Parity violation in molecular magnetic resonance properties

The Standard Model of particle physics consists of the quantum electrodynamics (QED) and the weak and strong nuclear interactions. The QED is the basis for molecular properties, and thus it defines much of the world we see. The weak nuclear interaction is responsible for decays of nuclei, among other things, and in principle, it should also effects at the molecular scale. The strong nuclear interaction is hidden in interactions inside nuclei. From the high-energy and atomic experiments it is known that the weak interaction does not conserve parity. Consequently, the weak interaction and specifically the exchange of the Z^0 boson between a nucleon and an electron induces small energy shifts of different sign for mirror image molecules. This in turn will make the other enantiomer of a molecule energetically favorable than the other and also shifts the spectral lines of the mirror image pair of molecules into different directions creating a split. Parity violation (PV) in molecules, however, has not been observed. The topic of this thesis is how the weak interaction affects certain molecular magnetic properties, namely certain parameters of nuclear magnetic resonance (NMR) and electron spin resonance (ESR) spectroscopies. The thesis consists of numerical estimates of NMR and ESR spectral parameters and investigations of the effects of different aspects of quantum chemical computations to them. PV contributions to the NMR shielding and spin-spin coupling constants are investigated from the computational point of view. All the aspects of quantum chemical electronic structure computations are found to be very important, which makes accurate computations challenging. Effects of molecular geometry are also investigated using a model system of polysilyene chains. PV contribution to the NMR shielding constant is found to saturate after the chain reaches a certain length, but the effects of local geometry can be large. Rigorous vibrational averaging is also performed for a relatively small and rigid molecule. Vibrational corrections to the PV contribution are found to be only a couple of per cents. PV contributions to the ESR g-tensor are also evaluated using a series of molecules. Unfortunately, all the estimates are below the experimental limits, but PV in some of the heavier molecules comes close to the present day experimental resolution.

Insights into the molecular genetics of celiac disease : Applying family- and population-based strategies

Celiac disease, or gluten intolerance, is triggered by dietary glutens in genetically susceptible individuals and it affects approximately 1% of the Caucasian population. The best known genetic risk factors for celiac disease are HLA DQ2 and DQ8 heterodimers, which are necessary for the development of the disease. However, they alone are not sufficient for disease induction, other risk factors are required. This thesis investigated genetic factors for celiac disease, concentrating on susceptibility loci on chromosomes 5q31-q33, 19p13 and 2q12 previously reported in genome-wide linkage and association studies. In addition, a novel genotyping method for the detection of HLA DQ2 and DQ8 coding haplotypes was validated. This study was conducted using Finnish and Hungarian family materials, and Finnish, Hungarian and Italian case-control materials. Genetic linkage and association were analysed in these materials using candidate gene and fine-mapping approaches. The results confirmed linkage to celiac disease on the chromosomal regions 5q31-q33 and 19p13. Fine-mapping on chromosome 5q31-q33 revealed several modest associations in the region, and highlighted the need for further investigations to locate the causal risk variants. The MYO9B gene on chromosome 19p13 showed evidence for linkage and association particularly with dermatitis herpetiformis, the skin manifestation of celiac disease. This implies a potential difference in the genetic background of the intestinal and skin forms of the disease, although studies on larger samplesets are required. The IL18RAP locus on chromosome 2q12, shown to be associated with celiac disease in a previous genome-wide association study and a subsequent follow-up, showed association in the Hungarian population in this study. The expression of IL18RAP was further investigated in small intestinal tissue and in peripheral blood mononuclear cells. The results showed that IL18RAP is expressed in the relevant tissues. Two putative isoforms of IL18RAP were detected by Western blot analysis, and the results suggested that the ratios and total levels of these isoforms may contribute to the aetiology of celiac disease. A novel genotyping method for celiac disease-associated HLA haplotypes was also validated in this thesis. The method utilises single-nucleotide polymorphisms tagging these HLA haplotypes with high sensitivity and specificity. Our results suggest that this method is transferable between populations, and it is suitable for large-scale analysis. In conclusion, this doctorate study provides an insight into the roles of the 5q31-q33, MYO9B, IL18RAP and HLA loci in the susceptibility to celiac disease in the Finnish, Hungarian and Italian populations, highlighting the need for further studies at these genetic loci and examination of the function of the candidate genes.

Molecular Interactions Chlorin Assemblies and NMR Separations

Photosynthesis is a chemical process in which the energy of the light quanta is transformed into chemical energy. Chlorophyll (Chl) molecules play a key role in photosynthesis; they function in the antennae systems and in the photosynthetic reaction center where the primary charge separation (CS) takes place. Bio-inspired mimicry of the CS is an essential unit in dye-sensitized solar cells. Aim of this study was to design and develop electron donor-acceptor (EDA) pairs from Chls and fullerenes (C60) or carbon nanotubes (CNT). The supramolecular approach was chosen, as long synthetic sequences required by the covalent approach lead to long reaction schemes and low yields. Here, a π-interaction between soluble CNTs and Chl was used in EDA construction. Also, a beta-face selective two-point bound Chl-C60 EDA was introduced. In addition, the photophysical properties of the supramolecular EDA dyads were analyzed. In organic chemistry, nuclear magnetic resonance (NMR) spectroscopy is the most vital analytical technique in use. Multi-dimensional NMR experiments have enabled a structural analysis of complex natural products and proteins. However, in mixture analysis NMR is still facing difficulties. In many cases overlapping signals can t be resolved even with the help of multi-dimensional experiments. In this work, an NMR tool based on simple host-guest chemistry between analytes and macromolecules was developed. Diffusion ordered NMR spectroscopy (DOSY) measures the mobilities of compounds in an NMR sample. In a liquid state NMR sample, each of the analytes has a characteristic diffusion coefficient, which is proportional to the size of the analyte. With normal DOSY experiment, provided that the diffusion coefficients of the analytes differ enough, individual spectra of analytes can be extracted. When similar sized analytes differ chemically, an additive can be introduced into the sample. Since macromolecules in a liquid state NMR sample can be considered practically stationary, even faint supramolecular interaction can change the diffusion coefficient of the analyte sufficiently for a successful resolution in DOSY. In this thesis, polyvinylpyrrolidone and polyethyleneglycol enhanced DOSY NMR techniques, which enable mixture analysis of similar in size but chemically differing natural products, are introduced.

Aspects and Applications of Pulse Sequence Design for Solution-State Nuclear Magnetic Resonance Spectroscopy

NMR spectroscopy enables the study of biomolecules from peptides and carbohydrates to proteins at atomic resolution. The technique uniquely allows for structure determination of molecules in solution-state. It also gives insights into dynamics and intermolecular interactions important for determining biological function. Detailed molecular information is entangled in the nuclear spin states. The information can be extracted by pulse sequences designed to measure the desired molecular parameters. Advancement of pulse sequence methodology therefore plays a key role in the development of biomolecular NMR spectroscopy. A range of novel pulse sequences for solution-state NMR spectroscopy are presented in this thesis. The pulse sequences are described in relation to the molecular information they provide. The pulse sequence experiments represent several advances in NMR spectroscopy with particular emphasis on applications for proteins. Some of the novel methods are focusing on methyl-containing amino acids which are pivotal for structure determination. Methyl-specific assignment schemes are introduced for increasing the size range of 13C,15N labeled proteins amenable to structure determination without resolving to more elaborate labeling schemes. Furthermore, cost-effective means are presented for monitoring amide and methyl correlations simultaneously. Residual dipolar couplings can be applied for structure refinement as well as for studying dynamics. Accurate methods for measuring residual dipolar couplings in small proteins are devised along with special techniques applicable when proteins require high pH or high temperature solvent conditions. Finally, a new technique is demonstrated to diminish strong-coupling induced artifacts in HMBC, a routine experiment for establishing long-range correlations in unlabeled molecules. The presented experiments facilitate structural studies of biomolecules by NMR spectroscopy.

CADASIL: molecular studies on the most common hereditary vascular dementing disorder

Cerebral Autosomal Dominant Arteriopathy with Subcortical Infarcts and Leukoencephalopathy (CADASIL) is the most common hereditary vascular dementia. CADASIL is a systemic disease of small and medium-sized arteries although the symptoms are almost exclusively neurological, including migraineous headache, recurrent ischemic episodes, cognitive impairment and, finally, subcortical dementia. CADASIL is caused by over 170 different mutations in the NOTCH3 gene, which encodes a receptor expressed in adults predominantly in the vascular smooth muscle cells. The function of NOTCH3 is not crucial for embryonic development but is needed after birth. NOTCH3 directs postnatal arterial maturation and helps to maintain arterial integrity. It is involved in regulation of vascular tone and in the wound healing of a vascular injury. In addition, NOTCH3 promotes cell survival by inducing expression of anti-apoptotic proteins. NOTCH3 is a membrane-spanning protein with a large extracellular domain (N3ECD) containing 34 epidermal growth factor-like (EGF) repeats and a smaller intracellular domain with six ankyrin repeats. All CADASIL mutations are located in the EGF repeats and the majority of the mutations cause gain or loss of one cysteine residue in one of these repeats leading to an odd number of cysteine residues, which in turn leads to misfolding of N3ECD. This misfolding most likely alters the maturation, targetting, degradation and/or function of the NOTCH3 receptor. CADASIL mutations do not seem to affect the canonical NOTCH3 signalling pathway. The main pathological findings are the accumulation of the NOTCH3 extracellular domain on degenerating vascular smooth muscle cells (VSMCs), accumulation of granular osmiophilic material (GOM) in the close vicinity of VSMCs as well as fibrosis and thickening of arterial walls. Narrowing of the arterial lumen and local thrombosis cause insufficient blood flow, mainly in small arteries of the cerebral white matter, resulting in tissue damage and lacunar infarcts. CADASIL is suspected in patients with a suggestive family history and clinical picture as well as characteristic white matter alterations in magnetic resonance imaging. A definitive verification of the diagnosis can be achieved by identifying a pathogenic mutation in the NOTCH3 gene or through the detection of GOM by electron microscopy. To understand the pathology underlying CADASIL, we have generated a unique set of cultured vascular smooth muscle cell (VSMC) lines from umbilical cord, placental, systemic and cerebral arteries of CADASIL patients and controls. Analyses of these VSMCs suggest that mutated NOTCH3 is misfolded, thus causing endoplasmic reticulum stress, activation of the unfolded protein response and increased production of reactive oxygen species. In addition, mutation in NOTCH3 causes alterations in actin cytoskeletal structures and protein expression, increased branching and abnormal node formation. These changes correlate with NOTCH3 expression levels within different VSMCs lines, suggesting that the phenotypic differences of SMCs may affect the vulnerability of the VSMCs and, therefore, the pathogenic impact of mutated NOTCH3 appears to vary in the arteries of different locations. Furthermore, we identified PDGFR- as an immediate downstream target gene of NOTCH3 signalling. Activation of NOTCH induces up-regulation of the PDGFR- expression in control VSMCs, whereas this up-regulation is impaired in CADASIL VSMCs and might thus serve as an alternative molecular mechanism that contributes to CADASIL pathology. In addition, we have established the congruence between NOTCH3 mutations and electron microscopic detection of GOM with a view to constructing a strategy for CADASIL diagnostics. In cases where the genetic analysis is not available or the mutation is difficult to identify, a skin biopsy is an easy-to-perform and highly reliable diagnostic method. Importantly, it is invaluable in setting guidelines concerning how far one should proceed with the genetic analyses.

Opioid dependence: Brain structure and function : a magnetic resonance imaging, neuropsychological, and electromagnetic study

Background: Opiod dependence is a chronic severe brain disorder associated with enormous health and social problems. The relapse back to opioid abuse is very high especially in early abstinence, but neuropsychological and neurophysiological deficits during opioid abuse or soon after cessation of opioids are scarcely investigated. Also the structural brain changes and their correlations with the length of opioid abuse or abuse onset age are not known. In this study the cognitive functions, neural basis of cognitive dysfunction, and brain structural changes was studied in opioid-dependent patients and in age and sex matched healthy controls. Materials and methods: All subjects participating in the study, 23 opioid dependents of whom, 15 were also benzodiazepine and five cannabis co-dependent and 18 healthy age and sex matched controls went through Structured Clinical Interviews (SCID) to obtain DSM-IV axis I and II diagnosis and to exclude psychiatric illness not related to opioid dependence or personality disorders. Simultaneous magnetoencephalography (MEG) and electroencephalography (EEG) measurements were done on 21 opioid-dependent individuals on the day of hospitalization for withdrawal therapy. The neural basis of auditory processing was studied and pre-attentive attention and sensory memory were investigated. During the withdrawal 15 opioid-dependent patients participated in neuropsychological tests, measuring fluid intelligence, attention and working memory, verbal and visual memory, and executive functions. Fifteen healthy subjects served as controls for the MEG-EEG measurements and neuropsychological assessment. The brain magnetic resonance imaging (MRI) was obtained from 17 patients after approximately two weeks abstinence, and from 17 controls. The areas of different brain structures and the absolute and relative volumes of cerebrum, cerebral white and gray matter, and cerebrospinal fluid (CSF) spaces were measured and the Sylvian fissure ratio (SFR) and bifrontal ratio were calculated. Also correlation between the cerebral measures and neuropsychological performance was done. Results: MEG-EEG measurements showed that compared to controls the opioid-dependent patients had delayed mismatch negativity (MMN) response to novel sounds in the EEG and P3am on the contralateral hemisphere to the stimulated ear in MEG. The equivalent current dipole (ECD) of N1m response was stronger in patients with benzodiazepine co-dependence than those without benzodiazepine co-dependence or controls. In early abstinence the opioid dependents performed poorer than the controls in tests measuring attention and working memory, executive function and fluid intelligence. Test results of the Culture Fair Intelligence Test (CFIT), testing fluid intelligence, and Paced Auditory Serial Addition Test (PASAT), measuring attention and working memory correlated positively with the days of abstinence. MRI measurements showed that the relative volume of CSF was significantly larger in opioid dependents, which could also be seen in visual analysis. Also Sylvian fissures, expressed by SFR were wider in patients, which correlated negatively with the age of opioid abuse onset. In controls the relative gray matter volume had a positive correlation with composite cognitive performance, but this correlation was not found in opioid dependents in early abstinence. Conclusions: Opioid dependents had wide Sylvian fissures and CSF spaces indicating frontotemporal atrophy. Dilatation of Sylvian fissures correlated with the abuse onset age. During early withdrawal cognitive performance of opioid dependents was impaired. While intoxicated the pre-attentive attention to novel stimulus was delayed and benzodiazepine co-dependence impaired sound detection. All these changes point to disturbances on frontotemporal areas.

X-ray and neutron scattering studies on some nanoscale structures in molecular biology

Scattering of X-rays and neutrons has been applied to the study of nanostructures with interesting biological functions. The systems studied were the protein calmodulin and its complexes, bacterial virus bacteriophage phi6, and the photosynthetic antenna complex from green sulfur bacteria, chlorosome. Information gathered using various structure determination methods has been combined to the low resolution information obtained from solution scattering. Conformational changes in calmodulin-ligand complex were studied by combining the directional information obtained from residual dipole couplings in nuclear magnetic resonance to the size information obtained from small-angle X-ray scattering from solution. The locations of non-structural protein components in a model of bacteriophage phi6, based mainly on electron microscopy, were determined by neutron scattering, deuterium labeling and contrast variation. New data are presented on the structure of the photosynthetic antenna complex of green sulfur bacteria and filamentous anoxygenic phototrophs, also known as the chlorosome. The X-ray scattering and electron cryomicroscopy results from this system are interpreted in the context of a new structural model detailed in the third paper of this dissertation. The model is found to be consistent with the results obtained from various chlorosome containing bacteria. The effect of carotenoid synthesis on the chlorosome structure and self-assembly are studied by carotenoid extraction, biosynthesis inhibition and genetic manipulation of the enzymes involved in carotenoid biosynthesis. Carotenoid composition and content are found to have a marked effect on the structural parameters and morphology of chlorosomes.

Sticking and erosion at carbon-containing plasma-facing materials in fusion reactors

Controlled nuclear fusion is one of the most promising sources of energy for the future. Before this goal can be achieved, one must be able to control the enormous energy densities which are present in the core plasma in a fusion reactor. In order to be able to predict the evolution and thereby the lifetime of different plasma facing materials under reactor-relevant conditions, the interaction of atoms and molecules with plasma first wall surfaces have to be studied in detail. In this thesis, the fundamental sticking and erosion processes of carbon-based materials, the nature of hydrocarbon species released from plasma-facing surfaces, and the evolution of the components under cumulative bombardment by atoms and molecules have been investigated by means of molecular dynamics simulations using both analytic potentials and a semi-empirical tight-binding method. The sticking cross-section of CH3 radicals at unsaturated carbon sites at diamond (111) surfaces is observed to decrease with increasing angle of incidence, a dependence which can be described by a simple geometrical model. The simulations furthermore show the sticking cross-section of CH3 radicals to be strongly dependent on the local neighborhood of the unsaturated carbon site. The erosion of amorphous hydrogenated carbon surfaces by helium, neon, and argon ions in combination with hydrogen at energies ranging from 2 to 10 eV is studied using both non-cumulative and cumulative bombardment simulations. The results show no significant differences between sputtering yields obtained from bombardment simulations with different noble gas ions. The final simulation cells from the 5 and 10 eV ion bombardment simulations, however, show marked differences in surface morphology. In further simulations the behavior of amorphous hydrogenated carbon surfaces under bombardment with D^+, D^+2, and D^+3 ions in the energy range from 2 to 30 eV has been investigated. The total chemical sputtering yields indicate that molecular projectiles lead to larger sputtering yields than atomic projectiles. Finally, the effect of hydrogen ion bombardment of both crystalline and amorphous tungsten carbide surfaces is studied. Prolonged bombardment is found to lead to the formation of an amorphous tungsten carbide layer, regardless of the initial structure of the sample. In agreement with experiment, preferential sputtering of carbon is observed in both the cumulative and non-cumulative simulations

Molecular dynamics studies of nanoparticle impacts

This thesis concerns the dynamics of nanoparticle impacts on solid surfaces. These impacts occur, for instance, in space, where micro- and nanometeoroids hit surfaces of planets, moons, and spacecraft. On Earth, materials are bombarded with nanoparticles in cluster ion beam devices, in order to clean or smooth their surfaces, or to analyse their elemental composition. In both cases, the result depends on the combined effects of countless single impacts. However, the dynamics of single impacts must be understood before the overall effects of nanoparticle radiation can be modelled. In addition to applications, nanoparticle impacts are also important to basic research in the nanoscience field, because the impacts provide an excellent case to test the applicability of atomic-level interaction models to very dynamic conditions. In this thesis, the stopping of nanoparticles in matter is explored using classical molecular dynamics computer simulations. The materials investigated are gold, silicon, and silica. Impacts on silicon through a native oxide layer and formation of complex craters are also simulated. Nanoparticles up to a diameter of 20 nm (315000 atoms) were used as projectiles. The molecular dynamics method and interatomic potentials for silicon and gold are examined in this thesis. It is shown that the displacement cascade expansionmechanism and crater crown formation are very sensitive to the choice of atomic interaction model. However, the best of the current interatomic models can be utilized in nanoparticle impact simulation, if caution is exercised. The stopping of monatomic ions in matter is understood very well nowadays. However, interactions become very complex when several atoms impact on a surface simultaneously and within a short distance, as happens in a nanoparticle impact. A high energy density is deposited in a relatively small volume, which induces ejection of material and formation of a crater. Very high yields of excavated material are observed experimentally. In addition, the yields scale nonlinearly with the cluster size and impact energy at small cluster sizes, whereas in macroscopic hypervelocity impacts, the scaling 2 is linear. The aim of this thesis is to explore the atomistic mechanisms behind the nonlinear scaling at small cluster sizes. It is shown here that the nonlinear scaling of ejected material yield disappears at large impactor sizes because the stopping mechanism of nanoparticles gradually changes to the same mechanism as in macroscopic hypervelocity impacts. The high yields at small impactor size are due to the early escape of energetic atoms from the hot region. In addition, the sputtering yield is shown to depend very much on the spatial initial energy and momentum distributions that the nanoparticle induces in the material in the first phase of the impact. At the later phases, the ejection of material occurs by several mechanisms. The most important mechanism at high energies or at large cluster sizes is atomic cluster ejection from the transient liquid crown that surrounds the crater. The cluster impact dynamics detected in the simulations are in agreement with several recent experimental results. In addition, it is shown that relatively weak impacts can induce modifications on the surface of an amorphous target over a larger area than was previously expected. This is a probable explanation for the formation of the complex crater shapes observed on these surfaces with atomic force microscopy. Clusters that consist of hundreds of thousands of atoms induce long-range modifications in crystalline gold.

Computer simulation of H and He effects in fusion reactor materials

Fusion power is an appealing source of clean and abundant energy. The radiation resistance of reactor materials is one of the greatest obstacles on the path towards commercial fusion power. These materials are subject to a harsh radiation environment, and cannot fail mechanically or contaminate the fusion plasma. Moreover, for a power plant to be economically viable, the reactor materials must withstand long operation times, with little maintenance. The fusion reactor materials will contain hydrogen and helium, due to deposition from the plasma and nuclear reactions because of energetic neutron irradiation. The first wall divertor materials, carbon and tungsten in existing and planned test reactors, will be subject to intense bombardment of low energy deuterium and helium, which erodes and modifies the surface. All reactor materials, including the structural steel, will suffer irradiation of high energy neutrons, causing displacement cascade damage. Molecular dynamics simulation is a valuable tool for studying irradiation phenomena, such as surface bombardment and the onset of primary damage due to displacement cascades. The governing mechanisms are on the atomic level, and hence not easily studied experimentally. In order to model materials, interatomic potentials are needed to describe the interaction between the atoms. In this thesis, new interatomic potentials were developed for the tungsten-carbon-hydrogen system and for iron-helium and chromium-helium. Thus, the study of previously inaccessible systems was made possible, in particular the effect of H and He on radiation damage. The potentials were based on experimental and ab initio data from the literature, as well as density-functional theory calculations performed in this work. As a model for ferritic steel, iron-chromium with 10% Cr was studied. The difference between Fe and FeCr was shown to be negligible for threshold displacement energies. The properties of small He and He-vacancy clusters in Fe and FeCr were also investigated. The clusters were found to be more mobile and dissociate more rapidly than previously assumed, and the effect of Cr was small. The primary damage formed by displacement cascades was found to be heavily influenced by the presence of He, both in FeCr and W. Many important issues with fusion reactor materials remain poorly understood, and will require a huge effort by the international community. The development of potential models for new materials and the simulations performed in this thesis reveal many interesting features, but also serve as a platform for further studies.

Irradiation effects in graphene and related materials

Nanomaterials with a hexagonally ordered atomic structure, e.g., graphene, carbon and boron nitride nanotubes, and white graphene (a monolayer of hexagonal boron nitride) possess many impressive properties. For example, the mechanical stiffness and strength of these materials are unprecedented. Also, the extraordinary electronic properties of graphene and carbon nanotubes suggest that these materials may serve as building blocks of next generation electronics. However, the properties of pristine materials are not always what is needed in applications, but careful manipulation of their atomic structure, e.g., via particle irradiation can be used to tailor the properties. On the other hand, inadvertently introduced defects can deteriorate the useful properties of these materials in radiation hostile environments, such as outer space. In this thesis, defect production via energetic particle bombardment in the aforementioned materials is investigated. The effects of ion irradiation on multi-walled carbon and boron nitride nanotubes are studied experimentally by first conducting controlled irradiation treatments of the samples using an ion accelerator and subsequently characterizing the induced changes by transmission electron microscopy and Raman spectroscopy. The usefulness of the characterization methods is critically evaluated and a damage grading scale is proposed, based on transmission electron microscopy images. Theoretical predictions are made on defect production in graphene and white graphene under particle bombardment. A stochastic model based on first-principles molecular dynamics simulations is used together with electron irradiation experiments for understanding the formation of peculiar triangular defect structures in white graphene. An extensive set of classical molecular dynamics simulations is conducted, in order to study defect production under ion irradiation in graphene and white graphene. In the experimental studies the response of carbon and boron nitride multi-walled nanotubes to irradiation with a wide range of ion types, energies and fluences is explored. The stabilities of these structures under ion irradiation are investigated, as well as the issue of how the mechanism of energy transfer affects the irradiation-induced damage. An irradiation fluence of 5.5x10^15 ions/cm^2 with 40 keV Ar+ ions is established to be sufficient to amorphize a multi-walled nanotube. In the case of 350 keV He+ ion irradiation, where most of the energy transfer happens through inelastic collisions between the ion and the target electrons, an irradiation fluence of 1.4x10^17 ions/cm^2 heavily damages carbon nanotubes, whereas a larger irradiation fluence of 1.2x10^18 ions/cm^2 leaves a boron nitride nanotube in much better condition, indicating that carbon nanotubes might be more susceptible to damage via electronic excitations than their boron nitride counterparts. An elevated temperature was discovered to considerably reduce the accumulated damage created by energetic ions in both carbon and boron nitride nanotubes, attributed to enhanced defect mobility and efficient recombination at high temperatures. Additionally, cobalt nanorods encapsulated inside multi-walled carbon nanotubes were observed to transform into spherical nanoparticles after ion irradiation at an elevated temperature, which can be explained by the inverse Ostwald ripening effect. The simulation studies on ion irradiation of the hexagonal monolayers yielded quantitative estimates on types and abundances of defects produced within a large range of irradiation parameters. He, Ne, Ar, Kr, Xe, and Ga ions were considered in the simulations with kinetic energies ranging from 35 eV to 10 MeV, and the role of the angle of incidence of the ions was studied in detail. A stochastic model was developed for utilizing the large amount of data produced by the molecular dynamics simulations. It was discovered that a high degree of selectivity over the types and abundances of defects can be achieved by carefully selecting the irradiation parameters, which can be of great use when precise pattering of graphene or white graphene using focused ion beams is planned.

Magnetically induced currents and magnetic response properties of molecules

The magnetically induced currents in organic monoring and multiring molecules, in Möbius shaped molecules and in inorganic all-metal molecules have been investigated by means of the Gauge-including magnetically induced currents (GIMIC) method. With the GIMIC method, the ring-current strengths and the ring-current density distributions can be calculated. For open-shell molecules, also the spin current can be obtained. The ring-current pathways and ring-current strengths can be used to understand the magnetic resonance properties of the molecules, to indirectly identify the effect of non-bonded interactions on NMR chemical shifts, to design new molecules with tailored properties and to discuss molecular aromaticity. In the thesis, the magnetic criterion for aromaticity has been adopted. According to this, a molecule which has a net diatropic ring current might be aromatic. Similarly, a molecule which has a net paratropic current might be antiaromatic. If the net current is zero, the molecule is nonaromatic. The electronic structure of the investigated molecules has been resolved by quantum chemical methods. The magnetically induced currents have been calculated with the GIMIC method at the density-functional theory (DFT) level, as well as at the self-consistent field Hartree-Fock (SCF-HF), at the Møller-Plesset perturbation theory of the second order (MP2) and at the coupled-cluster singles and doubles (CCSD) levels of theory. For closed-shell molecules, accurate ring-current strengths can be obtained with a reasonable computational cost at the DFT level and with rather small basis sets. For open-shell molecules, it is shown that correlated methods such as MP2 and CCSD might be needed to obtain reliable charge and spin currents. The basis set convergence has to be checked for open-shell molecules by performing calculations with large enough basis sets. The results discussed in the thesis have been published in eight papers. In addition, some previously unpublished results on the ring currents in the endohedral fullerene Sc3C2@C80 and in coronene are presented. It is shown that dynamical effects should be taken into account when modelling magnetic resonance parameters of endohedral metallofullerenes such as Sc3C2@C80. The ring-current strengths in a series of nano-sized hydrocarbon rings are related to static polarizabilities and to H-1 nuclear magnetic resonance (NMR) shieldings. In a case study on the possible aromaticity of a Möbius-shaped [16]annulene we found that, according to the magnetic criterion, the molecule is nonaromatic. The applicability of the GIMIC method to assign the aromatic character of molecules was confirmed in a study on the ring currents in simple monocylic aromatic, homoaromatic, antiaromatic, and nonaromatic hydrocarbons. Case studies on nanorings, hexaphyrins and [n]cycloparaphenylenes show that explicit calculations are needed to unravel the ring-current delocalization pathways in complex multiring molecules. The open-shell implementation of GIMIC was applied in studies on the charge currents and the spin currents in single-ring and bi-ring molecules with open shells. The aromaticity predictions that are made based on the GIMIC results are compared to other aromaticity criteria such as H-1 NMR shieldings and shifts, electric polarizabilities, bond-length alternation, as well as to predictions provided by the traditional Hückel (4n+2) rule and its more recent extensions that account for Möbius twisted molecules and for molecules with open shells.

Nanoscale studies of materials using x-ray synchrotron radiation and mesoscopic modelling

X-ray synchrotron radiation was used to study the nanostructure of cellulose in Norway spruce stem wood and powders of cobalt nanoparticles in cellulose support. Furthermore, the growth of metallic clusters was modelled and simulated in the mesoscopic size scale. Norway spruce was characterized with x-ray microanalysis at beamline ID18F of the European Synchrotron Radiation Facility in Grenoble. The average dimensions and the orientation of cellulose crystallites was determined using x-ray microdiffraction. In addition, the nutrient element content was determined using x-ray fluorescence spectroscopy. Diffraction patterns and fluorescence spectra were simultaneously acquired. Cobalt nanoparticles in cellulose support were characterized with x-ray absorption spectroscopy at beamline X1 of the Deutsches Elektronen-Synchrotron in Hamburg, complemented by home lab experiments including x-ray diffraction, electron microscopy and measurement of magnetic properties with a vibrating sample magnetometer. Extended x-ray absorption fine structure spectroscopy (EXAFS) and x-ray diffraction were used to solve the atomic arrangement of the cobalt nanoparticles. Scanning- and transmission electron microscopy were used to image the surfaces of the cellulose fibrils, where the growth of nanoparticles takes place. The EXAFS experiment was complemented by computational coordination number calculations on ideal spherical nanocrystals. The growth process of metallic nanoclusters on cellulose matrix is assumed to be rather complicated, affected not only by the properties of the clusters themselves, but essentially depending on the cluster-fiber interfaces as well as the morphology of the fiber surfaces. The final favored average size for nanoclusters, if such exists, is most probably a consequence of these two competing tendencies towards size selection, one governed by pore sizes, the other by the cluster properties. In this thesis, a mesoscopic model for the growth of metallic nanoclusters on porous cellulose fiber (or inorganic) surfaces is developed. The first step in modelling was to evaluate the special case of how the growth proceeds on flat or wedged surfaces.

Hyperfine effects in the nuclear magnetic resonance of paramagnetic molecules

Paramagnetic, or open-shell, systems are often encountered in the context of metalloproteins, and they are also an essential part of molecular magnets. Nuclear magnetic resonance (NMR) spectroscopy is a powerful tool for chemical structure elucidation, but for paramagnetic molecules it is substantially more complicated than in the diamagnetic case. Before the present work, the theory of NMR of paramagnetic molecules was limited to spin-1/2 systems and it did not include relativistic corrections to the hyperfine effects. It also was not systematically expandable. --- The theory was first expanded by including hyperfine contributions up to the fourth power in the fine structure constant α. It was then reformulated and its scope widened to allow any spin state in any spatial symmetry. This involved including zero-field splitting effects. In both stages the theory was implemented into a separate analysis program. The different levels of theory were tested by demonstrative density functional calculations on molecules selected to showcase the relative strength of new NMR shielding terms. The theory was also tested in a joint experimental and computational effort to confirm assignment of 11 B signals. The new terms were found to be significant and comparable with the terms in the earlier levels of theory. The leading-order magnetic-field dependence of shielding in paramagnetic systems was formulated. The theory is now systematically expandable, allowing for higher-order field dependence and relativistic contributions. The prevailing experimental view of pseudocontact shift was found to be significantly incomplete, as it only includes specific geometric dependence, which is not present in most of the new terms introduced here. The computational uncertainty in density functional calculations of the Fermi contact hyperfine constant and zero-field splitting tensor sets a limit for quantitative prediction of paramagnetic shielding for now.