A set of crude oil samples with different composition and characteristics is studied by means of Fast Field Cycling (FFC) 1H relaxometry, which probes the distribution of longitudinal relaxation times T1 as a function of the Larmor frequency. Investigation of T1 profiles at different temperatures is able to provide an insight into the dynamics and structural changes of oil components, with our particular interest being the high temperature behaviour of asphaltene. It is well-known that asphaltenes tend to form porous clusters in crude oils, which can cause severe problems for the process of oil extraction. Therefore, FFC experiments are conducted on Stelar Spinmaster FFC2000 in the temperature range 203K < T <443K, where the upper limit of 443K is aimed at approximating the typical maximal in-situ well temperatures. FFC relaxometry data of crude oils at such a high temperature are obtained for the first time with the use of a specially modified NMR probe. Inverse Laplace transformation is applied to the longitudinal agnetization decays, yielding T1 distributions at different frequencies. A comparative analysis of these distributions for different Larmor frequencies and temperatures showed that there is a systematic variation of the frequency dependence of T1 correlating with the asphaltene content in the samples, at temperatures similar to the well conditions.

We present nanoscale nuclear magnetic resonance (NMR) measurements performed with nitrogen-vacancy (NV) centers located down to about 2 nm from the diamond surface. NV centers were created by shallow ion implantation followed by a slow, nanometer-by-nanometer removal of diamond material using oxidative etching in air. The close proximity of NV centers to the surface yielded large 1H NMR signals of up to 3.4 lT-rms, corresponding to ~330 statistically polarized or ~10 fully polarized proton spins in a (1.8 nm)3 detection volume.

Arctic soils contain a large fraction of our planets terrestrial carbon (C) pool. When tundra soils become warmer and permafrost thaws, non-native geoengineering earthworms can enter these soils and ingest organic matter accumulated over long timescales. Previous studies have found that earthworms increase mineralization rates of soil organic matter into carbon dioxide (CO2) when introduced. Yet, this initial mineralization boost seems transient with time and it has been hypothesized that earthworms stimulate the formation of persistent C forms. In this study, I investigated how non-native, geoengineering earthworms affected the relative proportions of seven carbon forms in the O and A1 horizon of tundra soil and if their effect induced a change in pH. I used Nuclear Magnetic Resonance (NMR) spectroscopy to understand what happens to soil carbon compounds in two different tundra vegetation types (heath and meadow), that had been subjected to earthworm treatment for three summers. I found that O-aromatic C increased from 7.22% ± 0.24 (mean ± stderr) in the meadow soil lacking earthworms to 8.98% ± 0.30 in the meadow exposed to earthworms, and that aromatic C increased from 8.71% ± 0.23 to 9.93% ± 0.25. In similar, the result suggested that alkyl C decreased in this vegetation type from 20.43% ± 0.38 to 18.70% ± 0.25 due to earthworm activities. I found no effect on the chemical properties in the heath. I conclude that geoengineering earthworms affect the two vegetation types differently and that earthworms seem to enhance the accumulation of recalcitrant aromatic C forms.

Ribonuclease HI (RNase HI), a ubiquitous, non-sequence-specific endonuclease, cleaves the RNA strand in RNA/DNA hybrids. The enzyme has roles in replication, genome maintenance, and is the C-terminal domain of retroviral multi-domain reverse transcriptase (RT) proteins. Murine Leukemia Virus (MLV) and Human Immunodeficiency Virus (HIV) are two such retroviruses and their RNase HI (RNHI) domains are necessary for viral replication, making it an attractive drug target. RNase HI has a “handle region”, an extended loop with a large cluster of positive residues, that is critical for substrate recognition. MLV-RNHI is active in isolation and contains a handle region, but, HIV-RNHI is inactive in isolation and does not contain a handle region. HIV-RT, however, has a region in its polymerase domain (positive charge cluster and aromatic cluster) that makes contact with the RNHI domain that may be serving as a “pseudo” handle region; additionally, insertion of a handle region into isolated HIVRNHI restores its activity. Overall, a breadth of information exists on this region’s dynamics, but important gaps remain unfilled; gaps that may potentially lead to creating effective drugs to treat the above-mentioned viruses. Solution-state nuclear magnetic resonance (NMR) spectroscopy combined with Molecular Dynamic (MD) simulations suggest a model in which the extended handle region domain of the mesophilic Escherichia coli RNHI (EcRNHI) populates "open" (substrate-bindingcompetent) and "closed" (substrate-binding incompetent) states, while the thermophilic Thermus thermophilus RNHI (TtRNHI) mainly populates the closed state at 300 K. In addition, an in silico designed mutant Val98Ala (V98A) EcRNHI was predicted to populate primarily the closed state. Understanding the structural features and internal motions that lead RNase HI to adopt these various conformers is of central importance to better understanding RNase HI’s role in retroviral infection. To formulate a comprehensive model on handle region dynamics, an integrative approach of NMR spectroscopy, X-ray crystallography, and MD simulations is employed. The sensitivity to internal conformational dynamics at multiple time scales of NMR spectroscopy, molecular range and resolution of X-ray crystallography, and structural interpretations of dynamic processes by MD simulations create a synergistic trio capable of tackling this issue. First, the in silico 2-state Kinetic model is validated through NMR observables that correlate with the respective conformers, thus serving as experimental analogs. The NMR parameters also correlate with the Michaelis constants (KM) for RNHI homologs and help to confirm the in silico predictions of V98A EcRNHI. This study shows the important role of the handle region in modulation of substrate recognition. It also illustrates the power of NMR spectroscopy in dissecting the conformational preferences underlying enzyme function. Next, a deeper dive is taken into handle region dynamics, specifically focusing on residue 88 and the impact its identity has on this region. Its sidechain interactions are shown to directly correlate with handle region conformations and helps to amend the originally proposed in silico 2-state Kinetic model. Lastly, looking at RNHI handle region dynamics through an evolutionary lens opens the door to uncovering novel mutations that have been previously overlooked or not identified. Through a phylogenetic analysis, researchers have reconstructed seven ancestral RNHI mutants and three of them have been expressed here. The sequence identity of these three ancestral mutants range from 60-87% to extant homologs and this is reflected by similar peak positions in their 15N HSQC spectra. Requisite experiments to assign the NMR backbone have been completed.

The IR spectra of twenty-one transition metal complexes of 8-hydroxyquinoline over the range 700 - 50 cm⁻¹ are discussed in relation to their known or inferred structures. The complexes are of three types: (a) the bis(aquo) complexes of the first row transition metal(II) ions, [M(ox)₂(H₂O)₂] (M =Mn, Fe, Co, Ni, Cu, Zn); (b) the corresponding anhydrous complexes, [M(ox)₂]n (M=Mn, Co, Ni, Cu, Zn) and (c) the complexes of the metal(III) ions, [M(ox)₃] (M = Sc, V, Cr, Mn, Fe, Co, Ga, Rh and In). Deuterated 8-hydroxyquinoline was. synthesized by the Skraup synthesis and has been used to assist in the assignment of the metal-ligand modes. The assignment of these bands was further based on ⁶⁴,⁶⁸Zn labellihg of the bis(aquo) zinc chelate and on the effects of metal ion substitution in relation to structural considerations based on crystal field theory. An investigation of the IR spectra of a series of -tris, bis and mono(8-aminoquinoline) complexes of the first transition row metal(II) perchlorates and halides is reported.

Proteins are composed of a unique sequence of amino acids, whose order guides a protein to adopt its particular fold and perform a specific function. It has been shown that a protein's 3-dimensional structure is embedded within its primary sequence. The problem that remains elusive to biochemists is how a protein's primary sequence directs the folding to adopt such a specific conformation. In an attempt to gain a better understanding of protein folding, my research tests a novel model of protein packing using protein design. The model defines the knob-socket construct as the fundamental unit of packing within protein structure. The knob-socket model characterizes packing specificity in terms of amino acid preferences for sockets in different environments: sockets filled with a knob are involved in inter-helical interactions and free sockets are involved in intra-helical interactions. Equipped with this knowledge, I sought to design a unique protein, Ksα1.1, completely de novo. The sequence was selected to induce helix formation with a predefined tertiary packing interface. Circular dichroism showed that Ksα1.1 formed α-helical secondary structure as intended. The nuclear magnetic resonance studies demonstrated formation of a high order oligomer with increased protein concentration. These results and analysis prove that the knob-socket model is a predictive model for all α-helical protein packing. More importantly, the knob-socket model introduces a new protein design method that can potentially hold a solution to the folding problem.

The time-dependent visible spectra and the crystal structure of [Fe2(C20H24N8O2)(CH3CN)4]·PF6 (diketo-dimer) were studied. The spectra showed that the most significant chemistry occurred during the initial 1.5 hours of the synthetic reaction. The starting materials 343 nm peak shifted to a lower energy, at 360 nm, and a new shoulder appeared at 490 nm. This change suggests the formation of a new intermediate whose spectrum has an exceptional resemblance to the starting materials mixed valent species, [Fe2(TIED)(Cl)4]+1 (TIED = tetraiminethylene dimacrocycles). Two isosbestic points were found at 538 and 371 nm. The diketo-dimer's crystals appear to have individual colors, a physical characteristic called pleochroism. Pleochroism is a topic in the study of optical crystallography which is discussed and applied to the diketo-dimer. The extinction angle was estimated to be 14°, a value consistent for triclinic crystals. X-ray crystallography found that the diketo-dimer is triclinic, and has a space group of P-1. A noteworthy feature is the bond length, 1.406 Å, between the two linking bridgehead carbons. This bond length matches the value for partial double bonds of aromatic compounds. This argues for a delocalized electron circulating within the macrocycle. The NMR spectra of a diiron macrocycle, [Fe2(TIED)(CH3CN)4]4+, were examined. Temperature dependent, pH dependent, D+ substitution, selectively decoupled, and COSY 1H NMR experiments were performed. Two sets of structural equilibria were found. One set is temperature dependent, and the other is pH dependent. Of particular interest are the peaks centered at 9.7 ppm and assigned to the imine carbon protons H2. Its resonance indicates an imine proton in an extensively conjugated aromatic environment with an electron deficient metal.

Astrophysical observations indicate the existence of dark matter through its gravitational interaction, but since its other interactions remain undetected, its particle nature is still unknown. There are several dark matter candidates, one being a hypothetical particle called axion that can have three types of non-gravitational couplings: electromagnetic, electric dipole moment (EDM), and gradient. This dissertation presents experimental approaches and axionlike dark matter search results from two table-top experiments: Cosmic Axion Spin Precession Experiment (CASPEr-electric) sensitive to EDM and gradient couplings, and Search for Halo Axions with Ferromagnetic Toroids (SHAFT) sensitive to electromagnetic coupling. CASPEr-electric is a resonant search for axionlike dark matter through the induced nuclear spin precession. The experimental approach is measuring nuclear magnetic resonance (NMR) of the heavy atom in a ferroelectric crystal. Experimental setup is characterized using pulsed NMR calibration measurements. Recorded search data that is sensitive to axionlike dark matter is analyzed by optimal filtering and then setting a detection threshold based on the histogram of power spectral density modeled as a Gaussian distribution. The candidates above the threshold are all rejected through statistical fluctuations and scan/re-scan measurements. CASPEr-electric places the upper bounds on the EDM and gradient couplings of axionlike dark matter in the Compton frequency range from 39.1 MHz to 40.2 MHz. SHAFT is a broadband search for axionlike dark matter through the induced oscillatory magnetic field. The resultant magnetic flux is measured with a precision magnetometer called superconducting quantum interference device (SQUID), coupled to a coil placed on the inner surface of a ferromagnetic toroid. After analyzing the search data, all candidates are rejected and SHAFT places a limit on electromagnetic coupling of axionlike dark matter between 3 kHz and 3 MHz Compton frequencies. Finally, coupling limits placed by CASPEr-electric and SHAFT are evaluated in the wider parameter space, and possible future directions that both experiments could take to improve their sensitivities to axionlike dark matter are discussed. / 2022-09-27T00:00:00Z

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第18051号 / 理博第3929号 / 新制||理||1567(附属図書館) / 30909 / 京都大学大学院理学研究科物理学・宇宙物理学専攻 / (主査)教授 石田 憲二, 教授 前野 悦輝, 教授 松田 祐司 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DFAM

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第18060号 / 理博第3938号 / 新制||理||1567(附属図書館) / 30918 / 京都大学大学院理学研究科物理学・宇宙物理学専攻 / (主査)教授 石田 憲二, 教授 前野 悦輝, 教授 松田 祐司 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM