Crystal structure of (E)-2,3-dihydro-2-(R-phenylacylidene)-1,3,3-trimethyl- 1H-indole (R = 4-cn, 4-cl)

Article abstract of DOI:10.1007/s10870-010-9954-9

Two new 1,3,3-trimethyl-2-methylene-2,3-dyhidro-1H-indole derivatives, (E)-2,3-dihydro-2-(4-cyanophenylacylidene)-1,3,3-trimethyl-1H-indole, (I), and (E)-2,3-dihydro-2-(4-chlorophenylacylidene)-1,3,3-trimethyl-1H-indole, (II), have been synthesized and th

Full text of DOI:10.1007/s10870-010-9954-9

J Chem Crystallogr (2011) 41:419–424
DOI 10.1007/s10870-010-9954-9
COMMUNICATION
Crystal Structure of (E)-2,3-Dihydro-2-(R-Phenylacylidene)-1,3,3-
Trimethyl-1H-Indole (R 5 4-CN, 4-Cl)
•
Oscar F. Vazquez-Vuelvas David Morales-Morales
•
´
Juan M. German-Acacio Mikhail Tlenkopatchev
•
•
´
Armando Pineda-Contreras
Received: 30 July 2010 / Accepted: 30 December 2010 / Published online: 14 January 2011
Ó Springer Science+Business Media, LLC 2011
Abstract Two new 1,3,3-trimethyl-2-methylene-2,3-dyhi-
dro-1H-indole derivatives, (E)-2,3-dihydro-2-(4-cyanoph-
enylacylidene)-1,3,3-trimethyl-1H-indole, (I), and (E)-2,
3-dihydro-2-(4-chlorophenylacylidene)-1,3,3-trimethyl-1H-
indole, (II), have been synthesized and their crystal structure
determined by single crystal X-ray diffraction. (I), C20H18
N2O, crystallizes in a monoclinic space group, P21/c, with
unit cell parameters a = 9.882 (3), b = 15.614(4), c =
the crystals show, for (I) an antiparallel stacking mode
favored by the formation of weak C–Hꢀꢀꢀp interactions
involving the phenyl ring attached to the carbonyl group and
the phenyl of the indole fragment in a head-to-tail mode,
whereas, (II) present an weak C–HꢀꢀꢀHal interaction.
Keywords Crystal structure ꢀ Fischer base ꢀ
Enaminoketone ꢀ X-ray diffraction ꢀ s-cis Conformation
˚
11.181(3) A, b = 106.691(4)°, Z = 4. (II), C19H18Cl N O,
crystallizes in a monoclinic space group, P21/n, with unit cell
parameters a = 14.6722(19), b = 7.2597(9), c = 16.304
˚
Introduction
(2) A, b = 111.249 (2)°, Z = 4. The molecules consist of a
enaminoketone group formed by a Fischer base 1,3,3-tri-
methyl-2-methylene-2,3-dihydro-1H-indole bonded, at the
exocyclic electron-rich b-carbon atom of the indole moiety,
with the benzoyl chloride derivatives substituted at para-
positions with cyano and chloro groups. The molecules adopt
a s-cis conformation with respect to the C=O bond towards
the C=C bond, and a E configuration about the latter indole
exocyclic alkene C–C bond. Intermolecular arrangement of
The Fischer base, 1,3,3-trimethyl-2-methylene-2,3-dyhi-
dro-1H-indole and its derivatives recently have been
widely used in the organic synthesis related to prepare
different types of chemical switches. Products with dif-
ferent photochromic and thermochromic properties have
been reported in the literature because of the potential
practical applications of these products to a variety of
optoelectronics, molecular information devices and as
organic electroluminescence materials [1–4], as well as,
different products in the field of dyes [5]. Furthermore,
indole enaminoketones derivatives represent another ade-
quate route of synthesis, not only for photochromic deriv-
atives of the Fischer Base [6], but also acetylenic products
via indole enaminoketone fragmentation [7–9].
´
O. F. Vazquez-Vuelvas (&) ꢀ A. Pineda-Contreras
´
Facultad de Ciencias Quımicas, Universidad de Colima,
Km 9 Carr. Colima-Coquimatlan s/n, Coquimatlan,
´
Colima 28400, Mexico
e-mail: oscar_vazquez@ucol.mx
Some studies have reported the synthesis of 1,3,3-tri-
methyl-2-(phenylacylidene)-2,3-dyhidro-1H-indole deriva-
tives with different substituent in the phenyl ring [10].
Moreover, a spectroscopic study was carried out with
Fischer base indole enaminoketone derivatives in order to
establish the conformation of the enamino carbonyl frag-
ment [11]. However, no similar derivatives have been
reported previously using 1,3,3-trimethyl-2-methylene-2,
3-dyhidro-1H-indole in presence of the electrophiles
´
D. Morales-Morales ꢀ J. M. German-Acacio
´
Instituto de Quımica, Universidad Nacional Autonoma de
Mexico, Circuito Exterior, Ciudad Universitaria, Mexico,
´
´
DF 04510, Mexico
M. Tlenkopatchev
Instituto de Investigaciones en Materiales, Universidad Nacional
´
Autonoma de Mexico, Circuito Exterior, Ciudad Universitaria,
Mexico, DF 04510, Mexico
´
123

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J Chem Crystallogr (2011) 41:419–424
eliminated under vacuum. The 4-nitrobenzoyl chloride
obtained was dissolved in 15 mL of dry benzene, and this
solution was added to a mixture of the Fischer base 1,3,3-
trimethyl-2-methyleneindoline (1 eq., 2.35 g, 13.59 mmol)
and triethylamine (1.2 eq., 1.65 g, 16.31 mmol) in 20 mL of
dry benzene. The mixture was maintained at 40 °C for 2 h,
after that it was allowed to stand overnight at room tem-
perature. The final reaction mixture was first washed with
water and the organic phase was separated and removed by
vacuum. The resulting solid was washed successively with
isopropyl alcohol. The yellow product was purified using a
column chromatography with chloroform as a mobile phase.
Suitable crystals for X-ray diffraction were obtained from
toluene by slow evaporation. The yield was 2.94 g (71%);
m. p.: 184–186 °C. Elemental analysis for C20H18N2O:
[found(calc.)]: C 79.74 (79.44)%; H 6.00 (6.15)%; N 9.26
(9.79)%. GCMS m/z 302 (M?), 301 (100%) 287.
Scheme 1 Structure of (I)
Synthesis of (E)-2,3-Dihydro-2-
(4-Chlorophenylacylidene)-1,3,3-Trimethyl-1H-Indol (II)
Scheme 2 Structure of (II)
p-cyanobenzoyl chloride and p-chlorobenzoyl chloride.
Furthermore, single crystal structural studies of this type of
derivatives do not appear in the reported literature.
In the present study, we report the synthesis of two new
Fischer base enaminoketone derivatives and their molecu-
lar structure were determined using the X-ray diffraction
single crystal method to describe unambiguously the con-
formational arrangement. The structures of the Fischer base
enaminoketones are depicted in Schemes 1 and 2 for
(I) and (II), respectively.
The product was synthesized according to the procedure of
(I). The yield was 16.39 g (85%); m. p.: 146–148 °C.
GCMS m/z 311 (M?), 310 (100%) 296, 278, 209.
Structure Determination and Refinement
Suitable crystals for X-ray diffraction were mounted in
random orientation on glass fibers. The X-ray intensity data
were measured at 298 K on a Bruker SMART APEX
CCD-based three-circle X-ray diffractometer system
using graphite mono-chromated Mo–Ka radiation (k =
Experimental
˚
0.71073 A). The crystal structures were solved by direct
methods and refined by using SHELXS-97 and SHELXL-97
crystallographic software packages [12–14]. All non-
hydrogen atoms were refined anisotropically using reflec-
tions I [ 2r (I). Hydrogen atoms were located in ideal
positions. Geometric calculations and visualizations were
done using PLATON [15], MERCURY [16] and DIA-
MOND [17]. Crystal and experimental data of (I) and (II) are
listed in Table 1. Scheme 1 shows the molecular structures
of (I) and (II), respectively. Ortep diagrams [18] of the
asymmetric units and crystal packing of (I) and (II) are
displayed in Figs. 1, 2, 3 and 4, respectively. Selected geo-
metric parameters for (I) and (II) are listed in Table 2. The
geometric parameters associated with intra and intermolec-
ular D–HꢀꢀꢀA interactions are listed in Table 3.
4-cyanobenzoic acid, 4-chlorobenzoic acid and triethyl-
amine were purchased from Aldrich Chemical Co., 1,3,3-
trimethyl-2-methylene indoline was purchased from Fluka
and thionyl chloride was purchased from Alpha Aesar. All
reagents were used without further purification. All other
chemical substances were reagent grade commercial prod-
ucts. Benzene was dried over sodium benzophenone ketyl,
distilled and stored over activated molecular sieve 4A.
Synthesis of (E)-2,3-Dihydro-2-
(4-Cyanophenylacylidene)-1,3,3-Trimethyl-1H-Indol (I)
The methodology has already been reported in the literature
[8, 9]. In the present work, a mixture of 4-cyanobenzoic acid
(2 g, 13.59 mmol) and thionyl chloride (2 eq., 3.23 g,
27.19 mmol) in 8 mL of dry benzene was refluxed for 1.5 h,
afterward the excess thionyl chloride was evaporated under
vacuum. For complete removal of the thionyl chloride, 8 mL
of petroleum ether was added to the residue and then
Results and Discussion
The molecules (I) and (II) adopt a s-cis conformation with
respect to the C=O bond towards the C=C bond, and an
123

J Chem Crystallogr (2011) 41:419–424
421
Table 1 Crystal and
experimental data for (I) and
(II)
(I)
(II)
Empirical formula
C20 H18 N2 O
302.36
C19 H18 Cl N O
311.79
Formula weight
Temperature
Wavelength
298(2) K
298(2) K
˚
0.71073 A
˚
0.71073 A
Crystal system
Space group
Monoclinic
P 21/c
Monoclinic
P 21/n
˚
a (A)
9.882(3)
14.6722(19)
7.2597(9)
˚
b (A)
15.614(4)
˚
c (A)
11.181(16)
106.691(4)
1652.4(7)
16.304(2)
b (°)
Volume (A )
111.249(2)
1618.5(4)
3
˚
Z
4
4
Density (calculated) (Mg m-3
)
1.215
1.280
Absorption coefficient (mm-1
F(000)
)
0.076
0.237
640
656
Crystal size
0.34 9 0.31 9 0.07 mm
2.15°–25.38°
-11 B h B 11
-18 B k B 18
-13 B l B 13
13055
0.36 9 0.16 9 0.10 mm
2.34°–25.35°
-17 B h B 17
-8 B k B 8
-19 B l B 19
12891
Theta range for data collection
Index ranges
Reflections collected
Independent reflections
Data/parameters
3019 [R(int) = 0.0649]
3019/211
2964 [R(int) = 0.0713]
2964/203
Max. and min. Transmission
Final R indices [I [ 2sigma(I)]
Goodness-of-fit on F2
0.9774 and 0.9948
R1 = 0.0637, wR2 = 0.1408
1.03
0.956 and 0.977
R1 = 0.0466, wR2 = 0.1074
0.86
-3
-3
˚
0.146 and -0.137 e A
˚
0.168 and -0.189 e A
Largest diff. peak and hole
Fig. 1 The molecular structure and atom numbering of (I). Dis-
placements ellipsoidal of non-H atom are drawn at the 30% of
probability level. Intramolecular hydrogen bonds are depicted by
dashed lines
Fig. 2 The molecular structure and atom numbering of (II).
Displacements ellipsoidal of non-H atom are drawn at the 30% of
probability level. Intramolecular hydrogen bonds are depicted by
dashed lines
E configuration about the indole exocyclic alkene C–C bond.
The bond distances and angles of the indole moiety for both
crystals are similar to the reported by other crystal indole
derivatives [4, 19]. The bond distance of N3–C10 for (I) and
Due to the compounds reported here present N3–C4
˚
bond lengths of 1.368(3) A for (I) and 1.366(2) A for (II),
˚
˚
C4=C2 bond length of 1.370(4) A for (I) and 1.364(3) A
˚
˚
(II) are 1.402(4) and 1.404(3) A, respectively. These dis-
˚
for (II) and C1=O1 bond of 1.239(3) A for (I) and
˚
1.231(3) A for (II) (Table 2), a push–pull conjugation is
tance values are longer than those reported in the literature
for a Nsp3–Car indole bond with 1.372 A [20], and conse-
˚
present and the distance values are characteristic in ena-
minoketone molecular frameworks [21]. These bond dis-
tances are different with the corresponding ones reported
quently are similar to the N–C bonds of the Fisher base
structure derivative reported by Rok and coworkers [4].
123

422
J Chem Crystallogr (2011) 41:419–424
˚
Table 2 Selected bond distances (A), bond and torsion angles (8) for
(I) and (II)
Parameter
(I)
1.239(3)
(II)
O1–C1
1.230(3)
1.437(3)
1.508(4)
1.365(3)
1.365(2)
1.404(3)
1.454(3)
1.528(3)
1.512(3)
1.379(3)
1.732(4)
C1–C2
1.434(4)
1.507(5)
1.370(4)
1.368(3)
1.402(4)
1.458(3)
1.531(4)
1.511(4)
1.385(3)
C1–C15
C2–C4
N3–C4
N3–C10
N3–C12
C4–C5
C5–C11
C11–C10
C18–Cl1
C18–C21
1.439(5)
1.140(5)
125.7(3)
116.5(3)
127.9(2)
117.8(2)
129.9(2)
122.3(2)
107.7(2)
112.0(2)
125.0(2)
123.0(2)
120.6(2)
118.9(2)
15.7(5)
Fig. 3 The crystal packing of compound (I) and visualization of
intermolecular C–HꢀꢀꢀO hydrogen bond interactions
C21–N22
O1–C1–C2
O1–C1–C15
C1–C2–C4
C2–C1–C15
C2–C4–C5
N3–C4–C2
N3–C4–C5
C4–N3–C10
C4–N3–C12
C12–N3–C10
C17–C18–Cl1
C19–C18–Cl1
O1–C1–C2–C4
O1–C1–C15–C20
C1–C3–C4–N3
C1–C2–C4–C5
C2–C4–N3–C12
125.1(2)
117.6(2)
129.5(2)
117.3(2)
131.0(2)
121.2(2)
107.8(2)
112.1(2)
124.8(2)
123.1(2)
-0.6(4)
17.2(3)
179.8(2)
0.1(4)
21.8(4)
-178.7(3)
4.8(5)
Fig. 4 The crystal packing of compound (II) and visualization of
intermolecular C–HꢀꢀꢀO hydrogen bond interactions viewed down the
b axis
2.2(4)
-2.0(3)
2
in the literature for a Nsp3–Csp bond with 1.416 A), a
˚
˚
Table 3 Intra-intermolecular hydrogen bond distances (A) and bond
angles (8)
Csp2–Csp bond with 1.317 A and Csp2=O bond with
2
˚
˚
1.210 A [20, 22]. The aforementioned geometrical param-
D–HꢀꢀꢀA
d(D–H) d(HꢀꢀꢀA) d(DꢀꢀꢀA) \(DHA)
eters for (I) and (II) are present because the conjugative
delocalization of the nitrogen lone pair of the amino group
with the a,b-unsaturated carbonyl moiety, consequently, the
amino group presents a planar geometry for the reason that
the sum of the angles around the indole N3 atom is
360.0(6)° for (I) and 360.0(5)° for (II), indicating the ideal
sp2 hybridization in each compound [23]. All of the other
geometric parameters are within expected ranges [20].
The molecule presents a virtually planar conformation in
the indole moiety, showed by its interplanar angle of the
fused rings (C6–11 and N3–C4–C5–C10–C11) of 2.81° for
(I) and almost 1° for (II). Nevertheless, the exocyclic
carbon chain presents a distortion of the indole plane with
I
C13–H13BꢀꢀꢀO1a
C14–H14BꢀꢀꢀO1a
C9–H9ꢀꢀꢀO1i
0.96
0.96
0.93
0.96
0.96
0.96
0.96
0.93
2.337
2.300
2.642
2.780
2.723
2.328
2.362
2.787
2.672
2.995
3.094(4) 135.3
3.068(4) 136.5
3.487(3) 151.4
3.656(3) 152.1
3.446(3) 132.6
3.092(3) 136.0
3.113(3) 135.1
3.713(3) 173.4
3.603(2) 163.8
3.802(3) 152.0
C12–H12BꢀꢀꢀO1i
C14–H14CꢀꢀꢀO1ii
II C13–H13BꢀꢀꢀO1a
C14–H14BꢀꢀꢀO1a
C9–H9ꢀꢀꢀO1iii
C12–H12BꢀꢀꢀO1iii 0.96
C8–H8ꢀꢀꢀCl1iv
0.93
a
Intramolecular. i -x, y - 1/2, 1/2 - z; ii x, 1/2 - y, z ? 1/2; iii 1/
iv
2 ? x, 3/2 - y, 1/2 ? z; x, y, z - 1
123

J Chem Crystallogr (2011) 41:419–424
423
respect the carbonyl group O1–C1 when observed the
torsion angle C1–C2–C4–C5 with 4.8(5)° for (I), this
denotes that the molecule shows a tendency to twist around
the formal double bond. However, (II) does not present
the behavior mentioned, since the same dihedral angle
is coplanar (Table 2). Additionally, the dihedral angle
O1–C1–C2–C4 of 15.7(5)° shows the similar behavior of
deviation of C=C plane in molecule (I), whereas, molecule
(II) maintains planar geometry. Furthermore, the phenyl
ring (C15–C20) is twisted away with respect of the car-
bonyl C=O plane indicated by the torsion angle O1–C1–
C15–C20 with 21.8(4)° for compound (I), and 17.2(3) for
compound (II). The short C21–N22 triple bond in (I) is in
the range of a normal cyano bond, as well as, chloro atom
in (II) is for a Car–Cl bond [20].
Supplementary Material
CCDC 783910 and 784274 contain the supplementary
crystallographic data for this paper. These data can be
obtained free of charge via http://www.ccdc.cam.ac.uk/
conts/retrieving.html (or from the Cambridge Crystallo-
graphic Data Centre, 12, Union Road, Cambridge CB2
1EZ, UK; fax: ?44 1223 336033).
Acknowledgments This work was financially supported by CGIC-
´
´
´
UC (Coordinacion General de Investigacion Cientıfica de la Uni-
versidad de Colima, FRABA No. project 603/09) and by CONACyT
grant number 201625 for Ph.D. formation. Thanks to Felipe de Jesus
´
Martınez-Reyes to collaborate with the synthetic work to obtain his
Bachelor0s degree.
No classic hydrogen bonds are present, neither intra nor
intermolecular for both molecules (I) and (II). However,
according with the literature [24, 25], not only weak
C–HꢀꢀꢀO contacts, which are depicted in the supramolecu-
lar assembly (Fig. 3), but also C–Hꢀꢀꢀp interactions govern
intra and intermolecular crystal packing for (I). On the
other hand, crystal of (II) presents weak interactions of the
types C–HꢀꢀꢀO and C–HꢀꢀꢀHal.
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