Relating the chemical reactivity of supramolecular hydrogelators and the physical properties of their gels

This thesis reports a number of studies that examines low molecular weight hydrogelators forming through in situ chemical reactions and gel the water in which this reaction occurs. This in situ gelation process has allowed a number of chemical and physical reactions and assembly processes to be investigated. Pathway complexity, an exciting concept within chemical systems has been explored with a multi-reactive hydrazone based gelation system that allows different gels to be formed from a single starting point through navigation of the systems’ energy landscape. This work inspired the development of a large family of imine based gelators that would undergo an effectively irreversible tautomerisation. This allowed exploration and characterisation of the systems’ ability to self-sort and co-assemble, at both the molecular and macroscopic level. One particular imine inspired gelator featured a much slower in situ reaction. This allowed characterisation of its reaction kinetics and demonstrated its autocatalytic behaviour. This thesis highlights the link between the chemical reactions that form the individual gelator molecules and the supramolecular assembly process. By using one to control the other, an in-depth understanding of the presented systems has been developed, allowing for the accurate targeting of desired physical properties

A mathematical model for mechanically-induced deterioration of the binder in lithium-ion electrodes

This study is concerned with modeling detrimental deformations of the binder phase within lithium-ion batteries that occur during cell assembly and usage. A two-dimensional poroviscoelastic model for the mechanical behavior of porous electrodes is formulated and posed on a geometry corresponding to a thin rectangular electrode, with a regular square array of microscopic circular electrode particles, stuck to a rigid base formed by the current collector. Deformation is forced both by (i) electrolyte absorption driven binder swelling, and; (ii) cyclic growth and shrinkage of electrode particles as the battery is charged and discharged. The governing equations are upscaled in order to obtain macroscopic effective-medium equations. A solution to these equations is obtained, in the asymptotic limit that the height of the rectangular electrode is much smaller than its width, that shows the macroscopic deformation is one-dimensional. The confinement of macroscopic deformations to one dimension is used to obtain boundary conditions on the microscopic problem for the deformations in a 'unit cell' centered on a single electrode particle. The resulting microscale problem is solved using numerical (finite element) techniques. The two different forcing mechanisms are found to cause distinctly different patterns of deformation within the microstructure. Swelling of the binder induces stresses that tend to lead to binder delamination from the electrode particle surfaces in a direction parallel to the current collector, whilst cycling causes stresses that tend to lead to delamination orthogonal to that caused by swelling. The differences between the cycling-induced damage in both: (i) anodes and cathodes, and; (ii) fast and slow cycling are discussed. Finally, the model predictions are compared to microscopy images of nickel manganese cobalt oxide cathodes and a qualitative agreement is found.Comment: 25 pages, 11 figure

Role of MrgA in Peroxide and Light Stress in the Cyanobacterium Synechocystis sp. PCC 6803.

In the unicellular cyanobacterium Synechocystis sp. PCC 6803, the mrgA gene is part of the PerR regulon that is upregulated during peroxide stress. We determined that an ΔmrgA mutant was highly sensitive to low peroxide levels and that the mutant upregulated a gene cluster (sll1722-26) that encoded enzymes involved with exopolymeric substance (EPS) production. We made mutants in this EPS cluster in both a wild type and ΔmrgA background and studied the responses to oxidative stress by measuring cell damage with LIVE/DEAD stain. We show that Synechocystis sp. PCC 6803 becomes highly sensitive to oxidative stress when either mrgA or the sll1722-26 EPS components are deleted. The results suggest that the deletion of the EPS cluster makes a cell highly susceptible to cell damage, under moderate oxidative stress conditions. Mutations in either mrgA or the EPS cluster also result in cells that are more light and peroxide sensitive, and produce significantly less EPS material than in wild type. In this study, we show that in the absence of MrgA, which is known to be involved in the storage or mobilization of iron, cells can be more easily damaged by exogenous oxidative and light stress

Targetable Mechanical Properties by Switching between Self-Sorting and Co-assembly with In Situ Formed Tripodal Ketoenamine Supramolecular Hydrogels

A new family of supramolecular hydrogelators are introduced in which self-sorting and co-assembly can be utilised in the tuneability of the mechanical properties of the materials, a property closely tied to the nanostructure of the gel network. The in situ reactivity of the components of the gelators allows for system chemistry concepts to be applied to the formation of the gels and shows that molecular properties, and not necessarily the chemical identity, determines some gel properties in these family of gels

A homogenization study of the effects of cycling on the electronic conductivity of commercial lithium-ion battery cathodes

State-of-the-art image acquisition, image analysis, and modern homogenization theory are used to study the effects of cycling on commercial lithium-ion battery cathodes’ ability to conduct electronic current. This framework allows for a rigorous computation of an effective, or macroscale, electronic conductivity given an arbitrarily complicated three-dimensional microstructure comprised of three different material phases, i.e., active material, binder (polymer mixed with conductive carbon black), and electrolyte. The approach explicitly takes into account the geometry and is thus a vast improvement over the commonly used Bruggeman approximation. We apply our framework to two different types of lithium-ion battery cathodes before and after cycling. This leads us to predict an appreciable decrease in the effective electronic conductivity as a direct result of cycling. In addition, we present an ad-hoc “neighbor counting” methodology which meaningfully quantifies the effect of binder detaching from the surface of the active material due to the internal mechanical stresses experienced under operating conditions, thereby supporting the results of the homogenization calculations

Supramolecular Amino Acid Based Hydrogels: Probing the Contribution of Additive Molecules using NMR Spectroscopy

Supramolecular hydrogels are composed of self-assembled solid networks that restrict the flow of water. l-Phenylalanine is the smallest molecule reported to date to form gel networks in water, and it is of particular interest due to its crystalline gel state. Single and multi-component hydrogels of l-phenylalanine are used herein as model materials to develop an NMR-based analytical approach to gain insight into the mechanisms of supramolecular gelation. Structure and composition of the gel fibres were probed using PXRD, solid-state NMR experiments and microscopic techniques. Solution-state NMR studies probed the properties of free gelator molecules in an equilibrium with bound molecules. The dynamics of exchange at the gel/solution interfaces was investigated further using high-resolution magic angle spinning (HR-MAS) and saturation transfer difference (STD) NMR experiments. This approach allowed the identification of which additive molecules contributed in modifying the material properties

Halogen effects on the solid-state packing of phenylalanine derivatives and the resultant gelation properties

Phenylalanine is an important amino acid both biologically, essential to human health, and industrially, as a building block of artificial sweeteners. Our interest in this particular amino acid and its derivatives lies with its ability to form gels in a number of solvents. We present here the studies of the influence of halogen addition to the aromatic ring on the gelation properties and we analyse the crystal structures of a number of these materials to elucidate the trends in their behaviour based on the halogen addition to the aromatic group and the interactions that result

The Plot Thickens: Gelation by Phenylalanine in Water and Dimethyl Sulfoxide

Phenylalanine (Phe) is an amino acid of great interest as coupling of an aromatic group with a chiral hydrophilic region imparts a number of unique properties. Recently there has been an increased interest in the crystalline and gel forms of this compound, part as a result of the complex and undetermined structures of the resulting materials and the relationship of the solid forms of Phe with the disease phenylketonuria. In this report, we highlight the relationship between gelation, crystallization, and the dynamics of self-assembly processes of Phe. We do this by describing the gelation of the amino acid, the gel to crystal relationship, crystal structure predictions for this relatively simple compound, and the dynamics of assembly as determined by NMR in both water and dimethyl sulfoxide. This will provide guidance to future research into Phe assemblies, possible treatments for phenylketonuria, and diseases related to formation of amyloid-like fibers

Gelation Landscape Engineering Using a Multi-Reaction Supramolecular Hydrogelator System

Simultaneous control of the kinetics and thermodynamics of two different types of covalent chemistry allows pathway selectivity in the formation of hydrogelating molecules from a complex reaction network. This can lead to a range of hydrogel materials with vastly different properties, starting from a set of simple starting compounds and reaction conditions. Chemical reaction between a trialdehyde and the tuberculosis drug isoniazid can form one, two, or three hydrazone connectivity products, meaning kinetic gelation pathways can be addressed. Simultaneously, thermodynamics control the formation of either a keto or an enol tautomer of the products, again resulting in vastly different materials. Overall, this shows that careful navigation of a reaction landscape using both kinetic and thermodynamic selectivity can be used to control material selection from a complex reaction network

Emergence of novel cephalopod gene regulation and expression through large-scale genome reorganization

© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Schmidbaur, H., Kawaguchi, A., Clarence, T., Fu, X., Hoang, O. P., Zimmermann, B., Ritschard, E. A., Weissenbacher, A., Foster, J. S., Nyholm, S., Bates, P. A., Albertin, C. B., Tanaka, E., & Simakov, O. Emergence of novel cephalopod gene regulation and expression through large-scale genome reorganization. Nature Communications, 13(1), (2022): 2172, https://doi.org/10.1038/s41467-022-29694-7.Coleoid cephalopods (squid, cuttlefish, octopus) have the largest nervous system among invertebrates that together with many lineage-specific morphological traits enables complex behaviors. The genomic basis underlying these innovations remains unknown. Using comparative and functional genomics in the model squid Euprymna scolopes, we reveal the unique genomic, topological, and regulatory organization of cephalopod genomes. We show that coleoid cephalopod genomes have been extensively restructured compared to other animals, leading to the emergence of hundreds of tightly linked and evolutionary unique gene clusters (microsyntenies). Such novel microsyntenies correspond to topological compartments with a distinct regulatory structure and contribute to complex expression patterns. In particular, we identify a set of microsyntenies associated with cephalopod innovations (MACIs) broadly enriched in cephalopod nervous system expression. We posit that the emergence of MACIs was instrumental to cephalopod nervous system evolution and propose that microsyntenic profiling will be central to understanding cephalopod innovations.H.S., O.P.H., E.R., and O.S. were supported by the Austrian Science Fund (FWF) grant P30686-B29. O.S. was supported by Whitman Center Early Career Fellowship (Frank R. Lillie Quasi-Endowment Fund, L. & A. Colwin Summer Research Fellowship, Bell Research Award in Tissue Engineering). H.S. was supported by the short-term grant abroad (KWA) of the University of Vienna. H.S. and O.S. were supported by the University of Chicago/Vienna Strategic Partnership Programme Mobility Grant. A.K. was supported by the JSPS Postdoctoral Fellowship for Overseas Researchers program from Japan. C.B.A. was supported by the Hibbitt Early Career Fellowship. Eggs and paralarvae of E. scolopes were generated in part by support by the NASA Space Biology 80NSSC18K1465 awarded to J.S.F. S.V.N. was supported by the National Science Foundation IOS-1557914. This work was supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK (FC0001003), the UK Medical Research Council (FC001003), and the Wellcome Trust (FC001003)