Tetra­aqua­bis­{2-[4-(4-pyrid­yl)pyrimidin-2-ylsulfan­yl]acetato}­zinc

Zhu, H.-B.; Lu, X.

doi:10.1107/S160053681102993X

metal-organic compounds

CRYSTALLOGRAPHIC
COMMUNICATIONS

ISSN: 2056-9890

Volume 67| Part 8| August 2011| Page m1169

doi:10.1107/S160053681102993X

Open

access

Tetraaquabis{2-[4-(4-pyridyl)pyrimidin-2-ylsulfanyl]acetato}zinc

Hai-Bin Zhu ^a ^* and Xin Lu ^a

^aSchool of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, People's Republic of China
^*Correspondence e-mail: zhuhaibin@seu.edu.cn

(Received 13 July 2011; accepted 25 July 2011; online 30 July 2011)

In the title compound, [Zn(C₁₁H₈N₃O₂S)₂(H₂O)₄], the Zn^II ion lies on an inversion centre and is coordinated by four water molecules and two N atoms from two 2-[4-(4-pyridyl)pyrimidin-2-ylsulfanyl]acetate (L) ligands in a distorted octahedral geometry. In L, the pyridine and pyrimidine rings are twisted at an angle of 11.2 (1)°. The coordinated water molecules and the acetate groups are involved in the formation of a three-dimensional hydrogen-bonded network, which consolidates the crystal packing.

Related literature

For a related structure, see: Zhu et al. (2009 ).

Experimental

Crystal data

[Zn(C₁₁H₈N₃O₂S)₂(H₂O)₄]
M_r = 630.00
Orthorhombic, P b c a
a = 7.199 (7) Å
b = 11.792 (11) Å
c = 28.77 (3) Å
V = 2442 (4) Å³
Z = 4
Mo Kα radiation
μ = 1.24 mm⁻¹
T = 298 K
0.20 × 0.20 × 0.15 mm

Data collection

Bruker APEXII CCD area-detector diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2001 ) T_min = 0.780, T_max = 0.830
16776 measured reflections
2465 independent reflections
1836 reflections with I > 2σ(I)
R_int = 0.051

Refinement

R[F² > 2σ(F²)] = 0.033
wR(F²) = 0.086
S = 1.02
2465 reflections
190 parameters
4 restraints
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.23 e Å⁻³
Δρ_min = −0.45 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O4—H4WB⋯O2ⁱ	0.81 (2)	1.96 (2)	2.759 (3)	170 (3)
O4—H4WA⋯O1ⁱⁱ	0.82 (2)	1.82 (2)	2.632 (3)	172 (2)
O3—H3WB⋯O2ⁱⁱⁱ	0.84 (2)	1.89 (2)	2.728 (3)	176 (3)
O3—H3WA⋯O2^iv	0.82 (2)	2.24 (2)	3.060 (3)	172 (3)
Symmetry codes: (i) $[-x+{\script{1\over 2}}, -y+1, z+{\script{1\over 2}}]$ ; (ii) $[x+{\script{1\over 2}}, y, -z+{\script{1\over 2}}]$ ; (iii) $[-x, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (iv) $[-x-{\script{1\over 2}}, -y+1, z+{\script{1\over 2}}]$ .

Data collection: APEX2 (Bruker, 2007 ); cell refinement: SAINT-Plus (Bruker, 2007); data reduction: SAINT-Plus; 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: SHELXTL.

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S160053681102993X/cv5136sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S160053681102993X/cv5136Isup2.hkl

checkCIF report

Comment top

In our previous work, we have reported the crystal structure of mononuclear Mn(II) complex with the ligand of 2-(4-(pyridine-3-yl)pyrimidin-2-ylthio)acetic acid (Zhu et al., 2009). Herein, we present a Zn(II) complex with the ligand of 2-(4-(pyridine-4-yl)pyrimidin-2-ylthio)acetic acid.

Similar to the reported Mn(II) coordination compound (Zhu et al., 2009), the Zn(II) center in the title compound also adopts an octahedral coordination geometry defined by four water O atoms in equatorial positions and two N atoms in apical positions (Fig. 1). The Zn—O bond lengths vary from 2.070 (2) to 2.137 (2)Å, and the Zn—N bond length is 2.176 (2) Å. Intermolecular O—H···O hydrogen bonds (Table 1) consolidate the crystal packing.

Related literature top

For a related structure, see: Zhu et al. (2009).

Experimental top

The mixture of Zn(NO₃)₂ (0.1 mmol), L (0.2 mmol) and NaOH (0.2 mmol) in 10 ml of H₂O was stirred for 30 min at room temperature. After filtration, the mother liquid was stood for three weeks to give yellow crystals suitable for X-ray diffraction analysis.

Computing details top

Data collection: APEX2 (Bruker, 2007); cell refinement: SAINT-Plus (Bruker, 2007); data reduction: SAINT-Plus (Bruker, 2007); 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: SHELXTL (Sheldrick, 2008).

Figures top

Fig. 1. The coordination environment around Zn(II) in the title complex with the atom-labeling scheme [symmetry code: (A) -x, -y + 1, -z + 1]. Displacement ellipsoids for non-hydrogen atoms are drawn at the 50% probability level.

Tetraaquabis{2-[4-(4-pyridyl)pyrimidin-2-ylsulfanyl]acetato}zinc top

Crystal data top

[Zn(C₁₁H₈N₃O₂S)₂(H₂O)₄]	F(000) = 1296
M_r = 630.00	D_x = 1.714 Mg m⁻³
Orthorhombic, Pbca	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2ab	Cell parameters from 2465 reflections
a = 7.199 (7) Å	θ = 2.3–25.5°
b = 11.792 (11) Å	µ = 1.24 mm⁻¹
c = 28.77 (3) Å	T = 298 K
V = 2442 (4) Å³	Block, yellow
Z = 4	0.20 × 0.20 × 0.15 mm

Data collection top

Bruker APEXII CCD area-detector diffractometer	2465 independent reflections
Radiation source: fine-focus sealed tube	1836 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.051
ϕ and ω scans	θ_max = 27.1°, θ_min = 1.4°
Absorption correction: multi-scan (SADABS; Bruker, 2001)	h = −8→9
T_min = 0.780, T_max = 0.830	k = −14→14
16776 measured reflections	l = −34→32

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)] = 0.033	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.086	H atoms treated by a mixture of independent and constrained refinement
S = 1.02	w = 1/[σ²(F_o²) + (0.0432P)² + 0.3573P] where P = (F_o² + 2F_c²)/3
2465 reflections	(Δ/σ)_max < 0.001
190 parameters	Δρ_max = 0.23 e Å⁻³
4 restraints	Δρ_min = −0.45 e Å⁻³

Crystal data top

[Zn(C₁₁H₈N₃O₂S)₂(H₂O)₄]	V = 2442 (4) Å³
M_r = 630.00	Z = 4
Orthorhombic, Pbca	Mo Kα radiation
a = 7.199 (7) Å	µ = 1.24 mm⁻¹
b = 11.792 (11) Å	T = 298 K
c = 28.77 (3) Å	0.20 × 0.20 × 0.15 mm

Data collection top

Bruker APEXII CCD area-detector diffractometer	2465 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2001)	1836 reflections with I > 2σ(I)
T_min = 0.780, T_max = 0.830	R_int = 0.051
16776 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.033	4 restraints
wR(F²) = 0.086	H atoms treated by a mixture of independent and constrained refinement
S = 1.02	Δρ_max = 0.23 e Å⁻³
2465 reflections	Δρ_min = −0.45 e Å⁻³
190 parameters

Special details top

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 > 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 (Å²) top

	x	y	z	U_iso*/U_eq
Zn1	0.0000	0.5000	0.5000	0.02474 (14)
S1	0.01224 (8)	0.60147 (5)	0.17445 (2)	0.02955 (17)
N2	0.1353 (3)	0.80094 (16)	0.20795 (6)	0.0297 (5)
N1	0.0402 (3)	0.65524 (16)	0.26077 (6)	0.0264 (5)
O4	0.2360 (2)	0.41441 (14)	0.47861 (5)	0.0314 (4)
H4WB	0.307 (3)	0.396 (2)	0.4993 (7)	0.038*
H4WA	0.302 (3)	0.450 (2)	0.4603 (7)	0.038*
C1	0.0700 (3)	0.6981 (2)	0.21845 (8)	0.0256 (5)
C10	0.0382 (3)	0.6859 (2)	0.12255 (8)	0.0283 (5)
H10A	−0.0412	0.7522	0.1244	0.034*
H10B	0.1658	0.7114	0.1198	0.034*
O1	−0.0740 (3)	0.51902 (14)	0.08678 (6)	0.0396 (5)
C5	0.0435 (3)	0.67551 (18)	0.34366 (8)	0.0236 (5)
C4	0.0801 (3)	0.72292 (19)	0.29679 (7)	0.0241 (5)
C11	−0.0136 (3)	0.6163 (2)	0.08050 (8)	0.0269 (5)
N3	−0.0130 (2)	0.58138 (16)	0.43217 (6)	0.0255 (4)
O2	0.0038 (2)	0.66402 (14)	0.04128 (6)	0.0339 (4)
O3	−0.1746 (3)	0.36656 (14)	0.47517 (6)	0.0342 (4)
H3WB	−0.118 (3)	0.3056 (17)	0.4696 (9)	0.041*
H3WA	−0.269 (3)	0.355 (2)	0.4908 (8)	0.041*
C7	0.0205 (3)	0.6920 (2)	0.42625 (8)	0.0287 (6)
H7A	0.0259	0.7377	0.4525	0.034*
C3	0.1516 (3)	0.83095 (19)	0.28983 (8)	0.0295 (5)
H3B	0.1814	0.8781	0.3147	0.035*
C9	0.0026 (3)	0.5610 (2)	0.34959 (8)	0.0301 (6)
H9A	−0.0059	0.5135	0.3239	0.036*
C8	−0.0249 (3)	0.5184 (2)	0.39326 (8)	0.0309 (6)
H8A	−0.0534	0.4418	0.3962	0.037*
C2	0.1763 (4)	0.86515 (19)	0.24447 (8)	0.0311 (6)
H2B	0.2245	0.9372	0.2391	0.037*
C6	0.0476 (3)	0.7421 (2)	0.38362 (8)	0.0294 (5)
H6A	0.0685	0.8197	0.3815	0.035*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Zn1	0.0297 (2)	0.0257 (2)	0.0188 (2)	0.00061 (16)	0.00071 (16)	−0.00053 (15)
S1	0.0392 (4)	0.0303 (3)	0.0191 (3)	−0.0049 (3)	−0.0001 (3)	0.0019 (2)
N2	0.0318 (11)	0.0314 (11)	0.0259 (10)	−0.0026 (9)	−0.0017 (9)	0.0039 (9)
N1	0.0317 (12)	0.0287 (11)	0.0187 (10)	0.0006 (8)	−0.0007 (8)	0.0016 (8)
O4	0.0326 (10)	0.0363 (10)	0.0255 (9)	0.0049 (8)	0.0041 (8)	0.0036 (8)
C1	0.0233 (12)	0.0312 (13)	0.0222 (12)	0.0020 (10)	−0.0017 (9)	−0.0006 (10)
C10	0.0328 (14)	0.0304 (13)	0.0216 (12)	−0.0034 (10)	0.0017 (10)	0.0032 (10)
O1	0.0562 (12)	0.0353 (10)	0.0274 (10)	−0.0098 (9)	−0.0089 (9)	0.0006 (8)
C5	0.0238 (12)	0.0261 (12)	0.0210 (12)	0.0020 (9)	−0.0029 (9)	0.0013 (10)
C4	0.0218 (12)	0.0287 (12)	0.0217 (12)	0.0019 (10)	−0.0018 (10)	0.0008 (10)
C11	0.0275 (13)	0.0307 (13)	0.0226 (12)	0.0033 (10)	0.0000 (10)	0.0015 (10)
N3	0.0291 (11)	0.0275 (11)	0.0200 (10)	0.0010 (8)	−0.0004 (8)	−0.0019 (8)
O2	0.0474 (11)	0.0340 (10)	0.0203 (9)	0.0031 (8)	0.0014 (7)	0.0017 (7)
O3	0.0373 (11)	0.0329 (10)	0.0325 (10)	−0.0045 (8)	−0.0010 (8)	−0.0016 (8)
C7	0.0347 (14)	0.0288 (13)	0.0225 (12)	0.0031 (10)	−0.0018 (10)	−0.0062 (10)
C3	0.0339 (14)	0.0271 (13)	0.0276 (13)	−0.0002 (10)	−0.0047 (11)	−0.0022 (10)
C9	0.0393 (15)	0.0289 (13)	0.0220 (12)	−0.0023 (11)	−0.0014 (10)	−0.0066 (10)
C8	0.0436 (16)	0.0257 (12)	0.0233 (13)	−0.0046 (11)	−0.0005 (11)	−0.0001 (10)
C2	0.0328 (14)	0.0267 (13)	0.0339 (14)	−0.0042 (11)	−0.0028 (11)	0.0045 (11)
C6	0.0358 (14)	0.0247 (12)	0.0277 (13)	0.0001 (10)	−0.0036 (11)	−0.0015 (10)

Geometric parameters (Å, º) top

Zn1—O4	2.070 (2)	C5—C9	1.393 (3)
Zn1—O4ⁱ	2.070 (2)	C5—C6	1.392 (3)
Zn1—O3ⁱ	2.137 (2)	C5—C4	1.483 (3)
Zn1—O3	2.137 (2)	C4—C3	1.388 (3)
Zn1—N3ⁱ	2.176 (2)	C11—O2	1.267 (3)
Zn1—N3	2.176 (2)	N3—C7	1.337 (3)
S1—C1	1.753 (3)	N3—C8	1.346 (3)
S1—C10	1.804 (3)	O3—H3WB	0.843 (16)
N2—C2	1.328 (3)	O3—H3WA	0.822 (17)
N2—C1	1.335 (3)	C7—C6	1.375 (3)
N1—C1	1.336 (3)	C7—H7A	0.9300
N1—C4	1.339 (3)	C3—C2	1.377 (3)
O4—H4WB	0.810 (16)	C3—H3B	0.9300
O4—H4WA	0.821 (16)	C9—C8	1.367 (4)
C10—C11	1.508 (3)	C9—H9A	0.9300
C10—H10A	0.9700	C8—H8A	0.9300
C10—H10B	0.9700	C2—H2B	0.9300
O1—C11	1.240 (3)	C6—H6A	0.9300

O4—Zn1—O4ⁱ	180.00 (8)	C6—C5—C4	122.3 (2)
O4—Zn1—O3ⁱ	88.60 (9)	N1—C4—C3	121.0 (2)
O4ⁱ—Zn1—O3ⁱ	91.40 (9)	N1—C4—C5	116.1 (2)
O4—Zn1—O3	91.40 (9)	C3—C4—C5	122.9 (2)
O4ⁱ—Zn1—O3	88.60 (9)	O1—C11—O2	125.1 (2)
O3ⁱ—Zn1—O3	180.0	O1—C11—C10	118.2 (2)
O4—Zn1—N3ⁱ	90.94 (7)	O2—C11—C10	116.6 (2)
O4ⁱ—Zn1—N3ⁱ	89.06 (7)	C7—N3—C8	116.3 (2)
O3ⁱ—Zn1—N3ⁱ	89.99 (8)	C7—N3—Zn1	122.44 (15)
O3—Zn1—N3ⁱ	90.01 (8)	C8—N3—Zn1	120.33 (17)
O4—Zn1—N3	89.06 (7)	Zn1—O3—H3WB	113.9 (19)
O4ⁱ—Zn1—N3	90.94 (7)	Zn1—O3—H3WA	114.9 (19)
O3ⁱ—Zn1—N3	90.01 (8)	H3WB—O3—H3WA	111 (3)
O3—Zn1—N3	89.99 (8)	N3—C7—C6	123.9 (2)
N3ⁱ—Zn1—N3	180.0	N3—C7—H7A	118.0
C1—S1—C10	102.37 (13)	C6—C7—H7A	118.0
C2—N2—C1	114.66 (19)	C2—C3—C4	116.9 (2)
C1—N1—C4	116.4 (2)	C2—C3—H3B	121.5
Zn1—O4—H4WB	115.2 (19)	C4—C3—H3B	121.5
Zn1—O4—H4WA	114.8 (18)	C8—C9—C5	119.9 (2)
H4WB—O4—H4WA	104 (3)	C8—C9—H9A	120.0
N2—C1—N1	127.3 (2)	C5—C9—H9A	120.0
N2—C1—S1	120.71 (17)	N3—C8—C9	123.5 (2)
N1—C1—S1	111.96 (18)	N3—C8—H8A	118.2
C11—C10—S1	109.75 (17)	C9—C8—H8A	118.2
C11—C10—H10A	109.7	N2—C2—C3	123.6 (2)
S1—C10—H10A	109.7	N2—C2—H2B	118.2
C11—C10—H10B	109.7	C3—C2—H2B	118.2
S1—C10—H10B	109.7	C7—C6—C5	119.4 (2)
H10A—C10—H10B	108.2	C7—C6—H6A	120.3
C9—C5—C6	116.8 (2)	C5—C6—H6A	120.3
C9—C5—C4	121.0 (2)

Symmetry code: (i) −x, −y+1, −z+1.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O4—H4WB···O2ⁱⁱ	0.81 (2)	1.96 (2)	2.759 (3)	170 (3)
O4—H4WA···O1ⁱⁱⁱ	0.82 (2)	1.82 (2)	2.632 (3)	172 (2)
O3—H3WB···O2^iv	0.84 (2)	1.89 (2)	2.728 (3)	176 (3)
O3—H3WA···O2^v	0.82 (2)	2.24 (2)	3.060 (3)	172 (3)

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

Experimental details

Crystal data
Chemical formula	[Zn(C₁₁H₈N₃O₂S)₂(H₂O)₄]
M_r	630.00
Crystal system, space group	Orthorhombic, Pbca
Temperature (K)	298
a, b, c (Å)	7.199 (7), 11.792 (11), 28.77 (3)
V (Å³)	2442 (4)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	1.24
Crystal size (mm)	0.20 × 0.20 × 0.15

Data collection
Diffractometer	Bruker APEXII CCD area-detector diffractometer
Absorption correction	Multi-scan (SADABS; Bruker, 2001)
T_min, T_max	0.780, 0.830
No. of measured, independent and observed [I > 2σ(I)] reflections	16776, 2465, 1836
R_int	0.051
(sin θ/λ)_max (Å⁻¹)	0.641

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.033, 0.086, 1.02
No. of reflections	2465
No. of parameters	190
No. of restraints	4
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.23, −0.45

Computer programs: APEX2 (Bruker, 2007), SAINT-Plus (Bruker, 2007), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O4—H4WB···O2ⁱ	0.810 (16)	1.957 (17)	2.759 (3)	170 (3)
O4—H4WA···O1ⁱⁱ	0.821 (16)	1.818 (16)	2.632 (3)	172 (2)
O3—H3WB···O2ⁱⁱⁱ	0.843 (16)	1.886 (17)	2.728 (3)	176 (3)
O3—H3WA···O2^iv	0.822 (17)	2.243 (17)	3.060 (3)	172 (3)

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

Acknowledgements

The authors acknowledge the Teaching and Research Programme for Excellent Young Teachers of Southeast University (grant No. 3207041202).

References

Bruker (2001). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Bruker (2007). APEX2 and SAINT-Plus. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Zhu, H.-B., Xu, G. & Sun, Y.-Y. (2009). Acta Cryst. E65, m1126. Web of Science CSD CrossRef IUCr Journals Google Scholar