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The unknown relative configurations in the title compound, C13H13N3O4, of the acetal carbon and of the quaternary carbon bearing the azide were determined by X-ray crystallographic analysis; the absolute configuration was defined by the use of 2-C-methyl-D-lyxonolactone as a starting material. There are two molecules in the asymmetric unit (Z' = 2).
Supporting information
![]() | Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807014560/lh2348sup1.cif |
![]() | Structure factor file (CIF format) https://doi.org/10.1107/S1600536807014560/lh23485sup2.hkl |
CCDC reference: 647274
Computing details top
Data collection: COLLECT (Nonius, 2001); cell refinement: DENZO/SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO/SCALEPACK; program(s) used to solve structure: SIR92 (Altomare et al., 1994); program(s) used to refine structure: CRYSTALS (Betteridge et al., 2003); molecular graphics: CAMERON (Watkin et al., 1996); software used to prepare material for publication: CRYSTALS.
2-Azido-(R)-3,5-O-benzylidene-2-deoxy-2-C-methyl-D-xylono-
1,4-lactone top
Crystal data top
C13H13N3O4 | Dx = 1.362 Mg m−3 |
Mr = 275.26 | Mo Kα radiation, λ = 0.71073 Å |
Orthorhombic, P212121 | Cell parameters from 3025 reflections |
a = 9.7507 (2) Å | θ = 5–27° |
b = 10.4263 (2) Å | µ = 0.10 mm−1 |
c = 26.4090 (5) Å | T = 150 K |
V = 2684.84 (9) Å3 | Plate, colourless |
Z = 8 | 0.40 × 0.40 × 0.10 mm |
F(000) = 1152 |
Data collection top
Nonius KappaCCD diffractometer | 2414 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.055 |
ω scans | θmax = 27.6°, θmin = 5.4° |
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997) | h = −12→12 |
Tmin = 0.69, Tmax = 0.99 | k = −13→13 |
12730 measured reflections | l = −33→33 |
3360 independent reflections |
Refinement top
Refinement on F2 | Hydrogen site location: inferred from neighbouring sites |
Least-squares matrix: full | H-atom parameters constrained |
R[F2 > 2σ(F2)] = 0.044 | w = 1/[σ2(F2) + (0.05P)2 + 0.85P], where P = [max(Fo2,0) + 2Fc2]/3 |
wR(F2) = 0.119 | (Δ/σ)max = 0.004 |
S = 0.87 | Δρmax = 0.21 e Å−3 |
3360 reflections | Δρmin = −0.18 e Å−3 |
362 parameters | Extinction correction: Larson (1970), Equation 22 |
0 restraints | Extinction coefficient: 3314.893 |
Primary atom site location: structure-invariant direct methods |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
x | y | z | Uiso*/Ueq | ||
C1 | 0.5922 (3) | 0.8368 (3) | 0.56501 (11) | 0.0587 | |
C2 | 0.5707 (3) | 0.9098 (3) | 0.61377 (10) | 0.0561 | |
C3 | 0.6465 (4) | 0.8273 (3) | 0.65218 (12) | 0.0678 | |
O4 | 0.7600 (2) | 0.7754 (2) | 0.62420 (11) | 0.0772 | |
C5 | 0.7332 (4) | 0.7793 (3) | 0.57437 (16) | 0.0730 | |
O6 | 0.8099 (3) | 0.7366 (3) | 0.54353 (13) | 0.1168 | |
C7 | 0.6988 (4) | 0.9014 (4) | 0.69740 (13) | 0.0858 | |
O8 | 0.7623 (3) | 1.0189 (2) | 0.68232 (9) | 0.0773 | |
C9 | 0.6731 (3) | 1.0924 (3) | 0.65274 (11) | 0.0657 | |
O10 | 0.6413 (2) | 1.02832 (17) | 0.60689 (7) | 0.0587 | |
C11 | 0.7403 (3) | 1.2162 (3) | 0.63730 (11) | 0.0605 | |
C12 | 0.8701 (4) | 1.2159 (3) | 0.61683 (14) | 0.0773 | |
C13 | 0.9269 (4) | 1.3299 (4) | 0.59981 (16) | 0.0889 | |
C14 | 0.8560 (5) | 1.4413 (3) | 0.60341 (14) | 0.0820 | |
C15 | 0.7279 (5) | 1.4435 (3) | 0.62384 (14) | 0.0815 | |
C16 | 0.6693 (4) | 1.3296 (3) | 0.64103 (13) | 0.0730 | |
N17 | 0.4943 (3) | 0.7264 (3) | 0.56741 (11) | 0.0746 | |
N18 | 0.5080 (3) | 0.6487 (3) | 0.53294 (12) | 0.0788 | |
N19 | 0.5098 (5) | 0.5715 (3) | 0.50353 (16) | 0.1136 | |
C20 | 0.5793 (4) | 0.9114 (3) | 0.51646 (12) | 0.0809 | |
C101 | 0.6629 (3) | 0.7650 (4) | 0.32312 (11) | 0.0695 | |
C102 | 0.6434 (3) | 0.6251 (3) | 0.30903 (11) | 0.0644 | |
C103 | 0.7301 (3) | 0.6110 (3) | 0.26204 (11) | 0.0691 | |
O104 | 0.8458 (2) | 0.6983 (2) | 0.27092 (8) | 0.0741 | |
C105 | 0.8083 (3) | 0.7894 (4) | 0.30301 (12) | 0.0685 | |
O106 | 0.8806 (3) | 0.8814 (3) | 0.31213 (10) | 0.0875 | |
C107 | 0.7839 (4) | 0.4766 (3) | 0.25344 (12) | 0.0770 | |
O108 | 0.8227 (2) | 0.4155 (2) | 0.29978 (8) | 0.0747 | |
C109 | 0.7161 (3) | 0.4192 (3) | 0.33539 (12) | 0.0691 | |
O110 | 0.6941 (2) | 0.5511 (2) | 0.34969 (7) | 0.0664 | |
C111 | 0.7527 (3) | 0.3440 (3) | 0.38141 (13) | 0.0695 | |
C116 | 0.8045 (4) | 0.2209 (4) | 0.37538 (16) | 0.0844 | |
C115 | 0.8351 (5) | 0.1477 (4) | 0.41721 (19) | 0.1012 | |
C114 | 0.8173 (5) | 0.1959 (4) | 0.46476 (17) | 0.0989 | |
C113 | 0.7642 (6) | 0.3152 (4) | 0.47084 (16) | 0.1051 | |
C112 | 0.7319 (5) | 0.3903 (4) | 0.42933 (14) | 0.0906 | |
N117 | 0.5679 (3) | 0.8365 (4) | 0.28986 (11) | 0.0815 | |
N118 | 0.5814 (3) | 0.9550 (4) | 0.29177 (10) | 0.0796 | |
N119 | 0.5821 (4) | 1.0637 (4) | 0.29062 (12) | 0.1016 | |
C120 | 0.6465 (4) | 0.8011 (4) | 0.37851 (12) | 0.0776 | |
H21 | 0.4741 | 0.9199 | 0.6221 | 0.0658* | |
H31 | 0.5940 | 0.7550 | 0.6648 | 0.0809* | |
H71 | 0.7706 | 0.8514 | 0.7152 | 0.1037* | |
H72 | 0.6182 | 0.9217 | 0.7198 | 0.1045* | |
H91 | 0.5842 | 1.1104 | 0.6707 | 0.0789* | |
H121 | 0.9171 | 1.1383 | 0.6143 | 0.0935* | |
H131 | 1.0154 | 1.3271 | 0.5855 | 0.1069* | |
H141 | 0.8969 | 1.5187 | 0.5918 | 0.0985* | |
H151 | 0.6787 | 1.5203 | 0.6261 | 0.0978* | |
H161 | 0.5800 | 1.3332 | 0.6553 | 0.0884* | |
H201 | 0.6083 | 0.8589 | 0.4879 | 0.1217* | |
H202 | 0.6380 | 0.9880 | 0.5178 | 0.1212* | |
H203 | 0.4848 | 0.9373 | 0.5112 | 0.1222* | |
H1021 | 0.5516 | 0.6024 | 0.3024 | 0.0768* | |
H1031 | 0.6771 | 0.6374 | 0.2322 | 0.0815* | |
H1071 | 0.8613 | 0.4820 | 0.2307 | 0.0908* | |
H1072 | 0.7100 | 0.4193 | 0.2379 | 0.0914* | |
H1091 | 0.6333 | 0.3851 | 0.3183 | 0.0818* | |
H1161 | 0.8174 | 0.1913 | 0.3422 | 0.1018* | |
H1151 | 0.8672 | 0.0631 | 0.4129 | 0.1223* | |
H1141 | 0.8405 | 0.1462 | 0.4930 | 0.1191* | |
H1131 | 0.7493 | 0.3474 | 0.5033 | 0.1267* | |
H1121 | 0.6969 | 0.4710 | 0.4341 | 0.1089* | |
H1201 | 0.6577 | 0.8914 | 0.3832 | 0.1147* | |
H1202 | 0.7147 | 0.7560 | 0.3974 | 0.1157* | |
H1203 | 0.5552 | 0.7754 | 0.3888 | 0.1147* |
Atomic displacement parameters (Å2) top
U11 | U22 | U33 | U12 | U13 | U23 | |
C1 | 0.0539 (15) | 0.0523 (14) | 0.0699 (17) | −0.0124 (13) | 0.0065 (14) | 0.0002 (13) |
C2 | 0.0420 (12) | 0.0570 (14) | 0.0692 (16) | −0.0023 (12) | −0.0017 (13) | 0.0013 (13) |
C3 | 0.0609 (18) | 0.0652 (17) | 0.077 (2) | −0.0134 (17) | −0.0018 (17) | 0.0156 (15) |
O4 | 0.0562 (12) | 0.0658 (12) | 0.1094 (19) | 0.0086 (11) | −0.0037 (13) | 0.0168 (12) |
C5 | 0.0623 (18) | 0.0553 (16) | 0.102 (3) | −0.0013 (16) | 0.020 (2) | 0.0039 (17) |
O6 | 0.097 (2) | 0.104 (2) | 0.149 (2) | 0.0185 (18) | 0.052 (2) | −0.0073 (19) |
C7 | 0.098 (3) | 0.084 (2) | 0.076 (2) | −0.031 (2) | −0.0217 (19) | 0.0187 (18) |
O8 | 0.0803 (14) | 0.0738 (13) | 0.0777 (13) | −0.0157 (12) | −0.0247 (12) | 0.0142 (11) |
C9 | 0.0596 (17) | 0.0708 (17) | 0.0667 (17) | −0.0052 (16) | −0.0066 (15) | −0.0061 (15) |
O10 | 0.0578 (10) | 0.0500 (9) | 0.0684 (11) | −0.0051 (9) | −0.0075 (10) | 0.0019 (8) |
C11 | 0.0613 (18) | 0.0578 (15) | 0.0624 (17) | −0.0065 (15) | −0.0111 (14) | −0.0018 (13) |
C12 | 0.0623 (19) | 0.0655 (17) | 0.104 (2) | 0.0016 (16) | −0.0079 (19) | 0.0046 (18) |
C13 | 0.067 (2) | 0.083 (2) | 0.116 (3) | −0.021 (2) | −0.010 (2) | 0.017 (2) |
C14 | 0.094 (3) | 0.0656 (19) | 0.087 (2) | −0.017 (2) | −0.026 (2) | 0.0122 (17) |
C15 | 0.101 (3) | 0.0592 (17) | 0.084 (2) | 0.0007 (19) | −0.014 (2) | 0.0024 (16) |
C16 | 0.076 (2) | 0.0693 (18) | 0.0735 (19) | 0.0037 (18) | −0.0024 (18) | −0.0053 (15) |
N17 | 0.0781 (17) | 0.0651 (15) | 0.0807 (17) | −0.0233 (14) | 0.0127 (15) | −0.0063 (14) |
N18 | 0.090 (2) | 0.0533 (14) | 0.093 (2) | −0.0140 (15) | 0.0023 (18) | −0.0025 (16) |
N19 | 0.144 (3) | 0.0672 (19) | 0.130 (3) | −0.013 (2) | 0.005 (3) | −0.019 (2) |
C20 | 0.100 (3) | 0.077 (2) | 0.0656 (19) | −0.022 (2) | −0.0037 (18) | 0.0055 (16) |
C101 | 0.0459 (16) | 0.104 (2) | 0.0589 (16) | 0.0114 (17) | −0.0042 (14) | 0.0096 (17) |
C102 | 0.0477 (15) | 0.0838 (19) | 0.0617 (16) | 0.0024 (15) | −0.0056 (13) | 0.0055 (15) |
C103 | 0.0575 (17) | 0.092 (2) | 0.0577 (16) | −0.0016 (18) | −0.0023 (14) | 0.0029 (16) |
O104 | 0.0558 (12) | 0.0948 (15) | 0.0717 (13) | 0.0013 (12) | 0.0085 (11) | 0.0000 (12) |
C105 | 0.0526 (17) | 0.083 (2) | 0.0698 (19) | 0.0054 (17) | −0.0064 (15) | 0.0062 (18) |
O106 | 0.0687 (14) | 0.0952 (16) | 0.0985 (17) | −0.0011 (15) | −0.0034 (13) | 0.0035 (14) |
C107 | 0.071 (2) | 0.097 (2) | 0.0630 (19) | 0.006 (2) | −0.0007 (16) | −0.0054 (17) |
O108 | 0.0656 (13) | 0.0924 (15) | 0.0661 (12) | 0.0081 (12) | 0.0058 (11) | −0.0002 (11) |
C109 | 0.0541 (16) | 0.079 (2) | 0.074 (2) | −0.0014 (16) | −0.0027 (15) | −0.0059 (16) |
O110 | 0.0572 (12) | 0.0826 (13) | 0.0595 (11) | 0.0014 (11) | −0.0013 (10) | 0.0037 (10) |
C111 | 0.0553 (16) | 0.0799 (19) | 0.073 (2) | −0.0131 (16) | −0.0024 (16) | 0.0054 (16) |
C116 | 0.074 (2) | 0.088 (2) | 0.091 (2) | 0.007 (2) | 0.001 (2) | 0.001 (2) |
C115 | 0.090 (3) | 0.096 (3) | 0.119 (3) | 0.009 (3) | 0.003 (3) | 0.018 (3) |
C114 | 0.106 (3) | 0.094 (3) | 0.097 (3) | 0.000 (3) | −0.007 (3) | 0.021 (2) |
C113 | 0.139 (4) | 0.098 (3) | 0.078 (2) | −0.006 (3) | −0.007 (3) | 0.008 (2) |
C112 | 0.115 (3) | 0.084 (2) | 0.073 (2) | 0.003 (2) | −0.003 (2) | 0.0062 (19) |
N117 | 0.0663 (17) | 0.099 (2) | 0.0792 (19) | 0.0223 (18) | −0.0138 (15) | 0.0123 (16) |
N118 | 0.0583 (16) | 0.117 (3) | 0.0630 (17) | 0.0228 (19) | 0.0004 (13) | 0.0160 (17) |
N119 | 0.105 (3) | 0.113 (3) | 0.087 (2) | 0.043 (2) | 0.0005 (19) | 0.018 (2) |
C120 | 0.0705 (19) | 0.096 (2) | 0.0661 (18) | 0.018 (2) | 0.0003 (17) | 0.0014 (17) |
Geometric parameters (Å, º) top
C1—C2 | 1.510 (4) | C101—C102 | 1.517 (5) |
C1—C5 | 1.520 (5) | C101—C105 | 1.535 (5) |
C1—N17 | 1.497 (4) | C101—N117 | 1.478 (4) |
C1—C20 | 1.505 (4) | C101—C120 | 1.519 (4) |
C2—C3 | 1.521 (4) | C102—C103 | 1.509 (4) |
C2—O10 | 1.427 (3) | C102—O110 | 1.412 (3) |
C2—H21 | 0.973 | C102—H1021 | 0.942 |
C3—O4 | 1.437 (4) | C103—O104 | 1.468 (4) |
C3—C7 | 1.511 (5) | C103—C107 | 1.513 (5) |
C3—H31 | 0.970 | C103—H1031 | 0.981 |
O4—C5 | 1.342 (5) | O104—C105 | 1.324 (4) |
C5—O6 | 1.192 (4) | C105—O106 | 1.214 (4) |
C7—O8 | 1.429 (4) | C107—O108 | 1.430 (4) |
C7—H71 | 0.992 | C107—H1071 | 0.965 |
C7—H72 | 1.006 | C107—H1072 | 1.023 |
O8—C9 | 1.398 (4) | O108—C109 | 1.403 (4) |
C9—O10 | 1.418 (3) | C109—O110 | 1.442 (4) |
C9—C11 | 1.504 (4) | C109—C111 | 1.490 (5) |
C9—H91 | 1.005 | C109—H1091 | 0.991 |
C11—C12 | 1.376 (5) | C111—C116 | 1.389 (5) |
C11—C16 | 1.374 (4) | C111—C112 | 1.369 (5) |
C12—C13 | 1.386 (5) | C116—C115 | 1.375 (5) |
C12—H121 | 0.932 | C116—H1161 | 0.938 |
C13—C14 | 1.355 (5) | C115—C114 | 1.364 (6) |
C13—H131 | 0.943 | C115—H1151 | 0.943 |
C14—C15 | 1.361 (6) | C114—C113 | 1.356 (6) |
C14—H141 | 0.951 | C114—H1141 | 0.937 |
C15—C16 | 1.393 (5) | C113—C112 | 1.384 (5) |
C15—H151 | 0.936 | C113—H1131 | 0.931 |
C16—H161 | 0.950 | C112—H1121 | 0.916 |
N17—N18 | 1.226 (4) | N117—N118 | 1.244 (5) |
N18—N19 | 1.118 (4) | N118—N119 | 1.133 (5) |
C20—H201 | 0.975 | C120—H1201 | 0.956 |
C20—H202 | 0.983 | C120—H1202 | 0.955 |
C20—H203 | 0.970 | C120—H1203 | 0.968 |
C2—C1—C5 | 100.7 (3) | C102—C101—C105 | 101.0 (3) |
C2—C1—N17 | 105.2 (2) | C102—C101—N117 | 105.1 (3) |
C5—C1—N17 | 105.5 (2) | C105—C101—N117 | 106.8 (3) |
C2—C1—C20 | 117.1 (2) | C102—C101—C120 | 117.5 (3) |
C5—C1—C20 | 114.7 (3) | C105—C101—C120 | 112.9 (3) |
N17—C1—C20 | 112.3 (3) | N117—C101—C120 | 112.4 (3) |
C1—C2—C3 | 102.5 (2) | C101—C102—C103 | 103.0 (3) |
C1—C2—O10 | 105.1 (2) | C101—C102—O110 | 107.1 (2) |
C3—C2—O10 | 109.9 (2) | C103—C102—O110 | 112.1 (2) |
C1—C2—H21 | 112.5 | C101—C102—H1021 | 114.0 |
C3—C2—H21 | 112.3 | C103—C102—H1021 | 110.8 |
O10—C2—H21 | 113.7 | O110—C102—H1021 | 109.7 |
C2—C3—O4 | 104.1 (2) | C102—C103—O104 | 103.8 (2) |
C2—C3—C7 | 113.7 (3) | C102—C103—C107 | 114.1 (3) |
O4—C3—C7 | 109.8 (3) | O104—C103—C107 | 109.4 (3) |
C2—C3—H31 | 114.4 | C102—C103—H1031 | 109.7 |
O4—C3—H31 | 106.9 | O104—C103—H1031 | 111.0 |
C7—C3—H31 | 107.7 | C107—C103—H1031 | 108.8 |
C3—O4—C5 | 110.0 (3) | C103—O104—C105 | 109.6 (2) |
C1—C5—O4 | 110.4 (3) | C101—C105—O104 | 110.9 (3) |
C1—C5—O6 | 127.1 (4) | C101—C105—O106 | 126.8 (3) |
O4—C5—O6 | 122.4 (4) | O104—C105—O106 | 122.2 (3) |
C3—C7—O8 | 111.4 (3) | C103—C107—O108 | 112.0 (3) |
C3—C7—H71 | 110.1 | C103—C107—H1071 | 108.0 |
O8—C7—H71 | 106.1 | O108—C107—H1071 | 110.6 |
C3—C7—H72 | 108.0 | C103—C107—H1072 | 110.9 |
O8—C7—H72 | 108.8 | O108—C107—H1072 | 105.7 |
H71—C7—H72 | 112.5 | H1071—C107—H1072 | 109.6 |
C7—O8—C9 | 110.9 (3) | C107—O108—C109 | 111.4 (2) |
O8—C9—O10 | 110.8 (2) | O108—C109—O110 | 108.2 (3) |
O8—C9—C11 | 110.6 (2) | O108—C109—C111 | 110.8 (3) |
O10—C9—C11 | 105.6 (2) | O110—C109—C111 | 108.9 (3) |
O8—C9—H91 | 112.0 | O108—C109—H1091 | 106.8 |
O10—C9—H91 | 107.5 | O110—C109—H1091 | 109.9 |
C11—C9—H91 | 110.1 | C111—C109—H1091 | 112.2 |
C2—O10—C9 | 113.9 (2) | C109—O110—C102 | 112.0 (2) |
C9—C11—C12 | 120.3 (3) | C109—C111—C116 | 118.7 (3) |
C9—C11—C16 | 120.0 (3) | C109—C111—C112 | 122.2 (3) |
C12—C11—C16 | 119.6 (3) | C116—C111—C112 | 119.1 (3) |
C11—C12—C13 | 119.5 (3) | C111—C116—C115 | 120.0 (4) |
C11—C12—H121 | 118.8 | C111—C116—H1161 | 117.3 |
C13—C12—H121 | 121.7 | C115—C116—H1161 | 122.7 |
C12—C13—C14 | 120.6 (3) | C116—C115—C114 | 120.5 (4) |
C12—C13—H131 | 118.0 | C116—C115—H1151 | 119.6 |
C14—C13—H131 | 121.4 | C114—C115—H1151 | 119.9 |
C13—C14—C15 | 120.7 (3) | C115—C114—C113 | 119.7 (4) |
C13—C14—H141 | 119.4 | C115—C114—H1141 | 119.9 |
C15—C14—H141 | 119.9 | C113—C114—H1141 | 120.3 |
C14—C15—C16 | 119.4 (3) | C114—C113—C112 | 120.8 (4) |
C14—C15—H151 | 120.7 | C114—C113—H1131 | 120.0 |
C16—C15—H151 | 119.9 | C112—C113—H1131 | 119.2 |
C15—C16—C11 | 120.2 (3) | C113—C112—C111 | 119.9 (4) |
C15—C16—H161 | 118.1 | C113—C112—H1121 | 119.8 |
C11—C16—H161 | 121.6 | C111—C112—H1121 | 120.3 |
C1—N17—N18 | 114.1 (3) | C101—N117—N118 | 114.3 (3) |
N17—N18—N19 | 173.1 (4) | N117—N118—N119 | 173.1 (4) |
C1—C20—H201 | 110.2 | C101—C120—H1201 | 111.0 |
C1—C20—H202 | 109.9 | C101—C120—H1202 | 108.0 |
H201—C20—H202 | 108.4 | H1201—C120—H1202 | 109.7 |
C1—C20—H203 | 110.2 | C101—C120—H1203 | 107.4 |
H201—C20—H203 | 108.7 | H1201—C120—H1203 | 109.9 |
H202—C20—H203 | 109.4 | H1202—C120—H1203 | 111.0 |