京都大学 / 新制・課程博士 / 博士(理学) / 甲第22989号 / 理博第4666号 / 新制||理||1669(附属図書館) / 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 柳瀬 陽一, 教授 前野 悦輝 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

Synthetic molecular receptors find applications in the selective extraction, transport and detection of neutral or charged species and the study of these systems is an important facet of supramolecular chemistry. In this thesis, we focused our attention on a specific family of molecular receptors called calix[6]arenes. These receptors possess a hydrophobic cavity formed by 6 aromatic rings that can accommodate small organic molecules. They can furthermore be easily functionalized and give rise to for example ditopic receptors or sensing systems. We worked with two families of calix[6]arenes but also looked at the complexation properties of some related compounds: a homooxacalix[3]arene and a resorcin[4]arene derivatives. The first part of this thesis is devoted to the study of the complexation properties of a fluorescent calix[6]tris-pyrenylurea. The binding of anions, ion pairs, ion triads and phospholipids was monitored by 1H Nuclear Magnetic Resonance (NMR) and Emission Spectroscopy. Our results showed that the receptor exhibits a remarkable selectivity for the sulfate anion in DMSO for which a binding constant of the order of 103 M-1 was found. In chloroform the affinity for sulfate is of the order of 105 M-1 and the selective recognition of ammonium-TBASO4 triads was observed (TBA = tetra-n-butylammonium; ammonium = PrNH3+, HexNH3+ or DodNH3+). This work has been reported in the paper “Fluorescent Chemosensors for Anions and Contact Ion Pairs with a Cavity-Based Selectivity” Emilio Brunetti, Jean-François Picron, Karolina Flidrova, Gilles Bruylants, Kristin Bartik and Ivan Jabin J. Org. Chem. 2014, 79, 6179–6188. We also showed that calix[6]tris-pyrenylurea displays a remarkable selectivity in chloroform for phospholipids bearing a phosphatidylcholine head (PCs) over those bearing a phosphoethanolamine head (PEs). We were able to show that this fluorescent receptor is able to extract PCs from a water solution enabling their quantification. This work has been reported in the paper “A Selective Calix[6]arene-based Fluorescent Chemosensor for Phosphatidylcholine Type Lipids” Emilio Brunetti, Steven Moerkerke, Johan Wouters, Kristin Bartik and Ivan Jabin Org. Biomol. Chem. 2016. Accepted Manuscript. DOI: 10.1039/C6OB01880G.The second part of this thesis is devoted to the evaluation of the binding properties of different receptors incorporated into dodecylphosphocholine (DPC) micelles. This strategy was used to make the hydrophobic molecular receptors “water-compatible” without having to undertake synthetic modifications. Our results showed that a calix[6]azacryptand-based receptor can be incorporated into DPC micelles, either as a zinc complex or as a polyammonium at low pH. We observed that the zinc complex incorporated in the micelles is able to bind small and long linear primary amines in its cavity and we were able to highlight that complexation is driven by the hydrophobic effect. This work has been reported in the paper “Primary Amine Recognition in Water by a Calix[6]aza-cryptand Incorporated in Dodecylphosphocholine Micelles” Emilio Brunetti, Alex Inthasot, Flore Keymeulen, Olivia Reinaud, Ivan Jabin and Kristin Bartik Org. Biomol. Chem. 2015, 13, 2931-2938.We also validated the micellar incorporation strategy with a homooxacalix[3]tris-acid and with a resorcin[4]arene zinc complex bearing four methyl-imidazole moieties. Once incorporated into DPC micelles, we showed that the two receptors can bind small organic guests: the homooxacalix[3]arene derivative can bind tert-butylammonium or adamantylammonium, albeit with low affinity and the resorcin[4]arene-based zinc complex can bind acetate and acetylacetone.The final part of this thesis is devoted to the work undertaken in order to try and elucidate the guest exchange mechanism of calix[6]arene-zinc complexes where the zinc is tri-coordinated to the calixarene-based ligand and coordinates a guest molecule inside the calixarene cavity. The hypothesis that we put forward is that when the zinc is only tri-coordinated to the calixarene ligand, the guest exchange mechanism involves a zinc penta-coordinated intermediate where the zinc atom is simultaneous coordinated to an endo-complexed guest (inside the cavity) and an exo-complexed molecule (outside the cavity). 1D EXchange SpectroscopY experiments (EXSY) were undertaken with two calix[6]arene-zinc complexes where the zinc is tri-coordinated to the calixarene ligand and with a calix[6]arene-zinc complex where the zinc is tetra-coordinated to the calixarene ligand. The exchange of different guests (ethanol, dimethylformamide and acetonitrile) was monitored in deuterated dichloromethane. We observed that in all cases water accelerates guest exchange but that the guest residence times are highly dependent on the acidity of the metal center and on the nature of the guest buried inside the cavity. / Doctorat en Sciences de l'ingénieur et technologie / info:eu-repo/semantics/nonPublished

Title: NMR Study of Oligonucleotide Structures Author: Václav Římal Department: Department of Low-Temperature Physics Supervisor: Prof. RNDr. Helena Štěpánková, CSc., Department of Low- Temperature Physics Abstract: The dynamics of nucleic acids plays a fundamental role in the interactions with proteins. Some processes are governed by changes in DNA stability and flexibility caused by sequence alterations or chemical modifications without substantial structural impact. We employed line-shape analysis of variable-temperature 1H NMR spectra to deeply investigate the melting transition of DNA structures. We observed a significant influence of the sequence beyond the nearest neighbours on chemical shifts and thermodynamics of the double helix. The CpG motif is especially sensitive to its distant surroundings and for a particular oligonucleotide it was even found to undergo an unexpected local conformational transition. A strong cooperativity in the duplex dis- ruption was witnessed by both the equilibrium and kinetic aspects as well as by distant effects of cytosine methylation. We propose a two-state melt- ing scheme also for a fragment of a transcription element proved here to fold as a hairpin with a six-membered loop. In addition, we describe the properties of self-assemblies of riboguanosine and...

>Magister Scientiae - MSc / Retinoblastoma Binding Protein 6 (RBBP6) is a 200 KDa multi-domain protein that has been shown to play a role in mRNA processing, cell cycle arrest and apoptosis. RBBP6 interacts with tumour suppressor proteins such as p53 and pRb and has been shown cooperate with Murine Double Minute 2 (MDM2) protein in catalyzing ubiquitination and suppression of p53. Unpublished data from our laboratory has suggested that RBBP6 and MDM2 interact with each other through their RING finger domains. RBBP6 has also been shown to have its own E3 ubiquitin ligase activity, catalyzing ubiquitination of Y-Box Binding Protein 1 (YB-1) in vitro and in vivo. YB- 1 is a multifunctional oncogenic protein that is generally associated with poor prognosis in cancer, tumourigenesis, metastasis and chemotherapeutic resistance. Unpublished data from our laboratory shows that RBBP6 catalyzes poly-ubiquitination of YB-1, using Ubiquitin-conjugating enzyme H1 (UbcH1) as E2 ubiquitin conjugating enzyme. / 2022-02-25

NMR relaxation and Raman lineshape analysis are well known methods for the study of molecular reorientational dynamics in liquids. The combination of these two methods provides another approach to tackle the characterization of molecular dynamics in liquids. Investigations presented here include (1) NMR relaxation study of polycyclic compounds in solution, (2) the study of nitromethane reorientational dynamics using the NMR and Raman methods, and (3) Raman lineshape analysis of reorientation hexafluorobenzene/benzene mixtures.

Topical treatment containing undeclared corticosteroids and illegal topical treatment with corticosteroid content have been seen on the Swedish market. In creams and ointments corticosteroids in the category of glucocorticosteroids are used to reduce inflammatory reactions and itchiness in the skin. If the inflammation is due to bacterial infection or fungus, complementary treatment is necessary. Side effects of corticosteroids are skin reactions and if used in excess suppression of the adrenal gland function. Therefore the Swedish Medical Products Agency has published related warnings to make the public aware. There are many similar structures of corticosteroids where the anti-inflammatory effect is depending on substitutions on the corticosteroid molecular skeleton. In legal creams and ointments they can be found at concentrations of 0.025 ‑ 1.0 %, where corticosteroids with fluorine substitutions usually are found at concentrations up to 0.1 % due to increased potency. At the Medical Products Agency 19F-NMR and 1H-NMR have been used to detect and quantify corticosteroid content in creams and ointments. Nuclear Magnetic Resonance, NMR, is an analytical technique which is quite sensitive and can have a relative short experimental time. The low concentration of corticosteroids makes the signals detected in NMR small and in 1H‑NMR the signals are often overlapped by signals from the matrix. With 1H‑NMR characteristic signals could be detected in a less crowded spectral window between 5.96 ‑ 6.40 ppm where overlapping signals from the matrix often are absent. Since fluorine is less common in molecules, the option of using 19F‑NMR increases the possibility of finding fluorine-containing corticosteroids in creams and ointments. The corticosteroid signals in 19F‑NMR are detected at -165 ppm and -187 ppm, depending on where fluorine is located on the structure. Quantifying with 1H-NMR and 19F-NMR gave similar result with an accuracy of 98‑116 % and 89-106 % respectively, and RSD values between 2‑35 %, depending on the kind and amount of corticosteroid. Relations between the structure and some signals in 1H‑NMR were found, making it easier to determine the basic structure of unknown corticosteroids in creams and ointments. Screening experiments were performed on creams and ointments with known concentration corticosteroid in order to find minimum NS for analyzing products which might contain corticosteroids. In order to detect a corticosteroid concentration of 0.05 % 19F‑NMR needed 64 NS with an experimental time of 2 min and 1H-NMR needed 160 NS with an experimental time of 17 min. Concentrations of 0.025 % could for some corticosteroids be detected with these parameters. The possibility of spiking samples in order to discriminate between corticosteroids was also investigated. The corticosteroids available at the MPA could be discriminated from each other with at least one of the methods 1H‑NMR or 19F-NMR, and in most cases with both. A market research was done in order to search for counterfeits and salespersons in different health food stores were asked to recommend the best product to treat eczema or psoriasis. Nine recommended products were bought where one was found illegally containing a corticosteroid. In previous experiments at the MPA there had been occurrences of a split signal in 19F-NMR when analyzing creams. The split 19F‑NMR signal was shown to be related both to the presence of water and structural effects of the corticosteroid

No description available.

Nuclear magnetic resonance (NMR) experiments are reported at up to 30.5 GPa of pressure using radiofrequency (RF) micro-coils with anvil cell designs. These are the highest pressures ever reported with NMR, and are made possible through an improved gasket design based on nano-crystalline powders embedded in epoxy resin. Cubic boron-nitride (c-BN), corundum (α-Al2O3), or diamond based composites have been tested, also in NMR experiments. These composite gaskets lose about 1/2 of their initial height up to 30.5 GPa, allowing for larger sample quantities and preventing damages to the RF micro-coils compared to precipitation hardened CuBe gaskets. It is shown that NMR shift and resolution are less affected by the composite gaskets as compared to the more magnetic CuBe. The sensitivity can be as high as at normal pressure. The new, inexpensive, and simple to engineer gaskets are thus superior for NMR experiments at high pressures.

A new design of a non-magnetic high-pressure anvil cell for nuclear magnetic resonance (NMR) experiments at Giga-Pascal pressures is presented, which uses a micro-coil inside the pressurized region for high-sensitivity NMR. The comparably small cell has a length of 22 mm and a diameter of 18 mm, so it can be used with most NMR magnets. The performance of the cell is demonstrated with externalforce vs. internal-pressure experiments, and the cell is shown to perform well at pressures up to 23.5 GPa using 800 μm 6H-SiC large cone Boehler-type anvils. 1H, 23Na, 27Al, 69Ga, and 71Ga NMR test measurements are presented, which show a resolution of better than 4.5 ppm, and an almost maximum possible signal-to-noise ratio.

Nuclear Magnetic Resonance is used for the determination of the properties of porous media in Geophysics and oil exploration. As it stands, there is a challenge in understanding the connection between the times measured in Free Induction Decay Nuclear Magnetic Resonance experiments and the shape of samples. In this work, suspensions and watersaturated densely-packed porous media with the volume fraction of the glass solid phase in the range from 10–4 to ∼1 are found to exhibit FID decay rates proportional to the square root of the volume fraction of the solid phase of the samples. A model of spheres in liquid is proposed for the description of such behavior.