Dummy atoms are useful tools on a variety of fronts. Dummy atoms, represented as "X", are generally used to define geometries, particularly for structure optimizations. Gaussian94, for example, tends to "balk" with linear bond angles (180 degrees). We can, for example, cut the 180 angle in half through the use of a dummy atom as a bisector:
N C 1 cn X 2 1.0 1 90.0 H 2 ch 3 90.0 1 180.0 cn 1.20 ch 1.06
The angle between HNH and the CN bond is probably of interest in performing an optimization, but there is nothing to "anchor" the end of the angle. We can add a dummy atom, "X", which now becomes part of the CNX bond angle:
Dummy atoms are also frequently used with cyclic compounds, and molecules with centers of symmetry.
Bond distances are generally specified at 1.0 Å.
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