Construction of preorganized uracil based polytopic tectons for hydrogen-bonded supramolecular architectures

Article abstract of DOI:10.1016/j.molstruc.2012.02.012

Several polytopic ligands decorated with 1-methyluracil moieties at their ends have been synthesized in high yield. Single crystal X-ray diffraction analyses of bis-uracil conjugate (bis(1-methyluracilyl-5yl-)4-nitrobenzyl methane, 2) and tetra-uracil con

Full text of DOI:10.1016/j.molstruc.2012.02.012

Journal of Molecular Structure 1015 (2012) 99–105
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Journal of Molecular Structure
journal homepage: www.elsevier.com/locate/molstruc
Construction of preorganized uracil based polytopic tectons
for hydrogen-bonded supramolecular architectures
c
a,
Sourav Chakraborty a, Pablo J. Sanz Miguel b, , Francisca M. Albertí , Neeladri Das
⇑
⇑
a Department of Chemistry, Indian Institute of Technology, Patna, Patna 800 013, Bihar, India
b Departamento de Química Inorgánica, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), Universidad de Zaragoza – CSIC, 50009 Zaragoza, Spain
c Fakultät Chemie, Technische Universität Dortmund, 44221 Dortmund, Germany
a r t i c l e i n f o
a b s t r a c t
Article history:
Several polytopic ligands decorated with 1-methyluracil moieties at their ends have been synthesized in
high yield. Single crystal X-ray diffraction analyses of bis-uracil conjugate (bis(1-methyluracilyl-5yl-)4-
nitrobenzyl methane, 2) and tetra-uracil conjugate (1,3-bis[di(1-methyluracilyl)methyl]benzene, 3) indi-
cate presence of distinctly different hydrogen bonding patterns in the supramolecular framework. While
self-assembly of 2 utilizes a wobble type (mismatch) self-pairing, no base-pairing interaction of any kind
is observed in the packing of tetra-uracil conjugate 3. In the latter case, the presence of an acyclic water
trimer reinforces the supramolecular framework. However, in the presence of HClO4, molecules of 3 are
again associated via wobble (mismatched) complimentary self-base pairing. 3 represents the first nucle-
obase based tetratopic ligand till date. Investigation, as to how the hydrogen bonded supramolecular
framework is affected on increasing the number of hydrogen-bonding pendants, is reported here.
Ó 2012 Elsevier B.V. All rights reserved.
Received 26 December 2011
Received in revised form 3 February 2012
Accepted 3 February 2012
Available online 15 February 2012
Keywords:
Supramolecular structures
1-Methyluracil
Base-pairing
Wobble
Water cluster
H-bonding
1. Introduction
molecular self-assembly of supramolecules having uracil as tecton
utilize arrays of multiple hydrogen bonds for holding together the
Supramolecular chemistry and self-assembly are among the
frontier areas of research in molecular sciences, as evidenced by
the intense interest and the great surge of publications in this area
during the last decade [1]. Among the many building blocks uti-
lized to construct supramolecular architectures, the versatility
and potential of nucleobases has been widely studied [2]. This is
the case of uracil, which has also a biological importance because
of its presence in RNA [2a,e,3]. Literature has several reports
wherein uracil based molecules have exhibited medicinal proper-
ties, including antiviral activity [4]. In this context, it must be men-
tioned that 1-methyluracil (1-MeUH) is considered a model of
uridine and thymidine nucleobases, present in the biopolymer
RNA and DNA respectively [5]. In general, N1-alkylated nucleo-
bases have been reported to be pharmaceutically important
because of their potential application as anticancer agents [6]. Sev-
eral PdII and PtII organometallic complexes with anions of model
nucleobases including 1-methyluracil have demonstrated to be
more active than cisplatin [7].
individual building blocks [8]. Recently, Ganesh and coworkers
have reported the self-assembly of highly ordered structures
arising from hydrogen bonding interactions between uracil units
present in bis-uracil conjugates [9]. Champness et al. designed a
supramolecular building block containing two uracil units con-
nected by an aromatic spacer [10]. This tecton self-assembles with
another tecton (melamine) having complimentary hydrogen bond-
ing motif to yield a hydrogen-bonded sheet. From coordination
chemistry viewpoint, N1-substituted uracil ligands are interesting
because they contain several potential donor atoms for metal coor-
dination, namely O2, N3, O4, C5, and combinations thereof. This
has been documented by Lippert and others [11]. In this context,
Das et al. have reported synthesis of methylene-[5,50-bis-(1-meth-
yluracil)]. This ditopic ligand, with two 1-methyluracil units linked
via a methylene bridge through C5, has been used as building block
to self-assemble metallasupramolecules forming ‘‘hybrids between
classical organic calix[4]arenes and metallacalix[4]arenes’’ [12].
In view of the importance of multitopic uracil linkers as build-
ing blocks for supramolecular architectures, there is a need to
design ligands functionalized with multiple uracil moieties. One
of our research interests is the design of such uracil conjugates,
utilizing 1-MeUH as the synthon. The presence of triple hydrogen
bonding system in the form of acceptor–donor–acceptor (ADA)
array in 1-MeUH (Chart 1), offers several possibilities for forming
strong hydrogen bonded networks. Chart 1 shows representative
From a viewpoint of crystal engineering, uracil based ligands
are important because of their ability to form hydrogen bonds
using the endocyclic nitrogen and exocyclic oxygen centers. Often
⇑
Corresponding authors. Tel.: +91 612 2552023; fax: +91 612 2277383.
E-mail addresses: pablo.sanz@unizar.es (P.J. Sanz Miguel), neeladri@iitp.ac.in
(N. Das).
0022-2860/$ - see front matter Ó 2012 Elsevier B.V. All rights reserved.
doi:10.1016/j.molstruc.2012.02.012

100
S. Chakraborty et al. / Journal of Molecular Structure 1015 (2012) 99–105
4-nitrobenzylmethane (2), 1,3-bis[di(1-methyluracilyl)methyl]ben-
zene (3), and 1,4-bis[di(1-methyluracilyl)methyl]benzene (4). The
molecules designed can be classified into two types of tectons. One
class includes bis-uracil conjugates (1, 2) havingtwo hydrogen-bond-
ing appendages, while the other category (tetra-uracil conjugates: 3,
4) comprises of ligands with four H-bonding uracil units. This study
primarily aims to investigate how the hydrogen bonded supramolec-
ular framework is affected on increasing the number of hydrogen-
bonding pendants from two to four. Linkers (1–4) have been
characterized by NMR spectroscopy. Additionally, ligands 2 and 3
have been structurally characterized. To the best of our knowledge,
ligand 3 represents the first example of a nucleobase (uracil) based
tetratopic ligand till date.
2. Synthesis and characterization of multitopic uracil ligands
The synthesis of tectons 1–4 employed relatively simple reac-
tion pathways involving condensation of 1-MeUH [14] with an
aldehyde in the presence of concentrated acid under refluxing con-
dition (Scheme 1). The white precipitate thus obtained was col-
lected by filtration and washed with water to yield the desired
compounds in high purity. In all cases, the reaction was very clean
providing only one product with the yield of the reaction greater
than 80%.
Chart 1. (i) ADA array of 1-MeUH; (ii) Wobble type symmetrical self-base pairs via
two N3Hꢀ ꢀ ꢀO2 hydrogen bonds; [2a,9] (iii) Reverse Wobble type via two N3Hꢀ ꢀ ꢀO4
hydrogen bonds; [2a,9] (iv) Non-symmetrical N3Hꢀ ꢀ ꢀO4 and N3Hꢀ ꢀ ꢀO2 hydrogen
bonding mismatch [13].
Compounds 1–4 were characterized by 1H NMR (cf. Notes and
References). Compounds 1, and 3 exhibited limited solubility and
only dimethylsulfoxide (DMSO) provided adequate solubilization
to record 1H NMR spectra. For compounds 1 and 3, the N-methyl
proton peak was observed as a singlet at d = 3.2 ppm. Similarly,
the proton attached to C6 of uracil and the –CH–Ph– proton were
observed in the ranges 7.0–7.2 ppm, and 5.0–5.2 ppm, respectively.
1H NMR of 2 and 4 were recorded in NaOD solution because of its
extremely poor solubility in common organic solvents including
examples of self-base pairing for 1-MeUH such as (ii) Wobble, (iii)
reverse Wobble, and (iv) non-symmetrical types.
In continuation of our efforts to design new multitopic ligands
derived from 1-methyluracil, we herein report the facile synthesis
and characterization (1H NMR and single crystal X-ray crystallogra-
phy) of several uracil based (1–4) ligands in good yield: bis(1-methyl-
uracilyl-5yl-)3-nitrobenzylmethane (1), bis(1-methyluracilyl-5yl-)
Scheme 1. Synthesis of bis- and tetra-uracil derivatives in high yield.

S. Chakraborty et al. / Journal of Molecular Structure 1015 (2012) 99–105
101
DMSO-d6. For compounds 2 and 4, the N-methyl proton peak was
4. Crystal structure analysis of 3
observed as a singlet in the range 3.1–3.2 ppm, and the C6H proton
of uracil and the –CH–Ph– proton were observed in the ranges 6.7–
7.0 ppm, and 5.0–5.2 ppm, respectively.
Tetratopic ligand 3 (Fig. 3) was found to crystallize in two dif-
ferent modifications: 3a (3ꢀ4H2O), and 3b (3ꢀ2H2OꢀHClO4). The
asymmetric unit of 3a contains a molecule of 3 and four water mol-
ecules. The structure of 3a is related to 2, consisting on a benzene
ring to which, two bonded CH-methane groups (C1 and C2) are 1,3-
positioned. To each C1 and C2 groups, two 1-MeUH moieties are
attached, resulting in a tetra-1-methyluracilyl substituted struc-
ture. In 3a, all four uracil rings (labeled 1-MeUHA, 1-MeUHB,
1-MeUHC, 1-MeUHD) present different spatial orientations, as evi-
denced by the distances of their C5 sites to plane defined by the
benzene ring (ꢁ0.974(3) Å, C5a; 1.375(3) Å, C5b; ꢁ0.150(3) Å,
C5c; 1.126(3) Å, C5d). Dihedral angles of their pyrimidinic rings
with the planes defined by C11/C5a/C5b and C15/C5c/C5d (atoms
attached C1H and C2H, respectively) show different values:
51.48(6)° (1-MeUHA), 47.60(8)° (1-MeUHB), 71.50(6)° (benzene
ring), 49.42(7)° (1-MeUHC), 88.17(7)° (1-MeUHD), and 33.23(9)°
(benzene ring). Besides, dihedral angle values between by both
As compounds 1–4 exhibited limited solubility in common or-
ganic solvents, attempts to crystallize them were made under
hydrothermal conditions: in the presence of 3 mL of water at
180 °C, and then cooling the reaction mixture to ambient temper-
ature. Our efforts to obtain crystals suitable for X-ray structural
analysis were only successful for 2 and 3 (both crystallized as hy-
drates), whereas 1 and 4, despite of repeated attempts, did not
yield suitable crystals.
3. Crystal structure analysis of 2
Single crystal X-ray diffraction studies revealed that 2 crystal-
lized in the triclinic space group P–1 with three highly disordered
water molecules (cf. Notes and References). The crystal structure
analysis of 2ꢀ3H2O reveals no unusual bond lengths or angles with-
in the bitopic ligand 2. As shown in Fig. 1, the molecular structure
of 2 consists of a nitrobenzyl and two 1-MeUH moieties (1-MeUHA
and 1-MeUHB) bonded to the central C1H methane group. Mutual
orientations of the ring planes are not far from 90° (1-MeUHA/1-
MeUHB, 82.71(6)°; 1-MeUHA/benzyl 89.42(8)°; 1-MeUHB/benzyl,
88.98(8)°), while they form dihedral angles with the plane defined
by C5a/C5b/C11 (atoms bonded to C1H) within a small range:
57.89(1)° (benzyl), 49.80(8)° (1-MeUHA), and 50.97(7)° (1-MeUHB).
Mutual orientation of both Watson–Crick edges can be esti-
mated by the distances between N3a and the 1-MeUHB ring plane
(2.566(5) Å), which is almost identical as its corresponding N3b–1-
MeUHA value (2.543(5) Å), and the relative separation of their
atoms: O2a–O2b, 9.271(2) Å; N3a–N3b, 6.528(2) Å; and O4a–
O4b, 4.557(2) Å.
Both uracil moieties in 2 show different hydrogen bonding pat-
terns. 1-MeUHA is bonded via two N3aHꢀ ꢀ ꢀO2a0 (2.889(2) Å) hydro-
gen bonds with a symmetry related 1-MeUH0A entity, forming
wobble type (cf. Chart 1, (ii)) symmetrical pairs. Additionally,
O4a forms a H-bond with N3bH0 (2.884(2) Å) of a neighboring base.
Both nucleobases are twisted 82.71(6)°. Both O2b and O4b sites of
1-MeUHA are involved in H-bonding with the highly disordered
water molecules of the unit cell. The aforementioned intermolecu-
lar H-bonds generate infinite one-dimensional chains along the
[101] direction (Fig. 2).
Fig. 2. Association of ditopic ligand 2 through self-base pairing of wobble type and
Fig. 1. View of bis(1-methyluracilyl-5yl-)4-nitrobenzylmethane (2).
subsequent generation of infinite one-dimensional chains.

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S. Chakraborty et al. / Journal of Molecular Structure 1015 (2012) 99–105
1-MeUH ligands attached to the same (C1 or C2) group (1-MeUHA/
1-MeUHB, 75.32(5)°; 1-MeUHC/1-MeUHD, 53.94(5)°), are smaller
than in 2. This affects the mutual orientations of the Watson–Crick
The four 1-MeUH moieties in 3a exhibit different intermolecu-
lar hydrogen bonding patterns. 1-MeUHA is involved in two hydro-
gen bonds: O2wH0ꢀ ꢀ ꢀO4a (2.7384(18) Å), with a water molecule of
crystallization; and N3aHꢀ ꢀ ꢀO4b0 (2.8097(18) Å), with 1-MeUHB of
a neighboring ligand 3a, forming both interacting rings a dihedral
angle of 75.32(5)°. The O2 sites of 1-MeUHA and 1-MeUHB rings are
not involved in any hydrogen bonding. In case of 1-MeUHB, three
hydrogen bonding interactions are observed, namely N3bHꢀ ꢀ ꢀO2d0
(2.914(2) Å), with both rings twisted 65.93(6)°; and two different
interactions of O4b: O2w0Hꢀ ꢀ ꢀO4b (2.955(2) Å); and the upwards
mentioned N3aH0ꢀ ꢀ ꢀO4b. The O2, O4 and N3 sites of 1-MeUHC ex-
hibit hydrogen bonding interactions with three crystallized water
edges
of
the
1-MeUH
moieties
attached
to
the
same (C1 or C2) atom: N3a–1-MeUHB, 2.980(4) Å; N3b–1-MeUHA,
2.416(4) Å; N3c–1-MeUHD, 0.023(1) Å; N3d–1-MeUHC, 0.005(1) Å;
O2a–O2b,
8.837(2) Å;
N3a–N3b,
6.332(2) Å;
O4a–O4b,
4.493(2) Å; O2c–O2d, 9.830(2) Å; N3c–N3d, 6.880(2) Å; O4c–O4d,
5.4490(18) Å. Roughly, 1-MeUHA and 1-MeUHD are coplanar and
point toward opposite directions in different planes. 1-MeUHB
and 1-MeUHC can be also considered roughly coplanar, but their
pointing directions are 60° twisted, however.
Fig. 3. (a) View of 3a with atom numbering scheme. Hydrogen atoms have been omitted for clarity; (b) Water-mediated wobble type symmetrical self-base pairs exhibited
by 3a.
Fig. 4. Two different perspectives of 3b: (a) front view including ClOꢁ4 and O2w, and (b) ClO4ꢁ and ligand 3b along the c axis.

S. Chakraborty et al. / Journal of Molecular Structure 1015 (2012) 99–105
103
molecules: O3wH0ꢀ ꢀ ꢀO2c, 2.845(2) Å; N3cHꢀ ꢀ ꢀO3w, 2.858(2) Å; and
O1wH0ꢀ ꢀ ꢀO4c, 2.838(2) Å. For 1-MeUHD, the N3 and O4 sites form
H-bonds with water molecules (N3dHꢀ ꢀ ꢀO4w, 2.813(2) Å;
O1wHꢀ ꢀ ꢀO4d, 2.7602(19) Å), while O2 acts as proton acceptor for
N3b0. Thus, unlike molecule 2, in case of 3a none of the four uracil
rings exhibit self-base pairing shown in Chart 1.
In 3b, the 1-MeUHA moieties are engaged in wobble (mis-
matched) self-base pairing via N3aHꢀ ꢀ ꢀO2a0 (2.895(7) Å) H-bond-
ing with two neighboring molecules. This results in the assembly
of one-dimensional aggregates (Fig. 5). They are reinforced by
H-bonding of O2w, which bridges both O4b sites of the same
ligand (2.784(6) Å) (Figs. 4a and 5), and of O1w, connecting also
via H-bonding the O2b sites of two alternatively disposed ligands
(2.778(7) Å). Moreover, interaction of the O4a sites with two
Of the four water molecules of crystallization observed in the
crystal structure of compound 3a, three oxygen atoms (O1w,
O2w, and O4w) form an acyclic water trimer. It has been theoreti-
cally predicted that water trimers can exist in the form of cyclic
as well as acyclic structures [15]. In the present case, each water
molecule in the trimer forms three hydrogen bonds, with oxygen
acting as double donor and single acceptor. Each terminal oxygen
atom of the acyclic water trimer (O1w and O2w) acts as hydrogen
bond donor to two exocyclic O4 atoms of 3a and hydrogen bond
acceptor to the middle water molecule of the trimer. The central
oxygen atom (O4w) of the trimer acts as acceptor for N3dH. Thus,
tetra-coordination is not exhibited by any O atom in the trimeric
water cluster. Although each O atom in an assembly of water mol-
ecules tends to achieve four coordination, hydrogen-bond-deficient
water molecules are known to exist at the surface of ice [16]. Raman
scattering studies and X-ray absorption spectroscopy of liquid
water also indicate that significant numbers of O atoms show less
than tetra-coordination in liquid phase [17]. Overall, each water tri-
mer is hydrogen bonded to four neighboring molecules of 3a. The
OHꢀꢀꢀO distances of 2.837(2) Å (O4wꢀ ꢀ ꢀO1w0) and 2.731(2) Å
(O4wꢀ ꢀ ꢀO2w0) indicate the formation of acyclic water trimers
through short hydrogen bonding. For comparison, the OHꢀ ꢀ ꢀO dis-
tances in regular ice, in liquid water, and in the vapor phase are
2.74, 2.85, and 2.98 Å, respectively [18]. The O–O–O angle is found
to be 113.28(7)°, which is close to the theoretical value [15] of ca.
120° for the acyclic trimer in the gas phase. The fourth water mol-
ecule (that is not a part of the trimer) is H-bonded to two symmetry
related 3a molecules: N3cHꢀ ꢀ ꢀO3wHꢀ ꢀ ꢀO2c0.
5. Cocrystallization of tetra-uracil conjugate with HClO4 (3b)
Attempts were made to prepare metal–organic framework by
reaction of compound 3a and Ni(ClO4)2ꢀ6H2O under hydrothermal
conditions (180 °C, 3d) and then gradual cooling the reaction mix-
ture to ambient temperature. However no metal complex was
formed. Instead, this resulted in the crystallization of compound
3ꢀ2H2OꢀHClO4 (3b) (c.f. Notes and References). Metal binding was
not observed in this case, probably because of the low pH of the
resulting reaction mixture. Under these conditions, deprotonation
(or interchange) of the hydrogen atom attached to endocyclic N3
site is inhibited and hence metal coordination at this site is not
observed. X-ray single crystal analysis revealed that under the
reaction conditions, perchloric acid had ionized as evident
from the presence of a perchlorate anion in the unit cell. Interest-
ingly, cocrystallization of 3b with HClO4 results in marked
changes in its geometrical arrangement (Fig. 4), the ligand remain-
ing unprotonated, and in the nature of hydrogen bonding
interactions.
Compound 3b is bisected by a symmetry plane, perpendicular
to the benzene ring, and containing its 2 and 5 sites, relating both
C1H(1-MeUH)2 halves. As in 2, dihedral angles between rings
attached to C1 are close to 90° (1-MeUHA/1-MeUHB, 82.0(2)°;
1-MeUHA/benzyl 86.6(3)°; 1-MeUHB/benzyl, 83.0(3)°). Likewise,
dihedral angles of the plane defined by C5a/C5b/C11 (atoms
bonded to C1H), with their attached rings are 49.7(3)° (1-MeUHA),
50.5(2)° (1-MeUHB), and 65.1(3)° (benzyl), closer to those values of
2 than of 3a. Mutual orientations of the Watson–Crick edges are
almost perpendicular, N3a–1-MeUHB, 2.665(13) Å; N3b–1-MeUHA,
2.490(16) Å; O2a–O2b, 9.270(6); N3a–N3b, 6.499(7) Å; O4a–O4b,
4.543(6) Å.
Fig. 5. Packing detail of 3b based on two fold N3aHꢀ ꢀ ꢀO2a0 wobble (mismatched)
self-base pairing. ClOꢁ4 anions are omitted for clarity.

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S. Chakraborty et al. / Journal of Molecular Structure 1015 (2012) 99–105
additional ligands, via their N3b sites (2.808(6) Å), of parallel
threads, extends the 1D-aggregates to form two-dimensional lay-
ers. A further O1wꢀ ꢀ ꢀO2w H-bond (2.851(19) Å) connects parallel
threads on the layers. Perchlorate anions are not involved in clear
8. Notes
General: Linkers 1–4 were synthesized over 80% yield accord-
ing with slight modifications of the procedure reported in the liter-
ature [12].
H-bonding or anion–p interactions with the ligands or water mol-
1H NMR spectra were recorded on a Bruker 300 MHz and a Bru-
ker 400 MHz NMR spectrophotometers. IR spectra were recorded
as KBr pellets with a Shimadzu (IRAffinity-1) FT-IR spectrophotom-
eter. TGA were carried out with a SDT simultaneous TGA-DTA
instrument (Q600) by increasing temperature at the rate of
10 °C/min under a flow of nitrogen (100 mL/min). Elemental anal-
ysis were carried out with a Perkin-Elmer 2400 automatic carbon
hydrogen nitrogen and sulfur analyzer.
Bis(1-methyluracilyl-5yl-)3-nitrobenzyl methane (1): White solid;
Yield, 80%; mp > 300 °C. 1H NMR (DMSO-d6, 400 MHz): d 11.36 (s,
2H, H3), 8.10 (d, J = 11.2 Hz, 1H, H2-Ph), 7.94 (s, 1H, H4-Ph), 7.67
(d, J = 9.2 Hz, 1H, H6-Ph), 7.59 (t, J = 10.8 Hz, 1H, H5-Ph), 7.17 (s,
2H, H6), 5.18 (s, 1H, CH), 3.20 (s, 6H, CH3). IR (KBr): 3183, 3083,
2840, 1723, 1656, 1533, 1473, 1456, 1336, 1187, 1066, 759,
583 cmꢁ1. Elemental analysis calc. for C17H15N5O6: C, 52.99; H,
3.92; N, 18.17; O, 24.91. Found: C, 53.1; H, 4.0; N, 18.1; O, 24.9.
Bis(1-methyluracilyl-5yl-)4-nitrobenzyl methane (2): White solid;
Yield, 82%; mp > 300 °C. 1H NMR (NaOD, 400 MHz): d 8.09 (d,
J = 12 Hz, 2H, H3, 5-Ph), 7.30 (d, J = 11.6 Hz, 2H, H2, 6-Ph), 6.74
(s, 2H, H6), 5.19 (s, 1H, CH), 3.14 (s, 6H, CH3). IR (KBr): 3184,
3055, 2833, 1730, 1681, 1516, 1479, 1454, 1338, 1197, 1060,
754, 569 cmꢁ1. Elemental analysis calc. for C17H21N5O9 (3-hy-
drate): C, 46.47; H, 4.82; N, 15.94; O, 32.77. Found: C, 46.4; H,
4.7; N, 16.1; O, 32.9.
1,3-bis[di(1-methyluracilyl)methyl]benzene (3): White solid;
Yield, 92%; mp > 300 °C. 1H NMR (DMSO-d6, 300 MHZ): d 11.29
(s, 4H, H3), 7.27 (t, J = 5.7 Hz, 1H, H5-Ph), 7.07 (s, 4H, H6), 7.05
(d, J = 6 Hz, 2H, H4, 6-Ph), 7.02 (s, 1H, H2-Ph), 5.02 (s, 2H, CH),
3.19 (s, 12H, CH3). IR (KBr): 3167, 3047, 2810, 1681, 1481, 1456,
1413, 1336, 1197, 1068, 700, 561 cmꢁ1. Elemental analysis calc.
for C28H34N8O12 (4-hydrate): C, 49.85; H, 5.08; N, 16.61; O, 28.46.
Found: C, 49.7; H, 5.2; N, 16.7; O, 28.4.
1,4-bis[di(1-methyluracilyl)methyl]benzene (4): White solid;
Yield, 94%; mp > 300 °C. 1H NMR (NaOD, 300 MHZ): d 7.00 (s, 4H,
H6), 6.73 (d, J = 8.7 Hz, 4H, H-Ph), 5.06 (s, 2H, CH), 3.18 (s, 12H,
CH3). IR (KBr): 3168, 3036, 2831, 1730, 1653, 1481, 1458, 1427,
1331, 1192, 1062, 758, 579 cm–1. Elemental Analysis calc. for
ecules, residing in the triangular cavities of the sheets, probably
stabilized by electrostatics. It was not possible to identify a proton-
ated species in 3b in the Fourier difference map.
Thus, we tried to find a position to which the proton could be
reasonably attached. As ClOꢁ4 is not involved in hydrogen bonding,
and ligands are not expected to be protonated at their O2 and O4
sites (C2a–O2a, 1.232(7) Å; C4a–O4a, 1.246(7) Å; C2b–O2b,
1.236(8) A; C4b–O4b, 1.232(7) Å), a proton was tentatively posi-
tioned in O2w, pointing toward O1w, resulting in a H2Oꢀ ꢀ ꢀH3O+
system. The inverted system, with the proton at O1w seems to
be also reasonable.
6. Thermogravimetric analysis
The stability of ligand hydrates was studied by thermogravi-
metric analysis (TGA). In case of 2, a clean weight loss step in the
temperature range of 50–118 °C was observed. This corresponds
to the removal of three guest water molecules in the cavities
(calcd. 12.3%, found 12.6%). However, no weight loss was observed
between the temperature range of 120–300 °C, indicating that
guest-free compound 2 was stable. For compound 3a (3ꢀ4H2O), a
weight loss was found in the temperature range of 40–120 °C, cor-
responding to the loss of four guest water molecules (calcd. 10.9%,
found 11.4%). In this case, weight loss was not observed between
the temperature range of 130–370 °C, indicating the stability of
the guest-free compound 3 in this temperature range. The TGA
analyses of microcrystalline powder samples of compounds 1
and 4 were also carried out. Compound 1 was thermally stable
up to 340 °C and did not show loss of water. For compound 4, a
clean weight loss step in the temperature range of 40–100 °C
was observed. This corresponds to the removal of six guest water
molecules (calcd. 15.2%, found 15.5%). However, no weight loss
was observed between the temperature range of 100–450 °C, indi-
cating the high thermal stability of this compound.
7. Conclusion
C28H38N8O14 (6-hydrate): C, 47.32; H, 5.39; N, 15.77; O, 31.52.
Found: C, 47.5; H, 5.5; N, 15.7; O, 31.6.
In conclusion, this manuscript reports the design of hydrogen
bonding tectons containing multiple uracil moieties. These tectons
(1–4) have been projected to be building blocks for supramolecular
assemblies based on hydrogen bonding. Structural characterization
of a ditopic (2) and a tetratopic (3) compounds reveal interesting
deviations with respect to association adjacent molecules via
non-covalent interactions of uracil appendages. Molecule 2, having
two uracil appendages, exhibits dimerization via self-base (wobble
type mismatch) pairing. Conversely, molecule 3a, with four pen-
dant uracil rings does not associate with neighboring molecules
of 3a by any kind of self-base pairing. In this case, the presence
of an acyclic water trimer reinforces the supramolecular frame-
work. The presence of perchloric acid, changes the scenario com-
X-ray Crystallography: Data collections were performed on a
Bruker Kappa APEXII diffractometer (2), and on a Xcalibur S diffrac-
tometer (3a, and 3b), both with graphite mono-chromated Mo K
a
radiation (0.71073 Å). Data reduction was completed with the
APEX2 and CrysAlisPro software [19]. All three the structures were
solved by direct methods and full-matrix least-squares refined on
F2 using SHELXL-97 and WinGX software [20]. All non-hydrogen
atoms were refined anisotropically, and all hydrogen atoms were
positioned geometrically and refined with isotropic displacement
parameters according to the riding model. Distances and angles
calculations were performed with SHELXL-97 software [20b].
Refinement parameters are as follows:
2ꢀ3H2O: C17H21N5O9, M = 439.39, colorless blocks, triclinic, P–1,
pletely. In this case, 3b,
a
completely different H-bonding
a = 6.8253(2) Å, b = 12.1849(4) Å, c = 13.2516(4) Å, a = 68.220(2)°,
framework was observed, including association of neighboring
molecules via complimentary self-base pairing and water bridges.
TGA studies of crystalline samples of 2 and 3 indicated the stability
of the guest-free form over a wide temperature range. Our work
has the potential of leading the way to structurally related com-
pounds. We are presently investigating coordination properties of
these uracil based polytopic tectons with different metal ions.
b = 86.415(2)°,
c
= 87.924(2)°, V = 1021.30(5) Å3, Z = 2, Dcalc
(mmꢁ1) = 0.117, T = 293(2) K, 20,030 reflections col-
=
1.429 g/cm3,
l
lected, 3558 unique (Rint = 0.0303), R1 [I > 2s(I)] = 0.0497, wR2 (F,
all data) = 0.1472, GoF = 1.073. CCDC 838223.
3ꢀ4H2O (3a): C28H34N8O12, M = 674.63, colorless blocks, mono-
clinic, P21/c, a = 11.3152(4) Å, b = 13.1918(5) Å, c = 20.2265(9) Å,
b = 91.228(4)°, V = 3018.5(2) Å3, Z = 4, Dcalc = 1.485 g/cm3,
l

S. Chakraborty et al. / Journal of Molecular Structure 1015 (2012) 99–105
105
(mmꢁ1) = 0.118, T = 150(2) K, 26,433 reflections collected, 7315
unique (Rint = 0.0543), R1 [I > 2s(I)] = 0.0470, wR2 (F, all data) =
0.0862, GoF = 0.980. CCDC 838361.
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3ꢀ2H2OꢀHClO4 (3b): C28H31ClN8O14
,
M = 739.06, colorless
prisms, monoclinic, P21/m, a = 6.7352(18) Å, b = 18.512(5) Å, c =
13.040(2) Å, b = 92.52(2)°, V = 1624.2(6) Å3, Z = 2, Dcalc = 1.511
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Acknowledgments
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N.D. acknowledges SAIF, CDRI Lucknow (for providing NMR
facilities) and SAIF, IIT Madras (for recording single-crystal X-ray
crystallographic data for 2). P.J.S.M. thanks the FEDER fund and
the Spanish Ministerio de Economía y Competitividad for financial
support (CTQ2011-27593 and ‘‘Ramón y Cajal’’ Program). The
authors would like to thank Prof. Dr. Bernhard Lippert for his
continuous support.
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Appendix A. Supplementary material
Supplementary data associated with this article can be found, in
the online version, at doi:10.1016/j.molstruc.2012.02.012.
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