Synthesis, Crystal Structure, and Characterization of (Z) -2-(3-chlorophenyl)- N -hydroxyacetamidine

Article abstract of DOI:10.1080/15421406.2014.905087

The compound (Z)-2-(3-chlorophenyl)-N-hydroxyacetamidine, (2) was synthesized and characterized by ¹H NMR, FT-IR, TGA, UV-Visible Spectra, and elemental analysis. Its molecular structure was solved by single-crystal X-ray diffraction method. Th

Full text of DOI:10.1080/15421406.2014.905087

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Synthesis, Crystal Structure,
and Characterization of (Z)-2-(3-
chlorophenyl)-N’-hydroxyacetamidine
M. Prabhuswamya, Dineshab, M. M. M. Abdohc, K. J. Pampad, S.
Madan Kumara, G. K. Nagarajab & N. K. Lokanatha
a Department of Studies in Physics, University of Mysore, Mysore,
India
b Department of Chemistry, Mangalore University, Mangalore, India
c Department of Physics, Faculty of Science, An Najah National
University, Nabtus West Bank, Palestinian Territories
d Department of Studies in Microbiology, University of Mysore,
Mysore, India
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Published online: 15 Jan 2015.
To cite this article: M. Prabhuswamy, Dinesha, M. M. M. Abdoh, K. J. Pampa, S. Madan Kumar, G.
K. Nagaraja & N. K. Lokanath (2015) Synthesis, Crystal Structure, and Characterization of (Z)-2-(3-
chlorophenyl)-N’-hydroxyacetamidine, Molecular Crystals and Liquid Crystals, 606:1, 189-198, DOI:
10.1080/15421406.2014.905087
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Mol. Cryst. Liq. Cryst., Vol. 606: pp. 189–198, 2015
Copyright © Taylor & Francis Group, LLC
ISSN: 1542-1406 print/1563-5287 online
DOI: 10.1080/15421406.2014.905087
Synthesis, Crystal Structure, and Characterization
of (Z)-2-(3-chlorophenyl)-N’-hydroxyacetamidine
M. PRABHUSWAMY,1 DINESHA,2 M. M. M. ABDOH,3
K. J. PAMPA,4 S. MADAN KUMAR,1 G. K. NAGARAJA,2
AND N. K. LOKANATH1,∗
1Department of Studies in Physics, University of Mysore, Mysore, India
2Department of Chemistry, Mangalore University, Mangalore, India
3Department of Physics, Faculty of Science, An Najah National University,
Nabtus West Bank, Palestinian Territories
4Department of Studies in Microbiology, University of Mysore, Mysore, India
The compound (Z)-2-(3-chlorophenyl)-N’-hydroxyacetamidine, (2) was synthesized and
characterized by 1H NMR, FT-IR, TGA, UV-Visible Spectra, and elemental analysis. Its
molecular structure was solved by single-crystal X-ray diffraction method. The title
molecule, C8H9ClN2O is crystallized in the monoclinic crystal system with the space
group P21/c and with unit cell parameters a = 8.7092(4) Å, b = 8.2370(4) Å, c =
12.5256(6) Å, β = 102.252(3)◦, and Z = 4. The molecular and crystal structure of the
. . .
title molecule is stabilized by an intramolecular interaction of the type N—H O, and
. . .
. . .
the intermolecular interactions of types N—H N and O—H N.
Keywords Amidoxime; characterization; crystal structure; molecular interactions
Versatile heterocyclic compounds were generally synthesized from carbonitrile. The re-
action of carbonitrile with hydroxylamine hydrochloride gave amidoximes. Amidoximes
are compounds bearing both a hydroxyimino and an amino group at the same carbon atom
which makes them versatile building blocks for the synthesis of various heterocycles [1].
1,2,4-oxadiazole skeleton are pharmacologically active and constructed mainly based on
the coupling reaction of amidoximes with carbonyl compounds using various coupling
agents [2]. The importance of amidoximes in chemistry along with their rich biology, make
them an attractive target for medicinal chemists, biochemists, and biologists. Their numer-
ous pharmaceutical applications such as bactericidal and fungicidal [3], local anesthetics
[4], antitumor and antimalarial agents [5], and their ability to release NO were clarified,
giving a new insight to their mode of action and allowing the design of novel therapeutic
agents. Motivated by these reflections, it was contemplated to synthesize the title compound
(Z)-2-(3-chlorophenyl)-N’-hydroxyacetamidine which is well characterized by the single-
crystal X-ray diffraction, 1H NMR, FT-IR, thermogravimetric analysis (TGA), UV-Visible
Spectra, and elemental analysis.
∗Address correspondence to N. K. Lokanath, Department of Studies in Physics, University of
Mysore, Mysore 570006, India. E-mail: lokanath@physics.uni-mysore.ac.in
Color versions of one or more of the figures in the article can be found online at
www.tandfonline.com/gmcl.
189

190
M. Prabhuswamy et al.
2. Experimental
2.1. Materials and Methods
Melting point was taken in an open capillary tube and was uncorrected. The purity of the
compound was confirmed by thin-layer chromatography using Merck silica gel 60 F254
coated aluminum plates. IR spectrum was recorded on Shimadzu-FTIR Infrared spectrom-
eter in KBr (νmax in cm−1). 1H NMR (400 MHz) spectrum was recorded on a Bruker Avance
II 400 spectrometer, with 5 mm PABBO BB-1H TUBES, using CDCl3 as a solvent and
TMS as internal standard (chemical shift in δ ppm). A TA-SQT Q600 thermogravimetric
analy◦zer was used to obtain the TGA curve under nitrogen atmosphere with a heating rate
of 10 C min−1. The UV-Vis spectrum was recorded on a Shimadzu UV-2550 UV-Visible
spectrophotometer. Elemental analysis was carried out by using VARIO EL-III (Elementar
Analysensysteme GmBH).
Scheme 1. Synthesis of Compound (Z)-2-(3-chlorophenyl)-N’-hydroxyacetamidine.
2.2. Procedure for the Preparation of (Z)-2-(3-chlorophenyl)-N’-hydroxyacetamidine
(2)
Sodium bicarbonate (70 mmol, 5.88 g) was added in portions to a solution of hydroxy-
lamine hydrochloride (70 mmol, 4.79 g) in 15 ml of water. A solution of (3-Chlorophenyl)
acetonitrile (35 mmol, 4.14 ml) in 40 ml of ethanol was then added, and the mixture stirred
under reflux for 6 h. The precipitate formed was filtered off and recrystallized from ethanol.
Yield 82%, m.p. 108–110◦C.
Figure 1. FT-IR spectrum.

Characterization of (Z)-2-(3-chlorophenyl)-N’-hydroxyacetamidine
191
Figure 2. 1H NMR spectra.
Figure 3. TGA thermogram of compound.
Figure 4. UV-Visible spectrum.

192
M. Prabhuswamy et al.
Table 1. Elemental analysis for C8H9ClN2O
Element
Experimental (%)
Calculated (%)
Carbon
Nitrogen
Hydrogen
52.08
15.13
4.95
52.04
15.17
4.91
3. Results and Discussion
3.1. FT-IR Spectral Analysis
The FT-IR spectrum of the crystal structure was shown in Fig. 1. IR spectra showed strong
absorption bands at 3327 and 3462 cm−1 due to primary amine group and vibration band
at 3134 cm−1 due to the hydroxyl group. The absorption peak at 1670 cm−1 is due to the
stretching vibration that corresponds to C N group. The C H deformation vibration
in CH2 is observed at 1471 cm−1. The absorption at 948 cm−1 is characteristic of N-O
stretching vibration in amidoxime moiety.
3.2. 1H NMR Spectral Analysis
1
1
The H NMR spectrum of the crystal structure was shown in Fig. 2. H NMR spectrum
showed sharp singlet at δ 3.45, 4.50 and δ 10.10 ppm due to CH2, NH2, and OH pro-
tons, respectively. The four aromatic protons resonated as a multiplet in the region of
δ 7.17–7.32 ppm.
Figure 5. ORTEP view of the title molecule with atom numbering scheme. Displacement ellipsoids
for nonhydrogen atoms are drawn at 30% probability level. Dashed line indicates intramolecular
. . .
hydrogen bond of the type N
H
O.

Characterization of (Z)-2-(3-chlorophenyl)-N’-hydroxyacetamidine
193
Figure 6. Packing of molecules when viewed down a-axis.
3.3. Thermogravimetric Analysis (TGA)
The TG analysis thermogram (solid line) of the compound is shown in Fig. 3. TGA of
compound 2 has been performed in the temperature range 30◦C–600◦C at a rate of 10◦C
min−1 under N2 atmosphere. The TGA curve shows that compound 2 exhibits a remarkable
thermal stability at about 150◦C. The compound decomposes mainly into two stages on
heating between the room temperature and 470◦C. The following decomposition pattern
suggested explains the TGA. The first weight loss is 49.0% in the range of 150◦C–250◦C,
which is ascribed to the loss of hydroxycyanamide and chlorine atom (calculated 50.0%).
These results show that amidoxime bonds are weaker than parent nitrile bonds. With further
heating, the 28.0% of the compound (calculated 29.4%) decomposed between 250◦C and
470◦C, which is ascribed to the passing of an acetylene molecule. The differences between
the experimental and calculated weight losses in both stages of decomposition are small
and are within the experimental errors. Above 470◦C, 23% of the residue were left out
which is due to the charring of carbon. Hence, the TG study confirms the formation of the
compound in the stoichiometric ratio.
3.4. UV-Vis Spectral Analysis
LikeFT-IR spectroscopy, UVspectroscopy is alsouseful intheevaluationof thecompounds.
On UV, electronic spectrum compounds are analyzed based on the characteristic frequencies
corresponding to definite groups and it is shown in Fig. 4. The UV-Vis spectrum was
recorded by using methanol as a solvent. From the graph, it was observed that the compound
shows an absorption peak at 275 nm. The transmittance of the compound is due to the π–π∗
transition of the constituent group. Hence, the material may be useful for optoelectronic
applications.

194
M. Prabhuswamy et al.
Table 2. Crystal data and structure refinement
Parameter
Value
CCDC deposit No.
Empirical formula
Formula weight
945517
C8H9ClN2O
184.62
Temperature
296(2) K
Wavelength
1.54178 Å
Crystal system, space group
Unit cell dimensions
Monoclinic, P21/c
a = 8.7092(4) Å b = 8.2370(4) Å
β = 102.252(3) c = 12.5256(6) Å
878.09(7) Å3
Volume
Z, Calculated density
Absorption coefficient
F(000)
4, 1.397 Mg/m3
3.469 mm−1
384
Crystal size
Theta range for data collection
Limiting indices
0.23 × 0.20 × 0.19 mm
5.2 to 64.4◦
–10 ≤ h ≤ 9, –9 ≤ k ≤ 7, –14 ≤ l ≤ 11
5474 / 1442 [R(int) = 0.042]
97.8%
0.559 and 0.503
Full-matrix least-squares on F2
1442/0/110
Reflections collected / unique
Completeness to theta = 64.4◦
Max. and min. transmission
Refinement method
Data / restraints / parameters
Goodness-of-fit on F2
Final R indices [I>2sigma(I)]
R indices (all data)
1.07
R1 = 0.0541, wR2 = 0.1467
R1 = 0.0584, wR2 = 0.1520
0.0095(19)
0.30 and –0.44 e. Å−3
Extinction coefficient
Largest diff. peak and hole
3.5. Elemental Analysis
In order to confirm the chemical composition of the synthesized compound, Carbon (C),
Hydrogen (H), and Nitrogen (N) analysis was carried out. The experimental and calculated
percentages of C, H, and N are given in Table 1. The differences between experimental
Table 3. Selected bond lengths and angles (Å,◦)
Cl(12)–C(2)
O(11)–N(10)
1.745(3)
1.446(2)
N(10)–C(8)
1.285(3)
N(9)–C(8)
1.343(3)
C(8)–N(10)–O(11)
N(10)–C(8)–N(9)
N(10)–C(8)–C(7)
N(9)–C(8)–C(7)
C(1)–C(2)–Cl(12)
C(3)–C(2)–Cl(12)
110.19(19)
125.1(2)
116.4(2)
118.5(2)
119.14(19)
119.10(19)

Characterization of (Z)-2-(3-chlorophenyl)-N’-hydroxyacetamidine
195
Figure 7. Packing of molecules when viewed down b-axis.
Table 4. Selected torsion angles (◦)
N(10)–C(8)–C(7)–C(4)
102.9(3)
N(9)–C(8)–C(7)–C(4)
C(3)–C(4)–C(7)–C(8)
C(5)–C(4)–C(7)–C(8)
O(11)–N(10)–C(8)–C(7)
O(11)–N(10)–C(8)–N(9)
−78.6(3)
129.2(2)
−53.9(3)
179.71(19)
1.2(3)
Table 5. Hydrogen bond geometry (Å, ◦)
. . .
. . .
d(H A)
. . .
d(D A)
D—H
A
d(D—H)
<(DHA)
∗
. . .
N9—H9A O11
0.86
0.86
0.82
2.26
2.21
2.11
2.570(3)
3.039(3)
2.766(3)
101
162
137
. . .
N9—H9B O11(i)
. . .
O11—H1 N10(ii)
Symmetry codes: (i) 1−x, −1/2+y, 1/2−z; (ii) 1−x, 2−y, 1−z.
∗Intramolecular interaction.

196
M. Prabhuswamy et al.
Figure 8. Packing of molecules when viewed down c-axis.
and calculated percentages of C, H, and N were very close to each other and within
the experimental errors. This confirms the formation of the product in the stoichiometric
proportion.
3.6. Single Crystal X-Ray Diffraction Method
A colorless block-shaped single crystal of size 0.23 × 0.20 × 0.19 mm of the title compound
was selected for data collection. X-ray intensity data were collected for the title compound
at temperature 296 K, on Bruker AXS Proteum2 CCD diffractometer with X-ray generator
operating at 45 kV and 10 mA, using CuKα radiation of wavelength 1.54178 Å. Data were
collected for 24 frames per set with different settings of φ (0◦ and 90◦), keeping the scan
width of 0.5◦, exposure time of 5 s, the sample to detector distance of 45.10 mm, and 2θ
value at 46.6◦ [6]. A complete dataset is processed using the software SAINT PLUS [7].
The structure was solved by direct methods and refined by full-matrix least squares method

Characterization of (Z)-2-(3-chlorophenyl)-N’-hydroxyacetamidine
197
on F2 using SHELXS and SHELXL programs [8]. All nonhydrogen atoms were revealed in
the first difference Fourier map itself. All hydrogen atoms were positioned geometrically
(C–H = 0.93 Å, N–H = 0.86 Å, O–H = 0.82 Å) and refined using a riding model with
Uiso(H) = 1.2 Ueq (C,N) and Uiso(H) = 1.5 Ueq (O). After several cycles of refinement,
the final difference Fourier map showed peaks of no chemical significance and the residual
is saturated to 0.0541. The geometrical calculations were carried out using the program
PLATON [9]. The molecular and packing diagrams were generated using the software
MERCURY [10].
X-ray diffraction analysis revealed that the title compound is crystallized in the mono-
clinic crystal system with the space group P21/c. The unit cell parameters are a = 8.7092(4)
Å, b = 8.2370(4) Å, c = 12.5256(6) Å, β = 102.252(3)◦ and V = 878.09(7) Å3. The ORTEP
view of the title molecule with displacement ellipsoids drawn at 30% probability level is
shown in Fig. 5.
The packing of molecules when viewed down a-axis, b-axis, and c-axis are as given
in Fig. 6, Fig. 7, and Fig. 8, respectively. The crystal data and structure refinement details
are given in Table 2. Bond lengths and bond angles are given in Table 3. Torsion angles are
given in Table 4. Hydrogen-bond geometry is given in Table 5.
Torsional angles of 179.71(19)◦ about O11—N10—C8—C7 and 1.2(3)◦ about
O11—N10—C8—N9 confirm that C7 atom and the amidoxime chain are planar. The
chlorine-substituted phenyl ring, C1/C2/C3/C4/C5/C6 lies in the equatorial position with
respect to the plane described by the chain C7—C8—N9—N10—O11 containing amidx-
oime, confirmed by the dihedral angle 76.83(12)◦. The overall geometry is similar to the
molecule 4-Chlorobenzamidoxime [11].
. . .
An intramolecular interaction N9–H9A O11 forms a five membered planar ring
. . .
C8/N9/H9A/O11/N10 with amidoxime chain. The crystal structure exhibits N9–H9A
π
. . .
interaction (N9–H9A Cg(1) [where Cg(1) is the centroid of the ring C1/C2/C3/C4/C5/C6
. . .
angle of 139◦) and the structure is stabilized by the intermolecular hydrogen bond interac-
with a symmetry code 1–x,1/2+y, 1/2–z] with a N—Cg distance of 3.484(3) Å, N—H Cg
. . .
. . .
tions of types N—H O and O—H N, giving two-dimensional chains along bc-plane in
the crystal lattice.
4. Conclusion
The compound (Z)-2-(3-chlorophenyl)-N’-hydroxyacetamidine, (2) was synthesized and
characterized by means of 1H NMR, FT-IR, TGA and UV–visible spectroscopy data. The
molecular structure of this compound was determined by single crystal XRD method. The
crystal structure of the title compound reveals a potentially tautomeric amidoximes to be
the amino-oxime form and it adopts a nonplanar cis-syn configuration. Spectral data show
that the material may be useful for optoelectronic applications.
Acknowledgments
The authors thank the IOE X-ray diffraction facility, University of Mysore, Mysore, for
collecting the data.
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