Self-assembly of alternating left- and right-handed infinite Cd(II) helicates into a 2D open framework structure

Article abstract of DOI:10.1016/j.molstruc.2006.02.008

Pyrazine-2,3,5,6-tetracarboxylic acid (ptcH₄) reacts with Cd(NO₃)₂·6H₂O at room temperature in the presence of pyridine to form a 2D open framework built from alternating left- and right-handed helicates with the empirical formula, {[Cd₂(ptc)·(py)₅·H₂O]·5H₂O·py}_n, 1. Lattice water and pyridine molecules form an intricate array of H-bonding with the 2D sheets leading to a 3D structure. This compound crystallizes in the monoclinic space group C2/c with the following lattice parameters-a=24.103(2), b=13.480(5), c=29.176(4) A?, β=109.427(3)°, V=8940(4) A?³, Z=8, R1=0.0513, wR2=0.1552, S=1.085.

Full text of DOI:10.1016/j.molstruc.2006.02.008

Journal of Molecular Structure 796 (2006) 119–122
www.elsevier.com/locate/molstruc
Self-assembly of alternating left- and right-handed infinite Cd(II) helicates
into a 2D open framework structure
*
Sujit K. Ghosh, Parimal K. Bharadwaj
Department of Chemistry, Indian Institute of Technology, Kanpur 208016, Uttar Pradesh, India
Received 19 January 2006; received in revised form 31 January 2006; accepted 2 February 2006
Available online 27 March 2006
Abstract
Pyrazine-2,3,5,6-tetracarboxylic acid (ptcH4) reacts with Cd(NO3)2$6H2O at room temperature in the presence of pyridine to form a 2D open
framework built from alternating left- and right-handed helicates with the empirical formula, {[Cd2(ptc)$(py)5$H2O]$5H2O$py}n, 1. Lattice water
and pyridine molecules form an intricate array of H-bonding with the 2D sheets leading to a 3D structure. This compound crystallizes in the
˚
monoclinic space group C2/c with the following lattice parameters—aZ24.103(2), bZ13.480(5), cZ29.176(4) A, bZ109.427(3)8, VZ
3
˚
8940(4) A , ZZ8, R1Z0.0513, wR2Z0.1552, SZ1.085.
q 2006 Elsevier B.V. All rights reserved.
Keywords: X-ray crystallography; Supramolecular chemistry; Self-assembly; Metal-organic framework; Helical structure
1. Introduction
2. Experimental
2.1. General
Self-assembled helical structures are essence of life and are
of interest in supramolecular chemistry because helical
structures are reminiscent of DNA structures. Due to the
important roles of helicity in biology as well as in advanced
materials, helical organic, inorganic and metal-organic hybrid
compounds continue to attract a lot of attention [1–3]. In the
field of coordination chemistry, multidentate chelate ligands
have been used with great success for this purpose [4]. The
propensity for forming coordination polymers in the form of
helicates depends on the stereoelectronic molecular infor-
mation encoded in the ligand and reading of this information by
metal ions under suitable experimental conditions. While
coordination polymers are of great current interest in the field
of catalysis and biology as well as in the development and
understanding of self-assembly processes [5–10]. Helical
coordination networks in particular, are of great interest
owing to their potential utility in chiral separation, asymmetric
catalysis and non-linear optical applications [11–13]. We
present here, a 2D coordination polymer containing alternate
left-handed and right-handed infinite helical structures.
The metal salts and phenazine were acquired from Aldrich
and used as received. Spectroscopic data were collected as
follows: IR (KBr disk, 400–4000 cmK1) Perkin–Elmer Model
1320; X-ray powder pattern (Cu Ka radiation at a scan rate
of 38/min, 293 K) Siefert ISODEBYEFLEX-2002 X-ray
generator; thermogravimetric analysis (heating rate of
5 8C/min) Perkin-Elmer Pyris 6. Microanalyses for the
compounds were obtained from the Central Drug Research
Institute, Lucknow, India.
2.1.1. Synthesis of pyrazine-2,3,5,6-tetracarboxylic acid
(ptcH4)
This compound was synthesized in 55% yield by oxidation
of phenazine with aqueous KMnO4.
2.1.2. Synthesis of {[Cd2(ptc)$(py)5$H2O]$5H2O$py}n, 1
Reaction of Cd(NO3)2$4H2O (0.62 g; 2 mmol) and
pyrazine-2,3,5,6-tetracarboxylic acid (ptcH4) (0.26 g;
1 mmol) dissolved in 25 mL aqueous pyridine (1:1 v/v) to
obtain a colorless solution. After filtering the solution, the
filtrate is allowed to evaporate at room temperature whereupon
colorless crystals of 1 appeared after 10 days in the form of
rectangular parallelopiped in 65% yield. Anal. Calcd for
C38H37N8O14Cd2 (1054.56): C, 43.27; H, 3.53; N, 10.62%.
Found: C, 43.32; H, 3.55; N, 10.68%.
*
Corresponding author. Tel.: C91 512 259 7304; fax: C91 512 259 7436.
E-mail address: pkb@iitk.ac.in (P.K. Bharadwaj).
0022-2860/$ - see front matter q 2006 Elsevier B.V. All rights reserved.
doi:10.1016/j.molstruc.2006.02.008

120
S.K. Ghosh, P.K. Bharadwaj / Journal of Molecular Structure 796 (2006) 119–122
Table 2
Selected bond distances (A) and bond angles (8) in 1
2.2. X-ray crystallography
˚
Single crystal X-ray data on 1 were collected at 100 K on a
Bruker SMART APEX CCD diffractometer using graphite-
Cd1 OW6 2.304(3)
Cd1 N4 2.306(4)
Cd1 N3 2.334(4)
Cd1 N1 2.369(3)
Cd1 O1 2.438(3)
Cd1 O3 2.492(3)
˚
monochromated Mo Ka radiation (lZ0.71073 A). The linear
Cd1 O1 2.493(3)
Cd2 N7 2.328(4)
absorption coefficients, scattering factors for the atoms, and the
anomalous dispersion corrections were taken from Inter-
national Tables for X-ray Crystallography. The data integration
and reduction were processed with SAINT [14] software. An
empirical absorption correction was applied to the collected
reflections with SADABS [15] using XPREP [16]. The
structure was solved by the direct method using SHELXTL
[17] and was refined on F2 by full-matrix least-squares
technique using the SHELXL-97 [18] program package. Non-
hydrogen atoms were refined anisotropically. All hydrogen
atoms were located in successive difference Fourier maps and
they were treated as riding atoms using SHELXL default
parameters. The crystal and refinement data are collected in
Table 1. The selected bond lengths and bond angles are listed in
Table 2.
Cd2 N6 2.338(4)
Cd2 N5 2.346(4)
Cd2 O6 2.427(3)
Cd2 O7 2.446(3)
Cd2 O8 2.505(4)
Cd2 O5 2.515(3)
OW6 Cd1 N4 92.04(14)
N4 Cd1 N3 174.23(13)
N4 Cd1 N1 92.93(13)
OW6 Cd1 O1 81.59(12)
N3 Cd1 O1 88.49(12)
OW6 Cd1 O3 75.63(11)
N3 Cd1 O3 94.42(13)
O1 Cd1 O3 156.85(10)
N4 Cd1 O1 85.48(12)
N1 Cd1 O1 67.51(11)
O3 Cd1 O1 133.98(10)
N7 Cd2 N5 177.72(14)
N7 Cd2 O6 90.88(12)
N5 Cd2 O6 89.63(12)
N6 Cd2 O7 82.32(13)
O6 Cd2 O7 174.11(12)
N6 Cd2 O8 135.57(13)
O6 Cd2 O8 132.49(11)
N7 Cd2 O5 83.56(12)
N5 Cd2 O5 94.96(12)
O7 Cd2 O5 132.50(11)
OW6 Cd1 N3 87.25(14)
OW6 Cd1 N1 142.24(13)
N3 Cd1 N1 91.13(13)
N4 Cd1 O1 85.75(12)
N1 Cd1 O1 136.11(11)
N4 Cd1 O3 90.94(13)
N1 Cd1 O3 66.89(11)
OW6 Cd1 O1 150.24(11)
N3 Cd1 O1 92.29(12)
O1 Cd1 O1 68.66(11)
N7 Cd2 N6 90.80(14)
N6 Cd2 N5 91.40(14)
N6 Cd2 O6 91.80(13)
N7 Cd2 O7 89.19(12)
N5 Cd2 O7 90.54(12)
N7 Cd2 O8 91.70(12)
N5 Cd2 O8 86.32(12)
O7 Cd2 O8 53.39(12)
N6 Cd2 O5 144.37(12)
O6 Cd2 O5 53.32(11)
O8 Cd2 O5 79.90(11)
Crystallographic data for the structural analysis have been
deposited with the Cambridge Crystallographic Data Centre,
293349 for 1. Copies of this information may be obtained free
of charge at www.ccdc.cam.ac.uk/conts/retrieving.html [or
from the Cambridge Crystallographic Data Centre, 12, Union
Road, Cambridge CB2 1EZ, UK]; fax: C44 1223 336066;
e-mail: deposit@ccdc.cam.ac.uk.
air and insoluble in water as well as common organic solvents.
High yield of the product indicates that it is thermodynamically
stable under the prevailing reaction condition.
3. Results and discussion
The asymmetric unit of 1 consists of two Cd(II), one ptc4K
,
Compound {[Cd2(ptc)$(py)5$H2O]$5H2O$py}n, (1) is
readily formed by reacting a Cd(II) salt with pyrazine-
2,3,5,6-tetracarboxylic acid (ptcH4) at room temperature in
presence of pyridine in 65% yield. Once formed, it is stable in
six pyridine and six water molecules. Its structure can be
described as a 2D coordination polymer consisting of two
different types of hepta-coordinated Cd(II) centers with
pentagonal bipyramidal geometry (Fig. 1). The equatorial
coordination to Cd(1) ion is provided by two carboxylate O and
ring N on one side of the ligand, a bridging carboxylate O from
the neighboring ligand and a water molecule.
Table 1
Crystal and structure refinement data for 1
Empirical formula
Formula weight
Temperature
C38H37Cd2N8O14
1054.56
100 K
The two axial sites on the metal are occupied by two pyridine
molecules. The Cd(2) ion is equatorially coordinated to two
˚
Radiation, wavelength
Crystal system
Space group
Mo Ka, 0.71073 A
Monoclinic
C2/c
˚
a (A)
˚
b (A)
˚
c (A)
24.103(2)
13.480(5)
29.176(4)
109.427(5)
8940(4)
b (8)
3
˚
U (A )
Z
8
rcalc (Mg/m3)
1.567
m (mmK1
)
1.023
F(000)
4232
Refl. collected
Independent refl.
Refinement method
GOOF
29,394
9314
Full-matrix least-squares on F2
1.085
Final R indices
[IO2s(I)]
R indices
R1Z0.0513
wR2Z0.1552
R1Z0.0606
wR2Z0.1619
Fig. 1. An illustration showing the binding mode of the ligands with metals and
presence of three different type of water dimeric clusters.
(All data)

S.K. Ghosh, P.K. Bharadwaj / Journal of Molecular Structure 796 (2006) 119–122
121
carboxylate O from two different ptc4K ligands in the bi-dentate
fashion and one pyridine molecule. The two axial sites are again
occupied by two pyridine molecules. Two Cd(1) ions form a
carboxylate-bridged dimer. All Cd–O and Cd–N bond distances
are within normal ranges as found in other Cd(II) complexes [19].
Thesameligandandother similarligandssystemsarealsousedto
make many MOF structures [20].
The Cd(2) ions are arranged in infinite helices in spite of the
fact that the ligand has no intrinsic tendency to form such
structures. The Cd(1) dimers are present in between two helicates
to make the 2D sheet structure (Fig. 2). Interestingly, the structure
shows alternate right- and left-handed helical chains extending
along the crystallographic b axis(Fig. 2). The helicalstructure isa
result of metal–ligand interactions coupled with stereoelectronic
characteristics of the ligand and the conditions prevailing during
the synthesis. The stability of the final helical structure relies on
the coordinate bonds that each metal makes with the ligand. An
inspection of the structure of 1 leads to the belief that the metal
coordinated pyridine molecules play key roles in the formation of
the helices by acting as structure-directing agents to induce a
Fig. 2. The 2D structure including two types of helical chains.
Table 3
˚
Geometrical parameters of hydrogen-bonds (A, 8) of the three different dimers
in 1
˚
helical array. The width of each helix is calculated to be 13.5 A
˚
andthepitchis10.4 AwithtwoCd(2)ionsperturnatadistanceof
˚
7.87 A, while the distance between Cd ions in two helices are
˚
either 16.477 or 17.426 A. Both the width and the pitch are large
Ow1/Ow2
Ow3/Ow4
Ow5/Ow6
Ow1/O5
Ow2/O7
Ow2/N8
Ow3/O8
Ow4/O8
Ow5/O4
Ow5/O3
Ow6/O2
2.909(1)
2.770(3)
2.684(2)
2.905(4)
2.892(2)
2.864(2)
2.941(3)
2.846(3)
2.754(2)
2.790(3)
2.790(3)
Ow1–H/Ow2
Ow4–H/Ow3
Ow6–H/Ow5
Ow1–H/O5
Ow2–H/Ow2
Ow2–H/N8
Ow3–H/O8
Ow4–H/O6
Ow5–H/O4
Ow5–H/O3
Ow6–H/O2
168.02(6)
144.37(2)
160.77(3)
168.02(2)
168.02(4)
175.03(3)
145.06(2)
172.43(2)
159.31(3)
148.83(4)
161.25(2)
that is a result of the topology of the ligand and the electrostatic
repulsive interactions among Cd(III) ions. Similar kind 2D
structure with both left- and right-handed helicate are reported
[3,4c]. In one report [3], they synthesized a layered coordination
polymer of Co(II) containing two helical chains and the resultant
crystals were not racemic as evidenced by the observation of
strong signals in vibrational circular dichroism (VCD) spectra. In
other report [4c], carboxylate-bridged two terpyridine complex
are reported. Three different types of water dimers present in the
lattice are involved in H-bonding interactions (Table 3) with free
Fig. 3. A view of the overall 3D structure of 1 omitting H atoms for clarity.

122
S.K. Ghosh, P.K. Bharadwaj / Journal of Molecular Structure 796 (2006) 119–122
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Chem. Commun. (2002) 152;
carboxylate O of the sheet structures leading to a 3D motif
(Fig. 3).
Thermal gravimetric analyses performed under N2 atmos-
phere show that the compound 1 lost the encapsulated free
water and pyridine molecule within 200 8C. The FTIR
spectrum of 1 shows a broad band centered around
3500 cmK1 due to water molecules that vanishes on heating
the compound under vacuum (0.1 mm) at 180 8C for 2 h.
Powder X-ray diffraction patterns of 1 show changes in peak
positions as well as their intensities before and after water
expulsion although sharp peaks remain in the diffraction
pattern indicating a crystalline solid remains after water and
pyridine expulsion.
(c) J. Liang, G. Tian, G. Zhu, X. Yang, Q. Fang, M. Xue, J. Sun, Y. Wei,
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G. Christou, Angew. Chem. Int. Ed. 43 (2004) 2117.
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The structure of the compound 1 reported herein not only
contains helical chains but also possess left- and right-handed
helical chains in one compound. The structures of the
compound reported here show that infinite single helical
chains can be constructed with simpler ligand.
[14] SAINTC, 6.02ed. Bruker AXS, Madison, WI, 1999.
[15] G.M. Sheldrick, SADABS, Empirical Absorption Correction Program,
¨
University of Gottingen, Germany, 1997.
[16] XPREP, 5.1 ed. Siemens Industrial Automation Inc., Madison, WI, 1995.
[17] G.M. Sheldrick, SHELXTL e Reference Manual: Version 5.1, Bruker AXS,
Madison, WI, 1997.
Acknowledgements
[18] G.M. Sheldrick, SHELXL-97: Program for Crystal Structure Refinement,
¨
¨
University of Gottingen, Gottingen, Germany, 1997.
[19] X.-L. Wang, C.-Q. Qin, E.-B. Wang, L. Xu, Z.-M. Su, C.-W. Hu, Angew.
Chem. Int. Ed. 43 (2004) 5036.
We gratefully acknowledge the financial support received
from the Department of Science and Technology, New Delhi,
India (to P.K.B.) and Council of Scientific and Industrial
Research, New Delhi, India for a SRF to S.G.
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