X-ray Intensity Data Research Articles

A tetra-nitrato complex of platinum(II). Synthesis and crystal structure of K 2[Pt(NO 3) 4]· [formula omitted]H 2O

K 2[Pt(NO 3) 4]· 1 2 H 2O was prepared from ca 0.4 M solutions of platinum(II) perchlorate in perchloric acid by addition of KHCO 3 and KNO 3. Its crystal structure was determined from X-ray intensity data collected with a CAD-4 diffractometer. Monochromatic MoKα-radiation was used. The space group is I4/m with Z = 4; a = 7.5277(4) and c = 20.470(3) Å. The refinement converged to R = 0.036. The structure contains discrete complexes, [Pt(NO 3) 4] 2−, with symmetry C4. Pt coordinates four O from different unidentate nitrato groups. The PtO distance is 2.010(5) Å. The coordination around Pt is distorted square-planar, with Pt situated 0.14 Å above the plane formed by four O, so that a very flat, square pyramid is formed. Two such pyramids on each side of the mirror plane are packed together with their bases facing each other. The closest OO distance between them is 3.29(1) Å and the PtPt distance is 3.590(1) Å. The potassium ions are located between the pairs of complexes so that a three-dimensional packing of K + and 2×[Pt(NO 3) 4] 2− is formed.

Solid state and solution conformations of 1 -(β-D-2′,3′-secoribofuranosyl)-5,6-dichlorobenzimidazole, an acyclonucleoside analogue

The title compound crystallizes in the monoclinic space group P21, with two independent molecules in the asymmetric unit (Z = 4). The unit cell dimensions are a = 11.861(2), b = 7.897(1), c = 14.527(3) Å, β = 91.28(1)°. X-ray intensity data were measured on a diffractometer, and the crystal structure was determined by direct methods. Least-squares refinement converged at R = 0.036 for 2980 reflections. The glycosidic torsion angle [C(2)—N(1)—C(1′)—O(1′)] is 53.9° in molecule A and 129.8° in molecule B. In both molecules, the orientation of C(1′)—O(1′) to C(2′)—O(2′) is trans. The conformations about C(3′)—C(4′) and C(4′)—C(5′) are different in each of the two molecules. These features are compared with those of acyclonucleoside analogues with antiviral activity. The conformation in aqueous medium was examined with the aid of high-resolution 1H nmr spectroscopy, and the results are compared with those obtained from the X-ray analysis.

Bis(N-propyl-1,3-imidazolidine-2-thione)gold(I) chloride: Crystal and molecular structure

The crystal and molecular structures of bis(N-propyl-1,3-imidazolidine-2-thione)gold(I) chloride, [(PrImt)2Au]Cl, has been determined from three-dimensional x-ray intensity data collected on a CAD4 diffractometer. The compound crystallizes in the monoclinic space group P21/n witha=7.195(7),b=15.283(3),c=15.899(6) A, β=91.7(1) and Z = 4. Atomic parameters were refined by full-matrix least-squares methods to the R value of 6.2% for 2272 observed reflections. Gold(I) exhibits the usual linear coordination with S(1)-Au-S(10) angle of 177.7(1)°. The two [Prlmt] molecules are arranged intrans configuration which is attributed to the effects of intermolecular H-bonding between N-H and the halogen. The Au-S bond length is compared with the corresponding bond length in several known structures in order to evaluate thetrans influence of phosphorus, sulfur and chloride ligands on the Au-S bond.

X-ray structure refinement and pyroelectric investigation of fresnoite, Ba2TiSi2O8

Crystal structure parameters have been refined from single crystal x-ray intensity data collected on Ba2TiSi2O8 at 24 and 300°C. Anisotropic refinements in space group P4bm yielded residuals of 0.035 and 0.042 at 24 and 300°C, respectively. Pyroelectric measurements give a room temperature pyroelcctric coefficient of + 10 μC m -2 K -1. A structural mechanism for the pyroelectric effect is discussed in terms of large oxygen displacements. A sign reversal in the pyroeleetric coefficient occurs at 160°C, perhaps caused by the cancellation of primary and secondary effects.

The crystal and molecular structure of γ-hydroxy-β-amino butyric acid

The crystal structure of γ-hydroxy-β-aminobutyric acid was determined byMULTAN system with X-ray intensity data on a diffractometer and refined by the least-squares method to an Rvalue 0.034 for 711 reflections. The crystals were orthorhombic, space group P212121, Z=4, with a=10.220, b=8.257 and c=6.556A. The molecule takes the zwitterionic form and skeletal conformation is trans-trans form. The molecules are held together by intra-and intermolecular NH---O and OH---O hydrogen bonds.

Conformation of methyl 3,6-dideoxy-α-D-arabino-hexopyranoside, the immunodominant sugar of Salmonella serogroup D1: crystal structure, 1H nmr analysis, and semi-empirical calculations

Methyl 3,6-dideoxy-α-D-arabino-hexopyranoside (methyl tyveloside) crystallizes in the orthorhombic space group P212121 and the cell dimensions are a = 7.478(1), b = 7.933(1), c = 14.064(1) Å. X-ray intensity data were measured with a diffractometer and the structure was solved by direct methods. Least-squares refinement, which included all hydrogen atoms, converged at R = 0.038. The pyranose ring exists as an almost perfect 4C1 chair and the conformation adopted by the glycosidic methyl group is in agreement with the requirements of the exo-anomeric effect. Both acetal oxygen atoms act as hydrogen-bond acceptors, and the [Formula: see text] bond distances are in agreement with this feature. The 1H nmr spectrum shows that the conformation of the pyranose ring in aqueous solution is indistinguishable from that in the crystal. The minimum energy conformation of a pentasaccharide fragment of a Salmonella O-antigen, calculated with tyvelose coordinates obtained by bond modification, is in good agreement with the conformation which was calculated with tyvelose coordinates obtained from the X-ray analysis.

The crystal and molecular structures of dioxo mo(VI) complexes of tripodal, tetradentate N,S-donor ligands

The crystal and molecular structures of the complexes MoO 2((SCH 2CH 2) 2NCH 2CH 2SCH 3), I and MoO 2((SCH 2CH 2) 2NCH 2CH 2N(CH 3) 2), II, have been determined from X-ray intensity data collected by counter methods. Compound I crystallizes in two forms, Ia and Ib. In form Ia the space group is P2 1/n with cell parameters a = 7.235(2), b = 7.717(2), c = 24.527(6) Å, β = 119.86(2)°, V = 1188(1) Å 3, Z = 4. In form Ib the space group is P2 1/c with cell parameters a = 14.945(5), b = 11.925(5), c = 14.878(4) Å, β = 114.51(2)°, V = 2413(3) Å 3, Z = 8. The molecules of I in Ia and Ib are very similar having an octahedral structure with cis oxo groups, trans thiolates ( cis to both oxo groups) and N and thioether sulfur atoms trans to oxo groups. Average ditances are MoO = 1.70, MoS (thiolate) = 2.40, MoN = 2.40 and MoS (thioether) = 2.79 Å. Molecule II crystallizes in space group P2 12 12 1 with a = 7.188(1), b = 22.708(8), c = 7.746(2) Å, V = 1246(1) Å 3 and Z = 4. The coordination about Mo is octahedral with cis oxo groups, trans thiolates and N atoms trans to oxo. Distances in the first coordination sphere are MoO = 1.705(2), 1.699(2), MoS = 2.420(1), 2.409(1) and MoN = 2.372(2), 2.510(2) Å. The conformational features of the complexes are discussed. Complex I displays MoO and MoS distances which are very similar to those found by EXAFS in sulfite oxidase. This similarity is discussed.

Least-squares fitting of PIXE spectra with a digital filter treatment of the continuum

A set of aerosol spectra have been fitted both by HEX and by a new Guelph program that uses a top-hat filter; agreement is good. Improvements to lineshape descriptions and to the L X-ray intensity data base are suggested.

Polymorphism and phase transitions of K 2TeBr 6: A single crystal investigation of the high temperature phases (383–463 K)

From 383 to 463 K a single crystal measurement was performed in order to investigate lattice symmetry and lattice parameters of the high temperature phases. The 423 and 463 K X-ray intensity data were collected for the structural refinement of β-K 2TeBr 6 (Rb 2TeI 6-type structure, space group P4 mnc ) and α-K 2TeBr 6 (K 2PtCl 6-type structure, space group Fm3m). Orthorhombic γ-K 2TeBr 6, proposed in an earlier paper, could not be indicated. The tetragonal structure transforms directly into the monoclinic phase stable at room temperature (E g(X)-condensation of the rotary phonon).

Room- and high-pressure crystal chemistry of CoAs and FeAs

The MnP-type crystal structures of FeAs and CoAs have been studied at both room and high pressure. In the room-pressure study, refinements of both structures were carried out in space groups Pnam and Pna2~ using single-crystal integrated X-ray intensity data collected from a four-circle diffractometer. For CoAs, both space groups refined to a weighted residual, Rw = 0-054, whereas for FeAs, Rw = 0.030 for Pnam and 0-027 for Pna2~. The Hamilton significance test, applied to FeAs, shows a significant improvement in Rw for Pna2,. However, the Hamilton test is not a conclusive test for space-group identity. Comparison of interatomic distances, derived from Pnam and Pna2~ refinements for both CoAs and FeAs, shows no significant change in the structures. High-pressure X-ray data were collected from single crystals enclosed in a Merrill & Bassett-type diamond-anvil cell. Cell parameters and structures were refined at 2.80 (5), 3.70 (5), and 4.90 (5) GPa for CoAs, and at 2.25(5), 4.36 (5), 6-10(5), and 8.3(3) GPa for FeAs. Cell data were used to determine the elastic constants, isothermal bulk modulus and its pressure derivative (Kr and K~r, respectively), by least-squares fitting of the unit-cell volumes to a thirdorder Birch-Murnaghan equation of state. This gave Kr = 123 (6) GPa and K~r = 88(33) for CoAs. For FeAs, KT = 118 (4) GPa and K~r = 72 (1.8). Refinements in Pnam show that the structure remains an MnP-type throughout these pressure ranges. A precession photograph of CoAs at 7.8 GPa revealed previously sharp split and diffuse diffraction spots. Similar effects are known to occur in FeS when it undergoes a change from an MnP-type structure to a high-pressure phase above 6.8 GPa. Thus, these effects in CoAs may indicate the onset of a phase transition. Changes in both interatomic distances and atomic displacements from positions in an NiAs-type structure reveal some interesting aspects of the anisotropic compression these compounds undergo. These changes are correlated with high-pressure phase transitions that may occur in MnP-type structures.

Crystal Structure of β Poly(L-valine)

β Poly(L-valine) gave an excellent fiber photograph, and its crystal and molecular structures were determined on the basis of 72 X-ray intensity data. A molecular structure was constructed using the equations for helical parameters as functions of empirical internal coordinates. The crystal structure was refined by the R-value-map and least-squares methods with three parameters defining the packing scheme of the molecules. The crystal data: P212121, a=4.80, b=19.14, c=6.59 A. The final R value was 0.192. The crystal structure is fundamentally the same β-pleated sheet as that of poly(L-alanine). However, the molecule shows a considerable contraction (about 14%) along the fiber axis owing to the presence of a bulky isopropyl side chain.

Accuracy of linear polymer crystal structures determined from electron diffraction intensities: Problems with zonal data

In contrast to analyses based on X-ray and neutron diffraction intensity data, electron crystal structure determination for organic materials is only a crudely-developed procedure. Although the pioneering work of Vainshtein and co-workers has been very important for realization of the technique's advantages, self-consistent procedures based on earlier-derived diffraction theory have only recently emerged, enabling a reasonable estimate of what structural information might be obtained from a given microcrystalline organic specimen and how this might be best achieved. Problems which are unresolved include the optimal refinement procedure for an unknown structure and also the adequate identification of the correct crystal structure during this refinement process.The behavior of the crystallographic residual(R) during structure refinement is manifested by various minima in a multidimensional parameter space. The description of this space is more complicated for electron diffraction than for X-ray diffraction, although both cases include atomic position, atomic thermal vibration, atomic occupancy, “extinction”, and crystal distortion.

Structure of 2-(2,6-dimethoxyphenyl)-2,5-dimethylbicyclo[3.2.1]octane-6,8-dione

C18H2204, orthorhombic, P212~21, a = 7.343 (4), b = 11.251 (4), c = 19.357 (4)A, Z = 4, Dr, ' = 1.20, D e = 1.254 g cm -3, F(000) = 648, p(Mo Ka) = 0.94 cm -~. X-ray intensity data were collected on a Nonius CAD-4 diffractometer and the structure was solved by direct methods. Full-matrix least-squares refinement gave R = 0.052 (R w = 0.045) for 1053 observed reflections. The stereochemical configuration at C(2) has been shown to be 2-exo-methyl-2-endo- (2,6-dimethoxyphenyl), i.e. (3) in contrast to the structure (2) assigned earlier based on its ~H NMR data.

Crystal and molecular structure of pentachloromonoisopropylaminocyclotriphosphazatriene

Crystals of N3P3C15 (NHC3H7) are monoclinic:a=15.059(7),b=14.815(5),c=6.501(6) A, β=95.03(6)°, space groupP21/n, and Z=4. The atomic positions were determined by direct methods and refined by least-squares refinement from diffractometer X-ray intensity data toR=0.063 for 1530 reflections. In the structure, pairs of molecules mutually related by a center of symmetry are linked by N-H ⋯ N hydrogen bonds. The endocyclic P-N bonds range in length from 1.556 to 1.603 A depending on the location of the bond relative to the isopropylamino group, and the exocyclic P-N bond is only a little longer (1.617 A). The nongeminal P-Cl bond is significantly longer (2.036 A) than the remaining P-Cl bonds (1.988–2.013 A). The phosphazene ring shows only a very small departure from planarity. The isopropylamino group has a symmetrical conformation, with a Cl-P-N-C torsion angle of 90.5°.

The charge density in imidazole by X-ray diffraction at 103 and 293 K

The static charge density has been determined for imidazole, based on X-ray (Mo Ka) intensity data [1892 reflections with F o > 6ty(F) and sin 0/2 4o(F) and sin 0/2 < 0.8 A -1 at 293 K]. Full-matrix least-squares refinements were carried out using Stewart's rigid pseudoatom model. Fixed neutron values were assumed for the nuclear positional parameters, and for selected thermal parameters (Utj for H atoms and third-order Cjk I values for all atoms). The model gave a satisfactory fit to the X-ray data in terms of 150 variables which included population parameters for multipole expansions of the charge density as far as octapole terms for C and N atoms and quadrupoles for H atoms. Although ring-atom mean-square thermal vibrational amplitudes are considerably different at the two temperatures (U ~ 0.06 A 2 at 293 K; U ~ 0.02 A 2 at 103 K), the derived static charge distributions are in good agreement. This is attributed to the importance of the octapole deformation density for the imidazole-ring atoms. The charge density is consistent with a simple electrostatic theory for the strong NH...N hydrogen bond. It is also found that the approximate 2mm symmetry in the molecular geometry extends to the charge distribution, and that there are similarities with

Determination of defect structures by ion-channeling and by X-ray diffraction — A comparative study

Defect structures produced in V 3Si single crystals and polycrystalline films by irradiation have been analysed using ion channeling and X-ray diffraction measurements. The channeling data were analysed with computer simulations. The most prominent defect structures observed are randomly displaced lattice atoms and static contributions to the dynamical displacement amplitudes. The analysis of the X-ray intensity data with a modified Wilson plot shows an increase of the Debye-Waller factor with increasing ion fluence in agreement with the channeling data. At .ion fluences where the damage peak approaches the random spectrum in single crystals, the layers are found to be X-ray amorphous.

ChemInform Abstract: CRYSTALLOGRAPHIC STUDIES OF THE BORON‐NITROGEN BOND IN AMINOBORANES. PART 5. THE CRYSTAL AND MOLECULAR STRUCTURE OF 1,5,9‐TRIAZA‐13‐BORATRICYCLOTRIDECANE

Crystals of the title compound are orthorhombic, a= 8.69(1), b= 14.07(1), c= 8.48(1)A, space group P212121, and Z= 4. The atomic positions have been determined from diffractometer X-ray intensity data by the tangent refinement method and refined by full-matrix least-squares to R 0.050 for 414 reflections. The molecular symmetry is approximately C3v(3m). The BN3 system is almost planar but the carbon atoms lie out of this plane, by 0.3–0.4 A above for atoms in the 3-, 7-, and 11-positions and by smaller amounts below for the remaining carbon atoms. Mean bond lengths are : B–N 1.431 (6), C–N 1.446(4), C–C 1.521 (5)A and the B–N bond order obtained by molecular-orbital calculations is 1.4.

Comparison of solid state and solution conformations of R and S epimers of 8,5'-cycloadenosine and their relevance to some enzymatic reactions.

The C(5')-R epimer of 8,5'-cycloadenosine crystallizes in the monoclonic space group P2(1) (Z = 2) with unit cell dimensions a = 5.755 (1), b = 16.895 (1), and c = 5.511 (1) A and beta = 104.16 (1) degree. X-ray intensity data were measured on a diffractometer, and the crystal structure was determined by direct methods. Least-squares refinement converged at R = 0.037 for 1008 reflections. The conformation about the glycosyl bond is anti, as imposed by the 8,5' cyclization, with XCN = 29.8 degrees. The ribose ring adopts the unusual C(1')endo-O(4')exp (o1T) conformation with pseudo-rotation parameters P = 289.0 degrees and tau m = 490 degrees. The six-membered ring formed by the 8,5' linkage is approximately a half-chair with C(4') and O(4'), respectively, above and below a plane defined by the other four atoms. These results are compared with those previously reported for the corresponding S epimer [Haromy, T. P., Raleigh, J., & Sundaralingam, M. (1980) Biochemistry 19, 1718-1722]. The conformations of the sugar rings and the exocyclic groups of both epimers in the solid state are compared to the conformations in solution, as determined by analysis of the systems of proton-proton vicinal coupling constants from the 1H NMR spectra. The foregoing findings are employed to examine the role of the conformational parameters of adenosine and 5'-AMP in reactions catalyzed by the appropriate enzymes.

Electron density distribution in crystals of potassium trifluorocobaltate(II)

The electron density distribution in crystals of KCoF 3 was investigated on the basis of X-ray intensity data collected by diffractometry at 293 K. The characteristic residual electron density around the Co 2+ ion in the octahedral crystal field was observed on the difference Fourier maps when spherical scattering factors were used for the Co 2+ ion. With aspherical scattering factors for the 3d electrons of the Co 2+ ion, structure amplitudes were calculated for two electron configurations, i.e. high spin 4Tg(t2g)5(eg) 2 and low spin 2Eg(t2g)6(eg ). Refinement on the assumption of high spin decreased the R value significantly (0.0077) from that (0.0088) obtained with the spherical refinement, while assumption of low spin increased the value (0.0120). The difference density maps obtained after these refinements also showed that the high-spin (tEg)5(eg) 2 electron configuration is a good approximation of the electronic state for the Co 2+ ion in cubic KCoF 3 crystals at room temperature. [Crystal data: cubic, Pm3m, a = 4.0688 (7)A, V = 67.36 (3)/~3, Z = 1, D x = 3.821 Mg m -3, 2(MoKa) = 0.7107A, /~(Mo Ka) = 7.943 mm -~, T = 293 K; 743 reflections with IFI > 3trlFI.] crystal fields were observed in crystals of y-Co2SiO 4 (Marumo, Isobe & Akimoto, 1977) and CoA120 4 (Toriumi, Ozima, Akaogi & Saito, 1978) respectively. On the deformation density maps of y-C02SiO 4 eight positive peaks were observed around the Co 2+ ion on the lines along the (111 ) directions of the cubic lattice, and six negative peaks on the Co-O bonds. These peaks indicate that the electron density of the t2g orbitals is higher than that of the eg orbitals as a result of splitting of the d orbitals in a quasi-octahedral field. The deformation density around the Co 2÷ ion in CoA120 4 clearly shows that the density on the t2g orbitals is lower than that on the eg, giving an arrangement of negative and positive peaks reversed to that in an octahedral field. The present study was undertaken to increase knowledge on electron density distributions around the transition-metal ions in an octahedral field. In the octahedral crystal field, the ground state of a Co 2+ ion can be either high spin (t2g)5(eg) 2 or low spin (12g)6(eg) depending upon the strength of the crystal field. The refinements were performed for both configurations with aspherical scattering factors and the residual densities after these refinements were compared.

The effects of heating and dehydration on the crystal structure of hemimorphite up to 600° C

Abstract The crystal structure of hemimorphite, Zn4Si2O7(OH)2 · H2O, contracts upon dehydration caused by heating. X-ray intensity data were collected at 300°C, at 600°C and then at 22°C. Anisotropic least-squares refinements of 532, 255, and 432 reflections in the space group Imm2, and Z = 2, resulted in unweighted R-factors of 0.046, 0.074, and 0.061, respectively. The following cell parameters were obtained during crystal alignment on the diffractometer: 22°C1 300°C 600°C 22°C a 8.367(5) 8.337(5) 8.268(5) 8.206(4) b 10.730(6) 10.724(6) 10.784(8) 10.815(6) c 5.115(3) 5.116(4) 5.113(3) 5.089(2) V 459.2(4) 457.4(5) 455.9(5) 451.6(4) The structure is a framework consisting of interconnected corrugated sheets composed of 3-membered rings of one SiO4 and two Zn(OH)O3 tetrahedra. Contraction of the structure above 300°C is due to dehydration, and positive thermal expansion is observed in the dehydrated form. The structural mechanism of contraction is dependent upon the collapse of the cavities interconnected parallel to c towards the position of the expelled water molecule. The decrease in unit cell volume (ΔVuc ) is directly correlated with volume loss in the cavities (ΔVc ) and the increase in volume of the Zn tetrahedra (ΔVz ): ΔVuc ∼ 8ΔVz + 2ΔVc . Zeolites with structural characteristics like hemimorphite show similar changes during molecular exchange reactions.