DNA interactions with small solutes: change in the character of the binding of [Ru(NH3)5pz]2+ to DNA as a consequence of changes in the solvent

Kinetics and mechanism of formation of the complex [Ru(CN)5INH]3− through the ligand substitution reaction between the aquapentacyanoruthenate(II) anion and isoniazid

The formation kinetics of the complex, [Ru(CN)5INH]3−, formed through the ligand substitution reaction between isoniazid (INH) and aquapentacyanoruthenate(II) ([Ru(CN)5H2O]3−), have been investigated, under pseudo first-order conditions, as a function of concentrations of [INH] and [Ru(CN)5H2O]3−, ionic strength and temperature at pH = 4.0 ± 0.02 in 0.2 M NaClO4 spectrophotometrically at 502 nm ( λmax of intense yellow colour product [Ru(CN)5INH]3−) corresponding to metal-to-ligand charge-transfer transitions, in aqueous medium. The pseudo first-order condition was maintained by taking at least 10% excess of [INH] over [Ru(CN)5H2O]3−. The stoichiometry of the reaction product was found to be 1:1 which was further supported and characterized using elemental analysis, infrared, nuclear magnetic resonance and mass spectrometric techniques. Thermodynamic and kinetic parameters have also been computed, using the Eyring equation, and the values of ΔH≠, Ea, ΔG≠ and ΔS≠ were found to be 47.3 kJ mol−1, 49.8 kJ mol−1, −8.62 kJ mol−1 and 187.6 J K−1mol−1, respectively. The reaction was found to obey first-order kinetics with respect to [INH]. It exhibited a negative salt effect on the rate upon variation of ionic strength of the medium. A tentative mechanistic scheme was proposed on the basis of experimental findings.

Noncovalent interactions of tiopronin-protected gold nanoparticles with DNA: two methods to quantify free energy of binding

The binding of gold nanoparticles capped with N-(2-mercaptopropionyl)glycine (Au@tiopronin) with double-stranded DNA has been investigated and quantified in terms of free energies by using two different approaches. The first approach follows the DNA conformational changes induced by gold nanoparticles using the CD technique. The second methodology consists in the use of pyrene-1-carboxaldehyde as a fluorescent probe. This second procedure implies the determination of the "true" free energy of binding of the probe with DNA, after corrections through solubility measurements. Working at different salt concentrations, the nonelectrostatic and electrostatic components of the binding free energy have been separated. The results obtained revealed that the binding is of nonelectrostatic character, fundamentally. The procedure used in this work could be extended to quantify the binding affinity of other AuNPs/DNA systems.

Reaction and reorganization free energies of electron-transfer reactions under restricted geometry conditions

Electron-transfer reactions between iron and cobalt complexes were studied in beta-cyclodextrin (betaCD), 2-hydroxypropyl-beta-cyclodextrin (HbetaCD), and 18-crown-6 ether (18C6) solutions. The results were rationalized taking as the basis the Marcus-Hush formalism. We employed two different approaches, depending on the kind of receptor and solvent, to obtain the reorganization and reaction free energies that determine the reaction rate constant. The opposite trends in reactivity observed in betaCD and HbetaCD solutions and the behavior in solutions of 18C6 are explained.

Microheterogeneous catalysis

The catalytic effect of micelles, polymers (such as DNA, polypeptides) and nanoparticles, saturable receptors (cyclodextrins and calixarenes) and more complex systems (mixing some of the above mentioned catalysts) have been reviewed. In these microheterogeneous systems the observed changes in the rate constants have been rationalized using the Pseudophase Model. This model produces equations that can be derived from the Brönsted equation, which is the basis for a more general formulation of catalytic effects, including electrocatalysis. When, in the catalyzed reaction one of the reactants is in the excited state, the applicability (at least formally) of the Pseudophase Model occurs only in two limiting situations: the lifetime of the fluorophore and the distributions of the quencher and the probe are the main properties that define the different situations.

Cooperative and noncooperative binding of *Ru(bpy)3(2+) to DNA and SB4.5G dendrimers

The process *Ru(bpy)(3)(2+) + S(2)O(8)(2-) in two different reaction media, the SB4.5G dendrimer and DNA solutions, was studied. In both media, the receptors have anionic characteristics. This fact will produce a binding of the ruthenium complex to the two receptors by attractive electrostatic interactions. On the contrary, the peroxodisulfate ions will be preferentially located in the aqueous solution due to electrostatic repulsions with the receptors. Despite the similarities of the receptors, some differences are observed in these two reaction media. These differences arise from the fact that the binding of the *Ru(bpy)(3)(2+) complex to DNA shows a negative cooperativity, whereas the binding to the dendrimer is noncooperative in character. The anticooperative character of the binding that happens in DNA solutions becomes noncooperative when an electrolyte, NaNO(3), is added to the medium. This is related to a condensation of the salt's counterions on the surface of the DNA which produces a decrease of the equilibrium constant corresponding to the binding of the complex to the receptor. Therefore, it is shown that the ionic strength of the reaction medium exerts a great influence on the cooperative nature of the ligand/receptor binding. This also explains the different behavior observed in DNA and dendrimer solutions.