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.

Host Rock Classification (HRC) system for nuclear waste disposal in crystalline bedrock

A new rock mass classification scheme, the Host Rock Classification system (HRC-system) has been developed for evaluating the suitability of volumes of rock mass for the disposal of high-level nuclear waste in Precambrian crystalline bedrock. To support the development of the system, the requirements of host rock to be used for disposal have been studied in detail and the significance of the various rock mass properties have been examined. The HRC-system considers both the long-term safety of the repository and the constructability in the rock mass. The system is specific to the KBS-3V disposal concept and can be used only at sites that have been evaluated to be suitable at the site scale. By using the HRC-system, it is possible to identify potentially suitable volumes within the site at several different scales (repository, tunnel and canister scales). The selection of the classification parameters to be included in the HRC-system is based on an extensive study on the rock mass properties and their various influences on the long-term safety, the constructability and the layout and location of the repository. The parameters proposed for the classification at the repository scale include fracture zones, strength/stress ratio, hydraulic conductivity and the Groundwater Chemistry Index. The parameters proposed for the classification at the tunnel scale include hydraulic conductivity, Q´ and fracture zones and the parameters proposed for the classification at the canister scale include hydraulic conductivity, Q´, fracture zones, fracture width (aperture + filling) and fracture trace length. The parameter values will be used to determine the suitability classes for the volumes of rock to be classified. The HRC-system includes four suitability classes at the repository and tunnel scales and three suitability classes at the canister scale and the classification process is linked to several important decisions regarding the location and acceptability of many components of the repository at all three scales. The HRC-system is, thereby, one possible design tool that aids in locating the different repository components into volumes of host rock that are more suitable than others and that are considered to fulfil the fundamental requirements set for the repository host rock. The generic HRC-system, which is the main result of this work, is also adjusted to the site-specific properties of the Olkiluoto site in Finland and the classification procedure is demonstrated by a test classification using data from Olkiluoto. Keywords: host rock, classification, HRC-system, nuclear waste disposal, long-term safety, constructability, KBS-3V, crystalline bedrock, Olkiluoto

'A responsible nuclear weapons power' : Nuclear Weapons and Indian Foreign Policy

This thesis examines the interrelationship and dynamics between the Indian United Progressive Alliance government’s foreign policy and its nuclear weapons policy. The purpose of the study is to situate nuclear policy within a foreign policy framework, and the fundamental research problem is thus how does the Indian nuclear policy reflect and respond to the Indian foreign policy? The study examines the intentions in the Indian foreign and nuclear policies, and asks whether these intentions are commensurable or incommensurable. Moreover, the thesis asks whether the UPA government differs from its predecessors, most notably the Bharatiya Janata Party-led National Democratic Alliance government in its foreign and nuclear policies. Answers to these questions are based on the interpretation of political texts and speeches as suggested by Quentin Skinner’s notion of meaning3, what does a writer or speaker mean by what he or she says in a given text, and by J.L. Austin’s speech act theory. This linguistic perspective and the approach of intertextualizing, place the political acts within their contingent intellectual and political contexts. The notion of strategic culture is therefore introduced to provide context for these juxtapositions. The thesis firstly analyses the societal, historical and intellectual context of India’s foreign and nuclear policy. Following from this analysis the thesis then examines the foreign and nuclear policies of Prime Minister Manmo-han Singh’s UPA government. This analysis focuses on the texts, speeches and statements of Indian authorities between 2004 and 2008. This study forwards the following claims: firstly, the UPA Government conducts a foreign policy that is mainly and explicitly inclusive, open and enhancing, and it conducts a nuclear policy that is mainly and implicitly excluding, closed and protective. Secondly, despite the fact that the notion of military security is widely appreciated and does not, as such, necessarily collide with foreign policy, the UPA Government conducts a nuclear policy that is incommensurable with its foreign policy. Thirdly, the UPA Gov-ernment foreign and nuclear policies are, nevertheless, commensurable re-garding their internal intentions. Finally, the UPA Government is conduct-ing a nuclear policy that is gradually leading India towards having a triad of nuclear weapons with various platforms and device designs and a function-ing and robust command and control system encompassing political and military planning, decision-making and execution. Regarding the question of the possible differences between the UPA and NDA governments this thesis claims that, despite their different ideological roots and orientations in domestic affairs, the Indian National Congress Party conducts, perhaps surprisingly, quite a similar foreign and nuclear policy to the Bharatiya Janata Party.

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.