<p>Mass spectrometry-based techniques have been widely used in reaction monitoring due to their high sensitivity and ability to offer structure information by tandem mass spectrometry. We applied nanoelectrospray mass spectrometry (nanoESI-MS) to simultaneously monitor pre-catalysts, catalytic intermediates, reagents, and products of palladium catalyzed Suzuki-Miyaura cross-coupling reactions. A set of Pd cluster ions related to the monoligated Pd (0) active catalyst is detected, and its deconvoluted isotopic distribution reveals contributions from two neutral molecules. One is assigned to the generally accepted Pd (0) active catalyst, seen in MS as the protonated molecule, while the other is suggested to correspond to a deactivated form of Pd catalyst. Oxidative stress testing of the synthetic model catalyst XPhos Pd cyclo-octadiene, performed using oxygen and Fe(III), supported this assignment. Thus, the make-up of the monoligated set of Pd (0) ions appears to indicate the oxidation state of the system. The formation and removal of the oxidative addition intermediate during the catalytic cycle was monitored to provide information on the progress of the transmetalation step. </p> <p> </p> <p><a>Recently, microdroplets created by ambient ionization source have been used as reaction vessels to accelerate organic reactions. Field desorption mass spectrometry under ambient conditions is applied to study solution-phase organic reactions in micro-volumes. Compared to nanoelectrospray, it is noteworthy that radical cations and formation of radical cation products are observed. Three reactions, the hydrazone formation by phenyl hydrazine and indoline-2,3-dione, the Katritzky reaction between a pyrylium salt and anisidine, and the Hantzsch synthesis of 1,4-dihydropyridine, were investigated by this system and reaction acceleration was observed to different extents. The increase in rate relative to that for the corresponding bulk reactions is attributed to solvent evaporation which increases concentration, and to the increase of surface-to-volume ratio with enhanced interfacial reaction rate constants. Later work in this thesis describes explicit solvent calculations to study the energies and structures of the hydrazone formation reaction from phenylhydrazine and indoline-2,3-dione in acidic methanol with density functional tight binding (DFTB) methods. Additionally, the thesis covers MS based methods for determination of isoaspartate and aspartate in peptide by gas-phase chemistry and detection of S-nitrosoglutathione in exhaled breath condensate sample.</a></p>

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Master of Science / Department of Chemistry / Duy H. Hua / (+)-myriceric acid A is known as a non-peptide ETA receptor antagonist. It is isolated from the natural plant Myrica cerfera with 0.01% yield which is very low. The total synthesis of (+)-myriceric acid A is being pursued in Hua’s lab. (+)-myriceric acid A specifically blocks the vasoconstriction caused by endothelin-1 (ET-1). Because some derivatives of (+)-myriceric acid A were shown to have ET-1 receptor antagonistic effect, the tetracyclic terpenoid intermediates toward the total synthesis of (+)-myriceric acid A are postulated to have the similar antagonistic activities. The objective of this project is to study the release of vasoconstriction of these synthetic intermediates and compare their antagonistic potency. The ET-1 receptor antagonistic bioactivity of six (+)-myriceric acid A intermediates as well as (+)-myriceric acid A were evaluated by the in vitro spiral modiolar artery (SMA) bioassay. The synthetic intermediates which have not been reported in the literature were previously synthesized in Hua’s laboratory by Dr. Angelo Aguilar and Dr. Aibin Shi. Their synthesis was described in Dr. Aguilar’s PhD thesis. All the antagonistic effect evaluations were based on the SMA’s diameter changes. SMA’s diameter changes were induced by the superfusion of different extracellular solutions. The dose-response curves and straight lines were plotted to compare the antagonistic potency of these compounds. Based on the EC50 value of (+)-myriceric acid A intermediates (0.090 µM ~ 0.582 µM for the curves and 0.095 µM ~ 0.385 µM for the straight lines), all of the compounds have ET-1 receptor antagonistic activity, therefore the synthesis and screening of (+)-myriceric acid A intermediates is probably a promising route to develop new non-peptide ETA receptor antagonists.

Background The Red proteins of lambda phage mediate probably the simplest and most efficient homologous recombination reactions yet described. However the mechanism of dsDNA recombination remains undefined. Results Here we show that the Red proteins can act via full length single stranded intermediates to establish single stranded heteroduplexes at the replication fork. We created asymmetrically digestible dsDNA substrates by exploiting the fact that Redα exonuclease activity requires a 5' phosphorylated end, or is blocked by phosphothioates. Using these substrates, we found that the most efficient configuration for dsDNA recombination occurred when the strand that can prime Okazaki-like synthesis contained both homology regions on the same ssDNA molecule. Furthermore, we show that Red recombination requires replication of the target molecule. Conclusions Hence we propose a new model for dsDNA recombination, termed "beta" recombination, based on the formation of ssDNA heteroduplexes at the replication fork. Implications of the model were tested using (i) an in situ assay for recombination, which showed that recombination generated mixed wild type and recombinant colonies; and (ii) the predicted asymmetries of the homology arms, which showed that recombination is more sensitive to non-homologies attached to 5' than 3' ends. Whereas beta recombination can generate deletions in target BACs of at least 50 kb at about the same efficiency as small deletions, the converse event of insertion is very sensitive to increasing size. Insertions up to 3 kb are most efficiently achieved using beta recombination, however at greater sizes, an alternative Red-mediated mechanism(s) appears to be equally efficient. These findings define a new intermediate in homologous recombination, which also has practical implications for recombineering with the Red proteins.

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The presented master thesis is devoted to the investigation of reaction intermediates in homogeneous gold catalysis. Electrospray ionization mass spectrometry (ESI-MS) was used as the primary research technique in this study. Delayed reactant labeling was used as the main method. I have focused mainly on the hydration of 1-phenyl-1-propyne catalyzed by the gold complex [Au(IPr)(MeCN)]BF4 (IPr = 1,3-bis(2,6-di-iso-propylphenyl)imidazol-2- ylidene). I have detected two main intermediates containing one or two gold atoms, respectively (monoaurated and diaurated intermediate). I have obtained rate constants for the degradation of the reaction intermediates and their half-lives. I have derived kinetic isotope effects for the formation and the decomposition of the detected intermediates. I have shown that the kinetics of the degradation of both intermediates is identical, therefore I conclude that hydration of alkynes catalyzed by gold complex [Au(IPr)(MeCN)]BF4 proceeds most probably via neutral monoaurated intermediates. These neutral intermediates are detected by ESI-MS as protonated (monoaurated intermediate) or tagged by a second gold cation (diaurated intermediate). Key words: gold catalysis, reaction intermediates, electrospray ionization, mass spectrometry.

O sistema quimiluminescente peróxi-oxalato vem sendo estudado por diversos grupos de pesquisa ao redor do mundo desde os anos 60. Esse interesse em especial se deve ao fato de que em comparação com a maioria dos sistemas quimiluminescentes, que apresentam rendimentos quânticos da ordem de 1%, esse sistema apresenta rendimentos quânticos de emissão consideravelmente maiores, cerca de 30%. O sistema peróxi-oxalato consiste na reação de ésteres fenólicos substituídos derivados do ácido oxálico com peróxido de hidrogênio, catalisada por uma base e em presença de compostos aromáticos policondensados fluorescentes com baixo potencial de oxidação, chamados de ativadores (ACT). O mecanismo desta reação, apesar de intensamente estudado, ainda não se encontra completamente esclarecido. Especificamente, a estrutura do intermediário formado durante a reação, que é responsável pela quimiexcitação do ativador, não é conhecida ainda. No presente trabalho, foram completados estudos previamente efetuados no nosso grupo com derivados perácidos, intermediários na reação peróxi-oxalato. Foram sintetizados e caracterizados dois novos derivados perácido, o O,Ohidrogênio monoperóxi-oxalato de 3-clorofenila e o O,O-hidrogênio monoperóxioxalato de 3-nitrofenila. Dos estudos cinéticos da reação destes perácidos com imidazol, na presença de 9,10-difenilantraceno como ativador, foram obtidos constantes de velocidade de ciclização e rendimentos quânticos singlete. As constantes de velocidade determinadas, junto com os dados obtidos anteriormente no grupo, mostram correlação linear de energia livre com as constantes de substituintes de Hammett, obtendo-se um valor de = 2,18 ± 0,16, o que indica a formação de alta densidade de carga negativa no estado de transição do passo lento. A correlação linear entre as constantes de velocidade e os valores de pKa dos grupos de partida fenólicos levou à determinação do valor de &#946;GP = -1,07 ± 0,08, indicando que a quebra da ligação para o grupo de partida é muito avançada no estado de transição no passo lento da reação. Os rendimentos quânticos singlete mostram dependência com as propriedades eletrônicas dos substituintes, aumentando inicialmente com o aumento das propriedades de atração de elétron do substituinte, porém, com substituintes mais atraentes que hidrogênio, observa-se uma leve diminuição no rendimento quântico. O conjunto de dados apresentados neste trabalho, junto com os resultados obtidos anteriormente pelo grupo, demonstra claramente que a reação de ciclização dos perácidos, catalisada por imidazol, deve ocorrer de maneira concertada, ou seja, a saída do grupo de partida fenólico ocorre em conjunto com o ataque nucleofílico do íon percarboxilato à função éster no passo lento da reação. Conseqüentemente, foram obtidas neste trabalho evidências experimentais fundamentadas para a ocorrência da 1,2- dioxetanodiona como intermediário de alta energia na reação peróxi-oxalato. / The peroxyoxalate chemiluminescence has been intensely studied since the sixties by several research groups all around the world. This interest is mainly due to the fact that the peroxyoxalate system is highly efficient, showing quantum yields of around 30 %, much higher than other well known chemiluminescence reactions which commonly show quantum yields of around 1% or less. The peroxyoxalate system consists in the base catalyzed reaction of activated oxalate esters with hydrogen peroxide in the presence of highly fluorescent polycondensed aromatic hydrocarbons with low oxidation potentials, called activators (ACT). Although intensely investigated, the mechanism of this complex transformation is still not yet completely clarified. This is true specifically for the structure of the high-energy intermediate, formed during the reaction sequence, which is responsible for chemiexcitation, not known at all up to now. In the present work, former studies of our group on peracid derivatives, intermediates in the peroxyoxalate reaction, were completed. Two new peracid derivatives, 3-chlorophenyl O,O-hydrogen monoperoxyoxalate and 3- nitrophenyl O,O-hydrogen monoperoxyoxalate were synthesized and characterized. Kinetic studies on the reaction of these peracid derivatives with imidazole, in the presence of 9,10-diphenylanthracene as activator, led to the determination of cyclization rate constants and singlet quantum yields. These rate constants, together with data formerly obtained by our group, show linear free-energy correlation with the Hammett substituent constants, resulting in a reaction constant of = 2,18 ± 0,16, that indicates the formation of a high negative charge density in the transition state of the rate-limiting step. Similarly, the linear correlation of the rate constants with the pKa values of the phenolic leaving groups leads to the determination of a value &#946;GP = -1,07 ± 0,08, indicating a high degree of leaving group bond cleavage in the transition state of the rate-limiting step. The singlet quantum yields also show dependence on the electronic properties of the substituents, initially increasing with the increase in the electron withdrawing nature of the substituent, however, a slight decrease in the quantum yields is observed with substituents more electron withdrawing than hydrogen. The data accumulated in this work, together with results earlier obtained in our group, clearly demonstrate that the cyclization reaction of the peracid derivatives, catalyzed by imidazole, proceeds in a concerted manner, i.e. the phenolic leaving group departure occurs together with the nucleophilic percarboxylate attach to the ester function in the rate-limiting reaction step. Consequently, it was possible to obtain in this work solid experimental evidence for the occurrence of 1,2-dioxetandione as the high-energy intermediate in the peroxyoxalate reaction.

We report here the development of a Lewis acid catalyzed method for the dehydrative coupling of cyclic alcohols and nitriles to form amides with retention of configuration. By contrast, the formation of amides by nitrile trapping of carbocations (Ritter reaction) usually affords racemic product. The present reaction was accomplished by first converting alcohol starting materials to their corresponding chlorosulfites in situ. Even after an extensive search, only copper (II) salts were able to produce the desired conversion of these chlorosulfites to amides though with low catalytic turnover. Improving the turnover without deteriorating the stereochemical outcome was eventually accomplished by a careful selection of the reagent addition sequence and through the removal of gaseous byproducts. This Ritter-like coupling reaction proceeds in good yields with secondary cyclic alcohols under mild conditions. The stereochemical outcome likely due to fast nucleophilic capture of a non-planar carbocations (hyperconjomers) stabilized by ring hyperconjugation. / Includes bibliography. / Dissertation (Ph.D.)--Florida Atlantic University, 2014. / FAU Electronic Theses and Dissertations Collection