Specific isolation of N-terminal fragments from proteins and their high-fidelity de novo sequencing

A new method to determine N-terminal amino acid sequences of multiple proteins at low pmol level by a parallel processing has been developed. The method contains the following five steps: (1) reduction, S-alkylation and guanidination for targeted proteins; (2) coupling with sulfosucccimidyl-2-(biotinamido)ethyl-1,3-dithiopropionate(sulfo-NHS-SS-biotin) to N(alpha)-amino groups of proteins; (3) digestion of the modified proteins by an appropriate protease; (4) specific isolation of N-terminal fragments of proteins by affinity capture using the biotin-avidin system; (5) de novo sequence analysis of peptides by MALDI-TOF-/MALDI-TOF-PSD mass spectrometry with effective utilization of the CAF (chemically assisted fragmentation) method.1 This method is also effective for N-terminal sequencing of each protein in a mixture of several proteins, and for sequencing components of a multiprotein complex. It is expected to become an essential proteomics tool for identifying proteins, especially when used in combination with a C-terminal sequencing method.     

Ba-catalyzed direct Mannich-type reactions of a beta,gamma-unsaturated ester providing beta-methyl aza-Morita-Baylis-Hillman-type products

Barium-catalyzed direct Mannich-type reactions of a beta,gamma-unsaturated ester are described. The Ba-catalyst not only promoted the Mannich-type reactions, but also isomerized Mannich adducts to afford beta-methyl aza-Morita-Baylis-Hillman-type products in 61-88% yield from various aryl, heteroaryl, and alkyl imines. Preliminary trials on enantioselective variants with a chiral biaryldiol ligand gave products in up to 80% ee.     

Tubular structures bearing channels in organic crystals composed of adamantane-based macrocycles

Five macrocyclic molecules (1–5) were efficiently synthesized from the dimerization and trimerization of di-substituted adamantane derivatives, which were composed of three different aromatic units and two different linker groups. Three single-crystals were obtained from these macrocyclic molecules, including a set of pseudopolymorphs (3a and 3b) of macrocycle 3 and another macrocycle 5 (5a). Single crystal X-ray analysis revealed that the three monocyclic compounds were rectangular or square in shape with solvent molecules in the cavity. Macrocycle 3 in 3a formed stacks to produce tubular structures with channels that assembled into three-dimensional networks through CH/π interactions.     

Trapping of 1,8-biradical intermediates by molecular oxygen in photocycloaddition of naphthyl-N-(naphthylcarbonyl)carboxamides; formation of novel 1,8-epidioxides and evidence of stepwise aromatic cycloaddition.

The photocycloaddition reaction of naphthyl-N-(naphthylcarbonyl)carboxamides (1) was examined under argon and oxygen atmospheres. In addition to the [2 + 2] and [4 + 4] cycloadducts, 3 and 4, respectively, novel 1,8-epidioxides (5) were formed under oxygen atmosphere. The transient absorption at lambda max of 360 nm with the lifetime of 360 ns was observed by laser flash photolysis of 1c and was interpreted as the absorption of biradical intermediate 2. On the basis of the anti stereochemistry of 5, which was different from that of the major [4 + 4] cycloadducts, syn-4, it was deduced that equilibrium between biradical intermediates syn-2 and anti-2 would exist. Retro [2 + 2] cycloaddition of 3 was responsible for the efficient trapping of the biradical intermediate with molecular oxygen. The photocycloaddition of the anthryl derivatives, 9-anthryl-N-(methylethyl)-N-(naphthylcarbonyl)carboxamides (7), afforded the [4 + 4] cycloadducts (8) exclusively in a quantitative yield even under oxygen atmosphere. The absence of trapping with molecular oxygen was interpreted to be due to the lack of retro [4 + 4] cycloaddition of 8.     

Biphenyl ether and biphenyl quinolizidine lactone alkaloids from Heimia salicifolia

Three new biphenyl ether quinolizidine lactone alkaloids (1–3) and 13 new biphenyl quinolizidine lactone alkaloids (4–16) were isolated from Heimia salicifolia (Lythraceae) together with seven known alkaloids. Their structures were determined by spectroscopic analyses and chemical conversions.     

Synthesis of bicyclic lactones via I2-mediated intramolecular tandem C–C/C–O bond formation

The iodine/DMAP-mediated intramolecular tandem C–C/C–O bond forming reaction of malonate bearing alkene moiety proceeded to give bicyclic lactones with good diastereoselectivity in good yield. The mechanistic investigation was also discussed on the basis of various control experimental results.     

Structural features of aliphatic N-nitrosamines of 7-azabicyclo[2.2.1]heptanes that facilitate N-NO bond cleavage

N-Nitrosamines can be considered as potential nitric oxide (NO)/nitrosonium ion (NO(+)) donors. However, the relation of the structures of N-nitrosamines, in particular of aliphatic N-nitrosamines, to the characteristics of release of NO or NO(+) remains unclear. Here we show that aliphatic N-nitrosoamines of 7-azabicyclo[2.2.1]heptanes can undergo heterolytic N-NO bond cleavage. On the basis of the observation of reduced rotational barriers of the N-NO bonds in solution and nitrogen-pyramidal structures of the N-nitroso group in the solid state, we postulate that N-NO bond cleavage of N-nitrosamines is enhanced by a reduction of the resonance in the N-NO group. Computational studies suggest that these structural features of the N-nitrosamines of 7-azabicyclo[2.2.1]heptane are derived from angle strain imposed on the CNC angles.     

Colorimetric fluoride ion sensing by boron-containing pi-electron systems.

The boron-containing pi-conjugated systems, including tri(9-anthryl)borane (1) and tris[(10-dimesitylboryl)-9-anthryl]borane (2), have been investigated as a new type of fluoride chemosensor. Upon complexation of 1 with a fluoride ion, a significant color change from orange to colorless was observed and, in the UV-visible absorption spectra, the characteristic band of 1 at 470 nm disappeared and new bands around 360-400 nm assignable to pi-pi transitions of the anthryl moieties were observed. This change can be rationalized as a result of the interruption of the pi-conjugation extended through the vacant p-orbital of the boron atom by the formation of the corresponding fluoroborate. The binding constant of compound 1 with the fluoride ion was quite high [(2.8 +/- 0.3) x 10(5) M(-1)], whereas 1 only showed small binding constants with AcO- and OH- of around 10(3) M(-1) and no sensitivity to other halide ions such as Cl-, Br-, and I-, thus demonstrating its selective sensing ability to the fluoride ion. In contrast to the monoboron system 1, compound 2 having four boron atoms showed multistage changes in the absorption spectra by the stepwise complexation with fluoride ions.     

Comproportionation reaction and hindered rotation of coordinated pyridine rings in an acetate-bridged tetraplatinum(II) cluster with pyridine-based ligands in the cluster plane

A series of pyridine-substituted derivatives of octaacetatotetraplatinum(II), [Pt4(CH3COO)8-n(L)2n]n+ (L= 4-dimethylaminopyridine (dmap), pyridine (py), 4-cyanopyridine (cpy); n = 1-4) were prepared, and the tetra- and octasubstituted forms (n = 2 and 4) were isolated. 1HNMR spectra showed that this type of cluster undergoes a comproportionation reaction. Reactions between clusters in which n = 0 and 2, n = 0 and 4, and n = 2 and 4 afforded Pt4 clusters with n = 1, 2, and 3, respectively, as a main product in acetonitrile. The dmap-substituted clusters, trans-[Pt4(CH3COO)6(dmap)4](ClO4)2 x 3CH3NO2 (3a(ClO4)2 x 3CH3NO2) and [Pt4(CH3COO)4(dmap)8](ClO4)4 x 4 H2O (5a(ClO4)4-4H2O), have been structurally characterized. Both 3a and 5a have a square-planar cluster core comprised of four PtII ions, and all eight out-of-plane coordination sites are occupied by acetate ligands in a bridging mode. In 5a, all of the in-plane sites are occupied by dmap ligands. In 3a, four dmap ligands occupy the coordination sites at the two mutually opposite edges of the square planar cluster skeleton, giving a trans tetrasubstituted form of [Pt4(CH3COO)8-] (1). In octasubstituted 5a, adjacent dmap ligands are so closely arranged that the Pt-N distances (2.20(3), 2.30(3) A) are longer than those in tetrasubstituted 3a (2.13(1), 2.15(1) A) and related Pt4 clusters. Furthermore, rotation of the dmap ligand about the Pt-N bond in 5a was restricted, and the rate constant of the rotation was 4.5s(-1) at 20 degrees C from dynamic NMR study. Cluster [Pt4(CH3COO)5(dmap)6]3+ (4a) also exhibited similar hindered rotation with the rate constants of 2.0s(-1), 12s(-1) and approximately 10(4)s(-1) at 20 degrees C depending on the coordination sites of the dmap ligands in 4a.