Diss. (sammanfattning) Uppsala : Uppsala universitet, 2007. / Härtill 6 uppsatser.

Diss. (sammanfattning) Uppsala : Univ., 2007. / Härtill 4 uppsatser.

Diss. (sammanfattning) Uppsala : Univ., 2003. / Härtill 6 uppsatser.

Diss. (sammanfattning) Uppsala : Uppsala universitet, 2006. / Härtill 7 uppsatser.

<p>Chemical reactions are ubiquitous and very important for life and many other processes taking place on earth. In both theoretical and experimental studies of reactivity a transition state is often used to rationalise the outcome of such studies. The present thesis deals with calculations of transition states in radical cation rearrangements, and a principle of least motion study of the rearrangements in the barbaralyl cation.</p><p>In particular, alternative quadricyclane radical cation (<b>Q∙</b><b>+</b>) rearrangements are extensively studied. The rearrangement of <b>Q∙</b><b>+</b> to norbornadiene is extremely facile and is often used as a prototype for one-electron oxidations. However, electron spin resonance (ESR) experiments show that there are additional cations formed from <b>Q∙</b><b>+</b>. Two plausible paths for the rearrangement of <b>Q∙</b><b>+</b> to the 1,3,5-cycloheptatriene radical cation are located. The most favourable one is a multistep rearrangement with two shallow intermediates, which has a rate-limiting step of 16.5 kcal/mol. In addition, a special structure, the bicyclo[2.2.1]hepta-2-ene-5-yl-7-ylium radical cation, is identified on these alternative paths; and its computed ESR parameters agree excellently with the experimental spectrum assigned to another intermediate on this path. Moreover, this cation show a homoconjugative stabilization, which is uncommon for radical cations.</p><p>The bicyclopropylidene (<b>BCP</b>) radical cation undergoes ring opening to the tetramethyleneethane radical cation upon γ-irradiation of the neutral <b>BCP</b>. This rearrangement proceeds through a stepwise mechanism for the first ring opening with a 7.3 kcal/mol activation energy, while the second ring opening has no activation energy. The dominating reaction coordinate during each ring opening is an olefinic carbon rehybridization.</p><p>The principle of least motion is based on the idea that, on passing from reactant to product, the reaction path with the least nuclear change is the most likely. By using hyperspherical coordinates to define a distance measure between conformations on a potential energy surface, a possibility to interpret reaction paths in terms of distance arises. In applying this measure to the complex rearrangements of the barbaralyl cation, a correct ordering of the conformations on this surface is found.</p>

<p>In this thesis, quantum chemical calculations are undertaken mostly in order to interpret experimental results, but also to learn about computational techniques, their performance and their limitations. In paper I, the ionization-cleavage process of alkenes is investigated and two pathways are followed, one of initial cleavage and subsequent ionization and on the opposite, the other one of initial ionization and subsequent cleavage. The calculations reveal that ionization is best described by a vertical process, which is much faster than the relaxation of the molecule to its ionized structural minimum. Further, in paper II, the core hole excited state of ammonia is investigated and found to dissociate in an ultra-fast manner nicely explained by the calculated potential energy surface showing a very low barrier for dissociation. In paper III, the static and dynamic structures of two halogenated dimethyl ether radical cations are studied in ESR experiments, and it is found that, while the chlorinated molecule remains unaffected, the fluorinated molecule undergoes a dissociation or association reaction before the measurement takes place, the resulting fragments are searched for but not identified decisively. In paper IV, the stability of Jahn-Teller distorted selectively deuteriated benzene radical cation isotopomers is investigated by ESR experiments and density functional theory calculations. The temperature dependence, between 4.2 K and 77 K, of the ESR spectra is explained. Finally, in paper V, the hydrogen inversion in aziridine and methyl and dimethyl substituted aziridines is investigated. The rate constants and kinetic isotope effects are calculated using various techniques of transition state theory and tunneling correction methods.</p>

In this thesis, quantum chemical calculations are undertaken mostly in order to interpret experimental results, but also to learn about computational techniques, their performance and their limitations. In paper I, the ionization-cleavage process of alkenes is investigated and two pathways are followed, one of initial cleavage and subsequent ionization and on the opposite, the other one of initial ionization and subsequent cleavage. The calculations reveal that ionization is best described by a vertical process, which is much faster than the relaxation of the molecule to its ionized structural minimum. Further, in paper II, the core hole excited state of ammonia is investigated and found to dissociate in an ultra-fast manner nicely explained by the calculated potential energy surface showing a very low barrier for dissociation. In paper III, the static and dynamic structures of two halogenated dimethyl ether radical cations are studied in ESR experiments, and it is found that, while the chlorinated molecule remains unaffected, the fluorinated molecule undergoes a dissociation or association reaction before the measurement takes place, the resulting fragments are searched for but not identified decisively. In paper IV, the stability of Jahn-Teller distorted selectively deuteriated benzene radical cation isotopomers is investigated by ESR experiments and density functional theory calculations. The temperature dependence, between 4.2 K and 77 K, of the ESR spectra is explained. Finally, in paper V, the hydrogen inversion in aziridine and methyl and dimethyl substituted aziridines is investigated. The rate constants and kinetic isotope effects are calculated using various techniques of transition state theory and tunneling correction methods.

Chemical reactions are ubiquitous and very important for life and many other processes taking place on earth. In both theoretical and experimental studies of reactivity a transition state is often used to rationalise the outcome of such studies. The present thesis deals with calculations of transition states in radical cation rearrangements, and a principle of least motion study of the rearrangements in the barbaralyl cation. In particular, alternative quadricyclane radical cation (Q∙+) rearrangements are extensively studied. The rearrangement of Q∙+ to norbornadiene is extremely facile and is often used as a prototype for one-electron oxidations. However, electron spin resonance (ESR) experiments show that there are additional cations formed from Q∙+. Two plausible paths for the rearrangement of Q∙+ to the 1,3,5-cycloheptatriene radical cation are located. The most favourable one is a multistep rearrangement with two shallow intermediates, which has a rate-limiting step of 16.5 kcal/mol. In addition, a special structure, the bicyclo[2.2.1]hepta-2-ene-5-yl-7-ylium radical cation, is identified on these alternative paths; and its computed ESR parameters agree excellently with the experimental spectrum assigned to another intermediate on this path. Moreover, this cation show a homoconjugative stabilization, which is uncommon for radical cations. The bicyclopropylidene (BCP) radical cation undergoes ring opening to the tetramethyleneethane radical cation upon γ-irradiation of the neutral BCP. This rearrangement proceeds through a stepwise mechanism for the first ring opening with a 7.3 kcal/mol activation energy, while the second ring opening has no activation energy. The dominating reaction coordinate during each ring opening is an olefinic carbon rehybridization. The principle of least motion is based on the idea that, on passing from reactant to product, the reaction path with the least nuclear change is the most likely. By using hyperspherical coordinates to define a distance measure between conformations on a potential energy surface, a possibility to interpret reaction paths in terms of distance arises. In applying this measure to the complex rearrangements of the barbaralyl cation, a correct ordering of the conformations on this surface is found.

Theoretical studies on biological systems like nucleic acid and protein have been widely developed in the past 50 years and will continue to be a topic of interest in forefronts of natural science. In addition to experimental science, computational modeling can give useful information and help us to understand biochemical issues at molecular, atomic and even electronic levels. Deoxyribonucleic acid (DNA), the hereditary basis of life’s genetic identity, has always been major topic of discussions since its structure was built in 1953. However, harmful UV radiation from sunlight can make damage to DNA molecules and eventually give rise to DNA damaging biological consequences, like mutagenesis, carcinogenesis, and cell death. Photostability, photodamage, and photorepair are of vital importance in the photophysics and photochemistry of DNA. In this thesis, we have applied high level computer-aided theoretical methods to explore the underlying mechanisms for these three critical issues of DNA. Special attentions are paid to the following aspects: the properties of the excited states, the design of relevant computational models and the effects of biological environments. We have systematically studied the excited state properties of DNA from single base to base pair and oligonucleotides, where the concerted base pairing and base stacking effects was found to play important roles in DNA photostability. The UV-light induced isomerization mechanism between two photoproducts of DNA photodamage has been revealed in different biological environments. In association with DNA photodamage, the related photorepair processes have been proposed for different lesions in photolyase which is a catalytic enzyme for DNA, and the calculated results well explained the experimental observations. In particular, the internal and external properties of flavin cofactors have been extensively studied by combining the electronic structure and spectroscopic calculations. We have examined the effects of the intramolecular hydrogen bond on spectroscopic properties of flavins. The good agreements with the experimental spectra indicated that the biological self-regulation acted critical role in these biological systems. / QC 20110530

<p>The quantum chemical investigations presented in this thesis use hybrid density functional theory to shed light on the catalytic mechanisms of mononuclear non-heme iron oxygenases, accommodating a ferrous ion in their active sites. More specifically, the dioxygen activation process and the subsequent oxidative reactions in the following enzymes were studied: tetrahydrobiopterin-dependent hydroxylases, naphthalene 1,2-dioxygenase and α-ketoglutarate-dependent enzymes. In light of many experimental efforts devoted to the functional mimics of non-heme iron oxygenases, the reactivity of functional analogues was also examined.</p><p>The computed energetics and the available experimental data served to assess the feasibility of the reaction mechanisms investigated. Dioxygen activation in tetrahydrobiopterin- and α-ketoglutarate-dependent enzymes were found to involve a high-valent iron-oxo species, which was then capable of substrate hydroxylation. In the case of naphthalene 1,2-dioxygenase, the reactivity of an iron(III)-hydroxperoxo species toward the substrate was investigated and compared to the biomimetic counterpart.</p>