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.
Supporting information
CCDC reference: 159828
Key indicators
- Single-crystal X-ray study
- T = 110 K
- Mean (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.
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.
The absolute structure could not be determined reliably. Friedel pairs were
therefore merged in the refinement.
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.
lithium 1,2,3,6-tetrahydro-2,6-dioxo-4-pyrimidinecarboxylate monohydrate
top
Crystal data top
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) Å3 | 0.15 × 0.15 × 0.03 mm |
Data collection top
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 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)] = 0.030 | Hydrogen site location: difference Fourier map |
wR(F2) = 0.079 | H-atom parameters not refined |
S = 1.09 | w = 1/[σ2(Fo2) + (0.0464P)2 + 0.0193P] where P = (Fo2 + 2Fc2)/3 |
994 reflections | (Δ/σ)max = 0.031 |
118 parameters | Δρmax = 0.43 e Å−3 |
3 restraints | Δρmin = −0.27 e Å−3 |
Crystal data top
Li+·C5H3N2O4−·H2O | γ = 99.6012 (13)° |
Mr = 180.05 | V = 171.31 (1) Å3 |
Triclinic, P1 | Z = 1 |
a = 4.9745 (2) Å | Mo Kα radiation |
b = 5.3035 (2) Å | µ = 0.15 mm−1 |
c = 6.7548 (2) Å | T = 110 K |
α = 89.733 (2)° | 0.15 × 0.15 × 0.03 mm |
β = 102.717 (2)° | |
Data collection top
Nonius KappaCCD diffractometer | 948 reflections with I > 2σ(I) |
4219 measured reflections | Rint = 0.050 |
994 independent reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.030 | 3 restraints |
wR(F2) = 0.079 | H-atom parameters not refined |
S = 1.09 | Δρmax = 0.43 e Å−3 |
994 reflections | Δρmin = −0.27 e Å−3 |
118 parameters | |
Special details top
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 (Å2) top | 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 (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
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) top
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—H5i | 1.9062 | N1—H1 | 0.8134 |
O2—H1ii | 2.0982 | N2—C4 | 1.363 (2) |
O3—C4 | 1.225 (2) | N2—C2 | 1.372 (2) |
O3—Li1iii | 1.892 (3) | N2—H2 | 0.7958 |
O4—C5 | 1.2425 (19) | C1—C2 | 1.521 (2) |
O4—Li1iv | 1.950 (3) | C2—C3 | 1.351 (2) |
O4—H4v | 2.0916 | C3—C5 | 1.441 (2) |
O5—Li1 | 1.973 (4) | C3—H3 | 0.9199 |
O5—H2vi | 2.1444 | Li1—O3ii | 1.892 (3) |
O5—H4 | 0.8016 | Li1—O4vii | 1.950 (3) |
| | | |
C1—O1—Li1 | 133.32 (15) | O1—C1—C2 | 115.57 (15) |
C1—O2—H5i | 137.1 | O2—C1—C2 | 117.35 (15) |
C1—O2—H1ii | 126.5 | C3—C2—N2 | 120.97 (15) |
H5i—O2—H1ii | 88.1 | C3—C2—C1 | 124.60 (15) |
C4—O3—Li1iii | 142.65 (15) | N2—C2—C1 | 114.43 (15) |
C5—O4—Li1iv | 132.15 (14) | C2—C3—C5 | 119.27 (15) |
C5—O4—H4v | 130.2 | C2—C3—H3 | 120.6 |
Li1iv—O4—H4v | 97.3 | C5—C3—H3 | 120.0 |
Li1—O5—H2vi | 102.1 | O3—C4—N2 | 122.11 (15) |
Li1—O5—H4 | 111.5 | O3—C4—N1 | 122.45 (15) |
H2vi—O5—H4 | 99.3 | N2—C4—N1 | 115.44 (15) |
Li1—O5—H5 | 106.7 | O4—C5—N1 | 119.89 (14) |
H2vi—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—O3ii | 115.80 (17) |
C5—N1—H1 | 112.7 | O1—Li1—O4vii | 99.57 (15) |
C4—N1—H1 | 121.3 | O3ii—Li1—O4vii | 119.26 (17) |
C4—N2—C2 | 122.93 (14) | O1—Li1—O5 | 117.94 (17) |
C4—N2—H2 | 120.0 | O3ii—Li1—O5 | 99.21 (15) |
C2—N2—H2 | 117.0 | O4vii—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) |
H5i—O2—C1—O1 | −147.5 | C5—N1—C4—N2 | −2.4 (3) |
H1ii—O2—C1—O1 | −10.1 | Li1iv—O4—C5—N1 | −154.83 (19) |
H5i—O2—C1—C2 | 32.8 | H4v—O4—C5—N1 | 16.9 |
H1ii—O2—C1—C2 | 170.2 | Li1iv—O4—C5—C3 | 24.7 (3) |
C4—N2—C2—C3 | −0.4 (2) | H4v—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—O3ii | 49.2 (3) |
N2—C2—C3—C5 | −0.1 (2) | C1—O1—Li1—O4vii | 178.44 (18) |
C1—C2—C3—C5 | −179.97 (17) | C1—O1—Li1—O5 | −68.0 (3) |
Li1iii—O3—C4—N2 | −146.6 (2) | H2vi—O5—Li1—O1 | 40.9 |
Li1iii—O3—C4—N1 | 34.6 (3) | H2vi—O5—Li1—O3ii | −84.9 |
C2—N2—C4—O3 | −177.30 (15) | H2vi—O5—Li1—O4vii | 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) top
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O2iii | 0.81 | 2.10 | 2.8910 (19) | 164.8 |
N2—H2···O1 | 0.80 | 2.26 | 2.6326 (18) | 109.3 |
N2—H2···O5viii | 0.80 | 2.14 | 2.8941 (19) | 157.1 |
O5—H4···O1vi | 0.80 | 2.56 | 2.9738 (17) | 114.1 |
O5—H4···O4ix | 0.80 | 2.09 | 2.8797 (17) | 167.6 |
O5—H5···O2x | 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. |
Experimental details
Crystal data |
Chemical formula | Li+·C5H3N2O4−·H2O |
Mr | 180.05 |
Crystal system, space group | Triclinic, P1 |
Temperature (K) | 110 |
a, b, c (Å) | 4.9745 (2), 5.3035 (2), 6.7548 (2) |
α, β, γ (°) | 89.733 (2), 102.717 (2), 99.6012 (13) |
V (Å3) | 171.31 (1) |
Z | 1 |
Radiation type | Mo Kα |
µ (mm−1) | 0.15 |
Crystal size (mm) | 0.15 × 0.15 × 0.03 |
|
Data collection |
Diffractometer | Nonius KappaCCD diffractometer |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 4219, 994, 948 |
Rint | 0.050 |
(sin θ/λ)max (Å−1) | 0.703 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.030, 0.079, 1.09 |
No. of reflections | 994 |
No. of parameters | 118 |
No. of restraints | 3 |
H-atom treatment | H-atom parameters not refined |
Δρmax, Δρmin (e Å−3) | 0.43, −0.27 |
Selected geometric parameters (Å, º) topO1—C1 | 1.250 (2) | O3—Li1i | 1.892 (3) |
O1—Li1 | 1.881 (3) | O4—C5 | 1.2425 (19) |
O2—C1 | 1.252 (2) | O4—Li1ii | 1.950 (3) |
O3—C4 | 1.225 (2) | O5—Li1 | 1.973 (4) |
| | | |
O2—C1—C2—C3 | −4.2 (2) | | |
Symmetry codes: (i) x−1, y+1, z; (ii) x, y+1, z+1. |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O2i | 0.81 | 2.10 | 2.8910 (19) | 164.8 |
N2—H2···O1 | 0.80 | 2.26 | 2.6326 (18) | 109.3 |
N2—H2···O5iii | 0.80 | 2.14 | 2.8941 (19) | 157.1 |
O5—H4···O1iv | 0.80 | 2.56 | 2.9738 (17) | 114.1 |
O5—H4···O4v | 0.80 | 2.09 | 2.8797 (17) | 167.6 |
O5—H5···O2vi | 0.80 | 1.91 | 2.6928 (18) | 165.6 |
Symmetry codes: (i) x−1, y+1, z; (iii) x−1, y, z; (iv) x+1, y, z; (v) x+1, y−1, z−1; (vi) x, y, z−1. |
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 H2O 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.