Crystal structure of 2,4-di­amino-7-(hydroxy­meth­yl)pteridin-1-ium nitrate

Sivajeyanthi, P.; Balasubramani, K.; Jeevaraj, M.; Thanigaimani, K.; Khalib, N.C.; Razak, I.A.

doi:10.1107/S2056989015008397

organic compounds

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ISSN: 2056-9890

Volume 71| Part 6| June 2015| Pages o376-o377

doi:10.1107/S2056989015008397

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Crystal structure of 2,4-diamino-7-(hydroxymethyl)pteridin-1-ium nitrate

Palaniyappan Sivajeyanthi,^a Kasthuri Balasubramani,^a ^* Muthaiah Jeevaraj,^a Kaliyaperumal Thanigaimani,^b Nuridayanti Che Khalib ^b and Ibrahim Abdul Razak ^b ‡

^aDepartment of Chemistry, Government Arts College (Autonomous), Thanthonimalai, Karur 639 005, Tamil Nadu, India, and ^bSchool of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia
^*Correspondence e-mail: manavaibala@gmail.com

Edited by H. Stoeckli-Evans, University of Neuchâtel, Switzerland (Received 25 April 2015; accepted 28 April 2015; online 7 May 2015)

In the crystal of the title molecular salt, C₇H₉N₆O⁺·NO₃⁻, the cations and anions are linked via N—H⋯O and O—H⋯O hydrogen bonds, forming sheets parallel to (100). Within the sheets there are numerous hydrogen-bonding ring motifs.

Keywords: crystal structure; pteridine; 2,4-diaminopteridinium; pteridin-1-ium nitrate; hydrogen bonding; ring motifs.

CCDC reference: 1062258

1. Related literature

For background to and the biological activity of pteridine derivatives, see: Benkovic Annu (1980 ); Blakeley (1969 ); Van Beelen et al. (1984 ); Dolphin (1980 ); Pfleiderer (1982 ); Blakely & Cocco (1985 ); Pfleiderer & Taylor (1964 ); Müller et al. (1991 ); Weinstock et al. (1968 ). For related structures, see: Kuyper (1990 ); Schwalbe & Williams (1986 ); Robertson et al. (1998 ). For hydrogen-bond motifs, see: Etter (1990 ); Bernstein et al. (1995 ); Allen et al. (1998 ).

2. Experimental

2.1. Crystal data

C₇H₉N₆O⁺·NO₃⁻
M_r = 255.21
Orthorhombic, C m c 2₁
a = 6.4060 (17) Å
b = 14.960 (6) Å
c = 10.867 (3) Å
V = 1041.4 (6) Å³
Z = 4
Mo Kα radiation
μ = 0.14 mm⁻¹
T = 294 K
0.27 × 0.10 × 0.07 mm

2.2. Data collection

Bruker SMART APEXII Duo CCD area-detector diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2009 ) T_min = 0.964, T_max = 0.991
2866 measured reflections
862 independent reflections
720 reflections with I > 2σ(I)
R_int = 0.028

2.3. Refinement

R[F² > 2σ(F²)] = 0.030
wR(F²) = 0.074
S = 1.03
862 reflections
127 parameters
1 restraint
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.09 e Å⁻³
Δρ_min = −0.16 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N3—H1N3⋯O2	1.03 (5)	1.82 (5)	2.831 (5)	167 (4)
N6—H2N6⋯O4	0.98 (3)	2.06 (3)	3.019 (6)	167 (3)
O1—H1O1⋯O2ⁱ	0.95 (6)	1.93 (6)	2.846 (4)	163 (6)
N5—H1N5⋯O3ⁱⁱ	0.92 (4)	2.09 (4)	2.983 (6)	164 (4)
N5—H2N5⋯O1ⁱ	0.91 (5)	2.15 (5)	2.913 (5)	141 (4)
N6—H1N6⋯O3ⁱⁱⁱ	0.78 (5)	2.35 (4)	3.015 (5)	145 (5)
N6—H1N6⋯O4ⁱⁱⁱ	0.78 (5)	2.44 (5)	3.190 (6)	162 (5)
Symmetry codes: (i) $[-x+1, -y+1, z+{\script{1\over 2}}]$ ; (ii) x, y, z+1; (iii) $[-x+1, -y, z+{\script{1\over 2}}]$ .

Data collection: APEX2 (Bruker, 2009); cell refinement: SAINT (Bruker, 2009); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009 ).

Supporting information

CCDC reference: 1062258

Crystal structure: contains datablocks global, I. DOI: 10.1107/S2056989015008397/su5127sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S2056989015008397/su5127Isup2.hkl

Supporting information file. DOI: 10.1107/S2056989015008397/su5127Isup3.cml

checkCIF report

Structural commentary top

Pteridine derivatives are found as the core structure of folic acid flavin adenine dinucleotide (FAD) and function as cofactors for enzymes involved in hydroxylation (Benkovic & Annu,1980) and methyl transfer (Blakeley, 1969; Van Beelen et al., 1984), as redox mediators (Dolphin, 1980) and as pigments for eyes and wings in certain insects (Pfleiderer, 1982). Variation of the substituents on the pteridine core of folates has provided synthetic anticancer drugs (Blakely & Cocco, 1985; Pfleiderer & Taylor, 1964). Pterdines are metabolites formed by a bicyclic pyrimidine-pyrazine moiety that occurs in a wide range of living systems and contributes in relevant biological functions (Muller et al., 1991). Pteridine derivatives have good diuretic activity and are also used as simple models for therapeutically valuable antifolate drugs (Weinstock et al., 1968). In order to study potential hydrogen bonding interactions, the title compound was synthesized and we report herein on its crystal structure.

The title molecular salt, Fig. 1, consists of a 2,4-diamino-7-(hydroxymethyl)pteridinum cation and a nitrate anion. During the synthesis of the molecular salt a proton was transferred from the hydroxyl group of nitric acid to atom N3 of the pteridine ring. The pteridine ring system (C1—C7/N1—N6/O1) is planar with a maximum deviation of 0.001 (1) Å for all the non H atoms. The bond lengths and angles are close to those found for similar compounds, viz. 2,4-diamino-6,7-dimethylpteridine hydrochloride monohydrate (Schwalbe & Williams, 1986) and triamterenium tetraphenylborate acetonitrile solvate (Robertson et al., 1998).

In the crystal, Fig. 2, the protonated N3 atom and the protonated 2-amino group (N6) are hydrogen-bonded to the nitrate O atoms (O2 and O4) via a pair of N3—H1N3···O2 and N6—H2N6···O4 hydrogen bonds, forming an R₂²(8) ring motif (Bernstein et al., 1995). This type of interaction is similar to the carboxylate-trimethoprim interaction observed in the trimethoprim cation-dihydrofolate reductase complex (Kuyper, 1990) and to the cyclic hydrogen bonded motif observed in many organic crystal structures (Allen et al., 1998). An R₁²(4) ring motif indicates a bifurcated hydrogen bond formed by N6–H1N6 to the two acceptors (O3 and O4). The 4-amino group and the hydroxyl group form hydrogen bonds with the O atoms of the nitrate ion leading to an R₃³(8) ring. The three center and bifurcated hydrogen bonds and fork like interaction form an R₄⁴(12) ring. Two R₃³(8) motifs and an R₂²(8) ring motif generate a new R₃²(18) ring motif. The above interactions lead to the formation a two dimensional network parallel to the bc plane (Table 1 and Fig. 2).

Synthesis and crystallization top

A few drops of nitric acid were added to a hot methanol solution (20 ml) of 2,4-diamino-6-(hydroxymethyl)pteridine (43 mg, Aldrich) which had been warmed over a heating magnetic stirrer hotplate for a few minutes. The resulting solution was allowed to cool slowly at room temperature and crystals of the title molecular salt appeared after a few days.

Refinement top

Crystal data, data collection and structure refinement details are summarized in Table 2. The O– and N-bound H atoms were located in a difference Fourier map and freely refined (O–H = 0.94 (6) Å and N–H = 0.78 (5)– 1.03 (5) Å). The C-bound H atoms were positioned geometrically (C–H = 0.93–0.97 Å) and refined using a riding model with U_iso(H) = 1.2 U_eq(C).

Related literature top

For background to and the biological activity of pteridine derivatives, see: Benkovic Annu (1980); Blakeley (1969); Van Beelen et al. (1984); Dolphin (1980); Pfleiderer (1982); Blakely & Cocco (1985); Pfleiderer & Taylor (1964); Müller et al. (1991); Weinstock et al. (1968). For related structures, see: Kuyper (1990); Schwalbe & Williams (1986); Robertson et al. (1998). For hydrogen-bond motifs, see: Etter (1990); Bernstein et al. (1995); Allen et al. (1998).

Computing details top

Data collection: APEX2 (Bruker, 2009); cell refinement: SAINT (Bruker, 2009); data reduction: SAINT (Bruker, 2009); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (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 the title salt, with atom labelling. Displacement ellipsoids are drawn at the 50% probability level. The N-H···O hydrogen bonds are shown as dashed lines (see Table 1 for details).
	Fig. 2. A view along the a axis of the crystal packing of the title molecular salt. The N-H···O hydrogen bonds are shown as dashed lines (see Table 1 for details).

2,4-Diamino-7-(hydroxymethyl)pteridin-1-ium nitrate top

Crystal data top

C₇H₉N₆O⁺·NO₃⁻	F(000) = 528
M_r = 255.21	D_x = 1.628 Mg m⁻³
Orthorhombic, Cmc2₁	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: C 2c -2	Cell parameters from 1083 reflections
a = 6.4060 (17) Å	θ = 2.7–24.6°
b = 14.960 (6) Å	µ = 0.14 mm⁻¹
c = 10.867 (3) Å	T = 294 K
V = 1041.4 (6) Å³	Block, bronze
Z = 4	0.27 × 0.10 × 0.07 mm

Data collection top

Bruker SMART APEXII Duo CCD area-detector diffractometer	862 independent reflections
Radiation source: fine-focus sealed tube	720 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.028
ϕ and ω scans	θ_max = 25.0°, θ_min = 2.7°
Absorption correction: multi-scan (SADABS; Bruker, 2009)	h = −5→7
T_min = 0.964, T_max = 0.991	k = −17→17
2866 measured reflections	l = −8→12

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)] = 0.030	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.074	H atoms treated by a mixture of independent and constrained refinement
S = 1.03	w = 1/[σ²(F_o²) + (0.0382P)² + 0.1935P] where P = (F_o² + 2F_c²)/3
862 reflections	(Δ/σ)_max < 0.001
127 parameters	Δρ_max = 0.09 e Å⁻³
1 restraint	Δρ_min = −0.15 e Å⁻³

Crystal data top

C₇H₉N₆O⁺·NO₃⁻	V = 1041.4 (6) Å³
M_r = 255.21	Z = 4
Orthorhombic, Cmc2₁	Mo Kα radiation
a = 6.4060 (17) Å	µ = 0.14 mm⁻¹
b = 14.960 (6) Å	T = 294 K
c = 10.867 (3) Å	0.27 × 0.10 × 0.07 mm

Data collection top

Bruker SMART APEXII Duo CCD area-detector diffractometer	862 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2009)	720 reflections with I > 2σ(I)
T_min = 0.964, T_max = 0.991	R_int = 0.028
2866 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.030	1 restraint
wR(F²) = 0.074	H atoms treated by a mixture of independent and constrained refinement
S = 1.03	Δρ_max = 0.09 e Å⁻³
862 reflections	Δρ_min = −0.15 e Å⁻³
127 parameters

Special details top

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'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	0.5000	0.63088 (17)	0.8666 (3)	0.0557 (8)
O2	0.5000	0.2129 (2)	0.5161 (3)	0.0585 (9)
O3	0.5000	0.12875 (19)	0.3553 (3)	0.0584 (9)
O4	0.5000	0.06903 (19)	0.5342 (3)	0.0608 (9)
N1	0.5000	0.4061 (2)	0.9909 (3)	0.0415 (9)
N2	0.5000	0.1632 (3)	0.9791 (4)	0.0451 (9)
N3	0.5000	0.2207 (2)	0.7764 (3)	0.0447 (9)
N4	0.5000	0.3731 (2)	0.7360 (4)	0.0499 (10)
N5	0.5000	0.2581 (3)	1.1464 (4)	0.0524 (10)
H1N5	0.5000	0.210 (3)	1.199 (4)	0.042 (13)*
H2N5	0.5000	0.312 (3)	1.185 (5)	0.062 (14)*
N6	0.5000	0.0703 (3)	0.8120 (4)	0.0546 (11)
H1N6	0.5000	0.028 (3)	0.854 (5)	0.056 (15)*
H2N6	0.5000	0.060 (2)	0.723 (3)	0.020 (9)*
N7	0.5000	0.1359 (2)	0.4687 (4)	0.0448 (9)
C1	0.5000	0.5648 (3)	0.9606 (5)	0.0467 (11)
H1A	0.3776	0.5726	1.0120	0.056*	0.50
H1B	0.6224	0.5726	1.0120	0.056*	0.50
C2	0.5000	0.4726 (2)	0.9092 (4)	0.0390 (10)
C3	0.5000	0.3228 (3)	0.9449 (4)	0.0384 (11)
C4	0.5000	0.2451 (2)	1.0250 (4)	0.0401 (10)
C5	0.5000	0.1519 (2)	0.8573 (5)	0.0408 (11)
C6	0.5000	0.3074 (2)	0.8204 (5)	0.0391 (10)
C7	0.5000	0.4546 (3)	0.7834 (4)	0.0498 (13)
H7A	0.5000	0.5028	0.7293	0.060*
H1O1	0.5000	0.689 (4)	0.901 (6)	0.072 (14)*
H1N3	0.5000	0.208 (3)	0.683 (5)	0.046 (11)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0954 (19)	0.0284 (13)	0.0435 (17)	0.000	0.000	0.0045 (16)
O2	0.090 (2)	0.0310 (14)	0.054 (2)	0.000	0.000	−0.0078 (16)
O3	0.096 (2)	0.0401 (17)	0.039 (2)	0.000	0.000	−0.0029 (17)
O4	0.093 (2)	0.0323 (15)	0.057 (2)	0.000	0.000	0.0045 (15)
N1	0.0534 (19)	0.0299 (17)	0.041 (2)	0.000	0.000	0.0027 (15)
N2	0.062 (2)	0.0276 (17)	0.046 (2)	0.000	0.000	0.0055 (15)
N3	0.068 (2)	0.0304 (18)	0.035 (2)	0.000	0.000	0.0005 (14)
N4	0.082 (3)	0.0300 (15)	0.038 (2)	0.000	0.000	0.0011 (17)
N5	0.086 (2)	0.035 (2)	0.036 (2)	0.000	0.000	0.0041 (18)
N6	0.082 (3)	0.0308 (18)	0.051 (3)	0.000	0.000	−0.001 (2)
N7	0.058 (2)	0.036 (2)	0.040 (2)	0.000	0.000	−0.0012 (17)
C1	0.069 (3)	0.034 (2)	0.037 (2)	0.000	0.000	0.0015 (19)
C2	0.056 (2)	0.032 (2)	0.029 (2)	0.000	0.000	0.0006 (18)
C3	0.046 (2)	0.027 (2)	0.041 (3)	0.000	0.000	0.0013 (15)
C4	0.049 (2)	0.032 (2)	0.040 (3)	0.000	0.000	0.007 (2)
C5	0.049 (2)	0.029 (2)	0.044 (3)	0.000	0.000	0.006 (2)
C6	0.050 (2)	0.0322 (19)	0.035 (2)	0.000	0.000	−0.0005 (18)
C7	0.075 (3)	0.036 (2)	0.038 (3)	0.000	0.000	0.003 (2)

Geometric parameters (Å, º) top

O1—C1	1.422 (6)	N5—C4	1.333 (7)
O1—H1O1	0.94 (6)	N5—H1N5	0.92 (5)
O2—N7	1.262 (5)	N5—H2N5	0.91 (5)
O3—N7	1.237 (5)	N6—C5	1.317 (5)
O4—N7	1.228 (5)	N6—H1N6	0.78 (5)
N1—C2	1.334 (5)	N6—H2N6	0.98 (4)
N1—C3	1.342 (5)	C1—C2	1.487 (6)
N2—C4	1.322 (5)	C1—H1A	0.9700
N2—C5	1.334 (7)	C1—H1B	0.9700
N3—C5	1.353 (6)	C2—C7	1.394 (5)
N3—C6	1.383 (5)	C3—C6	1.372 (6)
N3—H1N3	1.03 (5)	C3—C4	1.454 (5)
N4—C7	1.323 (5)	C7—H7A	0.9300
N4—C6	1.344 (6)

C1—O1—H1O1	111 (4)	C2—C1—H1B	109.2
C2—N1—C3	116.4 (4)	H1A—C1—H1B	107.9
C4—N2—C5	119.5 (4)	N1—C2—C7	120.6 (3)
C5—N3—C6	119.3 (4)	N1—C2—C1	116.2 (4)
C5—N3—H1N3	120 (2)	C7—C2—C1	123.3 (3)
C6—N3—H1N3	121 (2)	N1—C3—C6	121.6 (4)
C7—N4—C6	114.1 (5)	N1—C3—C4	121.3 (4)
C4—N5—H1N5	120 (3)	C6—C3—C4	117.2 (4)
C4—N5—H2N5	126 (3)	N2—C4—N5	120.6 (3)
H1N5—N5—H2N5	114 (4)	N2—C4—C3	121.0 (5)
C5—N6—H1N6	122 (4)	N5—C4—C3	118.4 (4)
C5—N6—H2N6	121 (2)	N6—C5—N2	119.3 (4)
H1N6—N6—H2N6	117 (4)	N6—C5—N3	117.5 (5)
O4—N7—O3	120.5 (4)	N2—C5—N3	123.2 (4)
O4—N7—O2	120.4 (4)	N4—C6—C3	123.4 (4)
O3—N7—O2	119.0 (4)	N4—C6—N3	116.8 (4)
O1—C1—C2	112.0 (4)	C3—C6—N3	119.9 (4)
O1—C1—H1A	109.2	N4—C7—C2	124.1 (4)
C2—C1—H1A	109.2	N4—C7—H7A	118.0
O1—C1—H1B	109.2	C2—C7—H7A	118.0

C3—N1—C2—C7	0.000 (2)	C6—N3—C5—N6	180.000 (1)
C3—N1—C2—C1	180.000 (2)	C6—N3—C5—N2	0.000 (2)
O1—C1—C2—N1	180.000 (2)	C7—N4—C6—C3	0.000 (2)
O1—C1—C2—C7	0.000 (2)	C7—N4—C6—N3	180.000 (1)
C2—N1—C3—C6	0.000 (2)	N1—C3—C6—N4	0.000 (2)
C2—N1—C3—C4	180.000 (2)	C4—C3—C6—N4	180.000 (2)
C5—N2—C4—N5	180.000 (2)	N1—C3—C6—N3	180.000 (2)
C5—N2—C4—C3	0.000 (2)	C4—C3—C6—N3	0.000 (2)
N1—C3—C4—N2	180.000 (2)	C5—N3—C6—N4	180.000 (1)
C6—C3—C4—N2	0.000 (2)	C5—N3—C6—C3	0.000 (2)
N1—C3—C4—N5	0.000 (2)	C6—N4—C7—C2	0.000 (2)
C6—C3—C4—N5	180.000 (2)	N1—C2—C7—N4	0.000 (2)
C4—N2—C5—N6	180.000 (2)	C1—C2—C7—N4	180.000 (2)
C4—N2—C5—N3	0.000 (2)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N3—H1N3···O2	1.03 (5)	1.82 (5)	2.831 (5)	167 (4)
N6—H2N6···O4	0.98 (3)	2.06 (3)	3.019 (6)	167 (3)
O1—H1O1···O2ⁱ	0.95 (6)	1.93 (6)	2.846 (4)	163 (6)
N5—H1N5···O3ⁱⁱ	0.92 (4)	2.09 (4)	2.983 (6)	164 (4)
N5—H2N5···O1ⁱ	0.91 (5)	2.15 (5)	2.913 (5)	141 (4)
N6—H1N6···O3ⁱⁱⁱ	0.78 (5)	2.35 (4)	3.015 (5)	145 (5)
N6—H1N6···O4ⁱⁱⁱ	0.78 (5)	2.44 (5)	3.190 (6)	162 (5)

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

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N3—H1N3···O2	1.03 (5)	1.82 (5)	2.831 (5)	167 (4)
N6—H2N6···O4	0.98 (3)	2.06 (3)	3.019 (6)	167 (3)
O1—H1O1···O2ⁱ	0.95 (6)	1.93 (6)	2.846 (4)	163 (6)
N5—H1N5···O3ⁱⁱ	0.92 (4)	2.09 (4)	2.983 (6)	164 (4)
N5—H2N5···O1ⁱ	0.91 (5)	2.15 (5)	2.913 (5)	141 (4)
N6—H1N6···O3ⁱⁱⁱ	0.78 (5)	2.35 (4)	3.015 (5)	145 (5)
N6—H1N6···O4ⁱⁱⁱ	0.78 (5)	2.44 (5)	3.190 (6)	162 (5)

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

Footnotes

‡Thomson Reuters ResearcherID: A-5599-2009.

Acknowledgements

PS and KB thank the Department of Science and Technology (DST-SERB), grant No. SB/FT/CS–058/2013, New Delhi, India, for financial support. KT thanks the Academy of Sciences for the Developing World and USM for the TWAS–USM fellowship. The authors also thank the Malaysian Government and Universiti Sains Malaysia (USM) for the research facilities and a USM Short Term Grant, No. 304/PFIZIK/6312078, to conduct this work.

References

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Volume 71| Part 6| June 2015| Pages o376-o377

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