Two solid phases of pyrimidin-1-ium hydrogen chloranilate monohydrate determined at 225 and 120 K

The crystal structures of two solid phases of the title compound, C₄H₅N₂⁺·C₆HCl₂O₄⁻·H₂O, have been determined at 225 and 120 K. In the high-temperature phase, stable above 198 K, the transition temperature of which has been determined by ³⁵Cl nuclear quadrupole resonance and differential thermal analysis measurements, the three components are held together by O—H...O, N...H...O, C—H...O and C—H...Cl hydrogen bonds, forming a centrosymmetric 2+2+2 aggregate. In the N...H...O hydrogen bond formed between the pyrimidin-1-ium cation and the water mol­ecule, the H atom is disordered over two positions, resulting in two states, viz. pyrimidin-1-ium–water and pyrimidine–oxonium. In the low-temperature phase, the title compound crystallizes in the same monoclinic space group and has a similar mol­ecular packing, but the 2+2+2 aggregate loses the centrosymmetry, resulting in a doubling of the unit cell and two crystallographically independent mol­ecules for each component in the asymmetric unit. The H atom in one N...H...O hydrogen bond between the pyrimidin-1-ium cation and the water mol­ecule is disordered, while the H atom in the other hydrogen bond is found to be ordered at the N-atom site with a long N—H distance [1.10 (3) Å].

S1. Comment

The crystal structures of diazine (1,2-diazine, pyrimidine or 1,4-diazine)–chloranilic acid (2,5-dichloro-3,6-dihydroxy-1,4-benzoqinone) (2/1) systems have been determined at room temperature (Ishida & Kashino, 1999a,b) and recently re-determined at 110 K for the 1,2-diazine and 1,4-diazine compounds (Gotoh et al., 2008). In each compound, the diazine and chloranilic acid molecules are connected by strong N···H···O hydrogen bonds [N···O = 2.582 (3), 2.615 (2) and 2.590 (4) Å for the 1,2-diazine, pyrimidine and 1,4-diazine compounds, respectively, at room temperature] to afford a centrosymmetric 2:1 unit. Proton motions attributable to dynamically disordered H atoms in these hydrogen bonds have been detected by ¹H NMR and ³⁵Cl nuclear quadrupole resonance (NQR) measurements for the 1,2-diazine compound (Nihei et al., 2000a), the pyrimidine compound (Ikeda et al., 2005) and the 1,4-diazine compound (Nihei et al., 2000b). Recently, measurements of ¹⁴N NQR and multi-temperature X-ray diffraction were made for the 1,2-diazine compound and temperature dependence of the population ratio of two disordered sites of H atom in the N···H···O hydrogen bond, i.e. proton migration was determined (Seliger et al., 2009). On the other hand, in the crystal structures of 1,2-diazine–chloranilic acid (1/1) (Gotoh & Ishida, 2008) and 1,4-diazine–chloranilic acid (1/1) (Ishida & Kashino, 1999c), such short hydrogen bonds have not been observed. The hydrogen bonds between the base and the acid are fairly long [N···O = 2.6138 (13)–2.6621 (13) and 2.719 (3) Å, for the 1,2-diazine and 1,4-diazine compounds, respectively] and the H atoms are ordered.

In this communication, we report the structures of two solid phases of the title compound, which shows a solid–solid phase transition at about 198 K determined by ³⁵Cl NQR. In the ³⁵Cl NQR measurements in the temperature range of 77–328 K, two resonance lines were observed in the high-temperature range above 198 K; the ³⁵Cl NQR frequencies observed at 321 K are 35.973 and 35.449 MHz. Below 198 K, the resonance lines split into four lines (36.565, 36.357, 35.974 and 36.011 MHz at 77 K). This indicates that a phase transition occurs around 198 K, accompanying a change in the number of crystallographically independent Cl atoms, i.e. a change from two independent Cl atoms in the high-temperature phase to four in the low-temperature phase (Armstrong & van Driel, 1975). The detailed NQR results are reported elsewhere (Asaji, 2009). The phase transition was also detected by differential thermal analysis (DTA) operated in the range 150–295 K, which showed a broad and weak heat anomaly with onset and peak temperatures of 200 (1) and 206 (1) K, respectively, on heating, and 201 (1) and 197 (1) on cooling.

Fig. 1 shows the asymmetric unit in the high-temperature phase determined at 225 K, where the three components are held together by O—H···O, N···H···O and C—H···O hydrogen bonds (Table 1). The dihedral angle between the pyrimidine ring (N1/C7/N2/C8–C10) and the anion ring (C1–C6) is 30.43 (6)°. An acid–base interaction involving a proton transfer occurs through the water molecule. The transferred proton is shared by the pyrimidine and water molecules, resulting in two disordered states of pyrimidin-1-ium cation···water molecule and pyrimidine molecule···oxonium cation. This disordered feature in the short N···H···O hydrogen bond [N1···O5 2.5440 (15) Å] is confirmed in a difference Fourier map (Fig. 2a), where two distinct peaks are observed between the pyrimidin-1-ium cation and the water molecule. The asymmetric units related by an inversion centre are connected by O—H···O and C—H···Cl hydrogen bonds (Table 1), forming a centrosymmetric 2+2+2 aggregate (Fig. 3). These aggregates are further connected through an O—H···O hydrogen bond between the hydrogen chloranilate anions related by a twofold screw rotation axis (Fig. 4).

The asymmetric unit of the low-temperature phase determined at 120 K is shown in Fig. 5. This unit is a 2+2+2 aggregate of the three components; there are two crystallographically independent molecules for each component and the four independent Cl atoms in the crystal, being consistent with the ³⁵Cl NQR result. Although this phase crystallizes in the same space group and has a similar molecular packing, the centrosymmetry of the 2+2+2 aggregate (Fig. 3) and the twofold screw rotation symmetry between the anions (Fig. 4) in the high-temperature phase are lost, resulting in a doubling of the a axis as shown in Fig. 6. For the low-temperature phase, a non-standard setting of space group, P2₁/n, was selected in order to facilitate the comparison of the two phases. In the 2+2+2 aggregate, the pyrimidin-1-ium cation and the water molecule are connected by short hydrogen bonds [N1···O5 2.5207 (15) Å and N3···O10 2.5285 (15) Å; Table 2]. The difference Fourier map (Fig. 2b) shows two peaks between atoms N1 and O5. On the other hand, between atoms N3 and O10 only one diffused peak is observed near the centre of N···O (Fig. 2c). The maximum lies closer to atom N3 than O10, and a long N—H bond [N3—H3 1.10 (3) Å] is obtained. The dihedral angle between the pyrimidine ring (N3/C17/N4/C18–C20) and the anion ring (C11–C16) is 28.30 (5)° comparable with that of 30.43 (6)° in the high-temperature phase, while a larger dihedral angle of 54.12 (5)° is observed between the N1/C7/N2/C8–C10 and C1–C6 rings. The dihedral angles between the two base rings and between the two acid rings are 44.86 (6) and 1.49 (5)°, respectively. These angles indicate that the phase transition is accompanied by a considerable rotation of one pyrimidine molecule (N1/C7/N2/C8–C10) around the N···H···O hydrogen bond breaking the C—H···O and C—H···Cl hydrogen bonds.

Related literature

For related literature, see: Armstrong & van Driel (1975); Asaji (2009); Asaji et al. (2007); Gotoh & Ishida (2008); Gotoh, Asaji & Ishida (2008); Ikeda et al. (2005); Ishida & Kashino (1999a, 1999b, 1999c); Nihei et al. (2000a, 2000b); Seliger et al. (2009).

S2. Experimental

Single crystals of the title compound were obtained by slow evaporation from a methanol solution (120 ml) of chloranilic acid (0.84 g) with pyrimidine (0.32 g) at room temperature. As crystallization was not performed under anhydrous conditions, the presence of a hydrate water molecule in crystals of the title compound is not surprising. The same single crystal was used for the X-ray diffraction experiments at 225 and 120 K. This crystal was cooled from room temperature to 225 K within several minutes and the diffraction data were taken. After collection of the data, the crystal was further cooled to 120 K, and then the diffraction data were registered again.

For the ³⁵Cl NQR measurement a pulsed spectrometer base on a gated amplifier (Matec 525) was used. The sample temperature was controlled within ±0.5 K over the sample volume using an electronic controller (LakeShore 331) and measured with an accuracy of ±0.5 K by use of gold+0.07° ion versus chromel thermocouple (Asaji et al., 2007). DTA was performed by use of a home-made apparatus. The heating and cooling rates were circa 5 K min^-1. The samples used for NQR and DTA measurements were identified by comparing the observed X-ray powder pattern with the expected one from the present single-crystal data.

S3. Refinement

For both phases, all H atoms were found in difference Fourier maps, and then, C-bound H atoms were positioned geometrically (C—H = 0.94 Å at 225 K and 0.95 Å at 120 K) and treated as riding, with U_iso(H) = 1.2U_eq(C). The O-bound H atom in the hydrogen chloranilate anion was refined freely. In the high-temperature phase, the H atom in the N···H···O hydrogen bond was found to be disordered over two positions in a difference Fourier map. The positional parameters of the disordered H atom were refined, with bond restraints [O—H = 0.83 (2) and N—H = 0.87 (2) Å], and with U_iso(H) = 1.5U_eq(N or O). The site occupancies were initially refined, and then fixed at 0.5:0.5 in the final refinement. Other water H atoms were refined, with bond restraints [O—H = 0.83 (2) Å]. In the low-temperature phase, one of the H atoms in the N···H···O hydrogen bonds was found to be disordered. A similar treatment was applied, with bond restraints [O—H = 0.84 (2) and N—H = 0.88 (2) Å]. Other water H atoms were refined, with bond restraints [O—H = 0.84 (2) Å], while the ordered N-bound H atom was refined freely.

Computing details

For both compounds, data collection: PROCESS-AUTO (Rigaku/MSC, 2004); cell refinement: PROCESS-AUTO (Rigaku/MSC, 2004); data reduction: CrystalStructure (Rigaku/MSC, 2004); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 1997) and WinGX (Farrugia, 1999); software used to prepare material for publication: CrystalStructure (Rigaku/MSC, 2004) and PLATON (Spek, 2009).

Figures

	Fig. 1. A molecular view in the high-temperature phase (225 K) of the title compound, showing the atom-numbering scheme. Displacement ellipsoids are drawn at the 50% probability level and H atoms are shown as small spheres of arbitrary radii. The O—H···O, N···H···O and C—H···O hydrogen bonds are indicated by dashed lines.
	Fig. 2. Difference Fourier maps of the high-temperature phase (a) and the low-temperature phase (b), (c) associated with the N···H···O hydrogen bond between the pyrimidine and water molecules. Maps were calculated on the mean plane of O5/N1/C7 or O10/N3/C17 from a model containing all atoms apart from the H atom in the hydrogen bond. The contours are at 0.03 (a) and 0.05 e Å^-3 (b), (c) and dashed lines indicate negative contours.
	Fig. 3. A view of the centrosymmetric 2+2+2 aggregate in the high-temperature phase. The O—H···O, N···H···O, C—H···O and C—H···Cl hydrogen bonds are indicated by dashed lines. [Symmetry code: (ii) -x+1, -y+2, -z+1.]
	Fig. 4. A partial packing view of the hydrogen chloranilate anions in the high-temperature phase. The O—H···O hydrogen bonds are indicated by dashed lines. [Symmetry codes: (i) -x, y-1/2, -z+1/2; (iii) -x, y+1/2, -z+1/2.]
	Fig. 5. A molecular view in the low-temperature phase (120 K) of the title compound, showing the atom-numbering scheme. Displacement ellipsoids are drawn at the 50% probability level and H atoms are shown as small spheres of arbitrary radii. The O—H···O, N···H···O, C—H···O and C—H···Cl hydrogen bonds are indicated by dashed lines.
	Fig. 6. Packing diagrams of the high- (225 K) and low- (120 K) temperature phases, viewed down the b axis. The twofold screw axes and the inversion centres are shown by black symbols. The space group in the high-temperature phase is P21/c, while the space group in the low-temperature phase is taken to be P21/n in order to show the structural relation between the two phases. All H atoms have been omitted for clarity.

(I_225) pyrimidin-1-ium hydrogen chloranilate monohydrate

Crystal data

C4H5N2^+·C6HCl2O4^−·H2O	F(000) = 624.00
Mr = 307.09	Dx = 1.757 Mg m^−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71075 Å
Hall symbol: -P 2ybc	Cell parameters from 18188 reflections
a = 12.6621 (7) Å	θ = 3.1–30.1°
b = 3.75947 (18) Å	µ = 0.58 mm^−1
c = 26.7435 (16) Å	T = 225 K
β = 114.208 (2)°	Needle, dark
V = 1161.12 (11) Å^3	0.36 × 0.13 × 0.08 mm
Z = 4

Data collection

Rigaku RAXIS-RAPID II diffractometer	3061 reflections with I > 2σ(I)
Detector resolution: 10.00 pixels mm^-1	Rint = 0.016
ω scans	θmax = 30.0°
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	h = −17→17
Tmin = 0.890, Tmax = 0.955	k = −4→5
21678 measured reflections	l = −37→37
3377 independent reflections

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.027	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.075	H atoms treated by a mixture of independent and constrained refinement
S = 1.04	w = 1/[σ^2(Fo^2) + (0.0434P)^2 + 0.4181P] where P = (Fo^2 + 2Fc^2)/3
3377 reflections	(Δ/σ)max = 0.001
190 parameters	Δρmax = 0.53 e Å^−3
4 restraints	Δρmin = −0.17 e Å^−3

Special details

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.

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 (Ų)

	x	y	z	Uiso*/Ueq	Occ. (<1)
Cl1	0.41634 (2)	0.13406 (8)	0.271877 (10)	0.02200 (8)
Cl2	0.14851 (2)	0.73440 (8)	0.408348 (11)	0.02464 (8)
O1	0.51322 (6)	0.5145 (3)	0.37872 (3)	0.02687 (18)
O2	0.16484 (7)	0.0848 (3)	0.24451 (3)	0.02477 (18)
O3	0.05490 (6)	0.3410 (2)	0.30130 (3)	0.02336 (17)
O4	0.40346 (7)	0.7912 (3)	0.43597 (3)	0.02713 (18)
O5	0.63689 (8)	0.8783 (3)	0.48442 (4)	0.0317 (2)
H5C	0.678 (3)	0.969 (11)	0.4690 (15)	0.048*	0.50
N1	0.75684 (8)	1.0875 (3)	0.43354 (4)	0.0280 (2)
H1	0.716 (3)	1.031 (10)	0.4511 (14)	0.042*	0.50
N2	0.93241 (10)	1.3141 (4)	0.43578 (5)	0.0389 (3)
C1	0.40858 (8)	0.4738 (3)	0.36032 (4)	0.01800 (18)
C2	0.34264 (8)	0.2939 (3)	0.30885 (4)	0.01747 (18)
C3	0.22697 (8)	0.2515 (3)	0.29083 (4)	0.01753 (19)
C4	0.16093 (8)	0.3939 (3)	0.32250 (4)	0.01724 (18)
C5	0.22393 (8)	0.5715 (3)	0.37228 (4)	0.01818 (19)
C6	0.34312 (8)	0.6244 (3)	0.39306 (4)	0.01834 (19)
C7	0.86214 (12)	1.2300 (5)	0.45916 (5)	0.0377 (3)
H7	0.8883	1.2740	0.4969	0.045*
C8	0.89272 (10)	1.2522 (4)	0.38188 (5)	0.0282 (2)
H8	0.9407	1.3046	0.3638	0.034*
C9	0.78387 (10)	1.1142 (3)	0.35191 (5)	0.0276 (2)
H9	0.7567	1.0783	0.3139	0.033*
C10	0.71659 (10)	1.0312 (3)	0.37961 (5)	0.0269 (2)
H10	0.6422	0.9348	0.3606	0.032*
H2	0.1001 (18)	0.078 (6)	0.2396 (8)	0.054 (6)*
H5A	0.5684 (14)	0.828 (6)	0.4650 (8)	0.052 (5)*
H5B	0.6375 (17)	0.990 (5)	0.5117 (7)	0.054 (6)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Cl1	0.01880 (12)	0.02755 (14)	0.02334 (12)	0.00019 (9)	0.01239 (9)	−0.00203 (9)
Cl2	0.02129 (13)	0.03182 (15)	0.02559 (13)	−0.00189 (10)	0.01447 (10)	−0.00556 (10)
O1	0.0145 (3)	0.0372 (5)	0.0286 (4)	−0.0053 (3)	0.0085 (3)	−0.0070 (4)
O2	0.0147 (3)	0.0387 (5)	0.0204 (3)	−0.0050 (3)	0.0066 (3)	−0.0088 (3)
O3	0.0128 (3)	0.0330 (4)	0.0226 (4)	−0.0005 (3)	0.0055 (3)	−0.0008 (3)
O4	0.0197 (4)	0.0385 (5)	0.0238 (4)	−0.0079 (3)	0.0094 (3)	−0.0117 (3)
O5	0.0258 (4)	0.0462 (6)	0.0232 (4)	−0.0129 (4)	0.0101 (3)	−0.0089 (4)
N1	0.0214 (4)	0.0367 (6)	0.0285 (5)	−0.0028 (4)	0.0128 (4)	0.0000 (4)
N2	0.0255 (5)	0.0647 (8)	0.0265 (5)	−0.0160 (5)	0.0106 (4)	−0.0065 (5)
C1	0.0152 (4)	0.0197 (4)	0.0194 (4)	−0.0024 (3)	0.0074 (3)	0.0003 (4)
C2	0.0151 (4)	0.0208 (5)	0.0184 (4)	−0.0009 (3)	0.0088 (3)	−0.0004 (4)
C3	0.0155 (4)	0.0206 (5)	0.0164 (4)	−0.0013 (4)	0.0064 (3)	0.0002 (4)
C4	0.0142 (4)	0.0201 (5)	0.0178 (4)	0.0002 (3)	0.0069 (3)	0.0024 (4)
C5	0.0156 (4)	0.0223 (5)	0.0191 (4)	−0.0012 (4)	0.0096 (3)	−0.0014 (4)
C6	0.0160 (4)	0.0210 (5)	0.0187 (4)	−0.0026 (4)	0.0078 (3)	−0.0009 (4)
C7	0.0287 (6)	0.0624 (9)	0.0220 (5)	−0.0124 (6)	0.0105 (5)	−0.0053 (6)
C8	0.0240 (5)	0.0368 (6)	0.0264 (5)	−0.0046 (5)	0.0130 (4)	−0.0001 (5)
C9	0.0263 (5)	0.0332 (6)	0.0219 (5)	−0.0032 (5)	0.0086 (4)	−0.0029 (4)
C10	0.0185 (5)	0.0306 (6)	0.0295 (5)	−0.0025 (4)	0.0076 (4)	−0.0019 (5)

Geometric parameters (Å, º)

Cl1—C2	1.7223 (10)	N2—C8	1.3380 (16)
Cl2—C5	1.7243 (10)	C1—C2	1.4516 (14)
O1—C1	1.2192 (12)	C1—C6	1.5394 (14)
O2—C3	1.3217 (12)	C2—C3	1.3506 (13)
O2—H2	0.78 (2)	C3—C4	1.5113 (14)
O3—C4	1.2406 (12)	C4—C5	1.4084 (14)
O4—C6	1.2548 (13)	C5—C6	1.3922 (13)
O5—H5A	0.829 (15)	C7—H7	0.9400
O5—H5B	0.840 (15)	C8—C9	1.3803 (16)
O5—H5C	0.860 (19)	C8—H8	0.9400
N1—C7	1.3360 (16)	C9—C10	1.3745 (17)
N1—C10	1.3350 (15)	C9—H9	0.9400
N1—H1	0.851 (18)	C10—H10	0.9400
N2—C7	1.3186 (17)
C3—O2—H2	110.9 (15)	C5—C4—C3	117.94 (8)
H5A—O5—H5B	107.0 (19)	C6—C5—C4	123.11 (9)
H5A—O5—H5C	119 (3)	C6—C5—Cl2	118.97 (8)
H5B—O5—H5C	115 (3)	C4—C5—Cl2	117.92 (7)
C10—N1—C7	118.44 (10)	O4—C6—C5	126.18 (10)
C10—N1—H1	120 (3)	O4—C6—C1	115.85 (9)
C7—N1—H1	121 (3)	C5—C6—C1	117.96 (9)
C7—N2—C8	116.15 (11)	N2—C7—N1	125.35 (12)
O1—C1—C2	123.28 (9)	N2—C7—H7	117.3
O1—C1—C6	118.28 (9)	N1—C7—H7	117.3
C2—C1—C6	118.44 (8)	N2—C8—C9	122.38 (11)
C3—C2—C1	120.75 (9)	N2—C8—H8	118.8
C3—C2—Cl1	121.18 (8)	C9—C8—H8	118.8
C1—C2—Cl1	118.07 (7)	C10—C9—C8	117.66 (11)
O2—C3—C2	122.14 (9)	C10—C9—H9	121.2
O2—C3—C4	116.09 (8)	C8—C9—H9	121.2
C2—C3—C4	121.77 (9)	N1—C10—C9	119.99 (10)
O3—C4—C5	126.55 (9)	N1—C10—H10	120.0
O3—C4—C3	115.51 (9)	C9—C10—H10	120.0
O1—C1—C2—C3	178.96 (11)	C3—C4—C5—Cl2	179.91 (7)
C6—C1—C2—C3	−1.70 (15)	C4—C5—C6—O4	177.22 (11)
O1—C1—C2—Cl1	−0.59 (15)	Cl2—C5—C6—O4	−1.95 (16)
C6—C1—C2—Cl1	178.75 (7)	C4—C5—C6—C1	−1.30 (16)
C1—C2—C3—O2	−179.12 (10)	Cl2—C5—C6—C1	179.53 (7)
Cl1—C2—C3—O2	0.43 (15)	O1—C1—C6—O4	2.44 (15)
C1—C2—C3—C4	1.17 (16)	C2—C1—C6—O4	−176.93 (10)
Cl1—C2—C3—C4	−179.29 (8)	O1—C1—C6—C5	−178.89 (10)
O2—C3—C4—O3	−0.50 (14)	C2—C1—C6—C5	1.74 (15)
C2—C3—C4—O3	179.24 (10)	C8—N2—C7—N1	0.6 (3)
O2—C3—C4—C5	179.63 (9)	C10—N1—C7—N2	−1.7 (2)
C2—C3—C4—C5	−0.64 (15)	C7—N2—C8—C9	1.1 (2)
O3—C4—C5—C6	−179.12 (11)	N2—C8—C9—C10	−1.7 (2)
C3—C4—C5—C6	0.74 (16)	C7—N1—C10—C9	1.0 (2)
O3—C4—C5—Cl2	0.06 (16)	C8—C9—C10—N1	0.54 (19)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O5	0.86 (4)	1.69 (4)	2.5440 (15)	175 (4)
O2—H2···O3	0.78 (2)	2.19 (2)	2.6279 (12)	116.2 (18)
O2—H2···O3^i	0.78 (2)	2.02 (2)	2.6995 (12)	146 (2)
O5—H5A···O1	0.83 (2)	2.43 (2)	2.9467 (13)	122 (2)
O5—H5A···O4	0.83 (2)	1.91 (2)	2.7169 (14)	163 (2)
O5—H5B···O4^ii	0.84 (2)	1.87 (2)	2.6888 (14)	165 (2)
O5—H5C···N1	0.86 (4)	1.69 (4)	2.5440 (15)	171 (4)
C7—H7···Cl2^ii	0.94	2.76	3.6031 (13)	150
C10—H10···O1	0.94	2.46	3.2179 (16)	138

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

(I_120) pyrimidin-1-ium hydrogen chloranilate monohydrate

Crystal data

C4H5N2^+·C6HCl2O4^−·H2O	F(000) = 1248.00
Mr = 307.09	Dx = 1.787 Mg m^−3
Monoclinic, P21/n	Mo Kα radiation, λ = 0.71075 Å
Hall symbol: -P 2yn	Cell parameters from 31208 reflections
a = 25.5952 (9) Å	θ = 3.0–30.1°
b = 3.71581 (13) Å	µ = 0.59 mm^−1
c = 26.3761 (9) Å	T = 120 K
β = 114.5289 (13)°	Needle, dark
V = 2282.16 (14) Å^3	0.36 × 0.13 × 0.08 mm
Z = 8

Data collection

Rigaku RAXIS-RAPID II diffractometer	5959 reflections with I > 2σ(I)
Detector resolution: 10.00 pixels mm^-1	Rint = 0.021
ω scans	θmax = 30.0°
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	h = −35→35
Tmin = 0.867, Tmax = 0.954	k = −4→5
36273 measured reflections	l = −36→37
6635 independent reflections

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.029	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.078	H atoms treated by a mixture of independent and constrained refinement
S = 1.07	w = 1/[σ^2(Fo^2) + (0.0427P)^2 + 1.1405P] where P = (Fo^2 + 2Fc^2)/3
6635 reflections	(Δ/σ)max = 0.001
377 parameters	Δρmax = 0.76 e Å^−3
6 restraints	Δρmin = −0.25 e Å^−3

Special details

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.

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 (Ų)

	x	y	z	Uiso*/Ueq	Occ. (<1)
Cl1	0.202264 (11)	0.14112 (8)	0.264395 (11)	0.01364 (6)
Cl2	0.068417 (11)	0.72134 (8)	0.403400 (11)	0.01407 (6)
Cl3	0.290762 (11)	1.90740 (7)	0.726723 (11)	0.01279 (6)
Cl4	0.416720 (11)	1.34307 (8)	0.579382 (11)	0.01427 (6)
O1	0.24879 (3)	0.5379 (3)	0.37159 (4)	0.01657 (17)
O2	0.07692 (3)	0.0641 (2)	0.23708 (3)	0.01477 (16)
O3	0.02279 (3)	0.3068 (2)	0.29558 (3)	0.01390 (16)
O4	0.19398 (3)	0.8074 (2)	0.42982 (3)	0.01609 (17)
O5	0.30813 (4)	0.8681 (3)	0.48060 (4)	0.01854 (18)
H5C	0.3310 (13)	0.903 (10)	0.4651 (14)	0.028*	0.50
O6	0.23983 (3)	1.5234 (2)	0.61791 (3)	0.01567 (16)
O7	0.41457 (3)	1.9635 (3)	0.75124 (3)	0.01553 (17)
O8	0.46673 (3)	1.7159 (2)	0.69041 (3)	0.01522 (16)
O9	0.29174 (3)	1.2481 (2)	0.55753 (3)	0.01599 (17)
O10	0.17606 (4)	1.1463 (3)	0.51139 (4)	0.01762 (17)
N1	0.37554 (4)	0.9295 (3)	0.43348 (4)	0.0172 (2)
H1	0.3545 (13)	0.922 (10)	0.4518 (13)	0.026*	0.50
N2	0.46853 (4)	0.8389 (3)	0.43714 (4)	0.0186 (2)
N3	0.12019 (4)	0.9335 (3)	0.56542 (4)	0.01585 (19)
N4	0.03442 (4)	0.6949 (3)	0.56536 (4)	0.0193 (2)
C1	0.19707 (4)	0.4853 (3)	0.35336 (4)	0.01146 (19)
C2	0.16481 (4)	0.2947 (3)	0.30146 (4)	0.01114 (19)
C3	0.10771 (4)	0.2400 (3)	0.28370 (4)	0.01126 (19)
C4	0.07508 (4)	0.3757 (3)	0.31628 (4)	0.01077 (19)
C5	0.10571 (4)	0.5650 (3)	0.36630 (4)	0.01125 (19)
C6	0.16453 (4)	0.6315 (3)	0.38667 (4)	0.01159 (19)
C7	0.43019 (5)	0.8191 (3)	0.45889 (5)	0.0174 (2)
H7	0.4424	0.7193	0.4952	0.021*
C8	0.45016 (5)	0.9835 (4)	0.38589 (5)	0.0178 (2)
H8	0.4766	1.0060	0.3692	0.021*
C9	0.39425 (5)	1.1007 (3)	0.35647 (5)	0.0172 (2)
H9	0.3820	1.2001	0.3202	0.021*
C10	0.35698 (5)	1.0676 (3)	0.38184 (5)	0.0178 (2)
H10	0.3182	1.1425	0.3628	0.021*
C11	0.29168 (4)	1.5692 (3)	0.63524 (4)	0.01137 (19)
C12	0.32554 (4)	1.7519 (3)	0.68722 (4)	0.01103 (19)
C13	0.38277 (5)	1.7978 (3)	0.70412 (4)	0.01166 (19)
C14	0.41399 (4)	1.6631 (3)	0.66998 (4)	0.01129 (19)
C15	0.38126 (4)	1.4899 (3)	0.61885 (4)	0.01149 (19)
C16	0.32257 (4)	1.4235 (3)	0.60029 (4)	0.01160 (19)
C17	0.06823 (5)	0.7809 (4)	0.54027 (5)	0.0190 (2)
H17	0.0546	0.7304	0.5016	0.023*
C18	0.05503 (5)	0.7673 (3)	0.62017 (5)	0.0156 (2)
H18	0.0319	0.7120	0.6395	0.019*
C19	0.10863 (5)	0.9194 (3)	0.64959 (5)	0.0157 (2)
H19	0.1226	0.9651	0.6884	0.019*
C20	0.14100 (5)	1.0021 (3)	0.62028 (5)	0.0157 (2)
H20	0.1779	1.1074	0.6389	0.019*
H2A	0.0446 (9)	0.052 (6)	0.2323 (8)	0.040 (6)*
H3	0.1442 (12)	1.008 (9)	0.5409 (12)	0.092 (9)*
H5A	0.2735 (7)	0.830 (6)	0.4595 (8)	0.049 (6)*
H5B	0.3097 (8)	1.002 (5)	0.5067 (7)	0.038 (5)*
H7A	0.4477 (9)	1.970 (6)	0.7566 (9)	0.044 (6)*
H10A	0.2098 (6)	1.195 (5)	0.5307 (7)	0.031 (5)*
H10B	0.1760 (8)	1.030 (5)	0.4840 (7)	0.035 (5)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Cl1	0.01185 (11)	0.01646 (13)	0.01531 (12)	−0.00063 (9)	0.00832 (9)	−0.00258 (10)
Cl2	0.01209 (11)	0.01782 (13)	0.01509 (12)	−0.00040 (9)	0.00842 (9)	−0.00245 (10)
Cl3	0.01117 (11)	0.01577 (12)	0.01345 (11)	0.00012 (9)	0.00711 (9)	−0.00116 (9)
Cl4	0.01298 (12)	0.01737 (13)	0.01519 (12)	0.00112 (9)	0.00857 (9)	−0.00108 (10)
O1	0.0097 (3)	0.0221 (4)	0.0182 (4)	−0.0020 (3)	0.0060 (3)	−0.0043 (3)
O2	0.0094 (3)	0.0212 (4)	0.0135 (4)	−0.0026 (3)	0.0044 (3)	−0.0044 (3)
O3	0.0082 (3)	0.0179 (4)	0.0148 (4)	0.0001 (3)	0.0039 (3)	0.0002 (3)
O4	0.0119 (3)	0.0216 (4)	0.0150 (4)	−0.0033 (3)	0.0058 (3)	−0.0062 (3)
O5	0.0134 (4)	0.0274 (5)	0.0150 (4)	−0.0041 (3)	0.0061 (3)	−0.0064 (4)
O6	0.0094 (3)	0.0205 (4)	0.0170 (4)	−0.0024 (3)	0.0053 (3)	−0.0028 (3)
O7	0.0087 (3)	0.0237 (4)	0.0137 (4)	−0.0034 (3)	0.0042 (3)	−0.0054 (3)
O8	0.0082 (3)	0.0205 (4)	0.0162 (4)	−0.0001 (3)	0.0044 (3)	0.0003 (3)
O9	0.0124 (4)	0.0209 (4)	0.0149 (4)	−0.0030 (3)	0.0058 (3)	−0.0057 (3)
O10	0.0147 (4)	0.0250 (5)	0.0136 (4)	−0.0062 (3)	0.0063 (3)	−0.0051 (3)
N1	0.0142 (4)	0.0210 (5)	0.0186 (5)	−0.0022 (4)	0.0089 (4)	−0.0042 (4)
N2	0.0130 (4)	0.0259 (5)	0.0164 (4)	0.0012 (4)	0.0055 (4)	0.0004 (4)
N3	0.0131 (4)	0.0188 (5)	0.0170 (4)	0.0003 (4)	0.0076 (4)	0.0006 (4)
N4	0.0139 (4)	0.0275 (6)	0.0161 (4)	−0.0054 (4)	0.0058 (4)	−0.0021 (4)
C1	0.0103 (4)	0.0121 (5)	0.0127 (4)	−0.0003 (4)	0.0056 (4)	0.0002 (4)
C2	0.0099 (4)	0.0133 (5)	0.0120 (4)	0.0002 (4)	0.0063 (4)	−0.0004 (4)
C3	0.0105 (4)	0.0121 (5)	0.0112 (4)	0.0003 (4)	0.0045 (4)	0.0001 (4)
C4	0.0096 (4)	0.0110 (5)	0.0120 (4)	0.0012 (4)	0.0048 (4)	0.0025 (4)
C5	0.0098 (4)	0.0128 (5)	0.0129 (4)	0.0003 (4)	0.0066 (4)	−0.0011 (4)
C6	0.0104 (4)	0.0126 (5)	0.0124 (4)	0.0000 (4)	0.0054 (4)	0.0000 (4)
C7	0.0162 (5)	0.0208 (6)	0.0143 (5)	−0.0021 (4)	0.0054 (4)	−0.0010 (4)
C8	0.0150 (5)	0.0231 (6)	0.0169 (5)	−0.0004 (4)	0.0081 (4)	−0.0002 (5)
C9	0.0168 (5)	0.0175 (5)	0.0166 (5)	0.0007 (4)	0.0063 (4)	0.0017 (4)
C10	0.0129 (5)	0.0187 (5)	0.0208 (5)	0.0019 (4)	0.0060 (4)	−0.0011 (5)
C11	0.0104 (4)	0.0113 (5)	0.0124 (4)	−0.0003 (4)	0.0048 (4)	0.0007 (4)
C12	0.0103 (4)	0.0127 (5)	0.0116 (4)	−0.0001 (4)	0.0060 (4)	−0.0005 (4)
C13	0.0108 (4)	0.0130 (5)	0.0113 (4)	−0.0003 (4)	0.0047 (4)	0.0006 (4)
C14	0.0100 (4)	0.0119 (5)	0.0126 (4)	0.0007 (4)	0.0054 (4)	0.0019 (4)
C15	0.0101 (4)	0.0133 (5)	0.0132 (4)	0.0004 (4)	0.0070 (4)	−0.0005 (4)
C16	0.0112 (4)	0.0118 (5)	0.0123 (4)	−0.0003 (4)	0.0054 (4)	0.0004 (4)
C17	0.0159 (5)	0.0268 (6)	0.0137 (5)	−0.0032 (5)	0.0054 (4)	−0.0018 (5)
C18	0.0141 (5)	0.0180 (5)	0.0161 (5)	−0.0016 (4)	0.0078 (4)	0.0004 (4)
C19	0.0152 (5)	0.0171 (5)	0.0138 (5)	−0.0009 (4)	0.0049 (4)	−0.0017 (4)
C20	0.0119 (5)	0.0164 (5)	0.0177 (5)	−0.0007 (4)	0.0050 (4)	−0.0013 (4)

Geometric parameters (Å, º)

Cl1—C2	1.7259 (11)	N4—C17	1.3282 (16)
Cl2—C5	1.7266 (11)	N4—C18	1.3445 (15)
Cl3—C12	1.7268 (11)	C1—C2	1.4558 (15)
Cl4—C15	1.7291 (11)	C1—C6	1.5390 (15)
O1—C1	1.2218 (13)	C2—C3	1.3522 (14)
O2—C3	1.3250 (13)	C3—C4	1.5118 (15)
O2—H2A	0.79 (2)	C4—C5	1.4112 (15)
O3—C4	1.2444 (13)	C5—C6	1.3946 (14)
O4—C6	1.2563 (13)	C7—H7	0.9500
O5—H5A	0.841 (15)	C8—C9	1.3849 (16)
O5—H5B	0.837 (15)	C8—H8	0.9500
O5—H5C	0.851 (18)	C9—C10	1.3795 (17)
O6—C11	1.2228 (13)	C9—H9	0.9500
O7—C13	1.3216 (13)	C10—H10	0.9500
O7—H7A	0.80 (2)	C11—C12	1.4511 (15)
O8—C14	1.2437 (13)	C11—C16	1.5405 (15)
O9—C16	1.2572 (13)	C12—C13	1.3533 (14)
O10—H10A	0.821 (14)	C13—C14	1.5154 (15)
O10—H10B	0.842 (14)	C14—C15	1.4131 (15)
N1—C7	1.3402 (15)	C15—C16	1.3951 (14)
N1—C10	1.3442 (16)	C17—H17	0.9500
N1—H1	0.860 (18)	C18—C19	1.3856 (16)
N2—C7	1.3285 (15)	C18—H18	0.9500
N2—C8	1.3450 (16)	C19—C20	1.3821 (16)
N3—C17	1.3410 (15)	C19—H19	0.9500
N3—C20	1.3427 (15)	C20—H20	0.9500
N3—H3	1.10 (3)
C3—O2—H2A	111.0 (15)	N2—C8—H8	118.7
H5C—O5—H5A	117 (3)	C9—C8—H8	118.7
H5C—O5—H5B	120 (3)	C10—C9—C8	117.52 (11)
H5A—O5—H5B	108.6 (19)	C10—C9—H9	121.2
C13—O7—H7A	112.0 (15)	C8—C9—H9	121.2
H3—O10—H10A	115.6 (17)	N1—C10—C9	120.06 (11)
H3—O10—H10B	118.9 (18)	N1—C10—H10	120.0
H10A—O10—H10B	105.8 (17)	C9—C10—H10	120.0
C7—N1—C10	118.69 (10)	O6—C11—C12	123.24 (10)
C7—N1—H1	118 (2)	O6—C11—C16	118.33 (10)
C10—N1—H1	123 (2)	C12—C11—C16	118.44 (9)
C7—N2—C8	116.33 (10)	C13—C12—C11	120.69 (10)
C17—N3—C20	118.79 (10)	C13—C12—Cl3	121.19 (8)
C17—N3—H3	119.9 (15)	C11—C12—Cl3	118.12 (8)
C20—N3—H3	121.3 (16)	O7—C13—C12	121.87 (10)
C17—N4—C18	116.22 (10)	O7—C13—C14	116.23 (9)
O1—C1—C2	123.16 (10)	C12—C13—C14	121.90 (10)
O1—C1—C6	118.26 (10)	O8—C14—C15	126.30 (10)
C2—C1—C6	118.58 (9)	O8—C14—C13	115.82 (10)
C3—C2—C1	120.57 (10)	C15—C14—C13	117.87 (9)
C3—C2—Cl1	121.92 (9)	C16—C15—C14	122.73 (10)
C1—C2—Cl1	117.51 (8)	C16—C15—Cl4	119.39 (8)
O2—C3—C2	122.44 (10)	C14—C15—Cl4	117.84 (8)
O2—C3—C4	115.85 (9)	O9—C16—C15	126.15 (10)
C2—C3—C4	121.70 (10)	O9—C16—C11	115.59 (9)
O3—C4—C5	126.26 (10)	C15—C16—C11	118.25 (9)
O3—C4—C3	115.42 (9)	N4—C17—N3	124.95 (11)
C5—C4—C3	118.31 (9)	N4—C17—H17	117.5
C6—C5—C4	122.70 (10)	N3—C17—H17	117.5
C6—C5—Cl2	118.97 (8)	N4—C18—C19	122.61 (11)
C4—C5—Cl2	118.33 (8)	N4—C18—H18	118.7
O4—C6—C5	125.94 (10)	C19—C18—H18	118.7
O4—C6—C1	115.94 (9)	C20—C19—C18	117.50 (11)
C5—C6—C1	118.11 (9)	C20—C19—H19	121.3
N2—C7—N1	124.87 (11)	C18—C19—H19	121.3
N2—C7—H7	117.6	N3—C20—C19	119.93 (10)
N1—C7—H7	117.6	N3—C20—H20	120.0
N2—C8—C9	122.51 (11)	C19—C20—H20	120.0
O1—C1—C2—C3	179.07 (11)	O6—C11—C12—C13	−179.42 (11)
C6—C1—C2—C3	−1.58 (16)	C16—C11—C12—C13	0.98 (16)
O1—C1—C2—Cl1	−0.51 (16)	O6—C11—C12—Cl3	0.72 (16)
C6—C1—C2—Cl1	178.83 (8)	C16—C11—C12—Cl3	−178.88 (8)
C1—C2—C3—O2	−179.19 (10)	C11—C12—C13—O7	179.93 (10)
Cl1—C2—C3—O2	0.38 (16)	Cl3—C12—C13—O7	−0.22 (16)
C1—C2—C3—C4	0.56 (17)	C11—C12—C13—C14	0.14 (17)
Cl1—C2—C3—C4	−179.87 (8)	Cl3—C12—C13—C14	180.00 (8)
O2—C3—C4—O3	0.00 (15)	O7—C13—C14—O8	1.43 (15)
C2—C3—C4—O3	−179.76 (11)	C12—C13—C14—O8	−178.78 (11)
O2—C3—C4—C5	−179.99 (10)	O7—C13—C14—C15	−178.93 (10)
C2—C3—C4—C5	0.24 (16)	C12—C13—C14—C15	0.86 (16)
O3—C4—C5—C6	−179.91 (11)	O8—C14—C15—C16	176.34 (11)
C3—C4—C5—C6	0.08 (16)	C13—C14—C15—C16	−3.26 (16)
O3—C4—C5—Cl2	−0.21 (16)	O8—C14—C15—Cl4	−1.46 (16)
C3—C4—C5—Cl2	179.79 (8)	C13—C14—C15—Cl4	178.94 (8)
C4—C5—C6—O4	177.61 (11)	C14—C15—C16—O9	−174.36 (11)
Cl2—C5—C6—O4	−2.09 (17)	Cl4—C15—C16—O9	3.41 (17)
C4—C5—C6—C1	−1.10 (16)	C14—C15—C16—C11	4.37 (16)
Cl2—C5—C6—C1	179.19 (8)	Cl4—C15—C16—C11	−177.86 (8)
O1—C1—C6—O4	2.38 (16)	O6—C11—C16—O9	−3.94 (16)
C2—C1—C6—O4	−177.00 (10)	C12—C11—C16—O9	175.69 (10)
O1—C1—C6—C5	−178.77 (11)	O6—C11—C16—C15	177.20 (11)
C2—C1—C6—C5	1.85 (15)	C12—C11—C16—C15	−3.18 (15)
C8—N2—C7—N1	0.42 (19)	C18—N4—C17—N3	−0.4 (2)
C10—N1—C7—N2	0.8 (2)	C20—N3—C17—N4	1.1 (2)
C7—N2—C8—C9	−1.10 (19)	C17—N4—C18—C19	−0.65 (19)
N2—C8—C9—C10	0.6 (2)	N4—C18—C19—C20	0.94 (19)
C7—N1—C10—C9	−1.37 (19)	C17—N3—C20—C19	−0.78 (18)
C8—C9—C10—N1	0.72 (19)	C18—C19—C20—N3	−0.19 (18)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O5	0.86 (3)	1.67 (4)	2.5207 (15)	172 (4)
O2—H2A···O3	0.79 (2)	2.18 (2)	2.6246 (11)	116.1 (18)
O2—H2A···O8^i	0.79 (2)	2.09 (2)	2.7694 (11)	146 (2)
N3—H3···O10	1.10 (3)	1.44 (3)	2.5285 (15)	173 (3)
O5—H5A···O1	0.84 (2)	2.40 (2)	2.9075 (14)	120 (2)
O5—H5A···O4	0.84 (2)	1.86 (2)	2.6706 (14)	163 (2)
O5—H5B···O9	0.84 (2)	1.83 (2)	2.6446 (13)	163 (2)
O5—H5C···N1	0.85 (4)	1.67 (4)	2.5207 (15)	175 (4)
O7—H7A···O8	0.80 (3)	2.21 (2)	2.6423 (12)	114.4 (19)
O7—H7A···O3^ii	0.80 (3)	1.95 (2)	2.6606 (12)	148 (2)
O10—H10A···O6	0.82 (2)	2.43 (2)	2.9519 (12)	122 (1)
O10—H10A···O9	0.82 (2)	1.93 (2)	2.7201 (14)	163 (2)
O10—H10B···O4	0.84 (2)	1.87 (2)	2.6916 (13)	166 (2)
C9—H9···O2^iii	0.95	2.56	3.3331 (15)	139
C10—H10···O1^iv	0.95	2.39	3.1896 (16)	142
C17—H17···Cl2	0.95	2.76	3.6189 (13)	151
C20—H20···O6	0.95	2.44	3.2072 (15)	138

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