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For example, the cyclopentadienyl rings in ferrocene $\ce{Fe(}\eta^5 \ce{-C5H5)2}$ are often drawn with delocalized electron circles in them instead of explicit pi bonds.

ferrocene

The Wikipedia article for ferrocene provides the following SMILES string: [cH-]1cccc1.[cH-]1cccc1.[Fe+2]. In this SMILES string, the charge on the cyclopentadienyl ligands are explicitly attached to carbon atoms in the ring.

  1. Can explicit or implicit delocalization be stored in a SMILES string? For example, would c1cccc1.c1cccc1.Fe also be an acceptable SMILES string for ferrocene that can be parsed and understood?
  2. Does the localized version of the SMILES string provide enough information for the delocalization to be reconstructed when the string is parsed back into a structure? If not, how can this be done?
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  • $\begingroup$ If you mean the aromaticity of the cyclopentadienyl rings, I think SMILES doesn't capture such information, and in general it can only be noticed after rebuilding the structure. $\endgroup$ – Nicolau Saker Neto Dec 9 '14 at 13:05
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    $\begingroup$ As an example, the wikipedia article for ferrocene $\ce{Fe(}\eta^5 \ce{-C5H5)2}$ has the SMILES as [cH-]1cccc1.[cH-]1cccc1.[Fe+2], which as Nicolau mentions contains no such delocalization information. The charges on the cyclopentadienyl ligands are explicitly attached to carbon atoms. $\endgroup$ – Ben Norris Dec 9 '14 at 14:55
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    $\begingroup$ There is an excellent general question on what SMILES strings can and cannot convey buried in this question. I provided some improvements so that the question becomes answerable and the OP can still get the desired outcome. $\endgroup$ – Ben Norris Dec 9 '14 at 15:08
  • $\begingroup$ Thanks Ben. I could not have put it in a better way. It is not a homework question. I am coming to it from statistics/maths side and it is my first cheminformatics project. I was able to discover ferrocene by searching: delocalized qsar but when it's smiles notation is converted into structure, it gives positive charge on each C. I am reaching to conclusion that probably approaching this problem via SMILES is not the optimal way. $\endgroup$ – Kaustubh Kaluskar Dec 9 '14 at 15:30
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There are general problems representing delocalized bonding and organometallic compounds in cheminformatics (generally) and SMILES in specific.

To quote the Open SMILES standard:

This simple mental model [of a connection table between atoms using valence bonds] has little resemblance to the underlying quantum-mechanical reality of electrons, protons and neutrons, yet it has proved to be a remarkably useful approximation of how atoms behave in close proximity to one another. However, the valence model is an imperfect representation of molecular structure, and the SMILES language inherits these imperfections. Chemical bonds are often tautomeric, aromatic or otherwise fractional rather than neat integer multiples. Delocalized bonds, bond-centered bonds, hydrogen bonds and various other inter-atom forces that are well characterized by a quantum-mechanics description simply don’t fit into the valence model.

Other interesting cases are agostic interactions, 3-center 2-electron bonds (e.g., diborane).

There are several suggestions for advancing beyond the typical connection-table valence bond view, including:

That both papers were published 17+ years ago should be some indication of:

  • Chemists like the valence bond view of molecules, despite the limitations
  • How complicated bonding can be in non-organic chemistry
  • How far cheminformatics needs to go to properly handle organometallic and non-organic compounds

By the way... anyone interested in implementing such efforts should let me know.. Many people would be happy to help. :-)

UPDATE

I should point out that there are some practical solutions to representing such things. For example Alex Clark suggested recording zero-order bonds (and sometimes dummy atoms):

"Accurate Specification of Molecular Structures: The Case for Zero-Order Bonds and Explicit Hydrogen Counting" J. Chem. Inf. Model., 2011, 51 (12), pp 3149–3157

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