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Interstellar plasma — interstellar clouds in particular — play an important role in determining the structure and evolution of galaxies. Understanding the time evolution of such plasmas requires knowledge of the chemical processes that drive their dynamics. Two processes are studied in this dissertation: radiative electron attachment (REA) via dipole-bound states (DBSs) and dissociative recombination (DR). Of the several hundred molecules detected in the interstellar medium, only eight anions have been detected: CN-, C3N-, C5N-, C7N-, C4H-, C6H-, C8H-, and C10H-. Their production mechanism is not well known; REA was suggested as a possible formation pathway, but previous theoretical studies have found that REA rate coefficients were too low to explain the formation of CN-, C3N-, and C5N-. It was later suggested that including DBSs — an electron weakly bound at a large distance to the large dipole moment of a neutral molecule — could appreciably enhance the REA rate coefficients. The first portion of this study is dedicated to investigating the role of the large dipole moment of rotating C3N using an accurate \it ab initio approach with electronic and rotational resolution. DBS wavefunctions of C3N- are calculated and used to obtain REA cross sections that produce even smaller rate coefficients, suggesting that C3N- is efficiently formed by a different process. The second part of this study investigates DR in the difficult case of molecules with low-lying eletronic resonances, although these are not necessary for the approach. An approach to treat both direct and indirect mechanisms of DR in a diatomic ion with electronic, vibrational, and rotational resolution using R-matrix scattering calculations, frame transformation theory, and multichannel quantum defect theory is presented and applied to the CH+ and CF+ molecular ions at low collision energies. The calculated CH+ cross sections agree well with recent rotationally state-resolved experimental results and overall better than previous theoretical results. The calculated CF+ cross sections agree well with experimental results, although these do not have rotational resolution, and overall better than previous theoretical results at low energies. Additionally, the method can study rovibronic (de-)excitation — a process in competition with DR. These are calculated and compared to previous theoretical calculations for CH+, which which our results agree well with the exception of dipole-driven rotational excitation cross sections. This discrepancy is tentatively attibuted to negelcting the contribution of higher partial waves in the description of the incident electron, which will be incorporated in future studies.

The focus of the presented research is to examine the fundamental physics and chemistry of low-energy electron-stimulated reactions on adsorbate covered single crystal surfaces. Specifically, condensed SiCl₄ on the Si(111) surface and condensed H₂O on the TiO₂ (110) surface have been studied. By varying adsorbate film thicknesses, the coupling strength of the target molecule to the substrate and surrounding media dictates the progression of the electron induced reactions. To investigate the electron interactions with SiCl₄ on the Si(111) surface, desorbing cations and neutrals were detected via time of flight mass spectrometry (ToF-MS) where neutral chlorine atoms were ionized using a resonance enhanced multi-photon ionization (REMPI) technique. Structure in the cation and neutral yields were assigned to molecular excitations. At an incident electron energy of 10 eV, a resonance structure in the neutral yields was attributed to a negative ion resonance and observed in thick and thin films of SiCl₄. With monoenergetic electrons, specific surface reactions can be controlled which have implications for film growth, surface patterning and masking, and etching. For the H₂O/TiO₂ (110) system, the water interactions with the TiO₂ surface are revealed through the strong electron induced reaction dependencies on the water coverage. Understanding the nonthermal reaction landscape of H₂O on the TiO₂ (110) surface is crucial for developing the system as a catalytic source of hydrogen. The electron-stimulated oxidation of the TiO₂ (110) surface and electron induced sputtering of H ₂O was investigated. Irradiation of water films ([coverage]< 3 ML) oxidized the TiO₂ (110) surface similarly as surface oxidation via O₂ deposition. Each H₂O molecule in the first monolayer seems to be a target for the incoming electron initiating the oxidation. However, water coverages greater than a monolayer limited the oxidation process. The electron-stimulated desorption and sputtering yields of water from the TiO₂ (110) surface were measured as a function of water coverage. Surprisingly, the amount of water sputtered from the surface is nonlinearly dependent on water coverage.

Ribonucleotide reductases (RNR) are essential enzymes that catalyze the reduction of ribonucleotides to 2'-deoxyribonucleotides, which is a critical step that produces precursors for DNA replication and repair. The inactivation of RNR, logically, would discontinue producing the precursors of the DNA of viral or cancer cells, which then would consequently end the cycle of DNA replication. Among different compounds that were found to be inhibitors of RNR, 2'-azido-2'-deoxynucleotide diphosphates (N3NDPs) have been investigated in depth as potent inhibitors of RNR. Decades of investigation has suggested that the inactivation of RNR by N3NDPs is a result of the formation of a nitrogen-centered radical (N•) that is covalently attached to the nucleotide at C3' and cysteine molecule C225 [3'-C(R-S-N•-C-OH)]. Biomimetic simulation reactions for the generation of the nitrogen-centered radicals similar to the one observed during the inactivation of the RNR by azionuclotides was investigated. The study included several modes: (i) theoretical calculation that showed the feasibility of the ring closure reaction between thiyl radicals and azido group; (ii) synthesis of the model azido nucleosides with a linker attached to C3' or C5' having a thiol or vicinal dithiol functionality; (iii) generation of the thiyl radical under both physiological and radiolysis conditions whose role is important in the initiation on RNR cascades; and (iv) analysis of the nitrogen-centered radical species formed during interaction between the thiyl radical and azido group by electron paramagnetic resonance spectroscopy (EPR). Characterization of the aminyl radical species formed during one electron attachment to the azido group of 2'-azido-2'-deoxyuridine and its stereospecifically labelled 1'-, 2'-, 3'-, 4'- or 5,6-[2H2]-analogues was also examined. This dissertation gave insight toward understanding the mechanism of the formation of the nitrogen-centered radical during the inactivation of RNRs by azidonucleotides as well as the mechanism of action of RNRs that might provide key information necessary for the development of the next generation of antiviral and anticancer drugs.

L’étude des mécanismes de formation et de destruction des anions moléculaires est devenu un champ d’intérêt prononcé après la détection récente de six anions moléculaires (C4H-, C6H-, C8H-, CN-, C3N-, C5N-) dans le milieu interstellaire.Dans les environnements interstellaires où la densité d’électrons est relativement importante, le canal principal de formation de ces anions devrait être l’attachement électronique radiatif. Mais il manque aujourd’hui des données expérimentales et théoriques permettant d’évaluer cette hypothèse. D’autre part, le photodétachement est la principale cause de destruction de ces anions dans les nuages diffus et les régions de photodissociation. Une approche basée sur un développement monocentrique est appliquée à l’étude de ces deux processus opposés que sont le photodétachement et l’attachement électronique radiatif. Les résultats obtenus avec la présente méthode sont comparés à des données expérimentales et théoriques précédemment rapportées et montrent un bon accord. Cette méthode est ensuite utilisée pour déterminer les constantes de vitesse nécessaires pour confirmer si ces mécanismes sont cruciaux pour la chimie d’anions interstellaires. En plus des constantes de vitesse de formation et de destruction des anions, les constantes de vitesse d’excitation collisionnelle sont nécessaires pour modéliser les abondances observées des anions. Nous avons choisi de porter notre effort sur le calcul des constantes de vitesse de transition entre états rotationels de la molécule C3N- dans son état vibrationnel fondamental lors des collisions avec H2 et He en utilisant de nouvelles surfaces d’énergie potentielles. / The mechanisms of formation and destruction of molecular anions have become a field of special interest after the recent detection of six molecular anions (C4H-,C6H-, C8H-, CN-, C3N-, C5N-) in the interstellar medium. The main channel of formation of these anions is expected to be radiative electron attachment in environments where the density of electron is relatively important. There is however at themoment a lack of experimental and theoretical data allowing to assess this hypothesis. Photodetachment, on the other hand, is the main source of destruction of the anions in diffuse clouds and photodissociation regions. A single center expansion approach is applied to the study of both processes: photodetachment and radiative electron attachment. The results obtained with the present method are compared to previously reported experimental and theoretical data and show a good agreement.This method is then employed to determine the rate constants which are needed to confirm whether or not these mechanisms are crucial for the chemistry of the interstellar anions. Along with the formation and destruction rates, rotational excitation rate coefficients are needed to accurately model the observed anions abundances.We focus on the calculation of state-to-state rotational transitions rate coefficients of the C3N- molecule in its ground vibrational state in collisions with H2 and He using new potential energy surfaces

Kvantkemiska studier av reaktiviteten hos guldnanopartiklar Au3-Au11 och Au13 mot O- centrerade molekylradikaler OH , OOH , OCH3   och H2O undersöks. Olika molekylära ytegenskaper tas med i beräkningen, elektrostatiska ytpotentialen, den genomsnittliga lokala joniseringsenergin, electron attachment energy och spinndensiteten (VS(r), IS(r), TS(r), ES(r) och S(r)). De erhållna resultaten gäller slutna och öppna skalsystem. Där system med slutna skal bildas från växelverkan mellan en guldklusterradikal och en fri radikal, och system med öppna skal bildas från växelverkan mellan ett jämnt antal guldatomer med en fri radikal. För system med slutna skal Aux-R (där x = 3, 5, 7, 9 eller 11 och R är en O-centrerad radikal) finns det en övergripande trend av bindningsenergin gentemot ES(r), vilket återspeglar elektrofilictiten hos guldnanopartiklar. Multivariata modeller visar vidare hur de olika parametrarna korrelerar gentemot varandra för system med slutna skal.För strukturerna Aux-R (där x=3-11) medl ägst bindningsenergi, dvs. inklusive både slutna och öppna skalsystem, är den tydligaste trenden bindningsenergi vs minimum i ES(r) och parametern TS(r). Vid jämförelse av resultaten av interaktionerna med de fria radikalerna med H2O är trenden alltid tydligast för H2O. I linje med tidigare studier finns det även en korrelation av bindningsenergierna med VS,max och ES,min för H2O. Slutligen sträcker sig trenden med bindningsenergi vs ES,min vidare till systemet som innehåller den icke-plana Au13-strukturen. Denna studie visar kopplingen mellan reaktiviteten hos guldnanopartiklar mot fria radikaler till den lokala ES(r), samtidigt som bidraget från andra ytegenskaper visas. Detta kan vara av betydelse för fortsatta studier kring naturen av interaktioner av guldnanopartiklar. / The nature of gold nanoparticle interactions towards molecular radicals are investigated. Quantum chemical studies of the reactivity of gold nanoparticles Au3-Au11 and Au13 towards O-centered molecular radicals OH , OOH , OCH3   and H2O are performed. Different molecular surface properties are taken into account; the surface electrostatic potential, average local ionization energy, electron attachment energy and spin density (VS(r), IS(r), TS(r), ES(r) and S(r)). The obtained results concern closed and open shell systems. Where closed shell systems are formed from the interaction of a radical gold cluster and a free radical, and open shell systems are formed from the interaction of an even number of gold atoms with a free radical. For closed shell systems Aux-R (where x = 3, 5, 7, 9 or 11 and R is an O-centered radical) there is an overall trend of the binding energy vs the local electron attachment energy, reflecting the electrophilicity of the gold nanoparticles. Multivariate plots further show how the different parameters correlate together for closed shell systems. Looking at the lowest energy structures Aux-R (where x = 3-11), i.e. including closed and open shell systems, the clearest trend is of binding energy vs minima in the local electron attachment energy ES,min and the TS(r) parameter. When comparing the results of the interactions with the free radicals with H2O, the trend is always clearest for H2O. Concurring with previous trends, there is a correlation of the binding energies with VS,max and ES,min for H2O. Lastly, the trend of Binding energy vs ES,min further extends to systems containing the non-planar Au13 structure. This study extends the reactivity of gold nanoparticles towards free radicals to the local electron attachment energy, while showing the contribution of other surface properties. This might be of importance for further studies concerning the nature of gold nanoparticle interactions.

Title: Structure and dynamics of electronic defects in liquid water Author: Ondřej Maršálek Institute: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic Supervisor: prof. Mgr. Pavel Jungwirth, DSc. Supervisor's e-mail address: pavel.jungwirth@uochb.cas.cz Abstract: In this thesis we present ab inito molecular dynamics simulations of two different electronic defects in water. Photoionization of liquid water produces a cationic hole, which undergoes ultrafast dynamics and forms the hydrated proton and the hydroxyl radical as its products. We study both the dynamics and spectroscopy of this process. The hydrated electron is a key intermediate in radiation chemistry of aqueous systems. We simulate its equilibrium properties in anionic water clusters as well as the dynamics of vertical electron attachment to cold and warm clusters. The hydrated electron reacts with a hydrated proton to form a hydrogen atom. We examine this reaction at a finite temperature in a larger cluster as well as in more detail in a smaller cluster. Because both of the electronic defects studied here are challenging open-shell species, we put emphasis on benchmarking and testing our computational setup. Six published articles are attached to the thesis. Keywords: density functional theory,...

Les mono-couches auto-assemblées (SAMs) sont des systèmes de choix pour le développement de plateformes moléculaires aux propriétés physico-chimiques contrôlées. Il s’agit de monocouches organisées de molécules bi-fonctionnelles. Ces molécules se composent d’une fonction terminale modulable, séparée d’un groupement d’ancrage par un espaceur adapté. Ainsi, les propriétés des SAMs peuvent être ajustées pour le développement de systèmes électroniques moléculaires ou de capteurs (bio)-chimiques. De plus, des structurations chimiques supplémentaires peuvent être induites par irradiation.Les méthodes d’irradiation les plus courantes impliquent des particules de haute énergie. Les dommages induits résultent de plusieurs mécanismes en compétition (ionisations, excitations, dissociations). Dans cette thèse, les électrons lents (0-20 eV) sont utilisés comme particules primaires, et les processus d’interaction électron-SAM sont étudiés afin d’identifier les résonances d’attachement électronique. Aux énergies concernées, des processus dissociatifs sélectifs et efficaces peuvent être mis à profit pour proposer des stratégies d’irradiation menant à des modifications chimiques contrôlées et optimisées.Des SAMs modèles de thiols sur or sont étudiées par une technique de spectroscopie vibrationnelle de forte sensibilité de surface, la spectroscopie de perte d’énergie d’électrons lents (HREELS). Elle permet à la fois de caractériser les SAMs et de sonder les processus d'interaction électron-molécule. Les résultats obtenus concernent les : 1) SAMs aromatiques modèles de terphénylthiol (HS-(C₆H₄)₂-C₆H₅), stabilisables par réticulation sous irradiation. Une caractérisation vibrationnelle poussée de la SAM avant et après irradiation, en portant une attention particulière au comportement des modes d’élongation ν(CH), a permis d’opposer les processus de réactivité induite à 1, 6 et 50 eV.2) SAMs d’acide mercaptoundécanoïque (HS-(CH₂)₁ ₀ -COOH), les fonctions acides terminales permettant par exemple le greffage de peptides. L’interface SAM / environnement (COO-/COOH, eau résiduelle) a été caractérisée grâce à la forte sensibilité des modes d’élongation ν(OH) aux liaisons hydrogène. La démarche mise en place peut être facilement transposée à d’autres systèmes. / Self-Assembled Monolayers (SAMs) are good candidates to develop molecular platforms with controlled physico-chemical properties. A SAM is an ordered monolayer of bi-functionnal molecules. These molecules consist of an adjustable terminal function, separated from a headgroup by a chosen spacer chain. Thus, SAMs properties can be adjusted for the development of molecular electronic systems or (bio)-chemical sensors. Furthermore, additional chemical structuration can be induced by irradiation.Most current methods of irradiation involve high energy particles. The induced damages result from several competitive mechanisms (ionisations, excitations, dissociations). In this thesis, low energy electrons (0-20 eV) are used as primary particles, and the interaction processes between electrons and SAMs are studied in order to identify electron attachment resonances. At the associated energies, selective and effective dissociative processes can be induced to propose irradiation strategies leading to controlled and optimized chemical modifications.Model SAMs of thiols on gold are studied by a vibrational spectroscopy technique of strong surface sensibility, high resolution electron energy loss spectroscopy (HREELS). It allows at the same time to characterize SAMs and to probe electron-molecule interaction processes. The result obtained deal with : 1) Aromatic model SAMs of Terphenyl-thiol (HS-(C₆H₄)₂-C₆H₅), which can be stabilized by cross-linking under irradiation. Induced reactive processes at 1, 6 and 50 eV were compared and opposed, thanks to an advanced vibrational characterization of the SAM before and after irradiation, and by paying a particular attention to the stretching mode ν(CH) behaviour.2) Mercaptoundecanoic acid SAMs (HS-(CH₂)₁ ₀ -COOH), whose terminal functions allow for example the peptide anchoring. The interface SAM / environment (COO-/COOH, residual water) was characterized thanks to the strong sensitivity of the stretching modes ν(OH) to hydrogen bonding. The approach that was developped can be easily transposed to other systems.