Collision-energy-resolved Penning ionization electron spectroscopy of p-benzoquinone: study of electronic structure and anisotropic interaction with He(*)(2 (3)S) metastable atoms

Collision energy dependence of partial ionization cross sections (CEDPICS) of p-benzoquinone with He(*)(2 (3)S) metastable atoms indicates that interaction potentials between p-benzoquinone and He(*)(2 (3)S) are highly anisotropic in the studied collision energy range (100-250 meV). Attractive interactions were found around the C==O groups for in-plane and out-of-plane directions, while repulsive interactions were found around CH bonds and the benzenoid ring. Assignment of the first four ionic states of p-benzoquinone and an analogous methyl-substituted compound was examined with CEDPICS and anisotropic distributions of the corresponding two nonbonding oxygen orbitals (n(O) (+),n(O) (-)) and two pi(CC) orbitals (pi(CC) (+),pi(CC) (-)). An extra band that shows negative CEDPICS was observed at ca. 7.2 eV in Penning ionization electron spectrum.     

Deuterium isotope effects on hydrophobic interactions: the importance of dispersion interactions in the hydrophobic phase

Hydrogen/deuterium isotope effects on hydrophobic binding were examined by means of reversed-phase chromatographic separation of protiated and deuterated isotopologue pairs for a set of 10 nonpolar and low-polarity compounds with 10 stationary phases having alkyl and aryl groups bonded to the silica surface. It was found that protiated compounds bind to nonpolar moieties attached to silica more strongly than deuterated ones, demonstrating that the CH/CD bonds of the solutes are weakened or have less restricted motions when bound in the stationary phase compared with the aqueous solvent (mobile phase). The interactions responsible for binding have been further characterized by studies of the effects of changes in mobile phase composition, temperature dependence of binding, and QSRR (quantitative structure-chromatographic retention relationship) analysis, demonstrating the importance of enthalpic effects in binding and differentiation between the isotopologues. To explain our results showing the active role of the hydrophobic (stationary) phase we propose a plausible model that includes specific contributions from aromatic edge-to-face attractive interactions and attractive interactions of aliphatic groups with the pi clouds of aromatic groups present as the solute or in the stationary phase.     

Site-selective RNA cleavage by DNA bearing a base pair-mimic nucleoside

We have synthesized the deoxyadenosine derivative tethering a phenyl group (X), which mimics the Watson-Crick A/T base pair. The RNA/DNA hybrid duplexes containing X in the middle of the DNA sequence showed a similar thermal stability regardless of the ribonucleotide species (A, G, C, or U) opposite to X, probably because of the phenyl group stacking inside of the duplex accompanied by the opposite ribonucleotide base flipped in an extrahelical position. The RNA strand hybridized with the DNA strand bearing X was cleaved on the 3'-side of the ribonucleotide opposite to X in the presence of MgCl2, and the RNA sequence to be cleaved was not restricted. The site-specific RNA hydrolysis suggests that the DNA strand bearing X has the advantage of the site-selective base flipping in the target sequence and the development of a "universal deoxyribozyme" to exclusively cleave a target RNA sequence.     

Thermodynamic analysis of duplex formation of the heterochiral DNA with L-deoxyadenosine.

An L-DNA, the mirror-image isomer of natural DNA, has extraordinary nuclease resistance, and thus the molecules should be promising reagents for many applications, such as antisense technology. However, little is known about the structural and thermodynamic properties of DNAs with this modified nucleotide. In this study, we prepared the L-nucleotide (L-dA) and introduced it into oligodeoxyribonucleotides to assess the ability of the L-nucleotide as a functional molecule for many applications based on the DNA hybridization. Two decamers with an L-dA at the center were synthesized and duplexes with the complementary DNA strand were applied to structural and thermodynamic analyses. The structural study by CD spectra showed that the structures of both modified "L/D-D" duplexes were the typical B-form. This result suggests that the global structure of DNA was not collapsed by the introduction of an L-DNA. Thermodynamic parameters (deltaH degrees, deltaS degrees, and deltaG degrees 37) of the duplex formation, determined by UV melting experiments, indicated that the both duplexes were destabilized at about 2.5 to 3.0 kcal mol(-1) by the introduced L-dA, mainly due to an unfavorable enthalpic effect. In conjunction with information by other researchers, these results suggest that the L-DNA affect on the duplex structure and the stability vary locally; thus, the thermodynamic stability of modified L/D-D duplexes should be predictable by the nearest-neighbor thermodynamic parameters.     

Proposed mechanism for the reaction catalyzed by a diterpene cyclase,aphidicolan-16beta-ol synthase: experimental results on biomimetic cyclization and examination of the cyclization pathway by ab initio calculations

To examine the mechanism of the cyclization reaction catalyzed by aphidicolan-16beta-ol synthase (ACS), which is a key enzyme in the biosynthesis of diterpene aphidicolin, a specific inhibitor of DNA polymerase alpha, skeletal rearrangement of 2a and biomimetic cyclization of 4b were employed. The structures of the reaction products, which reflect penultimate cation intermediates, allowed us to propose a detailed reaction pathway for the Lewis acid-catalyzed cyclizations and rearrangements. Isolation of these products in an aphidicolin-producing fungus led us to speculate that the mechanism of the ACS-catalyzed cyclization reaction is the same as that of a nonenzymatic reaction. Ab initio calculations of the acid-catalyzed reaction intermediates and the transition states indicate that the overall reaction catalyzed by ACS is an exothermic process though the reaction proceeds via an energetically disfavored secondary cation-like transition state. In conjunction with the solvent effect in the acid-catalyzed reactions, this indicates that the actual role of ACS is to provide a template which enforces conformations of the intermediate cations leading to the productive cyclization although it has been believed that the cation-pi interaction between cation intermediates and aromatic amino acid residues in the active site is important for the enzymatic catalysis. This study provided important information on the role of various cationic species, especially secondary cation-like structures, in both nonenzymatic and enzymatic reactions.     

Optical microscopy and in situ Raman scattering of single crystalline ethylene hydrate and binary methane-ethylene hydrate at high pressures

Visual observations through a microscope and in situ Raman measurements have been made for single crystalline ethylene hydrate (EH) and binary methane-ethylene hydrate (MEH) at pressures up to 3.7 GPa and room temperature. Both hydrates showed pressure-induced phase transitions at 1.6, 2.0, and 3.0 GPa for EH and at 1.7, 2.1, and 3.3 GPa for MEH. The cubic sI phase of EH and MEH remains stable up to 1.6 and 1.7 GPa, respectively, which are more widely ranging values than the values for the methane hydrate sI phase. In this sI phase of binary MEH, the cage occupancies by methane and ethylene molecules are investigated from Raman spectra. Above P = 3.0 GPa for EH and 3.3 GPa for MEH, they decomposed by associating with the formation of the polyethylene.     

Efficient excitation energy transfer in long meso-meso linked Zn(II) porphyrin arrays bearing a 5,15-bisphenylethynylated Zn(II) porphyrin acceptor

Electronically coupled porphyrin arrays are suitable for artificial light harvesting antenna in light of a large absorption cross-section and fast excitation energy transfer (EET). Along this line, an artificial energy transfer model system has been synthesized, comprising of an energy donating meso-meso linked Zn(II) porphyrin array and an energy accepting 5,15-bisphenylethynylated Zn(II) porphyrin linked via a 1,4-phenylene spacer. This includes an increasing number of porphyrins in the meso-meso linked Zn(II) porphyrin array, 1, 2, 3, 6, 12, and 24 (Z1A, Z2A, Z3A, Z6A, Z12A, and Z24A). The intramolecular singlet-singlet EET processes have been examined by means of the steady-state and time-resolved spectroscopic techniques. The steady-state fluorescence comes only from the acceptor moiety in Z1A-Z12A, indicating nearly the quantitative EET. In Z24A that has a molecular length of ca. 217 A, the fluorescence comes largely from the acceptor moiety but partly from the long donor array, indicating that the intramolecular EET is not quantitative. The transient absorption spectroscopy has provided the EET rates in real time scale: (2.5 ps)(-1) for Z1A, (3.3 ps)(-1) for Z2A, (5.5 ps)(-1) for Z3A, (21 ps)(-1) for Z6A, (63 ps)(-1) for Z12A, and (108 ps)(-1) for Z24A. These results have been well explained by a revised F?rster equation (Sumi formula), which takes into account an exciton extending coherently over several porphyrin pigments in the donor array, whose length is not much shorter than the average donor-acceptor distance. Advantages of such strongly coupled porphyrin arrays in light harvesting and transmission are emphasized in terms of fast EET and a large absorption cross-section for incident light.     

Duplex dissociation of telomere DNAs induced by molecular crowding

Because of the importance of telomere DNAs, the structures of these DNAs in vivo are currently of great research interest in the medical, pharmaceutical, chemical, and industrial fields. To understand the structure of biomolecules in vivo, their properties studied in vitro are extrapolated to the in vivo condition, while the condition in a living cell is inherently molecularly crowded and a nonideal solution contains various biomolecules. We investigated the effect of molecular crowding, which is one of the most important cellular environmental conditions, on the structure and stability of the telomere and G-rich and C-rich DNAs using circular dichroism (CD) spectra, CD melting curves, and isothermal titration calorimetry (ITC). The CD spectra and CD melting curves of G-rich DNA, C-rich DNA, and the 1:1 mixture of G-rich and C-rich DNAs showed that each G-rich DNA, C-rich DNA, and the 1:1 mixture form the antiparallel G-quadruplex, I-motif, and duplex, respectively, in the noncrowding condition as previously considered. On the contrary, the G-rich and C-rich DNAs individually form the parallel G-quadruplex and I-motif, respectively, in the molecular crowding condition, and the 1:1 mixture folds into the parallel G-quadruplex and I-motif but does not form a duplex. The ITC measurements indicated that the thermodynamic stability (DeltaG degrees (20)) of the duplex formation between the G-rich and C-rich DNAs in the noncrowding condition was -10.2 kcal mol(-)(1), while only a small heat change was observed in the ITC measurements in the molecular crowding condition. These ITC results also demonstrated that the molecular crowding condition prevents any duplex formation between G-rich and C-rich DNAs. These results indicate that a structural polymorphism of the telomere DNAs is induced by molecular crowding in vivo.     

Lipase-catalyzed transformation of poly(lactic acid) into cyclic oligomers

Enzymatic transformations into cyclic oligomers were carried out with the objective of developing chemical recycling of poly(lactic acid)s, such as poly(D,L-lactic acid) (PDLLA), poly(D-lactic acid) (PDLA) and poly(L-lactic acid) (PLLA), which are typical biodegradable polymers. They were degraded by lipase in an organic solvent to produce the corresponding cyclic oligomer with a molecular weight of several hundreds. PDLLA (with a Mw of 84,000) was quantitatively transformed into cyclic oligomers by lipase RM (Lipozyme RM IM) in chloroform/hexane at 60 degrees C. PLLA (with a Mw of 120,000) was transformed into cyclic oligomer by lipase CA (Novozym 435) at a higher temperature of 100 degrees C in o-xylene. The oligomer structure was identified by 1H and 13C NMR spectroscopy and MALDI-TOF (matrix assisted laser desorption/ionization-time-of-flight) mass spectrometry.     

Ring‐Opening Reactions of 3‐Aryl‐1‐benzylaziridine‐2‐carboxylates and Application to the Asymmetric Synthesis of an Amphetamine‐Type Compound

Nucleophilic ring‐opening reactions of 3‐aryl‐1‐benzylaziridine‐2‐carboxylates were examined by using O‐nucleophiles and aromatic C‐nucleophiles. The stereospecificity was found to depend on substrates and conditions used. Configuration inversion at C(3) was observed with O‐nucleophiles as a major reaction path in the ring‐opening reactions of aziridines carrying an electron‐poor aromatic moiety, whereas mixtures containing preferentially the syn‐diastereoisomer were generally obtained when electron‐rich aziridines were used (Tables 1–3). In the reactions of electron‐rich aziridines with C‐nucleophiles, S_N2 reactions yielding anti‐type products were observed (Table 4). Reductive ring‐opening reaction by catalytic hydrogenation of (+)‐trans‐(2S,3R)‐3‐(1,3‐benzodioxol‐5‐yl)aziridine‐2‐carboxylate (+)‐trans‐ 3c afforded the corresponding α‐amino acid derivative, which was smoothly transformed into (+)‐tert‐butyl [(1R)‐2‐(1,3‐benzodioxol‐5‐yl)‐1‐methylethyl]carbamate((+)‐ 14 ) with high retention of optical purity (Scheme 6).