Effecting structural diversity in a series of Co(ii)-organic frameworks by the interplay between rigidity of a dicarboxylate and flexibility of bis(tridentate) spanning ligands

Article abstract of DOI:10.1039/d0dt02153a

In a one-pot self-assembly reaction of Co(OAc)2·4H2O, thiophene-2,5-dicarboxylic acid (H2tdc) and four different bis(tridentate) polypyridyl spanning ligands under ambient conditions, a series of structurally diverse metal-organic frameworks has been synt

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DOI: 10.1039/D0DT02153A
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ARTICLE
Effecting structural diversity in a series of Co(II)-organic
frameworks by the interplay between rigidity of a dicarboxylate
and flexibility of bis(tridentate) spanning ligands
Received 00th January 20xx,
Accepted 00th January 20xx
Biswajit Laha,a Sadhika Khullar,b Alisha Gogiaa and Sanjay K. Mandal*a
DOI: 10.1039/x0xx00000x
In a one-pot self-assembly reaction of Co(OAc)2·4H2O, thiophene-2,5-dicarboxylic acid (H2tdc) and four different
bis(tridentate) polypyridyl spanning ligands under ambient conditions, a series of structurally diverse metal-organic
frameworks has been synthesised and characterized by single crystal X-ray diffraction: {[Co2(tdc)2(tpbn)(H2O)2]·solvent}n
(solvent = 2H2O, 1; solvent = 2CH3OH, 2H2O, 1a), [Co2(tdc)2(tphn)]·solvent}n (solvent = H2O, 2; solvent = CH3OH, 2.5H2O, 2a),
{[Co2(tdc)2(tpchn)(H2O)2]·solvent}n (solvent = 5H2O, 3; solvent = C2H5OH, 2H2O, 3a), and {[Co2(tdc)2(tpxn)]·solvent}n (solvent
= 6H2O, 4; when no solvent, 4a), where tpbn = N1,N1,N4,N4-tetrakis(pyridin-2-ylmethyl)butane-1,4-diamine, tphn =
www.rsc.org/
N1,N1,N6,N6-tetrakis(pyridin-2-ylmethyl)hexane-1,6-diamine, tpchn
=
N,N'-(cyclohexane-1,4-diylbis(methylene))bis(1-
(pyridin-2-yl)-N-(pyridin-2-ylmethyl)methanamine) and tpxn = N,N'-(1,4-phenylenebis(methylene))bis(1-(pyridin-2-yl)-N-
(pyridin-2-ylmethyl)methanamine). There is a profound effect of the nature of spacer between the alkyl nitrogens in the
spanning ligands (flexible vs semiflexible) on the molecular structures of 1a-4a. The notable differences are (a) the binding
mode of the tridentate part of polypyridyl ligands to the Co(II) center is facial in 1a, 3a and 4a but meridional in 2a, (b) the
Co(II) centers in 1a-3a are hexacoordinated (with a coordinated water in 1a and 3a) but are pentacoordinated in 4a, and (c)
the binding mode of tdc linker is bis(monodentate) in 1a, 3a and 4a but chelated in one end and monodentate in the other
end in 2a. Thus, the overall framework structure of 1a, 2a, 3a and 4a is cis-decalin type 2D polymer, ladder-shaped 1D
polymer, hexagonal 2D net and cis-decalin type 2D polymer, respectively. Their thermal stabilities have been established by
thermogravimetric analysis (TGA). The presence of an unsaturated metal center in 4 has provided us an opportunity for its
use as an efficient Lewis acid catalyst for the Knoevenagel condensation reaction of malononitrile with various aldehydes
(100% conversion in 60 minutes with 2 mol% catalyst in methanol).
Introduction
The design and construction of coordination compounds, particularly becomes a three-component system), which primarily acts as the
coordination polymers (CPs) and metal-organic frameworks (MOFs), capping ligand to block the coordination sites on the metal center for
have attracted the scientist fraternity very much because of their controlling the outcome of structural features with different
structural and topological variation, and their multidimensional topologies, is desirable but challenging. With respect to synthetic
application in various fields like gas storage and separation1-9
magnetism10-15 drug delivery16-25 NLO,26,27 luminescence and ratio of the components, and anions of the starting metal salts have
,
innovations, reaction conditions (temperature, solvent, pH, etc.), the
,
,
sensing28-37, catalysis,38-53 etc. These MOFs are constructed through been found to be important parameters.55-64 However, the effect of
coordination bonds between the metal center and donor atoms of the capping ligands is also a major factor to control the structure and
the ligand and/or linkers. For the synthesis of CPs and MOFs, a topologies of these coordination compounds. A structural variation
combination of metal ions/clusters and multitopic carboxylates (the in the capping ligand, while keeping the metal ion and an organic
so-called two-component system) has been explored extensively.54 linker the same, can be studied in a systematic way to understand its
On the other hand, the inclusion of another component (thus it effect.
In the past few years, we focused on the three-component
approach to understand the chemistry of bis(tridentate) polypyridyl
ligands and their derivatives for their (i) flexibility and rigidity of the
spacer between the two alkyl nitrogens, and (ii) binding (facial vs
meridional) of each tridentate part. Given the proven stability of the
frameworks for the use of rigid carboxylates, we reported diverse
CPs and MOFs with both aliphatic and aromatic rigid dicarboxylates
where the carboxylate groups are aligned at 180°. For example, we
reported the chemistry of Mn(II) and the shortest rigid aliphatic
aDepartment of Chemical Sciences, Indian Institute of Science Education and
Research Mohali, Sector 81, Manauli PO, S.A.S. Nagar, Mohali, Punjab 140306,
India. E-mail: sanjaymandal@iisermohali.ac.in
bDepartment of Chemistry, Dr B R Ambedkar National Institute of Technology
Jalandhar, Jalandhar, Punjab 144011, India.
† Electronic supplementary information (ESI) available: Crystallographic data of 1a-
4a in CIF format (CCDC 2010036-2010039, respectively); FT-IR and NMR spectra,
PXRD of 1a and 2a, and additional SCXRD figures and tables for 1a-4a. For ESI and
crystallographic data in CIF or other electronic format see DOI: 10.1039/x0xx00000x
This journal is © The Royal Society of Chemistry 20xx
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dicarboxylate (acetylene dicarboxylate, adc2-),57 and of Zn(II) and 2,6- Knoevenagel condensation, which is conventionallyVicewatAarltyiczleeOdnlibnye
naphthalene dicarboxylate (2,6-ndc2-)34 using the flexible bases or Lewis acids.47,84,85 Thus, we have successfully utilized
DOI: 10.1039/D0DT02153A
bis(tridentate) ligands. Diversity in these examples is also due to compound 4 in the condensation reaction of malononitrile with
various binding modes of carboxylate groups.
various aldehydes reaction, where it is found that only 2 mol % of it
For continuing with the available variables in our chosen three- in methanol gives 100% conversion in 60 mins.
component system, we aimed at investigating the effect of rigid
Herein, we report the synthesis and structural characterization of
thiophene-2,5-dicarboxylate (tdc2-) that enforces the carboxylic acid 1-4 by elemental analysis, FTIR spectroscopy, single crystal and
groups to stay aligned at an exocyclic angle (148°) unlike the linearity powder X-ray diffraction, and thermogravimetric analysis (TGA), and
observed for adc2- and 2,6-ndc2-. Although quite a large number of the catalytic property of 4.
examples with tdc2- are available in the literature, these are primarily
multitopic carboxylate-based CPs or MOFs of lanthanides.65-70
Furthermore, other examples are mostly based on divalent metal
Experimental section
Materials and methods
ions with or without a bifunctional N-based ligand as the third
component.71-83 In addition to the well-established flexibility of the
methylene chain length in the bis(tridentate) ligands, further semi-
flexibility is introduced by changing the backbone from
tetramethylene or hexamethylene to 1,4-dimethylenecyclohexane
to 1,4-xylyl in the polydentate ancillary ligand shown in Fig. 1 to
explore the chemistry of Co(II). The idea was to combine the effect
of spacers with the angularity and rigidity of tdc2-. In doing so, diverse
structures (cis-decalin type 2D polymer, ladder-shaped 1D polymer,
hexagonal 2D net and cis-decalin type 2D polymer) were observed
for {[Co2(tdc)2(tpbn)(H2O)2]·solvent}n (solvent = 2H2O, 1; solvent =
2CH3OH, 2H2O, 1a), [Co2(tdc)2(tphn)]·solvent}n (solvent = H2O, 2;
solvent = CH3OH, 2.5H2O, 2a), {[Co2(tdc)2(tpchn)(H2O)2]·solvent}n
Metal salts and other reagent grade chemicals were procured
from Sigma-Aldrich and were used as received. All solvents
were obtained from Merck, India. These solvents were used
without further purification. All reactions were carried out
under aerobic conditions at room temperature. The tpbn, tphn,
tpchn and tpxn ligands were prepared following the literature
procedures.58
Physical measurements
The 1H NMR spectra were recorded on a Bruker ARX-400
spectrometer in CDCl3 at 25 °C; the chemical shifts are reported
relative to the residual solvent signals. TGA were carried out
from 30 to 500 °C (at a heating rate of 10 °C min-1) under a
dinitrogen atmosphere using a Shimadzu DTG-60H instrument.
Elemental analysis (C, H, N) was carried out using a Mettler
CHNS analyzer. FT-IR spectra (KBr pellet, 400−4000 cm−1) were
measured on a Perkin-Elmer Spectrum I spectrometer. For the
powder X-ray diffraction (PXRD) data, a Rigaku Ultima IV
diffractometer was used as described earlier from this
laboratory.86
(solvent
= 5H2O, 3; solvent = C2H5OH, 2H2O, 3a), and
{[Co2(tdc)2(tpxn)]·solvent}n (solvent = 6H2O, 4; when no solvent, 4a),
respectively.
N
N
N
N
N
N
N
N
N
N
N
N
(tpbn)
(tphn)
Synthesis of compounds
N
N
{[Co2(tdc)2(tpbn)(H2O)2]·2H2O}n (1). In a 10 mL round bottom flask,
22.5 mg (0.05 mmol) of tpbn was dissolved in 1.5 mL of methanol. To
this clear solution, 24.9 mg (0.1 mmol) of Co(OAc)2·4H2O was added
and stirred for few minutes followed by the addition of 17.2 mg (0.1
mmol) of H2tdc. The reaction mixture was stirred for 6 h at room
temperature. A precipitate obtained was filtered, washed with
methanol, and vacuum dried. Yield: 44 mg (89%). Anal. Calc. (%) for
C40H44N6O12S2Co2 (MW 982.1767): C, 48.88; H, 4.51; N, 8.55. Found:
C, 48.498; H, 3.954; N, 8.319. Selected FTIR peaks (KBr, cm-1): 3399
(br), 3235 (br), 1607 (m), 1585 (br), 1572 (br), 1361 (br), 1338 (br),
772 (s).
N
N
N
N
N
N
N
N
N
N
(tpchn)
(tpxn)
Fig. 1 Structures of the bis(tridentate) ligands with a variation in spacer type.
When conducting a systematic study to develop interesting diverse
structural features in MOFs due to the binding modes of both
spanning ligands and carboxylate linkers, one of the goals is to find
unusual coordination environments of a metal center. Such a goal
turns out to be a benefit for obtaining a MOF with unsaturated metal
centers that are of great importance in activating small molecules
through catalysis. Fortunately, compound 4 is found to contain
unsaturated cobalt centers with a trigonal bipyramidal geometry. For
the synthesis of several fine chemicals and pharmaceuticals, one of
the most useful C−C bond-forming reactions is between aldehydes
and compounds containing active methylene groups, known as
{[Co2(tdc)2(tphn)]·H2O}n (2). It was synthesised using the same
procedure as 1 except 24 mg (0.05 mmol) of tphn was used instead
of tpbn. Yield: 48 mg (96%). Anal. Calc. (%) for C42H46N6O11S2Co2 (MW
992.8446): C, 50.81; H, 4.67; N, 8.46. Found: C, 51.00; H, 4.54; N,
8.43. Selected FTIR peaks (KBr, cm-1): 1606 (s), 1574 (m), 1545 (m),
1402 (s), 1343 (s), 771 (s).
2 | J. Name., 2012, 00, 1-3
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{[Co2(tdc)2(tpchn)(H2O)2]·5H2O}n (3). It was synthesised using the and scaling of the data, fitting of reflection profiles, VaienwdAortbiclteaOinnilninge
same procedure as 1 except 25.3 mg (0.05 mmol) of tpchn was used values of F2 and σ(F2) for each reflection. All DreOqIu: 1ir0e.1d03c9o/rDre0cDtTio0n2s15f3oAr
instead of tpbn. Yield: 35 mg (65%). Anal. Calc. (%) for Lorentz and polarization effects and an absorption correction
C44H56N6O15S2Co2 (MW 1090.9430): C, 48.44; H, 5.17; N, 7.70. Found: (SADABS) were also applied. The subroutine XPREP87 was used to
C, 48.30; H, 5.11; N, 7.70. Selected FTIR peaks (KBr, cm-1): 3400 (br), determine the space group and to generate files necessary for
3221 (br), 1712 (s), 1605 (s), 1573 (br), 1361 (m), 773 (s).
solution and refinement. Using Olex2,88 the structure was solved with
the ShelXT89 structure solution program using Intrinsic Phasing and
refined with the ShelXL90 refinement package using least squares
minimisation. All the non-hydrogen atoms were refined with
anisotropic displacement parameters unless otherwise stated. In
case of 2a, the oxygen atom of a water molecule with half occupancy
was refined isotropically. On the other hand, hydrogen atoms were
placed at ideal positions, wherever possible, to get a convergence of
refinement. In 1a, hydrogen atoms for the two carbons of the
methylene group and for the methanol solvent molecule could not
{[Co2(tdc)2(tpxn)]·6H2O}n (4). It was synthesised using the same
procedure as 1 except 24 mg (0.05 mmol) of tpxn was used instead
of tpbn. Yield: 48 mg (90%). Anal. Calc. (%) for C44H48N6O14S2Co2 (MW
1066.8801): C, 49.53; H, 4.53; N, 7.88. Found: C, 49.89; H, 3.70; N,
7.72. Selected FTIR peaks (KBr, cm-1): 1603 (m), 1570 (m), 1366 (br),
770 (s). As compounds 1-4 were practically insoluble in most of the
solvents, their single crystals were obtained by the direct layering of
the reactants in a solvent mixture.
The formulae in the crystal structures (1a-4a) only differ by solvent be included for the convergence of refinement. In 2a, hydrogens for
of crystallization as confirmed by FTIR spectroscopy. As an example, the water molecule with partial occupancy were not included.
the procedure for 1a is described below.
Crystallographic parameters and basic information pertaining to data
collection and structure refinement for all compounds are
summarized in Table 1. The hydrogen bonding parameters with
symmetry codes were generated by PLATON.91,92 The final positional
and thermal parameters of the non-hydrogen atoms for all
compounds are listed in the CIF files.
A solution of tpbn (6 mg, 0.013 mmol) in 0.2 mL methanol was placed
in a narrow glass tube. A solution of Co(OAc)2·4H2O (6.5 mg, 0.025
mmol) and H2tdc (4.5 mg, 0.025 mmol) in 0.4 mL methanol was
added very carefully along the sides of the tube on the top of tpbn
solution and kept undisturbed. Pink crystals suitable for SCXRD
analysis were obtained after a week. Yield: 10 mg (85%).
Results and discussion
General Protocol used for the Knoevenagel condensation reaction
Prior to the catalytic study, 4 was activated in a vacuum oven at 120 Synthesis and spectroscopic characterization
°C for 10 h. In a 5 mL screw cap glass vial, a mixture of an aldehyde
Compounds 1-4 were synthesized in a one-pot self-assembly at room
(0.5 mmol) and malononitrile (1 mmol) with a specified amount of
catalyst (2 mol%) and solvent (1 mL) were stirrred for the indicated
time at 25-30 °C. After the desired time, the organic solvent was
removed under vacuum and the product was extracted with water
and ethyl acetate. The catalyst was removed from the reaction
temperature by taking metal salt, ligand, and thiophene dicarboxylic
acid in a ratio of 2:1:2 in methanol with continuous stirring for 6 h as
shown in Scheme 1. The acetic acid by-product was easily removed
by washing the precipitate with a 1:1 mixture of acetonitrile and
toluene. Thus, the formation of 2D MOFs in very pure form at room
temperature in 24 hours is remarkable.
The FTIR spectra of 1-4 were recorded in the solid-state as KBr
pellets at room temperature. These spectra are shown in Fig. S1.
Except 2, where both chelated and monodentate carboxylate groups
are present, the asymmetric and symmetric stretch of the
carboxylate group ( values are in the range of 210-230 cm-1)
confirms monodentate binding of the carboxylate group in 1, 3 and
4. Similarly, peaks due to coordinated (in case of 1 and 3) and lattice
water molecules (in case of 1-4) are also observed in region 3450-
3225 cm-1. These data corroborate well with the structural finding
from the single-crystal X-ray diffraction analyses (vide infra).
mixture by centrifugation followed by filtration, and the
%
1
conversion was determined with the help of H NMR spectroscopy.
For catalyst recycling, it was further washed with CH2Cl2 and dried in
a vacuum oven.
Single crystal X-ray data collection and refinements
Upon evaluating the crystals with the help of a microscope, initial
crystal evaluation and data collection were performed on an
automated Kappa APEX II diffractometer (Mo Kα radiation, λ =
0.71073 Å) equipped with a CCD detector which is controlled by the
APEX2 program.87 With the help of SAINT87 subroutine the collected
data was processed for the integration of the intensity of reflections
tpbn
{[Co2(tdc)2(tpbn)(H2O)2]·2H2O}n (1)
tphn
{[Co2(tdc)2(tphn)]·H2O}n (2)
CH3OH
Co(OAc)2·4H2O + H2tdc
Stir for 24 h at RT
tpchn
{[Co2(tdc)2(tpchn)(H2O)2]·5H2O}n (3)
tpxn
{[Co2(tdc)2(tpxn)]·6H2O}n (4)
Scheme 1 Synthesis of 1-4.
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DOI: 10.1039/D0DT02153A
Table 1 Crystal structure data and refinement parameters for 1a-4a
1a
2a
3a
4a
Chemical formula
Formula Weight
Temperature (K)
Wavelength (Å)
Crystal system
Space group
a (Å)
C21H26CoN3O7S
523.44
C43H48Co2N6O11.50S2
1014.85
100(2)
C46H56 Co2N6O13S2
1082.94
100(2)
C44H36Co2N6O8S2
958.77
100(2)
100(2)
0.71073
Monoclinic
P21/c
0.71073
Triclinic
P-1
0.71073
Monoclinic
P21/c
0.71073
Monoclinic
P21/n
8.0732(2)
15.1381(5)
18.8040(6)
90
9.911(18)
15.89(3)
16.97(3)
117.14(2)
90.21(3)
105.58(2)
2
9.1292(10)
16.1977(18)
17.632(2)
90
9.643(2)
14.622(4)
14.166(4)
90
b (Å)
c (Å)
α (°)
β (°)
94.055(2)
90
92.443(7)
90
93.433(16)
90
γ (°)
Z
4
2
2
Volume (Å3)
Density (g/cm3)
μ (mm-1)
2292.34(12)
1.517
2266.0(7)
1.487
2604.9(5)
1.381
1993.8(9)
1.597
0.887
0.891
0.782
0.0537
2.00 to 25.00°
984
Theta range
F(000)
1.73 to 25.03°
1088
1.36 to 25.14°
1052
1.71 to 25.03°
1128
Reflections collected
Independent reflections
Reflections with I >2σ(I)
Rint
19547
23875
19903
12474
4067
7966
4591
3483
3219
5018
3192
3073
0.0431
0.0819
0.0704
316
0.0537
280
Number of parameters
GOF on F2
311
589
0.974
1.067
1.031
0.894
a
b
R1 /wR2 (I > 2σ(I))
0.0629/0.1548
0.0638/0.1798
0.0698/0.1889
0.0330/0.1066
a
R1 /wR2b (all data)
0.0792/0.1680
0.1074/0.2098
0.1049/ 0.2130
0.0378/0.1142
Largest diff. peak and
hole (eÅ-3)
1.578 and -1.365
1.175 and -0.908
1.748 and -0.527
0.373 and -0.477
aR1 = ∑||Fo| - |Fc||/∑|Fo|. bwR2 = [∑w(Fo2 - Fc2)2/∑w(Fo2)2]1/2, where w = 1/[σ2(Fo2) + (aP)2 + bP], P = (Fo2 + 2Fc2)/3.
Description of structures
Compound 1a crystallizes in the monoclinic P21/c space group. In the
asymmetric unit, there are one Co(II), one-half of the tpbn ligand,
one tdc2-, a coordinated water molecule, one lattice water, and one
lattice methanol molecule (Fig. 2). A labelled diagram of 1a is shown
in Fig. S2. Each Co(II) ion is octahedrally surrounded with a N3O3
coordination environment where the N-donor atoms are from the
tpbn ligand, two O-donor atoms are from two different carboxylate
groups of tdc and the other O-donor atom is from a water molecule
(Fig. 2). The carboxylate binds in a monodentate syn-anti mode. Both
Co-Npyr bonds (2.106 Å and 2.113 Å) are shorter than the Co-Nalkyl
bond 2.216 Å. Similarly, the Co-Owater bond (2.167 Å) is longer than
the Co-Ocarb bonds (2.061 Å and 2.093 Å).
Fig. 2 Coordination environment around and geometry of the Co(II)
center with labelled donor atoms in the asymmetric unit of 1a
(solvent of crystallization are not shown for clarity).
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These values are in a range similar to those reported in the
literature.32,48,49,66-70 The Ocarb−Co−Npy angles are 89.37(14)°
(O1-Co1-N1), 97.62(14)° (O1-Co1-N3), 86.37(13)° (O3-Co1-
N3)and 166.25(14)° (O3-Co1-N3). The Ocarb−Co−Nalkyl angles are
in the range of 89.26(14)° to 165.63(14)°. Selected bond
distances and bond angles are listed in Table S1. Hydrogen bond
parameters are listed in Table S2. The distances between the
metal centers and uncoordinated oxygen atoms (Co1···O2 and
Co1···O4) are 3.373 Å and 3.442 Å in 1a, respectively. Two Co
centers connected by the tdc linker are separated by 10.764 Å,
whereas those connected by the spanning tpbn ligand are
separated by 8.843 Å. Each tridentate eDnOdI:o1f0t.1p0b3n9/bDi0nDdTs0i2n15a3A
facial manner (97.12°) to the metal centers while the tdc binds
to the metal ion in a monodentate fashion on both ends. On the
basis of this connectivity, six Co centers that form a cavity with
a dimension of 19.270 × 10.764 Å (distances between two tdc
linkers on opposite sides) adopt
a chair conformation,
extending to a cis-decalin type 2D polymer structure (Fig. 3a).
Its space-filling representation (Fig. 3b) further shows the
cavities in 1a.
Fig. 3 Schematic view of (a) 2D structure in 1a with a fused chair (cis-decalin) conformation, and (b) the corresponding space fill
representation.
1
Compound 2a crystallizes in the triclinic P space group. The
binds to the Co(II) centers in meridional fashion, which is
unit cell contains two independent molecules of 2a. Two and
one-half water molecules and a methanol molecule are also
found as solvent of crystallization per dinuclear repeat unit. A
labelled diagram of 2a is shown in Fig. S3. The coordination
environment around Co(II) is N3O3 (Fig. 4a), where one end of
the ligand provides three N-binding centers, and three O-atoms
are coming from two carboxylate groups of two different tdc2-,
one binding in chelating bidentate fashion and the other in
monodentate fashion. Each tridentate part of the tpbn ligand
evident from Npy-Co-Npy angles: N1-Co1-N4, 156.51 (19)° and
N2-Co2-N6, 156.6 (2)° Due to this change in the binding mode
.
of tphn compared to tpbn, the tdc2- binds to the Co(II) centers
in a monodentate and chelated manner. This does not allow any
coordinate water to bind to the Co(II) center. The Co2(tphn)
units are connected by tdc2-, almost in the perpendicular
direction of tphn. The overall structure of 2a is a ladder-shaped
1D polymer with Co(II), where tdc is along the sides of the
ladder and tphn forms the steps (Fig. 4a).
Fig. 4 (a) View of extended 1D ladder structure and coordination environment around the hexacoordinated Co(II) center of 2a; color
codes – cobalt: pink, sulphur: yellow, carbon: gray, nitrogen: blue, and oxygen: red. Hydrogen atoms of carbon are omitted for clarity.
(b) Schematic representation of the rectangular section, containing four Co centers at the corners, in 2a with dimensions.
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Fig. 5 Schematic representation of the overlap of two 1D ladders in 2a.
The bond distances are: Co-Npyr 2.087 Å and 2.107 Å; Co-Nalkyl
2.212 Å; Co-Ocarb 2.236 Å, 2.130 Å and 2.044 Å in one molecule
and Co-Npyr 2.096 Å and 2.125 Å; Co-Nalkyl 2.207 Å; Co-Ocarb
2.235 Å, 2.125 Å and 2.055 Å in the other molecule. These
values are similar to those for 1a. The Ocarb−Co−Npy angles are
102.50° (O1-Co1-N1), 93.16° (O4-Co1-N1), 91.28° (O2-Co1-N3)
and 93.58° (O2-Co1-N1). Selected bond distances and bond
angles are listed in Table S1. Hydrogen bond parameters are
listed in Table S2. The distance between the metal center and
uncoordinated oxygen atom (Co1···O3) is 3.406 Å. As shown in
Fig. 4b, the dimensions of the rectangle unit of the ladder
structure containing four Co centers in two independent
molecules are 9.911 Å x 12.600 Å and 9.911 Å x 12.582 Å (the
distances between two benzene rings of tphn and two tdc
linkers, respectively). In the overall structure of 2a, two such
ladders of the independent molecules are found to overlap as
shown in Fig. 5.
Based on the binding of tdc and tpchn, a hexagon consisting of
six Co(II) centers with dimensions of 21.528 Å x 10.558 Å
(distances between two tdc and two Co, respectively) is present
in the 2D polymeric structure of 3a (Fig. 7a). Its space-filling
representation (Fig. 7b) further shows the cavities in 3a.
Compound 3a crystallizes in the monoclinic P21/c space group.
The asymmetric unit consists of one Co(II), half of tpchn, one
tdc2-, one coordinated water and one half of ethanol molecule
and one water molecule of crystallization. The Co(II) is
octahedrally surrounded by N3O3 coordination environment
(Fig. 6). A labelled diagram of 3a is shown in Fig. S4. All the three
N-atoms are from one end of the ligand and O-atoms are from
two monodentate carboxylate groups (binds in a syn-anti
mode) and one coordinated water molecules. The bond
distances are 2.125 Å and 2.089 Å (Co-Npyr), 2.229 Å (Co-Nalkyl),
2.093 Å and 2.064 Å (Co-Ocarb) and 2.131 Å (Co-Ow). These
values are similar to those for 1a. The Ocarb−Co−Npy angles are
93.30(16)° (O3-Co1-N2), 93.21(16)° (O3-Co1-N1), 171.62(17)°
(O8-Co1-N2) and 86.59(17)° (O8-Co1-N1). The Ocarb−Co−Nalkyl
angles are in the range of 100.39(17)° to 164.73(16)°. Selected
bond lengths and bond angles are listed in Table S1. Hydrogen
bond parameters are listed in Table S2.
Fig. 6 Coordination environment around and geometry of the
Co(II) center with labelled donor atoms in the asymmetric unit
of 3a (solvent of crystallization are not shown for clarity).
Compound 4a crystallizes in the monoclinic P21/n space group.
The asymmetric unit contains one Co(II), half of tpxn and one
tdc2-. The Co(II) centers are pentacoordinated with N3O2
coordiantion environment (Fig. 8) in a trigonal bipyramidal
geometry ( = 0.94). A labelled diagram of 4a is shown in Fig.
S5. Each end of the bis(tridentate) ligand provides three N-
atoms and two O-atoms are from two monodentate tdc2- (binds
in syn-anti mode) which are bound to the Co(II) metal center
nearly at right angle. Each tridentate part of the tphn ligand
binds to the Co(II) centers in facial fashion, which is evident
from the N2-Co1-N3 angle 110.36(7)°.
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Fig. 7 Schematic view of (a) 2D structure in 3a with a fused chair (cis-decalin) conformation, and (b) the corresponding space fill
representation.
The Co(II)···Co(II) distances are 9.095 Å (connected by tpxn) and
10.542 Å (connected by tdc). Like 1a-3a, the Co−Npy distances
(2.057 − 2.073 Å) are shorter than Co−Nalkyl distance (2.283 Å)
which is longer than that in 1a. The two Co−Ocarb distances are
found to be almost similar, Co−O1 (1.981 Å) and Co−O4 (1.970
Å). The Ocarb−Co−Npy angles are 113.95(7)° (O1-Co1-N3),
103.57(7)° (O1-Co1-N2), 94.00(7)° (O4-Co1-N3) and 103.57(7)°
(O4-Co1-N2). The Ocarb−Co−Nalkyl angles are 85.14(7)° and
170.90(7)°. Selected bond lengths and bond angles are included
in Table S1. Hydrogen bond parameters are listed in Table S2.
given that the length of rigid tdc2- is almost constant (6.773 Å in
1a, 6.79 Å and 6.791 Å in 2a, 6.726 Å in 3a and 6.666 Å in 4a).
Furthermore, this remarkable feature to influence the
structural diversity is noteworthy as a paddlewheel core is
commonly observed for the divalent metal ions with
bifunctional spanning ligands.63,64,66-70 Both 1a and 2a have
hexacoordinated Co(II) centers with an N3O3 environment from
three nitrogen atoms of tpbn or tphn ligand and two
carboxylate oxygen atoms from two different tdc linkers and a
water molecules in 1a or three carboxylate oxygen atoms from
two different tdc linkers in 2a. However, the binding mode of
the tridentate part of polypyridyl ligands to the Co(II) center is
different in 1a and 2a facial (tpbn) vs. meridional (tphn) due to
an increase (1.5 times) of the methylene chain length; thus, the
binding mode of tdc to the Co(II) center differs:
bis(monodentate) in 1a and chelated in one end and
monodentate in the other end in 2a, which is reflected in the
Ocarb-Co-Ocarb angle (95.72° in 1a vs 107.1° in 2a) for
monodentate binding. Interestingly, the binding mode of tpbn
and tphn is just reverse when the carboxylate is ndc2- and the
metal center is Zn(II).32 This difference in binding modes of the
components has a profound effect on their structures: cis-
decalin type 2D polymer for 1a and ladder-shaped 1D polymer
for 2a. In order to confirm that the bulk of the material is phase
pure (i.e., there is no mixture of two different binding mode of
tpbn and tphn in 1a and 2a, respectively), the experimental
powder patterns of 1a and 2a were matched with the pattern
obtained from the single crystal structures (Fig. S6-S7). On the
other hand, for 3a and 4a containing the semiflexible
bis(tridentate) ligands, hexagonal net and chair-form (cis-
decalin) conformations of the six-membered ring within the 2D
network, respectively, were observed. This change caused by
the difference in the spacer (cyclohexylbis(methylene) vs xylyl,
respectively) in the spanning ligands, without a change in the
binding mode of each tridentate end (facial), has also
generated six-coordinated and five-coordinated Co(II) centers
in 3a and 4a, respectively. Both 3a and 4a have Co(II) centers
connected to two monodentate carboxylate groups from two
different tdc while the sixth coordination site in 3a is occupied
by a water molecule. Thus, the Ocarb-Co-Ocarb angle significantly
Fig. 8 Coordination environment around and geometry of the
Co(II) center with labelled donor atoms in the asymmetric unit
of 4a (solvent of crystallization are not shown for clarity).
The tdc2- carboxylates and Co(II) metal centers form zigzag
chains, and these chains are lying on two different planes. On
the basis of this connectivity, six Co centers that form a cavity
with a dimension of 16.980 × 10.542 Å2 (distances between two
Co and two tdc, respectively) adopt a chair conformation,
extending to a cis-decalin type 2D polymer structure (Fig. 9a).
Its space-filling representation (Fig. 9b) further shows the
cavities in 4a. The overlapped layers of such 2D frameworks are
shown in Fig. 9c.
Effect of the spacer in the bis(tridentate) ligands
For the series 1a-4a, a systematic change in the spacer between
the alkyl nitrogens of bis(tridentate) ligands has been
introduced to the three-component system, where the metal
center (Co(II)) and dicarboxylate (tdc2-) are kept the same. Thus,
the formation of different 2D ploymeric structures of 1a-4a is
clearly correlated to the flexibilty or semiflexibility of the spacer,
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Fig. 9 Schematic view of (a) 2D structure in 4a with a fused chair (cis-decalin) conformation, (b) the corresponding space fill
representation, and (c) overlapped layers of 4a.
Fig. 10 Topological views of 1a (a), 2a (b), 3a (c), and 4a (d).
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including CPs and MOFs have been explored. However, efforts
)
differs in 3a (91.78° and 4a (101.33°). If the semiflixibility is
considered in 3a and 4a, the difference in this outcome can be
understood based on the analysis of dihedral angle between
the planes containing the tdc where it widens from 67.08° to
72.35° (Fig. S8). Based on their topological represenations93
shown in Fig. 10, the conformational change in 1a-4a can be
visualized. 1a, 3a and 4a have the hcb topology belonging to the
uninodal 3-connected periodic Shubnikov hexagonal plane net
with the point symbol {63}, considering the metal center as a
three-coordinated node while both tdc and tpbn or tpchn or
tpxn as ditopic linkers. As mentioned above, 2 has the SP 1-
periodic net topology with the point symbol {42.6}.
Furthermore, there is a difference in the conformation of the
six-membered ring (three metal nodes present on each side of
for this reaction,75,76 homo- and heterogeneous metal catalysts
are dedicated in developing cost-effective and easy-to-make
CPs as heterogeneous catalysts for such reaction. As noted
earlier, compound 4 has coordinatively unsaturated metal
center that is suitable for Lewis acid catalysis. Thus, we have
tested its catalytic activity in the Knoevenagel condensation of
malononitrile with various aldehydes.
In a typical reaction, a mixture of an aldehyde (0.5 mmol) and
malononitrile (1 mmol) with a specified amount of activated 4
(2 mol%) and solvent (1 mL) was placed in a capped glass vial,
and then 1 mL of solvent was added to it. The mixture was
stirred at 25-30 °C for 60 minutes. Using the standard protocol,
the crude product was isolated and re-dissolved in CDCl3 and
analysed by H NMR spectroscopy. Both H NMR spectra and
related calculation of the percentage conversion by 4 in
methanol (entry 2, Table 2) are presented in Fig. S9. Using
benzaldehyde as the simplest substrate, various solvents were
screened for the reaction (entries 1-7, Table 2).
1
1
a
six-membered ring) in
conformation) reflecting flexible and semiflexible nature of the
spacer.
1
and
4
(perfect chair-like
Thermal properties
The TGA profiles of 1-4 are shown in Fig. 11. Compounds 1, 2
and 4 are remarkably stable up to 300 °C while compound 3 is
stable up to 280 °C. In all cases, a multi-step weight loss profile
is observed. In the first step, these compounds lose lattice
water molecule(s) followed by coordinated water molecule(s),
if present. For example, in case of 1 all four water molecules
(lattice and coordinated) are lost between 30-75 °C (calc. 7.33%,
found 6.73%). As compound 3 is found to lose more weight than
other compounds between 30-280 °C, it appears that its first
weight loss of five lattice water molecules between 30-75 °C
(calc. 8.24%, found 7.3%) is accompanied by the loss of two
coordinated water molecules and possibly a molecule of carbon
dioxide (calc. 8%, observed 7.7%). In the final step, for all
compounds a loss of the dicarboxylic acid is followed by the loss
of bis(tridentate) ligands before their final decomposition.
Table 2 Optimization of parameters for the Knoevenagel
condensation reaction catalysed by 4
NC
CN
Catalyst 4
CHO
+
NC
CN
25-30 °C
% Conversiona
Entry Catalyst amount Solvent Reaction time
(mol%)
(min)
1
2
Water
60
89
2
2
60
96
MeOH
3
2
60
92
EtOH
CH3CN
CHCl3
CH2Cl2
PhCH3
MeOH
MeOH
MeOH
MeOH
MeOH
MeOH
MeOH
MeOH
4
5
6
7
8
9
2
2
2
2
--
1
60
60
60
60
60
60
82
80
76
52
35
81
10
11
12
13
14
15
3
4
5
2
2
2
60
60
60
10
20
30
96
98
>99
40
55
62
16
17
18
2
2
2
2
40
50
70
78
86
MeOH
MeOH
MeOH
>99
19
20
80
60
>99
38
MeOH
MeOH
.
Fig. 11 TGA profiles of 1-4.
Co(OAc)2 4H2O
aCalculated by 1H NMR spectroscopy.
Catalysis studies
The best conversion (96%) was obtained in methanol while that
was poor (52%) in toluene. Next, the amount of catalyst (1-5
mol%) and the reaction time (10 min to 80 min) were varied to
optimize these parameters. An increase in the amount of
catalyst from 1 to 5 mol% enhanced the product conversion
from 81% to > 99% (entries 9−12, Table 2). On the other hand,
One of the most important C–C bond forming reactions that
afford α,β-unsaturated compounds for the valuable precursors
of fine chemicals and biological compounds is the Knoevenagel
condensation of aldehydes with active methylene compounds.
While bases or Lewis acids are commonly used as the catalysts
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Table 3 Substrate scope of the Knoevenagel condensation
reaction catalysed by 4
the conversion varied from 40% to >99% by increasing the time
(entries 13-19, Table 2); in fact, changing the time from 70 min
to 80 min did not make any difference. Based on these
experiments, optimized conditions (2 mol% catalyst, 60 min and
methanol) were chosen to explore further with other
substrates. A reaction was carried out without the catalyst to
show the conversion of 35% (entry 8, Table 2). Similarly, the
control experiment with Co(OAc)2·4H2O as the catalyst also
afforded similar results (entry 20, Table 2).
Catalyst 4
CN
CN
(2 mol%)
Ar
ArCHO
NC
CN
+
25-30 °C
60 min
Entry
Aldehyde
CHO
% Conversiona
TONb
Using the optimized conditions, a variety of substituted
F
1
100
50
aromatic aldehydes were reacted with malononitrile to obtain
the corresponding α,β-unsaturated compounds (Table 3 and
Fig. S10-S21). Both halogen and nitro substituted aldehydes
gave 100% conversion while methyl substituted aldehyde gave
an intermediate (75%) and methoxy substituted gave the
lowest conversion (60%). This corroborates well with the strong
accelerating influence of electron-withdrawing halogen or nitro
group in contrast to an electron-donating moiety for a reaction
involving nucleophilic attack at the carbonyl group. The
stronger is the electron-withdrawing ability of the substituent,
the faster is the activation of aldehyde for nucleophilic attack at
the carbonyl group and hence higher is the conversion.
Furthermore, an increase in ring size (entries 11 and 12 in
Tables 3) also provided 100% conversion.
100
100
75
Cl
CHO
CHO
2
3
50
50
Br
Me
CHO
CHO
CHO
CHO
4
37.5
MeO
O2N
5
6
60
30
50
100
7
100
100
50
50
O2N
N
CHO
8
9
In order to show the efficacy of the catalytic process at the
gram scale, the model reaction between benzaldehyde (663 L,
6.5 mmol) and malonitrile (858 mg, 13 mmol) with 2 mol% of 4
S
100
100
50
50
CHO
CHO
10
was
carried
out
to
isolate
the
product,
2-
Cl
benzylidenemalonitrile. As expected, a white crystalline solid
was obtained (904 mg; yield: 90%) after recrystallising it from a
3:1 CHCl3/MeOH solution. The product exhibits a sharp melting
point of 83.2 °C, which lies in the range of literature value of 83-
85 °C. Its FTIR spectrum, shown in Fig. S22, also matches with
the reported one.
CHO
100
50
11
12
CHO
100
50
aCalculated by 1H NMR spectroscopy. bNumber of moles of
product per mole of catalyst at 26-28 oC.
Based on the above results, a plausible mechanism of
Knoevenagel condensation reaction is depicted in Fig. 12. The
unsaturated Co(II) metal center (Lewis acidic site) interacts
with the carbonyl group of the benzaldehyde, resulting in
polarization of this group, which in turn increases the
electrophilic character of the carbonyl carbon atom. This
polarization accounts for attack by the nucleophile
(malononitrile). In order to prove this, a fine powdered sample
of 4 was activated by heating at 120 °C under vacuum was
added to a methanolic solution of benzaldehyde, stirred at 28
°C and dried to record its FTIR spectrum. Compared with the
neat benzaldehyde, there is a red-shift of 15 cm-1 for the CO
stretching frequency in the benzaldehyde complexed with 4
(Fig. S23). The interaction of a cyano group of malononitrile
with the Lewis acid site increases the acidity of the methylene
group, which further 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 attack the carbonyl
group of benzaldehyde resulting in the C−C bond formation
followed by dehydration.
Conclusion
A series of structurally diverse metal-organic frameworks has
been synthesised via one-pot self-assembly reaction of
Co(OAc)2·4H2O, thiophene-2,5-dicarboxylic acid (H2tdc) and
four different bis(tridentate) polypyridyl spanning ligands
under ambient conditions. Their structural diversity has been
correlated with the nature of spacer between the alkyl
nitrogens in the spanning ligands (flexible vs semiflexible), given
that the length of rigid tdc2- is almost constant. Both 1a and 2a
have hexacoordinated Co(II) centers but the binding mode of
tpbn and tphn is different - facial (tpbn) vs. meridional (tphn)
due to an increase (1.5 times) of the methylene chain length,
and the binding mode of tdc
is also different -
bis(monodentate) in 1a and chelated in one end and
monodentate in the other end in 2a, which allows a coordinated
water in 1a only. This difference in binding modes of the
components has a profound effect on their structures: cis-
decalin type 2D polymer for 1a and ladder-shaped 1D polymer
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for 2a. On the other hand, with semiflexible bis(tridentate)
ligands, hexagonal net and chair-form (cis-decalin)
conformations of the six-membered ring within the 2D
network, respectively, were observed for 3a and 4a. This
difference in the spacer (cyclohexylbis(methylene) vs xylyl,
respectively) in the spanning ligands, without a change in their
binding mode of the tridentate ends (facial), has also generated
six-coordinated and five-coordinated Co(II) centers in 3a and
4a, respectively. Both 3a and 4a have Co(II) centers coordinated
with two monodentate carboxylate groups from two different
tdc while the sixth coordination site in 3a is occupied by a water
molecule.
With an open Lewis acid site in 4, it was used as an efficient
heterogeneous catalyst for the KnoevDeOnaI:g1e0l.10c3o9n/dDe0nDsTa0t2io15n3A
reaction of malononitrile with various aldehydes in high yields
and low catalyst load (100% conversion in 60 minutes with 2
mol% catalyst in methanol). For the halogen and nitro-
substituted benzaldehydes, 4 gave 100% conversion. For
furthering this rich chemistry, we plan to explore it other metal
centers and different counter anions to identify other
interesting MOFs.
Fig. 12 Plausible mechanism for the Knoevenagel condensation reaction catalyzed by 4.
2
3
4
5
6
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Conflicts of interest
There are no conflicts to declare.
Acknowledgements
Funding for this work was provided by IISER, Mohali. B. L. is
grateful to MHRD, Govt. of India for a research fellowship. The
use of X-ray and NMR central facilities and other departmental
facilities at IISER Mohali is acknowledged.
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Table of Contents Artwork
Utilizing the angular and rigid thiophene dicarboxylate, diversity in metal organic frameworks of Co(II) is demonstrated based on the
flexible and semiflexible spacers in the bis(tridentate) spanning ligands.
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