Detecting Counterion Dynamics in DNA–Protein Association

Due to a high density of negative charges on its surface, DNA condenses cations as counterions, forming the so-called “ion atmosphere”. Although the release of counterions upon DNA–protein association has been postulated to have a major contribution to the binding thermodynamics, this release remains to be confirmed through a direct observation of the ions. Herein, we report the characterization of the ion atmosphere around DNA using NMR spectroscopy and directly detect the release of counterions upon DNA–protein association. NMR-based diffusion data reveal the highly dynamic nature of counterions within the ion atmosphere around DNA. Counterion release is observed as an increase in the apparent ionic diffusion coefficient, which directly provides the number of counterions released upon DNA–protein association.     

Several types of bilayer smectic liquid crystals with ferroelectric and antiferroelectric properties in binary mixture of dimeric compounds

The mesomorphic behavior and phase structure were examined in the mixture of two kinds of dimeric compounds, alpha,omega-bis(4-alkoxyanilinebenzylidene-4'-carbonyloxy)pentane (mOAM5AMOm), by optical microscopy, X-ray diffraction, polarization switching, and second-harmonic generation measurements. One compound is 4OAM5AMO4 with a short terminal alkyl chain that forms a single-layer smectic phase (SmCAs) with a random mixing of spacer and tail groups. Another compound is 16OAM5AMO16 with a long terminal alkyl chain that forms a chiral, anticlinic, and antiferroelectric bilayer phase (SmCAb) with the bent molecules tilted to the bilayer. By mixing these two compounds, the SmCAs phase of 4OAM5AMO4 is easily destabilized, leading to the wide content region of the bilayer phases. In the bilayer regime, three other smectic phases are newly induced. Two of them are antiferroelectric and ferroelectric phases in which the molecules lie perpendicularly with respect to the layer. The other shows no polar response to an external electric field and behaves like a smectic A. The new appearance of these bilayer phases is discussed as a mixing effect of long and short tail groups.     

Highly efficient total synthesis of the marine natural products (+)-avarone, (+)-avarol, (-)-neoavarone, (-)-neoavarol and (+)-aureol

Biologically important and structurally unique marine natural products avarone (1), avarol (2), neoavarone (3), neoavarol (4) and aureol (5), were efficiently synthesized in a unified manner starting from (+)-5-methyl-Wieland-Miescher ketone 10. The synthesis involved the following crucial steps: i) Sequential BF(3)Et(2)O-induced rearrangement/cyclization reaction of 2 and 4 to produce 5 with complete stereoselectivity in high yield (2 --> 5 and 4 --> 5); ii) strategic salcomine oxidation of the phenolic compounds 6 and 8 to derive the corresponding quinones 1 and 3 (6 --> 1 and 8 --> 3); and iii) Birch reductive alkylation of 10 with bromide 11 to construct the requisite carbon framework 12 (10 + 11 --> 12). An in vitro cytotoxicity assay of compounds 1-5 against human histiocytic lymphoma cells U937 determined the order of cytotoxic potency (3 > 1 > 5 > 2 > 4) and some novel aspects of structure-activity relationships.     

Controllable synthesis, magnetism and solubility enhancement of graphene nanosheets/magnetite hybrid material by covalent bonding

Hybrids of Fe(3)O(4) nanoparticles and surface-modified graphene nanosheets (GNs) were synthesized by a two-step process. First, graphene nanosheets were modified by SOCl(2) and 4-aminophenoxyphthalonitrile to introduce nitrile groups on their surface. Second, the nitrile groups of surface-modified graphene nanosheets were reacted with ferric ions on the surface of Fe(3)O(4) with the help of relatively high boiling point solvent ethylene glycol to form a GNs/Fe(3)O(4) hybrid. The covalent attachment of Fe(3)O(4) nanoparticles on the graphene nanosheet surface was confirmed by Fourier-transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), energy-dispersive X-ray spectrometer (EDS) and scanning electron microscopy (SEM). TEM and HRTEM observations indicated that the sizes of the nanoparticles and their coverage density on GNs could be easily controlled by changing the concentration of the precursor and the weight ratio to GNs. Magnetic measurements showed that magnetization of the hybrid materials is strongly influenced by the reaction conditions. Chemically bonded by phthalocyanine, the solubility of as-synthesized GNs/Fe(3)O(4) hybrid materials was greatly enhanced, which was believed to have potential for applications in the fields of composites, wastewater treatment and biomaterials.     

Effect of co-adsorbed CO and reaction temperature on the dynamics of N2 desorption under steady-state N2O-CO reaction on Rh(110)

We have investigated the effect of co-absorbed CO and reaction temperature on the angular distribution of N(2) desorption by N(2)O decomposition under the steady state of N(2)O-CO reaction on Rh(110). Spatial distributions of desorbing product N(2) emission have been measured at various surface temperatures and CO coverages. The decomposed N(2) collimates at 48°-61° off normal in the parallel plane to [001] and [110] directions, indicating that adsorbed N(2)O just before the decomposition is oriented along the [001] direction. Although the inclined and collimated N(2) desorption is always observed at any steady-state CO coverage and reaction temperature, the shape of the collimated N(2) distribution varied dependent on the co-adsorbed CO coverage. The distribution becomes sharp and shifts toward the surface normal direction with increasing CO coverage. These effects of adsorbed CO on the angular distribution of N(2) are interpreted by the collision of desorbed N(2) with co-adsorbed CO.     

Mechanism of enhancement in absorbance of vibrational bands of adsorbates at a metal mesh with subwavelength hole arrays

We have investigated the mechanism of enhanced absorption intensities of vibrational bands of adsorbates on copper meshes with subwavelength holes by measuring and simulating temporal profiles of infrared pulses transmitted through the meshes. As reported previously [Williams et al., J. Phys. Chem. B, 2003, 107, 11871], the absorption intensities of CH stretching bands of alkanethiolate adsorbed on the mesh increase substantially with decreasing hole size. The enhancements of absorption intensities are associated with temporal delays of infrared pulses transmitted through the mesh. Finite difference time domain calculations reproduce the observed pulse delays as a function of hole size. These facts indicate that the delays of transmitted pulses are not caused by coupling of infrared radiation to surface plasmon polaritons propagating on the front and rear surfaces of the mesh, but they are caused by the reduction in group velocity owing to coupling to waveguide modes of mesh holes. Consequently, the strong enhancements of the absorption intensities are attributed to adsorbates inside the holes rather than to those on the mesh surfaces that have been proposed previously.     

Synthesis and Cation-Binding Properties of (1→6)-2,5-Anhydro-D-glucitol with 3,4-Di-O-Pentyl and Decyl Groups by Cyclopolymerization of 1,2:5,6-Dianhydro-D-mannitols

Abstract

The cyclopolymerizations of 1,2:5,6-dianhydro-3,4-di-O-pentyl-D-mannitol (1b) and 1,2:5,6-dianhydro-3,4-di-O-decyl-D-mannitol (1c) were carried out using BF₃OEt₂ and t-BuOK. All the resulting polymers consisted of cyclic constitutional units, i.e., the extent of cyclization was 100%. The polymer structures for the polymerization with t-BuOK were (1→6)-2,5-anhydro-3,4-di-O-pentyl-D-glucitol (2b) and (1→6)-2,5-anhydro-3,4-di-O-decyl-D-glucitol (2c), whereas those with BF₃O-decyl₂ comprised 2,5-anhydro-D-glucitols as major units along with other cyclic ones. These polymers were soluble in n-hexane, CHCl₃, and THF, but insoluble in water, which differs from the amphiphilic solubility of (1→6)-2,5-anhydro-3,4-di-O-methyl-D-glucitol (2a). The cation-binding properties of 2b and 2c were examined using alkali-metal picrates in order to compare them with those of 2a. The extraction yields for each cation decreased in the order of 2c < 2b < 2a. Every polymer exhibited a similar cation-binding selectivity in the order Cs⁺ > Rb⁺ > K⁺ ? Na⁺ > Li⁺. The ratio of K⁺ and Na⁺, K⁺/Na⁺, was 4.6 for 2a, 5.1 for 2b, and 7.1 for 2c in the increasing order 2a < 2b > 2c.     

Synthetic Utilization of α-Phosphonovinyl Anions

The α-phosphonovinyl anions, generated in situ from treatment of β-hetero-substituted vinyl-phosphonates 1a-c with LDA (or LTMP), were trapped with various electrophiles such as chlorotriorganosilanes, chlorotrimethylgermane, chlorotriorganotins, dimethyl disulfide, and halogen to afford the corresponding β-hetero-substituted α-functionalized vinylphosphonates 2–14 in good to excellent yields. The Friedel-Crafts reaction of α-(silyl) or α-(germyl)phosphonoketene dithioacetals 2, 9 or 4 with acid chlorides gave α-acylated phosphonoketene dithioacetals 15–19 in 53–91 % yields. The palladium-catalyzed cross-coupling reaction of β-ethoxy-α-(tributylstannyl)vinylphosphonate 13 with a variety of organic halides (R = acyl, allyl, aryl etc.) provided β-ethoxy-α-substituted vinylphosphonates 20–25 in good to moderate yields. The palladium-mediated cross-coupling reaction of α-(iodo)-vinyl-phosphonates 7, 14 with terminal acetylenes afforded α-alkynylated vinylphosphonates 26–29 in 69–83 % yields.     

Preferential Uniplanar Orientation of Cellulose Microfibrils Reinvestigated by the FTIR Technique

A simple detection method to observe the uniplanar orientation behavior of native cellulose microfibrils to the cell wall surface by using Fourier transform infrared (FTIR) spectroscopy in the transmission mode is reported. Four bands at 1372, 1355, 1337, and 1317 cm⁻¹ (the latter two have been mentioned previously by Liang and Marchessault (1960, J. Polym. Sci. 43: 85–100)) were found to be sensitive to such orientation: the two middle bands at 1355 and 1337 cm⁻¹ increase remarkably when the 0.60–61 nm lattice planes lie parallel to the cell wall surfaces. The reverse was true when the 0.53–54 nm lattice planes oriented preferentially. Polarization of the two bands at 1372 and 1355 cm⁻¹ was parallel, while that of the other two bands at lower wavenumbers, i.e., at 1337 and 1317 cm⁻¹, was perpendicular to the molecular axis of cellulose. These bands were assigned to OH-related motion, probably to in-plane OH bending, as reported by Maréchal and Chanzy (2000, J. Mol. Spectrosc. 523: 183–196).