NMR Spectroscopic Investigations on Zintl Anions, Palladium Complexes, and Non-Classical Fullerene Topology

In this thesis the focus lied on the NMR spectroscopic investigation of silicon Zintl anions in solution. Surprisingly, despite other Zintl anions of different homologues being well studied in solid-state, the silicon Zintl phases have been elusive for detailed studies in solution thus far. By enrichment of 29Si (the only NMR active isotope for silicon), NMR spectroscopy as a tool for the investigation of their behavior became accessible. Three novel silicon cluster species are presented in this thesis. Furthermore, three endohedral 12-vertex tin-antimony clusters were characterized. Diffusion-ordered spectroscopy (DOSY) was used as a tool for the detection of supramolecular aggregates. Lastly, the first experimental approach for measurement of dispersive interactions in phosphoramidite palladium complexes was discussed. In chapter two the unprecedented protonated [HSi9]3– cluster was characterized. Using elegant 1D and 2D NMR spectroscopic methods, such as 1H29Si DEPT, 1H29Si HMQC and chemical exchange saturation transfer (CEST) experiments, the complete spin system of this unexpected species was found. Here, two resonances in the 29Si spectra were observed, i.e. one for the protonated Si-H moiety and one averaged for eight silicon atoms of a single Si8 entity. This was also verified by the observed coupling pattern (doublet of nonets at δ = -158.5 ppm for Si-H with 1JSiH = 156 Hz, = 22 Hz; and a doublet of doublets at δ = -358.5 ppm for the Si8 entity with = 22 Hz, = 3 Hz). Comparison of theoretical calculations for the chemical shifts and the scalar coupling constants with the experimental values showed good agreement. Only the calculated coupling constants involving the Si-H moiety significantly deviated from the experimental ones. Indeed, CEST experiments revealed a H hopping process that leads to the observed reduced coupling constants, which was also corroborated by theoretical calculations. Additionally, theoretical calculations predicted two possible scrambling processes for the averaging of the Si8 entity, which in combination leads to a complete scrambling of all silicon atoms. In conclusion, the highly dynamic behavior of the protonated [HSi9]3– cluster was demonstrated, that was previously thought of being rigid owing to the relative strong Si-Si bonds. Chapter three focuses on two additional silicon clusters found in solution, i.e. [µ-HSi4]3– and [Si5]2–. For [µ-HSi4]3– two 29Si resonances at δ = -327.8 ppm and δ = -404.5 ppm were observed. The former shows a triplet pattern (1JSi-Si = 45 Hz), the latter a doublet of triplets (1JSi-Si = 45 Hz, 1JSi-H = 12 Hz). Together with the extremely upfield shifted 1H resonance (triplet at δ = -10.61 ppm with 1JSi-H = 12 Hz) the structure of this protonated cluster was revealed to be a tetrahedral [Si4]4– with an H atom being bridged over two vertices of the silicon tetrahedron. Thus, this bridging protonation mode depicts the missing link to borane chemistry. ELI-D and NBO analysis predicted the formation of a 3c-2e bond between Si H Si being the driving force in the protonation of [Si4]4– enabling the delocalization of the highly negative charges in the cluster. For the trigonal bipyramidal [Si5]2– cluster two 29Si resonances were observed, i.e. a quartet at δ = +348.7 ppm and a triplet at δ = -347.8 ppm (1JSiSi = 41.8 Hz). Again, ELI-D and NBO analysis were performed, that revealed a non-classical Lewis structure with six electron-deficient 3c-2e bonds over each face of the cluster being highly delocalized. Thus, theoretical protonation in any position (terminally or bridging) leads to massive destabilization. In conclusion, delocalization of electrons proves to be the deciding factor for the easily achievable protonation of [Si4]4– and the unlikely protonation of [Si5]2–. Chapter four focuses on the synthesis and characterization of three new ternary intermetalloid clusters, i.e. the asymmetrically occupied endohedral 12-vertex cluster [Co@Sn6Rb6]3–, fully occupied [Co2@Sn5Sb7]3–, and [Ni2@Sn7Sb5]3–. Theoretical calculations and preliminary 119Sn NMR measurements were performed to investigate their behaviour in solution revealing their presence in solution. Chapter five and six focus on the synthesis and characterization of supramolecules beyond the fullerene topology. In chapter five P5 building blocks, i.e. CpBn-substituted pentaphosphaferrocene [CpBnFe(η5-P5)], were used. By self-assembly with copper(I) iodide spherical supramolecular aggregates are achieved. The inorganic scaffold consists of cyclo-P5 units and an expanded CuI framework with partial occupancies of few copper and iodine positions. It does not follow the fullerene-topology, because the CuI ladder structural motif provides no six-membered units, although twelve cyclo-P5 rings are present. The CpBn substituents enhance the solubility of these supramolecules thus, enabling NMR spectroscopic and MS investigations. Diffusion-ordered spectroscopy (DOSY) yielded a hydrodynamic radius rH of 20.72 Å, which is in line with the crystal-derived radius of 18.5 Å. Thus, clearly indicating the supramolecule being present and stable in solution. Chapter six addresses the reaction of cyclo-P4 building blocks, i.e. [CpRTa(CO)2(η4-P4)] (with CpR = Cp´´ or Cp´´´), with copper(I) halides yielding unprecedented supramolecules; truncated octahedrons, a peanut-shaped and a pear-shaped supramolecule. The reaction of the sterically more demanding Cp´´´-substituted cyclo-P4 building blocks with either copper(I) chloride or bromide yielded two truncated octahedron supramolecules with appropriate solubilty, thus, enabling NMR investigations. Again, diffusion-ordered spectroscopy (DOSY) was used to investigate their behaviour in solution. The hydrodynamic radii of both supramolecules was estimated to be 10.73 (with CuCl) and 9.45 Å (with CuBr). Despite the hydrodynamic radii being significantly smaller than the crystal-derived radii (12.5 and 12.7 Å, respectively), the DOSY experiments indicate the presence of intact spherical supramolecules in solution. In chapter seven dispersive interactions in phosphoramidite palladium complexes were investigated using the supramolecular balance. A structural change of one of the hetero complexes for the model system was found by theoretical calculations, thus rendering the supramolecular balance not applicable. Therefore, the synthesis of asymmetric phosphoramidite ligands was attempted to ensure the same structure of both hetero complexes

Enhancing Reaction-based de novo Design using Machine Learning

De novo design is a branch of chemoinformatics that is concerned with the rational design of molecular structures with desired properties, which specifically aims at achieving suitable pharmacological and safety profiles when applied to drug design. Scoring, construction, and search methods are the main components that are exploited by de novo design programs to explore the chemical space to encourage the cost-effective design of new chemical entities. In particular, construction methods are concerned with providing strategies for compound generation to address issues such as drug-likeness and synthetic accessibility. Reaction-based de novo design consists of combining building blocks according to transformation rules that are extracted from collections of known reactions, intending to restrict the enumerated chemical space into a manageable number of synthetically accessible structures. The reaction vector is an example of a representation that encodes topological changes occurring in reactions, which has been integrated within a structure generation algorithm to increase the chances of generating molecules that are synthesisable. The general aim of this study was to enhance reaction-based de novo design by developing machine learning approaches that exploit publicly available data on reactions. A series of algorithms for reaction standardisation, fingerprinting, and reaction vector database validation were introduced and applied to generate new data on which the entirety of this work relies. First, these collections were applied to the validation of a new ligand-based design tool. The tool was then used in a case study to design compounds which were eventually synthesised using very similar procedures to those suggested by the structure generator. A reaction classification model and a novel hierarchical labelling system were then developed to introduce the possibility of applying transformations by class. The model was augmented with an algorithm for confidence estimation, and was used to classify two datasets from industry and the literature. Results from the classification suggest that the model can be used effectively to gain insights on the nature of reaction collections. Classified reactions were further processed to build a reaction class recommendation model capable of suggesting appropriate reaction classes to apply to molecules according to their fingerprints. The model was validated, then integrated within the reaction vector-based design framework, which was assessed on its performance against the baseline algorithm. Results from the de novo design experiments indicate that the use of the recommendation model leads to a higher synthetic accessibility and a more efficient management of computational resources

Report / Institute für Physik

The 2016 Report of the Physics Institutes of the Universität Leipzig presents a hopefully interesting overview of our research activities in the past year. It is also testimony of our scientific interaction with colleagues and partners worldwide. We are grateful to our guests for enriching our academic year with their contributions in the colloquium and within our work groups

Large and multi scale mechanistic modeling of Diels-Alder reactions

The [4+2] cycloaddition reaction between conjugated dienes and substituted alkenes is known as the Diels-Alder (DA) reaction, in honor of two German chemists, Otto Diels and Kurt Alder, who first reported this marvelous chemical transformation. The DA reaction is one of the most popular reactions in organic chemistry, allowing for the regio- and stereospecific establishment of six-membered rings with up to four stereogenic centers. This pericyclic reaction has found many applications in areas as diverse as natural products chemistry, polymer chemistry, and agrochemistry. Over the past decades, the mechanism of the Diels-Alder (DA) reaction has been the subject of numerous studies, dealing with questions as diverse as the mechanistic pathway, the synchronicity, the use of catalysts, the effect of solvents and salts, etc. On the other hand, as an example, fullerenes (and particularly [60] fullerene) have been found to act as good dienophiles in DA reactions to the extent that many functionalized fullerenes with interesting applications are still synthesized by reacting C60 with dienes. However, despite the very abundant literature about the mechanism of the DA reaction, some pertinent questions have been still pending, including, without being restricted to, the prediction of transition state (TS) geometries and the modeling of DA reactions involving large systems, such as those of C60 fullerene. It must be emphasized that TSs are not easy to predict and the main reason is that many existing algorithms require that the search is initiated from a good starting point (guess TS), which must be very similar to the actual TS. This problem is even more difficult when many TSs are to be located as may be the case in large-scale studies. Moreover, due to the large size of the C60 molecule, the usage of accurate high-level computational methods in the investigation of its reactivity towards dienes is computationally costly, implying the need to find the best threshold between accuracy and computational cost. Therefore, the present study was carried out to contribute to solving the problems of large-scale prediction of DA transition state geometries and the multi-scale modeling of C60 fullerene DA reactions. To address the first problem (large-scale prediction of TSs), we have developed a python program named “AMADAR”, which predicts an unlimited number of DA transition states, using only the SMILES strings of the cycloadducts. AMADAR is customizable and allows for the description of intramolecular DA reactions as well as systems resulting in competing paths. In addition, The AMADAR tool contains two separate modules that perform reaction force analyses and atomic decomposition of energy derivatives from the predicted Intrinsic Reaction Coordinates (IRC) paths. The performance of AMADAR was assessed using 2000 DA cycloadducts and showed a success rate of ~ 95%. Most of the errors were due to basis set inconsistencies or convergence issues that we are still working on. Furthermore, a set of 150 IRC paths generated by the AMADAR program were analyzed to get insight into the (a)synchronicity of DA reactions. This investigation confirmed that the reaction force constant (second derivatives of the system energy with respect to the reaction coordinate) was a good indicator of synchronicity in DA reactions. A close inspection of the profile of has enabled us to propose an alternative classification of DA reactions based on their synchronicity degree, in terms of (quasi)-synchronous, moderate asynchronous, asynchronous, and likely two-steps DA reactions. Natural population analyses seemed to indicate that the global maximum of the reaction force constant could be identified with the formation of all the bonds in the reaction site. Finally, the atomic resolution of energy derivatives suggested that the mechanism of the DA reaction involves two inner elementary processes associated with the formation of each C-C bond. A striking mechanistic difference between synchronous and asynchronous DA reactions emerging from this study is that, in asynchronous reactions, the driving and retarding forces are mainly caused by the fast and slow-forming bonds (elementary process) respectively, while in the case of synchronous ones both elementary processes retard and drive the process concomitantly and equivalently. Regarding the DA reaction of C60 fullerene that was considered to illustrate the problem of multiscale modeling, we have constructed 12 ONIOM2 and 10 ONIOM3 models combining five semi-empirical methods (AM1, PM3, PM3MM, PDDG, PM6) and the LDA(SVWN) functional in conjunction with the B3LYP/6-31G(d) level. Then, their accuracy and efficiency were assessed in comparison with the pure B3LYP/6-31G(d) level considering first the DA reaction between C60 and cyclopentadiene whose experimental data are available. Further, different DFT functionals were employed in place of the B3LYP functional to describe the higher-layer of the best ONIOM partition, and the results obtained were compared to experimental data. At this step, the ONIOM2(M06-2X/6-31 G(d): SVWN/STO-3G) model, where the higher layer encompasses the diene and pyracyclene portion of C60, was found to provide the best tradeoff between accuracy and cost, with respect to experimental data. This model showed errors lower than 2.6 and 2.0 kcal/mol for the estimation of the activation and reaction enthalpies respectively. We have also demonstrated, by comparing several ONIOM2(DFT/6-31G(d): SVWN/STO-3G) models, the importance of dispersion corrections in the accurate estimation of reaction and activation energies. Finally, we have considered a set of 21 dienes, including anthracene, 1,3-butadiene, 1,3-cyclopentadiene, furan, thiophene, selenothiophene, pyrrole and their mono-cyano and hydroxyl derivatives to get insight into the DA reaction of C60 using the best ONIOM2(M06-2X/6-31 G(d): SVWN/STO-3G) model. For a given diene and its derivatives, the analysis of frontier molecular orbitals provides a consistent explanation for the substituent effect on the activation barrier. It revealed that electron-donating (withdrawing) groups such as -OH (–CN) cut down on the activation barrier of the reaction by lowering (extending) of the HOMOdiene – LUMOC60 gap and consequently enhancing (weakening) the interaction between the two reactants. Further, the decomposition of the activation energy into the strain and interaction components suggested that, for a given diene, electron-donating groups (here –OH) diminish the height of the activation barrier not only by favoring the attractive interaction between the diene and C60, but also by reducing the strain energy of the system; the opposite effect is observed for electron-withdrawing groups (here –CN). In contrast with some previous findings on typical DA reactions, we could not infer any general rule applicable to the entire dataset for the prediction of activation energies because the latter does not correlate well with either of the TS polarity, electrophilicity of the diene, or the reaction energy.Thesis (MSc) -- Faculty of Science, Chemistry, 202

The role of zinc on the chemistry of complex intermetallic compounds

Combining experiments and electronic structure theory provides the framework to design and discover new families of complex intermetallic phases and to understand factors that stabilize both new and known phases. Using solid state synthesis and multiple structural determinations, ferromagnetic β-Mn type Co8+xZn12-x was analyzed for their crystal and electronic structures. Inspection of the atomic arrangements of Co8+xZn12-x reveals that the β-Mn aristotype may be derived from an ordered defect, cubic Laves phase (MgCu2-type) structure. Structural optimization procedures using the Vienna Ab-initio Simulation Package (VASP) and starting from the undistorted, defect Laves phase structure achieved energy minimization at the observed β-Mn structure type, a result which offers greater insights into the &beta-Mn structure type and establishes a closer relationship with the corresponding α-Mn structure (cI58). Continuously, our research moved on Zn-rich γ-brasses Co-Zn system which has a homogeneity range Co2+xZn11-yVacanciesy-x including a small concentration of vacancies as the Co content increased as well as clear site preference of Co atoms in the structure. Inspired by the electronic structure calculated for Co2Zn11, substituting Pd atoms for Zn or Co atoms in the Co-Zn system leads to the discovery of a ferromagnetic (ferrimagnetic) Co2.5Pd2.5Zn8 γ-brass compound. To extend the research on Hume-Rothery phases, &gamma-brasses Fe-Pd-Zn system was also investigate to study the site preference of transition metals in Hume-Rothery phases. Additionally, establishing structure-property relationships for complex metal-rich materials, e.g., thermoelectric, magnetic and superconductors is related to both practical as well as fundamental issues. Cr22Sn24Zn72 and V23.3(1)Sn23.6(1)Zn68.4(1) crystallize in space group Fm3 ̅c, Z = 8, Pearson symbol cF944, with unit cell parameters, respectively, a = 25.184(4) Ã? and 25.080(3) Ã?. Their structures can be described as a cubic NaZn13-type packing of two distinct, yet condensed intermetallic clusters, or a simple cubic packing of I13 clusters condensed via extreme Zn sites with rhombic dodecahedra in the voids. Instead of using transition metals Cr/V, rare earth element, Ce, was also used to react with Zn and Sn. The new cerium-based ternary intermetallic phase, Ce(Sn1-xZnx)6 (0.45(1) \u3c x \u3c 0.49(1)) adopted to CeCu6-type structure. It exhibits a structural transition from orthorhombic to monoclinic around 150 K. Moreover, the magnetic properties of a sample analyzed as CeSn3.33(6)Zn2.67 shows it to be Langegin paramagnetic above 2K