bluuebunny/crossref_metadata_2025 huggingface dataset:
Structural and chemical variations in rathite, Pb8Pb4—x(Tl2As2)x(Ag2As2)As16S40: modulations of a parent structure
Authors: Berlepsch P. , Armbruster Th. , Topa D.
Published: December 2003

Members of the 4,4 sartorite homologues can be deduced from a topological parent structure with orthorhombic symmetry, space groupPmnb,a= 4.233,b= 7.918,c= 24.692 Å. The observed modulations in 4,4 sartorite homologues are associated with symmetry lowering of the parent structure and superstructure formation. The Pb, Tl, Ag, As, Sb sulfosalt rathite is a 4,4 member of the sartorite homologous series with space group symmetryP21/cand is isostructural to synthetic Ba12Sb18.64S40and closely related to Ba10.48Pb5.52Sb16S40of reduced symmetryP21. In these structures the two-fold screw axes run parallel tobof the parent structure. Isotopological is also dufrénoysite Pb16As16S40, another 4,4 homologue of the same series, of space group symmetryP21. In dufrénoysite, however, the two-fold screw axes run parallel tocof the parent structure. To elucidate the modulation of the parent structure, rathite has been structurally and chemically reinvestigated emphasising cation order/disorder relations. Single crystal X-ray structure refinement (space groupP21/c;a= 8.496(1),b= 7.969(1),c= 25.122(3) Å,β= 100.704(2)°;R1= 3.67% for 2718 reflections withI> 2σ[I]) yielded three split cation positions indicating heterovalent substitutions. Considering that isoelectronic Pb2+and Tl+cannot be distinguished in our diffraction experiment the chemical composition (Pb9.25Tl1.37)Σ=10.62Ag2.01(As19.09Sb0.83)Σ=19.92S40derived from electron microprobe analyses matches the formula Pb10.96Ag1.90(As18.09Sb1.06)Σ=19.15S40obtained from the structure refinement. The complex composition is caused by two independent heterovalent substitutions Ag++ As3+→ 2 Pb2+and Tl++ As3+→ 2 Pb2+leading to the simplified rathite formula Pb8Pb4–x(Tl2As2)x(Ag2As2)As16S40. The substitution involving Ag seems to be essential for the formation of rathite and distinguishes rathite from dufrénoysite Pb16As16S40. The Tl substitution in rathite appears to be optional. In addition, minor Sb3+may replace As3+.
Die Packungsdichte der Atome in Modifikationen von Kohlenstoff und Silicium
Authors: Trömel Martin , Hübner Sven
Published: December 2003

The crystal chemistry of carbon and silicon is discussed with respect to the packing density of atoms in their crystalline modifications. The reduced atomic volumes of metallic carbon as calculated from diamond, hexagonal diamond and buckminsterfullerene C60agree within less than 0.2, indicating the correctness of the reducing procedure. A much lower value calculated from graphite, rhombohedral graphite and a low-temperature modification of buckminsterfullerene remains unexplained. Two proposed crystal structures of a cubic body-centered form of carbon appear unacceptable. The reduced atomic volumes of diamond-type silicon and metastableγ-Si are in good agreement. Their values, calculated from six allotropic modifications (Si I, II, XI, V, VI, VII, and Si X) at pressures up to ≈200 GPa, are represented by an empirical exponential function of pressure. From this function, an isothermal equation of state is derived including the packing density of the atoms.
The crystal structure of Cu4Bi4Se9
Authors: Makovicky E. , Søtofte I. , Karup-Møller S.
Published: December 2003

The crystal structure of Cu4Bi4Se9, synthesized at 400 °C, was determined from single crystal X-ray diffraction data and refined to the R
1 value of 0.05. The compound is orthorhombic, with a = 32.692 Å, b = 4.120 Å, and c = 12.202 Å, space group Pnma. The structure contains three square pyramidal Bi sites, an octahedrally coordinated Bi site as well as two tetrahedrally and two irregularly coordinated Cu sites. The structure is an intergrowth of PbS-like slabs with irregularly configured slabs of Bi pyramids and Cu tetrahedra. It contains covalently bonded Se2 groups. Isotypy with Cu4Bi4S9 is connected with substantial changes in coordination details for two out of five distinct Cu sites. Modular relationships to the structures of the cuprobismutite series of Cu—Bi sulfosalts can be expressed as different ways of recombination of the same large structural fragment in the structures of Cu4Bi4Se9 and of the first cuprobismutite homologue, Cu4Bi5S10.
The crystal structure of Y2P4O13 from X-ray powder diffraction data
Authors: Ivashkevich L. S. , Lyakhov A. S. , Selevich A. F. , Ilieva D. , Lesnikovich A. I.
Published: December 2003

The crystal structure of Y2P4O13 has been determined from X-ray powder diffraction data. Y2P4O13 crystallizes in the orthorhombic space group C2221 (No. 20) with a = 17.2817(7) Å, b = 6.9823(4) Å, c = 8.5391(3) Å, V = 1030.38(8) Å3, and Z = 4. The structure has been solved by direct methods using EXPO program and refined by FULLPROF package. The final R
Bragg value was 9.1%. The tetraphosphate anion has the point group 2 symmetry. The yttrium atom is seven-coordinated forming strongly distorted octahedron with one bifurcated vertex. There are infinite chains of oxygen-bridged ittrium atoms running parallel to the b axis and linked together by the tetraphosphate anions with formation of three-dimensional network.
Dichloro-bis(2-chloro-2-phenyl-vinyl)Te(IV) and dibromo-bis(2-bromo-2-phenyl-vinyl)Te(IV): supramolecular self-assembly through different π-aryl interactions
Authors: Zukerman-Schpector Julio , Haiduc I. , Dabdoub M. J. , Biazzotto J. C. , Braga A. L. , Dornelles L. , Caracelli Ignez
Published: December 2003

C16H12Cl4Te, (1), Mr
= 473.66, P21/c, a = 8.3919(9), b = 14.474(1), c = 14.585(1) Å, β = 94.057(9)°, Z = 4, R
1 = 0.0378. C16H12Br4Te, (2), M
r = 651.50, Pnma, a = 19.159(2), b = 16.787(1), c = 5.781(1) Å, Z = 4, R
1 = 0.0437. In both compounds the primary geometry about the TeIV atom is a pseudo-trigonal-bipyramidal arrangement, with two halide atoms in apical positions, and the lone pair of electrons and C atoms in the equatorial plane. The TeIV atoms are involved in secondary interactions resulting in the self-assembly of a chain-like supramolecular array in (1) and into a three dimensional supramolecular array in (2). Compound (1) has a Z configuration with the chlorine atom and the tellurium moiety bonded at the same side in adjacent atoms. In (2) the bromine atom and the dibromotellurium moiety are bonded at adjacent carbons in a cis fashion.
Isomorphous phosphonoacetic acid salts with magnesium(II), manganese(II), cobalt(II), zinc(II) and copper(II)
Authors: Ślepokura K. , Piątkowska A. , Lis T.
Published: December 2003

All crystals of the title compounds, with general formula M2+(C2H4O5P–)2(H2O)2, (MAP), are isomorphous and crystallize in the space group P1̅ with Z = 2. The two crystallographically independent M2+ cations are situated on a center of symmetry and are octahedrally coordinated by two phosphonate monoanions and two water molecules. In the case of Cu2+ cation, Jahn-Teller effect causes strong extension of two Cu—O bonds. The mono anions coordinate the metal ions by one carboxylic and one phosphonate oxygen atom, which is facilitated by their specific overall conformation. In each monoanion, one of the phosphonate O atoms is nearly antiperiplanar ap to the carboxylic C atom, and the remaining phosphonate O atoms are nearly gauche (+sc and –sc) with respect to the mentioned C atom. The carboxylic O atoms are in positions close to +sc and –ac in relation to the phosphonate P atom. The complex molecules form well separated layers in all MAP compounds. The phosphonate and carboxylic groups act as donors in medium strong and weak intermolecular O—H...O hydrogen bonding and, as acceptors, in C—H...O hydrogen interactions in all structures. Additionally both crystallographically independent water molecules are donors of weak hydrogen bonding to phosphonate oxygen atoms from adjacent complex molecules.
Synthesis and structure of tris(triphenyltin)benzene-1,3,5-tricarboxylate and its tri-DMSO adduct
Authors: Dakternieks D. , Clarke D. J. , Tiekink Edward R. T.
Published: December 2003

The molecular structure of (Ph3SnO2C)3C6H3 reveals distorted tetrahedral C3O geometries for each tin atom. No intermolecular Sn...O associations occur between the molecules so that the trinuclear molecule may be considered monomeric. An increase in coordination number at tin is indicated by 119Sn NMR measurements conducted in d6-DMSO solution and this has been confirmed by a structure analysis of (DMSO·Ph3SnO2C)3C6H3·2 DMSO. In this structure, the tin atom geometries are distorted trigonal bipyramidal, existing within trans-C3O2 donor sets. Thus, while is it possible for the tin atoms to increase their coordination numbers in (Ph3SnO2C)3C6H3, molecular aggregation to form polymeric arrays is precluded, most likely due to steric constraints.
More power for direct methods: SIR2002
Authors: Burla M. C. , Carrozzini B. , Cascarano G. L. , Giacovazzo C. , Polidori G.
Published: December 2003

The program SIR2002, the heir of SIR2000-N, shows two important new features: a) a figure of merit which is able to recognize the trials potentially able to provide the correct solution; b) a procedure capable of exploiting electron density distributions misplaced with respect to the correct origin. The two features dramatically increase the power of direct methods for macromolecular crystallography.
Macromolecular phasing with SHELXE
Authors: Sheldrick G. M.
Published: December 2003

SHELXE was designed to provide a simple, fast and robust route from substructure sites found by the program SHELXD to an initial electron density map, if possible with an indication as to which heavy-atom enantiomorph is correct. This should be understood as a small contribution to high-throughput structural genomics. The new sphere of influence algorithm combined with a fuzzy solvent boundary enables some chemical knowledge to be incorporated into the density modification in a general and effective manner. In the special cases of high solvent content (greater than 0.6) or very high resolution data (better than 1.5 Å) high quality maps can be produced. This raises the possibility of a new paradigm for atomic resolution structure refinement: instead of alternating atom parameter refinement with weighted electron density maps calculated with the phases of the current model, which inevitably leads to some model bias, all model building should be based on the model free experimental density map!
Physical measurement of triplet invariants: present state of the experiment, data evaluation and future perspectives
Authors: Weckert E. , Müller R. , Zellner J. , Zegers I. , Loris R.
Published: December 2003

Invariant triplet phases can be determined experimentally by multi-beam interference experiments. In favourable conditions phases can also be determined from crystals of small macromolecules. The phase error is quite small, provided crystals of good quality are available. Single phases can be derived from triplet phases by means of maximum entropy based statistical methods. The number of experimental triplet phases necessary to solve a small protein crystal structure can be reduced by the application of an automatic refinement procedure. About 2.5 reflection phases per residue are necessary to solve the structure of a small protein if a high-resolution intensity data set is available.
Ab initio phasing starting from low resolution
Authors: Lunin V. Y. , Lunina N. , Podjarny A. , Bockmayr A. , Urzhumtsev A.
Published: December 2003

A single set of structure factor magnitudes complete at low resolution plus information of a general type are sufficient to get initial phases for macromolecular crystals which allow one to see the molecular packing and an approximate envelope. Followed by a more careful analysis based on the same information, these ab initio phases can be extended so that the corresponding maps show secondary structure elements.
Towards automated protein structure determination: BnP, the SnB-PHASES interface
Authors: Weeks C. M. , Blessing R. H. , Miller R. , Mungee R. , Potter S. A. , Rappleye J. , Smith G. D. , Xu H. , Furey W.
Published: December 2003

The direct-methods program SnB provides an efficient means for solving protein substructures containing many heavy-atom sites (current record: 160). In order to meet the high-throughput requirements of structural genomics projects, substructure determination needs to be tightly integrated with other aspects of the protein-phasing process. This has been accomplished through the design of a common Java interface, BnP, for SnB and components of PHASES, a popular and proven program suite that provides all the tools necessary to proceed from substructure refinement to the computation of an unambiguous protein electron-density map. Therefore, BnP will facilitate a high degree of automation and enable rapid structure determination by both experienced and novice crystallographers.
Direct way to anomalous scatterers
Authors: Dauter Z. , Nagem R. A. P.
Published: December 2003

The first step in solving macromolecular crystal structures by multi- or single-wavelength anomalous diffraction methods is the location of the anomalous scatterers. This can be done by direct methods, using either Bijvoet differences within the single data set, or anomalous scattering amplitudes estimated from measurements at several wavelengths. The calculations suggest that Bijvoet differences are equally successful for this purpose as anomalous amplitudes, F
A, which theoretically should be more suitable. The calculation of F
A values is susceptible to the accumulation of errors contained in the individual intensity measurements at several wavelengths and in the inaccurate estimation of the anomalous atomic scattering corrections, f′ and f″. Direct methods often give better results at resolution lower than the full extent of the diffraction data limit. This may be attributed to the enhanced accuracy of measurements of the strong, low resolution reflections and to more effective phase refinement and propagation through Σ2 relations.
The approach of the joint probability distribution functions: the SIR-MIR, SAD-MAD and SIRAS-MIRAS, cases
Authors: Giacovazzo C. , Ladisa M. , Siliqi D.
Published: December 2003

The method of the joint probability distribution functions has been recently applied to SIR-MIR, SAD-MAD and SIRAS-MIRAS cases. The capacity of the method to treat various forms of errors (i.e., errors in measurements, possible lack of isomorphism, errors in a substructure model when a model is a priori available, etc.) is the most innovative aspect of the approach. The description of the technique and the analysis of the conclusive formulas are dispersed in a number of papers; this contribution offers a unified point of view for all the cases and a perspective for future applications.
Direct-method phasing of anomalous diffraction from proteins
Authors: Gu Y. X. , Jiang F. , Sha B. D. , Fan H. F.
Published: December 2003

In dealing with anomalous diffraction data from proteins, the probability distribution of three-phase structure invariants provides additional information, which can be used to resolve the phase ambiguity intrinsic in single-wavelength anomalous diffraction (SAD) enabling solution of the protein structure. Based on this, direct methods have also been used in phasing multi-wavelength anomalous diffraction (MAD) data leading to better result than that from the conventional MAD phasing.
Molecular replacement and high-throughput structure determination
Authors: Navaza J. , Alzari P. M.
Published: December 2003

We describe the philosophy of the MR method as implemented in the AMoRe package. Fast rotation and translation functions are first used to obtain a meaningful sampling of solution space, whose elements are subsequently assessed by using more robust criteria. The introduction of fast and accurate algorithms for screening a large number of possible solutions opened the way to automation, thus bringing MR methods to the realm of high-throughput structure determination. Selected examples are discussed to illustrate specific aspects of the method.
Chemical short range order obtained from the atomic pair distribution function
Authors: Proffen Th. , Petkov V. , Billinge S. J. L. , Vogt T.
Published: December 2003

Many crystalline materials show chemical short range order and relaxation of neighboring atoms. Local structural information can be obtained by analyzing the atomic pair distribution function (PDF) obtained from powder diffraction data. In this paper, we present the successful extraction of chemical short range order parameters from the x-ray PDF of a quenched Cu3Au sample.
Refinement of the crystal structures of Cu3PS4and Cu3SbS4and a comment on normal tetrahedral structures
Authors: Pfitzner Arno , Reiser S.
Published: December 2003

The crystal structures of yellow Cu3PS4and of black Cu3SbS4were refined from single crystal X-ray diffraction data. Cu3PS4crystallizes orthorhombic in an ordered wurtzite superstructure type with the space groupPmn21(no. 31),a= 7.282(1) Å,b= 6.339(1) Å,c= 6.075(1) Å,V= 280.38(8) Å3, andZ= 2. The refinement converged toR= 0.0276, andwR2 = 0.0710 for 737 unique reflections and 44 parameters. Cu3SbS4crystallizes tetragonal in an ordered sphalerite superstructure type with the space groupI4̅2m(no. 121),a= 5.391(1) Å,c= 10.764(1) Å,V= 312.83(9) Å3, andZ= 2. The refinement converged toR= 0.0213, andwR2 = 0.0532 for 492 unique reflections and 14 parameters. The crystal structures of the title compounds and related normal tetrahedral structures are discussed with respect to the preference of either hexagonal or cubic packing of the anions.
Crystal structure of K1-

x
Cs
x
BSi2O6 (x = 0.12, 0.50) boroleucite solid solutions and thermal behaviour of KBSi2O6 and K0.5Cs0.5BSi2O6
Authors: Bubnova R. S. , Levin A. A. , Stepanov N. K. , Belger A. , Meyer D. C. , Polyakova I. G. , Filatov S. K. , Paufler P.
Published: December 2003

The crystal structures of two K1-

x
Cs
x
BSi2O6 solid solutions have been refined at room temperature by the Rietveld method: x = 0.12, a = 12.6858(4) Å, Rwp
= 7.66%, R
F = 5.56% and x = 0.50, a = 12.8480(2) Å, Rwp
= 7.64%, R
F = 3.10%. They are isostructural to cubic KBSi2O6 with the space group I4̅3d. The structure is built up from (Si,B)O4 tetrahedra linked in four-, six- and eightfold rings which are forming a three-dimensional borosilicate framework. The framework contains large cavities that are placed in continuous channels along the [111] directions. The Cs and K atoms occupy the positions in the channels statistically. Thermal behaviour of KBSi2O6 and K0.5Cs0.5BSi2O6 has been studied by high-temperature powder X-ray diffraction within the temperature range of 293-1073 K. A new tetragonal polymorph of KBSi2O6 has been found in situ under heating. The new polymorphic I4̅3d (cubic) – Ia3̅d (cubic) transition and the new Ia3̅d cubic polymorphic phase has been proposed for K1-

x
Cs

x

BSi2O6 from our experimental and literature data on crystal structures and thermal expansion of leucites. The structural relaxation under cationic (K, Cs) substitutions and under heating has been investigated.
The crystal structure of Na3HP2O7 ⋅ H2O from X-ray powder diffraction data
Authors: Ivashkevich L. S. , Selevich K. A. , Lyakhov A. S. , Selevich A. F. , Petrusevich Yu. I.
Published: December 2003

The crystal structure of Na3HP2O7 ⋅ H2O has been determined from X-ray powder diffraction data. The structure is monoclinic, space group P21/n (No. 14), with unit cell dimensions a = 10.4242(1) Å, b = 6.8707(1) Å, c = 10.0837(1) Å, β = 99.2258(7)°, V = 712.87(2) Å3, Z = 4, D
m = 2.43 g/cm3 and D
x = 2.41 g/cm3. The structure has been solved by direct methods using EXPO program and refined by FULLPROF package. The final R
Bragg value was 7.6%. Positions of hydrogen atoms were not defined. There are three sodium cations in the asymmetric unit. Two of them are five-coordinated and one cation has sixfold oxygen coordination. Each HP2O7
3– anion is hydrogen bonded to its two adjacent neighbours forming infinite chains parallel to the b axis. Water molecules are located in infinite channels extended along the b direction. The oxygen atom of the water molecule is connected with two sodium cations and hydrogen bonded with one oxygen atom of diphosphate group.
The glass transition in twinned ((phenyl)4As)2C60Cl crystals
Authors: Pilz K. , Jobst A. , Lam E. , Lüdecke J. , van Smaalen S. , Bao J. , Bietsch W. , Schwoerer M.
Published: December 2003

We have studied the crystal structure of ((phenyl)4As)2C60Cl at room temperature and below the phase transition at Tc
= 125 K by single-crystal x-ray diffraction. At room temperature tetragonal lattice parameters were found as a = b = 12.588(1)Å and c = 20.345(1)Å. At T = 120 K the lattice parameters were determined as a = b = 12.5060(1)Å and c = 20.4420(1)Å. The room temperature and low-temperature structures were found to be isostructural, with space group I4/m. Structure refinements were performed with restrictions on the C60 molecules according to the noncrystallographic isohedral point symmetry Ih
. Derivations from this symmetry could not be found, suggesting that any possible Jahn-Teller distortion of the C60 radical anions will be smaller than 0.01Å. The phase transition observed in ESR at Tc
= 125 K is proposed to be a glass transition. At room temperature there is dynamic disorder between two orientations of the C60 molecules as they are related by the 4-fold rotation. Below Tc
the disorder becomes static. Two types of twinning have been observed in different crystals. The first type is represented by a rotation over 180 about [1,1,1] axis. It results in different orientations of the 4-fold unique axes with angles of 82.4 degrees between them. Secondly, merohedral twinning was observed corresponding to the two orientations of the structure with 4/m symmetry on the tetragonal lattice. Both twinnings result in extra orientations of the C60 molecules, and they should be taken into account, when analysing the anisotropy of the physical properties of crystals of this compound.
Least-squares refinements of crystal structures: leverage analysis and the effects of truncating data
Authors: Merli M.
Published: December 2003

The treatment of weak intensities in the least-squares refinement of crystal structures is a quite controver-sial subject. According to the predominant opinion, all of the collected intensities should be used in the structure refinement process. Sometimes, however, the omission of the weakest data seems to be not influent, and sometimes it can even improve the refinement results. In the present work the effects of selectively excluding reflection with low I/u(I) ratio from both |Fo| and Fo
2 least-squares refinements are examined for Trimethopin-Sulfametoxypyridazine 1:1 and N′-(4-methoxyphenyl)-N-phenyl-N-oxyformamidinium. An interpretation of some observed features of the results of the least-squares refinements by means of the leverage analysis is proposed.
Monte Carlo Study of the quasicrystal-to-crystal transformation using an approach based on the Gummelt covering
Authors: Honal M. , Welberry T. R.
Published: December 2003

A tiling representation and associated possible tiling flips are developed for the "unit-cluster" description of decagonal quasicrystals with reference to the example of decagonal Al70Co15Ni15. A perfect P1 tiling is a suitable model of the ideal quasiperiodic structure and a 180° flip of a pentagon tile can be used as an analogue of the hexagon flips in Penrose rhomb tilings. Monte Carlo simulations and calculated diffraction patterns are used to study the effect of those tiling flips on the cluster scale for some example cases. Some of these have a special importance for the quasicrystal-to-crystal transformation. Starting with the perfect P1 tiling the system is allowed to evolve using phason fluctuations whose probabilities depend on the resulting local tile configurations. The degree of order/disorder introduced and its effects on the diffraction pattern are investigated.
Crystal structure analysis, pseudosymmetry and spectroscopic data of K4[Fe(CN)5NO2]⋅KNO2⋅H2O
Authors: Woike Th. , Himmelreich U. , Henke Henning , Bärnighausen H.
Published: December 2003

K4[Fe(CN)5NO2]⋅KNO2⋅H2O crystallizes in the non-centrosymmetric orthorhombic space group Bb21
m (no. 36) with a = 2698.2(3), b = 1415.7(1), c = 849.6(1) pm and Z = 8 at 291 K. Due to a high degree of pseudosymmetry the deviations from centrosymmetry are small. The gross arrangement of the iron and potassium atoms is that of the AlB2-type, discernible from the distorted hexagons of the boron-analogous part with the composition FeK3 while further potassium atoms are replacing Al in agreement with the formulation K2[FeK3]. The disorder of the free nitrite ions affiliated to KNO2 is characterized by means of additional data sets collected at temperatures of 173 K and 363 K. The results of the structure analysis are confirmed by infra-red spectroscopy. Especially the deformation modes δ(O-N-O) of the free nitrite and those of the nitro ligand show the expected frequency splitting. Mössbauer data serve as a check on chemical composition and give an independent estimate for the mean square displacement of the iron (57Fe) atoms comparable to the results from X-ray diffraction. The loss of crystal water above 400 K is registered using ther-mogravimetry and differential scanning calorimetry.
Stacking disorder in 2H-NbS2 and its intercalation compounds K
x
(H2O)
y
NbS2 I. Description and model calculations of stacking faults in the host lattice NbS2
Authors: Katzke H.
Published: December 2003

A quantitative modelling of the disorder phenomena in layered NbS2 is presented. The polytypes 2H and 3R are considered and the variations of the intensity profiles for their transformations into each other are calculated in terms of a one-dimensional disorder model.
[Cu(imidazole)2(CO3)]⋅H2O: an intermediate in the formation of the copper bis-imidazolate polymer (blue phase)
Authors: Masciocchi N. , Bruni S. , Cariati E. , Galli S. , Sironi A.
Published: December 2003

The crystal structure of [Cu(Him)2(CO3)]·H2O, determined from conventional X-ray powder diffraction methods, allowed to clarify, on the basis of a structural interpretation of the chemical transformation, the role of the title compound in the formation of the blue phase of Cu(im)2 [Cu(Him)2(CO3)]·H2O is triclinic, P1̅; a = 8.8565(7), b = 8.9579(5), c = 8.3705(6) Å, α = 105.728(4)°, β = 105.318(3)°, γ = 114.369(4)°; final Rwp
, Rp
and RF
agreement factors, for 4700 data collected in the 11–105° range, are 0.053, 0.036 and 0.078, respectively.
Search for structure-forming components in molecular crystals of binary compounds: a topological approach
Authors: Peresypkina E. V. , Blatov V. A.
Published: December 2003

Molecular crystal structures of 81 polymorphs of binary compounds are investigated with the method of coordination sequences and with the uniformity criterion for atomic sublattices. It is shown that using these tools one can estimate semi-quantitatively the relative force of inter-molecular interactions and to find so-called structure-forming lattice, i.e. the atomic sublattice, where the most stable long-wavelength phonons are likely to spread. When a crystal consists of molecules with distinguished central atoms, the polarizability of surrounding atoms is found to dictate mainly the composition of the structure-forming lattice. If the polarizability is small, crystal structure is formed by molecules as a whole, otherwise surrounding atoms form the structure basis themselves, and it is their lattice that often is one of the close packings. It is shown that if the central atom of a molecule has stereoactive lone pair the central atom can form the structure-forming lattice together with surrounding atoms.
On the treatment of settings of space-groups and crystal structures by spezialized short Hermann-Mauguin space-group symbols
Authors: Burzlaff H. , Zimmermann H.
Published: December 2003

From the short Hermann-Mauguin space-group symbol a set of generating operators can be derived. The matrix description of the operators depends on three free parameters related to the origin of the setting. Simple rules allow the specification of an origin, the origin of the symbol. The use of any other origin is notated by appending a shift vector from the symbol origin to the new one selected.
Phase extension to weaker reflections of proteins via a partial structure based tangent formula
Authors: Burla M. C. , Carrozzini B. , Cascarano G. L. , Giacovazzo C. , Polidori G.
Published: December 2003

When some molecular fragment is well located, the so called partial structure based tangent formula may be used to recovery the complete crystal structure. The formula has been extensively applied to small molecules and initial applications to proteins have also been performed. We will show in this paper that the formula may be successfully applied to macromolecules, to refine phase values and to extend the phase information to weaker reflections, even in absence of prior information (at atomic level) on part of the crystal structure. Experimental tests have been performed via a modified form of the program SIR2000.
Synthesis of zoning-free BaSO4-PbSO4 solid solution and its structural characterizations
Authors: Wang Hsiu-Ru , Lee Jiann-Shing , Yu Shu-Cheng
Published: December 2003

Natural Pb-bearing barite, (Ba,Pb)SO4 “hokutolite”, is a radioactive sulfate mineral occurring in hot-spring deposit. An attempt to synthesize (Ba,Pb)SO4 crystal with a flux-growth process was made in this study. BaSO4 and PbSO4 in various proportions were used as precursor materials with Na2SO4 as a flux agent. The growth was carried out in a platinum crucible at 750-850ºC and ambient pressure conditions. The nucleation and growth were activated by a slow-cooling process at 2ºC/hr cooling rate. The flux-grown (Ba,Pb)SO4 crystals up to 1 mm in dimension were obtained and their chemical compositions were found to cover the entire range between BaSO4 and PbSO4. Thus there does exist a complete solid solution series between the barite (BaSO4) and anglesite (PbSO4) binary system. This result is consistent with that reported for (Ba,Pb)SO4 synthesized with a hydrothermal method. Both natural and hydrothermally synthesized (Ba,Pb)SO4 crystals display a distinct domain structure in which the Ba/Pb ratio varied among different domains. This type of chemical zoning is recognized under an optical microscope to be a banded texture in which dark bands (Ba-rich area) alternate with bright bands (Pb-rich area). In contrast, the (Ba,Pb)SO4 samples synthesized in this work contain no detectable optical bands, and this dramatic difference is believed to be a direct consequence of different growth kinetics. The flux-grown (Ba,Pb)SO4 crystals were determined to be a barite type of structure with the Ba and Pb atoms substituting each other in a fully disordered arrangement. The cell parameters vary continuously and systematically from the Ba-rich end toward the Pb-rich end as dictated by an ideal solid solution series.
Stacking disorder in 2H-NbS2 and its intercalation compounds K
x
(H2O)
y
NbS2 II. Stacking disorder in K
x
(H2O)
y
NbS2
Authors: Katzke H.
Published: December 2003

The intercalation reaction of hydrated K+ ions into the layered structure of 2H-NbS2 was studied using in situ X-ray diffraction. A structurally complex intercalation mechanism was observed showing several highly one-dimensionally disordered intercalated phases. A quantitative modelling of the disorder in K
x
(H2O)
y
NbS2 is presented allowing a complete understanding of the intercalation mechanism.
Phase transformation of ammonium monomolybdate. The structure of the low temperature modification, (NH4)2[MoO4] (mP60, P21/a)
Authors: Schweda E. , Hofmann M. , Dittmann M. , Glaser J.
Published: December 2003

(NH4)2[MoO4] (mS60) undergoes on cooling a phase transition at 190 K. The investigation of this phase transition by means of time and temperature resolved X-ray powder diffraction showed that the phase transition appears on heating at a temperature of 250 K. From this hysteresis and the abrupt changes in the peak positions of the diffractograms it is assumed that this is a first order transition. A diffractogram of the low temperature modification was recorded between 10° and 100° in 2θ. The structure was determined using direct methods and was refined by Rietveld methods. The low temperature modification of (NH4)2[MoO4] (mP60, P21/a) crystallizes in space group P21/a (No. 14) and lattice constants a = 767.57(5) pm, b = 1120.53(7) pm, c = 712.64(4) pm and β = 115.727(2)°.
Topological analysis of DL-arginine monohydrate at 100 K
Authors: Kingsford-Adaboh R. , Dittrich B. , Wagner A. , Messerschmidt M. , Flaig R. , Luger P.
Published: December 2003

The charge density of DL-arginine monohydrate has been extracted from a synchrotron data set of 212121 reflections collected at 100 K with a Bruker CCD area detector up to a resolution of sin θ/λ = 1.40 Å-1 (d = 0.36 Å). DL-arginine monohydrate is characterised by a neutral α-amino group and a notable different hydrogen bond pattern compared to previously examined free arginine structures. All bond critical points of the electron density at the covalent and hydrogen bonds were located. We compare the local topological indices of ρ(r) with other amino acids. The conformation obtained from the experimental structure is found to be different from the Hartree-Fock (HF) optimization for the isolated molecule, thus the topology obtained from the static experimental charge density is compared to that derived from calculations at experimental and optimized geometry at HF and B3LYP levels of theory.
Synthesis, structural and spectral studies of bis-[N-(2,4-dimethoxy benzylidene)-2-mercaptoanilinato] Ni(II)
Authors: Şahin E. , İde S. , Ancın N. , Öztas S.G. , Tüzün M.
Published: December 2003

The Ni(II) complex of N-(2,4-dimethoxy ben-zylidene)-2-mercaptoaniline, [Ni(C15H14NO2S)2] was prepared and investigated. The structure derived from the two dimensional (2-D) NMR techniques, the infrared spectra, elemental analysis and mass spectra is consistent with that of the single crystal X-ray diffraction. Crystal system is monoclinic, space group Cc(no:9), number of formulae per unit cell Z=4. Cell parameters are a=14.283(4), b=13.828(4), c=14.345(5) Å, β=102.84(3)°, V= 2762(2) Å3. Two singly deprotonated ligands coordinate the metal atom in a distorted square planar geometry. The molecular geometry was also effected by C-H⋅⋅⋅N and C-H⋅⋅⋅O intramolecular hydrogen bonds.
Neural network investigation of borate crystal properties
Authors: Barber M. J. , Becker P.
Published: December 2003

Correlations between crystal chemical properties of anhydrous oxoborate crystals wereanalysed using artificial neural networks. Using structuralproperties of oxoborate crystal structures described inthe literature, we developed several neural network modelsthat capture statistical relations between crystalchemical properties of the anhydrous oxoborates from the existingdata sets. This indicates the suitability of neural networks forthe prediction of structural propertiesof crystals.
Influence of high hydrostatic pressure on lattice parameters of a single crystal of La3Nb0.5Ga5.5O14
Authors: Pavlovska A. , Werner S. , Boehler R.
Published: December 2003

Unit-cell parameters of La3Nb0.5Ga5.5O14 (langanite) have been determined at a number of pressures up to 23GPa in diamond anvil high pressure cells with single crystal X-ray diffraction techniques. The anisotropic behaviour of unit cell parameters of langanite is caused by differences of bonding strength in direction parallel to the a- and c-axis. Within the investigated pressure range, the c/a-ratio increases from 0.6232 to 0.6503. The volume compressibility of trigonal langanite (space group P321) is the 0.007 GPa-1, with calculated bulk modulus of 145(3)GPa (B'0=1.4(8)). At a pressure of 12.4(3)GPa a first-order phase transition was detected, characterised by a discontinuity in the pressure dependence of lattice parameter c. The high-pressure phase (presumably monoclinic, A2) with a volume compressibility of 0.011 GPa-1 (B0=93(2) GPa, B'0=1.9(9)) is more compressible as compared to the initial phase due to an abnormal pressure dependence of lattice parameter a.
Intramolecular hydrogen bond and proton transfer in 3-(2-benzimidazolylthio)-2,4-pentanedione. Crystallographic evidence and theoretical calculations
Authors: Smrčok L. , Tunega D. , Langer V. , Koóš M.
Published: December 2003

Crystal structure of the title compound is orthorhombic,Pbca,a=7.8689(2) Å,b=9.6519(3) Å,c=31.3579(9) Å. The structure was solved by direct methods and refined by a full-matrix least squares procedure to finalR(all)=0.0682 for 2853 unique diffractions merged from 24459 measured at 183(2)K. The molecule is formed by two planar moieties joined through an atom of sulphur. The short intramolecular O...O contact is 2.430(2) Å, the intramolecular hydrogen bond is slightly asymmetric. Theoretical ab initio calculations done at B3LYP/SVP and ONIOM(MP2/SVP:B3LYP/SVP) levels showed that the experimental geometry of pentanedione pseudoring is close to the geometry corresponding to a transition state on the asymmetric potential energy curve. Calculated energy difference between two minima is only –4.72 kJ/mol and the energy barrier –6.02 kJ/mol, which agrees well to ~6.6kJ/mol found in microwave spectroscopic study of malonaldehyde.
On the discovery of new low temperature monoclinic phases with Cm and Cc space groups in Pb(Zr0.52Ti0.48)O3: an overview
Authors: Pandey D. , agini R
Published: December 2003

The decades old phase diagram of the technologically important Pb(Zr
x
Ti1–

x
)O3 (PZT) ceramics in the vicinity of the morphotropic phase boundary has been under review during the last few years. This article summarises the results of the discoveries of two new mono clinic phases (F
M
HT) and (F
M
LT) with Cm and Cc space group by the Brookhaven group and our group, respectively, in the PZT ceramics.
Investigation of transition from decagonal to vacancy ordered phase on replacement of Co by Cu in Al70Co15–

x
Cu
x
Ni15
Authors: Yadav T. P. , Shaz M. A. , Tiwari R. S. , Srivastava O. N.
Published: December 2003

The alloy with composition Al70Co15Ni15 forms one of the important quasicrystalline phase exhibiting formation of decagonal variants [1, 2]. In the present investigation, copper has been substituted in place of cobalt i.e. the phases corresponding to Al70Co15–

x
Cu
x
Ni15, have been investigated. It is found that when copper concentration reaches to a value of 10 atomic percent with the composition corresponding to Al70Co5Cu10Ni15, the decagonal phase starts yielding to give rise to vacancy ordered phase. When all cobalt is replaced by copper i.e. when the composition corresponds to Al70Cu15Ni15, the decagonal phase disappears and the only phase observed is the vacancy ordered phase. It can thus be said that copper substitution brings in decagonal to vacancy ordered (VOP) phase transition. It has also been observed that gradual increase in concentration of Cu in Al70Co15–

x
Cu
x
Ni15 leads to cellular to dendritic transition in morphology.
White beam synchrotron X-ray topography studies of twinning in GdFeO3-type perovskite crystals
Authors: Savytskii D. , Senyshyn A. , Matkovskii A. , Vasylechko L. , Wieteska K. , Wierzchowski W. , Lukasiewicz T. , Bismayer U.
Published: December 2003

The twin structure of NdGaO3 and YAlO3 : Dy crystals was examined using white beam synchrotron X-ray topography. The relation of the orthorhombic lattice basis vectors has been obtained for every domain pair in the crystals with GdFeO3-type structure. A new computer program has been used to generate Laue simulation patterns and to calculate the image shifts in topographs. The proposed approach allow for the analysis of both, sample images for specified reflections and Laue patterns as a whole. Topography was used to map domain patterns, to show misorientations and to detect symmetric aspects of ferroelastic twins. Information on twin laws and the twin distribution was obtained simultaneously.
Synthesis, X-ray crystal structure and dielectric measurements of a tetragonal tungsten bronze: Pb0.75K1.80Li1.70Nb5O15
Authors: Elaatmani M. , Zegzouti A. , Capitelli F. , Moliterni A. G. G. , Migliori A. , Calestani G.
Published: December 2003

Typical crystals Pb0.75K1.80Li1.70Nb5O15, belonging to tetragonal tungsten bronze materials, were grown by the slow cooling technique. The crystals were characterized at room temperature by X-ray diffraction (XRD) and high resolution transmission electron microscopy (HREM). The structure, solved combining information obtained by HRTEM images and Direct Methods application to single crystal XRD data, was refined by full-matrix least-squares technique in the P4bm space group to a final R = 0.031. The lattice constants are a = 12.540(2), c = 4.037(1) Å, V = 634.8(2) Å3, at 293 K. There are two formulas per unit cell, for a calculated density of 4.928 Mg/m3. Dielectric measurements, carried out along the [001] direction in the frequency 103 Hz, showed the existence of the paraelectric-ferroelectric transition at 628 K and of a further maximum of ε′r (with a very weak intensity) at T
1 = 150 K.
Ab initio structure determination of In2H2(P2O7)(P4O12) from X-ray powder diffraction data
Authors: Ivashkevich L. S. , Lyakhov A. S. , Selevich A. F. , Lesnikovich A. I.
Published: December 2003

The crystal structure of In2H2(P2O7)(P4O12) has been determined from X-ray powder diffraction data. The structure is orthorhombic, space group Pmmn (No. 59), with unit cell dimensions a = 12.9398(2) Å, b = 11.3725(3) Å, c = 5.0385(1) Å, V = 741.45(3) Å3, Z = 2, and D
x = 3.23 g/cm3. The structure has been solved by direct methods using EXPO program and refined by FULLPROF package. The final R
Bragg value was 4.6%. Positions of hydrogen atoms were not defined. Indium cation has sixfold oxygen coordination being surrounded by two diphosphate and four cyclotetraphosphate groups. Probable scheme of hydrogen bonding is discussed.
EXAFS and XRD investigations of zeunerite and meta-zeunerite
Authors: Hennig C. , Reck G. , Reich T. , Roßberg A. , Kraus W. , Sieler J.
Published: December 2003

In this paper EXAFS was used to determine bond lengths in the structures of zeunerite and meta-zeunerite. The atomic distances between heavy and light scatterers observed using EXAFS in meta-zeunerite deviate approximately 0.1 Å from literature data of single-crystal X-ray diffraction measurements. Because this difference is significant higher than the error limits of EXAFS measurements, the complete crystal structure of meta-zeunerite, Cu[UO2AsO4]2·8 H2O, is revised by X-ray structure analysis. The bond length determinations by EXAFS and the revised XRD data agree within the experimental error limits. In this study EXAFS spectroscopy has proven to be an useful tool for determining precise local bond lengths in the environment of heavy atoms. Moreover, the crystal structure of zeunerite, Cu[UO2AsO4]2·12 H2O, hitherto not been described in the literature, was investigated. Reflex broadening effects and intergrowth relationship between zeunerite and meta-zeunerite show that meta-zeunerite grows in nature due to dehydration of zeunerite. The structural transition from zeunerite to meta-zeunerite is connected with a change in the uranyl arsenate layer arrangement and the crystal water content.
Crystal and molecular structures of 4-aryl-1,4-dihydropyrimidines: Novel calcium channel antagonists
Authors: Chandra Mohan K. , Ravikumar K. , Shetty M. M. , Velmurugan D.
Published: December 2003

The solid-state structures of three calcium channel antagonists viz. 1,4-dihydro-6-methyl-5-N-methyl-carbamoyl-4-(3′,4′-dichlorophenyl)-2(3 H)-pyrimidinethione, C13H13N3OSCl2 (1); 1,4-dihydro-6-methyl-5-N-methyl-carbamoyl-4-(4′-methoxyphenyl)-2(3 H)-pyrimidinethione, C14H17N3O2S (2) and 1,4-dihydro-6-methyl-5-N-methyl-carbamoyl-4-(2′,4′-dichlorophenyl)-2(3 H)-pyrimidineone monohydrate, C13H13N3O2Cl2·H2O (3), are reported here. The structures show that these compounds can adopt the important structural features of 1,4-dihydropyridine calcium channel blockers. In (2), the compound crystallized with three molecules in the asymmetric unit. The dihydropyrimidine ring adopts a half-chair in (1) and boat conformation in (2) and (3). The 4-aryl substituents occupies a pseudo-axial position approximately orthogonal to the plane of the dihydropyrimidine ring [95.1(2)° (1); 97.5(3)°, 79.8(2)° & 88.2(2)° (2) and 78.8(3)° (3)]. The C3 substituent, carbamoyl group, is in an extended conformation and oriented anticlinical in (1) and (3), but in (2) two molecules are anticlinal and the other one is synperiplanar, respectively. Intra- and inter- molecular interactions may be influencing the orientation of the C3 carbamoyl group. The 2-chlorophenyl substituent in (3) is in the axial synperiplanar orientation.
Crystal structure of anhydrous potassium O-n-propyldithiocarbonate. Theoretical calculations of O-alkyl dithiocarbonates
Authors: Buntine M. A. , Cox M. J. , Lim Y. X. , Yap T. C. , Tiekink Edward R. T.
Published: December 2003

The xanthate anion in the structure of K[S2COnPr] displays the expected features, i.e. planar S2CO chromophore and variation in C—S and C—O distances. The K cation exists in a distorted cubic geometry defined by an O2S6 donor set. Cubes are face-shared so as to form a layer structure with cohesion between layers afforded by hydrophobic interactions. A series of theoretical gas-phase structures have been calculated for isolated S2COR anions. These show that there is a remarkable consistency in geometric parameters across the series. This observation indicates that the nature of the R substituent does not influence greatly the electronic structure of the central S2CO chromophore.
Synthesis and crystal structure of diaquabis(diketohydrindene-diketohydrindamine)manganese(II)
Authors: Derebe M. G. , Retta N. , Moliterni A. G. G. , Capitelli F.
Published: December 2003

Diaquabis(diketohydrindene-diketohydrindamine)manganese(II), Mn(II) complex of Ruhemann's purple, a condensation product of ninhydrin andα, L-alanine (or anyα-amino acid), was synthesized for the first time and its structure determined by X-ray diffraction methods. The study revealed that the metal ion is seven-coordinated with two Ruhemann's purple ligands, one behaving as a didentate ON donor and another as a tridentate ONO donor, both monobasic, and two additional water ligands. The structure closely resembles a distorted pentagonal bipyramid (D5h) geometry.
Ab initio structure determination of cytochrome c6 by combined reciprocal space-real space approach
Authors: Chowdhury K. , Ghosh S. , Mukherjee M.
Published: December 2003

The direct method program SAYTAN has been applied successfully to redetermine the structure of cytochrome c6, a heme-containing redox protein with 89 amino acids, a Fe atom and 151 solvent water molecules in the asymmetric unit and data to 1.1 Å resolution. The crystal system is rhombohedral with space group R3, cell parameters a = b = c = 40.43(10) Å, α = β = γ = 80.25(5)°. Starting with initially random phases, useful phase sets could be obtained from multiple trials of direct methods based on reciprocal space. The E-map corresponding to the phase set with the lowest mean phase error, 45.4°, showed a distorted octahedral coordination around the Fe site. The phase estimates from the metal atom and a few neighbouring atoms in the initial E-map have been improved by density modification procedure (PERP) operating in direct space. The resulting electron density map can be interpreted readily by an automated procedure to build up the protein structure.
Tricalcium silicate Ca3SiO5, the major component of anhydrous Portland cement: on the conservation of distances and directions and their relationship to the structural elements
Authors: de Noirfontaine M.- N. , Dunstetter F. , Courtial M. , Gasecki G. , Signes-Frehel M.
Published: December 2003

Tricalcium silicate, the major component of Portland cement exhibits a complex phase diagram, surprisingly still not completely understood. In this letter, new results are highlighted including a comprehensive study of the superstructure relationship between the polymorphs, and new ideas about the structural analysis. The organisation of the silicate skeleton can be described in terms of 1-D or 2-D elements, from which arise new hypotheses about the cohesion and the chemical origin of the observed superstructures.