Crystal structure and Hirshfeld surface analysis of (E)-3-(2-chloro-4-fluoro­phen­yl)-1-(2,5-di­chloro­thio­phen-3-yl)prop-2-en-1-one

Sanjeeva Murthy, T.N.; Naveen, S.; Chidan Kumar, C.S.; Veeraiah, M.K.; Quah, C.K.; Siddaraju, B.P.; Warad, I.

doi:10.1107/S2056989018010216

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Volume 74| Part 8| August 2018| Pages 1134-1137

https://doi.org/10.1107/S2056989018010216

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Crystal structure and Hirshfeld surface analysis of (E)-3-(2-chloro-4-fluorophenyl)-1-(2,5-dichlorothiophen-3-yl)prop-2-en-1-one

T. N. Sanjeeva Murthy,^a S. Naveen,^b ^* C. S. Chidan Kumar,^c M. K. Veeraiah,^d Ching Kheng Quah,^e B. P. Siddaraju ^f and Ismail Warad ^g ^*

^aDepartment of Chemistry, Sri Siddhartha Academy of Higher Education, Tumkur 572 107, Karnataka, India, ^bDepartment of Physics, School of Engineering and Technology, Jain University, Bangalore 562 112, India, ^cDepartment of Engineering Chemistry, Vidya Vikas Institute of Engineering & Technology, Visvesvaraya Technological University, Alanahally, Mysuru 570 028, Karnataka, India, ^dDepartment of Chemistry, Sri Siddhartha Institute of Technology, Tumkur 572 105, Karnataka, India, ^eX-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia, ^fDepartment of Chemistry, Cauvery Institute of Technology, Mandya 571 402, Karnataka, India, and ^gDepartment of Chemistry, Science College, An-Najah National University, PO Box 7, Nablus, West Bank, Palestinian Territories
^*Correspondence e-mail: s.naveen@jainuniversity.ac.in, khalil.i@najah.edu

Edited by D.-J. Xu, Zhejiang University (Yuquan Campus), China (Received 4 July 2018; accepted 15 July 2018; online 24 July 2018)

In the title chalcone–thiophene derivative, C₁₃H₆Cl₃FOS, the aromatic rings are inclined to one another by 12.9 (2)°, and the thiophene ring is affected by π-conjugation. In the crystal, molecules are linked by C—H⋯F hydrogen bonds, forming an R₂²(8) ring motif. A Hirshfeld surface analysis was conducted to verify the contribution of the different intermolecular interactions. The shape-index surface clearly shows that the two sides of the molecules are involved in the same contacts with neighbouring molecules and the curvedness plots show flat surface patches characteristic of planar stacking.

Keywords: Thiophene chalcone; crystal structure; $[R_{2}^{2}]$ (8) ring motif; hydrogen bonding; Hirshfeld surface analysis.

CCDC reference: 1036795

1. Chemical context

Natural products are important sources in the search for new agents for cancer therapies with minimal side effects. Chalcones, considered to be the precursor of flavonoids and isoflavonoids, are abundant in edible plants. Compounds with the 1,3-diphenylprop-2-en-1-one framework are described by its generic term `chalcone'. They consist of open-chain flavonoids in which the two aromatic rings are joined by a three-carbon α,β-unsaturated carbonyl system. These are coloured compounds because of the presence of the –CO—CH=CH– chromophore, which depends in the presence of other auxochromes. Accumulating evidence has shown that chalcones and their derivatives could inhibit tumor initiation and progression. In view of the above, and as a part of our ongoing research on chalcone derivatives (Naveen et al., 2017 ; Lokeshwari et al., 2017 ; Tejkiran et al., 2016 ), we report herein the synthesis, crystal structure and Hirshfeld surface analysis of the title compound.

2. Structural commentary

The molecular structure of the title compound, shown in Fig. 1, is comprised of two aromatic rings (chlorofluorophenyl and dichlorothiophene) linked by C=C—C(=O)—C enone bridge. The bond lengths and bond angles are normal and the molecular conformation is characterized by a dihedral angle of 12.9 (2)° between the mean planes of the two aromatic rings. The olefinic double bond C6=C7 of 1.303 (6) Å is in an E configuration and is Csp² hybridized. The unsaturated keto group is in a syn-periplanar conformation with respect to the olefenic double bond, which is evident from the torsion angle value of −0.5 (8)° for the atoms O1—C5—C6—C7. The thiophene ring is affected by π conjugation. This can be explained by the longer C=S values of 1.703 (6) and 1.714 (4) Å for S1=C2 and S1=C1, respectively. The bond-angle values O1—C5—C6 [121.9 (4)°], O1—C5—C4 [118.2 (4)°] and C5—C6—C7 = 125.14 (4)° about C5 indicate that the carbon atom is in a distorted trigonal–planar configuration, which is due to steric hindrance of the oxygen atom. The molecular structure is stabilized by an intramolecular C6—-H6A⋯Cl1 hydrogen bond (Table 1) that closes an S(6) motif, as shown in Fig. 1.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C6—H6A⋯Cl1	0.93	2.47	3.207 (5)	136
C10—H10A⋯F1ⁱ	0.93	2.54	3.433 (6)	160
Symmetry code: (i) -x+3, -y+2, -z.

Figure 1
The molecular structure of the title compound, indicating the atom-numbering scheme. The intramolecular C—H⋯Cl hydrogen bond (dashed line) closes an S(6) motif. Displacement ellipsoids are drawn at the 50% probability level.

3. supramolecular features

In the crystal, the molecules are linked by C—H⋯F hydrogen bonds, forming an $[R_{2}^{2}]$ (8) ring motif as shown in Fig. 2. The structure also features π–π interactions: Cg1⋯Cg1(x − 1, y, z) = 3.956 (3) Å [α = 0°, β = 24.0°, γ = 24.0°, perpendicular distance of Cg1 on itself = 3.6131 (19) Å] and Cg2⋯Cg2(x + 1, y, z) = 3.957 (3) Å [α = 0°, β = 27.3°, γ = 27.3°] where Cg1 and Cg2 are the centroids of the S1/C1–C4 and C8–C13 rings, respectively.

Figure 2
The $[R_{2}^{2}]$ (8) ring motif.

4. Database survey

A survey of the Cambridge Structural Database (CSD, Version 5.39, last update November 2016; Groom et al., 2016 ) using (E)-3-(phenyl)-1-(2,5-dichlorothiophen-3-yl)prop-2-en-1-one as the main skeleton revealed the presence of three structures containing a similar 2,5-dichlorothiophene–chalcone moiety to the title compound but with different substituents on the terminal phenyl rings, viz. [(E)-1-(2,5-dichloro-3-thienyl)-3-(X)prop-2-en-1-one], where X = 4-(dimethylamino)phenyl (Dutkiewicz et al., 2010 ), 3,4-dimethoxyphenyl (Harrison et al., 2010a ) and 6-methoxy-2-naphthyl (Jasinski et al., 2010 ). In these three compounds, the dihedral angles between the central and terminal phenyl/naphthyl ring are in the range 2.13–11.90°. The difference may arise from the intermolecular hydrogen bonds between adjacent molecules.

5. Hirshfeld surface analysis

Hirshfeld surfaces and fingerprint plots were generated for the title compound based on the crystallographic information file (CIF) using CrystalExplorer (McKinnon et al., 2007 ). Hirshfeld surfaces enable the visualization of intermolecular interactions with different colours and colour intensity representing short or long contacts and indicating the relative strength of the interactions. Figs. 3 and 4 show the Hirshfeld surfaces mapped over d_norm (−0.139 to 1.120 a.u.) and shape-index (−1.0 to 1.0 a.u.), respectively. The calculated volume inside the Hirshfeld surface is 325.37 Å³ in the area of 310.17 Å³.

Figure 3
View of the three-dimensional Hirshfeld surface of the title compound mapped over d_norm.

Figure 4
Hirshfeld surface of the title compound mapped over (a) shape-index and (b) curvedness.

In Fig. 4, the dark spots near atoms Cl1 and F1 result from the C6—H6A⋯Cl1 and C10—H10A⋯F1 interactions, which play a significant role in the molecular packing of the title compound. The Hirshfeld surfaces illustrated in Fig. 4 also reflect the involvement of different atoms in the intermolecular interactions through the appearance of blue and red regions around the participating atoms, which correspond to positive and negative electrostatic potential, respectively. The shape-index surface clearly shows that the two sides of the molecules are involved in the same contacts with neighbouring molecules while the curvedness plots show flat surface patches characteristic of planar stacking.

The overall two-dimensional fingerprint plot for the title compound and those delineated into Cl⋯H/H⋯Cl, C⋯C, Cl⋯Cl, Cl⋯S/S⋯Cl, H⋯H, F⋯H/H⋯F, C⋯H/H⋯C contacts are illustrated in Fig. 5; the percentage contributions from the different interatomic contacts to the Hirshfeld surfaces are as follows: Cl⋯H (13.8%), C⋯C (12.7%), Cl⋯Cl (12.4%), Cl⋯S (10.7%), F⋯H (10.2%), H⋯H (10.1%), C⋯H (8.3%). The percentage contributions for other intermolecular contacts are less than 5% in the Hirshfeld surface mapping.

Figure 5
Two-dimensional fingerprint plots showing the percentage contributions of the various interactions.

6. Synthesis and crystallization

The title compound was synthesized as per the procedure reported earlier (Kumar et al., 2013a ,b ; Chidan Kumar et al., 2014 ). 1-(2,5-Dichlorothiophen-3-yl)ethanone (0.01 mol) (Harrison et al., 2010b ) and 2,4-dichlorobenzaldehyde (0.01 mol) were dissolved in 20 ml of methanol. A catalytic amount of NaOH was added to the solution dropwise with vigorous stirring. The reaction mixture was stirred for about 2 h at room temperature. The formed crude products were filtered off, washed successively with distilled water and recrystallized from methanol to give the title chalcone. The reaction scheme is shown in Fig. 6. The melting point (306–309 K) was determined using a Stuart Scientific (UK) apparatus.

Figure 6
Synthesis of the title compound.

7. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2. C-bound H atoms were positioned geometrically (C—H = 0.95–0.99 Å) and refined using a riding model with U_iso(H) = 1.2U_eq(C).

Table 2
Experimental details

Crystal data
Chemical formula	C₁₃H₆Cl₃FOS
M_r	335.60
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	294
a, b, c (Å)	3.9564 (8), 13.367 (2), 25.173 (5)
β (°)	93.363 (4)
V (Å³)	1329.0 (4)
Z	4
Radiation type	Mo Kα
μ (mm⁻¹)	0.84
Crystal size (mm)	0.44 × 0.19 × 0.14

Data collection
Diffractometer	Bruker APEXII DUO CCD area-detector
Absorption correction	Multi-scan (SADABS; Bruker, 2012 )
T_min, T_max	0.708, 0.894
No. of measured, independent and observed [I > 2σ(I)] reflections	3901, 3901, 2430
R_int	0.000
(sin θ/λ)_max (Å⁻¹)	0.707

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.076, 0.218, 1.04
No. of reflections	3901
No. of parameters	173
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.46, −0.48
Computer programs: APEX2 and SAINT (Bruker, 2012), SHELXS97 (Sheldrick, 2008 ), SHELXL2013 (Sheldrick, 2015 ), Mercury (Macrae et al., 2006 ) and PLATON (Spek, 2009 ).

Supporting information

CCDC reference: 1036795

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S2056989018010216/xu5930sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989018010216/xu5930Isup2.hkl

checkCIF report

Computing details top

Data collection: APEX2 (Bruker, 2012); cell refinement: SAINT (Bruker, 2012); data reduction: SAINT (Bruker, 2012); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2013 (Sheldrick, 2015); molecular graphics: SHELXL2013 (Sheldrick, 2015) and Mercury (Macrae et al., 2006); software used to prepare material for publication: SHELXL2013 (Sheldrick, 2015) and PLATON (Spek, 2009).

(E)-3-(2-Chloro-4-fluorophenyl)-1-(2,5-dichlorothiophen-3-yl)prop-2-en-1-one top

Crystal data top

C₁₃H₆Cl₃FOS	F(000) = 672
M_r = 335.60	D_x = 1.677 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 2430 reflections
a = 3.9564 (8) Å	θ = 1.6–30.2°
b = 13.367 (2) Å	µ = 0.84 mm⁻¹
c = 25.173 (5) Å	T = 294 K
β = 93.363 (4)°	Rectangle, green
V = 1329.0 (4) Å³	0.44 × 0.19 × 0.14 mm
Z = 4

Data collection top

Bruker APEXII DUO CCD area-detector diffractometer	3901 independent reflections
Radiation source: Rotating Anode	2430 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.0000
Detector resolution: 18.4 pixels mm^-1	θ_max = 30.2°, θ_min = 1.6°
φ and ω scans	h = −5→5
Absorption correction: multi-scan (SADABS; Bruker, 2012)	k = −18→18
T_min = 0.708, T_max = 0.894	l = −2→35
3901 measured reflections

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.076	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.218	H-atom parameters constrained
S = 1.04	w = 1/[σ²(F_o²) + (0.0673P)² + 2.8657P] where P = (F_o² + 2F_c²)/3
3901 reflections	(Δ/σ)_max < 0.001
173 parameters	Δρ_max = 0.46 e Å⁻³
0 restraints	Δρ_min = −0.48 e Å⁻³

Special details top

Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All su's are estimated from the variances of the (full) variance-covariance matrix. The cell esds are taken into account in the estimation of distances, angles and torsion angles

Refinement. Refinement on F² for ALL reflections except those flagged by the user for potential systematic errors. Weighted R-factors wR and all goodnesses of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The observed criterion of F² > 2sigma(F²) is used only for calculating -R-factor-obs etc. and is not relevant to the choice of reflections for refinement. R-factors based on F² are statistically about twice as large as those based on F, and R-factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
Cl1	0.3576 (4)	0.89705 (9)	0.29850 (5)	0.0644 (5)
Cl2	0.2067 (5)	1.14124 (14)	0.48102 (5)	0.0892 (6)
Cl3	1.1255 (5)	1.22982 (11)	0.10663 (6)	0.0863 (6)
S1	0.2273 (3)	0.97600 (10)	0.40296 (5)	0.0581 (4)
F1	1.3011 (10)	0.8888 (3)	0.03284 (14)	0.0890 (16)
O1	0.6247 (13)	1.2332 (3)	0.28547 (15)	0.0826 (16)
C1	0.3669 (11)	0.9974 (3)	0.34077 (16)	0.0452 (11)
C2	0.2951 (13)	1.0983 (4)	0.41922 (17)	0.0576 (15)
C3	0.4177 (12)	1.1522 (4)	0.37994 (16)	0.0518 (16)
C4	0.4643 (11)	1.0936 (3)	0.33320 (15)	0.0438 (11)
C5	0.6036 (13)	1.1423 (3)	0.28592 (16)	0.0503 (14)
C6	0.7148 (13)	1.0813 (3)	0.24247 (17)	0.0528 (14)
C7	0.8427 (14)	1.1157 (4)	0.19955 (16)	0.0553 (14)
C8	0.9626 (11)	1.0570 (3)	0.15588 (15)	0.0446 (11)
C9	1.0932 (12)	1.1014 (4)	0.11131 (17)	0.0505 (16)
C10	1.2095 (12)	1.0457 (4)	0.06983 (17)	0.0567 (16)
C11	1.1865 (13)	0.9448 (4)	0.0731 (2)	0.0621 (19)
C12	1.0579 (14)	0.8963 (4)	0.1151 (2)	0.0633 (17)
C13	0.9467 (13)	0.9528 (4)	0.15625 (18)	0.0535 (16)
H3A	0.46730	1.22000	0.38260	0.0620*
H6A	0.69310	1.01230	0.24550	0.0630*
H7A	0.85890	1.18480	0.19660	0.0660*
H10A	1.30020	1.07640	0.04070	0.0680*
H12A	1.04550	0.82680	0.11580	0.0760*
H13A	0.85860	0.92070	0.18510	0.0640*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cl1	0.0855 (10)	0.0491 (6)	0.0602 (7)	−0.0030 (6)	0.0169 (6)	−0.0015 (5)
Cl2	0.1049 (13)	0.1212 (13)	0.0442 (6)	−0.0094 (11)	0.0269 (7)	−0.0147 (7)
Cl3	0.1298 (15)	0.0642 (8)	0.0694 (8)	−0.0049 (9)	0.0430 (9)	0.0128 (6)
S1	0.0607 (8)	0.0698 (8)	0.0448 (6)	−0.0031 (6)	0.0114 (5)	0.0138 (5)
F1	0.098 (3)	0.096 (3)	0.076 (2)	0.013 (2)	0.030 (2)	−0.0231 (18)
O1	0.141 (4)	0.0503 (19)	0.060 (2)	−0.011 (2)	0.037 (2)	−0.0004 (16)
C1	0.043 (2)	0.054 (2)	0.0392 (18)	0.0025 (19)	0.0072 (16)	0.0064 (16)
C2	0.059 (3)	0.078 (3)	0.0365 (19)	−0.005 (3)	0.0095 (19)	−0.004 (2)
C3	0.056 (3)	0.060 (3)	0.040 (2)	−0.003 (2)	0.0078 (19)	−0.0031 (18)
C4	0.045 (2)	0.051 (2)	0.0357 (18)	−0.0023 (19)	0.0060 (16)	0.0001 (16)
C5	0.066 (3)	0.048 (2)	0.0378 (19)	−0.004 (2)	0.0118 (19)	0.0039 (17)
C6	0.067 (3)	0.051 (2)	0.042 (2)	0.000 (2)	0.017 (2)	0.0039 (18)
C7	0.076 (3)	0.052 (2)	0.039 (2)	0.000 (2)	0.013 (2)	0.0023 (17)
C8	0.041 (2)	0.056 (2)	0.0367 (18)	0.0005 (19)	0.0016 (16)	0.0010 (16)
C9	0.050 (3)	0.061 (3)	0.041 (2)	0.000 (2)	0.0061 (18)	0.0071 (18)
C10	0.050 (3)	0.081 (3)	0.040 (2)	0.002 (3)	0.0093 (19)	0.001 (2)
C11	0.052 (3)	0.081 (4)	0.054 (3)	0.009 (3)	0.010 (2)	−0.015 (2)
C12	0.061 (3)	0.059 (3)	0.071 (3)	0.010 (3)	0.013 (3)	−0.006 (2)
C13	0.057 (3)	0.057 (3)	0.047 (2)	0.006 (2)	0.008 (2)	0.0071 (19)

Geometric parameters (Å, º) top

Cl1—C1	1.711 (4)	C7—C8	1.453 (6)
Cl2—C2	1.713 (5)	C8—C9	1.395 (6)
Cl3—C9	1.726 (6)	C8—C13	1.394 (7)
S1—C1	1.714 (4)	C9—C10	1.383 (7)
S1—C2	1.703 (5)	C10—C11	1.355 (8)
F1—C11	1.359 (6)	C11—C12	1.364 (7)
O1—C5	1.218 (6)	C12—C13	1.375 (7)
C1—C4	1.359 (6)	C3—H3A	0.9300
C2—C3	1.337 (7)	C6—H6A	0.9300
C3—C4	1.434 (6)	C7—H7A	0.9300
C4—C5	1.490 (6)	C10—H10A	0.9300
C5—C6	1.453 (6)	C12—H12A	0.9300
C6—C7	1.303 (6)	C13—H13A	0.9300

C1—S1—C2	90.3 (2)	Cl3—C9—C10	117.0 (4)
Cl1—C1—S1	116.2 (2)	C8—C9—C10	122.2 (5)
Cl1—C1—C4	130.6 (3)	C9—C10—C11	117.6 (4)
S1—C1—C4	113.3 (3)	F1—C11—C10	118.5 (4)
Cl2—C2—S1	120.2 (3)	F1—C11—C12	118.2 (5)
Cl2—C2—C3	126.4 (4)	C10—C11—C12	123.4 (5)
S1—C2—C3	113.5 (4)	C11—C12—C13	118.3 (5)
C2—C3—C4	112.5 (5)	C8—C13—C12	121.8 (4)
C1—C4—C3	110.5 (4)	C2—C3—H3A	124.00
C1—C4—C5	130.3 (4)	C4—C3—H3A	124.00
C3—C4—C5	119.2 (4)	C5—C6—H6A	117.00
O1—C5—C4	118.2 (4)	C7—C6—H6A	117.00
O1—C5—C6	121.9 (4)	C6—C7—H7A	117.00
C4—C5—C6	119.9 (4)	C8—C7—H7A	117.00
C5—C6—C7	125.1 (4)	C9—C10—H10A	121.00
C6—C7—C8	126.6 (5)	C11—C10—H10A	121.00
C7—C8—C9	122.1 (4)	C11—C12—H12A	121.00
C7—C8—C13	121.2 (4)	C13—C12—H12A	121.00
C9—C8—C13	116.7 (4)	C8—C13—H13A	119.00
Cl3—C9—C8	120.7 (4)	C12—C13—H13A	119.00

C2—S1—C1—Cl1	−178.6 (3)	C4—C5—C6—C7	−179.4 (5)
C2—S1—C1—C4	0.7 (4)	C5—C6—C7—C8	178.7 (5)
C1—S1—C2—Cl2	179.7 (3)	C6—C7—C8—C9	179.5 (5)
C1—S1—C2—C3	−0.3 (4)	C6—C7—C8—C13	0.6 (8)
Cl1—C1—C4—C3	178.2 (4)	C7—C8—C9—Cl3	1.2 (6)
Cl1—C1—C4—C5	−1.8 (8)	C7—C8—C9—C10	179.6 (5)
S1—C1—C4—C3	−0.9 (5)	C13—C8—C9—Cl3	−179.9 (4)
S1—C1—C4—C5	179.0 (4)	C13—C8—C9—C10	−1.5 (7)
Cl2—C2—C3—C4	179.8 (4)	C7—C8—C13—C12	179.7 (5)
S1—C2—C3—C4	−0.2 (6)	C9—C8—C13—C12	0.8 (7)
C2—C3—C4—C1	0.7 (6)	Cl3—C9—C10—C11	179.8 (4)
C2—C3—C4—C5	−179.2 (4)	C8—C9—C10—C11	1.4 (7)
C1—C4—C5—O1	169.0 (5)	C9—C10—C11—F1	−179.7 (4)
C1—C4—C5—C6	−12.0 (8)	C9—C10—C11—C12	−0.5 (8)
C3—C4—C5—O1	−11.1 (7)	F1—C11—C12—C13	179.0 (5)
C3—C4—C5—C6	167.9 (4)	C10—C11—C12—C13	−0.2 (8)
O1—C5—C6—C7	−0.5 (8)	C11—C12—C13—C8	0.0 (8)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C6—H6A···Cl1	0.93	2.47	3.207 (5)	136
C10—H10A···F1ⁱ	0.93	2.54	3.433 (6)	160

Symmetry code: (i) −x+3, −y+2, −z.

Acknowledgements

The authors extend their appreciation to Vidya Vikas Research & Development Center for the provision of facilities and support.

References

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