Elements Available in PM6

Lanthanides^§:

*: Available as 3+ sparkles, if keyword SPARKLE is used. Hyperlink is to individual example data sets.
§: Hyperlink to a ZIP file containing example data sets for all the Lanthanides

In addition to the elements, other symbols used in geometry definition are:

Elements +, ++, -, and -- are the "Sparkles"; Tv is the translation vector for polymer calculations. The half-integer entities Fr and At are intended for use in simulating crystal fields for transition metal complex work, and should only be used in even numbers.

 Element 102, symbol Cb, is designed to satisfy valency requirements of atoms for which some bonds are not completed. Thus in "solid" diamond the usual way to complete the normal valency if the cluster model is not used is to use hydrogen atoms. This approach has the defect that the electronegativity of hydrogen is different from that of carbon. The "capped bond" atom, Cb, is designed to satisfy these valency requirements without acquiring a net charge.  

Cb behaves like a monovalent atom, with the exception that it can alter its electronegativity to achieve an exactly zero charge in whatever environment it finds itself. It is thus all things to all atoms. On bonding to hydrogen it behaves similarly to a hydrogen atom. On bonding to fluorine it behaves like a very electronegative atom. If several capped bond atoms are used, each will behave independently. Thus if the two hydrogen atoms in formic acid were replaced by Cbs, then each Cb would independently become electroneutral.

Capped bonds internal coordinates should not be optimized. A fixed bond-length of 1.7 Å is recommended; if two Cbs are on one atom, a contained angle of 109.471221 degrees is suggested, and if three Cbs are on one atom, a contained dihedral of -120 degrees (note sign) should be used.

   Element 99, X, or XX, is known as a dummy atom and is used in the definition of the geometry; it is deleted automatically from any Cartesian coordinate geometry files. Dummy atoms are pure mathematic points, and are useful in defining geometries; for example, in ammonia the definition of C_3v symmetry is facilitated by using one dummy atom and symmetry relating the three hydrogens to it.