On the possibility of tuning molecular edges to direct supramolecular self-assembly in coumarin derivatives through cooperative weak forces: Crystallographic and hirshfeld surface analyses

Article abstract of DOI:10.1021/cg2006343

Four organic compounds based on substituted coumarin derivatives (1 - 4) have been synthesized and characterized by X-ray structural studies with a detailed analysis of Hirshfeld surface and fingerprint plots facilitating a comparison of intermolecular interactions in building different supramole-cular architectures. The X-ray study reveals that in the molecular packing C - H · · ·O, π · · · π, and carbonyl (lone pair) · · · π interactions cooperatively take part. The recurring feature of the self-assembly in all the compounds is the appearance of the molecular ribbon through weak hydrogen bonding. These hydrogen bonded ribbons further stacked into molecular layers by π · · · π forces. The mode of cooperativity of the weak C - H · · · O and π · · · π forces is such that they operate in mutuallyperpen-dicular directions - hydrogen bonding in the plane of the molecule at their edges and π-stacking perpendicular to the molecular plane. Investigation of intermolecular interactions and crystal packing via Hirshfeld surface analyses reveals that more than two-thirds of the close contacts are associated with weak interactions. Hirshfeld surface and breakdown of the corresponding fingerprint plots of four coumarin structures clearly quantify the interactions within the crystal structures, revealing significant similarities in the interactions experienced by each compound. The binding energies associated with the weak interactions have been estimated using density functional theory calculations.

Full text of DOI:10.1021/cg2006343

ARTICLE
pubs.acs.org/crystal
On the Possibility of Tuning Molecular Edges To Direct
Supramolecular Self-Assembly in Coumarin Derivatives
through Cooperative Weak Forces: Crystallographic and
Hirshfeld Surface Analyses
Saikat Kumar Seth,†,§ Debayan Sarkar,‡ Atish Dipankar Jana,*,# and Tanusree Kar*,†
†Department of Materials Science, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
§Department of Physics, M. G. Mahavidyalaya, Bhupatinagar, Midnapore (East), West Bengal 721 425, India
‡Department of Chemistry, A. B. N. Seal College, Coochbehar 736101, W.B., India
#Department of Physics, Behala College, Parnasree, Kolkata-700060, India
S Supporting Information
b
ABSTRACT: Four organic compounds based on substituted
coumarin derivatives (1ꢀ4) have been synthesized and char-
acterized by X-ray structural studies with a detailed analysis of
Hirshfeld surface and fingerprint plots facilitating a comparison
of intermolecular interactions in building different supramole-
cular architectures. The X-ray study reveals that in the molecular
packing CꢀH O, π π, and carbonyl (lone pair)
π
3 3 3
3 3 3
3 3 3
interactions cooperatively take part. The recurring feature of
the self-assembly in all the compounds is the appearance of the
molecular ribbon through weak hydrogen bonding. These hy-
drogen bonded ribbons further stacked into molecular layers by
π
π forces. The mode of cooperativity of the weak CꢀH
O
3 3 3
3 3 3
and π π forces is such that they operate in mutually perpen-
3 3 3
dicular directions — hydrogen bonding in the plane of the molecule at their edges and π-stacking perpendicular to the molecular
plane. Investigation of intermolecular interactions and crystal packing via Hirshfeld surface analyses reveals that more than two-
thirds of the close contacts are associated with weak interactions. Hirshfeld surface and breakdown of the corresponding fingerprint
plots of four coumarin structures clearly quantify the interactions within the crystal structures, revealing significant similarities in the
interactions experienced by each compound. The binding energies associated with the weak interactions have been estimated using
density functional theory calculations.
’ INTRODUCTION
reactivity,14 that is, [2 + 2] photocycloaddition, and these are the
molecules long-known for their pharmacological importance.15
These molecules possess molecular backbones capable of edge-
Molecular self-assembly through weak noncovalent forces is
the hallmark of biological systems. An understanding of mutual
influence of more than one noncovalent force in the self-assembly of
molecules and ions is the key in successful utilization of these
forces in various branches of science such as crystal engineering,1
hostꢀguest chemistry,2 supramolecular electronics3 and nano-
scale technology,4 etc. Among a number of noncovalent forces
such as hydrogen bonding,5 π π,6 CꢀH π,7 cation π,8
to-edge self-association through weak but multiple CꢀH
O
3 3 3
hydrogen bonds. Also as these molecules possess two fused
aromatic rings, it is a common feature that molecular packing in a
direction perpendicular to the molecular plane is governed by π-
stacking interactions. Molecular assembly in these systems is the
result of mutual cooperation between hydrogen bonding forces
3 3 3
3 3 3
3 3 3
anion π,9 lone-pair π,10
S
S,11 Se Se,12 and various
and π π forces. Herein, we demonstrate how coumarin
3 3 3
3 3 3
3 3 3
3 3 3
3 3 3
metal metal interactions,13 hydrogen bonding interaction,
molecules may serve as remarkable skeletons for studying the
3 3 3
pattern of self-association via complementary sites of multiple
and π π interaction have been widely utilized in directing
3 3 3
weak bonding such as hydrogen bonding and π π interac-
3 3 3
molecular assembly for the construction of various supramole-
cular architectures. Proper organization of complementary donor
and acceptor atoms on the molecule is essential in utilizing
hydrogen bond to direct molecular self-assembly.
tions. The study of X-ray crystal structure of four coumarin based
Received: May 19, 2011
Substituted coumarin molecules are simple systems that have
been extensively studied in the context of solid state photochemical
Revised:
Published: September 22, 2011
September 11, 2011
r
2011 American Chemical Society
4837
dx.doi.org/10.1021/cg2006343 Cryst. Growth Des. 2011, 11, 4837–4849
|

Crystal Growth & Design
ARTICLE
Table 1. Crystal Data and Structure Refinement Parameters for Compounds C11H10O2 (1), C11H10O3 (2), C11H10O3 (3), and
C12H10O3 (4)a
compound (1)
compound (2)
compound (3)
compound (4)
formula weight
174.19
190.19
190.19
202.20
temperature
150(2) K
150 (2) K
150 (2) K
150(2) K
wavelength (Mo Kα)
crystal system space group
unit cell parameters
0.71073 Å
0.71073 Å
0.71073 Å
0.71073 Å
triclinic P1
monoclinic P21/c
a = 7.038(1) Å
b = 9.396(3) Å
c = 13.358(1) Å
α = 90.00°
β = 98.932(6)°
γ = 90.00°
872.6(3) Å3
monoclinic C2/c
a = 12.529(8) Å
b = 12.889(3) Å
c = 12.689(4) Å
α = 90.00°
β = 115.679(2)°
γ = 90.00°
1846.7(14) Å3
8, 1.368 Mg/m3
0.100 mmꢀ1
monoclinic P21/c
a = 4.1622(5) Å
b = 10.589(1) Å
c = 21.932(3 )Å
α = 90.00°
β = 91.696(4)°
γ = 90.00°
966.2(2) Å3
a = 7.0118(13) Å
b = 7.3848(17) Å
c = 9.9023(17) Å
α = 95.805(2)°
β = 106.502(3)°
γ = 110.677(2)°
448.21(15) Å3
2, 1.291 Mg/m3
0.088 mmꢀ1
volume
Z, calculated density
absorption coeff
F(000)
4, 1.448 Mg/m3
0.106 mmꢀ1
4, 1.390 Mg/m3
0.100 mmꢀ1
184
400
800
424
crystal size
0.21 ꢁ 0.13 ꢁ 0.08 mm
2.20ꢀ25.00°
0.19 ꢁ 0.12 ꢁ 0.07 mm
2.66ꢀ25.00°
0.25 ꢁ 0.16 ꢁ 0.09 mm
2.40ꢀ24.98°
ꢀ14 e h e 14
ꢀ15 e k e 15
ꢀ15 e l e 14
8466/1626 [R(int) = 0.0331]
100
0.21 ꢁ 0.18 ꢁ 0.13 mm
1.86ꢀ24.99°
θ-range for data collection
limiting indices
ꢀ8 e h e 7
ꢀ8 e h e 8
ꢀ4 e h e 4
ꢀ8 e k e 8
ꢀ11 e l e 11
3240/1563 [R(int) = 0.0138]
98.8
ꢀ11 e k e 11
ꢀ15 e l e 15
7715/1536 [R(int) = 0.0273]
99.9
ꢀ12 e k e 12
ꢀ26 e l e 26
8738/1692 [R(int) = 0.0353]
100.0
reflections collected/unique
completeness to θ (%)
refinement method
full-matrix least-squares on F2
full-matrix least-squares on F2
Full-matrix least-squares on F2 Full-matrix least-squares on F2
data/restraints/parameters
goodness-of-fit on F2
1563/0/120
1536/0/131
1626/0/129
1692/0/136
1.066
1.066
1.044
1.069
final R indices [I > 2σ(I)]
R indices (all data)
R1 = 0.0424, wR2 = 0.1160
R1 = 0.0552, wR2 = 0.1273
R1 = 0.0333, wR2 = 0.0945
R1 = 0.0444, wR2 = 0.1221
R1 = 0.0365, wR2 = 0.0898
R1 = 0.0345, wR2 = 0.0962
R1 = 0.0597, wR2 = 0.1363
R1 = 0.0473, wR2 = 0.0970
largest diff peak and hole
0.133 and ꢀ0.170 e Åꢀ3
0.188 and ꢀ0.224 e Åꢀ3
0.159 and ꢀ0.228 e Åꢀ3
0.139 and ꢀ0.246 e Åꢀ3
3
3
3
3
a R1 = ∑||Fo| ꢀ |Fc||/∑|Fo|, wR2 = [∑{(Fo ꢀ Fc2)2}/∑{w(Fo ) }]1/2, w = 1/{σ2(Fo ) + (aP)2 + bP}, where a = 0.0618 and b = 0.0549 for 1; a = 0.0552
2
2 2
2
and b = 0.2771 for 2; a = 0.0834 and b = 0.2841 for 3; and a = 0.0448 and b = 0.2312 for 4. P = (Fo2 + 2Fc2)/3 for all the title structures.
compounds reveals that hydrogen bonding and π π forces
ice-cold water was added. A yellow solid separated out which was filtered,
dried, and crystallized from methanol to yield 8 g (0.045 mol) of 1 in
3 3 3
operate in a particular mutually cooperative fashion. This study
also indicates the possibility of engineering the molecular edges
of the coumarin framework to obtain various coumarin based
self-assembled molecular architectures. The Hirshfeld surface
analysis and associated fingerprint plots have been presented to
explore the nature of intermolecular interactions in the title crystal
structures and offering considerable potential in the context of
crystal engineering.
51% yield as colorless plates. m.p. 154 °C; IR (KBr) νmax 1687 cmꢀ1
.
1H NMR (500 MHz, CDCl3) δ7.3 (d, J=8.2Hz,1H);6.8(d,J= 8.2 Hz, 1H),
6.7(S, 1H); 6.4(S,1H); 2.4(S, 3H); 2.35(S, 3H). 13C NMR (125 MHz,
CDCl3) δ 157.8, 150.2, 149.8, 135.6, 123.4, 122.8, 114.8, 113.7, 111.3,
23.6, 19.6. HRMS (EI) C11H10O2. MH+ Found: 175.0578, calculated:
175.0579. Anal. Calcd. for C11H10O2: C, 75.87; H, 5.74, Found: C,
75.90; H, 5.71.
Preparation of Compound 2. To a well stirred solution of 8 mL
of concentrated H2SO4 at 100 °C, a mixture of 3-methyl benzene 1, 2
diol (10 g, 0.0526 mol) and ethyl acetoacetate (10 g, 0.0789 mol) was
added and stirred for 3 h. Then the reaction mixture was cooled and ice-
cold water was added. A brown colored solid separated out which was
filtered, dried, and crystallized from ethanol to yield 6.2 g (0.0326 mol)
of 2 in 62% yield light brown crystals. m.p. 162 °C; IR (KBr) νmax 3321,
1690 cmꢀ1. 1H NMR (500 MHz, CDCl3) δ 7.6 (d, J = 8.2 Hz, 1H); 6.9
(d, J = 8.2 Hz, 1H); 6.6 (S, 1H); 5.5 (brs, 1H); 2.5 (S, 3H); 2.2 (S, 3H).
13C NMR (125 MHz, CDCl3) δ 159.8, 148.3, 147.8, 139.8, 128.4, 123.2,
’ EXPERIMENTAL SECTION
Materials and Measurements. All chemicals were of analytical
grade and used without further purification. Elemental analyses (C, H,
and N) were performed on a Perkin-Elmer 2400 elemental analyzer. IR
spectra were recorded on a Perkin-Elmer L120-00 FT-IR spectrophoto-
meter with the sample prepared as a KBr pellet. All NMR spectra were
recorded at 300 K on a Bruker DRX-300 spectrometer operating at the
frequencies of 300.0 MHz (1H), 75.0 MHz (13C). The spectra were mea-
sured in CDCl3 solution and the sample concentrations ranged from 40
to 70 mg per 0.4 mL of solvent, in a 5 mm sample tube.
118.8, 117.2, 112.6, 20.6, 17.3. HRMS (EI) C11H10O3 MH+ Found:
3
191.0531, calculated: 191.0528. Anal. Calcd. for C11H10O3: C, 69.46; H,
5.30, Found: C, 69.48; H, 5.32.
Preparation of Compound 1 (Literature Known).16. To a
well stirred solution of 8 mL of concentrated H2SO4 at 100 °C, a mixture
of m-cresol (10 g, 0.09 mol) and ethyl acetoacetate (17.01 g, 0.135 mol)
was added and stirred for 3 h. Then the reaction mixture was cooled and
Preparation of Compound 3. A solution of 6-hydroxy-7-methyl-
coumarin (1.52 g, 8.52 mol), anhydrous potassium carbonate (1.4 g,
10.14 mol), and methyl iodide (1.7 g, 11.9 mol) in acetone (20 mL) was
4838
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Crystal Growth & Design
ARTICLE
Figure 1. ORTEP view (granite stone) with atom numbering scheme of compounds 1ꢀ4 with displacement ellipsoids at the 30% probability level.
refluxed for 8 h. The reaction mixture was cooled and most of the acetone
was distilled off. The residue was poured into water and extracted
with chloroform (3ꢁ 30 mL) .The combined organic extract was
washed with water, dried, and concentrated to afford a yellow solid,
which was crystallized from ethanol to furnish 6-methoxy-7-methyl-
coumarin 3 (1.33 g, 82%) as a yellowish crystal. m.p. 132ꢀ134 °C.
IR (KBr) νmax 1716 cmꢀ1. 1H NMR (300 MHz, CDCl3) δ 7.65 (d,
J = 9.5 Hz, 1H); 7.12 (S, 1H); 6.79 (S, 1H); 6.36 (d, J = 9.5 Hz, 1H);
3.87 (S, 3H); 2.30 (S, 3H). 13C NMR (75 MHz, CDCl3) δ 161.2, 154.4,
143.1, 132.6, 120.7, 118.4, 116.2, 115.4, 106.4, 55.6, 16.6. Anal. Calcd. for
C11H10O3: C, 69.46; H, 5.30, Found: C, 69.43; H, 5.29.
Preparation of Compound 4. A solution of 7-hydroxy-2H-
chomen-2-one (1.5 g, 0.007 mol), anhydrous potassium carbonate
(1.02 g, 0.007 mol), and allyl bromide (0.8 g, 0.007 mol) in acetone
(20 mL) was refluxed for 10 h. The reaction mixture was cooled and
most of the acetone was distilled off. The residue was poured into water
and extracted with chloroform (3ꢁ 30 mL). The combined organic
extract was washed with water, dried, and concentrated to afford a colorless
solid, which was crystallized from ethanol to furnish 7-(allyloxy)-2H-
chromen-2-one 4 1.18 g (0.005 mol, 84%) as a white crystals. m.p.
59ꢀ60 °C. IR (KBr) νmax 1720 cmꢀ1. 1H NMR (300 MHz, CDCl3) δ
7.7 (d, J = 9.5 Hz, 1H); 7.6 (d, J = 8.2 Hz, 1H); 6.8 (S, 1H); 6.2 (m,
1H); 5.97 (d, J = 9.5 Hz, 1H); 5.11 (d, J = 14 Hz, 1H); 4.98 (d, J = 3
Hz, 1H); 4.68 (S, 3H). 13C NMR (75 MHz, CDCl3) δ 159.05, 150.2,
145.7, 132.9, 130.5, 123.5, 112.7, 109.2, 108.3, 107.6, 100.6, 66.2
Anal. Calcd. for C12H10O3: C, 71.28; H, 4.98, Found: C, 71.24;
H, 4.96.
X-ray Crystallography Study. X-ray diffraction intensity data of
the title compounds were collected at 150(2) K using a Bruker APEX-II
CCD diffractometer. Data reduction was carried out using the program
Bruker SAINT.17 The structure of the title compounds were solved by
direct method and refined by the full-matrix least-squares technique
on F2 using the programs SHELXS9718 and SHELXL97,19 respectively.
All the calculations were carried out using PLATON20 and WinGX
system Ver-1.64.21 All hydrogen atoms of the substituent groups were
located from difference Fourier map and refined isotropically whereas all
the hydrogen atoms attached to the ring carbons were placed at their
geometrically idealized positions. A summary of crystal data and relevant
refinement parameters are given in Table 1. CCDC 819048ꢀ819050
(1ꢀ3) and 777025 (4) contain the supplementary crystallographic
data for this paper. These data can be obtained free of charge from
the Cambridge Crystallographic Data Centre via www.ccdc.cam.ac.uk/
data_request/cif.
Computational Methods. For understanding the stability of various
hydrogen bonded and π-stacking motifs some calculations were carried
out. All calculations were performed using the PC GAMESS package.22
Initial geometries of the π-stacked dimers as well as hydrogen bonded
dimers (trimer in one case) of substituted coumarine derivatives were
taken from respective crystal structures. Starting from these initial geome-
tries all dimeric and trimeric motifs were optimized to their minimum
energy configurations. All calculations were performed at the density
functional theory (DFT) level using X3LYP functional and 6-311++G**
basis set. The stabilization energies of the n-meric (dimeric [n = 2] and
trimeric [n = 3]) motifs involving n number of coumarin based molecules
(ΔEn‑mer) is calculated from the formula ΔEn‑mer = En‑mer ꢀ (n ꢁ
Emonomer). Emonomer was calculated by optimizing a single molecule at
the same level of theory.
Hirshfeld Surface Analysis. Molecular Hirshfeld surfaces23ꢀ25,10p in
the crystal structure are constructed based on the electron distribution
calculated as the sum of spherical atom electron densities.26 For a given
crystal structure and set of spherical atomic electron densities, the Hirshfeld
surface is unique.27 The normalized contact distance (dnorm) based on both
de and di, and the vdW radii of the atom, given by eq 1 enables identification
of the regions of particular importance to intermolecular interactions.23
The combination of de and di in the form of a two-dimensional (2D)
fingerprint plot28 provides a summary of intermolecular contacts in the
crystal.23 The Hirshfeld surfaces are mapped with dnorm and 2D
fingerprint plots presented in this paper were generated using Crystal-
Explorer 2.1.29 In CrystalExplorer, the internal consistency is important
when comparing one structure with another; for the generation of
Hirshfeld surfaces all bond lengths to hydrogen (or deuterium) atoms
are set to typical neutron values (CꢀH = 1.083 Å, OꢀH = 0.983 Å,
NꢀH = 1.009 Å).30 Graphical plots of the molecular Hirshfeld surfaces
mapped with dnorm used a redꢀwhiteꢀblue color scheme, where red
highlights shorter contacts, white is used for contacts around the vdW
separation, and blue is for longer contacts. Moreover, two further colored
4839
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Crystal Growth & Design
Table 2. Selected Bond Lengths (Å) and Bond Angles (°) for C11H10O2 (1), C11H10O3 (2), C11H10O3 (3), and C12H10O3 (4)
ARTICLE
compound (1)
compound (2)
X-ray DFT
Bond Lengths
compound (3)
compound (4)
X-ray
DFT
X-ray
DFT
X-ray
DFT
mogul (mean)
O1ꢀC5
O1ꢀC9
O2ꢀC9
C8ꢀC9
C7ꢀC8
C6ꢀC7
C5ꢀC6
C7ꢀC11
C3ꢀC10
C4ꢀO3
C2ꢀO3
C11ꢀO3
C3ꢀO3
C10ꢀO3
1.375(2)
1.374(2)
1.205(2)
1.433(2)
1.334(2)
1.445(2)
1.395(2)
1.501(2)
1.507(2)
1.351
1.353
1.185
1.462
1.335
1.464
1.387
1.504
1.509
1.380(1)
1.375(1)
1.213(1)
1.444(2)
1.348(2)
1.450(2)
1.393(2)
1.496(2)
1.503(2)
1.359(2)
1.366
1.340
1.198
1.455
1.336
1.463
1.388
1.504
1.507
1.335
1.379(2)
1.374(2)
1.206(2)
1.434(3)
1.334(2)
1.422(2)
1.385(2)
1.357
1.350
1.185
1.468
1.331
1.452
1.376
1.381(2)
1.384(2)
1.215(2)
1.444(2)
1.342(2)
1.433(2)
1.390(2)
1.350
1.358
1.184
1.464
1.332
1.447
1.384
1.382
1.378
1.205
1.440
1.347
1.448
1.396
1.501
1.510
1.363
1.367
1.422
1.372
1.435
1.498(2)
1.507
1.363(2)
1.429(2)
1.351
1.399
1.364(2)
1.445(2)
1.339
1.411
Bond Angles
O1ꢀC9ꢀC8
O1ꢀC5ꢀC6
O1ꢀC9ꢀO2
C5ꢀO1ꢀC9
O2ꢀC9ꢀC8
C9ꢀC8ꢀC7
C2ꢀC3ꢀC4
C3ꢀC4ꢀC5
C2ꢀO3ꢀC11
C3ꢀO3ꢀC10
117.14(14)
121.21(13)
116.28(15)
121.43(12)
126.57(15)
123.24(15)
118.26(15)
120.37(14)
116.39
121.66
118.71
123.17
124.90
122.49
118.74
120.09
117.44(10)
122.03(10)
116.70(10)
120.97(9)
117.30
121.58
118.37
122.71
124.32
122.11
118.94
119.04
117.20(15)
120.95(16)
116.69(19)
121.55(14)
126.1(2)
116.29
121.65
119.09
123.39
124.62
121.21
118.84
120.53
119.77
117.16(13)
120.71(12)
116.19(13)
122.00(11)
126.64(14)
121.13(14)
121.10(13)
117.58(13)
116.27
121.12
118.44
123.77
125.29
120.83
120.36
118.55
117.06
121.51
116.33
121.86
125.94
123.03
117.98
119.94
117.59
117.89
125.86(10)
122.69(10)
118.55(10)
119.51(10)
121.65(18)
118.64(15)
120.45(14)
117.13(14)
116.78(11)
120.33
properties (shape index and curvedness) based on the local curvature of the
surface can be specified.31
are in the normal range (Table 2). Similar variations in the
geometric parameters of the lactone ring (L) of the coumarin
skeleton have been reported previously.34ꢀ43 The bond lengths
(Table 2) of the molecular fragment in 1ꢀ4 agree well with the
mean values of relevant bond distances obtained with MOGUL44
from searches based on related molecular fragments run on the
CSD.33 In 4, the allyloxy group at C(3) is nearly coplanar with the
benzenoid ring (B) as indicated by the C(10)ꢀO(3)ꢀC(3)ꢀ
C(4) torsion angle 3.26(2)°. This coplanarity is comparable with
the structures reported earlier with similar substituents.39ꢀ43
The wide-angle of C(4)ꢀC(3)ꢀO(3) and the narrow-angle of
O(3)ꢀC(3)ꢀC(2) show that the allyloxy group is slightly tilted
to the C(2) direction.
di ꢀ rivdw
de ꢀ revdw
dnorm
¼
þ
ð1Þ
rivdw
revdw
’ RESULTS AND DISCUSSION
Structural Description. The molecular views (ORTEP)32 of
the title coumarin derivatives 1ꢀ4 with atom numbering scheme
is shown in Figure 1. X-ray crystal structure reveals the presence
of a single coumarin molecule in the asymmetric unit of all
compounds. The asymmetric units of the title compounds are
composed of two fused rings with opposite polarity, namely, the
benzenoid ring (B) and lactone ring (L) with different substitu-
tions in 1ꢀ4. The planar geometry of benzene and lactone ring
together (benzolactone ring) supports the observation regarding
the aromatic character of coumarin derivatives found in the
Cambridge Structural Database33 reported previously for the
benzolactone ring.34ꢀ43 The geometric parameters of theoreti-
cally computed optimized structures of four compounds when
compared with the X-ray crystal structures do not show a large
difference; the largest deviation in bond distance is 0.03 Å
(Table 2). In the X-ray crystal structure of all the compounds,
the shortest bond length and the largest angle are observed for
C7ꢀC8 and C7ꢀC8ꢀC9, respectively, whereas the other angles
In the title compounds, the supramolecular aggregations are
stabilized by a combination of weak intermolecular CꢀH
O
3 3 3
hydrogen bonds (Table 3) and extensive π π stacking inter-
3 3 3
actions (Table 4). In 1, the lactone ring carbon atom C8 in the
molecule at (x, y, z) acts as a donor to the carbonyl oxygen atom
O2 of the partner molecule at (ꢀx, ꢀy, ꢀz) and forms a cyclic
2
hydrogen bonded dimer with R2 (8) hydrogen bonding synthon
(Figure S1, Supporting Information) in Etter’s graph notation.45
The interconnection of the monomeric units through π
π
3 3 3
stacking interaction (Table 4) between benzene and lactone
rings of the molecules define a well-connected column which
forms a supramolecular stacked ribbon in 1 (Figure 2). To optimize
the π-stacking interaction, successive molecules flip alternately
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Table 3. Relevant Hydrogen Bonding Parameters (Å, °)
DꢀH
A
DꢀH
H
A
D
A
DꢀH
A
symmetry
ꢀx, ꢀy, ꢀz
3 3 3
3 3 3
3 3 3
3 3 3
167
compound 1
compound 2
C8ꢀH8 O2
0.93
0.82
0.82
0.96
0.96
0.93
0.96
0.96
0.93
0.93
2.53
2.33
2.15
2.56
2.60
2.65
2.91
2.60
2.55
2.56
3.445(2)
2.738(2)
2.745(2)
3.356(2)
3.553(2)
3.573(2)
3.831(3)
3.090(3)
3.483(2)
3.472(2)
3 3 3
O3ꢀH3 O1
112
129
140
175
171
161
112
179
168
3 3 3
O3ꢀH3 O2
ꢀx, 1/2 + y, 3/2 ꢀ z
x, ꢀ1 + y, z
x, ꢀ1/2 ꢀy, 1/2 + z
3/2 ꢀ x, 1/2 + y, 3/2 ꢀ z
1 ꢀ x, ꢀy, 2 ꢀ z
1/2 + x, 1/2 ꢀ y, ꢀ1/2 + z
ꢀx, ꢀy, ꢀz
2 ꢀ x, ꢀ1/2 + y, 1/2 ꢀ z
3 3 3
C11ꢀH11A O3
3 3 3
C11ꢀH11B O2
3 3 3
compound 3
compound 4
C7ꢀH7 O3
3 3 3
C10ꢀH10A O2
3 3 3
C11ꢀH11B O2
3 3 3
C2ꢀH2 O3
3 3 3
C8ꢀH8 O1
3 3 3
Table 4. Geometrical Parameters (Å, °) for the π-Stacking Moieties Involved in the π π Interactions for the Title Compounds
3 3 3
(1ꢀ4)a
rings i-j
Rcb
R1vc
R2vd
αe
βf
γg
symmetry
compound 1
Cg(1) Cg(2)
3.6370(13)
3.6121(13)
3.9316(14)
3.8457(14)
3.5201(7)
3.4895(7)
3.5191(8)
3.4906(8)
3.5157(8)
3.4936(8)
3.5191(8)
3.4905(8)
0.29
14.84
14.72
26.48
24.82
14.56
14.97
26.48
24.82
ꢀx, ꢀy, 1 ꢀ z
3 3 3
Cg(1) Cg(2)
0.29
0.00
0.00
1 ꢀ x, ꢀy, 1 ꢀ z
ꢀx, ꢀy, 1 ꢀ z
3 3 3
Cg(2) Cg(2)
3 3 3
Cg(2) Cg(2)
1 ꢀ x, ꢀy, 1 ꢀ z
3 3 3
compound 2
Cg(1) Cg(2)
3.4778(13)
3.8249(14)
4.0495(14)
3.6391(13)
3.3270(4)
3.5329(4)
3.3541(4)
3.5058(4)
3.3228(4)
3.4923(4)
3.3541(4)
3.5058(4)
1.62
1.62
0.00
0.00
17.17
24.07
34.08
15.56
16.94
22.53
34.08
15.56
ꢀx, ꢀy, 2 ꢀ z
1 ꢀ x, ꢀy, 2 ꢀ z
ꢀx, ꢀy, 2 ꢀ z
1 ꢀ x, ꢀy, 2 ꢀ z
3 3 3
Cg(1) Cg(2)
3 3 3
Cg(2) Cg(2)
3 3 3
Cg(2) Cg(2)
3 3 3
compound 3
Cg(1) Cg(1)
4.0778(10)
3.9300(11)
3.9122(10)
3.7015(11)
3.5278(11)
3.3556(7)
3.3365(7)
3.3580(7)
3.3410(7)
3.4339(7)
3.3556(7)
3.3365(7)
3.4592(7)
3.3765(7)
3.4339(7)
4.55
0.00
3.06
1.81
1.00
34.63
31.90
27.84
25.49
13.25
34.63
31.90
30.87
25.49
13.25
1 ꢀ x, y, 3/2 ꢀ z
3 3 3
Cg(1) Cg(1)
3/2 ꢀ x, 1/2 ꢀy, 2 ꢀ z
1 ꢀ x, y, 3/2 ꢀ z
3 3 3
Cg(1) Cg(2)
3 3 3
Cg(1) Cg(2)
3/2 ꢀ x, 1/2 ꢀ y, 2 ꢀ z
1 ꢀ x, y, 3/2 ꢀ z
3 3 3
Cg(2) Cg(2)
3 3 3
compound 4
Cg(1) Cg(2)
3.6684(10)
3.3598(6)
3.3535(6)
1.50(7)
23.91
23.67
1 + x, y, z
3 3 3
a Cg(1) and Cg(2) are the centroids of the (O1/C5ꢀC9) and (C1ꢀC6) rings, respectively. b Centroid distance between ring i and ring j. c Vertical
distance from ring centroid i to ring j. d Vertical distance from ring centroid j to ring i. e Dihedral angle between the first ring mean plane and the second
ring mean plane of the partner molecule. f Angle between centroids of first ring and second ring mean planes. g Angle between the centroid of the first ring
and the normal to the second ring mean plane of the partner molecule.
an intercentroid separation of 3.6370(13) Å [ꢀx, ꢀy, 1 ꢀ z]. On
the other hand, the intercentroid separation of the lactone ring
(L) and benzene ring (B0) of the partner molecule is 3.6121(13)
Å [1 ꢀ x, ꢀy, 1 ꢀ z]. The benzene ring (B) is also engaged in π-
stacking interaction to the B0 ring of the partner molecule and
increases the stability of the self-assembly (Figure 2). This π-
stacking leads to the molecular aggregation along the (1 0 0)
direction. The cooperative π-stacking and hydrogen bonding
interaction give rise to the formation of supramolecular layer
architecture in 1 (Figure 2).
The molecule 2 has a similar chemical structure as that of 1
except for an additional ꢀOH group substituted in the benzene
Figure 2. Supramolecular layer in 1 via π π stacking and hydrogen
bonding interactions. Hydrogen atoms not involve in hydrogen bonding
has been omitted for the sake of clarity.
3 3 3
ring (B). Despite the close structural similarity between 1 and 2,
there are some significant differences in the nature of their
spontaneous self-assembly. In 2, the methyl carbon atom C11
in the molecule at (x, y, z) acts as donor to the carbonyl oxygen
and hydroxyl oxygen atoms in the molecule at (x, ꢀ1 + y, z) and
and increase the stability of the ribbon. The benzene ring (B) that
is in contact with the lactone ring (L0) of the partner molecule has
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Figure 5. Cooperative dispersive forces and π π stacking in 2.
3 3 3
the ꢀOH group has disrupted the cyclic hydrogen bonded motif
4
that was observed in 1. Instead, a R3 (12) cyclic hydrogen
bonding motif is established here between three adjacent mol-
ecules (Figure 3b). The hydrogen bonding parameters are given
in Table 3. The molecules are arranged in the (0 1 1) plane
through this hydrogen bonding. The combination of these self-
organized superstructures generated through above-mentioned
ring motifs leads to aggregation of molecules in the (0 1 1) plane
(Figure 4). Aided by π π stacking interactions (Table 4)
3 3 3
between the benzene and lactone rings, the molecules organize
themselves in well-connected columns (Figure 5).
The lactone ring (L) is in contact with the benzene ring (B)
through π-forces which give rise to the formation of the ribbon.
Moreover, the benzene rings (B) of the molecule are also in contact
with B0 ring of the partner molecule via π-stacking interaction.
This π-stacking leads to the molecular aggregation along crystal-
lographic a-axis (Figure 5).
Figure 3. Hydrogen bonded supramolecuar ribbon in 2.
On the edges of the stacked ribbon, molecules are recognized,
due to their self-complementarity, from layered assembly (Figure 5)
through cooperative hydrogen bonding (Table 3) and π
π
3 3 3
forces (Table 4). This dual recognition induced self-assembly of
the molecules, where π-forces are responsible for the formation
and strengthening of supramolecular layered assembly.
The molecules of 3 are arranged in 202 planes through multiple
CꢀH O hydrogen bonding (Figure 6) interaction. Two hydro-
3 3 3
gen bonding motifs exist in the supramolecular assembly, a
centrosymmetric motif with four hydrogen bonds is formed by
self-complementary association through the wider edge of the
molecule, and a cyclic hydrogen bonding motif (motif-A) is
established where the oxygen atom of the ꢀOMe group acts as a
hydrogen bond acceptor for the H7 hydrogen atom donated by
C7 carbon atom of the lactone ring and the C1 carbon atom
donates the H1 proton toward the C10 methyl group. One can
also visualize another motif where each molecule interacts with
the nearby molecule at their long edges. This gives rise to motif B
having four hydrogen bonding contacts. One can expect that
motif B will be stronger than motif A.
Figure 4. Formation of supramolecular assembly generated through
R4 (22) and R3 (12) ring motif in 2.
4
4
The molecular planes are stacked over each other due to
(x, ꢀ1/2 ꢀ y, 1/2 + z), respectively. These two self-comple-
π
π interaction (Figure 7). Two types of π-motifs exist in the
3 3 3
4
mentary hydrogen bonds result in a supramolecular R4 (22) ring
molecular packing. In one of the π-motifs, the methyl groups of
the two molecules are asymmetrically arranged (π-motif A), but
in the other it is more symmetrically arranged (π-motif B). The
benzene (B) and lactone (L) rings in the molecule at (x, y, z) are
in contact with another benzene (B0) and lactone (L0) rings of
motif in 2. The repetition of these ring motifs generate a 2D
supramolecular sheet in (0 1 1) plane (Figure 3a). Additional
hydrogen bonding between the hydroxyl oxygen and lactone
carbonyl oxygen results into another cyclic motif. Introduction of
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Figure 7. Monomeric units of 3 link one another by self-complemen-
tary hydrogen bonding and extensive π π interactions leading to the
3 3 3
formation of supramolecular layered assembly.
Figure 6. The 2D supramolecular sheet in 3.
the partner molecule at (1 ꢀ x, y, 3/2 ꢀ z) and generates π-motif
A. On the edges of the motif, the lactone ring carbon C7 in the
molecule at (x, y, z) acts as donor to the methoxy oxygen in the
molecule at (3/2 ꢀ x, 1/2 + y, 3/2 ꢀ z). The cooperative forces
of both hydrogen bonding and π-stacking interactions generate a
supramolecular layered assembly in 3 (Figure 7a). In another
substructure, the benzene ring and the lactone ring are in contact
via π-forces with the neighboring molecule at (1 ꢀ x, y, 3/2 ꢀ z)
and (3/2 ꢀ x, 1/2 ꢀ y, 2 ꢀ z) with intercentroid separations of
3.912(1) Å and 3.702(2) Å respectively to form π-motif B. Here
also the methoxy carbon atom acts as donor to the carbonyl
oxygen at (1/2 + x, 1/2 ꢀ y, ꢀ1/2 + z) and the combination of
these two types of weak forces results into a supramolecular
layered assembly (Figure 7b).
Figure 8. CꢀH O hydrogen bonded sheet (0 1 1 plane) in 4.
3 3 3
In 4, two coumarin molecules form a cyclic hydrogen bonded
2
dimer with R2 (8) hydrogen bonding motif (Figure S2, Supporting
are related to each other through an inversion center of sym-
metry. The interconnection between the rings in the molecules at
(x, y, z) and (ꢀ1 + x, y, z) are parallel, with ring centroid
separation of 3.6683(9) Å, forming homodimer and are in
agreement with parallel displaced or offset face-to-face π-stack-
ing interactions (Table 4).
Information) in Etter’s graph notation.45 In this self-complementary
hydrogen bond, the allyl oxygen aotm acts as acceptor to the H2
proton donated by C2 carbon atom. The hydrogen bonding
parameters are given in Table 3. Besides this cyclic motif, a chain
1
of hydrogen bonds with C1 (8) motif in Etter’s graph notation is
An unusual contact between CdO group and the π-system is
observed, which is responsible as well for strengthening the molecular
assembly. The carbonyl oxygen atom O(2) is in contact with the
lactone ring in the molecule at (1 + x, y, z). The distance between
O(2) and the centroid of ring L is 3.2804(14) Å [angle C9ꢀ
responsible for joining of successive dimeric motifs from oppo-
site sides along the b-aixs. This leads to a brick-wall architecture
of the molecular arrangement in the (0 1 1) plane (Figure 8). The
benzenoid ring B and the lactone ring L interact with the lactone
ring L0 and the benzenoid ring B0 of the partner molecule (prime for
partner molecule) through π π stacking interaction which
O2 Cg(1) = 89.44(10)°, C9 Cg(1) = 3.4870(18) Å,
3 3 3 3 3 3
3 3 3
where Cg(1) is the centroid of lactone ring]. This give rise to
forms a supramolecular stacked ribbon in 4, where both molecules
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the interaction of the lone-pair of O(2) atom with the electron-
Supporting Information) in 1. The molecular electrostatic po-
tential map is depicted in Figure S4, Supporting Information,
which shows the concentration of positive and negative charges
on the donor and acceptor atoms. DFT calculation shows that
the energy of the face to face π-stacked motif of two molecules in
1 is 8.74 kJ/mol (Figure S5, Supporting Information).
deficient lactone ring.46 These contacts are further supplemented
by face-to-face π π stacks leading to the formation of supra-
3 3 3
molecular self-assembly (Figure 9). This dual recognition in-
duced self-assembly of the monomeric units has been observed in
the literature.10jꢀn However, this carbonylꢀπ interaction has not
been thoroughly explored so far as a routine tool in the design
and construction of self-assembled structures.
DFT calculation shows that the stabilization energy for the
4
R3 (12) cyclic hydrogen bonding motif in 2 is 65.40 kJ/mol
The occurrence of these CdO(l.p.) π contacts produces a
(Figure S6, Supporting Information) and that of the face-to-
face π-stacked motif is 10.67 kJ/mol (Figure S7, Supporting
Information).
3 3 3
unique carbonyl π/π π topology to build up molecular
3 3 3
3 3 3
architectures. An analysis of the CSD for the lone pair
π
3 3 3
interaction10a showed a significant carbonylꢀπ stacking interac-
tion suggested by an angle ω ranging from 0° to 24°, ω being the
dihedral angle between CdO and the plane of the aromatic ring.
In 4, the orientation of the carbonyl group is almost parallel to the
ring (ω ≈ 1.5°). As stated by Egli and Sarkhel,10a this orientation
potentially allows hydrogen bonding interactions with the O lone
pairs. Moreover, the distance D (corresponding to the distance
between the carbonyl oxygen atom and the ring centroid) and
the angular distribution [deviation of the angle α (α is the angle
In compound 3 there are two types of hydrogen bonding and
π-stacking motifs. DFT analysis shows a small binding energy
of 1.80 kJ/mol (Figure S8, Supporting Information) for the
hydrogen bonded motif-A and somewhat larger stabilization
energy of 28.16 kJ/mol for motif-B (Figure S9, Supporting
Information). Though motif-A has small binding energy the
molecular electrostatic potential plot shows the accumulation of
the negative charge density on the oxygen atom of the ꢀOMe
group and a large positive charge density over the H7 hydrogen
atom is responsible for this contact (Figure S10a, Supporting
Information). The molecular electrostatic potential plot for
motif-B (Figure S10b, Supporting Information) shows that four
point contacts are not between the most positive (blue) edge and
most negative (red) edges of the molecules, but it is between the
same negatively charged wider edges of the partner molecules.
The contacts are between relatively less negative to more
negative regions on this edge of the molecule. In case of two
π-motifs in 3, methyl groups of the two molecules in one are
asymmetrically arranged (π-motif A) and in the other it is more
symmetrically arranged (π-motif B). The π-stacking energy
of the former motif is 18.16 kJ/mol (Figure S11, Supporting
Information) and that of the latter is 19.08 kJ/mol (Figure S12,
Supporting Information).
CdO Cg) from 120°] are 3.28 Å and 30.56°, respectively.
3 3 3
These values are within the mean values, that is, 3.58 Å and
30.6°,10a on the basis of favorable stacking CdO(l.p.)
π
3 3 3
interactions found in the CSD. This entire assembly as a whole
produces a rare supramolecular lone pair π/π π network
3 3 3
3 3 3
and illustrates the occurrence of an elegant combination of weak
forces in the solid-state structure of 4.
DFT Results Regarding Hydrogen Bonded and π-Stacked
Motifs. In Table 5 we have summarized the theoretical results
regarding the hydrogen bonding and π-stacked motifs observed
in the X-ray crystal structures of four compounds.
DFT calculation shows a stabilization energy of 25.02 kJ/mol
2
for the hydrogen bonded R2 (8) motif of two molecules (Figure S3,
In 4, the stabilization energy of the cyclic hydrogen bonded
2
dimer with R2 (8) motif is 8.91 kJ/mol (Figure S13, Supporting
Information). The MEP map of the hydrogen bonded dimer in 4
is displayed in Figure S14, Supporting Information. The energy
of the lone pair π stacking motif is 5.15 kJ/mol (Figure S15,
3 3 3
Supporting Information).
Hirshfeld Surfaces. The Hirshfeld surfaces of 1ꢀ4 are illu-
strated in Figure 10, showing surfaces that have been mapped
over a dnorm range of ꢀ0.5 to 1.5 Å, shape index (ꢀ1.0 to 1.0 Å)
and curvedness (ꢀ4.0 to 0.4 Å). The surfaces are shown as
transparent to allow visualization of the benzopyran moiety, in a
similar orientation for all the structures, around which they were
calculated. The information present in Table 3 is summarized
effectively in the spots, with the large circular depressions
(deep red) visible on the dnorm surfaces indicative of hydrogen bonding
contacts and other visible spots are due to H H contacts. The
Figure 9. Supramolecular layered-assembly generated through carbo-
nyl (l.p.) π/π π interactions in 4. Hydrogen atoms not involved
in hydrogen bonding have been omitted for the sake of clarity.
3 3 3
dominant interactions between hydroxyl OꢀH and carbonyl O
3 3 3
3 3 3
atom in 2 can be seen in Hirshfeld surface plots as the bright red
Table 5. Stabilization Energies of Hydrogen Bonded and π-Stacked Motifs of the Title Compounds 1ꢀ4a
1
2
3
4
hydrogen bonding motifs
25.02 kJ/mol
65.40 kJ/mol
H-motifA
H-motifB
8.91 kJ/mol
1.80 kJ/mol
π-motifA
28.16 kJ/mol
π-motifB
π-stacked motifs
8.74 kJ/mol
10.67 kJ/mol
5.15 kJ/mol
18.16 kJ/mol
19.08 kJ/mol
a For detailed calculations of energy values see Supporting Information.
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Figure 10. Hirshfeld surfaces mapped with dnorm (left), shape index
(middle) and curvedness (right) for the title coumarin derivatives 1ꢀ4.
area marked as 2b in Figure 11. The light red spots labeled as 1a,
2c, 2d, and 4a, 4b for compounds 1, 2, and 4 are due to Cꢀ
H
O interactions (Figure 10 and Table 3). The small extent of
3 3 3
area and light color on the surface indicates weaker and longer
contact other than hydrogen bonds.
Figure 11. Fingerprint plots of 1ꢀ4: Full (left) and resolved into
The OꢀH O and CꢀH O intermolecular interactions
3 3 3
3 3 3
O
H/H O (middle) and C H/H C (right) contacts show-
3 3 3
3 3 3
3 3 3
3 3 3
appear as two distinct spikes of almost equal lengths in the 2D
fingerprint plots in the region 2.03 Å < (de + di) < 2.47 Å labeled
correspondingly as a, b, etc. Complementary regions are visible
in the fingerprint plots where one molecule acts as a donor (de > di)
and the other as an acceptor (de < di). The fingerprint plots
can be decomposed to highlight particular atom pair close
contacts.47 This decomposition enables separation of contribu-
tions from different interaction types, which overlap in the full
fingerprint. The Hirshfeld surface analysis do not show a similar
ing the percentages of contacts contributed to the total Hirshfeld surface
area of molecules.
26.8% of total Hirshfeld surface due to O H/H O inter-
3 3 3
3 3 3
action. The spikes in the fingerprint plot represent lactone ring
oxygen acting as acceptor to the lactone ring carbon for the
formation of 1D chain and the allyl oxygen interacting with the
2
neighboring aryl carbon, forming R2 (8) motif. No significant
CꢀH π interaction has been observed for the substituted
proportion of O H interactions for each molecules ranging
3 3 3
3 3 3
coumarin derivatives (1ꢀ4), with CꢀH close contacts varying
from 14.7% to 18.4%. In all cases, the O H interactions are
3 3 3
from 9.0% in 1 to 17.3% in 4. A significant difference between the
represented by a spike in the bottom left (donor) area, whereas
molecular interactions in (1ꢀ4) in terms of H H interactions
the H O interactions are represented by a spike in the bottom
3 3 3
3 3 3
is reflected in the distribution of scattered points in the finger-
print plots, which spread only up to di = de = 1.197 Å in 1, di = de =
1.132 Å in 2, di = de = 1.147 Å in 3, and di = de = 1.067 Å in 4.
The relative contributions of the different interactions to the
Hirshfeld surfaces were calculated for 1ꢀ4 (Figure 12). From
the Hirshfeld surfaces, it is clear that the title coumarin derivatives
are related to one another where above the plane of the molecule,
inspection of the adjacent red and blue triangles on the shape
right region in the fingerprint plot and the proportion of H
O
3 3 3
interactions has less variety than its O H counterparts, ran-
3 3 3
ging from 11.6% to 14.0%.
The proportions of O H/H O interactions comprising
3 3 3
3 3 3
27.3% of the total Hirshfeld surface for each molecule of 1. The
points in the (di, de) regions of (1.357 Å, 1.026 Å) in the fin-
gerprint plots are due to CꢀH O interactions (Figure 11),
3 3 3
representing the lactone ring carbon interacting with carbonyl
2
index surface shows that the π π stacking interaction is almost
oxygen, forming a centrosymmetric R2 (8) hydrogen bonding
3 3 3
identical in the total crystal structures. The presence of π
π
motif. In 2, the O H/H O interactions comprise 30.6% of
3 3 3
3 3 3
3 3 3
stacking is evident since a flat region toward the bottom of both
sides of the molecules and is clearly visible on the curvedness
surface. On the de surface this feature appears as a relatively flat
green region, where the contact distances are all very similar. The
corresponding fingerprint plot in Figure 11 shows this interac-
tion as a region of blue/green color on the diagonal at around de
≈ di ≈ 1.78 Å. The pattern of red and blue triangles on the same
region of the shape index surface (Figure 10) is characteristic of
total Hirshfeld surface area. The O H interactions represented
3 3 3
by spike (di = 1.182 Å, de = 0.851 Å) represent the hydroxyl oxygen
acting as donor to carbonyl oxygen, forming a 1D zigzag chain
along the (0 1 0) direction. The H O interactions represented
3 3 3
by spike (di = 0.851 Å, de = 1.182 Å) represent the hydroxyl and
carbonyl O atoms acting as an acceptor to methyl carbon for the
formation of 2D sheet. Compound 3 does not exhibit any classical
hydrogen bonds but O H interaction comprises 32.4% of
3 3 3
π
π stacking and is used to determine the way in which the
Hirshfeld surface due to close contacts. In 4, each molecule comprises
3 3 3
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all the molecules at one corner of the rectangular molecular
framework. In compounds 1 and 2, the less acidic methyl group is
present at the 4 and 7 position. In 2, an addition ꢀOH substi-
tution is present on the lower edge of the molecule which can
possibly act both as donor and acceptor simultaneously because
the hydrogen of this group cannot perpendicularly align with
respect to the molecular lower edge. The effect of this substitu-
tion on the molecular packing is clearly seen by comparing the
2
hydrogen bonding arrangements in 1 and 2. While in 1 a R2 (8)
hydrogen bonding arrangement leads to dimeric association
4
among the molecules, a distinctly different cyclic R3 (12) hydrogen
bonding motif is enforced in 2 due to the OH substitution. The
hydroxyl group in 2 disrupts the dimeric motif observed in 1 and
4
enforces a R3 (12) cyclic motif involving three molecules by
simultaneously acting as donor for the carbonyl O atom present
on the lactone ring and acceptor for the one of the methyl
hydrogens substituted at the 4 position. This motif leads to the
ribbon architecture of the self-assembled molecular units in 2.
The ribbon propagates along the crystallographic b-axis. Two
sets of molecules are positioned symmetrically on both sides of
the ribbon, one set running opposite to the other. This arrange-
ment leads to the decoration of the edges of the ribbon by the
methyl groups substituted at the 7 position of the molecule. In
both 1 and 2, the cooperative π-stacking and hydrogen bonding
leads to molecular layers. There is a distinct characteristic of this
cooperation. The hydrogen bonding forces act in the molecular
plane and π-forces operate perpendicular to the molecular plane.
This mode of cooperation of relatively stronger hydrogen bonding
forces and comparatively weaker π-stacking forces is a recurring
feature observed in the packing of many molecular crystals. The
molecular layers observed in 1 is characteristically different from
the one observed in 2. In 1, the hydrogen bonded dimers are
glued by π-stacking forces leading to a stacked layer of brick wall
topology where each dimer is positioned over two other dimers.
The methyl groups substituted at 4 and 7 positions decorate the
two surfaces of the π-stacked layers. These methyl groups at the
molecular corners and other hydrogen atoms at the molecular
edges govern the interlayer stacking of the π-stacked layers through
dispersive forces. In 2, the stacked molecular ribbons lead to
molecular layers with a completely different topology. Each of the
ribbons is glued to two adjacent layers on the opposite faces of
the molecule at the two edges of the ribbon by π-stacking forces.
The topology of the layer is equivalent to that of the equilibrium
state of a set of books on a library rack when the support at one
end is removed. The uniqueness of this arrangement is in the
facilitation of the simultaneous operation of hydrogen bonding
forces and π-forces along the same direction. In this slided stacking
of hydrogen bonded ribbons not only do π-forces operate but
also the methyl group at the 4 position takes part in inter-ribbon
hydrogen bonding aiding the π-forces and acts parallel to it. So in
2 the hydrogen bonding forces operate both along the direction
of the π-forces and perpendicular to it. Interlayer sacking in this
case is governed solely by π-forces.
Figure 12. Relative contributions of various intermolecular contacts to
the Hirshfeld surface area in 1ꢀ4.
molecules overlap and make contact with each other. The pattern
of red and blue triangles on this region of both sides of the
molecule shows how adjacent molecules in the crystal are related
by translation. Blue triangles represent convex regions due to ring
carbon atoms of the molecule inside the surface, while red
triangles represent concave regions due to carbon atoms of the
π stacked molecule above it.
Figure 12 contains the percentages of contributions for a
variety of contacts in compounds 1ꢀ4. From these values, it can
be seen that the C C contacts, associated with π π stacking
3 3 3
3 3 3
interactions in the (di, de) ≈ (1.77 Å, 1.77 Å) region, are minimal
in 4 (only 6.5% of the surface is due to C C interactions
3 3 3
compared with the 11.1%, 11.4%, and 12.1% for 3, 2, and 1,
respectively). This quantatively verifies observations that are
obvious from inspecting the different structures. This conclusion
is further evident from the shape of the blue outline on the
curvedness surface (Figure 10), which unambiguously delineates
contacting patches of the molecules. Finally, these examples
underline the utility of Hirshfeld surface and in particular, finger-
print plot analysis for the “visual screening” and rapid detection
of unusual crystal structures features48 through a “whole struc-
ture” view of intermolecular interactions.49
’ STRUCTURAL DISCUSSION
Weak noncovalent forces are responsible for organizing organic
molecules in the solid state crystalline materials. Except for very
few cases, predicting the crystal structure of a given set of organic
molecules has remained a difficult task to date. The difficulty lies
in our lack of understanding regarding the self-assembly of
organic molecules in the presence of multiple noncovalent forces.
Understanding of self-assembling behavior of simple organic
molecules in the presence of multiple noncovalent forces is the
goal of the present study. Coumarin and substituted coumarines
being important in many fields, we have chosen a set of four
coumarin derivatives in the present study. The basic coumarin
framework possesses a benzenoid ring and a lactone ring. It is not
Interestingly, in 3 where all the substitution is on the benzenoid
ring, a methoxy group at the 6 position and the methyl group in
the 7 position leads to predominance of π-stacking forces in a
direction exactly perpendicular to the plane of the molecule and
difficult to foresee that π π stacking interactions will be one of
3 3 3
the main forces in governing the packing of these molecules in
the solid state, but our aim was to study the effect of hydrogen
bonding forces on the molecular packing by arranging various
donors and acceptors on the molecular edges of the coumarin
molecules. As one can easily see, there are four distinct edges on
the rectangular coumarin framework, two long one and two
short. The carbonyl O acceptor on the lactone ring is present in
multipoint CꢀH O hydrogen bonded contacts in the plane
3 3 3
of the molecule at it is four edges. It is very interesting to note that
two distinct sets of π-stacking motifs are present in 2. In one type
of stacking, the molecular rectangle is parallely stacked and in the
other a L-type stacking arrangement results where two molecular
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Crystal Growth & Design
ARTICLE
rectangles are rotated 90° with respect to each other around an a
axis passing through the benzenoid rings. Similarly, two sets of
hydrogen bonding motifs are present in the molecular plane. In
one set, the molecular rectangles are united along their self-
’ CONCLUSIONS
In summary, in our continuing effort to understand the role of
weak forces in the self-assembly of crystalline solid materials we
have studied four closely related coumarin based molecules by
X-ray structural analysis and DFT calculations. The crystal stru-
cture analysis reveals a particular mode of cooperativity of hydrogen
complementary long lower edge with four CꢀH O contacts.
3 3 3
Both the carbonyl O atom and the lactone ring O atom act as
acceptor for the methyl hydrogen at the 7-postion and the H4
hydrogen of C4 carbon atom on the benzenoid ring. The other
hydrogen bonded motif is the result of the long edge to short
edge hydrogen bonding association of the rectangular molecule.
The O atom of the methoxy group acts as a acceptor for the H7
hydrogen attached to C7 carbon atom on the upper long mole-
cular edge of the molecule. There is an unusual short contact
(2.942 Å) between the H1 hydrogen attached to C1 carbon atom
on the upper molecular edge and the methyl group at the 7
position. The preliminary DFT calculation also establishes the
authenticity of this hydrogen bonded motif having this unusual
contact confirming that it is not the artifact of packing effect. A
high level calculation is underway to establish the exact nature of
the forces associated with this short contact.
bonding forces and π π forces. Each molecule is associated in
3 3 3
homodimers through parallel displaced π-stacking interactions
between complementary rings of the coumarin backbone. Whereas
π-forces generally assemble coumarin based molecules perpen-
dicular to the molecular plane, hydrogen bonding forces unite
them in the plane of the molecules at their edges. The four edges
of the nearly rectangular molecules can be functionalized intelli-
gently and the architecture of the self-assembled hydrogen bonded
layer can be tuned accordingly. A R2 (8) hydrogen bonded motif
operates in the self-assembly among three of the four compounds
studied here. A result of the mutual cooperation of hydrogen
2
bonded forces with this motif and the π π forces is the ap-
pearance of self-assembled molecular ribbons. Widely asymmetric
positions of the substituent groups in compound 3 lead to four
3 3 3
In compound 4, the O atom of the substituted allyloxy group
and the lactone ring O atom are responsible for the two types
of hydrogen bonding motifs present in the structure. A cyclic
point contact at the long molecular edges through CꢀH
O
3 3 3
hydrogen bonding and molecular arrangement in a perfect plane.
The unique feature of this compound is the appearance of two
types of π-motifs due to orientation degrees of freedom of the
molecule satisfying the demand of the hydrogen bonding motifs
in the molecular plane. The simple coumarin based molecules
studied here reveal how finely the various weak forces such as
CꢀH O forces, π π forces, lone-pair π forces, and
2
R2 (8) hydrogen bonding motif leads to molecular dimers. This
hydrogen bonding force operates in the molecular plane and
joins two rectangular molecules at one of their short edges with
the two dangling allylic groups at the opposite end of the long
edges. π-stacking forces unite these molecular dimers along a
direction perpendicular to the molecular plane that leads to the
formation of molecular ribbons. This π-stacking is aided by the
3 3 3
3 3 3
3 3 3
dispersive forces cooperate with each other in crystal packing.
Generally hydrogen bonding forces and π π forces operate in
3 3 3
carbonyl (lone-pair) π interaction between the carbonyl O
3 3 3
mutually perpendicular but cooperative manner and assembly in
the molecular plane can be engineered intelligently influencing
the out of plane molecular stacking. This methodology has very
important promise for further study in the field of photoinduced
dimerization, molecular patterning on substrate surfaces, and
crystal engineering in general.
Hirshfeld surface is used to visualize the fidelity of computed
crystal structures. The nature of the interplay of the title
compounds are more easily understood using Hirshfeld surface
analyses. The Hirshfeld surface and its fingerprint plots provide
information not only about the areas of close contacts but also
about more distant contacts and areas where the interactions are
weakest. The fingerprint plots certainly allow a much more detailed
scrutiny in comparison to similar structures by displaying all the
intermolecular interactions within the crystal and are therefore
suitable for analyzing the changes in crystal packing due to different
substitutions in the coumarin skeleton.
atom on the lactone ring and the π-cloud of the lactone ring of
the symmetry related molecule. To facilitate this interaction the
π
π interaction is side wise displaced stacking type. Succes-
3 3 3
sive molecular ribbons are joined at their short edges due to the
formation of C2 (9) hydrogen bond chain motif among three
2
successive ribbons. This leads the brick wall architecture of the
ribbons in the three-dimensional packing in the crystal. Com-
pound 4 is a rare example where lone-pair π forces cooperate
3 3 3
with π π and hydrogen bonding forces.
3 3 3
All the molecules of 1ꢀ4 are self-associated through π-stacking
interactions forming homodimers. Each of the two molecules
interacts through parallel displaced π π interactions. The
3 3 3
intercentroid distances, the dihedral angle between the first ring
mean plane and the second ring mean plane of the neighboring
molecule, and the angle between the centroid of the first ring and
the normal to the second ring mean plane of the partner molecule
are in agreement with parallel displaced or offset face-to-face π-
stacking interactions. The values of the intercentroid distances
between two parallel rings correspond to the sum of the van der
Waals radii of two carbon atoms between two benzenoid
molecules.50 In the title compounds, four π-stacking interactions
’ ASSOCIATED CONTENT
S
Supporting Information. Four crystallographic files (CIF);
b
Figures S1ꢀS15 illustrating optimized hydrogen bonding, π-
stacking motifs and molecular electrostatic potential map of the
title compounds. Details of calculations of stabilization energies
for different motifs in 1ꢀ4 are described here. This material is
available free of charge via the Internet at http://pubs.acs.org.
like B L0, B0
3 3 3
L, B B0, and B0
3 3 3
B are found as common
features in the homodimers of 1, 2, and 3, whereas compound 4
3 3 3
3 3 3
exhibits only B L0 and B0
L type π-stacking interactions.
3 3 3
3 3 3
L0 type interactions. These types of interactions forming
homodimers are in agreement with the attractive interaction
between two rings with opposite polarity, followed by less repulsive
interaction between two rings with low electron density and
finally the most repulsive interaction between two rings with high
electron density.51
An exception is found for the homodimer of 3, which exhibits
L
3 3 3
’ AUTHOR INFORMATION
Corresponding Author
*E-mail: mstk@iacs.res.in (T.K.), atishdipankarjana@yahoo.in
(A.D.J.).
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ARTICLE
’ ACKNOWLEDGMENT
Chem. Soc. 2004, 126, 9862–9872. (c) Kim, D.; Hu, S.; Tarakeshwar, P.;
Kim, K. S.; Lisy, J. M. J. Phys. Chem. A 2003, 107, 1228–1238. (d) Ma,
J. C.; Dougherty, D. A. Chem. Rev. 1997, 97, 1303–1324. (e) Kim, K. S.;
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S.K.S. is grateful to the DST-funded National Single Crystal
X-ray Diffraction facility at the Department of Inorganic Chemistry,
Indian Association for the Cultivation of Science, India, for data
collection. The authors are grateful to Amalesh Roy, Department
of Organic Chemistry, IACS, Kolkata for his interest, help, and
discussions.
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