Anisotropic friction model of DNA electrophoresis in polymer solutions: Comparison with direct observations

The electrophoresis of DNA chains in uncrosslinked polymer solutions with a Brownian dynamics simulation with an anisotropic friction tensor was analyzed. According to the degree of anisotropy, three types of migration behavior are obtained: fluctuation without or with periodicity between U‐shaped and compact conformations, or migration with linear conformation. We found good agreement between our simulation results and the direct observations of DNA by fluorescence microscopy. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 1316–1322, 2003     

Changes in the near-edge X-ray absorption fine structure spectra of long-chain diacetylene derivatives through photopolymerization in Langmuir–Blodgett films

Photopolymerization of cadmium 10,12-pentacosadiynoate (CdDA) in Langmuir–Blodgett (LB) films, with the molecular packing well arranged by moderate preannealing, was investigated with near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. Greenish films of polydiacetylene with an absorption wavelength of 705 nm were obtained through the photopolymerization of preannealed monomer LB films, and this resulted in an extended π-conjugate system based on the well-ordered monomer in a two-dimensional arrangement. The electronic structures of the polydiacetylenes were found to be correlated to the variation of the molecular arrangements in the films from the changes in the NEXAFS spectra through photopolymerization in the LB films. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 2329–2336, 2004     

Direct observation of chemical oscillation at a water/nitrobenzene interface with a sodium-alkyl-sulfate system.

The oscillation of the interfacial tension and electrical potential at a water/nitrobenzene interface was observed with homologous anionic surfactant molecules, sodium-alkyl-sulfates. Concerning small molecules with a short hydrophobic carbon chain, the oscillation period and amplitude decreased with a decrease of the length of the alkyl chain. On the other hand, when surfactant molecules with a long hydrophobic carbon chain were used, no remarkable periodic oscillation occurred after the first oscillation. In all systems, an interfacial flow by Marangoni convection was observed when the oscillation took place. By monitoring the movement of carbon powder scattered on the liquid/liquid interface with a CCD camera, we could observe that the liquid/liquid interface expanded outward from the area on which the surfactant molecules adsorbed when the oscillation occurred. When the small molecule was used, the speed of expansion of the interface (flow speed) was small and shrinkage followed by expansion of the interface repeatedly occurred. However, when the large molecule was used, the flow speed was large and expansion occurred only one time. These results show that hydrodynamic factors and surface activities are important in chemical oscillation systems.     

Pseudo cyclic ionophores: ‘Binary-effect’ of quinolinyloxy groups at both ends of oligoethylene glycols on the conformational stabilization of their complexes with alkali metal salts

A series of noncyclic neutral ionophores has been synthesized by the reaction of oligoethylene glycol dihalides with 8-quinolinol. Complexation properties for alkali metal picrates were evaluated from solvent extraction and bulk liquid membrane transport experiments. Complexation profiles of the newly synthesized ionophores with a hexyl chain were similar to those of their homologues without the hexyl chain in the extraction experiments. Among them, the pentaethylene glycol derivatives showed the highest extraction efficiency and selectivity towards potassium ion. From the¹H NMR spectra (400 MHz), the change in chemical shifts of the aromatic protons upon the addition of alkali metal thiocyanates suggested the existence of a stabilization effect which is caused by intramolecular stacking conformations between the quinoline rings during complexation. Aryl stacking interactions depend on the size of the cations and on the chain length of the oligoethylene glycol. The relationship between transport ability towards alkali metal cations and lipophilicity of these ionophores is also discussed.     

Influence of moisture on the viscoelastic relaxations in long aliphatic chain contained semiaromatic polyamide, (PA9‐T) fiber

The effect of moisture on the mechanical relaxation processes of semiaromatic semicrystalline polyamides synthesized by a long‐chain aliphatic diamine and terephthalic acid was investigated by dynamic viscoelastic analysis (DVA) and differential scanning calorimetry (DSC). Moreover, the implication of moisture with the amorphous and crystalline domains was also examined by temperature‐dependent wide‐angle X‐ray diffraction and Fourier transform infrared spectra. The characteristics of the relaxations such as α, β, γ, and the pronounced peak shoulder appeared at 25–100 °C in DVA tan δ curves were found to be strongly susceptible to the presence of moisture. With moisture evaporation, the peak shoulder of 25–100 °C and the β‐relaxation disappeared. The former is anticipated to originate from to the side group motion of hydrogen‐bonded water, whereas the later one is from the motions of the amide–water complex units. With the disappearance of the β‐relaxation, the γ‐relaxation appeared simultaneously in much lower temperatures and ultimately coupled with the δ‐relaxation. The γ‐relaxation is attributed to be associated with the molecular motion of the amide group and δ‐relaxation with for the motion of the methylene units. The existence of two types of water was identified in the polymer, namely, tightly bound and loosely bound. The tightly bound water is believed to be directly connected by hydrogen bonding with the strong polar groups and the loosely bound water weakly links with those connected water making hydrogen bridges. The moisture acts as a plasticizer in the polymer matrix, which causes quite a large depression in its glass transition temperature (T_g). WAXD and FTIR studies corroborated the existence of water solely in amorphous regions, i.e., no rapport of water with the crystalline parts. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 2878–2891, 2003     

A rigorous control of logarithmic corrections in four-dimensional ϕ4 spin systems

Using Gawedzki and Kupiainen's rigorous block spin transformation method, we study critical phenomena in ⁴ spin systems in four dimensions. In Part I of this work we investigate in detail the renormalization group trajectory of the system not exactly at the critical point.     

A novel synthesis of (+)-biotin from L-cysteine

(+)-Biotin (1) was synthesized in 25% overall yield over 11 steps from L-cysteine. The contiguous asymmetric centers at C-3a and C-6a were formed through a novel and highly stereoselective Lewis base-catalyzed cyanosilylation of alpha-amino aldehyde 3 to provide anti-O-TMS-cyanohydrin 4 with high stereoselectivity and in high yield (anti/syn = 92:8, 96%). Treatment of 4 with a di-Grignard reagent, 1,4-bis(bromomagnesio)butane, followed by carbon dioxide, efficiently installed the 4-carboxybutyl chain at C-4 to give keto acid 5. The final cyclization to bicyclic compound 7b, a precursor to 1, was realized by a palladium-catalyzed intramolecular allylic amination of cis-allylic carbonate 6b that was elaborated from 5.     

Measurement of acid-catalyzed isomerization of unsaturated aldehyde-2,4-dinitrophenylhydrazone derivatives by high-performance liquid chromatography analysis

Aldehyde-2,4-dinitrophenylhydrazones exist as (E)- and (Z)-geometrical isomers, and adventitious isomerization during sample preparation can cause analytical errors. Purified alkenal-2,4-dinitrophenylhydrazone derivatives comprise only the (E)-isomer. However, partial isomerization to the (Z)-isomer occurs upon addition of acid to attain an equilibrium isomer ratio. The UV-visible spectral properties of the isomers differ; the (Z)-isomer exhibiting a 6-10 nm lower absorption maximum compared to the (E)-isomer. Alkenal-2,4-dinitrophenylhydrazones having a CC double bond at the 2- or 3-position of the alkenal exhibited similar absorption maxima with an equilibrium isomer ratio (0.035) that was much lower than those of other alkenals. The CC double bond at the 3-position migrates to a position of conjugation with the CN double bond during hydrazone synthesis to form a stabilized molecular structure. Alkenal-2,4-dinitrophenylhydrazones having a double bond at the 4-position or greater exhibited a similar absorption maxima equilibrium isomer ratio (0.14) to alkanal-2,4-dinitrophenylhydrazones. The quantitative analysis of carbonyl compounds in air or water using DNPH is usually conducted in the presence of an acid catalyst. Consequently, the solution of the direct extract prepared for HPLC or GC analysis contains both (E)- and (Z)-isomers.