Statistical mechanical modelling of chemical reactions in complex systems: the kinetics of the Haem carbon monoxide binding–unbinding reaction in Myoglobin

The free energy profile and the (classical) kinetics of chemical reactions in (soft) condensed phase may be well modelled theoretically by means of molecular dynamics simulations, the perturbed matrix method (PMM) and statistical mechanics, as we provided in previous articles. In this paper, we describe the theoretical framework, discussing thoroughly its crucial points, and apply the model to an important biochemical reaction: the Haem carbon monoxide binding–unbinding reaction in Myoglobin, specifically investigating the reaction step involving the carbon–iron chemical bond formation (disruption) which is of particular biochemical interest.     

Studies on the synthesis of heterocyclic compounds. Part VI. The action of methyl salicylate on some 5-aminopyrazoles

Some 1-phenyl-3-R-5-aminopyrazoles reacted with methyl salicylate to give N-(1-phenyl-3-R-pyrazol-5-yl)-2-methoxybenzamides ( 3a,b,c ), 1-phenyl-2-methyl-3-R-salicyloilimino-3-pyrazolines ( 4a,b,c ) together with 1-phenyl-3-R-5-methylamino pyrazoles ( 5a,b,c ). The structures of the new compounds 3 and 4 were determined on the basis of analytical and spectroscopic data as well as on the acid hydrolysis products.     

The reversible opening of water channels in cytochrome C modulates the heme iron reduction potential

Dynamic protein-solvent interactions are fundamental for life processes, but their investigation is still experimentally very demanding. Molecular dynamics simulations up to hundreds of nanoseconds can bring to light unexpected events even for extensively studied biomolecules. This paper reports a combined computational/experimental approach that reveals the reversible opening of two distinct fluctuating cavities in Saccharomyces cerevisiae iso-1-cytochrome c. Both channels allow water access to the heme center. By means of a mixed quantum mechanics/molecular dynamics (QM/MD) theoretical approach, the perturbed matrix method (PMM), that allows to reach long simulation times, changes in the reduction potential of the heme Fe(3+)/Fe(2+) couple induced by the opening of each cavity are calculated. Shifts of the reduction potential upon changes in the hydration of the heme propionates are observed. These variations are relatively small but significant and could therefore represent a tool developed by cytochrome c for the solvent driven, fine-tuning of its redox functionality.     

Alternative Fast and Slow Primary Charge-Separation Pathways in Photosystem II

Photosystem-II (PSII) is a multi-subunit protein complex that harvests sunlight to perform oxygenic photosynthesis. Initial light-activated charge separation takes place at a reaction centre consisting of four chlorophylls and two pheophytins. Understanding the processes following light excitation remains elusive due to spectral congestion, the ultrafast nature, and multi-component behaviour of the charge-separation process. Here, using advanced computational multiscale approaches which take into account the large-scale configurational flexibility of the system, we identify two possible primary pathways to radical-pair formation that differ by three orders of magnitude in their kinetics. The fast (short-range) pathway is dominant, but the existence of an alternative slow (long-range) charge-separation pathway hints at the evolution of redundancy that may serve other purposes, adaptive or protective, related to formation of the unique oxidative species that drives water oxidation in PSII.