The carbonate radical anion CO3•- is a potent reactive oxygen species (ROS) produced in vivo through enzymatic one-electron oxidation of bicarbonate or, mostly, via the reaction of CO2 with peroxynitrite. Due to the vitally essential role of the carbon dioxide/bicarbonate buffer system in regulation of physiological pH, CO3•- is arguably one of the most important ROS in biological systems. So far, the studies of reactions of CO3•- with DNA have been focused on the pathways initiated by oxidation of guanines in DNA. In this study, low-molecular products of attack of CO3•- on the sugar-phosphate backbone in vitro were analyzed by reversed phase HPLC. The selectivity of damage in double-stranded DNA (dsDNA) was found to follow the same pattern C4′ > C1′ > C5′ for both CO3•- and the hydroxyl radical, though the relative contribution of the C1′ damage induced by CO3•- is substantially higher. In single-stranded DNA (ssDNA) oxidation at C1′ by CO3•- prevails over all other sugar damages. An approximately 2000-fold preference for 8-oxoguanine (8oxoG) formation over sugar damage found in our study identifies CO3•- primarily as a one-electron oxidant with fairly low reactivity toward the sugar-phosphate backbone.

An O-methylated analog of protonated phenazine-di-N-oxide radical anion abstracts hydrogen from primary and secondary alcohols in a slow (k1 < 500 M-1 s-1) bimolecular reaction. No kinetic evidence has been found for the unimolecular release of free methoxyl radicals through the homolytic N-OMe bond cleavage in these species. DFT calculations at the UB3LYP 6-31G(d) level indicate that protonated and O-alkylated radical anions of pyrazine, quinoxaline and phenazine di-N-oxides are close analogues of aromatic nitroxyl radicals with the highest spin density localized on the oxygen and nitrogen of the nitrone moiety.

No description available.

Ultrahigh vacuum (UHV) surface science experiments were designed to study reaction kinetics and mechanisms of gas-phase NO₃ radicals with well-organized, highly characterized, organic thin films. The surface reactions were monitored in situ with reflection-absorption infrared spectroscopy (RAIRS). The oxidation states of surface-bound molecules were identified with X-ray photoelectron spectroscopy (XPS). Consumption of vinyl groups was observed concurrently with formation of organic nitrates in RAIRS. XPS spectra showed little oxidation of sulfur head groups. The observed rate constant was determined based on the consumption of carbon-carbon double bonds and the formation of organic nitrates. Using this rate constant, the initial reaction probability was determined to be (3 ± 1) X 10⁻³. This reaction probability is approximately two orders of magnitude higher than that for the reactions between the same surface and pure O₃, which is due to the higher electron affinity of NO₃ relative to O₃. These results led to the development of a proposed mechanism that involves electrophilic addition of NO₃ to the double bonds. Reactions between NO₃ and a methyl-terminated SAM were also monitored in situ with RAIRS. In the CH3-SAM studies, hydrogen abstraction was observed during NO3 exposure. The results presented in this thesis should help develop an understanding of the fundamental interfacial reaction dynamics of NO₃ radicals with organic surfaces. / Master of Science

[EN] Bile acids are a family of amphiphilic steroids that play a pivotal role in physiological functions such as elimination of cholesterol or solubilization of lipids. Chemically, they share a steroidal skeleton with an unusual cis fusion between rings A and B, a short lateral chain ending in a carboxylic acid moiety and different number of hydroxyl groups on the alpha-face. Hence, bile acids offer a versatile architecture that can be used to investigate photophysical processes of interest such as hydrogen atom transfer, through-bond energy trasfer, through-bond exciplex formation and DNA photodamage-related reactions. First, unmodified bile acids have been used to evaluate hydrogen atom trasfer to benzophenone-like triplet carbonyls. Dehydrogenation of bile acids at positions C-3 and/or C-7 by a radical-mediated mechanism from the excited state of benzophenone has been demonstrated. Moreover, synthesized lithocholic acid derivatives including benzophenone or carbazole as donors and a naphthalene, biphenyl or thymine as acceptors have been employed to investigate through-bond energy transfer and exciplex formation processes. Thus, energy transfer from benzophenone to naphthalene or biphenyl and extended through-bond exciplex formation in benzophenone/naphthalene and benzophenone/biphenyl linked systems has been demostrated by laser flash photolysis. Finally, bile acid derivatives incorporating one benzophenone and two thymine units with different degrees of freedom have been prepared to investigate the photochemical formation of oxetanes or thymine dimers. Photosensitized formation of cyclobutane pyrimidine dimers through the generation of a delocalized triplet excited state has been demonstrated in intermolecular systems, while oxetane formation is observed when the degrees of freedom are reduced. / [ES] Los ácidos biliares son una familia de esteroides anfifílicos que juegan un papel clave en diferentes funciones fisiológicas tales como la eliminación del colesterol o la solubilización de lípidos. Su estructura química está constituida por un esqueleto esteroideo con una fusión cis poco común entre los anillos A y B, una cadena lateral corta que termina con una función ácida y un número variable de grupos hidroxilo en la cara alfa. Por tanto, los ácidos biliares ofrecen una estructura versátil que puede ser utilizada para investigar procesos fotofísicos de interés como abstracción de hidrógeno, transferencia de energía y formación de exciplejos a larga distancia o reacciones relacionadas con el daño fotoinducido al ADN. En esta Tesis, en primer lugar, los ácidos biliares naturales se han utilizado para evaluar la abstracción de hidrógeno a carbonilos triplete en compuestos derivados de la benzofenona, demostrándose la deshidrogenación de los ácidos biliares en las posiciones C-3 y/o C-7 por un mecanismo radicalario desde el mencionado triplete de la benzofenona. En segundo lugar, se han preparado derivados de ácido litocólico que incluyen los dadores benzofenona o carbazol y los aceptores naftaleno, bifenilo o timina, que a continuación se han utilizado para investigar los procesos de transferencia de energía y formación de exciplejo intramolecular a larga distancia. De hecho, en los sistemas benzofenona/naftaleno y benzofenona/bifenilo, se demostró por fotólisis de destello láser la transferencia de energía desde benzofenona a naftaleno o bifenilo y la formación de exciplejo a larga distancia. Por último, se han preparado derivados de ácidos bliares que incorporan una unidad de benzofenona y dos de timina en diferentes posiciones del esqueleto para investigar la influencia de los diferentes grados de libertad en la formación fotosensibilizada de oxetanos o dímeros de timina. Gracias a ellos, se ha demostrado la formación fotosensibilizada de dímeros ciclobutánicos pirimidínicos a través de la generación de estados excitados triplete deslocalizados en sistemas en los que la benzofenona es intermolecular, mientras que se observa formación de oxetanos cuando los grados de libertad se ven reducidos. / [CAT] Els àcids biliars són una família d'esteroides anfifílics que juguen un paper clau en funcions fisiològiques com l'eliminació del colesterol o la solubilització de lípids. La seua estructura química està constituïda per un esquelet esteroïdal amb una fusió cis entre els anells A i B poc comuna, una cadena lateral curta que acaba amb una funció àcida i un nombre diferent de grups hidroxil en la cara alfa. D'aquesta manera, els àcids biliars ofereixen una estructura versàtil que pot ser utilitzada per investigar processos fotofísics d'interès com abstracció d'hidrogen, transferència d'energia i formació de exciplexes a llarga distància o reaccions relacionades amb el dany a l'ADN induït per llum. En primer lloc, els àcids biliars naturals s'han utilitzat per avaluar la abstracció d'hidrogen a carbonils triplets derivats de la benzofenona, demostrant-se la deshidrogenació dels àcids biliars en les posicions C-3 i/o C-7 per un mecanisme radicalari des de l'estat excitat de la benzofenona. A més, derivats d'àcid litocòlic que inclouen els donadors benzofenona o carbazol i els acceptors naftalé, bifenil o timina s'han utilitzat per investigar els processos de transferència d'energia i formació de exciplexe a llarga distància. En els sistemes benzofenona /naftalé i benzofenona/bifenil la fotòlisis làser va demostrar la transferència d'energia des de benzofenona a naftalé o bifenil i la formació d'exciplexe a llarga distància. Finalment, per tal d'investigar la formació fotosensibilitzada d'oxetans o dímers de timina, s'han preparat derivats d'àcids bliars que incorporen una unitat de benzofenona i dues de timina amb diferents graus de llibertat. La formació fotosensibilitzada de dímers ciclobutànics pirimidínics mitjançant la generació d'estats excitats triplet deslocalitzats ha estat demostrada en sistemes intermoleculars, mentre que la formació d'oxetans s'observa quan els graus de llibertat es veuen reduïts. / Miró Richart, P. (2016). Hydrogen-Abstraction, Energy Transfer and Exciplex Formation in Photoactive Systems Based on Bile Acids [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/64084 / TESIS

No description available.

The accuracy of a quantum chemical calculation inherently depends on the ability to account for the completeness of the one- and n-particle spaces. The size of the basis set used can be systematically increased until it reaches the complete one-particle basis set limit (CBS) while the n-particle space approaches its exact full configuration interaction (FCI) limit by following a hierarchy of electron correlation methods developed over the last seventy years. If extremely high accuracy is desired, properly correcting for very small effects such as those resulting the Born-Oppenheimer approximation and the neglect of relativistic effects becomes indispensable. For a series of chemically interesting and challenging systems, we identify the limits of conventional approaches and use state-of-the-art quantum chemical methods along with large basis sets to get the “right answer for the right reasons.” First, we quantify the importance of small effects that are ignored in conventional quantum chemical calculations and manage to achieve spectroscopic accuracy (agreement of 1 cm−1 or less with experimental harmonic vibrational frequencies) for BH, CH+ and NH. We then definitively resolve the global minimum structure for Li₆ , Li₆⁺ , and Li₆- using high accuracy calculations of the binding energies, ionization potentials, electron affinities and vertical excitation spectra for the competing isomers. The same rigorous approach is used to study a series of hydrogen transfer reactions and validate the necessary parameters for the hydrogen abstraction and donation steps in the mechanosynthesis of diamondoids. Finally, in an effort to overcome the steep computational scaling of most high-level methods, a new hybrid methodology which scales as O(N⁵) but performs comparably to O(N⁶) methods is benchmarked for its performance in the equilibrium and dissociation regimes.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / In this study, it has been carried out quantum molecular dynamics simulations for the hydrogen abstraction reaction from methane, silane, germane and stannane by H, F, Cl and I atoms and being or not being induced by femtosecond laser pulses with the aim to favor the dissociation of the M-H (M = C, Si, Ge and Sn). All the simulations have been performed using a simulation scheme based on ab initio calculations of molecular dynamics, where the motion of the atomic nuclei is described classically while the electrons are treated quantically by the Density Functional Theory (DFT). The results of the molecular dynamics simulations for the hydrogen abstraction reaction from methane, that is a very inert molecule, show that only the fluorine atom is able to promote the dissociation of the C-H bond. For the simulations performed in the presence of the electromagnetic radiation, it was possible to observe that the femtosecond laser pulse could induce the hydrogen abstraction from methane when the reaction occurs with the hydrogen or fluorine atom. The results of the molecular dynamics simulations for the hydrogen abstraction reaction from silane show that also the fluorine as the hydrogen atoms are able to dissociate effectively the Si-H bond in silane. In the case of the hydrogen abstraction from silane by the chlorine atom, the effective Si-H dissociation does not happen. In the simulations including the pulsed electromagnetic radiation, it is observed that it was possible to favor even more the hydrogen abstraction reaction from silane by the hydrogen and fluorine atoms, moreover, it was possible to turn effective the dissociation of the Si-H bond by the chlorine atom. The GeH4 and SnH4 molecules could be easily dissociated by the hydrogen, fluorine and chlorine atoms. About the iodine atom, it was not able to promote the hydrogen abstraction reaction in germane and stannane, even in the presence of the femtosecond laser pulse. / Neste trabalho foram realizadas simulações de dinâmica molecular quântica para as reações de abstração de hidrogênio nas moléculas de metano, silano, germano e estanano por átomos de H, F, Cl, e I sendo realizadas simulações sem e com o uso do pulso de laser de femtosegundos com o objetivo de favorecer a quebra das ligações M-H (M = C, Si, Ge ou Sn). Todas as simulações foram realizadas utilizando um esquema baseado em cálculos ab initio de dinâmica molecular, onde o movimento dos núcleos atômicos é descrito classicamente, enquanto os elétrons são tratados quanticamente pela Teoria do Funcional de Densidade (DFT). Os resultados das simulações de dinâmica molecular das reações de abstração de hidrogênio no metano mostram que, por esta molécula ser bastante inerte, somente o átomo de flúor é capaz de promover a dissociação da ligação C-H. Para as simulações realizadas na presença da radiação eletromagnética, foi possível observar que o pulso de laser consegue favorecer a abstração de hidrogênio no metano quando a reação acontece com o átomo de hidrogênio ou flúor. Os resultados das simulações de dinâmica molecular para a reação de abstração de hidrogênio no silano mostram que tanto o átomo de flúor quanto o de hidrogênio são capazes de promover a captura do átomo de hidrogênio promovendo a quebra da ligação Si-H. No caso da reação de abstração de hidrogênio na molécula de silano por átomo de cloro, a quebra efetiva da ligação Si-H não acontece. Nas simulações com a radiação eletromagnética pulsada observa-se que foi possível favorecer ainda mais as reações de abstração de hidrogênio no silano por átomos de flúor e hidrogênio, além de tornar efetiva a ruptura da ligação Si-H na reação com o átomo de cloro. As ligações químicas Ge-H e Sn-H nas moléculas de GeH4 e SnH4 conseguiram ser quebradas facilmente nas reações de abstração de hidrogênio por átomos de hidrogênio, flúor e cloro. Quanto ao átomo de iodo, este não foi capaz de promover a reação de abstração de hidrogênio nas moléculas de germano e estanano, mesmo na presença do pulso de laser de femtosegundos.

<p>Quantum chemical calculations have been performed to investigate radical cation rearrangement, radical carbonylation, and homolytic substitution reactions of organic molecules.</p><p>The rearrangement of the bicyclopropylidiene radical cation to the tetramethyleneethane radical cation is predicted to proceed with stepwise disrotatory opening of the two rings. Each ring opening is found to be combined with a striking pyramidalization of a carbon atom in the central bond.</p><p>The isomerization of the norbornadiene radical cation to the cycloheptatriene radical cation (<b>CHT</b><b>.+</b>), initialized by opening of a bridgehead–methylene bond, is investigated. The most favorable path involves concerted rearrangement to the norcaradiene radical cation followed by ring opening to <b>CHT</b><b>.+</b>. The barrier of this channel is found to be significantly reduced upon substitution of the methylene group with C(CH₃)₂.</p><p>Stepwise mechanisms are predicted to be favored over concerted isomerization for the McLafferty rearrangement of the radical cations of butanal and 3-fluorobutanal. The barrier for the concerted rearrangement is found to be lowered by 17.2 kcal/mol upon substitution, a result which is rationalized by the calculated dipole moments and atomic charges.</p><p>Recent experiments showed that photoinitiated carbonylation of alkyl iodides with [¹¹C]carbon monoxide may be significantly enhanced by using small amounts of ketones that have nπ* character of their excited triplet state. DFT calculations show the feasibility of an atom transfer type mechanism, proposed to explain these observations. Moreover, the computational results rationalize the observed differences in yield when using various alcohol solvents.</p><p>Finally, following photolysis of methyliodide, recent electron spin resonance spectroscopy experiments demonstrated that the S_H2 reaction ^•CD₃ + SiD₃CH₃ → CD₃SiD₃ + ^•CH₃ proceeds with high selectivity over the energetically more favorable D abstraction. The role of geometrical effects, especially the formation of prereactive complexes between methylsilane and methyliodide is studied, and a plausible explanation for the experimentally observed paradox is presented.</p>

Quantum chemical calculations have been performed to investigate radical cation rearrangement, radical carbonylation, and homolytic substitution reactions of organic molecules. The rearrangement of the bicyclopropylidiene radical cation to the tetramethyleneethane radical cation is predicted to proceed with stepwise disrotatory opening of the two rings. Each ring opening is found to be combined with a striking pyramidalization of a carbon atom in the central bond. The isomerization of the norbornadiene radical cation to the cycloheptatriene radical cation (CHT.+), initialized by opening of a bridgehead–methylene bond, is investigated. The most favorable path involves concerted rearrangement to the norcaradiene radical cation followed by ring opening to CHT.+. The barrier of this channel is found to be significantly reduced upon substitution of the methylene group with C(CH3)2. Stepwise mechanisms are predicted to be favored over concerted isomerization for the McLafferty rearrangement of the radical cations of butanal and 3-fluorobutanal. The barrier for the concerted rearrangement is found to be lowered by 17.2 kcal/mol upon substitution, a result which is rationalized by the calculated dipole moments and atomic charges. Recent experiments showed that photoinitiated carbonylation of alkyl iodides with [11C]carbon monoxide may be significantly enhanced by using small amounts of ketones that have nπ* character of their excited triplet state. DFT calculations show the feasibility of an atom transfer type mechanism, proposed to explain these observations. Moreover, the computational results rationalize the observed differences in yield when using various alcohol solvents. Finally, following photolysis of methyliodide, recent electron spin resonance spectroscopy experiments demonstrated that the SH2 reaction •CD3 + SiD3CH3 → CD3SiD3 + •CH3 proceeds with high selectivity over the energetically more favorable D abstraction. The role of geometrical effects, especially the formation of prereactive complexes between methylsilane and methyliodide is studied, and a plausible explanation for the experimentally observed paradox is presented.