Diaqua­bis(pyrimidine-2-carboxylic acid-κ2N,O)cobalt(II) dichloride

Xu, D.-J.; Zhang, B.-Y.; Yang, Q.; Nie, J.-J.

doi:10.1107/S1600536807063258

metal-organic compounds

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ISSN: 2056-9890

Volume 64| Part 1| January 2008| Page m77

https://doi.org/10.1107/S1600536807063258

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Diaquabis(pyrimidine-2-carboxylic acid-κ²N,O)cobalt(II) dichloride

Duan-Jun Xu,^a Bing-Yu Zhang,^a Qian Yang ^a and Jing-Jing Nie ^a ^*

^aDepartment of Chemistry, Zhejiang University, People's Republic of China
^*Correspondence e-mail: niejj@zju.edu.cn

(Received 24 November 2007; accepted 26 November 2007; online 6 December 2007)

In the title salt, [Co(C₅H₄N₂O₂)₂(H₂O)₂]Cl₂, the Co^II ion is located on an inversion center. It is chelated by two neutral pyrimidine-2-carboxylic acid molecules and is coordinated by two water molecules in an octahedral coordination geometry. The cations and anions are linked via O—H⋯Cl hydrogen bonds into a layer structure; an intramolecular O—H⋯N hydrogen bond connects the carboxylic acid group to the pyrimidine N atom.

Related literature

For general background, see: Cheng et al. (2000 ); Wu et al. (2003 ). For related structures, see: Rodriquez-Dieguez et al. (2007 ); Zhang et al. (2008 ).

Experimental

Crystal data

[Co(C₅H₄N₂O₂)₂(H₂O)₂]Cl₂
M_r = 414.07
Monoclinic, P 2₁ /n
a = 6.2803 (8) Å
b = 10.361 (2) Å
c = 11.906 (2) Å
β = 95.254 (15)°
V = 771.5 (2) Å³
Z = 2
Mo Kα radiation
μ = 1.49 mm⁻¹
T = 293 (2) K
0.25 × 0.12 × 0.10 mm

Data collection

Rigaku R-AXIS RAPID IP diffractometer
Absorption correction: multi-scan (ABSCOR; Higashi, 1995 ) T_min = 0.726, T_max = 0.862
7413 measured reflections
1763 independent reflections
1178 reflections with I > 2σ(I)
R_int = 0.052

Refinement

R[F² > 2σ(F²)] = 0.040
wR(F²) = 0.119
S = 1.12
1763 reflections
107 parameters
H-atom parameters constrained
Δρ_max = 0.70 e Å⁻³
Δρ_min = −0.72 e Å⁻³

Table 1
Selected geometric parameters (Å, °)

Co—O1	2.077 (3)
Co—O3	2.123 (3)
Co—N1	2.085 (3)

O1—Co—N1	78.92 (11)
O1—Co—O3	91.01 (12)
N1—Co—O3	87.84 (12)

Table 2
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O2—H2⋯N2	0.82	2.32	2.784 (5)	116
O3—H3A⋯Cl1ⁱ	0.95	2.20	3.140 (4)	168
O3—H3B⋯Cl1	0.97	2.34	3.273 (3)	161
Symmetry code: (i) $[-x+{\script{3\over 2}}, y-{\script{1\over 2}}, -z+{\script{3\over 2}}]$ .

Data collection: PROCESS-AUTO (Rigaku, 1998 ); cell refinement: PROCESS-AUTO; data reduction: CrystalStructure (Rigaku/MSC, 2002 ); program(s) used to solve structure: SIR92 (Altomare et al., 1993 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997 ); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997 ); software used to prepare material for publication: WinGX (Farrugia, 1999 ).

Supporting information

Crystal structure: contains datablocks I, global. DOI: https://doi.org/10.1107/S1600536807063258/ng2402sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536807063258/ng2402Isup2.hkl

checkCIF report

Comment top

As part of our ongoing investigation on the nature of aromatic stacking (Cheng et al., 2000; Wu et al., 2003), the title Co^II compound has recently been prepared and its crystal structure is presented here.

The molecular structure of the title compound is shown in Fig. 1. The crystal of the title compound consists of complex cations and Cl^- anions. The Co^II located on an inversion center is coordinated by two neutral pyrimidine-2-carboxylic acid and two water molecules with an octahedral geometry (Table 1). The Cl^- anions link with the complex cations via O—H···Cl hydrogen bonding (Table 2 and Fig. 1). The charge balance indicates that the pyrimidine-2-carboxylic acid is a neutral ligand but not an anion; and the significant difference in C—O bond distances (Table 1) also suggests that the carboxyl group is not deprotonated. This is obviously owing to the acidified solution environment in the preparation of the compound (see _publ_section_exptl_prep). The intra-molecular O—H···N hydrogen bonding exsits between the carboxyl group and adjacent pyrimidine-N atom (Fig. 1). Thus the pyrimidine-2-carboxylic acid can not play a role of bridge ligand in this structure, contrast to that found in pyrimidine-2-carboxylate complex of Co(II) reported previously (Rodriquez-Dieguez et al., 2007).

π-π stacking is not observed in this crystal structure, which is different from the situation in a related Cu^II complex with pyrimidine-2-carboxylate (Zhang et al., 2008). It may be due to extensive hydrogen bonding network involving coordinated water molecules and counter Cl^- anions.

Related literature top

For general background, see: Cheng et al. (2000); Wu et al. (2003). For related structures, see: Rodriquez-Dieguez et al. (2007); Zhang et al. (2008).

Experimental top

2-Cyanopyrimidine (0.19 g, 1.8 mmol), CoCl₂.6(H₂O) (0.24 g, 1 mmol) were dissolved in a mixture solution of water (15 ml) and ethanol (5 ml), then hydrochloric acid solution (3 ml, 37%) was added into the solution. The solution was refluxed for 5 h. Single crystals of the title compound were obtained after about one month.

Structure description top

For general background, see: Cheng et al. (2000); Wu et al. (2003). For related structures, see: Rodriquez-Dieguez et al. (2007); Zhang et al. (2008).

Computing details top

Data collection: PROCESS-AUTO (Rigaku, 1998); cell refinement: PROCESS-AUTO (Rigaku, 1998); data reduction: CrystalStructure (Rigaku/MSC, 2002); program(s) used to solve structure: SIR92 (Altomare et al., 1993); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997); software used to prepare material for publication: WinGX (Farrugia, 1999).

Figures top

Fig. 1. The molecular structure of the title compound with 30% probability displacement (arbitrary spheres for H atoms), dashed lines indicate hydrogen bonding [symmetry codes: (i) 1 - x,1 - y,1 - z].

Diaquabis(pyrimidine-2-carboxylic acid-κ²N,O)cobalt(II) dichloride top

Crystal data top

[Co(C₅H₄N₂O₂)₂(H₂O)₂]Cl₂	F(000) = 418
M_r = 414.07	D_x = 1.782 Mg m⁻³
Monoclinic, P2₁/n	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2yn	Cell parameters from 2668 reflections
a = 6.2803 (8) Å	θ = 3.5–24.5°
b = 10.361 (2) Å	µ = 1.49 mm⁻¹
c = 11.906 (2) Å	T = 293 K
β = 95.254 (15)°	Prism, pink
V = 771.5 (2) Å³	0.25 × 0.12 × 0.10 mm
Z = 2

Data collection top

Rigaku R-AXIS RAPID IP diffractometer	1763 independent reflections
Radiation source: fine-focus sealed tube	1178 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.052
Detector resolution: 10.0 pixels mm^-1	θ_max = 27.4°, θ_min = 3.4°
ω scans	h = −8→8
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	k = −12→13
T_min = 0.726, T_max = 0.862	l = −15→15
7413 measured reflections

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)] = 0.040	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.119	H-atom parameters constrained
S = 1.12	w = 1/[σ²(F_o²) + (0.0359P)² + 1.9784P] where P = (F_o² + 2F_c²)/3
1763 reflections	(Δ/σ)_max < 0.001
107 parameters	Δρ_max = 0.70 e Å⁻³
0 restraints	Δρ_min = −0.72 e Å⁻³

Crystal data top

[Co(C₅H₄N₂O₂)₂(H₂O)₂]Cl₂	V = 771.5 (2) Å³
M_r = 414.07	Z = 2
Monoclinic, P2₁/n	Mo Kα radiation
a = 6.2803 (8) Å	µ = 1.49 mm⁻¹
b = 10.361 (2) Å	T = 293 K
c = 11.906 (2) Å	0.25 × 0.12 × 0.10 mm
β = 95.254 (15)°

Data collection top

Rigaku R-AXIS RAPID IP diffractometer	1763 independent reflections
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	1178 reflections with I > 2σ(I)
T_min = 0.726, T_max = 0.862	R_int = 0.052
7413 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.040	0 restraints
wR(F²) = 0.119	H-atom parameters constrained
S = 1.12	Δρ_max = 0.70 e Å⁻³
1763 reflections	Δρ_min = −0.72 e Å⁻³
107 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
Co	0.5000	0.5000	0.5000	0.0257 (2)
Cl1	0.83609 (17)	0.85016 (10)	0.65401 (9)	0.0367 (3)
N1	0.6455 (5)	0.6498 (3)	0.4186 (3)	0.0250 (7)
N2	0.5891 (6)	0.8696 (3)	0.3695 (3)	0.0340 (8)
O1	0.3012 (4)	0.6537 (3)	0.5310 (2)	0.0329 (7)
O2	0.2425 (6)	0.8657 (3)	0.4995 (3)	0.0541 (9)
H2	0.2993	0.9247	0.4674	0.081*
O3	0.7051 (5)	0.5443 (3)	0.6466 (3)	0.0397 (7)
H3A	0.7018	0.4951	0.7142	0.060*
H3B	0.7642	0.6288	0.6649	0.060*
C1	0.3501 (6)	0.7589 (3)	0.4885 (3)	0.0268 (8)
C2	0.5395 (6)	0.7618 (4)	0.4203 (3)	0.0258 (8)
C3	0.7628 (8)	0.8641 (5)	0.3124 (4)	0.0415 (11)
H3	0.8027	0.9374	0.2746	0.050*
C4	0.8852 (7)	0.7540 (4)	0.3075 (4)	0.0381 (10)
H4	1.0058	0.7524	0.2677	0.046*
C5	0.8217 (6)	0.6467 (4)	0.3637 (3)	0.0323 (9)
H5	0.9021	0.5713	0.3635	0.039*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Co	0.0300 (4)	0.0184 (4)	0.0294 (4)	0.0009 (3)	0.0068 (3)	0.0022 (3)
Cl1	0.0399 (6)	0.0365 (6)	0.0339 (6)	−0.0014 (5)	0.0045 (4)	−0.0036 (4)
N1	0.0274 (16)	0.0192 (15)	0.0289 (17)	−0.0015 (14)	0.0056 (13)	−0.0003 (13)
N2	0.0376 (19)	0.0261 (18)	0.039 (2)	−0.0039 (16)	0.0045 (16)	0.0076 (15)
O1	0.0352 (15)	0.0248 (14)	0.0410 (17)	0.0033 (13)	0.0157 (13)	0.0007 (13)
O2	0.058 (2)	0.0387 (19)	0.067 (3)	0.0051 (18)	0.0102 (19)	−0.0011 (18)
O3	0.0529 (19)	0.0332 (16)	0.0317 (16)	−0.0045 (15)	−0.0028 (14)	0.0010 (13)
C1	0.030 (2)	0.0167 (17)	0.034 (2)	0.0004 (16)	0.0038 (17)	−0.0033 (16)
C2	0.031 (2)	0.0210 (18)	0.025 (2)	−0.0024 (17)	0.0017 (16)	0.0000 (15)
C3	0.047 (3)	0.037 (2)	0.041 (3)	−0.010 (2)	0.007 (2)	0.014 (2)
C4	0.037 (2)	0.042 (3)	0.037 (2)	−0.007 (2)	0.0124 (19)	0.005 (2)
C5	0.028 (2)	0.036 (2)	0.033 (2)	0.0004 (19)	0.0047 (17)	−0.0040 (18)

Geometric parameters (Å, º) top

Co—O1	2.077 (3)	O2—C1	1.309 (5)
Co—O1ⁱ	2.077 (3)	O2—H2	0.8200
Co—O3ⁱ	2.123 (3)	O3—H3A	0.9545
Co—O3	2.123 (3)	O3—H3B	0.9674
Co—N1ⁱ	2.085 (3)	C1—C2	1.501 (5)
Co—N1	2.085 (3)	C3—C4	1.379 (7)
N1—C5	1.337 (5)	C3—H3	0.9300
N1—C2	1.338 (5)	C4—C5	1.375 (6)
N2—C2	1.321 (5)	C4—H4	0.9300
N2—C3	1.338 (6)	C5—H5	0.9300
O1—C1	1.252 (5)

O1—Co—O1ⁱ	180.00 (16)	C1—O2—H2	109.5
O1—Co—N1ⁱ	101.08 (11)	Co—O3—H3A	121.3
O1ⁱ—Co—N1ⁱ	78.92 (11)	Co—O3—H3B	124.9
O1—Co—N1	78.92 (11)	H3A—O3—H3B	109.3
O1ⁱ—Co—N1	101.08 (11)	O1—C1—O2	123.2 (4)
N1ⁱ—Co—N1	180.00 (11)	O1—C1—C2	118.2 (3)
O1—Co—O3ⁱ	88.99 (12)	O2—C1—C2	118.6 (3)
O1ⁱ—Co—O3ⁱ	91.01 (12)	N2—C2—N1	126.0 (4)
N1ⁱ—Co—O3ⁱ	87.84 (12)	N2—C2—C1	119.7 (3)
N1—Co—O3ⁱ	92.16 (12)	N1—C2—C1	114.3 (3)
O1—Co—O3	91.01 (12)	N2—C3—C4	122.7 (4)
O1ⁱ—Co—O3	88.99 (12)	N2—C3—H3	118.6
N1ⁱ—Co—O3	92.16 (12)	C4—C3—H3	118.6
N1—Co—O3	87.84 (12)	C5—C4—C3	117.4 (4)
O3ⁱ—Co—O3	180.000 (1)	C5—C4—H4	121.3
C5—N1—C2	117.6 (3)	C3—C4—H4	121.3
C5—N1—Co	128.8 (3)	N1—C5—C4	120.5 (4)
C2—N1—Co	113.5 (2)	N1—C5—H5	119.7
C2—N2—C3	115.7 (4)	C4—C5—H5	119.7
C1—O1—Co	115.0 (2)

Symmetry code: (i) −x+1, −y+1, −z+1.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O2—H2···N2	0.82	2.32	2.784 (5)	116
O3—H3A···Cl1ⁱⁱ	0.95	2.20	3.140 (4)	168
O3—H3B···Cl1	0.97	2.34	3.273 (3)	161
C4—H4···Cl1ⁱⁱⁱ	0.93	2.79	3.670 (5)	159

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

Experimental details

Crystal data
Chemical formula	[Co(C₅H₄N₂O₂)₂(H₂O)₂]Cl₂
M_r	414.07
Crystal system, space group	Monoclinic, P2₁/n
Temperature (K)	293
a, b, c (Å)	6.2803 (8), 10.361 (2), 11.906 (2)
β (°)	95.254 (15)
V (Å³)	771.5 (2)
Z	2
Radiation type	Mo Kα
µ (mm⁻¹)	1.49
Crystal size (mm)	0.25 × 0.12 × 0.10

Data collection
Diffractometer	Rigaku R-AXIS RAPID IP
Absorption correction	Multi-scan (ABSCOR; Higashi, 1995)
T_min, T_max	0.726, 0.862
No. of measured, independent and observed [I > 2σ(I)] reflections	7413, 1763, 1178
R_int	0.052
(sin θ/λ)_max (Å⁻¹)	0.648

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.040, 0.119, 1.12
No. of reflections	1763
No. of parameters	107
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.70, −0.72

Computer programs: PROCESS-AUTO (Rigaku, 1998), CrystalStructure (Rigaku/MSC, 2002), SIR92 (Altomare et al., 1993), SHELXL97 (Sheldrick, 1997), ORTEP-3 for Windows (Farrugia, 1997), WinGX (Farrugia, 1999).

Selected geometric parameters (Å, º) top

Co—O1	2.077 (3)	O1—C1	1.252 (5)
Co—O3	2.123 (3)	O2—C1	1.309 (5)
Co—N1	2.085 (3)

O1—Co—N1	78.92 (11)	N1—Co—O3	87.84 (12)
O1—Co—O3	91.01 (12)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O2—H2···N2	0.82	2.32	2.784 (5)	116
O3—H3A···Cl1ⁱ	0.95	2.20	3.140 (4)	168
O3—H3B···Cl1	0.97	2.34	3.273 (3)	161

Symmetry code: (i) −x+3/2, y−1/2, −z+3/2.

Acknowledgements

The work was supported by the ZIJIN project of Zhejiang University, China.

References

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