| A heterocyclic metal ring contains metal-metal bonds that connect adjacent metal atoms of the ring structure. Such rings may also be considered as polynuclear complexes in which each metal atom is bound to its two nearest ring neighbors, but not to all other metal atoms of the ring (as in small metal clusters). In most cases, neither the metal-metal bonds nor the bonds between metal atoms and atoms of possible ligands are adequately represented by SMILES bond symbols. The CurlySMILES language overcomes this problem by providing the unspecified-bond symbol ~ as well as a format to include ligands and assign interactions between ligand-atoms and nuclei. The following example shows the notation for a six-membered heavy-atom heterocycle: | |||
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| The four metal atoms and the two antimony atoms are coordinated with ligands. This is indicated via the annotation {+L}, without including details. This notation serves as a template to encode the heterocycle [Re2(CO)8(μ-SbPh2)(μ-H)]2 (Ph = phenyl), which is shown below and has been prepared by palladium-catalyzed ring-opening cyclodimerization of the three-membered heterocycle Re(CO)8(μ-SbPh2)(μ-H) [2,3]. Its notation is derived by filling the notations for the carbonyl, phenyl and μ-H ligands into the template: | |||
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References
| [1] | A. Drefahl: CurlySMILES: a chemical language to customize and annotate encodings of molecular and nanodevice structures. J. Cheminf. 2011, 3:1; doi: 10.1186/1758-2946-3-1 . |
| [2] | R. D. Adams, W. C. Pearl, Jr. Y. O. Wong, Q. Zhang, M. B. Hall and J. R. Walensky: Tetrarhena-heterocycle from the Palladium-Catalyzed Dimerization of Re2(CO)8(μ-SbPh2)(μ-H) Exhibits an Unusual Host-Guest Behavior. J. Am. Chem. Soc. 2011, 133 (33), 12994-12997. doi: 10.1021/ja205515u . |
| [3] | S. Ritter: Heavy-Metal Ring Bags Metal Atom . Chem. & Eng. News 2011, 89 (32), 13. |
| Encoding of complexes |
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Ambidentate ligands |
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