The structures of 1-deoxy-1-(4-fluorophenyl)-β-
D-ribofuranose in two crystal forms, (I
a) and (I
b) (C
11H
13FO
4), 1-deoxy-1-(4-fluorophenyl)-β-
D-ribofuranose hemihydrate, (I
c) (C
11H
13FO
4·0.5H
2O) and 1-deoxy-1-(2,4-difluorophenyl)-β-
D-ribofuranose, (II) (C
11H
12F
2O
4), show two-dimensional networks of intermolecular hydrogen bonds between the hydroxyl groups. Weak intermolecular C—H
F—C and C—H
π
arene interactions complete the packing in the third dimension. The ribofuranose ring has a conformation intermediate between a C1′-
exo,C2′-
endo twist and a C2′-
endo envelope for (I
a) and (I
c), a conformation intermediate between a C2′-
endo,C3′-
exo twist and a C2′-
endo envelope for (I
b) and an unsymmetrical C2′-
exo,C3′-
endo twist conformation for (II).
Supporting information
CCDC references: 142751; 142752; 142753; 142754
The title compounds were prepared according to Krohn et al. (1992). Thus, 1-bromo-4-fluorobenzene [for (I)] or 1-bromo-2,4-difluorobenzene [for (II)] was lithiated and added to 2',3',5'-tri-O-benzyl-D-ribono-1,4-lactone (Barker & Fletcher, 1961; Timpe et al., 1975). The resulting intermediate lactol was directly dehydroxylated to yield a sterically uniform β-C-riboside. Debenzylation of the hydroxyl groups resulted in the unprotected C-nucleoside. Compound (I) was recrystallized from methanol, resuling in two different crystalline modifications, (Ia) and (Ib), while recrystallization from water yielded the hemihydrate (Ic). Compound (II) was also recrystallized from water.
For all compounds, data collection: SMART (Siemens, 1995); cell refinement: SMART; data reduction: SAINT (Siemens, 1995); program(s) used to solve structure: SHELXTL (Sheldrick, 1996); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: XP in SHELXTL; software used to prepare material for publication: CIF in SHELXL97.
(Ia) 1'-deoxy-1'-(4-fluorophenyl)-
β-
D-ribofuranose
top
Crystal data top
C11H13FO4 | Dx = 1.416 Mg m−3 |
Mr = 228.21 | Mo Kα radiation, λ = 0.71073 Å |
Orthorhombic, P212121 | Cell parameters from 279 reflections |
a = 5.4741 (9) Å | θ = 3–23° |
b = 7.3018 (7) Å | µ = 0.12 mm−1 |
c = 26.791 (3) Å | T = 134 K |
V = 1070.9 (2) Å3 | Plate, colourless |
Z = 4 | 1.30 × 0.64 × 0.15 mm |
F(000) = 480 | |
Data collection top
Siemens SMART diffractometer | 3273 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.084 |
Graphite monochromator | θmax = 31.3°, θmin = 2.9° |
ω scans | h = −7→8 |
18913 measured reflections | k = −10→10 |
3431 independent reflections | l = −38→35 |
Refinement top
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)] = 0.037 | Hydrogen site location: difference Fourier map |
wR(F2) = 0.111 | All H-atom parameters refined |
S = 1.39 | w = 1/[σ2(Fo2) + (0.06P)2] where P = (Fo2 + 2Fc2)/3 |
3431 reflections | (Δ/σ)max = 0.002 |
197 parameters | Δρmax = 0.36 e Å−3 |
0 restraints | Δρmin = −0.20 e Å−3 |
Crystal data top
C11H13FO4 | V = 1070.9 (2) Å3 |
Mr = 228.21 | Z = 4 |
Orthorhombic, P212121 | Mo Kα radiation |
a = 5.4741 (9) Å | µ = 0.12 mm−1 |
b = 7.3018 (7) Å | T = 134 K |
c = 26.791 (3) Å | 1.30 × 0.64 × 0.15 mm |
Data collection top
Siemens SMART diffractometer | 3273 reflections with I > 2σ(I) |
18913 measured reflections | Rint = 0.084 |
3431 independent reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.037 | 0 restraints |
wR(F2) = 0.111 | All H-atom parameters refined |
S = 1.39 | Δρmax = 0.36 e Å−3 |
3431 reflections | Δρmin = −0.20 e Å−3 |
197 parameters | |
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 | x | y | z | Uiso*/Ueq | |
O2 | 0.76882 (16) | 0.33447 (10) | 0.78927 (3) | 0.01865 (17) | |
F | 0.5477 (2) | 0.63072 (12) | 1.01688 (3) | 0.0391 (2) | |
O3 | 0.63932 (16) | −0.00392 (11) | 0.74918 (3) | 0.02119 (17) | |
O4 | 0.58996 (18) | −0.03869 (11) | 0.86967 (3) | 0.02431 (19) | |
O5 | 1.02384 (16) | −0.37191 (11) | 0.81932 (3) | 0.02209 (18) | |
C2 | 0.78380 (19) | 0.17676 (13) | 0.81964 (4) | 0.01504 (18) | |
C3 | 0.79950 (19) | −0.00591 (13) | 0.79128 (4) | 0.01600 (19) | |
C1 | 0.5644 (2) | 0.14795 (14) | 0.85402 (4) | 0.01712 (19) | |
C10 | 0.3775 (3) | 0.53286 (17) | 0.94093 (5) | 0.0290 (3) | |
C7 | 0.7353 (2) | 0.26211 (18) | 0.93564 (4) | 0.0237 (2) | |
C6 | 0.5575 (2) | 0.27333 (14) | 0.89837 (4) | 0.01727 (19) | |
C9 | 0.5541 (2) | 0.51538 (16) | 0.97721 (5) | 0.0257 (2) | |
C8 | 0.7339 (2) | 0.38401 (19) | 0.97552 (4) | 0.0271 (2) | |
C5 | 0.9144 (2) | −0.25106 (14) | 0.85456 (4) | 0.0212 (2) | |
C4 | 0.7080 (2) | −0.14229 (14) | 0.83058 (4) | 0.0185 (2) | |
C11 | 0.3813 (2) | 0.40980 (16) | 0.90120 (4) | 0.0234 (2) | |
H7 | 0.859 (4) | 0.161 (3) | 0.9349 (6) | 0.030 (4)* | |
H2 | 0.925 (3) | 0.191 (2) | 0.8403 (6) | 0.020 (4)* | |
H1 | 0.421 (3) | 0.171 (2) | 0.8320 (5) | 0.010 (3)* | |
H5B | 1.045 (4) | −0.164 (2) | 0.8646 (6) | 0.024 (4)* | |
H8 | 0.849 (4) | 0.380 (3) | 1.0015 (7) | 0.031 (4)* | |
H3 | 0.957 (3) | −0.0349 (19) | 0.7808 (5) | 0.014 (3)* | |
HO5 | 0.937 (5) | −0.454 (3) | 0.8111 (7) | 0.040 (5)* | |
H4 | 0.583 (3) | −0.224 (2) | 0.8160 (5) | 0.017 (3)* | |
H11 | 0.267 (4) | 0.415 (2) | 0.8775 (7) | 0.036 (5)* | |
H5A | 0.840 (4) | −0.319 (3) | 0.8835 (7) | 0.039 (5)* | |
H10 | 0.262 (5) | 0.639 (3) | 0.9446 (7) | 0.054 (6)* | |
HO3 | 0.733 (4) | 0.050 (3) | 0.7269 (7) | 0.045 (5)* | |
HO2 | 0.634 (5) | 0.346 (3) | 0.7739 (7) | 0.040 (5)* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
O2 | 0.0208 (4) | 0.0152 (3) | 0.0199 (3) | −0.0011 (3) | 0.0000 (3) | 0.0016 (3) |
F | 0.0458 (5) | 0.0397 (4) | 0.0318 (4) | −0.0062 (4) | 0.0017 (4) | −0.0213 (3) |
O3 | 0.0246 (4) | 0.0230 (4) | 0.0160 (3) | −0.0038 (3) | −0.0047 (3) | −0.0008 (3) |
O4 | 0.0354 (5) | 0.0159 (3) | 0.0215 (4) | 0.0003 (3) | 0.0104 (3) | 0.0006 (3) |
O5 | 0.0245 (4) | 0.0171 (4) | 0.0247 (4) | 0.0006 (3) | −0.0008 (3) | −0.0031 (3) |
C2 | 0.0155 (4) | 0.0147 (4) | 0.0150 (4) | −0.0002 (3) | −0.0005 (4) | −0.0012 (3) |
C3 | 0.0177 (4) | 0.0159 (4) | 0.0143 (4) | 0.0006 (3) | −0.0009 (3) | −0.0019 (3) |
C1 | 0.0169 (4) | 0.0169 (4) | 0.0176 (4) | −0.0001 (4) | 0.0010 (4) | −0.0023 (3) |
C10 | 0.0313 (6) | 0.0237 (5) | 0.0319 (6) | 0.0075 (5) | −0.0005 (5) | −0.0084 (4) |
C7 | 0.0217 (5) | 0.0305 (5) | 0.0188 (5) | 0.0064 (5) | −0.0020 (4) | −0.0031 (4) |
C6 | 0.0177 (4) | 0.0181 (4) | 0.0160 (4) | 0.0008 (4) | 0.0011 (4) | −0.0010 (3) |
C9 | 0.0301 (6) | 0.0251 (5) | 0.0219 (5) | −0.0058 (5) | 0.0027 (4) | −0.0088 (4) |
C8 | 0.0244 (5) | 0.0382 (6) | 0.0188 (5) | 0.0002 (5) | −0.0030 (4) | −0.0067 (4) |
C5 | 0.0294 (5) | 0.0176 (4) | 0.0165 (4) | 0.0012 (4) | −0.0028 (4) | −0.0005 (4) |
C4 | 0.0231 (5) | 0.0153 (4) | 0.0173 (4) | 0.0000 (4) | 0.0004 (4) | −0.0012 (3) |
C11 | 0.0229 (5) | 0.0241 (5) | 0.0232 (5) | 0.0062 (4) | −0.0036 (4) | −0.0052 (4) |
Geometric parameters (Å, º) top
O2—C2 | 1.4124 (12) | C1—C6 | 1.5004 (13) |
F—C9 | 1.3565 (12) | C10—C9 | 1.3770 (18) |
O3—C3 | 1.4286 (12) | C10—C11 | 1.3933 (15) |
O4—C1 | 1.4327 (13) | C7—C8 | 1.3907 (15) |
O4—C4 | 1.4445 (13) | C7—C6 | 1.3969 (15) |
O5—C5 | 1.4245 (13) | C6—C11 | 1.3888 (16) |
C2—C1 | 1.5282 (14) | C9—C8 | 1.3751 (19) |
C2—C3 | 1.5374 (13) | C5—C4 | 1.5235 (16) |
C3—C4 | 1.5333 (14) | | |
| | | |
C1—O4—C4 | 109.25 (8) | C11—C6—C7 | 119.14 (10) |
O2—C2—C1 | 114.44 (8) | C11—C6—C1 | 119.90 (10) |
O2—C2—C3 | 115.21 (8) | C7—C6—C1 | 120.85 (10) |
C1—C2—C3 | 102.85 (8) | F—C9—C8 | 118.52 (11) |
O3—C3—C4 | 110.37 (9) | F—C9—C10 | 118.50 (11) |
O3—C3—C2 | 110.30 (8) | C8—C9—C10 | 122.96 (10) |
C4—C3—C2 | 101.88 (7) | C9—C8—C7 | 118.40 (11) |
O4—C1—C6 | 110.56 (8) | O5—C5—C4 | 110.81 (8) |
O4—C1—C2 | 103.33 (8) | O4—C4—C5 | 107.39 (8) |
C6—C1—C2 | 114.40 (9) | O4—C4—C3 | 107.69 (8) |
C9—C10—C11 | 117.97 (11) | C5—C4—C3 | 112.69 (9) |
C8—C7—C6 | 120.52 (11) | C6—C11—C10 | 120.99 (11) |
| | | |
O2—C2—C3—O3 | −40.37 (11) | C11—C10—C9—F | −177.96 (12) |
C1—C2—C3—O3 | 84.83 (9) | C11—C10—C9—C8 | 0.7 (2) |
O2—C2—C3—C4 | −157.57 (9) | F—C9—C8—C7 | 177.92 (11) |
C1—C2—C3—C4 | −32.36 (10) | C10—C9—C8—C7 | −0.8 (2) |
C4—O4—C1—C6 | −153.22 (9) | C6—C7—C8—C9 | −0.13 (19) |
C4—O4—C1—C2 | −30.39 (11) | C1—O4—C4—C5 | 131.18 (9) |
O2—C2—C1—O4 | 164.70 (8) | C1—O4—C4—C3 | 9.57 (12) |
C3—C2—C1—O4 | 38.99 (10) | O5—C5—C4—O4 | 173.87 (8) |
O2—C2—C1—C6 | −75.05 (11) | O5—C5—C4—C3 | −67.70 (11) |
C3—C2—C1—C6 | 159.24 (8) | O3—C3—C4—O4 | −102.07 (10) |
C8—C7—C6—C11 | 1.04 (18) | C2—C3—C4—O4 | 15.08 (11) |
C8—C7—C6—C1 | 177.17 (11) | O3—C3—C4—C5 | 139.67 (9) |
O4—C1—C6—C11 | −133.56 (11) | C2—C3—C4—C5 | −103.18 (9) |
C2—C1—C6—C11 | 110.31 (12) | C7—C6—C11—C10 | −1.08 (18) |
O4—C1—C6—C7 | 50.33 (13) | C1—C6—C11—C10 | −177.25 (11) |
C2—C1—C6—C7 | −65.80 (13) | C9—C10—C11—C6 | 0.21 (19) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
O2—HO2···O3i | 0.85 (2) | 1.96 (2) | 2.729 (1) | 151 (2) |
O3—HO3···O5ii | 0.88 (2) | 1.91 (2) | 2.774 (1) | 169 (2) |
O5—HO5···O2iii | 0.80 (2) | 1.89 (2) | 2.682 (1) | 172 (2) |
Symmetry codes: (i) −x+1, y+1/2, −z+3/2; (ii) −x+2, y+1/2, −z+3/2; (iii) x, y−1, z. |
(Ib) 1'-deoxy-1'-(4-fluorophenyl)-
β-
D-ribofuranose
top
Crystal data top
C11H13FO4 | Dx = 1.461 Mg m−3 |
Mr = 228.21 | Mo Kα radiation, λ = 0.71073 Å |
Orthorhombic, P212121 | Cell parameters from 161 reflections |
a = 6.7109 (14) Å | θ = 3–23° |
b = 6.7653 (7) Å | µ = 0.12 mm−1 |
c = 22.846 (3) Å | T = 135 K |
V = 1037.2 (3) Å3 | Rod, colourless |
Z = 4 | 0.66 × 0.45 × 0.28 mm |
F(000) = 480 | |
Data collection top
Siemens SMART diffractometer | 3512 independent reflections |
Radiation source: fine-focus sealed tube | 2944 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.058 |
ω scans | θmax = 31.9°, θmin = 1.8° |
Absorption correction: numerical (SHELXTL; sheldrick, 1996) ? | h = −9→9 |
Tmin = 0.932, Tmax = 0.968 | k = −10→10 |
19895 measured reflections | l = −34→31 |
Refinement top
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.039 | All H-atom parameters refined |
wR(F2) = 0.090 | w = 1/[σ2(Fo2) + (0.05P)2] where P = (Fo2 + 2Fc2)/3 |
S = 1.11 | (Δ/σ)max = 0.001 |
3512 reflections | Δρmax = 0.30 e Å−3 |
198 parameters | Δρmin = −0.20 e Å−3 |
0 restraints | Extinction correction: SHELXL97 (Sheldrick, 1997), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.010 (3) |
Crystal data top
C11H13FO4 | V = 1037.2 (3) Å3 |
Mr = 228.21 | Z = 4 |
Orthorhombic, P212121 | Mo Kα radiation |
a = 6.7109 (14) Å | µ = 0.12 mm−1 |
b = 6.7653 (7) Å | T = 135 K |
c = 22.846 (3) Å | 0.66 × 0.45 × 0.28 mm |
Data collection top
Siemens SMART diffractometer | 3512 independent reflections |
Absorption correction: numerical (SHELXTL; sheldrick, 1996) ? | 2944 reflections with I > 2σ(I) |
Tmin = 0.932, Tmax = 0.968 | Rint = 0.058 |
19895 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.039 | 0 restraints |
wR(F2) = 0.090 | All H-atom parameters refined |
S = 1.11 | Δρmax = 0.30 e Å−3 |
3512 reflections | Δρmin = −0.20 e Å−3 |
198 parameters | |
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 | x | y | z | Uiso*/Ueq | |
O3 | 0.13084 (14) | 0.41021 (13) | 0.76631 (4) | 0.02036 (19) | |
O5 | 0.73253 (12) | 0.22777 (12) | 0.66755 (4) | 0.02106 (19) | |
F | 0.33765 (16) | 1.11352 (13) | 0.46221 (4) | 0.0454 (3) | |
O4 | 0.46441 (12) | 0.56444 (12) | 0.68270 (4) | 0.02004 (19) | |
O2 | −0.06632 (12) | 0.57415 (13) | 0.67107 (4) | 0.01943 (18) | |
C7 | 0.4733 (2) | 0.77456 (18) | 0.57821 (6) | 0.0244 (3) | |
C4 | 0.42437 (16) | 0.36681 (17) | 0.70464 (5) | 0.0159 (2) | |
C11 | 0.14812 (19) | 0.91003 (18) | 0.59712 (5) | 0.0215 (3) | |
C1 | 0.28136 (16) | 0.66180 (15) | 0.66811 (5) | 0.0154 (2) | |
C6 | 0.30337 (19) | 0.78431 (16) | 0.61310 (5) | 0.0178 (2) | |
C5 | 0.52017 (17) | 0.21584 (17) | 0.66459 (6) | 0.0189 (2) | |
C2 | 0.12640 (16) | 0.49594 (16) | 0.66321 (5) | 0.0153 (2) | |
C3 | 0.19792 (17) | 0.34891 (17) | 0.70967 (5) | 0.0159 (2) | |
C10 | 0.1592 (2) | 1.0222 (2) | 0.54614 (6) | 0.0281 (3) | |
C9 | 0.3288 (2) | 1.00628 (19) | 0.51258 (5) | 0.0303 (3) | |
C8 | 0.4866 (2) | 0.8878 (2) | 0.52740 (6) | 0.0311 (3) | |
H2 | 0.142 (2) | 0.437 (2) | 0.6228 (6) | 0.022 (4)* | |
H4 | 0.485 (2) | 0.3559 (18) | 0.7426 (5) | 0.007 (3)* | |
H1 | 0.239 (2) | 0.751 (2) | 0.7013 (6) | 0.016 (3)* | |
H3 | 0.148 (2) | 0.217 (2) | 0.7025 (5) | 0.014 (3)* | |
H11 | 0.022 (2) | 0.9189 (19) | 0.6210 (6) | 0.012 (3)* | |
HO5 | 0.775 (3) | 0.133 (3) | 0.6905 (7) | 0.028 (4)* | |
H5B | 0.483 (2) | 0.242 (2) | 0.6230 (7) | 0.030 (4)* | |
H5A | 0.472 (2) | 0.084 (2) | 0.6770 (6) | 0.020 (4)* | |
H7 | 0.582 (2) | 0.693 (3) | 0.5899 (6) | 0.028 (4)* | |
HO3 | 0.122 (3) | 0.317 (4) | 0.7873 (9) | 0.057 (6)* | |
H8 | 0.599 (2) | 0.885 (2) | 0.5036 (7) | 0.029 (4)* | |
H10 | 0.054 (3) | 1.100 (3) | 0.5344 (8) | 0.038 (5)* | |
HO2 | −0.152 (2) | 0.485 (3) | 0.6690 (7) | 0.036 (4)* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
O3 | 0.0240 (5) | 0.0182 (4) | 0.0189 (4) | −0.0025 (4) | 0.0051 (3) | 0.0011 (3) |
O5 | 0.0134 (4) | 0.0181 (4) | 0.0316 (5) | 0.0007 (3) | 0.0001 (3) | 0.0017 (4) |
F | 0.0740 (7) | 0.0364 (5) | 0.0260 (4) | −0.0143 (5) | 0.0018 (5) | 0.0117 (3) |
O4 | 0.0134 (4) | 0.0128 (4) | 0.0340 (5) | −0.0007 (3) | −0.0020 (3) | 0.0033 (3) |
O2 | 0.0121 (4) | 0.0173 (4) | 0.0289 (5) | −0.0002 (3) | −0.0001 (3) | −0.0014 (4) |
C7 | 0.0259 (7) | 0.0180 (5) | 0.0292 (6) | −0.0007 (5) | 0.0079 (5) | −0.0025 (5) |
C4 | 0.0147 (5) | 0.0147 (5) | 0.0182 (5) | −0.0008 (4) | −0.0010 (4) | 0.0005 (4) |
C11 | 0.0237 (6) | 0.0187 (5) | 0.0221 (6) | −0.0009 (5) | −0.0018 (5) | 0.0010 (4) |
C1 | 0.0139 (5) | 0.0138 (4) | 0.0185 (5) | −0.0012 (4) | −0.0001 (4) | −0.0017 (4) |
C6 | 0.0212 (6) | 0.0132 (5) | 0.0188 (5) | −0.0034 (4) | 0.0011 (4) | −0.0023 (4) |
C5 | 0.0144 (5) | 0.0166 (5) | 0.0258 (6) | −0.0003 (4) | 0.0002 (5) | −0.0039 (5) |
C2 | 0.0131 (5) | 0.0147 (5) | 0.0182 (5) | −0.0006 (4) | −0.0004 (4) | −0.0018 (4) |
C3 | 0.0150 (5) | 0.0144 (5) | 0.0183 (5) | −0.0017 (4) | 0.0021 (4) | −0.0010 (4) |
C10 | 0.0357 (8) | 0.0203 (6) | 0.0284 (7) | −0.0022 (5) | −0.0070 (6) | 0.0048 (5) |
C9 | 0.0515 (10) | 0.0206 (6) | 0.0186 (5) | −0.0115 (6) | 0.0005 (6) | 0.0027 (5) |
C8 | 0.0402 (9) | 0.0255 (7) | 0.0275 (7) | −0.0058 (6) | 0.0149 (6) | −0.0015 (5) |
Geometric parameters (Å, º) top
O3—C3 | 1.4314 (14) | C4—C3 | 1.5288 (16) |
O5—C5 | 1.4290 (14) | C11—C10 | 1.3920 (17) |
F—C9 | 1.3616 (14) | C11—C6 | 1.3937 (17) |
O4—C1 | 1.4332 (14) | C1—C6 | 1.5126 (15) |
O4—C4 | 1.4530 (14) | C1—C2 | 1.5340 (15) |
O2—C2 | 1.4089 (13) | C2—C3 | 1.5318 (16) |
C7—C6 | 1.3932 (17) | C10—C9 | 1.3762 (19) |
C7—C8 | 1.3938 (19) | C9—C8 | 1.371 (2) |
C4—C5 | 1.5146 (16) | | |
| | | |
C1—O4—C4 | 110.16 (8) | O5—C5—C4 | 110.89 (10) |
C6—C7—C8 | 120.18 (13) | O2—C2—C3 | 116.31 (9) |
O4—C4—C5 | 109.48 (9) | O2—C2—C1 | 109.77 (9) |
O4—C4—C3 | 106.42 (9) | C3—C2—C1 | 102.24 (9) |
C5—C4—C3 | 114.45 (10) | O3—C3—C4 | 110.95 (9) |
C10—C11—C6 | 120.78 (12) | O3—C3—C2 | 109.86 (9) |
O4—C1—C6 | 111.18 (9) | C4—C3—C2 | 102.00 (9) |
O4—C1—C2 | 105.18 (9) | C9—C10—C11 | 117.89 (13) |
C6—C1—C2 | 113.98 (9) | F—C9—C8 | 119.12 (13) |
C7—C6—C11 | 119.41 (11) | F—C9—C10 | 117.73 (13) |
C7—C6—C1 | 121.96 (11) | C8—C9—C10 | 123.15 (12) |
C11—C6—C1 | 118.62 (11) | C9—C8—C7 | 118.55 (13) |
| | | |
C1—O4—C4—C5 | 118.21 (10) | O4—C1—C2—C3 | 33.81 (11) |
C1—O4—C4—C3 | −5.98 (12) | C6—C1—C2—C3 | 155.85 (9) |
C4—O4—C1—C6 | −141.43 (9) | O4—C4—C3—O3 | −90.15 (11) |
C4—O4—C1—C2 | −17.61 (11) | C5—C4—C3—O3 | 148.78 (10) |
C8—C7—C6—C11 | −0.79 (18) | O4—C4—C3—C2 | 26.81 (11) |
C8—C7—C6—C1 | 179.09 (11) | C5—C4—C3—C2 | −94.26 (11) |
C10—C11—C6—C7 | 1.45 (17) | O2—C2—C3—O3 | −38.12 (13) |
C10—C11—C6—C1 | −178.44 (11) | C1—C2—C3—O3 | 81.44 (10) |
O4—C1—C6—C7 | 8.79 (14) | O2—C2—C3—C4 | −155.86 (9) |
C2—C1—C6—C7 | −109.87 (12) | C1—C2—C3—C4 | −36.30 (10) |
O4—C1—C6—C11 | −171.33 (10) | C6—C11—C10—C9 | −0.66 (18) |
C2—C1—C6—C11 | 70.01 (13) | C11—C10—C9—F | 178.85 (11) |
O4—C4—C5—O5 | 67.36 (13) | C11—C10—C9—C8 | −0.8 (2) |
C3—C4—C5—O5 | −173.29 (10) | F—C9—C8—C7 | −178.21 (12) |
O4—C1—C2—O2 | 157.86 (9) | C10—C9—C8—C7 | 1.5 (2) |
C6—C1—C2—O2 | −80.11 (11) | C6—C7—C8—C9 | −0.63 (19) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
O2—HO2···O5i | 0.83 (2) | 1.91 (2) | 2.706 (1) | 160 (1) |
O3—HO3···O2ii | 0.79 (2) | 1.94 (2) | 2.721 (1) | 170 (1) |
O5—HO5···O3iii | 0.88 (2) | 1.91 (2) | 2.782 (1) | 174 (1) |
Symmetry codes: (i) x−1, y, z; (ii) −x, y−1/2, −z+3/2; (iii) −x+1, y−1/2, −z+3/2. |
(Ic) 1'-deoxy-1'-(4-fluorophenyl)-
β-
D-ribofuranose hemihydrate
top
Crystal data top
C11H13FO4·0.5H2O | F(000) = 500 |
Mr = 237.22 | Dx = 1.378 Mg m−3 |
Monoclinic, C2 | Mo Kα radiation, λ = 0.71073 Å |
a = 29.356 (6) Å | Cell parameters from 185 reflections |
b = 5.3068 (7) Å | θ = 3–23° |
c = 7.3530 (11) Å | µ = 0.12 mm−1 |
β = 93.215 (10)° | T = 154 K |
V = 1143.7 (3) Å3 | Block, colourless |
Z = 4 | 0.45 × 0.44 × 0.40 mm |
Data collection top
Siemens SMART diffractometer | 2746 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.041 |
Graphite monochromator | θmax = 29.0°, θmin = 1.4° |
ω scans | h = −40→37 |
5566 measured reflections | k = −7→6 |
2827 independent reflections | l = −9→10 |
Refinement top
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.034 | All H-atom parameters refined |
wR(F2) = 0.100 | w = 1/[σ2(Fo2) + (0.05P)2] where P = (Fo2 + 2Fc2)/3 |
S = 1.49 | (Δ/σ)max = 0.001 |
2827 reflections | Δρmax = 0.35 e Å−3 |
207 parameters | Δρmin = −0.17 e Å−3 |
1 restraint | Extinction correction: SHELXL97 (Sheldrick, 1997), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.006 (2) |
Crystal data top
C11H13FO4·0.5H2O | V = 1143.7 (3) Å3 |
Mr = 237.22 | Z = 4 |
Monoclinic, C2 | Mo Kα radiation |
a = 29.356 (6) Å | µ = 0.12 mm−1 |
b = 5.3068 (7) Å | T = 154 K |
c = 7.3530 (11) Å | 0.45 × 0.44 × 0.40 mm |
β = 93.215 (10)° | |
Data collection top
Siemens SMART diffractometer | 2746 reflections with I > 2σ(I) |
5566 measured reflections | Rint = 0.041 |
2827 independent reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.034 | 1 restraint |
wR(F2) = 0.100 | All H-atom parameters refined |
S = 1.49 | Δρmax = 0.35 e Å−3 |
2827 reflections | Δρmin = −0.17 e Å−3 |
207 parameters | |
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 | x | y | z | Uiso*/Ueq | |
O1 | 1/2 | 0.4642 (3) | 0 | 0.0229 (3) | |
O5 | 0.42037 (3) | −0.29036 (19) | −0.12047 (12) | 0.0253 (2) | |
O2 | 0.44746 (3) | −0.0340 (2) | 0.59397 (11) | 0.0276 (2) | |
O3 | 0.47406 (3) | 0.1638 (2) | 0.27211 (12) | 0.0238 (2) | |
F | 0.23974 (4) | 0.0784 (2) | 0.88272 (15) | 0.0476 (3) | |
O4 | 0.36669 (3) | 0.0947 (2) | 0.22057 (12) | 0.0268 (2) | |
C11 | 0.34127 (5) | 0.2884 (3) | 0.67354 (19) | 0.0263 (3) | |
C1 | 0.38200 (4) | 0.1323 (2) | 0.40715 (15) | 0.0191 (2) | |
C5 | 0.38855 (5) | −0.2240 (3) | 0.01174 (16) | 0.0231 (3) | |
C6 | 0.34325 (4) | 0.1166 (2) | 0.53157 (15) | 0.0198 (2) | |
C2 | 0.41858 (4) | −0.0702 (2) | 0.43697 (15) | 0.0177 (2) | |
C4 | 0.40457 (4) | 0.0065 (2) | 0.12087 (16) | 0.0202 (2) | |
C3 | 0.44395 (4) | −0.0474 (2) | 0.26191 (15) | 0.0192 (2) | |
C7 | 0.31067 (5) | −0.0741 (3) | 0.5132 (2) | 0.0275 (3) | |
C10 | 0.30653 (6) | 0.2742 (3) | 0.79519 (19) | 0.0323 (3) | |
C9 | 0.27470 (5) | 0.0877 (3) | 0.77005 (19) | 0.0299 (3) | |
C8 | 0.27581 (5) | −0.0892 (3) | 0.6332 (2) | 0.0318 (3) | |
H2 | 0.4041 (6) | −0.231 (4) | 0.438 (2) | 0.018 (4)* | |
H11 | 0.3635 (5) | 0.418 (4) | 0.685 (2) | 0.017 (4)* | |
H1 | 0.3972 (5) | 0.299 (3) | 0.423 (2) | 0.012 (3)* | |
HO5 | 0.4459 (6) | −0.375 (4) | −0.069 (2) | 0.029 (4)* | |
HO3 | 0.5008 (7) | 0.113 (4) | 0.331 (2) | 0.035 (5)* | |
H5B | 0.3595 (6) | −0.192 (4) | −0.050 (2) | 0.025 (4)* | |
H3 | 0.4588 (6) | −0.204 (4) | 0.239 (2) | 0.023 (4)* | |
H5A | 0.3850 (6) | −0.374 (4) | 0.099 (2) | 0.026 (4)* | |
H4 | 0.4130 (5) | 0.140 (4) | 0.040 (2) | 0.023 (4)* | |
H8 | 0.2534 (7) | −0.214 (5) | 0.621 (2) | 0.039 (5)* | |
HO2 | 0.4345 (7) | −0.106 (4) | 0.686 (3) | 0.035 (5)* | |
H7 | 0.3135 (7) | −0.202 (4) | 0.423 (2) | 0.033 (5)* | |
H10 | 0.3038 (8) | 0.398 (6) | 0.887 (3) | 0.063 (7)* | |
HO1 | 0.5068 (7) | 0.369 (5) | −0.085 (3) | 0.044 (6)* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
O1 | 0.0309 (6) | 0.0205 (6) | 0.0179 (6) | 0 | 0.0077 (5) | 0 |
O5 | 0.0309 (5) | 0.0299 (5) | 0.0154 (4) | 0.0038 (4) | 0.0033 (3) | −0.0003 (4) |
O2 | 0.0207 (4) | 0.0466 (6) | 0.0154 (4) | −0.0057 (4) | 0.0004 (3) | 0.0052 (4) |
O3 | 0.0187 (4) | 0.0318 (5) | 0.0210 (4) | −0.0028 (4) | 0.0025 (3) | 0.0064 (3) |
F | 0.0421 (6) | 0.0542 (7) | 0.0497 (6) | −0.0022 (5) | 0.0306 (5) | 0.0068 (5) |
O4 | 0.0237 (4) | 0.0405 (6) | 0.0161 (4) | 0.0128 (4) | 0.0015 (3) | 0.0003 (4) |
C11 | 0.0292 (6) | 0.0256 (6) | 0.0250 (6) | −0.0041 (5) | 0.0087 (5) | −0.0055 (5) |
C1 | 0.0216 (5) | 0.0207 (6) | 0.0155 (5) | 0.0015 (4) | 0.0035 (4) | 0.0002 (4) |
C5 | 0.0242 (6) | 0.0276 (6) | 0.0177 (5) | −0.0019 (5) | 0.0027 (4) | −0.0003 (5) |
C6 | 0.0205 (5) | 0.0206 (6) | 0.0185 (5) | 0.0015 (4) | 0.0038 (4) | −0.0003 (4) |
C2 | 0.0172 (5) | 0.0215 (6) | 0.0145 (5) | 0.0001 (4) | 0.0017 (4) | 0.0034 (4) |
C4 | 0.0210 (5) | 0.0239 (6) | 0.0160 (5) | 0.0026 (4) | 0.0034 (4) | 0.0012 (4) |
C3 | 0.0198 (5) | 0.0224 (6) | 0.0155 (5) | 0.0024 (4) | 0.0027 (4) | 0.0014 (4) |
C7 | 0.0251 (6) | 0.0260 (7) | 0.0318 (7) | −0.0022 (5) | 0.0038 (5) | −0.0053 (6) |
C10 | 0.0368 (8) | 0.0360 (8) | 0.0252 (6) | 0.0002 (6) | 0.0123 (5) | −0.0060 (6) |
C9 | 0.0271 (6) | 0.0349 (7) | 0.0292 (7) | 0.0033 (6) | 0.0143 (5) | 0.0078 (6) |
C8 | 0.0252 (6) | 0.0288 (7) | 0.0419 (8) | −0.0050 (5) | 0.0076 (5) | 0.0005 (6) |
Geometric parameters (Å, º) top
O5—C5 | 1.4296 (14) | C1—C2 | 1.5261 (16) |
O2—C2 | 1.4066 (14) | C5—C4 | 1.5228 (18) |
O3—C3 | 1.4270 (16) | C6—C7 | 1.3936 (18) |
F—C9 | 1.3553 (13) | C2—C3 | 1.5277 (15) |
O4—C1 | 1.4335 (14) | C4—C3 | 1.5359 (17) |
O4—C4 | 1.4439 (14) | C7—C8 | 1.3905 (18) |
C11—C6 | 1.3897 (17) | C10—C9 | 1.367 (2) |
C11—C10 | 1.3959 (17) | C9—C8 | 1.378 (2) |
C1—C6 | 1.5016 (15) | | |
| | | |
C1—O4—C4 | 108.77 (9) | O4—C4—C5 | 107.70 (10) |
C6—C11—C10 | 120.58 (13) | O4—C4—C3 | 106.83 (10) |
O4—C1—C6 | 111.57 (9) | C5—C4—C3 | 113.88 (11) |
O4—C1—C2 | 102.71 (9) | O3—C3—C2 | 110.35 (9) |
C6—C1—C2 | 115.12 (10) | O3—C3—C4 | 109.25 (10) |
O5—C5—C4 | 111.21 (10) | C2—C3—C4 | 101.51 (9) |
C11—C6—C7 | 119.45 (11) | C8—C7—C6 | 120.41 (12) |
C11—C6—C1 | 119.10 (11) | C9—C10—C11 | 118.10 (13) |
C7—C6—C1 | 121.37 (11) | F—C9—C10 | 118.61 (13) |
O2—C2—C1 | 114.11 (10) | F—C9—C8 | 118.13 (13) |
O2—C2—C3 | 112.39 (9) | C10—C9—C8 | 123.25 (12) |
C1—C2—C3 | 101.28 (9) | C9—C8—C7 | 118.18 (13) |
| | | |
C4—O4—C1—C6 | −156.02 (10) | O2—C2—C3—O3 | −43.78 (13) |
C4—O4—C1—C2 | −32.17 (13) | C1—C2—C3—O3 | 78.40 (11) |
C10—C11—C6—C7 | −1.2 (2) | O2—C2—C3—C4 | −159.53 (11) |
C10—C11—C6—C1 | −177.95 (13) | C1—C2—C3—C4 | −37.35 (11) |
O4—C1—C6—C11 | −138.36 (13) | O4—C4—C3—O3 | −97.35 (11) |
C2—C1—C6—C11 | 105.12 (14) | C5—C4—C3—O3 | 143.88 (10) |
O4—C1—C6—C7 | 44.98 (16) | O4—C4—C3—C2 | 19.20 (13) |
C2—C1—C6—C7 | −71.54 (15) | C5—C4—C3—C2 | −99.56 (11) |
O4—C1—C2—O2 | 164.23 (10) | C11—C6—C7—C8 | 1.5 (2) |
C6—C1—C2—O2 | −74.31 (13) | C1—C6—C7—C8 | 178.14 (13) |
O4—C1—C2—C3 | 43.25 (11) | C6—C11—C10—C9 | −0.2 (2) |
C6—C1—C2—C3 | 164.71 (10) | C11—C10—C9—F | −177.30 (13) |
C1—O4—C4—C5 | 130.79 (11) | C11—C10—C9—C8 | 1.4 (2) |
C1—O4—C4—C3 | 8.08 (14) | F—C9—C8—C7 | 177.57 (13) |
O5—C5—C4—O4 | 167.32 (10) | C10—C9—C8—C7 | −1.1 (2) |
O5—C5—C4—C3 | −74.41 (13) | C6—C7—C8—C9 | −0.4 (2) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
O1—HO1···O3i | 0.84 (2) | 1.86 (2) | 2.701 (1) | 176 (2) |
O2—HO2···O5ii | 0.88 (2) | 1.79 (2) | 2.661 (1) | 167 (2) |
O3—HO3···O2iii | 0.92 (2) | 1.77 (2) | 2.669 (1) | 168 (2) |
O5—HO5···O1iv | 0.93 (2) | 1.85 (2) | 2.777 (1) | 172 (2) |
Symmetry codes: (i) −x+1, y, −z; (ii) x, y, z+1; (iii) −x+1, y, −z+1; (iv) x, y−1, z. |
(II) 1'-deoxy-1'-(2,4-difluorophenyl)-
β-
D-ribofuranose
top
Crystal data top
C11H12F2O4 | F(000) = 512 |
Mr = 246.21 | Dx = 1.536 Mg m−3 |
Monoclinic, C2 | Mo Kα radiation, λ = 0.71073 Å |
a = 14.684 (2) Å | Cell parameters from 217 reflections |
b = 4.6609 (6) Å | θ = 3–23° |
c = 15.772 (2) Å | µ = 0.14 mm−1 |
β = 99.476 (11)° | T = 134 K |
V = 1064.7 (2) Å3 | Thick plate, colourless |
Z = 4 | 0.75 × 0.70 × 0.20 mm |
Data collection top
Siemens SMART diffractometer | 2794 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.068 |
Graphite monochromator | θmax = 30.6°, θmin = 2.6° |
ω scans | h = −20→21 |
9578 measured reflections | k = −6→6 |
3048 independent reflections | l = −22→21 |
Refinement top
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)] = 0.046 | Hydrogen site location: difference Fourier map |
wR(F2) = 0.122 | All H-atom parameters refined |
S = 1.40 | w = 1/[σ2(Fo2) + (0.06P)2] where P = (Fo2 + 2Fc2)/3 |
3048 reflections | (Δ/σ)max < 0.001 |
202 parameters | Δρmax = 0.37 e Å−3 |
1 restraint | Δρmin = −0.25 e Å−3 |
Crystal data top
C11H12F2O4 | V = 1064.7 (2) Å3 |
Mr = 246.21 | Z = 4 |
Monoclinic, C2 | Mo Kα radiation |
a = 14.684 (2) Å | µ = 0.14 mm−1 |
b = 4.6609 (6) Å | T = 134 K |
c = 15.772 (2) Å | 0.75 × 0.70 × 0.20 mm |
β = 99.476 (11)° | |
Data collection top
Siemens SMART diffractometer | 2794 reflections with I > 2σ(I) |
9578 measured reflections | Rint = 0.068 |
3048 independent reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.046 | 1 restraint |
wR(F2) = 0.122 | All H-atom parameters refined |
S = 1.40 | Δρmax = 0.37 e Å−3 |
3048 reflections | Δρmin = −0.25 e Å−3 |
202 parameters | |
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 | x | y | z | Uiso*/Ueq | |
F2 | 0.02678 (6) | 0.7268 (3) | 0.21085 (7) | 0.0271 (3) | |
F1 | −0.10379 (8) | 1.4124 (3) | 0.00868 (7) | 0.0318 (3) | |
O5 | −0.37647 (7) | 0.8548 (3) | 0.42169 (8) | 0.0196 (2) | |
O4 | −0.23391 (7) | 0.5471 (3) | 0.27468 (7) | 0.0190 (3) | |
O3 | −0.15553 (8) | 0.8680 (3) | 0.48253 (8) | 0.0196 (3) | |
O2 | −0.06523 (8) | 0.4483 (3) | 0.40898 (8) | 0.0197 (3) | |
C6 | −0.13283 (10) | 0.8192 (4) | 0.19743 (10) | 0.0172 (3) | |
C7 | −0.20907 (11) | 0.9690 (4) | 0.15442 (11) | 0.0204 (3) | |
C2 | −0.09098 (10) | 0.6931 (4) | 0.35722 (10) | 0.0160 (3) | |
C9 | −0.11363 (13) | 1.2161 (4) | 0.07061 (11) | 0.0225 (3) | |
C4 | −0.25176 (10) | 0.6421 (4) | 0.35703 (11) | 0.0161 (3) | |
C3 | −0.17079 (10) | 0.8380 (4) | 0.39217 (10) | 0.0168 (3) | |
C10 | −0.03547 (11) | 1.0737 (4) | 0.10997 (11) | 0.0232 (4) | |
C5 | −0.34654 (11) | 0.7837 (4) | 0.34261 (11) | 0.0203 (3) | |
C1 | −0.13874 (10) | 0.6002 (4) | 0.26730 (10) | 0.0164 (3) | |
C11 | −0.04810 (10) | 0.8765 (4) | 0.17248 (10) | 0.0195 (3) | |
C8 | −0.20042 (12) | 1.1682 (4) | 0.09082 (12) | 0.0225 (4) | |
H2 | −0.0395 (13) | 0.810 (5) | 0.3560 (11) | 0.013 (5)* | |
H8 | −0.2511 (17) | 1.264 (7) | 0.0595 (15) | 0.036 (7)* | |
H7 | −0.2698 (19) | 0.939 (7) | 0.1719 (16) | 0.041 (7)* | |
H5B | −0.3434 (14) | 0.948 (6) | 0.3124 (12) | 0.016 (5)* | |
H5A | −0.3889 (13) | 0.643 (5) | 0.3089 (12) | 0.013 (5)* | |
HO5 | −0.3637 (15) | 0.722 (6) | 0.4545 (14) | 0.024 (6)* | |
H1 | −0.1144 (15) | 0.417 (5) | 0.2492 (13) | 0.024 (6)* | |
H10 | 0.025 (2) | 1.115 (8) | 0.0964 (16) | 0.047 (8)* | |
H4 | −0.2477 (13) | 0.489 (6) | 0.3949 (12) | 0.016 (5)* | |
H3 | −0.1834 (15) | 1.020 (6) | 0.3674 (13) | 0.021 (5)* | |
HO2 | −0.0089 (18) | 0.436 (7) | 0.4163 (15) | 0.038 (7)* | |
HO3 | −0.1447 (18) | 0.726 (7) | 0.5058 (16) | 0.033 (7)* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
F2 | 0.0161 (4) | 0.0324 (6) | 0.0341 (6) | 0.0064 (4) | 0.0074 (4) | 0.0093 (5) |
F1 | 0.0377 (6) | 0.0293 (7) | 0.0303 (6) | 0.0020 (5) | 0.0110 (5) | 0.0115 (5) |
O5 | 0.0170 (5) | 0.0194 (6) | 0.0239 (6) | 0.0058 (5) | 0.0074 (4) | 0.0023 (5) |
O4 | 0.0141 (5) | 0.0216 (6) | 0.0224 (6) | −0.0045 (4) | 0.0068 (4) | −0.0051 (5) |
O3 | 0.0230 (5) | 0.0159 (6) | 0.0201 (6) | 0.0005 (5) | 0.0037 (4) | −0.0020 (5) |
O2 | 0.0129 (5) | 0.0194 (6) | 0.0271 (6) | 0.0025 (4) | 0.0043 (4) | 0.0061 (5) |
C6 | 0.0165 (6) | 0.0161 (8) | 0.0191 (7) | 0.0003 (6) | 0.0039 (5) | −0.0024 (6) |
C7 | 0.0171 (6) | 0.0217 (8) | 0.0226 (8) | 0.0011 (6) | 0.0036 (6) | −0.0015 (6) |
C2 | 0.0137 (6) | 0.0155 (8) | 0.0191 (7) | −0.0006 (6) | 0.0039 (5) | 0.0004 (6) |
C9 | 0.0285 (8) | 0.0198 (9) | 0.0201 (8) | −0.0008 (7) | 0.0061 (6) | 0.0012 (6) |
C4 | 0.0137 (6) | 0.0140 (7) | 0.0212 (8) | 0.0006 (5) | 0.0050 (5) | −0.0007 (6) |
C3 | 0.0154 (6) | 0.0136 (7) | 0.0217 (8) | 0.0006 (6) | 0.0039 (5) | −0.0014 (6) |
C10 | 0.0223 (7) | 0.0243 (9) | 0.0249 (8) | −0.0014 (7) | 0.0096 (6) | 0.0029 (7) |
C5 | 0.0150 (6) | 0.0247 (9) | 0.0216 (8) | 0.0045 (6) | 0.0044 (6) | 0.0007 (6) |
C1 | 0.0135 (6) | 0.0163 (8) | 0.0204 (7) | −0.0018 (6) | 0.0059 (5) | −0.0015 (6) |
C11 | 0.0167 (6) | 0.0196 (9) | 0.0226 (8) | 0.0029 (6) | 0.0047 (6) | 0.0010 (6) |
C8 | 0.0222 (8) | 0.0222 (9) | 0.0226 (8) | 0.0035 (6) | 0.0017 (6) | −0.0001 (6) |
Geometric parameters (Å, º) top
F2—C11 | 1.3575 (18) | C6—C1 | 1.515 (2) |
F1—C9 | 1.363 (2) | C7—C8 | 1.388 (3) |
O5—C5 | 1.428 (2) | C2—C3 | 1.532 (2) |
O4—C4 | 1.4365 (19) | C2—C1 | 1.537 (2) |
O4—C1 | 1.4428 (17) | C9—C10 | 1.382 (3) |
O3—C3 | 1.4127 (19) | C9—C8 | 1.382 (2) |
O2—C2 | 1.418 (2) | C4—C5 | 1.523 (2) |
C6—C11 | 1.391 (2) | C4—C3 | 1.529 (2) |
C6—C7 | 1.397 (2) | C10—C11 | 1.383 (2) |
| | | |
C4—O4—C1 | 110.09 (11) | C5—C4—C3 | 115.62 (14) |
C11—C6—C7 | 116.71 (15) | O3—C3—C4 | 114.17 (13) |
C11—C6—C1 | 119.73 (14) | O3—C3—C2 | 113.77 (13) |
C7—C6—C1 | 123.55 (14) | C4—C3—C2 | 101.64 (13) |
C8—C7—C6 | 121.59 (15) | C9—C10—C11 | 116.16 (15) |
O2—C2—C3 | 107.15 (13) | O5—C5—C4 | 112.04 (13) |
O2—C2—C1 | 110.02 (14) | O4—C1—C6 | 110.28 (13) |
C3—C2—C1 | 101.32 (12) | O4—C1—C2 | 105.94 (12) |
F1—C9—C10 | 117.78 (15) | C6—C1—C2 | 114.16 (13) |
F1—C9—C8 | 118.98 (16) | F2—C11—C10 | 117.75 (13) |
C10—C9—C8 | 123.24 (17) | F2—C11—C6 | 118.15 (15) |
O4—C4—C5 | 107.27 (12) | C10—C11—C6 | 124.08 (15) |
O4—C4—C3 | 105.36 (12) | C9—C8—C7 | 118.20 (16) |
| | | |
C11—C6—C7—C8 | −0.9 (3) | C11—C6—C1—O4 | −172.31 (15) |
C1—C6—C7—C8 | 179.92 (16) | C7—C6—C1—O4 | 6.8 (2) |
C1—O4—C4—C5 | 139.81 (14) | C11—C6—C1—C2 | 68.57 (19) |
C1—O4—C4—C3 | 16.10 (17) | C7—C6—C1—C2 | −112.30 (17) |
O4—C4—C3—O3 | −157.35 (13) | O2—C2—C1—O4 | 83.09 (15) |
C5—C4—C3—O3 | 84.42 (18) | C3—C2—C1—O4 | −30.05 (16) |
O4—C4—C3—C2 | −34.42 (16) | O2—C2—C1—C6 | −155.36 (12) |
C5—C4—C3—C2 | −152.66 (13) | C3—C2—C1—C6 | 91.49 (15) |
O2—C2—C3—O3 | 46.40 (18) | C9—C10—C11—F2 | 178.22 (16) |
C1—C2—C3—O3 | 161.69 (14) | C9—C10—C11—C6 | −0.8 (3) |
O2—C2—C3—C4 | −76.80 (15) | C7—C6—C11—F2 | −177.64 (15) |
C1—C2—C3—C4 | 38.49 (15) | C1—C6—C11—F2 | 1.6 (2) |
F1—C9—C10—C11 | 179.95 (16) | C7—C6—C11—C10 | 1.4 (3) |
C8—C9—C10—C11 | −0.3 (3) | C1—C6—C11—C10 | −179.46 (17) |
O4—C4—C5—O5 | 172.73 (14) | F1—C9—C8—C7 | −179.58 (16) |
C3—C4—C5—O5 | −70.09 (19) | C10—C9—C8—C7 | 0.7 (3) |
C4—O4—C1—C6 | −114.97 (14) | C6—C7—C8—C9 | 0.0 (3) |
C4—O4—C1—C2 | 9.04 (18) | | |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
O2—HO2···O5i | 0.82 (2) | 1.97 (2) | 2.780 (1) | 171 (2) |
O3—HO3···O5ii | 0.76 (2) | 2.07 (2) | 2.827 (1) | 174 (2) |
O5—HO5···O3ii | 0.81 (2) | 1.92 (2) | 2.724 (1) | 171 (2) |
Symmetry codes: (i) x+1/2, y−1/2, z; (ii) −x−1/2, y−1/2, −z+1. |
Experimental details
| (Ia) | (Ib) | (Ic) | (II) |
Crystal data |
Chemical formula | C11H13FO4 | C11H13FO4 | C11H13FO4·0.5H2O | C11H12F2O4 |
Mr | 228.21 | 228.21 | 237.22 | 246.21 |
Crystal system, space group | Orthorhombic, P212121 | Orthorhombic, P212121 | Monoclinic, C2 | Monoclinic, C2 |
Temperature (K) | 134 | 135 | 154 | 134 |
a, b, c (Å) | 5.4741 (9), 7.3018 (7), 26.791 (3) | 6.7109 (14), 6.7653 (7), 22.846 (3) | 29.356 (6), 5.3068 (7), 7.3530 (11) | 14.684 (2), 4.6609 (6), 15.772 (2) |
α, β, γ (°) | 90, 90, 90 | 90, 90, 90 | 90, 93.215 (10), 90 | 90, 99.476 (11), 90 |
V (Å3) | 1070.9 (2) | 1037.2 (3) | 1143.7 (3) | 1064.7 (2) |
Z | 4 | 4 | 4 | 4 |
Radiation type | Mo Kα | Mo Kα | Mo Kα | Mo Kα |
µ (mm−1) | 0.12 | 0.12 | 0.12 | 0.14 |
Crystal size (mm) | 1.30 × 0.64 × 0.15 | 0.66 × 0.45 × 0.28 | 0.45 × 0.44 × 0.40 | 0.75 × 0.70 × 0.20 |
|
Data collection |
Diffractometer | Siemens SMART diffractometer | Siemens SMART diffractometer | Siemens SMART diffractometer | Siemens SMART diffractometer |
Absorption correction | – | Numerical (SHELXTL; Sheldrick, 1996) | – | – |
Tmin, Tmax | – | 0.932, 0.968 | – | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 18913, 3431, 3273 | 19895, 3512, 2944 | 5566, 2827, 2746 | 9578, 3048, 2794 |
Rint | 0.084 | 0.058 | 0.041 | 0.068 |
(sin θ/λ)max (Å−1) | 0.731 | 0.744 | 0.682 | 0.716 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.037, 0.111, 1.39 | 0.039, 0.090, 1.11 | 0.034, 0.100, 1.49 | 0.046, 0.122, 1.40 |
No. of reflections | 3431 | 3512 | 2827 | 3048 |
No. of parameters | 197 | 198 | 207 | 202 |
No. of restraints | 0 | 0 | 1 | 1 |
H-atom treatment | All H-atom parameters refined | All H-atom parameters refined | All H-atom parameters refined | All H-atom parameters refined |
Δρmax, Δρmin (e Å−3) | 0.36, −0.20 | 0.30, −0.20 | 0.35, −0.17 | 0.37, −0.25 |
Hydrogen-bond geometry (Å, º) for (Ia) top
D—H···A | D—H | H···A | D···A | D—H···A |
O2—HO2···O3i | 0.85 (2) | 1.96 (2) | 2.729 (1) | 151 (2) |
O3—HO3···O5ii | 0.88 (2) | 1.91 (2) | 2.774 (1) | 169 (2) |
O5—HO5···O2iii | 0.80 (2) | 1.89 (2) | 2.682 (1) | 172 (2) |
Symmetry codes: (i) −x+1, y+1/2, −z+3/2; (ii) −x+2, y+1/2, −z+3/2; (iii) x, y−1, z. |
Hydrogen-bond geometry (Å, º) for (Ib) top
D—H···A | D—H | H···A | D···A | D—H···A |
O2—HO2···O5i | 0.83 (2) | 1.91 (2) | 2.706 (1) | 160 (1) |
O3—HO3···O2ii | 0.79 (2) | 1.94 (2) | 2.721 (1) | 170 (1) |
O5—HO5···O3iii | 0.88 (2) | 1.91 (2) | 2.782 (1) | 174 (1) |
Symmetry codes: (i) x−1, y, z; (ii) −x, y−1/2, −z+3/2; (iii) −x+1, y−1/2, −z+3/2. |
Hydrogen-bond geometry (Å, º) for (Ic) top
D—H···A | D—H | H···A | D···A | D—H···A |
O1—HO1···O3i | 0.84 (2) | 1.86 (2) | 2.701 (1) | 176 (2) |
O2—HO2···O5ii | 0.88 (2) | 1.79 (2) | 2.661 (1) | 167 (2) |
O3—HO3···O2iii | 0.92 (2) | 1.77 (2) | 2.669 (1) | 168 (2) |
O5—HO5···O1iv | 0.93 (2) | 1.85 (2) | 2.777 (1) | 172 (2) |
Symmetry codes: (i) −x+1, y, −z; (ii) x, y, z+1; (iii) −x+1, y, −z+1; (iv) x, y−1, z. |
Hydrogen-bond geometry (Å, º) for (II) top
D—H···A | D—H | H···A | D···A | D—H···A |
O2—HO2···O5i | 0.82 (2) | 1.97 (2) | 2.780 (1) | 171 (2) |
O3—HO3···O5ii | 0.76 (2) | 2.07 (2) | 2.827 (1) | 174 (2) |
O5—HO5···O3ii | 0.81 (2) | 1.92 (2) | 2.724 (1) | 171 (2) |
Symmetry codes: (i) x+1/2, y−1/2, z; (ii) −x−1/2, y−1/2, −z+1. |
This paper presents the crystal structures of four ribofuranose-based compounds, namely, 1-deoxy-1-(4-fluorophenyl)-β-D-ribofuranose in two crystal forms, (Ia) and (Ib), 1-deoxy-1-(4-fluorophenyl)-β-D-ribofuranose hemihydrate, (Ic), and 1-deoxy-1-(2,4-difluorophenyl)-β-D-ribofuranose, (II).
The five-membered ribofuranose rings in (Ia) and (Ic) (Fig. 1) have rather similar conformations. The ring puckering parameters defined by Cremer & Pople (1975) are q = 0.375 Å and ϕ = 60.2° for (Ia), and q = 0.421 Å and ϕ = 63.4° for (Ic). This corresponds to a conformation intermediate between a C1'-exo, C2'-endo twist and a C2'-endo envelope. The hydroxyl group on O2 and the phenyl group attached to C1 are both in pseudo-equatorial positions, while the hydroxyl group on O3 is in a pseudo-axial position and the methanol group attached to C4 is in a bisecting position with respect to the five-membered ring. No short intramolecular contacts are observed for this conformation.
The five-membered ribofuranose ring in (Ib) (Fig. 1) is considerably different. It has a conformation intermediate between a C2'-endo,C3'-exo twist and a C2'-endo envelope. The ring puckering parameters are q = 0.368 Å and ϕ = 81.6°. The hydroxyl group on O2 and the phenyl group attached to C1 are in pseudo-equatorial positions, while the hydroxyl group on O3 and the methanol group attached to C4 are both in pseudo-axial positions with respect to the five-membered ring.
The five-membered ribofuranose ring in (II) (Fig. 1) is different again. It has approximately an unsymmetrical C2'-exo,C3'-endo twist conformation. The ring puckering parameters are q = 0.390 Å and ϕ = 274.8°. The hydroxyl group on O2 is in an axial position, the hydroxyl group on O3 is in an equatorial position, the methanol group attached to C4 is in a pseudo-equatorial position and the phenyl group attached to C1 is in a pseudo-axial position with respect to the five-membered ring.
Molecules (Ib) and (II) show a short intramolecular contact distance of 2.42 (2) for (Ib) and 2.44 (2) Å for (II) between O4 and H7. This distance is equal to the van der Waals contact distance of 2.4 Å between O and H. Each molecule of (Ia) and (Ib) is connected by intermolecular hydrogen bonding (Table 1, Table 2, Fig. 2, Fig. 3) to six neighbouring molecules, leading to a two-dimensional network in the ab direction.
For (Ic), a rather similar two-dimensional network is found in the bc direction. In this case, the water molecule is included in the network. Each molecule of (Ic) is connected by hydrogen bonding (Table 3, Fig. 4) to three neighbouring molecules of (Ic) and to two different water molecules.
Each molecule of (II) is connected by intermolecular hydrogen bonding (Table 4, Fig. 5) to four different neighbouring molecules, leading to a two-dimensional network in the ab direction. Two-dimensional networks of hydrogen bonds have also been observed in the crystal structures of 1-deoxy-1-phenyl-β-D-ribofuranose (Matulic Adamic, 1996), 1-deoxy-1-(2-fluorophenyl)-β-D-ribofuranose (Bats et al., 1999a) and 1-deoxy-1-(3-fluorophenyl)-β-D-ribofuranose (Bats et al., 1999b).
The packing in the direction of the long dimension of the unit cell consists entirely of intermolecular interactions between the fluorophenyl groups. Rather short intermolecular C—H···F—C contacts are observed in (Ia), (Ib) and (Ic). The intermolecular H10···F distance is 2.30 (2) in (Ia), 2.42 (2) in (Ib) and 2.38 (2) Å in (Ic). These distances are comparable to the van der Waals contact distance between F and H [2.35 Å according to Pauling (1960) or 2.47 Å according to Bondi (1964)]. Each 4-fluorophenyl group is involved in two of these contacts, resulting in zigzag chains of molecules (Fig. 6). In addition to these C—H···F—C interactions, the crystal packing of (Ia), (Ib) and (Ic) also shows intermolecular C—H···πarene interactions. The H8···Cg distance is 2.82 in (Ia), 2.84 in (Ib) and 2.82 Å in (Ic) (Cg is the centroid of the phenyl ring). Intermolecular C—H···πarene interactions play a significant role in crystal structures (Brady et al., 1998; Gallagher et al., 1998). Koch & Egert (1995) have shown these interactions to be of an electrostatic nature.
The crystal structure of (II) shows pairs of molecules related by a twofold axis, with intermolecular distances of 2.57 (2) Å between F1 and H10(-x, y, −z) (Fig. 7). These distances are longer than the van der Waals contact distance. No other intermolecular interactions between the phenyl groups are found in this case, which can explain the crystal packing in the c direction. Intermolecular F···H contacts have also been reported for other crystal structures (Karipides et al., 1988; Bruno et al., 1997; Antolić et al., 1996; Vij et al., 1996; Shimoni et al., 1994; Weiss et al., 1997). A search of the Spring 1999 release of the Cambridge Structural Data Base (Allen & Kennard, 1993?) for structures containing fluorophenyl groups, with H-atom coordinates included and no disorder reported, revealed 1144 crystal structures. Among those structures, 1596 different C—H···F—C contacts were found with H···F distances shorter than 2.6 Å (652 shorter than 2.5, 182 shorter than 2.4 and 37 shorter than 2.3 Å). About one third of these interactions were Cphenyl—H···F—Cphenyl contacts. The number of dimeric structures as found for (II) is rather small. Only 35 dimers were found with both C—H···F—C contacts shorter than 2.6 Å. Larsen & Marthi (1994) and Kubota & Ohba (1992) have shown the F atom in fluorophenyl groups to bear a small negative charge of about −0.1 e Å−3. Thus, the C—F bond is a likely candidate for electrostatic interactions with electropositive C—H bonds.
Howard et al. (1996) calculated the C—H···F—C interaction energy of a complex between CH3F and H4C to be approximately −0.2 kcalmol−1, which is an order of magnitude smaller than the corresponding value for a complex between CH3F and H2O. They termed the C—H···F—C interaction as a van der Waals interaction rather than a hydrogen bond. Thalladi et al. (1998) showed the packing in fluorobenzenes containing no elements other than C, H and F to be dominated by C—H···F—C interactions. They also showed the C—H···F interactions to have similar characteristics to those of weak C—H···O and C—H···N hydrogen bonds. These interactions are rather weak and thus are easily overridden by stronger intermolecular interactions. In the crystal structures reported here, however, stronger interactions are missing in one direction. Thus, weaker C—H···F—C and C—H···π interactions dominate the crystal packing in this direction.