Theoretical studies of the cross-linking mechanisms between cytosine and tyrosine

DNA-protein cross-linking is one of the many DNA lesions mediated by hydroxyl radicals, the most damaging among the reactive oxygen species in biological systems. Density functional theory methods are employed to investigate the complex reaction mechanisms of the formation of cytosine-tyrosine cross-links as observed in gamma-irradiated aqueous solutions of cytosine and tyrosine, as well as in gamma-irradiated nucleohistone. The majority of the radical addition mechanisms considered are found to have significant barriers and therefore to be thermodynamically unfavorable for the formation of the initial cross-linked product. Our calculated reaction potential energy surfaces suggest that a feasible complete mechanism consists of radical combination forming the initial cross-linked product, a hydrogen shuffle within the initial cross-linked product, and an acid-catalyzed dehydration reaction. Water and hydrogen-bonding interactions are suggested to play a key role in catalyzing the hydrogen-transfer step of the reaction.     

Aqueous Titanate Sols from Ti Alkoxide-α-Hydroxycarboxylic Acid System and Preparation of Titania Films from the Sols

Aqueous titanate sols were prepared by reactions of titanium tetraisopropoxide (TIP) with -hydroxycarboxylic acids in water. IR and Raman spectra, and elemental analyses of the precipitates obtained from the sols revealed that the carboxylates were chelated to titanium but the Ti species were polymerized to form a cluster that had a colloidal nature. Spin-coating of titania (TiO₂) thin films from these sols was also examined. Interestingly, it was found that (004) preferentially oriented anatase films with refractive index of 2.54 were obtained from TIP-lactic acid-NH₃ (1:1:1, molar ratio) aqueous sol. This crystallographic orientation was characteristic of the TIP-lactic acid-NH₃ (1:1:1) system, and was not affected by the kinds of substrates used and the heating rate of the film. TEM observation indicated that small anatase grains had already formed at 200°C. Therefore, the crystallographic orientation might depend strongly on the structure of the chemical species of the precursor solutions.     

Modeling the reaction mechanisms of the amide hydrolysis in an N-(o-carboxybenzoyl)-L-amino acid

Reaction mechanisms of the amide hydrolysis from the protonated, neutral, and deprotonated forms of N-(o-carboxybenzoyl)-l-amino acid have been investigated by use of the B3LYP density functional method. Our calculations reveal that in the amide hydrolysis the reaction barrier is significantly lower in solution than that in the gas phase, in contrast with the mechanism for imide formation in which the solvent has little influence on the reaction barrier. In the model reactions, the water molecules function both as a catalyst and as a reactant. The reaction mechanism starting from the neutral form of N-(o-carboxybenzoyl)-l-amino acid, which corresponds to pH 0-3, is concluded to be the most favored, and a concerted mechanism is more favorable than a stepwise mechanism. This conclusion is in agreement with experimental observations that the optimal pH range for amide hydrolysis of N-(o-carboxybenzoyl)-l-leucine is pH 0-3 where N-(o-carboxybenzoyl)-l-leucine is predominantly in its neutral form. We suggest that besides the acid-catalyzed mechanism the addition-elimination mechanism is likely to be an alternative choice for cleaving an amide bond. For the reaction mechanism initiated by protonation at the amidic oxygen (hydrogen ion concentration H(0) < -1), the reaction of the model compound with two water molecules lowers the transition barrier significantly compared with that involving a single water molecule.     

Determination of protein phosphorylation by extracellular signal-regulated kinase using capillary electrophoresis and matrix-assisted laser desorption ionization time-of-flight mass spectrometry

Extracellular signal-regulated kinase (ERK) is a key regulatory enzyme mediating cell responses to mitogenic stimulation and is one of the key components in linking growth factor receptor activation to serine/threonine protein phosphorylation processes. Phosphorylation reaction by ERK plays an important role in many signal transduction pathways. ERK phosphorylates numerous substrates such as MBP, microtubule-associated protein 2 (MAP2) and nuclear protein. In particular, MBP is a substrate commonly employed for the detection of ERK activity and contains the consensus primary sequence PRT97P. In this paper, we compared the degree of the phosphorylation reaction of MBP substrate peptides by ERK with the three different MBP substrate peptides, MBP1(KNIVTPRTPPPSQGK), MBP2(VPRTPGGRR) and MBP3(APRTPGGRR) in order to select an efficient substrate peptide for phosphorylation reaction by ERK. The results showed that the MBP3 peptide is the most efficient substrate for phosphorylation reaction by ERK. Using MBP3 peptide, the phosphorylation reaction of MBP by ERK was monitored with both matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and capillary electrophoresis (CE). Our results demonstrate the feasibility of the CE method, the method being a simple and reliable technique in determining and characterizing various kinds of enzyme reaction especially including kinase enzymes.     

Reaction of α-haloester having internal double bond with the low-valent metal complex

The α-haloester having an internal double bond was allowed to react with a catalytic amount of Pd(PPh₃)₄ to afford a cyclized product in a fairly good yield and the same product was obtained by treatment with Pd(OAc)₂ to ketene silyl acetal.     

Synthesis of Zeolite L. Tuning Size and Morphology

Summary. A convenient synthesis of zeolite L is presented. The size of the crystals can be tuned between 30 and 6000nm, spanning a volume range of seven orders of magnitude. The zeolite L crystals, which typically feature a cylindrical morphology, are synthesized with various aspect ratios ranging from elongated to disc-shaped. The importance of obtaining zeolite crystals with well-defined size and morphology is discussed in view of potential applications of zeolite L containing organic dye molecules as guests.This revised version was published online in February 2005. In the previous version the issue was not marked as a special issue, and the issue title and the editor was missing     

Determination of three compounds in Aloe vera by capillary electrophoresis

A capillary electrophoretic assay for determining aloe-emodin (AE), methyl p-coumarate (MC), and 3,4-dihydro-6,8-dihydroxyl-[(3s)-2'-acetyl-3'-hydroxyl-5'-methoxy-benzyl]-isocoumarin (DDI) in Aloe vera has been developed. Baseline separation was achieved within 15 min using a running buffer of 20 mm borax containing 10% (v/v) acetonitrile at pH 10.5. A linear relationship between the peak area and the concentration of the analytes was found in the ranges 5-500, 10-1000 and 2-1000 micro g/mL for AE, MC and DDI, respectively, with correlation coefficients of 0.9992-0.9998. The relative standard deviations of migration time and peak area were within 0.17-0.19 and 1.52-3.37%, respectively. The recoveries of AE, MC and DDI were 105, 102 and 96.4%. The contents of AE, MC and DDI in Aloe vera were measured to be 5.13, 0.768 and 1.30 mg/g, respectively.     

Studies on the Stereochemistry of 2-(Nitromethylidene)-Heterocycles

The ¹H-NMR spectra of 2-(nitromethylidene)pyrrolidine ( 7 ), 1-methyl-2-(nitromethylidene)imidazolidind ( 10 ) and 3-(nitromethylidene)tetrahydrothiazine ( 11 ) in CDCl₃ and (CD₃)₂SO indicate that these compounds have the intramolecularly H-bonded structures (Z)- 7 , (E)- 10 and (Z)- 11 while the N-methyl derivative 8 of 7 is (E)-configurated in both solvents. 1-Benzylamino-1-(methyltio)-2-nitroehtylene ( 13 ), an acylic model, has the H-bonded configuration (E)- 13 in CDCl₃ and in (CD₃)₂SO. 2-(Nitromethylidene)thiazolidine ( 3 ) has the (E)-configuration in CDCl₃ but exists in (CD₃)₂SO as a mixture of (Z)- and (E)-isomers with the former predominating. Both species are detected to varying proportions in a mixture of the two solvents. ¹⁵N-NMR spectroscopy of 3 ruled out unambiguously the nitronic acid structure 6 and the nitromethyleimine structure 5 . The N-methyl derivative 4 of 3 is (Z)-configurated in (CD₃)₂SO. Comparison of the olefinic proton shifts of (Z)- 3 and (Z)- 4 with those of analogues and also of 1,1-bis(methylti)-2-nitroethylene ( 12 ) shows decreased conjugation of the lone pair of electrons of the ring N-atom in (Z)- 3 and (Z)- 4 . This is also supported by ¹³C-NMR studies. Plausible explanations for the phenomenon are offered by postulating that the ring N-atoms are pyramidal in (Z)- 3 and (Z)- 4 and planar in other cases or, alternatively, that the conjugated nitroenamine system gets twisted due to steric interaction between the NO₂-group and the ring S-atom. Single-crystal X-ray studies of 3 and 8 show that the former exists in the (Z)-configuration and the latter in (E)-configuration; the ring N-atom in the former has slightly more pyramidal character than in the latter.     

An evaluation of various computational methods for the treatment of organoselenium compounds

A reliable computational method for the prediction of organoselenium geometries and bond dissociation energies (BDEs) has been determined on the basis of the performance of density functional theory (DFT: B3LYP and B3PW91) and ab initio molecular orbital procedures (Hartree-Fock (HF)) in conjunction with various Pople basis sets including (but not limited to) the 6-31G(d), 6-31G(d,p), 6-311G(d), 6-311G(d,p), 6-311G(2df,p), and 6-311G(3df,3pd) sets. Predicted geometries and BDEs are compared with available experimental data and quadratic configuration interaction including single and double substitutions (QCISD) results. The B3PW91/6-311G(2df,p) level of theory is recommended for the prediction of the geometries and energetics of organoselenium compounds.