Unimolecular reactions of the resonance-stabilized cyclopentadienyl radicals and their role in the polycyclic aromatic hydrocarbon formation

Resonance-stabilized cyclopentadienyl radicals are important intermediate species in the combustion of transportation fuels. It not only serves as precursors for polycyclic aromatic hydrocarbon (PAH) formation, but also involves in the formation of fundamental PAH precursors such as propargyl and acetylene. In this work, the unimolecular reactions of the cyclopentadienyl radicals are theoretically studied based on high-level quantum chemistry and RRKM/master equation calculations. Stationary points on the potential energy surface (PES) are calculated at the CCSD(T)/CBS//M06–2X/6–311++(d,p) level of theory. The branching ratios of unimolecular reactions of the cyclopentadienyl radicals are analyzed for a broad temperature range from 500 to 2500 K and pressures from 0.01 to 100 atm. It is found that the isomerization reaction of the cyclopentadienyl radical via 1,2-hydrogen transfer dominates at low temperatures and high pressures, while the well-skipping decomposition reaction which forms propargyl and acetylene is important at high temperatures and low pressures. Both the decomposition reaction of the cyclopentadienyl radicals and its reverse reaction show pronounced pressure dependence, and their reaction rate constants are compared against available low-pressure experimental measurements and theoretical studies. The temperature- and pressure-dependent rate coefficients for important reactions involved on the C₅H₅ PES are calculated and updated in a chemical kinetic model. Impacts of the unimolecular reactions of the cyclopentadienyl radicals on the PAH formation are explored by the numerical modeling of a low-pressure cyclopentene counterflow diffusion flame.     

Eulerian transported probability density function sub-filter model for large-eddy simulations of turbulent combustion

Reactive flow simulations using large-eddy simulations (LES) require modelling of sub-filter fluctuations. Although conserved scalars like mixture fraction can be represented using a beta-function, the reactive scalar probability density function (PDF) does not follow an universal shape. A one-point one-time joint composition PDF transport equation can be used to describe the evolution of the scalar PDF. The high-dimensional nature of this PDF transport equation requires the use of a statistical ensemble of notional particles and is directly coupled to the LES flow solver. However, the large grid sizes used in LES simulations will make such Lagrangian simulations computationally intractable. Here we propose the use of a Eulerian version of the transported-PDF scheme for simulating turbulent reactive flows. The direct quadrature method of moments (DQMOM) uses scalar-type equations with appropriate source terms to evolve the sub-filter PDF in terms of a finite number of delta-functions. Each delta-peak is characterized by a location and weight that are obtained from individual transport equations. To illustrate the feasibility of the scheme, we compare the model against a particle-based Lagrangian scheme and a presumed PDF model for the evolution of the mixture fraction PDF. All these models are applied to an experimental bluff-body flame and the simulated scalar and flow fields are compared with experimental data. The DQMOM model results show good agreement with the experimental data as well as the other sub-filter models used.     

Generalised scale-by-scale energy-budget equations and large-eddy simulations of anisotropic scalar turbulence at various Schmidt numbers

A necessary condition for the accurate prediction of turbulent flows using large-eddy simulation (LES) is the correct representation of energy transfer between the different scales of turbulence in the LES. For scalar turbulence, transfer of energy between turbulent length scales is described by a transport equation for the second moment of the scalar increment. For homogeneous isotropic turbulence, the underlying equation is the well-known Yaglom equation. In the present work, we study the turbulent mixing of a passive scalar with an imposed mean gradient by homogeneous isotropic turbulence. Both direct numerical simulations (DNS) and LES are performed for this configuration at various Schmidt numbers, ranging from 0.11 to 5.56. As the assumptions made in the derivation of the Yaglom equation are violated for the case considered here, a generalised Yaglom equation accounting for anisotropic effects, induced by the mean gradient, is derived in this work. This equation can be interpreted as a scale-by-scale energy-budget equation, as it relates at a certain scale r terms representing the production, turbulent transport, diffusive transport and dissipation of scalar energy. The equation is evaluated for the conducted DNS, followed by a discussion of physical effects present at different scales for various Schmidt numbers. For an analysis of the energy transfer in LES, a generalised Yaglom equation for the second moment of the filtered scalar increment is derived. In this equation, new terms appear due to the interaction between resolved and unresolved scales. In an a-priori test, this filtered energy-budget equation is evaluated by means of explicitly filtered DNS data. In addition, LES calculations of the same configuration are performed, and the energy budget as well as the different terms are thereby analysed in an a-posteriori test. It is shown that LES using an eddy viscosity model is able to fulfil the generalised filtered Yaglom equation for the present configuration. Further, the dependence of the terms appearing in the filtered energy-budget equation on varying Schmidt numbers is discussed.     

A joint volume-surface model of soot aggregation with the method of moments

In this work, a bivariate model of soot aggregation is formulated within the framework of the Method of Moments with Interpolative Closure (MOMIC). In the bivariate model, soot particles are represented by two independent variables: their volume and surface area. This joint formulation also allows for the blending of aggregation and coalescence with the two as limits. The new formulation is compared to the old formulation with the univariate model as well as both the Direct Quadrature Method of Moments (DQMOM) and Direct Simulation Monte Carlo (DSMC) for a laminar premixed ethylene flame. With the bivariate model, MOMIC is shown to predict volume fraction and number density very accurately and gives some insight into the properties of the aggregates.     

On Facts and Artefacts: The Difficulty to Evaluate an Artificial Nuclease

A number of promising synthetic catalysts for the hydrolytic degradation of RNA have been developed in recent years. Some of them show remarkable selectivity for pyrimidine nucleotides. The general problem of all these studies is to distinguish between real effects and artefacts caused by traces of contaminating natural ribonucleases. We show that methods representing the current state of the art (diethylpyrocarbonate treatment, sterilization, ultrafiltration, etc.) do not sufficiently protect against severe artefacts. However, an incorruptible assay could be found by comparing the cleavage of RNA and its mirror image. Enantiomeric RNA is completely resistant to enzymatic degradation, whereas achiral nonpeptide catalysts, by fundamental laws of symmetry, cannot distinguish between enantiomers and will induce exactly the same cleavage pattern with both substrates.     

Herstellung und 29Si-NMR-Untersuchung von Polymeren mit definierten Kieselsäurebaueinheiten

Preparation and ²⁹Si NMR Spectroscopic Investigation of Polymers with Definite Silicic Acid Units Three polymers were synthesized by additive reaction of the cage-like double fourring (D4R) silicic acid derivatives [(CH₃)₂HSi]₈Si₈O₂₀ and [CH₂?CH(CH₃)₂Si]₈Si₈O₂₀ resp., with the unsaturated diviyltetramethyldisiloxane or the multiple functional tetramethylcyclotetrasiloxane and polymethylhydrogensiloxane in a molar ratio of functional groups 1:1. By means of ²⁹Si solid state NMR spectroscopy was shown that the in organic solvents insoluble polymers are built up by D4R silicic acid units, which are connected by chain-like or cyclic siloxane bridges. With increasing functional groups of the reactants the sterical hindrance of the reaction of D4R derivates grows. The polymers show small surfaces of 1 to 8 m²/g.     

Bicyclo[3.2.1]amide-DNA: a chiral,nonchiroselective base-pairing system

The design, synthesis, and base-pairing properties of bicyclo[3.2.1]amide-DNA (bca-DNA), a novel phosphodiester-based DNA analogue, are reported. This analogue consists of a conformationally constrained backbone entity, which emulates a B-DNA geometry, to which the nucleo-bases were attached through an extended, acyclic amide linker. Homobasic adenine-containing bca decamers form duplexes with complementary oligonucleotides containing bca, DNA, RNA, and, surprisingly, also L-RNA backbones. UV and CD spectroscopic investigations revealed the duplexes with D- or L-complements to be of similar stability and enantiomorphic in structure. Bca oligonucleotides that contain all four bases form strictly antiparallel, left-handed complementary duplexes with themselves and with complementary DNA, but not with RNA. Base-mismatch discrimination is comparable to that of DNA, while the overall thermal stabilities of bca-oligonucleotide duplexes are inferior to those of DNA or RNA. A detailed molecular modeling study of left- and right-handed bca-DNA-containing duplexes showed only minor changes in the backbone structure and revealed a structural switch around the base-linker unit to be responsible for the generation of enantiomorphic duplex structures. The obtained data are discussed with respect to the structural and energetic role of the ribofuranose entities in DNA and RNA association.     

An Efficient Synthesis of Enantiomeric Ribonucleic Acids from D-Glucose

Enantiomeric oligoribonucleotides (= ent-RNA) up to a sequence length of thirty-five and consisting of the (L -configurated) nucleosides ent-adenosine, ent-guanosine, ent-cytidine, ent-uridine, and 1-(β-L -ribofuranosyl)thymine were prepared by automated synthesis from appropriate building blocks, carrying a known photo-labile 2′-O-protecting group. A simple large-scale synthesis of the new, prefunctionalized L -ribose derivative 5 from D -glucose (Scheme 1) and its straightforward conversion into the five phosphoramidites 28 – 32 and five solid supports 38 – 42 , respectively, were elaborated (Scheme 4). Within this project, a novel, superior strategy for the synthesis of the 2′-O-{[(2-nitrobenzyl)oxy]methyl}-substituted key intermediates 18 – 22 by regioselective alkylation of their 5′-O-dimethoxytritylated precursors 13 – 17 was developed. Furthermore, an improved set-up for the final light-induced cleavage of the 2′-O-protecting groups from the oligonucleotide sequences was designed (Scheme 5 and Fig. 1). The correct composition of all ent-oligoribonucleotides prepared was established by their MALDI-TOF mass spectra. The ¹H-NMR-spectroscopic data of a dodecameric ent-RNA sequence was in excellent agreement with the published data of its natural counterpart, synthesized by conventional methods. The known specific cleavage of a tetradecamer sequence by a 35mer ribozyme structure could be reproduced by ent-oligoribonucleotides, synthesized by the presented methods (Fig. 4).     

Palladium complexes in concentrated nitrate and acid solutions

A spectrophotometric study of palladium complexation in concentrated nitrate and acid solutions is presented. The water activity of the solutions was fixed to control activity coefficients. The existence of the species PdNO(+)(3), Pd(NO(3))(2) and PdOHNO(3) has been evidenced and their stability was evaluated. An activity diagram for the predominance of soluble palladium species is presented and the precipitation limit is drawn.     

Synthesis of 2′‐O‐[(Triisopropylsilyl)oxy]methyl (= tom)‐Protected Ribonucleoside Phosphoramidites Containing Various Nucleobase Analogues

The first results of a study aiming at an efficient preparation of a large variety of 2′‐O‐[(triisopropylsilyl)oxy]methyl(= tom)‐protected ribonucleoside phosphoramidite building blocks containing modified nucleobases are reported. All of the here presented nucleosides have already been incorporated into RNA sequences by several other groups, employing 2′‐O‐tbdms‐ or 2′‐O‐tom‐protected phosphoramidite building blocks (tbdms = (tert‐butyl)dimethylsilyl). We now optimized existing reactions, developed some new and shorter synthetic strategies, and sometimes introduced other nucleobase‐protecting groups. The 2′‐O‐tom, 5′‐O‐(dimethoxytrityl)‐protected ribonucleosides N²‐acetylisocytidine 5 , O²‐(diphenylcarbamoyl)‐N⁶‐isobutyrylisoguanosine 8 , N⁶‐isobutyryl‐N²‐(methoxyacetyl)purine‐2,6‐diamine ribonucleoside (= N⁸‐isobutyryl‐2‐[(methoxyacetyl)amino]adenosine) 11 , 5‐methyluridine 13 , and 5,6‐dihydrouridine 15 were prepared by first introducing the nucleobase protecting groups and the dimethoxytrityl group, respectively, followed by the 2′‐O‐tom group (Scheme 1). The other presented 2′‐O‐tom, 5′‐O‐(dimethoxytrityl)‐protected ribonucleosides inosine 17 , 1‐methylinosine 18 , N⁶‐isopent‐2‐enyladenosine 21 , N⁶‐methyladenosine 22 , N⁶,N⁶‐dimethyladenosine 23 , 1‐methylguanosine 25 , N²‐methylguanosine 27 , N²,N²‐dimethylguanosine 29 , N⁶‐(chloroacetyl)‐1‐methyladenosine 32 , N⁶‐{{{(1S,2R)‐2‐{[(tert‐butyl)dimethylsilyl]oxy}‐1‐{[2‐(4‐nitrophenyl)ethoxy]carbonyl}propyl}amino}carbonyl}}adenosine 34 (derived from L ‐threonine) and N⁴‐acetyl‐5‐methylcytidine 36 were prepared by nucleobase transformation reactions from standard, already 2′‐O‐tom‐protected ribonucleosides (Schemes 2–4). Finally, all these nucleosides were transformed into the corresponding phosphoramidites 37 – 52 (Scheme 5), which are fully compatible with the assembly and deprotection conditions for standard RNA synthesis based on 2′‐O‐tom‐protected monomeric building blocks.