Synthesis, molecular and solid state structure of 5-(5-nitro furan-2-ylmethylen), 3-N-(2-methoxy phenyl), 2-N′-(2-methoxyphenyl) imino thiazolidin-4-one: X-ray powder diffraction and DFT studies

Article abstract of DOI:10.1016/j.molstruc.2017.04.091

The 5-(5-nitro furan-2-ylmethylen), 3-N-(2-methoxy phenyl), 2-N′-(2-methoxyphenyl) imino thiazolidin-4-one compound has been synthesized and fully characterized by FT-IR, ¹H and ¹³C NMR spectroscopy. The crystal structure of the titl

Full text of DOI:10.1016/j.molstruc.2017.04.091

Accepted Manuscript
Synthesis, molecular and solid state structure of 5-(5-nitro furan-2-ylmethylen), 3-N-
(2-methoxy phenyl),2-N’-(2-methoxyphenyl) imino thiazolidin-4-one: X-ray powder
diffraction and DFT studies
Rachida Rahmani, Ahmed Djafri, Abdelkader Chouaih, Ayada Djafri, Fodil Hamzaoui,
Rosanna Rizzi, Angela Altomare
PII:
S0022-2860(17)30544-6
10.1016/j.molstruc.2017.04.091
MOLSTR 23714
DOI:
Reference:
To appear in: Journal of Molecular Structure
Received Date: 17 February 2017
Revised Date: 22 April 2017
Accepted Date: 23 April 2017
Please cite this article as: R. Rahmani, A. Djafri, A. Chouaih, A. Djafri, F. Hamzaoui, R. Rizzi, A.
Altomare, Synthesis, molecular and solid state structure of 5-(5-nitro furan-2-ylmethylen), 3-N-(2-
methoxy phenyl),2-N’-(2-methoxyphenyl) imino thiazolidin-4-one: X-ray powder diffraction and DFT
studies, Journal of Molecular Structure (2017), doi: 10.1016/j.molstruc.2017.04.091.
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Graphical abstract

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Synthesis, molecular and solid state structure of 5-(5-nitro furan-2-
ylmethylen), 3-N-(2-methoxy phenyl),2-N’-(2-methoxyphenyl) imino
thiazolidin-4-one: X-ray powder diffraction and DFT studies
Rachida Rahmania, Ahmed Djafria,b, Abdelkader Chouaiha, Ayada Djafric, Fodil Hamzaouia,
Rosanna Rizzid, Angela Altomared,
aLaboratory of Technology and Solid Properties, Faculty of Sciences and Technology, Abdelhamid Ibn Badis
University, BP 227 Mostaganem 27000, Algeria
bCentre de Recherche Scientifique et Technique en Analyses Physico-chimiques (CRAPC), BP 384-Bou-Ismail-
RP 42004, Tipaza-Algeria
cLaboratoire de Synthèse Organique Appliquée (LSOA), Département de Chimie, Faculté de Sciences,
University of Oran–Es-Sénia, 31000 Oran, Algeria
dCNR-IC Institute of Crystallography, Via Amendola 122/O, 70126 Bari, Italy.
Abstract
The 5-(5-nitro furan-2-ylmethylen), 3-N-(2-methoxy phenyl), 2-N’-(2-methoxyphenyl) imino
1
thiazolidin-4-one compound has been synthesized and fully characterized by FT-IR, H and
13C NMR spectroscopy. The crystal structure of the title compound was investigated by X-ray
powder diffraction (XRPD). The obtained structure is triclinic, space group P-1, with a =
11.4746(3), b = 10.9106(2),c = 8.8083(2) Å,
α = 103.6665(9)°β = 91.4910(13)° γ =
84.1433(12)°, V =1065.93(4)Å3 and Z = 2. The XRPD structural investigation has been
completed by a theoretical analysis performed using the density functional theory (DFT) via a
B3LYP functional at 6-311G(d,p) basis set. To highlight and establish the contribution of the
different intermolecular interactions, Hirshfeld surface analysis and fingerprint plots were
performed. The solid state molecular structure and packing are discussed.
Keywords: Molecular structure, Expo, thiazole, heterocycles, organic compounds
1. Introduction
Heterocyclic compounds with a thiazole moiety are one of the most important classes of
organic compounds which have attracted much attention for their biological activities [1-4].
Investigation of the absolute molecular configuration of organic compounds containing five-
membered heterocycles ring derivatives has been the subject of theoretical and experimental
studies [5-7].

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Thiazolidinone is obtained from the thiazolidine structure including heteroatoms in a five
membered cycle. It is contained in a variety of bioactive compounds, especially anti-HIV,
anti-bacterial, anti-tuberculosis, anti-tumor, anti-histaminic, or anti-convulsant agents [8-11].
Beyond these biological activities, the anti-inflammatory action of thiazolidinone-containing
compounds has recently become of particular interest [12]. As an example, the 5-arylidene-2-
imino-4- thiazolidinones [13] were synthesized by the reaction of thiazolidinones and
appropriate aldehydes under basic conditions in ethanol at reflux for about 2-7 hours. The
thiazolidinones in turn were obtained by Hantzsch cyclisation [14].
As a continuation of our studies on thiazole derivatives, we have sought to synthesize a novel
thiazolidinone compound incorporating thiazole unit [15-17]. We herein report the synthesis
and structure of 5-(5-nitro furan-2-ylmethylen), 3-N-(2-methoxy phenyl),2-N’-(2-
methoxyphenyl) imino thiazolidin-4-one, a simple molecule that belongs to the sulfur-
containing N,O-heterocycles. The title compound has been characterized by spectral data
(FTIR, 1H NMR and 13C NMR) and X-ray powder diffraction analysis. DFT calculations have
been executed to confirm the results.
2. Experimental and theoretical details
2.1. Synthesis
(N, N’) di(2-methoxy phenyl) thiourea (b) has been synthesized by condensation of 2-
methoxy phenyl amine (a) with carbon disulfide in dry ethanol. Compound (b), on treatment
with ethyl bromoacetate in absolute ethanol yielded to 3-N-(2-methoxy phenyl), 2-N’- (2-
methoxyphenyl)imino thiazolidin-4-one (c).
Compound (c), on reaction with 2-nitro furaldehyde in acetic acid leads to the formation of 5-
(5-nitro furan-2-ylmethylen), 3-N-(2-methoxy phenyl),2-N’-(2-methoxyphenyl) imino
thiazolidin-4-one (d) for 2h. (Scheme 1).

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Scheme 1. Synthetic route of 5-(5-nitro furan-2-ylmethylen), 3-N-(2-methoxy phenyl),2-N’-
(2-methoxyphenyl) imino thiazolidin-4-one (d)
2.2. Spectral Analysis
Melting points of all synthesized compounds were determined on a Köfler hot-stage
apparatus. The FT-IR spectrum of the title compound has been recorded as KBr pellets on a
JASCO FT/IR-4200 Fourier transform infrared spectrometer from the range of 4000-400 cm-1
in a solid phase at room temperature, number of scans 8, resolution 4 cm-1 and the reported
1
wavenumbers are given in cm−1. The H and 13C-NMR spectra were recorded on a Brüker
AC300 MHz instrument using CDCl3 as solvent and TMS as internal standard. All yields
refer to isolated products after purification.
Procedure for the preparation of (N, N’) di(2-methoxy phenyl) thiourea(b)
In dry ethanol, we added 0.01 mol of carbon disulfide to 0.02 mol of 2-methoxy phenyl amine
(a) and the mixture was refluxed for 2 hours. The resulting solid was washed with water and
recrystallized in ethanol to give (b).
White solid, Yield 70%, m.p. 132-132,5°C; IR (KBr) cm−1: 3400 (NH), 1600(C=C), 1340(C-
1
N),1210 (C=S); H-NMR (CDCl3): 8.2 (s, 2H, N-H), 7.4-7.1(m, 8H, ArH), 3.84(s, 6H,
OCH3); 13C-NMR (CDCl3): 179.60(C=S), 158.80(C-O-C), 114.40, 125.50, 121.20, 163.30,
125.10(C-N), 54.20 (OCH3).
Procedure for the preparation of 3-N-(2-methoxy phenyl), 2-N’- (2-methoxyphenyl)imino
thiazolidin-4-one(c)
A mixture of compound (b) (0.0035 mol) and ethyl bromoacetate (0.0035 mol) in absolute
ethanol (20 ml) was refluxed for 1 hour in the presence of sodium acetate (0.010 mol).The
obtained solid was recrystallized in ethanol to provide (c).

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White solid, Yield 74%, m.p. 207-208°C; IR (KBr) cm−1: 3064 (C-H), 1723(C=O),
1
1639(C=N), 1600 (C=C), 1378(C-N), 1111(C-O-C); H-NMR (CDCl3): 7.45-6.80(m, 8H,
ArH), 3.97(s, 2H, thiazolidin-4-one), 3.89(s, 3H, OCH3), 3.80(s, 3H, OCH3); 13C-
NMR(CDCl3): 171.34(C=O), 154.93(C=N), 148, 140.20, 135, 130.85, 129.82, 125.38,
123.49, 121.74, 121.14, 120.88, 112.50, 112.24, 55.90(OCH3), 55.85(OCH3), 33.03(CH2).
Procedure for the preparation of 5-(5-nitro furan-2-ylmethylen), 3-N-(2-methoxy phenyl),2-
N’-(2-methoxyphenyl) imino thiazolidin-4-one (d)
A mixture of compound (c) (0.001 mol) and 2-nitro-furaldehyde (0.001 mol) was refluxed in
acetic acid for 2 hours in presence of sodium acetate (0.002 mol). After cooling, the solid was
filtered and recrystallized in ethanol to yield the product (d).
Orange solid, Yield 60%, m.p. 224 °C; IR (KBr) cm−1: 3046 (C-H), 1710 (C=O), 1652(C=N),
1
1610 (C=C), 1110 (C-O-C); H-NMR (CDCl3): 7.56-6.75 (m, 10H), 7.38(d, 1H, C=C-H),
3.89(s, 3H, OCH3), 3.80(s, 3H, OCH3); 13C-NMR (CDCl3): 190.57 (C=O), 165.16 (C=N),
154.94, 152.20, 150.53, 150.04, 136.80, 131.16, 129.80, 128.34, 126.27, 123.03, 121.77,
121.16, 121.00, 116.04, 114.19, 113.50, 112.53, 112.17, 55.95(OCH3), 55.81(OCH3).
2.3. Powder data collection
The X-ray powder diffraction method was used to determine the crystal structure of the title
compound, which was prepared with a grain size less than 40 µm.
Powder diffraction data were collected at room temperature (296 K) by using an automated
Rigaku RINT2500 laboratory diffractometer (50 KV, 200 mA), equipped with an asymmetric
Johansson Ge(111) crystal to select the monochromatic Cu Kα1 radiation (λ=1.54056 Å). The
silicon strip Rigaku D/teX Ultra detector was used.
The angular range 7-70º (2θ) was scanned with a step size of 0.02º (2θ) and counting time of
6 s/step. The sample was introduced in a special glass capillary of 0.5 mm of diameter,
mounted on the axis of the diffractometer. During the measurement, it was put in rotation to
improve the randomization of the orientations of the individual crystallites in order to reduce
the effects of possible preferred orientation. The experimental powder diffraction pattern is
depicted in figure 1.
All the steps of the ab initio crystal structure solution process by powder diffraction data were
carried out by using EXPO2013 software [18], a package able to automatically execute the
full pathway of the solution process: 1) indexation; 2) space group determination; 3)

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integrated intensities extraction; 4) phasing process by Direct Methods and/or structure
solution in the direct space by simulated annealing; 5) Rietveld refinement [19].
Figure1 X-ray powder diffraction pattern
Table 1 Crystallographic data for C22H17O6N3S
Chemical formula
Mr
C22H17O6N3S
451
Crystal system
Space group, Z
a (Å)
b (Å)
c (Å)
Triclinic
P-1, 2
11.4746(3)
10.9106(2)
8.8083(2)
103.6665(9)
91.4910(13)
84.1433(12)
1065.93(4)
1.540560
7, 70
α
β
γ
(°)
(°)
(°)
V (Å3)
λ
(Å)
2
θmin, 2θmax(°)
Reflections
919
2.4. Computational analysis
Computational calculation was performed by using GaussView molecular visualized program
[20] and Gaussian03W package [21] on a personal computer. The molecular structure in the
ground state was optimized by Density Functional Theory using B3LYP/6−311G(d,p) basis
set [22, 23].

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2.5. Hirshfeld Surface analysis
The Hirshfeld Surface analyses [24] and the related 2D-fingerprint plots [25, 26] were
performed using Crystal Explorer program [27]
given by:
.
The normalized contact distance (dnorm) is
(ꢀꢅ − ꢆꢇꢈꢉ
)
(ꢀꢊ − ꢆꢇꢈꢉ
)
ꢊ
ꢅ
ꢀꢁꢂꢃꢄ
=
+
ꢆꢇꢈꢉ
ꢆꢇꢈꢉ
ꢊ
ꢅ
where ꢀꢅ is the distance from the point to the nearest nucleus internal to the surface, ꢀꢊ is the
corresponding distance to the nearest nucleus external to the surface. ꢆꢇꢈꢉ and ꢆꢇꢈꢉ are the
ꢊ
ꢅ
van der Waals radii of the atoms. Depending on the intermolecular contacts being shorter or
longer than the Van Der Waals distances, the value of dnorm can be negative or positive.
3. Results and discussion
3.1. Structural solution and refinement
All the crystal structure solution steps of the title compound were performed using the
EXPO2013 program. The indexation step was carried out by using the N-TREOR09 program
[28] integrated in EXPO2013. 69 lines of the diffraction pattern, with intensity values greater
than a default threshold, were automatically selected by the program. Among them, the first
25 low angle well defined peaks were used to find a feasible unit cell which was then refined
involving all the 69 peaks. A triclinic cell, characterized by values of M20 [29] and Fomnew
[28] figures of merit equal to 44 and 2.496 respectively, was obtained with cell parameters:
a=11.4803(17), b=10.9123(17), c=8.8103(18) Å, α=103.661(13)o, β=91.489(13)o,
γ=84.164(17)o and V = 1066.9(3)Å3. The space group P-1 was then selected. Detailed
crystallographic information are summarized in Table 1.
In order to carry out the structure solution, the experimental powder patter was decomposed
into single integrated intensities by using the Le Bail algorithm [30]. The obtained observed
amplitudes were successively used in the ab-initio solution process by Direct Methods [31] in
EXPO2013.
The hydrogen atoms were geometrically located in calculated positions. The constraint
Uiso(H) = kUiso(C), where k = 1.2 for methyl and k = 1.2 for aromatic H atoms, was applied.
The structure was then refined by the Rietveld method in EXPO2013.
The refinement procedure converged to the discrepancy indices reported in Table 2; the
values are indicative of reliable results and the agreement between the observed (blue line)

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and the calculated pattern (red line) is shown in Figure 2. The violet curve is the difference
pattern, plotted at the same scale as the other patterns.
The refined fractional atomic coordinates and the isotropic displacement parameters of the
title compound are reported in Table S3.
In Figure 3 the final refined crystal structures, as obtained at the end of the EXPO2013 run
(Fig. 3a) and via the DFT calculations (Fig. 3b), are shown.
The corresponding geometrical parameters (bond lengths, bond angles and torsion angles), are
given in Tables S4, S5 and S6, respectively.
Some values of C−N distances show the single bond character of these bonds. Whereas, other
bond lengths are intermediate between the classical lengths of single [C−N (1.47 Å)] and
double [C=N (1.27 Å)] bonds, which indicate that the thiazole moiety is an effective electron-
conjugated substructure. In the thiazole ring, the C–S distances are in agreement with a
C(sp2)−S single bond length which is about 1.76 Å. The C=O bond length is in good
agreement with the standard double bond value of 1.20 Å.
The bond angles values (see Table S5) indicate that the π electrons in the title molecule are
delocalized, while the torsion angles (see Table S6) indicate that the structure is formed by
three fragments, which are in three different planes.
The structure is stabilized by intramolecular hydrogen bonds, which link the molecules into a
three-dimensional supramolecular architecture. Figure 4 shows the C–H⋅⋅⋅O hydrogen bonds
which ensure crystal packing in the unit cell. In general, the results indicate the good
agreement between XRPD values and results from DFT. It is noteworthy that most of the
optimized parameters have slightly larger values than the corresponding experimental ones.
The small differences can be because theoretical calculations imply isolated molecule in
gaseous phase state while experimental results refer to the molecule in the solid state.
Table 2 Structure refinement parameters for C22H17O6N3S
χ2
Rp
Rwp
Rexp
Rpʹ
Rwpʹ
Rexpʹ
DW
RBragg RF
1.942 2.840 1.988 2.040 11.050 9.905 6.934 0.332
5.973 6.330

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Figure 2 Final Rietveld plot of the title compound: observed profile (blue line); calculated
profile (red line); difference profile (violet line); background (green line)
(a)
(b)
Figure 3 Structure of 5-(5-nitro furan-2-ylmethylen), 3-N-(2-methoxy phenyl),2-N’-(2-
methoxyphenyl) imino thiazolidin-4-on, with the atom numbering. (a): X-ray structure, (b):
via DFT calculations

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Figure 4 Crystal packing
3.2. Hirshfeld surface analysis
Intermolecular interactions in the crystal packing can be represented using Hirshfeld surface
(HS) analysis and the fingerprint plots, which provide quantitative information about the
individual contribution of each intermolecular interaction. In three-dimensional HS, red, white
and blue colors highlighted intermolecular contacts [32].
The HS of the title compound is illustrated in Figure 5, showing surfaces that have been
mapped over a dnorm range from−0.304 to 1.440 Å. The large and deep red spots on the dnorm
HS indicate the close-contact interactions, which are mainly responsible for the significant
hydrogen bonding contacts as can be seen in figure 6.The full 2D fingerprint plot is displayed
in figure 7, by using the expanded view (from 0.6 to 2.8 Å) with the de and di distance scales
on the graph axes. Excepting the H⋅⋅⋅H contacts on the surface, necessary for organic
molecules, the most important contacts are the H⋅⋅⋅O/O⋅⋅⋅H ones, which appear as highlighted
red spots on the HS (Figures 5 and 6). These spots indicate contact point with the atoms
forming the C–H⋅⋅⋅O intermolecular interactions, which correspond to weak hydrogen bonds.

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Figure 5 View of the HS for the title compound
Figure 6 HS mapped for thetitle compound with dnorm selected intermolecular contacts

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Figure 7 The full 2D fingerprint plot
4. Conclusion
In this work, we present for the first time the structure determination of a new organic
compound using X-ray powder diffraction and DFT methods. The compound 5-(5-nitro furan-
2-ylmethylen), 3-N-(2-methoxy phenyl), 2-N’-(2-methoxyphenyl) imino thiazolidin-4-one
1
13
was synthesized and characterized by means IR, H and C NMR spectroscopy. Its crystal
structure was determined using X-ray powder diffraction technique. The compound
crystallizes in the triclinic crystal system, space group P-1. The experimental structure was
complemented with quantum chemical calculations showing a good agreement. In the crystal
structure, molecules are packed through intermolecular hydrogen bonds. Hirshfeld surface
(HS) analysis and fingerprint plots are carried out in order to highlight and quantify
intermolecular interactions. The results indicate that excepting the H⋅⋅⋅H interactions, the
most important contacts are H⋅⋅⋅O/O⋅⋅⋅H. These latter constitute the C–H⋅⋅⋅O intermolecular
interactions corresponding to weak hydrogen bonds.
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ACCEPTED MANUSCRIPT
HIGHLIGHTS
ꢀ Synthesis and characterization of the title compound have been reported.
ꢀ Solid state X-ray structure of the title compound was determined.
ꢀ Molecular structure of the molecule has been obtained by DFT study.
ꢀ Intermolecular interactions were examined using Hirshfeld surface analysis.