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Acta Crystallogr Sect E Struct Rep Online. 2009 June 1; 65(Pt 6): o1298–o1299.
Published online 2009 May 14. doi:  10.1107/S1600536809017413
PMCID: PMC2969602

5-[(3,4-Dimethoxy­benzyl)­aminomethyl­ene]-2,2-dimethyl-1,3-dioxane-4,6-dione

Abstract

The title compound, C15H17NO6, is approximately planar, with dihedral angles of 3.11 (4) and 2.12 (4)° between the connecting amino­methyl­ene unit and the planar part of the dioxane ring, and between the dimethoxy­benzyl ring and the amino­methyl­ene group, respectively. The dioxane ring exhibits a half-boat conformation, in which the C atom between the dioxane O atoms is 0.5471 (8) Å out of the plane. The mol­ecule has an intra­molecular N—H(...)O hydrogen bond which may stabilize the planar conformation. In the crystal, weak inter­molecular C—H(...)O hydrogen-bonding contacts, result in the formation of sheets parallel to the ab plane.

Related literature

For the synthesis of related compounds, see: Cassis et al. (1985 [triangle]). For the synthesis of related anti­tumor precursors, see Ruchelman et al. (2003 [triangle]). For the structure of 5-(amino­methyl­ene)-2,2-dimethyl-1,3-dioxane-4,6-dione, see: da Silva et al. (2006 [triangle]). For Meldrum’s acid, see: Meldrum (1908 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-o1298-scheme1.jpg

Experimental

Crystal data

  • C15H17NO6
  • M r = 307.30
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o1298-efi1.jpg
  • a = 6.270 (4) Å
  • b = 12.486 (4) Å
  • c = 19.529 (5) Å
  • β = 106.31 (3)°
  • V = 1467.3 (11) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.11 mm−1
  • T = 292 K
  • 0.44 × 0.38 × 0.18 mm

Data collection

  • Enraf–Nonius CAD-4 diffractometer
  • Absorption correction: none
  • 2852 measured reflections
  • 2657 independent reflections
  • 1675 reflections with I > 2σ(I)
  • R int = 0.008
  • 3 standard reflections every 150 reflections intensity decay: 1.8%

Refinement

  • R[F 2 > 2σ(F 2)] = 0.056
  • wR(F 2) = 0.160
  • S = 1.03
  • 2657 reflections
  • 207 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.21 e Å−3
  • Δρmin = −0.26 e Å−3

Data collection: DIFRAC (Gabe & White, 1993 [triangle]); cell refinement: DIFRAC; data reduction: NRCVAX (Gabe et al., 1989 [triangle]); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: ORTEP-3 (Farrugia, 1997 [triangle]); software used to prepare material for publication: SHELXL97 and PLATON (Spek, 2009 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536809017413/si2171sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809017413/si2171Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

This research was supported financially by the State Key Laboratory of Drug Research (Shanghai Institute of Materia Medica, Chinese Academy of Sciences).

supplementary crystallographic information

Comment

The 4(1H)quinolone structure plays an extremely important role in the field of pharmaceutical chemistry. These compounds have been used as precursors for anticancer agents, anti-malarial agents and reversible (H+/K+) ATPase inhibitors (Ruchelman et al.,2003). 5-arylaminomethylene-2,2-dimethyl-1,3-dioxane-4,6-diones are the key intermediates which can be used to synthesize the 4(1H)quinolone derivatives by thermolysis (Cassis et al., 1985).

In the structure of the title molecule (Fig. 1), it is approximately planar with the dihedral angles of 3.11 (4)° and 2.12 (4)° between the connecting aminomethylene unit and the planar part of the dioxane ring, and between the dimethoxybenzyl ring and the aminomethylene group, respectively. Besides, the dioxane ring of the title compound exhibits a half-boat conformation, in which the C atom between the dioxane O atoms is -0.5471 (8) Å out-of-plane.

The intramolecular N—H···O hydrogen bond (Table 1) is stabilizing the planar conformation in the molecule. Intermolecular weak C—H···O hydrogen bonding contacts (Table 1) result in the formation of sheets running parallel to the a-b plane in the crystal structure (Fig. 2).

Experimental

A solution of 2,2-dimethyl-1,3-dioxane-4,6-dione (Meldrum's acid) and methylorthoformate was heated to reflux for two hours and immediately the arylamine was added in an equimolar amount relative to Meldrum's acid. The mixture was heated under reflux for another 5–8 h; single recrystallization from methanol gave the corresponding arylaminomethylene derivative as analytically pure material.

Refinement

H atoms were positioned geometrically (C—H = 0.93–0.98 Å) and refined using a riding model, with Uiso(H) = 1.2–1.5Ueq(C).

Figures

Fig. 1.
The molecular structure of the title compound, with displacement ellipsoids drawn at the 30% probability level.
Fig. 2.
A packing diagram of the title compound showing the layer-like aggregation of the title molecules in the unit cell.

Crystal data

C15H17NO6F(000) = 648
Mr = 307.30Dx = 1.391 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
a = 6.270 (4) ÅCell parameters from 29 reflections
b = 12.486 (4) Åθ = 4.4–7.7°
c = 19.529 (5) ŵ = 0.11 mm1
β = 106.31 (3)°T = 292 K
V = 1467.3 (11) Å3Block, yellow
Z = 40.44 × 0.38 × 0.18 mm

Data collection

Enraf–Nonius CAD-4 diffractometerRint = 0.008
Radiation source: fine-focus sealed tubeθmax = 25.4°, θmin = 2.0°
graphiteh = −7→7
ω/2θ scansk = −15→0
2852 measured reflectionsl = −23→8
2657 independent reflections3 standard reflections every 150 reflections
1675 reflections with I > 2σ(I) intensity decay: 1.8%

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.056Hydrogen site location: mixed
wR(F2) = 0.160H atoms treated by a mixture of independent and constrained refinement
S = 1.03w = 1/[σ2(Fo2) + (0.0954P)2] where P = (Fo2 + 2Fc2)/3
2657 reflections(Δ/σ)max < 0.001
207 parametersΔρmax = 0.21 e Å3
0 restraintsΔρmin = −0.26 e Å3

Special details

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)

xyzUiso*/Ueq
O10.0589 (3)0.78796 (12)0.14968 (8)0.0456 (5)
O2−0.0296 (3)0.60397 (13)0.13307 (9)0.0489 (5)
O30.3798 (3)0.84242 (14)0.22145 (9)0.0522 (5)
O40.2084 (3)0.47579 (14)0.18214 (10)0.0623 (6)
O51.4467 (3)0.80170 (14)0.40934 (10)0.0544 (5)
O61.5852 (3)0.60587 (14)0.42558 (9)0.0503 (5)
N10.7059 (3)0.69339 (19)0.27469 (10)0.0403 (5)
H1N0.677 (4)0.761 (2)0.2721 (13)0.046 (8)*
C1−0.2969 (4)0.7333 (2)0.08019 (14)0.0523 (7)
H1A−0.37970.67670.05130.078*
H1B−0.32420.79940.05400.078*
H1C−0.34270.74040.12290.078*
C20.0406 (5)0.7062 (3)0.03595 (15)0.0674 (9)
H2A0.19660.69030.05170.101*
H2B0.01870.77490.01310.101*
H2C−0.03430.65230.00270.101*
C3−0.0529 (4)0.70753 (19)0.09947 (12)0.0411 (6)
C40.2670 (4)0.7662 (2)0.19222 (12)0.0389 (6)
C50.3347 (4)0.65633 (19)0.20110 (11)0.0374 (6)
C60.1782 (4)0.5710 (2)0.17241 (13)0.0422 (6)
C70.5461 (4)0.6272 (2)0.24184 (12)0.0398 (6)
H70.57780.55440.24640.048*
C80.9280 (4)0.66471 (19)0.31291 (11)0.0374 (6)
C91.0729 (4)0.74811 (19)0.34299 (11)0.0388 (6)
H91.02190.81840.33840.047*
C101.2914 (4)0.72663 (18)0.37956 (11)0.0392 (6)
C111.3659 (4)0.61937 (18)0.38805 (11)0.0370 (6)
C121.2204 (4)0.5382 (2)0.35779 (12)0.0442 (6)
H121.26960.46760.36260.053*
C131.0014 (4)0.5605 (2)0.32015 (12)0.0445 (6)
H130.90500.50510.30000.053*
C141.3812 (5)0.9112 (2)0.39922 (15)0.0588 (8)
H14A1.33070.92660.34910.088*
H14B1.50560.95620.42120.088*
H14C1.26310.92450.42050.088*
C151.6708 (4)0.4995 (2)0.43247 (14)0.0535 (7)
H15A1.59730.45770.46030.080*
H15B1.82750.50120.45570.080*
H15C1.64510.46810.38600.080*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0390 (10)0.0379 (10)0.0492 (10)0.0012 (8)−0.0054 (8)−0.0002 (7)
O20.0380 (10)0.0398 (10)0.0585 (11)−0.0059 (8)−0.0036 (8)0.0011 (8)
O30.0468 (11)0.0371 (10)0.0602 (11)−0.0067 (8)−0.0054 (9)−0.0021 (8)
O40.0517 (12)0.0318 (11)0.0890 (14)−0.0007 (8)−0.0040 (10)0.0002 (9)
O50.0456 (11)0.0377 (10)0.0634 (11)−0.0014 (8)−0.0120 (8)−0.0020 (8)
O60.0388 (10)0.0459 (11)0.0550 (10)0.0053 (8)−0.0052 (8)−0.0005 (8)
N10.0345 (12)0.0390 (13)0.0417 (11)0.0005 (9)0.0012 (9)0.0041 (9)
C10.0384 (15)0.0603 (18)0.0493 (15)−0.0006 (13)−0.0025 (12)0.0020 (13)
C20.0541 (18)0.097 (2)0.0504 (15)−0.0023 (17)0.0130 (13)−0.0022 (16)
C30.0356 (13)0.0432 (14)0.0392 (12)−0.0032 (11)0.0017 (10)0.0001 (11)
C40.0371 (13)0.0408 (14)0.0357 (12)−0.0019 (11)0.0050 (10)0.0021 (10)
C50.0334 (13)0.0383 (13)0.0366 (12)−0.0023 (10)0.0034 (10)0.0010 (10)
C60.0338 (14)0.0417 (15)0.0471 (14)−0.0016 (11)0.0045 (11)−0.0025 (11)
C70.0364 (14)0.0424 (14)0.0382 (12)−0.0001 (11)0.0063 (11)0.0013 (10)
C80.0329 (13)0.0404 (14)0.0346 (12)0.0006 (11)0.0024 (9)0.0052 (10)
C90.0410 (14)0.0334 (13)0.0377 (12)0.0042 (11)0.0038 (10)0.0017 (10)
C100.0413 (14)0.0378 (14)0.0329 (11)−0.0028 (11)0.0011 (10)−0.0024 (10)
C110.0335 (13)0.0419 (14)0.0320 (11)0.0059 (11)0.0031 (10)0.0034 (10)
C120.0432 (15)0.0351 (14)0.0492 (14)0.0050 (11)0.0045 (11)0.0021 (11)
C130.0425 (15)0.0371 (14)0.0468 (14)−0.0042 (11)0.0011 (11)0.0043 (11)
C140.0604 (18)0.0389 (15)0.0644 (17)−0.0048 (13)−0.0030 (14)−0.0025 (13)
C150.0455 (16)0.0508 (16)0.0572 (15)0.0149 (13)0.0030 (12)0.0028 (13)

Geometric parameters (Å, °)

O1—C41.363 (3)C2—H2C0.9600
O1—C31.441 (3)C4—C51.432 (3)
O2—C61.376 (3)C5—C71.389 (3)
O2—C31.439 (3)C5—C61.450 (3)
O3—C41.227 (3)C7—H70.9300
O4—C61.211 (3)C8—C131.374 (4)
O5—C101.359 (3)C8—C91.398 (3)
O5—C141.425 (3)C9—C101.382 (3)
O6—C111.375 (3)C9—H90.9300
O6—C151.424 (3)C10—C111.413 (3)
N1—C71.318 (3)C11—C121.380 (3)
N1—C81.428 (3)C12—C131.392 (4)
N1—H1N0.86 (3)C12—H120.9300
C1—C31.504 (4)C13—H130.9300
C1—H1A0.9600C14—H14A0.9600
C1—H1B0.9600C14—H14B0.9600
C1—H1C0.9600C14—H14C0.9600
C2—C31.513 (4)C15—H15A0.9600
C2—H2A0.9600C15—H15B0.9600
C2—H2B0.9600C15—H15C0.9600
C4—O1—C3118.37 (18)N1—C7—C5126.0 (2)
C6—O2—C3118.82 (19)N1—C7—H7117.0
C10—O5—C14117.26 (19)C5—C7—H7117.0
C11—O6—C15117.28 (19)C13—C8—C9120.2 (2)
C7—N1—C8126.4 (2)C13—C8—N1122.7 (2)
C7—N1—H1N117.7 (17)C9—C8—N1117.1 (2)
C8—N1—H1N115.9 (17)C10—C9—C8120.4 (2)
C3—C1—H1A109.5C10—C9—H9119.8
C3—C1—H1B109.5C8—C9—H9119.8
H1A—C1—H1B109.5O5—C10—C9125.1 (2)
C3—C1—H1C109.5O5—C10—C11115.5 (2)
H1A—C1—H1C109.5C9—C10—C11119.5 (2)
H1B—C1—H1C109.5O6—C11—C12125.4 (2)
C3—C2—H2A109.5O6—C11—C10115.3 (2)
C3—C2—H2B109.5C12—C11—C10119.3 (2)
H2A—C2—H2B109.5C11—C12—C13121.0 (2)
C3—C2—H2C109.5C11—C12—H12119.5
H2A—C2—H2C109.5C13—C12—H12119.5
H2B—C2—H2C109.5C8—C13—C12119.7 (2)
O2—C3—O1110.38 (17)C8—C13—H13120.1
O2—C3—C1105.8 (2)C12—C13—H13120.1
O1—C3—C1106.7 (2)O5—C14—H14A109.5
O2—C3—C2110.5 (2)O5—C14—H14B109.5
O1—C3—C2109.8 (2)H14A—C14—H14B109.5
C1—C3—C2113.5 (2)O5—C14—H14C109.5
O3—C4—O1117.1 (2)H14A—C14—H14C109.5
O3—C4—C5125.1 (2)H14B—C14—H14C109.5
O1—C4—C5117.8 (2)O6—C15—H15A109.5
C7—C5—C4121.5 (2)O6—C15—H15B109.5
C7—C5—C6117.6 (2)H15A—C15—H15B109.5
C4—C5—C6120.7 (2)O6—C15—H15C109.5
O4—C6—O2117.6 (2)H15A—C15—H15C109.5
O4—C6—C5127.0 (2)H15B—C15—H15C109.5
O2—C6—C5115.4 (2)
C6—O2—C3—O1−48.6 (3)C6—C5—C7—N1−176.7 (2)
C6—O2—C3—C1−163.7 (2)C7—N1—C8—C13−0.4 (4)
C6—O2—C3—C273.1 (3)C7—N1—C8—C9179.0 (2)
C4—O1—C3—O245.3 (3)C13—C8—C9—C100.7 (4)
C4—O1—C3—C1159.8 (2)N1—C8—C9—C10−178.8 (2)
C4—O1—C3—C2−76.8 (3)C14—O5—C10—C9−2.9 (4)
C3—O1—C4—O3162.7 (2)C14—O5—C10—C11177.2 (2)
C3—O1—C4—C5−19.1 (3)C8—C9—C10—O5178.4 (2)
O3—C4—C5—C7−3.9 (4)C8—C9—C10—C11−1.7 (3)
O1—C4—C5—C7178.1 (2)C15—O6—C11—C121.5 (3)
O3—C4—C5—C6171.1 (2)C15—O6—C11—C10−177.0 (2)
O1—C4—C5—C6−6.9 (3)O5—C10—C11—O60.3 (3)
C3—O2—C6—O4−158.5 (2)C9—C10—C11—O6−179.6 (2)
C3—O2—C6—C524.7 (3)O5—C10—C11—C12−178.3 (2)
C7—C5—C6—O42.9 (4)C9—C10—C11—C121.9 (4)
C4—C5—C6—O4−172.3 (3)O6—C11—C12—C13−179.4 (2)
C7—C5—C6—O2179.3 (2)C10—C11—C12—C13−1.0 (4)
C4—C5—C6—O24.2 (3)C9—C8—C13—C120.2 (4)
C8—N1—C7—C5−175.7 (2)N1—C8—C13—C12179.6 (2)
C4—C5—C7—N1−1.6 (4)C11—C12—C13—C80.0 (4)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1N···O30.86 (3)2.11 (3)2.744 (3)130 (2)
C9—H9···O4i0.932.403.309 (4)164
C15—H15C···O3ii0.962.593.528 (4)166

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: SI2171).

References

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  • Farrugia, L. J. (1997). J. Appl. Cryst.30, 565.
  • Gabe, E. J., Le Page, Y., Charland, J.-P., Lee, F. L. & White, P. S. (1989). J. Appl. Cryst.22, 384–387.
  • Gabe, E. J. & White, P. S. (1993). DIFRAC American Crystallographic Association, Pittsburgh Meeting. Abstract PA104.
  • Meldrum, A. N. (1908). J. Chem. Soc. Trans.93, 598–601.
  • Ruchelman, A. L., Singh, S. K., Ray, A., Wu, X. H., Yang, J. M., Li, T. K., Liu, A., Liu, L. F. & LaVoie, E. J. (2003). Bioorg. Med. Chem.11, 2061–2073. [PubMed]
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Silva, L. E. da, Joussef, A. C., Silva, L. L., Foro, S. & Schmidt, B. (2006). Acta Cryst. E62, o3866–o3867.
  • Spek, A. L. (2009). Acta Cryst. D65, 148–155. [PMC free article] [PubMed]

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