Crystalline forms of 1,3,5-benzene-tri(pyridinyl)carboxamides: Isolated site hydrates as polymorphs and solvates

Article abstract of DOI:10.1016/j.molstruc.2011.02.011

The crystallization of 3-pyridyl (1) and 4-pyridyl (2) analogues of the title compound results in different crystalline hydrates and polymorphs and their crystal structures reveal that 1 and 2 exhibit conformational isomerism. The molecule 1 forms three c

Full text of DOI:10.1016/j.molstruc.2011.02.011

Journal of Molecular Structure 991 (2011) 97–102
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Journal of Molecular Structure
journal homepage: www.elsevier.com/locate/molstruc
Crystalline forms of 1,3,5-benzene-tri(pyridinyl)carboxamides: Isolated site
hydrates as polymorphs and solvates
⇑
Lalit Rajput, Kumar Biradha
Department of Chemistry, Indian Institute of Technology, Kharagpur 721 302, India
a r t i c l e i n f o
a b s t r a c t
Article history:
The crystallization of 3-pyridyl (1) and 4-pyridyl (2) analogues of the title compound results in different
crystalline hydrates and polymorphs and their crystal structures reveal that 1 and 2 exhibit conforma-
tional isomerism. The molecule 1 forms three crystalline forms from MeOH solution depending on con-
centration of the solution. Among these three forms, two are polymorphic monohydrates. However, the
crystallization of 2 was found to be dependent on the solvent of crystallization and resulted in new crys-
talline form from DMF as a dihydrate. The hydrates of both 1 and 2 can be classified as isolated site
hydrates. In these crystal structures, water molecules found to exhibit three types of coordination envi-
ronments with regard to hydrogen bonds.
Received 12 November 2010
Received in revised form 5 February 2011
Accepted 7 February 2011
Available online 4 March 2011
Keywords:
Amides
Hydrates
Polymorphs
Solvates
Ó 2011 Elsevier B.V. All rights reserved.
Conformations
Hydrogen bonds
1. Introduction
Prediction of periodic arrangements of organic molecules in
the crystal lattice via anticipated supramolecular synthons is al-
ways a challenge [1]. This is due to the dependency of the resul-
tant structure on several factors such as solvent, concentration,
temperature and technique of crystallization [2]. The existence
of several polymorphs or solvates for any given compound is
probably the most convincing example of this aspect [3]. Gener-
ally it is well accepted that the misbalance of number of accep-
tors and donors increases the probability of formation of solvates
or hydrates such that the balance between acceptors and donors
is achieved in the crystal lattice [4]. In such situations the inclu-
sion of water into the crystal lattice is more frequent due to its
abundance in the atmosphere and in some organic solvents,
small size and versatile hydrogen bonding ability. It has been
suggested that almost 33% of organic compounds form hydrates,
whereas inclusion of other solvents occurs only in 10% of organic
compounds [5]. In pharmaceutical industry almost 1/3rd of the
APIs are found to exhibit the tendency to form crystalline hy-
drates [6].
Hydrates are classified into three types: isolated site hydrates,
channel hydrates and metal-ion coordinated hydrates [7]. In iso-
lated site hydrates, the water molecules are not directly hydrogen
bonded to each other. Channel hydrates are the ones where water
molecules are hydrogen bonded to each other to form clusters or
networks within the channels formed by some other chemical
component(s). In metal-ion coordinated hydrates, water molecules
are coordinated to the metal ion. The Cambridge Structural Data-
base (CSD) analysis by Gillion et al. reveals that water molecules
exhibit eight different possible hydrogen bonding environments
in the crystal structures of hydrates [8]. In some cases, formation
of hydrate helps in stabilizing the crystal structures by the forma-
tion of diverse set of supramolecular synthons. In our previous
study we have observed that the compound 1 crystallizes in three
different forms (one unstable methanol solvate and two stable
⇑
Corresponding author.
E-mail address: kbiradha@yahoo.com (K. Biradha).
0022-2860/$ - see front matter Ó 2011 Elsevier B.V. All rights reserved.
doi:10.1016/j.molstruc.2011.02.011

98
L. Rajput, K. Biradha / Journal of Molecular Structure 991 (2011) 97–102
monohydrates) [9]. Out of these three, only two crystal structures
(Form 1A and 1B) were reported as the third form (Form 1C) did
not form suitable crystals for single crystal X-ray diffraction anal-
ysis. However, in the previous report the existence of the third
form was proved by TGA, DSC, powder-XRD and elemental analysis
[9,10]. Herein we report successful efforts in obtaining the single
crystals of the third form of 1 and also of a dihydrate of related ana-
logue 2 [11]. In case of 1 the three crystalline forms were obtained
from the same solvent such as MeOH at different initial concentra-
tions. While in case of 2 the crystallization did not exhibit any such
concentration dependency. Further, the compounds containing
multiple pyridine or carboxylic acids have been well known to
form versatile coordination polymers [12]. One of the primary
goals in engineering such structures is to incorporate catalytic
centres in crystal lattices with channels for solvents and substrates
[13].
Calculated: C, 62.91%; H, 4.94%; N, 18.26%; found: C, 63.14%; H,
4.57%; N, 18.54%.
2.3. Synthesis of 2
Similar procedure was adopted as of 1 and the product was
recrystallized from DMF. Yield: 78.37%.
2Á2H2O (2B): Calculated: C, 60.75%; H, 4.67%; N, 17.71%; Found:
C, 60.82%; H, 4.24%, N, 17.60%.
2.4. X-ray crystal structure determination
The single crystal data was collected on Bruker APEX-2 CCD X-
ray diffractometer that uses graphite monochromated Mo Ka radi-
ation (k = 0.71073 Å) by hemisphere method. The structures are
solved by direct methods and refined by least square methods on
F2 using SHELX-97 [14]. Non-hydrogen atoms were refined aniso-
tropically and hydrogen atoms were fixed at calculated positions
and refined using a riding model.
2. Experimental section
2.1. General
3. Results and discussion
FTIR spectra were recorded with an NEXUS-870 instrument,
Thermo Nicolet Corporation. Elemental analyses were obtained
with a Perkin–Elmer instrument, series II, CHNS/O analyzer 2400.
TGA data were recorded with a Perkin–Elmer instrument, Pyris
The compounds 1 and 2 are of our interest to understand the
interference of pyridine group in amide-to-amide hydrogen bond
formation [15]. These classes of compounds are also useful for
the construction of coordination polymers where amide-to-amide
Diamond TG/DTA. Powder XRD data were recorded with
XPERT-PRO PW3050/60 diffractometer.
a
Table 1
2.2. Synthesis of 1
Crystallographic parameters for compounds 1C and 2B.
Compound
1C
2B
The THF solution of 1,3,5-benzenetricarbonyl chloride
(0.5310 g, 2 mmol) was added drop wise to the THF solution
(25 mL) of 3-aminopyridine (0.5647 g, 6 mmol) and triethylamine
(1.0119 g, 10 mmol) at 0 °C with continuous stirring under nitro-
gen atmosphere. The solution was stirred overnight. THF was dis-
tilled off and the solid product thus obtained was washed with
water and recrystallized from MeOH. Yield: 85%. This product
was crystallized from MeOH as described in the results and discus-
sion and obtained the crystals of three forms.
Formula
M.wt.
T (K)
System
Space group
a (Å)
C
24H20N6O4
C24H22N6O5
474.48
293(2)
Orthorhombic
Pbca
7.593(4)
15.736(7)
36.327 (2)
90
456.46
293(2)
Orthorhombic
Pbca
8.1324(6)
22.0796(2)
24.1286(2)
90
b (Å)
c (Å)
a
(°)
b (°)
90
90
The elemental analysis of A-form is not reproducible as men-
tioned in the earlier report.
c
(°)
90
4332.5(6)
8
1.400
0.0499
0.1213
90
4340 (3)
8
1.452
0.0628
0.1903
V (Å3)
Z
1ÁH2O (1B): Calculated: C, 62.91%; H, 4.94%; N, 18.26%; found: C,
Dcalc (Mg/m3)
63.1%; H, 4.38%, N, 18.42%.
R1 (I>2
r(I))
wR2 (on F2, all data)
1ÁH2O (1C): Layering 25 mg of 1 in 3 mL MeOH over 6 mL of H2O
in a sealed test tube resulted into diffractable quality crystals.
Fig. 1. Honeycomb network via NAHÁ Á ÁN hydrogen bonds observed in: (a) 1A and (b) 2A.

L. Rajput, K. Biradha / Journal of Molecular Structure 991 (2011) 97–102
99
Fig. 2. Illustrations for the crystal structure of 1B: (a) interaction of water with 1, 1D-chain formed via amide-to-amide NAHÁ Á ÁO hydrogen bonds along c-axis; (b) side view
and (c) top view; (d) 2D-layer formed via CAHÁ Á ÁO and CAHÁ Á ÁN hydrogen bonds involving water molecules; (e) packing of the 2D-layers through water and amide-to-amide
hydrogen bonds.
Fig. 3. Illustrations for the crystal structure of 1C: (a) interaction of water with 1; (b) amide-to-amide hydrogen bonded column; (b) side view and (c) top view; (d) 2D-layer
formed via NAHÁ Á ÁN, CAHÁ Á ÁO hydrogen bonds and through water molecules and (e) joining of the zig-zag layers through water molecules.
recognition provides more control over the network geometries
[16]. Both the compounds have more number of acceptors (six)
than donors (three). To compensate such misbalance between
donors and acceptors these molecules tend to include solvent
molecules in their crystal lattice.
During the crystallization of 1 from MeOH, initially hexagonal
shaped crystals were formed and subsequently rectangular block
shaped crystals were observed in the same crystallization flask.
To understand this process in detail the crystallization studies for
1 and 2 were carried out by varying the concentration and/or sol-

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L. Rajput, K. Biradha / Journal of Molecular Structure 991 (2011) 97–102
Fig. 4. Illustrations for the crystal structure of 2B: (a) Interaction of water molecules with 2; (b) amide-to-amide hydrogen bonded 1D-chain, 2D-layer formed via NAHÁ Á ÁO
and NAHÁ Á ÁN hydrogen bonds; (c) top view and (d) side view; (1D-chains via amide-to-amide hydrogen bonds molecules are shown in one colour) and joining of the 2D-
layers through water molecules; (e) top view and (f) side view.
vent of crystallization. In case of 1, we have observed that high
concentrations of 1 in MeOH (5–37.5 mg/ml) results in MeOH sol-
vate of 1 (1A, 1Á3MeOH) which is unstable at room temperature,
crystal structure of this form was reported by Palmans et al.
(Fig. 1a) [10]. The moderate (3.5–4.2 mg/ml) and low concentra-
tions (0.5–3.5 mg/ml) of 1 in MeOH resulted in the crystals of
two stable forms 1B (1ÁH2O) and 1C (1ÁH2O) respectively. However
the crystals of 1C which were grown in this procedure are fibrous
in nature and not suitable for single crystal X-ray diffraction.
Therefore, good quality crystals of 1C were obtained by layering
MeOH solution of 1 over the H2O in a sealed test tube (Table 1).
The compound 2 earlier was reported by Dastidar et al. to form
single crystals (2A, 2Á0.16DMSOÁ0.33MeOH) from DMSO, the crys-
tal structure contains assembling of the molecules via NAHÁ Á ÁN
hydrogen bonds to form a network containing continuous channels
similar to the form 1A (Fig. 1b) [11]. Our studies by varying the
concentrations of 2 in DMSO always resulted in the crystals of
same form (2A) indicating that the formation of crystal forms does
not depend on the concentration. However, our efforts are success-
ful in obtaining another crystalline form (2B, 2Á2H2O) of 2 by
choosing a different solvent such as DMF.
In the crystal structure of form 1B, the molecule adopts T-shape
geometry and includes one water molecule in its asymmetric unit.
Water exhibits three coordination via hydrogen bonding: one to
amide ANH (NAHÁ Á ÁO: 1.980 Å, 152.09°, 2.770 Å) and two with
N-atoms of two pyridyl units (OAHÁ Á ÁN: 2.037 Å, 175.57°,
2.873 Å; 2.109 Å, 165.74°, 2.852 Å) (Fig. 2a). The other two NAH
groups of 1 are involved in amide-to-amide hydrogen bonds with
neighbouring molecules along c-axis such that it forms a linear
chain (Fig. 2b–c). One of the three pyridine units which is not in-
volved in OAHÁ Á ÁN hydrogen bond with water forms a CAHÁ Á ÁN
hydrogen bond (Fig. 2d). Overall each unit of 1 is hydrogen bonded
to three water molecules. In brief, the structure can be best de-
scribed as joining of 2D-layers, which are formed via CAHÁ Á ÁO
and CAHÁ Á ÁN hydrogen bonds, through water molecules and
amide-to-amide hydrogen bonds along c-axis (Fig. 2e). We note
here that the water molecules are present in between the layers
and no other significant weak interactions were observed between
1 and water molecules.
Form 1C is a polymorph of 1B and molecules in the crystal
structure of 1C exhibit similar T-shape as that of 1B. However
the inter-planar angles between amide and central C6-rings signif-

L. Rajput, K. Biradha / Journal of Molecular Structure 991 (2011) 97–102
101
icantly differ from those of form 1B (29.5° in 1A; 30°, 33.1°, 34.4 in
1B and 1.09°, 25.49°, 36.99° in 1C). These differences in the geom-
etry also reflected in their supramolecular aggregation with itself
and also with water. In this form water molecule exhibits five coor-
dination with respect to hydrogen bonds (Fig. 3a). The five hydro-
gen bonds include one NAHÁ Á ÁO (2.180 Å; 159.25°, 3.000 Å), two
OAHÁ Á ÁN (1.881 Å; 174.31°, 2.774 Å; 2.131 Å; 172.16°, 2.950 Å),
two CAHÁ Á ÁO hydrogen bonds one each of with CAH of central
phenyl (2.455 Å; 171.64°, 3.378 Å) and CAH of pyridine (2.619 Å;
129.17°, 3.287 Å). The molecules interact with each other via a sin-
gle amide-to-amide NAHÁ Á ÁO (2.223 Å, 150.89°, 3.006 Å) hydrogen
bond along a-axis (Fig. 3b–c) to form an offset stacks between cen-
tral C6 rings. These stacks are further connected with the adjacent
stacks in bc-plane via NAHÁ Á ÁN (2.300 Å, 160.69°, 3.125 Å),
CAHÁ Á ÁO (2.470 Å; 169.59°, 3.389 Å; 2.453 Å 137.57°, 3.201 Å)
hydrogen bonds and through water molecules (Fig. 3d). The 2D lay-
ers are linked along a-axis through water molecules, that are pres-
ent within the layer, and amide-to-amide hydrogen bonds (Fig. 3e).
It is important to note here that the single crystals suitable for
X-ray diffraction analysis for form-1C were obtained by using dif-
ferent conditions from the initially reported ones [9]. However, the
calculated powder X-ray pattern of 1C found to match exactly with
the initially reported experimental powder pattern of 1C.
show conformational isomerism which results in different crystal-
line forms. The stable crystalline forms were observed when the
molecules are including water in their crystal lattice compared to
other solvents. In the hydrate structures three different coordina-
tion environments for water are observed depending upon the po-
sition of water with respect to the molecular plane. The three
forms of 1 can be selectively achieved depending on its concentra-
tion in MeOH, whereas of 2 based on the solvent of crystallization.
Supporting information
The IR spectra, TGA and Powder XRD patterns of compounds.
CCDC 800565 and CCDC 800566 contain the supplementary crys-
tallographic data for this paper for 1C and 2B respectively. These
data can be obtained free of charge from the Cambridge Crystallo-
graphic Data Centre via www.ccdc.cam.ac.uk/data_request/cif.
Acknowledgement
We gratefully acknowledge DST for financial support and DST-
FIST for single crystal X-ray facility. L.R. thanks IIT (Kharagpur)
for research fellowship.
Compound 2 has poor solubility in common organic solvents
and soluble only in DMF or DMSO. The reported form 2A was ob-
tained from DMSO–MeOH solvent mixture [11]. We have obtained
the second form 2B by crystallizing 2 from DMF. The compound 2
crystallizes as a dihydrate from DMF. In the crystal structure of 2B,
the molecule exhibits T-shape geometry similar to the geometry of
1 in 1B or 1C. The water molecules have different coordination
through hydrogen bonding (Fig. 4a). One of the two exhibits five
coordination similar to the one observed in 1C: one NAHÁ Á ÁO
(2.043 Å; 164.10°, 2.880 Å) and two OAHÁ Á ÁN (2.015 Å; 170.42°,
2.927 Å; 2.093 Å, 166.21°, 2.777 Å) and two CAHÁ Á ÁO (with phenyl
2.402 Å; 140.50°, 3.175 Å and with pyridine 2.463 Å, 137.41°,
3.210 Å) hydrogen bonds. The second water molecule involved in
four significant interactions: one OAHÁ Á ÁO hydrogen bond with
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