<p>In the present thesis the density functional B3LYP has been used to study reactions of NO and O₂ in redox active enzymes.</p><p>Reduction of nitric oxide (NO) to nitrous oxide (N₂O) is an important part in the bacterial energy conservation (denitrification). The reduction of NO in three different bimetallic active sites leads to the formation of hyponitrous acid anhydride (N₂O₂^2-). The stability of this intermediate is crucial for the reaction rate. In the two diiron systems, respiratory and scavenging types of NOR, it is possible to cleave the N-O bond, forming N₂O, without any extra protons or electrons. In a heme-copper oxidase, on the other hand, both a proton and an electron are needed to form N₂O.</p><p>In addition to being an intermediate in the denitrification, NO is a toxic agent. Myoglobin in the oxy-form reacts with NO forming nitrate (NO₃ ^-) at a high rate, which should make this enzyme an efficient NO scavenger. Peroxynitrite (ONOO^-) is formed as a short-lived intermediate and isomerizes to nitrate through a radical reaction.</p><p>In the mechanism for pumping protons in cytochrome oxidase, thermodynamics, rather than structural changes, might guide protons to the heme propionate for further translocation.</p><p>The dioxygenation of arachidonic acid in prostaglandin endoperoxide H synthase forms the bicyclic prostaglandin G₂, through a cascade of radical reactions. The mechanism proposed by Hamberg and Samuelsson is energetically feasible.</p>

<p>The four-electron reduction of dioxygen to water is the most exothermic non-photochemical reaction available to biology. A detailed molecular description of this reaction is needed to understand oxygen-based redox processes. Horseradish peroxidase (HRP) is a haem-containing redox enzyme capable of catalysing the reduction of dioxygen to water. We developed instrumentation and experimental methodology to capture and characterise by X-ray crystallography transient reaction intermediates in this reaction. </p><p>An instrument was designed (“the vapour stream system”) to facilitate reaction initiation, monitoring and intermediate trapping. In combination with single crystal microspectrophotometry, it was used to obtain conditions for capturing a reactive dioxygen complex in HRP. X-ray studies on oxidised intermediates can be difficult for various reasons. Electrons re-distributed in the sample through the photoelectric effect during X-ray exposure can react with high-valency intermediates. In order to control such side reactions during data collection, we developed a new method based on an angle-resolved spreading of the X-ray dose over many identical crystals. Composite data sets built up from small chunks of data represent crystal structures which received different X-ray doses. As the number of electrons liberated in the crystal is dose dependent, this method allows us to observe and drive redox reactions electron-by-electron in the crystal, using X-rays.</p><p>The methods developed here were used to obtain a three-dimensional movie on the X-ray-driven reduction of dioxygen to water in HRP. Separate experiments established high resolution crystal structures for all intermediates, showing such structures with confirmed redox states for the first time. </p><p>Activity of HRP is influenced by small molecule ligands, and we also determined the structures of HRP in complex with formate, acetate and carbon monoxide.</p><p>Other studies established conditions for successfully trapping the M-intermediate in crystals of mutant bacteriorhodopsin, but the poor diffraction quality of these crystals prevented high-resolution structural studies.</p>

In the present thesis the density functional B3LYP has been used to study reactions of NO and O2 in redox active enzymes. Reduction of nitric oxide (NO) to nitrous oxide (N2O) is an important part in the bacterial energy conservation (denitrification). The reduction of NO in three different bimetallic active sites leads to the formation of hyponitrous acid anhydride (N2O22-). The stability of this intermediate is crucial for the reaction rate. In the two diiron systems, respiratory and scavenging types of NOR, it is possible to cleave the N-O bond, forming N2O, without any extra protons or electrons. In a heme-copper oxidase, on the other hand, both a proton and an electron are needed to form N2O. In addition to being an intermediate in the denitrification, NO is a toxic agent. Myoglobin in the oxy-form reacts with NO forming nitrate (NO3 -) at a high rate, which should make this enzyme an efficient NO scavenger. Peroxynitrite (ONOO-) is formed as a short-lived intermediate and isomerizes to nitrate through a radical reaction. In the mechanism for pumping protons in cytochrome oxidase, thermodynamics, rather than structural changes, might guide protons to the heme propionate for further translocation. The dioxygenation of arachidonic acid in prostaglandin endoperoxide H synthase forms the bicyclic prostaglandin G2, through a cascade of radical reactions. The mechanism proposed by Hamberg and Samuelsson is energetically feasible.

The four-electron reduction of dioxygen to water is the most exothermic non-photochemical reaction available to biology. A detailed molecular description of this reaction is needed to understand oxygen-based redox processes. Horseradish peroxidase (HRP) is a haem-containing redox enzyme capable of catalysing the reduction of dioxygen to water. We developed instrumentation and experimental methodology to capture and characterise by X-ray crystallography transient reaction intermediates in this reaction. An instrument was designed (“the vapour stream system”) to facilitate reaction initiation, monitoring and intermediate trapping. In combination with single crystal microspectrophotometry, it was used to obtain conditions for capturing a reactive dioxygen complex in HRP. X-ray studies on oxidised intermediates can be difficult for various reasons. Electrons re-distributed in the sample through the photoelectric effect during X-ray exposure can react with high-valency intermediates. In order to control such side reactions during data collection, we developed a new method based on an angle-resolved spreading of the X-ray dose over many identical crystals. Composite data sets built up from small chunks of data represent crystal structures which received different X-ray doses. As the number of electrons liberated in the crystal is dose dependent, this method allows us to observe and drive redox reactions electron-by-electron in the crystal, using X-rays. The methods developed here were used to obtain a three-dimensional movie on the X-ray-driven reduction of dioxygen to water in HRP. Separate experiments established high resolution crystal structures for all intermediates, showing such structures with confirmed redox states for the first time. Activity of HRP is influenced by small molecule ligands, and we also determined the structures of HRP in complex with formate, acetate and carbon monoxide. Other studies established conditions for successfully trapping the M-intermediate in crystals of mutant bacteriorhodopsin, but the poor diffraction quality of these crystals prevented high-resolution structural studies.

Antitumor pyrrolobenzodiazepines (PBDs), lincosamide antibiotics, quorum sensing molecule hormaomycin, and antituberculotic griselimycin are structurally and functionally diverse groups of actinobacterial metabolites. The common feature of these compounds is the incorporation of L-tyrosine- or L-leucine-derived 4-alkyl-L-proline derivatives (APDs) in their structures. APD biosynthesis involves a set of up to six homologous proteins. According to their proposed order in the biosynthesis of 4-propyl-L-proline, a model APD of lincosamide lincomycin, the homologous proteins were named Apd1 - Apd6. Here, we report that the last reaction in the biosynthetic pathway of APDs, catalyzed by F420H2-dependent Apd6 reductases, contributes to the structural diversity of APD precursors. Specifically, the heterologous overproduction and in vitro tests of six Apd6 enzymes demonstrated that Apd6 from the biosynthesis of PBDs and hormaomycin can reduce only an endocyclic imine double bond, whereas Apd6 LmbY and partially GriH from the biosyntheses of lincomycin and griselimycin, respectively, also reduce the more inert exocyclic double bond of the same 4-substituted Δ1 -pyrroline-2-carboxylic acid substrate, making LmbY and GriH unusual, if not unique, among reductases. The two successive F420H2-dependent reduction...

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Following a 15-year-long investigation on graphene, two-dimensional (2D) carbon-rich conjugated frameworks (CCFs) have attracted growing research interest as a new generation of multifunctional materials. Typical 2D CCFs include 2D π-conjugated polymers (also classified as 2D π-conjugated covalent organic frameworks) and 2D π-conjugated metal–organic frameworks, which are characterized by layer-stacked periodic frameworks with high in-plane π-conjugation. These unique structures endow 2D CCFs with regular porosities, large specific surface areas, and superior chemical stability. In addition, 2D CCFs exhibit certain notable properties (e.g., excellent electronic conductivity, designable topologies, and defined catalytic/redox-active sites), which have motivated increasing efforts to explore 2D CCFs for electrochemical energy applications. In this Perspective, the structural features and synthetic principles of 2D CCFs are briefly introduced. Moreover, we discuss recent achievements in 2D CCFs designed for various electrochemical energy conversion (electrocatalysis) and storage (supercapacitors and batteries) applications. Particular emphasis is placed on analyzing the precise structural regulation of 2D CCFs. Finally, we provide an outlook about the future development of synthetic 2D CCFs for electrochemical applications, which concerns novel monomer design, chemical methodology/strategy establishment, and a roadmap toward practical applications.

The thesis entitled “Design and Development of Synthetic Methods using Metal-mediated and Metal-free Redox Reactions: Novel C-H Activations, Reductions and Oxidative Transformations” is presented in 4 chapters Chapter 1; Iodine catalyzed amination of benzoxazoles: efficient metal free route to 2-aminobenzoxazoles under mild conditions. The Chapter 1 of this thesis describes iodine catalyzed C-H activation of benzoxazole with primary and secondary amines to form oxidative aminated products. Selective C-H oxidation is a frontline area of modern chemical research as it offers the opportunities to new avenues and more direct synthetic strategies for the synthesis of complex organic molecules.1 In this context, transition metals such as palladium copper, nickel etc, are used extensively for the functional group directed C-H activation, and thus provides new, rapid, low-cost, and environmentally benign protocols for the construction of new chemical bonds.2 During the past two decades iodine and hypervalent iodine have been focus of great attention as they provide mild, chemoselective and environmentally benign strategies in contrast to toxic metal oxidants.3 In this chapter, a facile metal-free route of oxidative amination of benzoxazole with secondary or primary amines in the presence of catalytic amount of iodine (5 mol%) in aq tert-butyl hydroperoxide (1equiv) and AcOH (1.1 equiv) at ambient temperature, under the solvent-free reaction condition is presented. This user-friendly method to form C-N bonds produces tert-butanol and water as the by-products, which are environmentally benign. A wide range of benzoxazole derivatives containing electron-donating and electron-withdrawing groups were coupled with both primary and secondary amines (Scheme 1). Application of this methodology is demonstrated by synthesizing therapeutically active benzoxazoles by reacting 5-chloro-7-methylbenzoxazole with N-methylpiperazine and N-ethylhomopiperazine to obtain corresponding N-aminatedbenzaxozoles, which exhibit antidiarrhetic activity (Scheme 2).4 Scheme 2 Chapter 2: NIS catalyzed reactions. amidation of acetophenones and oxidative amination of propiophenones Chapter 2 is divided in to 2 parts. Part 1 describes the synthesis of α-ketoamides by using acetophenone and secondary amine in the presence of N-iodosuccinamide and TBHP in acetonitrile at room temperature, whereas Part 2 reveals the synthesis of 2-aminoketones by reacting aryl alkyl ketones and suitable secondary amine in the presence of NIS and TBHP. Part 1: Oxidative amidation, synthesis of α-ketoamide: Alpha α-ketoamides are important intermediates in organic synthesis that are present in a variety of natural products, and pharmaceutically active compounds. Herein, a mild and efficient conversion of acetophenones to α-ketoamide is documented by using aq.TBHP and N-iodosuccinamide (NIS) as a catalyst, at ambient temperature. This amidation reaction was found to be versatile as several aetophenone derivitives containing electron-withdrawing and electron-donating substituents underwent a facile amidation. It was also found that acetyl derivatives of heterocylic compounds could be easily converted to their corresponding ketoamides (few examples are shown in Scheme 3).5 Scheme3 Part 2 of Chapter 2 narrates a novel amination of propiophenone and its derivatives catalysed by NIS in the presence of TBHP to furnish their corresponding 2-aminoketone derivatives (Scheme 4). These derivatives are ubiquitous scaffolds that are present in a wide variety of therapeutic agents. Some of these compounds are used in the treatment of depression, smoking cessation, as monoamine uptake inhibitors, rugs for cancer. They are photoinitiators, precursors to β-aminoalcohols, such as pseudoephedrine analogues. 2-Aminoacetophenone analogues are also important intermediates for the formation of several heterocyclic compounds and are active moieties in several important drugs such as ifenprodil, Scheme 4. Chapter 3: Efficient oxidation of primary azides to nitriles This Chapter is divided in to 2 parts, which presents the oxidation of primary azides to their corresponding nitriles. Part 1: An Efficient oxidation of primary azides catalyzed by copper iodide: a convenient method for the synthesis of nitriles In Part 1, an efficient oxidation of primary azides catalyzed by copper iodide to their corresponding nitriles is reported. Herein, the oxidation of primary azide to nitrile is performed using catalytic amount of copper iodide, and aq TBHP in water at 100 ° C. This methodology is compatible with a wide range of primary benzylic azides that contain electron-donating and electron-withdrawing functional groups. The oxidation was found to be selective and a number of oxidizable functional groups were well-tolerated during the reaction conditions (few examples are shown in Scheme 5).6 Scheme 6 Furthermore, oxidation of secondary azides furnished the corresponding ketones in excellent yields (Scheme 6).6 In the Part 2 of Chapter 3, a non-metal catalysed oxidation of primary azides to nitriles at ambient temperature is reported. This part reveals the oxidation of primary azides to nitriles by employing catalytic amounts of KI (25 mol%), DABCO (25 mol%) and aq. TBHP (3 equiv., 70% solution in water). This reaction provides a good selectivity, as double and triple bonds were not oxidized under the reaction conditions. Additionally, chemoselective oxidation of benzylicazides against aliphatic azides increases the potential application of the present method (Scheme 7).7 Chapter 4: Chemoeselective reduction of olefins Part 1: Iron chloride catalysed aerobic reduction of olefins using aqueous hydrazine at ambient temperature Chapter 4 describes the reduction olefins and acetylenes, which is presented in two Parts. Part 1 documents utility of hydrazine (1.5 equiv) for the chemoselective reduction of nonpolarised carbon-carbon bond using iron catalysts. In this part, a chemoselective reduction of alkenes and alkynes in the presence of a variety of reducible functional groups is demonstrated (Scheme 8). The highlight of the present method is that the reduction proceeds well at room temperature and requires only 1.5 equiv of hydrazine hydrate. The olefin reduction by hydrazine depends upon the controlled release of diimide during the reduction. Generally, metal catalyzed reduction of olefins employ a large excess of hydrazine (10-20 equiv), which might be attributed to uncontrolled release of diimide during the reduction.8 Scheme 8 Part 2: Guanidine catalyzed aerobic reduction: a selective aerobic hydrogenation of olefins using aqueous hydrazine In Chapter 4, part 2, organocatalytic generation of diimide and its utility to reduce the double bonds is presented. Generation of diimide in situ by using organo catalysts and its use for the reduction of carbon-carbon double bond is one of the interesting topics in organic chemistry. It has been shown in this part of the thesis that the reduction of olefin at room temperature can be efficiently performed by using 10 mol% of guanidine nitrate, 2 equiv of aqueous hydrazine in oxygen atmosphere. This method tolerates a variety of reducible functional groups such as nitro, azido, and bromo and protective groups such as methyl ethers, benzyl ethers, and Cbz groups. It is also shown that terminal olefin can be selectively reduced in the presence of internal olefin (Scheme 9). Unlike other methods that employ diimide strategy, the present method is shown to be efficient in reducing substrates those contain internal double bonds such as cinnamyl alcohol and its derivatives

Three-way catalysis (TWC) involves simultaneous removal of the three pollutants (i.e., CO, NOx, and HCs) which led to the branch of auto-exhaust catalysis. CeO2 has become the main component of TWC catalyst because of its oxygen storage storage (OSC) property to supply oxygen under excess fuel condition and store oxygen under lean condition. Substitution of smaller isovalent cations like Ti4+, Zr4+ and Hf4+ ions in CeO2 forming Ce1-xMxO2 (M = Ti, Zr &Hf) solid solution enhance the OSC property. XRD along with EXAFS study showed that cations arrange in FCC lattice but oxygen coordination around metal ions is split into 4 + 4 coordination in Ce1-xMxO2 instead of ideal 8 coordination in CeO2. The longer Ce/Ti/Zr – O bonds are weakly bound and can be easily removed by H2 giving high OSC value than pure CeO2. Among the three OSC systems studied here, Ce0.5Zr0.5O2 showed exceptionally high OSC which lead to formation of a new a pyrochlore, Ce2Zr2O6.3. This compound is nearly metallic. Ce0.85-xTi0.15PtxO2- (x = 0.01 & 0.02) crystallizes in fluorite structure and Pt is ionically substituted with 2+ and 4+ oxidation states. H/Pt atomic ratio at 30 oC over Ce0.84Ti0.15Pt0.01O2- is 5 and over Ce0.99Pt0.01O2-δ is 4 against just 0.078 for 8 nm Pt metal particles. Carbon monoxide and hydrocarbon oxidation activity are much higher over Ce1-x-yTixPtyO2 (x= 0.15, y= 0.01, 0.02) compared to Ce1-xPtxO2 (x= 0.01, 0.02). Synergistic involvement of Pt2+/Pt0 and Ti4+/Ti3+ redox couples in addition to Ce4+/Ce3+ due to the overlap of Pt(5d), Ti(3d), and Ce(4f) bands near EF is shown to be responsible for enhanced redox property and higher catalytic activity. On substitution of Pd ion in Ce1-xTixO2, more lattice oxygen is found to be more labile than Pd in CeO2. The easy removal of oxygen from the more reducible Ti4+ containing support plays a major role in showing higher catalytic activity of this material for CO oxidation, N2O and NO reduction by CO. The catalyst shows 100% N2 selectivity  240 oC in NO+CO reaction. It has been shown that oxide ion vacancy creation created by removal of lattice oxygen by CO is responsible for dissociation of NO or N2O at a lower temperature. Ionicity of Pd2+ ion in different support could be varied by varying the ionicity of the oxide support itself. Rates of CO oxidation increases or activation energy decreases over Ce1-xPdxO2-δ, Ti1-xPdxO2-δ and Ce1-x-yMxPdyO2-δ (M = Ti, Zr, Hf ; x = 0.25, 0.4 ; y = 0.02) is increased with ionicity of Pd2+ ion. The substitution of Sn in CeO2 forming Ce1-xSnxO2 (x = 0.1-0.5) solid solution was prepared using tin oxalate precursor by solution combustion method. These oxides can be promising support for noble metals because of the Sn4+  Sn2+ redox couple in addition to Ce3+/Ce4+. The two electron process involved in the redox reaction of Sn as well as easy reducibility of Sn4+ to Sn2+ offers a far better redox catalytic system hitherto not reported. Ce1-xSnxO2 solid solutions as well as Pd ion substituted Ce1-xSnxO2 was prepared for the first time.

Submitted by Pedro Silva Filho (pfsilva@ipen.br) on 2017-11-22T16:50:49Z No. of bitstreams: 0 / Made available in DSpace on 2017-11-22T16:50:49Z (GMT). No. of bitstreams: 0 / Eletrocatalisadores Pt/C, Pd/C, PtAu/C, PtIr/C, PdAu/C, PdIr/C, PtAuIr/C e PdAuIr/C foram preparados via redução por borohidreto de sódio em diferentes proporções atômicas, com 20% em massa de metal e suportados em carbono Vulcan XC72 de alta área superficial. Os materiais foram caracterizados pelas técnicas de espectroscopia de energia dispersiva de raios-X (EDX), análise de difração de raios-X (DRX) e microscopia eletrônica de transmissão (MET). A oxidação eletroquímica do etanol foi estudada por voltametria cíclica (VC) e cronoamperometria, utilizando a técnica do eletrodo de camada fina porosa e o estudo da oxidação eletroquímica de etanol \"in situ\" utilizando espectroscopia de infravermelho com transformada de Fourier (FTIR). Posteriormente os materiais foram testados em células à combustível alcalinas alimentadas diretamente com etanol. Os resultados demonstraram que houve formação de ligas, com tamanho médio de nanopartículas entre 4,0 - 10 nm. De acordo com os experimentos eletroquímicos os eletrocatalisadores ternários apresentaram maior atividade eletrocatalítica e os estudos em FTIR indicaram que o produto principal da oxidação eletroquímica de etanol em meio alcalino para todos eletrocatalisadores sintetizados foi o acetato, sugerindo que a oxidação ocorre de forma incompleta pelo mecanismo indireto. Os testes em célula mostraram os melhores resultados para PdAuIr/C (50:40:10) com o qual obteve-se potencial de circuito aberto de aproximadamente 0,78 V e densidade de potência máxima de aproximadamente 15 mW cm-2, cerca de 333% superior a Pd/C. / Tese (Doutorado em Tecnologia Nuclear) / IPEN/T / Instituto de Pesquisas Energéticas e Nucleares - IPEN-CNEN/SP