Coordination driven self-assembly of four new molecular boats using a flexible imidazole-containing donor linker

Article abstract of DOI:10.1039/b713783d

Using a metal-ligand coordination bonding approach, the self-assembly of four new metallamacrocycles from Pd(ii)-based 90° acceptors and a diimidazole donor ligand 1,3-bis(imidazole-1-ylmethyl)-2,4,6-trimethylbenzene (L) has been achieved. The assemblies are characterized fully by NMR and electrospray ionization-mass spectroscopic (ESI-MS) analysis and in two cases the X-ray single-crystal structure analysis established the gross structures. The selective formation of a diimidazole-based linker (L) containing macrocycle [(en)Pd(μ-L)₂Pd(en)]⁴⁺ from a 1:1:1 mixture of cis-Pd(en)(NO₃)₂, L and 1,2-bis(4-pyridyl)ethane is also established. Measuring the binding constants established the stronger Pd-L binding force compared to traditional Pd-N(pyridyl linker) interaction, which reveals the possibility of using imidazole donor ligands as potential linkers or even better ligands compared to the widely used pyridyl donor ligands in the construction of metal-based large supramolecular assemblies. The Royal Society of Chemistry.

Full text of DOI:10.1039/b713783d

PAPER
www.rsc.org/dalton | Dalton Transactions
Coordination driven self-assembly of four new molecular boats using a flexible
imidazole-containing donor linker†‡
Sushobhan Ghosh, Rajesh Chakrabarty and Partha Sarathi Mukherjee*
Received 7th September 2007, Accepted 19th December 2007
First published as an Advance Article on the web 6th February 2008
DOI: 10.1039/b713783d
Using a metal–ligand coordination bonding approach, the self-assembly of four new
metallamacrocycles from Pd(II)-based 90◦ acceptors and a diimidazole donor ligand
1,3-bis(imidazole-1-ylmethyl)-2,4,6-trimethylbenzene (L) has been achieved. The assemblies are
characterized fully by NMR and electrospray ionization-mass spectroscopic (ESI-MS) analysis and in
two cases the X-ray single-crystal structure analysis established the gross structures. The selective
formation of a diimidazole-based linker (L) containing macrocycle [(en)Pd(l-L)2Pd(en)]4+ from a
1 : 1 : 1 mixture of cis-Pd(en)(NO3)2, L and 1,2-bis(4-pyridyl)ethane is also established. Measuring the
binding constants established the stronger Pd–L binding force compared to traditional Pd–N(pyridyl
linker) interaction, which reveals the possibility of using imidazole donor ligands as potential linkers or
even better ligands compared to the widely used pyridyl donor ligands in the construction of
metal-based large supramolecular assemblies.
works have been reported in the last few years.1,3 The important
Introduction
requirement for this process is the use of rigid precursors of
From the beginning of the first organic chemistry reaction,
appropriate shapes and symmetries. Square planar Pt(II) and Pd(II)
enormous efforts have been made to discover of large and
have long been used as favorite acceptors in this area. In a majority
complicated synthetic molecules. During the last decades, chemists
of the cases, symmetrical and rigid polypyridyl ligands have been
have shown particular interest in the directional self-assembly
used as donors for this purpose with a few recent exceptions
where we used oxygen-donor linkers.4 On the other hand, flexible
linkers are less predictable in self-assembly and have a tendency to
form undesired polymers. However, flexible linkers may generate
pseudo-rigid assemblies5 that can distort their shapes to obtain
a more thermodynamically stable conformation for host–guest
interactions. As the use of pyridyl-donor ligands dominates the
present literature, our interest was in incorporating a different
kind of imidazole-type donor linker as well as the flexibility into
Pd(II)-based metallasupramolecules.
approach as an alternative way to build larger and more complex
molecules.1 This synthetic self-assembly may be guided by a range
of interactions like: H-bonding, p–p interaction, van der Waals
forces or by metal–ligand coordination. We are mainly interested
in the self-assembly via coordination.2 Coordination self-assembly
has been demonstrated to be a useful and powerful alternative for
the construction of predefined and well-organized architectures.
Several discrete assemblies including extended polymeric frame-
Here we report the self-assembly of four new molecular boats
(Scheme 1) of general formula [(AA)2Pd2(l-L)2](NO3)4 (2a–d)
using a flexible diimidazole donor ligand 1,3-bis(imidazole-1-
ylmethyl)-2,4,6-trimethylbenzene (L) and the corresponding cis-
blocked acceptors (AA)Pd(NO3)2 (1a–d) [where AA = 1,2-
ethanediamine (1a); 1,2-propanediamine (1b); 2,2ꢀ-bipyridyl (1c)
Department of Inorganic & Physical Chemistry, Indian Institute of Science,
Bangalore, 560012, India. E-mail: psm@ipc.iisc.ernet.in; Fax: +91 (0)80
23601552; Tel: +91 (0)80 22933352
† CCDC reference numbers 659976 and 659977. For crystallographic data
in CIF or other electronic format see DOI: 10.1039/b713783d
‡ Electronic supplementary information (ESI) available: 1H NMR spectra
of 2b–d. See DOI: 10.1039/b713783d
Scheme 1 Self-assembly of 2a–d from the analogous acceptors 1a–d and the donor L.
1850 | Dalton Trans., 2008, 1850–1856 This journal is The Royal Society of Chemistry 2008
©

and N,N,Nꢀ,Nꢀ-tetramethylethanediamine (1d)]. All these assem-
blies are characterized by NMR, mass spectrometry and in two
cases (2a and 2b), X-ray crystallography.† A preliminary investiga-
tion established that imidazole donor linkers could also be used as
potential bridging ligands in directed self-assembly and this could
be even better than the widely used pyridyl linkers. Despite the pos-
sibility of forming a bpe-bridged [bpe = 1,2-bis(4-pyridyl)ethane]
macrocycle [(en)Pd(l-bpe)2Pd(en)](NO3)4, the self-selection of 2a
[(en)Pd(l-L)2Pd(en)](NO3)4 was exclusively achieved by treating
a 1 : 1 mixture of L and 1,2-bis(4-pyridyl)ethane (bpe) with one
equivalent cis-[(en)Pd(NO3)2] (1a).
C38H56O12N16Pd2: C 39.97%; H 4.97%; N 19.63%. Found: C, 39.71;
H, 4.88; N, 19.40%.
2b: 1H NMR (MeOH-d4, 400 MHz): d 7.7 (dd, 4H, imidazole-
H), 7.43 (s, 4H, imidazole-H), 7.08 (s, 4H, imidazole-H), 7.05 (s,
2H, ArH), 5.28 (s, 8H, CH2), 3.34 (s, 4H, CH2), 2.75 (m, 2H, CH),
2.21 (s, 6H, CH3), 2.14 (d, 6H, CH3), 1.2 (d, 12H, CH3); Yield:
96%. Anal. calcd for C40H60N16O12Pd2: C 41.07%; H 5.17%; N
19.16%. Found: C, 40.91; H, 4.86; N, 19.32%
2c: 1H NMR (MeOH-d4, 400 MHz): 8.31 (m, 4H, bpy-H), 8.22
(m, 4H, bpy-H), 8.04 (s, 4H, imidazole-H), 7.6 (s, 4H, imidazole-
H), 7.49 (m, 8H, bpy-H), 7.31 (s, 4H, imidazole-H), 7.1 (s, 2H, Ar-
H), 5.37 (s, 8H, CH2), 2.4 (s, 6H, CH3), 2.14 (s, 12H, CH3); ESI-MS:
[M-2NO3]2+ [m/z = 604.2 (calcd 604.12)] and [M-4NO3]4+ [m/z =
271.1 (calcd 271.06)]. Yield: 90%. Anal. calcd for C54H56N16O12Pd2:
C 48.62%; H 4.23%; N 16.80%. Found: C, 48.69; H, 4.83; N,
16.49%.
Experimental
Synthesis
1
2d: H NMR (MeOH-d4, 400 MHz): 8.18 (s, 4H, imidazole-
1a–d were synthesized from the corresponding dichlorides by
treating with two equivalents of AgNO3 in distilled water.6 The
corresponding dichlorides were prepared using the published
procedure.6b–c All solvents were received from commercial sources
and distilled prior to use. Deuterated solvents and 1,2-bis(4-
pyridyl)ethane (bpe) were purchased from Aldrich. The elemental
analyses were done using a Thermo Finnigan Flash EA 1112
CHNSO analyzer. NMR spectra were recorded on a Bruker 400
H), 7.5 (s, 8H, imidazole-H), 7.06 (s, 2H, Ar-H), 5.29 (s, 8H,
CH2), 2.95 (s, 8H, CH2), 2.61 (s, 24H, NCH3), 2.41 (s, 6H,
CH3), 1.95 (s, 12H, CH3); ESI-MS: [M-2NO3]2+ [m/z = 564
(calcd 564.18)]; [M-3NO3]3+ [m/z = 355.5 (calcd 355.45)] and [M-
4NO3]4+ [m/z = 251.3 (calcd 251.09)]. Yield: 93%. Anal. calcd
for C46H72N16O12Pd2 : C 44.06%; H 5.79%; N 17.87%. Found: C,
44.39; H, 5.53; N, 17.65%.
1
spectrometer and H NMR chemical shifts (2a–d) are reported
relative to the residual protons of deuterated methanol (d 3.3
ppm). Mass spectra were obtained using an electrospray ionization
(ESI) source. UV-visible spectra were recorded on a Perkin-Elmer
spectrophotometer.
X-Ray data collection† and refinements
Colorless crystals of 2a and 2b were mounted on glass fiber
with traces of viscous oil and then transferred to a Bruker
SMART APEX CCD diffractometer, equipped with a fine-focus
sealed-tube Mo Ka X-ray source. SMART was used for data
acquisition, and SAINT was used for data extraction. The crystals
were positioned at 50 mm from the goneometer. Data for 2a
were collected at 150 K while for 2b data were collected at
293 K. The structures were solved by a combination of direct
methods and heavy atom using SIR 97.7 All of the non-hydrogen
atoms were refined with anisotropic displacement coefficients.
Hydrogen atoms were assigned isotropic displacement coefficients,
U(H) = 1.2U(C) or 1.5U(C-methyl), and their coordinates were
allowed to ride on their respective carbons using SHELXL97.8
The refinement converged to R1 = 0.0859 (2a) and 0.0999 (2b);
wR2 = 0.2250 (2a) and 0.2580 (2b). The completeness of data as
well as the quality of the structure of 2b was not very satisfactory
because of the very poor quality of the crystals. However, the
gross connectivity and the dimeric nature of the molecule were
clear from the present data set, which was also corroborated from
other spectroscopic data.
Synthesis of the ligand L
Imidazole (0.4 g, 6.0 mmol) and potassium hydroxide (1.4 g,
25 mmol) were dissolved in dimethylsulfoxide (DMSO) (15 ml)
and the solution was stirred for 2 h at room temperature, then
1,3-bis(bromomethyl)-2,4,6-trimethylbenzene (0.84 g, 3.0 mmol)
was added. After stirring for another 3 h at room temperature,
an equivalent volume of water was added to the mixture. The
aqueous solution was extracted with chloroform (4 × 10 ml)
and the chloroform solution was dried over anhydrous sodium
sulfate and filtered. Solvent was removed on a rotary evaporator
and excess diethyl ether was added to the residue. After standing
overnight at −10 ◦C, the white powder was filtered, washed with
1
diethyl ether and dried in a vacuum desiccator. Yield: 73%. H
NMR (CDCl3, ppm): d 2.19 (s, 6H, CH3), 2.33 (s, 3H, CH3), 5.15
(s, 4H, CH2), 6.74 (s, 2H, imidazole-H), 7.02 (s, 2H, imidazole-H),
7.04 (s, 1H, Ar-H), 7.30 (s, 2H, imidazole-H).
General procedure for the synthesis of assemblies 2a–d
Results and discussion
To a stirred solution of the appropriate corner linker (1a–d)
(0.06 mmol) in methanol was added a solution of L [L = 1,3-
bis(imidazole-1-ylmethyl)-2,4,6-trimethylbenzene] (16.82 mg, 0.06
mmol) in methanol and it was kept under stirring for 4 h.
Precipitating out by ether addition isolated the products.
2a: 1H NMR (MeOH-d4, 400 Mz): d 7.68 (s, 4H, imidazole-H),
7.44 (s, 4H, imidazole-H), 7.1 (s, 4H, imidazole-H); 7.05 (s, 2H,
ArH); 5.28 (s, 8H, CH2); 4.5(broad, 8H, NH2); 2.76 (s, 8H, CH2);
2.23 (s, 6H, CH3); 2.13 (s, 12H, CH3); Yield: 94%. Anal. calcd for
Synthesis and spectroscopic characterizations
When the methanolic solution of the ligand
L
[L
=
1,3-bis(imidazole-1-ylmethyl)-2,4,6-trimethylbenzene] was treated
with an equivalent amount of the linker 1a in methanol, the [2 + 2]
self-assembly of the metallamacrocycle 2a occurred. A 0.38 ppm
downfield shift of the proton signal of the C–H proton between
the imidazole nitrogens indicated the loss of electron density from
the donor L to palladium. A similar downfield shift of the other
This journal is
The Royal Society of Chemistry 2008
Dalton Trans., 2008, 1850–1856 | 1851
©

protons of the ligand was also observed upon the self-assembly
reaction. H NMR of the product also indicated the formation
determination of binding constants by the UV-vis spectroscopic
method in case of formation of 3 and 2a corroborated the result.
1
of a symmetrical product by the appearance of all the expected
peaks in the product (Fig. 1). Similar treatment of L with the
corresponding acceptors 1b–d yielded analogous macrocycles 2b–
d, which were also identified by 1H NMR. Despite the possibility
of formation of a mixture of isomeric products (syn and anti) due
to the presence of non-symmetric chelating amine in 1b, a single
isomeric product 2b was formed exclusively.
Structure descriptions
Diffusion of ether into the methanolic solution of 2a yielded a
feather-shaped crystalline material which was not suitable for X-
ray crystallography. The methanolic solution of the product was
treated with four equivalents of Et4NClO4 to precipitate out the
perchlorate salt of the product. Diffraction-quality single crystals
of 2a were grown by ether diffusion into the nitromethane solution
of the perchlorate salt of 2a. However, 2b was crystallized directly
by diffusing ether into the methanol solution of the product. Fig. 2
shows the molecular structures of 2a and 2b. Crystallographic
parameters are assembled in Table 1. The structure of 2a looks like
˚
a molecular boat with a Pd–Pd distance of 6.6 A. The geometry
around each palladium is square planar with N–Pd(1)–N bond
angles in the range of 85.2(4)–94.3(3)◦ and N–Pd(2)–N angles
are in the range of 85.2(4)–93.1(3)◦. The distance between the
˚
centroids of the opposite benzene rings in 2a is 7.44 A. The boat
accommodated a nitrate anion and a water molecule inside its
belly. The nitrate anion and the water molecule are H-bonded to
the NH2 protons. H-bonding between the counter anions, lattice
waters and the neighboring macrocyles helps to form an H-bonded
supramolecular polymeric network in the solid state.
Similarly, the crystal structure of 2b shows an identical boat-
shaped macrocycle. The geometry around each palladium was
almost square planar with the N–Pd(1)–N angles in the range of
85.4(4)–93.3(4)◦ and N–Pd(2)–N angles in the range of 86.9(5)–
92.8(5)◦. 1,3,5-Trimethylbenzene groups in the macrocycle are
aligning in anti-fashion to minimize the steric interactions among
the methyl groups. Similarly, the methyl groups of the 1,2-
diaminopropane ligands are also oriented in anti-fashion. The
distance between the centroids of two opposite benzene rings in
Fig. 1 1H NMR spectrum of the macrocycle 2a in d4-MeOH.
Moreover, when a methanolic slurry of the stable known
macrocycle 3 [3 = (en)2Pd2(l-bpe)2(NO3)4, where bpe = 1,2-bis(4-
pyridyl)ethane] was treated with L in a 1 : 2 molar ratio, the
macrocycle 2a was immediately formed exclusively along with
the release of ligand bpe (Scheme 2). The formation of 2a and
the free bpe was established by the solution-state NMR analysis.
˚
case of 2b is 7.52 A while the intramolecular Pd–Pd distance
1
˚
is 6.6 A. The packing diagram of 2a along the crystallographic
Although the H NMR is not much informative in this case, the
Scheme 2 Formation of 2a from 1a as well as from 3 [(en)2Pd2(l-bpe)2]4+
.
1852 | Dalton Trans., 2008, 1850–1856
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The Royal Society of Chemistry 2008
©

Fig. 2 View of the molecular structures of 2a (left) and 2b (right) with atom numbering. Green = Pd; blue = N; grey = C.
Table 1 Crystallographic data and refinement parameters of 2a and 2b†
of the 1,2-diaminopropane (Fig. 3). Selected bond parameters for
both 2a and 2b are assembled in Table 2.
Identification code
2a
2b
NMR spectroscopy generally provides a preliminary idea of
the metal–ligand coordination, the progress of the reaction and
the relative ratios of the reacting components. However, it does
not provide any information about the molecular weight and the
probable shape of this kind of product. ESI mass spectrometry
has proven to be a potential tool in the corroboration of
structural assignments for these kinds of self-assemblies.9 ESI mass
spectrometry clearly confirmed the 1c2L2 and 1d2L2 compositions
with the molecular weight of 1332.24 and 1252.36 for 2c and 2d
respectively. These compositions are analogous to the other two
assemblies, which are characterized fully by NMR and single-
crystal structure analysis.†
The ESI mass spectrum (Fig. 4) of 2c showed the signals
corresponding to the consecutive loss of nitrate counter anions
[M-2NO3]2+, [M-4NO3]4+; while 2d showed signals corresponding
to the consecutive loss of counter anions [M-2NO3]2+, [M-3NO3]3+
and [M-4NO3]4+ (M = molecular weight based on the 1c2L2 and
1d2L2 compositions). For 2c: [M-2NO3]2+ [m/z = 604.2 (calcd
604.12)] and [M-4NO3]4+ [m/z = 271.1 (calcd 271.06)]. For 2d:
[M-2NO3]2+ [m/z = 564 (calcd 564.18)]; [M-3NO3]3+ [m/z = 355.5
(calcd 355.45)] and [M-4NO3]4+ [m/z = 251.3 (calcd 251.09)].
These molecular compositions are fully consistent with the other
dimeric assemblies (2a and 2b). Several attempts to obtain
single crystals yielded only powder materials in the cases of 2c
and 2d.
Formula
Fw
C39.25H62.75Cl3N13.25O17.5Pd2
1308.59
100(2)
Monoclinic
P21/c
0.71073
14.786(2)
17.297(3)
21.718(3)
101.913(3)
5434.6(14)
4
C41H52N16O14Pd2
1205.79
100(2)
Monoclinic
P21/c
0.71073
14.723(5)
17.227(6)
22.223(7)
99.959(7)
5552(3)
4
Temp./K
Crystal system
Space group
˚
k/A (Mo-Ka)
˚
a/A
˚
b/A
˚
c/A
b/◦
3
˚
V/A
Z
qcalcd/mg m−3
l/mm−1
1.599
0.888
2653
37941
1.426
0.719
2428
39278
F(000)a
Total reflections
Unique data
R1
9561 [Rint = 0.0635]
9772 [Rint = 0.1200]
0.0859
0.0999
b
wR2
0.2250
0.2580
ꢀ
ꢀ
ꢀ
ꢀ
a R = ꢀFo| – |Fcꢀ/ |Fo|. b Rw = [ {w(Fo − Fc2)2}/ {w(Fo2)2}]1/2
.
2
c-axis showed the formation of a zigzag chain which is formed by
the weak interaction of the counter anions with the bowls. One
counter anion as well as a water molecule is entrapped inside the
bowl through the weak H-bond among them via the amine groups
Fig. 3 Packing diagram of 2a along the crystallographic c-axis.
The Royal Society of Chemistry 2008 Dalton Trans., 2008, 1850–1856 | 1853
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©

◦
˚
Table 2 Selected bond angles ( ) and bond distances (A) of 2a and 2b†
2a
Pd(1)–N(1)
Pd(1)–N(2)
Pd(1)–N(3)
Pd(1)–N(4)
Pd(2)–N(5)
Pd(2)–N(6)
Pd(2)–N(7)
Pd(2)–N(8)
2.036(8)
2.021(10)
2.027(8)
2.020(8)
2.031(9)
2.036(8)
2.002(8)
2.027(8)
N(4)–Pd(1)–N(2)
N(2)–Pd(1)–N(3)
N(2)–Pd(1)–N(1)
N(7)–Pd(2)–N(8)
N(8)–Pd(2)–N(5)
N(8)–Pd(2)–N(6)
92.9(4)
179.4(4)
85.2(4)
92.0(3)
174.9(3)
89.8(3)
N(4)–Pd(1)–N(3)
N(4)–Pd(1)–N(1)
N(3)–Pd(1)–N(1)
N(7)–Pd(2)–N(5)
N(7)–Pd(2)–N(6)
N(5)–Pd(2)–N(6)
87.6(3)
178.1(4)
94.3(3)
93.1(3)
177.6(3)
85.2(4)
2b
Pd(1)–N(1)
Pd(1)–N(2)
Pd(1)–N(3)
Pd(1)–N(4)
Pd(2)–N(5)
Pd(2)–N(6)
Pd(2)–N(7)
Pd(2)–N(8)
2.029(11)
2.042(9)
N(3)–Pd(1)–N(1)
N(1)–Pd(1)–N(4)
N(1)–Pd(1)–N(2)
N(8)–Pd(2)–N(7)
N(7)–Pd(2)–N(6)
N(7)–Pd(2)–N(5)
178.0(4)
92.9(4)
85.4(4)
92.8(5)
175.0(5)
88.1(5)
N(3)–Pd(1)–N(4)
N(3)–Pd(1)–N(2)
N(4)–Pd(1)–N(2)
N(8)–Pd(2)–N(6)
N(8)–Pd(2)–N(5)
N(6)–Pd(2)–N(5)
88.3(4)
93.3(4)
177.7(5)
92.1(5)
177.7(5)
86.9(5)
2.020(11)
2.033(10)
2.057(12)
2.048(11)
2.036(11)
1.989(14)
Fig. 4 ESI mass spectra of the complexes 2c (left) and 2d (right).
Fig. 5 Plots of optical density vs. wavelength for the formation of 2a (left) and 3 (right).
1854 | Dalton Trans., 2008, 1850–1856
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The Royal Society of Chemistry 2008
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Fig. 6 Plots of 1/DA vs. 1/[L] for the formations of 2a (left) and 3 (right).
UV-Visible spectroscopic studies and binding constants
determination for 2a and 3
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The binding constants for the formation of 2a and 3 were
measured separately by UV-visible spectroscopy. In both the cases
the ligand solution was added in small portions to a 3.0 ×
10−3 M concentrated solution of (en)Pd(NO3)2. The plots of optical
density vs. wavelength for the corresponding titrations are shown
in Fig. 5. The isosbestic points at 320 nm in both cases are due
to 1 : 1 binding for 2a and 3. Binding constants were determined
[976.55 and 608.34 M−1 for 2a and 3 respectively] by applying the
binding isotherm equation, and plotting 1/DA vs. 1/[L] as shown
in Fig. 6. It was found that the binding constant for the formation
of 2a is 1.6 times greater than that of 3. This may be due to the
stronger binding of the imidazole ligand than the widely used
pyridyl ligand with palladium.
In conclusion, we report here the synthesis and the spectral
and structural characterizations of a series of metallamacrocycles
derived from cis-blocked 90◦ Pd(II) acceptors and a diimidazole-
donor flexible ligand (L). NMR, ESI mass spectrometry and
single-crystal structure determination in two cases† clearly estab-
lished the formation of pseudo-boat-shaped macrocycles (2a–d).
Binding constants measurements as well as the facile formation of
2a from the stable dipyridyl analogue 3 revealed the possibility of
using the imidazole donor ligand as a potential linker or an even
better ligand compared to the widely used pyridyl donor ligands in
the construction of large metal-based supramolecular assemblies.
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Acknowledgements
We thank the Department of Science and Technology, New Delhi
(under the fast track scheme); and the Council for the Scientific
and Industrial Research (CSIR), New Delhi, India, for financial
support.
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