Diaqua­bis[(pyrimidin-2-ylsulfan­yl)acetato]copper(II) dihydrate

In the title compound, [Cu(C₆H₅N₂O₂S)₂(H₂O)₂]·2H₂O, the Cu atom lies on an inversion centre in a distorted square coordination geometry that consists of two O atoms of two (pyrimidin-2-ylsulfan­yl)acetate ligands [Cu-O = 1.953 (2) Å] and two O atoms of two water mol­ecules [Cu-O = 1.942 (3) Å].

Key indicators

• Single-crystal X-ray study
• T = 273 K
• Mean [sigma](C-C) = 0.007 Å
• R factor = 0.054
• wR factor = 0.125
• Data-to-parameter ratio = 14.4

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT042_ALERT_1_C Calc. and Rep. MoietyFormula Strings Differ ....          ?
PLAT232_ALERT_2_C Hirshfeld Test Diff (M-X)  Cu1    -   O1W     ..       8.48 su
PLAT241_ALERT_2_C Check High      Ueq as Compared to Neighbors for         O1
PLAT242_ALERT_2_C Check Low       Ueq as Compared to Neighbors for        Cu1
PLAT341_ALERT_3_C Low Bond Precision on C-C bonds (x 1000) Ang ...          7
PLAT720_ALERT_4_C Number of Unusual/Non-Standard Label(s) ........          4
PLAT731_ALERT_1_C Bond    Calc     0.84(4), Rep   0.845(10) ......       4.00 su-Rat
              O2W  -H2WA    1.555   1.555
PLAT731_ALERT_1_C Bond    Calc     0.85(3), Rep   0.847(10) ......       3.00 su-Rat
              O2W  -H2WB    1.555   1.555
PLAT731_ALERT_1_C Bond    Calc     0.86(3), Rep   0.858(10) ......       3.00 su-Rat
              O1W  -H1WA    1.555   1.555
PLAT731_ALERT_1_C Bond    Calc     0.85(4), Rep   0.860(10) ......       4.00 su-Rat
              O1W  -H1WB    1.555   1.555
PLAT732_ALERT_1_C Angle   Calc      110(5), Rep   110.3(18) ......       2.78 su-Rat
              H2WA -O2W  -H2WB    1.555   1.555   1.555
PLAT732_ALERT_1_C Angle   Calc      108(4), Rep   108.3(17) ......       2.35 su-Rat
              H1WA -O1W  -H1WB    1.555   1.555   1.555
PLAT735_ALERT_1_C D-H     Calc     0.84(4), Rep   0.845(10) ......       4.00 su-Rat
              O2W  -H2#     1.555   1.555
PLAT736_ALERT_1_C H...A   Calc     1.86(4), Rep   1.860(15) ......       2.67 su-Rat
              H2#  -O1      1.555   1.555

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

   9 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   3 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
   1 ALERT type 4 Improvement, methodology, query or suggestion

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S1. Comment

Following our studies of complexes of 2-pyrimidylthioacetic acid (Ng et al., 1993; Ma et al., 2004; Hao et al., 2005), we report the structure of the title compound, (I). The four-coordinate Cu atom is in a square coordination geometry that is made up of two O atoms of two carboxylate groups and two O atoms of two water molecules (Fig. 1). Hydrogen bonds connect the molecules and the solvent water molecules into a three-dimensional network structure.

S2. Experimental

Cupric nitrate (120.8 mg, 0.5 mmol) was dissolved in water (10 ml). Ammonium hydroxide was added until the solution turned blue. 2-Pyrimidylthioacetic acid (170.2 mg, 1 mmol) was suspended in a small volume of water–ethanol (1:1 v/v); ammonium hydroxide was added until the compound dissolved completely. The two solutions were then mixed. After three weeks, dark-blue crystals were obtained in 65% yield. Analysis found: C 30.41, H 3.83, N 11.82%; calculated for C₁₂H₁₈CuN₄O₈S₂: C 30.20, H 3.91, N 11.78%. IR (cm⁻¹): 3423 (ν_OH for H₂O), 1605, 1384 (ν_as and ν_s for COO⁻), 1551, 1309, 1280.

S3. Refinement

The water H atoms were located in difference Fourier maps and were refined with distance restraints of O—H = 0.85?(1) Å and H···H = 1.39?(1) Å [U_iso(H) = 0.85 Ų]. The aromatic and aliphatic H atoms were placed at calculated positions (C—H = 0.93 and 0.97 Å) and refined using the riding-model approximation, with U_iso(H) = 1.2U_eq(C).

Computing details

Data collection: SMART (Bruker, 2001); cell refinement: SAINT (Bruker, 2001); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEPII (Johnson, 1976); software used to prepare material for publication: SHELXL97.

Figures

Fig. 1. ORTEPII (Johnson, 1976) plot of (I). Displacement ellipsoids are drawn at the 30% probability level. [Symmetry code: (i) 1 − x, 1 − y, 1 − z.]

Diaquabis[(pyrimidin-2-ylsulfanyl)acetato]copper(II) dihydrate

Crystal data

[Cu(C6H5N2O2S)2(H2O)2]·2H2O	F(000) = 486
Mr = 473.96	Dx = 1.709 Mg m^−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 3246 reflections
a = 17.160 (5) Å	θ = 3.6–26.9°
b = 5.1577 (16) Å	µ = 1.46 mm^−1
c = 10.568 (3) Å	T = 273 K
β = 99.942 (5)°	Plate, blue
V = 921.3 (5) Å^3	0.27 × 0.16 × 0.07 mm
Z = 2

Data collection

Bruker APEX 2000 area-detector diffractometer	2009 independent reflections
Radiation source: fine-focus sealed tube	1874 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.056
ϕ and ω scans	θmax = 27.0°, θmin = 2.4°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	h = −21→21
Tmin = 0.694, Tmax = 0.905	k = −6→6
9709 measured reflections	l = −13→13

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)] = 0.054	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.125	H atoms treated by a mixture of independent and constrained refinement
S = 1.16	w = 1/[σ^2(Fo^2) + (0.0443P)^2 + 1.6524P] where P = (Fo^2 + 2Fc^2)/3
2009 reflections	(Δ/σ)max = 0.001
140 parameters	Δρmax = 0.54 e Å^−3
6 restraints	Δρmin = −0.66 e Å^−3

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 > 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 (Ų)

	x	y	z	Uiso*/Ueq
Cu1	0.5000	0.5000	0.5000	0.02570 (19)
S1	0.80407 (6)	0.7913 (2)	0.65446 (11)	0.0500 (3)
O2	0.57506 (14)	0.7306 (5)	0.6050 (2)	0.0319 (5)
O2W	0.62920 (16)	0.1061 (7)	0.3649 (3)	0.0473 (7)
O1	0.66342 (18)	0.4828 (6)	0.5426 (3)	0.0547 (8)
O1W	0.49139 (19)	0.7477 (6)	0.3599 (3)	0.0503 (7)
N2	0.79004 (18)	0.4420 (7)	0.8333 (3)	0.0389 (7)
C4	0.8364 (2)	0.5496 (8)	0.7638 (4)	0.0396 (9)
C6	0.6449 (2)	0.6676 (7)	0.6001 (3)	0.0310 (7)
C5	0.7052 (2)	0.8451 (7)	0.6747 (4)	0.0365 (8)
H5A	0.7024	0.8280	0.7652	0.044*
H5B	0.6911	1.0223	0.6499	0.044*
N1	0.9119 (2)	0.4954 (9)	0.7660 (4)	0.0634 (12)
C2	0.8996 (3)	0.2022 (11)	0.9288 (5)	0.0644 (14)
H2A	0.9225	0.0812	0.9891	0.077*
C3	0.8234 (3)	0.2669 (9)	0.9171 (4)	0.0488 (10)
H3A	0.7926	0.1861	0.9698	0.059*
C1	0.9414 (3)	0.3199 (13)	0.8494 (5)	0.0710 (16)
H1A	0.9942	0.2739	0.8540	0.085*
H1WA	0.5364 (15)	0.792 (9)	0.342 (5)	0.085*
H2WA	0.635 (3)	0.218 (9)	0.424 (4)	0.085*
H2WB	0.6734 (15)	0.074 (11)	0.343 (5)	0.085*
H1WB	0.466 (3)	0.886 (6)	0.371 (6)	0.085*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Cu1	0.0247 (3)	0.0229 (3)	0.0291 (3)	−0.0011 (2)	0.0033 (2)	−0.0005 (2)
S1	0.0337 (5)	0.0594 (7)	0.0555 (7)	−0.0110 (5)	0.0036 (4)	0.0132 (5)
O2	0.0270 (12)	0.0291 (13)	0.0376 (13)	−0.0027 (10)	−0.0003 (10)	−0.0025 (10)
O2W	0.0374 (15)	0.061 (2)	0.0435 (16)	−0.0114 (14)	0.0063 (12)	−0.0132 (14)
O1	0.0423 (16)	0.0485 (19)	0.073 (2)	−0.0024 (13)	0.0098 (15)	−0.0292 (16)
O1W	0.0525 (18)	0.0443 (17)	0.0548 (18)	−0.0013 (14)	0.0107 (15)	0.0078 (15)
N2	0.0314 (16)	0.0449 (19)	0.0402 (17)	0.0028 (14)	0.0057 (13)	−0.0016 (14)
C4	0.0280 (18)	0.047 (2)	0.043 (2)	−0.0017 (16)	0.0016 (15)	−0.0039 (17)
C6	0.0343 (18)	0.0246 (17)	0.0320 (18)	−0.0026 (14)	−0.0001 (14)	0.0011 (14)
C5	0.0314 (18)	0.0303 (19)	0.045 (2)	−0.0018 (15)	−0.0030 (15)	−0.0016 (16)
N1	0.0308 (18)	0.094 (4)	0.066 (3)	0.0047 (19)	0.0133 (17)	0.013 (2)
C2	0.055 (3)	0.083 (4)	0.053 (3)	0.025 (3)	0.005 (2)	0.013 (3)
C3	0.046 (2)	0.056 (3)	0.045 (2)	0.008 (2)	0.0080 (18)	0.005 (2)
C1	0.031 (2)	0.105 (5)	0.076 (3)	0.025 (3)	0.008 (2)	0.013 (3)

Geometric parameters (Å, º)

Cu1—O1W	1.942 (3)	N2—C4	1.297 (5)
Cu1—O1W^i	1.942 (3)	N2—C3	1.324 (5)
Cu1—O2	1.953 (2)	C4—N1	1.322 (5)
Cu1—O2^i	1.953 (2)	C6—C5	1.499 (5)
S1—C4	1.725 (4)	C5—H5A	0.9700
S1—C5	1.768 (4)	C5—H5B	0.9700
O2—C6	1.252 (4)	N1—C1	1.303 (7)
O2W—H2WA	0.845 (10)	C2—C3	1.333 (6)
O2W—H2WB	0.847 (10)	C2—C1	1.340 (7)
O1—C6	1.202 (4)	C2—H2A	0.9300
O1W—H1WA	0.858 (10)	C3—H3A	0.9300
O1W—H1WB	0.860 (10)	C1—H1A	0.9300
O1W—Cu1—O1W^i	180.0	O2—C6—C5	113.5 (3)
O1W—Cu1—O2	89.34 (12)	C6—C5—S1	115.5 (3)
O1W^i—Cu1—O2	90.66 (12)	C6—C5—H5A	108.4
O1W—Cu1—O2^i	90.66 (12)	S1—C5—H5A	108.4
O1W^i—Cu1—O2^i	89.34 (12)	C6—C5—H5B	108.4
O2—Cu1—O2^i	180.00 (11)	S1—C5—H5B	108.4
C4—S1—C5	103.70 (19)	H5A—C5—H5B	107.5
C6—O2—Cu1	111.1 (2)	C1—N1—C4	115.0 (4)
H2WA—O2W—H2WB	110.3 (18)	C3—C2—C1	116.8 (5)
Cu1—O1W—H1WA	113 (4)	C3—C2—H2A	121.6
Cu1—O1W—H1WB	114 (4)	C1—C2—H2A	121.6
H1WA—O1W—H1WB	108.3 (17)	N2—C3—C2	122.5 (4)
C4—N2—C3	115.7 (4)	N2—C3—H3A	118.8
N2—C4—N1	126.5 (4)	C2—C3—H3A	118.8
N2—C4—S1	122.1 (3)	N1—C1—C2	123.5 (4)
N1—C4—S1	111.4 (3)	N1—C1—H1A	118.3
O1—C6—O2	124.4 (3)	C2—C1—H1A	118.3
O1—C6—C5	122.1 (3)

Symmetry code: (i) −x+1, −y+1, −z+1.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O2W—H2WA···O1	0.85 (1)	1.86 (2)	2.695 (4)	169 (5)