Effect of solvation and confinement on the trans-gauche isomerization reaction in n-butane

Isomerization kinetics of flexible molecules in the gas phase: Atomistic versus coarse-grained sampling

Isomerization kinetics of molecules in the gas phase naturally falls on the microcanonical ensemble of statistical mechanics, which for small systems might significantly differ from the more traditional canonical ensemble. In this work, we explore the examples of cis-trans isomerization in butane and bibenzyl and to what extent the fully atomistic rate constants in isolated molecules can be reproduced by coarse-graining the system into a lower dimensional potential of mean force (PMF) along a reaction coordinate of interest, the orthogonal degrees of freedom acting as a canonical bath in a Langevin description. Time independent microcanonical rate constants can be properly defined from appropriate state residence time correlation functions; however, the resulting rate constants acquire some time dependence upon canonical averaging of initial conditions. Stationary rate constants are recovered once the molecule is placed into a real condensed environment pertaining to the canonical ensemble. The effective one-dimensional kinetics along the PMF, based on appropriately chosen inertia and damping parameters, quantitatively reproduces the atomistic rate constants at short times but deviates systematically over long times owing to the neglect of some couplings between the system and the bath that are all intrinsically present in the atomistic treatment. In bibenzyl, where stronger temperature effects are noted than in butane, the effective Langevin dynamics along the PMF still performs well at short times, indicating the potential interest of this extremely simplified approach for sampling high-dimensional energy surfaces and evaluating reaction rate constants.

Is There a General Rule for the Gauche Effect in the Conformational Isomerism of 1,2-Disubstituted Ethanes?

The stabilities of the gauche and anti conformations of butane, 1,2-dicyanoethane (DCE), and 1,2-dinitroethane (DNE) have been investigated through theoretical calculations. The gauche effect-the tendency of keeping close vicinal electronegative substituents (thetaX-C-C-X approximately 60 degrees ) in an ethane fragment-is expected to drive the conformational equilibrium of DCE and DNE toward the gauche conformation. It was found that, for butane, where the gauche effect is supposed to be poor/null, the hyperconjugation effect contributes mostly to the anti stabilization in opposition to the traditional sense that the methyl groups repel each other, and this should govern its conformational equilibrium. For DCE the equilibrium was shifted to the anti conformer, essentially due to a gauche repulsion, while for DNE, despite the higher electronic delocalization energies, a predominance of the gauche conformer was obtained, and this was attributed mainly to the attractive dipolar interaction between the two nitro groups. A full orbital energy analysis was performed using the natural bond orbital approach, which showed that bond bending and anti-C-H/C-X* hyperconjugation models, usually applied to explain the origin of the gauche effect in fluorinated derivatives, are not adequate to completely explain the conformational behavior of the titled compounds.