Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270104021602/sx1133sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S0108270104021602/sx1133Isup2.hkl |
CCDC reference: 257010
The title compound was prepared from the coupling reaction of methylsalicylchlorophosphane and 1-(2,4-difluoro-5-iodophenyl)-2-deoxy-β-D-ribofuranose, followed by oxidation using tert-butyl hydroperoxide (Sun et al., 2003) (m.p. 408–409 K; yield 20%). Spectroscopic analysis: 1H NMR (CDCl3, δ, p.p.m.): 7.86 (t, J = 7.6 Hz, 1H, difluorophenyl H), 7.19 (d, J = 6.9 Hz, 1H, saligenyl H4), 7.05 (dd, J = 7.3 and 6.9 Hz, 1H, saligenyl H5), 6.94 (d, J = 7.3 Hz, 1H, saligenyl H6), 6.82 (dd, J = 9.8 and 7.6 Hz, 1H, difluorophenyl H), 5.38 (d, J = 16.5 Hz, 2H, benzyl-CH2), 5.33 (dd, J = 10.4 and 6.1 Hz, 1H, H1'), 4.51 (ddd, J = 6.5, 3.4 and 3.1 Hz, 1H, H3'), 4.26–4.47 (m, 2H, H5'), 4.10–4.18 (m, 1H, H4'), 2.40 (ddt, J = 12.8, 5.8 and 1.8 Hz, 1H, H2'α), 2.30 (s, 3H, CH3), 1.89–2.00 (m, 1H, H2'β), 1.82 (br s, 1H, OH); 31P NMR (CDCl3, δ, p.p.m.): −8.69.
H atoms were treated as riding, with C—H = 0.95 and O—H = 0.93 Å, and with Uiso(H) = 1.3Ueq(C,O). Please check added text. In particular, please clarify the treatment of atom H18 - the CIF bond table gives no s.u.s, but Table 2 does. Please also check the symmetry operator in Table 2 - the CIF originally gave 3_656, but no symmetry code 3 was defined, nor is one possible for this space group, and symmetry code 2 was assumed.
Data collection: PROCESS-AUTO (Rigaku, 1998); cell refinement: PROCESS-AUTO; data reduction: CrystalStructure (Rigaku/MSC, 2004); program(s) used to solve structure: SIR92 (Altomare et al., 1994); program(s) used to refine structure: CRYSTALS (Watkin et al., 1996); molecular graphics: ORTEPII (Johnson, 1976); software used to prepare material for publication: CrystalStructure.
C19H18F2IO6P | F(000) = 532.00 |
Mr = 538.22 | Dx = 1.772 Mg m−3 |
Monoclinic, P21 | Mo Kα radiation, λ = 0.7107 Å |
Hall symbol: P 2yb | Cell parameters from 9501 reflections |
a = 14.552 (5) Å | θ = 3.3–27.5° |
b = 4.610 (2) Å | µ = 1.72 mm−1 |
c = 15.989 (5) Å | T = 123 K |
β = 109.86 (3)° | Needle, colorless |
V = 1008.9 (6) Å3 | 0.10 × 0.10 × 0.05 mm |
Z = 2 |
Rigaku R-AXIS RAPID diffractometer | 3621 reflections with F2 > 2σ(F2) |
Detector resolution: 10.00 pixels mm-1 | Rint = 0.053 |
ω scans | θmax = 27.5° |
Absorption correction: numerical (ABSCOR; Higashi, 1999) | h = −18→18 |
Tmin = 0.641, Tmax = 0.800 | k = −5→5 |
9720 measured reflections | l = −20→20 |
4063 independent reflections |
Refinement on F2 | (Δ/σ)max < 0.001 |
R[F2 > 2σ(F2)] = 0.037 | Δρmax = 2.12 e Å−3 |
wR(F2) = 0.096 | Δρmin = −2.03 e Å−3 |
S = 1.06 | Extinction correction: Larson (1970), eq. 22 |
4063 reflections | Extinction coefficient: 61 (6) |
282 parameters | Absolute structure: Flack (1983), with 1493 Friedel pairs |
H-atom parameters constrained | Absolute structure parameter: 0.02 (2) |
w = 1/[0.0002Fo2 + 0.6σ(Fo2)]/(4Fo2) |
C19H18F2IO6P | V = 1008.9 (6) Å3 |
Mr = 538.22 | Z = 2 |
Monoclinic, P21 | Mo Kα radiation |
a = 14.552 (5) Å | µ = 1.72 mm−1 |
b = 4.610 (2) Å | T = 123 K |
c = 15.989 (5) Å | 0.10 × 0.10 × 0.05 mm |
β = 109.86 (3)° |
Rigaku R-AXIS RAPID diffractometer | 4063 independent reflections |
Absorption correction: numerical (ABSCOR; Higashi, 1999) | 3621 reflections with F2 > 2σ(F2) |
Tmin = 0.641, Tmax = 0.800 | Rint = 0.053 |
9720 measured reflections |
R[F2 > 2σ(F2)] = 0.037 | H-atom parameters constrained |
wR(F2) = 0.096 | Δρmax = 2.12 e Å−3 |
S = 1.06 | Δρmin = −2.03 e Å−3 |
4063 reflections | Absolute structure: Flack (1983), with 1493 Friedel pairs |
282 parameters | Absolute structure parameter: 0.02 (2) |
Refinement. Refinement using all reflections. The weighted R-factor (wR) and goodness of fit (S) are based on F2. R-factor (gt) are based on F. The threshold expression of F2 > 2.0 σ(F2) is used only for calculating R-factor (gt). |
x | y | z | Uiso*/Ueq | ||
I1 | 0.50272 (2) | −0.0311 (2) | 0.60024 (2) | 0.03475 (9) | |
P1 | 0.94755 (9) | 0.6546 (3) | 0.81250 (8) | 0.0262 (3) | |
F1 | 0.4394 (2) | 0.6480 (8) | 0.9091 (2) | 0.0413 (9) | |
F2 | 0.3197 (2) | 0.0298 (8) | 0.6639 (2) | 0.044 (1) | |
O1 | 1.0313 (2) | 0.483 (1) | 0.8646 (2) | 0.0363 (9) | |
O2 | 0.9008 (2) | 0.8397 (7) | 0.8697 (2) | 0.0262 (9) | |
O3 | 0.8640 (2) | 0.469 (1) | 0.7479 (2) | 0.0297 (8) | |
O4 | 0.9737 (2) | 0.8855 (7) | 0.7524 (2) | 0.0293 (9) | |
O5 | 0.7089 (2) | 0.6939 (8) | 0.8730 (2) | 0.0298 (9) | |
O6 | 0.7742 (3) | 0.8890 (8) | 1.0968 (2) | 0.034 (1) | |
C1 | 0.5455 (3) | 0.503 (2) | 0.8349 (3) | 0.028 (1) | |
C2 | 0.4527 (3) | 0.498 (1) | 0.8422 (3) | 0.028 (1) | |
C3 | 0.3778 (4) | 0.335 (1) | 0.7887 (3) | 0.033 (1) | |
C4 | 0.3942 (4) | 0.188 (1) | 0.7202 (3) | 0.033 (1) | |
C5 | 0.4841 (4) | 0.187 (1) | 0.7077 (3) | 0.028 (1) | |
C6 | 0.5591 (4) | 0.352 (1) | 0.7659 (3) | 0.030 (1) | |
C7 | 0.6247 (3) | 0.684 (1) | 0.9001 (3) | 0.028 (1) | |
C8 | 0.6633 (4) | 0.556 (1) | 0.9942 (3) | 0.030 (1) | |
C9 | 0.7680 (4) | 0.669 (1) | 1.0327 (3) | 0.028 (1) | |
C10 | 0.7877 (3) | 0.789 (1) | 0.9496 (3) | 0.025 (1) | |
C11 | 0.8816 (3) | 0.686 (1) | 0.9421 (3) | 0.027 (1) | |
C12 | 0.7835 (4) | 0.628 (1) | 0.6828 (3) | 0.032 (1) | |
C13 | 0.8225 (4) | 0.821 (1) | 0.6290 (3) | 0.031 (1) | |
C14 | 0.7676 (4) | 0.889 (1) | 0.5406 (3) | 0.042 (2) | |
C15 | 0.8051 (5) | 1.077 (1) | 0.4926 (4) | 0.048 (2) | |
C16 | 0.8988 (5) | 1.187 (1) | 0.5296 (4) | 0.045 (2) | |
C17 | 0.9561 (4) | 1.121 (1) | 0.6161 (3) | 0.031 (1) | |
C18 | 0.9150 (3) | 0.937 (1) | 0.6634 (3) | 0.028 (1) | |
C19 | 1.0580 (5) | 1.236 (2) | 0.6572 (4) | 0.050 (2) | |
H1 | 0.3170 | 0.3227 | 0.7983 | 0.043* | |
H2 | 0.6206 | 0.3611 | 0.7575 | 0.038* | |
H3 | 0.6011 | 0.8748 | 0.9022 | 0.035* | |
H4 | 0.6625 | 0.3502 | 0.9923 | 0.038* | |
H5 | 0.6254 | 0.6216 | 1.0285 | 0.038* | |
H6 | 0.8117 | 0.5153 | 1.0586 | 0.036* | |
H7 | 0.7880 | 0.9948 | 0.9515 | 0.032* | |
H8 | 0.8775 | 0.4837 | 0.9302 | 0.034* | |
H9 | 0.9332 | 0.7225 | 0.9964 | 0.034* | |
H10 | 0.7503 | 0.7405 | 0.7134 | 0.038* | |
H11 | 0.7392 | 0.4931 | 0.6449 | 0.038* | |
H12 | 0.7046 | 0.8067 | 0.5136 | 0.049* | |
H13 | 0.7663 | 1.1299 | 0.4338 | 0.057* | |
H14 | 0.9242 | 1.3107 | 0.4951 | 0.059* | |
H15 | 1.0738 | 1.3540 | 0.6152 | 0.068* | |
H16 | 1.1025 | 1.0785 | 0.6743 | 0.068* | |
H17 | 1.0619 | 1.3485 | 0.7081 | 0.068* | |
H18 | 0.8353 | 0.9770 | 1.1197 | 0.044* |
U11 | U22 | U33 | U12 | U13 | U23 | |
I1 | 0.0441 (2) | 0.0384 (2) | 0.0269 (2) | 0.0037 (2) | 0.0187 (1) | −0.0005 (2) |
P1 | 0.0234 (6) | 0.0353 (8) | 0.0245 (6) | 0.0018 (5) | 0.0141 (5) | 0.0009 (6) |
F1 | 0.032 (2) | 0.055 (2) | 0.046 (2) | −0.005 (2) | 0.026 (1) | −0.018 (2) |
F2 | 0.037 (2) | 0.057 (3) | 0.041 (1) | −0.017 (2) | 0.016 (1) | −0.015 (2) |
O1 | 0.030 (2) | 0.052 (2) | 0.033 (1) | 0.009 (2) | 0.018 (1) | 0.010 (3) |
O2 | 0.028 (2) | 0.031 (2) | 0.027 (2) | −0.003 (1) | 0.018 (1) | −0.004 (1) |
O3 | 0.032 (2) | 0.032 (2) | 0.028 (1) | 0.005 (2) | 0.014 (1) | 0.007 (2) |
O4 | 0.030 (2) | 0.037 (2) | 0.025 (1) | −0.001 (1) | 0.015 (1) | 0.004 (1) |
O5 | 0.023 (2) | 0.041 (2) | 0.030 (2) | −0.005 (2) | 0.015 (1) | 0.002 (2) |
O6 | 0.028 (2) | 0.049 (3) | 0.032 (2) | −0.005 (1) | 0.018 (1) | −0.010 (2) |
C1 | 0.028 (2) | 0.028 (3) | 0.034 (2) | 0.001 (3) | 0.019 (2) | 0.008 (3) |
C2 | 0.034 (2) | 0.028 (3) | 0.029 (2) | −0.011 (3) | 0.018 (2) | −0.010 (3) |
C3 | 0.023 (3) | 0.042 (3) | 0.043 (3) | −0.003 (2) | 0.021 (2) | −0.004 (3) |
C4 | 0.031 (3) | 0.039 (3) | 0.029 (2) | −0.010 (2) | 0.011 (2) | −0.002 (2) |
C5 | 0.034 (3) | 0.029 (3) | 0.026 (2) | 0.004 (2) | 0.016 (2) | 0.007 (2) |
C6 | 0.026 (3) | 0.035 (3) | 0.035 (2) | 0.000 (2) | 0.017 (2) | 0.008 (2) |
C7 | 0.021 (2) | 0.036 (3) | 0.032 (2) | −0.002 (2) | 0.017 (2) | −0.002 (2) |
C8 | 0.034 (3) | 0.037 (3) | 0.025 (2) | −0.008 (2) | 0.018 (2) | −0.003 (2) |
C9 | 0.028 (3) | 0.035 (3) | 0.027 (2) | 0.001 (2) | 0.019 (2) | 0.004 (2) |
C10 | 0.026 (2) | 0.029 (3) | 0.026 (2) | −0.006 (2) | 0.015 (2) | −0.005 (2) |
C11 | 0.025 (2) | 0.034 (3) | 0.027 (2) | −0.001 (2) | 0.016 (2) | −0.001 (2) |
C12 | 0.027 (3) | 0.038 (3) | 0.030 (2) | 0.000 (2) | 0.007 (2) | −0.003 (2) |
C13 | 0.034 (3) | 0.031 (3) | 0.031 (2) | 0.009 (2) | 0.016 (2) | −0.002 (2) |
C14 | 0.039 (3) | 0.055 (4) | 0.030 (2) | 0.014 (3) | 0.008 (2) | −0.002 (2) |
C15 | 0.062 (4) | 0.057 (4) | 0.025 (2) | 0.026 (3) | 0.014 (3) | 0.009 (3) |
C16 | 0.074 (5) | 0.041 (3) | 0.031 (3) | 0.014 (3) | 0.032 (3) | 0.012 (3) |
C17 | 0.046 (3) | 0.029 (3) | 0.028 (2) | 0.003 (2) | 0.024 (2) | 0.000 (2) |
C18 | 0.035 (2) | 0.028 (3) | 0.024 (2) | 0.009 (2) | 0.016 (2) | 0.005 (3) |
C19 | 0.069 (4) | 0.055 (4) | 0.045 (3) | −0.012 (4) | 0.044 (3) | −0.003 (3) |
I1—C5 | 2.088 (5) | C13—C14 | 1.403 (7) |
P1—O1 | 1.454 (4) | C13—C18 | 1.378 (7) |
P1—O2 | 1.565 (4) | C14—C15 | 1.39 (1) |
P1—O3 | 1.557 (4) | C15—C16 | 1.386 (9) |
P1—O4 | 1.565 (4) | C16—C17 | 1.385 (7) |
F1—C2 | 1.341 (7) | C17—C18 | 1.399 (8) |
F2—C4 | 1.362 (6) | C17—C19 | 1.500 (9) |
O2—C11 | 1.463 (6) | O6—H18 | 0.9314 |
O3—C12 | 1.470 (6) | C3—H1 | 0.9500 |
O4—C18 | 1.410 (5) | C6—H2 | 0.9500 |
O5—C7 | 1.433 (7) | C7—H3 | 0.9500 |
O5—C10 | 1.433 (5) | C8—H4 | 0.9500 |
O6—C9 | 1.421 (6) | C8—H5 | 0.9501 |
C1—C2 | 1.395 (7) | C9—H6 | 0.9500 |
C1—C6 | 1.373 (8) | C10—H7 | 0.9500 |
C1—C7 | 1.515 (7) | C11—H8 | 0.9500 |
C2—C3 | 1.360 (7) | C11—H9 | 0.9500 |
C3—C4 | 1.375 (8) | C12—H10 | 0.9500 |
C4—C5 | 1.389 (8) | C12—H11 | 0.9500 |
C5—C6 | 1.394 (6) | C14—H12 | 0.9500 |
C7—C8 | 1.533 (6) | C15—H13 | 0.9499 |
C8—C9 | 1.528 (7) | C16—H14 | 0.9500 |
C9—C10 | 1.552 (7) | C19—H15 | 0.9500 |
C10—C11 | 1.488 (7) | C19—H16 | 0.9500 |
C12—C13 | 1.479 (8) | C19—H17 | 0.9500 |
I1···F2 | 3.170 (4) | O5···H7 | 1.9603 |
I1···C4 | 3.043 (6) | O5···H8 | 2.5036 |
I1···C6 | 3.055 (5) | O5···H9 | 3.1916 |
P1···C11 | 2.567 (6) | O5···H10 | 2.8228 |
P1···C12 | 2.579 (4) | O6···H3 | 3.2720 |
P1···C13 | 2.980 (5) | O6···H4 | 3.1240 |
P1···C18 | 2.615 (5) | O6···H4iv | 2.8477 |
F1···C1 | 2.343 (7) | O6···H5 | 2.4075 |
F1···C3 | 2.327 (6) | O6···H6 | 1.9658 |
F1···C4 | 3.562 (6) | O6···H6iv | 3.0384 |
F1···C6 | 3.584 (7) | O6···H7 | 2.4476 |
F1···C7 | 2.754 (6) | O6···H9 | 3.3226 |
F1···C8 | 3.105 (6) | C1···H1 | 3.2816 |
F2···C2 | 3.575 (6) | C1···H2 | 2.0170 |
F2···C3 | 2.352 (6) | C1···H3iii | 3.0975 |
F2···C5 | 2.367 (6) | C1···H3 | 2.0413 |
F2···C14i | 3.497 (6) | C1···H4 | 2.6103 |
F2···C15ii | 3.292 (7) | C1···H5 | 2.9650 |
F2···C15i | 3.582 (7) | C2···H1 | 2.0259 |
O1···O2iii | 3.539 (6) | C2···H2 | 3.2330 |
O1···O2 | 2.534 (6) | C2···H3iii | 3.5269 |
O1···O3 | 2.515 (4) | C2···H3 | 2.6818 |
O1···O4iii | 3.239 (6) | C2···H4 | 3.2517 |
O1···O4 | 2.517 (6) | C2···H5 | 3.2295 |
O1···C11 | 2.999 (7) | C4···H1 | 2.0389 |
O2···O1iv | 3.539 (6) | C4···H2 | 3.2422 |
O2···O3 | 2.508 (5) | C4···H12i | 3.5623 |
O2···O3iv | 3.433 (6) | C4···H13i | 3.4285 |
O2···O4 | 2.457 (5) | C5···H1 | 3.2855 |
O2···O5 | 2.890 (5) | C5···H2 | 2.0362 |
O2···C10 | 2.413 (7) | C5···H3iii | 3.3243 |
O2···C12 | 3.054 (5) | C6···H3iii | 3.0111 |
O2···C18 | 3.404 (6) | C6···H3 | 3.1661 |
O3···O2iii | 3.433 (6) | C6···H4 | 3.4161 |
O3···O4iii | 3.116 (6) | C7···H2 | 2.7064 |
O3···O4 | 2.481 (6) | C7···H4 | 2.0708 |
O3···C11 | 3.190 (6) | C7···H4iv | 3.3706 |
O3···C13iii | 3.482 (7) | C7···H5 | 2.0693 |
O3···C13 | 2.414 (6) | C7···H6 | 3.1223 |
O3···C17iii | 3.275 (7) | C7···H7 | 2.6555 |
O3···C18iii | 3.011 (8) | C8···H3iii | 3.4559 |
O3···C18 | 2.777 (7) | C8···H3 | 2.0583 |
O4···O1iv | 3.239 (6) | C8···H6 | 2.0610 |
O4···O3iv | 3.116 (6) | C8···H7iii | 3.3605 |
O4···C12 | 2.867 (6) | C8···H7 | 2.9472 |
O4···C13 | 2.424 (5) | C8···H18 | 3.2623 |
O4···C17 | 2.370 (6) | C9···H3 | 2.7759 |
O4···C19 | 2.776 (8) | C9···H4 | 2.0657 |
O5···O6 | 3.494 (5) | C9···H4iv | 3.4564 |
O5···C1 | 2.412 (6) | C9···H5 | 2.0658 |
O5···C6 | 2.762 (6) | C9···H7iii | 3.4202 |
O5···C8 | 2.339 (6) | C9···H7 | 2.0673 |
O5···C9 | 2.404 (6) | C9···H8 | 2.7801 |
O5···C11 | 2.377 (5) | C9···H9 | 2.6683 |
O5···C12 | 3.572 (7) | C9···H18iii | 3.4871 |
O6···C7 | 3.297 (5) | C9···H18 | 1.9950 |
O6···C8 | 2.419 (6) | C10···H3 | 2.5898 |
O6···C8iv | 3.599 (6) | C10···H4 | 2.9524 |
O6···C10 | 2.471 (6) | C10···H4iv | 3.3650 |
O6···C11 | 3.472 (7) | C10···H5 | 3.1287 |
C1···C3 | 2.424 (7) | C10···H6 | 2.0825 |
C1···C4 | 2.751 (7) | C10···H8 | 2.0142 |
C1···C5 | 2.410 (7) | C10···H8iv | 3.5131 |
C1···C8 | 2.554 (6) | C10···H9 | 2.0147 |
C2···C4 | 2.332 (7) | C10···H18 | 2.7114 |
C2···C5 | 2.748 (8) | C11···H6 | 2.5317 |
C2···C6 | 2.371 (8) | C11···H7iii | 3.4889 |
C2···C7 | 2.506 (7) | C11···H7 | 2.0104 |
C2···C8 | 3.212 (6) | C11···H10 | 3.5132 |
C3···C5 | 2.428 (9) | C11···H18 | 3.4081 |
C3···C6 | 2.784 (8) | C12···H2 | 3.2370 |
C4···C6 | 2.382 (7) | C12···H12 | 2.6855 |
C6···C7 | 2.542 (7) | C13···H10 | 2.0056 |
C6···C8 | 3.571 (6) | C13···H11 | 2.0057 |
C7···C9 | 2.418 (6) | C13···H11iv | 3.3680 |
C7···C10 | 2.283 (6) | C13···H12 | 2.0496 |
C7···C11 | 3.567 (7) | C13···H13 | 3.2719 |
C8···O6iii | 3.599 (6) | C14···H10 | 2.9387 |
C8···C10 | 2.411 (8) | C14···H11 | 2.5981 |
C8···C11 | 3.596 (8) | C14···H11iv | 3.3418 |
C9···C11 | 2.541 (8) | C14···H13 | 2.0315 |
C12···C14 | 2.514 (8) | C14···H14 | 3.2599 |
C12···C18 | 2.489 (8) | C15···H11iv | 3.4813 |
C13···O3iv | 3.482 (7) | C15···H12 | 2.0338 |
C13···C15 | 2.416 (8) | C15···H14 | 2.0301 |
C13···C16 | 2.795 (9) | C16···H12 | 3.2624 |
C13···C17 | 2.452 (8) | C16···H13 | 2.0316 |
C14···F2v | 3.497 (6) | C16···H15 | 2.5653 |
C14···C16 | 2.41 (1) | C16···H16 | 3.1194 |
C14···C17 | 2.807 (8) | C16···H17 | 3.1195 |
C14···C18 | 2.375 (6) | C17···H13 | 3.2643 |
C15···F2v | 3.582 (7) | C17···H14 | 2.0278 |
C15···F2vi | 3.292 (7) | C17···H15 | 2.0254 |
C15···C17 | 2.413 (7) | C17···H16 | 2.0241 |
C15···C18 | 2.731 (7) | C17···H17 | 2.0237 |
C16···C18 | 2.370 (8) | C18···H10 | 2.9158 |
C16···C19 | 2.523 (8) | C18···H11 | 3.2095 |
C17···O3iv | 3.275 (7) | C18···H11iv | 3.5609 |
C18···O3iv | 3.011 (8) | C18···H12 | 3.2383 |
C18···C19 | 2.527 (9) | C18···H14 | 3.2354 |
I1···H2 | 3.0989 | C18···H15 | 3.2921 |
I1···H10iii | 3.5967 | C18···H16 | 2.7535 |
I1···H12i | 3.3331 | C18···H17iii | 3.3783 |
P1···H8 | 2.5506 | C18···H17 | 2.7647 |
P1···H9 | 3.0341 | C19···H14 | 2.6827 |
P1···H10 | 2.7956 | H2···O5iii | 3.5932 |
P1···H11 | 3.3774 | H3···C1iv | 3.0975 |
P1···H17iii | 3.0719 | H3···C2iv | 3.5269 |
F1···H1 | 2.5322 | H3···C5iv | 3.3243 |
F1···H3 | 2.6116 | H3···C6iv | 3.0111 |
F1···H4 | 3.3565 | H3···C8iv | 3.4559 |
F1···H5 | 2.7345 | H4···O6iii | 2.8477 |
F2···H1 | 2.5497 | H4···C7iii | 3.3706 |
F2···H12i | 3.0215 | H4···C9iii | 3.4564 |
F2···H13ii | 2.4654 | H4···C10iii | 3.3650 |
F2···H13i | 3.2145 | H6···O6iii | 3.0384 |
F2···H16vii | 3.2285 | H7···O5iv | 3.5076 |
O1···H8 | 2.7762 | H7···C8iv | 3.3605 |
O1···H9 | 3.1212 | H7···C9iv | 3.4202 |
O1···H17iii | 2.7575 | H7···C11iv | 3.4889 |
O2···H7 | 2.5252 | H8···O2iii | 3.1761 |
O2···H8 | 1.9917 | H8···C10iii | 3.5131 |
O2···H8iv | 3.1761 | H10···I1iv | 3.5967 |
O2···H9 | 1.9926 | H11···C13iii | 3.3680 |
O2···H10 | 2.7442 | H11···C14iii | 3.3418 |
O3···H8 | 2.8555 | H11···C15iii | 3.4813 |
O3···H10 | 1.9971 | H11···C18iii | 3.5609 |
O3···H11 | 1.9978 | H12···I1v | 3.3331 |
O3···H17iii | 3.2018 | H12···F2v | 3.0215 |
O4···H10 | 3.1658 | H12···C4v | 3.5623 |
O4···H16 | 2.7312 | H13···F2v | 3.2145 |
O4···H17iii | 2.9832 | H13···F2vi | 2.4654 |
O4···H17 | 2.7064 | H13···C4v | 3.4285 |
O5···H2 | 2.4091 | H16···F2viii | 3.2285 |
O5···H2iv | 3.5932 | H17···P1iv | 3.0719 |
O5···H3 | 1.9682 | H17···O1iv | 2.7575 |
O5···H4 | 2.7345 | H17···O3iv | 3.2018 |
O5···H5 | 3.1343 | H17···O4iv | 2.9832 |
O5···H6 | 2.9509 | H17···C18iv | 3.3783 |
O5···H7iii | 3.5076 | H18···C9iv | 3.4871 |
I1—C5—C4 | 120.8 (3) | C16—C17—C18 | 116.8 (5) |
I1—C5—C6 | 121.4 (4) | C16—C17—C19 | 122.0 (6) |
O2—P1—O1 | 114.1 (2) | C19—C17—C18 | 121.3 (4) |
O3—P1—O1 | 113.3 (3) | O2—C11—H8 | 109.3906 |
O4—P1—O1 | 113.0 (2) | O2—C11—H9 | 109.4650 |
O3—P1—O2 | 106.9 (2) | O3—C12—H10 | 109.3402 |
O4—P1—O2 | 103.4 (2) | O3—C12—H11 | 109.4004 |
P1—O2—C11 | 115.9 (3) | O5—C7—H3 | 109.6849 |
O4—P1—O3 | 105.3 (2) | O5—C10—H7 | 109.0370 |
P1—O3—C12 | 116.8 (4) | O6—C9—H6 | 110.4086 |
P1—O4—C18 | 123.0 (3) | H18—O6—C9 | 114.3573 |
F1—C2—C1 | 117.7 (4) | C1—C6—H2 | 119.4290 |
F1—C2—C3 | 118.9 (5) | C1—C7—H3 | 109.6671 |
F2—C4—C5 | 118.7 (5) | C2—C3—H1 | 121.5308 |
F2—C4—C3 | 118.4 (5) | H1—C3—C4 | 121.4657 |
O2—C11—C10 | 109.7 (4) | C5—C6—H2 | 119.3931 |
O3—C12—C13 | 109.9 (4) | H3—C7—C8 | 109.7221 |
O4—C18—C13 | 120.8 (5) | C7—C8—H4 | 110.8091 |
O4—C18—C17 | 115.1 (4) | C7—C8—H5 | 110.6725 |
O5—C7—C1 | 109.8 (4) | H4—C8—C9 | 110.7524 |
O5—C7—C8 | 104.0 (4) | H5—C8—C9 | 110.7578 |
C10—O5—C7 | 105.6 (4) | C8—C9—H6 | 110.3483 |
O5—C10—C11 | 108.9 (4) | H5—C8—H4 | 109.4610 |
O5—C10—C9 | 107.3 (4) | C9—C10—H7 | 109.0865 |
O6—C9—C8 | 110.1 (4) | H6—C9—C10 | 110.3851 |
O6—C9—C10 | 112.3 (4) | C10—C11—H8 | 109.3943 |
C6—C1—C2 | 117.9 (5) | C10—C11—H9 | 109.4351 |
C1—C2—C3 | 123.2 (5) | H7—C10—C11 | 109.0632 |
C7—C1—C2 | 118.8 (5) | H9—C11—H8 | 109.4572 |
C1—C6—C5 | 121.2 (5) | H10—C12—C13 | 109.3617 |
C7—C1—C6 | 123.3 (5) | H11—C12—C13 | 109.3709 |
C1—C7—C8 | 113.8 (5) | H11—C12—H10 | 109.4646 |
C2—C3—C4 | 117.0 (5) | C13—C14—H12 | 119.9537 |
C3—C4—C5 | 122.9 (5) | H12—C14—C15 | 119.9574 |
C4—C5—C6 | 117.7 (5) | C14—C15—H13 | 119.7218 |
C7—C8—C9 | 104.3 (4) | H13—C15—C16 | 119.6723 |
C8—C9—C10 | 103.0 (3) | C15—C16—H14 | 119.5128 |
C9—C10—C11 | 113.4 (4) | H14—C16—C17 | 119.4041 |
C12—C13—C18 | 121.2 (4) | C17—C19—H16 | 109.3666 |
C12—C13—C14 | 121.5 (5) | C17—C19—H17 | 109.3295 |
C18—C13—C14 | 117.3 (5) | C17—C19—H15 | 109.4787 |
C13—C14—C15 | 120.1 (5) | H16—C19—H15 | 109.5921 |
C13—C18—C17 | 124.1 (4) | H17—C19—H15 | 109.5883 |
C14—C15—C16 | 120.6 (5) | H17—C19—H16 | 109.4715 |
C15—C16—C17 | 121.1 (6) | ||
O1—P1—O2—C11 | −48.3 (3) | F2—C4—C5—C6 | 179.7 (5) |
O3—P1—O2—C11 | 77.7 (3) | C3—C4—C5—I1 | −178.4 (4) |
O4—P1—O2—C11 | −171.4 (2) | C3—C4—C5—C6 | −2.5 (8) |
O1—P1—O3—C12 | −170.6 (3) | I1—C5—C6—C1 | 178.1 (4) |
O2—P1—O3—C12 | 62.8 (4) | C4—C5—C6—C1 | 2.2 (8) |
O4—P1—O3—C12 | −46.7 (4) | O5—C7—C8—C9 | 33.1 (5) |
O1—P1—O4—C18 | 136.5 (4) | C1—C7—C8—C9 | 152.5 (4) |
O2—P1—O4—C18 | −99.6 (4) | C7—C8—C9—O6 | 106.7 (4) |
O3—P1—O4—C18 | 12.4 (4) | C7—C8—C9—C10 | −13.3 (5) |
P1—O2—C11—C10 | −141.9 (3) | O6—C9—C10—O5 | −129.2 (4) |
P1—O3—C12—C13 | 56.3 (5) | O6—C9—C10—C11 | 110.6 (5) |
P1—O4—C18—C13 | 11.2 (8) | C8—C9—C10—O5 | −10.7 (5) |
P1—O4—C18—C17 | −171.4 (4) | C8—C9—C10—C11 | −130.9 (4) |
C10—O5—C7—C1 | −162.9 (4) | O5—C10—C11—O2 | 68.6 (5) |
C10—O5—C7—C8 | −40.8 (5) | C9—C10—C11—O2 | −172.1 (3) |
C7—O5—C10—C9 | 32.4 (5) | O3—C12—C13—C14 | 149.5 (5) |
C7—O5—C10—C11 | 155.5 (4) | O3—C12—C13—C18 | −29.4 (7) |
C6—C1—C2—F1 | −179.2 (5) | C12—C13—C14—C15 | 178.4 (6) |
C6—C1—C2—C3 | 5.4 (9) | C18—C13—C14—C15 | −2.7 (9) |
C7—C1—C2—F1 | −2.4 (8) | C12—C13—C18—O4 | −2.9 (9) |
C7—C1—C2—C3 | −177.7 (5) | C12—C13—C18—C17 | −180.0 (5) |
C2—C1—C6—C5 | −3.5 (8) | C14—C13—C18—O4 | 178.2 (5) |
C7—C1—C6—C5 | 179.8 (5) | C14—C13—C18—C17 | 1.1 (9) |
C2—C1—C7—O5 | −171.2 (5) | C13—C14—C15—C16 | 3 (1) |
C2—C1—C7—C8 | 72.7 (7) | C14—C15—C16—C17 | −2 (1) |
C6—C1—C7—O5 | 5.5 (8) | C15—C16—C17—C18 | 0.4 (9) |
C6—C1—C7—C8 | −110.6 (6) | C15—C16—C17—C19 | 179.4 (6) |
F1—C2—C3—C4 | 179.1 (5) | C16—C17—C18—O4 | −177.2 (5) |
C1—C2—C3—C4 | −5.6 (8) | C16—C17—C18—C13 | 0.0 (8) |
C2—C3—C4—F2 | −178.1 (5) | C19—C17—C18—O4 | 3.8 (8) |
C2—C3—C4—C5 | 4.1 (8) | C19—C17—C18—C13 | −179.0 (6) |
F2—C4—C5—I1 | 3.8 (7) |
Symmetry codes: (i) −x+1, y−1/2, −z+1; (ii) −x+1, y−3/2, −z+1; (iii) x, y−1, z; (iv) x, y+1, z; (v) −x+1, y+1/2, −z+1; (vi) −x+1, y+3/2, −z+1; (vii) x−1, y−1, z; (viii) x+1, y+1, z. |
D—H···A | D—H | H···A | D···A | D—H···A |
O6—H18···O1ix | 0.93 (1) | 1.87 (1) | 2.719 (5) | 150 (4) |
Symmetry code: (ix) −x+2, y+1/2, −z+2. |
Experimental details
Crystal data | |
Chemical formula | C19H18F2IO6P |
Mr | 538.22 |
Crystal system, space group | Monoclinic, P21 |
Temperature (K) | 123 |
a, b, c (Å) | 14.552 (5), 4.610 (2), 15.989 (5) |
β (°) | 109.86 (3) |
V (Å3) | 1008.9 (6) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 1.72 |
Crystal size (mm) | 0.10 × 0.10 × 0.05 |
Data collection | |
Diffractometer | Rigaku R-AXIS RAPID diffractometer |
Absorption correction | Numerical (ABSCOR; Higashi, 1999) |
Tmin, Tmax | 0.641, 0.800 |
No. of measured, independent and observed [F2 > 2σ(F2)] reflections | 9720, 4063, 3621 |
Rint | 0.053 |
(sin θ/λ)max (Å−1) | 0.649 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.037, 0.096, 1.06 |
No. of reflections | 4063 |
No. of parameters | 282 |
No. of restraints | ? |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 2.12, −2.03 |
Absolute structure | Flack (1983), with 1493 Friedel pairs |
Absolute structure parameter | 0.02 (2) |
Computer programs: PROCESS-AUTO (Rigaku, 1998), PROCESS-AUTO, CrystalStructure (Rigaku/MSC, 2004), SIR92 (Altomare et al., 1994), CRYSTALS (Watkin et al., 1996), ORTEPII (Johnson, 1976), CrystalStructure.
I1—C5 | 2.088 (5) | P1—O3 | 1.557 (4) |
P1—O1 | 1.454 (4) | P1—O4 | 1.565 (4) |
P1—O2 | 1.565 (4) | O4—C18 | 1.410 (5) |
O2—P1—O1 | 114.1 (2) | O3—P1—O2 | 106.9 (2) |
O4—P1—O1 | 113.0 (2) | O4—P1—O3 | 105.3 (2) |
C10—O5—C7—C8 | −40.8 (5) | C7—C8—C9—C10 | −13.3 (5) |
C7—O5—C10—C9 | 32.4 (5) | O6—C9—C10—C11 | 110.6 (5) |
C2—C1—C7—O5 | −171.2 (5) | C8—C9—C10—O5 | −10.7 (5) |
O5—C7—C8—C9 | 33.1 (5) | C9—C10—C11—O2 | −172.1 (3) |
D—H···A | D—H | H···A | D···A | D—H···A |
O6—H18···O1i | 0.931 (5) | 1.871 (5) | 2.719 (5) | 150 (4) |
Symmetry code: (i) −x+2, y+1/2, −z+2. |
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A group of synthetic 3-substituted (H, Me, OMe) cyclosaligenyl derivatives of 1-(2-deoxy-β-D-ribofuranosyl)-2,4-difluoro-5-iodo- (or -trifluoromethyl-) benzene, previously evaluated as antiviral and anticancer agents (Wang et al., 2001), have been synthesized. These cyclosaligenyl derivatives were designed to act as thymidine kinase-bypass pronucleotides that would give rise to the intracellular release of the monophosphate derivative of 1-(2-deoxy-β-D-ribofuranosyl)-2,4-difluoro-5-iodo- (or trifluoromethyl-) benzene (Meier De Clercq & Balzarini, 1998; Meier et al., 1999). The configuration of the phosphorus center in cyclosaligenyl phosphate has so far been assigned only by comparison with the known stereochemistry of the model compound using CD Please define spectroscopy (Meier Lorey et al., 1998). We now report the results of the X-ray crystal structure analysis for the title compound, (I), one of the two diastereomers of iodinated cyclosaligenyl phosphate produced in the reaction, in order to establish the absolute configuration at the asymmetric P center. \sch
Compound (I) was synthesized by the oxidation reaction of the coupled product of 1-(2-deoxy-β-D-ribofuranosyl)-2,4-difluoro-5-iodobenzene with 3-methylsaligenylchlorophosphane. Removal of the solvent in vacuo gave a residue which was purified by flash silica-gel column chromatography using CH2Cl2-EtOAc (1:1, v/v) as eluent, to give a 1:1 mixture of the respective S– and R-diastereomeric products. Optically pure (I) was obtained by fractional crystallization of an ether solution of the diastereomeric mixture. Single crystals for X-ray crystallographic analysis were prepared by the following procedure. Subsequent flash silica-gel column chromatography of the 1:1 mixture of S– [(I)] and R-diastereomeric isomers with CH2Cl2-EtOAc (3:2, v/v) as eluent gave the fast-eluting isomer, (I), and the slow-eluting isomer, respectively. The fast-eluting isomer, (I), was recrystallized from ether to afford optically pure crystals. Characterization of (I) by 1H and 31P NMR spectroscopy showed that the 31P resonance was more shielded (higher field), but in the1H NMR spectra, the benzylic-CH2 H atoms were less shielded than those of the slow-eluting isomer. Thus, the less polar diastereisomer, (I), was successfully crystallized from ether as colorless needles, which were subsequently subjected to X-ray crystallographic analysis. The crystallographic analysis afforded the assignment of the absolute configuration of the compound at the asymmetric P center in the cyclosaligenyl ring as S.
The molecular structure of (I) is shown in Fig. 1 and selected geometric parameters are listed in Table 1. The P1═O1 bond [1.454 (4) Å] indicates double-bond character and is shorter than P1—O2, P1—O3 and P1—O4 [1.565 (4), 1.557 (4) and 1.565 (4) Å, respectively]. The torsion angles at the phosphate, O1—P1—O2—C11, O1—P1—O3—C12 and O1—P1—O4—C18, are −48.3 (3), −170.6 (3) and 136.5 (4)°, respectively. The absolute stereochemistry of the iodinated molecule, (I), is confirmed by the value of the Flack (1983) parameter [0.02 (2)].
Our labeling of the deoxyribose ring differs from the standard labeling and therefore, in our description of its conformation, we use standard labels for the atoms followed by our labeling in parentheses. The O4' (O5)-endo conformation of the deoxyribose ring present in (I) is different from the C2'-endo conformation found in the structurally related compounds (E)-1-(2-deoxy-β-D-ribofuranosyl)-2,4-difluoro-5-(2-iodovinyl)benzene (Mark et al., 2001) and 1-(2-deoxy-β-D-ribofuranosyl)-2,4-difluoro-5-methylbenzene (Guckian & Kool, 1997). This O4' (O5)-endo conformation is consistent with the larger C3'-C4'-O4'-C1' (C9—C10—O5—C7) torsion angle of 32.4 (5)° relative to the smaller C1'-C2'-C3'-C4' (C7—C8—C9—C10) torsion angle of −13.3 (5)°. The 2,4-difluoro-5-iodobenzene ring in (I) is anti with respect to the deoxyribose, as measured by the O4'-C1'-C1—C2 (O5—C7—C1—C2) torsion angle of −171.2 (5)°.
Inspection of the packing structure of (I) reveals that intermolecular interactions are formed through hydrogen-bonding between a hydroxyl group (O6—H18) of the sugar ring and a phosphate O atom (P1═O1) (Fig. 2, Table 2), and also through π–π interactions between the methylsaligenyl aromatic ring, represented by the short intermolecular distance [3.011 (8) Å] between atoms O3 and C18 of the cyclosaligenyl rings and the molecules related by unit-cell translations along the crystallographic b axis·(Fig. 3) 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). The crystal structure of (I), however, shows no intermolecular hydrogen bonding involving the F atoms of the aryl ring.