Pentopyranosyl Oligonucleotide Systems. 9th Communication

Pyranosyl‐RNA (‘p‐RNA’ ) is an oligonucleotide system isomeric to natural RNA and composed of the very same building blocks as RNA. Its generational, chemical, and informational properties are deemed to be those of an alternative nucleic acid system that could have been a candidate in Nature's evolutionary choice of the molecular basis of genetic function. We consider the study of the chemistry of p‐RNA as etiologically relevant in the sense that knowledge of its structural, chemical, and informational properties on the chemical level offers both a perspective and reference points for the recognition of specific structural assets of the RNA structure that made it the (supposedly) superior system among possible alternatives and, therefore, the system that became part of biology as we know it today. The paper describes the chemical synthesis of β‐d‐ (and L )‐ribopyranosyl‐(4′→2′)‐oligonucleotide sequences, presents a resume of their structural and chemical properties, and cautiously discusses what we may and may not have learned from the pyranosyl isomer of RNA with respect to the conundrum of RNA's origin.     

Synthesis and structure of a stabilized 10-membered cyclic enediyne

The synthesis and structure of an acetal protected 10-membered cyclic enediyne-1,2-diol rac-10 is reported. The conformational constrain of the unsaturated macrocycle by the acetal protection group prevents the thermal cyclization reaction of the endiyne during synthesis and purification.     

Rotational fluctuations of water inside the nanopores of SBA-type molecular sieves

The rotational molecular dynamics of water confined to nanoporous molecular sieves of a regular hexagonal (SBA-15) and of a foamlike pore structure was studied by dielectric spectroscopy in the frequency range from 10(-2) to 10(9) Hz and in a broad temperature interval. Two relaxation processes were observed: the process at lower frequencies is related to water molecules forming a layer, which is strongly adsorbed at the pore surface, whereas the relaxation process at higher frequencies is assigned to fluctuations of water molecules situated close to the center of the pore. The relaxation times of the low-frequency process for both materials and of the high-frequency process for the SBA-15 material have an unusual saddlelike temperature dependence, reported here for the first time. To describe this temperature dependence, a model developed for water confined to nanoporous glasses by Ryabov et al. [J. Phys. Chem. B 2001, 105, 1845] was applied, which considers two competing effects. The characteristic features of these two competing processes were compared with those reported for other porous systems.     

Chemie von α-Aminonitrilen. 13. Mitteilung. Über die Bildung von 2-Oxoethyl-phosphaten (“Glycoladehyd-phosphaten”) aus rac-Oxirancarbonitril und anorganischem Phosphat und über (formale) Konstitutionelle Zusammenhänge zwischen 2-Oxoethyl-phosphaten und Oligo (hexo- und pentopyranosyl)nucleotid-Rückgraten

Chemistry of α-Aminonitriles. Formation of 2-Oxoethyl Phosphates (“Glycolaldehyde Phosphates”) from rac-Oxiranecarbonitrile and on (Formal) Constitutional Relationships between 2-Oxoethyl Phosphates and Oligo(hexo- and pentopyranosyl)nucleotide Backbones Oxiranecarbonitrile in basic acqueous solution at room temperature reacts regioselectively with inorganic phosphate to give the cyanohydrin of 2-oxoethyl phosphate (“glycolaldehyde phosphate”), a source of (the hydrate of) the free aldehyde, preferably in the presence of formaldehyde. In aqueous phosphate solution buffered to nearly neutral pH, oxiranecarbonitrile produces the phosphodiester of glycoladehyde as its bis-cyanohydrin in good yield. In contrast to mono- and dialkylation, trialkylation of phosphate with oxiranecarbonitrile is difficult, and the triester derivative is highly sensitive to hydrolysis. Glycolaldehyde phosphate per se is of prebiotic interest, since it had been shown [5] to aldomerize in basic aqueous solution regioselectively to rac-hexose 2, 4, 6-triphosphates and – in the presence of formaldehyde - mainly to rac-pentose 2, 4-diphosphates with, under appropriate conditions, rac-pentose 2, 4-diphosphates as the major reaction product. However, the question as to whether oxiranecarbonitrile itself has the potential of having been a prebiological natural constituent remains unanswered. Backbone structures of hexopyranosyl-oligonucleotides with phosphodiester linkages specifically between the positions 6′ → 4′, 6′ → 2′, or 4′ → 2′ of the sugar residues can formally be derived via the (hypothetical) aldomerization pathway, a combinatorial intermolecular aldomerization of glycoladehyde phosphate and bis(glycolaldehyde)-phosphodiester in a 1: 1 ratio. The constitutional relationships revealed by this synthetic analysis has played a decisive role as a selection criterion in the pursuit of our experimental studies toward a chemical etiology of the natural nucleic acids' structure. The Discussion in this paper delineates how the analysis contributed to the conception of the structure of p-RNA. The English Footnotes to Schemes 1–11 provide an extension of this summary.     

Electrochemical behavior of silver thin films interfaced with yttria-stabilized zirconia

Thin silver films (100–800 nm) were deposited by physical vapor deposition (PVD) on yttria-stabilized zirconia solid electrolyte. The electric percolation as a function of the film thickness was studied during deposition and annealing using a two-electrode in-situ resistance measurement technique. Electrical percolation was achieved in as-deposited films greater than 5.4?±?0.4 nm; however, thermal treatment (550 °C in air) resulted in film dewetting for Ag films as thick as 500 nm and formation of electronically isolated Ag nanoparticles, as was confirmed by SEM and XPS. In thermally treated samples, stable electronic conductivity associated with a continuous percolated network was only observed in samples greater than 600 nm in thickness. The effect of polarization on the electrochemical reactions at the three-phase (electrode-gas-electrolyte) and two-phase (electrode-electrolyte) boundaries of the electrode was investigated by solid electrolyte cyclic voltammetry (SECV) at 350 °C and P _O2?=?6 kPa. With the application of positive potential, silver oxide (Ag₂O) was found to form along the three-phase boundary and then extends within the bulk of the electrode with increasing anodic potentials. By changing the hold time at positive potential, passivating oxide layers are formed which results in a shift in favor of the oxygen evolution reaction at the working electrode. This oxide forms according to a logarithmic rate expression with thick oxides being associated with decrease in current efficiency for subsequent oxide formation.     

A consistent LES/filtered-density function formulation for the simulation of turbulent flames with detailed chemistry

A hybrid large-Eddy simulation/filtered-density function (LES–FDF) methodology is formulated for simulating variable density turbulent reactive flows. An indirect feedback mechanism coupled with a consistency measure based on redundant density fields contained in the different solvers is used to construct a robust algorithm. Using this novel scheme, a partially premixed methane/air flame is simulated. To describe transport in composition space, a 16-species reduced chemistry mechanism is used along with the interaction-by-exchange with the mean (IEM) model. For the micro-mixing model, typically a constant ratio of scalar to mechanical time-scale is assumed. This parameter can have substantial variations and can strongly influence the combustion process. Here, a dynamic time-scale model is used to prescribe the mixing time-scale, which eliminates the time-scale ratio as a model constant. Two different flame configurations, namely, Sandia flames D and E are studied. Comparison of simulated radial profiles with experimental data show good agreement for both flames. The LES–FDF simulations accurately predict the increased extinction near the inlet and re-ignition further downstream. The conditional mean profiles show good agreement with experimental data for both flames.     

Adjoint sensitivity analysis of kinetic,thermochemical, and transport data of nitrogen and ammonia chemistry

Many studies apply sensitivity analysis to explore the impact of reaction kinetic parameters on model predictions. The importance of thermochemical and transport data is often assumed to be relatively low. While this is true for specific combustion properties of hydrocarbons, the role of thermochemical and transport data in combustion processes of nitrogen-containing molecules remains to be investigated. Thus, this work applies adjoint sensitivity analysis to the complete set of parameters in combustion models, i.e., kinetics, thermodynamics, and transport data. This integral approach increases the number of parameters considered in the sensitivity analysis drastically. Compared to forward sensitivity analysis, the adjoint approach is very efficient for a large number of parameters, and analysis with several thousand parameters can be performed in seconds. Nitrogen oxide formation in methane/air flames and laminar burning velocities of ammonia/air flames are considered as prediction targets. Sensitivity analysis results for kinetic, thermochemical, and transport data are compared by jointly considering all appearing parameter uncertainties. The comparison reveals that, due to their importance for the equilibrium constants of elementary reactions, the optimization potential of thermodynamic properties is often similarly high as that of the kinetics parameters. Transport parameters are found to be of the lowest priority for the model development due to their low uncertainties, even though high sensitivities are determined for several of them. More specifically, the analysis for the laminar burning velocities of ammonia/air flames reveals a high optimization potential for parameters in the N₂-amine chemistry, including the molar heat capacities of N₂H₂, N₂H₃, and NH. Interestingly, analyses with different mechanisms reveal strongly diverging results, especially regarding the importance of reactions with OH, which is uncommon when considering the combustion of hydrocarbons.     

Highly radiating hydrogen flames: Effect of toluene concentration and phase

Adapting hydrogen as a carbon-free fuel for industrial applications requires new, innovative approaches, especially when radiant heat transfer is required. One possible option is to dope hydrogen with bio-oils, containing aromatics that help produce highly sooting flames. This study investigates the potential doping effects of toluene on a hydrogen-nitrogen (1:1 vol) flames. Flames with 1–5% toluene, based on the mole concentration of hydrogen, are measured using a combination of techniques including: still photographs and laser-based techniques. Toluene was mixed with hydrogen-nitrogen fuel mixture as either a vapour carried by nitrogen, or as a dilute spray. Spray flames are found to produce substantially more polycylic aromatic hydrocarbons, with significantly more soot near the nozzle exit plane, than the prevaporised flames. Increasing the dopant concentration from 1 to 3% of the hydrogen has a marked effect on soot loading in the flame, although the further increasing the dopant concentration to 5% has a far smaller effect on the soot produced in the flame. Simulations of laminar flames using detailed chemical kinetics support the above findings and reveal details of the competition between soot precursor formation and hydrocarbon oxidation. Correlations of formation rates are non-linear with toluene concentration in cases where toluene represents less than 10% of the fuel, although expected linear relationships are noted beyond this regime up to 1:1 toluene/hydrogen blends. The study provides insight and explanation into effects of toluene as a dopant, comparison between flame doping in gaseous or liquid phases and suggests that flame doping and blending should be treated as different regimes for their global effect on flame sooting characteristics.