<p>  </p> <p>Organic synthesis is the application of one or more reactions to the preparation of a particular target molecule, and can pertain to a single-step transformation or to a number of sequential chemical steps depicted by a scheme overall. The selection of a reaction or series of reactions while considering chemo-, regio-, and stereoselectivities in addition to protecting group strategies & redox manipulations highlights the complexity in designing & executing a synthetic plan while making a judgement about what is the most effective and efficient plan to synthesize any given chemical compound among numerous available options. To this end, chemical synthesis is the unifying theme of this thesis & was utilized and strategically applied to construct increasingly complex and diverse molecular architectures. </p> <p>Being the precise science that organic chemistry is, this discipline extends into many areas such as technology, biology & medicine, and even into the fine arts since it fosters unparalleled creativity and imagination in its practice. Research foci in chemical synthesis can encompass both the discovery and development of powerful reactions and the invention of strategies for the construction of defined target molecules, natural or man-made, more or less complex. Studies in the former area, synthetic methodology, fuel and enable studies in the latter area, target molecule and total synthesis campaigns, where the latter area offers a testing ground for the former. Consequently, the bulk of this research work is in organic methodology and will be covered in greater depth during chapters 2 and 3 where strategies, optimizations, & analyses are elaborated upon in light of searching & navigating the vast body of chemical literature in an effort to broaden and strengthen one's laboratory expertise as a synthetic chemist. Lastly, chapter 4 focuses not on traditional synthesis but on organic structure analysis relying on various techniques such as nuclear magnetic resonance (NMR), infrared (IR), ultraviolet-visible (UV-Vis) spectroscopy in combination with mass spectrometry (MS) and/or X-ray crystallography to hypothesize and confirm established structures, specifically phenolic oligomers. An ability to use spectroscopic data to evaluate organic structures by combining practical experience with fundamental knowledge will serve as a hallmark skill in one’s ability to problem-solve as an organic chemist.</p>

This Thesis describes the synthesis and characterisation of new alkaline earth- and rare earth-transition metal complexes. Experimental and computational studies were performed to investigate the structure and bonding in these complexes. Their reactivity was also studied. Chapter 1 introduces metal-metal bonded complexes and current alkaline earth- and rare earth-transition metal bonded complexes. Chapter 2 describes experimental and computational studies of new alkaline earth- and lanthanide-Fe complexes possessing the [CpFe(CO)2]- anion. Chapter 3 presents experimental studies of the reduction of Fe3(CO)12 with Ca. Chapter 4 describes experimental and computational studies of new alkaline earth- and lanthanide-Co complexes containing the [Co(CO)3(PR3)]- anion. Chapter 5 presents full experimental procedures and characterising data for the new complexes reported. Appendix describes the attempted synthesis of [Ca{CpRu(CO)2}2(THF)x]y and study by DFT of [CaRp2(THF)3]2 CD Appendix contains .cif files for all new crystallographically characterised complexes described.

Afin d'étudier la diffusion et la libération de molécules de tailles inférieures dans un gel polymère, les coefficients d'auto-diffusion d'une série de polymères en étoile avec un noyau d'acide cholique et quatre branches de poly(éthylène glycol) (PEG) ont été déterminés par spectroscopie RMN à gradient de champ pulsé dans des solutions aqueuses et des gels de poly(alcool vinylique). Les coefficients de diffusion obtenus ont été comparés avec ceux des PEGs linéaires et dendritiques pour étudier l'effet de l'architecture des polymères. Les polymères en étoile amphiphiles ont des profils de diffusion en fonction de la concentration similaires à leurs homologues linéaires dans le régime dilué. Ils diffusent plus lentement dans le régime semi-dilué en raison de leur noyau hydrophobe. Leurs conformations en solution ont été étudiées par des mesures de temps de relaxation spin-réseau T1 du noyau et des branches. L'imagerie RMN a été utilisée pour étudier le gonflement des comprimés polymères et la diffusion dans la matrice polymère. Les comprimés étaient constitués d'amidon à haute teneur en amylose et chargés avec de l'acétaminophène (de 10 à 40% en poids). Le gonflement des comprimés, ainsi que l'absorption et la diffusion de l'eau, augmentent avec la teneur en médicament, tandis que le pourcentage de libération du médicament est similaire pour tous les comprimés. Le gonflement in vitro des comprimés d'un complexe polyélectrolyte à base d'amidon carboxyméthylé et de chitosane a également été étudié par imagerie RMN. Ces comprimés sont sensibles au pH : ils gonflent beaucoup plus dans les milieux acides que dans les milieux neutres en raison de la dissociation des deux composants et de la protonation des chaînes du chitosane. La comparaison des résultats avec ceux d'amidon à haute teneur en amylose indique que les deux matrices ont des gonflements et des profils de libération du médicament semblables dans les milieux neutres, alors que les comprimés complexes gonflent plus dans les milieux acides en raison de la dissociation du chitosane et de l'amidon. / In an effort to study the diffusion and release of small molecules in a polymeric system, the self-diffusion coefficients of a series of star polymers with a cholic acid core bearing four poly(ethylene glycol) (PEG) arms in aqueous solutions and gels of poly(vinyl alcohol) were determined by pulsed gradient spin-echo NMR techniques. The results have been compared with those of linear and dendritic PEGs to elucidate the effect of the architecture of the polymers. The amphiphilic star polymers show similar concentration-dependent diffusion behaviors in the dilute regime to their linear homologues. They diffuse more slowly in the semi-dilute regime than the linear PEGs due to the presence of the hydrophobic core. The conformation of the star polymers in the solutions was studied by measuring the T1 values of the core and the arms of the diffusants. NMR imaging was used to study the swelling of polymeric tablets and diffusion in the polymer matrix. The tablets investigated were made of cross-linked high amylose starch (CHAS) and loaded with acetaminophen (10, 20 and 40 wt%). The swelling, water uptake and diffusion in the CHAS network are faster at higher drug loading levels, while the drug release rates are similar among all the tablets. The in vitro swelling of the tablets made of a polyelectrolyte complex based on chitosan and carboxymethylated starch has also been studied by NMR imaging. These tablets showed pH-sensitive behavior. They swelled much more in acidic media than in neutral media due to dissociation of the two components and the protonation of the amino groups in the chitosan residues. The comparison of the results with those obtained with the CHAS tablets indicates that the two matrices have similar swelling and drug release profile in neutral media, while the complex tablets showed a greater extent of swelling in acidic media due the dissociation of the chitosan from the complex.

Amino-functionalized organic–inorganic hybrid materials with a narrow distributed nanostructure of 2–4 nm in size were obtained by means of a template-free and non-aqueous procedure. Simultaneous twin polymerization of novel amino group containing twin monomers with 2,2′-spirobi[4H-1,3,2-benzodioxasiline] has been applied for this purpose. The amino groups of the organic–inorganic hybrid material are useful for post derivatization. / Dieser Beitrag ist aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.

A series of Fe2+ spin crossover (SCO) complexes [Fe(5/6)]2+ employing hexadentate ligands (5/6) with cis/trans-1,2-diamino cyclohexanes (4) as central building blocks were synthesised. The ligands were obtained by reductive amination of 4 with 2,2′-bipyridyl-6-carbaldehyde or 1,10-phenanthroline-2-carbaldehyde 3. The chelating effect and the rigid structure of the ligands 5/6 lead to exceptionally robust Fe2+ and Zn2+ complexes conserving their structure even in coordinating solvents like dmso at high temperatures. Their solution behavior was investigated using variable temperature (VT) 1H NMR spectroscopy and VT Vis spectroscopy. SCO behavior was found for all Fe2+ complexes in this series centred around and far above room temperature. For the first time we have demonstrated that the thermodynamics as well as kinetics for SCO can be deduced by using VT 1H NMR spectroscopy. An alternative scheme using a linear correction term C1 to model chemical shifts for Fe2+ SCO complexes is presented. The rate constant for the SCO of [Fe(rac-trans-5)]2+ obtained by VT 1H NMR was validated by Laser Flash Photolysis (LFP), with excellent agreement (1/(kHL + kLH) = 33.7/35.8 ns for NMR/LFP). The solvent dependence of the transition temperature T1/2 and the solvatochromism of complex [Fe(rac-trans-5)]2+ were ascribed to hydrogen bond formation of the secondary amine to the solvent. Enantiomerically pure complexes can be prepared starting with R,R- or S,S-1,2-diaminocyclohexane (R,R-trans-4 or S,S-trans-4). The high robustness of the complexes reduces a possible ligand scrambling and allows preparation of quasiracemic crystals of [Zn(R,R-5)][Fe(S,S-5)](ClO4)4·(CH3CN) composed of a 1 : 1 mixture of the Zn and Fe complexes with inverse chirality. / Dieser Beitrag ist aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.

The first identfied 2-oxoglutarate (2OG) dependent oxygenase was a collagen modifying enzyme in the work by Hutton et al. in 1967. Subsequent work has revealed that 2OG dependent oxygenases are a large family with diverse biological roles. With small molecule substrates, these enzymes catalyse a wide range of oxidative reactions, including those that form part of antibiotic biosynthetic pathways. The currently accepted consensus mechanism for catalysis by 2OG-dependent oxygenases is based on crystallographic data, kinetics and on quantum chemical calculations. The consensus mechanism involves oxidative decarboxylation of 2OG by reaction with an oxygen molecule producing CO₂, succinate and a reactive oxidising species that reacts with the 'prime' substrate. Deacetoxycephalosporin C synthase (DAOCS) is a 2OG-dependent oxygenase involved in cephalosporin biosynthesis. The mechanism of DAOCS is of particular interest because it has recently been proposed to be different from the consensus mechanism. The new mechanism proposal from Valeg ard et al. is primarily based on high-resolution crystallographic data with support from steady-state kinetic experiments and quantum-chemical calculations. The work in discussed in this thesis aimed to test the proposal of Valegård et al. by using a combination of spectroscopic and spectrometric methods analysing enzyme-substrate interactions. Substrate binding was investigated using both protein-observe (Chapter 3) and ligand-observe (Chapter 4.1 and 4.2) methods. Preliminary UV-visible data on enzyme-substrates complex formation was also obtained. The strength of substrate and cosubstrate binding was characterised through dissociation constant measurement. An activity assay (Chapter 2) that allows for direct and simultaneous monitoring of 2OG decarboxylation and penicillin ring expansion was optimised. Both the ligand-observe and protein-observe binding experiments as well as the preliminary UV-visible data indicate that the formation of a ternary complex between DAOCS, 2OG and the penicillin substrate is viable. The activity assay conclusively showed that in the presence of unnatural substrates, such as penicillin G, 2OG oxidation is significantly uncoupled from penicillin oxidation. Uncoupled turnover does not occur in the presence of the natural substrate, penicillin N, which is an aspect that should be considered in the analysis of the steady-state kinetic data. Overall, the results provide evidence that, the consensus mechanism for 2OG-dependent oxygenases is viable for DAOCS, at least in the presence of the natural substrate, penicillin N. It is possible that in the presence of an unnatural substrate, the catalytic process undergoes a more complex mechanism, possibly with the direct involvement of reducing agents in the system.

The human &alpha;-lactalbumin (&alpha;-LA) molten globule formed at low pH is a model for the study of protein folding intermediates. The molten globule lacks native-like side-chain interactions, resulting in a fluctuating ensemble of tertiary structures, characterisation of which has been precluded by severe line-broadening in NMR spectra and a lack of long-range NOEs. Paramagnetic relaxation enhancements (PREs) have been measured in a variant of &alpha;-LA in which all native cysteines have been mutated to alanine (all-Ala &alpha;-LA). Cysteine residues have been mutated into regions of interest and spin labelled with MTSL. These measurements have confirmed that all-Ala &alpha;-LA forms a compact molten globule. Transient, long-range interactions that are stabilising the compact fold have also been identified using PREs measured in urea-denatured states. This has identified several interactions formed by hydrophobic residues from both the &alpha;- and &beta;-domain, which could be important for initiating and driving folding. The molten globule’s 3D topology has been probed by measuring long-range distances between MTSL pairs using Double Electron-Electron Resonance (DEER). Broad distance distributions have been identified between elements of secondary structure, indicative of a fluctuating but compact fold. By contrast, a narrower distance distribution has been measured within one of the major helices, indicative of native-like secondary structure. The surface accessibility of all-Ala &alpha;-LA and that of two other variants ([28-111] &alpha;-LA and 4SS &alpha;-LA) has been probed using solvent PREs obtained using TEMPOL, a paramagnetic co-solute. This has revealed differences in the solvent-exposure of hydrophobic residues due to the removal of disulphide bonds. This method has also identified buried hydrophobic residues that contribute to forming the molten globule’s stable, native-like core.

This thesis describes the synthesis and characterisation of a series of cationic rhodium bis-phosphine complexes. The reactivity of these new complexes in the solid-state and in solution is reported. In <b>Chapter 2</b> the synthesis of a series of rhodium bis-phosphine diene complexes is presented and the reactions of these complexes with hydrogen in the solid-state are investigated. Several examples of zwitterionic complexes coordinating the [BAr^F4]^─ anion are produced by hydrogenation. A rare example of a sigma-alkane complex, [Rh(ⁱBu₂PCH₂CH₂PⁱBu₂)(eta²-_CH-eta²-_CH-NBA][BAr^F4]<sup>─</sup], is also formed in the solid-state, by a single crystal to single crystal transition driven by hydrogen. This complex is crystallographically characterised and displays two short Rh∙∙∙H−C sigma-interactions. Deuteration studies indicate that the agostic complex [Rh(ⁱBu₂PCH₂CH₂PⁱBu₂)(eta²-_CH-eta²-_CH-NBE][BAr^F4] may form as a short lived intermediate prior to the formation of the sigma-alkane complex. The temporal evolution of the solid-state hydrogenation reactions is monitored by powder X-ray diffraction methods. In <b>Chapter 3</b> the C−X activation of various aryl halides using the [Rh(ⁱBu₂PCH₂CH₂PⁱBu₂)]⁺ fragment is reported. The 'ligand innocence' of the phosphine with respect to intramolecular C−H activation is also discussed. A rare example of C−X activation in the solid-state is presented, which shows the formation of an isomer that is not observed by analogous solution routes. <b>Chapter 4</b> investigates solid-state ligand exchange reactions using ethene, butadiene, CO and NH3 gases. A solid-state transfer dehydrogenation reaction is reported within single crystals of [Rh(ⁱBu₂PCH₂CH₂PⁱBu₂)(C₂H₄)₂][BAr^F4]. H/D exchange of NH3 can also occur in the solid state in the bis-ammonia complex [Rh(ⁱBu₂PCH₂CH₂PⁱBu₂)(NH₃)₂][BAr^F4]. A variety of rhodium complexes are tested as heterogeneous catalysts for the hydrogenation of ethene and the isomerisation of butene. In <b>Chapter 5</b> the binding affinity of a variety of fluorinated arenes to rhodium bis-phosphine fragments is presented using ESI-MS methods. The dependence upon the arene substituents, phosphine substituents and phosphine bite angle are discussed.

This thesis expands the scope for using the permethylpentalene ligand and its precursors in the synthesis of organometallic complexes. <strong>Chapter one</strong> begins with a brief review of linked metallocenes, with which multimetallic compounds bridged by pentalene ligands have often been compared, followed by a comprehensive review of the routes used to make pentalenes and substituted pentalenes. Organometallic compounds of pentalenes are introduced, with a focus on bimetallic systems. <strong>Chapter two</strong> explores the diversification of substituents added to the permethylpentalene (Pn*) precursor WeissH₄, to include ethyl and isopropyl groups. Low-symmetry mono-, di-, tri- and tetraalkylated products are formed, eight such organic molecules have been identified by NMR spectroscopy, and two characterised crystallographically. It has been demonstrated that subsequent hydrolysis and decarboxylation of two of these products produces low-symmetry alkylpentalene precursors. The chapter concludes with discussions on the selectivity exhibited in these reactions, and the assignment of stereochemistry. <strong>Chapter three</strong> describes the synthesis of the first homoleptic double metallocene complex of iron. Fe₂Pn*₂ has been characterised by X ray diffraction, and cyclic voltammetry studies demonstrate four accessible oxidation states (-1, 0, +1, +2). Magnetic measurements in the solid and solution state reveal an unusual triplet configuration, and DFT calculations indicate the origin of a high magnetic moment likely resides in unquenched orbital angular momentum contributions from SOMOs which have metal d character. Fe₂Pn*₂ is EPR silent at 5, 40, and 300 K both in solution and the solid state, suggesting a large zero-field splitting parameter. The reaction of the di-iron complex with carbon monoxide, ethylene and H2 is reported; the bimetallic CO adduct, Fe₂(&mu; &eta;⁵,&eta;³ Pn*)(&mu; &eta;⁵,&eta;¹ Pn*)(CO)₂, has been crystallographically characterised, and contains a highly distorted allylic bonding motif, which to the author’s knowledge is believed to be unique among iron complexes. <strong>Chapter four</strong> discusses the interaction of the bidentate Pn* ligand in anti bimetallic fused metallocenes. A new ligand exchange route has been developed to access the complexes (MCp)₂Pn* (M = Co, Ni), and the isostructural complexes (MCp*)₂Pn* have been made for M = Fe, Co, Ni by salt metathesis reactions. All five complexes have been characterised by single crystal X-ray crystallography, and have diamagnetic ground states in solution in common with their Pn bridged analogues. Variable temperature NMR studies reveal a spin-equilibrium between S = 0 and S = 1 in the dinickel complexes. DFT calculations reproduce the spin states found, and suggest the distortion towards &eta;³ coordination observed on crossing from Fe, to Co, to Ni, results from population of orbitals with M―bridgehead antibonding character. The electronic structures show it is important to draw comparisons between isoelectronic linked metallocenes. Electrochemical studies on the diiron, dicobalt, and (NiCp)₂Pn* complexes reveal at least three redox events for each. <strong>Chapter five</strong> documents the successful synthesis and characterisation of monometallic complexes of iron and manganese with Pn*H ligands. The isostructural complexes Fe(Pn*H)₂ and Mn(Pn*H)₂ can have been characterised crystallographically, and are potential precursors for accessing heterometallic, and multimetallic complexes. Mn(Pn*H)₂ is a rare example of a manganese sandwich compound and magnetic studies on a single isomer in the solution and solid states suggest it adopts intermediate spin states of S = 2 in solution, and S = 3/2 in the solid state. <strong>Chapter six</strong> gives experimental details for all syntheses and studies described in the preceding chapters. <strong>Chapter seven</strong> provides characterising data for all new compounds. Fitting data for VT NMR and SQUID studies are provided in the <strong>appendix</strong> at the end of this thesis. Crystallographic data in the form of .cif files, DFT output files, and raw SQUID data, can be found in the <strong>electronic appendix</strong>.

Analogues of Antibacterial Natural Products Elizabeth Anne Heaviside, St Catherine’s College, University of Oxford DPhil Thesis, Trinity Term 2012 This thesis is concerned with the synthesis and biological evaluation of structural mimics for the natural products 16-methyloxazolomycin and lemonomycin which display potent biological activity including antibacterial and antitumour activity. Chapter 1 explores methods and approaches to the discovery of new antibacterial drugs and the challenges faced in this respect. It also gives an overview of the properties of the natural products investigated in the following chapters and summarises previous synthetic approaches to these molecules published in the scientific literature. Chapter 2 describes the work carried out towards the synthesis of the diazabicyclo[3.2.1]octane unit of the tetrahydroisoquinoline antitumour antibiotic lemonomycin. The intended retrosynthesis of the natural product led to a 2,5-disubstituted pyrrolidine bearing a 1ʹ-amino functional group; a series of routes were explored for the synthesis of this unit. Using (S)-pyroglutamic acid, strategies using Eschenmoser and thiolactim ether coupling reactions were investigated. A sequence based on the formation of a pyrrolidine ring from the cyclisation of an appropriately substituted oxime ether derived from L-phenylalanine was then implemented but a competing Beckmann rearrangement/Grob fragmentation prevented access to the desired heterocycle. Preliminary investigations were also carried out on the modification of cyclic imines derived from oxime ethers which did not undergo Beckmann rearrangement. Chapter 3 describes the synthesis of a library of densely functionalised tetramic acid and pyroglutamate mimics for the right-hand fragment of 16-methyloxazolomycin, and their coupling with a gem-dimethylamide unit mimicking the middle fragment of the natural product. Tetramates were accessed through the Dieckmann cyclisation of N-acyloxazolidines and were derivatised with various alkyl halides. The pyroglutamates were accessed via the highly diastereoselective aldol cyclisation of N-acyloxazolidines formed by the amide coupling of a threonine derived oxazolidine and β-keto-acids. A series of β-keto-acids were synthesised through the acylation and subsequent ring-opening/decarboxylation reaction of Meldrum’s acid. The formation of right-hand/middle fragment adducts was explored using cycloaddition, alkylation and Sonogashira chemistry before a Wittig protocol led to the formation of adducts (E)- and (Z)- 402 and 403. Biological evaluation of the compounds synthesised in this chapter was carried out using both broth and hole-plate bioassays and active compounds were identified. Of particular note was that the Wittig adducts displayed a higher level of activity against Gram-negative E. coli than either the pyroglutamate or amide motifs alone.