Irina L Andriichuk1, Liudmyla V Tsymbal1, Vladimir B Arion2, Yaroslaw D Lampeka1. 1. L. V. Pisarzhevskii Institute of Physical Chemistry of the National Academy of Sciences of Ukraine, Prospekt Nauki 31, 03028 Kiev, Ukraine. 2. Institute of Inorganic Chemistry of the University of Vienna, Wahringer Str., 42, 1090 Vienna, Austria.
Abstract
The asymmetric units of the title compounds, trans-di-aqua-(3-benzyl-1,3,5,8,12-penta-aza-cyclo-tetra-decane-κ4 N 1,N 5,N 8,N 12)copper(II) isophthalate monohydrate, [Cu(C16H29N5)(H2O)2](C8H4O4)·H2O, (I), and trans-di-aqua-[3-(pyridin-3-ylmeth-yl)-1,3,5,8,12-penta-aza-cyclo-tetra-decane-κ4 N 1,N 5,N 8,N 12]copper(II) iso-phthalate 0.9-hydrate, [Cu(C15H28N6)(H2O)2](C8H4O4)·0.9H2O, (II) consist of one di-aqua macrocyclic cation, one di-carboxyl-ate anion and uncoordinated water mol-ecule(s). In each compound, the metal ion is coordinated by the four secondary N atoms of the macrocyclic ligand and the mutually trans O atoms of the water mol-ecules in a tetra-gonally distorted octa-hedral geometry. The average equatorial Cu-N bond lengths are significantly shorter than the average axial Cu-O bond lengths [2.020 (9) versus 2.495 (12) Å and 2.015 (4) versus 2.507 (7) Å for (I) and (II), respectively]. The coordinated macrocyclic ligand in the cations of both compounds adopts the most energetically favorable trans-III conformation. In the crystals, the complex cations and counter-anions are connected via hydrogen-bonding inter-actions between the N-H groups of the macrocycles and the O-H groups of coordinated water mol-ecules as the proton donors and the O atoms of the carboxyl-ate as the proton acceptors. Additionally, as a result of O-H⋯O hydrogen bonding with the coordinated and water mol-ecules of crystallization, the isophthalate dianions form layers lying parallel to the (01) and (100) planes in (I) and (II), respectively.
The asymmetric units of the title compounds, trans-di-aqua-(3-benzyl-1,3,5,8,12-penta-aza-cyclo-tetra-decane-κ4 N 1,N 5,N 8,N 12)copper(II) isophthalate monohydrate, [Cu(C16H29N5)(H2O)2](C8H4O4)·H2O, (I), and trans-di-aqua-[3-(pyridin-3-ylmeth-yl)-1,3,5,8,12-penta-aza-cyclo-tetra-decane-κ4 N 1,N 5,N 8,N 12]copper(II) iso-phthalate 0.9-hydrate, [Cu(C15H28N6)(H2O)2](C8H4O4)·0.9H2O, (II) consist of one di-aqua macrocyclic cation, one di-carboxyl-ate anion and uncoordinated water mol-ecule(s). In each compound, the metal ion is coordinated by the four secondary N atoms of the macrocyclic ligand and the mutually trans O atoms of the water mol-ecules in a tetra-gonally distorted octa-hedral geometry. The average equatorial Cu-N bond lengths are significantly shorter than the average axial Cu-O bond lengths [2.020 (9) versus 2.495 (12) Å and 2.015 (4) versus 2.507 (7) Å for (I) and (II), respectively]. The coordinated macrocyclic ligand in the cations of both compounds adopts the most energetically favorable trans-III conformation. In the crystals, the complex cations and counter-anions are connected via hydrogen-bonding inter-actions between the N-H groups of the macrocycles and the O-H groups of coordinated water mol-ecules as the proton donors and the O atoms of the carboxyl-ate as the proton acceptors. Additionally, as a result of O-H⋯O hydrogen bonding with the coordinated and water mol-ecules of crystallization, the isophthalate dianions form layers lying parallel to the (01) and (100) planes in (I) and (II), respectively.
Transition-metal complexes of the versatile macrocyclic 14-membered tetraamine ligand cyclam (cyclam = 1,4,8,11-tetraazacyclotetradecane) are popular metal-containing building units for the construction of metal–organic frameworks (MOFs) possessing many promising applications (Lampeka & Tsymbal, 2004 ▸; Suh & Moon, 2007 ▸; Suh et al., 2012 ▸; Stackhouse & Ma, 2018 ▸; Lee & Moon, 2018 ▸). Such an interest is explained by the exceptionally high thermodynamic stability and kinetic inertness of these species (Melson, 1979 ▸; Yatsimirskii & Lampeka, 1985 ▸), implying a preservation of their structural features (equatorial arrangement of the macrocycle in the coordination sphere of the metal ion, availability of two trans vacant sites in the axial positions suitable for coordination of bridging ligands), thus making the architecture of MOFs more predictable. The complexes of N
3,N
10-disubstituted diazacyclam (diazacyclam = 1,3,5,8,10,12-hexaazacyclotetradecane), readily obtainable via template-directed Mannich condensation of bis(ethylenediamine) complexes with formaldehyde and primary amines (Costisor & Linert, 2000 ▸), also represent widespread systems in this kind of investigations. At the same time, the complexes of N
3-substituted azacyclam (azacyclam = 1,3,5,8,12-pentaazacyclotetradecane) – a middle member of this series of ligands – have attracted considerably less attention, presumably because of the necessity of using a more sophisticated non-cyclic precursor, i.e. 3,7-diazanonane-1,9-diamine, in the Mannich condensation (Rosokha et al., 1993 ▸).Though the isophthalate (1,3-benzenedicarboxylate) dianion is often used as bridging ligand in the construction of MOFs, a very limited number of its compounds with azamacrocyclic cations have been described to date and all they are complexes of the NiII ion.Herein, we describe the syntheses and crystal structures of the title CuII complexes with azacyclam ligands and an isophthalate dianion, namely, trans-diaqua(3-benzyl-1,3,5,8,12-pentaazacyclotetradecane-κ4
N)copper(II) isophthalate hydrate, [Cu(L1)(H2O)2](ip)·H2O, (I), and trans-diaqua[3-(pyridin-3-ylmethyl)-1,3,5,8,12-pentaazacyclotetradecane-κ4
N
1,N
5,N
8,N
12]copper(II) isophthalate 0.9-hydrate, [Cu(L2)(H2O)2](ip)·0.9(H2O), (II).
Structural commentary
Each CuII ion in the complex cations in the title compounds (I) and (II) is coordinated in the equatorial plane by four secondary amineN atoms of the azamacrocyclic ligand in a square-planar fashion, and by two O atoms from the water molecules in the axial positions, resulting in a tetragonally distorted octahedral geometry (Table 1 ▸, Fig. 1 ▸ and Fig. 2 ▸).
Table 1
Selected bond lengths (Å)
(I)
(II)
Cu1—N1
2.0146 (17)
2.011 (3)
Cu1—N2
2.0290 (17)
2.019 (3)
Cu1—N4
2.0119 (17)
2.019 (3)
Cu1—N5
2.0206 (17)
2.009 (3)
Cu1—O1W
2.5071 (16)
2.514 (2)
Cu1—O2W
2.4832 (15)
2.499 (2)
Figure 1
View of the asymmetric unit of (I), showing the atom-labelling scheme, with displacement ellipsoids drawn at the 30% probability level. H atoms attached to carbon atoms have been omitted for clarity.
Figure 2
View of the asymmetric unit of (II), showing the atom-labelling scheme, with displacement ellipsoids drawn at the 30% probability level. H atoms attached to carbon atoms have been omitted for clarity.
The average equatorial Cu—N bond lengths are significantly shorter than the average axial Cu—O bond lengths [2.020 (9) versus 2.495 (12) Å for (I) and 2.015 (4) versus 2.507 (7) Å for (II)], which can be attributed to a large Jahn–Teller distortion. The CuII ions are displaced from the nearly planar (r.m.s. deviations less than 0.01 Å) mean planes of the N4donor atoms towards the O1W water molecule by 0.024 and 0.033 Å in (I) and (II), respectively. Both coordinated macrocyclic ligands adopt the most energetically favourable trans-III (R,R,S,S) conformation (Bosnich et al., 1965 ▸) with the five-membered chelate rings in gauche [bite angles 86.28 (1) for (I) and 86.30 (7)° for (II)] and six-membered chelate rings in chair [bite angles 93.7 (2) for (I) and 93.7 (9)° for (II)] conformations. The methylene group of the substituent at the non-coordinated nitrogen atoms N3 in the six-membered chelate rings is axially oriented and the sum of the C—N—C angles around these atoms [345.6 and 348.1° for (I) and (II), respectively] indicates their partial sp character (Tsymbal et al., 2019 ▸).The isophthalate dianions in the title compounds counterbalance the charge of the complex cations. One carboxylic group of the isophthalate (O1/O2/C) is nearly coplanar with the mean plane of the aromatic fragment [dihedral angles being 2.4 (3) and 3.6 (4)° in (I) and (II), respectively], while the second (O3/O4/C) is tilted by 11.6 (3) and 21.1 (4)° in (I) and (II), respectively. The C—O bond lengths in the carboxylic groups are nearly equal, thus indicating essential electron delocalization.Among the water molecules of crystallization, O3W in (I) is fully occupied, while that in (II) has a site occupancy of 50%. Additionally, two positions for disordered water molecules (O4W and O5W), each with 20% population, were found in (II). Because of their low partial population, these were not considered further in the analysis of the hydrogen-bonding network.
Supramolecular features
Three secondary amino groups of the coordinated macrocycle in (I) act as proton donors by the formation of N—H⋯O hydrogen bonds with the carboxylic groups of three different adjacent anions, while the fourth group forms hydrogen bond with the water molecule of crystallization O3W (Fig. 3 ▸, Table 2 ▸). In turn, the coordinated water molecules donate protons to the carboxylic group of the anion {bifurcated hydrogen bonding O1W—H1WB⋯[O3,O4(x, y + 1, z)] and O2W—H2WA⋯O2(−x + , y + , −z + ) and O2W—H2WB⋯O3(x − 1, y + 1, z)}, as well as to the O3W molecule [O1W—H1WA⋯O3W(−x + , y + , −z + )]. Additionally, the uncoordinated water molecule O3W acts as a proton donor by the formation of bifurcated O3W—H3WB⋯(O1,O2) and O3W—H3WA⋯O1(−x + 1, −y + 1, −z + 1) hydrogen bonds.
Figure 3
Nearest surrounding of the macrocyclic cation in (I) formed by hydrogen bonding (dashed lines). [Symmetry codes: (i) x – 1, y + 1, z; (ii) x, y + 1, z; (iii) –x + , y + , –z + ; (iv) –x + , y + , –z + .]
Table 2
Hydrogen-bond geometry (Å, °) for (I)
D—H⋯A
D—H
H⋯A
D⋯A
D—H⋯A
N1—H1⋯O4i
0.98
2.04
2.950 (2)
154
N2—H2⋯O3ii
0.98
2.15
3.118 (2)
170
N4—H4⋯O2iii
0.98
2.00
2.949 (2)
161
N5—H5⋯O3Wiv
0.98
2.35
3.230 (3)
149
O1W—H1WB⋯O4ii
0.87
2.01
2.884 (2)
176
O1W—H1WB⋯O3ii
0.87
2.60
3.213 (2)
128
O1W—H1WA⋯O3Wiii
0.85
1.97
2.813 (2)
173
O2W—H2WA⋯O2iv
0.84
1.96
2.795 (2)
174
O2W—H2WB⋯O3i
0.85
1.95
2.798 (2)
178
O3W—H3WA⋯O1v
0.88
1.92
2.779 (2)
163
O3W—H3WB⋯O1
0.87
1.85
2.720 (2)
176
O3W—H3WB⋯O2
0.87
2.66
3.248 (2)
126
Symmetry codes: (i) ; (ii) ; (iii) ; (iv) ; (v) .
The hydrogen-bonded network in (II), though slightly different, has much in common with that in (I). In particular, all secondary amino groups of the macrocycle form N—H⋯O hydrogen bonds acting as proton donors with the carboxylic groups of four different adjacent anions (Fig. 4 ▸, Table 3 ▸). Each coordinated water molecule, as well as the water molecule of crystallization O3W, donates protons to two carboxylic groups of different isophthalate anions. Additionally, in the crystal of (II) there are a number of C—H⋯O and C—H⋯N contacts between the methylene and methine groups of the macrocyclic ligand and oxygen atoms of carboxylic groups, the water molecule O3W and atom N6 of the substituent in the neighbouring macrocycle (Table 3 ▸).
Figure 4
Nearest surrounding of the macrocyclic cation in (II) formed by hydrogen bonding (dashed lines). [Symmetry codes: (i) x + 1, y, z; (ii) x + 1, −y + , z + ; (iii) x, −y + , z + ; (iv) –x + 2, –y, –z + 1.] The contact C1—H1B⋯N6 (−x + 1, y + , −z + ) is not shown.
As can be seen from Figs. 3 ▸ and 4 ▸, because of the hydrogen bonding, two pairs of isophthalate anions are situated above and below the imaginary plane of the macrocyclic ligand. Each pair is further bound with symmetry-related partners via hydrogen bonding with the water molecule of crystallization, O3W, thus forming layers of anions lying parallel to the (01) and (100) planes in (I) and (II), respectively (Figs. 5 ▸ and 6 ▸), which thus are pillared with macrocyclic cations.
Figure 5
Sheets of isophthalate dianions parallel to the (01) plane in (I). Macrocyclic ligands and H atoms at carbon atoms of the carboxylate anions are omitted, only water molecules coordinated to CuII (balls) participating in the formation of a carboxylate layer are shown (O1W – green, O2W – dark blue, O3W – violet). Hydrogen bonds are shown as dashed lines.
Figure 6
Sheets of isophthalate dianions parallel to the (100) plane in (II). Macrocyclic ligands and H atoms at carbon atoms of the carboxylate anions are omitted, only water molecules coordinated to CuII (balls) participating in the formation of a carboxylate layer are shown (O1W – green, O2W – dark blue, O3W – violet). Hydrogen bonds are shown as dashed lines.
Database survey
A search of the Cambridge Structural Database (CSD, version 5.39, last update August 2018; Groom et al., 2016 ▸) indicated that only three CuII–perchlorate complexes of azacyclam macrocycles bearing N-alkyl groups decorated with aromatic rings have been reported (Tsymbal et al., 2010 ▸). In addition, four related dicopper(II) complexes with a p-xylylene-bridged bis(azacyclam) ligand and terephthalate anion have been described, none of which includes the diaqua CuII azacyclam cation (Park & Suh, 2012 ▸). At the same time, four complexes containing macrocyclic cations and an isophthalate dianion have been reported, all of them being formed by an NiII ion coordinated to a C-methyl-substituted cyclam. Thus, the title compounds (I) and (II) are the first examples of diaqua CuII azacyclam cations described so far.
Synthesis and crystallization
All chemicals and solvents used in this work were purchased from Sigma–Aldrich and used without further purification. The starting complexes, [Cu(L1)](ClO4)2 and [Cu(L2)](ClO4)2, were prepared by a method reported in the literature (Tsymbal et al., 2010 ▸) using benzylamine or 3-picolylamine, respectively, as locking reagents.Compound (I) was prepared as follows: To a hot solution of [Cu(L1)](ClO4)2 (138 mg, 0.25 mmol) in 8 ml of DMF were added 3 ml of an aqueous solution of Na2ip (84 mg, 40 mmol). A violet precipitate formed in 24 h; this was filtered off, washed with diethyl ether and dried in air. Yield: 27 mg (19%). Analysis calculated for C24H39N5CuO7: C 50.29, H 6.86, N 12.22%. Found: C 50.42, H 6.96, N 12.02%.Compound (II) was prepared analogously starting from [Cu(L2)](ClO4)2. Yield: 30 mg (21%). Analysis calculated for C23H37.8N6CuO6.9: C 48.12, H 6.67, N 14.64%. Found: C 48.31, H 6.84, N 14.32%. Violet plates of (I) and violet needles of (II) suitable for X-ray diffraction analysis were selected from the samples resulting from the syntheses.Safety note: perchlorate salts of n class="Chemical">metal complexes are potentially explosive and should be handled with care.
Refinement
Crystal data, data collection and structure refinement details are summarized in Table 4 ▸. All H atoms in (I) were placed in geometrically idealized positions and constrained to ride on their parent atoms, with C—H distances of 0.93 (ring H atoms) or 0.97 Å (open-chain H atoms), an N—H distance of 0.98 Å, and aqua O—H distances of 0.84–0.87 Å with U
iso(H) values of 1.2 or 1.5U
eq of the parent atoms. Water H atoms in (II) were positioned geometrically (O—H = 0.71–0.85 Å) and refined as riding with U
iso(H) = 1.5U
eq(O). All other H atoms were freely refined.
Table 4
Experimental details
(I)
(II)
Crystal data
Chemical formula
[Cu(C16H29N5)(H2O)2](C8H4O4)·H2O
[Cu(C15H28N6)(H2O)2](C8H4O4)·0.9H2O
Mr
573.14
572.33
Crystal system, space group
Monoclinic, P21/n
Monoclinic, P21/c
Temperature (K)
296
296
a, b, c (Å)
7.2625 (3), 17.8132 (7), 21.1511 (9)
7.1955 (3), 19.0463 (8), 19.4426 (8)
β (°)
92.159 (3)
94.276 (2)
V (Å3)
2734.34 (19)
2657.15 (19)
Z
4
4
Radiation type
Mo Kα
Mo Kα
μ (mm−1)
0.85
0.88
Crystal size (mm)
0.30 × 0.25 × 0.04
0.16 × 0.04 × 0.04
Data cocollection
Diffractometer
Bruker X8 APEXII CCD
Bruker X8 APEXII CCD
Absorption correction
Multi-scan (SADABS; Bruker, 2007 ▸)
Multi-scan (SADABS; Bruker, 2007 ▸)
Tmin, Tmax
0.785, 0.967
0.873, 0.966
No. of measured, independent and observed [I > 2σ(I)] reflections
137978, 5555, 4193
76082, 4532, 2834
Rint
0.070
0.106
(sin θ/λ)max (Å−1)
0.624
0.589
Refinement
R[F2 > 2σ(F2)], wR(F2), S
0.032, 0.084, 1.02
0.040, 0.097, 1.00
No. of reflections
5555
4532
No. of parameters
334
439
No. of restraints
9
0
H-atom treatment
H-atom parameters constrained
H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3)
0.25, −0.24
0.29, −0.34
Computer programs: APEX2 and SAINT (Bruker, 2007 ▸), SHELXS2014 (Sheldrick, 2015a
▸), SHELXL2014 (Sheldrick, 2015b
▸), Mercury (Macrae et al., 2008 ▸) and publCIF (Westrip, 2010 ▸).
Crystal structure: contains datablock(s) I, II. DOI: 10.1107/S2056989019008387/hb7828sup1.cifStructure factors: contains datablock(s) I. DOI: 10.1107/S2056989019008387/hb7828Isup2.hklStructure factors: contains datablock(s) II. DOI: 10.1107/S2056989019008387/hb7828IIsup3.hklCCDC references: 1922733, 1922732Additional supporting information: crystallographic information; 3D view; checkCIF report
Primary atom site location: structure-invariant direct methods
Least-squares matrix: full
Hydrogen site location: mixed
R[F2 > 2σ(F2)] = 0.032
H-atom parameters constrained
wR(F2) = 0.084
w = 1/[σ2(Fo2) + (0.0366P)2 + 1.2028P] where P = (Fo2 + 2Fc2)/3
S = 1.02
(Δ/σ)max = 0.001
5555 reflections
Δρmax = 0.25 e Å−3
334 parameters
Δρmin = −0.24 e Å−3
9 restraints
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes)
are estimated using the full covariance matrix. The cell esds are taken
into account individually in the estimation of esds in distances, angles
and torsion angles; correlations between esds in cell parameters are only
used when they are defined by crystal symmetry. An approximate (isotropic)
treatment of cell esds is used for estimating esds involving l.s. planes.
Primary atom site location: structure-invariant direct methods
Least-squares matrix: full
Hydrogen site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.040
H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.097
w = 1/[σ2(Fo2) + (0.0305P)2 + 2.3396P] where P = (Fo2 + 2Fc2)/3
S = 1.00
(Δ/σ)max = 0.001
4532 reflections
Δρmax = 0.29 e Å−3
439 parameters
Δρmin = −0.34 e Å−3
0 restraints
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes)
are estimated using the full covariance matrix. The cell esds are taken
into account individually in the estimation of esds in distances, angles
and torsion angles; correlations between esds in cell parameters are only
used when they are defined by crystal symmetry. An approximate (isotropic)
treatment of cell esds is used for estimating esds involving l.s. planes.