Implementation of pi-pi interactions in molecular dynamics simulation

No explicit pi-pi interaction term has been incorporated in the conventional molecular dynamics (MD) simulation programs in spite of its significant role in the folding of biomolecules and the clustering of organic chemicals. In this article, we propose a technique to emphasize the effect of pi-pi interactions using a function of energy and implement it into an MD simulation program. Several trial calculations show that the pi-pi incorporated program gives improved results consistent with experimental data on atom geometry and has no unfavorable interference with the conventional computational framework. This indicates an importance of the explicit consideration of pi-pi interactions in MD simulation.     

Chameleon reactivity of the allene bond of 4-vinylidene-2-oxazolidinone: novel through-space conjugative nucleophilic addition of electron-rich alkenes and hetero-nucleophiles

The Calpha==Cbeta double bond of allene carbamates 1 serves as an electron acceptor similar to the double bond of conjugated enones by means of a through-space interaction with the N--SO2 bond; the carbamate double bond is thus subject to nucleophilic addition for a wide variety of nucleophiles, which proceeds under mild conditions by heating at 70-100 degrees C. Depending on the kind of nucleophiles, 1 displays three different reaction modes: 1) Typically enol ethers and allylsilanes promote 1,3-sulfonyl migration of 1 and undergo the inverse electron demand Diels-Alder reaction with the 1-aza-1,3-butadiene intermediates II thus formed to furnish bicyclic 2-alkoxy-5-sulfonyltetrahydropyridines 2 and 2-silylmethyl-5-sulfonyltetrahydropyridines 3, respectively, with high regio- and stereoselectivity and retention of configuration of the double bonds of these electron-rich alkenes; 2) silanes (RnSiH4-n, n=1-3) and thiols deliver the hydride and the thiolate at the Cbeta carbon and promote the 1,3-sulfonyl migration, followed by protonation of the thus-formed carbamate anion (Z)-III to provide, for example, (Z)-4 a and (Z)-4 j, respectively; 3) alcohols simply add to the Calpha==Cbeta double bond and provide (E)-6. Usually, the reaction with alcohols is accompanied by the second pathway, giving rise to, for example, (Z)-4 b in addition to (E)-6 b. Phenol engages in the third pathway and provides (E)-6 g exclusively. Heteroaromatics, such as furans and benzofurans follow the first pathway, however, in a different regioselectivity from enol ethers and allylsilanes, delivering the oxygen atom at the 3-position of 5-sulfonyltetrahydropyridines (2 g and 2 h). Indoles, on the other hand, show a dichotomy, equally enjoying the first and the third pathways and provide mixtures of (E)-7 and (E)-8, respectively.     

Pyridylazulenes: synthesis, color changes, and structure of the colored product

A facile method for the synthesis of 1- and 2-pyridylazulenes, and of 1,3-dipyridylazulenes, is described. Color and spectral changes of these pyridylazulenes upon the addition of either acid or metal ions were investigated in detail. The color changed from blue to red upon the addition of trifluoroacetic acid or soft metal ions, depending on the substitution patterns of the pyridyl group on the azulene skeleton. The structures of the protonated or coordinated products were examined on the basis of the spectral data. It was found that the protonation or coordination of metal ions occurred on the nitrogen atom of the pyridine ring, but not on the carbon atom of azulene ring. The transition intervals of several pyridylazulenes for use as pH indicators were also determined.     

Shape Estimation of Anisometric Particles Using Size Measurement Techniques

This study was conducted to establish a simple method for evaluating the morphology of fine anisometric particles using size measurement techniques. The size distributions of mica particles and carbon fibers classified into narrower size ranges were measured by gravitational sedimentation and laser diffraction techniques. The ratio of mean diameters determined for flaky particles strongly depended on the aspect ratio, i.e. flatness. The relationship between particle shape and diameter is discussed theoretically. The experimental results were similar to those predicted. The flatness of fine particles can be evaluated by the ratio of the median diameter determined by laser diffraction to that determined by sedimentation.     

Observation of 18O/16O isotope effects at the cathode of a polymer electrolyte membrane fuel cell

¹⁸O/¹⁶O isotope effects were observed at the cathode of a polymer electrolyte membrane fuel cell at 25 and 35°C. Results of experiments in which the ¹⁸O/¹⁶O isotope ratios of the oxygen gases supplied to and exhausted from the cell were measured revealed that the lighter isotope ¹⁶O reacted more preferentially to form water molecules at the cathode than the heavier one, ¹⁸O. The value of the oxygen isotope separation factor, S₁, defined as the ratio of the ¹⁸O/¹⁶O isotope ratios of the oxygen gases supplied to and exhausted from the cell, ranged from 1.0030 to 1.0139, and tended to decrease with decreasing rate of oxygen utilisation (θ) and with increasing flow rate of the feed oxygen gas (D_F). The value of another separation factor, S₂, defined as the ratio of the ¹⁸O/¹⁶O isotope ratios of the exhausted oxygen gas and oxygen having reacted to form water molecules at the cathode, ranged from 1.0049 to 1.0304. The S₂ value was much less affected by the change in θ and D_F than the S₁ value with the majority of the S₂ value being in the range of 1.0240–1.0304.     

Measurement of non-DLVO force on a silicon substrate coated with ammonium poly(acrylic acid) using scanning probe microscopy

The repulsive force originating from steric hindrance of polymers in aqueous solvent was investigated using scanning probe microscopy (SPM). The contact angle (CA) of ammonium poly(acrylic acid) (PAA) solution on the Si surface was measured to estimate the state of the Si substrate. Results of CA measurement show that the Si surface was fully covered with PAA at 0.1 mass% in aqueous solution. The interaction force between the Si tip and the wafer was estimated using the SPM force curve mode. The force curve measured in the ion-exchanged purified water showed the typical relation predicted by Derjaguin-Landau-Verway-Overbeek (DLVO) theory. However, the force curve shape in the 0.1 mass% PAA solution was significantly different. Only a repulsive force was observed at less than about 4 nm of separation distance between the Si wafer and cantilever tip. This distance originated from the steric repulsions of PAA adsorbed onto the Si wafer and cantilever tip.     

Fluorophotometric Determination of Hydrogen Peroxide with Fluorescin in the Presence of Cobalt (II) and Reaction Against Other Reactive Oxygen Species

A fluorophotometric method for the determination of hydrogen peroxide (H₂O₂) using fluorescin was developed. This method was based on the oxidative reaction of fluorescin, a colorless, non-fluorescent lactoid fluorescein, by H₂O₂ to give highly fluorescein fluorescence emission. In the determination of H₂O₂, the calibration curve exhibited linearity over the H₂O₂ concentration range of 1.5–310 ng mL⁻¹ at an emission wavelength of 525 nm with an excitation of 500 nm and with relative standard deviations (n = 6) of 2.51%, 2.48%, and 1.31% for 3.1 ng mL⁻¹, 30.8 ng mL⁻¹, and for 308 ng mL⁻¹ of H₂O₂, respectively. The detection limit for H₂O₂ was 1.9 ng mL⁻¹ six blank determinations was performed (ρ = 6). This proposed method was applied to detection of other reactive oxygen species and nitrogen species (ROS/RNS) such as singlet oxygen (¹O₂), hydroxyl radical (^•OH), peroxynitrite (ONOO⁻) etc., and it was possible to detect them with a high sensitivity. In addition, this proposed method was applied to the recovery tests of H₂O₂ in calf serum, human saliva, rain water, and wheat noodles; the results were satisfactory.     

Rapid controlled hydrolytic degradation of poly(l-lactic acid) by blending with poly(aspartic acid-co-l-lactide)

Although poly(lactic acid) is known as a biodegradable polymer, its hydrolytic degradation is extremely slow, taking years in water and in the human body. In this study the effects of blending oligomeric poly(aspartic acid-co-lactide) (PALs) on the hydrolytic degradation of poly(l-lactic acid) (PLLA) were studied in detail. It was found that the addition of PAL did not accelerate the hydrolysis of the PLLA in air (25 °C, 60% relative humidity), but significantly accelerated it in a phosphate buffer solution. The degradation rate becomes higher for the blends containing PAL with higher molar ratios of lactide to aspartic acid units, [LA]/[Asp], when PLLA/PAL blends prepared with different PALs are compared at the same PAL concentration. TEM results, in which the distribution of PALs with higher [LA]/[Asp] occurs at a smaller scale in blends, imply that higher miscibility of the PAL with PLLA results in higher contact area between the components, thereby accelerating the degradation efficiently.