The mitochondrial membrane bound flavoenzymes monoamine oxidase A and B (MAO-A and MAO-B) catalyze the a-carbon oxidation of a variety of amines including neurotransmitters such as dopamine and serotonin. Although the primary structures of these enzymes have been established from the corresponding gene sequences, relatively little is known regarding the structural features of the active sites which lead to the selectivities observed with various substrates and inhibitors. In spite of many efforts, these enzymes have not been crystallized. In the absence of X-ray structures, the design, synthesis, and evaluation of biological activity remain the only way to assess a view of the active sites, through SAR and QSAR studies. The excellent MAO-A and/or B substrate and inhibitor properties of various 1,4-disubstituted-1,2,3,6-tetrahydropyridine derivatives offer an interesting opportunity to probe the active sites of MAO-A and MAO-B. In an effort to explore the spatial features of the active sites, we have synthesized series of substituted tetrahydropyridines, evaluated their biological activity with purified MAO-A and MAO-B, and carried out a topological analysis of the MAO active sites using molecular modeling. In addition, the results described in this thesis provide evidence that the MAO-A and MAO-B active sites differ in shape, regions of activity, and areas that tolerate polar interactions. The role of MAO in neurodegenerative processes such as Parkinson's Disease has been recognized for some time. The structurally unique parkinsonian inducing substrate 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) is bioactivated to neurotoxic metabolites. The mechanism of neurotoxicity has been studied extensively and it is known that MAO-B catalyzes the conversion of MPTP to the 2,3-dihydro-1-methyl-4-phenylpyridinium species (MPDP+) which undergoes further oxidation to the neurotoxic metabolite 1-methyl-4-phenyl pyridnium (MPP+). However, the role of MAO-A in mediating a neurotoxic response, has not been fully defined due to the lack of selective MAO-A substrates. In this thesis, we have investigated the neurotoxic potential of several tetrahydropyridines in C57Bl/6 mice and the ability of selective inhibitors to protect against the expression of MAO mediated neurotoxicity. / Ph. D.

<p dir="ltr">Partial methane oxidation (PMO) to methanol is a desirable route for upgrading natural and shale gas resources to liquid chemical intermediates and has been extensively studied on Cu-zeolites. Prior work has studied the stoichiometric PMO reaction on O₂-activated Cu-zeolites, leading to several proposals for candidate O_x-bridged Cu active site structures. More recent studies have investigated the catalytic PMO reaction and have reported that Cu-chabazite (CHA) zeolites tend to exhibit the highest methane oxidation rate (per Cu) among other Cu-zeolite topologies. Multiple studies have reported that decreasing the Cu site density and increasing the framework Al density increase the selectivity towards methanol, but have proposed different mechanistic explanations. Here, we study the influence of Cu active site distribution, which was altered by varying the extraframework Cu site density and the arrangement of framework Al atoms, on the kinetic parameters governing continuous PMO. The number of redox active Cu species was quantified through linear combination fitting of XANES spectra collected under <i>in situ</i> and transient conditions after reactant (O₂) cut-off, and the Cu speciation was investigated with XAS. Total methane oxidation rates and individual product formation rates (CH₃OH, CO, CO₂), normalized per total Cu, increased with Cu density because this influenced the speciation of Cu formed during the reaction. All Cu-CHA samples showed PMO rates that were nearly first-order in CH₄ pressure, consistent with prior reports that C-H activation in CH₄ is the rate limiting step. Samples with differing framework Al arrangement, but fixed extraframework Cu density, showed formation rates of over-oxidation products (e.g., CO₂) that had different apparent reaction orders in O₂, implying differences in the Cu active sites formed during reaction. Changes to Cu oxidation states were monitored with <i>in situ</i> XAS. Samples were first subjected to an oxidative pretreatment (723 K, 5 kPa O₂) and then to catalytic PMO conditions to reach steady-state. Steady-state XANES spectra collected after O₂ was removed from the reactant stream showed the expected reduction from Cu(II) to Cu(I), and the fraction of CH₄-reducible Cu(II) sites decreased with increasing Cu content; increasing the CH₄ pressure ten-fold increased the number of CH₄-reducible sites by a factor of ~1.5. These spectroscopic and kinetic observations suggest there are a mixture of Cu site types that are present during catalysis, each with different intrinsic reactivity toward CH₄ and selectivity to CH₃OH. To rationalize these observations, a reaction mechanism is proposed for a two-site model and used to derive rate expressions that describe apparent reaction orders for the total CH₄ oxidation rate and product formation rates on Cu-CHA zeolites of varying Cu content.</p><p dir="ltr">Additional routes for CH₄ activation include partial CH₄ oxidation over Fe zeolites that convert CH₄ at ambient temperature following an activation in nitrous oxide (N₂O), or through CH₄ dehydroaromatization (DHA) to benzene over Mo zeolites under non-oxidative conditions. Prior work on PMO over Fe-zeolites has identified candidate active site structures, but the influence of zeolite structural properties on ion-exchanged Fe speciation remains unclear. This work sought to understand the interaction of Fe with the zeolite framework during solvent-assisted deposition procedures and subsequent thermal treatments. In pursuit of this objective, Fe uptake isotherms were measured, and Fe speciation was characterized with UV-Vis spectroscopy and H₂ temperature programmed reduction (H₂ TPR). Increased framework Al site pairing increased the uptake of Fe in CHA zeolites, and high temperature treatments (723 K) resulted in the formation of oligomeric Fe structures as indicated by UV-vis. In CH₄ DHA over Mo-MFI, a principal challenge is the irreversible loss of catalytic reactivity with repeated reaction-regeneration cycles, attributed to dealumination of the zeolite structure during high-temperature oxidative regeneration treatments that produce steam. CHA zeolites are known to be more resistant to dealumination than MFI, but its smaller pore structure prevents diffusion of benzene and other aromatic products leading to rapid coking. This work attempted to address the diffusion limitations for benzene in Mo-CHA by synthesizing crystals with nanoscale dimensions by incorporating a surfactant into the crystallization procedure, generating solids with a flake-like morphology.</p><p dir="ltr">The overarching strategy in this work was to influence the speciation of metal sites and complexes in zeolites by controlling the density and arrangement of anionic Al anchoring sites within the framework and the density of extraframework metal species. In the case of Cu-zeolites, the amount of Cu present on the material influences the structures that form during catalysis that influences both the rate and selectivity of catalytic PMO.</p>

<p>In this dissertation a novel approach to protein-ligand docking is presented. First an existing method to predict putative active sites is employed. These predictions are then used to cut down the search space of an algorithm that uses the fast Fourier transform to calculate the geometrical and electrostatic complementarity between a protein and a small organic ligand. A simplified hydrophobicity score is also calculated for each active site. The docking method could be applied either to dock ligands in a known active site or to rank several putative active sites according to their biological feasibility. The method was evaluated on a set of 310 protein-ligand complexes. The results show that with respect to docking the method with its initial parameter settings is too coarse grained. The results also show that with respect to ranking of putative active sites the method works quite well.</p>

Les catalyseurs Ziegler Natta pour la polymérisation des oléfines sont généralement obtenus par réaction entre un complexe de métal de transition avec un alkylaluminium ou un autre co-catalyseur. Généralement, pour le catalyseur Ziegler-Natta moléculaire, l'espèce active est un complexe cationique. Cependant, la coordination de l'oléfine sur l'espèce active peut concurrencer avec le métal alkyl, le solvant, ou le contre-ion qui se trouvent dans le milieu réactionnel. Par conséquent la détermination de la fraction des sites actifs est un des principaux défis dans le domaine des polyoléfines. Plusieurs méthodes ont été étudiées pour mesurer les sites actifs. La méthode la plus fiable est celle basée sur la mesure du nombre des macromolécules dans les premiers instants de la polymérisation. Cette méthode nécessite de travailler dans un régime contrôlé où les réactions de transfert de chaîne sont négligeables. Pour certains catalyseurs Ziegler-Natta qui polymérisent dans conditions « extrêmes » (très basses températures), ce régime contrôlé dure plusieurs minutes. Pour la plupart des catalyseurs le régime contrôlé dure quelque secondes ou fractions de secondes. Dans ces cases il faut appliquer une technique cinétique très rapide : le Quenched Flow. Cette technique a toujours été mise en œuvre pour travailler dans des faibles conditions expérimentales. Le réacteur Quenched Flow utilisé dans cet étude a été conçu pour mesurer la constante de propagation de chaîne et surtout la fraction des sites actifs [M*]/[M]. La première partie de cette thèse est dédiée à l'étude des catalyseurs métallocène. Le comportement de ces catalyseurs dans les premiers instants de polymérisation avec différents activateurs a été observé. Une description cinétique a été possible pour certains systèmes catalytiques. La partie finale de la thèse a été dédiée à l'étude des catalyseurs post métallocène. La fraction des sites actifs, [M*]/[M], est la constante de propagation de chaînes, kp, ainsi les principaux paramètres d'activation S‡ et H‡ pour le complexe Bis(cumyl)[ONNO]ZrBz2 activé en utilisant MAO/tBu2-PhOH ont été déterminés sur un large plage de températures. Pour le complexe [N-(3-tert-butylsalicylidene)-2,3,4,5,6 pentafluoroanilinato] titanium activé par le MAO un changement de régime cinétique a été observé à hautes températures / Ziegler-Natta catalysts are generally obtained by the combination of a transition metal complex with an alkylaluminium compound and possibly another co-catalyst. For molecular Ziegler-Natta catalyst, generally, the active species is a cationic compound. However, in regards to the actives species, the olefin may compete in the polymerization medium with other metal alkyl, the solvent or the counteranion. Thus, it is not an easy task to determine the total active metal site fraction which remains an important challenge in the field of polyolefins. Several methods have been developed to perform this measurement. Among these the most reliable one is rely on the determination of number of macromolecules formed initially, and it requires working in initial controlled regime where the chain transfer reactions are very limited. It should be possible to achieve the controlled regime for molecular catalyst for time going from several milliseconds to fraction of second. This means that technically demanding fast kinetic techniques such as quenched flow technique are necessary for the investigation of kinetic parameters of olefin polymerization catalysts. Up to now this technique has been only implemented in very mild conditions. Recently a stopped flow reactor operating at high temperature and high pressure has been developed in Lyon. In the present study, the usefulness of this reactor for measuring the chain propagation rate constant kp and the fraction of metal active site [M*]/[M] is assessed. In the first part of this work we have focused on the investigation of some metallocene-based catalysts. In particular, we have observed how these catalysts behave at initial stage of polymerization, when they are activated with different co-catalyst and in some case a kinetic description was also possible. The last part of this work was dedicated to kinetic study of some post-metallocene catalysts such as amine bisphenolate and (bis phenoxy-imine) -Zr and -Ti based complexes activated with MAO in a large range of polymerization temperatures. A successful kinetic investigation of Bis(cumyl)[ONNO]ZrBz2 complex activated with MAO/tBu2-PhOH has been performed which allowed the determination of [M*]/[M], kp and activation parameters such as H‡ and S‡. In the case of [N-(3-tert-butylsalicylidene)-2,3,4,5,6 pentafluoroanilinato] titanium dichloride activated with MAO an original changing in kinetic regime is reported by increasing the polymerization temperature

京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第22456号 / 工博第4717号 / 新制||工||1737(附属図書館) / 京都大学大学院工学研究科物質エネルギー化学専攻 / (主査)教授 安部 武志, 教授 作花 哲夫, 教授 阿部 竜 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DGAM

Zeolites are crystalline microporous solid acids composed of silica-rich frameworks with aliovalent Al heteroatoms substituted in crystallographically-distinct location sand arrangements, which generate anionic lattice charges that can be compensated by protons and extra framework metal cations or complexes that behave as catalytic active sites. Protons that charge-compensate Al are similar in Brønsted acid strength, yet differ in reactivity because their bound intermediates and transition states are stabilized by van der Waals interactions with confining microporous cavities, and by electrostatic interactions with proximal heteroatoms and adjacent protons. A diverse array of framework Al and extra framework H⁺site ensembles are ubiquitous in low-silica and low-symmetry zeolite frameworks (e.g., MFI, MOR), which cause measured turnover rates to reflect the reactivity-weighted average of contributions from each distinct site ensemble. The reactivity of distinct sites can be further masked by diffusion barriers often imparted by microporous domains and secondary reactions of primary products, which become increasingly prevalent as products encounter higher numbers of active sites during diffusion prior to egress from zeolite crystallites. Consequently,catalytic behavior often depends on zeolite material properties at orders-of-magnitude different length scales, which depend on the specific protocols used in their synthesis and crystallization.<div><br></div><div><div>In this work, CHA zeolites that contain only one symmetrically-distinct lattice site for Al substitution are used as model materials to decouple the effects of proton</div><div>location and proximity in vibrational spectra and turnover rates for acid catalysis. Interactions between proximal protons influence their equilibrium distribution among anionic lattice O atoms in AlO⁻_4/2tetrahedra, and result in temperature-dependent changes to vibrational frequencies and intensities of the asymmetric OH stretching region in infrared spectra measured experimentally and computed by density functional theory (DFT). Protolytic propane cracking and dehydrogenation, a catalytic probe reaction of the intrinsic reactivity of Brønsted acid protons, occur with turnover rates (748 K, per H⁺) that are an order-of-magnitude higher on paired protons than isolated protons, resulting from entropic benefits provided to late carbonium ion-pair transition states by proximal protons. These results indicate that cationic transition states can be stabilized entropically through multi-ion interactions with lattice anion and cation sites. Precise interpretation and quantification of the reactivity of different types and ensembles of Brønsted acid protons in zeolites requires that protolytic chemistry prevails in the absence of secondary active sites or other kinetically-relevant processes, a requirement generally met for alkane cracking but not dehydrogenation on H-form zeolites. Propane dehydrogenation activation energies vary widely (by >100 kJ mol⁻¹) among H-form zeolites of different structure (MFI, MOR, CHA) and composition (Si/Al = 10 – 140) because reactant-derived carbonaceous deposits form in situ and catalyze alkane dehydrogenation under non-oxidative conditions through hydride transfer pathways. Contributions of reactant-derived active sites to propane dehydrogenation rates are quantified through a series of transient and steady-state kinetic experiments with co-fed alkene and dihydrogen products, and are found to depend on gradients in product pressures that are present in integral reactors under non-ideal plug-flow hydrodynamics. Propane dehydrogenation rates collected at initial time-on-stream and in the presence of co-fed H₂ solely reflect protolytic reaction events and can be used to interpret differences in the reactivity of distinct proton sites and ensembles for alkane activation catalysis. The reaction conditions identified here can be used to remove or suppress the reactivity of carbonaceous active sites during catalysis, or to engineer the formation of organocatalysts on zeolite surfaces for selective dehydrogenation or hydride transfer reactions.</div></div><div><br></div><div><div>Synthetic strategies to decouple bulk and active site properties at disparate length scales, which are typically correlated in MFI zeolites crystallized hydrothermally, are developed by adding a second heteroatom and organic structure directing agent (SDA) to synthesis media. Crystallite size and morphology are independently varied from Al content by incorporating B heteroatoms into zeolitic frameworks, which generate protons that are catalytically irrelevant compared to those compensating Al, and NH₃ temperature-programmed desorption methods are developed to differentiate between these two types of proton sites. The siting of Al heteroatoms in distinct locations and ensembles is influenced by the decrease in cationic charge density among occluded SDAs, in cases where ethylenediamine is co-occluded with tetra-<i>n</i>-propylammonium cations. The co-occlusion of organic SDAs enables crystallizing MFI zeolites with different bulk properties but similar Al distributions, or with similar bulk properties and different Al distributions. MFI zeolites crystallized with these methods provide model materials that can be interrogated to decouple the effects of bulk and atomicscale properties on acid catalysis, and open opportunities to exploit these material properties by designing active site ensembles and crystallite diffusion properties for catalytic chemistries that depend on coupled reaction-transport phenomena.</div></div>

<p>Proteini imaju osnovnu ulogu u&nbsp; životnim&nbsp;procesima, usled čega je isptivanje raznovrsnosti&nbsp;njihove strukture jedna od ključnih potreba&nbsp;modernih biolo&scaron;kih istraživanja. Cilj ove&nbsp;doktorske disertacije je predviđanje&nbsp;trodimenzionalne strukture beta-galaktozidaza&nbsp;odabranih bakterijskih sojeva (<em>Streptococcus&nbsp;thermophillus,&nbsp; Lactobacillus acidophilus</em>,&nbsp; i&nbsp;<em>Bifidobacterium animalis</em>&nbsp; ssp.&nbsp; <em>lactis</em>) kao i&nbsp;karakterizacija &nbsp;njihovih aktivnih mesta i&nbsp;određivanje aktivnih rezdua. Takođe, cilj&nbsp;disertacije obuhvata i ispitivanje beta-galaktozidaze&nbsp;<em> Bacteroides thetaiotaomicron</em>-a,&nbsp;kao i ispitivanje aktivnosti beta-galaktozidaze&nbsp;Kluyveromyces lactis-a. Na osnovu sličnosti&nbsp;<br />analizirane sekvence se mogu podeliti u dva&nbsp;klastera. Članovi klastera 1 pripadaju GH-2&nbsp;subfamiliji, dok članovi klastera 2 pripadaju GH-42 subfamiliji. Na osnovu klaster analize i poravnanja sekvenci&nbsp; predložene su&nbsp; katalitički&nbsp;aktivne rezidue beta-galaktozidaza ispitivanih&nbsp;sojeva: GLU458/GLU546 kod <em>S. thermophillus</em>-a,&nbsp;GLU148/GLU307 kod&nbsp;<em> L. Acidophilus-</em>a i&nbsp;GLU164/GLU324 kod<em> B. animalis</em> ssp.<em> lactis</em>-a.&nbsp;Konstruisani su homologi modeli beta-galaktozidaza<em> S. thermophilus, L. &nbsp;acidophilus, B.&nbsp;&nbsp; animalis</em>&nbsp; ssp.&nbsp;<em> lactis</em>.&nbsp; Iz rezultata simulacije&nbsp;molekularnog dokinga svih beta-galaktozidaza&nbsp;uočljivo je da se supstrat veže za aktivno mesto&nbsp;koje se nalazi u regionu visoke&nbsp;elektronegativnosti. Simulacije dokinga su&nbsp;potvrdile aktivna mesta predložena poravnanjem&nbsp;sekvenci i otkrile rezidue koje učestvuju u&nbsp;vezivanju laktoze i galaktoze kao supstrata.&nbsp;Obzirom da je objavljena samo jedna kristalna&nbsp;struktura beta-galaktozidaze sa laktozom u&nbsp;aktivnom mestu, analiza molekularnog dokinga&nbsp;laktoze kao supstrata je sprovedena i sa beta-alaktozidazama koje imaju određenu&nbsp;trodimenzionalnu strukturu. Na osnovu slučnosti&nbsp;sekvenci može se zaključiti da je nukleofilna&nbsp;rezidua beta-galaktozidaze <em>B. thetaiotaomicron</em>-a&nbsp;GLU259. Analizom konzervativnih regiona, kao i&nbsp;doking simulacije, može se zaključiti da ulogu&nbsp;proton donora ima rezidua GLU182. Hemijski&nbsp;sastav mleka za ispitivanje aktivnosti beta-galaktozidaze <em>Kluyveromyces lactis-</em>a je u skladu sa pravilnikom o kvalitetu proizvoda od mleka i&nbsp;starter kultura&nbsp; koji izdaje Ministarstvo&nbsp;<br />poljoprivrede i za&scaron;tite životne sredine Republike&nbsp;Srbije.&nbsp; Celokupna laktoza se razgradila u&nbsp;permeatu na temperaturi od 40&deg;C i pri&nbsp;koncentraciji enzima od 0,1% nakon 60 minuta od&nbsp;trenutka dodatka enzima. Maksimalna brzina&nbsp;postiže se toku prvih 10 minuta. Iz dobijenih&nbsp;rezultata može se zaključiti da beta-galaktozidaza&nbsp;<br /><em>K. lactis</em>-a ima visoku efikasnost prilikom&nbsp;razgradnje laktoze &scaron;to je čini pogodnom za&nbsp;<br />komercijalnu upotrebu u industriji mleka. U ovoj&nbsp;disertaciji predstavljen je protokol za&nbsp;<br />modelovanje komercijalno važnih beta-galaktozidaza i analiziranje njihovih &nbsp;interakcija sa laktozom kao supstratom. Dobijeni rezultati treba&nbsp;da pruže okvir za molekularna istraživanja&nbsp;vezivanja i razgradnje laktoze, kao i za buduće&nbsp;<br />dizajniranje komercijalno interesantnih beta-galaktzidaza.&nbsp;</p> / <p>Proteins have an essential role in all life&nbsp;processes. Therefore, investigation of their&nbsp;<br />structure diversity is one of the key focuses of&nbsp;modern biological researches. The aim of this&nbsp;PhD thesis is prediction of three-dimensional&nbsp;structure of&nbsp; beta-galactosidases of&nbsp; selected&nbsp;bacterial strains (<em>Streptococcus thermophillus,&nbsp;Lactobacillus acidophilus </em>and <em>Bifidobacterium&nbsp;animalis</em> ssp. <em>lactis</em>), as well as characterization&nbsp;of their active sites and active residues.&nbsp;Furthermore, this thesis include investigation&nbsp;<em>Bacteroides thetaiotaomicron</em>&nbsp; and&nbsp;<em>Kluyveromyces lactis</em> beta-galactosidases. Based&nbsp;on sequence &nbsp;similarity analyzed sequences can&nbsp;be clustered in two clusters. Members of cluster&nbsp;<br />1 belong to GH-2 subfamily, while members of&nbsp;cluster 2 belong to GH-42 subfamily. Cluster&nbsp;analysis and sequence alignment revealed&nbsp;potential active residues: GLU458/GLU546 - S.&nbsp;thermophillus,&nbsp; GLU148/GLU307&nbsp; -&nbsp; L.&nbsp;Acidophilus&nbsp; and&nbsp; GLU164/GLU324&nbsp; -&nbsp; B.&nbsp;animalis ssp. lactis.&nbsp; Homologous models of&nbsp;beta-galactosidases from&nbsp; <em>S. thermophilus,&nbsp; L.&nbsp;acidophilus,&nbsp; B. animalis&nbsp;</em> ssp.&nbsp; <em>lactis</em>&nbsp; are&nbsp;<br />constructed as a result of this PhD thesis.&nbsp;Molecular docking simulations of all beta-galactosidases revealed that substrate binds in&nbsp;region with high electronegativity. &nbsp;Furthermore,&nbsp;docking simulations confirmed active sites&nbsp;suggested by sequence alignment. As only one&nbsp;crystal structure with lactose in its active site&nbsp;has been published, docking simulations with&nbsp;lactose as a ligand were also performed with&nbsp;<br />experimentally determined beta-galactosidases&nbsp;structures. Also, lactose and &nbsp;alactose &nbsp;binding&nbsp;residues are predicted. Based on sequence&nbsp;similarity&nbsp; GLU259&nbsp; can be recognized as&nbsp;nucleophile of&nbsp;<em> B. thetaiotaomicron&nbsp;</em> beta-galactosidase. By analysis of conserved regions&nbsp;and docking simulation, GLU182 is predicted as&nbsp;a proton donor residue. Chemical composition&nbsp;of milk used for Kluyveromyces lactis&nbsp; beta-galactosidase research had appropriate quality&nbsp;according to directions of Ministry of&nbsp;<br />agriculture and environmental protection of&nbsp;Republic of Serbia. Total lactose content was&nbsp;degraded in permeate after 60 min using&nbsp;enzyme concentration of 0,1% at&nbsp; 40&deg;C.&nbsp;Maximal degradation was reached in the first 10&nbsp;min. Based on the results, it can be concluded&nbsp;that <em>Kluyveromyces lactis</em> beta-galactosidase has&nbsp;high efficiency for &nbsp;lactose degradation, which&nbsp;makes it commercially interesting for milk&nbsp;industry. Protocol for modeling of commercially&nbsp;important beta-galactosidases and their&nbsp;<br />interactions with lactose is developed as a result&nbsp;of this PhD thesis. Obtained results should&nbsp;provide the frame for molecular investigation of&nbsp;lactose binding and degradation, as well as for&nbsp;designing of commercially suitable beta-galactozidases.&nbsp;</p>

In this dissertation a novel approach to protein-ligand docking is presented. First an existing method to predict putative active sites is employed. These predictions are then used to cut down the search space of an algorithm that uses the fast Fourier transform to calculate the geometrical and electrostatic complementarity between a protein and a small organic ligand. A simplified hydrophobicity score is also calculated for each active site. The docking method could be applied either to dock ligands in a known active site or to rank several putative active sites according to their biological feasibility. The method was evaluated on a set of 310 protein-ligand complexes. The results show that with respect to docking the method with its initial parameter settings is too coarse grained. The results also show that with respect to ranking of putative active sites the method works quite well.

<p>Cu-zeolites have received renewed attention as catalytic materials that facilitate partial methane oxidation (PMO) to methanol, with a variety of mononuclear, binuclear, and multinuclear Cu active site motifs that have been proposed in prior literature. Our approach to more precisely identify and probe the Cu structures that activate O₂ and reduce in CH₄relies on the synthesis of model supports with varying composition and well-defined Cu speciation, which also facilitates connections between experimental data and theoretical models. Chabazite (CHA) zeolites are high-symmetry frameworks that contain a single lattice tetrahedral site (T-site), in which Cu²⁺ ions exchange at paired Al sites in a six-membered ring (6-MR) while CuOH⁺ species exchange at isolated 6-MR Al sites, the latter of which can react to form binuclear O/O₂-bridged Cu structures. In this work, Cu-CHA zeolites were synthesized to contain predominantly Cu²⁺ (Z₂Cu) or CuOH⁺ (ZCuOH) species of varying density, or a mixture of Z₂Cu and ZCuOH sites. Z₂Cu and ZCuOH sites were quantified by titration of residual Brønsted acid sites with NH₃, which respectively exchange with 2:1 or 1:1 H⁺:Cu²⁺ stoichiometry. Stoichiometric PMO reaction cycles on Cu-zeolites involved high-temperature (723 K) activation in O₂, and then moderate-temperature (473 K) reduction in CH₄ and treatment in H₂O (473 K) to extract CH₃OH. <i>I</i><i>n-situ</i> UV-Visible spectroscopy under oxidizing (O₂, 723 K) and reducing (CO, 523 K; CH₄, 473 K; He, 723 K) conditions detected the presence of mononuclear and binuclear Cu site types, while <i>in-situ</i> Cu K-edge X-ray absorption spectroscopy after such treatments was used to quantify Cu(I) and Cu(II) contents and <i>in situ</i> Raman spectroscopy was used to identify the Cu structures formed. ZCuOH, but not Z₂Cu sites, are precursors to binuclear O/O₂-bridged Cu sites that form upon O₂ activation and subsequently produce methanol after stoichiometric PMO cycles, at yields (per total Cu) that increased systematically with ZCuOH site density. The fraction of Cu(II) sites that undergo auto-reduction in inert at high temperatures (He, 723 K) is identical, within experimental error, to the fraction that reduces in CH₄ at temperatures relevant for PMO (473 K), providing a quantitative link between the binuclear Cu site motifs involved in both reaction pathways and motivating refinement of currently postulated PMO reaction mechanisms. These Cu-CHA zeolites were also studied for other redox chemistries including the selective catalytic reduction (SCR) of NO_x with NH₃. <i>In situ </i>UV-Visible and X-ray absorption spectroscopies were used to monitor and quantify the transient partial reduction of Cu(II) to Cu(I) during exposure to NH₃ (473 K), in concert with titration methods that use NO and NH₃ co-reductants to fully reduce all Cu(II) ions that remain after treatment in NH₃ alone to the Cu(I) state, providing quantitative evidence that both Z₂Cu and ZCuOH sites are able to reduce in NH₃ alone to similar extents as a function of time. These findings provide new insight into the reaction pathways and mechanisms in which NH₃ behaves as a reductant of mononuclear Cu(II) sites in zeolites, which are undesired side-reactions that occur during steady-state NO_x SCR and that often unintendedly result in Cu(II) reduction prior to spectroscopic or titrimetric characterization. Overall, the strategy in this dissertation employs synthetic methods to control framework Al density and arrangement in zeolite supports to emphasize extra-framework Cu site motifs of different structure and at different spatial densities, and to interrogate these model materials using a combination of <i>in situ</i> spectroscopic techniques together with theory, in order to elucidate active site structure and proximity requirements in redox catalysis. This work demonstrates how quantitative reactivity and site titration data, brought together with an arsenal of tools available in contemporary catalysis research, can provide detailed mechanistic insights into transition metal-catalyzed redox cycles on heterogeneous catalysts.</p>

L'enjeu de cette thèse réside dans la compréhension et l'amélioration de la sulfuration de catalyseurs à base de W. Elle a pour objectif la rationalisation des différentes étapes de préparation de catalyseurs d’hydrotraitement de type NiWS depuis la préparation jusqu'au test catalytique par une approche moléculaire (appelée «chimie de surface contrôlée» ou CSC), ce qui permet de proposer de nouvelles voies pour lever le verrou majeur, lié à la mauvaise sulfuration du W. Au cœur de cette approche se situe l'utilisation d'une méthode de préparation originale, ayant recours à des composés moléculaires métallo-organiques bien-définis comme précurseurs de la phase sulfurée WS2, combinée à une analyse poussée par spectroscopies multiples (IR, RMN, XPS) et chimie computationnelle.La famille des alcoxydes de tungstène a été sélectionnée ; les précurseurs mono ou di-nucléaires tels que W(OEt)6, [W(=O)(OEt)4]2 ou [W(OEt)5]2 ont été greffés sur silice-alumine partiellement deshydroxylée, et leur conversion en phase sulfure a montré que le type de précurseurs moléculaires influençaient peu les propriétés des catalyseurs non promus (WS2/ASA), en termes de taux de sulfuration (déterminé par XPS) ou d’activité catalytique, en hydrogénation du toluène en présence d’aniline. Le composé [W(OEt)5]2 a ensuite été sélectionné pour approfondir l’étude des catalyseurs préparés par CSC.L'approche visant à améliorer la compréhension des différentes espèces de surface formées a été réalisée par l'étude des matériaux avant et après sulfuration. L'augmentation de la quantité de W déposé sur les matériaux CSC a permis de révéler la formation de (1) une couche d’espèces greffées sur la surface de silice-alumine, puis (2) de couches successives, formées d'espèces plus mobiles. L'étude portant sur la sulfuration de ces matériaux en fonction de leur teneur en W, et de la température de sulfuration, a permis de les comparer aux catalyseurs sulfurés dits «conventionnels». Cette étude approfondie a mis en évidence une amélioration de la sulfuration du W pour les matériaux CSC aux températures habituellement utilisées (350°C). La vitesse intrinsèque d’hydrogénation des catalyseurs CSC, jusqu’à deux fois supérieure à celle des catalyseurs conventionnels, a en partie été expliquée par un meilleur taux de sulfuration, et par la morphologie 2D des feuillets WS2 (STEM-HAADF), de forme triangulaire tronquée, dans le cas d’un catalyseur conventionnel.Finalement, ayant démontré que l’emploi d’espèces moléculaires mono et binucléaires permettait d’améliorer les catalyseurs non promus par rapport à l’approche conventionnelle utilisant des clusters polyanioniques, les catalyseurs promus de type NiW/ASA ont été étudiés. Différents précurseurs ont été utilisés (par exemple Ni(acac)2) ainsi que différentes méthodes de dépôt (dépôt du nickel sur un matériau sulfuré, ou non) et quantités de nickel. Ces travaux ont permis d’estimer l’influence de ces paramètres sur la sulfurabilité du W et du Ni, ainsi que sur l’activité catalytique des catalyseurs, et montrer que l’emploi d'une approche moléculaire dans la préparation des phases NiWS supportées permet d’améliorer la promotion des feuillets sulfures par le nickel, mais aussi d'accéder à des catalyseurs pouvant avoir des vitesses intrinsèques d’hydrogénation quatre fois supérieures celles de catalyseurs conventionnelles de référence. Ces résultats catalytiques sont très probablement liés à une balance optimisée entre «nature» et «quantité» de sites actifs mixtes Ni-W. Cela démontre l’intérêt d’une approche moléculaire pour la préparation de catalyseurs d'hydrotraitement plus performants. / The aim of this thesis is to understand and improve the sulphidation of W-based hydrotreating catalysts by understanding and characterising each step of their preparation, from the synthesis to catalytic tests, via a controlled surface chemistry approach (or "CSC", also referred as surface organometallic chemistry, "SOMC", in the literature). This molecular approach opens new avenues for the improvement of W sulphidation, which is one strong limitation for using this metal in hydrotreatment. The core of this study is based on the use of well-defined metallo-organic precursors as precursors of the tungsten sulphide phase, each step of materials preparation being characterised by multiple spectroscopy techniques (IR, NMR, XPS) combined with ab initio molecular modelling.Mono or dinuclear tungsten alkoxides such as [W(OEt)5]2, W(OEt)6 or [W(=O)(OEt)4]2 were grafted on partially dehydroxylated amorphous silica-alumina. Their conversion into sulphide materials reveals that the precursor does not influence significantly the amount of WS2 phase formed (level of sulphidation observed by XPS) as well as catalytic properties in toluene hydrogenation in the presence of aniline. Only [W(OEt)5]2 was used in the following experiments.So as to better understand the genesis of the sulphide phase, CSC materials were characterised before and after sulphidation. Before sulphidation, the use of increasing amounts of W precursor reveals the formation of (1) first, a layer of tungsten surface species grafted on the surface, and (2) second, layers of more mobile species, more loosely bonded to the grafted species. Then, these CSC materials were sulphided into WS2 catalysts (with different W-loading, and different sulphidation temperatures) and were compared to conventionally prepared samples. The results reveal an improvement of tungsten sulphidation for CSC samples already at ambient sulphidation temperature and also at more usual sulphidation temperatures (350°C). Catalytic activities up to 2 times higher than conventional references were also obtained. They are explained in part by the better level of sulphidation of CSC samples and by a different 2D morphology of WS2 crystallites (STEM-HAADF), observed to be hexagonal-like for CSC samples while conventional ones have truncated triangle-like shapes.Then, as non-promoted CSC samples were more active than their conventional counterparts, nickel promoted catalysts (NiWS) were prepared, with the use of different Ni precursors (such as Ni(acac)2), different preparation methods and Ni amounts. This study gives insights into the sulphidation of W and Ni, and reveals that samples prepared via a molecular approach (CSC) can exhibit intrinsic hydrogenation rates up to four times higher than reference catalysts. These results are explained by an optimal balance between the nature of active Ni-W mixed sites and their amount. These interesting results, obtained for non-promoted and Ni-promoted catalysts, show that the use of a molecular approach is suitable to design highly active hydrotreating catalysts.