From: gilleain t. <gil...@gm...> - 2010-10-26 10:10:29
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Hi, About generating coordinates for structures with salts/counter ions; I think that this capability should definitely be in the SDG - perhaps in a subclass for now, but generally it should 'just do it'. The reasoning being that ions are closely (conceptually) tied to the other molecule. If you are laying out molecule sets, then the ion should not be separated from its - er, what is the term? - 'parent'. However, when it comes to placement, it would be nice to put the charged parts of the pair together, but not always possible. I can imagine situations where a parent has multiple charged groups - such as multiple carboxylates - and the ion can only be placed next to one or the other. Also, polydentate chelators may well have a fully 3D structure; a pair of EDTAs around a single metal ion may not project onto a planar diagram very well. In general, chemical diagrams are a mixture of symbology and geometric model - the bond lengths and angles are not accurate, but they roughly represent the three dimensional geometry. The placement of the counter-ion might not bear any relation to the actual chemical situation, and automated placement may well give the wrong idea if it is too smart. gilleain |