5-(Tri­fluoro­methyl)­uracil

The title compound, 5-tri­fluoro­methyl-1H-pyrimidine-2,4-dione, 5-CF₃-C₄H₃N₂O₂ or C₅H₃F₃N₂O₂, (I), displays marked differences in packing compared to the non-fluorinated parent mol­ecule, 5-CH₃-C₄H₃N₂O₂, i.e. thymine. Compound (I) forms a complicated three-dimensional array using hydrogen bonds [range 2.808 (3)-2.814 (3) Å], resulting in channels or voids parallel to [001], which are lined with F atoms from the CF₃ groups.

Key indicators

• Single-crystal X-ray study
• T = 213 K
• Mean [sigma](C-C) = 0.004 Å
• R factor = 0.049
• wR factor = 0.105
• Data-to-parameter ratio = 11.1

checkCIF/PLATON results

No syntax errors found



Alert level B
PLAT432_ALERT_2_B Short Inter X...Y Contact  O1     ..  C2      ..       2.88 Ang.

Alert level C
PLAT066_ALERT_1_C Predicted and Reported Transmissions Identical .          ?
PLAT125_ALERT_4_C No _symmetry_space_group_name_Hall Given .......          ?
PLAT601_ALERT_2_C Structure Contains Solvent Accessible VOIDS of .      50.00 A   3  

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

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

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S1. Comment

Compound (I), 5-CF₃—C₄H₃N₂O₂ (Fig. 1), is a partially fluorinated derivative of thymine. This compound has proven extremely useful in our continued research into fluorine chemistry (Gupta, Kirchmeier & Shreeve, 2000; Gupta, Twamley et al., 2000).

The structure of non-fluorinated thymine is well known (Ozeki et al., 1969; Portalone et al., 1999); it crystallizes in the common space group P2₁/c. In the solid state, the structure consists of planar sheets of thymine molecules held together by hydrogen bonding, with the molecules facing head-to-head. Sheets are stacked on top of each other, forming a regular array. Hydrogen-bond values are in the range 2.810–2.836 Å.

When the methyl group is fluorinated, the packing changes dramatically. Compound (I) now crystallizes in the trigonal space group R3 and the hydrogen-bonded sheet motif is no longer observed. In this case, a complicated three-dimensional `infinite' array is formed, with the uracil molecules hydrogen-bonding in pair-units, head-to-tail and side-by-side. These units are essentially planar with an out-of-plane r.m.s. deviation of 0.0241 Å (for all non-F atoms including H atoms). These pair-units then hydrogen bond to four other pair-units (Table 1). A section of the packing is shown in Fig. 2. This packing arrangement causes the CF<sub>3</sub> groups to form a symmetry-imposed pseudo-hexagonal channel. The F atoms become the lining for the channel, which is approximately 3.6 Å wide and extends parallel to [001]. The volume of these channels in the unit cell is approximately 50 Å<sup>3</sup>. Fig. 3 displays these channels outlined in green. The orientation of the CF<sub>3</sub> groups brings an F atom into close proximity to an H atom [H6A···F3<sup>iii</sup>; symmetry code: (iii) x-y, x, 1 − z] of a neighboring molecule. There is also a close intramolecular contact with the same H atom (F1···H6A). These distances are recorded in Table 1. Although these values are within the sum of the van der Waals radii of both fluorine and hydrogen, whether these are weak interactions is questionable. Intermolecular distances of d < 2.35 Å (d = H···F intermolecular distance) are generally accepted to be `true' weak hydrogen-bonding interactions (Desiraju & Steiner, 2001).

S2. Experimental

The sample was obtained commercially from Fluorochem (Cat. No. 3333), and recrystallized from CH₃CN.

S3. Refinement

H atoms were positioned geometrically and refined using a riding model, with U_iso values constrained to be 1.2U_eq of the carrier atom.

Computing details

Data collection: SMART (Bruker, 1999); cell refinement: SMART; data reduction: SAINT-Plus (Bruker, 1999); program(s) used to solve structure: XS in SHELXTL (Sheldrick, 2001); program(s) used to refine structure: XL in SHELXTL; molecular graphics: XP in SHELXTL; software used to prepare material for publication: XCIF in SHELXTL.

Figures

	Fig. 1. The molecular structure of (I). Atomic displacement ellipsoids are shown at the 30% probability level.
	Fig. 2. A ball-and-stick packing diagram of (I). Hydrogen bonding is indicated by dashed lines.
	Fig. 3. A space-filling representation of (I). F atoms are shown in green. The cell axes are shown separately for clarity.

(I)

Crystal data

C5H3F3N2O2	Dx = 1.831 Mg m^−3
Mr = 180.09	Mo Kα radiation, λ = 0.71073 Å
Trigonal, R3	Cell parameters from 2171 reflections
a = 25.5695 (17) Å	θ = 2.8–23.3°
c = 5.1934 (5) Å	µ = 0.20 mm^−1
V = 2940.5 (4) Å^3	T = 213 K
Z = 18	Fragment, colorless
F(000) = 1620	0.35 × 0.25 × 0.15 mm

Data collection

Bruker SMART 1K CCD diffractometer	1208 independent reflections
Radiation source: normal-focus sealed tube	896 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.045
Detector resolution: 8.3 pixels mm^-1	θmax = 25.5°, θmin = 2.8°
ω scans	h = −30→27
Absorption correction: multi-scan (SADABS; Sheldrick, 2001)	k = −28→30
Tmin = 0.935, Tmax = 0.971	l = −6→6
12551 measured reflections

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)] = 0.049	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.105	H-atom parameters constrained
S = 1.09	w = 1/[σ^2(Fo^2) + (0.0361P)^2 + 5.2597P] where P = (Fo^2 + 2Fc^2)/3
1208 reflections	(Δ/σ)max < 0.001
109 parameters	Δρmax = 0.20 e Å^−3
0 restraints	Δρmin = −0.24 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
C7	0.17115 (12)	0.07980 (13)	0.1700 (6)	0.0364 (7)
C5	0.22516 (11)	0.14030 (12)	0.1370 (5)	0.0281 (6)
C6	0.23448 (12)	0.18776 (12)	0.2825 (5)	0.0321 (6)
H6A	0.2059	0.1821	0.4093	0.039*
C2	0.32638 (12)	0.25598 (12)	0.0680 (5)	0.0283 (6)
C4	0.26913 (12)	0.14884 (12)	−0.0568 (5)	0.0282 (6)
F1	0.13535 (7)	0.07887 (8)	0.3585 (4)	0.0534 (5)
F2	0.13791 (7)	0.06005 (7)	−0.0429 (3)	0.0486 (5)
F3	0.18618 (8)	0.03764 (7)	0.2305 (3)	0.0496 (5)
N1	0.28352 (10)	0.24329 (10)	0.2530 (4)	0.0305 (5)
H1A	0.2880	0.2721	0.3558	0.037*
N3	0.31693 (9)	0.20712 (9)	−0.0761 (4)	0.0284 (5)
H3A	0.3440	0.2135	−0.1923	0.034*
O1	0.36988 (8)	0.30675 (8)	0.0350 (3)	0.0341 (5)
O2	0.26655 (8)	0.10907 (8)	−0.1992 (4)	0.0381 (5)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C7	0.0358 (16)	0.0405 (17)	0.0367 (17)	0.0220 (14)	0.0096 (13)	0.0107 (14)
C5	0.0286 (14)	0.0353 (15)	0.0259 (13)	0.0201 (12)	0.0074 (11)	0.0063 (12)
C6	0.0311 (15)	0.0443 (17)	0.0272 (14)	0.0236 (14)	0.0074 (12)	0.0049 (12)
C2	0.0334 (15)	0.0340 (15)	0.0245 (14)	0.0220 (14)	0.0013 (12)	0.0030 (11)
C4	0.0332 (14)	0.0321 (15)	0.0253 (14)	0.0208 (13)	0.0045 (11)	0.0055 (12)
F1	0.0456 (10)	0.0519 (11)	0.0569 (12)	0.0200 (9)	0.0282 (9)	0.0102 (9)
F2	0.0429 (10)	0.0410 (10)	0.0526 (11)	0.0140 (8)	−0.0064 (9)	0.0013 (8)
F3	0.0538 (11)	0.0410 (10)	0.0599 (12)	0.0280 (9)	0.0118 (9)	0.0194 (9)
N1	0.0347 (13)	0.0317 (13)	0.0277 (12)	0.0186 (11)	0.0041 (10)	−0.0034 (10)
N3	0.0312 (12)	0.0297 (12)	0.0264 (11)	0.0169 (10)	0.0095 (9)	0.0017 (9)
O1	0.0350 (11)	0.0327 (11)	0.0320 (11)	0.0151 (9)	0.0009 (8)	0.0002 (8)
O2	0.0453 (12)	0.0299 (10)	0.0382 (11)	0.0181 (9)	0.0144 (9)	−0.0012 (9)

Geometric parameters (Å, º)

C7—F2	1.331 (3)	C2—O1	1.228 (3)
C7—F1	1.332 (3)	C2—N1	1.369 (3)
C7—F3	1.350 (3)	C2—N3	1.370 (3)
C7—C5	1.481 (4)	C4—O2	1.232 (3)
C5—C6	1.346 (4)	C4—N3	1.380 (3)
C5—C4	1.442 (4)	N1—H1A	0.8700
C6—N1	1.353 (3)	N3—H3A	0.8700
C6—H6A	0.9400
F2—C7—F1	107.5 (2)	O1—C2—N1	122.9 (2)
F2—C7—F3	105.9 (2)	O1—C2—N3	122.8 (2)
F1—C7—F3	106.4 (2)	N1—C2—N3	114.3 (2)
F2—C7—C5	112.7 (2)	O2—C4—N3	120.1 (2)
F1—C7—C5	112.2 (2)	O2—C4—C5	125.3 (2)
F3—C7—C5	111.8 (2)	N3—C4—C5	114.6 (2)
C6—C5—C4	118.8 (2)	C6—N1—C2	122.7 (2)
C6—C5—C7	121.9 (2)	C6—N1—H1A	118.6
C4—C5—C7	119.2 (2)	C2—N1—H1A	118.6
C5—C6—N1	122.4 (2)	C2—N3—C4	127.0 (2)
C5—C6—H6A	118.8	C2—N3—H3A	116.5
N1—C6—H6A	118.8	C4—N3—H3A	116.5

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1A···O1^i	0.87	2.03	2.808 (3)	148
N3—H3A···O2^ii	0.87	1.94	2.814 (3)	176
C6—H6A···F1	0.94	2.35	2.697 (3)	101
C6—H6A···F3^iii	0.94	2.41	3.337 (3)	169

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