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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.
Supporting information
CCDC reference: 242352
Key indicators
- Single-crystal X-ray study
- T = 298 K
- Mean (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
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.
Crystal data top
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) Å3 | 0.16 × 0.16 × 0.08 mm |
Z = 8 | |
Data collection top
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 F2 > 2σ(F2) | l = −11→10 |
Refinement top
Refinement on F | All H-atom parameters refined |
R[F2 > 2σ(F2)] = 0.045 | w = 1/[0.0002Fo2 + σ(Fo2) + 0.015] |
wR(F2) = 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 top
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 (Å2) top | 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 (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
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) top
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) top
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···O5i | 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···O4ii | 0.90 (5) | 1.94 (4) | 2.826 (3) | 171 (4) |
O9—H6···O6ii | 0.95 (4) | 2.16 (4) | 2.932 (3) | 137 (3) |
O9—H6···O7ii | 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···O1iii | 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···O2iv | 0.92 (4) | 2.26 (4) | 2.947 (3) | 131 (3) |
O10—H11···O3iv | 0.92 (4) | 1.97 (4) | 2.776 (3) | 145 (4) |
O10—H12···O8iv | 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. |
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