X-ray, DFT, FTIR and NMR structural study of 2,3-dihydro-2-(R- phenylacylidene)-1,3,3-trimethyl-1H-indole

Article abstract of DOI:10.1016/j.molstruc.2010.12.001

Fischer base derivatives are widely used as precursor in the formation of different chemical switches. Besides, in the presence of acyl chlorides, indole enaminoketone derivatives can be prepared. 2,3-Dihydro-2-(R-phenylacylidene)-1, 3,3-trimethyl-1H-indole, R = 4-NO₂, 3,5-(NO₂)₂ and 4-OCH₃, have been characterized previously but only by ¹H NMR, thus further characterization was performed by FTIR, ¹³C NMR and when suitable crystals were obtained by single crystal X-ray diffraction analyses. The structures of the three molecules were additionally analyzed by DFT methods, B3LYP and PW91 functionals, using 6-311G(d,p) basis set. The optimized structures obtained were compared with those determined by crystallographic data. The probable assignments of the anharmonic experimental solid state vibrational frequencies for these molecules have been also made based on the calculated harmonic frequencies in vacuum at the same level of theory for the optimized structures. Correlations between experimental chemical shifts and GIAO calculated magnetic isotropic shielding constants with B3LYP and PW91 functionals using the 6-311++G(3df,3pd) basis set are also reported.

Full text of DOI:10.1016/j.molstruc.2010.12.001

Journal of Molecular Structure 987 (2011) 106–118
Contents lists available at ScienceDirect
Journal of Molecular Structure
journal homepage: www.elsevier.com/locate/molstruc
X-ray, DFT, FTIR and NMR structural study of
2,3-dihydro-2-(R-phenylacylidene)-1,3,3-trimethyl-1H-indole
a
b
c
Oscar F. Vázquez-Vuelvas a, , Julia V. Hernández-Madrigal , Rubén Gaviño , Mikhail A. Tlenkopatchev ,
David Morales-Morales b, Juan M. Germán-Acacio b, Zeferino Gomez-Sandoval a, Cesar Garcias-Morales d,
Armando Ariza-Castolo d, Armando Pineda-Contreras a
⇑
a Facultad de Ciencias Químicas, Universidad de Colima, km 9 Carr. Colima-Coquimatlán s/n, 28400 Coquimatlán, Colima, Mexico
b Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, México D.F. 04510, Mexico
c Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, México D.F. 04510, Mexico
d Centro de Investigación y de Estudios Avanzados del I.P.N., Apdo. Postal 14-740, México D.F. 07000, Mexico
a r t i c l e i n f o
a b s t r a c t
Article history:
Received 12 June 2010
Received in revised form 6 December 2010
Accepted 6 December 2010
Available online 15 December 2010
Fischer base derivatives are widely used as precursor in the formation of different chemical switches.
Besides, in the presence of acyl chlorides, indole enaminoketone derivatives can be prepared. 2,3-Dihy-
dro-2-(R-phenylacylidene)-1,3,3-trimethyl-1H-indole, R = 4-NO2, 3,5-(NO2)2 and 4-OCH3, have been
characterized previously but only by 1H NMR, thus further characterization was performed by FTIR,
13C NMR and when suitable crystals were obtained by single crystal X-ray diffraction analyses. The struc-
tures of the three molecules were additionally analyzed by DFT methods, B3LYP and PW91 functionals,
using 6-311G(d,p) basis set. The optimized structures obtained were compared with those determined
by crystallographic data. The probable assignments of the anharmonic experimental solid state vibra-
tional frequencies for these molecules have been also made based on the calculated harmonic frequencies
in vacuum at the same level of theory for the optimized structures. Correlations between experimental
chemical shifts and GIAO calculated magnetic isotropic shielding constants with B3LYP and PW91 func-
tionals using the 6-311++G(3df,3pd) basis set are also reported.
Keywords:
Fischer base
X-ray diffraction
Enaminoketone
FTIR
DFT
NMR
Ó 2010 Elsevier B.V. All rights reserved.
1. Introduction
the production of acetylenic products via indole enaminoketone
fragmentation [9–11].
The Fischer base, 2,3-dihydro-1H-1,3,3-trimethyl-2-methylen-
eindole and some derivatives have been widely used in organic
synthesis for the preparation of different types of chemical
switches [1]. Products with different photochromic and thermo-
chromic properties have been reported due to their potential prac-
tical application in optoelectronics, molecular information devices
and as organic electroluminescence materials [2–4]. Further appli-
cations include the use of different derivatives in the field of dyes
[5]. The spiropyran and spirooxazine derivatives of the Fischer base
have acquired in recent years industrial relevance in areas such as:
the production of polymer-based photochromic lenses, colorants
for textiles and surface coatings, including photochromic inks
and aesthetic uses [6,7] due to their photochemical properties.
These products can be conveniently prepared from indole enami-
noketones derivatives and this synthetic procedure is not limited
to the synthesis of spiropyrans and spirooxazines [8], but also for
The synthesis of Fischer base enaminoketone derivatives with
different acyl-substituted enamino carbonyl derivatives, as well
as their characterization by NMR and FTIR spectroscopies have
been previously studied in order to define conformational and con-
figurational structures [12].
Additionally, the synthesis and analysis in solution by 1H NMR
spectroscopy of several enaminoketones has also been reported
[13]. However, despite the great interest in Fischer base deriva-
tives, indole enaminoketones have been poorly studied and little
is known about their structures. The potential importance of these
species as precursors of chemical switches and arylacetylenes pro-
vides further motivation for the unambiguous structure determi-
nation of these compounds.
On this opportunity, we would like to report the full and
unequivocal characterization and solid structural studies of differ-
ent enaminoketone derivatives namely 2,3-dihydro-2-(R-phenyla-
cylidene)-1,3,3-trimethyl-1H-indole (1c, R = 4-NO2, 2c, 3,5-(NO2)2,
3c, 4-OCH3), (Fig. 1). In addition, DFT methods using the hybrid
B3LYP correlation and PW91 exchange-correlation functionals
were employed for the determination of calculated geometric
⇑
Corresponding author. Tel.: +52 312 316 11 63.
E-mail address: oscar_vazquez@ucol.mx (O.F. Vázquez-Vuelvas).
0022-2860/$ - see front matter Ó 2010 Elsevier B.V. All rights reserved.
doi:10.1016/j.molstruc.2010.12.001

O.F. Vázquez-Vuelvas et al. / Journal of Molecular Structure 987 (2011) 106–118
107
at a 4 cmꢀ1 resolution with 32 scans. 1H and 13C NMR for com-
pounds 1c and 2c were recorded in solution with CDCl3 and TMS
in a Varian 300 Unity Inova spectrometer at 300 MHz for 1H and
75 MHz for 13C. Compound 3c was recorded in a Bruker Avance
III spectrometer at 400 MHz for 1H and 100 MHz for 13C.
Suitable crystals for X-ray diffraction were obtained from its
toluene solution by slow evaporation. Crystals of 1c and 2c were
mounted in random orientation on glass fibers. The X-ray intensity
data were measured at 298 K and 123 K, for 1c and 2c, respectively,
on a Bruker SMART APEX CCD-based three-circle X-ray diffractom-
eter system using graphite mono-chromated Mo K
a radiation
(k = 0.71073 Å). The crystal structures were solved by direct meth-
ods and refined using SHELXS-97 and SHELXL-97 crystallographic
software packages [15–17]. All non-hydrogen atoms were refined
anisotropically using reflections I > 2r(I). Hydrogen atoms were lo-
cated in ideal positions. Geometric calculations were done using
PLATON [18]. Crystal of 3c was supported on a glass fiber. The dif-
fraction data were collected in an Enraf–Nonius CCD with Mo K
a
Fig. 1. Synthetic route and atom numbering of indole enaminoketones 1c, 2c and
3c. Hydrogen atom symbols have been omitted for clarity.
radiation (k = 0.71073 Å) with area detector. The software used
for data collection, indexing reflections, and parameter recording
for the lattice was CAD4 EXPRESS. Data reduction was performed
using WinGX [19] and SHELXS-97 crystallographic software pack-
ages [17]. Molecular graphics, visualization and analysis of the
three crystal structures were prepared using MERCURY [20].
The details of the structure determination are listed in Table 1,
selected bond lengths (Å), selected bond and dihedral angles (°) are
listed in Table 3. The atom numbering of crystal structures 1c, 2c
and 3c are depicted in Figs. 3a, 4a and 5a, respectively. CCDC
772890–772892 contains 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 Cam-
bridge Crystallographic Data Centre, 12, Union Road, Cambridge
CB2 1EZ, UK; fax: +44 1223 336033).
parameters, vibrational frequencies and chemical shifts, these re-
sults were analyzed and compared with those obtained from
experimental results.
2. Experimental
2.1. (E)-2,3-Dihydro-2-(4-nitrophenylacylidene)-1,3,3-trimethyl-1H-
indole (1c)
The synthesis of this compound has been previously reported
[13,14]. In the present work, to a solution of 1a (10 g, 59.84 mmol)
in 72 ml of dry benzene thionyl chloride (14.24 g, 119.68 mmol)
was added, the mixture was heated at reflux for 1.5 h. After the
prescribed reaction time, the reaction mixture was allowed to cool
down to room temperature, and both the solvent and excess of
thionyl chloride evaporated; for its complete removal, 30 ml of
petroleum ether was added and eliminated under a vacuum. A
solution of 1b in 50 ml of dry benzene was added to a mixture of
the Fischer base 2,3-dihydro-1H-1,3,3-trimethyl-2-methylenein-
dole (10.36 g, 59.84 mmol) and triethylamine (7.26 g, 71.78 mmol)
in 100 ml of dry benzene. The mixture was maintained at 40 °C for
2 h, and then allowed to stand overnight at room temperature. The
resulting precipitate was filtered and washed with water and iso-
propyl alcohol. The product was purified by column chromatogra-
phy using chloroform as eluent. The yield was 15.24 g (79%); m.p.:
194–196 °C. Literature [13]: 193–196 °C.
2.4. Computational details
The calculations were performed using the Gaussian 03 program
package [21]. The geometries of all structures were fully optimized
with two different functionals, B3LYP [22,23] and PW91 [24] in con-
junction with 6-311G(d,p) basis set without any symmetry restric-
tions. The calculations were carried out based on crystallographic
data from the three enaminoketone molecules 1c, 2c and 3c. The
minimum energy was verified by calculating the vibrational fre-
quencies for the optimized structures at the same level of theory
and compared with experimental FTIR data. Magnetic shielding ten-
sors were computed using the standard GIAO (Gauge-Independent
Atomic Orbital) DFT method as implemented in the Gaussian 03 pro-
grampackageemploying twodifferentfunctionals, B3LYPandPW91
using the 6-311++G(3df,3pd) basis set. The SCF convergence crite-
rion for the compound 2c was set to 10ꢀ7 on the density matrix
and to 10ꢀ5 au on the r.m.s. force for both functionals due to termi-
nationfailures inthecalculatingprocess. In order to getvisualization
of the shape of the different molecular vibrational modes and the
corresponding assignment of the calculated wavenumbers, the visu-
alization program for working with quantum chemistry computa-
tions Chemcraft software was used [25].
2.2. (E)-2,3-Dihydro-2-(3,5-dinitrophenylacylidene)-1,3,3-trimethyl-
1H-indole (2c)
Compound 2c was synthesized by the same procedure as that
described for compound 1c. Yield 65%; m.p. of 217–221 °C. Litera-
ture [13]: 215–220 °C.
2.3. (E)-2,3-Dihydro-2-(4-methoxyphenylacylidene)-1,3,3-trimethyl-
1H-indole (3c)
3. Results and discussion
Compound 3c from 3b was synthesized following the same pro-
cedure as that described above for compound 1c. Yield 59%; m.p.:
151–153 °C. Literature [13]: 148–150 °C.
3.1. Quantum chemical calculations
The infrared spectra of the three compounds were recorded in a
Varian 3100 FT-IR Excalibur Series spectrometer in the range of
4000–400 cmꢀ1. The solid substances were analyzed with an ATR
device, which was evacuated to avoid water and CO2 absorptions,
To support the experimental results, an extension of the study
was done by theoretical calculations. Regarding indole enaminok-
etones can exist in two conformations, s-cis and s-trans, and with
allowance for geometrical isomerism relative to exocyclic C@C

108
O.F. Vázquez-Vuelvas et al. / Journal of Molecular Structure 987 (2011) 106–118
Table 1
Structure refinement data for crystals of 1c, 2c and 3c compounds.
1c
2c
3c
Empirical formula
Formula weight
Temperature (K)
Wavelength (Å)
Crystal system
Space group
a (Å)
C
19H18N2O3
C19H17N3O5
367.36
123(2)
0.71073
Triclinic
P-1
6.9082(9)
C20H21NO2
307.38
293(2)
0.71073
Monoclinic
P 21/a
8.564
322.35
298(2)
0.71073
Triclinic
P-1
8.5784(13)
b (Å)
9.0870(13)
7.8601(11)
15.345
c (Å)
11.1379(16)
79.926(2)
15.578(2)
99.232(3)
12.936
90
a
(°)
b (°)
78.848(2)
91.361(3)
90.940
c
(°)
86.990(2)
838.5(2)
93.420(3)
832.97(19)
90
1699.75
Volume (Å3)
Z
2
2
4
Density (calculated) (Mg/m3)
Absorption coefficient (mmꢀ1
F(0 0 0)
1.277
0.087
340
1.465
0.108
384
1.201
0.077
656
)
Crystal size (mm)
Theta range for data collection (°)
0.372 ꢁ 0.164 ꢁ 0.126
0.388 ꢁ 0.212 ꢁ 0.104
0.4 ꢁ 0.4 ꢁ 0.4
1.89–5.37
2.63–5.45
3.1–7.71
Index ranges
ꢀ10 6 h 6 10
ꢀ10 6 k 6 10
ꢀ13 6 l 6 13
10,847
ꢀ8 6 h 6 8
ꢀ8 6 h 6 8
ꢀ9 6 k 6 9
ꢀ9 6 k 6 9
0 6 l 6 18
3076
0 6 l 6 18
12,007
Reflections collected
Independent reflections
Absorption correction
Max. and min. transmission
Refinement method
3076 [R(int) = 0.0313]
Semi-empirical from equivalents
0.9898 and 0.9726
Full-matrix least-squares on F2
3076/84/248
1.026
3076 [R(int) = 0.0397]
Semi-empirical from equivalents
0.989 and 0.870
Full-matrix least-squares on F2
3076/0/248
3444 [R(int) = 0.048]
None
0.97
Full-matrix least-squares on F2
3444/0/293
Data/restraints/parameters
Goodness-of-fit on F2
1.04
1.036
Final R indices [I > 2
R indices (all data)
Largest diff. peak and hole
r
(I)]
R1 = 0.0461, wR2 = 0.1150
R1 = 0.0655, wR2 = 0.1271
0.213 and ꢀ0.178 e Åꢀ3
R1 = 0.0409, wR2 = 0.0906
R1 = 0.0479, wR2 = 0.0941
0.229 and ꢀ0.173 e Åꢀ3
R1 = 0.0605 wR2 = 0.1354
R1 = 0.1002 wR2 = 0.1606
0.15 and ꢀ0.15 e Åꢀ3
Fig. 2. Analyzed structures of the enaminoketones, (a) (E) s-cis, (b) (E) s-trans, (c) (Z) s-cis, and (d) (Z) s-trans.
bond, there are four possible conformations to investigate. The
general structures of the four studied compounds are shown in
Fig. 2.
In the subsequent, the discussion will be referred to the ener-
getically most stable (E) s-cis structures of 1c, 2c and 3c
compounds.
Taking into account the DFT calculations, the lowest-energy iso-
mers were determined. The total energies E, relative
DE energies
3.2. Crystal structures
and relative Gibbs free energies G of the isomers at B3LYP and
D
PW91 levels are listed in Table 2. Calculated energies confirm that
the most stable structures are those with E configuration and s-cis
conformation for 1c, 2c and 3c compounds.
The enaminoketones 1c and 2c crystallized in a triclinic space
group P1, and 3c crystallized in a monoclinic space group P21/a. In
ꢀ
three cases the conformation observed for the molecules is (E) s-
cis. Selected bond distances and angles are listed on Table 3. For
the three structures, bond distances and angles of the indole moiety
are similar to those reported for other indole derivatives [4,26]. The
bond distances of N(3)AC(10) goes from 1.405(3) Å to 1.414(3) Å,
denoting a longer distance than that corresponding to a single
Nsp3ACsp2 bond of an indole. The same observation occurs with
the N(3)AC(4) bonds, with distances ranging from 1.354(3) Å to
1.369(2) Å [4,27]. In addition, the formally double C(2)AC(4) and
C(1)AO(1) bonds show 1.367(3)A1.379(3) Å, and 1.236(3)A
The data of calculated energy in Table 2 show that the lowest
values correspond to the energies calculated with B3LYP. The en-
ergy difference for (Z) s-cis structures was in the range of 1.67
and 1.90 kcal/mol for the three compounds with respect to the
(E) s-cis isomer. The difference showed in total energy by com-
pound 3c in the (Z) s-trans conformation, is high in comparison
with those for similar conformations in 1c and 2c due to 3c pre-
senting one imaginary frequency attributable to the highly steric
hindrance of this unstable isomer.

O.F. Vázquez-Vuelvas et al. / Journal of Molecular Structure 987 (2011) 106–118
109
Fig. 3. (a) Molecular structure of 1c at 30% of probability level and atom numbering. (b) Intramolecular hydrogen contacts, view along C(13)AC(5) bond. (c) Visualization of
CAHꢂ ꢂ ꢂO interactions as well as the intermolecular ring and chain formed, hydrogen atoms were omitted for clarity. (d) Packing pattern view along a axis, hydrogen atoms
were omitted for clarity.
1.243(3) Å bond distances respectively; the average of these dis-
tances being slightly longer than those reported for similar deriva-
tives [28]. Conversely, the C(2)AC(1) bonds are shorter than
expectedfor a typical CAC single bond, with bond distances between
1.424 (3) Å and 1.444(2) Å. These values can be attributed to conju-
gative delocalization of the lone pair of the nitrogen of the amino
N(1)AC(18)AC(17) of ꢀ13.6(3)° and C(18)AC(19)AN(2)AO(4) of
ꢀ15.8(3)°. The methoxy group of the crystal 3c has almost the
same
benzene
ring
plane,
the
torsion
angle
is
C(21)AO(2)AC(18)AC(17) = 2.9(3)°.
The geometric parameters associated with intra and intermo-
lecular DAHꢂ ꢂ ꢂA interactions are listed in Table 4. Non classic nei-
ther intra nor intermolecular hydrogen bonds are present.
However, weak CAHꢂ ꢂ ꢂO contacts, depicted in the supramolecular
assembly govern the intermolecular crystal packing. The main
interactions found in 1c and 2c, are of the type CAHꢂ ꢂ ꢂO of the ni-
tro group. Compound 3c presents short contacts of type CAHꢂ ꢂ ꢂO
involving the carbonyl and the methoxy groups (Table 4). The
aforementioned contacts determine the stacking mode of the mol-
ecules in the solid state due to the high coplanar difference of the
two-side aromatic rings and their substituents. Since the coplanar
angle between the rings is 38.29°, 17.61° and 31.06 for 1c, 2c and
group with the a,b-unsaturated carbonyl moiety and thus the amino
group exhibits a planar geometry (Table 3) [29]. In all cases, the mol-
ecules present a virtually planar conformation at the indole moiety,
this being showed by the value of their interplanar angles of the
adjacent rings [(C(6)AC(11) and N(3)AC(4)AC(5)AC(10)AC(11)] of
almost 1°. The exocyclic carbon chain in compound 1c presents a
minor distortion of the plane and this fact being reflected in the
dihedral angle C(1)AC(2)AC(4)AC(5), which denotes a tendency to
twist around the formal double bond with an angle of ꢀ3.5(3)°. In
addition, the dihedral angle O(1)AC(1)AC(2)AC(4) in 1c is
ꢀ6.3(3)°, whereas in 2c and 3c this angles are 5.8(4)° and 4.6(4)°
respectively, showing an inverted rotation of the carbonyl group in
1c with respect to the C@C bond (Table 3). For the same compound
the phenyl ring C(15)AC(20), is slightly twisted away from the car-
bonyl plane with a torsion angle O(1)AC(1)AC(15)AC(20) of
ꢀ32.1(2)° for 1c, ꢀ16.4(3)° in 2c and by an intermediate value of
24.8(3)° in 3c.
3c respectively, no short face-to-face p–p stacking interactions are
observed in the crystal packing of 1c and 2c, but they are present in
3c, exhibiting a CAHꢂ ꢂ ꢂO contact motif in a similar edge-to-face
fashion involving the methoxy group. For all the nitro groups in-
volved in short contacts, the CAHꢂ ꢂ ꢂO@N and Cꢂ ꢂ ꢂO@N distances
are shorter than the mean values reported in the literature [30].
Moreover, the not very basic nitro group acts as a CAHꢂ ꢂ ꢂO accep-
tor in the crystal structures of our unsaturated compounds, due to
the enhanced acceptor ability of the nitro group, this probably
being due to conjugation and cooperativity effects [31].
The nitro groups in 1c and 2c are rotated from the plane of the
adjacent aryl ring. In compound 1c, the nitro is twisted away from
the plane of C(15)AC(20) ring with ꢀ7(1)° denoted by the torsion
angle C(17)AC(18)AN(1)AO(2). Compound 2c presents an inter-
planar spacing with the torsion angle formed by O(1)A
The structures of the three compounds exhibit CAHꢂ ꢂ ꢂO inter-
molecular contacts in a bifurcated fashion with C(13) and C(14)

110
O.F. Vázquez-Vuelvas et al. / Journal of Molecular Structure 987 (2011) 106–118
Fig. 4. (a) Molecular structure of 2c at 50% of probability level and atom numbering. (b) Intramolecular hydrogen bonds, view along C(13)AC(5) bond. (c) Visualization of
CAHꢂ ꢂ ꢂO interactions as well as the intermolecular ring and chain formed, hydrogen atoms were omitted for clarity. (d) Packing patter view along a axis, hydrogen atoms
were omitted for clarity.
Table 2
Calculated B3LYP/6-311G(d,p) and PW91/6-311G(d,p) total E,
D
E and
D
G energies (kcal/mol) of the enaminoketone isomers.
Compound
Structure
B3LYP
PW91
E
D
E
D
G
E
D
E
DG
1c
(E) s-cis
(Z) s-cis
(Z) s-trans
(E) s-trans
ꢀ1070.216421
ꢀ1070.213767
ꢀ1070.204420
ꢀ1070.199097
0.00
1.67
7.53
0.00
1.64
7.63
ꢀ1069.846275
ꢀ1069.843568
ꢀ1069.835218
ꢀ1069.830098
0.00
1.70
6.94
0.00
2.14
7.72
10.87
10.45
10.15
10.43
2c
3c
(E) s-cis
(Z) s-cis
(Z) s-trans
(E) s-trans
ꢀ1274.768228
ꢀ1274.765389
ꢀ1274.755042
ꢀ1274.749926
ꢀ980.214913
ꢀ980.212174
ꢀ980.186022a
ꢀ980.199005
0.00
1.78
8.27
0.00
2.03
8.59
ꢀ1274.370640
ꢀ1274.367610
ꢀ1274.353537
ꢀ1274.353537
ꢀ979.836457
ꢀ979.833633
ꢀ979.809834a
ꢀ979.821320
0.00
1.90
7.68
0.00
1.77
7.73
11.48
11.51
10.73
10.53
(E) s-cis
(Z) s-cis
(Z) s-trans
(E) s-trans
0.00
1.72
18.13
9.98
0.00
1.51
9.72
9.63
0.00
1.77
16.71
9.50
0.00
1.80
11.44
9.82
a
There is one imaginary frequency for the structure, the local minimum has not been found.
as the donor atoms and the oxygen of carbonyl group O(1) as the
acceptor (Figs. 3b, 4b and 5b; Table 4). In 1c, the supramolecular
structure presents an arrangement antiparallel in a head-to-tail
stacking mode especially favored by the formation of a homodimer
determined by the CAHꢂ ꢂ ꢂO@C interactions. These are formed with
the donor C(20) atom at (x, y, z) and O(1) atom at (ꢀx, 1 ꢀ y, 1 ꢀ z),
and by inversion, it is formed a ring R22 (10) in graph notation [32]
(Fig. 3c; Table 4). Additionally, a CAHꢂ ꢂ ꢂO contact was observed
with the N(1B)AO(2B)AO(3B) atoms, whose occupancy exceeded
the nitro site. The contact is formed with the C(16) atom at (x, y,
z) as the donor and O(2B) at (1 ꢀ x, 1 ꢀ y, 2 ꢀ z) as the acceptor
of the interaction.
For compound 2c, the supramolecular assembly presents a
homodimer formed with the presence of CAHꢂ ꢂ ꢂO donor atom
C(12) at (x, y, z), interacting with the nitro O(3) atom in the molecule
at (ꢀx, ꢀy, 1 ꢀ z), and by inversion it forms a ring R22 (22) (Fig. 4c; Ta-
ble 4). At the same time, acceptor atom O(3) at (x, y, z) is engaged
with donor atom C(7) at (x, y, 1 + z) to form a suitable hydrogen con-
tact, and therefore propagation by inversion forms another ring R42
(18). Additionally, the donor C(8) atom at (x, y, z) interacts with
the acceptor O(4) atom at (x, ꢀ1 + y, ꢀ1 + z) to form the chains
C(13), as well as the C(7)AH(7)ꢂ ꢂ ꢂO(3) hydrogen contact form the
chain C(14) by motif propagation, consequently the formation oflay-
ers of the hydrogen contacts interlinked ribbon chains.

O.F. Vázquez-Vuelvas et al. / Journal of Molecular Structure 987 (2011) 106–118
111
Table 3
Experimental and calculated data with B3LYP/6-311G(d,p) and PW91/6-311G(d,p) of bond lengths (Å), bond angles and selected dihedral angles (°) for 1c, 2c and 3c.
Parameter
X-ray
B3LYP
PW91
X-ray
B3LYP
PW91
X-ray
B3LYP
PW91
Bond lengths
C(1)AO(1)
C(1)AC(2)
C(1)AC15
1c
2c
3c
1.243(3)
1.424(3)
1.525(3)
1.379(3)
1.414(3)
1.354(3)
1.456(3)
1.539(3)
1.519(3)
1.541(3)
1.536(3)
1.395(3)
1.376(3)
1.392(3)
1.393(3)
1.390(3)
1.382(3)
1.398(3)
1.394(3)
1.385(3)
1.384(3)
1.381(3)
1.380(3)
1.231
1.442
1.524
1.378
1.411
1.370
1.456
1.540
1.520
1.547
1.546
1.400
1.382
1.399
1.398
1.390
1.394
1.400
1.396
1.391
1.386
1.388
1.386
0.9963
1.243
1.442
1.524
1.384
1.411
1.375
1.452
1.538
1.520
1.547
1.546
1.405
1.389
1.398
1.402
1.395
1.401
1.405
1.402
1.395
1.391
1.393
1.391
0.9958
1.237(2)
1.432(2)
1.508(2)
1.368(2)
1.408(2)
1.365(2)
1.454(2)
1.535(2)
1.511(2)
1.538(2)
1.533(3)
1.388(3)
1.376(2)
1.374(3)
1.387(3)
1.380(2)
1.382(2)
1.388(2)
1.386(2)
1.376(3)
1.366(3)
1.372(3)
1.375(3)
1.232
1.448
1.518
1.375
1.409
1.374
1.450
1.541
1.520
1.548
1.544
1.400
1.384
1.392
1.398
1.390
1.395
1.401
1.401
1.390
1.390
1.392
1.387
0.9957
1.244
1.448
1.518
1.382
1.409
1.378
1.451
1.539
1.520
1.548
1.545
1.405
1.389
1.398
1.402
1.395
1.401
1.407
1.407
1.394
1.395
1.397
1.391
0.9950
1.236(3)
1.444(2)
1.502(3)
1.367(3)
1.405(3)
1.369(2)
1.445(3)
1.537(3)
1.513(3)
1.530(3)
1.538(4)
1.386(4)
1.381(3)
1.366(4)
1.386(4)
1.386(3)
1.379(3)
1.399(3)
1.382(3)
1.389(3)
1.378(3)
1.384(3)
1.372(3)
1.233
1.456
1.506
1.370
1.405
1.381
1.449
1.542
1.521
1.544
1.548
1.401
1.384
1.392
1.399
1.391
1.396
1.406
1.397
1.394
1.397
1.403
1.381
0.9953
1.246
1.455
1.506
1.377
1.406
1.384
1.449
1.540
1.520
1.544
1.548
1.405
1.388
1.398
1.403
1.396
1.402
1.411
1.403
1.398
1.404
1.408
1.385
C(2)AC(4)
N(3)AC(10)
N(3)AC(4)
N(3)AC(12)
C(4)AC(5)
C(5)AC(11)
C(5)AC(13)
C(5)AC(14)
C(6)AC(7)
C(6)AC(11)
C(7)AC(8)
C(8)AC(9)
C(9)AC(10)
C(10)AC(11)
C(15)AC(20)
C(16)AC(15)
C(16)AC(17)
C(17)AC(18)
C(18)AC(19)
C(19)AC(20)
ra
0.9942
Bond angles
O(1)AC(1)AC(15)
O(1)AC(1)AC(2)
C(1)AC(2)AC(4)
C(1)AC(15)AC(20)
C(1)AC(15)AC(16)
C(2)AC(4)AN(3)
C(2)AC(4)AC(5)
C(2)AC(1)AC(15)
N(3)AC(10)AC(11)
N(3)AC(4)AC(5)
N(3)C(10)AC(9)
C(4)AN(3)AC(10)
C(4)AC(5)AC(11)
C(4)AC(5)AC(13)
C(4)AC(5)AC(14)
C(4)AN(3)AC(12)
C(5)AC(11)AC(6)
C(5)AC(11)AC(10)
C(6)AC(7)AC(8)
117.0(1)
126.5(2)
128.9(2)
118.5(1)
122.8(1)
121.7(1)
130.3(1)
116.4(1)
108.7(1)
107.9(1)
128.9(2)
111.8(1)
101.6(1)
111.7(1)
111.2(1)
124.8(1)
130.4(2)
109.8(1)
120.6(2)
119.7(2)
121.4(2)
118.8(2)
117.0(2)
122.4(2)
123.3(1)
110.0(1)
110.1(1)
111.8(1)
120.7(2)
120.9(2)
118.8(2)
118.7(2)
122.2(2)
118.5(2)
117.3
125.9
128.4
117.3
123.8
121.1
130.8
116.8
108.8
108.1
129.2
111.9
101.5
111.1
111.9
124.1
130.5
109.6
120.2
120.0
121.1
119.2
117.6
121.9
124.0
110.1
111.9
111.1
120.9
121.0
118.7
118.9
121.3
118.6
117.4
125.9
128.4
117.0
124.1
121.0
130.8
116.7
108.7
108.1
129.3
111.9
101.7
111.0
111.7
123.9
130.6
109.6
120.3
119.9
121.2
119.1
117.5
122.0
124.2
110.1
112.0
111.0
120.9
121.0
118.7
118.9
122.0
118.9
115.6(2)
127.0(2)
127.7(2)
116.7(2)
124.3(2)
122.3(2)
129.3(2)
117.4(2)
108.9(2)
108.3(2)
128.8(2)
111.9(2)
101.4(2)
111.3(2)
112.1(2)
124.8(2)
130.2(2)
109.5(2)
119.8(2)
120.3(2)
121.7(2)
119.1(2)
116.8(2)
122.3(2)
123.3(2)
109.7(2)
110.1(2)
111.7(2)
119.1(2)
119.5(2)
123.2(2)
119.0(2)
116.2(2)
123.0(2)
116.6
126.4
128.2
116.8
124.5
121.0
130.8
117.0
108.8
108.3
129.2
111.9
101.5
111.2
111.7
124.0
130.5
109.6
120.3
119.9
121.1
119.2
117.6
122.0
124.1
110.7
110.3
111.1
119.7
119.8
122.6
118.7
116.6
122.6
116.7
126.4
128.2
116.5
124.8
120.9
130.9
116.7
108.6
108.3
129.2
111.9
101.7
111.2
111.5
124.0
130.6
109.6
120.4
119.8
121.1
119.1
117.4
122.1
124.1
110.4
110.7
111.0
119.7
119.8
122.7
118.7
116.6
122.7
118.3(2)
125.3(2)
129.4(2)
118.6(2)
123.9(2)
121.1(2)
130.9(2)
116.4(2)
108.9(2)
107.9(2)
128.6(2)
111.8(2)
101.4(2)
111.4(2)
111.0(2)
124.1(2)
130.9(2)
110.0(2)
120.3(2)
119.2(2)
121.8(2)
119.4(2)
116.8(2)
122.5(2)
124.0(2)
110.7(2)
109.8(2)
112.1(2)
121.7(2)
121.3(2)
119.4(2)
117.5(2)
119.9(2)
120.1(2)
118.2
124.6
128.5
117.6
124.6
121.2
130.9
117.2
108.9
107.9
129.3
111.9
101.6
112.0
111.1
124.0
130.5
109.6
120.2
119.9
121.1
119.3
117.7
121.8
124.2
110.9
110.0
111.0
121.6
121.4
119.6
117.8
119.5
120.1
118.2
124.6
128.4
117.3
124.8
121.1
131.0
117.2
108.8
107.9
129.4
111.9
101.8
111.8
111.0
123.8
130.5
109.6
120.2
119.9
121.2
119.2
117.6
121.9
124.3
111.0
110.0
110.9
121.6
121.4
119.6
117.8
119.6
120.5
C(6)AC(11)AC(10)
C(7)AC(8)AC(9)
C(7)AC(6)AC(11)
C(8)AC(9)AC(10)
C(9)AC(10)AC(11)
C(10)AN(3)AC(12)
C(11)AC(5)AC(13)
C(11)AC(5)AC(14)
C(13)AC(5)AC(14)
C(15)AC(16)AC(17)
C(15)AC(20)AC(19)
C(16)AC(17)AC(18)
C(16)AC(15)AC(20)
C(17)AC(18)AC(19)
C(18)AC(19)AC(20)
ra
0.9963
0.9960
0.9965
0.9961
0.9973
0.9969
Torsion angles
O(1)AC(1)AC(2)AC(4)
O(1)AC(1)AC(15)AC(20)
C(1)AC(2)AC(4)AC(5)
O(2)AN(1)AC(18)AC(17)
O(2)AN(1)AC(18)AC(17)
O(4)AN(2)AC(19)AC(18)
C(21)AO(2)AC(18)AC(17)
ꢀ6.3(3)
ꢀ32.1(2)
ꢀ3.5(3)
ꢀ7(1)
ꢀ5.96
ꢀ21.2
ꢀ3.1
0.1
ꢀ4.9
ꢀ19.4
ꢀ2.4
0.4
5.8(4)
ꢀ3.2
ꢀ14.6
ꢀ0.8
ꢀ2.2
ꢀ11.7
ꢀ0.2
4.6(4)
24.8(3)
3.0(4)
7.4
16.0
3.0
6.3
14.2
2.4
ꢀ16.4(3)
ꢀ0.7(4)
ꢀ13.6(3)
ꢀ15.8(3)
0.1
ꢀ0.3
ꢀ0.4
ꢀ0.1
2.9(3)
ꢀ0.4
ꢀ0.3
a
Correlation coefficient.

112
O.F. Vázquez-Vuelvas et al. / Journal of Molecular Structure 987 (2011) 106–118
Fig. 5. (a) Molecular structure of 3c at 30% of probability level and atom numbering. (b) Intramolecular hydrogen bonds, view along C(13)AC(5) bond. (c) Visualization of
CAHꢂ ꢂ ꢂO interactions as well as the intermolecular ring and chain formed. (d) Packing patter view along a axis, hydrogen atoms were omitted for clarity.
Table 4
Dimensions of short contacts of the crystal structures and the optimized geometries with B3LYP/6-311G(d,p) and PW91/6-311G(d,p) of 1c, 2c and 3c compounds.
Crystal
D–Hꢂ ꢂ ꢂA (symmetry codes)
D–H (Å)
Hꢂ ꢂ ꢂA (Å)
Dꢂ ꢂ ꢂA (Å)
DHꢂ ꢂ ꢂA (°)
1c
X-ray
C13AH13Cꢂ ꢂ ꢂO1a
0.960(2)
0.960(2)
0.930(2)
0.930(2)
2.333(1)
2.367(1)
2.579(1)
2.69(1)
3.099(2)
3.125(2)
3.343(2)
3.39(1)
136.3(1)
136.5(1)
139.7(1)
132.6(4)
C14AH14Bꢂ ꢂ ꢂO1a
C20AH20ꢂ ꢂ ꢂO2 (ꢀx, 1 ꢀ y, 1 ꢀ z)
C16AH16ꢂ ꢂ ꢂO2B (1 ꢀ x, 1 ꢀ y, 2 ꢀ z)
B3LYPa
PW91a
C13AH13Cꢂ ꢂ ꢂO1a
1.088
1.088
2.260
2.283
3.101
3.115
132.6
131.7
C14AH14Bꢂ ꢂ ꢂO1a
C13AH13Cꢂ ꢂ ꢂO1a
C14AH14Bꢂ ꢂ ꢂO1a
1.095
1.095
2.238
2.268
3.095
3.114
133.4
132.4
2c
X-ray
C13AH13Cꢂ ꢂ ꢂO1a
0.980(2)
0.980(2)
0.979(2)
0.949(2)
0.949(2)
2.278(1)
2.278(1)
2.565(1)
2.513(2)
2.691(2)
3.052(3)
3.053(2)
3.437(2)
3.417(3)
3.373(3)
135.2(1)
135.2(1)
148.3(1)
159.2(1)
129.3(8)
C14AH13Bꢂ ꢂ ꢂO1a
C12AH12Aꢂ ꢂ ꢂO3 (ꢀx, ꢀy, 1 ꢀ z)
C7AH7ꢂ ꢂ ꢂO3 (x, y,ꢀ1 + z)
C8AH8ꢂ ꢂ ꢂO4 (x, ꢀ1 + y, ꢀ1 + z)
B3LYP
PW91
C13AH13Cꢂ ꢂ ꢂO1a
1.088
1.088
2.258
2.280
3.097
3.111
132.4
131.6
C14AH14Bꢂ ꢂ ꢂO1a
C13AH13Cꢂ ꢂ ꢂO1a
C14AH14Bꢂ ꢂ ꢂO1a
1.095
1.095
2.241
2.265
3.095
3.111
133.2
132.4
3c
X-ray
C13AH13Aꢂ ꢂ ꢂO1a
1.03(3)
1.03(3)
0.99(3)
0.95(3)
0.93(2)
2.36(3)
2.32(3)
2.62(3)
2.65(3)
2.68(3)
3.100(3)
3.156(3)
3.533(3)
3.572(3)
3.532(3)
133(2)
131(2)
153(2)
165(2)
153(2)
C13AH13Aꢂ ꢂ ꢂO2a
C9AH9ꢂ ꢂ ꢂO1 (ꢀ1 + x, y, z)
C12AH12Aꢂ ꢂ ꢂO1 (ꢀ1 + x, y, z)
C17AH17ꢂ ꢂ ꢂO2 (ꢀ1/2 + x, 1/2 + y, z)
B3LYPa
PW91a
C13AH13Cꢂ ꢂ ꢂO1a
1.088
1.088
2.274
2.250
3.104
3.091
131.6
132.5
C14AH14Bꢂ ꢂ ꢂO1a
C13AH13Cꢂ ꢂ ꢂO1a
C14AH14Bꢂ ꢂ ꢂO1a
1.095
1.096
2.255
2.230
3.101
3.086
132.4
133.3
a
Intramolecular.

O.F. Vázquez-Vuelvas et al. / Journal of Molecular Structure 987 (2011) 106–118
113
For compound 3c, the supramolecular arrangement shows that
the C(9) and C(12A) atoms at (x, y, z) act as a contact donor with the
same carbonyl O(2) atom in the molecule at (ꢀ1 + x, y, z), and these
interactions lead to the formation of ring R12 (7) (Fig. 5c; Table 4). In
addition, the methoxy O(1) atom at (x, y, z) acts as an acceptor of
the donor C(11) atom at (1/2 + x, 1/2 ꢀ y, z), and by translation a
chain C(4) is formed. Both motifs are running parallel to a axis.
1.40° and 1.55° and for 3c, 1.20° and 1.26°, respectively. The corre-
lation coefficients r between the experimental and the different
calculated geometric parameters were processed for the two func-
tionals [33] (Table 3). The data reflect that the two methods corre-
late well for the bond lengths and angles, being the B3LYP
functional approach the best, indicating the calculation precision
to be satisfactory.
Selected dihedral angles (Table 3), presented a pronounced dif-
ference between experimental and calculated results. In compound
1c, the largest deviation of the torsion angle O(1)AC(1)A
C(15)AC(20) with B3LYP and PW91 is of 10.91° and 12.73°, respec-
tively. In the same manner, the nitro group presents a deviation of
about 7° in the calculated torsion angle O(2)AN(1)AC(18)AC(17) re-
spect to the experimental data. For compound 2c, the main differ-
ence between calculated and experimental data is denoted by the
inverted sense of rotation of the torsion angles O(1)AC(1)A
C(2)AC(4), which showed a deviation of 9° and 8°, with B3LYP and
PW91, respectively (Table 3). In spite of this, the angle torsion
O(1)AC(1)AC(15)AC(20) is only slightly different from the experi-
mental. Thetwonitrogroupsdonotshowa differenttrendofthepla-
narity deviation commented above, in fact, the difference is larger in
the torsion angle O(2)AN(1)AC(18)AC(17) being roughly 13°, and
15° for the O(4)AN(2)AC(19)AC(18) dihedral angle. For 3c, the larg-
est difference in torsion is present around the C(1)AC(15) bond com-
pare 8.78° and 10.64° in the torsion angle O(1)AC(1)AC(15)AC(20)
for B3LYP and PW91, respectively. However, the change in the tor-
sion angle C(21)AO(2)AC(18)AC(17) of the methoxy group is of only
3.2°, but in different sense of rotation.
3.3. Experimental FTIR results
The FTIR data of compounds 1c, 2c and 3c are listed in Table 5
and the spectra showed in Figs. 6i, iv and vii, respectively. The main
signals are grouped in two regions, in the range of 3200–
2800 cmꢀ1 and from 1700 cmꢀ1 to 550 cmꢀ1. The second region
shows vibrational bands strongly mixed, therefore, the assignment
of the experimental bands was made by comparison with a visual-
ization of the shape of the different molecular vibrational modes
theoretically calculated for each structure.
Region 3200–2800 cmꢀ1. The weak bands observed from 3150
to 3000 cmꢀ1, can be assigned to the aromatic CAH bonds in-plane
stretching modes, as well as those corresponding to CAH stretch-
ing vibrational modes of the exocyclic alkene of the indoline moi-
ety. From 3000 to 2800 cmꢀ1, the corresponding symmetric and
asymmetric CAH stretching bands of the methyl groups are ob-
served. These weak bands resemble the frequencies recently re-
ported in the literature for 2,20-(1,4-phenylenedivinylene)bis-
1,3,3-trimethyl-indolenine dichloride [3].
Region 1700–550 cmꢀ1. The bands observed here show a conju-
gated carbonyl weak stretching band between 1625 and
1615 cmꢀ1. Aromatic C@C stretching weak bands are observed in
the range of 1598 to 1542 cmꢀ1. The corresponding very strong
bands for aliphatic C@C bonds are located from 1527 to
1516 cmꢀ1 [28]. The band corresponding to the N@O asymmetric
stretching was not observed due to potential overlapping by C@C
phenyl stretching bands appearing on the same region.
3.5. Vibrational and structural analysis
The calculated frequencies for the three compounds are listed in
Table 5, these results reveal a substantial difference in comparison
with the experimental values, due to neglection of harmonicity in
real systems. The calculated frequencies using the B3LYP func-
tional present an overestimation slightly larger than the values cal-
culated with the PW91 functional.
The overestimation of the computed wavenumbers is system-
atic and can be corrected by applying appropriate scaling factors
or scaling equations [34]. The values of the wavenumbers scaled
Medium bands corresponding to asymmetric and symmetric
CAH bending modes of methyl groups can be observed in the inter-
val of 1500 and 1300 cmꢀ1. The N@O symmetric stretching band is
strong and observed around 1340 cmꢀ1 in both 1c and 2c. Aro-
matic CAH in-plane bending vibrations are typical of this spectral
region.
by two factors (mscal) for the data calculated with the B3LYP/6-
From to 1300 to 1000 cmꢀ1, the bands corresponding to sym-
metric and asymmetric CAOAC vibrations of the methoxy group
attached to the aromatic ring in 3c are observed. The symmetric
stretching vibration appears in 1248 cmꢀ1 and the asymmetric
311G(d,p) and PW91/6-311G(d,p) methods are listed in Table 5.
Scott and Radom recommended scaling factors for HF and DFT cal-
culated frequencies [35]. However, there is no scaling factor for
B3LYP/6-311G(d,p) and PW91/6-311G(d,p), so the corresponding
to B3LYP/6-31G(d) and B3PW91/6-31G(d) factors were used,
0.9614 and 0.9573, respectively. The scaling equation procedure
suggested by Alcolea Palafox was used to obtain the predicted fre-
one in 1032 cmꢀ1
.
The region below 1000 cmꢀ1, exhibits the out of plane bending
CAH bond vibrations of the aromatic and alkene carbon double
bonds.
quencies [36,37] and they are listed in Table 5 as
tions used were, for B3LYP/6-311G(d,p) scaleq = 17.8 + 0.9614mcalc
and for PW91/6-311G(d,p) scaleq = 24.8 + 0.9501 calc. Both func-
mscaleq. The equa-
m
3.4. Geometrical analysis
m
m
tionals and both scaling procedures, reproduce wavenumbers with
comparable r.m.s. errors also listed in Table 5, and both can be used
for theoretical prediction of the FTIR spectra. The FTIR vibrational
frequency for the carbonyl bond C1AO1 for the three structures
presents a maximum difference of 72 and 15 cmꢀ1 when the
B3LYP/6-311G(d,p) and PW91/6-311G(d,p) levels are applied.
The experimental absorption frequencies, corresponding to the
non-planar conjugated systems, show that the carbonyl, aromatic
and aliphatic carbon–carbon double bond stretching bands appear
in the region from 1630 cmꢀ1 to 1500 cmꢀ1 for the three com-
pounds (Fig. 6; Table 5). This region corresponds to the group of
frequencies that allow observing conformational transitions for
The calculated structural parameters of 1c, 2c and 3c are listed
in Table 3. These results clearly resemble those obtained by the
crystal structure data analysis, a clear evidence of the proper
choice of the applied model. From these data one can clearly real-
ize that in general the calculated bond distances and angles are
slightly larger than those determined by single crystal X-ray dif-
fraction techniques. This being mainly due to the fact that theoret-
ical calculations model isolated molecules in the gas phase, rather
than molecules in a close packing environment.
The largest differences between the experimental and calcu-
lated bond lengths are for 1c with B3LYP and PW91, 0.018 Å and
0.021 Å, for 2c, 0.024 Å and 0.029 Å, and for 3c, 0.026 Å
y
a,b-unsaturated compounds.
0.032 Å, respectively (Table 3). In addition, the largest angle value
Taking into account that the phenyl group of the ketone
differences are for 1c with B3LYP and PW91, 1.80° and 1.81°, for 2c,
decreases the planar conformation of the three structures due to

Table 5
Observed and calculated B3LYP/6-311G(d,p) and PW91/6-311G(d,p) vibrational frequencies (cmꢀ1) for 1c, 2c and 3c.
Exp
FTIR
1c
B3LYP
PW91
Exp
B3LYP
PW91
Exp
B3LYP
PW91
Assignments
a
b
c
d
a
b
c
d
a
b
c
d
mcalc
mscal
mscaleq mcalc
mscal
mscaleq FTIR
mcalc
mscal
mscaleq mcalc
mscal
mscaleq FTIR
mcalc
mscal
mscaleq mcalc
mscal
mscaleq
2c
3c
3086, vw 3207
3042, vw 3187
3007, vw 3166
2964, vw 3097
2922, vw 3076
3083
3064
3044
2977
2957
3101
3082
3062
2995
2975
3133
3129
3097
3053
3021
2999
2995
2965
2923
2892
3001
2998
2967
2925
2895
3110, vw 3236
3082, w 3191
3008, vw 3168
2960, w 3160
2925, vw 3080
3039
3111
3068
3046
3038
2961
2922
2919
3129
3086
3064
3056
2979
2939
2937
3158
3140
3110
3051
3025
2983
2981
3023
3006
2977
2921
2896
2856
2854
3025
3008
2980
2924
2899
2859
2857
3056, vw 3207
3042, vw 3203
3005, w 3135
2960, w 3149
2929, vw 3134
2919, w 3036
2884, vw 3015
2832, vw 3002
1622, w 1684
1598, m 1646
3083
3079
3014
3027
3013
2919
2899
2886
1619
1582
3101
3097
3032
3045
3031
2937
2916
2904
1637
1600
3136
3129
3106
3092
3002
3002
2980
2941
1624
1603
3002
2995
2973
2960
2874
2874
2853
2815
1555
1535
3004
2998
2976
2963
2877
2877
2856
2819
1568
1548
m
m
m
m
m
m
m
m
m
m
m
m
m
m
m
CAH ip of C@C
CAH ip of phenyls
CAH ip aromatic rings
asCAH of CH3
asCAH of CH3
sCAH of CH3
sCAH of CH3
sCAH of CH3
C@O
2884, vw 3035
2855, vw 3023
1625, w 1687
1594, w 1648
1643
2918
2906
1622
1584
1580
2936
2924
1640
1602
1597
2983
2965
1625
1603
1593
2856
2838
1556
1535
1525
2859
2842
1569
1548
1538
2865, vw 3036
1615, m 1687
1581, m 1654
1636
1622
1590
1573
1640
1608
1591
1628
1614
1581
1558
1545
1513
1572
1558
1527
C@C ip aromatic rings
C@C ip phenyl rings +
C@C ip aromatic rings
C@C ip phenyl rings +
C@C
m
asN@O
asN@O
1573, m 1604
1527, vs 1583
1542
1522
1560
1540
1564
1551
1497
1485
1511
1498
1542, sh 1609
1516, vs 1579
1547
1518
1565
1536
1546
1555
1480
1489
1494
1502
m
1518, vs 1578
1517
1535
1553
1533
1487
1468
1500
1481
asN@O
1504, m 1539
1493, m 1524
1452, m 1491
1437, w 1465
1405, w 1433
1480
1465
1433
1408
1378
1338
1322
1497
1483
1451
1426
1395
1356
1340
1491
1476
1451
1416
1394
1356
1340
1427
1413
1389
1356
1334
1298
1283
1441
1427
1403
1370
1349
1313
1298
dCAH ip phenyl ring
dasCAH of CH3
Indole skeletal vibration
1488, m 1523
1457, m 1490
1435, w 1466
1464
1432
1409
1482
1450
1427
1480
1451
1416
1417
1389
1356
1431
1403
1370
1485, m 1525
1450, m 1492
1419, w 1478
1378, m 1387
1466
1434
1421
1333
1484
1452
1439
1351
1478
1452
1440
1352
1415
1390
1379
1294
1429
1404
1393
1309
dsCAH of CH3
m
C@C ip phenyl rings
1369, m 1410
1356
1324
1275
1373
1342
1293
1349
1311
1301
1291
1255
1245
1306
1270
1261
1365, s
1351, s
1392
1375
dsCAH of CH3
dCAH ip indole ring
1343, s
1377
1337, s
1386
1375
1333
1322
1275
1350
1340
1293
1319
1311
1299
1263
1255
1244
1278
1270
1259
m
m
sN@O
sN@O
1317, m 1326
1293, m 1326
Skeletal vibration
C@C ip phenyl ring
1310, w 1348
1299, w 1330
1296
1279
1314
1296
1348
1304
1290
1248
1306
1264
m
1297, w 1297
1275, w 1264
1247
1215
1265
1233
1261
1226
1207
1174
1223
1190
1275, m 1299
1248, w 1263
1249
1214
1267
1232
1260
1226
1206
1174
1222
1190
dCAH ip aromatic rings
dsCAH of C(CH3)2
1248, s
1215, s
1281
1230
1232
1183
1249
1200
1250
1202
1197
1151
1212
1167
masCarAOACal
1207, s
1219
1172
1160
1190
1178
1188
1173
1137
1123
1154
1139
Phenyl skeletal vibration
dCAH ip phenyl ring
dsCAH of C(CH3)2
1233, w 1251
1203
1221
1200
1149
1165
1187, w 1207
1188, vs 1262
1213
1231
1226
1174
1190
1218, m 1230
1183, w 1207
1183
1160
1200
1178
1189
1172
1138
1122
1154
1138
dCAH ip phenyl ring
dsCAH of C(CH3)2
dCAH ip phenyl ring
dCAH ip indole ring
Skeletal vibration of indole
Skeletal vibration
Skeletal vibration
dCAH ip phenyl ring
dCAH ip phenyl ring
mCAN of phenyl ring and def
Skeletal vibration
Deformation vibration indole
Phenyl deformation vibration
1174, vs 1207
1154, w 1195
1160
1149
1178
1167
1172
1156
1122
1107
1138
1123
1176, w 1198
1160, w 1186
1132, m 1153
1152
1140
1108
1170
1158
1126
1159
1153
1121
1110
1104
1073
1126
1120
1090
1161, w 1185
1132, m 1152
1118, w 1143
1139
1108
1099
1157
1125
1117
1155
1122
1108
1106
1074
1061
1122
1091
1078
1134, m 1153
1117, m 1144
1108
1100
1126
1118
1121
1098
1073
1051
1090
1068
1106, w 1127
1083
1101
1083
1037
1054
1088, w 1110
1071, m 1082
1068
1067
1040
1027
1085
1058
1045
1070
1061
1044
1024
1016
999
1041
1033
1017
1068, m 1085
1068
1047
1049, w 1031
1043
1027
1007
991
1061
1045
1024
1009
1056
1042
1011
998
1028
1015
1068
1107, m 1132
1050, w 1068
1027
1088
1027
1045
1106
1045
1034
1074
1043
990
1028
998
1007
1045
1016
1024
980
998
1048, w 1046
1021, w 1016
1006
977
1023
995
1023
988
979
946
997
963
1032, s
978,w
1058
997
940
901
1017
959
904
866
1035
976
922
884
1031
959
920
877
987
918
881
840
1004
936
899
858
msCarAOACal
974, vw
982
944
962
944
904
922
dCAH oop indole ring
dCAH oop phenyl ring
Skeletal vibration
Phenyl def vibration
Indole skeletal vibration
Skeletal vibration
1010, w 1010
971
906
989
923
971
933
930
893
947
911
941, m
917, m
956
929
919
893
937
911
928
896
888
858
906
876
929, m
855, vs
933, m
942
903, m
861
828
846
833
797
816

837, m
793, m
815
778
784
748
801
766
785
776
751
743
771
762
848, vs
797, vs
868
823
834
791
852
809
836
792
800
758
819
777
dCAH oop@CH and ar CH
Skeletal vibration
dCAH oop phenyl ring
Skeletal vibration
dCAH oop@CH and ar CH
dCAH oop@CH and ar CH
dCAH oop indol phenyl ring
Indole skeletal vibration
Skeletal vibration
886, m
868, m
848, s
903
894
867
825
868
859
834
793
886
877
851
811
881
860
840
793
843
823
804
759
862
842
823
778
804, m
781, m
751, m
742, s
717, vs
684, m
765
755
739
705
608
735
726
710
678
585
753
744
728
696
602
737
727
718
685
591
706
696
687
656
566
725
716
707
676
586
744, s
718, m
754
726
725
698
743
716
726
700
695
670
715
690
744, vs
703, m
751
713
722
685
740
703
725
696
694
666
714
686
697, m
685, w
708
682
681
656
698
673
688
670
659
641
678
661
Skeletal vibration
dCAH oop@CH and ar CH
Skeletal vibration
679, m
637, m
702
685
675
659
693
676
678
661
649
633
669
653
649, w
488
469
487
472
452
473
70.8
29.4
25.7
44.6
62.0
48.5
74.3
47.0
41.3
53.3
72.7
58.5
78.7
28.0
30.5
46.3
54.1
41.6 R.m.s. error
Legends of bond types is as follows:
m, stretching; d, bending; ip, in-plane; oop, out of plane; s, symmetrical; as, asymmetrical; def, deformation.
s, strong; vs very strong; m, medium; w, weak; vw, very weak; sh, shoulder; blank, not observed o measured.
a
Scaling factor: 0.9614.
b
Scaling equation:
m
scaleq = 17.8 + 0.9614mcalc
.
.
c
Scaling factor: 0.9573.
Scaling equation: mscaleq = 24.8 + 0.9501mcalc
d

Table 6
Experimental (dexp) and predicted (dpred) rcalc) for compounds 1c, 2c and 3c.
1H and 13C chemical shifts (ppm), and calculated GIAO isotropic magnetic shielding tensors (
Parameter
B3LYP
PW91
B3LYP
PW91
B3LYP
PW91
e
f
f
e
f
f
e
f
f
dexp
dpred
rcalc
dpred
rcalc
dexp
dpred
rcalc
dpred
rcalc
dexp
dpred
rcalc
dpred
rcalc
Proton
1c
2c
3c
C(2)AH
C(6)AH
C(7)AH
C(8)AH
C(9)AH
C(12)AH
C(13)AH
C(14)AH
C(16)AH
C(17)AH
C(18)AH
C(19)AH
C(20)AH
C(21)AH
5.91
7.24
7.06
7.25
6.85
3.34
1.85
1.85
8.04
8.24
6.02
7.15
6.96
7.12
6.63
3.17
2.04
1.91
7.76
8.38
25.3082
6.35
7.10
6.91
7.05
6.57
3.14
2.01
1.91
7.76
8.33
24.5743
23.7931
23.9868
23.8447
24.3449
27.9500
29.1400
29.2500
23.0993
22.4915
5.92
7.27
7.12
7.31
6.92
3.42
1.86
1.86
9.06
6.04
7.04
6.92
7.05
6.62
3.30
2.08
2.01
9.01
25.2056
6.40
7.02
6.90
7.00
6.59
3.27
2.04
2.00
8.97
24.4568
5.94
7.18
6.99
7.19
6.77
3.29
1.78
1.78
7.94
6.91
6.10
7.18
6.93
7.14
6.60
3.12
1.82
2.01
7.86
6.58
25.2890
6.39
7.11
6.88
7.07
6.54
3.10
1.82
2.01
7.86
6.60
24.6061
24.0983
24.3042
24.1341
24.6618
28.3555
29.5630
29.7067
23.4489
22.7846
24.0950
24.2271
24.0825
24.5634
28.2429
29.5883
29.6613
21.9193
23.7785
23.9173
23.8009
24.2492
27.8322
29.1641
29.2129
21.6768
24.1605
24.4143
24.1974
24.7601
28.3986
29.7590
29.5543
23.4469
24.7875
23.8616
24.0973
23.9099
24.4517
28.0040
29.3176
29.1242
23.0903
24.3939
9.10
9.06
9.29
9.50
21.6087
21.3767
9.21
9.50
21.4166
21.0993
8.24
8.04
8.46
8.31
22.7047
22.8576
8.41
8.34
22.4073
22.4868
6.91
7.94
3.82
6.99
8.35
3.77
24.3593
22.9307
27.7157
6.94
8.35
3.78
24.0359
22.5861
27.3011
aa
bb
rc
29.688
29.717
28.810
29.024
30.295
30.259
ꢀ0.9351
ꢀ0.9507
ꢀ0.9034
ꢀ0.9252
ꢀ0.9569
ꢀ0.9700
ꢀ0.9970
ꢀ0.9951
ꢀ0.9961
ꢀ0.9944
ꢀ0.9963
ꢀ0.9946
d
R.m.s.
0.19
0.24
0.24
0.29
0.20
0.21
Carbon-13
C(1)
C(2)
C(4)
C(5)
C(6)
C(7)
C(8)
C(9)
C(10)
C(11)
C(12)
C(13)
C(14)
C(15)
C(16)
C(17)
C(18)
C(19)
C(20)
C(21)
184.2
90.4
174.1
48.7
123.0
121.9
127.5
108.0
147.7
140.1
29.8
180.2
ꢀ5.9976
86.8959
ꢀ0.6604
125.6995
53.9595
54.7782
48.8549
71.1312
31.9038
33.4965
152.9089
157.7915
160.7118
27.5437
52.3679
53.5303
25.6074
51.9507
46.6777
179.8
93.2
172.8
54.4
122.4
122.5
127.6
106.1
143.9
143.5
27.5
ꢀ2.4581
84.9245
4.5958
124.0462
55.4896
55.3649
50.2387
71.8593
33.7180
34.1742
180.1
88.7
175.5
49.1
123.5
119.7
127.6
108.4
145.6
140.0
30.7
175.3
ꢀ1.3824
90.8200
ꢀ2.4083
125.6913
54.2088
53.8441
48.3566
69.9601
32.2080
33.0995
152.3410
158.5203
160.1160
31.7578
49.3897
27.2185
55.5650
25.2613
44.7499
174.6
2.3822
88.0392
2.7775
185.6
90.4
171.7
48.5
121.9
114.0
127.3
107.4
143.6
139.8
29.7
180.4
ꢀ6.8491
86.9337
2.0765
179.7
92.2
169.8
53.7
122.1
121.1
127.0
105.2
143.8
143.1
27.7
ꢀ2.9073
85.9457
7.1132
91.1
175.1
53.9
122.7
121.9
127.6
106.2
143.8
142.3
27.8
87.2
176.3
53.9
122.2
122.5
127.8
107.1
143.2
142.3
28.4
90.1
174.2
54.6
121.7
122.7
127.4
106.7
143.3
143.5
28.5
91.1
171.9
53.1
122.4
120.5
127.0
105.3
143.8
142.0
28.3
124.0378
55.9452
54.9210
50.1741
71.1625
34.0647
33.8203
150.4767
157.6267
158.5761
32.9681
52.0076
27.4879
58.4611
25.3863
47.9522
126.7906
54.1069
56.0680
49.2348
72.0308
31.5489
33.4358
152.8858
160.3591
156.6607
40.7370
49.4251
72.1591
12.3591
60.3039
44.8659
126.2352
125.0925
55.5946
56.5565
50.5736
72.7832
33.5711
34.1921
151.4521
159.0486
155.3361
41.9427
51.5528
72.5135
13.7660
60.6610
47.0740
123.7528
1511830
156.6184
22.7
22.7
23.1
20.3
22.2
19.5
22.5
22.5
22.5
21.0
21.4
20.5
23.6
23.6
21.2
24.7
20.2
23.9
159.3081
30.7709
53.5829
54.6728
26.5576
52.9370
47.9444
142.9
128.1
123.3
148.7
123.3
128.1
148.0
124.2
123.1
149.9
124.6
129.7
146.8
124.2
123.2
151.0
124.9
129.8
142.6
127.4
148.3
121.9
148.3
127.4
143.6
126.8
148.0
120.9
149.8
131.2
144.4
125.6
149.8
119.2
151.9
129.6
132.6
129.3
113.1
162.1
113.1
129.3
55.6
135.1
126.8
105.2
162.1
116.5
131.2
53.7
135.5
126.1
105.4
163.2
117.1
130.5
55.0
a
174.42
177.33
173.98
176.90
173.89
176.80
b
r
ꢀ0.9591
ꢀ0.9908
ꢀ0.9557
ꢀ0.9862
ꢀ0.9524
ꢀ0.9844
ꢀ0.9985
ꢀ0.9982
ꢀ0.9988
ꢀ0.9983
ꢀ0.9977
ꢀ0.9972
R.m.s.
2.63
2.88
2.34
2.80
3.28
3.61
a
b
c
d
e
f
Slope.
Intercept.
Correlation coefficient.
Root mean square error.
Experimental.
Scaling equation: dpred = a + brcalc
.

O.F. Vázquez-Vuelvas et al. / Journal of Molecular Structure 987 (2011) 106–118
117
3.6. 1H and 13C NMR analysis
Acknowledgements
The relations between the experimental 1H and 13C chemical
shifts (dexp) and the (GIAO Gauge-Independent Atomic Orbital)
Financial support by CGIC-UC (Coordinación General de Investi-
gación Científica de la Universidad de Colima, FRABA No. project
603/09) and CONACyT Grant Number 201625 for PhD formation
are gratefully acknowledged. We would like to thank to Alejandri-
na Acosta for support in the running of the NMR spectra. Finally the
authors would like to thank the Universidad de Guanajuato for
allowing the use of the GAUSSIAN03.
magnetic isotropic shielding tensors (
used in efficient implementation [40,41], are usually linear and de-
scribed by the following equation: dexp = a + b calc. The slope and
intercept of the least-square correlation line is used to scale the
GIAO isotropic absolute shielding, , and to predict chemical shifts,
rcalc), which are now widely
r
r
dpred = a + brcalc (Fig. S1 of the Supplementary information). In the
present case, for the three compounds 1c, 2c and 3c, the r.m.s. error
denotes a very small difference when comparing calculated versus
experimental data, finding that the better calculations are obtained
with the B3LYP functional, for both 13C and 1H (Table 6). The same
behavior is showed by the correlation coefficients r, denoting that
the B3LYP/6-311++G(3df,3pd) and PW91/6-311++G(3df,3pd)
methods were suitably applied and reproduce well the experimen-
tal chemical shifts for both nuclei.
Appendix A. Supplementary material
Supplementary data associated with this article can be found, in
the online version, at doi:10.1016/j.molstruc.2010.12.001.
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