Poly[(μ2-nitrato-κ2O:O′)(μ2-pyrimidin­ium-2-carboxyl­ato-κ2O:O′)lithium(I)]

Starosta, W.; Leciejewicz, J.

doi:10.1107/S1600536811019520

metal-organic compounds

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doi:10.1107/S1600536811019520

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Poly[(μ₂-nitrato-κ²O:O′)(μ₂-pyrimidinium-2-carboxylato-κ²O:O′)lithium(I)]

Wojciech Starosta ^a and Janusz Leciejewicz ^a ^*

^aInstitute of Nuclear Chemistry and Technology, ul.Dorodna 16, 03-195 Warszawa, Poland
^*Correspondence e-mail: j.leciejewicz@ichtj.waw.pl

(Received 11 April 2011; accepted 23 May 2011; online 28 May 2011)

In the structure of the title compound, [Li(C₅H₄N₂O₂)(NO₃)]_n, the Li^I ion is coordinated by two carboxylate O atoms donated by two ligands and two nitrate O atoms in a distorted tetrahedral geometry. Li^I ions, bridged by carboxylate O atoms, form molecular ribbons composed of dimeric units. Two nitrate O atoms link the ribbons into molecular layers parallel to (001). Hydrogen bonds are active between protonated heterocyclic N atoms as donors and carboxylate O atoms as acceptors. The layers are held together by van der Waals interactions.

Related literature

For the polymeric structures of some metal complexes with a pyrimidine-2-carboxylate ligand, see: Rodríguez-Diéguez et al. (2007 , 2008 ); Zhao & Liu (2010 ); Zhang et al. (2008a ). For structures built of monomeric molecules, see: Kokunov & Gorbunova (2007 ); Antolić et al. (2000 ); Zhang et al. (2008b ); Suares-Varela et al. (2008 ).

Experimental

Crystal data

[Li(C₅H₄N₂O₂)(NO₃)]
M_r = 193.05
Orthorhombic, P b c a
a = 12.403 (3) Å
b = 9.3290 (19) Å
c = 12.810 (3) Å
V = 1482.2 (5) Å³
Z = 8
Mo Kα radiation
μ = 0.15 mm⁻¹
T = 293 K
0.49 × 0.48 × 0.14 mm

Data collection

Kuma KM-4 four-circle diffractometer
Absorption correction: analytical (CrysAlis RED; Oxford Diffraction,2008 $[Oxford Diffraction (2008). CrysAlis RED. Oxford Diffraction Ltd, Abingdon, England.]$ ) T_min = 0.782, T_max = 0.939
4248 measured reflections
2179 independent reflections
1504 reflections with I > 2σ(I)
R_int = 0.158
3 standard reflections every 200 reflections intensity decay: 3.8%

Refinement

R[F² > 2σ(F²)] = 0.050
wR(F²) = 0.153
S = 0.97
2179 reflections
131 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.43 e Å⁻³
Δρ_min = −0.32 e Å⁻³

Table 1
Selected bond lengths (Å)

O1—Li1	1.978 (3)
O11—Li1	1.967 (3)
Li1—O12ⁱ	2.001 (4)
Li1—O2ⁱⁱ	2.019 (3)
Symmetry codes: (i) -x+1, -y+1, -z+1; (ii) $[-x+{\script{3\over 2}}, y+{\script{1\over 2}}, z]$ .

Table 2
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N2—H2⋯O1ⁱⁱⁱ	0.90 (3)	1.68 (3)	2.5762 (17)	174 (3)
Symmetry code: (iii) $[-x+{\script{3\over 2}}, y-{\script{1\over 2}}, z]$ .

Data collection: KM-4 Software (Kuma, 1996 $[Kuma (1996). KM-4 Software. Kuma Diffraction Ltd, Wrocław, Poland.]$ ); cell refinement: KM-4 Software; data reduction: DATAPROC (Kuma, 2001 $[Kuma (2001). DATAPROC. Kuma Diffraction Ltd, Wrocław, Poland.]$ ); 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/S1600536811019520/kp2322sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536811019520/kp2322Isup2.hkl

checkCIF report

Comment top

The structure of the title compound contains Li^I ions, each coordinated by two ligand carboxylato and two nitrato O atoms at the apieces of a distorded trigonal pyramid. Its base is composed of coplanar carboxylato O1, nitrato O11 and O12^II atoms (Fig. 1). The Li^I ion is shifted by 0.0548 (2)Å above this plane. The carboxylato O2^III atom is at the apex of the pyramid. The Li—O bond distances fall in the range from 1.967 (3) to 2.019 (3) Å, commonly observed in the structures of Li complexes with carboxylate ligands (Table 1). The Li1—N1 bond distance of 2.467 (3)Å as too long was not allowed for in coordination of the Li ion The pyrimidine ring is planar with r.m.s. of 0.0074 (2) Å]. A hydrogen atom attached to the hetero-ring N2 atom, clearly visible on the Fourier map, maintains the charge balance. It links the N2 atom with the carboxylato O^I atom via a hydrogen bond of 2.5762 (17) Å. Bond distances and bond angles within the pyrimidine ring do not differ from those reported earlier in the structures of other metal complexes with the title ligand. The carboxylate group C7/O1/O2 makes with the ring a dihedral angle of 14.81 (2)°. Two Li^I ions, one coordinated by the carboxylato O1 atom, the other by the second carboxylato O2 atom of the same ligand form molecular ribbons composed of dimeric units (Fig. 2). The latter bridged by nitrato O11 and O12^II atoms give rise to molecular layers. While the nitrato O11 atom coordinates a Li^I ion in one ribbon plane, the O12 atom is bonded along the crystal c axis to a Li^I ion in an adjacent ribbon; the O11—N11—O12 bond angle is 120.44 (17)°. The third nitrato O13 atomis not involved in the coordination. The NO₃ group is planar with r.m.s. of 0.0023 (0) Å. It makes a dihedral angle of 28.8 (2)° with the ribbon plane. Since the bridging nitrate O12 atom is in a terminal position and it is bonded to the Li^I ion in the middle of an adjacent ribbon, a layer is formed. A sequence of open channels which propagate along crystal a direction form a layer parallel to the ab plane. The layers stacked along the crystal c direction are held together by van der Waals type interactions. A variety of polymeric molecular patterns have been recently observed in the structures of a number of divalent metal complexes with the title ligand, for example: Mn(II) (Rodríguez-Diéguez et al., 2008; Zhang et al., 2008a); Fe(II) and Co(II) (Rodríguez-Diéguez et al., 2007; Zhao & Liu, 2010); Ca(II) Zhang et al., 2008a), complexes. Structures built of monmeric molecules have been also reported: in a Ag(I) complex by Kokunov & Gorbunova, (2007); in a Cu(II) complex by Suares-Varela et al., (2008) and Zhang et al., (2008a). The structures of two Co(II) complexes have been determined by Antolić et al., (2000) and Zhang et al., (2008b).

Related literature top

For the polymeric structures of some metal complexes with a pyrimidine-2-carboxylate ligand, see: Rodríguez-Diéguez et al. (2007, 2008); Zhao & Liu (2010); Zhang et al. (2008a). For structures built of monmeric molecules, see: Kokunov & Gorbunova (2007); Antolić et al. (2000); Zhang et al. (2008b); Suares-Varela et al. (2008).

Experimental top

50 mL of an aqueous solution containing 1 mmol of pyrimidine-2-carbonitrile (Aldrich) and 1 mmol of lithium nitrate hydrate were boiled with constant stirring under reflux for 6 h. After cooling to room temperature 1 N HNO₃ was added dropwise until the pH reached 6. Then the solution was stirred for 3 h. After evaporation to dryness the residue was repeatedly dissolved in water and evaporated at room temperature until colourless single crystals of the title compound were deposited. The crystals were washed with cold methanol and dried in the air.

Computing details top

Data collection: KM-4 Software (Kuma, 1996); cell refinement: KM-4 Software (Kuma, 1996); data reduction: DATAPROC (Kuma, 2001); 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. A fragment of the structure with the atom labeling scheme. Non-hydrogen atoms are shown as 50% elipsoids. Symmetry code: (I) -x + 3/2, y - 1/2, z; (II) -x + 1, -y + 1, -z + 1; (III) -x + 3/2, y + 1/2, z.
	Fig. 2. Packing of molecular layers viewed along the a axis.

Poly[(µ₂-nitrato-κ²O:O')(µ₂-pyrimidinium-2-carboxylato- κ²O:O')lithium(I)] top

Crystal data top

[Li(C₅H₄N₂O₂)(NO₃)]	F(000) = 784
M_r = 193.05	D_x = 1.730 Mg m⁻³
Orthorhombic, Pbca	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2ab	Cell parameters from 25 reflections
a = 12.403 (3) Å	θ = 6–15°
b = 9.3290 (19) Å	µ = 0.15 mm⁻¹
c = 12.810 (3) Å	T = 293 K
V = 1482.2 (5) Å³	Plates, colorless
Z = 8	0.49 × 0.48 × 0.14 mm

Data collection top

Kuma KM-4 four-circle diffractometer	1504 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	R_int = 0.158
Graphite monochromator	θ_max = 30.1°, θ_min = 3.2°
profile data from ω/2θ scans	h = 0→17
Absorption correction: analytical (CrysAlis RED; Oxford Diffraction,2008)	k = 0→13
T_min = 0.782, T_max = 0.939	l = −18→18
4248 measured reflections	3 standard reflections every 200 reflections
2179 independent reflections	intensity decay: 3.8%

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)] = 0.050	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.153	H atoms treated by a mixture of independent and constrained refinement
S = 0.97	w = 1/[σ²(F_o²) + (0.0702P)² + 0.2975P] where P = (F_o² + 2F_c²)/3
2179 reflections	(Δ/σ)_max < 0.001
131 parameters	Δρ_max = 0.43 e Å⁻³
0 restraints	Δρ_min = −0.32 e Å⁻³

Crystal data top

[Li(C₅H₄N₂O₂)(NO₃)]	V = 1482.2 (5) Å³
M_r = 193.05	Z = 8
Orthorhombic, Pbca	Mo Kα radiation
a = 12.403 (3) Å	µ = 0.15 mm⁻¹
b = 9.3290 (19) Å	T = 293 K
c = 12.810 (3) Å	0.49 × 0.48 × 0.14 mm

Data collection top

Kuma KM-4 four-circle diffractometer	1504 reflections with I > 2σ(I)
Absorption correction: analytical (CrysAlis RED; Oxford Diffraction,2008)	R_int = 0.158
T_min = 0.782, T_max = 0.939	3 standard reflections every 200 reflections
4248 measured reflections	intensity decay: 3.8%
2179 independent reflections

Refinement top

R[F² > 2σ(F²)] = 0.050	0 restraints
wR(F²) = 0.153	H atoms treated by a mixture of independent and constrained refinement
S = 0.97	Δρ_max = 0.43 e Å⁻³
2179 reflections	Δρ_min = −0.32 e Å⁻³
131 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
N2	0.61057 (10)	0.04538 (11)	0.35126 (12)	0.0250 (3)
O1	0.71796 (9)	0.39321 (10)	0.32671 (12)	0.0323 (3)
O11	0.47373 (9)	0.63026 (13)	0.36709 (13)	0.0400 (4)
N1	0.52999 (10)	0.27071 (12)	0.37133 (13)	0.0294 (3)
C2	0.61507 (11)	0.18883 (13)	0.35586 (13)	0.0236 (3)
N11	0.38359 (10)	0.62115 (13)	0.40961 (13)	0.0300 (3)
C4	0.51530 (13)	−0.02147 (14)	0.35905 (15)	0.0290 (4)
H4	0.5115	−0.1208	0.3538	0.035*
O2	0.80624 (9)	0.18762 (11)	0.35001 (13)	0.0378 (4)
C7	0.72441 (11)	0.26027 (14)	0.34338 (14)	0.0258 (3)
C5	0.42357 (12)	0.05728 (16)	0.37473 (16)	0.0332 (4)
H5	0.3565	0.0135	0.3806	0.040*
C6	0.43471 (12)	0.20546 (16)	0.38159 (17)	0.0350 (4)
H6	0.3737	0.2610	0.3937	0.042*
O12	0.35866 (13)	0.51255 (13)	0.45999 (13)	0.0464 (4)
O13	0.32128 (12)	0.72177 (17)	0.4017 (2)	0.0755 (7)
Li1	0.6045 (2)	0.5149 (3)	0.3893 (3)	0.0362 (7)
H2	0.671 (2)	−0.005 (3)	0.339 (2)	0.044 (6)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N2	0.0196 (5)	0.0171 (5)	0.0382 (8)	−0.0002 (4)	−0.0020 (5)	−0.0003 (5)
O1	0.0227 (5)	0.0175 (4)	0.0567 (8)	−0.0023 (3)	0.0012 (5)	0.0000 (4)
O11	0.0233 (6)	0.0398 (6)	0.0568 (10)	0.0039 (4)	0.0078 (5)	0.0067 (6)
N1	0.0190 (6)	0.0212 (5)	0.0479 (9)	0.0021 (4)	−0.0008 (5)	−0.0048 (5)
C2	0.0200 (6)	0.0184 (5)	0.0323 (8)	−0.0005 (4)	−0.0018 (6)	−0.0018 (5)
N11	0.0230 (6)	0.0287 (6)	0.0384 (8)	−0.0003 (4)	−0.0009 (6)	0.0007 (5)
C4	0.0260 (7)	0.0200 (5)	0.0410 (10)	−0.0042 (5)	−0.0013 (7)	0.0014 (5)
O2	0.0183 (5)	0.0241 (5)	0.0710 (10)	0.0023 (4)	0.0002 (6)	0.0032 (5)
C7	0.0199 (6)	0.0186 (5)	0.0388 (8)	−0.0011 (4)	−0.0017 (6)	−0.0029 (5)
C5	0.0193 (6)	0.0304 (6)	0.0499 (11)	−0.0065 (5)	−0.0018 (7)	0.0000 (7)
C6	0.0191 (6)	0.0308 (7)	0.0551 (12)	0.0021 (5)	0.0020 (7)	−0.0064 (7)
O12	0.0557 (8)	0.0362 (6)	0.0474 (9)	−0.0142 (6)	0.0041 (8)	0.0043 (6)
O13	0.0321 (7)	0.0554 (8)	0.139 (2)	0.0210 (6)	0.0136 (10)	0.0267 (11)
Li1	0.0294 (13)	0.0305 (11)	0.0486 (19)	0.0042 (10)	0.0029 (13)	0.0051 (12)

Geometric parameters (Å, º) top

N2—C4	1.3399 (19)	N11—O12	1.2404 (18)
N2—C2	1.3406 (16)	C4—C5	1.369 (2)
N2—H2	0.90 (3)	C4—H4	0.9300
O1—C7	1.2610 (16)	O2—C7	1.2234 (17)
O1—Li1	1.978 (3)	O2—Li1ⁱ	2.019 (3)
O11—N11	1.2466 (18)	C5—C6	1.392 (2)
O11—Li1	1.967 (3)	C5—H5	0.9300
N1—C2	1.3178 (18)	C6—H6	0.9300
N1—C6	1.3357 (19)	O12—Li1ⁱⁱ	2.001 (4)
N1—Li1	2.469 (3)	Li1—O12ⁱⁱ	2.001 (4)
C2—C7	1.5194 (19)	Li1—O2ⁱⁱⁱ	2.019 (3)
N11—O13	1.2201 (18)

C4—N2—C2	119.87 (13)	O2—C7—C2	119.35 (12)
C4—N2—H2	120.5 (15)	O1—C7—C2	113.12 (11)
C2—N2—H2	119.5 (15)	C4—C5—C6	117.36 (14)
C7—O1—Li1	122.76 (14)	C4—C5—H5	121.3
N11—O11—Li1	129.73 (15)	C6—C5—H5	121.3
C2—N1—C6	117.33 (11)	N1—C6—C5	122.29 (14)
C2—N1—Li1	104.42 (11)	N1—C6—H6	118.9
C6—N1—Li1	137.95 (11)	C5—C6—H6	118.9
N1—C2—N2	123.50 (13)	N11—O12—Li1ⁱⁱ	123.35 (15)
N1—C2—C7	118.44 (11)	O11—Li1—O1	147.4 (2)
N2—C2—C7	118.06 (12)	O11—Li1—O12ⁱⁱ	113.43 (18)
O13—N11—O12	120.90 (16)	O1—Li1—O12ⁱⁱ	98.94 (15)
O13—N11—O11	118.66 (15)	O11—Li1—O2ⁱⁱⁱ	88.82 (12)
O12—N11—O11	120.44 (14)	O1—Li1—O2ⁱⁱⁱ	88.11 (14)
N2—C4—C5	119.61 (12)	O12ⁱⁱ—Li1—O2ⁱⁱⁱ	102.57 (16)
N2—C4—H4	120.2	O11—Li1—N1	100.51 (13)
C5—C4—H4	120.2	O1—Li1—N1	72.49 (10)
C7—O2—Li1ⁱ	156.13 (14)	O12ⁱⁱ—Li1—N1	93.28 (13)
O2—C7—O1	127.53 (13)	O2ⁱⁱⁱ—Li1—N1	156.71 (19)

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

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2···O1ⁱ	0.90 (3)	1.68 (3)	2.5762 (17)	174 (3)

Symmetry code: (i) −x+3/2, y−1/2, z.

Experimental details

Crystal data
Chemical formula	[Li(C₅H₄N₂O₂)(NO₃)]
M_r	193.05
Crystal system, space group	Orthorhombic, Pbca
Temperature (K)	293
a, b, c (Å)	12.403 (3), 9.3290 (19), 12.810 (3)
V (Å³)	1482.2 (5)
Z	8
Radiation type	Mo Kα
µ (mm⁻¹)	0.15
Crystal size (mm)	0.49 × 0.48 × 0.14

Data collection
Diffractometer	Kuma KM-4 four-circle diffractometer
Absorption correction	Analytical (CrysAlis RED; Oxford Diffraction,2008)
T_min, T_max	0.782, 0.939
No. of measured, independent and observed [I > 2σ(I)] reflections	4248, 2179, 1504
R_int	0.158
(sin θ/λ)_max (Å⁻¹)	0.706

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.050, 0.153, 0.97
No. of reflections	2179
No. of parameters	131
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.43, −0.32

Computer programs: KM-4 Software (Kuma, 1996), DATAPROC (Kuma, 2001), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Selected bond lengths (Å) top

O1—Li1	1.978 (3)	Li1—O12ⁱ	2.001 (4)
O11—Li1	1.967 (3)	Li1—O2ⁱⁱ	2.019 (3)

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

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2···O1ⁱⁱⁱ	0.90 (3)	1.68 (3)	2.5762 (17)	174 (3)

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

References

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doi:10.1107/S1600536811019520

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