C-H?O interactions are favoured in the crystal structures of imidazolin-5-ones

Article abstract of DOI:10.1016/j.molstruc.2005.05.044

The competing forces of a greater number of weak C-H?O interactions in the crystal structure of imidazolin-5-one analogues seem to tip the balance against the relatively stronger carbonyl-carbon (C=O ^δ-?C^δ+) electrostatic interaction previously observed and reported by us in the crystal structure of (4Z)-4-(4-methoxybenzylidene)-1,2-diphenyl-1,4-dihydro-5H-imidazolin-5-one [G. Bhattacharjya, G. Savitha, G. Ramanathan, Cryst. Eng. Commun. 6 (2004) 233].

Full text of DOI:10.1016/j.molstruc.2005.05.044

Journal of Molecular Structure 752 (2005) 98–103
www.elsevier.com/locate/molstruc
C–H/O interactions are favoured in the crystal structures
of imidazolin-5-ones
a
Gitalee Bhattacharjya , G. Savitha , Gurunath Ramanathan
a
a,b,
*
a
Department of Chemistry, Indian Institute of Technology, Kanpur 208016, UP, India
b
Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, UP, India
Received 17 April 2005; revised 15 May 2005; accepted 16 May 2005
Available online 20 July 2005
Abstract
The competing forces of a greater number of weak C–H/O interactions in the crystal structure of imidazolin-5-one analogues seem to tip
dK
dC
the balance against the relatively stronger carbonyl-carbon (CaO /C ) electrostatic interaction previously observed and reported by us
in the crystal structure of (4Z)-4-(4-methoxybenzylidene)-1,2-diphenyl-1,4-dihydro-5H-imidazolin-5-one [G. Bhattacharjya, G. Savitha, G.
Ramanathan, Cryst. Eng. Commun. 6 (2004) 233].
q 2005 Elsevier B.V. All rights reserved.
Keywords: Weak hydrogen bonding; Imidazolin-5-ones; C–H/O interaction; CaO/C interaction; Donor–acceptor interactions
1
. Introduction
Imidazolin-5-one and its analogues are known to exist as
flourophores in the green fluorescent protein (GFP) [22].
This chromophore is formed via a post-translational internal
Crystal packing in organic molecules by C–H/O
6
5
66
67
hydrogen bonding [2–4] in the absence of any other
competing strong electro-positive/negative groups is widely
accepted in structural chemistry [5–8] as well as in biology
cyclization of the Ser -Tyr -Gly tripeptide followed by
a,b-dehydrogenation of the tyrosine [23] in the protein [24].
The wide applicability of the green fluorescent protein
inspired us to design several imidazolin-5-ones and study
their potential as flourophores [25,26]. In this context, we
have examined the solution-state fluorescence properties of
these compounds and also determined their X-ray crystal
structures.
[
9]. Although it is premature to speculate on the driving
force between preferences in a mixed situation of
availability of both weak and strong partners, molecular
packing in crystals [10] offers an arena, where statistical
distributions of these interactions can be explored. In this
context, the CaO/CaO interaction [11,12] or the
CaO /C interaction [1] is not as common in crystal
packing as one would pre-suppose [13,14]. These so-called
donor–acceptor type [15–16] of electrostatic interactions
bears the potential to form supramolecular synthons [2]. The
inherent weakness and flexibility of the C–H/O hydrogen
bond often act as competing forces in crystal packing
Our recent studies on (4Z)-4-(4-methoxybenzylidene)-
1,2-diphenyl-1,4-dihydro-5H-imidazolin-5-one (1) brought
to light an interesting donor–acceptor interaction between
dK
dC
dK
dC
the carbonyl group and the carbon (CaO /C ) of the
imidazolinone ring. To investigate the persistence of this
electrostatic interaction in crystal packing and to study the
influence of the different substituents in the molecular
assembly, several analogues of (1) were synthesized.
We report here four crystal structures consisting of (4Z)-
[17,18], and has proved to be one of the challenges of crystal
engineering today [19–21].
4
-benzylidene-1-methyl-2-phenyl-1,4-dihydro-5H-imida-
zolin-5-one (2), (4Z)-4-benzylidene-1,2-di-phenyl-1,4-
dihydro-5H-imidazolin-5-one (3), (4Z)-4-(4-methoxyben-
zylidene)-1-methyl-2-phenyl-1,4-dihydro-5H-imidazolin-
*
Corresponding author. Address: Department of Chemistry, Indian
Institute of Technology, Kanpur 208016, UP, India. Tel.: C91 512 259
7
0
417; fax: C91 512 259 7436.
E-mail address: gurunath@iitk.ac.in (G. Ramanathan).
5-one (4) and (4Z)-4-(4-methoxybenzylidene)-2-methyl-1-
phenyl-1,4-dihydro-5H-imidazolin-5-one (5) as shown in
Fig. 1.
022-2860/$ - see front matter q 2005 Elsevier B.V. All rights reserved.
doi:10.1016/j.molstruc.2005.05.044

G. Bhattacharjya et al. / Journal of Molecular Structure 752 (2005) 98–103
99
6
O
6
22
O
21
9
7
20
CH3
8
5
23
10
9
7
4
1N
14
c
20
8
5
a
10
11
3
N
2
4
1N
2
24
11
13
a
3
N
25
15
12
13
15
16
12
14
2
19
b
3
16
19
b
17
18
17
18
6
24
O
23
2
5
9
7
22
c
5
10
8
4
1 N
16
26
a
3
N
2
27
11
1
3
15
1
2
H3C
17
O
14
18
21
b
1
19
20
6
O
6
19
9
7
O
18
2
2
8
5
20
10
CH3
4
1N
9
7
1
7
c
5
a
3
N
2
10
11
8
1
3
11
4
1N
21
15
1
O
2
H3C
2
22
17
a
3
N
1
3
14
16
12
15
H3C
1
6
18
O
14
CH3
2
1
b
5
4
19
20
Fig. 1. Molecular structure of 4Z-4-(4-methoxybenzylidene)-1,2-diphenyl-1,4-dihydro-5H-imidazolin-5-one and its analogues.
2
. Experimental
7.54 (m, 3H, Ar), 7.85 (d, 2H, Ar), 8.22 (d, 2H, Ar). IR (KBr)
925, 1715, 1645, 1597, 1429, 1372, 1286. For compound
2
The compounds (2–5) were synthesized with oxazolin-5-
one as the starting material, following reported procedures
27,28]. They were crystallized from distilled methanol by
(2), data collection: Bruker SMART; cell refinement: Bruker
SMART; data reduction: Bruker SAINT; program(s) used to
solve structure: SHELXS-97 [29]; program(s) used to refine
structure: SHELXL97 [29]; molecular graphics: Bruker
SHELXTL; software used to prepare material for publi-
cation: Bruker SHELXTL.
[
slow evaporation in air. X-ray data were collected at the
Bruker-Nonius SMARTAPEX CCD detector at the Depart-
ment of Chemistry, IIT Kanpur, India. The X-ray crystal
structure data obtained for the imidazolin-5-ones, com-
pounds (2–5), are shown in Table 1.
Compound (3) was synthesized by refluxing a mixture of
(4Z)-4-benzylidene-2-phenyl-oxazolin-5-one (1 g, 4.0
mmol), freshly distilled aniline (0.44 ml, 4.8 mmol) and
anhydrous zinc chloride (0.05 g, 0.40 mmol) for 1 h at
160 8C. Similar purification and crystallization procedure
Compound (2) was synthesized by refluxing a mixture of
4Z)-4-benzylidene-2-ethyl-oxazolin-5-one (1 g, 4.0 mmol),
(
methylamine in 40% solution (0.41 ml, 4.8 mmol) and
anhydrous zinc chloride (0.05 g, 0.40 mmol) for 1 h at
was applied to yield yellow crystalline product. Yield 60%,
1
m.p. 162–163 8C. H NMR (CDCl , 400 MHz) d 7.18 (s,
160 8C. The brown coloured reaction mixture was purified
by column chromatography and crystallized from distilled
methanol by slow evaporation in air to yield yellow crystals.
3
1H, aCHAr), 7.48 (m, 3H, Ar), 7.57 (d, 2H, Ar), 8.30 (d,
2H, Ar). IR (KBr) 3623, 2923, 1712, 1638, 1593, 1072.
For compound (3), data collection: Bruker SMART; cell
refinement: Bruker SMART; data reduction: Bruker
1
Yield 75%, m.p. 124–126 8C. H NMR (CDCl , 400 MHz):
3
d 3.35 (s, 3H, NCH ), 7.24 (s, 1H, aCHAr), 7.38 (m, 3H, Ar),
3

100
G. Bhattacharjya et al. / Journal of Molecular Structure 752 (2005) 98–103
Table 1
Crystallographic data on compounds 2–5
Compound
2
3
4
5
Empirical formula
Formula weight
Crystal system
Space group
˚
a (A)
˚
b (A)
C
17
H
14
N
2
O
C
22
H
16
N
2
O
C
18
H
16
N
2
O
2
C
18 16 2 2
H N O
262.30
324.37
Monoclinic
P2
292.33
Monoclinic
P2 /n
292.33
Orthorhombic
P2
Triclinic
PK1
9.6537(9)
1
1
1 1 1
2 2
5.5221(5)
14.8024(15)
9.8180(10)
93.330(2)
11.6285(12)
7.5291(8)
7.1302(15)
9.2894(19)
22.241(5)
90
9.8960(10)
14.0747(13)
95.190(2)
92.472(2)
101.638(2)
1309.0(2)
4
˚
c (A)
16.5896(17)
90.837(2)
b (8)
a (8)
g (8)
3
˚
V (A )
801.17(14)
2
1452.3(3)
4
1473.1(5)
4
Z
K3
D
c
(g cm
K1
)
1.331
1.344
1.337
1.317
m (mm
F(000)
)
0.084
0.084
0.088
0.087
552
340
616
616
Crystal dimensions
Theta range for data
collection (8)
0.2!0.2!0.2
2.11–28.37
0.2!0.1!0.1
2.49–28.30
0.2!0.2!0.2
2.12–28.27
0.1!0.1!0.1
1.83–28.34
Reflections measured
Independent reflections
Data/restraints/parameters
8454
5392
9026
9517
5920 [R(int)Z0.0169]
5920/0/361
2049 [R(int)Z0.0280]
2049/0/242
3443 [R(int)Z0.0499]
3443/0/199
2068 [R(int)Z0.0654]
2068/0/215
2
Goodness-of-fit on F
1.046
1.099
1.021
1.085
Final R indices
R1Z0.0599, wR2Z0.1510
R1Z0.0416, wR2Z0.0964
R1Z0.0748, wR2Z0.1714
R1Z0.0562, wR2Z0.1299
[
IO2sigma(I)]
R indices (all data)
R1Z0.0831, wR2Z0.1640
R1Z0.0439, wR2Z0.0977
R1Z0.1164, wR2Z0.1714
R1Z0.0743, wR2Z0.1375
For all compounds, X-ray diffraction data was collected on the Bruker-Nonius, SMART CCD detector, data reduction and processing: SAINTPLUS; empirical
absorption correction: SADABS; merging: XPREP; programs used to solve structure: WINGX32 Suite (version 1.64.05); structure refinement: SHELX97
2
refinement on F of all reflections); molecular graphics: DIAMOND (version 2). The CCDC reference numbers for the four crystal structures (2–5) are
(
249693, 249694, 249695 and 249696.
SAINT; program(s) used to solve structure: Bruker
SHELXTL; program(s) used to refine structure: SHELXL97
product with a solvent system of 10% ethyl acetate in pet
1
ether. Yield 81%, m.p. 131–132 8C. H NMR (CDCl , 400
3
[
29]; molecular graphics: Bruker SHELXTL; software used
MHz) d 2.26 (s, 3H, –CH ), 3.86 (s, 3H, OCH ), 6.94 (d,
3
3
to prepare material for publication: Bruker SHELXTL.
Compound (4) was synthesized by similar procedure in
which (4Z)-4-(4-methoxybenzylidene)-2-phenyl-oxazolin-
2H, Ar), 7.17 (s, 1H, aCHAr), 7.49 (m, 3H, Ar), 8.14 (d,
2H, Ar). IR (KBr) 3489, 2926, 1704, 1641, 1594, 1428,
1260, 1016. For compound (5), data collection: Bruker
SMART; cell refinement: Bruker SMART; data reduction:
Bruker SAINT; program(s) used to solve structure: Bruker
SHELXTL; program(s) used to refine structure:
SHELXL97 [29]; molecular graphics: Bruker SHELXTL;
software used to prepare material for publication: Bruker
SHELXTL.
5
-one (1 g, 0.36 mmol), methylamine in 40% solution
(
(
0.368 mL, 4.3 mmol) and anhydrous zinc chloride
0.049 g, 3.6 mmol) were used in the reaction mixture to
yield the product. Yellow crystals were obtained. Yield
1
8
0%, m.p. 137–139 8 C. H NMR (CDCl , 400 MHz) d 3.29
3
(
(
s, 3H, N–CH ), 3.79 (s, 3H, OCH ), 6.89 (d, 2H, Ar), 7.18
3 3
s, 1H, aCHAr), 7.48 (m, 3H, Ar), 7.79 (d, 2H,Ar), 8.15 (d,
2
1
H, Ar). IR (KBr) 2925, 1703, 1647, 1597, 1428, 1367,
256, 1015. For compound (4), data collection: SMART
3. Results and discussion
CCD; cell refinement: SAINTPLUS; data reduction:
XPREP; program(s) used to solve structure: SHELXS-97
Compound (2) consists of two molecules, which are
linked by C–H/O hydrogen bonds across the carbonyl and
methyl substituents of the imidazolinone forming self-
complexes (Fig. 2a).
[
29]; program(s) used to refine structure: SHELXL97 [30];
molecular graphics: ORTEP-3 for Windows [31]; software
used to prepare material for publication: WinGX publi-
cation routines [32].
˚
The perpendicular distance between the planes w3.3 A
Compound (5) was synthesized by refluxing (4Z)-4-(4-
and the stacking is staggered. The in-plane C–H/O
(C20–H20A/O6 is 2.94 A and C41–H41C/O27 is
˚
3.27 A) interaction is with symmetry-related molecules
˚
methoxybenzylidene)-2-methyl-oxazolin-5-one
.6 mmol), freshly distilled aniline (0.50 ml, 5.5 mmol)
and anhydrous zinc chloride (0.07 g, 5.0 mmol) for 1 h at
10 8C. The brown coloured reaction mixture was purified
by column chromatography to yield yellow crystalline
(1 g,
4
at (1Kx,1Ky,Kz), while C–H/N (C15–H15/N24Z
˚
3.56 A) interactions are with symmetry-related molecule
at (x,1Cy,z). This array emerges as lateral stacks of
1

G. Bhattacharjya et al. / Journal of Molecular Structure 752 (2005) 98–103
101
Fig. 2. (a) Structure of compound (2) showing C–H/O hydrogen bond between the carbonyl and the methyl substituent of the imidazolinone ring forming self-
complexes. (b) The packing diagram shows the edge-to-face orientation of the molecules in the crystal structure of compound (2).
the benzylidene–imidazolinone rings, with the phenyls
forming a edge-to-face orientation in the crystal (Fig. 2b).
The packing scheme shows formation of sheets along
In compound (4) the benzylidene–imidazolinone rings
are coplanar as in compound (1) with torsion angle C4–C7–
˚
C8–C15ZK0.68 tied by C15–H15/N5Z3.13 A intra-
molecular hydrogen bonding. The benzylidene rings are
(2 K2 K2) by the coplanar benzylidene–imidazolinone
rings. The intramolecular interaction within the two
linked by C–H/O hydrogen bonds to form self-pairs with
˚
molecules of the asymmetric unit is C9–H9/N3
C10–H10/O12Z3.49 A (Fig. 4a).
˚
˚
(
3.12 A) and C30–H30/N24 (3.06 A), respectively. In
fact, N24 co-ordinates as a bifurcated acceptor to H15–
The oxygen O6 of the carbonyl and methyl of the
imidazolinone have different roles this time, they are
involved in C–H/O hydrogen bonding with the carbonyl
O6 interacting with the methoxy-methyl and the methyl of
the imidazolinone interacting with the O12 of the
methoxy group forming stacks of the ring planes
(Fig. 4b). The hydrogen-bonding distance C13–H13b/
C15 and H30–C30 pair.
The crystal structure of compound (3) consists of mainly
C–H/O interactions. The carbonyl oxygen of the imida-
zolinone functions as a bifurcated acceptor having
simultaneous hydrogen-bonding interactions with sym-
metry-related molecules at (1Kx,1/2Cy,1Kz) and (K1C
x,y,z) as seen in (Fig. 3a), with C17–H17/O6 distance of
˚
˚
O6 is 3.31 A and C16–H16c/O12 is 3.44 A. The p–p
stacking achieved by perpendicular hydrogen bonding
involving the methoxy group and the methyl of the
˚
˚
3
.46 A and C21–H21/O6 distance of 3.32 A, respectively.
˚
imidazolinone is fairly strong with 2.7 A spacing. The
The overall crystal packing is by sheet formation by
intersecting planes (1 3 0) and (K1 3 0) (Fig. 3b). The
stacking of the benzylidene–imidazolinone rings is offset
and there is no strong interaction across the planes. The
benzylidene–imidazolinone ring system is also slightly
buckled with the internal torsional angle C4–C7–C8–
C13Z10.48. The intramolecular hydrogen bond across the
O12 of the methoxy group functions as a bifurcated
acceptor and forms stacking interactions between the
imidazolinone–benzylidene moiety in reverse orientation
alongside self-pairing interaction within the plane. The
overall packing is in parallel sheets in two planes (1 2 0)
and (K2 4 0) (Fig. 4b).
˚
benzylidene–imidazolinone ring (C13–H13/N3Z3.16 A)
In the crystal structure of compound (5), the 1-phenyl
forms edge-to-face interactions with the imidazolinone
is of the C–H/N type.
Fig. 3. (a) Structure of compound (3) showing simultaneous hydrogen bonding between the carbonyl of one molecule and the C–H of the benzene ring of two
other molecules with the imidazolinone functioning as a bifurcated acceptor. (b) Packing diagram shows sheet formation in the crystal structure of compound (3).

102
G. Bhattacharjya et al. / Journal of Molecular Structure 752 (2005) 98–103
Fig. 4. (a) Structure of compound (4) showing two types of hydrogen bonding. One between the O6 oxygen of the carbonyl of one molecule and the C–H of the
methoxy-methyl of the other molecule and the other interaction is between the methyl of the imidazolinone ring and the oxygen O12 of the methoxy group,
thereby forming self-pairs. (b) Packing diagram shows stack formation of the ring planes in compound (4).
Fig. 5. (a) Structure showing simultaneous C–H/O and C–H/N hydrogen bonding between the molecules of compound (5) holding them together in the
crystal lattice. (b) Packing diagram showing the edge-to-face orientation of the molecules of compound (5).
through C–H/O and C–H/N hydrogen bonds (C19–
H19/O6Z3.41 A and C22–H22/N3Z3.53 A) as shown
in (Fig. 5a).
bonding exists between C9–H9/N3 with a distance of
˚
˚
˚
3.14 A.
The hydrogen-bonding geometry of compounds (2–5)
are shown in Table 2.
Compound (1) [1] on the contrary consists of an
The benzylidene–imidazolinone rings are nearly copla-
nar (C4–C7–C8–C15Z8.48) forming sheets in the (5 0 0)
planes in the crystal (Fig. 5b). Intramolecular hydrogen
dK
dC
electrostatic donor–acceptor interaction of CaO /C
Table 2
˚
Hydrogen-bonding geometry (A, 8) for compounds 2–5
Compounds
D–H/A
D–H
H/A
D/A
D–H/A
Symmetry codes
2
C9–H9/N3
0.95
0.98
0.95
0.95
0.98
0.98
0.93
0.93
0.93
0.93
2.47
2.56
2.41
2.62
2.57
2.65
2.54
2.57
2.40
2.50
3.117 (3)
2.935 (2)
3.057 (3)
3.566 (3)
3.333 (2)
3.273 (2)
3.162 (3)
3.459 (3)
3.316 (3)
3.131 (4)
125.3
102.4
125.3
175.5
134.4
121.8
124.3
159.4
169.5
125.6
(i) x, yK1, z; (ii) 1Kx, 1Ky, 2Kz
C20–H20A/O6
C30–H30/N24
C15–H15/N24i
C41–H41B/O6ii
C41–H41C/O27ii
C13–H13/N3
C17–H17/O6i
C21–H21/O6ii
3
4
(i) 3Kx, yK1/2, 1Kz; (ii) 1Cx, y, z
(i) Kx, 2Ky, 2Kz; (ii) xK1/2, 3/2Ky, zK1/2;
iii) 1Kx, 2Ky, 2Kz
C15–H15/N3
C10–H10/O12i
C13–H13B/O6ii
C16–H16C/O12iii
C9–H9/N3
(
0.93
0.96
0.96
0.93
0.93
0.93
2.59
2.39
2.59
2.52
2.57
2.60
3.486 (3)
3.308 (3)
3.443 (4)
3.147 (4)
3.409 (4)
3.527 (4)
163.2
159.6
147.8
125.2
150.5
173.7
5
(i) xK1/2, K3/2Ky, K1Kz; (ii) 1/2Cx, K1/
2Ky, K1Kz
C19–H19/O6i
C22–H22/N3ii

G. Bhattacharjya et al. / Journal of Molecular Structure 752 (2005) 98–103
103
Acknowledgements
RG thanks CSIR for financial support. GB thanks the
council of scientific and industrial research (CSIR), New
Delhi for a junior research fellowship. The authors also
thank the SMART CCD X-ray facility, IIT Kanpur, India.
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[
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[
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All the compounds (2–5) reported here contain pre-
dominantly the C–H/O interaction involving the carbonyl-
oxygen of the imidazolinone ring. The phenyl rings do not
show any significant stacking interaction though they
appear as stacks looking down the packing schemes along
certain directions. Except for compound (1), the C–H/p
interaction across the benzylidenes, in addition to an
(
2001) 2382.
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[
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dK
dC
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electrostatic donor–acceptor interaction of CaO /C
[
[
[
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4423.
type across the imidazolinones to form infinite chains, was
not observed in any of the crystals of (2–5). The closest
analogue (3) also does not possess the viable carbonyl-
carbon interaction, indicating that the absence of the
methoxy group in the benzylidene at the far end of the
molecule is crucial in the formation of the unusual donor–
acceptor kind of interaction seen in (1). In other words, of all
the analogues studied in this work, (1) has the substituents in
the most favourable configuration in terms of functional
groups, and any alteration favours C–H/O interactions
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dK
dC
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over CaO /C
interaction. In conclusion, the co-
operative nature of the C–H/O interactions drives the
molecular packing despite the presence of donor–acceptor
groups in the imidazolinone crystal assembly to have
[
[
[
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dK
dC
potential CaO /C interactions.