This thesis concerns the development of software techniques for polycrystalline fibre diffraction analysis and the application of the techniques to the determination of the structures of target molecules. Fibre diffraction analysis is one of a powerful method for determining the structure of polycrystalline fibres. However, one of the main shortcomings of this method is the paucity of intensity data; the observed intensities need to be modelled using suitable methods. This particular problem is further complicated by the fact that no direct Fourier synthesis methods can be used because of the cylindrical averaging inherent in fibre diffraction patterns. An attractive strategy is to use software programs for performing semi-automated data extraction from fibre diffraction patterns using refined method of data stripping and modelling. Even though there are some software packages available to do part of this, process the best one, the CCP13 suite, required a great deal of improvement and development. In this thesis, the design, development and applicability of such a software package, FibreFix, are described. Using several practical examples, we show how this software package has aided in solving practical structure-determination problems. Covered in the thesis are: (i) Development,of several techniques as part of the CCP13 software for performing data stripping and structure analysis; (ii) Design and development of a new integrated CCP13 software package, FibreFix, incorporating these techniques; (iii) Evaluation of FibreFix to show that the analysis and modelling processes in data reduction for fibre diffraction can be simplified substantially using the FibreFix software. To show this two different, but related, case studies are described: crystalline natural rubber and E-DNA. Our results show that the structures modelled by the software package are well above our threshold for satisfactory modelling. This claim is supported by very satisfactory X-ray amplitude fitness and in reduction in the R-factor of the models. We have analysed the structure of oriented natural rubber, obtaining a very good fit with the observed X-ray amplitudes and a best R factor of 0.18. We have also analysed different possible models for E-DNA. The R-factors indicate that 172 D-DNA-like models are better than 152 models. We have a found a satisfactory structure for E-DNA, which gives a good fit with the X-ray amplitudes and a best R-factor 0f 28%. This project has substantially, improved the CCP13 fibre analysis software, now all incorporated within FibreFix, which can be used for data stripping of many forms of fibre diffraction pattern. The structures of rubber and E-DNA have also been used as targets to utilize and enhance the capability of the LALS (linked atom least-squares) modelling and refinement program.
| Identifer | oai:union.ndltd.org:bl.uk/oai:ethos.bl.uk:487950 |
| Date | January 2008 |
| Creators | Rajkumar, Ganeshalingam |
| Publisher | Imperial College London |
| Source Sets | Ethos UK |
| Detected Language | English |
| Type | Electronic Thesis or Dissertation |
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