Three crystalline forms of 1,3,5-benzene-tri(3-pyridinyl)carboxamide from the same solvent system

Article abstract of DOI:10.1016/j.molstruc.2007.07.006

The crystallization of the title compound from the MeOH resulted in three crystalline forms depending on the concentration of the solution, one of which contains N-H?N hydrogen bonds between pyridine and amide moieties, while the second one is constituted

Full text of DOI:10.1016/j.molstruc.2007.07.006

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Journal of Molecular Structure 876 (2008) 339–343
www.elsevier.com/locate/molstruc
Three crystalline forms of 1,3,5-benzene-tri(3-pyridinyl)
carboxamide from the same solvent system
*
Lalit Rajput, Kumar Biradha
Department of Chemistry, Indian Institute of Technology, Kharagpur-721302, India
Received 19 June 2007; received in revised form 3 July 2007; accepted 5 July 2007
Available online 14 July 2007
Abstract
The crystallization of the title compound from the MeOH resulted in three crystalline forms depending on the concentration of the
solution, one of which contains N–HÁ Á ÁN hydrogen bonds between pyridine and amide moieties, while the second one is constituted by
amide-to-amide N–HÁ Á ÁO hydrogen bonds and the third one crystallizes in a different crystalline phase (threads) and the phase could not
be identified. These three phases have shown different behaviours in TGA and DSC studies.
Ó 2007 Elsevier B.V. All rights reserved.
Keywords: Crystal engineering; Conformations; Amides
1. Introduction
compounds exhibit similar supramolecular structures con-
taining channels (Scheme 1) [4]. In contrast to the struc-
tures of bis amides, both 1a and 1b does not contain
amide-to-amide hydrogen bonds but contain N–HÁ Á ÁN
hydrogen bonds between pyridine and amide N–H groups.
To analyze these compounds further we have synthesized
1a and crystallized in MeOH.
The presence of multiple functional groups in a molecule
causes an interference in the formation of robust supramo-
lecular synthons [1,2]. The interference increases with
the presence of functional groups which are not self-com-
plimentary and also with the mismatch of donor and accep-
tors ratios. Recently, we have reported on the interference
of pyridine group in amide-to-amide hydrogen bonds by
analyzing the crystal structures bis(pyridinecarboxami-
do)alkane derivatives [3]. In those molecules the 2°-amide
groups are self complementary but not the pyridine groups
as they form relatively weak C–HÁ Á ÁN hydrogen bonded
synthons. Further, in bis(pyridinecarboxamido)alkane
derivatives, amide-to-amide hydrogen bonds occurred
more frequently while the pyridine moieties form
C–HÁ Á ÁN hydrogen bonds with aromatic C–H groups. In
continuation of our studies, we have focused on tris-amide
derivatives of trimesic acid containing 3-pyridine or 4-pyr-
idine moieties [1]. Recently the crystal structures of 1a and
1b have been reported and were shown that both these
R
R
N
R
N
H
N
O
O
H
H
H
O
H
O
H
N
O
R
R
O
H
N
R
H
N
O
N
H
H
R
1a: R = 3-Pyridyl; b: R= 4-Pyridyl
Synthon-I
2. Experimental
2.1. General
FTIR spectra were recorded with an NEXUS-870
instrument, Thermo Nicolet Corporation. Elemental anal-
yses were obtained with a Perkin-Elmer instrument, series
*
Corresponding author. Tel.: +91 3222 283346; fax: +91 3222 282252.
E-mail address: Kbiradha@chem.iitkgp.ernet.in (K. Biradha).
0022-2860/$ - see front matter Ó 2007 Elsevier B.V. All rights reserved.
doi:10.1016/j.molstruc.2007.07.006

340
L. Rajput, K. Biradha / Journal of Molecular Structure 876 (2008) 339–343
and hydrogen atoms were fixed at calculated positions
N
and refined using a riding model.
N
O
H
N
N
3. Results and Discussion
H
N
O
H
N
O
O
N
N
N
N
H
O
N
H
Our studies show that the compound 1a crystallizes
from MeOH in three forms but not in one form as it was
reported previously [4b]. One of the three is similar to the
reported structure (A-form, 1aÆ3MeOH), whereas as the
second one (B-form, 1aÆH2O) has an entirely different
structural characteristics and exhibits synthon-I (Table 1).
The third form (C-form, 1aÆH2O, polymorph of B-form)
we have obtained is not suitable for single crystal analysis
as it was crystallized as fine threads and characterized by
powder X-ray studies (Fig. 1). The CSD-analysis on the
tris-amide derivatives suggests that the synthon-I observed
here has an unique symmetry.
O
H
N
N
N
O
N
H
H
N
O
N
N
O
H
H
O
N
N
O
N
H
H
N
N
O
N
O
N
N
H
N
H
N
O
H
N
O
O
N
N
H
N
N
O
H
N
H
O
N
N
Scheme 1. Hydrogen bonding supramolecular structure observed for 1a in
A-form.
The process of crystallization has shown a dependency
on the concentration of solution and rate of evaporation.
In particular, highly concentrated solutions (5–37.5 mg/
ml) found to form crystals of A-form (1aÆ3MeOH), moder-
ate concentrations (3.5–4.2 mg/ml) were found to form
B-form (1aÆH2O) and dilute solutions (0.5–3.5 mg/ml) are
resulted in C-form (1aÆH2O, derived from elemental analy-
sis). However, we found that sometimes (two times out of
five trails) these concentration dependent results are not
repetitive as the rate of evaporation changes with atmo-
spheric conditions. Further, predominantly A-form was
obtained from concentrated solutions if the rate of evapo-
ration is faster. For example, if the rate of evaporation is
slower, it is observed that at 20 mg/ml concentration all
the three forms A, B and C, respectively, are obtained in
the same crystallization flask. The source for water of crys-
tallization could be from the washing of the product with
water prior to recrystallisation from methanol or from
atmospheric water. Similar results are reproduced by using
anhydrous MeOH.
II, CHNS/O analyzer 2400. TGA and DSC data were
recorded with a Perkin-Elmer instrument, Pyris Diamond
TG/DTA. Powder XRD data were recorded with a
XPERT-PRO PW3050/60 diffractometer.
2.2. Synthesis of 1a
3-Amino pyridine (1.44 mmol, 1.3436 g) was added to a
40 ml of 4-picoline solution of trimesic acid (4.8 mmol,
1 g), and the solution was stirred for 15 min. Triphenyl
phosphite (1.44 mmol, 4.4297 g) was added to this solution
and the mixture was refluxed for 5 h. The volume of the
solution was reduced to 5 ml by distilling out the picoline,
and a white precipitate was obtained. The solid was filtered
and washed with water and finally with acetone. Yield:
84.64%.
This product was crystallized from MeOH as described
in Results and discussion and obtained the three forms.
The elemental analysis of A-form is not reproducible as
mentioned in the earlier report. Whereas from the elemen-
tal analysis of B-form and C-form we can conclude that
both have the same composition water and they are
polymorphs.
B-form (1aÆH2O): Calcd (%): C, 62.91; H, 4.94; N, 18.26;
Obs (%): C, 63.15; H, 4.38, N, 18.42; C-form (1aÆH2O):
Calcd (%): C, 62.91; H, 4.94; N, 18.26; Obs (%): C,
63.33; H, 4.25; N, 18.70.
Table 1
Crystal data and structure refinement for B-form
Compound
Formula
M. wt.
T (K)
System
B-form
24H20N6O4
456.46
293 (2)
Monoclinic
Cc
C
Space group
˚
a (A)
17.761 (4)
14.571 (3)
8.3610 (17)
90
99.87 (3)
90
2131.8 (7)
4
1.422
˚
b (A)
˚
c (A)
2.3. Crystal structure determination
a (°)
b (°)
c (°)
The single crystal data was collected on Bruker-Nonius
Mach3 CAD4 X-ray diffractometer that uses graphite
3
˚
Vol. (A )
˚
monochromated Mo Ka radiation (k = 0.71073 A) by
Z
Dcalc (Mg/m3)
R1 (I > 2r(I))
wR2 (on F2, all data)
x-scan method. The structure was solved by direct methods
and refined by least square methods on F2 using SHELX-
97 [10]. Non-hydrogen atoms were refined anisotropically
0.0343
0.0980

L. Rajput, K. Biradha / Journal of Molecular Structure 876 (2008) 339–343
341
Fig. 1. Photographs of the crystals illustrating the morphological differences in three forms (a) form A became opaque as it looses the solvent; (b) form B
remains perfectly crystalline at room temperature; (c) form C (thin fibers), remains crystalline at room temperature.
In A-form, the molecule maintains a 3-fold symmetry
and hence it forms a honeycomb grid like structure via
N–HÁ Á ÁN hydrogen bonds. While in B-form the molecule
does not exhibit a 3-fold symmetry and exhibits a T-shape
geometry (Fig. 2). As a consequence they assemble via N–
HÁ Á ÁO (between amides, synthon-I), and O–HÁ Á ÁN
(between H2O and pyridine) hydrogen bonds. The inter-
planar angles between amide and central C6-rings are
about the same in both the forms (29.5° in A and 30°,
33.1°, 34.4 in B). However, the inter-planar angles of pyri-
dine with central C6 (9.6°, 8.4°, 27.5°) and with amide
plane in B (21.5°, 25.7°, 61.6°) are different from those in
A (68°, 38.7°).
hydrogen bonded layer structure formed by T-shaped mol-
ecules. These layers are joined together by synthon-I and
O–HÁ Á ÁO hydrogen bonding with water molecules (N–
HÁ Á ÁO and O–HÁ Á ÁN). The IR spectra clearly shows the
differences in carbonyl frequencies of the amide groups,
which confirms the fact that carbonyls are hydrogen
bonded in form B (1666 cmÀ1) but not in form A and C
(1682 cmÀ1) [5].
The C-form has thin threads like morphology and char-
acterized by powder X-ray diffraction. The X-ray powder
analysis confirms that the diffraction pattern for C-form
is different from those of form A and B (Fig. 4). Moreover,
B- and C-forms are crystalline at room temperature unlike
form A, which losses the solvent and there by the crystal-
line nature.
The three compounds have shown different melting
behaviours. The form A and C shows initial melting at
186–190 °C and the remaining solid (more in case of A-
form) sticks to the walls of the melting tube which finally
melts at 272–274 °C (A-form) and 278–280 °C (C-form).
However, B-form shows a single melting point at 272–
276 °C. To study this behaviour further we have investi-
gated TGA and DSC of these compounds (Fig. 5). In
TGA, the temperatures at which they loose the solvent
are different for all the three forms. A-form is loosing
absorbed water [6] at 126 °C, whereas B-form and C-form
loose the included water completely at about 162 and
185 °C, respectively. Therefore, up to 250 °C the weight
loss is different for all there forms. However, from 250 °C
Two of the three amide groups involve in the formation
of amide-to-amide hydrogen bonds with neighbouring
molecules along c-axis such that it forms a linear chain
(synthon-I, Fig. 3). We note here that the hydrogen bond-
ing synthon-I observed in this structure does not contain an
usual inversion centre but contains a glide plane (HÁ Á ÁO,
˚
˚
˚
NÁ Á ÁO, N–HÁ Á ÁO: 2.23 A, 3.066(2) A, 165°; 1.96 A,
˚
2.787(2) A, 162°). The third amide group of 1a forms N–
˚
HÁ Á ÁO hydrogen bonds with water molecule (1.98 A,
˚
2.770(3) A, 152°). Two out of the three pyridine moieties
˚
involved in O–HÁ Á ÁN hydrogen bonds with water (2.04 A,
˚
˚
˚
2.873(4) A, 175°; 2.11 A; 2.852(4) A, 165°) whereas the
third pyridine involved in C–HÁ Á ÁN hydrogen bonds
˚
˚
(2.97 A, 3.552(4) A, 122°). In brief, the structure can be
˚
˚
˚
described as a C–HÁ Á ÁO (2.79 A, 3.587(4) A, 145°; 2.84 A,
˚
˚
˚
3.477(4) A, 126°) and C–HÁ Á ÁN (2.85 A, 3.611(4) A, 139°)
Fig. 2. Molecular structures of 1a: (a) in the crystal structures of form B; and (b) form A; notice the difference in geometries.

342
L. Rajput, K. Biradha / Journal of Molecular Structure 876 (2008) 339–343
Fig. 3. Illustrations for the crystal structure of 1a in form B: (a) 1D-chain formed via synthon-I along c-axis; (b) top view of 1D-chain; (c) 2D-layer formed
via C–HÁ Á ÁO and C–HÁ Á ÁN hydrogen bonds; (d) unit cell showing the joining of the layers via hydrogen bonds, notice that the water molecules exist
between the layers.
transition. All the three forms have shown endotherms at
277–285 °C which may be the indication of decomposition
of the ligand.
a
In order to understand the unusual symmetry observed
for the synthon-I in B-form, we have used Cambridge
Structural Database (CSD) to study the structures of com-
b
pounds containing tris(amide), 1 [7]. The CSD search
resulted in 14 structures containing fragment-1 with vari-
ous R-groups. Out of 14, seven structures contain non-
pyridinyl groups as R-groups. In these seven structures,
c
only three structures contain the well-known triple-helix
structure (p-column) via amide-to-amide hydrogen bonds
(R = –CH2–CH2–OCH3 or –CH(COOMe)–CH2–CH2–
COOMe or CH(COOMe)CH(CH3)2) [8]. Further, none
10
20
30
of these seven structures exhibited synthon-I. In the
remaining seven structures, two corresponds to 1a (form
A) and 1b [4], four contain substituted 2-pyridine groups
as R-groups while one contains 2-picolyl group as R-
group. Interestingly, none of these pyridine containing
structures exhibit triple helix, but only one of them
(R = 4-methyl-2-pyridine) exhibit synthon-I (Fig. 6) [9].
Fig. 4. Powder X-ray diffraction patterns for (a) form A; (b) form B; and
(c) form C.
onwards the there forms show the similar type of thermal
behaviour.
˚
˚
In A-form an endotherm at 95 °C and a sharp endo-
therm at 126 °C are observed corresponding to loss of
water. Further, very small endo peaks at 196 and 226 °C
were observed which may correspond to phase transitions.
In B-form the mixture of exothermic and endothermic
events are observed at 219, 236 and 243 °C which may cor-
respond to the phase transitions. In form C, a sharp endo-
therm in the region of 204 and 212 °C indicates a phase
However, here the synthon-I (2.012 A, 2.877 A, 161.7°;
˚
˚
2.514 A, 3.097 A, 123°) has a translational symmetry unlike
in B-form.
In summery, the crystallization of the compound 1a was
shown to depend on its concentration in MeOH. The lower
concentrations of 1a lead to the formation of C-form, mod-
erate concentrations lead to B-form and highly concen-
trated solutions lead to crystallization of A-form. Crystal

L. Rajput, K. Biradha / Journal of Molecular Structure 876 (2008) 339–343
343
110
100
90
A-Form
b
a
B-Form
C-Form
60
50
40
30
20
10
0
C
A-Form
B-Form
C-Form
C
B
A
80
70
60
50
A
A
40
B
30
-10
50
100
150
200
250
300
0
100
200
300
400
500
Temperature (0C)
Temperature (0C)
Fig. 5. (a) TGA (b) DSC spectra for the three forms.
Supplementary data associated with this article can be
found, in the online version, at doi:10.1016/j.molstruc.
2007.07.006.
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Acknowledgements
[6] This compound has been reported to take up atmospheric water after
desorbtion of MeOH (Ref. [4b]). The elemental analysis after
desorbtion of MeOH shows that it can take up to 5 molecules of
water per one molecule of 1a: Found: C, 54.38%; H, 5.15%; N,
15.91%; Calcd: C, 54.54%; H, 5.30%; N, 15.90%.
[7] F.H. Allen, O. Kennard, Chem. Des. Autom. News 8 (1993) 31.
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We gratefully acknowledge financial support from the
Department of Science and Technology (DST) and DST-
FIST for single crystal X-ray facility. L.R. thanks IIT
(Kharagpur) for research fellowship.
Appendix A. Supporting information
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(2000) 289;
(c) P.P. Bose, M.G.B. Drew, A.K. Dasa, A. Banerjee, Chem.
Commun. (2006) 3196.
The IR spectra for three forms and crystallographic
tables for B-form. CCDC 624740 contain the supplemen-
tary crystallographic data for this paper. These data can
be obtained free of charge from The Cambridge Crystallo-
graphic Data Centre via www.ccdc.cam.ac.uk/data_
request/cif.
[9] M. Mazik, W. Sicking, Tetrahedron Lett. 45 (2004) 3117–3121.
[10] G.M. Sheldrick, SHELX-97, Program for the Solution and Refine-
ment of Crystal Structures, University of Go¨ttingen, Go¨ttingen,
Germany, 1997.