3 search hits
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Modulation of Incommensurately Modulated Structures Studied by the Maximum Entropy Method
(2011)
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Li Liang
- In this thesis, modulated properties of incommensurately modulated crystals are studied by the Maximum Entropy Method (MEM). This was done exemplarily on the compounds Rubidium tetrachlorozincate and Chromium pyrophosphate. To do so, the MEM derived (3+1)-dimensional superspace electron density was analysed to receive information on atomic positions and their modulation, and structure refinement by the method of least-squares and interpretation of the difference-Fourier maps were performed to better describe the atomic displacement parameters (ADPs) and to improve the applied structural models. All the MEM calculations are done by the computer program BayMEM. The analysis of this MEM reconstructed density map is done by the computer program EDMA. Our results suggest that the modulation of harmonic ADPs, anharmonic ADPs and its modulation form an intrinsic part of incommensurately modulated structures. We have shown that with a data set of certain resolution and satellite reflections of higher order, the inclusion of modulation of harmonic ADPs, the anharmonic ADPs and the modulation of anharmonic ADPs can significantly improve the fit of the structure model to the diffraction data. Such model then better represents the true nature of the structure under investigation.
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Accurate charge densities of amino acids and peptides by the Maximum Entropy Method
(2008)
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Jeanette Netzel
- In the present thesis accurate charge densities of several amino acids and peptides have been reconstructed by the Maximum Entropy Method (MEM) to study chemical bonds. The MEM model-independently determines the most probable electron density, which simultaneously maximizes the information entropy and fits the X-ray diffraction data. The quality of the MEM densities is enhanced by several extensions to the MEM such as the use of a non-uniform prior-density, the employment of the method of prior-derived F-constraint, static weighting and the choice of the optimal stopping criterion for the MEM iterations. The latter is achieved by inspection of difference Fourier maps and dynamic deformation maps. The reconstructed electron densities have been analyzed according to Baders Atoms in Molecules (AIM) theory to derive information about chemical bonds, in particular covalent bonds and hydrogen bonds. Local maxima of the densities, their associated atomic basins and charges, bond critical points (BCPs) and their densities and second derivatives, i.e. the eigenvalues and the Laplacians, have been determined according to the AIM theory. For all studied compounds it is shown that, providing the employment of the extensions to the MEM, the densities obtained from the MEM exhibit similar properties as those obtained from the multipole method. However, it is demonstrated that the features of hydrogen bonds are described more convincingly by the MEM than by the multipole method. By comparison of densities at BCPs from the MEM with the corresponding values from multipole refinement and from quantum chemical calculations it is shown that each method produces similar densities at BCPs. For all studied compounds it is demonstrated that for MEM densities, densities at BCPs of hydrogen bonds possess a larger magnitude than corresponding values from densities by the multipole method, while the opposite is true for covalent bonds. The values of the Laplacians at BCPs, especially of C–O bonds, show larger discrepancies between values from the MEM and from multipole refinement. These differences are caused by thermal motion which is present in dynamic MEM densities, but absent in static densities produced by the multipole method. The results of the extensive study of electron densities of amino acids and tripeptides show that densities and energetic properties at BCPs of covalent bonds and hydrogen bonds depend exponentially on their bond lengths. The functions of the dependencies of the densities on the bond lengths differ from the corresponding functions fitted to values from the multipole method. It is demonstrated that the ratio of the potential and kinetic energy densities at BCPs of hydrogen bonds reveals the possibility to classify them according to the distance between hydrogen atom and acceptor atom. Short hydrogen bonds possess covalent character, hydrogen bonds with intermediate distance have a mixed covalent-ionic character and long hydrogen bonds are ionic. This classification coincides with the usual classification of strong, intermediate and weak hydrogen bonds as proposed in the literature. The studied hydrogen bonds are classified as possessing mainly a mixed covalent-ionic character. However, for covalent bonds a classification according to the bond lengths does not suffice to characterize them. The results of the amino acids and tripeptides indicate that the prior density contributes a large part to the densities at BCPs. However, for the Laplacians and the energy densities at BCPs the differences between MEM and prior densities are larger than for the densities at BCPs. Densities at BCPs of hydrogen bonds from MEM densities show a different trend in their dependence on the bond distance than corresponding trends from prior densities. Thus, it is demonstrated that the analysis of the true density instead of the prior or procrystal density is recommended in order to extract information about chemical bonding. It is concluded from the results of the Accurate Charge Density studies reported in the present thesis, that the MEM allows a good characterization of chemical bonds and describes the electron density of hydrogen bonds more realistic than the multipole model. Chapter 3 of the present thesis has been published in Acta Crystallogr. B, 63, 285–295 (2007) and is reproduced with permission of the International Union of Crystallography (http://journals.iucr.org). Chapter 4 of the present thesis has been published in CrystEngComm, 10, 335–343 (2008) and is reproduced with permission of The Royal Society of Chemistry (RSC) (http://www.rsc.org).
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Maximum Entropy Method in Superspace Crystallography
(2003)
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Lukas Palatinus
- This thesis discusses several aspects of the combination of the Maximum Entropy Method (MEM) for the reconstructions of the electron density with the superspace approach to the description of structures of aperiodic crystals. It is shown that the MEM in superspace provides a parameter-free reconstruction of the modulation functions with sufficient accuracy. The MEM in superspace has been applied to diffraction data of several compounds. The computer program BayMEM was developed for this purpose. BayMEM allows electron densities of the ordinary 3D structures and the superspace electron densities of the aperiodic structures to be reconstructed using the same general principles. The program has been extended by adding features improving its versatility and accuracy of the results. The improvements include attaching of the set of subroutines MemSys5 to BayMEM, implementation of the method of the Generalized F-constraints and the static weighting, implementation of the G-constraints, of the Prior-derived F-constraints and of the two-channel entropy. The second major computer program EDMA is a software tool for analysis of the electron densities in arbitrary dimension. The program analyzes the MEM electron density and extracts quantitative information about the atoms according to Bader's formalism “Atoms in molecules“. Two new variants of the constraints in the MEM have been developed in order to solve the problems with artifacts in the MEM reconstructions. The two methods are the Generalized F-constraints and the Prior-derived F-constraints. The concept of the Generalized F-constraints is based in the observation, that the standard F-constraint is not sufficiently strong to constrain the histogram of the normalized residuals of the structure factors to the expected Gaussian shape. Higher moments of the distribution of the normalized residuals were therefore used as the constraint in the MEM calculations. With these constraints significantly improved histograms were obtained. The source of some artifacts in the MEM electron densities was identified to be the tendency of the MEM to estimate incorrectly those structure factors, that are not included in the experimental dataset. It is shown that the missing structure factors can successfully be replaced by the structure factors derived from the procrystal electron density. If the structure factors derived from the procrystal prior electron density (the Prior-derived F-constraints) are used as additional constraints in the MEM calculation, the result is free of sharp artifacts and the quality of the reconstruction of the electron density is comparable with the results of multipole refinements. To test the accuracy of the MEM in superspace, the method was applied to the dataset of the misfit-layer composite structure of (LaS)1.14NbS2. It has been shown, that the MEM on the model structure factors reproduces the model modulation functions with accuracy better that 10% of the pixel size of the grid, on which the electron density was sampled. The structure of the high-pressure phase III of Bi provided a prominent example illustrating the advantages of the MEM in superspace over the standard structure refinements. The MEM in superspace was applied to the diffraction data of Bi-III to extract more information about the modulation than obtained from the standard structure refinement. The modulation functions extracted from the MEM electron density revealed a block-wave-like shape of the modulation function of the Bi atom of the host structure that indicates shifts of the atom between two stable environments rather than smooth harmonic variation of the position indicated by the modulation function from the standard refinement. Secondly, the MEM modulation function of the Bi atoms in channels allowed to better understand the nature of the most prominent feature of the modulated structure - the occurrence of the pairs of Bi atoms along the channels. The incommensurately modulated structure of ammonium tetrafluoroberyllate (NH4)2BeF4, stable between 175K and 182K, was solved and refined in superspace. The known two-fold low-temperature superstructure of (NH4)2BeF4, that is stable below 175K has been described in superspace as a commensurately modulated structure. With aid of this description the close relationship between the two structures has been found. The MEM was applied to the incommensurate structure to test the appropriateness of the refined harmonic structure model. The MEM has shown that the harmonic model is very accurate. The MEM in superspace was established in this thesis as a reliable tool for the structure solutions of the modulated structure. The individual chapters together form a framework that allows to use the MEM in superspace to extract novel information from the diffraction data of both the periodic and aperiodic structures, that cannot be obtained from the structure refinements.
