metal-organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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

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 LiI ion is coordinated by two carboxyl­ate O atoms donated by two ligands and two nitrate O atoms in a distorted tetrahedral geometry. LiI 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[Rodríguez-Diéguez, A., Cano, J., Kivekas, R., Debdoubi, A. & Colacio, E. (2007). Inorg. Chem. 46, 2503-2510.], 2008[Rodríguez-Diéguez, A., Aouryaghal, H., Mota, A. J. & Colacio, E. (2008). Acta Cryst. E64, m618.]); Zhao & Liu (2010[Zhao, J.-P. & Liu, F.-C. (2010). Acta Cryst. E66, m1059.]); Zhang et al. (2008a[Zhang, J.-Y., Ma, Y., Cheng, A.-L., Yue, Q., Sun, Q. & Gao, E.-Q. (2008a). Dalton Trans. pp. 2061-2068.]). For structures built of monomeric mol­ecules, see: Kokunov & Gorbunova (2007[Kokunov, Yu. V. & Gorbunova, Yu. E. (2007). Zh. Neorg. Khim. 52, 1632-1637.]); Antolić et al. (2000[Antolić, S., Kojić-Prodić, B. & Lovrić, J. (2000). Acta Cryst. C56, e51-e52.]); Zhang et al. (2008b[Zhang, B.-Y., Yang, Q. & Nie, J.-J. (2008b). Acta Cryst. E64, m7.]); Suares-Varela et al. (2008[Suares-Varela, J., Mota, A. J., Luneau, D. & Colacio, E. (2008). Inorg. Chem. 47, 8143-8149.]).

[Scheme 1]

Experimental

Crystal data
  • [Li(C5H4N2O2)(NO3)]

  • Mr = 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.]) Tmin = 0.782, Tmax = 0.939

  • 4248 measured reflections

  • 2179 independent reflections

  • 1504 reflections with I > 2σ(I)

  • Rint = 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

  • Δρmax = 0.43 e Å−3

  • Δρmin = −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 DA 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[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXTL.

Supporting information


Comment top

The structure of the title compound contains LiI 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 O12II atoms (Fig. 1). The LiI ion is shifted by 0.0548 (2)Å above this plane. The carboxylato O2III 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 OI 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 LiI 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 O12II atoms give rise to molecular layers. While the nitrato O11 atom coordinates a LiI ion in one ribbon plane, the O12 atom is bonded along the crystal c axis to a LiI 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 LiI 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.

Refinement top

H atoms attached to pyridimiine-ring C atoms were placed at calculated positions with C—H=0.93 Å and treated as riding on the parent atoms with Uiso(H)=1.2Ueq(C). The H atom attached to pyrimidine ring N2 atom has been found from the Fourier map and refined isotropically.

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
[Figure 1] 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.
[Figure 2] 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
Mr = 193.05Dx = 1.730 Mg m3
Orthorhombic, PbcaMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2abCell parameters from 25 reflections
a = 12.403 (3) Åθ = 6–15°
b = 9.3290 (19) ŵ = 0.15 mm1
c = 12.810 (3) ÅT = 293 K
V = 1482.2 (5) Å3Plates, colorless
Z = 80.49 × 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 tubeRint = 0.158
Graphite monochromatorθmax = 30.1°, θmin = 3.2°
profile data from ω/2θ scansh = 017
Absorption correction: analytical
(CrysAlis RED; Oxford Diffraction,2008)
k = 013
Tmin = 0.782, Tmax = 0.939l = 1818
4248 measured reflections3 standard reflections every 200 reflections
2179 independent reflections intensity decay: 3.8%
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.050Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.153H atoms treated by a mixture of independent and constrained refinement
S = 0.97 w = 1/[σ2(Fo2) + (0.0702P)2 + 0.2975P]
where P = (Fo2 + 2Fc2)/3
2179 reflections(Δ/σ)max < 0.001
131 parametersΔρmax = 0.43 e Å3
0 restraintsΔρmin = 0.32 e Å3
Crystal data top
[Li(C5H4N2O2)(NO3)]V = 1482.2 (5) Å3
Mr = 193.05Z = 8
Orthorhombic, PbcaMo Kα radiation
a = 12.403 (3) ŵ = 0.15 mm1
b = 9.3290 (19) ÅT = 293 K
c = 12.810 (3) Å0.49 × 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)
Rint = 0.158
Tmin = 0.782, Tmax = 0.9393 standard reflections every 200 reflections
4248 measured reflections intensity decay: 3.8%
2179 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0500 restraints
wR(F2) = 0.153H atoms treated by a mixture of independent and constrained refinement
S = 0.97Δρmax = 0.43 e Å3
2179 reflectionsΔρmin = 0.32 e Å3
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
xyzUiso*/Ueq
N20.61057 (10)0.04538 (11)0.35126 (12)0.0250 (3)
O10.71796 (9)0.39321 (10)0.32671 (12)0.0323 (3)
O110.47373 (9)0.63026 (13)0.36709 (13)0.0400 (4)
N10.52999 (10)0.27071 (12)0.37133 (13)0.0294 (3)
C20.61507 (11)0.18883 (13)0.35586 (13)0.0236 (3)
N110.38359 (10)0.62115 (13)0.40961 (13)0.0300 (3)
C40.51530 (13)0.02147 (14)0.35905 (15)0.0290 (4)
H40.51150.12080.35380.035*
O20.80624 (9)0.18762 (11)0.35001 (13)0.0378 (4)
C70.72441 (11)0.26027 (14)0.34338 (14)0.0258 (3)
C50.42357 (12)0.05728 (16)0.37473 (16)0.0332 (4)
H50.35650.01350.38060.040*
C60.43471 (12)0.20546 (16)0.38159 (17)0.0350 (4)
H60.37370.26100.39370.042*
O120.35866 (13)0.51255 (13)0.45999 (13)0.0464 (4)
O130.32128 (12)0.72177 (17)0.4017 (2)0.0755 (7)
Li10.6045 (2)0.5149 (3)0.3893 (3)0.0362 (7)
H20.671 (2)0.005 (3)0.339 (2)0.044 (6)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N20.0196 (5)0.0171 (5)0.0382 (8)0.0002 (4)0.0020 (5)0.0003 (5)
O10.0227 (5)0.0175 (4)0.0567 (8)0.0023 (3)0.0012 (5)0.0000 (4)
O110.0233 (6)0.0398 (6)0.0568 (10)0.0039 (4)0.0078 (5)0.0067 (6)
N10.0190 (6)0.0212 (5)0.0479 (9)0.0021 (4)0.0008 (5)0.0048 (5)
C20.0200 (6)0.0184 (5)0.0323 (8)0.0005 (4)0.0018 (6)0.0018 (5)
N110.0230 (6)0.0287 (6)0.0384 (8)0.0003 (4)0.0009 (6)0.0007 (5)
C40.0260 (7)0.0200 (5)0.0410 (10)0.0042 (5)0.0013 (7)0.0014 (5)
O20.0183 (5)0.0241 (5)0.0710 (10)0.0023 (4)0.0002 (6)0.0032 (5)
C70.0199 (6)0.0186 (5)0.0388 (8)0.0011 (4)0.0017 (6)0.0029 (5)
C50.0193 (6)0.0304 (6)0.0499 (11)0.0065 (5)0.0018 (7)0.0000 (7)
C60.0191 (6)0.0308 (7)0.0551 (12)0.0021 (5)0.0020 (7)0.0064 (7)
O120.0557 (8)0.0362 (6)0.0474 (9)0.0142 (6)0.0041 (8)0.0043 (6)
O130.0321 (7)0.0554 (8)0.139 (2)0.0210 (6)0.0136 (10)0.0267 (11)
Li10.0294 (13)0.0305 (11)0.0486 (19)0.0042 (10)0.0029 (13)0.0051 (12)
Geometric parameters (Å, º) top
N2—C41.3399 (19)N11—O121.2404 (18)
N2—C21.3406 (16)C4—C51.369 (2)
N2—H20.90 (3)C4—H40.9300
O1—C71.2610 (16)O2—C71.2234 (17)
O1—Li11.978 (3)O2—Li1i2.019 (3)
O11—N111.2466 (18)C5—C61.392 (2)
O11—Li11.967 (3)C5—H50.9300
N1—C21.3178 (18)C6—H60.9300
N1—C61.3357 (19)O12—Li1ii2.001 (4)
N1—Li12.469 (3)Li1—O12ii2.001 (4)
C2—C71.5194 (19)Li1—O2iii2.019 (3)
N11—O131.2201 (18)
C4—N2—C2119.87 (13)O2—C7—C2119.35 (12)
C4—N2—H2120.5 (15)O1—C7—C2113.12 (11)
C2—N2—H2119.5 (15)C4—C5—C6117.36 (14)
C7—O1—Li1122.76 (14)C4—C5—H5121.3
N11—O11—Li1129.73 (15)C6—C5—H5121.3
C2—N1—C6117.33 (11)N1—C6—C5122.29 (14)
C2—N1—Li1104.42 (11)N1—C6—H6118.9
C6—N1—Li1137.95 (11)C5—C6—H6118.9
N1—C2—N2123.50 (13)N11—O12—Li1ii123.35 (15)
N1—C2—C7118.44 (11)O11—Li1—O1147.4 (2)
N2—C2—C7118.06 (12)O11—Li1—O12ii113.43 (18)
O13—N11—O12120.90 (16)O1—Li1—O12ii98.94 (15)
O13—N11—O11118.66 (15)O11—Li1—O2iii88.82 (12)
O12—N11—O11120.44 (14)O1—Li1—O2iii88.11 (14)
N2—C4—C5119.61 (12)O12ii—Li1—O2iii102.57 (16)
N2—C4—H4120.2O11—Li1—N1100.51 (13)
C5—C4—H4120.2O1—Li1—N172.49 (10)
C7—O2—Li1i156.13 (14)O12ii—Li1—N193.28 (13)
O2—C7—O1127.53 (13)O2iii—Li1—N1156.71 (19)
Symmetry codes: (i) x+3/2, y1/2, z; (ii) x+1, y+1, z+1; (iii) x+3/2, y+1/2, z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2···O1i0.90 (3)1.68 (3)2.5762 (17)174 (3)
Symmetry code: (i) x+3/2, y1/2, z.

Experimental details

Crystal data
Chemical formula[Li(C5H4N2O2)(NO3)]
Mr193.05
Crystal system, space groupOrthorhombic, Pbca
Temperature (K)293
a, b, c (Å)12.403 (3), 9.3290 (19), 12.810 (3)
V3)1482.2 (5)
Z8
Radiation typeMo Kα
µ (mm1)0.15
Crystal size (mm)0.49 × 0.48 × 0.14
Data collection
DiffractometerKuma KM-4 four-circle
diffractometer
Absorption correctionAnalytical
(CrysAlis RED; Oxford Diffraction,2008)
Tmin, Tmax0.782, 0.939
No. of measured, independent and
observed [I > 2σ(I)] reflections
4248, 2179, 1504
Rint0.158
(sin θ/λ)max1)0.706
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.050, 0.153, 0.97
No. of reflections2179
No. of parameters131
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)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—Li11.978 (3)Li1—O12i2.001 (4)
O11—Li11.967 (3)Li1—O2ii2.019 (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···AD—HH···AD···AD—H···A
N2—H2···O1iii0.90 (3)1.68 (3)2.5762 (17)174 (3)
Symmetry code: (iii) x+3/2, y1/2, z.
 

References

First citationAntolić, S., Kojić-Prodić, B. & Lovrić, J. (2000). Acta Cryst. C56, e51–e52.  Web of Science CSD CrossRef IUCr Journals Google Scholar
First citationKokunov, Yu. V. & Gorbunova, Yu. E. (2007). Zh. Neorg. Khim. 52, 1632–1637.  CAS Google Scholar
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First citationKuma (2001). DATAPROC. Kuma Diffraction Ltd, Wrocław, Poland.  Google Scholar
First citationOxford Diffraction (2008). CrysAlis RED. Oxford Diffraction Ltd, Abingdon, England.  Google Scholar
First citationRodríguez-Diéguez, A., Aouryaghal, H., Mota, A. J. & Colacio, E. (2008). Acta Cryst. E64, m618.  Web of Science CSD CrossRef IUCr Journals Google Scholar
First citationRodríguez-Diéguez, A., Cano, J., Kivekas, R., Debdoubi, A. & Colacio, E. (2007). Inorg. Chem. 46, 2503–2510.  Web of Science PubMed Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationSuares-Varela, J., Mota, A. J., Luneau, D. & Colacio, E. (2008). Inorg. Chem. 47, 8143–8149.  Web of Science PubMed Google Scholar
First citationZhang, J.-Y., Ma, Y., Cheng, A.-L., Yue, Q., Sun, Q. & Gao, E.-Q. (2008a). Dalton Trans. pp. 2061–2068.  CrossRef Google Scholar
First citationZhang, B.-Y., Yang, Q. & Nie, J.-J. (2008b). Acta Cryst. E64, m7.  Web of Science CSD CrossRef IUCr Journals Google Scholar
First citationZhao, J.-P. & Liu, F.-C. (2010). Acta Cryst. E66, m1059.  Web of Science CSD CrossRef IUCr Journals Google Scholar

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