Sonja M. Hammer

A Two-Dimensional Polymer from the Anthracene Dimer and Triptycene Motifs

A two-dimensional polymer (2DP) based on the dimerization of anthraceno groups arranged in a triptycene motif is reported. A photoinduced polymerization is performed in the crystalline state and gives a lamellar 2DP via a crystal-to-crystal (but not single-crystal to single-crystal) transformation. Solvent-induced exfoliation provides monolayer sheets of the 2DP. The 2DP is considered to be a tiling, a mathematical approach that facilitates structural elucidation.

Predicted and experimental crystal structures of ethyl-tert-butyl ether

Possible crystal structures of ethyl-tert-butyl ether (ETBE) were predicted by global lattice-energy minimizations using the force-field approach. 33 structures were found within an energy range of 2 kJmol(-1) above the global minimum. Low-temperature crystallization experiments were carried out at 80-160 K. The crystal structure was determined from X-ray powder data. ETBE crystallizes in C2/m, Z = 4, with molecules on mirror planes. The ETBE molecule adopts a trans conformation with a (CH(3))(3)C-O-C-C torsion angle of 180°. The experimental structure corresponds with high accuracy to the predicted structure with energy rank 2, which has an energy of 0.54 kJmol(-1) above the global minimum and is the most dense low-energy structure. In some crystallization experiments a second polymorph was observed, but the quality of the powder data did not allow the determination of the crystal structure. Possibilities and limitations are discussed for solving crystal structures from powder diffraction data by real-space methods and lattice-energy minimizations.

Crystal Structures of the Hydration States of Pigment Red 57:1

Today, most journals and newspapers are printed with Pigment Red 57:1 (P.R.57:1, 1). This is true for scientific journals like Angewandte Chemie and Zeitschrift f r Kristallographie as well as for newspapers such as The New York Times, The Sun, Bild, El Pa s, La Repubblica, Le Monde, and Shanghai Daily. P.R.57:1 is the most important organic red pigment with a production of more than 50 000 tons per year and an annual sales volume of more than 200 million Euro. 3] In printing ink the pigment is not dissolved, but finely dispersed. Consequently the solid-state properties are maintained. Most pigments, including P.R.57:1, occur in different crystal phases with different colors. Although P.R.57:1 has been industrially produced for more than 100 years, the crystal structures of P.R.57:1 have never been determined. 6] Here we report the crystal structures of three crystal phases of P.R.57:1 (Scheme 1). The compound is industrially synthesized in water by azo coupling and subsequent laking with CaCl2 (see Scheme 2). In the solid state all commercial “azo pigments” do not contain an azo group but adopt the tautomeric hydrazone form (Scheme 2). Thus the name “hydrazone pigments” is more

Structure determination from powder data without prior indexing, using a similarity measure based on cross-correlation functions.

A method to refine organic crystal structures from powder diffraction data with incorrect lattice parameters has been developed. The method is based on the similarity measure developed by de Gelder et al. [J. Comput. Chem. (2001), 22, 273-289], using the cross- and auto-correlation functions of a simulated and an experimental powder pattern. The lattice parameters, molecular position, molecular orientation and selected intramolecular degrees of freedom are optimized until the similarity measure reaches a maximum; subsequently, a Rietveld refinement is carried out. The program FIDEL (FIt with DEviating Lattice parameters) implements this method. The procedure is also suitable for unindexed powder data, powder diagrams of very low quality and powder diagrams of non-phase-pure samples. Various applications are shown, including structure determinations from powder data using crystal structure predictions by standard force-field methods. Other useful applications include the automatic structure determination from powder data starting from the crystal structures of isostructural compounds (e.g. a solvate, hydrate or chemical derivative), or from crystal data measured at a different temperature or pressure.

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.

Crystal structure of disordered nanocrystalline αII-quinacridone determined by electron diffraction

The nanocrystalline αII-phase of the industrially produced organic pigment quinacridone was studied by 3D electron diffraction of its crystals with a thickness of only 10 nm. The diffraction data showed strong diffuse scattering along one direction indicating severe stacking disorder. The average crystal structure was obtained from electron diffraction data using direct methods. In αII-quinacridone, the molecules are connected by a pair of hydrogen bonds thereby forming molecular chains, which are stacked, resulting in the formation of layers. The layers exhibit a stacking disorder with a mixture of herringbone and parallel arrangements, which explains the diffuse scattering. The crystal structure was confirmed by dispersion-corrected DFT calculations.

Crystal Structures of Pigment Red 57:1

Zeitschrift für Kristallographie, Angewandte Chemie, The New York Times, The Sun, El Pais, La Republica, Le Monde, Shanghai Daily, and many more journals and newspapers are printed with Pigment Red 57:1. P.R.57:1 (C18H12CaN2O6S ∙ n H2O, n = 0,1,3) is the most important organic red pigment with a production of more than 50,000 tons per year and an annual sales volume of more than 200 million Euro.[1] In printing ink the pigment is not dissolved, but finely dispersed. Consequently its solid-state properties are maintained. Like most pigments, P.R.57:1 occurs in different crystal phases with different colours. Upon synthesis a trihydrate is formed. Drying at 50 °C generates a monohydrate with magenta shade, which is used for printing inks. The monohydrate is thermally stable up to temperatures higher than 190 °C before it releases water to yield a hygroscopic anhydrous phase with dull dark magenta shade. For all three phases the growth of single crystals is impeded by the low solubility of the pigment in most media. The crystal structures of all three forms were determined from in-house X-ray powder data.[2] The structures were solved by real-space methods with simulated annealing. Subsequently a Rietveld refinement with restraints on bond lengths, bond angles and planar groups was performed. All three phases crystallize in space-group type P21/c, Z = 4. The trihydrate and the monohydrate show eightfold coordination of the Ca ions, the anhydrate a sevenfold one. Apparently the increasing anion-cation interactions lead to the observed colour shift. The arrangement of cations and anions is similar in all three forms. The crystal structures exhibit double layers, one polar, one nonpolar. The polar layer consists of water molecules, calcium ions, sulfonate, keto and carboxylate groups, held together mostly by hydrogen bonds and Coulomb interactions. The nonpolar layer contains naphthalene and toluene moieties.

Simulation of the interaction of terpenes and their oxidation products with ice

26th European Crystallographic Meeting, ECM 26, Darmstadt, 2010 Acta Cryst. (2010). A66, Page s75 s75 After equilibration the obtained structures are analyzed by clustering [2, 4]. It allows us to visualize the relationship between the idealized crystal structures and the obtained crystal structures in a classification tree. In dependence of the conditions we observe structural changes in the different polymorphs in accordance with the experimental phase diagram. At high pressure we find the structures VII and VIII stable, at low pressure ice I.

Absorption and adsorption of ETBE and mesitylene in and on ice

The design, properties and even definitions of cocrystals continue to receive considerable attention. Our understanding of the way in which molecules communicate and assemble is still incomplete, which means that supramolecular synthesis of discrete or extended molecular assemblies held together by noncovalent forces, remains a major fundamental scientific challenge. In this presentation, we outline a hypothesisdriven three-step protocol for the construction of ternary cocrystals and supermolecules where stoichiometry and primary intermolecular interactions can be readily rationalized [1-5].

Simulation of the absorption of acetone on ice at surfaces, bulk ice and small-angle grain boundaries

The thioredoxin redox system, consisting of the thioredoxin protein, thioredoxin reductase and NADPH, is ubiquitous in all living cells and is known to be important in a multitude of biological functions, including cell cycle regulation and maintaining an intracellular reduced state [1]. Studies in various human malignancies and cell lines in vitro have shown an up regulation of thioredoxin and have demonstrated a definite link between thioredoxin and cancer [2], [3]. Thioredoxin levels have also been shown to be raised in the presence of superoxide generating drugs, thus suggesting that inhibition of this redox system may also lead to improved efficiency of these drugs. The crystallisation of a variety of thioredoxin proteins has allowed comparisons to be made between crystal structures of mammalian and bacterial thioredoxins. Studies of existing human thioredoxin complexes have also enabled the understanding of the specificity requirements that thioredoxin has for its target proteins [4]. This has facilitated the design of potential novel inhibitors of the active site of this redox protein. There are currently two novel heteroaromatic quinol inhibitors, which have shown to have activity against thioredoxin, under development at the Cancer Research Laboratories of the University of Nottingham. These inhibitors are thought to have a novel mode of action, each containing a bis-micheal acceptor, allowing them to irreversibly bind to the active site, thus irreparably inactivating the protein. By studying the crystal structure of thioredoxin-inhibitor complex it will be possible to apply structure-activity relationships and thus enable not only the understanding of how these heteroaromatic quinols block the activity of thioredoxin, but also to develop these drugs with the intention of improving their affinity for the binding site. N labelled NMR HSQC experiments have also provided an insite into the binding of these quinols to the thioredoxin active site and thereby facilitating further drug design to improve affinity.