Radiation-induced cis–trans isomerization of polyisoprenes and temperature dependence of the equilibria

The cis-trans interconversion of polyisoprenes in solutions induced by γ-radiation in the presence of a sensitizer, which is any one of organic bromides or n-butyl mercaptan, was studied by using hevea and gutta percha as starting substances. The percentage cis remaining or converted after irradiation were determined by the infrared absorption. The equilibrium constants for the interconversion at 22, 60, and 100°C. were found to be 3.00, 5.25, and 7.33, respectively. The first-order rate constants for cis → trans and trans → cis isomerizations at 22°C. were calculated to be 9.05 and 2.91, respectively. The results were interpreted by the mechanism proposed by Golub, according to which the double bonds from π complexes with radiolytic fragments from sensitizers give a radical transition state capable of interconversion. However, our results showing that heating shifts the equilibrium toward trans isomer are not in accord with the mechanisms of the radiation-induced isomerization of polybutadiene of Golub and those for photoisomerization of aromatic azo compounds.     

Quantum tautomerization in porphycene and its isotopomers: Path-integral molecular dynamics simulations

Path-integral molecular dynamics simulations have been performed for porphycene and its isotopic variants in order to understand the effect of isotopic substitution of inner protons on the double proton transfer mechanism. We have used an on-the-fly direct dynamics technique at the semiempirical PM6 level combined with specific reaction parameterization. Our quantum simulations show that double proton transfer of the unsubstituted porphycene at T = 300 K mainly occurs via a so-called concerted mechanism through the D_2h second-order saddle point. In addition, we found that both isotopic substitution and temperature significantly affect the double proton transfer mechanism. For example, the contribution of the stepwise mechanism increases with a temperature increase. We have also carried out hypothetical simulations with the porphycene configurations being completely planar. It has been found that out-of-plane vibrational motions significantly decrease the contribution of the concerted proton transfer mechanism.     

Communication: A concerted mechanism between proton transfer of Zundel anion and displacement of counter cation

Ab initio path integral molecular dynamics simulation of M(+)(H(3)O(2)(-)) (M = Li, Na, and K) has been carried out to analyze how the structure and dynamics of a low-barrier hydrogen-bonded Zundel anion, H(3)O(2)(-), can be affected by the counter alkali metal cation, M(+). Our simulation predicts that the quantum proton transfer in Zundel anion can be strongly coupled to the motion of counter cation located nearby. A smaller cation can induce larger structural distortion of the Zundel anion fragment making the proton transfer barrier higher, and hence, lower the vibrational excitation energy. It is also argued that a large H∕D isotope effect is present.     

A Palladium-mediated DNA Base Pair of a β-C-Nucleoside Possessing a 2-Aminophenol as the Nucleobase

Abstract

An approach we have used in this study for the incorporation of metal ions into DNA, is the direct modification of a DNA base itself, turning it into a metal-chelating nucleobase wherein two nucleobases are paired through metal coordination. Herein we report the X-ray crystal structure of a synthetic intermediate 6 for the aminophenol bearing nucleoside 3 and its metal coordination properties with Pd²⁺. The anomeric configuration of the nucleoside was unequivocally determined to be β-form by the X-ray analysis of 6; the structure has been resolved by direct methods (S1R97) and expanded using Fourier techniques (DIRDIF94) using 2628 independent reflections with I>2.00 [sgrave](I) and 425 parameters. Final R (R_w) was 0.037 (0.043): orthorhombic, space group P2₁2₁2₁ (#19) with a=16.562(1) Å, b=16.933(1) Å, c=11.205(1) Å, and V=3142.2(4) ų; D_c =1.369g/cm³ for Z=4, and molecular weight 647.65. This result is consistent with the tentative assignment by our previous ¹H NOE differentiation experiments. Detailed ¹H NMR studies showed that the nucleoside forms a stable 2:1 complex with Pd²⁺ with concomitant deprotonation of its phenolic proton. Although there are two possible structures (cis or trans) for the square-planar Pd²⁺ complex, the ratio of cis to trans was approximately 1:1. The electrospray ionization time-of-flight mass spectrum of the complex also provided clear evidence for the 2:1 complexation.     

Nanotube nanoscience: A molecular-dynamics study

Carbon nanotubes, fullerenes, and other nanostructured carbon materials are now the most important material phases in the field of nanoscience and nanotechnology. We study the structural stabilities and the interconversion of carbon nanotubes and various other carbon nanostructured phases at elevated temperatures as well as under high pressure using the molecular dynamics method combined with a newly parametrized transferable tight-binding model. The model can deal with not only sp² and sp³ covalent bonds but also the interaction between sp² layers, which plays an important role in the structural and electronic properties of carbon nanostructured materials. It is found that, during a thermal transformation process of carbon nanotubes with C₆₀ fullerenes trapped inside into double-walled carbon nanotubes, the outer carbon-nanotube wall is chemically active and forms covalent bonds with inner carbon atoms, and that most vacancies on the initially imperfect outer tube wall are eventually filled with atoms migrated from inner fullerenes. It is also found that external pressure of about 20 GPa induces a variety of structural transformations in carbon nanostructures. On the other hand, pressure of 30 GPa or higher usually results in sp³-rich amorphous carbon materials. Finally, the rotational interlayer friction force in double-walled carbon nanotubes is studied for the system of (4,4)@(9,9), and the torque of the friction force per unit area acting on each nanotube of the system is found to be as small as . This small value indicates the importance of carbon nanostuctured materials not only for nanoelectronics but also for nanometer-scale machines in the future.     

Sub-5-fs real-time spectroscopy of transition states in bacteriorhodopsin during retinal isomerization

By using a sub-5-fs visible laser pulse, we have made the first observation of the vibrational spectra of the transition state during trans-cis isomerization in the retinal chromophore of bacteriorhodopsin (bR(S68). No instant isomerization of the retinal occurs in spite of electron promotion from the bonding pi-orbital to the anti-bonding pi*-orbital. The difference between the in-plane and out-of-plane vibrational frequencies (about 1150-1250 and 900-1000 cm(-1), respectively) is reduced during the first time period. The vibrational spectra after this period became very broad and weak and are ascribed to a "silent state." The silent state lasts for 700-900 fs until the chromophore isomerizes to the cis-C13 = C14 conformation. The frequency of the C = C stretching mode was modulated by the torsion mode of the C13 = C14 double bond with a period of 200 fs. The modulation was clearly observed for four to five periods. Using the empirical equation for the relation between bond length and stretching frequency, we determined the transitional C = C bond length with about 0.01 angstroms accuracy during the torsion motion around the double bond with 1-fs time resolution.     

Effect of surface interaction of silica nanoparticles modified by silane coupling agents on viscosity of methylethylketone suspension

In order to control the viscosity of a dense silica methylethylketone (MEK) suspension, the surfaces of silica nanoparticles were modified by 3-glycidoxypropyltrimethoxysilane (GPS) or hexyltrimethoxysilane (C6S) in MEK with the addition of a small amount of pH-controlled water. First, the effect of water addition on the amount of chemisorbed coupling agent was investigated. pH-controlled water enhanced the reactivity of the coupling agent in MEK. The amount of chemisorbed coupling agent increased slightly with the addition of pH 3 water and increased remarkably with the addition of pH 12 water. Next, the effect of the organic functional groups of the coupling agent, pH of the additive water, and additive amount of coupling agent on surface interaction were determined by colloid probe AFM. The steric repulsive force between the silica nanoparticles increased due to water addition, particularly when the pH was maintained at 3. The viscosity of the silica MEK suspension reduced effectively when this repulsive force appeared; however, the optimum condition for reducing the suspension viscosity was dependent on the coupling agent species. The viscosity of the dense silica MEK suspension can be controlled by the addition of small amounts of pH-controlled water and the functional groups of the coupling agent.     

Iron-catalyzed arylmagnesiation of aryl(alkyl)acetylenes in the presence of an N-heterocyclic carbene ligand

Addition of arylmagnesium bromides to aryl(alkyl)acetylenes proceeded in the presence of an iron catalyst and a N-heterocyclic carbene ligand to give high yields of the corresponding alkenylmagnesium reagents, which were transformed into tetrasubstituted alkenes by subsequent treatment with electrophiles. [reaction: see text]