5-Chloro-N′-cyclo­hexyl­idene-3-methyl-1H-indole-2-carbohydrazide

In the title compound, C₁₆H₁₈ClN₃O, the cyclo­hexane ring adopts a distorted chair conformation. In the crystal, pairs of mol­ecules are linked by N—H...O hydrogen bonds into inversion dimers, forming R₂²(10) ring motifs. These dimers are connected through C—H...N hydrogen bonds into chains along the a axis, forming layers parallel to (101).

Key indicators

• Single-crystal X-ray study
• T = 296 K
• Mean [sigma](C-C) = 0.004 Å
• R factor = 0.053
• wR factor = 0.129
• Data-to-parameter ratio = 15.0

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT029_ALERT_3_C _diffrn_measured_fraction_theta_full Low .......      0.971
PLAT242_ALERT_2_C Check Low       Ueq as Compared to Neighbors for        C11
PLAT340_ALERT_3_C Low Bond Precision on  C-C Bonds ...............     0.0043 Ang.
PLAT420_ALERT_2_C D-H Without Acceptor       N2     -   H2A    ...          ? Check
PLAT906_ALERT_3_C Large K value in the Analysis of Variance ......     22.333
PLAT906_ALERT_3_C Large K value in the Analysis of Variance ......      3.424
PLAT910_ALERT_3_C Missing # of FCF Reflections Below Th(Min) .....          1
PLAT911_ALERT_3_C Missing # FCF Refl Between THmin & STh/L=  0.600         73

Alert level G
PLAT005_ALERT_5_G No _iucr_refine_instructions_details  in the CIF          ? Do !
PLAT007_ALERT_5_G Note: Number of Unrefined Donor-H Atoms ........          1
PLAT063_ALERT_4_G Crystal Size Likely too Large for Beam Size ....       0.76 mm
PLAT912_ALERT_4_G Missing # of FCF Reflections Above STh/L=  0.600         13

   0 ALERT level A = Most likely a serious problem - resolve or explain
   0 ALERT level B = A potentially serious problem, consider carefully
   8 ALERT level C = Check. Ensure it is not caused by an omission or oversight
   4 ALERT level G = General information/check it is not something unexpected

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   2 ALERT type 2 Indicator that the structure model may be wrong or deficient
   6 ALERT type 3 Indicator that the structure quality may be low
   2 ALERT type 4 Improvement, methodology, query or suggestion
   2 ALERT type 5 Informative message, check

---

S1. Comment

Cyclohexylidenehydrazides are of interest, both as potential intermediates for the synthesis of novel heterocyclic systems and as pharmacologically active agents. We have recently reported on the synthesis, antitituberculosis and anticancer properties of cyclohexylidenehydrazides and spirothiazolidinones with an indole core (Cihan-Üstündağ & Çapan, 2012). As a continuation of our program directed towards the design, synthesis and characterization of bioactive indole derivatives (Akkurt et al., 2009, 2010; Güzel et al., 2006; Kaynak et al., 2005), we report here the synthesis, spectral and analytical data and crystal structure of the title compound.

In the title compound (I), (Fig. 1), the nine-membered 1H-indole ring (N1/C1–C8) is essentially planar with maximum deviations of 0.019 (3) Å for C3, 0.017 (3) Å for C7 and -0.017 (3) Å for C1]. The cyclohexane ring (C11–C16) of (I) adopts a distorted chair conformation [the puckering parameters (Cremer & Pople, 1975) are Q_T = 0.508 (4) Å, θ = 10.2 (5)° and φ = 193 (2) °]. The C7–C8–C10–N2, C7–C8–C10–O1, N1–C8–C10–O1, N1–C8–C10–N2, C8–C10–N2–N3 and C10–N2–N3–C11 torsion angles are -19.5 (5), 158.3 (3), -14.4 (4), 167.7 (3), -179.6 (2) and -172.8 (3)°, respectively.

In the crystal, pairs of N—H···O hydrogen bonds link molecules into inversion dimers, with the R²₂(10) ring motifs (Table 1, Fig. 2; Bernstein et al., 1995). These dimers connect to each other through C—H···N hydrogen bonds as chains along the a axis, forming layers parallel to the (101) plane. In the crystal structure, π-π and C—H···π interactions were not observed.

Related literature

For the design, synthesis and characterization of some bioactive indole derivatives, see: Akkurt et al. (2009, 2010); Cihan-Üstündağ & Çapan (2012); Güzel et al. (2006); Kaynak et al. (2005). For puckering analysis, see: Cremer & Pople (1975). For hydrogen-bond motifs, see: Bernstein et al. (1995).

S2. Experimental

A mixture of 5-chloro-3-methyl-1H-indole-2-carbohydrazide (0.005 mol) and cyclohexanone (0.006 mol) in 15 ml of absolute ethanol was heated under reflux for 3 h. The crude product obtained on cooling was filtered and purified by recrystallization from ethanol. [Yield: 91.4%, m.p.: 505–507 K].

S3. Refinement

H atoms bonded to C atoms were positioned geometrically with C—H = 0.93, 0.96 and 0.97 Å, and refined using a riding model with U_iso(H) = 1.2 or 1.5U_eq(C). The H atom (H1) of the one of the two amide groups was positioned geometrically with N—H = 0.86 Å, and refined using a riding model with U_iso(H) = 1.2U_eq(N). The H atom (H2A) of the other amide group was found in a difference Fourier map, restrained with N—H = 0.82 (3) Å and refined with U_iso = 1.2U_eq(N).

Computing details

Data collection: X-AREA (Stoe & Cie, 2002); cell refinement: X-AREA (Stoe & Cie, 2002); data reduction: X-RED32 (Stoe & Cie, 2002); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012); software used to prepare material for publication: WinGX (Farrugia, 2012).

Figures

	Fig. 1. The title molecule shown the atom labelling scheme. Displacement ellipsoids for non-H atoms are drawn at the 30% probability level.
	Fig. 2. View of the packing of the title compound with the N—H···O dimers, down the b axis. H atoms not participating in hydrogen bonding have been omitted for clarity and hydrogen bonds are drawn as dashed lines.

5-Chloro-N'-cyclohexylidene-3-methyl-1H-indole-2-carbohydrazide

Crystal data

C16H18ClN3O	Z = 2
Mr = 303.78	F(000) = 320
Triclinic, P1	Dx = 1.321 Mg m^−3
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 5.2727 (5) Å	Cell parameters from 9705 reflections
b = 9.7977 (9) Å	θ = 2.1–28.0°
c = 15.2380 (15) Å	µ = 0.25 mm^−1
α = 102.229 (7)°	T = 296 K
β = 95.732 (8)°	Plate, colourless
γ = 92.332 (7)°	0.76 × 0.36 × 0.02 mm
V = 763.94 (13) Å^3

Data collection

Stoe IPDS 2 diffractometer	2929 independent reflections
Radiation source: sealed X-ray tube, 12 x 0.4 mm long-fine focus	1684 reflections with I > 2σ(I)
Plane graphite monochromator	Rint = 0.065
Detector resolution: 6.67 pixels mm^-1	θmax = 26.0°, θmin = 2.1°
ω scans	h = −6→6
Absorption correction: integration (X-RED32; Stoe & Cie, 2002)	k = −12→12
Tmin = 0.831, Tmax = 0.995	l = −18→18
7177 measured reflections

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)] = 0.053	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.129	H atoms treated by a mixture of independent and constrained refinement
S = 1.01	w = 1/[σ^2(Fo^2) + (0.0554P)^2] where P = (Fo^2 + 2Fc^2)/3
2929 reflections	(Δ/σ)max < 0.001
195 parameters	Δρmax = 0.15 e Å^−3
0 restraints	Δρmin = −0.16 e Å^−3

Special details

Experimental. UV (EtOH) λ_max(nm)(ε) = 210.2 (11298); 230.6 (15341); 303.4 (14665). IR(KBr)ν = 3278 (N—H); 1639 (C=O);1624, 1537, 1514, 1471 (C=N, C=C) cm^-1. ¹H-NMR (500 MHz) (DMSO-d₆ / TMS) d =1.56–1.72 (6H, m, CH₂-cyc.*), 2.32 (2H, t, J=6.8 Hz, CH₂-cyc.) 2.42–2.48 (5H, m, CH₂-cyc. and 3-CH₃-ind.*), 7.20 (1H, dd, J=8.7, 1.9 Hz, H6-ind.), 7.41 (1H, d, J=8.7 Hz, H7-ind.), 7.66 (1H, d, J=1.9 Hz, H4-ind.), 10.30 (1H, s, CONH), 11.50 (1H, s, NH-ind.) p.p.m.. MS (ESI–) m/z (%) = 302 ([M—H]^-, 100). Analysis calculated for C₁₆H₁₈ClN₃O: C 63.26, H 5.97, N 13.83%. Found: C 63.12, H 5.97, N 13.86%.(*cyc. = cyclohexylidene, ind. = indole).

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 e.s.d.'s 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 > σ(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 (Ų)

	x	y	z	Uiso*/Ueq
Cl1	0.5891 (2)	0.46594 (11)	0.20802 (7)	0.1086 (4)
O1	0.1519 (4)	0.0786 (2)	0.61618 (12)	0.0717 (7)
N1	0.2262 (4)	0.1409 (2)	0.45351 (13)	0.0589 (8)
N2	0.5585 (5)	0.1489 (3)	0.67430 (15)	0.0597 (8)
N3	0.5305 (4)	0.1037 (2)	0.75354 (15)	0.0628 (8)
C1	0.2826 (5)	0.2059 (3)	0.38687 (17)	0.0538 (8)
C2	0.1513 (6)	0.1988 (3)	0.30110 (18)	0.0654 (10)
C3	0.2502 (6)	0.2795 (3)	0.24870 (19)	0.0705 (11)
C4	0.4744 (6)	0.3636 (3)	0.27889 (19)	0.0691 (11)
C5	0.6043 (5)	0.3719 (3)	0.3623 (2)	0.0648 (10)
C6	0.5060 (4)	0.2920 (3)	0.41855 (17)	0.0508 (8)
C7	0.5838 (4)	0.2775 (3)	0.50912 (16)	0.0512 (8)
C8	0.4070 (5)	0.1827 (3)	0.52722 (16)	0.0511 (8)
C9	0.8061 (5)	0.3606 (3)	0.5689 (2)	0.0686 (10)
C10	0.3624 (5)	0.1311 (3)	0.60883 (17)	0.0543 (9)
C11	0.7122 (5)	0.1360 (3)	0.81721 (18)	0.0597 (9)
C12	0.9530 (6)	0.2231 (4)	0.8204 (2)	0.0866 (13)
C13	1.0168 (7)	0.3247 (4)	0.9086 (2)	0.0993 (16)
C14	1.0052 (7)	0.2603 (4)	0.9900 (2)	0.0876 (13)
C15	0.7463 (6)	0.1875 (4)	0.9862 (2)	0.0837 (13)
C16	0.6818 (6)	0.0800 (4)	0.9003 (2)	0.0820 (11)
H1	0.09730	0.08260	0.45020	0.0710*
H2	0.00300	0.14140	0.28090	0.0790*
H2A	0.701 (5)	0.174 (3)	0.6650 (17)	0.054 (8)*
H3	0.16670	0.27840	0.19180	0.0850*
H5	0.75350	0.42900	0.38110	0.0780*
H9A	0.85040	0.44140	0.54590	0.1030*
H9B	0.94970	0.30360	0.56980	0.1030*
H9C	0.76010	0.39010	0.62910	0.1030*
H12A	0.93570	0.27410	0.77230	0.1040*
H12B	1.09240	0.16220	0.80990	0.1040*
H13A	0.89910	0.39870	0.91220	0.1190*
H13B	1.18740	0.36690	0.91050	0.1190*
H14A	1.13590	0.19360	0.99100	0.1050*
H14B	1.03740	0.33270	1.04480	0.1050*
H15A	0.74350	0.14270	1.03710	0.1010*
H15B	0.61810	0.25620	0.99110	0.1010*
H16A	0.50660	0.04370	0.89750	0.0980*
H16B	0.79110	0.00290	0.90090	0.0980*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Cl1	0.1362 (8)	0.1232 (8)	0.0844 (7)	−0.0039 (6)	0.0217 (6)	0.0607 (6)
O1	0.0767 (12)	0.0851 (14)	0.0498 (11)	−0.0264 (11)	−0.0034 (9)	0.0179 (10)
N1	0.0662 (13)	0.0625 (14)	0.0445 (12)	−0.0171 (11)	−0.0010 (10)	0.0109 (10)
N2	0.0590 (13)	0.0774 (16)	0.0448 (13)	−0.0043 (12)	0.0028 (11)	0.0210 (11)
N3	0.0722 (14)	0.0709 (15)	0.0491 (13)	−0.0018 (12)	0.0054 (12)	0.0236 (12)
C1	0.0654 (15)	0.0521 (15)	0.0427 (14)	0.0010 (13)	0.0064 (12)	0.0080 (12)
C2	0.0775 (17)	0.0694 (18)	0.0455 (15)	−0.0025 (15)	−0.0039 (14)	0.0102 (13)
C3	0.090 (2)	0.077 (2)	0.0444 (15)	0.0084 (17)	0.0005 (15)	0.0155 (14)
C4	0.0879 (19)	0.0721 (19)	0.0551 (18)	0.0077 (16)	0.0153 (16)	0.0274 (15)
C5	0.0675 (16)	0.0657 (17)	0.0633 (18)	−0.0028 (14)	0.0096 (14)	0.0193 (14)
C6	0.0536 (13)	0.0520 (15)	0.0471 (14)	0.0049 (12)	0.0050 (11)	0.0116 (12)
C7	0.0511 (13)	0.0536 (15)	0.0463 (14)	0.0012 (12)	0.0006 (11)	0.0079 (12)
C8	0.0570 (14)	0.0540 (15)	0.0407 (14)	0.0021 (13)	0.0014 (11)	0.0086 (12)
C9	0.0648 (16)	0.078 (2)	0.0613 (17)	−0.0071 (15)	−0.0059 (14)	0.0197 (15)
C10	0.0659 (16)	0.0502 (15)	0.0431 (14)	−0.0023 (13)	0.0016 (13)	0.0054 (12)
C11	0.0635 (15)	0.0719 (18)	0.0463 (15)	0.0060 (14)	0.0073 (13)	0.0177 (13)
C12	0.0652 (17)	0.143 (3)	0.0556 (18)	−0.0114 (19)	0.0048 (14)	0.0348 (19)
C13	0.112 (3)	0.122 (3)	0.065 (2)	−0.040 (2)	−0.0189 (19)	0.045 (2)
C14	0.099 (2)	0.112 (3)	0.0530 (18)	−0.013 (2)	−0.0066 (17)	0.0313 (18)
C15	0.092 (2)	0.116 (3)	0.0491 (17)	0.000 (2)	0.0086 (16)	0.0325 (18)
C16	0.097 (2)	0.092 (2)	0.0633 (19)	−0.0084 (19)	−0.0014 (17)	0.0386 (18)

Geometric parameters (Å, º)

Cl1—C4	1.754 (3)	C12—C13	1.492 (5)
O1—C10	1.230 (3)	C13—C14	1.511 (5)
N1—C1	1.358 (3)	C14—C15	1.504 (5)
N1—C8	1.378 (3)	C15—C16	1.495 (5)
N2—N3	1.390 (3)	C2—H2	0.9300
N2—C10	1.342 (4)	C3—H3	0.9300
N3—C11	1.272 (3)	C5—H5	0.9300
N1—H1	0.8600	C9—H9A	0.9600
N2—H2A	0.82 (3)	C9—H9B	0.9600
C1—C2	1.403 (4)	C9—H9C	0.9600
C1—C6	1.402 (4)	C12—H12A	0.9700
C2—C3	1.361 (4)	C12—H12B	0.9700
C3—C4	1.393 (4)	C13—H13A	0.9700
C4—C5	1.367 (4)	C13—H13B	0.9700
C5—C6	1.399 (4)	C14—H14A	0.9700
C6—C7	1.438 (4)	C14—H14B	0.9700
C7—C9	1.504 (4)	C15—H15A	0.9700
C7—C8	1.377 (4)	C15—H15B	0.9700
C8—C10	1.474 (4)	C16—H16A	0.9700
C11—C16	1.503 (4)	C16—H16B	0.9700
C11—C12	1.492 (4)
C1—N1—C8	109.6 (2)	C3—C2—H2	121.00
N3—N2—C10	120.0 (2)	C2—C3—H3	119.00
N2—N3—C11	117.5 (2)	C4—C3—H3	120.00
C8—N1—H1	125.00	C4—C5—H5	121.00
C1—N1—H1	125.00	C6—C5—H5	121.00
N3—N2—H2A	118.7 (18)	C7—C9—H9A	109.00
C10—N2—H2A	120.5 (18)	C7—C9—H9B	109.00
N1—C1—C6	107.7 (2)	C7—C9—H9C	109.00
C2—C1—C6	122.3 (3)	H9A—C9—H9B	109.00
N1—C1—C2	130.0 (3)	H9A—C9—H9C	109.00
C1—C2—C3	117.2 (3)	H9B—C9—H9C	110.00
C2—C3—C4	121.1 (3)	C11—C12—H12A	109.00
Cl1—C4—C3	118.5 (2)	C11—C12—H12B	109.00
Cl1—C4—C5	119.0 (2)	C13—C12—H12A	109.00
C3—C4—C5	122.5 (3)	C13—C12—H12B	109.00
C4—C5—C6	118.0 (3)	H12A—C12—H12B	108.00
C1—C6—C5	119.0 (2)	C12—C13—H13A	109.00
C5—C6—C7	133.4 (2)	C12—C13—H13B	109.00
C1—C6—C7	107.6 (2)	C14—C13—H13A	109.00
C6—C7—C8	105.7 (2)	C14—C13—H13B	109.00
C6—C7—C9	123.9 (2)	H13A—C13—H13B	108.00
C8—C7—C9	130.3 (2)	C13—C14—H14A	110.00
C7—C8—C10	133.6 (2)	C13—C14—H14B	110.00
N1—C8—C7	109.5 (2)	C15—C14—H14A	110.00
N1—C8—C10	116.6 (2)	C15—C14—H14B	110.00
O1—C10—C8	120.5 (2)	H14A—C14—H14B	108.00
N2—C10—C8	116.7 (2)	C14—C15—H15A	109.00
O1—C10—N2	122.8 (3)	C14—C15—H15B	109.00
N3—C11—C12	128.4 (3)	C16—C15—H15A	109.00
N3—C11—C16	116.3 (3)	C16—C15—H15B	109.00
C12—C11—C16	115.3 (2)	H15A—C15—H15B	108.00
C11—C12—C13	112.6 (3)	C11—C16—H16A	109.00
C12—C13—C14	113.9 (3)	C11—C16—H16B	109.00
C13—C14—C15	109.9 (3)	C15—C16—H16A	109.00
C14—C15—C16	111.7 (3)	C15—C16—H16B	109.00
C11—C16—C15	113.3 (3)	H16A—C16—H16B	108.00
C1—C2—H2	121.00
C1—N1—C8—C10	174.9 (2)	C4—C5—C6—C7	−177.9 (3)
C8—N1—C1—C2	−178.3 (3)	C5—C6—C7—C9	3.2 (5)
C8—N1—C1—C6	0.0 (3)	C5—C6—C7—C8	179.7 (3)
C1—N1—C8—C7	0.5 (3)	C1—C6—C7—C8	0.8 (3)
N3—N2—C10—C8	179.6 (2)	C1—C6—C7—C9	−175.7 (2)
N3—N2—C10—O1	1.8 (4)	C6—C7—C8—C10	−173.9 (3)
C10—N2—N3—C11	−172.8 (3)	C9—C7—C8—C10	2.3 (5)
N2—N3—C11—C16	−177.2 (3)	C9—C7—C8—N1	175.4 (3)
N2—N3—C11—C12	2.9 (4)	C6—C7—C8—N1	−0.8 (3)
N1—C1—C6—C7	−0.5 (3)	N1—C8—C10—N2	167.7 (3)
C6—C1—C2—C3	0.2 (4)	C7—C8—C10—O1	158.3 (3)
N1—C1—C6—C5	−179.6 (2)	C7—C8—C10—N2	−19.5 (5)
C2—C1—C6—C7	178.0 (3)	N1—C8—C10—O1	−14.4 (4)
C2—C1—C6—C5	−1.1 (4)	N3—C11—C12—C13	136.1 (3)
N1—C1—C2—C3	178.2 (3)	C16—C11—C12—C13	−43.7 (4)
C1—C2—C3—C4	1.0 (4)	N3—C11—C16—C15	−134.0 (3)
C2—C3—C4—Cl1	−179.5 (2)	C12—C11—C16—C15	45.9 (4)
C2—C3—C4—C5	−1.1 (5)	C11—C12—C13—C14	49.1 (4)
C3—C4—C5—C6	0.1 (4)	C12—C13—C14—C15	−55.6 (4)
Cl1—C4—C5—C6	178.5 (2)	C13—C14—C15—C16	56.2 (4)
C4—C5—C6—C1	1.0 (4)	C14—C15—C16—C11	−52.0 (4)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O1^i	0.86	2.03	2.826 (3)	153
C12—H12A···N2	0.97	2.47	2.842 (4)	102
C12—H12B···N3^ii	0.97	2.59	3.476 (4)	152

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