Effect of side chain length on the morphology of blends of 2,5‐bis(3‐alkylthiophen‐2‐yl)thieno[3,2‐b]thiophene oligomers and fullerene derivatives

Using molecular dynamics simulations we study blends of oligomers of 2,5‐bis(3‐alkylthiophen‐2‐yl)thieno[3,2‐b]thiophene, BTTT, and fullerene derivative based acceptors to understand the role of oligomer length and alkyl side chain (SC) length on the morphology of their blends. We use a validated coarse‐grained model of BTTT and fullerene derivatives presented in recent work along with direct comparison of morphology between simulations and experiments. In this article, we predict computationally that short alkyl SCs (6 alkyl groups) decrease the propensity of fullerene derivative acceptors to intercalate between SCs on the BTTT backbone compared to longer alkyl SCs (9 or 12 alkyl groups), and as a result increase acceptor aggregation. The decreasing acceptor intercalation and increasing acceptor aggregation do not significantly impact the positional or orientational order of the BTTT backbones. However, the BTTT oligomer backbones order better with increasing SC length in both neat systems and in blends, with the blends exhibiting higher positional order than neat systems. While these qualitative trends are similar both in 2mer blends and 4mer blends, we see a larger extent of acceptor intercalation and as a result, smaller acceptor cluster sizes in the 4mer blends. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016 , 54, 89–97     

The use of tunable diode laser absorption spectroscopy for rapid measurements of the δ13C of animal breath for physiological and ecological studies

In this study we introduce the use of tunable diode laser absorption spectroscopy (TDLAS) as a technique for making measurements of the δ¹³C of animal ‘breath’ in near real time. The carbon isotope ratios (δ¹³C) of breath CO₂ trace the carbon source of the materials being metabolized, which can provide insight into the use of specific food resources, e.g. those derived from plants using C₃ versus C₄ or CAM photosynthetic pathways. For physiological studies, labeled substrates and breath analyses provide direct evidence of specific physiological (e.g. fermentative digestion) or enzymatic (e.g. sucrase activity) processes. Although potentially very informative, this approach has rarely been taken in animal physiological or ecological research. In this study we quantify the utilization of different plant resources (photosynthetic types – C₃ or C₄) in arthropod herbivores by measuring the δ¹³C of their ‘breath’ and comparing it with bulk tissue values. We show that breath δ¹³C values are highly correlated with bulk tissues and for insect herbivores reflect their dietary guild, in our case C₃‐specialists, C₄‐specialists, or generalists. TDLAS has a number of advantages that will make it an important tool for physiologists, ecologists and behaviorists: it is non‐invasive, fast, very sensitive, accurate, works on animals of a wide range of body sizes, per‐sample costs are small, and it is potentially field‐deployable. Copyright © 2009 John Wiley & Sons, Ltd.     

A solver for the stochastic master equation applied to gene regulatory networks

An important driver of gene regulatory networks is noise arising from the stochastic nature of interactions of genes, their products and regulators. Thus, such systems are stochastic and can be modelled by the chemical master equations. A major challenge is the curse of dimensionality which occurs when one attempts to integrate these equations. While stochastic simulation techniques effectively address the curse, many repeated simulations are required to provide precise information about stationary points, bifurcation phenomena and other properties of the stochastic processes. An alternative way to address the curse of dimensionality is provided by sparse grid approximations. The sparse grid methodology is applied and the application demonstrated to work efficiently for up to 10 proteins. As sparse grid methods have been developed for the approximation of smooth functions, a variant for infinite sequences had to be developed together with a multiresolution analysis similar to Haar wavelets. Error bounds are provided which confirm the effectiveness of sparse grid approximations for smooth high-dimensional probability distributions.     

Oxidative coupling of bromo- and iodo-ferulic acid derivatives: synthesis of (±)-veraguensin

The phenolic coupling of halogen-containing ferulic acid and methyl ester derivatives was examined with particular reference to the synthesis of lignans of the aryltetralin and tetrahydrofuran classes. (±)-Isolariciresinol dimethyl ether (18) and (±)-veraguensin (27) have been synthesized.     

Contrasting photochemical and thermal reactivity of Ru(CO)2(PPh3)(dppe) towards hydrogen rationalised by parahydrogen NMR and DFT studies

The synthesis, characterisation and thermal and photochemical reactivity of Ru(CO)2(PPh3)(dppe) 1 towards hydrogen are described. Compound proved to exist in both fac (major) and mer forms in solution. Under thermal conditions, PPh3 is lost from 1 in the major reaction pathway and the known complex Ru(CO)2(dppe)(H)2 2 is formed. Photochemically, CO loss is the dominant process, leading to the alternative dihydride Ru(CO)(PPh3)(dppe)(H)2 3. The major isomer of 3, viz. 3a, contains hydride ligands that are trans to CO and trans to one of the phosphorus atoms of the dppe ligand but a second isomer, 3b, where both hydride ligands are trans to distinct phosphines, is also formed. On the NMR timescale, no interconversion of 3a and 3b was observed, although hydride site interchange is evident with activation parameters of DeltaH(double dagger) = 95 +/- 6 kJ mol(-1) and DeltaS(double dagger) = 26 +/- 17 J K(-1) mol(-1). Density functional theory confirms that the observed species are the most stable isomeric forms, and suggests that hydride exchange occurs via a transition state featuring an eta2-coordinated H2 unit.     

Ruthenium vinylidene and carbyne complexes containing a multifunctional tridentate ligand with a PNN donor set

The neutral, octahedral ruthenium vinylidene complexes mer,trans-[(PNN)Cl₂Ru(CCHR)] (PNN = N-(2-diphenylphosphinobenzylidene)-2-(2-pyridyl)ethylamine; R = Ph, 1a; R = ^tBu, 1b) are reported. An X-ray crystallographic study of 1a confirms the tridentate, meridional coordination mode of the PNN ligand. Compounds 1a and 1b undergo regioselective electrophilic addition with HBF₄ · Et₂O at C_β of the vinylidene ligand at low temperatures, and are cleanly and quantitatively converted to the ruthenium carbynes mer,trans-[(PNN)Cl₂Ru(CCH₂R)][BF₄] (R = Ph, 2a; R = ^tBu, 2b). Carbynes 2a and 2b are stable only at low temperatures (<−50 °C). Complex 1a undergoes ligand substitution with L to yield mer,trans-[(PNN)Cl₂Ru(L)] (L = MeCN, 3a; L = CO, 3b).     

A metabonomic analysis of plasma from Zucker rat strains using gas chromatography/mass spectrometry and pattern recognition

Plasma obtained from three strains of Zucker rats was analysed using capillary gas chromatography/mass spectrometry (GC/MS) to obtain global metabolite profiles as part of a series of metabonomic investigations of animal models of diabetes. Samples were obtained from 20-week-old male wild-type Zucker lean, (fa/fa) obese and lean/(fa) animals and were analysed following protein precipitation, using acetonitrile, and derivatisation. Subsequent data analysis using principal components analysis (PCA) and orthogonal projection to latent structures (OPLS) revealed differences between the plasma metabolite profiles of the three strains, with those of the Zucker lean and the lean/(fa) crosses being similar to each other whilst differing from the (fa/fa) obese strain.