Supercritical fluid clean-up of environmental samples for the analysis of polycyclic aromatic hydrocarbons using time-of-flight secondary ion mass spectrometry.

A novel sample-pretreatment method for time-of-flight secondary ion mass spectrometry (TOF-SIMS) was developed using supercritical fluid extraction (SFE). In SFE, the extraction efficiency of a certain organic matter is controlled by the pressure and temperature of supercritical CO2. Two-step SFE (1st step at 10 Mpa, 40 degrees C; 2nd step at 30 MPa, 120 degrees C) was applied to diesel exhaust particles containing many kinds of n-alkanes and aromatic species. n-Alkanes and polycyclic aromatic hydrocarbons (PAHs) were extracted in the 1st and 2nd steps, respectively. This selectivity was utilized for the sample preparation of TOF-SIMS analysis. Diesel exhaust particles after the 1st step of extraction were analyzed with TOF-SIMS, aiming at PAHs as analytical targets. The obtained spectrum was simplified, and mass peaks of individual PAHs were easily assigned, because unwanted compounds, like n-alkanes, were selectively removed by SFE. Furthermore, a simple calculation elucidated the outline of the spectrum.     

Synthesis and photophysical properties of novel push-pull-type solvatochromic 7-deaza-2′-deoxypurine nucleosides

We have synthesized two novel push-pull-type fluorescent 7-deazapurine nucleosides, ^CNZA and ^CNZG, and investigated their photophysical properties. In particular, ^CNZA was found to exhibit a remarkable solvatofluorochromicity (Δλ_fl.max = 60 nm). We incorporated ^CNZA into oligonucleotides and found that ^CNZA can form a stable base pair with both thymine and cytosine. Such environmentally sensitive fluorescent nucleosides have a potential as a fluorescence sensor for structural studies of nucleic acids.     

Roles of K151 and D180 in L‐2‐haloacid dehalogenase from Pseudomonas sp. YL: Analysis by molecular dynamics and ab initio fragment molecular orbital calculations

L ‐2‐haloacid dehalogenase (L ‐DEX) catalyzes the hydrolytic dehalogenation of L ‐2‐haloalkanoic acids to produce the corresponding D ‐2‐hydroxyalkanoic acids. This enzyme is expected to be applicable to the bioremediation of environments contaminated with halogenated organic compounds. We analyzed the reaction mechanism of L ‐DEX from Pseudomonas sp. YL (L ‐DEX YL) by using molecular modeling. The complexes of wild‐type L ‐DEX YL and its K151A and D180A mutants with its typical substrate, L ‐2‐chloropropionate, were constructed by docking simulation. Subsequently, molecular dynamics (MD) and ab initio fragment molecular orbital (FMO) calculations of the complexes were performed. The ab initio FMO method was applied at the MP2/6‐31G level to estimate interfragment interaction energies. K151 and D180, which are experimentally shown to be important for enzyme activity, interact particularly strongly with L ‐2‐chloropropionate, catalytic water, nucleophile (D10), and with each other. Our calculations suggest that K151 stabilizes substrate orientation and balances the charge around the active site, while D180 stabilizes the rotation of the nucleophile D10, fixes catalytic water around D10, and prevents K151 from approaching D10. Further, D180 may activate catalytic water on its own or with K151, S175, and N177. These roles are consistent with the previous results. Thus, MD and ab initio FMO calculations are powerful tools for the elucidation of the mechanism of enzymatic reaction at the molecular level and can be applied to other catalytically important residues. The results obtained here will play an important role in elucidating the reaction mechanism and rational design of L ‐DEX YL with improved enzymatic activity or substrate specificity. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

C2-substituted 8-aza-7-deaza-2′-deoxyadenosines as environmentally sensitive fluorescent nucleosides for discriminating apurinic/apyrimidinic sites in DNA duplex

We synthesized various C2-naphthylethynylated 8-aza-7-deaza-2′-deoxyadenosines 1a–1c as novel environmentally sensitive fluorescent (ESF) purine nucleosides. In particular, the N,N-dimethylamino-substituted derivative 1c exhibits a remarkably high solvatochromicity (Δ$\mathrm{\lambda }$ = 111 nm). 1c-containing oligodeoxynucleotide (ODN) probes clearly discriminated an apurinic/apyrimidinic site (AP site) in the complementary strand via a change in emission wavelength and intensity when hybridized with a target ODN.     

Synthesis of ethynylpyrene-modified 3-deaza-2′-deoxyguanosines as environmentally sensitive fluorescent nucleosides: Target DNA-sequence detection via changes in the fluorescence wavelength

Novel pyrene-labeled environmentally sensitive fluorescent (ESF) nucleosides [^1p3zG (1a) and ^2p3zG (1b)] possessing the 3-deazaguanine skeleton were synthesized. Among them, ^1p3zG (1a) exhibited longer fluorescence emission wavelengths compared with the previously reported naphthalene-modified ESF nucleoside ^3nzG (48–71?nm longer in polar solvents) and showed remarkable solvent-polarity-sensitive fluorescence properties. Oligodeoxynucleotide (ODN) probes containing ^1p3zG (1a) clearly discriminated target DNAs by the change in the emission wavelength and intensity through monitoring the microenvironmental change around the DNA minor groove. Thus, these pyrene-labeled ESF nucleosides can be applied in gene detection and molecular diagnostics, as well as in the structural analysis of nucleic acids.     

Cationic Rh(I)/modified-BINAP-catalyzed reactions of carbonyl compounds with 1,6-diynes leading to dienones and ortho-functionalized aryl ketones

We have determined that a cationic rhodium(I)/H8-BINAP complex catalyzes a [2 + 2 + 2] cycloaddition of both activated and unactivated carbonyl compounds with 1,6-diynes leading to dienones in high yields. On the other hand, unactivated aryl ketones react with 1,6-diynes in the presence of a cationic rhodium(I)/Segphos complex to give ortho-functionalized aryl ketones in high yields.     

Enantioselective synthesis of C2 -symmetric spirobipyridine ligands through cationic Rh(I)/modified-BINAP- catalyzed double [2 + 2 + 2] cycloaddition

[structure: see text]. Enantioenriched C2-symmetric spirobipyridine ligands were efficiently synthesized through a cationic rhodium(I)/(R)-Segphos or (R)-H8-BINAP complex-catalyzed enantioselective intramolecular double [2 + 2 + 2] cycloaddition of bis-diynenitriles.