Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270100018163/gd1119sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S0108270100018163/gd1119Isup2.hkl |
CCDC reference: 160014
Dimethyl acetylenedicarboxylate (1.28 g, 9.0 mmol) was added to a solution of 6-(tri-O-acetyl-β-D-xylopyranosylamino)-2-methoxy-3-methyl -4(3H)-pyrimidinone (1.85 g, 4.5 mmol) in acetonitrile (20 ml) containing a catalytic amount of trifluoroacetic acid (0.11 g, 1.2 mmol). The mixture was stirred in refluxing acetonitrile for 15.5 h. The solvent was evaporated under reduced pressure and the title compound was isolated by flash column chromatography on silica gel (toluene/acetone). Recrystallization from acetone afforded yellow crystals. It proved very difficult to obtain crystals of suitable quality for X-ray diffraction (m.p. 543 K). Analysis calculated for C22H25N3O12: C 50.5, H 4.8, N 8.0%; found: C 50.2, H 4.9, N 8.0%. 1H-NMR (CDCl3): 7.27 (d, 7.1 Hz, 1H, H—N), 5.58 (dd, 9.2 Hz, 8.4 Hz, 1H, H-1'), 5.38 (d, 8.6 Hz, 1H, H-3'), 5.08 (pst, 8.5 Hz, 1H, H-2'), 5.01 (m, 1H, H-4'), 4.15, (dd, 5.3 Hz, 11.8 Hz, 1H, H-5'eq), 4.03 (s, 3H, 6-OCH3), 3.94 (s, 3H, 7-COOCH3), 3.49 (dd, 9.3 Hz, 11.8 Hz, 1H, H-5'ax), 3.09 (s, 3H, N—CH3), 2.07 (s, 3H, OAc), 2.08 (s, 3H, OAc), 2.14 (s, 3H, OAc).
Compound (I) crystallized in the monoclinic system; space group C2 was assumed, and confirmed by the analysis. H atoms were treated as riding atoms with C—H 0.98 to 1.00 Å, N—H 0.88 Å. Methyl H atoms atoms were placed in calculated positions and these positions checked against contoured difference maps calculated in the plane of the calculated H atoms following a structure-factor calculation with the H atoms present with a site occupation factor of 0.0001. This technique was also used to confirm the position of the amino hydrogen H9.
The high R factor for the title compound is probably due to non-merohedral twinning involving a small secondary component. This possibility is indicated by the strange location of the residual peaks and the large proportion of the 50 most disagreeable reflections being of the type l = 1 with Fobs2 higher than Fcalc2. To check this, the diffraction images were examined and found to contain additional weak reflections and split faults in this direction. A symptom of these additional spots is the loss of 00 l reflections from the data file due to bad background during integration. Many of the twin reflections are close enough to the main reflections to contaminate the background and these will have been flagged as such and omitted from the final data set as unreliable. Due to the weak nature of the additional reflections, it is likely that the twin component is small and therefore a twin refinement was not attempted.
Data collection: Kappa-CCD server software (Nonius, 1997); cell refinement: DENZO (Otwinowski & Minor, 1997); data reduction: DENZO; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 2000); software used to prepare material for publication: SHELXL97 and WORDPERFECT macro PRPKAPPA (Ferguson, 1999).
Fig. 1. The asymmetric unit of (I) showing the the atom-labelling scheme and the intramolecular hydrogen bonds. Displacement ellipsoids are drawn at the 30% probability level. |
C22H25N3O12 | Dx = 1.479 Mg m−3 |
Mr = 523.45 | Melting point: 270 K |
Monoclinic, C2 | Mo Kα radiation, λ = 0.71073 Å |
a = 30.594 (6) Å | Cell parameters from 2704 reflections |
b = 10.285 (2) Å | θ = 2.7–27.6° |
c = 7.474 (1) Å | µ = 0.12 mm−1 |
β = 91.07 (3)° | T = 150 K |
V = 2351.4 (7) Å3 | Plate, yellow |
Z = 4 | 0.20 × 0.20 × 0.08 mm |
F(000) = 1096 |
Kappa-CCD diffractometer | 2704 independent reflections |
Radiation source: fine-focus sealed X-ray tube | 1621 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.080 |
ϕ scans and ω scans with κ offsets | θmax = 27.6°, θmin = 2.7° |
Absorption correction: multi-scan (SORTAV; Blessing, 1995, 1997) | h = −32→39 |
Tmin = 0.976, Tmax = 0.991 | k = −12→13 |
7395 measured reflections | l = −8→8 |
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)] = 0.082 | H-atom parameters constrained |
wR(F2) = 0.226 | w = 1/[σ2(Fo2) + (0.1363P)2] where P = (Fo2 + 2Fc2)/3 |
S = 1.00 | (Δ/σ)max = 0.042 |
2704 reflections | Δρmax = 0.42 e Å−3 |
328 parameters | Δρmin = −0.35 e Å−3 |
1 restraint | Extinction correction: SHELXL, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.017 (4) |
C22H25N3O12 | V = 2351.4 (7) Å3 |
Mr = 523.45 | Z = 4 |
Monoclinic, C2 | Mo Kα radiation |
a = 30.594 (6) Å | µ = 0.12 mm−1 |
b = 10.285 (2) Å | T = 150 K |
c = 7.474 (1) Å | 0.20 × 0.20 × 0.08 mm |
β = 91.07 (3)° |
Kappa-CCD diffractometer | 2704 independent reflections |
Absorption correction: multi-scan (SORTAV; Blessing, 1995, 1997) | 1621 reflections with I > 2σ(I) |
Tmin = 0.976, Tmax = 0.991 | Rint = 0.080 |
7395 measured reflections |
R[F2 > 2σ(F2)] = 0.082 | 1 restraint |
wR(F2) = 0.226 | H-atom parameters constrained |
S = 1.00 | Δρmax = 0.42 e Å−3 |
2704 reflections | Δρmin = −0.35 e Å−3 |
328 parameters |
x | y | z | Uiso*/Ueq | ||
C1 | 0.0578 (2) | 0.1076 (8) | 0.1858 (9) | 0.0284 (16) | |
O1 | 0.09636 (17) | 0.1158 (6) | 0.1454 (7) | 0.0366 (13) | |
N2 | 0.0306 (2) | 0.2164 (6) | 0.2158 (10) | 0.0340 (16) | |
C21 | 0.0460 (3) | 0.3506 (8) | 0.2140 (15) | 0.049 (2) | |
C3 | −0.0121 (3) | 0.1794 (8) | 0.2525 (10) | 0.0303 (18) | |
O3 | −0.0416 (2) | 0.2536 (6) | 0.2796 (9) | 0.0432 (15) | |
C4 | 0.0414 (2) | −0.1373 (7) | 0.1990 (9) | 0.0265 (17) | |
N4 | 0.0815 (2) | −0.1803 (6) | 0.1565 (8) | 0.0282 (15) | |
C3A | 0.0308 (2) | −0.0058 (7) | 0.2104 (9) | 0.0219 (16) | |
N5 | 0.01009 (19) | −0.2281 (6) | 0.2283 (8) | 0.0244 (13) | |
C6 | −0.0302 (2) | −0.1892 (8) | 0.2616 (9) | 0.0275 (17) | |
O6 | −0.06086 (16) | −0.2820 (5) | 0.2887 (7) | 0.0283 (12) | |
C61 | −0.04713 (13) | −0.4137 (3) | 0.2950 (4) | 0.0319 (18) | |
C7 | −0.04437 (14) | −0.0593 (3) | 0.2727 (7) | 0.0289 (18) | |
C71 | −0.09176 (11) | −0.0283 (3) | 0.3025 (5) | 0.0292 (18) | |
O71 | −0.09743 (12) | 0.0415 (3) | 0.4479 (4) | 0.0356 (14) | |
C72 | −0.14325 (11) | 0.0777 (3) | 0.4784 (6) | 0.046 (2) | |
O72 | −0.12016 (19) | −0.0648 (6) | 0.2027 (8) | 0.0457 (16) | |
C7A | −0.0116 (2) | 0.0343 (7) | 0.2491 (9) | 0.0222 (15) | |
C1' | 0.0929 (2) | −0.3159 (7) | 0.1526 (9) | 0.0257 (16) | |
C2' | 0.1339 (2) | −0.3360 (7) | 0.0402 (10) | 0.0260 (17) | |
O2' | 0.13422 (16) | −0.4742 (5) | 0.0100 (7) | 0.0292 (12) | |
C21' | 0.1591 (3) | −0.5189 (9) | −0.1263 (10) | 0.0345 (19) | |
O21' | 0.18110 (19) | −0.4452 (6) | −0.2138 (7) | 0.0379 (14) | |
C22' | 0.1546 (3) | −0.6604 (9) | −0.1477 (15) | 0.050 (2) | |
C3' | 0.1763 (2) | −0.2994 (7) | 0.1464 (10) | 0.0258 (16) | |
O3' | 0.17665 (17) | −0.1566 (5) | 0.1448 (7) | 0.0329 (13) | |
C31' | 0.2116 (3) | −0.0984 (9) | 0.0711 (11) | 0.0380 (19) | |
O31' | 0.2419 (2) | −0.1581 (6) | 0.0122 (11) | 0.0568 (19) | |
C32' | 0.2081 (3) | 0.0454 (9) | 0.0775 (14) | 0.047 (2) | |
C4' | 0.1766 (2) | −0.3396 (7) | 0.3397 (10) | 0.0279 (17) | |
O4' | 0.18377 (17) | −0.4781 (5) | 0.3491 (7) | 0.0309 (13) | |
C41' | 0.2260 (3) | −0.5157 (9) | 0.3775 (11) | 0.036 (2) | |
O41' | 0.2556 (2) | −0.4404 (7) | 0.3852 (11) | 0.070 (2) | |
C42' | 0.2288 (4) | −0.6576 (10) | 0.3994 (15) | 0.056 (3) | |
C5' | 0.1334 (3) | −0.3146 (9) | 0.4250 (10) | 0.0341 (19) | |
O5' | 0.09722 (16) | −0.3686 (5) | 0.3253 (6) | 0.0275 (12) | |
H21A | 0.0570 | 0.3745 | 0.3336 | 0.073* | |
H21B | 0.0218 | 0.4084 | 0.1793 | 0.073* | |
H21C | 0.0696 | 0.3592 | 0.1278 | 0.073* | |
H4 | 0.1016 | −0.1228 | 0.1298 | 0.034* | |
H61A | −0.0386 | −0.4417 | 0.1752 | 0.048* | |
H61B | −0.0712 | −0.4682 | 0.3364 | 0.048* | |
H61C | −0.0221 | −0.4222 | 0.3778 | 0.048* | |
H72A | −0.1577 | 0.0974 | 0.3635 | 0.069* | |
H72B | −0.1442 | 0.1545 | 0.5558 | 0.069* | |
H72C | −0.1583 | 0.0054 | 0.5361 | 0.069* | |
H1' | 0.0683 | −0.3629 | 0.0907 | 0.031* | |
H2' | 0.1317 | −0.2872 | −0.0752 | 0.031* | |
H22A | 0.1275 | −0.6797 | −0.2147 | 0.075* | |
H22B | 0.1536 | −0.7015 | −0.0296 | 0.075* | |
H22C | 0.1796 | −0.6942 | −0.2131 | 0.075* | |
H3' | 0.2026 | −0.3343 | 0.0852 | 0.031* | |
H32A | 0.2133 | 0.0813 | −0.0417 | 0.071* | |
H32B | 0.2299 | 0.0799 | 0.1627 | 0.071* | |
H32C | 0.1787 | 0.0700 | 0.1157 | 0.071* | |
H4' | 0.2004 | −0.2927 | 0.4069 | 0.033* | |
H42A | 0.2574 | −0.6881 | 0.3600 | 0.084* | |
H42B | 0.2057 | −0.6992 | 0.3271 | 0.084* | |
H42C | 0.2251 | −0.6800 | 0.5256 | 0.084* | |
H5'A | 0.1339 | −0.3522 | 0.5470 | 0.041* | |
H5'B | 0.1291 | −0.2195 | 0.4366 | 0.041* |
U11 | U22 | U33 | U12 | U13 | U23 | |
C1 | 0.020 (4) | 0.026 (4) | 0.039 (4) | 0.001 (3) | 0.003 (3) | 0.002 (3) |
O1 | 0.020 (3) | 0.035 (3) | 0.055 (3) | −0.004 (2) | 0.005 (2) | 0.004 (3) |
N2 | 0.025 (4) | 0.017 (4) | 0.060 (4) | 0.000 (3) | 0.004 (3) | 0.003 (3) |
C21 | 0.029 (5) | 0.016 (4) | 0.101 (7) | −0.003 (4) | 0.014 (5) | −0.003 (4) |
C3 | 0.025 (4) | 0.023 (4) | 0.043 (5) | 0.002 (3) | 0.009 (3) | 0.005 (3) |
O3 | 0.029 (3) | 0.028 (3) | 0.074 (4) | 0.009 (3) | 0.012 (3) | −0.004 (3) |
C4 | 0.022 (4) | 0.025 (4) | 0.032 (4) | 0.001 (3) | −0.001 (3) | 0.003 (3) |
N4 | 0.015 (3) | 0.025 (4) | 0.045 (4) | 0.003 (3) | 0.009 (3) | 0.001 (3) |
C3A | 0.012 (4) | 0.020 (4) | 0.034 (4) | 0.004 (3) | 0.003 (3) | −0.001 (3) |
N5 | 0.011 (3) | 0.025 (3) | 0.037 (3) | 0.007 (3) | 0.003 (2) | 0.000 (2) |
C6 | 0.014 (4) | 0.040 (5) | 0.029 (4) | 0.002 (3) | 0.006 (3) | −0.002 (3) |
O6 | 0.019 (3) | 0.020 (3) | 0.046 (3) | 0.003 (2) | 0.003 (2) | 0.003 (2) |
C61 | 0.022 (4) | 0.021 (4) | 0.053 (5) | 0.004 (3) | −0.001 (3) | −0.005 (3) |
C7 | 0.020 (4) | 0.039 (5) | 0.028 (4) | 0.007 (3) | 0.002 (3) | −0.002 (3) |
C71 | 0.022 (4) | 0.028 (4) | 0.037 (4) | 0.005 (3) | 0.006 (3) | 0.004 (3) |
O71 | 0.020 (3) | 0.048 (4) | 0.040 (3) | 0.010 (3) | 0.004 (2) | −0.007 (3) |
C72 | 0.040 (5) | 0.045 (6) | 0.052 (5) | 0.022 (5) | 0.014 (4) | 0.003 (4) |
O72 | 0.022 (3) | 0.049 (4) | 0.066 (4) | 0.002 (3) | −0.005 (3) | −0.017 (3) |
C7A | 0.015 (4) | 0.021 (4) | 0.030 (4) | 0.004 (3) | −0.001 (3) | 0.003 (3) |
C1' | 0.021 (4) | 0.025 (4) | 0.032 (4) | 0.000 (3) | 0.005 (3) | −0.002 (3) |
C2' | 0.021 (4) | 0.019 (4) | 0.038 (4) | 0.003 (3) | 0.002 (3) | −0.004 (3) |
O2' | 0.025 (3) | 0.020 (3) | 0.043 (3) | −0.002 (2) | 0.006 (2) | −0.005 (2) |
C21' | 0.022 (4) | 0.042 (5) | 0.039 (4) | −0.005 (4) | 0.001 (3) | −0.002 (4) |
O21' | 0.035 (3) | 0.040 (3) | 0.039 (3) | 0.010 (3) | 0.009 (2) | 0.001 (2) |
C22' | 0.037 (5) | 0.027 (5) | 0.087 (7) | 0.004 (4) | 0.009 (5) | −0.017 (5) |
C3' | 0.014 (4) | 0.018 (4) | 0.045 (4) | 0.000 (3) | −0.003 (3) | 0.000 (3) |
O3' | 0.023 (3) | 0.018 (3) | 0.059 (3) | −0.003 (2) | 0.011 (2) | −0.003 (2) |
C31' | 0.029 (5) | 0.031 (5) | 0.055 (5) | −0.002 (4) | 0.010 (4) | 0.008 (4) |
O31' | 0.037 (4) | 0.027 (4) | 0.108 (5) | −0.005 (3) | 0.038 (4) | −0.005 (3) |
C32' | 0.032 (5) | 0.035 (5) | 0.075 (6) | −0.005 (4) | 0.012 (4) | −0.004 (4) |
C4' | 0.015 (4) | 0.025 (4) | 0.043 (4) | 0.000 (3) | −0.005 (3) | −0.006 (3) |
O4' | 0.025 (3) | 0.019 (3) | 0.048 (3) | 0.004 (2) | −0.003 (2) | −0.001 (2) |
C41' | 0.023 (5) | 0.041 (5) | 0.046 (5) | 0.013 (4) | −0.001 (3) | −0.001 (4) |
O41' | 0.028 (4) | 0.055 (5) | 0.125 (6) | 0.008 (3) | −0.008 (4) | −0.012 (4) |
C42' | 0.052 (7) | 0.032 (5) | 0.084 (7) | 0.019 (5) | 0.000 (5) | 0.009 (5) |
C5' | 0.029 (5) | 0.042 (5) | 0.031 (4) | 0.008 (4) | −0.005 (3) | −0.006 (3) |
O5' | 0.017 (3) | 0.027 (3) | 0.039 (3) | −0.006 (2) | 0.004 (2) | 0.003 (2) |
C1—O1 | 1.226 (9) | C1'—C2' | 1.538 (10) |
C1—N2 | 1.415 (10) | C1'—H1' | 1.0000 |
C1—C3A | 1.443 (11) | C2'—O2' | 1.439 (9) |
N2—C3 | 1.393 (10) | C2'—C3' | 1.553 (10) |
N2—C21 | 1.459 (11) | C2'—H2' | 1.0000 |
C21—H21A | 0.9800 | O2'—C21' | 1.364 (9) |
C21—H21B | 0.9800 | C21'—O21' | 1.212 (10) |
C21—H21C | 0.9800 | C21'—C22' | 1.470 (13) |
C3—O3 | 1.203 (10) | C22'—H22A | 0.9800 |
C3—C7A | 1.492 (11) | C22'—H22B | 0.9800 |
C4—N4 | 1.349 (9) | C22'—H22C | 0.9800 |
C4—N5 | 1.357 (10) | C3'—O3' | 1.468 (9) |
C4—C3A | 1.393 (11) | C3'—C4' | 1.503 (11) |
N4—C1' | 1.438 (10) | C3'—H3' | 1.0000 |
N4—H4 | 0.8800 | O3'—C31' | 1.351 (9) |
C3A—C7A | 1.396 (10) | C31'—O31' | 1.203 (10) |
N5—C6 | 1.323 (9) | C31'—C32' | 1.483 (13) |
C6—O6 | 1.357 (9) | C32'—H32A | 0.9800 |
C6—C7 | 1.408 (9) | C32'—H32B | 0.9800 |
O6—C61 | 1.419 (6) | C32'—H32C | 0.9800 |
C61—H61A | 0.9800 | C4'—O4' | 1.443 (9) |
C61—H61B | 0.9800 | C4'—C5' | 1.501 (11) |
C61—H61C | 0.9800 | C4'—H4' | 1.0000 |
C7—C7A | 1.404 (8) | O4'—C41' | 1.362 (9) |
C7—C71 | 1.505 (2) | C41'—O41' | 1.191 (11) |
C71—O72 | 1.195 (7) | C41'—C42' | 1.471 (13) |
C71—O71 | 1.3163 (18) | C42'—H42A | 0.9800 |
O71—C72 | 1.4723 (13) | C42'—H42B | 0.9800 |
C72—H72A | 0.9800 | C42'—H42C | 0.9800 |
C72—H72B | 0.9800 | C5'—O5' | 1.434 (9) |
C72—H72C | 0.9800 | C5'—H5'A | 0.9900 |
C1'—O5' | 1.403 (9) | C5'—H5'B | 0.9900 |
O1—C1—N2 | 123.7 (7) | C2'—C1'—H1' | 107.3 |
O1—C1—C3A | 130.0 (7) | O2'—C2'—C1' | 103.0 (6) |
N2—C1—C3A | 106.3 (6) | O2'—C2'—C3' | 108.2 (6) |
C3—N2—C1 | 111.8 (6) | C1'—C2'—C3' | 111.7 (6) |
C3—N2—C21 | 124.4 (7) | O2'—C2'—H2' | 111.2 |
C1—N2—C21 | 123.8 (7) | C1'—C2'—H2' | 111.2 |
N2—C21—H21A | 109.5 | C3'—C2'—H2' | 111.2 |
N2—C21—H21B | 109.5 | C21'—O2'—C2' | 117.1 (6) |
H21A—C21—H21B | 109.5 | O21'—C21'—O2' | 121.0 (8) |
N2—C21—H21C | 109.5 | O21'—C21'—C22' | 127.7 (8) |
H21A—C21—H21C | 109.5 | O2'—C21'—C22' | 111.2 (7) |
H21B—C21—H21C | 109.5 | C21'—C22'—H22A | 109.5 |
O3—C3—N2 | 124.7 (7) | C21'—C22'—H22B | 109.5 |
O3—C3—C7A | 130.2 (8) | H22A—C22'—H22B | 109.5 |
N2—C3—C7A | 105.1 (6) | C21'—C22'—H22C | 109.5 |
N4—C4—N5 | 117.4 (7) | H22A—C22'—H22C | 109.5 |
N4—C4—C3A | 123.1 (7) | H22B—C22'—H22C | 109.5 |
N5—C4—C3A | 119.5 (7) | O3'—C3'—C4' | 106.4 (6) |
C4—N4—C1' | 123.0 (6) | O3'—C3'—C2' | 104.2 (6) |
C4—N4—H4 | 118.5 | C4'—C3'—C2' | 114.5 (6) |
C1'—N4—H4 | 118.5 | O3'—C3'—H3' | 110.5 |
C4—C3A—C7A | 121.1 (7) | C4'—C3'—H3' | 110.5 |
C4—C3A—C1 | 130.0 (7) | C2'—C3'—H3' | 110.5 |
C7A—C3A—C1 | 108.8 (6) | C31'—O3'—C3' | 116.9 (6) |
C6—N5—C4 | 119.0 (6) | O31'—C31'—O3' | 122.9 (8) |
N5—C6—O6 | 117.7 (7) | O31'—C31'—C32' | 125.2 (8) |
N5—C6—C7 | 126.0 (7) | O3'—C31'—C32' | 111.8 (7) |
O6—C6—C7 | 116.3 (6) | C31'—C32'—H32A | 109.5 |
C6—O6—C61 | 118.1 (5) | C31'—C32'—H32B | 109.5 |
O6—C61—H61A | 109.5 | H32A—C32'—H32B | 109.5 |
O6—C61—H61B | 109.5 | C31'—C32'—H32C | 109.5 |
H61A—C61—H61B | 109.5 | H32A—C32'—H32C | 109.5 |
O6—C61—H61C | 109.5 | H32B—C32'—H32C | 109.5 |
H61A—C61—H61C | 109.5 | O4'—C4'—C3' | 108.5 (6) |
H61B—C61—H61C | 109.5 | O4'—C4'—C5' | 106.4 (6) |
C7A—C7—C6 | 114.9 (5) | C3'—C4'—C5' | 111.8 (6) |
C7A—C7—C71 | 124.5 (3) | O4'—C4'—H4' | 110.0 |
C6—C7—C71 | 120.6 (4) | C3'—C4'—H4' | 110.0 |
O72—C71—O71 | 125.5 (3) | C5'—C4'—H4' | 110.0 |
O72—C71—C7 | 122.2 (5) | C41'—O4'—C4' | 115.5 (6) |
O71—C71—C7 | 112.3 (3) | O41'—C41'—O4' | 122.7 (8) |
C71—O71—C72 | 113.97 (6) | O41'—C41'—C42' | 126.7 (8) |
O71—C72—H72A | 109.5 | O4'—C41'—C42' | 110.5 (8) |
O71—C72—H72B | 109.5 | C41'—C42'—H42A | 109.5 |
H72A—C72—H72B | 109.5 | C41'—C42'—H42B | 109.5 |
O71—C72—H72C | 109.5 | H42A—C42'—H42B | 109.5 |
H72A—C72—H72C | 109.5 | C41'—C42'—H42C | 109.5 |
H72B—C72—H72C | 109.5 | H42A—C42'—H42C | 109.5 |
C3A—C7A—C7 | 119.4 (6) | H42B—C42'—H42C | 109.5 |
C3A—C7A—C3 | 108.0 (6) | O5'—C5'—C4' | 112.9 (6) |
C7—C7A—C3 | 132.5 (6) | O5'—C5'—H5'A | 109.0 |
O5'—C1'—N4 | 112.0 (6) | C4'—C5'—H5'A | 109.0 |
O5'—C1'—C2' | 112.7 (6) | O5'—C5'—H5'B | 109.0 |
N4—C1'—C2' | 110.0 (6) | C4'—C5'—H5'B | 109.0 |
O5'—C1'—H1' | 107.3 | H5'A—C5'—H5'B | 107.8 |
N4—C1'—H1' | 107.3 | C1'—O5'—C5' | 112.8 (6) |
O1—C1—N2—C3 | 177.5 (7) | C71—C7—C7A—C3A | −175.7 (6) |
C3A—C1—N2—C3 | −1.8 (8) | C6—C7—C7A—C3 | −179.2 (8) |
O1—C1—N2—C21 | −4.3 (12) | C71—C7—C7A—C3 | 2.6 (11) |
C3A—C1—N2—C21 | 176.4 (8) | O3—C3—C7A—C3A | 179.7 (8) |
C1—N2—C3—O3 | −178.7 (8) | N2—C3—C7A—C3A | −0.2 (8) |
C21—N2—C3—O3 | 3.2 (13) | O3—C3—C7A—C7 | 1.2 (15) |
C1—N2—C3—C7A | 1.2 (8) | N2—C3—C7A—C7 | −178.7 (7) |
C21—N2—C3—C7A | −176.9 (8) | C4—N4—C1'—O5' | −73.3 (8) |
N5—C4—N4—C1' | −4.1 (10) | C4—N4—C1'—C2' | 160.5 (6) |
C3A—C4—N4—C1' | 177.1 (7) | O5'—C1'—C2'—O2' | 68.8 (7) |
N4—C4—C3A—C7A | 177.9 (6) | N4—C1'—C2'—O2' | −165.4 (5) |
N5—C4—C3A—C7A | −0.9 (10) | O5'—C1'—C2'—C3' | −47.2 (8) |
N4—C4—C3A—C1 | −1.4 (12) | N4—C1'—C2'—C3' | 78.6 (7) |
N5—C4—C3A—C1 | 179.8 (7) | C1'—C2'—O2'—C21' | 161.8 (6) |
O1—C1—C3A—C4 | 1.7 (13) | C3'—C2'—O2'—C21' | −79.7 (8) |
N2—C1—C3A—C4 | −179.1 (8) | C2'—O2'—C21'—O21' | 2.4 (10) |
O1—C1—C3A—C7A | −177.7 (7) | C2'—O2'—C21'—C22' | −177.1 (7) |
N2—C1—C3A—C7A | 1.5 (8) | O2'—C2'—C3'—O3' | 171.0 (5) |
N4—C4—N5—C6 | −176.7 (6) | C1'—C2'—C3'—O3' | −76.2 (7) |
C3A—C4—N5—C6 | 2.1 (10) | O2'—C2'—C3'—C4' | −73.1 (8) |
C4—N5—C6—O6 | 179.4 (6) | C1'—C2'—C3'—C4' | 39.6 (8) |
C4—N5—C6—C7 | −1.0 (10) | C4'—C3'—O3'—C31' | 117.5 (7) |
N5—C6—O6—C61 | 5.3 (8) | C2'—C3'—O3'—C31' | −121.1 (7) |
C7—C6—O6—C61 | −174.3 (6) | C3'—O3'—C31'—O31' | −1.7 (12) |
N5—C6—C7—C7A | −1.3 (10) | C3'—O3'—C31'—C32' | 180.0 (7) |
O6—C6—C7—C7A | 178.3 (6) | O3'—C3'—C4'—O4' | −170.4 (5) |
N5—C6—C7—C71 | 177.0 (6) | C2'—C3'—C4'—O4' | 75.1 (8) |
O6—C6—C7—C71 | −3.5 (9) | O3'—C3'—C4'—C5' | 72.6 (8) |
C7A—C7—C71—O72 | 120.0 (7) | C2'—C3'—C4'—C5' | −41.9 (9) |
C6—C7—C71—O72 | −58.1 (7) | C3'—C4'—O4'—C41' | 95.4 (7) |
C7A—C7—C71—O71 | −60.2 (6) | C5'—C4'—O4'—C41' | −144.2 (6) |
C6—C7—C71—O71 | 121.7 (5) | C4'—O4'—C41'—O41' | −3.6 (11) |
O72—C71—O71—C72 | −2.2 (5) | C4'—O4'—C41'—C42' | 175.3 (7) |
C7—C71—O71—C72 | 178.0 | O4'—C4'—C5'—O5' | −66.5 (8) |
C4—C3A—C7A—C7 | −1.5 (10) | C3'—C4'—C5'—O5' | 51.8 (9) |
C1—C3A—C7A—C7 | 177.9 (6) | N4—C1'—O5'—C5' | −66.1 (7) |
C4—C3A—C7A—C3 | 179.8 (7) | C2'—C1'—O5'—C5' | 58.6 (8) |
C1—C3A—C7A—C3 | −0.8 (8) | C4'—C5'—O5'—C1' | −61.4 (8) |
C6—C7—C7A—C3A | 2.5 (9) |
D—H···A | D—H | H···A | D···A | D—H···A |
N4—H4···O1 | 0.88 | 2.46 | 3.081 (7) | 128 |
N4—H4···O3′ | 0.88 | 2.32 | 2.924 (8) | 126 |
Experimental details
Crystal data | |
Chemical formula | C22H25N3O12 |
Mr | 523.45 |
Crystal system, space group | Monoclinic, C2 |
Temperature (K) | 150 |
a, b, c (Å) | 30.594 (6), 10.285 (2), 7.474 (1) |
β (°) | 91.07 (3) |
V (Å3) | 2351.4 (7) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.12 |
Crystal size (mm) | 0.20 × 0.20 × 0.08 |
Data collection | |
Diffractometer | Kappa-CCD diffractometer |
Absorption correction | Multi-scan (SORTAV; Blessing, 1995, 1997) |
Tmin, Tmax | 0.976, 0.991 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 7395, 2704, 1621 |
Rint | 0.080 |
(sin θ/λ)max (Å−1) | 0.651 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.082, 0.226, 1.00 |
No. of reflections | 2704 |
No. of parameters | 328 |
No. of restraints | 1 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.42, −0.35 |
Computer programs: Kappa-CCD server software (Nonius, 1997), DENZO (Otwinowski & Minor, 1997), DENZO, SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), PLATON (Spek, 2000), SHELXL97 and WORDPERFECT macro PRPKAPPA (Ferguson, 1999).
C4—N4 | 1.349 (9) | ||
N4—C4—N5 | 117.4 (7) | N4—C4—C3A | 123.1 (7) |
N4—C1'—C2'—O2' | −165.4 (5) | C2'—C3'—C4'—O4' | 75.1 (8) |
O5'—C1'—C2'—C3' | −47.2 (8) | O3'—C3'—C4'—C5' | 72.6 (8) |
N4—C1'—C2'—C3' | 78.6 (7) | C2'—C3'—C4'—C5' | −41.9 (9) |
O2'—C2'—C3'—O3' | 171.0 (5) | O4'—C4'—C5'—O5' | −66.5 (8) |
C1'—C2'—C3'—O3' | −76.2 (7) | C3'—C4'—C5'—O5' | 51.8 (9) |
O2'—C2'—C3'—C4' | −73.1 (8) | N4—C1'—O5'—C5' | −66.1 (7) |
C1'—C2'—C3'—C4' | 39.6 (8) | C2'—C1'—O5'—C5' | 58.6 (8) |
O3'—C3'—C4'—O4' | −170.4 (5) | C4'—C5'—O5'—C1' | −61.4 (8) |
D—H···A | D—H | H···A | D···A | D—H···A |
N4—H4···O1 | 0.88 | 2.46 | 3.081 (7) | 128 |
N4—H4···O3' | 0.88 | 2.32 | 2.924 (8) | 126 |
Our investigations of the use of hetero Diels-Alder reactions have resulted in the preparation of novel substituted nucleobases compounds containing acetylated xylopyranose substituents (Low et al., 1996; Cobo et al., 1996). In these compounds, all the substituent acetyl groups on the sugar rings were found to be equatorial. In the title compound (I), all acetyl groups are axial to the sugar ring, Figure 1. Relevant torsion angles are given in Table 1. \sch
It is well known that β-xylopyranosides tend to adopt a chair conformation with all four substituents occupying equatorial positions (4C1 conformation). This is assumed to be the most stable of all possible conformations due to the relative low energy of the 1-equatorial:3-equatorial steric interactions between the hydroxyls (or functionalized hydroxyls) in comparison with the strong 1-axial:3-axial interaction found in the alternative chair conformation, the 1C4 conformation (Schwarz, 1973). The conformational features found in our previous work with β-D-(per-O-acetyl)xylopyranosylamino derivatives, cited above, are in agreement with the above statement, the 4C1 conformation being found in the crystal structures. In solution (DMSO-d6) at 293 K, the 4C1 conformation was also found for these compounds, as shown by the large values of the vicinal (3J) coupling constants between the hydrogen atoms of the pyranose rings measured in their 1H-NMR spectra; values around 10 Hz for the 3JH,H coupling constants between 1'-2', 2'-3', 3'-4', and 4'-5'ax are indicative of the all equatorial 4C1 conformation (Widmalm, 1998).
It was thus surprising to find an all axial conformation in the crystal structure of the (I) because its structural formula closely resembles that of our previously studied xylopyranosides, and its 1H-NMR data in CDCl3 solution indicated absolutely, the preferred all equatorial 4C1 conformation (see Experimental). After inspection of the Cambridge Structural Database (CSD; Allen & Kennard, 1993), no similar all axial conformation was found for any of the 15 β-D-(per-O-acetyl)xylopyranosides listed therein, thus confirming the unique features of the crystal structure described here. In fact, in all 15 β-D-xylopyranose structures listed in the CSD there is only one occurrence of an axial acetyl group, in 2,3,4-tri-O-acetyl-β-D-xylopyranosyl azide, (ACXPAZ10; Luger and Gyorgydeak, 1993).
The principal structural factors that contribute to explain the preference for a 1C4 conformation in compound (I) are: (i) the existence of a hydrogen bond between the 4-amino nitrogen atom and the oxygen atom of the acetate group at C3'; this leads to the formation of a six-membered ring which fixes the pyranoside ring in the 1C4 conformation. The same hydrogen atom participates in another intramolecular hydrogen bond involving a carbonyl oxygen of the pyrrolo[3,4-c]pyridine moiety (Fig. 1), which helps to block the free rotation around the N—C4 single bond and confers additional rigidity to the structure. The degree of planarity of the atoms involved in the N9–H9···O1,O3' hydrogen-bonding system can be seen when the O1···H4···O3' angle of 102° is considered in conjunction with the others at H4 (Table 1). The angle sum at H9 is 356° showing that the system is very close to being planar. ii) The anomeric effect (Eliel & Wilen, 1994), which favours the axial position of anomeric electronegative substituents. It is worth noting the absence of a type of called the exo-anomeric effect which usually operates in glycosylamine derivatives (Tvaroska & Carver, 1996). This is thought to be supported by the better electron-donor ability of the exocyclic nitrogen than that of the pyranose ring oxygen, thus cancelling the possibility of the 'anomeric effect' and favouring the equatorial conformation for the anomeric substituents on the base of steric reasons. However, no such effect can be found in (I) because the lone pair of the 4-amino nitrogen atom (directly linked to the anomeric position) is not available to help any exo-anomeric effect due to its large delocalization along the heterocyclic electron deficient π system. This delocalization is confirmed by the planar geometry found for the nitrogen atom and the short distance of its bond to the heterocyclic C4 atom (shorter than a common single bond, Table 1).
Examination of the structure with PLATON (Spek, 2000) showed that there were no solvent-accessible voids in the crystal lattice.