| Literature DB >> 29250365 |
Vijay Gayakhe1, Anant Ramakant Kapdi1, Yulia Borozdina2, Carola Schulzke2.
Abstract
The mol-ecule of the title compound, C21H18N2O6, has a bent rather than a linear conformation supported by three intra-molecular C-H⋯OEntities:
Keywords: Suzuki-Miyaura cross-coupling; catalysis; crystal structure; nucleoside; palladium; uridine
Year: 2017 PMID: 29250365 PMCID: PMC5730302 DOI: 10.1107/S2056989017013111
Source DB: PubMed Journal: Acta Crystallogr E Crystallogr Commun
Figure 1The molecular structure of the title compound, showing the atom labelling and 50% probability displacement ellipsoids. Atom C7 is in the C5 position of the pyrimidine base according to nucleoside/nucleotide nomenclature, atom C6 in C6.
Figure 2The crystal packing (Mercury; Macrae et al., 2006 ▸) viewed along the a axis showing the classical hydrogen bonds which lead to a two-dimensional network parallel to (010).
Hydrogen-bond geometry (Å, °)
|
|
| H⋯ |
|
|
|---|---|---|---|---|
| C4—H4 | 0.99 | 2.61 | 3.439 (6) | 142 |
| C6—H6⋯O6 | 0.95 | 2.34 | 2.915 (5) | 119 |
| C13—H13⋯O1 | 0.95 | 2.58 | 3.271 (6) | 130 |
| C21—H21⋯O5 | 0.95 | 2.33 | 2.876 (6) | 116 |
| C14—H14⋯O4ii | 0.95 | 2.45 | 3.115 (6) | 127 |
| O2—H2 | 1.00 (5) | 1.72 (5) | 2.716 (5) | 174 (5) |
| N2—H2 | 0.91 (5) | 2.30 (5) | 3.144 (5) | 154 (5) |
| O1—H1 | 0.92 (6) | 2.10 (6) | 2.922 (5) | 148 (6) |
Symmetry codes: (i) ; (ii) ; (iii) ; (iv) .
Experimental details
| Crystal data | |
| Chemical formula | C21H18N2O6 |
|
| 394.37 |
| Crystal system, space group | Orthorhombic, |
| Temperature (K) | 170 |
|
| 6.2899 (13), 15.167 (3), 17.938 (4) |
|
| 1711.2 (6) |
|
| 4 |
| Radiation type | Mo |
| μ (mm−1) | 0.11 |
| Crystal size (mm) | 0.46 × 0.09 × 0.09 |
| Data collection | |
| Diffractometer | Stoe IPDS2T |
| Absorption correction | Numerical face indexed ( |
|
| 0.388, 0.875 |
| No. of measured, independent and observed [ | 14640, 3696, 2704 |
|
| 0.110 |
| (sin θ/λ)max (Å−1) | 0.642 |
| Refinement | |
|
| 0.057, 0.143, 0.96 |
| No. of reflections | 3696 |
| No. of parameters | 274 |
| No. of restraints | 3 |
| H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
| Δρmax, Δρmin (e Å−3) | 0.34, −0.37 |
Computer programs: X-AREA (Stoe & Cie, 2010 ▸), SHELXT2014 (Sheldrick, 2015a ▸), SHELXL2013 (Sheldrick, 2015b ▸), XP in SHELXTL and CIFTAB (Sheldrick, 2008 ▸), Mercury (Macrae et al., 2006 ▸) and PLATON (Spek, 2009 ▸).
| C21H18N2O6 | |
| Mo | |
| Orthorhombic, | Cell parameters from 14682 reflections |
| θ = 6.5–54.3° | |
| µ = 0.11 mm−1 | |
| Needle, colourless | |
| 0.46 × 0.09 × 0.09 mm | |
| Stoe IPDS2T diffractometer | 3696 independent reflections |
| Radiation source: fine-focus sealed tube | 2704 reflections with |
| Detector resolution: 6.67 pixels mm-1 | |
| ω scans | θmax = 27.1°, θmin = 3.4° |
| Absorption correction: numerical face indexed (X-Red32 and X-Shape; Stoe & Cie, 2010) | |
| 14640 measured reflections |
| Refinement on | 3 restraints |
| Least-squares matrix: full | Hydrogen site location: mixed |
| H atoms treated by a mixture of independent and constrained refinement | |
| (Δ/σ)max < 0.001 | |
| 3696 reflections | Δρmax = 0.34 e Å−3 |
| 274 parameters | Δρmin = −0.37 e Å−3 |
| Experimental. The reaction was carried out in a Schlenk tube using Schlenk
techniques under a nitrogen atmosphere. All other reagents and solvents were
purchased commercially and used without any further purification. A
UV–visible spectrum of the title compound (10 µ |
| Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes. |
| O1 | 0.4367 (6) | 0.5659 (2) | 0.66750 (19) | 0.0316 (8) | |
| O2 | −0.1365 (5) | 0.6212 (3) | 0.62349 (19) | 0.0355 (8) | |
| O3 | 0.3555 (5) | 0.6634 (2) | 0.52801 (16) | 0.0251 (7) | |
| O4 | 0.0678 (6) | 0.6179 (2) | 0.33056 (18) | 0.0342 (8) | |
| O5 | 0.5541 (6) | 0.4112 (2) | 0.26958 (17) | 0.0319 (8) | |
| O6 | 0.6845 (5) | 0.4177 (2) | 0.54844 (17) | 0.0271 (7) | |
| N1 | 0.3167 (6) | 0.5825 (2) | 0.4169 (2) | 0.0244 (8) | |
| N2 | 0.3171 (7) | 0.5149 (3) | 0.3022 (2) | 0.0278 (8) | |
| C1 | 0.3630 (8) | 0.6543 (3) | 0.6624 (2) | 0.0268 (10) | |
| H1A | 0.4869 | 0.6946 | 0.6612 | 0.032* | |
| H1B | 0.2787 | 0.6685 | 0.7074 | 0.032* | |
| C2 | 0.2282 (7) | 0.6702 (3) | 0.5941 (2) | 0.0238 (9) | |
| H2 | 0.1672 | 0.7310 | 0.5970 | 0.029* | |
| C3 | 0.0472 (7) | 0.6046 (3) | 0.5800 (2) | 0.0256 (9) | |
| H3 | 0.0978 | 0.5428 | 0.5880 | 0.031* | |
| C4 | 0.0039 (7) | 0.6206 (3) | 0.4983 (3) | 0.0264 (9) | |
| H4A | −0.1046 | 0.6672 | 0.4915 | 0.032* | |
| H4B | −0.0458 | 0.5660 | 0.4735 | 0.032* | |
| C5 | 0.2197 (7) | 0.6500 (3) | 0.4670 (2) | 0.0253 (9) | |
| H5 | 0.2020 | 0.7067 | 0.4391 | 0.030* | |
| C6 | 0.4901 (7) | 0.5330 (3) | 0.4377 (2) | 0.0233 (9) | |
| H6 | 0.5481 | 0.5409 | 0.4862 | 0.028* | |
| C7 | 0.5806 (7) | 0.4735 (3) | 0.3914 (2) | 0.0239 (9) | |
| C8 | 0.4944 (7) | 0.4627 (3) | 0.3171 (3) | 0.0262 (9) | |
| C9 | 0.2231 (8) | 0.5755 (3) | 0.3485 (2) | 0.0282 (10) | |
| C10 | 0.7714 (7) | 0.4220 (3) | 0.4143 (2) | 0.0250 (9) | |
| C11 | 0.8132 (7) | 0.4001 (3) | 0.4874 (2) | 0.0256 (10) | |
| C12 | 0.7864 (8) | 0.3833 (3) | 0.6103 (2) | 0.0271 (10) | |
| C13 | 0.7096 (8) | 0.3830 (3) | 0.6814 (3) | 0.0296 (10) | |
| H13 | 0.5767 | 0.4090 | 0.6935 | 0.036* | |
| C14 | 0.8351 (8) | 0.3429 (3) | 0.7351 (3) | 0.0321 (10) | |
| H14 | 0.7868 | 0.3412 | 0.7853 | 0.039* | |
| C15 | 1.0316 (8) | 0.3047 (3) | 0.7172 (3) | 0.0310 (10) | |
| H15 | 1.1139 | 0.2775 | 0.7552 | 0.037* | |
| C16 | 1.1061 (8) | 0.3060 (3) | 0.6454 (3) | 0.0306 (10) | |
| H16 | 1.2393 | 0.2802 | 0.6334 | 0.037* | |
| C17 | 0.9829 (7) | 0.3460 (3) | 0.5904 (3) | 0.0262 (9) | |
| C18 | 0.9993 (7) | 0.3562 (3) | 0.5105 (3) | 0.0250 (9) | |
| C19 | 1.1478 (7) | 0.3293 (3) | 0.4577 (3) | 0.0280 (10) | |
| H19 | 1.2741 | 0.2993 | 0.4720 | 0.034* | |
| C20 | 1.1057 (7) | 0.3474 (3) | 0.3848 (3) | 0.0294 (10) | |
| H20 | 1.2028 | 0.3278 | 0.3477 | 0.035* | |
| C21 | 0.9242 (8) | 0.3939 (3) | 0.3626 (3) | 0.0281 (10) | |
| H21 | 0.9041 | 0.4067 | 0.3112 | 0.034* | |
| H2O | −0.097 (9) | 0.608 (4) | 0.676 (3) | 0.037 (15)* | |
| H2N | 0.266 (9) | 0.506 (4) | 0.255 (3) | 0.034 (14)* | |
| H1O | 0.567 (10) | 0.562 (5) | 0.644 (4) | 0.07 (2)* |
| O1 | 0.0278 (19) | 0.0285 (17) | 0.0385 (19) | 0.0033 (13) | −0.0009 (14) | 0.0040 (14) |
| O2 | 0.0208 (17) | 0.054 (2) | 0.0320 (19) | 0.0045 (15) | 0.0025 (13) | 0.0041 (16) |
| O3 | 0.0267 (17) | 0.0264 (15) | 0.0223 (16) | −0.0019 (12) | 0.0004 (12) | −0.0025 (12) |
| O4 | 0.0333 (19) | 0.0388 (18) | 0.0305 (17) | 0.0095 (15) | −0.0064 (14) | −0.0014 (15) |
| O5 | 0.0370 (19) | 0.0331 (17) | 0.0255 (16) | 0.0016 (14) | 0.0004 (14) | −0.0086 (14) |
| O6 | 0.0269 (17) | 0.0286 (16) | 0.0259 (15) | 0.0040 (13) | 0.0028 (13) | 0.0018 (12) |
| N1 | 0.024 (2) | 0.0249 (18) | 0.0243 (18) | 0.0037 (15) | −0.0004 (15) | 0.0000 (15) |
| N2 | 0.033 (2) | 0.0299 (19) | 0.0205 (19) | 0.0018 (16) | −0.0034 (16) | −0.0039 (15) |
| C1 | 0.029 (2) | 0.024 (2) | 0.028 (2) | −0.0031 (18) | 0.0007 (18) | −0.0005 (18) |
| C2 | 0.025 (2) | 0.021 (2) | 0.025 (2) | 0.0013 (16) | 0.0016 (18) | 0.0007 (17) |
| C3 | 0.022 (2) | 0.023 (2) | 0.031 (2) | 0.0002 (17) | 0.0024 (17) | 0.0028 (18) |
| C4 | 0.022 (2) | 0.026 (2) | 0.031 (2) | 0.0039 (17) | −0.0022 (19) | −0.0032 (18) |
| C5 | 0.032 (2) | 0.021 (2) | 0.023 (2) | 0.0024 (17) | −0.0011 (18) | −0.0010 (17) |
| C6 | 0.024 (2) | 0.023 (2) | 0.023 (2) | −0.0023 (16) | −0.0033 (16) | −0.0002 (16) |
| C7 | 0.024 (2) | 0.021 (2) | 0.026 (2) | −0.0018 (16) | 0.0020 (17) | 0.0012 (17) |
| C8 | 0.027 (2) | 0.024 (2) | 0.027 (2) | −0.0021 (17) | 0.0014 (18) | 0.0015 (17) |
| C9 | 0.032 (3) | 0.030 (2) | 0.023 (2) | −0.002 (2) | −0.0005 (18) | −0.0014 (18) |
| C10 | 0.026 (2) | 0.020 (2) | 0.029 (2) | −0.0015 (17) | 0.0010 (18) | −0.0024 (18) |
| C11 | 0.027 (3) | 0.020 (2) | 0.029 (2) | 0.0003 (17) | 0.0060 (18) | −0.0031 (16) |
| C12 | 0.029 (2) | 0.023 (2) | 0.030 (2) | 0.0016 (18) | −0.0041 (19) | 0.0003 (18) |
| C13 | 0.036 (3) | 0.023 (2) | 0.030 (2) | 0.0030 (19) | 0.001 (2) | 0.0011 (18) |
| C14 | 0.040 (3) | 0.027 (2) | 0.029 (2) | −0.004 (2) | −0.003 (2) | −0.0001 (19) |
| C15 | 0.030 (3) | 0.028 (2) | 0.036 (3) | 0.0010 (19) | −0.009 (2) | 0.0030 (19) |
| C16 | 0.030 (3) | 0.022 (2) | 0.040 (3) | 0.0015 (17) | −0.006 (2) | −0.004 (2) |
| C17 | 0.024 (2) | 0.023 (2) | 0.032 (2) | −0.0019 (17) | −0.0003 (19) | −0.0024 (18) |
| C18 | 0.025 (2) | 0.019 (2) | 0.031 (2) | −0.0012 (17) | 0.0012 (18) | 0.0005 (17) |
| C19 | 0.026 (2) | 0.017 (2) | 0.041 (3) | 0.0010 (16) | 0.004 (2) | −0.0001 (18) |
| C20 | 0.027 (2) | 0.029 (2) | 0.033 (3) | 0.0008 (18) | 0.0083 (19) | −0.0053 (19) |
| C21 | 0.033 (3) | 0.025 (2) | 0.026 (2) | −0.0032 (18) | 0.0028 (19) | −0.0045 (18) |
| O1—C1 | 1.423 (6) | C5—H5 | 1.0000 |
| O1—H1O | 0.92 (6) | C6—C7 | 1.353 (6) |
| O2—C3 | 1.417 (6) | C6—H6 | 0.9500 |
| O2—H2O | 1.00 (5) | C7—C8 | 1.447 (6) |
| O3—C5 | 1.403 (5) | C7—C10 | 1.489 (6) |
| O3—C2 | 1.435 (5) | C10—C11 | 1.379 (6) |
| O4—C9 | 1.213 (6) | C10—C21 | 1.402 (6) |
| O5—C8 | 1.216 (5) | C11—C18 | 1.408 (6) |
| O6—C12 | 1.384 (5) | C12—C13 | 1.364 (7) |
| O6—C11 | 1.387 (5) | C12—C17 | 1.405 (6) |
| N1—C9 | 1.366 (6) | C13—C14 | 1.386 (7) |
| N1—C6 | 1.375 (6) | C13—H13 | 0.9500 |
| N1—C5 | 1.492 (5) | C14—C15 | 1.403 (7) |
| N2—C9 | 1.373 (6) | C14—H14 | 0.9500 |
| N2—C8 | 1.393 (6) | C15—C16 | 1.370 (7) |
| N2—H2N | 0.91 (5) | C15—H15 | 0.9500 |
| C1—C2 | 1.508 (6) | C16—C17 | 1.394 (6) |
| C1—H1A | 0.9900 | C16—H16 | 0.9500 |
| C1—H1B | 0.9900 | C17—C18 | 1.445 (6) |
| C2—C3 | 1.533 (6) | C18—C19 | 1.391 (6) |
| C2—H2 | 1.0000 | C19—C20 | 1.364 (7) |
| C3—C4 | 1.511 (6) | C19—H19 | 0.9500 |
| C3—H3 | 1.0000 | C20—C21 | 1.399 (7) |
| C4—C5 | 1.535 (7) | C20—H20 | 0.9500 |
| C4—H4A | 0.9900 | C21—H21 | 0.9500 |
| C4—H4B | 0.9900 | ||
| C1—O1—H1O | 109 (5) | C6—C7—C10 | 121.3 (4) |
| C3—O2—H2O | 106 (3) | C8—C7—C10 | 119.8 (4) |
| C5—O3—C2 | 108.4 (3) | O5—C8—N2 | 118.5 (4) |
| C12—O6—C11 | 106.8 (3) | O5—C8—C7 | 127.0 (4) |
| C9—N1—C6 | 122.9 (4) | N2—C8—C7 | 114.4 (4) |
| C9—N1—C5 | 114.7 (4) | O4—C9—N1 | 122.9 (4) |
| C6—N1—C5 | 122.4 (4) | O4—C9—N2 | 122.8 (4) |
| C9—N2—C8 | 127.5 (4) | N1—C9—N2 | 114.2 (4) |
| C9—N2—H2N | 121 (4) | C11—C10—C21 | 115.1 (4) |
| C8—N2—H2N | 112 (4) | C11—C10—C7 | 122.8 (4) |
| O1—C1—C2 | 112.7 (4) | C21—C10—C7 | 122.0 (4) |
| O1—C1—H1A | 109.1 | C10—C11—O6 | 126.3 (4) |
| C2—C1—H1A | 109.1 | C10—C11—C18 | 123.5 (4) |
| O1—C1—H1B | 109.1 | O6—C11—C18 | 110.2 (4) |
| C2—C1—H1B | 109.1 | C13—C12—O6 | 125.9 (4) |
| H1A—C1—H1B | 107.8 | C13—C12—C17 | 123.2 (4) |
| O3—C2—C1 | 110.2 (4) | O6—C12—C17 | 110.8 (4) |
| O3—C2—C3 | 103.3 (3) | C12—C13—C14 | 116.8 (5) |
| C1—C2—C3 | 116.7 (4) | C12—C13—H13 | 121.6 |
| O3—C2—H2 | 108.8 | C14—C13—H13 | 121.6 |
| C1—C2—H2 | 108.8 | C13—C14—C15 | 121.5 (5) |
| C3—C2—H2 | 108.8 | C13—C14—H14 | 119.2 |
| O2—C3—C4 | 111.0 (4) | C15—C14—H14 | 119.2 |
| O2—C3—C2 | 113.5 (4) | C16—C15—C14 | 120.8 (5) |
| C4—C3—C2 | 101.0 (4) | C16—C15—H15 | 119.6 |
| O2—C3—H3 | 110.4 | C14—C15—H15 | 119.6 |
| C4—C3—H3 | 110.4 | C15—C16—C17 | 118.8 (5) |
| C2—C3—H3 | 110.4 | C15—C16—H16 | 120.6 |
| C3—C4—C5 | 104.0 (4) | C17—C16—H16 | 120.6 |
| C3—C4—H4A | 111.0 | C16—C17—C12 | 118.9 (4) |
| C5—C4—H4A | 111.0 | C16—C17—C18 | 135.2 (4) |
| C3—C4—H4B | 111.0 | C12—C17—C18 | 105.8 (4) |
| C5—C4—H4B | 111.0 | C19—C18—C11 | 119.8 (4) |
| H4A—C4—H4B | 109.0 | C19—C18—C17 | 133.7 (4) |
| O3—C5—N1 | 108.6 (3) | C11—C18—C17 | 106.4 (4) |
| O3—C5—C4 | 107.2 (3) | C20—C19—C18 | 117.6 (4) |
| N1—C5—C4 | 112.5 (4) | C20—C19—H19 | 121.2 |
| O3—C5—H5 | 109.5 | C18—C19—H19 | 121.2 |
| N1—C5—H5 | 109.5 | C19—C20—C21 | 122.2 (4) |
| C4—C5—H5 | 109.5 | C19—C20—H20 | 118.9 |
| C7—C6—N1 | 122.1 (4) | C21—C20—H20 | 118.9 |
| C7—C6—H6 | 118.9 | C20—C21—C10 | 121.7 (4) |
| N1—C6—H6 | 118.9 | C20—C21—H21 | 119.2 |
| C6—C7—C8 | 118.8 (4) | C10—C21—H21 | 119.2 |
| H··· | ||||
| C4—H4 | 0.99 | 2.61 | 3.439 (6) | 142 |
| C6—H6···O6 | 0.95 | 2.34 | 2.915 (5) | 119 |
| C13—H13···O1 | 0.95 | 2.58 | 3.271 (6) | 130 |
| C21—H21···O5 | 0.95 | 2.33 | 2.876 (6) | 116 |
| C13—H13···O4ii | 0.95 | 2.65 | 3.194 (6) | 117 |
| C14—H14···O4ii | 0.95 | 2.45 | 3.115 (6) | 127 |
| C1—H1 | 0.99 | 2.66 | 3.401 (6) | 132 |
| O2—H2 | 1.00 (5) | 1.72 (5) | 2.716 (5) | 174 (5) |
| N2—H2 | 0.91 (5) | 2.30 (5) | 3.144 (5) | 154 (5) |
| O1—H1 | 0.92 (6) | 2.10 (6) | 2.922 (5) | 148 (6) |