Solvent-Dependent Structural Variation of Zinc(II) Coordination Polymers and Their Catalytic Activity in the Knoevenagel Condensation Reaction

Article abstract of DOI:10.1021/acs.cgd.5b00948

The novel self-assembled zinc(II) coordination polymers [Zn(L)(H₂O)₂]_n (1), [Zn(L)(H₂O)₂]_n·n(formamide) (2), [Zn(L)(H₂O)₂]_n·n(N-methylformamide) (3), [Zn(L)

Full text of DOI:10.1021/acs.cgd.5b00948

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Solvent dependent structural variation of zinc(II) coordination polymers and
their catalytic activity in the Knoevenagel condensation reaction
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Anirban Karmakar,* Guilherme M. D. M. Rúbio, M. Fátima C. Guedes da Silva,* Susanta Hazra,
and Armando J. L. Pombeiro*
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Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais,
1049–001, Lisbon, Portugal. E-mail: anirbanchem@gmail.com; fatima.guedes@tecnico.ulisboa.pt;
pombeiro@tecnico.ulisboa.pt
Abstract
The novel self-assembled zinc(II) coordination polymers [Zn(L)(H2O)2]n (1), [Zn(L)(H2O)2]n·n(formamide)
(2), [Zn(L)(H2O)2]n·n(N-methylformamide) (3), [Zn(L)(H2O)(formamide)]n (4) and [Zn3(L)2(formate)2(4,4’-
bipyridine)3]n·2n(DMF)·2n(H2O) (5) (L = 5-acetamidoisophthalate) have been synthesized and
characterized by elemental microanalysis, IR spectroscopy, thermogravimetric analysis and X-ray single-
crystal diffraction. 1, 2 and 3 are 1D coordination polymers that crystallize in monoclinic P21, monoclinic
P21/m and triclinic P-1 systems, respectively, and are pseudo-polymorphic supramolecular isomers with
1 having a helical arrangement, and 2 and 3 exhibiting zig-zag type structures containing different guest
molecules. Compound 4 crystallizes in the triclinic P-1 space group and is a 1D coordination polymer that
exhibits fused 8-membered and 16-membered dimetallic rings. Compound 5 features a two-dimensional
network type polymer with trimetallic cores. Compounds 1 – 5 expand to 3D by means of H-bond
interactions. These coordination polymers act as effective heterogeneous catalysts, under mild
conditions, for the Knoevenagel condensation reaction of different aldehydes with an active methylene
compound (malononitrile) and can be recycled without losing activity.
Introduction
Coordination polymers represent a class of materials that can be constructed by assembly of metal
cations or their clusters as nodes and, usually, anionic organic ligands as linkers.1-11 Their attractive
architectures and topological networks account for their wide application in gas storage,12-15
separation,16 catalysis (see below), drug delivery,17,18 embedding of nanoparticles.19 Due to various
coordination modes they can be adjusted to satisfy the requirements of particular structural motifs.
However, identical chemical components may produce more than one superstructure, known as
supramolecular isomers.
Supramolecular isomers involve network structures that have identical chemical compositions but differ
in their structures.20-23 Pseudo polymorphic supramolecular isomers concern identical frameworks that
contain different counterions, solvent or guest molecules.20,22 Similar to polymorphism, this phenomena
results when different but energetically similar packing interactions can operate during crystallization;
induction by variation of temperature, solvent, conformation of the ligand, etc., has been well
established.24-27 A variety of examples of supramolecular isomerism in coordination polymers has been
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reported28-32 and this study is important not only in producing novel materials with interesting
properties but also in developing a fundamental understanding of the factors influencing crystal growth.
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Many isomeric zinc(II) imidazolates featuring zeolite-like topologies have been formed by using template
strategies.21 Two Zn(II) based 2D metal organic frameworks have recently been reported29 which are
pseudo-supramolecular isomeric pairs, and two heterometallic coordination polymers32 are good
examples of pseudo-polymorphic supramolecular isomers. A number of coordination polymers or metal
organic frameworks have been reported as supramolecular isomers, several being based on the co-
existence of different guest molecules.24-32
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Coordination polymers have recently been applied in heterogeneous catalysis33-38 and as catalysts for
several organic reactions,39-44 e.g., alkylation of aromatics,45 carbonyl–ene and Diels–Alder reaction,46
cyanotrimethylsilation,47 isomerization of α-pinene oxide,48 Mukaiyama–aldol reaction.49 Recently, we
have reported various coordination polymers which are catalytically active for the oxidation of alkanes,
alcohols or olefins.50-61 Acidic and basic polymers can exhibit high catalytic activity in condensation
reactions like the Pechmann,62 Knoevenagel,63-76 and Prins reactions.77 Coordination polymers can work
as catalysts through two different components, viz. the metal ions, which either provide the
coordinatively unsaturated nodes and/or form the active metal sites integrated into the linker ligand,
and the ligands. Depending on the nature of the ligands and binding metal ions, coordination polymers
can act as Lewis bases or acids in the catalytic medium.
Recently, we have been focusing on the rational designing of various types of coordination polymers and
discrete complexes using amido carboxylate ligands and different transition metal ions and their
catalytic activity in various organic transformations, namely the Henry reaction.78,79 The amido
carboxylate ligands are known to form interesting polymeric frameworks with metal ions.78,79 Besides,
the presence of carboxylate groups allows slight conformational changes for the potential assembly of
different network architectures.
Thus, the two main objectives of the current work are as follows: (i) to synthesize Zn(II)-coordination
polymers by using 5-acetamidoisophthalic acid linkers in presence or absence of auxiliary ligands, under
various hydrothermal conditions; (ii) to apply the synthesized coordination polymers as heterogeneous
catalysts for the Knoevenagel condensation reaction of different aldehydes with an active methylene
compound.
Hence, we now report the synthesis of the novel 5-acetamidoisophthalic acid (H2L) species which is then
applied to the preparation, under hydrothermal conditions, of new Zn(II)-coordination polymers. The
strategy successfully yielded the polymeric materials [Zn(L)(H2O)2]n (1), [Zn(L)(H2O)2]n·n(formamide) (2),
[Zn(L)(H2O)2]n·n(N-methylformamide)
(3),
[Zn(L)(H2O)(formamide)]n
(4)
and
[Zn3(L)2(4,4’-
bipyridine)3]n·2n(DMF)·2n(H2O) (5). The obtained frameworks act as heterogeneous catalysts in the
Knoevenagel condensation reaction of malononitrile with various aldehydes.
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Experimental
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The synthetic work was performed in air. All the chemicals were obtained from commercial sources and
used as received. The infrared spectra (4000–400 cm-1) were recorded on a Bruker Vertex 70 instrument
in KBr pellets; abbreviations: s = strong, m = medium, w = weak, bs = broad and strong, mb = medium
and broad. The 1H and 13C NMR spectra were recorded at ambient temperature on a Bruker Avance II +
300 (UltraShieldTMMagnet) spectrometer operating at 300.130 and 75.468 MHz for proton and carbon-
13, respectively. The chemical shifts are reported in ppm using tetramethylsilane as the internal
reference; abbreviations: s = singlet, d = doublet, t = triplet, q = quartet. Carbon, hydrogen and nitrogen
elemental analyses were carried out by the Microanalytical Service of the Instituto Superior Técnico.
Electrospray mass spectra (ESI-MS) were run with an ion-trap instrument (Varian 500-MS LC Ion Trap
Mass Spectrometer) equipped with an electrospray ion source. For electrospray ionization, the drying
gas and flow rate were optimized according to the particular sample with 35 p.s.i. nebulizer pressure.
Scanning was performed from m/z 100 to 1200 in methanol solution. The compounds were observed in
the positive mode (capillary voltage = 80–105 V). Thermal properties were analyzed with a Perkin-Elmer
Instrument system (STA6000) at a heating rate of 2˚C min-1 under a dinitrogen atmosphere. Powder X-
ray diffraction (PXRD) was conducted in a D8 Advance Bruker AXS (Bragg Brentano geometry) theta-
2theta diffractometer, with copper radiation (Cu Kα, λ = 1.5406 Å) and a secondary monochromator,
operated at 40 kV and 40 mA. Flat plate configuration was used and the typical data collection range
was between 5˚ and 40˚.
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Synthesis of 5-acetamidoisophthalic acid (H2L)
A 1.81 g (10 mmol) portion of 5-aminoisophtalic acid was dissolved in 20 mL of acetic anhydride and the
reaction mixture was refluxed for 4 h at 80 ˚C, after which 20 mL of water were added and the solution
further heated until boiling. After cooling, the obtained white solid product of 5-acetamidoisophthalic
acid (H2L) was filtered off and washed with water until total removal of acetic acid. Yield: 85% (1.54 g).
FT-IR (KBr, cm-1): 3546 (s), 3451(s), 3130(mb), 1723(s), 1673(s), 1616(s), 1583(s), 1459(m), 1407(m),
1372(w), 1338(m), 1308(s), 1255(s), 1208(s), 1130(w), 1109(w), 1031(m), 1001(w), 989(w), 924(s),
1
806(s), 782(m), 755(s), 676(s), 608(w), 587(w), 542(w), 505(s). H-NMR (DMSO-d6): 10.29 (1H, s, -NH),
8.38 (2H, s, Ar-H), 8.13 (1H, s, Ar-H), 2.0 (3H, s, -CH3). 13C-NMR (DMSO-d6): 169.5, 166.9, 140.2, 132.0,
124.8, 123.8, 24.3. MS (ESI): m/z: 246.0 [M+Na]+.
Synthesis of 1
A mixture of Zn(NO3)2.6H2O (29 mg, 0.10 mmol) and H2L (22 mg, 0.10 mmol) was dissolved in 1 mL of
DMF and methanol (1 : 1). The resulting mixture was sealed in an 8 mL glass vessel and heated at 75˚C
for 48 h. Subsequent gradual cooling to room temperature (0.2 ˚C min-1) afforded colorless crystals of 1.
Yield: 54% (based on Zn). Anal. Calcd. for C10H11NO7Zn (M = 322.59): C, 37.23; H, 3.44; N, 4.34; Found: C,
36.02; H,3.65; N, 4.02. FT-IR (KBr, cm-1): 3351 (bs), 1680 (s), 1634 (s), 1562 (s), 1420 (m), 1364 (s), 1326
(m), 1282 (m), 1238 (m), 1192 (w), 1103 (m), 1031 (m), 987 (w), 952 (m), 815 (s), 772 (s), 737(m), 538
(w), 460 (m).
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Synthesis of 2
Zn(NO3)2.6H2O (29 mg, 0.10 mmol) and H2L (22 mg, 0.10 mmol) were dissolved in 1 mL of formamide,
sealed in a capped glass vessel and heated to 75˚C for 48 h. Subsequent gradual cooling to room
temperature (0.2 ˚C min-1) afforded colorless crystals of 2 in ca. 77% yield (based on Zn). Anal. Calcd. for
C11H14N2O8Zn (M = 367.63): C, 35.94; H, 3.84; N, 7.62; Found: C, 36.11; H, 4.01; N, 7.45. FT-IR (KBr, cm-1):
3300 (bs), 2882 (w), 1679 (s), 1619 (s), 1580 (m), 1489 (s), 1451 (s), 1424 (m), 1352 (m), 1283 (m), 1221
(m), 1106 (w), 1069 (m), 1045 (m), 915 (w), 814 (s), 777 (s), 730 (m), 642 (m), 620 (m), 531 (m).
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Synthesis of 3
A mixture of Zn(NO3)2.6H2O (29 mg, 0.10 mmol) and H2L (22 mg, 0.10 mmol) was dissolved in 1 mL N-
methylformamide. The resulting mixture was sealed in an 8 mL glass vessel and heated at 75 ˚C for 48 h.
It was subsequently cooled to room temperature (0.2 ˚C min-1), affording plate-like colorless crystals of
3. Yield: 68% (based on Zn). Anal. Calcd. for C12H16N2O8Zn (M = 381.66): C, 37.77; H, 4.23; N, 7.34. Found:
C, 37.53; H, 3.92; N, 7.10. FT-IR (KBr, cm-1): 3367 (bs), 2883 (w), 1683 (s), 1613 (s), 1580 (m), 1560 (m),
1490 (s), 1417 (m), 1390 (s), 1347 (s), 1275 (w), 1216 (w), 1100 (w), 1072 (m), 1032 (m), 809 (s), 782 (s),
725 (s), 642 (m), 531 (m).
Synthesis of 4
A mixture of Zn(NO3)2.6H2O (58 mg, 0.20 mmol) and H2L (22 mg, 0.10 mmol) was dissolved in 1 mL of
formamide. The resulting mixture was sealed in an 8 mL glass vessel and heated at 85 ˚C for 48 h. It was
subsequently cooled to room temperature (0.2 ˚C min-1), affording colorless crystals of 4. Yield: 72%
(based on Zn). Anal. Calcd. for C11H12N2O7Zn (M = 349.60): C, 37.79; H, 3.46; N, 8.01. Found: C, 36.88; H,
3.01; N, 8.10. FT-IR (KBr, cm-1): 3373 (bs), 3177 (bs), 2916 (w), 1698 (s), 1637 (s), 1562 (s), 1444 (s), 1419
(m), 1384 (s), 1329 (s), 1283 (m), 1257 (w), 1112 (m), 1085 (m), 1034 (m), 935 (m), 799 (s), 782 (s), 725
(s), 634 (m), 542 (m), 474 (m).
Synthesis of 5
A mixture of Zn(NO3)2.6H2O (29 mg, 0.10 mmol), H2L (22 mg, 0.10 mmol) and 4,4’-bipyridine (15.6 mg,
0.10 mmol) was dissolved in 1 mL of DMF and methanol (1 : 1). A white precipitate was obtained when
0.5 mL of 28% aqueous ammonia solution was added to this reaction mixture. The precipitate was
dissolved upon the addition of additional 0.5 mL of 28% aqueous ammonia solution. Then, the resulting
mixture was sealed in an 8 mL glass vessel and heated at 75 ˚C for 48 h. It was subsequently cooled to
room temperature (0.2 ˚C min-1), affording plate-like colorless crystals of 5. Yield: 61% (based on Zn).
Anal. Calcd. for C58H58N10O18Zn3 (M = 1379.28): C, 50.51; H, 4.24; N, 10.16. Found: C, 49.83; H, 4.92; N,
10.09. FT-IR (KBr, cm-1): 3421 (bs), 2962 (w), 1676 (s), 1612 (s), 1571 (s), 1490 (w), 1417 (m), 1385 (s),
1282 (w), 1249 (w), 1217 (w), 1072 (m), 1047 (w), 809 (s), 783 (s), 717 (w), 642 (m), 532 (w).
Crystal structure determinations
X-ray quality single crystals of the compounds were immersed in cryo-oil, mounted in a nylon loop and
measured at room temperature (1-5). Intensity data were collected using a Bruker APEX-II PHOTON 100
diffractometer with graphite monochromated Mo-Kα (λ 0.71069) radiation. Data were collected using
phi and omega scans of 0.5° per frame and a full sphere of data was obtained. Cell parameters were
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retrieved using Bruker SMART80-82 software and refined using Bruker SAINT80 on all the observed
reflections. Absorption corrections were applied using SADABS.80 Structures were solved by direct
methods by using the SHELXS-97 package81 and refined with SHELXL-97.81 Calculations were performed
using the WinGX System–Version 1.80.03.82 The hydrogen atoms attached to carbon atoms and to the
nitrogen atoms were inserted at geometrically calculated positions and included in the refinement using
the riding-model approximation; Uiso(H) were defined as 1.2Ueq of the parent nitrogen atoms or the
carbon atoms for phenyl and methylene residues, and 1.5Ueq of the parent carbon atoms for the
methyl groups. The hydrogen atoms of coordinated water molecules were located from the final
difference Fourier map and the isotropic thermal parameters were set at 1.5 times the average thermal
parameters of the belonging oxygen atoms. Least square refinements with anisotropic thermal motion
parameters for all the non-hydrogen atoms and isotropic ones for the remaining atoms were employed.
Crystallographic data are summarized in Table S1 (Supplementary Information file) and selected bond
distances and angles are presented in Table S2. CCDC 1046910-1046914 contain the supplementary
crystallographic data for this paper. These data can be obtained free of charge from The Cambridge
Crystallographic Data Centre via www.ccdc.cam.ac.uk/data_request/cif.
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Results and Discussion
Syntheses and Characterization
The hydrothermal reaction, at 75oC, of 5-acetamidoisophthalic acid (H2L) with zinc(II) nitrate
hexahydrate (in stoichiometric amounts) in the presence of dimethyl formamide and methanol mixture,
formamide or N-methylformamide leads to the formation of [Zn(L)(H2O)2]n (1),
[Zn(L)(H2O)2]n·n(formamide) (2) or [Zn(L)(H2O)2]n·n(N-methylformamide) (3), respectively (L = 5-
acetamidoisophthalate) (Scheme 1). When the hydrothermal reaction of H2L with zinc(II) nitrate
hexahydrate is performed in a different molar ratio (1:2) and at a higher temperature (85oC),
[Zn(L)(H2O)(formamide)]n (4) is formed (Scheme 2). In the presence of 4,4’-bipyridine and in a mixture of
DMF and methanol, [Zn3(L)2(formate)(4,4’-bipyridine)3]n·2n(DMF)·2n(H2O) (5) is obtained (Scheme 2).
During the hydrothermal processes, DMF was hydrolyzed to dimethylamine and formic acid, the latter
coordinating the metal in the basic form.
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Scheme 1 Synthesis and structural representation (repeating units) of 1 – 3.
Due to their insolubility in common solvents, the NMR spectra of these frameworks could not be run,
but they were characterized by IR spectroscopy, single crystal X-ray diffraction, thermogravimetric and
elemental microanalysis.
Scheme 2 Synthesis and structural representation (repeating units) of 4 and 5.
In the IR spectra, the characteristic strong bands of coordinated carboxylate groups in 1-5 appear at
1580–1562 cm-1 and 1385-1326 cm-1 for the asymmetric and the symmetric stretching wavenumbers,
respectively. The bands in the regions of 1637–1612 cm-1 and 1424–1417 cm-1 are attributed to the C=C
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stretching frequency of the aromatic rings,83,84 and those at 1698-1676 cm-1 to the C=O of the amide
group.
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Crystal structure analysis
Compounds 1-5 crystallize in space groups P21 (1), P21/m (2), P-1 (3 and 4) and C2/c (5). Compound 1 has
a left-handed helix, while 2 and 3 have zig-zag type 1D chains; compound 4 features a 1D chain of fused
16- and 8-membered metallacycles and 5 a 2D architecture with 4, 4’-bipyridine as secondary ligand.
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Figure 1 A structural unit of the helical type 1D chain of 1 with partial atom labelling scheme.
The structural units of 1, 2 and 3 are similar. These polymers are pseudo-polymorphic species owing to
the absence (in 1) or presence of solvent molecules (in 2 and 3). The asymmetric units of 1-3 contain one
zinc(II) ion, one L2- ligand, two (or only one, in 2) coordinated water molecules and one non-coordinated
molecule of formamide (in 2) or N-methylformamide (in 3) (Scheme 1). The asymmetric unit of 4 also
contains one L2- ligand and one the Zn2+ ion and, additionally, one coordinated water and one
coordinated formamide molecules, while that of 5 encompasses one L2- ligand and one formate moiety,
two zinc cations, one and a half bypiridine and a non-coordinated DMF and water molecules.
A
B
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Figure 2 (A) Left-handed helical structure of 1. (B) Node-and-linker-type descriptions of the 1D
coordination framework in 1, the metal nodes being represented in green and the linkers in pink color.
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The Zn2+ ions assume tetrahedral geometries in 1 and 2 (τ4 = 0.93 and 0.83, respectively),85 trigonal
bipyramidal in 3 and 4 (τ5 = 0.54 and 0.62, respectively)86 and octahedral in 5 where Zn1 is in a more
distorted environment compared to Zn2, as demonstrated by the corresponding quadratic elongations
and angle variances (1.073 and 181.20 º2 against 1.001 and 2.32 º2, in this order).87
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A
B
C
Figure 3 Crystal structures of 2 (A) and 3 (B) with partial atom labelling schemes. (C) Node-and-linker-
type descriptions of the 1D coordination frameworks in 2 and 3, the metal nodes being represented in
green and the linkers in pink color.
The coordination types of the carboxylate groups in 1–5 are diverse, assuming the non-bridging
monodentate mode in 1 and 2. This type of linkage also occurs in 3 and 4 with, additionally, the
chelating bidentate fashion in the former and the bridging bidentate (syn-syn-μ-carboxylate) in the
latter. The bridging bidentate chelation mode (syn-syn-type) is the one present in 5.
The coplanarity of the carboxylate groups and the phenyl ring in L2‒ are worth to be mentioned being
expressed by the CaromaticCaromaticCcarboxylateO (hereafter denoted by CCCO) torsion angles. In 1 this
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parameter assumes values of 129.2(4)º and 178.7(4)º thus giving rise to ZnOCO torsion angles of
23.3(5)º and 11.0(5)º, in this order, ultimately resulting in the helical nature of this polymer (Fig. 2). The
CCCO and the ZnOCO torsion angles in 2 are of 180º and 0.0º, respectively, the reason why this 1D
polymer is markedly flat. Polymers 3 – 5 present CCCO and ZnOCO torsion angles that vary in the ranges
of 166.9(3) – 179.1(2)º and 3.1(3) – 18.2(6)º, respectively. Concerning the acetamido CaromaticNCC torsion
angles, they adopt values higher than 171.7(4)º evidencing the approximate coplanarity (precise, in the
case of 2) between this group and the phenyl ring.
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The Zn-O bond distances are in the usual range of 1.943(2) – 2.630(4) Å, the highest value only found in
5 and resulting from the chelating bidentate coordination mode of formate, but still within the sum of
the Van der Waals radii of Zn and O.
A
B
Figure 4 Hydrogen bonded networks of 2 (A) and 3 (B) with hydrogen bonding interaction drawn in black
dotted lines. N-methylformamide molecules (in B) are represented in spacefill model.
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O
O
NH2
Zn
O
H2O
O
O
NH2
O
H2O
O
HN
O
O
Zn
O
O
O
O
Zn
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O
O
NH
OH2
NH2
NH2
O
O
Zn
H2O
O
O
O
A
B
C
D
Figure 5 Perspective view with partial atom labelling scheme (A) and schematic representation (B) of a
fragment of polymer 4. (C) One dimensional structure of complex 4 running along the crystallographic c
axis. (D) Node-and-linker-type descriptions of 4, the metal nodes being represented in green and the
linkers in pink color.
In 4 the metal cations are involved in alternating condensed C2O4Zn2 and C10O4Zn2 metallacycles that
construct a 1D polymeric assembly (Figure 5C).
In 5, the μ3-L2‒ and the μ-formate ligands bridge the Zn atoms and form ~Zn1-(μ-COO)L-(μ-O)formate-Zn2-
(μ-COO)L-(μ-O)formate-Zn1~ trinuclear cores which are further inter-connected giving 16-membered
C10O4Zn2 rings, thus generating wave like chain motifs parallel to the ac plane (Figure 6B). These are
further extended into a 2D metal-organic layer by means of the µ-4,4’-bypiridine. The packing view of 5
is characterized by channels along the crystallographic a axis (Figure 6B) with approximate dimension of
11.39 x 7.59 Å2, which are occupied by DMF and water molecules.
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5
The minimum Zn···Zn separation in these polymers vary in the order 3.6878(6) (4) < 3.7905(5) (5) <
4.3935(5) (2) < 4.5627(5) (3) < 6.3870(7) (1) Å.
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A
B
C
Figure 6 (A) Trinuclear secondary building block unit of the coordination polymer 5 with partial atom
labelling scheme. (B) 2D packing diagram of 5 (water molecules are represented as spacefill model). (C)
Node-and-linker-type descriptions of 5, the metal nodes being represented in green, the linkers in pink,
4,4’-bipyridine in red and formate anion in blue color.
Non-covalent interactions (O–H···O, N–H···O and C–H···O. Table S2, supplementary information) are
found in 1 – 5, stabilizing the structures and extending them to 3D. The 1D chains of 1 are inter-
connected via intricate water···carboxylate contacts; the 1D chains of 2 are involved in a 2D network (in
the ac plane) by means of NH···O (acetamido···formamide, formamide··· acetamido and
formamide···carboxylate) interactions, ultimately expanding to the third dimension by means of
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water···carboxylate contacts; the 1D chains of 3 are also tangled in OH···O (water···methylformamide,
water···carboxylate and water···acetamido) and in NH···O (acetamido···methylformamide and
methylformamide···carboxylate) contacts.
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The non-covalent interactions in 4 (Table S2) are also of the expected types of OH···O (water···acetamido
and water···carboxylate) and N-H···O (formamide···carboxylate formamide···acetamido and
acetamido···formamide). The metal-organic network of 5 is reinforced via intermolecular H-bonds (Table
S2) involving the crystallization water molecules which simultaneously act as donors (to carboxylate
groups) and as acceptors (from the acetamido groups).
Structures 1 – 3 have similar types of topologies88,89 and can be represented as 2-connected uninodal
nets (Figure 2B and 3C) with topological type 2C1, 4 features a 3-connected uninodal net with a
topological type SP1-periodic net (Figure 5D) and 5 reveals a 2,2,2,3,5,6-connected hexanodal net.
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Catalytic activity of the Zn coordination polymers in the Knoevenagel condensation
The Knoevenagel condensation (Scheme 3) of aldehydes with active methylene compounds is one of the
most useful C–C bond forming reactions having wide applications for the synthesis of fine chemicals.63-76
This condensation is generally catalyzed by bases or Lewis acids and widely studied in homogeneous
systems.90,91 Only a few studies have employed heterogeneous catalysts including metal organic
frameworks.92-96 Recently, Kitagawa et al.73 and Zhou et al.76 reported that amide functionalized MOFs
are quite effective for Knoevenagel condensation. Besides that, some Zn-MOFs can also catalyze this
condensation in a heterogeneous way.35,64 Thus, the development of suitable MOFs or coordination
polymers based catalysts for this reaction is a topic of great interest.97,98 It is known that base and acid
sites can catalyze this reaction and that bifunctional catalysts (e.g., amide functionalized MOFs) with
adequate acid–base pairs are more active than either purely acid or base catalysts.99-101
Recently, a few amide functionalized MOFs and Zn-MOFs were separately reported to act as catalysts
for the Knoevenagel condensation. Thus, our idea was to produce zinc coordination polymers from an
amide functionalized ligand and test their catalytic behaviour on this type of reaction. Our newly
synthesized zinc(II) coordination polymers have both a Lewis acid (Zn2+) and a basic centre (amide
group), and thus they possibly can act as bifunctional catalysts for this condensation. Moreover, our zinc
polymers (1-5) have different structural dimensionalities (1D and 2D) and orientations. For example,
compounds 1-3 are pseudo-polymorphic supramolecular isomers, having similar 1D type structures but
with different structural arrangements and packing. Hence, it would be interesting to see how the
different structural features affect the catalytic behaviour. To our knowledge only a few examples of
supramolecular isomers are known which act as catalysts for the Knoevenagel condensation reactions.75
Thus, we have tested the catalytic activity of the coordination polymers 1-5 as solid heterogeneous
catalysts in the Knoevenagel condensation of malononitrile with various aldehydes. In a typical reaction,
a mixture of benzaldehyde (51 μL, 0.50 mmol), malononitrile (66 mg, 1.0 mmol) and Zn-catalyst (5 mg of
1, 5.5 mg of 2, 6 mg of 3, 5 mg of 4 or 21 mg of 5, 3 mol%) was placed in a capped glass vessel, and then
1 mL THF was added into it. The mixture was heated at 40 ˚C for 1.5 h, and subsequently quenched by
centrifugation and filtration at room temperature. The filtrate was evaporated in vacuum to give the
crude product. The residue was dissolved in CDCl3 and analyzed by 1H NMR. The 1H-NMR spectra and the
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calculation of the yield for compound 3 in the Knoevenagel reaction is presented in the supporting
information (Figure S3).
6
7
8
9
By using benzaldehyde as a test compound, we found that 3 led to the highest product yield, as
compared to the other polymers after the same reaction time and at the same temperature.
Consequently, the optimization of the reaction conditions (temperature, reaction time, amount of
catalyst, solvent) was carried out in a model malononitrile–benzaldehyde system with 3 as the catalyst
(Scheme 2 with typical reaction conditions; Table 1).
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CN
CHO
NC
Catalyst
+ NC CN
THF, 40oC, 90 min
Scheme 3 Knoevenagel condensation reaction of benzaldehyde with malononitrile
Under the above typical conditions (3 mol% of solid 3 at 40˚C with THF as the best solvent, as indicated
below), a conversion of 98% of benzaldehyde into 2-benzylidenemalononitrile is reached (entry 5, Table
1) after 1.5 h. With compounds 1, 2, 4 and 5, yields of 91%, 89%, 78% and 61% were obtained,
respectively. Hence, our five coordination polymers activities follow the order of 3 > 1 ≈ 2 > 4 > 5. The
relationship between structure and catalytic activity in the present study is not clearly understood.
However, the highest conversation shown by the compound 3 may be due its packing arrangement
where the 1D chains are hydrogen bonded with one another and form a 2D sheet. The N-methyl
formamide molecules trapped inside may eventually assist the substrate molecules (benzaldehyde and
malononitrile) to form acid base pairs with metal centres. In the other cases (for 1, 2, 4 and 5) the tight
packing doesn’t support the above hypothesis.
The plot of yield versus time for the Knoevenagel condensation reaction of benzaldehyde and
malononitrile with compound 3 is presented in Figure 8A.
A
B
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Figure 8 Plots of yield vs. time for the Knoevenagel condensation reaction of benzaldehyde and
malononitrile in the presence of catalyst 3. (A) In THF (black curve) and upon separation of catalyst 3
(red curve). (B) In the presence of several solvents.
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Blank reactions were tested with benzaldehyde in the absence of catalyst, at 40˚C in THF, and no
conversion of aldehyde into 2-benzylidenemalononitrile was detected, after 1.5 h (entry 19, Table 1).
The reaction also did not take place by using the free ligand H2L instead of catalyst 3 (entry 20, Table 1).
We have also checked the reactivity of different zinc(II) salts and ZnO in THF and the obtained reaction
yields are much lower, in the range of 22-43% (entries 21-25, Table 1). Moreover, we have performed
this condensation reaction by using 1:1 mixtures of ligand H2L and Zn(II) salts and the obtained yields lie
between 21 and 30% (entries 26-28, Table 1), not supporting a catalytic cooperative role. In addition, we
have also tested the activity of various metal oxides (different particle size) towards the same reaction
under similar conditions and the observed yields are in the 9-53% range (entries 29-34, Table 1). The
obtained results indicate that our catalyst 3 is much better than the tested metal oxides under
equivalent reaction conditions.
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Table 1
Optimization of the parameters of the Knoevenagel condensation reaction between benzaldehyde and malononitrile with 3
as the catalysta
Entry
Catalyst
Time (h)
Amount of
Catalyst (mol%)
3.0
T (˚C)
Solvent
Yield (%)b
TONc
1
2
3
4
5
3
3
3
3
3
0.25
0.5
0.75
1
40
40
40
40
40
THF
THF
THF
THF
THF
33
53
63
76
98
11
18
21
25
33
3.0
3.0
3.0
3.0
1.5
6
7
8
3
3
3
1.5
1.5
1.5
1.0
5.0
7.0
40
40
40
THF
THF
THF
77
97
98
77
18
14
9
3
3
3
1.5
1.5
1.5
3.0
3.0
3.0
40
40
40
CH3CN
CH2Cl2
MeOH
86
70
75
29
23
25
10
11
RT (15oC)
RT (15oC)
12
13
14
3
3
3
1.5
6.0
1.5
3.0
3.0
3.0
THF
THF
THF
40
97
88
13
32
29
25
15
16
17
18
1
2
4
5
1.5
1.5
1.5
1.5
3.0
3.0
3.0
3.0
40
40
40
40
THF
THF
THF
THF
91
89
78
61
30
29
26
20
19
Blank
1.5
-
40
THF
No Reaction
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20
H2L
Zn(NO3)2.6H2O
Zn(OAc)2.2H2O
ZnSO4.7H2O
ZnCl2
1.5
1.5
1.5
1.5
1.5
1.5
1.5
3.0
40
40
40
40
40
40
40
THF
THF
THF
THF
THF
THF
THF
No Reaction
-
21
3.0
3.0
3.0
3.0
3.0
3.0
41
39
22
29
43
24
14
13
7
22
23
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25
26
10
14
8
ZnO
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H2L +
Zn(NO3)2.6H2O
H2L +
ZnSO4.7H2O
H2L + ZnCl2
Al2O3
27
1.5
3.0
40
THF
21
7
28
29
30
31
32
33
1.5
1.5
1.5
1.5
1.5
1.5
1.5
3.0
3.0
3.0
3.0
3.0
3.0
3.0
40
40
40
40
40
40
40
THF
THF
THF
THF
THF
THF
THF
30
21
25
53
13
9
10
7
V2O5
8
CdO
17
4
MoO2
PbO2
3
34
HgO
26
8
a
Reaction conditions: 3.0 mol% of catalyst 3, solvent (THF) 1 mL, malononitrile (66 mg, 1.0 mmol) and
benzaldehyde (0.50 mmol). bCalculated by 1H NMR. c Number of moles of product per mole of catalyst.
The effects of temperature, catalyst amount and solvents were also tested. The increase of the amount
of catalyst 3 from 1.0 to 3.0 mol% enhances the product yield from 77 to 98%, but further increase
amount of catalyst leads to no significant increase in catalytic activity (entries 6–8, Table 1).
To select the most suitable solvent, experiments with various solvents (CH3CN, CH2Cl2, THF and MeOH)
have been carried out with compound 3, and the corresponding plots of yield vs. time are presented in
Figure 8B. The results indicate that THF (yield of 98%) is the best solvent, whereas the worst one is
CH2Cl2 (70% yield) for the same reaction time (1.5 h) (Table 1, entries 5 and 10). In methanol or
acetonitrile, the yield of 86% or 75%, respectively, was obtained (Table 1, entries 9 and 11) after 1.5 h.
Increasing the temperature from 15 to 40˚C improved the 2-benzylidenemalononitrile yield from 40 to
98% (entries 12 and 5, Table 1). However, we have obtained 97% of yield in 6 h at 15˚C (room
temperature) (entry 13, Table 1).
Table 2 Knoevenagel condensation reaction of various aldehydes with malononitrile
with catalyst 3a
Entry
compound
Yieldb(%)
100
TONc
33
1
2
26
8
3
4
5
94
70
86
31
23
28
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a Reaction conditions: 3.0 mol% of catalyst 3, solvent (THF) 1 mL, malononitrile (66 mg, 1.0 mmol) and
aldehyde (0.50 mmol); reaction time of 1.5 h. bCalculated by 1H NMR. c Number of moles of product per
mole of catalyst.
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We also investigated the catalytic activity of 3 with different types of substituted aromatic aldehydes in
the reaction with malononitrile. The results are summarized in Table 2. p-Nitrobenzaldehyde produced
the maximum yield (100%), while the lowest one (26%) was obtained for p-methoxybenzaldehyde,
suggesting that an electron-withdrawing substituent promotes the reactivity, in contrast to an electron-
donating moiety, what may be related with an increase of the electrophilicity of the substrate in the
former case.
In order to perform the catalyst recycling experiments, the used catalyst 3 (separated by centrifugation
of the supernatant solution) was washed with THF and dried in air. It was then reused for the
Knoevenagel condensation reaction as described above. The catalyst 3 was recycled in three consecutive
experiments, and its activity remained essentially the same (Figure S1). FT-IR spectra of catalyst 3 taken
before and after the reaction suggest that the structure of the solid was retained (Figure S2A). We have
also performed powder X-ray diffraction with internal standard (NaCl) of catalyst 3 before and after the
condensation reaction and observed only a slight difference (2%) in peak intensity after the reaction
(Figure S2B). These experiments are indicative that the material essentially remains intact during the
catalytic process.
To further verify the heterogeneity of the system, a procedure similar to that of Sheldon et al. was
followed.102 We performed a controlled experiment, removed the catalyst by centrifugation and the
catalyst free reaction solution was kept under the same conditions and monitored by NMR along the
time to determine whether the metal component dissolved appreciably from the solid structure of our
catalyst. In our experiment, the catalyst 3 was removed by filtration from the mixture once the
conversion was up to ca. 53% (after 30 min reaction time), whereupon the supernatant fluid was stirred
for an additional 1 h under the same reaction conditions. As shown in Fig. 8A, after separation of the
solid catalyst, no conversion of benzaldehyde is observed. These results demonstrate that the catalysis is
heterogeneous in nature. Additionally, the filtrate solution, after the separation of the catalyst, was
evaporated to dryness and the amount of zinc determined, being only 0.02% of the amount used in the
reaction, thus ruling out any significant leaching of the catalyst.
There are some reports on coordination polymers which are catalysts for this kind of reaction,63-76 and a
comparison with our catalyst 3 is shown in Table 3. The obtained yields in our system are usually higher
than for the other reported zinc(II) frameworks in which the reaction of benzaldehyde and
malononitrile, after a longer time and at a higher temperature, leads to an overall yield that is lower or
identical to ours (Table 3, entries 2,3).69,70 Similarly, a 3D metal–organic framework built from nickel(II)
ions as connectors and methanetetrabenzoate ligands produced 78% yield after 6 h at 130oC (Table 2,
entry 4).71 Moreover, when we performed the reaction at room temperature with our catalyst 3, a 97%
yield was reached only in 6 h (Table 3, entry 6), which is a much lower time than those for other
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reported Cd(II) and Pb(II)-MOFs (Table 3, entries 7 and 8).73,74 In comparison with other catalysts, ours
have the advantages of being rather cheap, easy-to-prepare and highly active at low temperature.
Moreover, they are recyclable without appreciable loss of activity.
Table 3: A comparison of catalytic activity of various coordination polymers in the Knoevenagel condensation
reaction of benzaldehydes and malononitrile
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Solvent/Temp/Time
THF/ 40°C/ 1.5 h
Aldehydes
Entry
1
Catalyst
Yield (%)
98
Reference
This work
3
Benzaldehyde
2
3
4
Zn2dobdc
Toluene/70°C/ 24 h
Ethanol/60°C/ 2 h
p-xylene/ 130°C/ 6 h
Benzaldehyde
Benzaldehyde
Benzaldehyde
77
99
78
69
70
71
Zn2(tpt)2(2-atp)I2
{[Ni4(μ6-MTB)2(μ2-
H2O)4(H2O)4]·10DMF·11H2O}n
[Tb(BTATB)(DMF).
5
CH3CN/ 60°C/ 24 h
Benzaldehyde
99
72
2(H2O)]·DMF·2H2O
6
7
3
THF/ RT/ 6 h
C6H6/RT /12 h
Benzaldehyde
Benzaldehyde
97
98
This work
[Cd(4-btapa)2(NO3)2]. 6H2O. 2DMF
Pb(cpna)2.2DMF.6H2O
3
73
74
8
CH3CN/ RT/ 24 h
THF/ 40°C/ 1.5 h
CH3CN/ 60 °C/ 6 h
Benzaldehyde
100
100
99
9
4-nitrobenzaldehyde
4-nitrobenzaldehyde
This work
75
10
{[Cd(NH2_bdc)(bphz)0.5]·DMF·H2O}n
dobdc = 2,5-dioxidoterephthalate; MTB = methanetetrabenzoate; DMF = N,N’-dimethylformamide; BTATB = 4,4′,4″-(benzene-1,3,5-
triyltris(azanediyl))tribenzoate; 4-btapa = 1,3,5-benzene tricarboxylic acid tris[N-(4-pyridyl)amide]; cpna = N-(4-carboxyphenyl)isonicotinamide
1-oxide; NH2_bdc = 2-aminobenzenedicarboxylic acid; bphz=1,2-bis(4-pyridylmethylene) hydrazine; tpt = tris (4-pyridyl) triazine; 2-atp = 2-
aminoterephthalate.
CN
CHO
H
NC
+
NC
CN
+
H2O
[
Zn
]
O
CN
CN
CN
H
C
C
H
C
H
H
C
C
O
H
N
H
O
[
]
Zn
O
[
]
O
Zn
Scheme 4: Proposed catalytic cycle for the Knoevenagel condensation reaction catalyzed by 1-5.
A possible mechanism for the Knoevenagel condensation catalyzed by 1-5 is presented in Scheme 4, on
the basis of reported proposals.103 In our coordination polymers, the zinc centre (Lewis acid site)
interacts with the carbonyl group of the benzaldehyde, producing a polarization of this group and thus
increasing the electrophilic character of the carbonylic carbon atom. This polarization favours the attack
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from the malononitrile. The interaction of a cyano group of malononitrile with the Lewis acid (zinc site)
increases the acidity of the methylene group which enhances the deprotonation of malononitrile. The
basic sites (carboxylate-O or amide-O) can abstract the proton from the methylenic group to generate
the corresponding nucleophilic species which attacks the carbonyl group of benzaldehyde with C-C bond
formation (aldol condensation) and dehydration. If the acid and basic sites of the bifunctional catalysts
are well balanced, a concerted and synergic action can take place.
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Conclusion
Five zinc(II) coordination polymers constructed with 5-acetamidoisophthalic acid (H2L) were synthesized.
They exhibit 1D (1, 2, 3 and 4) and 2D (5) structures, on account of the various coordination modes of
the ligand. Single-crystal X-ray diffraction analysis revealed that 1, 2 and 3 are pseudo-polymorphic
supramolecular isomers, with 1 having an helical assembly, but 2 and 3 exhibiting similar zig-zag type
structures containing different guest molecules (formamide in 2 and methylformamide in 3). Compound
4 is a 1D coordination polymer with fused 8-membered and 16-membered dimetallic rings, whereas
compound 5 shows a two dimensional layered structure with trimetallic cores. Zinc(II) coordination
numbers and geometries vary from tetrahedral (in 1 and 2) to trigonal bipyramidal (in 3 and 4) and to
octahedral (in 5).
These coordination polymers act as heterogeneous catalysts for the Knoevenagel condensation of
aldehydes with malononitrile, at low temperature. Among the five coordination polymers, 3 is the most
effective catalyst for this condensation reaction. It effectively catalyzes the reaction of various aldehydes
and malononitrile producing the corresponding benzylidenemalononitriles in high yields, which depend
on the electrophilicity of the substrate. Moreover, the catalyst is stable and recyclable. Moreover, the
present study displays an example of pseudo-polymorphic supramolecular isomers acting as
heterogeneous catalysts for the Knoevenagel condensation. It also presents the dependence of the
catalytic properties on the supramolecular structural arrangements.
This study also provides further evidence that zinc(II) coordination polymers can be utilized as effective
heterogeneous catalysts, under mild conditions, in this important organic reaction. Further explorations
into the uses of this catalyst family in other organic transformations, as well as mechanistic
investigations, are ongoing.
Supporting Information
CIF files and crystallographic data, bond distances, angles and hydrogen bonding tables for all
1
compounds (1-5), thermogravimetric analysis, FT-IR and PXRD before and after catalysis, H-NMR
spectra after catalysis, curve for recycling experiment. This material is available free of charge via the
Internet at http://pubs.acs.org.
Acknowledgements
This work has been supported by the Foundation for Science and Technology (FCT), Portugal (project
UID/QUI/00100/2013). Authors AK and SH express their gratitude to the FCT for post-doctoral
fellowships (Ref. No. SFRH/BPD/76192/2011 and SFRH/BPD/78264/2011). Authors MFCGS and AJLP also
acknowledge the Russian Science Foundation for support to the synthesis with malononitrile and for the
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help in organizing the International Laboratory (grant 14-43-00017). Thanks are also due to the
Portuguese NMR Network (IST-UL Centre) for access to the NMR facility, and the IST Node of the
Portuguese Network of mass-spectrometry (Dr. Conceição Oliveira) for the ESI-MS measurements.
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Solvent dependent structural variation of zinc(II) coordination polymers and
their catalytic activity in the Knoevenagel condensation reaction
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Anirban Karmakar,* Guilherme M. D. M. Rúbio, M. Fátima C. Guedes da Silva,* Susanta Hazra,
and Armando J. L. Pombeiro*
Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais,
1049–001, Lisbon, Portugal. E-mail: anirbanchem@gmail.com; fatima.guedes@tecnico.ulisboa.pt;
pombeiro@tecnico.ulisboa.pt
Synopsis
5-acetamidoisophthalic acid is used to synthesize five new zinc(II) complexes which act as
heterogeneous catalysts for the Knoevenagel condensation reaction of aldehydes with an active
methylene compound.
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