Dimethyl 2-[(acridin-9-yl)methyl­idene]malonate

Almeida, S.M.V. de; Pitta, I.R.; Lima, M. do C.A. de; Mendonça Junior, F.J.B.; Simone, C.A. de

doi:10.1107/S1600536813000500

organic compounds

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ISSN: 2056-9890

Volume 69| Part 2| February 2013| Page o224

doi:10.1107/S1600536813000500

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Dimethyl 2-[(acridin-9-yl)methylidene]malonate

Sinara M. V. de Almeida,^a Ivan R. Pitta,^b Maria do Carmo A. de Lima,^b Francisco J. B. Mendonça Junior ^c and Carlos A. de Simone ^d ^*

^aLaboratório de Imunopatologia Keizo Asami (LIKA), Departamento de Bioquímica, Universidade Federal de Pernambuco, 50670-901 Recife, PE, Brazil, ^bLaboratório de Síntese e Planejamento de Fármacos, Departamento de Antibióticos, Universidade Federal de Pernambuco, 50670-910 Recife, PE, Brazil, ^cLaboratório de Síntese e Vetorização de Moléculas Bioativas, Universidade Estadual da Paraíba, 58020-540 João Pessoa, PB, Brazil, and ^dDepartamento de Física e Informática, Instituto de Física de São Carlos, Universidade de São Paulo - USP, 13560-970 São Carlos, SP, Brazil
^*Correspondence e-mail: casimone@ifsc.usp.br

(Received 29 November 2012; accepted 6 January 2013; online 12 January 2013)

In the title compound, C₁₉H₁₅NO₄, the acridine system is essentially planar (r.m.s. deviation = 0.015 Å). The crystal packing exhibits π–π interactions between pairs of centrosymmetric molecules, one of them between the central heterocyclic rings and others between the outer benzene rings of the acridine systems, with centroid–centroid distances of 3.692 (1) and 3.754 (1) Å, respectively. These pairs are further linked by additional π–π interactions along the a-axis direction through one of the two outer benzene ring of neighboring molecules, with a centroid–centroid distance of 3.642 (2) Å.

Related literature

For background to acridines, see: Kumar et al. (2012 ). For the biological activity of acridine derivatives, see: Pigatto et al. (2011 ); Das et al. (2011 ); Kumar et al. (2012). For the synthesis of acridines, see: Tomar et al. (2010 ). For related structures, see: Buckleton & Waters (1984 ).

Experimental

Crystal data

C₁₉H₁₅NO₄
M_r = 321.32
Triclinic, $[P \overline 1]$
a = 8.3022 (2) Å
b = 9.0208 (3) Å
c = 12.0334 (4) Å
α = 96.468 (2)°
β = 93.652 (2)°
γ = 117.422 (2)°
V = 787.98 (4) Å³
Z = 2
Mo Kα radiation
μ = 0.10 mm⁻¹
T = 295 K
0.32 × 0.28 × 0.22 mm

Data collection

Nonius KappaCCD diffractometer
10674 measured reflections
3626 independent reflections
2805 reflections with I > 2σ(I)
R_int = 0.050

Refinement

R[F² > 2σ(F²)] = 0.052
wR(F²) = 0.148
S = 1.05
3626 reflections
218 parameters
H-atom parameters constrained
Δρ_max = 0.26 e Å⁻³
Δρ_min = −0.24 e Å⁻³

Data collection: COLLECT (Nonius, 1997 ); cell refinement: SCALEPACK (Otwinowski & Minor, 1997 ); data reduction: DENZO (Otwinowski & Minor, 1997) and SCALEPACK; 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).

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536813000500/lr2094sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536813000500/lr2094Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536813000500/lr2094Isup3.cml

checkCIF report

Comment top

The pharmacological uses of acridine derivatives have been well documented (Kumar et al. 2012). Amongst these applications can be highlighted: Proflavin an antibacterial agent against many Gram positive bacteria; Bucricaine which is used topically for surface anesthesia (Kumar et al. 2012); Quinacrine and 9-aminoacridine that act as antimalarial and disinfectant agents respectively (Das et al. 2011); and several antitumor agents as nitracrina, amsacrine and 9-arylacridines which are potent topoisomerase inhibitors (Pigatto et al. 2011).

In this work, we report the structure of the title compound synthesized by the reaction between acridine-9-carbaldehyde and dimethyl malonate. The mean plane analysis of molecule shows that the acridine ring is essentially planar. The deviation observed is maximum for the C5 [(0.0311 (2) Å].The crystal packing exhibits π- π interactions between pairs of centrosymmetric molecules, one of them between the central heterocyclic rings and others between the side benzene rings of the acridine moieties, with centroid-centroid distances of 3.692 (1) and 3.754 (1) Årespectively. These pairs are further linked by additional π- π interactions along the a axis through one of the two side benzene ring of neighboring molecules, with centroid-centroid distance of 3.642 (2) Å.

Related literature top

For background to acridines, see: Kumar et al. (2012). For the biological activity of acridine derivatives, see: Pigatto et al. (2011); Das et al. (2011); Kumar et al. (2012). For the synthesis of acridines, see: Tomar et al. (2010). For related structures, see: Buckleton & Waters (1984).

Experimental top

In a Dean-Stark apparatus, acridine-9-carbaldehyde (0.1 mmol), dimethyl malonate (0.1 mmol) and morpholine (0.01 mmol) were refluxed in toluene (10 ml). The reaction mixture was refluxed at 383 K for 24 h, and the solvent was evaporated under reduced pressure. The title compound was purified by flash chromatography on silica gel (230–400 mesh) Merck (Germany), eluting with n-hexane/ethyl acetate (9.5:0.5) to give analytically pure yellow crystals of 2-acridin-9-yl-methylene-malonic acid dimethyl ester; yield 33%, M.p. 405–407 K. Crystals suitable for suitable for single-crystal X-ray diffraction were grown by slow evaporation at 289 K of a solution of the pure title compound in absolute ethanol.

FTIR (KBr, cm^-1) Umax: 2954, 2924, 1730, 1628, 1435, 1266, 1232, 1076, 785, 749. NMR ¹H (300 MHz, DMSO-d₆) δ 3.15 (s, 3H), 3.92 (s, 3H), 7.65 (m, 2H), 7.89 (m, 2H), 7.99 (d, 2H,J = 8.6 Hz), 8.20 (d, 2H, J = 8.6 Hz), 8.70 (s, 1H). HRMS calcd for C₁₉H₁₅NO₄ = 321.1001, found = 322.0617.

Computing details top

Data collection: COLLECT (Nonius, 1997); cell refinement: SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO and SCALEPACK (Otwinowski & Minor, 1997); 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 top

	Fig. 1. The molecular structure of the title compound. with the ellipsoids drawn at the 50% probability level.
	Fig. 2. A partial view of the packing showing the π - π interactions.

Dimethyl 2-[(acridin-9-yl)methylidene]malonate top

Crystal data top

C₁₉H₁₅NO₄	Z = 2
M_r = 321.32	F(000) = 336
Triclinic, P1	D_x = 1.354 Mg m⁻³
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 8.3022 (2) Å	Cell parameters from 6418 reflections
b = 9.0208 (3) Å	θ = 2.5–27.5°
c = 12.0334 (4) Å	µ = 0.10 mm⁻¹
α = 96.468 (2)°	T = 295 K
β = 93.652 (2)°	Prism, yellow
γ = 117.422 (2)°	0.32 × 0.28 × 0.22 mm
V = 787.98 (4) Å³

Data collection top

Nonius KappaCCD diffractometer	2805 reflections with I > 2σ(I)
Radiation source: Enraf Nonius FR590	R_int = 0.050
Horizonally mounted graphite crystal monochromator	θ_max = 27.5°, θ_min = 2.6°
Detector resolution: 9 pixels mm^-1	h = −10→10
CCD rotation images,thick slices scans	k = −11→10
10674 measured reflections	l = −15→15
3626 independent reflections

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.052	H-atom parameters constrained
wR(F²) = 0.148	w = 1/[σ²(F_o²) + (0.0817P)² + 0.1056P] where P = (F_o² + 2F_c²)/3
S = 1.05	(Δ/σ)_max < 0.001
3626 reflections	Δρ_max = 0.26 e Å⁻³
218 parameters	Δρ_min = −0.24 e Å⁻³
0 restraints	Extinction correction: SHELXL97 (Sheldrick, 2008), Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.168 (19)

Crystal data top

C₁₉H₁₅NO₄	γ = 117.422 (2)°
M_r = 321.32	V = 787.98 (4) Å³
Triclinic, P1	Z = 2
a = 8.3022 (2) Å	Mo Kα radiation
b = 9.0208 (3) Å	µ = 0.10 mm⁻¹
c = 12.0334 (4) Å	T = 295 K
α = 96.468 (2)°	0.32 × 0.28 × 0.22 mm
β = 93.652 (2)°

Data collection top

Nonius KappaCCD diffractometer	2805 reflections with I > 2σ(I)
10674 measured reflections	R_int = 0.050
3626 independent reflections

Refinement top

R[F² > 2σ(F²)] = 0.052	0 restraints
wR(F²) = 0.148	H-atom parameters constrained
S = 1.05	Δρ_max = 0.26 e Å⁻³
3626 reflections	Δρ_min = −0.24 e Å⁻³
218 parameters

Special details top

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.

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

	x	y	z	U_iso*/U_eq
C2	0.18856 (17)	−0.04107 (16)	0.05238 (10)	0.0416 (3)
C8	0.27051 (18)	0.29435 (17)	0.10755 (11)	0.0439 (3)
C1	0.12960 (17)	0.00751 (16)	0.15015 (10)	0.0409 (3)
C16	0.25132 (19)	−0.00447 (18)	0.38809 (12)	0.0475 (3)
N1	0.32779 (16)	0.24918 (14)	0.01345 (9)	0.0477 (3)
C14	0.02296 (18)	−0.12607 (17)	0.21649 (11)	0.0455 (3)
H14	−0.0906	−0.2111	0.1815	0.055*
O4	−0.19557 (15)	−0.38893 (13)	0.31911 (9)	0.0630 (3)
C13	0.16978 (17)	0.17719 (16)	0.17992 (10)	0.0412 (3)
C12	0.11370 (19)	0.24024 (18)	0.27615 (11)	0.0484 (3)
H12	0.0464	0.1665	0.3236	0.058*
C11	0.1572 (2)	0.4058 (2)	0.29913 (12)	0.0544 (4)
H11	0.1202	0.4443	0.3625	0.065*
C6	0.3548 (2)	0.0411 (2)	−0.11100 (12)	0.0549 (4)
H6	0.4194	0.1228	−0.1546	0.066*
C9	0.3139 (2)	0.46746 (18)	0.13512 (13)	0.0538 (4)
H9	0.3808	0.5443	0.0892	0.065*
O2	0.22592 (15)	0.05138 (14)	0.48843 (9)	0.0593 (3)
O1	0.39648 (15)	0.04600 (18)	0.35414 (10)	0.0745 (4)
O3	0.02856 (18)	−0.31220 (15)	0.46082 (10)	0.0716 (4)
C7	0.28933 (18)	0.08723 (17)	−0.01311 (11)	0.0445 (3)
C18	−0.0314 (2)	−0.28576 (17)	0.37642 (11)	0.0488 (3)
C5	0.3247 (2)	−0.1193 (2)	−0.14145 (14)	0.0618 (4)
H5	0.3696	−0.1466	−0.2051	0.074*
C3	0.1592 (2)	−0.20857 (18)	0.01646 (12)	0.0508 (3)
H3	0.0939	−0.2935	0.0577	0.061*
C15	0.07425 (18)	−0.13590 (17)	0.32134 (11)	0.0452 (3)
C10	0.2585 (2)	0.52130 (19)	0.22792 (13)	0.0578 (4)
H10	0.2871	0.6345	0.2449	0.069*
C4	0.2252 (2)	−0.2462 (2)	−0.07701 (14)	0.0588 (4)
H4	0.2048	−0.3563	−0.0989	0.071*
C19	−0.3052 (3)	−0.5404 (2)	0.36533 (18)	0.0765 (5)
H19A	−0.4202	−0.6062	0.3179	0.115*
H19B	−0.3267	−0.5095	0.4398	0.115*
H19C	−0.2415	−0.6059	0.3690	0.115*
C17	0.3884 (3)	0.1685 (3)	0.56385 (16)	0.0767 (5)
H17A	0.3545	0.2006	0.6338	0.115*
H17B	0.4557	0.2672	0.5302	0.115*
H17C	0.4634	0.1156	0.5779	0.115*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C2	0.0385 (6)	0.0446 (7)	0.0367 (6)	0.0149 (5)	0.0014 (5)	0.0111 (5)
C8	0.0422 (7)	0.0438 (7)	0.0379 (6)	0.0126 (5)	0.0030 (5)	0.0124 (5)
C1	0.0387 (6)	0.0446 (7)	0.0350 (6)	0.0143 (5)	0.0027 (5)	0.0143 (5)
C16	0.0493 (7)	0.0517 (7)	0.0466 (7)	0.0249 (6)	0.0081 (6)	0.0219 (6)
N1	0.0484 (6)	0.0451 (6)	0.0397 (6)	0.0120 (5)	0.0080 (5)	0.0136 (5)
C14	0.0465 (7)	0.0429 (7)	0.0428 (7)	0.0157 (5)	0.0075 (5)	0.0136 (5)
O4	0.0636 (7)	0.0495 (6)	0.0614 (7)	0.0110 (5)	0.0127 (5)	0.0236 (5)
C13	0.0395 (6)	0.0448 (7)	0.0348 (6)	0.0153 (5)	0.0023 (5)	0.0117 (5)
C12	0.0506 (7)	0.0535 (8)	0.0411 (7)	0.0230 (6)	0.0081 (6)	0.0134 (6)
C11	0.0619 (9)	0.0575 (9)	0.0440 (7)	0.0291 (7)	0.0051 (6)	0.0058 (6)
C6	0.0510 (8)	0.0602 (9)	0.0419 (7)	0.0153 (6)	0.0115 (6)	0.0105 (6)
C9	0.0574 (8)	0.0425 (7)	0.0497 (8)	0.0127 (6)	0.0043 (6)	0.0139 (6)
O2	0.0593 (6)	0.0619 (7)	0.0536 (6)	0.0279 (5)	0.0027 (5)	0.0030 (5)
O1	0.0492 (6)	0.1023 (10)	0.0627 (7)	0.0255 (6)	0.0115 (5)	0.0222 (6)
O3	0.0931 (9)	0.0618 (7)	0.0579 (7)	0.0302 (6)	0.0085 (6)	0.0315 (5)
C7	0.0399 (6)	0.0491 (7)	0.0366 (6)	0.0137 (5)	0.0038 (5)	0.0109 (5)
C18	0.0622 (8)	0.0441 (7)	0.0440 (7)	0.0252 (6)	0.0168 (6)	0.0155 (6)
C5	0.0587 (9)	0.0693 (10)	0.0482 (8)	0.0241 (8)	0.0113 (7)	−0.0008 (7)
C3	0.0500 (8)	0.0477 (7)	0.0493 (8)	0.0180 (6)	0.0048 (6)	0.0107 (6)
C15	0.0502 (7)	0.0455 (7)	0.0425 (7)	0.0220 (6)	0.0119 (6)	0.0165 (5)
C10	0.0661 (9)	0.0442 (8)	0.0545 (8)	0.0204 (7)	0.0005 (7)	0.0048 (6)
C4	0.0603 (9)	0.0542 (8)	0.0561 (9)	0.0246 (7)	0.0041 (7)	0.0001 (7)
C19	0.0826 (12)	0.0459 (9)	0.0854 (13)	0.0120 (8)	0.0267 (10)	0.0254 (8)
C17	0.0776 (12)	0.0741 (11)	0.0667 (11)	0.0323 (9)	−0.0107 (9)	−0.0063 (9)

Geometric parameters (Å, º) top

C2—C1	1.4037 (18)	C6—C5	1.351 (2)
C2—C3	1.425 (2)	C6—C7	1.427 (2)
C2—C7	1.4345 (17)	C6—H6	0.9300
C8—N1	1.3482 (18)	C9—C10	1.358 (2)
C8—C9	1.424 (2)	C9—H9	0.9300
C8—C13	1.4356 (17)	O2—C17	1.441 (2)
C1—C13	1.4049 (19)	O3—C18	1.1981 (17)
C1—C14	1.4823 (16)	C18—C15	1.4899 (18)
C16—O1	1.1940 (17)	C5—C4	1.415 (2)
C16—O2	1.3226 (18)	C5—H5	0.9300
C16—C15	1.497 (2)	C3—C4	1.358 (2)
N1—C7	1.3381 (18)	C3—H3	0.9300
C14—C15	1.3315 (18)	C10—H10	0.9300
C14—H14	0.9300	C4—H4	0.9300
O4—C18	1.3293 (19)	C19—H19A	0.9600
O4—C19	1.4474 (18)	C19—H19B	0.9600
C13—C12	1.4301 (19)	C19—H19C	0.9600
C12—C11	1.355 (2)	C17—H17A	0.9600
C12—H12	0.9300	C17—H17B	0.9600
C11—C10	1.419 (2)	C17—H17C	0.9600
C11—H11	0.9300

C1—C2—C3	123.94 (12)	N1—C7—C6	117.91 (12)
C1—C2—C7	117.80 (12)	N1—C7—C2	123.52 (12)
C3—C2—C7	118.24 (12)	C6—C7—C2	118.55 (13)
N1—C8—C9	117.44 (12)	O3—C18—O4	124.20 (13)
N1—C8—C13	123.21 (12)	O3—C18—C15	123.33 (14)
C9—C8—C13	119.35 (12)	O4—C18—C15	112.42 (12)
C2—C1—C13	119.54 (11)	C6—C5—C4	120.40 (14)
C2—C1—C14	117.57 (12)	C6—C5—H5	119.8
C13—C1—C14	122.87 (12)	C4—C5—H5	119.8
O1—C16—O2	124.32 (15)	C4—C3—C2	121.06 (14)
O1—C16—C15	124.28 (14)	C4—C3—H3	119.5
O2—C16—C15	111.38 (11)	C2—C3—H3	119.5
C7—N1—C8	118.15 (11)	C14—C15—C18	122.41 (13)
C15—C14—C1	126.22 (12)	C14—C15—C16	122.17 (11)
C15—C14—H14	116.9	C18—C15—C16	115.18 (11)
C1—C14—H14	116.9	C9—C10—C11	120.38 (14)
C18—O4—C19	115.93 (13)	C9—C10—H10	119.8
C1—C13—C12	124.38 (12)	C11—C10—H10	119.8
C1—C13—C8	117.77 (12)	C3—C4—C5	120.61 (15)
C12—C13—C8	117.83 (12)	C3—C4—H4	119.7
C11—C12—C13	120.94 (13)	C5—C4—H4	119.7
C11—C12—H12	119.5	O4—C19—H19A	109.5
C13—C12—H12	119.5	O4—C19—H19B	109.5
C12—C11—C10	120.94 (14)	H19A—C19—H19B	109.5
C12—C11—H11	119.5	O4—C19—H19C	109.5
C10—C11—H11	119.5	H19A—C19—H19C	109.5
C5—C6—C7	121.14 (14)	H19B—C19—H19C	109.5
C5—C6—H6	119.4	O2—C17—H17A	109.5
C7—C6—H6	119.4	O2—C17—H17B	109.5
C10—C9—C8	120.55 (13)	H17A—C17—H17B	109.5
C10—C9—H9	119.7	O2—C17—H17C	109.5
C8—C9—H9	119.7	H17A—C17—H17C	109.5
C16—O2—C17	116.36 (13)	H17B—C17—H17C	109.5

Experimental details

Crystal data
Chemical formula	C₁₉H₁₅NO₄
M_r	321.32
Crystal system, space group	Triclinic, P1
Temperature (K)	295
a, b, c (Å)	8.3022 (2), 9.0208 (3), 12.0334 (4)
α, β, γ (°)	96.468 (2), 93.652 (2), 117.422 (2)
V (Å³)	787.98 (4)
Z	2
Radiation type	Mo Kα
µ (mm⁻¹)	0.10
Crystal size (mm)	0.32 × 0.28 × 0.22

Data collection
Diffractometer	Nonius KappaCCD diffractometer
Absorption correction	–
No. of measured, independent and observed [I > 2σ(I)] reflections	10674, 3626, 2805
R_int	0.050
(sin θ/λ)_max (Å⁻¹)	0.650

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.052, 0.148, 1.05
No. of reflections	3626
No. of parameters	218
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.26, −0.24

Computer programs: COLLECT (Nonius, 1997), DENZO and SCALEPACK (Otwinowski & Minor, 1997), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 for Windows (Farrugia, 2012), WinGX (Farrugia, 2012).

Acknowledgements

This work received partial support from CNPq and PROPESQ/UEPB. The authors thank the Instituto de Física de São Carlos – USP for allowing the use of the KappaCCD diffractometer.

References

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