Academic literature on the topic 'Hydride Transfer Chemistry'

Although molybdenum sulfide materials show promise as electrocatalysts for proton reduction, the hydrido species proposed as intermediates remain poorly characterized. We report herein the synthesis, reactions and spectroscopic properties of a molybdenum-hydride complex featuring an asymmetric Mo2S2 core. This molecule displays rich redox chemistry with electrochemical couples at E½ = −0.45, −0.78 and −1.99 V vs. Fc/Fc+. The corresponding hydrido-complexes for all three redox levels were isolated and characterized crystallographically. Through an analysis of solid-state bond metrics and DFT calculations, we show that the electron-transfer processes for the two more positive couples are centered predominantly on the pyridinediimine supporting ligand, whereas for the most negative couple electron-transfer is mostly Mo-localized.

Abstract In the present study, we have used computational quantum chemistry to explore the reduction of various types of substrates by group-13 hydrides. We use the high-level L-W1X method to obtain the energies for the constituent association and hydride transfer reactions. We find that the hydride transfer reactions are highly exothermic, while the preceding association reactions are less so. Thus, improving the thermodynamics of substrate association may improve the overall process. Among the various substrates, amine and imine show the strongest binding, while CO2 shows the weakest. Between the group-13 hydrides, alanes bind most strongly with the substrates, and they also have the most exothermic hydride transfer reactions. To facilitate CO2 binding, we have examined alanes with electron-withdrawing groups, and we indeed find CF3 groups to be effective. Drawing inspiration from the RuBisCO enzyme for CO2 fixation, we have further examined the activation of CO2 with two independent AlH(CF3)2 molecules, with the results showing an even more exothermic association. This observation may form the basis for designing an effective dialane reagent for CO2 reduction. We have also assessed a range of lower-cost computational methods for the calculation of systems in the present study. We find the DSD-PBEP86 double-hybrid DFT method to be the most suitable for the study of related medium-sized systems.

Gas phase ion/molecule reactions in a Fourier transform ion cyclotron resonance mass spectrometer have been carried out for reductions of isotopically labelled citraconic (methylmaleic), phenylmaleic, and ethoxymaleic anhydrides by BH4−. In citraconic anhydride the carbonyl group neighbouring the methyl substituent is reduced preferentially in agreement with the ab initio calculations, which show the higher LUMO coefficients at this site. Hydride ion transfer to the olefinic double bond occurs as well; however, in that case no preference for either of the carbon atoms is observed. In phenylmaleic anhydride strong indications are found for a theoretically unexpected hydride ion transfer to the phenyl ring. For ethoxymaleic anhydride experimental evidence is presented showing hydride ion transfer to the carbon atom carrying the ethoxy group, which is in agreement with the "best overlap" consideration predicting that this carbon atom bears the highest LUMO coefficient.Most of the hydride transfers from BH4− to the molecules studied seem, therefore, to take place under orbital control rather than under control of long-range ion-induced dipole interactions between reactants.

Cobalt(III) tetraphenylporphyrin catalyses a hydride transfer reaction from tributyltin hydride to 10-methylacridinium ion via the formation of hydridocobalt(III) tetraphenylporphyrin, which is the rate-determining step, followed by facile hydride transfer from the hydridocobalt(III) porphyrin to 10-methylacridinium ion in acetonitrile. Tributyltin hydride is also effective for the hydrometallation of alkenes and alkynes with cobalt(III) tetraphenylporphyrin to yield the corresponding organocobalt(III) porphyrins regioselectively. The hydrometallation is suggested to proceed via the hydride transfer from tributyltin hydride to cobalt(III) tetraphenylporphyrin to give the hydridocobalt(III) porphyrin, followed by the hydrogen transfer from hydridocobalt(III) porphyrin to alkenes and alkynes to yield the corresponding organocobalt(III) porphyrins. The regioselectivities are consistent with the stabilities of radicals generated by the hydrogen transfer from hydridocobalt(III) porphyrin to alkenes and alkynes. The rates of the electrophilic cleavage of cobalt-carbon bonds of organocobalt(III) porphyrins by trifluoroacetic acid in MeCN are also reported.

Enzymatic self-sufficient hydride transfer processes. The hydride shuttle used in catalytic quantities is typically a nicotinamide cofactor (full: reduced; empty: oxidized). Ideally, no electron is lost to ‘the outside’ and no waste is produced.

The tolyl analogue of Shvo's hydroxycyclopentadienyl ruthenium hydride (4) efficiently transfers a hydride and proton to benzaldehyde or acetophenone to produce an alcohol. This reduction can be performed in toluene, methylene chloride, and THF. Reduction of benzaldehyde in toluene and methylene chloride occurs approximately 300 times faster than in THF at 0 °C. Reduction of acetophenone occurs between 75 and 150 times slower than benzaldehyde at 0 °C in each respective solvent. Despite the differences in rate, mechanistic studies have provided evidence for a similar concerted transfer of acidic and hydridic hydrogens in each solvent. Addition of water to THF led to further rate decrease coupled with an increase in the OH/D kinetic isotope effect and a decrease in the RuH/D kinetic isotope effect. Addition of excess alcohol to toluene or methylene chloride results in the significant retardation of the rate of reduction. The slower rate in THF and in the presence of alcohol is attributed to the stabilization of the ground state of ruthenium hydride 4 by hydrogen bonding and the additional energy required to break these bonds prior to carbonyl reduction.Key words: ruthenium hydrogenation catalysis, hydrogenation mechanism, kinetic isotope effects, ligand–metal bifunctional catalysis.

The secondary kinetic isotope effects for the hydride transfer reactions from aliphatic alcohols to four carbocations (NAD⁺ models) in acetonitrile were determined. The results suggest that the hydride transfer takes place by tunneling and that the rehybridizations of both donor and acceptor carbons lag behind the H-tunneling. This is quite contrary to the observations in alcohol dehydrogenases where the importance of enzyme motions in catalysis is manifested.

It has been accepted that hydrogen-transfer reactions take place through a quantum mechanical tunneling mechanism, where H tunnels through its classical energy barrier in light of its wave form. There are several H-tunneling models proposed, including the contemporary Marcus-like H-tunneling model, which explains that the donor-acceptor distance (DAD) in the tunneling ready state (TRS) is shorter for a heavier isotope (e.g. deuterium (D)) then a lighter isotope (e.g., protium (H)). This model has been used to explain the kinetic isotopic effect observations in H-tunneling processes to provide mechanistic role of protein in enzyme catalysis. The purpose of the research is to test the hypothesis of “isotopically different DAD” concept by studying the hydrogen/deuterium-transfer reactions in solutions, given that hydride-transfer reactions account for over 50% of biological reactions. Our group’s previous results showed that the steric hindrance and hydrogen-bonding effect played a significant role in the different hydrogen vs deuterium tunneling-ready states. In general, the shorter DAD creates more spatial crowding effect which will affect the 2° C-H vibrations and decrease the 2° KIEs. In this thesis, different reaction systems were designed to test these effects by studying the 1° isotope dependence of 2° KIEs at the near and remote positions from the reaction center. It was found that the results are consistent with the hypothesis of the “isotopically different TRS structures”.

The nucleotide 2'-deoxythymidine 5'-monophosphate (thymidylate, dTMP) is phosphorylated twice to become a substrate for DNA polymerases, which copy a cell’s genetic information in advance of cell division. The main route to dTMP is mediated by the enzyme thymidylate synthase (TSase) and goes through 2'-deoxyuridine 5'-monophosphate (dUMP); dUMP’s heterocyclic aromatic pyrimidine ring loses a proton from its C5 position and gains a methylene and a hydride from the other reactant, methylene tetrahydrofolate (MTHF). In general, intricate knowledge of an enzyme’s mechanism can yield insight that leads to the development of precision-targeted inhibitors tailored exactly to thymidylate synthase. In fact, even more careful targeting could be achievable: Although E. coli TSase has served as a model system, investigators have increasingly been directing their lines of inquiry toward human TSase. A general enzymatic catalytic cascade is complex, comprising substrate binding, the chemical steps and product release; typically, the product release step is rate-limiting. TSase, however, is partially rate-limited by the chemistry portion of the process. The enzymatic mechanism has been considered for decades, yet recently has undergone a reassessment. After substrate binding – for which there is strong evidence for preference to dUMP as the first ligand in the wild-type E. coli enzyme – the important events are methylene transfer from MTHF to dUMP, proton abstraction and hydride transfer. The last of these – hydride transfer – is irreversible and rate-limiting (to a large degree without Mg2+, and to a small but noticeable degree with Mg2+). The studies described here are aimed at three therapeutically relevant questions: (a) determining the extent of negative charge accumulation at the O4 position of the hydride transfer acceptor; (b) expanding knowledge of the differential properties of E. coli and human TSase; and (c) gaining insight into the molecular origin of the drug resistance seen in a clinically relevant human TSase mutant. The properties touched on in this work include steady-state kinetics; inhibition constants toward 5-fluoro dUMP, substrate binding sequence and the temperature dependency of intrinsic hydride transfer kinetic isotope effects (KIEs). Intrinsic KIEs are a specialized measurement that permits the investigator to examine a particular hydrogen transfer step in isolation; it is achieved by labeling the bond to hydrogen broken in the reaction with protium (1H, also written as H), deuterium (2H, also written as D) or tritium (3H, also written as T). The latter is radioactive. The reaction is conducted with a mixture of two hydrogen isotopes at a time, and the extent to which the heavier isotope is disfavored against reaction is assessed; this covers multiple steps. Heavier isotopes directly participating in a chemical step react slower both because of zero-point vibrational energies if a semi-classical view is taken and because of the mass-dependence of tunneling probabilities if a quantum-mechanical view is taken. Each of the two-way isotopic comparisons mentioned above furnishes an observed KIE for that competition between two isotopes. Mathematical combination of two isotopic comparisons cancels out the effect of isotopically insensitive steps and provides rich insight into the hydride transfer alone. The ultimate result is the ratio of rate constants for the isotopologues; this ratio’s magnitude and variation with temperature report on the compactness of the active site and its resistance to thermal fluctuation, respectively. Our results reveal a possible role for E. coli asparagine 177 (N177) in the hydride transfer transition state (TS) stabilization, as revealed by its disruption in the aspartate mutant, N177D. This disruption was found to be alleviated to a high extent when the substrate was changed to dCMP, consistent with the N177 stabilizing partial negative charge at the TS for hydride transfer. This has drug design implications. Our work on human TSase underscores slightly weaker substrate binding preference, insensitivity to Mg2+ and mild alteration of hydride transfer TS when compared with E. coli TSase. Finally, analysis of the Y33H mutant of human TSase – the affected residue being remote from the active site – indicated the drug resistance was because of a higher inhibition constant for 5F-dUMP and that the hydride transfer step is disrupted, with a wider variation among donor-acceptor distances (between the two carbons involved in the hydride transfer at the TS for that step). Other researchers’ crystallographic evidence reveals greater positional uncertainty for a set of active-site side chains in the E. coli equivalent mutant. In totality, the data available implicate enzyme motions as relevant to drug binding and to catalysis for human TSase. In summary, the research described herein enriches the understanding of several aspects of the behavior of multiple TSase variants – the overall performance as seen via steady-state kinetics; the pattern of substrate binding as seen with observed KIEs for the proton abstraction step; and the efficiency of active site preparation for hydride transfer as evidenced in the temperature dependency of intrinsic hydride transfer KIEs.

Choline oxidase catalyzes the two-step oxidation of choline to glycine betaine, one of limited osmoprotectants, with the formation of betaine aldehyde as an enzyme bound intermediate. Glycine betaine accumulates in the cytoplasm of plants and bacteria as a defensive mechanism to withstand hyperosmolarity and elevated temperatures. This makes the genetic engineering of relevant plants which lack the property of salt accumulation of economic interest, and the biosynthetic pathway of the osmolyte a potential drug target in microbial infections. The reaction of alcohol oxidation occurs via a hydride ion tunneling transfer from the substrate donor to a flavin acceptor within a highly preorganized active site environment in which choline and FAD are in a rigidly close proximity. In this dissertation, factors contributing to the enzyme-substrate preorganization which is required for the hydride ion tunneling reaction mechanism in choline oxidase have been investigated. Crystallographic studies of wild-type choline oxidase revealed a covalent linkage between C8M atom of the FAD isoalloxazine ring and the N(3) atom of the side chain of a histidine at position 99, and a solvent excluded cavity in the substrate binding domain containing glutamic acid at position 312 as the only negatively charged amino acid residue in the active site of the enzyme. The role of the histidine residue and the contribution of the 8á-N(3)-histidyl covalent linkage of the flavin cofactor to the reaction of alcohol oxidation was investigated in a variant form of choline oxidase in which the histidine residue was replaced with an asparagine. The role of the glutamate residue and the importance of the spatial location of the negative charge at position 312 was investigated in variant forms of choline oxidase in which the negatively charged residue was replaced with glutamine and aspartate. Mechanistic data obtained for the variant enzymes and their comparison to previous data obtained for wild-type choline oxidase are consistent with the residues at positions 99 and 312 being important for relative positioning of the hydride ion donor and acceptor. The residues are important for the enzyme-substrate preorganization that is required for the hydride tunneling reaction in choline oxidase.

Enzymes direct chemical reactions with precision and speed, making life as we know it possible. How they do this is still not completely understood, but the relatively recent discovery of subpicosecond protein motion coupled to the reaction coordinate has provided a crucial piece of the puzzle. This type of motion is called a rate-promoting vibration (RPV) and has been seen in a number of different enzymatic systems. It typically involves a compression of the active site of the enzyme which lowers the barrier for the reaction to occur. In this work we present a number of studies that probe these motions in two dehydrogenase enzymes, yeast alcohol dehydrogenase (YADH) and homologs of lactate dehydrogenase (LDH). The goal of the study on the reaction of YADH was to probe the role of the protein in proton tunneling in the enzyme, which was suggested to occur from experimental kinetic isotope effect studies. We did this using transition path sampling (TPS), which perturbatively generates ensembles of reactive trajectories to observe transitions between stable states, such as chemical reactions. By applying a quantum method that can account for proton tunneling, centroid molecular dynamics, and generating reactive trajectory ensembles with and without the method, we were able to observe the change in barrier to proton transfer upon application of the tunneling method. We found that there was little change in the barrier, showing that classical over-the-barrier transfer is dominant over tunneling in the proton transfer in YADH. We also applied the knowledge of RPVs to identify a new class of allosteric molecules, which modulate enzymatic reaction not by changing a binding affinity, but by disrupting the reactive motion of enzymes. We showed, through design of a novel allosteric effector for human heart LDH, applying TPS to a system with and without the small molecule bound, and analysis of the reaction coordinate of the reactive trajectory ensemble, that the molecule was able to disrupt the motion of the protein such that it was no longer coupled to the reaction. We also examined the subpicosecond motions of two other LDHs, from Plasmodium falciparum and Cryptosporidium parvum, which evolved separately from previously studied LDHs. We found, using TPS and reaction coordinate identification, that while the LDH from C. parvum had similar dynamics to the earlier LDHs, the LDH from P. falciparum had a earlier transition-state associated with proton transfer, not hydride transfer. This is likely due to this LDH having a larger active site pocket, increasing the amount of motion necessary for proton transfer, and, thus, the barrier to proton transfer. More work is necessary in this system to determine whether the protein is coupled with the search for the reactive conformation for proton transfer. Protein motion coupled to the particle transfer in dehydrogenases plays an important role in their reactions and there is still much work to be done to understand the extent and role of RPVs.

Choline oxidase catalyzes the flavin-dependent, two-step oxidation of choline to glycine betaine via the formation of an aldehyde intermediate. The oxidation of choline includes two reductive half-reactions followed by oxidative half-reactions. In the first oxidation reaction, the alcohol substrate is activated to its alkoxide via proton abstraction and oxidized via transfer of a hydride from the alkoxide α-carbon to the N(5) atom of the enzyme-bound flavin. In the wild-type enzyme, proton and hydride transfers are mechanistically and kinetically uncoupled. The role of Ser101 was investigated in this dissertation. Replacement of Ser101 with threonine, alanine, cysteine, or valine demonstrated the importance of the hydroxyl group of Ser101 in proton abstraction and in hydride transfer. Moreover, the kinetic studies on the Ser101Ala variant have revealed the importance of a specific residue for the optimization of the overall turnover of choline oxidase. The UV-visbible absorbance of Ser101Cys suggests Cys101 can form an adduct with the C4a atom of the flavin. The mechanism of formation of the C4a-cysteinyl adduct has been elucidated. D-arginine dehydrogenase (DADH) catalyzes the oxidation of D-amino acids to the corresponding imino acids, which are non-enzymatically hydrolyzed to α-keto acids and ammonia. The enzyme is strick dehrogenase and deoesnot react with molecular oxygen. Steady state kinetic studies wirh D-arginine and D-histidine as a substrate and PMS as the electron acceptor has been investigated. The enzyme has broad substrate specificity for D-amino acids except aspartate, glutamate and glycine, with preference for arginine and lysine. Leucine is the slowest substrate in which steady state kinetic parameters can be obtained. The chemical mechanism of leucine dehydrogenation catalyzed by DADH was explored with a combination of pH, substrate and solvent kinetic isotope effects (KIE) and proton inventories by using rapid kinetics in a stopped-flow spectrophotometer. The data are discussed in the context of the crystallographic structures at high resolutions (<1.3 Å) of the enzyme in complex with iminoarginine or iminohistidine.

Nowadays, the modern chemical industry has to deal with increasing environmental concerns, including the disposal of waste and its economic impact, or the diminution of important worldwide resources such as transition metals. In this Ph.D. thesis, we aimed to bring improvement in this area by the development of green processes, based on the use of recyclable heterogeneous catalysts. By combining the catalytic properties of several metal cations with the properties of solid catalysts such as polyoxometalates or zeolites, we were able to set up new tools for organic synthesis. Silver-doped polyoxometalates proved to be very efficient catalysts in the rearrangement of alkynyloxiranes to furans. Acetals and spiroketals were synthetized by dihydroalkoxylation of alkynediols under catalysis with silver-zeolites. As a perspective, we highlighted the potential applications of such green procedures in the total synthesis of more complex molecules. The first results suggested that these environmental friendly processes should gain increasing interest in the future.

De nos jours, l’industrie chimique est de plus en plus confrontée à la question de son impact environnemental. Dans le même temps, elle doit faire face à la diminution des ressources de matières premières importantes tels que les métaux de transition, tout en respectant des contraintes économiques. Ces travaux de thèse avaient pour but de tenter de répondre à ces exigences, par le développement de méthodologies de synthèse basées sur l’utilisation de catalyseurs hétérogènes recyclables. En combinant les propriétés catalytiques de certains ions métalliques avec les propriétés de catalyseurs solides tels que les polyoxométallates ou les zéolithes, nous avons pu mettre au point de nouveaux outils pour la synthèse organique. Les polyoxométallates dopés à l’argent ont démontré leur efficacité dans le réarrangement d’alcynyloxiranes en furanes. La synthèse de spiroacétals et d’acétals par dihydroalkoxylation d’alcyne diols a été effectuée pour la première fois en catalyse à l’argent, via l’utilisation de zéolithes. En perspective, nous avons mis en évidence les applications potentielles de ces procédés verts dans la synthèse totale de molécules plus complexes. Les premiers résultats suggèrent que de telles synthèses plus respectueuses de l’environnement ont tout intérêt à être davantage utilisées à l’avenir
Nowadays, the modern chemical industry has to deal with increasing environmental concerns, including the disposal of waste and its economic impact, or the diminution of important worldwide resources such as transition metals. In this Ph.D. thesis, we aimed to bring improvement in this area by the development of green processes, based on the use of recyclable heterogeneous catalysts. By combining the catalytic properties of several metal cations with the properties of solid catalysts such as polyoxometalates or zeolites, we were able to set up new tools for organic synthesis. Silver-doped polyoxometalates proved to be very efficient catalysts in the rearrangement of alkynyloxiranes to furans. Acetals and spiroketals were synthetized by dihydroalkoxylation of alkynediols under catalysis with silver-zeolites. As a perspective, we highlighted the potential applications of such green procedures in the total synthesis of more complex molecules. The first results suggested that these environmental friendly processes should gain increasing interest in the future

AbstractPortland cement production is not regarded as environmentally friendly, because of its associated high carbon emissions, which are responsible for 5% of global emissions. An alternative is to substitute fly ash for Portland cement. Australia has an abundance of brown coal fly ash, as it is the main source of primary energy in the State of Victoria. Currently, the majority of this material is stored in landfills and currently there is no commercial use for it in the cement industry because brown coal fly ash cannot be used as a direct replacement material for Portland cement due to the high sulfur and calcium content and low aluminosilicate content. However, the potential exists to use brown coal fly ash as a geopolymeric material, but there remains a significant amount of research needed to be conducted. One possible application is the production of geopolymer concrete bricks. A research project was undertaken to investigate the use of brown coal fly ash from Latrobe Valley power stations in the manufacture of geopolymer masonry bricks. The research developed a detailed understanding of the fundamental chemistry behind the activation of the brown coal fly ash and the reaction mechanisms involved to enable the development of brown coal fly ash geopolymer concrete bricks. The research identified suitable manufacturing techniques to investigate relationships between compressive strength and processing parameters and to understand the reaction kinetics and microstructural developments. The first phase of the research determined the physical, chemical, and mineralogical properties of the Loy Yang and Yallourn fly ash samples to produce a 100% fly ash-based geopolymer mortar. Optimization of the Loy Yang and Yallourn geopolymer mortars was conducted to identify the chemical properties that were influential in the production of satisfactory geopolymer strength. The Loy Yang mortars were able to produce characteristic compressive strengths acceptable in load-bearing bricks (15 MPa), whereas the Yallourn mortars produced characteristic compressive strengths only acceptable as non-load-bearing bricks (5 MPa). The second phase of the research transposed the optimal geopolymer mortar mix designs into optimal geopolymer concrete mix designs while merging the mix design with the optimal Adbri Masonry (commercial partner) concrete brick mix design. The reference mix designs allowed for optimization of both the Loy Yang and Yallourn geopolymer concrete mix designs, with the Loy Yang mix requiring increased water content because the original mix design was deemed to be too dry. The key factors that influenced the compressive strength of the geopolymer mortars and concrete were identified. The amorphous content was considered a vital aspect during the initial reaction process of the fly ash geopolymers. The amount of unburnt carbon content contained in the fly ash can hinder the reactive process, and ultimately, the compressive strength because unburnt carbon can absorb the activating solution, thus reducing the particle to liquid interaction ratio in conjunction with lowering workability. Also, fly ash with a higher surface area showed lower flowability than fly ash with a smaller surface area. It was identified that higher quantity of fly ash particles <45 microns increased reactivity whereas primarily angular-shaped fly ash suffered from reduced workability. The optimal range of workability lay between the 110–150 mm slump, which corresponded with higher strength displayed for each respective precursor fly ash. Higher quantities of aluminum incorporated into the silicate matrix during the reaction process led to improved compressive strengths, illustrated by the formation of reactive aluminosilicate bonds in the range of 800–1000 cm–1 after geopolymerization, which is evidence of a high degree of reaction. In addition, a more negative fly ash zeta potential of the ash was identified as improving the initial deprotonation and overall reactivity of the geopolymer, whereas a less negative zeta potential of the mortar led to increased agglomeration and improved gel development. Following geopolymerization, increases in the quantity of quartz and decreases in moganite correlated with improved compressive strength of the geopolymers. Overall, Loy Yang geopolymers performed better, primarily due to the higher aluminosilicate content than its Yallourn counterpart. The final step was to transition the optimal geopolymer concrete mix designs to producing commercially acceptable bricks. The results showed that the structural integrity of the specimens was reduced in larger batches, indicating that reactivity was reduced, as was compressive strength. It was identified that there was a relationship between heat transfer, curing regimen and structural integrity in a large-volume geopolymer brick application. Geopolymer bricks were successfully produced from the Loy Yang fly ash, which achieved 15 MPa, suitable for application as a structural brick. Further research is required to understand the relationship between the properties of the fly ash, mixing parameters, curing procedures and the overall process of brown coal geopolymer concrete brick application. In particular, optimizing the production process with regard to reducing the curing temperature to ≤80 °C from the current 120 °C and the use of a one-part solid activator to replace the current liquid activator combination of sodium hydroxide and sodium silicate.

Each of the thirteen human vitamins brings unique and essential chemistry to enable nodal points in metabolic pathways to proceed. In a sense, each vitamin provides one (or more) snapshot(s) into human metabolic logic. Nine of the vitamins bring specialized heterocyclic chemistries to bear on key chemical conversion of metabolites. Ten of the thirteen mediate electron transfer processes, lowering barriers for carbanions, hydride transfers, or one electron pathways. We argue that most of the catabolic, energy yielding pathways in human metabolism center on redox chemistry, enabled by the vitamins. A vitamin-centric perspective also illuminates their roles in the flux of one-carbon metabolism in its several oxidation states for cellular economies. Several of the vitamins enable chemistry in both small molecule metabolic pathways and also for essential posttranslational modification of proteins.

This chapter begins a series of three chapters that examine the molecular logic of specific degradative or biosynthetic pathways involving three iconic metabolites: glucose, squalene, and porphobilinogen. This chapter examines three major metabolic roles for glucose, one catabolic, two anabolic. In the catabolic role of glucose-6-P as a major energy source the chemical and enzymatic logic for its complete oxidation to six CO2 with storage of its 24 bonding electrons are saved as 12 hydride equivalents in NADH and FADH2 are explored through both glycolysis and the citric acid cycle. The two biosynthetic pathways for glucose-6-P are the pentose-P pathway, generating ribose for all nucleic acid building blocks, and the transfer of glycosyl groups as electrophilic fragments at carbon 1 in polysaccharide biosynthesis. The array of hydroxycarbonyl group chemistry and the several alcohol to ketone oxidations of glucose illustrate a biologic universe of carbonyl chemistry.

Although methods both for reduction and for oxidation are well developed, there is always room for improvement. While ketones are usually reduced using metal hydrides, hydrogen gas is much less expensive on scale. Charles P. Casey of the University of Wisconsin has devised (J. Am. Chem. Soc. 2007, 129, 5816) an Fe-based catalyst that effects the transformation of 1 to 2. Note that the usually very reactive monosubstituted alkene is not reduced and does not migrate. Takeshi Oriyama of Ibaraki University has developed a catalyst, also Fe-based (Chemistry Lett. 2007, 38) for reducing aldehydes to ethers. Using this approach, an alcohol such as 3 can be converted into a variety of substituted benzyl ethers, including 5. Simple aliphatic aldehydes and alcohols also work well. Oxidation of alcohols to aldehydes or ketones is one of the most common of organic transformations. Several new processes catalytic in metal have been put forward. Tharmalingam Punniyamurthy of the Indian Institute of Technology, Guwahati has found (Adv. Synth. Cat. 2007, 349, 846) that catalytic V(IV) oxide on silica gel, stirred with t-butyl hydroperoxide in t-butyl alcohol at room temperature smoothly oxidized 6 to 7. After the reaction, the catalyst was separated by filtration. Another carbonyl can also serve as the hydride acceptor, but then the transfer can be reversible. Jonathan M. J. Williams of the University of Bath has shown (Tetrahedron Lett. 2007, 48, 3639) that with a Ru catalyst, methyl levulinate 9 could serve as the hydride acceptor, with the byproduct alcohol being drained off as the lactone 11. Hansjörg Grützmacher of the ETH Zürich developed an Ir catalyst (Angew. Chem. Int. Ed. 2007, 46, 3567) with benzoquinone as the net oxidant. that showed marked preference for the oxidation of primary over secondary alcohols. Yasuhiro Uozumi of the Institute for Molecular Science, Aichi, has devised (Angew. Chem. Int. Ed . 2007, 46, 704) a nanoencapsulated Pt catalyst that worked well with O2 or even with air. The catalyst was easily separated from the product, and maintained its activity over several cycles.

The reduction of pyridines offers an attractive approach to piperidine synthesis, and now Toshimichi Ohmura and Michinori Suginome of Kyoto University have developed (J. Am. Chem. Soc. 2012, 134, 3699) a rhodium-catalyzed hydroboration of pyridines, including the reaction of 1 to produce 3. Timothy J. Donohoe at the University of Oxford has found (Org. Lett. 2011, 13, 2074) that pyridinium silanes 4 undergo intramolecular hydride transfer by treatment with TBAF to produce dihydropyridones (e.g., 5) with good diastereoselectivity. Enantioselective amination of allylic alcohols has proven challenging, but Ross A. Widenhoefer at Duke University has reported (Angew. Chem. Int. Ed. 2012, 51, 1405) that a chiral gold catalyst can effect such intramolecular cyclizations with good enantioselectivity, as in the synthesis of 7 from 6. Alternatively, Masato Kitamura at Nagoya University has developed (Org. Lett. 2012, 14, 608) a ruthenium catalyst that operates at as low as 0.05 mol% loading for the conversion of substrates such as 8 to 9. Efforts to replace transition metal catalysts with alkaline earth metal-based alternatives have been gaining increasing attention, and Kai C. Hultzsch at Rutgers University has found (Angew. Chem. Int. Ed. 2012, 51, 394) that the magnesium complex 12 is capable of catalyzing intramolecular hydroamination (e.g., 10 to 11) with high enantioselectivity. Meanwhile, a stereoselective Wacker-type oxidation of tert-butanesulfinamides such as 13 to produce pyrrolidine derivatives 14 has been disclosed (Org. Lett. 2012, 14, 1242) by Shannon S. Stahl at the University of Wisconsin at Madison. Though highly desirable, Heck reactions have rarely proven feasible with alkyl halides due to competitive β-hydride elimination of the alkyl palladium intermediates. Sherry R. Chemler at the State University of New York at Buffalo has demonstrated (J. Am. Chem. Soc. 2012, 134, 2020) a copper-catalyzed enantioselective amination Heck-type cascade (e.g., 15 and 16 to 17) that is thought to proceed via radical intermediates. David L. Van Vranken at the University of California at Irvine has reported (Org. Lett. 2012, 14, 3233) the carbenylative amination of N-tosylhydrazones, which proceeds through η3-allyl Pd intermediates constructed via carbene insertion. This chemistry was applied to the two-step synthesis of caulophyllumine B from vinyl iodide 18 and N-tosylhydrazone 19.

This chapter on biologic nitrogenous heterocycles deals exclusively with the coenzymatically active forms of vitamins. Seven of the eight B vitamins use heterocyclic chemistry, each one a separate ring system, to mediate chemical transformations at key nodal metabolic intersections. The heterocycles include single ring heterocycles: the thiazolium ion in thiamin-PP, the cationic pyridinium in NAD(P)+, and the pyridine aldehyde in pyridoxal-P. Bis-heterocyclic rings include biotin and folate coenzymes. Riboflavin offers a tricyclic isoalloxazine ring system and B12 a tetrapyrrolic framework. The ranges of chemistry enabled include carbanion, carbocation, and carbon radical intermediates, as well as hydride ion transfers.

The three basic ingredients of our nanofabrication scheme on silicon surfaces are: (a) utilizing silicon hydride as the initial resist, (b) employing a scanning tunneling microscope (STM) as the e-beam source to desorb H-atoms of the resist to create patterns in an ultrahigh vacuum (UHV) environment, and (c) using either the original H-resist or an oxide-mask generated from (a) and (b) for further pattern transfer. Each of these ideas has been investigated independently by different research groups for different purposes. A brief summary seems appropriate to show how basic research may lead to the development of new technology and vice versa.

Increased research into the chemistry, physics and material science of hydrogen cycling compounds has led to the rapid growth of solid-phase hydrogen-storage options. The operating conditions of these new options span a wide range: system temperature can be as low as 70K or over 600K, system pressure varies from less than 100kPa to 35MPa, and heat loads can be moderate or can be measured in megawatts. While the intense focus placed on storage materials has been appropriate, there is also a need for research in engineering, specifically in containment, heat transfer, and controls. The DOE’s recently proposed engineering center of expertise underscores the growing understanding that engineering research will play a role in the success of advanced hydrogen storage systems. Engineering a hydrogen system will minimally require containment of the storage media and control of the hydrogenation and dehydrogenation processes, but an elegant system design will compensate for the storage media’s weaker aspects and capitalize on its strengths. To achieve such a complete solution, the storage tank must be designed to work with the media, the vehicle packaging, the power-plant, and the power-plant’s control system. In some cases there are synergies available that increase the efficiency of both subsystems simultaneously. In addition, system designers will need to make the hard choices needed to convert a technically feasible concept into a commercially successful product. Materials cost, assembly cost, and end of life costs will all shape the final design of a viable hydrogen storage system. Once again there is a critical role for engineering research, in this case into lower cost and higher performance engineering materials. Each form of hydrogen storage has its own, unique, challenges and opportunities for the system designer. These differing requirements stem directly from the properties of the storage media. Aside from physical containment of compressed or liquefied hydrogen, most storage media can be assigned to one of four major categories, chemical storage, metal hydrides, complex hydrides, or physisorption. Specific needs of each technology are discussed below. Physisorption systems currently operate at 77K with very fast kinetics and good gravimetric capacity; and as such, special engineering challenges center on controlling heat transfer. Excellent MLVSI is available, its cost is high and it is not readily applied to complex shape in a mass manufacture setting. Additionally, while the heat of adsorption on most physisorbents is a relatively modest 6–10kJ/mol H2, this heat must be moved up a 200K gradient. Physisorpion systems are also challenged on density. Consequently, methods for reducing the cost of producing and assembling compact, high-quality insulation, tank design to minimize heat transfer while maintaining manufacturability, improved methods of heat transfer to and from the storage media, and controls to optimize filling are areas of profitable research. It may be noted that the first two areas would also contribute to improvement of liquid hydrogen tanks. Metal hydrides are currently nearest application in the form of high pressure metal hydride tanks because of their reduced volume relative to compressed gas tanks of the same capacity and pressure. These systems typically use simple pressure controls, and have enthalpies of roughly 20kJ/mol H2 and plateau pressures of at most a few MPa. During filling, temperatures must be high enough to ensure fast kinetics, but kept low enough that the thermodynamically set plateau pressure is well below the filling pressure. To accomplish this balance the heat transfer system must handle on the order of 300kW during the 5 minute fill of a 10kg tank. These systems are also challenged on mass and the cost of the media. High value areas for research include: heat transfer inside a 35MPa rated pressure vessel, light and strong tank construction materials with reduced cost, and metals or other materials that do not embrittle in the presence of high pressure hydrogen when operated below ∼400K. The latter two topics would also have a beneficial impact on compressed gas hydrogen storage systems, the current “system to beat”. Complex hydrides frequently have high hydrogen capacity but also an enthalpy of adsorption >30kJ/mol H2, a hydrogen release temperature >370K, and in many cases multiple steps of adsorption/desorption with slow kinetics in at least one of the steps. Most complex hydrides are thermal insulators in the hydrided form. From an engineering perspective, improved methods and designs for cost effective heat transfer to the storage media in a 5 to 10MPa vessel is of significant interest, as are materials that resist embrittlement at pressures below 10MPa and temperatures below 500K. Chemical hydrides produce heat when releasing hydrogen; in some systems this can be managed with air cooling of the reactor, but in other systems that may not be possible. In general, chemical hydrides must be removed from the vehicle and regenerated off-board. They are challenged on durability and recycling energy. Engineering research of interest in these systems centers around maintaining the spent fuel in a state suitable for rapid removal while minimizing system mass, and on developing highly efficient recycling plant designs that make the most of heat from exothermic steps. While the designs of each category of storage tank will differ with the material properties, two common engineering research thrusts stand out, heat transfer and structural materials. In addition, control strategies are important to all advanced storage systems, though they will vary significantly from system to system. Chemical systems need controls primarily to match hydrogen supply to power-plant demand, including shut down. High pressure metal hydride systems will need control during filling to maintain an appropriately low plateau pressure. Complex hydrides will need control for optimal filling and release of hydrogen from materials with multi-step reactions. Even the relatively simple compressed-gas tanks require control strategies during refill. Heat transfer systems will modulate performance and directly impact cost. While issues such as thermal conductivity may not be as great as anticipated, the heat transfer system still impacts gravimetric efficiency, volumetric efficiency and cost. These are three key factors to commercial viability, so any research that improves performance or reduces cost is important. Recent work in the DOE FreedomCAR program indicates that some 14% of the system mass may be attributed to heat transfer in complex hydride systems. If this system is made to withstand 100 bar at 450K the material cost will be a meaningful portion of the total tank cost. Improvements to the basic shell and tube structures that can reduce the total mass of heat transfer equipment while maintaining good global and local temperature control are needed. Reducing the mass and cost of the materials of construction would also benefit all systems. Much has been made of the need to reduce the cost of carbon fiber in compressed tanks and new processes are being investigated. Further progress is likely to benefit any composite tank, not just compressed gas tanks. In a like fashion, all tanks have metal parts. Today those parts are made from expensive alloys, such as A286. If other structural materials could be proven suitable for tank construction there would be a direct cost benefit to all tank systems. Finally there is a need to match the system to the storage material and the power-plant. Recent work has shown there are strong effects of material properties on system performance, not only because of the material, but also because the material properties drive the tank design to be more or less efficient. Filling of a hydride tank provides an excellent example. A five minute or less fill time is desirable. Hydrogen will be supplied as a gas, perhaps at a fixed pressure and temperature. The kinetics of the hydride will dictate how fast hydrogen can be absorbed, and the thermodynamics will determine if hydrogen can be absorbed at all; both properties are temperature dependent. The temperature will depend on how fast heat is generated by absorption and how fast heat can be added or removed by the system. If the design system and material properties are not both well suited to this filling scenario the actual amount of hydrogen stored could be significantly less than the capacity of the system. Controls may play an important role as well, by altering the coolant temperature and flow, and the gas temperature and pressure, a better fill is likely. Similar strategies have already been demonstrated for compressed gas systems. Matching system capabilities to power-plant needs is also important. Supplying the demanded fuel in transients and start up are obvious requirements that both the tank system and material must be design to meet. But there are opportunities too. If the power-plant heat can be used to release hydrogen, then the efficiency of vehicle increases greatly. This efficiency comes not only from preventing hydrogen losses from supplying heat to the media, but also from the power-plant cooling that occurs. To reap this benefit, it will be important to have elegant control strategies that avoid unwanted feedback between the power-plant and the fuel system. Hydrogen fueled vehicles are making tremendous strides, as can be seen by the number and increasing market readiness of vehicles in technology validation programs. Research that improves the effectiveness and reduces the costs of heat transfer systems, tank construction materials, and control systems will play a key role in preparing advanced hydrogen storage systems to be a part of this transportation revolution.

Semiconductor and magnetic nanoparticles hold unique optical and magnetic properties, and great promise for bio-imaging and therapeutic applications. As part of their stable synthesis, the nanocrystal surfaces are usually capped by long chain organic moieties such as trioctylphosphine oxide. This capping serves two purposes: it saturates dangling bonds at the exposed crystalline lattice, and it prevents irreversible aggregation by stabilizing the colloid through entropic repulsion. These nanocrystals can be rendered water-soluble by either ligand exchange or overcoating, which hampers their widespread use in biological imaging and biomedical therapeutics. Here, we report a novel scheme of synthesizing fluorescent PbS and magnetic Fe3O4 nanoparticles using DNA oligonucleotides. Our method of PbS synthesis includes addition of Na2S to the mixture solution of DNA sequence and Pb acetate (at a fixed molar ratio of DNA/S2−/Pb2+ of 1:2:4) in a standard TAE buffer at room temperature in the open air. In the case of Fe3O4 particle synthesis, ferric and ferrous chloride were mixed with DNA in DI water at a molar ratio of DNA/Fe2+/Fe3+ = 1:4:8 and the particles were formed via reductive precipitation, induced by increasing pH to ∼11 with addition of ammonium hydroxide. These nanocrystals are highly stable and water-soluble immediately after the synthesis, due to DNA termination. We examined the surface chemistry between oligonucleotides and nanocrystals using FTIR spectroscopy, and found that the different chemical moieties of nucleobases passivate the particle surface. Strong coordination of primary amine and carbonyl groups provides the chemical and colloidal stabilities, leading to high particle yields (Figure 1). The resulting PbS nanocrystals have a distribution of 3–6 nm in diameter, while a broader size distribution is observed with Fe3O4 nanoparticles as shown in Figure 1b and c, respectively. A similar observation was reported with the pH change-induced Fe3O4 particles of a bimodal size distribution where superparamagnetic and ferrimagnetic magnetites co-exist. In spite of the differences, FTIR measurements suggest that the chemical nature of the oligonucleotide stabilization in this case is identical to the PbS system. As a particular application, we demonstrate that aptamer-capped PbS QD can detect a target protein based on selective charge transfer, since the oligonucleotide-templated synthesis can also serve the additional purpose of providing selective binding to a molecular target. Here, we use thrombin and a thrombin-binding aptamer as a model system. These QD have diameters of 3∼6 nm and fluoresce around 1050 nm. We find that a DNA aptamer can passivate near IR fluorescent PbS nanocrystals, rendering them water-soluble and stable against aggregation, and retain the secondary conformation needed to selectively bind to its target, thrombin, as shown in Figure 2. Importantly, we find that when the aptamer-functionalized nanoparticles binds to its target (only the target), there is a highly systematic and selective quenching of the PL, even in high concentrations of interfering proteins as shown in Figure 3a and b. Thrombin is detected within one minute with a detection limit of ∼1 nM. This PL quenching is attributed to charge transfer from functional groups on the protein to the nanocrystals. A charge transfer can suppress optical transition mechanisms as we observe a significant decrease in QD absorption with target addition (Figure 3c). Here, we rule out other possibilities including Forster resonance energy transfer (FRET) and particle aggregation, because thrombin absorb only in the UV, and we did not observe any significant change in the diffusion coefficient of the particles with the target analyte, respectively. The charge transfer-induced photobleaching of QD and carbon nanotubes was observed with amine groups, Ru-based complexes, and azobenzene compounds. This selective detection of an unlabeled protein is distinct from previously reported schemes utilizing electrochemistry, absorption, and FRET. In this scheme, the target detection by a unique, direct PL transduction is observed even in the presence of high background concentrations of interfering negatively or positively charged proteins. This mechanism is the first to selectively modulate the QD PL directly, enabling new types of label free assays and detection schemes. This direct optical transduction is possible due to oligonucleotidetemplated surface passivation and molecular recognition. This chemistry may lead to more nanoparticle-based optical and magnetic probes that can be activated in a highly chemoselective manner.