supplementary materials


bt6903 scheme

Acta Cryst. (2013). E69, o885    [ doi:10.1107/S1600536813012610 ]

Pyrimidine-4-carboxylic acid

K. Kiegiel, W. Starosta and J. Leciejewicz

Abstract top

The crystal structure of the title compound, C5H4N2O2, is built of acid molecules located on a mirror plane. They form sheets stacked along the b-axis direction. The molecules interact via O-H...N hydrogen bonds, forming [001] chains, and weak van der Waals interactions.

Comment top

The monoclinic structure of pyrimidine-4-carboxylic acid C5H4N2O2 is composed of molecular sheets stacked along [010] crystal direction (Fig.1). Within a sheet, hetero-ring and carboxylate group atoms are coplanar. Acid molecules interact via hydrogen bonds of 2.658 (3) A in which protonated carboxylate O atoms are as donors and hetero-ring N atoms in adjacent acid molecules act as acceptors. The C—C and C—N bond distances and bond angles within the acid molecule do not differ from those reported earlier in the structure of the Li complex with the title acid (Starosta & Leciejewicz, 2012). The sheets are held together by van der Waals interactions as indicated by the distance between adjacent sheets which is 3.171 (1) A.

Related literature top

For the structure of a Li complex with pyrimidine-4-carboxylate and aqua ligands, see: Starosta & Leciejewicz (2012).

Experimental top

75 ml of a hot (ca 350 K) aqueous solution containing 31.6 mmol of potassium permanganate was added dropwise during 3 h to 8 ml of stirred aqueous solution containing 21.3 mmol of 4-methylpyrimidine and 5 mmol of NaOH. After stirring for half an hour longer, 1 ml of methanol was added to decompose the excess of potassium permanganate. The hot solution was filtered and the solid washed twice with 5 ml of water. Then, the filtrate and the washings were concentrated to ca 15 ml and acidified to pH 2–3 with concentrated HCl. After cooling to room temperature the precipitate containing 10.5 mmol of crude pyrimidine-4-carboxylic acid was recrystalized from a mixture of water and methanol taken in 20:1 ratio to give 1.1 g. (8.9 mmol) of colourless crystal blocks of the title acid (yield 42%, m.p. 508–509 K).

Refinement top

The hydrogen atom attached to the carboxylic group was located in a difference map and refined isotropically, while the three H atoms attached to pyrimidine C atoms were located at a calculated positions and treated as riding on the parent atoms with C—H=0.93 Å.

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. Molecules of the title compound with atom labelling scheme and 50% probability displacement ellipsoids viewed along the b axis.
Pyrimidine-4-carboxylic acid top
Crystal data top
C5H4N2O2F(000) = 128
Mr = 124.10Dx = 1.559 Mg m3
Monoclinic, P21/mMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybCell parameters from 25 reflections
a = 6.0080 (12) Åθ = 6–15°
b = 6.3519 (13) ŵ = 0.12 mm1
c = 7.4834 (15) ÅT = 293 K
β = 112.20 (3)°Plate, colourless
V = 264.41 (9) Å30.17 × 0.16 × 0.06 mm
Z = 2
Data collection top
Kuma KM-4 four-circle
diffractometer
349 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.129
Graphite monochromatorθmax = 25.7°, θmin = 2.9°
profile data from ω/2θ scanh = 77
Absorption correction: analytical
(CrysAlis RED; Oxford Diffraction, 2008)
k = 77
Tmin = 0.973, Tmax = 0.994l = 99
1981 measured reflections3 standard reflections every 200 reflections
545 independent reflections intensity decay: 0.9%
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)] = 0.048Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.124H atoms treated by a mixture of independent and constrained refinement
S = 1.00 w = 1/[σ2(Fo2) + (0.0689P)2]
where P = (Fo2 + 2Fc2)/3
545 reflections(Δ/σ)max < 0.001
58 parametersΔρmax = 0.15 e Å3
0 restraintsΔρmin = 0.34 e Å3
Crystal data top
C5H4N2O2V = 264.41 (9) Å3
Mr = 124.10Z = 2
Monoclinic, P21/mMo Kα radiation
a = 6.0080 (12) ŵ = 0.12 mm1
b = 6.3519 (13) ÅT = 293 K
c = 7.4834 (15) Å0.17 × 0.16 × 0.06 mm
β = 112.20 (3)°
Data collection top
Kuma KM-4 four-circle
diffractometer
349 reflections with I > 2σ(I)
Absorption correction: analytical
(CrysAlis RED; Oxford Diffraction, 2008)
Rint = 0.129
Tmin = 0.973, Tmax = 0.994θmax = 25.7°
1981 measured reflections3 standard reflections every 200 reflections
545 independent reflections intensity decay: 0.9%
Refinement top
R[F2 > 2σ(F2)] = 0.048H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.124Δρmax = 0.15 e Å3
S = 1.00Δρmin = 0.34 e Å3
545 reflectionsAbsolute structure: ?
58 parametersFlack parameter: ?
0 restraintsRogers parameter: ?
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
O11.0036 (4)0.25000.2735 (3)0.0416 (6)
C40.8398 (5)0.25000.5171 (4)0.0308 (7)
N10.9072 (4)0.25000.8961 (3)0.0397 (7)
N31.0647 (4)0.25000.6476 (3)0.0371 (7)
O20.6049 (4)0.25000.1835 (3)0.0649 (8)
C70.8036 (5)0.25000.3063 (4)0.0364 (7)
C50.6416 (5)0.25000.5672 (4)0.0403 (8)
H50.48600.25000.47470.048*
C60.6868 (5)0.25000.7631 (4)0.0448 (9)
H60.55730.25000.80240.054*
C21.0847 (5)0.25000.8311 (4)0.0401 (8)
H41.24010.25000.92400.048*
H10.967 (6)0.25000.126 (5)0.064 (11)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0403 (11)0.0677 (13)0.0196 (9)0.0000.0145 (8)0.000
C40.0308 (14)0.0389 (14)0.0225 (13)0.0000.0097 (11)0.000
N10.0401 (13)0.0606 (16)0.0208 (11)0.0000.0142 (11)0.000
N30.0276 (11)0.0651 (16)0.0173 (12)0.0000.0071 (9)0.000
O20.0364 (12)0.130 (2)0.0206 (10)0.0000.0020 (9)0.000
C70.0366 (15)0.0507 (16)0.0217 (13)0.0000.0109 (12)0.000
C50.0287 (14)0.0613 (19)0.0293 (15)0.0000.0093 (13)0.000
C60.0325 (14)0.072 (2)0.0342 (15)0.0000.0179 (12)0.000
C20.0304 (13)0.0718 (19)0.0160 (12)0.0000.0062 (11)0.000
Geometric parameters (Å, º) top
O1—C71.314 (4)N3—C21.332 (3)
O1—H11.04 (4)O2—C71.200 (3)
C4—N31.335 (3)C5—C61.386 (4)
C4—C51.376 (4)C5—H50.9300
C4—C71.509 (3)C6—H60.9300
N1—C61.322 (4)C2—H40.9300
N1—C21.329 (4)
C7—O1—H1110.9 (19)C4—C5—C6116.4 (3)
N3—C4—C5122.8 (2)C4—C5—H5121.8
N3—C4—C7118.1 (2)C6—C5—H5121.8
C5—C4—C7119.1 (3)N1—C6—C5122.4 (3)
C6—N1—C2116.0 (2)N1—C6—H6118.8
C2—N3—C4115.2 (2)C5—C6—H6118.8
O2—C7—O1124.9 (2)N1—C2—N3127.3 (2)
O2—C7—C4120.6 (3)N1—C2—H4116.4
O1—C7—C4114.5 (2)N3—C2—H4116.4
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1···N1i1.04 (4)1.62 (4)2.660 (3)179 (3)
Symmetry code: (i) x, y, z1.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1···N1i1.04 (4)1.62 (4)2.660 (3)179 (3)
Symmetry code: (i) x, y, z1.
Acknowledgements top

No acknowledgments

references
References top

Kuma (1996). KM-4 Software. Kuma Diffraction Ltd, Wrocław, Poland.

Kuma (2001). DATAPROC. Kuma Diffraction Ltd, Wrocław, Poland.

Oxford Diffraction (2008). CrysAlis RED. Oxford Diffraction Ltd, Yarnton, England.

Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122.

Starosta, W. & Leciejewicz, J. (2012). Acta Cryst. E68, m1065–m1066.