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.     

The electronic structure and spectrum of tropone

The electronic structure and spectrum of tropone were studied by paying special attention to an assignment of the 300 m band. The band was shown to have a single ^* character overlapped by an n ^* transition from the following experimental and theoretical studies: (i) From the comparison of the observed transition energies and intensities with theoretical values obtained by the Pariser-Parr-Pople calculation in which the values of W _X ^2p (valence state ionization potential of the oxygen atom) and k (bond alternation parameter) taken as guiding parameters were changed widely and their adequateness was carefully examined, (ii) From the correlation among the electronic absorption spectra of tropone, troponeimine, and heptafulvene. (iii) From the finding that the 300 m band increases its intensity with the increasing polarity of the solvent. (iv) From the position and intensity of a band newly observed in the vacuum ultraviolet region.

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Zusammenfassung An Tropon wurden Elektronenstruktur und Spektrum untersucht, speziell die 300 m-Bande. Diese entsteht aus einem einzigen - ^*-Übergang, überlagert von einer schwachen n-^*-Bande, und nicht aus 2 - ^*-Banden. Als Stütze dienen: 1. eine PPP-Rechnung, bei der das Valenzzustandsionisationspotential von Sauerstoff und der Bindungsalternierungsparameter sorgfältig variiert wurden, 2. die Korrelation der Spektren von Tropon, Troponimin und Heptafulven, 3. der Lösungsmitteleinfluß auf die Bande, 4. eine neuaufgefundene UV-Bande.

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Résumé La structure électronique et le spectre de la tropolone ont été étudiés en accordant une attention particulière à l'identification de la bande à 300 m. Cette bande a été caractérisée comme résultant d'une transition ^* recouverte par une transition n ^*, à l'aide des arguments théoriques et expérimentaux suivants: 1. à partir de la comparaison des énergies et des intensités de transition observées, avec les valeurs théoriques obtenues par un calcul Pariser-Parr-Pople où les valeurs de W _X ^2p (potentiel d'ionisation de l'état de valence de l'atome d'oxygène) et de k (paramètre d'alternance des liaisons), considérés comme paramètres régulateurs, ont été largement variées et soigneusement analysées. 2. à partir de la corrélation entre les spectres d'absorption électronique de la tropolone, de la tropolonéimine et de l'heptafulène. 3. à partir du fait que la bande à 300 m voit son intensité croitre avec la polarité du solvent. 4. à partir de la position et de l'intensité d'une bande nouvelle observée dans la région de l'ultra-violet lointain.

     

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.     

Monolithic silica columns with various skeleton sizes and through-pore sizes for capillary liquid chromatography

Reduction of through-pore size and skeleton size of a monolithic silica column was attempted to provide high separation efficiency in a short time. Monolithic silica columns were prepared to have various sizes of skeletons (approximately 1-2 microm) and through-pores (approximately 2-8 microm) in a fused-silica capillary (50-200 microm I.D.). The columns were evaluated in HPLC after derivatization to C18 phase. It was possible to prepare monolithic silica structures in capillaries of up to 200 microm I.D. from a mixture of tetramethoxysilane and methyltrimethoxysilane. As expected, a monolithic silica column with smaller domain size showed higher column efficiency and higher pressure drop. High external porosity (> 80%) and large through-pores resulted in high permeability (K = 8 x 10(-14) -1.3 x 10(-12) m2) that was 2-30 times higher than that of a column packed with 5-mirom silica particles. The monolithic silica columns prepared in capillaries produced a plate height of about 8-12 microm with an 80% aqueous acetonitrile mobile phase at a linear velocity of 1 mm/s. Separation impedance, E, was found to be as low as 100 under optimum conditions, a value about an order of magnitude lower than reported for conventional columns packed with 5-microm particles. Although a column with smaller domain size generally resulted in higher separation impedance and the lower total performance, the monolithic silica columns showed performance beyond the limit of conventional particle-packed columns under pressure-driven conditions.     

WKB-like wave-functional for a string state and path-dependent phase factor

The variational calculation of the path-ordered phase factor is streamlined. We propose that the wave functional for a string state is approximately of the form

$\text{Ψ[x(σ)=}\text{Π}\text{σ′}\text{K(x(σ′))}\text{P exp}\text{ie∫}\text{A d}\text{x}$

.The real factor K is shown to be proportional to the square root of the dielectric permeability in the Kogut-Susskind-'t Hooft model of colour flux collimation.     

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.     

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).     

New photoswitching unit for magnetic interaction: diarylethene with 2,5-bis(arylethynyl)-3-thienyl group

Photoswitching of the intramolecular magnetic interaction was demonstrated using diarylethenes with 2,5-bis(arylethynyl)-4-methyl-3-thienyl side group. Two nitroxide radicals were placed at each end of the 2,5-bis(arylethynyl)-4-methyl-3-thienyl group. Three kinds of aryl groups, 2,5-thienylene, p-phenylene, and m-phenylene groups, were used in the arylethynyl moiety. The diarylethene photoswitching units have an extended pi-conjugated chain on one side of the diarylethene. The photochromic reactivity was dependent on the arylethynyl group. Diarylethenes with m-phenylene group showed an efficient photochromic reactivity. Along with the photochromic reaction the diarylethenes showed photoswitching of an ESR spectrum originating from the change in the magnetic interaction between two unpaired electrons. The open-ring isomer showed stronger exchange interaction than the photogenerated closed-ring isomer. The magnetic interaction between two radicals via the pi-conjugated chain was altered by photocyclization due to the change of the hybrid orbital at the 2-position of the thiophene ring from sp(2) to sp(3).     

Phenomenological analysis of elongational flow birefringence in semidilute solutions of hydroxypropylcellulose

The relaxation time of a polymer chain in an elongational flow field was investigated for hydroxypropylcellulose (HPC) semidilute solution systems by two methods: phenomenological analysis of elongational flow-induced birefringence, and dynamic light scattering (DLS) and rheological measurements. To understand the relaxation time of an entangled semiflexible polymer solution in an elongational flow field, scaling analysis of the elongational flow-induced birefringence curve was performed. The results of both temperature and concentration scaling analyses showed that birefringence curves at different temperatures and at several HPC concentrations were described well by a universal birefringence–strain rate curve. This scaling behavior was compared with the "fuzzy cylinder" model. The critical strain rate corresponded to the correlation time of the slow relaxation mode determined by DLS measurement and the relaxation spectrum obtained by dynamic viscoelasticity measurement. The elongational flow-induced birefringence observed in an HPC semidilute solution was concluded to be attributed to the orientation of the HPC segment in the entangled molecular system, because the dominant relaxation mode is found to be the concentration fluctuation of an entangled molecular cluster in a quiescent state.