Four independent structures of a pentacoordinate silicon species at different points on the Berry pseudorotation pathway

Article abstract of DOI:10.1039/c000803f

A new pentacoordinate silicon species containing two chelating ligands has been synthesized. The structures of four independent cations of the same compound correspond to different points on the Berry pseudorotation pathway. The percentage of square planar character varies between 19% and 40%.

Full text of DOI:10.1039/c000803f

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Four independent structures of a pentacoordinate silicon species
at different points on the Berry pseudorotation pathwayw
Alan R. Bassindale,*a M. Sohail,a Peter G. Taylor,*a Alexander A. Korlyukovb and
Dmitry E. Arkhipovb
Received (in Cambridge, UK) 12th January 2010, Accepted 16th March 2010
First published as an Advance Article on the web 30th March 2010
DOI: 10.1039/c000803f
A new pentacoordinate silicon species containing two chelating
ligands has been synthesized. The structures of four independent
cations of the same compound correspond to different points on
the Berry pseudorotation pathway. The percentage of square
planar character varies between 19% and 40%.
the extent to which related structures lie on the Berry or
turnstile processes.
In a landmark paper Corriu et al.19 demonstrated unambi-
guously that pentacoordinate silicon compounds can undergo
stereomutation by pseudorotation. Martin and co-workers20
were the first to study the pseudorotation of some penta-
coordinate siliconates and relate the structures of the anions to
positions on the pseudorotation pathway using dihedral
angle methods. Most pentacoordinate silicon structures, using
one or another dihedral angle method18 whether neutral,1a
zwitterionic,1b anionic,1c,7,15,21 or cationic1a appear to lie on
the TBP–SP continuum. The TBP geometry in silicon com-
pounds is generally very flexible with low energy differences
between TBP and SP (or more generally, rectangular pyramid
RP) structures.1a,b,21 There is a small number of cases where a
single pentacoordinate silicon species shows two different
forms in a single crystal with slightly different geometries7 as
is the case with a pair of siliconates in which all five atoms
attached to the silicon atom are carbon atoms. Martin observed
two forms of a fluorosiliconate with 23.2% and 31.6% RP
character20 as calculated by the d24 method.18 The most
spectacular difference in structure for independent forms of
a pentacoordinate silicon species was reported by Tacke and
co-workers1b,22 and is for a zwitterionic molecule with four
forms with distortions of 34.9, 70, 86.2 and 96.3% along the
Berry pathway. The first two forms are polymorphs from
separate crystals and the second two are found in a third
crystal form in which the two crystallographically independent
zwitterions in the unit cell are each hydrogen bonded to one
water molecule.
As a consequence of their structural and dynamic diver-
sity pentacoordinate silicon compounds are of great current
interest.1–7 There are two particularly challenging aspects to
the chemistry of pentacoordinate silicon: their use as transition
state and intermediate models in the commercially and academi-
cally important nucleophilic substitution reactions at tetra-
coordinate silicon;8–13 and the study of their stereochemical
non-rigidity.1,7,14,15
The stereochemical non-rigidity of pentacoordinate com-
pounds and the mechanism of stereomutation can frequently
be related to the X-ray crystal structures of a series of closely
related compounds. Muetterties and Guggenberger16 were the
first to relate the Berry pseudorotation pathway to the struc-
tures of real molecules in a quantitative manner. One Berry
pseudorotation with the limiting Berry structures of trigonal
bipyramid (TBP) and square pyramid (SP) is shown in Fig. 1.
Holmes,17,18 with particular reference to a large series of
pentacoordinate phosphorus compounds, extended and refined
the quantitative approach to the correlation of measured
structures with points on the Berry pseudorotation pathway.
In particular he demonstrated that for any pentacoordinate
species the sums of a set of dihedral angles formed by the
normals to adjacent polytopal faces may be used to quantify
Our previous work on mapping nucleophilic substitution
reported the use of coordinated pyridones as tuneable ligands
in which the electronic environment at silicon can be varied
without changing the particular set of atoms in the silicon
coordination sphere.8–10 For example in a series of compounds
shown in Fig. 210 the percentage O–Si bond formation with the
leaving group X = Cl varies from 40 (Y = 3-NO2) to 70%
Fig. 1 One Berry pseudorotation of a trigonal pyramidal complex via
a square pyramid resulting in permutational ligand exchange.
a Department of Chemistry and Analytical Sciences,
The Open University, Walton Hall, Milton Keynes,
MK7 6AA, UK. E-mail: a.bassindale@open.ac.uk
b X-Ray Structural Centre, A.N. Nesmeyanov Institute of
Organoelement Compounds (INEOS), Russian Academy of
Sciences, 28 Vavilov St., B-334, Moscow, 119991, Russia
w Electronic supplementary information (ESI) available: Synthesis,
characterisation and X-ray crystallographic data. CCDC 757287 (4a)
and 757286 (4b–d). For ESI and crystallographic data in CIF or other
electronic format see DOI: 10.1039/c000803f
Fig. 2 SN2 profile where the carbonyl O is the nucleophile and X is
the nucleofuge.
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Fig. 3 The synthesis of a new class of pentacoordinate ions contain-
ing two pyridone ‘responsive ligands’.
Fig. 4 ORTEP drawing of the cation in crystal structure of 4a
(Y = 6-Cl) with the thermal ellipsoids shown at the 50% probability
level. For clarity, one non-coordinating molecule of water and one
non-coordinating molecule of ligand, 6-chloropyridone, in the unit cell
have been removed from the figure.
(Y = 6-Me), while at the same time the configuration at the
silicon atom inverts from a structure on the 1–2 continuum
with 80% TBP character through a 100% TBP (2) (where Y = H)
to a structure on the 2–3 continuum with 81% TBP character.
So by varying only the substituent, Y, on the aromatic ring
approximately 40% of the SN2 profile is modelled by a closely
related series of compounds. Similarly the X may be varied
and a similar SN2 profile was observed in both the solid state
and in solution.8
29Si NMR solution shift of d = ꢁ48 ppm in CDCl3 between
ꢁ70 and +50 1C by contrast with some of the ions reported by
Kost and Kalikhman.1 The lack of silicon chlorine bonding, or
indeed interaction, is shown by the Siꢂ ꢂ ꢂCl distance of 410 pm
or more, compared with a typical Si–Cl bonding distance in
pentacoordinate silicon compounds of about 191–230 pm.
Other compounds of type 4 have been synthesised and the
effect of variations in the nature of the substituent Y on their
structures and dynamics are currently being evaluated.
In this work we introduce the use of a related tuneable
ligand to examine the effect of electronic changes at a silicon
atom with two pyridone ligands. The reaction shown in Fig. 3
could potentially have given either the pentacoordinate ion or
the neutral hexacoordinate structure in which there is a
covalent Si–Cl bond. Kost and Kalikhman1 have observed
both types of structure in similar, but not identical, series of
compounds. They also observed interconversion between the
two differently coordinated structures as parameters such as
temperature were varied. In all of the examples we have studied
only pentacoordinate ions of type 4 have been observed in the
solid state and in solution at all available temperatures.
The compound that is the main subject of this communi-
cation, the 6-Cl derivative of 4 has a temperature independent
The crystal structures of two salts containing cation 4
(Y = 6-Cl) have been determined by single crystal X-ray
diffraction.23 In one crystal there is only one form of 4
(Y = 6-Cl) in the unit cell (4a) (Fig. 4) whereas in the other
there are three independent structures of 4 (Y = 6-Cl) (4b–d)
each with widely different geometrical parameters. Strictly,
these salts are not polymorphs24 as the composition of each
crystal is slightly different. The crystal with three different
structures of the pentacoordinate ion also has in the indepen-
dent part of the unit cell two H3O+ cations, not hydrogen
Table 1 Structural parameters for compounds 4a–d as determined by X-ray crystallography and calculation of percentage SP for each
independent structure. More detailed information, in particular standard deviations for bonds and angles can be found in the ESIw
TBP (ideal)
4a (Y = 6-Cl)
4b (Y = 6-Cl)
4c (Y = 6-Cl)
4d (Y = 6-Cl)
SP (ideal)
Bond lengths/pm
Si–O
Si–C (endocyclic)
Si–C(Me)
184, 187
189, 189
184.7
185, 187
189, 189
186.1
185, 186
189, 189
185.3
185, 186
188, 191
184.2
Bond angles/1
O–Si–O/1, y15
C–Si–C/1, y24
d24
180
120
53.1
0
90
90
90, 90
90
120, 120
120
30
169
169.3
125.7
40.8
167.1
128.6
36.6
165.7
132.7
32.1
151
151
0
100
86
122.7
43.1
19
%SP
23
31
40
O–Si–C (endocyclic)
O–Si–C (exocyclic)
O–Si–Me y13,y35
Average (OSiMe)
C–Si–Me y32, y34
Average (CSiMe)
DAv/1
86.4, 85.3
89.4, 88.3
95.3, 95.4
95.35
119.8, 117.4
118.6
23.25
22.5
86.5, 85.6
89.8, 88.4
95.2, 95.4
95.3
117.8, 116.4
117.1
21.8
27.3
53
53
24
86.2, 85.9
89.9, 87.0
96.9, 96.0
96.45
119.3, 112
115.7
19.2
35.8
76.2
76.2
34.9
85.7, 85.2
89.1, 88.5
97.1, 97.2
97.15
115.0, 112.3
113.7
16.5
44.8
85
85
40
86
105, 105
105
105, 105
105
0
%SP
0
100
P
i|di(C) ꢁ di(TBP)|
%SPa
41.4
41.4
19
P
217.7 ꢁ
|di(C) ꢁ di(SP)|
i
0
100
D [1], the difference between angles y15 and y24 (for ligand numbering see Fig. 1: ligand 3, Me, is the pivot ligand); that is 601 for an ideal TBP and 01
in an ideal SP. DAv [1], the difference between average angles y32, y34 and y13, y35 that is 301 for an ideal TBP and 01 for an ideal SP.a Muetterties/
Holmes method (ref. 16 and 17).
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bonded to the cation, and a free pyridone ligand, together with
five chloride anions. The crystal with only one ion, 4a has one
water molecule, one neutral pyridone ligand and one chloride
ion in the unit cell. The results are discussed below.
Notes and references
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(b) R. Tacke, M. Pulm and B. Wagner, Adv. Organomet. Chem.,
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1999, 44, 221–273; (c) R. R. Holmes, Chem. Rev., 1990, 90, 17–31.
2 B. Theis, S. Metz, C. Burschka, R. Bertermann, S. Maisch and
R. Tacke, Chem.–Eur. J., 2009, 15, 7329–7338.
3 B. Theis, C. Burschka and R. Tacke, Chem.–Eur. J., 2008, 14,
4618–4630.
4 A. R. Bassindale, D. J. Parker, P. G. Taylor and R. E. Turtle, Z.
Anorg. Allg. Chem., 2009, 635, 1288–1294.
5 E. Brendler, T. Heine, A. F. Hill and J. Wagler, Z. Anorg. Allg.
Chem., 2009, 635, 1300.
6 V. V. Negrebetsky, P. G. Taylor, E. P. Kramarova, A. G. Shipov,
S. A. Pogozhikh, Y. E. Ovchinnikov, A. A. Korlyukov,
A. Bowden, A. R. Bassindale and Y. I. Baukov, J. Organomet.
Chem., 2008, 693, 1309–1320.
7 E. P. A. Couzijn, D. W. F. van den Engel, J. C. Slootweg, F. J.
J. De Kanter, A. W. Ehrlers, M. Schakel and K. Lammertsma,
J. Am. Chem. Soc., 2009, 131, 3741–3751.
8 A. R. Bassindale, D. J. Parker, P. G. Taylor, N. Auner and
B. Herrschaft, J. Organomet. Chem., 2003, 667, 66–72.
9 A. R. Bassindale and M. Borbaruah, J. Chem. Soc., Chem.
Commun., 1991, 1501–1503.
10 A. R. Bassindale, D. J. Parker, S. J. Glynn and P. G. Taylor,
J. Chem. Soc., Perkin Trans. 2, 1999, 2099–2109.
11 A. A. Macharashvili, V. E. Shklover, Y. T. Struchkov,
G. I. Oleneva, E. P. Kramarova, A. G. Shipov and
Y. I. Baukov, J. Chem. Soc., Chem. Commun., 1988, 683.
12 Y. E. Ovchinnikov, A. A. Macharashvili, Y. T. Struchkov,
A. G. Shipov and Y. I. Baukov, J. Struct. Chem., 1994, 35, 91–100.
13 V. F. Sidorkin, V. V. Vladimirov, M. G. Voronkov and
V. A. Pestunovich, J. Mol. Struct. (THEOCHEM), 1991, 74, 1–9.
14 D. Kost, B. Gostevskii, N. Kocher, D. Stalke and I. Kalikhman,
Angew. Chem., Int. Ed., 2003, 42, 1023–1026.
15 E. P. A. Couzijn, M. Schakel, F. J. J. De Kanter, A. W. Ehrlers,
M. Lutz, A. L. Spek and K. Lammertsma, Angew. Chem., Int. Ed.,
2004, 43, 3440–3442.
16 E. L. Muetterties and L. J. Guggenberger, J. Am. Chem. Soc.,
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17 R. R. Holmes and J. A. Dieters, J. Am. Chem. Soc., 1977, 99,
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18 R. R. Holmes, Acc. Chem. Res., 1979, 12, 257–265.
19 R. J. P. Corriu, A. Kpoton, M. Poirier, G. Royo and J. Y. Corey,
J. Organomet. Chem., 1984, 277, C25–C30.
20 W. H. Stevenson III, S. Wilson, J. C. Martin and W. B. Farnham,
J. Am. Chem. Soc., 1985, 107, 6340–6352.
21 J. J. Harland, R. O. Day, J. F. Vollano, A. C. Sau and
R. R. Holmes, J. Am. Chem. Soc., 1981, 103, 5269–5270.
The important structural parameters for 4a–d are shown in
Table 1. The bond lengths in 4a–d are almost invariant from
one to another structure. There are a number of bond angles
and dihedral angles associated with the change from TBP to
SP along the Berry pseudorotation profile. The bond angles
y15 and y24 are the angles O1–Si–O5 and C2–Si–C4 respec-
tively (see Fig. 1 for ligand numbering; the pivot ligand, Me, is
labelled 3). The angle y15 is the angle between axial ligands in
the trigonal bipyramid form, where it is 1801 and 1511 in a
square pyramid. The angle y24 is the angle between the non-
pivot equatorial ligands in the trigonal bipyramid form where
it is 1201 and again it is 1511 in a square pyramid. For
structures on the Berry pseudorotation pathway the angle will
be intermediate between the two limiting values. Measuring
the value of the difference between y15 and y24 allows the
estimation of the percentage SP character for each structure.17
As calculated by this method, the percentage SP character
varies between 22.5% for 4a and 44.8% for 4d. A similar set of
values was obtained by measuring the differences between the
average values of y32 and y34 and y13 and y35. The Holmes
dihedral angle method gives values varying between 19% for
4a and 40% for 4d (Table 1).
Holmes reported that the definitive method for determining
whether a series of related molecular structures, C, lie on the
Berry pathway is to compare each dihedral angle, di, for a
particular structure, with those of the corresponding TBP and
SP structures. The dihedral angle is that formed between
normals to the TBP faces sharing a common edge. If the
P
P
quantities i |di(C) ꢁ di(TBP)| and 217.7 ꢁ i |di(C) ꢁ di(SP)|
are found to be the same then the various structures are on the
TBP–SP Berry pseudorotation pathway.16–18 These two
quantities are identical for each of the structures 4a–d
(Table 1) showing that the four independent structures repre-
sent different points on an evolving Berry pseudorotation. The
percentages SP for each structure using this extended dihedral
angle method are 19, 24, 35 and 40%, respectively, for 4a, 4b,
4c and 4d. The more comprehensive dihedral angle methods
give slightly lower values for the extent of SP formation than
the bond angle methods.17 However, the degree of agreement
between all of the various methods for estimating TBP/SP
character is exceptionally good.
22 R. Tacke, M. Muhleisen and A. Lopez-Mras, Z. Anorg. Allg.
¨
Chem., 1995, 621, 779–788; R. Tacke, A. Lopez-Mras, J. Sperlich,
C. Strohmann, W. F. Kuhs, G. Mattern and A. Sebald, Chem.
Ber., 1993, 126, 851–861.
23 Crystal data for 4a. Crystals of C18H19Cl4N3O4Si are monoclinic,
space group P21/n, a = 7.6414(8) A, b = 21.915(2) A, c =
12.8697(14) A, b = 96.267(2)1 V = 2142.3(4) A3, Z = 4, M =
511.25. 26805 reflections were measured at 100 K, 6212 independent
reflections were used (Rint = 0.0325). The refinement converged to
wR2 = 0.0958 and GOF = 1.014 for all independent reflections
[R1 = 0.0374 for 5481 observed reflections with I 4 2s(I)]. CCDC
number: 757287. Crystal data for 4b–d. Crystals of C44H49Cl12N7O9-
There is no obvious reason beyond crystal packing forces
why in one unit cell there should be three independent
structures of the same molecule. It has been recognised
for some time that pentacoordinate structures are parti-
cularly easily deformed.1b,21 The four structures described here
are outstanding in illustrating that, when put under even the
small physical constraints involved in efficiently packing a
molecule in a crystal, pentacoordinate silicon compounds
deform along the lowest energy pathway—the Berry pseudo-
rotation pathway.
ꢀ
Si3 are triclinic, space group P1, a = 13.549(5) A, b = 15.753(6) A,
c = 16.005(7) A, a = 67.998(8)1, b = 74.146(9)1, g = 66.783(7)1,
V = 2879(2) A3, Z = 6 (Z0 = 2), M = 1329.57. 12 463 reflections
were measured at 100 K, 12355 independent reflections were used
(Rint = 0.01). The refinement converged to wR2 = 0.1408 and
GOF = 1.003 for all independent reflections [R1 = 0.0536 for 9987
observed reflections with I 4 2s(I)]. CCDC number: 757286.
24 J. Bernstein, Polymorphism in Molecular Crystals, Oxford University
Press, Oxford, 2002.
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3276 | Chem. Commun., 2010, 46, 3274–3276