Polarized molecular–electronic ­structures and supramolecular ­aggregation in 1-(6-amino-1,3-benzodioxol-5-yl)-3-aryl­prop-2-en-1-ones

Low, J.N.; Cobo, J.; Nogueras, M.; Cuervo, P.; Abonia, R.; Glidewell, C.

doi:10.1107/S0108270104020414

Volume 60
Part 10
Pages o744-o750
October 2004

Received 12 August 2004
Accepted 16 August 2004
Online 18 September 2004

Polarized molecular-electronic structures and supramolecular aggregation in 1-(6-amino-1,3-benzodioxol-5-yl)-3-arylprop-2-en-1-ones

John N. Low,^a Justo Cobo,^b Manuel Nogueras,^b Paola Cuervo,^c Rodrigo Abonia ^c and Christopher Glidewell ^d ^*

^aDepartment of Chemistry, University of Aberdeen, Meston Walk, Old Aberdeen AB24 3UE, Scotland,^bDepartamento de Química Inorgánica y Orgánica, Universidad de Jaén, 23071 Jaén, Spain,^cGrupo de Investigación de Compuestos Heterocíclicos, Departamento de Química, Universidad de Valle, AA 25360 Cali, Colombia, and ^dSchool of Chemistry, University of St Andrews, Fife KY16 9ST, Scotland
Correspondence e-mail: cg@st-andrews.ac.uk

Molecules of 1-(6-amino-1,3-benzodioxol-5-yl)-3-(4-methylphenyl)prop-2-en-1-one, C₁₇H₁₅NO₃, (I), 1-(6-amino-1,3-benzodioxol-5-yl)-3-(4-methoxyphenyl)prop-2-en-1-one, C₁₇H₁₅NO₄, (II), and 1-(6-amino-1,3-benzodioxol-5-yl)-3-[4-(trifluoromethyl)phenyl]prop-2-en-1-one, C₁₇H₁₂F₃NO₃, (III), all contain an intramolecular N-HO hydrogen bond and all exhibit polarized molecular-electronic structures. The molecules of (I) are linked into simple sheets, generated by translation, by means of one N-HO and one C-H [pi] (arene) hydrogen bond. Compound (II) crystallizes as two concomitant polymorphs, viz. (IIa), with Z' = 1 in P2₁/c, and (IIb), with Z' = 2 in P $[\overline 1]$ . In (IIa), intra- and intermolecular N-HO hydrogen bonds generate a helical chain of rings, and these chains are linked into sheets by simple helical chains built from a C-H [pi] (arene) hydrogen bond, while in (IIb), the molecules are linked into simple chains by a C-HO hydrogen bond. In (III), where Z' = 2, each type of molecule forms a simple N-HO hydrogen-bonded chain generated by translation and the two types of chain are linked by a single [pi] - [pi] stacking interaction.

Comment

A range of 2-aminochalcone derivatives have been prepared for use as intermediates in the synthesis of new 6,7-methylenedioxytetrahydroquinolin-4-ones, compounds with interesting biological and pharmacological properties (Donnelly & Farell, 1990; Prager & Thredgold, 1968; Kurasawa et al., 2002). We report here the molecular and supramolecular structures of three such compounds, (I)-(III), and compare them with two further examples, (IV) and (V) (Low et al., 2002).

Compounds (I) and (III) crystallize with Z' values of 1 and 2, respectively, while compound (II) forms two polymorphs, viz. monoclinic and triclinic, denoted (IIa) and (IIb), respectively, which crystallize concomitantly from dimethylformamide, with Z' values of 1 and 2, respectively (Figs. 1-4 ). Of the two polymorphs of (II), the monoclinic polymorph has a significantly higher density than the triclinic polymorph and hence is probably the thermodynamically more stable form (Burger & Ramberger, 1979).

There is significant bond fixation within the amino-substituted aryl rings of (I)-(III) (Table 1). In particular, the C3a-C4 and C7-C7a bonds are both short, while the C5-C6 and C6-C7 bonds are long. In addition, the C6-C8 bond is short for its type (mean value 1.488 Å; Allen et al., 1987), while C8-O8 is long (mean value 1.231 Å). These values point to the charge-separated form, (A) (see scheme below), as an important contributor to the overall molecular-electronic structure, alongside the delocalized form, (B). An entirely similar pattern of distances (Table 1) is observed in the analogous compounds (IV) and (V), the structures of which have recently been reported (Low et al., 2002), although this was not discussed or noted in the original report, which focused exclusively on the supramolecular aggregation of (IV) and (V).

In all cases, the molecular skeletons are fairly close to being planar but, as shown by the key torsion angles (Table 2), there are some significant deviations in most of the independent examples. The sole exception is the type 1 molecule (containing atom O11, etc.; Fig. 3a) of compound (III). The five-membered rings show some flexibility of conformational behaviour. Thus, this ring is planar in (IIa) [although not in (IIb)] and in the type 2 molecule of compound (III), but it adopts an envelope conformation, with a folding across the OO line, in (I), in both molecules of (IIb) and in the type 1 molecule of (III). For these rings, the ring-puckering parameter [varphi] ₂ (Cremer & Pople, 1975) takes the values 31.1 (15) and 30.5 (9)° in (I) and (III), respectively, and 30.9 (5) and 213.7 (5)° in the two independent molecules of (IIb). The two independent molecules in (IIb) exhibit different conformations at the methoxy substituent (Table 2), and this alone is sufficient to preclude the possibility of any additional symmetry

All of the molecules contain an intramolecular N-HO hydrogen bond (Tables 3-6 ), in each case generating an S(6) motif (Bernstein et al., 1995), and these may have some influence on the overall molecular conformations. The supramolecular structures of (I) and (IIa) both depend upon a combination of N-HO and C-H [pi] (arene) hydrogen bonds to generate sheets, but the structures differ considerably in detail. In compound (I), the amine atom N5 in the molecule at (x, y, z) acts as hydrogen-bond donor, via atom H5B, to ring atom O1 in the molecule at (x, y - 1, z), so generating by translation a C(7) chain running parallel to the [010] direction (Fig. 5). In addition, atom C2 in the molecule at (x, y, z) acts as hydrogen-bond donor, via atom H2A, to the C11-C16 ring in the molecule at (x - 1, y, z), so generating by translation a chain running parallel to the [100] direction (Fig. 6). The combination of the [100] and [010] chains generates a sheet parallel to (001), lying in the domain $[{1 \over 2}]$ < z < $[{3 \over 4}]$ (Fig. 7). Four sheets of this type pass through each unit cell, but there are no direction-specific interactions between adjacent sheets.

The monoclinic polymorph (IIa) of compound (II) exhibits two C-H [pi] (arene) hydrogen bonds in addition to the two N-HO interactions (Table 4). Amine atom N5 in the molecule at (x, y, z) acts as donor, again via atom H5B, but this time to carbonyl atom O8 in the molecule at (2 - x, y - $[{1 \over 2}]$ , $[{1 \over 2}]$ - z), so producing a helical C₂¹(4)C(6)[S(6)] chain of rings running parallel to the [010] direction and generated by the 2₁ screw axis along (1, y, $[{1 \over 4}]$ ) (Fig. 8). This chain of rings may be contrasted with the very simple chain formed by the N-HO hydrogen bonds in compound (I) (Fig. 5). Of the two C-H [pi] (arene) hydrogen bonds, that having atom C2 as the donor simply reinforces the foregoing [010] chain. However, that involving atom C13 in the molecule at (x, y, z) as donor to the C11-C16 ring in the molecule at (1 - x, y - $[{1 \over 2}]$ , $[{1 \over 2}]$ - z) not only generates a second chain running parallel to [010], this time generated by the 2₁ axis along ( $[{1 \over 2}]$ , y, $[{1 \over 4}]$ ) (Fig. 9), but also serves to link all of the chain of rings into an (001) sheet (Fig. 10). In the triclinic polymorph (IIb), the type 1 molecules (Fig. 3a) are linked by means of a single C-HO hydrogen bond into chains generated by translation, while the type 2 molecules (Fig. 3b) are pendent from these chains and linked to them by N-HO hydrogen bonds (Fig. 11)

Each of the two independent molecules in compound (III) forms a simple C(7) chain. The amine atoms N15 and N25 in the molecules at (x, y, z) act as donors to, respectively, the ring atoms O11 and O21 in the molecules at (x - 1, y, z), so generating C(7) chains by translation (Table 5 and Fig. 12). These two chains are linked by an aromatic [pi] - [pi] stacking interaction between the C111-C116 and C211-C216 rings within the asymmetric unit. The dihedral angle between the planes of these two rings is only 4.5 (2)°, the interplanar spacing is ca 3.5 Å and the centroid-centroid separation is 3.618 (2) Å. Propagation of this interaction then links the two independent translational chains (Fig. 12)

The simple and complex sheets in (I) and (IIa), the single chains in (IIb) and the paired chains in (III) may be briefly compared with the supramolecular structures of the analogues (IV) and (V) (Low et al., 2002). In (IV), where Z' = 1, the sole significant intermolecular interactions are a C-HO hydrogen bond with a ring O atom as acceptor, which generates zigzag C(10) chains, and a [pi] - [pi] stacking interaction linking these chains into sheets. In (V), where Z' = 2, two N-HO hydrogen bonds generate centrosymmetric R₈⁴(16) tetramers, which are weakly linked into chains by two rather long C-HO hydrogen bonds. Hence, for the five compounds (I)-(V), while their intramolecular properties are all very similar, their supramolecular aggregation patterns are all different. For no single example in this series could the supramolecular structure be predicted from a knowledge of the supramolecular structures of all the others.

Figure 1
The molecule of (I

), showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 30% probability level and H atoms are shown as small spheres of arbitrary radii.

Figure 2
The molecule of (IIa

), showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 30% probability level and H atoms are shown as small spheres of arbitrary radii.

Figure 3
The two independent molecules of (IIb

), showing the atom-labelling scheme for (a) the type 1 molecule and (b) the type 2 molecule. Displacement ellipsoids are drawn at the 30% probability level and H atoms are shown as small spheres of arbitrary radii.

Figure 4
The two independent molecules of (III

Figure 5
Part of the crystal structure of (I

), showing the formation of a chain parallel to [010]. For the sake of clarity, H atoms bonded to C atoms have been omitted. Atoms marked with an asterisk (*) or a hash (#) are at the symmetry positions (x, y - 1, z) and (x, 1 + y, z), respectively.

Figure 6
Part of the crystal structure of (I

), showing the formation of a chain parallel to [100]. For the sake of clarity, H atoms bonded to C atoms not involved in the motif shown have been omitted. Atoms marked with an asterisk (*) or a hash (#) are at the symmetry positions (x - 1, y, z) and (1 + x, y, z), respectively.

Figure 7
A stereoview of part of the crystal structure of (I

), showing the formation of a sheet parallel to (001). For the sake of clarity, H atoms bonded to C atoms not involved in the motif shown have been omitted.

Figure 8
Part of the crystal structure of polymorph (IIa

), showing the formation of a chain of rings parallel to [010]. For the sake of clarity, H atoms bonded to C atoms have been omitted. Atoms marked with an asterisk (*), a hash (#) or an ampersand (&) are at the symmetry positions (2 - x, y - $[{1 \over 2}]$ , $[{1 \over 2}]$ - z), (x, y - 1, z) and (2 - x, $[{1 \over 2}]$ + y, $[{1 \over 2}]$ - z), respectively.

Figure 9
A stereoview of part of the crystal structure of polymorph (IIa

), showing the formation of an [010] chain generated by C-H

(arene) hydrogen bonds. For the sake of clarity, H atoms not involved in the motif shown have been omitted.

Figure 10
A stereoview of part of the crystal structure of polymorph (IIa

), showing the formation of a sheet parallel to (001). For the sake of clarity, the intramolecular hydrogen bond and H atoms bonded to C atoms and not involved in the motif shown have been omitted.

Figure 11
A stereoview of part of the crystal structure of polymorph (IIb

), showing the formation of a C(8) chain along [100]. For the sake of clarity, the intramolecular hydrogen bond and H atoms bonded to C atoms and not involved in the motif shown have been omitted.

Figure 12
Part of the crystal structure of (III

), showing the formation of a [pi]

-stacked pair of chains parallel to [100]. For the sake of clarity, H atoms bonded to C atoms have been omitted. Atoms marked with an asterisk (*) or a hash (#) are at the symmetry positions (x - 1, y, z) and (1 + x, y, z), respectively.

Experimental

For the synthesis of (I), a solution of 6-amino-3,4-methylenedioxyacetophenone (0.5 g, 2.79 mmol), 4-tolualdehyde (0.33 g, 2.75 mmol), ethanol (10 ml) and aqueous NaOH (0.5 ml, 20%) was heated under reflux for 20 min. After cooling the mixture, the resulting precipitate was filtered off and washed with ethanol, yielding (I) as a yellow solid (yield 91%, m.p. 401 K). Spectroscopic analysis, IR (KBr disc, [nu] , cm^-1): 3454, 3278 (NH₂), 1646 (C=O), 1606 (C=C), 1224 (OCH₂O); ¹H NMR (DMSO-d₆, [delta] ): 2.33 (3H, s, CH₃), 5.96 (2H, s, OCH₂O), 6.35 (1H, s), 7.23 (2H, d, J = 8.0 Hz), 7.53 (1H, d, J = 15.4 Hz), 7.65 (1H, s), 7.67 (2H, br s, NH₂), 7.73 (2H, d, J = 8.0 Hz), 7.81 (1H, d, J = 15.4 Hz); ¹³C NMR (DMSO-d₆, [delta] ): 21.0 (CH₃), 95.8, 101.1 (OCH₂O), 108.0, 109.9, 122.7, 128.5, 129.4, 132.5, 137.7, 139.6, 141.0, 151.7, 152.7, 187.7 (C=O). MS (70 eV): m/e (%) 281 (41, [M⁺]), 190 (100, [M-C₇H₇]). Crystals of (I) suitable for single-crystal X-ray diffraction were grown from a solution in ethanol. For the synthesis of (II), a solution of 6-amino-3,4-methylenedioxyacetophenone (0.5 g, 2.79 mmol), 4-methoxybenzaldehyde (0.38 g, 2.79 mmol), ethanol (10 ml) and aqueous NaOH (0.5 ml, 20%) was heated under reflux for 30 min. After cooling the mixture, the resulting precipitate was filtered off and crystallized from ethanol, giving (II) as an orange solid (yield 50%, m.p. 405 K). Spectroscopic analysis, IR (KBr disc, [nu] , cm^-1): 3461, 3303 (NH₂), 1644 (C=O), 1603 (C=C), 1223 (OCH₂O); ¹H NMR (CDCl₃, [delta] ): 3.89 (3H, s, OCH₃), 5.93 (2H, s, OCH₂O), 6.19 (1H, s), 6.57 (2H, br s, NH₂), 6.91 (2H, d, J = 8.0 Hz), 7.26 (1H, s), 7.35 (1H, d, J = 15.4 Hz), 7.47 (2H, d, J = 8.0 Hz), 7.71 (1H, d, J = 15.4 Hz); ¹³C NMR (CDCl₃, [delta] ): 55.2 (OCH₃), 96.8, l01.5 (OCH₂O), 108.2, 112.0, 114.5, 121.2, 128.3, 130.0, 138.9, 142.1, 150.0, 153.5, 161.2, 189.0 (C=O). MS (70 eV): m/e (%) 297 (27, [M⁺]), 190 (100, [M-C₇H₇O]). Crystallization from dimethylformamide gave a mixture of the monoclinic polymorph (IIa) as red crystals (m.p. 382 K) and the triclinic polymorph (IIb) as yellow crystals (m.p. 389 K). For the synthesis of (III), a solution of 6-amino-3,4-methylenedioxyacetophenone (0.5 g, 2.79 mmol), 4-(trifluoromethyl)benzaldehyde (0.49 g, 2.79 mmol), ethanol (10 ml) and aqueous NaOH (0.5 ml, 20%) was heated under reflux for 25 min. After cooling the mixture, the resulting precipitate was filtered off and washed with ethanol, yielding (III) as an orange solid (yield 75%, m.p. 417 K). Spectroscopic analysis, IR (KBr disc, [nu] , cm^-1): 3468, 3305 (NH₂), 1646 (C=O), 1606 (C=C), 1228 (OCH₂O); ¹H NMR (DMSO-d₆, [delta] ): 5.94 (1H, s, H2), 5.98 (2H, s, OCH₂O), 6.38 (1H, s, H6), 7.6 (1H, d, H8, J = 15.0 Hz), 7.69 (2H, br s, NH₂), 7.76 (2H, d, J = 8.0 Hz), 8.02 (1H, d, J = 15.4 Hz), 8.15 (2H, d, J = 8.0 Hz); ¹³C NMR (DMSO-d₆, [delta] ): 95.8, 101.2 (OCH₂O), 108.0, 108.9, 113.5 (CF₃), 125.5, 126.7, 129.3, 138.0, 139.1, 139.4, 152.2, 153.2, 187.1 (C=O). MS (70 eV): m/e (%) 335 (100, [M⁺]). Crystals of (III) suitable for single-crystal X-ray diffraction were grown from a solution in ethanol.

Table 1
Selected bond distances (Å) for compounds (I)-(V)

Bond	(I)	(IIa)	(IIb)	(IIb)	(III)	(III)	(IV)	(V)	(V)
			Mol 1	Mol 2	Mol 1	Mol 2		Mol 1	Mol 2
x	nil	nil	1	2	1	2	nil	1	2
Cx3a-Cx4	1.368 (3)	1.357 (2)	1.357 (2)	1.359 (2)	1.358 (3)	1.355 (3)	1.361 (2)	1.358 (2)	1.351 (2)
Cx4-Cx5	1.402 (3)	1.416 (2)	1.418 (2)	1.418 (2)	1.415 (3)	1.417 (3)	1.417 (2)	1.419 (2)	1.418 (2)
Cx5-Cx6	1.424 (3)	1.430 (2)	1.423 (2)	1.422 (2)	1.429 (3)	1.419 (3)	1.426 (2)	1.426 (2)	1.431 (2)
Cx6-Cx7	1.428 (3)	1.430 (2)	1.420 (2)	1.435 (2)	1.428 (3)	1.421 (3)	1.428 (2)	1.426 (2)	1.423 (2)
Cx7-Cx7a	1.339 (3)	1.354 (2)	1.353 (2)	1.350 (2)	1.350 (3)	1.355 (3)	1.355 (2)	1.354 (2)	1.353 (2)
Cx7a-Cx3a	1.386 (3)	1.394 (2)	1.387 (2)	1.391 (2)	1.390 (3)	1.390 (3)	1.394 (2)	1.390 (2)	1.393 (2)
Cx5-Nx5	1.364 (3)	1.353 (2)	1.364 (2)	1.361 (2)	1.368 (2)	1.369 (3)	1.359 (2)	1.370 (2)	1.360 (2)
Cx6-Cx8	1.459 (3)	1.461 (2)	1.470 (2)	1.462 (2)	1.468 (2)	1.468 (3)	1.470 (2)	1.473 (2)	1.463 (2)
Cx8-Ox8	1.249 (3)	1.246 (2)	1.240 (2)	1.244 (2)	1.244 (4)	1.237 (2)	1.243 (2)	1.253 (2)	1.250 (2)

Table 2
Selected torsion angles (°) for compounds (I)-(III)

Parameter	(I)	(IIa)	(IIb)	(IIb)	(III)	(III)
			Mol 1	Mol 2	Mol 1	Mol 2
x	nil	nil	1	2	1	2
Cx5-Cx6-Cx8-Cx9	-177.8 (2)	179.63 (13)	-168.15 (13)	-175.23 (13)	-171.93 (18)	-156.36 (19)
Cx6-Cx8-Cx9-Cx10	-159.1 (2)	-175.03 (14)	-170.48 (13)	153.13 (14)	171.9 (2)	176.7 (2)
Cx8-Cx9-Cx10-Cx11	178.4 (2)	179.77 (14)	-178.12 (13)	-176.05 (13)	-177.59 (19)	-177.65 (19)
Cx9-Cx10-Cx11-Cx12	-9.0 (2)	5.1 (2)	-11.3 (2)	-16.8 (2)	0.7 (3)	-8.6 (3)
Cx13-Cx14-Ox14-Cx41		-175.91 (13)	1.4 (2)	-176.09 (14)

Compound (I)

Crystal data

C₁₇H₁₅NO₃
M_r = 281.30
Monoclinic, P2₁/n
a = 10.530 (5) Å
b = 7.362 (5) Å
c = 17.546 (5) Å
= 91.719 (5)°
V = 1359.6 (12) Å³
Z = 4
D_x = 1.374 Mg m^-3
Mo K radiation
Cell parameters from 3062 reflections
= 5.3-27.5°
= 0.10 mm^-1
T = 120 (2) K
Block, yellow
0.40 × 0.30 × 0.20 mm

Data collection

Nonius KappaCCD area-detector diffractometer
scans, and scans with offsets
Absorption correction: multi-scan (EvalCCD; Duisenberg et al., 2003) T_min = 0.958, T_max = 0.981
17 073 measured reflections
3062 independent reflections
2024 reflections with I > 2(I)
R_int = 0.065
_max = 27.5°
h = -13 12
k = -9 9
l = -22 22

Refinement

Refinement on F²
R[F² > 2(F²)] = 0.061
wR(F²) = 0.135
S = 1.11
3062 reflections
191 parameters
H-atom parameters constrained
w = 1/[²(F_o²) + (0.0198P)² + 1.4934P] where P = (F_o² + 2F_c²)/3
(/)_max < 0.001
_max = 0.24 e Å^-3
_min = -0.21 e Å^-3

Table 3
Hydrogen-bonding geometry (Å, °) for (I)

Cg1 is the centroid of the C11-C16 ring.

D-HA	D-H	HA	DA	D-HA
N5-H5AO8	0.96	1.88	2.612 (3)	131
N5-H5BO1ⁱ	0.96	2.07	3.032 (3)	178
C2-H2ACg1ⁱⁱ	0.99	2.86	3.644 (4)	137
Symmetry codes: (i) x,y-1,z; (ii) x-1,y,z.

Polymorph (IIa)