A second monoclinic polymorph of 2-(diformyl­methyl­idene)-3,3-dimethyl-2,3-dihydro-1H-indole

Khaledi, H.; Saharin, S.M.; Mohd Ali, H.; Robinson, W.T.; Abdulla, M.A.

doi:10.1107/S1600536809038495

organic compounds

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Volume 65| Part 10| October 2009| Page o2585

doi:10.1107/S1600536809038495

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A second monoclinic polymorph of 2-(diformylmethylidene)-3,3-dimethyl-2,3-dihydro-1H-indole

Hamid Khaledi,^a Siti Munirah Saharin,^a Hapipah Mohd Ali,^a ^* Ward T. Robinson ^a and Mahmood A. Abdulla ^b

^aDepartment of Chemistry, University of Malaya, 50603 Kuala Lumpur, Malaysia, and ^bDepartment of Molecular Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
^*Correspondence e-mail: hapipah@um.edu.my

(Received 10 September 2009; accepted 23 September 2009; online 30 September 2009)

The crystal structure of the title compound, C₁₃H₁₃NO₂, is a polymorph of the structure first reported by Helliwell et al. [Acta Cryst. (2006), E62, o737-o738]. It is also monoclinic (space group P2₁/c), but with completely different cell constants. The molecular conformations of these polymorphs differ by a 180° rotation of one formyl group. The present molecule is planar [maximum deviation 0.089 (2) Å] with the exception of the two methyl groups which lie on either side of the plane. There are strong intra- and intermolecular N—H⋯O hydrogen bonds. The latter link pairs of molecules across crystallographic centers of symmetry. Two aldehyde O atoms are brought close together [2.896 (4) Å in this arrangement but are not hydrogen bonded. In the earlier polymorph, one formyl group is rotated by 180° to yield intermolecular hydrogen bonding and an infinite polymeric chain. The other formyl group is involved in the same intramolecular hydrogen bonding as has been found here.

Related literature

For the crystal structure of the other polymorph, see: Helliwell et al. (2006 ). For a discussion of crystal growth conditions that can affect the occurrence of polymorphs, see: Hulliger et al. (1994 ). For chemistry involving 2-(diformylmethylidene)-3,3-dimethyl-2,3-dihydro-1H-indole, see: Baradarani et al. (2006 ).

Experimental

Crystal data

C₁₃H₁₃NO₂
M_r = 215.24
Monoclinic, P 2₁ /c
a = 6.9877 (10) Å
b = 18.688 (3) Å
c = 8.2154 (12) Å
β = 90.291 (3)°
V = 1072.8 (3) Å³
Z = 4
Mo Kα radiation
μ = 0.09 mm⁻¹
T = 103 K
0.57 × 0.37 × 0.03 mm

Data collection

Bruker APEXII CCD diffractometer
Absorption correction: multi-scan (SADABS; Sheldrick, 1996 ) T_min = 0.950, T_max = 0.997
4763 measured reflections
1865 independent reflections
1123 reflections with I > 2σ(I)
R_int = 0.072

Refinement

R[F² > 2σ(F²)] = 0.044
wR(F²) = 0.103
S = 0.92
1865 reflections
151 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.26 e Å⁻³
Δρ_min = −0.22 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1⋯O1	0.93 (3)	1.93 (3)	2.642 (3)	132 (2)
N1—H1⋯O1ⁱ	0.93 (3)	2.19 (3)	2.946 (2)	138 (2)
Symmetry code: (i) -x+1, -y+1, -z.

Data collection: APEX2 (Bruker, 2007 ); cell refinement: SAINT (Bruker, 2007); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXL97 and publCIF (Westrip, 2009 ).

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536809038495/om2278sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536809038495/om2278Isup2.hkl

checkCIF report

Related literature top

For the crystal structure of the other polymorph, see: Helliwell et al. (2006). For a discussion of crystal growth conditions that can affect the occurrence of polymorphs, see: Hulliger et al. (1994). For chemistry involving 2-(diformylmethylidene)-3,3-dimethyl-2,3-dihydro-1H-indole, see: Baradarani et al. (2006).

Experimental top

A solution of trimethylindolenine, (5.57 g, 35 mmol), in anhydrous dimethylformamide (15 ml) was cooled in an ice bath. A solution of phosphoryl chloride (10 ml) in dimethylformamide (15 ml) was added dropwise with stirring over a period of 1 h at below 283 K. The cooling bath was removed and the reaction mixture was stirred at 363 K for 2 h. The resulting solution was poured onto ice water (400 ml), the pH was adjusted to 9.0 by the addition of aqueous NaOH (35%) whereupon the solid product was precipitated. It was filtered, washed with hot water, dried and recrystallized from n-hexane/ethyl acetate to give a yellow solid in 4.35 g, 58% yield. Further recrystallization, from ethanol/water (3:1 v/v), led to a mixture of lath and prismatic habits. The prism cell dimensions confirmed the form reported earlier but the laths appeared new.

Computing details top

Data collection: APEX2 (Bruker, 2007); cell refinement: SAINT (Bruker, 2007); data reduction: SAINT (Bruker, 2007); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008) and publCIF (Westrip, 2009).

Figures top

Fig. 1. A perspective drawing of two molecules of the title compound showing dimerization through intermolecular H-bonds. Displacement ellipsoids are drawn at the 30% probability level. Symmetry code: A = 1-x, 1-y, -z

2-(diformylmethylidene)-3,3-dimethyl-2,3-dihydro-1H-indole top

Crystal data top

C₁₃H₁₃NO₂	F(000) = 456
M_r = 215.24	D_x = 1.333 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 864 reflections
a = 6.9877 (10) Å	θ = 2.2–24.7°
b = 18.688 (3) Å	µ = 0.09 mm⁻¹
c = 8.2154 (12) Å	T = 103 K
β = 90.291 (3)°	Lath, yellow
V = 1072.8 (3) Å³	0.57 × 0.37 × 0.03 mm
Z = 4

Data collection top

Bruker APEXII CCD diffractometer	1865 independent reflections
Radiation source: fine-focus sealed tube	1123 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.072
ω scans	θ_max = 25.1°, θ_min = 2.2°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	h = −5→8
T_min = 0.950, T_max = 0.997	k = −21→22
4763 measured reflections	l = −9→9

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)] = 0.044	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.103	H atoms treated by a mixture of independent and constrained refinement
S = 0.92	w = 1/[σ²(F_o²) + (0.0424P)²] where P = (F_o² + 2F_c²)/3
1865 reflections	(Δ/σ)_max < 0.001
151 parameters	Δρ_max = 0.26 e Å⁻³
0 restraints	Δρ_min = −0.22 e Å⁻³

Crystal data top

C₁₃H₁₃NO₂	V = 1072.8 (3) Å³
M_r = 215.24	Z = 4
Monoclinic, P2₁/c	Mo Kα radiation
a = 6.9877 (10) Å	µ = 0.09 mm⁻¹
b = 18.688 (3) Å	T = 103 K
c = 8.2154 (12) Å	0.57 × 0.37 × 0.03 mm
β = 90.291 (3)°

Data collection top

Bruker APEXII CCD diffractometer	1865 independent reflections
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	1123 reflections with I > 2σ(I)
T_min = 0.950, T_max = 0.997	R_int = 0.072
4763 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.044	0 restraints
wR(F²) = 0.103	H atoms treated by a mixture of independent and constrained refinement
S = 0.92	Δρ_max = 0.26 e Å⁻³
1865 reflections	Δρ_min = −0.22 e Å⁻³
151 parameters

Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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
O1	0.4035 (3)	0.49657 (9)	0.1554 (2)	0.0308 (5)
O2	0.4628 (3)	0.65460 (9)	0.6032 (2)	0.0346 (5)
N1	0.7133 (3)	0.57750 (10)	0.1457 (2)	0.0192 (5)
H1	0.637 (4)	0.5445 (14)	0.092 (3)	0.054 (9)*
C1	0.6569 (3)	0.60337 (11)	0.2893 (3)	0.0195 (5)
C2	0.8061 (3)	0.65754 (12)	0.3488 (3)	0.0199 (6)
C3	0.9518 (3)	0.65385 (12)	0.2146 (3)	0.0197 (6)
C4	1.1227 (3)	0.68961 (12)	0.1934 (3)	0.0225 (6)
H4	1.1673	0.7228	0.2725	0.027*
C5	1.2281 (4)	0.67584 (12)	0.0535 (3)	0.0253 (6)
H5	1.3459	0.7002	0.0373	0.030*
C6	1.1650 (4)	0.62761 (12)	−0.0621 (3)	0.0259 (6)
H6	1.2405	0.6190	−0.1560	0.031*
C7	0.9931 (3)	0.59154 (12)	−0.0434 (3)	0.0221 (6)
H7	0.9479	0.5585	−0.1226	0.027*
C8	0.8906 (3)	0.60609 (11)	0.0965 (3)	0.0196 (5)
C9	0.4879 (3)	0.57998 (12)	0.3639 (3)	0.0192 (6)
C10	0.3723 (4)	0.52662 (12)	0.2862 (3)	0.0258 (6)
H10	0.2591	0.5128	0.3415	0.031*
C11	0.4105 (4)	0.60552 (13)	0.5160 (3)	0.0257 (6)
H11	0.3018	0.5801	0.5539	0.031*
C12	0.7221 (4)	0.73372 (12)	0.3575 (3)	0.0262 (6)
H12A	0.8248	0.7679	0.3812	0.039*
H12B	0.6261	0.7359	0.4438	0.039*
H12C	0.6621	0.7458	0.2530	0.039*
C13	0.8926 (3)	0.63454 (12)	0.5131 (3)	0.0241 (6)
H13A	0.9436	0.5859	0.5039	0.036*
H13B	0.7932	0.6357	0.5968	0.036*
H13C	0.9961	0.6674	0.5433	0.036*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0343 (11)	0.0320 (10)	0.0261 (10)	−0.0086 (9)	−0.0002 (8)	−0.0040 (8)
O2	0.0367 (12)	0.0377 (11)	0.0295 (10)	−0.0023 (9)	0.0058 (9)	−0.0071 (9)
N1	0.0143 (12)	0.0217 (11)	0.0215 (11)	−0.0051 (9)	0.0010 (9)	−0.0019 (9)
C1	0.0213 (15)	0.0178 (12)	0.0192 (12)	0.0006 (11)	−0.0039 (11)	0.0024 (10)
C2	0.0234 (15)	0.0187 (12)	0.0176 (12)	−0.0011 (11)	0.0010 (11)	−0.0001 (10)
C3	0.0223 (15)	0.0183 (12)	0.0185 (12)	0.0021 (11)	0.0003 (11)	0.0028 (10)
C4	0.0205 (15)	0.0230 (13)	0.0239 (13)	−0.0023 (11)	−0.0024 (11)	0.0018 (10)
C5	0.0198 (15)	0.0262 (14)	0.0299 (14)	−0.0006 (11)	0.0033 (12)	0.0067 (11)
C6	0.0292 (17)	0.0253 (13)	0.0233 (13)	0.0041 (12)	0.0055 (12)	0.0039 (11)
C7	0.0227 (15)	0.0237 (13)	0.0201 (12)	−0.0017 (11)	0.0009 (11)	0.0000 (10)
C8	0.0208 (14)	0.0157 (12)	0.0223 (12)	0.0028 (11)	0.0000 (11)	0.0031 (10)
C9	0.0154 (14)	0.0216 (13)	0.0204 (12)	−0.0019 (11)	−0.0005 (11)	0.0033 (10)
C10	0.0235 (16)	0.0267 (14)	0.0271 (14)	−0.0004 (12)	0.0010 (12)	0.0077 (11)
C11	0.0207 (15)	0.0278 (14)	0.0286 (14)	0.0045 (12)	−0.0003 (12)	0.0040 (12)
C12	0.0313 (16)	0.0215 (13)	0.0259 (13)	0.0023 (12)	0.0020 (12)	−0.0006 (10)
C13	0.0214 (15)	0.0301 (14)	0.0207 (13)	−0.0033 (11)	−0.0011 (11)	0.0016 (10)

Geometric parameters (Å, º) top

O1—C10	1.233 (3)	C5—H5	0.9500
O2—C11	1.219 (3)	C6—C7	1.387 (3)
N1—C1	1.336 (3)	C6—H6	0.9500
N1—C8	1.410 (3)	C7—C8	1.384 (3)
N1—H1	0.93 (3)	C7—H7	0.9500
C1—C9	1.403 (3)	C9—C10	1.431 (3)
C1—C2	1.531 (3)	C9—C11	1.445 (3)
C2—C3	1.506 (3)	C10—H10	0.9500
C2—C13	1.538 (3)	C11—H11	0.9500
C2—C12	1.542 (3)	C12—H12A	0.9800
C3—C4	1.380 (3)	C12—H12B	0.9800
C3—C8	1.384 (3)	C12—H12C	0.9800
C4—C5	1.392 (3)	C13—H13A	0.9800
C4—H4	0.9500	C13—H13B	0.9800
C5—C6	1.380 (3)	C13—H13C	0.9800

C1—N1—C8	112.3 (2)	C6—C7—H7	121.7
C1—N1—H1	119.3 (17)	C3—C8—C7	123.3 (2)
C8—N1—H1	128.4 (17)	C3—C8—N1	108.2 (2)
N1—C1—C9	121.7 (2)	C7—C8—N1	128.5 (2)
N1—C1—C2	108.5 (2)	C1—C9—C10	119.8 (2)
C9—C1—C2	129.8 (2)	C1—C9—C11	126.5 (2)
C3—C2—C1	101.40 (18)	C10—C9—C11	113.8 (2)
C3—C2—C13	111.46 (19)	O1—C10—C9	127.1 (2)
C1—C2—C13	111.06 (18)	O1—C10—H10	116.4
C3—C2—C12	109.57 (18)	C9—C10—H10	116.4
C1—C2—C12	111.51 (19)	O2—C11—C9	130.1 (2)
C13—C2—C12	111.43 (18)	O2—C11—H11	114.9
C4—C3—C8	119.2 (2)	C9—C11—H11	114.9
C4—C3—C2	131.2 (2)	C2—C12—H12A	109.5
C8—C3—C2	109.6 (2)	C2—C12—H12B	109.5
C3—C4—C5	118.4 (2)	H12A—C12—H12B	109.5
C3—C4—H4	120.8	C2—C12—H12C	109.5
C5—C4—H4	120.8	H12A—C12—H12C	109.5
C6—C5—C4	121.4 (2)	H12B—C12—H12C	109.5
C6—C5—H5	119.3	C2—C13—H13A	109.5
C4—C5—H5	119.3	C2—C13—H13B	109.5
C5—C6—C7	121.0 (2)	H13A—C13—H13B	109.5
C5—C6—H6	119.5	C2—C13—H13C	109.5
C7—C6—H6	119.5	H13A—C13—H13C	109.5
C8—C7—C6	116.7 (2)	H13B—C13—H13C	109.5
C8—C7—H7	121.7

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O1	0.93 (3)	1.93 (3)	2.642 (3)	132 (2)
N1—H1···O1ⁱ	0.93 (3)	2.19 (3)	2.946 (2)	138 (2)

Symmetry code: (i) −x+1, −y+1, −z.

Experimental details

Crystal data
Chemical formula	C₁₃H₁₃NO₂
M_r	215.24
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	103
a, b, c (Å)	6.9877 (10), 18.688 (3), 8.2154 (12)
β (°)	90.291 (3)
V (Å³)	1072.8 (3)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.09
Crystal size (mm)	0.57 × 0.37 × 0.03

Data collection
Diffractometer	Bruker APEXII CCD diffractometer
Absorption correction	Multi-scan (SADABS; Sheldrick, 1996)
T_min, T_max	0.950, 0.997
No. of measured, independent and observed [I > 2σ(I)] reflections	4763, 1865, 1123
R_int	0.072
(sin θ/λ)_max (Å⁻¹)	0.596

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.044, 0.103, 0.92
No. of reflections	1865
No. of parameters	151
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.26, −0.22

Computer programs: APEX2 (Bruker, 2007), SAINT (Bruker, 2007), SHELXS97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008) and publCIF (Westrip, 2009).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O1	0.93 (3)	1.93 (3)	2.642 (3)	132 (2)
N1—H1···O1ⁱ	0.93 (3)	2.19 (3)	2.946 (2)	138 (2)

Symmetry code: (i) −x+1, −y+1, −z.

Acknowledgements

The authors thank the University of Malaya for funding this study (UMRG grant No. RG136/09HTM).

References

Baradarani, M. M., Afgan, A., Zebarjadi, F., Hasanzadeh, K. & Joule, J. A. (2006). J. Heterocycl. Chem. 43, 1591–1595. CrossRef CAS Google Scholar
Bruker (2007). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin,USA. Google Scholar
Helliwell, M., Afgan, A., Baradarani, M. M. & Joule, J. A. (2006). Acta Cryst. E62, o737–o738. Web of Science CSD CrossRef IUCr Journals Google Scholar
Hulliger, J. (1994). Angew. Chem. Int. Ed. Engl. 33, 143–162. CrossRef Web of Science Google Scholar
Sheldrick, G. M. (1996). SADABS. University of Göttingen, Germany. Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Westrip, S. P. (2009). publCIF. In preparation. Google Scholar

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CRYSTALLOGRAPHIC
COMMUNICATIONS

ISSN: 2056-9890

Volume 65| Part 10| October 2009| Page o2585

doi:10.1107/S1600536809038495

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		EndNote
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organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

A second monoclinic polymorph of 2-(di­formyl­methyl­­idene)-3,3-di­methyl-2,3-di­hydro-1H-indole

Related literature

Experimental

Crystal data

Data collection

Refinement

Supporting information

Acknowledgements

References

organic compounds

A second monoclinic polymorph of 2-(diformylmethylidene)-3,3-dimethyl-2,3-dihydro-1H-indole