Water templated hydrogen-bonded network of pyridine amide appended carbamate in solid state

Article abstract of DOI:10.1016/j.molstruc.2005.09.032

The pyridine amide appended carbamates 1 and 2 have been synthesized and their hydrogen-bonded self-assemblies in solid state have been described. The self-association pattern is dependent on the nature the anchored group of the carbamate moiety and influ

Full text of DOI:10.1016/j.molstruc.2005.09.032

Journal of Molecular Structure 785 (2006) 63–67
www.elsevier.com/locate/molstruc
Water templated hydrogen-bonded network of pyridine
amide appended carbamate in solid state
a,
a
*
, Suman Adhikari , Roland Fr o¨ hlich
b
Kumaresh Ghosh
a
Department of Chemistry, University of Kalyani, Kalyani, Nadia 741235, India
Organisch-Chemisches Institut, Universit a¨ t M u¨ nster, Corrensstrabe 40, D-48149, M u¨ nster
b
Received 7 August 2005; received in revised form 15 September 2005; accepted 22 September 2005
Available online 8 November 2005
Abstract
The pyridine amide appended carbamates 1 and 2 have been synthesized and their hydrogen-bonded self-assemblies in solid state have been
described. The self-association pattern is dependent on the nature the anchored group of the carbamate moiety and influenced by water inclusion.
Inclusion of water molecule gives a ladder type hydrogen bonded assemblies with cavities.
q 2005 Elsevier B.V. All rights reserved.
Keywords: Carbamate; Water-assembled structure; Ladder type assembly; Hydrogen bonding selectivity
1
. Introduction
within the simple structure of water. It can either function as
double hydrogen bond donor and a single hydrogen bond
acceptor in simple hydrate or double hydrogen bond donor and
double hydrogen bond acceptor in clathrate hydrates. There are
various reports on hydrogen-bonded water clusters in the form
of hexamers [17b], octamers [17c], decamers [17d] and one-
dimensional (1D) infinite water chains [17e] in different crystal
hosts. The structures of such hydrogen bonded water clusters
continue to attract attention since they play a crucial role in
contributing to the stability and function of biological
assemblies [17f]. In our continued research in molecular
recognition and supramolecular chemistry [18–19] we report
here the synthesis and solid state hydrogen bonding assembly
of the pyridine amide appended carbamates 1 and 2, for the first
time, with a view of establishing the hydrogen bonding nature
of carbamate with the complementary pyridine amide motif.
The compounds 1 and 2 were synthesized according to the
Scheme 1 and were isolated in good yield as white solids.
The rational design of new solid-state structures is central to a
wide variety of applications in crystal engineering and
supramolecular chemistry [1–4]. A particular goal, therefore,
involves the construction of solids with an appropriate ordered
and predictable arrangement of two or more molecular
components through specific noncovalent interaction, specifi-
cally hydrogen bond which has the pivotal role in molecular
recognition studies by synthetic receptors as well as in the
formation of supramolecular assembly due to its strength
anddirectionalnaturerelativetootherintermolecularinteractions
[
5–10]. Appropriate choice of molecules meeting both geometric
as well as energetic interactions allow the controlled formation of
different two- and three-dimensional shapes such as sheets [11],
ribbons [12], spheres [13], helices [14a], tubes [14b] and zeolite-
like 3D network structures with chiral channels [14c] fitted with
highly ordered water molecules etc. Such organization of
molecular components is controlled by proper hydrogen bonded
synthons as well as sometimes by inclusion of small molecules,
ions etc [15,16].
2. Experimental
In this aspect water is an important molecule, the inclusion
of which alters the molecular packing in the crystal [17a]. This
is due to various types of hydrogen-bonding possibility present
2
.1. General procedure
To a stirred solution of amine 4 [20] (1 equiv.) in dry
dichloromethane triphosgene (1 equiv.) was added. After stirring
for 1 h atroomtemperature dry alcohol (1 equiv.) was added drop
wise and the mixture was left overnight stirring. The reaction was
*
Corresponding author. Tel.: C91 33 25828750; fax: C91 33 25828282.
E-mail address: ghosh_k2003@yahoo.co.in (K. Ghosh).
quenched with aqueous NaHCO (20 ml), and the organic layer
3
0022-2860/$ - see front matter q 2005 Elsevier B.V. All rights reserved.
doi:10.1016/j.molstruc.2005.09.032
was separated. The aqueous layer was extracted with

64
K. Ghosh et al. / Journal of Molecular Structure 785 (2006) 63–67
Scheme 1.
dichloromethane and the combined organic layers were dried
Na SO ) and evaporated to white solid.
Carbamate 1: The compound was purified by column
5.23 (s, 2H), 2.48 (s, 3H). FT-IR (KBr) nmax: 3446, 3318, 1745,
K1
(
1665, 1595, 1226 cm
.
2
4
Single crystals of 1 and 2 were grown up by slow
evaporation of ethyl acetate-pet ether and chloroform-pet
ether combinations, respectively. All the crystallization
experiments were conducted in an unmodified atmosphere
and solvents were dried by standard methods, prior to use.
chromatography using 2:1 (pet ether: ethyl acetate) as eluant
1
and was collected as white solid, m.p 166 8C, 80% yield, H-
NMR (300 MHz, d -DMSO): d 10.49 (s, 1H), 9.97 (s, 1H), 7.99
6
(
d, JZ9 Hz, 3H), 7.70 (t, JZ9 Hz, 1H), 7.56 (d, JZ9 Hz, 2H),
7
2
1
.01(d, JZ9 Hz, 1H), 4.16 (q, JZ6 Hz, 2H), 3.35 (bs for H O),
2
.45 (s, 3H), 1.27 (t, JZ6 Hz, 3H). FT-IR (KBr) n
712, 1661, 1601, 1454, 1401 cm , Mass (FAB ): 316
3129,
max
C
K1
2.2. X-ray crystallography
C
C
[
(M CH O)K1], 300 (M C1), 282, 192, 227.
2
X-ray intensity data for a selected specimen were collected
on Nonius KappaCCD diffractometer, equipped with a rotating
anode generator Nonius FR591 (lZ0.71073 A˚ ). The following
Carbamate 2: The compound 2 was also purified by column
chromatography using 2:1 (pet ether: ethyl acetate) and was
1
obtained as white solid, m.p 156 8C, yield 75–80%. H-NMR
programs were used: data collection COLLECT [21], data
reduction Denzo-SMN [22], absorption correction SORTAV
(
(
300 MHz, CDCl ): d 8.42 (s, 1H), 8.16 (d, JZ10 Hz,1H), 7.89
d, JZ10 Hz 2H), 7.63 (t, JZ10 Hz,1H), 7.52 (d, JZ10 Hz,
H), 7.42–7.35 (m, 5H), 6.92 (d, JZ10 Hz, 2H), 6.85 (s, 1H),
3
[23], structure solution SHELXS-97 [24], structure refinement
2
Table 1
Crystal data and structure refinement for 1 and 2
1
2
Empirical formula
Formula weight
Temperature (K)
C
16
H
17
N
3
O
3
*H
2
O
21 19 3 3
C H N O
317.34
361.39
198(2)
293(2) K
0.71073
˚
Wavelength (A)
0.71073
Crystal system, space group
˚
Unit cell dimension (A)
Triclinic, P 1ꢀ (no. 2)
Triclinic, P1 (no.1)
˚
˚
aZ8.096(1) A, aZ92.43(1)8
aZ4.563(1) A, aZ92.76(1)8
˚
˚
bZ8.660(1) A, bZ107.04(1)8
bZ6.436(1) A, bZ91.94(1)8
˚
˚
cZ13.456 (1) A, gZ117.07(1)8
785.9(2)
cZ15.300(3) A, gZ92.70(1)8
448.0(2)
3
˚
Volume (A )
3
3
Z, calculated density
Absorption coefficient (m)
F(000)
2, 1.341 Mg/m
K1
0.098 mm
1, 1.339 Mg/m
K1
0.091 mm
336
190
Crystal size
0.30!0.20!0.15 mm
1.62–27.898
0.30!0.15!0.03 mm
2.67–27.838
Theta range for data collection
Limiting indices
K10%h%10,K11%k%11,K17%l%17
8175/3743 (R(int)Z0.054)
99.4%
K5%h%5,K8%k%8,K19%l%9
4479/2690 (R(int)Z0.0052)
88.8%
Reflections collected/unique
Completeness to theta
Max. and min. transmission
Refinement method
0.986 and 0.971
0.997 and 0.973
2
2
Full-matrix least-squares on F
Full-matrix least-squares on F
2
Goodness-of-fit on F
1.035
1.032
2
2
Final R indices [IO2sOI]
R indices (all data)
R1Z0.055, wR Z0.124
R1Z0.101, wR Z0.143
˚
0.22 and K0.20 eA
R1Z0.060, wR Z0.147
R1Z0.085, wR Z0.165
˚
0.21 and K0.18 eA
2
2
K3
K3
Largest diff. peak and hole

K. Ghosh et al. / Journal of Molecular Structure 785 (2006) 63–67
65
SHELXL-97 [25], graphics SCHAKAL [26]. The details and
results of the analysis are presented in Table 1.
3
. Results and discussion
Carbamates are interesting synthons in crystal engineering
on account of the fact that they exist as syn and anti rotamers
(
Fig. 1), with the anti rotamer favored by 1.0–1.5 kcal/mol for
Fig. 1. Carbamate rotamers.
steric and electrostatic reasons [27a]. These interesting features
of carbamates have been considered in the design of receptors
for theobromine alkaloid [27b]. The coupling of such
carbamate with complementary pyridine amide in specific
design is of keen interest in the context of building up of new-
engineered solid in crystal engineering. In this aspect the single
crystals of 1 and 2 were grow up by slow evaporation of ethyl
acetate-pet ether and chloroform-pet ether combinations,
respectively. The crystal data, data collection parameters and
analysis statistics are listed in the Table 1 [28].
2
Fig. 3. Hydrogen bonded three-dimensional arrangement of 1$H O.
forms (i) N–H/O hydrogen bond [N3–H3 0.85(2),
*
*
*
H3.O20 2.09(2), N3.O20 2.933(2) A˚ , N3–H3.O20
173(2)8, symmetry operation 1Kx, 1Ky, 1Kz] with the more
favored anti form of carbamate rotamer, (ii) O–H/N [O20–
H20A 0.80(2), H20A.N14 2.17(3), O20/N14
2.952(2) A˚ ,O20–H20A.N14 169(3)8] hydrogen bond with
In the crystal structure of 1 one molecule of water is bonded
as water of crystallization to the more basic pyridine nitrogen
ꢀ
and crystallizes in space group P1. The SCHAKAL plot with
pyridine ring nitrogen (iii) O–H/O hydrogen bond [O20–
*
*
**
H20B 0.90(3), H20B/O11
2.08(3), O20/O11
*
˚
2.977(2) A, O20–H20B/O11 171(2)8, symmetry operation
atom numbering scheme is shown in Fig. 2. The bound water
molecule typically functions as a double hydrogen bond donor
and a double hydrogen bond acceptor and exhibits a symmetric
dimer. Each neighbouring dimers are further assembled
through hydrogen bonds involving water as spacer in hydrogen
bonded network and executes nice water assisted ladder type
polymeric assembly (Fig. 3).
xK1, y, z] with pyridine amide carbonyl of the adjacent dimer
and (iv) C–H/O hydrogen bonds with H2AB (2.76 A˚ which
is about 0.14 A˚ shorter than the sum of the van der Waals
radii), where H2AB is one of the hydrogens at C2A (ethyl
group) thereby giving a tetrahedral arrangement. This
tetrahedral hydrogen bond co-ordination of water molecule
associates 1 as cyclic dimers via the two nitrogen–water
hydrogen bonds and is further connected via the oxygen–
water hydrogen bond in the third direction to give a ladder
type arrangement. However, in such assembly each macro-
cycle provides inwardly pointed two diagonal free N12–H12
hydrogen bond donors. These cavities may form inclusions of
a range of guest molecules that are both functionally and
dimensionally fitted into.
It is well known that the preferred hydrogen bond co-
ordination of the water molecule is tetrahedral or planar
trigonal [29]. In the present case, the water as bridging entity
A closer look on the geometrical parameters shows a
˚
distance of 3.72 A between the centers of neighbored pyridine
rings (symmetry operation Kx, Ky, Kz) indicating the
influence of p–p interactions. In contrast, there is no indication
*
**
for C–H/p interactions (closest distance from H2AA to the
˚
center of the benzene ring is 3.10 A; symmetry operation 2Kx,
2
Ky, 1Kz).
The presence of anchored water was also supported by the
C
appearance of the peak at 316 [(M CH O)K1] in mass
2
spectrum. The thermal stability of the water molecule in 1$H O
2
was studied by thermogravimetric analysis (TGA) (Fig. 4). The
weight loss for water is 5.7% that takes place in the temperature
region 25–140 8C and second weight loss occurs after 212 8C.
Fig. 2. SCHAKAL plot of 1 with atom numbering scheme.

66
K. Ghosh et al. / Journal of Molecular Structure 785 (2006) 63–67
Such arrangement is different from 1 where ethyl chain and
pyridine amide lie in opposite directions.
The selective combination of hydrogen bond donors and
acceptors of 2 governs the assembly indicating carbamate NH,
a better donor and pyridine amide carbonyl oxygen, a better
˚
acceptor. In the assembly pyridine rings are 4.563 A apart
(along a-axis) and do not show any p-stacking interaction.
The presence of phenyl ring in the carbamate moiety possibly
plays the key role not to allow any inclusion of water in the
network.
In summary, we have thus established that the inclusion of
water is dependent on the nature of the group anchored in the
carbamate moiety in our examples 1 and 2. Pyridine appended
carbamate having normal aliphatic group instead of aliphatic
chain containing pendent aromatic group, prefers water
inclusion that alters the molecular packing of carbamates.
2
Fig. 4. TGA plot showing the weight loss of the compound 1$H O on
increasing the temperature.
DSC experiment showed two endothermic peaks at 1378 and
71 8C. The first endotherm is, therefore, due to dehydration
and second one due to melting.
1
The compound 1$H O is stable hydrate above the boiling point
2
of water and exhibits a unique hydrogen bonding architecture
with cavities. Further exploration in this direction is in progress
in our laboratory.
Such water assisted hydrogen bonded architecture of 1 is
absent in 2 when benzyl group replaces the ethyl group of the
carbamate part. The SCHAKAL plot of 2, which crystallizes in
chiral space group P1, is presented in Fig. 5. The packing mode
Acknowledgements
(
Fig. 6) indicates a parallel arrangement of the molecules with
parallel hydrogen bonds keeping all the pyridines at one end
and phenyls on the other end and surprisingly the achiral
compound 2 crystallizes in an enantiomorphic space group.
Financial support from CSIR, New Delhi, India [Project No.
01(1922)/04/EMR-II] is gratefully acknowledged.
References
[
1] M.R. Bryce, A.J. Moore, M. Hasan, G.J. Ashwell, A.T. Fraser, W. Clegg,
M.B. Hursthouse, A.I. Karaulov, Angew. Chem. Int. Ed. Engl. 29 (1990)
1
450.
[
[
2] A.J. Moore, M.R. Bryce, J. Chem. Soc. Perkin Trans. 1 (1991) 157.
3] A.L. Lehninger, Biochemistry, Worth Publishers, New York, 1976.
Chapter 36.
[
[
[
[
4] G.A. Jeffery, W. Saenger, Hydrogen Bonding in Biological Structures,
Springer, New York, 1997.
5] Y. Yamashita, Y. Kobayashi, T. Miyashi, Angew. Chem. Int. Ed. Engl. 28
(
1989) 1052.
Fig. 5. SCHAKAL plot of 2 with atom numbering scheme.
6] F. Garcia-Tellado, S.J. Geib, S. Goswami, A.D. Hamilton, J. Am. Chem.
Soc. 113 (1991) 9265.
7] S. Hanessian, A. Gomtsyan, M. Simard, S. Roelens, J. Am. Chem. Soc.
1
16 (1994) 4495.
[
[
8] R. Horikoshi, C. Nambu, T. Mochida, New J. Chem. 28 (2004) 26.
9] T. Tanaka, T. Tasaki, Y. Aoyama, J. Am. Chem. Soc. 124 (2002)
1
2453.
[
[
10] Rebek Jr., Angew. Chem. Int. Ed. Engl. 29 (1990) 245.
11] X. Zhao, Y.-L. Cang, F.W. Fowler, J.W. Lauther, J. Am. Chem. Soc. 112
(
1990) 6627.
[
[
[
12] M.W. Hosseini, R. Ruppert, P. Schaeffer, A. de Cian, N. Kyritsaka,
J. Fischer, J. Chem. Soc. Chem. Commun. (1994) 2135.
13] R. Wyler, de Mendoza, Rebek Jr., Angew. Chem. Int. Ed. Engl. 32
(
1993) 1699.
14] (a) B. Sreenivasulu, J.J. Vittal, Angew. Chem. Int. Ed. Engl. 43 (2004)
769;
5
(
b) M.R. Ghadiri, J.R. Granja, R.A. Milligan, D.E. McRee,
N. Khazanovich, Nature 366 (1993) 324;
(
c) B. Zhao, P. Cheng, X. Chen, W. Shi, D. Liao, S. Yan, Z. Jiang,
J. Am. Chem. Soc. 126 (2004) 3012.
[
15] S.J. Geib, S.C. Hirst, C. Vicent, A.D. Hamilton, J. Chem. Soc. Chem.
Commun. (1991) 1283.
Fig. 6. Packing plot of 2.

K. Ghosh et al. / Journal of Molecular Structure 785 (2006) 63–67
67
[
16] (a) A. Mukherjee, M.K. Saha, M. Nethaji, A.R. Chakravarty, Chem.
[22] Z. Otwinowski, W. Minor, Methods Enzymol. 276 (1997) 307.
[23] (a) R.H. Blessing, Acta Crystallogr. A51 (1995) 33;
(b) R.H. Blessing, J. Appl. Crystallogr. 30 (1997) 421.
[24] G.M. Sheldrick, Acta Cryst. A46 (1990) 467.
Commun. (2004) 716;
(b) M.T. Ng, T.C. Deivaraj, W.T. Klooster, G.J. McIntyre, J.J. Vittal,
Chem. Eur. J. 10 (2004) 5853.
[
17] (a) S. Goswami, K. Ghosh, R. Mukherjee, Supramol. Chem. (1999)
91and references cited therein;
b) J.N. Moorthy, R. Natarajan, P. Venugopalan, Angew. Chem. 114
2002) 3567;
[25] Sheldrick G.M., SHELXLK97, Program for the refinement of crystal
structures from diffraction data, Universit a¨ t G o¨ ttingen, 1997
1
(
(
[26] E. Keller, SCHAKAL, A Computer Program for the Graphical
Representation of Molecular and Crystallographic Models, Universit a¨ t
Freiburg, 1997.
(
c) W.B. Blanton, S.W. Gordon-Wylie, G.R. Clark, K.K. Jordon,
J.T. Wood,U. Gieser, T.J. Collins,J. Am. Chem.Soc. 121(1999)3551;
d) L.J. Barbour, W.G. Orr, J.L. Atood, Nature 393 (1998) 671;
e) L. Infantes, J. Chisholm, S. Motherwell, Cryst. Eng. Comm. 5 (2003)
[27] (a) D. Marcovici-Mizarahi, H.E. Gottlieb, V. Marks, A. Nudelman,
J. Org. Chem. 61 (1996) 8402;
(
(
(b) S. Goswami, A. Mahapatra, R. Mukherjee, J. Chem. Soc. Perkin
Trans. 1 1 (2001) 2717.
480;
(
f) R. Ludwig, Angew. Chem. 113 (2001) 1856.
[28] Crystallographic data (excluding structure factors) have been deposited
with the Cambridge Crystallographic Data Centre as supplementary
publication CCDC-255451 and 277439. Copies of the data can be
obtained free of charge on application to The Director, CCDC, 12 Union
Road, CambridgeCB2 1EZ, UK (fax: int.codeC44(1223) 336-033, email:
deposit@ccdc.cam.ac.uk)
[
[
18] K. Ghosh, G. Masanta, Supramol. Chem. 17 (2005) 331.
19] N.C. Ganguly, M. Datta, K. Ghosh, A. Bond, Cryst. Eng. Comm. 34
(2005) 210.
[
[
20] S. Goswami, K. Ghosh, S. Dasgupta, J. Org. Chem. 65 (2000) 1907 and
procedure cited therein.
21] COLLECT, program for Collecting Data on CCD Area Detectors, Nonius
B.V., 1998.
[29] G.A. Jeffery, W. Saenger, Hydrogen Bonding in Biological Structures,
Springer, New York, 1997.