Characterization of molecular associations involving L-ornithine and α-ketoglutaric acid: crystal structure of L-ornithinium α-ketoglutarate.

Science.gov (United States)

Allouchi, H; Céolin, R; Berthon, L; Tombret, F; Rietveld, I B

2014-07-01

The crystal structure of L-ornithinium α-ketoglutarate (C5H13N2O2, C5H5O5) has been solved by direct methods using single crystal X-ray diffraction data. It crystallizes in the monoclinic system, space group P21, unit cell parameters a=15.4326(3), b=5.2015(1), c=16.2067(3) Å and β=91.986(1)°, containing two independent pairs of molecular ions in the asymmetric unit. An extensive hydrogen-bond network and electrostatic charges due to proton transfer provide an important part of the cohesive energy of the crystal. The conformational versatility of L-ornithine and α-ketoglutaric acid is illustrated by the present results and crystal structures available from the Cambridge Structural Database. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

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

Science.gov (United States)

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

2016-04-01

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

Syntheses and structure characterization of ten acid-base hybrid crystals based on imidazole derivatives and mineral acids

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Hu, Kaikai; Deng, Bowen; Jin, Shouwen; Ding, Aihua; Jin, Shide; Zhu, Jin; Zhang, Huan; Wang, Daqi

2018-04-01

Cocrystallization of the imidazole derivatives with a series of mineral acids gave a total of ten hybrid salts with the compositions: [(H2bzm)(Cl)2·3H2O] (1), [(H2bzm)(ClO4)2] (2), [(H2bze)(Cl)2·2H2O] (3), [(H2bze)(Br)2·2H2O] (4), [(H2bzp)(Cl)2·4H2O] (5), [(H2bzp)(Br)2·4H2O] (6), (2-(imidazol-1-yl)-1-phenylethanone): (phosphoric acid) [(Himpeta)+(H2PO4)-] (7), [(H2impd)(Br)2] (8), [(H2impd)(ClO4)2] (9), and [(Hbzml)(Cl)] (10). The ten salts have been characterised by X-ray diffraction analysis, IR, and elemental analysis, and the melting points of all the salts were also reported. And their structural and supramolecular aspects are fully analyzed. The result reveals that among the ten investigated crystals the ring N atoms of the imidazole are protonated when the acids are deprotonated, and the crystal packing is interpreted in terms of the strong charge-assisted classical H-bonds between the NH+ and deprotonated acidic groups. Further analysis of the crystal packing of the salts indicated that a different set of additional CHsbnd O, CH2sbnd O, CHsbnd Cl, CH2sbnd Cl, CHsbnd N, CHsbnd Br, CH2sbnd Br, Osbnd O, O-π, Br-π, CH-π, and π-π associations contribute to the stabilization and expansion of the total high-dimensional frameworks. For the coexistence of the various weak nonbonding interactions these structures adopted homo or hetero supramolecular synthons or both. Some classical supramolecular synthons, such as R21(7), R22(7), R22(8), and R42(8), usually observed in the organic solids, were again shown to be involved in constructing some of these H-bonding networks.

Crystal structure of (E-pent-2-enoic acid

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Tim Peppel

2015-05-01

Full Text Available The molecule of the title compound, C5H8O2, a low-melting α,β-unsaturated carboxylic acid, is essentially planar [maximum displacement = 0.0239 (13 Å]. In the crystal, molecules are linked into centrosymmetric dimers via pairs of O—H...O hydrogen bonds.

Synthesis, growth, morphology of the semiorganic nonlinear optical crystal L-glutamic acid hydrochloride and its structural, thermal and SHG characterizations

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Dhanasekaran, P.; Srinivasan, K. [Crystal Growth Laboratory, Department of Physics, School of Physical Sciences, Bharathiar University, Coimbatore-641 046, Tamil Nadu (India)

2012-12-15

One of the halide derivatives of L-glutamic acid which was identified as a semiorganic nonlinear optical material, L-glutamic acid hydrochloride [HOOC(CH{sub 2}){sub 2}CH(NH{sub 2})COOH.HCl], was grown as bulk single crystal and its significant properties were characterized. The stoichiometric title compound was synthesized and the solubility of its recrystallized form in DD water was determined in the temperature range 30-80 C by gravimetric method. Structural confirmation was carried out by powder X-ray diffraction study through lattice parameter verification. Optical quality smaller dimension single crystals were grown from aqueous solution by self nucleation through slow evaporation of solvent method and a large dimension single crystal was grown by slow cooling method with reversible seed rotation technique. Morphological importances of different growth facets of the as grown crystals were studied through optical goniometry. Unit cell structure of the grown crystal was refined by single crystal X-ray diffraction analysis, functional groups present in the crystal responsible for various modes of vibrations were confirmed by FTIR spectroscopy analysis, thermal stability of the grown crystal was analysed by TG/DTA and DSC and second harmonic generation (SHG) of a fundamental Nd:YAG laser beam by Kurtz technique. Results indicate that the grown crystal is in stoichiometric composition and has significant improvement in its thermal and SHG properties when compared to pure L-glutamic acid polymorphs. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

Structural elucidation and physicochemical properties of an organic NLO crystal: 4-Nitrotoluene-2-sulphonic acid dihydrate

Science.gov (United States)

Sangeetha, K.; Guru Prasad, L.; Mathammal, R.

2018-03-01

4-nitrotoluene-2-sulphonic acid dihydrate single crystals have been developed using slow evaporation technique in methanol. Lattice parameters of the NTSAD crystal have been calculated and it confirms the grown material. The intermolecular interactions are studied from the 3D Hirshfeld surface analysis and 2D fingerprint plots. The NMR spectral analysis has been carried out to confirm the molecular structure of the grown material. Optical properties have been obtained from UV-VIS spectral analysis and photoluminescence studies. Frequency conversion property of the NTSAD crystal was investigated with the aid of Kurtz and Perry method.

SYNTHESIS, CHARACTERIZATION, AND CRYSTAL STRUCTURE ...

African Journals Online (AJOL)

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KEY WORDS: Barium, Crystal structure, 2,6-Pyridinedicarboxylic acid .... The rational design of novel metal-organic frameworks has attracted great ..... Bond, A.D.; Jones, W. Supramolecular Organization and Materials Design, Jones, W.; Rao,.

Crystal Structures of Apo and Liganded 4-Oxalocrotonate Decarboxylase Uncover a Structural Basis for the Metal-Assisted Decarboxylation of a Vinylogous β-Keto Acid.

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Guimarães, Samuel L; Coitinho, Juliana B; Costa, Débora M A; Araújo, Simara S; Whitman, Christian P; Nagem, Ronaldo A P

2016-05-10

The enzymes in the catechol meta-fission pathway have been studied for more than 50 years in several species of bacteria capable of degrading a number of aromatic compounds. In a related pathway, naphthalene, a toxic polycyclic aromatic hydrocarbon, is fully degraded to intermediates of the tricarboxylic acid cycle by the soil bacteria Pseudomonas putida G7. In this organism, the 83 kb NAH7 plasmid carries several genes involved in this biotransformation process. One enzyme in this route, NahK, a 4-oxalocrotonate decarboxylase (4-OD), converts 2-oxo-3-hexenedioate to 2-hydroxy-2,4-pentadienoate using Mg(2+) as a cofactor. Efforts to study how 4-OD catalyzes this decarboxylation have been hampered because 4-OD is present in a complex with vinylpyruvate hydratase (VPH), which is the next enzyme in the same pathway. For the first time, a monomeric, stable, and active 4-OD has been expressed and purified in the absence of VPH. Crystal structures for NahK in the apo form and bonded with five substrate analogues were obtained using two distinct crystallization conditions. Analysis of the crystal structures implicates a lid domain in substrate binding and suggests roles for specific residues in a proposed reaction mechanism. In addition, we assign a possible function for the NahK N-terminal domain, which differs from most of the other members of the fumarylacetoacetate hydrolase superfamily. Although the structural basis for metal-dependent β-keto acid decarboxylases has been reported, this is the first structural report for that of a vinylogous β-keto acid decarboxylase and the first crystal structure of a 4-OD.

Crystal structure of olivetolic acid: a natural product from Cetrelia sanguinea (Schaer.).

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Ismed, Friardi; Farhan, Aulia; Bakhtiar, Amri; Zaini, Erizal; Nugraha, Yuda Prasetya; Dwichandra Putra, Okky; Uekusa, Hidehiro

2016-11-01

The title compound, C 12 H 16 O 4 (systematic name: 2,4-dihy-droxy-6-pentyl-benzoic acid) is a natural product isolated from C. sanguinea (Schaer.) and is reported to have various pharmacological activities. The mol-ecule is approximately planar (r.m.s. deviation for the non-H atoms = 0.096 Å) and features an intra-molecular O-H⋯O hydrogen bond. In the crystal, each olivetolic acid mol-ecule is connected to three neighbours via O-H⋯O hydrogen bonds, generating (10-1) sheets. This crystal is essentially isostructural with a related resorcinolic acid with a longer alkyl chain.

Crystal structure and hydrogen bonding in N-(1-deoxy-β-d-fructopyranos-1-yl-2-aminoisobutyric acid

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Valeri V. Mossine

2018-01-01

Full Text Available The title compound, alternatively called d-fructose-2-aminoisobutyric acid (FruAib, C10H19NO7, (I, crystallizes exclusively in the β-pyranose form, with two conformationally non-equivalent molecules [(IA and (IB] in the asymmetric unit. In solution, FruAib establishes an equilibrium, with 75.6% of the population consisting of β-pyranose, 10.4% β-furanose, 10.1% α-furanose, 3.0% α-pyranose and <0.7% the acyclic forms. The carbohydrate ring in (I has the normal 2C5 chair conformation and the amino acid portion is in the zwitterion form. Bond lengths and valence angles compare well with the average values from related pyranose structures. All carboxyl, hydroxy and ammonium groups are involved in hydrogen bonding and form a three-dimensional network of infinite chains that are connected through homodromic rings and short chains. Intramolecular hydrogen bonds bridge the amino acid and sugar portions in both molecules. A comparative Hirshfeld surfaces analysis of FruAib and four other sugar–amino acids suggests an increasing role of intramolecular heteroatom interactions in crystal structures with an increasing proportion of C—H bonds.

Phenylacetic acid co-crystals with acridine, caffeine, isonicotinamide and nicotinamide: Crystal structures, thermal analysis, FTIR spectroscopy and Hirshfeld surface analysis

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Amombo Noa, Francoise M.; Jacobs, Ayesha

2017-07-01

Co-crystals of phenylacetic acid (PAA) with acridine (ACR), caffeine (CAF), isonicotinamide (INM) and nicotinamide (NAM) have been successfully prepared and characterised by single crystal X-ray diffraction, FTIR spectroscopy, thermal analysis and Hirshfeld surface analysis. The ACR, INM and NAM co-crystals with PAA exhibit the carboxylic acid-pyridine heterosynthon. Furthermore the amide-amide supramolecular homosynthon is observed in the PAA co-crystals with INM and NAM as well as Nsbnd H⋯O interactions between the acid and the respective base. The CAF co-crystal exhibits hydrogen bonding between the imidazole nitrogen and the COOH group of the PAA. The compounds demonstrate different stoichiometries; for PAA·ACR and PAA·INM a 1:1 ratio is displayed, a 2:1 in 2PAA·CAF and a 2:2 in the case of 2PAA·2NAM.

Crystal structure of a bacterial homologue of the bile acid sodium symporter ASBT

Science.gov (United States)

Hu, Nien-Jen; Iwata, So; Cameron, Alexander D.; Drew, David

2011-01-01

High cholesterol levels greatly increase the risk of cardiovascular disease. By its conversion into bile acids, about 50% of cholesterol is eliminated from the body. However bile acids released from the bile duct are constantly recycled, being reabsorbed in the intestine via the Apical Sodium dependent Bile acid Transporter (ASBT). It has been shown in animal models that plasma cholesterol levels are significantly lowered by specific inhibitors of ASBT1,2, thus ASBT is a target for hypercholesterolemia drugs. Here, we describe the crystal structure of a bacterial homologue of ASBT from Neisseria meningitidis (ASBTNM) at 2.2Å. ASBTNM contains two inverted structural repeats of five transmembrane helices. A Core domain of six helices harbours two sodium ions while the remaining helices form a Panel-like domain. Overall the architecture of the protein is remarkably similar to the sodium-proton antiporter NhaA3 despite no detectable sequence homology. A bile acid molecule is situated between the Core and Panel domains in a large hydrophobic cavity. Residues near to this cavity have been shown to affect the binding of specific inhibitors of human ASBT4. The position of the bile acid together with the molecular architecture suggests the rudiments of a possible transport mechanism. PMID:21976025

Acid indium strontium phosphate SrIn2[PO3(OH)]4: synthesis and crystal structure

International Nuclear Information System (INIS)

Rusakov, D.A.; Bobylev, A.P.; Komissarova, L.N.; Filaretov, A.A.; Danilov, V.P.

2007-01-01

Acid indium-strontium phosphate SrIn 2 [PO 3 (OH)] 4 is synthesized and characterized. Crystal structure and lattice parameters ate determined. In atoms in SrIn 2 [PO 3 (OH)] 4 structure are in distorted InO 6 octahedrons and form with PO 3 (OH) tetrahedrons mixed paraskeleton {In 2 [PO 3 (OH)] 4 } 3∞ 2- with emptinesses occupied by big Sr 2+ cations. The compound is thermally stable up to 400 Deg C [ru

5-Arylidene derivatives of Meldrum's acid: Synthesis, structural characterization using single crystal and powder crystal X-ray diffraction, and electronic properties

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Dey, Tanusri; Ghosh, Soumen; Ghosh, Somnath; Mukherjee, Alok Kumar

2015-07-01

Four 5-arylidene derivatives of Meldrum's acid, 5-(4-chlorobenzylidene)-2,2-dimethyl-1,3-dioxane-4,6-dione (2), 5-(3-hydroxybenzylidene)-2,2-dimethyl-1,3-dioxane-4,6-dione (3), 5-(3,4-dimethoxybenzylidene)-2,2-dimethyl-1,3-dioxane-4,6-dione (4) and 5-(2,4-dimethoxy benzylidene)-2,2-dimethyl-1,3-dioxane-4,6-dione (5) have been synthesized and their crystal structures have been determined using single crystal X-ray diffractometry for 2, 4 and 5 and X-ray powder diffraction for 3. The nature of intermolecular interactions in 2-5 has been analyzed through Hirshfeld surfaces and 2D fingerprint plots. The DFT optimized molecular geometries in 2-5 agree closely with those obtained from the crystallographic studies. The crystal packing in 2-5 exhibits an interplay of Osbnd H⋯O, Csbnd H⋯O, Csbnd H⋯Cl and Csbnd H⋯π (arene) hydrogen bonds and π⋯π interactions, which assemble molecules into three-dimensional architecture in 2, 3 and 5 and two-dimensional framework in 4. The Hirshfeld surface analyses of 2-5, Meldrum's acid (1) and a few related 5-arylidene derivatives of Meldrum's acid retrieved from the Cambridge Structural Database (CSD) indicate that about 85% of the Hirshfeld surface area (72% in 2 where H⋯Cl contribution is about 13%) in this class of compounds are due to H⋯H, O⋯H and C⋯H contacts. The HOMO-LUMO energy gap (>2.2 eV) in 2-5 indicates a significant degree of internal charge transfer within the molecule.

Effect of L-aspartic acid on the growth, structure and spectral studies of Zinc (tris) Thiourea Sulphate (ZTS) single crystals

Science.gov (United States)

Samuel, Bincy Susan; Krishnamurthy, R.; Rajasekaran, R.

2014-11-01

Single crystals of pure and L-aspartic acid doped Zinc (Tris) Thiourea Sulphate (ZTS) were grown from aqueous solution by solution growth method. The cell parameters and structure of the grown crystals were determined by X-ray diffraction studies. The presence of functional group in the compound has been confirmed by FTIR and FT-Raman analysis. The optical transparency range has been studied through UV-Vis spectroscopy. TGA/DTA studies show thermal stability of the grown crystals. Microhardness study reveals that the hardness number (Hv) increases with load for pure and doped ZTS crystals. Dielectric studies have been carried out and the results are discussed. The second harmonic generation was confirmed for L-aspartic acid doped ZTS which is greater than pure ZTS.

Synthesis, structure, antitumor activity of novel pharmaceutical co-crystals based on bispyridyl-substituted α, β-unsaturated ketones with gallic acid

Science.gov (United States)

Liu, Lian-Dong; Liu, Shu-Lian; Liu, Zhi-Xian; Hou, Gui-Ge

2016-05-01

Three novel pharmaceutical co-crystals, (A)·(gallic acid) (1), (B)·(gallic acid) (2), and (C)·(gallic acid) (3) were generated based on 2,6-bis((pyridin-4-yl)methylene)cyclohexanone (A), N-methyl-3,5-bis((pyridin-3-yl)methylene)-4-piperidone (B), N-methyl-3,5-bis((pyridin-4-yl)methylene)-4-piperidone (C) with gallic acid, respectively. They are characterized by elemental analysis, FTIR spectroscopy, 1H NMR and single-crystal X-ray diffraction. Structural analysis reveals that two pharmaceutical ingredients link each other into H-bonding-driven 3D network in 1, 2, or 2D plane in 3. In addition, their antitumor activities against human neoplastic cell lines A549, SGC-7901, MCF-7, OVCA-433, HePG2 and cytotoxicity for HUVEC cell lines by CCK-8 method were evaluated primarily. Compared with gallic acid and free A, B and C, their antitumor activities have improved distinctly, while cytotoxicities have reduced markedly, especially for co-crystal 1. This is mainly because of the synergistic effect between pharmaceutical ingredients A, B, and C and gallic acid.

Syntheses and structure characterization of ten acid-base hybrid crystals based on N-containing aromatic brønsted bases and mineral acids

Science.gov (United States)

Lin, Zhihao; Jin, Shouwen; Li, Xiaoliang; Xiao, Xiao; Hu, Kaikai; Guo, Ming; Chi, Xinchen; Liu, Hui; Wang, Daqi

2017-10-01

Cocrystallization of the aromatic brønsted bases with a series of mineral acids gave a total of ten hybrid salts with the compositions: (2-methylquinoline)2: (hydrochloride acid): 3H2O [(HL1)+. (L1)·· (Cl-) · (H2O)3] (1), (6-bromobenzo[d]thiazol-2-amine): (hydrochloride acid) [(HL2)+. (Cl-)] (2), (6-bromobenzo[d]thiazol-2-amine): (nitric acid) [(HL2)+. (NO3-)] (3), (6-bromobenzo[d]thiazol-2-amine): (sulfuric acid) [(HL2)+ · (HSO4)-] (4), (6-bromobenzo[d]thiazol-2-amine): (phosphoric acid) [(HL2)+ · (H2PO4)-] (5), (5,7-dimethyl-1,8-naphthyridine-2-amine): (hydrochloride acid): 3H2O [(HL3)+ · (Cl-) (H2O)3] (6), (5,7-dimethyl-1,8-naphthyridine-2-amine): (hydrobromic acid): CH3OH [(HL3)+ · (Br)- · CH3OH] (7), (5,7-dimethyl-1,8-naphthyridine-2-amine): (sulfuric acid): H2O [(HL3)+ · (HSO4)- · H2O] (8), (2-aminophenol): (phosphoric acid) [(HL4)+ · (H2PO4)-] (9), and (2-amino-4-chlorophenol): (phosphoric acid) [(HL5)+ · (H2PO4)-] (10). The ten salts have been characterized by X-ray diffraction analysis, IR, and elemental analysis, and the melting points of all the salts were also reported. And their structural and supramolecular aspects are fully analyzed. The result reveals that among the ten investigated crystals the ring N of the heterocycle or the NH2 in the aminophenol are protonated when the acids are deprotonated, and the crystal packing is interpreted in terms of the strong charge-assisted classical hydrogen bonds between the NH+/NH3+ and deprotonated acidic groups. Further analysis of the crystal packing of the salts indicated that a different family of additional CHsbnd O, CHsbnd Cl, CH3sbnd N, CH3sbnd O, CHsbnd Br, CH3sbnd Br, Brsbnd Cl, Clsbnd S, Osbnd S, Osbnd O, Brsbnd S, Hsbnd H, and π-π associations contribute to the stabilization and expansion of the total high-dimensional frameworks. For the coexistence of the various weak nonbonding interactions these structures adopted homo or hetero supramolecular synthons or both. Some classical

Synthesis, characterization and crystal structure of (2RS,4R)-2-(2-hydroxy-3-methoxyphenyl)thiazolidine-4-carboxylic acid

Science.gov (United States)

Muche, Simon; Müller, Matthias; Hołyńska, Małgorzata

2018-03-01

The condensation reaction of ortho-vanillin and L-cysteine leads to formation of a racemic mixture of (2RS,4R)-2-(2-hydroxy-3-methoxyphenyl)thiazolidine-4-carboxylic acid and not, as reported in the available literature, to a Schiff base. The racemic mixture was fully characterized by 1D and 2D NMR techniques, ESI-MS and X-ray diffraction. Addition of ZnCl2 led to formation of crystals in form of colorless needles, suitable for X-ray diffraction studies. The measured crystals were identified as the diastereomer (2R,4R)-2-(2-hydroxy-3-methoxyphenyl)thiazolidine-4-carboxylic acid 1. The bulk material is racemic. Thiazolidine exists as zwitterion in solid state, as indicated by the crystal structure.

Crystal structure of a 2:1 piroxicam–gentisic acid co-crystal featuring neutral and zwitterionic piroxicam molecules

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Elizabeth M. Horstman

2016-12-01

Full Text Available A new 2:1 co-crystal of piroxicam and gentisic acid [systematic name: 4-hydroxy-1,1-dioxo-N-(pyridin-2-yl-2H-1λ6,2-benzothiazine-3-carboxamide–2-(4-oxido-1,1-dioxo-2H-1λ6,2-benzothiazine-3-amidopyridin-1-ium–2,5-dihydroxybenzoic acid, 2C15H13N3O4S·C7H6O4] has been synthesized using a microfluidic platform and initially identified using Raman spectroscopy. In the co-crystal, one piroxicam molecule is in its neutral form and an intramolecular O—H...O hydrogen bond is observed. The other piroxicam molecule is zwitterionic (proton transfer from the OH group to the pyridine N atom and two intramolecular N—H...O hydrogen bonds occur. The gentisic acid molecule shows whole-molecule disorder over two sets of sites in a 0.809 (2:0.191 (2 ratio. In the crystal, extensive hydrogen bonding between the components forms layers propagating in the ab plane.

Studies on the structural, optical and dielectric properties of samarium coordinated with salicylic acid single crystal

Science.gov (United States)

Singh, Harjinder; Slathia, Goldy; Gupta, Rashmi; Bamzai, K. K.

2018-04-01

Samarium coordinated with salicylic acid was successfully grown as a single crystal by low temperature solution technique using mixed solvent of methanol and water in equal ratio. Structural characterization was carried out by single crystal X-ray diffraction analysis and it crystallizes in centrosymmetric space group P121/c1. FTIR and UV-Vis-NIR spectroscopy confirmed the compound formation and help to determine the mode of binding of the ligand to the rare earth-metal ion. Dielectric constant and dielectric loss have been measured over the frequency range 100 Hz - 30MHz. The decrease in dielectric constant with increases in frequency is due to the transition from interfacial polarization to dipolar polarization. The small value of dielectric constant at higher frequency ensures that the crystal is good candidate for NLO devices. Dielectric loss represents the resistive nature of the material.

Pseudoracemic amino acid complexes: blind predictions for flexible two-component crystals.

Science.gov (United States)

Görbitz, Carl Henrik; Dalhus, Bjørn; Day, Graeme M

2010-08-14

Ab initio prediction of the crystal packing in complexes between two flexible molecules is a particularly challenging computational chemistry problem. In this work we present results of single crystal structure determinations as well as theoretical predictions for three 1 ratio 1 complexes between hydrophobic l- and d-amino acids (pseudoracemates), known from previous crystallographic work to form structures with one of two alternative hydrogen bonding arrangements. These are accurately reproduced in the theoretical predictions together with a series of patterns that have never been observed experimentally. In this bewildering forest of potential polymorphs, hydrogen bonding arrangements and molecular conformations, the theoretical predictions succeeded, for all three complexes, in finding the correct hydrogen bonding pattern. For two of the complexes, the calculations also reproduce the exact space group and side chain orientations in the best ranked predicted structure. This includes one complex for which the observed crystal packing clearly contradicted previous experience based on experimental data for a substantial number of related amino acid complexes. The results highlight the significant recent advances that have been made in computational methods for crystal structure prediction.

Crystal structure of a 2:1 piroxicam–gentisic acid co-crystal featuring neutral and zwitterionic piroxicam molecules

Energy Technology Data Exchange (ETDEWEB)

Horstman, Elizabeth M.; Bertke, Jeffery A.; Woods, Toby J.; Kenis, Paul J. A.

2016-11-04

A new 2:1 co-crystal of piroxicam and gentisic acid [systematic name: 4-hydroxy-1,1-dioxo-N-(pyridin-2-yl)-2H-1λ⁶,2-benzothiazine-3-carboxamide–2-(4-oxido-1,1-dioxo-2H-1λ⁶,2-benzothiazine-3-amido)pyridin-1-ium–2,5-dihydroxybenzoic acid, 2C₁₅H₁₃N₃O₄S·C₇H₆O₄] has been synthesized using a microfluidic platform and initially identified using Raman spectroscopy. In the co-crystal, one piroxicam molecule is in its neutral form and an intramolecular O—H...O hydrogen bond is observed. The other piroxicam molecule is zwitterionic (proton transfer from the OH group to the pyridine N atom) and two intramolecular N—H...O hydrogen bonds occur. The gentisic acid molecule shows whole-molecule disorder over two sets of sites in a 0.809(2):0.191(2) ratio. In the crystal, extensive hydrogen bonding between the components forms layers propagating in theabplane.

Crystal structure of ethylenedioxytetrathiafulvalene-4,5-bis(thiolbenzoic acid 0.25-hydrate

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Yuanyuan Zhang

2017-09-01

Full Text Available In the title compound (systematic name: 4,4′-{[2-(5,6-dihydro-[1,3]dithiolo[4,5-b][1,4]dioxin-2-ylidene-1,3-dithiole-4,5-diyl]bis(sulfanediyl}dibenzoic acid 0.25-hydrate, C22H14O6S6·0.25H2O, the tetrathiafulvalene (TTF core adopts a boat conformation, where the central S2C=CS2 plane makes dihedral angles of 31.34 (4 and 26.83 (6°, respectively, with the peripheral S2C=CS2 and S2C2O2 planes. In the crystal, the benzoic acid molecules are linked via O—H...O hydrogen bonds, forming inversion dimers with R22(8 motifs. The dimers are linked through weak C—H...O hydrogen bonds into a chain structure along [-101]. The chains stack along the a axis through S...S and S...C short contacts, forming layers parallel to the ac plane.

Comparative analysis of amino acids and amino-acid derivatives in protein crystallization

International Nuclear Information System (INIS)

Ito, Len; Shiraki, Kentaro; Yamaguchi, Hiroshi

2010-01-01

New types of aggregation suppressors, such as amino acids and their derivatives, were focused on as fourth-component additives. Data were obtained that indicated that the additives promote protein crystallization. Optimal conditions for protein crystallization are difficult to determine because proteins tend to aggregate in saturated solutions. This study comprehensively evaluates amino acids and amino-acid derivatives as additives for crystallization. This fourth component of the solution increases the probability of crystallization of hen egg-white lysozyme in various precipitants owing to a decrease in aggregation. These results suggest that the addition of certain types of amino acids and amino-acid derivatives, such as Arg, Lys and esterified and amidated amino acids, is a simple method of improving the success rate of protein crystallization

Synthesis, Crystal Structure, and Luminescence Properties of a New Calcium(II Coordination Polymer Based on L-Malic Acid

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Duraisamy Senthil Raja

2013-01-01

Full Text Available A new calcium coordination polymer [Ca(HL-MA]n (H3L-MA = L-malic acid has been solvothermally synthesized. The structure of the newly synthesized complex has been determined by single-crystal X-ray diffraction analysis and further characterized by elemental analysis, reflectance UV-Vis & IR spectra, powder X-ray diffraction (PXRD, and thermogravimetric analysis (TGA. The single crystal structure analysis showed that the complex forms three-dimensional framework. The new Ca(II complex has displayed very high thermal stability which was inferred from TGA and PXRD results. As far as the optical property of the new complex is concerned, the complex emitted its own characteristic sensitized luminescence.

Crystallization of a newly discovered histidine acid phosphatase from Francisella tularensis

Energy Technology Data Exchange (ETDEWEB)

Felts, Richard L. [Department of Chemistry, University of Missouri-Columbia, Columbia, Missouri 65211 (United States); Reilly, Thomas J. [Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri-Columbia, Columbia, Missouri 65212 (United States); Veterinary Medical Diagnostic Laboratory, College of Veterinary Medicine, University of Missouri-Columbia, Columbia, Missouri 65212 (United States); Calcutt, Michael J. [Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri-Columbia, Columbia, Missouri 65212 (United States); Tanner, John J., E-mail: tannerjj@missouri.edu [Department of Chemistry, University of Missouri-Columbia, Columbia, Missouri 65211 (United States); Department of Biochemistry, University of Missouri-Columbia, Columbia, Missouri 65211 (United States)

2006-01-01

A histidine acid phosphatase from the CDC Category A pathogen F. tularensis has been crystallized in space group P4{sub 1}2{sub 1}2, with unit-cell parameters a = 61.96, c = 210.78 Å. A 1.75 Å resolution data set was collected at Advanced Light Source beamline 4.2.2. Francisella tularensis is a highly infectious bacterial pathogen that is considered by the Centers for Disease Control and Prevention to be a potential bioterrorism weapon. Here, the crystallization of a 37.2 kDa phosphatase encoded by the genome of F. tularensis subsp. holarctica live vaccine strain is reported. This enzyme shares 41% amino-acid sequence identity with Legionella pneumophila major acid phosphatase and contains the RHGXRXP motif that is characteristic of the histidine acid phosphatase family. Large diffraction-quality crystals were grown in the presence of Tacsimate, HEPES and PEG 3350. The crystals belong to space group P4{sub 1}2{sub 1}2, with unit-cell parameters a = 61.96, c = 210.78 Å. The asymmetric unit is predicted to contain one protein molecule, with a solvent content of 53%. A 1.75 Å resolution native data set was recorded at beamline 4.2.2 of the Lawrence Berkeley National Laboratory Advanced Light Source. Molecular-replacement trials using the human prostatic acid phosphatase structure as the search model (28% amino-acid sequence identity) did not produce a satisfactory solution. Therefore, the structure of F. tularensis histidine acid phosphatase will be determined by multiwavelength anomalous dispersion phasing using a selenomethionyl derivative.

Crystallization of a newly discovered histidine acid phosphatase from Francisella tularensis

International Nuclear Information System (INIS)

Felts, Richard L.; Reilly, Thomas J.; Calcutt, Michael J.; Tanner, John J.

2005-01-01

A histidine acid phosphatase from the CDC Category A pathogen F. tularensis has been crystallized in space group P4 1 2 1 2, with unit-cell parameters a = 61.96, c = 210.78 Å. A 1.75 Å resolution data set was collected at Advanced Light Source beamline 4.2.2. Francisella tularensis is a highly infectious bacterial pathogen that is considered by the Centers for Disease Control and Prevention to be a potential bioterrorism weapon. Here, the crystallization of a 37.2 kDa phosphatase encoded by the genome of F. tularensis subsp. holarctica live vaccine strain is reported. This enzyme shares 41% amino-acid sequence identity with Legionella pneumophila major acid phosphatase and contains the RHGXRXP motif that is characteristic of the histidine acid phosphatase family. Large diffraction-quality crystals were grown in the presence of Tacsimate, HEPES and PEG 3350. The crystals belong to space group P4 1 2 1 2, with unit-cell parameters a = 61.96, c = 210.78 Å. The asymmetric unit is predicted to contain one protein molecule, with a solvent content of 53%. A 1.75 Å resolution native data set was recorded at beamline 4.2.2 of the Lawrence Berkeley National Laboratory Advanced Light Source. Molecular-replacement trials using the human prostatic acid phosphatase structure as the search model (28% amino-acid sequence identity) did not produce a satisfactory solution. Therefore, the structure of F. tularensis histidine acid phosphatase will be determined by multiwavelength anomalous dispersion phasing using a selenomethionyl derivative

Drug-drug cocrystals of antituberculous 4-aminosalicylic acid: Screening, crystal structures, thermochemical and solubility studies.

Science.gov (United States)

Drozd, Ksenia V; Manin, Alex N; Churakov, Andrei V; Perlovich, German L

2017-03-01

Experimental multistage cocrystal screening of the antituberculous drug 4-aminosalicylic acid (PASA) has been conducted with a number of coformers (pyrazinamide (PYR), nicotinamide (NAM), isonicotinamide (iNAM), isoniazid (INH), caffeine (CAF) and theophylline (TPH)). The crystal structures of 4-aminosalicylic acid cocrystals with isonicotinamide ([PASA+iNAM] (2:1)) and methanol solvate with caffeine ([PASA+CAF+MeOH] (1:1:1)) have been determined by single X-ray diffraction experiments. For the first time for PASA cocrystals it has been found that the structural unit of the [PASA+iNAM] cocrystal (2:1) is formed by 2 types of heterosynthons: acid-pyridine and acid-amide. The desolvation study of the [PASA+CAF+MeOH] cocrystal solvate (1:1:1) has been conducted. The correlation models linking the melting points of the cocrystals with the melting points of the coformers used in this paper have been developed. The thermochemical and solubility properties for all the obtained cocrystals have been studied. Cocrystallization has been shown to lead not only to PASA solubility improving but also to its higher stability against the chemical decomposition. Copyright © 2016 Elsevier B.V. All rights reserved.

Structural evolution of amino acid crystals under stress from a non-empirical density functional

International Nuclear Information System (INIS)

Sabatini, Riccardo; Küçükbenli, Emine; De Gironcoli, Stefano; Kolb, Brian; Thonhauser, T

2012-01-01

Use of the non-local correlation functional vdW-DF (from ‘van der Waals density functional’; Dion M et al 2004 Phys. Rev. Lett. 92 246401) has become a popular approach for including van der Waals interactions within density functional theory. In this work, we extend the vdW-DF theory and derive the corresponding stress tensor in a fashion similar to the LDA and GGA approach, which allows for a straightforward implementation in any electronic structure code. We then apply our methodology to investigate the structural evolution of amino acid crystals of glycine and l-alanine under pressure up to 10 GPa - with and without van der Waals interactions - and find that for an accurate description of intermolecular interactions and phase transitions in these systems, the inclusion of van der Waals interactions is crucial. For glycine, calculations including the vdW-DF (vdW-DF-c09x) functional are found to systematically overestimate (underestimate) the crystal lattice parameters, yet the stability ordering of the different polymorphs is determined accurately, at variance with the GGA case. In the case of l-alanine, our vdW-DF results agree with recent experiments that question the phase transition reported for this crystal at 2.3 GPa, as the a and c cell parameters happen to become equal but no phase transition is observed.

Synthesis,crystal structure and properties of inorganic-organic hybrid polymers based on 8-hydroxylquinoline-5-sulfonic acid

Institute of Scientific and Technical Information of China (English)

无

2009-01-01

Two new inorganic-organic hybrid polymers, Mn(QS)(H2O) (1) and Co(QS)(H2O)2 (2) (H2QS=8-hydroxyl-quinoline-5-sulfonic acid), based on 8-hydroxylquinoline-5-sulfonate ligand, have been synthesized under solvothermal conditions and their structures were solved by single-crystal X-ray diffraction analysis. Compound 1 is a three-dimensional open framework with rutile topology structure, and compound 2 is a three-dimensional supramolecular structure. These compounds were characterized by powder XRD, infrared spectroscopy, thermogravimetric analysis, fluorescence properties and magnetism properties.

New manganese (II) structures derived from 2,6-dichlorobenzoic acid: Syntheses, crystal structures and magnetism

International Nuclear Information System (INIS)

Esteves, D.; Tedesco, J.C.D.; Pedro, S.S.; Cruz, C.; Reis, M.S.; Brandão, P.

2014-01-01

One novel coordination polymer [Mn 2 (μ-2,6-DCBA) 3 (μ 2 -CH 3 CO 2 ) 2 (2H 2 O)]·2H 2 O (2,6-DCBA = 2,6-dichlorobenzoato) (compound 1) has been synthesized by self-assembly of bridging ligand 2,6-dichlorobenzoic acid and manganese acetate tetrahydrate. Single crystal X-ray diffraction analysis reveals that this compound crystallizes in space group P2 1 /c with a = 10.1547(7), b = 24.5829(2), c = 12.6606(2) Å, β = 93.707(3), V = 3153.9(3) Å 3 and Z = 4. The Mn(II) ions are connected by 2,6-DCBA and acetate group in μ-bridging mode to form 1D chains. Two water molecules are in the inter-layer space forming strong hydrogen bonds originating 2D layer structure. The preparation of this compound is very sensitive to the synthesis conditions, mainly to the solution pH and solvent yielding other two compounds 2 and 3. In compound 1 Mn(II) atoms in octahedral coordination are arranged in a zig–zag chain, with a trimeric structure repeated periodically along the chain, giving two exchange parameters: J 1 related to a syn–syn bond; and J 2 related to a bond of type anti–anti. A theoretical model was developed and then fitted to the magnetic susceptibility data, revealing an antiferromagnetic arrangement along the chain

Crystal structures of eight 3D molecular adducts derived from bis-imidazole, bis(benzimidazole), and organic acids

Science.gov (United States)

Ding, Aihua; Jin, Shouwen; Jin, Shide; Hu, KaiKai; Lin, Zhihao; Liu, Hui; Wang, Daqi

2018-01-01

Cocrystallization of the bis(imidazole)/bis(benzimidazole) with a series of organic acids gave a total of eight molecular adducts with the compositions: (3,6-bis(imidazole-1-yl)pyridazine): (trichloroacetic acid)2(1) [(H2L1)2+ · (tca-)2, L1 = 3,6-bis(imidazole-1-yl)pyridazine, tca- = trichloroacetate], (bis(N-imidazolyl)methane): (suberic acid) (2) [(L2) · (H2suba), L2 = bis(N-imidazolyl)methane, H2suba = suberic acid], bis(N-imidazolyl)methane: (3-nitrophthalic acid): 3H2O (3) [(H2L2)2+ · (3-Hnpa-)2 · 3H2O, 3-Hnpa- = 3-nitro hydrogenphthalate], (bis(N-imidazolyl)butane)0.5: (4-nitrophthalic acid): H2O (4) [(H2L3)0.5+ · (4-Hnpa-)- · H2O, L3 = bis(N-imidazolyl)butane, 4-Hnpa- = 4-nitro hydrogenphthalate], (1-(3-(1H-benzimidazol-1-yl)propyl)-1H-benzimidazole): (3,5-dinitrosalicylic acid) (5) [(HL4) · (3,5-dns-), L4 = 1-(3-(1H-benzimidazol-1-yl)propyl)-1H-benzimidazole, 3,5-dns- = 3,5-dinitrosalicylate], (1-(3-(1H-benzimidazol-1-yl)propyl)-1H-benzimidazole): (3-nitrophthalic acid) (6) [(H2L4) · (3-npa2-), L4 = 1-(3-(1H-benzimidazol-1-yl)propyl)-1H-benzimidazole, 3-npa2-=3-nitrogenphthalate], (bis(N-imidazolyl)butane): (pamoic acid) (7) [(H2L3) · (pam), pam = pamoate], and (3,6-bis(imidazole-1-yl)pyridazine): (1,5-naphthalenedisulfonic acid) [(H2L1)2+ · (npda)2- = 1,5-naphthalenedisulfonate] (8). The eight adducts have been characterized by X-ray diffraction technique, infrared spectrum, and elemental analysis, and the melting points of all adducts were also reported. And their structural and supramolecular aspects are fully analyzed. The result reveals that among the eight investigated crystals both the end ring N in the bis(imidazole) moieties are protonated when the organic acids are deprotonated except 2, and 5, and the crystal packing is interpreted in terms of the strong ionic Nsbnd H⋯O H-bond between the imidazolium and the deprotonated acidic groups. Except the Nsbnd H⋯O H-bond, the Osbnd H⋯O H-bonds were also found at the salts 3, 4

3.2.1. Synthesis, crystal and molecular structure of catena-(bis(µ1-oxalic acid-µ3-hydrogen oxalate-di-aqua-sodium(I.

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Olga Kovalchukova*, Sergey Aldoshin, Andrey Utenyshev, Konstantin Bogenko, Valeriy Tkachev

2015-07-01

Full Text Available The crystal and molecular structure of catena-(bis(µ- oxalic acid-µ-hydrogen oxalate-di-aqua-sodium(I was detected by X-Ray analysis. The compound crystallizes in the triclinic space group P-1, with a(Å 6.2378(12; b(Å 7,1115(14; c(Å 10.489(2; α(° 94.65(3; β(° 100.12(3; γ(° 97.78(3. The sodium cation in the title compound is eight coordinated and forms a square antiprism. It is surrounded by two molecules of oxalic acid, one hydrogen oxalate anion and one water molecule. Both oxalic acid and hydrogen oxalate anion act as polydentate bridging ligands. Centrosymmetric sodium cations are bounded by hydrogen oxalate anions through a system of H bonds involving the molecules of oxalic acid. In the lattice, the 3D structure stabilized by H bonds is formed.

Crystal Structures, Thermal Analysis, and Dissolution Behavior of New Solid Forms of the Antiviral Drug Arbidol with Dicarboxylic Acids

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Alex N. Manin

2015-12-01

Full Text Available Salts of the antiviral drug arbidol (umifenovir (Arb with maleate (Mlc and fumarate (Fum anions have been obtained, and their crystal structures have been described. The crystal structure of arbidol maleate has been redetermined by single crystal X-ray diffraction at 180K. A new arbidol cocrystal in zwitterion form with succinic acid (Suc has also been found and characterized. The arbidol zwitterion was not previously seen in any of the drug crystal forms, and the [Arb + Suc] cocrystal seems to be the first found instance. Analysis of the conformational preferences of the arbidol molecule in the crystal structures has shown that it adopts two types of conformations, namely “open” and “closed” ones. Thermal stability of the arbidol salts and cocrystal have been analyzed by means of differential scanning calorimetry, thermogravimetric, and mass-spectrometry analysis. The dissolution study of the arbidol salts and cocrystal performed in aqueous buffer solutions with pH 1.2 and 6.8 has shown that both the salts and the cocrystal dissolve incongruently to form an arbidol hydrochloride monohydrate at pH 1.2 and an arbidol base at pH 6.8, respectively. The cocrystal reaches the highest solubility level in both pH 1.2 and pH 6.8 solutions.

Synthesis and crystal structure of rare earth complexes with o-nitrobenzoic acid and N, N-dimethylformamide

Science.gov (United States)

Zhao, Lifang; Chen, Yashao; Bao, Lin

2010-03-01

The rare-earth compound [Ce 0.5Sm 0.5( o-NBA) 3(DMF) 2] 2 (where o-NBA = o-nitrobenzoic acid, DMF = N, N-dimethylformamide) has been synthesized and structurally characterized. The crystal structure of the compound is characterized by Fourier transfer infrared spectroscopy (FT-IR), fluorescent emission spectroscopy (FES) and single-crystal X-ray diffraction. The results show that the compound crystallizes in a triclinic system, space group P-1 with a = 11.8284 (6) Å, b = 12.5082 (7) Å, c = 13.0203 (7) Å, α = 63.9650 (10)°, β = 66.3900 (10)°, γ = 71.7380 (10)°, V = 1563.7 (14) Å 3, Dc = 1.677 g/cm 3, Z = 1, F(0 0 0) = 790. Each Ln (III) atom is bridged by four o-nitro-benzoates and chelated by one o-nitrobenzoate. The Ln (III) atom is eight-coordinated by six oxygen atoms from five o-nitro-benzoates and two oxygen atoms from two DMF molecules. Hydrogen bonds and aromatic π⋯ π stacking interactions assemble the compound into a three-dimensional network. Luminescence measurement shows that the compound emits fluorescence.

Crystal water as the mol-ecular glue for obtaining different co-crystal ratios: the case of gallic acid tris-caffeine hexa-hydrate.

Science.gov (United States)

Vella-Zarb, L; Baisch, U

2018-04-01

The crystal structure of the hexa-hydrate co-crystal of gallic acid and caffeine, C 7 H 6 O 5 ·3C 8 H 10 N 4 O 2 ·6H 2 O or GAL3CAF·6H 2 O , is a remarkable example of the importance of hydrate water acting as structural glue to facilitate the crystallization of two components of different stoichiometries and thus to compensate an imbalance of hydrogen-bond donors and acceptors. The water mol-ecules provide the additional hydrogen bonds required to form a crystalline solid. Whereas the majority of hydrogen bonds forming the inter-molecular network between gallic acid and caffeine are formed by crystal water, only one direct classical hydrogen bond between two mol-ecules is formed between the carb-oxy-lic oxygen of gallic acid and the carbonyl oxygen of caffeine with d ( D ⋯ A ) = 2.672 (2) Å. All other hydrogen bonds either involve crystal water or utilize protonated carbon atoms as donors.

Two-dimensional hydrogen-bonded polymers in the crystal structures of the ammonium salts of phenoxyacetic acid, (4-fluorophenoxyacetic acid and (4-chloro-2-methylphenoxyacetic acid

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Graham Smith

2014-12-01

Full Text Available The structures of the ammonium salts of phenoxyacetic acid, NH4+·C8H6O3−, (I, (4-fluorophenoxyacetic acid, NH4+·C8H5FO3−, (II, and the herbicidally active (4-chloro-2-methylphenoxyacetic acid (MCPA, NH4+·C9H8ClO3−·0.5H2O, (III have been determined. All have two-dimensional layered structures based on inter-species ammonium N—H...O hydrogen-bonding associations, which give core substructures consisting primarily of conjoined cyclic motifs. The crystals of (I and (II are isomorphous with the core comprising R12(5, R12(4 and centrosymmetric R42(8 ring motifs, giving two-dimensional layers lying parallel to (100. In (III, the water molecule of solvation lies on a crystallographic twofold rotation axis and bridges two carboxyl O atoms in an R44(12 hydrogen-bonded motif, creating two R43(10 rings, which together with a conjoined centrosymmetric R42(8 ring incorporating both ammonium cations, generate two-dimensional layers lying parallel to (100. No π–π ring associations are present in any of the structures.

Crystal structure of caesium hydrogen (L)-aspartate and an overview of crystalline compounds of aspartic acid with inorganic constituents

Energy Technology Data Exchange (ETDEWEB)

Fleck, M. [Universitaet Wien (Austria). Institut fuer Mineralogie und Kristallographie; Emmerich, R.; Bohaty, L. [Universitaet zu Koeln (Austria). Institut fuer Kristallographie

2010-08-15

The crystal structure of the new polar compound caesium hydrogen (L)-aspartate, Cs(C{sub 4}H{sub 6}NO{sub 4}), (abbreviated: Cs(L -AspH)) was determined from single crystal X-ray diffraction data; it comprises two crystallographically different L -AspH anions that are connected via caesium cations to form a three dimensional framework. The Cs ions are irregularly sevenfold[Cs1O{sub 7}] respectively eightfold[Cs2O{sub 8}] coordinated to all {alpha}- and {beta}- carboxylate oxygen atoms. Cs(L -AspH) represents a novel structure type of its own, as do most compounds of (L)-aspartic acid with inorganic constituents. A brief summary of such structurally known aspartates is given. (copyright 2010 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

Synthesis, crystal structure and Thermogravimetry of ortho-phthalic ...

Indian Academy of Sciences (India)

satisfied by two chelated carboxylates while fifth and sixth co-ordination positions are satisfied by monodentate ... Keywords. o-Phthalic acid; coordination polymer; X-ray crystal structure; Copper(II); EPR; TGA. 1. .... Absorption coefficient.

Amino Acid-Assisted Incorporation of Dye Molecules within Calcite Crystals.

Science.gov (United States)

Marzec, Bartosz; Green, David C; Holden, Mark A; Coté, Alexander S; Ihli, Johannes; Khalid, Saba; Kulak, Alexander; Walker, Daniel; Tang, Chiu; Duffy, Dorothy M; Kim, Yi-Yeoun; Meldrum, Fiona C

2018-05-23

Biomineralisation processes invariably occur in the presence of multiple organic additives, which act in combination to give exceptional control over structures and properties. However, few synthetic studies have investigated the cooperative effects of soluble additives. This work addresses this challenge and focuses on the combined effects of amino acids and coloured dye molecules. The experiments demonstrate that strongly coloured calcite crystals only form in the presence of Brilliant Blue R (BBR) and four of the seventeen soluble amino acids, as compared with almost colourless crystals using the dye alone. The active amino acids are identified as those which themselves effectively occlude in calcite, suggesting a mechanism where they can act as chaperones for individual molecules or even aggregates of dyes molecules. These results provide new insight into crystal-additive interactions and suggest a novel strategy for generating materials with target properties. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structural coloration of chitosan coated cellulose fabrics by electrostatic self-assembled poly (styrene-methyl methacrylate-acrylic acid) photonic crystals.

Science.gov (United States)

Yavuz, Gönül; Zille, Andrea; Seventekin, Necdet; Souto, Antonio P

2018-08-01

The structural coloration of a chitosan-coated woven cotton fabric obtained by glutaraldehyde-stabilized deposition of electrostatic self-assembled monodisperse and spherically uniform (250 nm) poly (styrene-methyl methacrylate-acrylic acid) photonic crystal nanospheres (P(St-MMA-AA)) was investigated. Bright iridescent coatings displaying different colors in function of the viewing angle were obtained. The SEM, diffuse reflectance spectroscopy, TGA, DSC and FTIR analyses confirm the presence of structural color and the glutaraldehyde and chitosan ability to provide durable chemical bonding between cotton fabric and photonic crystal (PCs) coating with the highest degradation temperature and the lowest enthalpy. The coatings are characterized by a mixture of face-centered cubic and hexagonal close-packed arrays alternating random packing regions. For the first time a cost-efficient structural coloration with high washing and light fastness using self-assembled P(St-MMA-AA) photonic crystals was successfully developed onto woven cotton fabric using chitosan and/or glutaraldehyde as stabilizing agent opening new strategies for the development of dye-free coloration of textiles. Copyright © 2018 Elsevier Ltd. All rights reserved.

Crystal structures of three co-crystals of 1,2-bis-(pyridin-4-yl)ethane with 4-alk-oxy-benzoic acids: 4-eth-oxy-benzoic acid-1,2-bis-(pyridin-4-yl)ethane (2/1), 4-n-propoxybenzoic acid-1,2-bis(pyridin-4-yl)ethane (2/1) and 4-n-but-oxy-benzoic acid-1,2-bis-(pyridin-4-yl)ethane (2/1).

Science.gov (United States)

Tabuchi, Yohei; Gotoh, Kazuma; Ishida, Hiroyuki

2015-11-01

The crystal structures of three hydrogen-bonded co-crystals of 4-alk-oxy-benzoic acid-1,2-bis-(pyridin-4-yl)ethane (2/1), namely, 2C9H10O3·C12H12N2, (I), 2C10H12O3·C12H12N2, (II), and 2C11H14O3·C12H12N2, (III), have been determined at 93, 290 and 93 K, respectively. In (I), the asymmetric unit consists of one 4-eth-oxy-benzoic acid mol-ecule and one half-mol-ecule of 1,2-bis-(pyridin-4-yl)ethane, which lies on an inversion centre. In (II) and (III), the asymmetric units each comprise two crystallographically independent 4-alk-oxy-benzoic acid mol-ecules and one 1,2-bis-(pyridin-4-yl)ethane mol-ecule. In each crystal, the two components are linked by O-H⋯N hydrogen bonds, forming a linear hydrogen-bonded 2:1unit of the acid and the base. Similar to the structure of 2:1 unit of (I), the units of (II) and (III) adopt nearly pseudo-inversion symmetry. The 2:1 units of (I), (II) and (III) are linked via C-H⋯O hydrogen bonds, forming tape structures.

A Standard Structure for Bile Acids and Derivatives

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Francisco Meijide

2018-02-01

Full Text Available The crystal structures of two ester compounds (a monomer in its methyl ester form, with an amino isophthalic group, and a dimer in which the two steroid units are linked by a urea bridge recrystallized from ethyl acetate/methanol derived from cholic acid are described. Average bond lengths and bond angles from the crystal structures of 26 monomers and four dimers (some of them in several solvents of bile acids and esters (and derivatives are used for proposing a standard steroid nucleus. The hydrogen bond network and conformation of the lateral chain are also discussed. This standard structure was used to compare with the structures of both progesterone and cholesterol.

Organic compounds containing methoxy and cyanoacrylic acid: Synthesis, characterization, crystal structures, and theoretical studies

Energy Technology Data Exchange (ETDEWEB)

Khalaji, A. D., E-mail: alidkhalaji@yahoo.com [Golestan University, Department of Chemistry, Faculty of Science (Iran, Islamic Republic of); Maddahi, E. [Iran University of Science & Technology, Ms.C Educated, Department of Chemistry (Iran, Islamic Republic of); Dusek, M.; Fejfarova, K. [Institute of Physics of the ASCR, v.v.i. (Czech Republic); Chow, T. J. [Academia Sinica, Institute of Chemistry (China)

2015-12-15

Metal-free organic compounds 24-SC ((E)-2-cyano-3-(2,4-dimethoxyphenyl)acrylic acid) and 34-SC ((E)-2-cyano-3-(3,4-dimethoxyphenyl)acrylic acid), containing methoxy groups as a donor and the acrylic acid as an acceptor were synthesized and characterized by CHN, FT-IR, UV-Vis, {sup 1}H-NMR and single crystal X-ray diffraction and used as photosensitizers for the application of dye-sensitized solar cells (DSSC). The sensitizing characteristics of them were evaluated. Both compounds contain the natural molecule, its anionic form and the piperidinium cation and they differ by number of these molecules in the asymmetric unit. To get further insight into the effect of molecular structure on the performance of DSSC, their geometry and energies of HOMO and LUMO were optimized by density functional theory calculation at the B3LYP/6-31G(d) level with Gaussian 03. Overall conversion efficiencies of 0.78 under full sunlight irradiation are obtained for DSSCs based on the new metal-free organic dyes 24-SC and 34-SC.

Crystal structures of carbamate kinase from Giardia lamblia bound with citric acid and AMP-PNP.

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Kap Lim

Full Text Available The parasite Giardia lamblia utilizes the L-arginine dihydrolase pathway to generate ATP from L-arginine. Carbamate kinase (CK catalyzes the last step in this pathway, converting ADP and carbamoyl phosphate to ATP and ammonium carbamate. Because the L-arginine pathway is essential for G. lamblia survival and absent in high eukaryotes including humans, the enzyme is a potential target for drug development. We have determined two crystal structures of G. lamblia CK (glCK with bound ligands. One structure, in complex with a nonhydrolyzable ATP analog, adenosine 5'-adenylyl-β,γ-imidodiphosphate (AMP-PNP, was determined at 2.6 Å resolution. The second structure, in complex with citric acid bound in the postulated carbamoyl phosphate binding site, was determined in two slightly different states at 2.1 and 2.4 Å resolution. These structures reveal conformational flexibility of an auxiliary domain (amino acid residues 123-170, which exhibits open or closed conformations or structural disorder, depending on the bound ligand. The structures also reveal a smaller conformational change in a region associated the AMP-PNP adenine binding site. The protein residues involved in binding, together with a model of the transition state, suggest that catalysis follows an in-line, predominantly dissociative, phosphotransfer reaction mechanism, and that closure of the flexible auxiliary domain is required to protect the transition state from bulk solvent.

Effect of amino acids and amino acid derivatives on crystallization of hemoglobin and ribonuclease A

International Nuclear Information System (INIS)

Ito, Len; Kobayashi, Toyoaki; Shiraki, Kentaro; Yamaguchi, Hiroshi

2008-01-01

The effect of the addition of amino acids and amino acid derivatives on the crystallization of hemoglobin and ribonuclease A has been evaluated. The results showed that certain types of additives expand the concentration conditions in which crystals are formed. Determination of the appropriate conditions for protein crystallization remains a highly empirical process. Preventing protein aggregation is necessary for the formation of single crystals under aggregation-prone solution conditions. Because many amino acids and amino acid derivatives offer a unique combination of solubility and stabilizing properties, they open new avenues into the field of protein aggregation research. The use of amino acids and amino acid derivatives can potentially influence processes such as heat treatment and refolding reactions. The effect of the addition of several amino acids, such as lysine, and several amino acid derivatives, such as glycine ethyl ester and glycine amide, on the crystallization of equine hemoglobin and bovine pancreatic ribonuclease A has been examined. The addition of these amino acids and amino acid derivatives expanded the range of precipitant concentration in which crystals formed without aggregation. The addition of such additives appears to promote the crystallization of proteins

Effect of amino acids and amino acid derivatives on crystallization of hemoglobin and ribonuclease A

Energy Technology Data Exchange (ETDEWEB)

Ito, Len, E-mail: len@ksc.kwansei.ac.jp; Kobayashi, Toyoaki [School of Science and Technology, Kwansei Gakuin University, 2-1 Gakuen, Sanda, Hyogo 669-1337 (Japan); Shiraki, Kentaro [Institute of Applied Physics, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573 (Japan); Yamaguchi, Hiroshi [School of Science and Technology, Kwansei Gakuin University, 2-1 Gakuen, Sanda, Hyogo 669-1337 (Japan)

2008-05-01

The effect of the addition of amino acids and amino acid derivatives on the crystallization of hemoglobin and ribonuclease A has been evaluated. The results showed that certain types of additives expand the concentration conditions in which crystals are formed. Determination of the appropriate conditions for protein crystallization remains a highly empirical process. Preventing protein aggregation is necessary for the formation of single crystals under aggregation-prone solution conditions. Because many amino acids and amino acid derivatives offer a unique combination of solubility and stabilizing properties, they open new avenues into the field of protein aggregation research. The use of amino acids and amino acid derivatives can potentially influence processes such as heat treatment and refolding reactions. The effect of the addition of several amino acids, such as lysine, and several amino acid derivatives, such as glycine ethyl ester and glycine amide, on the crystallization of equine hemoglobin and bovine pancreatic ribonuclease A has been examined. The addition of these amino acids and amino acid derivatives expanded the range of precipitant concentration in which crystals formed without aggregation. The addition of such additives appears to promote the crystallization of proteins.

An experimental screen for quinoline/fumaric acid salts and co-crystals

DEFF Research Database (Denmark)

Beko, S. L.; Schmidt, M. U.; Bond, A. D.

2012-01-01

. Characterised products include the previously published 1 : 1 salt, C9H8N+center dot C4H3O4-, and a new 2 : 1 quinoline/fumaric acid co-crystal, (C9H7N)(2)center dot C4H4O4. Attempts to influence the crystallisation outcome by addition of 6-methylquinoline yielded a second co-crystal, also with an inherent 2......An experimental screen has been carried out for salts and co-crystals of quinoline (C9H7N) and fumaric acid (C4H4O4), including solution-based co-crystallisation from a variety of solvents, solvent-assisted and solvent-free co-grinding, and direct co-crystallisation of the starting materials...... : 1 quinoline/fumaric acid ratio, as a solid solution containing ca. 75% 6-methylquinoline and 25% quinoline. The corresponding co-crystal with pure 6-methylquinoline, (C10H9N)(2)center dot C4H4O4, was prepared, but the analogous structure with pure quinoline could not be obtained. Energy minimisation...

3.2.1. Synthesis, crystal and molecular structure of catena-(bis(µ1-oxalic acid)-µ3-hydrogen oxalate-di-aqua-sodium(I)).

OpenAIRE

Olga Kovalchukova*, Sergey Aldoshin, Andrey Utenyshev, Konstantin Bogenko, Valeriy Tkachev

2015-01-01

The crystal and molecular structure of catena-(bis(µ- oxalic acid)-µ-hydrogen oxalate-di-aqua-sodium(I)) was detected by X-Ray analysis. The compound crystallizes in the triclinic space group P-1, with a(Å) 6.2378(12); b(Å) 7,1115(14); c(Å) 10.489(2); α(°) 94.65(3); β(°) 100.12(3); γ(°) 97.78(3). The sodium cation in the title compound is eight coordinated and forms a square antiprism. It is surrounded by two molecules of oxalic acid, one hydrogen oxalate anion and one water molecule. Both ox...

Crystallization of Δ1-tetrahydrocannabinolic acid (THCA) synthase from Cannabis sativa

International Nuclear Information System (INIS)

Shoyama, Yoshinari; Takeuchi, Ayako; Taura, Futoshi; Tamada, Taro; Adachi, Motoyasu; Kuroki, Ryota; Shoyama, Yukihiro; Morimoto, Satoshi

2005-01-01

Δ 1 -Tetrahydrocannabinolic acid (THCA) synthase from C. sativa was crystallized. The crystal diffracted to 2.7 Å resolution with sufficient quality for further structure determination. Δ 1 -Tetrahydrocannabinolic acid (THCA) synthase is a novel oxidoreductase that catalyzes the biosynthesis of the psychoactive compound THCA in Cannabis sativa (Mexican strain). In order to investigate the structure–function relationship of THCA synthase, this enzyme was overproduced in insect cells, purified and finally crystallized in 0.1 M HEPES buffer pH 7.5 containing 1.4 M sodium citrate. A single crystal suitable for X-ray diffraction measurement was obtained in 0.09 M HEPES buffer pH 7.5 containing 1.26 M sodium citrate. The crystal diffracted to 2.7 Å resolution at beamline BL41XU, SPring-8. The crystal belonged to the primitive cubic space group P432, with unit-cell parameters a = b = c = 178.2 Å. The calculated Matthews coefficient was approximately 4.1 or 2.0 Å 3 Da −1 assuming the presence of one or two molecules of THCA synthase in the asymmetric unit, respectively

Crystal structure of di-( N-methylmorpholine betaine)- L(+)-tartrate

Science.gov (United States)

Dega-Szafran, Z.; Dutkiewicz, G.; Kosturkiewicz, Z.; Szafran, M.

2002-11-01

The crystal structure of di-( N-methylmorpholine betaine)- L(+)-tartrate has been determined by X-ray diffraction method. Crystals are orthorhombic, space group P2 12 12 1, a=9.580(1), b=12.208(1), c=18.677(1) Å, Z=4, R=0.037. The molecule of L(+)-tartaric acid appears in the extended form with the hydroxyl groups as well as carboxyl groups in anti positions. The molecule is involved in a number of the intra- and intermolecular hydrogen bonds. The COOH groups of the tartaric acid link two non-equivalent N-methylmorpholine betaine molecules by a short, intermolecular O-H⋯O bonds of the lengths 2.456(1) and 2.510(1) Å. The OH groups form two different bifurcated hydrogen bonds, the intramolecular with the CO oxygen atoms (2.641(2) and 2.638(2) Å) and the intermolecular (2.919(2) and 3.084(2) Å) with neighbouring tartaric acid molecules, and link complexes in the zigzag ribbon parallel to the x-axis. The morpholine rings of both betaine molecules are in chair conformation with methyl groups in an axial position and CH 2COO - substituents in an equatorial one. In the crystals and the PM3-optimized structures there is no symmetry, both in the tartrate and N-methylmorpholine betaine moieties. FTIR spectrum confirms the complex structure of the investigated molecule.

Surface deterioration of ammonium acid phthalate crystals

Energy Technology Data Exchange (ETDEWEB)

Barrus, D.M.; Blake, R.L.; Burek, A.J.

1976-01-01

In working with various acid phthalate crystals for low energy X-ray spectroscopy, we have observed a relatively rapid surface degradation of ammonium acid phthalate in comparison with similar crystals was observed. It was found that two different samples degraded in a few days upon exposure to high vacuum (10/sup -6/ - 10/sup -7/ torr). The same crystals showed similar effects when exposed to room atmosphere for two to three weeks. One of these crystals deteriorated while kept constantly in a desiccator jar for about two years. The desiccator environment seems to be the most favorable. The observed difference in the surface of these crystals might be described as a change from a transparent, glasslike condition to a white, powderlike haze somewhat akin to frosted glass. A two week exposure to vacuum for a freshly cleaved crystal caused the integrated coefficient of reflection at 23.6 A to decrease by a factor of 2.5. The degraded surface areas tend to form definite rhombohedral patterns. Since the external symmetry of ammonium acid phthalate crystals is rhombohedral, this suggests that the degradation we observe takes place in the form of large etched figures. A possible mechanism may be sublimation, which would proceed more rapidly in vacuum than in air. It is concluded that ammonium acid phthalate should be kept in a desiccator environment as much as possible. Exposures to vacuum should be brief and critical diffraction measurements should be done using a freshly cleaved surface.

Theobromine inhibits uric acid crystallization. A potential application in the treatment of uric acid nephrolithiasis.

Science.gov (United States)

Grases, Felix; Rodriguez, Adrian; Costa-Bauza, Antonia

2014-01-01

To assess the capacity of methylxanthines (caffeine, theophylline, theobromine and paraxanthine) to inhibit uric acid crystallization, and to evaluate their potential application in the treatment of uric acid nephrolithiasis. The ability of methylxathines to inhibit uric acid nucleation was assayed turbidimetrically. Crystal morphology and its modification due to the effect of theobromine were evaluated by scanning electron microscopy (SEM). The ability of theobromine to inhibit uric acid crystal growth on calculi fragments resulting from extracorporeal shock wave lithotripsy (ESWL) was evaluated using a flow system. The turbidimetric assay showed that among the studied methylxanthines, theobromine could markedly inhibit uric acid nucleation. SEM images showed that the presence of theobromine resulted in thinner uric acid crystals. Furthermore, in a flow system theobromine blocked the regrowth of post-ESWL uric acid calculi fragments. Theobromine, a natural dimethylxanthine present in high amounts in cocoa, acts as an inhibitor of nucleation and crystal growth of uric acid. Therefore, theobromine may be clinically useful in the treatment of uric acid nephrolithiasis.

Direct investigations on strain-induced cold crystallization behavior and structure evolutions in amorphous poly(lactic acid) with SAXS and WAXS measurements

DEFF Research Database (Denmark)

Zhou, Chengbo; Li, Hongfei; Zhang, Wenyang

2016-01-01

scanning calorimetry (DSC) measurements. The data obtained from the stretched samples within 70-90 degrees C showed that all of the formed crystals are disordered alpha' form with more compact chain packing than that of the cold crystallization. Upon stretching at 70 degrees C, the mesocrystal appears......Strain-induced cold crystallization behavior and structure evolution of amorphous poly(lactic acid) (PLA) stretched within 70-90 degrees C were investigated via in situ synchrotron small-angle X-ray scattering (SAXS) and wide-angle X-ray scattering (WAXS) measurements as well as differential...... in strain-induced crystallization behavior of amorphous PLA within 70-90 degrees C can be attributed to the competition between chain orientation caused by stretching and chain relaxation. It was proposed that the strain-induced mesocrystal/crystal and the lamellae are formed from the mesophase originally...

Characterization of CeO{sub 2} crystals synthesized with different amino acids

Energy Technology Data Exchange (ETDEWEB)

Atla, Shashi B. [Department of Earth and Environmental Sciences, National Chung Cheng University, Minhsiung, Chiayi 621, Taiwan (China); Wu, Min-Nan; Pan, Wei; Hsiao, Yu Tang [Department of Physics, National Chung Cheng University, Minhsiung, Chiayi 621, Taiwan (China); Sun, An-Cheng [Department of Chemical Engineering and Materials Science, Yuan Ze University, No. 135 Yuan-Tung Road, Chungli, Taoyuan 320, Taiwan (China); Tseng, Min-Jen [Department of Life Science, National Chung Cheng University, 168 University Road, Minhsiung, Chiayi 621, Taiwan (China); Chen, Yen-Ju [Department of Earth and Environmental Sciences, National Chung Cheng University, Minhsiung, Chiayi 621, Taiwan (China); Chen, Chien-Yen, E-mail: yen@eq.ccu.edu.tw [Department of Earth and Environmental Sciences, National Chung Cheng University, Minhsiung, Chiayi 621, Taiwan (China); Department of Advanced Institute of Manufacturing with High-tech Innovations, National Chung Cheng University, Minhsiung, Chiayi 621, Taiwan (China)

2014-12-15

We investigated the relationship between the structures of the CeO{sub 2} products (particle size, morphology and their characteristics) prepared using different amino acids. Cerium hydroxide carbonate precursors were initially prepared by a hydrothermal method and were subsequently converted to CeO{sub 2} by its thermal decomposition. Various amino acids were used as structure-directing agents in the presence of cerium nitrate and urea as precursors. The results indicate morphology selectivity using different amino acids; CeO{sub 2} structures, such as quasi-prism-sphere, straw-bundle, urchin-flower like and polyhedron prisms, indeed could be produced. Raman and photoluminescence studies indicate the presence of oxygen vacancies in the CeO{sub 2} samples. Photoluminescence spectra of CeO{sub 2} with L-Valine exhibit stronger emission compared with other amino acids utilized under this study, indicating the higher degree of defects in these particles. This study clearly indicates that the degree of defects varied in the presence of different amino acids. Improved precision to control the crystal morphology is important in various material applications and our study provides a novel method to achieve this specificity. - Highlights: • We used urea hydrolysis of process for synthesis of CeO{sub 2}. • Structures have been directed using various amino acids. • We obtained straw bundle-like, quasi prism-sphere, polyhedron prisms and urchin flower-like based on amino acids. • We have found that amino acids could achieve the specificity of different degrees of defects. • This could provide the “tailor-make” of cerium crystals.

Hydrothermal synthesis and crystal structure of a new lanthanum(III coordination polymer with fumaric acid

Directory of Open Access Journals (Sweden)

Hayet Anana

2015-05-01

Full Text Available The title compound, poly[diaquatris(μ4-but-2-enedioato(μ2-but-2-enedioic aciddilanthanum(III], [La2(C4H2O43(C4H4O4(H2O2]n, was synthesized by the reaction of lanthanum chloride pentahydrate with fumaric acid under hydrothermal conditions. The asymmetric unit comprises an LaIII cation, one and a half fumarate dianions (L2−, one a half-molecule of fumaric acid (H2L and one coordinated water molecule. Each LaIII cation has the same nine-coordinate environment and is surrounded by eight O atoms from seven distinct fumarate moieties, including one protonated fumarate unit and one water molecule in a distorted tricapped trigonal–prismatic environment. The LaO8(H2O polyhedra centres are edge-shared through three carboxylate bridges of the fumarate ligand, forming chains in three dimensions to construct the MOF. The crystal structure is stabilized by O—H...O hydrogen-bond interactions between the coordinated water molecule and the carboxylate O atoms, and also between oxygen atoms of fumaric acid

Crystal structure of [propane-1,3-diylbis(piperidine-4,1-diyl]bis[(pyridin-4-ylmethanone]–4,4′-oxydibenzoic acid (1/1

Directory of Open Access Journals (Sweden)

Emily M. Low

2014-09-01

Full Text Available In the title co-crystal, C25H32N4O2·C14H10O5, molecules are connected into supramolecular chains aligned along [102] by O—H...N hydrogen bonding. These aggregate into supramolecular layers oriented parallel to (20-1 by C—H...O interactions. These layers then stack in an ABAB pattern along the c crystal direction to give the full three-dimensional crystal structure. The central chain in the dipyridylamide has an anti–anti conformation. The dihedral angle between the aromatic ring planes is 29.96 (3°. Disorder is noted in some of the residues in the structure and this is manifested in two coplanar dispositions of one statistically disordered carboxylic acid group.

Theobromine inhibits uric acid crystallization. A potential application in the treatment of uric acid nephrolithiasis.

Directory of Open Access Journals (Sweden)

Felix Grases

Full Text Available To assess the capacity of methylxanthines (caffeine, theophylline, theobromine and paraxanthine to inhibit uric acid crystallization, and to evaluate their potential application in the treatment of uric acid nephrolithiasis.The ability of methylxathines to inhibit uric acid nucleation was assayed turbidimetrically. Crystal morphology and its modification due to the effect of theobromine were evaluated by scanning electron microscopy (SEM. The ability of theobromine to inhibit uric acid crystal growth on calculi fragments resulting from extracorporeal shock wave lithotripsy (ESWL was evaluated using a flow system.The turbidimetric assay showed that among the studied methylxanthines, theobromine could markedly inhibit uric acid nucleation. SEM images showed that the presence of theobromine resulted in thinner uric acid crystals. Furthermore, in a flow system theobromine blocked the regrowth of post-ESWL uric acid calculi fragments.Theobromine, a natural dimethylxanthine present in high amounts in cocoa, acts as an inhibitor of nucleation and crystal growth of uric acid. Therefore, theobromine may be clinically useful in the treatment of uric acid nephrolithiasis.

Crystal structure, vibrational and DFT simulation studies of melaminium dihydrogen phosphite monohydrate

Science.gov (United States)

Arjunan, V.; Kalaivani, M.; Marchewka, M. K.; Mohan, S.

2013-08-01

The crystal structure investigations of melamine with phosphorous acid, namely melaminium dihydrogenphosphite monohydrate (C3N6H7·H2PO3·H2O) have been investigated by means of single crystal X-ray diffraction method. The title compound crystallizes in monoclinic crystal system, and the space group is P21/c with a = 10.069 Å, b = 21.592 Å, c = 12.409 Å and Z = 12. The vibrational assignments and analysis of melaminium dihydrogen phosphite monohydrate have also been performed by FTIR, FT-Raman and far-infrared spectral studies. The quantum chemical simulations were performed with DFT (B3LYP) method using 6-31G**, cc-pVTZ, and 6-311++G** basis sets to determine the energy, structural, thermodynamic parameters and vibrational frequencies of melaminium dihydrogen phosphite monohydrate. The hydrogen atom from phosphorous acid was transferred to the melamine molecule giving the singly protonated melaminium cation. The ability of ions to form spontaneous three-dimensional structure through weak Osbnd H···O and Nsbnd H···O hydrogen bonds shows notable vibrational effects.

Crystal structures of a manganese(I and a rhenium(I complex of a bipyridine ligand with a non-coordinating benzoic acid moiety

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Sheri Lense

2018-05-01

Full Text Available The structures of two facially coordinated Group VII metal complexes are reported, namely: fac-bromido[2-(2,2′-bipyridin-6-ylbenzoic acid-κ2N,N′]tricarbonylmanganese(I tetrahydrofuran monosolvate, [MnBr(C17H12N2O2(CO3]·C4H8O, I, and fac-[2-(2,2′-bipyridin-6-ylbenzoic acid-κ2N,N′]tricarbonylchloridorhenium(I tetrahydrofuran monosolvate, [ReCl(C17H12N2O2(CO3]·C4H8O, II. In both complexes, the metal ion is coordinated by three carbonyl ligands, a halide ion, and a 2-(2,2′-bipyridin-6-ylbenzoic acid ligand, in a distorted octahedral geometry. In manganese complex I, the tetrahydrofuran (THF solvent molecule could not be refined due to disorder. The benzoic acid fragment is also disordered over two positions, such that the carboxylic acid group is either positioned near to the bromide ligand or to the axial carbonyl ligand. In the crystal of I, the complex molecules are linked by a pair of C—H...Br hydrogen bonds, forming inversion dimers that stack up the a-axis direction. In the rhenium complex II, there is hydrogen bonding between the benzoic acid moiety and a disordered co-crystallized THF molecule. In the crystal, the molecules are linked by C—H...Cl hydrogen bonds, forming layers parallel to (100 separated by layers of THF solvent molecules.

Crystal structures of two erbium(III complexes with 4-aminobenzoic acid and 4-chloro-3-nitrobenzoic acid

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Graham Smith

2015-12-01

Full Text Available The crystal structures of two erbium(III complexes with 4-aminobenzoic acid (4-ABAH, namely bis(μ2-4-aminobenzoato-κ2O:O′bis[bis(4-aminobenzoato-κ2O,O′diaquaerbium(III] dihydrate, [Er2(C7H6NO26(H2O4]·2H2O, (I, and 4-chloro-3-nitrobenzoic acid (CLNBAH, namely poly[hexakis(μ2-4-chloro-3-nitrobenzoato-κ2O:O′bis(dimethyl sulfoxide-κOdierbium(III], [Er2(C7H3ClNO46(C2H6OS2]n, (II, have been determined. In the structure of solvatomorphic compound (I, the symmetry-related irregular ErO8 coordination polyhedra in the discrete centrosymmetric dinuclear complex comprise two monodentate water molecules and six carboxylate O-atom donors, four from two bidentate carboxylate O,O′-chelate groups and two from the bis-monodentate O:O′-bridging group of the third 4-ABA anion. The Er—O bond-length range is 2.232 (3–2.478 (3 Å and the Er...Er separation in the dinuclear complex unit is 4.7527 (4 Å. One of the coordinating water molecules is involved in an intra-unit O—H...O hydrogen-bonding association with an inversion-related carboxylate O-atom acceptor. In contrast, the anhydrous compound (II is polymeric, based on centrosymmetric dinuclear repeat units comprising ErO7 coordination polyhedra which involve four O-atom donors from two bidentate O:O′-bridging carboxylate groups, one O-atom donor from the monodentate dimethyl sulfoxide ligand and two O-atom donors from the third bridging CLNBA anion. The latter provides the inter-unit link in the one-dimensional coordination polymer extending along [100]. The Er—O bond-length range in (II is 2.239 (6–2.348 (6 Å and the Er...Er separation within the dinuclear unit is 4.4620 (6 Å. In the crystal of (I, extensive inter-dimer O—H...O and N—H...O hydrogen-bonding interactions involving both the coordinating water molecules and the solvent water molecules, as well as the amine groups of the 4-ABA anions, give an overall three-dimensional network structure. Within

Growth, morphology, spectral and thermal studies of gel grown diclofenac acid crystals

Science.gov (United States)

Ramachandran, E.; Ramukutty, S.

2014-03-01

The crystal growth of diclofenac acid in silica gel is the first to be reported in literature. The growth parameters were varied to optimize the suitable growth condition. Single crystal X-ray diffraction method was used for the conformation of the crystal structure. Morphology studies showed that the growth is prominent along the b-axis and the prominent face is {002}. Fourier transform infrared spectral study was performed to identify the functional groups present in the crystal. Thermal stability and decomposition of the material were analyzed using thermo calorimetry in the temperature range 30-500 °C.

Structural analysis of Bacillus pumilus phenolic acid decarboxylase, a lipocalin-fold enzyme

International Nuclear Information System (INIS)

Matte, Allan; Grosse, Stephan; Bergeron, Hélène; Abokitse, Kofi; Lau, Peter C. K.

2010-01-01

The crystal structure of phenolic acid decarboxylase from B. pumilus strain UI-670 has been determined and refined at 1.69 Å resolution. The enzyme is a dimer, with each subunit adopting a β-barrel structure belonging to the lipocalin fold. The decarboxylation of phenolic acids, including ferulic and p-coumaric acids, to their corresponding vinyl derivatives is of importance in the flavouring and polymer industries. Here, the crystal structure of phenolic acid decarboxylase (PAD) from Bacillus pumilus strain UI-670 is reported. The enzyme is a 161-residue polypeptide that forms dimers both in the crystal and in solution. The structure of PAD as determined by X-ray crystallography revealed a β-barrel structure and two α-helices, with a cleft formed at one edge of the barrel. The PAD structure resembles those of the lipocalin-fold proteins, which often bind hydrophobic ligands. Superposition of structurally related proteins bound to their cognate ligands shows that they and PAD bind their ligands in a conserved location within the β-barrel. Analysis of the residue-conservation pattern for PAD-related sequences mapped onto the PAD structure reveals that the conservation mainly includes residues found within the hydrophobic core of the protein, defining a common lipocalin-like fold for this enzyme family. A narrow cleft containing several conserved amino acids was observed as a structural feature and a potential ligand-binding site

Cloning, expression, purification, crystallization and X-ray crystallographic analysis of glucuronic acid dehydrogenase from Chromohalobacter salexigens

International Nuclear Information System (INIS)

Ahn, Jae-Woo; Lee, Shin Youp; Kim, Sangwoo; Cho, Sun Ja; Lee, Sun Bok; Kim, Kyung-Jin

2011-01-01

Recombinant glucuronic acid dehydrogenase from the halophilic bacterium Chromohalobacter salexigens has been crystallized and X-ray diffraction data collected to a maximum resolution of 2.1 Å. Glucuronic acid dehydrogenase (GluUADH), the product of the Csal-2474 gene from the halophilic bacterium Chromohalobacter salexigens DSM 3043, is an enzyme with potential use in the conversion of glucuronic acid in seaweed biomass to fuels and chemicals. GluUADH is an enzyme that catalyzes the oxidation of glucuronic acid (GluUA) and galacturonic acid (GalUA) and has a preference for NAD + rather than NADP + as a cofactor. Recombinant GluUADH was crystallized in the presence of 0.2 M calcium acetate, 0.1 M Tris–HCl pH 7.0 and 20% PEG 3000 at 295 K. X-ray diffraction data were collected to a maximum resolution of 2.1 Å. The GluUADH crystal belonged to space group P6 3 , with unit-cell parameters a = b = 122.58, c = 150.49 Å, γ = 120°. With one molecule per asymmetric unit, the crystal volume per unit protein weight (V M ) is 2.78 Å 3 Da −1 . The structure was solved by the single anomalous dispersion method and structure refinement is in progress

Study on the Reactivity of Amino Acid Chemosensor, NPFNP, with Ethanol: Structural Elucidation through Single Crystal XRD and DFT Calculations

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Beena Varghese

2017-01-01

Full Text Available A novel ethoxy derivative of an amino acid chemosensor, 3-naphthyl-1-phenyl-5-(2ʹ-fluoro-5ʹ-nitrophenyl-2-pyrazoline (NPFNP, has been synthesized and characterized by different spectroscopic methods.  A single crystal of the ethoxy derivative, 3-naphthyl-1-phenyl-5-(2ʹ-ethoxy-5ʹ-nitrophenyl-2-pyrazoline NPENP, has been obtained and characterized.  The structure holds interest as it carries biologically active pyrazoline as a central ring attaching to electron donating and withdrawing substituents. The major motivation for this work was to gain detailed insight into the structural parameters of this compound for investigating the influence of crystal packing and geometrical dimensions on optical properties. Time-dependent DFT calculations have been employed for comparing the XRD data with theoretical parameters. The results show that the DFT method at B3LYP/6-31G level can well reproduce the structure of the title compound.

Crystal structure of the MSMEG_4306 gene product from Mycobacterium smegmatis.

Science.gov (United States)

Kumar, Adarsh; Karthikeyan, Subramanian

2018-03-01

The MSMEG_4306 gene from Mycobacterium smegmatis encodes a protein of unknown function with 242 amino-acid residues that contains a conserved zinc-ribbon domain at its C-terminus. Here, the crystal structure of MSMEG_4306 determined by the single-wavelength anomalous dispersion method using just one zinc ion co-purified with the protein is reported. The crystal structure of MSMEG_4306 shows a coiled-coil helix domain in the N-terminal region and a zinc-ribbon domain in the C-terminal region. A structural similarity search against the Protein Data Bank using MSMEG_4306 as a query revealed two similar structures, namely CT398 from Chlamydia trachomatis and HP0958 from Helicobacter pylori, although they share only ∼15% sequence identity with MSMEG_4306. Based on comparative analysis, it is predicted that MSMEG_4306 may be involved in secretion systems, possibly by interacting with multiple proteins or nucleic acids.

Synthesis, crystal structure, vibrational spectra and theoretical calculations of quantum chemistry of a potential antimicrobial Meldrum's acid derivative

Science.gov (United States)

Campelo, M. J. M.; Freire, P. T. C.; Mendes Filho, J.; de Toledo, T. A.; Teixeira, A. M. R.; da Silva, L. E.; Bento, R. R. F.; Faria, J. L. B.; Pizani, P. S.; Gusmão, G. O. M.; Coutinho, H. D. M.; Oliveira, M. T. A.

2017-10-01

A new derivative of Meldrum's acid 5-((5-chloropyridin-2-ylamino)methylene)-2,2-dimethyl-1,3-dioxane-4,6-dione (CYMM) of molecular formula C12H11ClN2O4 was synthesized and structurally characterized using single crystal X-ray diffraction technique. The vibrational properties of the crystal were studied by Fourier Transform infrared (FT-IR), Fourier Transform Raman (FT-Raman) techniques and theoretical calculations of quantum chemistry using Density functional theory (DFT) and Density functional perturbation theory (DFPT). A comparison with experimental spectra allowed the assignment of all the normal modes. The descriptions of the normal modes were carried by means of potential energy distribution (PED). Additionally, analysis of the antimicrobial activity and antibiotic resistance modulatory activity was carried out to evaluate the antibacterial potential of the CYMM.

Co-crystal of (R,R)-1,2-cyclohexanediol with (R,R)-tartaric acid, a key structure in resolution of the ({+-})-trans-diol by supercritical extraction, and the related ternary phase system

Energy Technology Data Exchange (ETDEWEB)

Thorey, Paul [Department of Chemical and Environmental Process Engineering, Budapest University of Technology and Economics, H-1521 Budapest (Hungary); Bombicz, Petra [Institute of Structural Chemistry, Chemical Research Center, Hungarian Academy of Science, H-1525 Budapest (Hungary); Szilagyi, Imre Miklos [Material Structure and Modeling Research Group, Hungarian Academy of Sciences, H-1111 Budapest (Hungary); Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, H-1521 Budapest (Hungary); Molnar, Peter; Bansaghi, Gyoergy; Szekely, Edit; Simandi, Bela [Department of Chemical and Environmental Process Engineering, Budapest University of Technology and Economics, H-1521 Budapest (Hungary); Parkanyi, Laszlo [Institute of Structural Chemistry, Chemical Research Center, Hungarian Academy of Science, H-1525 Budapest (Hungary); Pokol, Gyoergy [Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, H-1521 Budapest (Hungary); Madarasz, Janos, E-mail: madarasz@mail.bme.hu [Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, H-1521 Budapest (Hungary)

2010-01-10

A novel co-crystal of trans-(R,R)-1,2-cyclohexanediol and (R,R)-tartaric acid (with 1:1 molar ratio, 1) has been found to be a key crystalline compound in the improved resolution of ({+-})-trans-1,2-cyclohexanediol by supercritical fluid extraction. The molecular and crystal structure of this co-crystal, which crystallizes in orthorhombic crystal system (space group P2{sub 1}2{sub 1}2{sub 1}, a = 6.7033(13) A, b = 7.2643(16), c = 24.863(5), Z = 4), has been solved by single crystal X-ray diffraction (R = 0.064). The packing arrangement consists of two dimensional layers of sandwich-like sheets, where the inner part is constructed by double layers of tartaric acids which hydrophilicity is 'covered' on both upper and bottom side by cyclohexanediols with the hydrophobic cyclohexane rings pointing outward. Thus, a rather complex hydrogen bonding pattern is constructed. The relatively high melting point (133 {sup o}C) observed by both simultaneous TG/DTA and DSC, and the main features of FTIR-spectrum of 1 are explained by the increased stability of this crystal structure. DSC studies on binary mixtures of co-crystal 1 with (R,R)-1,2-cyclohexanediol or (R,R)-tartaric acid, revealed eutectic temperatures of T{sub eu} = 100 or 131 {sup o}C, respectively. Between (S,S)-1,2-cyclohexanediol and (R,R)-tartaric acid a eutectic temperature of T{sub eu} = 85 {sup o}C have also been observed. The phase relations have been confirmed by powder X-ray diffraction, as well.

Crystallization of Δ{sup 1}-tetrahydrocannabinolic acid (THCA) synthase from Cannabis sativa

Energy Technology Data Exchange (ETDEWEB)

Shoyama, Yoshinari; Takeuchi, Ayako; Taura, Futoshi [Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582 (Japan); Tamada, Taro; Adachi, Motoyasu; Kuroki, Ryota [Neutron Science Research Center, Japan Atomic Energy Research Institute, 2-4 Shirakata-Shirane, Tokai, Ibaraki 319-1195 (Japan); Shoyama, Yukihiro; Morimoto, Satoshi [Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582 (Japan)

2005-08-01

Δ{sup 1}-Tetrahydrocannabinolic acid (THCA) synthase from C. sativa was crystallized. The crystal diffracted to 2.7 Å resolution with sufficient quality for further structure determination. Δ{sup 1}-Tetrahydrocannabinolic acid (THCA) synthase is a novel oxidoreductase that catalyzes the biosynthesis of the psychoactive compound THCA in Cannabis sativa (Mexican strain). In order to investigate the structure–function relationship of THCA synthase, this enzyme was overproduced in insect cells, purified and finally crystallized in 0.1 M HEPES buffer pH 7.5 containing 1.4 M sodium citrate. A single crystal suitable for X-ray diffraction measurement was obtained in 0.09 M HEPES buffer pH 7.5 containing 1.26 M sodium citrate. The crystal diffracted to 2.7 Å resolution at beamline BL41XU, SPring-8. The crystal belonged to the primitive cubic space group P432, with unit-cell parameters a = b = c = 178.2 Å. The calculated Matthews coefficient was approximately 4.1 or 2.0 Å{sup 3} Da{sup −1} assuming the presence of one or two molecules of THCA synthase in the asymmetric unit, respectively.

Synthesis of zeolite-like crystals by means of sorption of bases on polysilicic acids

Energy Technology Data Exchange (ETDEWEB)

Belyakova, L A; Il' in, V G; Peresun' ko, T F; Kryuchkova, I I; Neymark, I E [AN Ukrainskoj SSR, Kiev. Inst. Fizicheskoj Khimii

1974-11-21

Investigation into the sorption of bases on crystalline polysilicic acids is of particular interest from the viewpoint of synthesis of new types of porous zeolite-like materials. A synthesis of polysilicate acids was carried out by treating respective sodium polysilicates with mineral acid solutions. The sorption of alkali metal hydroxides in the neutral and alkaline pH region was studied by the method of potentiometric titration of individual weighed quantities. A marked sorption of alkali metal hydroxides on polysilicic acids starts in the weakly acid and neutral regions and reaches saturation at pH=10.5. The process of ion exchange is accompanied by a change in the crystal structure of polysilicic acids. The sorption of bases on polysilicic acids may be used as a method of synthesis of zeolite-like porous crystals in different cationic forms.

Synthesis of zeolite-like crystals by means of sorption of bases on polysilicic acids

International Nuclear Information System (INIS)

Belyakova, L.A.; Il'in, V.G.; Peresun'ko, T.F.; Kryuchkova, I.I.; Nejmark, I.E.

1974-01-01

Investigation into the sorption of bases on crystalline polysilicic acids is of particular interest from the viewpoint of synthesis of new types of porous zeolite-like materials. A synthesis of polysilicate acids was carried out by treating respective sodium polysilicates with mineral acid solutions. The sorption of alkali metal hydroxides in the neutral and alkaline pH region was studied by the method of potentiometric titration of individual weighed quantities. A marked sorption of alkali metal hydroxides on polysilicic acids starts in the weakly acid and neutral regions and reaches saturation at pHapproximately10.5. The process of ion exchange is accompanied by a change in the crystal structure of polysilicic acids. The sorption of bases on polysilicic acids may be used as a method of synthesis of zeolite-like porous crystals in different cationic forms

Preparation of three terbium complexes with p-aminobenzoic acid and investigation of crystal structure influence on luminescence property

International Nuclear Information System (INIS)

Ye Chaohong; Sun Haoling; Wang Xinyi; Li Junran; Nie Daobo; Fu Wenfu; Gao Song

2004-01-01

Three new rare earth p-aminobenzoic acid complexes, [Tb 2 L 6 (H 2 O) 2 ] n (1), [Tb 2 L 6 (H 2 O) 4 ].2H 2 O (2) and [Tb(phen) 2 L 2 (H 2 O) 2 ](phen)L·4H 2 O (3) (HL: p-aminobenzoic acid; phen: 1, 10-phenanthroline), with different structural forms are reported in this paper. Complex 1 is a polymolecule with a two-dimensional plane structure. Compound 2 is a binuclear molecule, and 3 appears to be a mononuclear complex. The fluorescence intensity, the fluorescence life-time and emission quantum yield of 2, which has two coordination water molecules, is better than those of 1, which has only one coordination water molecule. This is an unusual phenomenon for general fluorescent rare earth complexes. The fluorescence performance of 3 is the most unsatisfactory among the three complexes. Their crystal structures show that the coordination mode of the ligand is an important factor influencing the luminescence properties of a fluorescent rare earth complex

Origins of hydration differences in homochiral and racemic crystals of aspartic acid.

Science.gov (United States)

Juliano, Thomas R; Korter, Timothy M

2015-02-26

The propensity for crystalline hydrates of organic molecules to form is related to the strength of the interactions between molecules, including the chiral composition of the molecular solids. Specifically, homochiral versus racemic crystalline samples can exhibit distinct differences in their ability to form energetically stable hydrates. The focus of the current study is a comparison of the crystal structures and intermolecular forces found in solid-state L-aspartic acid, DL-aspartic acid, and L-aspartic acid monohydrate. The absence of experimental evidence for the DL-aspartic acid monohydrate is considered here in terms of the enhanced thermodynamic stability of the DL-aspartic acid anhydrate crystal as compared to the L-aspartic acid anhydrate as revealed through solid-state density functional theory calculations and terahertz spectroscopic measurements. The results indicate that anhydrous DL-aspartic acid is the more stable solid, not due to intermolecular forces alone but also due to the improved conformations of the molecules within the racemic solid. Hemihydrated and monohydrated forms of DL-aspartic acid have been computationally evaluated, and in each case, the hydrates produce destabilized aspartic acid conformations that prevent DL-aspartic acid hydrate formation from occurring.

Crystal structures of 2-(N,N-dimethylaminoalkyl)ferroceneboronic acids and their diol derivatives. The quest for a B-N intramolecular bond in the solid state

DEFF Research Database (Denmark)

Norrild, Jens Chr.; Søtofte, Inger

2001-01-01

The crystal structures of (S,S)-2-(N,N-dimethyl-1-aminoethyl)ferroceneboronic acid (2), (S,S)-1-(N,N-dimethyl-1-aminoethyl)-2-(4,4,5,5-tetraphenyl-1,3,2-dioxaborolan-2-yl)ferrocene (3), rac-2-(N,N-dimethylaminomethyl)-ferroceneboronic acid (rac-4), (S)-[(1S,2S,3R,5S)-pinane-1,2-diyl] 2-(N...

Investigation of supramolecular synthons and structural characterisation of aminopyridine-carboxylic acid derivatives.

Science.gov (United States)

Hemamalini, Madhukar; Loh, Wan-Sin; Quah, Ching Kheng; Fun, Hoong-Kun

2014-01-01

Co-crystal is a structurally homogeneous crystalline material that contains two or more neutral building blocks that are present in definite stoichiometric amounts. The main advantage of co-crystals is their ability to generate a variety of solid forms of a drug that have distinct physicochemical properties from the solid co-crystal components. In the present investigation, five co-crystals containing 2-amino-6-chloropyridine (AMPY) moiety were synthesized and characterized. The crystal structure of 2-amino-6-chloropyridine (AMPY) (I), and the robustness of pyridine-acid supramolecular synthon were discussed in four stoichiometry co-crystals of AMPY…BA (II), AMPY…2ABA (III), AMPY…3CLBA (IV) and AMPY…4NBA (V). The abbreviated designations used are benzoic acid (BA), 2-aminobenzoic acid (2ABA), 3-chlorobenzoic acid (3CLBA) and 4-nitrobenzoic acid (4NBA). All the crystalline materials have been characterized by (1)HNMR, (13)CNMR, IR, photoluminescence, TEM analysis and X-ray diffraction. The supramolecular assembly of each co-crystal is analyzed and discussed. Extensive N---H · · · N/N---H · · · O/O---H · · · N hydrogen bonds are found in (I-V), featuring different supramolecular synthons. In the crystal structure, for compound (I), the 2-amino-6-chloropyridine molecules are linked together into centrosymmetric dimers by hydrogen bonds to form homosynthon, whereas for compounds (II-V), the carboxylic group of the respective acids (benzoic acid, 2-aminobenzoic acid, 3-chlorobenzoic acid and 4-nitrobenzoic acid) interacts with pyridine molecule in a linear fashion through a pair of N---H · · · O and O---H · · · N hydrogen bonds, generating cyclic hydrogen-bonded motifs with the graph-set notation [Formula: see text] , to form heterosynthon. In compound (II), another intermolecular N---H · · · O hydrogen bonds further link these heterosynthons into zig-zag chains. Whereas in compounds (IV) and (V

Selenium Derivatization of Nucleic Acids for Phase and Structure Determination in Nucleic Acid X-ray Crystallography

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Zhen Huang

2008-03-01

Full Text Available Selenium derivatization (via selenomethionine of proteins for crystal structure determination via MAD phasing has revolutionized protein X-ray crystallography. It is estimated that over two thirds of all new crystal structures of proteins have been determined via Se-Met derivatization. Similarly, selenium functionalities have also been successfully incorporated into nucleic acids to facilitate their structure studies and it has been proved that this Se-derivatization has advantages over halogen strategy, which was usually used as a traditional method in this field. This review reports the development of site-specific selenium derivatization of nucleic acids for phase determination since the year of 2001 (mainly focus on the 2’-position of the ribose. All the synthesis of 2’-SeMe modified phosphoramidite building blocks (U, C, T, A, G and the according oligonucleotides are included. In addition, several structures of selenium contained nucleic acid are also described in this paper.

Preparation, crystallization and preliminary X-ray diffraction analysis of two intestinal fatty-acid binding proteins in the presence of 11-(dansylamino)undecanoic acid

International Nuclear Information System (INIS)

Laguerre, Aisha; Wielens, Jerome; Parker, Michael W.; Porter, Christopher J. H.; Scanlon, Martin J.

2011-01-01

Intestinal fatty-acid binding proteins from human and rat have been crystallized in complex with the fluorescent probe 11-(dansylamino)undecanoic acid. Diffraction data for the crystals were collected to 1.8 Å resolution (human) and 1.6 Å resolution (rat). Fatty-acid binding proteins (FABPs) are abundantly expressed proteins that bind a range of lipophilic molecules. They have been implicated in the import and intracellular distribution of their ligands and have been linked with metabolic and inflammatory responses in the cells in which they are expressed. Despite their high sequence identity, human intestinal FABP (hIFABP) and rat intestinal FABP (rIFABP) bind some ligands with different affinities. In order to address the structural basis of this differential binding, diffraction-quality crystals have been obtained of hIFABP and rIFABP in complex with the fluorescent fatty-acid analogue 11-(dansylamino)undecanoic acid

Synthesis and crystal structure of a polymeric zinc(II complex derived from 4-nitro- phenylacetic acid and propane-1,3-diamine

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G-H. Sheng

2014-05-01

Full Text Available A new polymeric zinc(II complex, [ZnL2(PDA]n, has been prepared by the reaction of zinc sulfate, 4-nitrophenylacetic acid, and propane-1,3-diamine (PDA in water. Structure of the complex has been characterized by single-crystal X-ray diffraction. The complex crystallizes as orthorhombic space group Pnma, with unit cell dimensions a = 15.732(1 Å, b = 23.912(1 Å, c = 5.5565(3 Å, V = 2090.2(2 Å3, Z = 4, R1 = 0.0427, wR2 = 0.0968, S = 1.048. The Zn atom is coordinated in a tetrahedral geometry. Single crystals of the complex are stabilized by hydrogen bonds and p···p interactions. DOI: http://dx.doi.org/10.4314/bcse.v28i2.17

Kinetics and enthalpy of crystallization of uric acid dihydrate

International Nuclear Information System (INIS)

Sádovská, Galina; Honcová, Pavla; Sádovský, Zdeněk

2013-01-01

Highlights: • The kinetic constant and growth order of crystallization of uric acid dihydrate was calculated. • The equation describing first-order crystal growth was derived. • The enthalpy of crystallization of uric acid dihydrate was determined. - Abstract: The kinetics of crystallization of uric acid dihydrate in aqueous solution with a constant ionic strength 0.3 mol dm −3 NaCl and at thermodynamic and physiological temperature (25 and 37 °C) was studied using isoperibolic reaction twin calorimeter. The enthalpy of crystallization Δ cr H = −47.3 ± 0.9 and −46.2 ± 1.4 kJ mol −1 and kinetic constant k g = 2.0 × 10 −8 and 9.6 × 10 −8 m 4 s −1 mol −1 were determined at 25 and 37 °C, respectively

Crystal structure of 5-hydroxy-5-propylbarbituric acid

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Thomas Gelbrich

2015-11-01

Full Text Available Molecules of the title compound, C7H10N2O4, systematic name 5-hydroxy-5-propylpyrimidine-2,4,6(1H,3H,5H-trione, form a hydrogen-bonded framework which is based on three independent hydrogen bonds, N—H...O(carbonyl, N—H...O(hydroxy and O—H...O(carbonyl. This framework has the topology of the 5-connected nov net. Each molecule is linked to five other molecules via six hydrogen bonds, and the descriptor of the hydrogen-bonded structure is F65[44.66-nov]. The crystal packing is isostructural with that of the previously reported 5-hydroxy-5-ethyl analogue.

Chromium(III) Complex Obtained from Dipicolinic Acid: Synthesis, Characterization, X-Ray Crystal Structure and Electrochemical Studies

Energy Technology Data Exchange (ETDEWEB)

Ghasemi, Khaled; Rezvani, Ali Reza; Ghasemi, Fatemeh [Univ. of Sistan and Baluchestan, Zahedan (Iran, Islamic Republic of); Razak, Ibrahim Abdul; Rosli, Mohd Mustaqim [Universiti Sains Malaysia, Penang (Malaysia)

2013-10-15

The synthesis, X-ray crystallography, spectroscopic (IR, UV-vis), and electrochemical properties of the title compound, [H{sub 3}O][Cr(dipic){sub 2}] [H{sub 3}O{sup +}.Cl{sup -}] (1), (H{sub 2}dipic = 2,6-pyridinedicarboxylic acid), are reported. This complex crystallizes in the monoclinic space group Cc with a = 14.9006(10) A, b = 12.2114(8) A, c = 8.6337(6) A, α = 90.00 .deg., β = 92.7460(10) .deg., γ = 90.00 .deg., and V = 1569.16(18) A3 with Z = 4. The hydrogen bonding and noncovalent interactions play roles in the stabilization of the structure. In order to gain a better understanding of the most important geometrical parameters in the structure of the complex, atoms in molecules (AIM) method at B3LYP/6-31G level of theory has been employed.

Crystal Structures of Active Fully Assembled Substrate- and Product-Bound Complexes of UDP-N-Acetylmuramic Acid:l-Alanine Ligase (MurC) from Haemophilus influenzae

OpenAIRE

Mol, Clifford D.; Brooun, Alexei; Dougan, Douglas R.; Hilgers, Mark T.; Tari, Leslie W.; Wijnands, Robert A.; Knuth, Mark W.; McRee, Duncan E.; Swanson, Ronald V.

2003-01-01

UDP-N-acetylmuramic acid:l-alanine ligase (MurC) catalyzes the addition of the first amino acid to the cytoplasmic precursor of the bacterial cell wall peptidoglycan. The crystal structures of Haemophilus influenzae MurC in complex with its substrate UDP-N-acetylmuramic acid (UNAM) and Mg2+ and of a fully assembled MurC complex with its product UDP-N-acetylmuramoyl-l-alanine (UMA), the nonhydrolyzable ATP analogue AMPPNP, and Mn2+ have been determined to 1.85- and 1.7-Å resolution, respective...

Crystal and macular structure of 1:1 complex of N-methylmorpholine betaine with salicylic acid

International Nuclear Information System (INIS)

Bartoszak-Adamska, E.; Dega-Szafran, Z.; Przedwojska, M.; Jaskolski, M.

2003-01-01

The structure of a 1:1 complexes of complex of N-methylmorpholine betaine (MMB) with salicylic acid (SAL) has been determined by a single crystal X-ray analysis. The crystals are orthorhombic, space group Pbca, with a 9.4702(6), b = 13.0559(7) and c = 45.226(2) A (at 140 K). The asymmetric unit is composed of two MMB + ·SAL - units (A and B) each formed by a short, nearly linear O-H...O hydrogen bond (2.542(2) and 2.474(2) A) between the carboxylic group of the betaine cation and carboxylate group of the anion. The salicylate anions form short intramolecular O-H...O hydrogen bonds of 2. 472(2) and 2.525(2) A (O-H...O angles 160(2) and 149(2) o ) for anion A and B, respectively, between the ortho hydroxyl donor and the COO - group, but the carboxylate acceptor O atom is in each case different. The morpholine rings are in a chair conformation with the -CH 2 COOH group in equatorial and the methyl group in axial positions. FTIR, and 1 H and 13 C NMR spectra of the complex are discussed. (author)

Crystal structure of Sus scrofa quinolinate phosphoribosyltransferase in complex with nicotinate mononucleotide.

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Hyung-Seop Youn

Full Text Available We have determined the crystal structure of porcine quinolinate phosphoribosyltransferase (QAPRTase in complex with nicotinate mononucleotide (NAMN, which is the first crystal structure of a mammalian QAPRTase with its reaction product. The structure was determined from protein obtained from the porcine kidney. Because the full protein sequence of porcine QAPRTase was not available in either protein or nucleotide databases, cDNA was synthesized using reverse transcriptase-polymerase chain reaction to determine the porcine QAPRTase amino acid sequence. The crystal structure revealed that porcine QAPRTases have a hexameric structure that is similar to other eukaryotic QAPRTases, such as the human and yeast enzymes. However, the interaction between NAMN and porcine QAPRTase was different from the interaction found in prokaryotic enzymes, such as those of Helicobacter pylori and Mycobacterium tuberculosis. The crystal structure of porcine QAPRTase in complex with NAMN provides a structural framework for understanding the unique properties of the mammalian QAPRTase active site and designing new antibiotics that are selective for the QAPRTases of pathogenic bacteria, such as H. pylori and M. tuberculosis.

Kinetics and enthalpy of crystallization of uric acid dihydrate

Energy Technology Data Exchange (ETDEWEB)

Sádovská, Galina, E-mail: galina.sadovska@upce.cz; Honcová, Pavla; Sádovský, Zdeněk

2013-08-20

Highlights: • The kinetic constant and growth order of crystallization of uric acid dihydrate was calculated. • The equation describing first-order crystal growth was derived. • The enthalpy of crystallization of uric acid dihydrate was determined. - Abstract: The kinetics of crystallization of uric acid dihydrate in aqueous solution with a constant ionic strength 0.3 mol dm{sup −3} NaCl and at thermodynamic and physiological temperature (25 and 37 °C) was studied using isoperibolic reaction twin calorimeter. The enthalpy of crystallization Δ{sub cr}H = −47.3 ± 0.9 and −46.2 ± 1.4 kJ mol{sup −1}and kinetic constant k{sub g} = 2.0 × 10{sup −8} and 9.6 × 10{sup −8} m{sup 4} s{sup −1} mol{sup −1} were determined at 25 and 37 °C, respectively.

Effect of amino acid doping on the growth and ferroelectric properties of triglycine sulphate single crystals

International Nuclear Information System (INIS)

Raghavan, C.M.; Sankar, R.; Mohan Kumar, R.; Jayavel, R.

2008-01-01

Effect of amino acids (L-leucine and isoleucine) doping on the growth aspects and ferroelectric properties of triglycine sulphate crystals has been studied. Pure and doped crystals were grown from aqueous solution by low temperature solution growth technique. The cell parameter values were found to significantly vary for doped crystals. Fourier transform infrared analysis confirmed the presence of functional groups in the grown crystal. Morphology study reveals that amino acid doping induces faster growth rate along b-direction leading to a wide b-plane and hence suitable for pyroelectric detector applications. Ferroelectric domain structure has been studied by atomic force microscopy and hysteresis measurements reveal an increase of coercive field due to the formation of single domain pattern

Crystal structures of Leishmania mexicana arginase complexed with α,α-disubstituted boronic amino-acid inhibitors

Energy Technology Data Exchange (ETDEWEB)

Hai, Yang; Christianson, David W.

2016-03-16

Leishmaniaarginase is a potential drug target for the treatment of leishmaniasis because this binuclear manganese metalloenzyme initiatesde novopolyamine biosynthesis by catalyzing the hydrolysis of L-arginine to generate L-ornithine and urea. The product L-ornithine subsequently undergoes decarboxylation to yield putrescine, which in turn is utilized for spermidine biosynthesis. Polyamines such as spermidine are essential for the growth and survival of the parasite, so inhibition of enzymes in the polyamine-biosynthetic pathway comprises an effective strategy for treating parasitic infections. To this end, two X-ray crystal structures ofL. mexicanaarginase complexed with α,α-disubstituted boronic amino-acid inhibitors based on the molecular scaffold of 2-(S)-amino-6-boronohexanoic acid are now reported. Structural comparisons with human and parasitic arginase complexes reveal interesting differences in the binding modes of the additional α-substituents,i.e.the D side chains, of these inhibitors. Subtle differences in the three-dimensional contours of the outer active-site rims among arginases from different species lead to different conformations of the D side chains and thus different inhibitor-affinity trends. The structures suggest that it is possible to maintain affinity while fine-tuning intermolecular interactions of the D side chain of α,α-disubstituted boronic amino-acid inhibitors in the search for isozyme-specific and species-specific arginase inhibitors.

Two-stage magnetic orientation of uric acid crystals as gout initiators

Science.gov (United States)

Takeuchi, Y.; Miyashita, Y.; Mizukawa, Y.; Iwasaka, M.

2014-01-01

The present study focuses on the magnetic behavior of uric acid crystals, which are responsible for gout. Under a sub-Tesla (T)-level magnetic field, rotational motion of the crystals, which were caused by diamagnetic torque, was observed. We used horizontal magnetic fields with a maximum magnitude of 500 mT generated by an electromagnet to observe the magnetic orientation of the uric acid microcrystals by a microscope. The uric acid crystals showed a perpendicular magnetic field orientation with a minimum threshold of 130 mT. We speculate that the distinct diamagnetic anisotropy in the uric acid crystals resulted in their rotational responses.

Crystallization and X-ray diffraction analysis of an ‘all-locked’ nucleic acid duplex derived from a tRNASer microhelix

International Nuclear Information System (INIS)

Behling, Katja; Eichert, André; Fürste, Jens P.; Betzel, Christian; Erdmann, Volker A.; Förster, Charlotte

2009-01-01

A completely ‘all-locked’ nucleic acid duplex was designed from an E. coli tRNA Ser microhelix. The helix consists exclusively of LNA building blocks and was crystallized. The crystals diffracted to 1.9 Å resolution. Modified nucleic acids are of great interest with respect to their nuclease resistance and enhanced thermostability. In therapeutical and diagnostic applications, such molecules can substitute for labile natural nucleic acids that are targeted against particular diseases or applied in gene therapy. The so-called ‘locked nucleic acids’ contain modified sugar moieties such as 2′-O,4′-C-methylene-bridged β-d-ribofuranose and are known to be very stable nucleic acid derivatives. The structure of locked nucleic acids in single or multiple LNA-substituted natural nucleic acids and in LNA–DNA or LNA–RNA heteroduplexes has been well investigated, but the X-ray structure of an ‘all-locked’ nucleic acid double helix has not been described to date. Here, the crystallization and X-ray diffraction data analysis of an ‘all-locked’ nucleic acid helix, which was designed as an LNA originating from a tRNA Ser microhelix RNA structure, is presented. The crystals belonged to space group C2, with unit-cell parameters a = 77.91, b = 40.74, c = 30.06 Å, β = 91.02°. A high-resolution and a low-resolution data set were recorded, with the high-resolution data showing diffraction to 1.9 Å resolution. The crystals contained two double helices per asymmetric unit, with a Matthews coefficient of 2.48 Å 3 Da −1 and a solvent content of 66.49% for the merged data

Cyanuric acid hydrolase from Azorhizobium caulinodans ORS 571: crystal structure and insights into a new class of Ser-Lys dyad proteins.

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Seunghee Cho

Full Text Available Cyanuric acid hydrolase (CAH catalyzes the hydrolytic ring-opening of cyanuric acid (2,4,6-trihydroxy-1,3,5-triazine, an intermediate in s-triazine bacterial degradation and a by-product from disinfection with trichloroisocyanuric acid. In the present study, an X-ray crystal structure of the CAH-barbituric acid inhibitor complex from Azorhizobium caulinodans ORS 571 has been determined at 2.7 Å resolution. The CAH protein fold consists of three structurally homologous domains forming a β-barrel-like structure with external α-helices that result in a three-fold symmetry, a dominant feature of the structure and active site that mirrors the three-fold symmetrical shape of the substrate cyanuric acid. The active site structure of CAH is similar to that of the recently determined AtzD with three pairs of active site Ser-Lys dyads. In order to determine the role of each Ser-Lys dyad in catalysis, a mutational study using a highly sensitive, enzyme-coupled assay was conducted. The 10⁹-fold loss of activity by the S226A mutant was at least ten times lower than that of the S79A and S333A mutants. In addition, bioinformatics analysis revealed the Ser226/Lys156 dyad as the only absolutely conserved dyad in the CAH/barbiturase family. These data suggest that Lys156 activates the Ser226 nucleophile which can then attack the substrate carbonyl. Our combination of structural, mutational, and bioinformatics analyses differentiates this study and provides experimental data for mechanistic insights into this unique protein family.

Crystal structure of (E-4-{2-[4-(allyloxyphenyl]diazenyl}benzoic acid

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Md. Lutfor Rahman

2014-12-01

Full Text Available The title compound, C16H14N2O3, has an E conformation about the azobenzene [—N=N– = 1.2481 (16 Å] linkage. The benzene rings are almost coplanar [dihedral angle = 1.36 (7°]. The O atoms of the carboxylic acid group are disordered over two sets of sites and were refined with an occupancy ratio of 0.5:0.5. The two disordered components of the carboxylic acid group make dihedral angles of 1.5 (14 and 3.8 (12° with the benzene ring to which they are attached. In the crystal, molecules are linked via pairs of O—H...O hydrogen bonds, forming inversion dimers. The dimers are connected via C—H...O hydrogen bonds, forming ribbons lying parallel to [120]. These ribbons are linked via C—H...π interactions, forming slabs parallel to (001.

Do carboximide–carboxylic acid combinations form co-crystals? The role of hydroxyl substitution on the formation of co-crystals and eutectics

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Ramanpreet Kaur

2015-05-01

Full Text Available Carboxylic acids, amides and imides are key organic systems which provide understanding of molecular recognition and binding phenomena important in biological and pharmaceutical settings. In this context, studies of their mutual interactions and compatibility through co-crystallization may pave the way for greater understanding and new applications of their combinations. Extensive co-crystallization studies are available for carboxylic acid/amide combinations, but only a few examples of carboxylic acid/imide co-crystals are currently observed in the literature. The non-formation of co-crystals for carboxylic acid/imide combinations has previously been rationalized, based on steric and computed stability factors. In the light of the growing awareness of eutectic mixtures as an alternative outcome in co-crystallization experiments, the nature of various benzoic acid/cyclic imide combinations is established in this paper. Since an additional functional group can provide sites for new intermolecular interactions and, potentially, promote supramolecular growth into a co-crystal, benzoic acids decorated with one or more hydroxyl groups have been systematically screened for co-crystallization with one unsaturated and two saturated cyclic imides. The facile formation of an abundant number of hydroxybenzoic acid/cyclic carboximide co-crystals is reported, including polymorphic and variable stoichiometry co-crystals. In the cases where co-crystals did not form, the combinations are shown invariably to result in eutectics. The presence or absence and geometric disposition of hydroxyl functionality on benzoic acid is thus found to drive the formation of co-crystals or eutectics for the studied carboxylic acid/imide combinations.

Crystal Structure of Na3MoCl6

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Martin Beran

2011-07-01

Full Text Available The ternary chloride Na3MoCl6 is obtained as red crystals from a disproportionation reaction of molybdenum dichloride, {Mo6}Cl12, in an acidic NaCl/AlCl3 melt at 350 °C. The crystal structure (trigonal, P-31c, a = 687.1(1, c = 1225.3(2 pm, Z = 2, V = 501,0(1 106 pm3 is that of Na3CrCl6: within a hexagonal closest-packing of chloride ions two thirds of the octahedral voids are filled between the AB double layers with Na+/Mo3+, and between the BA layers with Na+.

Synthesis, Crystal Structure and Anti-ischaemic Activity of (E)-1-{4 ...

African Journals Online (AJOL)

NICO

Mr = 476.98) (5) was synthesized and studied by the single crystal X-ray diffraction method. Its structure was ... The reaction of cinnamic acid chloride with 1-[bis(4-methoxy- .... Displacement ellipsoids are drawn at the 70 % probability level.

Synthesis, crystal structure and growth of a new inorganic- organic hybrid compound for nonlinear optical applications: Aquadiiodo (3-aminopropanoic acid) cadmium (II)

Science.gov (United States)

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

2017-12-01

The new inorganic-organic hybrid material aquadiiodo (3-aminopropanoic acid) cadmium (II) [ADI (3-AP) Cd] has been successfully synthesized and good quality crystals have been grown by slow evaporation solution technique. The structure was determined by single crystal X-ray diffraction at room temperature. The compound crystallizes in monoclinic crystal system with centro symmetric space group P21/c and four molecules in the unit cell. The structure of the title compound was further confirmed by 1H and 13C nuclear magnetic resonance spectral analysis. FT-IR spectroscopy was used to confirm the presence of various functional groups in the compound. The transmittance and optical parameters of the crystal were studied by UV- Visible-NIR spectroscopy. The thermal stability of the grown crystal was evaluated using thermogravimetric and differential thermal analyses. Mechanical hardness has been identified by Vickers micro hardness study and work hardening coefficient was calculated. Dielectric measurement was carried out as a function of frequency and results are discussed. The growth mechanism of the crystal was assessed by chemical etching studies. The third-order nonlinear optical susceptibility of [ADI (3-AP) Cd] was derived using the Z-scan technique, and it was 3.24955 × 10-8 esu. The positive nonlinear refractive index 2.48505 × 10-11 m2/W, is an indication of self-defocusing optical nonlinearity of the sample. It is believed that the [ADI (3-AP) Cd] is a promising new candidate for developing efficient nonlinear optical and optical power limiting devices.

Crystal engineering of novel cocrystals of a triazole drug with 1,4-dicarboxylic acids.

Science.gov (United States)

Remenar, Julius F; Morissette, Sherry L; Peterson, Matthew L; Moulton, Brian; MacPhee, J Michael; Guzmán, Héctor R; Almarsson, Orn

2003-07-16

Cocrystals of the poorly soluble antifungal drug cis-itraconazole (1) with 1,4-dicarboxylic acids have been prepared. The crystal structure of the succinic acid cocrystal with 1 was determined to be a trimer by single-crystal X-ray. The trimer is comprised of two molecules of 1 oriented in antiparallel fashion to form a pocket with a triazole at either end. The extended succinic acid molecule fills the pocket, bridging the triazole groups through hydrogen-bonding interactions rather than interacting with the more basic piperazine nitrogens. The solubility and dissolution rate of some of the cocrystals are approximately the same as those of the amorphous drug in the commercial formulation and are much higher than those for the crystalline free base. The results suggest that cocrystals of drug molecules have the possibility of achieving the higher oral bioavailability common for amorphous forms of water-insoluble drugs while maintaining the long-term chemical and physical stability that crystal forms provide.

Influence of VO2+ ions on structural and optical properties of potassium succinate-succinic acid single crystal for non-linear optical applications

Science.gov (United States)

Juliet sheela, K.; Subramanian, P.

2018-04-01

A transparent and good optical quality semi organic single crystal of vanadium doped potassium succinate-succinic acid (KSSA) was synthesized by slow evaporation technique at room temperature. The structural perfection was supported by the powder XRD of the KSSA-VO2+ single crystal. Optical behavior of the material was discovered from the absorption and transmission spectra of UV-vis-NIR characterization. Functional group and presence of metal ion in the specimen are depicted from FTIR traces. From the photoluminescence studies, emission of wavelength in the violet region (418 nm) at the excitation of 243 nm could be ascertained. EDAX, SEM measurements identify presence of elements and pictures the step-line growth and the imperfection presents in the grown crystal. EPR analysis extracts the information about the local site symmetry around the impurity ion, molecular orbital coefficients, admixture coefficients and ground state wave function of VO2+ doped KSSA single crystal. Second harmonic generation (SHG) efficiency of the grown crystal was investigated to explore the NLO characteristic of the material.

Expression, purification, crystallization and structure of human adipocyte lipid-binding protein (aP2)

International Nuclear Information System (INIS)

Marr, Eric; Tardie, Mark; Carty, Maynard; Brown Phillips, Tracy; Wang, Ing-Kae; Soeller, Walt; Qiu, Xiayang; Karam, George

2006-01-01

The crystal structure of human adipocyte lipid-binding protein (aP2) with a bound palmitate is reported at 1.5 Å resolution. Human adipocyte lipid-binding protein (aP2) belongs to a family of intracellular lipid-binding proteins involved in the transport and storage of lipids. Here, the crystal structure of human aP2 with a bound palmitate is described at 1.5 Å resolution. Unlike the known crystal structure of murine aP2 in complex with palmitate, this structure shows that the fatty acid is in a folded conformation and that the loop containing Phe57 acts as a lid to regulate ligand binding by excluding solvent exposure to the central binding cavity

In-situ Spectroscopic Studies and Modelling of Crystallization Processes of Sulphuric Acid Catalysts

DEFF Research Database (Denmark)

Oehlers, C.; Fehrmann, Rasmus; Masters, Stephen Grenville

1996-01-01

Deactivation of commercial and prototype sulphuric acid catalysts has been investigated in-situ by ESR spectroscopy. The influence of support pore structure,and the chemical composition of the catalyst and the gas phase was dicussed.A statistical lattice model was applied to describe the crystall......Deactivation of commercial and prototype sulphuric acid catalysts has been investigated in-situ by ESR spectroscopy. The influence of support pore structure,and the chemical composition of the catalyst and the gas phase was dicussed.A statistical lattice model was applied to describe...

Synthesis, crystal structure and optical property of three coordination polymer constructed from m-phenylenediacrylate acid

Energy Technology Data Exchange (ETDEWEB)

Xiao, YiFan; Wang, TingTing; Zeng, HePing, E-mail: hpzeng@scut.edu.cn

2015-01-15

Three new complexes of the wholly deprotonated flexible ligand m-phenylenediacrylate acid (H{sub 2}mpda), namely, [Zn (mpda) (H{sub 2}O)] [1], [Pr{sub 2}(mpda){sub 2}(H{sub 2}O){sub 2}(CHOO){sub 2}] [2], and [Mn{sub 2}(mpda){sub 2} (H{sub 2}O){sub 4}] [3], were synthesized by the solvothermal reaction. The complexes were characterized by IR spectroscopy, thermogravimetric analysis, and X-ray single-crystal diffraction. A mixed sample [Nd(mpda)(H{sub 2}O)(CHOO)·Pr(mpda)(H{sub 2}O)(CHOO)] [2{sup ]} was also synthesized and studied. Compounds [1] and [2] exhibit a selective sensing function with respect to acetone, and they are a potential luminescent sensory material for the selective detection of Zn{sup 2+} and Ni{sup 2+} ions, respectively. Furthermore, the fluorescent changes of compound [1] upon the addition of cations (Fe{sup 3+} and Zn{sup 2+}, Bi{sup 2+} and Zn{sup 2+}) are utilized to construct two logic gates at the molecular level. - Graphical abstract: Three new complexes of flexible ligand m-phenylenedicarboxylic acid were synthesized by solvothermal reaction. Three metal−organic frameworks exhibiting 1D, 2D, 3D structures, respectively. - Highlights: • Three new complexes of m-phenylenedicarboxylic acid were synthesized. • Three metal−organic frameworks exhibiting 1D, 2D, 3D structures, respectively. • [1] and [2] exhibits a very high quenching effect with acetone. • [1] and [2] are a potential luminescent sensory material for Zn{sup 2+}, Ni{sup 2+} ions. • Two logic gates have been constructed using compound [1].

Crystal structure and magnetic susceptibility of UOSe single crystals

International Nuclear Information System (INIS)

Kaczorowski, D.; Muenster Univ.; Poettgen, R.; Jeitschko, W.; Gajek, Z.; Zygmunt, A.

1993-01-01

The crystal structure and magnetic susceptibility behaviour of UOSe single crystals have been studied. UOSe crystalizes in the tetragonal PbFC1-type structure (space group P4/nmm) with the lattice parameters: a = 390.38(5) pm and c = 698.05(9) pm. It orders antiferromagnetically at T N =100±2 K and exhibits a very strong anisotropy in the susceptibility vs temperature variation. The magnetic and thermodynamic properties of UOSe are successfully interpreted in the framework of a perturbative ab initio crystal field approach. (Author)

Crystal structure and magnetic susceptibility of UOSe single crystals

Energy Technology Data Exchange (ETDEWEB)

Kaczorowski, D. (Polish Academy of Sciences, Wroclaw (Poland). Inst. for Low Temperature and Structure Research Muenster Univ. (Germany). Anorganisch-Chemisches Inst.); Poettgen, R.; Jeitschko, W. (Muenster Univ. (Germany). Anorganisch-Chemisches Inst.); Gajek, Z.; Zygmunt, A. (Polish Academy of Sciences, Wroclaw (Poland). Inst. for Low Temperature and Structure Research)

1993-01-01

The crystal structure and magnetic susceptibility behaviour of UOSe single crystals have been studied. UOSe crystalizes in the tetragonal PbFC1-type structure (space group P4/nmm) with the lattice parameters: a = 390.38(5) pm and c = 698.05(9) pm. It orders antiferromagnetically at T[sub N]=100[+-]2 K and exhibits a very strong anisotropy in the susceptibility vs temperature variation. The magnetic and thermodynamic properties of UOSe are successfully interpreted in the framework of a perturbative ab initio crystal field approach. (Author).

Carbamazepine-Fumaric Acid Co-Crystal Screening Using Solution Based Method

Directory of Open Access Journals (Sweden)

Abd Rahim Syarifah

2016-01-01

Full Text Available Co-crystals is a multi-component system which connected by non-covalent interactions, present physically as a solid form under ambient conditions. Nowadays, co-crystal has becoming as an alternative approach to improve the bioavailability of poor water soluble drugs especially for a weakly ionisable groups or neutral compounds. In this study the co-crystal screening was carried out for carbamazepine (CBZ and fumaric acid (FUM co-crystal former (CCF using non-stoichiometric method (addition of CBZ to CCF saturated solution and stoichiometric method (evaporation of 1:1 molar ratio of CBZ to CCF in acetonitrile, ethyl acetate, propanol, ethanol and formic acid solvent systems. The crystals produced from the screening were characterized using Powder X-ray Diffraction (PXRD, Differential Scanning Calorimetry (DSC and Fourier Transform Infrared (FT-IR. The PXRD analysis had confirmed that the co-crystal was successfully formed in both methods for all of the solvent system studied with an exception to formic acid in the stoichiometric method where no crystal was found precipitate. The findings from this study revealed that Form A and Form B of CBZ-FUM co-crystal had been successfully formed from different solvent systems.

Synthesis, Crystal Structure and Luminescence Property of a New Silver(I) Dimer with Isonicotinic Acid

International Nuclear Information System (INIS)

Yuan, Qi; Liu, Bing

2005-01-01

The absorption spectrum was calculated from reflection spectrum by the Kubelka.Munk function. The energy gap of the title compound determined by extrapolation from the linear portion of the absorption edge in a (α/S) versus energy plot is 1.91 eV, which suggests that the title compound behaves as semiconductor. Isonicotinic acid (Iso), namely 4.pyridinecarboxylate, a multi.functional chelating and/or bridging ligand, has proved to be very powerful for the construction of multi. dimensional metal.organic coordination networks. Furthermore, The isonicotinic acid complexes has raised many interests in fluorescence probing with numerous potential applications for studies of microsecond diffusion and dynamics of membranes. Metal centers are potential carriers of electrochemical, magnetic, catalytic, or optical properties that may be introduced into the inorganic.organic hybrid materials. d"1"0 metals with rich photophysical and photochemical character have focused attentions to synthesize polynuclear complexes. Considering the versatile coordination abilities of Iso, we employ the ligand to coordinate with silver nitrate to fabricate a coordination complex with excellent fluorescence property. Herein we report the synthesis, crystal structure and fluorescence property of a new d"1"0 coordination dimer [Ag_2(Iso)_2(NO_3)_2

Characterization of Crystal Chirality in Amino Acids Using Low-Frequency Raman Spectroscopy.

Science.gov (United States)

Aviv, Hagit; Nemtsov, Irena; Mastai, Yitzhak; Tischler, Yaakov R

2017-10-19

We present a new method for differentiating racemic crystals from enantiopure crystals. Recently, developments in optical filters have enabled the facile use of Raman spectroscopy to detect low-frequency vibrational (LFV) modes. Here, for the first time, we use Raman spectroscopy to characterize the LFV modes for crystalline organic materials composed of chiral molecules. The LF-Raman spectra of racemic and enantiopure crystals exhibit a significant variation, which we attribute to different hydrogen-bond networks in the chiral crystal structures. Across a representative set of amino acids, we observed that when comparing racemic versus enantiopure crystals, the available LFV modes and their relative scattering intensity are strong functions of side chain polarity. Thus, LF-Raman can be used as a method that is complementary to the currently used methods for characterizing crystal chirality due to simpler, faster, and more sensitive measurements, along with the small sample size required, which is limited by the laser-beam diameter in the focus.

Crystal structures of three anhydrous salts of the Lewis base 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU with the ring-substituted benzoic acid analogues 4-aminobenzoic acid, 3,5-dinitrobenzoic acid and 3,5-dinitrosalicylic acid

Directory of Open Access Journals (Sweden)

Graham Smith

2016-03-01

Full Text Available The anhydrous salts of the Lewis base 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU with 4-aminobenzoic acid [1-aza-8-azoniabicyclo[5.4.0]undec-7-ene 4-aminobenzoate, C9H17N2+·C7H6NO2− (I], 3,5-dinitrobenzoic acid [1-aza-8-azoniabicyclo[5.4.0]undec-7-ene 3,5-dinitrobenzoate, C9H17N2+·C7H3N2O6−, (II] and 3,5-dinitrosalicylic acid (DNSA [1-aza-8-azoniabicyclo[5.4.0]undec-7-ene 2-hydroxy-3,5-dinitrobenzoate, C9H17N2+·C7H3N2O7−, (III] have been determined and their hydrogen-bonded structures are described. In both (II and (III, the DBU cations have a common disorder in three of the C atoms of the six-membered ring moieties [site-occupancy factors (SOF = 0.735 (3/0.265 (3 and 0.686 (4/0.314 (4, respectively], while in (III, there is additional rotational disorder in the DNSA anion, giving two sites (SOF = 0.72/0.28, values fixed for the phenol group. In the crystals of (I and (III, the cation–anion pairs are linked through a primary N—H...Ocarboxyl hydrogen bond [2.665 (2 and 2.869 (3 Å, respectively]. In (II, the ion pairs are linked through an asymmetric three-centre R12(4, N—H...O,O′ chelate association. In (I, structure extension is through amine N—H...Ocarboxyl hydrogen bonds between the PABA anions, giving a three-dimensional structure. The crystal structures of (II and (III are very similar, the cation–anion pairs being associated only through weak C—H...O hydrogen bonds, giving in both overall two-dimensional layered structures lying parallel to (001. No π–π ring associations are present in any of the structures.

Crystal structure of 3-(4,4-difluoro-5,7-dimethyl-4-bora-3a,4a-diaza-s-indacen-3-ylpropanoic acid

Directory of Open Access Journals (Sweden)

Takuma Kato

2017-12-01

Full Text Available The crystal structure of the title compound, C14H15BF2N2O2, which comprises a boron–dipyrromethene (BODIPY backbone and a propionic acid group, has been determined at 100 K. The BODIPY fused-ring system is nearly planar, with a maximum deviation from the mean plane of 0.032 (2 Å. In the crystal, pairs of O—H...O hydrogen bonds connect the molecules, forming inversion dimers. The dimers are linked via C—H...O hydrogen bonds, forming a tape along the a axis. The tapes are stacked along the c axis through C—H...F hydrogen bonds and π–π interactions.

Crystal growth, structural, spectral, thermal, dielectric, linear and nonlinear optical characteristics of a new organic acentric material: L-Methionine-Succinic acid (2/1)

Science.gov (United States)

Nageshwari, M.; Kumari, C. Rathika Thaya; Vinitha, G.; Mohamed, M. Peer; Sudha, S.; Caroline, M. Lydia

2018-03-01

L-Methionine-Succinic acid (2/1) (LMSA), 2C5H11NO2S·C4H6O4, a novel nonlinear optical material which belongs to the class of organic category was grown-up for the first time by the technique of slow evaporation. Purity of LMSA was improved using repetitive recrystallization. LMSA was analyzed by single crystal and powder X-ray diffraction investigation to affirm the crystal structure and crystalline character. The single crystal XRD revealed that LMSA corresponds to the crystal system of triclinic with P1 as space group showing the asymmetric unit consists of a neutral succinic acid molecule and two methionine residues which are crystallographically independent existing in zwitterionic form. The functional groups existing in LMSA was accomplished using Fourier transform infrared spectroscopy. The optical transparency and the band gap energy were identified utilizing UV-Visible spectrum. The optical constants specifically reflectance and extinction coefficient clearly indicate the elevated transparency of LMSA. The thermal analyses affirmed its thermal stability. The luminescence behavior of LMSA has been analyzed by Photoluminescence (PL) spectral study. The mechanical, laser damage threshold and dielectric investigation of LMSA was done to suggest the material for practical applications. The second and third harmonic generation efficacy was confirmed by means of Kurtz-Perry and Z-scan procedure which attest its potentiality in the domain of nonlinear optics.

Structure of eight molecular salts assembled from noncovalent bonding between carboxylic acids, imidazole, and benzimidazole

Science.gov (United States)

Jin, Shouwen; Zhang, Huan; Liu, Hui; Wen, Xianhong; Li, Minghui; Wang, Daqi

2015-09-01

Eight organic salts of imidazole/benzimidazole have been prepared with carboxylic acids as 2-methyl-2-phenoxypropanoic acid, α-ketoglutaric acid, 5-nitrosalicylic acid, isophthalic acid, 4-nitro-phthalic acid, and 3,5-dinitrosalicylic acid. The eight crystalline forms reported are proton-transfer compounds of which the crystals and compounds were characterized by X-ray diffraction analysis, IR, mp, and elemental analysis. These structures adopted hetero supramolecular synthons, with the most common R22(7) motif observed at salts 2, 3, 5, 6 and 8. Analysis of the crystal packing of 1-8 suggests that there are extensive strong Nsbnd H⋯O, and Osbnd H⋯O hydrogen bonds (charge assisted or neutral) between acid and imidazolyl components in all of the salts. Except the classical hydrogen bonding interactions, the secondary propagating interactions also play important roles in structure extension. This variety, coupled with the varying geometries and number of acidic groups of the acids utilized, has led to the creation of eight supramolecular arrays with 1D-3D structure. The role of weak and strong noncovalent interactions in the crystal packing is analyzed. The results presented herein indicate that the strength and directionality of the Nsbnd H⋯O, and Osbnd H⋯O hydrogen bonds between acids and imidazole/benzimidazole are sufficient to bring about the formation of organic salts.

Metal complexes of salicylhydroxamic acid (H2Sha), anthranilic hydroxamic acid and benzohydroxamic acid. Crystal and molecular structure of [Cu(phen)2(Cl)]Cl x H2Sha, a model for a peroxidase-inhibitor complex.

Science.gov (United States)

O'Brien, E C; Farkas, E; Gil, M J; Fitzgerald, D; Castineras, A; Nolan, K B

2000-04-01

Stability constants of iron(III), copper(II), nickel(II) and zinc(II) complexes of salicylhydroxamic acid (H2Sha), anthranilic hydroxamic acid (HAha) and benzohydroxamic acid (HBha) have been determined at 25.0 degrees C, I=0.2 mol dm(-3) KCl in aqueous solution. The complex stability order, iron(III) > copper(II) > nickel(II) approximately = zinc(II) was observed whilst complexes of H2Sha were found to be more stable than those of the other two ligands. In the preparation of ternary metal ion complexes of these ligands and 1,10-phenanthroline (phen) the crystalline complex [Cu(phen)2(Cl)]Cl x H2Sha was obtained and its crystal structure determined. This complex is a model for hydroxamate-peroxidase inhibitor interactions.

Studies of the surface structures of molecular crystals and of adsorbed molecular monolayers on the (111) crystal faces of platinum and silver by low-energy electron diffraction

International Nuclear Information System (INIS)

Firment, L.E.

1977-01-01

The structures of molecular crystal surfaces were investigated for the first time by the use of low-energy electron diffraction (LEED). The experimental results from a variety of molecular crystals were examined and compared as a first step towards understanding the properties of these surfaces on a microscopic level. The method of sample preparation employed, vapor deposition onto metal single-crystal substrates at low temperatures in ultrahigh vacuum, allowed concurrent study of the structures of adsorbed monolayers on metal surfaces and of the growth processes of molecular films on metal substrates. The systems investigated were ice, ammonia, naphthalene, benzene, the n-paraffins (C 3 to C 8 ), cyclohexane, trioxane, acetic acid, propionic acid, methanol, and methylamine adsorbed and condensed on both Pt(111) and Ag(111) surfaces. Electron-beam-induced damage of the molecular surfaces was observed after electron exposures of 10 -4 A sec cm -2 at 20 eV. Aromatic molecular crystal samples were more resistant to damage than samples of saturated molecules. The quality and orientation of the grown molecular crystal films were influenced by substrate preparation and growth conditions. Forty ordered monolayer structures were observed. 110 figures, 22 tables, 162 references

Nitric acid adduct formation during crystallization of barium and strontium nitrates and their co-precipitation from nitric acid media

International Nuclear Information System (INIS)

Mishina, N.E.; Zilberman, B.Ya.; Lumpov, A.A.; Koltsova, T.I.; Puzikov, E.A.; Ryabkov, D.V.

2015-01-01

The molar solubilities of Ba, Sr and Pb nitrates in nitric acid as a function of total nitrate concentration is presented and described by the mass action law, indicating on formation of the adducts with nitric acid. Precipitates of Ba(NO 3 ) 2 and Sr(NO 3 ) 2 crystallized from nitric acid were studied by ISP OES and IR spectroscopy. The data obtained confirmed formation of metastable adducts with nitric acid. IR and X-ray diffraction studies of the mixed salt systems indicated conversion of the mixed salts into (Ba,Sr)(NO 3 ) 2 solid solution of discrete structure in range of total nitrate ion concentration ∼6 mol/L. (author)

Synthesis and crystal structure of two lead (II) complexes with 1,10-phenanthroline ligand

International Nuclear Information System (INIS)

Olivera, Fiorella L.; Santillan, Guillermo A.

2012-01-01

Two coordination complexes have been synthesized by the reaction of lead nitrate (II) with 1,10-phenanthroline in methanol/water. The crystals of these complexes were obtained by using the diffusion method and structurally characterized by X-ray single crystal diffraction. Both complexes crystallized in the monoclinic space group P2 1 /c. The analysis by crystal X-ray diffraction reveals that in both complexes the coordination around the lead (II) ion is a distorted octahedral structure where the ion is bonded to the heterocyclic nitrogen atoms of chelating ligand 1,10-phenanthroline, three oxygen atoms of three nitrate groups and one oxygen from the water molecule. The difference between the complexes lies in the way of nitrate ion in presence of carboxylic acid aromatics. In addition, the crystal structure of complexes can be regarded as a 3D coordination polymer through Pb-O weak interactions, hydrogen bonds and π-π stacking interactions. (author).

Systematic comparison of crystal and NMR protein structures deposited in the protein data bank.

Science.gov (United States)

Sikic, Kresimir; Tomic, Sanja; Carugo, Oliviero

2010-09-03

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.

Crystal Structure of Rat Carnitine Palmitoyltransferase II (CPT-II)

Energy Technology Data Exchange (ETDEWEB)

Hsiao,Y.; Jogl, G.; Esser, V.; Tong, L.

2006-01-01

Carnitine palmitoyltransferase II (CPT-II) has a crucial role in the {beta}-oxidation of long-chain fatty acids in mitochondria. We report here the crystal structure of rat CPT-II at 1.9 Angstroms resolution. The overall structure shares strong similarity to those of short- and medium-chain carnitine acyltransferases, although detailed structural differences in the active site region have a significant impact on the substrate selectivity of CPT-II. Three aliphatic chains, possibly from a detergent that is used for the crystallization, were found in the structure. Two of them are located in the carnitine and CoA binding sites, respectively. The third aliphatic chain may mimic the long-chain acyl group in the substrate of CPT-II. The binding site for this aliphatic chain does not exist in the short- and medium-chain carnitine acyltransferases, due to conformational differences among the enzymes. A unique insert in CPT-II is positioned on the surface of the enzyme, with a highly hydrophobic surface. It is likely that this surface patch mediates the association of CPT-II with the inner membrane of the mitochondria.

Amine free crystal structure: The crystal structure of d(CGCGCG)2 and methylamine complex crystal

International Nuclear Information System (INIS)

Ohishi, Hirofumi; Tsukamoto, Koji; Hiyama, Yoichi; Maezaki, Naoyoshi; Tanaka, Tetsuaki; Ishida, Toshimasa

2006-01-01

We succeeded in the crystallization of d(CGCGCG) 2 and methylamine Complex. The crystal was clear and of sufficient size to collect the X-ray crystallographic data up to 1.0 A resolution using synchrotron radiation. As a result of X-ray crystallographic analysis of 2F o - F c map was much clear and easily traced. It is First time monoamine co-crystallizes with d(CGCGCG) 2 . However, methylamine was not found from the complex crystal of d(CGCGCG) 2 and methylamine. Five Mg ions were found around d(CGCGCG) 2 molecules. These Mg ions neutralized the anion of 10 values of the phosphate group of DNA with five Mg 2+ . DNA stabilized only by a metallic ion and there is no example of analyzing the X-ray crystal structure like this. Mg ion stabilizes the conformation of Z-DNA. To use monoamine for crystallization of DNA, we found that we can get only d(CGCGCG) 2 and Mg cation crystal. Only Mg cation can stabilize the conformation of Z-DNA. The method of using the monoamine for the crystallization of DNA can be applied to the crystallization of DNA of long chain of length in the future like this

Synthesis, Crystal Structure and Luminescence Property of a New Silver(I) Dimer with Isonicotinic Acid

Energy Technology Data Exchange (ETDEWEB)

Yuan, Qi [Pharmacy College of Henan University, Kaifeng (China); Liu, Bing [Chinese Academy of Sciences, Fuzhou (China)

2005-10-15

The absorption spectrum was calculated from reflection spectrum by the Kubelka.Munk function. The energy gap of the title compound determined by extrapolation from the linear portion of the absorption edge in a (α/S) versus energy plot is 1.91 eV, which suggests that the title compound behaves as semiconductor. Isonicotinic acid (Iso), namely 4.pyridinecarboxylate, a multi.functional chelating and/or bridging ligand, has proved to be very powerful for the construction of multi. dimensional metal.organic coordination networks. Furthermore, The isonicotinic acid complexes has raised many interests in fluorescence probing with numerous potential applications for studies of microsecond diffusion and dynamics of membranes. Metal centers are potential carriers of electrochemical, magnetic, catalytic, or optical properties that may be introduced into the inorganic.organic hybrid materials. d{sup 10} metals with rich photophysical and photochemical character have focused attentions to synthesize polynuclear complexes. Considering the versatile coordination abilities of Iso, we employ the ligand to coordinate with silver nitrate to fabricate a coordination complex with excellent fluorescence property. Herein we report the synthesis, crystal structure and fluorescence property of a new d{sup 10} coordination dimer [Ag{sub 2}(Iso){sub 2}(NO{sub 3}){sub 2}].

CCDC 938820: Experimental Crystal Structure Determination : 9H-carbazole-3,6-dicarboxylic acid N,N-dimethylformamide solvate

KAUST Repository

Weselinski, Lukasz; Luebke, Ryan; Eddaoudi, Mohamed

2014-01-01

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

Optimization of methanol crystallization for highly efficient separation of palmitic acid from palm fatty acid mixture using response surface methodology

Directory of Open Access Journals (Sweden)

A. A.W. Japir

2018-01-01

Full Text Available The objective of the current study was to develop parameters for the separation of palmitic acid (PA from a crude palm oil saturated fatty acid (SFAs mixture by using the methanol crystallization method. The conditions of methanol crystallization were optimized by the response surface methodology (RSM with the D-optimal design. The procedure of developing the solvent crystallization method was based on various different parameters. The fatty acid composition was carried out using a gas chromatography flame ionization detector (GC-FID as fatty acid methyl esters. The highest percentage of SFAs was more than 96% with the percentage yield of 87.5% under the optimal conditions of fatty acids-to-methanol ratio of 1: 20 (w/v, the crystallization temperature of -15 °C, and the crystallization time of 24 hours, respectively. The composition of separated SFAs in the solid fraction contains 96.7% of palmitic acid (C16:0 as a dominant component and 3.3% of stearic acid (C18:0. The results showed that utilizing methanol as a crystallization solvent is recommended because of its high efficiency, low cost, stability, availability, comparative ease of recovery and its ability to form needle-like crystals which have good filtering and washing characteristics.

Optimization of methanol crystallization for highly efficient separation of palmitic acid from palm fatty acid mixture using response surface methodology

International Nuclear Information System (INIS)

Japir, A.A.W.; Salimon, J.; Derawi, D.; Yahaya, B.H.; Jamil, M.S.M.; Yusop, M.R.

2017-01-01

The objective of the current study was to develop parameters for the separation of palmitic acid (PA) from a crude palm oil saturated fatty acid (SFAs) mixture by using the methanol crystallization method. The conditions of methanol crystallization were optimized by the response surface methodology (RSM) with the D-optimal design. The procedure of developing the solvent crystallization method was based on various different parameters. The fatty acid composition was carried out using a gas chromatography flame ionization detector (GC-FID) as fatty acid methyl esters. The highest percentage of SFAs was more than 96% with the percentage yield of 87.5% under the optimal conditions of fatty acids-to-methanol ratio of 1: 20 (w/v), the crystallization temperature of -15 °C, and the crystallization time of 24 hours, respectively. The composition of separated SFAs in the solid fraction contains 96.7% of palmitic acid (C16:0) as a dominant component and 3.3% of stearic acid (C18:0). The results showed that utilizing methanol as a crystallization solvent is recommended because of its high efficiency, low cost, stability, availability, comparative ease of recovery and its ability to form needle-like crystals which have good filtering and washing characteristics. [es

Stereospecific ligands and their complexes. VI. The crystal structure of (S,S-ethylenediamine-N,N’-di-2-propanoic acid hydrochloride, (S,S-H2eddp•HCl

Directory of Open Access Journals (Sweden)

VERICA V. GLODJOVIĆ

2011-07-01

Full Text Available (S,S-Ethylenediamine-N,N’-di-2-propanoic acid hydrochloride, (S,S-H2eddp·HCl, was prepared and its crystal structure determined. The compound was characterized by infrared and 1H- and 13C-NMR spectroscopy. It forms P1 in the space group of a triclinic crystal system with a = 5.3902(2 Å, b = 5.8967(2 Å, c = 10.3319(2 Å, a = 99.625(2°, b = 91.645(2°, g = 109.995(2° and Z = 1.

The response of quartz crystals coated with thin fatty acid film to organic gases

CERN Document Server

Jin, C N; Kim, K H; Kwon, Y S

1999-01-01

We tried to apply a quartz crystal as a sensor by using the resonant frequency and the resistance properties of quartz crystals. Four kinds of fatty acids that have the same head groups were coated on the surfaces of the quartz crystals, and the shift of the resonant frequency and the resistance were observed based on the lengths of the tail groups. Myristic acid (C sub 1 sub 4), palmitic acid (C sub 1 sub 6), stearic acid (C sub 1 sub 8), and arachidic acid (C sub 2 sub 0) were deposited on the surfaces of quartz crystals by using the Langmuir-Blodgett (LB) method. As a result, the resonant frequency change was more sensitive to high molecular-weight fatty acids than to low molecular-weight ones. We also observed the effect of temperature on stearic acid LB films, and the response properties of quartz crystals coated with stearic-acid LB films to organic gases were investigated. As a result, the sensitivity of quartz crystals to organic gases was higher for higher molecular-weight gas, and we found that quar...

Crystallization Process of Protein Rv0731c from Mycobacterium Tuberculosis for a Successful Atomic Resolution Crystal Structure at 1.2 Angstrom

Energy Technology Data Exchange (ETDEWEB)

Zhu, Liang Cong

2009-06-08

Proteins are bio-macromolecules consisting of basic 20 amino acids and have distinct three-dimensional folds. They are essential parts of organisms and participate in every process within cells. Proteins are crucial for human life, and each protein within the body has a specific function, such as antibodies, contractile proteins, enzymes, hormonal proteins, structural proteins, storage proteins and transport proteins. Determining three-dimensional structure of a protein can help researchers discover the remarkable protein folding, binding site, conformation and etc, in order to understand well of protein interaction and aid for possible drug design. The research on protein structure by X-ray protein crystallography carried by Li-Wei Hung's research group in the Physical Bioscience Division at Lawrence Berkeley National Laboratory (LBNL) is focusing on protein crystallography. The research in this lab is in the process of from crystallizing the proteins to determining the three dimensional crystal structures of proteins. Most protein targets are selected from Mycobacterium Tuberculosis. TB (Tuberculosis) is a possible fatal infectious disease. By studying TB target protein can help discover antituberculer drugs, and find treatment for TB. The high-throughput mode of crystallization, crystal harvesting, crystal screening and data collection are applied to the research pipeline (Figure 1). The X-ray diffraction data by protein crystals can be processed and analyzed to result in a three dimensional representation of electron density, producing a detailed model of protein structure. Rv0731c is a conserved hypothetical protein with unknown function from Mycobacterium Tuberculosis. This paper is going to report the crystallization process and brief structure information of Rv0731c.

Photonic Crystal Laser-Driven Accelerator Structures

International Nuclear Information System (INIS)

Cowan, B

2004-01-01

The authors discuss simulated photonic crystal structure designs for laser-driven particle acceleration. They focus on three-dimensional planar structures based on the so-called ''woodpile'' lattice, demonstrating guiding of a speed-of-light accelerating mode by a defect in the photonic crystal lattice. They introduce a candidate geometry and discuss the properties of the accelerating mode. They also discuss the linear beam dynamics in the structure present a novelmethod for focusing the beam. In addition they describe ongoing investigations of photonic crystal fiber-based structures

Distribution of impurities during crystallization of tellurous acid

International Nuclear Information System (INIS)

Debska-Horecka, A.

1980-01-01

Crystallization has been used for purification of telluric acid and coprecipitation of Zn(2), Bi(3), Ni(2), Cr(3), Mg(2), Ca(2), Tl(1), Mn(2), Cu(2), Co(2), Cd(2) with telluric acid sediment has been investigated. The optimum conditions for obtaining the telluric acid of high purity have been established. (author)

Crystal structure of bile salt hydrolase from Lactobacillus salivarius.

Science.gov (United States)

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.

Influence of clay content on the melting behavior and crystal structure of nonisothermal crystallized poly(L-lactic acid)/nanocomposites

Czech Academy of Sciences Publication Activity Database

Ublekov, F.; Baldrian, Josef; Kratochvíl, Jaroslav; Steinhart, M.; Nedkov, E.

2012-01-01

Roč. 124, č. 2 (2012), s. 1643-1648 ISSN 0021-8995 Institutional research plan: CEZ:AV0Z40500505 Keywords : biopolymers * nanocomposite s * crystal structures Subject RIV: CD - Macromolecular Chemistry Impact factor: 1.395, year: 2012

Fabrication and characterization of poly(L-lactic acid) gels induced by fibrous complex crystallization with solvents

Energy Technology Data Exchange (ETDEWEB)

Matsuda, Yasuhiro [ORNL; Fukatsu, Akinobu [Shizuoka University, Hamamatsu, Japan; Wang, Yangyang [ORNL; Miyamoto, Kazuaki [Shizuoka University, Hamamatsu, Japan; Mays, Jimmy [University of Tennessee, Knoxville (UTK); Tasaka, Shigeru [Shizuoka University, Hamamatsu, Japan

2014-01-01

Complex crystal induced gelation of poly(L-lactic acid) (PLLA) solutions was studied for a series of solvents, including N,N-dimethylformamide (DMF). By cooling the solutions prepared at elevated temperatures, PLLA gels were produced in solvents that induced complex crystals ( -crystals) with PLLA. Fibrous structure of PLLA in the gel with DMF was observed by polarizing optical microscopy, field emission electron microscopy, and atomic force microscopy. Upon heating, the crystal form of PLLA in the DMF gel changed from -crystal to a-crystal, the major crystal form in common untreated PLLA films, but the morphology and high elastic modulus of the gel remained until the a-crystal dissolved at higher temperature. In addition, a solvent exchanging method was developed, which allowed PLLA gels to be prepared in other useful solvents that do not induce -crystals without losing the morphology and mechanical properties.

The crystal structure of human GDP-L-fucose synthase.

Science.gov (United States)

Zhou, Huan; Sun, Lihua; Li, Jian; Xu, Chunyan; Yu, Feng; Liu, Yahui; Ji, Chaoneng; He, Jianhua

2013-09-01

Human GDP-l-fucose synthase, also known as FX protein, synthesizes GDP-l-fucose from its substrate GDP-4-keto-6-deoxy-d-mannose. The reaction involves epimerization at both C-3 and C-5 followed by an NADPH-dependent reduction of the carbonyl at C-4. In this paper, the first crystal structure of human FX protein was determined at 2.37 Å resolution. The asymmetric unit of the crystal structure contains four molecules which form two homodimers. Each molecule consists of two domains, a Rossmann-fold NADPH-binding motif and a carboxyl terminal domain. Compared with the Escherichia coli GDP-l-fucose synthase, the overall structures of these two enzymes have four major differences. There are four loops in the structure of human FX protein corresponding to two α-helices and two β-sheets in that of the E. coli enzyme. Besides, there are seven different amino acid residues binding with NAPDH comparing human FX protein with that from E. coli. The structure of human FX reveals the key catalytic residues and could be useful for the design of drugs for the treatment of inflammation, auto-immune diseases, and possibly certain types of cancer.

Study of phosphoric acid crystallization using a focused beam reflectance measurement method

Energy Technology Data Exchange (ETDEWEB)

Ma, Yong [School of Chemistry and Resource Environment, Linyi Normal University, Linyi Shandong 276005 (China); Chen, Kui; Wu, Yanyang; Zhu, Jiawen [Chemical Engineering Research Center, East China University of Science and Technology, Shanghai 200237 (China); Sheng, Yong [SINOCHEN Fuling Chemical Industrial Co., Ltd, Chongqing 226005 (China)

2010-10-15

A way for restoring the crystal size distributions (CSD) from measured chord length distributions (CLD) was reported in this paper. The kinetics of phosphoric acid crystallization process was investigated in cooling mode using focused beam reflectance measurement (FBRM) and digital photo technique. In order to restore the CSD from measured CLD and verify the reliability of FBRM data, digital photo technique in real time and optical microscope were applied in large crystal size and small range, respectively. Results indicated a converting constant A existed between CLD and CSD when crystal growth follows size-independent growth (Mcabe's {delta}L law) law. It was verified by Malvern particles size analysis method. The converting constant A varied with crystal morphology. The crystal growth order increased with the stirring increasing speed during phosphoric acid crystallization process. The trend was especially notable at higher speed situations. It can illustrate that the state of phosphoric acid hemihydrate crystal growth was controlled by both diffusion and surface-integration with the increasing stirring speed. (copyright 2010 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

Propagation of biochirality: crossovers and nonclassical crystallization kinetics of aspartic acid in water.

Science.gov (United States)

Lee, Tu; Lin, Yu Kun; Tsai, Ya Chung; Lee, Hung Lin

2013-11-01

All experimental procedures discussed could be treated as a screening tool for probing the existence of molecular association among the chiral molecules and the solvent system. The molecular association phases of a racemic conglomerate solution (CS) and a racemic compound solution (RCS), and the templating effect of aspartic acid solid surface were observed to minimize the chance of redissolving racemic conglomerate and racemic compound aspartic acid in water and reforming an RCS in crossovers experiments. Only 1 %wt% of l-aspartic acid was adequate enough to induce a transformation from a racemic compound aspartic acid to a racemic conglomerate aspartic acid. This would make the propagation of biochirality more feasible and sound. However, tetrapeptide, (l-aspartic acid)4 , failed to induce enantioseparation as templates purely by crystallization. Nonclassical crystallization theory was needed to take into account the existence of a CS. Fundamental parameters of the crystallization kinetics such as the induction time, interfacial energy, Gibbs energetic barrier, nucleation rate, and critical size of stable nuclei of: (i) racemic compound aspartic acid, (ii) racemic compound aspartic acid seeded with 1 %wt% l-aspartic acid, (iii) racemic conglomerate aspartic acid, and (iv) l-aspartic acid were evaluated and compared with different initial supersaturation ratios. Morphological studies of crystals grown from the crystallization kinetics were also carried out. © 2013 Wiley Periodicals, Inc.

Two dialkylammonium salts of 2-amino-4-nitrobenzoic acid: crystal structures and Hirshfeld surface analysis

Directory of Open Access Journals (Sweden)

James L. Wardell

2016-12-01

Full Text Available The crystal structures of two ammonium salts of 2-amino-4-nitrobenzoic acid are described, namely dimethylazanium 2-amino-4-nitrobenzoate, C2H8N+·C7H5N2O4−, (I, and dibutylazanium 2-amino-4-nitrobenzoate, C8H20N+·C7H5N2O4−, (II. The asymmetric unit of (I comprises a single cation and a single anion. In the anion, small twists are noted for the carboxylate and nitro groups from the ring to which they are connected, as indicated by the dihedral angles of 11.45 (13 and 3.71 (15°, respectively; the dihedral angle between the substituents is 7.9 (2°. The asymmetric unit of (II comprises two independent pairs of cations and anions. In the cations, different conformations are noted in the side chains in that three chains have an all-trans [(+-antiperiplanar] conformation, while one has a distinctive kink resulting in a (+-synclinal conformation. The anions, again, exhibit twists with the dihedral angles between the carboxylate and nitro groups and the ring being 12.73 (6 and 4.30 (10°, respectively, for the first anion and 8.1 (4 and 12.6 (3°, respectively, for the second. The difference between anions in (I and (II is that in the anions of (II, the terminal groups are conrotatory, forming dihedral angles of 17.02 (8 and 19.0 (5°, respectively. In each independent anion of (I and (II, an intramolecular amino-N—H...O(carboxylate hydrogen bond is formed. In the crystal of (I, anions are linked into a jagged supramolecular chain by charge-assisted amine-N—H...O(carboxylate hydrogen bonds and these are connected into layers via charge-assisted ammonium-N—H...O(carboxylate hydrogen bonds. The resulting layers stack along the a axis, being connected by nitro-N—O...π(arene and methyl-C—H...O(nitro interactions. In the crystal of (II, the anions are connected into four-ion aggregates by charge-assisted amino-N—H...O(carboxylate hydrogen bonding. The formation of ammonium-N—H...O(carboxylate hydrogen bonds, involving

Synthesis, Crystal Structure and Anti-Fatigue Effects of Some Benzamide Derivatives

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Xianglong Wu

2014-01-01

Full Text Available A series of benzamide derivatives such as 1-(1,3-benzodioxol-5-ylcarbonyl piperidine (1-BCP were synthesized by the reaction of substituted benzoic acids with piperidine, morpholine or pyrrolidine using a novel method. The crystals of these benzamide derivatives were obtained by recrystallization. Structures of target and intermediate compounds were determined via FT-IR, 1H-NMR and elemental analysis and X-ray crystallography of select examples. The crystal structures of these compounds have potential applications to identify the binding site for allosteric modulators of the α-amino-3-hydroxy-5-methylisoxazole-4-propionic acid (AMPA receptor. The anti-fatigue effects of the benzamide derivatives in weight-loaded forced swimming mice were investigated in a swimming endurance capacity test used as an indicator of fatigue. The swimming times to exhaustion were longer in the b3, d3, and e3 groups than in the caffeine group (p < 0.05. In conclusion, b3, d3 and e3 enhanced the forced swimming capacity of mice. The mechanism of the anti-fatigue effects will be studied in the future.

Syntheses and Crystal Structures of Ferrocenoindenes

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Gerhard Laus

2013-02-01

Full Text Available Ferrocenoindenes display planar chirality and thus represent valuable ligands for asymmetric catalysis. Here, we report on the synthesis of novel 3-(1,1-dibromomethyleneferroceno[1,2-a]indene, (Z-3-(1-bromomethylene-6-iodoferroceno[1,2-a]indene, and benzo[5,6-f]ferroceno[2,3,a]inden-1-one. Any application-oriented design of chiral catalysts requires fundamental knowledge about the ligands involved, not only in terms of atom-connectivity, but also in terms of their three-dimensional structure and steric demand. Therefore, the crystal structures of 2-ferrocenylbenzoic acid, ferroceno[1,2-a]indene, and (Z-3-(1-bromomethylene-6-iodoferroceno[1,2-a]indene have been determined. The bond-lengths that can be retrieved therefrom also allow for an estimation of the reactivity of the aryl-iodo, bromo-methylidene and dibromomethylidene moieties.

Crystal structures of two solvates of (18-crown-6potassium acetate

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Phil Liebing

2016-12-01

Full Text Available The crystal and molecular strutures of two solvated forms of [K(18c6]OAc (18c6 = 18-crown-6 = 1,4,7,10,13,16-hexaoxacyclooctadecane and OAc = acetate were determined by single-crystal X-ray diffraction, namely (acetato-κ2O,O′(1,4,7,10,13,16-hexaoxacyclooctadecane-κ6Opotassium dihydrate, [K(CH3COO(C12H24O6]·2H2O (1 and (acetato-κ2O,O′aqua(1,4,7,10,13,16-hexaoxacyclooctadecane-κ6Opotassium acetic acid monosolvate [K(CH3COO(C12H24O6(H2O]·CH3COOH (2. In both compounds, the acetate anion is bonded to the potassium ion in a chelating fashion and the metal atom is consequently slightly displaced from the O6 plane of the crown ether. In the crystals, O—H...O hydrogen bonds lead to a polymeric ladder structure in the dihydrate 1, while the acetic acid hydrate 2 features inversion dimers.

Face-selective crystal growth behavior of L-aspartic acid in the presence of L-asparagine

Science.gov (United States)

Sato, Hiroyasu; Doki, Norihito; Yoshida, Saki; Yokota, Masaaki; Shimizu, Kenji

2016-02-01

The kinetic mechanism of L-asparagine (L-Asn) action on L-aspartic acid (L-Asp) crystal growth, namely the face-selective effect of L-Asn on the L-Asp crystal growth rate in each direction, was examined. In the a-axis direction, the effect of L-Asn on the L-Asp crystal growth rate was small. Enhancement and inhibition of L-Asp crystal growth, and interestingly the dissolution of the L-Asp crystal face, were observed in the b-axis direction, depending on the amount of L-Asn added. In the c-axis direction, the L-Asp crystal growth rate decreased with the increase in the amount of L-Asn added, and the experimental results were well fitted with a Langmuir adsorption isotherm. The study showed that there were crystal growth conditions where enhancement and inhibition, as well as inhibition and dissolution, coexisted in the presence of an additive with a structure similar to the growing crystal.

Crystallization and preliminary X-ray crystallographic studies of a Lys49-phospholipase A2 homologue from Bothrops pirajai venom complexed with rosmarinic acid

International Nuclear Information System (INIS)

Santos, Juliana I. dos; Santos-Filho, Norival A.; Soares, Andreimar M.; Fontes, Marcos R. M.

2010-01-01

PrTX-I, a noncatalytic and myotoxic Lys49-phospholipase A 2 from B. pirajai venom, was cocrystallized with the inhibitor rosmarinic acid from C. verbenacea. The crystals diffracted X-rays to 1.8 Å resolution and the structure was solved, indicating a remarkable electronic density for the ligand at the entrance to the hydrophobic channel. PrTX-I, a noncatalytic and myotoxic Lys49-phospholipase A 2 from Bothrops pirajai venom, was crystallized in the presence of the inhibitor rosmarinic acid (RA). This is the active compound in the methanolic extract of Cordia verbenacea, a plant that is largely used in Brazilian folk medicine. The crystals diffracted X-rays to 1.8 Å resolution and the structure was solved by molecular-replacement techniques, showing electron density that corresponds to RA molecules at the entrance to the hydrophobic channel. The crystals belong to space group P2 1 2 1 2 1 , indicating conformational changes in the structure after ligand binding: the crystals of all apo Lys49-phospholipase A 2 structures belong to space group P3 1 21, while the crystals of complexed structures belong to space groups P2 1 or P2 1 2 1 2 1

Copper(II) complexes with 4-(1H-1, 2, 4-trizol-1-ylmethyl) benzoic acid: Syntheses, crystal structures and antifungal activities

International Nuclear Information System (INIS)

Xiong, Pingping; Li, Jie; Bu, Huaiyu; Wei, Qing; Zhang, Ruolin; Chen, Sanping

2014-01-01

Reaction of Cu(II) with an asymmetric semi-rigid organic ligand 4-(1H-1, 2, 4-trizol-1-ylmethyl) benzoic acid (HL), yielded five compounds, [Cu 0.5 L] n (1), [Cu(HL) 2 Cl 2 ] n (2), [Cu(HL) 2 Cl 2 (H 2 O)] (3), [Cu(L) 2 (H 2 O)] n (4) and [Cu(L)(phen)(HCO 2 )] n (5), which have been fully characterized by infrared spectroscopy, elemental analysis, and single-crystal X-ray diffraction. As for compounds 1, 2 and 5, Cu(II) is bridged through HL, Cl - , and formic acid, respectively, featuring 1D chain-structure. In compound 3, Cu(II) with hexahedral coordination sphere is assembled through hydrogen-bonding into 3D supramolecular framework. In compound 4, 1D chain units –Cu–O–Cu–O– are ligand-bridged into a 3D network. All compounds were tested on fungi (Fusarium graminearum, Altemaria solani, Macrophoma kawatsukai, Alternaria alternata and Colletotrichum gloeosporioides). Compound 1 exhibits a better antifungal effect compared to other compounds. An effect of structure on the antifungal activity has also been correlated. - Graphical abstract: Copper(II) compounds with 4-(1H-1, 2, 4-trizol-1-ylmethyl) benzoic acid, were prepared, structurally characterized and investigated for antifungal activity. - Highlights: • The title compounds formed by thermodynamics and thermokinetics. • The five compounds show higher inhibition percentage than reactants. • The structure effect on the antifungal activity

Crystal structure of di?methyl?ammonium hydrogen oxalate hemi(oxalic acid)

OpenAIRE

Diallo, Waly; Gueye, Ndongo; Crochet, Aur?lien; Plasseraud, Laurent; Cattey, H?l?ne

2015-01-01

Single crystals of the title salt, Me2NH2 +?HC2O4 ??0.5H2C2O4, were isolated as a side product from the reaction involving Me2NH, H2C2O4 and Sn(n-Bu)3Cl in a 1:2 ratio in methanol or by the reaction of the (Me2NH2)2C2O4 salt and Sn(CH3)3Cl in a 2:1 ratio in ethanol. The asymmetric unit comprises a di?methyl?ammonium cation (Me2NH2 +), an hydrogenoxalate anion (HC2O4 ?), and half a mol?ecule of oxalic acid (H2C2O4) situated about an inversion center. From a supra?molecular point of view, the t...

Crystal and molecular structures of sixteen charge-assisted hydrogen bond-mediated diisopropylammonium salts from different carboxylic acids

Science.gov (United States)

Lin, Zhihao; Hu, Kaikai; Jin, Shouwen; Ding, Aihua; Wang, Yining; Dong, Lingfeng; Gao, Xingjun; Wang, Daqi

2017-10-01

salts were also reported. And their structural and supramolecular aspects are fully analyzed. The result reveals that among the sixteen investigated crystals the NH groups in the diisopropylamine are protonated when the carboxylic acids are deprotonated, and the crystal packing is interpreted in terms of the strong charge-assisted Nsbnd H⋯O hydrogen bond formation between the ammonium and the deprotonated COOH groups. Except the Nsbnd H⋯O hydrogen bond, the Osbnd H⋯O hydrogen bonds (charge assisted or neutral) were also found at the salts 6, 8, 9, 10, 12, 13, 14, 15, and 16. Further analysis of the crystal packing of the salts indicated that a different family of additional CHsbnd O/CH2sbnd O/CH3sbnd O, CH-π/CH3-π, CH3-Cπ, N-π, and π-π associations contribute to the stabilization and expansion of the total structures. For the coexistence of the various weak interactions these structures adopted homo or hetero supramolecular synthons or both.

Biosynthesis of l-Ascorbic Acid and Conversion of Carbons 1 and 2 of l-Ascorbic Acid to Oxalic Acid Occurs within Individual Calcium Oxalate Crystal Idioblasts1

Science.gov (United States)

Kostman, Todd A.; Tarlyn, Nathan M.; Loewus, Frank A.; Franceschi, Vincent R.

2001-01-01

l-Ascorbic acid (AsA) and its metabolic precursors give rise to oxalic acid (OxA) found in calcium oxalate crystals in specialized crystal idioblast cells in plants; however, it is not known if AsA and OxA are synthesized within the crystal idioblast cell or transported in from surrounding mesophyll cells. Isolated developing crystal idioblasts from Pistia stratiotes were used to study the pathway of OxA biosynthesis and to determine if idioblasts contain the entire path and are essentially independent in OxA synthesis. Idioblasts were supplied with various 14C-labeled compounds and examined by micro-autoradiography for incorporation of 14C into calcium oxalate crystals. [14C]OxA gave heavy labeling of crystals, indicating the isolated idioblasts are functional in crystal formation. Incubation with [1-14C]AsA also gave heavy labeling of crystals, whereas [6-14C]AsA gave no labeling. Labeled precursors of AsA (l-[1-14C]galactose; d-[1-14C]mannose) also resulted in crystal labeling, as did the ascorbic acid analog, d-[1-14C]erythorbic acid. Intensity of labeling of isolated idioblasts followed the pattern OxA > AsA (erythorbic acid) > l-galactose > d-mannose. Our results demonstrate that P. stratiotes crystal idioblasts synthesize the OxA used for crystal formation, the OxA is derived from the number 1 and 2 carbons of AsA, and the proposed pathway of ascorbic acid synthesis via d-mannose and l-galactose is operational in individual P. stratiotes crystal idioblasts. These results are discussed with respect to fine control of calcium oxalate precipitation and the concept of crystal idioblasts as independent physiological compartments. PMID:11161021

Method of fabricating patterned crystal structures

KAUST Repository

Yu, Liyang

2016-12-15

A method of manufacturing a patterned crystal structure for includes depositing an amorphous material. The amorphous material is modified such that a first portion of the amorphous thin-film layer has a first height/volume and a second portion of the amorphous thin-film layer has a second height/volume greater than the first portion. The amorphous material is annealed to induce crystallization, wherein crystallization is induced in the second portion first due to the greater height/volume of the second portion relative to the first portion to form patterned crystal structures.

Growth and characterization of KDP crystals doped with L-aspartic acid.

Science.gov (United States)

Krishnamurthy, R; Rajasekaran, R; Samuel, Bincy Susan

2013-03-01

Potassium Dihydrogen Phosphate (KDP) doped with L-aspartic acid has been grown by solvent slow evaporation technique from a mixture of aqueous solution of KDP and 0.7% of L-aspartic acid at room temperature. The grown crystals were characterized by powder X-ray diffraction, UV-visible, FTIR analysis. The doping of aspartic acid was confirmed by FTIR spectrum. The Nonlinear optical property (SHG) of L-aspartic acid doped KDP has been confirmed. Microhardness studies were carried out on the grown crystal. Copyright © 2012 Elsevier B.V. All rights reserved.

Effect of oxalic acid on the optical, thermal, dielectric and mechanical behaviour of ADP crystals

International Nuclear Information System (INIS)

Rajesh, P.; Ramasamy, P.

2009-01-01

The effect of the addition, over a concentration range from 1 to 5 mol%, of oxalic acid on the growth rate, optical transparency, hardness, dielectric behaviour, and SHG efficiency of ammonium dihydrogen phosphate single crystals grown by slow evaporation method has been investigated. UV-Vis studies show that the transparency of the oxalic acid added crystals decreased gradually. Thermal studies indicate that the decomposition temperatures of the crystal are decreased in oxalic acid added ADP crystals. It is observed from the dielectric measurements that the dielectric constant and dielectric loss increase with increase in temperature for all the crystals. Vicker's microhardness study reveals that the addition of higher concentration of oxalic acid decreases the hardness of the crystal. SHG efficiency of 1 mol% of oxalic acid is higher than the pure ADP.

Crystal structure of a β-aminopeptidase from an Australian Burkholderia sp.

Science.gov (United States)

John-White, Marietta; Dumsday, Geoff J; Johanesen, Priscilla; Lyras, Dena; Drinkwater, Nyssa; McGowan, Sheena

2017-07-01

β-Aminopeptidases are a unique group of enzymes that have the unusual capability to hydrolyze N-terminal β-amino acids from synthetic β-peptides. β-Peptides can form secondary structures mimicking α-peptide-like structures that are resistant to degradation by most known proteases and peptidases. These characteristics of β-peptides give them great potential as peptidomimetics. Here, the X-ray crystal structure of BcA5-BapA, a β-aminopeptidase from a Gram-negative Burkholderia sp. that was isolated from activated sludge from a wastewater-treatment plant in Australia, is reported. The crystal structure of BcA5-BapA was determined to a resolution of 2.0 Å and showed a tetrameric assembly typical of the β-aminopeptidases. Each monomer consists of an α-subunit (residues 1-238) and a β-subunit (residues 239-367). Comparison of the structure of BcA5-BapA with those of other known β-aminopeptidases shows a highly conserved structure and suggests a similar proteolytic mechanism of action.

Cryoprotection properties of salts of organic acids: a case study for a tetragonal crystal of HEW lysozyme.

Science.gov (United States)

Bujacz, Grzegorz; Wrzesniewska, Blanka; Bujacz, Anna

2010-07-01

Currently, the great majority of the data that are used for solving macromolecular structures by X-ray crystallography are collected at cryogenic temperatures. Selection of a suitable cryoprotectant, which ensures crystal stability at low temperatures, is critical for the success of a particular diffraction experiment. The effectiveness of salts of organic acids as potential cryoprotective agents is presented in the following work. Sodium formate, acetate, malonate and citrate were tested, as were sodium potassium tartrate and acetate in the form of potassium and ammonium salts. For each salt investigated, the minimal concentration that was required for successful cryoprotection was determined over the pH range 4.5-9.5. The cryoprotective ability of these organic salts depends upon the number of carboxylic groups; the lowest concentration required for cryoprotection was observed at neutral pH. Case-study experiments conducted using the tetragonal form of hen egg-white lysozyme (HEWL) confirmed that salts of organic acids can successfully act as cryoprotective agents of protein crystals grown from high concentrations of inorganic salts. When crystals are grown from solutions containing a sufficient concentration of organic acid salts no additional cryoprotection is needed as the crystals can safely be frozen directly from the crystallizing buffers.

Comparison of NMR and crystal structures highlights conformational isomerism in protein active sites

International Nuclear Information System (INIS)

Serrano, Pedro; Pedrini, Bill; Geralt, Michael; Jaudzems, Kristaps; Mohanty, Biswaranjan; Horst, Reto; Herrmann, Torsten; Elsliger, Marc-André; Wilson, Ian A.; Wüthrich, Kurt

2010-01-01

Tools for systematic comparisons of NMR and crystal structures developed by the JCSG were applied to two proteins with known functions: the T. maritima anti-σ factor antagonist TM1081 and the mouse γ-glutamylamine cyclotransferase A2LD1 (gi:13879369). In an attempt to exploit the complementarity of crystal and NMR data, the combined use of the two structure-determination techniques was explored for the initial steps in the challenge of searching proteins of unknown functions for putative active sites. The JCSG has recently developed a protocol for systematic comparisons of high-quality crystal and NMR structures of proteins. In this paper, the extent to which this approach can provide function-related information on the two functionally annotated proteins TM1081, a Thermotoga maritima anti-σ factor antagonist, and A2LD1 (gi:13879369), a mouse γ-glutamylamine cyclotransferase, is explored. The NMR structures of the two proteins have been determined in solution at 313 and 298 K, respectively, using the current JCSG protocol based on the software package UNIO for extensive automation. The corresponding crystal structures were solved by the JCSG at 100 K and 1.6 Å resolution and at 100 K and 1.9 Å resolution, respectively. The NMR and crystal structures of the two proteins share the same overall molecular architectures. However, the precision of the structure determination along the amino-acid sequence varies over a significantly wider range in the NMR structures than in the crystal structures. Thereby, in each of the two NMR structures about 65% of the residues have displacements below the average and in both proteins the less well ordered residues include large parts of the active sites, in addition to some highly solvent-exposed surface areas. Whereas the latter show increased disorder in the crystal and in solution, the active-site regions display increased displacements only in the NMR structures, where they undergo local conformational exchange on the

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

Science.gov (United States)

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

Cloning, sequencing, purification, and crystal structure of Grenache (Vitis vinifera) polyphenol oxidase.

Science.gov (United States)

Virador, Victoria M; Reyes Grajeda, Juan P; Blanco-Labra, Alejandro; Mendiola-Olaya, Elizabeth; Smith, Gary M; Moreno, Abel; Whitaker, John R

2010-01-27

The full-length cDNA sequence (P93622_VITVI) of polyphenol oxidase (PPO) cDNA from grape Vitis vinifera L., cv Grenache, was found to encode a translated protein of 607 amino acids with an expected molecular weight of ca. 67 kDa and a predicted pI of 6.83. The translated amino acid sequence was 99%, identical to that of a white grape berry PPO (1) (5 out of 607 amino acid potential sequence differences). The protein was purified from Grenache grape berries by using traditional methods, and it was crystallized with ammonium acetate by the hanging-drop vapor diffusion method. The crystals were orthorhombic, space group C222(1). The structure was obtained at 2.2 A resolution using synchrotron radiation using the 39 kDa isozyme of sweet potato PPO (PDB code: 1BT1 ) as a phase donor. The basic symmetry of the cell parameters (a, b, and c and alpha, beta, and gamma) as well as in the number of asymmetric units in the unit cell of the crystals of PPO, differed between the two proteins. The structures of the two enzymes are quite similar in overall fold, the location of the helix bundles at the core, and the active site in which three histidines bind each of the two catalytic copper ions, and one of the histidines is engaged in a thioether linkage with a cysteine residue. The possibility that the formation of the Cys-His thioether linkage constitutes the activation step is proposed. No evidence of phosphorylation or glycoslyation was found in the electron density map. The mass of the crystallized protein appears to be only 38.4 kDa, and the processing that occurs in the grape berry that leads to this smaller size is discussed.

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

International Nuclear Information System (INIS)

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

2001-01-01

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

Crystal structure of dimethylammonium hydrogen oxalate hemi(oxalic acid

Directory of Open Access Journals (Sweden)

Waly Diallo

2015-05-01

Full Text Available Single crystals of the title salt, Me2NH2+·HC2O4−·0.5H2C2O4, were isolated as a side product from the reaction involving Me2NH, H2C2O4 and Sn(n-Bu3Cl in a 1:2 ratio in methanol or by the reaction of the (Me2NH22C2O4 salt and Sn(CH33Cl in a 2:1 ratio in ethanol. The asymmetric unit comprises a dimethylammonium cation (Me2NH2+, an hydrogenoxalate anion (HC2O4−, and half a molecule of oxalic acid (H2C2O4 situated about an inversion center. From a supramolecular point of view, the three components interact together via hydrogen bonding. The Me2NH2+ cations and the HC2O4− anions are in close proximity through bifurcated N—H...(O,O hydrogen bonds, while the HC2O4− anions are organized into infinite chains via O—H...O hydrogen bonds, propagating along the a-axis direction. In addition, the oxalic acid (H2C2O4 molecules play the role of connectors between these chains. Both the carbonyl and hydroxyl groups of each diacid are involved in four intermolecular interactions with two Me2NH2+ and two HC2O4− ions of four distinct polymeric chains, via two N—H...O and two O—H...O hydrogen bonds, respectively. The resulting molecular assembly can be viewed as a two-dimensional bilayer-like arrangement lying parallel to (010, and reinforced by a C—H...O hydrogen bond.

Crystal structures of hibiscus acid and hibiscus acid dimethyl ester isolated from Hibiscus sabdariffa (Malvaceae)

OpenAIRE

Zheoat, Ahmed M.; Gray, Alexander I.; Igoli, John O.; Kennedy, Alan R.; Ferro, Valerie A.

2017-01-01

The biologically active title compounds have been isolated from Hibiscus sabdariffa plants, hibiscus acid as a dimethyl sulfoxide monosolvate [systematic name: (2S,3R)-3-hy?droxy-5-oxo-2,3,4,5-tetra?hydro?furan-2,3-di?carb?oxy?lic acid dimethyl sulfoxide monosolvate], C6H6O7?C2H6OS, (I), and hibiscus acid dimethyl ester [systematic name: dimethyl (2S,3R)-3-hy?droxy-5-oxo-2,3,4,5-tetra?hydro?furan-2,3-di?carboxyl?ate], C8H10O7, (II). Compound (I) forms a layered structure with alternating laye...

Reaction of hydrazine hydrate with oxalic acid: synthesis and crystal structure of dihydrazinium oxalate

OpenAIRE

Selvakumar, Rajendran; Premkumar, Thathan; Manivannan, Vadivelu; Saravanan, Kaliannan; Govindarajan, Subbiah

2014-01-01

The reaction of oxalic acid with hydrazine hydrate (in appropriate mole ratio) forms the dihydrazinium oxalate under specific experimental condition. The title compound is a molecular salt containing two discrete hydrazinium cations and an oxalate anion. The oxalate anion is perfectly planar and there is a crystallographic centre of symmetry in the middle of the C-C bond. The C-O bond distances are almost equal indicating the presence of resonance in the oxalate ion. The crystal packing is st...

The crystal structure and twinning of neodymium gallium perovskite single crystals

International Nuclear Information System (INIS)

Ubizskii, S.B.; Vasylechko, L.O.; Savytskii, D.I.; Matkovskii, A.O.; Syvorotka, I.M.

1994-01-01

By means of X-ray structure analysis, the crystal structure of neodymium gallium perovskite (NGP) single crystals (NdGaO 3 ) being used as a substrate for HTSC film epitaxy has been refined and the position of atoms has been determined. The possibility of YBa 2 Cu 3 O 7-x film epitaxy on the plane (110) of NGP crystal as well as its advantages and pitfalls are analysed from structural data. The twinning types in the NGP crystal were established. The twinning structure of NGP substrates is found to be stable up to a temperature of 1173 K, as differentiated from the LaGaO 3 and LaAlO 3 substrates. It is intimated that the twinning in the NGP substrates oriented as (001) can result in creation of 90 degrees twin bonds in a film, and in the case of (110)-oriented plates it is possible to ignore the twinning presence in substrate completely. (author)

Crystallization and preliminary X-ray crystallographic studies of a Lys49-phospholipase A{sub 2} homologue from Bothrops pirajai venom complexed with rosmarinic acid

Energy Technology Data Exchange (ETDEWEB)

Santos, Juliana I. dos [Departamento de Física e Biofísica, Instituto de Biociências, UNESP - Universidade Estadual Paulista, Botucatu-SP (Brazil); Instituto Nacional de Ciência e Tecnologia em Toxinas, CNPq (Brazil); Santos-Filho, Norival A.; Soares, Andreimar M. [Instituto Nacional de Ciência e Tecnologia em Toxinas, CNPq (Brazil); Departamento de Análizes Clínicas, Toxicológicas e Bromatológicas, FCFRP, USP, Ribeirão Preto-SP (Brazil); Fontes, Marcos R. M., [Departamento de Física e Biofísica, Instituto de Biociências, UNESP - Universidade Estadual Paulista, Botucatu-SP (Brazil); Instituto Nacional de Ciência e Tecnologia em Toxinas, CNPq (Brazil)

2010-06-01

PrTX-I, a noncatalytic and myotoxic Lys49-phospholipase A{sub 2} from B. pirajai venom, was cocrystallized with the inhibitor rosmarinic acid from C. verbenacea. The crystals diffracted X-rays to 1.8 Å resolution and the structure was solved, indicating a remarkable electronic density for the ligand at the entrance to the hydrophobic channel. PrTX-I, a noncatalytic and myotoxic Lys49-phospholipase A{sub 2} from Bothrops pirajai venom, was crystallized in the presence of the inhibitor rosmarinic acid (RA). This is the active compound in the methanolic extract of Cordia verbenacea, a plant that is largely used in Brazilian folk medicine. The crystals diffracted X-rays to 1.8 Å resolution and the structure was solved by molecular-replacement techniques, showing electron density that corresponds to RA molecules at the entrance to the hydrophobic channel. The crystals belong to space group P2{sub 1}2{sub 1}2{sub 1}, indicating conformational changes in the structure after ligand binding: the crystals of all apo Lys49-phospholipase A{sub 2} structures belong to space group P3{sub 1}21, while the crystals of complexed structures belong to space groups P2{sub 1} or P2{sub 1}2{sub 1}2{sub 1}.

Structural and electronic properties of L-amino acids

Science.gov (United States)

Tulip, P. R.; Clark, S. J.

2005-05-01

The structural and electronic properties of four L-amino acids alanine, leucine, isoleucine, and valine have been investigated using density functional theory (DFT) and the generalized gradient approximation. Within the crystals, it is found that the constituent molecules adopt zwitterionic configurations, in agreement with experimental work. Lattice constants are found to be in good agreement with experimentally determined values, although certain discrepancies do exist due to the description of van der Waals interactions. We find that these materials possess wide DFT band gaps in the region of 5 eV, with electrons highly localized to the constituent molecules. It is found that the main mechanisms behind crystal formation are dipolar interactions and hydrogen bonding of a primarily electrostatic character, in agreement with current biochemical understanding of these systems. The electronic structure suggests that the amine and carboxy functional groups are dominant in determining band structure.

Amino acids and glycine ethyl ester as new crystallization reagents for lysozyme

International Nuclear Information System (INIS)

Ito, Len; Shiraki, Kentaro; Yamaguchi, Hiroshi

2010-01-01

During the past two decades, amino acids and amino-acid derivatives have been applied in various fields of protein chemistry. The potential use of amino acids and their derivatives as new precipitating agents is described. Several amino acids and their derivatives are prominent additives in the field of protein chemistry. This study reports the use of charged amino acids and glycine ethyl ester as precipitants in protein crystallization, using hen egg-white lysozyme (HEWL) as a model. A discussion of the crystallization of HEWL using these reagents as precipitating agents is given

Interference effects from coexisting fatty acids on elaidic acid separation by fractionating crystallization: A model study

DEFF Research Database (Denmark)

Jala, Ram Chandra Reddy; Guo, Zheng; Bjerring, Thomas

2010-01-01

A multi-stage temperature-programmed fractionating crystallization process was carried out to examine the effects of the presence of stearic acid (SA), oleic acid (OA), and linoleic acid (LA) on the separation of elaidic acid (EA). The results showed that the efficiency of fractionating...

Alignment structures in ferroelectric liquid crystals

Energy Technology Data Exchange (ETDEWEB)

Islam, N.U

1998-07-01

Although for many years liquid crystals were of purely scientific interest, they have now become ubiquitous in everyday life. The use of the nematic liquid crystal phase in flat panel display applications has been the main factor in this popularity. However, with the advent of the SuperTwist Nematic (STN) device, the limits to which this phase could be exploited for display applications was perhaps reached. With the discovery by Clark et al. of the Surface Stabilised Ferroelectric Liquid Crystal (SSFLC) configuration, the possibility arose of using chiral smectic liquid crystals to create large area, passively addressed, fast switching, flat panel displays. Unfortunately, the structures that form within smectic liquid crystals, and the dynamics of the switching within these, are still not fully understood. In this thesis we address the former of these, making a detailed the study of the structures that form within tilted smectic liquid crystal devices. We present here the first complete theoretical and experimental study of various different ferroelectric liquid crystal materials, where we employed theoretical models based on a simple set of assumptions to understand the behaviour of a set of increasingly complex experimental systems. We started with the simplest of these, Freely Suspended Smectic Films (FSSFs) and then worked with progressively more realistic systems in the form of homeotropically, and later, homogeneously aligned liquid crystal cells. The equilibrium structures that form get particularly complex in the last case, taking the form of tilted and chevron layering structures. In each of these cases, the predictions of the modelling are compared with our experimental results. Further, we present here the first model of the chevron cusp that seeks to include the effects of biaxiality in the S{sub C} phase. We also present a model that seeks to analyse the stability of the chevron layering structure and its relationship with tilted layers. This includes

Alignment structures in ferroelectric liquid crystals

International Nuclear Information System (INIS)

Islam, N.U.

1998-01-01

Although for many years liquid crystals were of purely scientific interest, they have now become ubiquitous in everyday life. The use of the nematic liquid crystal phase in flat panel display applications has been the main factor in this popularity. However, with the advent of the SuperTwist Nematic (STN) device, the limits to which this phase could be exploited for display applications was perhaps reached. With the discovery by Clark et al. of the Surface Stabilised Ferroelectric Liquid Crystal (SSFLC) configuration, the possibility arose of using chiral smectic liquid crystals to create large area, passively addressed, fast switching, flat panel displays. Unfortunately, the structures that form within smectic liquid crystals, and the dynamics of the switching within these, are still not fully understood. In this thesis we address the former of these, making a detailed the study of the structures that form within tilted smectic liquid crystal devices. We present here the first complete theoretical and experimental study of various different ferroelectric liquid crystal materials, where we employed theoretical models based on a simple set of assumptions to understand the behaviour of a set of increasingly complex experimental systems. We started with the simplest of these, Freely Suspended Smectic Films (FSSFs) and then worked with progressively more realistic systems in the form of homeotropically, and later, homogeneously aligned liquid crystal cells. The equilibrium structures that form get particularly complex in the last case, taking the form of tilted and chevron layering structures. In each of these cases, the predictions of the modelling are compared with our experimental results. Further, we present here the first model of the chevron cusp that seeks to include the effects of biaxiality in the S C phase. We also present a model that seeks to analyse the stability of the chevron layering structure and its relationship with tilted layers. This includes an

Improved purification, crystallization and primary structure of pyruvate:ferredoxin oxidoreductase from Halobacterium halobium.

Science.gov (United States)

Plaga, W; Lottspeich, F; Oesterhelt, D

1992-04-01

An improved purification procedure, including nickel chelate affinity chromatography, is reported which resulted in a crystallizable pyruvate:ferredoxin oxidoreductase preparation from Halobacterium halobium. Crystals of the enzyme were obtained using potassium citrate as the precipitant. The genes coding for pyruvate:ferredoxin oxidoreductase were cloned and their nucleotide sequences determined. The genes of both subunits were adjacent to one another on the halobacterial genome. The derived amino acid sequences were confirmed by partial primary structure analysis of the purified protein. The structural motif of thiamin-diphosphate-binding enzymes was unequivocally located in the deduced amino acid sequence of the small subunit.

Copper(II) complexes with 4-(1H-1, 2, 4-trizol-1-ylmethyl) benzoic acid: Syntheses, crystal structures and antifungal activities

Energy Technology Data Exchange (ETDEWEB)

Xiong, Pingping [Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi' an 710069 (China); Li, Jie [Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), Shaanxi Provincial Key Laboratory of Biotechnology, Xi' an 710069 (China); Bu, Huaiyu, E-mail: 7213792@qq.com [Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), Shaanxi Provincial Key Laboratory of Biotechnology, Xi' an 710069 (China); Wei, Qing [Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi' an 710069 (China); Zhang, Ruolin [Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), Shaanxi Provincial Key Laboratory of Biotechnology, Xi' an 710069 (China); Chen, Sanping, E-mail: sanpingchen@126.com [Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi' an 710069 (China)

2014-07-01

Reaction of Cu(II) with an asymmetric semi-rigid organic ligand 4-(1H-1, 2, 4-trizol-1-ylmethyl) benzoic acid (HL), yielded five compounds, [Cu{sub 0.5}L]{sub n} (1), [Cu(HL){sub 2}Cl{sub 2}]{sub n} (2), [Cu(HL){sub 2}Cl{sub 2}(H{sub 2}O)] (3), [Cu(L){sub 2}(H{sub 2}O)]{sub n} (4) and [Cu(L)(phen)(HCO{sub 2})]{sub n} (5), which have been fully characterized by infrared spectroscopy, elemental analysis, and single-crystal X-ray diffraction. As for compounds 1, 2 and 5, Cu(II) is bridged through HL, Cl{sup -}, and formic acid, respectively, featuring 1D chain-structure. In compound 3, Cu(II) with hexahedral coordination sphere is assembled through hydrogen-bonding into 3D supramolecular framework. In compound 4, 1D chain units –Cu–O–Cu–O– are ligand-bridged into a 3D network. All compounds were tested on fungi (Fusarium graminearum, Altemaria solani, Macrophoma kawatsukai, Alternaria alternata and Colletotrichum gloeosporioides). Compound 1 exhibits a better antifungal effect compared to other compounds. An effect of structure on the antifungal activity has also been correlated. - Graphical abstract: Copper(II) compounds with 4-(1H-1, 2, 4-trizol-1-ylmethyl) benzoic acid, were prepared, structurally characterized and investigated for antifungal activity. - Highlights: • The title compounds formed by thermodynamics and thermokinetics. • The five compounds show higher inhibition percentage than reactants. • The structure effect on the antifungal activity.

Crystal structure of the HA3 subcomponent of Clostridium botulinum type C progenitor toxin.

Science.gov (United States)

Nakamura, Toshio; Kotani, Mao; Tonozuka, Takashi; Ide, Azusa; Oguma, Keiji; Nishikawa, Atsushi

2009-01-30

The Clostridium botulinum type C 16S progenitor toxin contains a neurotoxin and several nontoxic components, designated nontoxic nonhemagglutinin (HA), HA1 (HA-33), HA2 (HA-17), HA3a (HA-22-23), and HA3b (HA-53). The HA3b subcomponent seems to play an important role cooperatively with HA1 in the internalization of the toxin by gastrointestinal epithelial cells via binding of these subcomponents to specific oligosaccharides. In this study, we investigated the sugar-binding specificity of the HA3b subcomponent using recombinant protein fused to glutathione S-transferase and determined the three-dimensional structure of the HA3a-HA3b complex based on X-ray crystallography. The crystal structure was determined at a resolution of 2.6 A. HA3b contains three domains, domains I to III, and the structure of domain I resembles HA3a. In crystal packing, three HA3a-HA3b molecules are assembled to form a three-leaved propeller-like structure. The three HA3b domain I and three HA3a alternate, forming a trimer of dimers. In a database search, no proteins with high structural homology to any of the domains (Z score >10) were found. Especially, HA3a and HA3b domain I, mainly composed of beta-sheets, reveal a unique fold. In binding assays, HA3b bound sialic acid with high affinity, but did not bind galactose, N-acetylgalactosamine, or N-acetylglucosamine. The electron density of liganded N-acetylneuraminic acid was determined by crystal soaking. In the sugar-complex structure, the N-acetylneuraminic acid-binding site was located in the cleft formed between domains II and III of HA3b. This report provides the first determination of the three-dimensional structure of the HA3a-HA3b complex and its sialic acid binding site. Our results will provide useful information for elucidating the mechanism of assembly of the C16S toxin and for understanding the interactions with oligosaccharides on epithelial cells and internalization of the botulinum toxin complex.

Influence of media with different acidity on structure of FeNi nanotubes

Science.gov (United States)

Shumskaya, Alena; Kaniukov, Egor; Kutuzau, Maksim; Bundyukova, Victoria; Tulebayeva, Dinara; Kozlovskiy, Artem; Borgekov, Daryn; Kenzhina, Inesh; Zdorovets, Maxim

2018-04-01

A detailed analysis of the structure features of FeNi nanotubes exposed at environment with different acidity is carried out. It is demonstrated that the exposure of the nanostructures in the environment with high acidity causes the structure deformation, leading to sharply increasing of the presents of oxide phases and partial amorphization of nanotubes walls that determined the rate of FeNi nanotubes destruction. It was established that the evolution of the crystal structure parameters concerned with appearance of oxide phases and with formation of disorder regions as a result of oxidation processes.

Structural coloration of chitosan-cationized cotton fabric using photonic crystals

Science.gov (United States)

Yavuz, G.; Zille, A.; Seventekin, N.; Souto, A. P.

2017-10-01

In this work, poly (styrene-methyl methacrylate-acrylic acid) P(St-MMA-AA) composite nanospheres were deposited onto chitosan-cationized woven cotton fabrics followed by a second layer of chitosan. The deposited photonic crystals (PCs) on the fabrics were evaluated for coating efficiency and resistance, chemical analysis and color variation by optical and SEM microscopy, ATR-FTIR, diffuse reflectance spectroscopy and washing fastness. Chitosan deposition on cotton fabric provided cationic groups on the fiber surface promoting electrostatic interaction with photonic crystals. SEM images of the washed samples indicate that the PCs are firmly coated on the cotton surface only in the chitosan treated sample. The photonic nanospheres show an average diameter of 280 nm and display a face-centered cubic closepacking structure with an average thickness of 10 μm. A further chitosan post-treatment enhances color yield of the samples due to the chitosan transparent covering layer that induce bright reflections where the angles of incidence and reflection are the same. After washing, no photonic crystal can be detected on control fabric surface. However, the sample that received a chitosan post-treatment showed a good washing fastness maintaining a reasonable degree of iridescence. Chitosan fills the spaces between the polymer spheres in the matrix stabilizing the photonic structure. Sizeable variations in lattice spacing will allow color variations using more flexible non-close-packed photonic crystal arrays in chitosan hydrogels matrices.

Two new coordination polymers based on tartaric acid ligand: Syntheses, crystal structure and thermal stability

Energy Technology Data Exchange (ETDEWEB)

Chen, Fei-Yan; Lan, You-Zhao, E-mail: sky37@zjnu.cn; Han, Min-Min; Feng, Yun-Long, E-mail: lyzhao@zjnu.cn [Zhejiang Normal University, Zhejiang Key Laboratory for Reactive Chemistry on Solid Surfaces, Institute of Physical Chemistry (China)

2016-09-15

Two new coordination polymers [Cd{sub 3}(D-Tar){sub 3}]{sub n} (1) and [Pb(meso-Tar)]{sub n} (2) (H{sub 2}Tar = tartaric acid) have been synthesized by hydrothermal reaction and characterized by single crystal X-ray diffraction analysis and IR spectra. 1 crystallizes in the C222{sub 1} chiral space group and shows a 3D (4,4)-connected net with the (4.6.8{sup 4}){sub 4}(4.6{sup 2}.8{sup 2}.10)(4.6{sup 2}.8{sup 3})(4.6{sup 3}.8{sup 2})(4.6{sup 3}.8{sup 2}){sub 4}(4.8{sup 5}){sub 2} topology. 2 possesses a 3D (4,4)-connected net with the (4{sup 3}.6{sup 2}.8) topology. In addition, the thermogravimetric analyses (TGA) results for polymers are discussed.

Application of GPCR Structures for Modelling of Free Fatty Acid Receptors.

Science.gov (United States)

Tikhonova, Irina G

2017-01-01

Five G protein-coupled receptors (GPCRs) have been identified to be activated by free fatty acids (FFA). Among them, FFA1 (GPR40) and FFA4 (GPR120) bind long-chain fatty acids, FFA2 (GPR43) and FFA3 (GPR41) bind short-chain fatty acids and GPR84 binds medium-chain fatty acids. Free fatty acid receptors have now emerged as potential targets for the treatment of diabetes, obesity and immune diseases. The recent progress in crystallography of GPCRs has now enabled the elucidation of the structure of FFA1 and provided reliable templates for homology modelling of other FFA receptors. Analysis of the crystal structure and improved homology models, along with mutagenesis data and structure activity, highlighted an unusual arginine charge-pairing interaction in FFA1-3 for receptor modulation, distinct structural features for ligand binding to FFA1 and FFA4 and an arginine of the second extracellular loop as a possible anchoring point for FFA at GPR84. Structural data will be helpful for searching novel small-molecule modulators at the FFA receptors.

Revelation of endogenously bound Fe{sup 2+} ions in the crystal structure of ferritin from Escherichia coli

Energy Technology Data Exchange (ETDEWEB)

Thiruselvam, Viswanathan [Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025 (India); Sivaraman, Padavattan [RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148 (Japan); Kumarevel, Thirumananseri, E-mail: kumarevel.thirumananseri@riken.jp [RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148 (Japan); Structural Biology Laboratory, RIKEN Yokohama Institute, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045 (Japan); Ponnuswamy, Mondikalipudur Nanjappagounder, E-mail: mnpsy2004@yahoo.com [Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025 (India)

2014-10-24

Highlights: • Crystal structure of ferritin was determined. • Endogenously expressed iron’s were identified. • Binuclear iron sites were observed at A and B active sites. - Abstract: Ferritin is an iron regulatory protein. It is responsible for storage and detoxification of excess iron thereby it regulates iron level in the body. Here we report the crystal structure of ferritin with two endogenously expressed Fe atoms binding in both the sites. The protein was purified and characterized by MALDI-TOF and N-terminal amino acid sequencing. The crystal belongs to I4 space group and it diffracted up to 2.5 Å. The structural analysis suggested that it crystallizes as hexamer and confirmed that it happened to be the first report of endogenously expressed Fe ions incorporated in both the A and B sites, situated in between the helices.

Crystal Structure, Fluorescence Property and Theoretical Calculation of the Zn(II) Complex with o-Aminobenzoic Acid and 1,10-Phenanthroline

International Nuclear Information System (INIS)

Zhang, Zhongyu; Bi, Caifeng; Fan, Yuhua; Zhang, Xia; Zhang, Nan; Yan, Xingchen; Zuo, Jian

2014-01-01

A novel complex [Zn(phen)(o-AB) 2 ] [phen: 1,10-phenanthroline o-AB: o-aminobenzoic acid] was synthesized and characterized by elemental analysis and X-ray diffraction single-crystal analysis. The crystal crystallizes in monoclinic, space group P2(1)/c with a = 7.6397(6) A, b = 16.8761(18) A, c = 17.7713(19) A, α = 90 .deg., β = 98.9570(10) .deg., γ = 90 .deg., V = 2.2633(4) nm 3 , Z = 4, F(000) = 1064, S = 1.058, Dc = 1.520 g·cm -3 , R 1 = 0.0412, wR 2 = 0.0948, μ = 1.128 mm -1 . The Zn(II) is six coordinated by two nitrogen and four oxygen atoms from the 1,10-phenanthroline and o-aminobenzoic acid to furnish a distorted octahedron geometry. The complex exhibits intense fluorescence at room temperature. Theoretical studies of the title complex were carried out by density functional theory (DFT) B3LYP method. CCDC: 898291

Ambazone-lipoic acid salt: Structural and thermal characterization

Energy Technology Data Exchange (ETDEWEB)

Kacso, Irina [National Institute for Research and Development of Isotopic and Molecular Technologies, 65-103 Donath street, 400293 Cluj-Napoca (Romania); Racz, Csaba-Pal; Santa, Szabolcs [Babes-Bolyai' University, Faculty of Chemistry, 11 Arany Janos street, Cluj-Napoca (Romania); Rus, Lucia [' Iuliu Hatieganu' University of Medicine and Pharmacy, Faculty of Pharmacy, 6 Louis Pasteur street, 400349 Cluj-Napoca (Romania); Dadarlat, Dorin; Borodi, Gheorghe [National Institute for Research and Development of Isotopic and Molecular Technologies, 65-103 Donath street, 400293 Cluj-Napoca (Romania); Bratu, Ioan, E-mail: ibratu@gmail.com [National Institute for Research and Development of Isotopic and Molecular Technologies, 65-103 Donath street, 400293 Cluj-Napoca (Romania)

2012-12-20

Highlights: Black-Right-Pointing-Pointer Salt of Ambazone with lipoic acid obtained by solvent-drop grinding. Black-Right-Pointing-Pointer Ambazone lipoate salt crystallizes in monoclinic system. Black-Right-Pointing-Pointer FTIR data suggest the deprotonation of the lipoic acid. Black-Right-Pointing-Pointer Thermal behaviour different of ambazone salt as compared to the starting compounds. - Abstract: A suitable method for increasing the solubility, dissolution rate and consequently the bioavailability of poor soluble acidic or basic drugs is their salt formation. The aim of this study is to investigate the structural and thermal properties of the compound obtained by solvent drop grinding (SDG) method at room temperature, starting from the 1:1 molar ratios of ambazone (AMB) and {alpha}-lipoic acid (LA). The structural characterization was performed with X-ray powder diffraction (XRPD) and infrared spectroscopy (FTIR). The thermal behaviour of the obtained compound (AMB{center_dot}LA) was investigated by differential scanning calorimetry (DSC) and thermogravimetry (TG). The photopyroelectric calorimetry, in front detection configuration (FPPE), was applied to measure and compare the room temperature values of one dynamic thermal parameter (thermal effusivity) for starting and resulting compounds. Both structural and supporting calorimetric techniques pointed out a salt structure for AMB{center_dot}LA compound as compared to those of the starting materials.

Controlled synthesis of multi-morphology Te crystals by a convenient Lewis acid/base-assisted solvothermal method

International Nuclear Information System (INIS)

Wu Xiaoping; Yuan Lin; Zhou Shaomin; Lou Shiyun; Wang Yongqiang; Gao Tao; Liu YuBiao; Shi Xiaojing

2012-01-01

This paper reports on the controlled growth of multi-morphology Te crystals by a convenient Lewis acid/base-assisted solvothermal method for the first time. The morphological transformation from one-dimension (1D) nanostructures to 2D hierarchical flowerlike microarchitecture has been observed. The nanorods and nanowires with a well-defined crystallographical structure and the hierarchical flowers microarchitecture were obtained by changing the Lewis acids/bases. Lewis acids/bases were found to be crucial for the formation of the products by not only acting as the pH regulator but also as the shape controller, owing to their hydrolysis in the solvent to in situ form H + /OH − and hydrates. The results suggest that this should be an effective approach to the control the growth of t-Te crystals with interesting multiple morphologies, which are of interest for both theoretical investigations and practical applications.

Crystal Structure and Substrate Specificity of Drosophila 3,4-Dihydroxyphenylalanine Decarboxylase

Energy Technology Data Exchange (ETDEWEB)

Han, Q.; Ding, H; Robinson, H; Christensen, B; Li, J

2010-01-01

3,4-Dihydroxyphenylalanine decarboxylase (DDC), also known as aromatic L-amino acid decarboxylase, catalyzes the decarboxylation of a number of aromatic L-amino acids. Physiologically, DDC is responsible for the production of dopamine and serotonin through the decarboxylation of 3,4-dihydroxyphenylalanine and 5-hydroxytryptophan, respectively. In insects, both dopamine and serotonin serve as classical neurotransmitters, neuromodulators, or neurohormones, and dopamine is also involved in insect cuticle formation, eggshell hardening, and immune responses. In this study, we expressed a typical DDC enzyme from Drosophila melanogaster, critically analyzed its substrate specificity and biochemical properties, determined its crystal structure at 1.75 Angstrom resolution, and evaluated the roles residues T82 and H192 play in substrate binding and enzyme catalysis through site-directed mutagenesis of the enzyme. Our results establish that this DDC functions exclusively on the production of dopamine and serotonin, with no activity to tyrosine or tryptophan and catalyzes the formation of serotonin more efficiently than dopamine. The crystal structure of Drosophila DDC and the site-directed mutagenesis study of the enzyme demonstrate that T82 is involved in substrate binding and that H192 is used not only for substrate interaction, but for cofactor binding of drDDC as well. Through comparative analysis, the results also provide insight into the structure-function relationship of other insect DDC-like proteins.

Crystal structure and substrate specificity of Drosophila 3,4-dihydroxyphenylalanine decarboxylase.

Directory of Open Access Journals (Sweden)

Qian Han

2010-01-01

Full Text Available 3,4-Dihydroxyphenylalanine decarboxylase (DDC, also known as aromatic L-amino acid decarboxylase, catalyzes the decarboxylation of a number of aromatic L-amino acids. Physiologically, DDC is responsible for the production of dopamine and serotonin through the decarboxylation of 3,4-dihydroxyphenylalanine and 5-hydroxytryptophan, respectively. In insects, both dopamine and serotonin serve as classical neurotransmitters, neuromodulators, or neurohormones, and dopamine is also involved in insect cuticle formation, eggshell hardening, and immune responses.In this study, we expressed a typical DDC enzyme from Drosophila melanogaster, critically analyzed its substrate specificity and biochemical properties, determined its crystal structure at 1.75 Angstrom resolution, and evaluated the roles residues T82 and H192 play in substrate binding and enzyme catalysis through site-directed mutagenesis of the enzyme. Our results establish that this DDC functions exclusively on the production of dopamine and serotonin, with no activity to tyrosine or tryptophan and catalyzes the formation of serotonin more efficiently than dopamine.The crystal structure of Drosophila DDC and the site-directed mutagenesis study of the enzyme demonstrate that T82 is involved in substrate binding and that H192 is used not only for substrate interaction, but for cofactor binding of drDDC as well. Through comparative analysis, the results also provide insight into the structure-function relationship of other insect DDC-like proteins.

Structure and Chemical Durability of Lead Crystal Glass.

Science.gov (United States)

Angeli, Frédéric; Jollivet, Patrick; Charpentier, Thibault; Fournier, Maxime; Gin, Stéphane

2016-11-01

Silicate glasses containing lead, also called lead crystal glasses, are commonly used as food product containers, in particular for alcoholic beverages. Lead's health hazards require major attention, which can first be investigated through the understanding of Pb release mechanisms in solution. The behavior of a commercial crystal glass containing 10.6 mol % of PbO (28.3 wt %) was studied in a reference solution of 4% acetic acid at 22, 40, and 70 °C at early and advanced stages of reaction. High-resolution solid-state 17 O and 29 Si NMR was used to probe the local structure of the pristine and, for the first time, of the altered lead crystal glass. Inserted into the vitreous structure between the network formers as Si-O-Pb bonds, Pb does not form Pb-O-Pb clusters which are expected to be more easily leached. A part of K is located near Pb, forming mixed Si-O-(Pb,K) near the nonbridging oxygens. Pb is always released into the solution following a diffusion-controlled dissolution over various periods of time, at a rate between 1 and 2 orders of magnitude lower than the alkalis (K and Na). The preferential release of alkalis is followed by an in situ repolymerization of the silicate network. Pb is only depleted in the outermost part of the alteration layer. In the remaining part, it stays mainly surrounded by Si in a stable structural configuration similar to that of the pristine glass. A simple model is proposed to estimate the Pb concentration as a function of glass surface, solution volume, temperature, and contact time.

Three-Dimentional Structures of Autophosphorylation Complexes in Crystals of Protein Kinases

KAUST Repository

Dumbrack, Roland

2016-01-26

Protein kinase autophosphorylation is a common regulatory mechanism in cell signaling pathways. Several autophosphorylation complexes have been identified in crystals of protein kinases, with a known serine, threonine, or tyrosine autophosphorylation site of one kinase monomer sitting in the active site of another monomer of the same protein in the crystal. We utilized a structural bioinformatics method to identify all such autophosphorylation complexes in X-ray crystallographic structures in the Protein Data Bank (PDB) by generating all unique kinase/kinase interfaces within and between asymmetric units of each crystal and measuring the distance between the hydroxyl oxygen of potential autophosphorylation sites and the oxygen atoms of the active site aspartic acid residue side chain. We have identified 15 unique autophosphorylation complexes in the PDB, of which 5 complexes have not previously been described in the relevant publications on the crystal structures (N-terminal juxtamembrane regions of CSF1R and EPHA2, activation loop tyrosines of LCK and IGF1R, and a serine in a nuclear localization signal region of CLK2. Mutation of residues in the autophosphorylation complex interface of LCK either severely impaired autophosphorylation or increased it. Taking the autophosphorylation complexes as a whole and comparing them with peptide-substrate/kinase complexes, we observe a number of important features among them. The novel and previously observed autophosphorylation sites are conserved in many kinases, indicating that by homology we can extend the relevance of these complexes to many other clinically relevant drug targets.

Deducing 2D crystal structure at the liquid/solid interface with atomic resolution: a combined STM and SFG study.

Science.gov (United States)

McClelland, Arthur A; Ahn, Seokhoon; Matzger, Adam J; Chen, Zhan

2009-11-17

Sum frequency generation vibrational spectroscopy (SFG) has been applied to study two-dimensional (2D) crystals formed by an isophthalic acid diester on the surface of highly oriented pyrolytic graphite, providing complementary measurements to scanning tunneling microscopy (STM) and computational modeling. SFG results indicate that both aromatic and C=O groups in the 2D crystal tilt from the surface. This study demonstrates that a combination of SFG and STM techniques can be used to gain a more complete picture of 2D crystal structure, and it is necessary to consider solvent-2D crystal interactions and dynamics in the computer models to achieve an accurate representation of interfacial structure.

The solid-state structures of organic salts formed by calix[4]arene dihydroxyphosphonic acid with nucleic bases cations: adeninium, cytosinium, guaninium and uracilium

KAUST Repository

Shkurenko, Aleksander

2018-02-19

Calix[4]arene dihydroxyphosphonic acid has been demonstrated to possess an interesting range of biological properties, including atypical anti-cancer activity. The robustness of calix[4]arene dihydroxyphosphonic acid and its ubiquitous dimeric motif offers perspectives for pre-defined solid state complexation with small molecules. In the current article we describe co-crystals (organic salts) of calix[4]arene dihydroxyphosphonic acid with four nucleic base cations: adeninium, cytosinium, guaninium and uracilium. A number of characteristic interactions between the components in the four co-crystals are pointed out also using the Hirshfeld surface analysis. All the four co-crystals are based on layers of calix[4]arene dimers, alternating with layers of nucleic acid molecules. Two of the reported crystal structures (cytosinium and guaninium) are 1D channel-type structures, while the two others (adeninium and uracilium) represent 2D channel-type structures. In three out of four reported structures, interactions between the cations of nucleic bases are present generating 1D chains of cations. A constant motif is that the nucleic base is present in a type of cavity formed by one aromatic ring and a phosphonic acid moiety.

Synthesis and crystal structure of novel fluorescent 1,3,4-oxadiazole-containing carboxylate ligands

Science.gov (United States)

Mikhailov, Igor E.; Popov, Leonid D.; Tkachev, Valery V.; Aldoshin, Sergey M.; Dushenko, Galina A.; Revinskii, Yurii V.; Minkin, Vladimir I.

2018-04-01

Novel chelating ligands, 3-(5-aryl-1,3,4-oxadiazol-2-yl)acrylic acids and their zinc complexes were synthesized and their spectral and luminescent properties studied. The compounds intensively (quantum efficiencies φ = 0.18-0.76) luminesce in nonpolar solvents in the blue-green region (λmaxPL = 458-504 nm) of the spectrum. Molecular and crystal structures of 3-[5-(4-dimethylaminophenyl)-1,3,4-oxadiazol-2-yl]acrylic acid were established using X-ray crystallography. In crystal, the infinite chains of the molecules lie in the parallel planes and are arranged by the "head to tail" type to provide for strong π-π stacking interactions between the layers facilitating appearance of high electron transport properties and formation of excimers.

Synthesis, crystal structure, and magnetic properties of two-dimensional divalent metal glutarate/dipyridylamine coordination polymers, with a single crystal-to-single crystal transformation in the copper derivative

International Nuclear Information System (INIS)

Montney, Matthew R.; Supkowski, Ronald M.; Staples, Richard J.; LaDuca, Robert L.

2009-01-01

Hydrothermal reaction of divalent metal chlorides with glutaric acid and 4,4'-dipyridylamine (dpa) has afforded an isostructural family of coordination polymers with formulation [M(glu)(dpa)] n (M=Co (1), Ni (2), Cu (3); glu=glutarate). Square pyramidal coordination is seen in 1-3, with semi-ligation of a sixth donor to produce a '5+1' extended coordination sphere. Neighboring metal atoms are linked into 1D [M(glu)] n neutral chains through chelating/monodentate bridging glutarate moieties with a syn-anti binding mode, and semi-chelation of the pendant carboxylate oxygen. These chains further connect into 2D layers through dipodal dpa ligands. Neighboring layers stack into the pseudo 3D crystal structure of 1-3 through supramolecular hydrogen bonding between dpa amine units and the semi-chelated glutarate oxygen atoms. The variable temperature magnetic behavior of 1-3 was explored and modeled as infinite 1D Heisenberg chains. Notably, complex 3 undergoes a thermally induced single crystal-to-single crystal transformation between centric and acentric space groups, with a conformationally disordered unilayer structure at 293 K and an ordered bilayer structure at 173 K. All materials were further characterized via infrared spectroscopy and elemental and thermogravimetric analyses. - Graphical abstract: The coordination polymers [M(glu)(dpa)] n (M=Co (1), Ni (2), Cu (3); glu=glutarate, dpa=4,4'-dipyridylamine) exhibit 2D layer structures based on 1D [M(glu)] n chains linked through dpa tethers. Antiferromagnetic coupling is observed for 2 and 3, while ferromagnetism is predominant in 1. Compound 3 undergoes a thermally induced single crystal-to-single crystal transformation from an acentric to a centrosymmetric space group

Free radicals in dicarboxylic acids: an e.s.r. study of radical conversions in γ-irradiated single crystals of glutaric acid and glutaric-2,2,4,4-d4 acid

International Nuclear Information System (INIS)

Bergene, R.; Minegishi, A.; Riesz, P.

1980-01-01

The γ-radiation-induced free radicals in single crystals of glutaric acid and glutaric-2,2,4,4-d 4 acid were studied in the temperature range 77-300 K by e.s.r. techniques. At 77 K the decarboxylation radical and the anion are stabilized. At higher temperatures the decarboxylation radical is found to be converted into a hydrogen abstraction radical with an activation energy of 6.3 +- 0.5 kcal/mole for the non-deuterated crystal. This radical is stable at room temperature. The anion seems to be converted to a unidentified intermediate radical which in turn is converted to the σ-acyl radical. An analysis of the g-value anisotropy and of the 13 C hyperfine splitting variation for this radical in the deuterated crystal is consistent with the assigned radical structure. By heat treatment the σ-acyl radical is converted to another form of the hydrogen abstraction radical with an activation energy of 9.6 +- 0.6 kcal/mole in the deuterated crystal. U.V.-light (lambda= 254 nm) transforms one of the room temperature radicals into the other. (author)

Thermal, dielectric studies on pure and amino acid ( L-glutamic acid, L-histidine, L-valine) doped KDP single crystals

Science.gov (United States)

Kumaresan, P.; Moorthy Babu, S.; Anbarasan, P. M.

2008-05-01

Amino acids ( L-glutamic acid, L-histidine, L-valine) doped potassium dihydrogen phospate crystals are grown by solution growth technique. Slow cooling as well as slow evaporation methods were employed to grow these crystals. The concentration of dopants in the mother solution was varied from 0.1 mol% to 10 mol%. The solubility data for all dopants concentration were determined. There is variation in pH value and hence, there is habit modification of the grown crystals were characterized with UV-VIS, FT-IR studies, SHG trace elements and dielectric studies reveal slight distortion of lattice parameter for the heavily doped KDP crystals. UV-Visible spectra confirm the improvement in the transparency of these crystals on doping metal ions. FT-IR spectra reveal strong absorption band between 1400 and 1600 cm -1 for metal ion doped crystals. TGA-DTA studies reveal good thermal stability. The dopants increase the hardness value of the material and it also depends on the concentration of the dopants. Amino acids doping improved the NLO properties. The detailed results on the spectral parameters, habit modifications and constant values will be presented.

Optically induced structural phase transitions in ion Coulomb crystals

DEFF Research Database (Denmark)

Horak, Peter; Dantan, Aurelien Romain; Drewsen, Michael

2012-01-01

We investigate numerically the structural dynamics of ion Coulomb crystals confined in a three-dimensional harmonic trap when influenced by an additional one-dimensional optically induced periodical potential. We demonstrate that transitions between thermally excited crystal structures, such as b......We investigate numerically the structural dynamics of ion Coulomb crystals confined in a three-dimensional harmonic trap when influenced by an additional one-dimensional optically induced periodical potential. We demonstrate that transitions between thermally excited crystal structures...

Influence of media with different acidity on structure of FeNi nanotubes

Directory of Open Access Journals (Sweden)

Shumskaya Alena

2018-01-01

Full Text Available A detailed analysis of the structure features of FeNi nanotubes exposed at environment with different acidity is carried out. It is demonstrated that the exposure of the nanostructures in the environment with high acidity causes the structure deformation, leading to sharply increasing of the presents of oxide phases and partial amorphization of nanotubes walls that determined the rate of FeNi nanotubes destruction. It was established that the evolution of the crystal structure parameters concerned with appearance of oxide phases and with formation of disorder regions as a result of oxidation processes.

Crystal structures of three classes of non-steroidal anti-inflammatory drugs in complex with aldo-keto reductase 1C3.

Directory of Open Access Journals (Sweden)

Jack U Flanagan

Full Text Available Aldo-keto reductase 1C3 (AKR1C3 catalyses the NADPH dependent reduction of carbonyl groups in a number of important steroid and prostanoid molecules. The enzyme is also over-expressed in prostate and breast cancer and its expression is correlated with the aggressiveness of the disease. The steroid products of AKR1C3 catalysis are important in proliferative signalling of hormone-responsive cells, while the prostanoid products promote prostaglandin-dependent proliferative pathways. In these ways, AKR1C3 contributes to tumour development and maintenance, and suggest that inhibition of AKR1C3 activity is an attractive target for the development of new anti-cancer therapies. Non-steroidal anti-inflammatory drugs (NSAIDs are one well-known class of compounds that inhibits AKR1C3, yet crystal structures have only been determined for this enzyme with flufenamic acid, indomethacin, and closely related analogues bound. While the flufenamic acid and indomethacin structures have been used to design novel inhibitors, they provide only limited coverage of the NSAIDs that inhibit AKR1C3 and that may be used for the development of new AKR1C3 targeted drugs. To understand how other NSAIDs bind to AKR1C3, we have determined ten crystal structures of AKR1C3 complexes that cover three different classes of NSAID, N-phenylanthranilic acids (meclofenamic acid, mefenamic acid, arylpropionic acids (flurbiprofen, ibuprofen, naproxen, and indomethacin analogues (indomethacin, sulindac, zomepirac. The N-phenylanthranilic and arylpropionic acids bind to common sites including the enzyme catalytic centre and a constitutive active site pocket, with the arylpropionic acids probing the constitutive pocket more effectively. By contrast, indomethacin and the indomethacin analogues sulindac and zomepirac, display three distinctly different binding modes that explain their relative inhibition of the AKR1C family members. This new data from ten crystal structures greatly broadens

A new crystal lattice structure of Helicobacter pylori neutrophil-activating protein (HP-NAP)

International Nuclear Information System (INIS)

Tsuruta, Osamu; Yokoyama, Hideshi; Fujii, Satoshi

2012-01-01

A new crystal lattice structure of H. pylori neutrophil-activating protein has been determined. Iron loading causes a series of conformational changes at the ferroxidase centre. A new crystal lattice structure of Helicobacter pylori neutrophil-activating protein (HP-NAP) has been determined in two forms: the native state (Apo) at 2.20 Å resolution and an iron-loaded form (Fe-load) at 2.50 Å resolution. The highly solvated packing of the dodecameric shell is suitable for crystallographic study of the metal ion-uptake pathway. Like other bacterioferritins, HP-NAP forms a spherical dodecamer with 23 symmetry including two kinds of channels. Iron loading causes a series of conformational changes of amino-acid residues (Trp26, Asp52 and Glu56) at the ferroxidase centre

Damage and recovery of skin barrier function after glycolic acid chemical peeling and crystal microdermabrasion.

Science.gov (United States)

Song, Ji Youn; Kang, Hyun A; Kim, Mi-Yeon; Park, Young Min; Kim, Hyung Ok

2004-03-01

Superficial chemical peeling and microdermabrasion have become increasingly popular methods for producing facial rejuvenation. However, there are few studies reporting the skin barrier function changes after these procedures. To evaluate objectively the degree of damage visually and the time needed for the skin barrier function to recover after glycolic acid peeling and aluminum oxide crystal microdermabrasion using noninvasive bioengineering methods. Superficial chemical peeling using 30%, 50%, and 70% glycolic acid and aluminum oxide crystal microdermabrasion were used on the volar forearm of 13 healthy women. The skin response was measured by a visual observation and using an evaporimeter, corneometer, and colorimeter before and after peeling at set time intervals. Both glycolic acid peeling and aluminum oxide crystal microdermabrasion induced significant damage to the skin barrier function immediately after the procedure, and the degree of damage was less severe after the aluminum oxide crystal microdermabrasion compared with glycolic acid peeling. The damaged skin barrier function had recovered within 24 hours after both procedures. The degree of erythema induction was less severe after the aluminum oxide crystal microdermabrasion compared with the glycolic acid peeling procedure. The degree of erythema induced after the glycolic acid peeling procedure was not proportional to the peeling solution concentration used. The erythema subsided within 1 day after the aluminum oxide crystal microdermabrasion procedure and within 4 days after the glycolic acid peeling procedure. These results suggest that the skin barrier function is damaged after the glycolic acid peeling and aluminum oxide crystal microdermabrasion procedure but recovers within 1 to 4 days. Therefore, repeating the superficial peeling procedure at 2-week intervals will allow sufficient time for the damaged skin to recover its barrier function.

What makes a crystal structure report valid?

NARCIS (Netherlands)

Spek, Anthony L.|info:eu-repo/dai/nl/156517566

2018-01-01

Single crystal X-ray crystallography has developed into a unique, highly automated and accessible tool to obtain detailed information on molecular structures. Proper archival makes that referees, readers and users of the results of reported crystal structures no longer need to depend solely on the

Is the fenamate group a polymorphophore?: contrasting the crystal energy landscapes of fenamic and tolfenamic acids

NARCIS (Netherlands)

Uzoh, O.G.; Cruz-Cabeza, A.J.; Price, S. L.

2012-01-01

The concept of a polymorphophore was investigated by contrasting the crystal energy landscapes of monomorphic fenamic acid (2-(phenylamino)-benzoic acid, FA) and one of its highly polymorphic derivatives, tolfenamic acid (2-[(3-chloro-2-methylphenyl)amino]-benzoic acid, TA). The crystal energy

SYNTHESIS, CHARACTERIZATION AND CRYSTAL STRUCTURES ...

African Journals Online (AJOL)

B. S. Chandravanshi

ABSTRACT. Reaction of [VO(acac)2] (acac = acetylacetonate) with ... Single crystal X-ray structural studies indicate that the hydrazone ligands coordinate to ..... Molecular structure of complex (1) at 30% probability displacement. Figure 4.

Crystal structure of the yeast nicotinamidase Pnc1p.

Science.gov (United States)

Hu, Gang; Taylor, Alexander B; McAlister-Henn, Lee; Hart, P John

2007-05-01

The yeast nicotinamidase Pnc1p acts in transcriptional silencing by reducing levels of nicotinamide, an inhibitor of the histone deacetylase Sir2p. The Pnc1p structure was determined at 2.9A resolution using MAD and MIRAS phasing methods after inadvertent crystallization during the pursuit of the structure of histidine-tagged yeast isocitrate dehydrogenase (IDH). Pnc1p displays a cluster of surface histidine residues likely responsible for its co-fractionation with IDH from Ni(2+)-coupled chromatography resins. Researchers expressing histidine-tagged proteins in yeast should be aware of the propensity of Pnc1p to crystallize, even when overwhelmed in concentration by the protein of interest. The protein assembles into extended helical arrays interwoven to form an unusually robust, yet porous superstructure. Comparison of the Pnc1p structure with those of three homologous bacterial proteins reveals a common core fold punctuated by amino acid insertions unique to each protein. These insertions mediate the self-interactions that define the distinct higher order oligomeric states attained by these molecules. Pnc1p also acts on pyrazinamide, a substrate analog converted by the nicotinamidase from Mycobacterium tuberculosis into a product toxic to that organism. However, we find no evidence for detrimental effects of the drug on yeast cell growth.

Crystallization, X-ray diffraction analysis and preliminary structure determination of the polygalacturonase PehA from Agrobacterium vitis

International Nuclear Information System (INIS)

Vordtriede, Paul B.; Yoder, Marilyn D.

2008-01-01

The acidic polygalacturonase PehA from A. vitis has been crystallized. A molecular-replacement solution indicated a right-handed parallel β-helix fold. Polygalacturonases are pectate-degrading enzymes that belong to glycoside hydrolase family 28 and hydrolyze the α-1,4 glycosidic bond between neighboring galacturonasyl residues of the homogalacturonan substrate. The acidic polygalacturonase PehA from Agrobacterium vitis was overexpressed in Escherichia coli, where it accumulated in the periplasmic fraction. It was purified to homogeneity via a two-step chromatography procedure and crystallized using the hanging-drop vapour-diffusion technique. PehA crystals belonged to space group P2 1 , with unit-cell parameters a = 52.387, b = 62.738, c = 149.165 Å, β = 89.98°. Crystals diffracted to 1.59 Å resolution and contained two molecules per asymmetric unit. An initial structure determination by molecular replacement indicated a right-handed parallel β-helix fold

Fundamentals of poly(lactic acid) microstructure, crystallization behavior, and properties

Science.gov (United States)

Kang, Shuhui

Poly(lactic acid) is an environmentally-benign biodegradable and sustainable thermoplastic material, which has found broad applications as food packaging films and as non-woven fibers. The crystallization and deformation mechanisms of the polymer are largely determined by the distribution of conformation and configuration. Knowledge of these mechanisms is needed to understand the mechanical and thermal properties on which processing conditions mainly depend. In conjunction with laser light scattering, Raman spectroscopy and normal coordinate analysis are used in this thesis to elucidate these properties. Vibrational spectroscopic theory, Flory's rotational isomeric state (RIS) theory, Gaussian chain statistics and statistical mechanics are used to relate experimental data to molecular chain structure. A refined RIS model is proposed, chain rigidity recalculated and chain statistics discussed. A Raman spectroscopic characterization method for crystalline and amorphous phase orientation has been developed. A shrinkage model is also proposed to interpret the dimensional stability for fibers and uni- or biaxially stretched films. A study of stereocomplexation formed by poly(l-lactic acid) and poly(d-lactic acid) is also presented.

Crystal structure from one-electron theory

DEFF Research Database (Denmark)

Skriver, H. L.

1985-01-01

The authors have studied the crystal structure of all the 3d, 4d, and 5d transition metals at zero pressure and temperature by means of the linear muffin-tin orbital method and Andersen's force theorem. They find that, although the structural energy differences seem to be overestimated by the the......The authors have studied the crystal structure of all the 3d, 4d, and 5d transition metals at zero pressure and temperature by means of the linear muffin-tin orbital method and Andersen's force theorem. They find that, although the structural energy differences seem to be overestimated...

Poly(methacrylic acid)-mediated morphosynthesis of PbWO4 micro-crystals

International Nuclear Information System (INIS)

Yu, J.G.; Zhao, X.F.; Liu, S.W.; Li, M.; Mann, S.; Ng, D.H.L.

2007-01-01

PbWO 4 crystals with various morphologies were fabricated via a facile poly(methacrylic acid)-mediated hydrothermal route. Novel microsized PbWO 4 single crystals with a needle-like shape as well as other morphologies, such as a fishbone, dendrite, sphere, spindle, ellipsoid, rod, and dumbbell with two dandelion-like heads, could be produced. The presence of PMAA, [Pb 2+ ]/[WO 4 2- ] molar ratio (R), and aging temperature played key roles in the formation of the PbWO 4 needle-like structures. Between temperatures of 60 to 150 C, the length and photoluminescence intensities of the PbWO 4 micro needles significantly increased with aging temperature, while the diameter did not change remarkably. Time-dependent experiments revealed that the formation of PbWO 4 microneedles involved an unusual growth process, involving nucleation, oriented assembly and controlled mesoscale restructuring of nanoparticle building blocks. (orig.)

Topotactic decomposition and crystal structure of white molybdenum trioxide--monohydrate: prediction of structure by topotaxy

International Nuclear Information System (INIS)

Oswald, H.R.; Guenter, J.R.; Dubler, E.

1975-01-01

Single crystals of the white MoO 3 . H 2 O modification (''α-molybdic acid'') were transformed by heating to 160 0 C into perfect pseudomorphs built up from oriented MoO 3 crystallites of known structure. From the mutual orientation relationship of the unit cells of both phases involved in this topotactic reaction, as determined by X-ray photographs, a model for the so far unknown crystal structure of white MoO 3 . H 2 O could be deduced. Independently, this structure was determined by X-ray diffractometer data then: space group P anti 1, a = 7.388, b = 3.700, c = 6.673 A, α = 107.8, β = 113.6, γ = 91.2 0 , Z = 2. The structure was solved from the Patterson function and refined until R = 0.088. It is built up from isolated double chains of strongly distorted [MoO 5 (H 2 O)]-octahedra sharing two common edges with each other. This result agrees well with the model derived from topotaxy, and it becomes evident how the MoO 3 lattice is formed through corner linking of the isolated double chains after the water molecules are removed. The study of topotactic phenomena seems rather generally applicable to deduce the main features of structures involved and for better understanding of structural relationships. (U.S.)

Crystal structures of hibiscus acid and hibiscus acid dimethyl ester isolated from Hibiscus sabdariffa (Malvaceae).

Science.gov (United States)

Zheoat, Ahmed M; Gray, Alexander I; Igoli, John O; Kennedy, Alan R; Ferro, Valerie A

2017-09-01

The biologically active title compounds have been isolated from Hibiscus sabdariffa plants, hibiscus acid as a dimethyl sulfoxide monosolvate [systematic name: (2 S ,3 R )-3-hy-droxy-5-oxo-2,3,4,5-tetra-hydro-furan-2,3-di-carb-oxy-lic acid dimethyl sulfoxide monosolvate], C 6 H 6 O 7 ·C 2 H 6 OS, (I), and hibiscus acid dimethyl ester [systematic name: dimethyl (2 S ,3 R )-3-hy-droxy-5-oxo-2,3,4,5-tetra-hydro-furan-2,3-di-carboxyl-ate], C 8 H 10 O 7 , (II). Compound (I) forms a layered structure with alternating layers of lactone and solvent mol-ecules, that include a two-dimensional hydrogen-bonding construct. Compound (II) has two crystallographically independent and conformationally similar mol-ecules per asymmetric unit and forms a one-dimensional hydrogen-bonding construct. The known absolute configuration for both compounds has been confirmed.

Crystal Structure of Allophycocyanin from Marine Cyanobacterium Phormidium sp. A09DM.

Directory of Open Access Journals (Sweden)

Ravi Raghav Sonani

Full Text Available Isolated phycobilisome (PBS sub-assemblies have been widely subjected to X-ray crystallography analysis to obtain greater insights into the structure-function relationship of this light harvesting complex. Allophycocyanin (APC is the phycobiliprotein always found in the PBS core complex. Phycocyanobilin (PCB chromophores, covalently bound to conserved Cys residues of α- and β- subunits of APC, are responsible for solar energy absorption from phycocyanin and for transfer to photosynthetic apparatus. In the known APC structures, heterodimers of α- and β- subunits (known as αβ monomers assemble as trimer or hexamer. We here for the first time report the crystal structure of APC isolated from a marine cyanobacterium (Phormidium sp. A09DM. The crystal structure has been refined against all the observed data to the resolution of 2.51 Å to Rwork (Rfree of 0.158 (0.229 with good stereochemistry of the atomic model. The Phormidium protein exists as a trimer of αβ monomers in solution and in crystal lattice. The overall tertiary structures of α- and β- subunits, and trimeric quaternary fold of the Phormidium protein resemble the other known APC structures. Also, configuration and conformation of the two covalently bound PCB chromophores in the marine APC are same as those observed in fresh water cyanobacteria and marine red algae. More hydrophobic residues, however, constitute the environment of the chromophore bound to α-subunit of the Phormidium protein, owing mainly to amino acid substitutions in the marine protein.

SYNTHESIS, CHARACTERIZATION AND CRYSTAL STRUCTURE ...

African Journals Online (AJOL)

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Reaction of [MoO2(acac)2] (where acac = acetylacetonate) with N'-(2-hydroxy-4- ... Single crystal X-ray structural studies indicate that the hydrazone ligand coordinates .... Molecular structure of the complex at 30% probability displacement.

Crystal structure refinement with SHELXL

Energy Technology Data Exchange (ETDEWEB)

Sheldrick, George M., E-mail: gsheldr@shelx.uni-ac.gwdg.de [Department of Structural Chemistry, Georg-August Universität Göttingen, Tammannstraße 4, Göttingen 37077 (Germany)

2015-01-01

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

Two-dimensional photonic crystal accelerator structures

Directory of Open Access Journals (Sweden)

Benjamin M. Cowan

2003-10-01

Full Text Available Photonic crystals provide a method of confining a synchronous speed-of-light mode in an all-dielectric structure, likely a necessary feature in any optical accelerator. We explore computationally a class of photonic crystal structures with translational symmetry in a direction transverse to the electron beam. We demonstrate synchronous waveguide modes and discuss relevant parameters of such modes. We then explore how accelerator parameters vary as the geometry of the structure is changed and consider trade-offs inherent in the design of an accelerator of this type.

Two crystal forms of a helix-rich fatty acid- and retinol-binding protein, Na-FAR-1, from the parasitic nematode Necator americanus

International Nuclear Information System (INIS)

Gabrielsen, Mads; Rey-Burusco, M. Florencia; Griffiths, Kate; Roe, Andrew J.; Cooper, Alan; Smith, Brian O.; Kennedy, Malcolm W.; Corsico, Betina

2012-01-01

Na-FAR-1, a fatty acid- and retinol-binding protein, was expressed in bacteria, purified and crystallized. Crystals grew in two different morphologies under the same conditions. Na-FAR-1 is an unusual α-helix-rich fatty acid- and retinol-binding protein from Necator americanus, a blood-feeding intestinal parasitic nematode of humans. It belongs to the FAR protein family, which is unique to nematodes; no structural information is available to date for FAR proteins from parasites. Crystals were obtained with two different morphologies that corresponded to different space groups. Crystal form 1 exhibited space group P432 (unit-cell parameters a = b = c = 120.80 Å, α = β = γ = 90°) and diffracted to 2.5 Å resolution, whereas crystal form 2 exhibited space group F23 (unit-cell parameters a = b = c = 240.38 Å, α = β = γ = 90°) and diffracted to 3.2 Å resolution. Crystal form 2 showed signs of significant twinning

Solving nucleic acid structures by molecular replacement: examples from group II intron studies

International Nuclear Information System (INIS)

Marcia, Marco; Humphris-Narayanan, Elisabeth; Keating, Kevin S.; Somarowthu, Srinivas; Rajashankar, Kanagalaghatta; Pyle, Anna Marie

2013-01-01

Strategies for phasing nucleic acid structures by molecular replacement, using both experimental and de novo designed models, are discussed. Structured RNA molecules are key players in ensuring cellular viability. It is now emerging that, like proteins, the functions of many nucleic acids are dictated by their tertiary folds. At the same time, the number of known crystal structures of nucleic acids is also increasing rapidly. In this context, molecular replacement will become an increasingly useful technique for phasing nucleic acid crystallographic data in the near future. Here, strategies to select, create and refine molecular-replacement search models for nucleic acids are discussed. Using examples taken primarily from research on group II introns, it is shown that nucleic acids are amenable to different and potentially more flexible and sophisticated molecular-replacement searches than proteins. These observations specifically aim to encourage future crystallographic studies on the newly discovered repertoire of noncoding transcripts

Crystal structures of thiosemicarbazide diacetic acid and coordination compounds on its basis

International Nuclear Information System (INIS)

Burshtejn, I.F.; Petukhov, L.I.; Gehrbehlehu, N.V.; Volodina, G.F.; Bologa, O.A.

1985-01-01

Results of X-ray structure investigation of thiosemicarbazide diacetic acid (H 2 tscda) and its complex derivatives of the composition Mtscda (M=Cd, Co, Cu) have been reviewed. Structure characteristics of Cdtscdax4H 2 O are as follows: a=14.513, b=8.648, c=9.871 A, γ=98.46 deg, sp.gr. P2 1 /a, z=4. Cadmium complex structure represents a centrosymmetrical dimer with bridge oxygen atom of carboxylic group. Cd-Cd distance is 3.815 A. Cd atom has coordination number 7. Coordination Cd-polyhedron in the structure has configuration of trigonal one-cap prism

Crystallization and preliminary X-ray diffraction analysis of central structure domains from mumps virus F protein

International Nuclear Information System (INIS)

Liu, Yueyong; Xu, Yanhui; Zhu, Jieqing; Qiu, Bingsheng; Rao, Zihe; Gao, George F.; Tien, Po

2005-01-01

Single crystals of the central structure domains from mumps virus F protein have been obtained by the hanging-drop vapour-diffusion method. A diffraction data set has been collected to 2.2 Å resolution. Fusion of members of the Paramyxoviridae family involves two glycoproteins: the attachment protein and the fusion protein. Changes in the fusion-protein conformation were caused by binding of the attachment protein to the cellular receptor. In the membrane-fusion process, two highly conserved heptad-repeat (HR) regions, HR1 and HR2, are believed to form a stable six-helix coiled-coil bundle. However, no crystal structure has yet been determined for this state in the mumps virus (MuV, a member of the Paramyxoviridae family). In this study, a single-chain protein consisting of two HR regions connected by a flexible amino-acid linker (named 2-Helix) was expressed, purified and crystallized by the hanging-drop vapour-diffusion method. A complete X-ray data set was obtained in-house to 2.2 Å resolution from a single crystal. The crystal belongs to space group C2, with unit-cell parameters a = 161.2, b = 60.8, c = 40.1 Å, β = 98.4°. The crystal structure will help in understanding the molecular mechanism of Paramyxoviridae family membrane fusion

Oxidation kinetics of crystal violet by potassium permanganate in acidic medium

Science.gov (United States)

Khan, Sameera Razi; Ashfaq, Maria; Mubashir; Masood, Summyia

2016-05-01

The oxidation kinetics of crystal violet (a triphenylmethane dye) by potassium permanganate was focused in an acidic medium by the spectrophotometric method at 584 nm. The oxidation reaction of crystal violet by potassium permanganate is carried out in an acidic medium at different temperatures ranging within 298-318 K. The kinetic study was carried out to investigate the effect of the concentration, ionic strength and temperature. The reaction followed first order kinetics with respect to potassium permanganate and crystal violet and the overall rate of the reaction was found to be second order. Thermodynamic activation parameters like the activation energy ( E a), enthalpy change (Δ H*), free energy change (Δ G*), and entropy change (Δ S*) have also been evaluated.

Solid-state actinide acid phosphites from phosphorous acid melts

International Nuclear Information System (INIS)

Oh, George N.; Burns, Peter C.

2014-01-01

The reaction of UO 3 and H 3 PO 3 at 100 °C and subsequent reaction with dimethylformamide (DMF) produces crystals of the compound (NH 2 (CH 3 ) 2 )[UO 2 (HPO 2 OH)(HPO 3 )]. This compound crystallizes in space group P2 1 /n and consists of layers of uranyl pentagonal bipyramids that share equatorial vertices with phosphite units, separated by dimethylammonium. In contrast, the reaction of phosphorous acid and actinide oxides at 210 °C produces a viscous syrup. Subsequent dilution in solvents and use of standard solution-state methods results in the crystallization of two polymorphs of the actinide acid phosphites An(HPO 2 OH) 4 (An=U, Th) and of the mixed acid phosphite–phosphite U(HPO 3 )(HPO 2 OH) 2 (H 2 O)·2(H 2 O). α- and β-An(HPO 2 OH) 4 crystallize in space groups C2/c and P2 1 /n, respectively, and comprise a three-dimensional network of An 4+ cations in square antiprismatic coordination corner-sharing with protonated phosphite units, whereas U(HPO 3 )(HPO 2 OH) 2 (H 2 O) 2 ·(H 2 O) crystallizes in a layered structure in space group Pbca that is composed of An 4+ cations in square antiprismatic coordination corner-sharing with protonated phosphites and water ligands. We discuss our findings in using solid inorganic reagents to produce a solution-workable precursor from which solid-state compounds can be crystallized. - Graphical abstract: Reaction of UO 3 and H 3 PO 3 at 100 °C and subsequent reaction with DMF produces crystals of (NH 2 (CH 3 ) 2 )[UO 2 (HPO 2 OH)(HPO 3 )] with a layered structure. Reaction of phosphorous acid and actinide oxides at 210 °C produces a viscous syrup and further solution-state reactions result in the crystallization of the actinide acid phosphites An(HPO 2 OH) 4 (An=U, Th), with a three-dimensional network structure, and the mixed acid phosphite–phosphite U(HPO 3 )(HPO 2 OH) 2 (H 2 O) 2 ·(H 2 O) with a layered structure. - Highlights: • U(VI), U(IV) and Th(IV) phosphites were synthesized by solution

Photonics of liquid-crystal structures: A review

Energy Technology Data Exchange (ETDEWEB)

Palto, S. P., E-mail: palto@online.ru; Blinov, L M; Barnik, M I; Lazarev, V V; Umanskii, B A; Shtykov, N M [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)

2011-07-15

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

Synthesis and Molecular Structures of (E-non-2-enoic Acid and (E-dec-2-enoic Acid

Directory of Open Access Journals (Sweden)

Marcel Sonneck

2015-10-01

Full Text Available The molecular structures of (E-non-2-enoic acid (C9 and (E-dec-2-enoic acid (C10 are reported. The title compounds were crystallized by slow evaporation of ethanolic solutions at −30 °C. C9 crystallizes in the monoclinic space group P21/c and C10 in the triclinic space group P-1, each with 4 molecules in the unit cell. The unit cell parameters for C9 are: a = 10.6473(4 Å, b = 5.2855(2 Å, c = 17.0313(7 Å; β = 106.0985(10° and V = 920.87(6 Å3. The unit cell parameters for C10 are: a = 4.1405(2 Å, b = 15.2839(6 Å, c = 17.7089(7 Å; α = 68.3291(11°, β = 83.3850(13°, γ = 85.0779(12° and V = 1033.39(8 Å3.

Three coordination polymers constructed from 5-(4-(tetrazol-5-yl)phenyl)isophthalic acid: Synthesis, crystal structure and properties

Science.gov (United States)

Zhai, Dandan; Sun, Wujuan; Fan, Fei; Liao, Xuzhao; Chen, Sanping; Yang, Xuwu

2017-04-01

Three new coordination polymers, namely, {[Co2(TPA)(μ3-O)3]·0.5DMA}n (1), {[Co(H2TPA)(bibp)(H2O)3]·H2O}n (2) and {[Cd3(TPA)2(phen)4]·4H2O}n (3), (H3TPA = 5-(4-(tetrazol-5-yl)phenyl)isophthalic acid, bibp = 4,4'-bis(imidazolyl)biphenyl, phen = 1,10-phenanthroline and DMA = N,N-dimethylacetamide), have been synthesized under solvothermal conditions and structurally characterized by elemental analysis, IR spectroscopy, powder X-ray diffraction (PXRD) and single-crystal X-ray diffraction analysis. Polymer 1 exhibits a three-dimensional (3D) structure constructed from 5-connected secondary building units (SBUs) [Co3(μ3-O)] and 3-connected H3TPA ligands. Polymer 2 has a 1D zigzag polymer chain connected by H3TPA and bibp ligands. Polymer 3 features an unusual 3D framework with a (3,4,2)-connected {4; 6;8}{4; 62;83} topology. Moreover, the thermal stabilities of 1-3 and photoluminescence properties of 3 have been investigated. Magnetic susceptibility measurements indicate that polymers 1-2 display antiferromagnetic exchange properties.

On the origin of surface imposed anisotropic growth of salicylic and acetylsalicylic acids crystals during droplet evaporation

OpenAIRE

Przybyłek, Maciej; Cysewski, Piotr; Pawelec, Maciej; Ziółkowska, Dorota; Kobierski, Mirosław

2018-01-01

In this paper droplet evaporative crystallization of salicylic acid (SA) and acetylsalicylic acid (ASA) crystals on different surfaces, such as glass, polyvinyl alcohol (PVA), and paraffin was studied. The obtained crystals were analyzed using powder X-ray diffraction (PXRD) technique. In order to better understand the effect of the surface on evaporative crystallization, crystals deposited on glass were scraped off. Moreover, evaporative crystallization of a large volume of solution was perf...

Multicomponent hydrogen-bonding organic solids constructed from 6-hydroxy-2-naphthoic acid and N-heterocycles: Synthesis, structural characterization and synthon discussion

Science.gov (United States)

Zong, Yingxia; Shao, Hui; Pang, Yanyan; Wang, Debao; Liu, Kang; Wang, Lei

2016-07-01

Seven novel multicomponent crystals involving various substituted organic amine molecules and 6-hydroxy-2-naphthoic acid were prepared and characterized by using single crystal X-ray diffraction, infrared and thermogravimetric analyses (TGA). Crystal structures with 1,4-bis(imidazol) butane (L1) 1, 1,4-bis(imidazol-1-ylmethyl)benzene (L2) 2, 1-phenyl piperazine 3, 2-amino-4-hydroxy-6-methyl pyrimidine 4, 4,4'-bipyridine 5, 5,5'-dimethyl-2,2'-dipyridine 6, 2-amino-4,6-dimethyl pyrimidine 7 were determined. Among the seven molecular complexes, total proton transfer from 6-hydroxy-2-naphthoic acid to coformer has occurred in crystals 1-4, while the remaining were cocrystals. X-ray single-crystal structures of these complexes reveal that strong hydrogen bonding O-H···O/N-H···O/O-H···N and weak C-H···O/C-H···π/π···π intermolecular interactions direct the packing modes of molecular crystals together. The analysis of supramolecular synthons in the present structures shows that some classical supramolecular synthons like pyridine-carboxylic acid heterosynthon R22 (7) and aminopyridine-carboxylic acid heterosynthon R22 (8), are again observed in constructing the hydrogen-bonding networks in this paper. Besides, we noticed that water molecules act as a significant hydrogen-bonding connector in constructing supramolecular architectures of 3, 4, 6, and 7.

Structure of the human-heart fatty-acid-binding protein 3 in complex with the fluorescent probe 1-anilinonaphthalene-8-sulphonic acid

Energy Technology Data Exchange (ETDEWEB)

Hirose, Mika; Sugiyama, Shigeru, E-mail: sugiyama@chem.eng.osaka-u.ac.jp [Lipid Active Structure Project, 1-1 Machikaneyama-cho, Toyonaka 560-0043 (Japan); Osaka University, 1-1 Machikaneyama-cho, Toyonaka 560-0043 (Japan); Ishida, Hanako; Niiyama, Mayumi [Lipid Active Structure Project, 1-1 Machikaneyama-cho, Toyonaka 560-0043 (Japan); Osaka University, 2-1 Yamadaoka, Suita 565-0871 (Japan); Matsuoka, Daisuke; Hara, Toshiaki [Lipid Active Structure Project, 1-1 Machikaneyama-cho, Toyonaka 560-0043 (Japan); Osaka University, 1-1 Machikaneyama-cho, Toyonaka 560-0043 (Japan); Mizohata, Eiichi [Osaka University, 2-1 Yamadaoka, Suita 565-0871 (Japan); Murakami, Satoshi [Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama, Kanagaw 226-8501 (Japan); Inoue, Tsuyoshi [Osaka University, 2-1 Yamadaoka, Suita 565-0871 (Japan); Matsuoka, Shigeru; Murata, Michio [Lipid Active Structure Project, 1-1 Machikaneyama-cho, Toyonaka 560-0043 (Japan); Osaka University, 1-1 Machikaneyama-cho, Toyonaka 560-0043 (Japan)

2013-11-01

The crystal structure of human-heart-type fatty-acid-binding protein in complex with anilinonaphthalene-8-sulfonate was solved at 2.15 Å resolution revealing the detailed binding mechanism of the fluorescent probe 1-anilinonaphthalene-8-sulfonate. Heart-type fatty-acid-binding protein (FABP3), which is a cytosolic protein abundantly found in cardiomyocytes, plays a role in trafficking fatty acids throughout cellular compartments by reversibly binding intracellular fatty acids with relatively high affinity. The fluorescent probe 1-anilinonaphthalene-8-sulfonate (ANS) is extensively utilized for examining the interaction of ligands with fatty-acid-binding proteins. The X-ray structure of FABP3 was determined in the presence of ANS and revealed the detailed ANS-binding mechanism. Furthermore, four water molecules were clearly identified in the binding cavity. Through these water molecules, the bound ANS molecule forms indirect hydrogen-bond interactions with FABP3. The adipocyte-type fatty-acid-binding protein (FABP4) exhibits 67% sequence identity with FABP3 and its crystal structure is almost the same as that of FABP3. However, FABP4 can bind with a higher affinity to ANS than FABP3. To understand the difference in their ligand specificities, a structural comparison was performed between FABP3–ANS and FABP4–ANS complexes. The result revealed that the orientation of ANS binding to FABP3 is completely opposite to that of ANS binding to FABP4, and the substitution of valine in FABP4 to leucine in FABP3 may result in greater steric hindrance between the side-chain of Leu115 and the aniline ring of ANS.

Structure of the human-heart fatty-acid-binding protein 3 in complex with the fluorescent probe 1-anilinonaphthalene-8-sulphonic acid

International Nuclear Information System (INIS)

Hirose, Mika; Sugiyama, Shigeru; Ishida, Hanako; Niiyama, Mayumi; Matsuoka, Daisuke; Hara, Toshiaki; Mizohata, Eiichi; Murakami, Satoshi; Inoue, Tsuyoshi; Matsuoka, Shigeru; Murata, Michio

2013-01-01

The crystal structure of human-heart-type fatty-acid-binding protein in complex with anilinonaphthalene-8-sulfonate was solved at 2.15 Å resolution revealing the detailed binding mechanism of the fluorescent probe 1-anilinonaphthalene-8-sulfonate. Heart-type fatty-acid-binding protein (FABP3), which is a cytosolic protein abundantly found in cardiomyocytes, plays a role in trafficking fatty acids throughout cellular compartments by reversibly binding intracellular fatty acids with relatively high affinity. The fluorescent probe 1-anilinonaphthalene-8-sulfonate (ANS) is extensively utilized for examining the interaction of ligands with fatty-acid-binding proteins. The X-ray structure of FABP3 was determined in the presence of ANS and revealed the detailed ANS-binding mechanism. Furthermore, four water molecules were clearly identified in the binding cavity. Through these water molecules, the bound ANS molecule forms indirect hydrogen-bond interactions with FABP3. The adipocyte-type fatty-acid-binding protein (FABP4) exhibits 67% sequence identity with FABP3 and its crystal structure is almost the same as that of FABP3. However, FABP4 can bind with a higher affinity to ANS than FABP3. To understand the difference in their ligand specificities, a structural comparison was performed between FABP3–ANS and FABP4–ANS complexes. The result revealed that the orientation of ANS binding to FABP3 is completely opposite to that of ANS binding to FABP4, and the substitution of valine in FABP4 to leucine in FABP3 may result in greater steric hindrance between the side-chain of Leu115 and the aniline ring of ANS

Crystal structures and vibrational spectra of biuret co-crystals with cyanuric and glutaric acids, discussion of hydrogen bonding involving carbonyl groups

Czech Academy of Sciences Publication Activity Database

Matulková, I.; Mathauserová, J.; Císařová, I.; Němec, I.; Fábry, Jan

2016-01-01

Roč. 231, č. 5 (2016), s. 291-300 ISSN 2194-4946 R&D Projects: GA ČR GA14-05506S Institutional support: RVO:68378271 Keywords : biuret * crystal structure analysis * hydrogen bonding * vibrational spectroscopy * X-ray diffraction Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.179, year: 2016

Comparison of multiple crystal structures with NMR data for engrailed homeodomain

Energy Technology Data Exchange (ETDEWEB)

Religa, Tomasz L. [MRC Centre for Protein Engineering (United Kingdom)], E-mail: tlr25@mrc-lmb.cam.ac.uk

2008-03-15

Two methods are currently available to solve high resolution protein structures-X-ray crystallography and nuclear magnetic resonance (NMR). Both methods usually produce highly similar structures, but small differences between both solutions are always observed. Here the raw NMR data as well as the solved NMR structure were compared to the multiple crystal structures solved for the WT 60 residue three helix bundle engrailed homeodomain (EnHD) and single point mutants. There was excellent agreement between TALOS-predicted and crystal structure-observed dihedral angles and a good agreement for the {sup 3}J(H{sup N}H{sup {alpha}}) couplings for the multiple crystal structures. Around 1% of NOEs were violated for any crystal structure, but no NOE was inconsistent with all of the crystal structures. Violations usually occurred for surface residues or for residues for which multiple discreet conformations were observed between the crystal structures. Comparison of the disorder shown in the multiple crystal structures shows little correlation with dynamics under native conditions for this protein.

Crystallization and preliminary X-ray diffraction analysis of the sialic acid-binding domain (VP8*) of porcine rotavirus strain CRW-8

International Nuclear Information System (INIS)

Scott, Stacy A.; Holloway, Gavan; Coulson, Barbara S.; Szyczew, Alex J.; Kiefel, Milton J.; Itzstein, Mark von; Blanchard, Helen

2005-01-01

The sialic acid-binding domain (VP8*) component of the porcine CRW-8 rotavirus spike protein has been overexpressed in E. coli, purified and co-crystallized with an N-acetylneuraminic acid derivative. X-ray diffraction data have been collected to 2.3 Å, which has enabled determination of the structure by molecular replacement. Rotavirus recognition and attachment to host cells involves interaction with the spike protein VP4 that projects outwards from the surface of the virus particle. An integral component of these spikes is the VP8* domain, which is implicated in the direct recognition and binding of sialic acid-containing cell-surface carbohydrates and facilitates subsequent invasion by the virus. The expression, purification, crystallization and preliminary X-ray diffraction analysis of VP8* from porcine CRW-8 rotavirus is reported. Diffraction data have been collected to 2.3 Å resolution, enabling the determination of the VP8* structure by molecular replacement

Crystallization and preliminary X-ray diffraction analysis of the sialic acid-binding domain (VP8*) of porcine rotavirus strain CRW-8

Energy Technology Data Exchange (ETDEWEB)

Scott, Stacy A. [Institute for Glycomics, Griffith University (Gold Coast Campus) PMB 50, Gold Coast Mail Centre, Queensland 9726 (Australia); Holloway, Gavan; Coulson, Barbara S. [Department of Microbiology and Immunology, The University of Melbourne, Victoria 3010 (Australia); Szyczew, Alex J.; Kiefel, Milton J.; Itzstein, Mark von; Blanchard, Helen, E-mail: h.blanchard@griffith.edu.au [Institute for Glycomics, Griffith University (Gold Coast Campus) PMB 50, Gold Coast Mail Centre, Queensland 9726 (Australia)

2005-06-01

The sialic acid-binding domain (VP8*) component of the porcine CRW-8 rotavirus spike protein has been overexpressed in E. coli, purified and co-crystallized with an N-acetylneuraminic acid derivative. X-ray diffraction data have been collected to 2.3 Å, which has enabled determination of the structure by molecular replacement. Rotavirus recognition and attachment to host cells involves interaction with the spike protein VP4 that projects outwards from the surface of the virus particle. An integral component of these spikes is the VP8* domain, which is implicated in the direct recognition and binding of sialic acid-containing cell-surface carbohydrates and facilitates subsequent invasion by the virus. The expression, purification, crystallization and preliminary X-ray diffraction analysis of VP8* from porcine CRW-8 rotavirus is reported. Diffraction data have been collected to 2.3 Å resolution, enabling the determination of the VP8* structure by molecular replacement.

Crystal growth and structure of L-methionine L-methioninium hydrogen maleate-a new NLO material

International Nuclear Information System (INIS)

Natarajan, Subramanian; Rajan Devi, Neelamagam; Britto Dhas, Sathiya Dhas Martin; Athimoolam, Shanmuganarayanan

2008-01-01

A new organic nonlinear optical (NLO) crystal from the amino acid family, viz., L-methionine L-methioninium hydrogen maleate (LMMM), has been grown by slow evaporation method from aqueous solution. Bulk crystals were grown using submerged seed solution method. The structure was elucidated using the single crystal x-ray diffraction data. The compound crystallized in the space group P2 1 and the unit cell contains a protonated L-methioninium cation and a zwitterionic methionine residue plus a maleate anion. The backbone conformation angles Ψ 1 and Ψ 2 are in cis and trans configurations for both the methionine and methioninium residues, respectively. Amino and carboxyl groups of the methioninium and methionine residues are connected through N-H...O hydrogen bonds leading to a ring R 2 2 (10) motif.

Structure analysis on synthetic emerald crystals

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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.

Structure-property relationships in halogenbenzoic acids: Thermodynamics of sublimation, fusion, vaporization and solubility.

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Zherikova, Kseniya V; Svetlov, Aleksey A; Kuratieva, Natalia V; Verevkin, Sergey P

2016-10-01

Temperature dependences of vapor pressures for 2-, 3-, and 4-bromobenzoic acid, as well as for five isomeric bromo-methylbenzoic acids were studied by the transpiration method. Melting temperatures and enthalpies of fusion for all isomeric bromo-methylbenzoic acids and 4-bromobenzoic acid were measured with a DSC. The molar enthalpies of sublimation and vaporization were derived. These data together with results available in the literature were collected and checked for internal consistency using a group-additivity procedure and results from X-ray structural diffraction studies. Specific (hydrogen bonding) interactions in the liquid and in the crystal phase of halogenbenzoic acids were quantified based on experimental values of vaporization and sublimation enthalpies. Structure-property correlations of solubilities of halogenobenzoic acids with sublimation pressures and sublimation enthalpies were developed and solubilities of bromo-benzoic acids were estimated. These new results resolve much of the ambiguity in the available thermochemical and solubility data on bromobenzoic acids. The approach based on structure property correlations can be applied for the assessment of water solubility of sparingly soluble drugs. Copyright © 2016 Elsevier Ltd. All rights reserved.

Crystal Structure of an L-Carnitine Complex with Pyrogallol[4]arene

International Nuclear Information System (INIS)

Fujisawa, I; Takeuchi, D; Kitamura, Y; Okamoto, R; Aoki, K

2012-01-01

L-Carnitine is essential for the transport of long-chain fatty acids from cytosol into mitochondria for generating metabolic energy. The survey of crystal structures of carnitine-containing proteins in the Protein Data Bank reveals that carnitine can take several conformations with the quarternary trimethylammonium terminal being always bound to aromatic residues through cation-π interactions in acyltransferases or carnitine-binding proteins. In order to demonstrate the importance of cation-π interaction as a carnitine recognition mechanism in the artificial receptor-ligand system that mimics the carnitine-binding sites, we have determined the crystal structure of a complex formed between L-carnitine and pyrogallol[4]arene (pyrogallol cyclic tetramer: PCT) as a carnitine receptor, 2PCT·2(L-carnitine)·4EtOH. There form two crystallographically independent monomeric [PCT·L-carnitine] substructures, which further form an obliquely arranged capsule-like dimeric [PCT·L-carnitine] 2 structure through a pair of O-H (PCT)···O (L-carnitine) hydrogen bonds. This is the first report of PCT complex with chiral molecules. In each of the two monomeric [PCT·L-carnitine] substructures, the L-carnitine molecule takes the elongated form with an intramolecular hydrogen bond between the hydroxyl group and the carboxylate oxygen, and the cationic trimethylammonium moiety is incorporated into the cavity of the bowl-shaped PCT molecule through cation-π interactions. These features are similar to those at the D-carnitine-binding site in the crystal structure of the glycine betaine/carnitine/choline-binding protein complex.

Crystal structure of 2,5-dimethylanilinium salicylate

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A. Mani

2015-09-01

Full Text Available The title molecular salt, C8H12N+·C7H5O3− arose from the proton-transfer reaction between 2,5-xylidine and salicylic acid. In the anion, the dihedral angle between the planes of the aromatic ring and the –CO2− group is 11.08 (8°; this near planarity is consolidated by an intramolecular O—H...O hydrogen bond. In the crystal, the components are connected by N—H...O hydrogen bonds, with all three O atoms in the anion acting as acceptors; the result is a [100] chain. The structure also features weak C—H...O bonds and aromatic π–π stacking [centroid-to-centroid distance = 3.7416 (10 Å] interactions, which lead to a three-dimensional network.

Phosphate recovery through struvite-family crystals precipitated in the presence of citric acid: mineralogical phase and morphology evaluation.

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Perwitasari, D S; Edahwati, L; Sutiyono, S; Muryanto, S; Jamari, J; Bayuseno, A P

2017-11-01

Precipitation strategy of struvite-family crystals is presented in this paper to recover phosphate and potassium from a synthetic wastewater in the presence of citric acid at elevated temperature. The crystal-forming solutions were prepared from crystals of MgCl 2 and NH 4 H 2 PO 4 with a molar ratio of 1:1:1 for Mg +2 , [Formula: see text], and [Formula: see text], and the citric acid (C 6 H 8 O 7 ) was prepared (1.00 and 20.00 ppm) from citric acid crystals. The Rietveld analysis of X-ray powder diffraction pattern confirmed a mixed product of struvite, struvite-(K), and newberyite crystallized at 30°C in the absence of citric acid. In the presence of citric acid at 30° and 40°C, an abundance of struvite and struvite-(K) were observed. A minute impurity of sylvite and potassium peroxide was unexpectedly found in certain precipitates. The crystal solids have irregular flake-shaped morphology, as shown by scanning electron microscopy micrograph. All parameters (citric acid, temperature, pH, Mg/P, and N/P) were deliberately arranged to control struvite-family crystals precipitation.

Crystal structure of plant acetohydroxyacid synthase, the target for several commercial herbicides.

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Garcia, Mario Daniel; Wang, Jian-Guo; Lonhienne, Thierry; Guddat, Luke William

2017-07-01

Acetohydroxyacid synthase (AHAS, EC 2.2.1.6) is the first enzyme in the branched-chain amino acid biosynthesis pathway. Five of the most widely used commercial herbicides (i.e. sulfonylureas, imidazolinones, triazolopyrimidines, pyrimidinyl-benzoates and sulfonylamino-cabonyl-triazolinones) target this enzyme. Here we have determined the first crystal structure of a plant AHAS in the absence of any inhibitor (2.9 Å resolution) and it shows that the herbicide-binding site adopts a folded state even in the absence of an inhibitor. This is unexpected because the equivalent regions for herbicide binding in uninhibited Saccharomyces cerevisiae AHAS crystal structures are either disordered, or adopt a different fold when the herbicide is not present. In addition, the structure provides an explanation as to why some herbicides are more potent inhibitors of Arabidopsis thaliana AHAS compared to AHASs from other species (e.g. S. cerevisiae). The elucidation of the native structure of plant AHAS provides a new platform for future rational structure-based herbicide design efforts. The coordinates and structure factors for uninhibited AtAHAS have been deposited in the Protein Data Bank (www.pdb.org) with the PDB ID code 5K6Q. © 2017 Federation of European Biochemical Societies.

Studies on growth, crystal structure and characterization of novel organic nicotinium trifluoroacetate single crystals

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Dhanaraj, P.V. [Centre for Crystal Growth, SSN College of Engineering, Kalavakkam 603 110 (India); Rajesh, N.P., E-mail: rajeshnp@hotmail.com [Centre for Crystal Growth, SSN College of Engineering, Kalavakkam 603 110 (India); Sundar, J. Kalyana; Natarajan, S. [Department of Physics, Madurai Kamaraj University, Madurai 625 021 (India); Vinitha, G. [Department of Physics, Crescent Engineering College, Chennai 600 048 (India)

2011-09-15

Highlights: {yields} Good quality crystals of nicotinium trifluoroacetate in monoclinic system were grown for first time. {yields} Nicotinium trifluoroacetate crystal exhibits third order nonlinear optical properties. {yields} The optical spectrum of nicotinium trifluoroacetate crystal reveals the wide transmission in the entire range with cutoff wavelength at 286 nm. {yields} Nicotinium trifluoroacetate is a low dielectric constant material. - Abstract: An organic material, nicotinium trifluoroacetate (NTF) was synthesized and single crystals in monoclinic system were grown from aqueous solution for the first time. Its solubility and metastable zone width were estimated. The crystal structure of NTF was analyzed to reveal the molecular arrangements and the formation of hydrogen bonds in the crystal. High-resolution X-ray diffraction rocking curve measurements were performed to analyze the structural perfection of the grown crystals. Functional groups in NTF were identified by Fourier transform infrared spectral analysis. Thermal behaviour and stability of NTF were studied by thermogravimetric and differential thermal analysis and differential scanning calorimetry. Mechanical and dielectric properties of NTF crystals were analyzed. Optical studies reveal that NTF crystals are transparent in the wavelength range 286-1100 nm. The third order nonlinear optical parameters of NTF were derived by the Z-scan technique.

Relationship between mechanical properties and crystal structure in cocrystals and salt of paracetamol.

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Ahmed, Hamzah; Shimpi, Manishkumar R; Velaga, Sitaram P

2017-01-01

Objectives were to study mechanical properties of various solid forms of paracetamol and relate to their crystal structures. Paracetamol form I (PRA), its cocrystals with oxalic acid (PRA-OXA) and 4,4-bipyridine (PRA-BPY) and hydrochloride salt (PRA-HCL) were selected. Cocrystals and salt were scaled-up using rational crystallization methods. The resulting materials were subjected to different solid-state characterizations. The powders were sieved and 90-360 µm sieve fraction was considered. These powders were examined by scanning electron microscopy (SEM) and densities were determined. Tablets were made at applied pressures of 35-180 MPa under controlled conditions and the tablet height, diameter and hardness were measured. Tensile strength and porosity of the tablets were estimated using well known models. Crystal structures of these systems were visualized and slip planes were identified. Cocrystal and salt of PRA were physically pure. Sieved powders had comparable morphologies and particle size. The apparent and theoretical densities of powders were similar, but no clear trends were observed. The tensile strengths of these compacts were increased with increasing pressure whereas tabletability decreased in the order oxalic acid > PRA-HCL ≈ PRA-OXA > BPY > PRA-BPY. Tablet tensile strength decreases exponentially with increasing porosity with the exception of PRY-BPY and BPY. Slip plane prediction based on attachment energies may not be independently considered. However, it was possible to explain the improved mechanical properties of powders based on the crystal structure. Cocrystallization and salt formation have introduced structural features that are responsible for improved tableting properties of PRA.

Crystal Structure of the N-Benzyloxycarbonyl-alanyl-phenylalanyl-methyl Ester: The Importance of the H-Bonding Pattern

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Ignacio Alfonso

2011-08-01

Full Text Available Large crystals of the methyl ester of the N-a-benzyloxycarbonyl protected Ala-Phe dipeptide (Z-AF-OMe were obtained after the very slow evaporation of a solution of the corresponding carboxylic acid (Z-AF-OH in methanol containing an excess of HCl. The structure was confirmed by single crystal X-ray diffraction data. It crystallizes in the orthorhombic space group P212121 with unit cell dimensions a = 5.0655(6 Å, b = 8.4614(8 Å, c = 46.856(5 Å, V = 2008.3(4 Å3, Z = 4. In the crystal, the molecules form hydrogen bonded chains running along the a axis of the unit cell. Other secondary interactions are also discussed.

Preparation and crystal structure of carbonyltris (diethyldithiocarbamato) technetium (III): an unexpected source of co-ordinated carbon monoxide

International Nuclear Information System (INIS)

Baldas, J.; Bonnyman, J.; Pojer, P.M.; Williams, G.A.

1981-10-01

Tc(S 2 CNEt 2 ) 3 CO has been prepared by the reduction of NH 4 TcO 4 with formamidinesulphinic acid in the presence of NaS 2 CNEt 2 . It is suggested that the co-ordinated carbon monoxide is formed after co-ordination of formamidinesulphinic acid, or some decomposition product, with technetium. The crystal structure of Tc(S 2 CNEt 2 ) 3 CO has been determined by single-crystal X-ray diffraction methods at 17 deg. C. Diffractometry has provided significant Bragg intensities for 2045 independent reflections and the structure has been refined by full-matrix least-squares methods to R 0.049. The compound is isostructural with the rhenium analogue and consists of discrete Tc(S 2 CNEt 2 ) 3 CO molecules, each containing a terminal linear CO group. The technetium atom has a seven co-ordinate environment which is best described as a distorted pentagonal bipyramid

Crystal structures of active fully assembled substrate- and product-bound complexes of UDP-N-acetylmuramic acid:L-alanine ligase (MurC) from Haemophilus influenzae.

Science.gov (United States)

Mol, Clifford D; Brooun, Alexei; Dougan, Douglas R; Hilgers, Mark T; Tari, Leslie W; Wijnands, Robert A; Knuth, Mark W; McRee, Duncan E; Swanson, Ronald V

2003-07-01

UDP-N-acetylmuramic acid:L-alanine ligase (MurC) catalyzes the addition of the first amino acid to the cytoplasmic precursor of the bacterial cell wall peptidoglycan. The crystal structures of Haemophilus influenzae MurC in complex with its substrate UDP-N-acetylmuramic acid (UNAM) and Mg(2+) and of a fully assembled MurC complex with its product UDP-N-acetylmuramoyl-L-alanine (UMA), the nonhydrolyzable ATP analogue AMPPNP, and Mn(2+) have been determined to 1.85- and 1.7-A resolution, respectively. These structures reveal a conserved, three-domain architecture with the binding sites for UNAM and ATP formed at the domain interfaces: the N-terminal domain binds the UDP portion of UNAM, and the central and C-terminal domains form the ATP-binding site, while the C-terminal domain also positions the alanine. An active enzyme structure is thus assembled at the common domain interfaces when all three substrates are bound. The MurC active site clearly shows that the gamma-phosphate of AMPPNP is positioned between two bound metal ions, one of which also binds the reactive UNAM carboxylate, and that the alanine is oriented by interactions with the positively charged side chains of two MurC arginine residues and the negatively charged alanine carboxyl group. These results indicate that significant diversity exists in binding of the UDP moiety of the substrate by MurC and the subsequent ligases in the bacterial cell wall biosynthesis pathway and that alterations in the domain packing and tertiary structure allow the Mur ligases to bind sequentially larger UNAM peptide substrates.

Band structures in fractal grading porous phononic crystals

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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.

Thermal, Dielectric Studies on Pure and Amino Acid L-Glutamic Acid, L-Histidine L-Valine Doped Potassium Dihydrogen Phosphate Single Crystals

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Kumaresan, P.; Babu, S. Moorthy; Anbarasan, P. M.

Amino acids (L-Glutamic acid, L-Histidine, L-Valine) doped potassium dihydrogen phosphate crystals were grown by the solution growth technique. Slow cooling as well as slow evaporation methods were employed to grow these crystals. The concentration of dopants in the mother solution was varied from 0.1 mole % to 10 mole %. The solubility data for all dopant concentrations were determined. The variation in pH and the corresponding habit modification of the grown crystals were characterized with UV - VIS, FT-IR and SHG trace elements, and dielectric studies reveal slight distortion of lattice parameter for the heavily doped KDP crystals. TGA-DTA studies reveal good thermal stability. The dopants increase the hardness value of the material, which also depends on the concentration of the dopants. Amino acids doping improved the NLO properties. The detailed results on the spectral parameters, habit modifications and constant values will be presented.

Construction of crystal structure prototype database: methods and applications.

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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

International Nuclear Information System (INIS)

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

2017-01-01

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. (paper)

Hydrogen bonded 1D-3D supramolecular structures from Benzylamine and organic acidic components

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Gao, Xingjun; Li, XiaoLiang; Jin, Shouwen; Hu, Kaikai; Guo, Jianzhong; Guo, Ming; Xu, Weiqiang; Wang, Daqi

2018-03-01

Cocrystallization of the commonly available organic amine, benzylamine, with a series of organic acids afforded a total of seven organic salts with the compositions: (benzylamine)2: (p-nitrophenol)2: (H2O) (1) [(HL)2+⋯(npl-)2⋯(H2O), npl- = p-nitrophenolate], (benzylamine): (4-tert-butylbenzoic acid) (2) [(HL+)⋯(tba-), tba- = 4-tert-butylbenzoate], (benzylamine): (3,4-dichlorobenzoic acid) (3) [(HL+)⋯dcba-), dcba- = 3,4-dichlorobenzoate], (benzylamine): (2,5-dihydroxybenzoic acid) (4) [(HL+)⋯(dhba-), dhba- = 2,5-dihydroxybenzoate], (benzylamine): (2-bromo-but-2-enedioic acid) (5) [(HL+)⋯(Hbba-), Hbba- = 2-bromo-hydrogenbut-2-enedioate], (benzylamine): (2,6-pyridinedicarboxylic acid) (6) [(HL+)⋯(Hpdc-), Hpdc- = 2,6-pyridine hydrogendicarboxylate], and (benzylamine)2: (3-nitrophthalic acid): 2(H2O) (7) [(HL+)2⋯(npa2-)⋯(H2O)2, npa2- = 3-nitrophthalate]. The seven salts have been characterised by X-ray diffraction analysis, IR, and elemental analysis, and the melting points of all the salts were also reported. And their structural and supramolecular aspects are fully analyzed. The results reveal that among the seven investigated crystals the NH2 in the benzylamine are protonated when the organic acids are deprotonated, and the crystal packing is interpreted in terms of the strong charge-assisted Nsbnd H⋯O hydrogen bond between the NH3+ and deprotonated acidic groups. Except the Nsbnd H⋯O hydrogen bond, the Osbnd H⋯O hydrogen bonds (charge assisted or neutral) were also found at the salts 1, 4, 5, 6, and 7. Further analysis of the crystal packing of the salts indicated that a different family of additional CHsbnd O/CH2sbnd O, CH-π/CH2-π, Cπ-Cπ, Osbnd O, O-Cπ, O-π, and Cl-π associations also contribute to the stabilization and expansion of the total high-dimensional framework structures. For the coexistence of the various weak nonbonding interactions, these structures adopted a variety of

Design of co-crystals/salts of some Nitrogenous bases and some derivatives of thiophene carboxylic acids through a combination of hydrogen and halogen bonds.

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Jennifer, Samson Jegan; Muthiah, Packianathan Thomas

2014-01-01

The utility of N-heterocyclic bases to obtain molecular complexes with carboxylic acids is well studied. Depending on the solid state interaction between the N-heterocyclic base and a carboxylic acid a variety of neutral or ionic synthons are observed. Meanwhile, pyridines and pyrimidines have been frequently chosen in the area of crystal engineering for their multipurpose functionality. HT (hetero trimers) and LHT (linear heterotetramers) are the well known synthons that are formed in the presence of pyrimidines and carboxylic acids. Fourteen crystals involving various substituted thiophene carboxylic acid derivatives and nitrogenous bases were prepared and characterized by using single crystal X-ray diffraction. The 14 crystals can further be divided into two groups [1a-7a], [8b-14b] based on the nature of the nitrogenous base. Carboxylic acid to pyridine proton transfer has occurred in 3 compounds of each group. In addition to the commonly occurring hydrogen bond based pyridine/carboxylic acid and pyrimidine/carboxylic acid synthons which is the reason for assembly of primary motifs, various other interactions like Cl…Cl, Cl…O, C-H…Cl, C-H…S add additional support in organizing these supermolecules into extended architectures. It is also interesting to note that in all the compounds π-π stacking occurs between the pyrimidine-pyrimidine or pyridine-pyridine or acid-acid moieties rather than acid-pyrimidine/pyridine. In all the compounds (1a-14b) either neutral O-H…Npyridyl/pyrimidine or charge-assisted Npyridinium-H…Ocarboxylate hydrogen bonds are present. The HT (hetero trimers) and LHT (linear heterotetramers) are dominant in the crystal structures of the adducts containing N-heterocyclic bases with two proton acceptors (1a-7a). Similar type supramolecular ladders are observed in 5TPC44BIPY (8b), TPC44BIPY (9b), TPC44TMBP (11b). Among the seven compounds [8b-14b] the extended ligands are linear in all except for the TMBP (10b, 11b, 12b). The

Crystal structure of axolotl (Ambystoma mexicanum) liver bile acid-binding protein bound to cholic and oleic acid.

Science.gov (United States)

Capaldi, Stefano; Guariento, Mara; Perduca, Massimiliano; Di Pietro, Santiago M; Santomé, José A; Monaco, Hugo L

2006-07-01

The family of the liver bile acid-binding proteins (L-BABPs), formerly called liver basic fatty acid-binding proteins (Lb-FABPs) shares fold and sequence similarity with the paralogous liver fatty acid-binding proteins (L-FABPs) but has a different stoichiometry and specificity of ligand binding. This article describes the first X-ray structure of a member of the L-BABP family, axolotl (Ambystoma mexicanum) L-BABP, bound to two different ligands: cholic and oleic acid. The protein binds one molecule of oleic acid in a position that is significantly different from that of either of the two molecules that bind to rat liver FABP. The stoichiometry of binding of cholate is of two ligands per protein molecule, as observed in chicken L-BABP. The cholate molecule that binds buried most deeply into the internal cavity overlaps well with the analogous bound to chicken L-BABP, whereas the second molecule, which interacts with the first only through hydrophobic contacts, is more external and exposed to the solvent. (c) 2006 Wiley-Liss, Inc.

Structure of the Cyanuric Acid Hydrolase TrzD Reveals Product Exit Channel.

Science.gov (United States)

Bera, Asim K; Aukema, Kelly G; Elias, Mikael; Wackett, Lawrence P

2017-03-27

Cyanuric acid hydrolases are of industrial importance because of their use in aquatic recreational facilities to remove cyanuric acid, a stabilizer for the chlorine. Degradation of excess cyanuric acid is necessary to maintain chlorine disinfection in the waters. Cyanuric acid hydrolase opens the cyanuric acid ring hydrolytically and subsequent decarboxylation produces carbon dioxide and biuret. In the present study, we report the X-ray structure of TrzD, a cyanuric acid hydrolase from Acidovorax citrulli. The crystal structure at 2.19 Å resolution shows a large displacement of the catalytic lysine (Lys163) in domain 2 away from the active site core, whereas the two other active site lysines from the two other domains are not able to move. The lysine displacement is proposed here to open up a channel for product release. Consistent with that, the structure also showed two molecules of the co-product, carbon dioxide, one in the active site and another trapped in the proposed exit channel. Previous data indicated that the domain 2 lysine residue plays a role in activating an adjacent serine residue carrying out nucleophilic attack, opening the cyanuric acid ring, and the mobile lysine guides products through the exit channel.

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

Science.gov (United States)

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.

Nitrido-technetium(V) complexes with amino acids: Preparation and X-ray crystal structure of the L-cysteinate ethyl ester technetium(V) complex

International Nuclear Information System (INIS)

Marchi, A.; Rossi, R.; Marvelli, L.; Bertolasi, V.

1993-01-01

Technetium-99m is the radionuclide of choice in diagnostic nuclear medicine due to its ideal photon energy of 140 keV and half-life of 6 h. Neutral, stable, and lipophilic technetium complexes with diamino dithiol ligands (DADT) have been widely studied as potential brain perfusion agents and a 99m Tc complex of N,N'-1,2-ethylenediylbis(L-cysteine diethyl ester) (L,L-ECD) has been proposed as a marker of regional cerebral blood flow. It crosses the blood brain barrier (BBB) and is retained in the brain owing to enzymatic hydrolysis of one ester group yielding to a more polar species. More recently, 99m Tc-cysteine complex has been evaluated in animal distribution studies for tumor diagnosis, but its chemical structure has not been determined. A large number of transition metal complexes with amino acids and peptides have been synthesized and structurally characterized to understand their interactions with proteins and antibodies, as well as biocatalytic processes, but only a limited number of rhenium and technetium compounds have been reported. Up to now, the only technetium complex to be characterized by X-ray analysis that contains amino acids as ligand is [TcO(L,L-ECD)]. The author's interest in the nitrido-technetium chemistry is due to the discovery of a new method for preparing radiopharmaceuticals containing the [ 99m Tc triple-bond N] 2+ core. In this communication the authors report the synthesis and characterization of nitrido-technetium complexes with L-cysteine ethyl ester (CYS-OEt), L-cysteine (CYS) and cysteamine (CSA) and the first X-ray crystal structure of a [TcN] 2+ -amino acid complex

Synthesis, crystal structures and luminescence properties of new multi-component co-crystals of isostructural Co(II) and Zn(II) complexes

Science.gov (United States)

Tella, Adedibu C.; Owalude, Samson O.; Omotoso, Mary F.; Olatunji, Sunday J.; Ogunlaja, Adeniyi S.; Alimi, Lukman O.; Popoola, Olugbenga K.; Bourne, Susan A.

2018-04-01

Two novel isostructural compounds containing multi-component co-crystals [M(C6H4NO2)2(H2O)2](C9H6O6)2 (M = Co (1), Zn (2), C6H4NO2 = Picolinic acid, C9H6O6 = Trimesic acid) have been synthesized. The compounds were characterized by elemental analysis, FT-IR, UV-Visible and 1H NMR spectroscopies as well as thermal and single crystal X-ray diffraction analyses. Single crystal X-ray diffraction analysis reveals that 1 and 2 are isostructural. Compound 1 crystallizes in triclinic space group (P-1, with a = 5.154 (10) Å, b = 11.125 (2) Å, c = 14.113 (3) Å, α = 91.01 (3)°, β = 100.54 (3)°, and γ = 102.71 (3)°). In a similar fashion, compound 2 crystallizes in triclinic space group (P-1, with a = 5.1735 (3) Å, b = 11.0930 (10) Å, c = 14.1554 (8) Å, α = 91.70 (3)°, β = 100.26 (3)°, γ = 102.90 (3)°). The metal (II) cation presents distorted MN2O4 octahedral geometry with H2O molecules coordinated to the metal in equatorial position while the picolinic acid molecules are axially coordinated through the pyridine N atom. The two trimesic acid molecules are not part of the first coordination sphere. Compounds 1 and 2 constitute an example of a class of coordination compound of multicomponent crystals having trimesic acid outside the coordination sphere where it is neither protonated or deprotonated. The two compounds were investigated for luminiscence properties.

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

Science.gov (United States)

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

2016-04-01

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

Crystal structure of the starch-binding domain of glucoamylase from Aspergillus niger.

Science.gov (United States)

Suyama, Yousuke; Muraki, Norifumi; Kusunoki, Masami; Miyake, Hideo

2017-10-01

Glucoamylases are widely used commercially to produce glucose syrup from starch. The starch-binding domain (SBD) of glucoamylase from Aspergillus niger is a small globular protein containing a disulfide bond. The structure of A. niger SBD has been determined by NMR, but the conformation surrounding the disulfide bond was unclear. Therefore, X-ray crystal structural analysis was used to attempt to clarify the conformation of this region. The SBD was purified from an Escherichia coli-based expression system and crystallized at 293 K. The initial phase was determined by the molecular-replacement method, and the asymmetric unit of the crystal contained four protomers, two of which were related by a noncrystallographic twofold axis. Finally, the structure was solved at 2.0 Å resolution. The SBD consisted of seven β-strands and eight loops, and the conformation surrounding the disulfide bond was determined from a clear electron-density map. Comparison of X-ray- and NMR-determined structures of the free SBD showed no significant difference in the conformation of each β-strand, but the conformations of the loops containing the disulfide bond and the L5 loop were different. In particular, the difference in the position of the C α atom of Cys509 between the X-ray- and NMR-determined structures was 13.3 Å. In addition, the B factors of the amino-acid residues surrounding the disulfide bond are higher than those of other residues. Therefore, the conformation surrounding the disulfide bond is suggested to be highly flexible.

Crystal structure study of new lanthanide silicates with silico-carnotite structure

International Nuclear Information System (INIS)

Piccinelli, F.; Lausi, A.; Speghini, A.; Bettinelli, M.

2012-01-01

The crystal structures of new rare earth-based silicate compounds (Ca 3 Eu 2 Si 3 O 12 , Ca 3 Gd 2 Si 3 O 12 , Ca 3 Dy 2 Si 3 O 12 , Ca 3 Er 2 Si 3 O 12 and Ca 3 Lu 2 Si 3 O 12 ) have been determined using powder X-ray diffraction. From Rietveld refinement calculations on the collected powder patterns we observe a different distribution of the rare earth ions on the three available crystal sites characterized by different coordination numbers, depending on the ionic radius of the rare earth ion. The reasons of the instability of the silico-carnotite structure for lanthanide ions larger than Eu 3+ have been deduced. In addition, in order to detect crystal phase transitions, the powder patterns of Ca 3 Eu 2 Si 3 O 12 and Ca 3 Sm 2 Si 3 O 12 samples have been collected as a function of the temperature (RT-1000 °C range), but no phase transitions have been observed. - Graphical abstract: Synchrotron X-ray diffraction allows us the accurate determination of the RE 3+ ions distribution on the three available crystal sites of the silico-carnotite structure. Highlights: ► The structure of the Ca 3 M 2 Si 3 O 12 (M=Eu, Gd, Dy, Er and Lu) was determined. ► Different distribution of RE 3+ ions on the three available crystal sites was observed. ► The instability of the silico-carnotite structure for RE=La→Sm was discussed.

Crystal structure of aspartame anhydrate from powder diffraction data. Structural aspects of the dehydration process of aspartame

NARCIS (Netherlands)

Guguta, C.; Meekes, H.L.M.; Gelder, R. de

2006-01-01

Aspartame has three pseudo-polymorphic forms, two hydrates and a hemi-hydrate, for which crystal structures were determined from single-crystal diffraction data. This paper presents the crystal structure of the anhydrate, which was obtained by dehydrating the hemi-hydrate. The crystal structure of

Improved ferroelectric and pyroelectric parameters in iminodiacetic acid doped TGS crystal

Science.gov (United States)

Rai, Chitharanjan; Sreenivas, K.; Dharmaprakash, S. M.

2010-01-01

Single crystals of Iminodiacetic acid (HN(CH 2COOH) 2) doped Triglycine sulphate (IDATGS) has been grown from aqueous solution at constant temperature by slow evaporation technique. The concentration of the dopant in the TGS solution was 2 mol%. The X-ray diffraction analysis indicates that there is significant change in the lattice parameters compared to pure TGS crystal. The IDATGS crystal has larger transition temperature and observed higher and uniform figure of merit over most part of the ferroelectric phase. These crystals also exhibit higher internal bias field and micro-hardness number compared to pure TGS. Therefore IDATGS may be a potential material for IR detectors.

Structure, spectra and phase transition in p-nitroanilinium perchlorate crystal

Energy Technology Data Exchange (ETDEWEB)

Marchewka, M.K.; Drozd, M.; Pietraszko, A

2003-07-25

The first X-ray diffraction and vibrational spectroscopic analysis of a novel complex between p-nitroaniline and perchloric acid is reported. The structure was solved in 295 K. Room temperature powder infrared and Raman measurements for the p-nitroanilinium perchlorate (1:1) crystals were carried out. The vibrational spectra in the region of internal vibrations of ions corroborates the X-ray data which show that p-nitroaniline molecule is monoprotonated. DSC measurements on powder sample indicate the phase transition point at about 213 and 208 K for heating and cooling, respectively. No detectable signal was observed during powder test for second harmonic generation.

Crystal structure of actinide metals at high compression

International Nuclear Information System (INIS)

Fast, L.; Soederlind, P.

1995-08-01

The crystal structures of some light actinide metals are studied theoretically as a function of applied pressure. The first principles electronic structure theory is formulated in the framework of density functional theory, with the gradient corrected local density approximation of the exchange-correlation functional. The light actinide metals are shown to be well described as itinerant (metallic) f-electron metals and generally, they display a crystal structure which have, in agreement with previous theoretical suggestions, increasing degree of symmetry and closed-packing upon compression. The theoretical calculations agree well with available experimental data. At very high compression, the theory predicts closed-packed structures such as the fcc or the hcp structures or the nearly closed-packed bcc structure for the light actinide metals. A simple canonical band picture is presented to explain in which particular closed-packed form these metals will crystallize at ultra-high pressure

1.2.4. Synthesis, crystal structure and thermal stability property of Ni(aze(4,4′ –bipy(H2O based on longer-spanning azelaic acid and 4,4′ -bipyridine ligands

Directory of Open Access Journals (Sweden)

Ge Song, Feng Ying Bai*, Yan Xie, Yong Heng Xing.

2014-04-01

Full Text Available Abstract: One new three-dimensional (3D supramolecular longer-spanning azelaic acid (H2aze complex: Ni(aze(4,4′– bipy(H2O (4,4′-bipy = 4,4′-bipyridine has been synthesized using hydrothermal conditions and characterized by elemental analysis, IR spectroscopy, UV spectrum, powder X-ray diffraction, TG analysis and single crystal X–ray diffraction. Structural analysis reveals that the title complex is six-coordinate and connected by the azelaic acid and 4,4′-bipy ligands to generate a 2D planar structure, further linked through the interaction of hydrogen bond of C–H···O to form a 3D supramolecular structure . Supporting information: FT-IR, UV-Vis, X-Ray, Cif file

Study of the growth and pyroelectric properties of TGS crystals doped with aniline-family dipolar molecules

Science.gov (United States)

Zhang, Kecong; Song, Jiancheng; Wang, Min; Fang, Changshui; Lu, Mengkai

1987-04-01

TGS crystals doped with aniline-family dipolar molecules (aniline, 2-aminobenzoic acid, 3-aminobenzoic acid, 3-aminobenzene-sulphonic acid, 4-aminobenzenesulphonic acid and 4-nitroraniline) have been grown by the slow-cooling solution method. The influence of these dopants on the growth habits, crystal morphology pyroelectric properties, and structure parameters of TGS crystals has been systematically investigated. The effects of the domain structure of the seed crystal on the pyroelectric properties of the doped crystals have been studied. It is found that the spontaneous polarization (P), pyroelectric coefficient (lambda), and internal bias field of the doped crystals are slightly higher than those of the pure TGS, and the larger the dipole moment of the dopant molecule, the higher the P and lambda of the doped TGS crystal.

CCDC 1416891: Experimental Crystal Structure Determination : Methyl-triphenyl-germanium

KAUST Repository

Bernatowicz, Piotr; Shkurenko, Aleksander; Osior, Agnieszka; Kamieński, Bohdan; Szymański, Sławomir

2015-01-01

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from

Structural Color Patterns by Electrohydrodynamic Jet Printed Photonic Crystals.

Science.gov (United States)

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.

5,5'-Dithio-bis(2-nitrobenzoic acid) modification of cysteine improves the crystal quality of human chloride intracellular channel protein 2

International Nuclear Information System (INIS)

Mi Wei; Li Lanfen; Su Xiaodong

2008-01-01

Structural studies of human chloride intracellular channel protein 2 (CLIC2) had been hampered by the problem of generating suitable crystals primarily due to the protein containing exposed cysteines. Several chemical reagents were used to react with the cysteines on CLIC2 in order to modify the redox state of the protein. We have obtained high quality crystals that diffracted to better than 2.5 A at a home X-ray source by treating the protein with 5,5'-dithio-bis(2-nitrobenzoic acid) (DTNB). After solving the crystal structure of CLIC2, we found that the DTNB had reacted with the Cys 114 , and made CLIC2 in a homogenous oxidized state. This study demonstrated that the DTNB modification drastically improved the crystallization of CLIC2, and it implied that this method may be useful for other proteins containing exposed cysteines in general

Crystal structure of [1,1':3',1''-ter-phenyl]-2',3,3''-tri-carb-oxy-lic acid.

Science.gov (United States)

Decato, Daniel A; Berryman, Orion B

2015-09-01

The asymmetric unit of the title compound, C21H14O6, com-prises two symmetrically independent mol-ecules that form a locally centrosymmetric hydrogen-bonded dimer, with the planes of the corresponding carb-oxy-lic acid groups rotated by 15.8 (1) and 17.5 (1)° relative to those of the adjacent benzene rings. The crystal as a whole, however, exhibits a noncentrosymmetric packing, described by the polar space group Pca21. The dimers form layers along the ab plane, being inter-connected by hydrogen bonds involving the remaining carb-oxy-lic acid groups. The plane of the central carb-oxy-lic acid group forms dihedral angles of 62.5 (1) and 63.0 (1)° with those of the adjacent benzene rings and functions as a hydrogen-bond donor and acceptor. As a donor, it inter-connects adjacent layers, while as an acceptor it stabilizes the packing within the layers. The 'distal' carb-oxy-lic acid groups are nearly coplanar with the planes of the adjacent benzene rings, forming dihedral angles of 1.8 (1) and 7.1 (1)°. These groups also form intra- and inter-layer hydrogen bonds, but with 'reversed' functionality, as compared with the central carb-oxy-lic acid groups.

Crystallization and X-ray diffraction studies of a complete bacterial fatty-acid synthase type I

International Nuclear Information System (INIS)

Enderle, Mathias; McCarthy, Andrew; Paithankar, Karthik Shivaji; Grininger, Martin

2015-01-01

Bacterial and fungal type I fatty-acid synthases (FAS I) are evolutionarily connected, as bacterial FAS I is considered to be the ancestor of fungal FAS I. In this work, the production, crystallization and X-ray diffraction data analysis of a bacterial FAS I are reported. While a deep understanding of the fungal and mammalian multi-enzyme type I fatty-acid synthases (FAS I) has been achieved in recent years, the bacterial FAS I family, which is narrowly distributed within the Actinomycetales genera Mycobacterium, Corynebacterium and Nocardia, is still poorly understood. This is of particular relevance for two reasons: (i) although homologous to fungal FAS I, cryo-electron microscopic studies have shown that bacterial FAS I has unique structural and functional properties, and (ii) M. tuberculosis FAS I is a drug target for the therapeutic treatment of tuberculosis (TB) and therefore is of extraordinary importance as a drug target. Crystals of FAS I from C. efficiens, a homologue of M. tuberculosis FAS I, were produced and diffracted X-rays to about 4.5 Å resolution

Crystallization and X-ray diffraction studies of a complete bacterial fatty-acid synthase type I

Energy Technology Data Exchange (ETDEWEB)

Enderle, Mathias [Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main (Germany); Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried (Germany); McCarthy, Andrew [EMBL Grenoble, 71 Avenue des Martyrs, 38042 Grenoble CEDEX 9 (France); Paithankar, Karthik Shivaji, E-mail: paithankar@em.uni-frankfurt.de [Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main (Germany); Grininger, Martin, E-mail: paithankar@em.uni-frankfurt.de [Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main (Germany); Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried (Germany)

2015-10-23

Bacterial and fungal type I fatty-acid synthases (FAS I) are evolutionarily connected, as bacterial FAS I is considered to be the ancestor of fungal FAS I. In this work, the production, crystallization and X-ray diffraction data analysis of a bacterial FAS I are reported. While a deep understanding of the fungal and mammalian multi-enzyme type I fatty-acid synthases (FAS I) has been achieved in recent years, the bacterial FAS I family, which is narrowly distributed within the Actinomycetales genera Mycobacterium, Corynebacterium and Nocardia, is still poorly understood. This is of particular relevance for two reasons: (i) although homologous to fungal FAS I, cryo-electron microscopic studies have shown that bacterial FAS I has unique structural and functional properties, and (ii) M. tuberculosis FAS I is a drug target for the therapeutic treatment of tuberculosis (TB) and therefore is of extraordinary importance as a drug target. Crystals of FAS I from C. efficiens, a homologue of M. tuberculosis FAS I, were produced and diffracted X-rays to about 4.5 Å resolution.

Growth, structure, Hirshfeld surface and spectroscopic properties of 2-amino-4-hydroxy-6-methylpyrimidinium-2,3-pyrazinedicorboxylate single crystal

Science.gov (United States)

Faizan, Mohd; Alam, Mohammad Jane; Afroz, Ziya; Rodrigues, Vítor Hugo Nunes; Ahmad, Shabbir

2018-03-01

The present work is focused on the crystal structure, vibrational spectroscopy and DFT calculations of hydrogen bonded 2,3-pyrazinedicorboxylic acid and 2-amino-4-hydroxy-6-methylpyrimidine (PDCA-.AHMP+) crystal. The crystal structure has been determined using single crystal X-ray diffraction analysis which shows that the crystal belongs to monoclinic space group P21/n. The PDCA-.AHMP+ crystal has been characterized by FTIR, FT-Raman and FT-NMR spectroscopic techniques. The FTIR and FT-Raman spectra of the complex have unique spectroscopic feature as compared with those of the starting material to confirm salt formation. The theoretical vibrational studies have been performed to understand the modes of the vibrations of asymmetric unit of the complex by DFT methods. Hirschfeld surface and 2D fingerprint plots analyses were carried out to investigate the intermolecular interactions and its contribution in the building of PDCA-.AHMP+ crystal. The experimental and simulated 13C and 1H NMR studies have assisted in structural analysis of PDCA-.AHMP+ crystal. The electronic spectroscopic properties of the complex were explored by the experimental as well as theoretical electronic spectra simulated using TD-DFT/IEF-PCM method at B3LYP/6-311++G (d,p) level of theory. In addition, frontier molecular orbitals, molecular electrostatic potential map (MEP) and nonlinear optical (NLO) properties using DFT method have been also presented.

Crystal structure of enolase from Drosophila melanogaster.

Science.gov (United States)

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.

New co-crystal and salt form of sulfathiazole with carboxylic acid and ...

Indian Academy of Sciences (India)

e-mail: cmallareddy@gmail.com. MS received 14 May 2014; revised 8 July 2014; accepted 8 July 2014. Abstract. One co-crystal and one salt of an antibacterial drug sulfathiazole with 4-aminobenzamide and 2,4- dinitrobenzoic acid have been synthesized. These new forms are characterized by single crystal X-ray diffrac-.

Crystallization and Characterization of Galdieria sulphuraria RUBISCO in Two Crystal Forms: Structural Phase Transition Observed in P21 Crystal Form

Directory of Open Access Journals (Sweden)

Boguslaw Stec

2007-10-01

Full Text Available We have isolated ribulose-1,5-bisphosphate-carboxylase/oxygenase (RUBISCOfrom the red algae Galdieria Sulphuraria. The protein crystallized in two different crystalforms, the I422 crystal form being obtained from high salt and the P21 crystal form beingobtained from lower concentration of salt and PEG. We report here the crystallization,preliminary stages of structure determination and the detection of the structural phasetransition in the P21 crystal form of G. sulphuraria RUBISCO. This red algae enzymebelongs to the hexadecameric class (L8S8 with an approximate molecular weight 0.6MDa.The phase transition in G. sulphuraria RUBISCO leads from two hexadecamers to a singlehexadecamer per asymmetric unit. The preservation of diffraction power in a phasetransition for such a large macromolecule is rare.

Characterization of potassium bromide crystals grown in the aqueous solution of picric acid

Energy Technology Data Exchange (ETDEWEB)

Maheswari, J. Uma, E-mail: umak.anand@gmail.com [Department of Physics, The M.D.T.Hindu College, Tirunelveli 627010, Tamilnadu (India); Krishnan, C. [Department of Physics, Arignar Anna College, Aralvoymoli 629301, Tamilnadu (India); Kalyanaraman, S. [Physics Research Centre, Sri Paramakalyani College, Alwarkurichi 627412, Tamilnadu (India); Selvarajan, P. [Department of Physics, Aditanar College of Arts and Science, Tiruchendur 628216, Tamilnadu (India)

2016-12-01

Potassium bromide crystals were grown in the aqueous solution of picric acid by slow evaporation technique at room temperature. X-ray Diffraction (XRD) analysis ensures that the grown sample is in Fm3m space group and FCC structure. Energy Dispersive X-ray Spectroscopy (EDX) reveals the presence of elements in the title compound. UV–Vis-NIR spectrum reveals that the grown sample is a promising nonlinear optical (NLO) material. FTIR analysis confirms the functional groups present in the sample. The thermogravimetric (TG) and differential thermogravimetric (DTA) analyses ensure that the sample material is thermally stable up to 160 °C. The second harmonic efficiency of the sample is 1.3 times greater than that of standard KDP. The mechanical strength of the grown sample is estimated by Vickers microhardness tester. The electrical properties were investigated by impedance analysis and the results of various studies of the grown crystals are discussed.

Crystal structures of coordination polymers from CaI2 and proline

Directory of Open Access Journals (Sweden)

Kevin Lamberts

2015-06-01

Full Text Available Completing our reports concerning the reaction products from calcium halides and the amino acid proline, two different solids were found for the reaction of l- and dl-proline with CaI2. The enantiopure amino acid yields the one-dimensional coordination polymer catena-poly[[aqua-μ3-l-proline-tetra-μ2-l-proline-dicalcium] tetraiodide 1.7-hydrate], {[Ca2(C5H9NO25(H2O]I4·1.7H2O}n, (1, with two independent Ca2+ cations in characteristic seven- and eightfold coordination. Five symmetry-independent zwitterionic l-proline molecules bridge the metal sites into a cationic polymer. Racemic proline forms with Ca2+ cations heterochiral chains of the one-dimensional polymer catena-poly[[diaquadi-μ2-dl-proline-calcium] diiodide], {[Ca(C5H9NO22(H2O2]I2}n, (2. The centrosymmetric structure is built by one Ca2+ cation that is bridged towards its symmetry equivalents by two zwitterionic proline molecules. In both structures, the iodide ions remain non-coordinating and hydrogen bonds are formed between these counter-anions, the amino groups, coordinating and co-crystallized water molecules. While the overall composition of (1 and (2 is in line with other structures from calcium halides and amino acids, the diversity of the carboxylate coordination geometry is quite surprising.

Surface (glyco-)proteins: primary structure and crystallization under microgravity conditions

Science.gov (United States)

Claus, H.; Akca, E.; Schultz, N.; Karbach, G.; Schlott, B.; Debaerdemaeker, T.; De Clercq, J.-P.; König, H.

2001-08-01

The Archaea comprise microorganisms that live under environmental extremes, like high temperature, low pH value or high salt concentration. Their cells are often covered by a single layer of (glyco)protein subunits (S-layer) in hexagonal arrangement. In order to get further hints about the molecular mechanisms of protein stabilization we compared the primary and secondary structures of archaeal S-layer (glyco)proteins. We found an increase of charged amino acids in the S-layer proteins of the extreme thermophilic species compared to their mesophilic counterparts. Our data and those of other authors suggest that ionic interactions, e.g., salt bridges seem to be played a major role in protein stabilization at high temperatures. Despite the differences in the growth optima and the predominance of some amino acids the primary structures of S-layers revealed also a significant degree of identity between phylogenetically related archaea. These obervations indicate that protein sequences of S-layers have been conserved during the evolution from extremely thermophilic to mesophilic life. To support these findings the three-dimensional structure of the S-layer proteins has to be elucidated. Recently, we described the first successful crystallization of an extreme thermophilic surface(glyco)protein under microgravity conditions.

Photosensitive bent-core liquid crystals based on methyl substituted 3-hydroxybenzoic acid.

Czech Academy of Sciences Publication Activity Database

Kohout, M.; Alaasar, M.; Poryvai, A.; Novotná, Vladimíra; Poppe, S.; Tschierske, C.; Svoboda, J.

2017-01-01

Roč. 7, č. 57 (2017), s. 35805-35813 ISSN 2046-2069 R&D Projects: GA ČR GA16-12150S Institutional support: RVO:68378271 Keywords : liquid crystals * photosensitivity * bent-core liquid crystals * 3-hydroxybenzoic acid Subject RIV: JJ - Other Materials OBOR OECD: Nano-materials (production and properties) Impact factor: 3.108, year: 2016

Synthesis, Crystal Structure and Water Vapor Adsorption Properties of a Porous Supramolecular Architecture

Directory of Open Access Journals (Sweden)

Rui Qiao

2017-10-01

Full Text Available A new complex, [Cu4(HL4(H2O14] (1, H3L·HCl = 5-((4-carboxypiperidin-1-ylmethylisophthalic acid hydrochloride, has been prepared and characterized by single-crystal X-ray diffraction, elemental analysis, IR spectroscopy and powder X-ray diffraction (PXRD. The result of the X-ray diffraction analysis reveals that the complex crystallizes in monoclinic, space group C2/c and three unique Cu(II atoms that are connected by partially deprotonated HL2− anion to form a cyclic structure. The rich hydrogen bonding and π-π non-covalent packing interactions extend cyclic units into a three-dimensional (3D supramolecular polymer. Moreover, the thermogravimetric (TG analysis and water vapor adsorption property of 1 were also discussed.

Synthesis and crystal structure analysis of uranyl triple acetates

Energy Technology Data Exchange (ETDEWEB)

Klepov, Vladislav V., E-mail: vladislavklepov@gmail.com [Institute for Energy and Climate Research (IEK-6), Forschungszentrum Jülich GmbH, 52428 Jülich (Germany); Department of Chemistry, Samara National Research University, 443086 Samara (Russian Federation); Serezhkina, Larisa B.; Serezhkin, Victor N. [Department of Chemistry, Samara National Research University, 443086 Samara (Russian Federation); Alekseev, Evgeny V., E-mail: e.alekseev@fz-juelich.de [Institute for Energy and Climate Research (IEK-6), Forschungszentrum Jülich GmbH, 52428 Jülich (Germany); Institut für Kristallographie, RWTH Aachen University, 52066 Aachen (Germany)

2016-12-15

Single crystals of triple acetates NaR[UO{sub 2}(CH{sub 3}COO){sub 3}]{sub 3}·6H{sub 2}O (R=Mg, Co, Ni, Zn), well-known for their use as reagents for sodium determination, were grown from aqueous solutions and their structural and spectroscopic properties were studied. Crystal structures of the mentioned phases are based upon (Na[UO{sub 2}(CH{sub 3}COO){sub 3}]{sub 3}){sup 2–} clusters and [R(H{sub 2}O){sub 6}]{sup 2+} aqua-complexes. The cooling of a single crystal of NaMg[UO{sub 2}(CH{sub 3}COO){sub 3}]{sub 3}·6H{sub 2}O from 300 to 100 K leads to a phase transition from trigonal to monoclinic crystal system. Intermolecular interactions between the structural units and their mutual packing were studied and compared from the point of view of the stereoatomic model of crystal structures based on Voronoi-Dirichlet tessellation. Using this method we compared the crystal structures of the triple acetates with Na[UO{sub 2}(CH{sub 3}COO){sub 3}] and [R(H{sub 2}O){sub 6}][UO{sub 2}(CH{sub 3}COO){sub 3}]{sub 2} and proposed reasons of triple acetates stability. Infrared and Raman spectra were collected and their bands were assigned. - Graphical abstract: Single crystals of uranium based triple acetates, analytical reagents for sodium determination, were synthesized and structurally, spectroscopically and topologically characterized. The structures were compared with the structures of compounds from preceding families [M(H{sub 2}O){sub 6})][UO{sub 2}(CH{sub 3}COO){sub 3}]{sub 2} (M = Mg, Co, Ni, Zn) and Na[UO{sub 2}(CH{sub 3}COO){sub 3}]. Analysis was performed with the method of molecular Voronoi-Dirichlet polyhedra to reveal a large contribution of the hydrogen bonds into intermolecular interactions which can be a reason of low solubility of studied complexes.

Crystal structure of tris(hydroxylammonium orthophosphate

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Malte Leinemann

2015-11-01

Full Text Available The crystal structure of the title salt, ([H3NOH]+3·[PO4]3−, consists of discrete hydroxylammonium cations and orthophosphate anions. The atoms of the cation occupy general positions, whereas the anion is located on a threefold rotation axis that runs through the phosphorus atom and one of the phosphate O atoms. In the crystal structure, cations and anions are linked by intermolecular O—H...O and N—H...O hydrogen bonds into a three-dimensional network. Altogether, one very strong O—H...O, two N—H...O hydrogen bonds of medium strength and two weaker bifurcated N—H...O interactions are observed.

Optical and dielectric studies of KH2PO4 crystal influenced by organic ligand of citric acid and l-valine: A single crystal growth and comparative study

Directory of Open Access Journals (Sweden)

Mohd Anis

Full Text Available In the present study pure, citric acid (CA and l-valine (LV doped potassium dihydrogen phosphate (KDP crystals have been grown with the aim to investigate the nonlinear optical applications facilitated by UV–visible, third order nonlinear optical (TONLO and dielectric properties. The structural parameters of grown crystals have been confirmed by single crystal X-ray diffraction analysis. The enhancement in optical transparency of KDP crystal due to addition of CA and LV has been examined within 200–900 nm by means of UV–visible spectral analysis. In addition, the transmittance data have been used to evaluate the effect of dopants on reflectance, refractive index and extinction coefficient of grown crystals in the visible region. The Z-scan analysis has been performed at 632.8 nm to identify the nature of photoinduced nonlinear refraction and nonlinear absorption in doped KDP crystals. The influence of π-bonded ligand of dopant CA and LV on TONLO susceptibility (χ3, refractive index (n2 and absorption coefficient (β of KDP crystals has been evaluated to discuss laser assisted device applications. The decrease in dielectric constant and dielectric loss of KDP crystal due to addition of CA and LV has been explored using the temperature dependent dielectric studies. Keywords: Crystal growth, Nonlinear optical materials, UV–visible studies, Z-scan analysis, Dielectric studies

Ultrasmall-angle X-ray scattering analysis of photonic crystal structure

International Nuclear Information System (INIS)

Abramova, V. V.; Sinitskii, A. S.; Grigor'eva, N. A.; Grigor'ev, S. V.; Belov, D. V.; Petukhov, A. V.; Mistonov, A. A.; Vasil'eva, A. V.; Tret'yakov, Yu. D.

2009-01-01

The results of an ultrasmall-angle X-ray scattering study of iron(III) oxide inverse opal thin films are presented. The photonic crystals examined are shown to have fcc structure with amount of stacking faults varying among the samples. The method used in this study makes it possible to easily distinguish between samples with predominantly twinned fcc structure and nearly perfect fcc stacking. The difference observed between samples fabricated under identical conditions is attributed to random layer stacking in the self-assembled colloidal crystals used as templates for fabricating the inverse opals. The present method provides a versatile tool for analyzing photonic crystal structure in studies of inverse opals made of various materials, colloidal crystals, and three-dimensional photonic crystals of other types.

Crystal and NMR Structures of a Peptidomimetic β-Turn That Provides Facile Synthesis of 13-Membered Cyclic Tetrapeptides.

Science.gov (United States)

Cameron, Alan J; Squire, Christopher J; Edwards, Patrick J B; Harjes, Elena; Sarojini, Vijayalekshmi

2017-12-14

Herein we report the unique conformations adopted by linear and cyclic tetrapeptides (CTPs) containing 2-aminobenzoic acid (2-Abz) in solution and as single crystals. The crystal structure of the linear tetrapeptide H 2 N-d-Leu-d-Phe-2-Abz-d-Ala-COOH (1) reveals a novel planar peptidomimetic β-turn stabilized by three hydrogen bonds and is in agreement with its NMR structure in solution. While CTPs are often synthetically inaccessible or cyclize in poor yield, both 1 and its N-Me-d-Phe analogue (2) adopt pseudo-cyclic frameworks enabling near quantitative conversion to the corresponding CTPs 3 and 4. The crystal structure of the N-methylated peptide (4) is the first reported for a CTP containing 2-Abz and reveals a distinctly planar 13-membered ring, which is also evident in solution. The N-methylation of d-Phe results in a peptide bond inversion compared to the conformation of 3 in solution. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Synthesis, crystal structures, molecular docking, and in vitro biological activities evaluation of transition metal complexes with 4-(3,4-dichlorophenyl) piperazine-1-carboxylic acid

Science.gov (United States)

Chen, Zhi-Jian; Chen, Ya-Na; Xu, Chun-Na; Zhao, Shan-Shan; Cao, Qi-Yue; Qian, Shao-Song; Qin, Jie; Zhu, Hai-Liang

2016-08-01

Three novel mononuclear complexes, [MⅡ(L)2·2H2O], (M = Cu, Ni or Cd; HL = 4-(3,4-dichlorophenyl)piperazine-1-carboxylic acid)were synthesized and structurally determined by single-crystal X-ray diffraction. Molecular docking study preliminarily revealed that complex 1 had potential urease inhibitory activity. In accordance with the result of calculation, in vitro tests of the inhibitory activities of complexes 1-3 against jack bean urease showed complex 1 (IC50 = 8.17 ± 0.91 μM) had better inhibitory activities than the positive reference acetohydroxamic acid (AHA) (IC50 = 26.99 ± 1.43 μM), while complexes 2 and 3 showed no inhibitory activities., kinetics study was carried out to explore the mechanism of the inhibiting of the enzyme, and the result indicated that complex 1 was a competitive inhibitor of urease. Albumin binding experiment and in vitro toxicity evaluation of complex 1 were implemented to explore its Pharmacological properties.

Effects of the rate of supersaturation generation on polymorphic crystallization of m-hydroxybenzoic acid and o-aminobenzoic acid

Science.gov (United States)

He, Guangwen; Wong, Annie B. H.; Chow, Pui Shan; Tan, Reginald B. H.

2011-01-01

Effects of the rate of supersaturation generation on polymorphic crystallization have been investigated through evaporation and cooling crystallization experiments of m-hydroxybenzoic acid (m-HBA) in methanol, acetone and ethyl acetate, and o-aminobenzoic acid (o-ABA) in ethanol. The rate of supersaturation generation has been altered by systematically changing either the cooling rate or the evaporation rate of solvent using a jacketed crystallizer and a microfluidic evaporation device, respectively. The results have revealed that the rate of supersaturation generation and the tendency of the formation of the less stable polymorph are positively correlated. Kinetic effects are dominant when the rate of supersaturation generation is high, thereby producing the metastable polymorphs (orthorhombic m-HBA; Form II of o-ABA); on the contrary, more stable polymorphs (monoclinic m-HBA; Forms III and I of o-ABA) are formed when the rate of supersaturation generation is low and the thermodynamic effects are prevailing.

Crystal structure and solid-state properties of discrete hexa cationic ...

Indian Academy of Sciences (India)

Subsequently, weight loss of 33% in two stages from 242 to 691◦C can be assigned to the decomposition of triazole ligands. 3.3 Description of the crystal structure. The solid-state structure of ZnT was unambiguously determined by the single crystal X-ray diffraction tech- nique (figures 2 and 3). Compound ZnT crystallizes in.

Crystal structure and magnetism of UOsAl

Energy Technology Data Exchange (ETDEWEB)

Andreev, A.V., E-mail: andreev@fzu.cz [Institute of Physics, Academy of Sciences, Na Slovance 2, 182 21 Prague (Czech Republic); Daniš, S. [Department of Condensed Matter Physics, Charles University, Ke Karlovu 5, 121 16 Prague (Czech Republic); Šebek, J.; Henriques, M.S.; Vejpravová, J. [Institute of Physics, Academy of Sciences, Na Slovance 2, 182 21 Prague (Czech Republic); Gorbunov, D.I. [Institute of Physics, Academy of Sciences, Na Slovance 2, 182 21 Prague (Czech Republic); Dresden High Magnetic Field Laboratory (HLD-EMFL), Helmholtz-Zentrum, Dresden-Rossendorf, D-01314 Dresden (Germany); Havela, L. [Department of Condensed Matter Physics, Charles University, Ke Karlovu 5, 121 16 Prague (Czech Republic)

2017-04-15

Crystal structure, magnetization, and specific heat were studied on single crystal of uranium intermetallic compound UOsAl. It is a hexagonal Laves phase of MgZn{sub 2} type, space group P6{sub 3}/mmc, with lattice parameters a=536.4 pm, c=845.3 pm. Shortest inter-uranium distance 313 pm (along the c-axis) is considerably smaller than the Hill limit (340 pm). The compound is a weakly temperature-dependent paramagnet with magnetic susceptibility of ≈1.5*10{sup −8} m{sup 3} mol{sup −1} (at T=2 K), which is slightly higher with magnetic field along the a-axis compared to the c-axis. The Sommerfeld coefficient of electronic specific heat has moderate value of γ=36 mJ mol{sup −1} K{sup −2}. - Highlights: • Crystal structure and magnetic properties were studied on single crystal of UOsAl with hexagonal structure of MgZn{sub 2} type. • Shortest inter-uranium distance 313 pm (along the c-axis) is considerably smaller than the Hill limit (340 pm). • UOsAl has paramagnetic ground state as the compounds with T=Fe and Ru, i.e. 3d and 4d analogues of Os.

Salinomycin Hydroxamic Acids: Synthesis, Structure, and Biological Activity of Polyether Ionophore Hybrids.

Science.gov (United States)

Borgström, Björn; Huang, Xiaoli; Chygorin, Eduard; Oredsson, Stina; Strand, Daniel

2016-06-09

The polyether ionophore salinomycin has recently gained attention due to its exceptional ability to selectively reduce the proportion of cancer stem cells within a number of cancer cell lines. Efficient single step strategies for the preparation of hydroxamic acid hybrids of this compound varying in N- and O-alkylation are presented. The parent hydroxamic acid, salinomycin-NHOH, forms both inclusion complexes and well-defined electroneutral complexes with potassium and sodium cations via 1,3-coordination by the hydroxamic acid moiety to the metal ion. A crystal structure of an cationic sodium complex with a noncoordinating anion corroborates this finding and, moreover, reveals a novel type of hydrogen bond network that stabilizes the head-to-tail conformation that encapsulates the cation analogously to the native structure. The hydroxamic acid derivatives display down to single digit micromolar activity against cancer cells but unlike salinomycin selective reduction of ALDH(+) cells, a phenotype associated with cancer stem cells was not observed. Mechanistic implications are discussed.

Hydrothermal synthesis, crystal structures, and enantioselective adsorption property of bis(L-histidinato)nickel(II) monohydrate

Science.gov (United States)

Ramos, Christian Paul L.; Conato, Marlon T.

2018-05-01

Despite the numerous researches in metal-organic frameworks (MOFs), there are only few reports on biologically important amino acids, histidine in particular, on its use as bridging ligand in the construction of open-framework architectures. In this work, hydrothermal synthesis was used to prepare a compound based on Ni2+ and histidine. The coordination assembly of imidazole side chain of histidine with divalent nickel ions in aqueous condition yielded purple prismatic solids. Single crystal X-ray diffraction (XRD) analysis of the product revealed structure for Ni(C6H8N3O2)2 • H2O that has a monoclinic (C2) structure with lattice parameters, a = 29.41, b = 8.27, c = 6.31 Å, β = 90.01 ˚. Circular dichroism - optical rotatory dispersion (CD-ORD), Powder X-ray diffraction (PXRD) and Fourier transform - infrared spectroscopy (FT-IR) analyses are conducted to further characterize the crystals. Enantioselective adsorption analysis using racemic mixture of 2-butanol confirmed bis(L-histidinato)nickel(II) monohydrate MOF crystal's enantioselective property preferentially favoring the adsorption of (S)-2-butanol isomer.

Synthesis, spectroscopy and antimicrobial activity of vanadium(III) and vanadium(IV) complexes involving Schiff bases derived from tranexamic acid and X-ray structure of Zwitter ion of tranexamic acid

International Nuclear Information System (INIS)

Shahzadi, S.; Ali, S.; Badshah, A.; Parvez, M.; Ahmed, E.; Malik, A.

2007-01-01

The synthesis of six new vanadium complexes of Schiff base derived from Tranexamic acid is reported. All the complexes were characterized by elemental analysis, infrared, electronic spectra, and mass spectrometry. FTIR data reveals that the Schiff base acts as a bidentate and the complexes exhibit the hexa-coordinated geometry in solid state. These complexes were screened for their biological activity against various bacterial and fungal strains. All the ligands show higher activity after complexation. The crystal structure of the Zwitter ion of the Tranexamic acid has been determined by X-ray single crystal diffraction [ru

Pyroelectric properties of phosphoric acid-doped TGS single crystals

International Nuclear Information System (INIS)

Saxena, Aparna; Fahim, M; Gupta, Vinay; Sreenivas, K

2003-01-01

Pyroelectric properties of phosphoric acid (H 3 PO 4 )-doped triglycine sulfate (TGSP) single crystals grown from solutions containing 0.1-0.5 mol of H 3 PO 4 have been studied. Incorporation of H 3 PO 4 into the crystal lattice is found to induce an internal bias field (E b ) and is observed through the presence of a sustained polarization and pyroelectricity beyond the transition temperature. The internal bias field has been estimated theoretically by fitting the experimentally measured data on temperature dependence of the pyroelectric coefficient (λ), dielectric constant (ε') and polarization (P). A high E b value in the range 9 x 10 3 -15.5 x 10 4 V m -1 is obtained for crystals grown with 0.1-0.5 mol of H 3 PO 4 in the solution, and a specific concentration of 0.2-0.25 mol of H 3 PO 4 in the solution during crystal growth is found to be optimum for a high figure of merit for detectivity, F d = 428 μC m -2 K -1

Crystal Structures of KPC-2[beta]-Lactamase in Complex with 3-Nitrophenyl Boronic Acid and the Penam Sulfone PSR-3-226

Energy Technology Data Exchange (ETDEWEB)

Ke, Wei; Bethel, Christopher R.; Papp-Wallace, Krisztina M.; Pagadala, Sundar Ram Reddy; Nottingham, Micheal; Fernandez, Daniel; Buynak, John D.; Bonomo, Robert A.; van den Akker, Focco (Case Western); (Stokes); (SMU)

2012-08-01

Class A carbapenemases are a major threat to the potency of carbapenem antibiotics. A widespread carbapenemase, KPC-2, is not easily inhibited by {beta}-lactamase inhibitors (i.e., clavulanic acid, sulbactam, and tazobactam). To explore different mechanisms of inhibition of KPC-2, we determined the crystal structures of KPC-2 with two {beta}-lactamase inhibitors that follow different inactivation pathways and kinetics. The first complex is that of a small boronic acid compound, 3-nitrophenyl boronic acid (3-NPBA), bound to KPC-2 with 1.62-{angstrom} resolution. 3-NPBA demonstrated a Km value of 1.0 {+-} 0.1 {micro}M (mean {+-} standard error) for KPC-2 and blocks the active site by making a reversible covalent interaction with the catalytic S70 residue. The two boron hydroxyl atoms of 3-NPBA are positioned in the oxyanion hole and the deacylation water pocket, respectively. In addition, the aromatic ring of 3-NPBA provides an edge-to-face interaction with W105 in the active site. The structure of KPC-2 with the penam sulfone PSR-3-226 was determined at 1.26-{angstrom} resolution. PSR-3-226 displayed a K{sub m} value of 3.8 {+-} 0.4 {micro}M for KPC-2, and the inactivation rate constant (kinact) was 0.034 {+-} 0.003 s{sup -1}. When covalently bound to S70, PSR-3-226 forms a trans-enamine intermediate in the KPC-2 active site. The predominant active site interactions are generated via the carbonyl oxygen, which resides in the oxyanion hole, and the carboxyl moiety of PSR-3-226, which interacts with N132, N170, and E166. 3-NPBA and PSR-3-226 are the first {beta}-lactamase inhibitors to be trapped as an acyl-enzyme complex with KPC-2. The structural and inhibitory insights gained here could aid in the design of potent KPC-2 inhibitors.

Neutron crystallographic studies of amino acids and nucleic acids

International Nuclear Information System (INIS)

Kashiwagi, Tatsuki

2014-01-01

Neutron crystallographic studies of two representative umami materials were executed utilizing iBLX at MLF/J-PARC. The results of them will be summarized in this report. At first, structure analysis of the alpha form crystal of L-glutamic acid was performed in order to assess the usefulness of neutron crystallography at iBIX to our company's R and D. Neutron crystal structure of it was successfully determined at 0.6 A resolution. All hydrogen atoms were clearly observed. Next, the mixed crystal of disodium Inosine-5'-phosphate (IMP · 2Na) and disodium Guanosine-5'-phosphate (GMP · 2Na) was analyzed by neutron crystallography. Neutron crystal structure of the mixed crystal of IMP and GMP (IM/GMP rate = 1.7) was successfully determined at 0.8 A resolution. In the neutron crystal structure of the mixed crystal, the hydrogen atom bonded to the C2 atom of purine base in IMP and the nitrogen atom bonded to the C2 atom of purine base in GMP were clearly observed in the nuclear density map, structurally demonstrating that this crystal is the mixed crystal. (author)

Crystal structure of Clostridium difficile toxin A

Energy Technology Data Exchange (ETDEWEB)

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

2016-01-11

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

Programmatic conversion of crystal structures into 3D printable files using Jmol

OpenAIRE

Scalfani, Vincent F.; Williams, Antony J.; Tkachenko, Valery; Karapetyan, Karen; Pshenichnov, Alexey; Hanson, Robert M.; Liddie, Jahred M.; Bara, Jason E.

2016-01-01

Background Three-dimensional (3D) printed crystal structures are useful for chemistry teaching and research. Current manual methods of converting crystal structures into 3D printable files are time-consuming and tedious. To overcome this limitation, we developed a programmatic method that allows for facile conversion of thousands of crystal structures directly into 3D printable files. Results A collection of over 30,000 crystal structures in crystallographic information file (CIF) format from...

Crystal structure and crystal growth of the polar ferrimagnet CaBaFe4O7

Science.gov (United States)

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 structure of 5-[(4-carboxybenzyloxy]isophthalic acid

Directory of Open Access Journals (Sweden)

Md. Serajul Haque Faizi

2016-08-01

Full Text Available The molecular shape of the title compound, C16H12O7, is bent around the central CH2—O bond. The two benzene rings are almost perpendicular to one another, making a dihedral angle of 87.78 (7°. In the crystal, each molecule is linked to three others by three pairs of O—H...O hydrogen bonds, forming undulating sheets parallel to the bc plane and enclosing R22(8 ring motifs. The sheets are linked by C—H...O hydrogen bonds and C—H...π interactions, forming a three-dimensional network.

Solving crystal structures with the symmetry minimum function

International Nuclear Information System (INIS)

Estermann, M.A.

1995-01-01

Unravelling the Patterson function (the auto-correlation function of the crystal structure) (A.L. Patterson, Phys. Rev. 46 (1934) 372) can be the only way of solving crystal structures from neutron and incomplete diffraction data (e.g. powder data) when direct methods for phase determination fail. The negative scattering lengths of certain isotopes and the systematic loss of information caused by incomplete diffraction data invalidate the underlying statistical assumptions made in direct methods. In contrast, the Patterson function depends solely on the quality of the available diffraction data. Simpson et al. (P.G. Simpson et al., Acta Crystallogr. 18 (1965) 169) showed that solving a crystal structure with a particular superposition of origin-shifted Patterson functions, the symmetry minimum function, is advantageous over using the Patterson function alone, for single-crystal X-ray data.This paper describes the extension of the Patterson superposition approach to neutron data and powder data by (a) actively using the negative regions in the Patterson map caused by negative scattering lengths and (b) using maximum entropy Patterson maps (W.I.F. David, Nature 346 (1990) 731). Furthermore, prior chemical knowledge such as bond lengths and angles from known fragments have been included. Two successful structure solutions of a known and a previously unknown structure (M. Hofmann, J. Solid State Chem., in press) illustrate the potential of this new development. ((orig.))

Crystal and molecular structure of N-(4-nitrophenyl)-β-alanine—Its vibrational spectra and theoretical calculations

Science.gov (United States)

Marchewka, M. K.; Drozd, M.; Janczak, J.

2011-08-01

The N-(4-nitrophenyl)-β-alanine in crystalline form directly by the addition of 4-nitroaniline to the acrylic acid in aqueous solution has been obtained. The title β-alanine derivative crystallizes in the P2 1/ c space group of monoclinic system with four molecules per unit cell. The X-ray geometry of β-alanine derivative molecule has been compared with those obtained by molecular orbital calculations corresponding to the gas phase. In the crystal the molecules related by an inversion center interact via symmetrically equivalent O-H⋯O hydrogen bonds with O⋯O distance of 2.656(2) Å forming a dimeric structure. The dimers of β-alanine derivative weakly interact via N-H⋯O hydrogen bonds between the H atom of β-amine groups and one of O atom of nitro groups. The room temperature powder vibrational (infrared and Raman) measurements are in accordance with the X-ray analysis. In aqueous solution of 4-nitroaniline and acrylic acid, the double C dbnd C bond of vinyl group of acrylic acid breaks as result of 4-nitroaniline addition.

CCDC 1416891: Experimental Crystal Structure Determination : Methyl-triphenyl-germanium

KAUST Repository

Bernatowicz, Piotr

2015-01-01

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

CCDC 1408042: Experimental Crystal Structure Determination : 6,13-dimesitylpentacene

KAUST Repository

Shi, Xueliang

2015-01-01

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

CCDC 1475929: Experimental Crystal Structure Determination : trimethylammonium tribromo-tin(iv)

KAUST Repository

Dang, Yangyang; Zhong, Cheng; Zhang, Guodong; Ju, Dianxing; Wang, Lei; Xia, Shengqing; Xia, Haibing; Tao, Xutang

2016-01-01

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from

CCDC 1475930: Experimental Crystal Structure Determination : trimethylammonium trichloro-tin(iv)

KAUST Repository

Dang, Yangyang; Zhong, Cheng; Zhang, Guodong; Ju, Dianxing; Wang, Lei; Xia, Shengqing; Xia, Haibing; Tao, Xutang

2016-01-01

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from

CCDC 1475931: Experimental Crystal Structure Determination : trimethylammonium trichloro-tin(iv)

KAUST Repository

Dang, Yangyang; Zhong, Cheng; Zhang, Guodong; Ju, Dianxing; Wang, Lei; Xia, Shengqing; Xia, Haibing; Tao, Xutang

2016-01-01

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from

CCDC 1482638: Experimental Crystal Structure Determination : trimethylammonium trichloro-tin(iv)

KAUST Repository

Dang, Yangyang; Zhong, Cheng; Zhang, Guodong; Ju, Dianxing; Wang, Lei; Xia, Shengqing; Xia, Haibing; Tao, Xutang

2016-01-01

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from

Artemin Crystal Structure Reveals Insights into Heparan Sulfate Binding

Energy Technology Data Exchange (ETDEWEB)

Silvian,L.; Jin, P.; Carmillo, P.; Boriack-Sjodin, P.; Pelletier, C.; Rushe, M.; Gong, B.; Sah, D.; Pepinsky, B.; Rossomando, A.

2006-01-01

Artemin (ART) promotes the growth of developing peripheral neurons by signaling through a multicomponent receptor complex comprised of a transmembrane tyrosine kinase receptor (cRET) and a specific glycosylphosphatidylinositol-linked co-receptor (GFR{alpha}3). Glial cell line-derived neurotrophic factor (GDNF) signals through a similar ternary complex but requires heparan sulfate proteoglycans (HSPGs) for full activity. HSPG has not been demonstrated as a requirement for ART signaling. We crystallized ART in the presence of sulfate and solved its structure by isomorphous replacement. The structure reveals ordered sulfate anions bound to arginine residues in the pre-helix and amino-terminal regions that were organized in a triad arrangement characteristic of heparan sulfate. Three residues in the pre-helix were singly or triply substituted with glutamic acid, and the resulting proteins were shown to have reduced heparin-binding affinity that is partly reflected in their ability to activate cRET. This study suggests that ART binds HSPGs and identifies residues that may be involved in HSPG binding.

Nonlinear coherent structures in granular crystals

Science.gov (United States)

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.

Unique Reversible Crystal-to-Crystal Phase Transition – Structural and Functional Properties of Fused Ladder Thienoarenes

KAUST Repository

Abe, Yuichiro

2017-08-15

Donor-acceptor type molecules based on fused ladder thienoarenes, indacenodithiophene (IDT) and dithienocyclopenta-thienothiophene (DTCTT), coupled with benzothiadiazole, are prepared and their solid-state structures are investigated. They display a rich variety of solid phases ranging from amorphous glass states to crystalline states, upon changes in the central aromatic core and side group structures. Most notably, the DTCTT-based derivatives showed reversible crystal-to-crystal phase transitions in heating and cooling cycles. Unlike what has been seen in π−conjugated molecules variable temperature XRD revealed that structural change occurs continuously during the transition. A columnar self-assembled structure with slip-stacked π−π interaction is proposed to be involved in the solid-state. This research provides the evidence of unique structural behavior of the DTCTT-based molecules through the detailed structural analysis. This unique structural transition paves the way for these materials to have self-healing of crystal defects, leading to improved optoelectronic properties.

Unique Reversible Crystal-to-Crystal Phase Transition – Structural and Functional Properties of Fused Ladder Thienoarenes

KAUST Repository

Abe, Yuichiro; Savikhin, Victoria; Yin, Jun; Grimsdale, Andrew C.; Soci, Cesare; Toney, Michael F.; Lam, Yeng Ming

2017-01-01

Donor-acceptor type molecules based on fused ladder thienoarenes, indacenodithiophene (IDT) and dithienocyclopenta-thienothiophene (DTCTT), coupled with benzothiadiazole, are prepared and their solid-state structures are investigated. They display a rich variety of solid phases ranging from amorphous glass states to crystalline states, upon changes in the central aromatic core and side group structures. Most notably, the DTCTT-based derivatives showed reversible crystal-to-crystal phase transitions in heating and cooling cycles. Unlike what has been seen in π−conjugated molecules variable temperature XRD revealed that structural change occurs continuously during the transition. A columnar self-assembled structure with slip-stacked π−π interaction is proposed to be involved in the solid-state. This research provides the evidence of unique structural behavior of the DTCTT-based molecules through the detailed structural analysis. This unique structural transition paves the way for these materials to have self-healing of crystal defects, leading to improved optoelectronic properties.

Photonic Crystal Laser-Driven Accelerator Structures

International Nuclear Information System (INIS)

Cowan, Benjamin M.

2007-01-01

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

Two Voriconazole salts: Syntheses, crystal structures, solubility and bioactivities

Science.gov (United States)

Tang, Gui-Mei; Wang, Yong-Tao

2018-01-01

Two Voriconazole salts, namely, (H2FZ)2+·2(Cl-) (1) and (HFZ)+·NO3- (2) (FZ = (2R,3S)-2-(2,4-difluorophenyl)-3-(5-fluoro-4-pyrimidiny)-1-(1H-1,2,4-triazol-1-yl)-2-butanol) have been obtained through the reaction of Voriconazole, hydrochloric acid and nitrate acid, respectively. They were structurally characterized by FT-IR, elemental analyses (EA), single crystal X-ray diffraction, and thermogravimetric analysis (TGA). A variety of hydrogen bonds (Osbnd H⋯N, Nsbnd H⋯Cl/O, Csbnd H⋯N/OF/Cl) were observed in the compounds 1 and 2, through which a 3D supramolecular architecture is generated. Both two salts 1 and 2 show the promising bioactivities against Aspergillus species (Aspergillus niger, Aspergillus terreus, Aspergillus fumigatus and Aspergillus flavus) and Candida ones (Candida albicans, Candida krusei, Candida glabrata and Cryptococcus neoformans), which is obviously more excellent than that of FZ. Additionally, the solubility of two salts is considerably higher than that of the drug Voriconazole.

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

Energy Technology Data Exchange (ETDEWEB)

Cornaby, Sterling [School of Applied and Engineering Physics, Cornell University, Ithaca, New York (United States); CHESS (Cornell High Energy Synchrotron Source), Cornell University, Ithaca, New York (United States); Szebenyi, Doletha M. E. [MacCHESS (Macromolecular Diffraction Facilities at CHESS), Cornell University, Ithaca, New York (United States); Smilgies, Detlef-M. [CHESS (Cornell High Energy Synchrotron Source), Cornell University, Ithaca, New York (United States); Schuller, David J.; Gillilan, Richard; Hao, Quan [MacCHESS (Macromolecular Diffraction Facilities at CHESS), Cornell University, Ithaca, New York (United States); Bilderback, Donald H., E-mail: dhb2@cornell.edu [School of Applied and Engineering Physics, Cornell University, Ithaca, New York (United States); CHESS (Cornell High Energy Synchrotron Source), Cornell University, Ithaca, New York (United States)

2010-01-01

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 Laue 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.

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

International Nuclear Information System (INIS)

Cornaby, Sterling; Szebenyi, Doletha M. E.; Smilgies, Detlef-M.; Schuller, David J.; Gillilan, Richard; Hao, Quan; Bilderback, Donald H.

2010-01-01

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 Laue 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

Structure of rat acidic fibroblast growth factor at 1.4 Å resolution

International Nuclear Information System (INIS)

Kulahin, Nikolaj; Kiselyov, Vladislav; Kochoyan, Arthur; Kristensen, Ole; Kastrup, Jette Sandholm; Berezin, Vladimir; Bock, Elisabeth; Gajhede, Michael

2007-01-01

The structure of rat acidic fibroblast growth factor was determined and compared with those of human, bovine and newt origin. The rat and human structures were found to be very similar. Fibroblast growth factors (FGFs) constitute a family of 22 structurally related heparin-binding polypeptides that are involved in the regulation of cell growth, survival, differentiation and migration. Here, a 1.4 Å resolution X-ray structure of rat FGF1 is presented. Two molecules are present in the asymmetric unit of the crystal and they coordinate a total of five sulfate ions. The structures of human, bovine and newt FGF1 have been published previously. Human and rat FGF1 are found to have very similar structures

Structural basis for olivetolic acid formation by a polyketide cyclase from Cannabis sativa.

Science.gov (United States)

Yang, Xinmei; Matsui, Takashi; Kodama, Takeshi; Mori, Takahiro; Zhou, Xiaoxi; Taura, Futoshi; Noguchi, Hiroshi; Abe, Ikuro; Morita, Hiroyuki

2016-03-01

In polyketide biosynthesis, ring formation is one of the key diversification steps. Olivetolic acid cyclase (OAC) from Cannabis sativa, involved in cannabinoid biosynthesis, is the only known plant polyketide cyclase. In addition, it is the only functionally characterized plant α+β barrel (DABB) protein that catalyzes the C2-C7 aldol cyclization of the linear pentyl tetra-β-ketide CoA as the substrate, to generate olivetolic acid (OA). Herein, we solved the OAC apo and OAC-OA complex binary crystal structures at 1.32 and 1.70 Å resolutions, respectively. The crystal structures revealed that the enzyme indeed belongs to the DABB superfamily, as previously proposed, and possesses a unique active-site cavity containing the pentyl-binding hydrophobic pocket and the polyketide binding site, which have never been observed among the functionally and structurally characterized bacterial polyketide cyclases. Furthermore, site-directed mutagenesis studies indicated that Tyr72 and His78 function as acid/base catalysts at the catalytic center. Structural and/or functional studies of OAC suggested that the enzyme lacks thioesterase and aromatase activities. These observations demonstrated that OAC employs unique catalytic machinery utilizing acid/base catalytic chemistry for the formation of the precursor of OA. The structural and functional insights obtained in this work thus provide the foundation for analyses of the plant polyketide cyclases that will be discovered in the future. Structural data reported in this paper are available in the Protein Data Bank under the accession numbers 5B08 for the OAC apo, 5B09 for the OAC-OA binary complex and 5B0A, 5B0B, 5B0C, 5B0D, 5B0E, 5B0F and 5B0G for the OAC His5Q, Ile7F, Tyr27F, Tyr27W, Val59M, Tyr72F and His78S mutant enzymes, respectively. © 2016 Federation of European Biochemical Societies.

Structural and morphological characterization of fullerite crystals prepared from the vapor phase

International Nuclear Information System (INIS)

Haluska, M.; Fejdi, P.; Vybornov, M.; Kuzmany, H.

1993-01-01

Crystal structure, habits and surface structures of fullerite crystals prepared from vapor phase were characterized by X-ray analysis, interfacial angle measurements and optical and scanning electron microscopy (SEM). The study of selected C 60 crystals confirmed the fcc structure at room temperature. The crystal habit is determined by two types of morphological faces, namely {100} and {111}. SEM was used for the observation of thermal etched surfaces. (orig.)

Structural properties of a family of hydrogen-bonded co-crystals formed between gemfibrozil and hydroxy derivatives of t-butylamine, determined directly from powder X-ray diffraction data

International Nuclear Information System (INIS)

Cheung, Eugene Y.; David, Sarah E.; Harris, Kenneth D.M.; Conway, Barbara R.; Timmins, Peter

2007-01-01

We report the formation and structural properties of co-crystals containing gemfibrozil and hydroxy derivatives of t-butylamine H 2 NC(CH 3 ) 3- n (CH 2 OH) n , with n=0, 1, 2 and 3. In each case, a 1:1 co-crystal is formed, with transfer of a proton from the carboxylic acid group of gemfibrozil to the amino group of the t-butylamine derivative. All of the co-crystal materials prepared are polycrystalline powders, and do not contain single crystals of suitable size and/or quality for single crystal X-ray diffraction studies. Structure determination of these materials has been carried out directly from powder X-ray diffraction data, using the direct-space Genetic Algorithm technique for structure solution followed by Rietveld refinement. The structural chemistry of this series of co-crystal materials reveals well-defined structural trends within the first three members of the family (n=0, 1, 2), but significantly contrasting structural properties for the member with n=3. - Graphical abstract: Structural properties of a family of co-crystals containing gemfibrozil and hydroxy derivatives of t-butylamine are discussed and rationalized

Ibuprofen-Amino Acids Co-Crystal Screening Via Co-Grinding Methods

Directory of Open Access Journals (Sweden)

Othman Muhamad Fitri

2016-01-01

Full Text Available The importance of pharmaceutical co-crystals now has been recognized in order to improve the research and development in pharmaceutical industries. Low solubility of active pharmaceutical ingredient (API has led to the growth of new pharmaceutical co-crystals formation as it enhances the physicochemical properties of the API. In this works, preparation of new co-crystal formation between ibuprofen (IBP with selected amino acid compounds were performed by using dry grinding and liquid assisted grinding (LAG techniques. Ibuprofen (IBP was selected as the API meanwhile glycine (GLY, L-alanine (ALA and L-proline (PRO were selected as co-crystal former (CCF agents. The products of IBP-co-former from grinding experiments for the formation of co-crystals were characterized and verified using X-Ray Powder Diffraction (XRPD, Differential Scanning Calorimetry (DSC and Fourier Transform Infra-Red Spectroscopy (FTIR. The finding reveals that the IBP-PRO co-crystals have successfully formed. For IBP-PRO system, new crystalline peaks from XRPD were recorded at 2θ values of 4.374°, 5.436° and 10.944° from dry grinding technique and 4.41°, 5.436° and 10.962° for liquid assisted grinding (LAG technique. A new melting point of 257.49 °C was discovered for IBP-ALA indicates the possibility of co-crystals formation. On the other hand, the analysis for IBP-GLY shows that no co-crystals formed in the system.

Crystal structure of product-bound complex of UDP-N-acetyl-d-mannosamine dehydrogenase from Pyrococcus horikoshii OT3.

Science.gov (United States)

Pampa, K J; Lokanath, N K; Girish, T U; Kunishima, N; Rai, V R

2014-10-24

UDP-N-acetyl-d-mannosamine dehydrogenase (UDP-d-ManNAcDH) belongs to UDP-glucose/GDP-mannose dehydrogenase family and catalyzes Uridine-diphospho-N-acetyl-d-mannosamine (UDP-d-ManNAc) to Uridine-diphospho-N-acetyl-d-mannosaminuronic acid (UDP-d-ManNAcA) through twofold oxidation of NAD(+). In order to reveal the structural features of the Pyrococcus horikoshii UDP-d-ManNAcADH, we have determined the crystal structure of the product-bound enzyme by X-ray diffraction to resolution of 1.55Å. The protomer folds into three distinct domains; nucleotide binding domain (NBD), substrate binding domain (SBD) and oligomerization domain (OD, involved in the dimerization). The clear electron density of the UDP-d-ManNAcA is observed and the residues binding are identified for the first time. Crystal structures reveal a tight dimeric polymer chains with product-bound in all the structures. The catalytic residues Cys258 and Lys204 are conserved. The Cys258 acts as catalytic nucleophile and Lys204 as acid/base catalyst. The product is directly interacts with residues Arg211, Thr249, Arg244, Gly255, Arg289, Lys319 and Arg398. In addition, the structural parameters responsible for thermostability and oligomerization of the three dimensional structure are analyzed. Copyright © 2014 Elsevier Inc. All rights reserved.

Two rhodamine 6G derivative compounds: a structural and fluorescence single-crystal study.

Science.gov (United States)

Di Paolo, Matias; Bossi, Mariano L; Baggio, Ricardo; Suarez, Sebastián A

2016-10-01

The synthesis, characterization, structural analysis and fluorescence properties of two rhodamine 6G derivatives are described, namely a propargylamine derivative, 3',6'-bis(ethylamino)-2',7'-dimethyl-2-(methylcyanide)spiro[isoindole-1,9'-xanthen]-3(2H)-one (I), and a γ-aminobutyric acid (GABA) derivative, 3',6'-bis(ethylamino)-2',7'-dimethyl-3-oxospiro[isoindole-1,9'-xanthen]-2(3H)-yl)butyricacid (II). Both structures are compared with four similar ones from the Cambridge Structural Database (CSD), and the interactions involved in the stabilization are analyzed using the atoms in molecules (AIM) theory. Finally, a single-crystal in-situ reaction study is presented, carried out by fluorescence methods, which enabled the `opening' of the spirolactam ring in the solid phase.

Crystal structure of product-bound complex of UDP-N-acetyl-D-mannosamine dehydrogenase from Pyrococcus horikoshii OT3

Energy Technology Data Exchange (ETDEWEB)

Pampa, K.J., E-mail: sagarikakj@gmail.com [Department of Studies in Microbiology, University of Mysore, Mysore 570 006 (India); Lokanath, N.K. [Department of Studies in Physics, University of Mysore, Mysore 570 006 (India); Girish, T.U. [Department of General Surgery, JSS Medical College and Hospital, JSS University, Mysore 570 015 (India); Kunishima, N. [Advanced Protein Crystallography Research Group, RIKEN SPring-8 Center, Harima Institute, Hyogo 679-5148 (Japan); Rai, V.R. [Department of Studies in Microbiology, University of Mysore, Mysore 570 006 (India)

2014-10-24

Highlights: • Determined the structure of UDP-D-ManNAcADH to a resolution of 1.55 Å. • First complex structure of PhUDP-D-ManNAcADH with UDP-D-ManMAcA. • The monomeric structure consists of three distinct domains. • Cys258 acting as catalytic nucleophilic and Lys204 acts as acid/base catalyst. • Oligomeric state plays an important role for the catalytic function. - Abstract: UDP-N-acetyl-D-mannosamine dehydrogenase (UDP-D-ManNAcDH) belongs to UDP-glucose/GDP-mannose dehydrogenase family and catalyzes Uridine-diphospho-N-acetyl-D-mannosamine (UDP-D-ManNAc) to Uridine-diphospho-N-acetyl-D-mannosaminuronic acid (UDP-D-ManNAcA) through twofold oxidation of NAD{sup +}. In order to reveal the structural features of the Pyrococcus horikoshii UDP-D-ManNAcADH, we have determined the crystal structure of the product-bound enzyme by X-ray diffraction to resolution of 1.55 Å. The protomer folds into three distinct domains; nucleotide binding domain (NBD), substrate binding domain (SBD) and oligomerization domain (OD, involved in the dimerization). The clear electron density of the UDP-D-ManNAcA is observed and the residues binding are identified for the first time. Crystal structures reveal a tight dimeric polymer chains with product-bound in all the structures. The catalytic residues Cys258 and Lys204 are conserved. The Cys258 acts as catalytic nucleophile and Lys204 as acid/base catalyst. The product is directly interacts with residues Arg211, Thr249, Arg244, Gly255, Arg289, Lys319 and Arg398. In addition, the structural parameters responsible for thermostability and oligomerization of the three dimensional structure are analyzed.

NMR structure of the protein NP-247299.1: comparison with the crystal structure

International Nuclear Information System (INIS)

Jaudzems, Kristaps; Geralt, Michael; Serrano, Pedro; Mohanty, Biswaranjan; Horst, Reto; Pedrini, Bill; Elsliger, Marc-André; Wilson, Ian A.; Wüthrich, Kurt

2010-01-01

Comparison of the NMR and crystal structures of a protein determined using largely automated methods has enabled the interpretation of local differences in the highly similar structures. These differences are found in segments of higher B values in the crystal and correlate with dynamic processes on the NMR chemical shift timescale observed in solution. The NMR structure of the protein NP-247299.1 in solution at 313 K has been determined and is compared with the X-ray crystal structure, which was also solved in the Joint Center for Structural Genomics (JCSG) at 100 K and at 1.7 Å resolution. Both structures were obtained using the current largely automated crystallographic and solution NMR methods used by the JCSG. This paper assesses the accuracy and precision of the results from these recently established automated approaches, aiming for quantitative statements about the location of structure variations that may arise from either one of the methods used or from the different environments in solution and in the crystal. To evaluate the possible impact of the different software used for the crystallographic and the NMR structure determinations and analysis, the concept is introduced of reference structures, which are computed using the NMR software with input of upper-limit distance constraints derived from the molecular models representing the results of the two structure determinations. The use of this new approach is explored to quantify global differences that arise from the different methods of structure determination and analysis versus those that represent interesting local variations or dynamics. The near-identity of the protein core in the NMR and crystal structures thus provided a basis for the identification of complementary information from the two different methods. It was thus observed that locally increased crystallographic B values correlate with dynamic structural polymorphisms in solution, including that the solution state of the protein involves

PDF analysis on re-crystallized structure from amorphous BiT

Energy Technology Data Exchange (ETDEWEB)

Yoneda, Yasuhiro [Japan Atomic Energy Research Institute, Synchrotron Radiation Research Center, Kouto 1-1-1, Mikazuki-cho, Sayo-gun, Hyogo 679-5148 (Japan)]. E-mail: yoneda@spring8.or.jp; Kohara, Shinji [Synchrotron Radiation Research Laboratory, Japan Synchrotron Radiation, Research Institute, Kouto 1-1-1, Mikazuki-cho, Sayo-gun, Hyogo 679-5198 (Japan); Hamazaki, Shin' ichi [Department of Electronics, Iwaki Meisei University, Iino 5-5-1, Chuohdai, Fukushima 970-8551 (Japan); Takashige, Masaaki [Department of Electronics, Iwaki Meisei University, Iino 5-5-1, Chuohdai, Fukushima 970-8551 (Japan); Mizuki, Jun' ichiro [Japan Atomic Energy Research Institute, Synchrotron Radiation Research Center, Kouto 1-1-1, Mikazuki-cho, Sayo-gun, Hyogo 679-5148 (Japan)

2005-08-15

A glass sample of composition Bi{sub 4}Ti{sub 3}O{sub 12} was prepared by rapid quenching. The as-quenched sample was confirmed to be amorphous by synchrotron X-ray measurements. The crystallization process of the amorphous sample was also investigated by high-energy X-ray diffraction and by atomic pair distribution function analysis. The perovskite layer in the crystal Bi{sub 4}Ti{sub 3}O{sub 12} is transformed to a pyrochlore structure in the amorphous sample. The amorphous sample first crystallized to a metastable phase by acquiring long-range ordering of the pyrochlore structure at T {sub cryst1}, and then secondary crystallized into a reverted Bi{sub 4}Ti{sub 3}O{sub 12} structure at T {sub cryst2}.

Nucleation of colloidal crystals on configurable seed structures

NARCIS (Netherlands)

Hermes, M; Vermolen, E.C.M.; Leunissen, M.E.; Vossen, D.L.J.; van Oostrum, P.D.J.; Dijkstra, M.; van Blaaderen, A.

2011-01-01

Nucleation is an important stage in the growth of crystals. During this stage, the structure and orientation of a crystal are determined. However, short time- and length-scales make nucleation poorly understood. Micrometer-sized colloidal particles form an ideal model system to study nucleation due

Crystal structure of MboIIA methyltransferase.

Science.gov (United States)

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.

Pyroelectric properties of phosphoric acid-doped TGS single crystals

Energy Technology Data Exchange (ETDEWEB)

Saxena, Aparna; Fahim, M; Gupta, Vinay; Sreenivas, K [Department of Physics and Astrophysics, University of Delhi, Delhi 110007 (India)

2003-12-21

Pyroelectric properties of phosphoric acid (H{sub 3}PO{sub 4})-doped triglycine sulfate (TGSP) single crystals grown from solutions containing 0.1-0.5 mol of H{sub 3}PO{sub 4} have been studied. Incorporation of H{sub 3}PO{sub 4} into the crystal lattice is found to induce an internal bias field (E{sub b}) and is observed through the presence of a sustained polarization and pyroelectricity beyond the transition temperature. The internal bias field has been estimated theoretically by fitting the experimentally measured data on temperature dependence of the pyroelectric coefficient ({lambda}), dielectric constant ({epsilon}') and polarization (P). A high E{sub b} value in the range 9 x 10{sup 3}-15.5 x 10{sup 4} V m{sup -1} is obtained for crystals grown with 0.1-0.5 mol of H{sub 3}PO{sub 4} in the solution, and a specific concentration of 0.2-0.25 mol of H{sub 3}PO{sub 4} in the solution during crystal growth is found to be optimum for a high figure of merit for detectivity, F{sub d} = 428 {mu}C m{sup -2} K{sup -1}.

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

Science.gov (United States)

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.

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

International Nuclear Information System (INIS)

Streek, Jacco van de; Neumann, Marcus A.

2010-01-01

The accuracy of a dispersion-corrected density functional theory method is validated against 241 experimental organic crystal structures from Acta Cryst. Section E. 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 Å 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

Experimental evidence for a chiral symmetry-breaking mechanism in aspartic acid: Lattice and sub-lattice matching

Science.gov (United States)

Teschke, Omar; Soares, David Mendez

2017-10-01

A mother crystal formed from a transient molecular structure of (D+L) aspartic acid in solution is reported. Hexagonal structures with a lattice constant of 1.04 nm were crystallized from a solution in which three aspartic acid species coexist: right- and left-handed enantiomorphs, denoted D-aspartic and L-aspartic, respectively, and transitory (D+L) aspartic acid specie. Atomic force microscopy images of the crystalline deposits reveal domains of the transitory (D+L) aspartic acid crystal forming the substrate deposit on silicon wafers, and on top of this hexagonal lattice only L-aspartic acid is observed to conform and crystallize. A preferential crystallization mechanism is then observed for (D+L) aspartic acid crystals that seed only L-aspartic deposits by the geometrical matching of their multiple hexagonal lattice structures with periodicities of 1.04 nm and 0.52 nm, respectively.

A unified picture of the crystal structures of metals

Science.gov (United States)

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.

A unified picture of the crystal structures of metals

International Nuclear Information System (INIS)

Soederlind, P.; Eriksson, O.; Johansson, B.; Wills, J.M.; Boring, A.M.

1995-01-01

The crystal structures of the light actinides have intrigued physicists and chemists for several decades. Simple metals and transition metals have close-packed, high-symmetry structures, such as body-centred cubic, face-centred cubic 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 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 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. (author)

Lanthanide complexes with 2,3-dimethoxybenzoic acid and terpyridine. Crystal structures, thermal properties, and antibacterial activities

Energy Technology Data Exchange (ETDEWEB)

Shen, Pan-Pan; Wu, Xiao-Hui; Zhang, Jian-Jun [Testing and Analysis Center, Hebei Normal University, Shijiazhuang (China); College of Chemistry and Material Science, Hebei Normal University, Shijiazhuang (China); Ren, Ning [College of Chemical Engineering and Material, Handane College (China); Wang, Shu-Ping [College of Chemistry and Material Science, Hebei Normal University, Shijiazhuang (China)

2017-08-03

The lanthanide coordination complexes Er(2,3-DMOBA){sub 3}(terpy)(H{sub 2}O) (1) and [Nd(2,3-DMOBA){sub 3}(terpy)(H{sub 2}O)]{sub 2} (2) (2,3-DMOBA = 2,3-dimethoxybenzoate; terpy = 2,2':6',2{sup ''}-terpyridine) were synthesized and characterized by IR spectroscopy, powder X-ray diffraction (XRD), single-crystal X-ray diffraction, and thermogravimetric analysis. Complex 1 crystallizes in the triclinic system, space group P1, and the mononuclear subunits form a 1D chain structure along the a axis by hydrogen bonds. Complex 2 crystallizes in the monoclinic system, space group P2{sub 1}/c, and the dinuclear subunits are further linked via the offset face-to-face π..π weak stacking interactions to form a supramolecular 2D layered structure. Thermal analysis showed that the complexes have three decomposition steps. The first step is the loss of coordination water molecules. The neutral terpy ligands and partial 2,3-DMOBA ligands are lost in the second step. The remaining 2,3-DMOBA ligands are lost in the third step. The 3D stacked plots for the FT-IR spectra of the evolved gases are recorded and the gaseous products are identified by the typical IR spectra obtained at different temperatures from the 3D stacked plots. Meanwhile, the results of the antibacterial action tests show that 1 and 2 have better antibacterial activities to Candida albicans than to Escherichia coli or Staphylococcus aureus. In addition, complex 2 has better antibacterial action to Candida albicans than complex 1. (copyright 2017 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

Crystal structure of rac-3-[2,3-bis(phenylsulfanyl-3H-indol-3-yl]propanoic acid

Directory of Open Access Journals (Sweden)

Wayland E. Noland

2015-11-01

Full Text Available The title compound, C23H19NO2S2, was obtained as an unexpected regioisomer from an attempted synthesis of an intermediate for a substituent-effect study on ergot alkaloids. This is the first report of a 1H-indole monothioating at the 2- and 3-positions to give a 3H-indole. In the crystal, the acid H atom is twisted roughly 180° from the typical carboxy conformation and forms centrosymmetric O—H...N hydrogen-bonded dimers with the indole N atom of an inversion-related molecule. Together with a weak C—H...O hydrogen bond involving the carbonyl O atom, chains are formed along [100].

Five new Zn(II) and Cd(II) coordination polymers constructed by 3,5-bis-oxyacetate-benzoic acid: Syntheses, crystal structures, network topologies and luminescent properties

International Nuclear Information System (INIS)

Jiang Xianrong; Yuan Hongyan; Feng Yunlong

2012-01-01

Five Zn(II) and Cd(II) coordination polymers, [Zn 2 (BOABA)(bpp)(OH)]·0.5H 2 O (1), [Cd 3 (BOABA) 2 (bpp) 2 (H 2 O) 6 ]·2H 2 O (2), [Cd 3 (BOABA) 2 (2,2′-bipy) 3 (H 2 O) 4 ]·5.5H 2 O (3), [CdNa(BOABA)(H 2 O)] 2 ·H 2 O (4) and [Cd 2 (BOABA)(bimb)Cl(H 2 O) 2 ]·H 2 O (5) (H 3 BOABA=3,5-bis-oxyacetate-benzoic acid, bpp=1,3-bi(4-pyridyl)propane, 2,2′-bipy=2,2′-bipyridine, bimb=1,4-bis(imidazol-1′-yl)butane), have been solvothermally synthesized and characterized by single-crystal X-ray diffraction, elemental analyses, IR spectra and TG analyses. 1 is an uninodal 4-connected 2D square grid network based on binuclear zinc clusters. 2 is 2D wavelike layer structure and further linked by hydrogen bonds into the final 3D (5,6,6)-connected topology network. 3 is 3-connected 2D topology network and the 2,2′-bipy ligands decorate in two different types. 4 is a (4,8)-connected 2D topology network with heterocaryotic {Cd 2 Na 2 } clusters and BOABA 3– ligands. 5 can be rationalized as a (3,10)-connected 3D topology network with tetranuclear {Cd 4 Cl 2 } clusters and BOABA 3– ligands. Meanwhile, photoluminescence studies revealed that these five coordination polymers display strong fluorescent emission bands in the solid state at room temperature. - Graphical abstract: Five new d 10 metal(II) coordination polymers based on H 3 BOABA ligand were obtained and characterized. They display different topological structures and luminescent properties. Highlights: ► Five d 10 metal(II) polymers based on 3,5-bis-oxyacetate-benzoic acid were obtained. ► The polymers were structurally characterized by single-crystal X-ray diffraction. ► Polymers 1–5 display different topological structures. ► They show strong fluorescent emission bands in the solid state.

Detection of anomalies in NLO sulphamic acid single crystals by ...

Indian Academy of Sciences (India)

The ultrasonic pulse echo overlap technique (PEO) has been used to measure the ... acid single crystals in the range of 300–400 K. This study evaluated all the elastic stiff- .... tic constants C11, C22, C33, C44, C55 and C66 have direct rela-.

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

Science.gov (United States)

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.

Multi-structure docking analysis of BACE1 crystal structures and non-peptidic ligands.

Science.gov (United States)

Haghighijoo, Zahra; Hemmateenejad, Bahram; Edraki, Najmeh; Miri, Ramin; Emami, Saeed

2017-09-01

In order to design novel non-peptidic inhibitors of BACE1, many research groups have attempted using computational studies including docking analyses. Since there are too many 3D structures for BACE1 in the protein database, the selection of suitable crystal structures is a key prerequisite for the successful application of molecular docking. We employed a multi-structure docking protocol. In which 615 ligands' structures were docked into 150 BACE1 structures. The large number of the resultant docking scores were post-processed by different data analysis methods including exploratory data analysis, regression analysis and discriminant analysis. It was found that using one crystal structure for docking did not result in high accuracy for predicting activity of the BACE1 inhibitors. Instead, using of the multi-structural docking scores, post-processed by chemometrics methods arrived to highly accurate predictive models. In this regards, the PDB accession codes of 4B70, 4DVF and 2WEZ could discriminate between active and inactive compounds, with higher accuracy. Clustering of the BACE1 structures based on principal component analysis of the crystallographic structures the revealed that the discriminant structures are in the center of the clusters. Thus, these structures can be selected as predominant crystal structures for docking studies of non-peptidic BACE1 inhibitors. Copyright © 2017 Elsevier Inc. All rights reserved.

Crystal structure of 2,5-di-methyl-anilinium salicylate.

Science.gov (United States)

Mani, A; Kumar, P Praveen; Chakkaravarthi, G

2015-09-01

The title mol-ecular salt, C8H12N(+)·C7H5O3 (-) arose from the proton-transfer reaction between 2,5-xylidine and salicylic acid. In the anion, the dihedral angle between the planes of the aromatic ring and the -CO2 (-) group is 11.08 (8)°; this near planarity is consolidated by an intra-molecular O-H⋯O hydrogen bond. In the crystal, the components are connected by N-H⋯O hydrogen bonds, with all three O atoms in the anion acting as acceptors; the result is a [100] chain. The structure also features weak C-H⋯O bonds and aromatic π-π stacking [centroid-to-centroid distance = 3.7416 (10) Å] inter-actions, which lead to a three-dimensional network.

Biophysical characterization and crystal structure of the Feline Immunodeficiency Virus p15 matrix protein.

Science.gov (United States)

Serrière, Jennifer; Robert, Xavier; Perez, Magali; Gouet, Patrice; Guillon, Christophe

2013-06-24

Feline Immunodeficiency Virus (FIV) is a viral pathogen that infects domestic cats and wild felids. During the viral replication cycle, the FIV p15 matrix protein oligomerizes to form a closed matrix that underlies the lipidic envelope of the virion. Because of its crucial role in the early and late stages of viral morphogenesis, especially in viral assembly, FIV p15 is an interesting target in the development of potential new therapeutic strategies. Our biochemical study of FIV p15 revealed that it forms a stable dimer in solution under acidic conditions and at high concentration, unlike other retroviral matrix proteins. We determined the crystal structure of full-length FIV p15 to 2 Å resolution and observed a helical organization of the protein, typical for retroviral matrix proteins. A hydrophobic pocket that could accommodate a myristoyl group was identified, and the C-terminal end of FIV p15, which is mainly unstructured, was visible in electron density maps. As FIV p15 crystallizes in acidic conditions but with one monomer in the asymmetric unit, we searched for the presence of a biological dimer in the crystal. No biological assembly was detected by the PISA server, but the three most buried crystallographic interfaces have interesting features: the first one displays a highly conserved tryptophan acting as a binding platform, the second one is located along a 2-fold symmetry axis and the third one resembles the dimeric interface of EIAV p15. Because the C-terminal end of p15 is involved in two of these three interfaces, we investigated the structure and assembly of a C-terminal-truncated form of p15 lacking 14 residues. The truncated FIV p15 dimerizes in solution at a lower concentration and crystallizes with two molecules in the asymmetric unit. The EIAV-like dimeric interface is the only one to be retained in the new crystal form. The dimeric form of FIV p15 in solution and its extended C-terminal end are characteristic among lentiviral matrix proteins

Crystal structure of isomeric boron difluoride acetylnaphtholates

International Nuclear Information System (INIS)

Bukvetskij, B.V.; Fedorenko, E.V.; Mirochnik, A.G.; Karasev, V.E.

2006-01-01

Crystal structures of luminescent isomeric acetylnaphtholates of boron difluoride are investigated. Full X-ray structural analysis is done at 293 K. Coordinated of atoms, bond angles, bond lengths, interatomic distances are determined. Results of comparative evaluations of the isomers are represented [ru

Effect of Cooling Rates on Shape and Crystal Size Distributions of Mefenamic Acid Polymorph in Ethyl Acetate

Science.gov (United States)

Mudalip, S. K. Abdul; Adam, F.; Parveen, J.; Abu Bakar, M. R.; Amran, N.; Sulaiman, S. Z.; Che Man, R.; Arshad, Z. I. Mohd; Shaarani, S. Md.

2017-06-01

This study investigate the effect of cooling rates on mefenamic acid crystallisation in ethyl acetate. The cooling rate was varied from 0.2 to 5 °C/min. The in-line conductivity system and turbidity system were employed to detect the onset of the crystallization process. The crystals produced were analysed using optical microscopy and Fourier transform infrared spectroscopy (FTIR). It was found that the crystals produced at different cooling rates were needle-like and exhibit polymorphic form type I. However, the aspect ratio and crystal size distributions were varied with the increased of cooling rate. A high crystals aspect ratio and narrower CSD (100-900 μm) was obtained at cooling rate of 0.5 °C/min. Thus, can be suggested as the most suitable cooling rate for crystallization of mefenamic acid in ethyl acetate.

Lanthanum tris[di(chloromethyl)phosphinate] dihydrate: crystal structure

International Nuclear Information System (INIS)

Aleksandrov, G.G.; Sergienko, V.S.; Afonin, E.G.

2001-01-01

X-ray diffraction analysis of the LaL 3 · 2H 2 O crystals, HL - di(chloromethyl)phosphinic acid, is conducted. Every of two crystallografically non-equivalent atoms La(1), La(2) is bound with six O(P) atoms of six L - anions performing function of bidentate μ 2 -bridge ligand in the top of pentagonal bipyramid and with O(w) atom of water molecule. La(H 2 O)L 3 particles of the both types are associated in polymer chains along the x axis of the crystal. Chains are conducted through hydrogen bonds O-H···O between coordinated and crystallization molecules of water as well as through short contacts Cl···Cl. Monophase state of polycrystal sample of complex was shown by method of X-ray diffraction of powder [ru

Structure of a designed, right-handed coiled-coil tetramer containing all biological amino acids.

Science.gov (United States)

Sales, Mark; Plecs, Joseph J; Holton, James M; Alber, Tom

2007-10-01

The previous design of an unprecedented family of two-, three-, and four-helical, right-handed coiled coils utilized nonbiological amino acids to efficiently pack spaces in the oligomer cores. Here we show that a stable, right-handed parallel tetrameric coiled coil, called RH4B, can be designed entirely using biological amino acids. The X-ray crystal structure of RH4B was determined to 1.1 Angstrom resolution using a designed metal binding site to coordinate a single Yb(2+) ion per 33-amino acid polypeptide chain. The resulting experimental phases were particularly accurate, and the experimental electron density map provided an especially clear, unbiased view of the molecule. The RH4B structure closely matched the design, with equivalent core rotamers and an overall root-mean-square deviation for the N-terminal repeat of the tetramer of 0.24 Angstrom. The clarity and resolution of the electron density map, however, revealed alternate rotamers and structural differences between the three sequence repeats in the molecule. These results suggest that the RH4B structure populates an unanticipated variety of structures.

Saturated fatty acids and fatty acid esters promote the polymorphic transition of clarithromycin metastable form I crystal.

Science.gov (United States)

Watanabe, Miteki; Mizoguchi, Midori; Aoki, Hajime; Iwao, Yasunori; Noguchi, Shuji; Itai, Shigeru

2016-10-15

The phase transition of active pharmaceutical ingredients should be taken into account during manufacturing, processing- and storage, because different crystal forms lead to different physical properties of formulations. The phase transition of clarithromycin (CAM) metastable form I to stable form II was investigated on heating with additives such as fatty acids or fatty acid esters. Differential scanning calorimetry analyses revealed that when form I was heated with additives, the phase transition temperature of form I decreased close to the melting points of the additives. Powder X-ray diffraction analyses indicated the tentative presence of a non-crystalline component during the transition of form I to form II on heating with additives. These observations implied that CAM form I dissolved in the melted additives on heating and the dissolved CAM crystallized to form II. Reduction of transition temperatures in the presence of additives were also observed for the crystals of nifedipine form B and carbamazepine form III. These results suggested that the phenomena can be widely applicable for simultaneous crystalline phase transition and granulation using binder additives. Copyright © 2016 Elsevier B.V. All rights reserved.

Crystal Structure of Methylornithine Synthase (PylB): Insights into the Pyrrolysine Biosynthesis

KAUST Repository

Quitterer, Felix

2011-11-16

Made by the barrel load: The biosynthetic pathway of the recently discovered 22nd amino acid, pyrrolysine, starts with an isomerization of lysine to methylornithine, catalyzed by PylB. The X-ray crystal structure of PylB is determined (see picture) and shows it has a TIM barrel fold. The sealed central cavity contains a [4Fe-4S] cluster, S-adenosylmethionine (SAM), and methylornithine, whose 2R,3R configuration could be confirmed. The data suggest a fragmentation-recombination mechanism via a glycyl radical intermediate. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Crystal structure of the UBR-box from UBR6/FBXO11 reveals domain swapping mediated by zinc binding.

Science.gov (United States)

Muñoz-Escobar, Juliana; Kozlov, Guennadi; Gehring, Kalle

2017-10-01

The UBR-box is a 70-residue zinc finger domain present in the UBR family of E3 ubiquitin ligases that directly binds N-terminal degradation signals in substrate proteins. UBR6, also called FBXO11, is an UBR-box containing E3 ubiquitin ligase that does not bind N-terminal signals. Here, we present the crystal structure of the UBR-box domain from human UBR6. The dimeric crystal structure reveals a unique form of domain swapping mediated by zinc coordination, where three independent protein chains come together to regenerate the topology of the monomeric UBR-box fold. Analysis of the structure suggests that the absence of N-terminal residue binding arises from the lack of an amino acid binding pocket. © 2017 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

Crystal structure analysis of C-phycoerythrin from marine cyanobacterium Phormidium sp. A09DM.

Science.gov (United States)

Kumar, Vinay; Sonani, Ravi R; Sharma, Mahima; Gupta, Gagan D; Madamwar, Datta

2016-07-01

The role of unique sequence features of C-phycoerythrin, isolated from Phormidium sp. A09DM, has been investigated by crystallographic studies. Two conserved indels (i.e. inserts or deletions) are found in the β-subunit of Phormidium phycoerythrin that are distinctive characteristics of large number of cyanobacterial sequences. The identified signatures are a two-residue deletion from position 21 and a nine-residue insertion at position 146. Crystals of Phormidium phycoerythrin were obtained at pH values of 5 and 8.5, and structures have been resolved to high precision at 1.95 and 2.1 Å resolution, respectively. In both the structures, heterodimers of α- and β- subunits assemble as hexamers. The 7-residue insertion at position 146 significantly reduces solvent exposure of π-conjugated A-C rings of a phycoerythrobilin (PEB) chromophore, and can influence energy absorption and energy transfer characteristics. The structural analyses (with 12-fold redundancy) suggest that protein micro-environment alone dictates the conformation of bound chromophores. The low- and high-energy absorbing chromophores are identified based on A-B ring coplanarity. The spatial distribution of these is found to be similar to that observed in R-phycoerythrin, suggesting the direction of energy transfer from outer-surface of hexamer to inner-hollow cavity in the Phormidium protein. The crystal structures also reveal that a commonly observed Hydrogen-bonding network in phycobiliproteins, involving chromophore bound to α-subunit and amino acid at position 73 of β-subunit, may not be essential for structural and functional integrity of C-phycoerythrin orthologs. In solution, the protein displays slight red shift and decrease in fluorescence emission at acidic pH. The mechanism for which may be static and correlates with the proximity of +ve electric field of Arg148 to the C-ring of a PEB chromophore.

Structure of a second crystal form of Bence-Jones protein Loc: Strikingly different domain associations in two crystal forms of a single protein

International Nuclear Information System (INIS)

Schiffer, M.; Ainsworth, C.; Xu, Z.B.; Carperos, W.; Olsen, K.; Solomon, A.; Stevens, F.J.; Chang, C.H.

1989-01-01

The authors have determined the structure of the immunoglobulin light-chain dimer Loc in a second crystal form that was grown from distilled water. The crystal structure was determined to 2.8-angstrom resolution; the R factor is 0.22. The two variable domains are related by local 2-fold axes and form an antigen binding pocket. The variable domain-variable domain interaction observed in this crystal form differs from the one exhibited by the protein when crystallized from ammonium sulfate in which the two variable domains formed a protrusion. The structure attained in the distilled water crystals is similar to, but not identical with, the one observed for the Mcg light-chain dimer in crystals grown from ammonium sulfate. Thus, two strikingly different structures were attained by this multisubunit protein in crystals grown under two different, commonly used, crystallization techniques. The quaternary interactions exhibited by the protein in the two crystal forms are sufficiently different to suggest fundamentally different interpretations of the structural basis for the function of this protein. This observation may have general implications regarding the use of single crystallographic determinations for detailed identification of structural and functional relationships. On the other hand, proteins whose structures can be altered by manipulation of crystallization conditions may provide useful systems for study of fundamental structural chemistry

Overexpression, purification, crystallization and preliminary structural studies of catabolic ornithine transcarbamylase from Lactobacillus hilgardii

Energy Technology Data Exchange (ETDEWEB)

Rivas, Blanca de las; Rodríguez, Héctor [Instituto de Fermentaciones Industriales, CSIC, Juan de la Cierva 3, 28006 Madrid (Spain); Angulo, Iván [Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto Rocasolano, CSIC, Serrano 119, 28006 Madrid (Spain); Muñoz, Rosario [Instituto de Fermentaciones Industriales, CSIC, Juan de la Cierva 3, 28006 Madrid (Spain); Mancheño, José M., E-mail: xjosemi@iqfr.csic.es [Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto Rocasolano, CSIC, Serrano 119, 28006 Madrid (Spain); Instituto de Fermentaciones Industriales, CSIC, Juan de la Cierva 3, 28006 Madrid (Spain)

2007-07-01

The catabolic ornithine transcarbamylase (cOTC) from L. hilgardii has been overexpressed in E. coli, purified and crystallized under two different experimental conditions. The structure has been solved by the molecular-replacement method using the atomic coordinates of catabolic ornithine transcarbamylase from P. aeruginosa as the search model. The catabolic ornithine transcarbamylase (cOTC; EC 2.1.3.3) from the lactic acid bacteria Lactobacillus hilgardii is a key protein involved in the degradation of arginine during malolactic fermentation. cOTC containing an N-terminal His{sub 6} tag has been overexpressed in Escherichia coli, purified and crystallized under two different experimental conditions using the hanging-drop vapour-diffusion method. Crystals obtained from a solution containing 8%(w/v) PEG 4000, 75 mM sodium acetate pH 4.6 belong to the trigonal space group P321 and have unit-cell parameters a = b = 157.04, c = 79.28 Å. Conversely, crystals grown in 20%(v/v) 2-methyl-2,4-pentanediol, 7.5%(w/v) PEG 4000, 100 mM HEPES pH 7.8 belong to the monoclinic space group C2 and have unit-cell parameters a = 80.06, b = 148.90, c = 91.67 Å, β = 100.25°. Diffraction data were collected in-house to 3.00 and 2.91 Å resolution for trigonal and monoclinic crystals, respectively. The estimated Matthews coefficient for the crystal forms were 2.36 and 2.24 Å{sup 3} Da{sup −1}, respectively, corresponding to 48% and 45% solvent content. In both cases, the results are consistent with the presence of three protein subunits in the asymmetric unit. The structure of cOTC has been determined by the molecular-replacement method using the atomic coordinates of cOTC from Pseudomonas aeruginosa (PDB code) as the search model.

Overexpression, purification, crystallization and preliminary structural studies of catabolic ornithine transcarbamylase from Lactobacillus hilgardii

International Nuclear Information System (INIS)

Rivas, Blanca de las; Rodríguez, Héctor; Angulo, Iván; Muñoz, Rosario; Mancheño, José M.

2007-01-01

The catabolic ornithine transcarbamylase (cOTC) from L. hilgardii has been overexpressed in E. coli, purified and crystallized under two different experimental conditions. The structure has been solved by the molecular-replacement method using the atomic coordinates of catabolic ornithine transcarbamylase from P. aeruginosa as the search model. The catabolic ornithine transcarbamylase (cOTC; EC 2.1.3.3) from the lactic acid bacteria Lactobacillus hilgardii is a key protein involved in the degradation of arginine during malolactic fermentation. cOTC containing an N-terminal His 6 tag has been overexpressed in Escherichia coli, purified and crystallized under two different experimental conditions using the hanging-drop vapour-diffusion method. Crystals obtained from a solution containing 8%(w/v) PEG 4000, 75 mM sodium acetate pH 4.6 belong to the trigonal space group P321 and have unit-cell parameters a = b = 157.04, c = 79.28 Å. Conversely, crystals grown in 20%(v/v) 2-methyl-2,4-pentanediol, 7.5%(w/v) PEG 4000, 100 mM HEPES pH 7.8 belong to the monoclinic space group C2 and have unit-cell parameters a = 80.06, b = 148.90, c = 91.67 Å, β = 100.25°. Diffraction data were collected in-house to 3.00 and 2.91 Å resolution for trigonal and monoclinic crystals, respectively. The estimated Matthews coefficient for the crystal forms were 2.36 and 2.24 Å 3 Da −1 , respectively, corresponding to 48% and 45% solvent content. In both cases, the results are consistent with the presence of three protein subunits in the asymmetric unit. The structure of cOTC has been determined by the molecular-replacement method using the atomic coordinates of cOTC from Pseudomonas aeruginosa (PDB code) as the search model

Structure of initial crystals formed during human amelogenesis

Science.gov (United States)

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.

Structures of the OmpF porin crystallized in the presence of foscholine-12.

Science.gov (United States)

Kefala, Georgia; Ahn, Chihoon; Krupa, Martin; Esquivies, Luis; Maslennikov, Innokentiy; Kwiatkowski, Witek; Choe, Senyon

2010-05-01

The endogenous Escherichia coli porin OmpF was crystallized as an accidental by-product of our efforts to express, purify, and crystallize the E. coli integral membrane protein KdpD in the presence of foscholine-12 (FC12). FC12 is widely used in membrane protein studies, but no crystal structure of a protein that was both purified and crystallized with this detergent has been reported in the Protein Data Bank. Crystallization screening for KdpD yielded two different crystals of contaminating protein OmpF. Here, we report two OmpF structures, the first membrane protein crystal structures for which extraction, purification, and crystallization were done exclusively with FC12. The first structure was refined in space group P21 with cell parameters a = 136.7 A, b = 210.5 A, c = 137 A, and beta = 100.5 degrees , and the resolution of 3.8 A. The second structure was solved at the resolution of 4.4 A and was refined in the P321 space group, with unit cell parameters a = 215.5 A, b = 215.5 A, c = 137.5 A, and gamma = 120 degrees . Both crystal forms show novel crystal packing, in which the building block is a tetrahedral arrangement of four trimers. Additionally, we discuss the use of FC12 for membrane protein crystallization and structure determination, as well as the problem of the OmpF contamination for membrane proteins overexpressed in E. coli.

Mitigating crystallization of saturated FAMES (fatty acid methyl esters) in biodiesel: 4. The phase behavior of 1,3-dioleoyl-2-palmitoyl glycerol – Methyl stearate binary system

International Nuclear Information System (INIS)

Mohanan, Athira; Bouzidi, Laziz; Narine, Suresh S.

2016-01-01

The present study examines the phase behavior of a model binary system made of OPO (1,3-dioleoyl-2-palmitoyl glycerol); a TAG (triacylglycerol) highly effective in depressing onset of crystallization of biodiesel, and MeS (methyl stearate); a prevalent saturated FAMEs (fatty acid methyl esters) in biodiesel. The thermal behavior, crystal structure and microstructure of the OPO/MeS mixtures were investigated with DSC (differential scanning calorimetry), XRD (X-ray diffraction) and PLM (polarized light microscope). The OPO/MeS system presented a phase diagram with peritectic and eutectic transitions. A simple thermodynamic modeling of the liquidus line indicated a relatively complex mixing behavior, and highlighted the prevailing effect of the peritectic compound on solubility. Different types of microstructures that were more or less influenced by MeS, OPO or/and compound microstructures were observed in the mixtures. They are associated with the crystal phases and the thermal transitions. Furthermore, MeS, OPO and compound crystal structures (monoclinic, orthorhombic and triclinic, respectively) served as templates for the crystal forms of the coexisting phases. The singularities in the liquidus line are attributed to chain length mismatch between the palmitic acid and the FAME (fatty acid methyl ester). The phase diagram achieved for OPO/MeS system is complete and can help in designing additive formulations to improve the cold flow behavior of biodiesel. - Highlights: • 1,3-dioleoyl-2-palmitoyl glycerol/methyl stearate (OPO/MeS) studied in detail. • Phase diagram with thermal transitions, polymorphism, microstructure achieved. • Phase trajectory singularities attributed to length mismatch of linear chains. • Mechanism for disruption of crystallization of biodiesel evidenced and explained.

Growth, spectral and optical characterization of a novel nonlinear optical organic material: D-Alanine DL-Mandelic acid single crystal

Science.gov (United States)

Jayaprakash, P.; Mohamed, M. Peer; Caroline, M. Lydia

2017-04-01

An organic nonlinear optical single crystal, D-alanine DL-mandelic acid was synthesized and successfully grown by slow evaporation solution growth technique at ambient temperature using solvent of aqueous solution. The unit cell parameters were assessed from single crystal X-ray diffraction analysis. The presence of diverse functional groups and vibrational modes were identified using Fourier Transform Infra Red and Fourier Transform Raman spectral analyses. The chemical structure of grown crystal has been identified by Nuclear Magnetic Resonance spectroscopic study. Ultraviolet-visible spectral analysis reveal that the crystal has lower cut-off wavelength down to 259 nm, is a key factor to exhibit second harmonic generation signal. The electronic optical band gap and Urbach energy is calculated as 5.31 eV and 0.2425 eV respectively from the UV absorption profile. The diverse optical properties such as, extinction coefficient, reflectance, linear refractive index, optical conductivity was calculated using UV-visible data. The relative second harmonic efficiency of the compound is found to be 0.81 times greater than that of KH2PO4 (KDP). The thermal stability of the grown crystal was studied by thermogravimetric analysis and differential thermal analysis techniques. The luminescence spectrum exhibited two peaks (520 nm, 564 nm) due to the donation of protons from carboxylic acid to amino group. The Vickers microhardness test was carried out employing one of the as-grown hard crystal and there by hardness number (Hv), Meyer's index (n), yield strength (σy), elastic stiffness constant (C11) and Knoop hardness number (HK) were assessed. The dielectric behaviour of the as-grown crystal was analyzed for different temperatures (313 K, 333 K, 353 K, and 373 K) at different frequencies.

The effect of amino acid backbone length on molecular packing: crystalline tartrates of glycine, β-alanine, γ-aminobutyric acid (GABA) and DL-α-aminobutyric acid (AABA).

Science.gov (United States)

Losev, Evgeniy; Boldyreva, Elena

2018-02-01

We report a novel 1:1 cocrystal of β-alanine with DL-tartaric acid, C 3 H 7 NO 2 ·C 4 H 6 O 6 , (II), and three new molecular salts of DL-tartaric acid with β-alanine {3-azaniumylpropanoic acid-3-azaniumylpropanoate DL-tartaric acid-DL-tartrate, [H(C 3 H 7 NO 2 ) 2 ] + ·[H(C 4 H 5 O 6 ) 2 ] - , (III)}, γ-aminobutyric acid [3-carboxypropanaminium DL-tartrate, C 4 H 10 NO 2 + ·C 4 H 5 O 6 - , (IV)] and DL-α-aminobutyric acid {DL-2-azaniumylbutanoic acid-DL-2-azaniumylbutanoate DL-tartaric acid-DL-tartrate, [H(C 4 H 9 NO 2 ) 2 ] + ·[H(C 4 H 5 O 6 ) 2 ] - , (V)}. The crystal structures of binary crystals of DL-tartaric acid with glycine, (I), β-alanine, (II) and (III), GABA, (IV), and DL-AABA, (V), have similar molecular packing and crystallographic motifs. The shortest amino acid (i.e. glycine) forms a cocrystal, (I), with DL-tartaric acid, whereas the larger amino acids form molecular salts, viz. (IV) and (V). β-Alanine is the only amino acid capable of forming both a cocrystal [i.e. (II)] and a molecular salt [i.e. (III)] with DL-tartaric acid. The cocrystals of glycine and β-alanine with DL-tartaric acid, i.e. (I) and (II), respectively, contain chains of amino acid zwitterions, similar to the structure of pure glycine. In the structures of the molecular salts of amino acids, the amino acid cations form isolated dimers [of β-alanine in (III), GABA in (IV) and DL-AABA in (V)], which are linked by strong O-H...O hydrogen bonds. Moreover, the three crystal structures comprise different types of dimeric cations, i.e. (A...A) + in (III) and (V), and A + ...A + in (IV). Molecular salts (IV) and (V) are the first examples of molecular salts of GABA and DL-AABA that contain dimers of amino acid cations. The geometry of each investigated amino acid (except DL-AABA) correlates with the melting point of its mixed crystal.

High-Resolution Crystal Structure of a Silver(I)-RNA Hybrid Duplex Containing Watson-Crick-like C-Silver(I)-C Metallo-Base Pairs.

Science.gov (United States)

Kondo, Jiro; Tada, Yoshinari; Dairaku, Takenori; Saneyoshi, Hisao; Okamoto, Itaru; Tanaka, Yoshiyuki; Ono, Akira

2015-11-02

Metallo-base pairs have been extensively studied for applications in nucleic acid-based nanodevices and genetic code expansion. Metallo-base pairs composed of natural nucleobases are attractive because nanodevices containing natural metallo-base pairs can be easily prepared from commercially available sources. Previously, we have reported a crystal structure of a DNA duplex containing T-Hg(II)-T base pairs. Herein, we have determined a high-resolution crystal structure of the second natural metallo-base pair between pyrimidine bases C-Ag(I)-C formed in an RNA duplex. One Ag(I) occupies the center between two cytosines and forms a C-Ag(I)-C base pair through N3-Ag(I)-N3 linear coordination. The C-Ag(I)-C base pair formation does not disturb the standard A-form conformation of RNA. Since the C-Ag(I)-C base pair is structurally similar to the canonical Watson-Crick base pairs, it can be a useful building block for structure-based design and fabrication of nucleic acid-based nanodevices. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Crystal structure of vanadite: Refinement of anisotropic displacement parameters

Czech Academy of Sciences Publication Activity Database

Laufek, F.; Skála, Roman; Haloda, J.; Císařová, I.

2006-01-01

Roč. 51, 3-4 (2006), s. 271-275 ISSN 1210-8197 Institutional research plan: CEZ:AV0Z30130516 Keywords : anisotropic displacement parameter * crystal structure * single-crystal X-ray refinement * vanadinite Subject RIV: DB - Geology ; Mineralogy

Crystal structure of N-(quinolin-6-ylhydroxylamine

Directory of Open Access Journals (Sweden)

Anuruddha Rajapakse

2014-11-01

Full Text Available The title compound, C9H8N2O, crystallized with four independent molecules in the asymmetric unit. The four molecules are linked via one O—H...N and two N—H...N hydrogen bonds, forming a tetramer-like unit. In the crystal, molecules are further linked by O—H...N and N—H...O hydrogen bonds forming layers parallel to (001. These layers are linked via C—H...O hydrogen bonds and a number of weak C—H...π interactions, forming a three-dimensional structure. The crystal was refined as a non-merohedral twin with a minor twin component of 0.319.

Physicochemical and crystal structure analyses of the antidiabetic agent troglitazone.

Science.gov (United States)

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.