Twofold Symmetry Axis Research Articles

Indium(III) thiolate-bridged molybdenocene complexes: crystal structure of [InCl 2MoCp 2(η-SEt) 22][BPh 4] · (CH 3) 2CO

The reaction of [MoCp 2(SR) 2] (R=CH 3, C 2H 5, n-C 14H 29 or C 6H 5) with InCl 3 in ethanol affords new compounds which, after treatment with NH 4PF 6, were fully characterized as the hexafluorophosphate salts [InMoCp 2(μ-SR) 2 3] [PF 6] 3. A new monocation [InCl 2MoCp 2(μ-SR) 2 2] + was isolated as a tetraphenylborate salt and structurally characterized by a single-crystal X-ray diffraction study. The molybdenum atoms exhibit the usual bent metallocene structure with a distorted tetrahedron around each metal atom. The coordination around the indium atom is cis-octahedral. The InS 4Cl 2 core has a pseudo two-fold symmetry axis through the In atom bisecting the midpoint of the Cl- Cl edge of the coordination polyhedron. This pseudosymmetry extends to the Mo atoms and to some extent to the Cp ligands. The In-Mo distances, 4.0401(5) and 4.0703(5)A˚, and the large In-S-Mo angles indicate no interaction between the two different metal centres.

Structure of recombinant bovine interferon-gamma at 3.0 A resolution.

The three-dimensional crystal structure of recombinant bovine interferon-gamma was determined using the multiple isomorphous replacement method at 3.0 A and refined to an R factor of 19.2%. This protein crystallizes in space group P2(1)2(1)2(1) with unit-cell parameters of a = 42.8, b = 79.9 and c = 85.4 A. There is one functional dimer in the asymmetric unit. The two polypeptide chains are related by a non-crystallographic twofold symmetry axis. The secondary structure is predominantly alpha-helical with extensive interdigitation of the alpha-helical segments of the polypeptide chains that make up the dimer. The secondary structure, tertiary structure and topology of this molecule are identical to the previously reported structures of recombinant rabbit interferon-gamma and recombinant human interferon-gamma. The molecular topology is also similar to that of murine interferon-beta. These structural similarities strongly indicate the presence of a unique topological feature (fold) among gamma-interferons from different species, and also among the different classes of interferons.

Structure of 4,7-bis(4-mercaptobenzoyl)-1-tosyl-1,4,7-triazacyclononane

Bis(4-mercaptobenzoyl)-l-tosyl-l,4,7- triazacyclononane-n-hexane (2/1), C27H29N304S3 .- 0.5C6H14, Mr = 598.8, monoclinic, P21/-7, a = 24.113(5), b=ll.020(5), c=12.065 (4) /~, fl= 100.07 (2) °, V = 3156.7 A 3, Z = 4, Dx = 1.260 g cm -3, A(Mo Ka) = 0.71069 A,/., = 2.6 cm- F(000)=1268, T=293K, R=0.085 for 2493 observed reflections. The triazacyclononane ring has a 'twist-chair-chair' conformation, with a pseudo- twofold symmetry axis in the ring. Two of the sub- stituent groups are directed to opposite sides of the ring, the third is more equatorially orientated; all are at approximately sp2-hybridized N atoms. The two thiol groups form S--H..-O hydrogen bonds connec- ting molecules in chains. Introduction. Recently we synthesized the novel tri- dentate trithiol, 1,4,7-tris(4-mercaptobenzoyl)-l,4,7- triazacyclononane, which acts as a tripodal ligand to Fe4S4 metal clusters generating a site-differentiated Fe site (Evans, Leigh & Santana, 1991; Evans, Garcia, Leigh, Newton & Santana, 1992). As a minor product in the preparation of this molecule, we obtained crystals of the title compound (I). Presumably a small amount of 1-tosyl-l,4,7-tri- azacyclononane had been present in the 1,4,7-tri-

Structures of 1-ferrocenyl-1-phenylethanol, ferrocenyl(diphenyl)methanol and ferrocene-1,1'-diylbis(diphenylmethanol)

Racemic 1-ferrocenyl- 1-phenylethanol, [(CsHs)Fe- (CsHa)]CPhMeOH (I), crystallizes as discrete molecules which are not involved in hydrogen bondinog; the shortest intermolecular O-..O contact is 3.768(3) A and the hydroxyl H atom is orientated towards the unsubstituted cyclopentadienyl ring. Ferrocenyl(diphenyl)methanol, [(CsHs)Fe(CsHa)]CPh2OH (II) is hydrogen bonded to form centrosynunetric dimers with O...O 2.816(1) and H...O 2.52 ]k. Ferrocene-l,l~-diylbis(diphenylmeth - anol), Fe[(CsHa)C(Ph)2COH]2 (III) crystallizes as a dimeric aggregate with the Fe atoms on twofold crystallographic symmetry axes and the four O atoms defining a folded trapezium with O...O 2.762(2), 2.714(2) and 2.865(2) A,. The four hydroxyl groups are disordered equally over two orientations such that there are two halfoccupancy H-atom sites between each hydrogen-bonded oxygen pair.

The structure of an idarubicin-d(TGATCA) complex at high resolution.

The crystal structure of the DNA hexamer d(TGATCA) complexed with the anthracycline antibiotic idarubicin has been determined at 1.6 A resolution. The asymmetric unit consists of a single hexamer oligonucleotide strand, one drug molecule and 35 water molecules. The complex crystallizes in the tetragonal space group P4(1)2(1)2, Z = 8 with lattice dimensions of a = b = 28.19 (3), c = 52.77 (4) A, V = 41 935 A(3). The structure is isomorphous with a series of hexamer-anthracycline complexes and was solved by molecular replacement. Restrained least-squares methods interspersed with computer-graphics map inspection and model manipulation were used to refine the structure. The R factor is 0.22 for 2032 reflections with F >/= 3sigma(F) in the resolution range 8.0-1.6 A. The self-complementary DNA forms a distorted B-DNA double helix with two idarubicin molecules intercalated in the d(TpG) steps of the duplex. The duplex is formed by utilization of a crystallographic twofold axis of symmetry. The idarubicin chromophore is oriented at right angles to the long axis of the DNA base pairs with the anthracycline amino-sugar moiety positioned in the minor groove. Our structure determination allows for comparison with a d(CGATCG)-idarubicin complex recently reported. Despite the sequence alteration at the intercalation step, the structures are very similar. The geometry of the intercalation and the nature of the interactions are conserved irrespective of the DNA sequence involved in the binding.

Surface Wave Propagation In A Slowly Varying Anisotropic Waveguide

SUMMARY We present a JWKB theory which describes the propagation of seismic surface waves in a laterally heterogeneous, anisotropic waveguide. We introduce a local dispersion relation and local vertical eigenfunctions which depend explicitly on the direction of the local wavevector as a consequence of the anisotropy. the variation of amplitude along a surface wave ray path is determined by a conservation law for the surface wave energy. Apart from the usual dynamical phase, which is the integral of the local wavevector along a ray path, there is an additional variation in phase in a general anisotropic waveguide. This additional phase, which is an analogue of the Berry phase in adiabatic quantum mechanics, vanishes in a waveguide with a local vertical two-fold symmetry axis or a local horizontal mirror plane.

The 0.25-nm X-ray structure of the Bowman-Birk-type inhibitor from mung bean in ternary complex with porcine trypsin.

The structure of the Bowman-Birk-type inhibitor from mung bean Phaseolus aureus has been determined in ternary complex with porcine trypsin. The complex formed crystals of the trigonal space group P3(1)21 which diffracted to a resolution of 250 pm. Each of the two mung bean protease reactive sites is bound to trypsin according to the standard mechanism for serine proteinase inhibition. The binding loops thereby adopt the canonical conformation for the standard mechanism; however, the sub-van der Waals contact between the active-site serine O gamma (195) and the P1 carbonyl carbon of both loops is significantly smaller (210 pm) than hitherto observed, with continuous electron density connecting the two atoms. The inhibitor is formed by two double-stranded antiparallel beta-sheets, which are connected into a moderately twisted beta-sheet by a network of hydrogen bonds involving main-chain atoms and two water molecules. All contacts with neighbors in the crystal lattice occur between trypsin molecules. This apparently gives rise to an unusual form of disorder where the complexes pack in two orientations Ta:MaMb:Tb and Tb:MbMa:Ta (Ta, Tb = trypsin, Ma = mung bean loop I, Mb = mung bean loop II), such that the asymmetric unit consists of the ternary complex in two orientations, each with half occupancy. This is nearly equivalent to an asymmetric unit which has one trypsin molecule with full occupancy and one mung bean inhibitor with half occupancy and a crystallographic twofold symmetry axis through its center. Because of the approximate twofold symmetry of the inhibitor itself, however, the electron density was interpretable for most of the inhibitor (17 residues at the termini were not resolved) and shows evidence of its double orientation.

Refined Structure of the Pyruvoyl-dependent Histidine Decarboxylase from Lactobacillus 30a

The crystal structure of the pyruvoyl-dependent histidine decarboxylase from Lactobacillus 30a has been refined to an R-value of 0·15 (for the 5·0 to 2·5 Å resolution shell) and 0·17 (for the 10·0 to 2·5 Å resolution shell). A description of the overall structure is presented, focusing on secondary structure and subunit association. The enzyme is a hexamer of αβ subunits. Separate α and β-chains arise from an autocatalytic cleavage reaction between two serine residues, which results in the pyruvoyl cofactor. The central core of the αβ subunit is a β-sandwich which consists of two face-to-face three-stranded antiparallel β- sheets, flanked by α-helices on each side. The β-sandwich creates a stable fold that allows conformational strain to be introduced across an internal cleavage region between the α and β chains and places the pyruvoyl cofactor in a position for efficient electron withdrawal from the substrate. Three αβ subunits are related by a molecular three-fold symmetry axis to form a trimer whose interfaces have complementary surfaces and extensive molecular interactions. Each of the interfaces contains an active site and a solvent channel that leads from the active site to the exterior of the molecule. The trimers are related by a crystallographic twofold symmetry axis to form the hexamer with an overall dumbbell shape. The interface between trimers has few molecular interactions.

Diffuse scattering in icosahedral phase AlMnSi

Neutron powder diffraction patterns are calculated from a random cluster model (RCM) for icosahedral phase AlMnSi for comparison with experimental intensity data. The diffuse scattering seen experimentally under the groups of strong peaks is revealed selectively in the calculated partial intensities for AlAl, MnMn and AlMn correlations. This diffuse intensity is known to result from the enhancement of the dense background of weak peaks by the structure factor of a single atomic cluster, rather than from substitutional chemical disorder or orientational disorder. A single crystal diffraction pattern normal to a two-fold symmetry axis is also calculated to determine the distribution of diffuse intensity in reciprocal space. This intensity is found to be in agreement with experimental transmission electron diffraction patterns in that the diffuse scattering is centered around the expected positions for the most intense superlattice reflections found in fci quasicrystals.

Sandramycin, a novel antitumor antibiotic produced by a Nocardioides sp. II. Structure determination.

The structure of sandramycin, a novel antitumor antibiotic, was established by spectroscopic analysis and chiral chromatography of its acid hydrolysate. It was determined to be a cyclic decadepsipeptide with a two-fold axis of symmetry and 3-hydroxyquinaldic acid as an appended chromophore.

Orientation dependence of the Fe 2+-NO and Fe 3+ EPR signals associated with the non-heme iron of Photosystem II

We have examined the orientation dependence of two EPR signals associated with the iron of the ferroquinone complex of Photosystem II. The first signal with g values (4.09, 3.95 and approx. 2.0) results from the reversible interaction of the ferrous ion with NO (Petrouleas et al. (1990) Biochim. Biophys. Acta 1015, 131–140). Studies of oriented spinach BBY membranes treated with NO show that g x lies on the membrane plane, g y is oriented at 30° and g z is oriented at 60° with respect to the membrane plane. The latter, most likely, indicates the approximate direction of the Fe-NO bond. Since NO displaces CO 2/HCO − 3 upon binding (Diner et al. (1990) Biochim. Biophys. Acta 1015, 141–149), the latter physiological ligand is probably well above the membrane plane containing the iron. This places CO 2/HCO − 3 at an approximately homologous position with the bacterial glutamate ligand (Deisenhofer and Michel (1989) EMBO J. 8, 2149–2169); it is not known, however, whether CO 2/HCO − 3 binds as a monodentate or bidentate ligand. The second signal with characteristic g values in the region 5.6–8.1 results from the oxidized non-heme iron (Fe 3+) [3]. The orientation results show that the g x = 8.1 and g z = 5.6 resonances have both maxima in the plane of the membrane. The g y axis is, therefore, perpendicular to the plane of the membrane and runs along the homologous direction of the bacterial twofold symmetry axis. Based on the strong effect that molecules bound at the Q B binding site have on the x- y plane anisotropy ( E D ) but not on the axial field strength, D, and assuming basic similarities with the bacterial reaction center, it is suggested that, the x- y plane is defined by the two oxygen ligands and the two nitrogens from the histidine imidazoles which have contacts with the Q A and Q B site. The g z -axis lies then along the N-Fe-N direction defined by the nitrogen ligands from the other two histidines. An unusual finding is that the process of membrane orientation (slow drying of the membranes) induces an axial signal, g xy = 6, in a fraction of centers. The axial plane of the latter is perpendicular to the membrane in agreement with the orientation results of the more rhombic signals. A possible arrangement of the nitrogen and oxygen ligands in the equatorial plane (vertical to the membrane) as to impose pseudo-C 3 symmetry is discussed.

Crystal structure of N(1)-methyl-α-isosparteine iodide and 1,16-endomethylene-α-isosparteine diiodide

The crystal and molecular structures of mono- and di-quaternary salts ofa-isosparteine have been determined by X-ray analysis. Both N(1)-methyl-α-isosparteine iodide and 1,16-endomethyleneα-isosparteine diiodide crystallize in the space groupC2221. The N-methylation does not change the configuration of parenttrans-cisoid-trans-α-isosparteine. The crystallographic twofold symmetry axis coincides with molecular symmetry of the diquaternary cation. Thetrans-cisoid-trans-1,16-endomethylene-α-isosparteine diiodide and its stereoisomer,trans-cisoid-cis-1,16-endo-methylenesparteine diiodide, form isomorphous crystals. Short cation-anion contacts in crystal structures suggest existence of C-H-⋯-I− hydrogen bonds in the solid state. In the N(1)-methyl-α-isosparteine iodide crystal, 7C⋯I− distances in the range 3.85-4.15 A have been found, while 17 distances of this type have been observed in 1,16-endomethylene-α-isosparteine diiodide.

Structural domains of phytochrome deduced from homologies in amino acid sequences.

A method of semiempirical identification of structural domains is proposed. The procedure is based on the comparison of amino acid sequences in groups of homologous proteins. This approach was tested using 32 known protein sequences from different cytochrome b5, cytochrome c, lysozyme, hemoglobin, and myoglobin proteins. The method presented was able to identify all structural domains of these reference proteins. A consensus secondary structure provided information on structural content of these domains predicting correctly 21 of 23 (91%) of alpha-helices. We applied this method to six homologous phytochrome sequences from Avena, Arabadopsis, Cucurbita, Maize, Oryza, and Pisum. Some of the identified domains can be assigned to the known tertiary structure categories. For example, an alpha/beta domain is localized in the region known to stabilize the phytochrome chromophore in the red light absorbing form (Pr). One alpha-helical and one alpha/beta domains are localized in regions important for the chromophore stabilization in the far-red absorbing form (Pfr). From an analysis of noncovalent interaction patterns in another domain it is proposed that a phytochrome dimer contact involves two segments localized between residues 730 and 821 (using numbering of aligned sequences). Also, a possible antiparallel beta-sheet structure of this region has been suggested. According to this model, the long axis of the interacting structures is perpendicular to a twofold symmetry axis of the phytochrome dimer.

Synthesis, nuclear magnetic resonance, and X-ray structural investigations of 1,6-diaza-9,12-dioxacyclotetradeca-2,5-dione

The molecular structure of l,6-diaza-9,12-dioxacyclotetradeca-2,5-dione has been investigated by X-ray and NMR methods. The crystals are monoclinic:C2/c,Z=4,a=8.5571(3),b=14.468(1),c=10.092(2) A,β=113.38(1)°. The structure was solved by direct methods, and refined toR=0.051 on 1082 unique reflections. The molecule exhibits a crystallographic twofold symmetry axis, the axis bisecting the 3C-4C and 10C-11C bonds, which is in full agreement with NMR findings.

Bis(N,N) chelated rhenium(III): the [ReL2Cl2]Cl family [L = 2-(arylazo)pyridine

The reaction of mer-[Re(MeCN)(PPh3)2Cl3] with 2-(arylazo)pyridines (L) affords dark green, diamagnetic, 1 : 1 electrolytes [ReL2Cl2]Cl (aryl of L = Ph, m-MeC6H4 or p-ClC6H4). The ReCl2 moiety is cis(two Re–Cl stretches) and the cation has an overall two-fold symmetry axis (1H NMR spectra). The co-ordinated pyridine-nitrogen atoms and azo-nitrogen atoms of each ligand are assigned relative trans and cis geometries respectively. The NN stretching frequencies are low (1280–1290 cm–1) implying significant Re(t2)–azo(π*) back bonding. In MeCN solution three nearly reversible redox couples occur with E½ values of ≈ 0.9 V [rhenium(IV)–rhenium(III)] and ≈–0.4, ≈–0.8 V (azo redox)vs. the saturated calomel electrode (SCE). A metal-to-ligand charge-transfer (m.l.c.t.) absorption is observed near 600 nm. The reduction potentials and m.l.c.t. frequencies are mutually consistent. The remarkable spectral and electrochemical similarities between [ReIIIL2Cl2]Cl and [OsIIL2Cl2] are noted and rationalised.

Copper(I) and gold(I) complexes with cis-bis(diphenylphosphino)ethylene. Crystal structures and 31P cross-polarization magic angle spinning nuclear magnetic resonance studies

The synthesis, structural and solid-state 31P cross-polarization magic angle spinning (CP MAS) NMR characterization of cis-bis(diphenylphosphino)ethylene (dppey) and the copper(I) and gold(I) complexes [M(dppey)2]PF6 has been carried out. The complexes, which have been shown to exhibit cytotoxic and antitumour activity, belong to the relatively rare class of copper(I) and gold(I) complexes with tetrahedral CuP4 and AuP4 co-ordination spheres. Crystals of dppey 1 are monoclinic with space group P21/c and a= 12.861(8), b= 13.097(2), c= 14.228(8)A, β= 116.15(3)°; R was 0.047 for 3117 ‘observed’ reflections. The solid-state CP MAS 31P NMR spectrum consists of an AB multiplet with δ(PA)–24.2, δ(PB)–27.2 and J(P–P)= 126 Hz. Crystals of [Cu(dppey)2]PF62 are orthorhombic with space group P212121 and a= 14.479(5), b= 16.703(4), c= 20.891(4)A; R was 0.046 for 3138 ‘observed’ reflections. The CuP4 co-ordination sphere is regular within the constraints of chelation with Cu–P in the range 2.276(2)–2.289(2)A. The copper atom lies on a pseudo two-fold axis of symmetry bisecting the C[double bond, length half m-dash]C bonds. Charge-transfer interactions between phenyl rings on each ligand contribute to the stabilization of the structure of the cation. The solid-state 31P NMR spectrum consists of four broad bands (Δν½= 300 Hz) centred at δ 8 with J(Cu–P)≈ 820 Hz. Distortion of the quartet spacings by quadrupolar interaction with the copper nuclei is minimal. Crystals of [Au(dppey)2]PF63 are isomorphous with 2 with a= 14.644(4), b= 16.703(1), c= 20.699(5)A; R was 0.025 for 3947 ‘observed’ reflections. The Au–P distances lie in the narrow range 2.377(2)–2.388(2)A. Solid-state CP MAS 31P NMR of this complex and the analogous nitrate and chloride complexes at magnetic field strengths of 2.11, 7.05 and 9.40 T reveal splitting of the phosphorus signal into a quartet ascribed to Au–P spin–spin coupling effects with J(Au–P) estimated to be 200 Hz. As for the copper complex, distortion of the quartet spacings is minimal and indicative of a small 197Au quadrupolar coupling constant. Solution and solid-state 31P NMR chemical shift parameters are similar, supporting the hypothesis that the tetrahedral bis(chelated) cations are also stable in solution. Spin–spin coupling to the quadrupolar (197Au or 63/65Cu) nuclei was not resolved in the solution spectra, however, due to rapid quadrupolar relaxation.

Crystallization of diphtheria toxin

Two new crystal forms (forms III and IV) have been grown of diphtheria toxin (DT), which kills susceptible cells by catalyzing the ADP-ribosylation of elongation factor 2, thereby stopping protein synthesis. Forms III and IV diffract to 2·3 Å and 2·7 Å resolution, respectively. Both forms belong to space group C2; the unit cell parameters for form III are a = 107·3 A ̊ , b = 91·7 A ̊ , c = 66·3 A ̊ and β = 94·7 ° and those for form IV are a = 108·3 A ̊ , b = 92·3 A ̊ , c = 66·1 A ̊ and β = 90·4 ° . Both forms have one protein chain per asymmetric unit with the dimeric molecule on a twofold axis of symmetry. Form IV is exceptional among all crystal forms of DT in that it can be grown reproducibly. Thus the form IV crystals should yield a crystallographic structure giving insight into the catalytic, receptor-binding and membrane-insertion properties of DT.

Structure and properties of lanthanide catalysts: the crystal and molecular structure of SmBr3�4iPr(OH)

The crystal of the title compound is monoclinic (space group C2/c), with a = 22,067(17), b = 10.111 (10), c = 16.886(11) A,β=142.95(5)°, and Z = 4. Its structure is based on the packing of SmBr3·4iPr(OH) (iPr = isopropyl) molecules. The metal atom is coordinated by three Br ions and by the oxygen atoms of the four iPr(OH) ligands. The coordination polyhedron is a distorted pentagonal bipyramid of C2 symmetry, with Sm and one of the Br atoms lying on the twofold axis of crystallographic symmetry. Polymerization experiments are reported showing that the activity of the catalytic system based on the title complex is much lower than that shown by systems based on similar Nd complexes. A possible rationalization of this fact is given in terms of the oxidation capacity of the rare-earth ions.

Ab initio CI study of the optical rotatory strengths of HSSH

The optical rotatory strengths for the four lower-lying electronic transitions of dihydrogen disulfide (HSSH) have been studied by a large ab initio multi-reference CI (MR CI) calculation. The dependence of the optical property on the rotation with respect to the twofold axis of symmetry has been examined. For the two lowest-lying transitions, the empirical C2-rule and the “quadrant rule” may be confirmed. However, for dihedral angles near 90°, a significant net contribution of rotatory strengths is calculated, whereas the two excited states are nearly degenerate.

An electron microscopic study of two-hexameric hemocyanins from the crab Cancer pagurus and the tarantula Eurypelma californicum: Determination of their quaternary structure using image processing and simulation models based on X-ray diffraction data

Two dodecameric hemocyanin (Hc) structures from species belonging to different taxonomic classes, one Crustacean (the crab Cancer pagurus) and one Cheliceratan (the tarantula Eurypelma californicum), were studied by electron microscopy. The relative orientation and position of the hexamers were determined by the combination of data from electron microscopy and X-ray diffraction. Computer model building using the determined parameters shows for both Hc's the presence of a twofold symmetry axis running through the interhexameric contact areas perpendicular to their long axis. The threefold axes of the hexamers in the two-hexameric structures are nearly perpendicular to each other. In Cancer He one of the three twofold axes of each hexamer is nearly parallel to the long axis of the two-hexamer. In the Eurypelma two-hexamer, one of the three twofold axes in both hexamers is almost perpendicular to the long axis. In both Cancer and Eurypelma Hc's at least four subunits are involved in the interhexameric binding. The subunit interaction for the Cancer He involves mainly domain 3, while for the Eurypelma He domains 1 and 3 are involved. The difference in hexamer interaction observed for Cancer and Eurypelma Hc's is probably caused by a 21-residue loop which may be absent in Eurypelma.