Estimated MP2 and CCSD(T) interaction energies of n-alkane dimers at the basis set limit: comparison of the methods of Helgaker et al. and Feller

The MP2 (the second-order M?ller-Plesset calculation) and CCSD(T) (coupled cluster calculation with single and double substitutions with noniterative triple excitations) interaction energies of all-trans n-alkane dimers were calculated using Dunning's [J. Chem. Phys. 90, 1007 (1989)] correlation consistent basis sets. The estimated MP2 interaction energies of methane, ethane, and propane dimers at the basis set limit [EMP2(limit)] by the method of Helgaker et al. [J. Chem. Phys. 106, 9639 (1997)] from the MP2/aug-cc-pVXZ (X=D and T) level interaction energies are very close to those estimated from the MP2/aug-cc-pVXZ (X=T and Q) level interaction energies. The estimated EMP2(limit) values of n-butane to n-heptane dimers from the MP2/cc-pVXZ (X=D and T) level interaction energies are very close to those from the MP2/aug-cc-pVXZ (X=D and T) ones. The EMP2(limit) values estimated by Feller's [J. Chem. Phys. 96, 6104 (1992)] method from the MP2/cc-pVXZ (X=D, T, and Q) level interaction energies are close to those estimated by the method of Helgaker et al. from the MP2/cc-pVXZ (X=T and Q) ones. The estimated EMP2(limit) values by the method of Helgaker et al. using the aug-cc-pVXZ (X=D and T) are close to these values. The estimated EMP2(limit) of the methane, ethane, propane, n-butane, n-pentane, n-hexane, n-heptane, n-octane, n-nonane, and n-decane dimers by the method of Helgaker et al. are -0.48, -1.35, -2.08, -2.97, -3.92, -4.91, -5.96, -6.68, -7.75, and -8.75 kcal/mol, respectively. Effects of electron correlation beyond MP2 are not large. The estimated CCSD(T) interaction energies of the methane, ethane, propane, and n-butane dimers at the basis set limit by the method of Helgaker et al. (-0.41, -1.22, -1.87, and -2.74 kcal/mol, respectively) from the CCSD(T)/cc-pVXZ (X=D and T) level interaction energies are close to the EMP2(limit) obtained using the same basis sets. The estimated EMP2(limit) values of the ten dimers were fitted to the form m0+m1X (X is 1 for methane, 2 for ethane, etc.). The obtained m0 and m1 (0.595 and -0.926 kcal/mol) show that the interactions between long n-alkane chains are significant. Analysis of basis set effects shows that cc-pVXZ (X=T, Q, or 5), aug-cc-pVXZ (X=D, T, Q, or 5) basis set, or 6-311G** basis set augmented with diffuse polarization function is necessary for quantitative evaluation of the interaction energies between n-alkane chains.     

Trypanocidal constituents of Dracocephalum komarovi

Trypanocidal constituents of Dracocephalum komarovi were investigated. Under guidance of the in vitro trypanocidal activity against epimastigotes of Trypanosoma cruzi, the causative agent of Chagas' disease, two new diterpenes, dracocequinones A (1) and B (2), and two known triterpene acids, ursonic acid and ursolic acid, were isolated as trypanocidal constituents, in addition to previously reported diterpenes, cyclocoulterone (4), komaroviquinone (5), dracocephalone A (6) and komarovispirone (7). Furthermore a new diterpene, komarovinone A (3), was isolated, together with four known terpenes. Among these compounds, komaroviquinone (5) showed the most potent activity with minimum lethal concentration of 0.4 μM. Structure elucidation of the new diterpenes 1-3 was described.     

High performance liquid chromatography/electron spin resonance/mass spectrometry analyses of radicals formed in an anaerobic reaction of 9- (or 13-) hydroperoxide octadecadienoic acids with ferrous ions

The oxidation of linoleic acid yields isomeric acyl hydroperoxides. In order to clarify the relation between the lipid peroxide-derived radicals and the toxicity of the lipid peroxide, identification of the lipid-derived radicals is essential. In this paper, high performance liquid chromatography/electron spin resonance/mass spectrometry (HPLC/EPR/MS) analysis of the radicals was performed for the reaction mixture containing 9-hydroperoxy-(10E,12E)-octadeca-10,12-dienoic acid (9EE-OOH) [or 13-hydroperoxy-(9Z,11E)-octadeca-9,11-dienoic acid (13ZE-OOH)] under an aerobic condition or an anaerobic condition. Following radicals were identified from 9EE-OOH (or 13EZ-OOH) by using high performance liquid chromatography/electron spin resonance spectrometry (HPLC/EPR) and HPLC/EPR/MS: pentyl radical and isomers of epoxylinoleic acid radicals from 13EZ-OOH under an anaerobic condition; 7-carboxyheptyl radical and pentyl radical from 13EZ-OOH under an aerobic condition; 7-carboxyheptyl radical and pentyl radical from 9EE-OOH under an aerobic condition; 7-carboxyheptyl radical from 9EE-OOH under an anaerobic condition. These results showed that the formation of the respective radical species depends on oxygen concentration in the reaction mixtures to a great extent.     

Cation-pi interaction in the polyolefin cyclization cascade uncovered by incorporating unnatural amino acids into the catalytic sites of squalene cyclase

It has been assumed that the pi-electrons of aromatic residues in the catalytic sites of triterpene cyclases stabilize the cationic intermediates formed during the polycyclization cascade of squalene or oxidosqualene, but no definitive experimental evidence has been given. To validate this cation-pi interaction, natural and unnatural aromatic amino acids were site-specifically incorporated into squalene-hopene cyclase (SHC) from Alicyclobacillus acidocaldarius and the kinetic data of the mutants were compared with that of the wild-type SHC. The catalytic sites of Phe365 and Phe605 were substituted with O-methyltyrosine, tyrosine, and tryptophan, which have higher cation-pi binding energies than phenylalanine. These replacements actually increased the SHC activity at low temperature, but decreased the activity at high temperature, as compared with the wild-type SHC. This decreased activity is due to the disorganization of the protein architecture caused by the introduction of the amino acids more bulky than phenylalanine. Then, mono-, di-, and trifluorophenylalanines were incorporated at positions 365 and 605; these amino acids reduce cation-pi binding energies but have van der Waals radii similar to that of phenylalanine. The activities of the SHC variants with fluorophenylalanines were found to be inversely proportional to the number of the fluorine atoms on the aromatic ring and clearly correlated with the cation-pi binding energies of the ring moiety. No serious structural alteration was observed for these variants even at high temperature. These results unambiguously show that the pi-electron density of residues 365 and 605 has a crucial role for the efficient polycyclization reaction by SHC. This is the first report to demonstrate experimentally the involvement of cation-pi interaction in triterpene biosynthesis.     

Synthesis and characterization of transparent silica-based aerogels using methyltrimethoxysilane precursor

Silica-based aerogels with high transparency and high bending strength were prepared using methyltrimethoxysilane and non-ionic surfactant under supercritical drying condition of CO₂. Non-ionic surfactant, ethylene oxide/propylene oxide block copolymer, was appropriate to form the three dimensional-connected thinner fibers of silica skeletons, which was extruded by soaking the wet gel in hot water at 50 °C, resulting in the formation of porous materials having small pores with narrow size distribution. The transparency of aerogels increased with decreasing the pore size, reaching to higher than 65 and 88% at 400 and 600 nm wavelength, respectively, for 10 mm thickness of sample. The formation of fiber skeletons were discussed using small angle X-ray scattering experiments.     

Analysis of carbohydrates in glycoproteins by high-performance liquid chromatography and high-performance capillary electrophoresis

We describe two methods for the analysis of oligosaccharide chains in glycoproteins by high-performance liquid chromatography (HPLC) and high-performance capillary electrophoresis (HPCE).O-andN-glycosidically linked oligosaccharides released from glycoproteins can be identified as their borohydride-reduced forms by anion-exchange HPLC with pulsed amperometric detection.N-Glycosidically linked oligosaccharides can also be analyzed as 2-aminopyridine derivatives by HPCE in direct zone electrophoresis mode in an acidic phosphate buffer and zone electrophoresis mode as borate complexes in an alkaline buffer. We also present a convenient procedure for the analysis of the constituent monosaccharides of these oligosaccharides chains by HPLC based on reversed-phase partition mode as 1-phenyl-3-methyl-5-pyrazolone derivatives.     

Stimulatory effect of red light on starch accumulation in a marine green alga,chlamydomonas sp. strain MGA161

A marine green alga,Chlamydomonas sp. strain MGA161 was cultivated under illumination of red and white lights. The growth rate under red light illumination was almost the same as that in the basic conditions under white light illumination, but red light-grown cells accumulated almost twice as much starch as white light-grown cells. Although there was a slight decrease in carbonic anhydrase activity, red light-illuminated cells had almost 2.3 times the fructose-l,6-diphos-phatase activity of white light-illuminated cells. Red light might stimulate starch accumulation by increasing the amounts of enzymes related to carbon fixation through the phytochrome system. Cells grown under red light degraded 1.6 times as much starch and produced 1.7 times as much hydrogen and 1.6 times as much ethanol compared with cells grown under white light during 12 h of dark anaerobic fermentation.     

Trace metal enrichment by automated on-line column preconcentration for flow-injection atomic absorption spectrometry

An on-line column preconcentration technique for flow-injection atomic absorption spectrometry was developed. Diverse metal ions (Cd²⁺, Zn²⁺, Cu²⁺, Mn²⁺, Pb²⁺, Fe³⁺ and Cr³⁺) in solution were concentrated quantitatively by a microcolumn (7-mm × 4-mm i.d.) packed with Muromac A-1, which is an iminodiacetate chelate resin, in a flow-injection system. From the pH dependence of the uptake of the ions, all the divalent metals examined were recovered quantitatively in the pH range 3–5 and the trivalent metals were recovered at a maximum pH of 1. Enrichment factors using 20-ml samples were in the range 90–180-fold for the seven elements and the sampling rate was 13 h^?1. The 3σ detection limits were in the range 0.14–2.1 μg l^?1 and the relative standard deviations for replicate measurements (n=3–4) were in the range 0.7–1.7%. The method was compared with flame and graphite furnace atomic absorption spectrometry. Application to the determination of cadmium and copper in several standard reference materials is described.     

Protonation and methylation of an Anderson-type polyoxoanion [IMo6O24]5-

A series of protonated and methylated Anderson-type molybdoperiodates as well as the unprotonated [IMo6O24]5- have been synthesized and structurally characterized as tetra-n-butylammonium salts: [(n-C4H9)4N]5[IMo6O24] [monoclinic, space group C2/c, a = 33.6101(3) A, b = 15.2575(1) A, c = 24.0294(2) A, beta = 126.9569(3) degrees , Z = 4], [(n-C4H9)4N]4[IMo6O23(OH)] [monoclinic, space group P21/c, a = 9.5587(1) A, b = 24.1364(2) A, c = 18.2788(2) A, beta = 90.1562(5) degrees , Z = 2], [(n-C4H9)4N]3[IMo6O22(OH)2].2DMF [monoclinic, space group P21/a, a = 17.6105(4) A, b = 15.5432(5) A, c = 29.3316(9) A, beta = 91.475(3) degrees , Z = 4], [(n-C4H9)4N]4[IMo6O23(OMe)].3H2O [orthorhombic, space group Pbca, a = 17.0679(4) A, b = 25.6998(6) A, c = 20.7428(4) A, Z = 4], [(n-C4H9)4N]3[IMo6O22(OMe)2] [monoclinic, space group P21/n, a = 10.4009(1) A, b = 14.6658(3) A, c = 23.5395(4) A, beta = 100.324(1) degrees , Z = 2]. In all of these compounds, the [IMo6O24]5- anion is protonated or methylated selectively at O atoms shared by two Mo atoms. The results have also revealed that the protonated Anderson-type molybdoperiodates readily react with methanol in a very selective manner, while the unprotonated [IMo6O24]5- anion does not react with methanol under similar conditions.     

RBM band shift-evidenced dispersion mechanism of single-wall carbon nanotube bundles with NaDDBS

The dispersion process of single-wall carbon nanotube (SWNT) by using sodium dodecylbenzene sulfonate (NaDDBS) was studied by means of surface tension measurements, ultraviolet-visible (UV-Vis) spectroscopy, scanning electron microscopy (SEM), and transmission electron spectroscopy (TEM). The critical micelle concentration (CMC) and the concentration where the surface tension begins to drop increase by the presence of SWNT. The isotherm of NaDDBS amount adsorbed on SWNT shows the plateau region at 0.2-6 mM and the saturated region above 40 mM. The external surface of SWNT bundle is fully covered with adsorbed NaDDBS at the plateau region, showing that SWNTs can be dispersed with the bundle form. On the other hand, SWNTs are dispersed in individual tubes at the saturated region, where the adsorption amount corresponds to coating of individual tube surfaces with NaDDBS. This dispersion state was confirmed by SEM and TEM observations. The effect of the dispersion state of SWNTs on radial breathing mode in Raman spectrum gave inherent peak shifts, being the in situ evidences on the step-wise dispersion mechanism of the SWNT bundle to the individual tubes.