Reaction of sulphate radical anion (SO<Superscript>.</Superscript><Subscript>4</Subscript><Superscript>-</Superscript>) with hydroxy-and methyl-substituted pyrimidines: a pulse radiolysis study

Reactions of sulphate radical anion (SO·₄ ^-) with 4,6-dihydroxy-2-methyl pyrimidine (DHMP), 2,4-dimethyl-6-hydroxy pyrimidine (DMHP), 6-methyl uracil (MU) and 5,6-dimethyl uracil (DMU) have been studied by pulse radiolysis at pH 3 and at pH 10. The transient intermediate spectra were compared with those from the reaction of hydroxyl radical (·OH). It is proposed that SO·₄ ^- produces radical cations of these pyrimidines in the initial stage. These radical cations are short-lived except in the case of DMHP where a relatively longer lived radical cation is proposed to be formed. When there is a hydrogen atom attached to the N(1) or N(3) position, a deprotonation from these sites is highly favored. When there is no hydrogen attached to these sites, deprotonation from a substituted methyl group is favored. At acidic pH, deprotonation from nitrogen is observed for DHMP, MU and DMU. At basic pH, the radical cation reacts with OH^- leading to the formation of OH adducts.     

Identification of archaeal proteins that affect the exosome function in vitro

Background  

The archaeal exosome is formed by a hexameric RNase PH ring and three RNA binding subunits and has been shown to bind and degrade RNA in vitro. Despite extensive studies on the eukaryotic exosome and on the proteins interacting with this complex, little information is yet available on the identification and function of archaeal exosome regulatory factors.     

High precision delta(17)O isotope measurements of oxygen from silicates and other oxides: method and applications

The use of infrared laser-assisted fluorination to release oxygen from milligram quantities of silicates or other oxide mineral grains is a well-established technique. However, relatively few studies have reported the optimisation of this procedure for oxygen-17 isotope measurements. We describe here details of an analytical system using infrared (10 μm) laser-assisted fluorination, in conjunction with a dual inlet mass spectrometer of high resolving power ( approximately 250) to provide (17)O and (18)O oxygen isotope measurements from 0.5-2 mg of silicates or other oxide mineral grains. Respective precisions (1) of typically 0.08 and 0.04 per thousand are obtained for the complete analytical procedure. Departures from the mass-dependent oxygen isotope fractionation line are quantified by Delta(17)O; our precision (1) of such measurements on individual samples is shown to be +/-0.024 per thousand. In turn, this permits the offset between parallel, mass-dependent fractionation lines to be characterised to substantially greater precision than has been possible hitherto. Application of this system to investigate the (17)O versus (18)O relationship for numerous terrestrial whole-rock and mineral samples, of diverse geological origins and age, indicates that the complete data set may be described by a single, mass-dependent fractionation line of slope 0.5244+/- 0.00038 (standard error). Copyright 1999 John Wiley & Sons, Ltd.     

A NEW FINITE ELEMENT APPROXIMATION OF A STATE-CONSTRAINED OPTIMAL CONTROL PROBLEM

In this paper, we study numerical methods for an optimal control problem with pointwise state constraints. The traditional approaches often need to deal with the deltasingularity in the dual equation, which causes many difficulties in its theoretical analysis and numerical approximation. In our new approach we reformulate the state-constrained optimal control as a constrained minimization problems only involving the state, whose optimality condition is characterized by a fourth order elliptic variational inequality. Then direct numerical algorithms （nonconforming finite element approximation） are proposed for the inequality, and error estimates of the finite element approximation are derived. Numerical experiments illustrate the effectiveness of the new approach.     

Reaction of hydroxyl radicals with azacytosines: a pulse radiolysis and theoretical study

Pulse radiolysis and density functional theory (DFT) calculations at B3LYP/6-31+G(d,p) level have been carried out to probe the reaction of the water-derived hydroxyl radicals (*OH) with 5-azacytosine (5Ac) and 5-azacytidine (5Acyd) at near neutral and basic pH. A low percentage of nitrogen-centered oxidizing radicals, and a high percentage of non-oxidizing carbon-centered radicals were identified based on the reaction of transient intermediates with 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonate), ABTS2-. Theoretical calculations suggests that the N3 atom in 5Ac is the most reactive center as it is the main contributor of HOMO, whereas C5 atom is the prime donor for the HOMO of cytosine (Cyt) where the major addition site is C5. The order of stability of the adduct species were found to be C6-OH_5Ac*>C4-OH_5Ac*>N3-OH_5Ac*>N5-OH_5Ac* both in the gaseous and solution phase (using the PCM model) respectively due to the additions of *OH at C6, C4, N3, and N5 atoms. These additions occur in direct manner, without the intervention of any precursor complex formation. The possibility of a 1,2-hydrogen shift from the C6 to N5 in the nitrogen-centered C6-OH_5Ac* radical is considered in order to account for the experimental observation of the high yield of non-oxidizing radicals, and found that such a conversion requires activation energy of about 32 kcal/mol, and hence this possibility is ruled out. The hydrogen abstraction reactions were assumed to occur from precursor complexes (hydrogen bonded complexes represented as S1, S2, S3, and S4) resulted from the electrostatic interactions of the lone pairs on the N3, N5, and O8 atoms with the incoming *OH radical. It was found that the conversion of these precursor complexes to their respective transition states has ample barrier heights, and it persists even when the effect of solvent is considered. It was also found that the formation of precursor complexes itself is highly endergonic in solution phase. Hence, the abstraction reactions will not occur in the present case. Finally, the time dependent density functional theory (TDDFT) calculations predicted an absorption maximum of 292 nm for the N3-OH_5Ac* adduct, which is close to the experimentally observed spectral maxima at 290 nm. Hence, it is assumed that the addition to the most reactive center N3, which results the N3-OH_5Ac* radical, occurs via a kinetically driven process.     

Reactions of hydroxyl radical (·OH) and oxide radical anion (O·−) with 2-aminopurine in aqueous medium

Pulse radiolysis has been used to investigate the reaction of hydroxyl radical (^·OH) and oxide radical anion (O^·−) with 2-aminopurine (2AP), a fluorescent analogue of adenine, in aqueous medium. The second-order rate constant for the reaction of ^·OH with 2AP was determined to be 3 × 10⁹ dm³ mol⁻¹s⁻¹ and for the reaction of O^·− it was 7.1 × 10⁸ dm³ mol⁻¹s⁻¹. The transient absorption spectrum obtained in the reaction of ^·OH at pH 7 has absorption maxima at 370 and 470 nm. The spectrum undergoes a time-dependent transformation at higher time-scale. The intermediate species was found to react with N,N,N′,N′-tetramethyl-p-phenylenediamine (TMPD). The yield of TMPD^·+ was calculated in terms of G(TMPD^·+) to be 3.3 × 10⁻⁷ mol J⁻¹ at pH 7. The ^·OH reactions were also carried out at pH 10 and the transient absorption spectra have λ _max at 400 and 480 nm. The transient spectra obtained in the reaction of O^·− at pH ≈14 have maxima at 400 and 480 nm. The transient intermediate species at pH 7 are assigned to the formation of 2AP-4-OH^· (54%), 2AP-5-OH^· (7%) and 2AP-8-OH^· (39%) based on the spectral evidence and TMPD^·+ build-up. Both 2AP-4-OH^· and 2AP-5-OH^· undergo OH⁻ elimination to form a radical cation. At higher pH (pH 10), the dehydration reaction of these OH-adducts leads to a N-centered radical (2AP-N(9)^·, 71%). Formation of 2AP-8-OH^· (29%) is also proposed at this pH. In the reaction of O^·− with 2AP, it is proposed that a similar nitrogen centered 2AP-N(9)^· radical is formed by an electron-transfer reaction at N(9).     

Reaction of oxide radical ion (O.–) with substituted pyrimidines

Pulse radiolysis technique has been used to investigate the reaction of oxide radical ion (O^.–) with 4,6-dihydroxy-2-methyl pyrimidine (DHMP), 2,4-dimethyl-6-hydroxy pyrimidine (DMHP), 5,6-dimethyl uracil (DMU) and 6-methyl uracil (MU) in strongly alkaline medium. The second-order rate constants for the reaction of O^.– with these compounds are in the range 2-5 × 10⁸ dm³ mol^–1 s^–1. The transient absorption spectra obtained with DHMP have two maxima at 290 and 370 nm and with DMHP have maxima at 310 and 470 nm. The transient spectrum from DMU is characterized by its absorption maxima at 310 and 520 nm and that of MU by its single maximum at 425 nm. The intermediate species were found to react with N,N,N,N-tetramethyl-p-phenylenediamine (TMPD) with high G(TMPD^.+) values ranged between 3.9 × 10^–7 molJ^–1 and 4.8 × 10^–7 molJ^–1. These radicals undergo decay by second-order kinetics (2k/ = 1.0-1.7 × 10⁶ s^–1). The reaction of O^.– with the selected pyrimidines is proposed to proceed through a hydrogen abstraction from the methyl group forming allyl type radicals. These are mainly oxidizing radicals and hence readily undergo electron transfer reactions with TMPD.     

Reaction of hydroxyl radicals with S-nitrosothiols: Formation of thiyl radical (RS?) as the intermediate

The decomposition studies of S-nitrosothiols (RSNO) are important due to their potential role in vivo in connection with the storage and transport of nitric oxide (^•NO) within the body. Reactions of hydroxyl radicals (^•OH) with a number of RSNOs (S-nitroso derivatives of N-acetyl-dl-penicillamine, l-cysteinemethylester, N-acetylcysteamine, and dl-penicillamine) in aqueous medium at neutral and acidic pH have been reported in the present study. Radiation chemical technique (steady state and pulse radiolysis) has been utilized for the determination of the reaction rate constants, the end product analyses, and the transient intermediate species. The rate constants for the reaction of ^•OH with the selected RSNOs were determined using a competition kinetic method with 2′-deoxy-d-ribose as the competitor. All the rate constants were found to be of the order of diffusion controlled (10¹⁰ M⁻¹ s⁻¹). The degradation yield of RSNOs was found to be quantitative (i.e., G(–RSNO) ≈ G(^•OH)) at neutral and acidic pH. The major products of decomposition were the respective disulfide (RSSR) and nitrite (NO₂ ⁻). A good material balance is also obtained between the degradation yield and the formation of the products (i.e., G(–RSNO) ≈ G(RSSR) + G(NO₂ ⁻)). The major transient intermediate was the thiyl radical (RS^•). Its intermediacy was confirmed by making use of the electron transfer reaction of 2,2′-azinobis(3-ethylbenzothiazoline-6-sulfonate) (ABTS²⁻) to RS^•, which results in the formation of ABTS^•− having a transient absorption spectrum with λ_max at 410 nm. Based on these results, a generalized reaction mechanism is deduced for the reaction of ^•OH with RSNO.