tert-Butyl 2,3-di­hydro-1H-cyclo­penta­[b]indole-4-carboxyl­ate

Jordon, J.A.; Badenock, J.C.; Gribble, G.W.; Kaur, M.; Jasinski, J.P.

doi:10.1107/S2414314616014681

organic compounds

IUCrDATA

ISSN: 2414-3146

Volume 1| Part 9| September 2016| x161468

doi:10.1107/S2414314616014681

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tert-Butyl 2,3-dihydro-1H-cyclopenta[b]indole-4-carboxylate

Jason A. Jordon,^a Jeanese C. Badenock,^a Gordon W. Gribble,^b Manpreet Kaur ^c and Jerry P. Jasinski ^c ^*

^aDepartment of Biological and Chemical Sciences, University of the West Indies, Cave Hill, Barbados, ^bDepartment of Chemistry, Dartmouth College, Hanover, NH 03755-3564, USA, and ^cDepartment of Chemistry, Keene State College, 229 Main Street, Keene, NH 03435-2001, USA
^*Correspondence e-mail: jjasinski@keene.edu

Edited by R. J. Butcher, Howard University, USA (Received 1 September 2016; accepted 16 September 2016; online 27 September 2016)

In the title molecule, C₁₆H₁₉NO₂, all the non-hydrogen atoms except two of the C atoms of the tert-butyl group lie on a crystallographic mirror plane. No classical hydrogen bonds are observed. The crystal packing is influenced by weak π–π and C—H⋯π interactions.

Keywords: crystal structure; π–π stacking interactions; C—H⋯π interactions; mirror plane.

CCDC reference: 1504684

Structure description

We report herein the crystal structure of the title compound, which confirms the previously assigned structure in which it was envisioned that the coupling of an indole with a protected hydroxyl benzaldehyde appendage would install the required vinyl group found in the target molecules Prenostodione, Scytonemin and Nostodione (Macor et al., 1989 ; Badenock et al., 2013 ). As such, and in preparation for the coupling, commercially available 1,2,3,4-tetrahydrocyclopenta[b]indole was converted to the N-BOC derivative using a standard protection protocol in 87% yield. All the atoms except C15 (see Fig. 1) lie on a crystallographic mirror plane: the second methyl group outside the mirror plane is symmetry related and generates the third methyl group in the tert-butyl group.

Figure 1
The molecular structure of the title compound, showing the atom-labeling scheme. Displacement ellipsoids are drawn at the 50% probability level.

In the crystal, the molecules are in parallel layers alternately inverted along the c axis, parallel to the ac plane (Fig2. 2 and 3). The crystal packing is influenced by weak π–π [Cg1–Cg1 and Cg1–Cg2; Cg1–Cg1 = 3.8718 (5) Å and Cg1–Cg2 = 3.7142 (4) Å, where Cg1 is the centroid of the N1/C1/C5/C6/C11 eing and Cg2 is the centroid of the C1–C5 ring] stacking interactions involving the pyrrole and cyclopentyl moieties and C2—H2(A/B)⋯Cg3(π) [C—H⋯π distance = 2.8 (8) Å; symmetry code: −x + 1, y + $[{1\over 2}]$ (H2A) or y − $[{1\over 2}]$ (H2B), −z + 2; where Cg3 is the centroid of the C6–C11 ring] interactions involving the benzene ring.

Figure 2
The packing of the title compound, viewed along the b axis.

Figure 3
Part of the crystal structure of the title compound, showing the planes of molecules arranged in parallel layers alternately inverted along the c axis, parallel to the ac plane.

Synthesis and crystallization

To a stirred solution of 1,2,3,4-tetrahydrocyclopenta[b]indole (2.48 g, 15.7 mmol, 1.0 equivalent) in freshly distilled THF (75 ml) was added DMAP (0.10 g, 0.79 mmol, 0.05 equivalents) and di-tert-butyl dicarbonate (5.31 g, 24.3 mmol, 1.5 equivalents), and the resulting mixture allowed to stir at room temperature overnight (Grehn & Ragnarsson, 1984 ). The solvent was removed via rotary evaporation and the subsequent brown residue was absorbed directly onto silica and purified using flash column chromatography (9:1 hexanes–ethyl acetate). tert-Butyl 2,3-dihydro-1H-cyclopenta[b]indole-4-carboxylate was obtained as a pale-yellow solid (yield 3.53 g, 87%). Crystals suitable for X-ray diffraction were recrystallized from methanol solution (m.p. 389.0–389.4 K). ¹H NMR (CDCl₃): δ 8.15–8.17 (d, J = 7.5 Hz, 1H), 7.33–7.35 (m, 1H), 7.16–7.23 (m, 2H), 3.04–3.07 (m, 2H), 2.72–2.76 (m, 2H), 2.42–2.49 (m, 2H), 1.63 (s, 9H); ¹³C NMR (CDCl₃): δ 150.1, 144.1, 140.2, 126.9, 124.5, 122.9, 122.6, 118.6, 115.8, 83.0, 29.2, 28.3, 27.5, 24.1; IR ν film) 3315, 3053, 2980, 2860, 1727, 1611,1476, 1453 cm⁻¹; UV λ_max (95% EtOH) 204, 230, 272 nm. Analysis calculated for C₁₆H₁₉NO₂: C 74.68, H 7.44, N 5.44%; found: C 74.63, H 7.33, N 5.50.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 1.

Table 1
Experimental details

Crystal data
Chemical formula	C₁₆H₁₉NO₂
M_r	257.32
Crystal system, space group	Orthorhombic, Pnma
Temperature (K)	173
a, b, c (Å)	19.6761 (11), 7.2330 (4), 9.9258 (7)
V (Å³)	1412.61 (15)
Z	4
Radiation type	Mo Kα
μ (mm⁻¹)	0.08
Crystal size (mm)	0.38 × 0.26 × 0.15

Data collection
Diffractometer	Rigaku-Oxford Diffraction
Absorption correction	Multi-scan (CrysAlis PRO & CrysAlis RED; Rigaku-Oxford Diffraction, 2012 $[Rigaku-Oxford Diffraction (2012). CrysAlis PRO and CrysAlis RED. Rigaku Americas Corporation, The Woodlands, Texas, USA.]$ )
T_min, T_max	0.970, 0.988
No. of measured, independent and observed [I > 2σ(I)] reflections	12388, 1808, 1486
R_int	0.029
(sin θ/λ)_max (Å⁻¹)	0.658

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.056, 0.147, 1.11
No. of reflections	1808
No. of parameters	113
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.16, −0.18
Computer programs: CrysAlis PRO (Rigaku-Oxford Diffraction, 2012 $[Rigaku-Oxford Diffraction (2012). CrysAlis PRO and CrysAlis RED. Rigaku Americas Corporation, The Woodlands, Texas, USA.]$ ), CrysAlis RED (Rigaku-Oxford Diffraction, 2012 $[Rigaku-Oxford Diffraction (2012). CrysAlis PRO and CrysAlis RED. Rigaku Americas Corporation, The Woodlands, Texas, USA.]$ ), SHELXL2014 (Sheldrick, 2015b ), SHELXT (Sheldrick, 2015a ) and OLEX2 (Dolomanov et al., 2009 ).

Structural data

CCDC reference: 1504684

Crystal structure: contains datablock I. DOI: 10.1107/S2414314616014681/bv4003sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S2414314616014681/bv4003Isup2.hkl

Supporting information file. DOI: 10.1107/S2414314616014681/bv4003Isup3.cml

checkCIF report

Computing details top

Data collection: CrysAlis PRO (Rigaku-Oxford Diffraction, 2012); cell refinement: CrysAlis PRO (Rigaku-Oxford Diffraction, 2012); data reduction: CrysAlis RED (Rigaku-Oxford Diffraction, 2012); program(s) used to solve structure: SHELXT2014 (Sheldrick, 2015b); program(s) used to refine structure: SHELXL (Sheldrick, 2015a); molecular graphics: OLEX2 (Dolomanov et al., 2009); software used to prepare material for publication: OLEX2 (Dolomanov et al., 2009).

tert-Butyl 2,3-dihydro-1H-cyclopenta[b]indole-4-carboxylate top

Crystal data top

C₁₆H₁₉NO₂	D_x = 1.210 Mg m⁻³
M_r = 257.32	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, Pnma	Cell parameters from 4596 reflections
a = 19.6761 (11) Å	θ = 3.5–32.3°
b = 7.2330 (4) Å	µ = 0.08 mm⁻¹
c = 9.9258 (7) Å	T = 173 K
V = 1412.61 (15) Å³	Block, colourless
Z = 4	0.38 × 0.26 × 0.15 mm
F(000) = 552

Data collection top

Rigaku-Oxford Diffraction diffractometer	1486 reflections with I > 2σ(I)
Detector resolution: 16.1500 pixels mm^-1	R_int = 0.029
ω scans	θ_max = 27.9°, θ_min = 3.5°
Absorption correction: multi-scan (CrysAlis PRO & CrysAlis RED; Rigaku-Oxford Diffraction, 2012)	h = −25→24
T_min = 0.970, T_max = 0.988	k = −9→8
12388 measured reflections	l = −12→13
1808 independent reflections

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.056	H-atom parameters constrained
wR(F²) = 0.147	w = 1/[σ²(F_o²) + (0.0562P)² + 0.394P] where P = (F_o² + 2F_c²)/3
S = 1.11	(Δ/σ)_max < 0.001
1808 reflections	Δρ_max = 0.16 e Å⁻³
113 parameters	Δρ_min = −0.18 e Å⁻³
0 restraints

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq	Occ. (<1)
O1	0.32442 (9)	0.2500	1.10343 (19)	0.0736 (6)
O2	0.35771 (8)	0.2500	0.88593 (17)	0.0631 (5)
N1	0.43643 (8)	0.2500	1.04482 (17)	0.0438 (4)
C1	0.49003 (10)	0.2500	0.9521 (2)	0.0408 (4)
C2	0.49512 (11)	0.2500	0.8034 (2)	0.0484 (5)
H2A	0.4739	0.3616	0.7640	0.058*	0.5
H2B	0.4739	0.1384	0.7640	0.058*	0.5
C3	0.57309 (12)	0.2500	0.7828 (2)	0.0586 (6)
H3A	0.5869	0.1391	0.7311	0.070*	0.5
H3B	0.5869	0.3609	0.7311	0.070*	0.5
C4	0.60802 (11)	0.2500	0.9211 (2)	0.0547 (6)
H4A	0.6366	0.1385	0.9331	0.066*	0.5
H4B	0.6366	0.3615	0.9331	0.066*	0.5
C5	0.54989 (10)	0.2500	1.0164 (2)	0.0442 (5)
C6	0.53714 (12)	0.2500	1.1579 (2)	0.0490 (5)
C7	0.57817 (15)	0.2500	1.2717 (3)	0.0674 (7)
H7	0.6263	0.2500	1.2632	0.081*
C8	0.5485 (2)	0.2500	1.3961 (3)	0.0874 (10)
H8	0.5765	0.2500	1.4741	0.105*
C9	0.4784 (2)	0.2500	1.4109 (3)	0.0863 (10)
H9	0.4594	0.2500	1.4989	0.104*
C10	0.43543 (15)	0.2500	1.3003 (2)	0.0652 (7)
H10	0.3874	0.2500	1.3104	0.078*
C11	0.46572 (12)	0.2500	1.1746 (2)	0.0471 (5)
C12	0.36713 (10)	0.2500	1.0180 (2)	0.0513 (5)
C13	0.28904 (12)	0.2500	0.8262 (3)	0.0673 (7)
C14	0.30593 (17)	0.2500	0.6773 (3)	0.0996 (12)
H14A	0.2638	0.2500	0.6248	0.149*
H14B	0.3325	0.3606	0.6554	0.149*	0.5
H14C	0.3325	0.1394	0.6554	0.149*	0.5
C15	0.25196 (10)	0.0761 (3)	0.8664 (2)	0.0919 (8)
H15A	0.2814	−0.0311	0.8514	0.138*
H15B	0.2106	0.0635	0.8121	0.138*
H15C	0.2397	0.0830	0.9620	0.138*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0494 (9)	0.0972 (14)	0.0743 (12)	0.000	0.0089 (8)	0.000
O2	0.0406 (8)	0.0872 (12)	0.0614 (10)	0.000	−0.0137 (7)	0.000
N1	0.0427 (9)	0.0436 (9)	0.0450 (9)	0.000	−0.0029 (7)	0.000
C1	0.0421 (10)	0.0340 (9)	0.0463 (11)	0.000	−0.0026 (8)	0.000
C2	0.0525 (12)	0.0462 (11)	0.0466 (11)	0.000	−0.0054 (9)	0.000
C3	0.0579 (13)	0.0584 (13)	0.0596 (14)	0.000	0.0092 (11)	0.000
C4	0.0433 (11)	0.0507 (12)	0.0701 (15)	0.000	−0.0006 (10)	0.000
C5	0.0453 (10)	0.0363 (9)	0.0511 (11)	0.000	−0.0081 (9)	0.000
C6	0.0559 (12)	0.0384 (10)	0.0526 (12)	0.000	−0.0109 (10)	0.000
C7	0.0740 (17)	0.0687 (15)	0.0596 (15)	0.000	−0.0255 (13)	0.000
C8	0.111 (3)	0.097 (2)	0.0548 (16)	0.000	−0.0305 (17)	0.000
C9	0.122 (3)	0.095 (2)	0.0414 (13)	0.000	−0.0040 (15)	0.000
C10	0.0810 (17)	0.0641 (15)	0.0506 (13)	0.000	0.0058 (12)	0.000
C11	0.0584 (13)	0.0382 (10)	0.0447 (11)	0.000	−0.0059 (9)	0.000
C12	0.0426 (11)	0.0509 (12)	0.0603 (13)	0.000	−0.0022 (10)	0.000
C13	0.0450 (12)	0.0737 (16)	0.0832 (18)	0.000	−0.0249 (12)	0.000
C14	0.079 (2)	0.140 (3)	0.081 (2)	0.000	−0.0380 (17)	0.000
C15	0.0649 (12)	0.0779 (14)	0.133 (2)	−0.0129 (10)	−0.0315 (12)	0.0047 (13)

Geometric parameters (Å, º) top

O1—C12	1.194 (3)	C6—C11	1.415 (3)
O2—C12	1.324 (3)	C7—H7	0.9500
O2—C13	1.476 (3)	C7—C8	1.365 (4)
N1—C1	1.400 (3)	C8—H8	0.9500
N1—C11	1.411 (3)	C8—C9	1.388 (5)
N1—C12	1.389 (3)	C9—H9	0.9500
C1—C2	1.479 (3)	C9—C10	1.385 (4)
C1—C5	1.340 (3)	C10—H10	0.9500
C2—H2A	0.9900	C10—C11	1.383 (3)
C2—H2B	0.9900	C13—C14	1.515 (4)
C2—C3	1.548 (3)	C13—C15ⁱ	1.508 (3)
C3—H3A	0.9900	C13—C15	1.508 (3)
C3—H3B	0.9900	C14—H14A	0.9800
C3—C4	1.536 (3)	C14—H14B	0.9800
C4—H4A	0.9900	C14—H14C	0.9800
C4—H4B	0.9900	C15—H15A	0.9800
C4—C5	1.484 (3)	C15—H15B	0.9800
C5—C6	1.427 (3)	C15—H15C	0.9800
C6—C7	1.388 (3)

C12—O2—C13	121.74 (19)	C7—C8—H8	119.3
C1—N1—C11	107.02 (16)	C7—C8—C9	121.4 (3)
C12—N1—C1	127.82 (18)	C9—C8—H8	119.3
C12—N1—C11	125.16 (18)	C8—C9—H9	119.3
N1—C1—C2	135.00 (17)	C10—C9—C8	121.5 (3)
C5—C1—N1	110.42 (18)	C10—C9—H9	119.3
C5—C1—C2	114.58 (19)	C9—C10—H10	121.5
C1—C2—H2A	111.5	C11—C10—C9	116.9 (3)
C1—C2—H2B	111.5	C11—C10—H10	121.5
C1—C2—C3	101.51 (17)	N1—C11—C6	107.37 (18)
H2A—C2—H2B	109.3	C10—C11—N1	130.4 (2)
C3—C2—H2A	111.5	C10—C11—C6	122.2 (2)
C3—C2—H2B	111.5	O1—C12—O2	127.2 (2)
C2—C3—H3A	109.9	O1—C12—N1	123.7 (2)
C2—C3—H3B	109.9	O2—C12—N1	109.11 (19)
H3A—C3—H3B	108.3	O2—C13—C14	101.0 (2)
C4—C3—C2	108.96 (19)	O2—C13—C15	109.67 (14)
C4—C3—H3A	109.9	O2—C13—C15ⁱ	109.67 (14)
C4—C3—H3B	109.9	C15ⁱ—C13—C14	111.38 (16)
C3—C4—H4A	111.2	C15—C13—C14	111.38 (16)
C3—C4—H4B	111.2	C15ⁱ—C13—C15	113.0 (2)
H4A—C4—H4B	109.1	C13—C14—H14A	109.5
C5—C4—C3	103.01 (17)	C13—C14—H14B	109.5
C5—C4—H4A	111.2	C13—C14—H14C	109.5
C5—C4—H4B	111.2	H14A—C14—H14B	109.5
C1—C5—C4	111.95 (19)	H14A—C14—H14C	109.5
C1—C5—C6	108.33 (19)	H14B—C14—H14C	109.5
C6—C5—C4	139.71 (19)	C13—C15—H15A	109.5
C7—C6—C5	134.3 (2)	C13—C15—H15B	109.5
C7—C6—C11	118.8 (2)	C13—C15—H15C	109.5
C11—C6—C5	106.85 (18)	H15A—C15—H15B	109.5
C6—C7—H7	120.4	H15A—C15—H15C	109.5
C8—C7—C6	119.1 (3)	H15B—C15—H15C	109.5
C8—C7—H7	120.4

N1—C1—C2—C3	180.000 (1)	C6—C7—C8—C9	0.000 (1)
N1—C1—C5—C4	180.000 (1)	C7—C6—C11—N1	180.000 (1)
N1—C1—C5—C6	0.000 (1)	C7—C6—C11—C10	0.000 (1)
C1—N1—C11—C6	0.000 (1)	C7—C8—C9—C10	0.000 (1)
C1—N1—C11—C10	180.000 (1)	C8—C9—C10—C11	0.000 (1)
C1—N1—C12—O1	180.000 (1)	C9—C10—C11—N1	180.000 (1)
C1—N1—C12—O2	0.000 (1)	C9—C10—C11—C6	0.000 (1)
C1—C2—C3—C4	0.000 (1)	C11—N1—C1—C2	180.000 (1)
C1—C5—C6—C7	180.000 (1)	C11—N1—C1—C5	0.000 (1)
C1—C5—C6—C11	0.000 (1)	C11—N1—C12—O1	0.000 (1)
C2—C1—C5—C4	0.000 (1)	C11—N1—C12—O2	180.000 (1)
C2—C1—C5—C6	180.000 (1)	C11—C6—C7—C8	0.000 (1)
C2—C3—C4—C5	0.000 (1)	C12—O2—C13—C14	180.000 (1)
C3—C4—C5—C1	0.000 (1)	C12—O2—C13—C15ⁱ	62.35 (18)
C3—C4—C5—C6	180.000 (1)	C12—O2—C13—C15	−62.35 (18)
C4—C5—C6—C7	0.000 (1)	C12—N1—C1—C2	0.000 (1)
C4—C5—C6—C11	180.000 (1)	C12—N1—C1—C5	180.000 (1)
C5—C1—C2—C3	0.000 (1)	C12—N1—C11—C6	180.000 (1)
C5—C6—C7—C8	180.000 (1)	C12—N1—C11—C10	0.000 (1)
C5—C6—C11—N1	0.000 (1)	C13—O2—C12—O1	0.000 (1)
C5—C6—C11—C10	180.000 (1)	C13—O2—C12—N1	180.000 (1)

Symmetry code: (i) x, −y+1/2, z.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C10—H10···O1	0.95	2.40	2.931 (3)	115
C15—H15C···O1	0.98	2.49	3.025 (3)	114

Acknowledgements

JCB wishes to thank the School of Graduate Studies and Research, UWI and the Government of Barbados for the funding of this research. JPJ acknowledges the NSF–MRI program (grant No. CHE-0619278) for funds to purchase the X-ray diffractometer.

References

Badenock, J. C., Jordan, J. A. & Gribble, G. W. (2013). Tetrahedron Lett. 54, 2759–2762. CrossRef CAS Google Scholar
Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339–341. Web of Science CrossRef CAS IUCr Journals Google Scholar
Grehn, L. & Ragnarsson, U. (1984). Angew. Chem. Int. Ed. 96, 296–301. CrossRef Google Scholar
Macor, J. E., Ryan, K. & Newman, M. E. (1989). Tetrahedron Lett. 30, 2509–2512. CrossRef CAS Google Scholar
Rigaku-Oxford Diffraction (2012). CrysAlis PRO and CrysAlis RED. Rigaku Americas Corporation, The Woodlands, Texas, USA. Google Scholar
Sheldrick, G. M. (2015a). Acta Cryst. A71, 3–8. Web of Science CrossRef IUCr Journals Google Scholar
Sheldrick, G. M. (2015b). Acta Cryst. C71, 3–8. Web of Science CrossRef IUCr Journals Google Scholar

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