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This analysis of the title compound, C13H13F2IO3, establishes the orientation of (E)-5-(CH=CH—I) as antiperiplanar (ap) to the C—C bond (5–6 position) of the 2,4-di­fluoro­phenyl ring system, with the (E)-5-(CH=CH—I) H atom located in close proximity (2.17 Å) to the F4 atom of the 2,4-di­fluoro­phenyl moiety.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270101005029/da1180sup1.cif
Contains datablocks I, DA1180

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S0108270101005029/da1180Isup2.hkl
Contains datablock I

CCDC reference: 166999

Comment top

The development of 2'-deoxyuridine derivatives possessing novel 2-carbon substituents at the C-5 position, which are potent and selective antiviral agents, represents an important area of antiviral drug design. Accordingly, (E)-5-(2-iodovinyl)-2'-deoxyuridine (IVDU) was identified as a highly specific inhibitor of herpesvirus replication due to its specific phosphorylation by virus-encoded thymidine kinase (TK) in virus-infected, but not in uninfected, host cells (De Clercq, 1983). 2,4-Difluoro-5-methyl-1-(2'-deoxy-β-D-ribofuranosyl)benzene (DFT) was designed as a nonpolar hydrophobic unnatural thymidine mimic that retains a close structural, steric and isoelectronic relationship to natural thymidine (T) (Schweitzer & Kool, 1994). DFT was envisaged to be a valuable model compound to determine the importance of hydrogen bonding and base stacking in the formation of stable DNA duplex structures. The 2,4-difluoro-5-methylphenyl moiety of DFT is isosteric with the thymine (5-methyluracil) base moiety of thymidine where F is the isosteric replacement for O, CH replaces NH, and the thymine N1 is replaced by an sp2 hybridized C. Although aromatic-substituted F atoms can participate in weak intramolecular hydrogen bonds (Jones & Watkinson, 1964), NMR titration experiments using 2,4-difluorotoluene (the aryl moiety of DFT) did not show any evidence of hydrogen bonding with potential complementary partners (Schweitzer & Kool, 1995). Nonetheless, the 5'-triphosphate of DFT (DFTTP) is a good substrate for the Klenow fragment (KF, exo- mutant) of E. coli DNA polymerase 1 and is inserted into replicating DNA strands. Steady-state measurements indicated that DFTTP was inserted into a template opposite adenine (A) with an efficacy (Vmax/Km) only 40-fold lower than that for the 5'-triphosphate of thymidine. Furthermore, DFTTP was inserted opposite A, relative to cytidine (C), guanidine (G) or thymidine (T), with a selectivity (fidelity) nearly as high as that for the 5'-triphosphate of thymidine (Moran et al., 1997). \sch

We now describe the X-ray analysis of 2,4-difluoro-5-methyl-1-(2'-deoxy-β-D-ribofuranosyl)benzene, (I), to determine the orientation of the (E)-5-(2-iodovinyl) substituent, and whether a potential intramolecular hydrogen-bonding interaction between the (E)—CHCH—I moiety and the F4 substituent exists. The title compound, which is an unnatural mimic of (E)-5-(2-iodovinyl)-2'-deoxyuridine, warrants evaluation as an antiviral agent.

The overall conformation of the title compound is similar to that found in other nucleosides. The glycosidic torsion angle χ (O4'-C1'-C1—C6) is 18.5 (7)° (anti-conformation), and the sugar ring adopts a C2' endo conformation with a displacement of C2' 0.60 (2) Å from the least-squares plane through the other four ring atoms, given by the equation 0.7607x + 0.6453y - 0.0707z = -5.5105

The root mean square deviation of the four atoms in this plane is 0.015 Å with a maximum deviation of 0.018 Å. The orientation of the C5'-O5' bond is trans to C4'-O4' and gauche to C3'-C4'. This trans-gauche orientation of the C5'-O5' bond and C2' endo conformation of the sugar ring is most similar to the crystal structure of 2'-deoxyuridine (Rahman & Wilson, 1972) and differs from the C3' exo conformation seen in the crystal structure of (E)-5-(2-bromovinyl)-2'-deoxyuridine (Párkányi et al., 1983).

Bond lengths for the 2,4-difluoro-(E)-5-(2-iodovinyl)benzene base mimic are nearly identical with analogous bond lengths for the thymine base (Young et al., 1969) and a 2,4-difluorotoluene base mimic from a deoxynucleoside analogue recently described by Guckian and Kool (1997). Aside from the 5-(2-iodovinyl) substituent, all bond lengths within the base mimic of the title compound are within 0.07 Å of the analogous bond lengths for the thymine base and the 2,4-difluorotoluene base mimic. However, as observed in the crystal structure of the 2,4-difluorotoluene deoxynucleoside (Guckian & Kool, 1997), the F—C bond lengths of the 2,4-difluorotoluene base mimic (both 1.37 Å) and the analogous bond lengths in the title compound (both 1.36 Å) differ substantially from the CO bond lengths of thymine (1.23 and 1.21 Å).

The 2-iodovinyl group of the title compound is antiperiplanar (ap) to the C5—C6 bond of the 2,4-difluorobenzene ring. The least squares plane of the 2-iodovinyl group is angled 5.3 (8)° from the least squares plane of the 2,4-difluorobenzene ring. The X-ray crystal structure for (E)-5-(2-bromovinyl)-2'-deoxyuridine has a similar conformational feature; the best plane of the 2-bromovinyl moiety is angled 6° from the plane of the uracil ring. In contrast to the ap conformation seen for the 2-bromo and 2-iodovinyl substituents of the compounds described above, the X-ray crystal structure for 5-vinyl-2'-deoxyuridine showed the unsubstituted vinyl group to be synperiplanar (sp) to the 5,6-olefinic bond and inclined 12° to the best plane of the uracil ring (Hamor et al., 1978).

The X-ray crystal structure of (E)-5-(2-bromovinyl)-2'-deoxyuridine indicates that the positively charged H8 of the (E)-5-(C7HC8H—Br) substituent donates an intramolecular hydrogen bond to the uracil O4 atom (Párkányi et al., 1983). A similar hydrogen-bonding interaction appears in the title compound as evidenced by the 2.17 Å intramolecular distance observed between H8 and F4 (Fig. 1).

Intermolecular C—H···F—C hydrogen-bonding interactions have been observed in the crystal structure of 1-deoxy-1-(2,4-difluorophenyl)-β-D-ribofuranose (Bats et al., 2000) and related fluorobenzene crystal structures (Thalladi et al., 1998). The crystal structure of the title compound contains no intermolecular hydrogen bonds involving fluorine atoms of the aryl ring. The only intermolecular hydrogen-bonding interactions formed in the crystal structure are between 3' and 5' hydroxyls of the sugar rings. Intermolecular interactions of the 5-(2-iodovinyl)-2,4-difluorobenzene base mimic of the title compound appear to be limited to nonpolar van der Waals contacts. A similar hydrogen-bonding network is observed in the crystal structure of the 2,4-difluorotoluene deoxynucleoside analogue, where only the sugar ring hydroxyls are involved in intermolecular hydrogen-bonding interactions (Guckian & Kool, 1997).

Experimental top

The title compound (Wang et al., 1999) was dissolved in a minimum amount of methylene chloride and then diluted with an equal volume of hexanes. Slow evaporation of the methylene chloride from this solution resulted in recrystallization of the title compound. Yellow crystals of appropriate size were obtained after 1–2 d.

Computing details top

Data collection: SMART (Siemens, 1996); cell refinement: SMART (Siemens, 1996); data reduction: SHELXTL (Sheldrick, 1996); program(s) used to solve structure: DIRDIF99 (Beurskens et al., 1998); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997b); molecular graphics: ZORTEP (Zsolnai & Huttner, 1994).

Figures top
[Figure 1] Fig. 1. ZORTEP (Zsolnai & Huttner, 1994) diagram of the title compound showing the atom-labelling scheme. Displacement ellipsoids are at a 50% probability level.
2,4-Difluoro-(E)-5-(2-iodovinyl)-1-(2'-deoxy-β-D-ribofuranosyl)benzene top
Crystal data top
C13H13F2IO3Dx = 1.911 Mg m3
Mr = 382.13Melting point = 358–360 K
Monoclinic, P21Mo Kα radiation, λ = 0.71073 Å
a = 9.2884 (8) ÅCell parameters from 4139 reflections
b = 6.7527 (6) Åθ = 1.9–25.7°
c = 10.6582 (9) ŵ = 2.44 mm1
β = 96.5141 (14)°T = 193 K
V = 664.19 (10) Å3Plate, clear pale yellow
Z = 20.23 × 0.18 × 0.04 mm
F(000) = 372
Data collection top
Bruker SMART CCD
diffractometer
2464 independent reflections
Radiation source: fine-focus sealed tube2334 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.025
ϕ and ω scansθmax = 25.7°, θmin = 1.9°
Absorption correction: multi-scan
(SADABS; Sheldrick, 1997a)
h = 1111
Tmin = 0.560, Tmax = 0.862k = 88
4141 measured reflectionsl = 1212
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.037H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.095 w = 1/[σ2(Fo2) + (0.069P)2]
where P = (Fo2 + 2Fc2)/3
S = 1.02(Δ/σ)max < 0.001
2464 reflectionsΔρmax = 0.97 e Å3
174 parametersΔρmin = 0.31 e Å3
1 restraintAbsolute structure: Flack (1983)
Primary atom site location: structure-invariant direct methodsAbsolute structure parameter: 0.04 (3)
Crystal data top
C13H13F2IO3V = 664.19 (10) Å3
Mr = 382.13Z = 2
Monoclinic, P21Mo Kα radiation
a = 9.2884 (8) ŵ = 2.44 mm1
b = 6.7527 (6) ÅT = 193 K
c = 10.6582 (9) Å0.23 × 0.18 × 0.04 mm
β = 96.5141 (14)°
Data collection top
Bruker SMART CCD
diffractometer
2464 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 1997a)
2334 reflections with I > 2σ(I)
Tmin = 0.560, Tmax = 0.862Rint = 0.025
4141 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.037H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.095Δρmax = 0.97 e Å3
S = 1.02Δρmin = 0.31 e Å3
2464 reflectionsAbsolute structure: Flack (1983)
174 parametersAbsolute structure parameter: 0.04 (3)
1 restraint
Special details top

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 (Å2) top
xyzUiso*/Ueq
C1'0.3620 (6)0.6186 (7)0.1474 (5)0.0250 (10)
H1'0.41370.74810.15070.030*
O4'0.4659 (4)0.4616 (5)0.1352 (3)0.0284 (9)
C2'0.2724 (6)0.5816 (9)0.2732 (5)0.0322 (12)
H2A'0.19660.48090.26530.039*
H2B'0.22630.70510.30800.039*
C3'0.3851 (5)0.5068 (11)0.3548 (4)0.0281 (9)
H3A'0.34000.42520.42710.034*
O3'0.4620 (5)0.6716 (6)0.3970 (4)0.0404 (10)
H3'0.47700.65360.47240.061*
C4'0.4816 (6)0.3807 (7)0.2590 (5)0.0252 (10)
H4'0.58480.39470.27590.030*
C5'0.4428 (6)0.1640 (8)0.2587 (5)0.0298 (11)
H5A'0.33620.14790.26860.036*
H5B'0.48240.10270.17760.036*
O5'0.5023 (5)0.0713 (6)0.3601 (4)0.0340 (10)
H5'0.46280.03960.37450.051*
C10.2751 (6)0.6183 (8)0.0351 (5)0.0265 (10)
C20.1946 (7)0.7827 (8)0.0110 (6)0.0331 (12)
F20.2025 (4)0.9461 (5)0.0850 (4)0.0481 (10)
C30.1057 (7)0.7922 (9)0.0835 (6)0.0362 (13)
H30.04920.90640.09560.043*
C40.1027 (6)0.6278 (9)0.1597 (5)0.0328 (12)
F40.0133 (4)0.6362 (5)0.2516 (3)0.0431 (8)
C50.1823 (6)0.4566 (8)0.1446 (5)0.0297 (12)
C70.1875 (6)0.2832 (9)0.2286 (5)0.0339 (12)
H70.24280.17380.20500.041*
C80.1247 (7)0.2612 (9)0.3326 (6)0.0372 (13)
H80.06590.36620.35720.045*
I80.14684 (4)0.01161 (7)0.44498 (3)0.04307 (15)
C60.2672 (6)0.4565 (7)0.0432 (5)0.0273 (11)
H60.32100.34100.02810.033*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C1'0.032 (3)0.017 (2)0.027 (3)0.003 (2)0.007 (2)0.0013 (19)
O4'0.0348 (19)0.029 (2)0.0219 (17)0.0066 (14)0.0033 (14)0.0036 (13)
C2'0.033 (3)0.040 (3)0.025 (3)0.007 (2)0.006 (2)0.007 (2)
C3'0.042 (2)0.021 (2)0.0221 (19)0.000 (3)0.0081 (17)0.008 (3)
O3'0.073 (3)0.0210 (19)0.032 (2)0.0044 (19)0.026 (2)0.0015 (16)
C4'0.027 (3)0.025 (3)0.024 (3)0.001 (2)0.008 (2)0.005 (2)
C5'0.041 (3)0.023 (2)0.024 (3)0.001 (2)0.002 (2)0.002 (2)
O5'0.052 (3)0.021 (2)0.032 (2)0.0029 (15)0.0147 (18)0.0023 (14)
C10.027 (3)0.027 (3)0.026 (3)0.000 (2)0.004 (2)0.002 (2)
C20.041 (3)0.028 (3)0.031 (3)0.006 (2)0.005 (2)0.000 (2)
F20.060 (2)0.036 (2)0.053 (2)0.0172 (16)0.0250 (19)0.0146 (16)
C30.040 (3)0.035 (3)0.034 (3)0.008 (2)0.008 (2)0.002 (2)
C40.031 (3)0.042 (3)0.027 (3)0.000 (2)0.009 (2)0.007 (2)
F40.048 (2)0.049 (2)0.0359 (19)0.0022 (16)0.0210 (15)0.0050 (16)
C50.030 (3)0.034 (3)0.025 (2)0.004 (2)0.004 (2)0.0008 (19)
C70.034 (3)0.036 (3)0.032 (3)0.000 (2)0.008 (2)0.004 (2)
C80.044 (3)0.036 (3)0.034 (3)0.000 (2)0.013 (3)0.008 (2)
I80.0498 (2)0.0495 (2)0.0312 (2)0.0069 (3)0.01021 (14)0.0101 (2)
C60.030 (3)0.025 (3)0.027 (2)0.0011 (18)0.002 (2)0.0035 (18)
Geometric parameters (Å, º) top
C1—C21.379 (8)C2'—H2A'0.9900
C2—C31.373 (8)C2'—H2B'0.9900
C3—C41.378 (9)C3'—O3'1.423 (7)
C4—C51.391 (8)C3'—C4'1.537 (7)
C5—C61.409 (7)C3'—H3A'1.0000
C6—C11.382 (7)O3'—H3'0.8400
C1—C1'1.518 (7)C4'—C5'1.508 (7)
C2—F21.363 (7)C4'—H4'1.0000
C4—F41.355 (6)C5'—O5'1.415 (7)
C5—C71.471 (8)C5'—H5A'0.9900
C7—C81.318 (8)C5'—H5B'0.9900
C8—I82.064 (6)O5'—H5'0.8400
C1'—O4'1.429 (6)C3—H30.9500
C1'—C2'1.517 (8)C7—H70.9500
C1'—H1'1.0000C8—H80.9500
O4'—C4'1.450 (6)C6—H60.9500
C2'—C3'1.521 (7)
C1—C2—F2118.6 (5)O4'—C4'—C3'106.5 (4)
C3—C2—F2117.6 (5)C5'—C4'—C3'114.7 (5)
C3—C4—F4116.6 (5)O4'—C4'—H4'109.0
C5—C4—F4119.7 (5)C5'—C4'—H4'109.0
C4—C5—C7124.9 (5)C3'—C4'—H4'109.0
C6—C5—C7118.9 (5)O5'—C5'—C4'108.3 (4)
C5—C7—C8127.9 (6)O5'—C5'—H5A'110.0
C7—C8—I8123.7 (5)C4'—C5'—H5A'110.0
O4'—C1'—C2'104.8 (4)O5'—C5'—H5B'110.0
O4'—C1'—C1110.0 (4)C4'—C5'—H5B'110.0
C2'—C1'—C1114.2 (4)H5A'—C5'—H5B'108.4
O4'—C1'—H1'109.3C5'—O5'—H5'109.5
C2'—C1'—H1'109.3C2—C1—C6117.2 (5)
C1—C1'—H1'109.3C2—C1—C1'119.6 (5)
C1'—O4'—C4'109.5 (4)C6—C1—C1'123.1 (5)
C1'—C2'—C3'102.5 (4)C3—C2—C1123.9 (5)
C1'—C2'—H2A'111.3C2—C3—C4116.7 (5)
C3'—C2'—H2A'111.3C2—C3—H3121.7
C1'—C2'—H2B'111.3C4—C3—H3121.7
C3'—C2'—H2B'111.3C3—C4—C5123.6 (5)
H2A'—C2'—H2B'109.2C4—C5—C6116.1 (5)
O3'—C3'—C2'108.9 (5)C8—C7—H7116.1
O3'—C3'—C4'111.6 (4)C5—C7—H7116.1
C2'—C3'—C4'101.1 (4)C7—C8—H8118.1
O3'—C3'—H3A'111.6I8—C8—H8118.1
C2'—C3'—H3A'111.6C1—C6—C5122.4 (5)
C4'—C3'—H3A'111.6C1—C6—H6118.8
C3'—O3'—H3'109.5C5—C6—H6118.8
O4'—C4'—C5'108.4 (4)
O4'—C1'—C2'—C3'37.3 (5)O3'—C3'—C4'—O4'89.7 (5)
C1'—C2'—C3'—C4'37.8 (5)O3'—C3'—C4'—C5'150.5 (4)
C2'—C3'—C4'—O4'25.9 (6)C6—C1—C2—F2178.7 (5)
C3'—C4'—O4'—C1'3.2 (5)C1'—C1—C2—F23.8 (8)
C4'—O4'—C1'—C2'21.3 (5)C6—C1—C2—C31.6 (9)
O4'—C4'—C5'—O5'160.8 (4)C1'—C1—C2—C3175.9 (6)
C3'—C4'—C5'—O5'80.4 (5)F2—C2—C3—C4178.0 (5)
C2'—C1'—C1—C278.4 (6)C1—C2—C3—C42.2 (9)
O4'—C1'—C1—C2164.2 (5)C2—C3—C4—F4179.0 (5)
C2'—C1'—C1—C698.9 (6)C2—C3—C4—C50.8 (9)
O4'—C1'—C1—C618.5 (7)F4—C4—C5—C6177.1 (5)
C4—C5—C7—C82.8 (10)C3—C4—C5—C61.1 (8)
C6—C5—C7—C8174.8 (6)F4—C4—C5—C75.3 (8)
C5—C7—C8—I8177.9 (5)C3—C4—C5—C7176.5 (6)
C2'—C3'—C4'—C5'93.9 (5)C2—C1—C6—C50.5 (8)
C1—C1'—O4'—C4'144.4 (4)C1'—C1—C6—C5177.9 (5)
C1—C1'—C2'—C3'157.7 (5)C4—C5—C6—C11.8 (8)
C1'—C2'—C3'—O3'79.8 (5)C7—C5—C6—C1176.0 (5)
C1'—O4'—C4'—C5'120.7 (4)

Experimental details

Crystal data
Chemical formulaC13H13F2IO3
Mr382.13
Crystal system, space groupMonoclinic, P21
Temperature (K)193
a, b, c (Å)9.2884 (8), 6.7527 (6), 10.6582 (9)
β (°) 96.5141 (14)
V3)664.19 (10)
Z2
Radiation typeMo Kα
µ (mm1)2.44
Crystal size (mm)0.23 × 0.18 × 0.04
Data collection
DiffractometerBruker SMART CCD
diffractometer
Absorption correctionMulti-scan
(SADABS; Sheldrick, 1997a)
Tmin, Tmax0.560, 0.862
No. of measured, independent and
observed [I > 2σ(I)] reflections
4141, 2464, 2334
Rint0.025
(sin θ/λ)max1)0.610
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.037, 0.095, 1.02
No. of reflections2464
No. of parameters174
No. of restraints1
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.97, 0.31
Absolute structureFlack (1983)
Absolute structure parameter0.04 (3)

Computer programs: SMART (Siemens, 1996), SHELXTL (Sheldrick, 1996), DIRDIF99 (Beurskens et al., 1998), SHELXL97 (Sheldrick, 1997b), ZORTEP (Zsolnai & Huttner, 1994).

Selected geometric parameters (Å, º) top
C1—C21.379 (8)C1—C1'1.518 (7)
C2—C31.373 (8)C2—F21.363 (7)
C3—C41.378 (9)C4—F41.355 (6)
C4—C51.391 (8)C5—C71.471 (8)
C5—C61.409 (7)C7—C81.318 (8)
C6—C11.382 (7)C8—I82.064 (6)
C1—C2—F2118.6 (5)C4—C5—C7124.9 (5)
C3—C2—F2117.6 (5)C6—C5—C7118.9 (5)
C3—C4—F4116.6 (5)C5—C7—C8127.9 (6)
C5—C4—F4119.7 (5)C7—C8—I8123.7 (5)
O4'—C1'—C2'—C3'37.3 (5)C2'—C1'—C1—C278.4 (6)
C1'—C2'—C3'—C4'37.8 (5)O4'—C1'—C1—C2164.2 (5)
C2'—C3'—C4'—O4'25.9 (6)C2'—C1'—C1—C698.9 (6)
C3'—C4'—O4'—C1'3.2 (5)O4'—C1'—C1—C618.5 (7)
C4'—O4'—C1'—C2'21.3 (5)C4—C5—C7—C82.8 (10)
O4'—C4'—C5'—O5'160.8 (4)C6—C5—C7—C8174.8 (6)
C3'—C4'—C5'—O5'80.4 (5)C5—C7—C8—I8177.9 (5)
 

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