In this research the so-called potential morphing method was used to generate reliable interaction potential energy surfaces for weakly bound complexes. The potential morphing method is based on the optimization of modified computed ab initio potential energy surfaces to give predicted spectroscopic data, in agreement with the experimental values. In the standard potential morphing procedure the computed ab initio potential is adjusted by scaling, shifting, and dilating transformations to reproduce the experimental data. In this research, selected systems have been chosen to be studied based on the availability of varied and accurate sets of experimental data. In the present work, accurate interaction potential energy surfaces are obtained for the weakly bound complexes: Ne:HCl, OC:HX (X = F, Cl, Br, I) and HI:CO2. A comprehensive study on the interaction potential of these systems provides fundamental perspectives on the influence of different intermolecular forces. In addition the ground state isotopic isomerization observed in the OC:HI system may suggest a possible structural change of proteins, and other biological macromolecules, in deuterated solvents. In this dissertation, an alternative approach to morphing the potential energy surfaces of non-covalent interactions is also presented. In this approach the morphed potential is generated as a linear combination of ab initio potentials, that are computed at different levels of theory. This new morphing approach is applied to OC:HCl and is found to be of similar accuracy to that of the previous morphing method. In addition, this new method is also extended from four-dimensions to six-dimensions and is applied to the OC:HF system to obtain a vibrationally-complete six-dimensional morphed potential.

Structure properties of water clusters are investigated in this study by means of molecular dynamics simulations. The oxygen density profile, dipole moment and hydrogen bond properties of water clusters are all examined. The temperature dependence and size dependence of the structure properties are also explored in the present study. Upon the molecular dynamics simulations, the flexible three-centered (F3C) water potential is used to model the inter- and intra-actions of the water molecule. It is found that as the temperature rises, the density of the oxygen and the average number of hydrogen bonds per water molecule will decrease. The effect of cluster size, however, is less significant on the structure properties. The differences between the structural properties for the surface region and those for the interior region of the cluster are also investigated. It is found that as the temperature rises, the average number of hydrogen bonds per water molecule decreases, but the ratio of surface water molecules increases. After comparing the water densities in interior regions and the average number of hydrogen bonds in those regions, we find there is no apparent size effect on water molecules in the interior region, whereas the size of the water cluster has a significant influence on the behavior of water molecules at the surface region.

京都大学 / 新制・課程博士 / 博士(理学) / 甲第23728号 / 理博第4818号 / 新制||理||1689(附属図書館) / 京都大学大学院理学研究科化学専攻 / (主査)教授 北川 宏, 教授 吉村 一良, 教授 竹腰 清乃理 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

Despite the prevalence of supramolecular architectures derived from metal-ligand or hydrogen-bonding interactions, few studies have focused on the simultaneous use of these two strategies to form discrete metal-ligand hydrogen-bonded (MLHB) assemblies. The design, synthesis, and characterization of 2-quinolone based hybrid subunits, 7-DPQ and 5-PYQ, that contain phosphine and pyridyl metal binding sites, respectively, is reported. Both subunits give two-fold symmetric hydrogen-bonded tectons that assemble with metal precursors to give hybrid MLHB structures. Treatment of [Cp*RhCl2]2 with the 7-DPQ subunit yields hybrid MLHB assemblies with closed topology. 1H diffusion ordered spectroscopy experiments established the stability of the structures in solution, and the measured hydrodynamic radii match those determined crystallographically, suggesting that the closed topology is maintained in solution and the solid state. In order to further explore possible MLHB architectures and test the selectivity boundaries of our quinolone-based subunits we report the selective assembly of 5-PYQ with mono- and bis-platinated anthracene precursors. Addition of 5-PYQ to [1-trans-Pt(PEt3)2NO3]-8-chloroanthracene yielded a hybrid MLHB structure with preorganization for a hybrid MLHB polymer. Despite the systems preorganization for the hybrid polymeric structure the assembly of 5-PYQ with 1,8-bis(trans-Pt(PEt3)2NO3)anthracene selects only for one discrete closed self-assembled macrocycle. The strong π-π stacking interactions of the 5-PYQ subunits erode the hydrogen-bonding fidelity to favor ambidentate coordination modes of 5-PYQ and give the non-hybrid macrocycle. In the course of investigating the intricacies of hybrid MLHB supramolecular structures we observed that, in addition to metal-ligand and hydrogen-bond interactions, the π-π stacking interactions of the 7-DPQ and 5-PYQ subunits played a critical role in determining the final assemblies. In fact, the prominent π-π interactions were typically found to be more favorable than the quinolone interligand hydrogen-bonding interactions. These results contribute to the overall knowledge of the design principles, synthesis, characterization, and fundamental assembly trends when exploiting both hydrogen-bonding and metal-ligand interactions to form stable supramolecular architectures. These studies have provided the foundation for expanding the accessible space of supramolecular chemistry to include rationally designed hybrid MLHB systems to give structures that more closely mimic the complex supramolecular systems observed in Nature. This dissertation includes both previously published/unpublished and co-authored material. / 10000-01-01

Abstract The triosephosphate isomerase (TIM) barrel superfamily is a broad family of proteins, most of which are enzymes. At the amino-acid-sequence level, many of the members of this family share little, if any, homology. Yet, they adopt the same three-dimensional (βα)8 fold. The TIM barrel fold seems to be a good framework for many different kinds of enzymes, providing unique possibilities for both natural and human-designed evolution, as the catalytic center and the stabilizing features are separated to different ends of the barrel. Indeed, in the light of most recent studies, it seems likely that at least most of the different TIM barrel enzymes, catalyzing a huge variety of reactions, have evolved from a common ancestor. TIM can be considered a real text-book enzyme — its catalytic properties and stucture-function relationships have been studied for decades. Still, at present, we are quite far from understanding the structural features that make TIM and other enzymes such superior catalysts in both efficiency and precision. TIM is a dimeric enzyme that consists of two identical subunits of 250 residues. It catalyzes the interconversion of dihydroxyacetone phosphate and D-glyceraldehyde-3-phosphate in glycolysis. The basics of this reaction are well known, but there is ongoing discussion about the details of the proton transfer steps, and three alternative pathways have been suggested. In addition, it is a fascinating question how the enzyme succeeds in abstracting a highly stable proton from a carbon atom of the substrate. This study was undertaken to shed light on some of the questions concerning the structure-function relationships in TIM. The most important findings are the elucidation of the role of Asn11 as a catalytic residue and the meaning of the flexibility of both the catalytic Glu167 side chain as well as the substrate during catalysis, and the presence of a low-barrier hydrogen bond between Glu167 and a transition-state analogue, 2-phosphoglycolate. Furthermore, significant results were obtained on the importance of a conserved salt bridge, 20 Å away from the active site and the dimer interface, for the stability and folding of TIM as well as on the factors influencing the opening of the flexible loop 6 upon product release.

No description available.

Le trifluoroéthanol (TFE) et l'hexafluoroisopropanol (HFIP) présentent des propriétés physicochimiques particulières comme un fort pouvoir ionisant élevé, une forte capacité à donner des liaisons hydrogène, et une faible nucléophilie. Ces différentes propriétés ont été avantageusement exploitées dans plusieurs réactions sans la présence de catalyseur. Dans un premier temps, l'étude de l'amination électrophile sélective d'aromatiques avec les azodicarboxylates a été réalisée dans l'HFIP pour conduire à une famille d'hydrazines aromatiques. Ensuite l'alkylation de Friedel-Crafts avec des hétéroaromatiques et des β-nitroalcènes a conduit à des dérivées de tryptamines. Ensuite, l'halogénation sélective d'aromatiques et d'hétérocycles en présence de N-halosuccinimides (NIS, NBS et NCS) a été développée. Egalement, nous avons étudié un nouveau système combinant l'HFIP et le KHSO4 qui est un sel inorganique peu coûteux. L'association de l'HFIP et de KHSO4 (10 mol%) est un système catalytique doux et efficace pour promouvoir certaines réactions. En particulier nous avons montré que ce système catalytique a été appliqué avec succès pour l'amination directe d'aromatiques peu activés avec des azodicarboxylates pour conduire à d'autres dérivés hydrazines. Ce système a aussi montré son efficacité dans la réaction directe de benzylation de Friedel-Crafts avec des alcools benzyliques. Ainsi une grande variétés de composés diarylméthanes dissymétriques a pu être obtenue avec une excellente régiosélectivité. / Due to the electron-withdrawing character of fluoroalkyl groups, fluorinated alcohols such as trifluoroethanol (TFE) and hexafluoroisopropanol (HFIP) exhibit a nearly unique set of properties that include high ionizing power, strong hydrogen bond donating ability, mild acidity, and low nucleophilicity. All of these properties have been exploited without the need of an external catalyst. At first, the para-selective amination of free anilines with azodicarboxylates in HFIP led to hydrazine derivatives. The Friedel-Crafts alkylation of indoles and electron-rich arenes with β-nitroalkenes succeeded to afford tryptamines derivatives. Then the regioselective halogenation of arenes and heterocycles with N-halosuccinimides (NIS, NBS, NCS) have been developed. Meanwhile, we have disclosed a new mild system between HFIP and KHSO4 which is a green, inexpensive and readily available inorganic salt. The association of HFIP/KHSO4 (10 mol%) is an efficient and mild catalytic system in order to promote some reactions. In particular, we showed that this system allowed the direct amination of slightly activated and neutral arenes with azodicarboxylates in order to give other families of hydrazines. This mild system has been applied successfully for the Friedel-Crafts benzylation with benzylic alcohols. These mild conditions provided a straightforward synthesis of a variety of unsymmetrical diarylmethanes in high yield with good to high regioselectivity

Yes / Literature solubilities and NMR and IR studies have been used to obtain properties or descriptors of edaravone. These show that edaravone has a significant hydrogen bond acidity so that it must exist in solution partly as the OH and NH forms, as found by Freyer et al. Descriptors have been assigned to the keto form which has a low hydrogen bond acidity, and which is the dominant form in nonpolar solvents. Physicochemical properties of the keto form can be been calculated such as solubilities in nonpolar solvents, partition coefficients from water to nonpolar solvents, and partition coefficients from air to biological phases.

No description available.

No description available.