Scientific Publications 2009
2009. "Catalytic Hydroprocessing of Chemical Models for Bio-oil." Energy and Fuels 23(2):631-637. doi:10.1021/ef8007773 Abstract Bio-oil (product liquids from fast pyrolysis of biomass) is a complex mixture of oxygenates derived from the thermal breakdown of the bio-polymers in biomass. In the case of lignocellulosic biomass, the structures of three major components, cellulose, hemicellulose and lignin, are well represented by the bio-oil components. In order to study the chemical mechanisms of catalytic hydroprocessing of bio-oil, three model compounds were chosen to represent those components. Guaiacol represents the large number of mono- and di-methoxy phenols found in bio-oil derived from softwood or hardwood, respectively. Furfural represents a major pyrolysis product group from cellulosics. Acetic acid is a major product from biomass pyrolysis, derived from the hemicellulose, which has important impacts on the further processing of the bio-oil because of the acidic character. These three compounds were processed using palladium or ruthenium catalyst over a temperature range from 150C to 300C. The batch reactor was sampled during each test over a period of four hours. The samples were analyzed by gas chromatography with both a mass selective detector and a flame ionization detector. The products were determined and the reaction pathways for their formation are suggested based on these results. Both temperature and catalyst metal have significant effects on the product composition.
2009. "A Dianionic Phosphorane Intermediate and Transition States in an Associative AN+DN Mechanism for the RibonucleaseA Hydrolysis Reaction." Journal of the American Chemical Society 131(11):3869-3871. doi:10.1021/ja807940y Abstract The ubiquitous presence of phosphoryl transfer as central step in many metabolic, signaling, energy storage, etc. enzymatic reactions requires that the details of the reaction mechanisms (e.g. reaction paths, transition state stabilization and structure, etc.) that leads to their remarkable rates in protein catalytic environments be understood1. It is expected that most of these reactions proceed through a pathway that includes a penta- coordinated phosphorane species. However, the nature of the bonding and the protonation of the structure in this region and the possibility of stable intermediates as the system passes along the reaction path through the transitions state (TS) are currently topics of considerable debate1a,b,c. Typically nucleophilic substitution reactions are classified in terms of extremes of two bonding situations along the reaction path: in a dissociative mechanism the substrate phosphate bridging bond is broken and the bond to the entering nucleophilic group is not yet formed leaving a metastable metaphosphate (PO3−) intermediate (a DN+AN reaction); in an associative mechanism in the extreme case a metastable pentacoordinated phosphorane species with nearly equivalent bonds is present in the TS, whose subsequent dissociation leads to the product state (an AN+DN reaction). Recently we published a computational study of the phosphoryl transfer step of a major class of enzymes, the serine kinases2a,b involved in signal transduction. These calculations2b support a dissociative mechanism (DNAN,) for this family of enzymes with unstable metaphosphate structure in loose transition state with total bond order of 22%.
2009. "A Dianionic Phosphorane Intermediate and Transition States in an Associative AN+DN Mechanism for the RibonucleaseA Hydrolysis Reaction." Journal of the American Chemical Society 131(11):3869-3871. doi:10.1021/ja807940y Abstract The RNaseA enzyme efficiently cleaves phosphodiester bonds in the RNA backbone. Phosphoryl transfer plays a central role in many biochemical reactions, and this is one of the most studied enzymes. However, there remains considerable controversy about the reaction mechanism. Most of this debate centers around the roles of the conserved residues, structures of the transition state or states, the possibility of a stable intermediate, and the charge and structure of this intermediate. In this communication we report calculations of the mechanism of the hydrolysis step in this reaction using a comprehensive QM/MM theoretical approach that includes a high level calculation of the interactions in the QM region, free energy estimates along an NEB optimized reaction path, and the inclusion of the interaction of the protein surroundings and solvent. Contrary to prior calculations we find a stable pentacoordinated dianionic phosphorane intermediate in the reaction path supporting an AN+DN reaction mechanism. In the transition state in the path from the reactant to the intermediate state (with barrier of 3.96 kcal/mol and intermediate stability of 2.21 kcal/mol) a proton from the attacking water is partially transferred to the His119 residue and the PO bond only partially formed from the remaining nucleophilic OH− species (bond order (BO) 0.11). In passing from the intermediate to the product state (barrier 13.22 kcal/mol) the PO bond on the cyclic phosphorane intermediate is nearly broken (BO 0.28) and the transfer of the proton from the Lys41 is almost complete (Lys41-H BO 0.87). In the product state a proton has been transferred from Lys41 to the O2′ position of the sugar. The role of Lys41 as the catalytic acid is a result of the relative positioning of the Lys41 and His12 in the catalytic site. This configuration is supported by calculations and docking studies.
2009. "Engineering Performance in TCO Films for Energy Applications." ECS Transactions 19(18): 29-42. doi:10.1149/1.3246846 Abstract Thin film materials that exhibit both good electrical conductivity and high transparency owe this duality to careful control of the chemical state of the constituents and the attendant structure. Through manipulation of deposition conditions n- or p-type semi-conducting oxide films readily can be prepared. Such films enable the performance of energy conversion devices and promote development of architectural elements including smart energy efficient windows. This paper summarizes current TCO research trends, reviews processing approaches, and offers guidelines for engineering high performance TCO films. Also provided is a glimpse of optical engineering approaches where impedance matching and quantum mechanical tunneling offer alternative avenues to further improvement of film properties.