2,6-Di­amino-4-chloro­pyrimidinium 4-carb­oxy­butano­ate

Bellarmin Edison; Kasthuri Balasubramani; Kaliyaperumal Thanigaimani; Nuridayanti Che Khalib; Suhana Arshad; Ibrahim Abdul Razak

doi:10.1107/S1600536814015220

. 2014 Jul 5;70(Pt 8):o857–o858. doi: 10.1107/S1600536814015220

2,6-Diamino-4-chloropyrimidinium 4-carboxybutanoate

Bellarmin Edison ^a, Kasthuri Balasubramani ^a,^*, Kaliyaperumal Thanigaimani ^b, Nuridayanti Che Khalib ^b, Suhana Arshad ^b, Ibrahim Abdul Razak ^b,^‡

PMCID: PMC4158549 PMID: 25249908

Abstract

In the title molecular salt, C₄H₆ClN₄ ⁺·C₅H₇O₄ ⁻, the cation is essentially planar, with a maximum deviation of 0.037 (1) Å for all non-H atoms. The anions are self-assembled through O—H⋯O hydrogen bonds, forming a supramolecular zigzag chain with graph-set notation C(8). In the crystal, the protonated N atom and the 2-amino group of the cation are hydrogen bonded to the carboxylate O atoms of the anion via a pair of N—H⋯O hydrogen bonds with an R ₂ ²(8) ring motif. This motif further self-organizes through N—H⋯O and O—H⋯O hydrogen bonds, generating an array of six hydrogen bonds, the rings having graph-set notation R ₃ ²(8), R ₂ ²(8), R ₄ ²(8), R ₂ ²(8) and R ₃ ²(8). In addition, another type of R ₂ ²(8) motif is formed by inversion-related pyrimidinium cations via N—H⋯N hydrogen bonds, forming a two-dimensional network parallel to (101).

Keywords: crystal structure

Related literature

For applications of pyrimidine derivatives, see: Condon et al. (1993 ▶); Maeno et al. (1990 ▶); Gilchrist (1997 ▶). For applications of glutaric acid, see: Windholz (1976 ▶). For the conformation of glutaric acid, see: Saraswathi et al. (2001 ▶); Stanley et al. (2002 ▶). For related structures, see: Thanigaimani et al. (2012a ▶,b ▶); Thanigaimani & Muthiah (2010 ▶). For hydrogen-bond motifs, see: Bernstein et al. (1995 ▶). For bond-length data, see: Allen et al. (1987 ▶). graphic file with name e-70-0o857-scheme1.jpg

Experimental

Crystal data

C₄H₆ClN₄ ⁺·C₅H₇O₄ ⁻
M _r = 276.68
Monoclinic,
a = 5.1582 (1) Å
b = 23.2339 (5) Å
c = 9.8858 (2) Å
β = 94.7949 (12)°
V = 1180.62 (4) Å³
Z = 4
Mo Kα radiation
μ = 0.34 mm⁻¹
T = 296 K
0.54 × 0.24 × 0.21 mm

Data collection

Bruker SMART APEXII DUO CCD area-detector diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2009 ▶) T _min = 0.838, T _max = 0.932
31054 measured reflections
3121 independent reflections
2402 reflections with I > 2σ(I)
R _int = 0.030

Refinement

R[F ² > 2σ(F ²)] = 0.040
wR(F ²) = 0.099
S = 1.04
3121 reflections
187 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.24 e Å⁻³
Δρ_min = −0.27 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

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536814015220/sj5418sup1.cif

e-70-0o857-sup1.cif^{(22.1KB, cif)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536814015220/sj5418Isup2.hkl

e-70-0o857-Isup2.hkl^{(153.2KB, hkl)}

Click here for additional data file.^{(4.8KB, cml)}

Supporting information file. DOI: 10.1107/S1600536814015220/sj5418Isup3.cml

CCDC reference: 1010934

Additional supporting information: crystallographic information; 3D view; checkCIF report

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

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N4—H1N4⋯O2ⁱ	0.91 (2)	1.99 (2)	2.7950 (19)	147.4 (18)
N2—H2N2⋯N3ⁱⁱ	0.85 (2)	2.23 (2)	3.079 (2)	176.9 (18)
N2—H1N2⋯O4ⁱⁱⁱ	0.87 (2)	2.15 (2)	3.0140 (18)	175.5 (18)
N4—H2N4⋯O2^iv	0.87 (2)	1.92 (2)	2.7904 (18)	175 (2)
N1—H1N1⋯O1^iv	0.90 (2)	1.80 (2)	2.6924 (17)	177 (2)
O4—H1O4⋯O1^v	0.94 (3)	1.67 (3)	2.5480 (15)	155 (3)

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

Acknowledgments

The authors thank the Malaysian Government and Universiti Sains Malaysia (USM) for the research facilities and Fundamental Research Grant Scheme (FRGS) No. 203/PFIZIK/6711171 to conduct this work. KT thanks The Academy of Sciences for the Developing World and USM for the TWAS–USM fellowship.

supplementary crystallographic information

S1. Comment

Pyrimidine derivatives are very important molecules in biology and have many application in the areas of pesticide and pharmaceutical agents (Condon et al., 1993). For example, imazosulfuron, ethirmol and mepanipyrim have been commercialized as agrochemicals (Maeno et al., 1990). Pyrimidine derivatives have also been developed as antiviral agents, such as AZT, which is the most widely-used anti-AIDS drug (Gilchrist, 1997). Glutaric acid (pentanedioic acid) is a dicarboxylic acid with five carbon atoms, occurring in plant and animal tissues. Glutaric acid is found in the blood and urine. It is used in the synthesis of phamaceuticals, surfactants and metal finishing compounds. Alpha-ketoglutaic acid is used in dietary supplements to improve protein synthesis (Windholz, 1976). The related crystal structures of Bis(2,6-diamino-4-chloropyrimidin-1-ium) fumarate (Thanigaimani et al., 2012a) and 2,6-diamno-4-chloropyrimidine-benzoic acid (1/1) (Thanigaimani et al., 2012b) have been recently reported. In order to study some interesting hydrogen bonding interactions, the crystal structure determination of the title compound, (I), was carried out.

The asymmetric unit of the title compound consists of a 2,6-diamino-4-chloropyrimidinium cation and a hydrogen glutarate anion (Fig. 1). The 2,6-diamino-4-chloropyrimidinium cation is essentially planar, with a maximum deviation of 0.016 (1) Å for atom N1. In the 2,6-diamino-4-chloropyrimidinium cation, a wider than normal angle [C1–N1–C6 = 121.44 (12)°] is subtented at the protonated N1 atom. In the hydrogen glutarate anion, C5/C6/C7/C8/C9 plane makes a dihedral angle of 9.67 (12) ° with 2,6-diamino-4-chloropyrimidinium cation. The backbone conformation of the hydrogen glutarate anion can be described by the two torsion angles C5–C6–C7–C8 of -171.89 (13)° and C6–C7–C8–C9 of -176.36 (13)°. As evident from the torsion angles, the hydrogenglutarate anion is in a fully extended conformation (Saraswathi et al., 2001) of the two carboxyl groups, one is deprotonated while the other is not. The bond lengths and angles (Allen et al., 1987) are within normal ranges.

In the crystal packing, the protonated N atom the 2-amino group of the cation are hydrogen bonded to the carboxylate O atoms of the anion via a pair of N1—H1N1···O1^iv and N4—H2N4···O2^iv hydrogen bonds (symmetry code in Table 1), forming R₂²(8) (Bernstein et al., 1995) ring motif. This motif further self organizes through N4—H1N4···O2ⁱ, N2—H1N2···O4ⁱⁱⁱ and O4—H1O4···O1^v hydrogen bonds (symmetry code in Table 1), to generate an array of six hydrogen bonds with the rings having the graph-set notations of R₃²(8), R₂²(8), R₄²(8), R₂²(8) and R₃²(8). The hydrogen glutarate anion self-assemble via O4—H1O4···O1 hydrogen bonds to form a one-dimensional supramolecular zigzag infinite chain, with the graph-set notation C(8); this is shown in Fig. 2. This type of head-to-tail fashion of hydrogen glutarate ions has also been observed in the crystal structure of pyrimethamine hydrogen glutarate (Stanley et al., 2002). The inversion-centre-related to the 2,6-diamino-4-chloropyrimidinium cations are also base-paired via N2—H2N2···N3ⁱⁱ hydrogen bonds involving the unprotonated pyrimidine N atom and the 2-amino group (symmetry code in Table 1). This type of base pairing, also with an R₂²(8) motif, has been observed in many diaminopyrimidiniumcarboxylate salts (Thanigaimani & Muthiah, 2010). These ring motifs extend to give a sheet parallel to (101) plane as shown in Fig 3.

S2. Experimental

Hot methanol solutions (20 ml) of 2,6-diamino-4-chloropyrimidine (36 mg, Aldrich) and glutaric acid (33 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.