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Reported Structures (reported + structure)
Selected AbstractsChemInform Abstract: Synthesis of Elemane Bis-lactones from Santonin , Synthesis of the Reported Structure of seco-Isoerivanin Pseudo Acid and Formal Synthesis of (+)-8-Deoxyvernolepin.CHEMINFORM, Issue 3 2001Gonzalo Blay Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a "Full Text" option. The original article is trackable via the "References" option. [source] High resolution structure and catalysis of O -acetylserine sulfhydrylase isozyme B from Escherichia coliFEBS JOURNAL, Issue 20 2007Georg Zocher The crystal structure of the dimeric O -acetylserine sulfhydrylase isozyme B from Escherichia coli (CysM), complexed with the substrate analog citrate, has been determined at 1.33 Å resolution by X-ray diffraction analysis. The C1-carboxylate of citrate was bound at the carboxylate position of O -acetylserine, whereas the C6-carboxylate adopted two conformations. The activity of the enzyme and of several active center mutants was determined using an assay based on O -acetylserine and thio-nitrobenzoate (TNB). The unnatural substrate TNB was modeled into the reported structure. The substrate model and the observed mutant activities may facilitate future protein engineering attempts designed to broaden the substrate spectrum of the enzyme. A comparison of the reported structure with previously published CysM structures revealed large conformational changes. One of the crystal forms contained two dimers, each of which comprised one subunit in a closed and one in an open conformation. Although the homodimer asymmetry was most probably caused by crystal packing, it indicates that the enzyme can adopt such a state in solution, which may be relevant for the catalytic reaction. [source] Pitfalls of data mining: triclinic polymorph of 2,2-aziridinedicarboxamide revisitedACTA CRYSTALLOGRAPHICA SECTION B, Issue 1 2007Marcin Podsiad Several procedures have been employed for validating structural models refined on poor quality single-crystal diffraction data. Analysis of intra- and intermolecular distances in the structures of 2,2-aziridinedicarboxamide polymorphs proved to be a robust means, and a means independent of the chosen unit cell and symmetry, of detecting several incorrect atom-type assignments in the reported structure of the triclinic polymorph of 2,2-aziridinedicarboxamide [Brückner (1982). Acta Cryst. B38, 2405,2408]. The corrected model, refined in the space group , rules out the existence of any conformational polymorphism in this compound. Small differences in the powder-diffraction patterns calculated for the original and corrected structures of the triclinic polymorph illustrate the sensitivity of the above method for polymorph validation. [source] K3TaF8 from laboratory X-ray powder dataACTA CRYSTALLOGRAPHICA SECTION C, Issue 2 2010ubomír Smr The crystal structure of tripotassium octafluoridotantalate, K3TaF8, determined from laboratory powder diffraction data by the simulated annealing method and refined by total energy minimization in the solid state, is built from discrete potassium cations, fluoride anions and monocapped trigonal,prismatic [TaF7]2, ions. All six atoms in the asymmetric unit are in special positions of the P63mc space group: the Ta and one F atom in the 2b (3m) sites, the K and two F atoms in the 6c (m) sites, and one F atom in the 2a (3m) site. The structure consists of face-sharing K6 octahedra with a fluoride anion at the center of each octahedron, forming chains of composition [FK3]2+ running along [001] with isolated [TaF7]2, trigonal prisms in between. The structure of the title compound is different from the reported structure of Na3TaF8 and represents a new structure type. [source] 1,3-Bis(ethylamino)-2-nitrobenzene, 1,3-bis(n -octylamino)-2-nitrobenzene and 4-ethylamino-2-methyl-1H -benzimidazoleACTA CRYSTALLOGRAPHICA SECTION C, Issue 5 2008Christopher P. Walczak 1,3-Bis(ethylamino)-2-nitrobenzene, C10H15N3O2, (I), and 1,3-bis(n -octylamino)-2-nitrobenzene, C22H39N3O2, (II), are the first structurally characterized 1,3-bis(n -alkylamino)-2-nitrobenzenes. Both molecules are bisected though the nitro N atom and the 2-C and 5-C atoms of the ring by twofold rotation axes. Both display intramolecular N,H...O hydrogen bonds between the amine and nitro groups, but no intermolecular hydrogen bonding. The nearly planar molecules pack into flat layers ca 3.4,Å apart that interact by hydrophobic interactions involving the n -alkyl groups rather than by ,,, interactions between the rings. The intra- and intermolecular interactions in these molecules are of interest in understanding the physical properties of polymers made from them. Upon heating in the presence of anhydrous potassium carbonate in dimethylacetamide, (I) and (II) cyclize with formal loss of hydrogen peroxide to form substituted benzimidazoles. Thus, 4-ethylamino-2-methyl-1H -benzimidazole, C10H13N3, (III), was obtained from (I) under these reaction conditions. Compound (III) contains two independent molecules with no imposed internal symmetry. The molecules are linked into chains via N,H...N hydrogen bonds involving the imidazole rings, while the ethylamino groups do not participate in any hydrogen bonding. This is the first reported structure of a benzimidazole derivative with 4-amino and 2-alkyl substituents. [source] Form I of desloratadine, a tricyclic antihistamineACTA CRYSTALLOGRAPHICA SECTION C, Issue 6 2006Prashant M. Bhatt The title compound [systematic name: 8-chloro-11-(piperidin-4-ylidene)-6,11-dihydro-5H -benzo[4,5]cyclohepta[2,1- b]pyridine], C19H19ClN2, was crystallized from ethyl acetate. The interesting feature of the reported structure is that it does not contain any strong hydrogen bonds, although the molecule contains a secondary NH group, which is a good hydrogen-bond donor. [source] Structure validation in chemical crystallographyACTA CRYSTALLOGRAPHICA SECTION D, Issue 2 2009Anthony L. Spek Automated structure validation was introduced in chemical crystallography about 12,years ago as a tool to assist practitioners with the exponential growth in crystal structure analyses. Validation has since evolved into an easy-to-use checkCIF/PLATON web-based IUCr service. The result of a crystal structure determination has to be supplied as a CIF-formatted computer-readable file. The checking software tests the data in the CIF for completeness, quality and consistency. In addition, the reported structure is checked for incomplete analysis, errors in the analysis and relevant issues to be verified. A validation report is generated in the form of a list of ALERTS on the issues to be corrected, checked or commented on. Structure validation has largely eliminated obvious problems with structure reports published in IUCr journals, such as refinement in a space group of too low symmetry. This paper reports on the current status of structure validation and possible future extensions. [source] How to Produce a Chemical Defense: Structural Elucidation and Anatomical Distribution of Aplysioviolin and Phycoerythrobilin in the Sea Hare Aplysia californicaCHEMISTRY & BIODIVERSITY, Issue 5 2010Michiya Kamio Abstract We previously used bioassay-guided fractionation to identify phycoerythrobilin (1) and its monomethyl ester, aplysioviolin (2), as components in the ink secretion of a marine gastropod, the sea hare Aplysia californica, that act as chemical deterrents against predatory blue crabs. This was the first report of 1 as a natural product. Compound 2 was previously reported as a natural product from three species of Aplysia (A. fasciata, A. dactylomela, and A. parvula), but the reported structure and composition of stereoisomers of 2 are different among these species. Sea hares are thought to produce 2 from phycoerythrin, a photosynthetic pigment in their red-algal diet composed of a phycobiliprotein covalently linked to the chromophore 1, by cleavage of the covalent bond and methylation of 1, but neither the sequence nor the anatomical location of the cleavage and methylation is known. In this study, we clarify the structure of 1 and 2 in ink secretion of A. californica, and describe the distribution of 1 and 2 in the tissues of sea hares. We conclude that cleavage of the covalent bond in phycoerythrin occurs first, forming 1 in the digestive gland, followed by methylation of 1 to yield 2 in the ink gland. [source] Spectroscopic investigations and computational study of 2-[acetyl(4-bromophenyl)carbamoyl]-4-chlorophenyl acetateJOURNAL OF RAMAN SPECTROSCOPY, Issue 6 2010C. Yohannan Panicker Abstract The Fourier transform Raman (FT-Raman) and Fourier transform infrared (FT-IR) spectra of 2-[acetyl(4-bromophenyl)carbamoyl]-4-chlorophenyl acetate were studied. The vibrational wavenumbers were examined theoretically using the Gaussian03 set of quantum chemistry codes, and the normal modes were assigned by potential energy distribution (PED) calculations. The simultaneous Raman and infrared (IR) activations of the CO stretching mode in the carbamoyl moiety show a charge transfer interaction through a ,-conjugated path. From the optimized structure, it is clear that the hydrogen bonding decreases the double bond character of the CO bond and increases the double bond character of the CN bonds. The first hyperpolarizability and predicted IR intensities are reported. The calculated first hyperpolarizability is comparable with the reported values of similar structures, which makes this compound an attractive object for future studies of nonlinear optics. Optimized geometrical parameters of the compound are in agreement with similar reported structures. Copyright © 2009 John Wiley & Sons, Ltd. [source] Structural conservation in the major facilitator superfamily as revealed by comparative modelingPROTEIN SCIENCE, Issue 7 2004Eyal Vardy Abstract The structures of membrane transporters are still mostly unsolved. Only recently, the first two high-resolution structures of transporters of the major facilitator superfamily (MFS) were published. Despite the low sequence similarity of the two proteins involved, lactose permease and glycerol-3-phosphate transporter, the reported structures are highly similar. This leads to the hypothesis that all members of the MFS share a similar structure, regardless of their low sequence identity. To test this hypothesis, we generated models of two other members of the MFS, the Tn10-encoded metal-tetracycline/H+ antiporter (TetAB) and the rat vesicular monoamine transporter (rVMAT2). The models are based on the two MFS structures and on experimental data. The models for both proteins are in good agreement with the data available and support the notion of a shared fold for all MFS proteins. [source] Hexaaquanickel(II) disulfato(1,4,8,11-tetraazacyclotetradecane)nickelate(II) dihydrateACTA CRYSTALLOGRAPHICA SECTION C, Issue 9 2010Andrew James Churchard The title compound, [Ni(H2O)6][Ni(SO4)2(C10H24N4)]·2H2O, is an unusual compound in that it is composed of a hexaaqua complex, formally a dication, and a mixed-donor complex (four N and two O atoms), formally a dianion, with substantial charge separation between the two nickel centres (6.536,Å). The homoleptic dication complex consists of the weaker-field ligands, whilst the dianion retains the coordination of all the higher-field donors. Both nickel ions are located at centres of symmetry. This rare compound is placed in the context of previously reported structures which emphasizes its peculiarity. [source] Luminescence properties of the structure built from 3-cyano-4-dicyanomethylene-5-oxo-4,5-dihydro-1H -pyrrol-2-olate and caesium(I)ACTA CRYSTALLOGRAPHICA SECTION C, Issue 2 2010Viktor A. Tafeenko The structure of caesium(I) 3-cyano-4-dicyanomethylene-5-oxo-4,5-dihydro-1H -pyrrol-2-olate (CsA), Cs+·C8HN4O2,, is related to its luminescence properties. The structure of CsA (triclinic, P) is not isomorphous with previously reported structures (monoclinic, P21/c) of the KA and RbA salts. Nevertheless, the coordination numbers of the metals are equal for all salts (nine). Each anion in the CsA salt is connected by pairs of inversion-related N,H...O hydrogen bonds to another anion, forming a centrosymmetric dimer. The dimers are linked into infinite ribbons, stacked by means of ,,, interactions, thus building up an anionic wall. Time-dependent density functional theory calculations show that the formation of the dimer shifts the wavelength of the luminescence maximum to the blue region. Shortening the distance between stacked anions in the row [from 3.431,(5),Å for RbA to 3.388,(2),Å for KA to 3.244,(10),Å for CsA] correlates with a redshift of the luminescence maximum from 574 and 580,nm to 596,nm, respectively. [source] Manganese(II) and cobalt(II) complexes of 1,4-bis(diphenylphosphinoyl)butaneACTA CRYSTALLOGRAPHICA SECTION C, Issue 1 2009Anthony M. J. Lees The title complexes, catena -poly[[[diaquadiethanolmanganese(II)]-,-1,4-bis(diphenylphosphinoyl)butane-,2O:O,] dinitrate 1,4-bis(diphenylphosphinoyl)butane solvate], {[Mn(C2H6O)2(C28H28O2P2)(H2O)2](NO3)2·C28H28O2P2}n, (I), and catena -poly[[[diaquadiethanolcobalt(II)]-,-1,4-bis(diphenylphosphinoyl)butane-,2O:O,] dinitrate 1,4-bis(diphenylphosphinoyl)butane solvate], {[Co(C2H6O)2(C28H28O2P2)(H2O)2](NO3)2·C28H28O2P2}n, (II), are isostructural and centrosymmetric, with the MII ions at centres of inversion. The coordination geometry is octahedral, with each metal ion coordinated by two trans ethanol molecules, two trans water molecules and two bridging 1,4-bis(diphenylphosphinoyl)butane ligands which link the coordination centres to form one-dimensional polymeric chains. Parallel chains are linked by hydrogen bonds to uncoordinated 1,4-bis(diphenylphosphinoyl)butane molecules, which are bisected by a centre of inversion. Further hydrogen bonds, weak C,H...O interactions to nitrate anions, and weak C,H..., interactions serve to stabilize the structure. This study reports a development of the coordination chemistry of bis(diphenylphosphinoyl)alkanes, with the first reported structures of complexes of the first-row transition metals with 1,4-bis(diphenylphosphinoyl)butane. [source] The new three-dimensional supramolecule bis{,-2-[(4-hydroxybenzoyl)hydrazonomethyl]phenolato}bis[aquacopper(II)] dinitrateACTA CRYSTALLOGRAPHICA SECTION C, Issue 10 2008Hua Yin In the title centrosymmetric binuclear complex, [Cu2(C14H11N2O3)2(H2O)2](NO3)2, the two metal centres are bridged by the phenolate O atoms of the ligand, forming a Cu2O2 quadrangle. Each Cu atom has a distorted square-pyramidal geometry, with the basal donor atoms coming from the O,N,O,-tridentate ligand and a symmetry-related phenolate O atom. The more weakly bound apical donor O atom is supplied by a coordinated water molecule. When a further weak Cu...O interaction with the 4-hydroxy O atom of a neighbouring cation is considered, the extended coordination sphere of the Cu atom can be described as distorted octahedral. This interaction leads to two-dimensional layers, which extend parallel to the (100) direction. The two-dimensional polymeric structure contrasts with other reported structures involving salicylaldehyde benzoylhydrazone ligands, which are usually discrete mono- or dinuclear Cu complexes. The nitrate anions are involved in a three-dimensional hydrogen-bonding network, featuring intermolecular N,H...O and O,H...O hydrogen bonds. [source] Three new enantiomerically pure ferrocenylphosphole compoundsACTA CRYSTALLOGRAPHICA SECTION C, Issue 5 2006Eric Manoury The absolute configurations of three new enantiomerically pure ferrocenylphosphole compounds, namely (2S,4S,SFc)-4-methoxymethyl-2-[2-(9-thioxo-9,5 -phosphafluoren-9-yl)ferrocenyl]-1,3-dioxane, [Fe(C5H5)(C23H22O3PS)], (III), (SFc)-[2-(9-thioxo-9,5 -phosphafluoren-9-yl)ferrocenyl]methanol, [Fe(C5H5)(C18H14OPS)], (V), and (SFc)-diphenyl[2-(9-thioxo-9,5 -phosphafluoren-9-yl]ferrocenylmethyl]phosphine, [Fe(C5H5)(C30H23P2)], (VIII), have been unambiguously established. All three ligands contain a planar chiral ferrocene group, bearing a dibenzophosphole and either a dioxane, a methanol or a diphenylphosphinomethane group on the same cyclopentadienyl. In compound (V), the occurrence of O,H,S and C,H,S hydrogen bonds results in the formation of a two-dimensional network parallel to (001). The geometry of the ferrocene frameworks agrees with related reported structures. [source] Observation of a calcium-binding site in the ,-class carbonic anhydrase from Pyrococcus horikoshiiACTA CRYSTALLOGRAPHICA SECTION D, Issue 10 2008Jeyaraman Jeyakanthan Carbonic anhydrases are zinc-containing metalloenzymes that catalyze the interconversion of carbon dioxide and bicarbonate. Three crystal structures of ,-class carbonic anhydrase (one of which is bound to a bicarbonate molecule) from the aerobic OT3 strain of the hyperthermophilic archeon Pyrococcus horikoshii have been solved by molecular replacement in space group F4132. The asymmetric unit contains a monomer of 173 amino acids and a catalytic Zn2+ ion. The protein fold is a regular prism formed by a left-handed ,-helix, similar to previously reported structures. The active-site Zn2+ ion located at the interface between the two monomers is bound to three histidyl residues and a water molecule in a tetrahedral fashion. In addition to the 20 ,-strands comprising the ,-helix, there is also a long C-terminal ,-helix. For the first time, Ca2+ ions have been observed in addition to the catalytic Zn2+ ion. It is hypothesized that Tyr159 (which corresponds to the catalytically important Asn202 in previously reported structures) utilizes C,H..., interactions to fulfill its functions. This study may shed light on the catalytic mechanism of the enzyme and throw open new questions on the mechanism of product removal in carbonic anhydrases. [source] Structural flexibility, an essential component of the allosteric activation in Escherichia coli glucosamine-6-phosphate deaminaseACTA CRYSTALLOGRAPHICA SECTION D, Issue 1 2002E. Rudiño-Piñera A new crystallographic structure of the free active-site R conformer of the allosteric enzyme glucosamine-6-phosphate deaminase from Escherichia coli, coupled with previously reported structures of the T and R conformers, generates a detailed description of the heterotropic allosteric transition in which structural flexibility plays a central role. The T conformer's external zone [Horjales et al. (1999), Structure, 7, 527,536] presents higher B values than in the R conformers. The ligand-free enzyme (T conformer) undergoes an allosteric transition to the free active-site R conformer upon binding of the allosteric activator. This structure shows three alternate conformations of the mobile section of the active-site lid (residues 163,182), in comparison to the high B values for the unique conformation of the T conformer. One of these alternate R conformations corresponds to the active-site lid found when the substrate is bound. The disorder associated with the three alternate conformations can be related to the biological regulation of the Km of the enzyme for the reaction, which is metabolically required to maintain adequate concentrations of the activator, which holds the enzyme in its R state. Seven alternate conformations for the active-site lid and three for the C-terminus were refined for the T structure using isotropic B factors. Some of these conformers approach that of the R conformer in geometry. Furthermore, the direction of the atomic vibrations obtained with anisotropic B refinement supports the hypothesis of an oscillating rather than a tense T state. The concerted character of the allosteric transition is also analysed in view of the apparent dynamics of the conformers. [source] Trypanosoma brucei UDP-galactose-4,-epimerase in ternary complex with NAD+ and the substrate analogue UDP-4-deoxy-4-fluoro-,- d -galactoseACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 9 2006Magnus S. Alphey The structure of the NAD-dependent oxidoreductase UDP-galactose-4,-epimerase from Trypanosoma brucei in complex with cofactor and the substrate analogue UDP-4-deoxy-4-fluoro-,- d -galactose has been determined using diffraction data to 2.7,Å resolution. Despite the high level of sequence and structure conservation between the trypanosomatid enzyme and those from humans, yeast and bacteria, the binding of the 4-fluoro-,- d -galactose moiety is distinct from previously reported structures. Of particular note is the observation that when bound to the T. brucei enzyme, the galactose moiety of this fluoro-derivative is rotated approximately 180° with respect to the orientation of the hexose component of UDP-glucose when in complex with the human enzyme. The architecture of the catalytic centre is designed to effectively bind different orientations of the hexose, a finding that is consistent with a mechanism that requires the sugar to maintain a degree of flexibility within the active site. [source] X-ray structure of glutathione S -transferase from Schistosoma japonicum in a new crystal form reveals flexibility of the substrate-binding siteACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 3 2005Arne Christian Rufer The crystal structure of the 26,kDa glutathione S -transferase from Schistosoma japonicum (SjGST) was determined at 3,Å resolution in the new space group P212121. The structure of orthorhombic SjGST reveals unique features of the ligand-binding site and dimer interface when compared with previously reported structures. SjGST is recognized as the major detoxification enzyme of S. japonicum, a pathogenic helminth causing schistosomiasis. As resistance against the established inhibitor of SjGST, praziquantel, has been reported these results might prove to be valuable for the development of novel drugs. [source] Synthesis of Oligo(thienylfuran)s with Thiophene Rings at Both Ends and Their Structural, Electronic, and Field-Effect PropertiesCHEMISTRY - AN ASIAN JOURNAL, Issue 12 2007Yasuo Miyata Dr. Abstract Oligo(thienylfuran)s with thiophene rings at both ends (SOSOSOS, DE-SOSOS, DH-SOSOS, DE-SOSOSOS, and DH-SOSOSOS; S and O denote thiophene and furan rings, respectively, DE and DH denote diethyl- and dihexyl-substituted, respectively) were newly synthesized by repetitive Stille coupling reactions. The UV/Vis maximum absorptions of the oligomers, SO, SOSO, SOSOS, SOSOSO, and SOSOSOS, exhibited a clear bathochromic shift with increasing number of heterocycles. The value of the oxidation peak potential (Epa1) determined by cyclic voltammetry decreased with an increase in the number of heterocycles by 0.06,0.08,V per heterocycle. The crystal-packing structures of DE-SOSOS and DH-SOSOS determined by X-ray crystallography have a herringbone motif and are denser than the reported structures of pentacene and ,-sexithiophene. The morphologies of thin films prepared by vacuum deposition and spin coating were investigated by atomic force microscopy and X-ray diffraction. Among these films, those of DE-SOSOS and DH-SOSOS exhibited highly ordered arrangements. The devices based on vacuum-deposited and spin-coated films of DE-SOSOS and DH-SOSOS displayed the highest FET mobilities of 10,2,10,3,cm2,V,1,s,1 among the oligomers reported in this study. [source] | ||||||||||