Synthesis, crystal structure and properties of a new 3D supramolecular unsymmetrical tetradentate Schiff bases copper (II) framework with stable tunnels

Article abstract of DOI:10.1016/j.molstruc.2016.07.024

Flexible unsymmetrical Schiff base ligand (L) which is derived from the half unit Y?=?C₆H₅COCH₂C(N[Formula presented]CH₂C₆H₄NH₂)CH₃ (obtained from the reaction of benz

Full text of DOI:10.1016/j.molstruc.2016.07.024

Accepted Manuscript
Synthesis, crystal structure and properties of a new 3D supramolecular
unsymmetrical tetradentate Schiff bases copper (II) framework with stable tunnels
Mousa Al-Noaimi, Firas F. Awwadi, Raiid Al-Razagg, Fatima T. Esmadi
PII:
S0022-2860(16)30695-0
10.1016/j.molstruc.2016.07.024
MOLSTR 22727
DOI:
Reference:
To appear in: Journal of Molecular Structure
Received Date: 31 May 2016
Revised Date: 1 July 2016
Accepted Date: 8 July 2016
Please cite this article as: M. Al-Noaimi, F.F. Awwadi, R. Al-Razagg, F.T. Esmadi, Synthesis, crystal
structure and properties of a new 3D supramolecular unsymmetrical tetradentate Schiff bases
copper (II) framework with stable tunnels, Journal of Molecular Structure (2016), doi: 10.1016/
j.molstruc.2016.07.024.
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ACCEPTED MANUSCRIPT
The reported complex in this paper crystallizes in two different space groups; P21/n and P-1. The crystal
structure of the P-1phase indicates the presence of tunnels; the volume of these tunnels is 157 Å3 which is big
enough to accommodate solvent molecules.

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Synthesis, Crystal Structure and Properties of a New 3D
Supramolecular Unsymmetrical Tetradentate Schiff Bases
Copper (II) Framework with Stable Tunnels
Mousa Al-Noaimi*a, Firas F. Awwadib, Raiid Al-Razaggc, Fatima T. Esmadi*c
aDepartment of Chemistry, Hashemite University, P.O.Box 150459, Zarqa-13115-Jordan
b Departmentof Chemistry, The University of Jordan, Amman 11942, Jordan.
cDepartment of Chemistry, Yarmouk University, Irbid, Jordan.
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Abstract
Flexible unsymmetrical Schiff base Ligand (L) which is derived from the half unit Y =
C6H5COCH2C(N=CH2C6H4NH2)CH3 (obtained from the reaction of benzoylacetone and 2-
aminobenzylamine) and 2- quinolinecarboxaldehyde have been successfully co-assembled with
Cu(ClO4)2 to give out the [Cu(L)]ClO4 complex. The complex crystallizes in two different
space groups; P21/n and P-1. The crystal structure of the P-1 phase indicates the presence of
tunnels; the volume of these tunnels is 157 Å3 which is big enough to accommodate solvent
molecules. The X-ray data indicates that these tunnels are most probably filled by highly
disorded solvent molecules or solvent molecules with partial occupancy. The tunneled structure
is stabilized via π–π stacking interactions to give a supramolecular MOF with 1D rhomboidal
tunnels array. The copper(II) atom assumes a distorted-square pyrimidal coordination geometry
where the perchlorate is located on the apex of the pyramide. In addition, this work presents and
discusses the spectroscopic (IR, UV/vis), electro-chemical (cyclic voltammetry) behavior of the
Cu(II) complexes. The Cu(II) oxidation state is stabilized by the novel tetradentate ligands,
showing Cu(I/II) couple around 0.1 vs. Cp2Fe/Cp2Fe+.
Key words: copper , Electrochemistry, supramolecular MOF, polymorphs
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1.Introduction
Metal-complexes containing Schiff-base ligands have been extensively investigated due to
their novel structures and potential applications in many fields [1, 2]. These Schiff-base
ligands may act as a bidentate [3], multidentate ligands [4] to form homo- and heterometallic
complexes with varied stereochemistry [5]. Also, these complexes can be used as single-
molecule magnets [6], a luminescent material [7] and as catalysts for DNA cleavage reactions
[8,9]. Crystal engineering of metal complexes, especially coordination polymers with open-
framework structures have received more attention in the past decades [10-11]. In contrast, the
research about flexible ligands is still few due to the difficulty of crystallization [12–14]. In
this paper, Cu (II) complex of unsymmetrical flexible tetradentate Schiff bases was prepared
by the reaction of 1-half unit (Y) prepared from (benzoylacetone and 2-aminobenzylamine)
and 2- quinolinecarboxaldehyde with Cu(ClO4)2. The redox (cyclic voltametry) and
spectroscopic behavior for this complex was investigated. The complex was characterized on
the basis of their molar conductance, magnetic susceptibility, IR, UV-Vis, cyclic voltametry
and single crystal X-ray structure determination.
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2.Experimental
2.1.Materials
Benzoylacetone, 2-aminobenzylamine, benzoylacetone and 2- quinolinecarboxaldehyde,
Cu(ClO4)2.6H2O were purchased from Aldrich. Perchlorate salts are potentially explosive.
They should be handled with caution and small quantities only. The half unit (Y=
C6H5COCH2C(N=CH2C6H4NH2)CH3) was prepared by a method similar to that reported in the
literature [15].
2.2.Preparation of [Cu(L)]ClO4.
(370.50 g, 1mmol) of the Cu(ClO4)2.6H2O in ethanol (10ml) was added to a solution of of the
2- Quinolinecarboxaldehyde (0.16g, 1 mmol) and a half unit(Y) (0.57 g, 1 mmol) in 20 ml
solution of (1:1 ml dichloromethane:ethanol). The mixture was refluxed for 3 hours and then
stirred overnight at room temperature. The products was filtered and recrystallized from
ethanol. Yield. (0.3 g, 42%). Anal. Calc. for CuC27H22ClN3O5: C, 57.14; H, 3.91; N, 7.41%.
Found: C, 57.30; H, 3.96; N, 7.55%.UV–Vis in dichloromethane: λmax(nm) (εmax/ M-1cm-1):
243 (4.7×104), 290 (2.9×104), 364 (1.3×104), 420 (1.1×104). IR: ν(N=N) 1470, ν(C=N) 1615,
ν(C=O) 1701 cm-1.
2.3.Instrumentation.
1H-NMR spectra were recorded using NMR–spectrometer, Bruker advanced III 400MZ . IR
spectra were measured by Bruker Vertex 70. Elemental analyses were carried out on a
Eurovector E.A.3000 instrument using copper sample-tubes. UV-Vis SHIMADZU UV-
spectrophotometer for 3.3×10-4 M solutions in DMF. Melting points were measured on an
electrothermal melting point apparatus (Staffordshire, UK). Magnetic susceptibility
measurements were done using an instrument obtained from Sherwood Scientific Ltd
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(Cambridge, UK). Cyclic voltammograms were recorded using a PGSTAT 204 apparatus.
The electrochemical cell consisted of a double-jacketed glass container, which was charged
with approximately 15 mL of solvent. The cell temperature was set at 25 °C by means of a
Haake D8-G refrigerated bath and circulator (accuracy 0.02 °C). The cell was fitted with a
Teflon cap that had four holes to permit insertion of electrodes and an argon gas bubbler
into the cell. Three electrodes were utilized in this system, two platinum-disk working and
counter (auxiliary) electrodes (1.6-mm diameter), and a silver wire pseudo-reference
electrode with ferrocene as an internal reference. The potential was controlled by the BAS
CV-27. Tetrabutylammonium hexafluorophosphate (TBAHF, 0.1 M) was used as
supporting electrolyte. TBAHF was recrystallized twice from ethanol:water (1:1) and
vacuum-dried at 110 °C overnight. Referencing was done with an addition of one crystal of
ferrocene (Cp2Fe) as an internal standard to the analyte solution after all data of interest had
been acquired. The platinum working-electrode was manually cleaned with 1 mM diamond
polish before each scan. Solvents used in all cyclic voltammetry experiment was
deoxygenated by bubbling with argon for 15 min. Conductivity measurement was obtained
using a CyberScan 540 conductivity meter for 1×10-3 M solutions in DMF at 25°C.
.
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2.4.Crystallography
[Cu(L)]ClO4 complex crystallizes into two types of crystals; parallelepiped and sword shaped
crystals with roughly 50:50 percent (by inspection). Suitable crystals of the two polymorphs
were mounted on a glass fiber and the data collected at room temperature employing enhanced
Mo radiation, λ = 0.71073 Å, using Xcalibur/Oxford Diffractometer equipped with Eos CCD
detector. The space group of parallelepiped shaped crystals is P-1while it is P21/n for the
sword shaped crystals. CrysAlis Pro software was used for data collection, absorption
correction and data reduction to give SHELX-format-hkl files, [16]. 'Multi-scan' absorption
corrections were applied with Min and Max transmission factors of 0.80809 and 1.000 for the
P21/n phase and 0.73172 and 1.000 for the P-1 phase, respectively [16]. Cell parameters
were retrieved using 6419 for P21/n phase and 2230 for the P-1 phase reflections. The
structure was solved using SHELXTL program package [17]. All nonhydrogen atoms were
refined anisotropically except hydrogen atoms which were placed in calculated positions and
refined using a riding model. CheckCif program of the cif file of the P-1 phase gave alert B
which indicates the presence void volume ( 157 Å3) (~12% of the total volume), this volume is
big enough to accommodate a solvent molecule. The R-indices are R = 5.8% and wR2 = 0.1744
and the largest diff. peak and hole 0.845 and -0.346 e.Å-3. Analysis of electron density map
using Olex2 program package indicated the presence of unidentified electron density is
accommodated inside the tunnels (Figure 1). Therefore, the void space was squeezed using
Platon program [18]. The refining parameters have improved significantly, R-indices after
squeezing the void volume has been reduced to R = 4.95% and wR2 = 0.1323 , the details of
refining parameters are given in Table 1. Details of data collection and refinement for the two
phases are given in Table 1.
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3. Results and Discussion
3.1.Synthesis
The half unit (Y) was prepared by refluxing benzoylacetone and 2-aminobenzylamine in
ethanol (Scheme 1) [15]. The milky white powder half unit which melts at 170°C has IR
spectrum stretching frequencies at 1520, 1597 and 3462 cm-1 which are assigned to C=C, C=N
and NH2, respectively. The 1H-NMR spectrum of this compound shows a singlet at 2.12 ppm
due to methyl group, a doublet in the 4.42-4.41 ppm range due to benzyl protons, and a singlet
at 5.77 ppm due N=C-H proton. A multiplet in the 6.72-7.90 ppm range is due to aromatic
protons. A broad peak at 3.78 ppm ppm is assigned to NH2 protons, and a broad peak at 11.53
ppm is attributed to O-H proton, indicating that the compound is present in the enol form [15].
Reaction of this half unit (Y) with 2-quinolinecarboxaldehyde produce unsymmtrical
tetradentate Schiff base ligand (L). The ligand (L) has neither been isolated nor characterized
spectroscopically due to its stablity. Therefore, preparation of the Cu(II) complex was carried
out by the reaction of of the half-unit (Y) with the 2-quinolinecarboxaldehyde in the presence
of the Cu(ClO4)2 (Scheme 1). The obtained complex was analyzed by infrared and UV–
Visible spectroscopy. In the IR spectrum, the formation of the complex was confirmed by the
absent of NH2 for the half unite (Y), the shift of the imine (C=/N) at (1597 cm-1) cm-1 to lower
energy (1590 cm-1). The complex shows a band at 1088 cm-1 suggesting the presence of
perchlorate as counter anion[19]. The formation of the MꢀN bonds were further supported by
the appearance of the ν(MꢀN) band at 620 cm-1 (Figure 2)[20].
.
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O
H2N
N
O
ethanol
+
O
H2N
NH2
Y
N
O
H2N
Cu(ClO4)2.6H2O
N
N
Cu
N
N
ethanol
+
O
O
L
Y
Scheme 1: synthesis of the [Cu(L)]ClO4 complex
Electrical conductivity and magnetic susceptibility measurements were also carried out for the
complex. The molar conductivity values in DMF solvent is (2.1) supports the formulation of
the complexes as ionic. Magnetic susceptibility for [Cu(L)](ClO4) is 1.65 BM indicate that
each Cu has one unpaired electron with a d9 square planar geometry. Similar results were
obtained with other unsymmetrical Schiff bases containing 2-quinolinecarboxaldehyde [21].
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3.2.Crystal structure
[Cu(L)](ClO4) crystallizes in two different packing PSEUDO polymorphs, the polymorph 2
crystallizes in P-1 space group and polymorph 1 crystallizes in P21/n space group. The
asymmetric unit of P-1 consists of one molecule, while the asymmetric unit of the P21/n
consist of two molecules. The crystal structures of the two polymorphs are shown in Figure 3
and 4. The perchlorate anion is disordered on two positions with 54:46 ratio in the P21/n
phase. There is no significant difference in the molecular structure in the two polymorphs as
shown in Figure 5. In both polymorphs, the geometry around the copper center is 4+1 via the
nitrogen and oxygen atoms of the ligand L and the fifth position via the interaction with the
oxygen atoms of the perchlorate anions. It is noteworthy that the Cu…O-ClO3 distance in the
P-1 phase is significantly than the corresponding distances in the P21/n phase by 0.33 Å.
Selected crystallographic and structural parameters are listed in Tables 1. Selected bond
distances and bond angles are given in (Table 2). The X-ray structure analysis verified the
formation of the unsymmetrical Schiff-base copper(II) complex formed from half unit and 2-
quinolinecarboxaldehyde. In [Cu(L)](ClO4), the deprotonated ligand L is quadridentate
forming one five-membered chelate ring, and two six-membered chelate rings. The copper(II)
ions have square-pyrimidal coordination, the perchlorate anion is located on the apex of the
complex. The six-membered chelate ring comprising the Cu atom and the ketoimine residue
O(31)-Cu-N(20)) is planar (mean deviation of component atoms from plane are 0.05 Å for the
P-1 phase and 0.03 Å and 0.05 Å for the two crystallographically different molecules in the
P21/n phase). The bond distances of C(23)-C(24) and C(23)-C(21), C(21)-N(20), and C(24)-
O(31) of the chelate ring are intermediate between their single and double-bond distances,
indicating that the chelate ring is conjugated. The bond distance Cu-N(20) is somewhat shorter
than Cu-N(12) and Cu(1)-N(1).
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The molecular units of both polymorphs are connected mainly by C-H O-Cl nonclassical
hydrogen bonding interactions, whereas π-π stacking interactions plays less important role.
The data summarizing hydrogen bond interactions are listed in Table 3. Olex2 program was
used to analyze π-π stacking interactions, the data are listed in Table 4, it can be seen that the
role of the π-π stacking interactions in the P-1phase is more significant than its corresponding
role in the P21/n phase; there is one π-π stacking interaction in the P21/n phase while there are
two in the P-1 phase (Table 4).
The three dimensional structure of the P-1 phase indicates the presence of void space, partially
filled or filled with highly disordered solvent molecules. (Figure 1).These tunnel structure is
stabilized by π-π stacking interactions (Figure 1).
3.3.Electronic structure
UV-Vis spectrum of [Cu(L)]ClO4 was recorded in the range of (200-800) nm in
dichloromethane solution ((Figure 6). The spectrum of the complex shows two strong
absorption bands at 243 nm and 290 nm, which are assigned as intraligand absorption, π→π*
and n→π* of both conjugated and azomethine group, respectively [22]. The absorption band
at 360 nm is assigned as metal ligand charge transfer transition (MLCT). In most cases, d–d
transition cannot be detected since they are obscured by the broad charge transfer transition
tailing into the visible spectrum [22].
3.4.Electrochemistry
The electrochemical behavior of the complex is investigated by cyclic voltammetry (CV) in
the presence of [NBu4][PF6] in dichloromethane at scan rate 100 mV S-1 (Figure 7).
Referencing was done with an addition of ~1 mg crystal of ferrocene (Cp2Fe) as an internal
standard to the analyte solution. The Cu(II/I) couples were calculated from average of the E˚1/2
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values for the anodic and cathodic waves from cyclic voltammetry. Complexes show a
quasireversible electron reduction at (0.10 eV) is assigned to CuII/I reduction couple . The
second reduction at -1.8 V is assigned to the second reduction peak is due to L0/-1
.
4.Conclusions
Therefore, preparation of the [Cu(L)]ClO4 complex was carried out by the reaction of the
half-unit (Y) with the 2-quinolinecarboxaldehyde in the presence of the Cu(ClO4)2. The
coordination geometry of the central metal is square-pyrimidal in which the ligand L acts as a
monoanionic N3O donor via the carbonyl oxygen, deprotonated enamine nitrogen and pyridyl
nitrogen atom. [Cu(L)](ClO4) crystallizes in two different pseudo polymorphs (P-1 and P21/n
space groups). In both polymorphs, the geometry around the copper center is 4+1 via the N3O
donor atoms of the ligand L and the oxygen atoms of the perchlorate anions. The three
dimensional structure of the P-1 phase indicates the presence of void space can accomadate a
solvent with a volume (157 Å3). These tunnel structure is stabilized by π-π stacking
interactions. The electrochemical properties and electronic absorption in dichloromethane
have been obtained.
Supplementary material
Crystallographic data have been deposited with the Cambridge Crystallographic Data Center; CCDC
No. 1482426 for polymorph 2 and 1482427 for polymorph 1, Copies of this information may be
obtained from the director, CCDC, 12 Union Road, Cambridge CB2 1EZ, UK. Tel.: +44 1223 762910;
fax: +44 1223 336 033; e-mail: deposit@ccdc.cam.ac.uk or on the web www:
http//www.ccdc.cam.ac.uk/deposit.
Acknowledgements
M. Al-Noaimi and Fatima T. Esmadi would like to thank Hashemite University and Yarmouk
University in Jordan.
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Table 1: Crystallographic Data and Structure Refinement Parameters for Polymorph 1 and 2 of
[Cu(L)]ClO4.
Polymorph 1
Polymorph 2
Empirical formula
C27H22ClCuN3O5
C27H22ClCuN3O5
Formula weight
Temperature
567.47
567.47
293(2) K
293(2) K
Wavelength
0.71073 Å
0.71073 Å
Crystal system
Space group
Monoclinic
Triclinic
P 1 21/n 1
P-1
a = 8.0605(5)Å, α= 110.318(6)°
b = 12.1232(8)Å, β= 96.349(5)°.
c = 14.8171(10)Å, γ = 97.657(5)°
1326.41(15) Å3
Unit cell dimensions
a = 19.2533(7) Å, α= 90°
b = 12.9019(7) Å, β=102.881(4) Å
c = 20.2340(8) Å γ = 90°
4899.7(4) Å3
Volume
Z
8
2
Density (calculated)
Absorption coefficient
F(000)
1.539 Mg/m3
1.421 Mg/m3
1.046 mm-1
0.966 mm-1
2328
582
Crystal size
Theta range for data
collection
0.31 x 0.18 x 0.12 mm3
3.04 to 26.30°.
0.32 x 0.22 x 0.12 mm3
2.97 to 26.30°.
Index ranges
-24 ≤ h ≤ 21, -13 ≤ k ≤ 16,
-25 ≤ l ≤ 25
-8 ≤ h ≤ 10, -15 ≤ k ≤ 14,
-17 ≤ l ≤ 18
Reflections collected
Independent reflections
Completeness to theta =
25.00°
23848
7552
9927[R(int) = 0.0277]
99.8 %
4826 [R(int) = 0.0189]
89.9 %
Absorption correction
Semi-empirical from equivalents
Semi-empirical from equivalents
1.00000 and 0.73172
Full-matrix least-squares on F2
4826 / 0 / 335
Max. and min. transmission 1.00000 and 0.80809
Refinement method
Full-matrix least-squares on F2
Data / restraints / parameters 9927 / 0 / 713
Goodness-of-fit on F2
Final R indices
1.097
1.078
R1 = 0.0427, wR2 = 0.1047
R1 = 0.0495, wR2 = 0.1323
[I>2sigma(I)]
R indices (all data)
Largest diff. peak and hole
R1 = 0.0674, wR2 = 0.1203
0.489 and -0.333e.Å-3
R1 = 0.0633, wR2 = 0.1423
0.526 and -0.329 Å-3
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Table 2: Bond length and Bond angle for Polymorph 1 and 2 of [Cu(L)]ClO4.
Polymorph 1
Polymorph 2
Bond length [Å]
Cu(1)-O(31)
Cu(1)-N(20)
Cu(1)-N(12)
Cu(1)-N(1)
Cu(1)-O(31)
1.888(2)
1.915(2)
2.018(2)
2.024(3)
1.291(4)
1.367(4)
1.307(4)
1.889(2)
1.935(3)
2.010(3)
2.112(3)
1.289(4)
1.366(5)
1.312(4)
Cu(1)-N(20)
Cu(1)-N(12)
Cu(1)-N(1)
O(31)-C(24)
C(23)-C(24)
N(20)-C(21)
O(31)-C(24)
C(24)-C(23)
N(20)-C(21)
Bond angles
O(31)-Cu(1)-N(20)
O(31)-Cu(1)-N(12)
N(20)-Cu(1)-N(12)
O(31)-Cu(1)-N(1)
N(20)-Cu(1)-N(1)
N(12)-Cu(1)-N(1)
C(24)-O(31)-Cu(1)
C(10)-N(1)-Cu(1)
C(2)-N(1)-Cu(1)
94.48(10)
150.62(11)
93.30(11)
96.17(10)
166.26(11)
81.60(11)
125.7(2)
O(31)-Cu(1)-N(20)
O(31)-Cu(1)-N(12)
N(20)-Cu(1)-N(12)
O(31)-Cu(1)-N(1)
N(20)-Cu(1)-N(1)
N(12)-Cu(1)-N(1)
C(24)-O(31)-Cu(1)
C(10)-N(1)-Cu(1)
C(2)-N(1)-Cu(1)
94.07(11)
155.41(12)
91.04(12)
99.13(11)
164.51(12)
80.30(12)
124.7(2)
111.6(2)
110.0(3)
129.7(2)
131.9(2)
C(11)-N(12)-Cu(1)
C(13)-N(12)-Cu(1)
112.3(2)
C(11)-N(12)-Cu(1)
C(13)-N(12)-Cu(1)
113.6(3)
124.1(2)
124.2(2)
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Table 5. Hydrogen bonding parameters in Polymorph 2 phase.
Hydrogen bond
C4-H4…O3
C11-H11…O2
C14-H14…O3
C15-H15…O1
C19-H19a…O1
C…O
3.503
3.237
3.553
2.95
H…O
2.674
2.447
2.652
2.555
2.517
C-H…O
148.96
142.72
163.34
136.75
139.24
3.313
Table 4. ππ interaction parameters
Polymorph
Centeroide-centroide
distance
Polymorph 2
3.585
Polymorph 1
3.671
Shift distance
Centeroide-centroide
diatance
0.477
3.792
1.071
Shift distance
1.676
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Figure 1. Three dimensional structure of Polymorph 2 phase viewed along the a-axis showing the
unidentified electrondensity in the tunnels (above) and in spacefill format (below), dash lines depict
π-π bonds.
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Figure 2 : IR spectrum of complex [Cu(L)]ClO4
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Figure 3. Thermal ellipsoid drawing (50%) of polymorph 1
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Figure 4. Thermal ellipsoid drawing (50%) of polymorph 2
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Figure 5. The overlaid molecular cations of the two phases.
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50000
40000
30000
20000
10000
0
300
400
wavelength (nm)
Figure 6: UV-visible for [Cu(L)]ClO4 in dichloromethane
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Figure 7. Cyclic voltammogram of [Cu(L)]ClO4 vs. ferrocene (Cp2Fe) (TBAHF, 0.1M,
dichloromethane, 25˚C).
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Research highlights
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[Cu(L)]ClO4 crystallizes in two different space groups; P21/n and P-1.
P-1 polymorph has tunnels with a volume of 157 Å3.
The tunneled structure is stabilized via π–π stacking interactions to give MOF
[Cu(L)]ClO4 has a distorted-square pyrimidal coordination geometry
The complex has Cu(I/II) couple around 0.1 vs. Cp2Fe/Cp2Fe+.