La nicotianamine est une molécule naturelle qui joue un rôle essentiel dans la régulation des concentrations en métaux de transition dans les plantes. Sa structure comprend trois acides carboxyliques et trois fonctions amines. L'objectif du travail présenté dans ce manuscrit est d'établir un protocole permettant de reproduire les propriétés de chélation de cette molécule grâce à des calculs de chimie quantique. L'intérêt est d'appliquer ce protocole à des analogues synthétiques de la nicotianamine, afin de prédire leurs propriétés.Le protocole que nous avons mis au point s'articule autour de quatre axes : le calcul des pKa, l'étude des propriétés de chélation, le calcul de tenseur g de résonance paramagnétique électronique et l'analyse des propriétés vibrationnelles. Ces différents points ont nécessité le développement de méthodes de calcul et d'outils innovants. Les calculs de chimie quantique qui ont été effectués sont basés sur la théorie de la fonctionnelle de la densité. On a utilisé des fonctionnelles hybrides, associées à un modèle de solvant implicite ou semi-explicite qui permet de prendre en compte l'effet du milieu.Nous avons proposé une méthode graphique originale adaptée à la nicotianamine permettant le calcul de ses six pKa ainsi que celui des pka des complexes formés avec les métaux de transition. Cette méthode conduit à une bonne précision sur les calcul de pKa dans l'intervalle de pH physiologique. Ces pKa renseignent sur le comportement de la nicotianamine dans différents milieux végétaux. Nous avons aussi envisagé plusieurs protocoles pour l'étude des propriétés de chélation de la nicotianamine.Pour compléter l'étude des complexes de la nicotianamine, nous avons paramétré une méthode simple et rapide de calcul du tenseur g de systèmes moléculaires contenant du cuivre paramagnétique. Enfin, nous avons développé un programme graphique permettant l'analyse des modes de vibration infrarouges de systèmes moléculaires comme les complexes métal-nicotianamine étudiés. / Nicotianamine is a triamino acid that plays an essential role in regulation and transportation of transition metals in plants by a chelation process. Functional analogues of this molecule have already been synthesised that we hope to use for selective soil decontamination thanks to their property changes with respect to nicotianamine. Therefore, the aim of the present work is to find a predictive protocol for the chelating properties of these analogues, using the know example of nicotianamine. We worked out a predictive protocol focusing on the four following points : pKas, chelation, EPR tensors and vibrational properties. It uses quantum chemistry methods such as hybrid DFT functionals and implicit solvent models.The pKa calculations for nicotianamine and metal-nicotianamine complexes were performed using a novel graphical method well suited to these systems. The pKas are useful to understand the effect of the various plants pHs on the complexes. Then we computed the chelation constants and the structures of metal-nicotianamine complexes. As a complement to the study of these complexes, we set up protocols to calculate the EPR tensors of the copper-nicotianamine complex and to analyse the infra-red vibrations of the complexes, using respectively a parametrised method and a local code.

Humic acids are part of humus material abounded in nature. Humic acids are generally aromatic stuffs with sidechains and there can be linked various functional groups as carboxylic and fenolic mainly. This functional groups are able to form transitions elements ions and complexes of different stability. This property can be used in the environment, because certain polutants should be imobilized in nature. Diploma thesis studies adsorption of metal ions Cu2+, Cd2+, Zn2+ and Pb2+ on humic acids by electroanalytical method called flow – through coulometry.

This diploma thesis is focused on the study of diffusion of metal ions in hydrogel of humic acid. The objective of this thesis was to investigate the effect of the concentration of metal ions supply source and duration of diffusion on transport through the gel using method of diffusion couple. Cupric, nickel and cobalt ions were esed like the diffusion medium. All these ions were selected thanks to their high affinity for the humic acids and because they are ideal to investigate the diffusion through the humic gel. Chloride salts of these metals, namely CuCl2, NiCl2 and CoCl2, were used like supply sources. Three different concentrations of each solution were compared, specifically 0,05M, 0,1M and 1M, and also were three different durations of diffusion, specifically 10 hours, 1 day and 3 days. Metal ions were compared with each other in order to determine which one has the best transport properties through the humic hydrogel. The data, necessary for calculation, were obtained by UV-VIS spectrophotometry. Diffusion coefficients and duffusive flux of individual metal ions were determined from measured data.

MSc (Chemistry) / Department of Chemistry / The corrosion potential of three ionic liquids (ILs) namely, 5-(Trifluoromethyl)dibenzothiophenium tetrafluoroborate (TDTB), 5-(Trifluoromethyl)dibenzothiophenium trifluoromethanesulfonate (TDTM) and 1-Ethyl-3-methylimidazolium ethyl sulfate [EMIM][ESO4] was studied for mild steel and zinc corrosion in 1.0 M hydrochloric acid using electrochemical, spectroscopic and gravimetric techniques. The studied ILs showed appreciable inhibition efficiencies at the considered concentration range. The highest inhibition efficiencies were observed at 30°C when inhibitor concentration was 8.0 × 10-2 M. The gravimetric data revealed that inhibition efficiencies decreased with an increase in temperature, the lowest inhibition efficiencies for mild steel and zinc were observed at 50°C. The potentiodynamic polarization results indicated that all three inhibitors are mixed-type inhibitors, with TDTM being a predominantly anodic inhibitor. The orders of inhibition efficiency at 8.0 × 10-2 M were TDTM > TDTB > [EMIM][ESO4] and TDTB > TDTM > [EMIM]ESO4] for mild steel and zinc, respectively. All inhibitors showed superior performance in mild steel than in zinc. The adsorption of the studied ILs on mild steel and zinc obeyed the Langmuir adsorption isotherm. The Gibbs free energy of adsorption (ΔG°ads) indicated that the adsorption process was spontaneous, and that corrosion inhibition occurred by a physical adsorption process. Surface morphology analysis through scanning electron microscopy (SEM) and energy dispersive spectroscopy (EDS) revealed a great improvement in the surface morphologies of mild steel and zinc specimens in the inhibited systems. The Fourier transform infrared spectroscopy studies confirmed the chemical interactions between the metal surface and the ILs. This is observed by means of the disappearance of characteristic absorption bands in the adsorption film FTIR spectra. / NRF

iv Abstract Subject: Determination of structure and dynamics of biomolecules by theoretical calcu- lations of NMR spectroscopic parameters Author: Ladislav Benda, ladislav.benda@gmail.com Department/Institute: Institute of Organic Chemistry and Biochemistry, AS CR Supervisor: Dr. Vladim'ır Sychrovsk'y, Institute of Organic Chemistry and Biochemistry, AS CR, vladimir.sychrovsky@uochb.cas.cz Abstract: This doctoral work was focused on theoretical modeling of nuclear magnetic resonance (NMR) parameters in peptides and nucleic acids. Dependences of NMR para- meters on molecular structure and solvation were primarily modeled. Great emphasis was put on the comparison of the calculated data with the NMR experiment. The molecular models studied included the l-alanyl-l-alanine di-peptide (AA) and the phosphate group of nucleic acid backbone. Conformations of all three charged forms of AA in solution were determined and the respective pH-induced changes of experimental NMR chemical shifts and nuclear spin-spin coupling constants were explained. Dependences of NMR cross-correlated relaxation rates on the AA backbone geometry were calibrated. The 31 P NMR parameters in nucleic acid phosphate were systematically calculated in dependence on the backbone conformation and the phosphate solvation pattern. Qualitative rules...

The present study involves the determination of traces of thallium and mercury in aqueous solution by forming ion-association complexes of these metals with rhodamine 6G (R6G) in the presence of iodide. Thallium(lll) and mercury(Il) are able to quench the fluorescence of R6G in the presence of iodide by forming ion—association complexes, and the degree of quenching correlates with the thallium(III) or mercury(II) concentrations . By using this method, the minimum amount of thallium- (III) that can be determined in aqueous solutions is approximately 4.00 X 10-6m, while the minimum amount of mercury(II) is approximately 3.00 X 10-6m. Thallium(I) cannot be determined by this method because it is not possible to form ion-association complexes under similar experimental conditions therefore, this method can be used to differentiate between Tl(I) and Tl(III) in aqueous solution. To elucidate the composition of the ion-association complexes in aqueous solutions two spectrophotometric methods are used: the mole-ratio method and the continuous- variation method. The experimental results seem to indicate that two complexes are formed for the mercury(II)-R6G-iodide system. The empirical compositions of these complexes are tentatively determined to be [(R6G)HgI3] and [(R6G)2HgI4).

京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第18995号 / 工博第4037号 / 新制||工||1621(附属図書館) / 31946 / 京都大学大学院工学研究科材料化学専攻 / (主査)教授 田中 勝久, 教授 平尾 一之, 教授 三浦 清貴 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DGAM

No description available.

The copper-binding ability of the prion protein may be closely connected to its function. Identifying the exact function of the prion protein can clarify the underlying mechanism in prion diseases. In this work, the copper-binding octapeptide region in the human prion protein has been studied. The structural characteristics of the binding site are examined by quantum chemical structural optimization. The calculations aim at identifying a substitute for copper(II) to be used in NMR-spectroscopic studies of the copper-binding region. The dynamical and structural features of the peptide region are investigated in molecular dynamics simulations. Aspects of importance in the development of model systems in molecular dynamics simulation are addressed. / QC 20101220

Metabolism is a subset of chemistry that allows cells to defy thermodynamic equilibrium, a fundamental process that must have been in place from the very beginning of biology. Before evolution produced efficient catalysts in the form of complex protein machinery, short metal binding peptides might have preceded modern metalloproteins. Such prebiotic, metal-binding motifs have been hypothesized to have existed through analyses of extant protein sequences. However, it is unclear how metal-binding motifs might have evolved in the harsh prebiotic environment. Here, we show how certain environments, in particular seawater-like environments rich in divalent cations and especially Mg2+, support the survival of short peptides upon extreme temperatures as high as 150 °C. Moreover, while Mg2+ does not offer the same protection from UV light, peptides are protected from both heat and irradiation when bound to a metal ion. The results suggest that specific environments rich in metal ions may be better suited for the emergence of complex systems in the path toward life. Additionally, the conditional degradation of peptides depending on their ability of binding metals might have enabled a selection mechanism that would favor the survival of metal-binding motifs which resemble the motifs found in modern proteins. These short sequences could have acted as early, simple catalysts able to facilitate a restricted set of chemical reactions, which would shape the emergence and biology of the Last Universal Common Ancestor.