Empirical Absorption Correction Research Articles

Synthesis and crystal structure of copper(I) iodine complexes with 1-allyl-1H-benzimidazole

By reaction of acetonitrile solution of 1-allyl-4-benzimidazole, iodine and copper under alternating current technique in 1 day the dark red crystals of [(C 7 H 5 N 2 (C 3 H 5 )) 4 Cu 4 I 4 ] (I) compound was obtained and structurally characterized by X-ray single crystal method: space group , Z = 2, a = 11,3260(5), b = 12,2730(5), c = 16,3601(6) Å, α = 96,407(3), β = 95,572(3), γ = 99,260(4) o , V = 2215,1(2) Å 3 , r обч. = 2,089 г/см 3 , New Gemini, Dual , m(Mo K a ) = 4,72 мм −1 , empirical absorption correction, q max. = 29,0°, 26095 measured, 9674 used reflections, R ( F 2 ) = 0,024, Rw ( F 2 ) = 0,053, S = 1,07. Structures was solved by direct methods and refined by least-squares method on F 2 by SHELXL-2014 with following graphical user interfaces of OLEX 2 . In the crystal structure of compound I, the copper(I) atoms possess a deformed tetrahedral coordination environment formed by nitrogen atom (Cu-N distances 1,990–2,014 Å) of organic ligand and three iodine atoms (Cu-I distances 2,629–2,787 Å). Due to the fact that each I atom of four independent ones connects three copper(I) atoms, globular units {Cu 4 I 4 } – are appearing. Bonding of nitrogen atom of ligand moieties with Cu(I) closed coordination environments causes an appearance of the {C 7 H 5 N 2 (C 3 H 5 )CuI} 4 topological block. An interesting feature of the compound structure is the lack of coordination of copper atoms with the unsaturated C=C bond of the allyl group of the 1-allyl-1H-benzimidazole cation. This feature of the crystal structure topology can be explained by a steric hindrance from iodine atoms and the extremely weak power of hydrogen and Cu....Cu contacts. Confirmation of this approval is the lack of literature information about π-complexes of Cu(I), in which the coordination environment of metal atoms included three iodide ions together with C=C bond. Keywords : 1-allyl-1H-benzimidazole, copper(І), iodine coordination compounds, crystal structure.

Hydrothermal synthesis and crystal structure of a novel compound: [Ni(phen) 3] 2[SiMo 10V IV2O 40(V IVO) 2]·2H 2O

A novel compound [Ni(phen) 3] 2[SiMo 10V IV 2O 40(V IVO) 2]·2H 2O has been hydrothermally synthesized and structurally characterized by single-crystal X-ray diffraction. The compound crystallizes in the triclinic system, space group P-1, a=12.378(4) A ̊ , b=14.148(5) A ̊ , c=14.316(2) A ̊ , α=105.91(2)°, β=95.31(2)°, γ=96.89(3)°, V=2373.0(12) A ̊ 3 , Z=1, (λ Mo Kα )=0.71073 A ̊ , R1( wR2)=0.0869(0.2174). Data were collected on a Siemens P4 four-circle diffractometer at 293 K in the range of 1.51< θ<22.50° using the ω-scan technique. Empirical absorption correction (ψ scan) was applied. The structure was solved by the direct method and refined by the Full-matrix least-squares on F 2 using the SHELXL-97 software. X-ray crystallographic study showed that the title compound contained a bi-capped α-Keggin-type [SiMo 10V IV 2O 40(V IVO) 2] 4− polyoxoanion.

Structure of dysprosium polysulfide DyS1.83 (Dy6S11) according to x-ray diffraction analysis

The crystal structure of a single crystal of dysprosium polysulfide DyS1.83 = Dy6S11 is determined. The unit cell parameters are similar to those established for DyS1.76 = Dy4S7, but the composition is different. The unit cell is monoclinic, space group P21/m, a = 11.009(2), b = 11.531(2), c = 11.023(1) A, β = 91.152(8)∘, V= 1398.1(4) A3; for Z = 4 this gives the composition Dy6S11, regarding the experimental values of the partial statistic of the S atoms and dcalc = 6.303 g/cm3 (EnrafNonius CAD-4 automatic diffractometer, γMoKα, Raniso = 0.0349 for 6381 unique Ihkl > 2σI of 9804 measured ones). An empirical absorption correction was applied based on transmission curves and habit data. The polysulfide is a PbFCl type structure; the monoclinic unit cell parameters are related to a0 and c0 of the tetragonal cell of PbFCl as [101] ≅ 4a0, [010] ≅3a0, [101] ≅2c0. The crystal is a twin with the ratio of components k2 = 1-k1 = 0.243(2) and a transition matrix 001/010/100. The composition DyS1.83±0.02 agrees with the chemical analysis data and the experimental value dexp = 6.30±0.08 g/cm3. The phase individuality of the polysulfide is confirmed by the form of the P-T projection of the P-T-X diagram of the Dy-S system.

XABS2: an empirical absorption correction program

The XABS2 Fortran program calculates an empirical absorption correction based on minimization of the 2 differences between F2obs and F2calc. The basic algorithm has been used in the crystallography laboratory at the University of California, Davis for over a decade, in the form of the program XABS. XABS relied upon an approximately linear relationship for spherical crystals between the transmission factor and sin2 θ for θ ≃ 30° when μR ≃ 5. In XABS2, deviations from linearity are accounted for by a cubic equation in sin2 θ, which makes it applicable over the whole range of diffraction angle. The program needs no data in addition to the unique set but assumes a bisecting (symmetric) data-collection mode on a four-circle diffractometer. Since it does not require knowledge of the diffractometer setting angles, it can be applied even in cases where details of the original data collection are unknown.

Structure of triaqua(nitrilotriacetato)vanadium(III) tetrahydrate

Structure of triaqua(nitrilotriacetato)vanadium(III) tetrahydrate

Structure of dicarbonylbis(η2-dimethyl 7-acetyl-7-azabicyclo[2.2.1]hept-2-ene-2,3-dicarboxylate-κN)molybdenum(0)

[Mo(C24H34N2O10)(CO)2], Mr = 66251, monoclinic, C2/c, a = 61.3502 (41), b = 10.4370 (4), c = 17.7387 (14) A, /~ = 99.742 (6) °, V = 11194.5 (18) ,~3, Z = 16, Dx = 1.57 g c m -3, a(Cu Ka) = 1.54056 ,~, # = 44.7 cm-~, F(000) = 5472, T = 298 K, R = 0-046 for 7459 reflections with I > 30-(/). There are two independent molecules per unit cell. In each molecule, two CO groups are cis to each other with M o C O distances from 1.955 (5) to 1.982(7)fit. Two substituted double bonds are bound to the Mo atom [Mo-C from 2.193 (6) to 2.238 (6)A]. The C C distances for bound and non-bound double bonds are 1.437 (8) and 1.34 (1),~, respectively. The M o N distances are 2.336 (4), 2.347 (5), 2.361 (5) and 2.339 (5) A. Experimental. The title compound, C26H34MoN2OI2 , was synthesized as reported by Sun & Chow (1988). Yellow crystals were grown from Et20. A suitable prism crystal with dimensions 0.15 x 0.20 x 0.30 mm was mounted on a glass fiber with epoxy resin. Cell constants were derived from least-squares refinement of 25 reflections having 50 < 20 < 52 °. Intensity data were collected at room temperature using the 0/20 scanning technique on an Enraf-Nonius CAD-4 diffractometer with monochromated Cu Ka radiation. A total of 9595 reflections were measured with 0 < * To whom correspondence should be addressed. 0108-2701/91 / 112459-03503.00 2 0 < 1 3 0 ° (h = 72 to 70, k = 0 t o 12, l = 0 t o 2 0 ) , which were averaged to 9305 unique reflections with Rin t = 0019. Three standard reflections (17 3 6, 173 6, 647) were measured every 7200 s and only small ( < 3%) random variations were observed. Lorentz and polarization corrections were applied. An empirical absorption correction based on a series of ~ scans was applied to the data: Tmin = 0863, Tmax = 0999. The space group, C2/c, was determined by systematic absences (hkl, h + k = odd; 0k0, k = odd; hOl, 1 = odd). The structure was solved by heavy-atom methods using SHELXS86 (Sheldrick, 1986) which revealed two independent positions of Mo. The remaining non-H atoms were located in successive difference Fourier syntheses. H atoms were not included in calculations. Atomic scattering factors including anomalous dispersion were taken from International Tables for X-ray Crystallography (1974, Vol. IV). The structure was refined with full-matrix least squares using Personal SDP (B. A. Frenz & Associates, Inc., 1989) on a 80386-based IBM compatible PC. All atoms were refined anisotropically. Y.w(IFol IFcl) 2 was minimized, where w = 4FoZ/[0-z(1) + 0.01Fo2]. A secondary-extinction coefficient refined to a value of X = 2.22 × 10 -7, where the correction factor (1 + xlc)-~ was applied to Ft. The final R = 0.046, wR = 0.061, Ral I ---0059 and S = 3.137 were obtained using 740 variables and 7459 observed © 1991 International Union of Crystallography 2460 [ ] V I o ( C 2 4 H 3 4 N 2 0 1 o ) ( C O ) 2 1 Table 1. Positional parameters and their e.s.d. 's A n i s o t r o p i c a l l y r e f i n e d a t o m s a r e g i v e n in t h e f o r m o f t h e i s o t r o p i c e q u i v a l e n t d i s p l a c e m e n t p a r a m e t e r d e f i n e d as : (4 /3 ) [a2 f l (1 ,1 ) + b2/3(2,2) + c2/3(3,3) + a b ( c o s y ) f l ( 1 , 2 ) + ac(cosfl)~(1,3) + bc(cosa)fl(2,3)].

Two crystal modifications of hexamethylcyclotristannatellurane

[(CH3)2SnTe]3, C6HI8Sn3Te3, Mr = 8291, Mo Ka radiation, h. = 0.71069 A, T = 293 K: (1) monoclinic, P21/c, a = 14-681 (2), b = 10.2775 (8), c =13.561(3) A, fl=112-087(12) ° , V =1896-0A 3, Z = 4, Dx = 2.905 Mg m-3, /.1, = 8.45 mm-1, F(000) = 1439.9, R=0.034 for 1968 observed data; (2) tetragonal, 141/a, a = 12-710 (3), c = 22.757 (4) A, V=3676.3A 3, Z = 8 , Dx=2996Mgm-3 , /z= 8-72 ram-l , F(000) = 2879.8, R = 0-024 for 1507 observed data. In each form the molecule adopts a twist-boat conformation which, in the case of the tetragonal modification, displays crystallographic twofold symmetry. Experimental. [(CH3)2SnTe]3 was obtained in petroleum solution by Soxhlet extraction of the crude reaction product (Blecher & Drfiger, 1979; Gay, Jones & Sharma, 1989). Evaporation of the solvent at room temperature yielded a sample consisting mainly of thin yellow-green sheets and a few thicker plates of amber colour. The solid state l l9Sn and lZSTe NMR spectra (Gay et al., 1989) displayed multiple resonances suggesting that more than one crystalline form was present. A plate selected from this sample for X-ray analysis was found to have crystallized in the space group P2~/c. A different yellow crystal modification was formed exclusively when a saturated petroleum solution of [(CH3)2SnTe]3 was cooled to 255 K, as confirmed by its solid state !19Sn and ~25Te NMR spectra (Gay et al., 1989). X-ray analysis showed these crystals to be tetragonal, space group I4~/a. Attempts to convert this phase to the monoclinic form by heating were unsuccessful. At 343 K the solid material appeared to fuse to give an apparently polymeric material of negligible solubility in petroleum ether. In either case the crystals became black upon exposure to air for several mintues. Crystals were mounted on Pyrex filaments with five-minute epoxy resin and were protected from air exposure by a thin coating of resin. Cell-parameter determination (25 reflections 15.1 _< 0_< 19.1 °, P21/c; 24 reflections 20.3 _ 0_ 25-7 °, I41/a) and data acquisition were performed using an Enraf-Nonius CAD-4F diffractometer with Mo Ka radiation and a graphite monochromator. The symmetry of the intensity-weighted reciprocal lattices and the systematic absences were determined using the diffractometer. Two standard intensities were measured every hour of acquisition time and showed no systematic variations. An empirical absorption correction (North, Phillips & Mathews, 1968) was applied to the data in the case of the I4~/a modification because the irregular shape of the crystal made measurement of crystal faces impracticable. The correction factors applied to the intensities ranged from 1.0 to 0.813. In the P2~/c case, an analytical absorption correction (de Meulenaer & Tompa, 1965) was made (transmission coefficients ranging from 0.614 to 0.248). Data reduction, including Lorentz and polarization corrections, was performed. In both cases the coordinates for the Te and Sn atoms were determined by direct methods (Main, Woolfson & Germain, 1971). The C-atom positions were revealed by electron density difference Fourier syntheses. H atoms were fixed at calculated positions with assigned isotropic temperature factors, basing the rotational conformation of each CH3 group upon the positions of the strongest peaks near the C atoms from a difference Fourier map. The final, full-matrix least-squares refinement, minimizing 0108-2701/89/111813-03503.00 © 1989 International Union of Crystallography 1814 HEXAMETHYLCYCLOTRISTANNATELLURANE Table 1. Data-acquisition and refinement details for two modifications of [(CH3)2SnTe]3

1,2-diaminobenzene adducts of nickel(II) 1,3-diketonates: Their role in dibenzotetraaza[14]annulence macrocycle formation

The attempted preparation of the macrocyclic ligand,6,8,15,17-tetraphenyldibenzo[b,i][1,4,8,11]tetraazacyclotetradecine from 1,2-diaminobenzene, 1,3-diphenyl-1,3-propanedione, and nickel(II)acetate via a template condensation is unsuccessful because of severe steric interactions in the desired product. The product isolated from this reaction, in high yield, is the bis(1,2-diaminobenzene) adduct of bis(1,3-diphenyl-1,3-propanedionato) nickel(II). Crystals of the adduct are monoclinic with a = 7.425(1), b = 12.221(3), c = 19.194(3) Å, β = 97.01°, Z = 2, V = 1728.7 Å 3, and space group P2 1/ n. The structure was solved by the heavy atom method and difference Fourier techniques, and refined by the block-diagonal least-squares method to a final R of 0.0379 for 2218 reflections with I>2σ( I). An empirical absorption correction was made via ψ-scan of 5 reflections with 2θ-values between 5 and 90°, and χ close to 90°. The compound consists of a square planar Ni(II)O 4 array with two molecules of axially coordinated diamine. The monodentate trans arrangement of a diamine molecules gives the compound the overall pseudo-octahedral geometry that is common to adducts of metal 1,3-diketonates. The 6,8,15,17-tetramethyl macrocycle is readily formed via template condensation when the diketone employed is 2,4-pentanedione. The bis(1,2-diaminobenzene) adduct of bis(2,4-pentanedionato)nickel(II) has also been prepared. A small amount of macrocycle can be detected by refluxing this latter adduct in alcohol. The principal product is (1,2-diaminobenzene) tetrakis(2,4-pentanedionato)dinickel(II).

Structure of guanidinium bicarbonate: a model for the bicarbonate anion binding site of the transferrins

Structure of guanidinium bicarbonate: a model for the bicarbonate anion binding site of the transferrins

Structures of mercury(I) nitrite and lithium disilver trinitrite

Structures of mercury(I) nitrite and lithium disilver trinitrite

Measurement of absorption curves for protein single crystals on the oscillation camera with time decaying incident-beam intensity and variable-wavelength synchrotron X-radiation

The correction of intensity data from protein single crystals for sample absorption effects is important for refinement and interpretation of atomic parameters. Synchrotron X-radiation sources are extensively used to provide high-resolution data and their tuneability utilized to collect data with optimized anomalous dispersion. At longer wavelengths the sample absorption effects become increasingly important. Previous methods of determining the absorption correction using the oscillation camera relied upon film methods, which cannot readily take account of the decay in incident-beam intensity of synchrotron sources. The use of a sensitive ion chamber to measure the transmitted intensity and monitoring of the incident intensity allows an empirical absorption correction to be calculated directly.

A Fortran computer program to collect X-ray diffraction data on macromolecules

A Fortran minicomputer program for the collection of X-ray diffraction data from protein crystals is described. Data collection efficiency has been achieved by means of: ω step scans for reflection intensity, radial step scan along 2θ to estimate background intensity and preselected reflection files. The program includes a standard reflection monitor, a means for slight misalignment compensation, empirical absorption correction data, Bijvoet pair collection, and the ability to collect data for the crystal lifetime without operator intervention.

Comments on the short communication,A statistical evaluation of absorptionby C. Katayama, N. Sakabe &amp; K. Sakabe

In a recent paper by Katayama, Sakabe & Sakabe [Acta Cryst. (1972), A28, 293] some principles of an empirical absorption correction method are described. These have been published previously [Kopfmann & Huber (1968). Acta Cryst. A24, 348].