{"id":5104,"date":"2011-10-13T11:22:58","date_gmt":"2011-10-13T10:22:58","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=5104"},"modified":"2011-10-13T12:47:59","modified_gmt":"2011-10-13T11:47:59","slug":"bonds","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5104","title":{"rendered":"Bonds."},"content":{"rendered":"
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Bonds are a good example of something all chemists think they can recognise when they see them. But they are also remarkably dependent on context. We are running a molecular modelling course at the moment, and I found myself explaining to someone how very context-sensitive they can be. I thought it might be useful to collect my thoughts here.<\/p>\n

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  1. The most primitive bond is the connection type<\/em>. This is used in chemical informatics to define a connection table<\/em> for a molecule, which is used by all the major chemical databases to index and hence search for molecules. It is also used by the InChI identifier to create the InChI key, and of course SMILES strings. The connection bond has no other properties (such as its bond order etc), but it is assumed to be covalent rather than ionic.<\/li>\n
  2. The next is the display bond<\/em>. This is used by chemical visualisation programs; it is normally created by the code based on very simple rules, such as how far apart the two (or more) atoms are. Such bonds are normally drawn with straight lines, of which there can be up to five (or six at a pinch) nowadays. There is however only a fuzzy convention for how non-integer bond orders are represented. A dashed line can be added (and it might be the only line for weaker types such as hydrogen bonds), but its clear this display convention is suffering at this stage.\n