In a MOZYME calculation, some elements might need to be defined as not having any covalent bonds when building the Lewis structure. This can be in order to generate a sensible Lewis structure for the user or, in rare instances, to generate an acceptable Lewis structure for MOZYME.
Consider ferrocene. In ferrocene, iron has 8 valence electrons, so if it is allowed to bond to the carbon atoms, it would form 8 covalent sigma bonds. In such a system, iron would thus be Fe(VIII). In a zinc finger, if Zn bonds to the four ligands, it would have a formal charge of -2. Such unusual oxidation states or charges might be of concern to users, however in most cases they would not affect the MOZYME calculation.
Individual elements and individual atoms can be re-defined as not forming any covalent bonds by use of METAL. In building Lewis structures, all elements of Groups I and II are considered as being fully ionic. If they need to be considered as covalent, use CVB to define bonds.
Individual elements are specified by their chemical symbol, individual atoms are specified by the atom-number of the real atom. (Real atoms numbers exclude any dummy atoms)
|METAL=(Fe)||Re-define all iron atoms are being 100% ionic|
|METAL=(Fe,Zn)||Re-define all iron and zinc atoms are being 100% ionic|
|METAL=(3423)||Re-define atom 3423 as being 100% ionic|
|METAL=(Zn,6222)||Re-define all zinc atoms and atom 6222 as being 100% ionic|
|METAL=(22,54)||Re-define atoms 22 and 55 as being 100% ionic|
Related key-words: LEWIS,
CHARGE, CHARGES, and MOZYME
See also: Lewis Structures, MOZYME introduction, Lewis metal atom charges