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Some potential energy functions accurately describe the geometries of important classes of structures

In molecular mechanical systems, behavior depends on the shape and elastic properties of parts, rather than directly on their energies. Although the shape of conformationally flexible molecules can depend sensitively on the relative energies of different configurations, the shape of a stiff molecule depends only on its bond lengths and bond angles. Modern molecular mechanics methods describe these geometric parameters with high accuracy for a wide range of structures. A previous-generation system (MM2) typically predicts experimental bond lengths to within ~0.0003 nm and bond angles to within ~0.6° (hence angular positions to within ~0.0015 nm) for diverse hydrocarbons [1]. A leading vendor of modeling software (Accelrys) claims that their current Class II force field (CFF) has rms errors in bond lengths ~0.001 nm, bond angles ~1.2°, and torsion angles ~1.3°, “nearly independent of molecule type” for a wide range of organic structures [2].

What are “conformationally flexible” molecules?

Link  Most large molecules made by conventional synthesis are floppy

What are “stiff” molecules?

Link  Large molecules made by mechanosynthesis can be stiff


[1] Burkert, U. and Allinger, N. L (1982) Molecular Mechanics ACS Monograph 177, American Chemical Society.

[2] CFF - Accelrys’ Class II Forcefield