Molecular mechanics cross terms

Assisted model building with energy refinement (AMBER) is the name of both a force field and a molecular mechanics program. It was parameterized specifically for proteins and nucleic acids. AMBER uses only five bonding and nonbonding terms along with a sophisticated electrostatic treatment. No cross terms are included. Results are very good for proteins and nucleic acids, but can be somewhat erratic for other systems. 

In expression 3, (Tab is the average cross relaxation rate between protons a and b Xl is the mole fraction of one of the conformers, and aiab and a2ab are the cross relaxation rates for the individual conformers. In expression 4, Ei and E2 are the molecular mechanics energies for the conformers, k is the Boltzmann constant and T is the temperature at which the data were obtained. The pseudoenergy term may be... 

We briefly note in passing that because of the sum over molecular states 9j in (9), there is the possibility that cross-terms may contribute, thereby leading to quantum mechanical interference effects, 3 1S>. 

In the original molecular mechanics work, a steric energy, E, for a molecule was defined as the sum of the potentials for bond stretch, angle bend, Ee, torsional strain, E, nonbonded interactions, Ey f, and other terms, such as Urey-Bradley terms, cross-interaction terms, and electrostatic terms, (8). 

The primary conclusion that can be drawn is that there is a fundamental similarity in all three cytochrome molecules, which permits an appreciable amount of cross-reactivity to occur. We are therefore justified in looking to the common features of these three molecules for the essential regions in terms of molecular mechanism. Four secondary observations can aid our search even more ... 

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