Kinetics of transient end-to-end contact of single-stranded DNAs

The formation of the pyrene (Py) dimer radical cation (Py(2)(*+)) was used to measure the kinetics of the intrastrand end-to-end contact rates of single-stranded DNAs (ssDNAs) in the 10 nanoseconds to the tens of microseconds time range. ssDNAs labeled with Py at both ends with the lengths of 3, 6, and 9 mer were synthesized, and the two-photon ionization method was employed to generate a Py(*+), which enables the measurements of the end-to-end contact rates from 10 ns. The formation rate of Py(2)(*+) depended on the length and the sequence of the ssDNAs, and about 1 order of magnitude faster rates were observed for the T-rich ssDNAs compared to those for the corresponding length of A-rich ssDNAs, showing that ssDNA made from adenines is much more rigid than that composed of thymidines. As for the T-rich ssDNAs, the formation of Py(2)(*+) attributed to the misfolded structures was also observed, which is consistent with the configurational diffusion model suggested by Ansari and co-workers.     

1,1-bis(trimethylsilyl)-1-alkanols as silylcarbene equivalent

Silylcarbenes are generated by the pyrolysis of 1,1-bis(trimethylsilyl)-1-alkanols with elimination of trimethylsilanol.     

Studies of the polymerization of diallyl compounds. XXII. Polymerization of diallyl oxalate in the evolution of carbon dioxide at elevated temperatures

The polymerization of diallyl oxalate was conducted in the presence of radical initiators at a high temperature range of 80–180°C; a large decrease in degree of polymerization, an increase in residual unsaturation of the resulting polymer, and the evolution of carbon dioxide were observed with the elevation of temperature. These findings were reasonably interpreted by considering the dismutation of the uncyclized growing radical to yield the allyl radical, carbon dioxide, and polymer carrying a terminal double bond. The kinetics of the polymerization of diallyl oxalate in the evolution of carbon dioxide at elevated temperatures were also discussed in detail.     

Diffusion-controlled stress-relaxation in polymers,I

Summary The “chemical” relaxation of stress either in Amilan (6-Nylon) or polyvinyl alcohol caused by penetration of water vapor was studied at 40% R. H. and temperatures 15, 30, and 50° C. A theory was presented of the chemical relaxation in a polymer which comprises penetrant-sensitive bonds as the crosslinkages between the molecular chains. This theory assumes the diffusion coefficient of penetrant in the polymer to he independent of concentration and any other factors. It was found that the system Amilan-water behaves in exact conformity with the theory over the ranges of elongation and temperature studied. The diffusion coefficient,D, of water in Amilan could thus be evaluated from the chemical relaxation data, using the theory presented, as functions of elongation and temperature. An ordinary sorption experiment was carried out for this system at 40% R. H. and 16.8° C and demonstrated that the diffusion of water in Amilan was Fickian with a constant diffusion coefficient. Both diffusion coefficients from the chemical relaxation data and the sorption. data were found to agree quite well when the former was extrapolated to zero-strain. The chemical relaxation behavior in the system polyvinyl alcohol-water was markedly different from that expected from the theory, suggesting primarily that the diffusion coefficient of water in this polymer was not constant. A parallel evidence for this fact was obtained from sorption measurements on this system, which demonstrated the diffusion in this system to be dependent both on concentration and time. From these results it may be concluded that the chemical relaxation technique, when combined properly with an adequate theory, can be used not only to evaluate the diffusion coefficient of penetrant in a given polymer solid but also to investigate, at least qualitatively, the type of sorption behavior characteristic of the system under given experimental conditions.

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Zusammenfassung Die chemische Spannungsrelaxation in Amilan (6-Nylon) und Polyvinylalkohol, verursacht durch Eindringen von Wasserdampf, wurde bei 40% r. F. und Temperaturen von 15, 30 und 50° C untersucht. Es wird eine Theorie der chemischen Relaxation von Polymeren vorgelegt, die als empfindliche Bindungen auf das eindringende Niedermolekulare die Vernetzungen zwischen den molekularen Ketten betrachtet. Diese Theorie setzt voraus, da? der Diffusionskoeffizient im Polymeren für die eindringende Substanz unabh?ngig von Konzentration und anderen Faktoren ist. Das System Amilan-Wasser benimmt sich vollkommen entsprechend dieser Theorie in den studierten Verstreckungs- und Temperaturbereiche. Der Diffusionskoeffizient von Wasser in Amilan konnte daher aus der chemischen Relaxation als Funktion von Dehnung und Temperatur ausgewertet werden. Ein normales Quellungsexperiment wurde für das System bei 40% r. F. und 16,8° C ausgeführt und zeigte, da? die Diffusion von Wasser in Amilan dem Fickschen Gesetz mit konstantem Diffusionskoeffizienten folgt. Beide Diffusionskoeffizienten, der aus chemischer Relaxation und der aus Quellungsdaten gewonnene, stimmten sehr gut überein, falls der erstere auf die Dehnung 0 extrapoliert wurde. Die chemische Relaxation des Systems Polyvinylalkohol-Wasser war merklich anders als nach der Theorie erwartet und lie? in erster Linie vermuten, da? der Diffusionskoeffizient von Wasser in diesem Polymeren nicht konstant ist. Eine entsprechende Andeutung wurde aus Quellungsmessungen an diesem System erhalten. Die Diffusion h?ngt von Konzentration und Zeit ab. Aus diesen Resultaten kann gefolgert werden, da? die Technik der Untersuchungen der chemischen Relaxation unter Verwendung einer geeigneten Theorie nicht nur dazu angewendet werden kann, Diffusionskoeffizienten von kleinen Molekülen in einem gegebenen festen Polymeren zu messen, sondern zumindest auch qualitativ den Typ des Quellungsverhaltens festzustellen, der das System unter den gegebenen experimentellen Bedingungen charakterisiert.

     

Chemical reaction dynamics of PeCB and TCDD decomposition: A tight‐binding quantum chemical molecular dynamics study with first‐principles parameterization

The decomposition reaction dynamics of 2,3,4,4′,5‐penta‐chlorinated biphenyl (2,3,4,4′,5‐PeCB), 3,3′,4,4′,5‐penta‐chlorinated biphenyl (3,3′,4,4′,5‐PeCB), and 2,3,7,8‐tetra‐chlorinated dibenzo‐p‐dioxin (2,3,7,8‐TCDD) was clarified for the first time at atomic and electronic levels, using our novel tight‐binding quantum chemical molecular dynamics method with first‐principles parameterization. The calculation speed of our new method is over 5000 times faster than that of the conventional first‐principles molecular dynamics method. We confirmed that the structure, energy, and electronic states of the above molecules calculated by our new method are quantitatively consistent with those by first‐principles calculations. After the confirmation of our methodology, we investigated the decomposition reaction dynamics of the above molecules and the calculated dynamic behaviors indicate that the oxidation of the 2,3,4,4′,5‐PeCB, 3,3′,4,4′,5‐PeCB, and 2,3,7,8‐TCDD proceeds through an epoxide intermediate, which is in good agreement with the previous experimental reports and consistent with our static density functional theory calculations. These results proved that our new tight‐binding quantum chemical molecular dynamics method with first‐principles parameterization is an effective tool to clarify the chemical reaction dynamics at reaction temperatures. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Structure of aszonalenin,a new metabolite of aspergillus zonatus

Aszonalenin ($\text{1}$) has been isolated from $\text{Aspergillus zonatus}$ together with LL-S490β ($\text{2}$) and the structure of $\text{1}$ has been established by spectroscopic evidences and chemical transformation.     

Molecular dynamics study of the methanol effect on the membrane morphology of perfluorosulfonic ionomers

The membranes of a perfluorosulfonic acid polymer swollen in 10-80 wt % methanol solution were investigated to elucidate the methanol effect on their morphologies, such as size of the solvent cluster, solvent location, and polymer structure, by using isothermal-isobaric molecular dynamics simulations. In higher methanol concentrations, we found less-spherical solvent aggregation and a more spread polymer structure because of the ampholytic nature of methanol. The partial radial distribution functions between solvent oxygen and fluorocarbons, which are composed of the main chain, clearly show that methanol is located closer to the polymer matrix than water. On the other hand, water is preferentially located in the vicinity of an acidic headgroup, SO(3)(-), compared with methanol, although both have similar attractive interaction energies to the acidic group. Furthermore, we discussed solvent dynamics and hydrogen bonding between sulfonic oxygen and solvent O-H groups.     

Total synthesis of cis-solamin

[structure: see text] A convergent total synthesis of cis-solamin and its diastereomer was accomplished using VO(acac)2-catalyzed diastereoselective epoxidation followed by cyclization of bis-homoallylic alcohol as the key step. By comparison of the optical rotation of two possible diastereomers, it is suggested that the absolute configuration of natural cis-solamin is 1a.     

Regiospecific allylation of acetals with allylsilanes catalyzed by iodotrimethylsilane. Synthesis of homoallylethers

Allylation of acetals with allylsilanes is catalyzed by iodotrimethylsilane to give the corresponding homoallyl ethers, with regiospecific transposition of the allyl group.     

Polymerization of allyl esters of unsaturated acids. V. Cyclopolymerization of methyl allyl fumarate

The kinetics of radical polymerization of methyl allyl fumarate (MAF) is discussed in terms of cyclopolymerization and compared with the polymerization results of methyl allyl maleate (MAM) as a cis isomer. In the polymerization of MAF, the rate and degree of polymerization were quite enhanced compared with MAM, and gelation occurred at low conversion. The content of the unreacted allylic double bonds of the MAF polymer was quite large; whereas those of the unreacted fumaric double bonds and the cyclic structural units showed reverse tendencies. Only a slight presence of a five-membered ring was observed in the MAF polymer. The cyclization constants K_A and K_V, the ratios of the rate constants of the unimolecular cyclization reaction to those of the bimolecular propagation reaction of the uncyclized allylic and fumaric radicals, were estimated to be 2.73 and 1.48 mole/liter, respectively. These values suggest the great difference in the cyclopolymerization behavior between two isomeric monomers. These results are discussed in detail in connection with the high reactivity of the fumaric double bond compared to the maleic double bond. In addition, the formation mode and the sequence distribution of the structural units of the polymer produced are discussed on the basis of these analytical results. Thus, for the MAF polymer obtained in the bulk polymerization, about 60% of the cyclic structure can be formed via the intramolecular attack of the uncyclized fumaric radical on the allylic double bond, as opposed to the case of MAM via the predominant intramolecular attack (ca. 90%) of the uncyclized allylic radical on the maleic double bond; these results and the low probability for the succession of cyclic structures and the rather high probability of a vinyl-to-vinyl addition are presented.