Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536802015295/wn6118sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536802015295/wn6118Isup2.hkl |
CCDC reference: 197487
Key indicators
- Single-crystal X-ray study
- T = 213 K
- Mean (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
The sample was obtained commercially from Fluorochem (Cat. No. 3333), and recrystallized from CH3CN.
H atoms were positioned geometrically and refined using a riding model, with Uiso values constrained to be 1.2Ueq of the carrier atom.
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.
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) Å3 | T = 213 K |
Z = 18 | Fragment, colorless |
F(000) = 1620 | 0.35 × 0.25 × 0.15 mm |
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 on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.049 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.105 | H-atom parameters constrained |
S = 1.09 | w = 1/[σ2(Fo2) + (0.0361P)2 + 5.2597P] where P = (Fo2 + 2Fc2)/3 |
1208 reflections | (Δ/σ)max < 0.001 |
109 parameters | Δρmax = 0.20 e Å−3 |
0 restraints | Δρmin = −0.24 e Å−3 |
C5H3F3N2O2 | Z = 18 |
Mr = 180.09 | Mo Kα radiation |
Trigonal, R3 | µ = 0.20 mm−1 |
a = 25.5695 (17) Å | T = 213 K |
c = 5.1934 (5) Å | 0.35 × 0.25 × 0.15 mm |
V = 2940.5 (4) Å3 |
Bruker SMART 1K CCD diffractometer | 1208 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 2001) | 896 reflections with I > 2σ(I) |
Tmin = 0.935, Tmax = 0.971 | Rint = 0.045 |
12551 measured reflections |
R[F2 > 2σ(F2)] = 0.049 | 0 restraints |
wR(F2) = 0.105 | H-atom parameters constrained |
S = 1.09 | Δρmax = 0.20 e Å−3 |
1208 reflections | Δρmin = −0.24 e Å−3 |
109 parameters |
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 | ||
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) |
U11 | U22 | U33 | U12 | U13 | U23 | |
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) |
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 |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1A···O1i | 0.87 | 2.03 | 2.808 (3) | 148 |
N3—H3A···O2ii | 0.87 | 1.94 | 2.814 (3) | 176 |
C6—H6A···F1 | 0.94 | 2.35 | 2.697 (3) | 101 |
C6—H6A···F3iii | 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. |
Experimental details
Crystal data | |
Chemical formula | C5H3F3N2O2 |
Mr | 180.09 |
Crystal system, space group | Trigonal, R3 |
Temperature (K) | 213 |
a, c (Å) | 25.5695 (17), 5.1934 (5) |
V (Å3) | 2940.5 (4) |
Z | 18 |
Radiation type | Mo Kα |
µ (mm−1) | 0.20 |
Crystal size (mm) | 0.35 × 0.25 × 0.15 |
Data collection | |
Diffractometer | Bruker SMART 1K CCD diffractometer |
Absorption correction | Multi-scan (SADABS; Sheldrick, 2001) |
Tmin, Tmax | 0.935, 0.971 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 12551, 1208, 896 |
Rint | 0.045 |
(sin θ/λ)max (Å−1) | 0.605 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.049, 0.105, 1.09 |
No. of reflections | 1208 |
No. of parameters | 109 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.20, −0.24 |
Computer programs: SMART (Bruker, 1999), SMART, SAINT-Plus (Bruker, 1999), XS in SHELXTL (Sheldrick, 2001), XL in SHELXTL, XP in SHELXTL, XCIF in SHELXTL.
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1A···O1i | 0.87 | 2.03 | 2.808 (3) | 148 |
N3—H3A···O2ii | 0.87 | 1.94 | 2.814 (3) | 176 |
C6—H6A···F1 | 0.94 | 2.35 | 2.697 (3) | 101 |
C6—H6A···F3iii | 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. |
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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 CF3 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 Å3. Fig. 3 displays these channels outlined in green. The orientation of the CF3 groups brings an F atom into close proximity to an H atom [H6A···F3iii; 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).