When CHARGES is present, all ionized sites in the system will be identified and printed. The run will then be stopped. This operation is useful during the preparation of a data set, in that it is very easy for even experienced users to have incorrect charges on large systems, particularly complicated organic species such as enzymes and organometallics.
The method for identifying charged atoms is very powerful. So although you might be quite certain that you have the charges correct, if CHARGES indicates that you have made a mistake, please check the system using the information printed. In 100% of the cases where users have complained that MOPAC reported faulty charges, CHARGES identified errors in the user's structure.
In MOPAC, many common Lewis structures involve hypervalent systems being represented as ions. Thus the sulfur atom in sulfuric acid would be represented as S+ and there would be a counter-charge of O-. Be aware that during a geometry optimization "salt bridges" can form, e.g. -COOH ... H2N- can convert to -[COO]- ... [H2N]+-. Such structures should not be regarded as faults. Also, metal ions might be reported as having an unexpected charge, thus Zn with four oxygen atoms as ligands might be reported as [Zn]2-. If this causes any concern, add keyword METAL, and all bonds to metal ions will be broken, so for example Zn with four ligands would be reported as [Zn]2+ and all four ligands would each acquire a negative charge.
The choice of which nitrogen atoms in the heterocycle in histidine have attached hydrogen atoms is often not immediately obvious. But in many cases, the choice is important - the wrong choice will always result in a high-energy structure, and be accompanied by severe rotation of the heterocycle, as it tries to relieve the stress. CHARGES cannot help with identifying the right choice.
Related key-words: LEWIS,
CVB, METAL, VDWM,
CHARGE, and MOZYME
See also: Lewis Structures,
MOZYME introduction