

PubMed

Grzyb, Tomasz; Runowski, Marcin; Dąbrowska, Krystyna; Giersig, Michael; Lis, Stefan

2013-01-01

Terbium fluoride nanocrystals, covered by a shell, composed of cerium fluoride were synthesized by a co-precipitation method. Their complex structure was formed spontaneously during the synthesis. The surface of these core/shell nanocrystals was additionally modified by silica. The properties of TbF 3 @CeF 3 and TbF 3 @CeF 3 @SiO 2 nanocrystals, formed in this way, were investigated. Spectroscopic studies showed that the differences between these two groups of products resulted from the presence of the SiO 2 shell. X-ray diffraction patterns confirmed the trigonal crystal structure of TbF 3 @CeF 3 nanocrystals. High resolution transmission electron microscopy in connection with energy-dispersive X-ray spectroscopy showed a complex structure of the formed nanocrystals. Crystallized as small discs, 'the products', with an average diameter around 10 nm, showed an increase in the concentration of Tb 3+ ions from surface to the core of nanocrystals. In addition to photo-physical analyses, cytotoxicity studies were performed on HSkMEC (Human Skin Microvascular Endothelial Cells) and B16F0 mouse melanoma cancer cells. The cytotoxicity of the nanomaterials was neutral for the investigated cells with no toxic or antiproliferative effect in the cell cultures, either for normal or for cancer cells. This fact makes the obtained nanocrystals good candidates for biological applications and further modifications of the SiO 2 shell. .

Structural, spectroscopic and cytotoxicity studies of TbF3@CeF3 and TbF3@CeF3@SiO2 nanocrystals

NASA Astrophysics Data System (ADS)

Grzyb, Tomasz; Runowski, Marcin; Dąbrowska, Krystyna; Giersig, Michael; Lis, Stefan

2013-10-01

Terbium fluoride nanocrystals, covered by a shell, composed of cerium fluoride were synthesized by a co-precipitation method. Their complex structure was formed spontaneously during the synthesis. The surface of these core/shell nanocrystals was additionally modified by silica. The properties of TbF3@CeF3 and TbF3@CeF3@SiO2 nanocrystals, formed in this way, were investigated. Spectroscopic studies showed that the differences between these two groups of products resulted from the presence of the SiO2 shell. X-ray diffraction patterns confirmed the trigonal crystal structure of TbF3@CeF3 nanocrystals. High resolution transmission electron microscopy in connection with energy-dispersive X-ray spectroscopy showed a complex structure of the formed nanocrystals. Crystallized as small discs, `the products', with an average diameter around 10 nm, showed an increase in the concentration of Tb3+ ions from surface to the core of nanocrystals. In addition to photo-physical analyses, cytotoxicity studies were performed on HSkMEC (Human Skin Microvascular Endothelial Cells) and B16F0 mouse melanoma cancer cells. The cytotoxicity of the nanomaterials was neutral for the investigated cells with no toxic or antiproliferative effect in the cell cultures, either for normal or for cancer cells. This fact makes the obtained nanocrystals good candidates for biological applications and further modifications of the SiO2 shell.

Crystal Structure of Toxoplasma gondii Porphobilinogen Synthase

PubMed Central

Jaffe, Eileen K.; Shanmugam, Dhanasekaran; Gardberg, Anna; Dieterich, Shellie; Sankaran, Banumathi; Stewart, Lance J.; Myler, Peter J.; Roos, David S.

2011-01-01

Porphobilinogen synthase (PBGS) is essential for heme biosynthesis, but the enzyme of the protozoan parasite Toxoplasma gondii (TgPBGS) differs from that of its human host in several important respects, including subcellular localization, metal ion dependence, and quaternary structural dynamics. We have solved the crystal structure of TgPBGS, which contains an octamer in the crystallographic asymmetric unit. Crystallized in the presence of substrate, each active site contains one molecule of the product porphobilinogen. Unlike prior structures containing a substrate-derived heterocycle directly bound to an active site zinc ion, the product-bound TgPBGS active site contains neither zinc nor magnesium, placing in question the common notion that all PBGS enzymes require an active site metal ion. Unlike human PBGS, the TgPBGS octamer contains magnesium ions at the intersections between pro-octamer dimers, which are presumed to function in allosteric regulation. TgPBGS includes N- and C-terminal regions that differ considerably from previously solved crystal structures. In particular, the C-terminal extension found in all apicomplexan PBGS enzymes forms an intersubunit β-sheet, stabilizing a pro-octamer dimer and preventing formation of hexamers that can form in human PBGS. The TgPBGS structure suggests strategies for the development of parasite-selective PBGS inhibitors. PMID:21383008

Crystal structure and crystal growth of the polar ferrimagnet CaBaFe4O7

NASA Astrophysics Data System (ADS)

Perry, R. S.; Kurebayashi, H.; Gibbs, A.; Gutmann, M. J.

2018-05-01

Magnetic materials are a cornerstone for developing spintronic devices for the transport of information via magnetic excitations. To date, relatively few materials have been investigated for the purpose of spin transport, mostly due to the paucity of suitable candidates as these materials are often chemically complex and difficult to synthesize. We present the crystal growth and a structure solution on the high-temperature crystal structure of the layered, polar ferrimagnet CaBaFe4O7 , which is a possible new contender for spintronics research. The space group is identified as P 3 by refinement of single crystal and powder neutron diffraction data. At 400 K, the trigonal lattice parameters are a =11.0114 (11 )Å and c =10.330 (3 )Å . The structure is similar to the low-temperature phase with alternating layers of triangular and Kagome-arranged Fe-O tetrahedra. We also present details of the crystal growth by traveling solvent method.

Crystal structures of sialyltransferase from Photobacterium damselae

DOE PAGES

Huynh, Nhung; Li, Yanhong; Yu, Hai; ...

2014-11-15

Sialyltransferase structures fall into either GT-A or GT-B glycosyltransferase fold. Some sialyltransferases from the Photobacterium genus have been shown to contain an additional N-terminal immunoglobulin (Ig)-like domain. Photobacterium damselae α2–6-sialyltransferase has been used efficiently in enzymatic and chemoenzymatic synthesis of α2–6-linked sialosides. In this paper, we report three crystal structures of this enzyme. Two structures with and without a donor substrate analog CMP-3F(a)Neu5Ac contain an immunoglobulin (Ig)-like domain and adopt the GT-B sialyltransferase fold. The binary structure reveals a non-productive pre-Michaelis complex, which are caused by crystal lattice contacts that prevent the large conformational changes. The third structure lacks themore » Ig-domain. Finally, comparison of the three structures reveals small inherent flexibility between the two Rossmann-like domains of the GT-B fold.« less

A Two-Tailed Phosphopeptide Crystallizes to Form a Lamellar Structure.

PubMed

Pellach, Michal; Mondal, Sudipta; Harlos, Karl; Mance, Deni; Baldus, Marc; Gazit, Ehud; Shimon, Linda J W

2017-03-13

The crystal structure of a designed phospholipid-inspired amphiphilic phosphopeptide at 0.8 Å resolution is presented. The phosphorylated β-hairpin peptide crystallizes to form a lamellar structure that is stabilized by intra- and intermolecular hydrogen bonding, including an extended β-sheet structure, as well as aromatic interactions. This first reported crystal structure of a two-tailed peptidic bilayer reveals similarities in thickness to a typical phospholipid bilayer. However, water molecules interact with the phosphopeptide in the hydrophilic region of the lattice. Additionally, solid-state NMR was used to demonstrate correlation between the crystal structure and supramolecular nanostructures. The phosphopeptide was shown to self-assemble into semi-elliptical nanosheets, and solid-state NMR provides insight into the self-assembly mechanisms. This work brings a new dimension to the structural study of biomimetic amphiphilic peptides with determination of molecular organization at the atomic level. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Tailoring the Crystal Structure Toward Optimal Super Conductors

DTIC Science & Technology

2016-06-23

AFRL-AFOSR-VA-TR-2016-0210 TAILORING THE CRYSTAL STRUCTURE TOWARD OPTIMAL SUPERCONDUCTORS Emilia Morosan WILLIAM MARSH RICE UNIV HOUSTON TX Final...TAILORING THE CRYSTAL STRUCTURE TOWARD OPTIMAL SUPERCONDUCTORS 5a. CONTRACT NUMBER FA9550-11-1-0023 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6...studied the properties of layered transition metal compounds in search of unconventional superconductors . The aim is to identify ground states competing

Crystal structure of a poly(rA) staggered zipper at acidic pH: evidence that adenine N1 protonation mediates parallel double helix formation

DOE PAGES

Gleghorn, Michael L.; Zhao, Jianbo; Turner, Douglas H.; ...

2016-06-10

We have solved at 1.07 Å resolution the X-ray crystal structure of a polyriboadenylic acid (poly(rA)) parallel and continuous double helix. Fifty-nine years ago, double helices of poly(rA) were first proposed to form at acidic pH. Here, we show that 7-mer oligo(rA), i.e. rA 7, hybridizes and overlaps in all registers at pH 3.5 to form stacked double helices that span the crystal. Under these conditions, rA 7 forms well-ordered crystals, whereas rA 6 forms fragile crystalline-like structures, and rA 5, rA 8 and rA 11 fail to crystallize. Our findings support studies from ~50 years ago: one showed usingmore » spectroscopic methods that duplex formation at pH 4.5 largely starts with rA 7 and begins to plateau with rA 8; another proposed a so-called ‘staggered zipper’ model in which oligo(rA) strands overlap in multiple registers to extend the helical duplex. While never shown, protonation of adenines at position N1 has been hypothesized to be critical for helix formation. Bond angles in our structure suggest that N1 is protonated on the adenines of every other rAMP–rAMP helix base pair. Lastly, our data offer new insights into poly(rA) duplex formation that may be useful in developing a pH sensor.« less

Crystal structure of a poly(rA) staggered zipper at acidic pH: evidence that adenine N1 protonation mediates parallel double helix formation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gleghorn, Michael L.; Zhao, Jianbo; Turner, Douglas H.

We have solved at 1.07 Å resolution the X-ray crystal structure of a polyriboadenylic acid (poly(rA)) parallel and continuous double helix. Fifty-nine years ago, double helices of poly(rA) were first proposed to form at acidic pH. Here, we show that 7-mer oligo(rA), i.e. rA 7, hybridizes and overlaps in all registers at pH 3.5 to form stacked double helices that span the crystal. Under these conditions, rA 7 forms well-ordered crystals, whereas rA 6 forms fragile crystalline-like structures, and rA 5, rA 8 and rA 11 fail to crystallize. Our findings support studies from ~50 years ago: one showed usingmore » spectroscopic methods that duplex formation at pH 4.5 largely starts with rA 7 and begins to plateau with rA 8; another proposed a so-called ‘staggered zipper’ model in which oligo(rA) strands overlap in multiple registers to extend the helical duplex. While never shown, protonation of adenines at position N1 has been hypothesized to be critical for helix formation. Bond angles in our structure suggest that N1 is protonated on the adenines of every other rAMP–rAMP helix base pair. Lastly, our data offer new insights into poly(rA) duplex formation that may be useful in developing a pH sensor.« less

How evolutionary crystal structure prediction works--and why.

PubMed

Oganov, Artem R; Lyakhov, Andriy O; Valle, Mario

2011-03-15

Once the crystal structure of a chemical substance is known, many properties can be predicted reliably and routinely. Therefore if researchers could predict the crystal structure of a material before it is synthesized, they could significantly accelerate the discovery of new materials. In addition, the ability to predict crystal structures at arbitrary conditions of pressure and temperature is invaluable for the study of matter at extreme conditions, where experiments are difficult. Crystal structure prediction (CSP), the problem of finding the most stable arrangement of atoms given only the chemical composition, has long remained a major unsolved scientific problem. Two problems are entangled here: search, the efficient exploration of the multidimensional energy landscape, and ranking, the correct calculation of relative energies. For organic crystals, which contain a few molecules in the unit cell, search can be quite simple as long as a researcher does not need to include many possible isomers or conformations of the molecules; therefore ranking becomes the main challenge. For inorganic crystals, quantum mechanical methods often provide correct relative energies, making search the most critical problem. Recent developments provide useful practical methods for solving the search problem to a considerable extent. One can use simulated annealing, metadynamics, random sampling, basin hopping, minima hopping, and data mining. Genetic algorithms have been applied to crystals since 1995, but with limited success, which necessitated the development of a very different evolutionary algorithm. This Account reviews CSP using one of the major techniques, the hybrid evolutionary algorithm USPEX (Universal Structure Predictor: Evolutionary Xtallography). Using recent developments in the theory of energy landscapes, we unravel the reasons evolutionary techniques work for CSP and point out their limitations. We demonstrate that the energy landscapes of chemical systems have an

Nonlinear coherent structures in granular crystals

NASA Astrophysics Data System (ADS)

Chong, C.; Porter, Mason A.; Kevrekidis, P. G.; Daraio, C.

2017-10-01

The study of granular crystals, which are nonlinear metamaterials that consist of closely packed arrays of particles that interact elastically, is a vibrant area of research that combines ideas from disciplines such as materials science, nonlinear dynamics, and condensed-matter physics. Granular crystals exploit geometrical nonlinearities in their constitutive microstructure to produce properties (such as tunability and energy localization) that are not conventional to engineering materials and linear devices. In this topical review, we focus on recent experimental, computational, and theoretical results on nonlinear coherent structures in granular crystals. Such structures—which include traveling solitary waves, dispersive shock waves, and discrete breathers—have fascinating dynamics, including a diversity of both transient features and robust, long-lived patterns that emerge from broad classes of initial data. In our review, we primarily discuss phenomena in one-dimensional crystals, as most research to date has focused on such scenarios, but we also present some extensions to two-dimensional settings. Throughout the review, we highlight open problems and discuss a variety of potential engineering applications that arise from the rich dynamic response of granular crystals.

Crystal structure of simple metals at high pressures

NASA Astrophysics Data System (ADS)

Degtyareva, Olga

2010-09-01

The effects of pressure on the crystal structure of simple (or sp-) elements are analysed in terms of changes in coordination number, packing density, and interatomic distances, and general rules are established. In the polyvalent elements from groups 14-17, the covalently bonded structures tend to transform to metallic phases with a gradual increase in coordination number and packing density, a behaviour normally expected under pressure. Group 1 and 2 metallic elements, however, show a reverse trend towards structures with low packing density due to intricate changes in their electronic structure. Complex crystal structures such as host-guest and incommensurately modulated structures found in these elements are given special attention in this review in an attempt to determine their role in the observed phase-transition sequences.

Structural and spectroscopic studies of a commercial glassy carbon

NASA Astrophysics Data System (ADS)

Parker, Stewart F.; Imberti, Silvia; Callear, Samantha K.; Albers, Peter W.

2013-12-01

Glassy carbon is a form of carbon made by heating a phenolic resin to high temperature in an inert atmosphere. It has been suggested that it is composed of fullerene-like structures. The aim of the present work was to characterize the material using both structural (neutron diffraction and transmission electron microscopy) and spectroscopic (inelastic neutron scattering, Raman and X-ray photoelectron spectroscopies) methods. We find no evidence to support the suggestion of fullerene-like material being present to a significant extent, rather the model that emerges from all of the techniques is that the material is very like amorphous carbon, consisting of regions of small graphite-like basic structural units of partly stacked but mismatched structure with the edges terminated by hydrogen or hydroxyls. We do find evidence for the presence of a small quantity of water trapped in the network and suggest that this may account for batch-to-batch variation in properties that may occur.

How large B-factors can be in protein crystal structures.

PubMed

Carugo, Oliviero

2018-02-23

Protein crystal structures are potentially over-interpreted since they are routinely refined without any restraint on the upper limit of atomic B-factors. Consequently, some of their atoms, undetected in the electron density maps, are allowed to reach extremely large B-factors, even above 100 square Angstroms, and their final positions are purely speculative and not based on any experimental evidence. A strategy to define B-factors upper limits is described here, based on the analysis of protein crystal structures deposited in the Protein Data Bank prior 2008, when the tendency to allow B-factor to arbitrary inflate was limited. This B-factor upper limit (B_max) is determined by extrapolating the relationship between crystal structure average B-factor and percentage of crystal volume occupied by solvent (pcVol) to pcVol =100%, when, ab absurdo, the crystal contains only liquid solvent, the structure of which is, by definition, undetectable in electron density maps. It is thus possible to highlight structures with average B-factors larger than B_max, which should be considered with caution by the users of the information deposited in the Protein Data Bank, in order to avoid scientifically deleterious over-interpretations.

Crystal structure and crystal chemistry of melanovanadite, a natural vanadium bronze.

USGS Publications Warehouse

Konnert, J.A.; Evans, H.T.

1987-01-01

The crystal structure of melanovanadite from Minas Ragra, Peru, has been determined in space group P1. The triclinic unit cell (non-standard) has a 6.360(2), b 18.090(9), c 6.276(2) A, alpha 110.18(4)o, beta 101.62(3)o, gamma 82.86(4)o. A subcell with b' = b/2 was found by crystal-structure analysis to contain CaV4O10.5H2O. The subcell has a layer structure in which the vanadate sheet consists of corner-shared tetrahedral VO4 and double square-pyramidal V2O8 groups, similar to that previously found in synthetic CsV2O5. Refinement of the full structure (R = 0.056) showed that the Ca atom, which half-occupies a general position in the subcell, is 90% ordered at one of these sites in the whole unit cell. Bond length-bond strength estimates indicate that the tetrahedra contain V5+, and the square pyramids, V4+.-J.A.Z.

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

Clathrate Structure Determination by Combining Crystal Structure Prediction with Computational and Experimental 129Xe NMR Spectroscopy

PubMed Central

Selent, Marcin; Nyman, Jonas; Roukala, Juho; Ilczyszyn, Marek; Oilunkaniemi, Raija; Bygrave, Peter J.; Laitinen, Risto; Jokisaari, Jukka

2017-01-01

Abstract An approach is presented for the structure determination of clathrates using NMR spectroscopy of enclathrated xenon to select from a set of predicted crystal structures. Crystal structure prediction methods have been used to generate an ensemble of putative structures of o‐ and m‐fluorophenol, whose previously unknown clathrate structures have been studied by 129Xe NMR spectroscopy. The high sensitivity of the 129Xe chemical shift tensor to the chemical environment and shape of the crystalline cavity makes it ideal as a probe for porous materials. The experimental powder NMR spectra can be used to directly confirm or reject hypothetical crystal structures generated by computational prediction, whose chemical shift tensors have been simulated using density functional theory. For each fluorophenol isomer one predicted crystal structure was found, whose measured and computed chemical shift tensors agree within experimental and computational error margins and these are thus proposed as the true fluorophenol xenon clathrate structures. PMID:28111848

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…

Spectroscopic investigation on the efficient organic nonlinear crystals of pure and diethanolamine added DAST.

PubMed

Karthikeyan, C; Haja Hameed, A S; Sagaya Agnes Nisha, J; Ravi, G

2013-11-01

4-N,N'-dimethylamino-N-methyl-4-stilbazolium toyslate (DAST) and diethanolamine (DEA) added DAST crystals are grown by slow cooling method. The corresponding powder samples are examined by characterization studies such as XRD, FT-IR, FT-Raman, UV-Vis-NIR and photoluminescence studies. From the powder X-ray diffraction, their lattice parameter values are found out. Since the vibrational spectra of the molecules are considerably contributed to their linear and nonlinear optical effects, Infrared and Raman spectroscopic studies are carried out for the samples. The UV-Vis-NIR absorption spectra of the samples are used to find the nature of transitions occurred in the samples. Using the density functional theory, highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) analyses are done in order to explain the transition and density of states (DOS). The first order hyperpolarizability is calculated by HF and B3LYP/6-311 G(d,p) basis sets for the DAST molecule. From the photoluminescence (PL) spectral studies, the strong excitation emissions are observed. Copyright © 2013 Elsevier B.V. All rights reserved.

Crystal structure of MboIIA methyltransferase.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Osipiuk, J.; Walsh, M. A.; Joachimiak, A.

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 inmore » 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.« less

Crystal structure of MboIIA methyltransferase.

PubMed

Osipiuk, Jerzy; Walsh, Martin A; Joachimiak, Andrzej

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 A resolution the crystal structure of a beta-class DNA MTase MboIIA (M.MboIIA) from the bacterium Moraxella bovis, the smallest DNA MTase determined to date. M.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.MboIIA is not bound to DNA. The overall structure of the enzyme closely resembles that of M.RsrI. However, the cofactor-binding pocket in M.MboIIA forms a closed structure which is in contrast to the open-form structures of other known MTases.

Validation of experimental molecular crystal structures with dispersion-corrected density functional theory calculations.

PubMed

van de Streek, Jacco; Neumann, Marcus A

2010-10-01

This paper describes the validation of a dispersion-corrected density functional theory (d-DFT) method for the purpose of assessing the correctness of experimental organic crystal structures and enhancing the information content of purely experimental data. 241 experimental organic crystal structures from the August 2008 issue of Acta Cryst. Section E were energy-minimized in full, including unit-cell parameters. The differences between the experimental and the minimized crystal structures were subjected to statistical analysis. The r.m.s. Cartesian displacement excluding H atoms upon energy minimization with flexible unit-cell parameters is selected as a pertinent indicator of the correctness of a crystal structure. All 241 experimental crystal structures are reproduced very well: the average r.m.s. Cartesian displacement for the 241 crystal structures, including 16 disordered structures, is only 0.095 Å (0.084 Å for the 225 ordered structures). R.m.s. Cartesian displacements above 0.25 A either indicate incorrect experimental crystal structures or reveal interesting structural features such as exceptionally large temperature effects, incorrectly modelled disorder or symmetry breaking H atoms. After validation, the method is applied to nine examples that are known to be ambiguous or subtly incorrect.

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.

Powder diffraction and crystal structure prediction identify four new coumarin polymorphs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shtukenberg, Alexander G.; Zhu, Qiang; Carter, Damien J.

Coumarin, a simple, commodity chemical isolated from beans in 1820, has, to date, only yielded one solid state structure. Here, we report a rich polymorphism of coumarin grown from the melt. Four new metastable forms were identified and their crystal structures were solved using a combination of computational crystal structure prediction algorithms and X-ray powder diffraction. With five crystal structures, coumarin has become one of the few rigid molecules showing extensive polymorphism at ambient conditions. We demonstrate the crucial role of advanced electronic structure calculations including many-body dispersion effects for accurate ranking of the stability of coumarin polymorphs and themore » need to account for anharmonic vibrational contributions to their free energy. As such, coumarin is a model system for studying weak intermolecular interactions, crystallization mechanisms, and kinetic effects.« less

Powder diffraction and crystal structure prediction identify four new coumarin polymorphs

DOE PAGES

Shtukenberg, Alexander G.; Zhu, Qiang; Carter, Damien J.; ...

2017-05-15

Coumarin, a simple, commodity chemical isolated from beans in 1820, has, to date, only yielded one solid state structure. Here, we report a rich polymorphism of coumarin grown from the melt. Four new metastable forms were identified and their crystal structures were solved using a combination of computational crystal structure prediction algorithms and X-ray powder diffraction. With five crystal structures, coumarin has become one of the few rigid molecules showing extensive polymorphism at ambient conditions. We demonstrate the crucial role of advanced electronic structure calculations including many-body dispersion effects for accurate ranking of the stability of coumarin polymorphs and themore » need to account for anharmonic vibrational contributions to their free energy. As such, coumarin is a model system for studying weak intermolecular interactions, crystallization mechanisms, and kinetic effects.« less

Exploring Molecular Speciation and Crystallization Mechanism of Amorphous 2-Phenylamino Nicotinic Acid.

PubMed

Kalra, Arjun; Lubach, Joseph W; Munson, Eric J; Li, Tonglei

2018-02-07

Molecular understanding of phase stability and transition of the amorphous state helps in formulation and manufacturing of poorly-soluble drugs. Crystallization of a model compound, 2-phenylamino nicotinic acid (2PNA), from the amorphous state was studied using solid-state analytical methods. Our previous report suggests that 2PNA molecules mainly develop intermolecular -COOH∙∙∙pyridine N (acid-pyridine) interactions in the amorphous state. In the current study, the molecular speciation is explored with regard to the phase transition from the amorphous to the crystalline state. Using spectroscopic techniques, the molecular interactions and structural evolvement during the recrystallization from the glassy state were investigated. The results unveiled that the structurally heterogeneous amorphous state contains acid-pyridine aggregates - either as hydrogen-bonded neutral molecules or as zwitterions - as well as a population of carboxylic acid dimers. Phase transition from the amorphous state results in crystal structures composed of carboxylic acid dimer (acid-acid) synthon or acid-pyridine chains depending on the crystallization conditions employed. The study underlines the structural evolvement, as well as its impact on the metastability, of amorphous samples from local, supramolecular assemblies to long-range intermolecular ordering through crystallization.

High-pressure crystal structures of an insensitive energetic crystal: 1,1-diamino-2,2-dinitroethene

DOE PAGES

Dreger, Zbigniew A.; Stash, Adam I.; Yu, Zhi -Gang; ...

2015-12-03

Understanding the insensitivity/stability of insensitive high explosive crystals requires detailed structural information at high pressures and high temperatures of interest. Synchrotron single crystal x-ray diffraction experiments were used to determine the high-pressure structures of 1,1-diamino-2,2-dinitroethene (FOX-7), a prototypical insensitive high explosive. The phase transition around 4.5 GPa was investigated and the structures were determined at 4.27 GPa (α’-phase) and 5.9 GPa (ε-phase). The α’-phase (monoclinic, P2 1/ n), structurally indistinguishable from the ambient α-phase, transforms to the new ε-phase (triclinic, P1). The most notable features of the ε-phase, compared to the α’-phase, are: formation of planar layers and flattening ofmore » molecules. Density functional theory (DFT-D2) calculations complemented the experimental results. Furthermore, the results presented here are important for understanding the molecular and crystalline attributes governing the high-pressure insensitivity/stability of insensitive high explosive crystals.« less

High-pressure crystal structures of an insensitive energetic crystal: 1,1-diamino-2,2-dinitroethene

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dreger, Zbigniew A.; Stash, Adam I.; Yu, Zhi -Gang

Understanding the insensitivity/stability of insensitive high explosive crystals requires detailed structural information at high pressures and high temperatures of interest. Synchrotron single crystal x-ray diffraction experiments were used to determine the high-pressure structures of 1,1-diamino-2,2-dinitroethene (FOX-7), a prototypical insensitive high explosive. The phase transition around 4.5 GPa was investigated and the structures were determined at 4.27 GPa (α’-phase) and 5.9 GPa (ε-phase). The α’-phase (monoclinic, P2 1/ n), structurally indistinguishable from the ambient α-phase, transforms to the new ε-phase (triclinic, P1). The most notable features of the ε-phase, compared to the α’-phase, are: formation of planar layers and flattening ofmore » molecules. Density functional theory (DFT-D2) calculations complemented the experimental results. Furthermore, the results presented here are important for understanding the molecular and crystalline attributes governing the high-pressure insensitivity/stability of insensitive high explosive crystals.« less

Feasibility of one-shot-per-crystal structure determination using Laue diffraction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cornaby, Sterling; CHESS; Szebenyi, Doletha M. E.

Structure determination was successfully carried out using single Laue exposures from a group of lysozyme crystals. The Laue method may be a viable option for collection of one-shot-per-crystal data from microcrystals. Crystal size is an important factor in determining the number of diffraction patterns which may be obtained from a protein crystal before severe radiation damage sets in. As crystal dimensions decrease this number is reduced, eventually falling to one, at which point a complete data set must be assembled using data from multiple crystals. When only a single exposure is to be collected from each crystal, the polychromatic Lauemore » technique may be preferable to monochromatic methods owing to its simultaneous recording of a large number of fully recorded reflections per image. To assess the feasibility of solving structures using single Laue images from multiple crystals, data were collected using a ‘pink’ beam at the CHESS D1 station from groups of lysozyme crystals with dimensions of the order of 20–30 µm mounted on MicroMesh grids. Single-shot Laue data were used for structure determination by molecular replacement and correct solutions were obtained even when as few as five crystals were used.« less

Hydrogen-bond coordination in organic crystal structures: statistics, predictions and applications.

PubMed

Galek, Peter T A; Chisholm, James A; Pidcock, Elna; Wood, Peter A

2014-02-01

Statistical models to predict the number of hydrogen bonds that might be formed by any donor or acceptor atom in a crystal structure have been derived using organic structures in the Cambridge Structural Database. This hydrogen-bond coordination behaviour has been uniquely defined for more than 70 unique atom types, and has led to the development of a methodology to construct hypothetical hydrogen-bond arrangements. Comparing the constructed hydrogen-bond arrangements with known crystal structures shows promise in the assessment of structural stability, and some initial examples of industrially relevant polymorphs, co-crystals and hydrates are described.

Structural investigation of (2E)-2-(ethoxycarbonyl)-3-[(4-methoxyphenyl)amino]prop-2-enoic acid: X-ray crystal structure, spectroscopy and DFT

NASA Astrophysics Data System (ADS)

Venkatesan, Perumal; Rajakannan, Venkatachalam; Venkataramanan, Natarajan S.; Ilangovan, Andivelu; Sundius, Tom; Thamotharan, Subbiah

2016-09-01

The title compound, (2E)-2-(ethoxycarbonyl)-3-[(4-methoxyphenyl)amino]prop-2-enoic acid is characterized by means of X-ray crystallography, spectroscopic methods and quantum chemical calculations. The title compound crystallizes in centrosymmetric space group P21/c. Moreover, the crystal structure is primarily stabilized through intramolecular Nsbnd H⋯O and Osbnd H⋯O and intermolecular Nsbnd H⋯O and Csbnd H⋯O interactions along with carbonyl⋯carbonyl and Csbnd H⋯C contacts. These intermolecular interactions are analysed and quantified by using Hirshfeld surface analysis, PIXEL energy, NBO, AIM and DFT calculations. The overall lattice energies of the title and parent compounds suggest that the title compound is stabilized by a 4.5 kcal mol-1 higher energy than the parent compound. The additional stabilization force comes from the methoxy substitution on the title molecule, which is evident since the methoxy group is involved in the intermolecular Csbnd H⋯O interaction as an acceptor. The vibrational modes of the interacting groups are investigated using both experimental and theoretical FT-IR and FT-Raman spectra. The experimental and theoretical UV-Vis spectra agree well. The time dependent DFT spectra show that the ligand-to-ligand charge transfer is responsible for the intense absorbance of the compound.

Synthesis, crystal structure, spectroscopic characterization, Hirshfeld surface analysis, and DFT calculations of 1,4-dimethyl-2-oxo-pyrimido[1,2-a]benzimidazole hydrate

NASA Astrophysics Data System (ADS)

El Bakri, Youness; Anouar, El Hassane; Ramli, Youssef; Essassi, El Mokhtar; Mague, Joel T.

2018-01-01

Imidazopyrimidine derivatives are organic synthesized compounds with a pyrimido[1,2-a]benzimidazole as basic skeleton. They are known for their various biological properties and as an important class of compounds in medicinal chemistry. A new 1,4-dimethyl-2-oxo-pyrimido[1,2-a]benzimidazole hydrate derivative of the tilted group has been synthesized and characterized by spectroscopic techniques NMR and FT-IR; and by a single crystal X-ray diffraction. The X-ray results showed that the tricyclic core of the title compound, C12H11N3O·H2O, is almost planar. The molecules stack along the a-axis direction in head-to- tail fashion through π-stacking interactions involving all three rings. The stacks are tied together by direct Csbnd H⋯O hydrogen bonds and by Osbnd H⋯O, Osbnd N⋯N and Csbnd H⋯O hydrogen bonds with the lattice water. DFT calculations at B3LYP/6-311++G(d,p) in gas phase an polarizable continuum model have been carried out to predict the spectral and geometrical data of the tilted compound. The obtained results showed relatively good correlations between the predicted and experimental data with correlation coefficients higher than 98%.

Multiple solvent crystal structures of ribonuclease A: An assessment of the method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dechene, Michelle; Wink, Glenna; Smith, Mychal

2010-11-12

The multiple solvent crystal structures (MSCS) method uses organic solvents to map the surfaces of proteins. It identifies binding sites and allows for a more thorough examination of protein plasticity and hydration than could be achieved by a single structure. The crystal structures of bovine pancreatic ribonuclease A (RNAse A) soaked in the following organic solvents are presented: 50% dioxane, 50% dimethylformamide, 70% dimethylsulfoxide, 70% 1,6-hexanediol, 70% isopropanol, 50% R,S,R-bisfuran alcohol, 70% t-butanol, 50% trifluoroethanol, or 1.0M trimethylamine-N-oxide. This set of structures is compared with four sets of crystal structures of RNAse A from the protein data bank (PDB) andmore » with the solution NMR structure to assess the validity of previously untested assumptions associated with MSCS analysis. Plasticity from MSCS is the same as from PDB structures obtained in the same crystal form and deviates only at crystal contacts when compared to structures from a diverse set of crystal environments. Furthermore, there is a good correlation between plasticity as observed by MSCS and the dynamic regions seen by NMR. Conserved water binding sites are identified by MSCS to be those that are conserved in the sets of structures taken from the PDB. Comparison of the MSCS structures with inhibitor-bound crystal structures of RNAse A reveals that the organic solvent molecules identify key interactions made by inhibitor molecules, highlighting ligand binding hot-spots in the active site. The present work firmly establishes the relevance of information obtained by MSCS.« less

Synthesis, structural and spectral characterization of a novel NLO crystal N,N‧-diphenylguanidinium picrate: diacetone solvate

NASA Astrophysics Data System (ADS)

Shanmugavadivu, T.; Dhandapani, M.; Naveen, S.; Lokanath, N. K.

2017-09-01

An organic NLO active material N,N‧-diphenylguanidinium picrate: diacetone solvate (C13H14N3+. C6H2N3O7-. 2C3H6O) (DPGPD) was synthesized and single crystals were grown by slow evaporation-solution growth technique at room temperature. DPGPD crystallizes in monoclinic crystal system with noncentrosymmetric space group, Cc confirmed by single crystal X-ray diffraction analysis. The presence of various functional groups was identified from FT-IR spectral analysis and the proton transfer during the formation of compound was confirmed by NMR spectroscopic techniques. The thermal stability was investigated by TG/DTA analyses. Optical transmittance was measured by UV-Vis-NIR spectroscopy and band gap energy was calculated. Photoluminescence spectrum was used to explore its applicability towards laser diodes. Dielectric property of the material was ascertained at different temperatures and it is found that the grown crystal has higher dielectric constant in low frequencies. Photoconductivity study revealed that DPGPD exhibits positive photoconductivity. SHG property was found to be 0.6 times higher than that of KDP.

Chiral lactic hydrazone derivatives as potential bioactive antibacterial agents: Synthesis, spectroscopic, structural and molecular docking studies

NASA Astrophysics Data System (ADS)

Noshiranzadeh, Nader; Heidari, Azam; Haghi, Fakhri; Bikas, Rahman; Lis, Tadeusz

2017-01-01

A series of novel chiral lactic-hydrazone derivatives were synthesized by condensation of (S)-lactic acid hydrazide with salicylaldehyde derivatives and characterized by elemental analysis and spectroscopic studies (FT-IR, 1H NMR and 13C NMR spectroscopy). The structure of one compound was determined by single crystal X-ray analysis. Antibacterial activity of the synthesized compounds was studied against Staphylococcus aureus, Streptococcus pneumonia, Escherichia coli and Pseudomonas aeruginosa as bacterial cultures by broth microdilution method. All of the synthesized compounds showed good antibacterial activity with MIC range of 64-512 μg/mL. Compounds (S,E)-2-hydroxy-N-(2-hydroxy-5-nitrobenzylidene)propanehydrazide (5) and (S,E)-2-hydroxy-N-((3-hydroxy-5-(hydroxymethyl)-2-methylpyridin-4-yl)propanehydrazide (7) were the most effective antibacterial derivatives against S. aureus and E. coli respectively with a MIC value of 64 μg/mL. Bacterial biofilm formation assay showed that these compounds significantly inhibited biofilm formation of P. aeruginosa. Also, in silico molecular docking studies were performed to show lipoteichoic acid synthase (LtaS) inhibitory effect of lactic hydrazone derivatives. The association between electronic and structural effects of some substituents on the benzylidene moiety and the biological activity of these chiral compounds were studied. Structural studies show that compound with higher hydrogen bonding interactions show higher antibacterial activity. The results show chiral hydrazone derivatives based on lactic acid hydrazide could be used as potential lead compounds for developing novel antibacterial agents.

Crystal Structure Variations of Sn Nanoparticles upon Heating

NASA Astrophysics Data System (ADS)

Mittal, Jagjiwan; Lin, Kwang-Lung

2018-04-01

Structural changes in Sn nanoparticles during heating below the melting point have been investigated using differential scanning calorimetry (DSC), x-ray diffraction (XRD) analysis, electron diffraction (ED), and high-resolution transmission electron microscopy (HRTEM). DSC revealed that the heat required to melt the nanoparticles (28.43 J/g) was about half compared with Sn metal (52.80 J/g), which was attributed to the large surface energy contribution for the nanoparticles. ED and XRD analyses of the Sn nanoparticles revealed increased intensity for crystal planes having large interplaner distances compared with regular crystal planes with increasing heat treatment temperature (HTT). HRTEM revealed an increase in interlayer spacing at the surface and near joints between nanoparticles with the HTT, leading to an amorphous structure of nanoparticles at the surface at 220°C. These results highlight the changes that occur in the morphology and crystal structure of Sn nanoparticles at the surface and in the interior with increase of the heat treatment temperature.

Structural colored gels for tunable soft photonic crystals.

PubMed

Harun-Ur-Rashid, Mohammad; Seki, Takahiro; Takeoka, Yukikazu

2009-01-01

A periodically ordered interconnecting porous structure can be embodied in chemical gels by using closest-packed colloidal crystals as templates. The interconnecting porosity not only provides a quick response but also endows the porous gels with structural color arising from coherent Bragg optical diffraction. The structural colors revealed by porous gels can be regulated by several techniques, and thus, it is feasible to obtain desirable, smart, soft materials. A well-known thermosensitive monomer, N-isopropylacrylamide (NIPA), and other minor monomers were used to fabricate various structural colored gels. The selection of minor monomers depended on the targeted properties. This review focuses on the synthesis of templates, structural colored porous gels, and the applications of structural colored gel as smart soft materials for tunable photonic crystals. (c) 2009 The Japan Chemical Journal Forum and Wiley Periodicals, Inc.

Crystal structure of simple metals at high pressures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Degtyareva, Olga

2010-10-22

The effects of pressure on the crystal structure of simple (or sp-) elements are analysed in terms of changes in coordination number, packing density, and interatomic distances, and general rules are established. In the polyvalent elements from groups 14-17, the covalently bonded structures tend to transform to metallic phases with a gradual increase in coordination number and packing density, a behaviour normally expected under pressure. Group 1 and 2 metallic elements, however, show a reverse trend towards structures with low packing density due to intricate changes in their electronic structure. Complex crystal structures such as host-guest and incommensurately modulated structuresmore » found in these elements are given special attention in this review in an attempt to determine their role in the observed phase-transition sequences.« less

Novel Red-Orange Phosphors Na2BaMg(PO4)2:Pr3+: Synthesis, Crystal Structure and Photoluminescence Performance

NASA Astrophysics Data System (ADS)

Pan, Lu; Yang, Xiaozhan; Xiong, Chaoyue; Deng, Dashen; Qin, Chunlin; Feng, Wenlin

2018-01-01

A series of new red-orange emission phosphors Na2BaMg(PO4)2:Pr3+ were synthesised by a high-temperature solid-state reaction. The crystal structure and photoluminescence properties of these samples were characterised by X-ray diffraction and spectroscopic measurements. This compound holds P3̅m1 space group of the trigonal system with the lattice parameters of hexagonal cell a=0.5304(3) nm and c=0.6989(3) nm. The phosphor emits the strongest peak at 606 nm when excited by 449 nm. The average Commission Internationale de l'Eclairage chromaticity coordinates calculated for the phosphors are (0.52, 0.46). The results demonstrate the potential application of these phosphors in solid-state lighting and other fields.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kaoua, Saida; Krimi, Saida; Pechev, Stanislav

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{submore » 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

Structure of initial crystals formed during human amelogenesis

NASA Astrophysics Data System (ADS)

Cuisinier, F. J. G.; Voegel, J. C.; Yacaman, J.; Frank, R. M.

1992-02-01

X-ray diffraction analysis revealed only the existence of carbonated hydroxyapatite (c.HA) during amelogenesis, whereas conventional transmission electron microscopy investigations showed that developing enamel crystals have a ribbon-like habit. The described compositional changes could be an indication for the presence of minerals different from c.HA. However, the absence of identification of such a mineral shows the need of studies by high resolution electron microscopy (HREM) of initial formed human enamel crystals. We demonstrate the existence of two crystal families involved in the early stages of biomineralization: (a) nanometer-size particles which appeared as a precursor phase; (b) ribbon-like crystals, with a structure closely related to c.HA, which by a progressive thickening process tend to attain the mature enamel crystal habit.

Crystal structure, magnetism, and luminescent properties of two isostructural pcu MOFs based on a triangular ligand

NASA Astrophysics Data System (ADS)

Yan, Pen-Ji; Yao, Xiao-Qiang; Xie, Hua; Xiao, Guo-Bin; Liu, Jia-Cheng; Xu, Xin-Jian

2018-05-01

Two isomorphous metal-organic frameworks, {[M(TIPA) (btec)½]H2O}n, [M = Co (1) or Zn (2)] were synthesized hydrothermally based on a semi-rigid N-center triangular ligand TIPA, where TIPA = tris(4-(1H-imidazol-1-yl)-phenyl)amine, H4btec = 1,2,4,5-benzenetetracarboxylic acid. Single crystal structural analyses show that complexes 1 and 2 are isostructural and both feature a twofold interpenetrated pcu topology. In 1 and 2, the btec4- ligand adopting μ2-η2:η1 and μ1-η1:η0 coordination modes connect adjacent dinuclear Co/Zn units to form a 1D straight polymeric chain. Then these chains arranged in parallel/parallel fashion were further extended to a 3D network by exo-tridentate ligand TIPA with μ2-κ2N:N‧ coordination mode. The magnetic property of 1 and the luminescent property of 2 were investigated. Furthermore, the structure and spectroscopic property of 2 were further investigated by DFT and TD-DFT calculations.

Synthesis, spectroscopic characterization and structural investigations of new adduct compound of carbazole with picric acid: DNA binding and antimicrobial studies

NASA Astrophysics Data System (ADS)

Saravanabhavan, Munusamy; Sathya, Krishnan; Puranik, Vedavati G.; Sekar, Marimuthu

2014-01-01

Carbazole picrate (CP), a new organic compound has been synthesized, characterized by various analytical and spectroscopic technique such as FT-IR, UV-Vis, 1H and 13C NMR spectroscopy. An orthorhombic geometry was proposed based on single crystal XRD study. The thermal stability of the crystal was studied by using thermo-gravimetric and differential thermal analyses and found that it was stable up to 170 °C. Further, the newly synthesized title compound was tested for its in vitro antibacterial and antifungal activity against various bacterial and fungal species. Also, the compound was tested for its binding activity with Calf thymus (CT) DNA and the results show a considerable interaction between CP and CT-DNA.

Mueller matrix spectroscopic ellipsometry study of chiral nanocrystalline cellulose films

NASA Astrophysics Data System (ADS)

Mendoza-Galván, Arturo; Muñoz-Pineda, Eloy; Ribeiro, Sidney J. L.; Santos, Moliria V.; Järrendahl, Kenneth; Arwin, Hans

2018-02-01

Chiral nanocrystalline cellulose (NCC) free-standing films were prepared through slow evaporation of aqueous suspensions of cellulose nanocrystals in a nematic chiral liquid crystal phase. Mueller matrix (MM) spectroscopic ellipsometry is used to study the polarization and depolarization properties of the chiral films. In the reflection mode, the MM is similar to the matrices reported for the cuticle of some beetles reflecting near circular left-handed polarized light in the visible range. The polarization properties of light transmitted at normal incidence for different polarization states of incident light are discussed. By using a differential decomposition of the MM, the structural circular birefringence and dichroism of a NCC chiral film are evaluated.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sankari, R. Siva, E-mail: sivasankari.sh@act.edu.in; 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.

Synthesis, crystal structure, NLO and Hirshfeld surface analysis of 1,2,3-triazolyl chalcone single crystal

NASA Astrophysics Data System (ADS)

Shruthi, C.; Ravindrachary, V.; Guruswamy, B.; Lokanath, N. K.; Kumara, Karthik; Goveas, Janet

2018-05-01

Needle shaped brown coloured single crystal of the title compound was grown by slow evaporation technique using methanol as solvent. The grown crystal was characterized using FT-IR, Single crystal XRD, UV-visible and NLO studies. Crystal structure was confirmed by FT-IR study and the functional groups were identified. XRD study reveals that the crystal belongs to orthorhombic crystal system with pnaa space group and the corresponding cell parameters were calculated. UV-visible spectrum shows that the crystal is transparent in the entire visible region and absorption takes place in the UV-range. NLO efficiency of the crystal obtained 0.66 times that of urea was determined by SHG test. The intermolecular interaction and percentage contribution of each individual atom in the crystal lattice was quantized using Hirshfeld surface and 2D finger print analysis.

Impact of Supramolecular Aggregation on the Crystallization Kinetics of Organic Compounds from the Supercooled Liquid State.

PubMed

Kalra, Arjun; Tishmack, Patrick; Lubach, Joseph W; Munson, Eric J; Taylor, Lynne S; Byrn, Stephen R; Li, Tonglei

2017-06-05

Despite numerous challenges in their theoretical description and practical implementation, amorphous drugs are of growing importance to the pharmaceutical industry. One such challenge is to gain molecular level understanding of the propensity of a molecule to form and remain as a glassy solid. In this study, a series of structurally similar diarylamine compounds was examined to elucidate the role of supramolecular aggregation on crystallization kinetics from supercooled liquid state. The structural similarity of the compounds makes it easier to isolate the molecular features that affect crystallization kinetics and glass forming ability of these compounds. To examine the role of hydrogen-bonded aggregation and motifs on crystallization kinetics, a combination of thermal and spectroscopic techniques was employed. Using variable temperature FTIR, Raman, and solid-state NMR spectroscopies, the presence of hydrogen bonding in the melt and glassy state was examined and correlated with observed phase transition behaviors. Spectroscopic results revealed that the formation of hydrogen-bonded aggregates involving carboxylic acid and pyridine nitrogen (acid-pyridine aggregates) between neighboring molecules in the melt state impedes crystallization, while the presence of carboxylic acid dimers (acid-acid dimers) in the melt favors crystallization. This study suggests that glass formation of small molecules is influenced by the type of intermolecular interactions present in the melt state and the kinetics associated with the molecules to assemble into a crystalline lattice. For the compounds that form acid-pyridine aggregates, the formation of energy degenerate chains, produced due to conformational flexibility of the molecules, presents a kinetic barrier to crystallization. The poor crystallization tendency of these aggregates stems from the highly directional hydrogen-bonding interactions needed to form the acid-pyridine chains. Conversely, for the compounds that form acid

Physicochemical and crystal structure analyses of the antidiabetic agent troglitazone.

PubMed

Kobayashi, Katsuhiro; Fukuhara, Hiroshi; Hata, Tadashi; Sekine, Akiko; Uekusa, Hidehiro; Ohashi, Yuji

2003-07-01

The antidiabetic agent troglitazone has two asymmetric carbons located at the chroman ring and the thiazolidine ring and is produced as a mixture of equal amounts of four optical isomers, 2R-5S, 2S-5R, 2R-5R, and 2S-5S. The crystalline powdered drug substance consists of two diastereomer pairs, 2R-5R/2S-5S and 2R-5S/2S-5R. There are many types of crystals obtained from various crystallization conditions. The X-ray structure analysis and the physicochemical analyses of troglitazone were performed. The solvated crystals of the 2R-5R/2S-5S pair were crystallized from several solutions: methanol, ethanol, acetonitrile, and dichloromethane. The ratio of solvent and troglitazone was 1 : 2 (L1/2-form). The monohydrate crystals were obtained from aqueous acetone solution (L1-form). On the other hand, only an anhydrate crystal of the 2R-5S/2S-5R pair was crystallized from various solutions (H0-form). The dihydrous mixed crystal (MA2-form) was obtained from a mixture of the two diastereomer pairs of 2R-5R/2S-5S and 2R-5S/2S-5R in equal amounts by the slow evaporation of aqueous acetone solution. The crystal structure of the MA2-form is similar to the H0-form. When the MA2 crystal was kept under low humidity, it was converted into the dehydrated form (MA0-form) with retention of the single crystal form. The structure of the MA0-form is isomorphous to the H0-form. The MA2-form was converted into the MA0-form and vice versa with retention of the single crystal under low and high humidity, respectively. The crystallization and storage conditions of the drug substances were successfully analyzed.

Raman, AFM and SNOM high resolution imaging of carotene crystals in a model carrot cell system.

PubMed

Rygula, Anna; Oleszkiewicz, Tomasz; Grzebelus, Ewa; Pacia, Marta Z; Baranska, Malgorzata; Baranski, Rafal

2018-05-15

Three non-destructive and complementary techniques, Raman imaging, Atomic Force Microscopy and Scanning Near-field Optical Microscopy were used simultaneously to show for the first time chemical and structural differences of carotenoid crystals. Spectroscopic and microscopic scanning probe measurements were applied to the released crystals or to crystals accumulated in a unique, carotenoids rich callus tissue growing in vitro that is considered as a new model system for plant carotenoid research. Three distinct morphological crystal types of various carotenoid composition were identified, a needle-like, rhomboidal and helical. Raman imaging using 532 and 488 nm excitation lines provided evidence that the needle-like and rhomboidal crystals had similar carotenoid composition and that they were composed mainly of β-carotene accompanied by α-carotene. However, the presence of α-carotene was not identified in the helical crystals, which had the characteristic spatial structure. AFM measurements of crystals identified by Raman imaging revealed the crystal topography and showed the needle-like and rhomboidal crystals were planar but they differed in all three dimensions. Combining SNOM and Raman imaging enabled indication of carotenoid rich structures and visualised their distribution in the cell. The morphology of identified subcellular structures was characteristic for crystalline, membraneous and tubular chromoplasts that are plant organelles responsible for carotenoid accumulation in cells. Copyright © 2018 Elsevier B.V. All rights reserved.

Synthesis, crystal structure, Hirshfeld surface analysis, spectroscopic characterization, reactivity study by DFT and MD approaches and molecular docking study of a novel chalcone derivative

NASA Astrophysics Data System (ADS)

Arshad, Suhana; Pillai, Renjith Raveendran; Zainuri, Dian Alwani; Khalib, Nuridayanti Che; Razak, Ibrahim Abdul; Armaković, Stevan; Armaković, Sanja J.; Panicker, C. Yohannan; Van Alsenoy, C.

2017-05-01

In the present study, the title compound named as (E)-1-(4-bromophenyl)-3-(4-(trifluoromethyl)phenyl)prop-2-en-1-one was synthesized and structurally characterized by single-crystal X-ray diffraction. The compound crystallizes in monoclinic crystal system in P21/c space group, unit cell parameters a = 16.7629 (12) Å, b = 13.9681 (10) Å, c = 5.8740 (4) Å, β = 96.3860 (12)° and Z = 4. Hirshfeld surface analysis revealed that the molecular structure is dominated by H⋯H, C⋯H/H⋯C, Br⋯F/F⋯Br and F⋯F contacts. The FT-IR spectrum was recorded and interpreted in details with the aid of Density Functional Theory (DFT) calculations and Potential Energy Distribution (PED) analysis. Average local ionization energies (ALIE) and Fukui functions have been used as quantum-molecular descriptors to locate the molecule sites that could be of importance from the aspect of reactivity. Degradation properties have been assessed by calculations of bond dissociation energies (BDE) for hydrogen abstraction and the rest of the single acyclic bonds, while molecular dynamics (MD) simulations were used in order to calculate radial distribution functions and determine the atoms with significant interactions with water. In order to understand how the title molecule inhibits and hence increases the catalytic efficiency of MOA-B enzyme, molecular docking study was performed.

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.

Model representations of kerogen structures: An insight from density functional theory calculations and spectroscopic measurements.

PubMed

Weck, Philippe F; Kim, Eunja; Wang, Yifeng; Kruichak, Jessica N; Mills, Melissa M; Matteo, Edward N; Pellenq, Roland J-M

2017-08-01

Molecular structures of kerogen control hydrocarbon production in unconventional reservoirs. Significant progress has been made in developing model representations of various kerogen structures. These models have been widely used for the prediction of gas adsorption and migration in shale matrix. However, using density functional perturbation theory (DFPT) calculations and vibrational spectroscopic measurements, we here show that a large gap may still remain between the existing model representations and actual kerogen structures, therefore calling for new model development. Using DFPT, we calculated Fourier transform infrared (FTIR) spectra for six most widely used kerogen structure models. The computed spectra were then systematically compared to the FTIR absorption spectra collected for kerogen samples isolated from Mancos, Woodford and Marcellus formations representing a wide range of kerogen origin and maturation conditions. Limited agreement between the model predictions and the measurements highlights that the existing kerogen models may still miss some key features in structural representation. A combination of DFPT calculations with spectroscopic measurements may provide a useful diagnostic tool for assessing the adequacy of a proposed structural model as well as for future model development. This approach may eventually help develop comprehensive infrared (IR)-fingerprints for tracing kerogen evolution.

The Crystal Structure of GXGD Membrane Protease FlaK

DOE Office of Scientific and Technical Information (OSTI.GOV)

J Hu; Y Xue; S Lee

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.more » 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.« less

The crystal structure of GXGD membrane protease FlaK

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu, Jian; Xue, Yi; Lee, Sangwon

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.more » 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.« less

Crystal structure optimisation using an auxiliary equation of state

NASA Astrophysics Data System (ADS)

Jackson, Adam J.; Skelton, Jonathan M.; Hendon, Christopher H.; Butler, Keith T.; Walsh, Aron

2015-11-01

Standard procedures for local crystal-structure optimisation involve numerous energy and force calculations. It is common to calculate an energy-volume curve, fitting an equation of state around the equilibrium cell volume. This is a computationally intensive process, in particular, for low-symmetry crystal structures where each isochoric optimisation involves energy minimisation over many degrees of freedom. Such procedures can be prohibitive for non-local exchange-correlation functionals or other "beyond" density functional theory electronic structure techniques, particularly where analytical gradients are not available. We present a simple approach for efficient optimisation of crystal structures based on a known equation of state. The equilibrium volume can be predicted from one single-point calculation and refined with successive calculations if required. The approach is validated for PbS, PbTe, ZnS, and ZnTe using nine density functionals and applied to the quaternary semiconductor Cu2ZnSnS4 and the magnetic metal-organic framework HKUST-1.

Field-controlled structures in ferromagnetic cholesteric liquid crystals.

PubMed

Medle Rupnik, Peter; Lisjak, Darja; Čopič, Martin; Čopar, Simon; Mertelj, Alenka

2017-10-01

One of the advantages of anisotropic soft materials is that their structures and, consequently, their properties can be controlled by moderate external fields. Whereas the control of materials with uniform orientational order is straightforward, manipulation of systems with complex orientational order is challenging. We show that a variety of structures of an interesting liquid material, which combine chiral orientational order with ferromagnetic one, can be controlled by a combination of small magnetic and electric fields. In the suspensions of magnetic nanoplatelets in chiral nematic liquid crystals, the platelet's magnetic moments orient along the orientation of the liquid crystal and, consequently, the material exhibits linear response to small magnetic fields. In the absence of external fields, orientations of the liquid crystal and magnetization have wound structure, which can be either homogeneously helical, disordered, or ordered in complex patterns, depending on the boundary condition at the surfaces and the history of the sample. We demonstrate that by using different combinations of small magnetic and electric fields, it is possible to control reversibly the formation of the structures in a layer of the material. In such a way, different periodic structures can be explored and some of them may be suitable for photonic applications. The material is also a convenient model system to study chiral magnetic structures, because it is a unique liquid analog of a solid helimagnet.

Unsupervised learning of structure in spectroscopic cubes

NASA Astrophysics Data System (ADS)

Araya, M.; Mendoza, M.; Solar, M.; Mardones, D.; Bayo, A.

2018-07-01

We consider the problem of analyzing the structure of spectroscopic cubes using unsupervised machine learning techniques. We propose representing the target's signal as a homogeneous set of volumes through an iterative algorithm that separates the structured emission from the background while not overestimating the flux. Besides verifying some basic theoretical properties, the algorithm is designed to be tuned by domain experts, because its parameters have meaningful values in the astronomical context. Nevertheless, we propose a heuristic to automatically estimate the signal-to-noise ratio parameter of the algorithm directly from data. The resulting light-weighted set of samples (≤ 1% compared to the original data) offer several advantages. For instance, it is statistically correct and computationally inexpensive to apply well-established techniques of the pattern recognition and machine learning domains; such as clustering and dimensionality reduction algorithms. We use ALMA science verification data to validate our method, and present examples of the operations that can be performed by using the proposed representation. Even though this approach is focused on providing faster and better analysis tools for the end-user astronomer, it also opens the possibility of content-aware data discovery by applying our algorithm to big data.

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.

Fabrication of large binary colloidal crystals with a NaCl structure

PubMed Central

Vermolen, E. C. M.; Kuijk, A.; Filion, L. C.; Hermes, M.; Thijssen, J. H. J.; Dijkstra, M.; van Blaaderen, A.

2009-01-01

Binary colloidal crystals offer great potential for tuning material properties for applications in, for example, photonics, semiconductors and spintronics, because they allow the positioning of particles with quite different characteristics on one lattice. For micrometer-sized colloids, it is believed that gravity and slow crystallization rates hinder the formation of high-quality binary crystals. Here, we present methods for growing binary colloidal crystals with a NaCl structure from relatively heavy, hard-sphere-like, micrometer-sized silica particles by exploring the following external fields: electric, gravitational, and dielectrophoretic fields and a structured surface (colloidal epitaxy). Our simulations show that the free-energy difference between the NaCl and NiAs structures, which differ in their stacking of the hexagonal planes of the larger spheres, is very small (≈0.002 kBT). However, we demonstrate that the fcc stacking of the large spheres, which is crucial for obtaining the pure NaCl structure, can be favored by using a combination of the above-mentioned external fields. In this way, we have successfully fabricated large, 3D, oriented single crystals having a NaCl structure without stacking disorder. PMID:19805259

4-Methyl-1H-Indazole-5-Boronic acid: Crystal structure, vibrational spectra and DFT simulations

NASA Astrophysics Data System (ADS)

Dikmen, Gökhan

2017-12-01

Molecular structure, conformer forms, geometric parameters and vibrational assignments and properties of 4-Methyl-1H-Indazole-5-Boronic Acid (4M1HI5BA) were theoretically and experimentally studied using Raman, FT-IR, XRD spectroscopic methods and quantum chemical calculations. Raman and FT-IR spectra were examined range from 4000 to 400 cm-1. Moreover, single crystals of 4M1HI5BA were prepared in order to use in XRD experiments. Vibrational assignments were carried out using total energy distribution (TED) values. Furthermore, HOMO and LUMO were calculated for 4M1HI5BA. Four different conformations of 4M1HI5BA were calculated in only gas phase. The theoretical and experimental results show that in order to predict vibrational wavenumbers B3LYP/6-311++G(d,p) may provide acceptable results and the most stable conformer of 4M1HI5BA is predicted to be envelope conformer.

Crystal structure and vibrational spectra of piperazinium bis(4-hydroxybenzenesulphonate) molecular-ionic crystal

NASA Astrophysics Data System (ADS)

Marchewka, M. K.; Pietraszko, A.

2008-02-01

The piperazinium bis(4-hydroxybenzenesulphonate) crystallizes from water solution at room temperature in P2 1/ c space group of monoclinic system. The crystals are built up of doubly protonated piperazinium cations and ionized 4-hydroxybenzenesulphonate anions that interact through weak hydrogen bonds of O-H⋯O and N-H⋯O type. Mutual orientation of anions is determined by non-conventional hydrogen bonds of C-H⋯π type. Room temperature powder FT IR and FT Raman measurements were carried out. The vibrational spectra are in full agreement with the structure obtained from X-ray crystallography. The big single crystals of the title salt can be grown.

Crystal structure of κ-Ag2Mg5

NASA Astrophysics Data System (ADS)

Castro, Facundo J.; Primo, Gastón A.; Urretavizcaya, Guillermina

2018-02-01

The structure of κ-Ag2Mg5 has been refined based on X-ray powder diffraction measurements (Rwp = 0.083). The compound has been prepared by combining mechanical alloying techniques and thermal treatments. The intermetallic presents the prototypical structure of Co2Al5, an hexagonal crystal with the symmetries of space group P63/mmc, and belongs to the family of kappa-phase structure compounds. The unit cell dimensions are a=8.630(1) Å and c=8.914(1) Å. Five crystallographically independent sites are occupied, Wyckoff positions 12k, 6h and 2a are filled with Mg, another 6h site is occupied with Ag, and the 2c site presents mixed Ag/Mg occupancy. The crystal chemistry of the structure and bonding are briefly discussed in the paper.

Confirming the Revised C-Terminal Domain of the MscL Crystal Structure

PubMed Central

Maurer, Joshua A.; Elmore, Donald E.; Clayton, Daniel; Xiong, Li; Lester, Henry A.; Dougherty, Dennis A.

2008-01-01

The structure of the C-terminal domain of the mechanosensitive channel of large conductance (MscL) has generated significant controversy. As a result, several structures have been proposed for this region: the original crystal structure (1MSL) of the Mycobacterium tuberculosis homolog (Tb), a model of the Escherichia coli homolog, and, most recently, a revised crystal structure of Tb-MscL (2OAR). To understand which of these structures represents a physiological conformation, we measured the impact of mutations to the C-terminal domain on the thermal stability of Tb-MscL using circular dichroism and performed molecular dynamics simulations of the original and the revised crystal structures of Tb-MscL. Our results imply that this region is helical and adopts an α-helical bundle conformation similar to that observed in the E. coli MscL model and the revised Tb-MscL crystal structure. PMID:18326638

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rao Popuri, Srinivasa; University of Bordeaux, ICMCB, UPR 9048, F-33608 Pessac; National Institute for Research and Development in Electrochemistry and Condensed Matter, Timisoara, Plautius Andronescu Str. No. 1, 300224 Timisoara

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 reversiblemore » 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.« less

Ab initio calculations of the electronic structure and specific optical features of β-LiNH4SO4 single crystals

NASA Astrophysics Data System (ADS)

Rudysh, M. Ya.; Brik, M. G.; Stadnyk, V. Yo.; Brezvin, R. S.; Shchepanskyi, P. A.; Fedorchuk, A.; Khyzhun, O. Y.; Kityk, I. V.; Piasecki, M.

2018-01-01

In the present work complex experimental and theoretical studies of electronic and optical properties for β-lithium-ammonium sulfate crystals of good optical quality are performed using the X-ray photoelectron spectroscopy (XPS) and X-ray emission spectroscopy (XES). Standard immersion and spectroscopic techniques accompanied by the theoretical quantum-chemical calculations in the density functional theory (DFT) framework were applied. Calculations of band structure and related properties were carried out within a framework of local density and generalized gradient approximations as well as hybrid B3LYP functionals. The energy levels features and their origin are established from the DFT calculations and they were ferified by XPS and XES measurements. Theoretical and experimental refractive indices dispersions along the principal crystallographic directions (nx, ny and nz) as well as birefringence dispersion (Δnx, Δny and Δnz) in the visible spectral range are obtained. It was found a closeness of nx and ny curves for the titled crystals. More precise birefringence examining predicts their intersection at λ ≈ 190 nm.

Effects of thermo-order-mechanical coupling on band structures in liquid crystal nematic elastomer porous phononic crystals.

PubMed

Yang, Shuai; Liu, Ying

2018-08-01

Liquid crystal nematic elastomers are one kind of smart anisotropic and viscoelastic solids simultaneously combing the properties of rubber and liquid crystals, which is thermal sensitivity. In this paper, the wave dispersion in a liquid crystal nematic elastomer porous phononic crystal subjected to an external thermal stimulus is theoretically investigated. Firstly, an energy function is proposed to determine thermo-induced deformation in NE periodic structures. Based on this function, thermo-induced band variation in liquid crystal nematic elastomer porous phononic crystals is investigated in detail. The results show that when liquid crystal elastomer changes from nematic state to isotropic state due to the variation of the temperature, the absolute band gaps at different bands are opened or closed. There exists a threshold temperature above which the absolute band gaps are opened or closed. Larger porosity benefits the opening of the absolute band gaps. The deviation of director from the structural symmetry axis is advantageous for the absolute band gap opening in nematic state whist constrains the absolute band gap opening in isotropic state. The combination effect of temperature and director orientation provides an added degree of freedom in the intelligent tuning of the absolute band gaps in phononic crystals. Copyright © 2018 Elsevier B.V. All rights reserved.

Crystal structure and optical properties of silver nanorings

NASA Astrophysics Data System (ADS)

Zhou, Li; Fu, Xiao-Feng; Yu, Liao; Zhang, Xian; Yu, Xue-Feng; Hao, Zhong-Hua

2009-04-01

We report the polyol synthesis and crystal structure characterization of silver nanorings, which have perfect circular shape, smooth surface, and elliptical wire cross-section. The characterization results show that the silver nanorings have well-defined crystal of singly twinned along the whole ring. The spatial distribution of the scattering of a silver nanoring with slanted incidence reveals the unique focus effect of the nanoring, and the focus scattering varies with the incident wavelength. The silver nanorings with perfect geometry and well-defined crystal have potential applications in nanoscaled photonics, plasmonic devices, and optical manipulation.

Accurate structural and spectroscopic characterization of prebiotic molecules: The neutral and cationic acetyl cyanide and their related species.

PubMed

Bellili, A; Linguerri, R; Hochlaf, M; Puzzarini, C

2015-11-14

In an effort to provide an accurate structural and spectroscopic characterization of acetyl cyanide, its two enolic isomers and the corresponding cationic species, state-of-the-art computational methods, and approaches have been employed. The coupled-cluster theory including single and double excitations together with a perturbative treatment of triples has been used as starting point in composite schemes accounting for extrapolation to the complete basis-set limit as well as core-valence correlation effects to determine highly accurate molecular structures, fundamental vibrational frequencies, and rotational parameters. The available experimental data for acetyl cyanide allowed us to assess the reliability of our computations: structural, energetic, and spectroscopic properties have been obtained with an overall accuracy of about, or better than, 0.001 Å, 2 kcal/mol, 1-10 MHz, and 11 cm(-1) for bond distances, adiabatic ionization potentials, rotational constants, and fundamental vibrational frequencies, respectively. We are therefore confident that the highly accurate spectroscopic data provided herein can be useful for guiding future experimental investigations and/or astronomical observations.

Syntheses, spectroscopic characterization, SOD-like properties and antibacterial activities of dimer copper (II) and nickel (II) complexes based on imine ligands containing 2-aminothiophenol moiety: X-ray crystal structure determination of disulfide Schiff bases

NASA Astrophysics Data System (ADS)

Bharti, Sulakshna; Choudhary, Mukesh; Mohan, Bharti; Rawat, S. P.; Sharma, S. R.; Ahmad, K.

2018-07-01

A series of new dimer complexes of copper (II) and nickel (II) were designed and synthesized using the Schiff base ligands which was formed by the condensation of 2-aminothiophenol with 2- methoxybenzaldehyde, 3-formylbenzonitrile and 3-bromo-2-hydroxy-5-nitrobenzaldehyde, respectively. The synthesized metallic complexes were characterized by using different physicochemical and spectroscopic methods. The most plausible geometry for the 1:2 complexes appeared to be distorted square-planar or tetrahedral environments. All the synthesized metal complexes are found to be binuclear and confirmed by elemental analyses, magnetic susceptibility measurements and ESR spectroscopy. The Schiff base ligands (HL1/HL2/H2L) were coordinated to the metal ions through the ONS/SNN and/or N, S donor atoms. In order to prevent the oxidation of the thiol group during the formation of Schiff bases and its complexes, all of the reactions were carried out under an inert atmosphere of argon. The X-ray structures of the Schiff base ligands showed that in the crystalline form the SH groups were oxidized to produce a disulfide Schiff bases as a new double Schiff base ligands (L1a/L2a/H2La). The L1b ligand is a bicyclic ring system of N, S-containing heterocyclic. The crystal structures of the double Schiff bases were determined by single crystal X-ray diffraction. The molar conductivity values of the complexes in DMSO implied the presence of non-electrolyte species. The SOD-like activity of Schiff bases and its complexes were investigated by NBT-DMSO assay and IC50 values were evaluated. Their biological properties have also been studied. These complexes were also tested for their in vitro antibacterial screening activities against three bacteria (Streptococcus aureus, Salmonella typhi, and Escherichia coli) comparing with the Schiff base ligands. Most of the complexes have higher antibacterial activities than those of the free Schiff bases, double Schiff bases and the control.

Studying the orientation of bio-objects by nematic liquid crystals

NASA Astrophysics Data System (ADS)

Zubtsova, Yu. A.; Kamanin, A. A.; Kamanina, N. V.

2017-05-01

We have studied the ability of a liquid-crystal (LC) matrix to visualize and orient DNA molecules. It is established that the relief of the interface between the LC mesophase and conducting contact can be improved without using an additional high-ohmic polymer layer. Spectroscopic and ellipsometric techniques revealed changes in the refractive properties and structure of composites. The obtained results can be used in creating devices for rapid DNA testing with retained form of biostructures.

Discovery of a diamond-based photonic crystal structure in beetle scales.

PubMed

Galusha, Jeremy W; Richey, Lauren R; Gardner, John S; Cha, Jennifer N; Bartl, Michael H

2008-05-01

We investigated the photonic crystal structure inside iridescent scales of the weevil Lamprocyphus augustus. By combining a high-resolution structure analysis technique based on sequential focused ion beam milling and scanning electron microscopy imaging with theoretical modeling and photonic band-structure calculations, we discovered a natural three-dimensional photonic structure with a diamond-based crystal lattice operating at visible wavelengths. Moreover, we found that within individual scales, the diamond-based structure is assembled in the form of differently oriented single-crystalline micrometer-sized pixels with only selected lattice planes facing the scales' top surface. A comparison of results obtained from optical microreflectance measurements with photonic band-structure calculations reveals that it is this sophisticated microassembly of the diamond-based crystal lattice that lends Lamprocyphus augustus its macroscopically near angle-independent green coloration.

Monomer structure of a hyperthermophilic β-glucosidase mutant forming a dodecameric structure in the crystal form

PubMed Central

Nakabayashi, Makoto; Kataoka, Misumi; Watanabe, Masahiro; Ishikawa, Kazuhiko

2014-01-01

One of the β-glucosidases from Pyrococcus furiosus (BGLPf) is found to be a hyperthermophilic tetrameric enzyme that can degrade cellooligosaccharides. Recently, the crystal structures of the tetrameric and dimeric forms were solved. Here, a new monomeric form of BGLPf was constructed by removing the C-terminal region of the enzyme and its crystal structure was solved at a resolution of 2.8 Å in space group P1. It was discovered that the mutant enzyme forms a unique dodecameric structure consisting of two hexameric rings in the asymmetric unit of the crystal. Under biological conditions, the mutant enzyme forms a monomer. This result helps explain how BGLPf has attained its oligomeric structure and thermostability. PMID:25005077

Structural and optical properties of WTe2 single crystals synthesized by DVT technique

NASA Astrophysics Data System (ADS)

Dixit, Vijay; Vyas, Chirag; Pathak, V. M.; Soalanki, G. K.; Patel, K. D.

2018-05-01

Layered transition metal di-chalcogenide (LTMDCs) crystals have attracted much attention due to their potential in optoelectronic device applications recently due to realization of their monolayer based structures. In the present investigation we report growth of WTe2 single crystals by direct vapor transport (DVT) technique. These crystals are then characterized by energy dispersive analysis of x-rays (EDAX) to study stoichiometric composition after growth. The structural properties are studied by x-ray diffraction (XRD) and selected area electron diffraction (SAED) is used to confirm orthorhombic structure of grown WTe2 crystal. Surface morphological properties of the crystals are also studied by scanning electron microscope (SEM). The optical properties of the grown crystals are studied by UV-Visible spectroscopy which gives direct band gap of 1.44 eV for grown WTe2 single crystals.

Metalloprotein Crystallography: More than a Structure.

PubMed

Bowman, Sarah E J; Bridwell-Rabb, Jennifer; Drennan, Catherine L

2016-04-19

Metal ions and metallocofactors play important roles in a broad range of biochemical reactions. Accordingly, it has been estimated that as much as 25-50% of the proteome uses transition metal ions to carry out a variety of essential functions. The metal ions incorporated within metalloproteins fulfill functional roles based on chemical properties, the diversity of which arises as transition metals can adopt different redox states and geometries, dictated by the identity of the metal and the protein environment. The coupling of a metal ion with an organic framework in metallocofactors, such as heme and cobalamin, further expands the chemical functionality of metals in biology. The three-dimensional visualization of metal ions and complex metallocofactors within a protein scaffold is often a starting point for enzymology, highlighting the importance of structural characterization of metalloproteins. Metalloprotein crystallography, however, presents a number of implicit challenges including correctly incorporating the relevant metal or metallocofactor, maintaining the proper environment for the protein to be purified and crystallized (including providing anaerobic, cold, or aphotic environments), and being mindful of the possibility of X-ray induced damage to the proteins or incorporated metal ions. Nevertheless, the incorporated metals or metallocofactors also present unique advantages in metalloprotein crystallography. The significant resonance that metals undergo with X-ray photons at wavelengths used for protein crystallography and the rich electronic properties of metals, which provide intense and spectroscopically unique signatures, allow a metalloprotein crystallographer to use anomalous dispersion to determine phases for structure solution and to use simultaneous or parallel spectroscopic techniques on single crystals. These properties, coupled with the improved brightness of beamlines, the ability to tune the wavelength of the X-ray beam, the availability of

A hybrid computational-experimental approach for automated crystal structure solution

NASA Astrophysics Data System (ADS)

Meredig, Bryce; Wolverton, C.

2013-02-01

Crystal structure solution from diffraction experiments is one of the most fundamental tasks in materials science, chemistry, physics and geology. Unfortunately, numerous factors render this process labour intensive and error prone. Experimental conditions, such as high pressure or structural metastability, often complicate characterization. Furthermore, many materials of great modern interest, such as batteries and hydrogen storage media, contain light elements such as Li and H that only weakly scatter X-rays. Finally, structural refinements generally require significant human input and intuition, as they rely on good initial guesses for the target structure. To address these many challenges, we demonstrate a new hybrid approach, first-principles-assisted structure solution (FPASS), which combines experimental diffraction data, statistical symmetry information and first-principles-based algorithmic optimization to automatically solve crystal structures. We demonstrate the broad utility of FPASS to clarify four important crystal structure debates: the hydrogen storage candidates MgNH and NH3BH3; Li2O2, relevant to Li-air batteries; and high-pressure silane, SiH4.

Synthesis, spectroscopic characterization and structural investigations of new adduct compound of carbazole with picric acid: DNA binding and antimicrobial studies.

PubMed

Saravanabhavan, Munusamy; Sathya, Krishnan; Puranik, Vedavati G; Sekar, Marimuthu

2014-01-24

Carbazole picrate (CP), a new organic compound has been synthesized, characterized by various analytical and spectroscopic technique such as FT-IR, UV-Vis, (1)H and (13)C NMR spectroscopy. An orthorhombic geometry was proposed based on single crystal XRD study. The thermal stability of the crystal was studied by using thermo-gravimetric and differential thermal analyses and found that it was stable up to 170°C. Further, the newly synthesized title compound was tested for its in vitro antibacterial and antifungal activity against various bacterial and fungal species. Also, the compound was tested for its binding activity with Calf thymus (CT) DNA and the results show a considerable interaction between CP and CT-DNA. Copyright © 2013 Elsevier B.V. All rights reserved.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Choudhury, Rajul Ranjan, E-mail: rajul@barc.gov.in; 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.

Picosecond fluorescence of intact and dissolved PSI-LHCI crystals.

PubMed

van Oort, Bart; Amunts, Alexey; Borst, Jan Willem; van Hoek, Arie; Nelson, Nathan; van Amerongen, Herbert; Croce, Roberta

2008-12-15

Over the past several years, many crystal structures of photosynthetic pigment-protein complexes have been determined, and these have been used extensively to model spectroscopic results obtained on the same proteins in solution. However, the crystal structure is not necessarily identical to the structure of the protein in solution. Here, we studied picosecond fluorescence of photosystem I light-harvesting complex I (PSI-LHCI), a multisubunit pigment-protein complex that catalyzes the first steps of photosynthesis. The ultrafast fluorescence of PSI-LHCI crystals is identical to that of dissolved crystals, but differs considerably from most kinetics presented in the literature. In contrast to most studies, the data presented here can be modeled quantitatively with only two compartments: PSI core and LHCI. This yields the rate of charge separation from an equilibrated core (22.5 +/- 2.5 ps) and rates of excitation energy transfer from LHCI to core (k(LC)) and vice versa (k(CL)). The ratio between these rates, R = k(CL)/k(LC), appears to be wavelength-dependent and scales with the ratio of the absorption spectra of LHCI and core, indicating the validity of a detailed balance relation between both compartments. k(LC) depends slightly but nonsystematically on detection wavelength, averaging (9.4 +/- 4.9 ps)(-1). R ranges from 0.5 (<690 nm) to approximately 1.3 above 720 nm.

Myelin structures formed by thermotropic smectic liquid crystals

NASA Astrophysics Data System (ADS)

Peddireddy, Karthik Reddy; Kumar, Pramoda; Thutupalli, Shashi; Herminghaus, Stephan; Bahr, Christian

2014-03-01

We report on transient structures, formed by thermotropic smectic-A liquid crystals, resembling the myelin figures of lyotropic lamellar liquid crystals. The thermotropic myelin structures form during the solubilization of a smectic-A droplet in an aqueous phase containing a cationic surfactant at concentrations above the critical micelle concentration. Similar to the lyotropic myelin figures, the thermotropic myelins appear in an optical microscope as flexible tube-like structures growing at the smectic/aqueous interface. Polarizing microscopy and confocal fluorescence microscopy show that the smectic layers are parallel to the tube surface and form a cylindrically bent arrangement around a central line defect in the tube. We study the growth behavior of this new type of myelins and discuss similarities and differences to the classical lyotropic myelin figures.

Crystal structure of alpha poly-p-xylylene.

NASA Technical Reports Server (NTRS)

Kubo, S.; Wunderlich, B.

1971-01-01

A crystal structure of alpha poly-p-xylylene is proposed with the help of data of oriented crystals grown during polymerization. The unit cell is monoclinic with the parameters a = 8.57 A, b = 10.62 A, c = 6.54 A (chain axis), and beta = 101.3 deg. Four repeating units per cell lead to a calculated density of 1.185 g/cu cm and a packing density of 0.71. The probable space group is P2 sub 1/m.

Gallium arsenide single crystal solar cell structure and method of making

NASA Technical Reports Server (NTRS)

Stirn, Richard J. (Inventor)

1983-01-01

A production method and structure for a thin-film GaAs crystal for a solar cell on a single-crystal silicon substrate (10) comprising the steps of growing a single-crystal interlayer (12) of material having a closer match in lattice and thermal expansion with single-crystal GaAs than the single-crystal silicon of the substrate, and epitaxially growing a single-crystal film (14) on the interlayer. The material of the interlayer may be germanium or graded germanium-silicon alloy, with low germanium content at the silicon substrate interface, and high germanium content at the upper surface. The surface of the interface layer (12) is annealed for recrystallization by a pulsed beam of energy (laser or electron) prior to growing the interlayer. The solar cell structure may be grown as a single-crystal n.sup.+ /p shallow homojunction film or as a p/n or n/p junction film. A Ga(Al)AS heteroface film may be grown over the GaAs film.

Synthesis, crystal growth and characterization of bioactive material: 2- Amino-1H-benzimidazolium pyridine-3-carboxylate single crystal- a proton transfer molecular complex

NASA Astrophysics Data System (ADS)

Fathima, K. Saiadali; Kavitha, P.; Anitha, K.

2017-09-01

The 1:1 molecular adducts 2- Amino-1H-benzimidazolium pyridine-3-carboxylate (2ABPC) was synthesized and grown as single crystal where 2-aminobenzimidazole (ABI) acts as a donor and nicotinic acid (NA) acts as an acceptor. The presence of proton and carbon were predicted using 1H and 13C NMR spectral analysis. The molecular structure of the crystal was elucidated by subjecting the grown crystals to the single crystal x-ray diffraction analysis and was refined by full matrix least-squares method to R = 0.038 for 2469 reflections. The vibrational modes of functional group have been studied using FTIR and Raman spectroscopic analysis. The UV-Vis spectrum exhibited a visible band at 246 nm for 2ABPC due to the nicotinate anion of the molecule. Further, the antimicrobial activity of 2ABPC complex against B. subtilis, klebsiella pneumonia, Pseudomonas eruginos and E. coli pathogens was investigated. Minimum Inhibitory Concentration (MIC) for this crystal was obtained using UV spectrometer against MRSA pathogen. It was found that the benzimidazole with aminogroup at position 2 increases the general antimicrobial activities of 2ABPC crystal.

CMOS-Compatible Fabrication for Photonic Crystal-Based Nanofluidic Structure.

PubMed

Peng, Wang; Chen, Youping; Ai, Wu; Zhang, Dailin; Song, Han; Xiong, Hui; Huang, Pengcheng

2017-12-01

Photonic crystal (PC)-based devices have been widely used since 1990s, while PC has just stepped into the research area of nanofluidic. In this paper, photonic crystal had been used as a complementary metal oxide semiconductors (CMOS) compatible part to create a nanofluidic structure. A nanofluidic structure prototype had been fabricated with CMOS-compatible techniques. The nanofluidic channels were sealed by direct bonding polydimethylsiloxane (PDMS) and the periodic gratings on photonic crystal structure. The PC was fabricated on a 4-in. Si wafer with Si 3 N 4 as the guided mode layer and SiO 2 film as substrate layer. The higher order mode resonance wavelength of PC-based nanofluidic structure had been selected, which can confine the enhanced electrical field located inside the nanochannel area. A design flow chart was used to guide the fabrication process. By optimizing the fabrication device parameters, the periodic grating of PC-based nanofluidic structure had a high-fidelity profile with fill factor at 0.5. The enhanced electric field was optimized and located within the channel area, and it can be used for PC-based nanofluidic applications with high performance.

Solvent effects on the crystal growth structure and morphology of the pharmaceutical dirithromycin

NASA Astrophysics Data System (ADS)

Wang, Yuan; Liang, Zuozhong

2017-12-01

Solvent effects on the crystal structure and morphology of pharmaceutical dirithromycin molecules were systematically investigated using both experimental crystallization and theoretical simulation. Dirithromycin is one of the new generation of macrolide antibiotics with two polymorphic forms (Form I and Form II) and many solvate forms. Herein, six solvates of the dirithromycin, including acetonitrile, acetonitrile/water, acetone, 1-propanol, N,N-dimethylformamide (DMF) and cyclohexane, were studied. Experimentally, we crystallized the dirithromycin molecules in different solvents by the solvent evaporating method and measured the crystal structures with the X-ray diffraction (XRD). We compared these crystal structures of dirithromycin solvates and analyzed the solvent property-determined structure evolution. The solvents have a strong interaction with the dirithromycin molecule due to the formation of inter-molecular interactions (such as the hydrogen bonding and close contacts (sum of vdW radii)). Theoretically, we calculated the ideal crystal habit based on the solvated structures with the attachment growth (AE) model. The predicted morphologies and aspect ratios of dirithromycin solvates agree well with the experimental results. This work could be helpful to better understand the structure and morphology evolution of solvates controlled by solvents and guide the crystallization of active pharmaceutical ingredients in the pharmaceutical industry.

DFT calculations in the assignment of solid-state NMR and crystal structure elucidation of a lanthanum(iii) complex with dithiocarbamate and phenanthroline.

PubMed

Gowda, Vasantha; Laitinen, Risto S; Telkki, Ville-Veikko; Larsson, Anna-Carin; Antzutkin, Oleg N; Lantto, Perttu

2016-12-06

The molecular, crystal, and electronic structures as well as spectroscopic properties of a mononuclear heteroleptic lanthanum(iii) complex with diethyldithiocarbamate and 1,10-phenanthroline ligands (3 : 1) were studied by solid-state 13 C and 15 N cross-polarisation (CP) magic-angle-spinning (MAS) NMR, X-ray diffraction (XRD), and first principles density functional theory (DFT) calculations. A substantially different powder XRD pattern and 13 C and 15 N CP-MAS NMR spectra indicated that the title compound is not isostructural to the previously reported analogous rare earth complexes with the space group P2 1 /n. Both 13 C and 15 N CP-MAS NMR revealed the presence of six structurally different dithiocarbamate groups in the asymmetric unit cell, implying a non-centrosymmetric packing arrangement of molecules. This was supported by single-crystal X-ray crystallography showing that the title compound crystallised in the triclinic space group P1[combining macron]. In addition, the crystal structure also revealed that one of the dithiocarbamate ligands has a conformational disorder. NMR chemical shift calculations employing the periodic gauge including projector augmented wave (GIPAW) approach supported the assignment of the experimental 13 C and 15 N NMR spectra. However, the best correspondences were obtained with the structure where the atomic positions in the X-ray unit cell were optimised at the DFT level. The roles of the scalar and spin-orbit relativistic effects on NMR shielding were investigated using the zeroth-order regular approximation (ZORA) method with the outcome that already the scalar relativistic level qualitatively reproduces the experimental chemical shifts. The electronic properties of the complex were evaluated based on the results of the natural bond orbital (NBO) and topology of the electron density analyses. Overall, we apply a multidisciplinary approach acquiring comprehensive information about the solid-state structure and the metal

Simultaneous electrical transport and Raman spectroscopic measurements on individual nanowires of WxV1 - xO2

NASA Astrophysics Data System (ADS)

Wu, Tai-Lung; Whittaker, Luisa; Patridge, C. J.; Banerjee, S.; Sambandamurthy, G.

2011-03-01

Vanadium oxide is a well-know material to study the metal-insulator transition (MIT) in correlated electron systems. Upon heating to about 340 K, VO2 undergoes orders of magnitude drop in resistance from an insulating phase (I) to a metallic phase (M) and accompanies a lattice structural phase transition from a low-temperature monoclinical phase (M1) to a high-temperature tetragonal phase (R). We present results from combined electrical transport and Raman spectroscopic measurements to discern the effects of doping in controllably tuning the MIT in individual nanowires of single crystal WxV1 - xO2 . The MIT temperature (Tc) in our WxV1 - xO2 nanowires can be tuned through a wide range from 280 to 330 K by controlling the dopant concentration. The M-I transition can also driven electrically in these nanowires. Our simultaneous measurement of electrical transport and Raman spectroscopic measurement help us understand the role of structural transition in affecting the macroscopic electrical transition in individual wires.

Model representations of kerogen structures: An insight from density functional theory calculations and spectroscopic measurements

DOE PAGES

Weck, Philippe F.; Kim, Eunja; Wang, Yifeng; ...

2017-08-01

Molecular structures of kerogen control hydrocarbon production in unconventional reservoirs. Significant progress has been made in developing model representations of various kerogen structures. These models have been widely used for the prediction of gas adsorption and migration in shale matrix. However, using density functional perturbation theory (DFPT) calculations and vibrational spectroscopic measurements, we here show that a large gap may still remain between the existing model representations and actual kerogen structures, therefore calling for new model development. Using DFPT, we calculated Fourier transform infrared (FTIR) spectra for six most widely used kerogen structure models. The computed spectra were then systematicallymore » compared to the FTIR absorption spectra collected for kerogen samples isolated from Mancos, Woodford and Marcellus formations representing a wide range of kerogen origin and maturation conditions. Limited agreement between the model predictions and the measurements highlights that the existing kerogen models may still miss some key features in structural representation. A combination of DFPT calculations with spectroscopic measurements may provide a useful diagnostic tool for assessing the adequacy of a proposed structural model as well as for future model development. This approach may eventually help develop comprehensive infrared (IR)-fingerprints for tracing kerogen evolution.« less

Model representations of kerogen structures: An insight from density functional theory calculations and spectroscopic measurements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weck, Philippe F.; Kim, Eunja; Wang, Yifeng

Molecular structures of kerogen control hydrocarbon production in unconventional reservoirs. Significant progress has been made in developing model representations of various kerogen structures. These models have been widely used for the prediction of gas adsorption and migration in shale matrix. However, using density functional perturbation theory (DFPT) calculations and vibrational spectroscopic measurements, we here show that a large gap may still remain between the existing model representations and actual kerogen structures, therefore calling for new model development. Using DFPT, we calculated Fourier transform infrared (FTIR) spectra for six most widely used kerogen structure models. The computed spectra were then systematicallymore » compared to the FTIR absorption spectra collected for kerogen samples isolated from Mancos, Woodford and Marcellus formations representing a wide range of kerogen origin and maturation conditions. Limited agreement between the model predictions and the measurements highlights that the existing kerogen models may still miss some key features in structural representation. A combination of DFPT calculations with spectroscopic measurements may provide a useful diagnostic tool for assessing the adequacy of a proposed structural model as well as for future model development. This approach may eventually help develop comprehensive infrared (IR)-fingerprints for tracing kerogen evolution.« less

DFT simulation, quantum chemical electronic structure, spectroscopic and structure-activity investigations of 4-acetylpyridine

NASA Astrophysics Data System (ADS)

Atilgan, A.; Yurdakul, Ş.; Erdogdu, Y.; Güllüoğlu, M. T.

2018-06-01

The spectroscopic (UV-Vis and infrared), structural and some electronic property observations of the 4-acetylpyridine (4-AP) were reported, which are investigated by using some spectral methods and DFT calculations. FT-IR spectra were obtained for 4-AP at room temperature in the region 4000 cm-1- 400 cm-1. In the DFT calculations, the B3LYP functional with 6-311G++G(d,p) basis set was applied to carry out the quantum mechanical calculations. The Fourier Transform Infrared (FT-IR) and FT-Raman spectra were interpreted by using of normal coordinate analysis based on scaled quantum mechanical force field. The present work expands our understanding of the both the vibrational and structural properties as well as some electronic properties of the 4-AP by means of the theoretical and experimental methods.

Temperature-dependent dielectric functions and interband critical points of sulfur-rich TlIn(S1-xSex)2 layered solid solution crystals

NASA Astrophysics Data System (ADS)

Gomonnai, O. O.; Gordan, O.; Guranich, P. P.; Slivka, A. G.; Gomonnai, A. V.; Zahn, D. R. T.

2017-12-01

Real and imaginary parts of the dielectric function of TlIn(S1-xSex)2 (x = 0.05, 0.08, 0.25) single crystals were determined in the spectral range from 1 to 5 eV within a temperature interval 140-293 K from spectroscopic ellipsometry measurements. The energies of interband transitions (critical points) of the TlIn(S1-xSex)2 crystals were obtained from the second derivative of the real and imaginary parts of dielectric function. Structural phase transitions are behind the observed change of electronic band structure.

Synthesis and Crystal Structure Study of 2’-Se-Adenosine-Derivatized DNA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sheng, J.; Salon, J; Gan, J

2010-01-01

The selenium derivatization of nucleic acids is a novel and promising strategy for 3D structure determination of nucleic acids. Selenium can serve as an excellent anomalous scattering center to solve the phase problem, which is one of the two major bottlenecks in macromolecule X-ray crystallography. The other major bottleneck is crystallization. It has been demonstrated that the incorporated selenium functionality at the 2'-positions of the nucleosides and nucleotides is stable and does not cause significant structure perturbation. Furthermore, it was observed that the 2'-Se-derivatization could facilitate crystallization of oligonucleotides with fast crystal growth and high diffraction quality. Herein, we describemore » a convenient synthesis of the 2'-Se-adenosine phosphoramidite, and report the first synthesis and X-ray crystal structure determination of the DNA containing the 2'-Se-A derivatization. The 3D structure of 2'-Se-A-DNA decamer [5'-GTACGCGT(2'-Se-A)C-3']{sub 2} was determined at 1.75 {angstrom} resolution, the 2'-Se-functionality points to the minor groove, and the Se-modified and native structures are virtually identical. Moreover, we have observed that the 2'-Se-A modification can greatly facilitate the crystal growth with high diffraction quality. In conjunction with the crystallization facilitation by the 2'-Se-U and 2'-Se-T, this novel observation on the 2'-Se-A functionality suggests that the 2'-Se moiety is sole responsible for the crystallization facilitation and the identity of nucleobases does not influence the crystal growth significantly.« less

Crystal structure of hexagonal MnAl(4).

PubMed

Pauling, L

1987-06-01

A structure is proposed for the hexagonal form of MnAl(4), with a(H) = 28.4 A and c(H) = 12.43 A, on the basis of a high-resolution electron micrograph and comparison with crystals of known structures. The proposed structure involves seven 104-atom complexes of 20 Friauf polyhedra, sharing some atoms with one another. It is closely related to the 23.36-A cubic structure of MnAl(4) and to the 14.19-A cubic structure of Mg(32)(Al,Zn)(49).

Magnetic assembly of nonmagnetic particles into photonic crystal structures.

PubMed

He, Le; Hu, Yongxing; Kim, Hyoki; Ge, Jianping; Kwon, Sunghoon; Yin, Yadong

2010-11-10

We report the rapid formation of photonic crystal structures by assembly of uniform nonmagnetic colloidal particles in ferrofluids using external magnetic fields. Magnetic manipulation of nonmagnetic particles with size down to a few hundred nanometers, suitable building blocks for producing photonic crystals with band gaps located in the visible regime, has been difficult due to their weak magnetic dipole moment. Increasing the dipole moment of magnetic holes has been limited by the instability of ferrofluids toward aggregation at high concentration or under strong magnetic field. By taking advantage of the superior stability of highly surface-charged magnetite nanocrystal-based ferrofluids, in this paper we have been able to successfully assemble 185 nm nonmagnetic polymer beads into photonic crystal structures, from 1D chains to 3D assemblies as determined by the interplay of magnetic dipole force and packing force. In a strong magnetic field with large field gradient, 3D photonic crystals with high reflectance (83%) in the visible range can be rapidly produced within several minutes, making this general strategy promising for fast creation of large-area photonic crystals using nonmagnetic particles as building blocks.

Synthesis, growth, structural, spectral, thermal, chemical etching, linear and nonlinear optical and mechanical studies of an organic single crystal 4-chloro 4-nitrostilbene (CONS): a potential NLO material.

PubMed

Dinakaran, Paul M; Kalainathan, S

2013-07-01

4-Chloro 4-nitrostilbene (CONS) a new organic nonlinear optical material has been synthesized. Employing slow evaporation method, good optical quality single crystals (dimensions up to 6×2×3 mm(3)) have been grown using ethyl methyl ketone (EMK) as a solvent. The grown crystals have been subjected to various characterizations such as single crystal X-ray diffraction, powder XRD, Fourier Transform Infrared spectroscopy (FTIR), proton NMR, solid UV absorption, SHG studies. Single crystal X-ray diffraction reveals that the crystal system belongs to monoclinic with noncentrosymmetric space group P21. The UV-Vis absorption spectrum has been recorded and found that the cut off wavelength is 380 nm. Functional groups and the structure of the title compound have been confirmed by FTIR and (1)H NMR spectroscopic analyses respectively. Molecular mass of the CONS confirmed by the high resolution mass spectral analysis .The thermal behavior of the grown crystal has been studied by TG/DTA analysis and it shows the melting point is at 188.66 °C. Dislocations and growth pattern present in the grown crystal revealed by the etching study. The mechanical strength of the CONS crystal has been studied by Vicker's hardness measurement. The SHG efficiency of the grown crystal has been determined by Kurtz and Perry powder test which revealed that the CONS crystal (327 mV) has 15 times greater efficiency than that of KDP (21.7 mV). Copyright © 2013 Elsevier B.V. All rights reserved.

Exploring Solid-State Structure and Physical Properties: A Molecular and Crystal Model Exercise

ERIC Educational Resources Information Center

Bindel, Thomas H.

2008-01-01

A crystal model laboratory exercise is presented that allows students to examine relations among the microscopic-macroscopic-symbolic levels, using crystalline mineral samples and corresponding crystal models. Students explore the relationship between solid-state structure and crystal form. Other structure-property relationships are explored. The…

A STUDY OF DISLOCATION STRUCTURE OF SUBBOUNDARIES IN MOLYBDENUM SINGLE CRYSTALS,

DTIC Science & Technology

MOLYBDENUM, *DISLOCATIONS), GRAIN STRUCTURES(METALLURGY), SINGLE CRYSTALS, ZONE MELTING, ELECTRON BEAM MELTING, GRAIN BOUNDARIES, MATHEMATICAL ANALYSIS, ETCHED CRYSTALS, ETCHING, ELECTROEROSIVE MACHINING, CHINA

Survey and analysis of crystal polymorphism in organic structures

PubMed Central

Kaur, Ramanpreet

2018-01-01

With the intention of producing the most comprehensive treatment of the prevalence of crystal polymorphism among structurally characterized materials, all polymorphic compounds flagged as such within the Cambridge Structural Database (CSD) are analysed and a list of crystallographically characterized organic polymorphic compounds is assembled. Classifying these structures into subclasses of anhydrates, salts, hydrates, non-hydrated solvates and cocrystals reveals that there are significant variations in polymorphism prevalence as a function of crystal type, a fact which has not previously been recognized in the literature. It is also shown that, as a percentage, polymorphic entries are decreasing temporally within the CSD, with the notable exception of cocrystals, which continue to rise at a rate that is a constant fraction of the overall entries. Some phenomena identified that require additional scrutiny include the relative prevalence of temperature-induced phase transitions among organic salts and the paucity of polymorphism in crystals with three or more chemical components. PMID:29765601

Structural evolution in the crystallization of rapid cooling silver melt

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tian, Z.A., E-mail: ze.tian@gmail.com; Laboratory for Simulation and Modelling of Particulate Systems School of Materials Science and Engineering, University of New South Wales, Sydney, NSW 2052; Dong, K.J.

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 temperaturemore » 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.« less

Crystal structure of spinach plastocyanin at 1.7 A resolution.

PubMed Central

Xue, Y.; Okvist, M.; Hansson, O.; Young, S.

1998-01-01

The crystal structure of plastocyanin from spinach has been determined using molecular replacement, with the structure of plastocyanin from poplar as a search model. Successful crystallization was facilitated by site-directed mutagenesis in which residue Gly8 was substituted with Asp. The region around residue 8 was believed to be too mobile for the wild-type protein to form crystals despite extensive screening. The current structure represents the oxidized plastocyanin, copper (II), at low pH (approximately 4.4). In contrast to the similarity in the core region as compared to its poplar counterpart, the structure shows some significant differences in loop regions. The most notable is the large shift of the 59-61 loop where the largest shift is 3.0 A for the C(alpha) atom of Glu59. This results in different patterns of electrostatic potential around the acidic patches for the two proteins. PMID:9792096

Crystal Structures of the β2-Adrenergic Receptor

NASA Astrophysics Data System (ADS)

Weis, William I.; Rosenbaum, Daniel M.; Rasmussen, Søren G. F.; Choi, Hee-Jung; Thian, Foon Sun; Kobilka, Tong Sun; Yao, Xiao-Jie; Day, Peter W.; Parnot, Charles; Fung, Juan J.; Ratnala, Venkata R. P.; Kobilka, Brian K.; Cherezov, Vadim; Hanson, Michael A.; Kuhn, Peter; Stevens, Raymond C.; Edwards, Patricia C.; Schertler, Gebhard F. X.; Burghammer, Manfred; Sanishvili, Ruslan; Fischetti, Robert F.; Masood, Asna; Rohrer, Daniel K.

G protein coupled receptors (GPCRs) constitute the largest family of membrane proteins in the human genome, and are responsible for the majority of signal transduction events involving hormones and neuro-transmitters across the cell membrane. GPCRs that bind to diffusible ligands have low natural abundance, are relatively unstable in detergents, and display basal G protein activation even in the absence of ligands. To overcome these problems two approaches were taken to obtain crystal structures of the β2-adrenergic receptor (β2AR), a well-characterized GPCR that binds cate-cholamine hormones. The receptor was bound to the partial inverse agonist carazolol and co-crystallized with a Fab made to a three-dimensional epitope formed by the third intracellular loop (ICL3), or by replacement of ICL3 with T4 lysozyme. Small crystals were obtained in lipid bicelles (β2AR-Fab) or lipidic cubic phase (β2AR-T4 lysozyme), and diffraction data were obtained using microfocus technology. The structures provide insights into the basal activity of the receptor, the structural features that enable binding of diffusible ligands, and the coupling between ligand binding and G-protein activation.

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.

Structure and spectroscopic properties of neutral and cationic tetratomic [C,H,N,Zn] isomers: A theoretical study

NASA Astrophysics Data System (ADS)

Redondo, Pilar; Largo, Antonio; Vega-Vega, Álvaro; Barrientos, Carmen

2015-05-01

The structure and spectroscopic parameters of the most relevant [C,H,N,Zn] isomers have been studied employing high-level quantum chemical methods. For each isomer, we provide predictions for their molecular structure, thermodynamic stabilities as well as vibrational and rotational spectroscopic parameters which could eventually help in their experimental detection. In addition, we have carried out a detailed study of the bonding situations by means of a topological analysis of the electron density in the framework of the Bader's quantum theory of atoms in molecules. The analysis of the relative stabilities and spectroscopic parameters suggests two linear isomers of the neutral [C,H,N,Zn] composition, namely, cyanidehydridezinc HZnCN (1Σ) and hydrideisocyanidezinc HZnNC (1Σ), as possible candidates for experimental detections. For the cationic [C,H,N,Zn]+ composition, the most stable isomers are the ion-molecule complexes arising from the direct interaction of the zinc cation with either the nitrogen or carbon atom of either hydrogen cyanide or hydrogen isocyanide, namely, HCNZn+ (2Σ) and HCNZn+ (2Σ).

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).

Synthesis and structural characterization of bulk Sb2Te3 single crystal

NASA Astrophysics Data System (ADS)

Sultana, Rabia; Gahtori, Bhasker; Meena, R. S.; Awana, V. P. S.

2018-05-01

We report the growth and characterization of bulk Sb2Te3 single crystal synthesized by the self flux method via solid state reaction route from high temperature melt (850˚C) and slow cooling (2˚C/hour) of constituent elements. The single crystal X-ray diffraction pattern showed the 00l alignment and the high crystalline nature of the resultant sample. The rietveld fitted room temperature powder XRD revealed the phase purity and rhombohedral structure of the synthesized crystal. The formation and analysis of unit cell structure further verified the rhombohedral structure composed of three quintuple layers stacked one over the other. The SEM image showed the layered directional growth of the synthesized crystal carried out using the ZEISS-EVOMA-10 scanning electron microscope The electrical resistivity measurement was carried out using the conventional four-probe method on a quantum design Physical Property Measurement System (PPMS). The temperature dependent electrical resistivity plot for studied Sb2Te3 single crystal depicts metallic behaviour in the absence of any applied magnetic field. The synthesis as well as the structural characterization of as grown Sb2Te3 single crystal is reported and discussed in the present letter.

Synthesis, crystal structure and electronic structure of the binary phase Rh2Cd5

NASA Astrophysics Data System (ADS)

Koley, Biplab; Chatterjee, S.; Jana, Partha P.

2017-02-01

A new phase in the Rh-Cd binary system - Rh2Cd5 has been identified and characterized by single crystal X-ray diffraction and Energy dispersive X-ray analysis. The stoichiometric compound Rh2Cd5 crystallizes with a unit cell containing 14 atoms, in the orthorhombic space group Pbam (55). The crystal structure of Rh2Cd5 can be described as a defect form of the In3Pd5 structure with ordered vacancies, formed of two 2D atomic layers with the stacking sequence: ABAB. The A type layers consist of (3.6.3.6)-Kagomé nets of Cd atoms while the B type layers consist of (35) (37)- nets of both Cd and Rh atoms. The stability of this line phase is investigated by first principle electronic structure calculations on the model of ordered Rh2Cd5.

Dry-growth of silver single-crystal nanowires from porous Ag structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Chuantong, E-mail: chenchuantong@sanken.osaka-u.ac.jp; Nagao, Shijo; Jiu, Jinting

A fabrication method of single crystal Ag nanowires in large scale is introduced without any chemical synthesis in wet processes, which usually generates fivefold twinned nanowires of fcc metals. Dense single-crystal nanowires grow on a mechanically polished surface of micro-porous Ag structure, which is created from Ag micro-particles. The diameter and the length of the nanowires can be controlled simply by changing the temperature and the time of the heating during the nanowire growth in air. Unique growth mechanism is described in detail, based on stress-induced migration accelerated by the micro-porous structure where the origin of Ag nanowires growth ismore » incubated. Transmission electron microscopy analysis on the single crystal nanowires is also presented. This simple method offered an alternative preparation for metallic nanowires, especially with the single crystal structure in numerous applications.« less

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.

Synthesis and crystal structures of three new benzotriazolylpropanamides

PubMed Central

Amenta, Donna S.; Liebing, Phil; Biero, Julia E.; Sherman, Robert J.; Gilje, John W.

2017-01-01

The base-catalyzed Michael addition of 2-methyl­acryl­amide to benzotriazole afforded 3-(1H-benzotriazol-1-yl)-2-methyl­propanamide, C10H12N4O (1), in 32% yield in addition to small amounts of isomeric 3-(2H-benzotriazol-2-yl)-2-methyl­propanamide, C10H12N4O (2). In a similar manner, 3-(1H-benzotriazol-1-yl)-N,N-di­methyl­propanamide, C11H14N4O (3), was prepared from benzotriazole and N,N-di­methyl­acryl­amide. All three products have been structurally characterized by single-crystal X-ray diffraction. The crystal structures of 1 and 2 comprise infinite arrays formed by N—H⋯O and N—H⋯N bridges, as well as π–π inter­actions, while the mol­ecules of 3 are aggregated to simple π-dimers in the crystal. PMID:28638650

Investigations on structural, optical, electrical, mechanical and third-order nonlinear behaviour of 3-aminopyridinium 2,4-dinitrophenolate single crystal

NASA Astrophysics Data System (ADS)

Mohanbabu, B.; Bharathikannan, R.; Siva, G.

2017-10-01

The single crystals of 3-aminopyridinium 2,4-dinitrophenolate (APDP) have been synthesized and grown by slow evaporation technique at room temperature. The crystal system was identified and lattice dimensions were measured from the single-crystal X-ray diffraction (SXRD) analysis. UV-visible absorption and transmittance spectra have been recorded in the region between 250 and 1100 nm. The different vibrational modes of the molecule were studied by Fourier transform infrared (FTIR) spectroscopic analysis. The decreasing tendency of dielectric constant with increasing frequency was analysed in dielectric study. The polarizability value calculated using Penn analysis well agrees with the value calculated using Clausius-Mossotti equation. The photoconductivity and photoluminescence behaviour were also studied on grown APDP crystal. The mechanical strength of the crystal has been studied using a Vickers' microhardness test. The stiffness constant and yield strength of the crystal were also calculated from the microhardness test. The third-order nonlinear optical parameters such as refractive index, absorption coefficient and third-order susceptibility were estimated by Z-scan studies.

Crystal-Structure-Guided Design of Self-Assembling RNA Nanotriangles.

PubMed

Boerneke, Mark A; Dibrov, Sergey M; Hermann, Thomas

2016-03-14

RNA nanotechnology uses RNA structural motifs to build nanosized architectures that assemble through selective base-pair interactions. Herein, we report the crystal-structure-guided design of highly stable RNA nanotriangles that self-assemble cooperatively from short oligonucleotides. The crystal structure of an 81 nucleotide nanotriangle determined at 2.6 Å resolution reveals the so-far smallest circularly closed nanoobject made entirely of double-stranded RNA. The assembly of the nanotriangle architecture involved RNA corner motifs that were derived from ligand-responsive RNA switches, which offer the opportunity to control self-assembly and dissociation. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Temperature influence on spectroscopic properties and 2.7-μm lasing of Er:YAP crystal

NASA Astrophysics Data System (ADS)

Švejkar, Richard; Šulc, Jan; Němec, Michal; Jelínková, Helena; Nejezchleb, Karel; Čech, Miroslav

2018-02-01

The spectroscopic and laser properties of Er:YAP crystal, that is appropriate for generation at 2.7 μm, in temperature range 78 - 400 K are presented. The sample of Er:YAP (1 at. % of Er3+) had face-polished plan-parallel faces without anti-reflection coatings (thickness 4.47 mm). During experiments the Er:YAP was attached to temperature controlled copper holder and it was placed in vacuum chamber. The transmission and emission spectra together with the fluorescence decay time were measured depending on temperature. The Er:YAP crystal was longitudinally pumped by radiation from laser diode that works in pulse regime (repetition rate 66.6 Hz, pulse duration 1.5 ms, pump wavelength 972.5 nm) or in CW regime. Laser resonator was hemispherical, 145 mm in length with flat pumping mirror (HR @ 2.7 μm) and spherical output coupler (r = 150 mm, R = 95 % @ 2.5 - 2.8 μm). The fluorescence decay time of manifold 4I11/2 (upper laser level) became shorter and intensity of up-conversion radiation was increasing with decreasing temperature. In pulsed regime, the highest slope efficiency with respect to absorbed mean power was 1.27 % at 78 K. The maximum output of mean power was 3.5 mW at 78 K, i.e. 8.7 times higher than measured this value at 300 K. The maximal output power 27 mW with slope efficiency up to 3.5 % was achieved in CW. The radiation generated by Er:YAP laser (2.73 μm) is close to absorption peak of water (3 μm) thus this wavelength can be use in medicine and spectroscopy.

Crystal structure of hexagonal MnAl4

PubMed Central

Pauling, Linus

1987-01-01

A structure is proposed for the hexagonal form of MnAl4, with aH = 28.4 Å and cH = 12.43 Å, on the basis of a high-resolution electron micrograph and comparison with crystals of known structures. The proposed structure involves seven 104-atom complexes of 20 Friauf polyhedra, sharing some atoms with one another. It is closely related to the 23.36-Å cubic structure of MnAl4 and to the 14.19-Å cubic structure of Mg32(Al,Zn)49. Images PMID:16593837

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

PubMed Central

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

2015-01-01

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. PMID:26198974

Synthesis, characterization, crystal structure and HSA binding of two new N,O,O-donor Schiff-base ligands derived from dihydroxybenzaldehyde and tert-butylamine

NASA Astrophysics Data System (ADS)

Khosravi, Iman; Hosseini, Farnaz; Khorshidifard, Mahsa; Sahihi, Mehdi; Rudbari, Hadi Amiri

2016-09-01

Two new o-hydroxy Schiff-bases compounds, L1 and L2, were derived from the 1:1 M condensation of 2,3-dihydroxybenzaldehyde and 2,4-dihydroxybenzaldehyde with tert-butylamine and were characterized by elemental analysis, FT-IR, 1H and 13C NMR spectroscopies. The crystal structure of L2 was also determined by single crystal X-ray analysis. The crystal structure of L2 showed that the compound exists as a zwitterionic form in the solid state, with the H atom of the phenol group being transferred to the imine N atom. It adopts an E configuration about the central Cdbnd N double bond. Furthermore, binding of these Schiff base ligands to Human Serum Albumin (HSA) was investigated by fluorescence quenching, absorption spectroscopy, molecular docking and molecular dynamics (MD) simulation methods. The fluorescence emission of HSA was quenched by ligands. Also, suitable models were used to analyze the UV-vis absorption spectroscopy data for titration of HSA solution by various amounts of Schiff bases. The spectroscopic studies revealed that these Schiff bases formed 1:1 complex with HSA. Energy transfer mechanism of quenching was discussed and the values of 3.35 and 1.57 nm as the mean distances between the bound ligands and the HSA were calculated for L1 and L2, respectively. Molecular docking results indicated that the main active binding site for these Schiff bases ligands is in subdomain IB. Moreover, MD simulation results suggested that this Schiff base complex can interact with HSA, with a slight modification of its tertiary structure.

Crystal Structures of Aedes Aegypt Alanine Glyoxylate Aminotransferase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Han,Q.; Robinson, H.; Gao, Y.

Mosquitoes are unique in having evolved two alanine glyoxylate aminotransferases (AGTs). One is 3-hydroxykynurenine transaminase (HKT), which is primarily responsible for catalyzing the transamination of 3-hydroxykynurenine (3-HK) to xanthurenic acid (XA). Interestingly, XA is used by malaria parasites as a chemical trigger for their development within the mosquito. This 3-HK to XA conversion is considered the major mechanism mosquitoes use to detoxify the chemically reactive and potentially toxic 3-HK. The other AGT is a typical dipteran insect AGT and is specific for converting glyoxylic acid to glycine. Here we report the 1.75{angstrom} high-resolution three-dimensional crystal structure of AGT from themore » mosquito Aedes aegypti (AeAGT) and structures of its complexes with reactants glyoxylic acid and alanine at 1.75 and 2.1{angstrom} resolution, respectively. This is the first time that the three-dimensional crystal structures of an AGT with its amino acceptor, glyoxylic acid, and amino donor, alanine, have been determined. The protein is dimeric and adopts the type I-fold of pyridoxal 5-phosphate (PLP)-dependent aminotransferases. The PLP co-factor is covalently bound to the active site in the crystal structure, and its binding site is similar to those of other AGTs. The comparison of the AeAGT-glyoxylic acid structure with other AGT structures revealed that these glyoxylic acid binding residues are conserved in most AGTs. Comparison of the AeAGT-alanine structure with that of the Anopheles HKT-inhibitor complex suggests that a Ser-Asn-Phe motif in the latter may be responsible for the substrate specificity of HKT enzymes for 3-HK.« less

Low-temperature crystal and magnetic structure of α – RuCl 3

DOE PAGES

Cao, Huibo B.; Yan, Jiaqiang; Bridges, Craig A.; ...

2016-04-19

Here, single crystals of the Kitaev spin-liquid candidate α – RuCl 3 have been studied to determine the low-temperature bulk properties, the structure, and the magnetic ground state. Refinements of x-ray diffraction data show that the low-temperature crystal structure is described by space group C2/m with a nearly perfect honeycomb lattice exhibiting less than 0.2% in-plane distortion. The as-grown single crystals exhibit only one sharp magnetic transition at T N = 7 K. The magnetic order below this temperature exhibits a propagation vector of k=(0,1,1/3), which coincides with a three-layer stacking of the C2/m unit cells. Magnetic transitions at highermore » temperatures up to 14 K can be introduced by deformations of the crystal that result in regions in the crystal with a two-layer stacking sequence. The best-fit symmetry-allowed magnetic structure of the as-grown crystals shows that the spins lie in the ac plane, with a zigzag configuration in each honeycomb layer. The three-layer repeat out-of-plane structure can be refined as a 120° spiral order or a collinear structure with a spin direction of 35° away from the a axis. The collinear spin configuration yields a slightly better fit and also is physically preferred. The average ordered moment in either structure is less than 0.45(5) μB per Ru 3+ ion.« less

Crystal Structure of Two V-shaped Ligands with N-Heterocycles

NASA Astrophysics Data System (ADS)

Wang, Gao-Feng; Sun, Shu-Wen; Zhang, Xiao; Sun, Shu-Gang

2017-12-01

Two V-shaped ligands with N-heterocycles, bis(4-(1 H-imidazol-1-yl) phenyl)methanone ( 1), and bis(4-(1 H-benzo[d]imidazol-1-yl)phenyl)methanone ( 2) have been synthesized and characterized by elemental analyses, IR and 1 H NMR spectroscopy. Crystal structures of 1 and 2 have been determined by X-ray diffraction. The crystal of 1 is monoclinic, sp. gr. P21/ c, Z = 4. The crystal of 2 is orthorhombic, sp. gr. Fdd2, Z = 8. X-ray diffraction analyses show that the V-shaped angles of 1 and 2 are 122.72(15)° and 120.7(4)°, respectively. Intermolecular C-H···O, C-H···N, C-H···π, and π···π interactions link the components into three-dimensional networks in the crystal structures.

Glutamate receptors as seen by light: Spectroscopic studies of structure-function relationships

PubMed Central

Mankiewicz, Kimberly A.; Jayaraman, Vasanthi

2010-01-01

Ionotropic glutamate receptors are major excitatory receptors in the central nervous system and also have far reaching influence in other areas of the body. Their modular nature has allowed for the isolation of the ligand binding domain and subsequent structural studies using a variety of spectroscopic techniques. This review will discuss the role of specific ligand:protein interactions in mediating activation in the α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) subtype of glutamate receptors as established by various spectroscopic investigations of the GluR2 and GluR4 subunits of this receptor. Specifically, this review will provide an introduction of the insight gained from X-ray crystallography and nuclear magnetic resonance (NMR) investigations and then go on to focus on studies utilizing vibrational spectroscopy and fluorescence resonance energy transfer (FRET) to study the behavior of the isolated ligand binding domain in solution and discuss the importance of specific ligand:protein interactions in the mechanism of receptor activation. PMID:17934637

Synthesis, crystal structure, thermal and nonlinear optical properties of new metal-organic single crystal: Tetrabromo (piperazinium) zincate (II) (TBPZ)

NASA Astrophysics Data System (ADS)

Boopathi, K.; Babu, S. Moorthy; Ramasamy, P.

2018-04-01

Tetrabromo (piperazinium) zincate, a new metal-organic crystal has been synthesized and its single crystal grown by slow evaporation method. The grown crystal has characterized by structural, spectral, thermal, linear and nonlinear optical properties. Single crystal X-ray diffractions study reveals that grown crystal belongs to orthorhombic crystal system with space group P212121. The presence of functional groups is identified by FT-IR spectral analysis. Thermal stability of the crystal was ascertained by TG-DTA measurement. The second order harmonic generation efficiency was measured using Kurtz and Perry technique and it was found to be 1.5 times that of KDP.

Design, Synthesis, Structural and Spectroscopic Studies of Push-Pull Two-Photon Absorbing Chromophores with Acceptor Groups of Varying Strength

PubMed Central

Morales, Alma R.; Frazer, Andrew; Woodward, Adam W.; Ahn-White, Hyo-Yang; Fonari, Alexandr; Tongwa, Paul; Timofeeva, Tatiana; Belfield, Kevin D.

2013-01-01

A new series of unsymmetrical diphenylaminofluorene-based chromophores with various strong π-electron acceptors were synthesized and fully characterized. The systematic alteration of the structural design facilitated the investigation of effects such as molecular symmetry and strength of electron-donating and/or withdrawing termini have on optical nonlinearity. In order to determine the electronic and geometrical properties of the novel compounds, a thorough investigation was carried out by a combination of linear and nonlinear spectroscopic techniques, single crystal X-ray diffraction, and quantum chemical calculations. Finally, on the basis of two-photon absorption (2PA) cross sections, the general trend for π -electron accepting ability, i.e., ability to accept charge transfer from diphenylamine was: 2-pyran-4-ylidene malononitrile (pyranone) > dicyanovinyl > bis(dicyanomethylidene)indane > 1-(thiophen-2-yl)propenone > dicyanoethylenyl > 3-(thiophen-2-yl)propenone. An analog with the 2-pyran-4-ylidene malononitrile acceptor group exhibited a nearly three-fold enhancement of the 2PA< δ (1650 GM at 840 nm), relative to other members of the series. PMID:23305555

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)

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.

Theoretical exploration of various lithium peroxide crystal structures in a Li-air battery

DOE PAGES

Lau, Kah; Qiu, Dantong; Luo, Xiangyi; ...

2015-01-14

We describe a series of metastable Li₂O₂ crystal structures involving different orientations and displacements of the O₂²⁻ peroxy ions based on the known Li₂O₂ crystal structure. Within the vicinity of the chemical potential ΔG ~ 0.20 eV/Li from the thermodynamic ground state of the Li₂O₂ crystal structure (i.e., Föppl structure), all of these newly found metastable Li₂O₂ crystal structures are found to be insulating and high-k materials, and they have a common unique signature of an O₂²⁻ O-O vibration mode (ω ~ 799–865 cm⁻¹), which is in the range of that commonly observed in Li-air battery experiments, regardless of themore » random O₂²⁻ orientations and the symmetry in the crystal lattice. From XRD patterns analysis, the commercially available Li₂O₂ powder is confirmed to be the thermodynamic ground state Föppl-like structure. However, for Li₂O₂ compounds that are grown electrochemically under the environment of Li-O₂ cells, we found that the XRD patterns alone are not sufficient for structural identification of these metastable Li₂O₂ crystalline phases due to the poor crystallinity of the sample. In addition, the commonly known Raman signal of O₂²⁻ vibration mode is also found to be insufficient to validate the possible existence of these newly predicted Li₂O₂ crystal structures, as all of them similarly share the similar O₂²⁻ vibration mode. However considering that the discharge voltage in most Li-O₂ cells are typically several tenths of an eV below the thermodynamic equilibrium for the formation of ground state Föppl structure, the formation of these metastable Li₂O₂ crystal structures appears to be thermodynamically feasible.« less

Structural investigation of cooperite (PtS) crystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rozhdestvina, V. I., E-mail: veronika@ascnet.ru; Udovenko, A. A.; Rubanov, S. V.

2016-03-15

The single-crystal structure of cooperite, a natural platinum sulfide PtS, is studied by X-ray diffraction supported by high-resolution scanning transmission electron microscopy and X-ray spectrum microanalysis. It is found that, in addition to the main reflections corresponding to the known tetragonal cell (a = 3.47 and c = 6.11 Å; space group P4{sub 2}/mmc), many weak reflections with intensities I ≤ 60σ(I) are clearly observed. These reflections fit the tetragonal cell (space group I4/mmm) with doubled parameters. In structures with small (P4{sub 2}/mmc) and large (I4/mmm) cells, the S atoms occupy statistically two special positions. It is shown that themore » chemical composition of the cooperite crystals deviates from the stoichiometric composition: sulfur-deficient specimens predominate.« less

Ab initio NMR Confirmed Evolutionary Structure Prediction for Organic Molecular Crystals

NASA Astrophysics Data System (ADS)

Pham, Cong-Huy; Kucukbenli, Emine; de Gironcoli, Stefano

2015-03-01

Ab initio crystal structure prediction of even small organic compounds is extremely challenging due to polymorphism, molecular flexibility and difficulties in addressing the dispersion interaction from first principles. We recently implemented vdW-aware density functionals and demonstrated their success in energy ordering of aminoacid crystals. In this work we combine this development with the evolutionary structure prediction method to study cholesterol polymorphs. Cholesterol crystals have paramount importance in various diseases, from cancer to atherosclerosis. The structure of some polymorphs (e.g. ChM, ChAl, ChAh) have already been resolved while some others, which display distinct NMR spectra and are involved in disease formation, are yet to be determined. Here we thoroughly assess the applicability of evolutionary structure prediction to address such real world problems. We validate the newly predicted structures with ab initio NMR chemical shift data using secondary referencing for an improved comparison with experiments.

Structure and spectroscopic propierties of imine acetaldehyde: a possible interstellar molecule

NASA Astrophysics Data System (ADS)

Redondo, Pilar; Largo, Antonio; Barrientos, Carmen

2018-05-01

A previous theoretical study shows that imine acetaldehyde can be obtained from the reaction between protonated vinyl alcohol and azanone. Therefore, imine acetaldehyde could be considered as a good molecule candidate to be found in space and could evolve to more complex organic molecules of prebiotic interest. In the present work, we carried out a computational study of the different conformers of imine acetaldehyde. For characterize its conformers we apply a composite approach which considers the extrapolation to the complete basis set (CBS) limit and core-valence (CV) electron correlation corrections at the at the CC level including single and double excitations and a perturbative treatment of triple excitations (CCSD(T)). This approach provides bond distances with an accuracy of 0.001-0.002 Åand angles accurate to 0.05-0.1°. Vibrational harmonic and anharmonic frequencies and IR intensities are also reported at the CCSD level. The most stable structure corresponds to an antiperiplanar disposition of the oxygen atom and of NH group with the hydrogen atom of the NH group addressed outside the skeleton. Interconversion processes between the four conformers characterized are studied. The lowest isomerization barrier is estimated to be around 1.2 kcal mol-1, making these processes unlikely under low temperature conditions, such as those reigning in the interstellar medium. The reported, at "spectroscopic" accuracy, stabilities, molecular structures, as well as spectroscopic parameters for the four imine acetaldehyde conformers that could help in their laboratory or astronomical detection.

Ab initio molecular crystal structures, spectra, and phase diagrams.

PubMed

Hirata, So; Gilliard, Kandis; He, Xiao; Li, Jinjin; Sode, Olaseni

2014-09-16

Conspectus Molecular crystals are chemists' solids in the sense that their structures and properties can be understood in terms of those of the constituent molecules merely perturbed by a crystalline environment. They form a large and important class of solids including ices of atmospheric species, drugs, explosives, and even some organic optoelectronic materials and supramolecular assemblies. Recently, surprisingly simple yet extremely efficient, versatile, easily implemented, and systematically accurate electronic structure methods for molecular crystals have been developed. The methods, collectively referred to as the embedded-fragment scheme, divide a crystal into monomers and overlapping dimers and apply modern molecular electronic structure methods and software to these fragments of the crystal that are embedded in a self-consistently determined crystalline electrostatic field. They enable facile applications of accurate but otherwise prohibitively expensive ab initio molecular orbital theories such as Møller-Plesset perturbation and coupled-cluster theories to a broad range of properties of solids such as internal energies, enthalpies, structures, equation of state, phonon dispersion curves and density of states, infrared and Raman spectra (including band intensities and sometimes anharmonic effects), inelastic neutron scattering spectra, heat capacities, Gibbs energies, and phase diagrams, while accounting for many-body electrostatic (namely, induction or polarization) effects as well as two-body exchange and dispersion interactions from first principles. They can fundamentally alter the role of computing in the studies of molecular crystals in the same way ab initio molecular orbital theories have transformed research practices in gas-phase physical chemistry and synthetic chemistry in the last half century. In this Account, after a brief summary of formalisms and algorithms, we discuss applications of these methods performed in our group as compelling

Structure, dielectric and electric properties of diisobutylammonium hydrogen sulfate crystal

NASA Astrophysics Data System (ADS)

Bednarchuk, Tamara J.; Kinzhybalo, Vasyl; Markiewicz, Ewa; Hilczer, Bożena; Pietraszko, Adam

2018-02-01

Diisobutylammonium hydrogen sulfate, a new organic-inorganic hybrid compound, was successfully synthesized and three structural phases in 298-433 K temperature range were revealed by differential scanning calorimetry and X-ray powder diffraction studies. Single crystal X-ray diffraction data were used to describe the crystal structures in each particular case. In phase III (below 336/319 K on heating/cooling) the crystal arrangement appears to be within the triclinic symmetry with P-1 space group. During heating in the 336-339 K region (and 319-337 K on cooling) the crystal exists in the phase II, characterized by monoclinic symmetry with P21/c space group. Consequently, above 339 K (during heating, and 337 K during cooling temperature sequences), i.e. in phase I the crystal exhibits orthorhombic symmetry (Cmce space group). Ferroelastic domain structure was observed in phase III. These phase boundaries (III→II and II→I) were accompanied by the presence of small anomalies, apparent in the dielectric permittivity and electric conductivity experimental data. Fast proton transport with activation energy of 0.23 eV was observed in the high temperature phase I and related to phonon assisted proton diffusion conditioned by disorder of diisobutylammonium (diba) cations, as well as by high thermal displacements of oxygen and sulfur atoms of hydrogen sulfate anion (hs).

Eukaryotic major facilitator superfamily transporter modeling based on the prokaryotic GlpT crystal structure.

PubMed

Lemieux, M Joanne

2007-01-01

The major facilitator superfamily (MFS) of transporters represents the largest family of secondary active transporters and has a diverse range of substrates. With structural information for four MFS transporters, we can see a strong structural commonality suggesting, as predicted, a common architecture for MFS transporters. The rate for crystal structure determination of MFS transporters is slow, making modeling of both prokaryotic and eukaryotic transporters more enticing. In this review, models of eukaryotic transporters Glut1, G6PT, OCT1, OCT2 and Pho84, based on the crystal structures of the prokaryotic GlpT, based on the crystal structure of LacY are discussed. The techniques used to generate the different models are compared. In addition, the validity of these models and the strategy of using prokaryotic crystal structures to model eukaryotic proteins are discussed. For comparison, E. coli GlpT was modeled based on the E. coli LacY structure and compared to the crystal structure of GlpT demonstrating that experimental evidence is essential for accurate modeling of membrane proteins.

Quantum-mechanical calculations of magnesium aspartate arginine structure and spectroscopic characteristics

NASA Astrophysics Data System (ADS)

Marcoin, W.; Pasterny, K.; Wrzalik, R.

2005-05-01

Theoretical calculations of magnesium aspartate-arginine (Mg[Asp-Arg]) structure and spectroscopic characteristics have been performed in the gas phase with the GAUSSIAN 98 software package using density functional theory (DFT) at the B3PW91 level. The 6-31+G* basis set was selected due to their reasonable quality and size. The comparison with corresponding results for magnesium aspartate-glycine (Mg[Asp-Gly]) is presented. NMR and IR measurements were carried out and obtained experimental 1H and 13C chemical shifts and IR spectra are compared with calculated spectral parameters.

Spectroscopic and calorimetric characterization of spermine oxidase and its association forms.

PubMed

Leonetti, Alessia; Cervoni, Laura; Polticelli, Fabio; Kanamori, Yuta; Yurtsever, Zuleyha Nihan; Agostinelli, Enzo; Mariottini, Paolo; Stano, Pasquale; Cervelli, Manuela

2017-12-14

Spermine oxidase (SMOX) is a flavin-containing enzyme that oxidizes spermine to produce spermidine, 3-aminopropanaldehyde, and hydrogen peroxide. SMOX has been shown to play key roles in inflammation and carcinogenesis; indeed, it is differentially expressed in several human cancer types. Our previous investigation has revealed that SMOX purified after heterologous expression in Escherichia coli actually consists of monomers, covalent homodimers, and other higher-order forms. All association forms oxidize spermine and, after treatment with dithiothreitol, revert to SMOX monomer. Here, we report a detailed investigation on the thermal denaturation of SMOX and its association forms in native and reducing conditions. By combining spectroscopic methods (circular dichroism, fluorescence) and thermal methods (differential scanning calorimetry), we provide new insights into the structure, the transformation, and the stability of SMOX. While the crystal structure of this protein is not available yet, experimental results are interpreted also on the basis of a novel SMOX structural model, obtained in silico exploiting the recently solved acetylspermine oxidase crystal structure. We conclude that while at least one specific intermolecular disulfide bond links two SMOX molecules to form the homodimer, the thermal denaturation profiles can be justified by the presence of at least one intramolecular disulfide bond, which also plays a critical role in the stabilization of the overall three-dimensional SMOX structure, and in particular of its flavin adenine dinucleotide-containing active site. © 2017 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

Atomic resolution of structural changes in elastic crystals of copper(II) acetylacetonate

NASA Astrophysics Data System (ADS)

Worthy, Anna; Grosjean, Arnaud; Pfrunder, Michael C.; Xu, Yanan; Yan, Cheng; Edwards, Grant; Clegg, Jack K.; McMurtrie, John C.

2018-01-01

Single crystals are typically brittle, inelastic materials. Such mechanical responses limit their use in practical applications, particularly in flexible electronics and optical devices. Here we describe single crystals of a well-known coordination compound—copper(II) acetylacetonate—that are flexible enough to be reversibly tied into a knot. Mechanical measurements indicate that the crystals exhibit an elasticity similar to that of soft materials such as nylon, and thus display properties normally associated with both hard and soft matter. Using microfocused synchrotron radiation, we mapped the changes in crystal structure that occur on bending, and determined the mechanism that allows this flexibility with atomic precision. We show that, under strain, the molecules in the crystal reversibly rotate, and thus reorganize to allow the mechanical compression and expansion required for elasticity and still maintain the integrity of the crystal structure.

Machine learning for autonomous crystal structure identification.

PubMed

Reinhart, Wesley F; Long, Andrew W; Howard, Michael P; Ferguson, Andrew L; Panagiotopoulos, Athanassios Z

2017-07-21

We present a machine learning technique to discover and distinguish relevant ordered structures from molecular simulation snapshots or particle tracking data. Unlike other popular methods for structural identification, our technique requires no a priori description of the target structures. Instead, we use nonlinear manifold learning to infer structural relationships between particles according to the topology of their local environment. This graph-based approach yields unbiased structural information which allows us to quantify the crystalline character of particles near defects, grain boundaries, and interfaces. We demonstrate the method by classifying particles in a simulation of colloidal crystallization, and show that our method identifies structural features that are missed by standard techniques.

Formation of crystal-like structures and branched networks from nonionic spherical micelles

NASA Astrophysics Data System (ADS)

Cardiel, Joshua J.; Furusho, Hirotoshi; Skoglund, Ulf; Shen, Amy Q.

2015-12-01

Crystal-like structures at nano and micron scales have promise for purification and confined reactions, and as starting points for fabricating highly ordered crystals for protein engineering and drug discovery applications. However, developing controlled crystallization techniques from batch processes remain challenging. We show that neutrally charged nanoscale spherical micelles from biocompatible nonionic surfactant solutions can evolve into nano- and micro-sized branched networks and crystal-like structures. This occurs under simple combinations of temperature and flow conditions. Our findings not only suggest new opportunities for developing controlled universal crystallization and encapsulation procedures that are sensitive to ionic environments and high temperatures, but also open up new pathways for accelerating drug discovery processes, which are of tremendous interest to pharmaceutical and biotechnological industries.

Crystal structure and dynamics of a lipid-induced potential desensitized-state of a pentameric ligand-gated channel

DOE Office of Scientific and Technical Information (OSTI.GOV)

Basak, Sandip; Schmandt, Nicolaus; Gicheru, Yvonne

Desensitization in pentameric ligand-gated ion channels plays an important role in regulating neuronal excitability. Here, we show that docosahexaenoic acid (DHA), a key ω-3 polyunsaturated fatty acid in synaptic membranes, enhances the agonist-induced transition to the desensitized state in the prokaryotic channel GLIC. We determined a 3.25 Å crystal structure of the GLIC-DHA complex in a potentially desensitized conformation. The DHA molecule is bound at the channel-periphery near the M4 helix and exerts a long-range allosteric effect on the pore across domain-interfaces. In this previously unobserved conformation, the extracellular-half of the pore-lining M2 is splayed open, reminiscent of the openmore » conformation, while the intracellular-half is constricted, leading to a loss of both water and permeant ions. These findings, in combination with spin-labeling/EPR spectroscopic measurements in reconstituted-membranes, provide novel mechanistic details of desensitization in pentameric channels.« less

Potassium and magnesium succinatouranilates – Synthesis and crystal structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Novikov, S.A., E-mail: serg.alex.novikov@gmail.com; Grigoriev, M.S.; Serezhkina, L.B.

2017-04-15

Single crystal X-ray diffraction has been applied to determine the structures of two new uranyl coordination polymers: K{sub 2}[(UO{sub 2}){sub 2}(C{sub 4}H{sub 4}O{sub 4}){sub 3}] (1) and [Mg(H{sub 2}O){sub 6}] [(UO{sub 2}){sub 2}(C{sub 4}H{sub 4}O{sub 4}){sub 3}]·2H{sub 2}O (2), where C{sub 4}H{sub 4}O{sub 4}{sup 2-} is succinate anion. Crystals of 1 and 2 contain polymeric complex anions [(UO{sub 2}){sub 2}(C{sub 4}H{sub 4}O{sub 4}){sub 3}]{sup 2-} with the same A{sub 2}Q{sup 02}{sub 3} crystallochemical formula (A=UO{sub 2}{sup 2+}, Q{sup 02}=C{sub 4}O{sub 4}H{sub 4}{sup 2-}), and have layered (1) or chain (2) structure. It has been found, that conformation of succinate ionsmore » is one of the factors, which affects the structure of [(UO{sub 2}){sub 2}(C{sub 4}H{sub 4}O{sub 4}){sub 3}]{sup 2-} anions. IR spectra of these new compounds are in good agreement with crystallographic data. Topological analysis of the uranium dicarboxylates with A{sub 2}Q{sup 02}{sub 3} crystallochemical formula has shown the presence of five isomers which differ from each other in coordination sequences and / or dimensionality. - Graphical abstract: Crystal structures of two new uranium(VI) coordination polymers with succinate linkers, namely K{sub 2}[(UO{sub 2}){sub 2}(C{sub 4}H{sub 4}O{sub 4}){sub 3}] (1) and [Mg(H{sub 2}O){sub 6}][(UO{sub 2}){sub 2}(C{sub 4}H{sub 4}O{sub 4}){sub 3}]·2H{sub 2}O (2), were determined by single-crystal XRD. Crystals of studied compounds are based on 2D or 1D structural units with the same composition and crystallochemical formula. Topological isomerism in A{sub 2}Q{sup 02}{sub 3} crystallochemical group and conformations of succinate anions in uranyl complexes are under discussion. - Highlights: • Two new uranium coordination polymers were synthesized. • Their structural units have the same composition and crystallochemical formula. • In spite the same composition and CCF dimensionality of units is different. • Structural features of

Molecular Dynamic Simulation of Space and Earth-Grown Crystal Structures of Thermostable T1 Lipase Geobacillus zalihae Revealed a Better Structure.

PubMed

Ishak, Siti Nor Hasmah; Aris, Sayangku Nor Ariati Mohamad; Halim, Khairul Bariyyah Abd; Ali, Mohd Shukuri Mohamad; Leow, Thean Chor; Kamarudin, Nor Hafizah Ahmad; Masomian, Malihe; Rahman, Raja Noor Zaliha Raja Abd

2017-09-25

Less sedimentation and convection in a microgravity environment has become a well-suited condition for growing high quality protein crystals. Thermostable T1 lipase derived from bacterium Geobacillus zalihae has been crystallized using the counter diffusion method under space and earth conditions. Preliminary study using YASARA molecular modeling structure program for both structures showed differences in number of hydrogen bond, ionic interaction, and conformation. The space-grown crystal structure contains more hydrogen bonds as compared with the earth-grown crystal structure. A molecular dynamics simulation study was used to provide insight on the fluctuations and conformational changes of both T1 lipase structures. The analysis of root mean square deviation (RMSD), radius of gyration, and root mean square fluctuation (RMSF) showed that space-grown structure is more stable than the earth-grown structure. Space-structure also showed more hydrogen bonds and ion interactions compared to the earth-grown structure. Further analysis also revealed that the space-grown structure has long-lived interactions, hence it is considered as the more stable structure. This study provides the conformational dynamics of T1 lipase crystal structure grown in space and earth condition.

On the crystal structure of the vaterite polymorph of CaCO3: a calcium-43 solid-state NMR and computational assessment.

PubMed

Burgess, Kevin M N; Bryce, David L

2015-02-01

The vaterite polymorph of CaCO3 has puzzled crystallographers for decades in part due to difficulties in obtaining single crystals. The multiple proposed structures for the vaterite polymorph of CaCO3 are assessed using a combined (43)Ca solid-state nuclear magnetic resonance (SSNMR) spectroscopic and computational approach. A combination of improved experimental and computational methods, along with a calibrated chemical shift scale and (43)Ca nuclear quadrupole moment, allow for improved insights relative to our earlier work (Bryce et al., J. Am. Chem. Soc. 2008, 130, 9282). Here, we synthesize a (43)Ca isotopically-enriched sample of vaterite and perform high-resolution quadrupolar SSNMR experiments including magic-angle spinning (MAS), double-rotation (DOR), and multiple-quantum (MQ) MAS experiments at magnetic field strengths of 9.4 and 21.1T. We identify one crystallographically unique Ca(2+) site in vaterite with a slight distribution in both chemical shifts and quadrupolar parameters. Both the experimental (43)Ca electric field gradient tensor and the isotropic chemical shift for vaterite are compared to those calculated with the gauge-including projector-augmented-wave (GIPAW) DFT method in an attempt to identify the model that best represents the crystal structure of vaterite. Simulations of (43)Ca DOR and MAS NMR spectra based on the NMR parameters computed for a total of 18 structural models for vaterite allow us to distinguish between these models. Among these 18, the P3221 and C2 structures provide simulated spectra and diffractograms in best agreement with all experimental data. Copyright © 2014 Elsevier Inc. All rights reserved.

Sixty years from discovery to solution: crystal structure of bovine liver catalase form III

DOE Office of Scientific and Technical Information (OSTI.GOV)

Foroughi, Leila M.; Kang, You-Na; Matzger, Adam J.

2012-03-27

The crystallization and structural characterization of bovine liver catalase (BLC) has been intensively studied for decades. Forms I and II of BLC have previously been fully characterized using single-crystal X-ray diffraction. Form III has previously been analyzed by electron microscopy, but owing to the thinness of this crystal form an X-ray crystal structure had not been determined. Here, the crystal structure of form III of BLC is presented in space group P212121, with unit-cell parameters a = 68.7, b = 173.7, c = 186.3 {angstrom}. The asymmetric unit is composed of the biological tetramer, which is packed in a tetrahedronmore » motif with three other BLC tetramers. This higher resolution structure has allowed an assessment of the previously published electron-microscopy studies.« less

The molecular structure of the borate mineral rhodizite (K, Cs)Al4Be4(B, Be)12O28 - A vibrational spectroscopic study

NASA Astrophysics Data System (ADS)

Frost, Ray L.; López, Andrés; Xi, Yunfei; Scholz, Ricardo; Souza, Larissa; Lana, Cristiano

2014-07-01

We have studied the borate mineral rhodizite (K, Cs)Al4Be4(B, Be)12O28 using a combination of DEM with EDX and vibrational spectroscopic techniques. The mineral occurs as colorless, gray, yellow to white crystals in the triclinic crystal system. The studied sample is from the Antandrokomby Mine, Sahatany valley, Madagascar. The mineral is prized as a semi-precious jewel. Semi-quantitative chemical composition shows a Al, Ca, borate with minor amounts of K, Mg and Cs. The mineral has a characteristic borate Raman spectrum and bands are assigned to the stretching and bending modes of B, Be and Al. No Raman bands in the OH stretching region were observed.

Synthesis, spectroscopic and structural characterization of 5-benzoyl-4-phenyl-2-methylthio-1H-pyrimidine with theoretical calculations using density functional theory

NASA Astrophysics Data System (ADS)

İnkaya, Ersin; Dinçer, Muharrem; Şahan, Emine; Yıldırım, İsmail

2013-10-01

In this paper, we will report a combined experimental and theoretical investigation of the molecular structure and spectroscopic parameters (FT-IR, 1H NMR, 13C NMR) of 5-benzoyl-4-phenyl-2-methylthio-1H-pyrimidine. The compound crystallizes in the triclinic space group P-1 with Z = 2. The molecular geometry was also optimized using density functional theory (DFT/B3LYP) method with the 6-311G(d,p) and 6-311++G(d,p) basis sets in ground state and compared with the experimental data. All the assignments of the theoretical frequencies were performed by potential energy distributions using VEDA 4 program. Information about the size, shape, charge density distribution and site of chemical reactivity of the molecules has been obtained by mapping electron density isosurface with electrostatic potential (ESP). Also, non-linear optical properties of the title compound were performed at B3LYP/6-311++G(d,p) level. The theoretical results showed an excellent agreement with the experimental values.

Crystal growth, structural, low temperature thermoluminescence and mechanical properties of cubic fluoroperovskite single crystal (LiBaF3)

NASA Astrophysics Data System (ADS)

Daniel, D. Joseph; Ramasamy, P.; Ramaseshan, R.; Kim, H. J.; Kim, Sunghwan; Bhagavannarayana, G.; Cheon, Jong-Kyu

2017-10-01

Polycrystalline compounds of LiBaF3 were synthesized using conventional solid state reaction route and the phase purity was confirmed using powder X-ray diffraction technique. Using vertical Bridgman technique single crystal was grown from melt. Rocking curve measurements have been carried out to study the structural perfection of the grown crystal. The single peak of diffraction curve clearly reveals that the grown crystal was free from the structural grain boundaries. The low temperature thermoluminescence of the X-ray irradiated sample has been analyzed and found four distinguishable peaks having maximum temperatures at 18, 115, 133 and 216 K. Activation energy (E) and frequency factor (s) for the individual peaks have been studied using Peak shape method and the computerized curve fitting method combining with the Tmax- TStop procedure. Nanoindentation technique was employed to study the mechanical behaviour of the crystal. The indentation modulus and Vickers hardness of the grown crystal have values of 135.15 GPa and 680.81 respectively, under the maximum indentation load of 10 mN.

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)

Crystal growth, spectral, structural and optical studies of π-conjugated stilbazolium crystal: 4-bromobenzaldehyde-4'-N'-methylstilbazolium tosylate.

PubMed

Krishna Kumar, M; Sudhahar, S; Bhagavannarayana, G; Mohan Kumar, R

2014-05-05

Nonlinear optical (NLO) organic compound, 4-bromobenzaldehyde-4'-N'-methylstilbazolium tosylate was synthesized by reflux method. The formation of molecular complex was confirmed from (1)H NMR, FT-IR and FT-Raman spectral analyses. The single crystals were grown by slow evaporation solution growth method and the crystal structure and atomic packing of grown crystal was identified. The morphology and growth axis of grown crystal were determined. The crystal perfection was analyzed using high resolution X-ray diffraction study on (001) plane. Thermal stability, decomposition stages and melting point of the grown crystal were analyzed. The optical absorption coefficient (α) and energy band gap (E(g)) of the crystal were determined using UV-visible absorption studies. Second harmonic generation efficiency of the grown crystal was examined by Kurtz powder method with different particle size using 1064 nm laser. Laser induced damage threshold study was carried out for the grown crystal using Nd:YAG laser. Copyright © 2014 Elsevier B.V. All rights reserved.

Structural transformation of synthetic hydroxyapatite under simulated in vivo conditions studied with ATR-FTIR spectroscopic imaging

NASA Astrophysics Data System (ADS)

Sroka-Bartnicka, Anna; Borkowski, Leszek; Ginalska, Grazyna; Ślósarczyk, Anna; Kazarian, Sergei G.

2017-01-01

Hydroxyapatite and carbonate-substituted hydroxyapatite are widely used in bone tissue engineering and regenerative medicine. Both apatite materials were embedded into recently developed ceramic/polymer composites, subjected to Simulated Body Fluid (SBF) for 30 days and characterized using ATR-FTIR spectroscopic imaging to assess their behaviour and structures. The specific aim was to detect the transition phases between both types of hydroxyapatite during the test and to analyze the surface modification caused by SBF. ATR-FTIR spectroscopic imaging was successfully applied to characterise changes in the hydroxyapatite lattice due to the elastic properties of the scaffolds. It was observed that SBF treatment caused a replacement of phosphates in the lattice of non-substituted hydroxyapatite by carbonate ions. A detailed study excluded the formation of pure A type carbonate apatite. In turn, CO32- content in synthetic carbonate-substituted hydroxyapatite decreased. The usefulness of ATR-FTIR spectroscopic imaging studies in the evaluation of elastic and porous β-glucan hydroxyapatite composites has been demonstrated.

Crystal and molecular structure of 2,6-dibromo-3-chloro-4-fluoroaniline

NASA Astrophysics Data System (ADS)

Betz, R.

2015-12-01

The crystal and molecular structure of 2,6-dibromo-3-chloro-4-fluoroaniline is determined. The crystals are monoclinic, a = 3.8380(3), b = 13.1010(12), c = 8.0980(8) Å, β = 96.010(4)°, V = 404.94(6) Å3, Z = 2, sp. gr. P21. Classical intra- and intermolecular hydrogen bonds of the N-H··· Hal type are observed next to a series of dispersive halogen···halogen interactions in the crystal structure.

Highly sensitive quartz crystal microbalance based biosensor using Au dendrite structure

NASA Astrophysics Data System (ADS)

Asai, Naoto; Terasawa, Hideaki; Shimizu, Tomohiro; Shingubara, Shoso; Ito, Takeshi

2018-02-01

A Au dendrite structure was obtained by only electroplating under a suitable potential. A blanch like nanostructure was formed along the crystal orientation. In this study, we attempted to fabricate a Au dendrite structure on the electrode of a quartz crystal by electroplating to increase the specific surface area. We estimated the effective surface area by cyclic voltammetry (CV) and monitored the frequency shift induced by antigen-antibody interaction by the quartz crystal microbalance (QCM) method. The dendrite structure with the largest surface area was formed under -0.95 V for 5 min. In the measurement of the antigen-antibody interaction, the frequency shifts of 40, 80, and 110 Hz were obtained with the dendrite structured QCM chips formed at the above potential for 1, 1.5, and 2.0 min, respectively. The sensitivity was improved compared with that QCM chip having a flat surface electrode.

Syntheses, characterization, superoxide dismutase, antimicrobial, crystal structure and molecular studies of copper (II) and nickel (II) complexes with 2-((E)-(2, 4-dibromophenylimino) methyl)-4-bromophenol as Schiff base ligand

NASA Astrophysics Data System (ADS)

Bharti, Sulakshna; Choudhary, Mukesh; Mohan, Bharti; Rawat, S. P.; Sharma, S. R.; Ahmad, Khursheed

2017-12-01

Three new copper (II) and nickel (II) complexes viz. [Cu(L)2](1a), [Cu(L)2](1b) and [Ni(L)2].DMF(2), where HL = 2-((E)-(2, 4-dibromophenylimino) methyl)-4-bromophenol, have been synthesized and characterized by using various physico-chemical and spectroscopic techniques. The crystal structures of Schiff base (HL) and their metal complexes (1a), (1b) and (2) were determined by single crystal X-ray diffraction. IR and UV-Vis spectra and magnetic susceptibility measurements agree with the observed crystal structures. The crystallographic and spectroscopic studies confirmed four coordinate environments around the metal (II) ions. The synthesized Schiff base ligand (HL) crystallizes in the orthorhombic system of the space group Pbca. Complex (1a) of HL was crystallized in the monoclinic system of the space group P21/c, a = 10.1712(9) Å, b = 10.9299(10) Å,c = 12.7684(11) Å,α = 90̊,β = 104.649(2)̊, γ = 90̊ and Z = 2 whereas complex (1b) and (2) crystallized in the triclinic system of the space group P-1, a = 11.499(5)Å, b = 11.598(5)Å, c = 12.211(5)Å, α = 98.860(5), β = 115.653(5),γ = 100.906(5) and Z = 2 for (1b), a = 9.080(6) Å, b = 9.545(8)Å, c = 9.545(8)Å, α = 101.43(4)º,β = 99.63(3)̊, γ = 117.71(2)º and Z = 1 for (2). The synthesized ligand (HL) was behaved as monobasic bidentate Schiff base ligand having N and O donor sites. The electron paramagnetic resonance spectra indicate a dx2-y2ground state (g|| > g⊥> 2.0023) for (1a) and (1b). Copper (II) complexes display X-band EPR spectra in 100% DMSO and 77 K, giving indicating dx2-y2ground state. Superoxide dismutase-like activities of HL and its complexes were investigated by nitrobluetetrazolium chloride-DMSO assay and IC50 values were evaluated. These complexes were also tested for their in vitro antimicrobial activities against two bacteria (E. coli and Salmonella typhi) and two fungi (Pencillium, Aspergillus sp.) comparing with the Schiff base. The antimicrobial results showed that the

Low-loss Ca{sub 5-x}Sr{sub x}A{sub 2}TiO{sub 12} [A=Nb,Ta] ceramics: Microwave dielectric properties and vibrational spectroscopic analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bijumon, Pazhoor Varghese; Sebastian, Mailadil Thomas; Dias, Anderson

2005-05-15

Complex perovskite-type Ca{sub 5-x}Sr{sub x}A{sub 2}TiO{sub 12} [A=Nb,Ta] (0{<=}x{<=}5) ceramics were prepared by conventional solid-state ceramic route. The crystal structure, microwave dielectric properties, and vibrational spectroscopic characteristics of these materials are reported. The structure and microstructure were investigated by x-ray diffraction and scanning electron microscopy techniques. The microwave dielectric properties were measured in the 3-5-GHz frequency range by the resonance method. Structural evolutions from orthorhombic to an averaged pseudocubic phase, with associated changes in dielectric properties, were observed as a function of composition. The structure-property relationships in these ceramics were established using Raman and Fourier transform infrared spectroscopic techniques. Ramanmore » analysis showed characteristic bands of ordered perovskite materials, with variation in both intensity and frequency as a function of composition.« less

Investigations of the optical and EPR data and local structure for the trigonal tetrahedral Co2+ centers in LiGa5O8: Co2+ crystal

NASA Astrophysics Data System (ADS)

He, Jian; Liao, Bi-Tao; Mei, Yang; Liu, Hong-Gang; Zheng, Wen-Chen

2018-01-01

In this paper, we calculate uniformly the optical and EPR data for Co2+ ion at the trigonal tetrahedral Ga3+ site in LiGa5O8 crystal from the complete diagonalization (of energy matrix) method founded on the two-spin-orbit-parameter model, where the contributions to the spectroscopic data from both the spin-orbit parameter of dn ion (in the classical crystal field theory) and that of ligand ions are contained. The calculated ten spectroscopic data (seven optical bands and three spin-Hamiltonian parameters g//, g⊥ and D) with only four adjustable parameters are in good agreement with the available observed values. Compared with the host (GaO4)5- cluster, the great angular distortion and hence the great trigonal distortion of (CoO4)6- impurity center obtained from the calculations are referred to the large charge and size mismatch substitution. This explains reasonably the observed great g-anisotropy Δg (= g// - g⊥) and zero-field splitting D for the (CoO4)6- cluster in LiGa5O8: Co2+ crystal.

IR spectroscopic studies in microchannel structures

NASA Astrophysics Data System (ADS)

Guber, A. E.; Bier, W.

1998-06-01

By means of the various microengineering methods available, microreaction systems can be produced among others. These microreactors consist of microchannels, where chemical reactions take place under defined conditions. For optimum process control, continuous online analytics is envisaged in the microchannels. For this purpose, a special analytical module has been developed. It may be applied for IR spectroscopic studies at any point of the microchannel.

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

PubMed

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

2016-02-05

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. Copyright © 2015 Elsevier B.V. All rights reserved.

Growth and structural, optical, and electrical properties of zincite crystals

NASA Astrophysics Data System (ADS)

Kaurova, I. A.; Kuz'micheva, G. M.; Rybakov, V. B.

2013-03-01

An X-ray diffraction study of ZnO crystals grown by the hydrothermal method has revealed reflections that give grounds to assign them to the sp. gr. P3 rather than to P63 mc. The distribution of Zn1, Zn2, O1, and O2 over structural positions, along with vacancies and incorporated zinc atoms, explains the dissymmetrization observed in terms of the kinetic (growth) phase transition of the order-disorder type, which is caused by ordering Zn and O atoms over structural positions. The color of crystals of refined compositions (Zn0.975□0.025)Zn i(0.015)(O0.990□0.010) (green) and (Zn0.965□0.035)Zn i(0.035)O (bright green) is related to different oxygen contents, which is confirmed by the results of electron probe X-ray microanalysis and absorption spectroscopy. The degree of the structural quality of crystals, their resistivity, and activation energy are also related to oxygen vacancies.

Synthesis, electrochemical, structural, spectroscopic and biological activities of mixed ligand copper (II) complexes with 2-{[(Z)-(5-bromo-2-hydroxyphenyl)methylidene]amino}benzoic acid and nitrogenous bases

NASA Astrophysics Data System (ADS)

Choudhary, Mukesh; Patel, R. N.; Rawat, S. P.

2014-02-01

Three new copper (II) complexes viz. [Cu(L1)(bipy)]ṡ2H2O 1, [Cu(L1)(dmp)]ṡCH3CN 2, [Cu(L1)(phen)] 3 where L1H2 = 2-{[(Z)-(5-bromo-2-hydroxyphenyl)methylidene]amino}benzoic acid, bipy = 2,2‧-bipyridine; dmp = 2,9-dimethyl 1,10-phenanthroline, phen = 1,10-phenanthroline have been synthesized and characterized by physic-chemical and spectroscopic methods. The solid-state structures of 1 and 2 were determined by single crystal X-ray crystallography, which revealed distorted square pyramidal geometry. In solid-state structure, 1 is self-assembled via intermolecular π…π stacking and the distances between centroids of aromatic ring is 3.525 Å. L1H2 is a diprotic tridentate Schiff base ligand having ONO donor site. Infrared spectra, ligand field spectra and magnetic susceptibility measurements agree with the observed crystal structures. The EPR spectra of these complexes in frozen DMSO solutions showed a single at g ca. 2. The trend in g-value (g|| > g⊥ > 2.0023) suggests that the unpaired electron on copper (II) has d character. Copper (II) complexes 1-3 yielded an irreversible couple corresponding to the Cu (II)/Cu (I) redox process. Superoxide dismutase activity of all these complexes has been revealed to catalyze the dismutation of superoxide (O2-) and IC50 values were evaluated and discussed. Antimicrobial and antifungal activities of these complexes were also investigated.

Synthesis, crystal structure and properties of a new 3D supramolecular unsymmetrical tetradentate Schiff bases copper (II) framework with stable tunnels

NASA Astrophysics Data System (ADS)

Al-Noaimi, Mousa; Awwadi, Firas F.; Al-Razagg, Raiid; Esmadi, Fatima T.

2016-12-01

Flexible unsymmetrical Schiff base ligand (L) which is derived from the half unit Y = C6H5COCH2C(Ndbnd CH2C6H4NH2)CH3 (obtained from the reaction of benzoylacetone and 2-aminobenzylamine) and 2- quinolinecarboxaldehyde have been successfully co-assembled with Cu(ClO4)2 to give out the [Cu(L)]ClO4 complex. The complex crystallizes in two different space groups; P21/n and P-1. The crystal structure of the P-1 phase indicates the presence of tunnels; the volume of these tunnels is 157 Å3 which is big enough to accommodate solvent molecules. The X-ray data indicates that these tunnels are most probably filled by highly disordered solvent molecules or solvent molecules with partial occupancy. The tunneled structure is stabilized via π-π stacking interactions to give a supramolecular MOF with 1D rhomboidal tunnels array. The copper(II) atom assumes a distorted-square pyrimidal coordination geometry where the perchlorate is located on the apex of the pyramide. In addition, this work presents and discusses the spectroscopic (IR, UV/vis), electro-chemical (cyclic voltammetry) behavior of the Cu(II) complexes. The Cu(II) oxidation state is stabilized by the novel tetradentate ligands, showing Cu(I/II) couple around 0.1 vs. Cp2Fe/Cp2Fe+.

Structural characterization and DFT study of a new optical crystal: 2-amino-3-methylpyridinium-3,5-dinitrobenzoate

NASA Astrophysics Data System (ADS)

Sathya, K.; Dhamodharan, P.; Dhandapani, M.

2018-05-01

A new proton transfer complex was synthesized by the reaction between 2-amino-3-methyl pyridine with 3,5-dinitro benzoic acid in methanol solvent at room temperature. Chemical composition and stoichiometry of the synthesized complex 2-amino-3-methylpyridinium 3,5-dinitrobenzoate (AMPDB) were verified by CHN analysis. The AMPDB crystals were subjected to FT-IR spectral analysis to confirm the functional groups in the compound. UV-Vis-NIR spectral studies revealed that the AMPDB has a large optical transparency window. Single crystal XRD analysis reveals that AMPDB belongs to a monoclinic system with P21/c space group. NMR spectroscopic data indicate the exact carbon skeleton and hydrogen environment in the molecular structure of AMPDB. The thermal stability of the compound was investigated by thermogravimetry (TG). Computational studies such as optimisation of molecular geometry, natural bond analysis (NBO), Mulliken population analysis and HOMO-LUMO analysis were performed using Gaussian 09 software by B3LYP method at 6-311 G(d p) basis set. The first order hyperpolarizability (β) value is 37 times greater than that of urea. The optical nonlinearities of AMPDB have been investigated by Z-scan technique with He-Ne laser radiation of wavelength 632.8 nm. Hirshfeld analysis indicate O⋯H/H⋯O interactions are the superior interactions confirming intensive hydrogen bond net work.

Co-crystal and crystal: Supramolecular arrangement obtained from 4-aminosalicylic acid, bpa ligand and cobalt ion

NASA Astrophysics Data System (ADS)

Garcia, Humberto C.; Cunha, Ronaldo T.; Diniz, Renata; de Oliveira, Luiz Fernando C.

2012-02-01

In this study, the synthesis, spectroscopic properties (infrared and Raman) and crystal structures of two new compounds co-crystal and crystal named HASbpa (1) and [Co(bpa)(H2O)4]AS2ṡ4H2O (2) have been reported, where bpa is trans-1,2-bis(4-pyridyl)ethane, HAS is 4-aminosalicylic acid and AS- is aminosalicylate anion. The crystalline arrangement of the compound 1 exhibits a triclinic system with space group P1¯. The formation of a structure known as co-crystal, composed by building blocks in their neutral form; being the first work of this type involving the HAS and nitrogen ligand as bpa. For compound 2, a monoclinic system was observed with P21/c space group. The crystalline arrangement of the structure consisted of a covalent one-dimensional cationic [Co(bpa)(H2O)4]2+ chain, which interacts by hydrogen bonding, π-stacking and electrostatic interactions with aminosalicylate anions and water molecules that were trapped in the crystal. These interactions form supramolecular cavities denominated as pseudo honeycombs. For compound 1, the infrared spectrum revealed the presence of bands at 1643 and 1601 cm-1 assigned to the stretching mode of CO [ν(CO)] and CC/CN groups [ν(CC/CN)]. For the Raman spectrum, these same modes appear around 1644 and 1602 cm-1 related to HAS and bpa blocks, respectively. For compound 2, the largest displacement of the bands compared to free ligand suggested the formation of covalent bonds between bpa ligand and metallic site and loss of the proton in HAS molecule. In the infrared spectrum we can observe the presence of bands around 1635 and 1618 cm-1 attributed to the stretching ν(COO-) and ν(CC/CN), for the Raman spectrum these same modes appear around 1631 and 1619 cm-1 related to AS- and bpa ligand respectively.

Visualization of Hyperconjugation and Subsequent Structural Distortions through 3D Printing of Crystal Structures.

PubMed

Mithila, Farha J; Oyola-Reynoso, Stephanie; Thuo, Martin M; Atkinson, Manza Bj

2016-01-01

Structural distortions due to hyperconjugation in organic molecules, like norbornenes, are well captured through X-ray crystallographic data, but are sometimes difficult to visualize especially for those applying chemical knowledge and are not chemists. Crystal structure from the Cambridge database were downloaded and converted to .stl format. The structures were then printed at the desired scale using a 3D printer. Replicas of the crystal structures were accurately reproduced in scale and any resulting distortions were clearly visible from the macroscale models. Through space interactions or effect of through space hyperconjugation was illustrated through loss of symmetry or distortions thereof. The norbornene structures exhibits distortion that cannot be observed through conventional ball and stick modelling kits. We show that 3D printed models derived from crystallographic data capture even subtle distortions in molecules. We translate such crystallographic data into scaled-up models through 3D printing.

Nontypical iodine–halogen bonds in the crystal structure of (3 E )-8-chloro-3-iodomethylidene-2,3-dihydro-1,4-oxazino[2,3,4- ij ]quinolin-4-ium triiodide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bartashevich, E. V.; Batalov, V. I.; Yushina, I. D.

2016-03-23

Two kinds of iodine–iodine halogen bonds are the focus of our attention in the crystal structure of the title salt, C 12H 8ClINO +·I 3 -, described by X-ray diffraction. The first kind is a halogen bond, reinforced by charges, between the I atom of the heterocyclic cation and the triiodide anion. The second kind is the rare case of a halogen bond between the terminal atoms of neighbouring triiodide anions. The influence of relatively weakly bound iodine inside an asymmetric triiodide anion on the thermal and Raman spectroscopic properties has been demonstrated.

Nontypical iodine–halogen bonds in the crystal structure of (3 E )-8-chloro-3-iodomethylidene-2,3-dihydro-1,4-oxazino[2,3,4- ij ]quinolin-4-ium triiodide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bartashevich, E. V.; Batalov, V. I.; Yushina, I. D.

2016-04-29

Two kinds of iodine–iodine halogen bonds are the focus of our attention in the crystal structure of the title salt, C 12H 8ClINO +·I 3 -, described by X-ray diffraction. The first kind is a halogen bond, reinforced by charges, between the I atom of the heterocyclic cation and the triiodide anion. The second kind is the rare case of a halogen bond between the terminal atoms of neighbouring triiodide anions. Lastly, the influence of relatively weakly bound iodine inside an asymmetric triiodide anion on the thermal and Raman spectroscopic properties has been demonstrated.

Synthesis, crystal growth, structural, thermal, optical and mechanical properties of solution grown 4-methylpyridinium 4-hydroxybenzoate single crystal.

PubMed

Sudhahar, S; Krishna Kumar, M; Sornamurthy, B M; Mohan Kumar, R

2014-01-24

Organic nonlinear optical material, 4-methylpyridinium 4-hydroxybenzoate (4MPHB) was synthesized and single crystal was grown by slow evaporation solution growth method. Single crystal and powder X-ray diffraction analyses confirm the structure and crystalline perfection of 4MPHB crystal. Infrared, Raman and NMR spectroscopy techniques were used to elucidate the functional groups present in the compound. TG-DTA analysis was carried out in nitrogen atmosphere to study the decomposition stages, endothermic and exothermic reactions. UV-visible and Photoluminescence spectra were recorded for the grown crystal to estimate the transmittance and band gap energy respectively. Linear refractive index, birefringence, and SHG efficiency of the grown crystal were studied. Laser induced surface damage threshold and mechanical properties of grown crystal were studied to assess the suitability of the grown crystals for device applications. Copyright © 2013 Elsevier B.V. All rights reserved.

Synthesis of rhenium nitride crystals with MoS2 structure

NASA Astrophysics Data System (ADS)

Kawamura, Fumio; Yusa, Hitoshi; Taniguchi, Takashi

2012-06-01

Rhenium nitride (ReN2) crystals were synthesized from a metathesis reaction between ReCl5 and Li3N under high pressure. The reaction was well controlled by the addition of a large amount of NaCl as reaction inhibitor to prevent a violent exothermic reaction. The largest rhenium nitride crystals obtained had a millimeter-order size with a platelet shape. X-ray diffraction analysis revealed that rhenium nitride has MoS2 structure similar to hexagonal rhenium diboride (ReB2) which has recently been investigated as an ultra-hard material. The structure was different from any structures previously predicted for ReN2 by theoretical calculations.

Amino acid based MOFs: synthesis, structure, single crystal to single crystal transformation, magnetic and related studies in a family of cobalt and nickel aminoisophthales.

PubMed

Sarma, Debajit; Ramanujachary, K V; Lofland, S E; Magdaleno, Travis; Natarajan, Srinivasan

2009-12-21

Four new 5-aminoisophthalates of cobalt and nickel have been prepared employing hydro/solvothermal methods: [Co(2)(C(8)H(5)NO(4))(2)(C(4)H(4)N(2))(H(2)O)(2)].3H(2)O (I), [Ni(2)(C(8)H(5)NO(4))(2)(C(4)H(4)N(2))(H(2)O)(2)].3H(2)O (II), [Co(2)(H(2)O)(mu(3)-OH)(2)(C(8)H(5)NO(4))] (III), and [Ni(2)(H(2)O)(mu(3)-OH)(2)(C(8)H(5)NO(4))] (IV). Compounds I and II are isostructural, having anion-deficient CdCl(2) related layers bridged by a pyrazine ligand, giving rise to a bilayer arrangement. Compounds III and IV have one-dimensional M-O(H)-M chains connected by the 5-aminoisophthalate units forming a three-dimensional structure. The coordinated as well as the lattice water molecules of I and II could be removed and inserted by simple heating-cooling cycles under the atmospheric conditions. The removal of the coordinated water molecule is accompanied by changes in the coordination environment around the M(2+) (M = Co, Ni) and color of the samples (purple to blue, Co; green to dark yellow, Ni). This change has been examined by a variety of techniques that include in situ single crystal to single crystal transformation studies and in situ IR and UV-vis spectroscopic studies. Magnetic studies indicate antiferromagnetic behavior in I and II, a field-induced magnetism in III, and a canted antiferromagnetic behavior in IV.

Structure, Energetics, and Dynamics of Screw Dislocations in Even n-Alkane Crystals.

PubMed

Olson, Isabel A; Shtukenberg, Alexander G; Hakobyan, Gagik; Rohl, Andrew L; Raiteri, Paolo; Ward, Michael D; Kahr, Bart

2016-08-18

Spiral hillocks on n-alkane crystal surfaces were observed immediately after Frank recognized the importance of screw dislocations for crystal growth, yet their structures and energies in molecular crystals remain ill-defined. To illustrate the structural chemistry of screw dislocations that are responsible for plasticity in organic crystals and upon which the organic electronics and pharmaceutical industries depend, molecular dynamics was used to examine heterochiral dislocation pairs with Burgers vectors along [001] in n-hexane, n-octane, and n-decane crystals. The cores were anisotropic and elongated in the (110) slip plane, with significant local changes in molecular position, orientation, conformation, and energy. This detailed atomic level picture produced a distribution of strain consistent with linear elastic theory, giving confidence in the simulations. Dislocations with doubled Burgers vectors split into pairs with elementary displacements. These results suggest a pathway to understanding the mechanical properties and failure associated with elastic and plastic deformation in soft crystals.

Localized and Spectroscopic Orbitals: Squirrel Ears on Water.

ERIC Educational Resources Information Center

Martin, R. Bruce

1988-01-01

Reexamines the electronic structure of water considering divergent views. Discusses several aspects of molecular orbital theory using spectroscopic molecular orbitals and localized molecular orbitals. Gives examples for determining lowest energy spectroscopic orbitals. (ML)

The crystal structure and crystal chemistry of fernandinite and corvusite

USGS Publications Warehouse

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

1994-01-01

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

Synthesis and Crystal Structure of a Chalcone Derivative

NASA Astrophysics Data System (ADS)

Singh, Vikram D.; Salian, Vinutha V.; Narayana, B.; Sarojini, B. K.; Kamni; Anthal, Sumati; Kant, Rajni

2017-12-01

(2E)-3-(anthrance-9-yl)-1-(3,4-dichlorophenyl)prop-2-en-1-one [C23H14OCl2] is synthesized and its crystal structure is determined by single X-ray diffraction. There exist two molecules in the asymmetric unit. The dihedral angle between the benzene and anthracene moiety of the molecule A and B is 86.51(12)° and 76.42(13)°, respectively. No classical hydrogen bonds are observed and only van der Waals forces stabilize the crystal packing.

Spectroscopic analyses of Fe and water in clays: A Martian surface weathering study

NASA Technical Reports Server (NTRS)

Bishop, J. L.; Pieters, Carle M.; Edwards, J. O.; Coyne, L. M.; Chang, S.

1991-01-01

Martian surface morphology suggests the presence of liquid H2O on Mars in the past. Reflectance spectra of the Martian surface include features which correspond to the crystal field transitions of iron, as well as features supporting the presence of ice and minerals containing structural OH and surface water. Researchers initiated further spectroscopic studies of surface iron and water and structural OH in clays in order to determine what remotely obtained spectra can indicate about the presence of clays on Mars based on a clearer understanding of the factors influencing the spectral features. Current technology allows researchers to better correlate the low frequency fundamental stretching and bending vibrations of O-H bonds with the diagnostic near infrared overtone and combination bands used in mineral characterization and identification.

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.

Ultrafast photodimerization dynamics in α-cyano-4-hydroxycinnamic and sinapinic acid crystals

NASA Astrophysics Data System (ADS)

Hoyer, Theo; Tuszynski, Wilfried; Lienau, Christoph

2007-07-01

We report a sub-picosecond time-resolved fluorescence spectroscopic study of different cinnamic acid crystals, model systems for solid-state photodimerization reactions. For α-cyano-4-hydroxycinnamic acid (α-CHC), we identify the emission spectra of both monomers and dimers, allowing us to directly probe the photoinduced dynamics of both species. The dimerization occurs on a timescale of 10 ps and results in a long-lived dimer product, stable for hours. For sinapinic acid, we find an extremely fast, sub-picosecond dimerization reaction and a short-lived dimer. This first sub-picosecond time-resolved dimerization study in cinnamic acid crystals provides a new basis for relating their structural properties and microscopic reaction dynamics.

Crystal structure of bile salt hydrolase from Lactobacillus salivarius.

PubMed

Xu, Fuzhou; Guo, Fangfang; Hu, Xiao Jian; Lin, Jun

2016-05-01

Bile salt hydrolase (BSH) is a gut-bacterial enzyme that negatively influences host fat digestion and energy harvesting. The BSH enzyme activity functions as a gateway reaction in the small intestine by the deconjugation of glycine-conjugated or taurine-conjugated bile acids. Extensive gut-microbiota studies have suggested that BSH is a key mechanistic microbiome target for the development of novel non-antibiotic food additives to improve animal feed production and for the design of new measures to control obesity in humans. However, research on BSH is still in its infancy, particularly in terms of the structural basis of BSH function, which has hampered the development of BSH-based strategies for improving human and animal health. As an initial step towards the structure-function analysis of BSH, C-terminally His-tagged BSH from Lactobacillus salivarius NRRL B-30514 was crystallized in this study. The 1.90 Å resolution crystal structure of L. salivarius BSH was determined by molecular replacement using the structure of Clostridium perfringens BSH as a starting model. It revealed this BSH to be a member of the N-terminal nucleophile hydrolase superfamily. Crystals of apo BSH belonged to space group P21212, with unit-cell parameters a = 90.79, b = 87.35, c = 86.76 Å (PDB entry 5hke). Two BSH molecules packed perfectly as a dimer in one asymmetric unit. Comparative structural analysis of L. salivarius BSH also identified potential residues that contribute to catalysis and substrate specificity.

Hierarchically structured photonic crystals for integrated chemical separation and colorimetric detection.

PubMed

Fu, Qianqian; Zhu, Biting; Ge, Jianping

2017-02-16

A SiO 2 colloidal photonic crystal film with a hierarchical porous structure is fabricated to demonstrate an integrated separation and colorimetric detection of chemical species for the first time. This new photonic crystal based thin layer chromatography process requires no dyeing, developing and UV irradiation compared to the traditional TLC. The assembling of mesoporous SiO 2 particles via a supersaturation-induced-precipitation process forms uniform and hierarchical photonic crystals with micron-scale cracks and mesopores, which accelerate the diffusion of developers and intensify the adsorption/desorption between the analytes and silica for efficient separation. Meanwhile, the chemical substances infiltrated to the voids of photonic crystals cause an increase of the refractive index and a large contrast of structural colors towards the unloaded part, so that the sample spots can be directly recognized with the naked eye before and after separation.

Atomic density functional and diagram of structures in the phase field crystal model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ankudinov, V. E., E-mail: vladimir@ankudinov.org; Galenko, P. K.; Kropotin, N. V.

2016-02-15

The phase field crystal model provides a continual description of the atomic density over the diffusion time of reactions. We consider a homogeneous structure (liquid) and a perfect periodic crystal, which are constructed from the one-mode approximation of the phase field crystal model. A diagram of 2D structures is constructed from the analytic solutions of the model using atomic density functionals. The diagram predicts equilibrium atomic configurations for transitions from the metastable state and includes the domains of existence of homogeneous, triangular, and striped structures corresponding to a liquid, a body-centered cubic crystal, and a longitudinal cross section of cylindricalmore » tubes. The method developed here is employed for constructing the diagram for the homogeneous liquid phase and the body-centered iron lattice. The expression for the free energy is derived analytically from density functional theory. The specific features of approximating the phase field crystal model are compared with the approximations and conclusions of the weak crystallization and 2D melting theories.« less

Crystal orientation dependence of femtosecond laser-induced periodic surface structure on (100) silicon.

PubMed

Jiang, Lan; Han, Weina; Li, Xiaowei; Wang, Qingsong; Meng, Fantong; Lu, Yongfeng

2014-06-01

It is widely believed that laser-induced periodic surface structures (LIPSS) are independent of material crystal structures. This Letter reports an abnormal phenomenon of strong dependence of the anisotropic formation of periodic ripples on crystal orientation, when Si (100) is processed by a linearly polarized femtosecond laser (800 nm, 50 fs, 1 kHz). LIPSS formation sensitivity with a π/2 modulation is found along different crystal orientations with a quasi-cosinusoid function when the angle between the crystal orientation and polarization direction is changed from 0° to 180°. Our experiments indicate that it is much easier (or more difficult) to form ripple structures when the polarization direction is aligned with the lattice axis [011]/[011¯] (or [001]). The modulated nonlinear ionization rate along different crystal orientations, which arises from the direction dependence of the effective mass of the electron is proposed to interpret the unexpected anisotropic LIPSS formation phenomenon. Also, we demonstrate that the abnormal phenomenon can be applied to control the continuity of scanned ripple lines along different crystal orientations.

Crystal growth, structure and morphology of hydrocortisone methanol solvate

NASA Astrophysics Data System (ADS)

Chen, Jianxin; Wang, Jiangkang; Zhang, Ying; Wu, Hong; Chen, Wei; Guo, Zhichao

2004-04-01

Hydrocortisone (HC), an important grucocorticoid, was crystallized from methanol solvent in the form of its methanol solvate. Its crystal structure belongs to orthorhombic, space group P2 12 12 1, with the unit cell parameters a=7.712(3) Å, b=14.392(5) Å, c=18.408(6) Å, Z=4. The methanol takes part in intermolecular hydrogen bonding, so if we change the solvent, the crystal habit of HC maybe different. The long parallelepiped morphology was also predicted by Cerius 2TM simulation program. The influence of intermolecular interaction was taken into account in the attachment energy model. The morphology calculation performed on the potential energy minimized model using a generic DREIDING 2.21 force field and developed minimization protocol with derived partial charges fits the experimental crystal shape well.

Atomically-thick two-dimensional crystals: electronic structure regulation and energy device construction.

PubMed

Sun, Yongfu; Gao, Shan; Xie, Yi

2014-01-21

Atomically-thick two-dimensional crystals can provide promising opportunities to satisfy people's requirement of next-generation flexible and transparent nanodevices. However, the characterization of these low-dimensional structures and the understanding of their clear structure-property relationship encounter many great difficulties, owing to the lack of long-range order in the third dimensionality. In this review, we survey the recent progress in fine structure characterization by X-ray absorption fine structure spectroscopy and also overview electronic structure modulation by density-functional calculations in the ultrathin two-dimensional crystals. In addition, we highlight their structure-property relationship, transparent and flexible device construction as well as wide applications in photoelectrochemical water splitting, photodetectors, thermoelectric conversion, touchless moisture sensing, supercapacitors and lithium ion batteries. Finally, we outline the major challenges and opportunities that face the atomically-thick two-dimensional crystals. It is anticipated that the present review will deepen people's understanding of this field and hence contribute to guide the future design of high-efficiency energy-related devices.

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

NASA Astrophysics Data System (ADS)

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

2007-06-01

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

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.

Structures, Energetics and Spectroscopic Fingerprints of Water Clusters n=2-24

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yoo, Soohaeng; Xantheas, Sotiris S.

This chapter discusses the structures, energetics, and vibrational spectra of the first few (n$24) water clusters obtained from high-level electronic structure calculations. The results are discussed in the perspective of being used to parameterize/assess the accuracy of classical and quantum force fields for water. To this end, a general introduction with the classification of those force fields is presented. Several low-lying families of minima for the medium cluster sizes are considered. The transition from the “all surface” to the “fully coordinated” cluster structures occurring at nD17 and its spectroscopic signature is presented. The various families of minima for nD20 aremore » discussed together with the low energy networks of the pentagonal dodecahedron (H2O)20 water cage. Finally, the low-energy networks of the tetrakaidecahedron (T-cage) (H2O)24 cluster are shown and their significance in the construction of periodic lattices of structure I (sI) of the hydrate lattices is discussed.« less

Synthesis, characterization, crystal structure, superoxide dismutase and biological activities of nickel (II) complexes with bidentate ligands possessing N and O donor atoms

NASA Astrophysics Data System (ADS)

Sangeeta, S.; Ahmad, K.; Noorussabah, N.; Bharti, S.; Mishra, M. K.; Sharma, S. R.; Choudhary, M.

2017-12-01

Two new Schiff bases 2-((E)-(4-bromo-2-chlorophenylimino)methyl)-4-bromophenol(HL1) and1-((E)-(4-bromo-2-chlorophenylimino)methyl)naphthalene-2-ol (HL2) and their new nickel (II) complexes [Ni(L1)2]·DMF(1) and [Ni(L2)2] (2) have been synthesized and characterized by various physico- chemical and spectroscopic methods. The solid-state structures of synthesized compounds were determined by single crystal X-ray crystallography, which revealed square planar geometry around Ni (II) ion. Infrared spectra, UV-Vis, thermal analysis and magnetic susceptibility measurements agreed with the observed crystal structures. The ligand (HL1) crystallized in the Orthorhombic system of the space group Pbca,a = 7.5485(4)Å, b = 11.5514(5) Å, c = 30.1370(14)Å, α = 90°, β = 90°, γ = 90°and Z = 8. Complex[Ni(L1)2]·DMF(1) crystallized in the Triclinic system of the space group P-1, a = 8.9954(3) Å, b = 9.4593(4) Å, c = 13.2657(5) Å, α = 101.478°, β = 99.595°, γ = 117.651°and Z = 2, whereas complex [Ni(L2)2]·(2) crystallized in the Monoclinic system of the space group P21/c, a = 9.301(9)Å, b = 12.149(8)Å, c = 13.792(10)Å, α = 90°, β = 106.35(4).°, γ = 90°and Z = 2. The Schiff bases (HL1and HL2) behaved as monobasic bidentate ligands possessing N and O donor atoms. The SOD activities of HL1 and its Ni (II) complex[Ni(L1)2]·DMF(1) have been measured using xanthine-xanthine oxidase as a source of superoxide radical and NBT assay as O2- scavenger. In vitro antimicrobial activities of the Ni(II) complexes (1) and (2)against Bacillus cereus and Staphylococcus aureus as Gram + ve and Salmonella typhi, Klebsiella pneumonia and Escherichia coli as Gram-ve species have been investigated comparing with the Schiff base ligands (HL1and HL2).

Crystal structure and hydrogen-bonding patterns in 5-fluoro-cytosinium picrate.

PubMed

Mohana, Marimuthu; Thomas Muthiah, Packianathan; McMillen, Colin D

2017-03-01

In the crystal structure of the title compound, 5-fluoro-cytosinium picrate, C 4 H 5 FN 3 O + ·C 6 H 2 N 3 O 7 - , one N heteroatom of the 5-fluoro-cytosine (5FC) ring is protonated. The 5FC ring forms a dihedral angle of 19.97 (11)° with the ring of the picrate (PA - ) anion. In the crystal, the 5FC + cation inter-acts with the PA - anion through three-centre N-H⋯O hydrogen bonds, forming two conjoined rings having R 2 1 (6) and R 1 2 (6) motifs, and is extended by N-H⋯O hydrogen bonds and C-H⋯O inter-actions into a two-dimensional sheet structure lying parallel to (001). Also present in the crystal structure are weak C-F⋯π inter-actions.

Free-standing nanomechanical and nanophotonic structures in single-crystal diamond

NASA Astrophysics Data System (ADS)

Burek, Michael John

Realizing complex three-dimensional structures in a range of material systems is critical to a variety of emerging nanotechnologies. This is particularly true of nanomechanical and nanophotonic systems, both relying on free-standing small-scale components. In the case of nanomechanics, necessary mechanical degrees of freedom require physically isolated structures, such as suspended beams, cantilevers, and membranes. For nanophotonics, elements like waveguides and photonic crystal cavities rely on light confinement provided by total internal reflection or distributed Bragg reflection, both of which require refractive index contrast between the device and surrounding medium (often air). Such suspended nanostructures are typically fabricated in a heterolayer structure, comprising of device (top) and sacrificial (middle) layers supported by a substrate (bottom), using standard surface nanomachining techniques. A selective, isotropic etch is then used to remove the sacrificial layer, resulting in free-standing devices. While high-quality, crystalline, thin film heterolayer structures are readily available for silicon (as silicon-on-insulator (SOI)) or III-V semiconductors (i.e. GaAs/AlGaAs), there remains an extensive list of materials with attractive electro-optic, piezoelectric, quantum optical, and other properties for which high quality single-crystal thin film heterolayer structures are not available. These include complex metal oxides like lithium niobate (LiNbO3), silicon-based compounds such as silicon carbide (SiC), III-V nitrides including gallium nitride (GaN), and inert single-crystals such as diamond. Diamond is especially attractive for a variety of nanoscale technologies due to its exceptional physical and chemical properties, including high mechanical hardness, stiffness, and thermal conductivity. Optically, it is transparent over a wide wavelength range (from 220 nm to the far infrared), has a high refractive index (n ~ 2.4), and is host to a vast

Crystal structure, electronic structure, temperature-dependent optical and scintillation properties of CsCe 2Br 7

DOE PAGES

Wu, Yuntao; Shi, Hongliang; Chakoumakos, Bryan C.; ...

2015-10-05

CsCe 2Br 7 is a self-activated inorganic scintillator that shows promising performance, but the understanding of the important structure-property relationships is lacking. In this work, we conduct a comprehensive study on CCsCe 2Br 7. The crystal structure of CsCe 2Br 7 is refined using single crystal X-ray study for the first time. It crystallizes into the orthorhombic crystal system with Pmnb space group. Its electronic structure is revealed by Density Functional Theory (DFT) calculations. Two cerium emission centers are identified and the energy barriers related to the thermal quenching to 4f ground states of Ce 3+ for these two Cemore » centers are evaluated. CsCe 2Br 7 single crystal has better light yield and energy resolution than CsCe 2Cl 7, but with an additional slow decay component of 1.7 s. The existence of a deep trap with a depth of 0.9 eV in CsCe 2Cl 7 contributes to its higher afterglow level in comparison to that of CsCe 2Br 7. The most possible point defects in CsCe 2Cl 7 and CsCe 2Br 7 are proposed by considering the vapour pressure in the growth atmosphere upon melting point.« less

Experimental and theoretical studies on the structural, spectroscopic and hydrogen bonding on 4-nitro-n-(2,4-dinitrophenyl) benzenamine

NASA Astrophysics Data System (ADS)

Subhapriya, G.; Kalyanaraman, S.; Jeyachandran, M.; Ragavendran, V.; Krishnakumar, V.

2018-04-01

Synthesized 4-nitro-N-(2,4-dinitrophenyl) benzenamine (NDPBA) molecule was confirmed applying the tool of NMR. Theoretical prediction addressed the NMR chemical shifts and correlated well with the experimental data. The molecule subjected to theoretical DFT at 6-311++G** level unraveled the spectroscopic and structural properties of the NDPBA molecule. Moreover the structural features proved the occurrence of intramolecular Nsbnd H· · O hydrogen bonding in the molecule which was further confirmed with the help of Frontier molecular orbital analysis. Vibrational spectroscopic characterization through FT-IR and Raman experimentally and theoretically gave an account for the vibrational properties. An illustration of the topology of the molecule theoretically helped also in finding the hydrogen bonding energy.

Circularly polarized vacuum field in three-dimensional chiral photonic crystals probed by quantum dot emission

NASA Astrophysics Data System (ADS)

Takahashi, S.; Ota, Y.; Tajiri, T.; Tatebayashi, J.; Iwamoto, S.; Arakawa, Y.

2017-11-01

The modification of a circularly polarized vacuum field in three-dimensional chiral photonic crystals was measured by spontaneous emission from quantum dots in the structures. Due to the circularly polarized eigenmodes along the helical axis in the GaAs-based mirror-asymmetric structures we studied, we observed highly circularly polarized emission from the quantum dots. Both spectroscopic and time-resolved measurements confirmed that the obtained circularly polarized light was influenced by a large difference in the photonic density of states between the orthogonal components of the circular polarization in the vacuum field.

Synthesis, growth, crystal structure, optical and third order nonlinear optical properties of quinolinium derivative single crystal: PNQI

NASA Astrophysics Data System (ADS)

Karthigha, S.; Krishnamoorthi, C.

2018-03-01

An organic quinolinium derivative nonlinear optical (NLO) crystal, 1-ethyl-2-[2-(4-nitro-phenyl)-vinyl]-quinolinium iodide (PNQI) was synthesized and successfully grown by slow evaporation solution growth technique. Formation of a crystalline compound was confirmed by single crystal X-ray diffraction. The quinolinium compound PNQI crystallizes in the triclinic crystal system with a centrosymmetric space group of P-1 symmetry. The molecular structure of PNQI was confirmed by 1H NMR and 13C NMR spectral studies. The thermal properties of the crystal have been investigated by thermogravimetric (TG) and differential scanning calorimetry (DSC) studies. The optical characteristics obtained from UV-Vis-NIR spectral data were described and the cut-off wavelength observed at 506 nm. The etching study was performed to analyse the growth features of PNQI single crystal. The third order NLO properties such as nonlinear refractive index (n2), nonlinear absorption coefficient (β) and nonlinear susceptibility (χ (3)) of the crystal were investigated using Z-scan technique at 632.8 nm of Hesbnd Ne laser.

Synthesis, high-resolution NMR spectroscopic analysis, and single-crystal X-ray diffraction of isoxazoline tetracycles.

PubMed

Fascio, Mirta L; Alvarez-Larena, Angel; D'Accorso, Norma B

2002-11-29

Three isoxazoline tetracycles were obtained enantiomerically pure by intramolecular 1,3-dipolar cycloaddition. The characterization of the new compounds was performed by high-resolution 1H and 13C NMR spectroscopy. The relative configuration of the new chiral centers was determined by NOESY experiments and confirmed by single-crystal X-ray structural analysis.

Boron Arsenide and Boron Phosphide for High Temperature and Luminescent Devices. [semiconductor devices - crystal growth/crystal structure

NASA Technical Reports Server (NTRS)

Chu, T. L.

1975-01-01

The crystal growth of boron arsenide and boron phosphide in the form of bulk crystals and epitaxial layers on suitable substrates is discussed. The physical, chemical, and electrical properties of the crystals and epitaxial layers are examined. Bulk crystals of boron arsenide were prepared by the chemical transport technique, and their carrier concentration and Hall mobility were measured. The growth of boron arsenide crystals from high temperature solutions was attempted without success. Bulk crystals of boron phosphide were also prepared by chemical transport and solution growth techniques. Techniques required for the fabrication of boron phosphide devices such as junction shaping, diffusion, and contact formation were investigated. Alloying techniques were developed for the formation of low-resistance ohmic contacts to boron phosphide. Four types of boron phosphide devices were fabricated: (1) metal-insulator-boron phosphide structures, (2) Schottky barriers; (3) boron phosphide-silicon carbide heterojunctions; and (4) p-n homojunctions. Easily visible red electroluminescence was observed from both epitaxial and solution grown p-n junctions.

The molecular structure of the borate mineral rhodizite (K, Cs)Al4Be4(B, Be)12O28--a vibrational spectroscopic study.

PubMed

Frost, Ray L; López, Andrés; Xi, Yunfei; Scholz, Ricardo; Souza, Larissa; Lana, Cristiano

2014-07-15

We have studied the borate mineral rhodizite (K, Cs)Al4Be4(B, Be)12O28 using a combination of DEM with EDX and vibrational spectroscopic techniques. The mineral occurs as colorless, gray, yellow to white crystals in the triclinic crystal system. The studied sample is from the Antandrokomby Mine, Sahatany valley, Madagascar. The mineral is prized as a semi-precious jewel. Semi-quantitative chemical composition shows a Al, Ca, borate with minor amounts of K, Mg and Cs. The mineral has a characteristic borate Raman spectrum and bands are assigned to the stretching and bending modes of B, Be and Al. No Raman bands in the OH stretching region were observed. Copyright © 2014 Elsevier B.V. All rights reserved.

Syntheses and crystal structures of the rare-earth metal(III) bromide ortho-oxidotungstates(VI) with the formula REBr[WO4] (RE = Y, Gd-Yb)

NASA Astrophysics Data System (ADS)

Schustereit, Tanja; Schleid, Thomas; Hartenbach, Ingo

2015-10-01

The rare-earth metal(III) bromide ortho-oxidotungstates(VI) with the formula REBr[WO4] crystallize triclinically in space group P 1 bar (a = 689-693, b = 715-728, c = 1074-1107 pm, α = 103-106, β ≈ 108 and γ = 93-95°, Z = 4) for RE = Y, Gd-Yb. Their crystal structure is isotypic with the most examples of the formally analogous lanthanoid(III) bromide oxidomolybdates(VI) REBr[MoO4] with RE = Y, Pr, Nd, Sm, Gd-Lu. It contains two crystallographically different rare-earth metal(III) cations with coordination numbers of seven plus one for (RE1)3+ and seven for (RE2)3+. The (RE1)3+ cations are surrounded by three Br- and four plus one O2- anions forming distorted trigonal dodecahedra, while the (RE2)3+ cations exhibit a coordination environment of one Br- and six O2- anions in the shape of a monocapped trigonal prism. Furthermore, the structure contains two crystallographically independent, isolated tetrahedral [WO4]2- units. All these polyhedra are fused together to form 1 ∞ {REBr[WO4]} chains running along [012]. Since the title compounds, synthesized by solid-state reactions from the underlying binaries, emerge as pure phases according to X-ray powder diffractometry, spectroscopic and magnetic measurements were performed.

Synthesis, spectroscopic, and molecular structure characterizations of some azo derivatives of 2-hydroxyacetophenone

NASA Astrophysics Data System (ADS)

Albayrak, Çiğdem; Gümrükçüoğlu, İsmail E.; Odabaşoğlu, Mustafa; İskeleli, Nazan Ocak; Ağar, Erbil

2009-08-01

Some novel azo compounds were prepared by the reaction of 2-hydroxyacetophenone with aniline and its substituted derivatives. The structures of synthesized azo compounds were determined by IR, UV-Vis, 1H NMR and 13C NMR spectroscopic techniques and the structures of some of these compounds were also determined by X-ray diffraction studies. Structural analysis using IR in solid state shows that the azo form is favoured in the azo compounds whereas UV-Vis analysis of the azo compounds in solution has shown that there is a azo and ionic form. The azo compounds in the basic solvents dimethylformamide (DMF) and dimethylsulfoxide (DMSO) are both azo and ionic form while these compounds in ethyl alcohol (EtOH) and chloroform (CHCl 3) are only azo form.

Synthesis, Structural and Antioxidant Studies of Some Novel N-Ethyl Phthalimide Esters

PubMed Central

Chandraju, Siddegowda; Win, Yip-Foo; Tan, Weng Kang; Quah, Ching Kheng; Fun, Hoong-Kun

2015-01-01

A series of N-ethyl phthalimide esters 4(a-n) were synthesized and characterized by spectroscopic studies. Further, the molecular structure of majority of compounds were analysed by single crystal X-ray diffraction studies. The X-ray analysis revealed the importance of substituents on the crystal stability and molecular packing. All the synthesized compounds were tested for in vitro antioxidant activity by DPPH radical scavenging, FRAP and CUPRAC methods. Few of them have shown good antioxidant activity. PMID:25742494

Synthesis, structural and antioxidant studies of some novel N-ethyl phthalimide esters.

PubMed

Chidan Kumar, C S; Loh, Wan-Sin; Chandraju, Siddegowda; Win, Yip-Foo; Tan, Weng Kang; Quah, Ching Kheng; Fun, Hoong-Kun

2015-01-01

A series of N-ethyl phthalimide esters 4(a-n) were synthesized and characterized by spectroscopic studies. Further, the molecular structure of majority of compounds were analysed by single crystal X-ray diffraction studies. The X-ray analysis revealed the importance of substituents on the crystal stability and molecular packing. All the synthesized compounds were tested for in vitro antioxidant activity by DPPH radical scavenging, FRAP and CUPRAC methods. Few of them have shown good antioxidant activity.

Band gap structures for 2D phononic crystals with composite scatterer

NASA Astrophysics Data System (ADS)

Qi, Xiao-qiao; Li, Tuan-jie; Zhang, Jia-long; Zhang, Zhen; Tang, Ya-qiong

2018-05-01

We investigated the band gap structures in two-dimensional phononic crystals with composite scatterer. The composite scatterers are composed of two materials (Bragg scattering type) or three materials (locally resonance type). The finite element method is used to calculate the band gap structure, eigenmodes and transmission spectrum. The variation of the location and width of band gap are also investigated as a function of material ratio in the scatterer. We have found that the change trends the widest band gap of the two phononic crystals are different as the material ratio changing. In addition to this, there are three complete band gaps at most for the Bragg-scattering-type phononic crystals in the first six bands; however, the locally resonance-type phononic crystals exist only two complete band gap at most in the first six bands. The gap-tuning effect can be controlled by the material ratio in the scatterer.

Synthesis, crystal structure and bioactivity of manganese complexes with asymmetric chiral Schiff base

NASA Astrophysics Data System (ADS)

Zhang, Enfeng; Wei, Yi; Huang, Fuping; Yu, Qing; Bian, Hedong; Liang, Hong; Lei, Fuhou

2018-03-01

A couple of chiral unsymmtrical Schiff base ligands, (1R,2R) (-)chxn (salH) (naftalH) and (1S,2S) (-)chxn (salH) (naftalH) had been synthesized by the condensation of salicylaldehyde and 2-hydroxy-1-naphthaldehyde with two isomers of (1R,2R)-trans-1,2-cyclohexanediamin and (1S,2S)-trans-1,2-cyclohexanediamin, respectively. At the same time, two manganese complexes have been synthesized and fully characterized by FT-IR spectrum, elemental analyses, single crystal X-ray diffraction. The interaction of the two Mn (III) complexes with bovine serum albumin (BSA) was investigated by spectroscopic techniques. The result reveals that the complexes can strongly quench the intrinsic fluorescence of BSA through a static quenching mechanism. The binding constant and binding mode has been determined. The secondary structure and the amino acid residues microenvironment of BSA change in the presence of these complexes. SOD-like activity and ABTS free radical scavenging ability were also studied. The antioxidant capacity of the compounds showed that the complexes and their corresponding BSA adducts showed some SOD activity. The results of ABTS free radical scavenging showed that the activity of the BSA adduct was more obvious than that of the complex.

Machine learning for the structure-energy-property landscapes of molecular crystals.

PubMed

Musil, Félix; De, Sandip; Yang, Jack; Campbell, Joshua E; Day, Graeme M; Ceriotti, Michele

2018-02-07

Molecular crystals play an important role in several fields of science and technology. They frequently crystallize in different polymorphs with substantially different physical properties. To help guide the synthesis of candidate materials, atomic-scale modelling can be used to enumerate the stable polymorphs and to predict their properties, as well as to propose heuristic rules to rationalize the correlations between crystal structure and materials properties. Here we show how a recently-developed machine-learning (ML) framework can be used to achieve inexpensive and accurate predictions of the stability and properties of polymorphs, and a data-driven classification that is less biased and more flexible than typical heuristic rules. We discuss, as examples, the lattice energy and property landscapes of pentacene and two azapentacene isomers that are of interest as organic semiconductor materials. We show that we can estimate force field or DFT lattice energies with sub-kJ mol -1 accuracy, using only a few hundred reference configurations, and reduce by a factor of ten the computational effort needed to predict charge mobility in the crystal structures. The automatic structural classification of the polymorphs reveals a more detailed picture of molecular packing than that provided by conventional heuristics, and helps disentangle the role of hydrogen bonded and π-stacking interactions in determining molecular self-assembly. This observation demonstrates that ML is not just a black-box scheme to interpolate between reference calculations, but can also be used as a tool to gain intuitive insights into structure-property relations in molecular crystal engineering.

High-brightness tapered laser diodes with photonic crystal structures

NASA Astrophysics Data System (ADS)

Li, Yi; Du, Weichuan; Kun, Zhou; Gao, Songxin; Ma, Yi; Tang, Chun

2018-02-01

Beam quality of tapered laser diodes is limited by higher order lateral mode. On purpose of optimizing the brightness of tapered laser diodes, we developed a novel design of tapered diodes. This devices based on InGaAs/AlGaAs asymmetry epitaxial structure, containing higher order lateral mode filtering schemes especially photonic crystal structures, which fabricated cost effectively by using standard photolithography and dry etch processes. Meanwhile, the effects of photonic crystal structures on mode control are also investigated theoretically by FDBPM (Finite-Difference Beam Propagation Method) calculation. We achieved a CW optical output power of 6.9W at 940nm for a single emitter with 4 mm cavity length. A nearly diffraction limited beam of M2 ≍1.9 @ 0.5W has been demonstrated, and a highest brightness of β =75MW/(cm2 ·sr) was reached.

Spectroscopic properties of Nd3+ doped transparent oxyfluoride glass ceramics.

PubMed

Yu, Yunlong; Chen, Daqin; Ma, En; Wang, Yuansheng; Hu, Zhongjian

2007-07-01

In this paper, the spectroscopic properties of Nd(3+) doped transparent oxyfluoride glass ceramics containing LaF(3) nano-crystals were systematically studied. The formation and distribution of LaF(3) nano-crystals in the glass matrix were investigated by X-ray diffraction (XRD) and transmission electron microscopy (TEM). Based on Judd-Ofelt theory, the intensity parameters Omega(t) (t=2, 4, 6), spontaneous emission probability, radiative lifetime, radiative quantum efficiency, width of the emission line and stimulated emission cross-section of Nd(3+) were evaluated. Particularly, the effect of Nd(3+) doping level on them was discussed. With the increase of Nd(3+) concentration in the glass ceramic, the experimental luminescence lifetime, radiative quantum efficiency and stimulated emission cross-section vary from 353.4 micros, 78.3% and 1.86 x 10(-20)cm(2) to 214.7 micros, 39.9% and 1.52 x 10(-20)cm(2), respectively. The comparative study of Nd(3+) spectroscopic parameters in different hosts suggests that the investigated glass ceramic system is potentially applicable as laser materials for 1.06 microm emission.

Self-assembled ordered structures in thin films of HAT5 discotic liquid crystal.

PubMed

Morales, Piero; Lagerwall, Jan; Vacca, Paolo; Laschat, Sabine; Scalia, Giusy

2010-05-20

Thin films of the discotic liquid crystal hexapentyloxytriphenylene (HAT5), prepared from solution via casting or spin-coating, were investigated by atomic force microscopy and polarizing optical microscopy, revealing large-scale ordered structures substantially different from those typically observed in standard samples of the same material. Thin and very long fibrils of planar-aligned liquid crystal were found, possibly formed as a result of an intermediate lyotropic nematic state arising during the solvent evaporation process. Moreover, in sufficiently thin films the crystallization seems to be suppressed, extending the uniform order of the liquid crystal phase down to room temperature. This should be compared to the bulk situation, where the same material crystallizes into a polymorphic structure at 68 °C.

“Skin-Core-Skin” Structure of Polymer Crystallization Investigated by Multiscale Simulation

PubMed Central

Ruan, Chunlei

2018-01-01

“Skin-core-skin” structure is a typical crystal morphology in injection products. Previous numerical works have rarely focused on crystal evolution; rather, they have mostly been based on the prediction of temperature distribution or crystallization kinetics. The aim of this work was to achieve the “skin-core-skin” structure and investigate the role of external flow and temperature fields on crystal morphology. Therefore, the multiscale algorithm was extended to the simulation of polymer crystallization in a pipe flow. The multiscale algorithm contains two parts: a collocated finite volume method at the macroscopic level and a morphological Monte Carlo method at the microscopic level. The SIMPLE (semi-implicit method for pressure linked equations) algorithm was used to calculate the polymeric model at the macroscopic level, while the Monte Carlo method with stochastic birth-growth process of spherulites and shish-kebabs was used at the microscopic level. Results show that our algorithm is valid to predict “skin-core-skin” structure, and the initial melt temperature and the maximum velocity of melt at the inlet mainly affects the morphology of shish-kebabs. PMID:29659516

Structure and functionality of nanostructured triacylglycerol crystal networks.

PubMed

Ramel, Pere R; Co, Edmund D; Acevedo, Nuria C; Marangoni, Alejandro G

2016-10-01

In this review, recent advances in the characterization of the nanoscale structure of fat crystal networks are outlined. The effect of different factors on the properties of crystalline nanoplatelets (CNPs) is comprehensively described. These are discussed together with the observed changes in polymorphism and micro- or mesostructural properties so as to have a complete understanding of the influence of different internal and external factors on the material properties of fats. The relationship between the nanostructure and the material properties of fats (i.e., oil binding capacity and rheology) is also described. Characterization of the nanostructure of fats has provided a new dimension to the analysis of fat crystal networks and opportunities for nanoengineering that could result in innovations in the food industry with regards to processing and structuring fatty materials. Copyright © 2016 Elsevier B.V. All rights reserved.

Surface modes and reconstruction of diamond structure crystals

NASA Astrophysics Data System (ADS)

Goldammer, W.; Ludwig, W.; Zierau, W.

1986-08-01

Applying our recently proposed Green function method we calculate the surface phonon spectra for the (111) surfaces of the diamond structure crystals C, Si, Ge and α-Sn on the basis of a phenomenological force constant model. Allowing for changes in the surface force constants we investigate the possibility of a surface phonon softening. Relating these soft modes to surface reconstructions we find evidence for a Si (7 × 7), Ge (8 × 8) and α-Sn (3 × 3) reconstruction, while diamond does not exhibit a soft mode behavior at all. We can thus explain the occurrence of different surface structures in these geometrically identical crystals as being determined to a great extent already by bulk properties. Finally, we derive models of the reconstructed surfaces and discuss our model for the Si (7 × 7) surface with respect to experimental TED patterns.

HeI photoelectron spectroscopic studies on the electronic structure of alkyl nitrosamines

NASA Astrophysics Data System (ADS)

Jiang, Peng; Qian, Ximei; Li, Chunhui; Qiao, Chunhua; Wang, Dianxun

1997-10-01

HeI photoelectron spectroscopic (PES) studies on the electronic structure of alkyl nitrosamines R 2N 2O (R = CH 3-, CH 3CH 2-, and CH 3CH 2CH 2-) are reported. The assignment of the PES bands for this series of compounds has been made with the aid of the band shapes, the band intensity and ab initio SCF MO calculations based on the 631 ∗ G basis sets. Both PES experiment and the ab initio SCF MO calculations show that the detoxification ability of nitrosamine with longer alkyl chain is stronger.

Crystal Structure of Cocosin, A Potential Food Allergen from Coconut (Cocos nucifera).

PubMed

Jin, Tengchuan; Wang, Cheng; Zhang, Caiying; Wang, Yang; Chen, Yu-Wei; Guo, Feng; Howard, Andrew; Cao, Min-Jie; Fu, Tong-Jen; McHugh, Tara H; Zhang, Yuzhu

2017-08-30

Coconut (Cocos nucifera) is an important palm tree. Coconut fruit is widely consumed. The most abundant storage protein in coconut fruit is cocosin (a likely food allergen), which belongs to the 11S globulin family. Cocosin was crystallized near a century ago, but its structure remains unknown. By optimizing crystallization conditions and cryoprotectant solutions, we were able to obtain cocosin crystals that diffracted to 1.85 Å. The cocosin gene was cloned from genomic DNA isolated from dry coconut tissue. The protein sequence deduced from the predicted cocosin coding sequence was used to guide model building and structure refinement. The structure of cocosin was determined for the first time, and it revealed a typical 11S globulin feature of a double layer doughnut-shaped hexamer.

Synthesis and characterization of a novel schiff base of 1,2-diaminopropane with substituted salicyaldehyde and its transition metal complexes: Single crystal structures and biological activities

NASA Astrophysics Data System (ADS)

Tadavi, Samina K.; Yadav, Abhijit A.; Bendre, Ratnamala S.

2018-01-01

A novel schiff base H2L derived from simple condensation of 2-hydroxy-6-isopropyl-3-methyl benzaldehyde and 1,2-diaminopropane in 2:1 M ratio and its [MnL], [CoL] and [NiL]2 complexes have been prepared and characterized by spectroscopic technique, elemental analysis, SEM-EDX analysis, and cyclic voltammetry. Additionally, single crystal X-ray diffraction technique has been applied to the schiff base ligand H2L and its nickel complex. The structure of nickel complex exhibited dimeric form with formula [NiL]2 with distorted square planar geometry around each nickel center. Furthermore, all the synthesized compounds were screened for their antimicrobial and antioxidant and DNA cleavage activities.

Low-Temperature Crystal Structures of the Hard Core Square Shoulder Model.

PubMed

Gabriëlse, Alexander; Löwen, Hartmut; Smallenburg, Frank

2017-11-07

In many cases, the stability of complex structures in colloidal systems is enhanced by a competition between different length scales. Inspired by recent experiments on nanoparticles coated with polymers, we use Monte Carlo simulations to explore the types of crystal structures that can form in a simple hard-core square shoulder model that explicitly incorporates two favored distances between the particles. To this end, we combine Monte Carlo-based crystal structure finding algorithms with free energies obtained using a mean-field cell theory approach, and draw phase diagrams for two different values of the square shoulder width as a function of the density and temperature. Moreover, we map out the zero-temperature phase diagram for a broad range of shoulder widths. Our results show the stability of a rich variety of crystal phases, such as body-centered orthogonal (BCO) lattices not previously considered for the square shoulder model.

Effects of cyclic structure inhibitors on the morphology and growth of tetrahydrofuran hydrate crystals

NASA Astrophysics Data System (ADS)

Li, Sijia; Wang, Yanhong; Lang, Xuemei; Fan, Shuanshi

2013-08-01

Morphology and growth of hydrate crystals with cyclic structure inhibitors at a hydrate-liquid interface were directly observed through a microscopic manipulating apparatus. Tetrahydrofuran (THF) hydrate was employed as an objective. The effects of four kind of cyclic structure inhibitors, polyvinylpyrrolidone (PVP), poly(N-vinyl-2-pyrrolidone-co-2-vinyl pyridine) (PVPP), poly(2-vinyl pyridine-co-N-vinylcaprolactam) (PVPC) and poly(N-vinylcaprolactam) (PVCap), were investigated. Morphological patterns between each hydrate crystal growth from hydrate-liquid interface into droplet were found differ significantly. Lamellar structure growth of hydrate crystal was observed without inhibitor, while with PVP was featheriness-like, PVPP was like long dendritic crystal, PVPC was Mimosa pudica leaf-like and PVCap was like weeds. The growth rate of hydrate crystal without inhibitor was 0.00498 mm3/s, while with PVPP, PVPC and PVCap, were 0.00339 mm3/s, 0.00350 mm3/s, 0.00386 mm3/s and 0.00426 mm3/s, respectively. Cyclic structure inhibitors can decrease the growth rate, degree of reduction in growth rate of hydrate crystals decrease with the increase of cylinder number.

Exchange-Hole Dipole Dispersion Model for Accurate Energy Ranking in Molecular Crystal Structure Prediction.

PubMed

Whittleton, Sarah R; Otero-de-la-Roza, A; Johnson, Erin R

2017-02-14

Accurate energy ranking is a key facet to the problem of first-principles crystal-structure prediction (CSP) of molecular crystals. This work presents a systematic assessment of B86bPBE-XDM, a semilocal density functional combined with the exchange-hole dipole moment (XDM) dispersion model, for energy ranking using 14 compounds from the first five CSP blind tests. Specifically, the set of crystals studied comprises 11 rigid, planar compounds and 3 co-crystals. The experimental structure was correctly identified as the lowest in lattice energy for 12 of the 14 total crystals. One of the exceptions is 4-hydroxythiophene-2-carbonitrile, for which the experimental structure was correctly identified once a quasi-harmonic estimate of the vibrational free-energy contribution was included, evidencing the occasional importance of thermal corrections for accurate energy ranking. The other exception is an organic salt, where charge-transfer error (also called delocalization error) is expected to cause the base density functional to be unreliable. Provided the choice of base density functional is appropriate and an estimate of temperature effects is used, XDM-corrected density-functional theory is highly reliable for the energetic ranking of competing crystal structures.

Crystal Structure Predictions Using Adaptive Genetic Algorithm and Motif Search methods

NASA Astrophysics Data System (ADS)

Ho, K. M.; Wang, C. Z.; Zhao, X.; Wu, S.; Lyu, X.; Zhu, Z.; Nguyen, M. C.; Umemoto, K.; Wentzcovitch, R. M. M.

2017-12-01

Material informatics is a new initiative which has attracted a lot of attention in recent scientific research. The basic strategy is to construct comprehensive data sets and use machine learning to solve a wide variety of problems in material design and discovery. In pursuit of this goal, a key element is the quality and completeness of the databases used. Recent advance in the development of crystal structure prediction algorithms has made it a complementary and more efficient approach to explore the structure/phase space in materials using computers. In this talk, we discuss the importance of the structural motifs and motif-networks in crystal structure predictions. Correspondingly, powerful methods are developed to improve the sampling of the low-energy structure landscape.

Towards the Structure Determination of a Modulated Protein Crystal: The Semicrystalline State of Profilin:Actin

NASA Technical Reports Server (NTRS)

Borgstahl, G.; Lovelace, J.; Snell, E. H.; Bellamy, H.

2003-01-01

One of the remaining challenges to structural biology is the solution of modulated structures. While small molecule crystallographers have championed this type of structure, to date, no modulated macromolecular structures have been determined. Modulation of the molecular structures within the crystal can produce satellite reflections or a superlattice of reflections in reciprocal space. We have developed the data collection methods and strategies that are needed to collect and analyze these data. If the macromolecule's crystal lattice is composed of physiologically relevant packing contacts, structural changes induced under physiological conditions can cause distortion relevant to the function and biophysical processes of the molecule making up the crystal. By careful measurement of the distortion, and the corresponding three-dimensional structure of the distorted molecule, we will visualize the motion and mechanism of the biological macromolecule(s). We have measured the modulated diffraction pattern produced by the semicrystalline state of profilin:actin crystals using highly parallel and highly monochromatic synchrotron radiation coupled with fine phi slicing (0.001-0.010 degrees) for structure determination. These crystals present these crystals present a unique opportunity to address an important question in structural biology. The modulation is believed to be due to the formation of actin helical filaments from the actin beta ribbon upon the pH-induced dissociation of profilin. To date, the filamentous state of actin has resisted crystallization and no detailed structures are available. The semicrystalline state profilin:actin crystals provides a unique opportunity to understand the many conformational states of actin. This knowledge is essential for understanding the dynamics underlying shape changes and motility of eukaryotic cells. Many essential processes, such as cytokinesis, phagocytosis, and cellular migration depend upon the capacity of the actin

Crystal Structures of MEK1 Binary and Ternary Complexes with Nucleotides and Inhibitors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fischmann, Thierry O.; Smith, Catherine K.; Mayhood, Todd W.

MEK1 is a member of the MAPK signal transduction pathway that responds to growth factors and cytokines. We have determined that the kinase domain spans residues 35-382 by proteolytic cleavage. The complete kinase domain has been crystallized and its X-ray crystal structure as a complex with magnesium and ATP-{gamma}S determined at 2.1 {angstrom}. Unlike crystals of a truncated kinase domain previously published, the crystals of the intact domain can be grown either as a binary complex with a nucleotide or as a ternary complex with a nucleotide and one of a multitude of allosteric inhibitors. Further, the crystals allow formore » the determination of costructures with ATP competitive inhibitors. We describe the structures of nonphosphorylated MEK1 (npMEK1) binary complexes with ADP and K252a, an ATP-competitive inhibitor (see Table 1), at 1.9 and 2.7 {angstrom} resolution, respectively. Ternary complexes have also been solved between npMEK1, a nucleotide, and an allosteric non-ATP competitive inhibitor: ATP-{gamma}S with compound 1 and ADP with either U0126 or the MEK1 clinical candidate PD325089 at 1.8, 2.0, and 2.5 {angstrom}, respectively. Compound 1 is structurally similar to PD325901. These structures illustrate fundamental differences among various mechanisms of inhibition at the molecular level. Residues 44-51 have previously been shown to play a negative regulatory role in MEK1 activity. The crystal structure of the integral kinase domain provides a structural rationale for the role of these residues. They form helix A and repress enzymatic activity by stabilizing an inactive conformation in which helix C is displaced from its active state position. Finally, the structure provides for the first time a molecular rationale that explains how mutations in MEK may lead to the cardio-facio-cutaneous syndrome.« less

Probing the crystal structure landscape by doping: 4-bromo, 4-chloro and 4-methylcinnamic acids.

PubMed

Desiraju, Gautam R; Chakraborty, Shaunak; Joseph, Sumy

2018-06-11

Accessing the data points in the crystal structure landscape of a molecule is a challenging task, either experimentally or computationally. We have charted the crystal structure landscape of 4-bromocinnamic acid (4BCA) experimentally and computationally: experimental doping is achieved with 4-methylcinnamic acid (4MCA) to obtain new crystal structures; computational doping is performed with 4-chlorocinnamic acid (4CCA) as a model system, because of the difficulties associated in parameterizing the Br-atom. The landscape of 4CCA is explored experimentally in turn, also by doping it with 4MCA, and is found to bear a close resemblance to the landscape of 4BCA, justifying the ready miscibility of these two halogenated cinnamic acids to form solid solutions without any change in crystal structure. In effect, 4MCA, 4CCA and 4BCA form a commutable group of crystal structures, which may be realized experimentally or computationally, and constitute the landscape. Unlike the results obtained by Kitaigorodskii and others, all but two of the multiple solid solutions obtained in the methyl-doping experiments take structures that are different from the hitherto observed crystal forms of the parent compounds. Even granted that the latter might be inherently polymorphic, this unusual observation provokes the suggestion that solid solution formation may be used to probe the crystal structure landscape. The influence of pi...pi interactions, weak hydrogen bonds and halogen bonds in directing the formation of these new structures is also seen. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Fabrication and Analysis of Photonic Crystals

ERIC Educational Resources Information Center

Campbell, Dean J.; Korte, Kylee E.; Xia, Younan

2007-01-01

These laboratory experiments are designed to explore aspects of nanoscale chemistry by constructing and spectroscopically analyzing thin films of photonic crystals. Films comprised of colloidal spheres and polydimethylsiloxane exhibit diffraction-based stop bands that shift reversibly upon exposure to some common solvents. Topics covered in these…

Photonic guiding structures in lithium niobate crystals produced by energetic ion beams

NASA Astrophysics Data System (ADS)

Chen, Feng

2009-10-01

A range of ion beam techniques have been used to fabricate a variety of photonic guiding structures in the well-known lithium niobate (LiNbO3 or LN) crystals that are of great importance in integrated photonics/optics. This paper reviews the up-to-date research progress of ion-beam-processed LiNbO3 photonic structures and reports on their fabrication, characterization, and applications. Ion beams are being used with this material in a wide range of techniques, as exemplified by the following examples. Ion beam milling/etching can remove the selected surface regions of LiNbO3 crystals via the sputtering effects. Ion implantation and swift ion irradiation can form optical waveguide structures by modifying the surface refractive indices of the LiNbO3 wafers. Crystal ion slicing has been used to obtain bulk-quality LiNbO3 single-crystalline thin films or membranes by exfoliating the implanted layer from the original substrate. Focused ion beams can either generate small structures of micron or submicron dimensions, to realize photonic bandgap crystals in LiNbO3, or directly write surface waveguides or other guiding devices in the crystal. Ion beam-enhanced etching has been extensively applied for micro- or nanostructuring of LiNbO3 surfaces. Methods developed to fabricate a range of photonic guiding structures in LiNbO3 are introduced. Modifications of LiNbO3 through the use of various energetic ion beams, including changes in refractive index and properties related to the photonic guiding structures as well as to the materials (i.e., electro-optic, nonlinear optic, luminescent, and photorefractive features), are overviewed in detail. The application of these LiNbO3 photonic guiding structures in both micro- and nanophotonics are briefly summarized.

Crystal structure of triosephosphate isomerase from Trypanosoma cruzi in hexane

PubMed Central

Gao, Xiu-Gong; Maldonado, Ernesto; Pérez-Montfort, Ruy; Garza-Ramos, Georgina; de Gómez-Puyou, Marietta Tuena; Gómez-Puyou, Armando; Rodríguez-Romero, Adela

1999-01-01

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-Å 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 Å 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. PMID:10468562

Crystal structure of triosephosphate isomerase from Trypanosoma cruzi in hexane.

PubMed

Gao, X G; Maldonado, E; Pérez-Montfort, R; Garza-Ramos, G; de Gómez-Puyou, M T; Gómez-Puyou, A; Rodríguez-Romero, A

1999-08-31

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-A 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 A 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.

Structure and Dynamics of Freely Suspended Liquid Crystals

NASA Technical Reports Server (NTRS)

Clark, Noel A.

2004-01-01

Smectic liquid crystals are phases of rod shaped molecules organized into one dimensionally (1 D) periodic arrays of layers, each layer being between one and two molecular lengths thick. In the least ordered smectic phases, the smectics A and C, each layer is a two dimensional (2D) liquid. Additionally there are a variety of more ordered smectic phases having hexatic short range translational order or 2D crystalline or quasi long range translational order within the layers. The inherent fluid-layer structure and low vapor pressure of smectic liquid crystals enables the long term stabilization of freely suspended, single component, layered fluid films as thin as 30A, a single molecular layer. The layering forces the films to be an integral number of smectic layers thick, quantizing their thickness in layer units and forcing a film of a particular number of layers to be physically homogeneous with respect to its layer structure over its entire area. Optical reflectivity enables the precise determination of the number of layers. These ultrathin freely suspended liquid crystal films are structures of fundamental interest in condensed matter and fluid physics. They are the thinnest known stable fluid structures and have the largest surface-to-volume ratio of any stable fluid preparation, making them ideal for the study of the effects of reduced dimensionality on phase behavior and on fluctuation and interface phenomena. Their low vapor pressure and quantized thickness enable the effective use of microgravity to extend the study of basic capillary phenomena to ultrathin fluid films. Freely suspended films have been a wellspring of new LC physics. They have been used to provide unique experimental conditions for the study of condensed phase transitions in two dimensions. They are the only system in which the hexatic has been unambiguously identified as a phase of matter, and the only physical system in which fluctuations of a 2D XY system and Kosterlitz Thouless phase

The effect of ultrasonic intensity on the crystal structure of palm oil.

PubMed

Patrick, Maria; Blindt, Renoo; Janssen, Jo

2004-05-01

It has been known for a long time that both the crystal structure and kinetics of crystallisation can be affected by ultrasound. In the past systems used have relied on high power ultrasonic probes to produce crystals. The majority of these probes produce cavitation in the system and it has been difficult to differentiate between effects caused by the ultrasound alone or by the cavitation produced by ultrasound on the crystal structure. Some materials, such as fats, are very susceptible to the production of free radicals that lead to "off-flavours" being obtained. These "off-flavours" are easily produced when the standard high power probes are used. This has meant that, although the crystal structure of the final product might be improved, the presence of 'off' flavours has prevented ultrasound being considered as a commercial technique for the crystallisation of edible fats. At Unilever R&D a system has been developed which can investigate the effect of ultrasound on the crystallisation of fats under controlled conditions covering a range of intensities and cooling rates. The intensity levels used were both below and above the cavitational threshold. By keeping the cooling regime constant it has been possible to show that the structure of the final product can vary from a material looking similar to cottage cheese through to a fine cream simply by varying the ultrasonic intensity. This paper describes the effect of ultrasound on both the crystal structure and kinetics of palm oil crystallisation at intensities below and above the cavitational threshold.

Stochastic generation of complex crystal structures combining group and graph theory with application to carbon