2,4-Dioxo-1,2,3,4-tetra­hydro­pyrimidine-5-carboxyl­ic acid monohydrate

The title compound, C₅H₄N₂O₄·H₂O, a uracil derivative, contains several important functional groups, which give rise to its use in biomedical applications. The crystal structure consists of mol­ecules held together by extensive intermolec­ular hydrogen bonding between neighbouring pyrimidine rings and between the acid groups and water mol­ecules, resulting in a layered sheet structure. The asymmetric unit contains two molecules of the carboxylic acid and two water molecules.

Key indicators

• Single-crystal X-ray study
• T = 298 K
• Mean [sigma](C-C) = 0.003 Å
• R factor = 0.045
• wR factor = 0.047
• Data-to-parameter ratio = 7.7

checkCIF/PLATON results

No syntax errors found



Alert level A
PLAT355_ALERT_3_A Long    O-H Bond (0.82A)   O2     -   H1     ...       1.15 Ang.

Author Response: We believe that there is some exchange of the H between the carboxylate acid group and the solvate water, thus the O-H bond was found to be much longer than ordinary O-H bond.

PLAT355_ALERT_3_A Long    O-H Bond (0.82A)   O6     -   H7     ...       1.15 Ang.

Author Response: We believe that there is some exchange of the H between the carboxylate acid group and the solvate water, thus the O-H bond was found to be much longer than ordinary O-H bond.

Alert level B
REFNR01_ALERT_3_B  Ratio of reflections to parameters is < 8 for a
            centrosymmetric structure
            sine(theta)/lambda                0.6493
            Proportion of unique data used    0.6500
            Ratio reflections to parameters   7.7358
PLAT088_ALERT_3_B Poor Data / Parameter Ratio ....................       7.74
PLAT417_ALERT_2_B Short Inter D-H..H-D       H1     ..  H5      ..       2.05 Ang.
PLAT417_ALERT_2_B Short Inter D-H..H-D       H1     ..  H6      ..       1.97 Ang.
PLAT417_ALERT_2_B Short Inter D-H..H-D       H7     ..  H11     ..       1.95 Ang.
PLAT417_ALERT_2_B Short Inter D-H..H-D       H7     ..  H12     ..       2.07 Ang.
PLAT420_ALERT_2_B D-H Without Acceptor       O2     -   H1     ...          ?
PLAT420_ALERT_2_B D-H Without Acceptor       O6     -   H7     ...          ?

Alert level C
PLAT029_ALERT_3_C _diffrn_measured_fraction_theta_full Low .......       0.98
PLAT166_ALERT_4_C S.U's Given on Coordinates for calc-flagged ....         H1
PLAT166_ALERT_4_C S.U's Given on Coordinates for calc-flagged ....         H2
PLAT166_ALERT_4_C S.U's Given on Coordinates for calc-flagged ....         H3
PLAT166_ALERT_4_C S.U's Given on Coordinates for calc-flagged ....         H4
PLAT166_ALERT_4_C S.U's Given on Coordinates for calc-flagged ....         H5
PLAT166_ALERT_4_C S.U's Given on Coordinates for calc-flagged ....         H6
PLAT166_ALERT_4_C S.U's Given on Coordinates for calc-flagged ....         H7
PLAT166_ALERT_4_C S.U's Given on Coordinates for calc-flagged ....         H8
PLAT166_ALERT_4_C S.U's Given on Coordinates for calc-flagged ....         H9
PLAT166_ALERT_4_C S.U's Given on Coordinates for calc-flagged ....        H10
PLAT166_ALERT_4_C S.U's Given on Coordinates for calc-flagged ....        H11
PLAT166_ALERT_4_C S.U's Given on Coordinates for calc-flagged ....        H12
PLAT250_ALERT_2_C Large U3/U1 Ratio for Average U(i,j) Tensor ....       2.49
PLAT250_ALERT_2_C Large U3/U1 Ratio for Average U(i,j) Tensor ....       2.73
PLAT790_ALERT_4_C Centre of Gravity not Within Unit Cell: Resd.  #          3
              H2 O
PLAT790_ALERT_4_C Centre of Gravity not Within Unit Cell: Resd.  #          4
              H2 O

   2 ALERT level A = In general: serious problem
   8 ALERT level B = Potentially serious problem
  17 ALERT level C = Check and explain
   0 ALERT level G = General alerts; check

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   8 ALERT type 2 Indicator that the structure model may be wrong or deficient
   5 ALERT type 3 Indicator that the structure quality may be low
  14 ALERT type 4 Improvement, methodology, query or suggestion

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Computing details

Data collection: SMART (Bruker, 1998); cell refinement: SAINT (Bruker, 1999); data reduction: CrystalStructure (Rigaku/MSC, 2003); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: CRYSTALS (Watkin et al., 1996); molecular graphics: ORTEP-3 for Windows (Farrugia, 2001); software used to prepare material for publication: CrystalStructure.

(I)

Crystal data

C5H4N2O4·H2O	F(000) = 720.00
Mr = 174.11	Dx = 1.702 Mg m^−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.7107 Å
Hall symbol: -P 2ybc	Cell parameters from 16902 reflections
a = 7.876 (2) Å	θ = 1.0–27.5°
b = 20.352 (4) Å	µ = 0.16 mm^−1
c = 8.664 (2) Å	T = 298 K
β = 101.87 (1)°	Block, pale yellow
V = 1359.1 (5) Å^3	0.16 × 0.16 × 0.08 mm
Z = 8

Data collection

CCD diffractometer	Rint = 0.032
ω scans	θmax = 27.5°
16902 measured reflections	h = −10→10
3154 independent reflections	k = −26→23
2050 reflections with F^2 > 2σ(F^2)	l = −11→10

Refinement

Refinement on F	All H-atom parameters refined
R[F^2 > 2σ(F^2)] = 0.045	w = 1/[0.0002Fo^2 + σ(Fo^2) + 0.015]
wR(F^2) = 0.047	(Δ/σ)max < 0.001
S = 1.09	Δρmax = 0.29 e Å^−3
3154 reflections	Δρmin = −0.24 e Å^−3
265 parameters

Special details

Refinement. Refinement using reflections with F² > 2.0 σ(F²). The weighted R-factor(wR), goodness of fit (S) and R-factor (gt) are based on F, with F set to zero for negative F. The threshold expression of F² > 2.0 σ(F²) is used only for calculating R-factor (gt).

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
O1	0.6791 (3)	0.48050 (9)	0.9239 (3)	0.0583 (6)
O2	0.5790 (3)	0.38139 (9)	0.9597 (2)	0.0523 (6)
O3	0.3468 (2)	0.32829 (8)	0.7142 (2)	0.0462 (5)
O4	0.0685 (3)	0.46881 (9)	0.3413 (2)	0.0489 (6)
O5	−0.2338 (3)	0.12755 (8)	0.1300 (3)	0.0567 (6)
O6	−0.2188 (3)	0.23545 (8)	0.1543 (3)	0.0572 (6)
O7	0.0318 (3)	0.28639 (8)	0.3913 (2)	0.0499 (6)
O8	0.3559 (2)	0.14159 (8)	0.7243 (2)	0.0501 (6)
O9	0.8075 (3)	0.37734 (11)	1.2129 (3)	0.0690 (7)
O10	−0.4738 (3)	0.23826 (12)	−0.0720 (3)	0.0764 (8)
N1	0.2120 (3)	0.39985 (10)	0.5327 (3)	0.0394 (6)
N2	0.2840 (3)	0.50961 (10)	0.5339 (3)	0.0398 (6)
N3	0.1588 (3)	0.10124 (11)	0.5164 (3)	0.0433 (7)
N4	0.1871 (3)	0.21255 (10)	0.5544 (3)	0.0393 (6)
C1	0.5759 (3)	0.43635 (11)	0.8811 (3)	0.0383 (7)
C2	0.4372 (3)	0.44123 (11)	0.7380 (3)	0.0340 (7)
C3	0.3352 (3)	0.38552 (11)	0.6669 (3)	0.0340 (7)
C4	0.1794 (3)	0.46002 (12)	0.4600 (3)	0.0370 (7)
C5	0.4057 (3)	0.50061 (12)	0.6665 (3)	0.0370 (7)
C6	−0.1677 (3)	0.17629 (11)	0.1985 (3)	0.0380 (7)
C7	−0.0253 (3)	0.17176 (11)	0.3383 (3)	0.0340 (7)
C8	0.0601 (3)	0.22800 (11)	0.4243 (3)	0.0353 (7)
C9	0.2426 (3)	0.15126 (12)	0.6079 (3)	0.0379 (7)
C10	0.0309 (3)	0.11097 (12)	0.3893 (3)	0.0384 (7)
H1	0.687 (4)	0.3813 (13)	1.072 (3)	0.052 (8)*
H2	0.470 (3)	0.5395 (13)	0.710 (3)	0.042 (7)*
H3	0.267 (4)	0.548 (2)	0.489 (4)	0.061 (9)*
H4	0.147 (4)	0.368 (1)	0.484 (3)	0.052 (8)*
H5	0.896 (6)	0.405 (2)	1.246 (5)	0.12 (2)*
H6	0.848 (5)	0.334 (2)	1.239 (5)	0.10 (1)*
H7	−0.329 (4)	0.2338 (12)	0.044 (3)	0.046 (7)*
H8	−0.016 (3)	0.0716 (13)	0.331 (3)	0.047 (8)*
H9	0.196 (4)	0.064 (1)	0.542 (3)	0.051 (9)*
H10	0.240 (4)	0.244 (2)	0.614 (4)	0.066 (10)*
H11	−0.494 (6)	0.278 (2)	−0.123 (5)	0.12 (2)*
H12	−0.524 (5)	0.204 (2)	−0.141 (5)	0.092 (12)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O1	0.0559 (13)	0.0323 (10)	0.073 (2)	−0.0133 (9)	−0.0188 (11)	−0.0006 (9)
O2	0.0564 (12)	0.0358 (10)	0.0517 (12)	−0.0112 (9)	−0.0191 (10)	0.0084 (9)
O3	0.0541 (12)	0.0234 (9)	0.0495 (12)	−0.0039 (8)	−0.0161 (9)	0.0029 (8)
O4	0.0511 (11)	0.0364 (10)	0.0490 (12)	0.0008 (8)	−0.0134 (10)	0.0051 (8)
O5	0.0621 (13)	0.0313 (10)	0.0628 (13)	−0.0041 (9)	−0.0193 (11)	−0.0096 (9)
O6	0.0623 (13)	0.0279 (10)	0.064 (1)	0.0032 (9)	−0.0286 (11)	−0.0010 (9)
O7	0.0564 (12)	0.0222 (9)	0.0571 (13)	−0.0025 (8)	−0.0213 (10)	0.0004 (8)
O8	0.0499 (12)	0.0353 (10)	0.0542 (13)	0.0035 (8)	−0.0148 (10)	0.0033 (9)
O9	0.075 (2)	0.0356 (12)	0.074 (2)	−0.0023 (11)	−0.0353 (13)	0.0056 (11)
O10	0.089 (2)	0.0394 (12)	0.076 (2)	0.0022 (12)	−0.041 (1)	0.0010 (12)
N1	0.0449 (13)	0.0250 (11)	0.0404 (13)	−0.0046 (9)	−0.0098 (10)	0.0002 (9)
N2	0.0406 (13)	0.0232 (11)	0.050 (1)	0.0003 (9)	−0.0027 (10)	0.0061 (10)
N3	0.0445 (13)	0.0222 (11)	0.055 (2)	0.0039 (10)	−0.0087 (11)	0.0022 (10)
N4	0.0412 (13)	0.0244 (10)	0.0441 (13)	−0.0018 (9)	−0.0103 (11)	−0.0025 (9)
C1	0.038 (1)	0.0257 (12)	0.046 (2)	−0.0015 (11)	−0.0016 (12)	−0.0051 (11)
C2	0.034 (1)	0.0244 (12)	0.040 (1)	−0.0023 (10)	0.0004 (11)	−0.0020 (10)
C3	0.0336 (13)	0.0262 (12)	0.038 (1)	0.0005 (10)	−0.0023 (11)	−0.0008 (10)
C4	0.039 (1)	0.0284 (12)	0.040 (2)	0.0012 (10)	0.0002 (12)	0.0015 (11)
C5	0.036 (1)	0.0259 (12)	0.046 (2)	−0.0015 (10)	0.0012 (12)	−0.0036 (11)
C6	0.038 (1)	0.0285 (13)	0.042 (2)	−0.0011 (11)	−0.0043 (12)	−0.0026 (11)
C7	0.0332 (13)	0.0254 (12)	0.039 (1)	−0.0014 (10)	−0.0026 (11)	−0.0015 (10)
C8	0.0346 (13)	0.0263 (12)	0.040 (1)	−0.0017 (10)	−0.0045 (11)	−0.0007 (11)
C9	0.036 (1)	0.0287 (13)	0.044 (2)	0.0020 (10)	−0.0026 (12)	0.0020 (11)
C10	0.038 (1)	0.0266 (13)	0.046 (2)	−0.0019 (11)	−0.0024 (12)	−0.0021 (11)

Geometric parameters (Å, º)

O1—C1	1.217 (3)	N2—C4	1.375 (3)
O2—C1	1.307 (3)	N2—C5	1.349 (3)
O2—H1	1.15 (3)	N2—H3	0.87 (3)
O3—C3	1.232 (3)	N3—C9	1.373 (3)
O4—C4	1.218 (3)	N3—C10	1.345 (3)
O5—C6	1.216 (3)	N3—H9	0.83 (3)
O6—C6	1.302 (3)	N4—C8	1.381 (3)
O6—H7	1.15 (2)	N4—C9	1.371 (3)
O7—C8	1.232 (3)	N4—H10	0.87 (3)
O8—C9	1.217 (3)	C1—C2	1.477 (3)
O9—H5	0.90 (4)	C2—C3	1.452 (3)
O9—H6	0.95 (4)	C2—C5	1.358 (3)
O10—H11	0.93 (5)	C5—H2	0.97 (3)
O10—H12	0.95 (4)	C6—C7	1.475 (3)
N1—C3	1.383 (3)	C7—C8	1.453 (3)
N1—C4	1.377 (3)	C7—C10	1.357 (3)
N1—H4	0.87 (3)	C10—H8	0.98 (3)
C1—O2—H1	111 (1)	O3—C3—C2	126.9 (2)
C6—O6—H7	110 (1)	N1—C3—C2	115.1 (2)
H5—O9—H6	108 (3)	O4—C4—N1	123.5 (2)
H11—O10—H12	109 (3)	O4—C4—N2	122.9 (2)
C3—N1—C4	127.2 (2)	N1—C4—N2	113.7 (2)
C3—N1—H4	119 (1)	H2—C5—N2	116 (1)
C4—N1—H4	113 (1)	H2—C5—C2	121 (1)
C4—N2—C5	123.4 (2)	N2—C5—C2	122.7 (2)
C4—N2—H3	115 (1)	C7—C6—O5	121.8 (2)
C5—N2—H3	121 (1)	C7—C6—O6	115.9 (2)
C9—N3—C10	123.6 (2)	O5—C6—O6	122.4 (2)
C9—N3—H9	115 (1)	C8—C7—C10	117.8 (2)
C10—N3—H9	121 (1)	C8—C7—C6	124.4 (2)
C8—N4—C9	127.6 (2)	C10—C7—C6	117.8 (2)
C8—N4—H10	119 (2)	O7—C8—N4	118.4 (2)
C9—N4—H10	113 (2)	O7—C8—C7	126.8 (2)
C2—C1—O1	122.6 (2)	N4—C8—C7	114.9 (2)
C2—C1—O2	115.2 (2)	O8—C9—N3	122.8 (2)
O1—C1—O2	122.2 (2)	O8—C9—N4	123.8 (2)
C3—C2—C5	117.9 (2)	N3—C9—N4	113.4 (2)
C3—C2—C1	123.6 (2)	H8—C10—N3	116 (1)
C5—C2—C1	118.5 (2)	H8—C10—C7	120 (1)
O3—C3—N1	118.0 (2)	N3—C10—C7	122.7 (2)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O2—H1···O9	1.15 (3)	1.39 (3)	2.537 (3)	175 (3)
N2—H3···O5^i	0.87 (4)	1.91 (4)	2.775 (3)	174 (3)
N1—H4···O7	0.88 (2)	1.98 (2)	2.852 (3)	170 (2)
O9—H5···O4^ii	0.90 (5)	1.94 (4)	2.826 (3)	171 (4)
O9—H6···O6^ii	0.95 (4)	2.16 (4)	2.932 (3)	137 (3)
O9—H6···O7^ii	0.95 (4)	2.00 (4)	2.795 (3)	140 (3)
O6—H7···O10	1.15 (3)	1.36 (3)	2.502 (4)	170 (3)
N3—H9···O1^iii	0.83 (2)	1.96 (2)	2.768 (3)	168 (3)
N4—H10···O3	0.87 (4)	2.03 (4)	2.886 (3)	169 (3)
O10—H11···O2^iv	0.92 (4)	2.26 (4)	2.947 (3)	131 (3)
O10—H11···O3^iv	0.92 (4)	1.97 (4)	2.776 (3)	145 (4)
O10—H12···O8^iv	0.95 (4)	1.85 (4)	2.795 (3)	174 (4)

Symmetry codes: (i) −x, y+1/2, −z+1/2; (ii) x+1, y, z+1; (iii) −x+1, y−1/2, −z+3/2; (iv) x−1, y, z−1.