Anisotropic refinement of the structure of Thermoascus aurantiacusxylanase I

The isotropic crystallographic model of the structure of xylanase I from Thermoascus aurantiacus (TAXI) has now been refined anisotropically at 1.14 Å resolution to a standard residual of R = 11.1% for all data. TAXI is amongst the five largest proteins deposited in the Protein Data Bank to have been refined with anisotropic displacement parameters (ADPs) at this level of resolution. The anisotropy analysis revealed a more isotropic distribution of anisotropy than usually observed previously. Adding ADPs resulted in high-quality electron-density maps which revealed discrepancies from the previously suggested primary sequences for this enzyme. Side-chain conformational disorder was modelled for 16 residues, including Trp275, a bulky residue at the active site. An unrestrained refinement was consistent with the protonation of the catalytic acid/base glutamate and the deprotonation of the nucleophile glutamate, as required for catalysis. The thermal stability of TAXI is reinterpreted in the light of the new refined model.

Determination by MAD-DM of the structure of the DNA duplex d[ACGTACG(5-BrU)]2 at 1.46 Å and 100 K

A four-wavelength MAD experiment on a new brominated octanucleotide is reported here. d[ACGTACG(5-BrU)], C77H81BrN30O32P7, (DNA) = 2235, tetragonal, P43212 (No. 96), a = 43.597, c = 26.268 Å, V = 49927.5 Å3, Z = 8, T = 100 K, R = 10.91% for 4312 reflections between 15.0 and 1.46 Å resolution. The self-complementary brominated octanucleotide d[ACGTACG(5-BrU)]2 has been crystallized and data measured to 1.45 Å at both 293 K and a second crystal flash frozen at 100 K. The latter data collection was carried out to the same resolution at the four wavelengths 0.9344, 0.9216, 0.9208 and 0.9003 Å, around the Br K edge at 0.92 Å and the structure determined from a map derived from a MAD data analysis using pseudo-MIR methodology, as implemented in the program MLPHARE. This is one of the first successful MAD phasing experiments carried out at Sincrotrone Elettra in Trieste, Italy. The structure was refined using the data measured at 0.9003 Å, anisotropic temperature factors and the restrained least-squares refinement implemented in the program SHELX96, and the helical parameters are compared with those previously determined for the isomorphous d(ACGTACGT)2 analogue. The asymmetric unit consists of a single strand of octamer with 96 water molecules. No countercations were located. The A-DNA helix geometry obtained has been analysed using the CURVES program.

The synthesis of dicobalt and dinickel complexes of trimethylsilylethynyl-1, 2-dihydrofullerene; characterisation by n.m.r. and structure of the first acyclic metal fullerene derivative: molecular structure of [η2-{2-H-1-(Me3SiC ≡ C)-C60}Ni2(η-C5H5)2]

The synthesis and characterisation of the complexes [η2-{2-H-1-(Me3SiC ≡ C)-C60}Co2(CO)6] (2)} and [η-2-{2-H-1-(Me3SiC ≡ C)-C60}Ni2η-C5H5)2] (3)} is reported, together with a single-crystal molecular structure for (3). This provides the first structural data for an acyclic metal derivative of [60]-fullerene.

Structure of the DNA octanucleotide d(ACGTACGT)2

d(ACGTACGT), C78H84N30O32P7.20H2O, Mr (DNA) = 2170, tetragonal, P43212 (No 96), a = 42.845 (1), b = 42.845(1), c = 24.804 (1) Å, V = 45532.5 (2) Å3, z = 8,(MoK) = 0.71069 Å,µ(MoK) = 0.10 mm-1, T = 295 K, R = 0.18 for 1994 unique reflections between 5.0 and 1.9 Å resolution. The self-complementary octanucleotide d(ACGTACGT)2 has been crystallized and its structure determined to a resolution of 1.9 Å. The asymmetric unit consists of a single strand of octamer with 20 water molecules. It is only the second example of an octanucleotide having terminal A·T base pairs whose structure has been determined by X-ray crystallography. The sequence adopts the modified A-type conformation found for all octanucleotide duplexes studied to date with the helix bent by approximately 15° and an average tilt angle of 0°. Unusually the data collection was carried out using a 3 kW molybdenum sealed-tube source. The conformational details are discussed in comparison with other closely related sequences.

Synthesis, X-ray crystal structure and catalytic activity of the manganese(II) complex [Mn(bdoa)(H2O)3](bdoaH2 =benzene-1,2-dioxyacetic acid)

Benzene-1,2-dioxyacetic acid (bdoaH2) reacts with Mn(CH3CO2)2·4H2O in an ethanol-water mixture to give the manganese(II) complex [Mn(bdoa)(H2O)3]. The X-ray crystal structure of the complex shows the metal to be pseudo seven-coordinate. The quadridentate bdoa2− dicar☐ylate ligand forms an essentially planar girdle around the metal, being strongly bondedtransoid by a car☐ylate oxygen atom from each of the two car☐ylate moieties (mean MnO 2.199A˚) and also weakly chelated by the two internal ether oxygen atoms (mean MnO 2.413A˚). The coordination sphere about the manganese is completed by three water molecules (mean MnO 2.146A˚) lying in a meridional plane orthogonal to that of the bdoa2− ligand. Magnetic, conductivity and voltammetry data for the complex are given, and its use as a catalyst for the disproportionisation of H2O2 is described.

Synthesis, X-ray crystal structure and reactivity of the polymeric copper(II) dicarboxylic acid complex {Cu2(η1η1μ2-oda)2(py)4(H2O)2}n(odaH2 = octanedioic acid, PY = pyridine)

An aqueous solution of the α-ω-dicarboxylic acid octanedioic acid (odaH2) reacts with [Cu2(μ-O2CCH3)4(H2O)2] in the presence of an excess of pyridine (py) to give the crystalline copper(II) complex {Cu2(η1η1μ2-oda)2(py)4(H2O)2}n (1). structure of 1, as determined by X-ray crystallography, consists of polymeric chains in which bridging oda2− anions link two crystallographically identical copper atoms. The copper atoms are also ligated by two transoidal pyridine nitrogens and an oxygen atom from an apical water molecule, giving the metals an overall N2O3 square-pyramidal geometry. If the blue solid 1 is gently heated, or if it is left to stand in its mother liquor for prolonged periods, it loses one molecule of pyridine and half a molecule of water and the green complex {Cu (oda)(py)(H2O)0.5}n (2) is formed. Spectroscopic and magnetic data for both complexes are given, together with the electrochemical and thermogravimetric measurements for 1.

Synthesis and X-ray crystal structure of the triethylammonium magnesium β-octamolybdate(VI)salt[Et3NH]2[Mg(H2O)6Mo8O26]·2H2O

[Et3NH]4[Mo8O26] reacted with MgCl2 giving the triethylammonum magnesium β-octamolybdate(VI) salt [Et3NH]2[Mg(H2O)6Mo8O26]·2H2O (3) and the triethylammonium hydronium β-octaamolybdate(VI) salt [Et3NH]3[(H3O)Mo8O26·2H2O (4), respectively. A small amount of [Et3NH]2[Mo6O269] was formed as a by-product. The salts 3 and 4 were characterized by X-ray crystallography. The [Mg(H2O)6Mo8O26]2− moiety in 3 is polymeric, with each octahedral [Mg(H2O)6]2+ ion sandwiched between two β[Mo8O26]4− ions, being hydrogen bonded to three terminal MOO oxygen atoms on one face of each β[Mo8O26]4− ion. The X-ray crystal structure of 4 corresponds to the reported previously. IR and conductivity data are given for 3 and 4.

Synthesis and X-ray crystal structure of the copper(I) dicarboxylic acid complex [Cu(η1-bdoaH)(PPh3)3] (bdoaH2 = benzene-1,2- dioxyacetic acid)

The copper(II) complex [Cu(bdoa)(H2O)2] (bdoaH2 = benzene-1,2-dioxyacetic acid) reacts with triphenylphosphine (1:4 mol ratio) to give the colourless copper(I) complex [Cu(η1-bdoaH)(PPh3)3] (1) in good yield. The X-ray crystal structure of the complex shows the copper atom at the centre of a distorted tetrahedron, and is ligated by the phosphorus atoms of the three triphenylphosphines and one carboxylate oxygen atom of the bdoaH− ligand. Significant intermolecular hydrogen-bonding exists between the pendant carboxylate OH function of one molecule and the uncoordinated “ketonic” oxygen of a neighbouring molecule. Complex 1 is non-conducting in chloroform but ionizes readily in acetonitrile. The cyclic voltammogram of an acetonitrile solution of 1 shows a single irreversible anodic peak for the oxidation of the PPh3 ligands and the copper(I) centre, and a single irreversible cathodic peak for the reduction of the bdoaH− ion. IR and mass spectral data for 1 are given.

Synthesis and reactions of [Et3NH]4[Mo8O6]: X-ray crystal structure of [Et3NH]3[NaMo8O26]

[Et3NH]4[Mo8O26] (1) was prepared by reacting triethylamine with either molybdenum trioxide dihydrate or with a solution of ammonium molybdate in aqueous HCl. An aqueous solution of complex 1 reacted with an excess of sodium chloride to give a mixture of [Et3NH]3[NaMo8O26] (2) and [Et3NH]2[Mo6O19] (3). Complex 2 was also formed on reacting sodium molybdate with triethylamine in aqueous HCl. In the reaction of 1 with potassium chloride the nature of the product obtained was critically dependent upon reaction time. After a 5.5 h reflux period a mixture of [Et3NH]3[KMo8O26] (4) and 3 was obtained, whereas upon prolonged reflux (24 h) only K4Mo8O26 · H2O (5) was precipitated. The X-ray crystal structure of 2 shows it to be polymeric, with each Na+ ion sandwiched between two β[Mo8O26]4− ions. Four oxygen atoms on one face of each β[Mo8O26]4− ion are coordinated to a Na+ ion, and four oxygens from the opposite face are bonded to the next Na+ ion in the polymer chain. This produces a zig-zag arrangement of Na+ ions throughout the molecular structure. Spectral, conductivity and voltammetry data are given.

Copper(II) complexes of benzene-1,2-dioxyacetic acid (bdoaH2): X-ray crystal structure of [Cu2(bdoa)(phen)4]bdoa·13H2O (phen = 1,10-phenanthroline)

Copper(II) acetate reacts with benzene-1,2-dioxyacetic acid (bdoaH2) in aqueous media to give [Cu(bdoa)(H2O)2] (1). Complex 1 reacts with the N-donor ligands pyridine (py), ammonia and 1,10-phenanthroline (phen) to give [Cu(bdoa)(NH3)2]·H2O (2), [Cu(bdoa)(py)2]·H2O (3) and [Cu2(bdoa)(phen)4]bdoa·13H2O (4), respectively. The X-ray crystal structure of the dicopper(II,II) complex 4 shows each copper atom at the centre of a distorted trigonal bipyramid comprising four nitrogen atoms from two chelating phen ligands and a single oxygen atom from one of the carboxylate moieties of the bridging bdoa2− ligand. The cyclic voltammogram of 4 shows a single reversible wave for the Cu2+/Cu+ couple at E = + 115 mV (vs Ag/AgCl). Spectroscopic and magnetic data for the complexes are given.

Synthesis of water-soluble and ether-soluble tetra-μ-acetatodiruthenium(II,III) complexes and X-ray crystal structure of [Ru2(μ-O2CC6H5)4(C2H5OH)2][Ru2(μ-O2CC6H5)4(HSO4)2]

[Ru2(μ-O2CCH3)4Cl] reacts readily with aqueous Ag2SO4 (2: 1 molar ratio) to give the sulphate salt [Ru2(μ-O2CCH3)4(H2O)2]2(SO4) (1). Addition of NaBPh4 to an aqueous solution of 1 produces the ether-soluble tetraphenylborate salt [Ru2(μ-O2CCH3)4(H2O)2][BPh4] (2). A methanolic solution of 1 reacts with Ba(C6H5CCCO2)2 · H2O to give the tetraacetatemonophenylpropynoate complex [Ru2(μ-O2CCH3)4(O2CCCC6H5)] · H2O (3). The reaction of an ethanolic suspension of [Ru2(μ-O2CC6H5)4Cl] with Ag2SO4 and H2SO4 (2 : 1 : 1 molar ratio) leads to the tetra-μ-benzoatodiruthenium(II,III) double complex salt [Ru2(μ-O2CC6H5)4(C2H5OH)2][Ru2(μ-O2CC6H5)4(HSO4)2] (4). Complex 4 is also obtained by reacting an ethanolic solution of 1 with an excess of benzoic acid in the presence of H2SO4. The X-ray crystal structure of 4 shows it to consist of [Ru2(μ-O2CC6H5)4(C2H5OH)2]+ and [Ru2(μ-O2CC6H5)4(HSO4)2]− ions, which are linked together by hydrogen bonds into an infinite polymeric chain. The RuRu distances in the cation and anion are very similar [2.265(2) and 2.272(2) Å, respectively]. Spectroscopic, magnetic, conductivity and cyclic voltammetry data are given for the complexes.

Possible pre-dissociation of diorganotin dihalide complexes: relationship between antitumour activity and structure

An examination of crystallographic data has indicated that the structure/activity relationship for diorganotin dihalide complexes is different from that of other metal dihalides, in that the SnN bond lengths appear to determine the antitumour activity.

Spectroscopic properties of alkenylferrocenes; crystal and molecular structure of (Z)-(1,2-diphenylethenyl)ferrocene

Studies of the 1H n.m.r. and electronic spectra of a series of alkenylferrocenes including (E) and (Z) stereoisomers of various styrylferrocenes, have provided methods of structure elucidation. Crystals of the title compound are monoclinic, space group P21/c with Z= 4 in a unit cell of dimensions a= 17.603(2), b= 10.218(2), c= 10.072 Å, β= 103.27(2)°. The structure has been determined by the heavy-atom method from diffractometer data and refind by full-matrix least-squares techniques to R= 0.043 for 2 219 unique reflections.

Unsaturated σ-hydrocarbyl transition-metal complexes. Part 4. Crystal and molecular structure of trans-chlorobis(diethylphenylphosphine)-(phenylethynyl)platinum(II) and comments on the relative trans influence of various carbon ligands

The molecular structure of trans-[PtCl(CCPh)(PEt2Ph)2] has been determined by X-ray diffraction methods. The crystals are monoclinic, space group P21, with a= 12.359(3), b= 13.015(3), c= 9.031(2)Å, β= 101.65(2)°, and Z= 2. The structure has been solved by the heavy-atom method and refined by full-matrix least squares to R 0.046 for 1 877 diffractometric intensity data. The crystals contain discrete molecules in which the platinum coordination is square planar. The phenylethynyl group is non-linear, with a Pt–CC angle of 163(2)°. Selected bond lengths are Pt–Cl 2.407(5) and Pt–C 1.98(2)Å. The structural trans influences of CCPh, CHCH2, and CH2SiMe3 ligands in platinum(II) complexes are compared; there is only a small dependence on hybridization at the ligating carbon atom.

Unsaturated σ-hydrocarbyl transition-metal complexes. Part 3. Crystal and molecular structure of trans-chlorobis(diethylphenylphosphine)(vinyl)platinum(II)

The molecular structure of trans-[PtCl(CHCH2)(PEt2Ph)2] has been determined by X-ray diffraction methods. The crystals are orthorhombic, space group Pbcn, with a= 10.686(2), b= 13.832(4), c= 16.129(4)Å, and Z= 4. The structure has been solved by the heavy-atom method and refined by full-matrix least squares to R 0.044 for 1 420 diffractometric intensity data. The crystals contain discrete molecules in which the platinum co-ordination is square planar. The Pt–Cl bond vector coincides with a crystallographic diad axis about which the atoms of the vinyl group are disordered. Selected bond lengths (Å) are Pt–Cl 2.398(4), Pt–P 2.295(3), and Pt–C 2.03(2). The Pt–CC angle is 127(2)°. From a survey of the available structural data it is concluded that there is little, if any, back donation from platinum to carbon in platinum–alkenyl linkages.