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ISSN: 2056-9890

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

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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 ππ inter­action in (I) and a ππ inter­action in (II) further stabilize these crystal structures.

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[Rajam, A., Muthiah, P. T., Butcher, R. J., Jasinski, J. P. & Glidewell, C. (2017). Acta Cryst. C73, 862-868.]). 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[Hunt, W. E., Schwalbe, C. H., Bird, K. & Mallinson, P. D. (1980). Biochem. J. 187, 533-536.]; Baker & Santi, 1965[Baker, B. R. & Santi, D. V. (1965). J. Pharm. Sci. 54, 1252-1257.]). The mol­ecules are often self-assembled by hydrogen bonding, halogen bonding, cation⋯π, anion⋯π and ππ stacking inter­actions. Among these inter­actions, halogen bonding is of particular current inter­est (Cavallo et al., 2016[Cavallo, G., Metrangolo, P., Milani, R., Pilati, T., Priimagi, A., Resnati, G. & Terraneo, G. (2016). Chem. Rev. 116, 2478-2601.]). 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[Mohana, M., Thomas Muthiah, P. & Butcher, R. J. (2017). Acta Cryst. C73, 536-540.]). 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.

[Scheme 1]

2. Structural commentary

The salt of compound (I)[link] crystallizes with one CDAPY (2,6-di­amino-4-chloro­pyrimidinium) cation and one CSA (5-chloro­salicylate) anion in the asymmetric unit (Fig. 1[link]). The pyrimidinium cation is protonated at the N1 position (see Fig. 1[link] 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)[link] 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[link]), 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[Liu, M.-L. (2012). Acta Cryst. E68, o342.]; Xu, 2012[Xu, Q. (2012). Acta Cryst. E68, o1733.]; Liu & Chen, 2012[Liu, M.-L. & Chen, Z.-Q. (2012). Acta Cryst. E68, o1745.]). The pyrimidinium cation is again protonated at the N1 position (see Fig. 2[link] 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]
Figure 1
ORTEP view of compound (I)[link] with the atom-numbering scheme. Displacement ellipsoids are drawn at 50% probability level. Dashed lines represent hydrogen bonds.
[Figure 2]
Figure 2
ORTEP view of compound (II)[link], with the atom-numbering scheme. Displacement ellipsoids are drawn at 50% probability level. Dashed lines represent hydrogen bonds.

3. Supra­molecular features

In salt (I)[link], the protonated N1 atom and the amino hydrogen (N6) atom of CDAPY are hydrogen bonded via two N—H⋯O bonds (Table 1[link]) 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[Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N. L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555-1573.]; Prabakaran et al., 2001[Prabakaran, P., Murugesan, S., Mu­thiah, P. T., Bocelli, G. & Righi, L. (2001). Acta Cryst. E57, o933-o936.]; Panneerselvam et al., 2002[Panneerselvam, P., Stanley, N. & Mu­thiah, P. T. (2002). Acta Cryst. E58, o180-o182.]) (Fig. 1[link]). 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[Mohana, M., Thomas Muthiah, P. & Butcher, R. J. (2017). Acta Cryst. C73, 536-540.]). However, in compound (I)[link] 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[Edison, B., Balasubramani, K., Thanigaimani, K., Khalib, N. C., Arshad, S. & Razak, I. A. (2014). Acta Cryst. E70, o857-o858.]), 2,6-di­amino-4-chloro­pyrimidine-benzoic acid (Thanigaimani et al., 2012a[Thanigaimani, K., Khalib, N. C., Arshad, S. & Razak, I. A. (2012a). Acta Cryst. E68, o3442-o3443.]) and bis­(2,6-di­amino-4-chloro­pyrimidin-1-ium) fumarate (Thanigaimani et al., 2012b[Thanigaimani, K., Khalib, N. C., Farhadikoutenaei, A., Arshad, S. & Razak, I. A. (2012b). Acta Cryst. E68, o3321-o3322.]). The 2,6-di­amino-4-chloro­pyrimidinium 5-chloro­salicylate units are linked via a Cl⋯Cl inter­action (a type I inter­action; Cavallo et al., 2016[Cavallo, G., Metrangolo, P., Milani, R., Pilati, T., Priimagi, A., Resnati, G. & Terraneo, G. (2016). Chem. Rev. 116, 2478-2601.]) with a distance and angle of 3.3505 (12) Å and 151.37 (10)°, respectively (Durka et al., 2015[Durka, K., Kliś, T. & Serwatowski, J. (2015). Acta Cryst. E71, 1471-1474.]) (Fig. 3[link]). 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[Muthukumaran, J., Parthiban, A., Kannan, M., Rao, H. S. P. & Krishna, R. (2011). Acta Cryst. E67, o898-o899.]) further stabilize this crystal structure (Fig. 4[link]).

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

D—H⋯A D—H H⋯A DA 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]
Figure 3
Supra­molecular layered structure extended as a chain via Cl⋯Cl inter­actions in (I)[link].
[Figure 4]
Figure 4
A weak C—Cl⋯π inter­action and ππ stacking inter­actions.

In salt (II)[link], 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[Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N. L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555-1573.]; Balasubramani et al., 2007[Balasubramani, K., Thomas Muthiah, P. & Lynch, D. E. (2007). Chem. Cent. J. 1, 28.]). All units of the CDAPY and NSA ions are hydrogen bonded (Table 2[link]) to generate a quadruple DDAA array with fused ring motifs R22(8), R42(8) and R22(8) (Fig. 5[link]). This type of array has also been reported earlier (Robert et al., 2001[Robert, J. J., Raj, S. B. & Muthiah, P. T. (2001). Acta Cryst. E57, o1206-o1208.]; Umadevi et al., 2002[Umadevi, B., Prabakaran, P. & Muthiah, P. T. (2002). Acta Cryst. C58, o510-o512.]; Raj et al., 2003[Raj, S. B., Muthiah, P. T., Rychlewska, U. & Warzajtis, B. (2003). CrystEngComm, 5, 48-53.]; Subashini et al., 2007[Subashini, A., Muthiah, P. T., Bocelli, G. & Cantoni, A. (2007). Acta Cryst. E63, o3775.]; Thanigaimani et al., 2007[Thanigaimani, K., Muthiah, P. T. & Lynch, D. E. (2007). Acta Cryst. E63, o4555-o4556.]; Liu & Chen, 2012[Liu, M.-L. & Chen, Z.-Q. (2012). Acta Cryst. E68, o1745.]). In addition, the NSA anions also generate R32(10) and R33(21) ring motifs via N—H⋯O bonds. Weak ππ 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[link]).

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

D—H⋯A D—H H⋯A DA 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]
Figure 5
Formation of a quadruple DDAA array in (II)[link] via N—H⋯O hydrogen bonds.
[Figure 6]
Figure 6
A view of the ππ 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[Zhang, J., Jin, S., Tao, L., Liu, B. & Wang, D. (2014). J. Mol. Struct. 1072, 208-220.]), 4-amino-5-chloro-2,6-di­methyl­pyrimidinium 5-chloro-2-hy­droxy­benzoate (Rajam et al., 2017[Rajam, A., Muthiah, P. T., Butcher, R. J., Jasinski, J. P. & Glidewell, C. (2017). Acta Cryst. C73, 862-868.]) and 2-amino-4,6-di­methyl­pyrimidinium 5-chloro­salicylate (Ebenezer & Mu­thiah, 2012[Ebenezer, S. & Muthiah, P. T. (2012). Cryst. Growth Des. 12, 3766-3785.]). 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[Liu, M.-L. (2012). Acta Cryst. E68, o342.]), bis­(3-methyl­anilinium) naphthalene-1,5-di­sulfonate (Liu & Chen, 2012[Liu, M.-L. & Chen, Z.-Q. (2012). Acta Cryst. E68, o1745.]) and bis­(2-methyl­piperidinium) naphthalene-1,5-di­sulfonate (Xu, 2012[Xu, Q. (2012). Acta Cryst. E68, o1733.]).

5. Synthesis and crystallization

Compounds (I)[link] and (II)[link] were synthesized by mixing hot ethano­lic solutions (1:1) of 2,6-di­amino-4-chloro­pyrimidine (36 mg) with 5-chloro­salicylic acid (43 mg) (I)[link]/naphthalene-1,5-di­sulfonic acid (72 mg) (II)[link]. 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[link]. 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 Uiso(H) = kUeq(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−
Mr 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)
V3) 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[Agilent. (2013). CrysAlis PRO. Agilent Technologies UK Ltd, Yarnton, England.]) Multi-scan (CrysAlis PRO; Agilent, 2013[Agilent. (2013). CrysAlis PRO. Agilent Technologies UK Ltd, Yarnton, England.])
Tmin, Tmax 0.644, 1.000 0.527, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections 7906, 3144, 2137 10382, 2735, 2274
Rint 0.027 0.028
(sin θ/λ)max−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
Δρmax, Δρmin (e Å−3) 0.29, −0.40 0.49, −0.59
Computer programs: CrysAlis PRO (Agilent, 2013[Agilent. (2013). CrysAlis PRO. Agilent Technologies UK Ltd, Yarnton, England.]), SHELXT2014 (Sheldrick, 2015a[Sheldrick, G. M. (2015a). Acta Cryst. A71, 3-8.]), SHELXL2014 (Sheldrick, 2015b[Sheldrick, G. M. (2015b). Acta Cryst. C71, 3-8.]), PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]) and Mercury (Macrae et al., 2008[Macrae, C. F., Bruno, I. J., Chisholm, J. A., Edgington, P. R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., van de Streek, J. & Wood, P. A. (2008). J. Appl. Cryst. 41, 466-470.]).

Supporting information


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+·C7H4ClO3F(000) = 648
Mr = 317.13Dx = 1.534 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
a = 13.9203 (14) ÅCell parameters from 1734 reflections
b = 7.0285 (6) Åθ = 3.9–27.5°
c = 15.4294 (14) ŵ = 0.49 mm1
β = 114.544 (12)°T = 293 K
V = 1373.2 (3) Å3Needle, colorless
Z = 40.40 × 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 Source2137 reflections with I > 2σ(I)
Mirror monochromatorRint = 0.027
Detector resolution: 10.4933 pixels mm-1θmax = 27.5°, θmin = 2.9°
ω scansh = 1817
Absorption correction: multi-scan
(CrysAlis PRO); Agilent, 2013)
k = 79
Tmin = 0.644, Tmax = 1.000l = 2019
7906 measured reflections
Refinement top
Refinement on F20 restraints
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.048H-atom parameters constrained
wR(F2) = 0.128 w = 1/[σ2(Fo2) + (0.0482P)2 + 0.5033P]
where P = (Fo2 + 2Fc2)/3
S = 1.04(Δ/σ)max < 0.001
3144 reflectionsΔρmax = 0.29 e Å3
182 parametersΔρmin = 0.40 e Å3
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
xyzUiso*/Ueq
Cl10.25461 (6)0.27636 (11)0.00641 (5)0.0674 (2)
N10.38557 (14)0.2707 (3)0.12207 (13)0.0386 (4)
H10.41280.37920.14500.046*
N20.50448 (17)0.2485 (3)0.05504 (16)0.0566 (6)
H2B0.53130.18950.02150.068*
H2A0.52930.35730.07960.068*
N30.38700 (15)0.0032 (3)0.03064 (13)0.0442 (5)
N60.27205 (16)0.3072 (3)0.19347 (15)0.0503 (5)
H6A0.30230.41410.21570.060*
H6B0.22070.26870.20630.060*
C20.42485 (18)0.1715 (3)0.06889 (16)0.0404 (5)
C40.30522 (17)0.0606 (3)0.04713 (16)0.0414 (5)
C50.26096 (16)0.0273 (3)0.09993 (15)0.0398 (5)
H50.20480.02660.10890.048*
C60.30401 (16)0.2033 (3)0.14025 (15)0.0368 (5)
Cl20.50995 (6)1.29096 (12)0.45221 (5)0.0745 (3)
O10.49261 (13)0.5917 (2)0.18881 (13)0.0534 (5)
O20.38734 (12)0.6467 (2)0.26174 (12)0.0501 (4)
O30.62982 (14)0.8382 (3)0.19368 (15)0.0617 (5)
H30.59810.73650.18050.093*
C70.46259 (17)0.6930 (3)0.24184 (16)0.0393 (5)
C80.51962 (15)0.8751 (3)0.27862 (15)0.0362 (5)
C90.60003 (17)0.9377 (4)0.25339 (17)0.0437 (6)
C100.65092 (19)1.1105 (4)0.28915 (19)0.0563 (7)
H100.70381.15270.27180.068*
C110.6235 (2)1.2181 (4)0.34943 (19)0.0580 (7)
H110.65761.33300.37290.070*
C120.54500 (19)1.1548 (4)0.37507 (17)0.0488 (6)
C130.49410 (17)0.9865 (3)0.34066 (16)0.0412 (5)
H130.44170.94580.35900.049*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl10.0648 (4)0.0561 (5)0.0783 (5)0.0240 (3)0.0267 (4)0.0292 (4)
N10.0432 (10)0.0303 (10)0.0503 (10)0.0045 (8)0.0274 (9)0.0059 (9)
N20.0670 (13)0.0480 (13)0.0795 (15)0.0198 (11)0.0551 (12)0.0247 (12)
N30.0479 (11)0.0401 (11)0.0490 (11)0.0089 (9)0.0245 (9)0.0100 (10)
N60.0527 (11)0.0418 (12)0.0747 (14)0.0065 (10)0.0448 (11)0.0087 (11)
C20.0460 (12)0.0383 (13)0.0442 (12)0.0032 (11)0.0258 (10)0.0027 (11)
C40.0403 (12)0.0346 (13)0.0421 (11)0.0045 (10)0.0099 (10)0.0031 (11)
C50.0337 (11)0.0385 (13)0.0477 (12)0.0050 (10)0.0176 (10)0.0007 (11)
C60.0354 (11)0.0341 (12)0.0433 (11)0.0029 (9)0.0187 (10)0.0030 (10)
Cl20.0751 (5)0.0685 (5)0.0735 (5)0.0006 (4)0.0245 (4)0.0334 (4)
O10.0566 (10)0.0395 (10)0.0798 (12)0.0057 (8)0.0439 (9)0.0171 (9)
O20.0519 (10)0.0380 (9)0.0762 (11)0.0081 (8)0.0425 (9)0.0081 (9)
O30.0555 (11)0.0592 (13)0.0892 (13)0.0074 (9)0.0487 (10)0.0126 (11)
C70.0401 (12)0.0314 (12)0.0494 (12)0.0037 (10)0.0216 (10)0.0012 (10)
C80.0315 (10)0.0326 (12)0.0427 (11)0.0022 (9)0.0136 (9)0.0001 (10)
C90.0351 (11)0.0427 (14)0.0539 (13)0.0011 (10)0.0192 (10)0.0002 (12)
C100.0436 (13)0.0566 (17)0.0695 (16)0.0126 (13)0.0242 (13)0.0008 (15)
C110.0517 (15)0.0456 (15)0.0638 (16)0.0121 (13)0.0112 (13)0.0105 (14)
C120.0451 (13)0.0436 (14)0.0485 (13)0.0009 (11)0.0102 (11)0.0088 (12)
C130.0356 (11)0.0399 (13)0.0466 (12)0.0005 (10)0.0156 (10)0.0032 (11)
Geometric parameters (Å, º) top
Cl1—C41.731 (2)Cl2—C121.747 (3)
N1—C21.353 (3)O1—C71.279 (3)
N1—C61.362 (3)O2—C71.251 (3)
N1—H10.8600O3—C91.352 (3)
N2—C21.328 (3)O3—H30.8200
N2—H2B0.8600C7—C81.488 (3)
N2—H2A0.8600C8—C131.392 (3)
N3—C21.329 (3)C8—C91.400 (3)
N3—C41.342 (3)C9—C101.399 (4)
N6—C61.307 (3)C10—C111.370 (4)
N6—H6A0.8600C10—H100.9300
N6—H6B0.8600C11—C121.382 (4)
C4—C51.357 (3)C11—H110.9300
C5—C61.402 (3)C12—C131.368 (3)
C5—H50.9300C13—H130.9300
C2—N1—C6121.80 (19)C9—O3—H3109.5
C2—N1—H1119.1O2—C7—O1122.8 (2)
C6—N1—H1119.1O2—C7—C8119.9 (2)
C2—N2—H2B120.0O1—C7—C8117.29 (19)
C2—N2—H2A120.0C13—C8—C9118.4 (2)
H2B—N2—H2A120.0C13—C8—C7119.85 (19)
C2—N3—C4115.1 (2)C9—C8—C7121.7 (2)
C6—N6—H6A120.0O3—C9—C10118.0 (2)
C6—N6—H6B120.0O3—C9—C8122.3 (2)
H6A—N6—H6B120.0C10—C9—C8119.7 (2)
N2—C2—N3119.6 (2)C11—C10—C9120.6 (2)
N2—C2—N1117.5 (2)C11—C10—H10119.7
N3—C2—N1122.8 (2)C9—C10—H10119.7
N3—C4—C5126.4 (2)C10—C11—C12119.5 (2)
N3—C4—Cl1114.28 (18)C10—C11—H11120.2
C5—C4—Cl1119.28 (18)C12—C11—H11120.2
C4—C5—C6116.8 (2)C13—C12—C11120.7 (2)
C4—C5—H5121.6C13—C12—Cl2119.5 (2)
C6—C5—H5121.6C11—C12—Cl2119.8 (2)
N6—C6—N1117.7 (2)C12—C13—C8121.0 (2)
N6—C6—C5125.3 (2)C12—C13—H13119.5
N1—C6—C5117.0 (2)C8—C13—H13119.5
C4—N3—C2—N2178.7 (2)O1—C7—C8—C92.6 (3)
C4—N3—C2—N11.2 (3)C13—C8—C9—O3179.9 (2)
C6—N1—C2—N2180.0 (2)C7—C8—C9—O30.7 (3)
C6—N1—C2—N30.2 (3)C13—C8—C9—C101.2 (3)
C2—N3—C4—C51.7 (3)C7—C8—C9—C10179.5 (2)
C2—N3—C4—Cl1178.08 (16)O3—C9—C10—C11179.5 (2)
N3—C4—C5—C60.9 (3)C8—C9—C10—C110.7 (4)
Cl1—C4—C5—C6178.93 (16)C9—C10—C11—C120.1 (4)
C2—N1—C6—N6179.0 (2)C10—C11—C12—C130.2 (4)
C2—N1—C6—C51.1 (3)C10—C11—C12—Cl2179.8 (2)
C4—C5—C6—N6179.5 (2)C11—C12—C13—C80.3 (4)
C4—C5—C6—N10.6 (3)Cl2—C12—C13—C8179.61 (17)
O2—C7—C8—C134.7 (3)C9—C8—C13—C121.1 (3)
O1—C7—C8—C13176.68 (19)C7—C8—C13—C12179.7 (2)
O2—C7—C8—C9176.1 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O10.861.822.664 (3)168
N2—H2A···O10.862.563.223 (3)135
N2—H2B···N3i0.862.132.970 (3)165
O3—H3···O10.821.832.557 (3)146
N6—H6A···O20.861.972.824 (3)172
N6—H6B···O2ii0.861.962.819 (3)172
C10—H10···O3iii0.932.513.358 (4)151
Symmetry codes: (i) x+1, y, z; (ii) x+1/2, y1/2, 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+·C10H6O6S22F(000) = 592
Mr = 577.42Dx = 1.604 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
a = 9.1696 (4) ÅCell parameters from 3749 reflections
b = 13.0848 (7) Åθ = 3.7–30.1°
c = 9.9663 (5) ŵ = 0.50 mm1
β = 90.526 (5)°T = 293 K
V = 1195.73 (10) Å3Prism, colorless
Z = 20.40 × 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 Source2274 reflections with I > 2σ(I)
Mirror monochromatorRint = 0.028
Detector resolution: 10.4933 pixels mm-1θmax = 27.5°, θmin = 3.0°
ω scansh = 811
Absorption correction: multi-scan
(CrysAlis PRO; Agilent, 2013)
k = 1615
Tmin = 0.527, Tmax = 1.000l = 1212
10382 measured reflections
Refinement top
Refinement on F20 restraints
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.038H-atom parameters constrained
wR(F2) = 0.102 w = 1/[σ2(Fo2) + (0.0444P)2 + 0.5881P]
where P = (Fo2 + 2Fc2)/3
S = 1.05(Δ/σ)max < 0.001
2735 reflectionsΔρmax = 0.49 e Å3
163 parametersΔρmin = 0.59 e Å3
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
xyzUiso*/Ueq
Cl10.10474 (6)0.91005 (5)0.13497 (8)0.0693 (2)
N10.47951 (17)0.72194 (12)0.24106 (15)0.0379 (4)
H10.55410.68390.25720.045*
N20.4259 (2)0.61789 (16)0.0635 (2)0.0675 (7)
H2A0.37340.60060.00470.081*
H2B0.50130.58230.08530.081*
N30.27559 (18)0.75496 (14)0.10314 (17)0.0437 (4)
N60.54208 (19)0.81915 (14)0.42350 (17)0.0444 (4)
H6A0.61480.77890.43760.053*
H6B0.52750.87010.47610.053*
C20.3908 (2)0.69909 (16)0.1347 (2)0.0420 (5)
C40.2528 (2)0.83590 (15)0.1817 (2)0.0393 (4)
C50.3328 (2)0.86453 (15)0.2911 (2)0.0377 (4)
H50.30890.92150.34220.045*
C60.45350 (19)0.80277 (14)0.32183 (18)0.0333 (4)
S10.80386 (5)0.55638 (4)0.21480 (4)0.03723 (15)
O10.75993 (16)0.65802 (11)0.25770 (15)0.0491 (4)
O20.68017 (17)0.49952 (12)0.15999 (15)0.0517 (4)
O30.92854 (18)0.55687 (13)0.12748 (14)0.0541 (4)
C70.7936 (2)0.40041 (15)0.39206 (19)0.0379 (4)
H70.71840.37610.33750.045*
C80.86088 (18)0.49007 (14)0.36151 (17)0.0307 (4)
C90.97829 (18)0.52894 (13)0.44251 (17)0.0293 (4)
C101.0523 (2)0.62150 (15)0.41375 (19)0.0385 (4)
H101.02500.65950.33880.046*
C111.1626 (2)0.65540 (16)0.4944 (2)0.0427 (5)
H111.20970.71630.47390.051*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl10.0446 (3)0.0740 (4)0.0888 (5)0.0223 (3)0.0221 (3)0.0052 (4)
N10.0362 (8)0.0366 (8)0.0405 (8)0.0056 (7)0.0128 (7)0.0061 (7)
N20.0709 (13)0.0633 (13)0.0676 (13)0.0230 (11)0.0364 (11)0.0346 (11)
N30.0371 (9)0.0485 (10)0.0454 (9)0.0019 (7)0.0144 (7)0.0041 (8)
N60.0459 (10)0.0451 (9)0.0420 (9)0.0073 (8)0.0150 (8)0.0107 (7)
C20.0415 (11)0.0420 (11)0.0424 (10)0.0010 (8)0.0122 (9)0.0066 (8)
C40.0275 (9)0.0429 (11)0.0474 (11)0.0012 (8)0.0047 (8)0.0052 (9)
C50.0347 (9)0.0367 (10)0.0416 (10)0.0032 (8)0.0022 (8)0.0028 (8)
C60.0327 (9)0.0338 (9)0.0333 (9)0.0023 (7)0.0023 (7)0.0000 (7)
S10.0411 (3)0.0401 (3)0.0303 (2)0.0063 (2)0.00909 (19)0.00095 (18)
O10.0499 (8)0.0425 (8)0.0545 (9)0.0128 (7)0.0185 (7)0.0033 (7)
O20.0563 (9)0.0532 (9)0.0451 (8)0.0030 (7)0.0252 (7)0.0052 (7)
O30.0625 (10)0.0643 (10)0.0356 (8)0.0090 (8)0.0075 (7)0.0121 (7)
C70.0326 (9)0.0426 (11)0.0382 (10)0.0054 (8)0.0048 (8)0.0017 (8)
C80.0295 (8)0.0349 (9)0.0276 (8)0.0026 (7)0.0017 (7)0.0004 (7)
C90.0279 (8)0.0325 (9)0.0276 (8)0.0019 (7)0.0002 (6)0.0012 (7)
C100.0415 (10)0.0380 (10)0.0361 (9)0.0029 (8)0.0033 (8)0.0086 (8)
C110.0437 (11)0.0387 (10)0.0456 (11)0.0133 (8)0.0023 (9)0.0073 (8)
Geometric parameters (Å, º) top
Cl1—C41.7290 (19)S1—O31.4431 (16)
N1—C61.352 (2)S1—O11.4550 (15)
N1—C21.363 (2)S1—O21.4584 (15)
N1—H10.8600S1—C81.7749 (17)
N2—C21.319 (3)C7—C81.361 (3)
N2—H2A0.8600C7—C11i1.403 (3)
N2—H2B0.8600C7—H70.9300
N3—C21.321 (3)C8—C91.433 (2)
N3—C41.335 (3)C9—C101.419 (3)
N6—C61.311 (2)C9—C9i1.427 (3)
N6—H6A0.8600C10—C111.361 (3)
N6—H6B0.8600C10—H100.9300
C4—C51.361 (3)C11—C7i1.403 (3)
C5—C61.402 (3)C11—H110.9300
C5—H50.9300
C6—N1—C2121.84 (16)O3—S1—O1113.34 (10)
C6—N1—H1119.1O3—S1—O2113.21 (10)
C2—N1—H1119.1O1—S1—O2111.10 (9)
C2—N2—H2A120.0O3—S1—C8105.66 (8)
C2—N2—H2B120.0O1—S1—C8106.56 (8)
H2A—N2—H2B120.0O2—S1—C8106.34 (9)
C2—N3—C4115.40 (16)C8—C7—C11i120.15 (17)
C6—N6—H6A120.0C8—C7—H7119.9
C6—N6—H6B120.0C11i—C7—H7119.9
H6A—N6—H6B120.0C7—C8—C9121.31 (16)
N2—C2—N3121.08 (18)C7—C8—S1118.35 (13)
N2—C2—N1116.65 (18)C9—C8—S1120.31 (13)
N3—C2—N1122.27 (18)C10—C9—C9i119.00 (19)
N3—C4—C5127.02 (18)C10—C9—C8123.19 (15)
N3—C4—Cl1114.47 (14)C9i—C9—C8117.8 (2)
C5—C4—Cl1118.51 (16)C11—C10—C9120.90 (17)
C4—C5—C6115.80 (18)C11—C10—H10119.6
C4—C5—H5122.1C9—C10—H10119.6
C6—C5—H5122.1C10—C11—C7i120.83 (18)
N6—C6—N1118.48 (17)C10—C11—H11119.6
N6—C6—C5123.87 (18)C7i—C11—H11119.6
N1—C6—C5117.64 (16)
C4—N3—C2—N2179.1 (2)O3—S1—C8—C7116.17 (16)
C4—N3—C2—N10.7 (3)O1—S1—C8—C7122.99 (16)
C6—N1—C2—N2179.4 (2)O2—S1—C8—C74.41 (18)
C6—N1—C2—N30.8 (3)O3—S1—C8—C961.75 (17)
C2—N3—C4—C51.8 (3)O1—S1—C8—C959.08 (16)
C2—N3—C4—Cl1178.00 (16)O2—S1—C8—C9177.67 (14)
N3—C4—C5—C61.3 (3)C7—C8—C9—C10179.44 (18)
Cl1—C4—C5—C6178.48 (14)S1—C8—C9—C101.6 (2)
C2—N1—C6—N6178.92 (19)C7—C8—C9—C9i0.6 (3)
C2—N1—C6—C51.3 (3)S1—C8—C9—C9i178.50 (17)
C4—C5—C6—N6179.95 (19)C9i—C9—C10—C110.3 (3)
C4—C5—C6—N10.3 (3)C8—C9—C10—C11179.62 (19)
C11i—C7—C8—C90.8 (3)C9—C10—C11—C7i0.1 (3)
C11i—C7—C8—S1178.73 (16)
Symmetry code: (i) x+2, y+1, z+1.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O10.861.922.708 (2)152
N2—H2A···O2ii0.862.082.868 (3)152
N2—H2B···O20.862.102.953 (2)174
N6—H6A···N3iii0.862.252.943 (2)138
N6—H6B···O3iv0.862.012.808 (2)154
Symmetry codes: (ii) x+1, y+1, z; (iii) x+1/2, y+3/2, z+1/2; (iv) x1/2, 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).

References

First citationAgilent. (2013). CrysAlis PRO. Agilent Technologies UK Ltd, Yarnton, England.  Google Scholar
First citationBaker, B. R. & Santi, D. V. (1965). J. Pharm. Sci. 54, 1252–1257.  CrossRef CAS PubMed Web of Science Google Scholar
First citationBalasubramani, K., Thomas Muthiah, P. & Lynch, D. E. (2007). Chem. Cent. J. 1, 28.  CSD CrossRef PubMed Google Scholar
First citationBernstein, J., Davis, R. E., Shimoni, L. & Chang, N. L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555–1573.  CrossRef CAS Web of Science Google Scholar
First citationCavallo, G., Metrangolo, P., Milani, R., Pilati, T., Priimagi, A., Resnati, G. & Terraneo, G. (2016). Chem. Rev. 116, 2478–2601.  Web of Science CrossRef CAS PubMed Google Scholar
First citationDurka, K., Kliś, T. & Serwatowski, J. (2015). Acta Cryst. E71, 1471–1474.  CSD CrossRef IUCr Journals Google Scholar
First citationEbenezer, S. & Muthiah, P. T. (2012). Cryst. Growth Des. 12, 3766–3785.  Web of Science CSD CrossRef CAS Google Scholar
First citationEdison, B., Balasubramani, K., Thanigaimani, K., Khalib, N. C., Arshad, S. & Razak, I. A. (2014). Acta Cryst. E70, o857–o858.  CSD CrossRef IUCr Journals Google Scholar
First citationHunt, W. E., Schwalbe, C. H., Bird, K. & Mallinson, P. D. (1980). Biochem. J. 187, 533–536.  CSD CrossRef CAS PubMed Web of Science Google Scholar
First citationLiu, M.-L. (2012). Acta Cryst. E68, o342.  Web of Science CSD CrossRef IUCr Journals Google Scholar
First citationLiu, M.-L. & Chen, Z.-Q. (2012). Acta Cryst. E68, o1745.  CSD CrossRef IUCr Journals Google Scholar
First citationMacrae, C. F., Bruno, I. J., Chisholm, J. A., Edgington, P. R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., van de Streek, J. & Wood, P. A. (2008). J. Appl. Cryst. 41, 466–470.  Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
First citationMohana, M., Thomas Muthiah, P. & Butcher, R. J. (2017). Acta Cryst. C73, 536–540.  CSD CrossRef IUCr Journals Google Scholar
First citationMuthukumaran, J., Parthiban, A., Kannan, M., Rao, H. S. P. & Krishna, R. (2011). Acta Cryst. E67, o898–o899.  CSD CrossRef IUCr Journals Google Scholar
First citationPanneerselvam, P., Stanley, N. & Mu­thiah, P. T. (2002). Acta Cryst. E58, o180–o182.  Web of Science CSD CrossRef IUCr Journals Google Scholar
First citationPrabakaran, P., Murugesan, S., Mu­thiah, P. T., Bocelli, G. & Righi, L. (2001). Acta Cryst. E57, o933–o936.  Web of Science CSD CrossRef IUCr Journals Google Scholar
First citationRaj, S. B., Muthiah, P. T., Rychlewska, U. & Warzajtis, B. (2003). CrystEngComm, 5, 48–53.  CAS Google Scholar
First citationRajam, A., Muthiah, P. T., Butcher, R. J., Jasinski, J. P. & Glidewell, C. (2017). Acta Cryst. C73, 862–868.  Web of Science CSD CrossRef IUCr Journals Google Scholar
First citationRobert, J. J., Raj, S. B. & Muthiah, P. T. (2001). Acta Cryst. E57, o1206–o1208.  Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
First citationSheldrick, G. M. (2015a). Acta Cryst. A71, 3–8.  Web of Science CrossRef IUCr Journals Google Scholar
First citationSheldrick, G. M. (2015b). Acta Cryst. C71, 3–8.  Web of Science CrossRef IUCr Journals Google Scholar
First citationSpek, A. L. (2009). Acta Cryst. D65, 148–155.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationSubashini, A., Muthiah, P. T., Bocelli, G. & Cantoni, A. (2007). Acta Cryst. E63, o3775.  Web of Science CSD CrossRef IUCr Journals Google Scholar
First citationThanigaimani, K., Khalib, N. C., Arshad, S. & Razak, I. A. (2012a). Acta Cryst. E68, o3442–o3443.  CSD CrossRef IUCr Journals Google Scholar
First citationThanigaimani, K., Khalib, N. C., Farhadikoutenaei, A., Arshad, S. & Razak, I. A. (2012b). Acta Cryst. E68, o3321–o3322.  CSD CrossRef IUCr Journals Google Scholar
First citationThanigaimani, K., Muthiah, P. T. & Lynch, D. E. (2007). Acta Cryst. E63, o4555–o4556.  Web of Science CSD CrossRef IUCr Journals Google Scholar
First citationUmadevi, B., Prabakaran, P. & Muthiah, P. T. (2002). Acta Cryst. C58, o510–o512.  Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
First citationXu, Q. (2012). Acta Cryst. E68, o1733.  CSD CrossRef IUCr Journals Google Scholar
First citationZhang, J., Jin, S., Tao, L., Liu, B. & Wang, D. (2014). J. Mol. Struct. 1072, 208–220.  CSD CrossRef CAS Google Scholar

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