The twinned crystal structure of 3-indolyl­acetic acid

Crystals of the title compound, C₁₀H₉NO₂, whose structure has already been determined four times by different research groups, were found to be twinned. Satisfactory refinement is only possible if the twinning is taken into account. This kind of twinning in the monoclinic crystal system can, in principle, occur if the following condition is met: a·|cosβ| = c/2, i.e. if the short diagonal of the ac plane is of the same length as a or c itself.

Key indicators

• Single-crystal X-ray study
• T = 100 K
• Mean [sigma](C-C) = 0.002 Å
• R factor = 0.029
• wR factor = 0.074
• Data-to-parameter ratio = 13.7

checkCIF results

No syntax errors found

ADDSYM reports no extra symmetry


 Alert Level C:



PLAT_420  Alert C D-H Without Acceptor       N(1)   -   H(1)              ?


 0 Alert Level A = Potentially serious problem

 0 Alert Level B = Potential problem

 1 Alert Level C = Please check

---

S1. Comment

The structure of the title compound, (I), has already be determined (Karle et al., 1964; Chandrasekhar & Raghunathan, 1982; Pfeiffer et al., 1987; Nigovic et al., 2000), but none of the authors has described any twinning.

Surprisingly, we encountered a twinned crystal and satisfactory refinement was only possible when the correct twin law (101/010/001) was applied. This case of twinning is characterized by the fact that one of the face diagonals is of the same length as one of the axes bordering the face. As a result of that, the face diagonal can be an axis of the twin unit cell, whereas the other axis runs in its opposite direction. The present kind of twinning in the monoclinic crystal system can in principle occur if the following condition is met: a^.cos(β) = c/2. The structure determinations of Chandrasekhar & Raghunathan (1982), Pfeiffer et al. (1987) and Nigovic et al. (2000) have led to acceptable results. However, Karle et al. (1964), who had used Equi-inclination Weissenberg photographs and zero-level precession photographs on a thin plate-like crystal to collect the diffracted intensities, ascribed the relatively high R value to the shape of the crystal and to the difficulty to estimate the density of the diffraction spots.

S2. Experimental

The title compound was purchased from Fluka and recrystallized from diethyl ether.

S3. Refinement

After having encountered severe problems during structure solution, anisotropic refinement remained stuck at R1 = 0.28. It was therefore assumed that the crystal was twinned and applying the twin law (101/010/001), which is equivalent to (101/010/001) provided the ultimate success (R1 dropped below 0.1). All H atoms could now be located by difference Fourier synthesis. They were refined with fixed individual displacement parameters [U(H) = 1.2U_eq(C)] using a riding model with C—H(aromatic) = 0.95 Å or C—H(methylene) = 0.99 Å. H atoms bonded to N and O atoms were refined isotropically. The twin ratio refined to 0.416 (1)/0.584 (1).

Computing details

Data collection: X-AREA (Stoe & Cie, 2001); cell refinement: X-AREA; data reduction: X-AREA; program(s) used to solve structure: SHELXS97 (Sheldrick, 1990); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 1990).

Figures

Fig. 1. Perspective view of (I) with the atom numbering; displacement ellipsoids are at the 50% probability level.

(I)

Crystal data

C10H9NO2	F(000) = 368
Mr = 175.18	Dx = 1.356 Mg m^−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71073 Å
a = 17.848 (2) Å	Cell parameters from 10779 reflections
b = 5.2214 (7) Å	θ = 1.7–26.5°
c = 9.568 (1) Å	µ = 0.10 mm^−1
β = 105.70 (1)°	T = 100 K
V = 858.39 (17) Å^3	Block, colourless
Z = 4	0.40 × 0.30 × 0.20 mm

Data collection

Stoe IPDS-II two-circle diffractometer	1476 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.050
Graphite monochromator	θmax = 26.4°, θmin = 2.2°
ω scans	h = −22→22
11341 measured reflections	k = −6→6
1756 independent reflections	l = −11→11

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.029	H atoms treated by a mixture of independent and constrained refinement
wR(F^2) = 0.074	w = 1/[σ^2(Fo^2) + (0.0454P)^2 + 0.0141P] where P = (Fo^2 + 2Fc^2)/3
S = 1.01	(Δ/σ)max < 0.001
1756 reflections	Δρmax = 0.12 e Å^−3
128 parameters	Δρmin = −0.12 e Å^−3
0 restraints	Extinction correction: SHELXL97, Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.046 (5)

Special details

Experimental. ;

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
N1	0.78667 (9)	0.2286 (3)	0.31213 (17)	0.0508 (4)
H1	0.8077 (14)	0.099 (5)	0.276 (3)	0.087 (8)*
C1	0.71228 (10)	0.3206 (3)	0.2555 (2)	0.0492 (4)
H1A	0.6752	0.2530	0.1730	0.059*
C2	0.70028 (9)	0.5233 (3)	0.33589 (18)	0.0421 (4)
C3	0.77160 (8)	0.5603 (3)	0.44932 (16)	0.0356 (3)
C4	0.79686 (9)	0.7378 (3)	0.56268 (19)	0.0428 (4)
H4	0.7625	0.8676	0.5775	0.051*
C5	0.87205 (10)	0.7234 (3)	0.6530 (2)	0.0496 (4)
H5	0.8889	0.8439	0.7294	0.060*
C6	0.92328 (9)	0.5336 (3)	0.6329 (2)	0.0522 (4)
H6	0.9745	0.5264	0.6961	0.063*
C7	0.90057 (9)	0.3563 (3)	0.5222 (2)	0.0491 (4)
H7	0.9355	0.2276	0.5084	0.059*
C8	0.82467 (9)	0.3714 (3)	0.43107 (19)	0.0405 (4)
C9	0.62743 (9)	0.6794 (3)	0.3094 (2)	0.0500 (4)
H9B	0.5993	0.6681	0.2051	0.060*
H9A	0.6420	0.8610	0.3311	0.060*
C10	0.57321 (8)	0.6008 (3)	0.39668 (18)	0.0395 (3)
O1	0.58057 (7)	0.4048 (2)	0.46829 (14)	0.0512 (3)
O2	0.51619 (7)	0.7638 (2)	0.38738 (15)	0.0548 (3)
H2	0.4854 (14)	0.697 (5)	0.444 (3)	0.084 (7)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
N1	0.0638 (9)	0.0389 (7)	0.0580 (9)	−0.0064 (7)	0.0308 (8)	−0.0095 (6)
C1	0.0536 (9)	0.0515 (9)	0.0460 (10)	−0.0176 (7)	0.0192 (9)	−0.0014 (8)
C2	0.0411 (8)	0.0452 (8)	0.0453 (9)	−0.0084 (6)	0.0207 (7)	0.0063 (7)
C3	0.0362 (7)	0.0326 (7)	0.0442 (8)	−0.0049 (5)	0.0213 (7)	0.0033 (6)
C4	0.0470 (8)	0.0353 (7)	0.0546 (10)	−0.0013 (7)	0.0281 (8)	−0.0027 (7)
C5	0.0511 (9)	0.0454 (9)	0.0553 (11)	−0.0147 (8)	0.0197 (8)	−0.0075 (7)
C6	0.0379 (8)	0.0556 (10)	0.0629 (11)	−0.0063 (7)	0.0134 (8)	0.0063 (9)
C7	0.0423 (8)	0.0414 (8)	0.0700 (12)	0.0062 (7)	0.0263 (9)	0.0061 (8)
C8	0.0461 (8)	0.0303 (7)	0.0525 (10)	−0.0047 (6)	0.0259 (7)	−0.0012 (7)
C9	0.0401 (8)	0.0579 (10)	0.0551 (11)	−0.0036 (7)	0.0181 (8)	0.0168 (8)
C10	0.0331 (7)	0.0454 (8)	0.0397 (8)	−0.0040 (6)	0.0093 (7)	0.0057 (7)
O1	0.0438 (6)	0.0571 (7)	0.0582 (7)	0.0055 (5)	0.0233 (6)	0.0199 (6)
O2	0.0484 (6)	0.0542 (6)	0.0688 (9)	0.0067 (5)	0.0278 (6)	0.0212 (6)

Geometric parameters (Å, º)

N1—C8	1.376 (2)	C5—H5	0.9500
N1—C1	1.378 (2)	C6—C7	1.382 (3)
N1—H1	0.89 (3)	C6—H6	0.9500
C1—C2	1.359 (2)	C7—C8	1.401 (2)
C1—H1A	0.9500	C7—H7	0.9500
C2—C3	1.445 (2)	C9—C10	1.497 (2)
C2—C9	1.497 (2)	C9—H9B	0.9900
C3—C4	1.405 (2)	C9—H9A	0.9900
C3—C8	1.410 (2)	C10—O1	1.2187 (18)
C4—C5	1.388 (2)	C10—O2	1.3110 (19)
C4—H4	0.9500	O2—H2	0.94 (3)
C5—C6	1.396 (2)
C8—N1—C1	110.06 (14)	C7—C6—H6	119.5
C8—N1—H1	124.9 (17)	C5—C6—H6	119.5
C1—N1—H1	125.0 (17)	C6—C7—C8	118.21 (14)
C2—C1—N1	109.37 (16)	C6—C7—H7	120.9
C2—C1—H1A	125.3	C8—C7—H7	120.9
N1—C1—H1A	125.3	N1—C8—C7	131.40 (14)
C1—C2—C3	106.70 (14)	N1—C8—C3	106.51 (14)
C1—C2—C9	126.21 (16)	C7—C8—C3	122.07 (15)
C3—C2—C9	127.09 (15)	C2—C9—C10	114.78 (13)
C4—C3—C8	118.09 (14)	C2—C9—H9B	108.6
C4—C3—C2	134.52 (14)	C10—C9—H9B	108.6
C8—C3—C2	107.36 (14)	C2—C9—H9A	108.6
C5—C4—C3	119.93 (14)	C10—C9—H9A	108.6
C5—C4—H4	120.0	H9B—C9—H9A	107.5
C3—C4—H4	120.0	O1—C10—O2	123.14 (14)
C4—C5—C6	120.77 (16)	O1—C10—C9	123.81 (14)
C4—C5—H5	119.6	O2—C10—C9	113.04 (13)
C6—C5—H5	119.6	C10—O2—H2	106.4 (14)
C7—C6—C5	120.92 (16)
C8—N1—C1—C2	−0.17 (18)	C1—N1—C8—C7	−178.52 (16)
N1—C1—C2—C3	0.17 (17)	C1—N1—C8—C3	0.09 (17)
N1—C1—C2—C9	179.20 (14)	C6—C7—C8—N1	178.32 (16)
C1—C2—C3—C4	177.99 (15)	C6—C7—C8—C3	−0.1 (2)
C9—C2—C3—C4	−1.0 (3)	C4—C3—C8—N1	−178.45 (12)
C1—C2—C3—C8	−0.11 (15)	C2—C3—C8—N1	0.01 (15)
C9—C2—C3—C8	−179.13 (14)	C4—C3—C8—C7	0.3 (2)
C8—C3—C4—C5	−0.2 (2)	C2—C3—C8—C7	178.78 (14)
C2—C3—C4—C5	−178.18 (16)	C1—C2—C9—C10	96.2 (2)
C3—C4—C5—C6	−0.1 (2)	C3—C2—C9—C10	−84.92 (19)
C4—C5—C6—C7	0.3 (3)	C2—C9—C10—O1	−10.3 (2)
C5—C6—C7—C8	−0.2 (2)	C2—C9—C10—O2	170.32 (15)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O2—H2···O1^i	0.94 (3)	1.70 (3)	2.6372 (16)	172 (2)

Symmetry code: (i) −x+1, −y+1, −z+1.