Supra­molecular hydrogen-bonding patterns in the organic–inorganic hybrid compound bis­(4-amino-5-chloro-2,6-di­methyl­pyrimidinium) tetra­thio­cyanato­zinc(II)–4-amino-5-chloro-2,6-di­methyl­pyrimidine–water (1/2/2)

Zinc thio­cyanate complexes have been found to be biologically active compounds. Zinc is also an essential element for the normal function of most organisms and is the main constituent in a number of metalloenzyme proteins. Pyrimidine and amino­pyrimidine derivatives are biologically very important as they are components of nucleic acids. Thio­cyanate ions can bridge metal ions by employing both their N and S atoms for coordination. They can play an important role in assembling different coordination structures and yield an inter­esting variety of one-, two- and three-dimensional polymeric metal–thio­cyanate supra­molecular frameworks. The structure of a new zinc thio­cyanate–amino­pyrimidine organic–inorganic compound, (C₆H₉ClN₃)₂[Zn(NCS)₄]·2C₆H₈ClN₃·2H₂O, is reported. The asymmetric unit consist of half a tetra­thio­cyanato­zinc(II) dianion, an uncoordinated 4-amino-5-chloro-2,6-di­methyl­pyrimidinium cation, a 4-amino-5-chloro-2,6-di­methyl­pyrimidine mol­ecule and a water mol­ecule. The Zn^II atom adopts a distorted tetra­hedral coordination geometry and is coordinated by four N atoms from the thio­cyanate anions. The Zn^II atom is located on a special position (twofold axis of symmetry). The pyrimidinium cation and the pyrimidine mol­ecule are not coordinated to the Zn^II atom, but are hydrogen bonded to the uncoordinated water mol­ecules and the metal-coordinated thio­cyanate ligands. The pyrimidine mol­ecules and pyrimidinium cations also form base-pair-like structures with an R₂²(8) ring motif via N—H...N hydrogen bonds. The crystal structure is further stabilized by inter­molecular N—H...O, O—H...S, N—H...S and O—H...N hydrogen bonds, by intra­molecular N—H...Cl and C—H...Cl hydrogen bonds, and also by π–π stacking inter­actions.

Computing details

Data collection: APEX2 (Bruker, 2014); cell refinement: SAINT (Bruker, 2014); data reduction: SAINT (Bruker, 2014); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2013 (Sheldrick, 2015) and SHELXLE (Hübschle et al., 2011); molecular graphics: PLATON (Spek, 2009); software used to prepare material for publication: PLATON (Spek, 2009) and publCIF (Westrip, 2010).

Bis(4-amino-5-chloro-2,6-dimethylpyrimidinium) tetrathiocyanatozinc(II)–4-amino-5-chloro-2,6-dimethylpyrimidine–water (1/2/2)

Crystal data

(C6H9ClN3)[Zn(NCS)4]·2C6H8ClN3·2H2O	F(000) = 1984
Mr = 966.15	Dx = 1.477 Mg m^−3
Monoclinic, C2/c	Mo Kα radiation, λ = 0.71073 Å
a = 19.4354 (7) Å	Cell parameters from 8426 reflections
b = 16.7556 (6) Å	θ = 2.4–30.5°
c = 15.3266 (6) Å	µ = 1.05 mm^−1
β = 119.4829 (11)°	T = 100 K
V = 4344.8 (3) Å^3	Block, colourless
Z = 4	0.27 × 0.21 × 0.13 mm

Data collection

Bruker D8 Quest CMOS diffractometer	6507 independent reflections
Radiation source: I-mu-S microsource X-ray tube	4548 reflections with I > 2σ(I)
Laterally graded multilayer (Goebel) mirror monochromator	Rint = 0.054
ω and φ scans	θmax = 30.6°, θmin = 2.4°
Absorption correction: multi-scan (APEX2; Bruker, 2014)	h = −27→25
Tmin = 0.664, Tmax = 0.746	k = −23→23
25175 measured reflections	l = −19→21

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)] = 0.046	Hydrogen site location: mixed
wR(F^2) = 0.095	H atoms treated by a mixture of independent and constrained refinement
S = 1.02	w = 1/[σ^2(Fo^2) + (0.0317P)^2 + 7.8231P] where P = (Fo^2 + 2Fc^2)/3
6507 reflections	(Δ/σ)max < 0.001
259 parameters	Δρmax = 0.43 e Å^−3
2 restraints	Δρmin = −0.41 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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
C1	0.11718 (13)	0.10092 (13)	0.38335 (17)	0.0229 (5)
C2	0.04852 (13)	0.36488 (14)	0.15248 (17)	0.0225 (5)
N1	0.08331 (12)	0.15844 (12)	0.34275 (17)	0.0326 (5)
N2	0.03536 (12)	0.30479 (12)	0.17978 (16)	0.0297 (5)
O1	0.24989 (10)	−0.01341 (10)	0.21097 (13)	0.0255 (4)
H1A	0.2945 (12)	−0.0248 (17)	0.2575 (17)	0.038*
H1B	0.2567 (17)	0.0244 (14)	0.180 (2)	0.038*
S1	0.16709 (4)	0.02232 (3)	0.44438 (5)	0.02800 (14)
S2	0.06662 (4)	0.44762 (3)	0.11161 (4)	0.02462 (13)
Zn1	0.0000	0.23105 (2)	0.2500	0.02289 (10)
N1A	0.34484 (10)	0.36431 (10)	0.37009 (13)	0.0184 (4)
H1N	0.3164	0.4078	0.3593	0.022*
C2A	0.41367 (13)	0.36956 (13)	0.36986 (16)	0.0192 (4)
N3A	0.45872 (10)	0.30678 (10)	0.38336 (13)	0.0179 (4)
C4A	0.43393 (12)	0.23410 (12)	0.39739 (16)	0.0170 (4)
C5A	0.36274 (13)	0.22810 (12)	0.40210 (16)	0.0174 (4)
C6A	0.31731 (12)	0.29419 (13)	0.38638 (16)	0.0177 (4)
C7A	0.43807 (14)	0.44973 (13)	0.3525 (2)	0.0269 (5)
H7AA	0.4931	0.4476	0.3672	0.040*
H7AB	0.4331	0.4889	0.3965	0.040*
H7AC	0.4040	0.4653	0.2824	0.040*
C8A	0.23945 (13)	0.29757 (14)	0.38287 (18)	0.0237 (5)
H8AA	0.2002	0.3220	0.3196	0.036*
H8AB	0.2443	0.3296	0.4391	0.036*
H8AC	0.2225	0.2434	0.3875	0.036*
Cl1A	0.33386 (3)	0.13573 (3)	0.42265 (5)	0.02680 (13)
N4A	0.47755 (11)	0.17171 (11)	0.40456 (15)	0.0233 (4)
H4A1	0.5208	0.1779	0.4003	0.028*
H4A2	0.4635	0.1238	0.4136	0.028*
N1B	0.28300 (10)	0.11725 (11)	0.13255 (14)	0.0191 (4)
C2B	0.35036 (12)	0.12117 (12)	0.12934 (16)	0.0168 (4)
N3B	0.38674 (10)	0.18820 (10)	0.12723 (13)	0.0167 (4)
C4B	0.35258 (12)	0.25812 (12)	0.12673 (15)	0.0165 (4)
C5B	0.28012 (12)	0.25815 (12)	0.12759 (16)	0.0170 (4)
C6B	0.24691 (12)	0.18685 (13)	0.13106 (16)	0.0179 (4)
C7B	0.38767 (14)	0.04338 (13)	0.12699 (19)	0.0244 (5)
H7BA	0.4131	0.0491	0.0858	0.037*
H7BB	0.3469	0.0019	0.0983	0.037*
H7BC	0.4273	0.0283	0.1953	0.037*
C8B	0.17104 (14)	0.17983 (14)	0.13403 (19)	0.0259 (5)
H8BA	0.1420	0.2304	0.1126	0.039*
H8BB	0.1828	0.1675	0.2025	0.039*
H8BC	0.1387	0.1370	0.0889	0.039*
Cl1B	0.23541 (3)	0.34875 (3)	0.12316 (4)	0.02473 (13)
N4B	0.38898 (11)	0.32520 (10)	0.12500 (14)	0.0226 (4)
H4B1	0.4339	0.3228	0.1242	0.027*
H4B2	0.3680	0.3718	0.1246	0.027*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C1	0.0204 (11)	0.0214 (11)	0.0217 (12)	−0.0055 (9)	0.0062 (10)	−0.0041 (9)
C2	0.0179 (10)	0.0260 (12)	0.0193 (11)	0.0077 (9)	0.0060 (9)	−0.0005 (9)
N1	0.0258 (11)	0.0246 (11)	0.0343 (12)	0.0006 (9)	0.0048 (10)	0.0048 (9)
N2	0.0263 (11)	0.0291 (11)	0.0319 (12)	0.0061 (9)	0.0130 (9)	0.0062 (9)
O1	0.0242 (8)	0.0232 (8)	0.0265 (9)	−0.0089 (7)	0.0104 (7)	0.0021 (7)
S1	0.0309 (3)	0.0168 (3)	0.0271 (3)	0.0021 (2)	0.0072 (3)	−0.0002 (2)
S2	0.0273 (3)	0.0199 (3)	0.0242 (3)	0.0060 (2)	0.0107 (3)	0.0025 (2)
Zn1	0.01937 (19)	0.01837 (18)	0.0243 (2)	0.000	0.00560 (16)	0.000
N1A	0.0158 (9)	0.0164 (9)	0.0205 (10)	0.0052 (7)	0.0070 (8)	0.0006 (7)
C2A	0.0190 (10)	0.0180 (10)	0.0183 (11)	0.0024 (8)	0.0074 (9)	0.0004 (8)
N3A	0.0178 (9)	0.0177 (9)	0.0175 (9)	0.0021 (7)	0.0082 (7)	0.0012 (7)
C4A	0.0189 (10)	0.0185 (10)	0.0137 (10)	0.0030 (8)	0.0082 (8)	0.0012 (8)
C5A	0.0198 (10)	0.0169 (10)	0.0163 (10)	0.0002 (8)	0.0094 (9)	0.0006 (8)
C6A	0.0168 (10)	0.0211 (10)	0.0143 (10)	0.0005 (8)	0.0069 (9)	−0.0022 (8)
C7A	0.0253 (12)	0.0171 (11)	0.0397 (15)	0.0019 (9)	0.0169 (11)	0.0026 (10)
C8A	0.0180 (11)	0.0259 (12)	0.0283 (13)	0.0009 (9)	0.0122 (10)	−0.0020 (10)
Cl1A	0.0304 (3)	0.0187 (3)	0.0396 (3)	0.0007 (2)	0.0235 (3)	0.0031 (2)
N4A	0.0258 (10)	0.0169 (9)	0.0364 (12)	0.0057 (8)	0.0223 (9)	0.0063 (8)
N1B	0.0195 (9)	0.0184 (9)	0.0220 (10)	−0.0009 (7)	0.0124 (8)	−0.0009 (7)
C2B	0.0171 (10)	0.0167 (10)	0.0170 (11)	−0.0001 (8)	0.0088 (9)	−0.0004 (8)
N3B	0.0176 (9)	0.0159 (8)	0.0182 (9)	−0.0006 (7)	0.0099 (7)	0.0000 (7)
C4B	0.0199 (10)	0.0165 (10)	0.0119 (10)	0.0003 (8)	0.0070 (8)	−0.0002 (8)
C5B	0.0200 (10)	0.0169 (10)	0.0143 (10)	0.0042 (8)	0.0085 (9)	−0.0012 (8)
C6B	0.0165 (10)	0.0220 (11)	0.0144 (10)	0.0000 (8)	0.0071 (9)	−0.0017 (8)
C7B	0.0254 (12)	0.0182 (11)	0.0364 (14)	0.0027 (9)	0.0205 (11)	0.0023 (10)
C8B	0.0222 (11)	0.0302 (12)	0.0314 (14)	0.0006 (10)	0.0179 (11)	−0.0024 (10)
Cl1B	0.0307 (3)	0.0211 (3)	0.0240 (3)	0.0088 (2)	0.0147 (2)	0.0002 (2)
N4B	0.0258 (10)	0.0154 (9)	0.0296 (11)	−0.0016 (7)	0.0160 (9)	−0.0010 (8)

Geometric parameters (Å, º)

C1—N1	1.160 (3)	C8A—H8AA	0.9800
C1—S1	1.630 (2)	C8A—H8AB	0.9800
C2—N2	1.166 (3)	C8A—H8AC	0.9800
C2—S2	1.629 (3)	N4A—H4A1	0.8800
N1—Zn1	1.964 (2)	N4A—H4A2	0.8800
N2—Zn1	1.971 (2)	N1B—C2B	1.336 (3)
O1—H1A	0.829 (17)	N1B—C6B	1.355 (3)
O1—H1B	0.840 (17)	C2B—N3B	1.336 (3)
Zn1—N1^i	1.964 (2)	C2B—C7B	1.501 (3)
Zn1—N2^i	1.971 (2)	N3B—C4B	1.345 (3)
N1A—C2A	1.342 (3)	C4B—N4B	1.335 (3)
N1A—C6A	1.364 (3)	C4B—C5B	1.415 (3)
N1A—H1N	0.8800	C5B—C6B	1.371 (3)
C2A—N3A	1.318 (3)	C5B—Cl1B	1.734 (2)
C2A—C7A	1.491 (3)	C6B—C8B	1.502 (3)
N3A—C4A	1.365 (3)	C7B—H7BA	0.9800
C4A—N4A	1.316 (3)	C7B—H7BB	0.9800
C4A—C5A	1.424 (3)	C7B—H7BC	0.9800
C5A—C6A	1.362 (3)	C8B—H8BA	0.9800
C5A—Cl1A	1.727 (2)	C8B—H8BB	0.9800
C6A—C8A	1.489 (3)	C8B—H8BC	0.9800
C7A—H7AA	0.9800	N4B—H4B1	0.8800
C7A—H7AB	0.9800	N4B—H4B2	0.8800
C7A—H7AC	0.9800
N1—C1—S1	177.7 (2)	C6A—C8A—H8AC	109.5
N2—C2—S2	178.4 (2)	H8AA—C8A—H8AC	109.5
C1—N1—Zn1	161.95 (19)	H8AB—C8A—H8AC	109.5
C2—N2—Zn1	159.1 (2)	C4A—N4A—H4A1	120.0
H1A—O1—H1B	106 (3)	C4A—N4A—H4A2	120.0
N1—Zn1—N1^i	103.44 (12)	H4A1—N4A—H4A2	120.0
N1—Zn1—N2^i	112.20 (9)	C2B—N1B—C6B	117.74 (18)
N1^i—Zn1—N2^i	113.50 (9)	N1B—C2B—N3B	125.61 (19)
N1—Zn1—N2	113.50 (9)	N1B—C2B—C7B	116.88 (18)
N1^i—Zn1—N2	112.20 (9)	N3B—C2B—C7B	117.51 (18)
N2^i—Zn1—N2	102.37 (12)	C2B—N3B—C4B	117.83 (18)
C2A—N1A—C6A	122.56 (18)	N4B—C4B—N3B	117.94 (19)
C2A—N1A—H1N	118.7	N4B—C4B—C5B	122.64 (19)
C6A—N1A—H1N	118.7	N3B—C4B—C5B	119.42 (18)
N3A—C2A—N1A	122.2 (2)	C6B—C5B—C4B	119.32 (19)
N3A—C2A—C7A	120.1 (2)	C6B—C5B—Cl1B	121.87 (16)
N1A—C2A—C7A	117.66 (19)	C4B—C5B—Cl1B	118.81 (16)
C2A—N3A—C4A	118.54 (18)	N1B—C6B—C5B	120.05 (19)
N4A—C4A—N3A	117.31 (19)	N1B—C6B—C8B	116.09 (19)
N4A—C4A—C5A	122.80 (19)	C5B—C6B—C8B	123.9 (2)
N3A—C4A—C5A	119.88 (18)	C2B—C7B—H7BA	109.5
C6A—C5A—C4A	119.67 (19)	C2B—C7B—H7BB	109.5
C6A—C5A—Cl1A	121.35 (17)	H7BA—C7B—H7BB	109.5
C4A—C5A—Cl1A	118.92 (16)	C2B—C7B—H7BC	109.5
C5A—C6A—N1A	117.02 (19)	H7BA—C7B—H7BC	109.5
C5A—C6A—C8A	126.6 (2)	H7BB—C7B—H7BC	109.5
N1A—C6A—C8A	116.35 (19)	C6B—C8B—H8BA	109.5
C2A—C7A—H7AA	109.5	C6B—C8B—H8BB	109.5
C2A—C7A—H7AB	109.5	H8BA—C8B—H8BB	109.5
H7AA—C7A—H7AB	109.5	C6B—C8B—H8BC	109.5
C2A—C7A—H7AC	109.5	H8BA—C8B—H8BC	109.5
H7AA—C7A—H7AC	109.5	H8BB—C8B—H8BC	109.5
H7AB—C7A—H7AC	109.5	C4B—N4B—H4B1	120.0
C6A—C8A—H8AA	109.5	C4B—N4B—H4B2	120.0
C6A—C8A—H8AB	109.5	H4B1—N4B—H4B2	120.0
H8AA—C8A—H8AB	109.5
C6A—N1A—C2A—N3A	1.4 (3)	C6B—N1B—C2B—N3B	1.7 (3)
C6A—N1A—C2A—C7A	−179.2 (2)	C6B—N1B—C2B—C7B	−177.67 (19)
N1A—C2A—N3A—C4A	0.4 (3)	N1B—C2B—N3B—C4B	−1.1 (3)
C7A—C2A—N3A—C4A	−178.9 (2)	C7B—C2B—N3B—C4B	178.3 (2)
C2A—N3A—C4A—N4A	176.0 (2)	C2B—N3B—C4B—N4B	179.76 (19)
C2A—N3A—C4A—C5A	−3.1 (3)	C2B—N3B—C4B—C5B	−0.5 (3)
N4A—C4A—C5A—C6A	−174.9 (2)	N4B—C4B—C5B—C6B	−178.9 (2)
N3A—C4A—C5A—C6A	4.0 (3)	N3B—C4B—C5B—C6B	1.4 (3)
N4A—C4A—C5A—Cl1A	2.4 (3)	N4B—C4B—C5B—Cl1B	1.6 (3)
N3A—C4A—C5A—Cl1A	−178.60 (15)	N3B—C4B—C5B—Cl1B	−178.10 (15)
C4A—C5A—C6A—N1A	−2.2 (3)	C2B—N1B—C6B—C5B	−0.8 (3)
Cl1A—C5A—C6A—N1A	−179.51 (16)	C2B—N1B—C6B—C8B	179.6 (2)
C4A—C5A—C6A—C8A	176.3 (2)	C4B—C5B—C6B—N1B	−0.7 (3)
Cl1A—C5A—C6A—C8A	−1.0 (3)	Cl1B—C5B—C6B—N1B	178.75 (16)
C2A—N1A—C6A—C5A	−0.4 (3)	C4B—C5B—C6B—C8B	178.9 (2)
C2A—N1A—C6A—C8A	−179.1 (2)	Cl1B—C5B—C6B—C8B	−1.6 (3)

Symmetry code: (i) −x, y, −z+1/2.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1A···S2^ii	0.83 (2)	2.49 (2)	3.316 (2)	175 (3)
O1—H1B···N1B	0.84 (3)	1.89 (3)	2.723 (2)	170 (3)
N1A—H1N···O1^iii	0.88	1.79	2.623 (2)	158
N4A—H4A1···N3B^iv	0.88	2.05	2.922 (3)	173
N4B—H4B1···N3A^iv	0.88	2.16	3.041 (3)	175
N4B—H4B2···S1^iii	0.88	2.69	3.4766 (18)	150
N4A—H4A2···Cl1A	0.88	2.60	3.000 (2)	109
N4B—H4B2···Cl1B	0.88	2.60	2.997 (2)	109
C8A—H8AC···Cl1A	0.98	2.66	3.161 (2)	112
C8B—H8BA···Cl1B	0.98	2.64	3.132 (2)	111

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