Simulations d'une structure cristalline incommensurable à caractère désordonné

Incommensurate crystal structures do not display three-dimensional periodicity. Discovered in the 1960's, a mathematical model has been established in 1974 only. Incommensurate structures belong to the big family of aperiodic structures. The modulation of incommensurate structures manifests itself as satellite reflections around the main peaks on X-rays diffractograms. Short range order correlations in crystals lead to diffuse scattering between Bragg peaks in the diffraction pattern. The computing power available today allows for very time consuming simulations of the incommensurate or disordered crystal structures. Simulations based on Monte-Carlo and the molecular dynamic techniques have been performed. The former is based on stochastic algorithms, whereas the latter is deterministic. This PhD thesis strove to combine these two methods, using a four-isomermodel, in order to study the incommensurate, disordered polymorph of p-azoxydiphenetol (PAP), which crystallises below 356 K. One of the main features of the PAP molecule is its dative bond. A Monte-Carlo program, using true empirical potentials, has been developed in order to explain the behaviour of PAP. This code (6000 lines), written in C, uses the GSL and OpenMP libraries. Using numerical and experimental tools, this thesis provides explanations for the origin, from an atomic point of view, of the incommensurate and disordered behaviour of PAP. Calculations have been performed on the clusters of École Polytechnique Fédérale de Lausanne. Simulated diffraction patterns have been compared to experimental data, collected before and during this study. Moreover, a set of differential scanning calorimetry (DSC) measurements has been carried out during this work, the results of which have been analysed based on Arrhenius's law. For a better understanding of the role played by the dative bond, and the relation between the complexity of the molecule and the structure, DFT and ab initio calculations have been performed. This work has successfully woven the results from different experimental and numerical techniques into a comprehensive model for this very complex system indeed.

Development of X-Ray Powder Diffraction Methods for Biomolecules

Sebastian Basso

The comparable order of magnitude between interatomic distances in a crystal and the wavelength of X-rays make X-ray crystallography the ideal analytical tool to gain insight into the structure of crystalline material, including biomolecules. Nevertheless, biomolecular crystallography has until now relied on the successful growth of single crystals of suitable size and quality. These remain the exception rather than the rule, since biomolecules often produce polycrystalline precipitate instead. Yet, an interest in making use of the once-discarded polycrystalline material, through the technique of powder diffraction, has only recently emerged. This can be accounted for by the information deficit which powder diffraction data suffers from in comparison with that of single crystal. The paucity of information in powder data stems from the compression of the three-dimensional reciprocal space onto the one-dimension of a powder pattern. In spite of this, powder diffraction holds the potential for application in biomolecular crystallography as is shown in the two different studies presented herein. Both studies were carried out with methods which do not rely on employing previously determined crystal-structures as molecular models. This therefore allowed the objective assessment of the quality of information that powder diffraction data can contribute to the structural investigation of biomolecules. In the first project, the traditional single-crystal structure-solution process is applied to data extracted from protein powder diffraction patterns measured on a synchrotron source. The use of models is avoided by employing the de novo phasing method of isomorphous replacement. With two protein test-cases, namely hen egg white lysozyme and porcine pancreatic elastase, it is demonstrated that protein powder diffraction data can afford structural information up to medium resolution. Indeed, a single isomorphous replacement analysis generated molecular envelopes accurately describing the crystal packing of both protein systems, while a multiple isomorphous replacement experiment, carried out only on lysozyme, revealed an electron density map in which elements of the secondary structure could be located. In fact, the resolution of the latter was discovered to be sufficient to determine the chirality of the protein molecule it represented. In addition to being encouraging, these results do not reflect the full potential of biomolecular powder diffraction, due, in large part, to the ultimately unsuitable nature of one type of phasing method, single crystal, being applied to another type of data, powder. An alternative approach to extract information from protein powder diffraction data is to employ powder-specific structure-solution techniques, such as global optimization methods. Although these methods make use of a starting "model", it is a molecular description of the system under study based on known chemical quantities rather than a related molecular configuration based on a previously determined crystal structure. Since their conception, global optimization methods have continuously been developed to enable the tackling of increasingly complex crystal structures. However, the immense complexity of biomacromolecules has kept proteins well out of reach of such methods. In an attempt to further reduce the gap separating the two levels of complexity, the second study reported herein puts forth the implementation of Ramachandran plot restraints into the algorithm of a global optimization method, i.e. that of simulated annealing. More specifically, the Ramachandran plot was approximated using a two-dimensional Fourier series which was subsequently expressed as a penalty function and incorporated into the search algorithm.

EPFL2011

Development of X-Ray Powder Diffraction Methods for Biomolecules

Sebastian Basso

EPFL2011