Recognition of dicarboxylic acids by a bis pyrimidine amine linked xylene spacer: A unique gauche dimeric complex of host and adipic acid detected by X-ray

Article abstract of DOI:10.1007/s10847-010-9810-8

A pyrimidine based receptor (pyrimidine amine linked xylene spacer) has been synthesized for recognition of dicarboxylic acids. Binding studies have been performed by UV-vis method by varying the chain length of dicarboxylic acids. The downfield chemical shift of amine protons of receptor in presence of adipic acid or glutaric acid and the 1:1 dimeric crystal structure of the receptor and adipic acid reveal the strong binding interaction.

Full text of DOI:10.1007/s10847-010-9810-8

J Incl Phenom Macrocycl Chem (2010) 68:461–466
DOI 10.1007/s10847-010-9810-8
ORIGINAL ARTICLE
Recognition of dicarboxylic acids by a bis pyrimidine amine linked
xylene spacer: a unique gauche dimeric complex of host and adipic
acid detected by X-ray
•
Shyamaprosad Goswami Anita Hazra
•
Hoong-Kun Fun
Received: 9 March 2010 / Accepted: 25 May 2010 / Published online: 9 June 2010
Ó Springer Science+Business Media B.V. 2010
Abstract A pyrimidine based receptor (pyrimidine amine
linked xylene spacer) has been synthesized for recognition
of dicarboxylic acids. Binding studies have been performed
by UV–vis method by varying the chain length of dicar-
boxylic acids. The downfield chemical shift of amine
protons of receptor in presence of adipic acid or glutaric
acid and the 1:1 dimeric crystal structure of the receptor
and adipic acid reveal the strong binding interaction.
amide group is frequently used functionality for designing
extended self-assemblies with conventional hydrogen
bonding patterns with the dicarboxylic acids [8–13]. To
date, various receptors have been designed for selective
binding of carboxylic acids [14–22]. Recognition of
dicarboxylic acids having appropriate chain length selec-
tively bind pyridylamide-based ditopic receptor to form a
1:1 syn–syn dimeric complex (1) [23, 24] whereas
increasing the chain length of dicarboxylic acids, 1:1
polymeric complexes having ribbon structure are observed
instead of dimeric complex [25, 26]. Previously Hamilton
et al. [27] has shown that a syn–syn helical supramolecular
structure is formed by the complexation of dicarboxylic
acids with a receptor (2) having pyridylamide separated by
an isophthaloyl spacer. Etter et al. [28] has demonstrated
first the complexation of carboxylic acid using 2-amino
pyrimidine. Here in this paper, for the first time we discuss
the recognition of dicarboxylic acids by pyrimidine amine
linked-xylene spacer (3) and report solid state 1:1 dimeric
supramolecular structure of receptor 3 and adipic acid by
showing the conformation of receptor in gauche form.
Keywords Molecular recognition ꢀ
Supramolecular network ꢀ Host–guest interaction ꢀ
Hydrogen bonding
Introduction
In molecular recognition [1, 2] synthesis of an artificial
receptor for binding dicarboxylic acid is a massive inter-
esting area of research due to the biological importance and
the wide application of pharmaceutical science such as
receptor-based drug design [3, 4]. Recognition of carbox-
ylic acids is mainly based on hydrogen bonding interac-
tions [5–7]. Among the all hydrogen-bonding groups, the
O
O
O
O
N
N
N
H
H
N
N
N
N
N
N
N
H
H
H
H
O
H
H
O
N
N
Electronic supplementary material The online version of this
article (doi:10.1007/s10847-010-9810-8) contains supplementary
material, which is available to authorized users.
N
N
O
O
1
2
3
S. Goswami (&) ꢀ A. Hazra
Department of Chemistry, Bengal Engineering and Science
University, Shibpur, Howrah, West Bengal 711103, India
e-mail: spgoswamical@yahoo.com
Experimental
H.-K. Fun (&)
Receptor 3 has been synthesized in our laboratory [29] and
it was crystallized with adipic acid. Melting points were
recorded by hot coil stage melting point apparatus and were
X-ray Crystallography Unit, School of Physics, Universiti Sains
Malaysia, 11800 USM, Penang, Malaysia
e-mail: hkfun@usm.my
123

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J Incl Phenom Macrocycl Chem (2010) 68:461–466
1
uncorrected. H NMR spectra were recorded on 500 MHz
spectrometer. FT-IR spectra were recorded on a JASCO
FT/IR-460 plus spectrometer using KBr discs.
C6H10O4; Formula weight 494.59 g mol-1; Crystal system
˚
triclinic; Space group P-1; T = 100 K; a = 7.3487(2) A;
˚
˚
b = 8.8661(2) A; c = 19.4497(5) A; a = 91.745(2)°;
Intensity data of the crystal structure was collected on
Bruker SMART APEXII CCD area-detector diffractometer
[30]. Data reductions were performed using SAINT. The
structures were solved by direct methods and refined by
full-matrix least squares on F2 using the SHELXTL
package [31]. The softwares used to prepare material for
publication were SHELXTL and PLATON [32]. All
hydrogen atoms were located from the difference Fourier
maps and refined freely. The figures were plotted with the
aid of ORTEP [33] and Mercury 1.4.1 software. Crystal-
lographic data for the structural analysis have been
deposited with the Cambridge Crystallographic Data
Center No. CCDC 757534.
b = 90.02(2)°; c = 97.147(2)°; Z = 2; V = 1256.79(6)
3
A ; I = 0.71073 A; Dcalc = 1.307 g/cm3; F [000] = 528;
˚
˚
Crystal size = 0.05 9 0.12 9 0.37; h min–max = 1.0–
26.5°; l = 0.090 mm-1
; Index ranges -9 B h B 9;
-11 B k B 11; -24 B l B 24; Reflections collected 23571;
Unique reflections 5149; Observed reflections [I [ 2.0r(I)]
3567; R1 [I [ 2r(I)] 0.0415; wR2 0.1109; GOF 1.02.
Result and discussions
Receptor 3 has been easily synthesized in solid phase by
microwave irradiation according to our recently reported
procedure (Scheme 1) [29]. The compound is characterized
by spectral analysis. The single crystal X-ray structure of
receptor 3 and adipic acid is reported here.
General procedure for UV–vis titration
Stock solution of the receptor 3 was prepared in the order
of 1.11 9 10-4 M in acetonitrile. The solutions of guest
acids were also prepared in ca 1 9 10-3 M order in ace-
tonitrile. Then the guest solution was added to the receptor
solution (taking 2 mL in the UV-cell) and continuous
decreases of absorbance in UV spectra were recorded each
time. Association constants were calculated by plotting
1/DI versus 1/[G].
Receptor 3 having two pyrimidine amines linked by a
xylene spacer has two donor acceptor arrays for binding
dicarboxylic acids. In receptor 3, the benzylic carbons are
sp3 instead of sp2 which makes the receptor 3 more flexible
and as a result receptor 3 is free to rotate to adjust its
conformation to a stable gauche dimeric complex with
adipic acid (Fig. 1d as proved by X-ray structure deter-
mination) to match mutual size selectivity rather than the
formation of polymeric (Fig. 1a: hypothetical) or tetra-
meric complex (Fig. 1b: hypothetical). Due to the small
cavity of the syn form of receptor 3, syn–syn dimeric
complex is not observed (Fig. 1c: hypothetical).
Crystallization procedure of the co-crystal of receptor 3
and adipic acid
A 1:1 mixture of receptor 3 (20.1 mg, 0.06 mmol) and
adipic acid (8.8 mg, 0.06 mmol) was dissolved in a mix-
ture of chloroform methanol and hexane solution. The
single crystals were grown by slow evaporation of solvent.
Mp 120–122 °C; IR: 3434, 3295, 2914, 2851, 1679,
The 1:1 dimeric complex crystallized out in space group
P-1. The binding pattern of receptor 3 and adipic acid shows
that both the receptor and the guest adipic acid accommo-
date each other by taking the advantage of the flexibility of
the spacer methylenes attached in between the benzene ring
and the pyrimidine amine moieties of the receptor and also
the four methylenes between the carboxyl groups of the
guest adipic acid (Fig. 2a). The receptor 3 interacts with the
guest adipic acid in solid state by two eight-membered
cyclic hydrogen bonding network. Each cyclic hydrogen
bonding network contains (i) hydrogen bonding between
1
1578, 1450, 1367, 1295, 1152, 1028, 787 cm-1. H NMR
(500 MHz, CDCl3): 7.35 (s, 1H), 7.29–7.26 (m, 3H), 7.08
(bs, 2H), 6.29 (s, 2H), 4.62 (d, 4H, J = 5.60 Hz), 2.30
(t, 4H, J = 8.32 Hz), 2.28 (s, 12H), 1.63 (t, 4H,
J = 2.85 Hz).
Crystallographic data and structure refinement parame-
ters of the co-crystal: Empirical formula C20H24N6.
Scheme 1 Reagents and
conditions: (i) K2CO3,
450 Watt, 25 min, MW;
NH2
(i)
(ii) acetyl acetone, 300 W,
8 min, MW
H2SO4
+
N
N
(ii)
H
H
HN
SMe
N
N
2
N
N
NH2
NH2
4
5
Receptor 3
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J Incl Phenom Macrocycl Chem (2010) 68:461–466
463
Fig. 1 a Hypothetical anti–anti
1:1 polymeric structure; b
hypothetical syn–syn 2:2
tetrameric structure; c
hypothetical syn–syn 1:1
dimeric structure; d gauche 1:1
dimeric structure (ORTEP
diagram with 50% probability)
(co-crystal structure of receptor
3 with adipic acid)
N
N
N
N
N
N
H
N
H
N
N
N
H
N
N
H
H
O
H
O
H
O
O
O
O
O
O
O
O
H
O
O
H
N
H
N
H
H
N
H
N
H
N
N
N
N
N
N
N
N
(a)
(b)
N
N
N
N
H
O
H
O
N
N
H
O
H
O
(c)
(d)
Fig. 2 a 1:1 Gauche top–
bottom bound complex of
receptor 3 with adipic acid
along the crystallographic a
axis; b chair-like motif viewed
down crystallographic c axis.
Hydrogen bonds are shown in
dashed line
the pyrimidine amine of receptor 3 and the ‘O’ of carboxylic
˚
Previously Hamilton et al. [23] reported a syn–syn 1:1
acid moiety [N3–H1N3ꢀꢀꢀO3, 2.857(2) A; N4–H1N4ꢀꢀꢀO2,
dimeric co-crystal of adipic acid with pyridine amine
linked with a terephthaloyl spacer. Here in our case the
gauche 1:1 top–bottom bound dimeric co-crystal is
observed (Fig. 2). One asymmetric unit interacts with other
asymmetric units by secondary CH–p and C–HꢀꢀꢀO
˚
2.879(2) A; Table 1] and (ii) hydrogen bonding between the
pyrimidine nitrogen and the hydroxy group of carboxylic
˚
˚
acid [O1–H1ꢀꢀꢀN6, 2.650(2) A; O4–H4ꢀꢀꢀN2, 2.638(2) A;
Table 1].
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J Incl Phenom Macrocycl Chem (2010) 68:461–466
˚
Table 1 Hydrogen-bond parameters (A, °) of co-crystal of receptor 3
and adipic acid
D–HꢀꢀꢀA
d(HꢀꢀꢀA)
d(DꢀꢀꢀA)
h(D–HꢀꢀꢀA)
O1–H1ꢀꢀꢀN6
1.84
2.650(2)
2.857(2)
2.879(2)
2.638(2)
3.468(3)
3.523(2)
3.615(2)
168
N3–H1N3ꢀꢀꢀO3
N4–H1N4ꢀꢀꢀO2
O4–H4ꢀꢀꢀN2
2.00(2)
2.01(2)
1.83
173(2)
177.7(16)
168
C22–H22AꢀꢀꢀO3i
C18–H18CꢀꢀꢀCg3ii
C20–H20BꢀꢀꢀCg3iii
2.53
163
2.81
131
2.83
140
Symmetry codes: (i) -1 ? x, y, z; (ii) x, 1 ? y, z; (iii) x, -1 ? y, z;
Cg3 is the centroids of the ring C6/C7/C8/C9/C10/C11
interactions to make chair like supramolecular architecture
(Fig. 2b) [34, 35]. Thus, this case of complexation shows
unique conformational adjustments of host and guest to
compliment each other and this would have not been
possible with rigid small spacer.
Fig. 3 Partial 1H NMR (500 MHz) spectra of receptor 3 (a); addition
of equivalent amount of adipic acid (b); and addition of equivalent
amount of glutaric acid (c) in CDCl3
1
In H NMR spectrum, the amine protons of receptor 3
1
appear at 5.26 ppm in CDCl3. The 1:1 H NMR spectra of
receptor 3 with different carboxylic acids were performed in
CDCl3 solution. Generally dicarboxylic acids are insoluble
in chloroform but upon addition of equivalent amount of
solid adipic acid to the CDCl3 solution of receptor 3, the
adipic acid is soluble in the solution of receptor 3 and the
amine protons get shifted downfield with d value at
7.08 ppm (Fig. 3). The amine proton of receptor 3 shifts
downfield at 7.64 ppm upon addition of equivalent amount
of glutaric acid and is readily soluble in the CDCl3 solution
of receptor 3. The solubility of these acids in the receptor
solution points toward strong binding interaction between
host–guest. But in the case of 1,4-phenylenediacetic acid
only small amount of chemical shift (0.34 ppm) occurs (see
supporting information) and it is also only sparingly soluble
in the CDCl3 solution of receptor 3. The large chemical shift
of 2.38, 1.82 ppm for glutaric acid and adipic acid respec-
tively indicate the strong hydrogen bonding complexation
of receptor 3 with those acids and the above crystal structure
is the evidence of this observation.
The binding behavior of receptor 3 with different
dicarboxylic acids has been studied by UV–vis method.
A strong absorbance at kmax = 295 nm is observed for
receptor 3 (1.11 9 10-4 M) which is gradually decreased
upon addition of guest acid solution (ca 1 9 10-3 M)
(Fig. 4). To observe the binding affinity of receptor 3
towards dicarboxylic acids we have taken different acid
solutions having different chain lengths. The association
constant of receptor 3 with dicarboxylic acids are deter-
mined in acetonitrile (Fig. 5a) [36]. The binding constant
of receptor 3 with adipic acid and glutaric acid are higher
than those of other dicarboxylic acids (Table 2). From Job
plots, a prominent 1:1 complexation between receptor 3
and adipic acid or glutaric acid are observed since the
Fig. 4 UV–vis titration spectra
of receptor 3 with a glutaric
acid and b adipic acid
(a)
(b)
0.9
0.6
0.3
0.0
0.9
0.6
0.3
0.0
270
300
330
270
300
330
Wavelength (nm)
Wavelength (nm)
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J Incl Phenom Macrocycl Chem (2010) 68:461–466
465
Fig. 5 a Binding constant
(a)
(b)
calculation curves of receptor 3
with different dicarboxylic acids
by UV–vis method; b Jobs plots
of receptor 3 with different
dicarboxylic acids at
120
90
60
30
0
Pimelic acid
1,4-Phenylenediacetic acid
Glutaric acid
0.18
0.12
0.06
0.00
Adipic acid
kmax = 295 nm
Malonic acid
Succinic acid
Glutaric acid
Adipic acid
Pimelic acid
1,4-Phenylenediacetic acid
0
15
30
45
60
0.0
0.2
0.4
0.6
0.8
1.0
1/[G] x 103
Xhost
Table 2 Binding constants [Ka (M-1)] of receptor 3 with dicarbox-
ylic acids by UV–vis method
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All errors are 10%
complex concentration goes maximum when molar frac-
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Acknowledgments We thank CSIR [No. 01(2292)/09/EMR-II],
Government of India for financial support. A. H. thanks the CSIR,
Government of India for a research fellowship. We would also like to
thank the Malaysian Government and Universiti Sains Malaysia for a
Research University Golden Goose grant No. 1001/PFIZIK/811012.
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