Crystal structure of 2-amino-4,6-di-meth-oxy-pyrimidinium thio-phene-2-carboxyl-ate.

In the title salt, C6H10N3O2 (+)·C5H3O2S(-), the 2-amino-4,6-di-meth-oxy-pyrimidinium cation inter-acts with the carboxyl-ate group of the thio-phene-2-carboxyl-ate anion through a pair of N-H⋯O hydrogen bonds, forming an R 2 (2)(8) ring motif. These motifs are centrosymmetrically paired via N-H⋯O hydrogen bonds, forming a complementary DDAA array. The separate DDAA arrays are linked by π-π stacking inter-actions between the pyrimidine rings, as well as by a number of weak C-H⋯O and N-H⋯O inter-actions. In the anion, the dihedral angle between the ring plane and the CO2 group is 11.60 (3)°. In the cation, the C atoms of methoxy groups deviate from the ring plane by 0.433 (10) Å.

Related literature

For the role played by non-covalent inter­actions in mol­ecular recognition porcesses, see: Desiraju (1989 ▸). For amino­pryimidine–carboxylate interactions in protein–nucleic acid recognition and protein–drug binding inteactions, see: Hunt et al. (1980 ▸); Alkorta & Elguero (2003 ▸). For 1:1 salts between 2-amino­pyrimidine and mono- and di­carb­oxy­lic acids, see: Etter & Adsmond (1990 ▸). For self-assembly of 2-amino­pyrimidine compounds, see: Scheinbeim & Schempp (1976 ▸). For carb­oxy­lic acid and 2-amino heterocyclic ring system synthons, see: Lynch & Jones (2004 ▸). For crystal structures of related salts, see: Ebenezer et al. (2012 ▸); Jennifer & Mu­thiah (2014 ▸). DDAA arrays have been observed in trimeth­oprim hydrogen glutarate (Robert et al., 2001 ▸), trimetho­prim formate (Umadevi et al., 2002 ▸), trimethoprim-m-chloro­benzoate (Raj et al., 2003 ▸), pyrimethaminium 3,5-di­nitro­benzoate (Subashini et al., 2007 ▸) and 2-amino-4,6-di­meth­oxy­pyrimidinum-salicylate (Thanigaimani et al., 2007 ▸).

Experimental

Crystal data

C6H10N3O2 +·C5H3O2S−

M = 283.30

Monoclinic,

a = 6.7335 (3) Å

b = 7.6307 (4) Å

c = 25.0638 (10) Å

β = 93.928 (4)°

V = 1284.78 (10) Å3

Z = 4

Mo Kα radiation

μ = 0.27 mm−1

T = 173 K

0.32 × 0.28 × 0.14 mm

Data collection

Agilent Eos Gemini diffractometer

Absorption correction: multi-scan (CrysAlis RED; Agilent, 2012 ▸) T min = 0.789, T max = 1.000

8844 measured reflections

4245 independent reflections

3071 reflections with I > 2σ(I)

R int = 0.028

Refinement

R[F 2 > 2σ(F 2)] = 0.062

wR(F 2) = 0.186

S = 1.05

4245 reflections

174 parameters

H-atom parameters constrained

Δρmax = 0.79 e Å−3

Δρmin = −0.55 e Å−3

Data collection: CrysAlis PRO (Agilent, 2012 ▸); cell refinement: CrysAlis PRO; data reduction: CrysAlis RED (Agilent, 2012 ▸); program(s) used to solve structure: SUPERFLIP (Palatinus & Chapuis, 2007 ▸; Palatinus & van der Lee, 2008 ▸; Palatinus et al., 2012 ▸); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015 ▸); molecular graphics: OLEX2 (Dolomanov et al., 2009 ▸); software used to prepare material for publication: OLEX2.

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S2056989015010907/hg5442sup1.cif

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989015010907/hg5442Isup2.hkl

Click here for additional data file.

Supporting information file. DOI: 10.1107/S2056989015010907/hg5442Isup3.cml

Click here for additional data file.

. DOI: 10.1107/S2056989015010907/hg5442fig1.tif

The asymmetric unit of the title compound, showing 30% probability displacement ellipsoids.

Click here for additional data file.

b . DOI: 10.1107/S2056989015010907/hg5442fig2.tif

A view of DDAA array along the b axis formed by independent N—H⋯O hydrogen bonds. Symmetry codes are given in Table 1. Dashed lines represent hydrogen bonds.

Click here for additional data file.

Cg Cg Cg . DOI: 10.1107/S2056989015010907/hg5442fig3.tif

A view of infinite number of DDAA arrays inter­connected by π–π stacking inter­actions indicated by dotted lines. Cg1⋯Cg1 = 3.4689 (12) Å, where Cg1 represents the centroid of the ring N1/C1/N2/C2/C3/C4.

CCDC reference: 1405154

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

C6H10N3O2+·C5H3O2S−	F(000) = 592
Mr = 283.30	Dx = 1.465 Mg m−3
Monoclinic, P21/n	Mo Kα radiation, λ = 0.71073 Å
a = 6.7335 (3) Å	Cell parameters from 2092 reflections
b = 7.6307 (4) Å	θ = 4.0–32.4°
c = 25.0638 (10) Å	µ = 0.27 mm−1
β = 93.928 (4)°	T = 173 K
V = 1284.78 (10) Å3	Irregular, colourless
Z = 4	0.32 × 0.28 × 0.14 mm

Agilent Eos Gemini diffractometer	4245 independent reflections
Radiation source: Enhance (Mo) X-ray Source	3071 reflections with I > 2σ(I)
Detector resolution: 16.0416 pixels mm-1	Rint = 0.028
ω scans	θmax = 32.7°, θmin = 3.3°
Absorption correction: multi-scan (CrysAlis RED; Agilent, 2012)	h = −7→9
Tmin = 0.789, Tmax = 1.000	k = −11→10
8844 measured reflections	l = −36→33

Refinement on F2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.062	H-atom parameters constrained
wR(F2) = 0.186	w = 1/[σ2(Fo2) + (0.0861P)2 + 0.9218P] where P = (Fo2 + 2Fc2)/3
S = 1.05	(Δ/σ)max < 0.001
4245 reflections	Δρmax = 0.79 e Å−3
174 parameters	Δρmin = −0.55 e Å−3
0 restraints

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.

	x	y	z	Uiso*/Ueq
O1	0.3208 (2)	0.1426 (2)	0.38775 (6)	0.0280 (3)
O2	0.2312 (2)	0.1346 (2)	0.57319 (6)	0.0324 (4)
N1	0.5394 (2)	0.2619 (2)	0.44749 (6)	0.0228 (3)
H1	0.6074	0.2925	0.4202	0.027*
N2	0.5086 (2)	0.2608 (2)	0.54146 (6)	0.0240 (3)
N3	0.7832 (3)	0.3787 (3)	0.50524 (7)	0.0329 (4)
H3A	0.8323	0.4043	0.5377	0.039*
H3B	0.8504	0.4053	0.4775	0.039*
C1	0.6093 (3)	0.3005 (3)	0.49820 (8)	0.0230 (4)
C2	0.3645 (3)	0.1761 (3)	0.43926 (8)	0.0223 (4)
C3	0.2549 (3)	0.1307 (3)	0.48120 (8)	0.0257 (4)
H3	0.1315	0.0706	0.4763	0.031*
C4	0.3372 (3)	0.1789 (3)	0.53174 (8)	0.0242 (4)
C5	0.1469 (3)	0.0367 (3)	0.37450 (9)	0.0333 (5)
H5A	0.1320	0.0186	0.3357	0.050*
H5B	0.0286	0.0966	0.3862	0.050*
H5C	0.1617	−0.0769	0.3926	0.050*
C6	0.3184 (4)	0.1689 (4)	0.62628 (9)	0.0352 (5)
H6A	0.3659	0.2903	0.6284	0.053*
H6B	0.4305	0.0890	0.6342	0.053*
H6C	0.2182	0.1507	0.6523	0.053*
S1	−0.15194 (10)	0.54563 (10)	0.26469 (2)	0.0427 (2)
O1A	−0.0066 (2)	0.4332 (2)	0.41417 (6)	0.0326 (4)
O2A	−0.2775 (2)	0.3607 (3)	0.36279 (6)	0.0361 (4)
C1A	0.0377 (5)	0.6516 (4)	0.23842 (10)	0.0434 (6)
H1A	0.0295	0.7014	0.2036	0.052*
C2A	0.2037 (4)	0.6582 (4)	0.27227 (11)	0.0431 (6)
H2A	0.3227	0.7142	0.2631	0.052*
C3A	0.1860 (3)	0.5737 (3)	0.32322 (8)	0.0268 (4)
H3AA	0.2874	0.5637	0.3513	0.032*
C4A	−0.0153 (3)	0.5071 (3)	0.32345 (8)	0.0253 (4)
C5A	−0.1048 (3)	0.4276 (3)	0.37009 (8)	0.0250 (4)

	U11	U22	U33	U12	U13	U23
O1	0.0286 (7)	0.0348 (8)	0.0209 (7)	−0.0082 (6)	0.0042 (5)	−0.0050 (6)
O2	0.0321 (8)	0.0437 (10)	0.0228 (7)	−0.0045 (7)	0.0110 (6)	0.0022 (6)
N1	0.0241 (7)	0.0250 (8)	0.0196 (7)	−0.0027 (6)	0.0044 (6)	0.0006 (6)
N2	0.0269 (8)	0.0271 (8)	0.0185 (7)	0.0015 (6)	0.0054 (6)	0.0015 (6)
N3	0.0316 (9)	0.0479 (12)	0.0193 (8)	−0.0135 (8)	0.0023 (7)	−0.0005 (8)
C1	0.0267 (9)	0.0229 (9)	0.0198 (8)	0.0003 (7)	0.0039 (7)	0.0016 (7)
C2	0.0241 (9)	0.0214 (9)	0.0217 (8)	−0.0009 (7)	0.0032 (7)	−0.0006 (7)
C3	0.0241 (9)	0.0279 (10)	0.0256 (9)	−0.0034 (7)	0.0062 (7)	0.0015 (8)
C4	0.0275 (9)	0.0243 (9)	0.0217 (9)	0.0032 (7)	0.0079 (7)	0.0029 (7)
C5	0.0321 (10)	0.0379 (12)	0.0296 (11)	−0.0087 (9)	0.0009 (8)	−0.0066 (9)
C6	0.0372 (11)	0.0494 (14)	0.0202 (9)	0.0037 (10)	0.0101 (8)	−0.0003 (9)
S1	0.0476 (4)	0.0578 (5)	0.0226 (3)	0.0000 (3)	0.0015 (2)	0.0018 (3)
O1A	0.0325 (8)	0.0457 (10)	0.0194 (7)	−0.0082 (7)	−0.0006 (6)	0.0043 (6)
O2A	0.0340 (8)	0.0530 (11)	0.0213 (7)	−0.0147 (7)	0.0015 (6)	0.0006 (7)
C1A	0.0661 (17)	0.0416 (14)	0.0241 (11)	0.0038 (12)	0.0141 (11)	0.0050 (10)
C2A	0.0517 (15)	0.0439 (15)	0.0354 (13)	−0.0110 (11)	0.0155 (11)	0.0029 (11)
C3A	0.0409 (11)	0.0239 (9)	0.0170 (8)	−0.0072 (8)	0.0112 (7)	0.0013 (7)
C4A	0.0311 (10)	0.0277 (10)	0.0171 (8)	0.0014 (8)	0.0026 (7)	0.0002 (7)
C5A	0.0291 (9)	0.0277 (10)	0.0186 (8)	−0.0026 (7)	0.0034 (7)	−0.0002 (7)

O1—C2	1.329 (2)	C5—H5B	0.9800
O1—C5	1.443 (3)	C5—H5C	0.9800
O2—C4	1.343 (2)	C6—H6A	0.9800
O2—C6	1.441 (3)	C6—H6B	0.9800
N1—H1	0.8800	C6—H6C	0.9800
N1—C1	1.357 (2)	S1—C1A	1.683 (3)
N1—C2	1.351 (3)	S1—C4A	1.708 (2)
N2—C1	1.352 (2)	O1A—C5A	1.249 (2)
N2—C4	1.321 (3)	O2A—C5A	1.272 (3)
N3—H3A	0.8800	C1A—H1A	0.9500
N3—H3B	0.8800	C1A—C2A	1.357 (4)
N3—C1	1.315 (3)	C2A—H2A	0.9500
C2—C3	1.370 (3)	C2A—C3A	1.443 (3)
C3—H3	0.9500	C3A—H3AA	0.9500
C3—C4	1.396 (3)	C3A—C4A	1.448 (3)
C5—H5A	0.9800	C4A—C5A	1.481 (3)
C2—O1—C5	116.97 (16)	H5A—C5—H5C	109.5
C4—O2—C6	117.66 (17)	H5B—C5—H5C	109.5
C1—N1—H1	120.3	O2—C6—H6A	109.5
C2—N1—H1	120.3	O2—C6—H6B	109.5
C2—N1—C1	119.40 (16)	O2—C6—H6C	109.5
C4—N2—C1	115.98 (17)	H6A—C6—H6B	109.5
H3A—N3—H3B	120.0	H6A—C6—H6C	109.5
C1—N3—H3A	120.0	H6B—C6—H6C	109.5
C1—N3—H3B	120.0	C1A—S1—C4A	92.37 (12)
N2—C1—N1	122.80 (18)	S1—C1A—H1A	123.6
N3—C1—N1	118.20 (17)	C2A—C1A—S1	112.83 (19)
N3—C1—N2	119.00 (18)	C2A—C1A—H1A	123.6
O1—C2—N1	111.98 (16)	C1A—C2A—H2A	122.5
O1—C2—C3	126.99 (18)	C1A—C2A—C3A	115.0 (2)
N1—C2—C3	121.02 (18)	C3A—C2A—H2A	122.5
C2—C3—H3	122.3	C2A—C3A—H3AA	126.4
C2—C3—C4	115.38 (18)	C2A—C3A—C4A	107.1 (2)
C4—C3—H3	122.3	C4A—C3A—H3AA	126.4
O2—C4—C3	115.91 (18)	C3A—C4A—S1	112.68 (14)
N2—C4—O2	118.68 (18)	C3A—C4A—C5A	125.34 (18)
N2—C4—C3	125.40 (17)	C5A—C4A—S1	121.78 (16)
O1—C5—H5A	109.5	O1A—C5A—O2A	124.37 (18)
O1—C5—H5B	109.5	O1A—C5A—C4A	117.69 (18)
O1—C5—H5C	109.5	O2A—C5A—C4A	117.92 (18)
H5A—C5—H5B	109.5
O1—C2—C3—C4	178.67 (19)	C6—O2—C4—N2	−4.2 (3)
N1—C2—C3—C4	−0.2 (3)	C6—O2—C4—C3	174.98 (19)
C1—N1—C2—O1	−177.64 (17)	S1—C1A—C2A—C3A	0.3 (3)
C1—N1—C2—C3	1.3 (3)	S1—C4A—C5A—O1A	−167.06 (17)
C1—N2—C4—O2	179.44 (18)	S1—C4A—C5A—O2A	11.8 (3)
C1—N2—C4—C3	0.4 (3)	C1A—S1—C4A—C3A	−1.39 (18)
C2—N1—C1—N2	−1.8 (3)	C1A—S1—C4A—C5A	173.67 (19)
C2—N1—C1—N3	177.7 (2)	C1A—C2A—C3A—C4A	−1.3 (3)
C2—C3—C4—O2	−179.84 (19)	C2A—C3A—C4A—S1	1.7 (2)
C2—C3—C4—N2	−0.7 (3)	C2A—C3A—C4A—C5A	−173.1 (2)
C4—N2—C1—N1	0.9 (3)	C3A—C4A—C5A—O1A	7.3 (3)
C4—N2—C1—N3	−178.5 (2)	C3A—C4A—C5A—O2A	−173.8 (2)
C5—O1—C2—N1	174.26 (18)	C4A—S1—C1A—C2A	0.6 (2)
C5—O1—C2—C3	−4.7 (3)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O1Ai	0.88	2.83	3.479 (2)	132
N1—H1···O2Ai	0.88	1.76	2.637 (2)	175
N3—H3A···O1Aii	0.88	2.04	2.826 (2)	148
N3—H3B···O1Ai	0.88	1.92	2.798 (2)	173
C5—H5B···O1A	0.98	2.68	3.369 (3)	128
C6—H6B···O1iii	0.98	2.52	3.434 (3)	155
C1A—H1A···O1iv	0.95	2.60	3.365 (3)	138
C1A—H1A···O2Av	0.95	2.60	3.383 (3)	140

Table 1

Hydrogen-bond geometry (, )

DHA	DH	HA	D A	DHA
N1H1O2A i	0.88	1.76	2.637(2)	175
N3H3AO1A ii	0.88	2.04	2.826(2)	148
N3H3BO1A i	0.88	1.92	2.798(2)	173
C6H6BO1iii	0.98	2.52	3.434(3)	155
C1AH1AO1iv	0.95	2.60	3.365(3)	138
C1AH1AO2A v	0.95	2.60	3.383(3)	140

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