bluuebunny/crossref_metadata_2025 huggingface dataset:
Modulated Structure of the Composite Crystal Urea/n-Heptadecane
Authors: Weber Th. , Boysen H. , Frey F. , Neder R. B.
Published: July 2002

The structure of the composite crystal urea/heptadecane was determined by single-crystal X-ray diffraction. The lattice constants of the hexagonal substructures are a = 8.218 (2), b = 8.218 (3), c

h
= 11.017 (3) Å for the urea (host) structure and c

g
= 23.713 (1) Å for the heptadecane (guest) structure, respectively. The (3+ 1)-dimensional space group is P6122(00\rho)011. Refinements on 786 reflections converged to wR = 0.0232 for 608 main host reflections, wR = 0.1506 for 10 main guest reflections, wR = 0.0328 for 49 common main reflections and wR = 0.753 for 119 pure satellite reflections. A comparison of the refinement of only the urea substructure and a refinement of the whole composite crystal, including the guest subsystem and the mutual modulations of both subsystems, shows that the main reflections, previously assigned to the urea host exclusively, are affected by a nonnegligible contribution of the heptadecane satellite scattering. The modulation of the guest structure has a maximum when the CH2 groups of the heptadecane molecule are facing the channel walls at heights corresponding to troughs in this wall. Thus, the modulation of the guest structure can be interpreted by an adaptation of the guest molecules to the host structure. The modulation of the host structure was found to be very weak, as the satellite scattering of the host structure is low. \psi-scans of the 00 l reflections revealed that the observed violation of the 61 screw axis extinction rule of the host structure and guest structure modulation can be explained by considerable umweganregung.
Retrieval of Structure-Factor Phases in Non-centrosymmetric Space Groups. Model Studies Using Multipole Refinements
Authors: Spackman M. A. , Byrom P. G.
Published: July 2002

Structure factors with known magnitude and phase are constructed for seven different molecular crystals in non-centrosymmetric space groups and used to calibrate the retrieval of structure-factor phase information with several different scattering factor models. Monopole models are confirmed to be inadequate, yielding poor estimates of phases and underestimating the Fourier deformation electron density by as much as 50%. Multipole models are generally successful, with the conspicuous exception of hexamethylenetetramine (HMT). The results confirm the known difficulty of phasing structure-factor magnitudes for HMT, but reveal a broad spectrum of behaviour of phase retrieval in various non-centrosymmetric space groups, depending partly on the number of reflections with restricted phases. For several systems (urea, hydrogen peroxide, L-alanine and borazine) the results confirm that multipole refinements of scattering factor models against experimental data are capable of yielding highly accurate phases and hence reliable electron distributions. For the exceptional case of HMT a simple eigenvalue filtering technique enables retrieval of phases and electron densities with an accuracy comparable to the best of the other non-centrosymmetric systems studied.
Structural Systematics of the High-Pressure Phases of Phosphorus, Arsenic, Antimony and Bismuth
Authors: Iwasaki H. , Kikegawa T.
Published: July 2002

New structural systematics of the high-pressure phases of the title elements are given on the basis of the results obtained in our diffraction studies and the results from the literature. Although the structural transition sequence with increasing pressure appears to be different for the four elements, reinterpretation of the structure data has shown that it is expressed in a systematic way as follows P A17–A7–PSC As A7–PSC–dist. BCC–BCC Sb A7–dist. BCC–BCC Bi A7–dist. PSC–dist. BCC–BCC. Notations used are A17 (orthorhombic layered structure), A7 (rhombohedral layered structure), PSC (primitive simple cubic structure), dist. PSC (monoclinic structure which is regarded as a distorted PSC), BCC (body-centered cubic structure) and dist. BCC (tetragonal structure which is regarded as a distorted BCC). Phosphorus lacks the post-PSC phases, but it is likely that the same transition sequence as that of arsenic is seen under extremely high pressure. Discussion is made on how the network of the densest atomic plane changes through the structural transition sequence.
Low-Temperature Neutron Diffraction Study of the Silver Perchlorate–Benzene π Complex
Authors: McMullan R. K. , Koetzle T. F. , Fritchie C. J.
Published: July 2002

The crystal structure of the AgClO4.C6H6 \pi complex, earlier determined by X-ray diffraction at room temperature, has been redetermined at 18, 78 and 158 K by neutron diffraction. Crystal data: orthorhombic, space group Cmcm, Z = 4, F(000) = 225.318 fm, T: 18, 17, 158 K; D

x
= 2.591 (2), 2.570 (1), 2.523 (1) g cm−1; \mu
n
= 0.166, 0.165, 0.162 cm−1; a = 7.913 (1), 7.973 (1), 8.100 (1), 8.336 (1) Å (at 295 K); b = 7.837 (2), 7.857 (1), 7.902 (1), 7.996 (1) Å (at 295 K); c = 11.798 (3), 11.777 (2), 11.739 (2), 11.638 (2) Å (at 295 K); wR(F
2) = 0.037, 0.035, 0.045, S = 1.18, 1.08, 1.10 for 782, 628, 800 reflections and 51 variable parameters. This study confirms the principal features reported in the X-ray investigation and reveals details of structure not observable at room temperature. Distortions of the benzene molecule from D
6h
symmetry ascribed to Ag+...C6H6 interactions are small, but significant. At 18 K the two C—C bonds complexed by Ag+ are 1.405 (1) Å in length; the other four are 1.398 (1) Å. The C—H bonds are equal in length at 1.087 (2) (two) and 1.089 (1) Å (four). The H atoms nearest to Ag+ are displaced 0.064 (1) Å from the C6 plane, away from the silver. The shortest Ag+...C distance of the complex is 2.565 (1) Å. This value and bond lengths of the benzene molecule are invariant between 18 and 158 K within 2 e.s.d.'s or less. The nonequivalent bond lengths of ClO^{-}_4, 1.451 (1) (two) and 1.441 (1) Å (two) at 18 K, are foreshortened by −0.007 and −0.005 Å at 158 K by effects of thermal motion. The O—Cl—O angles, 109.08 (7), 109.98 (2) and 107.83 (8)° at 18 K, are virtually unchanged by temperature. The Ag+...ClO^{-}_4 interactions occur at Ag+...O distances of 2.785 (1) and 2.612 (1) Å (18 K), where the shorter values involve ClO^{-}_4 acting as a bidentate group. Rigid-body and riding-motion models do not adequately account for the observed temperature dependence of bond lengths in ClO^{-}_4 nor provide significant corrections to the C6H6 bond lengths at 18, 78 and 158 K beyond their uncertainty limits. A harmonic potential rationalizes the motion of Ag+ at these three temperatures.
Structural and Thermodynamic Relationships Between Optically Active and Racemic Compounds. The Crystal Structures of Optically Active Chloro- and Bromo-Substituted 3-Hydroxy-3-phenylpropionic Acids
Authors: Larsen S. , Marthi K.
Published: July 2002

The crystal structures of the isostructural optically active R-(+)-meta-chloro- and meta-bromo-substituted 3-hydroxy-3-phenylpropionic acids have been determined from low-temperature [122.0 (5) K] X-ray [\lambda(Cu K\alpha) = 1.54184 Å] diffraction data. (R)-(+)-3-Hydroxy-3-(3′-chlorophenyl)propionic acid (C9H9ClO3, M

r
= 200.61), orthorhombic, P212121, a = 5.6938 (7), b = 5.7913 (7), c = 27.052 (4) Å, Z = 4, m.p. = 365.8 (5) K. 3-Hydroxy-3-(3′-bromophenyl)propionic acid (C9H9BrO3, M

r
= 245.07), orthorhombic, P212121, a = 5.8020 (8), b = 5.8638 (8), c = 27.345 (4) Å, Z = 4, m.p. = 350.3 (5) K. The O—H...O hydrogen-bond pattern found in these acids is identical to those found in the equivalent racemic compounds with hydrogen-bonded chains parallel to the a axis. The enantiomeric and racemic crystals differ only in the orientation of these chains. Short contact distances are found between the halogen atoms and one of the H atoms of the phenyl group. Statistical data show that these interactions are of repulsive character. The structural results are related to the thermodynamic measurements, which show that the conglomerate and racemic compound are in equilibrium for the chloro-substituted acid. The formation of a racemic compound for the bromo-substituted acid appears to be favoured by repulsive H...Br interactions in the enantiomeric crystals, giving the latter a higher enthalpy.
Hydrogen Bonding to Thiocyanate Anions: Statistical and Quantum-Chemical Analyses
Authors: Lommerse J. P. M. , Cole J. C.
Published: July 2002

A statistical analysis of entries from the CSD (Cambridge Structural Database) showed that the average hydrogen-bond geometry to the nitrogen acceptor atom of the thiocyanate anion was not collinear with respect to the molecular axis of the anion and so not collinear with the nitrogen lone pair [Tchertanov & Pascard (1996). Acta Cryst. B52, 685–690]. This somewhat unexpected result has been investigated further using theoretical energy calculations applying Intermolecular Perturbation Theory in combination with a more detailed statistical analysis of an appropriate CSD dataset. The energy calculations pointed to the formation of the strongest hydrogen bonds in the nitrogen lone-pair direction. The statistical analysis showed that this directionality occurs in cases where the N atom accepts one hydrogen bond only. The non-linear average hydrogen-bond geometry observed in the earlier study can be attributed to multiple hydrogen bonding to the N atom. In such cases, there is a shift away from the optimum orientation.
Structures and Phase Transitions of the A
7PSe6 (A = Ag, Cu) Argyrodite-Type Ionic Conductors. I. Ag7PSe6
Authors: Evain M. , Gaudin E. , Boucher F. , Petricek V. , Taulelle F.
Published: July 2002

The crystal structures of the two polymorphic forms of the argyrodite Ag7PSe6 compound are analysed by means of single-crystal X-ray diffraction. Above the phase transition at 453 K leading to the ionic conducting phase, γ-Ag7PSe6 crystallizes in cubic symmetry, space group F4¯3m, with a = 10.838 (3) Å, V = 1273.1 (12) Å3 and Z = 4 at 473 K. The refinement of the 473 K structure leads to a reliability factor of R = 0.0326 for 192 independent reflections and 33 variables. Diffusion paths for silver d
10 ions are evidenced by means of a combination of a Gram–Charlier development of the atomic displacement factors and a split model. Below the phase transition β-Ag7PSe6 crystallizes again in cubic symmetry, but with the space group P213 and a = 10.772 (2) Å, V = 1250.1 (6) Å3 and Z = 4 at room temperature. The refinement of the 293 K structure leads to a reliability factor of R = 0.0267 for 1125 independent reflections and 68 variables. In the β-Ag7PSe6 ordered phase the silver cations are found in various sites corresponding to the most pronounced probability density locations of the high-temperature diffusion paths. Those positions correspond to low coordination (2, 3 and 4) sites, in agreement with the silver preference for such environments. In addition, the Ag atoms are found slightly displaced from the true linear, triangular or tetrahedral coordination, as expected from second-order Jahn–Teller effects.
Order and Disorder in Niobium Tungsten Oxides of the Tetragonal Tungsten Bronze Type
Authors: Krumeich F.
Published: July 2002

Two superstructures of the TTB type (tetragonal tungsten bronze) exist in the system Nb2O5/WO3. They are caused by an ordered arrangement of pentagonal tunnels filled with metal–oxygen strings. Besides the well known 4:9 phase (Nb8W9O47), which has a tripled b axis, evidence for a new orthorhombic structure, Nb6W8O39 (a = b = 27.3 Å), has been found. The oxidation products of Nb7W10O47 and Nb4W13O47 frequently comprise less-ordered arrangements of filled tunnels, causing diffuse scattering. In Nb7W10O47.5 the electron diffraction patterns (along [001]) of many crystal fragments show circular diffuse scattering, which appears around the main reflections of the TTB substructure with two distinct radii (r*). r* \simeq 0.33a* indicates the predominance of 4:9-type domains, whereas r* \simeq 0.41a* corresponds to Nb6W8O39. In Nb4W13O49 the diffuse scattering pattern is cross-shaped; this is due to the presence of long slabs of diamond-linked pentagonal columns. Structure models for these particular states of order have been derived from high-resolution transmission electron microscopy images. Some general principles for the formation of the different arrangements are deduced. Apparently, two distinct types of link between the filled pentagonal tunnels are important features which lead to the stability of these structures.
Neutron powder diffraction study of α-Ti(HPO4)2.H2O and α-Hf(HPO4)2.H2O; H-atom positions. Erratum
Authors: Salvadó M. A. , Pertierra P. , García-Granda S. , García J. R. , Rodríguez J. , Fernández-Díaz M. T.
Published: July 2002

The H-atom coordinates were omitted from Tables 2 and 3 on p. 897 [Salvadó, Pertierra, García-Granda, García, Rodríguez & Fernández-Díaz, Acta Cryst. (1996), B52, 896–898]. The values are now listed.
Structure of Gallobicchulite. A Combined EXAFS/Neutron Powder Diffraction Refinement
Authors: Binsted N. , Dann S. E. , Pack M. J. , Weller M. T.
Published: July 2002

A new model for the structure of gallobicchulite, Ca8(Ga2SiO6)4(OH)8, has been derived from a combined refinement of EXAFS and neutron powder diffraction data. The structure is based on a pseudo-cubic ordered unit cell, related to that of tugtupite, with long-range disorder owing to domains in three orientations parallel to the cubic faces.
Pressure-Induced Octahedron Strain in VF3-Type Compounds
Authors: Sowa H. , Ahsbahs H.
Published: July 2002

High-pressure X-ray investigations on crystal powders of the TiF3, titanium trifluoride, and FeF3, iron trifluoride, phases with VF3-type structures were performed up to 7.67 (7) and 9.00 (7) GPa, respectively. Both compounds are highly compressible and show strong anisotropic behavior. While the hexagonal a lattice parameters are shortened under pressure, the c parameters are elongated. These changes are associated with distortions of the TiF6 and FeF6 coordination octahedra, whereby the octahedron strain is stronger in TiF3 than in FeF3. The high-pressure behavior is characterized by cooperative tiltings of the octahedra, while simultaneously repulsive interactions between the cations probably cause the octahedral distortions.
Is There Evidence for Non-Linear Thiocyanate or Selenocyanate Ions?
Authors: Marsh R. E.
Published: July 2002

The structure of a mixed-valence copper complex with 1,10-phenanthroline, [CuII(phen)2]–NC–[CuI(phen)((Se,S)CN)]- [(Se,S)CN].0.5(C2H5OH), μ-cyano-1κN:2κC-(seleno,thio)cyanato-2κN-tris(1,10-phenanthroline)-1κ4
N,N′;2κ2
N,N′-dicopper(I,II) (seleno,thio)cyanate semiethanolate, has been revised from space group Cc to C2/c. Refinement in C2/c has shown that, contrary to the Cc results, the (Se,S)CN anions can be described as approximately linear, as expected.
Energetic Study of the Disordered Solvent in the Crystal Structure of an Isoxazole Derivative
Authors: Pani M. , Carnasciali M. M. , Mugnoli A. , Beltrame P. , Cadoni E. , Gelli G.
Published: July 2002

In the crystal structure of ethyl (Z)-3-{[3-(3,5-dichloro-2,4,6-trimethylphenyl)isoxazol-4-yl]-2-butenylidene}carbazate–ethyl acetate solvate, C19H21Cl2N3O3.0.34-C4H8O2 (R
1 = 0.072, wR
2 = 0.228), the host molecules are linked by intermolecular N—H...N hydrogen bonds, giving rise to infinite channels which contain molecules of ethyl acetate. Packing potential energy calculations carried out for host–guest model crystals account for the disorder of the solvent molecules in the crystal state.
Synchrotron X-ray study of the electron density in RFeO3 (R = Nd, Dy)
Authors: Streltsov Victor A. , Ishizawa Nobuo
Published: July 2002

Structure factors for small hydrothermally grown orthorhombic neodymium and dysprosium iron oxides RFeO3 (R = Nd, Dy) were measured with focused λ = 0.84 Å synchrotron radiation using a fast avalanche photodiode (APD) counter. Higher symmetry in the deformation electron density (Δρ) maps reflects the coordination of the magnetic atoms in the structure and implies that Δρ is sensitive to the cation–cation magnetic interactions. Within a given compound the local Δρ topographies around the R and Fe atoms are similar, but differ markedly between compounds. The difference in Δρ near the Nd and Dy atoms is associated with the different type of spin reorientation transitions in these compounds. The R–Fe magnetic interactions determine the magnetic phase transitions and consequently affect the electron distribution. Synchrotron radiation diffraction imaging of the electron density provides an additional tool for probing the magnetic properties of materials.
Concerning the κ Phase of Al–Cr–Ni
Authors: Marsh R. E.
Published: July 2002

The structure of a new hexagonal phase aluminium–chromium–nickel, of reported composition Al14.4Cr3.4Ni1.1, has recently been described and refined in space group P63; most of the atom sites were described as disordered between various pairs of metal atoms [Sato et al. (1997). Acta Cryst. C53, 1531–1533]. A simpler structure, in space group P63/m, leads to better refinement. In the revised structure most of the atom sites are ordered. There is no indication of Ni in any of these ordered sites, but one partially occupied site may contain Ni, octahedrally coordinated to six Al atoms. Disordering along a chain of four atoms, parallel to the c axis, prevents a determination of the exact chemical composition; the approximate cell contents are Al177Cr49Ni.
Structure of mono-acid even-numbered β-triacylglycerols
Authors: van Langevelde Arjen , van Malssen Kees , Hollander Frank , Peschar René , Schenk Henk
Published: July 2002

The crystal structure of the β polymorph of tripalmitin (1,2,3-trihexadecanoylglycerol, β-PPP) has been determined by single-crystal X-ray diffraction. The molecules crystallize in space group P1¯ in an asymmetric tuning-fork conformation. This structure and the already-known crystal structures of β-tricaprin (β-CCC) and β-trilaurin (β-LLL) could be matched in an overlap model. Apart from a difference in chain length, the three structures are almost identical. The overlap model can be used to predict the crystal structure of the other members of the C
n
C
n
C
n
-type (n = even) TAG series reasonably accurately. This is demonstrated by predicting the crystal structure for β-trimyristin (β-MMM) and successively comparing the experimental and calculated X-ray powder diagrams.
Elucidation of the crystal structure of oxyapatite by high-resolution electron microscopy
Authors: Alberius Henning Peter , Landa-Cánovas Angel R. , Larsson Ann-Kristin , Lidin Sven
Published: July 2002

High-resolution electron-microscopy (HREM) images from different hydroxyapatite (OHAp) samples showed p3 projection symmetry along [001] instead of the p6 projection symmetry compatible with the space group P6_3/m of OHAp. Image processing was used to establish without ambiguity that threefold symmetry dominates the images along [001]. OHAp crystals decompose in the transmission electron microscope and it is concluded that the threefold symmetry observed corresponds to an early step in the decomposition process, the dehydration of OHAp to oxyapatite (OAp). A structural model for OAp where every second O atom along the 63 axis in OHAp is removed has the maximal space-group symmetry P\bar6. This is compatible with the p3 projection symmetry observed. Atomic shifts in this OAp model compared to the OHAp structure were estimated using the HREM images and geometric optimizations of the atomic structure. No refinements of the atomic coordinates against diffraction data were possible but the simulated HREM images of this crude model fit well with the experimental images.
Electron density distribution and Madelung potential in α-spodumene, LiAl(SiO3)2, from two-wavelength high-resolution X-ray diffraction data
Authors: Kuntzinger Sandrine , Ghermani Nour Eddine
Published: July 2002

The electron density distribution in α-spodumene, LiAl(SiO3)2, was derived from high-resolution X-ray diffraction experiments. The results obtained from both Mo Kα- and Ag Kα-wavelength data sets are reported. The features of the Si—O and Al—O bonds are related to the geometrical parameters of the Si—O—Al and Si—O—Si bridges on the one hand and to the O...Li+ interaction on the other. Kappa refinements against the two data sets yielded almost the same net charges for the Si (+1.8 e) and O (−1.0 e) atoms in spodumene. However, the Al net charge obtained from the Ag Kα data (+1.9 e) is larger than the net charge derived from the Mo Kα data (+1.5 e). This difference correlates with a more contracted Al valence shell revealed by the shorter X-ray wavelength (κ = 1.4 for the Ag Kα data set). The derived net charges were used to calculate the Madelung potential at the spodumene atomic sites. The electrostatic energy for the chemical formula LiAl(SiO3)2 was −8.60 e2 Å−1 (−123.84 eV) from the net charges derived from the Ag Kα data and −6.97 e2 Å−1 (−100.37 eV) from the net charges derived from the Mo Kα data.
Arrangement of C atoms in the SiC–C solid solution
Authors: Mykhaylyk O. O. , Gadzira M. P.
Published: July 2002

The microstructure of a silicon carbide–carbon solid-solution powder (SiC–C), obtained from a fine powder of silicon and thermal expansive graphite, is investigated by X-ray powder diffraction methods. The microstructure is characterized by Williamson–Hall analysis and the strain-field model suggested by van Berkum et al. [Acta Cryst. (1996), A52, 730–747]. SiC–C adopts a layered structure like the solid solutions formed by compounds possessing a diamond-like structure, e.g. SiC–AlN. Superstoichiometric C atoms are located as planar defects. The SiC–C solid solution is destroyed on heating in a vacuum in the temperature range of graphitization of diamond but is maintained after sintering at high pressure (4–8 GPa) and high temperature (1673 and 2073 K). However, at the higher temperature (2073 K), it is observed that planar defects formed by C atoms decompose to non-correlated point defects accompanied simultaneously by a decrease in the lattice parameter from 4.3540 (2) to 4.35234 (5) Å.
Crystal engineering using bisphenols and trisphenols. Complexes with 1,10-phenanthroline: hydrogen-bonded chains in adducts with 4,4′-biphenol (1/1) and 4,4′-sulfonyldiphenol (2/3), π–π stacked chains in the (1/2) adduct with 4,4′-thiodiphenol, and pairwise-interwoven nets in 1,1,1-tris(4-hydroxyphenyl)ethane–1,10-phenanthroline–methanol (1/1/1)
Authors: Ferguson George , Glidewell Christopher , Lavender Emma S.
Published: July 2002

In 4,4′-biphenol–1,10-phenanthroline (1/1) [systematic name: 4,4′-biphenyldiol–1,10-phenanthroline (1/1)] the diphenol molecules lie across centres of inversion and the phenanthroline molecules lie across twofold rotation axes; the phenanthroline molecules act as chain-building units and the molecular components are linked into steeply zigzag C(16) chains parallel to [101] by means of O—H...N hydrogen bonds. In the structure of 4,4′-thiodiphenol–1,10-phenanthroline (1/2) the phenanthroline molecules act as chain-terminating units; the supramolecular aggregation is finite, with the bisphenol linked to each phenanthroline molecule by means of a single O—H...N hydrogen bond. π−π stacking interactions between the phenanthroline molecules in neighbouring hydrogen-bonded aggregates serve to link these aggregates into a continuous two-dimensional array. The phenanthroline molecules in 4,4′-sulfonyldiphenol–1,10-phenanthroline (2/3) play two roles: molecules in general positions act as chain-terminating units and are linked to the sulfonyldiphenol molecules by means of three-centre O—H...(N)2 hydrogen bonds, while those lying across twofold rotation axes act as chain builders and are linked to two different sulfonyldiphenol molecules by means of a two-centre O—H...N hydrogen bond in each case; the resulting U-shaped five-component aggregates are further linked by C—H...O=S hydrogen bonds into a C_3^3(17)[R_2^2(12)] `chain of rings' along [001]. In 1,1,1-tris(4-hydroxyphenyl)ethane–1,10-phenanthroline–methanol (1/1/1) [systematic name: 4,4′,4′′-ethylidynetriphenol–1,10-phenanthroline–methanol (1/1/1)] the phenanthroline molecules again act as chain-terminating units: the trisphenol molecules and the methanol molecules are linked by O—H...O hydrogen bonds into two-dimensional nets built from R_6^6(42) rings, and pairs of these nets are interwoven. The formation of each net utilizes two hydroxyl groups per trisphenol molecule as hydrogen-bond donors and the remaining hydroxyl group acts as donor to the phenanthroline molecule in a three-centre O—H...(N)2 hydrogenbond.
Charge density in NiCl2.4H2O at 295 and 30 K
Authors: Ptasiewicz-Bak H. , Olovsson I. , McIntyre G. J.
Published: July 2002

The charge distribution has been determined by multipole refinements against single-crystal X-ray diffraction data. In the refinements a comparison was made between the densities based on H-atom parameters from X-ray and neutron data, respectively. X-ray study: λ(Mo Kα) = 0.71073 Å, F(000) = 408; at 30 K: R(F) = 0.015 for 6686 reflections; at 295 K: R(F) = 0.022 for 4630 reflections. The nickel ion is octahedrally surrounded by four water molecules and two chloride ions, forming a locally neutral Ni(H2O)4Cl2 complex. Two of the water molecules are coordinated to nickel approximately in one of the tetrahedral (`lone-pair') directions; the other two are trigonally coordinated. At 30 K one H atom in one of the trigonally coordinated water molecules is disordered, with equal occupation of two different positions. Owing to the polarizing influence of the nickel ion there are two peaks in the lone-pair plane of the water molecules when these are tetrahedrally coordinated; for those trigonally coordinated there is just one peak. The individual (`partial') charge densities, calculated from the deformation functions of only nickel or the separate water molecules, have also been calculated to study the effects of superposition of the individual densities. In the individual density of nickel an excess is observed in the diagonal directions and a deficiency in the ligand directions. However, owing to the influence of the whole crystalline environment, the maxima around nickel are not found in the planes defined by nickel and the six ligands.
N-n-Alkyl N,N-dimethylammonioacetic acid bromides: the first complete series of crystal and molecular structure determinations of an amphiphilic compound with alkyl chain lengths n = 1,..., 16
Authors: Rudert Rainer , Schulz Burkhard , Reck Günter , Vollhardt Dieter , Kriwanek Jörg
Published: July 2002

The molecular and crystal structures of 16 N-n-alkyl N,N-dimethylammonioacetic acid bromides with chain lengths between n = 1 and n = 16 have been determined. All compounds from n = 5 to n = 16 form bilayers with interdigitated chains. The even-numbered chains display the chain packing type M
2
II. The chain packing of the odd-numbered chain compounds is less regular. The head groups of all compounds are connected via electrostatic N+...Br− interactions, and by OH...Br− hydrogen bonds. The compounds with short chains are packed in different ways. Their molecular conformation depends on the crystal packing.
Preferred conformations in the solid state of some α-(p-phenylsulfinyl)-p-substituted acetophenones
Authors: Olivato Paulo R. , Guerrero Sandra A. , Zukerman-Schpector J.
Published: July 2002

Information on the geometrical structures of α-(p-phenylsulfinyl)-p-substituted acetophenones X—PhC(O)CH2S(O)Ph—Y [X = OMe, Y = H (1); X = NO2, Y = OMe (2); X = OMe, Y = NO2 (3); IUPAC names: (1) 4-methoxyphenyl phenylsulfinylmethyl ketone; (2) 4-nitrophenyl 4-methoxyphenylsulfinylmethyl ketone; (3) 4-methoxyphenyl 4-nitrophenylsulfinylmethyl ketone] have been obtained from X-ray diffraction analyses. A comparison of these results with those previously obtained from X-ray diffraction and ab initio computations of α-methylsulfinylacetophenone, PhC(O)CH2S(O)Me, indicated that (1) and (2) adopt in the crystal a cis
1 conformation and (3) assumes a quasi-gauche geometry. The stabilization of these conformations in the crystal is discussed in terms of the dipole moment coupling, Coulombic and intramolecular charge transfer interactions between the oppositely charged atoms of the C=O and S=O dipoles. The p-substituted benzene ring is quasi-coplanar with the sulfinyl group for (1) and (3), but is quasi-perpendicular for (2). Conjugation and repulsion between the sulfinyl sulfur lone pair and the π-benzene ring seem to be responsible for the observed geometries.
Volumetric measure of isostructurality
Authors: Fábián László , Kálmán Alajos
Published: July 2002

The numerical descriptors of isostructurality are critically reviewed and to overcome their limitations a new volumetric measure is proposed. It is defined as the percentage ratio of the overlapping volume of molecules in the analyzed structures to the average of the corresponding molecular volumes. For the calculation of this index a numerical approach is presented, which is also capable of treating disordered structures. The use of isostructurality calculations is demonstrated using a series of examples. Homologous 9-alkylthiophenanthrenes are used as simple illustrations of the necessity and applicability of the new descriptor. The structural changes in the inclusion compounds of 5-methoxysulfadiazine with chloroform, dioxane and tetrahydrofuran are analyzed and rationalized with the aid of isostructurality indices. The diverse relationships among a series of helical tubuland diols cocrystallized with simple phenols are also characterized. The modifications in molecular and crystal structures are correlated with the calculated degree of isostructurality.
P1 or P1¯? Or something else?
Authors: Marsh Richard E.
Published: July 2002

The October 1998 release of the Cambridge Structural Database (1992) contains structural details (unit-cell dimensions and atom coordinates) for nearly 1300 distinct entries under space group P1 (No. 1); for 279 of these entries, the space-group designation is incorrect. The most common type of error, occurring for 157 entries with Z > 1, seems to have resulted from a simple misprint – the omission of the `overline' in the symbol P\overline{1} as it appears in the original publication; in these cases the reported coordinates, when applied to space group P\overline{1} rather than P1, lead to reasonable intermolecular distances and to apparently reliable structures. In the remaining 123 cases the space group is incorrect for more fundamental reasons and the atom coordinates should be revised. In approximately one-third of the structures in which chiral molecules crystallize in P1 with Z = 2, the two molecules are related by an approximate center of inversion. In some cases this pseudocenter is surprisingly exact, with r.m.s. deviations from centrosymmetry as small as 0.1 Å, and may result in the same sort of refinement difficulties that inevitably arise when truly centrosymmetric structures are mistakenly refined in space group P1. It appears as though, for typical molecular compounds, standard crystal-structure techniques may be unable to distinguish between P1 and P\overline{1} if the r.m.s. deviation from centrosymmetry is less than ∼0.1 Å.
Structure of Cu6PbO8
Authors: Winkler Björn , Chall Michael , Pickard Chris J. , Milman Victor , White Jim
Published: July 2002

First-principles quantum mechanical calculations based on density functional theory were performed for Cu_6PbO_8, hexacopper lead octaoxide, murdochite. The computed lattice parameter, density and bond lengths at ambient pressure are in good agreement with experimental data for murdochite. At about 18 GPa a phase transition is predicted, when a polymorph with a Suzuki-type structure, i.e. a close-packed structure with ordered vacancies, is proposed to become stable. The pressure dependence of the structural parameters has been calculated for the two polymorphs and their bulk moduli have been predicted. It is argued that the incorporation of halogen atoms is not a precondition for the stability of murdochite.
Two different three-dimensional hydrogen-bonded framework structures in two hydrated adducts meso-5,5,7,12,12,14-hexamethyl-1,4,8,11-tetraazacyclotetradecane–terephthalic acid–water (1/1/4) and (1/1/6)
Authors: Lough Alan J. , Gregson Richard M. , Ferguson George , Glidewell Christopher
Published: July 2002

Co-crystallization of meso-5,5,7,12,12,14-hexamethyl-1,4,8,11-tetraazacyclotetradecane, C16H36N4, with terephthalic acid (1,4-benzenedicarboxylic acid), C8H6O4, from ethanol yields the tetrahydrate (C16H36N4).(C8H6O4).(H2O)4 (1), meso-5,5,7,12,12,14-hexamethyl-1,4,8,11-tetraazacyclotetradecane–terephthalic acid–water (1/1/4), while similar co-crystallization from methanol yields the hexahydrate (C16H36N4).(C8H6O4).(H2O)6 (2), meso-5,5,7,12,12,14-hexamethyl-1,4,8,11-tetraazacyclotetradecane–terephthalic acid–water (1/1/6). Both compounds are salts, [C16H38N4]2+.[C8H4O4]2−.4H2O (1) and [C16H38N4]2+.[C8H4O4]2−.6H2O (2): in (2) both ionic components lie across centres of inversion and in both salts there are two protons held within the N4 cavity of the cation. In the structure of (1), the cations and anions are linked into chains by means of paired N—H...O hydrogen bonds, and the water molecules are linked into continuous chains by means of O—H...O hydrogen bonds, in which each of the H atoms is independently disordered over two equally populated sites. The water chains link the ionic chains into a continuous three-dimensional framework by means of further O—H...O hydrogen bonds. In (2) the cations and anions are linked by single N—H...O hydrogen bonds, again into chains: at the same time the anions and the water molecules are linked by multiple O—H...O hydrogen bonds into continuous two-dimensional nets, which are linked by the cations, by means of N—H...O hydrogen bonds into a three-dimensional framework, entirely different from that in (1).
The assignment and validation of metal oxidation states in the Cambridge Structural Database
Authors: Shields Gregory P. , Raithby Paul R. , Allen Frank H. , Motherwell W. D. Samuel
Published: July 2002

A methodology has been developed for the semi-automatic assignment and checking of formal oxidation states for metal atoms in the majority of metallo-organic complexes stored in the Cambridge Structural Database (CSD). The method uses both chemical connectivity and bond-length data, via ligand donor group templates and bond-valence sums, respectively. In order to use bond-length data, the CSD program QUEST has been modified to allow the coordination sphere of metal atoms to be recalculated using user-defined criteria at search time. The new methodology has been used successfully to validate the +1, +2 and +3 oxidation states in 743 four-coordinate copper complexes in the CSD for which atomic coordinates are available in ca 99% of structures using one or other method, and both succeed for >86% of structures.
Novel infinite three-dimensional network of neutral fullerene molecules in (C60)8(twin-TDAS)6
Authors: Penicaud Alain , Boubekeur Kamal , Kotov Alexander I. , Yagubskii Eduard B.
Published: July 2002

The crystal structure of (C60)8(twin-TDAS)6 [twin-TDAS = C4S6N4 = 3,3′,4,4′-tetrathiobis(1,2,5-thiadiazole)] has been redetermined at low temperature in the correct space group [I23, a = 18.849 (1) Å]. Structural analysis reveals a novel three-dimensional close-contact network of C60 molecules with tetrahedral holes similar to pristine C60.
Molecular coordination numbers in crystal structures of organic compounds
Authors: Peresypkina E. V. , Blatov V. A.
Published: July 2002

The calculation of molecular coordination numbers (MCNs), and topological and geometrical analysis of the environment of molecules in the crystal structures of 23 067 organic compounds, shows that Kitaigorodskii's close-packing model, assuming the predominance of MCN = 12, works correctly in only a few cases, whereas MCN = 14 is the most frequent. To explain this fact the close-packing model is extended with the model of the thinnest covering of space by deformable molecules. It is shown that the packing of molecules of arbitrary shape and composition can be better described with geometrical, but not topological, parameters of their short-range environment, which is conveniently characterized by molecular Voronoi–Dirichlet polyhedra.
Testing aspherical atom refinements on small-molecule data sets
Authors: Hansen N. K. , Coppens P.
Published: July 2002

X-ray data on silicon, tetracyanoethylene, p-nitropyridine N-oxide and ammonium thiocyanate are refined with a generalized aspherical-atom formalism as introduced by Stewart, but modified to have a spherical valence more similar to the unperturbed HF valence shell. Several types of radial dependences of the multipole functions are tested and criteria are developed for judging the adequacy of the aspherical-atom refinement. The aspherical-atom model leads to a significant decrease in the least-squares error function, a reduction of features in the residual map, and an improvement in thermal parameters when comparison is made with the neutron results or when the rigid-bond postulate proposed by Hirshfeld is applied. Positional parameters are often improved except in the case of terminal atoms for which discrepancies, attributed to correlation between dipole-population and positional parameters, are sometimes observed. Deformation maps based on the aspherical-atom least-squares parameters contain less noise than X -- N maps and benefit from inclusion of calculated values of weak structure amplitudes in the summation. In the cases studied, deformation maps including terms beyond the experimental resolution do not yield additional information.
Analysis of molecular motion with allowance for intramolecular torsion
Authors: Trueblood K. N.
Published: July 2002

The one-parameter model of Dunitz & White [Acta Cryst. (1973), A29, 93-94] for the analysis of torsional degrees of freedom within an otherwise rigid body has been applied to data for a number of representative compounds. The model gives results not significantly different from those of more elaborate models for librations about bonds, even when the r.m.s, amplitudes of these librations are as great as 24°. The limitations of this kind of analysis and some of the problems in applying it are discussed.
Enhanced electron-density envelopes by extended solvent definition
Authors: Blom Nick , Sygush Jurgen
Published: July 2002

Extended delineation of water molecules, monitored using R
free values, afforded considerable improvement in quality of electron-density maps for structure determination of mammalian class I and E. coli class II aldolases. Augmented solvent definition results in an additional decrease in R
free values of 3–4% and is reflected in significantly enhanced electron-density envelopes enabling tracing of amino-acid sequences through regions of otherwise discontinuous or weak electron density.
Purification, crystallization and preliminary X-ray diffraction data from selenomethionine glycinamide ribonucleotide synthetase
Authors: Weaver Todd M. , Wang Weiru , Ealick Steven E.
Published: July 2002

In this study, the overexpression, purification and crystallization of selenomethionine (SeMet) incorporated glycinamide ribonucleotide synthetase (GAR-syn) from Escherichia coli are reported. The overexpression of SeMet GAR-syn was placed under the control of the isopropylthio-β-galactoside (IPTG) inducible T7 RNA-polymerase system. The newly developed construct contained a removable histidine tag on the amino terminus of GAR-syn, which allowed rapid purification using metal-chelate chromatography techniques. The SeMet GAR-syn crystals were grown by hanging-drop vapor diffusion and belong to the space group P212121 with unit-cell parameters a = 56.2, b = 62.4 and c = 129.8 Å and a single monomer in the asymmetric unit. The crystals diffract to 1.6 Å resolution and have led to the determination of multiple-wavelength anomalous diffraction phases to 2.2 Å resolution.
Determination by MAD-DM of the structure of the DNA duplex d[ACGTACG(5-BrU)]2 at 1.46 Å and 100 K
Authors: Todd Alan K. , Adams Adrienne , Powell Harold R. , Wilcock Deborah J. , Thorpe James H. , Lausi Andrea , Zanini Franco , Wakelin Laurence P. G. , Cardin Christine J.
Published: July 2002

A four-wavelength MAD experiment on a new brominated octanucleotide is reported here. d[ACGTACG(5-BrU)], C77H81BrN30O32P7, M_r (DNA) = 2235, tetragonal, P43212 (No. 96), a = 43.597, c = 26.268 Å, V = 49927.5 Å3, Z = 8, T = 100 K, R = 10.91% for 4312 reflections between 15.0 and 1.46 Å resolution. The self-complementary brominated octanucleotide d[ACGTACG(5-BrU)]2 has been crystallized and data measured to 1.45 Å at both 293 K and a second crystal flash frozen at 100 K. The latter data collection was carried out to the same resolution at the four wavelengths 0.9344, 0.9216, 0.9208 and 0.9003 Å, around the Br K edge at 0.92 Å and the structure determined from a map derived from a MAD data analysis using pseudo-MIR methodology, as implemented in the program MLPHARE. This is one of the first successful MAD phasing experiments carried out at Sincrotrone Elettra in Trieste, Italy. The structure was refined using the data measured at 0.9003 Å, anisotropic temperature factors and the restrained least-squares refinement implemented in the program SHELX96, and the helical parameters are compared with those previously determined for the isomorphous d(ACGTACGT)2 analogue. The asymmetric unit consists of a single strand of octamer with 96 water molecules. No countercations were located. The A-DNA helix geometry obtained has been analysed using the CURVES program.
Refined structure of the FKBP12–rapamycin–FRB ternary complex at 2.2 Å resolution
Authors: Liang Jun , Choi Jungwon , Clardy Jon
Published: July 2002

The structure of the FKBP12–rapamycin–FRB ternary complex has now been refined at 2.2 Å resolution. The cell-cycle arrest agent rapamycin binds FK506-binding protein (FKBP12) and the FKBP12–rapamycin binding (FRB) domain of FKBP12–rapamycin associated protein (FRAP) simultaneously, and the inhibition of FRAP is responsible for rapamycin's biological activity. The conformation of rapamycin in the ternary complex is very similar to that observed in the FKBP12–rapamycin binary complex, with an r.m.s. difference of only 0.30 Å. However, a slight (9°) rotation repositions the FRB-binding face of rapamycin in the ternary complex. There are extensive rapamycin–protein interactions and relatively few interactions between the two protein partners FKBP12 and FRB, these interactions mainly involving residues in the 40s and 80s loops of FKBP12 and α1 and α4 of FRB. The high-resolution refinement has revealed the crucial role of several buried waters in the formation of the ternary complex.
Structures of orthorhombic lysozyme grown at basic pH and its low-humidity variant
Authors: Sukumar N. , Biswal B. K. , Vijayan M.
Published: July 2002

The structures of orthorhombic lysozyme grown at basic pH and its low-humidity variant have been solved and refined at 1.9 and 2.0 Å resolution, respectively. A comparison of the native structure with those of crystals grown at acidic pH does not show any systematic pH-dependent difference in the molecular geometry. The conformations, mutual orientation and interactions of the catalytic residues Glu35 and Asp52 also remain unchanged. However, comparison between the native and low-humidity forms in the orthorhombic form show that the changes in molecular geometry which accompany the water-mediated transformation to the low-humidity form are more pronounced in the C-terminal residues than in the other regions of the molecule. During the transformation from the native to the low-humidity form, the locations of only about half the water molecules in the hydration shell remain unchanged, but the hydration shell as a whole moves along with the protein molecule.
Crystallization and preliminary X-ray diffraction analysis of the regulatory subunit of human protein kinase CK2
Authors: Chantalat Laurent , Leroy Didier , Filhol Odile , Quitaine Nora , Chambaz Edmond M. , Cochet Claude , Dideberg Otto
Published: July 2002

Protein kinase CK2 is a tetramer composed of two α catalytic subunits and two β regulatory subunits. A C-terminal truncated form of the β subunit has been overproduced in Escherichia coli and purified to homogeneity. Two crystal forms of the truncated protein which diffract to at least 2 Å resolution have been obtained. Form I belongs to the monoclinic space group P21, with unit-cell parameters a = 49.9, b = 92.9, c = 53.7 Å, β = 96.3°, and yields plate-like crystals. Form II belongs to the tetragonal space group P42212, with unit-cell parameters a = 132.19, b = 132.19, c = 63.79 Å, and produces rod-shaped crystals. Both crystal forms have a functional dimer in the crystal asymmetric unit.
Crystallization, X-ray diffraction and preliminary structure analysis of Mycobacterium tuberculosis chaperonin 10
Authors: Roberts Michael M. , Coker Alun R. , Fossati Gianluca , Mascagni Paolo , Coates Anthony R. M. , Wood Steve P.
Published: July 2002

The Mycobacterium tuberculosis chaperonin 10 (Mtcpn10) has been crystallized by the sitting-drop vapour-diffusion method. The crystals belong to the monoclinic space group P21, with unit-cell parameters a = 76.5, b = 87.9, c = 124.4 Å, β = 106.8°. X-ray diffraction data were collected to 2.8 Å. The self-rotation function and the molecular-replacement solution show that the asymmetric unit contains a dimer of heptamers related by twofold non-crystallographic symmetry. The two heptamers interact through interleaving flexible loops in a similar fashion to M. leprae and Gp31 cpn10. In addition to its role in protein folding, Mtcpn10 has unique effects on the growth of host cells and is a major immunogen in tuberculosis infections. The structure determination will permit the analysis of the amino acids identified as important for the protein-folding and cell-signalling activity of Mtcpn10.
Crystallization and preliminary X-ray analysis of wild-type and V103L mutant Myb R2 DNA-binding domain
Authors: Tahirov Tahir H. , Morii Hisayuki , Uedaira Hatsuho , Sarai Akinori , Ogata Kazuhiro
Published: July 2002

The R2 subdomain of the mouse c-Myb DNA-binding domain and its V103L mutant have been crystallized by the vapour-diffusion method using highly concentrated sodium citrate at pH 6.8 as a precipitant. Using ammonium sulfate as precipitant in MES buffer only produced crystals for the mutant R2. All crystals are isomorphous and belong to space group P212121. The unit-cell dimensions for wild-type R2 crystals grown from sodium citrate precipitant are a = 28.83, b = 40.18, c = 49.23 Å. Crystals contain one R2 molecule per asymmetric unit. They are stable during 3 d exposure to X-rays and diffract to 1.37–1.45 Å resolution.
Feasibility study for the measurement of a large set of triplet phases from a small protein
Authors: Weckert Edgar , Hölzer Kerstin , Schroer Klaus , Zellner Johannes , Hümmer Kurt
Published: July 2002

The feasibility of measuring a set of triplet phases large enough to solve the structure of a small protein has been evaluated. A total of about 850 triplet phases have been measured from the tetragonal form of hen egg-white lysozyme. From these triplet phases, about 750 single phases can be derived. The experimental details of these measurements as well as the results, the values of the measured triplet phases, are reported. Additional experimental data from other small proteins are also presented.
Derivative manipulation in the structure solution of the integral membrane LH2 complex
Authors: Prince S. M. , McDermott G. , Freer A. A. , Papiz M. Z. , Lawless A. M. , Cogdell R. J. , Isaacs N. W.
Published: July 2002

The structure of the peripheral light-harvesting complex from Rhodopseudomonas acidophila strain 10050 was determined by multiple isomorphous replacement methods. The derivatization of the crystals was augmented by the addition of a backsoaking stage. The soak/backsoaked data comparison had greater isomorphism and showed simpler Patterson maps than the standard native/soak comparison. Amplitudes from the derivatized then backsoaked crystals and from the derivatized crystals were compared in order to extract a subset of heavy-atom sites. Using this information, the full array of sites were found from a derivative/native comparison, eventually leading to excellent electron-density maps.