2-Azido­methyl-3-methyl-1-phenyl­sulfonyl-1H-indole

Karthikeyan, S.; Sethusankar, K.; Rajeswaran, G.G.; Mohanakrishnan, A.K.

doi:10.1107/S1600536811030601

2-Azidomethyl-3-methyl-1-phenylsulfonyl-1H-indole

S. Karthikeyan, K. Sethusankar, G. G. Rajeswaran and A. K. Mohanakrishnan

In the title compound, C₁₆H₁₄N₄O₂S, the plane of the indole ring is twisted by 70.4 (2)° with respect to the plane of the azidomethyl substituent. As a result of the electron-withdrawing character of the phenylsulfonyl groups, the N—C bond lengths are slightly longer than the anticipated value of approximately 1.355 Å for an N atom with a planar configuration. The indole ring is essentially planar, with a maximum deviation of 0.0296 Å. The azide group is almost linear, the N—N—N angle being 171.4 (3)°. The methyl group on the azide-substituted C atom is in a flagpole position. The phenyl ring of the sulfonyl substituent makes a dihedral angle of 87.07 (10)° with the best plane of the indole moiety. The crystal packing is stabilized by intermolecular C—H

O interactions, which link the molecules into infinite chains running parallel to the b axis. The crystal packing is further stabilized by C—H

π interactions.

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536811030601/rk2287sup1.cif Contains datablocks global, I
	Structure factor file (CIF format) https://doi.org/10.1107/S1600536811030601/rk2287Isup2.hkl Contains datablock I
	Chemical Markup Language (CML) file https://doi.org/10.1107/S1600536811030601/rk2287Isup3.cml Supplementary material

CCDC reference: 845314

checkCIF report

Key indicators

Single-crystal X-ray study
T = 295 K
Mean (C-C) = 0.004 Å
R factor = 0.047
wR factor = 0.166
Data-to-parameter ratio = 20.2

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT242_ALERT_2_C Check Low       Ueq as Compared to Neighbors for         N3
PLAT910_ALERT_3_C Missing # of FCF Reflections Below Th(Min) .....          1
PLAT912_ALERT_4_C Missing # of FCF Reflections Above STh/L=  0.600          7

Alert level G
PLAT005_ALERT_5_G No _iucr_refine_instructions_details in CIF ....          ?

   0 ALERT level A = Most likely a serious problem - resolve or explain
   0 ALERT level B = A potentially serious problem, consider carefully
   3 ALERT level C = Check. Ensure it is not caused by an omission or oversight
   1 ALERT level G = General information/check it is not something unexpected

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   1 ALERT type 2 Indicator that the structure model may be wrong or deficient
   1 ALERT type 3 Indicator that the structure quality may be low
   1 ALERT type 4 Improvement, methodology, query or suggestion
   1 ALERT type 5 Informative message, check

Comment top

The phenylsulfonyl indole compounds inhibit the HIV–1 RT enzyme in vitro and HTLVIIIb viral spread in MT–4 human T–lymphoid cells (Williams, et al., 1993). The Cu(I)–catalyzed 1,3–dipolar cycloaddition reaction between alkynes and azides has been suitable for the synthesis of a large number of modified nucleosides, nucleotides and oligonucleotides with a broad range of applications (Amblard et al., 2009). A lot of sulfur containing compounds, exhibit insecticidal, germicidal, antimicrobial and antibacterial activities (De-Benedetti et al., 1985).

In the title compound C₁₆H₁₄N₄O₂S, the molecular conformation (Fig. 1) is preferred with the plane of indole ring twisted by 70.4 (2)° with respect to the plane of the azido group bound to the methyl substituent. The indole ring is essentially planar with a maximum deviation 0.0296 (17)Å for the atom N1. The bond angle around N3, in the chain of atom N2–N3–N4, is 171.4 (3)° and thus the azidomethyl side chain is almost linear. The methyl group on the azide substituted C atom is in a flag pole position.

The phenyl ring of the sulfonyl substituent makes a dihedral angle of 87.07 (10)° with the indole moiety. The deviation of atoms S1 and C10 from the indole mean plane is 0.453 (5)Å and -0.0618 (24)Å, respectively. As a result of electron–withdrawing character of the phenylsulfonyl group, the bond lengths N1—C8 = 1.432 (2)Å and N1—C1 = 1.416 (2)Å in the molecule are longer than the mean value of 1.355 (14)Å (Allen et al., 1987). Due to Thorpe–Ingold effect (Bassindale, 1984), bond angles around atom S1 show significant deviations from the ideal tetrahedral value, with significant deviations, widening of angle O1═S1═O2 = 119.71 (10)° and narrowing of angle N1—S1—C11 = 105.36 (8)°. The title molecule exhibits structural similarities with the already reported related structure (Fernandes et al., 2005).

In crystal packing, the molecule is stabilized by intermolecular C—H···O interactions which link the molecules into infinite chains running parallel to b axis. The crystal packing is further stabilized by C—H···π interaction, where Cg3 is centroid of C11–C16. The symmetry codes: (i) -1/2-x, 1/2+y, z; (ii) -x, 1-y, 1-z. The packing view of the title compound is shown in the Fig. 2.

Related literature top

For the biological activity of compounds containing an indole ring system, sulfur, azides, see: Williams et al. (1993); Amblard et al. (2009); De-Benedetti et al. (1985). For related structures, see: Fernandes et al. (2005). For comparison of molecular dimensions, see: Bassindale (1984); Allen et al. (1987).

Experimental top

To a solution of 2–(bromomethyl)–3–methyl–1–phenylsulfonyl–indole (1 mmol) in DMF (3 ml) was added sodium azide (2 mmol) and stirred for 2 h at room temperature. After consumption of the 2–(bromomethyl)–3–methyl–1–phenylsulfonyl–indole (monitored by TLC), reaction mass was poured into ice water (20 ml). The solid obtained was filtered and dried (CaSO₄). Then the crude product was recrystalized with MeOH (5 ml) afforded the 2–(azidomethyl)–3–methyl–1–phenylsulfonyl–indole as a colourless solid. Yield: 0.28 g (92%).

Computing details top

Data collection: APEX2 (Bruker, 2004); cell refinement: SAINT (Bruker, 2004); data reduction: SAINT (Bruker, 2004); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009).

Figures top

	Fig. 1. The molecular structure of the title compound with the atom numbering scheme. Displacement ellipsoids are drawn at 30% probability level. H atoms are present as a small spheres of arbitary radius.
	Fig. 2. The packing arrangement of the title compound viewed down a axis. The dashed lines indicate C—H···O intermolecular interactions, which is running parallel to b axis. Initial symmetry code: (i) -1/2-x, 1/2+y, z.

2-Azidomethyl-3-methyl-1-phenylsulfonyl-1H-indole top

Crystal data top

C₁₆H₁₄N₄O₂S	F(000) = 1360
M_r = 326.38	D_x = 1.393 Mg m⁻³
Orthorhombic, Pbca	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2ab	Cell parameters from 4231 reflections
a = 11.0337 (4) Å	θ = 1.0–29.3°
b = 12.1424 (4) Å	µ = 0.22 mm⁻¹
c = 23.2234 (9) Å	T = 295 K
V = 3111.37 (19) Å³	Block, colourless
Z = 8	0.30 × 0.25 × 0.25 mm

Data collection top

Bruker Kappa APEXII CCD diffractometer	2776 reflections with I > 2σ(I)
Radiation source: fine–focus sealed tube	R_int = 0.049
Graphite monochromator	θ_max = 29.3°, θ_min = 2.6°
ω scans	h = −15→13
37510 measured reflections	k = −16→12
4231 independent reflections	l = −31→31

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.047	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.166	H-atom parameters constrained
S = 0.99	w = 1/[σ²(F_o²) + (0.0987P)² + 0.4179P] where P = (F_o² + 2F_c²)/3
4231 reflections	(Δ/σ)_max < 0.001
209 parameters	Δρ_max = 0.37 e Å⁻³
0 restraints	Δρ_min = −0.35 e Å⁻³

Crystal data top

C₁₆H₁₄N₄O₂S	V = 3111.37 (19) Å³
M_r = 326.38	Z = 8
Orthorhombic, Pbca	Mo Kα radiation
a = 11.0337 (4) Å	µ = 0.22 mm⁻¹
b = 12.1424 (4) Å	T = 295 K
c = 23.2234 (9) Å	0.30 × 0.25 × 0.25 mm

Data collection top

Bruker Kappa APEXII CCD diffractometer	2776 reflections with I > 2σ(I)
37510 measured reflections	R_int = 0.049
4231 independent reflections

Refinement top

R[F² > 2σ(F²)] = 0.047	0 restraints
wR(F²) = 0.166	H-atom parameters constrained
S = 0.99	Δρ_max = 0.37 e Å⁻³
4231 reflections	Δρ_min = −0.35 e Å⁻³
209 parameters

Special details top

Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'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
C1	0.07440 (17)	0.32220 (15)	0.44968 (8)	0.0419 (4)
C2	−0.0143 (2)	0.25607 (19)	0.47362 (10)	0.0566 (5)
H2	−0.0569	0.2052	0.4516	0.068*
C3	−0.0368 (3)	0.2688 (2)	0.53153 (12)	0.0719 (7)
H3	−0.0958	0.2253	0.5488	0.086*
C4	0.0252 (3)	0.3435 (3)	0.56443 (11)	0.0807 (8)
H4	0.0075	0.3495	0.6034	0.097*
C5	0.1128 (2)	0.4095 (2)	0.54104 (10)	0.0690 (7)
H5	0.1548	0.4600	0.5636	0.083*
C6	0.13730 (18)	0.39903 (16)	0.48237 (9)	0.0478 (5)
C7	0.22068 (19)	0.45506 (16)	0.44500 (9)	0.0513 (5)
C8	0.20845 (16)	0.41425 (15)	0.39159 (8)	0.0424 (4)
C9	0.3091 (3)	0.5412 (2)	0.46516 (13)	0.0844 (9)
H9A	0.3390	0.5816	0.4326	0.127*
H9B	0.3756	0.5062	0.4846	0.127*
H9C	0.2691	0.5908	0.4912	0.127*
C10	0.2829 (2)	0.4427 (2)	0.34045 (9)	0.0529 (5)
H10A	0.3110	0.5181	0.3441	0.064*
H10B	0.2328	0.4382	0.3062	0.064*
C11	−0.08441 (17)	0.36552 (16)	0.33108 (8)	0.0433 (4)
C12	−0.0704 (2)	0.46737 (18)	0.30491 (9)	0.0547 (5)
H12	0.0048	0.4893	0.2910	0.066*
C13	−0.1695 (3)	0.5355 (2)	0.29992 (11)	0.0711 (7)
H13	−0.1615	0.6043	0.2828	0.085*
C14	−0.2791 (3)	0.5020 (3)	0.32010 (13)	0.0801 (9)
H14	−0.3457	0.5484	0.3164	0.096*
C15	−0.2932 (2)	0.4012 (3)	0.34580 (12)	0.0780 (8)
H15	−0.3690	0.3797	0.3592	0.094*
C16	−0.19488 (19)	0.3311 (2)	0.35192 (11)	0.0609 (6)
H16	−0.2033	0.2628	0.3696	0.073*
N1	0.12022 (14)	0.32780 (13)	0.39281 (6)	0.0405 (3)
N2	0.38932 (18)	0.3686 (2)	0.33357 (9)	0.0696 (6)
N3	0.37305 (17)	0.2784 (2)	0.31151 (9)	0.0632 (5)
N4	0.3730 (2)	0.1938 (2)	0.29245 (13)	0.0975 (8)
O1	0.00404 (15)	0.17244 (11)	0.35322 (7)	0.0599 (4)
O2	0.11681 (14)	0.29357 (13)	0.28769 (6)	0.0590 (4)
S1	0.04241 (4)	0.27961 (4)	0.33704 (2)	0.04300 (17)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0427 (10)	0.0382 (9)	0.0449 (10)	−0.0001 (8)	0.0005 (8)	0.0030 (7)
C2	0.0576 (13)	0.0529 (11)	0.0593 (13)	−0.0137 (10)	0.0052 (10)	0.0041 (10)
C3	0.0766 (17)	0.0759 (17)	0.0633 (15)	−0.0133 (13)	0.0191 (13)	0.0112 (12)
C4	0.103 (2)	0.0881 (19)	0.0509 (14)	−0.0151 (17)	0.0197 (14)	−0.0017 (12)
C5	0.0830 (17)	0.0747 (15)	0.0494 (12)	−0.0168 (14)	0.0032 (12)	−0.0107 (11)
C6	0.0500 (11)	0.0466 (11)	0.0468 (10)	−0.0046 (9)	−0.0014 (8)	−0.0035 (8)
C7	0.0491 (11)	0.0467 (11)	0.0580 (12)	−0.0103 (9)	−0.0008 (9)	−0.0061 (9)
C8	0.0363 (9)	0.0417 (9)	0.0490 (10)	−0.0026 (7)	−0.0004 (7)	0.0029 (7)
C9	0.0866 (19)	0.0825 (18)	0.0841 (19)	−0.0432 (16)	0.0045 (15)	−0.0183 (14)
C10	0.0471 (11)	0.0592 (12)	0.0524 (12)	−0.0067 (10)	0.0018 (9)	0.0077 (9)
C11	0.0385 (9)	0.0463 (10)	0.0452 (10)	0.0038 (8)	−0.0076 (8)	−0.0100 (8)
C12	0.0605 (13)	0.0535 (12)	0.0501 (11)	0.0067 (10)	−0.0110 (10)	−0.0028 (9)
C13	0.089 (2)	0.0627 (14)	0.0613 (14)	0.0285 (14)	−0.0205 (13)	−0.0114 (11)
C14	0.0729 (19)	0.089 (2)	0.0786 (18)	0.0410 (16)	−0.0250 (15)	−0.0325 (15)
C15	0.0385 (12)	0.107 (2)	0.0881 (19)	0.0117 (13)	−0.0040 (11)	−0.0294 (16)
C16	0.0414 (11)	0.0694 (15)	0.0719 (14)	0.0003 (10)	−0.0048 (10)	−0.0123 (11)
N1	0.0381 (8)	0.0434 (8)	0.0400 (8)	−0.0047 (6)	−0.0029 (6)	0.0015 (6)
N2	0.0389 (10)	0.0972 (17)	0.0728 (14)	−0.0009 (11)	0.0019 (9)	−0.0075 (11)
N3	0.0461 (10)	0.0842 (17)	0.0594 (12)	0.0081 (11)	0.0006 (9)	0.0063 (11)
N4	0.0768 (17)	0.0868 (18)	0.129 (2)	0.0254 (14)	−0.0104 (16)	−0.0159 (17)
O1	0.0639 (10)	0.0375 (8)	0.0783 (10)	−0.0019 (7)	−0.0153 (8)	−0.0086 (7)
O2	0.0488 (8)	0.0817 (11)	0.0463 (8)	0.0069 (7)	0.0009 (6)	−0.0149 (7)
S1	0.0380 (3)	0.0433 (3)	0.0478 (3)	0.00322 (19)	−0.00599 (19)	−0.00836 (18)

Geometric parameters (Å, º) top

C1—C2	1.383 (3)	C10—H10A	0.9700
C1—C6	1.389 (3)	C10—H10B	0.9700
C1—N1	1.416 (2)	C11—C16	1.377 (3)
C2—C3	1.376 (4)	C11—C12	1.387 (3)
C2—H2	0.9300	C11—S1	1.7509 (19)
C3—C4	1.369 (4)	C12—C13	1.376 (3)
C3—H3	0.9300	C12—H12	0.9300
C4—C5	1.368 (4)	C13—C14	1.359 (4)
C4—H4	0.9300	C13—H13	0.9300
C5—C6	1.395 (3)	C14—C15	1.371 (4)
C5—H5	0.9300	C14—H14	0.9300
C6—C7	1.436 (3)	C15—C16	1.386 (3)
C7—C8	1.342 (3)	C15—H15	0.9300
C7—C9	1.505 (3)	C16—H16	0.9300
C8—N1	1.432 (2)	N1—S1	1.6604 (15)
C8—C10	1.485 (3)	N2—N3	1.222 (3)
C9—H9A	0.9600	N3—N4	1.119 (3)
C9—H9B	0.9600	O1—S1	1.4190 (16)
C9—H9C	0.9600	O2—S1	1.4200 (15)
C10—N2	1.488 (3)

C2—C1—C6	121.61 (19)	C8—C10—H10B	109.1
C2—C1—N1	130.98 (18)	N2—C10—H10B	109.1
C6—C1—N1	107.41 (16)	H10A—C10—H10B	107.9
C3—C2—C1	117.1 (2)	C16—C11—C12	121.6 (2)
C3—C2—H2	121.5	C16—C11—S1	119.92 (17)
C1—C2—H2	121.5	C12—C11—S1	118.48 (16)
C4—C3—C2	122.0 (2)	C13—C12—C11	119.0 (2)
C4—C3—H3	119.0	C13—C12—H12	120.5
C2—C3—H3	119.0	C11—C12—H12	120.5
C5—C4—C3	121.3 (2)	C14—C13—C12	119.9 (3)
C5—C4—H4	119.4	C14—C13—H13	120.0
C3—C4—H4	119.4	C12—C13—H13	120.0
C4—C5—C6	118.1 (2)	C13—C14—C15	121.2 (2)
C4—C5—H5	120.9	C13—C14—H14	119.4
C6—C5—H5	120.9	C15—C14—H14	119.4
C1—C6—C5	119.90 (19)	C14—C15—C16	120.3 (3)
C1—C6—C7	107.95 (17)	C14—C15—H15	119.9
C5—C6—C7	132.2 (2)	C16—C15—H15	119.9
C8—C7—C6	108.61 (17)	C11—C16—C15	118.0 (3)
C8—C7—C9	127.5 (2)	C11—C16—H16	121.0
C6—C7—C9	123.8 (2)	C15—C16—H16	121.0
C7—C8—N1	108.70 (16)	C1—N1—C8	107.24 (14)
C7—C8—C10	126.69 (18)	C1—N1—S1	121.74 (13)
N1—C8—C10	124.23 (17)	C8—N1—S1	126.47 (12)
C7—C9—H9A	109.5	N3—N2—C10	118.10 (19)
C7—C9—H9B	109.5	N4—N3—N2	171.4 (3)
H9A—C9—H9B	109.5	O1—S1—O2	119.71 (10)
C7—C9—H9C	109.5	O1—S1—N1	105.72 (9)
H9A—C9—H9C	109.5	O2—S1—N1	106.78 (9)
H9B—C9—H9C	109.5	O1—S1—C11	109.20 (10)
C8—C10—N2	112.42 (17)	O2—S1—C11	109.09 (9)
C8—C10—H10A	109.1	N1—S1—C11	105.36 (8)
N2—C10—H10A	109.1

C6—C1—C2—C3	−0.7 (3)	C13—C14—C15—C16	0.3 (4)
N1—C1—C2—C3	178.5 (2)	C12—C11—C16—C15	0.3 (3)
C1—C2—C3—C4	0.1 (4)	S1—C11—C16—C15	−179.36 (17)
C2—C3—C4—C5	0.1 (5)	C14—C15—C16—C11	−0.6 (4)
C3—C4—C5—C6	0.2 (4)	C2—C1—N1—C8	177.9 (2)
C2—C1—C6—C5	1.0 (3)	C6—C1—N1—C8	−2.8 (2)
N1—C1—C6—C5	−178.3 (2)	C2—C1—N1—S1	20.4 (3)
C2—C1—C6—C7	−179.01 (19)	C6—C1—N1—S1	−160.34 (14)
N1—C1—C6—C7	1.6 (2)	C7—C8—N1—C1	3.1 (2)
C4—C5—C6—C1	−0.8 (4)	C10—C8—N1—C1	176.49 (18)
C4—C5—C6—C7	179.3 (2)	C7—C8—N1—S1	159.22 (15)
C1—C6—C7—C8	0.3 (2)	C10—C8—N1—S1	−27.4 (3)
C5—C6—C7—C8	−179.7 (2)	C8—C10—N2—N3	80.5 (3)
C1—C6—C7—C9	−177.3 (2)	C1—N1—S1—O1	−48.72 (17)
C5—C6—C7—C9	2.7 (4)	C8—N1—S1—O1	158.31 (15)
C6—C7—C8—N1	−2.1 (2)	C1—N1—S1—O2	−177.23 (14)
C9—C7—C8—N1	175.4 (2)	C8—N1—S1—O2	29.80 (18)
C6—C7—C8—C10	−175.29 (19)	C1—N1—S1—C11	66.85 (16)
C9—C7—C8—C10	2.2 (4)	C8—N1—S1—C11	−86.12 (17)
C7—C8—C10—N2	91.2 (3)	C16—C11—S1—O1	12.21 (19)
N1—C8—C10—N2	−81.0 (2)	C12—C11—S1—O1	−167.48 (15)
C16—C11—C12—C13	0.2 (3)	C16—C11—S1—O2	144.74 (17)
S1—C11—C12—C13	179.90 (16)	C12—C11—S1—O2	−34.96 (17)
C11—C12—C13—C14	−0.5 (3)	C16—C11—S1—N1	−100.94 (17)
C12—C13—C14—C15	0.3 (4)	C12—C11—S1—N1	79.36 (16)

Hydrogen-bond geometry (Å, º) top

Cg3 is the centroid of the C11–C16 ring.

D—H···A	D—H	H···A	D···A	D—H···A
C14—H14···O1ⁱ	0.93	2.46	3.322 (3)	154
C5—H5···Cg3ⁱⁱ	0.93	2.89	3.714 (3)	148

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

Experimental details

Crystal data
Chemical formula	C₁₆H₁₄N₄O₂S
M_r	326.38
Crystal system, space group	Orthorhombic, Pbca
Temperature (K)	295
a, b, c (Å)	11.0337 (4), 12.1424 (4), 23.2234 (9)
V (Å³)	3111.37 (19)
Z	8
Radiation type	Mo Kα
µ (mm⁻¹)	0.22
Crystal size (mm)	0.30 × 0.25 × 0.25

Data collection
Diffractometer	Bruker Kappa APEXII CCD diffractometer
Absorption correction	–
No. of measured, independent and observed [I > 2σ(I)] reflections	37510, 4231, 2776
R_int	0.049
(sin θ/λ)_max (Å⁻¹)	0.687

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.047, 0.166, 0.99
No. of reflections	4231
No. of parameters	209
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.37, −0.35

Computer programs: APEX2 (Bruker, 2004), SAINT (Bruker, 2004), SHELXS97 (Sheldrick, 2008), ORTEP-3 (Farrugia, 1997), SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009).