Methyl (2S)-2-[2-(5-fluoro-2,4-dioxo-1,2,3,4-tetra­hydro­pyrimidin-1-yl)acetamido]propionate monohydrate

In the title compound, C₁₀H₁₂FN₃O₅·H₂O, the crystal packing is stabilized by an extensive three-dimensional network of inter­molecular O—H...O and N—H...O hydrogen bonds.

Key indicators

• Single-crystal X-ray study
• T = 298 K
• Mean [sigma](C-C) = 0.004 Å
• R factor = 0.043
• wR factor = 0.107
• Data-to-parameter ratio = 7.7

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT089_ALERT_3_C Poor Data / Parameter Ratio (Zmax .LT. 18) .....       7.70
PLAT220_ALERT_2_C Large Non-Solvent    C     Ueq(max)/Ueq(min) ...       2.79 Ratio
PLAT222_ALERT_3_C Large Non-Solvent    H     Ueq(max)/Ueq(min) ...       3.11 Ratio
PLAT242_ALERT_2_C Check Low       Ueq as Compared to Neighbors for         C8
PLAT431_ALERT_2_C Short Inter HL..A Contact  F1     ..  O3      ..       2.95 Ang.

Alert level G
REFLT03_ALERT_4_G 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.
           From the CIF: _diffrn_reflns_theta_max           25.21
           From the CIF: _reflns_number_total               1455
           Count of symmetry unique reflns         1456
           Completeness (_total/calc)             99.93%
           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

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

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

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Computing details

Data collection: SMART (Bruker, 2002); cell refinement: SAINT (Bruker, 2002); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL (Bruker, 2002); software used to prepare material for publication: SHELXL97.

(2S)-Methyl 2-[2-(5-fluoro-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)acetamido]propionate

Crystal data

C10H12FN3O5·H2O	F(000) = 608
Mr = 291.24	Dx = 1.446 Mg m^−3
Orthorhombic, P212121	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2ab	Cell parameters from 2999 reflections
a = 4.7472 (6) Å	θ = 2.5–24.2°
b = 11.2103 (14) Å	µ = 0.13 mm^−1
c = 25.139 (3) Å	T = 298 K
V = 1337.8 (3) Å^3	Block, colourless
Z = 4	0.43 × 0.28 × 0.20 mm

Data collection

Bruker APEX area-detector diffractometer	1455 independent reflections
Radiation source: fine-focus sealed tube	1410 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.000
φ and ω scans	θmax = 25.2°, θmin = 1.6°
Absorption correction: multi-scan (SADABS; Bruker, 2002)	h = 0→5
Tmin = 0.947, Tmax = 0.970	k = 0→13
1455 measured reflections	l = 0→30

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.043	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.107	H atoms treated by a mixture of independent and constrained refinement
S = 1.19	w = 1/[σ^2(Fo^2) + (0.0488P)^2 + 0.3758P] where P = (Fo^2 + 2Fc^2)/3
1455 reflections	(Δ/σ)max < 0.001
189 parameters	Δρmax = 0.15 e Å^−3
3 restraints	Δρmin = −0.19 e Å^−3

Special details

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 (Ų)

	x	y	z	Uiso*/Ueq
F1	1.0958 (5)	0.25277 (16)	0.67114 (8)	0.0684 (6)
O1	0.5539 (6)	0.65480 (19)	0.71796 (9)	0.0634 (7)
O2	1.2041 (6)	0.4614 (2)	0.61754 (9)	0.0674 (7)
O3	0.8244 (4)	0.49148 (19)	0.83307 (8)	0.0461 (5)
O4	0.7580 (6)	0.5153 (2)	0.98650 (9)	0.0683 (7)
O5	0.4545 (7)	0.3982 (2)	0.94528 (10)	0.0777 (9)
O6	0.9518 (8)	0.7745 (2)	0.61696 (13)	0.0839 (10)
N1	0.6161 (5)	0.4574 (2)	0.73216 (8)	0.0361 (5)
N2	0.8754 (5)	0.5563 (2)	0.66756 (9)	0.0412 (6)
H2	0.9105	0.6214	0.6507	0.049*
N3	0.4102 (5)	0.5603 (2)	0.86283 (8)	0.0379 (6)
H3	0.2350	0.5725	0.8560	0.045*
C1	0.6733 (7)	0.5626 (2)	0.70643 (10)	0.0396 (7)
C2	1.0294 (6)	0.4571 (3)	0.65232 (10)	0.0409 (7)
C3	0.9551 (7)	0.3535 (2)	0.68276 (11)	0.0399 (7)
C4	0.7599 (6)	0.3545 (2)	0.72040 (10)	0.0382 (7)
H4	0.7198	0.2848	0.7390	0.046*
C5	0.4243 (6)	0.4611 (3)	0.77733 (10)	0.0396 (7)
H5A	0.3520	0.3816	0.7841	0.048*
H5B	0.2660	0.5124	0.7689	0.048*
C6	0.5714 (5)	0.5074 (2)	0.82691 (10)	0.0333 (6)
C7	0.5253 (7)	0.5978 (3)	0.91328 (11)	0.0414 (7)
H7	0.7093	0.6343	0.9064	0.050*
C8	0.5722 (7)	0.4912 (3)	0.94948 (11)	0.0459 (7)
C9	0.8164 (13)	0.4202 (5)	1.02476 (15)	0.0932 (16)
H9A	0.8817	0.3506	1.0062	0.140*
H9B	0.6474	0.4011	1.0439	0.140*
H9C	0.9586	0.4463	1.0493	0.140*
C10	0.3413 (9)	0.6910 (3)	0.93995 (14)	0.0660 (11)
H10A	0.1566	0.6587	0.9458	0.099*
H10B	0.3277	0.7601	0.9175	0.099*
H10C	0.4230	0.7133	0.9734	0.099*
H6A	1.066 (7)	0.824 (3)	0.6291 (15)	0.079*
H6B	0.838 (7)	0.806 (3)	0.5957 (13)	0.079*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
F1	0.0774 (15)	0.0459 (10)	0.0821 (13)	0.0224 (11)	0.0188 (13)	−0.0085 (9)
O1	0.0820 (19)	0.0387 (12)	0.0694 (14)	0.0209 (14)	0.0229 (15)	−0.0027 (11)
O2	0.0658 (16)	0.0760 (16)	0.0604 (13)	0.0072 (15)	0.0326 (13)	0.0028 (13)
O3	0.0310 (10)	0.0535 (12)	0.0539 (12)	0.0024 (11)	−0.0001 (10)	−0.0072 (10)
O4	0.0756 (16)	0.0856 (18)	0.0436 (11)	−0.0171 (17)	−0.0195 (13)	0.0071 (12)
O5	0.106 (2)	0.0625 (15)	0.0641 (15)	−0.0244 (17)	−0.0261 (18)	0.0062 (13)
O6	0.107 (3)	0.0548 (16)	0.0903 (19)	−0.0246 (18)	−0.035 (2)	0.0233 (14)
N1	0.0403 (13)	0.0341 (12)	0.0340 (10)	−0.0029 (11)	0.0062 (10)	−0.0027 (9)
N2	0.0509 (14)	0.0329 (11)	0.0398 (11)	−0.0019 (12)	0.0096 (12)	0.0044 (10)
N3	0.0251 (10)	0.0550 (14)	0.0335 (10)	−0.0001 (12)	−0.0005 (10)	−0.0046 (11)
C1	0.0468 (16)	0.0354 (14)	0.0365 (13)	0.0018 (15)	0.0037 (14)	−0.0016 (12)
C2	0.0385 (15)	0.0495 (16)	0.0347 (13)	0.0018 (14)	0.0073 (13)	−0.0045 (13)
C3	0.0446 (17)	0.0318 (13)	0.0431 (14)	0.0046 (14)	0.0020 (14)	−0.0075 (12)
C4	0.0441 (17)	0.0306 (13)	0.0398 (14)	−0.0036 (13)	0.0005 (14)	−0.0006 (12)
C5	0.0347 (14)	0.0467 (16)	0.0375 (14)	−0.0057 (14)	0.0047 (13)	−0.0041 (12)
C6	0.0283 (13)	0.0337 (13)	0.0379 (13)	−0.0020 (12)	0.0046 (12)	0.0043 (11)
C7	0.0341 (14)	0.0513 (17)	0.0388 (14)	−0.0085 (14)	0.0022 (13)	−0.0064 (13)
C8	0.0470 (16)	0.0578 (18)	0.0330 (13)	−0.0061 (17)	0.0026 (14)	−0.0075 (14)
C9	0.110 (4)	0.118 (4)	0.052 (2)	−0.008 (4)	−0.021 (3)	0.024 (2)
C10	0.063 (2)	0.075 (2)	0.059 (2)	0.008 (2)	−0.010 (2)	−0.0298 (18)

Geometric parameters (Å, º)

F1—C3	1.344 (3)	N3—H3	0.8600
O1—C1	1.214 (4)	C2—C3	1.435 (4)
O2—C2	1.206 (3)	C3—C4	1.325 (4)
O3—C6	1.224 (3)	C4—H4	0.9300
O4—C8	1.311 (4)	C5—C6	1.520 (4)
O4—C9	1.463 (5)	C5—H5A	0.9700
O5—C8	1.187 (4)	C5—H5B	0.9700
O6—H6A	0.833 (18)	C7—C10	1.518 (4)
O6—H6B	0.838 (18)	C7—C8	1.519 (4)
N1—C4	1.373 (4)	C7—H7	0.9800
N1—C1	1.373 (4)	C9—H9A	0.9600
N1—C5	1.456 (3)	C9—H9B	0.9600
N2—C1	1.371 (4)	C9—H9C	0.9600
N2—C2	1.385 (4)	C10—H10A	0.9600
N2—H2	0.8600	C10—H10B	0.9600
N3—C6	1.324 (3)	C10—H10C	0.9600
N3—C7	1.444 (3)
C8—O4—C9	116.4 (3)	C6—C5—H5B	109.4
H6A—O6—H6B	112 (2)	H5A—C5—H5B	108.0
C4—N1—C1	121.5 (2)	O3—C6—N3	123.1 (3)
C4—N1—C5	120.2 (2)	O3—C6—C5	120.3 (3)
C1—N1—C5	117.8 (2)	N3—C6—C5	116.5 (2)
C1—N2—C2	127.5 (2)	N3—C7—C10	111.8 (3)
C1—N2—H2	116.3	N3—C7—C8	110.6 (2)
C2—N2—H2	116.3	C10—C7—C8	111.2 (3)
C6—N3—C7	120.7 (2)	N3—C7—H7	107.7
C6—N3—H3	119.6	C10—C7—H7	107.7
C7—N3—H3	119.6	C8—C7—H7	107.7
O1—C1—N2	122.8 (3)	O5—C8—O4	124.1 (3)
O1—C1—N1	121.8 (3)	O5—C8—C7	124.7 (3)
N2—C1—N1	115.4 (2)	O4—C8—C7	111.2 (3)
O2—C2—N2	122.1 (3)	O4—C9—H9A	109.5
O2—C2—C3	126.0 (3)	O4—C9—H9B	109.5
N2—C2—C3	111.9 (2)	H9A—C9—H9B	109.5
C4—C3—F1	120.7 (3)	O4—C9—H9C	109.5
C4—C3—C2	123.1 (3)	H9A—C9—H9C	109.5
F1—C3—C2	116.2 (3)	H9B—C9—H9C	109.5
C3—C4—N1	120.6 (3)	C7—C10—H10A	109.5
C3—C4—H4	119.7	C7—C10—H10B	109.5
N1—C4—H4	119.7	H10A—C10—H10B	109.5
N1—C5—C6	111.2 (2)	C7—C10—H10C	109.5
N1—C5—H5A	109.4	H10A—C10—H10C	109.5
C6—C5—H5A	109.4	H10B—C10—H10C	109.5
N1—C5—H5B	109.4
C2—N2—C1—O1	178.1 (3)	C5—N1—C4—C3	−173.3 (3)
C2—N2—C1—N1	−1.2 (4)	C4—N1—C5—C6	93.8 (3)
C4—N1—C1—O1	−177.4 (3)	C1—N1—C5—C6	−78.3 (3)
C5—N1—C1—O1	−5.4 (4)	C7—N3—C6—O3	−2.9 (4)
C4—N1—C1—N2	2.0 (4)	C7—N3—C6—C5	174.5 (2)
C5—N1—C1—N2	174.0 (2)	N1—C5—C6—O3	−29.3 (4)
C1—N2—C2—O2	−179.7 (3)	N1—C5—C6—N3	153.2 (2)
C1—N2—C2—C3	0.0 (4)	C6—N3—C7—C10	160.6 (3)
O2—C2—C3—C4	−179.7 (3)	C6—N3—C7—C8	−75.0 (3)
N2—C2—C3—C4	0.6 (4)	C9—O4—C8—O5	−0.8 (5)
O2—C2—C3—F1	0.3 (5)	C9—O4—C8—C7	178.6 (3)
N2—C2—C3—F1	−179.4 (2)	N3—C7—C8—O5	−22.2 (4)
F1—C3—C4—N1	−179.9 (3)	C10—C7—C8—O5	102.6 (4)
C2—C3—C4—N1	0.1 (4)	N3—C7—C8—O4	158.4 (3)
C1—N1—C4—C3	−1.5 (4)	C10—C7—C8—O4	−76.8 (3)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O6—H6B···O5^i	0.84 (2)	2.01 (2)	2.845 (4)	171 (4)
O6—H6A···O3^ii	0.83 (2)	2.17 (3)	2.936 (4)	153 (4)
N3—H3···O3^iii	0.86	2.23	2.981 (3)	147
N2—H2···O6	0.86	1.92	2.781 (3)	173

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