Unclassical hydrogen bonds of C-H...N and C-H...Cl in the crystal structures of 2-((E)-1,3-diarylallylidene) malononitriles

Article abstract of DOI:10.1007/s10870-010-9837-0

The 2-((E)-3-(2-nitrophenyl)-1-(4-methoxyphenyl) allylidene)malononitrile and 2-((E)-3-(2-chlorophenyl)-1-(4-bromophenyl)allylidene)malononitrile were synthesized and characterized by IR, ¹H NMR, and elemental analysis. The molecular structures

Full text of DOI:10.1007/s10870-010-9837-0

J Chem Crystallogr (2011) 41:59–63
DOI 10.1007/s10870-010-9837-0
ORIGINAL PAPER
Unclassical Hydrogen Bonds of C–H_N and C–H_Cl
in the Crystal Structures of 2-((E)-1,3-diarylallylidene)
malononitriles
•
•
•
Xiang-Shan Wang Qing Li Jian-Rong Wu
Mei-Mei Zhang
Received: 3 January 2008 / Accepted: 19 June 2010 / Published online: 2 July 2010
Ó Springer Science+Business Media, LLC 2010
Abstract The 2-((E)-3-(2-nitrophenyl)-1-(4-methoxyphenyl)
allylidene)malononitrile and 2-((E)-3-(2-chlorophenyl)-1-
(4-bromophenyl)allylidene)malononitrile were synthesized
and characterized by IR, 1H NMR, and elemental analysis.
The molecular structures were further confirmed by X-ray
diffraction analysis. The former 1, C19H13N3O3, is triclinic,
space group P-1, a = 7.3834(13), b = 10.901(3), c =
C–H_X hydrogen bonds by spectroscope. A survey of
crystal structures containing short C–H_O was firstly con-
ducted by Sutor in 1963 [5]. In the recent years, more and
more C–H_X hydrogen bonds [6–12] (especially C–H_O)
have been postulated in the crystal structure, sometimes they
are generally considered as un-classical or non-classical
hydrogen bonds [13–15] in the literature. However, the
symbol X in C–H_X hydrogen bonds is usually limited to
be O [6–12], N [16, 17], or F [18–20], and seldom to be Cl
[21, 22] or I [23]. It was well known that as potential
hydrogen bond acceptors, 2-((E)-3-(2-nitrophenyl)-1-
(4-methoxyphenyl)allylidene)malononitrile 1 contains the
cyano group, methoxy group and the benzene ring moiety,
while 2 contains cyano group, the benzene ring moiety and
halogen. However, as hydrogen bond donors, they carry no
O–H group or N–H group. This raises an interesting ques-
tion: do what kinds of forces make the molecules together in
the crystals if no classical hydrogen bonds? In this paper, we
present the crystal structures of 2-((E)-3-(2-nitrophenyl)-
1-(4-methoxyphenyl)allylidene)malononitrile 1 and 2-((E)-
3-(2-chlorophenyl)-1-(4-bromophenyl) allylidene)malononit-
rile 2, which were prepared by the reaction of aromatic
aldehydes and 1-arylethylidene malononitriles in ionic
liquid catalyzed by 10 mol% malononitrile. It is found that
the unclassical hydrogen bonds of C–H_N in 1, C–H_N
and C–H_Cl in 2 link the molecules forming polymers.
˚
11.227(2) A, a = 88.64(2), b = 71.596(14), c = 78.186
3
(18), Z = 2, V = 838.5(3) A . The unclassical hydrogen
˚
bond of C–H_N links the molecules forming polymers.
The latter 2, C36H20Br2Cl2N4, is orthorhombic, space
group Pnma, a = 20.900 (4), b = 7.0710 (11), c =
3
˚
˚
10.9170 (18) A, Z = 2, V = 1613.4(5) A . The same
hydrogen bond of C–H_N and another type of C–H_Cl
hydrogen bond link the adjacent molecules forming poly-
mers along a axis.
Keywords Hydrogen bond ꢀ Allylidenemalononitrile ꢀ
Infrared ꢀ NMR
Introduction
The ability of carbon atoms to act as proton donors in
hydrogen bonds has been recognized in recent years [1, 2],
Harmon et al. [3] and Kobayashi et al. [4] studied the
Experimental
X.-S. Wang (&) ꢀ Q. Li ꢀ J.-R. Wu
School of Chemistry and Chemical Engineering,
Xuzhou Normal University, Xuzhou 221116,
Jiangsu, People’s Republic of China
e-mail: xswang1974@yahoo.com
Synthesis of 2-((E)-3-(2-nitrophenyl)-1-(4-methoxy
phenyl)allylidene)malononitrile 1 and 2-((E)-3-(2-chlo-
rophenyl)-1-(4-bromophenyl)allylidene)malononitrile 2
X.-S. Wang ꢀ M.-M. Zhang
A dry 50 mL flask was charged with aromatic aldehyde
(2.0 mmol), malononitrile (0.013 g, 0.2 mmol), 1-arylethy
The Key Laboratory of Biotechnology on Medical Plant
of Jiangsu Province, Xuzhou 221116, China
123

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J Chem Crystallogr (2011) 41:59–63
lidenemalononitrile (2.0 mmol), and ionic liquid of
[bmim?][BF4-] (1 mL). The reaction mixture was stirred
at 90 °C for 3–8 h, and then 5 mL water was added to the
mixture, the solid was isolated by filtration to remove the
ionic liquid. The crude yellow products were washed with
water and purified by recrystallization from a mixture of
DMF and water to give 1 or 2. 1: Pale yellow crystals,
96%, mp 182–184 °C. IR (KBr): 3061, 2221, 1602, 1561,
1532, 1485, 1469, 1444, 1391, 1338, 1323, 1286, 1098,
1345, 1292, 1254, 1210, 1177, 1103, 1025, 983, 857, 838,
794, 749, 704. Anal. Calcd for C19H13N3O3: C 68.88, H
3.95, N 12.68; found C 69.01, H 3.87, N 12.57.
X-ray Analysis
A summary of the crystallographic data was given in
Table 1. The structure was solved by direct method using
SHELXTL [24] program and expanded using Fourier tech-
nique. The non-hydrogen atoms were refined anisotropi-
cally, the hydrogen atoms were positioned geometrically and
1
1071, 1039, 1011, 966, 824, 766, 750. H NMR (DMSO-
d6) d: 7.16 (d, J = 15.6 Hz, 1H, CH=), 7.47 * 7.55 (m,
5H, ArH), 7.58 (d, J = 15.6 Hz, 1H, CH=), 7.85 (d,
J = 8.4 Hz, 2H, ArH), 8.01 * 8.03 (m, 1H, ArH). Anal.
Calcd for C18H10BrClN2: C 58.49, H 2.73, N 7.58; found C
58.62, H 2.70, N 7.54. 2: Pale yellow crystals, 95%, mp
˚
refined as riding [C–H = 0.93–0.96 A and Uiso(H) = 1.2
Ueq(C)]. A full-matrix least-squares refinement gave final
R = 0.0500 and xR = 0.1284 (R = 0.0494 and xR =
0.1146 for 2) with x = 1/[r2 (Fo2) ? (0.0793P)2] (x = 1/[r 2
(F2o) ? (0.0514P)2 ? 2.4803P]for2),whereP = (Fo2 ?2F2c)/3.
1
188–190 °C. H NMR (DMSO-d6, d, ppm): 3.87 (s, 3H,
CH3O), 7.16 (d, J = 8.4 Hz, 2H, ArH), 7.36 (d,
J = 15.6 Hz, 1H, CH), 7.42 (d, J = 15.6 Hz, 1H, CH),
7.57 (d, J = 8.4 Hz, 2H, ArH), 7.70 * 7.71 (m, 1H, ArH),
7.85 * 7.89 (m, 1H, ArH), 7.98 (d, J = 8.0 Hz, 1H, ArH),
8.10 (d, J = 8.0 Hz, 1H, ArH); IR (KBr, m, cm-1): 3084,
3004, 2972, 2839, 2223, 1602, 1569, 1518, 1439, 1420,
Analysis
Melting points were determined in open capillaries and are
uncorrected. IR spectra were recorded on a TENSOR 27
spectrometer in KBr pellet. 1H NMR spectra were obtained
Table 1 Crystallographic data for 1 and 2
Compounds
1
2
Empirical formula
CCDC deposit no.
Color/shape
C19 H13 N3 O3
672173
C36 H20 Br2 Cl2 N4
672174
Pale yellow/Block
331.32
Pale yellow/Block
739.28
Formula weight
Temperature
298(2) K
294(2) K
Crystal system
Space group
Triclinic
Orthorhombic
P-1
Pnma
˚
˚
Unit cell dimensions
a = 7.3834(13) A, a = 88.64(2)°
a = 20.900(4) A, a = 90°
˚
˚
b = 10.901(3) A, b = 71.596(14)°
b = 7.0710(11) A, b = 90°
˚
˚
c = 11.227(2) A, c = 78.186(18)°
838.5(3) A
c = 10.9170(18) A, c = 90°
1613.4(5) A
3
˚
3
˚
Volume
Z
2
2
Density (calculated), Mg/m3
Absorption coefficient, mm-1
Diffractometer/scan
F(000)
1.312
1.522
0.091
2.710
Rigaku Mercury/x
344
CCD area detector/p and x
736
Crystal size
0.80 9 0.70 9 0.30 mm
0.28 9 0.26 9 0.12 mm
Theta range for data collection
Limiting indices
3.18–25.35°
-8 B h B 8, -13 B k B 13, -11 B l B 13
8120
2.10–26.36°
-26 B h B 23, -6 B k B 8, -13 B l B 12
8904
Reflections collected
Independent reflections
Data/restraints/parameters
Goodness-of-fit on F2
Final R indices [I [ 2 r (I)]
R indices (all data)
Largest diff. peak and hole
3047 [R(int) = 0.0384]
3047/0/228
1782 [R(int) = 0.00455]
1782/2/145
1.005
1.010
R1 = 0.0500, wR2 = 0.1284
R1 = 0.0714, wR2 = 0.1434
0.297 and -0.235 e A-3
R1 = 0.0494, wR2 = 0.1146
R1 = 0.0945, wR2 = 0.1402
0.969 and -0.906 e A-3
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J Chem Crystallogr (2011) 41:59–63
61
1
from solution in DMSO-d6 with Me4Si as internal standard
using an Inova-400 spectrometer. Elemental analyses were
carried out using Perkin-Elmer 2400 II analyzer.
The H NMR spectrum of 1 exhibited a doublet identified
as hydrogen on the double bond at 7.16 ppm (J = 15.6 Hz,
7.36 ppm (J = 15.6 Hz) for 2). Another coupling proton
was observed at 7.58 ppm with the same coupling constant
(J = 15.6 Hz, 7.42 (J = 15.6 Hz) for 2). Obviously, the
bigger coupling constant (15.6 Hz) also indicated that
compounds 1 and 2 were all trans-alkenes.
Results and Discussion
In the infrared spectrography of 1, it was observed a sharp
band at 2221 cm-1 (2223 cm-1for 2) for the cyano group.
The selected bond lengths and bond angles of 1 and 2 are
given in Table 2. The structures of 1 and 2, packing
˚
Table 2 Selected bond lengths (A) and selected bond angles (°) for 1 and 2
Selected bond lengths for 2
Selected bond lengths for 1
Br(1)–C(16)
Cl(1)–C(1)
N(1)–C(11)
N(2)–C(12)
C(1)–C(2)
C(1)–C(6)
C(2)–C(3)
C(3)–C(4)
C(4)–C(5)
C(5)–C(6)
C(6)–C(7)
C(7)–C(8)
C(8)–C(9)
C(9)–C(10)
C(9)–C(13)
1.896(6)
1.740(6)
1.133(8)
1.128(8)
1.378(8)
1.390(7)
1.366(8)
1.385(9)
1.373(8)
1.389(8)
1.454(7)
1.327(7)
1.422(7)
1.355(8)
1.491(8)
C(10)–C(11)
1.433(9)
1.443(8)
1.312(10)
1.312(10)
1.429(11)
1.429(11)
1.387(13)
2.01(2)
O(1)–C(10)
O(1)–C(13)
O(2)–N(3)
O(3)–N(3)
N(1)–C(5)
N(2)–C(6)
N(3)–C(15)
C(1)–C(2)
C(1)–C(5)
C(1)–C(6)
C(2)–C(3)
C(2)–C(7)
C(3)–C(4)
1.368(2)
1.415(3)
1.214(2)
1.216(3)
1.145(2)
1.136(2)
1.469(3)
1.363(2)
1.431(3)
1.436(2)
1.450(2)
1.482(2)
1.328(2)
C(4)–C(14)
C(7)–C(8)
1.462(2)
1.379(2)
1.401(2)
1.385(2)
1.381(2)
1.385(3)
1.371(2)
1.394(2)
1.399(2)
1.375(3)
1.381(3)
1.362(3)
1.374(3)
C(10)–C(12)
C(13)–C(14)#1
C(7)–C(12)
C(8)–C(9)
C(13)–C(14)
C(13)–C(140)#1
C(13)–C(140)
C(14)–C(15)
C(9)–C(10)
C(10)–C(11)
C(11)–C(12)
C(14)–C(19)
C(14)–C(15)
C(15)–C(16)
C(16)–C(17)
C(17)–C(18)
C(18)–C(19)
C(14)–C(14)#1
C(15)–C(16)
1.298(12)
2.02(2)
C(15)–C(15)#1
C(140)–C(150)
C(150)–C(16)
C(16)–C(15)#1
C(16)–C(150)#1
#1: x, -y ? 1/2, z
1.386(13)
1.413(12)
1.298(12)
1.413(12)
Selected bond angles for 2
Selected bond angles for 1
C(2)–C(1)–C(6)
C(2)–C(1)–Cl(1)
C(6)–C(1)–Cl(1)
C(3)–C(2)–C(1)
C(2)–C(3)–C(4)
C(5)–C(4)–C(3)
C(4)–C(5)–C(6)
C(1)–C(6)–C(5)
C(1)–C(6)–C(7)
C(5)–C(6)–C(7)
C(8)–C(7)–C(6)
C(7)–C(8)–C(9)
C(10)–C(9)–C(8)
C(10)–C(9)–C(13)
C(8)–C(9)–C(13)
C(9)–C(10)–C(11)
C(9)–C(10)–C(12)
C(11)–C(10)–C(12)
N(1)–C(11)–C(10)
N(2)–C(12)–C(10)
122.7(6) C(14)–C(13)–C(140)#1 118.3(6)
117.3(4) C(14)#1–C(13)–C(140) 118.3(6)
120.0(4) C(140)#1–C(13)–C(140) 108.9(8)
C(10)–O(1)–C(13)
O(2)–N(3)–O(3)
O(2)–N(3)–C(15)
O(3)–N(3)–C(15)
C(2)–C(1)–C(5)
C(2)–C(1)–C(6)
C(5)–C(1)–C(6)
117.92(15) C(7)–C(8)–C(9)
122.2(2) C(10)–C(9)–C(8)
119.42(19) O(1)–C(10)–C(9)
118.3(2) O(1)–C(10)–C(11)
122.86(15) C(9)–C(10)–C(11)
121.57(16)
119.10(16)
124.29(16)
115.52(15)
120.19(16)
119.7(6) C(14)#1–C(13)–C(9)
119.4(6) C(14)–C(13)–C(9)
120.2(6) C(140)#1–C(13)–C(9)
121.9(6) C(140)–C(13)–C(9)
116.1(5) C(13)–C(14)–C(15)
121.6(5) C(13)–C(14)–C(14)#1
122.2(5) C(15)–C(14)–C(14)#1
126.8(5) C(16)–C(15)–C(14)
125.1(5) C(16)–C(15)–C(15)#1
120.5(5) C(14)–C(15)–C(15)#1
119.1(5) C(150)–C(140)–C(13)
120.4(5) C(140)–C(150)–C(16)
121.8(5) C(15)#1–C(16)–C(15)
123.0(5)
123.0(5)
118.7(5)
118.7(5)
121.89(15) C(12)–C(11)–C(10) 120.27(16)
115.25(15) C(11)–C(12)–C(7) 120.45(16)
119.39(15) C(19)–C(14)–C(15) 115.21(16)
122.5(10) C(1)–C(2)–C(3)
40.1(4)
90.2(6)
C(1)–C(2)–C(7)
C(3)–C(2)–C(7)
120.25(15) C(19)–C(14)–C(4)
120.36(15) C(15)–C(14)–C(4)
120.52(16)
124.20(16)
120.8(10) C(4)–C(3)–C(2)
124.55(16) C(16)–C(15)–C(14) 122.71(18)
39.1(5)
89.8(6)
C(3)–C(4)–C(14)
N(1)–C(5)–C(1)
C(8)–C(7)–C(12)
C(8)–C(7)–C(2)
C(12)–C(7)–C(2)
124.16(15) C(16)–C(15)–N(3)
178.35(19) C(14)–C(15)–N(3)
118.35(15) C(15)–C(16)–C(17)
116.70(18)
120.57(17)
119.4(2)
119.2(9)
118.4(9)
101.9(9)
120.83(15) C(18)–C(17)–C(16) 120.00(19)
120.79(15) C(17)–C(18)–C(19) 119.92(19)
123.8(5) C(15)#1–C(16)–C(150) 120.7(7)
114.4(5) C(15)–C(16)–C(150)#1 120.7(7)
179.1(6) C(150)–C(16)–C(150)#1 110.6(8)
C(18)–C(19)–C(14) 122.79(18)
177.7(7) C(15)#1–C(16)–Br(1)
C(150)#1–C(16)–Br(1) 118.3(5) C(15)–C(16)–Br(1)
C(150)–C(16)–Br(1)
118.3(5) #1: x, -y ? 1/2, z
120.9(5)
120.9(5)
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J Chem Crystallogr (2011) 41:59–63
Table 3 Unclassical hydrogen bonds geometry for 1 and 2
˚
D–H (A)
˚
˚
(D–H_A)
H_A (A)
D_A (A)
D–H_A(°)
Symmetry codes
C(18)–H(18)_N(1)
C(15)–H(15A)_Cl(1)
C(14)–H(14A)_N(2)
0.93
0.93
0.93
2.61
2.90
2.56
3.348(3)
3.793(2)
3.313(2)
137.2
161.0
138.8
x - 1, y ? 1, z
1 - x, -y, 1 - z
1 - x, -0.5 ? y, -z
Fig. 1 The molecular structure of 1 showing 50% probability
displacement ellipsoids
Fig. 3 The packing arrangement in a unit cell of 1 along a
Fig. 4 The packing arrangement in a unit cell of 2 along a
benzene rings are the other side of double bonds, forming
trans-conformation. The basal plane of the alkene makes
dihedral rings to benzene rings C(14)–C(19) and C(7)–C(12)
of 22.9(1)° and 62.4(1)°, respectively. The benzene rings
make a dihedral angle of 52.7(1)° with one another. In 2, the
alkene also forms trans-conformation. However, the benzene
ring and the atoms C(6)–C(9)/H(7)/H(8) are coplanar, which
makes a dihedral angle of 67.0(1)° with benzene ring C(13)–
C(16)/C(14B)/C(15B).
Fig. 2 The molecular structure of 2 showing 50% probability
displacement ellipsoids
arrangement in a unit cell of 1 and 2 are shown in Figs. 1, 2, 3,
and 4 respectively. In 1, the atoms C(14)/C(4)/H(14)/C(3)/
H(3)/C(2) are coplanar, and two larger groups containing
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63
References
The X-ray determination indicates that two types of
unclassical hydrogen bonds C–H_Cl and C–H_N are
presented in 2. From Table 3, it is clear to find that the
distance from H(15A) to Cl(1) in the adjacent molecules is
1. Allen FH, Lommerse JPM, Hoy VJ, Howard JAK, Desiraju GR
(1996) Acta Crystallogr B52:734
2. Braga D, Grepioni F, Biradha K, Pedireddi VR, Desiraju GR
(1995) J Am Chem Soc 117:3156
˚
2.90 A, which is obviously shorter than the sum of the van
˚
der Waals radii for Cl and H (3.00 A), indicating the
3. Harmon KM, Gennick I, Maderira SL (1974) J Phys Chem
78:2585
4. Kobayashi K, Ishii K, Sakamoto S, Shirasaka T, Yamaguchi K
(2003) J Am Chem Soc 125:10615
5. Sutor DJ (1963) J Chem Soc 1105
6. Zhang R, Li H, Li Y, Han S (2004) J Mol Struct 693:17
7. Venkatesan V, Fujii A, Ebata T, Mikami N (2004) Chem Phys
Lett 394:45
presence of unclassical hydrogen bonds C–H_Cl. On the
other hand, there is another different type of intermolecular
hydrogen bonds in the vicinal molecules to be found:
C(14)–H(14A)_N(2) according to the distance measure-
˚
ment (2.56 A for H(14A)_N(2)) and the related bond
angles (138.8° for C(14)–H(14A)_N(2)) (Table 3). In 1,
the intermolecular hydrogen bond of C(18)–H(18)_N(1)
is observed according to the data listed in Table 3, The
unclassical hydrogen bonds of C–H_N in 1 and the
C–H_N and C–H_Cl hydrogen bonds in 2 all link the
molecules forming polymers, respectively (Figs. 3 and 4).
8. Siebrand W, Smedarchina Z (2004) J Phys Chem 108:4185
9. Zhang R, Li H, Lei Y, Han S (2004) J Phys Chem 108:12596
10. Klaholz BP, Moras D (2002) Structure 10:1197
11. Gupta BD, Singh V, Yamuna R, Barclay T, Cordes W (2003)
Organometallics 22:2670
12. Chang H, Jiang J, Chuang C, Lin H (2004) Chem Phys Lett
397:205
13. Zhu XQ, Wang JS, Cheng JP (2005) Tetrahedron Lett 46:877
14. Wang XS, Zeng ZS, Shi DQ, Tu SJ, Wei XY, Zong ZM (2005) J
Chem Crystallogr 35:1011
15. Shi Z, Olson CA, Bell AJ, Kallenbach NR (2002) Biophys Chem
101–102:267
Supplementary Material
16. Cappelli A, Giorgi G, Anzini M, Vomero S, Ristori S, Rossi C,
Donati A (2004) Chem Eur J 10:3177
17. Taylor R, Kennard O (1982) J Am Chem Soc 104:5063
18. Vangala VR, Nangia A, Lynch VM (2002) Chem Commun
(12):1304
19. Casas JM, Beatriz BE, Falvello LR, Fomies J, Martin A, Rueda
AJ (2004) Dalton Trans (17):2733
20. Zhu S, Jin G, Li Z (2005) Tetrahedron Lett 46:2713
21. Spaniel T, Gorls H, Scholz J (1998) Angew Chem Int Ed Engl
37:2862
Crystallographic data for the structures reported in this
paper have been deposited with the Cambridge Crystallo-
graphic Data Centre as supplementary publication no.
CCDC-672173 and CCDC-672174. Copies of available
material can be obtained, free of charge, on application to
the Director, CCDC, 12 Union Road, Cambridge CB2 1EZ,
UK, (fax: ?44-(0) 1223-336033 or e-mail: deposit@ccdc.
cam.ac.uk).
22. Navon O, Bernstein J, Khodorkovsky V (1997) Angew Chem Int
Ed Engl 36:601
23. Gibb CLD, Stevens ED, Gibb BC (2001) J Am Chem Soc
123:5849
24. Sheldrick GM (2008) Acta Crystallogr A64:112
Acknowledgments We are grateful to the National Natural Science
foundation of China (20802061), the Natural Science foundation
(08KJD150019) and Qing Lan Project (08QLT001) of Jiangsu Edu-
cation Committee for financial support.
123