Methyl indole-3-carboxylate

The title compound, C₁₀H₉NO₂, was isolated and characterized from an EtOAc extract of marine Streptomyces sp. 060524. All atoms, except the methyl H atoms, are nearly coplanar. There is an inter­molecular N—H...O hydrogen bond in the crystal stucture. The compound is cytotoxic against K562 human chronic leukaemia.

Key indicators

• Single-crystal X-ray study
• T = 298 K
• Mean [sigma](C-C) = 0.003 Å
• R factor = 0.056
• wR factor = 0.152
• Data-to-parameter ratio = 14.4

checkCIF/PLATON results

No syntax errors found



Alert level C
CELLV02_ALERT_1_C  The supplied cell volume s.u. differs from that
            calculated from the cell parameter s.u.'s by > 2
            Calculated cell volume su =       8.88
            Cell volume su given      =       6.00
RINTA01_ALERT_3_C  The value of Rint is greater than 0.10
            Rint given   0.146
PLAT020_ALERT_3_C The value of Rint is greater than 0.10 .........       0.15
PLAT029_ALERT_3_C _diffrn_measured_fraction_theta_full Low .......       0.98
PLAT066_ALERT_1_C Predicted and Reported Transmissions Identical .          ?
PLAT125_ALERT_4_C No _symmetry_space_group_name_Hall Given .......          ?
PLAT152_ALERT_1_C Supplied and Calc Volume s.u. Inconsistent .....          ?
PLAT230_ALERT_2_C Hirshfeld Test Diff for    C7     -   C8      ..       6.16 su

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   8 ALERT level C = Check and explain
   0 ALERT level G = General alerts; check

   3 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
   3 ALERT type 3 Indicator that the structure quality may be low
   1 ALERT type 4 Improvement, methodology, query or suggestion

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Computing details

Data collection: SMART (Siemens, 1996); cell refinement: SAINT (Siemens, 1996); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997a); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997a); molecular graphics: SHELXTL (Sheldrick, 1997b); software used to prepare material for publication: SHELXTL.

Methyl indole-3-carboxylate

Crystal data

C10H9NO2	F(000) = 736
Mr = 175.18	Dx = 1.347 Mg m^−3
Monoclinic, C2/c	Mo Kα radiation, λ = 0.71073 Å
a = 21.382 (4) Å	Cell parameters from 1009 reflections
b = 7.4070 (15) Å	θ = 2.9–26.5°
c = 13.372 (3) Å	µ = 0.10 mm^−1
β = 125.34 (3)°	T = 298 K
V = 1727.6 (6) Å^3	Prism, colourless
Z = 8	0.45 × 0.41 × 0.38 mm

Data collection

Siemens SMART CCD area-detector diffractometer	1752 independent reflections
Radiation source: fine-focus sealed tube	1315 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.146
φ and ω scans	θmax = 26.5°, θmin = 2.3°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	h = −26→26
Tmin = 0.959, Tmax = 0.965	k = −9→5
5009 measured reflections	l = −16→16

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.056	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.152	H-atom parameters constrained
S = 1.06	w = 1/[σ^2(Fo^2) + (0.0677P)^2 + 0.0691P] where P = (Fo^2 + 2Fc^2)/3
1752 reflections	(Δ/σ)max < 0.001
122 parameters	Δρmax = 0.34 e Å^−3
1 restraint	Δρmin = −0.33 e Å^−3

Special details

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 (Ų)

	x	y	z	Uiso*/Ueq
O1	0.23931 (6)	0.28869 (16)	0.36724 (11)	0.0529 (4)
O2	0.35102 (5)	0.43096 (16)	0.49706 (10)	0.0534 (4)
N1	0.23271 (7)	0.90625 (17)	0.35139 (12)	0.0478 (4)
C1	0.16367 (8)	0.6504 (2)	0.28083 (12)	0.0403 (4)
C2	0.15931 (8)	0.8388 (2)	0.27359 (13)	0.0433 (4)
C3	0.09050 (9)	0.9314 (3)	0.19884 (15)	0.0564 (5)
H3	0.0888	1.0569	0.1952	0.068*
C4	0.02488 (10)	0.8286 (3)	0.13045 (17)	0.0658 (5)
H4	−0.0223	0.8859	0.0795	0.079*
C5	0.02772 (9)	0.6419 (3)	0.13603 (16)	0.0626 (5)
H5	−0.0178	0.5770	0.0889	0.075*
C6	0.09592 (8)	0.5490 (3)	0.20931 (14)	0.0517 (4)
H6	0.0970	0.4234	0.2113	0.062*
C7	0.24359 (7)	0.6066 (2)	0.36797 (12)	0.0400 (4)
C8	0.28203 (9)	0.7678 (2)	0.40701 (15)	0.0461 (4)
H8	0.3347	0.7798	0.4639	0.055*
C9	0.27562 (8)	0.4288 (2)	0.40758 (13)	0.0401 (4)
C10	0.38748 (10)	0.2590 (2)	0.54184 (19)	0.0615 (5)
H10A	0.3610	0.1897	0.5671	0.092*
H10B	0.4398	0.2762	0.6104	0.092*
H10C	0.3862	0.1958	0.4780	0.092*
H1	0.2455 (10)	1.0248 (15)	0.3644 (18)	0.080*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O1	0.0529 (6)	0.0330 (7)	0.0656 (7)	−0.0009 (5)	0.0302 (6)	0.0007 (5)
O2	0.0436 (6)	0.0418 (7)	0.0631 (7)	0.0047 (4)	0.0242 (5)	0.0034 (5)
N1	0.0514 (7)	0.0300 (8)	0.0571 (8)	−0.0024 (5)	0.0286 (6)	−0.0030 (6)
C1	0.0463 (8)	0.0319 (9)	0.0442 (7)	0.0009 (6)	0.0271 (6)	0.0008 (6)
C2	0.0487 (8)	0.0366 (10)	0.0463 (7)	0.0021 (6)	0.0284 (7)	0.0010 (6)
C3	0.0577 (9)	0.0429 (10)	0.0642 (10)	0.0129 (7)	0.0327 (8)	0.0066 (8)
C4	0.0484 (9)	0.0645 (15)	0.0713 (11)	0.0126 (9)	0.0270 (8)	0.0084 (10)
C5	0.0435 (8)	0.0579 (13)	0.0695 (10)	−0.0033 (8)	0.0228 (8)	0.0020 (10)
C6	0.0490 (8)	0.0390 (10)	0.0597 (9)	−0.0052 (7)	0.0272 (7)	0.0010 (7)
C7	0.0434 (7)	0.0313 (8)	0.0449 (8)	−0.0018 (6)	0.0252 (6)	−0.0022 (6)
C8	0.0434 (7)	0.0392 (10)	0.0520 (8)	−0.0009 (6)	0.0254 (7)	−0.0018 (6)
C9	0.0421 (7)	0.0354 (8)	0.0451 (7)	−0.0004 (6)	0.0266 (6)	−0.0009 (6)
C10	0.0506 (9)	0.0546 (13)	0.0710 (11)	0.0151 (7)	0.0304 (9)	0.0138 (8)

Geometric parameters (Å, º)

O1—C9	1.2189 (18)	C4—C5	1.384 (3)
O2—C9	1.3415 (18)	C4—H4	0.9300
O2—C10	1.4312 (19)	C5—C6	1.381 (3)
N1—C8	1.345 (2)	C5—H5	0.9300
N1—C2	1.3808 (19)	C6—H6	0.9300
N1—H1	0.906 (10)	C7—C8	1.370 (2)
C1—C2	1.398 (2)	C7—C9	1.437 (2)
C1—C6	1.406 (2)	C8—H8	0.9300
C1—C7	1.4421 (19)	C10—H10A	0.9600
C2—C3	1.390 (2)	C10—H10B	0.9600
C3—C4	1.379 (3)	C10—H10C	0.9600
C3—H3	0.9300
C9—O2—C10	116.44 (13)	C5—C6—C1	117.76 (18)
C8—N1—C2	109.06 (13)	C5—C6—H6	121.1
C8—N1—H1	125.4 (12)	C1—C6—H6	121.1
C2—N1—H1	125.5 (12)	C8—C7—C9	127.25 (14)
C2—C1—C6	119.04 (13)	C8—C7—C1	106.32 (13)
C2—C1—C7	106.33 (12)	C9—C7—C1	126.41 (13)
C6—C1—C7	134.64 (15)	N1—C8—C7	110.36 (15)
N1—C2—C3	129.18 (16)	N1—C8—H8	124.8
N1—C2—C1	107.93 (12)	C7—C8—H8	124.8
C3—C2—C1	122.89 (14)	O1—C9—O2	122.29 (14)
C4—C3—C2	116.87 (18)	O1—C9—C7	124.85 (14)
C4—C3—H3	121.6	O2—C9—C7	112.85 (13)
C2—C3—H3	121.6	O2—C10—H10A	109.5
C3—C4—C5	121.32 (15)	O2—C10—H10B	109.5
C3—C4—H4	119.3	H10A—C10—H10B	109.5
C5—C4—H4	119.3	O2—C10—H10C	109.5
C6—C5—C4	122.12 (16)	H10A—C10—H10C	109.5
C6—C5—H5	118.9	H10B—C10—H10C	109.5
C4—C5—H5	118.9
C8—N1—C2—C3	179.28 (14)	C2—C1—C7—C8	−0.25 (14)
C8—N1—C2—C1	−0.50 (15)	C6—C1—C7—C8	−179.87 (15)
C6—C1—C2—N1	−179.86 (12)	C2—C1—C7—C9	178.33 (13)
C7—C1—C2—N1	0.46 (12)	C6—C1—C7—C9	−1.3 (2)
C6—C1—C2—C3	0.35 (18)	C2—N1—C8—C7	0.34 (18)
C7—C1—C2—C3	−179.34 (13)	C9—C7—C8—N1	−178.62 (12)
N1—C2—C3—C4	−179.58 (14)	C1—C7—C8—N1	−0.05 (17)
C1—C2—C3—C4	0.2 (2)	C10—O2—C9—O1	1.1 (2)
C2—C3—C4—C5	−0.2 (2)	C10—O2—C9—C7	−179.98 (12)
C3—C4—C5—C6	−0.3 (3)	C8—C7—C9—O1	−177.58 (14)
C4—C5—C6—C1	0.8 (2)	C1—C7—C9—O1	4.1 (2)
C2—C1—C6—C5	−0.84 (19)	C8—C7—C9—O2	3.5 (2)
C7—C1—C6—C5	178.74 (14)	C1—C7—C9—O2	−174.74 (11)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O1^i	0.91 (1)	1.96 (1)	2.8381 (18)	162 (2)

Symmetry code: (i) x, y+1, z.