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

Li, B.; Li, W.; Ye, L.; Hou, G.-F.; Wu, L.-X.

doi:10.1107/S1600536810045836

metal-organic compounds

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ISSN: 2056-9890

Volume 66| Part 12| December 2010| Page m1546

https://doi.org/10.1107/S1600536810045836

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

Bao Li,^a Wen Li,^a Ling Ye,^a Guang-Feng Hou ^a and Li-Xin Wu ^a ^*

^aState Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, People's Republic of China
^*Correspondence e-mail: wulx@jlu.edu.cn

(Received 5 November 2010; accepted 8 November 2010; online 13 November 2010)

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.

Related literature

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

Experimental

Crystal data

[Na₂(C₄H₃N₂O₂S)Cl(H₂O)₂]
M_r = 260.61
Orthorhombic, I m m a
a = 16.815 (3) Å
b = 6.5938 (13) Å
c = 8.8587 (18) Å
V = 982.2 (3) Å³
Z = 4
Mo Kα radiation
μ = 0.68 mm⁻¹
T = 290 K
0.12 × 0.11 × 0.09 mm

Data collection

Rigaku R-AXIS RAPID diffractometer
Absorption correction: multi-scan (ABSCOR; Higashi, 1995 ) T_min = 0.923, T_max = 0.942
4752 measured reflections
633 independent reflections
581 reflections with I > 2σ(I)
R_int = 0.017

Refinement

R[F² > 2σ(F²)] = 0.024
wR(F²) = 0.062
S = 1.09
633 reflections
46 parameters
H-atom parameters constrained
Δρ_max = 0.26 e Å⁻³
Δρ_min = −0.30 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

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⋯O1ⁱ	0.89	1.94	2.8164 (19)	169
O2—H2B⋯S1ⁱⁱ	0.87	2.49	3.3545 (15)	176
Symmetry codes: (i) $[-x+{\script{1\over 2}}, -y+{\script{1\over 2}}, -z+{\script{5\over 2}}]$ ; (ii) $[x-{\script{1\over 2}}, -y+{\script{1\over 2}}, -z+{\script{3\over 2}}]$ .

Data collection: RAPID-AUTO (Rigaku, 1998 ); cell refinement: RAPID-AUTO; 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 ).

Supporting information

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S1600536810045836/hy2376sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536810045836/hy2376Isup2.hkl

checkCIF report

Comment top

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 top

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

Experimental top

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.

Structure description top

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

Computing details top

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 top

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)] top

Crystal data top

[Na₂(C₄H₃N₂O₂S)Cl(H₂O)₂]	F(000) = 528
M_r = 260.61	D_x = 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) Å³	Block, colorless
Z = 4	0.12 × 0.11 × 0.09 mm

Data collection top

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

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.024	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.062	H-atom parameters constrained
S = 1.09	w = 1/[σ²(F_o²) + (0.0282P)² + 1.0461P] where P = (F_o² + 2F_c²)/3
633 reflections	(Δ/σ)_max = 0.002
46 parameters	Δρ_max = 0.26 e Å⁻³
0 restraints	Δρ_min = −0.30 e Å⁻³

Crystal data top

[Na₂(C₄H₃N₂O₂S)Cl(H₂O)₂]	V = 982.2 (3) Å³
M_r = 260.61	Z = 4
Orthorhombic, Imma	Mo Kα radiation
a = 16.815 (3) Å	µ = 0.68 mm⁻¹
b = 6.5938 (13) Å	T = 290 K
c = 8.8587 (18) Å	0.12 × 0.11 × 0.09 mm

Data collection top

Rigaku R-AXIS RAPID diffractometer	633 independent reflections
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	581 reflections with I > 2σ(I)
T_min = 0.923, T_max = 0.942	R_int = 0.017
4752 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.024	0 restraints
wR(F²) = 0.062	H-atom parameters constrained
S = 1.09	Δρ_max = 0.26 e Å⁻³
633 reflections	Δρ_min = −0.30 e Å⁻³
46 parameters

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
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 (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
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) top

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—Cl1ⁱ	2.7625 (4)
C2—N1	1.400 (2)	Na1—Na1ⁱⁱ	3.2969 (6)
C3—H3	0.9300	O2—H2A	0.8885
Cl1—Na1	2.7625 (4)	O2—H2B	0.8701

N1ⁱⁱⁱ—C1—N1	115.5 (2)	O2—Na1—Cl1ⁱ	95.07 (3)
N1ⁱⁱⁱ—C1—S1	122.25 (11)	O2ⁱⁱ—Na1—Cl1ⁱ	82.47 (3)
N1—C1—S1	122.25 (11)	O1ⁱⁱ—Na1—Cl1ⁱ	82.60 (3)
O1—C2—C3	127.48 (16)	O1—Na1—Cl1ⁱ	100.18 (3)
O1—C2—N1	115.99 (15)	Cl1—Na1—Cl1ⁱ	176.03 (3)
C3—C2—N1	116.53 (15)	O2—Na1—Na1ⁱⁱ	133.74 (3)
C2ⁱⁱⁱ—C3—C2	121.0 (2)	O2ⁱⁱ—Na1—Na1ⁱⁱ	46.26 (3)
C2ⁱⁱⁱ—C3—H3	119.5	O1ⁱⁱ—Na1—Na1ⁱⁱ	48.87 (2)
C2—C3—H3	119.5	O1—Na1—Na1ⁱⁱ	131.13 (2)
Na1—Cl1—Na1^iv	180.0	Cl1—Na1—Na1ⁱⁱ	126.636 (8)
Na1—Cl1—Na1^v	73.272 (15)	Cl1ⁱ—Na1—Na1ⁱⁱ	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)	O2ⁱⁱ—Na1—Na1^v	133.74 (3)
Na1^iv—Cl1—Na1^vi	73.272 (16)	O1ⁱⁱ—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	Cl1ⁱ—Na1—Na1^v	126.636 (8)
C2—N1—H1	117.4	Na1ⁱⁱ—Na1—Na1^v	180.00 (5)
O2—Na1—O2ⁱⁱ	103.98 (6)	C2—O1—Na1^v	121.29 (7)
O2—Na1—O1ⁱⁱ	173.45 (5)	C2—O1—Na1	121.29 (7)
O2ⁱⁱ—Na1—O1ⁱⁱ	81.84 (4)	Na1^v—O1—Na1	82.26 (4)
O2—Na1—O1	81.84 (4)	Na1—O2—Na1^v	87.48 (5)
O2ⁱⁱ—Na1—O1	173.45 (5)	Na1—O2—H2A	122.5
O1ⁱⁱ—Na1—O1	92.53 (5)	Na1^v—O2—H2A	122.5
O2—Na1—Cl1	82.47 (3)	Na1—O2—H2B	110.7
O2ⁱⁱ—Na1—Cl1	95.07 (3)	Na1^v—O2—H2B	110.7
O1ⁱⁱ—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) top

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.

Experimental details

Crystal data
Chemical formula	[Na₂(C₄H₃N₂O₂S)Cl(H₂O)₂]
M_r	260.61
Crystal system, space group	Orthorhombic, Imma
Temperature (K)	290
a, b, c (Å)	16.815 (3), 6.5938 (13), 8.8587 (18)
V (Å³)	982.2 (3)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.68
Crystal size (mm)	0.12 × 0.11 × 0.09

Data collection
Diffractometer	Rigaku R-AXIS RAPID
Absorption correction	Multi-scan (ABSCOR; Higashi, 1995)
T_min, T_max	0.923, 0.942
No. of measured, independent and observed [I > 2σ(I)] reflections	4752, 633, 581
R_int	0.017
(sin θ/λ)_max (Å⁻¹)	0.647

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.024, 0.062, 1.09
No. of reflections	633
No. of parameters	46
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.26, −0.30

Computer programs: RAPID-AUTO (Rigaku, 1998), CrystalStructure (Rigaku/MSC, 2002), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008), PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top

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···O1ⁱ	0.89	1.94	2.8164 (19)	169
O2—H2B···S1ⁱⁱ	0.87	2.49	3.3545 (15)	176

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

Acknowledgements

This work was supported financially by the National Basic Research Program of China (grant No. 2007CB808003) and the National Natural Science Foundation of China (grant Nos. 20973082, 20921003, 20703019).

References

Carballo, R., Casas, J. S., Garcia-Tasende, M. S., Sanchez, A., Sordo, J. & Vazquez-Lopez, E. M. (1996). J. Organomet. Chem. 525, 49–55. CSD CrossRef CAS Web of Science Google Scholar
Higashi, T. (1995). ABSCOR. Rigaku Corporation, Tokyo, Japan. Google Scholar
Rigaku (1998). RAPID-AUTO. Rigaku Corporation, Tokyo, Japan. Google Scholar
Rigaku/MSC (2002). CrystalStructure. Rigaku/MSC Inc., The Woodlands, Texas, USA. Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Spek, A. L. (2009). Acta Cryst. D65, 148–155. Web of Science CrossRef CAS IUCr Journals Google Scholar

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