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     

Sympathetic cooling rate of gas-phase ions in a radio-frequency-quadrupole ion trap

We theoretically investigated the mass dependence of the sympathetic cooling rate of gas-phase ions trapped in a linear radio-frequency-quadrupole ion trap. Using an a priori molecular dynamical calculation, tracing numerically with Newtonian equations of motion, we found that ions with a mass greater than 0.54±0.04 times that of the laser-cooled ions are sympathetically cooled; otherwise, they are heated. To understand the mass dependence obtained using the molecular-dynamical calculation, we made a heat-exchange model of sympathetic cooling, which shows that the factor of 0.54±0.04 is a consequence of absence of micro-motion along the axis of the linear ion trap. Received: 10 December 2001 / Revised version: 28 January 2002 / Published online: 14 March 2002     

Synthesis and simple separation of β-pyrrole sulfonated porphycenes

New water-soluble porphycenes having sulfonic acid groups at the β-pyrrolic positions were synthesized and characterized by UV-vis, NMR, IR, and mass spectroscopy as well as elemental analyses. The series of mono- to tri-sulfonato derivatives were simply separated by the extraction method.     

Mechanism of gold adsorption by persimmon tannin gel.

Gold adsorption by persimmon tannin (PT) gel from a solution containing hydrogen tetrachloroaurate(III) was examined. A flow-rate examination in a column system indicated the reduction of Au(III) ion to Au(0). XRD patterns clarified the existence of Au(0) on the gel which adsorbed gold. The gel could also adsorb colloidal Au(0) prepared independently. A model consisting of ligand exchange, Au(III) reduction to Au(0), and resulting Au(0) adsorption by PT gel was presented for the gold adsorption mechanism.     

Fluorogenic probes for detecting deacylase and demethylase activity towards post-translationally-modified lysine residues

Reversible enzymatic post-translational modification of the ε-amino groups of lysine residues (e.g. N-acylation reactions) plays an important role in regulating the cellular activities of numerous proteins. This study describes how enzyme catalyzed N-deprotection of lysine residues of non-fluorescent peptide-coumarin probes can be used to generate N-deprotected peptides that undergo spontaneous O- to N-ester transfer reactions (uncatalyzed) to generate a highly fluorescent N-carbamoyl peptide. This enables detection of enzyme catalyzed N-deacetylation, N-demalonylation, N-desuccinylation and N-demethylation reactions activities towards the N-modified lysine residues of these probes using simple ‘turn on’ fluorescent assays.

We developed “turn-on” fluorescent probes that detect enzymatic lysine deacylation and demethylation critical for epigenetic and other cellular phenomena, using intramolecular O- to N-ester transfer reactions.     

Fluorination of 2-alkyl-substituted oxanes. The synthesis and purification of perfluoro(2-alkyl-substituted oxane)s

Five kinds of 2-alkyl-substituted oxanes like 2-ethyloxane, 2-n-propyloxane, 2-iso-propyloxane, 2-n-butyloxane and 2-n-amyloxane were fluorinated electrochemically to give the corresponding perfluoro(2-alkyloxane)s. The perfluoro(2-alkyloxane)s were obtained in good yields from these starting materials together with isomeric perfluoro(2-alkyloxolane)s, perfluoro(2-alkyl-5-methyloxolane)s and perfluoro(dialkyl ether)s. The purification of the perfluoro(2-alkyloxane)s which contained small amounts of isomeric perfluoro(2-alkyloxolane)s was successfully achieved by recovering the former unreacted after treating these mixture with anhydrous aluminum chloride at 150 /sR 160 °C during /sR 48 hrs in order to convert the latter into the easy-separable perfluoro(2,5,5- trichloro-2-alkyloxolane)s. Small quantities of new perfluoro(5,5-dichloroalkanoyl chloride)s were also among the chlorination products. The spectroscopic data as well as the physical properties of these new fluorination products, and perfluoro(2,5,5-trichloro-2-alkyloxolane)s and perfluoro(5,5-dichloroalkanoyl chloride)s are presented.     

Sub-Doppler rotationally resolved spectroscopy of lower vibronic bands of benzene with Zeeman effects

Sub-Doppler high-resolution excitation spectra and the Zeeman effects of the 6(0)(1), 1(0)(1)6(0)(1), and 1(0)(2)6(0)(1) bands of the S1(1)B2u<--S(0)(1)A1g transition of benzene were measured by crossing laser beam perpendicular to a collimated molecular beam. 1593 rotational lines of the 1(0) (1)6(0) (1) band and 928 lines of the 1(0)(2)6(0)(1) band were assigned, and the molecular constants of the excited states were determined. Energy shifts were observed for the S1(1)B2u(v1=1,v6=1,J,Kl=-11) levels, and those were identified as originating from a perpendicular Coriolis interaction. Many energy shifts were observed for the S1(1)B2u(v1=2,v6=1,J,Kl) levels. The Zeeman splitting of a given J level was observed to increase with K and reach the maximum at K=J, which demonstrates that the magnetic moment lies perpendicular to the molecular plane. The Zeeman splittings of the K=J levels were observed to increase linearly with J. From the analysis, the magnetic moment is shown to be originating mostly from mixing of the S1(1)B2u and S2(1)B1u states by the J-L coupling (electronic Coriolis interaction). The number of perturbations was observed to increase as the excess energy increases, and all the perturbing levels were found to be a singlet state from the Zeeman spectra.     

Catalytic transformation of methane over in-loaded ZSM-5 zeolite in the presence of ethene

Methane is shown to react with ethene over In-loaded ZSM-5 to higher hydrocarbons such as propene and toluene at around 673 K. Such methane conversion is not catalyzed by proton-exchanged ZSM-5 (H-ZSM-5) under the same conditions, only C2H4 being converted to higher hydrocarbons. By using 13C-labeled methane (13CH4) as a reactant, the reaction paths for the formation of propene, benzene and toluene were examined. 13C-labeled propene (13CC2H6) is formed by the reaction of 13CH4 with C2H4. The lack of 13C-labeled benzene revealed that propene is not transformed to benzene, which instead originates entirely from C2H4. The 13C atom is inserted both into the methyl group and benzene ring in the toluene formed. This indicates that toluene is formed by two reaction paths; the reaction of 13CC2H6 with butenes formed by the dimerization of C2H4 and the reaction of benzene with 13CH4. The existence of the latter path was proved by the direct reaction of 13CH4 with benzene. The reaction of methane with benzene was also carried out in a continuous flow system over In-loaded ZSM-5. The reaction afforded 7.6% and 0.9% yields of toluene and xylenes, respectively, at 623 K.     

Determination of plutonium by solvent extraction—Liquid scintillation method

A combined solvent extraction—liquid scintillation method is suggested for the determination of plutonium. The quenching by twenty four extracting reagents was examined systematically, and the organo phosphorus extractants such as tributylphosphate (TBP), bis-(2-ethyhexyl) phosphoric acid (HDEHP), and tri-n-octylphosphineoxide (TOPO) were shown to be least quenching compared with amines and beta-diketones. Using TOPO, plutonium from 1 ng to 2 μg was determined within 5% of standard deviation, and the detection limit was 3·10⁻¹⁰ g of²³⁹Pu. The quenching by the different ions and the effects of the radioactive elements were also shown.