Unequal effect of ethanol-water on the stability of ct-DNA, poly[(dA-dT)]2 and poly(rA)·poly(rU). Thermophysical properties.

Ethanol affects unequally the thermal stability of DNA and RNA. It stabilizes RNA, while destabilizing DNA. The variation of the relative viscosity (η/η0) of [poly(dA-dT)]2 with temperature unveils transitions close to the respective denaturation temperature, calculated spectrophotometrically and calorimetrically. From the raw data densities and speeds of sound, the volumetric observables were calculated. In all cases studied, a change in sign from low to high ethanol content occurred for both partial molar volume (ϕV) and partial molar adiabatic compressibility (ϕK(S)). The minima, close to 10%, should correspond to the highest solvation and the maxima, close to 30%, to the lowest solvation. For 40-50% ethanol, the solvation increases again. The complex structure of ethanol-water, for which changes are observed in regions close to such critical concentrations, justifies the observed behaviour. The variation of ϕV and ϕK(S) was sharper for RNA compared with respect to DNA, indicating that the solvation sequence is poly(rA)·poly(rU) < ct-DNA < [poly(dA-dT)]2.

RNA triplex-to-duplex and duplex-to-triplex conversion induced by coralyne.

Spectrophotometric, circular dichroism, calorimetric, displacement assay and kinetic analyses of the binding of the fluorescent dye coralyne to poly(A)2poly(U) have served to enlighten the ability of the dye to produce dramatic changes in the RNA structure. The sets of data assembled convey that coralyne is able to induce the triplex-to-duplex conversion and also the duplex-to-triplex conversion according to a non-reversible cycle governed by temperature, provided that the [dye]/[polymer] ratio (CD/CP) is maintained constant above unity. Alternatively, at room temperature the triplex is formed at (roughly) CD/CP < 1 and the duplex at CD/CP > 1.

Microwave dielectric relaxation spectroscopy study of alkan-1-ol/alkylbenzoate binary solvents.

The structure and dynamics of alkan-1-ol/alkylbenzoate binary mixtures have been studied by microwave dielectric relaxation spectroscopy in the 200 MHz to 20 GHz frequency range. The binary mixtures of methanol, ethanol, propan-1-ol, butan-1-ol, and pentan-1-ol with methyl, ethyl, propyl, and butyl benzoates were studied at 298.15 K. The relaxational response of the pure alcohols, pure esters, and their binary mixtures over the full composition range is properly described by the Havriliak-Negami model. The alcohol content, alcohol length, and alkyl side-chain effects on the relaxational properties have been studied for these mixtures over the whole composition range. From the experimental readings, the effective and the corrective Kirkwood and Bruggeman correlation factors have been calculated. The data gathered have been interpreted in terms of the alkyl side-chain effect and their reliance on the mixture composition.

Heat capacity behavior and structure of alkan-1-ol/alkylbenzoate binary solvents.

Heat capacities for the binary mixtures of methanol with (C(1)-C(4)) alkylbenzoates and methylbenzoate with (C(1)-C(11)) alkan-1-ols have been measured over the whole composition range at 298.15 K under atmospheric pressure. From the experimental measurements, the derived excess molar heat capacities and partial excess molar heat capacities at infinite dilution have been calculated. A Redlich-Kister-type equation was fitted to these data, and the fitting parameters and standard deviations have been evaluated. Likewise, the IR spectra for the same systems have been recorded as a function of composition. The sets of experimental data gathered contribute to shed light onto the solvent structure and the underlying molecular interactions between the mixture constituents. The conclusions drawn have been established in terms of solute-solvent and solvent-solvent interactions and the ensuing structural effects between the solvent constituents.

Preferential solvation in alkan-1-ol/alkylbenzoate binary mixtures by solvatochromic probes.

The binary mixtures of methanol with (C(1)-C(4)) alkylbenzoates and of (C(1), C(3), C(5), C(7), C(9), C(11)) alkan-1-ols with methylbenzoate were used as solvents to look into the preferential solvation and intermolecular interactions of the solvatochromic indicators 2-nitroanisole, 4-nitroaniline, 4-nitrophenol, and Reichardt's dye by UV-vis measurements. The experimental data at 298.15 K have served to deduce the corresponding Reichardt and Kamlet-Taft parameters of the mixed solvents. The solvation effects exerted on the solvatochromic probes by the solvents used, either pure or binary mixed, were analyzed by means of the preferential solvation model. Likewise, the (1)H NMR, (13)C NMR, and IR spectroscopic parameters measured for the mixed solvents corroborate the structural effects. The sets of experimental data gathered shed abundant light on the underlying solute-solvent and solvent-solvent interactions. The alkanol/methylbenzoate mixtures display stronger solvation ability than the pure solvents.

Phosphine and thiophene cyclopalladated complexes: hydrolysis reactions in strong acidic media.

The mechanisms for the hydrolysis of organopalladium complexes [Pd(CNN)R]BF(4) (R=P(OPh)(3), PPh(3), and SC(4)H(8)) were investigated at 25 °C by using UV/Vis absorbance measurements in 10 % v/v ethanol/water mixtures containing different sulphuric acid concentrations in the 1.3-11.7 M range. In all cases, a biphasic behavior was observed with rate constants k(1obs), which corresponds to the initial step of the hydrolysis reaction, and k(2obs), where k(1obs)>k(2obs). The plots of k(1obs) and k(2obs) versus sulfuric acid concentration suggest a change in the reaction mechanism. The change with respect to the k(1obs) value corresponds to 35 %, 2 %, and 99 % of the protonated complexes for R=PPh(3), P(OPh)(3), and SC(4)H(8), respectively. Regarding k(2obs), the change occurred in all cases at about 6.5 M H(2)SO(4) and matched up with the results reported for the hydrolysis of the 2-acetylpyridinephenylhydrazone (CNN) ligand. By using the excess acidity method, the mechanisms were elucidated by carefully looking at the variation of k(i),(obs) (i=1,2) versus cH+. The rate-determining constants, k(0,A-1), k(0,A-2), and k(0,A-SE2) were evaluated in all cases. The R=P(OPh)(3) complex was most reactive due to its π-acid character, which favors the rupture of the trans nitrogen-palladium bond in the A-2 mechanism and also that of the pyridine nitrogen-palladium bond in the A-1 mechanism. The organometallic bond exerts no effect on the relative basicity of the complexes, which are strongly reliant on the substituent.

Hydrolysis mechanisms for the organopalladium complex [Pd(CNN)P(OMe)3]BF4 in sulfuric acid.

The acid-catalyzed hydrolysis of the organopalladium complex [Pd(CNN)P(OMe)3]BF4 species was monitored spectrophotometrically at different sulfuric acid concentrations (3.9 and 11.0 M) in 10% v:v ethanol-water over the 25-45 degrees C temperature range and in 30% and 50% (v/v) ethanol-water at 25 degrees C. Two acidity regions (I and II) could be differentiated. In each of the two regions the kinetic data pairs yielded two different rate constants, k(1obs) and k(2obs), the former being faster. These constants were fitted by an Excess Acidity analysis to different hydrolyses mechanisms: A-1, A-2, and A-SE2. In region I ([H2SO4] < 7.0 M), the k(1obs) values remained constant k(1obs)(av) = 1.6 x 10(-3) s(-1) and the set of k(2obs) values nicely matched an A-SE2 mechanism, yielding a rate-determining constant k(0,ASE2) = 2.4 x 10(-7) M(-1) s(-1). In region II ([H2SO4] > 7.0 M), a switchover was observed from an A-1 mechanism (k(0,A1) = 1.3 x 10(-4) s(-1)) to an A-2 mechanism (k(0,A2) = 3.6 x 10(-3) M(-1) s(-1)). The temperature effect on the rate constants in 10% (v/v) ethanol-water yielded positive DeltaH and negative DeltaS values, except for the A-1 mechanism, where DeltaS adopted positive values throughout. The solvent permittivity effect, epsilonr, revealed that k(1obs)(av) and k(0,A2) dropped with a fall in epsilonr, whereas the k(0,ASE2) value remained unaffected. The set of results deduced is in line with the schemes put forward.

Structural NMR and ab initio study of salicylhydroxamic and p-hydroxybenzohydroxamic acids: evidence for an extended aggregation.

The acid-base behavior and self-aggregation of salicylhydroxamic (SHA) and p-hydroxybenzohydroxamic acids (PHBHA)have been investigated by UV and 1HNMR spectroscopy, respectively. The acid-base parameters, measured in H2O at 25 degrees C and I=0.1 M, were pK1=7.56, pK2=9.85 for SHA and pK1=8.4, pK2=9.4 for PHBHA. The 1H NMR signals for salicylhydroxamic and p-hydroxybenzohydroxamic acids measured in acetone indicate that both acids self-aggregate according to a mechanism where two monomers produce planar E-E dimers stabilized by horizontal H-bonds. Further dimer aggregation yields sandwich-like tetramer structures stabilized by vertical H-bonds and pi-pi interactions. The p-hydroxybenzohydroxamic tetramers, less stable than those of salicylhydroxamic, contain two water molecules in their structures. The gas-phase structures of salicylhydroxamic acid and its anions were investigated by ab initio calculations using the density functional theory at the B3LYP/AUG-cc-pVDZ level. The SHA most stable gas-phase conformer is the A-Z amide, a structure with all three phenolate (OP), carboxylate (OC), and hydroxamate (OH) oxygen atoms in the cis position. The B-Z amide, with the OP oxygen trans to OC, lies 5.4 kcal above the A-Z amide. The most stable monoanion is the N-deprotonated A-Z amide.

Thermodynamics and kinetics of the nickel(II)-salicylhydroxamic acid system. Phenol rotation induced by metal ion binding.

The kinetics and the equilibria of Ni(II) binding to p-hydroxybenzohydroxamic acid (PHBHA) and salicylhydroxamic acid (SHA) have been investigated in an aqueous solution at 25 degrees C and I=0.2 M by the stopped-flow method. Two reaction paths involving metal binding to the neutral acid and to its anion have been observed. Concerning PHBHA, the rate constants of the forward and reverse steps are k1=(1.9+/-0.1)x10(3) M-1 s-1 and k-1=(1.1+/-0.1)x10(2) s-1 for the step involving the undissociated PHBHA and k2=(3.2+/-0.2)x10(4) M-1 s-1 and k-2=1.2+/-0.2 s-1 for the step involving the anion. Concerning SHA, the analogous rate constants are k1=(2.6+/-0.1)x10(3) M-1 s-1, k-1=(1.3+/-0.1)x10(3) s-1, k2=(5.4+/-0.2)x10(3) M-1 s-1, and k-2=6.3+/-0.5 s-1. These values indicate that metal binding to the anions of the two acids concurs with the Eigen-Wilkins mechanism and that the phenol oxygen is not involved in the chelation. Moreover, a slow effect was observed in the SHA-Ni(II) system, which has been put down to rotation of the benzene ring around the C-C bond. Quantum mechanical calculations at the B3LYP/lanL2DZ level reveal that the phenol group in the most stable form of the Ni(II) chelate is in trans position relative to the carbonyl oxygen, contrary to the free SHA structure, where the phenol and carbonyl oxygen atoms both have cis configuration. These results bear out the idea that the complex formation is coupled with phenol rotation around the C-C bond.