Molecular Rate Coefficients Research Articles

Effect of Hofmeister cosolutes on the photocycle of photoactive yellow protein at moderately alkaline pH

The photocycle of photoactive yellow protein was studied by kinetic absorption spectroscopy from below 100ns to seconds, at moderately alkaline pH, in the presence of high concentrations of various salts. Chemometric analysis combined with multiexponential fit of the flash-induced difference spectra provided evidence for five intermediates, including a spectrally silent form before the final recovery of the parent state, but only three with significantly distinct spectra. The calculated intermediate spectra constituted the input for the following spectrotemporal model fit using a sufficiently complex photocycle scheme with reversible transitions. This yielded the rate coefficients of the molecular transitions, the final spectra and the kinetics of the intermediates. Except for the transition between the two red shifted (early) intermediates (pR1 and pR2) and the final photocycle step, all reactions appeared to be reversible. Kosmotropic and chaotropic cosolutes had a systematic effect on the molecular rate coefficients. The largest effect, associated presumably with the exposure of the hydrophobic interior of the protein, accompanies the transition between the second red-shifted and the first blue-shifted intermediate (pR2 and pB1, respectively), i.e. it coincides with the chromophore protonation. The dependence of the rate coefficients on the Hofmeister cosolutes suggests that the conformational change of photoactive yellow protein leading eventually to the most unfolded signaling state takes place in several steps, and starts already with the relaxation after the chromophore isomerization in the microsecond time domain.

Molecular and phenomenological rate coefficients of fast reactions in solutions

The paper is concerned with the problem of formulating chemical rate equations for reversible reactions in solution in terms of concentration-independent, phenomenological rate coefficients. These time-dependent rate coefficients approach, after an initial transient, the rate constants that can be obtained in a relaxation experiment. We start with the coupled evolution equations for the macroscopic concentrations, and for the two-particle distribution functions describing association–dissociation (A+B=C), bimolecular isomerization (A+B=B+C), and double decomposition (A+B=C+D). The effects of interparticle forces and long-ranged reactivity are included. We derive general identities linking the reactants and products radial distribution functions. For association–dissociation this leads to relations among the molecular rate coefficients which are valid for both contact and long ranged reactivities. For the other two reaction types, we were able to derive analogous relations only for contact reactivities. We demonstrate how the phenomenological rate coefficients can be defined via the solutions of the corresponding diffusional boundary-value problems. This approach is quite general, and valid for both contact and long-ranged reactivities and if interaction forces are included.

Monomer–excimer kinetics in solution. II. Statistical nonequilibrium thermodynamic approach

The statistical nonequilibrium thermodynamic theory of diffusion-influenced reactions is employed to study reversible excimer formation in solution. Three types of rate coefficients for bimolecular excimer formation are discussed: (i) molecular rate coefficients defined by one-way reactive fluxes, (ii) phenomenological rate constants based on form of the macroscopic rate equations, and (iii) modified, time-dependent phenomenological rate coefficients. Relations are derived linking: (i) the molecular rate coefficients for reversible and irreversible excimer formation rates, and (ii) the steady-state molecular rate constant and the Laplace transform of the time resolved irreversible rate coefficient. The relationship between the present approach and the microscopic–stochastic theory of excimer formation is discussed.

The chemistry of nitroso-compounds. Part V. Encounter control for the nitrosation of indoles in dilute acid

Rates of nitrosation of 1,2-dimethyl-, 2-phenyl-, 2-methyl-, 2-methyl-5-nitro-, 5-cyano-, 5-nitro-, and 1-methyl-5-nitro-indole in dilute aqueous acid under various conditions are reported. Reaction to form the 3-nitroso-product may be brought about by various reagents, including nitrous anhydride, the nitrous acidium ion, and nitrosyl chloride, depending on the conditions. Examination of kinetic hydrogen isotope effects and chloride ion catalysis shows that these reactions follow the expected A–SE2 pathway characteristic of aromatic electrophilic substitution, but that the rate-limiting step depends on the basicity of the substrate. For basic compounds (pKA–3·5) either formation of the reagent (in the case of nitrous anhydride) or diffusion of the reactants is rate limiting: molecular rate coefficients for the reaction of nitrosyl chloride with the neutral substrate are of the order of 1010 l mol–1 min–1 at 0 °C. For less basic compounds (pKA⩽–6·0), proton expulsion from the Wheland-type intermediate is slow as is usual for aromatic nitrosation. Generally, indole compounds are much more reactive than aromatic amines (diazotisation) towards these nitrosating agents, and this suggests that nitrosation of the former may involve initial substitution of the heterocyclic N atom, with rearrangement to the 3-nitroso-product.