Although structural descriptors such as we’ve seen in the names of boron hydrides, for example catena or closo, provide information on atomic connectivity, they tell us little or nothing about the geometry of the molecule.
Have a look at the structures (a) and (b):
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| (a) | (b) |
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Both of them can be named additively pentaoxidotungstate(4−). Yet, as you can see, they have very different shapes. We can tell one from another with the help of special descriptors known as polyhedral symbols. The molecule (a) adopts a pentacoordinate square pyramidal (SPY-5) geometry, while (b) is a pentacoordinate trigonal bipyramid (TBPY-5). Therefore, their corresponding — and more informative — names will be (SPY-5)-pentaoxidotungstate(4−) and (TBPY-5)-pentaoxidotungstate(4−).
For coordination numbers 2 to 9, IUPAC recommends the following polyhedral symbols [1, IR-9.3.2.1, Table IR-9.2]:
| Coordination polyhedron | Coordination number | Polyhedral symbol |
|---|---|---|
| Angular | 2 | A-2 |
| Linear | 2 | L-2 |
| Trigonal plane | 3 | TP-3 |
| Trigonal pyramid | 3 | TPY-3 |
| T-shape | 3 | TS-3 |
| Square plane | 4 | SP-4 |
| Square pyramid | 4 | SPY-4 |
| See-saw | 4 | SS-4 |
| Tetrahedron | 4 | T-4 |
| Square pyramid | 5 | SPY-5 |
| Trigonal bipyramid | 5 | TBPY-5 |
| Octahedron | 6 | OC-6 |
| Trigonal prism | 6 | TPR-6 |
| Octahedron, face monocapped | 7 | OCF-7 |
| Pentagonal bipyramid | 7 | PBPY-7 |
| Trigonal prism, square face monocapped | 7 | TPRS-7 |
| Cube | 8 | CU-8 |
| Dodecahedron | 8 | DD-8 |
| Hexagonal bipyramid | 8 | HBPY-8 |
| Octahedron, trans-bicapped | 8 | OCT-8 |
| Square antiprism | 8 | SARP-8 |
| Trigonal prism, square-face bicapped | 8 | TPRS-8 |
| Trigonal prism, triangular-face bicapped | 8 | TPRT-8 |
| Heptagonal bipyramid | 9 | HBPY-9 |
| Trigonal prism, square-face tricapped | 9 | TPRS-9 |
More polyhedral symbols have been proposed for higher coordination numbers [2]. In organic compounds, commonly encountered polyhedra include TPY-3, TS-3, T-4, SP-4, SS-4, TBPY-5, SPY-5 and OC-6 [3, P-93.3.2, Table 9.1]; the symbol (T-4) — tetrahedron being the default coordination polyhedron for carbon — is not used in organic nomenclature [3, P-93.3.3.2].
Let us represent the coordination complexes in the form [Maibj...], where M is the central atom, ‘a’, ‘b’, etc. are different types of ligands, and i, j, etc. indicate the number of ligands. For complexes of the form [Mai], that is, if all the ligands are the same, as is the case with structures (a)—(c)*, there is no need to add anything to the polyhedral symbol. Ditto for [Maib1] , i.e. if only one ligand of type ‘b’ is present in polyhedra such as T-4, SP-4 and OC-6, as in the case of (OC-6)-amminepentacyanidoferrate(3−) (d). But for [Maibj] (where i>1, j>1), that is, if we add another ligand of type ‘b’, the situation could change dramatically.
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| (c) | (d) |
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Consider the isomers (e) and (f). The complex (e) is known as cisplatin and is used to treat some types of cancer. Its isomer (f), transplatin, does not show comparable anticancer activity.
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| (e) | (f) |
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Square planar complexes of the form [Ma2b2] are commonly differentiated by the descriptors cis and trans [1, IR-9.3.3.3], so (e) and (f) can be called cis-diamminedichloridoplatinum(II) and trans-diamminedichloridoplatinum(II), respectively. However, if we need to distinguish between isomers of the form [Mabcd], or if we want to use (SP-4) symbol, we can follow a more general procedure recommended by IUPAC [1, IR-9.3.3.3].
Each donor atom in the complex is assigned a priority number according to the Cahn–Ingold–Prelog (CIP) sequence rules. These priority numbers are then used to form the configuration index which is the single digit corresponding to the priority number of the donor atom trans to the priority ① donor. The configuration index follows the polyhedral symbol (SP-4). In case of (e), the priority ② atom (nitrogen) is trans to the priority ① atom (chlorine), so the configuration index will be ‘2’: (SP-4-2)-diamminedichloridoplatinum, while for (f), the priority ① atoms (chlorine) are trans to each other, thus the configuration index is ‘1’: (SP-4-1)-diamminedichloridoplatinum.
Similar rules are used to name octahedral systems, although the configuration index now consists of two digits that follow the polyhedral symbol (OC-6) [1, IR-9.3.3.4]. Let’s see how it works with the isomers (g) and (h). Warning: it can get a bit tedious; feel free to skip it.
2(PMe2Ph)4%5D.png) |
2(PMe2Ph)4%5D.png){kind=spacer} |
| (g) | (h) |
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First, let’s assign the priority numbers. There are only two types of ligands in (g) and (h) to the central molybdenum atom: dimethyl(phenyl)phosphane and dinitrogen. According to the CIP rules, the priority numbers for their respective donor atoms are ① (phosphorus) and ② (nitrogen).
The pairs of donor atoms at the opposite vertices of an octahedron are said to be trans to each other. There are three C4 symmetry axes passing through these vertices. The reference axis of the octahedron is the one connecting the priority ① atom and the lowest priority (and therefore highest numerical value) atom trans to it. In (g), there are two identical axes ①—② (phosphorus—nitrogen), so we can choose either of them as a reference axis.
The reference axis will give us the first digit of the configuration index: it is the priority number of the donor atom trans to the priority ① donor atom. In case of (g), the priority ② (N) is trans to the priority ① atom (P), so the first digit of the configuration index is ‘2’.
The second digit of the configuration index is the priority number of the donor atom trans to the most preferred donor atom in the plane that is perpendicular to the reference axis. If there is a choice, the lowest priority (highest numerical value) number is selected. For (g), in the plane perpendicular to the reference axis ①—②, we have two other axes: ①—② (P—N) and ①—① (P—P). We choose the priority number which has the highest numerical value, i.e. ②. Thus the configuration index for (g) is ‘22’ and the complete name will be (OC-6-22)-tetrakis[dimethyl(phenyl)phosphane]bis(dinitrogen)molybdenum.
In case of (h), the priority ① atoms (P) are always trans to each other, so the two reference axes are ①—① and the first digit of the configuration index will be ‘1’. In the plane perpendicular to the reference axis ①—① there are two other axes: ①—① (P—P) and ②—② (N—N). Since the atom trans to the priority ① atom also has the priority ①, the second digit is ‘1’ and the configuration index for (h) will be ‘11’, thus (OC-6-11)-tetrakis[dimethyl(phenyl)phosphane]bis(dinitrogen)molybdenum.
The Red Book also provides the rules for TS-3, SS-4, SPY-4, SPY-5, TBPY-5, PBPY-7, HBPY-8 and HBPY-9 systems [1, pp. 183—185]. As you can imagine, the more vertices there are, the more complex the configuration index grows. For coordination numbers higher than 6, the configuration indices consist of two segments divided by a hyphen. Hartshorn et al. furnish an example descriptor ‘SAPRS-10-49-135827106-A’, where SAPRS-10 is the proposed polyhedral symbol for decacoordinate square-face bicapped square antiprism, 49-135827106 is the configuration index, and A is the absolute configuration stereodescriptor [2]. The authors thought it necessary to underscore ‘10’ in the configuration index “in order to avoid any ambiguity with two separate designators, 1 and 0”, although there is no such thing as priority ⓪ atoms. Still, they have a point: for coordination numbers above 10, we’ll need a system to differentiate between one-digit and two-digit numbers, say by enclosing the latter in commas or something. Maybe there is a good reason why IUPAC didn’t recommend anything (so far) beyond coordination number 9.
| * | See [3, P-93.3.2] for more examples. |
References
- Connelly, N.G., Hartshorn R.M., Damhus, T. and Hutton, A.T. Nomenclature of Inorganic Chemistry: IUPAC Recommendations 2005. Royal Society of Chemistry, Cambridge, 2005.
- Hartshorn, R.M., Hey-Hawkins, E., Kalio, R. and Leigh, G.J. (2007) Representation of configuration in coordination polyhedra and the extension of current methodology to coordination numbers greater than six (IUPAC Technical Report). Pure and Applied Chemistry 79, 1779—1799.
- Favre, H.A. and Powell, W.H. Nomenclature of Organic Chemistry: IUPAC Recommendations 2013 and Preferred IUPAC Names. Royal Society of Chemistry, Cambridge, 2014.
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