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The title compound, C22H21N3O7, was prepared by reaction of podophyllotoxin and hydrogen azide. Each of the five-membered rings displays an envelope conformation. Weak C—H...O and C—H...N hydrogen bonding helps to stabilize the crystal structure.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536806015388/xu2019sup1.cif
Contains datablocks I, global

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536806015388/xu2019Isup2.hkl
Contains datablock I

CCDC reference: 621534

Key indicators

  • Single-crystal X-ray study
  • T = 298 K
  • Mean [sigma](C-C) = 0.004 Å
  • Disorder in main residue
  • R factor = 0.040
  • wR factor = 0.112
  • Data-to-parameter ratio = 8.8

checkCIF/PLATON results

No syntax errors found



Alert level C PLAT222_ALERT_3_C Large Non-Solvent H Ueq(max)/Ueq(min) ... 3.08 Ratio PLAT241_ALERT_2_C Check High Ueq as Compared to Neighbors for O1 PLAT241_ALERT_2_C Check High Ueq as Compared to Neighbors for O2 PLAT241_ALERT_2_C Check High Ueq as Compared to Neighbors for O4 PLAT241_ALERT_2_C Check High Ueq as Compared to Neighbors for N1 PLAT241_ALERT_2_C Check High Ueq as Compared to Neighbors for C20A PLAT242_ALERT_2_C Check Low Ueq as Compared to Neighbors for N2 PLAT242_ALERT_2_C Check Low Ueq as Compared to Neighbors for C18B PLAT242_ALERT_2_C Check Low Ueq as Compared to Neighbors for C19A PLAT301_ALERT_3_C Main Residue Disorder ......................... 14.00 Perc. PLAT366_ALERT_2_C Short? C(sp?)-C(sp?) Bond C15 - C16 ... 1.39 Ang. PLAT366_ALERT_2_C Short? C(sp?)-C(sp?) Bond C16 - C17 ... 1.38 Ang. PLAT390_ALERT_3_C Deviating Methyl C11B X-C-H Bond Angle ...... 101.70 Deg.
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 27.50 From the CIF: _reflns_number_total 2735 Count of symmetry unique reflns 2751 Completeness (_total/calc) 99.42% 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
0 ALERT level A = In general: serious problem 0 ALERT level B = Potentially serious problem 13 ALERT level C = Check and explain 1 ALERT level G = General alerts; check 0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 10 ALERT type 2 Indicator that the structure model may be wrong or deficient 3 ALERT type 3 Indicator that the structure quality may be low 1 ALERT type 4 Improvement, methodology, query or suggestion

Computing details top

Data collection: PROCESS-AUTO (Rigaku, 1998); cell refinement: PROCESS-AUTO; data reduction: CrystalStructure (Rigaku/MSC, 2004); program(s) used to solve structure: SIR92 (Altomare et al., 1993); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: WinGX (Farrugia, 1999).

4-β-Azido-4-desoxypodophyllotoxin top
Crystal data top
C22H21N3O7F(000) = 920
Mr = 439.42Dx = 1.385 Mg m3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71075 Å
Hall symbol: P 2ac 2abCell parameters from 15464 reflections
a = 8.998 (2) Åθ = 3.2–27.0°
b = 12.880 (5) ŵ = 0.11 mm1
c = 18.184 (5) ÅT = 298 K
V = 2107.4 (11) Å3Chunk, colorless
Z = 40.31 × 0.19 × 0.12 mm
Data collection top
Rigaku R-AXIS RAPID
diffractometer
2050 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.035
Graphite monochromatorθmax = 27.5°, θmin = 3.2°
Detector resolution: 10.0 pixels mm-1h = 1011
ω scansk = 1616
20804 measured reflectionsl = 2323
2735 independent reflections
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.040H-atom parameters constrained
wR(F2) = 0.112 w = 1/[σ2(Fo2) + (0.0578P)2 + 0.1971P]
where P = (Fo2 + 2Fc2)/3
S = 1.05(Δ/σ)max < 0.001
2735 reflectionsΔρmax = 0.14 e Å3
311 parametersΔρmin = 0.17 e Å3
0 restraintsExtinction correction: SHELXL97, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0117 (17)
Special details top

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.

Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/UeqOcc. (<1)
C10.4205 (3)0.41569 (19)0.63477 (12)0.0503 (6)
H10.35280.43510.67470.060*
C20.4092 (3)0.29867 (19)0.62421 (13)0.0506 (6)
H20.42110.26730.67290.061*
C30.5328 (3)0.2559 (2)0.57653 (13)0.0554 (6)
H30.53810.29820.53180.066*
C40.6801 (3)0.2658 (2)0.61647 (16)0.0605 (6)
H40.76010.25420.58080.073*
C50.6980 (3)0.3733 (2)0.64804 (12)0.0522 (6)
C60.8432 (3)0.4039 (2)0.66873 (15)0.0618 (7)
H60.92450.36100.66010.074*
C70.8601 (3)0.4979 (3)0.70160 (16)0.0661 (7)
C80.7402 (3)0.5612 (2)0.71562 (16)0.0674 (7)
C90.6005 (3)0.5351 (2)0.69481 (14)0.0622 (7)
H90.52120.57980.70330.075*
C100.5784 (3)0.4391 (2)0.66022 (12)0.0497 (5)
C120.3767 (3)0.4784 (2)0.56702 (12)0.0527 (6)
C130.4792 (3)0.5016 (2)0.51187 (14)0.0603 (6)
H130.57650.47780.51550.072*
C140.4359 (4)0.5602 (2)0.45151 (15)0.0675 (7)
C150.2905 (4)0.5965 (2)0.44545 (16)0.0714 (8)
C160.1900 (4)0.5728 (2)0.50077 (17)0.0711 (8)
C170.2324 (3)0.5146 (2)0.56100 (15)0.0621 (7)
H170.16370.49960.59770.074*
C18A0.6917 (11)0.5865 (8)0.4116 (5)0.100 (3)*0.50
H18A0.72320.51610.41930.151*0.50
H18B0.71140.62660.45500.151*0.50
H18C0.74520.61560.37080.151*0.50
C18B0.6683 (8)0.5469 (6)0.3924 (4)0.0786 (19)*0.50
H18D0.72570.57210.43320.118*0.50
H18E0.71520.56690.34720.118*0.50
H18F0.66200.47250.39480.118*0.50
C19A0.2237 (9)0.6085 (6)0.3213 (4)0.0744 (18)*0.50
H19A0.31320.57610.30400.112*0.50
H19B0.18960.65780.28550.112*0.50
H19C0.14870.55660.32890.112*0.50
C19B0.1577 (9)0.6147 (6)0.3361 (4)0.084 (2)*0.50
H19D0.20650.55640.31380.126*0.50
H19E0.13350.66490.29890.126*0.50
H19F0.06820.59190.35990.126*0.50
O5A0.039 (2)0.5901 (10)0.4954 (13)0.093 (4)0.50
C20A0.0005 (15)0.6954 (7)0.5112 (8)0.124 (4)0.50
H20A0.05820.71960.55220.185*0.50
H20B0.10330.69950.52300.185*0.50
H20C0.02080.73780.46890.185*0.50
O5B0.057 (2)0.6250 (10)0.4899 (11)0.098 (4)0.50
C20B0.0294 (11)0.6396 (10)0.5500 (6)0.107 (3)0.50
H20D0.06410.57360.56760.161*0.50
H20E0.11300.68230.53730.161*0.50
H20F0.02770.67310.58770.161*0.50
C210.2718 (3)0.2514 (2)0.59096 (14)0.0592 (6)
C220.4714 (3)0.1507 (2)0.55581 (18)0.0708 (7)
H22A0.51200.12740.50920.085*
H22B0.49400.09950.59330.085*
O10.7858 (2)0.6487 (2)0.75179 (14)0.0934 (7)
O20.9880 (2)0.5444 (2)0.72602 (13)0.0910 (7)
O30.5280 (3)0.5884 (2)0.39538 (12)0.0949 (8)
O40.2527 (3)0.66022 (18)0.38842 (12)0.0962 (8)
O60.1445 (2)0.27522 (18)0.59737 (11)0.0726 (6)
O70.3120 (2)0.16779 (17)0.55030 (11)0.0725 (5)
N10.6893 (4)0.1825 (2)0.67428 (18)0.0874 (8)
N20.6947 (3)0.2087 (2)0.73758 (19)0.0791 (8)
N30.7014 (5)0.2229 (3)0.7981 (2)0.1307 (15)
C11A0.9484 (8)0.6259 (6)0.7688 (4)0.0805 (19)*0.50
H11A1.00950.68590.75770.097*0.50
H11B0.96050.60870.82040.097*0.50
C11B0.9402 (8)0.6594 (5)0.7403 (4)0.0730 (17)*0.50
H11C0.98930.68780.78340.088*0.50
H11D0.96130.70320.69820.088*0.50
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0461 (12)0.0617 (15)0.0431 (11)0.0077 (11)0.0012 (10)0.0073 (10)
C20.0477 (12)0.0598 (14)0.0443 (10)0.0048 (11)0.0003 (10)0.0011 (10)
C30.0582 (13)0.0554 (14)0.0525 (12)0.0042 (12)0.0067 (11)0.0065 (11)
C40.0551 (14)0.0584 (15)0.0680 (15)0.0102 (12)0.0056 (12)0.0015 (13)
C50.0479 (12)0.0584 (14)0.0503 (12)0.0073 (11)0.0037 (11)0.0014 (11)
C60.0458 (13)0.0744 (18)0.0652 (15)0.0061 (12)0.0048 (12)0.0022 (14)
C70.0483 (13)0.083 (2)0.0667 (15)0.0062 (14)0.0004 (12)0.0113 (15)
C80.0579 (15)0.0751 (19)0.0692 (16)0.0038 (14)0.0011 (13)0.0207 (14)
C90.0532 (13)0.0702 (17)0.0631 (14)0.0094 (13)0.0021 (12)0.0174 (13)
C100.0456 (12)0.0599 (14)0.0437 (10)0.0062 (11)0.0014 (10)0.0028 (10)
C120.0560 (13)0.0534 (13)0.0485 (12)0.0072 (11)0.0098 (11)0.0073 (10)
C130.0607 (14)0.0641 (16)0.0561 (13)0.0079 (13)0.0040 (12)0.0047 (12)
C140.086 (2)0.0598 (16)0.0569 (14)0.0007 (14)0.0077 (15)0.0042 (12)
C150.094 (2)0.0546 (16)0.0658 (15)0.0095 (15)0.0292 (17)0.0003 (13)
C160.0710 (17)0.0651 (17)0.0771 (18)0.0185 (14)0.0275 (16)0.0122 (15)
C170.0547 (14)0.0670 (16)0.0646 (15)0.0127 (13)0.0074 (13)0.0082 (13)
O5A0.073 (4)0.063 (6)0.143 (10)0.030 (5)0.049 (6)0.022 (6)
C20A0.123 (8)0.080 (7)0.167 (12)0.036 (7)0.029 (9)0.027 (7)
O5B0.098 (7)0.098 (11)0.099 (5)0.045 (8)0.030 (5)0.003 (8)
C20B0.087 (5)0.120 (8)0.114 (7)0.048 (6)0.018 (5)0.017 (6)
C210.0608 (16)0.0632 (16)0.0537 (13)0.0017 (13)0.0006 (12)0.0025 (12)
C220.0720 (17)0.0636 (18)0.0768 (17)0.0019 (14)0.0047 (15)0.0124 (15)
O10.0668 (12)0.0981 (17)0.1152 (17)0.0094 (13)0.0032 (13)0.0480 (15)
O20.0546 (11)0.1130 (19)0.1054 (16)0.0112 (12)0.0002 (11)0.0340 (15)
O30.1135 (18)0.1010 (18)0.0703 (12)0.0015 (14)0.0021 (13)0.0311 (12)
O40.137 (2)0.0650 (13)0.0865 (14)0.0055 (13)0.0510 (15)0.0100 (11)
O60.0530 (10)0.0879 (15)0.0770 (13)0.0001 (10)0.0084 (10)0.0034 (11)
O70.0693 (11)0.0705 (12)0.0776 (12)0.0055 (10)0.0038 (11)0.0156 (10)
N10.103 (2)0.0636 (16)0.0953 (19)0.0150 (15)0.0212 (18)0.0083 (15)
N20.0614 (14)0.0787 (18)0.097 (2)0.0094 (13)0.0099 (16)0.0249 (17)
N30.173 (4)0.131 (3)0.089 (2)0.045 (3)0.019 (3)0.033 (2)
Geometric parameters (Å, º) top
C1—C21.523 (4)C18A—H18B0.9600
C1—C121.525 (3)C18A—H18C0.9600
C1—C101.525 (3)C18B—O31.372 (8)
C1—H10.9800C18B—H18D0.9600
C2—C211.504 (4)C18B—H18E0.9600
C2—C31.514 (3)C18B—H18F0.9600
C2—H20.9800C19A—O41.414 (7)
C3—C221.512 (4)C19A—H19A0.9600
C3—C41.516 (4)C19A—H19B0.9600
C3—H30.9800C19A—H19C0.9600
C4—N11.505 (4)C19B—O41.407 (8)
C4—C51.507 (4)C19B—H19D0.9600
C4—H40.9800C19B—H19E0.9600
C5—C101.388 (3)C19B—H19F0.9600
C5—C61.416 (4)O5A—C20A1.429 (16)
C6—C71.359 (4)C20A—H20A0.9600
C6—H60.9300C20A—H20B0.9600
C7—O21.372 (3)C20A—H20C0.9600
C7—C81.375 (4)O5B—C20B1.35 (2)
C8—C91.355 (4)C20B—H20D0.9600
C8—O11.368 (4)C20B—H20E0.9600
C9—C101.401 (4)C20B—H20F0.9600
C9—H90.9300C21—O61.191 (3)
C12—C171.384 (3)C21—O71.356 (4)
C12—C131.395 (4)C22—O71.455 (3)
C13—C141.388 (4)C22—H22A0.9700
C13—H130.9300C22—H22B0.9700
C14—O31.364 (4)O1—C11B1.412 (7)
C14—C151.393 (5)O1—C11A1.523 (8)
C15—O41.366 (3)O2—C11A1.354 (7)
C15—C161.387 (5)O2—C11B1.565 (7)
C16—O5A1.379 (19)N1—N21.201 (4)
C16—C171.381 (4)N2—N31.118 (5)
C16—O5B1.391 (19)C11A—H11A0.9700
C17—H170.9300C11A—H11B0.9700
C18A—O31.503 (10)C11B—H11C0.9700
C18A—H18A0.9600C11B—H11D0.9700
C2—C1—C12113.89 (19)C17—C16—C15120.9 (3)
C2—C1—C10107.3 (2)C17—C16—O5B127.9 (9)
C12—C1—C10112.4 (2)C15—C16—O5B110.7 (9)
C2—C1—H1107.7C16—C17—C12120.3 (3)
C12—C1—H1107.7C16—C17—H17119.8
C10—C1—H1107.7C12—C17—H17119.8
C21—C2—C3103.10 (19)O3—C18A—H18A109.5
C21—C2—C1120.4 (2)O3—C18A—H18B109.5
C3—C2—C1112.5 (2)O3—C18A—H18C109.5
C21—C2—H2106.7O3—C18B—H18D109.5
C3—C2—H2106.7O3—C18B—H18E109.5
C1—C2—H2106.7H18D—C18B—H18E109.5
C22—C3—C2101.5 (2)O3—C18B—H18F109.5
C22—C3—C4121.0 (2)H18D—C18B—H18F109.5
C2—C3—C4109.7 (2)H18E—C18B—H18F109.5
C22—C3—H3108.0O4—C19A—H19A109.5
C2—C3—H3108.0O4—C19A—H19B109.5
C4—C3—H3108.0O4—C19A—H19C109.5
N1—C4—C5112.5 (2)O4—C19B—H19D109.5
N1—C4—C3108.8 (3)O4—C19B—H19E109.5
C5—C4—C3110.7 (2)O4—C19B—H19F109.5
N1—C4—H4108.2C16—O5A—C20A112.2 (12)
C5—C4—H4108.2C20B—O5B—C16116.5 (14)
C3—C4—H4108.2O6—C21—O7120.9 (3)
C10—C5—C6120.2 (2)O6—C21—C2130.3 (3)
C10—C5—C4122.6 (2)O7—C21—C2108.8 (2)
C6—C5—C4117.1 (2)O7—C22—C3104.0 (2)
C7—C6—C5117.9 (2)O7—C22—H22A111.0
C7—C6—H6121.1C3—C22—H22A111.0
C5—C6—H6121.1O7—C22—H22B111.0
C6—C7—O2128.7 (3)C3—C22—H22B111.0
C6—C7—C8121.5 (3)H22A—C22—H22B109.0
O2—C7—C8109.8 (3)C8—O1—C11B107.7 (3)
C9—C8—O1128.1 (3)C8—O1—C11A103.1 (3)
C9—C8—C7121.9 (3)C11A—O2—C7107.6 (4)
O1—C8—C7110.0 (2)C7—O2—C11B103.7 (3)
C8—C9—C10118.4 (3)C14—O3—C18B118.9 (4)
C8—C9—H9120.8C14—O3—C18A116.4 (4)
C10—C9—H9120.8C15—O4—C19B114.5 (4)
C5—C10—C9120.0 (2)C15—O4—C19A114.7 (3)
C5—C10—C1123.6 (2)C21—O7—C22110.2 (2)
C9—C10—C1116.3 (2)N2—N1—C4118.1 (3)
C17—C12—C13119.4 (2)N1—N2—N3173.0 (4)
C17—C12—C1119.0 (2)O2—C11A—O1106.6 (5)
C13—C12—C1121.6 (2)O2—C11A—H11A110.4
C14—C13—C12120.0 (3)O1—C11A—H11A110.4
C14—C13—H13120.0O2—C11A—H11B110.4
C12—C13—H13120.0O1—C11A—H11B110.4
O3—C14—C13124.5 (3)H11A—C11A—H11B108.6
O3—C14—C15114.9 (3)O1—C11B—O2101.7 (4)
C13—C14—C15120.6 (3)O1—C11B—H11C111.4
O4—C15—C16121.3 (3)O2—C11B—H11C111.4
O4—C15—C14119.8 (3)O1—C11B—H11D111.4
C16—C15—C14118.8 (3)O2—C11B—H11D111.4
O5A—C16—C17114.6 (9)H11C—C11B—H11D109.3
O5A—C16—C15123.7 (10)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C6—H6···O6i0.932.543.433 (4)161
C18A—H18A···O7ii0.962.563.517 (11)176
C18A—H18C···N3iii0.962.523.349 (11)145
Symmetry codes: (i) x+1, y, z; (ii) x+1/2, y+1/2, z+1; (iii) x+3/2, y+1, z1/2.
 

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