Structural investigation of (2E)-2-(ethoxycarbonyl)-3-[(4-methoxyphenyl)amino]prop-2-enoic acid: X-ray crystal structure, spectroscopy and DFT

Article abstract of DOI:10.1016/j.molstruc.2016.04.090

The title compound, (2E)-2-(ethoxycarbonyl)-3-[(4-methoxyphenyl)amino]prop-2-enoic acid is characterized by means of X-ray crystallography, spectroscopic methods and quantum chemical calculations. The title compound crystallizes in centrosymmetric space g

Full text of DOI:10.1016/j.molstruc.2016.04.090

Journal of Molecular Structure 1119 (2016) 259e268
Contents lists available at ScienceDirect
Journal of Molecular Structure
journal homepage: http://www.elsevier.com/locate/molstruc
Structural investigation of (2E)-2-(ethoxycarbonyl)-3-[(4-
methoxyphenyl)amino]prop-2-enoic acid: X-ray crystal
structure, spectroscopy and DFT
Perumal Venkatesan a, Venkatachalam Rajakannan b, Natarajan S. Venkataramanan c,
,
, *
Andivelu Ilangovan a **, Tom Sundius d, Subbiah Thamotharan e
a School of Chemistry, Bharathidasan University, Tiruchirappalli, 620 024, Tamilnadu, India
b Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Chennai, 600 025, India
c Centre for Computational Chemistry and Materials Science, SASTRA University, Thanjavur, 613 401, India
d Department of Physics, University of Helsinki, P.O. Box 64, FIN-00014, Helsinki, Finland
e Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA University, Thanjavur, 613 401,
India
a r t i c l e i n f o
a b s t r a c t
Article history:
The title compound, (2E)-2-(ethoxycarbonyl)-3-[(4-methoxyphenyl)amino]prop-2-enoic acid is charac-
terized by means of X-ray crystallography, spectroscopic methods and quantum chemical calculations.
The title compound crystallizes in centrosymmetric space group P21/c. Moreover, the crystal structure is
primarily stabilized through intramolecular NeH/O and OeH/O and intermolecular NeH/O and
CeH/O interactions along with carbonyl/carbonyl and CeH/C contacts. These intermolecular in-
teractions are analysed and quantified by using Hirshfeld surface analysis, PIXEL energy, NBO, AIM and
DFT calculations. The overall lattice energies of the title and parent compounds suggest that the title
compound is stabilized by a 4.5 kcal molꢀ1 higher energy than the parent compound. The additional
stabilization force comes from the methoxy substitution on the title molecule, which is evident since the
methoxy group is involved in the intermolecular CeH/O interaction as an acceptor. The vibrational
modes of the interacting groups are investigated using both experimental and theoretical FT-IR and FT-
Raman spectra. The experimental and theoretical UVeVis spectra agree well. The time dependent DFT
spectra show that the ligand-to-ligand charge transfer is responsible for the intense absorbance of the
compound.
Received 24 December 2015
Received in revised form
25 April 2016
Accepted 25 April 2016
Available online 27 April 2016
Keywords:
Malonic acid halfeester
Hirshfeld surface
Intermolecular interactions
PIXEL
HOMO-LUMO
© 2016 Elsevier B.V. All rights reserved.
1. Introduction
geminal half-ester family, have numerous applications as in-
termediates in the synthesis of virantmycin [2], amino acids [3],
Ester hydrolysis is one of the most fundamental reactions in
organic chemistry [1]. The reaction of partial hydrolysis of diesters
generates half-esters, which consist of both a carboxylic acid and an
ester moiety. Half-esters can be classified as geminal, vicinal,
vinylic, aromatic and simple half-esters depending on the substi-
tution positions of acid and ester moieties. Half-esters are versatile
building blocks for a variety of natural products and biologically
active compounds. Malonic acid half-esters, which belong to the
behydroxy esters or beamino esters [4] and tri-carbonyl com-
pounds [5]. The synthesis of functionalized malonic acid half-ester
derivatives has been reported by our group [6]. The crystal struc-
tures of these derivatives and the invariant and variable intermo-
lecular interactions in them have been examined using Hirshfeld
surfaces and PIXEL energy calculations [7]. We have also studied
the crystal structure of the L-phenylalanine derivative (2E)-2-
(ethoxycarbonyl)-3-[(1-methoxy-1-oxo-3-phenylpropan-2-yl)
amino] prop-2-enoic acid, wherein we observed a pushepull
network formed by the geminal methylene malonic acid and amine
group at vicinal position of the double bond. The presence of a
chiral center in the phenylalanine and the push pull environment
helps to show good second harmonic generation (SHG) activity [8].
* Corresponding author.
** Corresponding author.
E-mail addresses: ilangovanbdu@yahoo.com (A. Ilangovan), thamu@scbt.sastra.
edu (S. Thamotharan).
http://dx.doi.org/10.1016/j.molstruc.2016.04.090
0022-2860/© 2016 Elsevier B.V. All rights reserved.

260
P. Venkatesan et al. / Journal of Molecular Structure 1119 (2016) 259e268
In this work, we present the crystal and molecular structure of
2.2. Single crystal X-ray diffraction
one of the malonic acid half-ester derivatives, (2E)-2-(ethox-
ycarbonyl)-3-[(4-methoxyphenyl) amino] prop-2-enoic acid. The
structure of the title compound is optimized in the gas phase using
the DFT level of theory with a 6-31þG(d) basis set. The harmonic
vibrational frequencies are calculated for this compound at the
same level of theory. The calculated spectra of this compound are
compared with experimentally observed FT-IR and Raman spectra.
Furthermore, the intermolecular interactions in the crystal struc-
ture of the title compound are visualized using a Hirshfeld surface
diagram [9,10]. The relative contributions of various intermolecular
interactions are quantified using decomposed two dimensional
fingerprint plots [11,12]. Furthermore, we have used the PIXEL
method [13e15] to quantify the strengths of the various intermo-
lecular interactions present in the crystal structure of the title
compound. Atoms-in-molecules (AIM) and natural bond orbitals
(NBO) analysis shows the existence of various intra- and intermo-
lecular interactions.
Xeray intensity data were collected for the title compound at
room temperature (296 K) using a Bruker SMART APEXeII CCD
diffractometer (MoK
a,
l
¼ 0.71073 Å). The crystal structure of the
title compound was solved by the SIR92 program [16] and all the
non-hydrogen atoms were refined anisotropically using the
SHELXL2014 program [17]. The positions of the amine and hydroxy
hydrogen atoms were located from a difference Fourier map and
refined freely along with their isotropic displacement parameters.
The methyl hydrogen atoms were constrained to an ideal geometry
(CeH ¼ 0.98 Å), with Uiso(H) ¼ 1.5Ueq(C), but were allowed to rotate
freely about the CeC bonds. The remaining H atoms were placed in
idealized geometrical positions and constrained to ride on their
parent atoms. The thermal ellipsoidal and crystal packing figures
were produced using the programs PLATON [18] and MERCURY
[19], respectively. CCDC 1438183 contains the supplementary
crystallographic data for this paper. These data can be obtained free
of charge from The Cambridge Crystallographic Data Centre via
www.ccdc.cam.ac.uk/data_request/cif.
2. Experimental
2.1. Synthesis of (2E)-2-(ethoxycarbonyl)-3-[(4-methoxyphenyl)
amino] prop-2-enoic acid
2.3. Computational details
All the density functional theory calculations were performed
with the Gaussian 09 program package [20]. From the X-ray crystal
structure analysis and PIXEL energy calculation, four different
dimeric pairs were identified based on their interaction energies.
These four dimers were further subjected to structural optimization
without any geometrical constraints using a dispersion corrected
M05-2X functional [21]. In previous studies, the use of the M05-2X
functional has provided accurate prediction of the molecular ge-
ometries and binding energies for materials with hydrogen
bonding interactions [22,23]. To include the effect of the ethanol
solvent, we used the CPCM method, with sphere radii optimized for
COSMO-RS, as proposed by Klamt [24]. In order to confirm the
proper convergence to minima and to compute the IR spectra,
vibrational frequencies were computed and we confirmed that no
negative frequencies were present.
The interaction energy Eint was computed for four different di-
mers after incorporating the zero point vibrational energy (ZPVE)
and counterpoise correction [25]. Partial charges were computed at
the M05-2X/6-31þG(d) level of theory using the natural bond or-
bitals (NBO) program as implemented in Gaussian 09 program. The
quantitative molecular electrostatic potentials (MESP) for all sys-
tems were computed on the 0.001 a.u. isodensity surface. AIM to-
pological analysis was carried out using the AIM2000 package. For
the optical part, the calculations of the properties have been carried
out in the framework of time dependent-DFT (TDDFT) by extracting
a minimum of 100 roots with the time dependent Kohn-Sham
formalism [26]. For comparison, the calculated discrete spectra
have been normalized and their peaks broadened with a Gaussian
function of fwhm ¼ 0.02 eV.
The title compound was prepared by BF3$OEt2 mediated hy-
drolysis of the geminal diester (Scheme 1) [6]. To a solution of
diethyl 2-[(4-methoxyphenyl)amino] methylene malonate (1.0 g,
3.4 mmol, 1.0 equiv.) in CHCl3 (3 ꢁ w/v), BF3$OEt2 (856
mL,
3.4 mmol, 1.0 equiv.) was added and stirred at 296 K and the
progress of the reaction was monitored by TLC. The reaction
mixture was quenched with water (1 ꢁ w/v) and extracted with
chloroform (3 ꢁ 10 mL). The combined organic layer was dried
(anhydrous Na2SO4) and evaporated in a rotary evaporator under
vacuum. The crude product obtained was passed through a short
silica gel column using a hexane and ethyl acetate mixture (8:2, v/v)
as eluent to obtain a yellow solid (mp: 110 ꢂC, 0.80 g, yield 90%). The
title compound recrystallized from ethanol by the slow evaporation
method. 1H NMR (400 MHz, CDCl3)
d
:1.37 (t, 3H, J ¼ 7.2 Hz), 3.82 (s,
3H), 4.33 (q, 2H, J ¼ 7.2 Hz), 6.94 (d, 2H, J ¼ 12.0 Hz), 7.13 (d, 2H,
J ¼ 12.0 Hz), 8.39 (d, 1H, J ¼ 13.6 Hz), 11.64 (d, 1H, J ¼ 13.6 Hz), 13.01
(s, 1H). 13C NMR (100 MHz, CDCl3)
119.5, 131.9, 152.0, 157.9, 170.1, 170.8.
d: 14.3, 55.6, 61.3, 88.7, 115.1,
The infrared spectra of the title compound were recorded in the
frequency region 4000e400 cmꢀ1 on the Perkin Elmer FTeIR
spectrophotometer with a resolution of 1 cmꢀ1 using the KBr pellet
technique. The Raman spectrum was recorded using the iRaman
Plus Raman spectrometer (B &W Tek, USA) and the 532 nm laser
line was used for excitation. The spectral resolution was 4 cmꢀ1. The
1H (Fig. S1) and 13C NMR spectra (Fig. S2) for the title compound are
presented in the supplementary information (SI) section. The
UVeVis absorption spectrum was recorded (200e700 nm) on a
Eppendorf Biospectrophotometer in ethanol solvent.
Scheme 1. Synthesis of malonic acid half-ester. Parent compound R¼ eH and title compound R¼ eOCH3.

P. Venkatesan et al. / Journal of Molecular Structure 1119 (2016) 259e268
261
3. Results and discussion
bonding interactions. The methoxy oxygen atom (O5) is also
participating in an intermolecular CeH/O interaction. As observed
in related malonic acid half-ester derivatives [7], two invariant
intramolecular NeH/O and OeH/O hydrogen bonding in-
teractions are seen in the crystal structure of the title molecule. As
shown in the ORTEP diagram (Fig. 1), these intramolecular
hydrogen bonding interactions are generating two fused pseudo
six-membered rings. These rings can be described as S(6)eS(6)
graph-set motifs [27].
3.1. Description of crystal structure
Single crystal X-ray analysis of the title compound reveals that
the crystal has the space group P21/c and belongs to the monoclinic
system. The crystal data and refinement parameters are presented
in Table 1. The hydrogen bonding interactions that stabilize the
crystal structure are listed in Table 2. We have determined a series
of crystal structures of malonic acid half-ester derivatives by X-ray
crystallography earlier and analysed how different functional
groups substituted at different positions on the phenyl ring alter
the crystal packing in detail [7]. The malonic acid half-ester de-
rivatives which include the title compound have a common skeletal
framework consisting of acid and ester groups at the geminal po-
sition and an N-vinyl aniline moiety. In the title compound, a
methoxy group is substituted at the para-position on N-vinyl ani-
line moiety.
The dihedral angles between the mean planes formed by
different sets of atoms for the title molecule and its parent molecule
are given in Table S1. Briefly, the phenyl ring is coplanar with the
acid, ester and methoxy moieties. The dihedral angle is in the range
of 2e5ꢂ. In the parent molecule, the phenyl ring is oriented at an
angle of ~34ꢂ with both acid and ester moieties. This clearly in-
dicates that the phenyl ring is undergoing a slight rotational
movement. This observation is further supported by the variations
of two torsion angles C7eN1eC1eC2 [177.97(14)ꢂ in the title
compound and 147.45(11)ꢂ in the parent compound] and
C7eN1eC1eC6 [e2.3(2)ꢂ in the title compound and ꢀ32.44(16)ꢂ in
the parent compound]. The root mean square deviation (RMSD)
between the pair of title and parent molecules is 0.129 Å. The
structural superimposition of the title and the parent compounds is
shown in Fig. S3.
In the crystal structure, molecules dimerize with R22 ð12Þ motif
through an invariant intermolecular NeH/O hydrogen bonding
interaction between the amine group and the carbonyl group of the
carboxylic acid moiety as observed in the parent compound
(Fig. 2(a)). This dimer is further stabilized by three additional non-
covalent interactions. Two of them are intermolecular CeH/O
interactions (C2eH2/O2 and C2eH2/O1) and
a carbon-
yl/carbonyl (C]O/O]C) contact with a distance of 2.896 Å. This
distance is slightly longer in the title compound when compared
with its parent crystal structure (2.789 Å). Moreover, the inter-
molecular C2eH2/O2 and C2eH2/O1 interactions produce two
independent R22ð16Þ motif as shown in Fig. 2(b). The former inter-
molecular interaction is observed in the crystal structure of the
parent molecule, while the latter interaction is only observed in the
title molecule. The substitution of the 4-methoxy group on the
phenyl ring provides an additional stabilization to the crystal
structure. As mentioned earlier, the methoxy oxygen (O5) is
involved in an intermolecular C6eH6/O5 interaction. This inter-
action links the molecules into a C(5) chain motif which runs par-
allel to the b axis as displayed in Fig. 3(c).
It is worthy to note that even though the title and its parent
molecules superimpose well, there is a difference observed in these
structures for the interconnection of NeH/O hydreon bonded
dimeric molecules. In the parent crystal structure, adjacent dimers
are interconnected by C11/O3 contacts. In contrast, this interac-
tion is absent in the title molecule. However, dimeric molecules in
one layer are interconnected by dimeric molecules in an adjacent
layer by C11eH11A/C9 interactions. As shown in Fig. 3(a), this
In the crystal structure of the title compound, amine and hy-
droxy groups act as donors and carbonyl groups (atoms O2 and O3)
of carboxylic acid and ester moieties act as acceptors for various
intra-and intermolecular NeH/O, OeH/O and CeH/O hydrogen
Table 1
The crystal data and refinement parameters of the title compound.
Empirical formula
C13 H15 N O5
Formula weight
T (K)
265.26
296(2)
Wavelength (Ǻ)
Crystal system
Space group
a (Ǻ)
0.71073
Monoclinic
P21/c
7.7905(2)
b (Ǻ)
7.3567(2)
c (Ǻ)
23.7906(7)
90
98.358(2)
90
a
b
g
(ꢂ)
(ꢂ)
(ꢂ)
V (Ǻ3)
1349.01(6)
Z
4
Calculated density (Mg/m3)
1.306
0.101
560
Absorption (mmꢀ1
F(0 0 0)
)
Crystal size (mm)
q
0.25 ꢁ 0.20 ꢁ 0.20
(ꢂ)
2.643e28.417
Limiting indices
Reflections collected/unique, (Rint
ꢂ)/Completeness (%)
ꢀ10 ⩽ h ⩽ 9, ꢀ8 ⩽ k ⩽ 9, ꢀ31 ⩽ l ⩽ 31
3313/2261, (0.0241)
(25.42)/99.9
)
(q
Refinement method
full-matrix least-squares on F2
3313/0/181
Data/restraints/parameters
Goodness-of-fit (GOF) on F2
1.054
Final R indices [I > 2
s
(I)]
R1 ¼ 0.0449, wR2 ¼ 0.1280
R1 ¼ 0.0669, wR2 ¼ 0.1435
0.157 and ꢀ0.147
R indices (all data)
Largest difference in peak and hole (e Aꢀ3
)

262
P. Venkatesan et al. / Journal of Molecular Structure 1119 (2016) 259e268
Table 2
Various intra- and intermolecular interactions observed in the crystal structure of the title compound and key contacts visible on the HS are labelled.
DeH/A
DeH
H/A
D/A
DeH/A
Symmetry
Label
O1eH1O/O3]C10
N1eH1N/O2]C9
N1eH1N/O2]C9
C2eH2/O1eC9
C2eH2/O2]C9
C9]O2/O2]C9
C8/C9
0.899(19)
0.875(16)
0.875(16)
0.93
1.70(2)
2.046(16)
2.608(17)
2.62
2.5466(19)
2.6845(16)
3.4122(19)
3.441(2)
155.3(17)
129.0(13)
153.2(13)
147.0
ꢀx+2, ꢀy, ꢀz
1
2
3
4
5
6
7
ꢀx+2, ꢀy, ꢀz
0.93
2.48
3.333(2)
153.3
ꢀx+2, ꢀy, ꢀz
2.8958(17)
3.3869(21)
3.755(2)
ꢀx+2, ꢀy, ꢀz
ꢀx+2, ꢀy+1, ꢀz
ꢀx+1, ꢀy+1, ꢀz
ꢀx+2, y+1/2, ꢀz+1/2
C11eH11A/C9
C6eH6/O5
0.97
0.93
2.90
2.69
147.5
146.6
3.505(2)
compound are 2.9, 2.0 and 3.3%.
The intermolecular potential is evaluated using PIXEL method
[13e15] which deals with the energy partitioned into Coulombic,
polarization, dispersion and repulsion terms. The interaction en-
ergy is calculated for different pairs of molecules that are inter-
connected by various intermolecular interactions. The distances
involving hydrogen atoms are moved to their neutron values before
the calculation. The electron density of the molecule has been ob-
tained at the MP2/6-31G** level of theory using Gaussian 09. The
overall lattice energies of the title compound and its parent com-
pound are summarized in Table 3. The lattice energies of these
structures suggest that the title compound is stabilized by
4.5 kcal molꢀ1 more than the parent compound. This additional
stabilization is achieved by the involvement of methoxy substitu-
tion in the intermolecular interaction as mentioned earlier. It is also
interesting to note that the dispersion contribution is nearly the
same in both the title and parent crystal structures. However, there
are variations (from 5.6 to 8.1 kcal molꢀ1) in the energies of the
Coulombic, polarization and repulsion energies observed in these
crystal structures.
Fig. 1. The ORTEP diagram and atomic labelling scheme of the title compound. The
intramolecular NeH/O and OeH/O hydrogen bonding interactions are indicated by
dashed lines.
interaction can be described as a R22ð12Þ motif. The molecular di-
mers are arranged as layers and adjacent layers are further inter-
connected by C8/C9 contacts as observed in the parent compound
(Fig. 3(b)).
Various energy components for interacting molecular pairs
along with the centroid-to-centroid distance between the inter-
acting pair of molecules are listed in Table 4. As mentioned earlier,
the invariant intermolecular NeH/O hydrogen bonding interac-
tion along with additional CeH/O interactions forms a molecular
dimer. The interaction energy (ꢀ12.4 kcal molꢀ1) for this dimer is
found to be similar with a related structure where the methyl group
is substituted at the para position on the phenyl ring [7]. Based on
the energetics, this interaction makes a more significant contribu-
tion to the crystal packing when compared to other types of in-
teractions observed in the crystal structure. As mentioned earlier, a
non-covalent interaction is observed between atom C8 in one layer
and atom C9 in the adjacent layer. The energy for this interaction
is ꢀ10.5 kcal molꢀ1. The second most significant contribution to the
crystal packing comes from this interaction. The strength of this
interaction is found to be similar to related structures [7]. Another
interaction is (C11eH11A/C9), which links the adjacent layers in a
similar way as the C8/C9 interaction (Fig. 3(b)). The interaction
energy for the former is being ꢀ7.0 kcal molꢀ1. It is worthy to note
that this contact is not visible on the HS and the distance between
the interacting atoms is slightly longer (the sum of the van der
Waals radiiþ0.1 Å). The methoxy group is participating in an
3.2. Hirshfeld surface analysis and PIXEL energy calculation
The Hirshfeld surface (HS) and the two dimensional fingerprint
plots are generated based on the de and di distances using Crystal
Explorer 3.1 [28]. The former is the distance from the HS to the
nearest atom outside the surface, while the latter is the distance
from the nearest atom inside the surface. This analysis is used to
identify the various intermolecular contacts and their relative
contributions in the crystal structure. The HS diagram, decomposed
two dimensional fingerprint plots and the relative contributions of
the various intermolecular interactions to the HS area for the
crystal structure of the title compound are displayed in Fig. 4. The
result suggests that the intermolecular H/H contacts have a major
contribution (42.8%) to the crystal packing of the title compound as
observed in related structures [7]. These contacts are relatively
comparable (44.2%) with that of the parent compound. The relative
contributions of the O/H/H/O and C/H/H/C contacts are 29.2%
and 18.9%, respectively. The relative contributions of the corre-
sponding contacts are 27% and 18.6% in the parent compound. It is
of interest to note that the O/H/H/O contacts are slightly
increased (~2%) in the title compound. This increment is a conse-
quence of the presence of the methoxy substitution on the phenyl
ring. The other intermolecular contacts such as O/C/C/O, N/H/
H/N and C/C contacts are contributing 2.8, 2.3 and 1.9%,
respectively to the crystal packing of the title compound. The
relative contributions of the corresponding contacts in the parent
intermolecular
C6eH6/O5
interaction. This
interaction
scores ꢀ6.1 kcal molꢀ1. As can be seen from Table 4, the least
contribution to the crystal packing comes from this interaction.
However, this interaction provides an additional stabilization to the
crystal structure.
3.3. DFT and wavefunction analysis
The bond lengths, angles and torsion angles derived from gas

P. Venkatesan et al. / Journal of Molecular Structure 1119 (2016) 259e268
263
Fig. 2. (a) Part of the crystal structure showing various intermolecular interactions forming a molecular dimer with R22ð12Þ for NeH/O interaction. (b) Intermolecular CeH/O
interaction forming a molecular dimer with R22ð16Þ motif. (c) An intermolecular CeH/O interaction links the molecules into a C(5) chain motif.
phase DFT study are compared with the geometric parameters
determined from X-ray analysis. The comparative geometric pa-
rameters are listed in Table S2. The structural overlay is performed
in order to compare the experimental structure with that obtained
from the gas phase geometry optimization (Fig. S4, SI). The RMSD
between X-ray and optimized structures is 0.269 Å. It is of interest
to note that the 4eOMe substituted phenyl ring shows a twist by
~30ꢂ when compared with the optimized structure. This larger
deviation might be a consequence of the involvement of atom O5 in
an intermolecular interaction in the crystal structure. Obviously, no
such interaction exists in the isolated molecule. Two torsion angles
(C7eN1eC1eC2 and C7eN1eC1eC6) indicate this deviation
(Table S2, SI). Moreover, the inclusion of intrinsic solvent (ethanol)
has only a marginal effect.
To understand the nature of interaction between the monomers
(within dimers) and the relative strength of the four different
dimeric pairs that were identified as mentioned earlier, they are
subjected to complete optimization. The optimized structure of
dimer-I is shown in Fig. S5(a) , which is found to be stabilized by
two NeH/O type hydrogen bonds, and four CeH/O type in-
teractions as observed in the crystal structure. The dimer-II
(Fig. S5(b)) is found to be 0.002 kcal molꢀ1 higher in energy than
the dimer-I. It is of interest to note that the energy difference be-
tween dimer-I and dimer-II is calculated to be 1.9 kcal molꢀ1 using
PIXEL method. Fig. S5(c and d) show the optimized geometries of
dimer-III and dimer-IV, respectively. The former dimer is
0.803 kcal molꢀ1 higher in energy than dimer-I, while the latter is
5.589 kcal molꢀ1 higher in energy than dimer-I. The optimized
structure of dimer-III has four intermolecular hydrogen bonding
interactions, whereas dimer-IV has two interactions. Thus, it is
evident that with the increase in the number of intermolecular
interactions, and the interaction energy of the dimers increases.
Fig. S6(a) shows the molecular electrostatic potential (MEP) of
the isolated monomer where the location of the various most
positive and negative potentials is indicated, and the electrostatic
potential maxima with the atom numbering and the values desig-
nated as Vs,max and Vs,min, are listed in Table 5. To understand the
nature of interactions, and to identify the reason for the nearly iso-
energetic geometries of dimer-I and dimer-II (Fig. S6(b and c)), we
analysed the quantitative MEP. As shown in Table 5 and Fig. S6(a),
the favourable sites for electrophilic attack are concentrated to the
regions around the carboxylic group, the carbonyl group and on the
oxygen atom. On the contrary, regions of positive electrostatic
potential are found on the hydrogen atoms on the benzene ring and
on the methyl group. The most striking feature of Fig. S6(b) is the
positive electrostatic potential at the end benzene hydrogen atoms
that are capped by the negative potentials of the carboxylic group
with a large electronegative domain, thereby giving rise to a
directional interaction. In dimer-II, we observed that the negative
potentials on the carboxylic group are capped by the positive re-
gions on the alkyl chain. Thus the dimers are formed by interactions
of opposite electrostatic regions.
To contemplate the ESP results, we carried out AIM analysis on
the dimer-I and dimer-II. The molecular graphs of these dimers

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P. Venkatesan et al. / Journal of Molecular Structure 1119 (2016) 259e268
Fig. 3. (a) Part of the crystal structure showing an intermolecular C11eH11A/C9 interaction links the neighbouring molecular dimers with R22ð12Þ motif. (b) The intermolecular
C8/C9 and C11eH11A/C9 interactions links two adjacent layers.
show the existence of different types of bonding (Fig. 5). In dimer-I,
we observed seven intermolecular bond critical bonds (BCP's). The
computed topological electron density at the BCP's are in the range
of 0.021e0.017 a.u. These values are comparable with those of
predicted values for hydrogen bonding interactions [29]. Further-
more, an intermolecular BCP between the carbonyls (C]O/O]C)
is observed with an electron density of 0.010 a.u. Thus in dimer-I,
the major attractive interactions are the hydrogen bonds. In
dimer-II, nine BCP's are observed which includes N/O, C/C, C/O
types of bonds in addition to the hydrogen bonds. This accounts for
the near degeneracy in the interaction energy between dimer-I and
II. The existence of intermolecular C/C bonds which are rarely
observed have been identified in this crystal structure.
Delocalization of the electron density between occupied bonds
or lone pair NBO orbitals and unoccupied antibonding orbitals
correspond to stabilizing donoreacceptor interactions. Further-
more, the larger the second-order perturbation (E(2)) value, the
more intensive is the interaction between the donor and the
acceptor. The most important acceptoredonor interactions with
high E(2) for dimer-I and II are presented in Table 6. In dimer-I, the
highest interaction energy (8.49 kcal molꢀ1) is observed for the
transfer of the lone pair electrons of the oxygen atom (O2) into the
antibonding orbital of the amine hydrogen. We have also observed
charge transfer from the lone pair electrons of the oxygen atom
(O1) to the antibonding orbital of the hydrogen atom (H2) of the
benzene ring with an interaction energy of 1.23 kcal molꢀ1. It is
worthy to note that these two intermolecular interactions are
relatively more stabilizing dimer-I than other interactions. The
optimized dimer-II is mainly stabilized by a C8/C9 intermolecular
contact with an interaction energy of 1.36 kcal molꢀ1, which sup-
ports what was found from the AIM analysis.
monomer's in the crystal structure, we considered the most stable
dimer-I and dimer-II for the simulation of IR and Raman spectra.
The experimental and the simulated FT-IR and Raman spectra are
displayed in Fig. 6. It is clearly visible from the figure that the
simulated spectra resemble the experimental spectra. The sec-
ondary amine NeH stretching and carboxylic acid OeH vibrations
are usually observed in the range of 3400e3250 and 3300-
2500 cmꢀ1, respectively [30]. In the monomer, the computed NeH
stretching is observed at 3437 cmꢀ1. The corresponding vibration is
calculated at 3477 cmꢀ1 in the dimer-I complex and at 3502 cmꢀ1 in
the dimer-II. The OeH stretching is calculated at 3409, 3348
3280 cmꢀ1 in the monomer, dimer-I and dimer-II, respectively. In
the FT-IR spectrum, a peak is observed at 3214 cmꢀ1, which could
be assigned for NeH or OeH vibrations. It is of interest to note that
both NeH and OeH groups are involved in intra-and intermolec-
ular hydrogen bonding interactions. The spectral blue shift in-
dicates the involvement of the band in hydrogen bond formation
between the intermolecular species. The C2eH2 stretching is
observed at 3070 cmꢀ1 in IR and at 3079 cmꢀ1 in Raman. The
corresponding vibration is calculated at 3240 cmꢀ1 in the monomer
and at 3265 cmꢀ1 in the dimer-I. Again there is a spectral blue shift
supporting the possible involvement of a hydrogen bonding inter-
action and an intermolecular C2eH2/O interaction in the dimer-I
formation. The C8eC9 stretching is calculated at 1688, 1700 and
1692 cmꢀ1 in the monomer, dimer-I and dimer-II, respectively.
There is a peak observed at 1603 cmꢀ1 in Raman which could be
assigned for this vibration. The computed stretching frequency for
the C8eC9 in the monomer is at 1521 cmꢀ1, which gets red shifted
to 1527 cmꢀ1 in dimer-II. This shows that dimer-II, which is a part of
the crystal structure is stabilized by a C8/C9 intermolecular
interaction.
The absorption spectrum of the title compound is computed in
ethanol solvent using the TDDFT method. In Fig. 7(a), we have
plotted the experimental and theoretical spectra, which are in good
agreement. The optical properties are governed by the frontier
3.4. Spectral analysis
To understand the nature of interaction between the

P. Venkatesan et al. / Journal of Molecular Structure 1119 (2016) 259e268
265
Fig. 4. (aec) Different orientations of Hirshfeld surface mapped with dnorm and potential intermolecular contacts are labelled (see Table 2). (dej) Two dimensional fingerprint plots
for various intermolecular interactions. Various reciprocal close contacts and their contributions are indicated. (k) The relative contributions (in %) of various intermolecular
contacts.

266
P. Venkatesan et al. / Journal of Molecular Structure 1119 (2016) 259e268
Table 3
molecular orbitals compositions and the HOMO and LUMO energy
levels (Fig. 7(b)). The HOMO orbitals are localized over the phenyl
rings, while the LUMO orbitals are localized over the alkyl and the
carbonyl groups. The simulated spectra show an intense absor-
bance at the ultraviolet wavelength of 301 nm, which is mainly due
to the transfer of charge from the HOMO orbital to the LUMO orbital
Lattice energies (kcal molꢀ1) partitioned into Coulombic, polarization, dispersion
and repulsion contributions for title and parent compounds.
Compound
ECoul
Epol
ꢀ4.4
EDisp
Erep
ETot
Parent compound [7]
Present study
ꢀ13.7
ꢀ5.6
ꢀ30.9
ꢀ31.4
19.8
14.2
ꢀ29.3
ꢀ33.8
ꢀ11.0
Table 4
PIXEL intermolecular interaction energies (kcal molꢀ1) between molecular pairs related by a symmetry operation in the crystal structure.
Centroid-to-centroid distance of molecular pair
7.175
Ecoul
Epol
Edisp
Erep
Etot
Symmetry
Important interactions
Label
ꢀ11.4
ꢀ4.4
ꢀ6.7
10.1
ꢀ12.4
ꢀx+2, ꢀy, ꢀz
N1eH1N/O2]C9
C2eH2/O2]C9
C9]O2/O2]C9
C2eH2/O1eC9
C8/C9
Dimer-I
5.615
8.349
7.793
ꢀ5.0
ꢀ3.1
ꢀ1.9
ꢀ1.8
ꢀ1.0
ꢀ0.8
ꢀ9.8
ꢀ5.7
ꢀ7.0
6.1
2.8
3.6
ꢀ10.5
ꢀ7.0
ꢀ6.1
ꢀx+2, ꢀy+1, ꢀz
Dimer-II
Dimer-III
Dimer-IV
ꢀx+1, ꢀy+1, ꢀz
C11eH11A/C9
C6eH6/O5
ꢀx+2, y+1/2, ꢀz+1/2
Table 5
with a 98% contribution. Furthermore, the calculated oscillator
strengths are 0.696 for this charge transfer. The next absorption
occurs at excitation energies of 188 and 177 nm with much lower
oscillator strengths of 0.115 and 0.123, respectively, compared to
the 301 nm excitation (Table S3, SI). Thus, in the title molecule the
intense absorbance that occurs at 301 nm is mainly due to ligand-
to-ligand charge transfer (LLCT).
Computed electrostatic potential maxima (Vs,max) and minima (Vs,min) on 0.001
a.u. molecular surface for the monomer.
Monomer
Atom
Vs,max
Atom
Vs,min
H6
28.12
26.50
23.16
19.78
H12B
O2
O1
15.28
H13B
H1N
H2
ꢀ46.2594
ꢀ28.7853
ꢀ17.3296
O5
Fig. 5. Molecular topography analysis obtained from AIM analysis for (a) dimer-I and (b) dimer-II. Bond critical points (BCP) are denoted by red dots. (For interpretation of the
references to colour in this figure legend, the reader is referred to the web version of this article.)
Table 6
he intermolecular acceptoredonor interactions (E(i) e E(j)) and second order perturbation energies (E(2)) (in kcal molꢀ1) for Dimer-I and Dimer - II. The symbol ($) denotes
atom-numbering of the second monomer in the dimer.
Donor (i)
Dimer-I
Acceptor (j)
E(2)
E(i) e E(j)
F(i,j)
Donor (i)
Dimer-II
Acceptor (j)
E(2)
E(i) e E(j)
F(i,j)
s
(1)O2eC9
RY*H1N$
s
s
s
0.77
1.23
8.49
0.82
0.77
1.24
8.38
0.87
2.33
1.26
1.32
0.94
2.33
1.26
1.32
0.94
0.038
0.035
0.095
0.026
0.038
0.035
0.094
0.026
s
s
(2)O2eC9
(2)C7eC8
s
s
s
s
s
s
s
s
*(2)O3$-C10$
*(2)O2$-C9$
*(1)C6$-H6$
*(2)C7$-C8$
*(2) O3eC10
*(2) O1eC9
*(1) C6eH6
*(2)C7eC8
0.63
1.39
0.72
0.96
0.65
1.36
0.72
0.97
0.48
0.37
1.23
0.42
0.48
0.37
1.23
0.42
0.017
0.020
0.027
0.019
0.017
0.020
0.027
0.019
LP(1)O1
LP(1)O2
LP(2)O2
* C2$eH2$
* N1$eH1N$
* C2$eH2$
LP (1)O1
LP (2)O1
s
(1)O2$-C9$
RY*(1)H1N
s
s
(2)O2$-C9$
(2)C7$-C8$
LP(1)O1$
LP(1)O2$
LP(2)O2$
s
s
s
*(1) C2eH2
*(1) N1eH1N
*(1) C2eH2
LP (1)O1$
LP (2)O1$

P. Venkatesan et al. / Journal of Molecular Structure 1119 (2016) 259e268
267
Fig. 6. Spectra of the title molecule (a) FT-IR (b) FT-Raman.
Fig. 7. (a) The observed and calculated UVeVis absorption spectra (b) HOMO and LUMO orbitals.
4. Conclusions
The experimental and computed IR and Raman spectra show the
presence of NeH/O and OeH/O bonding in the crystals. The
HOMO-LUMO diagram suggests that a charge transfer process is
going on within the molecule.
The title compound, one of the malonic acid half-ester de-
rivatives, is synthesized and characterized by experimental and
theoretical methods. The crystal structure of the 4-methoxy de-
rivative is primarily stabilized by intramolecular NeH/O and
OeH/O hydrogen bonds and intermolecular NeH/O, CeH/O
interactions along with CeH/C, O/O and C/C contacts. The
strengths of the various intermolecular interactions energies are
calculated. We found that an invariant molecular dimer generated
through intermolecular NeH1N/O2]C9, C2eH2/O2]C9, C9]
O2/O2]C9 and C1eH1/O1eC9 interactions provides the highest
contribution to the crystal-packing. Interestingly, the C/C inter-
action has a much higher contribution in comparison with some of
the intermolecular CeH/O interactions. The methoxy substitution
on the phenyl ring gives an additional stabilization to the crystal
structure as is evident from the involvement of methoxy group in
the intermolecular CeH/O interaction. Furthermore, the overall
lattice energies of the methoxy and the parent structures suggest
that the methoxy structure is stabilized by 4.5 kcal molꢀ1 higher
energy than the parent crystal structure. AIM and NBO analysis
show the presence of an intermolecular C/C contact in the dimer.
Acknowledgements
The authors PV and AI thank the Department of Science and
Technology (DST)-FIST programs for the use the 400 MHz NMR
facility at the School of Chemistry, Bharathidasan University. ST is
highly grateful to the management of SASTRA University for their
encouragement and financial support (Prof. TRR fund). ST also
thanks the DST-SERB (SB/YS/LS-19/2014) for research funding.
Authors thank Dr. V. Ramanathan for providing access to the facility
of Raman spectrometer supported by DST-SERB (SB/FT/CS-007/
2013).
Appendix A. Supplementary data
Supplementary data related to this article can be found at http://
dx.doi.org/10.1016/j.molstruc.2016.04.090.

268
P. Venkatesan et al. / Journal of Molecular Structure 1119 (2016) 259e268
J.R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G.A. Petersson,
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