2,3-Diamino­pyridinium hydrogen malonate

Kaliyaperumal Thanigaimani; Nuridayanti Che Khalib; Suhana Arshad; Ibrahim Abdul Razak

doi:10.1107/S1600536812050386

. 2012 Dec 15;69(Pt 1):o92–o93. doi: 10.1107/S1600536812050386

2,3-Diaminopyridinium hydrogen malonate

Kaliyaperumal Thanigaimani ^a, Nuridayanti Che Khalib ^a, Suhana Arshad ^a, Ibrahim Abdul Razak ^a,^*,^‡

PMCID: PMC3588255 PMID: 23476473

Abstract

In the title molecular salt, C₅H₈N₃ ⁺·C₃H₃O₄ ⁻, the cation is essentially planar, with a maximum deviation of 0.005 (1) Å for all non-H atoms. In the anion, an intramolecular O—H⋯O hydrogen bond generates an S(6) ring. In the crystal, the cations and anions are connected via N—H⋯O hydrogen bonds and a weak C—H⋯O interaction, forming layers parallel to the ab plane.

Related literature

For backgroup to the chemistry of substituted pyridines, see: Amr et al. (2006 ▶); Bart et al. (2001 ▶); Shinkai et al. (2000 ▶). For related structures, see: Betz et al. (2011 ▶); Hemamalini et al. (2011 ▶); Balasubramani & Fun (2009 ▶); Fun & Balasubramani (2009 ▶). For the conformation of the malonate ion, see: Djinović et al. (1990 ▶). For hydrogen-bond motifs, see: Bernstein et al. (1995 ▶). For bond-length data, see: Allen et al. (1987 ▶). For stability of the temperature controller used for the data collection, see: Cosier & Glazer (1986 ▶). graphic file with name e-69-00o92-scheme1.jpg

Experimental

Crystal data

C₅H₈N₃ ⁺·C₃H₃O₄ ⁻
M _r = 213.20
Monoclinic,
a = 5.0843 (1) Å
b = 8.0771 (1) Å
c = 11.1928 (2) Å
β = 91.214 (1)°
V = 459.55 (1) Å³
Z = 2
Mo Kα radiation
μ = 0.13 mm⁻¹
T = 100 K
0.28 × 0.25 × 0.14 mm

Data collection

Bruker SMART APEXII CCD area-detector diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2009 ▶) T _min = 0.966, T _max = 0.983
6631 measured reflections
1778 independent reflections
1695 reflections with I > 2σ(I)
R _int = 0.024

Refinement

R[F ² > 2σ(F ²)] = 0.037
wR(F ²) = 0.094
S = 1.07
1778 reflections
160 parameters
1 restraint
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.35 e Å⁻³
Δρ_min = −0.26 e Å⁻³

Data collection: APEX2 (Bruker, 2009 ▶); cell refinement: SAINT (Bruker, 2009 ▶); 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 ▶).

Supplementary Material

Click here for additional data file.^{(20.1KB, cif)}

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536812050386/is5228sup1.cif

e-69-00o92-sup1.cif^{(20.1KB, cif)}

Click here for additional data file.^{(87.5KB, hkl)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536812050386/is5228Isup2.hkl

e-69-00o92-Isup2.hkl^{(87.5KB, hkl)}

Click here for additional data file.^{(4.1KB, cml)}

Supplementary material file. DOI: 10.1107/S1600536812050386/is5228Isup3.cml

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O3—H1O3⋯O1	0.93 (4)	1.63 (3)	2.5208 (16)	159 (3)
N3—H2N3⋯O4ⁱ	0.88 (3)	2.16 (3)	2.9133 (19)	143 (2)
N2—H2N2⋯O2ⁱⁱ	0.87 (3)	2.15 (3)	3.0066 (18)	168 (2)
N1—H1N1⋯O1ⁱⁱⁱ	0.92 (3)	1.87 (3)	2.7782 (16)	168 (3)
N2—H1N2⋯O2ⁱⁱⁱ	0.88 (3)	2.12 (3)	2.9470 (18)	157 (3)
N3—H1N3⋯O2ⁱⁱ	0.87 (2)	2.18 (2)	3.0574 (19)	178 (3)
C7—H7B⋯O2^iv	0.99	2.46	3.3532 (19)	149

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Symmetry codes: (i) Inline graphic ; (ii) ; (iii) ; (iv) .

Acknowledgments

The authors thank the Malaysian Government and Universiti Sains Malaysia (USM) for the research facilities and USM Short Term Grant No. 304/PFIZIK/6312078 to conduct this work. KT thanks The Academy of Sciences for the Developing World and USM for a TWAS–USM fellowship.

supplementary crystallographic information

Comment

Pyridine and its derivatives continue to attract great interest due to the wide variety of interesting biological activities observed for these compounds, such as anticancer, analgesic, antimicrobial and antidepressant activities (Amr et al., 2006; Bart et al., 2001; Shinkai et al., 2000). They are also often involved in hydrogen-bond interactions. The related crystal structures of 2,3-diaminopyridinium 2-hydroxybenzoate (Hemamalini et al., 2011), 2,3-diaminopyrimidinium benzoate (Balasubramani & Fun, 2009) and 2,3-diaminopyridinium 4-hydroxybenzoate (Fun & Balasubramani, 2009) have been recently reported. In order to study potential hydrogen bonding interactions, the crystal structure determination of the title compound (I) was carried out.

The asymmetric unit (Fig. 1) contains one 2,3-Diaminopyridinium cation and one hydrogen malonate anion. The proton transfers from one of the carboxyl group oxygen atom (O1) to atom N1 of 2,3-diaminopyridine resulted in widening of C1—N1—C5 angle of the pyridinium ring to 123.69 (13)°, compared to the corresponding angle of 118.97 (15)° in neutral 2,3-diaminopyridine (Betz et al., 2011). The 2,4-diaminopyrinium cation is planar, with a maximum deviation of 0.005 (1) Å for atom N1. The bond lengths (Allen et al., 1987) and angles are normal.

In the crystal packing (Fig. 2), the protonated N1 atom and the 2-amino group (N2) is hydrogen-bonded to the carboxylate oxygen atoms (O1 and O2) via a pair of intermolecular N1—H1N1···O1ⁱⁱⁱ and N2—H1N2···O2ⁱⁱⁱ hydrogen bonds (symmetry code in Table 1), forming a ring motif R₂²(8) (Bernstein et al., 1995). Atom O3 of the carboxyl group of the hydrogen malonate anion forms an intramolecular O3—H1O3···O1 hydrogen bond with the O atom of the carboxylate group (O1) [with graph-set notation S(6)], leading to a folded conformation. A similar intramolecular hydrogen bond has been observed in the crystal structures of benzylammonium hydrogen malonate and 4-picolinium hydrogen malonate (Djinović et al., 1990). The 2-amino groups (N2 and N3) are involved in the intermolecular N—H···O hydrogen bonds with hydrogen malonate oxygen atom (O2), forming an R₂¹(7) ring motif. The crystal structure is further stabilized by a weak C7—H7B···O2^iv interaction (symmetry code in Table 1), forming a layer lying parallel to the ab plane.

Experimental

Hot methanol solutions (20 ml) of 2,3-diaminopyrimidine (27 mg, Aldrich) and malonic acid (26 mg, Merck) were mixed and 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 compound (I) appeared after a few days.