Redetermination of orotic acid monohydrate.

The crystal structure of the title compound, which is also known as vitamin B(13) (systematic name: 2,6-dioxo-1,2,3,6-tetra-hydro-pyrimidine-4-carboxylic acid monohydrate), C(5)H(4)N(2)O(4)·H(2)O, was reported for the first time by Takusagawa & Shimada [Bull. Chem. Soc. Jpn (1973 ▶), 46, 2011-2019]. The present redetermination provides more precise values of the mol-ecular geometry. The asymmetric unit comprises a planar diketo tautomer and a solvent water mol-ecule. In the crystal structure, mol-ecules are connected by O-H⋯O, N-H⋯O and C-H⋯O hydrogen bonds involving NH groups, two carbonyl O atoms and the solvent water mol-ecule.

Related literature

For the previous structure determination, see: Takusagawa & Shimada (1973 ▶). For a general approach to the use of multiple hydrogen-bonding DNA/RNA nucleobases as potential supra­molecular reagents, see: Portalone et al. (1999 ▶); Brunetti et al. (2000 ▶, 2002 ▶); Portalone & Colapietro (2007 ▶ and references therein). For the computation of ring patterns formed by hydrogen bonds in crystal structures, see: Etter et al. (1990 ▶); Bernstein et al. (1995 ▶); Motherwell et al. (1999 ▶).

Experimental

Crystal data

C5H4N2O4·H2O

M = 174.12

Triclinic,

a = 5.89854 (14) Å

b = 6.92921 (15) Å

c = 9.59160 (18) Å

α = 74.6778 (12)°

β = 72.3232 (16)°

γ = 68.447 (2)°

V = 342.21 (1) Å3

Z = 2

Mo Kα radiation

μ = 0.15 mm−1

T = 298 (2) K

0.20 × 0.15 × 0.15 mm

Data collection

Oxford Diffraction Xcalibur S CCD diffractometer

Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2006 ▶) T min = 0.977, T max = 0.985

64781 measured reflections

2340 independent reflections

2048 reflections with I > 2σ(I)

R int = 0.017

Refinement

R[F 2 > 2σ(F 2)] = 0.044

wR(F 2) = 0.133

S = 1.08

2340 reflections

133 parameters

All H-atom parameters refined

Δρmax = 0.19 e Å−3

Δρmin = −0.22 e Å−3

Data collection: CrysAlis CCD (Oxford Diffraction, 2006 ▶); cell refinement: CrysAlis RED (Oxford Diffraction, 2006 ▶); data reduction: CrysAlis RED; program(s) used to solve structure: SIR97 (Altomare et al., 1999 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: ORTEP3 (Farrugia, 1997 ▶); software used to prepare material for publication: WinGX (Farrugia, 1999 ▶).

Crystal structure: contains datablocks I, global. DOI: 10.1107/S160053680800562X/kp2160sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S160053680800562X/kp2160Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

C5H4N2O4·H2O	Z = 2
Mr = 174.12	F000 = 180
Triclinic, P1	Dx = 1.690 Mg m−3
Hall symbol: -P 1	Mo Kα radiation λ = 0.71073 Å
a = 5.89854 (14) Å	Cell parameters from 64781 reflections
b = 6.92921 (15) Å	θ = 3.2–32.0º
c = 9.59160 (18) Å	µ = 0.15 mm−1
α = 74.6778 (12)º	T = 298 (2) K
β = 72.3232 (16)º	Plate, colourless
γ = 68.447 (2)º	0.20 × 0.15 × 0.15 mm
V = 342.207 (13) Å3

Oxford Diffraction Xcalibur S CCD diffractometer	2340 independent reflections
Radiation source: Enhance (Mo) X-ray source	2048 reflections with I > 2σ(I)
Monochromator: graphite	Rint = 0.017
Detector resolution: 16.0696 pixels mm-1	θmax = 32.0º
T = 298(2) K	θmin = 3.2º
ω and φ scans	h = −8→8
Absorption correction: multi-scan(CrysAlis RED; Oxford Diffraction, 2006)	k = −10→10
Tmin = 0.977, Tmax = 0.985	l = −14→14
64781 measured reflections

Refinement on F2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.044	All H-atom parameters refined
wR(F2) = 0.133	w = 1/[σ2(Fo2) + (0.0846P)2 + 0.0376P] where P = (Fo2 + 2Fc2)/3
S = 1.08	(Δ/σ)max < 0.001
2340 reflections	Δρmax = 0.19 e Å−3
133 parameters	Δρmin = −0.22 e Å−3
Primary atom site location: structure-invariant direct methods	Extinction correction: none

Experimental. Empirical absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm.

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.

	x	y	z	Uiso*/Ueq
O1	−0.14403 (15)	0.19593 (14)	0.87497 (9)	0.0437 (2)
O2	0.33017 (14)	0.40869 (13)	0.43298 (8)	0.0402 (2)
O3	0.67729 (18)	−0.25757 (17)	0.92057 (11)	0.0575 (3)
O4	0.94015 (16)	−0.17721 (14)	0.70790 (10)	0.0430 (2)
H4	1.045 (5)	−0.276 (4)	0.759 (3)	0.072 (6)*
N1	0.27952 (15)	0.03091 (13)	0.83018 (9)	0.03108 (19)
H1	0.248 (4)	−0.038 (3)	0.918 (2)	0.052 (4)*
C2	0.06502 (18)	0.17428 (15)	0.79307 (10)	0.0302 (2)
N3	0.09988 (15)	0.29328 (13)	0.65310 (8)	0.03059 (19)
H3	−0.050 (4)	0.391 (3)	0.630 (2)	0.054 (5)*
C4	0.32531 (17)	0.28849 (14)	0.55477 (10)	0.0284 (2)
C5	0.54286 (17)	0.13666 (14)	0.60218 (10)	0.0295 (2)
H5	0.689 (3)	0.127 (3)	0.540 (2)	0.042 (4)*
C6	0.51057 (17)	0.01317 (13)	0.73716 (9)	0.02706 (19)
C7	0.72006 (19)	−0.15575 (15)	0.79814 (11)	0.0325 (2)
O5	1.28887 (17)	−0.45822 (16)	0.81521 (11)	0.0523 (3)
H51	1.421 (5)	−0.460 (4)	0.757 (3)	0.080 (7)*
H52	1.313 (5)	−0.528 (4)	0.896 (3)	0.082 (7)*

	U11	U22	U33	U12	U13	U23
O1	0.0285 (4)	0.0499 (5)	0.0329 (4)	−0.0054 (3)	−0.0022 (3)	0.0094 (3)
O2	0.0291 (4)	0.0447 (4)	0.0298 (4)	−0.0065 (3)	−0.0079 (3)	0.0154 (3)
O3	0.0390 (5)	0.0612 (6)	0.0449 (5)	−0.0062 (4)	−0.0138 (4)	0.0266 (4)
O4	0.0302 (4)	0.0449 (4)	0.0385 (4)	−0.0003 (3)	−0.0112 (3)	0.0054 (3)
N1	0.0289 (4)	0.0311 (4)	0.0247 (3)	−0.0063 (3)	−0.0080 (3)	0.0067 (3)
C2	0.0277 (4)	0.0308 (4)	0.0252 (4)	−0.0071 (3)	−0.0065 (3)	0.0037 (3)
N3	0.0245 (4)	0.0319 (4)	0.0258 (3)	−0.0047 (3)	−0.0077 (3)	0.0070 (3)
C4	0.0260 (4)	0.0289 (4)	0.0244 (4)	−0.0064 (3)	−0.0078 (3)	0.0041 (3)
C5	0.0243 (4)	0.0308 (4)	0.0258 (4)	−0.0045 (3)	−0.0072 (3)	0.0029 (3)
C6	0.0268 (4)	0.0251 (4)	0.0257 (4)	−0.0045 (3)	−0.0106 (3)	0.0014 (3)
C7	0.0306 (4)	0.0297 (4)	0.0322 (4)	−0.0049 (3)	−0.0137 (3)	0.0038 (3)
O5	0.0287 (4)	0.0598 (6)	0.0426 (5)	0.0010 (4)	−0.0082 (3)	0.0118 (4)

O1—C2	1.2241 (12)	N3—C4	1.3716 (12)
O2—C4	1.2418 (10)	N3—H3	0.94 (2)
O3—C7	1.2056 (13)	C4—C5	1.4387 (12)
O4—C7	1.3040 (13)	C5—C6	1.3525 (12)
O4—H4	0.89 (3)	C5—H5	0.879 (19)
N1—C6	1.3656 (12)	C6—C7	1.5012 (12)
N1—C2	1.3702 (12)	O5—H51	0.81 (3)
N1—H1	0.85 (2)	O5—H52	0.82 (3)
C2—N3	1.3772 (11)
C7—O4—H4	104.3 (16)	N3—C4—C5	115.74 (8)
C6—N1—C2	122.36 (8)	C6—C5—C4	118.56 (8)
C6—N1—H1	126.4 (14)	C6—C5—H5	124.1 (11)
C2—N1—H1	111.2 (14)	C4—C5—H5	117.3 (11)
O1—C2—N1	123.81 (8)	C5—C6—N1	122.13 (8)
O1—C2—N3	121.35 (8)	C5—C6—C7	124.03 (9)
N1—C2—N3	114.83 (8)	N1—C6—C7	113.84 (8)
C4—N3—C2	126.29 (7)	O3—C7—O4	125.70 (9)
C4—N3—H3	120.3 (12)	O3—C7—C6	120.28 (10)
C2—N3—H3	113.3 (12)	O4—C7—C6	114.02 (8)
O2—C4—N3	119.61 (8)	H51—O5—H52	110 (2)
O2—C4—C5	124.64 (9)
C6—N1—C2—O1	−178.86 (10)	C4—C5—C6—N1	−1.20 (15)
C6—N1—C2—N3	2.20 (15)	C4—C5—C6—C7	178.02 (9)
O1—C2—N3—C4	177.12 (10)	C2—N1—C6—C5	0.18 (16)
N1—C2—N3—C4	−3.91 (15)	C2—N1—C6—C7	−179.11 (9)
C2—N3—C4—O2	−178.17 (10)	C5—C6—C7—O3	178.85 (12)
C2—N3—C4—C5	2.97 (15)	N1—C6—C7—O3	−1.87 (15)
O2—C4—C5—C6	−179.05 (10)	C5—C6—C7—O4	−1.13 (15)
N3—C4—C5—C6	−0.26 (14)	N1—C6—C7—O4	178.15 (9)

D—H···A	D—H	H···A	D···A	D—H···A
O4—H4···O5	0.89 (3)	1.65 (3)	2.5231 (11)	166 (2)
N1—H1···O1i	0.85 (2)	2.03 (2)	2.8824 (11)	175.2 (19)
N3—H3···O2ii	0.94 (2)	1.87 (2)	2.8112 (11)	174.6 (18)
O5—H51···O2iii	0.81 (3)	2.00 (3)	2.7786 (12)	161 (3)
O5—H52···O3iv	0.82 (3)	1.98 (3)	2.7787 (12)	164 (2)
C5—H5···O4iii	0.879 (19)	2.740 (19)	3.5922 (13)	163.7 (15)

Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O4—H4⋯O5	0.89 (3)	1.65 (3)	2.5231 (11)	166 (2)
N1—H1⋯O1i	0.85 (2)	2.03 (2)	2.8824 (11)	175.2 (19)
N3—H3⋯O2ii	0.94 (2)	1.87 (2)	2.8112 (11)	174.6 (18)
O5—H51⋯O2iii	0.81 (3)	2.00 (3)	2.7786 (12)	161 (3)
O5—H52⋯O3iv	0.82 (3)	1.98 (3)	2.7787 (12)	164 (2)
C5—H5⋯O4iii	0.879 (19)	2.740 (19)	3.5922 (13)	163.7 (15)

Symmetry codes: (i) ; (ii) ; (iii) ; (iv) .