Efficient identification and quantification of proteins using isotope-coded 1-(6-methylnicotinoyloxy)succinimides by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

We describe a convenient and useful method for the identification and relative quantification of proteins using light and heavy reagents, 1-(6-methylnicotinoyloxy)succinimides (6-CH(3)-Nic-NHS and 6-CD(3)-Nic-NHS, respectively). This method is based on the chemical derivatization of amino groups of tryptic peptides with these reagents, i.e., the basic moiety of the reagents thus incorporated into both the N-terminal amino group and the epsilon-amino group of the lysine residue would improve the ionization efficiency of tryptic peptides. An increase in protein sequence coverage is achieved by derivatization with these reagents or by combination of mass values before and after derivatization. Since a combination of 6-CH(3)-Nic-NHS and d(3)-labeled reagent (6-CD(3)-Nic-NHS) generates a 3 Da mass difference per reaction site, the d(3)-labeled reagent shifts the mass values of d(0)-labeled peptides according to the number of reactive amino groups in the peptides. In the case of tryptic peptides, the mass values of C-terminal arginine and lysine peptides are shifted by 3 and 6 Da, respectively. Further, the 3 Da mass difference between 6-CH(3)-Nic-NHS and 6-CD(3)-Nic-NHS offers a means for the relative quantification of protein by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.     

Chiral spherical molecule constructed from aromatic amides: facile synthesis and highly ordered network structure in the crystal

A novel chiral spherical molecule composed of aromatic amide was synthesized in short steps. The molecule is constructed from four benzene rings connected by six amide bonds and has multiple functionalizable points and an asymmetric structure. The racemic spherical molecule constructed channel network structures in the crystalline state.     

Encapsulation and dynamic behavior of two H2 molecules in an open-cage C70

An open-cage C70 derivative having a 13-membered ring opening (2) was synthesized by a three-step reaction; thermal reaction of C70 with a pyridazine derivative, oxidative cleavage of the CC double bond, and insertion of a sulfur atom to the opening. The structure of 2 was determined by X-ray analysis. One H2 molecule was introduced into 2 to give H2@2 in 97% yield. Furthermore, two H2 molecules were encapsulated in 2 in 3% yield. The positional exchange of two H2 molecules inside 2 was clearly observed by the dynamic low-temperature NMR measurements.     

2-(4,5,6,7-Tetrafluorobenzimidazol-2-yl)-4,4,5,5-tetramethyl-4,5-dihydro-1- H-imidazole-3-oxide-1-oxyl, a hydrogen-bonded organic quasi-1D ferromagnet

The title radical (F4BImNN) is a stable nitronylnitroxide that forms hydrogen-bonded NH... ON chains in the solid state. The chains assemble the F4BImNN molecules to form stacked contacts between the radical groups, in a geometry that is expected to exhibit ferromagnetic (FM) exchange based on spin polarization (SP) models. The experimental magnetic susceptibility of F4BImNN confirms the expectation, showing 1-D Heisenberg chain FM exchange behavior over 1.8-300 K with an intrachain exchange constant of Jchain/k = +22 K. At lower temperatures, ac magnetic susceptibility and variable field heat capacity measurements show that F4BImNN acts as a quasi-1-D ferromagnet. The dominant ferromagnetic exchange interaction is attributable to overlap between spin orbitals of molecules within the hydrogen-bonded chains, consistent with the SP model expectations. The chains appear to be antiferromagnetically exchange coupled, giving cusps in the ac susceptibility and zero field heat capacity at lower temperatures. The results indicate that the sample orders magnetically at about 0.7 K. The magnetic heat capacity ordering cusp shifts to lower temperatures as external magnetic field increases, consistent with forming a bulk antiferromagnetic phase below a Néel temperature of TN(0) = 0.72 K, with a critical field of Hc approximately 1800 Oe. The interchain exchange is estimated to be zJ/k congruent with (-)0.1 K.     

Three new furoquinoline alkaloids from the leaves of Boninia glabra

Three novel furoquinoline alkaloid oxogeranyl ethers (1-3) and one known furoquinoline alkaloid (4) were isolated from the leaves of Boninia glabra, an endemic plant of the Bonin Islands. Their structures were elucidated on the basis of spectroscopic analysis.     

Orientation of fluorinated cholesterol in lipid bilayers analyzed by 19F tensor calculation and solid-state NMR

6-F-cholesterol was reported to exhibit biological and interfacial properties similar to unmodified cholesterol. We have also found that 6-F-cholesterol mimicked the cholesterol activity observed in the systems of amphotericin B and lipid rafts. However, to use 6-F-cholesterol as a molecular probe to explore molecular recognition in membranes, it is indispensable to have detailed knowledge of the dynamic and orientation properties of the molecule in membrane environments. In this paper, we present the molecular orientation of 6-F-cholesterol (30 mol %) in dimyristoylphosphatidylcholine (DMPC) bilayers revealed by combined use of 19F chemical shift anisotropy (CSA), 2H NMR, and C-F rotational echo double resonance (REDOR) experiments. The axis of rotation of 6-F-cholesterol was shown to be in a similar direction to that of cholesterol in DMPC bilayers, which is almost parallel to the long axis of the molecular frame. The molecular order parameter of 6-F-cholesterol was determined to be ca. 0.85, which is within the range of reported values of cholesterol. These findings suggest that the dynamic properties of 6-F-cholesterol in DMPC are quite similar to those of unmodified cholesterol; therefore, the introduction of a fluorine atom at C6 has virtually no effect on cholesterol dynamics in membranes. In addition, this study demonstrates the practical utility of theoretical calculations for determining the 19F CSA principal axes, which would be extremely difficult to obtain experimentally. The combined use of quantum calculations and solid-state 19F NMR will make it possible to apply the orientation information of 19F CSA tensors to membrane systems.     

Sonication-assisted supramolecular nanorods of meso-diaryl-substituted porphyrins

Supramolecular nanorods of 5,15-diaryl-substituted porphyrins prepared by sonication method exhibit a broad absorption property, which is confirmed by photocurrent generation measurement in a photoelectrochemical cell.     

Combinatorial synthesis of the 1,5-polyol system based on cross metathesis: structure revision of amphidinol 3

Combinatorial synthesis of a 1,5-polyol system corresponding to the C1-C14 unit of amphidinol 3 (AM3) and its diastereomers was achieved via chemoselective cross metathesis as the key step. Comparison of (13)C NMR data of the synthetic specimens with that of AM3 led to a controversy regarding the originally proposed structure. From GC-MS analysis of the degradation product, the absolute configuration at C2 of AM3 has been revised to be R.     

2D layered supramolecular host system derived from a 21-helical column, composed of 1,2-diphenylethylenediamine and N-phenyliminodiacetic acid

A supramolecular host system composed of a 2D layered structure was developed by combining 1,2-diphenylethylenediamine and N-phenyliminodiacetic acid. This 2D layered structure was formed by a hydrogen- and ionic-bonded network between 2(1)-helical columns.     

Distribution analysis for single molecule FRET measurement

A new numerical analysis method for experimental single-pair fluorescence resonance energy transfer (sp-FRET) data is proposed. In this method, every single data point was plotted in a style of a cumulative distribution function and dedicated to curve-fitting analysis, so that the analysis does not depend on bin size. A series of numerical simulations showed that this analysis has a more efficient and accurate resolvability of components than a fitting method based on Gaussian functions to a histogram plot. A simulated data based on experimental FRET distributions were also used to discuss the fitting errors of this method. The proposed method was applied to sp-FRET experiments of doubly dye-labeled double-strand DNA with a short sequence. Mixtures of up to three species were analyzed, and the contributions up to four subpopulations were successfully resolved.