Structure determination of organic compounds by a fit to the pair distribution function from scratch without prior indexing.

A method for the ab initio crystal structure determination of organic compounds by a fit to the pair distribution function (PDF), without prior knowledge of lattice parameters and space group, has been developed. The method is called 'PDF-Global-Fit' and is implemented by extension of the program FIDEL (fit with deviating lattice parameters). The structure solution is based on a global optimization approach starting from random structural models in selected space groups. No prior indexing of the powder data is needed. The new method requires only the molecular geometry and a carefully determined PDF. The generated random structures are compared with the experimental PDF and ranked by a similarity measure based on cross-correlation functions. The most promising structure candidates are fitted to the experimental PDF data using a restricted simulated annealing structure solution approach within the program TOPAS, followed by a structure refinement against the PDF to identify the correct crystal structure. With the PDF-Global-Fit it is possible to determine the local structure of crystalline and disordered organic materials, as well as to determine the local structure of unindexable powder patterns, such as nanocrystalline samples, by a fit to the PDF. The success of the method is demonstrated using barbituric acid as an example. The crystal structure of barbituric acid form IV solved and refined by the PDF-Global-Fit is in excellent agreement with the published crystal structure data.

Comparison and evaluation of pair distribution functions, using a similarity measure based on cross-correlation functions.

An approach for the comparison of pair distribution functions (PDFs) has been developed using a similarity measure based on cross-correlation functions. The PDF is very sensitive to changes in the local structure, i.e. small deviations in the structure can cause large signal shifts and significant discrepancies between the PDFs. Therefore, a comparison based on pointwise differences (e.g. R values and difference curves) may lead to the assumption that the investigated PDFs as well as the corresponding structural models are not in agreement at all, whereas a careful visual inspection of the investigated structural models and corresponding PDFs may reveal a relatively good match. To quantify the agreement of different PDFs for those cases an alternative approach is introduced: the similarity measure based on cross-correlation functions. In this paper, the power of this application of the similarity measure to the analysis of PDFs is highlighted. The similarity measure is compared with the classical R wp values as representative of the comparison based on pointwise differences as well as with the Pearson product-moment correlation coefficient, using polymorph IV of barbituric acid as an example.

Absolute Configuration of Pharmaceutical Research Compounds Determined by X-ray Powder Diffraction.

The absolute configuration of active pharmaceutical ingredients (APIs) was determined by generating salts of the active pharmaceutical ingredient (API) with counterions of known chirality, and determining the crystal structures by X-ray powder diffraction. This approach avoids the (often tedious) growth of single crystals, and is successful with very limited quantities of material (less than 1 mg). The feasibility of the method is demonstrated on five examples, and its limitations are discussed as well.

Anionic silicate organic frameworks constructed from hexacoordinate silicon centres.

Crystalline frameworks composed of hexacoordinate silicon species have thus far only been observed in a few high pressure silicate phases. By implementing reversible Si-O chemistry for the crystallization of covalent organic frameworks, we demonstrate the simple one-pot synthesis of silicate organic frameworks based on octahedral dianionic SiO6 building units. Clear evidence of the hexacoordinate environment around the silicon atoms is given by 29Si nuclear magnetic resonance analysis. Characterization by high-resolution powder X-ray diffraction, density functional theory calculation and analysis of the pair-distribution function showed that those anionic frameworks-M2[Si(C16H10O4)1.5], where M = Li, Na, K and C16H10O4 is 9,10-dimethylanthracene-2,3,6,7-tetraolate-crystallize as two-dimensional hexagonal layers stabilized in a fully eclipsed stacking arrangement with pronounced disorder in the stacking direction. Permanent microporosity with high surface area (up to 1,276 m2 g-1) was evidenced by gas-sorption measurements. The negatively charged backbone balanced with extra-framework cations and the permanent microporosity are characteristics that are shared with zeolites.

Towards solution and refinement of organic crystal structures by fitting to the atomic pair distribution function.

A method towards the solution and refinement of organic crystal structures by fitting to the atomic pair distribution function (PDF) is developed. Approximate lattice parameters and molecular geometry must be given as input. The molecule is generally treated as a rigid body. The positions and orientations of the molecules inside the unit cell are optimized starting from random values. The PDF is obtained from carefully measured X-ray powder diffraction data. The method resembles `real-space' methods for structure solution from powder data, but works with PDF data instead of the diffraction pattern itself. As such it may be used in situations where the organic compounds are not long-range-ordered, are poorly crystalline, or nanocrystalline. The procedure was applied to solve and refine the crystal structures of quinacridone (ß phase), naphthalene and allopurinol. In the case of allopurinol it was even possible to successfully solve and refine the structure in P1 with four independent molecules. As an example of a flexible molecule, the crystal structure of paracetamol was refined using restraints for bond lengths, bond angles and selected torsion angles. In all cases, the resulting structures are in excellent agreement with structures from single-crystal data.