Structural Chemistry

Charge-density studies of energetic materials: CL-20 and FOX-7. Corrigendum.

Publication Date: 2008 Aug PMID: 18641455
Authors: Meents, A. - Dittrich, B. - Johnas, S. K. - Thome, V. - Weckert, E. F.
Journal: Acta Crystallogr B

A corrigendum to the paper by Meents et al. (2008), Acta Cryst. B64, 42-49 to correct the nomenclature for CL-20.

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On the correlations between the polyhedron eccentricity parameters and the bond-valence sums for the cations with one lone electron pair.

Publication Date: 2008 Aug PMID: 18641454
Authors: Sidey, V.
Journal: Acta Crystallogr B

Applicability of the Wang-Liebau polyhedron eccentricity parameter in the bond-valence model [Wang & Liebau (2007). Acta Cryst. B63, 216-228] has been found to be doubtful: the correlations between the values of the polyhedron eccentricity parameters and the bond-valence sums calculated for the cations with one lone electron pair are probably an artifact of the poorly determined bond-valence parameters.

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Hydrogen-bond motifs in the crystals of hydrophobic amino acids.

Publication Date: 2008 Aug PMID: 18641453
Authors: Fabian, L. - Chisholm, J. A. - Galek, P. T. - Motherwell, W. D. - Feeder, N.
Journal: Acta Crystallogr B

A computer program has been developed to survey a set of crystal structures for hydrogen-bond motifs. Possible ring and chain motifs are generated automatically from a user-defined list of interacting molecular fragments and intermolecular interactions. The new program was used to analyse the hydrogen-bond networks in the crystals of 52 zwitterionic alpha-amino acids. All the possible chain motifs (repeating 1-4 molecules) are frequent, while the frequency of ring motifs (2-6 molecules) ranges from 0 to 85% of the structures. The list of motifs displayed by each structure reveals structural similarities and it can be used to compare polymorphs. The motifs formed in cocrystals of alpha-amino acids and in crystals of beta- and gamma-amino acids are similar to those of alpha-amino acids.

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Role of the gauche effect and local 1,3-dipole-dipole interactions in stabilizing an unusual conformation of tartarodinitriles.

Publication Date: 2008 Aug PMID: 18641452
Authors: Rychlewska, U. - Wascinska, N. - Warzajtis, B. - Gawronski, J.
Journal: Acta Crystallogr B

This paper reports the synthesis, X-ray and NMR investigations of chiral and meso dinitriles of tartaric acid (tartarodinitriles) and their O,O'-diacetyl and O,O'-dibenzoyl derivatives. While in chiral tartaric acid its esters and NH amides the four-atom carbon chain is overwhelmingly trans, it is gauche in chiral tartarodinitriles. Conversely, meso-tartaric acid, its esters and amides display a tendency for the gauche conformation, but meso-tartarodinitriles usually have the trans conformation. The NMR studies of tartarodinitriles reveal the presence of a conformational equilibrium in solution with a preference for those conformers found in crystals. The gauche conformation of meso-tartarodinitriles seems to be stabilized by local dipolar interactions, intramolecular C-H...O hydrogen bonds and by a tendency for maximization of the gauche effect, the latter effect also operating in chiral tartarodinitriles. Stabilization of the trans conformers of tartarodinitriles in the crystals seems to originate from specific intermolecular interactions.

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Interaction geometries and energies of hydrogen bonds to C=O and C=S acceptors: a comparative study.

Publication Date: 2008 Aug PMID: 18641451
Authors: Wood, P. A. - Pidcock, E. - Allen, F. H.
Journal: Acta Crystallogr B

The occurrence, geometries and energies of hydrogen bonds from N-H and O-H donors to the S acceptors of thiourea derivatives, thioamides and thiones are compared with data for their O analogues - ureas, amides and ketones. Geometrical data derived from the Cambridge Structural Database indicate that hydrogen bonds to the C=S acceptors are much weaker than those to their C=O counterparts: van der Waals normalized hydrogen bonds to O are shorter than those to S by approximately 0.25 A. Further, the directionality of the approach of the hydrogen bond with respect to S, defined by the C=S...H angle, is in the range 102-109 degrees , much lower than the analogous C=O...H angle which lies in the range 127-140 degrees . Ab initio calculations using intermolecular perturbation theory show good agreement with the experimental results: the differences in hydrogen-bond directionality are closely reproduced, and the interaction energies of hydrogen bonds to S are consistently weaker than those to O, by approximately 12 kJ mol(-1), for each of the three compound classes. There are no CSD examples of hydrogen bonds to aliphatic thiones, (Csp(3))(2)C=S, consistent with the near-equality of the electronegativities of C and S. Thioureas and thioamides have electron-rich N substituents replacing the Csp(3) atoms. Electron delocalization involving C=S and the N lone pairs then induces a significant >C(delta+)=S(delta-) dipole, which enables the formation of the medium-strength C=S...H bonds observed in thioureas and thioamides.

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Conformational richness and multiple Z' in salt co-crystal of N-methylpiperidine betaine with N-methylpiperidine betaine hexafluorosilicate.

Publication Date: 2008 Aug PMID: 18641450
Authors: Thaimattam, R. - Szafran, M. - Dega-Szafran, Z. - Jaskolski, M.
Journal: Acta Crystallogr B

The co-crystal structure of N-methylpiperidine betaine with N-methylpiperidine betaine hexafluorosilicate represents an unusual case of a salt co-crystal with a high Z' value (3), unexpected conformational variability, and with nearly 50% of its contents disordered. The betaine units from the salt and co-crystal formers are paired into several homoconjugated dimers via very short, linear O(-)...H(+)...O(-) bridges. These hydrogen bonds are the dominating interactions in the co-crystal structure, in variance with the simple hexafluorosilicate salt, which has a structure governed by COOH...F hydrogen bonds. The SiF;{2-}_6 anion in the co-crystal structure has only C-H...F interactions with the betaine units. The zwitterion:cation:anion stoichiometry is 3:3:1.5. Some of the betaine units display disorder, but each case is different. One of the SiF_6;{2-} anions is ordered while possessing exact crystallographic symmetry. The other one is disordered in a general position. In addition, there are three water molecules in the crystal structure. One is fully ordered, one has an H atom disordered in two positions and the third one occupies two alternative positions with unequal populations.

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Pressure-freezing with conformational conversion of 3-aminopropan-1-ol molecules.

Publication Date: 2008 Aug PMID: 18641449
Authors: Gajda, R. - Katrusiak, A.
Journal: Acta Crystallogr B

3-Aminopropan-1-ol, NH(2)(CH(2))(3)OH, was pressure-frozen and its structure determined at 0.2, 0.9 and 1.31 GPa by single-crystal X-ray diffraction. The freezing pressure of 0.13 GPa at 296 K was measured by ruby fluorescence in the diamond-anvil cell and from compressibility measurement in the piston-and-cylinder reaction press. The molecules assume an extended conformation in the crystalline state, different from the pseudo-ring conformers, with the terminal groups linked by an intramolecular hydrogen bond, present in the gaseous and liquid states. The polar arrangement in the 3-aminopropan-1-ol crystals is explained in terms of the pattern of intermolecular hydrogen bonds.

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High-pressure structural study of L-alpha-glutamine and the use of Hirshfeld surfaces and graph-set notation to investigate the hydrogen bonding present in the structure up to 4.9 GPa.

Publication Date: 2008 Aug PMID: 18641448
Authors: Lozano-Casal, P. - Allan, D. R. - Parsons, S.
Journal: Acta Crystallogr B

The crystal structure of L-alpha-glutamine has been elucidated at room temperature at pressures between 0 and 4.9 GPa by using single-crystal high-pressure X-ray diffraction techniques. The structure is primarily stabilized by five N-H...O intermolecular interactions, which link molecules in a herringbone-like layer arrangement, giving rise to voids within the solid. The application of pressure on the structure results in a reduction in the size of the voids, as a consequence of the shortening of the N-H...O hydrogen bonds, which compress to minimum N...O distances of around 2.6 A, without driving the crystal structure to a phase transition. The decrease in the hydrogen-bond distances is due to the necessary stabilization of the structure, which arises from molecules modifying their positions to optimize electrostatic contacts and minimize the occupied space. Hirshfeld surfaces and fingerprint plots have been used to rapidly assess the structural changes that occur on application of pressure.

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X-ray diffuse scattering from HMTA: analysis via a Monte Carlo model.

Publication Date: 2008 Aug PMID: 18641447
Authors: Goossens, D. J. - Heerdegen, A. P. - Welberry, T. R.
Journal: Acta Crystallogr B

Hexamethylenetetramine (HMT, C(6)H(12)N(4), also referred to as urotropin) and azelaic acid [A, HOOC-(CH(2))(7)-COOH] form a co-crystal or adduct (HMTA, also referred to as urotropin azelate) which exhibits several structural phases as a function of temperature. At room temperature, the structure is orthorhombic, but shows substantial disorder. Here, this disorder is explored by analyzing the diffuse scattering from single crystals of HMTA via Monte Carlo simulation. The disorder is in part occupational, with two orientations of azelaic acid occurring, and in part thermally induced, which is to say dynamic. The occupational disorder can be thought of as a combination of limited-range in-plane (bc plane) negative correlations combined with effectively zero correlation between planes (along a), rather like stacking faults. Size effect, the cross-correlation between molecular orientation and displacement from average position, is required to reproduce the observed diffuse scattering.

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Special features of intermolecular bonding A...D(A = Si, Ge and D = nucleophile) in crystal structures.

Publication Date: 2008 Aug PMID: 18641446
Authors: Vologzhanina, A. V. - Korlyukov, A. A. - Antipin, M. Y.
Journal: Acta Crystallogr B

An investigation of the crystal structures of 3346 silicon- and 718 germanium-containing compounds was carried out with a geometrical-topological analysis. The descriptors of inter- and intramolecular contacts A...D are given. Information on the descriptors of T-A...D (where T = leaving group) interactions in terms of a stereoatomic model of crystal structures was described as being helpful in modelling S(N)2 reactions. It was established that the formation of multiple intermolecular contacts in crystal structures is unfavorable. The dependence of the descriptors of intermolecular contacts T-A...D was studied as a function of the nature of T (leaving group in substitution reactions) and D (nucleophile atom or group of atoms) groups, and the coordination number of an A atom. The constancy of the T-A and A...D bond-order sum in crystal structures was demonstrated.

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Order, disorder and structural modulations in Bi-Fe-W-O-Br Sillen-Aurivillius intergrowths.

Publication Date: 2008 Aug PMID: 18641445
Authors: Avila-Brande, D. - Landa-Canovas, A. R. - Otero-Diaz, L. C.
Journal: Acta Crystallogr B

Transmission electron microscopy observations on a new complex oxybromide with nominal composition Bi(4)Fe(1/3)W(2/3)O(8)Br, heated at high temperature, reveal the transformation of its basic structure yielding two types of crystals. The first crystal type shows ordered and disordered extended defects leading to a new family of intergrowths between one Sillen block and n Aurivillius blocks and occasionally between one Aurivillius block and n Sillen blocks. The second type presents a compositionally modulated structure, determined by electron diffraction, with an average composition Bi(4)Fe(1/2)W(1/2)O(8 - delta)Br and unit-cell parameters a = (1/gamma) 3.8, b = 3.8, c = 14.5 A (gamma = 0.10-0.15) in the superspace group Immm[(1 - gamma)00] no. 71.1.

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Inorganic structures in space group P3m1; coordinate analysis and systematic prediction of new ferroelectrics.

Publication Date: 2008 Aug PMID: 18641444
Authors: Abrahams, S. C.
Journal: Acta Crystallogr B

ICSD Release 2007/1 contains 47 families of inorganic crystal structures, some single-member only, within the 311 entries listed under the polar space group P3m1. Coordinate analysis reveals 12 such families to be candidate ferroelectrics, over a range of confidence levels. Selection is based on the detection of an approach to nonpolar supergroup symmetry, within specified limits, by the atomic arrangement as reported in a confirmed polar space group. The primary source of uncertainty in such predictions is the reliability of the underlying structural determination. The candidates include In(2)ZnS(4), TlSn(2)F(5), Cu(7)Te(4), NaMnSe(2), Na(2)In(2)(Mo(3)O(8))(MoO(4))(2), Nb(3)Br(7)S, Nb(3)TeI(7), fencooperite, Bi(HCOO)(3), Li(NpO(2))(CO(3))(H(2)O)(2), LiPtD(0.66) and Ag(3)(MoO(3)F(3))(Ag(3)(MoO(4))Cl). A total of 20 structures examined are likely to be nonpolar, a further 20 have reduced predictive properties and three others are more likely to retain P3m1 symmetry over a wide thermal range. Substantial uncertainties associated with many of the listed 163 CdI(2), 69 ZnS and 10 SiC polytype structures, together with their low potential for use as possible ferroelectrics, led to their exclusion from fuller analysis.

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Incommensurate structure of Ca(2)Al(2)O(5) at high temperatures - structure investigation and Raman spectroscopy.

Publication Date: 2008 Aug PMID: 18641443
Authors: Lazic, B. - Kruger, H. - Kahlenberg, V. - Konzett, J. - Kaindl, R.
Journal: Acta Crystallogr B

A high-temperature X-ray diffraction study revealed that brownmillerite-type Ca(2)Al(2)O(5) transforms to an incommensurately modulated structure at elevated temperatures. Single crystals of Ca(2)Al(2)O(5) were synthesized in an end-loaded piston cylinder press at 2.5 GPa and 1273 K. The diffraction pattern observed at 1090 (10) K by in situ single-crystal diffraction experiments can be indexed by an I-centred orthorhombic cell and a modulation wavevector of q = 0.595 (1)c(*). A (3 + 1)-dimensional model in superspace group Imma(00gamma)s00 was used to refine the modulated structure. The structure is assembled from two building units: (i) layers of corner-sharing [AlO(6)] octahedra, stacked along b alternate with (ii) layers of zweier single chains of [AlO(4)] tetrahedra running along a. The modulated structure arises from an aperiodic sequence of two different configurations of the chains within the tetrahedral layers. The modulated high-temperature phase of Ca(2)Al(2)O(5) is isotypic to the modulated high-temperature modification of Ca(2)Fe(2)O(5). A large hysteresis was found in the phase-transition temperature. On heating, the transition occurs at ca 1075 (10) K; on cooling, satellite reflections can be observed down to 975 (10) K. The characterization of Ca(2)Al(2)O(5) is completed by Raman spectroscopy, including a partial interpretation of the spectra.

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Incommensurate structure of InAl(1 - x)Ti(x)O(3 + x/2)[x = 0.701 (1)]: comparison between modulated and composite models.

Publication Date: 2008 Aug PMID: 18641442
Authors: Bereciartua, P. J. - Zuniga, F. J. - Breczewski, T.
Journal: Acta Crystallogr B

The structure of the monoclinic phase of the compound InAl(1 - x)Ti(x)O(3 + x/2) with x = 0.701 (1) has been analyzed within the (3 + 1)-dimensional superspace formalism. Two different models were refined describing the structure as an incommensurate modulated layer and modulated composite, respectively. Both models include the same composition-structure relation. In the composite approach it is derived from the mismatching between the two subsystems. In the incommensurate modulated system, it is derived from a closeness condition between O atomic domains. The distribution and coordination of the cations is discussed and compared with previously proposed models for similar compounds.

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