Academic literature on the topic 'Mass spectrometers; structure elucidation; ion-molecular reactions'

Gas chromatography–high-resolution mass spectrometry (GC–HRMS) is a powerful nontargeted screening technique that promises to accelerate the identification of environmental pollutants. Currently, most GC–HRMS instruments are equipped with electron ionization (EI), but atmospheric pressure ionization (API) ion sources have attracted renewed interest because: (i) collisional cooling at atmospheric pressure minimizes fragmentation, resulting in an increased yield of molecular ions for elemental composition determination and improved detection limits; (ii) a wide range of sophisticated tandem (ion mobility) mass spectrometers can be easily adapted for operation with GC–API; and (iii) the conditions of an atmospheric pressure ion source can promote structure diagnostic ion–molecule reactions that are otherwise difficult to perform using conventional GC–MS instrumentation. This literature review addresses the merits of GC–API for nontargeted screening while summarizing recent applications using various GC–API techniques. One perceived drawback of GC–API is the paucity of spectral libraries that can be used to guide structure elucidation. Herein, novel data acquisition, deconvolution and spectral prediction tools will be reviewed. With continued development, it is anticipated that API may eventually supplant EI as the de facto GC–MS ion source used to identify unknowns.

Lipid A, the membrane-bound phosphoglycolipid component of bacteria, is held responsible for the clinical syndrome of gram-negative sepsis. In this study, the fragmentation behavior of a set of synthetic lipid A derivatives was studied by electrospray ionization multistage mass spectrometry (ESI-MSn), in conjunction with tandem mass spectrometry (MS/MS), using low-energy collision-induced dissociation (CID). Genealogical insight about the fragmentation pathways of the deprotonated 4’-monophosphoryl lipid A structural analogs led to proposals of a number of alternative dissociation routes that have not been reported previously. Each of the fragment ions was interpreted using various possible mechanisms, consistent with the principles of reactions described in organic chemistry. Specifically, the hypothesized mechanisms are: (i) cleavage of the C-3 primary fatty acid leaves behind an epoxide group attached to the reducing sugar; (ii) cleavage of the C-3’ primary fatty acid (as an acid) generates a cyclic phosphate connected to the nonreducing sugar; (iii) cleavage of the C-2’ secondary fatty acid occurs both in acid and ketene forms; iv) the C-2 and C-2’ primary fatty acids are eliminated as an amide and ketene, respectively; (v) the 0,2A2 cross-ring fragment contains a four-membered ring (oxetanose); (vi) the 0,4A2 ion is consecutively formed from the 0,2A2 ion by retro-aldol, retro-cycloaddition, and transesterification; and (vii) formations of H2PO4− and PO3− are associated with the formation of sugar epoxide. An understanding of the relation between 0,2A2 and 0,4A2-type sugar fragments and the different cleavage mechanisms of the two ester-linked primary fatty acids is invaluable for distinguishing lipid A isomers with different locations of a single ester-linked fatty acid (i.e., at C-3 or C-3’). Thus, in addition to a better comprehension of lipid A fragmentation processes in mass spectrometers, our observations can be applied for a more precise elucidation of naturally occurring lipid A structures.

Abstract A reversed-phase liquid chromatographic method combined with fluorescence and multiple mass spectrometric detection in series is presented for the separation and structure elucidation of bisphenol A diglycidyl ether (BADGE) and novolac glycidyl ether (NOGE) derivatives. Atmospheric pressure chemical ionization in the positive ion mode and collision induced fragmentation in the ion trap allowed identification of BADGE- and NOGE-related compounds originating from reactions of the glycidyl ethers with bisphenols, solvents, and chain stoppers. Two extracts from food-can coatings were investigated in detail. It was possible to elucidate the structures of many substances and consequently to draw conclusions about the production of the lacquers.

The energy barrier for the keto–enol isomerization of the isolated acetone ion to its distonic (enol) isomer lies above its lowest dissociation limit and so the spontaneous isomerization can never be observed. Keto–enol isomerizations can be catalyzed within appropriate ion–molecule complexes. The present study involved two systems, [(CH3)2C=O···H+···O(H)CH2·] (ion 1) and [(CH3)2C=O···H+····OCH3] (ion 2), in both stable and metastable adducts. When acetone is bound to ·CH2OH though a proton bridge, shown as ion 1, an enol acetone ion is produced. This reaction results from a proton attaching to the acetone, which then gives an H· atom back to the radical site by a 1,6-H transfer, involving a transition state of low energy requirement. In contrast, when the acetone is protonated and bound to the radical CH3O· (ion 2), the above rearrangement does not take place. The metastable complex ion 2 loses a methyl radical, producing a new [C3H7O2]+ isomer of structure [CH3C+(O)···(H)OCH3]. Tandem mass spectrometry combined with ab initio calculations were used to investigate the two systems. Potential energy surface diagrams were obtained by calculations at the MP2/6-31+G(d) level of theory to aid further elucidation of the reaction mechanisms. Key words: ion–molecule complexes, keto–enol mechanisms, ion rearrangements and structures.

The stereochemistry of organic ions in the gas phase can be regarded from two different points of view: (i) stereoselectivity in ion formation and (ii) stereospecifity of ion fragmentations. Fast ionization by electron or photon impact shows little stereoselection. Differences in the ionization energies and cross sections between stereoisomers are generally small, save for a few exceptions. Proton or larger ion transfer, as employed in chemical ionization mass spectrometry, gives more possibilities for stereoselection. Bi- or polyfunctional molecules can capture the proton in a hydrogen-bond stabilized [M + H]+ ion, which is feasible only with a favourable spatial orientation of the chelating groups. Adduct ions [M + R]+ can also be formed stereoselectively. The use of a chiral ionizing medium adds a new dimension, since enantiomers can be distinguished, or even independently identified. The stereochemistry of even-electron cations in the gas-phase is most pronounced with polyfunctional species. The stereochemical behaviour is ruled by two reactivity principles, i.e. the geometry-dependent stabilization of [M + H]+ ions by chelation, and the anchimeric assistance by neighbouring groups in elimination of small molecules (water, ammonia, alcohols, acetic acid, etc.). The stereochemistry of odd-electron cations seems to be governed by three principles, i.e. the thermochemistry of decompositions proceeding with simple-bond cleavage, stereoelectronic effects on bond dissociations in the presence of a control orbital, and long-range interactions resulting in transfer of a hydrogen atom or a larger group. All these three reaction classes have limited areas of application. The stereochemistry of even-electron anions has been developing rapidly. The reactivity of gas-phase anions finds numerous analogies in their chemistry in solution, e.g. hydride transfer reactions and nucleophilic substitution. The applications of mass spectrometry to configurational assignment and structure elucidation remain restricted to selected classes of organic compounds.

A structural investigation of perfluorocarboxylic acid derivatives formed in the reaction with N,N-dimethylformamide dialkylacetals employing several techniques of mass spectrometry (MS) is described. Two derivatizing reagents, dimethylformamide dimethyl acetal (DMF-DMA) and dimethylformamide diethylacetal (DMF-DEA) were used. In contrast to carboxylic acids, perfluorocarboxylic acids are not able to form alkyl esters as the main product in this reaction. We found that perfluorooctanoic acid (PFOA) forms a salt with N,N-dimethylformamide dialkylacetals. This salt undergoes a further reaction inside the injection block of a gas chromatograph (GC) by loss of CO2 and then forms 1,1-perfluorooctane-(N,N,N,N-tetramethyl)-diamine. The GC-MS experiments using both electron ionization (EI) and positive-ion chemical ionization (PCI) revealed that the same reaction products are formed with either derivatizing reagent. Subjecting the perfluorocarboxylic acid derivative to electrospray ionization (ESI) and direct analysis in real time (DART), both positive- and negative-ion modes indicated that cluster ions are formed. In the positive-ion mode, this cluster ion consists of two iminium cations and one PFOA anion, while in the negative-ion mode, it comprises two PFOA anions and one cation. The salt structure was further confirmed by liquid injection field desorption/ionization (LIFDI) as well as infrared (IR) spectroscopy. We propose a simple mechanism of N,N,N′,N′-tetramethylformamidinium cation formation. The structure elucidation is supported by specific fragment ions as obtained by GC-EI-MS and GC-PCI-MS analyses.

Abstract. Guaiacol (2-methoxyphenol) and its derivatives can be emitted into the atmosphere by thermal degradation (i.e., burning) of wood lignins. Due to its volatility, guaiacol is predominantly distributed atmospherically in the gaseous phase. Recent studies have shown the importance of aqueous-phase reactions in addition to the dominant gas-phase and heterogeneous reactions of guaiacol, in the formation of secondary organic aerosol (SOA) in the atmosphere. The main objectives of the present study were to chemically characterize the main products of the aqueous-phase photonitration of guaiacol and examine their possible presence in urban atmospheric aerosols. The aqueous-phase reactions were carried out under simulated sunlight and in the presence of hydrogen peroxide and nitrite. The formed guaiacol reaction products were concentrated by solid-phase extraction and then purified with semi-preparative high-performance liquid chromatography (HPLC). The fractionated individual compounds were isolated as pure solids and further analyzed with liquid-state proton, carbon-13 and two-dimensional nuclear magnetic resonance (NMR) spectroscopy, and direct infusion negative ion electrospray ionization tandem mass spectrometry ((−)ESI-MS/MS). The NMR and product ion (MS2) spectra were used for unambiguous product structure elucidation. The main products of guaiacol photonitration are 4-nitroguaiacol (4NG), 6-nitroguaiacol (6NG), and 4,6-dinitroguaiacol (4,6DNG). Using the isolated compounds as standards, 4NG and 4,6DNG were unambiguously identified in winter PM10 aerosols from the city of Ljubljana (Slovenia) by means of HPLC/(−)ESI-MS/MS. Owing to the strong absorption of ultraviolet and visible light, 4,6DNG could be an important constituent of atmospheric "brown" carbon, especially in regions affected by biomass burning.

Abstract. Guaiacol (2-methoxyphenol) and its derivatives can be emitted into the atmosphere by thermal degradation (i.e. burning) of wood lignins. Due to its volatility, guaiacol is predominantly distributed in the atmospheric gaseous phase. Recent studies have shown the importance of aqueous-phase reactions in addition to the dominant gas-phase and heterogeneous reactions of guaiacol, in the formation of secondary organic aerosol (SOA) in the atmosphere. The main objectives of the present study were to chemically characterize the low-volatility SOA products of the aqueous-phase photonitration of guaiacol and examine their possible presence in urban atmospheric aerosols. The aqueous-phase reactions were carried out under simulated sunlight and in the presence of H2O2 and nitrite. The formed guaiacol reaction products were concentrated by using solid-phase extraction (SPE) and then purified by means of semi-preparative high-performance liquid chromatography (HPLC). The fractionated individual compounds were isolated as pure solids and further analyzed with liquid-state 1H, 13C and 2D nuclear magnetic resonance (NMR) spectroscopy and direct infusion negative ion electrospray ionization tandem mass spectrometry ((–)ESI-MS/MS). The NMR and product ion (MS2) spectra were used for unambiguous product structure elucidation. The main products of guaiacol photonitration are 4-nitroguaiacol (4NG), 6-nitroguaiacol (6NG), and 4,6-dinitroguaiacol (4,6DNG). Using the isolated compounds as standards, 4NG and 4,6DNG were unambiguously identified in winter PM10 aerosols from the city of Ljubljana (Slovenia) by means of HPLC/(–)ESI-MS/MS. Owing to the strong absorption of UV and visible light, 4,6DNG could be an important constituent of atmospheric "brown" carbon, especially in regions affected by biomass burning.

Abstract. Chemical ionization mass spectrometry with the nitrate reagent ion (NO3- CIMS) was used to investigate the products of the nitrate radical (NO3) initiated oxidation of four monoterpenes in laboratory chamber experiments. α-Pinene, β-pinene, Δ-3-carene, and α-thujene were studied. The major gas-phase species produced in each system were distinctly different, showing the effect of monoterpene structure on the oxidation mechanism and further elucidating the contributions of these species to particle formation and growth. By comparing groupings of products based on the ratios of elements in the general formula CwHxNyOz, the relative importance of specific mechanistic pathways (fragmentation, termination, and radical rearrangement) can be assessed for each system. Additionally, the measured time series of the highly oxidized reaction products provide insights into the ratio of relative production and loss rates of the high-molecular-weight products of the Δ-3-carene system. The measured effective O:C ratios of reaction products were anticorrelated with new particle formation intensity and number concentration for each system; however, the monomer : dimer ratios of products had a small positive trend. Gas-phase yields of oxidation products measured by NO3- CIMS correlated with particle number concentrations for each monoterpene system, with the exception of α-thujene, which produced a considerable amount of low-volatility products but no particles. Species-resolved wall loss was measured with NO3- CIMS and found to be highly variable among oxidized reaction products in our stainless steel chamber.

Fungi produce a wide variety of biologically active compounds/metabolites that could be used for medicinal and pharmaceutical purposes. Mitorubrines, members of the family of azaphilones, constitute a particularly interesting set of structurally diverse secondary metabolites, exhibiting a wide range of biological activities (e. G. Antimicrobial, antibacterial, antimalarial). This work describes the development of several mass spectrometry-based approaches to solve the natural structural diversity and complexity of azaphilones extracted from Hypoxylon fragiforme fungus. The first part of this manuscript is dedicated to the development and validation of an analytical methodology involving liquid chromatography coupled to high resolution mass spectrometry for the efficient and accurate detection of trace-level azaphilones in complex fungal extracts. Further collision-induced dissociation and hydrogen/deuterium exchange experiments were performed to fully elucidate and characterize the azaphilones and their nitrogenized analogues from Hypoxylon fragiforme. The second part is devoted to the application of these different analytical strategies to the in-depth characterization of a novel family of secondary metabolites derived from azaphilones, the mitorubramines. Lastly, these different secondary metabolites were further purified to confirm their chemical structures by NMR spectroscopy
Les champignons produisent une grande variété de composés/métabolites biologiquement actifs qui peuvent être utilisés à des fins médicinales et pharmaceutiques. Les mitorubrines, membres de la famille des azaphilones, constituent un ensemble particulièrement intéressant de métabolites secondaires, présentant une grande étendue d’activités biologiques (e. G. Antimicrobienne, antibactérienne, antipaludique). Ce travail présente le développement de plusieurs approches de spectrométrie de masse permettant de résoudre la diversité structurelle naturelle et la complexité des azaphilones extraits des champignons Hypoxylon fragiforme. La première partie de ce manuscrit est dédiée au développement et à la validation d’une méthodologie analytique impliquant la chromatographie liquide couplée à la spectrométrie de masse haute résolution pour la détection efficace et précise de traces d’azaphilones dans des extraits fongiques complexes. En outre, des expériences de spectrométrie de masse en mode tandem (par dissociation induite par collision, CID) et d'échange hydrogène/deutérium ont été effectuées pour élucider et caractériser les azaphilones et leurs analogues azotés chez Hypoxylon fragiforme. La deuxième partie est consacrée à l'application de ces différentes stratégies analytiques pour la caractérisation approfondie d'une nouvelle famille de métabolites secondaires dérivés des azaphilones, les mitorubramines. Enfin, ces différents métabolites secondaires ont été purifiés pour confirmer leur structure chimique par spectroscopie RMN

Doutoramento em Bioquímica
Os polissacarídeos são os componentes maioritários dos grãos de café verde e torrado e da bebida de café. Os mais abundantes são as galactomananas, seguindo-se as arabinogalactanas. Durante o processo de torra, as galactomananas e arabinogalactanas sofrem modificações estruturais, as quais estão longe de estar completamente elucidadas devido à sua diversidade e à complexidade estrutural dos compostos formados. Durante o processo de torra, as galactomananas e arabinogalactanas reagem com proteínas, ácidos clorogénicos e sacarose, originando compostos castanhos de alto peso molecular contendo nitrogénio, designados de melanoidinas. As melanoidinas do café apresentam diversas atividades biológicas e efeitos benéficos para a saúde. No entanto, a sua estrutura exata e os mecanismos envolvidos na sua formação permanecem desconhecidos, bem como a relação estrutura-atividade biológica. A utilização de sistemas modelo e a análise por espectrometria de massa permitem obter uma visão global e, simultaneamente, detalhada das modificações estruturais nos polissacarídeos do café promovidas pela torra, contribuindo para a elucidação das estruturas e mecanismos de formação das melanoidinas. Com base nesta tese, oligossacarídeos estruturalmente relacionados com a cadeia principal das galactomananas, (β1→4)-Dmanotriose (Man3), e as cadeias laterais das arabinogalactanas, (α1→5)-Larabinotriose (Ara3), isoladamente ou em misturas com ácido 5-Ocafeoilquínico (5-CQA), o ácido clorogénico mais abundante nos grãos de café verde, e péptidos compostos por tirosina e leucina, usados como modelos das proteínas, foram sujeitos a tratamento térmico a seco, mimetizando o processo de torra. A oxidação induzida por radicais hidroxilo (HO•) foi também estudada, uma vez que estes radicais parecem estar envolvidos na modificação dos polissacarídeos durante a torra. A identificação das modificações estruturais induzidas por tratamento térmico e oxidativo dos compostos modelo foi feita por estratégias analíticas baseadas principalmente em espectrometria de massa, mas também em cromatografia líquida. A cromatografia de gás foi usada na análise de açúcares neutros e ligações glicosídicas. Para validar as conclusões obtidas com os compostos modelo, foram também analisadas amostras de polissacarídeos do café obtidas a partir de resíduo de café e café instantâneo. Os resultados obtidos a partir dos oligossacarídeos modelo quando submetidos a tratamento térmico (seco), assim como à oxidação induzida por HO• (em solução), indicam a ocorrência de despolimerização, o que está de acordo com estudos anteriores que reportam a despolimerização das galactomananas e arabinogalactanas do café durante a torra. Foram ainda identificados outros compostos resultantes da quebra do anel de açúcares formados durante o tratamento térmico e oxidativo da Ara3. Por outro lado, o tratamento térmico a seco dos oligossacarídeos modelo (individualmente ou quando misturados) promoveu a formação de oligossacarídeos com um maior grau de polimerização, e também polissacarídeos com novos tipos de ligações glicosídicas, evidenciando a ocorrência de polimerização através reações de transglicosilação não enzimática induzidas por tratamento térmico a seco. As reações de transglicosilação induzidas por tratamento térmico a seco podem ocorrer entre resíduos de açúcares provenientes da mesma origem, mas também de origens diferentes com formação de estruturas híbridas, contendo arabinose e manose como observado nos casos dos compostos modelo usados. Os resultados obtidos a partir de amostras do resíduo de café e de café instantâneo sugerem a presença de polissacarídeos híbridos nestas amostras de café processado, corroborando a ocorrência de transglicosilação durante o processo de torra. Além disso, o estudo de misturas contendo diferentes proporções de cada oligossacarídeo modelo, mimetizando regiões do grão de café com composição distinta em polissacarídeos, sujeitos a diferentes períodos de tratamento térmico, permitiu inferir que diferentes estruturas híbridas e não híbridas podem ser formadas a partir das arabinogalactanas e galactomananas, dependendo da sua distribuição nas paredes celulares do grão e das condições de torra. Estes resultados podem explicar a heterogeneidade de estruturas de melanoidinas formadas durante a torra do café. Os resultados obtidos a partir de misturas modelo contendo um oligossacarídeo (Ara3 ou Man3) e 5-CQA sujeitas a tratamento térmico a seco, assim como de amostras provenientes do resíduo de café, mostraram a formação de compostos híbridos compostos por moléculas de CQA ligadas covalentemente a um número variável de resíduos de açúcar. Além disso, os resultados obtidos a partir da mistura contendo Man3 e 5-CQA mostraram que o CQA atua como catalisador das reações de transglicosilação. Por outro lado, nas misturas modelo contendo um péptido, mesmo contendo também 5-CQA e sujeitas ao mesmo tratamento, observou-se uma diminuição na extensão das reações transglicosilação. Este resultado pode explicar a baixa extensão das reações de transglicosilação não enzimáticas durante a torra nas regiões do grão de café mais ricas em proteínas, apesar dos polissacarídeos serem os componentes maioritários dos grãos de café. A diminuição das reações de transglicosilação na presença de péptidos/proteínas pode dever-se ao facto de os resíduos de açúcares redutores reagirem preferencialmente com os grupos amina de péptidos/proteínas por reação de Maillard, diminuindo o número de resíduos de açúcares redutores disponíveis para as reações de transglicosilação. Além dos compostos já descritos, uma diversidade de outros compostos foram formados a partir dos sistemas modelo, nomeadamente derivados de desidratação formados durante o tratamento térmico a seco. Em conclusão, a tipificação das modificações estruturais promovidas pela torra nos polissacarídeos do café abre o caminho para a compreensão dos mecanismos de formação das melanoidinas e da relação estrutura-atividade destes compostos.
Polysaccharides are the major components of green and roasted coffee beans, and coffee brew. The most abundant ones are galactomannans, followed by arabinogalactans. During the roasting process, galactomannans and arabinogalactans undergo structural modifications that are far to be completely elucidated due to their diversity and complexity of the compounds formed. During the roasting process, galactomannans and arabinogalactans react with proteins, chlorogenic acids, and sucrose, originating high molecular weight brown compounds containing nitrogen, known as melanoidins. Several biological activities and beneficial health effects have been attributed to coffee melanoidins. However, their exact structures and the mechanisms involved in their formation remain unknown, as well as the structure-biological activity relationship. The use of model systems and mass spectrometry analysis allow to obtain an overall view and, simultaneously, detailed, of the structural modifications in coffee polysaccharides promoted by roasting, contributing to the elucidation of the structures and formation mechanisms of melanoidins. Based on this thesis, oligosaccharides structurally related to the backbone of galactomannans, (β1→4)-D-mannotriose, and the side chains of arabinogalactans, (α1→5)-Larabinotriose, alone or in mixtures with 5-O-caffeoylquinic acid, the most abundant chlorogenic acid in green coffee beans, and dipeptides composed by tyrosine and leucine, used as models of proteins, were submitted to dry thermal treatments, mimicking the coffee roasting process. The oxidation induced by hydroxyl radicals (HO•) was also studied, since these radicals seem to be involved in the modification of the polysaccharides during roasting. The identification of the structural modifications induced by thermal and oxidative treatment of the model compounds was performed mostly by mass spectrometry-based analytical strategies, but also using liquid chromatography. Gas chromatography was used in the analysis of neutral sugars and glycosidic linkages. To validate the conclusions achieved with the model compounds, coffee polysaccharide samples obtained from spent coffee grounds and instant coffee were also analysed. The results obtained from the model oligosaccharides when submitted to thermal treatment (dry) or oxidation induced by HO• (in solution) indicate the occurrence of depolymerization, which is in line with previous studies reporting the depolymerization of coffee galactomannans and arabinogalactans during roasting. Compounds resulting from sugar ring cleavage were also formed during thermal treatment and oxidative treatment of Ara3. On the other hand, the dry thermal treatment of the model oligosaccharides (alone or when mixed) promoted the formation of oligosaccharides with a higher degree of polymerization, and also polysaccharides with new type of glycosidic linkages, evidencing the occurrence of polymerization via non-enzymatic transglycosylation reactions induced by dry thermal treatment. The transglycosylation reactions induced by dry thermal treatment can occur between sugar residues from the same origin, but also of different origins, with formation of hybrid structures, containing arabinose and mannose in the case of the model compounds used. The results obtained from spent coffee grounds and instant coffee samples suggest the presence of hybrid polysaccharides in these processed coffee samples, corroborating the occurrence of transglycosylation during the roasting process. Furthermore, the study of mixtures containing different proportions of each model oligosaccharide, mimicking coffee bean regions with distinct polysaccharide composition, subjected to different periods of thermal treatment, allowed to infer that different hybrid and non-hybrid structures may be formed from arabinogalactans and galactomannans, depending on their distribution in the bean cell walls and on roasting conditions. These results may explain the heterogeneity of melanoidins structures formed during coffee roasting. The results obtained from model mixtures containing an oligosaccharide (Ara3 or Man3) and 5-CQA and subjected to dry thermal treatment, as well as samples derived from spent coffee grounds, showed the formation of hybrid compounds composed by CQA molecules covalently linked to a variable number of sugar residues. Moreover, the results obtained from the mixture containing Man3 and 5-CQA showed that CQA acts as catalyst of transglycosylation reactions. On the other hand, in the model mixtures containing a peptide, even if containing 5-CQA and subjected to the same treatment, it was observed a decrease in the extent of transglycosylation reactions. This outcome can explain the low extent of non-enzymatic transglycosylation reactions during roasting in coffee bean regions enriched in proteins, although polysaccharides are the major components of the coffee beans. The decrease of transglycosylation reactions in the presence of peptides/proteins can be related with the preferential reactivity of reducing residues with the amino groups of peptides/proteins by Maillard reaction, decreasing the number of reducing residues available to be directly involved in the transglycosylation reactions. In addition to the compounds already described, a diversity of other compounds were formed from model systems, namely dehydrated derivatives formed during dry thermal treatment. In conclusion, the identification of the structural modifications in coffee polysaccharides promoted by roasting pave the way to the understanding of the mechanisms of formation of melanoidins and structure-activity relationship of these compounds.

This thesis is comprised of two parts with all the work carried out centred around the use of two mass spectrometers with vastly differing capabilities and with the experimental results obtained supported or refuted with the aid of theoretical quantum chemical calculations. For the last two decades our research group has been interested in cumulenes and hetero-cumulenes, some detected and some not as yet in their interstellar environs. The work discussed in the first part of this thesis is a continuation of some of that work and a comparison with the new work undertaken within. Our interest is predominantly orientated towards the neutral systems and their rearrangements. Our work on interstellar molecules is of interest because some of the systems investigated here and in the past, along with their precursor molecules are already known interstellar molecules and some have been implicated as possible precursors for the building blocks of life and some as possible antibiotics. The first part of this thesis uses a combination of mass spectrometric techniques using a VG ZAB 2HF mass spectrometer (mainly charge reversal mass spectrometry) and/or theoretical quantum calculations to investigate the structures and energetics of the neutral tetra-atomic and hetero-cumulenic systems CCCN, CCCSi, CCCP, H₂CCCN, and ONCS (a possible primordial antibiotic). The second part of this thesis involves the modification of a Finnigan LCQ ion trap mass spectrometer in order to perform gas phase ion-molecule reactions between selectively generated carbanions and carbon disulfide. The investigation carried out in the second part of this thesis is a revisit on our earlier group research on the gas phase ipso (Smiles) rearrangement. It was proposed that the adducts formed between the carbanions and CS₂ undergo Smiles type rearrangements via ipso intermediates upon collision induced dissociation CID.
Thesis (Ph.D.) -- University of Adelaide, School of Chemistry and Physics, 2012