Dynamical and statistical effects of the intrinsic curvature of internal space of molecules

The Hamilton dynamics of a molecule in a translationally and/or rotationally symmetric field is kept rigorously constrained in its phase space. The relevant dynamical laws should therefore be extracted from these constrained motions. An internal space that is induced by a projection of such a limited phase space onto configuration space is an intrinsically curved space even for a system of zero total angular momentum. In this paper we discuss the general effects of this curvedness on dynamics and structures of molecules in such a manner that is invariant with respect to the selection of coordinates. It is shown that the regular coordinate originally defined by Riemann is particularly useful to expose the curvature correction to the dynamics and statistical properties of molecules. These effects are significant both qualitatively and quantitatively and are studied in two aspects. One is the direct effect on dynamics: A trajectory receives a Lorentz-like force from the curved space as though it was placed in a magnetic field. The well-known problem of the trapping phenomenon at the transition state is analyzed from this point of view. By showing that the trapping force is explicitly described in terms of the curvature of the internal space, we clarify that the physical origin of the trapped motion is indeed originated from the curvature of the internal space and hence is not dependent of the selection of coordinate system. The other aspect is the effect of phase space volume arising from the curvedness: We formulate a general expression of the curvature correction of the classical density of states and extract its physical significance in the molecular geometry along with reaction rate in terms of the scalar curvature and volume loss (gain) due to the curvature. The transition state theory is reformulated from this point of view and it is applied to the structural transition of linear chain molecules in the so-called dihedral angle model. It is shown that the curvature effect becomes large roughly linearly with the size of molecule.     

Kinetic study of the quenching reaction of singlet oxygen by flavonoids in ethanol solution

The quenching rate of singlet oxygen (1O2) by seven kinds of flavonoids (flavone, flavonol, chrysin, apigenin, rutin, quercetin, and myricetin) with 2,3-double bonds has been measured spectrophotometrically in ethanol at 35 degrees C. The overall rate constants kQ (= kq + kr, physical quenching + chemical reaction) increased as the number of OH groups substituted to the flavone skeleton (that is, the total electron-donating capacity of flavonoids) increases. The existence of catechol or pyrogallol structure in the B-ring is essential for the 1O2 quenching of flavonoids. Log kQ was found to correlate with their peak oxidation potentials, E(P); the flavonoids that have smaller E(P) values show higher reactivities. Similarly, log kQ values of flavonoids correlate with the energy level of the highest occupied molecular orbital (E(HOMO)), calculated by the PM3 MO method, and the longest wavelength pi pi* excitation energy (E(ex)). The contribution of the chemical reaction (kr) was found to be negligible in these flavonoids. The kQ values of rutin, quercetin, and myricetin [(1.21 approximately 5.12) x 10(8) M(-1) s(-1)] were found to be larger than those of lipids [(0.9 approximately 6.4) x 10(4) M(-1) s(-1)], amino acids (<3.7 x 10(7) M(-1) s(-1)), and DNA (5.1 x 10(5) M(-1) s(-1)). The result suggests that these flavonoids may contribute to the protection of oxidative damage in foods and plants, by quenching 1O2.     

Interface interactions in modulated phases,and upsilon points

Certain features in Frenkel-Kontorova and other models of phases with a one-dimensional modulation can be analyzed by assuming parallel interfaces separating sets of lattice planes belonging to two different phases, and treating the free energy to create interfaces, as well as the interaction of two, three, or more interfaces, as phenomenological parameters. A strategy employed by Fisher and Szpilka for interacting defects can be extended to the case of interfaces, allowing a systematic study of the phase diagram by ignoring all interface interactions, and then successively taking into account pair, triple, and higher-order terms. The possible phase diagrams which can occur near the point where =0 include: various sorts of endpoints analogous to critical endpoints, an accumulation point of first-order transitions and triple points, and a self-similar structure which we call an upsilon point, which turns out to be an accumulation point of an infinite number of segments of first-order transition lines, each of which terminates in two upsilon points.     

Synthesis of 5H-pyrido[2,3-a]phenoxazin-5-one and 5H-pyrido[3,2-a]phenoxazin-5-one derivatives

The 5H-pyrido[2,3-a]phenoxazin-5-one derivatives and 5H-pyrido[3,2-a]phenoxazin-5-one derivatives were prepared by the condensation of substituted 2-aminophenols with 6,7-dibromo-5,8-quinolinequinone followed by dehalogenation in the presence of sodium hydrosulfite dissolved in aqueous pyridine under a nitrogen atmosphere.     

Synthesis of marine guanidine alkaloids and their application as chemical/biological tools

Ptilomycalin A and crambescidins, novel marine guanidine alkaloids, have a unique pentacyclic guanidine structure, and exhibit a considerable array of biological activities. The first method developed for the synthesis of the pentacyclic guanidine core structure involved successive 1,3-dipolar cycloaddition reactions and resulted in the first total synthesis of crambescidin 359. The synthesis of other pentacyclic guanidine derivatives has been based on this methodology and applied as tools for studying biological activities, and as chemical reaction catalysts.     

Determination of saccharides in sake by high-performance liquid chromatography with polarized photometric detection

A high-performance liquid chromatographic method has been developed for the determination of saccharides in sake, an alcoholic beverage brewed from rice. Saccharides in sake were separated on a normal phase (carbamoyl bonded silica) column using a linear gradient elution of water in acetonitrile. Seven saccharides, glucose, maltose, isomaltose, maltotriose, panose, isomaltotriose and ethyl alpha-D-glucoside, were determined by a polarized photometric detector. Unidentified peaks suggesting saccharides with polymerization degrees over 4 were also observed. The proposed method did not require any sample clean-up treatment. As an application, saccharide compositions in various kinds of sake were compared.     

Trapping effect of eugenol on hydroxyl radicals induced by L-DOPA in vitro

Many researchers have stated that eugenol might inhibit lipid peroxidation at the stage of initiation, propagation, or both, and many attempts have been made to elucidate the mechanism of its antioxidant activity. Nevertheless, details of its mechanism are still obscure. This study was carried out to investigate the trapping effect of eugenol on hydroxyl radical generated from L-3,4-dihydroxyphenylalanine (DOPA) in MiliQ water and the generation mechanism of the hydroxyl radical by this system which uses no metallic factor. This was studied by adding L-DOPA and 5,5-dimethyl-1-pyrroline N-oxide (DMPO) to phosphate buffered saline (PBS) or MiliQ water, and the generation of hydroxyl radical was detected on an ESR spectrum. By this method, the effect of antioxidants was detected as a modification of ESR spectra. We found that the eugenol trapped hydroxyl radicals directly, because it had no iron chelating action, did not trap L-DOPA semiquinone radical and inhibited hydroxyl radicals with or without iron ion.     

Polyether-bridged sexithiophene as a complexation-gated molecular wire for intramolecular photoinduced electron transfer

The porphyrin-sexithiophene-fullerene triad 2, where the two central thiophene units of the sexithiophene spacer are bridged with a crown-ether-like polyether chain, undergoes efficient intramolecular electron transfer from the photoexcited porphyrin moiety to the fullerene through the sexithiophene. However, complexation with a sodium cation in the crown ether ring causes complete suppression of electron transfer as a result of a drastic conformational change of the sexithiophene backbone. Furthermore, decomplexation resumes the photoinduced electron transfer. This on/off switching phenomenon indicates that the polyether-bridged sexithiophene can function as a complexation-gated molecular wire.     

Improvement of an automatic HPLC system for nitropolycyclic aromatic hydrocarbons: removal of an interfering peak and increase in the number of analytes.

An automatic HPLC system for analyzing nitropolycyclic aromatic hydrocarbons (NPAHs, nitroarenes) in airborne particulates was previously described (Anal. Chim. Acta, 2001, 445, 20). Some problems with this system were that it generated a peak originating from an ascorbic acid solution that elutes at a retention time close to that of 1,6-dinitropyrene (DNP), and that it was able to analyze only 1,3-, 1,6-, 1,8-DNPs and 1-nitropyrene (I-NP). Here, we describe an improved system that effectively removes the interfering peak by introducing an ODS column just after the pump for the ascorbic acid solution, and which is capable of analyzing several additional compounds (2-, 4-NPs, 2-nitrofluorene. 6-nitrochrysene, 7-nitrobenz[a]anthracene, 3-nitroperylene and 6-nitrobenzo[a]pyrene etc.). The improved sensitivities were achieved by concentrating the compounds in a benzene-ethanol extract from airborne particulates, by increasing the loading time of the sample solution from 20 to 38 min, and by increasing the flow rate of an ascorbic acid solution from 1.3 to 1.8 mL/min.     

Morphological change of gold-dendrimer nanocomposites by laser irradiation

Gold-dendrimer nanocomposites are prepared in aqueous solutions in the presence of poly(amidoamine)dendrimers (PAMAM) (generation 3 and 5) or poly(propyleneimine)dendrimers (PPI) (generation 3 and 4) by wet chemical NaBH(4) method. Thus prepared gold-dendrimer nanocomposites are irradiated by laser at 532 nm. UV-vis absorption spectroscopy and transmission electron microscopy reveal that the gold nanoparticles grow with the laser irradiation time as well as the fluence of the laser; in particular, the gold nanoparticles prepared at lower concentrations of PAMAM dendrimer as well as lower generations of PAMAM grow significantly. On the other hand, in the case of PPI dendrimers, the gold nanoparticles hardly grow by irradiation. In addition, dynamic light-scattering measurements show that the laser irradiation markedly promotes the association of the gold-PAMAM G3 dendrimer nanocomposites compared to that of the gold-PAMAM G5 dendrimer nanocomposites, while the sizes of association for the gold-PPI G3, G4 dendrimer nanocomposites hardly change by laser irradiation.