Crystal structure of 4-amino­pyridinium 5-(5-chloro-2,4-dinitrophenyl)-1,3-dimethyl-2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-olate hemihydrate

Vaduganathan, M.; Doraisamyraja, K.

doi:10.1107/S1600536814021084

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ISSN: 2056-9890

Volume 70| Part 10| October 2014| Pages 256-258

doi:10.1107/S1600536814021084

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Crystal structure of 4-aminopyridinium 5-(5-chloro-2,4-dinitrophenyl)-1,3-dimethyl-2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-olate hemihydrate

Manickkam Vaduganathan ^a and Kalaivani Doraisamyraja ^a ^*

^aPG and Research Department of Chemistry, Seethalakshmi Ramaswami College, Tiruchirappalli 620 002, Tamil Nadu, India
^*Correspondence e-mail: kalaivbalaj@yahoo.co.in

Edited by H. Stoeckli-Evans, University of Neuchâtel, Switzerland (Received 12 September 2014; accepted 22 September 2014; online 27 September 2014)

The title molecular salt, C₅H₇N₂⁺·C₁₂H₈ClN₄O₇⁻·0.5H₂O, crystallizes as a hemihydrate. The two rings in the barbiturate anion are not coplanar but make a dihedral angle of 43.17 (16)°. The two nitro groups deviate from the ring to which they are attached; the nitro group ortho with respect to the ring junction is more deviated [39.3 (4)°] than that in the para position [4.2 (5)°], probably to overcome steric hindrance. As a result of this, the latter nitro group is more involved in delocalizing the negative charge of the anion than the former nitro group. In the crystal, the cations and anions are linked via N—H⋯O hydrogen bonds forming zigzag chains along [10-1]. The chains are linked by O—H⋯O and C—H⋯O hydrogen bonds, forming slabs lying parallel to (10-1). Further C—H⋯O hydrogen bonds link the slabs, forming a three-dimensional structure.

Keywords: crystal structure; barbiturate; 4-aminopyridinium; molecular salt; hydrogen bonding.

CCDC reference: 1008376

1. Chemical context

Barbiturates occupy an important place in pharmacopoeia due to their central nervous system (CNS) depressing nature (Nogrady, 1988 ; Ashutoshkar, 1993 ; Hardman et al., 2001 ; Yadav, 2004 ; Nadkarni et al., 2005 ). Many barbiturates are ideal drugs for treating major epilepsy (Olsen et al., 1986 ; Dhiman, 2013 ). In a continuation of our previous work on the synthesis of crystalline barbiturates and, in particular, similar nitro-substituted aromatic compounds (Babykala et al., 2014 ), we report herein on the synthesis and crystal structure of the title molecular salt.

2. Structural commentary

The molecular structure of the title salt is depicted in Fig. 1. The two rings in the barbiturate anion (N3/N4/C7–C10 and C1–C6) are not coplanar but are inclined to one another by 43.17 (16)°. The two nitro groups on the benzene ring (N1/O1/O2 and N2/O3/O4) deviate to different extents from the plane of the ring. The dihedral angle for the former group, adjacent to the ring junction, is 39.3 (4)° while for the later it is 4.2 (5)°. as a result of this, the latter nitro group is more involved in delocalizing the negative charge of the anion than the former. The cation is protonated at the pyridine N atom, as has been observed previously (Babykala et al., 2014).

Figure 1
A view of the molecular structure of the title salt, with atom labelling. Displacement ellipsoids are drawn at the 30% probability level.

3. Supramolecular features

In the crystal, the cations and anions are linked via N—H⋯O hydrogen bonds (Fig. 2 and Table 1) forming zigzag chains along [10 $[\overline{1}]$ ]. The chains are linked by O—H⋯O and C—H⋯O hydrogen bonds, forming slabs lying parallel to (10 $[\overline{1}]$ ). Further C—H⋯O hydrogen bonds link the slabs, forming a three-dimensional structure (Fig. 2 and Table 1).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N6—H6A⋯O8ⁱ	0.90 (2)	2.09 (2)	2.947 (4)	158 (4)
N6—H6B⋯O9ⁱⁱ	0.90 (2)	2.05 (2)	2.918 (4)	162 (4)
N5—H5A⋯O7ⁱⁱⁱ	0.91 (2)	1.89 (4)	2.667 (4)	141 (5)
O9—H9A⋯O6^iv	0.89 (2)	1.99 (5)	2.707 (3)	136 (6)
O9—H9B⋯O6	0.90 (2)	1.83 (3)	2.707 (3)	167 (9)
C15—H15⋯O4^v	0.93	2.41	3.276 (5)	156
C16—H16⋯O2	0.93	2.46	3.190 (5)	136
C17—H17⋯O8ⁱ	0.93	2.56	3.290 (4)	136
Symmetry codes: (i) $[-x+{\script{5\over 2}}, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (ii) -x+2, -y, -z; (iii) -x+2, -y+1, -z; (iv) $[-x+2, y, -z+{\script{1\over 2}}]$ ; (v) $[-x+{\script{3\over 2}}, y-{\script{1\over 2}}, -z-{\script{1\over 2}}]$ .

Figure 2
A view along the b axis of the crystal packing of the title compound. Hydrogen bonds are shown as dashed lines (see Table 1

for details; H atoms not involved in hydrogen bonding have been omitted for clarity).

4. Database survey

A search of the Cambridge Structural Database (Version 5.35, last update May 2014; Allen, 2002 ) indicated the presence of 31 hits for barbiturate salts. These including five with a substituted benzene ring in position 5 of the barbiturate. In these five compounds, the organic cations vary: triethylammonium with 1,3-dimethyl-2,6-dioxo-5-(2,4,6-trinitrophenyl)-1,2,3,6-tetrahydropyrimidin-4-olate (LEGWIF; Rajamani & Kalaivani, 2012 ), 2-aminopyridinium with 5-(5-chloro-2,4-dinitrophenyl)-1,3-dimethyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-6-olate (OCEWUQ; Babykala et al., 2014), 2-methylpyridinium with 5-(2,4-dinitrophenyl)-1,3-dimethyl-2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-olate (YAVSOF; Sridevi & Kalaivani, 2012 ), N,N-dimethylanilinium with 1,3-dimethyl-2,6-dioxo-5-(2,4,6-trinitrophenyl)-1,2,3,6-tetrahydropyrimidin-4-olate (JOKGIB; Babykala et al., 2014) and quinolinium with 1,3-dimethyl-2,6-dioxo-5-(2,4,6-trinitrophenyl)-1,2,3,6-tetrahydropyrimidin-4-olate monohydrate (JOKGUN; Babykala et al., 2014). Compound OCEWUQ is composed of the same barbiturate anion as in the title compound. The difference lies in the nature of the cation, 2-aminopyrdinium in OCEWUQ and 4-aminopyridinium in the title salt.

The dihedral angle between the benzene ring and the barbiturate ring varies from ca 42.64° in YAVSOF to ca 51.88° in OCEWUQ, compared to only 43.17 (16)° in the title salt. This difference is surprising considering that the barbiturate anion is the same in both OCEWUQ and the title salt.

5. Synthesis and crystallization

To 1,3-dichloro-4,6-dinitrobenzene (2.36 g, 0.01 mol) dissolved in 20 ml of absolute alcohol, was added 1,3-dimethylbarbituric acid (0.01 mol, 1.56 g) dissolved in 30 ml of absolute alcohol. The mixture was heated to 313 K and 4-aminopyridine (0.02 mol, 1.88 g) dissolved in 20 ml of absolute ethanol was added. The mixture was shaken well for 2–3 h and kept as such at 298 K. After 24 h, the excess of solvent was removed by distillation under reduced pressure and to the resulting slurry was added to 50 ml of dry ether and the mixture was refrigerated for 5 h. The maroon-red-coloured solid obtained was filtered, powdered well and washed with 50 ml of dry ether. The dry solid was recrystallized from absolute ethanol and slow evaporation of this solvent at 293 K yielded good quality single crystals (yield 75%; m.p. 488 K).

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2. The cation NH and NH₂ H atoms were located in a difference Fourier map and freely refined. The water H atoms were also located in a difference Fourier map and refined with U_iso(H) = 1.2U_eq(O). The C-bound H atoms were included in calculated positions and treated as riding atoms: C—H = 0.93–0.98 Å with U_iso(H) = 1.5U_eq(C) for methyl H atoms and = 1.2U_eq(C) for other H atoms.

Table 2
Experimental details

Crystal data
Chemical formula	C₅H₇N₂⁺·C₁₂H₈ClN₄O₇⁻·0.5H₂O
M_r	459.81
Crystal system, space group	Monoclinic, C2/c
Temperature (K)	293
a, b, c (Å)	17.7242 (5), 14.2576 (5), 17.4321 (7)
β (°)	116.259 (3)
V (Å³)	3950.6 (2)
Z	8
Radiation type	Mo Kα
μ (mm⁻¹)	0.25
Crystal size (mm)	0.35 × 0.35 × 0.30

Data collection
Diffractometer	Bruker APEXII CCD
Absorption correction	Multi-scan (SADABS; Bruker, 2004 )
T_min, T_max	0.911, 0.930
No. of measured, independent and observed [I > 2σ(I)] reflections	38331, 3868, 2686
R_int	0.029
(sin θ/λ)_max (Å⁻¹)	0.617

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.056, 0.175, 1.07
No. of reflections	3868
No. of parameters	306
No. of restraints	7
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.47, −0.46
Computer programs: APEX2, SAINT and XPREP (Bruker, 2004), SIR92 (Altomare et al., 1993 ), ORTEP-3 for Windows (Farrugia, 2012 ), Mercury (Macrae et al., 2008 ), SHELXL97 (Sheldrick, 2008 ), PLATON (Spek, 2009 ) and publCIF (Westrip, 2010 ).

Supporting information

CCDC reference: 1008376

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536814021084/su2786sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536814021084/su2786Isup2.hkl

checkCIF report

Chemical context top

Barbiturates occupy an important place in pharmacopoeia due to their central nervous system (CNS) depressing nature (Nogrady, 1988; Ashutoshkar, 1993; Hardman et al., 2001; Yadav, 2004; Nadkarni et al., 2005). Many barbiturates are ideal drugs for treating major epilepsy (Olsen et al., 1986; Dhiman, 2013). In a continuation of our previous work on the synthesis of crystalline barbiturates and, in particular, similar nitro-substituted aromatic compounds (Babykala et al., 2014), we report herein on the synthesis and crystal structure of the title molecular salt.

Structural commentary top

The molecular structure of the title salt is depicted in Fig 1. The two rings in the barbiturate anion (N3/N4/C7–C10 and C1–C6) are not coplanar but are inclined to one another by 43.17 (16)°. The two nitro groups on the benzene ring (N1/O1/O2 and N2/O3/O4) deviate to different extents from the plane of the ring. The dihedral angle for the former group, adjacent to the ring junction, is 39.3 (4)° while for the later it is 4.2 (5)°. as a result of this, the latter nitro group is more involved in delocalizing the negative charge of the anion than the former. The cation is protonated at the pyridine N atom, as has been observed previously (Babykala et al., 2014).

Supramolecular features top

In the crystal, the cations and anions are linked via N—H···O hydrogen bonds (Fig. 2 and Table 1) forming zigzag chains along [101]. The chains are linked by O—H···O and C—H···O hydrogen bonds, forming slabs lying parallel to (101). Further C—H···O hydrogen bonds link the slabs, forming a three-dimensional structure (Fig. 2 and Table 1).

Database survey top

A search of the Cambridge Structural Database (Version 5.35, last update May 2014; Allen, 2002) indicated the presence of 31 hits for barbiturate salts. These including five with a substituted benzene ring in position 5 of the barbiturate. In these five compounds, the organic cations vary: triethylammonium with 1,3-dimethyl-2,6-dioxo-5-(2,4,6-trinitrophenyl)-1,2,3,6-tetrahydropyrimidin-4-olate (LEGWIF; Rajamani & Kalaivani, 2012), 2-aminopyridinium with 5-(5-chloro-2,4-dinitrophenyl)-1,3-dimethyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-6-olate (OCEWUQ; Babykala et al., 2014), 2-methylpyridinium with 5-(2,4-dinitrophenyl)-1,3-dimethyl-2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-olate (YAVSOF; Sridevi & Kalaivani, 2012), N,N-dimethylanilinium with 1,3-dimethyl-2,6-dioxo-5-(2,4,6-trinitrophenyl)-1,2,3,6-tetrahydropyrimidin-4-olate (JOKGIB; Babykala et al., 2014) and quinolinium with 1,3-dimethyl-2,6-dioxo-5-(2,4,6-trinitrophenyl)-1,2,3,6-tetrahydropyrimidin-4-olate monohydrate (JOKGUN; Babykala et al., 2014). Compound OCEWUQ is composed of the same barbiturate anion as in the title compound. The difference lies in the nature of the cation, 2-aminopyrdinium in OCEWUQ and 4-aminopyridinium in the title salt.

Synthesis and crystallization top

Refinement top

Related literature top

For related literature, see: Allen (2002); Ashutoshkar (1993); Babykala et al. (2014); Dhiman (2013); Hardman & Limbird (2001); Kalaivani & Rajamani (2012); Nadkarni et al. (2005); Nogrady (1988); Olsen et al. (1986); Sridevi & Kalaivani (2012); Yadav (2004).

Computing details top

Data collection: APEX2 (Bruker, 2004); cell refinement: APEX2 and SAINT (Bruker, 2004); data reduction: SAINT and XPREP (Bruker, 2004); program(s) used to solve structure: SIR92 (Altomare et al., 1993); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012) and Mercury (Macrae et al., 2008); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008), PLATON (Spek, 2009) and publCIF (Westrip, 2010).

Figures top

	Fig. 1. A view of the molecular structure of the title salt, with atom labelling. Displacement ellipsoids are drawn at the 30% probability level.
	Fig. 2. A view along the b axis of the crystal packing of the title compound. Hydrogen bonds are shown as dashed lines (see Table 1 for details; H atoms not involved in hydrogen bonding have been omitted for clarity).

4-Aminopyridinium 5-(5-chloro-2,4-dinitrophenyl)-1,3-dimethyl-2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-olate hemihydrate top

Crystal data top

C₅H₇N₂⁺·C₁₂H₈ClN₄O₇⁻·0.5H₂O	F(000) = 1896
M_r = 459.81	D_x = 1.546 Mg m⁻³
Monoclinic, C2/c	Mo Kα radiation, λ = 0.71073 Å
a = 17.7242 (5) Å	Cell parameters from 9949 reflections
b = 14.2576 (5) Å	θ = 2.6–29.5°
c = 17.4321 (7) Å	µ = 0.25 mm⁻¹
β = 116.259 (3)°	T = 293 K
V = 3950.6 (2) Å³	Block, red
Z = 8	0.35 × 0.35 × 0.30 mm

Data collection top

Bruker APEXII CCD diffractometer	3868 independent reflections
Radiation source: fine-focus sealed tube	2686 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.029
ω and ϕ scan	θ_max = 26.0°, θ_min = 1.9°
Absorption correction: multi-scan (SADABS; Bruker, 2004)	h = −21→21
T_min = 0.911, T_max = 0.930	k = −17→17
38331 measured reflections	l = −21→21

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.056	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.175	w = 1/[σ²(F_o²) + (0.0628P)² + 9.3104P] where P = (F_o² + 2F_c²)/3
S = 1.07	(Δ/σ)_max < 0.001
3868 reflections	Δρ_max = 0.47 e Å⁻³
306 parameters	Δρ_min = −0.46 e Å⁻³
7 restraints	Extinction correction: SHELXL, Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.0010 (2)

Crystal data top

C₅H₇N₂⁺·C₁₂H₈ClN₄O₇⁻·0.5H₂O	V = 3950.6 (2) Å³
M_r = 459.81	Z = 8
Monoclinic, C2/c	Mo Kα radiation
a = 17.7242 (5) Å	µ = 0.25 mm⁻¹
b = 14.2576 (5) Å	T = 293 K
c = 17.4321 (7) Å	0.35 × 0.35 × 0.30 mm
β = 116.259 (3)°

Data collection top

Bruker APEXII CCD diffractometer	3868 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2004)	2686 reflections with I > 2σ(I)
T_min = 0.911, T_max = 0.930	R_int = 0.029
38331 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.056	7 restraints
wR(F²) = 0.175	H atoms treated by a mixture of independent and constrained refinement
S = 1.07	Δρ_max = 0.47 e Å⁻³
3868 reflections	Δρ_min = −0.46 e Å⁻³
306 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)
C1	0.9919 (2)	0.4245 (2)	0.09141 (19)	0.0514 (7)
C2	0.9091 (2)	0.4328 (3)	0.0311 (2)	0.0629 (9)
H2	0.8833	0.3839	−0.0069	0.075*
C3	0.8647 (2)	0.5132 (3)	0.0273 (2)	0.0601 (9)
C4	0.90337 (19)	0.5859 (3)	0.0836 (2)	0.0547 (8)
C5	0.98582 (19)	0.5748 (2)	0.14353 (19)	0.0495 (7)
H5	1.0111	0.6239	0.1814	0.059*
C6	1.03389 (18)	0.4946 (2)	0.15101 (17)	0.0437 (7)
C7	1.11882 (18)	0.48772 (19)	0.22105 (18)	0.0430 (6)
C8	1.14416 (18)	0.4037 (2)	0.26856 (18)	0.0455 (7)
C9	1.27389 (19)	0.4806 (2)	0.3673 (2)	0.0513 (7)
C10	1.17194 (19)	0.5664 (2)	0.2441 (2)	0.0477 (7)
C11	1.3064 (2)	0.6394 (3)	0.3416 (3)	0.0748 (11)
H11A	1.2939	0.6791	0.3790	0.112*
H11B	1.2989	0.6741	0.2915	0.112*
H11C	1.3635	0.6180	0.3707	0.112*
C12	1.2465 (3)	0.3194 (2)	0.3945 (2)	0.0692 (10)
H12A	1.2993	0.3299	0.4436	0.104*
H12B	1.2522	0.2683	0.3615	0.104*
H12C	1.2043	0.3044	0.4128	0.104*
C13	0.9905 (2)	0.0191 (2)	−0.1371 (2)	0.0523 (7)
C14	0.9221 (2)	0.0263 (2)	−0.2186 (2)	0.0554 (8)
H14	0.9062	−0.0250	−0.2554	0.067*
C15	0.8793 (2)	0.1080 (3)	−0.2431 (2)	0.0681 (10)
H15	0.8345	0.1122	−0.2974	0.082*
C16	0.9629 (3)	0.1772 (2)	−0.1155 (2)	0.0678 (10)
H16	0.9761	0.2303	−0.0811	0.081*
C17	1.0100 (2)	0.1002 (2)	−0.0844 (2)	0.0611 (9)
H17	1.0543	0.0998	−0.0296	0.073*
N1	1.0356 (3)	0.3400 (2)	0.08368 (18)	0.0696 (9)
N2	0.7784 (2)	0.5168 (4)	−0.0404 (2)	0.0866 (11)
N3	1.24936 (15)	0.55831 (17)	0.31628 (17)	0.0516 (6)
N4	1.22188 (16)	0.40446 (17)	0.34170 (16)	0.0501 (6)
N5	0.8988 (2)	0.1819 (2)	−0.1926 (2)	0.0717 (9)
N6	1.0343 (2)	−0.0582 (2)	−0.1099 (2)	0.0680 (8)
O1	1.1078 (2)	0.34820 (19)	0.09283 (19)	0.0855 (9)
O2	0.9948 (2)	0.26692 (19)	0.06391 (18)	0.1055 (12)
O3	0.7499 (2)	0.4483 (3)	−0.0835 (2)	0.1351 (16)
O4	0.7378 (2)	0.5880 (3)	−0.0505 (3)	0.1303 (15)
Cl1	0.85552 (6)	0.68966 (8)	0.08676 (7)	0.0830 (4)
O6	1.10297 (16)	0.33059 (16)	0.25208 (15)	0.0653 (7)
O7	1.15599 (14)	0.64213 (15)	0.20372 (16)	0.0623 (6)
O8	1.34014 (15)	0.47883 (18)	0.43275 (16)	0.0736 (7)
O9	1.0000	0.1893 (2)	0.2500	0.0645 (9)
H9A	0.948 (2)	0.211 (4)	0.235 (6)	0.077*	0.50
H9B	1.032 (3)	0.233 (4)	0.242 (5)	0.077*	0.50
H6A	1.076 (2)	−0.063 (3)	−0.0563 (14)	0.101 (16)*
H6B	1.027 (3)	−0.108 (2)	−0.144 (2)	0.094 (14)*
H5A	0.863 (3)	0.230 (3)	−0.219 (4)	0.15 (2)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.064 (2)	0.0464 (17)	0.0424 (16)	−0.0042 (14)	0.0222 (15)	0.0029 (13)
C2	0.071 (2)	0.065 (2)	0.0419 (17)	−0.0195 (18)	0.0153 (16)	0.0024 (15)
C3	0.0458 (18)	0.082 (3)	0.0455 (17)	−0.0061 (17)	0.0142 (15)	0.0130 (17)
C4	0.0445 (17)	0.071 (2)	0.0501 (17)	0.0070 (15)	0.0222 (14)	0.0110 (16)
C5	0.0481 (17)	0.0539 (17)	0.0468 (16)	0.0012 (14)	0.0213 (14)	0.0007 (14)
C6	0.0488 (16)	0.0450 (15)	0.0390 (14)	−0.0011 (12)	0.0211 (13)	0.0025 (12)
C7	0.0428 (15)	0.0395 (14)	0.0443 (15)	0.0008 (12)	0.0170 (13)	0.0007 (12)
C8	0.0475 (17)	0.0426 (16)	0.0468 (16)	−0.0002 (13)	0.0213 (14)	0.0027 (12)
C9	0.0446 (17)	0.0486 (17)	0.0564 (18)	0.0052 (13)	0.0184 (15)	−0.0006 (14)
C10	0.0465 (16)	0.0365 (15)	0.0583 (18)	0.0049 (12)	0.0214 (14)	−0.0016 (13)
C11	0.051 (2)	0.052 (2)	0.109 (3)	−0.0096 (16)	0.023 (2)	−0.006 (2)
C12	0.076 (2)	0.056 (2)	0.065 (2)	0.0086 (17)	0.0219 (19)	0.0184 (17)
C13	0.0562 (19)	0.0458 (17)	0.0588 (19)	−0.0003 (14)	0.0289 (16)	0.0030 (14)
C14	0.067 (2)	0.0455 (17)	0.0488 (17)	−0.0005 (15)	0.0206 (16)	−0.0062 (14)
C15	0.075 (2)	0.064 (2)	0.059 (2)	0.0048 (19)	0.0240 (19)	0.0018 (18)
C16	0.084 (3)	0.0486 (19)	0.067 (2)	0.0006 (17)	0.031 (2)	−0.0085 (16)
C17	0.064 (2)	0.0541 (19)	0.0539 (19)	−0.0043 (16)	0.0157 (16)	−0.0057 (15)
N1	0.114 (3)	0.0483 (17)	0.0422 (15)	0.0056 (18)	0.0302 (17)	0.0011 (12)
N2	0.056 (2)	0.130 (3)	0.057 (2)	−0.009 (2)	0.0095 (17)	0.006 (2)
N3	0.0410 (13)	0.0394 (13)	0.0662 (16)	−0.0003 (10)	0.0164 (12)	−0.0025 (12)
N4	0.0502 (15)	0.0428 (13)	0.0506 (14)	0.0046 (11)	0.0163 (12)	0.0071 (11)
N5	0.089 (2)	0.0544 (18)	0.070 (2)	0.0143 (16)	0.0329 (19)	0.0057 (15)
N6	0.072 (2)	0.0522 (17)	0.070 (2)	0.0058 (15)	0.0228 (17)	0.0007 (15)
O1	0.128 (3)	0.0666 (17)	0.085 (2)	0.0329 (18)	0.069 (2)	0.0169 (14)
O2	0.165 (3)	0.0499 (16)	0.0685 (18)	−0.0136 (18)	0.0213 (19)	−0.0118 (13)
O3	0.074 (2)	0.177 (4)	0.100 (3)	−0.016 (2)	−0.010 (2)	−0.039 (3)
O4	0.069 (2)	0.168 (4)	0.107 (3)	0.027 (2)	−0.0044 (19)	0.009 (3)
Cl1	0.0616 (6)	0.0980 (8)	0.0897 (7)	0.0296 (5)	0.0339 (5)	0.0120 (6)
O6	0.0729 (16)	0.0525 (13)	0.0598 (14)	−0.0150 (11)	0.0197 (12)	0.0101 (11)
O7	0.0590 (14)	0.0386 (12)	0.0809 (16)	0.0041 (10)	0.0232 (12)	0.0085 (11)
O8	0.0564 (15)	0.0718 (16)	0.0683 (16)	0.0030 (12)	0.0055 (13)	0.0030 (13)
O9	0.074 (2)	0.0376 (17)	0.091 (3)	0.000	0.044 (2)	0.000

Geometric parameters (Å, º) top

C1—C2	1.382 (5)	C12—N4	1.466 (4)
C1—C6	1.396 (4)	C12—H12A	0.9600
C1—N1	1.469 (5)	C12—H12B	0.9600
C2—C3	1.374 (5)	C12—H12C	0.9600
C2—H2	0.9300	C13—N6	1.311 (4)
C3—C4	1.384 (5)	C13—C14	1.405 (5)
C3—N2	1.463 (5)	C13—C17	1.421 (4)
C4—C5	1.379 (4)	C14—C15	1.352 (5)
C4—Cl1	1.718 (4)	C14—H14	0.9300
C5—C6	1.397 (4)	C15—N5	1.316 (5)
C5—H5	0.9300	C15—H15	0.9300
C6—C7	1.463 (4)	C16—N5	1.322 (5)
C7—C10	1.404 (4)	C16—C17	1.340 (5)
C7—C8	1.412 (4)	C16—H16	0.9300
C8—O6	1.231 (3)	C17—H17	0.9300
C8—N4	1.403 (4)	N1—O1	1.224 (4)
C9—O8	1.223 (4)	N1—O2	1.228 (4)
C9—N4	1.365 (4)	N2—O3	1.199 (5)
C9—N3	1.367 (4)	N2—O4	1.210 (5)
C10—O7	1.251 (4)	N5—H5A	0.91 (2)
C10—N3	1.397 (4)	N6—H6A	0.898 (18)
C11—N3	1.469 (4)	N6—H6B	0.896 (18)
C11—H11A	0.9600	O9—H9A	0.89 (2)
C11—H11B	0.9600	O9—H9B	0.90 (2)
C11—H11C	0.9600

C2—C1—C6	122.8 (3)	H12A—C12—H12B	109.5
C2—C1—N1	115.2 (3)	N4—C12—H12C	109.5
C6—C1—N1	121.8 (3)	H12A—C12—H12C	109.5
C3—C2—C1	120.0 (3)	H12B—C12—H12C	109.5
C3—C2—H2	120.0	N6—C13—C14	122.4 (3)
C1—C2—H2	120.0	N6—C13—C17	121.0 (3)
C2—C3—C4	119.9 (3)	C14—C13—C17	116.7 (3)
C2—C3—N2	116.1 (4)	C15—C14—C13	119.6 (3)
C4—C3—N2	123.9 (4)	C15—C14—H14	120.2
C5—C4—C3	118.5 (3)	C13—C14—H14	120.2
C5—C4—Cl1	116.6 (3)	N5—C15—C14	122.2 (3)
C3—C4—Cl1	124.9 (3)	N5—C15—H15	118.9
C4—C5—C6	124.3 (3)	C14—C15—H15	118.9
C4—C5—H5	117.9	N5—C16—C17	123.6 (3)
C6—C5—H5	117.9	N5—C16—H16	118.2
C1—C6—C5	114.5 (3)	C17—C16—H16	118.2
C1—C6—C7	125.9 (3)	C16—C17—C13	118.4 (3)
C5—C6—C7	119.5 (3)	C16—C17—H17	120.8
C10—C7—C8	120.7 (3)	C13—C17—H17	120.8
C10—C7—C6	119.8 (3)	O1—N1—O2	124.7 (4)
C8—C7—C6	119.3 (3)	O1—N1—C1	118.2 (3)
O6—C8—N4	117.5 (3)	O2—N1—C1	116.9 (4)
O6—C8—C7	125.4 (3)	O3—N2—O4	122.2 (4)
N4—C8—C7	117.1 (3)	O3—N2—C3	118.5 (4)
O8—C9—N4	121.3 (3)	O4—N2—C3	119.3 (4)
O8—C9—N3	121.4 (3)	C9—N3—C10	123.8 (3)
N4—C9—N3	117.2 (3)	C9—N3—C11	117.7 (3)
O7—C10—N3	117.7 (3)	C10—N3—C11	118.4 (3)
O7—C10—C7	124.9 (3)	C9—N4—C8	123.6 (2)
N3—C10—C7	117.3 (3)	C9—N4—C12	118.8 (3)
N3—C11—H11A	109.5	C8—N4—C12	117.6 (3)
N3—C11—H11B	109.5	C15—N5—C16	119.5 (3)
H11A—C11—H11B	109.5	C15—N5—H5A	110 (4)
N3—C11—H11C	109.5	C16—N5—H5A	130 (4)
H11A—C11—H11C	109.5	C13—N6—H6A	121 (3)
H11B—C11—H11C	109.5	C13—N6—H6B	122 (2)
N4—C12—H12A	109.5	H6A—N6—H6B	116 (3)
N4—C12—H12B	109.5	H9A—O9—H9B	111 (3)

C6—C1—C2—C3	0.9 (5)	C13—C14—C15—N5	−0.8 (6)
N1—C1—C2—C3	−173.8 (3)	N5—C16—C17—C13	0.5 (6)
C1—C2—C3—C4	0.4 (5)	N6—C13—C17—C16	−179.8 (4)
C1—C2—C3—N2	178.1 (3)	C14—C13—C17—C16	−0.5 (5)
C2—C3—C4—C5	−1.0 (5)	C2—C1—N1—O1	137.5 (3)
N2—C3—C4—C5	−178.5 (3)	C6—C1—N1—O1	−37.2 (4)
C2—C3—C4—Cl1	−179.4 (3)	C2—C1—N1—O2	−38.7 (4)
N2—C3—C4—Cl1	3.1 (5)	C6—C1—N1—O2	146.5 (3)
C3—C4—C5—C6	0.5 (5)	C2—C3—N2—O3	5.4 (5)
Cl1—C4—C5—C6	179.1 (2)	C4—C3—N2—O3	−177.0 (4)
C2—C1—C6—C5	−1.3 (4)	C2—C3—N2—O4	−175.4 (4)
N1—C1—C6—C5	173.0 (3)	C4—C3—N2—O4	2.2 (6)
C2—C1—C6—C7	174.5 (3)	O8—C9—N3—C10	−175.5 (3)
N1—C1—C6—C7	−11.2 (5)	N4—C9—N3—C10	5.3 (5)
C4—C5—C6—C1	0.6 (4)	O8—C9—N3—C11	1.4 (5)
C4—C5—C6—C7	−175.5 (3)	N4—C9—N3—C11	−177.8 (3)
C1—C6—C7—C10	143.2 (3)	O7—C10—N3—C9	178.3 (3)
C5—C6—C7—C10	−41.2 (4)	C7—C10—N3—C9	−3.4 (4)
C1—C6—C7—C8	−41.3 (4)	O7—C10—N3—C11	1.4 (4)
C5—C6—C7—C8	134.4 (3)	C7—C10—N3—C11	179.7 (3)
C10—C7—C8—O6	−178.1 (3)	O8—C9—N4—C8	178.1 (3)
C6—C7—C8—O6	6.4 (5)	N3—C9—N4—C8	−2.7 (4)
C10—C7—C8—N4	3.5 (4)	O8—C9—N4—C12	0.2 (5)
C6—C7—C8—N4	−172.0 (2)	N3—C9—N4—C12	179.4 (3)
C8—C7—C10—O7	177.0 (3)	O6—C8—N4—C9	179.9 (3)
C6—C7—C10—O7	−7.5 (5)	C7—C8—N4—C9	−1.6 (4)
C8—C7—C10—N3	−1.2 (4)	O6—C8—N4—C12	−2.2 (4)
C6—C7—C10—N3	174.3 (3)	C7—C8—N4—C12	176.4 (3)
N6—C13—C14—C15	180.0 (3)	C14—C15—N5—C16	0.8 (6)
C17—C13—C14—C15	0.7 (5)	C17—C16—N5—C15	−0.6 (6)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N6—H6A···O8ⁱ	0.90 (2)	2.09 (2)	2.947 (4)	158 (4)
N6—H6B···O9ⁱⁱ	0.90 (2)	2.05 (2)	2.918 (4)	162 (4)
N5—H5A···O7ⁱⁱⁱ	0.91 (2)	1.89 (4)	2.667 (4)	141 (5)
O9—H9A···O6^iv	0.89 (2)	1.99 (5)	2.707 (3)	136 (6)
O9—H9B···O6	0.90 (2)	1.83 (3)	2.707 (3)	167 (9)
C15—H15···O4^v	0.93	2.41	3.276 (5)	156
C16—H16···O2	0.93	2.46	3.190 (5)	136
C17—H17···O8ⁱ	0.93	2.56	3.290 (4)	136

Symmetry codes: (i) −x+5/2, y−1/2, −z+1/2; (ii) −x+2, −y, −z; (iii) −x+2, −y+1, −z; (iv) −x+2, y, −z+1/2; (v) −x+3/2, y−1/2, −z−1/2.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N6—H6A···O8ⁱ	0.898 (18)	2.09 (2)	2.947 (4)	158 (4)
N6—H6B···O9ⁱⁱ	0.896 (18)	2.05 (2)	2.918 (4)	162 (4)
N5—H5A···O7ⁱⁱⁱ	0.91 (2)	1.89 (4)	2.667 (4)	141 (5)
O9—H9A···O6^iv	0.89 (2)	1.99 (5)	2.707 (3)	136 (6)
O9—H9B···O6	0.90 (2)	1.83 (3)	2.707 (3)	167 (9)
C15—H15···O4^v	0.93	2.41	3.276 (5)	156
C16—H16···O2	0.93	2.46	3.190 (5)	136
C17—H17···O8ⁱ	0.93	2.56	3.290 (4)	136

Symmetry codes: (i) −x+5/2, y−1/2, −z+1/2; (ii) −x+2, −y, −z; (iii) −x+2, −y+1, −z; (iv) −x+2, y, −z+1/2; (v) −x+3/2, y−1/2, −z−1/2.

Experimental details

Crystal data
Chemical formula	C₅H₇N₂⁺·C₁₂H₈ClN₄O₇⁻·0.5H₂O
M_r	459.81
Crystal system, space group	Monoclinic, C2/c
Temperature (K)	293
a, b, c (Å)	17.7242 (5), 14.2576 (5), 17.4321 (7)
β (°)	116.259 (3)
V (Å³)	3950.6 (2)
Z	8
Radiation type	Mo Kα
µ (mm⁻¹)	0.25
Crystal size (mm)	0.35 × 0.35 × 0.30

Data collection
Diffractometer	Bruker APEXII CCD diffractometer
Absorption correction	Multi-scan (SADABS; Bruker, 2004)
T_min, T_max	0.911, 0.930
No. of measured, independent and observed [I > 2σ(I)] reflections	38331, 3868, 2686
R_int	0.029
(sin θ/λ)_max (Å⁻¹)	0.617

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.056, 0.175, 1.07
No. of reflections	3868
No. of parameters	306
No. of restraints	7
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.47, −0.46

Computer programs: APEX2 (Bruker, 2004), APEX2 and SAINT (Bruker, 2004), SAINT and XPREP (Bruker, 2004), SIR92 (Altomare et al., 1993), ORTEP-3 for Windows (Farrugia, 2012) and Mercury (Macrae et al., 2008), SHELXL97 (Sheldrick, 2008), PLATON (Spek, 2009) and publCIF (Westrip, 2010).

Acknowledgements

The authors are grateful to the SERB–DST, New Delhi, for financial support and the SAIF, IIT Madras, for the data collection.

References

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Volume 70| Part 10| October 2014| Pages 256-258

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research communications\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Crystal structure of 4-amino­pyridinium 5-(5-chloro-2,4-di­nitro­phenyl)-1,3-di­methyl-2,6-dioxo-1,2,3,6-tetra­hydropyrimidin-4-olate hemihydrate

1. Chemical context

2. Structural commentary

3. Supra­molecular features

4. Database survey

5. Synthesis and crystallization

6. Refinement

Supporting information

Acknowledgements

References

research communications

Crystal structure of 4-aminopyridinium 5-(5-chloro-2,4-dinitrophenyl)-1,3-dimethyl-2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-olate hemihydrate

3. Supramolecular features