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Coordination networks of Cu2+ ions with 1,3-bis[2-(4pyridyl)ethyl]benzene: strong structure-directing role of the
counter ion (nitrate, acetate and sulphate), leading to clusters,
sheets and chains
M. John Plater, Ben M. De Silva, Mark R. St J. Foreman
and William T. A. Harrison
Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE,
Scotland (e-mail: [email protected])
Submitted to Polyhedron
Abstract
The crystal structures of three compounds formed from the crystallisation of different
copper(II) salts (nitrate, acetate and sulphate) with the new ligand 1,3-bis[2-(4pyridyl)ethyl]-benzene, C 20H20N2 (L) are reported. The anion is incorporated into each
strructure,
but
it
plays
a
completely
different
role
in
each
case:
[Cu2L4(NO3)(H2O)2]·3(NO3) (1) contains discrete ‘paddlewheel’ bimetallic clusters
incorporating a nitrate ion at their centres. [Cu 2L(Ac)3(OH)] n (2) contains unusual tetrametallic clusters in which the acetate ions display three different coordination modes: the
L ligands link the clusters into (100) sheets. [CuL2(SO4)]n·2n(H2O) (3) contains looped
[010] chains in which both the L ligands and sulphate ions bridge adjacent metal ions.
Crystal data: 1, C80H84Cu2N12O14, Mr = 1564.67, tetragonal, space group I4/m, a = 15.2358
(4) Å, c = 16.5372 (6) Å, V = 3838.8 (2) Å 3, Z = 2, R(F) = 0.054, wR(F2) = 0.142. 2,
C26H30Cu2N2O7, Mr = 609.60, monoclinic, space group P21/c, a = 15.9076 (6) Å, b =
11.8299 (4) Å, c = 14.4234 (4) Å,  = 107.646 (1), V = 2586.56 (15) Å 3, Z = 4, R(F) =
0.043, wR(F2) = 0.109. 3, C40H44CuN4O6S, Mr = 772.39, triclinic, space group 𝑃1̅, a =
10.513 (2) Å, b = 12.925 (4) Å, c = 14.769 (4) Å,  = 91.126 (11),  = 109.749 (9),  =
100.658 (9), V = 1848.9 (8) Å3, Z = 2, R(F) = 0.108, wR(F2) = 0.274.
1 Introduction
Flexible dipyridyl bridging ligands, in which the pyridine rings are linked by an alkyl chain,
are versatile ligands for constructing MOFs and coordination networks [1–20]. Such ligands
can yield networks that can clathrate guest species because the flexible ligand may be able to
‘breathe’ to accommodate the guest, whilst maintaining its crystalline structure [21]. This
might be termed an ‘induced-fit,’ resembling the binding of a substrate at the active site of an
enzyme. Our previous crystallographic studies on a series of flexible dipyridyl alkanes showed
that longer chains tend to be disordered although the gross structural features of the networks
were easily discerned [22–24]. Flexible ligands, which can ‘fold back’ on themselves, may
also offer an opportunity to form a discrete complex or a cluster [25]. An important
consequence of using neutral dipyridyl ligands as metal-linkers rather than anions such as
dicarboxylates is the requirement for charge-balancing anions, which may exert their own
influence on the structure [26].
In this paper, we report three structures formed from the crystallisation of different
copper(II) salts (nitrate, acetate and sulphate) with the new ligand 1,3-bis[2-(4pyridyl)ethyl]-benzene, C20H20N2 (see scheme below), in which the anion plays a key, but
completely different, role in each case. So far as we are aware, this ligand is novel and no
crystal structures containing it have been reported previously.
2 Experimental
Synthesis of 1,3-Bis[2-(4-pyridyl)ethyl]benzene (L)
Pyridine-4-carboxaldehyde (2.72 g, 25.4 mmol) was added to a solution of 1,3bis(methyltriphenylphosphonium)benzene di-bromide (10 g, 12.7 mmol) in dry ethanol (50
ml). A fresh solution of sodium ethoxide was slowly added to the stirred mixture over 30 min.
After a further 3.5 h the ethanol was removed and water (80 ml) followed by CH2Cl2 (8 ml)
was added. The triphenylphosphine oxide that remained as a precipitate was filtered off and
washed with water. The aqueous washings were combined and neutralized with sodium
hydroxide (2 M) and the mixture was extracted with CH2Cl2 (2  50 ml). The CH2Cl2 was
removed in vacuo to give a brown solid, which was dissolved in ethanol (15 ml) to which 10%
palladium on carbon (200 mg) was added. This vigorously stirred mixture was hydrogenated
at 1 atm pressure and at 24 °C until no more hydrogen was absorbed. The ethanol was removed
and the crude product was purified by column chromatography (silica gel; eluent 90%
ethanol:10% ethyl acetate) to give L (2.2 g, 62 %) as a light brown solid, m.p. 86–89 C.
(KBr)/cm–1 3010s, 2928s, 2866w, 1556s, 1454s, 1413s, 1217w, 990w and 704s; H(250 MHz;
CDCl3) 2.86(8H, s), 6.87–7.20(8H, m) and 4.00(4H, d, J 1.9); C(62.9 MHz; CDCl3) 36.5, 37.1,
124.0, 126.3, 128.6, 140.9, 150.0, 150.4 (one resonance is missing); m/z 289.1705 (C20H20N2
requires 289.1704).
Synthesis of [Cu2L4(H2O)2(NO3)]·3(NO3) (1)
L (0.10 g, 0.35 mmol) was dissolved in ethanol (5 ml) and carefully layered onto a solution of
Cu(NO3)2·2.5H2O (0.081 g, 0.35 mmol) in water (5 ml) in a sample vial, which was then sealed.
The mixture was left to stand for two weeks and during this time royal blue crystals of 1 grew
at the layer interface. The crystals were harvested by filtration and air dried (0.106 g, 59%);
(KBr)/cm–1 3382s, 3050m, 3016m, 2922s, 2856s, 1672s, 1430s, 1228s, 1184w, 1066m,
1030m, 936w, 822s, 773s and 698s.
Synthesis of [Cu2L(OAc)3(OH)]n (2)
L (0.10 g, 0.35 mmol) was dissolved in EtOH (5 ml) and layered onto a solution of
Cu(OAc)2·H2O (0.070 g, 0.35 mmol) in water (5 ml). The vial was sealed and the solution was
left to stand for two weeks: during this time turquoise crystals of 2 grew at the layer interface,
which were collected and air dried (0.138 g, 74%); (KBr)/cm–1 3430s, 3060m, 2922s, 2858s,
1617s, 1436s, 1229s, 1050s, 1032s, 967s, 825s, 795s, 704s and 613s.
Synthesis of [CuL2(SO4)]n·2n(H2O) (3)
L (0.10 g, 0.35 mmol) was dissolved in ethanol (5 ml) and layered onto a solution of
CuSO4·5H2O (0.086 g, 0.35 mmol) in water (5 ml). The solution was left to stand for two
weeks in a sealed vial and during this time blue crystals of 3 grew at the layer interface. The
crystals were collected and air dried (0.095 g, 59%). (Found: C, 51.7; H, 5.0; N, 4.55.
C26H30Cu2N2O7 requires C, 51.2; H, 5.0; N, 4.6%) (KBr)/cm–1 3445m, 1603s, 1506w, 1445s,
1332s, 1224s, 1070s, 1037s, 910w, 819w, 705w and 671s.
X-Ray Crystallography
Intensity data for 1–3 were collected at 120 K using graphite-monochromated MoK
radiation ( = 0.71073 Å) on a Bruker-Nonius KappaCCD diffractometer. The structures
were solved by direct methods and completed and optimised by least-squares refinement
against F2 with SHELXL-97 [27]. The C-bound H atoms were geometrically placed (C–
H = 0.95–0.99 Å) and refined as riding atoms. The O-bound H atoms were located in
difference maps and refined as riding atoms in their as-found relative positions. The
constraint Uiso(H) = 1.2Ueq(carrier) was applied in all cases.
The nitrate ion at the centre of the ‘paddlewheel’ cluster in 1 (vide infra) is disordered by
symmetry over four orientations rotated by 90. The three charge-balancing
(uncoordinated) nitrate ions in 1 were found to be highly disordered and after unsuccessful
attempts to plausibly model them, their contribution to the scattering was remved with the
SQUEEZE option incorporated in PLATON [28]. The H atoms of the each of the –CH3
groups of the acetate anions in 2 were modelled as being disordered over two sets of sites
related by a 60 rotation about the H3C–C bond axis. One of the Cu 2+ ions in 3 is statistically
disordered over two sites adjacent to an inversion centre. One of the uncoordinated water
molecules in 3 is disordered over three adjacent positions; its H atoms could not be located.
The key crystallographic and data collection parameters for 1–3 are summarized in Table
1 and full details are available in the archived cifs.
3 Results
Structure of [Cu2L4(NO3)(H2O)2]·3NO3 (1)
The crystal structure of 1 contains novel cationic ‘paddlewheel’ [Cu 2L4(NO3)(H2O)2]3+
clusters, which are templated by nitrate ions at their centres. The copper(II) ion, which lies
on a fourfold rotation axis, is bonded to a square-plane of four symmetry equivalent ligand
N1 atoms [Cu–N = 2.025 (3) Å] and its Jahn–Teller, asymmetrically axially-distorted
octahedral CuN4O2 coordination sphere is completed by a water molecule and the O atom
of a nitrate group [Cu–O = 2.289 (5) and 2.620 (5) Å, respectively]. The asymmetric unit
(Fig. 1) of 1 contains half an L ligand, which is completed by mirror symmetry. The dihedral
angle between the planes of any two adjacent py rings of the ligands bonded to Cu is 77.92
(9), and the metal ion is displaced from the mean plane of each py ring by 0.386 (4) Å.
The conformation of the ethyl chain linking the aromatic rings of the ligand is gauche [C3–
C6–C7–C8 torsion angle = –63.9 (4)] and the dihedral angle between the central benzene
ring and the terminal pyridyl ring is 44.5 (2). Each ligand is twisted back to bond to a
second, symmetry equivalent metal ion; the nitrate group at the centre of the cluster, which
is disorderd about the [001] 4-fold axis also bonds to the second copper ion, to result in a
‘paddleweel’ (Fig. 2) arrangement for the cluster: its O–CuCu–O axis lies in the [001]
direction and the complete cluster has 4/m point symmetry. The axial water molecules
probably form O–HO hydrogen bonds to the disordered charge-balancing nitrate groups.
The unit-cell packing shows (Fig. 3) shows that the clusters stack in the [001] direction;
the disordered (and unmodelled) nitrate ions separate adjacent clusters in the c-dirction.
Structure of [Cu2L(OAc)3(OH)]n (2)
The crystal structure of 2 consists of unusual tetra-metallic copper–acetate–hydroxo clusters
connected into (100) sheets by the L ligands. Cu1 (Fig. 4) has four near-neighbours arranged
in a square plane: one ligand N atom [Cu–N = 1.977 (2) Å], two cis hydroxide groups [Cu–O
= 1.948 (2) and 1.973 (2) Å] and an acetate O atom [1.925 (2) Å]. Its axially distorted octahedral
coordination geometry is completed by two further acetate O atoms [2.543 (2) and 2.678 (2)
Å]: the bond angle for the axial O–Cu–O grouping is 163.33 (7). Cu2 has five near-neighbours
in a square pyramidal arrangement: one N atom [2.018 (3) Å], a hydroxide group trans to N
[1.989 (2) Å] and two acetate O atoms [1.973 (2) and 2.002 (2) Å] form the base of the pyramid
and another acetate (O2) atom [2.198 (2) Å] the apex. A highly distorted octahedron is
completed by the long Cu2–O5 bond [2.647 (2) Å]: the O2–Cu2–O5 bond angle is 149.94 (7).
The hydroxide ion plays a key role is constructing the cluster: it bridges the two Cu1 atoms (as
part of a centrosymmetric Cu2O2 square) and also bonds to Cu2. It is notable that the three
acetate groups have very different coordination environments: the C21-containing ion is 1 +
1 bridging between Cu1 and Cu2, whereas the C23 ion is chelating to Cu2 [O–Cu–O = 54.88
(8)] and also bridges to Cu1 from both its’ oxygen atoms (i.e. 2 + 2). Finally, the C25
acetate ion is simple monodentate (1) to Cu2; its uncoordinated O atom accepts a hydrogen
bond [HO = 1.85 (4) Å; O–HO = 165 (4)] from the hydroxide group at the centre of the
cluster. Overall, a centrosymmetric [Cu4(OH)2(OAc)6N4] entity arises (Fig. 5), where N is part
of the ligand. The Cu1Cu1i (i = 1–x, 2–y, –z) and Cu1Cu2 separations are 2.9851 (5) Å
and 3.0920 (5) Å, respectively.
In terms of the L ligand in 2, the dihedral angles between the central ring and the N1 and N2
pyridine rings are 8.72 (15) and 45.26 (9), respectively. The conformation of the C3–C6–C7–
C8 inter-ring link is anti [torsion angle = 179.9 (3)] whereas the C18–C15–C14–C10 link is
gauche [–67.0 (4)].
The extended structure of 2 results in (100) infinite sheets (Fig. 6), in which the clusters are
linked by the contorted ligands in the [010] and [001] directions. Inter-sheet bonding occurs
via van der Waals’ contacts between the ligand atoms. There are no aromatic – stacking
interactions in 2 (shortest centroid–centroid separation > 4.3 Å).
Structure of [CuL2(SO4)]n·2n(H2O) (3)
The crystal structure of 3 (Fig. 7) consists of infinite [010] chains with adjacent copper ions
bridged by both L ligands and sulphate ions. Cu1 (site symmetry ̅1) is coordinated by four L
nitrogen atoms in a square planar arrangement (mean Cu–N = 2.030 Å) and its Jahn–Teller
axially-distorted octahedral geometry is completed by two sulphate O atoms [Cu–O = 2.414
(6) Å]. Cu2, which is disordered over adjacent sites [CuCu = 0.957 (4) Å] related by
inversion, has essentially the same coordination mode. The N1 ligand has a gauche
conformation for both the C3–C6–C7–C8 [50.5 (12)°] and C10–C14–C15–C18 [63.0 (12)°]
linking groups. The dihedral angles between the central ring and the N1 and N2 pyridine rings
are 61.2 (4) and 38.5 (4)°, respectively. For the N3 ligand, both its linking ethyl groups are
gauche [C23–C26–C27–C28 = 54.0 (12)° and C30–C34–C35–C38 = 61.9 (12)°] and the
central ring subtends dihedral angles of 43.2 (3) and 68.4 (3)° with the N3- and N4-pyridine
rings, respectively. Because of the coordination of the N2- and N3-rings to Cu2 and Cu1,
respectively (Fig. 7), the ring planes are well aligned for aromatic – stacking with a short
centroid–centroid separation of 3.486 (6) Å; the angle between the ring planes is 4.9 (5).
Each Cu1 atom in the [010] chain is linked to two Cu2 atoms via a pair of L ligands and a
bridging sulphate ion and, mutatis mutandis, Cu2 has the same situation with respect to
Cu1 (Fig. 8). The separation of adjacent copper ions in the chain is either 6.073 (3) or 6.863
(3) Å, depending on which disorder component of Cu2 is considered. The crystal of 3 is
consolidated by water-to-sulphate O5–HO hydrogen bonds, which link adjacent chains
in the [xxx] direction.
4 Conclusion
The room-temperature interface syntheses of the new flexible ligand 1,3-bis[2-(4pyridyl)ethyl]benzene with different Cu2+ salts has generated single crystals of a novel
cluster, a sheet and a chain structure. The flexibility of the ligand has been demonstrated,
with both gauche and anti conformations for the ethyl linkers and a variety of dihedral
angles between the aromatic rings. The meta-attachment of the side chains to the central
benzene ring of the ligand leads to a “bent back” (rather than extended) conformation in
each case: in 1 and 3 the ligand bonds to two metal ions bridged by an anion [in 1, CuCu
= 7.4229 (12) Å; in 3, CuCu = 6.073 (3) or 6.863 (3) Å] whereas in 2, even though the
CuCu separation of 7.3061 (5) Å is slightly shorter than in 1, the metal ions are in
separate clusters. The structural role of the anion in these structures is notable, with each
species generating a completely different structure.
Acknowledgements
We thank the EPSRC National Mass Spectrometry Facility (University of Swansea) for the
high-resolution mass spectrometry data and the EPSRC National Crystallography Service
(University of Southampton) for the X-ray data collections and preliminary structural
analyses.
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Table 1: key crystallographic parameters for 1–3
1
Chemical formula
Formula Mass
Crystal system
a (Å)
b (Å)
c (Å)
α (°)
β (°)
γ (°)
V (Å3)
T (K)
Space group
Z
Reflections
measured
Independent
reflections
RInt
R(F) [I > 2σ(I)]
wR(F2) (all data)
CCDC deposition
number
2
3
C80H84Cu2N12O14
1564.67
Tetragonal
15.2358 (4)
15.2358 (4)
16.5372 (6)
90.00
90.00
90.00
3838.8 (2)
120 (2)
I4/m (No. 87)
2
6489
C26H30Cu2N2O7
609.60
Monoclinic
15.9076 (6)
11.8299 (4)
14.4234 (4)
90.00
107.646 (1)
90.00
2586.56 (15)
120 (2)
P21/c (No. 14)
4
24917
C40H44CuN4O6S
772.39
Triclinic
10.513 (2)
12.925 (4)
14.769 (4)
91.126 (11)
109.749 (9)
100.658 (9)
1848.9 (8)
120 (2)
𝑃1̅ (No. 2)
2
10508
1765
5070
6232
0.053
0.054
0.142
1032648
0.094
0.043
0.109
1032649
0.136
0.108
0.274
1032650
Fig. 1: The asymmetric unit of 1 extended to show the complete L ligand showing 50%
displacement ellipsoids. Only one orientation of the disordered nitrate ion is shown. The
complete ligand is generated by the symmetry operation (x, y, –z).
Fig. 2: A [Cu2L4(H2O)2(NO3)]3+ paddlewheel cluster in 1. Only one orientation of the
disordered nitrate ion at the centre of the cluster is shown. The C-bound H atoms are omitted
for clarity.
Fig. 3: The unit-cell packing in 1 viewed down the fourfold c-axis. The Cu–O and Cu–N
bonds are highlighted in yellow.
Fig. 4: the asymmetric unit of 2 showing 50% displacement ellipsoids. The O–HO
hydrogen bond is indicated by a double-dashed line.
Fig. 5: the tetra-metallic cluster in 2 (atom colours: Cu orange, C dary grey, O red, N blue,
H white).
Fig. 6: the packing in 2 showing part of a (100) sheet of clusters connected by the L ligands.
Fig. 7: the asymmetric unit of 3 showing 50% displacement ellipsoids. The H atoms of the
disordered water molecule O6a/O6b/O6c could not be located.
Fig. 8: fragment of a [010] chain in 3 showing that adjacent copper ions are each bridged
by a sulphate ion and a pair of contorted L ligands.