| dc.contributor.advisor | Stalke, Dietmar Prof. Dr. | |
| dc.contributor.author | Hey, Jakob | |
| dc.date.accessioned | 2013-10-11T08:28:52Z | |
| dc.date.available | 2013-10-11T08:28:52Z | |
| dc.date.issued | 2013-10-11 | |
| dc.identifier.uri | http://hdl.handle.net/11858/00-1735-0000-0001-BBE1-7 | |
| dc.identifier.uri | http://dx.doi.org/10.53846/goediss-4081 | |
| dc.language.iso | eng | de |
| dc.publisher | Niedersächsische Staats- und Universitätsbibliothek Göttingen | de |
| dc.rights.uri | http://creativecommons.org/licenses/by-nc-nd/3.0/ | |
| dc.subject.ddc | 540 | de |
| dc.title | From X-ray diffraction data annealing to comprehensive charge density analysis | de |
| dc.type | doctoralThesis | de |
| dc.contributor.referee | Stalke, Dietmar Prof. Dr. | |
| dc.date.examination | 2013-07-01 | |
| dc.description.abstracteng | The current thesis focuses on three detailed experimental QTAIM charge density studies on small molecules based on high resolution X-ray diffraction experiments. Each of the three studies required the application of different analytical methods.
The first of the studies (chapter 3) deals with the experimentally challenging piano stool complex tris(ammine)cyclopentadienyl sodium. The anticipated highly ionic character of the metal–cyclopentadienyl interaction was confirmed by means of the integrated atomic charges and the atomic Source Function contributions in a QTAIM analysis. An out-of-plane bending of the cyclopentadienyl hydrogen atoms, apparently violating traditional theoretical predictions, was experimentally observed. More sophisticated theoretical calculations taking the lattice environment into account were carried out by our cooperation partner Diego Andrada from the Mata workgroup. The calculations exactly reproduced the experimentally observed bending angle. The out-of-plane-bending was explained by the charge reorganization and accumulation on top of the Cp ring, caused by strong intermolecular N–H∙∙∙π interactions with adjacent ammonia molecules. These in-termolecular interactions were visualised by a state-of-the-art Hirshfeld surface analysis and traced by the recently published NCI (non-covalent interactions) method and the Source Function. The results confirm the excellent quality of the acquired data and the appropriateness of the refined model despite a 50:50 disorder in one out of three ammonia groups. Those experimental data might even serve for benchmarking in the development of new, more resilient theoretical methods.
It was demonstrated that the sodium/cyclopentadienyl as well as the N–H∙∙∙π interactions have a strongly polarising effect on the partially delocalised valence density of the cyclopentadienyl anion. This is visible in plots of the deformation density as well as of the Laplacian distribution. It can be postulated that the strength of the polarising effect of the cation and the ammonia protons compete on similar levels.
The second charge density study elucidates the bis(2-benzothiazolyl)phosphane, a sec-ondary phosphane in an unusual tautomeric form. Embarking on the primary goal to characterize the ambiguous character of the P–C bonds (chapter 4), the investigations turned out to have account for the even more general issue of conjugation and heteroaromaticity. The Source Function as a tool for the quantification of delocalisation was evaluated, and the first results on the fuzzy set of heteroaromaticity were presented.
Several complementary measures for aromaticity confirmed the aromaticity of the five- and six-membered rings. They were applied in cooperation with specialists from the Institute of Physical Chemistry (R. A. Mata and J. Dieterich) and from the University of Oslo (H. Fliegl).
It was shown that the interpretation of valence shell charge concentrations as VSEPR-concept lone pairs and the deduction of hybridisation states of third-row elements from these features of the charge density map are accepted in the experimental charge density community. The physical appropriateness of this interpretation was questioned and disproved in this thesis, which is in accordance with other opinions.
Weak intermolecular C–H∙∙∙S and C–H∙∙∙P interactions in the crystal packing of bis-(2-benzothiazolyl)-phosphane were identified as attractive interactions by means of the NCI descriptor. The existence of the corresponding intermolecular bond paths underlines this conclusion.
The experimental charge density study on N-benzyl-2-(hydroxymethyl)benzamide had the aim to provide a rationale for the inert behaviour of this compound towards hydridic reduction agents (chapter 5).
A QTAIM analysis of the benzamide 3 was carried out, confirming the long known electron delocalisation in the bonds of the C(=O)–N amide group by their topological bond orders. No double bond character could be found in the C(amide)–phenyl bond and thus a stabilising conjugation of the amide group to the phenyl ring can be ruled out. A variety of relatively strong intermolecular interactions was characterised, among them two C–H∙∙∙O interactions.
The analysis of the electrostatic potential around the molecule revealed that an envelope of negative potential together with a steric shielding of the positive potential regions by the ortho hydrogen atom of the phenyl ring prevents the reaction of the carboxy carbon atom with hydridic reduction agents.
The last two chapters of this thesis (chapters 6 and 7) deal with some sources of errors in modern single crystal X-ray diffraction experiments:
The problems and the observed irregularities in the data sets from a synchrotron source were shown in chapter 6. Different strategies for data acquisition and data procession were evaluated. A discussion of possible errors was provided and future investigations were suggested.
A hitherto largely neglected flaw in the design of modern focusing optics was subject of chapter 7: the low-energy contamination of the used radiation by total reflection of bremsstrahlung from the target of the X-ray source.
The chapter provided evidence based on data statistics suggesting that the effect of the contamination should not be neglected in the future. A simple filter insert for the beam path of a diffractometer was designed that enables the filtering of the contamination.
Two multipole refinements against datasets of tris(ammine)cyclopentadienyl sodium with and without contamination were compared. While a bond path between the sodium atom and the cyclopentadienyl moiety was observed when the model from the non-contaminated data was analysed, this path was absent in the result from the refinement against contaminated data, which highlighted the importance of accurately measured data.
The current thesis provides several links and cues to possible future projects. Charge density studies are generally considered to be mature, but it became clear that some of the used methods in the analysis of the results require further development. A lot more studies on the delocalisation in heteroaromatic systems using the Source Function and the delocalisation index as the measures for delocalisation are needed.
More investigations are needed to enable the efficient exploitation of the enormous potential of the beamline 15 ID-B at the Advanced Photon Source. The source of the observed error remains unresolved yet, but the range of potential errors has been narrowed down so that the combined efforts of the German (Stalke) and the Danish group (Iversen) will eventually lead to success.
The influence of the low energy contamination in multilayer focused X-ray beams will have to be further investigated. The future will show whether the effect should best be tackled by hardware (filter foils) or by software that remains to be developed. | de |
| dc.contributor.coReferee | Meyer, Franc Prof. Dr. | |
| dc.contributor.thirdReferee | Farrugia, Louis J. Prof Dr | |
| dc.subject.eng | Single xrystal X-ray diffraction | de |
| dc.subject.eng | Charge density analysis | de |
| dc.subject.eng | QTAIM | de |
| dc.subject.eng | Quantum theory of atoms in molecules | de |
| dc.subject.eng | Aromaticity | de |
| dc.identifier.urn | urn:nbn:de:gbv:7-11858/00-1735-0000-0001-BBE1-7-3 | |
| dc.affiliation.institute | Fakultät für Chemie | de |
| dc.subject.gokfull | Chemie (PPN62138352X) | de |
| dc.identifier.ppn | 769803369 | |