Bis(2,3-diamino­pyridinium) succinate trihydrate

Fun, H.-K.; Balasubramani, K.; Yeap, C.S.

doi:10.1107/S1600536809026439

organic compounds

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ISSN: 2056-9890

Volume 65| Part 8| August 2009| Pages o1854-o1855

doi:10.1107/S1600536809026439

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Bis(2,3-diaminopyridinium) succinate trihydrate

Hoong-Kun Fun,^a ^*‡ Kasthuri Balasubramani ^a and Chin Sing Yeap ^a §

^aX-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia
^*Correspondence e-mail: hkfun@usm.my

(Received 24 June 2009; accepted 7 July 2009; online 15 July 2009)

In the title salt, 2C₅H₈N₃⁺·C₄H₄O₄²⁻·3H₂O, the asymmetric unit contains a protonated 2,3-diaminopyridinium cation, half of a succinate dianion (disposed about a centre of inversion), and one and a half water molecules. One of the water molecules is disordered over two sites with occupancies of 0.670 (17) and 0.330 (17). The other water molecule has an occupancy of 0.5 (from refinement). The pyridine N atom of the 2,3-diaminopyridine molecule is protonated. The protonated N atom and one of the 2-amino H atoms are hydrogen bonded to the succinate anion through a pair of N—H⋯O hydrogen bonds, forming an R₂²(8) ring motif. In the crystal, molecules are consolidated into a three-dimensional network by N—H⋯O and O—H⋯O interactions.

Related literature

For substituted pyridines, see: Pozharski et al. (1997 ); Katritzky et al. (1996 ); Jeffrey & Saenger (1991 ); Jeffrey (1997 ); Scheiner (1997 ). For related structures, see: De Cires-Mejias et al. (2004 ); Fun & Balasubramani (2009 ); Balasubramani & Fun (2009a ,b ). For the stability of the temperature controller used in the data collection, see: Cosier & Glazer (1986 ). For hydrogen-bond motifs, see: Bernstein et al. (1995 ).

Experimental

Crystal data

2C₅H₈N₃⁺·C₄H₄O₄²⁻·3H₂O
M_r = 195.20
Monoclinic, P 2₁ /c
a = 12.7159 (4) Å
b = 3.9024 (1) Å
c = 18.7734 (6) Å
β = 94.933 (2)°
V = 928.13 (5) Å³
Z = 4
Mo Kα radiation
μ = 0.11 mm⁻¹
T = 100 K
0.17 × 0.13 × 0.06 mm

Data collection

Bruker SMART APEXII CCD area-detector diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2005 ) T_min = 0.981, T_max = 0.993
10934 measured reflections
2121 independent reflections
1364 reflections with I > 2σ(I)
R_int = 0.056

Refinement

R[F² > 2σ(F²)] = 0.062
wR(F²) = 0.129
S = 1.06
2121 reflections
178 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.26 e Å⁻³
Δρ_min = −0.24 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N2—H2N2⋯O1ⁱ	0.90 (3)	2.14 (3)	2.978 (3)	155 (3)
N3—H1N3⋯O1ⁱ	0.85 (3)	2.14 (3)	2.993 (3)	176 (3)
N3—H2N3⋯O1WAⁱⁱ	0.91 (3)	2.34 (3)	3.243 (6)	172 (2)
O1WA—H2WA⋯O2	0.85	1.93	2.764 (5)	165
N2—H1N2⋯O1	0.89 (3)	2.04 (3)	2.929 (3)	175 (2)
N1—H1N1⋯O2	0.96 (3)	1.69 (3)	2.643 (3)	171 (2)
Symmetry codes: (i) $[-x, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (ii) $[x, -y+{\script{1\over 2}}, z-{\script{1\over 2}}]$ .

Data collection: APEX2 (Bruker, 2005); cell refinement: SAINT (Bruker, 2005); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 ); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009 ).

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809026439/tk2489sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536809026439/tk2489Isup2.hkl

checkCIF report

Comment top

Pyridine and its derivatives play an important role in heterocyclic chemistry (Pozharski et al., 1997; Katritzky et al., 1996). Further, pyridine and its substituted derivatives are often involved in hydrogen-bond interactions (Jeffrey & Saenger, 1991; Jeffrey, 1997;Scheiner, 1997). The crystal structures of 2,3-diaminopyridinium 4-hydroxybenzoate (Fun & Balasubramani, 2009), 2,3-diaminopyridinium 4-nitrobenzoate (Balasubramani & Fun, 2009a) and 2,3-diaminopyridinium benzoate (Balasubramani & Fun, 2009b) have been reported by us recently. In the hope to study some interesting hydrogen-bonding interactions, the title compound (I) was synthesized. Its molecular and crystal structure is presented here.

The asymmetric unit of (I) (Fig. 1), contains a protonated 2,3-diaminopyridinium cation, a half molecule of succinate anion (disposed about a centre of inversion), and one and half water molecules. In the 2,3-diaminopyridinium cation, protonatation N1 atom has lead to a slight increase (ca. 4 °) in the C1—N1—C5 angle to 123.6 (2)° compared with the unprotonated structure (De Cires-Mejias et al., 2004). The 2,3-diaminopyridinium cation is planar, with a maximum deviation of 0.004 (2) Å for atom C2.

In the crystal packing (Fig. 2), the protonated N1 atom and a nitrogen atom of the 2-amino group (N2) are hydrogen-bonded to the succinate oxygen atoms (O2 and O1) via a pair of N—H···O hydrogen bonds forming a ring motif R₂²(8) (Bernstein et al., 1995). The 2-amino groups (N2 and N3) are involved in N—H···O hydrogen-bonding interactions to form a R₂¹(7) ring motif. The crystal structure is further stabilized by water molecules via O(water)—H···O and N—H···O(water) hydrogen bonding (Table 1 and Fig. 2).

Related literature top

For substituted pyridines, see: Pozharski et al. (1997); Katritzky et al. (1996); Jeffrey & Saenger (1991); Jeffrey (1997); Scheiner (1997). For related structures, see: De Cires-Mejias et al. (2004); Fun & Balasubramani (2009); Balasubramani & Fun (2009a,b). For the stability of the temperature controller used in the data collection, see: Cosier & Glazer (1986). For hydrogen-bond motifs, see: Bernstein et al. (1995).

Experimental top

An aqueous solution of hot methanol (10 ml/ 10 ml) of 2,3-diaminopyridine (27 mg, Aldrich) and succinic acid (29 mg, Merck) were mixed and warmed over a heating magnetic stirrer for 5 minutes. The resulting solution was allowed to cool slowly at room temperature. Crystals of (I) appeared from the mother liquor after a few days.

Computing details top

Data collection: APEX2 (Bruker, 2005); cell refinement: SAINT (Bruker, 2005); data reduction: SAINT (Bruker, 2005); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).

Figures top

	Fig. 1. The molecular structure of (I), showing 50% probability displacement ellipsoids and the atom numbering scheme. Dashed lines indicate the hydrogen bonding. The O1 water molecule is disordered over two positions. Symmetry operation A:-x, 2-y, 1-z.
	Fig. 2. Part of the crystal packing showing the overall 3-D hydrogen-bonding network in (I). Dashed lines indicate the hydrogen bonding.

Bis(2,3-diaminopyridinium) succinate trihydrate top

Crystal data top

2C₅H₈N₃⁺·C₄H₄O₄²⁻·3H₂O	F(000) = 416
M_r = 195.20	D_x = 1.397 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 2108 reflections
a = 12.7159 (4) Å	θ = 2.2–30.0°
b = 3.9024 (1) Å	µ = 0.11 mm⁻¹
c = 18.7734 (6) Å	T = 100 K
β = 94.933 (2)°	Block, brown
V = 928.13 (5) Å³	0.17 × 0.13 × 0.06 mm
Z = 4

Data collection top

Bruker SMART APEXII CCD area-detector diffractometer	2121 independent reflections
Radiation source: fine-focus sealed tube	1364 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.056
ϕ and ω scans	θ_max = 27.5°, θ_min = 2.6°
Absorption correction: multi-scan (SADABS; Bruker, 2005)	h = −16→16
T_min = 0.981, T_max = 0.993	k = −4→5
10934 measured reflections	l = −24→21

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)] = 0.062	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.129	H atoms treated by a mixture of independent and constrained refinement
S = 1.06	w = 1/[σ²(F_o²) + (0.041P)² + 0.7373P] where P = (F_o² + 2F_c²)/3
2121 reflections	(Δ/σ)_max < 0.001
178 parameters	Δρ_max = 0.26 e Å⁻³
0 restraints	Δρ_min = −0.24 e Å⁻³

Crystal data top

2C₅H₈N₃⁺·C₄H₄O₄²⁻·3H₂O	V = 928.13 (5) Å³
M_r = 195.20	Z = 4
Monoclinic, P2₁/c	Mo Kα radiation
a = 12.7159 (4) Å	µ = 0.11 mm⁻¹
b = 3.9024 (1) Å	T = 100 K
c = 18.7734 (6) Å	0.17 × 0.13 × 0.06 mm
β = 94.933 (2)°

Data collection top

Bruker SMART APEXII CCD area-detector diffractometer	2121 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2005)	1364 reflections with I > 2σ(I)
T_min = 0.981, T_max = 0.993	R_int = 0.056
10934 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.062	0 restraints
wR(F²) = 0.129	H atoms treated by a mixture of independent and constrained refinement
S = 1.06	Δρ_max = 0.26 e Å⁻³
2121 reflections	Δρ_min = −0.24 e Å⁻³
178 parameters

Special details top

Experimental. The crystal was placed in the cold stream of an Oxford Cryosystems Cobra open-flow nitrogen cryostat (Cosier & Glazer, 1986) operating at 100.0 (1) K.

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

Refinement. Refinement of F² against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The threshold expression of F² > σ(F²) is used only for calculating R-factors(gt) 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	Occ. (<1)
O1	0.02464 (12)	0.7567 (4)	0.37851 (8)	0.0251 (4)
O2	0.18198 (12)	0.6548 (5)	0.43615 (8)	0.0264 (4)
N1	0.25383 (14)	0.2963 (5)	0.33114 (10)	0.0204 (5)
N2	0.10876 (15)	0.4334 (6)	0.25459 (12)	0.0243 (5)
N3	0.20743 (19)	0.1167 (7)	0.14153 (12)	0.0328 (6)
C1	0.20422 (17)	0.2863 (6)	0.26523 (12)	0.0201 (5)
C2	0.25526 (17)	0.1188 (6)	0.20981 (12)	0.0221 (6)
C3	0.35320 (18)	−0.0256 (7)	0.22796 (13)	0.0243 (6)
C4	0.40151 (18)	−0.0059 (7)	0.29740 (13)	0.0248 (6)
C5	0.35068 (18)	0.1562 (7)	0.34840 (13)	0.0241 (6)
C6	0.08824 (17)	0.7727 (6)	0.43321 (12)	0.0207 (5)
C7	0.05630 (18)	0.9358 (7)	0.50147 (12)	0.0207 (5)
O1WA	0.3424 (4)	0.840 (3)	0.5375 (3)	0.082 (3)	0.670 (17)
H1WA	0.3803	0.6625	0.5341	0.123*	0.670 (17)
H2WA	0.2898	0.8222	0.5066	0.123*	0.670 (17)
O1WB	0.3443 (6)	0.583 (4)	0.5327 (3)	0.039 (4)	0.330 (17)
H1WB	0.3312	0.7954	0.5365	0.058*	0.330 (17)
H2WB	0.3173	0.5182	0.4919	0.058*	0.330 (17)
O2W	0.4593 (3)	0.248 (2)	0.5467 (3)	0.110 (3)	0.50
H1W2	0.5119	0.3543	0.5322	0.165*	0.50
H2W2	0.4462	0.0794	0.5187	0.165*	0.50
H4A	0.4676 (19)	−0.100 (7)	0.3090 (12)	0.027 (7)*
H5A	0.3781 (17)	0.185 (6)	0.3960 (13)	0.022 (6)*
H3A	0.3854 (18)	−0.140 (7)	0.1902 (13)	0.030 (7)*
H7B	0.0722 (17)	0.759 (6)	0.5381 (12)	0.020 (6)*
H7A	0.1062 (18)	1.118 (7)	0.5145 (12)	0.026 (7)*
H2N2	0.076 (2)	0.445 (8)	0.2102 (16)	0.047 (9)*
H1N3	0.142 (2)	0.154 (7)	0.1337 (14)	0.037 (8)*
H1N2	0.0799 (19)	0.537 (7)	0.2905 (14)	0.028 (7)*
H2N3	0.239 (2)	−0.022 (8)	0.1105 (15)	0.045 (9)*
H1N1	0.2213 (19)	0.418 (7)	0.3676 (13)	0.030 (7)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0211 (8)	0.0345 (11)	0.0203 (8)	0.0028 (8)	0.0054 (7)	−0.0005 (7)
O2	0.0188 (8)	0.0361 (11)	0.0253 (9)	0.0030 (8)	0.0074 (7)	−0.0010 (8)
N1	0.0177 (10)	0.0213 (12)	0.0235 (10)	−0.0029 (9)	0.0084 (8)	−0.0007 (9)
N2	0.0203 (11)	0.0296 (13)	0.0239 (11)	0.0020 (10)	0.0066 (9)	−0.0041 (10)
N3	0.0263 (13)	0.0450 (16)	0.0277 (12)	0.0052 (12)	0.0056 (10)	−0.0071 (11)
C1	0.0172 (11)	0.0179 (13)	0.0259 (12)	−0.0052 (10)	0.0067 (9)	0.0016 (10)
C2	0.0219 (12)	0.0213 (14)	0.0242 (12)	−0.0050 (11)	0.0074 (10)	−0.0006 (10)
C3	0.0229 (12)	0.0215 (15)	0.0304 (13)	−0.0033 (11)	0.0134 (10)	−0.0025 (11)
C4	0.0153 (12)	0.0234 (14)	0.0366 (14)	−0.0026 (11)	0.0067 (10)	0.0008 (12)
C5	0.0204 (12)	0.0251 (15)	0.0269 (13)	−0.0031 (11)	0.0028 (10)	0.0024 (11)
C6	0.0219 (12)	0.0185 (14)	0.0229 (12)	−0.0022 (11)	0.0082 (10)	0.0049 (10)
C7	0.0207 (12)	0.0212 (14)	0.0204 (12)	−0.0003 (11)	0.0035 (10)	0.0027 (11)
O1WA	0.068 (3)	0.111 (8)	0.061 (3)	−0.030 (3)	−0.026 (2)	0.022 (3)
O1WB	0.031 (4)	0.064 (9)	0.020 (3)	0.009 (4)	−0.002 (2)	−0.009 (3)
O2W	0.039 (3)	0.210 (8)	0.078 (4)	−0.015 (4)	−0.016 (3)	−0.006 (4)

Geometric parameters (Å, º) top

O1—C6	1.253 (3)	C4—H4A	0.93 (2)
O2—C6	1.274 (3)	C5—H5A	0.94 (2)
N1—C1	1.340 (3)	C6—C7	1.517 (3)
N1—C5	1.361 (3)	C7—C7ⁱ	1.513 (4)
N1—H1N1	0.96 (3)	C7—H7B	0.98 (2)
N2—C1	1.342 (3)	C7—H7A	0.97 (3)
N2—H2N2	0.90 (3)	O1WA—H1WA	0.8500
N2—H1N2	0.89 (3)	O1WA—H2WA	0.8501
N3—C2	1.371 (3)	O1WA—H1WB	0.2257
N3—H1N3	0.85 (3)	O1WB—H1WA	0.5518
N3—H2N3	0.91 (3)	O1WB—H2WA	1.2381
C1—C2	1.431 (3)	O1WB—H1WB	0.8500
C2—C3	1.383 (3)	O1WB—H2WB	0.8502
C3—C4	1.395 (3)	O2W—H1W2	0.8500
C3—H3A	0.96 (3)	O2W—H2W2	0.8501
C4—C5	1.357 (3)

C1—N1—C5	123.6 (2)	C4—C5—H5A	124.5 (14)
C1—N1—H1N1	118.5 (14)	N1—C5—H5A	115.7 (14)
C5—N1—H1N1	117.9 (14)	O1—C6—O2	123.6 (2)
C1—N2—H2N2	120.3 (18)	O1—C6—C7	120.8 (2)
C1—N2—H1N2	120.5 (15)	O2—C6—C7	115.61 (19)
H2N2—N2—H1N2	119 (2)	C7ⁱ—C7—C6	115.4 (2)
C2—N3—H1N3	120.8 (18)	C7ⁱ—C7—H7B	113.3 (13)
C2—N3—H2N3	114.7 (17)	C6—C7—H7B	104.0 (13)
H1N3—N3—H2N3	118 (3)	C7ⁱ—C7—H7A	111.3 (14)
N1—C1—N2	118.2 (2)	C6—C7—H7A	107.7 (14)
N1—C1—C2	118.5 (2)	H7B—C7—H7A	104.4 (18)
N2—C1—C2	123.2 (2)	H1WA—O1WA—H2WA	107.4
N3—C2—C3	123.1 (2)	H1WA—O1WA—H1WB	73.7
N3—C2—C1	119.4 (2)	H2WA—O1WA—H1WB	54.6
C3—C2—C1	117.5 (2)	H1WA—O1WB—H2WA	91.7
C2—C3—C4	121.5 (2)	H1WA—O1WB—H1WB	67.4
C2—C3—H3A	116.1 (14)	H2WA—O1WB—H1WB	35.9
C4—C3—H3A	122.3 (14)	H1WA—O1WB—H2WB	118.6
C5—C4—C3	119.1 (2)	H2WA—O1WB—H2WB	72.5
C5—C4—H4A	119.8 (15)	H1WB—O1WB—H2WB	107.4
C3—C4—H4A	121.1 (15)	H1W2—O2W—H2W2	107.4
C4—C5—N1	119.7 (2)

C5—N1—C1—N2	180.0 (2)	C1—C2—C3—C4	−0.8 (4)
C5—N1—C1—C2	0.2 (3)	C2—C3—C4—C5	0.6 (4)
N1—C1—C2—N3	−177.7 (2)	C3—C4—C5—N1	0.0 (4)
N2—C1—C2—N3	2.6 (4)	C1—N1—C5—C4	−0.4 (4)
N1—C1—C2—C3	0.4 (3)	O1—C6—C7—C7ⁱ	1.6 (4)
N2—C1—C2—C3	−179.4 (2)	O2—C6—C7—C7ⁱ	−177.9 (3)
N3—C2—C3—C4	177.2 (2)

Symmetry code: (i) −x, −y+2, −z+1.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2N2···O1ⁱⁱ	0.90 (3)	2.14 (3)	2.978 (3)	155 (3)
N3—H1N3···O1ⁱⁱ	0.85 (3)	2.14 (3)	2.993 (3)	176 (3)
N3—H2N3···O1WAⁱⁱⁱ	0.91 (3)	2.34 (3)	3.243 (6)	172 (2)
O1WA—H2WA···O2	0.85	1.93	2.764 (5)	165
N2—H1N2···O1	0.89 (3)	2.04 (3)	2.929 (3)	175 (2)
N1—H1N1···O2	0.96 (3)	1.69 (3)	2.643 (3)	171 (2)

Symmetry codes: (ii) −x, y−1/2, −z+1/2; (iii) x, −y+1/2, z−1/2.

Experimental details

Crystal data
Chemical formula	2C₅H₈N₃⁺·C₄H₄O₄²⁻·3H₂O
M_r	195.20
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	100
a, b, c (Å)	12.7159 (4), 3.9024 (1), 18.7734 (6)
β (°)	94.933 (2)
V (Å³)	928.13 (5)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.11
Crystal size (mm)	0.17 × 0.13 × 0.06

Data collection
Diffractometer	Bruker SMART APEXII CCD area-detector diffractometer
Absorption correction	Multi-scan (SADABS; Bruker, 2005)
T_min, T_max	0.981, 0.993
No. of measured, independent and observed [I > 2σ(I)] reflections	10934, 2121, 1364
R_int	0.056
(sin θ/λ)_max (Å⁻¹)	0.650

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.062, 0.129, 1.06
No. of reflections	2121
No. of parameters	178
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.26, −0.24

Computer programs: APEX2 (Bruker, 2005), SAINT (Bruker, 2005), SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2N2···O1ⁱ	0.90 (3)	2.14 (3)	2.978 (3)	155 (3)
N3—H1N3···O1ⁱ	0.85 (3)	2.14 (3)	2.993 (3)	176 (3)
N3—H2N3···O1WAⁱⁱ	0.91 (3)	2.34 (3)	3.243 (6)	172 (2)
O1WA—H2WA···O2	0.85	1.93	2.764 (5)	165
N2—H1N2···O1	0.89 (3)	2.04 (3)	2.929 (3)	175 (2)
N1—H1N1···O2	0.96 (3)	1.69 (3)	2.643 (3)	171 (2)

Symmetry codes: (i) −x, y−1/2, −z+1/2; (ii) x, −y+1/2, z−1/2.

Footnotes

‡Thomson Reuters ResearcherID: A-3561-2009.

§Thomson Reuters ResearcherID: A-5523-2009.

Acknowledgements

HKF and KBS thank the Malaysian Government and Universiti Sains Malaysia for Science Fund grant No. 305/PFIZIK/613312. KBS thanks Universiti Sains Malaysia for a post–doctoral research fellowship. HKF also thanks Universiti Sains Malaysia for the Research University Golden Goose grant No. 1001/PFIZIK/811012.

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