Poly[di-μ₂-aqua-μ₄-chlorido-μ₄-(2-mercaptopyrimidine-4,6-diolato-κ⁴O:O:O′:O′)-disodium(I)]

In the title coordination polymer, [Na₂(C₄H₃N₂O₂S)Cl(H₂O)₂]_n, the Na^I ion lies on a twofold rotation axis and the chloride anion on an inversion center. The Na^I ion is six-coordinated by two O atoms from two zwitterionic 2-mercaptopyrimidine-4,6-diolate ligands (mm2 symmetry), two water O atoms (m symmetry) and two Cl atoms in a distorted octa­hedral geometry. Adjacent Na^I ions are bridged by an olate group, a water mol­ecule and a chloride anion into a three-dimensional network. The crystal structure is further stabil­ized by N—H...Cl, O—H...O and O—H...S hydrogen bonds.

Key indicators

• Single-crystal X-ray study
• T = 290 K
• Mean [sigma](C-C) = 0.002 Å
• R factor = 0.024
• wR factor = 0.062
• Data-to-parameter ratio = 13.8

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT250_ALERT_2_C Large U3/U1 Ratio for Average U(i,j) Tensor ....       2.23
PLAT420_ALERT_2_C D-H Without Acceptor       N1     -   H1     ...          ?
PLAT910_ALERT_3_C Missing # of FCF Reflections Below Th(Min) .....          2

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   3 ALERT level C = Check and explain
   0 ALERT level G = General alerts; check

   0 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
   0 ALERT type 5 Informative message, check

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S1. Comment

2-Mercaptopyrimidine-4,6-diol and its derivatives have been used widely to build organic-inorganic hybrids due to their diverse properties (Carballo et al. 1996). During the course of on-going crystal engineering studies on nickel salts, we obtained two types of crystals different in color, green and colorless. We herein report the crystal structure of the colorless one, the title compound.

The coordination environment around Na^I ion is shown in Fig. 1, with atom numbering scheme. The Na^I ion is six-coordinated in a distorted octahedral geometry by two O atoms from two 2-mercaptopyrimidine-4,6-diolate ligands, two water O atoms and two Cl atoms. The 2-mercaptopyrimidine-4,6-diolate anion serving as a bridging ligand coordinates to four Na^I ions. The crystal structure is stabilized by N—H···Cl, O—H···O and O—H···S hydrogen bonds (Table 1).

Related literature

For organic–inorganic hybrid compounds with 2-mercaptopyrimidine-4,6-diol derivatives, see: Carballo et al. (1996).

S2. Experimental

2-Mercaptopyrimidine-4,6-diol (1.44 g, 10 mmol) and NiCl₂.6H2O (3.28 g, 10 mmol) were dissolved in hot water (20 ml) and the pH value was adjusted to about 5 by using dilute NaOH solution with stirring. The mixture was heated for one hour and then cooled to room temperature. The precipitate was washed by dilute HCl and the filtrate was allowed to evaporate at room temperature for two weeks, generating two types of block crystals, one was colorless and the other was green.

S3. Refinement

C- and N-bound H atoms were positioned geometrically (C—H = 0.93, N—H = 0.86 Å) and refined as riding atom, with U_iso(H) = 1.2U_eq(C,N). Water H atoms were located in a difference Fourier map and refined as riding, with U_iso(H) = 1.5U_eq(O).

Computing details

Data collection: RAPID-AUTO (Rigaku, 1998); cell refinement: RAPID-AUTO (Rigaku, 1998); data reduction: CrystalStructure (Rigaku/MSC, 2002); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: PLATON (Spek, 2009).

Figures

Fig. 1. The asymmetric unit of the title compound, with symmetry-related atoms to complete the ligand and Na coordination. Displacement ellipsoids are drawn at the 30% probability level. [Symmetry codes: (A): 1-x, 1/2-y, z; (B): x, 1-y, 2-z; (C): x, -1/2+y, 2-z; (D): 1/2-x, 1-y, 1/2+z; (E): 1/2-x, -y, 1/2+z; (F) x, -y, 2-z.]

Poly[di-µ₂-aqua-µ₄-chlorido-µ₄-(2-mercaptopyrimidine-4,6-diolato- κ⁴O:O:O':O')-disodium(I)]

Crystal data

[Na2(C4H3N2O2S)Cl(H2O)2]	F(000) = 528
Mr = 260.61	Dx = 1.762 Mg m^−3
Orthorhombic, Imma	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -I 2b 2	Cell parameters from 4272 reflections
a = 16.815 (3) Å	θ = 3.3–27.4°
b = 6.5938 (13) Å	µ = 0.68 mm^−1
c = 8.8587 (18) Å	T = 290 K
V = 982.2 (3) Å^3	Block, colorless
Z = 4	0.12 × 0.11 × 0.09 mm

Data collection

Rigaku R-AXIS RAPID diffractometer	633 independent reflections
Radiation source: rotation anode	581 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.017
ω scans	θmax = 27.4°, θmin = 3.9°
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	h = −21→19
Tmin = 0.923, Tmax = 0.942	k = −8→8
4752 measured reflections	l = −11→11

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)] = 0.024	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.062	H-atom parameters constrained
S = 1.09	w = 1/[σ^2(Fo^2) + (0.0282P)^2 + 1.0461P] where P = (Fo^2 + 2Fc^2)/3
633 reflections	(Δ/σ)max = 0.002
46 parameters	Δρmax = 0.26 e Å^−3
0 restraints	Δρmin = −0.30 e Å^−3

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

	x	y	z	Uiso*/Ueq
C1	0.5000	0.2500	0.7898 (3)	0.0222 (5)
C2	0.42785 (10)	0.2500	1.02887 (18)	0.0174 (3)
C3	0.5000	0.2500	1.1064 (3)	0.0199 (5)
H3	0.5000	0.2500	1.2113	0.024*
Cl1	0.2500	0.2500	0.7500	0.02138 (17)
N1	0.43218 (8)	0.2500	0.87105 (16)	0.0204 (3)
H1	0.3881	0.2500	0.8220	0.025*
Na1	0.25570 (4)	0.5000	1.0000	0.0256 (2)
O1	0.35874 (7)	0.2500	1.08459 (14)	0.0242 (3)
O2	0.16839 (8)	0.2500	1.10168 (15)	0.0294 (3)
H2A	0.1533	0.2500	1.1978	0.044*
H2B	0.1232	0.2500	1.0538	0.044*
S1	0.5000	0.2500	0.60136 (8)	0.0531 (3)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C1	0.0155 (11)	0.0313 (13)	0.0197 (11)	0.000	0.000	0.000
C2	0.0158 (7)	0.0182 (7)	0.0182 (8)	0.000	0.0019 (6)	0.000
C3	0.0178 (11)	0.0262 (12)	0.0158 (10)	0.000	0.000	0.000
Cl1	0.0201 (3)	0.0286 (3)	0.0154 (3)	0.000	−0.0028 (2)	0.000
N1	0.0127 (7)	0.0314 (8)	0.0172 (7)	0.000	−0.0013 (5)	0.000
Na1	0.0288 (4)	0.0236 (4)	0.0245 (4)	0.000	0.000	−0.0031 (3)
O1	0.0141 (6)	0.0382 (7)	0.0204 (6)	0.000	0.0030 (5)	0.000
O2	0.0206 (6)	0.0449 (8)	0.0225 (6)	0.000	0.0013 (5)	0.000
S1	0.0199 (3)	0.1243 (10)	0.0150 (3)	0.000	0.000	0.000

Geometric parameters (Å, º)

C1—N1	1.3484 (19)	N1—H1	0.8600
C1—S1	1.670 (3)	Na1—O2	2.3842 (11)
C2—O1	1.263 (2)	Na1—O1	2.5062 (11)
C2—C3	1.394 (2)	Na1—Cl1^i	2.7625 (4)
C2—N1	1.400 (2)	Na1—Na1^ii	3.2969 (6)
C3—H3	0.9300	O2—H2A	0.8885
Cl1—Na1	2.7625 (4)	O2—H2B	0.8701
N1^iii—C1—N1	115.5 (2)	O2—Na1—Cl1^i	95.07 (3)
N1^iii—C1—S1	122.25 (11)	O2^ii—Na1—Cl1^i	82.47 (3)
N1—C1—S1	122.25 (11)	O1^ii—Na1—Cl1^i	82.60 (3)
O1—C2—C3	127.48 (16)	O1—Na1—Cl1^i	100.18 (3)
O1—C2—N1	115.99 (15)	Cl1—Na1—Cl1^i	176.03 (3)
C3—C2—N1	116.53 (15)	O2—Na1—Na1^ii	133.74 (3)
C2^iii—C3—C2	121.0 (2)	O2^ii—Na1—Na1^ii	46.26 (3)
C2^iii—C3—H3	119.5	O1^ii—Na1—Na1^ii	48.87 (2)
C2—C3—H3	119.5	O1—Na1—Na1^ii	131.13 (2)
Na1—Cl1—Na1^iv	180.0	Cl1—Na1—Na1^ii	126.636 (8)
Na1—Cl1—Na1^v	73.272 (15)	Cl1^i—Na1—Na1^ii	53.364 (8)
Na1^iv—Cl1—Na1^v	106.728 (15)	O2—Na1—Na1^v	46.26 (3)
Na1—Cl1—Na1^vi	106.728 (15)	O2^ii—Na1—Na1^v	133.74 (3)
Na1^iv—Cl1—Na1^vi	73.272 (16)	O1^ii—Na1—Na1^v	131.13 (2)
Na1^v—Cl1—Na1^vi	180.0	O1—Na1—Na1^v	48.87 (2)
C1—N1—C2	125.23 (16)	Cl1—Na1—Na1^v	53.364 (8)
C1—N1—H1	117.4	Cl1^i—Na1—Na1^v	126.636 (8)
C2—N1—H1	117.4	Na1^ii—Na1—Na1^v	180.00 (5)
O2—Na1—O2^ii	103.98 (6)	C2—O1—Na1^v	121.29 (7)
O2—Na1—O1^ii	173.45 (5)	C2—O1—Na1	121.29 (7)
O2^ii—Na1—O1^ii	81.84 (4)	Na1^v—O1—Na1	82.26 (4)
O2—Na1—O1	81.84 (4)	Na1—O2—Na1^v	87.48 (5)
O2^ii—Na1—O1	173.45 (5)	Na1—O2—H2A	122.5
O1^ii—Na1—O1	92.53 (5)	Na1^v—O2—H2A	122.5
O2—Na1—Cl1	82.47 (3)	Na1—O2—H2B	110.7
O2^ii—Na1—Cl1	95.07 (3)	Na1^v—O2—H2B	110.7
O1^ii—Na1—Cl1	100.18 (3)	H2A—O2—H2B	102.6
O1—Na1—Cl1	82.60 (3)

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

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···Cl1	0.86	2.41	3.2457 (15)	165
O2—H2A···O1^vii	0.89	1.94	2.8164 (19)	169
O2—H2B···S1^viii	0.87	2.49	3.3545 (15)	176

Symmetry codes: (vii) −x+1/2, −y+1/2, −z+5/2; (viii) x−1/2, −y+1/2, −z+3/2.