Synthesis and reactivity of alpha-thio-beta-chloroacrylamides and alpha-thio-beta-chloroenones

Development of novel synthetic methodology for selective transformation of organic compounds is a central element underpinning organic synthesis with control of chemo-, regio- and stereoselectivity a very high priority. Reactions which can be conducted under mild reaction conditions and, ideally in an environmentally attractive manner, are particularly advantageous. The principal objective of this thesis was to explore the synthesis, reactivity and synthetic utility of a series of α,β-thio-β-chloroenones. The stereochemical features of these transformations and the potential of this novel series of compounds in the synthesis of bioactive compounds were of particular interest. In exploring the reactivity of these compounds, the key transformations included nucleophilic additions and Stille cross-coupling at the β-carbon. Chapter 1 reviews the literature relevant to the research conducted, and focuses in particular on the synthesis of β-chloroenones and related unsaturated carbonyl compounds. The synthesis of chalcone compounds from various precursors is also discussed, with particular emphasis on the use of palladium cross-coupling reactions in the preparation of these compounds. The biological activity of chalcones is also summarised in this chapter. The second chapter delineates the stereoselective synthesis of the novel α-thio-β-chloroenones from the corresponding α-thioketones in a multistep reaction cascade initiated by a NCS-mediated chlorination. A range of both alkyl and aryl β-chloroenones were prepared in this work and the oxidation of these compounds to the corresponding sulfoxides and sulfones is also outlined. The electrophilicity of the β-carbon of the enones was examined in nucleophilic addition/substitution reactions with successful access to a variety of synthetically useful novel adducts including acetals and enaminoketones. Investigation of the synthetic potential of the Stille cross-coupling reaction with the novel α-thio-β-chloroenones was explored and provided an efficient route for the synthesis of a novel series of chalcones. Most importantly this new methodology provided a new and synthetically powerful approach for carbon-carbon bond formation at the β-carbon under mild neutral conditions. A preliminary investigation into the use of these β-chloroenones as dienophiles in Diels-Alder cycloaddition reactions is also discussed in this chapter. Chapter 2 also reports the nucleophilic addition of N, O, S and C nucleophiles to previously described β-chloroacrylamides and their corresponding sulfoxide derivatives. This work builds on previous research carried out in this programme and the reactivity of these β-chloroacrylamides at the sulfide and sulfoxide level is compared. Comparison of the reactivity of the β-chloroacrylamides, in nucleophilic substitution and Stille-coupling, with that of the novel β-chloroenones is of interest. Finally, the biological activity of both the β-chloroenones and the β-chloroacrylamides in terms of cytotoxicity is summarised in Chapter 2. The final chapter, Chapter 3, details the full experimental procedures, including spectroscopic and analytical data for the compounds prepared during this research.

Synthesis of 4-substituted-3(2H)-furanones with novel luminescence properties

The objective of this project was to prepare a range of 4-substituted 3-(2H)-furanones, and to investigate the relationship between their molecular structures and photoluminescence properties. The effects of substituents and conjugated linker unit were also investigated. After generation of the key 3(2H)-furanone heterocycle, extension of the conjugated framework at the C-4 position was achieved through Pd(0)-catalysed coupling reactions. Chapter one of the thesis comprises a review of the relavent literature and is split into three sections. These include information about the prevalence of 3-(2H)-furanones as natural products and synthetic routes to 3-(2H)-furanones in general. The synthetic routes are divided according to the synthetic precursor employed. The final section of chapter one outlines the fundamental principles and application of photoluminescence to organic compounds in general. Chapter two contains the results of the research achieved in the course of this work and a discussion of the findings. Two routes were successfully employed to generate 4-unsubstituted 3-(2H)-furanone moieties: (i) base induced cyclisation of hydroxyenones and (ii) isoxazole chemistry. A number of methods which proved ineffective in the production of furanones with the desired substitution pattern are also detailed. The majority of this study was focused on the introduction of substituents at the C-4 position of the 3-(2H)-furanone ring. This was achieved through the use of Sonogashira and Suzuki cross coupling protocols for Pd(0) catalysed C-C bond formation. The further functionalisation of some compounds was performed using transfer hydrogenation and “click chemistry” methodologies. Finally, the photophysical properties of 3-(2H)-furanones prepared in this project are discussed and the effect of substitution patterns in a complementary “push push” and “push pull” manner have also been investigated. All the experimental data and details of the synthetic methods employed, for the compounds prepared during the course of this research is contained in chapter three together with the spectroscopic and analytical properties of the compounds prepared.

Does an incremental filling technique reduce polymerization shrinkage stresses

It is widely accepted that volumetric contraction and solidification during the polymerization process of restorative composites in combination with bonding to the hard tissue result in stress transfer and inward deformation of the cavity walls of the restored tooth. Deformation of the walls decreases the size of the cavity during the filling process. This fact has a profound influence on the assumption-raised and discussed in this paper-that an incremental filling technique reduces the stress effect of composite shrinkage on the tooth. Developing stress fields for different incremental filling techniques are simulated in a numerical analysis. The analysis shows that, in a restoration with a well-established bond to the tooth-as is generally desired-incremental filling techniques increase the deformation of the restored tooth. The increase is caused by the incremental deformation of the preparation, which effectively decreases the total amount of composite needed to fill the cavity. This leads to a higher-stressed tooth-composite structure. The study also shows that the assessment of intercuspal distance measurements as well as simplifications based on generalization of the shrinkage stress state cannot be sufficient to characterize the effect of polymerization shrinkage in a tooth-restoration complex. Incremental filling methods may need to be retained for reasons such as densification, adaptation, thoroughness of cure, and bond formation. However, it is very difficult to prove that incrementalization needs to be retained because of the abatement of shrinkage effects.

C-H activations via palladacycles

Summary: This chapter contains sections titled: * Introduction: CC Bond Formation via Cyclopalladation Reactions * Stoichiometric CH Activation Chemistry * Catalytic Chemistry * Arylations * Direct CH CH Coupling Reactions * Alkylations * Other Reactions * Conclusion * References

Structure of the adenylation domain of an NAD+-dependent DNA ligase

Background: DNA ligases catalyse phosphodiester bond formation between adjacent bases in nicked DNA, thereby sealing the nick. A key step in the catalytic mechanism is the formation of an adenylated DNA intermediate. The adenyl group is derived from either ATP (in eucaryotes and archaea) or NAD+4 (in bacteria). This difference in cofactor specificity suggests that DNA ligase may be a useful antibiotic target.

Results: The crystal structure of the adenylation domain of the NAD+-dependent DNA ligase from Bacillus stearothermophilus has been determined at 2.8 Å resolution. Despite a complete lack of detectable sequence similarity, the fold of the central core of this domain shares homology with the equivalent region of ATP-dependent DNA ligases, providing strong evidence for the location of the NAD+-binding site.

Conclusions: Comparison of the structure of the NAD+4-dependent DNA ligase with that of ATP-dependent ligases and mRNA-capping enzymes demonstrates the manifold utilisation of a conserved nucleotidyltransferase domain within this family of enzymes. Whilst this conserved core domain retains a common mode of nucleotide binding and activation, it is the additional domains at the N terminus and/or the C terminus that provide the alternative specificities and functionalities in the different members of this enzyme superfamily.

Carboxyl-Functionalized Task-Specific Ionic Liquids for Solubilizing Metal Oxides

Imidazolium, pyridinium, pyrrolidinium, piperidinium, morpholinium, and quaternary ammonium bis(trifluoromethyl-sulfonyl)imide salts were functionalized with a carboxyl group. These ionic liquids are useful for the selective dissolution of metal oxides and hydroxides. Although these hydrophobic ionic liquids are immiscible with water at room temperature, several of them form a single phase with water at elevated temperatures. Phase separation occurs upon cooling. This thermomorphic behavior has been investigated by H-1 NMR, and it was found that it can be attributed to the temperature-dependent hydration and hydrogen-bond formation of the ionic liquid components. The crystal structures of four ionic liquids and five metal complexes have been determined.

Molecular rearrangement reactions in the gas phase triggered by electron attachment

Bond formation and rearrangement reactions in gas phase electron attachment were studied through dissociative electron attachment (DEA) to pentafluorotoluene (PFT), pentafluoroaniline (PFA) and pentafluorophenol (PFP) in the energy range 0-14 eV. In the case of PFA and PFP, the dominant processes involve formation of [M - HF](-) through the loss of neutral HF. This fragmentation channel is most efficient at low incident electron energy and for PFP it is accompanied by a substantial conformational change of the anionic fragment. At higher energy, HF loss is also observed as well as a number of other fragmentation processes. Thermochemical threshold energies have been computed for all the observed fragments and classical trajectories of the electron attachment process were calculated to elucidate the fragmentation mechanisms. For the dominant reaction channel leading to the loss of HF from PFP, the minimum energy path was calculated using the nudged elastic band method.

Development of new methodologies for C-H insertion

Tese de doutoramento, Farmácia (Química Farmacêutica e Terapêutica), Universidade de Lisboa, Faculdade de Farmácia, 2014

Boronic acids as partners in multicomponent reactions

Tese de doutoramento, Farmácia (Química Farmacêutica e Terapêutica), Universidade de Lisboa, Faculdade de Farmácia, 2014

A mass spectrometric study of some pesticides /|nK. S. Subramanian. -- 260 St. Catharines, Ont. : [s. n.],

The fragmentation processes in the mass spectra of a series of organophosphorus, organochlorine, thio and dithiocarbamate as well as a number of miscellaneous pesticides have been studied i n detail by using the Bendix timeof- flight, MS-12 single-focussing and MS-30 double-focussing mass spectrometers. Interpretation of all the spectra have been presented; their mode s of dissociation elucidated, aided by metastable transitions wherever possible and the structures of the various f ragmentation species postulated wherever f easible. The fragmentation mechanisms are based on the concepts of inductive, resonance and steric ef~ects. Multiple bond cleavages accompanied by simultaneous bond formation and rearrangement reactions involving cycli c t r ansition states have clarified t he formation of various ions . Due emphasis has been placed on the effect of the functional groups or substituents in altering the mass spectral behaviour of the pesticides as they form the basis for the identifi cation of the otherwise identical pesticides. The organophosphorus pesticides which have been studied include i) the phosphates (eg: DDVP and Phosdrin ); ii) phosphorothionates (eg: Parathion, 0-2, 4 dichloro phenyl 0, O-diethyl thionophosphate); iii) phosphorothioites (eg: Tributyl phosphorotrithioite); i V) phosphorothioates (eg: Ethion) and v) phosphorodithioates (eg: Carbophenolthion). Cleavages and rearrangements of the ester moiety dominate the spectrum of phosdrin while that of DDVP is + dominated by t he fragmentation modes of the (OH30)2P=0 + moiety. Fragmentation §f the (CH30)2P=S characterises the spectrum of (OH30)2"P -Cl while cleavages of the + (C2H50 )2P=S species mark the spectra of parathion and 0-2, 4- di chlorophenyl O, O-diethyl thiophosphate. The 0(, cl eavages of the thioether f unction rather than + cleavages of the (C2H50)2P=S signify the spectrum of carbophenolthion. Tributyl phosphorotrithioite behaves more like an aliphatic hydrocarbon than like the corresponding phosphites. The isopropyl and butyl esters of 2, 4 dichlorophenoxy acetic acid show cleavage and rearrangement ions typical of an ester. In spite of its structural similari ty to pp' - DDT and pp' - DDD, Kalthane has a completely different mass spectral behaviour due to the influence of its hydroxyl function. The thiocarbamate pesticides studied include Eptam and Perbulate. Both are structurally similar but having different alkyl substituents on nitrogen and sulphur. This structurQlsimilarity leads to similar types of (N-C), (O-S) and (S-alkyl cleavages). However, perbulate differs from Eptam in showing a rearrangement ion at mle 161 and in forming an isocyanate ion as the base peak. In Eptam the base peak i s the alkyl ion. The dithiocarbamate, Vegadex, resembles the thiocarbamates in undergoing simple cleavages but it differs from them in having a weak parent ion; in the formation of its base peak and in undergoing a series of rearrangement reactions. The miscellaneous pesticides studied include 1-Naphthalene acetic aCid- methyl ester, Fiperonyl butoxide and Allethrin. The ester i s stable to electron impact and shows only fewer ions. Piper onyl butoxide, a polyether, shows characteristics of an et her, alcohol and aldehyde . Allethrin is regarded as an ester of the type R-C-O-R1 with n R being a substituted cyclopr opane moiety and o Rt, a substituted cyclopentenone mOiety. Accordingly it shows cleavage ions typical of an aliphatic ester and undergoes bond ruptures of the cyclic moieties to give unusual ions. Its base peak is an odd electron ion, quite contrary to expectations.

Experimental and Computational Studies on Copper and Hydrobenzoin Derivatives in Catalytic Asymmetric Reactions

The use of theory to understand and facilitate catalytic enantioselective organic transformations involving copper and hydrobenzoin derivatives is reported. Section A details the use of theory to predict, facilitate, and understand a copper promoted amino oxygenation reaction reported by Chemler et al. Using Density Functional Theory (DFT), employing the hybrid B3LYP functional and a LanL2DZ/6-31G(d) basis set, the mechanistic details were studied on a N-tosyl-o-allylaniline and a [alpha]-methyl-[gamma]-alkenyl sulfonamide substrate. The results suggest the N-C bond formation proceeds via a cisaminocupration, and not through a radical-type mechanism. Additionally, the origin of diastereoselection observed with [alpha]-methyl-[gamma]-alkenyl sulfonamide arises from avoidance of unfavourable steric interactions between the methyl substituent and the N -protecting group. Section B details the computationally guided, experimental investigation of two hydrobenzoin derivatives as ligands/ catalysts, as well as the attempted synthesis of a third hydrobenzoin derivative. The bis-boronic acid derived from hydrobenzoin was successful as a Lewis acid catalyst in the Bignielli reaction and the Conia ene reaction, but provided only racemic products. The chiral diol derived from hydrobenzoin successfully increased the rate of the addition of diethyl zinc to benzaldehyde in the presence of titanium tetraisopropoxide, however poor enantioinduction was obseverved. Notably, the observed reactivity was successfully predicted by theoretical calculations.

(A) BODIPY as a versatile fluorophore (B) Synthesis of PNAs via Staudinger reaction

(A) In recent years, 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) fluorophores have attracted considerable interest due to their unique photochemical properties. However detailed studies on the stability of BODIPY and analogues under acidic and basic conditions have been lacking. Thus the stability of a series of BODIPY analogues in acidic (di- and trichloroacetic acid) and basic (aqueous ammonium hydroxide) conditions was investigated using 11B NMR spectroscopy. Among the analogues tested, 4,4-diphenyl BODIPY was the most stable under the conditions used in the experiments. It was found that reaction of 4,4-dimethoxy BODIPY with dichloroacetic acid gave mixed anhydride 4,4-bis(dichloroacetoxy) BODIPY in good yields. Treatment of the latter mixed anhydride with alcohols such as methanol and ethanol in the presence of a base afforded corresponding borate esters, whereas treatment with 1,2-diols such as ethylene glycol and catechol in the presence of a base gave corresponding cyclic borate esters. Furthermore treatment of 4,4-difluoro-8-methyl-BODIPY with secondary amines in dihalomethane resulted in carbon–carbon bond formation at the meso-methyl position of BODIPY via Mannich-type reactions. The resulting modified BODIPY fluorophores possess high fluorescent quantum yields. Five BODIPY analogues bearing potential ion-binding moieties were synthesized via this Mannich-type reaction. Among these, the BODIPY bearing an aza-18-crown-5 tether was found to be selective towards copper (II) ion, resulting in a large blue shift in absorption and sharp fluorescent quenching, whereas aza-15-crown-4 analogue was selected towards fluoride ion, leading to effective florescent quenching and blue shift. (B) Peptide nucleic acids (PNA), as mimics of natural nucleic acids, have been widely applied in molecular biology and biotechnology. Currently, the preparation of PNA oligomers is commonly achieved by a coupling reaction between carboxyl and amino groups in the presence of an activator. In this thesis attempts were made towards the synthesis of PNA through the Staudinger ligation reactions between C-terminal diphenylphosphinomethanethiol thioesters and N-terminal α-azido PNA building blocks.

Mirroring Enzymes: The Role of H-Bonding In HQuin-BAM Catalyzed Asymmetric Aza-Henry Reactions: A DFT Study into the Reactivity, Mechanism, and Origins of Selectivity

The exact mechanistic understanding of various organocatalytic systems in asymmetric reactions such as Henry and aza-Henry transformations is important for developing and designing new synthetic organocatalysts. The focus of this dissertation will be on the use of density functional theory (DFT) for studying the asymmetric aza-Henry reaction. The first part of the thesis is a detailed mechanistic investigation of a poorly understood chiral bis(amidine) (BAM) Brønsted acid catalyzed aza-Henry reaction between nitromethane and N-Boc phenylaldimine. The catalyst, in addition to acting as a Brønsted base, serves to simultaneously activate both the electrophile and the nucleophile through dual H-bonding during C-C bond formation and is thus essential for both reaction rate and selectivity. Analysis of the H-bonding interactions revealed that there was a strong preference for the formation of a homonuclear positive charge-assisted H-bond, which in turn governed the relative orientation of substrate binding. Attracted by this well-defined mechanistic investigation, the other important aspect of my PhD research addressed a detailed theoretical analysis accounting for the observed selectivity in diastereoselective versions of this reaction. A detailed inspection of the stereodetermining C-C bond forming transition states for monoalkylated nitronate addition to a range of electronically different aldimines, revealed that the origins of stereoselectivity were controlled by a delicate balance of different factors such as steric, orbital interactions, and the extent of distortion in the catalyst and substrates. The structural analysis of different substituted transition states established an interesting dependency on matching the shape and size of the catalyst (host molecule) and substrates (guest molecules) upon binding, both being key factors governing selectivity, in essence, offering an analogy to positive cooperative binding effect of catalytic enzymes and substrates in Nature. In addition, both intra-molecular (intra-host) and inter-molecular (host-guest, guest-guest) stabilizing interactions play a key role to the high π-facial selectivity. The application of dispersion-corrected functionals (i.e., ωB97X-D and B3LYP-D3) was essential for accurately modeling these stabilizing interactions, indicating the importance of dispersion effects in enantioselectivity. As a brief prelude to more extensive future studies, the influence of a triflate counterion on both reactivity and selectivity in this reaction was also addressed.

New insights into the substrate specificities of microbial transglutaminase: a biocatalytic perspective

La transglutaminase microbienne (Microbial transglutaminase : MTG) est fortement exploitée dans l’industrie textile et alimentaire afin de modifier l’apparence et la texture de divers produits. Elle catalyse la formation de liaisons iso-peptidiques entre des protéines par l’entremise d’une réaction de transfert d’acyle entre le groupement γ-carboxamide d’une glutamine provenant d’un substrat donneur d’acyle, et le groupement ε-amino d’une lysine provenant d’un substrat accepteur d’acyle. La MTG est tolérante à un large éventail de conditions réactionnelles, ce qui rend propice le développement de cette enzyme en tant que biocatalyseur. Ayant pour but le développement de la MTG en tant qu’alternative plus soutenable à la synthèse d’amides, nous avons étudié la réactivité d’une gamme de substrats donneurs et accepteurs non-naturels. Des composés chimiquement diversifiés, de faible masse moléculaire, ont été testés en tant que substrats accepteurs alternatifs. Il fut démontré que la MTG accepte une large gamme de composés à cet effet. Nous avons démontré, pour la première fois, que des acides aminés non-ramifiés et courts, tels la glycine, peuvent servir de substrat accepteur. Les α-acides aminés estérifiés Thr, Ser, Cys et Trp, mais pas Ile, sont également réactifs. En étendant la recherche à des composés non-naturels, il fut observé qu’un cycle aromatique est bénéfique pour la réactivité, bien que les substituants réduisent l’activité. Fait notable, des amines de faible masse moléculaire, portant les groupements de forte densité électronique azidure ou alcyne, sont très réactives. La MTG catalyse donc efficacement la modification de peptides qui pourront ensuite être modifiés ou marqués par la chimie ‘click’. Ainsi, la MTG accepte une variété de substrats accepteurs naturels et non-naturels, élargissant la portée de modification des peptides contenant la glutamine. Afin de sonder le potentiel biocatalytique de la MTG par rapport aux substrats donneurs, des analogues plus petits du peptide modèle Z-Gln-Gly furent testés; aucun n’a réagi. Nous avons toutefois démontré, pour la première fois, la faible réactivité d’esters en tant que substrats donneurs de la MTG. L’éventuelle amélioration de cette réactivité permettrait de faire de la MTG un biocatalyseur plus général pour la synthèse d’amides. Mots clés: Lien amide, biocatalyse, biotransformation, transglutaminase, arrimage moléculaire, criblage de substrats, ingénierie de substrats.

First Example of Organocatalysis by Polystyrene-Supported PAMAM Dendrimers: Highly Efficient and Reusable Catalyst for Knoevenagel Condensations

This paper describes the first use of polystyrene-supported poly(amidoamine) (PAMAM) dendrimers as heterogeneous basic organocatalysts for carbon–carbon bond formation. Polystyrene-supported PAMAM dendrimers of first, second and third generations have been used as reusable base catalysts in Knoevenagel condensations of carbonyl compounds with active methylene compounds. The reactions proceed in short periods of time and with 100% selectivity. This novel catalyst eliminates the use of aromatic and halogenated solvents, as well as complex purification processes. The catalysts can be recycled ten times.