Methyl group dynamics in the crystalline alanine dipeptide: A combined computer simulation and inelastic neutron scattering analysis

Kneller, G. R.; Doster, W.; Settles, M.; Cusack, S.; Smith, J. C.
December 1992
Journal of Chemical Physics;12/15/1992, Vol. 97 Issue 12, p8864
Academic Journal
The dynamics of the methyl groups in the crystalline alanine dipeptide is examined over a wide range of temperatures using elastic and inelastic neutron scattering experiments and molecular dynamics (MD) simulations of the full crystal. Neutron scattering spectra are calculated from the simulations and directly compared to the experimental profiles. The N-ter and C-ter methyl groups in the molecule have low rotational barriers, i.e., ≲1 kcal/mol. They undergo rotations that are activated on time scales faster than ≊1 ns at temperatures as low as 50–100 K and are on the picosecond time scale at 150 and 300 K. At 300 K the rotational motion becomes strongly diffusive in the simulation. In contrast, the side-chain methyls possess a significant intramolecular intrinsic torsional barrier, ≊3 kcal/mol. As a result, their dynamics consists of librations and rare jumps between wells. The simulations are further analyzed to characterize in detail the motions giving rise to the calculated scattering. Using a quaternion-based method the simulated methyl dynamics is decomposed into rigid-body rotational and translational components. The decomposed motions and their contributions to the calculated neutron profiles are examined.


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