Methyl rotational tunneling dynamics of p-xylene confined in a crystalline zeolite host

Methyl rotor quantum states and the effect of chemical environment in organic crystals: γ-picoline and toluene

Using a set of first-principles calculations, we have studied the methyl tunnel splitting for molecular crystals of γ-picoline and toluene. The effective rotational potential energy surface of the probe methyl rotor along the tunneling path is evaluated using first-principles electronic structure calculations combined with the nudged elastic band method. The tunnel splitting is calculated by an explicit diagonalization of the one-dimensional time-independent Hamiltonian matrix. The effects of chemical environment and rotor-rotor coupling on the rotational energy barriers were investigated. It is found that more dense packing of the molecules in toluene compared to that in γ-picoline gives rise to a larger rotational barrier which in turn yields a considerably smaller tunnel splitting. Moreover, it turned out that coupled motion of the face-to-face methyl groups in γ-picoline has a significant effect on the reduction of the rotational barrier. Our results are in good agreement with the experimentally observed tunnel splitting.

Three entropic classes of side chain in a globular protein

The relationship between the NMR methyl group axial order parameter and the side chain conformational entropy is investigated in inhibitor-bound and apo human HIV protease using molecular dynamics simulation. Three distinct entropic classes of methyl-bearing side chains, determined by the topological distance of the methyl group from the protein backbone (i.e., the number of χ-bonds between the Cα and the carbon of the CH3 group), are revealed by atomistic trajectory analyses performed in the local frame of reference of individual methyl probes. The results demonstrate that topologically equivalent methyl groups experience similar nonbonded microenvironments regardless of the type of residues to which they are attached. Similarly, methyl groups that belong to the same side chain but that are not topologically equivalent exhibit different thermodynamic and dynamic properties. The two-parameter classification (based upon entropy and methyl axial order parameter) of side chains described here permits improved estimates of the conformational entropies of proteins from NMR motional parameters.

Van der waals interactions and decrease of the rotational barrier of methyl-sized rotators: a theoretical study

Rotational barriers of methyl-sized molecular rotators are investigated theoretically using ab initio and empirical force field calculations in molecular models simulating various environmental conditions experienced by the molecular rotors. Calculations on neopentane surrounded by methyl groups suggest that the neopentane's methyl rotational potential energy barrier can be reduced by up to an order of magnitude by locating satellite functional groups around the rotator at a geometry that destabilizes the staggered conformation of the rotator through van der Waals repulsive interactions and reduces the staggered/eclipsed relative energy difference. Molecular mechanics and molecular dynamics calculations indicate that this barrier-reducing geometry can also be found in molecular rotators surface mounted on graphite surfaces or carbon nanotube models. In these models, molecular dynamics simulations show that the rotation of methyl-sized functional groups can be catalyzed by van der Waals interactions, thus making very rigid rotators become thermally activated at room temperature. These results are discussed in the context of design of nanostructures and use of methyl groups as markers for microenvironmental conditions.