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Acta Crystallogr Sect E Struct Rep Online. 2008 June 1; 64(Pt 6): o998.
Published online 2008 May 7. doi:  10.1107/S1600536808012762
PMCID: PMC2961616

Dimethyl 2-(amino­methyl­ene)malonate

Abstract

In the title compound, C6H9NO4, which is an example of a push–pull alkene, N—H(...)O inter­actions stabilize the crystal structure.

Related literature

For related literature, see: Bouzard (1990 [triangle]); Chemla & Zyss (1987 [triangle]); Cook (1969 [triangle]); Freeman (1981 [triangle]); Nalwa et al. (1997 [triangle]); Shmueli et al. (1973 [triangle]).

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Object name is e-64-0o998-scheme1.jpg

Experimental

Crystal data

  • C6H9NO4
  • M r = 159.14
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-64-0o998-efi1.jpg
  • a = 9.3410 (19) Å
  • b = 6.9000 (14) Å
  • c = 11.725 (2) Å
  • β = 97.58 (3)°
  • V = 749.1 (3) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.12 mm−1
  • T = 100 K
  • 0.43 × 0.27 × 0.06 mm

Data collection

  • Oxford Diffraction GEMINI R diffractometer
  • Absorption correction: analytical (CrysAlis RED; Oxford Diffraction, 2006 [triangle]) T min = 0.892, T max = 0.998
  • 14185 measured reflections
  • 1368 independent reflections
  • 841 reflections with I > 2σ(I)
  • R int = 0.089

Refinement

  • R[F 2 > 2σ(F 2)] = 0.091
  • wR(F 2) = 0.261
  • S = 0.99
  • 1368 reflections
  • 102 parameters
  • H-atom parameters constrained
  • Δρmax = 0.62 e Å−3
  • Δρmin = −0.38 e Å−3

Data collection: CrysAlis CCD (Oxford Diffraction, 2006 [triangle]); cell refinement: CrysAlis CCD; data reduction: CrysAlis RED (Oxford Diffraction, 2006 [triangle]); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXS97 (Sheldrick, 2008 [triangle]); molecular graphics: DIAMOND (Brandenburg, 1998 [triangle]); software used to prepare material for publication: enCIFer (Allen et al., 2004 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536808012762/bt2703sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536808012762/bt2703Isup2.hkl

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

Acknowledgments

The authors thank the Grant Agency of the Slovak Republic, grant Nos. APVT-20–007304 and VEGA 1/0817/08, for support.

supplementary crystallographic information

Comment

The title compound (I), aminomethylene-malonic acid dimethyl ester belongs to the family of so-called push-pull ethylenes. Push-pull ethylenes with the general formula R1X—CR2=CR3R4 are highly reactive organic compounds with electron donor groups at one end and strong electron acceptor groups at the other end of ethylenic C=C double bond. Very often R2 = H and for X = NH or NR1 and X = O as the electron donor groups R1 can be hydrogen, alkyl, cycloalkyl, aryl or hetero(aryl) groups. On the other side as the electron acceptors R3, R4 are groups such as –CN, –COR, –COOR, –SO2CH3, and –NO2. Mainly enamines (X = NH, NR1) are frequently used as reactants or intermediates in chemical syntheses of drugs, polymers and dyes (Bouzard et al., 1990, Cook et al., 1969). But also alkoxymethylenes (X = O) are often used in organic synthesis (Freeman et al., 1981).

Due to the opposite character of the substituents, the olefinic C=C double bond order is reduced and accompanied by increased bond orders of bonds between the olefinic carbon atoms and their electron donor and electron acceptor groups. This leads to the substantial decrease of the rotational barrier about the C=C double bond and to the increase of an analogues barrier about the adjacent bonds. These changes are connected with the separation of positive and negative charges and electron delocalization within the π-electron system. Such compounds belong to the most developed structures in the search for new compounds with non-linear optics responses (Nalwa et al., 1997, Chemla et al., 1987).

The study of a similar compound, dimethyl-(dimethylaminomethylene)-malonate, has been done (Shmueli et al., 1973). This study revealed that dimethyl-(dimethylaminomethylene)-malonate exists in solid phase as ZE conformer (Z denotes towards to C=C double bond orientation of the carbonyl oxygen in trans position; E denotes away from C=C double bond orientation of the carbonyl oxygen in cis position). The study of aminomethylene-malonic acid dimethyl ester revealed that this compound exists in solid phase as EZ conformer. The =C—N bond length of 1.301 (4)Å in the title compound is somewhat shorter than in the case of dimethyl-(dimethylaminomethylene)-malonate (1.337 Å). The C=C bond length of 1.385 (5)Å is slightly longer than in the case of dimethyl-(dimethylaminomethylene)-malonate (1.380 Å). The =C—C trans and cis bond lengths are 1.470 (4)/1.456 (5)Å, respectively in the title compound and 1.442/1.488 Å in dimethyl-(dimethylaminomethylene)-malonate.

Experimental

To dimethyl 3-methoxymethylenemalonate (1.74 g, 10 mmol) in methanol (10 ml), an aqueous solution of ammonia (12 mmol) was added dropwise (amount according to concentration and density) over a period of 30 min with stirring. The slightly warmed mixture was stirred overnight at room temperature. The reaction mixture was then briefly heated to reflux (ca. 20 min). After ensuring that no starting derivative remained (thin-layer chromatography; Silufol 254, Kavalier Czechoslovakia; eluent chloroform-methanol 10:1 v/v, detection UV light 254 nm), the reaction mixture was evaporated on a vacuum evaporator and chromatographed on silica gel (eluent dichloromethane-methanol 10:1 v/v). Obtained product was recrystallized from minimal amount of chloroform and n-hexane mixture in refrigerator.

The solid phase mid-IR vibrational spectrum was recorded with a Nicolet model NEXUS 470 FTIR spectrometer at room temperature. The measurement was performed after mixing the powdered sample with KBr into a pellet.

The mid-IR vibrational frequencies of aminomethylene-malonic acid dimethyl ester are (in cm-1): 3460 w; 3358 s; 3296 vw; 3271 vw; 3222 s; 3135 w, sh; 3025 m; 3017 vw, sh; 2993 vw; 2962 m; 2924 vw; 2907 vw; 1683 vs; 1658 vs; 1637 vs; 1576 vw, sh; 1534 m; 1507 s; 1499 s; 1474 vw, sh; 1461 w, sh; 1440 s; 1433 w, sh; 1373 s; 1331 s; 1293 w; 1286 s; 1221 s; 1193 m; 1176 w, sh; 1150 w, sh; 1141 s; 1070 s, b; 1033 w; 982 m; 942 w; 828 w; 822 m; 783 s; 772 w; 750 vw; 715 s, b; 669 w; 649 w, b; 617 m, sh, b; 589 s; 480 s; 440 m.

Refinement

All H atoms were positioned geometrically and allowed to ride on their corresponding parent atoms at distances of Cmethyl-H = 0.96Å, Caromatic-H = 0.93Å and N-H =0.86 Å, with Uiso(H) = 1.2Ueq(C,N) or Uiso(H) = 1.5Ueq(Cmethyl). Methyl groups were allowed to rotate but not to tip.

Figures

Fig. 1.
The atom-numbering scheme of aminomethylene-malonic acid dimethyl ester. Displacement ellipsoids are drawn at the 50% probability level.
Fig. 2.
Packing diagram of aminomethylene-malonic acid dimethyl ester. Hydrogen-bond interactions are indicated by dashed lines.

Crystal data

C6H9NO4F000 = 336
Mr = 159.14Dx = 1.411 Mg m3
Monoclinic, P21/cMo Kα radiation λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 2135 reflections
a = 9.3410 (19) Åθ = 3.4–29.6º
b = 6.9000 (14) ŵ = 0.12 mm1
c = 11.725 (2) ÅT = 100 K
β = 97.58 (3)ºBlock, colorless
V = 749.1 (3) Å30.43 × 0.27 × 0.06 mm
Z = 4

Data collection

Oxford Diffraction GEMINI R diffractometer1368 independent reflections
Radiation source: fine-focus sealed tube841 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.089
T = 100 Kθmax = 25.3º
Rotation method data acquisition using ω and [var phi] scansθmin = 4.2º
Absorption correction: analytical(CrysAlis RED; Oxford Diffraction, 2006)h = −10→11
Tmin = 0.892, Tmax = 0.998k = −8→8
14185 measured reflectionsl = −14→14

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.091H-atom parameters constrained
wR(F2) = 0.261  w = 1/[σ2(Fo2) + (0.1927P)2] where P = (Fo2 + 2Fc2)/3
S = 0.99(Δ/σ)max = 0.005
1368 reflectionsΔρmax = 0.62 e Å3
102 parametersΔρmin = −0.38 e Å3
Primary atom site location: structure-invariant direct methodsExtinction correction: none

Special details

Experimental. face-indexed (CrysAlis RED; Oxford Diffraction, 2006)
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
O40.9175 (3)0.2420 (3)0.85543 (19)0.0639 (9)
O20.8250 (3)−0.0207 (4)0.92664 (19)0.0657 (9)
C30.8357 (3)0.1536 (5)0.9256 (3)0.0475 (9)
N10.7287 (3)0.6345 (4)1.0263 (3)0.0648 (10)
H1B0.67170.61271.07680.078*
H1A0.74860.75171.00890.078*
C20.7644 (3)0.2942 (5)0.9935 (3)0.0460 (9)
C40.7847 (4)0.4902 (5)0.9761 (3)0.0511 (9)
H4A0.84550.52250.92220.061*
C50.9912 (5)0.1154 (5)0.7845 (3)0.0685 (12)
H5C1.04550.19160.73680.082*
H5B0.92160.03840.73680.082*
H5A1.05550.03190.83270.082*
O10.6120 (3)0.3524 (4)1.1347 (2)0.0773 (10)
O30.6559 (3)0.0457 (3)1.0934 (2)0.0594 (8)
C10.6714 (4)0.2365 (5)1.0780 (3)0.0515 (10)
C60.5661 (4)−0.0100 (6)1.1793 (3)0.0705 (12)
H6C0.5600−0.14871.18240.085*
H6B0.47110.04331.15960.085*
H6A0.60750.03851.25310.085*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O40.0949 (19)0.0289 (14)0.0785 (17)−0.0010 (12)0.0514 (14)−0.0019 (11)
O20.094 (2)0.0233 (15)0.0884 (18)−0.0009 (11)0.0449 (15)0.0022 (11)
C30.065 (2)0.027 (2)0.0544 (18)−0.0036 (14)0.0236 (16)0.0017 (13)
N10.090 (2)0.0235 (17)0.088 (2)−0.0033 (14)0.0392 (18)−0.0022 (14)
C20.057 (2)0.0255 (17)0.0580 (18)−0.0039 (14)0.0172 (16)0.0018 (14)
C40.067 (2)0.0299 (19)0.0601 (18)−0.0043 (15)0.0210 (17)0.0008 (15)
C50.099 (3)0.037 (2)0.079 (2)0.0036 (19)0.049 (2)0.0008 (18)
O10.111 (2)0.0312 (15)0.104 (2)−0.0012 (13)0.0689 (17)−0.0028 (13)
O30.0900 (18)0.0217 (14)0.0756 (15)−0.0054 (10)0.0445 (13)0.0026 (10)
C10.062 (2)0.030 (2)0.066 (2)−0.0002 (14)0.0221 (17)−0.0043 (14)
C60.101 (3)0.039 (2)0.081 (2)−0.012 (2)0.047 (2)0.0024 (19)

Geometric parameters (Å, °)

O4—C31.342 (4)C5—H5C0.9600
O4—C51.442 (4)C5—H5B0.9600
O2—C31.206 (4)C5—H5A0.9600
C3—C21.470 (4)O1—C11.219 (4)
N1—C41.301 (4)O3—C11.340 (4)
N1—H1B0.8600O3—C61.445 (4)
N1—H1A0.8600C6—H6C0.9600
C2—C41.385 (5)C6—H6B0.9600
C2—C11.456 (5)C6—H6A0.9600
C4—H4A0.9300
C3—O4—C5115.6 (3)H5C—C5—H5B109.5
O2—C3—O4120.9 (3)O4—C5—H5A109.5
O2—C3—C2127.5 (3)H5C—C5—H5A109.5
O4—C3—C2111.6 (3)H5B—C5—H5A109.5
C4—N1—H1B120.0C1—O3—C6116.0 (3)
C4—N1—H1A120.0O1—C1—O3120.4 (3)
H1B—N1—H1A120.0O1—C1—C2123.1 (3)
C4—C2—C1118.3 (3)O3—C1—C2116.5 (3)
C4—C2—C3119.0 (3)O3—C6—H6C109.5
C1—C2—C3122.8 (3)O3—C6—H6B109.5
N1—C4—C2127.6 (3)H6C—C6—H6B109.5
N1—C4—H4A116.2O3—C6—H6A109.5
C2—C4—H4A116.2H6C—C6—H6A109.5
O4—C5—H5C109.5H6B—C6—H6A109.5
O4—C5—H5B109.5
C5—O4—C3—O2−0.8 (5)C3—C2—C4—N1178.6 (3)
C5—O4—C3—C2−179.6 (3)C6—O3—C1—O10.1 (5)
O2—C3—C2—C4−176.8 (3)C6—O3—C1—C2178.6 (3)
O4—C3—C2—C41.9 (4)C4—C2—C1—O1−0.8 (5)
O2—C3—C2—C12.5 (5)C3—C2—C1—O1180.0 (3)
O4—C3—C2—C1−178.8 (3)C4—C2—C1—O3−179.2 (3)
C1—C2—C4—N1−0.7 (6)C3—C2—C1—O31.5 (5)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1B···O10.862.032.638 (2)128
N1—H1A···O2i0.862.022.848 (2)161

Symmetry codes: (i) x, y+1, z.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: BT2703).

References

  • Allen, F. H., Johnson, O., Shields, G. P., Smith, B. R. & Towler, M. (2004). J. Appl. Cryst.37, 335–338.
  • Bouzard, D. (1990). Recent Progress in the Chemical Synthesis of Antibiotics, p. 249. München: Springer-Verlag.
  • Brandenburg, K. (1998). DIAMOND Crystal Impact GbR, Bonn, Germany.
  • Chemla, D. & Zyss, J. (1987). Optical Properties of Organic Molecules and Crystals, Vol. 1, pp. 23–187. New York: Academic Press.
  • Cook, A. G. (1969). Enamines: Syntheses, Structure and Reactions. New York: Marcel Dekker.
  • Freeman, F. (1981). LONZA Reaction of Malononitrile Derivatives, p. 925. Stuttgart: Georg Thieme Verlag.
  • Nalwa, H. S., Watanabe, T. & Miyata, S. (1997). Nonlinear Optics of Organic Molecules and Polymers, pp. 87–329. Boca Ranton: CRC Press.
  • Oxford Diffraction (2006). CrysAlis CCD and CrysAlis RED Oxford Diffraction Ltd, Abingdon, Oxfordshire, England.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Shmueli, U., Shanan-Atidi, H., Horwitz, H. & Shvo, Y. (1973). J. Chem. Soc. Perkin Trans. 2, pp. 657–662.

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