The guanosine monophosphate synthetase (GMPS) is a class I glutamine amidotransferase, involved in the de-novo purine nucleotide biosynthesis. The enzyme catalyzes the biochemical transformation of xantosine (XMP) into guanosine monophosphate (GMP) in presence of ATP, Mg2+ and glutamine. All GMPSs consist of two catalytic sites 1) for GATase activity 2) for the ATPPase activity. The two catalytic sites may be housed in the same polypeptide (two-domain-type) or in separate polypeptides (two-subunit-type). Most of the studies have been performed on two-domain-type GMPSs, while only one study has been reported from two-subunit-type GMPS (Maruoka et al. 2009). The two-subunit-type GMPS presents an example where the component reactions of a single enzymatic reaction are carried out by two distinct subunits. In order to get better understanding of structural aspects and mechanistic principle that governs the GMPS activity in two-subunit-type GMPSs, we initiated the study by taking GMPS of Methanocaldococcus jannaschii as a model system. The GMPS of M. jannaschii (Mj) is a two-subunit-type protein. The GATase subunit catalyzes the hydrolysis of glutamine to produce glutamate and ammonia. The ATPPase subunit catalyses the amination of XMP to produce GMP using the ammonia generated in GATase subunit. Since the two component reactions are catalysed by two separate subunits and are coupled in the way that product of one reaction (ammonia) acts as a nucleophile in the second reaction. The cross-talk between these two subunits in order to maximise the efficiency of overall GMPS warrants investigation. The GATase activity is tightly regulated by the interaction with ATPPase domain/subunit, in all GMPS except in the case of P. falciparum. This interaction is facilitated by substrate binding to the ATPPase domain/subunit. Though, the conditions for the interaction between two subunits is known in a two-subunit-type GMP synthetase from P. horikoshii, the structural basis of substrate dependent interaction is not known. As a first step to understand the structural basis of interaction between the Mj GATase and Mj ATPPase subunits, we have determined the structure of Mj GATase (21 kDa) subunit using high resolution, multinuclear, multidimensional NMR spectroscopy. Sequence specific resonance assignments were obtained through analysis of various 2D and 3D hetero-nuclear multidimensional NMR experiments. NMR based distance restraints were obtained from assignment of correlations observed in NOE based experiments. Data were acquired on isotopically enriched samples of Mj GATase. The structure of Mj GATase (2lxn) was solved by using cyana-3.0 using NMR based restraints as input for the structure calculation. The ensemble of 20 lowest-energy structures showed root-mean-square deviations of 0.35±0.06 Å for backbone atoms and 0.8±0.06 Å for all heavy atoms. Attempts were also made to obtain assignments for the 69.6 kDa dimeric ATPPase subunit. Partial assignments have been obtained for this subunit. The GATase subunit is catalytically inactive. So far, there has been only one published report on a two-subunit-type GMPS from P. horikashii. The study has shown that the catalytic activity of GATase is regulated by the GATase-ATPPase interaction which is facilitated by the substrate binding to the ATPPase subunit. For the first time, we have provided the structural basis of interaction between GATase-ATPPase (112 kDa) in a two-subunit-type GMPS. Observed line width changes were used to identify residues in GATase residues that are involved in the Mj GATase-ATPPase interaction. Our data provides a possible explanation for conformational changes observed in the Mj GATase subunit upon GATase-ATPPase interaction that lead to GATase activation. Ammonia is generated in GATase subunit and is very reactive and labile. Thus, the faithful transportation of ammonia from GATase to ATPPase subunit is very crucial for optimal GMPS activity. Till date, a PDB query for GMPS retrieves only one structure which belongs to two-subunit-type GMPS, where authors have determined the structures of GATase and ATPPase subunits separately. However, the structure of holo-GMPS is not determined yet. Using interface information from experimental data and HADDOCK, we have constructed a model for the holo-GMPS from M. jannaschii. A possible ammonia channel has been deduced using the programs MOLE 2.0 and CAVER 2.0. This ammonia channel has a length of 46 Å, which is well within the range of the lengths calculated for similar channels in other glutamine amidotransferase. It had been suggested earlier that in addition to the magnesium required for charge stabilization of ATP, additional binding sites were present on GMPS. The effect of excess Mg2+ requirement on the GMPS activity has been studied in two-domain-type GMPS. However, the interaction between GATase and Mg2+ has been not investigated in any GMPS. This prompted us to investigate the effect of MgCl2 on Mj GATase subunit. For the first time, using chemical shift perturbation, we have established interaction between Mj GATase and Mg2+. The dissociation constant (Kd) of the Mj GATase-Mg2+ interaction was determined. The Kd value was found to be 1 mM, which indicates a very weak interaction. The substrate of the GATase subunit is glutamine. The condition of the hydrolysis of the glutamine is known in GMPS. However, the binding of the glutamine and associated conformational changes in GATase have been not studied in GMPS. Furthermore, till date there is no structure available for the glutamine bound GMPS/GATase. Using isotope edited one dimensional and two-dimensional NMR spectroscopy; we have shown that the Mj GATase catalytic residues are not in a compatible conformation to bind with glutamine. Thus, a conformational change in Mj GATase subunit is a pre-requisite condition for the binding of glutamine. These conformational changes are brought by the Mj GATase-ATPPase interaction.

<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>.