Substitution Of Oxygen Atoms Research Articles

Stabilizing contributions of sulfur-modified nucleotides: crystal structure of a DNA duplex with 2'-O-[2-(methoxy)ethyl]-2-thiothymidines

Substitution of oxygen atoms by sulfur at various locations in the nucleic acid framework has led to analogs such as the DNA phosphorothioates and 4′-thio RNA. The phosphorothioates are excellent mimics of DNA, exhibit increased resistance to nuclease degradation compared with the natural counterpart, and have been widely used as first-generation antisense nucleic acid analogs for applications in vitro and in vivo. The 4′-thio RNA analog exhibits significantly enhanced RNA affinity compared with RNA, and shows potential for incorporation into siRNAs. 2-Thiouridine (s2U) and 5-methyl-2-thiouridine (m5s2U) are natural nucleotide analogs. s2U in tRNA confers greater specificity of codon–anticodon interactions by discriminating more strongly between A and G compared with U. 2-Thio modification preorganizes the ribose and 2′-deoxyribose sugars for a C3′-endo conformation, and stabilizes heteroduplexes composed of modified DNA and complementary RNA. Combination of the 2-thio and sugar 2′-O-modifications has been demonstrated to boost both thermodynamic stability and nuclease resistance. Using the 2′-O-[2-(methoxy)ethyl]-2-thiothymidine (m5s2Umoe) analog, we have investigated the consequences of the replacement of the 2-oxygen by sulfur for base-pair geometry and duplex conformation. The crystal structure of the A-form DNA duplex with sequence GCGTAT*ACGC (T* = m5s2Umoe) was determined at high resolution and compared with the structure of the corresponding duplex with T* = m5Umoe. Notable changes as a result of the incorporation of sulfur concern the base-pair parameter ‘opening’, an improvement of stacking in the vicinity of modified nucleotides as measured by base overlap, and a van der Waals interaction between sulfur atoms from adjacent m5s2Umoe residues in the minor groove. The structural data indicate only minor adjustments in the water structure as a result of the presence of sulfur. The observed small structural perturbations combined with the favorable consequences for pairing stability and nuclease resistance (when combined with 2′-O-modification) render 2-thiouracil-modified RNA a promising candidate for applications in RNAi.

Optical properties and energetics of oxygenated silicon ring-shaped clusters

The optical absorption spectra of equilibrium Si-based ring-shaped clusters have been calculated with the semi-empirical quantum mechanical Intermediate Neglect of Differential Overlap method and Configuration Interaction. The Neglect of the Diatomic Differential Overlap based AM1 geometry optimization calculations show that it is energetically favorable to attach the OH group to an isolated Si ring and to further incorporate the oxygenated Si clusters into an amorphous silica matrix. Substitution of oxygen atoms with nitrogen in such clusters lowers the binding energy of the participating atoms and therefore compromises the stability of the molecule. The calculated optical absorption spectra of the oxygenated Si-based rings consistently exhibit three peaks in the neighborhood of 200, 260 and 320 nm that are not influenced by the presence or absence of nitrogen atoms. A comparison has been made between the experimental results obtained and the properties of the spark-processed Si. The calculations suggest that Si ring clusters are contributing to the optical properties of this material.

A Phospholipase with a Novel Catalytic Triad.

Catalytic triads are a long-standing paradigm of enzyme catalysis. By using a "matched mutation" approach, that is, a simultaneous exchange of the protein (through mutagenesis) and the substrate (through substitution of oxygen atoms by sulfur atoms) followed by enzyme kinetic analysis, a novel catalytic triad (see figure) with an unusual amino acid composition is now proposed for a phospholipase that fulfills a dual function in catalysis.

Remediation of the Earth's atmosphere through photoinitiated destruction of freons on the alkaline earth oxide components of tropospheric aerosols

Interaction of some freons with the ambient air-exposed surface of magnesium oxide and calcium hydroxycarbonate in darkness and under mild UV radiation, corresponding to solar light in the troposphere, can result in efficient irreversible destructive adsorption of some freons. The above photoadsorption activity appears to be related to the optical absorption, detected at wavelengths ranging within 300–400 nm and caused presumably by surface carbonates or some other surface compounds. The irreversible adsorption is observed for H-containing freons like CF 3CH 2F and CHF 2Cl, while for hydrogen-free ozone-depleting freons like CF 2Cl 2 no adsorption is detected. We suggest that at the photostimulated adsorption, fluorine and chlorine atoms substitute oxygen atoms in the magnesium oxide lattice and hydroxyl groups of calcium hydroxycarbonates. It was also found that most of the observed photoadsorption phenomena might be related to the presence of a certain amount of N 2O natively adsorbed on the alkaline earth oxides exposed to ambient air. Also under discussion is a possible impact of the solar light driven photoadsorption on solid tropospheric aerosols, containing magnesium oxide and calcium hydroxycarbonate, on the natural non-technogeneous remediation of the Earth's atmosphere from freons.

The effects of heteroatom substitution on the singlet–triplet energy differences in diradicals—ab initio calculations of ΔEST in meta-benzoquinomethane and in 1,3-naphthoquinomethane

The large effects on the singlet–triplet energy difference, ΔEST, of substituting oxygen atoms for one or two methylene groups in trimethylenemethane and in 2,4-dimethylenecyclobutane-1,3-diyl are discussed. In contrast, CASSCF and CASPT2N/6-31G* calculations predict only small changes in ΔEST on substituting oxygen atoms for one or two methylene groups in m-benzoquinodimethane. After corrections for differences in zero-point energies and heat capacities, CASPT2N/6-31G* calculations give ΔEST = 11.0 kcal mol–1 for m-benzoquinodimethane, which is very close to the experimental value of ΔEST = 9.6 ± 0.2 kcal mol–1. At the same level of theory ΔEST = 9.3 and 11.8 kcal mol–1 are computed for, respectively, m-benzoquinomethane and m-benzoquinone. The reasons why substitution of oxygen atoms for one or two methylene groups is predicted to have such a small effect on ΔEST in these three diradicals is discussed. As expected, for 1,3-naphthoquinomethane CASPT2N predicts a value of ΔEST that is only slightly larger than that in m-benzoquinomethane. However, the calculated value of ΔEST = 11.6 kcal mol–1 is 7 kcal mol–1 lower than the value measured by photoacoustic calorimetry.

X-ray emission spectra of fluorinated Bi2223 compound

The results of measurements of FKα X-ray emission spectra of Bi 1.65Pb 0.35Sr 2Ca 2Cu 3O y F 0.75 and related compounds CaF 2, SrF 2, CuF 2, PbF 2, BiF 3 and BiOF are presented. It is found that the width of F Kα X-ray emission spectrum, and fine structure and intensity of K 1 L 1 high energy satellite of Bi2223:F are very close to those of SrF 2 and quite different in comparison with other F-containing compounds. It is concluded that in Bi2223:F the doped F-atoms substitute oxygen atoms in SrO planes and form mainly FSr bonds.

Possibility of sulphur-oxygen substitution in YBa 2Cu 3O 6+xS y analyzed by means of X-ray emission spectroscopy

The analysis of substitution effects upon doping of YBa 2Cu 3O 6+xS y by sulphur is given on the basis of investigation of SKα 1,2 and SKß 1 x-ray emission spectra. It is found that sulphur can enter the lattice of YBa 2Cu 3O 7 and substitute oxygen atoms. With increasing sulphur concentration from y>0.5 to 2.0 S atoms form isolated sulphate groups which do not have a long order but can be detected by x-ray emission spectroscopy.

Sulphur-oxygen substitution in YBa 2Cu 3O 6+xS y analyzed by means of X-ray emission spectroscopy

The analysis of substitution effects upon doping of YBa 2Cu 3O 6+ x S y by sulphur is given on the basis of the investigation of S Kα 1,2 and S Kβ 1 X-ray emission spectra. It is found that sulphur can enter the lattice of YBa 2Cu 3O 7 and substitute oxygen atoms. With increasing sulphur concentration from y > 0.5 to 2.0 S atoms form isolated sulphate groups which do not have a long order but can be detected by X-ray emission spectroscopy.

TG study on the reaction of γ-Al 2O 3 by CCl 4. Part I. Kinetic model for the chlorination process

Thermogravimetric (TG) measurements were carried out to study the chlorination of γ-alumina by gaseous CCl 4 in the temperature range 650–1123 K at 10 2–10 4 Pa CCl 4 partial pressure. Experimental results indicate that the reaction involves two main steps: the substitution of oxygen atoms on the surface by chlorine leading to a mass gain and the volatilization of the main gaseous product, aluminium chloride, with a mass loss of the sample. These processes take place simultaneously during the course of the reaction. A kinetic model is proposed to describe these two steps providing a simple method for linearization of the initial part of the isothermal TG curves. Temperature and partial pressure dependence of the reaction rate and of the steady-state surface coverage are discussed on the basis of the proposed kinetic model. Activation energies and reaction orders are calculated for these two steps.

Constitution of the surface lipid from the leaves of Brassica oleracea (var. capitata ) ( Winnigstadt )) - III. Nonacosane and its derivatives

The constitution of the hydrocarbon fraction has been determined by gas/liquid chromatography. Ten alkanes containing both odd and even numbers of carbon atoms have been found. Nonacosane (93 %) and hentriacontane (3 %) are the main components. The constitution of the nonacosane derivatives has been elucidated by subjecting each fraction to modified Baeyer-Villiger oxidation and identifying the key fragments by a combination of adsorption and reversed-phase partition chromatography on films of adsorbent supported on glass plates. A pair of isomers has been found in each group. Those from the ketone and secondary alcohol are derived by substitution of oxygen atoms in the 10- and 15-positions. In the ketol the oxygen substituents are also in the 10- and 15-positions and the isomers are derived by interchanging the positions of the hydroxyl and carbonyl groups.