Novel metal template strategies for the construction of rotaxanes and catenanes

The template synthesis of rotaxanes and catenanes has allowed a detailed study of their intrinsically novel and interesting properties. A key strategy has been the deployment of transition metal ions with their well-defined coordination geometries allowing high-yielding and facile preparation of interlocked architectures. Knowledge of how to exploit the coordination sphere of metal ions and the design of ligands for the creation of intermediates that are pre-disposed to undergo ‘stoppering’ or ‘clipping’ has been a crucial requirement for this approach. This Thesis is in three parts describing the use of three dimensional, two dimensional and one dimensional coordination geometries in the synthesis of interlocked architectures. Firstly, the octahedral coordination geometry of cobalt(III) was utilized to organize dianionic pyridine-2,6-dicarboxamido ligands in a mutually orthogonal arrangement such that ring closing metathesis macrocyclizations gave access to interlocked or entwined products. A ‘figure-of-eight’ complex was obtained from a double macrocyclizations, whereas a catenate was accessed through a single macrocyclization. The topology of the isomers was proved by X-ray crystallography. An analogous [2]rotaxane was synthesized and the interlocked nature of the rotaxane demonstrated by 1H NMR spectroscopy and mass spectrometry. Secondly, an “active” metal template strategy, in which the metal ion plays a dual role – acting to both organize ligands and catalyze mechanical bond formation – allowed rotaxanes be constructed using the square planar coordination geometry and Lewis acidic nature of a palladium(II) complex. The interlocked nature of the rotaxane was proved by X-ray crystallography, demonstrating that a nitrile group present in the thread acted as a “station” for the Pd(II)-macrocycle. This observation led to the construction of a two “station” degenerate molecular shuttle in which the dynamics of translocation were controlled by reagent addition and observed by 1H NMR techniques. Lastly, the linear coordination geometry of gold(I) was successfully used as a template for construction of rotaxanes and catenanes via a ‘clipping’ strategy. The linear coordination geometry and the interlocked nature of the gold(I)-catenate was proved by X-ray crystallography, the rotaxane architecture was proved by 1H NMR spectroscopy and mass spectrometry. Chapters Two, Three and Four are in the form of articles that have been published in peer-reviewed journals, and are reproduced, in their published format, in the Appendix. No attempt has been made to rewrite the published work; as a consequence the numbering of compounds, whilst consistent within each Chapter, is not consistent throughout this Thesis. Another consequence is that the many failed synthetic routes have been left out. I hope the reader will forgive these omissions as well as the slight repetition that occurs in the introduction and bibliography of each chapter. Additionally, preceding each Chapter is a brief synopsis that places the work in context and acknowledges the contributions of my fellow researchers

Using evolutionary algorithms and machine learning to explore sequence space for the discovery of antimicrobial peptides

We present a proof-of-concept methodology for efficiently optimizing a chemical trait by using an artificial evolutionary workflow. We demonstrate this by optimizing the efficacy of antimicrobial peptides (AMPs). In particular, we used a closed-loop approach that combines a genetic algorithm, machine learning, and in vitro evaluation to improve the antimicrobial activity of peptides against Escherichia coli. Starting with a 13-mer natural AMP, we identified 44 highly potent peptides, achieving up to a ca. 160-fold increase in antimicrobial activity within just three rounds of experiments. During these experiments, the conformation of the peptides selected was changed from a random coil to an α-helical form. This strategy not only establishes the potential of in vitro molecule evolution using an algorithmic genetic system but also accelerates the discovery of antimicrobial peptides and other functional molecules within a relatively small number of experiments, allowing the exploration of broad sequence and structural space

Candidate Proteins, Metabolites and Transcripts in the Biomarkers for Spinal Muscular Atrophy (BforSMA) Clinical Study

Spinal Muscular Atrophy (SMA) is a neurodegenerative motor neuron disorder resulting from a homozygous mutation of the survival of motor neuron 1 (SMN1) gene. The gene product, SMN protein, functions in RNA biosynthesis in all tissues. In humans, a nearly identical gene, SMN2, rescues an otherwise lethal phenotype by producing a small amount of full-length SMN protein. SMN2 copy number inversely correlates with disease severity. Identifying other novel biomarkers could inform clinical trial design and identify novel therapeutic targets.To identify novel candidate biomarkers associated with disease severity in SMA using unbiased proteomic, metabolomic and transcriptomic approaches.A cross-sectional single evaluation was performed in 108 children with genetically confirmed SMA, aged 2-12 years, manifesting a broad range of disease severity and selected to distinguish factors associated with SMA type and present functional ability independent of age. Blood and urine specimens from these and 22 age-matched healthy controls were interrogated using proteomic, metabolomic and transcriptomic discovery platforms. Analyte associations were evaluated against a primary measure of disease severity, the Modified Hammersmith Functional Motor Scale (MHFMS) and to a number of secondary clinical measures.A total of 200 candidate biomarkers correlate with MHFMS scores: 97 plasma proteins, 59 plasma metabolites (9 amino acids, 10 free fatty acids, 12 lipids and 28 GC/MS metabolites) and 44 urine metabolites. No transcripts correlated with MHFMS.In this cross-sectional study, "BforSMA" (Biomarkers for SMA), candidate protein and metabolite markers were identified. No transcript biomarker candidates were identified. Additional mining of this rich dataset may yield important insights into relevant SMA-related pathophysiology and biological network associations. Additional prospective studies are needed to confirm these findings, demonstrate sensitivity to change with disease progression, and assess potential impact on clinical trial design.Clinicaltrials.gov NCT00756821

Novel metal template strategies for the construction of rotaxanes and catenanes

The template synthesis of rotaxanes and catenanes has allowed a detailed study of their intrinsically novel and interesting properties. A key strategy has been the deployment of transition metal ions with their well-defined coordination geometries allowing high-yielding and facile preparation of interlocked architectures. Knowledge of how to exploit the coordination sphere of metal ions and the design of ligands for the creation of intermediates that are pre-disposed to undergo ‘stoppering’ or ‘clipping’ has been a crucial requirement for this approach. This Thesis is in three parts describing the use of three dimensional, two dimensional and one dimensional coordination geometries in the synthesis of interlocked architectures. Firstly, the octahedral coordination geometry of cobalt(III) was utilized to organize dianionic pyridine-2,6-dicarboxamido ligands in a mutually orthogonal arrangement such that ring closing metathesis macrocyclizations gave access to interlocked or entwined products. A ‘figure-of-eight’ complex was obtained from a double macrocyclizations, whereas a catenate was accessed through a single macrocyclization. The topology of the isomers was proved by X-ray crystallography. An analogous [2]rotaxane was synthesized and the interlocked nature of the rotaxane demonstrated by 1H NMR spectroscopy and mass spectrometry. Secondly, an “active” metal template strategy, in which the metal ion plays a dual role – acting to both organize ligands and catalyze mechanical bond formation – allowed rotaxanes be constructed using the square planar coordination geometry and Lewis acidic nature of a palladium(II) complex. The interlocked nature of the rotaxane was proved by X-ray crystallography, demonstrating that a nitrile group present in the thread acted as a “station” for the Pd(II)-macrocycle. This observation led to the construction of a two “station” degenerate molecular shuttle in which the dynamics of translocation were controlled by reagent addition and observed by 1H NMR techniques. Lastly, the linear coordination geometry of gold(I) was successfully used as a template for construction of rotaxanes and catenanes via a ‘clipping’ strategy. The linear coordination geometry and the interlocked nature of the gold(I)-catenate was proved by X-ray crystallography, the rotaxane architecture was proved by 1H NMR spectroscopy and mass spectrometry. Chapters Two, Three and Four are in the form of articles that have been published in peer-reviewed journals, and are reproduced, in their published format, in the Appendix. No attempt has been made to rewrite the published work; as a consequence the numbering of compounds, whilst consistent within each Chapter, is not consistent throughout this Thesis. Another consequence is that the many failed synthetic routes have been left out. I hope the reader will forgive these omissions as well as the slight repetition that occurs in the introduction and bibliography of each chapter. Additionally, preceding each Chapter is a brief synopsis that places the work in context and acknowledges the contributions of my fellow researchers.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Rapid and selective spiro-cyclisations of O-centred radicals onto aromatic acceptors

Substituted benzyloxycarbonyloxyl radicals were generated by sensitised photolyses of benzyl oxime carbonates. EPR spectroscopy showed they ring closed exclusively by spiro-cyclisation onto the ipso-C-atoms of the aromatic rings. β-Scission of the alkoxycarbonyloxyls to CO₂ and benzyloxyl radicals increasingly competed and became dominant above 270 K. The first rate parameters for spiro-cyclisations of O-centred radicals onto aromatics were obtained by the steady-state kinetic EPR method. Pentafluoro-substitution of the ring substantially reduced the spiro-cyclisation rate. Activation barriers of the spiro-cyclisations were computed by DFT to be about half those of the alternative ortho-cyclisations. Consideration of the TS structures suggested the preference for spiro- over ortho-cyclisation resulted from better overlap of the oxyl SOMO with the aromatic π-system during spiro closure.8 page(s

An All-purpose preparation of oxime carbonates and resultant insights into the chemistry of alkoxycarbonyloxyl radicals

Oxime carbonates have been synthesised and their potential studied as a new class of radical precursor. A general synthetic route, avoiding laboratory use of phosgene, was developed. Alkyl or aryl 1H-imidazole-1-carboxylates were prepared from the corresponding alcohols and 1,1-carbonyldiimidazole, then reacted with oximes in the presence of base. UV photolyses of oxime carbonates released particular N- and O-centred radicals suitable for spectroscopic examination. Spiro-cyclisations of alkoxycarbonyloxyl radicals onto aromatic acceptors and 5-exo cyclisations onto alkene acceptors were studied by EPR spectroscopy. EPR data also provided insight to the loss of CO₂ from alkoxycarbonyloxyl radicals. The conformational preferences of 2-oxo-1,3-dioxolan-4-yl-methyl and related radicals were established. Modest yields of cyclic carbonates were obtained from preparative scale photolyses.9 page(s

Ligand-assisted nickel-catalysed sp(3)-sp(3) homocoupling of unactivated alkyl bromides and its application to the active template synthesis of rotaxanes

An efficient, mild and operationally simple Ni-catalysed sp3-carbon-to-sp3-carbon homocoupling of unactivated alkyl bromides has been developed and utilised in the active metal template synthesis of an alkyl chain axle [2]rotaxane. The key to the transformation is the use of tridentate nitrogen-donor-atom (terpy or pybox derived) ligands which inhibit competing ?-hydride elimination of alkyl-Ni intermediates