Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807039414/rt2004sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536807039414/rt2004Isup2.hkl |
CCDC reference: 660287
5-phenyluridine was prepared by the Suzuki coupling reaction of 5-iodouridine (0.277 g, 0.75 mmol) and phenylboronic acid (0.081 g, 0.90 mmol) (Flynn et al. 1991), yield 0.203 g (84%). Analytical data are identical with that published. The final product was obtained from slow evaporation of an aqueous solution (10 mg ml-1) at room temperature. MS: m/z 321.
The aromatic, methylene, methine, amine and hydroxyl H atoms were placed in geometrically idealized positions (C—H = 0.93–0.98, N—H = 0.86 and O—H = 0.82 Å) and constrained to ride on their parent atoms with Uiso(H) = 1.2Ueq(C,N,O). Water molecules O1W and O3W refined with large thermal vibrations and were subsequently refined disordered over two sites as O1W/O1W' and O3W/O3W' respectively. Refinement was kept stable with the use of anisotropic restraints and free variables were incorporated to refine occupation parameters to one. Possible hydogen coordinates from the Fourier difference map could not be refined satisfactory. Refinement of the Flack parameter (Flack, 1983) led to an inconclusive value (Flack & Bernardinelli, 2000) of -10 (10). This is generally the case with light atom Mo Kα data where f" is nearly zero. The Friedel equivalents were therefore merged before final refinement with a MERG 4 command. The conformation of the title compound was assigned from the absolute configuration of the starting material.
Research has been focused towards finding biologically active analogues of uridine, a naturally occurring compound, and modification of the uracil ring concentrates on position 5. Examples of the latest investigations for the development of new drugs include e.g. the synthesis of ethynyl uridine derivatives as antiviral drugs against Flaviviridae (Aucagne et al., 2006), especially HCV, studies of other alkynyl-uridines as potent inhibitors of Mycobacteria (Rai et al., 2005), and e.g. uridine and estradiol conjugates exhibiting binding affinity and cytotoxicity against cell lines with and without an estrogen receptor (Ali, H. et al., 2006). Modern synthetic methods include coupling reactions with catalysis by organometallic compounds, which enables the introduction of diverse substituents of an aliphatic or aromatic nature. Although the synthesis and biological activity of uridine derivatives has been studied intensively, their structural parameters from crystallographic measurements, important for behavior in biological systems, have rarely been discussed and published. In this paper we describe the structural properties of 5-phenyluridine prepared by the Suzuki coupling from 5-iodouridine and phenylboronic acid.
A selection of geometric parameters is given in Table 1. The heterocyclic base moiety is almost planar, with a maximum deviation of 0.019 (3) Å for the C1 atom. The N-glycosidic torsion angle χ (C1–N1–C1'–O4') is -169.8 (2)° which corresponds to an anti orientation of the base moiety. The sugar ring, C1'–C2'–C3'–C4'–O4', adopts a mixed twisted- envelope 3T2/3E conformation (C3'-exo / C2'-endo) with puckering parameters q2 = 0.384 (3) Å and φ2 = 64.2 (4)° (Cremer & Pople, 1975). The conformation of the side chain, as defined by the torsion angle O5'–C5'–C4'–C3' of 53.5 (3)°, is +sc. The phenyl and uracil rings are not co-planar (Fig.1), with a dihedral angle between the mean planes of 38.02 (9)°. The crystal packing is determined by a network of hydrogen bonds (Table 2) with π-π interactions (3.455 Å) observed between the phenyl and uracil moieties. This packing creates channels along the a axis which hosts the solvent molecules (Fig. 2).
For related literature, see: Ali et al. (2006); Aucagne et al. (2006); Cremer & Pople (1975); Flack (1983); Flack & Bernardinelli (2000); Flynn et al. (1991); Rai et al. (2005).
Data collection: KappaCCD Server Software (Nonius, 1997); cell refinement: DENZO-SMN (Otwinowski & Minor, 1997); data reduction: DENZO-SMN; program(s) used to solve structure: SIR97 (Altomare et al., 1999); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: DIAMOND (Brandenburg & Putz, 2005); software used to prepare material for publication: WinGX (Farrugia, 1999).
Fig. 1. The structure of (1) showing the displacement ellipsoids parameters at 50% probability. | |
Fig. 2. The crystal packing of (1) viewed down the crystallographic a axis |
C15H16N2O6·3H2O | F(000) = 792 |
Mr = 374.35 | Dx = 1.433 Mg m−3 |
Orthorhombic, P212121 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2ac 2ab | Cell parameters from 2838 reflections |
a = 7.3627 (1) Å | θ = 3.9–30° |
b = 14.0874 (3) Å | µ = 0.12 mm−1 |
c = 16.7287 (3) Å | T = 295 K |
V = 1735.12 (5) Å3 | Prismatic, colourless |
Z = 4 | 0.45 × 0.24 × 0.14 mm |
Nonius KappaCCD diffractometer | 2338 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.022 |
Graphite monochromator | θmax = 30.0°, θmin = 1.9° |
φ and ω scans | h = −10→10 |
5050 measured reflections | k = −19→19 |
2879 independent reflections | l = −23→23 |
Refinement on F2 | 12 restraints |
Least-squares matrix: full | H-atom parameters constrained |
R[F2 > 2σ(F2)] = 0.053 | w = 1/[σ2(Fo2) + (0.1267P)2] where P = (Fo2 + 2Fc2)/3 |
wR(F2) = 0.185 | (Δ/σ)max < 0.001 |
S = 1.16 | Δρmax = 0.63 e Å−3 |
2879 reflections | Δρmin = −0.63 e Å−3 |
255 parameters |
C15H16N2O6·3H2O | V = 1735.12 (5) Å3 |
Mr = 374.35 | Z = 4 |
Orthorhombic, P212121 | Mo Kα radiation |
a = 7.3627 (1) Å | µ = 0.12 mm−1 |
b = 14.0874 (3) Å | T = 295 K |
c = 16.7287 (3) Å | 0.45 × 0.24 × 0.14 mm |
Nonius KappaCCD diffractometer | 2338 reflections with I > 2σ(I) |
5050 measured reflections | Rint = 0.022 |
2879 independent reflections |
R[F2 > 2σ(F2)] = 0.053 | 12 restraints |
wR(F2) = 0.185 | H-atom parameters constrained |
S = 1.16 | Δρmax = 0.63 e Å−3 |
2879 reflections | Δρmin = −0.63 e Å−3 |
255 parameters |
Experimental. The diffraction data were collected at room temperature using a Nonius Kappa CCD diffractometer with graphite-monochromated Mo Kα (λ = 0.7107 Å) using an exposure time of 40 s/frame. A total of 204 frames were collected with a frame width of 2.0° covering up to θ = 30.04° with 99.6% completeness accomplished. |
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. |
x | y | z | Uiso*/Ueq | Occ. (<1) | |
O1 | 0.8933 (4) | 0.55845 (14) | 0.57391 (13) | 0.0405 (5) | |
O2 | 0.7725 (3) | 0.33876 (14) | 0.38352 (11) | 0.0349 (5) | |
N1 | 0.9232 (3) | 0.40257 (16) | 0.60850 (12) | 0.0262 (4) | |
N2 | 0.8299 (3) | 0.44486 (15) | 0.48118 (14) | 0.0296 (5) | |
H2 | 0.7984 | 0.4885 | 0.448 | 0.036* | |
C1 | 0.8832 (4) | 0.47460 (19) | 0.55542 (16) | 0.0283 (5) | |
C2 | 0.8209 (4) | 0.35266 (17) | 0.45353 (15) | 0.0254 (5) | |
C3 | 0.8698 (4) | 0.28058 (17) | 0.51060 (15) | 0.0246 (5) | |
C4 | 0.9212 (4) | 0.30928 (18) | 0.58495 (15) | 0.0250 (5) | |
H4 | 0.9567 | 0.2633 | 0.6216 | 0.03* | |
C5 | 0.8662 (4) | 0.17852 (19) | 0.48985 (16) | 0.0286 (5) | |
C6 | 0.9221 (4) | 0.1455 (2) | 0.41495 (19) | 0.0365 (6) | |
H6 | 0.9593 | 0.1886 | 0.3762 | 0.044* | |
C7 | 0.9225 (5) | 0.0498 (3) | 0.3980 (2) | 0.0496 (9) | |
H7 | 0.9604 | 0.0289 | 0.348 | 0.059* | |
C8 | 0.8669 (5) | −0.0158 (2) | 0.4549 (3) | 0.0585 (11) | |
H8 | 0.8687 | −0.0804 | 0.4433 | 0.07* | |
C9 | 0.8084 (6) | 0.0157 (2) | 0.5297 (3) | 0.0521 (9) | |
H9 | 0.7698 | −0.0275 | 0.5681 | 0.063* | |
C10 | 0.8083 (5) | 0.1124 (2) | 0.5461 (2) | 0.0392 (7) | |
H10 | 0.7687 | 0.1334 | 0.5958 | 0.047* | |
C1' | 0.9934 (4) | 0.43348 (18) | 0.68847 (14) | 0.0255 (5) | |
H1' | 1.0928 | 0.4789 | 0.6812 | 0.031* | |
C2' | 0.8448 (4) | 0.47799 (17) | 0.73959 (15) | 0.0264 (5) | |
H2' | 0.75 | 0.5086 | 0.7076 | 0.032* | |
O2' | 0.9353 (3) | 0.54254 (13) | 0.79151 (12) | 0.0327 (5) | |
H2O' | 0.8655 | 0.5595 | 0.8269 | 0.039* | |
C3' | 0.7751 (4) | 0.39195 (18) | 0.78564 (15) | 0.0285 (5) | |
H3' | 0.6943 | 0.3544 | 0.7515 | 0.034* | |
O3' | 0.6828 (3) | 0.41854 (14) | 0.85632 (14) | 0.0433 (6) | |
H3O' | 0.6012 | 0.3804 | 0.8654 | 0.052* | |
C4' | 0.9494 (4) | 0.33734 (19) | 0.80117 (15) | 0.0307 (6) | |
H4' | 1.0118 | 0.3665 | 0.8467 | 0.037* | |
O4' | 1.0571 (3) | 0.35341 (14) | 0.73006 (11) | 0.0318 (4) | |
C5' | 0.9330 (5) | 0.2329 (2) | 0.81655 (18) | 0.0395 (7) | |
H51' | 1.0535 | 0.2055 | 0.8211 | 0.047* | |
H52' | 0.8706 | 0.2229 | 0.8669 | 0.047* | |
O5' | 0.8359 (3) | 0.18558 (16) | 0.75411 (14) | 0.0437 (6) | |
H5O' | 0.8947 | 0.1397 | 0.7387 | 0.052* | |
O1W | 0.831 (2) | 0.7382 (6) | 0.5078 (5) | 0.083 (4) | 0.63 (3) |
O1W' | 0.715 (5) | 0.7221 (11) | 0.5193 (16) | 0.114 (7) | 0.37 (3) |
O2W | 0.5372 (5) | 0.6628 (3) | 0.7329 (2) | 0.0838 (12) | |
O3W | 0.6219 (14) | 0.8252 (13) | 0.6464 (15) | 0.107 (6) | 0.43 (3) |
O3W' | 0.549 (3) | 0.7790 (12) | 0.6033 (9) | 0.118 (7) | 0.57 (3) |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0665 (14) | 0.0226 (9) | 0.0324 (10) | −0.0004 (9) | −0.0019 (11) | −0.0011 (8) |
O2 | 0.0495 (11) | 0.0311 (9) | 0.0242 (9) | 0.0031 (9) | −0.0093 (9) | 0.0009 (7) |
N1 | 0.0367 (11) | 0.0226 (9) | 0.0192 (9) | 0.0029 (9) | −0.0005 (9) | −0.0021 (7) |
N2 | 0.0426 (12) | 0.0211 (9) | 0.0251 (10) | 0.0032 (9) | −0.0038 (10) | 0.0027 (8) |
C1 | 0.0362 (13) | 0.0233 (11) | 0.0253 (12) | 0.0017 (10) | 0.0000 (10) | 0.0018 (9) |
C2 | 0.0302 (12) | 0.0228 (11) | 0.0232 (11) | −0.0002 (10) | −0.0016 (9) | −0.0008 (9) |
C3 | 0.0285 (11) | 0.0216 (10) | 0.0237 (11) | 0.0007 (9) | 0.0005 (10) | 0.0012 (9) |
C4 | 0.0312 (12) | 0.0214 (10) | 0.0223 (11) | 0.0023 (10) | −0.0004 (10) | −0.0005 (9) |
C5 | 0.0302 (12) | 0.0247 (12) | 0.0310 (13) | 0.0036 (10) | −0.0073 (10) | −0.0027 (10) |
C6 | 0.0360 (14) | 0.0333 (14) | 0.0402 (15) | 0.0040 (12) | −0.0022 (13) | −0.0079 (12) |
C7 | 0.0438 (17) | 0.0410 (17) | 0.064 (2) | 0.0118 (15) | −0.0104 (17) | −0.0229 (16) |
C8 | 0.057 (2) | 0.0272 (14) | 0.091 (3) | 0.0060 (15) | −0.029 (2) | −0.0150 (17) |
C9 | 0.065 (2) | 0.0270 (13) | 0.064 (2) | −0.0065 (15) | −0.019 (2) | 0.0062 (15) |
C10 | 0.0516 (17) | 0.0263 (13) | 0.0398 (15) | −0.0017 (13) | −0.0094 (14) | 0.0039 (11) |
C1' | 0.0319 (11) | 0.0246 (11) | 0.0201 (11) | 0.0000 (10) | −0.0009 (9) | −0.0017 (9) |
C2' | 0.0345 (11) | 0.0219 (10) | 0.0228 (11) | 0.0007 (10) | −0.0003 (10) | −0.0030 (9) |
O2' | 0.0423 (10) | 0.0277 (9) | 0.0280 (9) | −0.0076 (8) | 0.0058 (8) | −0.0098 (8) |
C3' | 0.0364 (12) | 0.0233 (10) | 0.0257 (11) | −0.0026 (10) | 0.0032 (11) | −0.0065 (9) |
O3' | 0.0565 (13) | 0.0341 (10) | 0.0394 (11) | −0.0134 (10) | 0.0207 (10) | −0.0118 (9) |
C4' | 0.0435 (14) | 0.0290 (12) | 0.0195 (11) | 0.0016 (12) | −0.0015 (10) | −0.0011 (9) |
O4' | 0.0359 (9) | 0.0343 (9) | 0.0251 (9) | 0.0084 (8) | −0.0018 (8) | 0.0004 (7) |
C5' | 0.0590 (18) | 0.0265 (12) | 0.0329 (13) | 0.0037 (14) | −0.0046 (14) | 0.0040 (11) |
O5' | 0.0514 (12) | 0.0286 (10) | 0.0512 (14) | 0.0065 (10) | −0.0038 (11) | −0.0063 (10) |
O1W | 0.108 (9) | 0.060 (4) | 0.080 (4) | 0.015 (5) | −0.009 (4) | 0.018 (3) |
O1W' | 0.113 (17) | 0.084 (8) | 0.146 (13) | −0.011 (9) | −0.050 (13) | 0.024 (8) |
O2W | 0.075 (2) | 0.122 (3) | 0.0549 (18) | 0.036 (2) | −0.0032 (16) | −0.0002 (19) |
O3W | 0.046 (5) | 0.096 (9) | 0.178 (14) | 0.021 (5) | 0.011 (7) | 0.008 (10) |
O3W' | 0.125 (11) | 0.108 (9) | 0.121 (9) | 0.054 (9) | 0.045 (8) | 0.049 (7) |
O1—C1 | 1.223 (3) | C9—H9 | 0.93 |
O2—C2 | 1.240 (3) | C10—H10 | 0.93 |
N1—C4 | 1.372 (3) | C1'—O4' | 1.406 (3) |
N1—C1 | 1.380 (3) | C1'—C2' | 1.524 (4) |
N1—C1' | 1.499 (3) | C1'—H1' | 0.98 |
N2—C1 | 1.368 (3) | C2'—O2' | 1.423 (3) |
N2—C2 | 1.380 (3) | C2'—C3' | 1.525 (4) |
N2—H2 | 0.86 | C2'—H2' | 0.98 |
C2—C3 | 1.439 (3) | O2'—H2O' | 0.82 |
C3—C4 | 1.362 (3) | C3'—O3' | 1.414 (3) |
C3—C5 | 1.479 (4) | C3'—C4' | 1.519 (4) |
C4—H4 | 0.93 | C3'—H3' | 0.98 |
C5—C10 | 1.391 (4) | O3'—H3O' | 0.82 |
C5—C6 | 1.398 (4) | C4'—O4' | 1.447 (3) |
C6—C7 | 1.378 (4) | C4'—C5' | 1.499 (4) |
C6—H6 | 0.93 | C4'—H4' | 0.98 |
C7—C8 | 1.389 (6) | C5'—O5' | 1.430 (4) |
C7—H7 | 0.93 | C5'—H51' | 0.97 |
C8—C9 | 1.395 (7) | C5'—H52' | 0.97 |
C8—H8 | 0.93 | O5'—H5O' | 0.82 |
C9—C10 | 1.389 (4) | ||
C4—N1—C1 | 121.1 (2) | C5—C10—H10 | 119.2 |
C4—N1—C1' | 122.6 (2) | O4'—C1'—N1 | 108.89 (19) |
C1—N1—C1' | 115.7 (2) | O4'—C1'—C2' | 107.0 (2) |
C1—N2—C2 | 127.3 (2) | N1—C1'—C2' | 111.9 (2) |
C1—N2—H2 | 116.3 | O4'—C1'—H1' | 109.7 |
C2—N2—H2 | 116.3 | N1—C1'—H1' | 109.7 |
O1—C1—N2 | 122.9 (2) | C2'—C1'—H1' | 109.7 |
O1—C1—N1 | 122.3 (3) | O2'—C2'—C1' | 105.6 (2) |
N2—C1—N1 | 114.8 (2) | O2'—C2'—C3' | 110.9 (2) |
O2—C2—N2 | 118.6 (2) | C1'—C2'—C3' | 101.4 (2) |
O2—C2—C3 | 125.9 (2) | O2'—C2'—H2' | 112.7 |
N2—C2—C3 | 115.4 (2) | C1'—C2'—H2' | 112.7 |
C4—C3—C2 | 117.8 (2) | C3'—C2'—H2' | 112.7 |
C4—C3—C5 | 120.5 (2) | C2'—O2'—H2O' | 109.5 |
C2—C3—C5 | 121.7 (2) | O3'—C3'—C4' | 113.4 (2) |
C3—C4—N1 | 123.4 (2) | O3'—C3'—C2' | 111.9 (2) |
C3—C4—H4 | 118.3 | C4'—C3'—C2' | 101.8 (2) |
N1—C4—H4 | 118.3 | O3'—C3'—H3' | 109.8 |
C10—C5—C6 | 118.3 (3) | C4'—C3'—H3' | 109.8 |
C10—C5—C3 | 119.8 (3) | C2'—C3'—H3' | 109.8 |
C6—C5—C3 | 121.9 (3) | C3'—O3'—H3O' | 109.5 |
C7—C6—C5 | 120.7 (3) | O4'—C4'—C5' | 109.8 (2) |
C7—C6—H6 | 119.7 | O4'—C4'—C3' | 104.1 (2) |
C5—C6—H6 | 119.7 | C5'—C4'—C3' | 117.3 (3) |
C6—C7—C8 | 120.7 (4) | O4'—C4'—H4' | 108.4 |
C6—C7—H7 | 119.7 | C5'—C4'—H4' | 108.4 |
C8—C7—H7 | 119.7 | C3'—C4'—H4' | 108.4 |
C7—C8—C9 | 119.5 (3) | C1'—O4'—C4' | 110.48 (19) |
C7—C8—H8 | 120.2 | O5'—C5'—C4' | 111.8 (2) |
C9—C8—H8 | 120.2 | O5'—C5'—H51' | 109.2 |
C10—C9—C8 | 119.3 (4) | C4'—C5'—H51' | 109.2 |
C10—C9—H9 | 120.3 | O5'—C5'—H52' | 109.2 |
C8—C9—H9 | 120.3 | C4'—C5'—H52' | 109.2 |
C9—C10—C5 | 121.5 (3) | H51'—C5'—H52' | 107.9 |
C9—C10—H10 | 119.2 | C5'—O5'—H5O' | 109.5 |
C2—N2—C1—O1 | 177.3 (3) | C8—C9—C10—C5 | −0.3 (5) |
C2—N2—C1—N1 | −3.4 (4) | C6—C5—C10—C9 | 1.2 (5) |
C4—N1—C1—O1 | −176.1 (3) | C3—C5—C10—C9 | −178.0 (3) |
C1'—N1—C1—O1 | −4.5 (4) | C4—N1—C1'—O4' | 1.7 (3) |
C4—N1—C1—N2 | 4.5 (4) | C1—N1—C1'—O4' | −169.9 (2) |
C1'—N1—C1—N2 | 176.2 (2) | C4—N1—C1'—C2' | −116.3 (3) |
C1—N2—C2—O2 | −178.6 (3) | C1—N1—C1'—C2' | 72.1 (3) |
C1—N2—C2—C3 | 1.5 (4) | O4'—C1'—C2'—O2' | 88.5 (2) |
O2—C2—C3—C4 | 179.5 (3) | N1—C1'—C2'—O2' | −152.3 (2) |
N2—C2—C3—C4 | −0.7 (4) | O4'—C1'—C2'—C3' | −27.3 (2) |
O2—C2—C3—C5 | 0.0 (4) | N1—C1'—C2'—C3' | 91.9 (2) |
N2—C2—C3—C5 | 179.8 (2) | O2'—C2'—C3'—O3' | 47.3 (3) |
C2—C3—C4—N1 | 2.1 (4) | C1'—C2'—C3'—O3' | 159.1 (2) |
C5—C3—C4—N1 | −178.4 (2) | O2'—C2'—C3'—C4' | −74.2 (2) |
C1—N1—C4—C3 | −4.2 (4) | C1'—C2'—C3'—C4' | 37.6 (2) |
C1'—N1—C4—C3 | −175.3 (2) | O3'—C3'—C4'—O4' | −155.9 (2) |
C4—C3—C5—C10 | 38.3 (4) | C2'—C3'—C4'—O4' | −35.4 (2) |
C2—C3—C5—C10 | −142.2 (3) | O3'—C3'—C4'—C5' | 82.7 (3) |
C4—C3—C5—C6 | −140.9 (3) | C2'—C3'—C4'—C5' | −156.9 (2) |
C2—C3—C5—C6 | 38.7 (4) | N1—C1'—O4'—C4' | −115.8 (2) |
C10—C5—C6—C7 | −1.1 (4) | C2'—C1'—O4'—C4' | 5.3 (3) |
C3—C5—C6—C7 | 178.1 (3) | C5'—C4'—O4'—C1' | 145.6 (2) |
C5—C6—C7—C8 | 0.2 (5) | C3'—C4'—O4'—C1' | 19.3 (3) |
C6—C7—C8—C9 | 0.7 (6) | O4'—C4'—C5'—O5' | −64.2 (3) |
C7—C8—C9—C10 | −0.6 (6) | C3'—C4'—C5'—O5' | 54.2 (4) |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2···O3′i | 0.86 | 2.02 | 2.842 (3) | 159 |
O2′—H2O′···O2ii | 0.82 | 2 | 2.740 (3) | 151 |
O3′—H3O′···O3Wiii | 0.82 | 1.83 | 2.600 (9) | 157 |
O3′—H3O′···O3W′iii | 0.82 | 1.88 | 2.691 (9) | 169 |
O5′—H5O′···O2′iv | 0.82 | 1.92 | 2.735 (3) | 171 |
Symmetry codes: (i) −x+3/2, −y+1, z−1/2; (ii) −x+3/2, −y+1, z+1/2; (iii) −x+1, y−1/2, −z+3/2; (iv) −x+2, y−1/2, −z+3/2. |
Experimental details
Crystal data | |
Chemical formula | C15H16N2O6·3H2O |
Mr | 374.35 |
Crystal system, space group | Orthorhombic, P212121 |
Temperature (K) | 295 |
a, b, c (Å) | 7.3627 (1), 14.0874 (3), 16.7287 (3) |
V (Å3) | 1735.12 (5) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.12 |
Crystal size (mm) | 0.45 × 0.24 × 0.14 |
Data collection | |
Diffractometer | Nonius KappaCCD |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 5050, 2879, 2338 |
Rint | 0.022 |
(sin θ/λ)max (Å−1) | 0.704 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.053, 0.185, 1.16 |
No. of reflections | 2879 |
No. of parameters | 255 |
No. of restraints | 12 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.63, −0.63 |
Computer programs: KappaCCD Server Software (Nonius, 1997), DENZO-SMN (Otwinowski & Minor, 1997), DENZO-SMN, SIR97 (Altomare et al., 1999), SHELXL97 (Sheldrick, 1997), DIAMOND (Brandenburg & Putz, 2005), WinGX (Farrugia, 1999).
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2···O3'i | 0.86 | 2.02 | 2.842 (3) | 159.1 |
O2'—H2O'···O2ii | 0.82 | 2 | 2.740 (3) | 150.6 |
O3'—H3O'···O3Wiii | 0.82 | 1.83 | 2.600 (9) | 156.5 |
O3'—H3O'···O3W'iii | 0.82 | 1.88 | 2.691 (9) | 168.5 |
O5'—H5O'···O2'iv | 0.82 | 1.92 | 2.735 (3) | 171.1 |
Symmetry codes: (i) −x+3/2, −y+1, z−1/2; (ii) −x+3/2, −y+1, z+1/2; (iii) −x+1, y−1/2, −z+3/2; (iv) −x+2, y−1/2, −z+3/2. |
Research has been focused towards finding biologically active analogues of uridine, a naturally occurring compound, and modification of the uracil ring concentrates on position 5. Examples of the latest investigations for the development of new drugs include e.g. the synthesis of ethynyl uridine derivatives as antiviral drugs against Flaviviridae (Aucagne et al., 2006), especially HCV, studies of other alkynyl-uridines as potent inhibitors of Mycobacteria (Rai et al., 2005), and e.g. uridine and estradiol conjugates exhibiting binding affinity and cytotoxicity against cell lines with and without an estrogen receptor (Ali, H. et al., 2006). Modern synthetic methods include coupling reactions with catalysis by organometallic compounds, which enables the introduction of diverse substituents of an aliphatic or aromatic nature. Although the synthesis and biological activity of uridine derivatives has been studied intensively, their structural parameters from crystallographic measurements, important for behavior in biological systems, have rarely been discussed and published. In this paper we describe the structural properties of 5-phenyluridine prepared by the Suzuki coupling from 5-iodouridine and phenylboronic acid.
A selection of geometric parameters is given in Table 1. The heterocyclic base moiety is almost planar, with a maximum deviation of 0.019 (3) Å for the C1 atom. The N-glycosidic torsion angle χ (C1–N1–C1'–O4') is -169.8 (2)° which corresponds to an anti orientation of the base moiety. The sugar ring, C1'–C2'–C3'–C4'–O4', adopts a mixed twisted- envelope 3T2/3E conformation (C3'-exo / C2'-endo) with puckering parameters q2 = 0.384 (3) Å and φ2 = 64.2 (4)° (Cremer & Pople, 1975). The conformation of the side chain, as defined by the torsion angle O5'–C5'–C4'–C3' of 53.5 (3)°, is +sc. The phenyl and uracil rings are not co-planar (Fig.1), with a dihedral angle between the mean planes of 38.02 (9)°. The crystal packing is determined by a network of hydrogen bonds (Table 2) with π-π interactions (3.455 Å) observed between the phenyl and uracil moieties. This packing creates channels along the a axis which hosts the solvent molecules (Fig. 2).