Diaqua­bis(pyrimidine-2-carboxylic acid-κ² N,O)cobalt(II) dichloride

Abstract

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,

• a = 6.2803 (8) Å

• b = 10.361 (2) Å

• c = 11.906 (2) Å

• β = 95.254 (15)°

• V = 771.5 (2) ų

• 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[F ² > 2σ(F ²)] = 0.040

• wR(F ²) = 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

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 ▶).

Supplementary Material

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

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) .

supplementary crystallographic information

Comment

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.

Experimental

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.

Refinement

Hydroxy and water H atoms were located in a difference Fourier map and refined as riding in as-found relative positions, with U_iso(H) = 1.5U_eq(O). Other H atoms were placed in calculated positions with C—H = 0.93 Å and refined in riding mode with U_iso(H) = 1.2U_eq(C).

Figures

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].

Crystal data

[Co(C5H4N2O2)2(H2O)2]Cl2	F000 = 418
Mr = 414.07	Dx = 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 = 3.5–24.5º
b = 10.361 (2) Å	µ = 1.49 mm−1
c = 11.906 (2) Å	T = 293 (2) K
β = 95.254 (15)º	Prism, pink
V = 771.5 (2) Å3	0.25 × 0.12 × 0.10 mm
Z = 2

Data collection

Rigaku R-AXIS RAPID IP diffractometer	1763 independent reflections
Radiation source: fine-focus sealed tube	1178 reflections with I > 2σ(I)
Monochromator: graphite	Rint = 0.052
Detector resolution: 10.0 pixels mm-1	θmax = 27.4º
T = 291(2) K	θmin = 3.4º
ω scans	h = −8→8
Absorption correction: multi-scan(ABSCOR; Higashi, 1995)	k = −12→13
Tmin = 0.726, Tmax = 0.862	l = −15→15
7413 measured reflections

Refinement

Refinement on F2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.040	H-atom parameters constrained
wR(F2) = 0.119	w = 1/[σ2(Fo2) + (0.0359P)2 + 1.9784P] where P = (Fo2 + 2Fc2)/3
S = 1.12	(Δ/σ)max < 0.001
1763 reflections	Δρmax = 0.70 e Å−3
107 parameters	Δρmin = −0.72 e Å−3
Primary atom site location: structure-invariant direct methods	Extinction correction: none

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
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 (Ų)

	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, °)

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 codes: (i) −x+1, −y+1, −z+1.

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···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.