Torsional angle rotation

A separation of the through-bond interactions (Ed) into bond stretching ( b), angle bending (E ) and torsional angle rotation (Ej) is only possible if these terms are not... 

Arachidonic acid (5 ,8 , HE, 14 -eicosatetraenoic acid) is a precursor for the biosynthesis of prostaglandins. Apply torsion angle rotations involving bond C9-C10 and C10-C11 to search for the prostaglandin-like conformation. 

A separation of the through-bond interactions (Ed) into bond stretching (Eb), angle bending (Eg), out-of-plane deformation (E ), torsional angle rotation (Ef) and other terms is only possible if these terms are not coupled, and this is most likely if the force constants are very different. This is generally true and leads to largely decoupled local oscillators. In cases where this requirement is violated correction terms have to be added. This can be done by the inclusion of cross-terms which will be discussed later. 

One could completely describe the three-dimensional structure of a protein by placing it in a Cartesian coordinate system and listing (x, y, z) coordinates for each atom in the protein. Indeed, this is how experimentally determined protein structures are stored in the Protein Data Bank at the Brookhaven National Laboratory in the United States of America. However, the structure of a protein can be more succinctly described by listing the angles of rotation (torsion angles) of each of the bonds in the protein (see Fig. 4-4). For example, the backbone conformation of an amino acid residue can be specified by listing the torsion angles (rotation around the N—Ca bond), (rotation around the Ca—C bond), and ca (rotation around the N—C bond). 

For example, the backbone conformation of an amino acid residue can be specified by listing the torsion angles ( ) (rotation aronnd the N—C bond), / (rotation around the C —C bond), and 0) (rotation about the N—C bond). 

At the time of writing we can optimise on five classes of observables geometry expressed as the Internal coordinates bond lengths, valence angles and torsional angles rotational constants atomic charges dipole moment and Internal frequencies of vibration. 

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