4-β-Azido-4-desoxypodophyllotoxin

Chen, X.; Liang, J.; Shang, Z.-C.

doi:10.1107/S1600536806015388

4-β-Azido-4-desoxypodophyllotoxin

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.

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536806015388/xu2019sup1.cif Contains datablocks I, global
	Structure factor file (CIF format) https://doi.org/10.1107/S1600536806015388/xu2019Isup2.hkl Contains datablock I

CCDC reference: 621534

checkCIF report

Key indicators

Single-crystal X-ray study
T = 298 K
Mean (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

C₂₂H₂₁N₃O₇	F(000) = 920
M_r = 439.42	D_x = 1.385 Mg m⁻³
Orthorhombic, P2₁2₁2₁	Mo Kα radiation, λ = 0.71075 Å
Hall symbol: P 2ac 2ab	Cell parameters from 15464 reflections
a = 8.998 (2) Å	θ = 3.2–27.0°
b = 12.880 (5) Å	µ = 0.11 mm⁻¹
c = 18.184 (5) Å	T = 298 K
V = 2107.4 (11) Å³	Chunk, colorless
Z = 4	0.31 × 0.19 × 0.12 mm

Data collection top

Rigaku R-AXIS RAPID diffractometer	2050 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	R_int = 0.035
Graphite monochromator	θ_max = 27.5°, θ_min = 3.2°
Detector resolution: 10.0 pixels mm^-1	h = −10→11
ω scans	k = −16→16
20804 measured reflections	l = −23→23
2735 independent reflections

Refinement top

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)] = 0.040	H-atom parameters constrained
wR(F²) = 0.112	w = 1/[σ²(F_o²) + (0.0578P)² + 0.1971P] where P = (F_o² + 2F_c²)/3
S = 1.05	(Δ/σ)_max < 0.001
2735 reflections	Δρ_max = 0.14 e Å⁻³
311 parameters	Δρ_min = −0.17 e Å⁻³
0 restraints	Extinction correction: SHELXL97, Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction 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

	x	y	z	U_iso*/U_eq	Occ. (<1)
C1	0.4205 (3)	0.41569 (19)	0.63477 (12)	0.0503 (6)
H1	0.3528	0.4351	0.6747	0.060*
C2	0.4092 (3)	0.29867 (19)	0.62421 (13)	0.0506 (6)
H2	0.4211	0.2673	0.6729	0.061*
C3	0.5328 (3)	0.2559 (2)	0.57653 (13)	0.0554 (6)
H3	0.5381	0.2982	0.5318	0.066*
C4	0.6801 (3)	0.2658 (2)	0.61647 (16)	0.0605 (6)
H4	0.7601	0.2542	0.5808	0.073*
C5	0.6980 (3)	0.3733 (2)	0.64804 (12)	0.0522 (6)
C6	0.8432 (3)	0.4039 (2)	0.66873 (15)	0.0618 (7)
H6	0.9245	0.3610	0.6601	0.074*
C7	0.8601 (3)	0.4979 (3)	0.70160 (16)	0.0661 (7)
C8	0.7402 (3)	0.5612 (2)	0.71562 (16)	0.0674 (7)
C9	0.6005 (3)	0.5351 (2)	0.69481 (14)	0.0622 (7)
H9	0.5212	0.5798	0.7033	0.075*
C10	0.5784 (3)	0.4391 (2)	0.66022 (12)	0.0497 (5)
C12	0.3767 (3)	0.4784 (2)	0.56702 (12)	0.0527 (6)
C13	0.4792 (3)	0.5016 (2)	0.51187 (14)	0.0603 (6)
H13	0.5765	0.4778	0.5155	0.072*
C14	0.4359 (4)	0.5602 (2)	0.45151 (15)	0.0675 (7)
C15	0.2905 (4)	0.5965 (2)	0.44545 (16)	0.0714 (8)
C16	0.1900 (4)	0.5728 (2)	0.50077 (17)	0.0711 (8)
C17	0.2324 (3)	0.5146 (2)	0.56100 (15)	0.0621 (7)
H17	0.1637	0.4996	0.5977	0.074*
C18A	0.6917 (11)	0.5865 (8)	0.4116 (5)	0.100 (3)*	0.50
H18A	0.7232	0.5161	0.4193	0.151*	0.50
H18B	0.7114	0.6266	0.4550	0.151*	0.50
H18C	0.7452	0.6156	0.3708	0.151*	0.50
C18B	0.6683 (8)	0.5469 (6)	0.3924 (4)	0.0786 (19)*	0.50
H18D	0.7257	0.5721	0.4332	0.118*	0.50
H18E	0.7152	0.5669	0.3472	0.118*	0.50
H18F	0.6620	0.4725	0.3948	0.118*	0.50
C19A	0.2237 (9)	0.6085 (6)	0.3213 (4)	0.0744 (18)*	0.50
H19A	0.3132	0.5761	0.3040	0.112*	0.50
H19B	0.1896	0.6578	0.2855	0.112*	0.50
H19C	0.1487	0.5566	0.3289	0.112*	0.50
C19B	0.1577 (9)	0.6147 (6)	0.3361 (4)	0.084 (2)*	0.50
H19D	0.2065	0.5564	0.3138	0.126*	0.50
H19E	0.1335	0.6649	0.2989	0.126*	0.50
H19F	0.0682	0.5919	0.3599	0.126*	0.50
O5A	0.039 (2)	0.5901 (10)	0.4954 (13)	0.093 (4)	0.50
C20A	0.0005 (15)	0.6954 (7)	0.5112 (8)	0.124 (4)	0.50
H20A	0.0582	0.7196	0.5522	0.185*	0.50
H20B	−0.1033	0.6995	0.5230	0.185*	0.50
H20C	0.0208	0.7378	0.4689	0.185*	0.50
O5B	0.057 (2)	0.6250 (10)	0.4899 (11)	0.098 (4)	0.50
C20B	−0.0294 (11)	0.6396 (10)	0.5500 (6)	0.107 (3)	0.50
H20D	−0.0641	0.5736	0.5676	0.161*	0.50
H20E	−0.1130	0.6823	0.5373	0.161*	0.50
H20F	0.0277	0.6731	0.5877	0.161*	0.50
C21	0.2718 (3)	0.2514 (2)	0.59096 (14)	0.0592 (6)
C22	0.4714 (3)	0.1507 (2)	0.55581 (18)	0.0708 (7)
H22A	0.5120	0.1274	0.5092	0.085*
H22B	0.4940	0.0995	0.5933	0.085*
O1	0.7858 (2)	0.6487 (2)	0.75179 (14)	0.0934 (7)
O2	0.9880 (2)	0.5444 (2)	0.72602 (13)	0.0910 (7)
O3	0.5280 (3)	0.5884 (2)	0.39538 (12)	0.0949 (8)
O4	0.2527 (3)	0.66022 (18)	0.38842 (12)	0.0962 (8)
O6	0.1445 (2)	0.27522 (18)	0.59737 (11)	0.0726 (6)
O7	0.3120 (2)	0.16779 (17)	0.55030 (11)	0.0725 (5)
N1	0.6893 (4)	0.1825 (2)	0.67428 (18)	0.0874 (8)
N2	0.6947 (3)	0.2087 (2)	0.73758 (19)	0.0791 (8)
N3	0.7014 (5)	0.2229 (3)	0.7981 (2)	0.1307 (15)
C11A	0.9484 (8)	0.6259 (6)	0.7688 (4)	0.0805 (19)*	0.50
H11A	1.0095	0.6859	0.7577	0.097*	0.50
H11B	0.9605	0.6087	0.8204	0.097*	0.50
C11B	0.9402 (8)	0.6594 (5)	0.7403 (4)	0.0730 (17)*	0.50
H11C	0.9893	0.6878	0.7834	0.088*	0.50
H11D	0.9613	0.7032	0.6982	0.088*	0.50

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0461 (12)	0.0617 (15)	0.0431 (11)	0.0077 (11)	0.0012 (10)	−0.0073 (10)
C2	0.0477 (12)	0.0598 (14)	0.0443 (10)	0.0048 (11)	0.0003 (10)	−0.0011 (10)
C3	0.0582 (13)	0.0554 (14)	0.0525 (12)	0.0042 (12)	0.0067 (11)	−0.0065 (11)
C4	0.0551 (14)	0.0584 (15)	0.0680 (15)	0.0102 (12)	0.0056 (12)	−0.0015 (13)
C5	0.0479 (12)	0.0584 (14)	0.0503 (12)	0.0073 (11)	0.0037 (11)	0.0014 (11)
C6	0.0458 (13)	0.0744 (18)	0.0652 (15)	0.0061 (12)	0.0048 (12)	−0.0022 (14)
C7	0.0483 (13)	0.083 (2)	0.0667 (15)	−0.0062 (14)	0.0004 (12)	−0.0113 (15)
C8	0.0579 (15)	0.0751 (19)	0.0692 (16)	−0.0038 (14)	0.0011 (13)	−0.0207 (14)
C9	0.0532 (13)	0.0702 (17)	0.0631 (14)	0.0094 (13)	−0.0021 (12)	−0.0174 (13)
C10	0.0456 (12)	0.0599 (14)	0.0437 (10)	0.0062 (11)	0.0014 (10)	−0.0028 (10)
C12	0.0560 (13)	0.0534 (13)	0.0485 (12)	0.0072 (11)	−0.0098 (11)	−0.0073 (10)
C13	0.0607 (14)	0.0641 (16)	0.0561 (13)	0.0079 (13)	−0.0040 (12)	0.0047 (12)
C14	0.086 (2)	0.0598 (16)	0.0569 (14)	0.0007 (14)	−0.0077 (15)	0.0042 (12)
C15	0.094 (2)	0.0546 (16)	0.0658 (15)	0.0095 (15)	−0.0292 (17)	−0.0003 (13)
C16	0.0710 (17)	0.0651 (17)	0.0771 (18)	0.0185 (14)	−0.0275 (16)	−0.0122 (15)
C17	0.0547 (14)	0.0670 (16)	0.0646 (15)	0.0127 (13)	−0.0074 (13)	−0.0082 (13)
O5A	0.073 (4)	0.063 (6)	0.143 (10)	0.030 (5)	−0.049 (6)	−0.022 (6)
C20A	0.123 (8)	0.080 (7)	0.167 (12)	0.036 (7)	−0.029 (9)	−0.027 (7)
O5B	0.098 (7)	0.098 (11)	0.099 (5)	0.045 (8)	−0.030 (5)	0.003 (8)
C20B	0.087 (5)	0.120 (8)	0.114 (7)	0.048 (6)	−0.018 (5)	−0.017 (6)
C21	0.0608 (16)	0.0632 (16)	0.0537 (13)	−0.0017 (13)	0.0006 (12)	0.0025 (12)
C22	0.0720 (17)	0.0636 (18)	0.0768 (17)	0.0019 (14)	0.0047 (15)	−0.0124 (15)
O1	0.0668 (12)	0.0981 (17)	0.1152 (17)	−0.0094 (13)	−0.0032 (13)	−0.0480 (15)
O2	0.0546 (11)	0.1130 (19)	0.1054 (16)	−0.0112 (12)	−0.0002 (11)	−0.0340 (15)
O3	0.1135 (18)	0.1010 (18)	0.0703 (12)	−0.0015 (14)	0.0021 (13)	0.0311 (12)
O4	0.137 (2)	0.0650 (13)	0.0865 (14)	0.0055 (13)	−0.0510 (15)	0.0100 (11)
O6	0.0530 (10)	0.0879 (15)	0.0770 (13)	0.0001 (10)	−0.0084 (10)	−0.0034 (11)
O7	0.0693 (11)	0.0705 (12)	0.0776 (12)	−0.0055 (10)	−0.0038 (11)	−0.0156 (10)
N1	0.103 (2)	0.0636 (16)	0.0953 (19)	0.0150 (15)	−0.0212 (18)	0.0083 (15)
N2	0.0614 (14)	0.0787 (18)	0.097 (2)	−0.0094 (13)	−0.0099 (16)	0.0249 (17)
N3	0.173 (4)	0.131 (3)	0.089 (2)	−0.045 (3)	−0.019 (3)	0.033 (2)

Geometric parameters (Å, º) top

C1—C2	1.523 (4)	C18A—H18B	0.9600
C1—C12	1.525 (3)	C18A—H18C	0.9600
C1—C10	1.525 (3)	C18B—O3	1.372 (8)
C1—H1	0.9800	C18B—H18D	0.9600
C2—C21	1.504 (4)	C18B—H18E	0.9600
C2—C3	1.514 (3)	C18B—H18F	0.9600
C2—H2	0.9800	C19A—O4	1.414 (7)
C3—C22	1.512 (4)	C19A—H19A	0.9600
C3—C4	1.516 (4)	C19A—H19B	0.9600
C3—H3	0.9800	C19A—H19C	0.9600
C4—N1	1.505 (4)	C19B—O4	1.407 (8)
C4—C5	1.507 (4)	C19B—H19D	0.9600
C4—H4	0.9800	C19B—H19E	0.9600
C5—C10	1.388 (3)	C19B—H19F	0.9600
C5—C6	1.416 (4)	O5A—C20A	1.429 (16)
C6—C7	1.359 (4)	C20A—H20A	0.9600
C6—H6	0.9300	C20A—H20B	0.9600
C7—O2	1.372 (3)	C20A—H20C	0.9600
C7—C8	1.375 (4)	O5B—C20B	1.35 (2)
C8—C9	1.355 (4)	C20B—H20D	0.9600
C8—O1	1.368 (4)	C20B—H20E	0.9600
C9—C10	1.401 (4)	C20B—H20F	0.9600
C9—H9	0.9300	C21—O6	1.191 (3)
C12—C17	1.384 (3)	C21—O7	1.356 (4)
C12—C13	1.395 (4)	C22—O7	1.455 (3)
C13—C14	1.388 (4)	C22—H22A	0.9700
C13—H13	0.9300	C22—H22B	0.9700
C14—O3	1.364 (4)	O1—C11B	1.412 (7)
C14—C15	1.393 (5)	O1—C11A	1.523 (8)
C15—O4	1.366 (3)	O2—C11A	1.354 (7)
C15—C16	1.387 (5)	O2—C11B	1.565 (7)
C16—O5A	1.379 (19)	N1—N2	1.201 (4)
C16—C17	1.381 (4)	N2—N3	1.118 (5)
C16—O5B	1.391 (19)	C11A—H11A	0.9700
C17—H17	0.9300	C11A—H11B	0.9700
C18A—O3	1.503 (10)	C11B—H11C	0.9700
C18A—H18A	0.9600	C11B—H11D	0.9700

C2—C1—C12	113.89 (19)	C17—C16—C15	120.9 (3)
C2—C1—C10	107.3 (2)	C17—C16—O5B	127.9 (9)
C12—C1—C10	112.4 (2)	C15—C16—O5B	110.7 (9)
C2—C1—H1	107.7	C16—C17—C12	120.3 (3)
C12—C1—H1	107.7	C16—C17—H17	119.8
C10—C1—H1	107.7	C12—C17—H17	119.8
C21—C2—C3	103.10 (19)	O3—C18A—H18A	109.5
C21—C2—C1	120.4 (2)	O3—C18A—H18B	109.5
C3—C2—C1	112.5 (2)	O3—C18A—H18C	109.5
C21—C2—H2	106.7	O3—C18B—H18D	109.5
C3—C2—H2	106.7	O3—C18B—H18E	109.5
C1—C2—H2	106.7	H18D—C18B—H18E	109.5
C22—C3—C2	101.5 (2)	O3—C18B—H18F	109.5
C22—C3—C4	121.0 (2)	H18D—C18B—H18F	109.5
C2—C3—C4	109.7 (2)	H18E—C18B—H18F	109.5
C22—C3—H3	108.0	O4—C19A—H19A	109.5
C2—C3—H3	108.0	O4—C19A—H19B	109.5
C4—C3—H3	108.0	O4—C19A—H19C	109.5
N1—C4—C5	112.5 (2)	O4—C19B—H19D	109.5
N1—C4—C3	108.8 (3)	O4—C19B—H19E	109.5
C5—C4—C3	110.7 (2)	O4—C19B—H19F	109.5
N1—C4—H4	108.2	C16—O5A—C20A	112.2 (12)
C5—C4—H4	108.2	C20B—O5B—C16	116.5 (14)
C3—C4—H4	108.2	O6—C21—O7	120.9 (3)
C10—C5—C6	120.2 (2)	O6—C21—C2	130.3 (3)
C10—C5—C4	122.6 (2)	O7—C21—C2	108.8 (2)
C6—C5—C4	117.1 (2)	O7—C22—C3	104.0 (2)
C7—C6—C5	117.9 (2)	O7—C22—H22A	111.0
C7—C6—H6	121.1	C3—C22—H22A	111.0
C5—C6—H6	121.1	O7—C22—H22B	111.0
C6—C7—O2	128.7 (3)	C3—C22—H22B	111.0
C6—C7—C8	121.5 (3)	H22A—C22—H22B	109.0
O2—C7—C8	109.8 (3)	C8—O1—C11B	107.7 (3)
C9—C8—O1	128.1 (3)	C8—O1—C11A	103.1 (3)
C9—C8—C7	121.9 (3)	C11A—O2—C7	107.6 (4)
O1—C8—C7	110.0 (2)	C7—O2—C11B	103.7 (3)
C8—C9—C10	118.4 (3)	C14—O3—C18B	118.9 (4)
C8—C9—H9	120.8	C14—O3—C18A	116.4 (4)
C10—C9—H9	120.8	C15—O4—C19B	114.5 (4)
C5—C10—C9	120.0 (2)	C15—O4—C19A	114.7 (3)
C5—C10—C1	123.6 (2)	C21—O7—C22	110.2 (2)
C9—C10—C1	116.3 (2)	N2—N1—C4	118.1 (3)
C17—C12—C13	119.4 (2)	N1—N2—N3	173.0 (4)
C17—C12—C1	119.0 (2)	O2—C11A—O1	106.6 (5)
C13—C12—C1	121.6 (2)	O2—C11A—H11A	110.4
C14—C13—C12	120.0 (3)	O1—C11A—H11A	110.4
C14—C13—H13	120.0	O2—C11A—H11B	110.4
C12—C13—H13	120.0	O1—C11A—H11B	110.4
O3—C14—C13	124.5 (3)	H11A—C11A—H11B	108.6
O3—C14—C15	114.9 (3)	O1—C11B—O2	101.7 (4)
C13—C14—C15	120.6 (3)	O1—C11B—H11C	111.4
O4—C15—C16	121.3 (3)	O2—C11B—H11C	111.4
O4—C15—C14	119.8 (3)	O1—C11B—H11D	111.4
C16—C15—C14	118.8 (3)	O2—C11B—H11D	111.4
O5A—C16—C17	114.6 (9)	H11C—C11B—H11D	109.3
O5A—C16—C15	123.7 (10)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C6—H6···O6ⁱ	0.93	2.54	3.433 (4)	161
C18A—H18A···O7ⁱⁱ	0.96	2.56	3.517 (11)	176
C18A—H18C···N3ⁱⁱⁱ	0.96	2.52	3.349 (11)	145

Symmetry codes: (i) x+1, y, z; (ii) x+1/2, −y+1/2, −z+1; (iii) −x+3/2, −y+1, z−1/2.

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