Jürgen Glinnemann

The Thermodynamically Stable Form of Solid Barbituric Acid: The Enol Tautomer

Barbituric acid, which has been known since 1863, is drawn in textbooks always as the keto tautomeric form 1 (Scheme 1). Indeed, this is the most stable form in the gas phase and in solution. Also in the solid state, the keto tautomer is observed in the metastable phase I, the commercial phase II, and a high-temperature phase III, as well as in its dihydrates. In contrast, we now observe that the recently discovered tautomeric polymorph IV consists of molecules in the enol form 2, and that this polymorph is actually the thermodynamically stable phase at ambient conditions. The preference for the enol form in the solid state is explained by the formation of an additional strong hydrogen bond in the crystal, leading to a more favorable lattice energy. Polymorph IV is obtained from phase II by grinding or milling. Solid-state NMR (SSNMR), IR, and Raman experiments revealed this to be a tautomeric polymorph, which does not consist of the keto tautomer 1, but of one of the enol forms. The spectroscopic data suggested the trienol tautomer, but other enol tautomers could not be ruled out. All attempts to obtain single crystals of phase IV by recrystallization failed, and dehydration of the dihydrate yielded only phase II. The grinding or milling processes resulted in powders of poor crystallinity. However, it was possible to index the laboratory X-ray powder data and to solve the crystal structure by simulated annealing, while refinement was carried out by the Rietveld method from synchrotron data (Figure 1). The bond lengths in the OCN framework revealed phase IV to consist of molecules in the enol form 2. Scheme 1. Barbituric acid in the keto (1) and enol (2) tautomeric forms.

Electron diffraction, X-ray powder diffraction and pair-distribution-function analyses to determine the crystal structures of Pigment Yellow 213, C23H21N5O9

The crystal structure of the nanocrystalline alpha phase of Pigment Yellow 213 (P.Y. 213) was solved by a combination of single-crystal electron diffraction and X-ray powder diffraction, despite the poor crystallinity of the material. The molecules form an efficient dense packing, which explains the observed insolubility and weather fastness of the pigment. The pair-distribution function (PDF) of the alpha phase is consistent with the determined crystal structure. The beta phase of P.Y. 213 shows even lower crystal quality, so extracting any structural information directly from the diffraction data is not possible. PDF analysis indicates the beta phase to have a columnar structure with a similar local structure as the alpha phase and a domain size in column direction of approximately 4 nm.

Explanation for the stacking disorder in tris(bicyclo[2.1.1]hexeno)benzene using lattice-energy minimisations

Abstract The stacking disorder in the hexagonal polymorph of tris(bicyclo[2.1.1]hexeno)benzene, C18H18, is explained by lattice-energy minimisations. The compound crystallises in layers with P(-6)2m layer-group symmetry. Each layer can be placed in one of three possible positions. Possible stacking sequences were derived from order-disorder (OD) theory and by a combinatorial approach. The resulting periodic model structures were optimised by lattice-energy minimisations. The calculations show that eclipsed arrangements of layers (sequence e.g. ABA) are energetically less favourable than non-eclipsed ones (sequence e.g. ABC). The reason was found in the deviation from P(-6)2m symmetry. Molecules in eclipsed layers are almost parallel to the layer plane, whereas molecules in non-eclipsed layers are inclined to it by about 3° leading to a more efficient packing. The influence of the next-nearest layers was found to be not a direct one, but mediated by the distortion of the layers between them. Using Boltzmann statistics, the stacking probabilities for all four-layer sequences were calculated. The results match well with the probabilities derived from the diffuse scattering by Bürgi et al. (2005) (Z. Kristallogr. 220, 1066–1075). The lattice-energy minimisations allowed to determine the actual local structures in all individual layers including packing effects like rotation of molecules, lateral shifts, and to calculate the stacking layer thickness, depending on the actual layer sequences. The diffraction pattern, calculated from a lattice-energy optimised structure with 54 layers, is similar to the experimental one, and even approximates the diffuse scattering.

Predicted crystal structures of tetramethylsilane and tetramethylgermane and an experimental low-temperature structure of tetramethylsilane

No crystal structure at ambient pressure is known for tetramethylsilane, Si(CH(3))(4), which is used as a standard in NMR spectroscopy. Possible crystal structures were predicted by global lattice-energy minimizations using force-field methods. The lowest-energy structure corresponds to the high-pressure room-temperature phase (Pa3, Z = 8). Low-temperature crystallization at 100 K resulted in a single crystal, and its crystal structure has been determined. The structure corresponds to the predicted structure with the second lowest energy rank. In X-ray powder analyses this is the only observed phase between 80 and 159 K. For tetramethylgermane, Ge(CH(3))(4), no experimental crystal structure is known. Global lattice-energy minimizations resulted in 47 possible crystal structures within an energy range of 5 kJ mol(-1). The lowest-energy structure was found in Pa3, Z = 8.

Simulation of absorption sites of acetone at ice: (0001) surface, bulk ice and small-angle grain boundaries

Local structures and energies were calculated for the interaction of acetone molecules with ice Ih at the (0001) surface, in the bulk and at small-angle grain boundaries. Force-field methods were used; for the surface additionally ab initio calculations were done. An ordered crystal-structure model of ice Ih in space groupP1121 (Z = 8) was used. The small-angle grain boundary was set up as a series of line defects with Burgers vectors of [2/3 1/3 1/2] (in the hexagonal lattice of ice Ih). All calculations were carried out with one or two acetone molecules in a sufficiently large simulation box containing up to 4608 water molecules, representing the low concentration of acetone in the atmosphere. The adsorption on the surface is energetically preferred. The acetone molecule is bound to the surface by two hydrogen bonds. This result is in contrast to earlier works with high acetone concentrations where only one hydrogen bond is formed. With two hydrogen bonds the adsorption enthalpy is calculated as −41.5 kJ mol−1, which is in agreement with experimental results. The interaction at small-angle grain boundaries is energetically less favourable than at the surface but much more favourable than in the bulk ice. In bulk ice and at small-angle grain boundaries the acetone molecule is bound by two hydrogen bonds like at the surface. The incorporation of acetone in bulk ice distorts the crystal structure significantly, whereas an incorporation at a small-angle grain boundary leads only to a minor distortion.

Explanation of the stacking disorder in the β-phase of Pigment Red 170.

The β-phase of Pigment Red 170, C26H22N4O4, which is used industrially for the colouration of plastics, crystallizes in a layer structure with stacking disorder. The disorder is characterized by a lateral translational shift between the layers with a component ty of either +0.421 or -0.421. Order-disorder (OD) theory is used to derive the possible stacking sequences. Extensive lattice-energy minimizations were carried out on a large set of structural models with different stacking sequences, containing up to 2688 atoms. These calculations were used to determine the actual local structures and to derive the stacking probabilities. It is shown that local structures and energies depend not only on the arrangement of neighbouring layers, but also next-neighbouring layers. Large models with 100 layers were constructed according to the derived stacking probabilities. The diffraction patterns simulated from those models are in good agreement with the experimental single-crystal and powder diffraction patterns. Electron diffraction investigation on a nanocrystalline industrial sample revealed the same disorder. Hence the lattice-energy minimizations are able to explain the disorder and the diffuse scattering.

Packing of tetrahedral EX4 molecules with E = C, Si, Ge, Sn, Pb and X = F, Cl, Br, I

The crystal structures of EX4 molecules with E = C, Si, Ge, Sn, Pb and X = F, Cl, Br and I were investigated by geometrical packing analysis, lattice-energy minimisations and analysis of the halogen–halogen interactions. The 18 known crystal structures group into seven different structure types. In most cases the halogen atoms as well as the molecules themselves are arranged in distorted close-sphere packings. The sphericity of the molecules seems to determine which structure types are adopted by the individual compounds. Lattice-energy minimisations show a high number of possible polymorphs. For EX4 compounds the same types of halogen–halogen interactions as for halogenated organic compounds were found but with different ranges for the E–X⋯X angle values.

Local structure in the disordered solid solution of cis- and trans-perinones.

The cis- and trans-isomers of the polycyclic aromatic compound perinone, C26H12N4O2, form a solid solution (Vat Red 14). This solid solution is isotypic to the crystal structures of cis-perinone (Pigment Red 194) and trans-perinone (Pigment Orange 34) and exhibits a combined positional and orientational disorder: In the crystal, each molecular position is occupied by either a cis- or trans-perinone molecule, both of which have two possible molecular orientations. The structure of cis-perinone exhibits a twofold orientational disorder, whereas the structure of trans-perinone is ordered. The crystal structure of the solid solution was determined by single-crystal X-ray analysis. Extensive lattice-energy minimizations with force-field and DFT-D methods were carried out on combinatorially complete sets of ordered models. For the disordered systems, local structures were calculated, including preferred local arrangements, ordering lengths, and probabilities for the arrangement of neighbouring molecules. The superposition of the atomic positions of all energetically favourable calculated models corresponds well with the experimentally determined crystal structures, explaining not only the atomic positions, but also the site occupancies and anisotropic displacement parameters.

Local atomic order in sodium p-chlorobenzenesulfonate monohydrate studied by pair distribution function analyses and lattice-energy minimisations

Abstract Routine X-ray single-crystal structure analysis of Na[C6H4ClO3S]·H2O resulted in an orthorhombic layer structure with space group Pnma, Z=4. In this crystal structure the phenyl rings in a single layer are disordered over two mutually perpendicular orientations with occupancies of 0.500(4) each. Structure determination including superstructure reflections and irregular shaped reflections revealed a twinned, ordered, monoclinic structure, P21/c, Z=8. Here, within a layer the phenyl rings are arranged alternatingly perpendicular. Pair distribution function analysis (PDF) and lattice-energy calculations confirmed this arrangement. Faint diffuse scattering streaks point to a one-dimensional disorder (concerning the layer-stacking sequence). Application of the order-disorder (OD) approach led to three polytype structures with maximum degree of order (MDO); one of them is the experimental monoclinic structure. This structure was found to have the most favourable energy in the lattice-energy minimisations. However, the energy differences between different polytypes with different stacking sequences are rather small. Hence, the lattice-energy minimisations confirmed the monoclinic P21/c structure with stacking disorder.

4-Cyanopyridine, a versatile mono- and bidentate ligand. Crystal structures of related coordination polymers determined by X-ray powder diffraction

4-Cyanopyridine (4-CNpy, also known as isonicotinonitrile) can act as a monodentate ligand in transition metal complexes via the pyridine nitrogen atom (Npy), or as a bidentate ligand via both nitrogen atoms (Npy and NCN), resulting in a linear bridge between two metal atoms. Seven new polymeric transition metal compounds, [CuCl2(4-CNpy)]n (1b), [MnCl2(4-CNpy)]n (2b), [NiCl2(4-CNpy)2]n (3a), [NiCl2(4-CNpy)]n (3b), [CoBr2(4-CNpy)2]n (4a), [NiBr2(4-CNpy)2]n (5a) and [NiBr2(4-CNpy)]n (5b), are reported. Compounds 1b, 2b, 3b and 5b were obtained from the corresponding [M(II)X2(4-CNpy)2]n compounds by careful thermal decomposition under controlled conditions. Compounds 3a, 4a and 5a were synthesized from 4-cyanopyridine and transition metal halides. For all compounds, IR-spectroscopy was used to distinguish between mono- or bi-coordination of the 4-cyanopyridine ligand: in bi-coordinated compounds the asymmetric stretching vibrations of the cyano group vas(CN) are shifted to higher frequencies. All crystal structures were determined from X-ray powder diffraction data. Compounds 1b, 3a, 4a and 5a consist of polymeric chains of octahedra (double chains for 1b; single chains for 3a, 4a and 5a), in which 4-cyanopyridine acts as a monodentate ligand via the Npy atom. Compound 1b exists in two polymorphs, a triclinic (α-1b) and a monoclinic phase (β-1b); both exhibit a strong Jahn–Teller distortion of the CuCl5N-octahedra. On the other hand, 2b, 3b and 5b exhibit layered structures, in which the 4-cyanopyridine acts as a bidentate ligand. Both nitrogen atoms coordinate to metal atoms, resulting in a linear M(II)-py-CN–M(II) bridge. These are the first examples of Mn and Ni compounds in which two 3d metal atoms are connected by a 4-cyanopyridine bridge. Due to the linearity of this bridge, 4-cyanopyridine lends itself to the construction of new metal–organic frameworks.