Metal-Organic Frameworks in Germany: from Synthesis to Function

Metal-organic frameworks (MOFs) are constructed from a combination of inorganic and organic units to produce materials which display high porosity, among other unique and exciting properties. MOFs have shown promise in many wide-ranging applications, such as catalysis and gas separations. In this review, we highlight MOF research conducted by Germany-based research groups. Specifically, we feature approaches for the synthesis of new MOFs, high-throughput MOF production, advanced characterization methods and examples of advanced functions and properties

New initiators for the ring-opening polymerisation of lactones

This thesis describes the preparation of new yttrium and indium phosphasalen catalysts for the stereocontrolled ring-opening polymerisation of rac-lactide. Systematic ligand modification was performed by changing the size of the phosphine substituents, the identity of the central donor of the diimine bridge, and through increasing the steric bulk at the ortho and para phenolate positions. The coordination chemistry of the final complexes was then explored with full characterisation by multinuclear NMR spectroscopy, elemental analysis or high-resolution mass spectrometry, and in most cases, single crystal X-ray diffraction. Yttrium phosphasalen compounds were found to be active initiators for the ring-opening polymerisation of rac-lactide, affording moderately isotactic polymers. The level of stereocontrol was shown to be influenced by the nature of the phosphine substituents, the diimine bridge, and to a limited extent, the size of the ortho phenolate substituents. The stereocontrol was observed to change when the diimine bridge donor atom was changed, with an NH substituent yielding isotactic enchainment (Pi = 0.72) and an O donor yielding moderately heterotactic (Ps = 0.73) enchainment. Indium phosphasalen compounds were similarly active for ROP, affording isotactic polymers, with one exception, which afforded atactic PLA. The level of stereocontrol was found to correlate with the flexibility of the diimine bridge and largely by the size of the ortho phenolate substituents. In the best cases, highly isotactic polylactide was afforded (Pi = 0.87 at 298 K) concurrent with fast rates, showcasing one of the best performing initiators in the stereocontrolled ring-opening polymerisation of raclactide. Finally, an yttrium phosphasalen complex was applied for the ring-opening polymerisation of three large macrolactones: ω-pentadecalactone (C15), ω-nonadecalactone (C19) and ω- tricosalactone (C23). A comparison is made between yttrium phosphasalen and aluminium salen complexes as initiators for these monomers, showing that with the former, higher rates (minute vs. hour timescales) are observed. The polymerisations of macrolactones are generally more challenging as they are entropically driven, hence the thermodynamic parameters are also uncovered, showing that high conversions (near-quantitative) remain feasible, with molecular weights up to 32 kg mol-1, even using ring sizes up to C23.Open Acces

Analysing Novel Structures of Protein Complexes Requiring the Central Plant Immune Regulator EDS1

Plants as sessile organisms are constantly attacked by pathogens and have evolved a complex immune system to cope with this challenge. The first inducible layer of plant immunity recognises pathogens outside each plant cell and activates a resistance response that is usually sufficient to halt pathogen infection. Many pathogens, however, produce effector molecules that suppress these defences and thus allow successful invasion of the plant. A second layer of plant immunity relies on the specific recognition of these effectors through intracellular immune receptors, the so-called R (resistance) proteins. Effector recognition triggers a fast and strong immune response that is often associated with localised cell death at the site of infection. To prevent spreading cell death and to reduce the cellular costs of an activated immune system, these activities have to be tightly regulated. The nucleo-cytoplasmic protein EDS1, which exists in all higher plant species, has emerged as a central regulator downstream of effector recognition. EDS1 physically interacts with two sequence-related proteins, PAD4 and SAG101, that share an organisation into an N-terminal domain that is related to eukaryotic lipases and a C-terminal domain that has no obvious sequence homologs. The EDS1 protein family, as defined by this organisation, is involved in multiple plant stress signalling pathways. While recent studies have helped to genetically position EDS1, PAD4 and SAG101, their biochemical mode of action remained elusive. To gain mechanistic insights into their functions, the structures of EDS1-containing complexes should be elucidated by means of X-ray crystallography. This thesis describes the preparation of recombinant proteins, their characterisation and the de novo structure solution of a functional complex between EDS1 and SAG101. I found that EDS1, despite being closely related to eukaryotic lipases at sequence and structure level, does not utilise conserved lipase features to bind or process a (lipid-derived) signalling molecule in central immune pathways of the model plant Arabidopsis. The lipase-like half of the protein is rather optimised for protein-protein interactions within the EDS1 family. The interactions between EDS1 and SAG101 were characterised in vitro and in vivo and used to infer a homology model of PAD4. EDS1, PAD4 and SAG101 loss-of-interaction variants were proposed on the basis of this structural information and could be verified experimentally. These will help to further discriminate between the functions of single components and protein complexes within EDS1-dependent pathways. While interactions within the EDS1 protein family are largely driven by the lipase-like half, the C-terminal EP domain is sequentially and structurally unique but reveals a distant relation to proteins that exist in multi-protein complexes. This domain potentially acts as a binding platform for proteins outside the EDS1 family and could gain importance as the number of experimentally characterised EDS1 interactors is constantly growing

Structural studies of two outer membrane proteins: OmpT from Escherichia coli and NspA from Neisseria meningitidis

This Thesis describes the three-dimensional structures of two outer membrane proteins (OMPs), OmpT and NspA, from two pathogenic Gram-negative bacteria. These structures reveal information about the functioning of these proteins and can potentially be used for the design of antimicrobial drugs or vaccines, since they are exposed to the outside of the bacterium. OmpT is present in Escherichia coli, a bacterium that is commensally present in the intestines, and which is the main cause of urinary tract disease. Homologues of OmpT, called omptins, are found in for example Yersinia pestis and Salmonella typhimurium. Omptins are proteases that can cleave extracellular proteins between two consecutive basic amino acids. They are implicated in pathogenicity of several bacteria, since they can cleave plaminogen, which results in fibrinolysis and subsequently the spread of the bacteria. Furthermore, OmpT inactivates defensins, antimicrobial compounds excreted by the epithelial cells of the urinary tract. OmpT had been classified as a serine protease (involving a Ser-His-Asp triad). This classification is, however, controversial. Indeed, site directed mutagenesis studies showed that mutation of Ser99 and His212 led to a significant reduction of catalytic activity. In contrast, commonly used serine protease inhibitors fail to inhibit OmpT activity. Furthermore, OmpT's activity dependent is on the presence of lipopolysaccharide (LPS), a molecule in the outer membrane. To learn more about OmpT's catalytic mechanism and about its LPS dependence, we solved the crystal structure of OmpT (described in chapter 2). The structure reveals a very long ten-stranded b-barrel, with the putative active site in a large cleft at the extracellular extremity. Surprisingly, the earlier identified active site serine and histidine are very far (~9 Å) apart, which questions their involvement in the same catalytic triad. Since, no unambiguous identification of the active site could be made, we investigated the roles of all acidic residues in activity (described in chapter 3). Three acidic residues (Asp83, Asp85 and Asp210) like His212 turned out to be essential for catalysis. Asp210 forms a couple with His212 on one side of the active site that faces the Asp83-Asp85 couple on the other side. We propose that these four residues constitute a catalytic site, which has not been observed in proteases before. Based on this, we propose a novel catalytic mechanism, which involves the activation of a water molecule by the His-Asp couple, similar to the activation of the serine in serine proteases. Furthermore, we propose that the Asp-Asp couple is involved in stabilization of the oxyanion, similar to which is proposed for aspartic proteases. We solved the crystal structure of OmpT in complex with an inhibitor, zinc (described in chapter 4). Although the zinc binding sites are not very specific, this structure does supports our hypothesis on the catalytic site. Also based on the structure of OmpT, and that of another OMP in complex with LPS, we identified an LPS-binding site in OmpT. Based on the location of this site, we conclude that LPS must have an indirect effect on catalysis, for example by inducing a slight conformational change. NspA of Neisseria meningitidis, the main cause of life-threatening meningitis, has been found to be well-conserved and to elicit bactericidal and protective antibodies in mice. These findings makes NspA a very attractive vaccine candidate. We solved the crystal structure of NpsA (described in chapter 5) in order to know the exact three-dimensional conformation of the loop (loop 3) against which the antibodies are directed. This conformation can form the basis for the design of cyclic peptides that adopt this conformation. These peptides may be used as vaccine against Neisseria meningitidis. The structure of NspA furthermore reveals a hydrophobic cleft with a detergent molecule bound. This might be related to the yet unknown function of NspA. In conclusion, the structure NspA can be used as a basis for the design of a vaccine, and the structure of OmpT can form a basis for antimicrobial drug design

Cosmology at Low Frequencies: The 21 cm Transition and the High-Redshift Universe

Observations of the high-redshift Universe with the 21 cm hyperfine line of neutral hydrogen promise to open an entirely new window onto the early phases of cosmic structure formation. Here we review the physics of the 21 cm transition, focusing on processes relevant at high redshifts, and describe the insights to be gained from such observations. These include measuring the matter power spectrum at z~50, observing the formation of the cosmic web and the first luminous sources, and mapping the reionization of the intergalactic medium. The epoch of reionization is of particular interest, because large HII regions will seed substantial fluctuations in the 21 cm background. We also discuss the experimental challenges involved in detecting this signal, with an emphasis on the Galactic and extragalactic foregrounds. These increase rapidly toward low frequencies and are especially severe for the highest redshift applications. Assuming that these difficulties can be overcome, the redshifted 21 cm line will offer unique insight into the high-redshift Universe, complementing other probes but providing the only direct, three-dimensional view of structure formation from z~200 to z~6.Comment: extended review accepted by Physics Reports, 207 pages, 44 figures (some low resolution); version with high resolution figures available at http://pantheon.yale.edu/~srf28/21cm/index.htm; minor changes to match published versio

Solvothermal Preparation and Characterization of Superstructures of Nanoscopic CdS and CdSe

Micrometer-sized superparticles, self-assembled from metallic or semiconducting nanoclusters, can be used as convenient building blocks for preparing functional materials, utilizing the electronic and photophysical properties resulting from the quantum confinement as well as from the coupling between individual nanoscopic constituents. This research aimed at developing a novel approach utilizing the conversion of a cadmium phenylchalcogenolate precursor (Me4N)2[Cd(EPh)4] (where E = S or Se) under solvothermal conditions for the preparation of nanoscopic CdE, including both crystalline superlattices of large discrete nanoclusters and superstructures with more complex morphology. In particular, 3D cubic superlattices of molecular CdS nanoclusters of 1.9 and 2.3 nm in diameter were prepared and characterized by a set of techniques, including UV−vis absorption and photoluminescence studies under various conditions, Raman spectroscopy, and thermogravimetric analysis. Structural information was obtained by methods complementary to single crystal X-ray diffraction such as 111Cd SSNMR spectroscopy, electron microscopy, and electron tomographic reconstruction. Observed structural features demonstrate the significance of the prepared materials as a transition point from known families of smaller CdS nanoclusters to unexplored larger ones. Even more unusual 3D superstructures comprised of nanoscopic constituents, i.e., spherical CdS superparticles and porous CdSe single crystal, were reported and possible mechanisms of formation were discussed. The importance of this research lies in improving the ability to manipulate the size and organization of primary nanocluster building blocks into particular superstructures and to tailor the photophysical properties of the resulting material, which enables the creation of new multifunctional systems and broadens potential areas of application