Crystal structure of (Z)-ethyl 3-[2-(5-methyl-7-nitro-1H-indole-2-carbon-yl)hydrazinyl-idene]butano-ate.

The reaction of 5-methyl-7-nitro-1H-indole-2-carbohydrazide with ethyl aceto-acetate yielded the title mol-ecule, C16H18N4O5, in which the indole ring is almost planar, with the greatest deviation from the mean plane being 0.006 (2) Å. The nine atoms of the indole ring are almost perpendicular to the mean plane through the ethyl acetate group, as indicated by the dihedral angle of 87.02 (4)° between them. In the crystal, centrosymmetric supra-molecular dimers are formed via N-H⋯O hydrogen bonds and eight-membered amide {⋯HNCO}2 synthons. These are consolidated into a three-dimensional architecture by C-H⋯O contacts, and by π-π inter-actions between six-membered rings [inter-centroid distance = 3.499 (2) Å].

Related literature

For biochemical properties of indoles, see: Kuethe et al. (2005 ▸); Smith et al. (1998 ▸). For medicinal activity, see: El Kihel et al. (2007 ▸, 2013 ▸); Penning et al. (1997 ▸); Dumas et al. (2000 ▸). For starting materials, see: El Ouar et al. (1995 ▸).

Experimental

Crystal data

C16H18N4O5

M = 346.34

Triclinic,

a = 8.4716 (9) Å

b = 8.4722 (7) Å

c = 13.0971 (9) Å

α = 108.695 (4)°

β = 91.865 (4)°

γ = 106.886 (4)°

V = 843.80 (13) Å3

Z = 2

Mo Kα radiation

μ = 0.10 mm−1

T = 296 K

0.35 × 0.30 × 0.27 mm

Data collection

Bruker X8 APEX diffractometer

Absorption correction: multi-scan (SADABS; Bruker, 2009 ▸) T min = 0.589, T max = 0.746

18286 measured reflections

3676 independent reflections

3120 reflections with I > 2σ(I)

R int = 0.033

Refinement

R[F 2 > 2σ(F 2)] = 0.043

wR(F 2) = 0.124

S = 1.07

3676 reflections

226 parameters

H-atom parameters constrained

Δρmax = 0.30 e Å−3

Δρmin = −0.24 e Å−3

Data collection: APEX2 (Bruker, 2009 ▸); cell refinement: SAINT (Bruker, 2009 ▸); data reduction: SAINT; 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: PLATON (Spek, 2009 ▸) and publCIF (Westrip, 2010 ▸).

Crystal structure: contains datablock(s) I. DOI: 10.1107/S2056989015015054/tk5378sup1.cif

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989015015054/tk5378Isup2.hkl

Click here for additional data file.

Supporting information file. DOI: 10.1107/S2056989015015054/tk5378Isup3.cml

Click here for additional data file.

. DOI: 10.1107/S2056989015015054/tk5378fig1.tif

Plot of the mol­ecule with the atom-labelling scheme. Displacement ellipsoids are drawn at the 50% probability level.

Click here for additional data file.

. DOI: 10.1107/S2056989015015054/tk5378fig2.tif

A view of the crystal packing of the title compound, showing inter­molecular π—π inter­actions between six-membered rings (dashed green lines) and inter­molecular hydrogen bonds (dashed blue lines).

CCDC reference: 1418363

Additional supporting information: crystallographic information; 3D view; checkCIF report

C16H18N4O5	Z = 2
Mr = 346.34	F(000) = 364
Triclinic, P1	Dx = 1.363 Mg m−3
a = 8.4716 (9) Å	Mo Kα radiation, λ = 0.71073 Å
b = 8.4722 (7) Å	Cell parameters from 3676 reflections
c = 13.0971 (9) Å	θ = 2.5–27.1°
α = 108.695 (4)°	µ = 0.10 mm−1
β = 91.865 (4)°	T = 296 K
γ = 106.886 (4)°	Block, yellow
V = 843.80 (13) Å3	0.35 × 0.30 × 0.27 mm

Bruker X8 APEX diffractometer	3676 independent reflections
Radiation source: fine-focus sealed tube	3120 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.033
φ and ω scans	θmax = 27.1°, θmin = 2.5°
Absorption correction: multi-scan (SADABS; Bruker, 2009)	h = −10→10
Tmin = 0.589, Tmax = 0.746	k = −10→10
18286 measured reflections	l = −16→16

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)] = 0.043	Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.124	H-atom parameters constrained
S = 1.07	w = 1/[σ2(Fo2) + (0.059P)2 + 0.3197P] where P = (Fo2 + 2Fc2)/3
3676 reflections	(Δ/σ)max < 0.001
226 parameters	Δρmax = 0.30 e Å−3
0 restraints	Δρmin = −0.24 e Å−3

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.

	x	y	z	Uiso*/Ueq
C1	0.17198 (16)	0.64599 (17)	0.94250 (11)	0.0241 (3)
C2	0.12573 (17)	0.78350 (18)	1.00943 (12)	0.0266 (3)
H2	0.0884	0.8540	0.9793	0.032*
C3	0.13423 (17)	0.81836 (18)	1.12214 (12)	0.0272 (3)
C4	0.18973 (17)	0.71346 (18)	1.16710 (11)	0.0265 (3)
H4	0.1948	0.7356	1.2416	0.032*
C5	0.23851 (16)	0.57373 (17)	1.10067 (10)	0.0233 (3)
C6	0.22965 (16)	0.54061 (16)	0.98701 (10)	0.0215 (3)
C7	0.0821 (2)	0.9697 (2)	1.19212 (14)	0.0366 (4)
H7A	0.1600	1.0786	1.1935	0.055*
H7B	0.0803	0.9670	1.2648	0.055*
H7C	−0.0270	0.9596	1.1625	0.055*
C8	0.30024 (17)	0.44531 (18)	1.12041 (11)	0.0250 (3)
H8	0.3193	0.4334	1.1875	0.030*
C9	0.32627 (16)	0.34231 (17)	1.02184 (11)	0.0228 (3)
C10	0.39564 (16)	0.19582 (17)	1.00510 (10)	0.0227 (3)
C11	0.39038 (17)	0.03684 (19)	0.72021 (11)	0.0264 (3)
C12	0.4537 (2)	−0.1170 (2)	0.69488 (12)	0.0343 (3)
H12A	0.5004	−0.1320	0.6280	0.052*
H12B	0.3634	−0.2211	0.6877	0.052*
H12C	0.5378	−0.0967	0.7527	0.052*
C13	0.3494 (2)	0.0920 (2)	0.62686 (12)	0.0360 (4)
H13A	0.4517	0.1398	0.6004	0.043*
H13B	0.2990	0.1842	0.6527	0.043*
C14	0.2322 (2)	−0.0586 (2)	0.53418 (12)	0.0394 (4)
C15	−0.0299 (2)	−0.2793 (3)	0.48056 (15)	0.0516 (5)
H15A	0.0177	−0.3734	0.4529	0.062*
H15B	−0.0586	−0.2445	0.4206	0.062*
C16	−0.1808 (3)	−0.3393 (3)	0.5309 (2)	0.0656 (6)
H16A	−0.2618	−0.4381	0.4773	0.098*
H16B	−0.2271	−0.2453	0.5575	0.098*
H16C	−0.1508	−0.3731	0.5901	0.098*
N1	0.15863 (16)	0.61115 (16)	0.82643 (10)	0.0296 (3)
N2	0.28297 (14)	0.40043 (14)	0.94143 (9)	0.0223 (2)
H2N	0.2888	0.3552	0.8733	0.027*
N3	0.41081 (15)	0.09582 (15)	0.90428 (9)	0.0247 (3)
H3N	0.4466	0.0082	0.8968	0.030*
N4	0.36975 (14)	0.13223 (15)	0.81339 (9)	0.0251 (3)
O1	0.10064 (17)	0.70060 (17)	0.78835 (10)	0.0465 (3)
O2	0.20654 (16)	0.49110 (15)	0.76987 (8)	0.0386 (3)
O3	0.43926 (13)	0.16440 (13)	1.08520 (8)	0.0298 (2)
O4	0.2639 (2)	−0.1084 (3)	0.44345 (11)	0.0763 (5)
O5	0.08886 (16)	−0.13058 (17)	0.56453 (9)	0.0447 (3)

	U11	U22	U33	U12	U13	U23
C1	0.0223 (6)	0.0229 (6)	0.0240 (6)	0.0050 (5)	0.0025 (5)	0.0060 (5)
C2	0.0232 (7)	0.0218 (6)	0.0336 (7)	0.0075 (5)	0.0029 (5)	0.0079 (5)
C3	0.0228 (7)	0.0218 (6)	0.0312 (7)	0.0062 (5)	0.0048 (5)	0.0023 (5)
C4	0.0260 (7)	0.0256 (7)	0.0225 (6)	0.0069 (5)	0.0047 (5)	0.0023 (5)
C5	0.0216 (6)	0.0228 (6)	0.0216 (6)	0.0055 (5)	0.0030 (5)	0.0039 (5)
C6	0.0195 (6)	0.0201 (6)	0.0215 (6)	0.0053 (5)	0.0033 (5)	0.0037 (5)
C7	0.0363 (8)	0.0299 (8)	0.0398 (8)	0.0162 (6)	0.0074 (7)	0.0017 (6)
C8	0.0258 (7)	0.0269 (7)	0.0211 (6)	0.0082 (5)	0.0035 (5)	0.0067 (5)
C9	0.0213 (6)	0.0224 (6)	0.0229 (6)	0.0066 (5)	0.0026 (5)	0.0057 (5)
C10	0.0217 (6)	0.0227 (6)	0.0223 (6)	0.0067 (5)	0.0035 (5)	0.0061 (5)
C11	0.0244 (7)	0.0314 (7)	0.0218 (6)	0.0104 (6)	0.0030 (5)	0.0060 (5)
C12	0.0435 (9)	0.0382 (8)	0.0241 (7)	0.0221 (7)	0.0063 (6)	0.0061 (6)
C13	0.0445 (9)	0.0442 (9)	0.0261 (7)	0.0230 (7)	0.0069 (6)	0.0126 (6)
C14	0.0464 (10)	0.0562 (10)	0.0224 (7)	0.0294 (8)	0.0039 (6)	0.0107 (7)
C15	0.0524 (11)	0.0524 (11)	0.0374 (9)	0.0216 (9)	−0.0083 (8)	−0.0040 (8)
C16	0.0566 (13)	0.0561 (12)	0.0642 (14)	0.0105 (10)	−0.0010 (10)	0.0021 (11)
N1	0.0331 (7)	0.0295 (6)	0.0266 (6)	0.0106 (5)	0.0026 (5)	0.0098 (5)
N2	0.0246 (6)	0.0223 (5)	0.0190 (5)	0.0090 (4)	0.0039 (4)	0.0042 (4)
N3	0.0292 (6)	0.0250 (6)	0.0219 (6)	0.0137 (5)	0.0035 (5)	0.0063 (5)
N4	0.0253 (6)	0.0290 (6)	0.0208 (5)	0.0110 (5)	0.0022 (4)	0.0064 (5)
O1	0.0654 (8)	0.0529 (7)	0.0374 (6)	0.0334 (7)	0.0064 (6)	0.0237 (6)
O2	0.0557 (7)	0.0387 (6)	0.0236 (5)	0.0232 (5)	0.0058 (5)	0.0062 (5)
O3	0.0398 (6)	0.0314 (5)	0.0231 (5)	0.0184 (5)	0.0058 (4)	0.0094 (4)
O4	0.0659 (10)	0.1143 (14)	0.0251 (6)	0.0216 (9)	0.0100 (6)	−0.0011 (7)
O5	0.0476 (7)	0.0525 (7)	0.0261 (5)	0.0178 (6)	0.0013 (5)	0.0019 (5)

C1—C2	1.3827 (19)	C11—C12	1.496 (2)
C1—C6	1.3943 (19)	C11—C13	1.505 (2)
C1—N1	1.4465 (18)	C12—H12A	0.9600
C2—C3	1.404 (2)	C12—H12B	0.9600
C2—H2	0.9300	C12—H12C	0.9600
C3—C4	1.385 (2)	C13—C14	1.510 (2)
C3—C7	1.5100 (19)	C13—H13A	0.9700
C4—C5	1.4059 (18)	C13—H13B	0.9700
C4—H4	0.9300	C14—O4	1.195 (2)
C5—C6	1.4188 (18)	C14—O5	1.327 (2)
C5—C8	1.4234 (19)	C15—O5	1.453 (2)
C6—N2	1.3585 (16)	C15—C16	1.490 (3)
C7—H7A	0.9600	C15—H15A	0.9700
C7—H7B	0.9600	C15—H15B	0.9700
C7—H7C	0.9600	C16—H16A	0.9600
C8—C9	1.3729 (18)	C16—H16B	0.9600
C8—H8	0.9300	C16—H16C	0.9600
C9—N2	1.3778 (17)	N1—O1	1.2276 (17)
C9—C10	1.4803 (19)	N1—O2	1.2347 (16)
C10—O3	1.2325 (16)	N2—H2N	0.8600
C10—N3	1.3547 (17)	N3—N4	1.3798 (16)
C11—N4	1.2793 (17)	N3—H3N	0.8600
C2—C1—C6	119.89 (13)	C11—C12—H12B	109.5
C2—C1—N1	119.77 (13)	H12A—C12—H12B	109.5
C6—C1—N1	120.34 (12)	C11—C12—H12C	109.5
C1—C2—C3	121.06 (13)	H12A—C12—H12C	109.5
C1—C2—H2	119.5	H12B—C12—H12C	109.5
C3—C2—H2	119.5	C11—C13—C14	112.44 (13)
C4—C3—C2	119.56 (12)	C11—C13—H13A	109.1
C4—C3—C7	121.18 (13)	C14—C13—H13A	109.1
C2—C3—C7	119.26 (14)	C11—C13—H13B	109.1
C3—C4—C5	120.34 (13)	C14—C13—H13B	109.1
C3—C4—H4	119.8	H13A—C13—H13B	107.8
C5—C4—H4	119.8	O4—C14—O5	123.36 (17)
C4—C5—C6	119.39 (13)	O4—C14—C13	124.16 (18)
C4—C5—C8	134.22 (13)	O5—C14—C13	112.47 (13)
C6—C5—C8	106.39 (11)	O5—C15—C16	107.43 (15)
N2—C6—C1	132.14 (12)	O5—C15—H15A	110.2
N2—C6—C5	108.10 (12)	C16—C15—H15A	110.2
C1—C6—C5	119.76 (12)	O5—C15—H15B	110.2
C3—C7—H7A	109.5	C16—C15—H15B	110.2
C3—C7—H7B	109.5	H15A—C15—H15B	108.5
H7A—C7—H7B	109.5	C15—C16—H16A	109.5
C3—C7—H7C	109.5	C15—C16—H16B	109.5
H7A—C7—H7C	109.5	H16A—C16—H16B	109.5
H7B—C7—H7C	109.5	C15—C16—H16C	109.5
C9—C8—C5	107.13 (12)	H16A—C16—H16C	109.5
C9—C8—H8	126.4	H16B—C16—H16C	109.5
C5—C8—H8	126.4	O1—N1—O2	122.89 (13)
C8—C9—N2	109.32 (12)	O1—N1—C1	119.29 (12)
C8—C9—C10	125.34 (12)	O2—N1—C1	117.82 (12)
N2—C9—C10	125.31 (12)	C6—N2—C9	109.07 (11)
O3—C10—N3	119.72 (12)	C6—N2—H2N	125.5
O3—C10—C9	118.74 (12)	C9—N2—H2N	125.5
N3—C10—C9	121.53 (12)	C10—N3—N4	121.12 (11)
N4—C11—C12	127.75 (13)	C10—N3—H3N	119.4
N4—C11—C13	114.81 (13)	N4—N3—H3N	119.4
C12—C11—C13	117.42 (12)	C11—N4—N3	118.81 (12)
C11—C12—H12A	109.5	C14—O5—C15	115.98 (13)

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3N···O3i	0.86	2.04	2.8815 (15)	167
C12—H12C···O3i	0.96	2.39	3.1723 (18)	139
C4—H4···O4ii	0.93	2.51	3.4019 (19)	161
C13—H13A···O4iii	0.97	2.56	3.407 (2)	146

Table 1

Hydrogen-bond geometry (, )

DHA	DH	HA	D A	DHA
N3H3NO3i	0.86	2.04	2.8815(15)	167
C12H12CO3i	0.96	2.39	3.1723(18)	139
C4H4O4ii	0.93	2.51	3.4019(19)	161
C13H13AO4iii	0.97	2.56	3.407(2)	146

Symmetry codes: (i) ; (ii) ; (iii) .