Journal of Coordination Chemistry

ISSN: 0095-8972 (Print) 1029-0389 (Online) Journal homepage: http://www.tandfonline.com/loi/gcoo20

Shapes of undecanuclear clusters and

undecacoordinated metal complexes

Santiago Alvarez

To cite this article: Santiago Alvarez (2018): Shapes of undecanuclear clusters

and undecacoordinated metal complexes, Journal of Coordination Chemistry, DOI:
10.1080/00958972.2018.1442003

To link to this article: https://doi.org/10.1080/00958972.2018.1442003

Accepted author version posted online: 16

Feb 2018.

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Publisher: Taylor & Francis
Journal: Journal of Coordination Chemistry
DOI: http://doi.org/10.1080/00958972.2018.1442003

Shapes of undecanuclear clusters and undecacoordinated metal complexes

SANTIAGO ALVAREZ*

Departament de Química Inorgànica i Orgànica, Secció de Química Inorgànica, and Institut de Química Teòrica i
Computacional (IQTC-UB), Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona (Spain)

Dedicated to Prof. Juan Faus

The structures of molecules that arrange eleven identical atoms in one, two or three dimensions
are analyzed by means of continuous shape measures. In the case of three-dimensional
molecules, they comprise metallic clusters, boranes, supramolecular architectures and metal
coordination spheres, examples of eight different polyhedra have been identified, and in some
cases, also structures that fall along the minimal interconversion pathway between two such
polyhedra are discussed.

Keywords: Continuous shape measures; Stereochemistry; Transition metals; Lanthanides;

Clusters; Supramolecular architectures; Coordination compounds

A variety of polyhedra are used by chemists to describe the molecular structures of

metallic clusters, ligand-bridged polynuclear complexes, or the coordination sphere around metal
atoms [1]. When we wish to describe the structures of groups of eleven atoms, however, we are
devoid of regular reference polyhedra, and very little systematic classifications can be found in
the literature. In a classical book devoted to the stereochemistry of coordination compounds [2],
for instance, coordination numbers from 4 to 12 are considered, but undecacoordination is
skipped. Similarly, only a handful of 11-vertex clusters are described in a monograph, and their
shapes are described mostly as fused polyhedral [3].

*Corresponding author. Email: santiago@qi.ub.es

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Table 1. Eleven-vertex polygonal and polyhedral reference structures used in this work.

Abbreviation Name(s)‡ Edges Faces†

HP-11 Planar Hendecagon 11 -
cPPR-11 Elongated pentagonal pyramid (J9) 20 53 + 54 +15 = 11
or Capped pentagonal prism
cPAPR-11 Gyroelongated pentagonal pyramid (J11) 25 153 +15 = 16
or Capped pentagonal antiprism, or Vacant icosahedron
aPPR-11 Augmented pentagonal prism (J52) 19 43 + 44 + 25 = 10
aSPC-11 Augmented sphenocorona (J87) 26 163 +14 = 17
vCOC-11 Vacant cuboctahedron 22 83 + 54 = 13
hcTBPY-11 Hexacapped trigonal bipyramid 27 183 = 18
pcTPR-11 Pentacapped trigonal prism 27 183 = 18

†The faces are identified by Nx symbols, where x indicates the order of the faces and N is the
number of faces. For example, the symbol 25 indicates the presence of two pentagonal faces.
‡ The common numbers assigned to Johnson polyhedra are given in parentheses.

To find possible regularities in the geometries of 11-atom groups, extensive searches for
structures of clusters, polynuclear complexes and coordination spheres have been carried out in
the structural databases CSD [4] and ICSD [5]. For the study of coordination spheres,  bonded
ligands and metal-metal bonds have been disregarded. To identify the closest ideal geometry for
each set of 11 atoms, continuous shape measures (CShM's) [6] have been calculated with the
Shape program [7]. In brief, a shape measure compares the geometry of a group of points
(atoms) with that of an ideal shape (IS) and gives a numerical value S(IS) that is zero if the two
shapes are identical, and adopts increasing values as the problem and ideal shapes increasingly
differ from each other. Symmetry measures for each analyzed crystal structure have been
calculated relative to the ideal polyhedra shown in figure 1, whose geometrical characteristics
are summarized in table 1, and only those that have a small shape measure relative to one of the
ideal polyhedra will be discussed here.

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Figure 1. Ideal 11-vertex polyhedra considered in this work: Planar hendecagon (HP-11), capped
pentagonal antiprism (cPAPR-11), capped pentagonal prism (cPPR-11), augmented pentagonal
prism (aPPR-11), augmented sphenocorona (aSPC-11), vacant cuboctahedron (vCOC-11),
hexacapped trigonal bipyramid (hcTBPY-11), pentacapped trigonal prism (pcTPR-11), and
trioctahedron (triOC-11). The dashed lines in vCOC-11 indicate the vacant site of the
cuboctahedron.

a b

Figure 2. Linear structure of a Ni11 chain (a) subtended by four poly(naphthyridine-amine)

ligands arranged in a helical way [8], and planar ring structure (b) of a phenylthiolato-bridged
Ni11 compound [9].

3
Clusters and polynuclear complexes
A simple symmetric way of arranging eleven atoms is in a one-dimensional chain, and
that is the shape in which two Ni11 complexes appear (figure 2a), assembled by four
poly(naphthyridine-amino) ligands that form helices around the nickel chain [8]. The Ni11 groups
are astonishingly close to an equispaced linear chain, with shape measures of at most 0.01.
Moving to two-dimensional structures, two planar phenyl-thiolato bridged Ni11 rings have been
identified [9] that differ only in the number of THF solvation molecules. These rings (figure 2b)
present slightly distorted hendecagonal geometries (shape measures of 0.60 and 1.47).
The capped pentagonal antiprism is also named gyroelongated pentagonal pyramid
(abbreviated J11, i.e., Johson polyhedron number 11), although it can equivalently be viewed as
an icosahedron with a vacant position. Only four clusters have been found to present structures
close to the ideal shape, that of the B11H132- undecaborate, and those of three Ti11
polyoxotitanates with nitrato and alkoxide ligands (figure 3), in some of which the vacant site of
the icosahedron is occupied by a lanthanide ion. Shape measures data and references are given in
table 2.

Table 2. Continuous shape measures for some clusters with vacant icosahedral (or, equivalently,
capped pentagonal antiprism, cPAPR-11) geometry, and of the corresponding icosahedral
clusters with a lanthanide occupying the twelfth vertex of the icosahedron (IC-12).

ClusterRefcode cPAPR-11 Icosahedron IC-12 Ref.

B11 cstmab 0.07 - - 10
Ti11 yavjoy 1.04 - - 11
Ti11 oxejei 1.15 SmTi11 1.40 12
Ti11 oxejim 1.17 EuTi11 1.40 12
Ti11 oxejos 1.15 GdTi11 1.38 12

Figure 3. Capped square antiprismatic geometry of a Ti11 polyoxotungstate [11].

4
 Two structures found for a family of Cu11 and Ag11 clusters can be described as the
composition of one polyhedron and its dual. A trigonal bipyramid capped by six atoms that form
a trigonal prism can be called a hexacapped trigonal bipyramid (hcTBP-11), while the opposite
composition gives a pentacapped trigonal prism (pcTPR-11), both shown in figure 4. Although
those structures are similar to "stellated" polyhedra, they do not fit into the geometric definition
of stellated polyhedral [13] and for that reason they will be referred to here as "capped"
polyhedra.

Table 3. Continuous shape measures of several undecanuclear groups relative to the hexacapped
trigonal bipyramid (hcTBPY) and the pentacapped trigonal prism (pcTPR), together with their
deviations from the minimum distortion interconversion path (Path Dev.) and the degree of
distortion (% pcTPR) from hcTBPY to pcTPR (values given in square bracket must be taken as
rough indications because of the large path deviations).

Central Path Distortion

M Atom Refcode hcTBPY pcTPR Dev. (%) % pcTPR L (or
compd.) Ref.
Ag11 H uyaced 0.40 17.75 12.2 14.2 dtc 14
In11 - 370033 0.49 15.46 6.8 15.8 Rb8In11 15
In11 - 370002 0.51 15.49 7.2 16.1 K8In11 16
Ga11 - 165305 0.51 15.13 6.0 16.0 Cs8Ga11 17
Tl11 - 370009 0.54 14.85 5.6 16.5 K8Tl11 18
Tl11 - 370035 0.56 14.83 5.9 16.9 Rb8Tl11 19
Ag11 S vulcou01 2.36 13.11 18.2 [34.7] dtc 20
Ag11 S vulcou 3.13 11.08 16.5 [40.0] dtc 21
Ag11 Se jaqniy 4.77 8.70 17.0 [49.6] dtc 22
SmD11 Sm 416785 4.77 9.96 21.9 [49.6] SmD3 23
Ag11 I lecbig 7.03 4.31 7.5 60.5 P2SR2 24
Ag11 Se veyroh 10.07 1.64 1.7 72.8 PSe2(OEt)2 25
Cu11 Se xublah 10.48 1.53 2.2 74.3 PSe2(OEt)2 26
Cu11 Se xahmau 10.97 1.24 1.2 76.0 PSe2(OEt)2 27
Ag11 Se ukajew11.56 1.28 3.7 78.1 PSe2(OPr)2 28
Ag11 Se xefgar 11.90 1.27 4.7 79.3 PSe2(OPr)2 29
Ag11 Se xefgev 12.05 1.29 5.5 79.8 PSe2(OBu)2 29

5
 The CShM values for these and other M11 clusters (table 3) reveal some structures that are
very close to one of the two polyhedra considered. Two examples of Ag11 clusters with those
two structures are shown in figure 4a, one with hcTBPY-11 geometry [14] and the other one
with the pcTPR-11 shape [29]. Other clusters, however, appear to be significantly distorted with
respect the two ideal polyhedra, although some of them are close to their minimal distortion
interconversion path (see path deviation values in table 3), a fact that can be best appreciated in a
shape map (figure 5a). Clusters of the group 11 metals with PSe2(OR)2 ligands have similar
geometries (≈ 70% pcTPR-11), while other clusters present variable geometries that correlate
with the size of the atom (H, S, Se or I) at the cluster center (figure 5b).

a b
Figure 4. Hexacapped trigonal bipyramid of a H-centered Ag11 cluster [14] (a) and tricapped
trigonal prism of a Se-centered Ag11 cluster [29] (b).

a b
Figure 5. (a) Shape map in the (hcTBPY-11, pcTPR-11) space for the M11 clusters of table 3.
(b) Deviation from the pc-TPR-11 ideal shape of the M11 (M = Cu, Ag) clusters as a function of
the atomic radius of central atom of the cluster (H, S, Se, I). Clusters with PSe2(OR)2 ligands are
represented by open circles, clusters with other ligands by filled circles.

6
 Interestingly, even if one might think that the interconversion between the two polyhedra
retains the three-fold symmetry axis, the minimal distortion path follows a different way,
retaining only a symmetry plane that contains the two axial and one equatorial atoms of the
trigonal bipyramid (labelled 3, 6 and 8 in figure 6a) and two of its capping atoms (7 and 9 in
figure 6a). These five atoms occupy the pentacapped trigonal prism (figure 6b) one edge parallel
to the three-fold axis, two axial capping atoms and one equatorial capping atom.

a b
Figure 6. Correspondence of the vertices of the hexacapped trigonal bipyramid (a) and the
pentacapped trigonal prism (b) for the interconversion through the minimal distortion pathway.
The shaded pentagons show the symmetry plane preserved throughout the path, the ball and stick
atoms represent the basic polyhedra (trigonal bipyramid and trigonal prism, respectively), and
the light spheres represent the capping atoms.

When the trigonal bipyramid of a hcTBPY-11 is compressed along the trigonal axis to
the point that the two axial atoms form a bond, the structure becomes trioctahedral, i.e., that of
three octahedra sharing faces, as found in Rh11 clusters [30, 31] (figure 7), triOC-11. Since three
regular octahedra cannot share faces in the way shown in figure 7, each of the octahedra is
slightly distorted in our ideal triOC-11 (octahedral shape measures of 0.27).

Figure 7. Trioctahedral structure of the [Rh11(CO)23]3- cluster [30].

7
 Another geometry, that of a tricapped cube (or, equivalently, a vacant cuboctahedron,
vCOC-11) is found in a family of polyoxotungstates (table 4), derived from the M12 α-Keggin
structure by removing a metal atom (figure 8). While in all the examples shown with nearly
perfect vCOC-11 shape there is always a centering main group atom (Si, Ge or P), the vacant site
of the cuboctahedron may be empty or occupied by a lanthanide (La or Ce).

Table 4. Shape measures relative to the vacant capped octahedron (vCOC-11), or tricapped cube,
for a family of W11 polyoxotungstates.

Metal core Refcode vCOC-11 Ref.

Si@CeW11 415003 0.17 32
Si@LaW11 415004 0.17 32
Si@CeW11 411198 0.16 33
P@W11 imozug 0.01 34
Si@W11 henzoq0.11 35
Ge@W11 - 0.12, 0.16 36

a b

Figure 8. Tricapped square antiprismatic (or vacant cuboctahedral) structure of a W11

polyoxotungstate [34] in two alternative views: (a) showing the polyhedron formed by the
tungsten atoms and (b) showing the coordination polyhedra of the tungsten atoms.

Coordination spheres of ML11 complexes

Such a high and unusual coordination number is found in a significant amount only for
the lanthanides, while in a small number of actinide and transition metal complexes

8
undecacoordination seems to be favored by side-on coordination of carbaborates or by small bite
bidentate or tridentate ligands such as NO3-, NO2- and BH4-. The actinide and transition metal
compounds found present highly irregular coordination spheres and none of them could be
neatly associated to one of the reference polyhedra used in this work. In contrast, a good sample
of lanthanide complexes can be reasonably described as distorted vacant icosahedra (or capped
pentagonal antiprism), as shown in table 5. The presence of small bite bidentate ligands can be
responsible for both the high coordination number and the deviations of the shape measures by
2 - 3 units from the ideal polyhedron. The different occupation of the edges of the cPAPR-11 by
bi- and multinuclear ligands (figure 9 and table 5) suggests that such a coordination geometry is
a rather stable one for undecacoordinated lanthanides.

Table 5. Shape measures of ML11 coordination spheres relative to the capped pentagonal
antiprism. For ligand topologies see figure 9.

Refcode M Ligands Topology cPAPR-11 Ref.

Penta- or Hexa-dentate macrocycles
HERCOX Sm1 [M(N6-macrocycle)(NO3)2(MeOH)]+ 1 2.14 37
HERCUD La1 [M(N6-macrocycle)(NO3)2(MeOH)]+ 2 2.37 37
CABLEW Nd1 [M(crown-5)(NO3)3] 3 2.39 38
XAVWUM Pr1 [M(crown-5)(NO3)3] 3 2.41 39
HEBFUP La2 [M(crown-5)(NO3)3] 3 2.47 40
SIXBIK La1 [M(crown-5)(NO3)3] 3 2.50 41
BUTRUD Ce1 [M(crown-5)(NO3)3] 3 2.51 42
CABLAS La1 [M(crown-5)(NO3)3] 3 2.58 43
CABLAS01 La1 [M(crown-5)(NO3)3] 3 2.58 44
BEKWUJ Eu1 [M(crown-5)(NO3)3] 3 2.63 45

Other combinations of mono-, bi- and multidentate ligands

USEBAX Ce3 (N4-ligand)(NO3)3(H2O) 4 2.18 46
FEZPOR Ce (O4-ligand)(NO3)3(MeOH) 4 2.80 47
EXASIF La1 (N3-ligand)(NO3)3(H2O) 5 2.73 48
WEFWIO Nd1 (NO3)5(H2O) 6 2.93 49
XOLMAM Ce1 (NO3)5(H2O) 6 2.77 50
QAVVOY La1 (phen)(NO3)4(H2O) 7 2.84 51
CUCWOM Pr3 (NO3)5(O-NO2) 8 2.27 52
CUCWIG La3 (NO3)5(O-NO2) 8 2.35 52

9
 Another coordination geometry found is that of the vacant cuboctahedron, vCOC-11, or
tricapped cube, whose best examples correspond to a Pr [53], (figure 10a) and two La [54]
compounds, with shape measures between 1.86 and 2.72. These three compounds have two open
chain pentadentate ligands with the arrangement shown in figure 10b.

Figure 9. Coordination topology of several undecacoordinated lanthanide complexes with the

arrangement of bi- and multidentate ligands (thick lines) on the edges of the vacant icosahedral
(or cPAPR-11) coordination sphere.

a b

Figure 10. (a) Tricapped cubic (or vacant cuboctahedral) coordination geometry of an
undecacoordinated Pr complex and (b) schematic depiction of the arrangement of its two
pentadentate ligands (thick lines).

Concluding remarks
The continuous shape analysis of eleven-vertex molecular structures shows that in most
cases they present quite irregular shapes. However, examples have been found of structures that
are close to one of the ideal geometries studied here and that may serve as references for the

10
stereochemical description of other more distorted molecules. Those reference shapes are (i) a
linear chain, (ii) a planar hendecagon, (iii) a capped pentagonal antiprism (or vacant
icosahedron), (iv) a capped pentagonal prism, (v) a square-face augmented pentagonal prism,
(vi) an augmented sphenocorona, (vii) a vacant cubocthedron (or tricapped cube), (viii) a
hexacapped trigonal bipyramid, (ix) a pentacapped trigonal prism, and (x) a trioctahedron. The
capped pentagonal prism, or vacant icosahedron, is seen to be a rather robust core for
undecacoordinated lanthanide complexes, on which bi- and multidentate ligands can be arranged
in a variety of topologies. The minimal distortion interconversion path between the hexacapped
trigonal bipyramid and the pentacapped trigonal prism has been found to preserve a plane of
symmetry but not the three-fold symmetry axis, and several clusters, as well as the coordination
sphere of Sm in SmD3, present structures that are intermediate between the two ideal polyhedra.

Acknowledgements
This work was supported by the Spanish Ministerio de Economía y Competitividad, grant
CTQ2015-64579-C3-1-P.

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