Supra­molecular inter­actions in 2,6-di­amino-4-chloro­pyrimidin-1-ium 5-chloro­salicylate and bis­(2,6-di­amino-4-chloro­pyrimidin-1-ium) naphthalene-1,5-di­sulfonate

Swinton Darious, R.; Thomas Muthiah, P.; Perdih, F.

doi:10.1107/S2056989018001196

research communications

CRYSTALLOGRAPHIC
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ISSN: 2056-9890

Volume 74| Part 2| February 2018| Pages 237-241

https://doi.org/10.1107/S2056989018001196

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Supramolecular interactions in 2,6-diamino-4-chloropyrimidin-1-ium 5-chlorosalicylate and bis(2,6-diamino-4-chloropyrimidin-1-ium) naphthalene-1,5-disulfonate

Robert Swinton Darious,^a Packianathan Thomas Muthiah ^a ^* and Franc Perdih ^b

^aSchool of Chemistry, Bharathidasan University, Tiruchirappalli 620 024, Tamilnadu, India, and ^bFaculty of Chemistry and Chemical Technology, University of Ljubljana, Večna, pot 113, PO Box 537, SI-1000 Ljubljana, Slovenia
^*Correspondence e-mail: tommtrichy@yahoo.co.in

Edited by M. Zeller, Purdue University, USA (Received 12 January 2018; accepted 19 January 2018; online 26 January 2018)

The crystals of two new salts, 2,6-diamino-4-chloropyrimidin-1-ium 5-chlorosalicylate, C₄H₆ClN₄⁺·C₇H₄ClO₃⁻, (I), and bis(2,6-diamino-4-chloropyrimidin-1-ium) naphthalene-1,5-di-sulfonate, 2C₄H₆ClN₄⁺·C₁₀H₆O₆S₂²⁻, (II), have been synthesized and characterized by single-crystal X-ray diffraction. In both compounds, the N atom of the pyrimidine group in between the amino substituents is protonated and the pyrimidinium cation forms a pair of N—H⋯O hydrogen bonds with the carboxylate/sulfonate ion, leading to a robust R₂²(8) motif (supramolecular heterosynthon). In compound (I), a self-complementary base pairing involving the other pyrimidinium ring nitrogen atom and one of the amino groups via a pair of N—H⋯N hydrogen bonds [R₂²(8) homosynthon] is also present. In compound (II), the crystallographic inversion centre coincides with the inversion centre of the naphthalene-1,5-disulfonate ion and all the sulfonate O atoms are hydrogen-bond acceptors, generating fused-ring motifs and a quadruple DDAA array. A halogen-bond (Cl⋯Cl) interaction is present in (I) with a distance and angle of 3.3505 (12) Å and 151.37 (10)°, respectively. In addition, a C—Cl⋯π interaction and a π–π interaction in (I) and a π–π interaction in (II) further stabilize these crystal structures.

Keywords: crystal structure; hydrogen bonding; supramolecular architecture; halogen–halogen interaction; quadruple array; homosynthon; heterosynthon.

CCDC references: 1817972; 1817971

1. Chemical context

The study of supramolecular interactions in the crystals of pyrimidinium salts continues to be an active field since the pyrimidine fragment is a component of nucleobases and many drug molecules. The pyrimidine group offers two protonation sites (the two ring nitrogens) and the site of protonation depends on the nature of the substituents. Tautomerism of the pyrimidinium cation has also been reported recently (Rajam et al., 2017 ). The pyrimidinium–carboxylate interaction is also of fundamental importance in biology since it is involved in protein–nucleic acid interactions and drug-receptor recognition (Hunt et al., 1980 ; Baker & Santi, 1965 ). The molecules are often self-assembled by hydrogen bonding, halogen bonding, cation⋯π, anion⋯π and π–π stacking interactions. Among these interactions, halogen bonding is of particular current interest (Cavallo et al., 2016 ). Various substituted pyrimidines and their interactions with different acids have been studied systematically in our laboratory. The variation in supramolecular architectures resulting from the different substituents in the base and the acid is being investigated, and crystal structures of 2,6-diamino-4-chloropyrimidinium salts with carboxylate/sulfonate have been reported recently from our laboratory (Mohana et al., 2017 ). The same pyrimidine derivative has been used to prepare the title compounds in order to further study the supramolecular architectures and the role of the halogen bond.

2. Structural commentary

The salt of compound (I) crystallizes with one CDAPY (2,6-diamino-4-chloropyrimidinium) cation and one CSA (5-chlorosalicylate) anion in the asymmetric unit (Fig. 1). The pyrimidinium cation is protonated at the N1 position (see Fig. 1 for atom numbering) and this is confirmed by an increase in the internal bond angle. The C2—N3—C4 angle at the unprotonated N3 atom is 115.1 (2)°, while for the protonated N1 atom, the C2—N1—C6 angle is 121.8 (2)°. The ion-pair (CDAPY and CSA) is almost planar [dihedral angle = 4.22 (11)°]. The carboxylate group of CSA is twisted slightly with respect to the remainder of the anion [dihedral angle= 3.9 (3)°]. The salt of compound (II) crystallizes with one CDAPY (2,6-diamino-4-chloropyrimidinium) cation and half a molecule of NSA (naphthalene-1,5-disulfonate) anion in the asymmetric unit (Fig. 2), the other half of NSA being generated by an inversion centre. A crystallographic inversion centre coinciding with the inversion centre of the NSA ion has also been reported earlier (Liu, 2012 ; Xu, 2012 ; Liu & Chen, 2012 ). The pyrimidinium cation is again protonated at the N1 position (see Fig. 2 for atom numbering) and this is confirmed by an increase in the internal bond angle. The C2—N3—C4 angle at the unprotonated N3 atom is 115.40 (16)°, while the angle at the protonated N1 atom (C2—N1—C6) is 121.84 (16)°. All of the sulfonate oxygen atoms of the NSA anion are involved in hydrogen bonding. The S1—O1, S1—O2 and S1—O3 distances are similar [1.4550 (15), 1.4584 (15) and 1.4431 (16) Å respectively].

Figure 1
ORTEP view of compound (I)

with the atom-numbering scheme. Displacement ellipsoids are drawn at 50% probability level. Dashed lines represent hydrogen bonds.

Figure 2
ORTEP view of compound (II)

, with the atom-numbering scheme. Displacement ellipsoids are drawn at 50% probability level. Dashed lines represent hydrogen bonds.

3. Supramolecular features

In salt (I), the protonated N1 atom and the amino hydrogen (N6) atom of CDAPY are hydrogen bonded via two N—H⋯O bonds (Table 1) forming a robust R₂²(8) ring motif (heterosynthon) involving the carboxylate group. The typical intramolecular hydrogen-bond S(6) motif (involving the carboxyl group and the phenolic –OH) observed in salicylates/salicylic acid is also present (Bernstein et al., 1995 ; Prabakaran et al., 2001 ; Panneerselvam et al., 2002 ) (Fig. 1). The 2-amino hydrogen atom of CDAPY interacts with the carboxylate oxygen O1 of CSA via an N—H⋯O hydrogen bond forming an R₂¹(6) ring motif. Thus, the O1 oxygen atom acts as a trifurcated acceptor. A similar set of three fused rings was observed in the crystal structure of 2,6-diamino-4-chloropyrimidinium 2-carboxy-3-nitrobenzoate (Mohana et al., 2017). However, in compound (I) the role of the 2-amino and 6-amino groups has been reversed. A self-complementary base pairing via a pair of N2—H⋯N3ⁱ (homosynthon) hydrogen bonds forming an R₂²(8) ring motif is also been observed. This type of base pairing is also observed in the crystal structures of 2,6-diamino-4-chloropyridinium 4-carboxybutanoate (Edison et al., 2014 ), 2,6-diamino-4-chloropyrimidine-benzoic acid (Thanigaimani et al., 2012a ) and bis(2,6-diamino-4-chloropyrimidin-1-ium) fumarate (Thanigaimani et al., 2012b ). The 2,6-diamino-4-chloropyrimidinium 5-chlorosalicylate units are linked via a Cl⋯Cl interaction (a type I interaction; Cavallo et al., 2016) with a distance and angle of 3.3505 (12) Å and 151.37 (10)°, respectively (Durka et al., 2015 ) (Fig. 3). Furthermore, a weak C—H⋯Oⁱⁱⁱ hydrogen-bonding interaction is present in this crystal structure. In addition, a weak stacking interaction with Cg1⋯Cg2 [3.6624 (14) Å; symmetry code: x, −1 + y, z; Cg1 and Cg2 are the centroids of the N1/C2/N3/C4/C5/C6 and C8–C13 rings, respectively] and C—Cl⋯π interactions [3.4469 (13) Å with an angle of 152.24 (9)°; symmetry code: − $[{1\over 2}]$ + x, $[{1\over 2}]$ − y, − $[{1\over 2}]$ + z] (Muthukumaran et al., 2011 ) further stabilize this crystal structure (Fig. 4).

Table 1
Hydrogen-bond geometry (Å, °) for (I)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1⋯O1	0.86	1.82	2.664 (3)	168
N2—H2A⋯O1	0.86	2.56	3.223 (3)	135
N2—H2B⋯N3ⁱ	0.86	2.13	2.970 (3)	165
O3—H3⋯O1	0.82	1.83	2.557 (3)	146
N6—H6A⋯O2	0.86	1.97	2.824 (3)	172
N6—H6B⋯O2ⁱⁱ	0.86	1.96	2.819 (3)	172
C10—H10⋯O3ⁱⁱⁱ	0.93	2.51	3.358 (4)	151
Symmetry codes: (i) -x+1, -y, -z; (ii) $[-x+{\script{1\over 2}}, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (iii) $[-x+{\script{3\over 2}}, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]$ .

Figure 3
Supramolecular layered structure extended as a chain via Cl⋯Cl interactions in (I)

Figure 4
A weak C—Cl⋯π interaction and π–π stacking interactions.

In salt (II), the sulfonate group mimics the role of the carboxylate oxygen atoms in generating an R₂²(8) motif (heterosynthon) involving the aminopyrimidinium cation (CDAPY) (Bernstein et al., 1995; Balasubramani et al., 2007 ). All units of the CDAPY and NSA ions are hydrogen bonded (Table 2) to generate a quadruple DDAA array with fused ring motifs R₂²(8), R₄²(8) and R₂²(8) (Fig. 5). This type of array has also been reported earlier (Robert et al., 2001 ; Umadevi et al., 2002 ; Raj et al., 2003 ; Subashini et al., 2007 ; Thanigaimani et al., 2007 ; Liu & Chen, 2012). In addition, the NSA anions also generate R₃²(10) and R₃³(21) ring motifs via N—H⋯O bonds. Weak π–π stacking interactions [Cg1⋯Cg4 = 3.4781 (11) Å; symmetry code: $[{3\over 2}]$ − x, − $[{1\over 2}]$ + y, $[{1\over 2}]$ − z and Cg4⋯Cg2 =3.4781 (11) Å; symmetry code: $[{1\over 2}]$ + x, $[{3\over 2}]$ − y, $[{1\over 2}]$ + z; Cg1, Cg2 and Cg4 are the centroids of the C7/C8/C9/C9′/C10′/C11′, C9/C10/C11/C7′/C8′/C9′ and N1/C2/N3/C4/C5/C6 rings, respectively] is also present (Fig. 6).

Table 2
Hydrogen-bond geometry (Å, °) for (II)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1⋯O1	0.86	1.92	2.708 (2)	152
N2—H2A⋯O2ⁱ	0.86	2.08	2.868 (3)	152
N2—H2B⋯O2	0.86	2.10	2.953 (2)	174
N6—H6A⋯N3ⁱⁱ	0.86	2.25	2.943 (2)	138
N6—H6B⋯O3ⁱⁱⁱ	0.86	2.01	2.808 (2)	154
Symmetry codes: (i) -x+1, -y+1, -z; (ii) $[x+{\script{1\over 2}}, -y+{\script{3\over 2}}, z+{\script{1\over 2}}]$ ; (iii) $[x-{\script{1\over 2}}, -y+{\script{3\over 2}}, z+{\script{1\over 2}}]$ .

Figure 5
Formation of a quadruple DDAA array in (II)

via N—H⋯O hydrogen bonds.

Figure 6
A view of the π–π stacking interactions between the pyrimidinium cation and the anion.

4. Database survey

Various salts of 5-chlorosalicylate have been reported: 2-methylquinolinium 5-chloro-2-hydroxybenzoate (Zhang et al., 2014 ), 4-amino-5-chloro-2,6-dimethylpyrimidinium 5-chloro-2-hydroxybenzoate (Rajam et al., 2017) and 2-amino-4,6-dimethylpyrimidinium 5-chlorosalicylate (Ebenezer & Muthiah, 2012 ). Similarly, various salts of half a molecule of naphthalene-1,5-disulfonate have been reported: bis(2-trifluoromethyl-1H-benzimidazole-3-ium) naphthalene-1,5-disulfonate (Liu, 2012), bis(3-methylanilinium) naphthalene-1,5-disulfonate (Liu & Chen, 2012) and bis(2-methylpiperidinium) naphthalene-1,5-disulfonate (Xu, 2012).

5. Synthesis and crystallization

Compounds (I) and (II) were synthesized by mixing hot ethanolic solutions (1:1) of 2,6-diamino-4-chloropyrimidine (36 mg) with 5-chlorosalicylic acid (43 mg) (I)/naphthalene-1,5-disulfonic acid (72 mg) (II). These mixtures were warmed to 333 K for 25 min. Colourless crystals separated out from the mother liquor at room temperature after a week.

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 3. All H atoms were initially located readily in difference-Fourier maps and were treated as riding atoms with C—H = 0.93 Å (aromatic), N—H = 0.86 Å and O—H = 0.82 Å with U_iso(H) = kU_eq(C,N,O), where k = 1.5 for hydroxy and 1.2 for all other H atoms.

Table 3
Experimental details

	(I)	(II)
Crystal data
Chemical formula	C₄H₆ClN₄⁺·C₇H₄ClO₃⁻	2C₄H₆ClN₄⁺·C₁₀H₆O₆S₂²⁻
M_r	317.13	577.42
Crystal system, space group	Monoclinic, P2₁/n	Monoclinic, P2₁/n
Temperature (K)	293	293
a, b, c (Å)	13.9203 (14), 7.0285 (6), 15.4294 (14)	9.1696 (4), 13.0848 (7), 9.9663 (5)
β (°)	114.544 (12)	90.526 (5)
V (Å³)	1373.2 (3)	1195.73 (10)
Z	4	2
Radiation type	Mo Kα	Mo Kα
μ (mm⁻¹)	0.49	0.50
Crystal size (mm)	0.40 × 0.10 × 0.03	0.40 × 0.40 × 0.06

Data collection
Diffractometer	Agilent SuperNova Dual Source diffractometer with an Atlas detector	Agilent SuperNova Dual Source diffractometer with an Atlas detector
Absorption correction	Multi-scan (CrysAlis PRO); Agilent, 2013 )	Multi-scan (CrysAlis PRO; Agilent, 2013)
T_min, T_max	0.644, 1.000	0.527, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections	7906, 3144, 2137	10382, 2735, 2274
R_int	0.027	0.028
(sin θ/λ)_max (Å⁻¹)	0.649	0.649

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.048, 0.128, 1.04	0.038, 0.102, 1.05
No. of reflections	3144	2735
No. of parameters	182	163
H-atom treatment	H-atom parameters constrained	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.29, −0.40	0.49, −0.59
Computer programs: CrysAlis PRO (Agilent, 2013), SHELXT2014 (Sheldrick, 2015a ), SHELXL2014 (Sheldrick, 2015b ), PLATON (Spek, 2009 ) and Mercury (Macrae et al., 2008 ).

Supporting information

CCDC references: 1817972; 1817971

Crystal structure: contains datablocks I, II. DOI: https://doi.org/10.1107/S2056989018001196/zl2723sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989018001196/zl2723Isup2.hkl

Structure factors: contains datablock II. DOI: https://doi.org/10.1107/S2056989018001196/zl2723IIsup3.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2056989018001196/zl2723Isup4.cml

checkCIF report

Computing details top

For both structures, data collection: CrysAlis PRO (Agilent, 2013); cell refinement: CrysAlis PRO (Agilent, 2013); data reduction: CrysAlis PRO (Agilent, 2013); program(s) used to solve structure: SHELXT2014 (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015b); molecular graphics: PLATON (Spek, 2009), Mercury (Macrae et al., 2008); software used to prepare material for publication: PLATON (Spek, 2009).

2,6-Diamino-4-chloropyrimidin-1-ium 2-chloro-6-hydroxybenzoate (I) top

Crystal data top

C₄H₆ClN₄⁺·C₇H₄ClO₃⁻	F(000) = 648
M_r = 317.13	D_x = 1.534 Mg m⁻³
Monoclinic, P2₁/n	Mo Kα radiation, λ = 0.71073 Å
a = 13.9203 (14) Å	Cell parameters from 1734 reflections
b = 7.0285 (6) Å	θ = 3.9–27.5°
c = 15.4294 (14) Å	µ = 0.49 mm⁻¹
β = 114.544 (12)°	T = 293 K
V = 1373.2 (3) Å³	Needle, colorless
Z = 4	0.40 × 0.10 × 0.03 mm

Data collection top

Agilent SuperNova Dual Source diffractometer with an Atlas detector	3144 independent reflections
Radiation source: SuperNova (Mo) X-ray Source	2137 reflections with I > 2σ(I)
Mirror monochromator	R_int = 0.027
Detector resolution: 10.4933 pixels mm^-1	θ_max = 27.5°, θ_min = 2.9°
ω scans	h = −18→17
Absorption correction: multi-scan (CrysAlis PRO); Agilent, 2013)	k = −7→9
T_min = 0.644, T_max = 1.000	l = −20→19
7906 measured reflections

Refinement top

Refinement on F²	0 restraints
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.048	H-atom parameters constrained
wR(F²) = 0.128	w = 1/[σ²(F_o²) + (0.0482P)² + 0.5033P] where P = (F_o² + 2F_c²)/3
S = 1.04	(Δ/σ)_max < 0.001
3144 reflections	Δρ_max = 0.29 e Å⁻³
182 parameters	Δρ_min = −0.40 e Å⁻³

Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
Cl1	0.25461 (6)	−0.27636 (11)	−0.00641 (5)	0.0674 (2)
N1	0.38557 (14)	0.2707 (3)	0.12207 (13)	0.0386 (4)
H1	0.4128	0.3792	0.1450	0.046*
N2	0.50448 (17)	0.2485 (3)	0.05504 (16)	0.0566 (6)
H2B	0.5313	0.1895	0.0215	0.068*
H2A	0.5293	0.3573	0.0796	0.068*
N3	0.38700 (15)	0.0032 (3)	0.03064 (13)	0.0442 (5)
N6	0.27205 (16)	0.3072 (3)	0.19347 (15)	0.0503 (5)
H6A	0.3023	0.4141	0.2157	0.060*
H6B	0.2207	0.2687	0.2063	0.060*
C2	0.42485 (18)	0.1715 (3)	0.06889 (16)	0.0404 (5)
C4	0.30522 (17)	−0.0606 (3)	0.04713 (16)	0.0414 (5)
C5	0.26096 (16)	0.0273 (3)	0.09993 (15)	0.0398 (5)
H5	0.2048	−0.0266	0.1089	0.048*
C6	0.30401 (16)	0.2033 (3)	0.14025 (15)	0.0368 (5)
Cl2	0.50995 (6)	1.29096 (12)	0.45221 (5)	0.0745 (3)
O1	0.49261 (13)	0.5917 (2)	0.18881 (13)	0.0534 (5)
O2	0.38734 (12)	0.6467 (2)	0.26174 (12)	0.0501 (4)
O3	0.62982 (14)	0.8382 (3)	0.19368 (15)	0.0617 (5)
H3	0.5981	0.7365	0.1805	0.093*
C7	0.46259 (17)	0.6930 (3)	0.24184 (16)	0.0393 (5)
C8	0.51962 (15)	0.8751 (3)	0.27862 (15)	0.0362 (5)
C9	0.60003 (17)	0.9377 (4)	0.25339 (17)	0.0437 (6)
C10	0.65092 (19)	1.1105 (4)	0.28915 (19)	0.0563 (7)
H10	0.7038	1.1527	0.2718	0.068*
C11	0.6235 (2)	1.2181 (4)	0.34943 (19)	0.0580 (7)
H11	0.6576	1.3330	0.3729	0.070*
C12	0.54500 (19)	1.1548 (4)	0.37507 (17)	0.0488 (6)
C13	0.49410 (17)	0.9865 (3)	0.34066 (16)	0.0412 (5)
H13	0.4417	0.9458	0.3590	0.049*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cl1	0.0648 (4)	0.0561 (5)	0.0783 (5)	−0.0240 (3)	0.0267 (4)	−0.0292 (4)
N1	0.0432 (10)	0.0303 (10)	0.0503 (10)	−0.0045 (8)	0.0274 (9)	−0.0059 (9)
N2	0.0670 (13)	0.0480 (13)	0.0795 (15)	−0.0198 (11)	0.0551 (12)	−0.0247 (12)
N3	0.0479 (11)	0.0401 (11)	0.0490 (11)	−0.0089 (9)	0.0245 (9)	−0.0100 (10)
N6	0.0527 (11)	0.0418 (12)	0.0747 (14)	−0.0065 (10)	0.0448 (11)	−0.0087 (11)
C2	0.0460 (12)	0.0383 (13)	0.0442 (12)	−0.0032 (11)	0.0258 (10)	−0.0027 (11)
C4	0.0403 (12)	0.0346 (13)	0.0421 (11)	−0.0045 (10)	0.0099 (10)	−0.0031 (11)
C5	0.0337 (11)	0.0385 (13)	0.0477 (12)	−0.0050 (10)	0.0176 (10)	0.0007 (11)
C6	0.0354 (11)	0.0341 (12)	0.0433 (11)	0.0029 (9)	0.0187 (10)	0.0030 (10)
Cl2	0.0751 (5)	0.0685 (5)	0.0735 (5)	0.0006 (4)	0.0245 (4)	−0.0334 (4)
O1	0.0566 (10)	0.0395 (10)	0.0798 (12)	−0.0057 (8)	0.0439 (9)	−0.0171 (9)
O2	0.0519 (10)	0.0380 (9)	0.0762 (11)	−0.0081 (8)	0.0425 (9)	−0.0081 (9)
O3	0.0555 (11)	0.0592 (13)	0.0892 (13)	−0.0074 (9)	0.0487 (10)	−0.0126 (11)
C7	0.0401 (12)	0.0314 (12)	0.0494 (12)	0.0037 (10)	0.0216 (10)	0.0012 (10)
C8	0.0315 (10)	0.0326 (12)	0.0427 (11)	0.0022 (9)	0.0136 (9)	0.0001 (10)
C9	0.0351 (11)	0.0427 (14)	0.0539 (13)	0.0011 (10)	0.0192 (10)	0.0002 (12)
C10	0.0436 (13)	0.0566 (17)	0.0695 (16)	−0.0126 (13)	0.0242 (13)	−0.0008 (15)
C11	0.0517 (15)	0.0456 (15)	0.0638 (16)	−0.0121 (13)	0.0112 (13)	−0.0105 (14)
C12	0.0451 (13)	0.0436 (14)	0.0485 (13)	0.0009 (11)	0.0102 (11)	−0.0088 (12)
C13	0.0356 (11)	0.0399 (13)	0.0466 (12)	0.0005 (10)	0.0156 (10)	−0.0032 (11)

Geometric parameters (Å, º) top

Cl1—C4	1.731 (2)	Cl2—C12	1.747 (3)
N1—C2	1.353 (3)	O1—C7	1.279 (3)
N1—C6	1.362 (3)	O2—C7	1.251 (3)
N1—H1	0.8600	O3—C9	1.352 (3)
N2—C2	1.328 (3)	O3—H3	0.8200
N2—H2B	0.8600	C7—C8	1.488 (3)
N2—H2A	0.8600	C8—C13	1.392 (3)
N3—C2	1.329 (3)	C8—C9	1.400 (3)
N3—C4	1.342 (3)	C9—C10	1.399 (4)
N6—C6	1.307 (3)	C10—C11	1.370 (4)
N6—H6A	0.8600	C10—H10	0.9300
N6—H6B	0.8600	C11—C12	1.382 (4)
C4—C5	1.357 (3)	C11—H11	0.9300
C5—C6	1.402 (3)	C12—C13	1.368 (3)
C5—H5	0.9300	C13—H13	0.9300

C2—N1—C6	121.80 (19)	C9—O3—H3	109.5
C2—N1—H1	119.1	O2—C7—O1	122.8 (2)
C6—N1—H1	119.1	O2—C7—C8	119.9 (2)
C2—N2—H2B	120.0	O1—C7—C8	117.29 (19)
C2—N2—H2A	120.0	C13—C8—C9	118.4 (2)
H2B—N2—H2A	120.0	C13—C8—C7	119.85 (19)
C2—N3—C4	115.1 (2)	C9—C8—C7	121.7 (2)
C6—N6—H6A	120.0	O3—C9—C10	118.0 (2)
C6—N6—H6B	120.0	O3—C9—C8	122.3 (2)
H6A—N6—H6B	120.0	C10—C9—C8	119.7 (2)
N2—C2—N3	119.6 (2)	C11—C10—C9	120.6 (2)
N2—C2—N1	117.5 (2)	C11—C10—H10	119.7
N3—C2—N1	122.8 (2)	C9—C10—H10	119.7
N3—C4—C5	126.4 (2)	C10—C11—C12	119.5 (2)
N3—C4—Cl1	114.28 (18)	C10—C11—H11	120.2
C5—C4—Cl1	119.28 (18)	C12—C11—H11	120.2
C4—C5—C6	116.8 (2)	C13—C12—C11	120.7 (2)
C4—C5—H5	121.6	C13—C12—Cl2	119.5 (2)
C6—C5—H5	121.6	C11—C12—Cl2	119.8 (2)
N6—C6—N1	117.7 (2)	C12—C13—C8	121.0 (2)
N6—C6—C5	125.3 (2)	C12—C13—H13	119.5
N1—C6—C5	117.0 (2)	C8—C13—H13	119.5

C4—N3—C2—N2	−178.7 (2)	O1—C7—C8—C9	2.6 (3)
C4—N3—C2—N1	1.2 (3)	C13—C8—C9—O3	179.9 (2)
C6—N1—C2—N2	−180.0 (2)	C7—C8—C9—O3	0.7 (3)
C6—N1—C2—N3	0.2 (3)	C13—C8—C9—C10	−1.2 (3)
C2—N3—C4—C5	−1.7 (3)	C7—C8—C9—C10	179.5 (2)
C2—N3—C4—Cl1	178.08 (16)	O3—C9—C10—C11	179.5 (2)
N3—C4—C5—C6	0.9 (3)	C8—C9—C10—C11	0.7 (4)
Cl1—C4—C5—C6	−178.93 (16)	C9—C10—C11—C12	0.1 (4)
C2—N1—C6—N6	179.0 (2)	C10—C11—C12—C13	−0.2 (4)
C2—N1—C6—C5	−1.1 (3)	C10—C11—C12—Cl2	179.8 (2)
C4—C5—C6—N6	−179.5 (2)	C11—C12—C13—C8	−0.3 (4)
C4—C5—C6—N1	0.6 (3)	Cl2—C12—C13—C8	179.61 (17)
O2—C7—C8—C13	4.7 (3)	C9—C8—C13—C12	1.1 (3)
O1—C7—C8—C13	−176.68 (19)	C7—C8—C13—C12	−179.7 (2)
O2—C7—C8—C9	−176.1 (2)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O1	0.86	1.82	2.664 (3)	168
N2—H2A···O1	0.86	2.56	3.223 (3)	135
N2—H2B···N3ⁱ	0.86	2.13	2.970 (3)	165
O3—H3···O1	0.82	1.83	2.557 (3)	146
N6—H6A···O2	0.86	1.97	2.824 (3)	172
N6—H6B···O2ⁱⁱ	0.86	1.96	2.819 (3)	172
C10—H10···O3ⁱⁱⁱ	0.93	2.51	3.358 (4)	151

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

Bis(2,6-diamino-4-chloropyrimidin-1-ium) naphthalene-1,5-disulfonate (II) top

Crystal data top

2C₄H₆ClN₄⁺·C₁₀H₆O₆S₂²⁻	F(000) = 592
M_r = 577.42	D_x = 1.604 Mg m⁻³
Monoclinic, P2₁/n	Mo Kα radiation, λ = 0.71073 Å
a = 9.1696 (4) Å	Cell parameters from 3749 reflections
b = 13.0848 (7) Å	θ = 3.7–30.1°
c = 9.9663 (5) Å	µ = 0.50 mm⁻¹
β = 90.526 (5)°	T = 293 K
V = 1195.73 (10) Å³	Prism, colorless
Z = 2	0.40 × 0.40 × 0.06 mm

Data collection top

Agilent SuperNova Dual Source diffractometer with an Atlas detector	2735 independent reflections
Radiation source: SuperNova (Mo) X-ray Source	2274 reflections with I > 2σ(I)
Mirror monochromator	R_int = 0.028
Detector resolution: 10.4933 pixels mm^-1	θ_max = 27.5°, θ_min = 3.0°
ω scans	h = −8→11
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2013)	k = −16→15
T_min = 0.527, T_max = 1.000	l = −12→12
10382 measured reflections

Refinement top

Refinement on F²	0 restraints
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.038	H-atom parameters constrained
wR(F²) = 0.102	w = 1/[σ²(F_o²) + (0.0444P)² + 0.5881P] where P = (F_o² + 2F_c²)/3
S = 1.05	(Δ/σ)_max < 0.001
2735 reflections	Δρ_max = 0.49 e Å⁻³
163 parameters	Δρ_min = −0.59 e Å⁻³

Special details top

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
Cl1	0.10474 (6)	0.91005 (5)	0.13497 (8)	0.0693 (2)
N1	0.47951 (17)	0.72194 (12)	0.24106 (15)	0.0379 (4)
H1	0.5541	0.6839	0.2572	0.045*
N2	0.4259 (2)	0.61789 (16)	0.0635 (2)	0.0675 (7)
H2A	0.3734	0.6006	−0.0047	0.081*
H2B	0.5013	0.5823	0.0853	0.081*
N3	0.27559 (18)	0.75496 (14)	0.10314 (17)	0.0437 (4)
N6	0.54208 (19)	0.81915 (14)	0.42350 (17)	0.0444 (4)
H6A	0.6148	0.7789	0.4376	0.053*
H6B	0.5275	0.8701	0.4761	0.053*
C2	0.3908 (2)	0.69909 (16)	0.1347 (2)	0.0420 (5)
C4	0.2528 (2)	0.83590 (15)	0.1817 (2)	0.0393 (4)
C5	0.3328 (2)	0.86453 (15)	0.2911 (2)	0.0377 (4)
H5	0.3089	0.9215	0.3422	0.045*
C6	0.45350 (19)	0.80277 (14)	0.32183 (18)	0.0333 (4)
S1	0.80386 (5)	0.55638 (4)	0.21480 (4)	0.03723 (15)
O1	0.75993 (16)	0.65802 (11)	0.25770 (15)	0.0491 (4)
O2	0.68017 (17)	0.49952 (12)	0.15999 (15)	0.0517 (4)
O3	0.92854 (18)	0.55687 (13)	0.12748 (14)	0.0541 (4)
C7	0.7936 (2)	0.40041 (15)	0.39206 (19)	0.0379 (4)
H7	0.7184	0.3761	0.3375	0.045*
C8	0.86088 (18)	0.49007 (14)	0.36151 (17)	0.0307 (4)
C9	0.97829 (18)	0.52894 (13)	0.44251 (17)	0.0293 (4)
C10	1.0523 (2)	0.62150 (15)	0.41375 (19)	0.0385 (4)
H10	1.0250	0.6595	0.3388	0.046*
C11	1.1626 (2)	0.65540 (16)	0.4944 (2)	0.0427 (5)
H11	1.2097	0.7163	0.4739	0.051*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cl1	0.0446 (3)	0.0740 (4)	0.0888 (5)	0.0223 (3)	−0.0221 (3)	−0.0052 (4)
N1	0.0362 (8)	0.0366 (8)	0.0405 (8)	0.0056 (7)	−0.0128 (7)	−0.0061 (7)
N2	0.0709 (13)	0.0633 (13)	0.0676 (13)	0.0230 (11)	−0.0364 (11)	−0.0346 (11)
N3	0.0371 (9)	0.0485 (10)	0.0454 (9)	0.0019 (7)	−0.0144 (7)	−0.0041 (8)
N6	0.0459 (10)	0.0451 (9)	0.0420 (9)	0.0073 (8)	−0.0150 (8)	−0.0107 (7)
C2	0.0415 (11)	0.0420 (11)	0.0424 (10)	0.0010 (8)	−0.0122 (9)	−0.0066 (8)
C4	0.0275 (9)	0.0429 (11)	0.0474 (11)	0.0012 (8)	−0.0047 (8)	0.0052 (9)
C5	0.0347 (9)	0.0367 (10)	0.0416 (10)	0.0032 (8)	−0.0022 (8)	−0.0028 (8)
C6	0.0327 (9)	0.0338 (9)	0.0333 (9)	−0.0023 (7)	−0.0023 (7)	0.0000 (7)
S1	0.0411 (3)	0.0401 (3)	0.0303 (2)	0.0063 (2)	−0.00909 (19)	0.00095 (18)
O1	0.0499 (8)	0.0425 (8)	0.0545 (9)	0.0128 (7)	−0.0185 (7)	−0.0033 (7)
O2	0.0563 (9)	0.0532 (9)	0.0451 (8)	0.0030 (7)	−0.0252 (7)	−0.0052 (7)
O3	0.0625 (10)	0.0643 (10)	0.0356 (8)	0.0090 (8)	0.0075 (7)	0.0121 (7)
C7	0.0326 (9)	0.0426 (11)	0.0382 (10)	−0.0054 (8)	−0.0048 (8)	−0.0017 (8)
C8	0.0295 (8)	0.0349 (9)	0.0276 (8)	0.0026 (7)	−0.0017 (7)	0.0004 (7)
C9	0.0279 (8)	0.0325 (9)	0.0276 (8)	0.0019 (7)	−0.0002 (6)	0.0012 (7)
C10	0.0415 (10)	0.0380 (10)	0.0361 (9)	−0.0029 (8)	−0.0033 (8)	0.0086 (8)
C11	0.0437 (11)	0.0387 (10)	0.0456 (11)	−0.0133 (8)	−0.0023 (9)	0.0073 (8)

Geometric parameters (Å, º) top

Cl1—C4	1.7290 (19)	S1—O3	1.4431 (16)
N1—C6	1.352 (2)	S1—O1	1.4550 (15)
N1—C2	1.363 (2)	S1—O2	1.4584 (15)
N1—H1	0.8600	S1—C8	1.7749 (17)
N2—C2	1.319 (3)	C7—C8	1.361 (3)
N2—H2A	0.8600	C7—C11ⁱ	1.403 (3)
N2—H2B	0.8600	C7—H7	0.9300
N3—C2	1.321 (3)	C8—C9	1.433 (2)
N3—C4	1.335 (3)	C9—C10	1.419 (3)
N6—C6	1.311 (2)	C9—C9ⁱ	1.427 (3)
N6—H6A	0.8600	C10—C11	1.361 (3)
N6—H6B	0.8600	C10—H10	0.9300
C4—C5	1.361 (3)	C11—C7ⁱ	1.403 (3)
C5—C6	1.402 (3)	C11—H11	0.9300
C5—H5	0.9300

C6—N1—C2	121.84 (16)	O3—S1—O1	113.34 (10)
C6—N1—H1	119.1	O3—S1—O2	113.21 (10)
C2—N1—H1	119.1	O1—S1—O2	111.10 (9)
C2—N2—H2A	120.0	O3—S1—C8	105.66 (8)
C2—N2—H2B	120.0	O1—S1—C8	106.56 (8)
H2A—N2—H2B	120.0	O2—S1—C8	106.34 (9)
C2—N3—C4	115.40 (16)	C8—C7—C11ⁱ	120.15 (17)
C6—N6—H6A	120.0	C8—C7—H7	119.9
C6—N6—H6B	120.0	C11ⁱ—C7—H7	119.9
H6A—N6—H6B	120.0	C7—C8—C9	121.31 (16)
N2—C2—N3	121.08 (18)	C7—C8—S1	118.35 (13)
N2—C2—N1	116.65 (18)	C9—C8—S1	120.31 (13)
N3—C2—N1	122.27 (18)	C10—C9—C9ⁱ	119.00 (19)
N3—C4—C5	127.02 (18)	C10—C9—C8	123.19 (15)
N3—C4—Cl1	114.47 (14)	C9ⁱ—C9—C8	117.8 (2)
C5—C4—Cl1	118.51 (16)	C11—C10—C9	120.90 (17)
C4—C5—C6	115.80 (18)	C11—C10—H10	119.6
C4—C5—H5	122.1	C9—C10—H10	119.6
C6—C5—H5	122.1	C10—C11—C7ⁱ	120.83 (18)
N6—C6—N1	118.48 (17)	C10—C11—H11	119.6
N6—C6—C5	123.87 (18)	C7ⁱ—C11—H11	119.6
N1—C6—C5	117.64 (16)

C4—N3—C2—N2	−179.1 (2)	O3—S1—C8—C7	−116.17 (16)
C4—N3—C2—N1	0.7 (3)	O1—S1—C8—C7	122.99 (16)
C6—N1—C2—N2	−179.4 (2)	O2—S1—C8—C7	4.41 (18)
C6—N1—C2—N3	0.8 (3)	O3—S1—C8—C9	61.75 (17)
C2—N3—C4—C5	−1.8 (3)	O1—S1—C8—C9	−59.08 (16)
C2—N3—C4—Cl1	178.00 (16)	O2—S1—C8—C9	−177.67 (14)
N3—C4—C5—C6	1.3 (3)	C7—C8—C9—C10	179.44 (18)
Cl1—C4—C5—C6	−178.48 (14)	S1—C8—C9—C10	1.6 (2)
C2—N1—C6—N6	178.92 (19)	C7—C8—C9—C9ⁱ	−0.6 (3)
C2—N1—C6—C5	−1.3 (3)	S1—C8—C9—C9ⁱ	−178.50 (17)
C4—C5—C6—N6	−179.95 (19)	C9ⁱ—C9—C10—C11	−0.3 (3)
C4—C5—C6—N1	0.3 (3)	C8—C9—C10—C11	179.62 (19)
C11ⁱ—C7—C8—C9	0.8 (3)	C9—C10—C11—C7ⁱ	0.1 (3)
C11ⁱ—C7—C8—S1	178.73 (16)

Symmetry code: (i) −x+2, −y+1, −z+1.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O1	0.86	1.92	2.708 (2)	152
N2—H2A···O2ⁱⁱ	0.86	2.08	2.868 (3)	152
N2—H2B···O2	0.86	2.10	2.953 (2)	174
N6—H6A···N3ⁱⁱⁱ	0.86	2.25	2.943 (2)	138
N6—H6B···O3^iv	0.86	2.01	2.808 (2)	154

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

Acknowledgements

The EN–FIST Centre of Excellence, Ljubljana, Slovenia, is thanked for the use of the SuperNova diffractometer.

Funding information

RSD thanks the UGC–BSR India for the award of an RFSMS. PTM thanks UGC, New Delhi, for a UGC Emeritus fellowship. FP thanks the Slovenian Research Agency for financial support (PI-0230–0175).

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Volume 74| Part 2| February 2018| Pages 237-241

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

Supra­molecular inter­actions in 2,6-di­amino-4-chloro­pyrimidin-1-ium 5-chloro­salicylate and bis­­(2,6-di­amino-4-chloro­pyrimidin-1-ium) naphthalene-1,5-di­sulfonate

1. Chemical context

2. Structural commentary

3. Supra­molecular features

4. Database survey

5. Synthesis and crystallization

6. Refinement

Supporting information

Acknowledgements

Funding information

References

research communications

Supramolecular interactions in 2,6-diamino-4-chloropyrimidin-1-ium 5-chlorosalicylate and bis(2,6-diamino-4-chloropyrimidin-1-ium) naphthalene-1,5-disulfonate

3. Supramolecular features