Helix external parameters

Here k is the Boltzmann constant, T is the absolute temperature, C is the number of peptide residues per cubic centimeter of solution, / and s are the helical fraction and the Zimm-Bragg parameter for the polypeptide molecule in the absence of external field, and ft is a parameter which represents the average correlation between the helix unit at the end of a helical sequence and the random-coil unit next to it. Though a detailed account of this parameter is left for Ref. (124), we note here that / = 0 corresponds to the complete absence of correlation between these two units, while ft — 1 corresponds to the case in which the dipole moment of a random coil unit points in the same direction as the axis of the preceding helix unit. 

For the description of a given helix, we have a natural basis. One refers to the screw sjmmietry and just specifles the screw operation that maps the molecule onto itself. Screw operations comprise a turn about a certain angle, say AC, together with a simultaneous longitudinal shift, say Az. These two values that describe the move from one monomer unit to the adjacent one constitute the external helix parameters. For polyethylene we have AC =... 

The relative geometries of DNA and the transition moment of an externally bound chromophore are defined by the parameters r, a, and y, in Figure 2B. r and y define the position of the external chromophore s transition moment relative to the DNA helical axis and a and describe the orientation of the transition moment a is the angle between the z-axis (DNA helical axis) and the transition moment and is the angle between the projection of the transition moment onto the xy plane and the vector r the distance from the helix axis to the position of the transition moment. 

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