3-(4-Chloro­but­yl)-3H-indole-5-carbo­nitrile

Manikandan, D.; Gomathi, S.; Nirmalram, J.S.; Tagore, S.S.; Sethuraman, V.; Agim, J.; Butcher, R.

doi:10.1107/S2414314617003765

organic compounds

IUCrDATA

ISSN: 2414-3146

Volume 2| Part 3| March 2017| x170376

https://doi.org/10.1107/S2414314617003765

Open

access

3-(4-Chlorobutyl)-3H-indole-5-carbonitrile

Devakumar Manikandan,^a Sundaramoorthy Gomathi,^a Jeyaraman Selvaraj Nirmalram,^b Sadasivam Sharmila Tagore,^a Velusamy Sethuraman,^a ^* Joseph Agim ^c and Ray Butcher ^c

^aDepartment of Chemistry, Periyar Maniammai University, Thanjavur 613 403, Tamil Nadu, India, ^bCentre for Research and Development, PRIST University, Thanjavur 613 403, Tamil Nadu, India, and ^cInorganic & Structural Chemistry, Howard University, Washington, DC 20059, USA
^*Correspondence e-mail: lvsethu13@gmail.com

Edited by P. C. Healy, Griffith University, Australia (Received 3 March 2017; accepted 8 March 2017; online 17 March 2017)

In the title compound, C₁₃H₁₂ClN₂, the indole moiety and the chloroalkyl substituent are nearly coplanar, making a dihedral angle of 1.27 (10)°. In the crystal, a supramolecular sheet parallel to the ab plane is generated via weak C—H⋯Cl hydrogen bonds, aromatic π–π stacking [centroid–centroid distances of 3.5563 (13) and 3.6792 (13) Å] and C—H⋯π interactions.

Keywords: crystal structure; 3-(4-chlorobutyl)-3H-indole-5-carbonitrile,non-covalent interactions; supramolecular sheet.

CCDC reference: 1536778

Structure description

The synthesis of indoles currently is of great interest because of their potential in acting as β-blockers, anti-arrhythmic, antiviral, anti-asthmatic, opioid antagonist and also sexual dysfunction drugs (Biswal et al., 2012 ). The title compound, an indole derivative, is a key intermediate in the synthesis of the antidepressant drug vilazodone hydrochloride (Smith et al., 1981 ). The present study focuses on its crystal structure and the non-covalent interactions present in it.

An ORTEP view of the title compound is shown in Fig. 1. The indole moiety (N1/C2–C9) and the chloroalkyl substituent (C11–C14/Cl1) are nearly coplanar, making a dihedral angle of 1.27 (10)°. The C11—C12—C13—C14 and C12—C13—C14—Cl1 torsion angles are −179.08 (14)° and 178.06 (12)° respectively.

Figure 1
The asymmetric unit, shown in 50% probability displacement ellipsoids.

In the crystal, neighboring molecules self-assemble through weak C—H⋯Cl interactions (Table 1), forming zigzag supramolecular C(9) chains extending along the b-axis direction, as shown in Fig. 2a. π–π stacking interactions are observed between the five- (N1/C2/C3/C9/C8; centroid Cg1) and six-membered rings (C4–C9, centroid Cg2) of symmetry-related molecules [Cg1⋯Cg2^iv = 3.6792 (13) Å, perpendicular distance = 3.3537 (7) Å, slip angle = 23.4°; Cg2⋯Cg2^iv = 3.5563 (13) Å, perpendicular distance = 3.3648 (7) Å, slip angle = 18.9°; symmetry code: (iv) −x, 1 − y, 1 − z] (Fig. 2b). Adjacent chains are linked by weak C—H⋯π interactions (Fig. 2c, Table 1), generating a supramolecular sheet-like architecture parallel to the ab plane.

Table 1
Hydrogen-bond geometry (Å, °)

Cg1 and Cg2 are the centroids of the N1/C2/C3/C9/C8 and C4–C9 rings, respectively.

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C4—H4⋯Cl1ⁱ	0.95	2.80	3.750 (2)	178
C13—H13B⋯Cg2ⁱⁱ	0.99	2.83	3.729 (2)	151
C14—H14A⋯Cg1ⁱⁱⁱ	0.99	2.70	3.619 (2)	154
Symmetry codes: (i) $[-x+1, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (ii) -x+1, -y+1, -z+1; (iii) $[x, -y+{\script{3\over 2}}, z-{\script{1\over 2}}]$ .

Figure 2
A view of a supramolecular sheet (a) generated via weak intermolecular C—H⋯Cl hydrogen bonds, aromatic π–π (b) and weak C—H⋯π interactions (c). [Symmetry codes: (i) 1 − x, − $[{1\over 2}]$ + y, $[{1\over 2}]$ − z; (ii) 1 − x, 1 − y, 1 − z; (iii) x, $[{3\over 2}]$ − y, − $[{1\over 2}]$ + z; (iv) −x, 1 − y, 1 − z.]

Synthesis and crystallization

Crystals of the title compound were obtained by dissolving 3-(4-chlorobutyl)-3H-indole-5-carbonitrile (purchased from the Tokyo Chemical Industry Co. Ltd; 58.17 mg, 0.25 mmol) in 20 ml of hot DMF, warming the resultant solution over a water bath for half an hour and then allowing it to evaporate slowly. After a couple of weeks, colourless block-shaped crystals were obtained.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2.

Table 2
Experimental details

Crystal data
Chemical formula	C₁₃H₁₂ClN₂
M_r	231.70
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	100
a, b, c (Å)	8.870 (2), 9.271 (2), 14.498 (3)
β (°)	100.236 (4)
V (Å³)	1173.3 (4)
Z	4
Radiation type	Mo Kα
μ (mm⁻¹)	0.30
Crystal size (mm)	0.18 × 0.17 × 0.15

Data collection
Diffractometer	Bruker APEX2
Absorption correction	Multi-scan (SADABS; Sheldrick, 2008 )
T_min, T_max	0.618, 0.745
No. of measured, independent and observed [I > 2σ(I)] reflections	7342, 1952, 1632
R_int	0.039
(sin θ/λ)_max (Å⁻¹)	0.586

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.039, 0.114, 1.04
No. of reflections	1952
No. of parameters	145
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.77, −0.26
Computer programs: APEX2 and SAINT (Bruker, 2008 ), SHELXS97 (Sheldrick, 2008), SHELXL2014 (Sheldrick, 2015 ), PLATON (Spek, 2009 ), Mercury (Macrae et al., 2008 ), POV-RAY (Cason, 2004 ) and publCIF (Westrip, 2010 ).

Structural data

CCDC reference: 1536778

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S2414314617003765/hg4020sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314617003765/hg4020Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2414314617003765/hg4020Isup3.cml

checkCIF report

Computing details top

Data collection: APEX2 (Bruker, 2008); cell refinement: SAINT (Bruker, 2008); data reduction: SAINT (Bruker, 2008); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: PLATON (Spek, 2009), Mercury (Macrae et al., 2008) and POV-RAY (Cason, 2004); software used to prepare material for publication: PLATON (Spek, 2009) and publCIF (Westrip, 2010).

3-(4-Chlorobutyl)-3H-indole-5-carbonitrile top

Crystal data top

C₁₃H₁₂ClN₂	F(000) = 484
M_r = 231.70	D_x = 1.312 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 1952 reflections
a = 8.870 (2) Å	θ = 2.6–24.6°
b = 9.271 (2) Å	µ = 0.30 mm⁻¹
c = 14.498 (3) Å	T = 100 K
β = 100.236 (4)°	Block, colourless
V = 1173.3 (4) Å³	0.18 × 0.17 × 0.15 mm
Z = 4

Data collection top

Bruker APEX2 diffractometer	1632 reflections with I > 2σ(I)
Detector resolution: 18.4 pixels mm^-1	R_int = 0.039
ω scans	θ_max = 24.6°, θ_min = 2.6°
Absorption correction: multi-scan (SADABS; Sheldrick, 2008)	h = −10→10
T_min = 0.618, T_max = 0.745	k = −10→10
7342 measured reflections	l = −17→16
1952 independent reflections

Refinement top

Refinement on F²	0 restraints
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.039	H-atom parameters constrained
wR(F²) = 0.114	W = 1/[Σ²(FO²) + (0.0787P)² + 0.103P] where P = (FO² + 2FC²)/3
S = 1.04	(Δ/σ)_max = 0.001
1952 reflections	Δρ_max = 0.77 e Å⁻³
145 parameters	Δρ_min = −0.26 e Å⁻³

Special details top

Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All su's are estimated from the variances of the (full) variance-covariance matrix. The cell esds are taken into account in the estimation of distances, angles and torsion angles

Refinement. Refinement on F² for ALL reflections except those flagged by the user for potential systematic errors. Weighted R-factors wR and all goodnesses of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The observed criterion of F² > 2sigma(F²) is used only for calculating -R-factor-obs 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
Cl1	0.64037 (6)	0.62791 (5)	0.10556 (3)	0.0374 (2)
N1	0.17148 (16)	0.77777 (15)	0.56156 (10)	0.0201 (5)
N2	0.11010 (18)	0.07016 (16)	0.63996 (10)	0.0253 (5)
C2	0.24695 (19)	0.77015 (18)	0.48563 (12)	0.0196 (5)
C3	0.27340 (19)	0.62955 (18)	0.46458 (12)	0.0180 (5)
C4	0.19954 (19)	0.39639 (19)	0.54477 (12)	0.0167 (5)
C5	0.12932 (19)	0.34712 (18)	0.61728 (12)	0.0171 (5)
C6	0.07011 (19)	0.44444 (18)	0.67723 (11)	0.0185 (5)
C7	0.0791 (2)	0.59138 (18)	0.66467 (12)	0.0191 (5)
C8	0.14883 (19)	0.63995 (18)	0.59107 (12)	0.0176 (5)
C9	0.21102 (18)	0.54455 (19)	0.53132 (11)	0.0153 (5)
C10	0.11668 (19)	0.19390 (19)	0.63026 (12)	0.0191 (5)
C11	0.34870 (18)	0.56955 (19)	0.38841 (11)	0.0182 (5)
C12	0.4092 (2)	0.68144 (18)	0.32641 (12)	0.0203 (5)
C13	0.4845 (2)	0.60776 (18)	0.25126 (11)	0.0190 (5)
C14	0.5469 (2)	0.71641 (19)	0.19066 (12)	0.0215 (5)
H2	0.27617	0.85126	0.45284	0.0240*
H4	0.23902	0.33015	0.50508	0.0200*
H6	0.02363	0.40800	0.72665	0.0220*
H7	0.03952	0.65724	0.70453	0.0230*
H11A	0.27405	0.50708	0.34793	0.0220*
H11B	0.43526	0.50774	0.41744	0.0220*
H12A	0.32352	0.74294	0.29572	0.0240*
H12B	0.48507	0.74416	0.36575	0.0240*
H13A	0.40796	0.54622	0.21144	0.0230*
H13B	0.56877	0.54487	0.28208	0.0230*
H14A	0.46219	0.77712	0.15794	0.0260*
H14B	0.62104	0.78010	0.23056	0.0260*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cl1	0.0600 (4)	0.0245 (3)	0.0365 (3)	0.0068 (2)	0.0330 (3)	0.0054 (2)
N1	0.0249 (8)	0.0132 (8)	0.0242 (8)	−0.0009 (6)	0.0095 (6)	−0.0002 (6)
N2	0.0355 (9)	0.0163 (9)	0.0265 (9)	0.0014 (7)	0.0123 (7)	0.0007 (6)
C2	0.0229 (9)	0.0149 (9)	0.0223 (9)	−0.0021 (7)	0.0074 (7)	0.0028 (7)
C3	0.0170 (9)	0.0180 (10)	0.0196 (9)	−0.0001 (7)	0.0053 (7)	0.0007 (7)
C4	0.0177 (9)	0.0154 (9)	0.0178 (9)	0.0020 (7)	0.0053 (7)	−0.0023 (7)
C5	0.0203 (9)	0.0125 (9)	0.0186 (9)	0.0001 (7)	0.0038 (7)	0.0006 (6)
C6	0.0202 (9)	0.0190 (9)	0.0182 (9)	−0.0007 (7)	0.0087 (7)	0.0012 (7)
C7	0.0219 (9)	0.0157 (9)	0.0213 (9)	0.0011 (7)	0.0079 (7)	−0.0024 (7)
C8	0.0182 (9)	0.0144 (10)	0.0203 (9)	0.0005 (7)	0.0036 (7)	−0.0007 (7)
C9	0.0153 (8)	0.0152 (9)	0.0160 (8)	0.0005 (6)	0.0043 (7)	−0.0001 (7)
C10	0.0206 (9)	0.0197 (10)	0.0187 (9)	0.0018 (7)	0.0078 (7)	−0.0003 (7)
C11	0.0209 (9)	0.0158 (9)	0.0194 (9)	0.0002 (7)	0.0074 (7)	0.0018 (7)
C12	0.0235 (10)	0.0179 (9)	0.0207 (9)	0.0004 (8)	0.0074 (7)	0.0027 (7)
C13	0.0236 (9)	0.0162 (9)	0.0186 (9)	−0.0006 (7)	0.0072 (7)	0.0009 (7)
C14	0.0279 (10)	0.0173 (9)	0.0218 (9)	0.0009 (7)	0.0113 (8)	−0.0002 (7)

Geometric parameters (Å, º) top

Cl1—C14	1.8018 (19)	C12—C13	1.536 (2)
N1—C2	1.388 (2)	C13—C14	1.505 (2)
N1—C8	1.374 (2)	C2—H2	0.9500
N2—C10	1.159 (2)	C4—H4	0.9500
C2—C3	1.369 (2)	C6—H6	0.9500
C3—C9	1.433 (2)	C7—H7	0.9500
C3—C11	1.496 (2)	C11—H11A	0.9900
C4—C5	1.391 (2)	C11—H11B	0.9900
C4—C9	1.394 (3)	C12—H12A	0.9900
C5—C6	1.417 (2)	C12—H12B	0.9900
C5—C10	1.440 (2)	C13—H13A	0.9900
C6—C7	1.379 (2)	C13—H13B	0.9900
C7—C8	1.400 (2)	C14—H14A	0.9900
C8—C9	1.417 (2)	C14—H14B	0.9900
C11—C12	1.531 (2)

C2—N1—C8	108.51 (14)	C9—C4—H4	121.00
N1—C2—C3	110.57 (15)	C5—C6—H6	120.00
C2—C3—C9	105.73 (15)	C7—C6—H6	120.00
C2—C3—C11	129.47 (16)	C6—C7—H7	121.00
C9—C3—C11	124.80 (15)	C8—C7—H7	121.00
C5—C4—C9	118.89 (16)	C3—C11—H11A	108.00
C4—C5—C6	121.27 (15)	C3—C11—H11B	108.00
C4—C5—C10	118.59 (15)	C12—C11—H11A	108.00
C6—C5—C10	120.14 (15)	C12—C11—H11B	108.00
C5—C6—C7	120.78 (15)	H11A—C11—H11B	107.00
C6—C7—C8	117.55 (15)	C11—C12—H12A	109.00
N1—C8—C7	130.22 (16)	C11—C12—H12B	109.00
N1—C8—C9	107.21 (15)	C13—C12—H12A	109.00
C7—C8—C9	122.57 (15)	C13—C12—H12B	109.00
C3—C9—C4	133.08 (16)	H12A—C12—H12B	108.00
C3—C9—C8	107.97 (15)	C12—C13—H13A	109.00
C4—C9—C8	118.93 (15)	C12—C13—H13B	109.00
N2—C10—C5	178.24 (19)	C14—C13—H13A	109.00
C3—C11—C12	115.51 (14)	C14—C13—H13B	109.00
C11—C12—C13	110.93 (14)	H13A—C13—H13B	108.00
C12—C13—C14	111.58 (14)	Cl1—C14—H14A	109.00
Cl1—C14—C13	110.89 (12)	Cl1—C14—H14B	109.00
N1—C2—H2	125.00	C13—C14—H14A	109.00
C3—C2—H2	125.00	C13—C14—H14B	109.00
C5—C4—H4	121.00	H14A—C14—H14B	108.00

C8—N1—C2—C3	0.3 (2)	C5—C4—C9—C8	−0.9 (2)
C2—N1—C8—C7	179.71 (18)	C4—C5—C6—C7	0.7 (3)
C2—N1—C8—C9	−0.42 (19)	C10—C5—C6—C7	−178.91 (16)
N1—C2—C3—C9	−0.1 (2)	C5—C6—C7—C8	−0.2 (3)
N1—C2—C3—C11	179.14 (16)	C6—C7—C8—N1	178.92 (17)
C2—C3—C9—C4	178.35 (18)	C6—C7—C8—C9	−0.9 (3)
C2—C3—C9—C8	−0.18 (19)	N1—C8—C9—C3	0.37 (19)
C11—C3—C9—C4	−0.9 (3)	N1—C8—C9—C4	−178.40 (15)
C11—C3—C9—C8	−179.45 (16)	C7—C8—C9—C3	−179.75 (16)
C2—C3—C11—C12	1.9 (3)	C7—C8—C9—C4	1.5 (3)
C9—C3—C11—C12	−179.01 (15)	C3—C11—C12—C13	179.74 (14)
C9—C4—C5—C6	−0.1 (3)	C11—C12—C13—C14	−179.08 (14)
C9—C4—C5—C10	179.47 (16)	C12—C13—C14—Cl1	178.06 (12)
C5—C4—C9—C3	−179.31 (18)

Hydrogen-bond geometry (Å, º) top

Cg1 and Cg2 are the centroids of the N1/C2/C3/C9/C8 and C4–C9 rings, respectively.

D—H···A	D—H	H···A	D···A	D—H···A
C4—H4···Cl1ⁱ	0.95	2.80	3.750 (2)	178
C13—H13B···Cg2ⁱⁱ	0.99	2.83	3.729 (2)	151
C14—H14A···Cg1ⁱⁱⁱ	0.99	2.70	3.619 (2)	154

Symmetry codes: (i) −x+1, y−1/2, −z+1/2; (ii) −x+1, −y+1, −z+1; (iii) x, −y+3/2, z−1/2.

Acknowledgements

The authors wish to acknowledge the assistance of Dr Matthias Zeller with the data collection and NSF Grant CHE 0087210, Ohio Board of Regents Grant CAP-491, and Youngstown State University for funds to purchase the X-ray diffractometer. RJB wishes to acknowledge NSF award 1205608, Partnership for Reduced Dimensional Materials, for partial funding of this research.

References

Biswal, S., Sahoo, U., Sethy, S., Kumar, H. K. S. & Banerjee, M. (2012). Asian J. Pharm. Clin. Res. 5, 1–6. CAS Google Scholar
Bruker (2008). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Cason, C. J. (2004). POV-RAY for Windows. Persistence of Vision, Raytracer Pty. Ltd, Victoria, Australia. URL: https://www.povray.org. Google Scholar
Macrae, C. F., Bruno, I. J., Chisholm, J. A., Edgington, P. R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., van de Streek, J. & Wood, P. A. (2008). J. Appl. Cryst. 41, 466–470. Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Sheldrick, G. M. (2015). Acta Cryst. C71, 3–8. Web of Science CrossRef IUCr Journals Google Scholar
Smith, C. B., Garcia-Sevilla, J. A. & Hollingsworth, P. J. (1981). Brain Res. 210, 413–418. CrossRef CAS PubMed Google Scholar
Spek, A. L. (2009). Acta Cryst. D65, 148–155. Web of Science CrossRef CAS IUCr Journals Google Scholar
Westrip, S. P. (2010). J. Appl. Cryst. 43, 920–925. Web of Science CrossRef CAS IUCr Journals Google Scholar

This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.

IUCrDATA

ISSN: 2414-3146

Volume 2| Part 3| March 2017| x170376

https://doi.org/10.1107/S2414314617003765

Open

access

Format		BIBTeX
		EndNote
		RefMan
		Refer
		Medline
		CIF
		SGML
		Plain Text
		Text

Format		BIBTeX
		EndNote
		RefMan
		Refer
		Medline
		CIF
		SGML
		Plain Text
		Text

Search IUCr Journals		doi		Advanced search
Author		volume	page

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

3-(4-Chloro­but­yl)-3H-indole-5-carbo­nitrile

Structure description

Synthesis and crystallization

Refinement

Structural data

Acknowledgements

References

organic compounds

3-(4-Chlorobutyl)-3H-indole-5-carbonitrile