(E)-3-Dimethyl­amino-2-(1H-indol-3-yl­carbon­yl)acrylonitrile: a chain of edge-fused rings built from a three-centre N—H...(N,O) hydrogen bond

In the title compound, C₁₄H₁₃N₃O, the intra­molecular distances provide evidence for polarization of the mol­ecular–electronic structure. A single three-centre N—H...(N,O) hydrogen bond links the mol­ecules into chains of edge-fused R₂²(16) and R₂⁴(12) rings. Comparison with a number of related structures identifies factors of significance controlling the pattern of supra­molecular aggregation.

S1. Comment

Indolylpyrimidines, which are analogues of the marine natural product meridianin D (Radwan & El-Sherbiny, 2007), are promising bioactive compounds (Jiang et al., 2001). In order to introduce this interesting naturally occurring indole group as a substituent in other heterocyclic frameworks, with the aim of testing its biological influence, we have prepared the α-β-unsaturated 1-indolylketone (I) as a useful synthetic intermediate, using a condensation reaction between 3-(1H-indol-3-yl)-3-oxo-propionitrile and dimethylformamidedimethyacetal. We report here the structure of the title compound, (I), for comparison with three closely-related amino-substituted derivatives (II) [Cambridge Structural Database (CSD; Allen, 2002) refcode LEMSUS (Hashmi et al., 2006)], (III) (AMIMZF10; Adhikesavalu & Venkatesan, 1981) and (IV) (PELZUC; Langer et al., 2006), as well as those of the thienyl analogues (V)–(IX) (Cobo et al., 2005; Cobo, Quiroga et al., 2006; Cobo, Cobo et al., 2006).

The molecule of (I) (Fig. 1) is very nearly planar, as indicated by the torsion angles defining the conformation of the open-chain portion (Table 1). For the atoms forming the spine of this portion, the deviations from the mean plane of the five-membered ring range from 0.207 (2) Å for atom C32 to 0.006 (2) Å for atom C33. The bond distances within the exocyclic portion of the molecule provide evidence for polarization of the molecular–electronic structure. While the C3—C31 bond length is entirely typical of its type (mean value 1.464 Å; Allen et al., 1987), the C32—C33 bond is long for its type, while C33—N33 is short (mean values 1.340 and 1.355 Å, respectively); in addition, the C31—O31 bond is long for an amide carbonyl group (mean value 1.231 Å). These observations point to the importance of the polarized form (Ia) as a contributor to the overall molecular–electronic structure. Furthermore, the C32—C321 bond is rather shorter than the corresponding bonds in (V)–(IX), where the distances range from 1.443 (2) Å in (VI) to 1.448 (3) Å in (V), while the C321—N322 bond is rather longer than the corresponding bonds in (V)–(IX), which range from 1.143 (4) Å in (VI) to 1.1499 (18) Å in (IX), supporting a contribution to the overall molecular–electronic structure of (I) from the polarized form (Ib). Forms analogous to (Ib) are not possible for (V)–(IX), but they are possible in (II)–(IV), which do, in fact, all show values for the corresponding bond lengths that are very similar to those in (I).

A single three-centre N—H···(N,O) hydrogen bond (Table 2) links the molecules of (I) into a chain of edge-fused rings. The N—H···N component of this system links pairs of molecules into centrosymmetric R₂²(16) (Bernstein et al., 1995) rings, while the N—H···O component links molecules related by the C-centring translation into C(6) chains running parallel to the [110] direction. In combination, these two interactions generate a chain of centrosymmetric rings along [110] in which R₂²(16) rings centred at (1/2n + 1/4, 1/2n + 1/4, 1/2), where n represents zero or an integer, alternate with R₂⁴(12) rings centred at (1/2n, 1/2n, 1/2), where n represents zero or an integer (Fig. 2). Two chains of this type, related to one another by the action of the twofold rotation axes, pass through each unit cell, but there are no direction-specific interaction between the chains; in particular, there are no C—H···π(arene) hydrogen bonds and no aromatic π–π stacking interactions.

In the crystal structures of (II) (Hashmi et al., 2006) and (III) (Adhikesavalu & Venkatesan, 1981), both close related to (I), there are no significant direction-specific intermolecular interactions of any kind, and neither the carbonyl O atoms nor the nitrile N atoms act as hydrogen-bond acceptors. In (IV) (Langer et al., 2006), there is an intermolecular N—H···O hydrogen bond; while the original report of this compound listed intermolecular C—H···O and C—H···N hydrogen bonds, no analysis or discussion was provided on the resulting supramolecular aggregation. Analysis of this structure using the published atomic coordinates shows that the molecules are linked into sheets lying parallel to (101) and built from alternating centrosymmetric R₂²(10) and R⁶₆(38) rings (Fig. 3).

The marked difference in the pattern of supramolecular aggregation in (I) as compared with those in (II)–(IV) may be traced to two significant factors. First, neither of compounds (II) and (III) contains an N—H bond, which acts as the sole hydrogen-bond donor in (I), while the N—H bond in (IV) is effectively masked by the formation of the intramolecular hydrogen bond. Secondly, the configuration about the C═C double bond places the amino substituent remote from the carbonyl group in each of (I) and (II), but close to it in each of (III) and (IV). Intermolecular hydrogen bonding with the carbonyl O atom as acceptor may be prevented in (III) by the steric effects of the adjacent methyl group. However, it is unclear why there are no intermolecular C—H···O hydrogen bonds formed in (II) between the C—H bonds of the aryl ring and either the carbonyl O atom or the nitrile N atom.

Related literature

For related literature, see: Adhikesavalu & Venkatesan (1981); Allen (2002); Allen et al. (1987); Bernstein et al. (1995); Cobo et al. (2005); Cobo, Cobo, Low & Glidewell (2006); Cobo, Quiroga, de la Torre, Cobo, Low & Glidewell (2006); Hashmi et al. (2006); Langer et al. (2006).

S2. Experimental

A solution of 3-(1H-indol-3-yl)-3-oxopropionitrile (3.2 mmol) in dry toluene (6 ml) was added to dimethylformamidedimethylacetal (5 mmol), and the mixture was heated under reflux for 30 min. After cooling the mixture to ambient temperature, the product (I) was collected by filtration, washed with ethanol, dried and recrystallized from ethanol to afford crystals suitable for single-crystal X-ray diffraction (yellow plates [colourless laths according to CIF], yield 68%, m.p. 474–476 K). MS m/z (relative abundance, %): 239 (M⁺, 40), 238 (100), 222 (16), 144 (93), 116 (46), 89 (46); 42 (19).

S3. Refinement

The systematic absences permitted C2/c and Cc as possible space groups. C2/c was selected, and confirmed by the subsequent structure refinement. All H atoms were located in difference maps and then treated as riding atoms in geometrically idealized positions, with C—H distances of 0.95 Å (ring or alkene H) or 0.98 Å (methyl) and N—H distances of 0.88 Å, and with U_iso(H) = kU_eq(carrier), where k = 1.5 for the methyl groups and k = 1.2 for all other H atoms.

Computing details

Data collection: COLLECT (Hooft, 1999); cell refinement: DIRAX/LSQ (Duisenberg et al., 2000); data reduction: EVALCCD (Duisenberg et al., 2003); program(s) used to solve structure: SIR2004 (Burla et al., 2005); program(s) used to refine structure: OSCAIL (McArdle, 2003) and SHELXL97 (Sheldrick, 2008); molecular graphics: PLATON (Spek, 2003); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008) and PRPKAPPA (Ferguson, 1999).

Figures

	Fig. 1. The molecular structure of (I), showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 30% probability level.
	Fig. 2. A stereoview of part of the crystal structure of (I), showing the formation of a hydrogen-bonded chain of edge-fused rings along [110]. For the sake of clarity, H atoms not involved in the motifs shown have been omitted.
	Fig. 3. A stereoview of part of the crystal structure of compound (IV), showing the formation of a hydrogen-bonded sheet parallel to (101). The original atomic coordinates (Langer et al., 2006) have been used and, for the sake of clarity, the H atoms not involved in the motifs shown have been omitted.

(E)-3-Dimethylamino-2-(1H-indol-3-ylcarbonyl)acrylonitrile

Crystal data

C14H13N3O	F(000) = 1008
Mr = 239.27	Dx = 1.371 Mg m^−3
Monoclinic, C2/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2yc	Cell parameters from 2660 reflections
a = 11.5945 (5) Å	θ = 3.1–27.5°
b = 8.6412 (6) Å	µ = 0.09 mm^−1
c = 23.1522 (18) Å	T = 120 K
β = 92.325 (7)°	Plate, light yellow
V = 2317.7 (3) Å^3	0.44 × 0.43 × 0.12 mm
Z = 8

Data collection

Bruker–Nonius KappaCCD diffractometer	2660 independent reflections
Radiation source: Bruker-Nonius FR591 rotating anode	1543 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.054
Detector resolution: 9.091 pixels mm^-1	θmax = 27.5°, θmin = 3.1°
ϕ and ω scans	h = −14→15
Absorption correction: multi-scan (SADABS; Sheldrick, 2003)	k = −11→11
Tmin = 0.965, Tmax = 0.989	l = −30→30
15301 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)] = 0.067	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.225	H-atom parameters constrained
S = 1.06	w = 1/[σ^2(Fo^2) + (0.1203P)^2 + 3.0772P] where P = (Fo^2 + 2Fc^2)/3
2660 reflections	(Δ/σ)max < 0.001
165 parameters	Δρmax = 0.35 e Å^−3
0 restraints	Δρmin = −0.34 e Å^−3

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
O31	0.45342 (17)	0.7995 (2)	0.54321 (8)	0.0359 (5)
N1	0.1956 (2)	0.4076 (3)	0.56594 (10)	0.0330 (6)
N33	0.49745 (19)	0.8176 (3)	0.37120 (10)	0.0306 (6)
N322	0.3580 (2)	0.4297 (3)	0.39828 (11)	0.0398 (7)
C2	0.2492 (2)	0.4816 (3)	0.52315 (12)	0.0316 (7)
C3	0.3311 (2)	0.5838 (3)	0.54636 (11)	0.0284 (6)
C3A	0.3254 (2)	0.5701 (3)	0.60841 (11)	0.0284 (6)
C4	0.3829 (2)	0.6398 (3)	0.65610 (12)	0.0318 (7)
C5	0.3538 (2)	0.5952 (3)	0.71116 (12)	0.0347 (7)
C6	0.2705 (3)	0.4818 (4)	0.72033 (13)	0.0365 (7)
C7	0.2136 (2)	0.4104 (3)	0.67444 (12)	0.0339 (7)
C7A	0.2407 (2)	0.4571 (3)	0.61909 (12)	0.0303 (6)
C31	0.4043 (2)	0.6922 (3)	0.51570 (12)	0.0281 (6)
C32	0.4196 (2)	0.6776 (3)	0.45317 (11)	0.0282 (6)
C33	0.4804 (2)	0.7938 (3)	0.42665 (11)	0.0289 (6)
C34	0.5786 (3)	0.9358 (4)	0.35323 (13)	0.0371 (7)
C35	0.4405 (3)	0.7289 (4)	0.32441 (12)	0.0365 (7)
C321	0.3837 (2)	0.5418 (3)	0.42298 (12)	0.0304 (6)
H1	0.1378	0.3416	0.5638	0.040*
H2	0.2332	0.4661	0.4830	0.038*
H4	0.4405	0.7160	0.6508	0.038*
H5	0.3916	0.6431	0.7436	0.042*
H6	0.2530	0.4539	0.7587	0.044*
H7	0.1579	0.3320	0.6803	0.041*
H33	0.5152	0.8678	0.4522	0.035*
H34A	0.5992	1.0031	0.3861	0.056*
H34B	0.5427	0.9977	0.3219	0.056*
H34C	0.6483	0.8858	0.3396	0.056*
H35A	0.4849	0.6347	0.3174	0.055*
H35B	0.4360	0.7917	0.2892	0.055*
H35C	0.3624	0.7007	0.3353	0.055*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O31	0.0375 (11)	0.0385 (12)	0.0314 (11)	−0.0083 (9)	−0.0012 (9)	−0.0012 (9)
N1	0.0299 (13)	0.0355 (13)	0.0338 (13)	−0.0072 (10)	0.0040 (10)	−0.0008 (11)
N33	0.0294 (12)	0.0365 (13)	0.0262 (12)	0.0000 (10)	0.0034 (9)	−0.0019 (10)
N322	0.0412 (15)	0.0379 (15)	0.0408 (15)	−0.0063 (12)	0.0084 (12)	−0.0064 (12)
C2	0.0325 (15)	0.0338 (15)	0.0287 (14)	−0.0050 (12)	0.0036 (11)	−0.0004 (12)
C3	0.0249 (13)	0.0316 (14)	0.0286 (14)	0.0031 (11)	0.0018 (11)	0.0023 (12)
C3A	0.0272 (14)	0.0316 (15)	0.0265 (14)	0.0020 (11)	0.0021 (11)	0.0001 (12)
C4	0.0296 (15)	0.0345 (15)	0.0311 (15)	0.0035 (12)	−0.0012 (11)	−0.0035 (12)
C5	0.0320 (15)	0.0432 (17)	0.0284 (15)	0.0080 (13)	−0.0025 (12)	−0.0065 (13)
C6	0.0367 (16)	0.0425 (17)	0.0305 (15)	0.0087 (14)	0.0058 (12)	0.0031 (13)
C7	0.0334 (15)	0.0352 (16)	0.0335 (15)	0.0020 (12)	0.0069 (12)	0.0032 (13)
C7A	0.0288 (14)	0.0325 (15)	0.0297 (14)	0.0045 (12)	0.0016 (11)	−0.0015 (12)
C31	0.0209 (13)	0.0329 (15)	0.0302 (14)	0.0006 (11)	−0.0039 (10)	0.0003 (12)
C32	0.0268 (14)	0.0323 (15)	0.0256 (14)	0.0001 (11)	0.0009 (10)	−0.0036 (11)
C33	0.0264 (14)	0.0341 (15)	0.0262 (14)	−0.0005 (11)	−0.0007 (10)	0.0006 (12)
C34	0.0364 (16)	0.0410 (17)	0.0343 (16)	−0.0051 (13)	0.0060 (13)	0.0015 (14)
C35	0.0429 (17)	0.0376 (16)	0.0289 (15)	0.0008 (14)	0.0008 (12)	−0.0055 (13)
C321	0.0261 (14)	0.0345 (16)	0.0310 (14)	−0.0012 (12)	0.0049 (11)	0.0016 (13)

Geometric parameters (Å, º)

N1—C2	1.352 (4)	O31—C31	1.249 (3)
N1—C7A	1.385 (3)	C32—C321	1.420 (4)
C2—C3	1.388 (4)	C321—N322	1.158 (4)
C3—C3A	1.446 (4)	N1—H1	0.88
C3A—C4	1.403 (4)	C2—H2	0.95
C4—C5	1.387 (4)	C4—H4	0.95
C5—C6	1.398 (4)	C5—H5	0.95
C6—C7	1.373 (4)	C6—H6	0.95
C7—C7A	1.391 (4)	C7—H7	0.95
C3A—C7A	1.414 (4)	C33—H33	0.95
C3—C31	1.467 (4)	C34—H34A	0.98
C31—C32	1.471 (4)	C34—H34B	0.98
C32—C33	1.385 (4)	C34—H34C	0.98
C33—N33	1.323 (3)	C35—H35A	0.98
N33—C34	1.460 (4)	C35—H35B	0.98
N33—C35	1.463 (3)	C35—H35C	0.98
C33—N33—C34	120.6 (2)	C33—C32—C31	117.3 (2)
C33—N33—C35	123.8 (2)	C321—C32—C31	120.7 (2)
C34—N33—C35	115.6 (2)	C4—C5—C6	122.0 (3)
C2—N1—C7A	109.7 (2)	C4—C5—H5	119.0
C2—N1—H1	129.6	C6—C5—H5	119.0
C7A—N1—H1	120.6	C5—C4—C3A	118.6 (3)
N1—C2—C3	110.2 (2)	C5—C4—H4	120.7
N1—C2—H2	124.9	C3A—C4—H4	120.7
C3—C2—H2	124.9	N1—C7A—C7	129.6 (3)
N33—C33—C32	129.9 (3)	N1—C7A—C3A	107.3 (2)
N33—C33—H33	115.0	C7—C7A—C3A	123.0 (3)
C32—C33—H33	115.0	C6—C7—C7A	117.6 (3)
C4—C3A—C7A	118.1 (2)	C6—C7—H7	121.2
C4—C3A—C3	135.0 (3)	C7A—C7—H7	121.2
C7A—C3A—C3	106.9 (2)	N33—C35—H35A	109.5
O31—C31—C3	119.2 (2)	N33—C35—H35B	109.5
O31—C31—C32	119.7 (2)	H35A—C35—H35B	109.5
C3—C31—C32	121.1 (2)	N33—C35—H35C	109.5
N322—C321—C32	177.9 (3)	H35A—C35—H35C	109.5
C2—C3—C3A	105.9 (2)	H35B—C35—H35C	109.5
C2—C3—C31	128.2 (2)	N33—C34—H34A	109.5
C3A—C3—C31	125.7 (2)	N33—C34—H34B	109.5
C7—C6—C5	120.7 (3)	H34A—C34—H34B	109.5
C7—C6—H6	119.7	N33—C34—H34C	109.5
C5—C6—H6	119.7	H34A—C34—H34C	109.5
C33—C32—C321	121.7 (2)	H34B—C34—H34C	109.5
C2—C3—C31—C32	−15.7 (4)	N33—C33—C32—C321	13.6 (5)
C3—C31—C32—C33	173.5 (2)	O31—C31—C32—C33	−5.7 (4)
C31—C32—C33—N33	−172.9 (3)	O31—C31—C32—C321	167.9 (3)
C32—C33—N33—C34	−171.2 (3)	C7—C6—C5—C4	−0.3 (4)
C2—C3—C31—O31	163.5 (3)	C6—C5—C4—C3A	0.9 (4)
C3—C31—C32—C321	−12.9 (4)	C7A—C3A—C4—C5	−0.2 (4)
C32—C33—N33—C35	7.6 (5)	C3—C3A—C4—C5	−179.6 (3)
C7A—N1—C2—C3	−0.5 (3)	C2—N1—C7A—C7	−178.5 (3)
N1—C2—C3—C3A	−0.4 (3)	C2—N1—C7A—C3A	1.1 (3)
N1—C2—C3—C31	−176.7 (3)	C4—C3A—C7A—N1	179.2 (2)
C4—C3A—C3—C2	−179.6 (3)	C3—C3A—C7A—N1	−1.3 (3)
C7A—C3A—C3—C2	1.0 (3)	C4—C3A—C7A—C7	−1.2 (4)
C4—C3A—C3—C31	−3.1 (5)	C3—C3A—C7A—C7	178.3 (3)
C7A—C3A—C3—C31	177.5 (2)	C5—C6—C7—C7A	−1.1 (4)
O31—C31—C3—C3A	−12.1 (4)	N1—C7A—C7—C6	−178.6 (3)
C32—C31—C3—C3A	168.7 (3)	C3A—C7A—C7—C6	1.9 (4)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O31^i	0.88	2.20	2.985 (3)	148
N1—H1···N322^ii	0.88	2.50	3.099 (4)	126

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