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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

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807014560/lh2348sup1.cif
Contains datablocks 5, global

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536807014560/lh23485sup2.hkl
Contains datablock 5

CCDC reference: 647274

Key indicators

  • Single-crystal X-ray study
  • T = 150 K
  • Mean [sigma](C-C) = 0.005 Å
  • R factor = 0.044
  • wR factor = 0.119
  • Data-to-parameter ratio = 9.3

checkCIF/PLATON results

No syntax errors found



Alert level B ABSTM02_ALERT_3_B The ratio of expected to reported Tmax/Tmin(RR') is < 0.75 Tmin and Tmax reported: 0.690 0.990 Tmin(prime) and Tmax expected: 0.959 0.990 RR(prime) = 0.720 Please check that your absorption correction is appropriate. PLAT061_ALERT_3_B Tmax/Tmin Range Test RR' too Large ............. 0.72 PLAT230_ALERT_2_B Hirshfeld Test Diff for C101 - C102 .. 9.44 su
Alert level C PLAT029_ALERT_3_C _diffrn_measured_fraction_theta_full Low ....... 0.96 PLAT125_ALERT_4_C No _symmetry_space_group_name_Hall Given ....... ? PLAT230_ALERT_2_C Hirshfeld Test Diff for N117 - N118 .. 6.49 su PLAT340_ALERT_3_C Low Bond Precision on C-C bonds (x 1000) Ang ... 5 PLAT720_ALERT_4_C Number of Unusual/Non-Standard Label(s) ........ 13
Alert level G REFLT03_ALERT_4_G Please check that the estimate of the number of Friedel pairs is correct. If it is not, please give the correct count in the _publ_section_exptl_refinement section of the submitted CIF. From the CIF: _diffrn_reflns_theta_max 27.56 From the CIF: _reflns_number_total 3360 Count of symmetry unique reflns 3507 Completeness (_total/calc) 95.81% TEST3: Check Friedels for noncentro structure Estimate of Friedel pairs measured 0 Fraction of Friedel pairs measured 0.000 Are heavy atom types Z>Si present no PLAT791_ALERT_1_G Confirm the Absolute Configuration of C1 = . S PLAT791_ALERT_1_G Confirm the Absolute Configuration of C2 = . S PLAT791_ALERT_1_G Confirm the Absolute Configuration of C3 = . S PLAT791_ALERT_1_G Confirm the Absolute Configuration of C9 = . R PLAT791_ALERT_1_G Confirm the Absolute Configuration of C101 = . S PLAT791_ALERT_1_G Confirm the Absolute Configuration of C102 = . S PLAT791_ALERT_1_G Confirm the Absolute Configuration of C103 = . S PLAT791_ALERT_1_G Confirm the Absolute Configuration of C109 = . R
0 ALERT level A = In general: serious problem 3 ALERT level B = Potentially serious problem 5 ALERT level C = Check and explain 9 ALERT level G = General alerts; check 8 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 2 ALERT type 2 Indicator that the structure model may be wrong or deficient 4 ALERT type 3 Indicator that the structure quality may be low 3 ALERT type 4 Improvement, methodology, query or suggestion 0 ALERT type 5 Informative message, check

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
C13H13N3O4Dx = 1.362 Mg m3
Mr = 275.26Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, P212121Cell parameters from 3025 reflections
a = 9.7507 (2) Åθ = 5–27°
b = 10.4263 (2) ŵ = 0.10 mm1
c = 26.4090 (5) ÅT = 150 K
V = 2684.84 (9) Å3Plate, colourless
Z = 80.40 × 0.40 × 0.10 mm
F(000) = 1152
Data collection top
Nonius KappaCCD
diffractometer
2414 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.055
ω scansθmax = 27.6°, θmin = 5.4°
Absorption correction: multi-scan
(DENZO/SCALEPACK; Otwinowski & Minor, 1997)
h = 1212
Tmin = 0.69, Tmax = 0.99k = 1313
12730 measured reflectionsl = 3333
3360 independent reflections
Refinement top
Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullH-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 = 0.87Δρmax = 0.21 e Å3
3360 reflectionsΔρmin = 0.18 e Å3
362 parametersExtinction correction: Larson (1970), Equation 22
0 restraintsExtinction coefficient: 3314.893
Primary atom site location: structure-invariant direct methods
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
C10.5922 (3)0.8368 (3)0.56501 (11)0.0587
C20.5707 (3)0.9098 (3)0.61377 (10)0.0561
C30.6465 (4)0.8273 (3)0.65218 (12)0.0678
O40.7600 (2)0.7754 (2)0.62420 (11)0.0772
C50.7332 (4)0.7793 (3)0.57437 (16)0.0730
O60.8099 (3)0.7366 (3)0.54353 (13)0.1168
C70.6988 (4)0.9014 (4)0.69740 (13)0.0858
O80.7623 (3)1.0189 (2)0.68232 (9)0.0773
C90.6731 (3)1.0924 (3)0.65274 (11)0.0657
O100.6413 (2)1.02832 (17)0.60689 (7)0.0587
C110.7403 (3)1.2162 (3)0.63730 (11)0.0605
C120.8701 (4)1.2159 (3)0.61683 (14)0.0773
C130.9269 (4)1.3299 (4)0.59981 (16)0.0889
C140.8560 (5)1.4413 (3)0.60341 (14)0.0820
C150.7279 (5)1.4435 (3)0.62384 (14)0.0815
C160.6693 (4)1.3296 (3)0.64103 (13)0.0730
N170.4943 (3)0.7264 (3)0.56741 (11)0.0746
N180.5080 (3)0.6487 (3)0.53294 (12)0.0788
N190.5098 (5)0.5715 (3)0.50353 (16)0.1136
C200.5793 (4)0.9114 (3)0.51646 (12)0.0809
C1010.6629 (3)0.7650 (4)0.32312 (11)0.0695
C1020.6434 (3)0.6251 (3)0.30903 (11)0.0644
C1030.7301 (3)0.6110 (3)0.26204 (11)0.0691
O1040.8458 (2)0.6983 (2)0.27092 (8)0.0741
C1050.8083 (3)0.7894 (4)0.30301 (12)0.0685
O1060.8806 (3)0.8814 (3)0.31213 (10)0.0875
C1070.7839 (4)0.4766 (3)0.25344 (12)0.0770
O1080.8227 (2)0.4155 (2)0.29978 (8)0.0747
C1090.7161 (3)0.4192 (3)0.33539 (12)0.0691
O1100.6941 (2)0.5511 (2)0.34969 (7)0.0664
C1110.7527 (3)0.3440 (3)0.38141 (13)0.0695
C1160.8045 (4)0.2209 (4)0.37538 (16)0.0844
C1150.8351 (5)0.1477 (4)0.41721 (19)0.1012
C1140.8173 (5)0.1959 (4)0.46476 (17)0.0989
C1130.7642 (6)0.3152 (4)0.47084 (16)0.1051
C1120.7319 (5)0.3903 (4)0.42933 (14)0.0906
N1170.5679 (3)0.8365 (4)0.28986 (11)0.0815
N1180.5814 (3)0.9550 (4)0.29177 (10)0.0796
N1190.5821 (4)1.0637 (4)0.29062 (12)0.1016
C1200.6465 (4)0.8011 (4)0.37851 (12)0.0776
H210.47410.91990.62210.0658*
H310.59400.75500.66480.0809*
H710.77060.85140.71520.1037*
H720.61820.92170.71980.1045*
H910.58421.11040.67070.0789*
H1210.91711.13830.61430.0935*
H1311.01541.32710.58550.1069*
H1410.89691.51870.59180.0985*
H1510.67871.52030.62610.0978*
H1610.58001.33320.65530.0884*
H2010.60830.85890.48790.1217*
H2020.63800.98800.51780.1212*
H2030.48480.93730.51120.1222*
H10210.55160.60240.30240.0768*
H10310.67710.63740.23220.0815*
H10710.86130.48200.23070.0908*
H10720.71000.41930.23790.0914*
H10910.63330.38510.31830.0818*
H11610.81740.19130.34220.1018*
H11510.86720.06310.41290.1223*
H11410.84050.14620.49300.1191*
H11310.74930.34740.50330.1267*
H11210.69690.47100.43410.1089*
H12010.65770.89140.38320.1147*
H12020.71470.75600.39740.1157*
H12030.55520.77540.38880.1147*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0539 (15)0.0523 (14)0.0699 (17)0.0124 (13)0.0065 (14)0.0002 (13)
C20.0420 (12)0.0570 (14)0.0692 (16)0.0023 (12)0.0017 (13)0.0013 (13)
C30.0609 (18)0.0652 (17)0.077 (2)0.0134 (17)0.0018 (17)0.0156 (15)
O40.0562 (12)0.0658 (12)0.1094 (19)0.0086 (11)0.0037 (13)0.0168 (12)
C50.0623 (18)0.0553 (16)0.102 (3)0.0013 (16)0.020 (2)0.0039 (17)
O60.097 (2)0.104 (2)0.149 (2)0.0185 (18)0.052 (2)0.0073 (19)
C70.098 (3)0.084 (2)0.076 (2)0.031 (2)0.0217 (19)0.0187 (18)
O80.0803 (14)0.0738 (13)0.0777 (13)0.0157 (12)0.0247 (12)0.0142 (11)
C90.0596 (17)0.0708 (17)0.0667 (17)0.0052 (16)0.0066 (15)0.0061 (15)
O100.0578 (10)0.0500 (9)0.0684 (11)0.0051 (9)0.0075 (10)0.0019 (8)
C110.0613 (18)0.0578 (15)0.0624 (17)0.0065 (15)0.0111 (14)0.0018 (13)
C120.0623 (19)0.0655 (17)0.104 (2)0.0016 (16)0.0079 (19)0.0046 (18)
C130.067 (2)0.083 (2)0.116 (3)0.021 (2)0.010 (2)0.017 (2)
C140.094 (3)0.0656 (19)0.087 (2)0.017 (2)0.026 (2)0.0122 (17)
C150.101 (3)0.0592 (17)0.084 (2)0.0007 (19)0.014 (2)0.0024 (16)
C160.076 (2)0.0693 (18)0.0735 (19)0.0037 (18)0.0024 (18)0.0053 (15)
N170.0781 (17)0.0651 (15)0.0807 (17)0.0233 (14)0.0127 (15)0.0063 (14)
N180.090 (2)0.0533 (14)0.093 (2)0.0140 (15)0.0023 (18)0.0025 (16)
N190.144 (3)0.0672 (19)0.130 (3)0.013 (2)0.005 (3)0.019 (2)
C200.100 (3)0.077 (2)0.0656 (19)0.022 (2)0.0037 (18)0.0055 (16)
C1010.0459 (16)0.104 (2)0.0589 (16)0.0114 (17)0.0042 (14)0.0096 (17)
C1020.0477 (15)0.0838 (19)0.0617 (16)0.0024 (15)0.0056 (13)0.0055 (15)
C1030.0575 (17)0.092 (2)0.0577 (16)0.0016 (18)0.0023 (14)0.0029 (16)
O1040.0558 (12)0.0948 (15)0.0717 (13)0.0013 (12)0.0085 (11)0.0000 (12)
C1050.0526 (17)0.083 (2)0.0698 (19)0.0054 (17)0.0064 (15)0.0062 (18)
O1060.0687 (14)0.0952 (16)0.0985 (17)0.0011 (15)0.0034 (13)0.0035 (14)
C1070.071 (2)0.097 (2)0.0630 (19)0.006 (2)0.0007 (16)0.0054 (17)
O1080.0656 (13)0.0924 (15)0.0661 (12)0.0081 (12)0.0058 (11)0.0002 (11)
C1090.0541 (16)0.079 (2)0.074 (2)0.0014 (16)0.0027 (15)0.0059 (16)
O1100.0572 (12)0.0826 (13)0.0595 (11)0.0014 (11)0.0013 (10)0.0037 (10)
C1110.0553 (16)0.0799 (19)0.073 (2)0.0131 (16)0.0024 (16)0.0054 (16)
C1160.074 (2)0.088 (2)0.091 (2)0.007 (2)0.001 (2)0.001 (2)
C1150.090 (3)0.096 (3)0.119 (3)0.009 (3)0.003 (3)0.018 (3)
C1140.106 (3)0.094 (3)0.097 (3)0.000 (3)0.007 (3)0.021 (2)
C1130.139 (4)0.098 (3)0.078 (2)0.006 (3)0.007 (3)0.008 (2)
C1120.115 (3)0.084 (2)0.073 (2)0.003 (2)0.003 (2)0.0062 (19)
N1170.0663 (17)0.099 (2)0.0792 (19)0.0223 (18)0.0138 (15)0.0123 (16)
N1180.0583 (16)0.117 (3)0.0630 (17)0.0228 (19)0.0004 (13)0.0160 (17)
N1190.105 (3)0.113 (3)0.087 (2)0.043 (2)0.0005 (19)0.018 (2)
C1200.0705 (19)0.096 (2)0.0661 (18)0.018 (2)0.0003 (17)0.0014 (17)
Geometric parameters (Å, º) top
C1—C21.510 (4)C101—C1021.517 (5)
C1—C51.520 (5)C101—C1051.535 (5)
C1—N171.497 (4)C101—N1171.478 (4)
C1—C201.505 (4)C101—C1201.519 (4)
C2—C31.521 (4)C102—C1031.509 (4)
C2—O101.427 (3)C102—O1101.412 (3)
C2—H210.973C102—H10210.942
C3—O41.437 (4)C103—O1041.468 (4)
C3—C71.511 (5)C103—C1071.513 (5)
C3—H310.970C103—H10310.981
O4—C51.342 (5)O104—C1051.324 (4)
C5—O61.192 (4)C105—O1061.214 (4)
C7—O81.429 (4)C107—O1081.430 (4)
C7—H710.992C107—H10710.965
C7—H721.006C107—H10721.023
O8—C91.398 (4)O108—C1091.403 (4)
C9—O101.418 (3)C109—O1101.442 (4)
C9—C111.504 (4)C109—C1111.490 (5)
C9—H911.005C109—H10910.991
C11—C121.376 (5)C111—C1161.389 (5)
C11—C161.374 (4)C111—C1121.369 (5)
C12—C131.386 (5)C116—C1151.375 (5)
C12—H1210.932C116—H11610.938
C13—C141.355 (5)C115—C1141.364 (6)
C13—H1310.943C115—H11510.943
C14—C151.361 (6)C114—C1131.356 (6)
C14—H1410.951C114—H11410.937
C15—C161.393 (5)C113—C1121.384 (5)
C15—H1510.936C113—H11310.931
C16—H1610.950C112—H11210.916
N17—N181.226 (4)N117—N1181.244 (5)
N18—N191.118 (4)N118—N1191.133 (5)
C20—H2010.975C120—H12010.956
C20—H2020.983C120—H12020.955
C20—H2030.970C120—H12030.968
C2—C1—C5100.7 (3)C102—C101—C105101.0 (3)
C2—C1—N17105.2 (2)C102—C101—N117105.1 (3)
C5—C1—N17105.5 (2)C105—C101—N117106.8 (3)
C2—C1—C20117.1 (2)C102—C101—C120117.5 (3)
C5—C1—C20114.7 (3)C105—C101—C120112.9 (3)
N17—C1—C20112.3 (3)N117—C101—C120112.4 (3)
C1—C2—C3102.5 (2)C101—C102—C103103.0 (3)
C1—C2—O10105.1 (2)C101—C102—O110107.1 (2)
C3—C2—O10109.9 (2)C103—C102—O110112.1 (2)
C1—C2—H21112.5C101—C102—H1021114.0
C3—C2—H21112.3C103—C102—H1021110.8
O10—C2—H21113.7O110—C102—H1021109.7
C2—C3—O4104.1 (2)C102—C103—O104103.8 (2)
C2—C3—C7113.7 (3)C102—C103—C107114.1 (3)
O4—C3—C7109.8 (3)O104—C103—C107109.4 (3)
C2—C3—H31114.4C102—C103—H1031109.7
O4—C3—H31106.9O104—C103—H1031111.0
C7—C3—H31107.7C107—C103—H1031108.8
C3—O4—C5110.0 (3)C103—O104—C105109.6 (2)
C1—C5—O4110.4 (3)C101—C105—O104110.9 (3)
C1—C5—O6127.1 (4)C101—C105—O106126.8 (3)
O4—C5—O6122.4 (4)O104—C105—O106122.2 (3)
C3—C7—O8111.4 (3)C103—C107—O108112.0 (3)
C3—C7—H71110.1C103—C107—H1071108.0
O8—C7—H71106.1O108—C107—H1071110.6
C3—C7—H72108.0C103—C107—H1072110.9
O8—C7—H72108.8O108—C107—H1072105.7
H71—C7—H72112.5H1071—C107—H1072109.6
C7—O8—C9110.9 (3)C107—O108—C109111.4 (2)
O8—C9—O10110.8 (2)O108—C109—O110108.2 (3)
O8—C9—C11110.6 (2)O108—C109—C111110.8 (3)
O10—C9—C11105.6 (2)O110—C109—C111108.9 (3)
O8—C9—H91112.0O108—C109—H1091106.8
O10—C9—H91107.5O110—C109—H1091109.9
C11—C9—H91110.1C111—C109—H1091112.2
C2—O10—C9113.9 (2)C109—O110—C102112.0 (2)
C9—C11—C12120.3 (3)C109—C111—C116118.7 (3)
C9—C11—C16120.0 (3)C109—C111—C112122.2 (3)
C12—C11—C16119.6 (3)C116—C111—C112119.1 (3)
C11—C12—C13119.5 (3)C111—C116—C115120.0 (4)
C11—C12—H121118.8C111—C116—H1161117.3
C13—C12—H121121.7C115—C116—H1161122.7
C12—C13—C14120.6 (3)C116—C115—C114120.5 (4)
C12—C13—H131118.0C116—C115—H1151119.6
C14—C13—H131121.4C114—C115—H1151119.9
C13—C14—C15120.7 (3)C115—C114—C113119.7 (4)
C13—C14—H141119.4C115—C114—H1141119.9
C15—C14—H141119.9C113—C114—H1141120.3
C14—C15—C16119.4 (3)C114—C113—C112120.8 (4)
C14—C15—H151120.7C114—C113—H1131120.0
C16—C15—H151119.9C112—C113—H1131119.2
C15—C16—C11120.2 (3)C113—C112—C111119.9 (4)
C15—C16—H161118.1C113—C112—H1121119.8
C11—C16—H161121.6C111—C112—H1121120.3
C1—N17—N18114.1 (3)C101—N117—N118114.3 (3)
N17—N18—N19173.1 (4)N117—N118—N119173.1 (4)
C1—C20—H201110.2C101—C120—H1201111.0
C1—C20—H202109.9C101—C120—H1202108.0
H201—C20—H202108.4H1201—C120—H1202109.7
C1—C20—H203110.2C101—C120—H1203107.4
H201—C20—H203108.7H1201—C120—H1203109.9
H202—C20—H203109.4H1202—C120—H1203111.0
 

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