Synthesis, molecular structure, and spectral analyses of ethyl-4-[(2,4-dinitrophenyl)-hydrazonomethyl]-3,5-dimethyl-1H-pyrrole-2- carboxylate

Article abstract of DOI:10.1007/s11224-012-0112-1

Ethyl-4-[(2,4-dinitrophenyl)-hydrazonomethyl]-3,5-dimethyl-1H-pyrrole-2- carboxylate (3) has been newly synthesized by the condensation of ethyl-4-formyl-3,5-dimethyl-1H-pyrrole-2-carboxylate and 2,4- dinitrophenylhydrazine, characterized by FT-IR, ¹H NMR, UV-Vis, DART Mass and elemental analysis. The formation of compound (3) and its properties have been evaluated by quantum chemical calculations. The calculated thermodynamic parameters show that the formation reaction of (3) is exothermic and spontaneous at room temperature. The vibrational analysis indicates that (3) forms dimer in the solid state by heteronuclear double hydrogen bonding (N-H···O). Topological parameters electron density (ρ _BCP), Laplacian of electron density (x² ρ _BCP), and total electron energy density (H _BCP) at bond critical points (BCP) have been analyzed using atoms in molecules (AIM) theory. The interaction energies of dimer formation using DFT and AIM calculations are found to be -14.6509 and -15.5308 kcal/mol, respectively. AIM ellipticity analysis confirms the presence of resonance-assisted hydrogen bonding in dimer. The global electrophilicity index (ω = 5.91 eV) shows that title molecule is a strong electrophile. The local reactivity descriptors Fukui functions (f _k ⁺, f _k ^-), softness (s _k ⁺, s _k ^-), and electrophilicity indices (ω _k ⁺, ω _k ^-) analyses are performed to determine the reactive sites within molecule.

Full text of DOI:10.1007/s11224-012-0112-1

Struct Chem
DOI 10.1007/s11224-012-0112-1
ORIGINAL RESEARCH
Synthesis, molecular structure, and spectral analyses
of ethyl-4-[(2,4-dinitrophenyl)-hydrazonomethyl]-3,
5-dimethyl-1H-pyrrole-2-carboxylate
•
R. N. Singh Amit Kumar R. K. Tiwari
•
•
•
Poonam Rawat Rajiv Manohar
Received: 26 February 2012 / Accepted: 13 August 2012
ꢀ Springer Science+Business Media, LLC 2012
Abstract Ethyl-4-[(2,4-dinitrophenyl)-hydrazonometh-
yl]-3,5-dimethyl-1H-pyrrole-2-carboxylate (3) has been
newly synthesized by the condensation of ethyl-4-formyl-
3,5-dimethyl-1H-pyrrole-2-carboxylate and 2,4-dinitro-
phenylhydrazine, characterized by FT-IR, 1H NMR,
UV–Vis, DART Mass and elemental analysis. The formation
of compound (3) and its properties have been evaluated by
quantum chemical calculations. The calculated thermody-
namic parameters show that the formation reaction of (3) is
exothermic and spontaneous at room temperature. The
vibrational analysis indicates that (3) forms dimer in the solid
state by heteronuclear double hydrogen bonding (N–HꢀꢀꢀO).
Topological parameters electron density (qBCP), Laplacian
electrophilicity indices (x?k , x-k ) analyses are performed to
determine the reactive sites within molecule.
Keywords Density functional theory ꢀ
Vibrational spectra ꢀ Hydrogen bonded dimer ꢀ
AIM calculation ꢀ Reactivity descriptors ꢀ Ellipticity
Introduction
The carboxaldehydes of pyrrole form important class of
precursors for synthesis of hydrazones and their deriva-
tives. Pyrrole fragment is a constituent of many biological
systems. The pyrrole-a-carboxaldehyde has been used for
the development of potential chemosensors [1]. Hydra-
zones are an important class of compounds due to their
various properties and applications. They are used as
antimicrobial, antitubercular [2–6], and antidiabetic agents
[7]. They have strong coordinating ability toward different
metal ions [8, 9]. In addition, aroyl hydrazones and their
mode of chelation with transition metal ions present in the
living system have been of significant interest [10, 11]. The
chemical stability of hydrazones and their high melting
points have recently made them attractive as prospective
new material for opto-electronic applications [1]. The
nitrophenyl hydrazones exhibit a series of good organic
nonlinear optical (NLO) properties [12–15]. Hydrazones
having frame –CH=N–NH– constitute an important class of
compounds for [2?2] cycloadditions and 1,3 dipolar cyc-
loadditions and have been turned into a valuable tool for
the synthesis of azetidinones and pyrazoles, respectively
[16, 17] and various other N, O, or S containing hetero-
cyclic compounds such as oxadiazolines, thiazolidinones,
triazolines [18–24]. The ethyl-4-formyl-3,5-dimethyl-1H-
pyrrole-2-carboxylate is a suitable precursor for the
2
of electron density (r qBCP), and total electron energy
density (HBCP) at bond critical points (BCP) have been ana-
lyzed using ‘‘atoms in molecules’’ (AIM) theory. The interac-
tion energies of dimer formation using DFT and AIM
calculations are found to be-14.6509 and -15.5308 kcal/mol,
respectively. AIM ellipticity analysis confirms the pres-
ence of resonance-assisted hydrogen bonding in dimer. The
global electrophilicity index (x = 5.91 eV) shows that title
molecule is a strong electrophile. The local reactivity
descriptors Fukui functions (f?k , fk-), softness (sk?, sk-), and
Electronic supplementary material The online version of this
article (doi:10.1007/s11224-012-0112-1) contains supplementary
material, which is available to authorized users.
R. N. Singh (&) ꢀ A. Kumar ꢀ R. K. Tiwari ꢀ P. Rawat
Department of Chemistry, University of Lucknow, University
Road, Lucknow 226007, India
e-mail: rnsvk.chemistry@gmail.com
R. Manohar
Department of Physics, University of Lucknow, University
Road, Lucknow 226007, India
123

Struct Chem
synthesis of hydrazones; however, its derivative with
2,4-dinitrophenylhydrazine has not been reported. In this
article, we report the synthesis, characterization, and
molecular dimer structure of ethyl-4-[(2,4-dinitrophenyl)-
hydrazonomethyl]-3,5-dimethyl-1H-pyrrole-2-carboxylate
(3). Experimental work is accompanied by quantum
chemical calculations providing information on chemi-
cal reactivity and several other properties of the title
compound.
heavy atoms and ‘‘p’’ polarization functions on hydrogen
atoms are used for better description of polar bonds of nitro
group [30, 31]. It should be emphasized that ‘‘p’’ polari-
zation functions on hydrogen atoms are used for repro-
ducing the out of plane vibrations involving hydrogen
atoms. Convergence criterion in which both the maximum
force and displacement are smaller than the cutoff values of
0.000450 and 0.001800 and r.m.s. force and displacement
are less than the cut-off values of 0.000300 and 0.001200
are used in the calculations. The absence of imaginary
frequency verified that stationary points correspond to
minima of the potential energy surfaces. The time-depen-
dent density functional theory (TD-DFT) is carried out to
find the electronic transitions. The optimized geometrical
parameters are used in the calculation of vibrational
wavenumbers to characterize all stationary points as min-
ima and their harmonic vibrational wavenumbers are
positive. All molecular structures are visualized using
software Chemcraft [32] and Gauss-View [33]. Potential
energy distribution (PED) along internal coordinates is
calculated by Gar2ped software [34]. Internal coordinate
system recommended by Pulay et al. [35] is used for the
assignment of vibrational modes. To estimate the enthalpy
and Gibbs free energy values, thermal corrections to
enthalpy and Gibbs free energy calculated at B3LYP/6-
31G(d,p) level were added to the calculated total energies.
The wave function file generated at B3LYP/6-31G(d,p)
basis set from the optimized coordinate was used to cal-
culate the topological parameters by AIM 2000 1.0 soft-
ware [36]. The atoms in molecules (AIM) method gives the
opportunity to have an insight into a region of a system.
The theory of AIM efficiently describes H-bonding and its
concept without border. One of the advantages of the AIM
theory is that one can obtain information on changes in the
electron density distribution as result of either bond for-
mation or complexes formation. With respect to change of
both the method used and the basis set the reliability and
stability of values of AIM parameters have been studied
and found that they were almost independent of basis set in
case of used functional B3LYP in DFT [37].
Experimental section
Procedures and synthesis of ethyl-4-[(2,4-
dinitrophenyl)-hydrazonomethyl]-3,5-dimethyl-1H-
pyrrole-2-carboxylate (3)
Analytical grade 2,4-dinitrophenylhydrazine was pur-
chased from s.d. fine. The solvent methanol was dried and
distilled before use according to the standard procedure
[25]. Ethyl-4-formyl-3,5-dimethyl-1H-pyrrole-2-carboxyl-
ate was prepared by an earlier reported method [26]. A
solution of 2,4-dinitrophenyl hydrazine (0.1015 g,
0.5125 mmol) in 15 ml methanol was added dropwise with
stirring in solution of 20 ml methanol. Reaction mixture
was stirred at room temperature for 24 h. After 24 h stir-
ring, precipitate of brown color was appeared. The pre-
cipitate was filtered off, washed with methanol, and dried
in air. Percentage yield: 20.81. Compound decomposes
above 268 ꢁC without melting. The elemental analysis was
carried out using Elemental Analyser Vario EL-III. Anal-
ysis for C16H17N5O6: Found C 49.92, H 4.63, N 18.91 %,
1
Calculated C 51.18, H 4.56, N 18.66 %. The H NMR
spectrum was recorded in DMSO-d6 on Bruker DRX-300
spectrometer using TMS as an internal reference. The
UV–Vis absorption spectrum (1 9 107 M in DMSO) was
recorded on ELICO SL-164 spectrophotometer. The FT-IR
spectrum was recorded in KBr medium on a Bruker
spectrometer. The DART-Mass spectrum was recorded on
JMS-T100LC, Accu TOF mass spectrometer. DART Mass:
Calc. 375.1178, Found m/z 375.13 [M?].
Computational methods
Results and discussions
The theoretical calculations for the synthesized compound
were carried out with Gaussian 03 program package [27] to
Thermodynamic properties
1
predict the molecular structure, H NMR chemical shifts,
For the simplicity reactants ethyl-3,5-dimethyl-4-formyl-
1H-pyrrole-2-carboxylate, 2,4-dinitrophenylhydrazine, pro-
duct (3), and water (byproduct) are abbreviated as 1, 2, 3,
and 4, respectively. The calculated enthalpy (H), Gibbs free
energy (G), and entropy (S) of 1, 2, 3, 4 and reaction at
room temperature are listed in Table 1. The enthalpy
change of reaction (DHreaction), Gibbs free energy change
and vibrational wavenumbers using density functional
theory (DFT), B3LYP functional and 6-31G(d,p) basis set.
B3LYP invokes Becke’s three parameters (local, non local,
Hartree–Fock) hybrid exchange functional (B3) [28] with
Lee–Yang–Parr correlation functional (LYP) [29]. The
basis set 6-31G(d,p) with ‘‘d’’ polarization functions on
123

Struct Chem
Table 1 Calculated enthalpy (H), Gibbs free energy (G), and entropy (S) of reactants (1, 2), products (3, 4) and reaction at room temperature,
using B3LYP/6-31G(d,p)
Parameters
1
2
3
4
Reaction
H (a.u.)
-669.126528
-669.185894
124.946
-751.78676
-751.838537
108.974
-1344.524162
-1344.611253
183.298
-76.394588
-76.416024
45.116
-0.005462
-0.002846
-5.506
G (a.u.)
S (cal/mol K)
Table 2 Enthalpy (H), Gibbs free energy (H), entropy (H), their change and equilibrium constant of conversion from monomer to dimer
Thermodynamic parameters H (a.u.) G (a.u.) S (cal/mol K) DH (kcal/mol) DG (kcal/mol) DS (cal/mol K) Keq
29 Monomer
-2,689.048324 -2,689.222506 366.596
-2,689.069059 -2,689.224971 328.146
-13.01140
-1.54681
-38.45
13.60
Dimer
Molecular geometry
of reaction (DGreaction), and entropy change of reaction
(DSreaction) are calculated from thermodynamic parameters
of reactants and products at room temperature. For overall
reaction the enthalpy change of reaction (DHreaction), Gibbs
free energy change of reaction (DGreaction), and entropy
change of reaction (DSreaction) are found to be -3.4275,
-1.7859 kcal/mol and -5.506 cal/mol K, respectively.
The calculated negative values for DHreaction and DGreaction
show that reaction is exothermic and spontaneous at room
temperature. Thermodynamic relation between equilibrium
constant (KT) and Gibbs free energy change of reaction
(DGreaction) at temperature (T) is given as
Geometry of all the reactants and products involved in
chemical reaction were computed at B3LYP/6-31G(d,p)
level. The calculated ground state syn, and anti conformers
of the product (3) have the energy -1,344.88546024 and
-1,344.88472880 a.u., respectively, at room temperature.
They have energy difference 0.4589 kcal/mol and exist in
ratio 68.6, 31.4 %, respectively, at room temperature. The
difference of dihedral angle s(C3C2C9O12, 178.9051)
between syn (179.99925ꢁ) and anti (0.0125ꢁ) conformers
brings carbonyl oxygen (O12) closer to hydrogen (H33) of
b-methyl of pyrrole in anti conformer, and the conse-
quences are repulsion between atom O12 and H33, increase
of the angle C2C9O12 (126.0704ꢁ), decrease in hardness,
and overall higher in energy. In case of the syn conformer,
the angle C2C9O12 (122.2857ꢁ) is less than anti resulting
to stabilization of the syn conformer. Furthermore, the syn
conformer has geometrical suitability for intermolecular
hydrogen bonding by having pyrrolic NH and ester CO on
same side and their role lie in molecular association
resulting into dimer. The asymmetry of the N1–C2 and
N1–C5 bonds can be explained by electron withdrawing
character of the ethoxycarbonyl group and conjugation of
the N1–C5 with C4–C3–C2 skeleton. It leads to the elon-
gation of N1–C2 bond. These effects are not only seen in
quantum calculation but also reflect in crystal structure
of the ethyl-3,5-dimethyl-1H-pyrrole-2-carboxylate [39],
methyl 4-p-tolyl-1H-pyrrole-2-carboxylate [40]. The N=O
bonds in N22-nitro group are more unsymmetrical due to
the formation of intramolecular hydrogen bond (N11–
H36ꢀꢀꢀO23). This is not only observed in our theoretical
study but also reported in crystal structure of hydrazones
[41]. Optimized geometry of dimer is shown in Fig. 1, with
atom numbering. Selected optimized geometrical parame-
ters of molecular dimer of (3) are listed in Table TS1 in
Supplementary material. In dimer, heteronuclear intermo-
lecular hydrogen bonding (N–HꢀꢀꢀO) between pyrrolic
KT ¼ eꢁDG=RT
The value of equilibrium constant (KT) determines the
nature of reaction (i) if KT [ 1, reaction is favored in
forward direction, (ii) if KT = 0, reaction is in equilibrium
state, (iii) if KT \ 1, reaction is favored in backward
direction. Using above equation, equilibrium constant (KT)
for title reaction is calculated as 20.37 at room temperature.
Therefore, reaction is favored in forward direction at room
temperature. This confirms the formation of product (3) at
room temperature.
The binding energy of dimer is calculated as
-14.6509 kcal/mol using DFT calculation. The calculated
hydrogen binding energy of dimer formation has been
corrected for the basis set superposition error (BSSE) via
the standard counterpoise method [38] and found to be
-10.5485 kcal/mol. The calculated changes in thermody-
namic quantities during the dimer formation in gaseous
phase have the negative values of DH (kcal/mol),
DG (kcal/mol), and DS (cal/mol K) and incorporated in
Table 2, indicating that the dimer formation is exothermic
and spontaneous. The calculated equilibrium constant
between monomer and dimer is quite high (K = 13.60)
indicating that dimer formation is highly preferred and as a
result even anti conformer gets converted to syn and finally
forms the dimer.
123

Struct Chem
Fig. 1 The molecular structure
of dimer for syn-conformer of
(3) using B3LYP/6-31G(d,p)
Table 3 Experimental and calculated GIAO 1H NMR chemical
shifts of (3) using B3LYP/6-31G(d,p) in DMSO-d6 as the solvent
(25 ꢁC)
(N–H) and carbonyl (C=O) oxygen of ester form two
hydrogen bonds. In intermolecular hydrogen bonds, the
N–H bond acts as proton donor and C=O bond as proton
acceptor. According to the Etter terminology [42], the
cyclic ester dimer form the ten member pseudo ring
denoted as R22(10) or more extended sixteen member pseudo
ring R22(16) consisting of atoms O12, C9, C2, C3, C4, C5, N1,
C55, C53, C54, C57, C60, C58, N56. The superscript des-
ignates the number of acceptor centers and the subscript the
number of donors in the motif. In dimer, due to intermolec-
ular hydrogen-bond formation both proton donor (N–H
bond) and proton acceptor (C=O bond) are elongated from
Atom no.
d calc.
(ppm)
d exp.
(ppm)
Assignment
H28
H29
H30
H31
H32
H33
H34
H35
H36
9.2597
2.3092
2.6527
2.6524
8.0748
3.0491
2.1274
2.1272
11.9065
11.513
2.475
(s, 1H, pyrrole-NH)
(s, 3H, pyrrole-CH3)
8.758
2.409
(s, 1H, CH=N)
(s, 3H, pyrrole-CH3)
˚
˚
1.0111 to 1.0207 A, 1.2230 to 1.2321 A, respectively. Total
energy of the monomer (syn-conformer) and its dimer
are calculated as -1,344.88546024, -2,689.79426826 a.u.,
respectively.
11.798
(s, 1H, hydrazide
–NH)
H37
H38
H39
H40
H41
H42
H43
H44
4.3239
4.3217
1.2095
1.4739
1.4741
8.5518
7.8691
9.3416
4.200–4.271
(q, 2H, CH2 ester)
1H NMR spectroscopy
1.281–1.327
(t, 3H, CH3 ester)
The geometry of the title compound, together with that of
tetramethylsilane (TMS) is fully optimized. 1H NMR chem-
ical shifts are calculated with GIAO approach using B3LYP
functional and 6-31G(d,p)basisset [43]. Chemicalshift ofany
proton is the difference between isotropic magnetic shielding
7.793–8.346
8.845
(m, 2H, Ar–H)
(s, 1H, Ar–H)
123

Struct Chem
1
Fig. 2 The experimental H
NMR spectrum of (3)
(IMS) of TMS and that proton. Experimental and calculated
1H NMR chemical shifts of the title compound are listed in
Table 3. The experimental 1H NMR chemical shifts are
shown in Fig. 2. To compare the chemical shifts correlation
graph between the experimental and calculated chemical
shifts was drawn. The correlation graph follows the linear
equation (y = 1.05505x - 0.13678), where y is the experi-
mental 1H NMR chemical shift, x is the calculated 1H NMR
chemical shift. The high value of correlation coefficient
(R2 = 0.9613) shows that a good agreement exist between
experimental and calculated chemical shifts. The hydrogen
experiencemoredeshielding effectwhenhydrogenbondingis
strong and less deshielded when hydrogen bonding is dimin-
ished. Thus, the presenceofthe intramolecularhydrogenbond
N11–H35ꢀꢀꢀO23 is supported by the 1H NMR spectrum where
the signal of N11–H35 proton appeared with the high value of
chemical shift at 11.798 ppm.
Fig. 1 in Supplementary material. The FMOs are important
in determining the ability of a molecule to absorb light and
molecular reactivity. The vicinal orbitals of HOMO and
LUMO play the role of electron donor and electron acceptor,
respectively. The kmax is a function of substitution, the
stronger the acceptor character of the substituents, the more
electron withdraw from the ring, the shorter the kmax. From
the charge transfer viewpoint, the high value of |eHOMO
|
means that the ionization is more difficult, that is to say, that
molecule is hard to lose electron. The HOMO–LUMO
energy gap is an important stability index. The HOMO–
LUMO energy gap of title molecule reflects the chemical
stability of the molecule.
HOMO energy ¼ ꢁ5:8613 eV
LUMO energy ¼ ꢁ2:7355 eV
HOMO-LUMO energy gap ¼ 3:1258 eV
TD-DFT calculations using B3LYP/6-31G(d,p) predict
three intense electronic transitions at kmax = 240 nm,
UV–Vis spectroscopy
f = 0.4021; kmax = 303 nm, f = 0.3958 and kmax
=
439.49 nm, f = 0.7145. The calculated electronic transi-
tions at kmax = 240, 303, and 439 nm are in agreement with
the experimental electronic transitions observed at kmax 251,
293, and 401 nm, respectively. The calculated values for
wavelength of maximum absorption (kmax) are also in
agreement with the reported kmax in literature [44].
According to the TD-DFT calculations, the experimental
bands at 251, 293, and 401 nm originate mainly due to the
The nature of the transitions observed in the UV–Vis spec-
trum of (3) has been studied by the TD-DFT. The values of
calculated electronic transitions of high oscillatory strength
and observed are listed in Table TS2 in Supplementary
material. The both absorption graph experimental and the-
oretical UV–Vis spectrum are shown in Fig. 3a. Selected
molecular orbital plots involved in electronic excitations are
shown in Fig. 3b. The theoretical spectrum of (3) is given in
123

Struct Chem
Fig. 3 a UV–Vis spectra (experimental and theoretical) for (3).
b Selected molecular orbital plots involved in electronic excitations
for (3)
c
Homo-1 ? Lumo?4, Homo ? Lumo?3 and Homo
? Lumo?2 excitations, respectively. Figure 4b predicts
that Homo and Lomo?2 orbitals are localized over pyrrole
ring and benzene ring, respectively. Homo ? Lumo?3 are
localized over C2–C3C8–C4 of pyrrole ring and N25–O26 of
nitro group, respectively. The theoretical transition at
293 nm arises due to transition Homo ? Lumo?3. The
Homo-5 orbital are localized over the benzene ring and
Lumo over the nitro group. On the basis of molecular orbital
coefficients analyses and molecular plots, these electronic
excitations show p ? p*, p ? p*, and n ? p* transition,
respectively.
Vibrational spectroscopy
The experimental and theoretical (selected) vibrational
wavenumbers of dimer at B3LYP/6-31G(d,p) level and their
assignments using PED are given in Table 4. The calculated
(monomer, dimer) and the experimental FT-IR spectra of (3)
in the region 4,000–400 cm-1 are shown graphically in
Fig. 4a, b. The total number of atoms in monomer and dimer
are 44 and 88 which give 126 and 258, (3n - 6) vibrational
modes for monomer and dimer, respectively. The calculated
vibrational wavenumbers have higher values than their
experimental for the majority of the normal modes. Two
factors may be responsible for the discrepancies between the
experimental and computed wavenumbers of this com-
pound. The first is caused by difference of the environment
(gas and solid phase) and the second is due to the fact that the
experimental values are anharmonic wavenumbers while the
calculated values are harmonic ones. Therefore, calculated
wavenumbers at B3LYP/6-31G(d,p) level are scaled down
using single scaling factor 0.9608 [45], to discard the an-
harmonicity present in real system. The observed wave-
numbers are in good agreement with the calculated
wavenumbers of dimer than monomer. Therefore, observed
wavenumbers are assigned using dimer PED.
N–H vibrations
The elongation of N–H bond and red shift of corresponding
band positions are observed in the dimer, as compared to
the monomer. In the experimental FT-IR spectrum of (3),
the N–H stretch of pyrrole (mNH
) is observed at
3,290 cm-1, whereas it is calculated as 3,334 cm-1 in
dimer and 3,496 cm-1 in monomer. The observed wave-
number at 3,290 cm-1 is in good agreement with the cal-
culated wavenumber of dimer. The observed value of mNH
also correlates with the earlier reported strong absorption at
123

Struct Chem
3,358 cm-1 for hydrogen bonded pyrrole-2-carboxylic acid
dimer recorded in KBr pellet, but it deviates to the reported
free mNH band at higher wavenumber 3,465 cm-1, recorded
in CCl4 solution [46]. Therefore, solid state spectrum of (3)
attributes to the vibration of hydrogen bonded N–H group.
The observed N–H wagging mode of pyrrole at 796 cm-1
is calculated at same wavenumber in theoretical IR-
spectrum. The observed N–H deformation of pyrrole at
1,563 cm-1 agrees well with the calculated wavenumber at
pyrrole N–H deformation observed at 1,282 cm-1 agrees well
with thecalculated wavenumber at1,271 cm-1. The observed
rocking mode of Me at 1,022 cm-1 corresponds to the cal-
culated wavenumber at 1,088 cm-1. Asymmetric deforma-
tion of Me1 observed at 1,420 cm-1 agrees well with the
calculated wavenumber at 1,412 cm-1
.
C–O vibrations
1,544 cm-1
.
The stretching mode of carbonyl group (mC=O) is observed
at 1,679 cm-1, whereas it is calculated as 1,656 cm-1 in
dimer and 1,693 cm-1 in monomer. The observed mC=O
agrees well with the earlier reported wavenumber at
1,665 cm-1 for dimer of syn-pyrrole-2-carboxylic acid
[46]. The observed mC=O absorption band at 1,679 cm-1 is
also in good agreement with the calculated wavenumber of
dimer. Therefore, mC=O stretching mode in (3) confirms the
involvement of C=O group in intermolecular hydrogen
bonding. The observed C9–O13 stretching mode at
1,141 cm-1 corresponds to the calculated wavenumber at
1,176 cm-1 with 8 % contribution in dimer PED.
C–H vibrations
Three methyl groups are present in the molecule. They are
abbreviated as Me, Me1, and Me2. Me1 and Me2 are directly
attached to the C5 and C3 carbon of pyrrole ring. Me is
attached to the CH2 of ester group. The observed C–H
stretching vibrations of benzene ring, ester methyl, and Schiff
C–H at 3101, 2983, and 2930 cm-1 are in agreement with the
calculated wavenumber at 3139, 3018, and 2945 cm-1
,
respectively. A combination band of CH2 wagging and
Fig. 4 a FT-IR spectra
(experimental and calculated)
for (3) in the region
500–1,800 cm-1. b FT-IR
spectra (experimental and
calculated) for (3) in the region
2,800–3,600 cm-1
123

Struct Chem
Table 4 Positions of experimental and theoretical (selected) vibrational bands of dimer using B3LYP/6-31G(d,p) and their assignments
[harmonic vibrational wavenumbers (cm-1), IRint (K mmol-1)]
Mode
no.
Positions of scaled
theoretical bands
IRint
Exp.
bands
Assignment (PED) C 5 %
1
2
3
4
5
6
7
8
3,334
3,139
3,018
2,945
1,656
1,604
1,587
1,544
3,071.47
49.35
3,290
3,101
2,983
2,930
1,679
1,615
1,586
1,563
m(N1H28)(52) - m(N56H59)(48)
m(C79H83)(61) - m(C21H44)(38)
57.83
m(C15H41)(26) - m(C15H40)(24) - m(C46H48)(19) m(C46H49)(18)
m(C7H32)(50) - m(C63H71)(48)
74.57
1,760.65
1,968.11
834.89
912.7
m(C53O55)(33) - m(C9O12)(33) - m(C53C54)(5)
m(C17C18)(8) - m(C75C77)(8) ? m(C20C21)(5) - m(C76C79)(5)
m(N86O88)(11) - m(N25O27)(11) - m(N86O87)(11) ? m(N25O26)(11)
d(C54H59N56)(12) - d(C2H28N1)(12) - m(C4C5)(8) ? m(C58C60)(8) ?
m(C2C3)(7) - m(C54C57)(7)
9
1,507
1,085.05
1,506
m(N11C19)(6) - m(C73N72)(6) ? m(C16C17)(6) - m(C77C81)(6)
- m(C58N56)(5) ? m(N1C5)(5)
10
11
1,412
1,327
278.06
1,616.4
1,420
1,323
(das-Me1)(5) - (das-Me1)(5)
m(N86O88)(8) - m(N25O27)(8) ? m(N86O87)(6) - m(N25O26)(6)
- m(C81N86)(5) ? m(C16N25)(5)
12
13
1,271
1,250
1,230.87
531.37
1,282
1,235
d(C54H59N56)(12) - d(C2H28N1)(11) - m(C9O13)(6) ? m(C53O50)(6)
? (x-C14H37H38)(5) - (x-C47H51H52)(5) - m(C53C54)(5) ? m(C2C9)(5)
m(N80O84)(10) - m(N22O24)(10) - d(C76H83C79)(6) - d(C16H44C21)(6)
- d(C81H82C77)(5) ? d(C16H42C17)(5) - (q-N72C74)(5) - (q-N11H36)
(5) - m(C76N80)(5) ? m(C20N22)(5)
14
15
16
1,213
1,197
1,176
330.25
119.2
1,217
1,191
1,141
m(N1C2)(12) - m(C54N56)(11) - m(C5C6)(6) ? m(C58C62)(5) ? m(C5C6)(5)
- m(C60C63)(5)
d(C73H78C75)(11) ? d(C17H43C18)(11) - d(C76H83C79)(7)
- d(C16H44C21)(7) ? (q-N72C74)(6) ? (q-N11H36)(6)
657.52
m(C53O50)(8) - m(C54N56)(8) - m(C9O13)(8) ? m(N1C2)(8)
- d(C54H59N56)(7) ? d(C2H28N1)(7)
17
18
19
20
1,113
1,088
1,036
1,004
511.73
609.56
54.29
1,101
1,022
951
d(C81H82C77)(18) - d(C16H42C17)(17) ? d(C73H78C75)(9) ? d(C17H43C18)(9)
m(N10N11)(7) - m(N70N72)(7)
(s-C9C2)(16) ? (s-C53C54)(12) - (s-R)(6) - d(C16H44C21)(5) - (s-R)(5)
68.42
921
m(C14C15)(20) - m(O13C14)(16) - m(C46C47)(12)
- (s-C9C2)(10) ? m(C47H51)(9)
21
908
39.36
881
m(C81N86)(7) - m(C16N25)(7) - m(C76N80)(6) - (dtrigonal-R1)(6) m(C20N22)(6)
- (dtrigonal-R1)(6)
22
23
24
25
796
777
716
647
116.07
93.82
796
769
713
644
(x-N56H59)(24) ? (x-N1H28)(24) - (s-O12H59)(22) - (s-O55H28)(21)
(s-C9C2)(10) ? (s-C53C54)(10) ? (x-C2C9)(6) ? (x-C53C54)(6)
(x-C53C54)22) ? (s-C53C54)(22) ? (x-C2C9)(19) ? (s-C9C2)(19)
44.74
156.85
(s-R)(16) - (s-C58C62)(15) ? (s-R)(14) - (s-C5C6)(14) - (s-C53C54)(10)
- (s-C9C2)(9) ? (x-C58C62)(5)
26
27
607
515
11.52
17.11
600
506
(x-C2C9)(14) ? (x-C53C54)14) - (s-R)(8) - (s-R)(7) ? (s-C5C6)(6)
? (s-H67O12)(6) ? (s-H29O55)(6) ? (s-C58C62)(6)
(q-C16N25)(25) ? d(O87C81N86)(22) ? d(C77N86C81)(5)
- d(C17N25C16)(5)
Proposed assignment and PED for vibrational modes: types of vibrations: m—stretching, q—rocking (in-plane vibration), x—wagging (out of
plane vibration), d—deformation, das—asymmetric deformation, s—torsion. R—pyrrole ring, R1—benzene ring
N=O vibrations
vibrations as asymmetric and symmetric. Asymmetric
stretching vibrations are always observed at higher wave-
number than symmetric stretching vibrations. The observed
asymmetric stretching vibrations of nitro group (mN=O) at
The molecule under investigation possesses two nitro
groups. The nitro groups show two type of stretching
123

Struct Chem
2
1,586 cm-1 agrees well with the calculated wavenumber at
1,587 cm-1. Symmetric stretching vibration of mN=O is
observed at 1235, 1323 cm-1, whereas it is calculated as
1250, 1327 cm-1, respectively. The observed wavenum-
bers are in agreement with the earlier reported wavenum-
bers for asymmetric and symmetric vibration of nitro group
at 1,600 and 1,319 cm-1, respectively [47].
(iii) weak H-bonds: having (r qBCP) [ 0 and HBCP [ 0,
mainly electrostatic in nature and the distance between
interacting atoms is greater than the sum of van der Waal’s
radii of these atoms.
Molecular graph of the dimer using AIM program at
B3LYP/6-31G(d,p) level is shown in Fig. 5. According to
these parameters, there exist three types of interactions as
(i) O23ꢀꢀꢀH36, O84ꢀꢀꢀH74 are medium hydrogen bonds, (ii)
O12ꢀꢀꢀH59, O55ꢀꢀꢀH28 are weak hydrogen bonds, (iii)
O50ꢀꢀꢀH64, O13ꢀꢀꢀH33, O12ꢀꢀꢀH67, O55ꢀꢀꢀH29, C6ꢀꢀꢀN10,
C62ꢀꢀꢀN70 are weak interactions. AIM topological (density
and energetic) parameters of various interactions of
molecular complex are tabulated in Table TS3 in Supple-
mentary material. Espinosa [49] proposed proportionality
between hydrogen bond energy (E) and potential energy
density (VBCP) at HꢀꢀꢀO contact: E = ‘ (VBCP). The
intermolecular interaction energy of dimer formation as per
DFT calculation found to be -14.6509 kcal/mol and after
BSSE correction is -10.5485 kcal/mol and as per AIM
calculations is -15.5307 kcal/mol, respectively. The het-
eronuclear intramolecular N–HꢀꢀꢀO hydrogen bond energy
is calculated as -9.4035 kcal/mol using AIM calculations.
The strength of H-bonds in dimer is often resulting of the
existence of dynamic disorder, orientational disorder, and
mesomeric effect but may also be explained within the
conditions related to the resonance-assisted H-bonding
(RSHB). In dimer, often there is equalization of certain
bonds, potential double movement of protons between
electronegativity atoms of electron excess. In RAHBs
model, there is an effective mixing in two forms. The ellip-
ticity (e) at bond critical points (BCP) is a sensitive index to
monitor the p-character of bond. The e is related to k1 and k2,
which correspond to the eigen values of Hessian and defined
as by a relationship: e = (k1/k2) - 1. To investigate the
effect of p-electron delocalization in bonds associated with
N and O atoms of N–HꢀꢀꢀO heteronuclear inter and intra-
molecular hydrogen bonds, the analysis of the bond ellip-
ticity is performed. In dimer, inter and intramolecular
hydrogen bonds are associated with the sixteen member and
six member pseudo rings, respectively. These rings are
abbreviated as Ring1 and Ring2, respectively. The e values
for bonds involved in Ring1 and Ring2 are given in
Table TS4 in Supplementary material. In Ring1, the values
of e for bonds O12–C9, C9–C2, C2–C3, C3–C4, C4–C5,
C5–N1 associated with the N1–H28ꢀꢀꢀO55 and for bonds
O55–C53, C53–C54, C54–C57, C57–C60, C60–C58, C58–
N56 associated with the N56–H59ꢀꢀꢀO12 are in the range
0.1005–0.2904. In Ring2, the values of e for bonds N11–C19,
C19–C20, C20–N22, N22–O23 associated with the N11–
H36ꢀꢀꢀO23 are in the range 0.1131–0.2301. These values of e
correspond to the aromatic bonds reported in literature [50].
The e values confirm the presence of resonance-assisted
intermolecular and intramolecular hydrogen bonds because
C–N and C–C vibrations
The observed C19–N11 stretching vibration at 1,506 cm-1
agrees well with the calculated wavenumber at 1,507 cm-1
.
The observed C16–N25 rocking mode at 881 cm-1 corre-
sponds to the calculated wavenumber at 908 cm-1. The
observed C–C stretches in benzene ring at 1,615 cm-1 cor-
responds to the calculated wavenumber at 1,604 cm-1
,
respectively. A combination band of C–C stretching and
C2H28N1 deformation in pyrrole ring is observed at
1,563 cm-1, whereas it is calculated as 1,544 cm-1
AIM calculation
.
The experimental and computational data show that
H-bonding exerts substantial changes on the molecular
geometry of the distant parts of the system. These changes
are related to the variations in p-electron delocalization and
reflect the strength of H-bonding. In both intramolecular
and intermolecular H-bonding p-electron delocalization
effects are detectable and characterized with the use of the
QTAIM methods. There are several interacting effects such
as dynamic disorder, orientational disorder, and mesomeric
effect connected with hydrogen bonding especially in
crystal structures. Geometrical as well as topological
parameters are useful tool to characterize the strength of
hydrogen bond. The geometrical criteria for the existence
of hydrogen bond are as follows: (i) The distance between
proton (H) and acceptor (A) to be less than the sum of their
van der Waal’s radii of these atoms, (ii) the ‘‘donor
(D)–proton (H)ꢀꢀꢀacceptor (A)’’ angle to be [90ꢁ, (iii) the
elongation of ‘‘donor (D)–proton(H)’’ bond length to be
observed. These criteria are frequently considered as
insufficient; therefore, the existence of hydrogen bond
could be supported further by Koch and Popelier criteria
[48] based on ‘‘AIM’’ theory (i) The existence of bond
critical point for the ‘‘proton (H)ꢀꢀꢀacceptor (A)’’ contact,
(ii) the value of electron density (qH…A) should be within
the range 0.002–0.040 a.u., (iii) the corresponding Lapla-
2
cian (r qBCP) should be within the range 0.024–0.139 a.u.
According to Rozas et al. [48], the H-bonding may be
2
classified as (i) Strong H-bonds: having (r qBCP) \ 0 and
HBCP \ 0, covalent in nature, (ii) medium H-bonds: having
2
(r qBCP) [ 0 and HBCP \ 0, partially covalent in nature,
123

Struct Chem
Fig. 5 Molecular graph of (3)
dimer: bond critical points
(small red spheres), ring critical
points (small yellow sphere),
bond paths (pink lines) (Color
figure online)
Local reactivity descriptors
both N and O atoms are interconnected by a system of
p-conjugated double bonds.
Fukui functions (fk?, fk-, fk0), local softnesses (s?k , sk-, s0k), and
local electrophilicity indices (x?k , xk-, xk0) have been
described earlier in literature [54, 55]. Using Hirshfeld
population analyses of neutral, cation and anion state of
molecule, Fukui Functions are calculated at same calcula-
tion method B3LYP/6-31G(d,p) using Eqs. (7–9):
Chemical reactivity
Global reactivity descriptors
On the basis of Koopman’s theorem [51], global reactivity
descriptors electronegativity (v), chemical potential (l),
global hardness (g), global softness (S), and global elec-
trophilicity index (x) are calculated using the energies of
frontier molecular orbitals eHOMO, eLUMO and given by Eqs.
(1–5) [51–55]:
fkþ ¼ ½qðN þ 1Þ ꢁ qðNÞꢂ for nucleophilic attack
fk ¼ ½qðNÞ ꢁ qðN ꢁ 1Þꢂ for electrophilic attack
fk0 ¼ 1=2½qðN þ 1Þ þ qðN ꢁ 1Þꢂ for radical attack,
ð7Þ
ð8Þ
ð9Þ
where N, N - 1, N ? 1 are total electrons present in
neutral, cation, and anion state of molecule, respectively.
Local softnesses and electrophilicity indices are calcu-
lated using the following equations (10, 11).
v ¼ 1=2ðeLUMO þ eHOMO
l ¼ v ¼ 1=2ðeLUMO þ eHOMO
g ¼ 1=2ðeLUMO ꢁ eHOMO
S ¼ 1=2g
x ¼ l2=2g
Þ
ð1Þ
ð2Þ
ð3Þ
ð4Þ
ð5Þ
Þ
Þ
skþ ¼ Sfkþ; skꢁ ¼ Sfkꢁ; sk0 ¼ Sfk0
ð10Þ
ð11Þ
xþk ¼ xfkþ; xk ¼ xfkꢁ; x0k ¼ xfk0;
where ?, -, 0 signs show nucleophilic, electrophilic, and
Electrophilicity index (x) measures the stabilization in
energy when the system acquires an additional electronic
charge (DNmax) from the environment. The energies of
frontier molecular orbitals (eHOMO, eLUMO), energy gap
(eLUMO - eHOMO), electronegativity (v), chemical potential
(l), global hardness (g), global softness (S), and global
electrophilicity index (x) for reactants 1, 2, and product (3)
are listed in Table TS5 in Supplementary material. The
calculated high value of (x) for (3) shows that the title
molecule to be a strong electrophile than reactants 1 and 2.
radical attack respectively.
Fukui functions (fk?, fk-), local softnesses (sk?, s-k ), local
electrophilicity indices (x?k , x-k ) for selected atomic sites
of (3) are listed in Tables TS6 and TS7 in Supplementary
material, using Mulliken and Hirshfeld population analy-
ses, respectively. The maximum values of all the three
local electrophilic reactivity descriptors (f?k , sk?, xk?) at
C(7) indicate that this site is more prone to nucleophilic
attack. The calculated local reactivity descriptors of
123

Struct Chem
11. Affan MA, Foo IPP, Fasihuddin BA, Sim EUH, Hapipah MA
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synthesized molecule (3) favor the formation of new het-
erocyclic compounds such as azetidinones, oxadiazolines,
and thiazolidinones etc. by attack of nucleophilic part of
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Conclusions
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17. Deng X, Mani NS (2008) J Org Chem 73:2412
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1
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1
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NMR chemical shifts are in good agreement to each other.
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intra and intermolecular hydrogen bonds in dimer. In
addition, theoretical results from reactivity descriptors are
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type of compounds. The local electronic reactivity
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reactive site for nucleophilic attack and may be used as
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