Exo-bonded six-membered heterocycle in the crystal structures of RE7Co2Ge4(RE = La–Nd)

The stability of the heterocyclic {Co₄Ge₆} clusters in RE₇Co₂Ge₄(RE = La–Nd) is determined by strong interactions with the surrounding RE atoms in the structures.

Synthesis, crystal structure, and bonding analysis of the hypoelectronic cubic phase Ca5Pd6Ge6

The title compound, Ca5Pd6Ge6, was obtained during a systematic investigation of the Ca-Pd-Ge ternary phase diagram. The crystal structure was determined and refined from single-crystal X-ray diffraction data. It crystallizes in a new structure variant of the Y4PdGa12-type structure (Im3̅m, a = 8.7764(4) Å) that features an arrangement of vertex-sharing body-centered cubes of calcium, Ca@Ca8, with a hierarchical bcc network, interpenetrating a second (Pd6Ge6) network consisting of Ge2 dumbbells surrounded by Pd in a strongly flattened octahedron with Pd(μ(2)-η(2),η(4)-Ge2)-like motifs. These octahedra are condensed through the Pd to form a 3D open fcc network. Theoretical band structure calculations suggested that the compound is hypoelectronic with predominantly multicenter-type interatomic interactions involving all three elements and essentially a Hume-Rothery-like regime of electronic stabilization. The similar electronegativity between germanium and palladium atoms has a decisive impact on the bonding picture of the system.

Antimalarial activity of ruthenium(ii) and osmium(ii) arene complexes with mono- and bidentate chloroquine analogue ligands

Thirteen new ruthenium and osmium half-sandwich complexes with chloroquine analogue ligands have been synthesized and evaluated for anti-malarial properties.

A short designed semi-aromatic organic nanotube--synthesis, chiroptical characterization, and host properties

The first generation of an organic nanotube based on the enantiomerically pure bicyclo[3.3.1]nonane framework is presented. The helical tube synthesised is the longest to date having its aromatic systems oriented parallel to the axis of propagation (length ∼26 Å and inner diameter ∼11 Å according to molecular dynamics simulations in chloroform). The synthesis of the tube, a heptamer, is based on a series of Friedländer condensations and the use of pyrido[3,2-d]pyrimidine units as masked 2-amino aldehydes, as a general means to propagate organic tubular structures and the introduction of a methoxy group for modification toward solubility and functionalization are described. The electronic CD spectra of the tube and molecular intermediates are correlated with theoretical spectra calculated with time-dependent density functional theory to characterize the chirality of the tube. Both experimental (NMR-titrations) and theoretical (molecular dynamics simulations) techniques are used to investigate the use of the tube as a receptor for the acetylcholine and guanidinium cations, respectively.

Synthesis and crystal structure of a series of incommensurately modulated composite oxohalide compounds

Transparent, needle-like single crystals of the isostructural compounds [Sb4O7+3δX4][Zn3]1+δ (X = Cl, Br, I) δ ≈ 0.2 were obtained from chemical reactions in evacuated and sealed silica tubes. First, the average structure was solved in P21/n but the model refined poorly and a lowering of the symmetry to the 3 + 1 dimensional space group P21(α0γ)0 gave a significantly better fit to the data. This model used second order positional modulations for all the atoms. Whereas Sb, Cl (Br, I) and most O positions were well behaved, there was a mismatch with Zn that was better described in a sub-cell, thus yielding a composite structure. The composite nature of the structure leads to a charge imbalance that is compensated by oxygen vacancies.

Cu3Sn - understanding the systematic absences

The intermetallic compound Cu3Sn has previously been described as a long-period antiphase boundary superstructure of the Cu3Ti structure type. While the compound itself has been reported as a tenfold and an eightfold superstructure, ternary doped alloys show shorter repetitions. Interestingly, the diffraction patterns of these compounds show non-crystallographic absences that cannot be explained using the superstructure models. Since the compound exhibits phase broadening, these models are not satisfactory because the paucity of observed data does not allow for a refinement of the composition. Here, an alternative, superspace model in the orthorhombic space group Xmcm(0β0)000 is proposed, with the centering vectors (0,0,0,0) and (½,0,0,½). The presence of the non-crystallographic absences is explained as a result of a dominating occupational modulation that is accompanied by a weaker displacive modulation. In consistency with the EDXS results, the composition has been refined to Cu3 + xSn from single-crystal X-ray diffraction data. It is further demonstrated that by varying the length and the direction of the modulation wavevector in the superspace model, the ternary Cu3Sn compounds and other colored hexagonal close packing (h.c.p.) structures can be produced.

Y-brass related composite structures : a (3+1)-dimensional space description

The γ-brass Hume-Rothery [1] phases which adopt at VEC values near about 21/13 presently attract attention due to their structural complexity and challenge for the understanding of the underlying stabilization mechanism. Morton, by electron microscopy studies, revealed that the γ-brass regions of Cu-Zn, Ni-Zn and Pd-Zn do not only accommodate the γ-brass phase but also a bundle of structurally related, complex phases with lower symmetry than that of the γ-phase. A bundle of γ-brass related phases in the Zn-rich region of the Ni-Zn, Pd-Zn, Pt-Zn phase diagram is investigated. Their structures have been refined from single crystal X-ray diffraction data in the conventional 3D space group using supercells [2,3]. In the course of a previous investigation of the Pd-Zn system, the structures of two γ-brass related composite compounds- Pd24.3Zn75.7 and Pd21.2Zn78.8 have been described with the (3+1) dimensional space description (superspace group Xmmm(00γ)0s0 with the following lattice parameters, a = 12.929(3) Å, b = 9.112(4) Å, c = 2.5631(7) Å, q = 8/13 c* and a = 12.909(3) Å, b = 9.115(3) Å, c = 2.6052(6) Å, q = 11/18 c*, respectively) [3]. The aim of this study is to represent the structure of these previously reported phases in a coherent, modulated description to make them more readily comparable. A refinement model with a variety of modulation vectors allows to refine any intergrowth structure in the Zn rich region of the M-Zn (M=Ni,Pd,Pt) system. In order to gain an insight into expressions, cause and mechanism and structure-composition relationship for such phases, we also study the impact of substitution on the evolution of the structure of ternary derivatives of M-Zn composite compounds by the use of (3+1) formalism. For instance, substitution of zero-valent palladium and bi-valent zinc by zero-valent platinum in the structure of Pd24.3Zn75.7. This presentation will discuss about the understanding of the complexity of the atomic arrangement through the various modulation which correlates with the variation of composition of the binary and ternary phases.

Freeze Frames vs. Movies

Sometimes, model building in crystallography is like resolving a puzzle: All obvious symmetrical or methodological errors are excluded, you apparently understand the measured patterns in 3D, but the structure solution and/or refinement is just not working. One such nerve-stretching problem arises from metrically commensurate structures (MCS). This expression means that the observed values of the components of the modulation wave vectors are rational by chance and not because of a lock-in. Hence, it is not a superstructure - although the boundaries between the two descriptions are blurry. Using a superstructure model for a MCS decreases the degrees of freedom, and forces the atomic arrangement to an artificial state of ordering. Just imagine it as looking at a freeze frame from a movie instead of watching the whole film. The consequences in structure solution and refinement of MCS are not always as dramatically as stated in the beginning. On the contrary, treating a superstructure like a MCS might be a worthwhile idea. Converting from a superstructure model to a superspace model may lead to a substantial decrease in the number of parameters needed to model the structure. Further, it can permit for the refinement of parameters that the paucity of data does not allow in a conventional description. However, it is well known that families of superstructures can be described elegantly by the use of superspace models that collectively treat a whole range of structures, commensurate and incommensurate. Nevertheless, practical complications in the refinement are not uncommon. Instances are overlapping satellites from different orders and parameter correlations. Notably, MCS occur in intermetallic compounds that are important for the performance of next-generation electronic devices. Based on examples of their (pseudo)hexagonal 3+1D and 3+2D structures, we will discuss the detection and occurrence of MCS as well as the benefits and limitations of implementing them artificially.

News from the world of modulated intermetallics

The number of modulated structures with more than one modulation vector is small, and such structures often pose special problems in solving and refining. This talk will be concentrated on three such cases; The 3+4 dimensionally modulated cubic structure of digenite, the 3+2 dimensionally modulated structure of Cu3In2, the 3+2 dimensionally modulated structure of AuZn3 and the 3+2 dimensionally modulated structure of Se(Sn4)2K10. The three former cases are interesting because they are relatively weakly ordered structures where modelling is straight-forward, but the model itself is less than obvious to understand while the latter case appears highly ordered, but presents formal modelling difficulties. From these and previously known multi dimensional cases it would appear that higher order modulations are very prone to disorder. The image shows the hk0 layer from Se(Sn4)2K10.

Structural Study of the Disordered RECd6 Quasicrystal Approximants (RE = Tb, Ho, Er, Tm and Lu)

The crystal structures of approximants RECd6 (RE = Tb, Ho, Er, Tm and Lu) have been refined from single crystal X-ray diffraction data. This work is a continuation of a previous study of MCd6 approximants [1] in which the different types of disorder of the central Cd4 tetrahedra located in the dodecahedral cavities were examined. The structures of the title compounds are all similar to GdCd6 and disorder was observed in all these compounds. There is a correlation between the anisotropic displacement parameter and the unit cell dimension

Imaging techniques. Mapping bond orientations with polarized x-rays

Regions of bond order and disorder are revealed [Also see Report by Palmer et al. ]

LiZn(4 - x) (x = 0.825) as a (3 + 1)-dimensional modulated derivative of hexagonal close packing

The (3+1)-dimensional modulated structure of the LiZn(4 - x) (x = 0.825) binary compound has been determined in the superspace. The compound crystallizes in the orthorhombic superspace group Cmcm(α00)0s0 with a = 2.7680 (6), b = 4.7942 (6), c = 4.3864 (9) Å, modulation wavevector: q ≃ 4/7a*. The structure is a derivative from the hexagonal close packing. The cubo-octahedron as a coordination polyhedron (c.n. = 12) is typical for all atoms. Bonding between atoms is explored by means of the TB-LMTO-ASA program package. The absence of strong interatomic interactions in LiZn(4 - x) is the main reason for the possible structure transformations.

Au10Mo4Zn89: a fully ordered complex intermetallic compound analyzed by TOPOS

The compound Au10Mo4Zn89 has been synthesized, and its structure has been analyzed by single-crystal X-ray diffraction. The compound crystallizes in cubic space group F43m (No. 216) with a unit cell that contains 412 atoms. The structure is largely tetrahedrally closely packed, but an octahedral arrangement of atoms is incompatible with tetrahedral close packing. The structure of the ordered Au10Mo4Zn89 compound has been described by using the algorithm of automatic geometric and topological analysis that is implemented in TOPOS as the "Nanoclustering" procedure.

Allotwinning in a molecular crystal: (1R,3S)-dimethyl 2-oxocyclohexane-1,3-dicarboxylate

Two polytypic modifications of (1R,3S)-dimethyl 2-oxocyclohexane-1,3-dicarboxylate intergrow to form allotwins. One phase shows monoclinic symmetry, Cc, while the other is orthorhombic Pmc21. The structures may be considered as two different modes of superstructure ordering of an underlying, disordered structure. Considered in the same metrically orthorhombic unit cell a = 37.8883, b = 4.7233, c = 11.6835 Å, the two can be conveniently distinguished by their non-standard centering, Cc being represented as Xc with the centering vectors (0 0 0); (½ 0 ½); (¼ ½ ¾); (¾ ½ ¼); and Pmc21 as Xmc21 with the centering vectors (0 0 0); (½ 0 0). The difference between the allotwin domains lies only in the relationship between next-nearest neighbors along the stacking direction 100 and hence the conformations and packing efficiencies are identical for both phases and all three domains. The stacking sequences for the two phases correspond to ABAB for the orthorhombic stacking and ABA'B'/AB'A'B for the two (equivalent) monoclinic stackings. The monoclinic phase dominates comprising ca 80% of the total volume. Within the monoclinic phase, the ratio between the two possible orientations is highly unbalanced (6:1) indicating relatively large domains. The allotwinning detected in this sample may appear exotic in molecular compounds, but we suggest that the rarity of such examples in the literature is a reflection of the paucity of software that can identify and handle such cases. It is easy to overlook the possibility that a complex diffraction pattern originates from allotwinning and assume that normal mono-component twinning is the cause. The underlying mechanism in this case is the formation of two-dimensional layers of molecules that allow for two equivalent, but in terms of absolute geometry, different, ways of stacking.