Crystal structure of 2-amino-5-methyl­sulfanyl-1,3,4-thia­diazol-3-ium chloride monohydrate

The title salt, C₃H₆N₃S₂⁺·Cl⁻·H₂O, crystallized with two organic cations, two chloride anions and two water mol­ecules in the asymmetric unit. The methyl C atoms deviate from their respective bound ring planes by 0.081 and 0.002 Å. In the crystal, the components are connected via N—H...O, N—H...Cl and O—H...Cl hydrogen bonds, forming sheets lying parallel to (100). The sheets are linked into bilayers by O—H...Cl hydrogen bonds involving the chloride ions and water mol­ecules. Within the bilayers there are π–π inter­actions [inter-centroid distances = 3.4654 (4) and 3.4789 (4) Å] involving inversion-related cations.

Key indicators

• Single-crystal X-ray study
• T = 110 K
• Mean [sigma](N-C) = 0.001 Å
• R factor = 0.020
• wR factor = 0.054
• Data-to-parameter ratio = 37.5

checkCIF/PLATON results

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Alert level B
PLAT417_ALERT_2_B Short Inter D-H..H-D       H11    ..  H18A    ..       2.08 Ang.

Alert level C
PLAT417_ALERT_2_C Short Inter D-H..H-D       H3     ..  H17A    ..       2.12 Ang.
PLAT910_ALERT_3_C Missing # of FCF Reflections Below Th(Min) .....          5 Why ?

Alert level G
PLAT005_ALERT_5_G No _iucr_refine_instructions_details  in the CIF     Please Do !
PLAT042_ALERT_1_G Calc. and Reported MoietyFormula Strings  Differ     Please Check

   0 ALERT level A = Most likely a serious problem - resolve or explain
   1 ALERT level B = A potentially serious problem, consider carefully
   2 ALERT level C = Check. Ensure it is not caused by an omission or oversight
   2 ALERT level G = General information/check it is not something unexpected

   1 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   2 ALERT type 2 Indicator that the structure model may be wrong or deficient
   1 ALERT type 3 Indicator that the structure quality may be low
   0 ALERT type 4 Improvement, methodology, query or suggestion
   1 ALERT type 5 Informative message, check

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S1. Chemical context

The amine under investigation, 2-amino-5-(methyl­thio)-1,3,4-thia­diazole, belongs to the larger family of heterocyclic compounds with potential medicinal importance and broad spectra of biological activities. Among these types of organic molecules are several isomers of thia­diazole (Demirbas et al., 2009). 1,3,4-thia­diazo­les represent one of the most biologically active classes of compounds with a wide spectrum of activities. A large number of 1,3,4-thia­diazo­les have been patented in the agricultural field as herbicides and bactericides (Wei et al., 2006). In the present investigation, we report the synthesis and crystal structure of a new organic-inorganic hybrid compound prepared from the reaction of the title amine with the hydro­chloric acid in aqueous medium.

S2. Structural commentary

As shown in Fig. 1, the asymmetric unit of the title compound contains two 2-amino-5-(methyl­thio)-1,3,4-thia­diazol-3-ium cations, two chloride anions and two water molecules. These entities are connected by N—H···Cl, N—H···O and O—H···Cl hydrogen bonds, forming sheets parallel to (100) (Table 1 and Fig. 2). The layers are connect through O—H···Cl contacts, forming bilayers (Figs. 2 and 3).

Examination of the geometrical features of the organic cations shows that the exocyclic C—N bond lengths are similar in length to those of the thia­diazole rings, probably due to delocalization of the ring π density with the p-orbital electrons of the amino group. These C—N distances, ca. 1.33 Å, are compatible to that of [C₃H₆N₃S₂]H₂PO₄ which contains the same organic entity (Mrad et al., 2012).

S3. Supra­molecular features

The crystal packing is also influenced by inter­molecular π–π stacking inter­actions between inversion-related anti-parallel organic cations within the bilayers (Fig. 3); Cg1···Cg1ⁱ = 3.4654 (4) Å [Cg1 is the centroid of the S1/N3/N4/C2/C5 ring; symmetry code: (i) -x, -y+2, -z+1] and Cg2···Cg2ⁱⁱ = 3.4789 (4) Å [Cg2 is the centroid of the S9/N11/N12/C10/C13 ring; symmetry code: -x+1, -y+1, -z+1].

S4. Synthesis and crystallization

An aqueous 1 M HCl solution and 2-amino-5-(methyl­thio)-1,3,4-thia­diazole in a 1:1 molar ratio were mixed and dissolved in sufficient ethanol. Crystals of the title salt grew as the ethanol evaporated at room temperature over the course of a few days.

S5. Refinement

The N- and O-bound H atoms were located in difference Fourier maps and freely refined. The C-bound H atoms were included in calculated positions and treated as riding atoms: C—H = 0.98 Å with U_iso(H) = 1.2Ueq(C). Experimental details are given in Table 2.

Related literature

For the medicinal importance and biological activity of thiadiazol isomers, see: Demirbas et al. (2009). For applications of 1,3,4 thiadiazoles in agriculture, see: Wei et al. (2006). For C—N bond lengths in the 2-amino-5-methylsulfanyl-1,3,4-thiadiazol-3-ium cation, see: Mrad et al. (2012).

Computing details

Data collection: CrysAlis PRO (Agilent, 2012); cell refinement: CrysAlis PRO (Agilent, 2012); data reduction: CrysAlis PRO (Agilent, 2012); program(s) used to solve structure: SIR92 (Altomare et al., 1994); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009).

Figures

	Fig. 1. A view of molecular structure of the title salt, with atom labelling. Displacement ellipsoids are drawn at the 50% probability level.
	Fig. 2. A view along the b axis of the crystal packing of the title compound. The hydrogen bonds are shown as dashed lines (see Table 1 for details).
	Fig. 3. A partial view along the b axis of the crystal packing of the title compound, showing the intermolecular π–π stacking interactions between inversion-related organic cations.

2-Amino-5-methylsulfanyl-1,3,4-thiadiazol-3-ium chloride monohydrate

Crystal data

C3H6N3S2^+·Cl^−·H2O	F(000) = 832
Mr = 201.69	Dx = 1.586 Mg m^−3
Monoclinic, P2/n	Mo Kα radiation, λ = 0.7107 Å
Hall symbol: -P 2yac	Cell parameters from 30742 reflections
a = 13.3826 (2) Å	θ = 2.9–37.8°
b = 9.4258 (1) Å	µ = 0.89 mm^−1
c = 13.5762 (2) Å	T = 110 K
β = 99.453 (1)°	Prism, colorless
V = 1689.27 (4) Å^3	0.42 × 0.31 × 0.15 mm
Z = 8

Data collection

Agilent SuperNova (Dual, Cu at zero, Atlas) diffractometer	8394 independent reflections
Radiation source: SuperNova (Mo) X-ray Source	7745 reflections with I > 2σ(I)
Mirror monochromator	Rint = 0.021
Detector resolution: 10.4508 pixels mm^-1	θmax = 36.7°, θmin = 2.9°
ω scans	h = −22→22
Absorption correction: analytical [CrysAlis PRO (Agilent, 2012), using a multi-faceted crystal model based on expressions derived by Clark & Reid (1995)]	k = −15→15
Tmin = 0.769, Tmax = 0.894	l = −22→22
65950 measured reflections

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.020	H atoms treated by a mixture of independent and constrained refinement
wR(F^2) = 0.054	w = 1/[σ^2(Fo^2) + (0.0211P)^2 + 0.370P] where P = (Fo^2 + 2Fc^2)/3
S = 1.12	(Δ/σ)max = 0.003
8394 reflections	Δρmax = 0.47 e Å^−3
224 parameters	Δρmin = −0.28 e Å^−3
0 restraints	Extinction correction: SHELXL97 (Sheldrick, 2008), Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.00111 (13)

Special details

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

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 > 2σ(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
S7	0.127439 (13)	1.268596 (18)	0.444671 (12)	0.01782 (3)
Cl2	0.386288 (13)	0.472130 (17)	0.838806 (12)	0.01897 (3)
S1	0.129775 (12)	1.086700 (17)	0.628112 (12)	0.01498 (3)
S9	0.353350 (12)	0.596116 (17)	0.572019 (12)	0.01549 (3)
S15	0.370685 (15)	0.777122 (18)	0.392656 (13)	0.02012 (3)
Cl1	0.112933 (13)	0.978631 (17)	0.878768 (12)	0.01911 (3)
O18	0.39361 (4)	0.11409 (5)	0.40860 (4)	0.01921 (9)
O17	0.10727 (4)	0.60603 (5)	0.44691 (4)	0.01852 (9)
N12	0.38085 (4)	0.49199 (6)	0.40204 (4)	0.01616 (9)
N3	0.12906 (4)	0.87190 (6)	0.51663 (4)	0.01608 (9)
N6	0.13116 (5)	0.81093 (7)	0.68457 (4)	0.01909 (10)
N11	0.37722 (4)	0.38126 (6)	0.46775 (4)	0.01566 (9)
N14	0.35554 (5)	0.32153 (6)	0.63065 (4)	0.01771 (9)
N4	0.12853 (4)	0.98357 (6)	0.45103 (4)	0.01622 (9)
C10	0.36248 (5)	0.41383 (6)	0.55932 (5)	0.01406 (9)
C5	0.12929 (5)	1.10218 (7)	0.49890 (5)	0.01482 (9)
C13	0.36960 (5)	0.61102 (7)	0.44630 (5)	0.01494 (10)
C2	0.13012 (5)	0.90405 (7)	0.61203 (5)	0.01490 (10)
C16	0.38878 (6)	0.72871 (9)	0.26821 (5)	0.02396 (13)
H16B	0.4528	0.6771	0.2715	0.036*
H16A	0.3906	0.8146	0.2279	0.036*
H16C	0.3327	0.6681	0.2376	0.036*
C8	0.13379 (6)	1.21799 (9)	0.31782 (5)	0.02475 (13)
H8B	0.1962	1.1643	0.3161	0.037*
H8A	0.1335	1.3033	0.2765	0.037*
H8C	0.0751	1.1589	0.2919	0.037*
H18B	0.4504 (11)	0.0902 (15)	0.3960 (11)	0.045 (4)*
H18A	0.3831 (10)	0.0703 (14)	0.4546 (10)	0.033 (3)*
H6A	0.1303 (9)	0.8410 (13)	0.7431 (9)	0.028 (3)*
H14B	0.3640 (10)	0.2376 (14)	0.6235 (10)	0.033 (3)*
H14A	0.3506 (9)	0.3519 (14)	0.6907 (9)	0.031 (3)*
H6B	0.1286 (10)	0.7247 (14)	0.6724 (10)	0.036 (3)*
H17B	0.0504 (11)	0.5876 (15)	0.4157 (11)	0.045 (4)*
H17A	0.1117 (10)	0.5630 (15)	0.4979 (10)	0.037 (3)*
H3	0.1242 (9)	0.7870 (14)	0.4929 (9)	0.033 (3)*
H11	0.3851 (10)	0.2905 (15)	0.4467 (10)	0.043 (4)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
S7	0.02231 (7)	0.01564 (6)	0.01558 (6)	−0.00113 (5)	0.00333 (5)	−0.00038 (5)
Cl2	0.02398 (7)	0.01862 (7)	0.01352 (6)	0.00121 (5)	0.00077 (5)	−0.00314 (5)
S1	0.01744 (6)	0.01459 (6)	0.01294 (6)	−0.00041 (5)	0.00259 (5)	−0.00314 (5)
S9	0.01931 (7)	0.01389 (6)	0.01357 (6)	0.00047 (5)	0.00357 (5)	−0.00272 (5)
S15	0.02861 (8)	0.01529 (7)	0.01681 (7)	−0.00147 (6)	0.00476 (6)	0.00022 (5)
Cl1	0.02353 (7)	0.01790 (6)	0.01740 (6)	−0.00308 (5)	0.00778 (5)	−0.00374 (5)
O18	0.0268 (2)	0.01509 (19)	0.0167 (2)	0.00361 (17)	0.00633 (18)	0.00171 (16)
O17	0.0251 (2)	0.0155 (2)	0.01450 (19)	−0.00279 (17)	0.00197 (17)	0.00079 (15)
N12	0.0187 (2)	0.0157 (2)	0.0147 (2)	−0.00090 (17)	0.00432 (17)	−0.00181 (17)
N3	0.0205 (2)	0.0144 (2)	0.0132 (2)	−0.00115 (17)	0.00220 (17)	−0.00289 (16)
N6	0.0265 (3)	0.0163 (2)	0.0143 (2)	−0.0013 (2)	0.00311 (19)	−0.00122 (18)
N11	0.0194 (2)	0.0141 (2)	0.0139 (2)	−0.00025 (17)	0.00404 (17)	−0.00234 (16)
N14	0.0241 (2)	0.0152 (2)	0.0137 (2)	0.00121 (19)	0.00275 (18)	−0.00082 (17)
N4	0.0190 (2)	0.0158 (2)	0.0137 (2)	−0.00094 (17)	0.00235 (17)	−0.00223 (17)
C10	0.0144 (2)	0.0141 (2)	0.0135 (2)	0.00004 (17)	0.00170 (18)	−0.00237 (17)
C5	0.0149 (2)	0.0160 (2)	0.0135 (2)	−0.00038 (18)	0.00204 (18)	−0.00209 (18)
C13	0.0159 (2)	0.0150 (2)	0.0140 (2)	−0.00095 (18)	0.00286 (18)	−0.00155 (18)
C2	0.0153 (2)	0.0154 (2)	0.0139 (2)	−0.00111 (18)	0.00202 (18)	−0.00291 (18)
C16	0.0260 (3)	0.0305 (4)	0.0159 (3)	0.0014 (3)	0.0047 (2)	0.0019 (2)
C8	0.0297 (3)	0.0296 (4)	0.0161 (3)	−0.0003 (3)	0.0069 (2)	0.0003 (2)

Geometric parameters (Å, º)

S7—C5	1.7312 (7)	N3—H3	0.861 (13)
S7—C8	1.8024 (7)	N6—C2	1.3176 (9)
S1—C2	1.7355 (6)	N6—H6A	0.846 (12)
S1—C5	1.7593 (6)	N6—H6B	0.829 (13)
S9—C10	1.7331 (6)	N11—C10	1.3264 (8)
S9—C13	1.7613 (6)	N11—H11	0.913 (14)
S15—C13	1.7278 (7)	N14—C10	1.3164 (9)
S15—C16	1.8043 (8)	N14—H14B	0.808 (13)
O18—H18B	0.836 (15)	N14—H14A	0.876 (13)
O18—H18A	0.780 (14)	N4—C5	1.2923 (8)
O17—H17B	0.827 (15)	C16—H16B	0.9800
O17—H17A	0.796 (14)	C16—H16A	0.9800
N12—C13	1.2932 (8)	C16—H16C	0.9800
N12—N11	1.3791 (8)	C8—H8B	0.9800
N3—C2	1.3280 (8)	C8—H8A	0.9800
N3—N4	1.3781 (8)	C8—H8C	0.9800
C5—S7—C8	99.61 (3)	N11—C10—S9	110.27 (5)
C2—S1—C5	87.51 (3)	N4—C5—S7	124.86 (5)
C10—S9—C13	87.75 (3)	N4—C5—S1	115.35 (5)
C13—S15—C16	100.21 (3)	S7—C5—S1	119.78 (4)
H18B—O18—H18A	108.1 (13)	N12—C13—S15	125.50 (5)
H17B—O17—H17A	105.6 (13)	N12—C13—S9	115.05 (5)
C13—N12—N11	109.69 (5)	S15—C13—S9	119.45 (4)
C2—N3—N4	117.01 (5)	N6—C2—N3	125.04 (6)
C2—N3—H3	124.4 (8)	N6—C2—S1	124.52 (5)
N4—N3—H3	118.4 (8)	N3—C2—S1	110.44 (5)
C2—N6—H6A	118.6 (8)	S15—C16—H16B	109.5
C2—N6—H6B	120.6 (9)	S15—C16—H16A	109.5
H6A—N6—H6B	120.6 (12)	H16B—C16—H16A	109.5
C10—N11—N12	117.23 (5)	S15—C16—H16C	109.5
C10—N11—H11	123.5 (9)	H16B—C16—H16C	109.5
N12—N11—H11	119.3 (9)	H16A—C16—H16C	109.5
C10—N14—H14B	122.1 (9)	S7—C8—H8B	109.5
C10—N14—H14A	119.6 (8)	S7—C8—H8A	109.5
H14B—N14—H14A	117.7 (12)	H8B—C8—H8A	109.5
C5—N4—N3	109.70 (5)	S7—C8—H8C	109.5
N14—C10—N11	125.16 (6)	H8B—C8—H8C	109.5
N14—C10—S9	124.57 (5)	H8A—C8—H8C	109.5
C13—N12—N11—C10	0.74 (8)	C2—S1—C5—S7	179.35 (4)
C2—N3—N4—C5	0.04 (8)	N11—N12—C13—S15	179.19 (5)
N12—N11—C10—N14	178.94 (6)	N11—N12—C13—S9	−0.16 (7)
N12—N11—C10—S9	−0.95 (7)	C16—S15—C13—N12	0.81 (7)
C13—S9—C10—N14	−179.23 (6)	C16—S15—C13—S9	−179.87 (4)
C13—S9—C10—N11	0.67 (5)	C10—S9—C13—N12	−0.29 (5)
N3—N4—C5—S7	−179.17 (5)	C10—S9—C13—S15	−179.68 (4)
N3—N4—C5—S1	−0.44 (7)	N4—N3—C2—N6	−179.72 (6)
C8—S7—C5—N4	−3.94 (7)	N4—N3—C2—S1	0.37 (7)
C8—S7—C5—S1	177.38 (4)	C5—S1—C2—N6	179.60 (6)
C2—S1—C5—N4	0.55 (5)	C5—S1—C2—N3	−0.49 (5)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3···O17	0.861 (13)	1.818 (13)	2.6778 (7)	176.4 (12)
N6—H6A···Cl1	0.846 (12)	2.296 (12)	3.1178 (6)	164.2 (11)
N6—H6B···Cl2^i	0.829 (13)	2.392 (13)	3.2139 (7)	171.4 (13)
N11—H11···O18	0.914 (14)	1.751 (14)	2.6632 (7)	176.7 (13)
N14—H14A···Cl2	0.877 (12)	2.289 (12)	3.1287 (6)	160.3 (11)
N14—H14B···Cl1^ii	0.807 (13)	2.461 (13)	3.2648 (6)	173.6 (13)
O17—H17A···Cl2^i	0.796 (14)	2.373 (14)	3.1593 (5)	169.8 (14)
O17—H17B···Cl2^iii	0.826 (15)	2.340 (15)	3.1649 (6)	175.5 (14)
O18—H18A···Cl1^ii	0.780 (13)	2.414 (13)	3.1708 (5)	163.8 (13)
O18—H18B···Cl1^iv	0.837 (15)	2.318 (15)	3.1517 (6)	174.1 (14)

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