organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2056-9890

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

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 ππ 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 ππ 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[Kumar, R., Kaur, M. & Kumari, M. (2012). Acta Pol. Pharm. 69, 3-9.]). For the biological activity of acridine derivatives, see: Pigatto et al. (2011[Pigatto, M. C., Lima, M. C. A., Galdino, S. L., Pitta, I. R., Vessecchi, R., Assis, M. D., Santos, J. S., Costa, T. C. T. D. & Lopes, P. N. (2011). Eur. J. Med. Chem. 1, 4245-4251.]); Das et al. (2011[Das, S., Kundu, S. & Suresh, K. G. (2011). DNA Cell Biol. 30, 525-535.]); Kumar et al. (2012[Kumar, R., Kaur, M. & Kumari, M. (2012). Acta Pol. Pharm. 69, 3-9.]). For the synthesis of acridines, see: Tomar et al. (2010[Tomar, V., Bhattacharjee, G., Uddin, K., Rajakumar, S., Srivastava, K. & Puri, S. K. (2010). Eur. J. Med. Chem. 45, 745-751.]). For related structures, see: Buckleton & Waters (1984[Buckleton, J. S. & Waters, T. N. (1984). Acta Cryst. C40, 1587-1589.]).

[Scheme 1]

Experimental

Crystal data
  • C19H15NO4

  • Mr = 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)

  • Rint = 0.050

Refinement
  • R[F2 > 2σ(F2)] = 0.052

  • wR(F2) = 0.148

  • S = 1.05

  • 3626 reflections

  • 218 parameters

  • H-atom parameters constrained

  • Δρmax = 0.26 e Å−3

  • Δρmin = −0.24 e Å−3

Data collection: COLLECT (Nonius, 1997[Nonius (1997). COLLECT. Nonius BV, Delft, The Netherlands.]); cell refinement: SCALEPACK (Otwinowski & Minor, 1997[Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M. Sweet, pp. 307-326. New York: Academic Press.]); data reduction: DENZO (Otwinowski & Minor, 1997[Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M. Sweet, pp. 307-326. New York: Academic Press.]) and SCALEPACK; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012[Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849-854.]); software used to prepare material for publication: WinGX (Farrugia, 2012[Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849-854.]).

Supporting information


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.

Refinement top

All H-atoms were included in the refinement at calculated positions [C—H = 0.93 Å (aromatic) and 0.96 Å (methyl), with Uiso(H) = 1.2Ueq(aromatic C) or 1.5Ueq(methyl C)],also using a riding-model approximation. The maximum and minimum residual electron density peaks were located 0.16 and 0.77 Å, from the C9 and H14 atoms respectively.

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
[Figure 1] Fig. 1. The molecular structure of the title compound. with the ellipsoids drawn at the 50% probability level.
[Figure 2] Fig. 2. A partial view of the packing showing the π - π interactions.
Dimethyl 2-[(acridin-9-yl)methylidene]malonate top
Crystal data top
C19H15NO4Z = 2
Mr = 321.32F(000) = 336
Triclinic, P1Dx = 1.354 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 8.3022 (2) ÅCell parameters from 6418 reflections
b = 9.0208 (3) Åθ = 2.5–27.5°
c = 12.0334 (4) ŵ = 0.10 mm1
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 FR590Rint = 0.050
Horizonally mounted graphite crystal monochromatorθmax = 27.5°, θmin = 2.6°
Detector resolution: 9 pixels mm-1h = 1010
CCD rotation images,thick slices scansk = 1110
10674 measured reflectionsl = 1515
3626 independent reflections
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.052H-atom parameters constrained
wR(F2) = 0.148 w = 1/[σ2(Fo2) + (0.0817P)2 + 0.1056P]
where P = (Fo2 + 2Fc2)/3
S = 1.05(Δ/σ)max < 0.001
3626 reflectionsΔρmax = 0.26 e Å3
218 parametersΔρmin = 0.24 e Å3
0 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.168 (19)
Crystal data top
C19H15NO4γ = 117.422 (2)°
Mr = 321.32V = 787.98 (4) Å3
Triclinic, P1Z = 2
a = 8.3022 (2) ÅMo Kα radiation
b = 9.0208 (3) ŵ = 0.10 mm1
c = 12.0334 (4) ÅT = 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 reflectionsRint = 0.050
3626 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0520 restraints
wR(F2) = 0.148H-atom parameters constrained
S = 1.05Δρmax = 0.26 e Å3
3626 reflectionsΔρmin = 0.24 e Å3
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
xyzUiso*/Ueq
C20.18856 (17)0.04107 (16)0.05238 (10)0.0416 (3)
C80.27051 (18)0.29435 (17)0.10755 (11)0.0439 (3)
C10.12960 (17)0.00751 (16)0.15015 (10)0.0409 (3)
C160.25132 (19)0.00447 (18)0.38809 (12)0.0475 (3)
N10.32779 (16)0.24918 (14)0.01345 (9)0.0477 (3)
C140.02296 (18)0.12607 (17)0.21649 (11)0.0455 (3)
H140.09060.21110.18150.055*
O40.19557 (15)0.38893 (13)0.31911 (9)0.0630 (3)
C130.16978 (17)0.17719 (16)0.17992 (10)0.0412 (3)
C120.11370 (19)0.24024 (18)0.27615 (11)0.0484 (3)
H120.04640.16650.32360.058*
C110.1572 (2)0.4058 (2)0.29913 (12)0.0544 (4)
H110.12020.44430.36250.065*
C60.3548 (2)0.0411 (2)0.11100 (12)0.0549 (4)
H60.41940.12280.15460.066*
C90.3139 (2)0.46746 (18)0.13512 (13)0.0538 (4)
H90.38080.54430.08920.065*
O20.22592 (15)0.05138 (14)0.48843 (9)0.0593 (3)
O10.39648 (15)0.04600 (18)0.35414 (10)0.0745 (4)
O30.02856 (18)0.31220 (15)0.46082 (10)0.0716 (4)
C70.28933 (18)0.08723 (17)0.01311 (11)0.0445 (3)
C180.0314 (2)0.28576 (17)0.37642 (11)0.0488 (3)
C50.3247 (2)0.1193 (2)0.14145 (14)0.0618 (4)
H50.36960.14660.20510.074*
C30.1592 (2)0.20857 (18)0.01646 (12)0.0508 (3)
H30.09390.29350.05770.061*
C150.07425 (18)0.13590 (17)0.32134 (11)0.0452 (3)
C100.2585 (2)0.52130 (19)0.22792 (13)0.0578 (4)
H100.28710.63450.24490.069*
C40.2252 (2)0.2462 (2)0.07701 (14)0.0588 (4)
H40.20480.35630.09890.071*
C190.3052 (3)0.5404 (2)0.36533 (18)0.0765 (5)
H19A0.42020.60620.31790.115*
H19B0.32670.50950.43980.115*
H19C0.24150.60590.36900.115*
C170.3884 (3)0.1685 (3)0.56385 (16)0.0767 (5)
H17A0.35450.20060.63380.115*
H17B0.45570.26720.53020.115*
H17C0.46340.11560.57790.115*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C20.0385 (6)0.0446 (7)0.0367 (6)0.0149 (5)0.0014 (5)0.0111 (5)
C80.0422 (7)0.0438 (7)0.0379 (6)0.0126 (5)0.0030 (5)0.0124 (5)
C10.0387 (6)0.0446 (7)0.0350 (6)0.0143 (5)0.0027 (5)0.0143 (5)
C160.0493 (7)0.0517 (7)0.0466 (7)0.0249 (6)0.0081 (6)0.0219 (6)
N10.0484 (6)0.0451 (6)0.0397 (6)0.0120 (5)0.0080 (5)0.0136 (5)
C140.0465 (7)0.0429 (7)0.0428 (7)0.0157 (5)0.0075 (5)0.0136 (5)
O40.0636 (7)0.0495 (6)0.0614 (7)0.0110 (5)0.0127 (5)0.0236 (5)
C130.0395 (6)0.0448 (7)0.0348 (6)0.0153 (5)0.0023 (5)0.0117 (5)
C120.0506 (7)0.0535 (8)0.0411 (7)0.0230 (6)0.0081 (6)0.0134 (6)
C110.0619 (9)0.0575 (9)0.0440 (7)0.0291 (7)0.0051 (6)0.0058 (6)
C60.0510 (8)0.0602 (9)0.0419 (7)0.0153 (6)0.0115 (6)0.0105 (6)
C90.0574 (8)0.0425 (7)0.0497 (8)0.0127 (6)0.0043 (6)0.0139 (6)
O20.0593 (6)0.0619 (7)0.0536 (6)0.0279 (5)0.0027 (5)0.0030 (5)
O10.0492 (6)0.1023 (10)0.0627 (7)0.0255 (6)0.0115 (5)0.0222 (6)
O30.0931 (9)0.0618 (7)0.0579 (7)0.0302 (6)0.0085 (6)0.0315 (5)
C70.0399 (6)0.0491 (7)0.0366 (6)0.0137 (5)0.0038 (5)0.0109 (5)
C180.0622 (8)0.0441 (7)0.0440 (7)0.0252 (6)0.0168 (6)0.0155 (6)
C50.0587 (9)0.0693 (10)0.0482 (8)0.0241 (8)0.0113 (7)0.0008 (7)
C30.0500 (8)0.0477 (7)0.0493 (8)0.0180 (6)0.0048 (6)0.0107 (6)
C150.0502 (7)0.0455 (7)0.0425 (7)0.0220 (6)0.0119 (6)0.0165 (5)
C100.0661 (9)0.0442 (8)0.0545 (8)0.0204 (7)0.0005 (7)0.0048 (6)
C40.0603 (9)0.0542 (8)0.0561 (9)0.0246 (7)0.0041 (7)0.0001 (7)
C190.0826 (12)0.0459 (9)0.0854 (13)0.0120 (8)0.0267 (10)0.0254 (8)
C170.0776 (12)0.0741 (11)0.0667 (11)0.0323 (9)0.0107 (9)0.0063 (9)
Geometric parameters (Å, º) top
C2—C11.4037 (18)C6—C51.351 (2)
C2—C31.425 (2)C6—C71.427 (2)
C2—C71.4345 (17)C6—H60.9300
C8—N11.3482 (18)C9—C101.358 (2)
C8—C91.424 (2)C9—H90.9300
C8—C131.4356 (17)O2—C171.441 (2)
C1—C131.4049 (19)O3—C181.1981 (17)
C1—C141.4823 (16)C18—C151.4899 (18)
C16—O11.1940 (17)C5—C41.415 (2)
C16—O21.3226 (18)C5—H50.9300
C16—C151.497 (2)C3—C41.358 (2)
N1—C71.3381 (18)C3—H30.9300
C14—C151.3315 (18)C10—H100.9300
C14—H140.9300C4—H40.9300
O4—C181.3293 (19)C19—H19A0.9600
O4—C191.4474 (18)C19—H19B0.9600
C13—C121.4301 (19)C19—H19C0.9600
C12—C111.355 (2)C17—H17A0.9600
C12—H120.9300C17—H17B0.9600
C11—C101.419 (2)C17—H17C0.9600
C11—H110.9300
C1—C2—C3123.94 (12)N1—C7—C6117.91 (12)
C1—C2—C7117.80 (12)N1—C7—C2123.52 (12)
C3—C2—C7118.24 (12)C6—C7—C2118.55 (13)
N1—C8—C9117.44 (12)O3—C18—O4124.20 (13)
N1—C8—C13123.21 (12)O3—C18—C15123.33 (14)
C9—C8—C13119.35 (12)O4—C18—C15112.42 (12)
C2—C1—C13119.54 (11)C6—C5—C4120.40 (14)
C2—C1—C14117.57 (12)C6—C5—H5119.8
C13—C1—C14122.87 (12)C4—C5—H5119.8
O1—C16—O2124.32 (15)C4—C3—C2121.06 (14)
O1—C16—C15124.28 (14)C4—C3—H3119.5
O2—C16—C15111.38 (11)C2—C3—H3119.5
C7—N1—C8118.15 (11)C14—C15—C18122.41 (13)
C15—C14—C1126.22 (12)C14—C15—C16122.17 (11)
C15—C14—H14116.9C18—C15—C16115.18 (11)
C1—C14—H14116.9C9—C10—C11120.38 (14)
C18—O4—C19115.93 (13)C9—C10—H10119.8
C1—C13—C12124.38 (12)C11—C10—H10119.8
C1—C13—C8117.77 (12)C3—C4—C5120.61 (15)
C12—C13—C8117.83 (12)C3—C4—H4119.7
C11—C12—C13120.94 (13)C5—C4—H4119.7
C11—C12—H12119.5O4—C19—H19A109.5
C13—C12—H12119.5O4—C19—H19B109.5
C12—C11—C10120.94 (14)H19A—C19—H19B109.5
C12—C11—H11119.5O4—C19—H19C109.5
C10—C11—H11119.5H19A—C19—H19C109.5
C5—C6—C7121.14 (14)H19B—C19—H19C109.5
C5—C6—H6119.4O2—C17—H17A109.5
C7—C6—H6119.4O2—C17—H17B109.5
C10—C9—C8120.55 (13)H17A—C17—H17B109.5
C10—C9—H9119.7O2—C17—H17C109.5
C8—C9—H9119.7H17A—C17—H17C109.5
C16—O2—C17116.36 (13)H17B—C17—H17C109.5

Experimental details

Crystal data
Chemical formulaC19H15NO4
Mr321.32
Crystal system, space groupTriclinic, 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)
V3)787.98 (4)
Z2
Radiation typeMo Kα
µ (mm1)0.10
Crystal size (mm)0.32 × 0.28 × 0.22
Data collection
DiffractometerNonius KappaCCD
diffractometer
Absorption correction
No. of measured, independent and
observed [I > 2σ(I)] reflections
10674, 3626, 2805
Rint0.050
(sin θ/λ)max1)0.650
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.052, 0.148, 1.05
No. of reflections3626
No. of parameters218
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)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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First citationTomar, V., Bhattacharjee, G., Uddin, K., Rajakumar, S., Srivastava, K. & Puri, S. K. (2010). Eur. J. Med. Chem. 45, 745–751.  Web of Science CrossRef CAS PubMed

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Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
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