When nuclear fuel, fabricated for the purpose of transmuting spent fuel is irradiated, significant amounts of He is produced from alpha particles mainly emitted when 242Cm decays into 238Pu. From irradiation experiments it is known that the presence of He in the solids alters the swelling behaviour of the material. The thesis presents the theoretical background from which nucleation models of He bubbles can be formulated. Such models are presented for He in metals, and the case of He in Mo is studied as an example. MgO, which together with Mo is suggested as a matrix material in transmutation fuel is also studied and the stability of He containing bubbles in this material is discussed. By calculating parameters for a rate theory model derived from atomistic modelling, it is shown that He can stabilise vacancy clusters and cause cluster growth at temperatures and irradiation doses where nucleation and growth would not otherwise occur. At the initial stages of nucleation He can stabilise small bubbles while larger bubbles are unstable. This results in an incubation time of swelling, which implies that He does not always cause increased swelling, but can at certain irradiation conditions slow down the growth of large vacancy clusters and thereby delay swell\-ing beyond the time of the irradiation. When comparing the behaviour of bubble nucleation in Mo and MgO, it is found that He has a significant impact even at very low concentrations in Mo. In contrast, the concentration of He has to be considerably higher in MgO to affect the swelling behaviour. For an inert matrix fuel, designed for transmutation purposes, this implies that the Mo matrix will have a tendency to swell considerably at rather high temperatures due to He stabilised vacancy clusters. If operated at lower temperatures, the swelling could instead be reduced due to the incubation time. In a MgO matrix, the swelling behaviour will instead depend largely on the production rate of He. For a low production rate, the material will have a swelling behaviour similar to the one seen when He is not present in the material. A high production rate implies that He will remain in vacancy clusters, thereby stabilising the clusters and enhancing the growth and swelling.

The desire for low cost electronics has led to a huge increase in research focused on organic materials. These materials are appealing due to their unique electrical and material-processing properties and are rapidly being adopted in old and new electronic applications. To create practical devices requires a further understanding of the charge transport properties of the unique anisotropic molecular crystal structures. This work looks at how doping with the transition-metal element manganese can alter the electronic structure of the organic material pentacene. It has been found that using manganese as a dopant provides novel physical characteristics previously not encountered in organic field effect transistors based on pentacene. These organic thin films were characterized using X-ray absorption spectroscopy and the results compared to computational density functional theory analysis.

Vgeu casresum1de1.pdf

El treball que es presenta en aquesta tesi és la continuació i ampliació de la feina feta en el nostre grup de recerca en els darrers anys sobre derivats de l’o-carborà que porten grups rics en electrons. L’objectiu global de la tesi és la síntesis i l’estudi teòric d’aquests derivats. Gairebé tots els compostos sintetitzats en aquest treball s’han obtingut directament a partir de l’o-carborà. La funcionalització dels àtoms de carboni de l’o-carborà es fa en dos etapes. En un primer pas, s’afegeix un agent per arrancar el protons, com són els compostos organolitiats, les amides alcalines, els hidrurs alcalins; i tot seguit, s’afegeix un electròfil (diòxid de carboni, calcogen, halogen, halurs, epòxids, aldehids). Tot i que la substitució dels dos àtoms de carboni del clúster d’o-carborà S’obté pràcticament sempre, la monosubstitució no és gens trivial, perquè sempre ve acompanyada de la disubstitució. Per això, el primer objectiu d’aquest treball ha sigut l’estudi experimental i teòric de la influencia dels dissolvents eterats (Et2O, THF or DME) en la formació dels compostos organolitiats, utilitzant com a plataforma el 1,2-C2B10H12. Tot i que les fosfines de l’o-carborà són uns dels derivats més estudiats, la investigació de les seves propietats electròniques no ho ha sigut tant. Les carboranilfosfines varen ésser sintetitzades per primer cop fa més de 50 anys, però cap estudi sistemàtic i exhaustiu sobre les reaccions d’oxidació s’havia fet fins ara. Per tant, un altre objectiu d’aquest treball ha sigut l’estudi de les reaccions d’oxidació de les carboranilfosfines amb peròxid d’hidrogen, sofre i seleni; i la seva avaluació com a lligands. Un cop sintetitzats aquests compostos, hem fet un estudi teòric que ha tingut els següents objectius: i) veure la influència dels grups fosfina i fosfina oxidada en els efects electrònics del clúster d’o-carborà; ii) veure els efectes electrònics en les closo-carboranilmonofosfines; iii) veure la labilitat del enllaç fòsfor-calcogen en els monocalcògens dels carboranilmono- i carboranildifosfines; iv) estudiar dels processos de oxidació i degradació; v) estudiar la comunicació intramolecular en les carboranildifosfines aniòniques oxidades. Un altre grup ric en electrons és el grup formil (-CHO), que una vegada afegit a un clúster d’o-carborà, veure les seves propietats altament modificades. Tot i que el carboranilformaldehid es coneix des de fa temps, hi ha pocs estudis sobre la seva reactivitat. Per tant un altre objectiu d’aquest treball ha sigut l’estudi de la reactivitat d’aquest compost amb la finalitat d’obtenir nous derivats. Per això hem estudiat: i) l’addició nucleofílica al grup carbonílic del derivat litiat de l’o-carborà per obtenir derivats amb múltiples clústers d’o-carborà; ii) la substitució electrofílica dels substrats aromàtics emprant el carboranilformaldehid activat amb la finalitat d’obtenir derivats de l’o-carborà amb propietats luminescents; iii) les reaccions de Wittig i Horner-Wadaworth-Emmons emprant ja sigui el carboranilformaldehid ó els derivats de l’o-carborà amb grups fosfonat i sals de fosfoni. Per l’últim hem estudiat la síntesis de nous derivats utilitzant com a plataforma la carboranilpiridina. Les reaccions estudiades han sigut: i) la metal·lació de la carboranilpiridina amb complexos de Pd(II), Ir(III), Rh(III) i Ru(II); ii) la síntesis de lligands híbrids carboranilpiridina-fosfina i les seves reaccions de complexació amb Pd(II) i Rh(I); iii) la síntesis de un derivat de la carboranilpiridina que inclou un grup borà; iv) la síntesis de un derivat cobaltabis(dicarballur)-dipiridina. / The work presented in this manuscript is the continuation and extension of the work done in our group during the last years on the carborane derivatives with electron rich moieties. The main objective of this work is to synthesize and to study by computational means new derivatives of carborane with electron rich moieties. Almost all the compounds synthesized in this work are directly achieved from o-carborane. The direct modification of the C vertexes of the o-carborane is done in two steps. First a deprotonating agent as organolithium compounds, alkali-metal amides or alkali-metal hydrides is added, followed by the addition of a suitable electrophile (carbon dioxide, chalcogens, halogens, halides, epoxides, aldehydes). Although the substitution at the both carbon atoms is always achieved, the monosubstitution is not so trivial, being almost always accompanied by the disubstituted derivative. For that, the first specific objective of this work was to study both experimentally and by computational means the influence of ethereal solvents (Et2O, THF or DME) on the formation of organolithiated compounds, based on the 1,2-C2B10H12 platform. Though the o-carborane derivatives with phosphorus moieties were the most studied synthetically and some of their properties were exploited, still work has to be done to understand their electronic properties that may ultimate lead to a rationalized design of new derivatives. The carboranylphosphines are known for more than 50 years ago, but no systematic and comprehensive investigation on their oxidation reactions were found in the literature as well as investigations on the electronic properties of these phosphines. For that the second specific objective was the study of the oxidation of carboranylphsophines with hydrogen peroxide, sulphur and selenium and to examine their properties as ligands. Once the synthetic study on the carboranylphosphines and their oxides and chalcogenides was completed, we proceeded with the third specific objective that was the computational study of the carboranylphosphines and their oxides and chalcogenides. The computational study contains: i) the contribution of phosphine and oxidized phosphine moieties to the electronic effects on the o-carborane cluster; ii) electronic effects in closo-carboranylmonophosphines; iii) the lability of the phosphorus-chalcogen bonds in carboranylmono- and carboranyldiphsophine monochalcogenides; iv) the oxidation/degradation processes study; and v) intramolecular communication in oxidized anionic carboranyldiphosphines. Other moiety that is rich in electrons is the formyl group, that once attached to o-carborane cluster its properties are highly modified. Though the carboranylformadehyde is long known in the literature, studies on its reactivity are rare. For that, the fourth objective was to understand the reactivity carboranylformaldehyde as platform for new derivatives. For that we studied: i) the nucleophilic addition to the carbonyl group with lithated carborane in order to synthesize “confined space” multi-cage compounds; ii) the electrophilic substitution reactions of aromatic substrates with activated carboranylformaldehyde, in order to obtain derivatives with luminescent properties; and iii) the Wittig and Horner-Wadaworth-Emmons reaction using carboranylformaldehyde and carborane containing phosphonates and phosphonium salts. The fifth specific objective was the study of carboranylpyridine as platform for new derivatives, for which we studied: i) the metalation reaction of carboranylpyridine with Pd(II), Ir(III), Rh(III) and Ru(II); ii) synthesis of carboranylpyridine-phosphine hybrid ligands and complexation reactions of these ligands through Pd(II) and Rh(I) complexes; iii) synthesis of carboranylpyridine-borane derivative; and iv) synthesis of cobalta(bisdicarbollide)-pyridine derivative.

The desire for low cost electronics has led to a huge increase in research focused on organic materials. These materials are appealing due to their unique electrical and material-processing properties and are rapidly being adopted in old and new electronic applications. To create practical devices requires a further understanding of the charge transport properties of the unique anisotropic molecular crystal structures. This work looks at how doping with the transition-metal element manganese can alter the electronic structure of the organic material pentacene. It has been found that using manganese as a dopant provides novel physical characteristics previously not encountered in organic field effect transistors based on pentacene. These organic thin films were characterized using X-ray absorption spectroscopy and the results compared to computational density functional theory analysis.

This dissertation investigates three topics in the field of multiple-bonded metal chemistry. The first topic concerns the synthetic and theoretical considerations of ditungsten formamidinates and guanidinates compounds. This work presents an enhanced synthetic path to the W2(hpp)4 molecule (Hhpp = 1,3,4,6,7,8-hexahydro-2H-pyrimido[1,2-a]pyrimidine). The reflux of W(CO)6 with Hhpp in o-dichlorobenzene at 200 oC produces W2(hpp)4Cl2 in a one-pot reaction in 92% yield. This compound is stable and easily stored for further use, and it can be efficiently reduced in a one-step reaction to the most easily ionized compound W2(hpp)4. This work also examines the electronic structure and geometry of the intermediates W2(µ-CO)2(µ- hpp)2(η2-hpp)2 and W2(hpp)4Cl2. The second topic concerns the theoretical investigation by DFT of the electronic structure of [Mo2] units bridged by oxamidate ligands or bridging hydride ions ([Mo2] = (Mo2(DArF)3, where DArF is the anion of a diarylformamidine). It is shown that the effect of the gauche conformation of the α oxamidate isomers is due to steric interactions, and that the planar β oxamidate isomers have an electronic structure similar to that of naphthalene when it is doubly oxidized. The [Mo2](µ-H)2[Mo2] compound shows interdimetal unit interactions between the δ orbitals of the two [Mo2] units. These interactions are theoretically predicted and experimentally observed by a decrease in the [Mo2]---[Mo2] distance with a one-electron oxidation of [Mo2](µ- H)2[Mo2]. The final topic concerns the magnetic and structural properties of two Ru2(DArF)4Cl compounds. The compounds with Ar = p-anisyl (para) and m-anisyl (meta) both show different temperature dependence of their molar magnetic susceptibility, χ. For the para compound, there is a Boltzmann distribution between a π*3 ground state and a δ*2π* upper state, and this is confirmed by a temperature dependence of the Ru-Ru bond length: 2.4471(5) àat 23 K and 2.3968(5) àat 300 K. For the meta compound, a δ*2π*configuration persists over the range of 23-300 K as shown by an invariant Ru-Ru bond length and its molar magnetic susceptibility.

In the last few years the quest towards a hydrogen based economy has intensified interest for effective and less expensive catalysts for fuel cell applications. Due to its slow kinetics, alternative catalysts for the oxygen electroreduction reaction are actively researched. Platinum alloys with different transition metals (for example: Ni, Co and Fe) have shown improved activity over pure Pt. The design of a Pt-free catalysts is also highly desirable, and different alternatives including metalloporphyrins and Pd-based catalysts are being researched. Pd-based catalysts constitute an attractive alternative to Pt alloys in some fuel cell applications, not only because of lower costs but also because of the lower reactivity of Pt alloys towards methanol, which is important for improved methanol crossover tolerance on direct methanol fuel cells. In this work we apply density functional theory (DFT) to the study of four catalysts for oxygen electroreduction. The electronic structure of these surfaces is characterized together with their surface reconstruction properties and their interactions with oxygen electroreduction intermediates both in presence and absence of water. The energetics obtained for the intermediates is combined with entropy data from thermodynamic tables to generate free energy profiles for two representative reaction mechanisms where the cell potential is included as a variable. The study of the barriers in these profiles points to the elementary steps in the reaction mechanisms that are likely to be rate-determining. The highest barrier in the series pathway is located at the first proton and charge transfer on all four catalytic surfaces. This is in good agreement with observed rate laws for this reaction. The instability of hydrogen peroxide on all surfaces, especially compared with the relatively higher stability of other intermediates, strongly points at this intermediate as the most likely point where the oxygen bond is broken during oxygen reduction. This adds to the argument that this path might be active during oxygen electroreduction. A better understanding behind the reaction mechanism and reactivities on these representative surfaces will help to find systematic ways of improvement of currently used catalysts in the oxygen electroreduction reaction.

A recently developed chemical vapor deposition (CVD) synthesis process called CoMoCAT yields single-wall carbon nanotubes (SWCNT)s of controlled diameter and chirality, making them extremely attractive for technological applications. In this dissertation, we use molecular dynamics simulations and density functional theory to study the selective growth mechanisms. In the CoMoCAT process, growth of SWCNTs happens on Co clusters with diameters of about 1 �. Effective force fields for Ni-C interactions developed by Yamaguchi and Maruyama for the formation of metallofullerenes and the reactive empirical bond order Brenner potential for C-C interactions are modified to describe interactions in such system. Classical molecular dynamics (MD) simulations using this force field are carried out to study the growth of SWCNT on floating and supported metal clusters. The effect of metal-cluster interactions on the growth process is discussed. The energy of forming one more ring at the open end of one-end-closed nanotubes with different chiralities, which is believed to be the basic step of nanotube elongation, are studied as a function of tube length. The energy and shape of the frontier highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of armchair nanotubes are studied and used to explain the change of reaction energy with tube length. Another property, the aromaticity of the rings forming a tube is also studied using Nucleus Independent Chemical Shift (NICS) as probe. NICS of rings in one-end-closed nanotubes with different chirality are studied as a function of tube length. NICS behavior of one-end-closed nanotube is compared with that of two-ends-open nanotube with the same chirality for nanotubes (6, 5) and (9, 1). Also (8, 3) nanotubes with one end open and the other end bonded to three different kinds of cap structures are compared. Since from both experimental observation and from our MD simulation results, the growth process of SWCNT can be affected by the interaction between Co clusters and their substrate, the performance of a series of CoN Clusters (N=1-4, 7, 10, 14, 15) adsorbed on MoC surface are studied with density functional theory.

We investigated the reactivity of difluorovinylidene groups (C2F2) on Cu(111) under ultrahigh vacuum conditions. Difluorovinylidene moieties bonded to surface were generated by the dissociative adsorption of 1,1-dibromodifluoroethylene. Temperature Programmed desorption (TPD) and reflection-adsorption infrared spectroscopy (RAIRS) revealed the thermal reaction pathways, and a variety of intermediates were identified or inferred. The major desorption product, hexafluoro-2-butyne (C4F6), was detected at 445 K. It invokes a step of fluoride addition to difluorovinylidene to render the intermediacy of C2F3. However, differences exist when the vibration data from F + C=CF2 were compared with those from C−CF3 and CF=CF2 in previous literature, implying that the form is neither ethylidyne nor vinyl. Based on the concept of fluorine hyperconjugation, density function theory (DFT) calculations were utilized to obtain two transition states, quasi-vinyl and -ethylidyne, which can account for the differences present in the IR spectra. The relative thermal stability follows the trend of vinyl > quasi-ethylidyne > quasi-vinyl > vinylidene > ethylidyne suggested by IR and DFT calculations. Finally, the end product, CF3C¡ÝCCF3, might be formed by coupling of two quasi-ethylidyne species via the partial allenic forms.

Computational methods have become an integral part of drug development and can help bring new and better drugs to the market faster. The process of predicting the biological activity of large compound collections is known as virtual screening, and has been instrumental in the development of several drugs today in the market. Computational methods can also be used to elucidate the energies associated with chemical reactivity and predict how to improve a synthetic protocol. These two applications of computational medicinal chemistry is the focus of this thesis. In the first part of this work, quantum mechanics has been used to probe the energy surface of palladium(II)-catalyzed decarboxylative reactions in order to gain a better understating of these systems (paper I-III). These studies have mapped the reaction pathways and been able to make accurate predictions that were verified experimentally. The other focus of this work has been to develop virtual screening methodology. Our first study in the area (paper IV) investigated if the results from several virtual screening methods could be combined using data fusion techniques in order to get a more consistent result and better performance. The study showed that the results obtained from data fusion were more consistent than the results from any single method. The data fusion methods also for several target had a better performance than any of the included single methods. Next, we developed a dataset suitable for evaluating the performance of virtual screening methods when applied to large compound collection as a replacement or complement for high throughput screening (paper V). This is the first benchmark dataset of its kind. Finally, a method for using computationally derived reaction coordinates as basis for virtual screening was developed. The aim was to find inhibitors that resemble key steps in the mechanism (paper VI). This initial proof of concept study managed to locate several known and one previously not reported reaction mimetics against insulin regulated amino peptidase.