Low-temperature redetermination of 1H-indole-3-carbaldehyde

This high precision study has confirmed the previous structure [Golubev & Kondrashev (1984). Zh. Strukt. Khim. 25, 145–149] of the title compound, C₉H₇NO, and the H atoms have been located. In the crystal structure, mol­ecules are linked by an N—H...O hydrogen bond [N...O = 2.826 (2) Å] into a helical chain running along the polar c axis of the ortho­rhom­bic unit cell.

Key indicators

• Single-crystal X-ray study
• T = 173 K
• Mean [sigma](C-C) = 0.003 Å
• R factor = 0.036
• wR factor = 0.096
• Data-to-parameter ratio = 8.5

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT141_ALERT_4_C su on a - Axis Small or Missing (x 100000) .....         10 Ang.
PLAT153_ALERT_1_C The su's on the Cell Axes are Equal (x 100000) .         10 Ang.
PLAT180_ALERT_3_C Check Cell Rounding: # of Values Ending with 0 =          3

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           30.00
           From the CIF: _reflns_number_total               1086
           Count of symmetry unique reflns         1088
           Completeness (_total/calc)             99.82%
           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
   3 ALERT level C = Check and explain
   1 ALERT level G = General alerts; check

   1 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   0 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
   2 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

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S1. Comment

The crystal structure of the title compound, (I), indole-3-carboxaldehyde was refined to R(F) = 0.053 from room-temperature diffraction measurements (Golubev & Kondrashev, 1984). This re-refinement represents an improvement; all H atoms were located and refined. In the crystal structure, the molecules are linked by an N—H···O hydrogen bond (Table 1) to form a helical C(6) chain that propagates along the c axis.

Related literature

For related literature, see: Golubev & Kondrashev (1984).

S2. Experimental

Commercially available indole-3-carboxaldehyde was recrystallized from ethanol to yield crystals of (I).

S3. Refinement

Anomalous dispersion was negligible and Friedel pairs were merged before refinement. All the H atoms were located in difference maps and their positions and U_iso values were freely refined.

Computing details

Data collection: APEXII (Bruker, 2004); cell refinement: SAINT (Bruker, 2004); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: X-SEED (Barbour, 2001); software used to prepare material for publication: publCIF (Westrip, 2007).

Figures

Fig. 1. View of a fragment of a chain of molecules of (I) connected by hydrogen bonds (dashed lines). Displacement ellipsoids are drawn at the 70% probability level, and H atoms are shown as spheres of arbitrary radius.

1H-indole-3-carbaldehyde

Crystal data

C9H7NO	F(000) = 304
Mr = 145.16	Dx = 1.376 Mg m^−3
Orthorhombic, Pca21	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2c -2ac	Cell parameters from 4178 reflections
a = 13.9016 (1) Å	θ = 2.9–29.8°
b = 5.8655 (1) Å	µ = 0.09 mm^−1
c = 8.5928 (1) Å	T = 173 K
V = 700.66 (2) Å^3	Needle, colorless
Z = 4	0.40 × 0.12 × 0.09 mm

Data collection

Bruker APEXII CCD diffractometer	966 reflections with I > 2σ(I)
Radiation source: medium-focus sealed tube	Rint = 0.041
Graphite monochromator	θmax = 30.0°, θmin = 2.9°
φ and ω scans	h = −19→19
11794 measured reflections	k = −8→8
1086 independent reflections	l = −12→12

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)] = 0.036	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.096	All H-atom parameters refined
S = 1.10	w = 1/[σ^2(Fo^2) + (0.0608P)^2 + 0.0666P] where P = (Fo^2 + 2Fc^2)/3
1086 reflections	(Δ/σ)max = 0.001
128 parameters	Δρmax = 0.27 e Å^−3
1 restraint	Δρmin = −0.16 e Å^−3

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
O1	0.26655 (11)	0.4245 (2)	0.49999 (18)	0.0281 (3)
N1	0.29363 (13)	1.0779 (3)	0.2067 (2)	0.0246 (4)
C1	0.37908 (13)	0.9581 (3)	0.1919 (2)	0.0203 (4)
C2	0.45965 (15)	1.0078 (3)	0.1013 (2)	0.0244 (4)
C3	0.53265 (15)	0.8489 (4)	0.0993 (2)	0.0257 (4)
C4	0.52637 (14)	0.6458 (3)	0.1862 (2)	0.0258 (4)
C5	0.44695 (14)	0.5987 (3)	0.2777 (2)	0.0216 (4)
C6	0.37122 (13)	0.7567 (3)	0.28066 (19)	0.0190 (3)
C7	0.27630 (14)	0.7600 (3)	0.3492 (2)	0.0201 (4)
C8	0.23266 (15)	0.9593 (3)	0.2984 (2)	0.0244 (4)
C9	0.22880 (14)	0.5972 (3)	0.4472 (2)	0.0219 (4)
H1	0.281 (2)	1.216 (5)	0.153 (4)	0.047 (8)*
H2	0.4644 (19)	1.148 (4)	0.042 (3)	0.028 (7)*
H3	0.590 (2)	0.870 (5)	0.027 (4)	0.044 (9)*
H4	0.5805 (19)	0.540 (5)	0.183 (4)	0.037 (7)*
H5	0.4432 (17)	0.461 (4)	0.334 (3)	0.020 (6)*
H8	0.169 (2)	1.007 (5)	0.316 (4)	0.036 (7)*
H9	0.1626 (17)	0.638 (4)	0.466 (3)	0.022 (6)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O1	0.0332 (8)	0.0218 (6)	0.0292 (7)	0.0000 (6)	0.0022 (6)	0.0071 (6)
N1	0.0322 (9)	0.0182 (7)	0.0233 (8)	0.0048 (6)	0.0001 (7)	0.0052 (6)
C1	0.0276 (9)	0.0155 (7)	0.0179 (7)	−0.0005 (6)	−0.0032 (7)	0.0002 (7)
C2	0.0330 (10)	0.0197 (9)	0.0204 (8)	−0.0069 (7)	−0.0017 (8)	0.0016 (7)
C3	0.0234 (9)	0.0307 (10)	0.0231 (8)	−0.0064 (7)	0.0010 (7)	−0.0013 (8)
C4	0.0249 (9)	0.0262 (9)	0.0262 (9)	0.0017 (7)	−0.0009 (8)	0.0003 (8)
C5	0.0258 (9)	0.0187 (8)	0.0203 (7)	0.0005 (7)	−0.0028 (7)	0.0016 (7)
C6	0.0253 (8)	0.0170 (7)	0.0147 (7)	−0.0022 (6)	−0.0026 (7)	0.0002 (6)
C7	0.0254 (9)	0.0179 (7)	0.0169 (7)	0.0009 (6)	−0.0006 (6)	0.0016 (6)
C8	0.0290 (10)	0.0226 (8)	0.0217 (8)	0.0050 (7)	0.0007 (7)	0.0023 (7)
C9	0.0257 (10)	0.0220 (8)	0.0182 (8)	−0.0001 (7)	0.0028 (7)	−0.0020 (7)

Geometric parameters (Å, º)

O1—C9	1.228 (2)	C4—C5	1.383 (3)
N1—C8	1.350 (3)	C4—H4	0.98 (3)
N1—C1	1.386 (2)	C5—C6	1.403 (3)
N1—H1	0.95 (3)	C5—H5	0.94 (2)
C1—C2	1.395 (3)	C6—C7	1.445 (3)
C1—C6	1.410 (2)	C7—C8	1.388 (3)
C2—C3	1.378 (3)	C7—C9	1.434 (3)
C2—H2	0.97 (3)	C8—H8	0.94 (3)
C3—C4	1.409 (3)	C9—H9	0.96 (2)
C3—H3	1.02 (3)
C8—N1—C1	109.28 (16)	C4—C5—C6	118.50 (17)
C8—N1—H1	127.1 (19)	C4—C5—H5	120.5 (15)
C1—N1—H1	123.5 (19)	C6—C5—H5	121.0 (15)
N1—C1—C2	129.28 (17)	C5—C6—C1	119.06 (17)
N1—C1—C6	108.00 (16)	C5—C6—C7	134.52 (16)
C2—C1—C6	122.63 (17)	C1—C6—C7	106.27 (15)
C3—C2—C1	117.20 (17)	C8—C7—C9	122.99 (18)
C3—C2—H2	121.1 (16)	C8—C7—C6	106.37 (16)
C1—C2—H2	121.7 (16)	C9—C7—C6	130.62 (17)
C2—C3—C4	121.29 (19)	N1—C8—C7	110.08 (18)
C2—C3—H3	120.1 (17)	N1—C8—H8	122.1 (18)
C4—C3—H3	118.4 (17)	C7—C8—H8	127.6 (18)
C5—C4—C3	121.32 (19)	O1—C9—C7	124.71 (18)
C5—C4—H4	120.4 (17)	O1—C9—H9	123.4 (15)
C3—C4—H4	118.3 (17)	C7—C9—H9	111.9 (15)
C8—N1—C1—C2	175.59 (18)	N1—C1—C6—C7	0.35 (18)
C8—N1—C1—C6	−0.8 (2)	C2—C1—C6—C7	−176.38 (17)
N1—C1—C2—C3	−175.09 (19)	C5—C6—C7—C8	−174.9 (2)
C6—C1—C2—C3	0.9 (3)	C1—C6—C7—C8	0.25 (19)
C1—C2—C3—C4	−0.5 (3)	C5—C6—C7—C9	3.4 (3)
C2—C3—C4—C5	−0.4 (3)	C1—C6—C7—C9	178.53 (19)
C3—C4—C5—C6	1.0 (3)	C1—N1—C8—C7	1.0 (2)
C4—C5—C6—C1	−0.6 (3)	C9—C7—C8—N1	−179.22 (18)
C4—C5—C6—C7	174.08 (19)	C6—C7—C8—N1	−0.8 (2)
N1—C1—C6—C5	176.42 (17)	C8—C7—C9—O1	−176.6 (2)
C2—C1—C6—C5	−0.3 (2)	C6—C7—C9—O1	5.4 (3)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O1^i	0.95 (3)	1.91 (3)	2.826 (2)	161 (3)

Symmetry code: (i) −x+1/2, y+1, z−1/2.