Tetrapodal amidoxime ligands I. Coordination isomerism due to self-complementary dimerization of a pyramidal cobalt(iii) coordination module

Article abstract of DOI:10.1039/c2dt11847e

A bis-μ-amidoximato-bridged cobalt(iii) dimer obtained with a new tetrapodal ligand possesses interesting structural parameters as a consequence of intramolecular hydrogen bonding intentionally built into the complex. Its synthesis and properties are described. The new ligand type combines attributes of two previously described ligand classes: It binds a metal ion in a tetrapodal pentadentate fashion and forms a pseudomacrocycle through hydrogen bonds, characteristic of chelating oxime ligands. Coordination isomerism, which is a consequence of dimer formation, has been analyzed by means of X-ray crystallography and carbon-13 nuclear magnetic resonance spectroscopy. The Royal Society of Chemistry 2012.

Full text of DOI:10.1039/c2dt11847e

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PAPER
Tetrapodal amidoxime ligands I. Coordination isomerism due to
self-complementary dimerization of a pyramidal cobalt(III) coordination
module†‡
John P. Boyd,* Elisabeth Irran and Andreas Grohmann*
Received 29th September 2011, Accepted 21st November 2011
DOI: 10.1039/c2dt11847e
A bis-m-amidoximato-bridged cobalt(III) dimer obtained with a new tetrapodal ligand possesses
interesting structural parameters as a consequence of intramolecular hydrogen bonding intentionally
built into the complex. Its synthesis and properties are described. The new ligand type combines
attributes of two previously described ligand classes: It binds a metal ion in a tetrapodal pentadentate
fashion and forms a pseudomacrocycle through hydrogen bonds, characteristic of chelating oxime
ligands. Coordination isomerism, which is a consequence of dimer formation, has been analyzed by
means of X-ray crystallography and carbon-13 nuclear magnetic resonance spectroscopy.
in effect compensates positive charge brought into the compound
Introduction
upon metal ion coordination (formation of an “inner salt”).
The application of effects arising from peripheral hydrogen
The connectivity of the oxime functions in a system of our design
bonding in transition metal complexes is of growing importance.
necessarily differs from that of the well-known glyoxime (i.e. 1,2-
Such interactions are instrumental in bioinorganic chemistry and
dioxime) ligands and related pseudomacrocyclic ligands, which
catalysis, where secondary bonding can create a “coordination
have also been used as bridged pairs, especially for coenzyme B12
modelling (“cobaloximes”, see Fig. 1, 1a, 1c).9 While 1,3-dioxime
pocket”, tune metal as well as substrate reactivity, stabilize reactive
intermediates, and facilitate intra- and intermolecular proton
(including malonamidoxime, i.e., 1,3-diamidoxime; 1e) ligands
transfer reactions.1,2 Two limiting cases of intramolecular hydro-
gen bonding may be distinguished: H-bonding between a metal-
coordinated species and the ligand periphery,3,4 and H-bonding
within the ligand periphery.5 Additionally, hydrogen bonds have
been used to incorporate transition metal complexes into host
structures, such as cyclodextrins,6 and to tune the strength of
metal ion extractants.7 Methodologies to create ligands that
add hydrogen bond-mediated properties to known coordination
geometries thus constitute a useful addition to the coordination
chemist’s toolbox.
Our approach aims at linking equatorial oxime donors via an ax-
ial N-heterocycle, thereby generating a tetrapodal pentadentate N5
ligand which forms a square pyramidal coordination environment.
The capping ligand thus obtained is reinforced by two hydrogen
bonds at the basis of the pyramid. This combination is attractive
for at least two reasons: Firstly, pentadentate tetrapodands enforce
a donor pattern that may, for reasons of kinetic lability, otherwise
be unavailable for first row transition metal complexes;8 secondly,
dioxime ligands can form strong hydrogen bonds resulting in pseu-
domacrocyclic arrangements. This involves deprotonation, which
form hydrogen bonds that are energetically10 and geometrically11
similar to those found in 1,2-dioxime complexes, they lack conju-
gation and therefore show decreased p-backbonding character.
Amidoximes (e.g. malonamidoxime12) are easily prepared from
nitriles by reaction with hydroxylamine (Tiemann reaction).13 By
varying a nucleophilic aromatic substitution methodology that
was established in the context of intramolecular [4 + 2] Diels–
Alder/retro-Diels–Alder ring transformations,14 we gained access
to a pyrimidine-derived nitrile precursor and from it obtained the
prototype of a new ligand class (Fig. 1, 4). We describe the synthesis
of the ligand and the properties of its cobalt(III) complex, and show
that the new type of complex possesses features characteristic of
both the hydrogen bond-forming dioxime ligands (Fig. 1, 1a, 1c;
1e) and ligands of the tetrapodal pentadentate topology (2, 3).15,16
Experimental
Research chemicals were obtained from commercial suppliers and
used without further purification. THF was saturated with dry
dinitrogen, dried over potassium hydroxide for four weeks and
used without further purification. Potassium hydroxide (5 wt%)
was dissolved in ethanol and the solution stored for several
weeks to decompose 2-butanone present as a denaturing agent;
the solvent was then distilled in vacuo. Routine NMR spec-
tra were measured on a Bruker ARX 200 spectrometer, while
Institut fu¨r Chemie, Technische Universita¨t Berlin, Straße des 17. Juni 135,
10623, Berlin, Germany
† Electronic supplementary information (ESI) available. CCDC reference
numbers 825623–825624. For ESI and crystallographic data in CIF or
other electronic format see DOI: 10.1039/c2dt11847e
1
‡ Dedicated to Martin A. Bennett
the 13C{ H}-spectrum of 11 was measured on a Bruker AV
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Fig. 1 “Capped” (1a,17 1b18) and “bridged”(1c,9 1d19) pseudomacrocyclic and macrocyclic ligands; conceptual combination of the malonamidoxime pair
(1e11) and tetrapodal pentadentate ligands (2,15 316) in ligand 4.
400 spectrometer (cf. Fig. 4). EI-MS measurements were con-
ducted using a Finnegan MAT95S instrument. ESI-MS source
spectra and collision induced dissociation (CID) spectra were
acquired on a Thermo LTQ Orbitrap XL FT-spectrometer
(XCalibur software). Combustion analysis was performed using a
Thermo Finnigan Flash 1112 apparatus (EAGER 300 software).
IR spectra were measured with KBr disks on a Perkin–Elmer Spec-
trum 100 Series FT-IR spectrometer. A PAR263A potentiostat was
used for electrochemical data acquisition. The quality of iR-drop
compensation was analyzed using the RL0 algorithm.20 Melting
and decomposition points were determined on a Kofler apparatus
and calibrated against azobenzene, acetanilide and phenacetine,
as applicable. X-ray diffraction: Diffraction data were obtained
on an Oxford Diffraction Xcalibur S instrument equipped with
a Sapphire CCD-detector using graphite-monochromated Mo-
parameters of hydrogen atoms were tied to those of their carrier
atoms. Supplementary crystallographic data can be obtained free
of charge from The Cambridge Crystallographic Data Centre,
CCDC 825623 (10) and CCDC 825624 (11). Molecular graphics
were created using Ortep 3v2.24
Methylmalonamide (6)
2-Pyridone (1 g, 1 mol%)25 was dissolved in 30% aqueous ammonia
(400 mL), diethyl methylmalonate (5) added (200 mL, 1.16 mol,
202 g), and the biphasic reaction mixture stirred vigorously
overnight. A fine colourless precipitate was collected on a Buchner
funnel, washed with ethanol, and dried overnight in air. Colourless
solid (80 g, 60%).
Mp. 209–211 ◦C (lit.26 210 ◦C). Anal. found: C, 41.67, H, 7.11,
N, 24.19%, calcd for C4H8N2O2: C, 41.37, H, 6.94, N, 24.12%. 1H-
NMR (d6-DMSO): 7.23 (s br, 2 H, NH), 6.98 (s br, 2 H, NH), 3.06
(q, 3J (HH) = 7.2 Hz, 1 H, CH), 1.55 (d, 3J (HH) = 7.2 Hz, 3 H,
CH3); 13C-NMR (d6◦-DMSO): 172.4 (CO), 46.7 (CH), 15.0 (CH3);
EI-MS (70 eV, 120 C): 116 (M+, ~3%), 99 (M - NH3, ~2%), 73
˚
Ka radiation with l = 0.71073 A. Suitable crystals were attached
to glass fibers using perfluoropolyalkylether oil and transferred
to a goniometer where they were cooled to 150 K for data
collection. Software packages used: CrysAlis CCD for data
collection, CrysAlis Pro (for cell refinement and data reduction).
Empirical absorption corrections (multiscan based on symmetry-
related measurements) were applied using CrysAlis Pro software.21
Space groups were determined from systematic absences and
confirmed by the successful solution of the structure. Structures
were solved by direct methods using the program Sir2004.22
+
(M - HOCN, 100%), 55 (M - HOCN/CO, 20%), 44 (CONH2 ,
50%); IR: 1674 cm-1 (CO).
Methylmalononitrile (7)
The compound was prepared according to a literature procedure26
by reactive vacuum dehydration/distillation of methylmalon-
amide (6) over phosphorous pentoxide at 15 mm Hg/250 ◦C.
Colourless solid, max. yield 65%.
2
Subsequent full-matrix least-squares refinement of Fo data was
carried out using SHELXL-97.23 All non-hydrogen atoms were
refined anisotropically. Treatment of hydrogen atoms: Carbon-
bound hydrogen atoms were placed in positions of optimized ge-
ometry, and isotropic displacement parameters were tied to those
of the corresponding carrier atoms. Oxygen- and nitrogen-bound
hydrogen atoms were located in the difference Fourier map and
freely refined. Hydrogen atoms belonging to water molecules were
refined using distance and angle restraints. Thermal displacement
Mp. 35 ◦C (lit.27 32–36 ◦C). Anal. found: C, 59.82, H, 4.55, N,
35.18%, calcd for C4H4N2: C, 59.99, H, 5.03, N. 34.98%. 1H-NMR
(CDCl3): 3.80 (q, 3J(HH) = 7.3 Hz, 1H, CH), 1.79 (d, 3J(HH) = 7.3
Hz, 3 H, CH3); 13C-NMR (CDCl3): 113.0 (CN), 16.7 (CH), 16.5
(CH3); EI-MS (70 eV, 29 ◦C): 79 (M–1, 40%), 53 (M - HCN, 95%),
28 (HCNH+, 100%); IR: 2262 cm-1 (CN) (lit.27 2255–2260 cm-1).
2478 | Dalton Trans., 2012, 41, 2477–2485
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2,4-Dichloropyrimidine (9)
course of the reaction. The mixture was allowed to cool to room
temperature and then quenched with water (10 mL) to dissolve
precipitated lithium chloride. Concentrated aqueous ammonium
chloride solution (20 mL) and dichloromethane (50 mL) were
added subsequently. The phases were separated, and the aqueous
phase extracted with additional dichloromethane (20 mL). The
combined extracts were dried over sodium sulfate, filtered over
neutral alumina (II–III), and volatiles were removed in vacuo. The
remaining oil (8.9 g, 94%) crystallized rapidly. Melting point and
elemental analysis data (below) were determined for this material,
and it was also used in the subsequent synthetic steps without
further purification. The material can be recrystallized from a ten-
fold amount of benzene to yield 10 as a colourless crystalline solid
(cf. Table 1).
In a 250 mL flask, uracil (5.0 g, 45 mmol) and tetraethyl
ammonium chloride (1.1 g, 15 mol%) were suspended in phos-
phorous oxychloride (10 mL), and heated to 120 ◦C for 1 h
(CAUTION: vigorous evolution of hydrogen chloride gas). The
mixture was subsequently allowed to cool, while stirring was
continued overnight. The brown solution was poured on crushed
ice (100 g) and stirred until a yellowish solid appeared. The solid
was collected at 0 ◦C by filtration (CAUTION: The hydrolysis
of phosphorous oxychloride at 0 ◦C is incomplete; a strongly
exothermic reaction occurs in the aqueous filtrate upon warming)
and washed with ice water, dissolved in chloroform (80 mL), dried
over sodium sulfate and filtered through neutral alumina (II–
III). After volatiles had been removed in vacuo, the residual oil
crystallized upon cooling. Yellowish rods (2.4 g, 36%).
Mp. (unrecrystallized material): 112 ◦C; Anal. found (unrecrys-
tallized material): C, 60.13, H, 3.47, N, 35.25%, calcd for C12H8N6:
C, 61.01, H, 3.41, N, 35.58%. 1H-NMR (CDCl3): 9.12 (d, 3J = 5.2
Mp. 61 ◦C (lit.28 61–62 ◦C). Anal. found: C, 32.89, H, 1.37, N,
18.88%, calcd for C4H2N2Cl2: C, 32.25, H, 1.35, N, 18.80%. H-
NMR (CDCl3): 8.53 (d, 3J = 5.3 Hz, 1 H), 7.35 (d, 3J = 5.3 Hz, 1 H);
13C-NMR (CDCl3): 162.7 and 161.0 (CCl), 160.0 and 120.3 (CH);
HR-EI-MS (370 K) M+ calcd: 147.95950 m/z; found: 147.95919
m/z.
1
3
Hz, 1 H, CH), 7.89 (d, J = 5.3 Hz, 1 H, CH), 2.29 (s, 3 H,
CH3), 2.26 (s, 3 H, CH3); 13C-NMR (CDCl3): 162.8 and 161.9
(quaternary aromatic C), 161.6 and 118.1 (CH), 113.7 and 113.2
(CN), 40.3 and 37.9 (quaternary aliphatic C), 26.4 and 26.3 (CH3);
HR-EI-MS (370 K): M+ calcd: 236.08104 m/z; found: 236.07989
m/z; IR: 2260 cm-1 (CN).
2,2¢-(Pyrimidine-2,4-diyl)bis(2-methylmalononitrile) (10)
Under an atmosphere of dry dinitrogen, commercial lithium
hydride (640 mg, 80 mmol) was suspended in dry THF (20 mL) at
20 ◦C with stirring, in a reaction flask on a water bath. A solution
of methylmalononitrile (7) (6.57 g, 82 mmol) in THF (15 mL)
was added during 15 min, which resulted in hydrogen evolution.
The temperature was maintained between 25 and 35 ◦C during
addition. After the evolution of hydrogen had ceased, a slightly
yellow solution had formed. The water bath was replaced with
an oil bath, and a solution of 2,4-dichloropyrimidine (9) (5.97 g,
40 mmol) in THF (5–10 mL) was added rapidly. The exothermic
reaction warmed the mixture to 70 ◦C instantaneously, and the
oil bath was then heated to hold the reaction mixture at reflux
temperature for an additional 30 min. A precipitate formed in the
2,2¢-(Pyrimidine-2,4-diyl)bis(N¢1,N¢3-dihydroxy-2-
methylmalonamidoxime) (4)
Unrecrystallized nitrile 10 (7.91 g, 33 mmol) was crushed into
small pieces and suspended in ethanol (50 mL; purified to remove
2-butanone). Aqueous hydroxylamine (50 wt%, 10 mL, 166 mmol)
was added. The nitrile began to dissolve after a brief initiation
period, and an exothermic reaction brought the mixture to reflux.
A precipitate formed. The mixture was left to cool and stirred
for an additional 24 h at room temperature. The precipitate was
collected, washed with a small amount of ethanol and dried in air.
Very fine colourless powder (10 g, 85%), decomposes at ~190 ◦C.
Table 1 Summary of crystallogaphic data
Empirical formula
C12H8N6 (10)
C32 H62 Co2 F12 N20 O28 (11·12H2O)
Formula weight
236.34
150(2)
0.71073
Monoclinic
1520.88
150(2)
T/K
˚
l/A
0.71073
Triclinic
Crystal system
Space group
¯
P21/n
P1
˚
˚
˚
a/A, b/A, c/A
6.6056(2), 10.9046(4), 16.8884(5)
90, 97.859(3), 90
1205.07(7)
9.2213(4), 12.9948(6), 13.4621(8)
69.118(5), 83.997(4), 73.435(4)
1444.63(12)
a (◦), b (◦), g (◦)
3
˚
U/A
Z
4
1
Dc/Mg m-3
1.302
0.086
488
1.748
0.716
780
m/mm-1
F(000)
Crystal size/mm
0.60 ¥ 0.33 ¥ 0.30
3.07 to 25.00
-7 to 7, -12 to 12, -17 to 20
2107 [R(int) = 0.0185]
2107/16/181
1.045
R1 = 0.0349, wR2 = 0.0760
R1 = 0.0473, wR2 = 0.0800
0.148 and -0.146
0.40 ¥ 0.22 ¥ 0.11
3.28 to 25.00
-10 to 10, -12 to 15, -11 to 15
5065 [R(int) = 0.0292]
5065/110/535
H range/◦
Range h, k, l
Independent reflections
Data/restraints/parameters
Goodness-of-fit on F2
Final R indices [I > 2s(I)]
R indices (all data)
0.973
R1 = 0.0389, wR2 = 0.0892
R1 = 0.0534, wR2 = 0.0928
0.555 and -0.327
-3
˚
Largest diff. peak and hole/e A
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Anal. found: C, 40.03, H, 5.73, N, 37.27%, calcd for
C12H20N10O4: C, 39.13, H, 5.47, N, 38.03%. 1H-NMR (d6-DMSO):
for the preparation of methylmalondiamide (6) was modified in
two ways: 2-Pyridone was used as a bifunctional catalyst,25 and
aqueous ammonia as the solvent instead of a mixture of methanol
and liquid ammonia. This decreases the yield (from 99%, as
published, to 60%), but the reaction time is shortened considerably
(from several weeks to 12 h). Uracil (8) is converted to 2,4-
dichloropyrimidine (9) by the action of phosphorous oxychloride.
We modified the available procedures28 (see Experimental section)
by using tetraalkylammonium chlorides instead of aniline deriva-
tives as additives. Specifically, the reaction product contained less
of a lachrymatory impurity when the exposure of uracil to hot
phosphorous oxychloride was limited to 1 h.
3
9.36 (s br, 2 H, OH), 9.23 (s br, 2 H, OH), 8.65 (d, J(HH) =
3
5.3 Hz, 1 H, CH), 7.31 (d, J(HH) = 5.3 Hz, 1 H, CH), 5.32
(s br, 4 H, NH), 5.23 (s br, 4 H, NH), 1.71 (s, 3 H, CH3),
1.65 (s, 3 H, CH3); selected 2D 1H-1H NOESY cross peaks:
7.31/1.65 (pyrimidine-C5-H/methyl), 1.65/5.32 (methyl/amino),
5.32/9.36 (amino/hydroxyl); 13C-NMR (d6-DMSO): 169.67 and
168.21 (quaternary aromatic C), 157.26 (CH), 155.18 and 154.53
(quaternary oxime C), 119.21(CH), 54.30 and 52.74 (quaternary
aliphatic C), 22.11 and 21.89 (CH3); HR-ESI-MS (RT): MH+
calcd: 369.17418 m/z; found: 369.17334 m/z; IR: 1676 and 1657
(C Noxime), 947 and 935 (N–O).
Chlorodiazines are highly reactive with respect to nucleophilic
aromatic substitution of the Cl substituents by deprotonated
geminal dinitriles.14 In our case, the reaction of the lithium salt
of methylmalononitrile with 2,4-dichloropyrimidine (9) in THF
produces tetranitrile 10. The lithium salt of 7 is conveniently
prepared at temperatures above 15 ◦C by the reaction with
commercial lithium hydride. The reaction is relatively insensitive
to moisture which can be attributed to the low pKa of geminal
dinitriles,29 their high nucleophilicity30 and the essential inertness
of commercial LiH.31 10 is converted to the corresponding
tetraamidoxime (4) by reaction with aqueous hydroxylamine in
ethanol (Fig. 2). Although the addition of hydroxylamine to this
nitrile is an exothermic reaction, the four-fold addition goes to
near completion only upon prolonged exposure of the tetranitrile
to hydroxylamine solution at room temperature, owing to the low
solubility of the higher addition products. Combustion analysis
and ESI-MS indicate that three-fold addition products are present
in the compound as minor impurities. 1H-NMR spectroscopy
(d6-DMSO) shows well-resolved signals of the magnetically in-
equivalent methyl, hydroxyl and amide groups (see Supporting
information†). Ligand 4 is sparingly soluble in common laboratory
solvents and may be stored in air for extended periods of time
without decomposition.◦ It decomposes with evolution of gas
when heated above 190 C. Although no adverse behaviour was
observed in the course of our study, it should be noted that oximes
generally pose a fire and explosion hazard. Attempts to prepare
cobalt(II) compounds of 4 under conditions otherwise known to
produce cobaloximes failed, and we propose reasons for this in
the following. In air, however, a rapid reaction occurs between
cobalt(II)acetate tetrahydrate and 4, and a cobalt(III) compound is
formed. In the presence of excess trifluoroacetic acid, the carboxy-
late counter ions are exchanged, and 11 is obtained which forms
single crystals of its dodecahydrate upon slow evaporation of water
from the aqueous solution at 5 ◦C (11·12H2O, cf. Fig. 3 and Fig. 6).
{CoIII2[4–H]2}(OCOCF3)4 (11)
In air, solid 4 (830 mg, 2.25 mmol) and solid cobalt(II) acetate
tetrahydrate (560 mg, 2.25 mmol) were dissolved in a stirred
mixture of trifluoroacetic acid (2 mL) and ethanol (10 mL) at
room temperature. The brown solution that formed was stirred
◦
for 1 h and then poured on cold diethylether (40 mL, 5 C). An
orange–brown solid was collected by filtration, washed with cold
diethylether (30 mL), and dried in vacuo (690 mg, 47%). Additional
product can be obtained by slow evaporation of the filtrate. The
exchange of acetate for trifluoroacetate proceeds to approx. 93%,
1
as estimated from the resonance of remaining acetate in the H-
NMR spectrum. 11 decomposes at 150 ◦C.
Anal. found: C, 29.70; H, 2.65; N, 20.88%, calcd for C32 H38
Co2 F12 N20 O16: C, 29.46; H, 2.94; N, 21.47%. HR-ESI MS
(MeOH; m/z;%): [CoIII2(4 - 2H)2]2+ (425.08(3); 100%), {[CoIII(4
+
- 2H)]2(OCOCF3)} (963.15(3); 10%), [CoIII2(4 - 2H)(4 - 3H)]+
(849.15(9); 5%), {CoIII(4 - H)(OCOCF3)} (539.07(6); < 1%);
+
1H-NMR (d6-DMSO): 9.70 (m, 1 H, OH), 9.09 (d, J(HH) =
3
6 Hz, 1 H, CH), 7.85 (d, 3J(HH) = 6 Hz, 1 H, CH), 8.20,
7.54, 7.35, 7.08 (four s br, 8 H, NH), 2.12, 2.08 (two s br, 6 H,
CH3). The compound was dissolved in absolute trifluoroacetic
acid, dried in vacuo and crystallized by slow evaporation of a
highly dilute aqueous solution at 5 ◦C to obtain single crystals
of the dodecahydrate (11·12H2O) suitable for X-ray diffraction
measurements (cf. Table 1).
Results and discussion
Ligand and complex synthesis
Methylmalononitrile (7) was prepared from 5 in a sequence of
ester ammonolysis and dehydration.26 The published procedure
Fig. 2 i) NH4OH, cat. 2-pyridone, rt, 24 h, 60%; ii) P2O5 on sand, 250 ◦C, 15 torr, 65%; iii) POCl3, NEt4Cl, 120 ◦C, 1 h, 36%; iv) LiH, THF, reflux,
45 min, 94%; v) NH2OH, EtOH, 24 h, 85%.
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Fig. 3 Three different views of the disordered structure of the formal tetracation in 11·12H2O (ellipsoids at the 50% probability level; cf. Fig. 5; primed
symbols refer to equivalent positions 1 - x, 1 - y, 1 - z).
Oxidation pathways
positions) could not be assigned unambiguously on the basis of
the diffraction data. In P1, the asymmetric unit contains one
¯
The ligand does not dissolve in the reaction mixture when its com-
plexation is attempted in the absence of oxygen. When micromolar
amounts of 4 and cobaltous acetate are mixed in a 1 : 1 molar
ratio at high dilution in the absence of additional trifluoroacetic
acid in air, an instantaneous reaction occurs, producing an orange
solution. ESI mass spectra of this crude mixture are dominated by
an ionof thecomposition [CoIII2(4 - 2H)2]2+ which is also dominant
in ESI spectra of the purified compound. Additionally, a trinuclear
cluster [Co3(O2)(4 - 2H)2]+ accompanied by a protonated dication
[Co3(O2)(4 - 2H)(4 - H)]2+ is observed which is not present in
the spectra of material prepared in the presence of trifluoroacetic
acid. CID (collision-induced dissociation) experiments with the
monocation reveal interesting behaviour, as only the simultaneous
loss of two water molecules is observed at high collision energies,
whereas a signal corresponding to the loss of a single water
molecule is not observed. It is therefore unlikely that 4 first
coordinates Co(II) in square-pyramidal fashion and then reacts
with molecular oxygen. Rather, the data points to a complex acid-
promoted oxidation mechanism involving cluster compounds that
are finally trapped in the form of the very stable “quasi-cryptand”
dimer described in the following. The cobalt(III) compound shows
an irreversible reduction peak in its cyclic voltammogram (dry
DMF, 298 K, 50–800 mV s-1, glassy carbon working electrode) at
voltages more negative than –2.7 V vs. ferrocene. This unexpected
recalcitrance with respect to stabilization of cobalt(II) can be
explained by the lack of p-backbonding in a,g-dioximes and the
rigidity of the dimer which cannot easily accommodate an increase
in ionic radius.
disordered half of the dimer that is related to the other half by
a centre of symmetry. A similar disorder was encountered during
refinement of the crystal structure of the tetranitrile precursor
10 (see Supporting information†). Both possible orientations
(with respect to one cobalt ion) produced unexceptional thermal
¯
ellipsoids in P1 as well as in P1 but, in the difference Fourier
map, had residual electron density in the vicinity of the atom
assigned as carbon (cf. Fig. 4). Although the structure, as discussed
in the following, represents an average, the thermal ellipsoids
are unexceptional. Disorder in 11 can be explained by invoking
the presence of four stereoisomeric forms. Of these, two are
centrosymmetric (cf. Fig. 4, B and C), and the remaining two
are a pair of enantiomers (cf. Fig. 4, A and A*). In the following,
we discuss three limiting cases, i)–iii); i) Only one enantiomer,
A or A*, is present (spontaneous racemate resolution). Then, a
¯
solution in P1necessarily leads to a diagnosis of pseudosymmetry;
¯
ii) both A and A* are present. In this case, a solution in P1 leads
to a diagnosis of pseudosymmetry and disorder; the disorder,
however, could only be solved in the lower-symmetric space group
P1; iii) all four stereoisomeric forms are present, such that the
observed pseudosymmetry contains both point groups, C1 and
Ci. Then, the observed stereoisomerism cannot be resolved in
a centrosymmetric space group due to the presence of non-
centrosymmetric enantiomers. For this reason, the site occupancy
factors of the isomers were refined in P1 for comparison. The chiral
forms A and A* (Fig. 4) converged to approximately 75% of the
whole, indicating isomerism. By restraining the occupation of the
1- and 5-positions of the pyrimidine ring to 50 : 50 (N : CH) each, a
¯
disordered solution in P1 was obtained as a compromise, because
Structural analysis (part 1)
refinement in P1 was not feasible without strongly restraining the
atomic displacement parameters. Within this solution, identical
CH distances (within estimated standard deviations) were deter-
mined for both disordered positions, whereas H atoms collapsed
on their carrier atoms, with unrealistic distances, when the
disorder was ignored. This solution is compatible with all limiting
cases i)–iii).
X-ray structural analysis revealed a complex of the composition
[CoIII2(4–H)2](OCOCF3)4·12H2O (11·12H2O). The dinuclear tetra-
cation contains two capping ligands, each of which is deprotonated
at one of its hydroxyl groups, forming a bis-m-amidoximato-
bridged core (Fig. 3). The orientation of the pyrimidine heterocycle
(the uncoordinated nitrogen atom may be in one of two different
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Fig. 4 Electron density maps of the pyrimidine plane in 10 and 11·12H2O; (a) experimental electron density; (b/c) residual density resulting from ignored
disorder; (d) minor fluctuation in the difference density maps of the solutions incorporating disorder, with peaks occurring at bonding critical points
(note the different scales). The position of the cobalt ion (residual electron density) can be seen in figure (a) (at right). (e) Top: Possible stereoisomers in
1
11 (m denotes a mirror plane, i a centre of symmetry and A* an enantiomer). Below: Symmetry interpretation of the 13C{ H}-NMR (100 MHz) signals
assigned to amidoxime groups of 11 in D2O (cf. Fig. 3).
1
Coordination isomerism and 13C{ H}-NMR (in D2O)
point group symmetry and are a pair of enantiomers, such that
all eight amidoxime functions have slightly different chemical en-
Unlike ligand 4, ligands of the tetrapodal pentadentate class usu-
ally have C2v point group symmetry, which renders all equatorial
donor functions magnetically equivalent. In ligand 4, the “true”
point group is Cs, the only symmetry element other than identity
being a mirror plane which coincides with the pyrimidine ring
plane, i.e., the two-fold rotation axis, as found in C2v, is missing.
However, the breaking of symmetry in 4 occurs not in the first coor-
dination sphere but in the ligand periphery, as all equatorial donor
functions are amidoxime groups. Therefore, we may call 4 “pseudo-
C2v symmetric”, i.e. dimerization can still occur with monomers
having their pyrimidine rings in every possible orientation (cf.
Fig. 4). For a truely C2v symmetric ligand, dimerization of the
present kind would result in a dimer belonging to point group
Ci. This means that in each monomeric motif, all four amidoxime
functions would have a slightly different chemical environment,
but each environment would occur twice per molecule, as a
consequence of inversion symmetry. Consequently, this point
group occurs only in two out of four conceivable cases for a
“pseudo-C2v symmetric”, in actual fact Cs symmetric, ligand.
These two cases are composed of two different isomers that have
different chemical environments. The other two cases show C1
vironments. Taking into consideration the previous explanations
for an isomeric mixture of four different compounds, 16 different
1
13C{ H}-resonances belonging to amidoxime functions are to be
expected, four for each of the two Ci dimers and eight for each
enantiomer, indistinguishable from one another in achiral media.
This behaviour can indeed be observed over a chemical shift
range of 7 ppm (cf. Fig. 4). The 16 observed signals can easily be
ordered into four groups, based on their chemical shifts, line widths
and fitted integrals ( 10% maximum integration deviation). The
four groups correspond to four different chemical environments
expected for the simplified case of a single molecule in the Ci point
group. Within each group there are two signals of comparable
intensity. In the context of the previous rationale, these can
be assigned to the C1 forms, since eight magnetically different
amidoxime groups are to be expected in the enantiomers, which
have identity (E) as the only symmetry element. Moreover, each
of the two signals of comparable intensity within each of the
four groups resembles another signal in terms of chemical shift,
that consequently belongs to one of the Ci symmetric forms.
This observation can be elegantly explained, as each half of the
enantiomers resembles the orientation in one of the Ci isomers.
2482 | Dalton Trans., 2012, 41, 2477–2485
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◦
˚
Table 2 Selected interatomic distances (A) and angles ( ) for 11·12 H2O
Further, this hypothesis is consistent with the chemical shift
difference observed in the Cs-symmetric ligand 4. In conclusion,
a
Co1 ◊ ◊ ◊ Co1¢
3.812(1)
N2–O3–Co1¢
Co1–N2–O3
O3¢–Co1–N2
Co1–N2–O3–Co1¢
N4–Co1–O3¢
N4–Co1–N2
N4–Co1–N6
N4–Co1–N5
N4–Co1–N7
N5–Co1–N2–O3
O3–H8–O8
119.33(14)
122.14(15)
90.93(8)
67.9(2)
173.73(9)
89.39(9)
88.61(9)
86.71(9)
87.11(9)
45.7(2)
1
the appearance of the amidoxime resonances in the 13C{ H}-
spectrum of 11 is fully consistent with the picture of isomerism as
deduced from the X-ray diffraction data. The distribution of these
isomers is not fully probabilistic, as in this case all 16 signals would
be of equal intensity due to equal population of the four forms.
Co1–N2
N2–O3
1.907(2)
1.385(3)
1.919(2)
1.909(2)
1.911(2)
1.919(2)
1.913(2)
2.726(3)
2.587(4)
2.848(2)
O3¢–Co1
Co1–N4
Co1–N6
Co1–N5
Co1–N7
O8 ◊ ◊ ◊ O3
O10 ◊ ◊ ◊ O11
O3¢ ◊ ◊ ◊ O10
Structural analysis (part 2)
162(4)
169(4)
In the structure of 11 (Fig. 3), the apical pyrimidine donor N4 oc-
cupies the position trans to the m-oximato oxygen atom. The cation
charge is compensated by four trifluoroacetate counterions which
form intermolecular hydrogen bonds to the cation’s hydroxyl and
amino functions. The monomeric motif is self-complementary; in
the dimer, the metal ions are coordinatively saturated in reciprocal
fashion by deprotonated hydroxyl groups of the other half of the
molecule.
O11–H10–O10
Intermolecular distances:
O11 ◊ ◊ ◊ O31
N14 ◊ ◊ ◊ O32
N14 ◊ ◊ ◊ O800
2.490(1)
N13 ◊ ◊ ◊ O400
O400 ◊ ◊ ◊ O500
O500 ◊ ◊ ◊ O800
2.915(1)
2.840(1)
2.717(2)
2.902(1)
2.928(1)
a The angle N2–O3–Co1¢ defines the parameter a, which has been used to
characterize bis-m-oximato bridging (see text).33 Primed symbols refer to
equivalent positions 1 - x, 1 - y, 1 - z.
Most notably, the structure of 11 is reminiscent of cryptate
complexes, with the two cobalt(III) ions completely shielded from
their surroundings as a consequence of dimerization. The geom-
etry which results from dimerization is best described in terms
of a least-squares planes analysis. In the asymmetric octahedral
motif, three best planes can be defined by the coordinates of N2,
N5, N6, N7 (plane 1), N2, O3¢, N6, N4 (plane 2) and O3¢, N5,
N4, N7 (plane 3) (cf. Fig. 5). The cobalt ion surrounded by these
can be clearly distinguished from the type of out-of-plane bis-
m-oximato bridging found in copper glyoxime compounds where
the relation is approximately rectangular.33 Additional interatomic
distances and angles are given in Table 2.
Intramolecular H-bonding in the solid state
The hydrogen bonds in 11 are longer than in nickel dimethylgly-
34
˚
˚
˚
atoms deviates from the planes by 0.0683(11) A, 0.0578(12) A
oxime (O ◊ ◊ ◊ O: 2.45 A ) and not equivalent. However, there is no
˚
and 0.0184(11) A, respectively, while the interplanar angles are
doubt that hydrogen bonding is present as the O ◊ ◊ ◊ O interatomic
86.63(06)◦ (planes 1/2), 88.41(06)◦ (planes 2/3), and 89.85(06)◦
(planes 3/1). This characterizes a slightly distorted octahedral
coordination environment around cobalt. The symmetry-related
second cobalt ion (by inversion) is displaced from the planes
distances are significantly smaller than the sum of the van der
35
˚
˚
Waals radii (2 ¥ 1.52 A vs. 2.73 and 2.59 A, respectively; see
Table 2). Geometric variations of hydrogen bonding param-
eters can arise due to secondary interactions with water of
crystallization,36 but in the present case the hydrogen bonding
pattern formed by the oxime functions is rather characteristic
of a bis-m-oximato bridged dimer. The hydrogen bond formed
between the bridging oxygen atom and the adjacent hydroxyl
group has a larger interatomic distance (“central” O3 ◊ ◊ ◊ O8)
than the hydrogen bond formed between the non-coordinating
hydroxyl functions (“peripheral” O11 ◊ ◊ ◊ O10). This behaviour is
also observed in copper dimethylglyoxime37 and can be explained
by a decreased hydrogen bond donor capability of the coordinated
oxygen atom (O3¢). Further, as there is a short contact between
˚
˚
˚
by 2.7209(24) A, 0.8478(30) A and 2.6908(21) A, respectively,
which defines a “slipped cofacial dimer”. This term was coined
previously32 and indicates that there are pairs of parallel faces in
two octahedra (in the present case due to inversion symmetry)
while the centres of the octahedra are displaced (“slipped”) with
respect to one another.
Two other planes can be defined by the atomic coordinates of
N2, Co1, O3¢ and N2, O3, O3¢, N2¢ to further characterize the out-
of-plane displacement of the bis-m-oximato bridge (see Fig. 5). The
angle defined by these planes is 43.21(10)◦. The bridging motif
Fig. 5 Simplified representation of the coordination octahedra and H-bonding in [CoIII2(4–H)2](OCOCF3)4·12H2O] (outer coordination sphere omitted
for clarity). A) Intramolecular H-bonding pattern in the dimer. B) Intermolecular H-bonding pattern in the asymmetric unit (this motif, when doubled,
produces the structure of the whole molecule).
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Fig. 6 Schematic representation of cation structures and hydrogen bond motifs in 11·12H2O.
O3¢ and O10 (cf. Table 2 and Fig. 5), the presence of bifurcated H-
bonds involving the hydroxyl group O10–H10 and oxygen atoms
O11/O3¢ (and symmetry equivalents) cannot be ruled out. Such
hydrogen bonding may provide an additional link between the two
halves of the molecule.
metal ions. The influence of coordination isomerism, which
derives from the use of a pyrimidine core (as opposed to an
azine of higher symmetry38), on the overall geometry of the
complex cation is subtle. The presence of trifluoroacetic acid
during complexation does not impede the single deprotonation
of the capping ligand. Overall, dimerization produces a formal
tetracation [Co2(4 - H)2]4+, with both strong and weak hydrogen
bonds to its trifluoroacetate counterions in the solid state. In
ESI mass spectra, the predominant ion is the dication [Co2(4 -
2H)2]2+ which is a result of further deprotonation of the ligand.
Mononuclear ions are observed but their intensity is negligible (cf.
Experimental section). We compare the structure of the dimer to
that of copper glyoxime dimers, as there appear to be no literature
examples of related bis-m-oximato-bridged cobalt complexes of
dioximes. An explanation for their absence might be that, in
cobaloximes, significant out-of-plane placement of the hydroxyl
functions is regularly accompanied by dislocation of the metal
ion in the opposite direction.39 Yet, since malonamidoxime itself,
which can be viewed as the parent compound of the present
ligand, shows out-of-plane location of the hydroxyl function in
combination with in-plane location of the metal ion in certain
metal complexes,11 it can be assumed that this particular motif is
prone to form in cobalt(III) compounds of 1,3-dioxime ligands.
In summary, amidoxime ligands of this kind indeed combine
certain properties of tetrapodal pentadentate ligands and macro-
cyclic oxime ligands. However, while amidoxime functions are
known to act as versatile bridging donors,40 the encapsulation of
the metal ions upon dimerization in 11 is an example of synergism.
In effect, compound 4 can be considered an “open prison ligand”41
or a “pseudo-cryptand”, as the shielding depends on the self-
complementarity of the mononuclear ion-ligand fragment rather
than on the ligand alone.
Intermolecular H-bonding in the solid state
The presence of amidoxime functions makes intermolecular
hydrogen bonding in 11·12H2O diverse. Two of the four triflu-
oroacetate anions per formula unit form strong hydrogen bonds
to the hydroxyl functions serving as acceptors for the peripheral
macrocyclic intramolecular hydrogen bonds (cf. Fig. 5 B, Fig. 6).
The short contact indicates that trifluoroacetate may, alternatively,
be interpreted as trifluoroacetic acid (TFA) acting as a hydrogen
bond donor (instead of trifluoroacetate acting as an acceptor).
Based on this argument, the compound can be reformulated
as a trifluoroacetic acid adduct of the composition {[CoIII(4 -
2H)]2[OCOCF3]2·2TFA}. This explains why the dication [CoIII(4
2+
- 2H)]2 is observed in ESI mass spectra as the dominant signal,
whereas a tetracation is not observed (see Experimental section).
The other two trifluoroacetate anions form weak hydrogen bonds
to an amino function (not shown in Fig. 5). Six of the twelve water
molecules of crystallization form two ‘hydrogen bond arches’,
related by inversion symmetry, which connect the amino functions
of the methylmalonamidoxime residue that does not contain the
bridging m-oximato function (cf. Fig. 5 A/B, Table 2). The residual
six water molecules form hydrogen bonds with the weakly bound
trifluoroacetate ions. There are no hydrogen bonds involving the
non-coordinating nitrogen atoms of the pyrimidine ring.
Conclusions
Future studies will focus on the exploration of other
transition metal complexes of tetrapodal amidoxime ligands,
their reactivity, and ligand variations in order to prevent
dimerization/coordination isomerism as observed in the present
case. The potential of such complexes in electrocatalytic water
splitting will be studied.42,43
Compound 4 binds to cobalt(III) ions in tetrapodal pentadentate
fashion, with formation of a dinuclear complex containing a six-
membered out-of-plane bis-m-amidoximato metallacycle and a
macrobicyclic structure based on hydrogen bonds. This unex-
pected dimerization results in efficient shielding of the central
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21 Oxford Diffraction, CrysAlis CCD and CrysAlisPro, Version
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26 T. Matsumoto, D. Yoshida and H. Tomita, Agric. Biol. Chem., 1981,
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Acknowledgements
Support by the Deutsche Forschungsgemeinschaft (GR 1247/7-
1) is gratefully acknowledged. Thomas Hamfler and Manfred
Detlaff are thanked for technical assistance, and Dr Josef Seiffert,
Dr Gerald Ho¨rner, Dr Maria Schlangen and Professor Aris
Chatzidimitriou-Dreismann are thanked for helpful discussions.
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