The coupling between librational motions and conformational transitions in chain molecules. A phenomenological analysis

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Abstract
By analyzing the barrier crossing problem according to the Kramers theory, one derives that a conformational transition leads to reorientations in a small portion only of the chain. Therefore one must consider the librational motions, i.e., the fluctuations of the internal coordinates about the minima of the intramolecular potential, in order to describe the relaxation to the equilibrium after a transition. A phenomenological treatment is proposed for the model system of the rotor chain. It is shown that a conformational transition generates reorientations of the chain units, which propagate with increasing time delays. Since the time delays can be comparable or even greater than the lifetimes of the conformational states, the coupling between the librational and the conformational motions must be taken into account in order to describe the rotational relaxation in long chain molecules. This problem requires a generalized master equation (GME) for the distribution function on both the the torsional angle displacements and the conformational states. An approximate method of solution of the GME is presented, which allows the calculation of the orientational correlation functions