Avoiding negative populations in explicit Poisson tau-leaping

The explicit tau-leaping procedure attempts to speed up the stochastic simulation of a chemically reacting system by approximating the number of firings of each reaction channel during a chosen time increment tau as a Poisson random variable. Since the Poisson random variable can have arbitrarily large sample values, there is always the possibility that this procedure will cause one or more reaction channels to fire so many times during tau that the population of some reactant species will be driven negative. Two recent papers have shown how that unacceptable occurrence can be avoided by replacing the Poisson random variables with binomial random variables, whose values are naturally bounded. This paper describes a modified Poisson tau-leaping procedure that also avoids negative populations, but is easier to implement than the binomial procedure. The new Poisson procedure also introduces a second control parameter, whose value essentially dials the procedure from the original Poisson tau-leaping at one extreme to the exact stochastic simulation algorithm at the other; therefore, the modified Poisson procedure will generally be more accurate than the original Poisson procedure.     

How to Control the Chemoselectivity of the Catalytic Formation of Chiral γ-Lactams or 2,3-Disubstituted Pyrroles by the Choice of Solvent

Summary. The reaction of the unsaturated imine methyl(3-phenylallylidene)amine with ethylene and carbon monoxide in the presence of catalytical amounts of Ru₃(CO)₁₂ leads to the formation of two heterocyclic products. One of the products is a chiral γ-lactam, the other one a 2,3-disubstituted pyrrole derivative, in which only the carbon atom from carbon monoxide is incorporated. The selectivity in the formation of the products may be controlled by the choice of solvent. In general, in nonpolar solvents the formation of the lactam is preferred whereas the use of more polar solvents enhances the yield of the pyrrole. For most of the solvents used there is a linear dependence of the product ratio on the relative permittivity of the corresponding solvent. Typically, polar aprotic solvents do not follow this rule.     

IN VIVO CHLOROPHYLL a FLUORESCENCE TRANSIENTS AND THE CIRCADIAN RHYTHM OF PHOTOSYNTHESIS IN GONYAULAX POLYEDRA

Abstract— The intensity of chlorophyll a fluorescence during the early part of fluorescence induction at O , initial fluorescence, and P, peak fluorescence, was higher during the day phase of the circadian cycle than during the night phase in continuous light (LL) conditions and was positively correlated with the rate of oxygen evolution. The circadian rhythm in fluorescence in LL persisted in the presence of 10μM 3–(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU), which blocks electron flow from photo-system (PS) II in photosynthesis. The rhythmic changes in fluorescence intensity are consistent with a lower rate constant for radiationless transitions during the day phase than during the night phase of the circadian rhythmicity. The circadian changes in the intensity of fluorescence were abolished at 77K, which may indicate the importance of structural changes in membranes in circadian oscillations.     

Characterization and transport properties of Nafion/polyaniline composite membranes

Nafion membranes were modified by chemical polymerization of aniline using ammonium peroxodisulfate as the oxidant. The Nafion-polyaniline composite membranes were extensively characterized using scanning electron microscopy (SEM), atomic force microscopy (AFM), infrared (FTIR-ATR) and X-ray photoelectron spectroscopy (XPS), thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), and ion-exchange capacity measurements. The transport properties were also evaluated by conductivity and electrodialysis measurements. The data show that when a high oxidant concentration (1 M (NH4)2S2O8) is used, polyaniline is mostly formed at the surface of the Nafion membrane with a higher proportion of oligomers. On the contrary, when 0.1 M oxidant is used, polyaniline is mostly formed inside the ionic domains of Nafion, blocking the pathway to ion transport and thus reducing the transport of Zn2+ as well as the transport of H+. These data were also compared to the data obtained with poly(styrene sulfonate)-PANI composite membranes.     

Synthesis of [4.2]cyclophanes

Vinyl $\text{p}$-xylylene cross-dimerizes with other xylylene-type intermediates to yield cycloadducts of the [8+6] and [6+6] type. This reaction provides a simple entry to the [4.2]paracyclophane system as well as the analogous [4.2]cyclophanes containing furan and pyrrole moieties.     

New aspects of the protonation of biliverdins

Biliverdins undergo appreciable self association in acidic solutions especially if solvents like benzene or chloroform are employed. The population of aggregates further depends on the concentration of both the acid and the solute. In chloroform and benzene solutions at high acidity a doubly protonated species is formed. This is concluded from a combinatory evaluation of the CD and electronic absorption spectra of chiral optically active biliverdins (1–6) in benzene, chloroform, and ethanol solutions containing trifluoroacetic acid or hydrochloric acid. The aggregates formed at medium acid concentrations exhibit largeCotton effects in the long-wavelength absorption bands and thus dominate the CD spectra. Similarly, agrregates are the main contributors to theCotton effects of achiral, protonated biliverdins in (S)-(–)-ethyl lactate (SICD) at usual concentrations. The consequence and relevance of these findings with regard to the recent literature is briefly discussed.Dedicated to Prof. Dr.Karl Schlögl on occasion of his 60^th birthday.     

New dehydration in the pyrrolo[1,2–6-b]isoquinoline series. Preparation and structural identification of 3,5-dihydrobenz[f]indolizin-3-one

3,5-Dihydrobenz[f]indolizin-3-one was prepared by a novel dehydration reaction involving the heating of 1,2,3,5,10,10a-hexahydro[f]indolizine-3,10-dione with polyphosphoric acid. The structure of this new compound was established by X-ray crystallography, by nmr spectroscopy and by reduction to the known products 1,2,3,5-tetrahydrobenz[f]indolizin-3-one and 1,2,3,5,10,10a-hexahydrobenz[f]indolizin-3-one.     

Surface enrichment of proteins at quartz/water interfaces: a neutron reflectivity study

Neutron reflectivity (NR) was used to study the adsorption of human serum albumin and human fibrinogen on quartz. The proteins were individually and sequentially adsorbed from heavy water and heavy water/methanol mixtures at pH 4 and 7.0. The technique allows for the subnanometer resolution of the adsorbed layer thickness and gross morphology. Under the conditions of our measurements we found that fibrinogen formed a distinct layer that we interpret as a mat of the protein three layers thick whereas albumin formed only diffuse layers. The adsorption pattern of the two proteins changed radically when one protein was adsorbed on top of the other (previously adsorbed). In general our measurements indicate that the adsorbed protein layers on quartz are rather loosely bound and that these layers, incorporating as much as 80% water, extend further into the bulk fluid than might have been expected.     

Intermediates in the Dehydrogenation of Hydroaromatic Compounds with Quinones

Dehydrogenation of hydroaromatic compounds with quinones was reinvestigated in the light of recent criticism of the reaction mechanism. Kinetic and spectroscopic evidence shows that disappearance of substrate proceeds at the same rate as the product-forming step. A mechanism consisting in fast formation followed by slow decomposition of an intermediate can be ruled out. The order of reactivities of 1,4-cyclohexadiene ( 1 ), 1,4-dihydronaphthalene ( 8 ) and 9,10-dihydroanthracene ( 11 ) changes in going from benzoquinone to chloranil or 2,3-dichloro-5,6-dicyanobenzoquinone. It is suggested that this behaviour could be due to contribution of CT-complexes or HOMO-LUMO interactions for determining the reactivity of the substrates.     

Selective Si--C bond cleavage as synthetic entry to a functionalized lithiosilane

Treatment of the phenyl-substituted silane 4 with lithium metal afforded the functionalized lithiosilane rac-2 by selective cleavage of one Si-C bond between silicon and a phenyl group. The resulting lithiosilane rac-2 crystallizes as the dimer (2.THF)2, which represents the first example of a dimeric organyl-substituted lithiosilane in the presence of THF.