Publisher Summary A polypeptide chain can assume an extremely large number of conformations because of the possibility of rotations about the single bonds of the backbone and side chains. The totality of these conformations, in random sequence along a chain, constitutes the so-called “random coil;” this concept is very familiar to those dealing with synthetic polymers. In the random-coil form, the polypeptide chain has a considerable amount of conformational entropy. However, under appropriate conditions of temperature, pH, solvent, etc., the various intramolecular interactions may cause the chain to adopt a rather limited number of conformations, despite the considerable reduction of conformational entropy. Presumably, the native form of most proteins is a member of this small class of relatively ordered conformations. This chapter discusses the computation of the internal energy for any arbitrary conformation. In principle, in a computation, conformations of equal energy can be grouped, and thereby information about the entropy can be obtained, and hence free energy, of the system. Computations are currently being carried out under the “assumption” that the native protein has a narrow distribution of conformations about an equilibrium one, and that this distribution has the highest statistical weight.

Calculations of Conformations of Polypeptides

Periodic potential functions for pseudorotation and internal rotation

A simple formula is presented for calculating the approximate partition function of a hindered internal rotational mode of a polyatomic molecule. The formula gives useful accuracy over the whole range from harmonic oscillator to hindered rotator to free rotator.

A simple approximation for the vibrational partition function of a hindered internal rotation

Flexible models for intramolecular motion, a versatile treatment and its application to glyoxal☆

The N.M.R. spectrum of o-chlorotoluene, dissolved in the nematic phase of 4-methoxybenzylidene-4-amino-α-methylcinnamic acid n-propylester is analysed and the shape of the proton skeleton determined. The position of lowest energy of the potential barrier to methyl rotation is found to be that in which the chlorine atom is staggered to the methyl group, and the height of the barrier is of the order of 5·0 kJ mol-1 (1200 cal/mole).

Jerome D. Swalen

Papers

Internal Rotation and Microwave Spectroscopy