VDWM(text)

In MOZYME,  the LEWIS structure is constructed from the topology of the system.  Atoms are considered to be connected if they are within 10% of the addition of the two radii, or within twice the heavy-atom radius if one of the atoms is hydrogen.  Values for all radii used are shown in the Table below.

The criterion of whether atoms are connected or not can be changed by modifying the radii. using the VDWM keyword.   The format of the command is:

VDWM(<chemical symbol₁>=n.nn;<chemical symbol₂>=n.nn;<chemical symbol₃>=n.nn;...)

For example, if a hydrogen atom should be regarded as connected to a nitrogen, but the N-H distance is 1.62 Angstroms, then VDWM(N=0.85) would override the default values of the van der Waals radii of nitrogen (0.75), and result in the hydrogen being connected (the N-H distance of 1.62 being less than 2*0.85).

If a fluorine atom should be connected to a bromine, but the F-Br distance is 2.1 Angstroms, i.e., it is too large for the two atoms to be regarded as being connected (2.1 > 1.1(0.71 + 1.14), then either the F radius, or the Br radius, or both, could be increased.  One possible change would be to use keyword VDWM(F=0.75;Br=1.2)

Entries for different elements should be separated by a colon, a comma, or a semi-colon.

 Table 1: Default radii (Angstroms) used in MOZYME

Related key-words:  LEWIS, CVB, SETPI, METAL, CHARGE, CHARGES, and MOZYME
See also: Lewis Structures, MOZYME introduction