The addition of hydrogen to the carbon-carbon double bond of 2-butenes adsorbed on Pd(111) was studied within the density functional theory (DFT) and using a periodic slab model. For that purpose, the Horiuti-Polanyi mechanisms for both complete hydrogenation and isomerization were considered. The hydrogenation of cis and trans-2-butene to produce butane proceeds via the formation of eclipsed and staggered -2-butyl intermediates, respectively. In both cases, a relatively high energy barrier to produce the half-hydrogenated intermediate makes the first hydrogen addition the slowest step of the reaction. The competitive production of trans-2-butene from cis-2-butene requires the conversion from the eclipsed -2-butyl to the staggered -2-butyl isomer. As the corresponding energy barrier is relatively small and because the first of these isomers is less stable than the second, an easy conversion is predicted.

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In this work, we assess a previously advanced hypothesis that predicts the existence of ion channels in the capsid of small and non-enveloped icosahedral viruses. With this purpose we examine Triatoma Virus (TrV) as a case study. This virus has a stable capsid under highly acidic conditions but disassembles and releases the genome in alkaline environments. Our calculations range from a subtle sub-atomic proton interchange to the dismantling of a large-scale system representing several million of atoms. Our results provide structure-based explanations for the three roles played by the capsid to enable genome release. First, we observe, for the first time, the formation of a hydrophobic gate in the cavity along the five-fold axis of the wild-type virus capsid, which can be disrupted by an ion located in the pore. Second, the channel enables protons to permeate the capsid through a unidirectional Grotthuss-like mechanism, which is the most likely process through which the capsid senses pH. Finally, assuming that the proton leak promotes a charge imbalance in the interior of the capsid, we model an internal pressure that forces shell cracking using coarse-grained simulations. Although qualitatively, this last step could represent the mechanism of capsid opening that allows RNA release. All of our calculations are in agreement with current experimental data obtained using TrV and describe a cascade of events that could explain the destabilization and disassembly of similar icosahedral viruses.