Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270100000998/bm1390sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S0108270100000998/bm1390Isup2.hkl |
CCDC reference: 144654
Compound (I) was synthesized by the reaction of (E)-5-(2-ethoxy carbonyl vinyl)-2'-deoxyuridine with I2 and potassium iodate, as illustrated in the Scheme, according to the method of Kumar et al. (1989). Crystals of (I) were obtained from methanol by slow evaporation at room temperature.
The structure was solved by direct methods and successive Fourier syntheses. All H atoms attached to C or N were located geometrically and refined as part of a riding model, with Uiso(H) = 0.078 (6) Å2. All H atoms attached to hydroxyl-O atoms were located in circular difference Fourier syntheses and thereafter refined freely with Uiso(H) = 0.078 (6) Å2. The atom-numbering scheme used in Fig. 1 is consistent with the rules of the IUPAC-IUB Joint Commission on Biochemical Nomenclature (IUPAC-IUB, 1983).
Data collection: CAD-4 Software (Enraf-Nonius, 1988); cell refinement: CAD-4 Software; data reduction: CAD-4 Software; program(s) used to solve structure: SHELXS86 (Sheldrick, 1990); program(s) used to refine structure: SHELXL93 (Sheldrick, 1993); molecular graphics: ORTEPII (Johnson, 1976); software used to prepare material for publication: SHELXL93.
Fig. 1. An ORTEPII (Johnson, 1976) plot of the molecule of (I) drawn at the 30% probability level. |
C14H19IN2O8 | F(000) = 468 |
Mr = 470.21 | Dx = 1.763 Mg m−3 |
Monoclinic, P21 | Mo Kα radiation, λ = 0.71069 Å |
a = 6.748 (3) Å | Cell parameters from 25 reflections |
b = 10.466 (4) Å | θ = 10.3–14.4° |
c = 12.555 (4) Å | µ = 1.85 mm−1 |
β = 92.36 (3)° | T = 293 K |
V = 885.9 (6) Å3 | Block, colourless |
Z = 2 | 0.35 × 0.25 × 0.20 mm |
Enraf-Nonius CAD-4 diffractometer | 1545 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.046 |
Graphite monochromator | θmax = 25°, θmin = 2.5° |
ω–2θ scans | h = −8→8 |
Absorption correction: empirical (using intensity measurements) via ψ scan (North et al., 1968) | k = 0→12 |
Tmin = 0.607, Tmax = 0.690 | l = 0→14 |
3290 measured reflections | 3 standard reflections every 100 reflections |
1649 independent reflections | intensity decay: none |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.036 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.137 | Calculated w = 1/[σ2(Fo2) + (0.0399P)2] where P = (Fo2 + 2Fc2)/3 |
S = 0.93 | (Δ/σ)max = 0.002 |
1585 reflections | Δρmax = 0.34 e Å−3 |
231 parameters | Δρmin = −0.31 e Å−3 |
2 restraints | Absolute structure: Flack (1983) |
Primary atom site location: structure-invariant direct methods | Absolute structure parameter: −0.04 (3) |
C14H19IN2O8 | V = 885.9 (6) Å3 |
Mr = 470.21 | Z = 2 |
Monoclinic, P21 | Mo Kα radiation |
a = 6.748 (3) Å | µ = 1.85 mm−1 |
b = 10.466 (4) Å | T = 293 K |
c = 12.555 (4) Å | 0.35 × 0.25 × 0.20 mm |
β = 92.36 (3)° |
Enraf-Nonius CAD-4 diffractometer | 1545 reflections with I > 2σ(I) |
Absorption correction: empirical (using intensity measurements) via ψ scan (North et al., 1968) | Rint = 0.046 |
Tmin = 0.607, Tmax = 0.690 | 3 standard reflections every 100 reflections |
3290 measured reflections | intensity decay: none |
1649 independent reflections |
R[F2 > 2σ(F2)] = 0.036 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.137 | Δρmax = 0.34 e Å−3 |
S = 0.93 | Δρmin = −0.31 e Å−3 |
1585 reflections | Absolute structure: Flack (1983) |
231 parameters | Absolute structure parameter: −0.04 (3) |
2 restraints |
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 on F2 for ALL reflections except for 64 with very negative F2 or flagged by the user for potential systematic errors. Weighted R-factors wR and all goodnesses of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The observed criterion of F2 > σ(F2) is used only for calculating _R_factor_obs 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 | ||
I | 0.51789 (7) | 0.26018 (12) | 0.01926 (3) | 0.0832 (2) | |
C7 | 0.4084 (6) | 0.2547 (6) | 0.2528 (3) | 0.0343 (10) | |
H17 | 0.3148 | 0.3235 | 0.2339 | 0.078* | |
C8 | 0.4137 (9) | 0.1655 (7) | 0.1570 (5) | 0.0497 (15) | |
H8 | 0.4965 | 0.0908 | 0.1743 | 0.078* | |
C9 | 0.1980 (10) | 0.1229 (7) | 0.1259 (5) | 0.056 (2) | |
O9 | 0.0584 (7) | 0.1941 (6) | 0.1303 (5) | 0.075 (2) | |
O10 | 0.1990 (9) | 0.0011 (6) | 0.1003 (5) | 0.086 (2) | |
C10 | −0.0022 (14) | −0.0469 (11) | 0.0599 (10) | 0.091 (3) | |
H110 | −0.1066 | −0.0138 | 0.1030 | 0.078* | |
H210 | −0.0069 | −0.1395 | 0.0609 | 0.078* | |
O7 | 0.3284 (5) | 0.1857 (4) | 0.3382 (3) | 0.0417 (9) | |
H7 | 0.402 (6) | 0.126 (5) | 0.355 (4) | 0.078 (6)* | |
C5 | 0.6034 (8) | 0.3167 (5) | 0.2837 (4) | 0.0352 (12) | |
C4 | 0.7684 (8) | 0.2403 (5) | 0.3159 (4) | 0.0376 (11) | |
C6 | 0.6265 (9) | 0.4433 (6) | 0.2849 (4) | 0.0371 (12) | |
H6 | 0.5173 | 0.4946 | 0.2674 | 0.078* | |
N1 | 0.8052 (6) | 0.5013 (4) | 0.3110 (3) | 0.0318 (9) | |
O4 | 0.7598 (7) | 0.1216 (4) | 0.3218 (4) | 0.0605 (13) | |
C1' | 0.8355 (8) | 0.6415 (5) | 0.3127 (4) | 0.0344 (12) | |
H1' | 0.9521 | 0.6638 | 0.2726 | 0.078* | |
C4' | 0.6169 (9) | 0.8133 (6) | 0.3213 (5) | 0.0427 (14) | |
H4' | 0.6152 | 0.8855 | 0.2716 | 0.078* | |
O4' | 0.6644 (6) | 0.6983 (4) | 0.2648 (3) | 0.0427 (10) | |
C5' | 0.4137 (9) | 0.7976 (6) | 0.3648 (6) | 0.057 (2) | |
H15' | 0.3230 | 0.7637 | 0.3099 | 0.078* | |
H25' | 0.4196 | 0.7379 | 0.4239 | 0.078* | |
O5' | 0.3449 (6) | 0.9175 (5) | 0.3996 (6) | 0.077 (2) | |
H5' | 0.236 (6) | 0.933 (4) | 0.371 (5) | 0.078 (6)* | |
C3' | 0.7830 (8) | 0.8316 (6) | 0.4036 (5) | 0.042 (2) | |
H13' | 0.7328 | 0.8673 | 0.4694 | 0.078* | |
C2' | 0.8541 (10) | 0.6965 (5) | 0.4209 (5) | 0.043 (2) | |
H12' | 0.9906 | 0.6946 | 0.4483 | 0.078* | |
H22' | 0.7714 | 0.6512 | 0.4698 | 0.078* | |
O2 | 1.1324 (5) | 0.4784 (4) | 0.3499 (4) | 0.0477 (10) | |
N3 | 0.9445 (6) | 0.3015 (4) | 0.3385 (4) | 0.0356 (10) | |
H3 | 1.0449 | 0.2551 | 0.3577 | 0.078* | |
C2 | 0.9729 (7) | 0.4295 (6) | 0.3331 (4) | 0.0370 (12) | |
C11 | −0.0237 (16) | 0.0033 (12) | −0.0535 (10) | 0.096 (4) | |
H111 | −0.1490 | −0.0234 | −0.0850 | 0.078* | |
H211 | 0.0817 | −0.0298 | −0.0945 | 0.078* | |
H311 | −0.0175 | 0.0950 | −0.0527 | 0.078* | |
O3' | 0.9423 (6) | 0.9034 (5) | 0.3691 (5) | 0.0630 (14) | |
H3' | 0.902 (2) | 0.956 (6) | 0.325 (5) | 0.078 (6)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
I | 0.0614 (3) | 0.1360 (6) | 0.0528 (3) | 0.0082 (4) | 0.0080 (2) | 0.0103 (5) |
C7 | 0.027 (2) | 0.028 (2) | 0.048 (2) | 0.002 (3) | −0.004 (2) | 0.001 (3) |
C8 | 0.039 (3) | 0.059 (4) | 0.050 (3) | 0.003 (3) | −0.005 (2) | −0.005 (3) |
C9 | 0.066 (4) | 0.058 (4) | 0.044 (3) | −0.018 (4) | −0.009 (3) | −0.020 (3) |
O9 | 0.041 (2) | 0.076 (3) | 0.104 (4) | 0.014 (3) | −0.022 (2) | −0.040 (3) |
O10 | 0.092 (4) | 0.069 (4) | 0.098 (4) | −0.026 (4) | 0.018 (3) | −0.026 (4) |
C10 | 0.075 (6) | 0.106 (8) | 0.091 (7) | −0.040 (6) | −0.008 (5) | −0.030 (7) |
O7 | 0.028 (2) | 0.038 (2) | 0.060 (2) | −0.001 (2) | 0.008 (2) | 0.008 (2) |
C5 | 0.025 (3) | 0.030 (3) | 0.050 (3) | 0.016 (2) | 0.001 (2) | 0.008 (2) |
C4 | 0.038 (3) | 0.021 (2) | 0.054 (3) | −0.011 (3) | 0.003 (2) | −0.006 (3) |
C6 | 0.033 (3) | 0.040 (3) | 0.039 (3) | 0.009 (2) | 0.006 (2) | 0.000 (3) |
N1 | 0.023 (2) | 0.028 (2) | 0.044 (3) | −0.001 (2) | −0.002 (2) | 0.002 (2) |
O4 | 0.034 (2) | 0.033 (2) | 0.113 (4) | 0.004 (2) | −0.016 (2) | 0.016 (3) |
C1' | 0.031 (3) | 0.031 (3) | 0.040 (3) | 0.003 (2) | −0.003 (2) | 0.003 (2) |
C4' | 0.032 (3) | 0.041 (3) | 0.055 (4) | 0.002 (2) | −0.002 (3) | 0.004 (3) |
O4' | 0.049 (2) | 0.027 (2) | 0.050 (2) | 0.011 (2) | −0.020 (2) | −0.004 (2) |
C5' | 0.037 (3) | 0.032 (3) | 0.102 (5) | 0.004 (3) | −0.005 (3) | −0.012 (3) |
O5' | 0.028 (2) | 0.055 (3) | 0.147 (5) | 0.012 (2) | 0.002 (3) | −0.030 (3) |
C3' | 0.025 (3) | 0.051 (4) | 0.050 (3) | 0.014 (3) | −0.008 (2) | −0.012 (3) |
C2' | 0.045 (4) | 0.030 (3) | 0.051 (4) | 0.000 (3) | −0.019 (3) | −0.014 (3) |
O2 | 0.026 (2) | 0.038 (2) | 0.080 (3) | 0.001 (2) | −0.002 (2) | −0.007 (2) |
N3 | 0.023 (2) | 0.018 (2) | 0.065 (3) | 0.007 (2) | −0.005 (2) | 0.009 (2) |
C2 | 0.024 (3) | 0.045 (3) | 0.042 (3) | 0.006 (3) | 0.004 (2) | 0.009 (2) |
C11 | 0.088 (7) | 0.105 (8) | 0.095 (7) | −0.049 (7) | 0.012 (6) | −0.023 (7) |
O3' | 0.023 (2) | 0.046 (3) | 0.119 (5) | 0.003 (2) | −0.007 (2) | −0.006 (3) |
I—C8 | 2.137 (6) | C1'—C2' | 1.476 (8) |
C7—O7 | 1.419 (6) | C1'—H1' | 0.98 |
C7—C5 | 1.504 (7) | C4'—O4' | 1.440 (7) |
C7—C8 | 1.524 (8) | C4'—C3' | 1.505 (8) |
C7—H17 | 0.98 | C4'—C5' | 1.506 (9) |
C8—C9 | 1.557 (8) | C4'—H4' | 0.98 |
C8—H8 | 0.98 | C5'—O5' | 1.414 (8) |
C9—O9 | 1.204 (7) | C5'—H15' | 0.97 |
C9—O10 | 1.315 (9) | C5'—H25' | 0.97 |
O10—C10 | 1.516 (10) | O5'—H5' | 0.82 |
C10—C11 | 1.519 (13) | C3'—O3' | 1.395 (8) |
C10—H110 | 0.97 | C3'—C2' | 1.506 (8) |
C10—H210 | 0.97 | C3'—H13' | 0.98 |
O7—H7 | 0.82 | C2'—H12' | 0.97 |
C5—C6 | 1.334 (8) | C2'—H22' | 0.97 |
C5—C4 | 1.416 (7) | O2—C2 | 1.203 (7) |
C4—O4 | 1.245 (6) | N3—C2 | 1.355 (7) |
C4—N3 | 1.370 (7) | N3—H3 | 0.86 |
C6—N1 | 1.378 (7) | C11—H111 | 0.96 |
C6—H6 | 0.93 | C11—H211 | 0.96 |
N1—C2 | 1.377 (7) | C11—H311 | 0.96 |
N1—C1' | 1.482 (7) | O3'—H3' | 0.82 |
C1'—O4' | 1.411 (6) | ||
O7—C7—C5 | 112.4 (4) | N1—C1'—H1' | 110 |
O7—C7—C8 | 107.8 (5) | O4'—C4'—C3' | 105.7 (5) |
C5—C7—C8 | 114.8 (4) | O4'—C4'—C5' | 108.2 (5) |
O7—C7—H17 | 107 | C3'—C4'—C5' | 115.3 (6) |
C5—C7—H17 | 107 | O4'—C4'—H4' | 109 |
C8—C7—H17 | 107 | C3'—C4'—H4' | 109 |
C7—C8—C9 | 108.8 (5) | C5'—C4'—H4' | 109 |
C7—C8—I | 111.9 (4) | C1'—O4'—C4' | 109.7 (4) |
C9—C8—I | 105.3 (4) | O5'—C5'—C4' | 109.3 (5) |
C7—C8—H8 | 110 | O5'—C5'—H15' | 110 |
C9—C8—H8 | 110 | C4'—C5'—H15' | 110 |
I—C8—H8 | 110 | O5'—C5'—H25' | 110 |
O9—C9—O10 | 128.6 (7) | C4'—C5'—H25' | 110 |
O9—C9—C8 | 122.4 (6) | H15'—C5'—H25' | 108 |
O10—C9—C8 | 108.9 (6) | C5'—O5'—H5' | 110 |
C9—O10—C10 | 112.9 (7) | O3'—C3'—C4' | 114.6 (6) |
O10—C10—C11 | 104.4 (9) | O3'—C3'—C2' | 107.8 (5) |
O10—C10—H110 | 111 | C4'—C3'—C2' | 101.7 (5) |
C11—C10—H110 | 111 | O3'—C3'—H13' | 111 |
O10—C10—H210 | 111 | C4'—C3'—H13' | 111 |
C11—C10—H210 | 111 | C2'—C3'—H13' | 111 |
H110—C10—H210 | 109 | C1'—C2'—C3' | 102.6 (6) |
C7—O7—H7 | 109 | C1'—C2'—H12' | 111 |
C6—C5—C4 | 117.9 (5) | C3'—C2'—H12' | 111 |
C6—C5—C7 | 122.1 (5) | C1'—C2'—H22' | 111 |
C4—C5—C7 | 120.0 (5) | C3'—C2'—H22' | 111 |
O4—C4—N3 | 119.8 (5) | H12'—C2'—H22' | 109 |
O4—C4—C5 | 122.8 (5) | C2—N3—C4 | 125.1 (4) |
N3—C4—C5 | 117.4 (4) | C2—N3—H3 | 117 |
C5—C6—N1 | 122.7 (5) | C4—N3—H3 | 117 |
C5—C6—H6 | 119 | O2—C2—N3 | 122.6 (5) |
N1—C6—H6 | 119 | O2—C2—N1 | 121.7 (6) |
C2—N1—C6 | 120.8 (5) | N3—C2—N1 | 115.6 (5) |
C2—N1—C1' | 115.2 (4) | C10—C11—H111 | 109 |
C6—N1—C1' | 123.9 (4) | C10—C11—H211 | 109 |
O4'—C1'—C2' | 105.4 (5) | H111—C11—H211 | 109 |
O4'—C1'—N1 | 107.5 (4) | C10—C11—H311 | 109 |
C2'—C1'—N1 | 113.9 (5) | H111—C11—H311 | 109 |
O4'—C1'—H1' | 110 | H211—C11—H311 | 109 |
C2'—C1'—H1' | 110 | C3'—O3'—H3' | 109 |
O7—C7—C8—C9 | 61.1 (6) | C2—N1—C1'—C2' | −77.2 (6) |
C5—C7—C8—C9 | −172.8 (5) | C6—N1—C1'—C2' | 105.7 (6) |
O7—C7—C8—I | 177.1 (3) | C2'—C1'—O4'—C4' | 19.4 (6) |
C5—C7—C8—I | −56.8 (6) | N1—C1'—O4'—C4' | 141.3 (4) |
C7—C8—C9—O9 | 37.7 (9) | C3'—C4'—O4'—C1' | 4.9 (6) |
I—C8—C9—O9 | −82.5 (7) | C5'—C4'—O4'—C1' | −119.1 (6) |
C7—C8—C9—O10 | −139.7 (6) | O4'—C4'—C5'—O5' | −167.1 (5) |
I—C8—C9—O10 | 100.2 (6) | C3'—C4'—C5'—O5' | 74.9 (7) |
O9—C9—O10—C10 | 7.6 (12) | O4'—C4'—C3'—O3' | 89.7 (6) |
C8—C9—O10—C10 | −175.3 (7) | C5'—C4'—C3'—O3' | −150.9 (5) |
C9—O10—C10—C11 | 76.7 (9) | O4'—C4'—C3'—C2' | −26.3 (7) |
O7—C7—C5—C6 | −116.0 (6) | C5'—C4'—C3'—C2' | 93.1 (7) |
C8—C7—C5—C6 | 120.3 (7) | O4'—C1'—C2'—C3' | −35.6 (6) |
O7—C7—C5—C4 | 62.1 (7) | N1—C1'—C2'—C3' | −153.2 (5) |
C8—C7—C5—C4 | −61.6 (7) | O3'—C3'—C2'—C1' | −83.5 (5) |
C6—C5—C4—O4 | 176.9 (6) | C4'—C3'—C2'—C1' | 37.4 (7) |
C7—C5—C4—O4 | −1.2 (9) | O4—C4—N3—C2 | 178.8 (6) |
C6—C5—C4—N3 | −4.7 (8) | C5—C4—N3—C2 | 0.4 (8) |
C7—C5—C4—N3 | 177.1 (5) | C4—N3—C2—O2 | −177.1 (5) |
C4—C5—C6—N1 | 3.2 (9) | C4—N3—C2—N1 | 5.3 (8) |
C7—C5—C6—N1 | −178.7 (5) | C6—N1—C2—O2 | 175.5 (5) |
C5—C6—N1—C2 | 2.8 (8) | C1'—N1—C2—O2 | −1.7 (7) |
C5—C6—N1—C1' | 179.8 (5) | C6—N1—C2—N3 | −6.8 (7) |
C2—N1—C1'—O4' | 166.4 (4) | C1'—N1—C2—N3 | 175.9 (5) |
C6—N1—C1'—O4' | −10.8 (7) |
D—H···A | D—H | H···A | D···A | D—H···A |
C6—H6···O4′ | 0.93 | 2.35 | 2.694 (8) | 101 |
O5′—H5′···O3′i | 0.82 | 2.01 | 2.732 (6) | 147 |
O7—H7···O5′ii | 0.82 | 2.29 | 2.912 (7) | 133 |
O3′—H3′···O4iii | 0.82 | 1.98 | 2.650 (7) | 138 |
N3—H3···O7iv | 0.86 | 2.07 | 2.860 (6) | 152 |
Symmetry codes: (i) x−1, y, z; (ii) x, y−1, z; (iii) x, y+1, z; (iv) x+1, y, z. |
Experimental details
Crystal data | |
Chemical formula | C14H19IN2O8 |
Mr | 470.21 |
Crystal system, space group | Monoclinic, P21 |
Temperature (K) | 293 |
a, b, c (Å) | 6.748 (3), 10.466 (4), 12.555 (4) |
β (°) | 92.36 (3) |
V (Å3) | 885.9 (6) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 1.85 |
Crystal size (mm) | 0.35 × 0.25 × 0.20 |
Data collection | |
Diffractometer | Enraf-Nonius CAD-4 diffractometer |
Absorption correction | Empirical (using intensity measurements) via ψ scan (North et al., 1968) |
Tmin, Tmax | 0.607, 0.690 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 3290, 1649, 1545 |
Rint | 0.046 |
(sin θ/λ)max (Å−1) | 0.595 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.036, 0.137, 0.93 |
No. of reflections | 1585 |
No. of parameters | 231 |
No. of restraints | 2 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.34, −0.31 |
Absolute structure | Flack (1983) |
Absolute structure parameter | −0.04 (3) |
Computer programs: CAD-4 Software (Enraf-Nonius, 1988), CAD-4 Software, SHELXS86 (Sheldrick, 1990), SHELXL93 (Sheldrick, 1993), ORTEPII (Johnson, 1976), SHELXL93.
C5—C7—C8—C9 | −172.8 (5) | C8—C9—O10—C10 | −175.3 (7) |
C7—C8—C9—O10 | −139.7 (6) | C9—O10—C10—C11 | 76.7 (9) |
D—H···A | D—H | H···A | D···A | D—H···A |
O5'—H5'···O3'i | 0.82 | 2.01 | 2.732 (6) | 147 |
O7—H7···O5'ii | 0.82 | 2.29 | 2.912 (7) | 133 |
O3'—H3'···O4iii | 0.82 | 1.98 | 2.650 (7) | 138 |
N3—H3···O7iv | 0.86 | 2.07 | 2.860 (6) | 152 |
Symmetry codes: (i) x−1, y, z; (ii) x, y−1, z; (iii) x, y+1, z; (iv) x+1, y, z. |
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The title compound, (I), is an example of the 5-vinyl-2'-deoxyuridine derivatives, which have been found to inhibit replication of the herpes simplex virus type I (De Clercq et al., 1979). Studies of the structure-activity relationships of these 5-substituted derivatives indicated that the activity is associated with analogues in which the 5-substituent is conjugated with the pyrimidine ring (Griengl et al., 1985). The structural analysis of the compound (I) is a continuation of our earlier work involving systematic conformational studies on modified nucleosides with the aim of understanding structure-function relationships. \scheme
The absolute configuration of the structure has been determined, as indicated by the Flack parameter of -0.04 (3) (Flack, 1983) (Friedel number = ?). The 5-substituent is an aliphatic chain with a terminal carboxyl ethoxy group and it is twisted away from the N1—C6 ring [C4—C5—C7—C8 torsion angle = -61.6 (7)°], allowing the bulky I atom to lie out of the plane of the ring. The chain skeleton has an extended conformation. The terminal ethoxy group has a gauche conformation with respect to the skeleton [C9—O10—C10—C11 = 76.7 (9)°]. The C—I bond distance of 2.137 (6) Å compares closely with the value of 2.139 Å found for CH3I (Bowen et al., 1958).
The heterocyclic base moiety is almost planar, the r.m.s. deviation of the atoms from their least-squares mean plane being 0.027 (5) Å and the maximum deviation being 0.044 (5) Å for C2. The bond lengths and angles for the nucleoside analogue are normal (Allen et al., 1987) with no significant deviation, indicating that the substitution at C5 has no effect on the molecular geometry. The C4=O4 [1.245 (6) Å] bond is 0.042 (6) Å longer than the C2=O2 [1.203 (7) Å] and C9=O9 [1.204 (7) Å] bonds; this elongation is attributed to the formation of a hydrogen bond between O4 and O3'; O2 and O9 do not form any hydrogen bonds in the structure of (I). Similar effects have been reported for the 1:1 complex of thiourea and parabanic acid (TUPA; Weber et al., 1987).
The glycosyl torsion angle τ (C2—N1—C1'-O4'), showing the relative orientation of the base with respect to the sugar ring, has a value of 166.4 (4)°, which lies at the extreme end of the range -160 to -175° for torsion angles τ observed in active anti-HIV nucleosides (Van Roey et al., 1989). This glycosyl angle τ places the C1'-O4' bond close to the plane of the conjugated system of the base, bringing O4' into close contact with hydrogen H6 on C6 of the base [H6···O4' = 2.352 (7) Å], resulting in steric hindrance between the base and sugar ring. The structural effects include lengthening of the C1'-N1 bond, which has a value 1.482 (7) Å in (I). Saenger (1984) has correlated the C1'-N1 bond length with the angle τ, and for τ near -167°, the expected N1—C1' bond length is 1.48 Å.
The C1'-O4' [1.411 (6) Å] bond is shorter than C4'-O4' [1.440 (7) Å], due to the anomeric effect (Kirby, 1983), which is a common feature of nucleosides. The pseudo rotation phase angle P [168.3 (6)°] and the maximum torsion angle νmax [38.2 (7)°] are calculated from intraring torsion angles to describe the puckering of the five-membered ring of the sugar moiety; these values indicate an unsymmetrical twist of the sugar ring with C2'-endo/C3'-exo (2T3; Saenger,1984) and are similar to those of active anti-HIV compounds, which have P values in the range 165–220° with C2'-endo/C3'-exo (Van Roey et al., 1989). The active conformer of 3'-azido-3'-deoxythymidine (known as AZT) has P = 175° with C2'-endo/C3'-exo (Dyer et al., 1988). The C3'-exo conformation places C5' in an axial position. The torsion angle Γ (uc?) [C3'-C4'-C5'-O5'= 74.9 (7)°] describing the orientation of the 5'-hydroxyl group relative to the sugar ring shows that C5'-O5' is in a gauche-gauche orientation (+sc) (Van Roey et al., 1989).
Each molecule in the crystal structure of (I) has four H atoms available for hydrogen-bond formation. These are bonded to three hydroxyl O atoms, O3', O5' and O7, and to the pyrimidine nitrogen N3. The hydroxyl groups act as both hydrogen-bond donors and acceptors. The hydroxyl groups and the ring N atom N3 form O—H···O and N—H···O hydrogen bonds with molecules related by translational symmetry along the a and b axes (Table 2), resulting in a two-dimensional network in the ab plane.