Crystal structure of 4-amino-5-chloro-2,6-di-methyl-pyrimidinium thio-phene-2,5-di-carboxyl-ate.

In the title salt, C6H9ClN3 (+)·C6H3O4S(-), the cations and anions are linked via O-H⋯O and N-H⋯O hydrogen bonds, forming R 6 (6)(37) ring motifs that are inter-connected with each other, producing sheets. Separate parallel inversion-related sheets are linked through N-H⋯N and π-π stacking inter-actions [centroid-centroid distance = 3.5414 (13) Å], forming double layers parallel to (101). Weak C-H⋯O and C-H⋯S hydrogen bonds, as well as C-H⋯π inter-actions, connect the double layers into a three-dimensional network.

Chemical context

In crystal engineering, non-covalent inter­actions, such as hydrogen bonding, play a key role in mol­ecular recognition processes (Desiraju, 1989 ▸). Pyrimidine derivatives have gained considerable importance because of their remarkable bio­logical properties, for example as anti-fungal, anti­viral, anti­cancer and anti-allergenic agents (Ding et al., 2004 ▸). Thio­phene­carb­oxy­lic acid and its derivatives have attracted attention because of their wide range of pharmacological properties and numerous applications, such as the preparation of DNA hybridization indicators, single-mol­ecule magnets, photoluminescence materials and the treatment of osteoporosis as inhibitors of bone resorption in the tissue culture (Bharti et al., 2003 ▸; Taş et al., 2014 ▸; Boulsourani et al., 2011 ▸). The present study investigates the hydrogen-bonding patterns in 4-amino-5-chloro-2,6-di­methyl­pyrimidinium thio­phene-2,5-di­carboxyl­ate (I).

Structural commentary

The asymmetric unit of C6H9ClN3 +·C6H3O4S−, (I), contains one 4-amino-5-chloro-2,6-di­methyl­pyrimidinium cation and one thio­phene-2,5-di­carboxyl­ate anion (Fig. 1 ▸). Protonation of the pyrimidine occurs at atom N1, leading to a C2B—N1B—C6B angle of 122.5 (2)° which an increase of ca 3.8° compared to the C2B—N3B—C4B angle 118.7 (2)° involving the unprotonated N3 atom.

Figure 1

The asymmetric unit of the title compound, showing 30% probability displacement ellipsoids. The dashed line indicates a hydrogen bond.

Supra­molecular features

The carboxyl­ate group of the thio­phene-2,5-di­carboxyl­ate anion inter­acts with the protonated N1 atom of the pyrimidinium moiety with a single point heterosynthon via N—H⋯O hydrogen bonds (Table 1 ▸). In addition, the components are connected through O—H⋯O and N—H⋯O hydrogen bonds (Table 1 ▸) to form an (37) ring graph set motif. This motif includes anions connected by O—H.·O hydrogen bonds along [10] and involves the cations along [010] to form a 2D sheet (Fig. 2 ▸). Two separate 2D sheets (which are indicated in red and yellow in Fig. 3 ▸) are inter­connected by a self-complementary base pair between the pyrimidinium moiety through N—H⋯N hydrogen bond inter­actions with an (8) ring graph set motif and π–π stacking inter­actions between the pyrimidinium ring and the thio­phene ring with an observed inter­planar distance of 3.4188 (10) Å, a centroid-to-centroid (Cg1–Cg2) distance of 3.5414 (13) Å (where Cg1 is the centroid of the ring N1B/C2B–C6B and Cg2 is the centroid of the ring S1A/C2A–C5A) and slip angle (the angle between the centroid vector and the normal to the plane) of 18.0°; these are typical aromatic stacking values (Hunter, 1994 ▸). Through these inter­actions, parallel inversion-related sheets are connected into double layers parallel to (101). In addition, weak C—H⋯O, C—H⋯S and C—H⋯π inter­molecular inter­actions connect the double layers into a three-dimensional network (Fig. 3 ▸).

Table 1

Hydrogen-bond geometry (Å, °)

Cg is the centroid of the S1A/C2A–C5A ring.

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O3A—H3A⋯O2A i	1.04 (4)	1.44 (4)	2.475 (2)	176 (4)
N1B—H1B⋯O1A	0.85 (3)	1.87 (3)	2.719 (3)	178 (3)
N4B—H4B1⋯N3B ii	0.86 (3)	2.40 (3)	3.218 (3)	158 (3)
N4B—H4B2⋯O4A iii	0.94 (3)	1.86 (3)	2.784 (3)	170 (3)
C7B—H7BB⋯S1A iv	0.98	2.86	3.807 (2)	164
C8B—H8BB⋯O3A v	0.98	2.53	3.281 (3)	134
C8B—H8BC⋯O2A vi	0.98	2.47	3.301 (3)	143
C7B—H7BB⋯Cg iv	0.98	2.69	3.556 (3)	148

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

Figure 2

Packing diagram for (I), viewed along the a axis, showing a single sheet formed by O—H⋯O and N—H⋯O hydrogen bonds. Symmetry codes are given in Table 1 ▸. Dashed lines represent hydrogen bonds.

Figure 3

A view along the b axis, showing double layers (indicated in red and yellow) formed by hydrogen bonds and π–π stacking inter­actions. The weak C—H⋯O and C—H⋯S hydrogen bonds connect the double layers to form a three-dimensional network. Dotted lines represent N—H⋯N, C—H⋯O and C—H⋯S inter­actions. Solid lines indicate the stacking inter­actions.

Database survey

The crystal structures of amino­pyrimidine derivatives (Schwalbe & Williams, 1982 ▸) and amino­pyrimidine carboxyl­ates (Hu et al., 2002 ▸), have been reported. Several co-crystals/salts of amino­pyrimidine derivatives have been reported from our laboratory including co-crystals/salts of amino­pyrimidines with carb­oxy­lic acid (Mu­thiah et al., 2006 ▸; Devi & Mu­thiah, 2007 ▸; Subashini et al., 2008 ▸; Thanigaimani et al., 2009 ▸; Ebenezer & Mu­thiah, 2010 ▸, 2012 ▸; Ebenezer et al., 2011 ▸), amino­pyrimidines–thio­phene­carb­oxy­lic acid (Jegan Jennifer et al., 2014 ▸), the crystal structure of 2-amino-4,6-di­meth­oxy­pyrimidiniumthio­phene-2-carboxyl­ate (Rajam et al., 2015 ▸) and metal complexes with 4-amino-5-chloro-2,6-di­methyl­pyrimidine (Karthikeyan et al., 2016 ▸)

Synthesis and crystallization

A hot DMF solution of 4-amino-5-chloro-2,6-di­methyl­pyrimidine (39 mg, Alfa Aesar) and thio­phene-2,5-di­carb­oxy­lic acid (43 mg, Alfa Aesar) were mixed and warmed for half an hour over a water bath. The mixture was cooled slowly and kept at room temperature. After a few days colourless plate-like crystals were obtained.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2 ▸. The N—H and O—H H atoms were located in difference Fourier maps and refined isotropically. All other H atoms were placed in calculated positions and refined using a riding-model approximation with C—H = 0.95 Å (CH) or 0.98 Å (CH3). Isotropic displacement parameters for these atoms were set to 1.2 (CH) or 1.5 (CH3) times U eq of the parent atom. Idealized Me H atoms were refined as rotating groups. There are larger than expected residual density peaks close to the Cl and S atoms but these are not chemically sensible and are assumed to be related to the quality of the crystal.

Table 2

Experimental details

Crystal data
Chemical formula	C6H9ClN3 +·C6H3O4S−
M r	329.76
Crystal system, space group	Monoclinic, P21/n
Temperature (K)	100
a, b, c (Å)	7.9948 (3), 11.3928 (4), 15.7757 (6)
β (°)	98.520 (2)
V (Å3)	1421.04 (9)
Z	4
Radiation type	Mo Kα
μ (mm−1)	0.44
Crystal size (mm)	0.23 × 0.19 × 0.06
Data collection
Diffractometer	Bruker AXS D8 Quest CMOS
Absorption correction	Multi-scan (SADABS; Krause et al., 2015 ▸)
T min, T max	0.424, 0.746
No. of measured, independent and observed [I > 2σ(I)] reflections	10749, 3911, 2862
R int	0.053
(sin θ/λ)max (Å−1)	0.704
Refinement
R[F 2 > 2σ(F 2)], wR(F 2), S	0.060, 0.185, 1.10
No. of reflections	3911
No. of parameters	208
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3)	1.59, −0.69

Computer programs: APEX2 and SAINT (Bruker, 2014 ▸), SIR92 (Altomare et al., 1993 ▸), SHELXL2014 (Sheldrick, 2015 ▸), SHELXLE (Hübschle et al., 2011 ▸), Mercury (Macrae et al., 2008 ▸) and PLATON (Spek, 2009 ▸).

Crystal structure: contains datablock(s) I. DOI: 10.1107/S2056989016010148/lh5814sup1.cif

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989016010148/lh5814Isup2.hkl

Click here for additional data file.

Supporting information file. DOI: 10.1107/S2056989016010148/lh5814Isup3.cml

CCDC reference: 1486940

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

C6H9ClN3+·C6H3O4S−	F(000) = 680
Mr = 329.76	Dx = 1.541 Mg m−3
Monoclinic, P21/n	Mo Kα radiation, λ = 0.71073 Å
a = 7.9948 (3) Å	Cell parameters from 6601 reflections
b = 11.3928 (4) Å	θ = 3.1–30.0°
c = 15.7757 (6) Å	µ = 0.44 mm−1
β = 98.520 (2)°	T = 100 K
V = 1421.04 (9) Å3	Plate, colourless
Z = 4	0.23 × 0.19 × 0.06 mm

Bruker AXS D8 Quest CMOS diffractometer	3911 independent reflections
Radiation source: I-mu-S microsource X-ray tube	2862 reflections with I > 2σ(I)
Laterally graded multilayer (Goebel) mirror monochromator	Rint = 0.053
ω and φ scans	θmax = 30.0°, θmin = 2.6°
Absorption correction: multi-scan (SADABS; Krause et al., 2015)	h = −11→9
Tmin = 0.424, Tmax = 0.746	k = −15→16
10749 measured reflections	l = −21→21

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)] = 0.060	Hydrogen site location: mixed
wR(F2) = 0.185	H atoms treated by a mixture of independent and constrained refinement
S = 1.10	w = 1/[σ2(Fo2) + (0.1146P)2] where P = (Fo2 + 2Fc2)/3
3911 reflections	(Δ/σ)max < 0.001
208 parameters	Δρmax = 1.59 e Å−3
0 restraints	Δρmin = −0.69 e Å−3

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

	x	y	z	Uiso*/Ueq
S1A	0.83375 (7)	0.63795 (4)	0.43028 (4)	0.01808 (18)
O1A	0.6790 (2)	0.57301 (14)	0.58125 (10)	0.0252 (4)
O2A	0.6743 (2)	0.75418 (14)	0.63699 (10)	0.0218 (4)
O3A	1.0617 (2)	0.81066 (15)	0.26723 (10)	0.0227 (4)
H3A	1.110 (5)	0.780 (3)	0.214 (2)	0.060 (11)*
O4A	0.9244 (3)	0.63757 (15)	0.25678 (12)	0.0309 (4)
C1A	0.7104 (3)	0.6802 (2)	0.58237 (14)	0.0178 (4)
C2A	0.7953 (3)	0.7287 (2)	0.51203 (14)	0.0187 (4)
C3A	0.8446 (3)	0.84283 (19)	0.49963 (15)	0.0204 (5)
H3AA	0.8325	0.9054	0.5381	0.024*
C4A	0.9151 (3)	0.85594 (18)	0.42313 (15)	0.0199 (5)
H4AA	0.9568	0.9282	0.4046	0.024*
C5A	0.9166 (3)	0.75252 (19)	0.37866 (14)	0.0182 (4)
C6A	0.9689 (3)	0.7288 (2)	0.29484 (14)	0.0198 (5)
Cl1B	0.43554 (7)	0.14586 (5)	0.77201 (3)	0.02236 (18)
N1B	0.6246 (2)	0.34003 (17)	0.60286 (13)	0.0206 (4)
H1B	0.639 (4)	0.413 (3)	0.5956 (19)	0.031 (7)*
N3B	0.6059 (2)	0.14982 (16)	0.54703 (13)	0.0205 (4)
N4B	0.5127 (3)	−0.00013 (17)	0.62434 (14)	0.0242 (4)
H4B1	0.512 (4)	−0.043 (3)	0.5793 (19)	0.040 (9)*
H4B2	0.478 (4)	−0.039 (3)	0.671 (2)	0.045 (9)*
C2B	0.6450 (3)	0.2616 (2)	0.54118 (15)	0.0204 (5)
C4B	0.5460 (3)	0.1121 (2)	0.61845 (15)	0.0205 (5)
C5B	0.5201 (3)	0.1938 (2)	0.68398 (14)	0.0196 (4)
C6B	0.5592 (3)	0.3099 (2)	0.67489 (15)	0.0191 (4)
C7B	0.7142 (3)	0.3044 (2)	0.46395 (15)	0.0235 (5)
H7BA	0.6941	0.2453	0.4185	0.035*
H7BB	0.8360	0.3181	0.4787	0.035*
H7BC	0.6579	0.3778	0.4439	0.035*
C8B	0.5357 (3)	0.4046 (2)	0.73702 (15)	0.0250 (5)
H8BA	0.4198	0.4019	0.7502	0.037*
H8BB	0.5563	0.4810	0.7120	0.037*
H8BC	0.6156	0.3931	0.7898	0.037*

	U11	U22	U33	U12	U13	U23
S1A	0.0222 (3)	0.0148 (3)	0.0193 (3)	−0.00038 (18)	0.0096 (2)	−0.00055 (19)
O1A	0.0324 (9)	0.0188 (8)	0.0273 (9)	−0.0044 (7)	0.0142 (7)	0.0021 (7)
O2A	0.0242 (8)	0.0230 (8)	0.0207 (8)	−0.0008 (6)	0.0118 (6)	−0.0003 (6)
O3A	0.0267 (8)	0.0229 (8)	0.0217 (8)	−0.0026 (7)	0.0140 (7)	−0.0021 (7)
O4A	0.0445 (11)	0.0221 (9)	0.0308 (10)	−0.0068 (7)	0.0212 (8)	−0.0064 (7)
C1A	0.0186 (9)	0.0192 (10)	0.0164 (10)	0.0001 (8)	0.0054 (8)	−0.0009 (8)
C2A	0.0169 (9)	0.0197 (10)	0.0207 (10)	0.0010 (8)	0.0064 (8)	−0.0006 (9)
C3A	0.0234 (11)	0.0193 (10)	0.0199 (11)	−0.0029 (8)	0.0078 (9)	−0.0015 (8)
C4A	0.0208 (10)	0.0183 (11)	0.0218 (11)	−0.0040 (8)	0.0076 (9)	−0.0013 (8)
C5A	0.0166 (9)	0.0184 (10)	0.0210 (11)	−0.0010 (8)	0.0081 (8)	−0.0002 (8)
C6A	0.0212 (10)	0.0203 (11)	0.0197 (11)	0.0030 (8)	0.0089 (8)	0.0015 (9)
Cl1B	0.0281 (3)	0.0207 (3)	0.0200 (3)	−0.0013 (2)	0.0090 (2)	−0.0002 (2)
N1B	0.0218 (9)	0.0168 (9)	0.0239 (10)	−0.0020 (7)	0.0055 (8)	0.0024 (8)
N3B	0.0225 (9)	0.0188 (10)	0.0212 (10)	0.0004 (7)	0.0059 (8)	0.0018 (7)
N4B	0.0349 (11)	0.0171 (10)	0.0227 (10)	0.0003 (8)	0.0116 (9)	0.0000 (8)
C2B	0.0165 (9)	0.0210 (11)	0.0235 (11)	0.0009 (8)	0.0021 (8)	0.0015 (9)
C4B	0.0183 (10)	0.0215 (11)	0.0228 (11)	0.0013 (8)	0.0071 (8)	0.0006 (9)
C5B	0.0201 (10)	0.0187 (10)	0.0207 (11)	0.0003 (8)	0.0050 (8)	0.0002 (9)
C6B	0.0176 (9)	0.0163 (10)	0.0233 (11)	0.0006 (8)	0.0026 (8)	−0.0003 (9)
C7B	0.0240 (10)	0.0208 (11)	0.0273 (12)	0.0000 (9)	0.0094 (9)	0.0024 (10)
C8B	0.0327 (12)	0.0177 (11)	0.0256 (12)	0.0009 (9)	0.0078 (10)	−0.0044 (9)

S1A—C2A	1.716 (2)	N1B—H1B	0.85 (3)
S1A—C5A	1.722 (2)	N3B—C2B	1.318 (3)
O1A—C1A	1.247 (3)	N3B—C4B	1.358 (3)
O2A—C1A	1.269 (3)	N4B—C4B	1.312 (3)
O3A—C6A	1.306 (3)	N4B—H4B1	0.86 (3)
O3A—H3A	1.04 (4)	N4B—H4B2	0.94 (3)
O4A—C6A	1.226 (3)	C2B—C7B	1.492 (3)
C1A—C2A	1.490 (3)	C4B—C5B	1.429 (3)
C2A—C3A	1.381 (3)	C5B—C6B	1.372 (3)
C3A—C4A	1.414 (3)	C6B—C8B	1.488 (3)
C3A—H3AA	0.9500	C7B—H7BA	0.9800
C4A—C5A	1.372 (3)	C7B—H7BB	0.9800
C4A—H4AA	0.9500	C7B—H7BC	0.9800
C5A—C6A	1.470 (3)	C8B—H8BA	0.9800
Cl1B—C5B	1.721 (2)	C8B—H8BB	0.9800
N1B—C2B	1.348 (3)	C8B—H8BC	0.9800
N1B—C6B	1.363 (3)
C2A—S1A—C5A	91.32 (10)	H4B1—N4B—H4B2	115 (3)
C6A—O3A—H3A	109 (2)	N3B—C2B—N1B	122.3 (2)
O1A—C1A—O2A	126.5 (2)	N3B—C2B—C7B	119.5 (2)
O1A—C1A—C2A	117.76 (19)	N1B—C2B—C7B	118.2 (2)
O2A—C1A—C2A	115.72 (19)	N4B—C4B—N3B	117.9 (2)
C3A—C2A—C1A	128.7 (2)	N4B—C4B—C5B	122.1 (2)
C3A—C2A—S1A	111.97 (17)	N3B—C4B—C5B	120.0 (2)
C1A—C2A—S1A	119.24 (16)	C6B—C5B—C4B	119.5 (2)
C2A—C3A—C4A	112.3 (2)	C6B—C5B—Cl1B	120.89 (18)
C2A—C3A—H3AA	123.9	C4B—C5B—Cl1B	119.55 (17)
C4A—C3A—H3AA	123.9	N1B—C6B—C5B	116.8 (2)
C5A—C4A—C3A	112.36 (19)	N1B—C6B—C8B	117.9 (2)
C5A—C4A—H4AA	123.8	C5B—C6B—C8B	125.2 (2)
C3A—C4A—H4AA	123.8	C2B—C7B—H7BA	109.5
C4A—C5A—C6A	130.0 (2)	C2B—C7B—H7BB	109.5
C4A—C5A—S1A	112.08 (16)	H7BA—C7B—H7BB	109.5
C6A—C5A—S1A	117.83 (16)	C2B—C7B—H7BC	109.5
O4A—C6A—O3A	125.4 (2)	H7BA—C7B—H7BC	109.5
O4A—C6A—C5A	119.7 (2)	H7BB—C7B—H7BC	109.5
O3A—C6A—C5A	114.8 (2)	C6B—C8B—H8BA	109.5
C2B—N1B—C6B	122.5 (2)	C6B—C8B—H8BB	109.5
C2B—N1B—H1B	121 (2)	H8BA—C8B—H8BB	109.5
C6B—N1B—H1B	116 (2)	C6B—C8B—H8BC	109.5
C2B—N3B—C4B	118.7 (2)	H8BA—C8B—H8BC	109.5
C4B—N4B—H4B1	118 (2)	H8BB—C8B—H8BC	109.5
C4B—N4B—H4B2	127 (2)
O1A—C1A—C2A—C3A	−179.2 (2)	C4B—N3B—C2B—N1B	−1.3 (3)
O2A—C1A—C2A—C3A	2.2 (3)	C4B—N3B—C2B—C7B	178.83 (19)
O1A—C1A—C2A—S1A	3.9 (3)	C6B—N1B—C2B—N3B	−1.3 (3)
O2A—C1A—C2A—S1A	−174.75 (16)	C6B—N1B—C2B—C7B	178.6 (2)
C5A—S1A—C2A—C3A	0.03 (18)	C2B—N3B—C4B—N4B	−177.9 (2)
C5A—S1A—C2A—C1A	177.43 (18)	C2B—N3B—C4B—C5B	2.5 (3)
C1A—C2A—C3A—C4A	−177.4 (2)	N4B—C4B—C5B—C6B	179.2 (2)
S1A—C2A—C3A—C4A	−0.4 (3)	N3B—C4B—C5B—C6B	−1.2 (3)
C2A—C3A—C4A—C5A	0.6 (3)	N4B—C4B—C5B—Cl1B	−2.4 (3)
C3A—C4A—C5A—C6A	176.1 (2)	N3B—C4B—C5B—Cl1B	177.20 (17)
C3A—C4A—C5A—S1A	−0.6 (3)	C2B—N1B—C6B—C5B	2.4 (3)
C2A—S1A—C5A—C4A	0.31 (18)	C2B—N1B—C6B—C8B	−177.5 (2)
C2A—S1A—C5A—C6A	−176.79 (17)	C4B—C5B—C6B—N1B	−1.2 (3)
C4A—C5A—C6A—O4A	−162.8 (2)	Cl1B—C5B—C6B—N1B	−179.59 (16)
S1A—C5A—C6A—O4A	13.7 (3)	C4B—C5B—C6B—C8B	178.8 (2)
C4A—C5A—C6A—O3A	17.1 (3)	Cl1B—C5B—C6B—C8B	0.4 (3)
S1A—C5A—C6A—O3A	−166.44 (16)

D—H···A	D—H	H···A	D···A	D—H···A
O3A—H3A···O2Ai	1.04 (4)	1.44 (4)	2.475 (2)	176 (4)
N1B—H1B···O1A	0.85 (3)	1.87 (3)	2.719 (3)	178 (3)
N4B—H4B1···N3Bii	0.86 (3)	2.40 (3)	3.218 (3)	158 (3)
N4B—H4B2···O4Aiii	0.94 (3)	1.86 (3)	2.784 (3)	170 (3)
C7B—H7BB···S1Aiv	0.98	2.86	3.807 (2)	164
C8B—H8BB···O3Av	0.98	2.53	3.281 (3)	134
C8B—H8BC···O2Avi	0.98	2.47	3.301 (3)	143
C7B—H7BB···Cgiv	0.98	2.69	3.556 (3)	148