Christian Buchsbaum

Microscopic modeling of a spin crossover transition

In spin crossover materials, an abrupt phase transition between a low-spin state and a high-spin (HS) state can be driven by temperature, pressure or by light irradiation. Of special relevance are Fe(II) based coordination polymers where, in contrast to molecular systems, the phase transition between a spin S=0 and 2 state shows a pronounced hysteresis which is desirable for technical applications. A satisfactory microscopic explanation of this large cooperative phenomenon has been sought for a long time. The lack of x-ray data has been one of the reasons for the absence of microscopic studies. In this work, we present an efficient route to prepare reliable model structures and within an ab initio density functional theory analysis and effective model considerations we show that in polymeric spin crossover compounds magnetic exchange between HS Fe(II) centers is as important as elastic couplings for understanding the phase transition. We discuss the relevance of these interactions for the cooperative behavior in these materials.

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.

Rietveld refinement of a wrong crystal structure.

Rietveld refinements are generally used to confirm crystal structures solved from powder diffraction data. If the Rietveld refinement converges with low R values and with a smooth difference curve, and the structure looks chemically sensible, the resulting structure is generally considered to be close to the correct crystal structure. Here we present a counter example: The Rietveld refinement of the X-ray powder pattern of gamma-quinacridone with the crystal structure of beta-quinacridone gives quite a smooth difference curve; the resulting crystal structure looks reasonable in terms of molecular conformation, molecular packing and intermolecular hydrogen bonds. However, neither the lattice parameters, the molecular packing nor the conformation of the molecules show any similarity with the actual structure, which was determined from single-crystal data. This example shows that a successful Rietveld refinement is not always final proof of the correctness of a crystal structure; in special cases the resulting crystal structure may still be wrong.

Pigment Orange 5 : crystal structure determination from a non-indexed X-ray powder diagram

Pigment Orange 5, also known as “Dinitroaniline Orange”, is an industrially produced azo pigment. The structure was solved from routinely measured lab X-ray powder data without indexing, by means of a newly developed combination of lattice energy minimization and simultaneous fit to the X-ray powder diagram. Finally, the structure was refined by Rietveld methods using restraints. Pigment Orange 5 crystallizes in space group P21/a with a = 16.365(5) Å, b = 12.874(4) Å, c = 6.924(2) Å, β = 100.143(2)°, Z = 2. The molecules are almost planar and form stacks along the c axis.

Structure determination of 6,6′-bis(trifluoromethyl)-thiazine-indigo from laboratory powder data and lattice-energy minimisation

Abstract 6,6′-bis(trifluoromethyl)-thiazine-indigo, C18H8F6N2O2S2, is a yellow derivative of the thiazine-indigo pigments. Due to its insolubility single crystals could not be grown; the structure had to be determined from powder diffraction data. The X-ray powder pattern – measured on a laboratory diffractometer in routine manner – could be indexed, although the crystallite size was only about 20 nm. The crystal struc ture was solved by lattice-energy minimisation using the program CRYSCA. Subsequently, the structure was refined by the Rietveld method using restraints. The compound crys tallises in space group P21/c with a = 15.4136(12), b = 7.8384(5), c = 7.7102(6) Å, β = 112.736(6)°, Z = 2, with molecules on inversion centres. The molecules are connected by double hydrogen bonds, resulting in planar chains. These chains form stacks in [001] direction. The density is unusually high (ϱ = 1.7875 g/cm3), this explains the observed insolubility of the compound.

Crystal structures of thiazine-indigo pigments, determined from single-crystal and powder diffraction data

Abstract The crystal structures of two polymorphs of thiazine-indigo, C16H10N2O2S2 were determined by single crystal X-ray diffraction. 7,7′-dimethyl-thiazine-indigo, 7,7′-dimethoxy-thiazine-indigo and 7-monochloro-thiazine-indigo are isostructural to β-thiazine-indigo and 7,7′-dichloro-thiazine-indigo; their structures are refined by Rietveld methods. 7-monochloro-thiazine-indigo shows a head-to-tail-disorder. 6,6′-bis(trifluoromethyl)-thiazine-indigo is not isotypic to any other thiazine-indigo compound. Polymorph screenings were performed; three of the six compounds are polymorphic. In all determined structures the molecules are essentially planar; all molecules are connected by double hydrogen bonds to form parallel chains, but there are three different arrangement of chains. The structures are compared with the chain-structures of other organic pigments like indigo, quinacridone and diketopyrrolopyrrole derivatives.

Data Bases, the Base for Data Mining

Data collections provide a basis for solving numerous problems by data mining approach. The advantages of data mining consists in the retrieving of a new knowledge from existing information. The comprehensiveness of the data collection, the structure and quality of the data, and the selection of relevant data sets are extremely important to get correct results. In the crystallographic field, scientists will find several databases dealing with crystal structures of inorganic and organic compounds, or proteins. Usually databases have detailed data evaluation mechanisms integrated in their database production process and offer comprehensive and reliable data sets. The CIF standard enables the scientists to exchange the data. As an example, the Inorganic Crystal Structure Database (ICSD), a source of information for crystallographers, mineralogists, physicists, and chemists will be presented here. The ICSD contains about 120,000 entries (March 2009) of fully determined crystal structures. This chapter gives a detailed description of data collection, the contents of the data fields, data evaluation, and finally search the functionality of the ICSD database.

Crystal-structure determination of the fluorescent bisazomethine pigment C36H26N4O4 from X-ray powder data

The compound C36H26N4O4, a derivative of Pigment Yellow 101, is one of the few organic pigments that show fluorescence in the solid state. Since single crystals could not be grown, the structure was determined from powder data. The X-ray powder pattern could be indexed with an orthorhombic unit cell. The space group remained ambiguous. The crystal structure was solved by lattice energy minimisation in different space groups using the program CRYSCA. Subsequently, the structure was refined by the Rietveld method using restraints. The compound crystallises in a herringbone pattern in Pbcn with a = 30.117(1) Å, b = 9.723(2) Å, c = 9.511(3) Å, Z = 4 with the molecule on an inversion centre. The insolubility and the solid-state fluorescence can be explained from the crystal structure.

Cu-based metalorganic systems: an ab initio study of the electronic structure

Within a first principles framework, we study the electronic structure of the recently synthesized polymeric coordination compound Cu(II)-2,5-bis(pyrazol-1-yl)-1,4-dihydroxybenzene (CuCCP), which has been suggested to be a good realization of a Heisenberg spin-1/2 chain with antiferromagnetic coupling. By using a combination of classical with ab initio quantum mechanical methods, we design on the computer reliable modified structures of CuCCP aimed at studying effects of Cu–Cu coupling strength variations on this spin-1/2 system. For this purpose, we performed two types of modifications on CuCCP. In one case, we replaced H in the linker by (i) an electron donating group (NH2) and (ii) an electron withdrawing group (CN), while the other modification consisted of adding H2O and NH3 molecules in the structure which change the local coordination of the Cu(II) ions. With the Nth order muffin tin orbital (NMTO) downfolding method, we provide a quantitative analysis of the modified electronic structure and the nature of the Cu–Cu interaction paths in these new structures and discuss its implications for the underlying microscopic model.