Coordination-driven self-assembly in a single pot

Article abstract of DOI:10.1016/j.tetlet.2010.06.084

New multinuclear discrete heteroleptic complexes have been synthesized by mixing Pd(II), 2,2′-bipyridine and N,N′-(1,2-phenylene) diisonicotinamide in a single pot as a new approach. A dimeric molecular rhombus and a trimer in equilibrium are obtained where the dimer is the major product. Similar equilibrium is also observed when classical method is employed for the synthesis. The equilibrium is shifted exclusively in favour of the dimer upon addition of benzene. The complexes are characterized by NMR and ESI-MS methods. Crystal structure of the benzene encapsulated rhombus is presented.

Full text of DOI:10.1016/j.tetlet.2010.06.084

Tetrahedron Letters 51 (2010) 4449–4451
Contents lists available at ScienceDirect
Tetrahedron Letters
journal homepage: www.elsevier.com/locate/tetlet
Coordination-driven self-assembly in a single pot
*
Niladri B. Debata, Debakanta Tripathy, V. Ramkumar, Dillip Kumar Chand
Department of Chemistry, Indian Institute of Technology Madras, Chennai 600 036, Tamilnadu, India
a r t i c l e i n f o
a b s t r a c t
New multinuclear discrete heteroleptic complexes have been synthesized by mixing Pd(II), 2,20-bipyridine
and N,N0-(1,2-phenylene)diisonicotinamide in a single pot as a new approach. A dimeric molecular rhom-
bus and a trimer in equilibrium are obtained where the dimer is the major product. Similar equilibrium is
also observed when classical method is employed for the synthesis. The equilibrium is shifted exclusively
in favour of the dimer upon addition of benzene. The complexes are characterized by NMR and ESI-MS
methods. Crystal structure of the benzene encapsulated rhombus is presented.
Article history:
Received 23 April 2010
Revised 15 June 2010
Accepted 17 June 2010
Available online 20 June 2010
Keywords:
Palladium
Ó 2010 Elsevier Ltd. All rights reserved.
Self-assembly
One-pot synthesis
Molecular rhombus
Self-assembly is one of the beautiful aspects of supramolecular
chemistry.1 Based on the nature of self-assembly several metal-as-
sisted multinuclear discrete architectures are reported in the liter-
ature.2 Generally partially protected metal is further complexed
with a suitable ligand to get the assembly. The number of accept-
ing sites for the metal centre is lowered by blocking with the pro-
tecting units which commonly are chelating in nature. In this work
various components consisting of Pd(II), 2,20-bipyridine (bpy) and
N,N0-(1,2-phenylene) diisonicotinamide are combined in a single
pot which results in the formation of exclusive discrete product(s).
In comparison with classical method,2 the one-pot method is less
time consuming.
the formed Pd(bpy)(NO3)2 upon complexation with ligand 1 at
room temperature for 24 h in CH3CN medium gave rise to the sim-
ilar equilibrium mixture. The comparison between classical and
one-pot method is given in Table 1.
The ESI-MS in water/methanol (1:5) mixture showed peaks cor-
responding to the loss of four nitrate anions for complex 2 at m/z
290.42 [2—(NO3)4]4+ and loss of six nitrate anions for complex 3
at m/z 290.84 [3—(NO3)6]6+
.
Cl
Cl
ONO2
ONO2
N
N
N
N
H2O, pH = 1
AgNO3
N
CH3CN, Δ
Pd
Pd
+
PdCl2
Equimolar mixture of N,N0-(1,2-phenylene) diisonicotinamide,
13 along with Pd(II) and bpy in CH3CN/H2O (1:1) solvent system
in a single pot at 70 °C for 30 min gave rise to an equilibrium mix-
ture of binuclear compound 2 as a major product along with a tri-
nuclear complex 3 (Scheme 1b).4 Concentration variation was
studied for the equilibrium of 2 and 3 at 5 and 10 mM of Pd, which
gave the ratio as 96:4 and 89:11, respectively. This observation is
in accordance with the entropy factor.5
N
ONO2
N
N
+
Pd
ONO2
+
4(NO3)
6(NO3)
The equilibrium mixture was shifted towards 2 by the addition
of benzene to this solution (Fig. 1). The upfield shift of 2 in 1H NMR
suggests that there is a host guest complexation. When the synthe-
sis was attempted by classical method the same equilibrium mix-
ture of 2 and 3 was observed. In this method bpy was added to a
hot acetonitrile solution of PdCl2 to prepare Pd(bpy)Cl2 (Scheme
1a).6 The chloride anion of the isolated Pd(bpy)Cl2 was then ex-
changed with nitrate by adding AgNO3 in aq HNO3 at pH 1.6 Thus
2
3
N
+
+
Pd(NO3)2
N
N
N
O
O
Pd
=
=
NH NH
1
N
N
* Corresponding author. Tel.: +91 44 2257 4224; fax: +91 44 2257 4202.
E-mail address: dillip@iitm.ac.in (D.K. Chand).
Scheme 1. Synthesis of 2 and 3 by (a) classical method (b) one-pot method.
0040-4039/$ - see front matter Ó 2010 Elsevier Ltd. All rights reserved.
doi:10.1016/j.tetlet.2010.06.084

4450
N. B. Debata et al. / Tetrahedron Letters 51 (2010) 4449–4451
Figure 1. 1H NMR spectra in D2O of (a) a mixture of 2 (major) and 3, (b) benzene ꢁ 2 emerged from the equilibrium upon addition of benzene.
moieties of a given ligand are almost perpendicular to the square
planes of the complexed Pd-centres and point trans to amide oxy-
Table 1
Comparison between classical and one-pot method for the synthesis of the mixtures 2
and 3
gen of the other ligand unit of the rhombus. Each oxygen form a
hydrogen bond (ꢀ2.9 Å) intermolecularly with amide NH. Thus
one molecule of benzene ꢁ 2 ꢂ 4H2O possesses eight H-bonds by
connecting with four neighbouring molecules. The benzene mole-
cule is trapped almost at the centroid of the hydrophobic cavity
of this molecular rhombus. Each Pd(II) ion adopts a square planar
geometry with Pd–N bond distance of ꢀ2.0 Å and the Pd to Pd dis-
tance is ꢀ11.9 Å. The pyridine rings of the ligands are situated
orthogonally to the 2,20-bipyridine ring. The o-phenylenediamine
moiety of the complexed ligand remains perpendicular to the pyr-
idine rings and slightly out of plane to adjust the geometrical de-
mand of the metal centre. While two nitrates are located the
other two are not found.
Method
Classical
Step
Time (h)
Temperature (°C)
Yield (%)
1st
2nd
3rd
1
0.5
24
60
60
rt
92
83
92a,b
One pot
one
0.5
70
95b
a
Over all yield is 70%.
similar product ratio of 2 and 3.
b
Single crystals were formed within one week by layering ben-
zene to an aqueous solution of the complexes at room tempera-
ture. The crystal structure showed a binuclear rhombus structure
having a benzene molecule encapsulated in the cavity (Fig. 2).7 This
binuclear complex resembles a rare rhombus architecture where
two adjacent arms are occupied by one ligand unit and the square
planes of the metal centres are coplanar. The two amide oxygen
This method was further established with ligand 1,4-bis(40-pyr-
idylmethyl)-2,3,5,6-tetrafluorobenzene, 4. Bidentate non-chelating
ligand 4, Pd(NO3)2 and bpy at a ratio of 1:1:1 in CH3CN/H2O (1:1)
gave a single dimeric complex 5 (Scheme 2), which was character-
ized by 1H NMR and ESI-MS.8,9 The ESI-MS in water/methanol (1:5)
Figure 2. Extensive intermolecular hydrogen bonding seen in the crystal structure of benzene ꢁ 2 ꢂ 4H2O. Counter anions, hydrogen atoms and water are omitted for clarity.
Benzene is shown in space filling style.

N. B. Debata et al. / Tetrahedron Letters 51 (2010) 4449–4451
4451
Coord. Chem. Rev. 2002, 225, 91–121; (d) Fujita, M.; Tominaga, M.; Hori, A.;
Therrien, B. Acc. Chem. Res. 2005, 38, 371–380.
CH3CN:H2O (1:1)
rt, 6 h
N
N
3. Burchell, T. J.; Eisler, D. J.; Puddephatt, R. J. Inorg. Chem. 2004, 43, 5550–5557.
4. 2,20-Bipyridine (0.0078 g, 0.05 mmol) and N,N0-(1,2-phenylene)diisonic-
otinamide (0.0159 g, 0.05 mmol) were taken in 5 mL of CH3CN/H2O (1:1). To
this suspension, Pd(NO3)2 (0.0138 g, 0.06 mmol) was added and stirred for
30 min at 70 °C. The suspension was changed to a green coloured solution.
Then it was evaporated by N2 flushing and dried under vacuum giving rise to a
pale green solid as the product (0.0335 g, yield 95%). 1H NMR (400 MHz, D2O,
external TMS/CDCl3): for 2: d 9.39 (d, J = 5.2 Hz, 8H, a), 8.54 (d, J = 8.0 Hz, 4H,
a0), 8.44 (t, J = 7.6 Hz, 4H, b0), 8.20 (d, J = 5.6 Hz, 8H, b), 7.67–7.57 (m, 12H, c, d
and c0) 7.32 (d, J = 5.6 Hz, 4H, d0), for 3: 9.22 (d, J = 5.6 Hz, 12H, a), 8.05 (d,
J = 5.6 Hz, 12H, trimer b), other signals are merged with 2. 13C NMR (100 MHz,
D2O, external TMS/CDCl3) for 2: 165.0 (CO), 156.8 (Cqpy), 152.6 (a), 149.8 (d0),
145.6 (Cq(bpy/bz)), 143.0 (b0), 130.8 (Cq(bpy/bz)), 128.9, 128.3, 127.2 (c,d,c0), 126.0
(b), 124.6 (a0). Anal. Calcd for C28H22N8O8Pdꢂ4H2O: C, 43.28; H, 3.89; N, 14.42.
Found: C, 43.37; H, 3.53; N, 14.16.
+
+
Pd(NO3)2
4(NO3)
5
F
F
F
F
N
Pd
=
=
N
4
N
N
Scheme 2. Synthesis of complex 5 by one-pot method.
5. (a) Lee, S. B.; Hwang, S.; Chung, D. S.; Yun, H.; Hong, J.-I. Tetrahedron Lett. 1998,
39, 873–876; (b) Yamamoto, T.; Arif, A. M.; Stang, P. J. J. Am. Chem. Soc. 2003,
125, 12309–12317; (c) Ferrer, M.; Mounir, M.; Rossell, O.; Ruiz, E.; Maestro, M.
A. Inorg. Chem. 2003, 42, 5890–5899; (d) Chand, D. K.; Biradha, K.; Kawano, M.;
Sakamoto, S.; Yamaguchi, K.; Fujita, M. Chem. Asian. J. 2006, 1–2, 82–90; (e)
Ghosh, S.; Mukherjee, P. S. Inorg. Chem. 2009, 48, 2605–2613.
showed a peak corresponding to the loss of four nitrate anions at
m/z 297.0 [5—(NO3)4]4+
.
In conclusion, steric crowding generated by bpy10 during com-
plexation along with the labile nature of co-ordinate bond between
Pd and N was successfully utilized for the preparation of discrete
product in a single pot.
6. Wimmer, S.; Castan, P.; Wimmer, F. L.; Johnson, N. P. J. Chem. Soc., Dalton Trans.
1989, 403–412.
7. X-ray crystal data of benzene ꢁ 2 ꢂ 4H2O: C62H58N16O20Pd2, Mr = 1560.04,
crystal dimensions 0.25 ꢃ 0.21 ꢃ 0.16 mm3, monoclinic, space group
P21/c, a = 17.6614(7) Å, b = 20.6665(8) Å, c = 9.9004(4) Å, b = 96.374(2)°, V =
3591.3(2) Å3, Z = 2,
= 0.581 mmꢄ1
k(MoK
measured and independent reflections 26849/8834, Rint = 0.0396, R1
q
calcd = 1.443 g cmꢄ3
,
linear absorption coefficient
Acknowledgement
l
,
a) = 0.71073 Å, T = 223(2) K, 2hmax = 56.64°, no. of
(I > 2r(I)) = 0.1043, wR2 = 0.3461, GOF = 1.108, max/min residual density
This project is supported by Department of Science and Tech-
nology, India (No. SR/S1/IC-28/2009).
5.894/ꢄ1.190 e Åꢄ3, the data were collected using paraffin oil. The structure
was solved by direct methods (SHELXL-97) and refined by full-matrix least
squares methods on F2 with 418 parameters. CCDC 767855 contains the
Supplementary crystallograhic data for this Letter.
Supplementary data
8. Sahoo, H. S.; Chand, D. K.; Debata, N. B. Inorg. Chim. Acta 2007, 360, 31–38.
9. 2,20-Bipyridine (0.0078 g, 0.05 mmol) and 1,4-bis(40-pyridylmethyl)-2,3,5,6-
tetrafluorobenzene (0.0166 g, 0.05 mmol) were dissolved in 5 mL of CH3CN/
H2O (1:1). To this solution, Pd(NO3)2 (0.0138 g, 0.06 mmol) was added and
stirred for 6 h at room temperature. The pale coloured solution was evaporated
by N2 flushing and dried under vacuum. The solid was washed with acetone,
ether and dried again to give rise to a pale solid as the product (0.0281 g, yield
78%). 1H NMR (400 MHz, DMSO-d6, external TMS/CDCl3): d 9.72 (d, J = 6.4 Hz,
8H, a), 9.32 (d, J = 8.0 Hz, 4H, a0), 9.04 (dt, J = 7.9 and 1.0 Hz, 4H, b0), 8.24–8.28
(m, 12H, b and c0), 8.04 (d, J = 5.6 Hz, 4H, d0), 4.84 (s, 8H, –CH2–).
Supplementary data associated with this article can be found, in
the online version, at doi:10.1016/j.tetlet.2010.06.084.
References and notes
1. Steed, J. W.; Atwood, J. L. Supramolecular Chemistry, 2nd ed.; John Wiley & Sons
Ltd, 2009.
2. (a) Stang, P. J.; Olenyuk, B. Acc. Chem. Res. 1997, 30, 502–518; (b) Seidel, S. R.;
Stang, P. J. Acc. Chem. Res. 2002, 35, 972–983; (c) Swiegers, G. F.; Malefetse, T. J.
10. (a) Hinamoto, M.; Ooi, S.; Kuroya, H. J. Chem. Soc., Chem. Commun. 1972, 356–
357; (b) Chieh, P. C. J. Chem. Soc., Dalton Trans. 1972, 1643–1646.