Abstract In this thesis nuclear magnetic resonance (NMR) and magneto-optical rotation (MOR) parameters are investigated for water, paying special attention to the effect of solvation from gaseous to liquid phase. Nuclear magnetic shielding and quadrupole coupling tensors of NMR spectroscopy are studied for gaseous and liquid water. Liquid state is modelled by a 32-molecule Car-Parrinello molecular dynamics simulation, followed by property calculations for the central molecules in clusters cut out from the simulation trajectory. Gaseous state is similarly represented by a one-molecule simulation. Gas-to-liquid shifts for shielding constants obtained this way are in good agreement with experiments. To get insight into the local environment and its effect on the properties the clusters are divided into groups of distinct local features, namely the number of hydrogen bonds. The analysis shows in detail how the NMR tensors evolve as the environment changes gradually from the gas to liquid upon increasing the number of hydrogen bonds to the molecule of interest. The study sheds light on the usefulness of NMR experiments in investigating the local coordination of liquid water. To go a bit further, the above mentioned NMR parameters along with the spin-spin coupling constant are examined for water dimer in various geometries to have insight into solvation and hydrogen bonding phenomena from bottom to top. Characteristic changes in the properties are monitored as the geometry of the dimer is systematically varied from very close encounter of the monomers to distances and orientations where hydrogen bonding between monomers ceases to exist. No rapid changes during the hydrogen bond breaking are observed indicating that the hydrogen bonding is a continuous phenomenon rather than an on-off situation. However, for analysis purposes we provide an NMR-based hydrogen bond definition, expressed geometrically, based on the behaviour of the NMR properties as a function of dimer geometry. Our definition closely resembles widely used definitions and thus reinforces their validity. Magneto-optical rotation parameters, the nuclear spin optical rotation (NSOR) and the Verdet constant, are computed for gaseous and liquid water, in the same manner as the NMR properties above. Recent pioneering experiments including NSOR for hydrogen nuclei in liquid water and liquid xenon have demonstrated that this technique has a potential to be a useful new probe of molecular structure. We reproduce computationally, applying a first-principles theory developed recently in the group, the experimental NSOR for hydrogen nuclei in liquid water, and predict hydrogen NSOR in gaseous water along with the oxygen NSOR in liquid and gaseous water. NSOR is an emerging experimental technique that needs interplay between theory and computation for validation, steering and insight.

Positively charged aromatic carbon-centered σ-type mono-and biradicals have been studied previously in the gas phase. However, very little is known about the properties of related polyradicals. In this dissertation, the reactions of series of quinolinium-and acridinium-based bi-, tri-, and tetraradicals were studied with cyclohexane and allyl iodide in the gas phase by using tandem mass spectrometry. I atom abstraction and allyl group abstraction were observed as dominant reactions for all the studied radicals upon reactions with allyl iodide. Sequential H atom abstractions were observed as the major reactions for the studied bi-and tetraradicals upon reactions with cyclohexane. Surprisingly, triradicals appeared to undergo addition followed by elimination of a H atom as one of the major reactions upon interactions with cyclohexane. Vertical electron affinity and spin-spin coupling between radical sites were found to control the radical reactivities.<div><br></div><div>The radical site(s) which react first with cyclohexane were experimentally determined. For the studied biradicals, the first reacting radical sites were found to be the ones that are predicted to be more reactive based on the reactivities of related monoradicals. For the studied triradicals, the first reacting radical sites are the ones that are least strongly coupled to the other radical sites. For tetraradicals, the first two sites reacting with cyclohexane are more weakly coupled than the other two radical sites.<br></div><div><br></div><div>The mechanisms for the reactions of the triradicals with cyclohexane were proposed based on tandem mass spectrometry experiments and supported by quantum chemical calculations. Briefly, the least strongly coupled radical site of a triradical reacts with cyclohexane first by abstracting a H atom. The more reactive radical site insome of the produced biradicals will then abstract a H atom from the cyclohexyl radical within the product collision complex to generate a monoradical and cyclohexene. Some of these monoradicals undergo addition to cyclohexene within this product complex,followed by elimination of a H atom. When allowed to react with allyl iodide, all of the monoradicals and most of the biradicals demonstrated predominant I atom abstraction. The quinolinium-based meta-and para-benzynes exhibited allyl group abstraction as the major reaction. The triradicals with a meta-benzyne moiety in the pyridinium ring demonstrated dominant allyl group abstraction, which is likely to occur at the pyridinium moiety. The reaction efficienciesof these triradicals toward allyl iodide are correlated with their calculated vertical electron affinities. The other triradicals showed I atom abstraction as the major reaction. These triradicals react with allyl iodide through different mechanisms compared to those mainly abstract an allyl group. Therefore, their reactivities are not directly related to their calculated vertical electron affinities.<br></div><div><br></div><div>In the tetraradicals, spin-spin coupling between all the radical sites affects their reactivities. The coupling of the radicals in a benzyne moiety is weakened by the couplings of radical sites between two benzyne moieties. This interaction results in higher reaction efficiencies for the tetraradicals than the related benzynes. Particularly, the 2,4,7,8-tetradehydroquinolinium cation was found to have much higher reactivity than the related meta-benzyne, the 2,4-didehydroquinolinium cation. This was rationalized based on the low distortion energy of the meta-benzyne moiety in the tetraradical.<br></div><div><br></div><div>Spin-spin coupling between the radical sites in bi-, tri-, and tetraradicals significantly affect their reactivity. To better understand the relation between the effects of spin-spin coupling and the spatial distance between two radical sites, a series of acridinium-based mono-and biradicals were studied in the gas phase. The acridinium-based monoradicals are less reactive than the related quinolinium-based monoradicals, which is possibly because of the steric hindrance of the additional benzene ring. Unlike quinolinium-based biradicals, which are less reactive than the related monoradicals, acridinium-based biradicals showed higher reactivities than the monoradicals with similar vertical electron affinities. In order to better illustrate the coupling strength in the studied biradicals, the natural logarithm of their total reaction efficiencies toward cyclohexane was plotted as a function of their calculated vertical electron affinities. The plots indicate that the coupling of quinolinium-based biradicals hinders the radical reactivity, while for acridinium-based biradicals, the coupling is negligibly weak and the biradicals react as two individual monoradicals.<br></div>

Ce travail présente une étude théorique des spectres RMN de molécules biologiques. Dans la première partie, les calculs DFT des paramètres RMN (déplacements chimiques et constantes de couplage spin-spin) pour les protons liés à des atomes de carbone ont été réalisés pour quatre métabolites de la prostate: la putrescine, la spermidine, la spermine, et la sarcosine, et trois métabolites du cerveau: l'acétate, l'alanine et la sérine. Une étude théorique systématique, dans l'approche DFT, des paramètres de RMN des métabolites a montré que la méthode B3LYP/6- 311++G** est un bon compromis entre la précision et les coûts. Les contributions du solvant ont été évaluées en utilisant le modèle PCM, les effets des isomères, pondérés dans l'approximation de Boltzmann, ont été pris en compte, et les corrections de vibration de point zéro ont été estimées en utilisant une approche perturbative au second ordre. La comparaison avec l'expérience a démontré que tous ces effets sont nécessaires pour améliorer l'accord entre les données calculées et expérimentales, aboutissant à des résultats de grande précision. Dans la deuxième partie, nous avons développé un nouveau modèle, BioShift, qui permet la prédiction des déplacements chimiques des différents noyaux (H, N, C ...) pour des molécules biologiques (protéines, ADN, ARN, polyamine ...). Il est simple, rapide, et comporte un nombre limité de paramètres. La comparaison avec des modèles sophistiqués conçus spécialement pour la prédiction des déplacements chimiques des protéines a montré que Bioshift est concurrentiel avec de tels modèles.

In this thesis a computational complement to experimental observables will be presented. Computational tools such as molecular dynamics and quantum chemical tools will be used to aid in the interpretation of experimentally (NMR) obtained structural data. The techniques are applied to study the dynamical features of biologically important carbohydrates and their interaction with proteins. When evaluating conformations, molecular mechanical methods are commonly used. Paper I, highlights some important considerations and focuses on the force field parameters pertaining to carbohydrate moieties. Testing of the new parameters on a trisaccharide showed promising results. In Paper II, a conformational analysis of a part of the repeating unit of a Shigella flexneri bacterium lipopolysaccharide using the modified force field revealed two major conformational states. The results showed good agreement with experimental data. In Paper III, a trisaccharide using Langevin dynamics was investigated. The approach used in the population analysis included a least-square fit technique to match T1 elaxation parameters. The results showed good agreement with experimental T-ROE build-up curves, and three states were concluded to be involved. In Paper IV, carbohydrate moieties were used in the development of prodrug candidates, to “hide” peptide opioid receptor agonists. Langevin dynamics and quantum chemical methods were employed to elucidate the structural preference of the compound. The results showed a chemical shift difference between hydrogens across the ring for the two isomers as well as a difference in the coupling constant, when taking the dynamics into account. In Paper V, the interaction of the Salmonella enteritidis bacteriophage P22 with its host bacterium, involves an initial hydrolysis of the O-antigenic polysaccharide (O-PS). Docking calculations were used to examine the binding between the Phage P22 tail-spike protein and the O-PS repeating unit. Results indicated a possible active site in conjunction with NMR measurements.

<p>This thesis presents quantum chemical calculations, applications of the response function formalism recently implemented within the framework of density functional theory (DFT) by our research group. The purpose of the calculations is to assess the performance of this perturbative approach to determining heavy atom effects on magnetic resonance parameters. Relativistic corrections can be generated by spin-orbit interactions or by scalar relativistic effects due to high velocity electrons in the atomic core region of heavy atoms. In this work, the evaluation of nuclear magnetic resonance (NMR) parameters is considered, the nuclear shielding tensor and the indirect nuclear spin-spin coupling tensor. For series of homologous compounds, it is found that both types of corrections to these parameters are increasing in size upon substitution of a constituent atom by a heavier element, but that their relative importance is system dependent. The obtained results are compatible with the ones provided by electron correlated <em>ab initio</em> methods, and a qualitative agreement with experimentally determined parameters is overall achieved. The methodology presented in this thesis aims to be a practical approach which can be applied in the study of molecular properties of large systems.</p><p>This thesis also addresses the calculation of hyperfine coupling constants, and evaluates a novel approach to the treatment of spin-polarization in spin restricted calculations without the spin contamination associated with spin unrestricted calculations.</p>

To fully exploit the capability of NV centers in diamond as magnetic sensors and quantum bits, the optimum production recipe as well as the method to enhance its optical performance has been studied in this work. The NV centers in bulk diamond were prepared by ion implantation and electron irradiation, and the optimum dose and temperature are found by comparing its optical and magnetic performance both experimentally and theoretically. In addition, the enhancement of optical performance and size characterization of NV centers in nanodiamonds will be discussed in this work.

Abstract In this thesis, the theory of static magnetic resonance spectral parameters of nuclear magnetic resonance (NMR) and electron spin resonance (ESR) spectroscopy is investigated in terms of the molecular Breit-Pauli Hamiltonian, which is obtained from the relativistic Dirac equation via the Foldy-Wouthuysen transformation. A leading-order perturbational relativistic theory of NMR nuclear shielding and spin-spin coupling tensors, and ESR electronic g-tensor, is presented. In addition, the possibility of external magnetic-field dependency of NMR parameters is discussed. Various first-principles methods of electronic structure theory and the role of one-electron basis sets and their performance in magnetic resonance properties in terms of their completeness profiles are discussed. The presented leading-order perturbational relativistic theories of NMR nuclear shielding tensors and ESR electronic g-tensors, as well as the theory of the magnetic-field dependent NMR shielding and quadrupole coupling are evaluated using first-principles wave function and density-functional theories.

Abstract The subjects of this thesis are the dynamics of liquid crystals in external electric and magnetic fields as well as the magnetic properties of small molecules, both studied by liquid crystal nuclear magnetic resonance (LC NMR) spectroscopy. Director dynamics of a liquid crystal 5CB in external magnetic and electric fields was studied by deuterium NMR and spectral simulations. A new theory was developed to explain the peculiar oscillations observed in the experimental spectra collected during fast director rotation. A spectral simulation program based on this new theory was developed and the outcome of the simulations was compared with the experimental results to verify the tenability of the theory. In the studies on the properties of small solute molecules, LC NMR was utilised to obtain information about anisotropic nuclear magnetic interaction tensors. The nuclear magnetic shielding tensor was studied in methyl halides, the spin-spin coupling tensor in methyl mercury halides and the quadrupolar coupling tensor in deuterated benzenes. The effects of small-amplitude molecular motions and solvent interactions on the obtained parameters were considered in each case. Finally, the experimental results were compared to the corresponding computational NMR parameters calculated in parallel with the experimental work.

Magnetic nanoparticles have received extensive attention in the biomedical research, e.g. as prospective contrast agents for T2-weighted magnetic resonance imaging. The ability of a contrast agent to enhance the relaxation rate of 1 H in its vicinity is quantified by relaxivity. The main aim of this thesis is to evaluate the transversal re- laxivity of ε-Fe2−x Alx O3 nanoparticles coated with amorphous silica or citrate - its dependence on external magnetic field, temperature and thickness of silica coating - by means of nuclear magnetic resonance. The aluminium content x = 0.23(1) was determined from XRF, the material was further characterised by XRPD, Möss- bauer spectroscopy, DLS, TEM and magnetic measurements. The size of magnetic cores was ∼ 21 nm, the thickness of silica coating ∼ 6,10,17 and 21 nm. Magne- tization of the ε-Fe2−x Alx O3 nanoparticles increased by ∼ 30 % when compared to ε-Fe2O3. The saturating dependence of relaxivity on external magnetic field and on the linear decrease with increase of thickness of silica coating contravene the theo- retical model of motional averaging regime (MAR); nevertheless, the temperature dependence acquired in 0.47 T and 11.75 T may be explained by MAR. In compari- son to ε-Fe2O3 nanoparticles, the relaxivity of examined samples was higher for par-...

This thesis presents quantum chemical calculations, applications of the response function formalism recently implemented within the framework of density functional theory (DFT) by our research group. The purpose of the calculations is to assess the performance of this perturbative approach to determining heavy atom effects on magnetic resonance parameters. Relativistic corrections can be generated by spin-orbit interactions or by scalar relativistic effects due to high velocity electrons in the atomic core region of heavy atoms. In this work, the evaluation of nuclear magnetic resonance (NMR) parameters is considered, the nuclear shielding tensor and the indirect nuclear spin-spin coupling tensor. For series of homologous compounds, it is found that both types of corrections to these parameters are increasing in size upon substitution of a constituent atom by a heavier element, but that their relative importance is system dependent. The obtained results are compatible with the ones provided by electron correlated ab initio methods, and a qualitative agreement with experimentally determined parameters is overall achieved. The methodology presented in this thesis aims to be a practical approach which can be applied in the study of molecular properties of large systems. This thesis also addresses the calculation of hyperfine coupling constants, and evaluates a novel approach to the treatment of spin-polarization in spin restricted calculations without the spin contamination associated with spin unrestricted calculations. / QC 20101122