Imperial College London

Henry Rzepa

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.

1.  The most primitive bond is the *connection type*. This is used in
    chemical informatics to define a *connection table* 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.
2.  The next is the *display bond*. 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.
    - Perhaps to keep the synthetic chemists happy, I should add two
      flavours to this category, the *stereochemical display bond,*
      which attempts to add a 3D context but in truth does this less
      than perfectly and the *retrosynthetic bond*. I will not dwell.
3.  Then there is what I call the *mechanical bond*. This is used in
    molecular mechanics force fields. It is a declared bond, *i.e.* you
    declare where you want the bond to be, and once that is done, it
    remains there (it is thus never broken). Each declaration is
    associated with (quadratic) force constants, which taken as a whole
    define the force field.
4.  Next comes the *quantum chemical bond.* This is defined by a
    wavefunction, which in turn tells us about the electron density.
    This, to be frank, can be a can of worms. There must be dozens of
    ways of interpreting the electron density in terms of a bond type. I
    have used just one of these on this blog, the ELF procedure, which
    gives an estimate of how many electrons are involved in any bond
    (and these are always non-integers). Books could be written about
    this topic, but I will mention just three varieties which indicate
    how confusing quantum bonds can become. These are the
    *homo(aromatic) bond,* which itself comes in two varieties, *bond
    and no-bond* types
    (DOI: [10.1021/jp026521l](http://dx.doi.org/10.1021/jp026521l){target="_blank"}), *bent
    bonds and transition state bonds. *Phew!
5.  The *quantum topological bond* emerges from  [Bader's QTAIM
    procedure](http://www.ch.imperial.ac.uk/rzepa/blog/?p=4987){target="_blank"},
    which provides a formal topological framework for defining what a
    bond is. As I noted in earlier posts, it is controversial, since it
    does not always reflect what chemists might regard as a useful
    definition that helps them do chemistry.
6.  Finally (?), I could add *Rydberg bonds*, which are mysterious
    formations on excited state surfaces, and which can be
    extraordinarily long (\> 500Å), thus defying application of simple
    distance rules as noted in type 2 above.

<div>

It is a taken that the moment anyone tries to define boundaries and
rules for bonds, people will argue against the scheme. But if you have
your own type which is missing above, do let me know!

</div>

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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.

Messaggi di Rogue Scholar

Bonds.