organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2414-3146

Methyl 4-amino-3-meth­­oxy­isoxazole-5-carboxyl­ate

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aFaculty of Applied Sciences, Universiti Teknologi MARA, 40450 Shah Alam, Selangor, Malaysia, and bEaStCHEM School of Chemistry, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom
*Correspondence e-mail: abdfatah@uitm.edu.my

Edited by W. T. A. Harrison, University of Aberdeen, United Kingdom (Received 14 July 2023; accepted 16 July 2023; online 1 August 2023)

The title compound, C6H8N2O4, a new derivative of isoxazole, has been synthesized and structurally characterized. The crystal structure shows the mol­ecule to be almost planar (r.m.s. deviation for the non-hydrogen atoms = 0.029 Å), this conformation being supported by an intra­molecular N—H⋯O hydrogen bond. In the extended structure, the mol­ecules are linked by N—H⋯O hydrogen bonds into chains propagating along [010].

3D view (loading...)
[Scheme 3D1]
Chemical scheme
[Scheme 1]

Structure description

Isoxazoles, five-membered heterocyclic compounds containing adjacent nitro­gen and oxygen atoms, have many applications including in photochromic components (Pu et al., 2011[Pu, S., Li, H., Liu, G., Liu, W., Cui, S. & Fan, C. (2011). Tetrahedron, 67, 438-1447.]), liquid crystals (Kauhanka et al., 2006[Kauhanka, U. M. & Kauhanka, M. M. (2006). Liq. Cryst. 33, 121-127.]), solar cells (Yoon et al., 2022[Yoon, J., Liu, X. & Lee, E. C. (2022). ACS Omega, 7, 34278-34285.]), high energy materials (Lal et al., 2023[Lal, S., Staples, R. J. & Shreeve, J. M. (2023). Dalton Trans. 52, 3449-3457.]), pesticides and insecticides (Wang et al., 2022[Wang, L., Huang, M., Wu, Z., Huang, M., Yan, Y., Song, B., Li, X. & Li, Q. X. (2022). J. Agric. Food Chem. 70, 4871-4880.]) and pharmaceuticals (Zhu et al., 2018[Zhu, J., Mo, J., Lin, H. Z., Chen, Y. & Sun, H. P. (2018). Bioorg. Med. Chem. 26, 3065-3075.]). In a continuation of our previous work on isoxazole derivatives (Abdul Manan et al., 2023[Abdul Manan, M. A. F., Cordes, D. B., Slawin, A. M. Z. & O'Hagan, D. (2023). IUCrData, 8, x230300.]), we now present the synthesis and structure of the title compound.

The title compound, C6H8N2O4, crystallizes in space group P21/c with one mol­ecule in the asymmetric unit (Fig. 1[link]). All of the non-hydrogen atoms lie almost in the same plane, with an r.m.s. deviation of 0.029 Å and a maximum deviation of 0.060 (1) Å for C8. An intra­molecular N—H⋯Oe (e = ester) hydrogen bond (Table 1[link]) helps to ensure the near co-planarity of the isoxazole and ester moieties. This whole-mol­ecule planarity, assisted by an intra­molecular hydrogen bond, is similar to what was observed in the related compounds ethyl 5-amino-3-methyl­isoxazole-4-carboxyl­ate (Sony et al., 2005[Sony, S. M. M., Charles, P., Ponnuswamy, M. N., Yathirajan, H. S. & Nethaji, M. (2005). Acta Cryst. E61, o198-o200.]), ethyl 5-amino-3-(di­fluoro­meth­yl)isoxazole-4-carboxyl­ate (Schmitt et al., 2015[Schmitt, E., Rugeri, B., Panossian, A., Vors, J.-P., Pazenok, S. & Leroux, F. R. (2015). Org. Lett. 17, 4510-4513.]) and 5-amino-3-methyl­isoxazole-4-carbohydrazide (Regiec et al., 2018[Regiec, A., Wojciechowski, P., Pietraszko, A. & Mączyński, M. (2018). J. Mol. Struct. 1161, 320-338.]). The relative orientation of the ester and amine groups, allowing the formation of the intra­molecular hydrogen bond to the ester oxygen atom rather than the carbonyl oxygen atom, is, however, different to what is seen in ethyl 5-amino-3-methyl­isoxazole-4-carboxyl­ate (Sony et al., 2005[Sony, S. M. M., Charles, P., Ponnuswamy, M. N., Yathirajan, H. S. & Nethaji, M. (2005). Acta Cryst. E61, o198-o200.]), ethyl 5-amino-3-(di­fluoro­meth­yl)isoxazole-4-carboxyl­ate (Schmitt et al., 2015[Schmitt, E., Rugeri, B., Panossian, A., Vors, J.-P., Pazenok, S. & Leroux, F. R. (2015). Org. Lett. 17, 4510-4513.]), ethyl 5-amino-3-[fluoro(tri­fluorometh­oxy)meth­yl]isoxazole-4-carboxyl­ate (Schmitt et al., 2017[Schmitt, E., Bouvet, S., Pégot, B., Panossian, A., Vors, J.-P., Pazenok, S., Magnier, E. & Leroux, F. R. (2017). Org. Lett. 19, 4960-4963.]) and 1-(cyclo­hexyl­carbamo­yl)cyclo­hexyl 5-amino-3-methyl­isoxazole-4-carboxyl­ate (Bąchor et al., 2019[Bąchor, U., Ryng, S., Mączyński, M., Artym, J., Kocięba, M., Zaczyńska, E., Kochanowska, I., Tykarska, E. & Zimecki, M. (2019). Acta Pol. Pharm. 76, 251-263.]).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N4—H4A⋯O6i 0.89 (1) 2.30 (2) 2.9765 (16) 133 (1)
N4—H4B⋯O1i 0.91 (1) 2.31 (2) 3.0233 (15) 136 (1)
N4—H4B⋯O7 0.91 (1) 2.30 (2) 2.8734 (16) 121 (1)
Symmetry code: (i) [-x, y-{\script{1\over 2}}, -z+{\script{3\over 2}}].
[Figure 1]
Figure 1
The mol­ecular structure of the title compound, showing displacement ellipsoids drawn at the 50% probability level.

In the crystal of the title compound, adjacent mol­ecules are linked by N—H⋯Oc (c = carbon­yl) and N—H⋯Oi (i = isoxazole) hydrogen bonds, forming an R22 (7) loop, which generates chains of mol­ecules running along the crystallographic b-axis direction (Fig. 2[link]). No additional directional inter­actions exist between chains. This combination of hydrogen bonds leading to chain formation is not seen in related isoxazole compounds as a result of the different relative position of the amine group on the isoxazole ring. While the combination of two inter- and one intra­molecular hydrogen bond has been seen previously in related isoxazoles (Sony et al., 2005[Sony, S. M. M., Charles, P., Ponnuswamy, M. N., Yathirajan, H. S. & Nethaji, M. (2005). Acta Cryst. E61, o198-o200.]; Regiec et al., 2018[Regiec, A., Wojciechowski, P., Pietraszko, A. & Mączyński, M. (2018). J. Mol. Struct. 1161, 320-338.]; Bąchor et al., 2019[Bąchor, U., Ryng, S., Mączyński, M., Artym, J., Kocięba, M., Zaczyńska, E., Kochanowska, I., Tykarska, E. & Zimecki, M. (2019). Acta Pol. Pharm. 76, 251-263.]), the pattern of hydrogen bonds is either different or has additional hydrogen bonds contributing to it, and the resulting supra­molecular motifs differ as well. One-dimensional chain motifs have been seen in two of the related isoxazoles (Schmitt et al., 2015[Schmitt, E., Rugeri, B., Panossian, A., Vors, J.-P., Pazenok, S. & Leroux, F. R. (2015). Org. Lett. 17, 4510-4513.], 2017[Schmitt, E., Bouvet, S., Pégot, B., Panossian, A., Vors, J.-P., Pazenok, S., Magnier, E. & Leroux, F. R. (2017). Org. Lett. 19, 4960-4963.]), although the pattern of hydrogen bonds that leads to the chains is different.

[Figure 2]
Figure 2
View down the [101] axis of the [010] chain formed by N—H⋯O hydrogen bonds, which are shown as dashed lines.

Synthesis and crystallization

Synthesis of the methyl 3-meth­oxy-4-nitro­isoxazole-5-carb­oxyl­ate precursor

The starting material, methyl 3-meth­oxy­isoxazole-5-carboxyl­ate, was prepared according to the previously described literature procedure with minor modifications (Melikian et al., 1992[Melikian, A., Schlewer, G., Chambon, J. P. & Wermuth, C. G. (1992). J. Med. Chem. 35, 4092-4097.]). K2CO3 (2.9 g, 21.0 mmol, 1.5 eq) and CH3I (1.3 ml, 21.0 mmol, 1.5 eq) were added to a solution of methyl 3-hy­droxy­isoxazole-5-carboxyl­ate (2.0 g, 13.9 mmol, 1.0 eq) in di­methyl­formamide (DMF) (10 ml) at 0°C. After 14 h stirring at room temperature, the mixture was poured into an ice-cold aqueous solution of HCl (0.5 M, 100 ml) and extracted into Et2O (5 × 80 ml). The combined organic layers were washed with a saturated aqueous solution of Na2CO3 (80 ml), dried over MgSO4, filtered and concentrated under reduced pressure to afford a light yellow crystalline solid, which was purified by silica gel column chromatography (petroleum ether/Et2O, 80:20), affording methyl 3-meth­oxy­isoxazole-5-carboxyl­ate (1.45 g, 66%) as a colourless crystalline solid.

Triflic anhydride (5.9 g, 21.0 mmol, 3.0 eq) was added to a solution of tetra­methyl­ammonium nitrate (2.9 g, 21.0 mmol, 3.0 eq) in DCM (3 ml) at room temperature. The suspension was stirred for 2 h, then a solution of methyl 3-meth­oxy­isoxazole-5-carboxyl­ate (1.1 g, 7.0 mmol, 1.0 eq) in di­chloro­methane (DCM) (10 ml) was added. After 48 h stirring under reflux, the mixture was cooled to room temperature and partitioned between water (30 ml) and DCM (40 ml). The organic layer was separated and washed with water (50 ml). The aqueous layer was extracted with DCM (3 × 50 ml). The combined organic layers were washed with brine (50 ml), dried over MgSO4, filtered and concentrated under reduced pressure. The resulting yellow residue was purified by silica gel column chromatography (petroleum ether/DCM, 50:50) to afford methyl 3-meth­oxy-4-nitro­isoxazole-5-carboxyl­ate (0.9 g, 70%) as yellowish oil: Rf = 0.41 (petroleum ether/Et2O, 80:20, UV/KMnO4); 1H (500 MHz, CDCl3), δ: (p.p.m): 4.14 (3H, s), 4.02 (3H, s); 13C (125 MHz, CDCl3), δ: (p.p.m): 164.0, 157.4, 155.0, 127.7, 58.9, 54.2; HRMS m/z (APCI+), found: [M + H]+ 203.0295, C6H7N2O6 requires [M + H]+ 203.0299.

Synthesis of methyl 4-amino-3-meth­oxy­isoxazole-5-carboxyl­ate

Iron powder (267 mg, 4.86 mmol, 5.0 eq) was added to a solution of methyl 3-meth­oxy-4-nitro­isoxazole-5-carboxyl­ate (196 mg, 0.97 mmol, 1.0 eq) in AcOH/H2O (AcOH = acetic acid) (3:1 v/v mixture, 12 ml). After stirring at 50°C for 2 h, the solution was cooled to room temperature and the solvent was removed under reduced pressure. The residue was partitioned between water (20 ml) and ethyl acetate (EtOAc) (20 ml). The mixture was basified with a saturated aqueous solution of Na2CO3 and further extracted with EtOAc (3 × 20 ml). The combined organic layers were washed with brine (20 ml), dried over MgSO4, filtered and concentrated under reduced pressure to afford a pale-yellow solid, which was purified by silica gel column chromatography (DCM, 100), affording methyl 4-amino-3-meth­oxy­isoxazole-5-carboxyl­ate (139 mg, 83%) as a colourless crystalline solid: Rf = 0.74 (DCM/EtOAc, 90:10, UV/ninhydrin); m.p. 111–112°C; 1H (500 MHz, CDCl3), δ: (p.p.m): 4.15 (br s, 2H), 4.05 (3H, s), 3.92 (3H, s); 13C (125 MHz, CDCl3), δ: (p.p.m): 164.5, 159.1, 138.4, 125.6, 57.5, 51.9; HRMS m/z (ESI+), found: [M + Na]+ 195.0373, C6H8N2O4Na requires [M + Na]+ 195.0382.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2[link].

Table 2
Experimental details

Crystal data
Chemical formula C6H8N2O4
Mr 172.14
Crystal system, space group Monoclinic, P21/c
Temperature (K) 173
a, b, c (Å) 7.0425 (18), 11.555 (3), 9.654 (2)
β (°) 106.629 (6)
V3) 752.7 (3)
Z 4
Radiation type Mo Kα
μ (mm−1) 0.13
Crystal size (mm) 0.27 × 0.06 × 0.06
 
Data collection
Diffractometer Rigaku XtaLAB P200
Absorption correction Multi-scan (CrystalClear; Rigaku, 2014[Rigaku (2014). CrystalStructure and CrystalClear. Rigaku Americas Corporation, The Woodlands, Texas, USA, and Rigaku Corporation, Tokyo, Japan.])
Tmin, Tmax 0.695, 0.992
No. of measured, independent and observed [F2 > 2.0σ(F2)] reflections 9048, 1388, 1223
Rint 0.051
(sin θ/λ)max−1) 0.604
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.030, 0.083, 1.09
No. of reflections 1388
No. of parameters 119
No. of restraints 2
H-atom treatment H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3) 0.17, −0.20
Computer programs: CrystalClear and CrystalStructure (Rigaku, 2014[Rigaku (2014). CrystalStructure and CrystalClear. Rigaku Americas Corporation, The Woodlands, Texas, USA, and Rigaku Corporation, Tokyo, Japan.]), SIR2011 (Burla et al., 2012[Burla, M. C., Caliandro, R., Camalli, M., Carrozzini, B., Cascarano, G. L., Giacovazzo, C., Mallamo, M., Mazzone, A., Polidori, G. & Spagna, R. (2012). J. Appl. Cryst. 45, 357-361.]), SHELXL2018/3 (Sheldrick, 2015[Sheldrick, G. M. (2015). Acta Cryst. C71, 3-8.]), Mercury (Macrae et al., 2020[Macrae, C. F., Sovago, I., Cottrell, S. J., Galek, P. T. A., McCabe, P., Pidcock, E., Platings, M., Shields, G. P., Stevens, J. S., Towler, M. & Wood, P. A. (2020). J. Appl. Cryst. 53, 226-235.]) and publCIF (Westrip, 2010[Westrip, S. P. (2010). J. Appl. Cryst. 43, 920-925.]).

Structural data


Computing details top

Data collection: CrystalClear (Rigaku, 2014); cell refinement: CrystalClear (Rigaku, 2014); data reduction: CrystalClear (Rigaku, 2014); program(s) used to solve structure: SIR2011 (Burla et al., 2012); program(s) used to refine structure: SHELXL2018/3 (Sheldrick, 2015); molecular graphics: Mercury (Macrae et al., 2020); software used to prepare material for publication: CrystalStructure (Rigaku, 2014) and publCIF (Westrip, 2010).

Methyl 4-amino-3-methoxyisoxazole-5-carboxylate top
Crystal data top
C6H8N2O4F(000) = 360.00
Mr = 172.14Dx = 1.519 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71075 Å
a = 7.0425 (18) ÅCell parameters from 2384 reflections
b = 11.555 (3) Åθ = 2.8–25.4°
c = 9.654 (2) ŵ = 0.13 mm1
β = 106.629 (6)°T = 173 K
V = 752.7 (3) Å3Prism, colorless
Z = 40.27 × 0.06 × 0.06 mm
Data collection top
Rigaku XtaLAB P200
diffractometer
1388 independent reflections
Radiation source: Rotating Anode, Rigaku FR-X1223 reflections with F2 > 2.0σ(F2)
Rigaku Osmic Confocal Optical System monochromatorRint = 0.051
Detector resolution: 11.628 pixels mm-1θmax = 25.4°, θmin = 2.8°
ω scansh = 88
Absorption correction: multi-scan
(CrystalClear; Rigaku, 2014)
k = 1313
Tmin = 0.695, Tmax = 0.992l = 1111
9048 measured reflections
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.030Hydrogen site location: mixed
wR(F2) = 0.083H atoms treated by a mixture of independent and constrained refinement
S = 1.09 w = 1/[σ2(Fo2) + (0.0426P)2 + 0.1362P]
where P = (Fo2 + 2Fc2)/3
1388 reflections(Δ/σ)max < 0.001
119 parametersΔρmax = 0.17 e Å3
2 restraintsΔρmin = 0.20 e Å3
Primary atom site location: structure-invariant direct methods
Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Refinement. Refinement was performed using all reflections. The weighted R-factor (wR) and goodness of fit (S) are based on F2. R-factor (gt) are based on F. The threshold expression of F2 > 2.0 sigma(F2) is used only for calculating R-factor (gt).

Carbon-bound H atoms were included in calculated positions (C—H = 0.98 Å) and refined as riding atoms with Uiso(H) = 1.2Ueq(C). The nitrogen-bound hydrogen atoms were located from difference Fourier maps and refined isotropically subject to a distance restraint.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.02039 (14)0.26697 (7)0.62559 (10)0.0332 (3)
O30.32430 (13)0.09325 (8)0.53449 (10)0.0333 (3)
O60.30018 (14)0.23906 (8)0.77949 (11)0.0376 (3)
O70.19751 (14)0.05355 (8)0.82206 (10)0.0355 (3)
N20.12840 (17)0.25137 (9)0.55608 (12)0.0321 (3)
N40.11557 (19)0.02825 (9)0.71104 (14)0.0380 (3)
H4A0.201 (2)0.0715 (13)0.6805 (17)0.044 (4)*
H4B0.039 (2)0.0582 (14)0.7641 (17)0.046 (4)*
C30.18521 (18)0.14406 (10)0.58185 (13)0.0275 (3)
C40.08233 (18)0.08329 (10)0.66715 (13)0.0271 (3)
C50.04431 (18)0.16376 (10)0.69055 (14)0.0289 (3)
C60.19340 (18)0.16034 (10)0.76742 (14)0.0297 (3)
C70.3398 (2)0.03562 (12)0.90147 (17)0.0396 (4)
H7A0.3133270.0897740.9828920.048*
H7B0.3292010.0439680.9379680.048*
H7C0.4737270.0488460.8375610.048*
C80.4105 (2)0.16335 (12)0.44464 (16)0.0375 (3)
H8A0.4718160.2321230.4985670.045*
H8B0.3068590.1871860.3578680.045*
H8C0.5114350.1183840.4163980.045*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0415 (5)0.0222 (4)0.0413 (5)0.0044 (4)0.0205 (4)0.0028 (4)
O30.0375 (5)0.0275 (5)0.0410 (6)0.0027 (4)0.0211 (4)0.0030 (4)
O60.0383 (5)0.0303 (5)0.0495 (6)0.0026 (4)0.0209 (5)0.0031 (4)
O70.0399 (5)0.0281 (5)0.0451 (6)0.0013 (4)0.0227 (4)0.0007 (4)
N20.0385 (6)0.0262 (6)0.0360 (6)0.0012 (4)0.0178 (5)0.0013 (4)
N40.0473 (7)0.0223 (6)0.0534 (8)0.0053 (5)0.0291 (6)0.0077 (5)
C30.0299 (6)0.0245 (6)0.0291 (7)0.0004 (5)0.0102 (5)0.0018 (5)
C40.0294 (7)0.0231 (6)0.0283 (6)0.0013 (5)0.0077 (5)0.0013 (5)
C50.0340 (7)0.0224 (6)0.0309 (7)0.0018 (5)0.0104 (6)0.0006 (5)
C60.0316 (7)0.0260 (6)0.0318 (7)0.0026 (5)0.0098 (5)0.0042 (5)
C70.0421 (8)0.0377 (8)0.0469 (9)0.0057 (6)0.0252 (7)0.0002 (6)
C80.0398 (8)0.0368 (7)0.0427 (8)0.0006 (6)0.0227 (6)0.0057 (6)
Geometric parameters (Å, º) top
O1—C51.3801 (15)N4—H4B0.910 (14)
O1—N21.4083 (15)C3—C41.4275 (18)
O3—C31.3302 (15)C4—C51.3514 (17)
O3—C81.4417 (16)C5—C61.4493 (19)
O6—C61.2070 (15)C7—H7A0.9800
O7—C61.3456 (16)C7—H7B0.9800
O7—C71.4403 (17)C7—H7C0.9800
N2—C31.3048 (16)C8—H8A0.9800
N4—C41.3560 (17)C8—H8B0.9800
N4—H4A0.893 (13)C8—H8C0.9800
C5—O1—N2108.07 (9)O6—C6—O7124.71 (12)
C3—O3—C8115.92 (10)O6—C6—C5126.27 (12)
C6—O7—C7115.91 (10)O7—C6—C5109.01 (10)
C3—N2—O1105.08 (10)O7—C7—H7A109.5
C4—N4—H4A120.1 (11)O7—C7—H7B109.5
C4—N4—H4B117.4 (11)H7A—C7—H7B109.5
H4A—N4—H4B122.2 (15)O7—C7—H7C109.5
N2—C3—O3124.73 (11)H7A—C7—H7C109.5
N2—C3—C4113.51 (11)H7B—C7—H7C109.5
O3—C3—C4121.76 (11)O3—C8—H8A109.5
C5—C4—N4131.68 (12)O3—C8—H8B109.5
C5—C4—C3103.07 (11)H8A—C8—H8B109.5
N4—C4—C3125.24 (11)O3—C8—H8C109.5
C4—C5—O1110.27 (11)H8A—C8—H8C109.5
C4—C5—C6132.56 (12)H8B—C8—H8C109.5
O1—C5—C6117.18 (11)
C5—O1—N2—C30.22 (13)N4—C4—C5—C61.7 (2)
O1—N2—C3—O3179.64 (11)C3—C4—C5—C6179.23 (13)
O1—N2—C3—C40.08 (14)N2—O1—C5—C40.46 (14)
C8—O3—C3—N22.12 (18)N2—O1—C5—C6179.30 (10)
C8—O3—C3—C4177.58 (11)C7—O7—C6—O60.80 (19)
N2—C3—C4—C50.35 (14)C7—O7—C6—C5179.66 (10)
O3—C3—C4—C5179.38 (11)C4—C5—C6—O6179.16 (14)
N2—C3—C4—N4178.81 (12)O1—C5—C6—O60.53 (19)
O3—C3—C4—N41.45 (19)C4—C5—C6—O70.32 (19)
N4—C4—C5—O1178.61 (13)O1—C5—C6—O7179.37 (10)
C3—C4—C5—O10.48 (13)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N4—H4A···O6i0.89 (1)2.30 (2)2.9765 (16)133 (1)
N4—H4B···O1i0.91 (1)2.31 (2)3.0233 (15)136 (1)
N4—H4B···O70.91 (1)2.30 (2)2.8734 (16)121 (1)
Symmetry code: (i) x, y1/2, z+3/2.
 

Funding information

The authors acknowledge Universiti Teknologi MARA for financial support.

References

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