Residual Electron Density Research Articles

A comparative structural study of a flux-grown crystal of K0.86Rb0.14TiOPO4 and an ion-exchanged crystal of K0.84Rb0.16TiOPO4

The crystal structures of a flux-grown crystal, K 0.86 Rb 0.14 TiOPO 4 , and an Rb/Ba ion-exchanged KTiOPO 4 crystal, K 0.84 Rb 0.16 TiOPO 4 , are refined and compared. Both crystals are isostructural with potassium titanyl phosphate, KTiOPO 4 . In both crystals, Rb substitutes for K only on the K(2) site with the crystallographically distinct K(1) site being solely occupied by K. However, in the ion-exchanged crystal, a residual electron density (2.6 e A -3 ) is found on a site that is normally a void in the KTiOPO 4 structure and that has been suggested as an essential site in the process of domain inversion by ion exchange in KTiOPO 4

Synthesis, characterization and Rietveld refinement of the tetragonal variant of AlPO 4-16 prepared in fluoride medium

The tetragonal variant of AlPO 4-16 isostructural of the clathrasil octadecasil was obtained by using quinuclidine as a template in the presence of fluoride anions. The as-synthesized material was characterized by 13C, 19F, 27Al and 31P nuclear magnetic resonance (NMR) spectroscopy. The structure was refined in the space group I4̄ [ a = 9.3423(1) Å, c = 13.4760(2) Å] from powder X-ray data. The position parameters of the four highest maxima of the residual electron density representative of the disordered organic species were used in the refinement procedure. Part of the fluoride present in the material was found in the D4R units of the structure. The final Rietveld residuals are R F = 0.034 and R wp = 0.114.

Stereo- und regioselektive Mehrfachadditionen an komplexgebundenes Cyclooctatetraen in [CpFe(η 6-Cot)] +

The cationic complex [CpFe(η 6-Cot)] + (Cot = cyclooctatetraene) 1 has been shown to be very suitable for high yield nucleophilic additions. The nucleophiles Nu − (Nu  HC(CO 2Me) 2, 2a; HC(CO 2Et) 2, 2b; NMe 2, 2c; H, 2d) add exclusively at the Cot ring, and stereoselectively in exo position with respect to the metal centre. Subsequently, the electrophilic addition of H + to the neutral compound CpFe(2-6-η-C 8H 8- 1- exo-Nu) generates the new cationic product [CpFe(2-7-η-C 8H 9-1- exo-Nu)] + ( 4), which can add a second nucleophile revealing an exo, exo-1,7-disubstituted cyclooctadienyl ligand. The X-ray structure analysis of the methyl malonate compound 2a (space group P2 1/ c, a = 19.083(1) å, b = 7.9169(5) Å, c = 11.278(2) Å, β = 106.77(1)°, R merge = 0.062) shows the η 2–6 coordination mode of the cyclo-C 8-ligand, the exo-position of the Nu-substituent, and the endo-position of the hydrogen atom at the sp 3 carbon atom of the C 8-ring confirmed by residual electron density. The cyclo-C 8-ring is bent, and the angle between the two best planes, which are defined by C-7, C-8, C-1 and C-2—C-6, amounts to 122.7°.

Residual electron density study of chromium sesquioxide by crystal structure and scattering factor refinement

The crystal structure of chromium sesquioxide, Cr 2O 3, has been refined from single crystal X-ray diffraction intensity data. Refinement of the scattering factors of Cr and oxygen in the anisotropic stage enabled extension of refinement up to anharmonic terms of the fourth rank tensors ( R=0.012). Difference Fourier synthesis shows d-electrons of ∼ 0.4ρ A ̊ 3 height situated in six of the eight cube-corner positions around Cr at ∼ 0.7 A ̊ distances; absent at the two positions along the three-fold axis. A prominent peak of 0.9ρÅ 3 height, interpreted as being due to electrons contributing to antiferromagnetic exchange, is situated between Cr pairs of face-sharing CrO 6 octahedra. No residual is detected between edge-sharing pairs.

Residual electron density study of α-aluminum oxide through refinement of experimental atomic scattering factors

The residual electron density distribution in α-Al 2O 3 has been studied with single-crystal X-ray diffraction intensity data. In addition to conventional least-squares anharmonic refinement up to the fourth-rank tensors ( R=0.0081), a method for obtaining experimental atomic scattering factors by utilizing occupation parameter refinement was tested. It has been found that this method is convergent once the basic crystal structure is well established ( R=0.0066). Although there were no prominent electron density residuals, several weak ( ∼ 0.1e A ̊ −3 in height) residuals including some resembling those due to bonding electrons were detected.

Electron distribution in pseudomorphic Al0.30Ga0.70As/ In0.15Ga0.85As/GaAs δ-doped heterostructures

We have investigated the electronic properties of the δ-modulation-doped Al0.30Ga0.70As/In0.15Ga0.85As heterojunction for a variety of different configurations. Experimental findings are compared with theoretical predictions based on the two-band effective mass approximation including strain, many-body, finite temperature, and DX center effects. We have also examined the case where the δ doping is placed in an embedded GaAs well within the Al0.30Ga0.70As. This is intended to reduce the effects of DX centers. In this instance, as the doping concentration is increased, experimentally determined channel density, ns, suggests higher saturation values, which may leave a residual electron density in the GaAs well. This residual charge density is parallel with the electron density in the InGaAs well and represents an additional conducting path. The features of the theoretical channel density versus doping density curves are confirmed by 300 and 1.6 K resistivity and Hall measurements, and Shubnikov–de Haas measurements made at 1.6 K.

Three-dimensional structure of rat acid phosphatase.

The crystal structure of recombinant rat prostatic acid phosphatase was determined to 3 A resolution with protein crystallographic methods. The enzyme subunit is built up of two domains, an alpha/beta domain consisting of a seven-stranded mixed beta-sheet with helices on both sides of the sheet and a smaller alpha domain. Two disulfide bridges between residues 129-340 and 315-319 were found. Electron density at two of the glycosylation sites for parts of the carbohydrate moieties was observed. The dimer of acid phosphatase is formed through two-fold interactions of edge strand 3 from one subunit with strand 3 from the second subunit, thus extending the beta-sheet from seven to 14 strands. Other subunit-subunit interactions involve conserved residues from loops between helices and beta-strands. The fold of the alpha/beta domain is similar to the fold observed in phosphoglycerate mutase. The active site is at the carboxy end of the parallel strands of the alpha/beta domain. There is a strong residual electron density at the phosphate binding site which probably represents a bound chloride ion. Biochemical properties and results from site-directed mutagenesis experiments of acid phosphatase are correlated to the three-dimensional structure.

The crystal structure of garnets (I): The residual electron density distribution in pyrope

The crystal structure of garnets (I): The residual electron density distribution in pyrope

Crystal structure of lead silver tribismuth sulfide, PbAgBi3S6

Crystallization in orthorhombic Cmcm space group with lattice parameters a = 4.077(2), b = 13.477 (7), c = 19.88 (2)A, Z = 4; the final R value is 0.076. Strong differences between weighted R-value and unit weighted R-value are caused by very small crystals and few observed reflections. Therefore the residual electron density was also calculated based on the observed reflections only. Natural gustavite show Ag-Bi ordering, whereas synthetic gustavite show statistical distribution

Refined Crystal Structure of LiNH4SO4Including Hydrogen Atoms in Phases II and III

Crystal structure of LiNH 4 SO 4 was refined in phase II (room temperature) and phase III (190 K) by the use of X-ray diffraction intensity with including hydrogen atoms. The least-squares calculations converged with residual parameter R =0.0362 and 0.0378 for phases II and III, respectively. At room temperature, thermal parameters of hydrogen atoms are large and residual electron density is notable around ammonium ions. This may indicate a partial disorderness of the ammonium ions. In the monoclinic phase III, the calculation was performed with considering the effect of twin domains. In the refined superstructure, ammonium ions with hydrogen atoms are perfectly ordered. Hydrogen atoms link nitrogen and oxygen of sulphate ions.

Cobalt atoms at M(2) site in C2/c clinopyroxenes of the system CaMgSi2O6(Di)-CaCoSi2O6(CaCoPx).

Single crystals of clinopyroxenes with two different compositions in the system CaMgSi2O6–CaCoSi2O6 were synthesized under the condition where the crystals were coexiting with the melts. The compositions of the obtained crystals are [Ca0.970Co0.030][Mg0.831Co0.169]Si2O6 (abbreviated CaCoPx20) and [Ca0.951Co0.049][Mg0.486Co0.514]Si2O6 (abbreviated CaCoPx70). The crystals have the same structure as diopside (space group C2/c) with the cell dimensions a=0.97527(10), b=0.89261(8), c=0.52486(7) nm, β=105.856(9)°, Z=4, Dx=3.370(1) g·cm−3 in CaCoPx20, and a=0.97700(10), b=0.89395(8), c=0.52451(7)nm, β=105.720(9)°, Z=4, Dx=3.544(1) g·cm−3 in CaCoPx70.The X-ray structure analyses gave unusually high residual electron densities up to about 6.9×103 e·nm−3 for CaCoPx20 and 1.3×104 e·nm−3 for CaCoPx70 at the position apart from the M(2) sites by about 0.04 nm along the b-axis in the difference Fourier maps based on the diopside model, where all of the Co2+ ions were located at the M(1) sites. These residual electron densities are due to partial replacement of Ca2+ by Co2+ at the M(2) sites, which amount to 3.0(4)% in CaCoPx20 and 4.9(4)% in CaCoPx70. The replacement was qualitatively confirmed by the ALCHEMI method under the condition of the (020) planar channeling.

The crystal structure of garnets (I): The residual electron density distribution in pyrope

Abstract The crystal structure of pyrope, Mg3Al2Si3O12, was refined by the X-ray diffraction method with anharmonic thermal vibration considered, applying the Gram-Charlier series expansion up to the fourth-rank tensors (R = 0.015 for 688 reflexions). A positive electron density residue due to bonding electrons 0.7 eÅ−3 in height was observed between the silicon and oxygen atoms. Crystal data: [Natural specimen from Parigi, Martiniana Po, Cuneo, Italy; Cubic garnet structure; Ia[unk]d; Z = 8; a o = 11.4582(6) Å; V = 1504.35 Å3; Dx = 3.560 g cm−3; μ = 11.88 cm−1; λ(MoKα) = 0.71069 Å, F(000) = 1600; T = 296 K].

Molecular organization in crystalline [Co2(CO)8] and [Fe2(CO)9] and a search for alternative packings for [Co2(CO)8

The molecular organization in crystals of [Co2(CO)8] and [Fe2(CO)9] has been investigated by means of packing potential-energy calculations and computer graphic analysis. It is shown that the two molecules pack in nearly identical ways in their crystals. However, while crystalline [Fe2(CO)9] is compact, solid [Co2(CO)8] presents large empty channels (van der Waals width between 2.4 and 4.5 A, at room temperature) corresponding to the approximate location of possible residual electron density (whether due to Co–Co bonding electrons or to lone pairs on the Co atoms). Alternative crystal packings for [Co2(CO)8] have been generated, using improved atomic potential parameters adapted to carbonyl compounds. On purely steric grounds, it is shown that the [Co2(CO)8] molecule is compatible with more close-packed crystal arrangements than the one actually observed. In two alternative triclinic and monoclinic crystal structures the ‘empty’ bridging sites are shown to be available for molecular interlocking.

Single-crystal X-ray diffraction study on Ce 1 − xLa xB 6 solid solutions

Single crystals of Ce 1 − x La x B 6, with x = 0, 0.25, 0.50 and 0.75, prepared by crystallization from solutions in molten aluminium, were investigated by X-ray diffraction. Experimental data were corrected for thermal diffuse scattering, absorption and extinction effects. Structural parameters were refined and the residual electron densities were calculated. Vacancies at the boron position were established for all the compounds.

Comparison of the binding of glucose and glucose 1-phosphate derivatives to T-state glycogen phosphorylase b

The binding of T-state- and R-state-stabilizing ligands to the catalytic C site of T-state glycogen phosphorylase b has been investigated by crystallographic methods to study the interactions made and the conformational changes that occur at the C site. The compounds studied were alpha-D-glucose, 1, a T-state-stabilizing inhibitor of the enzyme, and the R-state-stabilizing phosphorylated ligands alpha-D-glucose 1-phosphate (2), 2-deoxy-2-fluoro-alpha-D-glucose 1-phosphate (3), and alpha-D-glucose 1-methylenephosphonate (4). The complexes have been refined, giving crystallographic R factors of less than 19%, for data between 8 and 2.3 A. Analysis of the refined structures shows that the glucosyl portions of the phosphorylated ligands bind in the same orientation as glucose and retain most of the interactions formed between glucose and the enzyme. However, the phosphates of the phosphorylated ligands adopt different conformations in each case; the stability of these conformations have been studied by using computational methods to rationalize the different binding modes. Binding of the phosphorylated ligands is accompanied by movement of C-site residues, most notably a shift of a loop out of the C site and toward the exterior of the protein. The C-site alterations do not include movement of Arg569, which has been observed in both the refined complex with 1-deoxy-D-gluco-heptulose 2-phosphate (5) [Johnson, L. N., et al (1990) J. Mol. Biol. 211, 645-661] and in the R-state enzyme [Barford, D. & Johnson, L. N. (1989) Nature 340, 609-616]. Refinement of the ligand complexes has also led to the observation of additional electron density for residues 10-19 at the N-terminus which had not previously been localized in the native structure. The conformation of this stretch of residues is different from that observed in glycogen phosphorylase a.

Stereochemistry of carbon monoxide binding to normal human adult and Cowtown haemoglobins

The structures of carbonmonoxyhaemoglobins A and Cowtown (His146β → Leu) have been refined at 2.2 Å (1 Å = 0.1 nm) and 2.3 Å resolution, respectively. The least squares fit to the FeCO line makes an angle to the haem normal of about 6 °. The FeCO group is bent from linearity by about 7 °. The porphyrins in the CO liganded haemoglobins are ruffled. This deformation of the haem and the distortion of the FeCO group may explain the low CO affinity of haemoglobin. The electron density for the C-terminal residues is low but sufficient to distinguish the histidyl and leucyl residues clearly. The similarity between these two structures, apart from 146β, means that the reduced alkaline Bohr effect is due solely to the replacement of histidine by a leucine.

Crystal structure of chicken liver basic fatty acid-binding protein at 2.7 � resolution

The three-dimensional structure of chicken liver basic fatty acid-binding protein has been determined at 2.7 A resolution by X-ray crystallography. Phases were calculated using the multiple isomorphous replacement procedure and a preliminary model was built. This model, with an initial R-factor of 0.57, was then improved by a cycle of refinement by simulated annealing which brought the R factor down to 0.32. The protein is structured as a compact 10-stranded-beta-barrel which encapsulates a residual electron density that can be interpreted as a fatty acid molecule. The NH2-terminus portion of the molecule contains two short alpha-helices. The structure of this liver protein appears very similar to that of the Escherichia coli derived rat intestinal FABP recently determined by X-ray diffraction methods.

X-ray structure refinement of single crystals of CeB 6 and Ce 0.75La 0.25B 6 solid solution grown by the solution method

Single crystals of CeB 6 and Ce 0.75La 0.25B 6, prepared by crystallization from solutions in molten aluminium, were investigated using X-ray diffractometry. Experimental data were corrected for thermal diffuse scattering and extinction effects. Structural parameters were refined and the residual electron density was calculated. The results were compared with previous studies. Vacancies at the boron position were established for both compounds.

Electron-density distribution in ilmenite-type crystals. IV. Iron(II) titanium(IV) trioxide, FeTiO3.

The electron-density distribution in a crystal of FeTiO3 has been investigated by means of the single crystal X-ray diffraction method. A small amount of partial disorder was observed in the cation arrangement of the examined crystal. The crystal has the cell dimensions a=5.08854(7), c=14.0924(3) Å, with the space group R-3, Z=6, Dx=4.789 g cm−3, and μ(Mok α)=103.40 cm−1. Residual electron densities observed around the Fe2+ ion after refinement based on the spherical atom model are qualitatively explained with a configuration of 3d electrons near the high-spin state. Population analysis with the assumption of the 3(C3) crystal field yielded the electron populations of 1.31, 2.33, and 2.36 for the a, e(t2g) and e(eg) orbitals, respectively. The subsequent refinement with anharmonic thermal parameters for cations markedly reduced the residual densities around Fe2+ ion.

Anharmonic thermal vibration in a crystal of lithium(I) tantalum(V) trioxide, LiTaO3.

The electron-density distribution in a crystal of LiTaO3 has been investigated with the single-crystal X-ray diffraction method. The crystal has the cell dimensions a=5.15329(7) and c=13.7806(5) A with the space group R3c and Z=6. Residual electron densities due to anharmonic thermal vibration were observed around the Ta5+ ion. Refinement with anharmonic thermal parameters improved the coincidence of the observed and calculated structure factors significantly. The C333 (the coefficient of Δz3) value of Ta5+ is most significant among the third and fourth order anharmonic potential parameters. It has revealed that significant errors are sometimes introduced into positional parameters if contributions of odd order terms of anharmonic potentials are ignored.