Crystal structure of a methyl(methoxy)carbene complex of nickel(II), trans-[Ni(C6Cl5)(PMe2Ph)2{C(OMe)Me}]BF4

The structure of a nickel(II) complex, trans-[Ni(C₆Cl₅)(PMe₂Ph)₂{C(OMe)Me}]BF₄, containing the simplest alkyl(alkoxy)carbene ligand has been determined by X-ray crystallography (R = 0.091). The geometry around the nickel atom is square-planar. The comparatively short NiC(1) bond length of 1.843(10) Å showed the presence of π-bonding in the nickel-carbene bond.     

Synthesis and isomerization of conjugated oligomers containing azoimidazole unit

The Suzuki (for O1 – O3 ) and Stille (for O4 ) coupling polymerization of 2‐(phenylazo)imidazole bearing the benzyl protecting group at the 1‐position gave conjugated oligomers. The transformation from the neutral imidazole in the conjugated oligomer O2 , consisted of the alternating 2,5‐didecyl‐1,4‐phenylene unit, to the cationic imidazolium salt O2S was performed. Depending on the chemical structure of coupling partners, the absorption maximum of conjugated oligomers showed red shift or blue shift from that of the model compound M with the benzene ring at the 4,5‐positions. The absorption maximum wavelength of the cationic conjugated oligomer O2S showed a blue shift from that of the neutral conjugated oligomer O2 . The trans‐to‐cis photoisomerization of the azoimidazole unit in conjugated oligomers was observed by irradiating the light at 436 nm, and the conversion degree to the cis structure had a rough correlation with the maximum absorption wavelength of materials. The trans‐to‐cis photoisomerization in the film state was sluggish. On the other hand, the cis‐to‐trans thermal isomerization of the azoimidazole unit was confirmed and the absorbance returned to the initial state before the photoisomerization. The trans‐to‐cis photoisomerization of the cationic conjugated oligomer O2S required large energy, and the prolonged light irradiation might decompose the azoimidazole unit. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011.     

Measurement of acid-catalyzed isomerization of unsaturated aldehyde-2,4-dinitrophenylhydrazone derivatives by high-performance liquid chromatography analysis

Aldehyde-2,4-dinitrophenylhydrazones exist as (E)- and (Z)-geometrical isomers, and adventitious isomerization during sample preparation can cause analytical errors. Purified alkenal-2,4-dinitrophenylhydrazone derivatives comprise only the (E)-isomer. However, partial isomerization to the (Z)-isomer occurs upon addition of acid to attain an equilibrium isomer ratio. The UV-visible spectral properties of the isomers differ; the (Z)-isomer exhibiting a 6-10 nm lower absorption maximum compared to the (E)-isomer. Alkenal-2,4-dinitrophenylhydrazones having a CC double bond at the 2- or 3-position of the alkenal exhibited similar absorption maxima with an equilibrium isomer ratio (0.035) that was much lower than those of other alkenals. The CC double bond at the 3-position migrates to a position of conjugation with the CN double bond during hydrazone synthesis to form a stabilized molecular structure. Alkenal-2,4-dinitrophenylhydrazones having a double bond at the 4-position or greater exhibited a similar absorption maxima equilibrium isomer ratio (0.14) to alkanal-2,4-dinitrophenylhydrazones. The quantitative analysis of carbonyl compounds in air or water using DNPH is usually conducted in the presence of an acid catalyst. Consequently, the solution of the direct extract prepared for HPLC or GC analysis contains both (E)- and (Z)-isomers.     

Nuclear quantum effect on the hydrogen-bonded structure of guanine�Ccytosine pair

The structure of Watson?CCrick type guanine?Ccytosine (G?CC) base pair has been studied by classical hybrid Monte Carlo (HMC) and quantum path integral hybrid Monte Carlo (PIHMC) simulations on the semiempirical PM6 potential energy surface. For the three NH?X hydrogen-bonded moieties, the intramolecular NH bonds are found systematically longer while the H?X distance shorter in the PIHMC simulation than in the HMC simulation. We found that the hydrogen bonded length N?X correlates with the H?X distance, but not with the NH distance. A correlation is also between the neighboring hydrogen bonds in the G?CC base pair.     

Quantum proton transfer in hydrated sulfuric acid clusters: a perspective from semiempirical path integral simulations

We have carried out path-integral molecular dynamics simulations for hydrated sulfuric acid clusters to understand acid-dissociation and hydrogen-bonded structural rearrangement processes in these clusters from a quantum mechanical viewpoint. The simulations were performed using the PM6 semiempirical electronic structure level whose parameters were modified on the basis of the specific reaction parameters strategy so that relative energies of optimized structures, as well as water binding energies reproduce ab initio and density-functional theory calculations. We have found that the acid dissociation processes, first and second deprotonation, effectively occur in a hydrated cluster with a specific cluster size. The mechanisms of the proton-transfer processes were analyzed in detail and it was found that the distance between O in sulfuric acid and O in the proton-accepting water is playing an important role. We also found that the water coordination number of the poton-accepting water is important in the proton-transfer processes.     

Identification of oligosaccharides from histopathological sections by MALDI imaging mass spectrometry

Direct tissue analysis using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) provides the means for in situ molecular analysis of a wide variety of biomolecules. This technology—known as imaging mass spectrometry (IMS)—allows the measurement of biomolecules in their native biological environments without the need for target-specific reagents such as antibodies. In this study, we applied the IMS technique to formalin-fixed paraffin-embedded samples to identify a substance(s) responsible for the intestinal obstruction caused by an unidentified foreign body. In advance of IMS analysis, some pretreatments were applied. After the deparaffinization of sections, samples were subjected to enzyme digestion. The sections co-crystallized with matrix were desorbed and ionized by a laser pulse with scanning. A combination of α-amylase digestion and the 2,5-dihydroxybenzoic acid matrix gave the best mass spectrum. With the IMS Convolution software which we developed, we could automatically extract meaningful signals from the IMS datasets. The representative peak values were m/z 1,013, 1,175, 1,337, 1,499, 1,661, 1,823, and 1,985. Thus, it was revealed that the material was polymer with a 162-Da unit size, calculated from the even intervals. In comparison with the mass spectra of the histopathological specimen and authentic materials, the main component coincided with amylopectin rather than amylose. Tandem MS analysis proved that the main components were oligosaccharides. Finally, we confirmed the identification of amylopectin by staining with periodic acid-Schiff and iodine. These results for the first time show the advantages of MALDI-IMS in combination with enzyme digestion for the direct analysis of oligosaccharides as a major component of histopathological samples.     

Synthesis of new azonia-helicenes with a quaternary nitrogen at the inner helix skeleton

The 16c-azonia[6]helicene salts, in which a carbon atom at the inner helix skeleton of [6]helicene is replaced by a quaternary nitrogen atom, have been synthesized by photo-induced intramolecular quater-nization of 2-[2-(1-chloronaphthyl)vinyl]benzo[h]quinolines in acetonitrile.     

Synthesis and reactivities of 10-S-3 trithiadiazapentalene derivatives

1,3-Bis(p-substituted-phenylthiocarbamoyl)-2-imidazolidinethiones 3a-f reacted with bromine to give trithiadiazapentalene derivatives 5a-f , bearing the exocyclic C-N double bonds, in moderate yields. The molecular structure of 5b was elucidated by the X-ray crystallographic analysis. The treatment of 5b-f with hydrochloric acid gave the ring-opening products, 1,3-bis(p-substituted-phenylthiocarbamoyl)-2-imidazo-lidinones 9b-f , accompanied by the production of elemental sulfur. Reduction of 5b , 5d , and 5e with sodium borohydride gave the ring-opening compounds, 1,3-bis(p-substituted-phenylthiocarbamoyl)-2-imidazolidines 13b , 13d , and 13e respectively.