Hydrogen-bonded supramolecular array in the crystal structure of ethyl 7-hydroxy-2-oxo-2h-chromene-3-carboxylate monohydrate

Article abstract of DOI:10.4067/S0717-97072011000100005

The crystal structure of ethyl 7-hydroxy-2-oxo-2H-chromene-3-carboxylate monohydrate (1), C₁₂H₁₀O₅.H₂O, was established by X-ray crystallographic analysis. The molecule of the title compound is essentially planar except for the carboxylate substituent group. The crystal packing supramolecular array arises from hydrogen bonds and intermolecular C-H...O=C contacts of the organic molecules and solvent water molecules, with graph-set descriptor)R²₄(8), R ²₁(6), R⁴₄(20)and5 (C) motifs. The water molecules are involved as donors and acceptors. The hydrogen bond and intermolecular interaction network is reinforced by stacking of the sheet through π-π interactions.

Full text of DOI:10.4067/S0717-97072011000100005

J. Chil. Chem. Soc., 56, Nº 1 (2011)
HYDROGEN-BONDED SUPRAMOLECULAR ARRAY IN THE CRYSTAL STRUCTURE OF ETHYL
-HYDROXY-2-OXO-2H-CHROMENE-3-CARBOXYLATE MONOHYDRATE
7
1
,
3
1,2
ANTONIO GALDÁMEZ, * OLIMPO GARCÍA-BELTRÁN AND BRUCE K. CASSELS
1
Departamento de Química, Facultad de Ciencias, Universidad de Chile.
Casilla 653, Santiago, Chile
Millennium Institute for Cell Dynamics and Biotechnology, Santiago, Chile
2
3
Departamento de Ciencias Químicas, Facultad de Ecología y Recursos Naturales, Universidad Andrés Bello, Avenida Rpública 275, Piso 3, Santiago, Chile
(Received: December 3, 2010 - Accepted: March 14, 2011)
ABSTRACT
The crystal structure of ethyl 7-hydroxy-2-oxo-2H-chromene-3-carboxylate monohydrate (1), C H O .H O, was established by X-ray crystallographic
1
2
10
5
2
analysis. The molecule of the title compound is essentially planar except for the carboxylate substituent group. The crystal packing supramolecular array arises
2
4
2
1
from hydrogen bonds and intermolecular C-H···O=C contacts of the organic molecules and solvent water molecules, with graph-set descriptor
, R (6) ,
R (8)
4
R ( 202 0) andC(5) motifs. The water molecules are involved as donors and acceptors. The hydrogen bond and intermolecular interaction network is reinforced by
4
stacking of the sheet through p-p interactions.
Keywords: Crystal structure, Coumarins, X-ray diffraction
INTRODUCTION
(Sheldrick, 1990); program used to refine structure: SHELXL97 (Sheldrick,
8
-9
1
997). Molecular graphics: DIAMOND (Brandenburg, 1999); software used
10, 11
The coumarins, compounds that occur naturally in many plant families,
play an important role in organic chemistry. These compounds have been
tested in a wide range of pharmacological models, and many derivatives
have potentially useful biological activities among which are: antimicrobial,
antithrombotic, anti-inflammatory, antimutagenic, antitumor, and enzyme
to prepare material for publication: PLATON (Spek, 2003).
Table 1. Crystal data and details of the structure determination for
compound 1.
Crystal data
1
-4
inhibitory (cyclooxygenase, lipoxygenase, and monoamine oxidase). In
addition to their broad biological interest, the coumarins are sometimes colored
and generally exhibit intense fluorescence, which has attracted interest for the
development of new technological applications in areas such as liquid crystals
C
H
O
. H
O
d = 99.388(5) º
V = 583.3(2) Å
Z = 2
12
10
5
2
3
Mr = 252.22
5
for use in photoelectronic devices. In the present study, an X-ray analysis
Triclinic, P-1 (Nº 2)
a = 6.7177(17) Å
b =7.2637(18) Å
c =12.618(3) Å
of ethyl 7-hydroxy-2-oxo-2H-chromene-3-carboxylate monohydrate (1) was
performed in order to determine its inherent conformation and describe the
crucial role of hydrogen bonds to water and weak intermolecular interactions
in the assembly of its supramolecular architecture.
MoKa radiation
-
1
m = 0.117 mm
T = 298 K
a = 104.064(4) º
b = 95.506(5) º
0.32 x 0.14 x 0.05 mm
EXPERIMENTAL
Synthesis
Ethyl 7-hydroxy-2-oxo-2H-chromene-3-carboxylate monohydrate was
synthesized in two steps. First, resorcinol was formylated (Vilsmeier-Haack),
Data collection
6
and subsequently condensed with ethyl malonate (Knoevenagel) and cyclized
in a single step. The solid was recrystallized in EtOH (5.6 g, 52%) to afford
7
Bruker SMART CCD diffractometer 1057 reflections with I > 2s(I)
aggregates of yellow prisms (Scheme 1).
4269 measured reflections
035 independent reflections
Rint = 0.043
2
Refinement
H atoms treated by a mixture
of independent and constrained
refinement
Scheme 1. Reagents and conditions: (a) POCl , DMF, ACN, 2 h; (b)
piperidine, AcOH, EtOH, reflux, 6 h.
2
2
3
R [(F > 2s (F )] = 0.040
2
wR(F ) = 0.062
180 parameters
Refinement
-3
S = 0.96
Drmax = 0.15e Å
H atoms attached to C3, O3 and O1W were located in a Fourier map and
their positions and isotropic displacement parameters were refined freely. All
other H atoms were positioned geometrically and constrained to ride on their
-3
2
035 reflections
Drmim = -0.15 e Å
parent atoms (C—H: 0.93–0.97 Å). Displacement factors were taken as U (H)
iso
=
kU (C); k = 1.2–1.5. The crystal data, data collection and refinement are
eq
summarized in Table 1.
RESULTS AND DISCUSSION
Computing details
The asymmetric unit of the title compound (1) consists of one C H O
12 10 5
Data collection: Bruker SMART (BRUKER 1996); cell refinement: Bruker
SAINTPLUS V6.02 (BRUKER 1997); data reduction: Bruker SHELXTL
V6.10 (BRUKER 2000); program used to solve structure: SHELXS97
organic molecule and one solvent water molecule. A perspective view of the
molecular structure with the atom labels is depicted in Figure 1. A search in the
Cambridge Structural Database (CSD version 5.31, August 2010) of coumarin
e-mail: agaldamez@uchile.cl
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46

J. Chil. Chem. Soc., 56, Nº 1 (2011)
and derivates revealed the regioisomer ethyl 7-hydroxy-4-coumarinacetate
2) [CSD refcode SICREB (Subramanian et al. 1990)] and 7-hydroxy-4-
coumarinacetic acid monohydrate (3) [CSD refcode SICRIF (Sivakumar et al.
Table 3. Hydrogen-bond and intermolecular contact interaction geometry
(Å, º).
(
D-X...A
d(D-X)
d(X...A)
d(D...A)
<(DXA)
12,13
1
990)].
Selected bond lengths and angles of molecule 1 with their estimated
standard deviations (esd`s) are given in Table 2.
i
O1W-H1W···O2 0.81 (3)
2.24 (3)
2.26 (3)
2.13 (3)
1.81 (3)
2.534 (16)
2.876 (3)
2.963 (3)
2.976 (3)
2.648 (3)
3.452 (3)
135 (3)
145 (3)
174 (3)
170 (3)
156.7 (13)
i
O1W-H1W···O4 0.81 (3)
ii
O1W-H2W···O4 0.85 (3)
iii
O3-H3B···O1W
0.85 (2)
iv
C3-H3···O2
0.976 (15)
Symmetry code : (i) 2-x,1-y,1-z, (ii) x,y,z , (iii) x,y,z-1, (iv) x-1,y,z
Figure 1. The structure of 1 showing the atom numbering scheme.
Displacement ellipsoids are drawn at the 50% probability level and H atoms
are shown as small spheres of arbitrary radius.
Table 2. Selected geometric parameters (Å, º)
O1-C1
1.395 (2)
1.368 (3)
1.349 (2)
1.508 (2)
121.69 (19)
120.8 (2)
C2-C3-C9
122.2 (2)
123.1 (2)
0.9 (3)
C4-C5
C7-C8-C9
O3-C6
C8-O1-C1-C2
C3-C2-C10-O4
C11-O5-C10-O4
C11-C12
C3-C2-C10
C2-C3-C9
−162.9 (2)
2.6 (3)
C10-O5-C11-C12 −178.85 (18)
The molecule (1) is essentially planar except for the carboxylate
substituent group at C2 with a C3-C2-C10-O5 torsion angle of 16.1(3)º.
The torsion angles C2-C3-C10-C11 of the corresponding substituent (at C3:
ethoxycarbonylmethyl in 2 and acetic acid residue in 3), are -97.7(3)º and
1
2
03.6(3)º, respectively. The C2=C3 bond distances in 1 [1.353(3) Å] and in
[1.358(4) Å] are similar. However, the bond distance in 3 [1.341(4) Å] is
Figure 3. A partial packing of the crystal structure of 1: (a) A view of
the formation of a hydrogen-bonded sheet running parallel to the ac plane. (b)
A view of the hydrogen bonds in the central core linking the components into
centrosymmetric six-molecule aggregates consisting of two water molecules
and four C H O molecules. Dashed lines represent hydrogen bonds.
shorter than in 1 and 2, which can be attributed to the acetic acid moiety. All the
other relevant structural parameters (bond distances and angles) are as expected
and in acceptable agreement with the recently described analogues (Table 2).
1
2
10
5
The hydrogen bonds of the water molecules that are involved in the two-
2
donor centers H1W···O=C generate two graph-set descriptor R (6) motifs
1
(
figure 3b). This graph-set is formed by the linkage of water bonds, O1W-
H1W···O2 [symmetry code: 2-x,1-y,1-z] and O1W-H1W···O4 [symmetry
code: 2-x,1-y,1-z], with both O=C carbonyl groups of one molecule (Table
3
). Besides, these two-dimensional sheets are additionally stabilized by the
combinations of two O3-H3B···O1W and two O1W-H1W···O2 hydrogen
bonds. The links of two water molecules with two C H O molecules generate
The three-dimensional supramolecular architecture of compound 1
can be analyzed in terms of various components such as motifs, chains and
stacking interactions.The crystal structure of 1 is assembled from the C H O
1
2
10
5
4
17-19
a graph-set descriptor R ( 220 0) motif in the ac plane (Figure 3a).
4
1
2
10
5
molecules with solvent water molecules via hydrogen-bonding interactions.
Hydrogen bonds, p-p interactions and weak intermolecular contacts are
The crystal packing structure contains chains that run along the
crystallographic a-axis generated by intermolecular C-H···O=C contacts
1
4-17
responsible for the crystal packing.
In the asymmetric unit, two water
(
Table 3). The H···O contact distance is 2.543 (15) Å and the C···O distance
molecules are related forming an inversion centre. The two water molecules
serve to link four C H O molecules forming a two-dimensional array running
18-19
is 3.452 (3) Å, both within the C–H···O distance and angle range.
The
12
10
5
intermolecular C3-H3···O2 [-1+x,y,z] interactions form a graph-set descriptor
C(5) motif (Figure 2). The packing structure contains an additional weak
intermolecular contact O1···H4 [1+x,y,z] with a bond distance of 2.62(2) Å
and an angle of 113.4(4)º.
parallel to the [010] plane (Figure 3). The water molecules are involved as
hydrogen bond donors and acceptors. Each water molecule acts as a single
acceptor, in an O-H···OW hydrogen bond, and as a triple donor forming a
two-center H1W···O=C bond and single-center H2W···O=C bond (Table 3).
2
4
17-19
The central core constitutes a graph-set descriptor R (8) motif (Figure 3b).
5
47

J. Chil. Chem. Soc., 56, Nº 1 (2011)
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[
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centroid Cg1) and C4-C9 (centroid Cg2). The perpendicular Cg1···Cg2
(
distance is 3.5688 (15) Å (Figure 3). A similar packing interaction has been
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2
0
[centroid-centroid distance of 3.8380 (15)Å].
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a
b
Figure 3. A partial packing view of the crystal structure of 1 showing the
formation of weak intermolecular contacts between Cg1...Cg2 [symmetry code
i): 1-x,1-y,-z] in the bc-plane (a). The centroids Cg are denoted by small black
(
spheres and dashed lines represent intermolecular interactions. (b) Shows
parallel stacking between neighboring coumarin rings in the ac plane.
ACKNOWLEDGMENTS
M. T. Garland and A. Ibáñez are thanked for the X-ray measurements
and FONDAP Grant Nº 11980002 for the purchase of the Bruker SMART
CCD single crystal diffractometer. O. G.-B. is the recipient of a CONICYT
fellowship, This work was funded by ICM grant Nº P05-001-F.
Supplementary Information: Crystallographic data (excluding structure
factors) for the structural analysis have been deposited in the Cambridge
Crystallographic Data Centre, CCDC 801740. These data can be obtained free
of charge from the Cambridge Crystallographic Data Centre; Postal Address:
CCDC, 12 Union Road, Cambridge CB21EZ, UK, Telephone: (44) 01223
7
62910, Fax: (44) 01223 336033, e-mail: deposit@ccdc.cam.ac.uk.
5
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