Showing papers in "Acta Crystallographica Section B-structural Science in 1986"

A systematic pairwise comparison of geometric parameters obtained by X-ray and neutron diffraction

Abstract: The effects of X-ray atomic asphericity on derived molecular geometry have been examined for ten common substructures involving C, N, O. The Cambridge Structural Database has been used to locate pairs of X-ray (X) and neutron (N) structure determinations of the same compound. Rigid criteria based on experimental temperature, refinement procedures, crystalline form and precision have been applied in selecting suitable X, N structure pairs. Corresponding X and N values for derived parameters have been paired for 46 chemically unique subsets (39 bond-length sets and 7 valence-angle sets). The statistical significance of the distribution of X N differences (Di) has been assessed in each case via a Wilcoxon matched-pairs signed-ranks test. The signed magnitude of the mean difference (/5) is large, as expected, for bonds to H, ranging from -0.096 (7) A for C-H to -0.155 (10) A for O-H. Some highly significant differences are also observed for bonds involving C, N, O alone. Representative /) values (A) are -0.0096 (9) for C--C (ethylenic), -0.0052(9) for C---C (benzenoid), -0.0078 (16) for C_----N, +0.0035 (12) for C-OH (carboxyl), +0.0046 (10) for N---O (nitro), +0.0054 (8) 0108-7681 / 86/050515-08 $01.50 for C-O (carbohydrate) and +0.0082 (21) for C-C (C-C----N); the significance of the Di distribution for C = O (keto) was marginal. No significant differences were observed for C = O (COOH and COO-), nor for any of the valence angles tested. Some implications for the combination or comparison of structural results obtained from different techniques are noted.

Charge density in cuprite, Cu2O

Abstract: Etude de l'influence des procedures de reduction de donnees, des modeles de facteur de temperature et des modeles de deformation sur les resultats

The refined structure of beef liver catalase at 2·5 Å resolution

Abstract: The crystal structure of beef liver catalase [Murthy, Reid, Sicignano, Tanaka & Rossmann (1981). J. Mol. Biol. 152, 465-499] has now been refined by a restrained parameter least-squares method [Konnert & Hendrickson (1980). Acta Cryst. A36, 344-350] with respect to 2.5 A data. Some extra density was discovered during the refinement process. This was interpreted in terms of a bound NADP molecule [Kirkman & Gaetani (1984). Proc. Natl Acad. Sci. USA, 81, 4343-4348; Fita & Rossmann (1985). Proc. Natl Acad. Sci. USA, 82, 1604-1608]. When the noncrystallographic symmetry was imposed as a constraint, the R factor was reduced to 21.2%. However, refinement of the two crystallographic independent subunits gave a final R factor of 19.1%. The refined coordinates have been re-analyzed for main-chain and side-chain hydrogen bonding, charge distribution, secondary structural element interactions, subunit contacts and molecular packing. The fractional accessibility and the temperature-factor variation are also discussed. The oligomerization process is considered in terms of the unusual quaternary structure. The organization of the heme channel and its relation to the enzyme's catalytic properties have been discussed elsewhere [Fita & Rossmann (1985). J. Mol. Biol. 185, 21-37].

Hydrogen bonding and thermal vibrations in crystalline phosphate salts of histidine and imidazole

Abstract: Salts of composition Im.H3PO4 and L-His.2H3PO4 were prepared and analyzed by X-ray crystallography. The Im salt forms a rather complicated crystal structure with two chemical formula units in the crystal chemical unit and the crystals of the His salt contain unionized molecular H3PO4. There are networks of short strong hydrogen bonds in both crystals, and the hydrogen bonding noticeably affects the O-atom thermal vibrations. The hydrogenbonding geometries indicate that N-H...O-P and P-O-H...O-P bonds are generally the strongest N-H...O and O-H...O bonds that can form in biochemical systems, and the strong hydrogen bonding significantly affects the P-O bond strengths. Crystal data: L-histidinium dihydrogen orthophosphate 10N302 .H2PO4 .Ha PO4,

Neutron diffraction study of MgNH4PO4.6H2O (struvite) and survey of water molecules donating short hydrogen bonds

Abstract: MgNH4PO4.6H20 (struvite), Mr=245'4, Pmn2, a=6.955(1), b=6.142(1), c=11.218(2)A, V= 479.2 (2) ]k 3, Z = 2, Dx = 1.70 Mg m -3, neutrons, A 1.179/~, /z = 0.03 mm -t, room temperature. The structure was refined from 685 unique neutron diffraction data to R -- 0.032. The ammonium group is completely ordered and linked by one single and several polyfurcated N...O hydrogen bonds varying from 2.800 (5) to 3"498 (5) ~. Six out of eight W...O hydrogen bonds donated by the water molecules are in the range 2.630 (4)-2.649 (5) A. A survey of hydrogen bonds studied by neutron diffraction reveals, on

An analysis of the structural characteristics of hollandite compounds

Abstract: Etude par diffraction de neutrons sur 7 composes Ba x (M 3+ Ti 4+ ) 8 O 16 . Influence des ions trivalents tels que Al, Fe, Ga sur les variations de l'environnement des sites tunnel et la nature de la transformation monoclinique-quadratique dans les hollandites

The β⇄α' transition in Sr2SiO4 (and Ca2SiO4, K2SeO4 etc.), involving a modulated structure

Abstract: Examen des legeres differences entre les structures des phases β et α' afin d'interpreter l'apparition d'une modulation dans la transition β⇄α'

Centrosymmetric or noncentrosymmetric

Abstract: In cases where diffraction data do not provide a clear choice between a centrosymmetric and a noncentrosymmetric space group, it is better to opt for the centrosymmetric description even though disorder may result. The disorder model implies that the crystal is a composite of two or more molecular structures that cannot be distinguished from one another. On the other hand, attempts to refine a single, ordered model in the noncentrosymmetric space group (which should lead to poor convergence because of near singularities) may lead to the erroneous conclusion that a unique structure has been found. Three examples of this latter situation are given.

Electron Density of Orthoboric Acid Determined by X-ray Diffraction at 105 K and ab initio Calculations

Abstract: The charge distribution in orthoboric acid, B(OH)3, Mr=61.83, has been investigated experimentally using low-temperature X-ray diffraction data and theoretically by ab initio calculations. Crystal data at 105 K, triclinic, space group P1, a = 7.0187 (14), b = 7.035 (2), c=6.3472 (12) A, a =92.49 (12), /3-- 101.46 (2), 3/=119"76(2) °, V= 262"90 (1)/~ 3, Z=4, Dx = 1.562 (1) g cm -3, Mo Ka, h = 0.71073/~, /x = 1.51 cm -1, F(000) = 128, R = 0.038 for 3370 observed reflections. The two independent B(OH)3 molecules are identical and planar, each having threefold symmetry. (B-O) = 1.368 (1) ~, (O-B-O) = 120.00 (7) °. The structural parameters for B and O, determined from high-order refinement, are virtually identical to those obtained from a multipole refinement using all the data. The static deformation density in the B-O bonds as determined from a multipole refinement agrees well with the theoretical deformation density obtained from an ab initio calculation beyond the Hartree-Fock level, which had peaks with a density of 0.3 e A-3. The features around the O atoms, especially in the lone-pair regions, agree less well.

On a possible substitution of p‐xylene by toluene in p‐xylene crystals. The crystal structure of p‐xylene, C8H10, at 180 K

Abstract: Mr=106.17, monoclinic, P21/n, a=5.806(2), b= 5.023 (1), c=11.215 (2)/~, fl=100.48(2) ° , V= 321.61 (14) A3, Z = 2, Dx = 1.096 gcm -3, A(Mo Ka)=0.71069/~,, /x =0.66cm -1, F(000) = 116, T= 180 K, R = 0.045 for 926 reflections [I > 2.5o-(I)]. The cell dimensions are confirmed by powder diffraction. No phase transition is observed between 110 and 273 K. The crystal data reported by Biswas [Indian J. Phys. (1960), 34, 263-271] are incorrect. The bond lengths and bond angles in p-xylene are equal to the corresponding values in toluene within experimental error. The aromatic ring is essentially planar and slightly deformed at the substituent side. The centre of symmetry in p-xylene coincides with the space-group centre. The p-xylene molecules are packed into chains along b by nearly equal van der Waals contacts between the six ring C atoms and one methyl H of a neighbouring molecule. The chains are held together by van der Waals forces. Because of the great resemblance of packing in p-xylene and a-toluene crystals, the possibility of the existence of solid solutions of toluene in p-xylene is proposed. This proposal is verified by measuring the p-xylenerich part of the phase diagram of the toluene/p-xylene system. Separation of pure p-xylene crystals from a mixture containing toluene seems unlikely.

Neutron low-temperature (4 and 20 K) and X-ray high-pressure (6.5 x 102 and 9.8 x 102 MPa) structures of the organic superconductor di(2,3,6,7-tetramethyl-1,4,5,8-tetraselenafulvalenium) hexafluorophosphate, (TMTSF)2PF6

Abstract: Description de l'evolution de l'empilement cristallin sous contrainte. La temperature et la pression conduisent a une diminution des distances intra- et interstrates dans le rapport 1:1,5. Description de la mise en ordre de l'anion PF 6

The determination of the incommensurately modulated structure of niobium tetratelluride

Abstract: A complete analysis of the modulated structure of NbTe4 is presented, using the newly developed formalism of de Wolff [Acta Cryst. (1974). A30, 777-785] and Yamamoto [Acta Cryst. (1982). A38, 87-92]. The diffraction pattern was measured at room temperature, including first-order and second-order satellites. The superspace group of the complete structure is |'l/Pa/mcc,, 1 T I 1" The final R~ value is 0.095 (0.044 for main reflections only), for a total of 3894 unique reflections (923 main reflections). The average structure found previously [Selte & Kjekshus (1964). Acta Chem. Scand. 18, 690-696] is confirmed. In addition, the modulation wave is determined; it resides mainly on the Nb atoms, which have an amplitude of 0.33/~. The results show that the displacements are correlated in such a way as to keep the Te-Te bonding distance constant and to minimize the variation in the shortest Nb-Te distance. It is found possible to refine at least up to the fifth harmonic in the modulation wave. However, the values found for higher harmonics do not describe the real modulation wave, but assume values to account for the variation in intensities due to experimental errors. Therefore, only the amplitudes up to the second order are considered to be reliable.

Accuracy of crystal structure error estimates

Abstract: A statistical analysis of 100 crystal structures retrieved from the Cambridge Structural Database is reported. Each structure has been determined independently by two different research groups. Comparison of the independent results leads to the following conclusions: (a) The e.s.d.'s of non-hydrogen-atom positional parameters are almost invariably too small. Typically, they are underestimated by a factor of 1.4-1-45. (b) The extent to which e.s.d.'s are underestimated varies significantly from structure to structure and from atom to atom within a structure. (c) Errors in the positional parameters of atoms belonging to the same chemical residue tend to be positively correlated. (d) The e.s.d.'s of heavy-atom positions are less reliable than those of light-atom positions. (e) Experimental errors in atomic positional parameters are normally, or approximately normally, distributed. (f) The e.s.d.'s of cell parameters are grossly underestimated, by an average factor of about 5 for cell lengths and 2.5 for cell angles. There is marginal evidence that the accuracy of atomic-coordinate e.s.d.'s also depends on diffractometer geometry, refinement procedure, whether or not the structure has a centre of symmetry, and the degree of precision attained in the structure determination.

Pseudo-weak-phase-object approximation in high-resolution electron microscopy. II: Feasibility of directly observing Li+

Abstract: Images of Li2Ti307 were calculated with the multislice method and observed with a JEM-200CX electron microscope Both calculated and observed images show that Li ÷ ions can be seen intuitively under an optimum imaging condition as is predicted by the theory of the pseudo-weak-phase-object approxi- mation 1 Introduction In the earlier papers in this study (Li & Tang, 1984, 1985) the dependence of image contrast on crystal thickness was discussed When the crystal is too thick to allow the weak-phase-object approximation (WPOA) to hold, it was shown that with increasing crystal thickness the image contrast of light atoms increases more rapidly than that of heavy atoms Hence, crystals too thick for weak-phase-object approximation to hold but thinner than the critical thickness have been treated as pseudo-weak phase objects Under the optimum imaging condition the image intensity can be expressed as I(r)= 1- 2o'~o'(r) (1) Here ~o'(r) is the modified projected potential distri- bution function (PPDF) which can be treated as the PPDF of an imaginary isomorph of the examined crystal where real atoms are replaced by imaginary ones The constituent heavy and light atoms of the imaginary isomorph are respectively lighter and heavier than those of the real crystal This indicates the possibility of preferentially revealing different kinds of atoms by choosing observation regions of different thicknesses in the crystal examined It was found by the HREM (high-resolution elec- tron microscopy) observation on the mineral cebaite BasCe2(CO3)sFz that within a certain range of crystal thicknesses the image contrast is sensitive to the posi- tions of light atoms (C, O, F) and hence the positions of these light atoms were determined by HREM (Li * Projects supported by the Science Fund of the Chinese Academy of Sciences t Present address: Beijing Electron Microscope Laboratory, PO Box 2724, Beijing, China

Structural investigations of phosphorus–nitrogen compounds. 2. The structures of N3P3(NH2)2Cl4, N3P3(NPPh3)(NH2)Cl4 and N3P3(NPPh3)Cl5 and a comparison with other phosphazenylphosphazenes. The relationship of conformation in the solid state to conformation in solution

Abstract: Discussion sur la conformation a l'etat solide determinee a partir des angles diedus des substituants phosphazenyl par rapport au cycle et sur les conformations preferentielles en solution mesurees a partir des constantes de couplage spin-spin 4 J(PP)

The immanent chaotization of crystal structures and the resulting diffuse scattering. I. Mathematical scheme and physical models

Abstract: Developpement de la theorie de la diffusion en diffraction RX observee par la methode de Laue dans certains cristaux ioniques. Discussion sur les causes du phenomene

Symmetry rules for the stereochemistry of the lone-pair electrons in TeX62− (X=Cl, Br, I) and the structures of 1,2-ethanediammonium hexachlorotellurate(IV) and 1,2-ethanediammonium hexachlorostannate(IV)

Abstract: Ces deux composes sont isostructuraux et cristallisent dans le systeme triclinique, groupe P 1 . Observation de tres petites deformations par rapport a la symetrie m 3 m