Spray flame dynamics with oscillating flow and droplet grouping

The co-flow laminar spray diffusion flame in an oscillating flow field is investigated. Mild slip is permitted between the droplets and their host surroundings and droplet grouping resulting from the host flow oscillations is accounted for. The spray is modelled using the sectional approach and a perturbation analysis using a small sectional Stokes number is utilised for solving the liquid phase governing equations. The effect of droplet grouping is described through a specially constructed model for the vaporisation Damkohler number. The large chemical Damkohler number assumption is adopted and a formal analytical solution is developed for Schwab-Zeldovitch parameters through which the dynamics of the spray flame front shapes and thermal fields are deduced. Computed results based on the solutions demonstrate how the phenomenon of droplet grouping can lead to the existence of multiple flame sheets as a result of the dynamic change in the type of the main homogeneous flame from under- to over-ventilated as the flow field oscillates. Concomitant fluctuating thermal fields are also shown to be present indicating a potential impact on undesirable pollutants production.     

Synthesis and analysis of oligonucleotides containing abasic site analogues

DNA damage results in the formation of abasic sites from the formal hydrolysis of the glycosidic bond (AP) and several oxidized abasic lesions. Previous studies on AP sites revealed that DNA polymerases preferentially incorporated dA opposite them in approximately 80% of the replication events in Escherichia coli. These results were consistent with the hypothesis that the AP sites are noninstructive lesions due to the absence of a Watson-Crick base whose bypass adheres to the "A-rule." Recent replication studies of the oxidized abasic lesion, 2-deoxyribonolactone (L), revealed that DNA polymerase(s) does not apply the A-rule when bypassing it and incorporates large amounts of dG opposite L. These studies suggested that abasic sites such as L do direct polymerases to selectively incorporate nucleotides opposite them. However, it was not possible to determine the structural basis for this molecular recognition from these experiments. A group of oligonucleotides containing analogues of the AP and L lesions were synthesized and characterized as probes to gain insight into the structural basis for the distinct effect of 2-deoxyribonolactone on replication. These molecules will be useful tools for studying replication in cells and in vitro.     

Highly efficient antibody-catalyzed deuteration of carbonyl compounds

Antibody 38C2 efficiently catalyzes deuterium-exchange reactions at the alpha position of a variety of ketones and aldehydes, including substrates that have a variety of sensitive functional groups. In addition to the regio- and chemoselectivity of these reactions, the catalytic rates (kcat) and rate-enhancement values (kcat/kun) are among the highest values ever observed with catalytic antibodies. Comparison of the substrate range of the catalytic antibody with highly evolved aldolase enzymes, such as rabbit-muscle aldolase, highlights the much broader practical scope of the antibody, which accepts a wide range of substrates. The hydrogen-exchange reaction was used for calibration and mapping of the antibody active site. Isotope-exchange experiments with cycloheptanone reveal that the formation of the Schiff base species (as concluded from the 16O/18O exchange rate at the carbonyl oxygen) is much faster than the formation of the enamine intermediate (as concluded from the H/D exchange rate), and both steps are faster than the antibody-catalyzed aldol addition reaction.     

Stereoselective C-X and regioselective C-H activation to,and selective C(sp2)-C(sp3) reductive elimination from,platinum compounds with thiophene-derived ligands

Several thiophene-based N^C ligands were synthesized. Strategically, a bromide was incorporated on the 2-position of the thiophene ring. When allowed to react with the platinum tetramethyl dimer, [Pt₂Me₄(µ-SMe₂)₂], platinum(IV) platinacycles were formed by oxidative addition of the C(sp²)-X bond. These platinum(IV) compounds were characterized by NMR and HRMS. The platinum (IV) compounds were subsequently subjected to thermolysis. A series of reactions occurred, including selective C-C reduction elimination and selective C-H oxidative addition, giving mixtures of platinum(II) products with varying degrees of regioselectivity.     

Synthesis, DNA polymerase incorporation, and enzymatic phosphate hydrolysis of formamidopyrimidine nucleoside triphosphates

The nucleoside triphosphates of N6-(2-deoxy-alpha,beta-d-erythro-pentofuranosyl)-2,6-diamino-4-hydroxy-5-formamidopyrimidine (Fapy.dGTP) and its C-nucleoside analogue (beta-C-Fapy.dGTP) were synthesized. The lability of the formamide group required that nucleoside triphosphate formation be carried out using an umpolung strategy in which pyrophosphate was activated toward nucleophilic attack. The Klenow fragment of DNA polymerase I from Escherichia coli accepted Fapy.dGTP and beta-C-Fapy.dGTP as substrates much less efficiently than it did dGTP. Subsequent extension of a primer containing either modified nucleotide was less affected compared to when the native nucleotide is present at the 3'-terminus. The specificity constants are sufficiently large that nucleoside triphosphate incorporation could account for the level of Fapy.dG observed in cells if 1% of the dGTP pool is converted to Fapy.dGTP. Similarly, polymerase-mediated introduction of beta-C-Fapy.dG could be useful for incorporating useful amounts of this nonhydrolyzable analogue for use as an inhibitor of base excision repair. The kinetic viability of these processes is enhanced by inefficient hydrolysis of Fapy.dGTP and beta-C-Fapy.dGTP by MutT, the E. coli enzyme that releases pyrophosphate and the corresponding nucleoside monophosphate upon reaction with structurally related nucleoside triphosphates.     

Biologically Relevant Molecular Transducer with Increased Computing Power and Iterative Abilities

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