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.     

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.     

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.     

Enantioselective synthesis of gabapentin analogues via organocatalytic asymmetric Michael addition of α-branched aldehydes to β-nitroacrylates

Michael addition reaction of α-branched aldehydes to β-nitroacrylates was successfully carried out by using a mixed catalyst consisting of a primary amino acid, L-phenylalanine, and its lithium salt to give β-formyl-β'-nitroesters having a quaternary carbon centre in good yields (up to 85%) with high enantioselectivity (up to 98% ee). By using benzyl β-nitroacrylates as Michael acceptors, the obtained β-formyl-β'-nitroesters were converted into various 4,4-disubstituted pyrrolidine-3-carboxylic acids including analogues of gabapentin (Neurotin(?)) in one step from the Michael adducts in high yields.     

Mechanistic study of asymmetric Michael addition of malonates to enones catalyzed by a primary amino acid lithium salt

A mechanistic study was carried out for the asymmetric Michael addition reaction of malonates to enones catalyzed by a primary amino acid lithium salt to elucidate the origin of the asymmetric induction. A primary β-amino acid salt catalyst, O-TBDPS β-homoserine lithium salt, exhibited much higher enantioselectivity than that achieved with the corresponding catalysts derived from α- and γ-amino acids for this reaction. Detailed studies of the transition states with DFT calculations revealed that the lithium cation and carboxylate group of the β-amino acid salt catalyst have important roles in achieving high enantioselectivity in the Michael addition reaction of malonates to enones.     

Synthesis of novel 4′-C-methyl-1′,3′-dioxolane pyrimidine nucleosides and evaluation of its anti-HIV-1 activity

The key glycosyl donor for the target molecule 12 was prepared by two-step sequences; (1) acetalization of tert-butyldimethylsilyloxyacetaldehyde with 3-bromopropanediol, (2) DBN-initiated β-elimination of the resulting 2-(tert-butyldimethylsilyloxy)methyl-4-bromomethyl-1,3-dioxolane 11. Electrophilic glycosidation between 12 and silylated pyrimidine nucleobase proceeded efficiently to provide a mixture of β- and α-anomers of the respective glycosides 14 and 15. Tin radical-mediated reduction of the bromomethyl functional group of 14 and 15 gave protected 4′-C-methyl-dioxorane uracil- 16 and thymine nucleoside 17. The respective cytosine nucleoside 18 was synthesized from 16. De-silylation of 4′-methyl-1′,3′-dioxolane pyrimidine nucleosides 16–18 gave the target molecules. Evaluation of the anti-HIV-1 activity of the β- and α-anomers of the novel 4′-C-methyl-1′,3′-dioxolane nucleosides 22β,α–24β,α revealed that none of the nucleoside derivatives possess anti-viral activity against HIV-1 and show cytotoxicity against MT-4 cells at 100 μM.     

Isomerization of aldehyde-2,4-dinitrophenylhydrazone derivatives and validation of high-performance liquid chromatographic analysis

The most widely used method for qualitative and quantitative analysis of carbonyl compounds is the 2,4-dinitrophenylhydrazine method through the formation of 2,4-dinitrophenylhydrazone derivatives. However, this method may cause an analytical error because 2,4-dinitrophenylhydrazones have both E- and Z-stereoisomers. Purified aldehyde-2,4-dinitrophenylhydrazone demonstrated only the E-isomer. However under UV irradiation and the addition of acid, both E- and Z-isomers were seen. The spectral patterns of Z-isomers were different from those of E-isomers and the absorption maximum wavelengths were shifted towards shorter wavelengths by 5-8 nm. An equilibrium Z/E isomer ratio was observed in 0.02-0.2% (v/v) phosphoric acid solutions. In the case of acetaldehyde- and propanal-2,4-dinitrophenylhydrazones, the equilibrium Z/E isomer ratios were 0.32 and 0.14, respectively. However, when irradiated with ultraviolet light at 364 nm, the isomer ratios were increased beyond this constant ratio and reached 0.55 and 0.33, respectively. Zero-order rates for decreases of aldehyde derivatives were observed under UV irradiation (364 nm), however the decreases of concentration were not observed in phosphoric acid solutions. The best method for the determination of aldehyde-2,4-dinitrophenylhydrazones by HPLC is to add phosphoric acid to both the sample and the standard solution, to form a 0.02-1% acid solution.     

DNA sensor: A novel electrochemical gene detection method using carbon electrode immobilized DNA probes

Abstract

The authors have developed a novel, rapid, convenient, and specific gene detection method, named the ‘DNA sensor,’ using a graphite electrode loaded with DNA probes. Synthesized oligonucleotide (5-TGCAGTTCCGGTGGCTGATC-3′) complementary to oncogene v-myc was employed for a model probe. The oligonucleotide was chemically adsorbed on a basal plane pyrolytic graphite (BPPG) electrode. The sensor was able to be applied to a hybridization reaction (40°C) in a linearized pVM623 solution carrying the Pst I fragment of v-myc (1.5 kbp).

After the hybridization reaction, the sensor was immersed into an acridine orange solution (1 μM) and washed with a phosphate buffer (pH 7.0). Acridine orange intercalated between base pairs of the formed double stranded DNAs on the electrode. The anodic peak potential of acridine orange that interacted with the DNAs on the electrode was measured. The positive shift of the peak potential increased in proportional to the pVM623 concentration in the hybridization reaction. 10^?1 g/ml of pVM623 was able to be detected in the buffer solution using the sensor. This gene detection was completed within an hour.     

Simons electrochemical fluorination of substituted homopiperazines(hexahydro-1,4-diazepines) and piperazines

Simons electrochemical fluorination (ECF) of 1,4-dimethyl-1,4-homopiperazine, methyl 4-ethylhomopiperazin-1-ylacetate and 1,4-bis(methoxycarbonylmethyl)-1,4-homopiperazine was studied. For comparison, ECF of three piperazines with a N-(methoxycarbonylmethyl) group(s) was also studied. ECF of 1,4-dimethyl-1,4-homopiperazine gave a low yield of corresponding perfluoro(1,4-dimethyl-1,4-homopiperazine) together with perfluoro(2,6-diaza-2,6-dimethylheptane) as the major product. Corresponding perfluoro(homopiperazines) with mono- and/or di-(fluorocarbonyldifluoromethyl) groups [CF₂C(O)F] at the 1- and/or 4-position were formed in low yields from methyl 4-ethylhomopiperazin-1-ylacetate and 1,4-bis(methoxycarbonylmethyl)-1,4-homopiperazine, respectively. These new seven-membered perfluoro(1,4-dialkyl-1,4-homopiperazines) were accompanied by the formation of mono- and/or di-basic linear perfluoroacid fluorides resulting from the CC bond scission at the 2- and 3-positions of the ring. From mono- and/or di-N-(methoxycarbonylmethyl)-substituted piperazines, corresponding perfluoropeperazines having the acid fluoride group(s) were formed in low yields.