Lithium orotate monohydrate

The X-ray crystal structure of the title compound, lithium 1,2,3,6-tetra­hydro-2,6-dioxo-4-pyrimidine­carboxyl­ate monohydrate, Li⁺·C₅H₃N₂O₄^-·H₂O, was redetermined at a temperature of 110 (2) K. It was now possible to locate all H atoms in the difference Fourier map. The hydrogen-bonding pattern can now be completely described, as well as the coordination mode of the water mol­ecule to the lithium center.

Key indicators

• Single-crystal X-ray study
• T = 110 K
• Mean [sigma](C-C) = 0.002 Å
• R factor = 0.030
• wR factor = 0.079
• Data-to-parameter ratio = 8.4

checkCIF results

No syntax errors found

ADDSYM reports no extra symmetry

General Notes



REFLT_03
         From the CIF: _diffrn_reflns_theta_max           30.00
         From the CIF: _reflns_number_total                994
         Count of symmetry unique reflns          997
         Completeness (_total/calc)             99.70%
         TEST3: Check Friedels for noncentro structure
         Estimate of Friedel pairs measured         0
         Fraction of Friedel pairs measured     0.000
         Are heavy atom types Z>Si present           no
          Please check that the estimate of the number of Friedel pairs is
          correct. If it is not, please give the correct count in the
          _publ_section_exptl_refinement section of the submitted CIF.

---

S1. Comment

The room-temperature structure of lithium orotate monohydrate was first reported by Bach et al. (1990). One H atom of the water molecule was missing in that publication, because it could not be located in the difference Fourier synthesis, neither could it be introduced in a calculated position.

With the present data, measured at a low temperature of 110 (2) K, all H-atom positions could be determined unambiguously from the difference Fourier map (Fig. 1). With this information, the crystal structure can be completely described. The lithium center links the orotate and the water molecules to form a two-dimensional layer which is defined by the base vectors [101] and [011]. Thereby the lithium is in a tetrahedral environment of four O atoms (Fig. 2). Two of these are carbonyl O atoms [Li—O 1.892 (3) and 1.950 (3) Å], one is from the carboxylate group [Li—O 1.881 (3) Å], and the fourth is the water molecule [Li—O 1.973 (4) Å].

The two-dimensional layers formed by the lithium coordination are linked by O—H···O and N—H···O hydrogen bonds (see Table 2) to build up a three-dimensional network. According to the geometrical definition of Jeffrey (1997), H2 and H4 are involved in bifurcated hydrogen bonds with angle sums at these H atoms of 351 and 359°, respectively.

As can be seen from the Li—O bond lengths, the donor ability of the two carbonyl groups is quite different. This effect is a consequence of the hydrogen bonding. While O4 accepts a strong hydrogen bond from a water molecule, O3 is not involved in hydrogen bonding. The donor strength of O3 is therefore larger, leading to a shorter Li—O bond. Much smaller but still significant, is this effect reflected in the C═O double-bond lengths of 1.225 (2) Å for O3 and 1.2425 (19) Å for O4.

The carboxylate O atoms have different environments; while the first one coordinates to the lithium, the second one acts as an acceptor for two nearly linear hydrogen bonds. Surprisingly, this difference is not reflected in the bond distances of C1—O1 1.250 (2) Å and C1—O2 1.252 (2) Å.

The water molecule coordinates to the lithium via the tetrahedral `lone pair' direction. The β-angle between the H<sub>2</sub>O plane and the oxygen–metal direction (Ptasiewicz-Bak et al., 1999), amounts to 58.7°. The second `lone pair' is an acceptor for a hydrogen bond.

S2. Experimental

Lithium orotate monohydrate as obtained from Fluka Chemie AG (Buchs, Switzerland) was dissolved in water. The solution was then evaporated at a temperature of 330 K until crystal formation resulted.

S3. Refinement

The absolute structure could not be determined reliably. Friedel pairs were therefore merged in the refinement.

Computing details

Data collection: COLLECT (Nonius, 1998); cell refinement: HKL-2000 (Otwinowski & Minor, 1997); data reduction: HKL-2000 (Otwinowski & Minor, 1997); program(s) used to solve structure: coordinates taken from literature (Bach et al., 1990); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 2001); software used to prepare material for publication: manual editing of SHELXL97 output.

Figures

	Fig. 1. Difference Fourier map in the H2O plane. Friedel pairs were merged. H4 and H5 were omitted from structure-factor calculations. Contour level: 0.1 e Å^-3.
	Fig. 2. Coordination environment of the Li atom. Displacement ellipsoids drawn at the 50% probability level. [Symmetry codes: (i) x, y - 1, z - 1; (ii) x + 1, y - 1, z.]

lithium 1,2,3,6-tetrahydro-2,6-dioxo-4-pyrimidinecarboxylate monohydrate

Crystal data

Li^+·C5H3N2O4^−·H2O	Z = 1
Mr = 180.05	F(000) = 92
Triclinic, P1	Dx = 1.745 Mg m^−3
a = 4.9745 (2) Å	Mo Kα radiation, λ = 0.71073 Å
b = 5.3035 (2) Å	Cell parameters from 2473 reflections
c = 6.7548 (2) Å	θ = 3.1–30.0°
α = 89.733 (2)°	µ = 0.15 mm^−1
β = 102.717 (2)°	T = 110 K
γ = 99.6012 (13)°	Plate, colourless
V = 171.31 (1) Å^3	0.15 × 0.15 × 0.03 mm

Data collection

Nonius KappaCCD diffractometer	948 reflections with I > 2σ(I)
Radiation source: rotating anode	Rint = 0.050
Graphite monochromator	θmax = 30.0°, θmin = 3.1°
ϕ and ω scans with 2° scan width and a crystal–detector distance of 40 mm	h = −6→6
4219 measured reflections	k = −7→7
994 independent reflections	l = −9→9

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)] = 0.030	Hydrogen site location: difference Fourier map
wR(F^2) = 0.079	H-atom parameters not refined
S = 1.09	w = 1/[σ^2(Fo^2) + (0.0464P)^2 + 0.0193P] where P = (Fo^2 + 2Fc^2)/3
994 reflections	(Δ/σ)max = 0.031
118 parameters	Δρmax = 0.43 e Å^−3
3 restraints	Δρmin = −0.27 e Å^−3

Special details

Experimental. The non-standard setting of the triclinic unit cell was chosen to allow a better comparison with the publication of Bach et al. (1990).

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
O1	0.4976 (3)	0.8088 (2)	0.7934 (2)	0.0144 (3)
O2	0.7888 (3)	0.8660 (2)	1.10006 (19)	0.0134 (3)
O3	−0.1398 (3)	1.3798 (3)	0.7411 (2)	0.0144 (3)
O4	0.3434 (3)	1.5475 (3)	1.3940 (2)	0.0146 (3)
O5	0.9590 (3)	0.8413 (3)	0.50562 (19)	0.0145 (3)
N1	0.1107 (3)	1.4682 (3)	1.0664 (2)	0.0104 (3)
N2	0.2182 (3)	1.1671 (3)	0.8621 (2)	0.0101 (3)
C1	0.5855 (3)	0.9115 (3)	0.9669 (3)	0.0102 (3)
C2	0.4264 (3)	1.1143 (3)	1.0188 (3)	0.0097 (3)
C3	0.4784 (4)	1.2366 (3)	1.2017 (3)	0.0116 (3)
C4	0.0518 (3)	1.3416 (3)	0.8802 (3)	0.0102 (3)
C5	0.3124 (3)	1.4253 (3)	1.2317 (2)	0.0104 (3)
Li1	0.6638 (7)	0.6384 (6)	0.6212 (5)	0.0147 (6)
H1	0.0108	1.5639	1.0932	0.050*
H2	0.1921	1.0859	0.7588	0.050*
H3	0.6112	1.1938	1.3084	0.050*
H4	1.0759	0.7589	0.4932	0.050*
H5	0.8892	0.8639	0.3891	0.050*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O1	0.0168 (6)	0.0157 (6)	0.0121 (6)	0.0078 (5)	0.0019 (5)	−0.0039 (5)
O2	0.0146 (6)	0.0167 (6)	0.0100 (6)	0.0088 (5)	0.0006 (5)	−0.0015 (5)
O3	0.0148 (6)	0.0157 (6)	0.0119 (6)	0.0070 (5)	−0.0019 (5)	−0.0021 (5)
O4	0.0152 (6)	0.0192 (6)	0.0101 (6)	0.0080 (5)	0.0002 (5)	−0.0057 (5)
O5	0.0156 (6)	0.0189 (6)	0.0102 (6)	0.0085 (5)	0.0014 (5)	−0.0011 (5)
N1	0.0100 (6)	0.0112 (6)	0.0106 (7)	0.0054 (5)	0.0010 (5)	−0.0013 (5)
N2	0.0113 (6)	0.0111 (7)	0.0081 (7)	0.0041 (5)	0.0010 (5)	−0.0027 (5)
C1	0.0102 (7)	0.0098 (7)	0.0119 (8)	0.0034 (5)	0.0037 (6)	−0.0004 (6)
C2	0.0096 (7)	0.0102 (7)	0.0106 (8)	0.0042 (6)	0.0032 (6)	0.0004 (6)
C3	0.0112 (7)	0.0138 (8)	0.0100 (8)	0.0056 (6)	0.0003 (6)	−0.0012 (6)
C4	0.0110 (7)	0.0112 (7)	0.0088 (8)	0.0030 (6)	0.0023 (6)	−0.0001 (6)
C5	0.0095 (7)	0.0128 (8)	0.0087 (8)	0.0021 (6)	0.0016 (6)	−0.0009 (6)
Li1	0.0151 (14)	0.0171 (14)	0.0124 (14)	0.0072 (11)	0.0008 (12)	−0.0009 (11)

Geometric parameters (Å, º)

O1—C1	1.250 (2)	O5—H5	0.8045
O1—Li1	1.881 (3)	N1—C5	1.373 (2)
O2—C1	1.252 (2)	N1—C4	1.378 (2)
O2—H5^i	1.9062	N1—H1	0.8134
O2—H1^ii	2.0982	N2—C4	1.363 (2)
O3—C4	1.225 (2)	N2—C2	1.372 (2)
O3—Li1^iii	1.892 (3)	N2—H2	0.7958
O4—C5	1.2425 (19)	C1—C2	1.521 (2)
O4—Li1^iv	1.950 (3)	C2—C3	1.351 (2)
O4—H4^v	2.0916	C3—C5	1.441 (2)
O5—Li1	1.973 (4)	C3—H3	0.9199
O5—H2^vi	2.1444	Li1—O3^ii	1.892 (3)
O5—H4	0.8016	Li1—O4^vii	1.950 (3)
C1—O1—Li1	133.32 (15)	O1—C1—C2	115.57 (15)
C1—O2—H5^i	137.1	O2—C1—C2	117.35 (15)
C1—O2—H1^ii	126.5	C3—C2—N2	120.97 (15)
H5^i—O2—H1^ii	88.1	C3—C2—C1	124.60 (15)
C4—O3—Li1^iii	142.65 (15)	N2—C2—C1	114.43 (15)
C5—O4—Li1^iv	132.15 (14)	C2—C3—C5	119.27 (15)
C5—O4—H4^v	130.2	C2—C3—H3	120.6
Li1^iv—O4—H4^v	97.3	C5—C3—H3	120.0
Li1—O5—H2^vi	102.1	O3—C4—N2	122.11 (15)
Li1—O5—H4	111.5	O3—C4—N1	122.45 (15)
H2^vi—O5—H4	99.3	N2—C4—N1	115.44 (15)
Li1—O5—H5	106.7	O4—C5—N1	119.89 (14)
H2^vi—O5—H5	134.7	O4—C5—C3	124.16 (15)
H4—O5—H5	101.6	N1—C5—C3	115.95 (15)
C5—N1—C4	125.42 (14)	O1—Li1—O3^ii	115.80 (17)
C5—N1—H1	112.7	O1—Li1—O4^vii	99.57 (15)
C4—N1—H1	121.3	O3^ii—Li1—O4^vii	119.26 (17)
C4—N2—C2	122.93 (14)	O1—Li1—O5	117.94 (17)
C4—N2—H2	120.0	O3^ii—Li1—O5	99.21 (15)
C2—N2—H2	117.0	O4^vii—Li1—O5	105.70 (16)
O1—C1—O2	127.08 (16)
Li1—O1—C1—O2	−22.7 (3)	C2—N2—C4—N1	1.6 (2)
Li1—O1—C1—C2	156.93 (18)	C5—N1—C4—O3	176.49 (16)
H5^i—O2—C1—O1	−147.5	C5—N1—C4—N2	−2.4 (3)
H1^ii—O2—C1—O1	−10.1	Li1^iv—O4—C5—N1	−154.83 (19)
H5^i—O2—C1—C2	32.8	H4^v—O4—C5—N1	16.9
H1^ii—O2—C1—C2	170.2	Li1^iv—O4—C5—C3	24.7 (3)
C4—N2—C2—C3	−0.4 (2)	H4^v—O4—C5—C3	−163.6
C4—N2—C2—C1	179.45 (16)	C4—N1—C5—O4	−178.48 (16)
O1—C1—C2—C3	176.07 (18)	C4—N1—C5—C3	1.9 (3)
O2—C1—C2—C3	−4.2 (2)	C2—C3—C5—O4	179.83 (17)
O1—C1—C2—N2	−3.8 (2)	C2—C3—C5—N1	−0.6 (2)
O2—C1—C2—N2	175.87 (16)	C1—O1—Li1—O3^ii	49.2 (3)
N2—C2—C3—C5	−0.1 (2)	C1—O1—Li1—O4^vii	178.44 (18)
C1—C2—C3—C5	−179.97 (17)	C1—O1—Li1—O5	−68.0 (3)
Li1^iii—O3—C4—N2	−146.6 (2)	H2^vi—O5—Li1—O1	40.9
Li1^iii—O3—C4—N1	34.6 (3)	H2^vi—O5—Li1—O3^ii	−84.9
C2—N2—C4—O3	−177.30 (15)	H2^vi—O5—Li1—O4^vii	151.1

Symmetry codes: (i) x, y, z+1; (ii) x+1, y−1, z; (iii) x−1, y+1, z; (iv) x, y+1, z+1; (v) x−1, y+1, z+1; (vi) x+1, y, z; (vii) x, y−1, z−1.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O2^iii	0.81	2.10	2.8910 (19)	164.8
N2—H2···O1	0.80	2.26	2.6326 (18)	109.3
N2—H2···O5^viii	0.80	2.14	2.8941 (19)	157.1
O5—H4···O1^vi	0.80	2.56	2.9738 (17)	114.1
O5—H4···O4^ix	0.80	2.09	2.8797 (17)	167.6
O5—H5···O2^x	0.80	1.91	2.6928 (18)	165.6

Symmetry codes: (iii) x−1, y+1, z; (vi) x+1, y, z; (viii) x−1, y, z; (ix) x+1, y−1, z−1; (x) x, y, z−1.