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Acta Cryst. (2007). E63, o4015    [ doi:10.1107/S1600536807043383 ]

Ethyl 4-amino-5-cyano-6-[(2-hydroxyethyl)amino]-2-methylnicotinate

Q.-Y. Ren, H.-W. He, C.-F. Jin and Y.-C. Gu

Abstract top

In the title compound, C12H16N4O3, all bond lengths and angles are within normal ranges. An O-H...N and an N-H...O intramolecular hydrogen bond contribute to the approximately planar molecular conformation. In the crystal structure, intermolecular N-H...O and N-H...N hydrogen bonds link the molecules into ribbons parallel to the [1\overline{1}0] direction.

Comment top

Pyridine derivatives are important compounds because of their presence in numerous natural products. For example, nicotine is found in a wide variety of plants, playing an important role in metabolism and possessing a wide spectrum of biological activities (Yildiz, 2004). We report here the crystal structure of the title compound, (I).

In (I), all bond lengths and angles are within normal ranges (Allen et al., 1987). Two intramolecular hydrogen bonds - O—H···N and N—H···O (Table 1), respectively, contribute to the approximately planar molecular conformation. In the crystal, intermolecular N—H···O and N—H···N hydrogen bonds (Table 1) link the molecules into ribbons parallel to direction [1–10] (Fig. 2).

Related literature top

For biological functions of nicotine, see: Yildiz (2004). For normal ranges of molecular bond lengths and angles in organic compounds, see: Allen et al. (1987).

Experimental top

2-[Amino-(2-hydroxy-ethylamino)-methylene]-malononitrile (1.52 g, 10 mmol) and ethyl acetoacetate (1.6 g, 12 mmol) were added to a solution of Zinc nitrate (3.56 g, 20 mmol) in ethanol (15 ml) at room temperature while stirring. The mixture was then refluxed for 12 h. The precipitate was filtered and washed with water, recrystallized from ethanol to give the title compound (yield 39%). Crystals of (I) suitable for X-ray structure analysis were grown from ethanol.

Refinement top

C-bound H atoms were placed in calculated positions, with C—H distances in the range 0.93–0.97 Å, and included in the final cycles of refinement using a riding-model approximation, with Uiso(H) = 1.2–1.5Ueq(C). The rest H atoms were located on a difference map, and refined with bond restraints O—H = 0.85 (2) Å, N—H = 0.85 (2) Å (for H4A) or 0.88 (2) Å (for H2A and H2B), with Uiso(H)=1.2Ueq(N) or 1.5Ueq(O).

Computing details top

Data collection: SMART (Bruker, 2000); cell refinement: SAINT (Bruker, 2000); data reduction: SAINT (Bruker, 2000); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL (Bruker, 2000); software used to prepare material for publication: SHELXTL (Bruker, 2000).

Figures top
[Figure 1] Fig. 1. The molecular structure of (I) showing 50% probability displacement ellipsoids and the atom-numbering scheme.
[Figure 2] Fig. 2. A portion of the crystal packing showing hydrogen bonds as dashed lines.
Ethyl 4-amino-5-cyano-6-[(2-hydroxyethyl)amino]-2-methylnicotinate top
Crystal data top
C12H16N4O3Z = 2
Mr = 264.29F000 = 280
Triclinic, P1Dx = 1.352 Mg m−3
Hall symbol: -p 1Mo Kα radiation
λ = 0.71073 Å
a = 7.8350 (7) ÅCell parameters from 1450 reflections
b = 9.1368 (9) Åθ = 3.2–20.8º
c = 10.3272 (10) ŵ = 0.10 mm−1
α = 79.720 (2)ºT = 302 (2) K
β = 77.381 (2)ºBlock, colourless
γ = 64.657 (2)º0.35 × 0.20 × 0.10 mm
V = 648.97 (11) Å3
Data collection top
Bruker SMART CCD area detector
diffractometer		2767 independent reflections
Radiation source: fine-focus sealed tube1991 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.033
T = 302(2) Kθmax = 27.0º
phi and ω scansθmin = 2.0º
Absorption correction: multi-scan
(SADABS; Bruker, 2000)		h = −10→10
Tmin = 0.966, Tmax = 0.990k = −11→11
4521 measured reflectionsl = −11→13
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)] = 0.058H atoms treated by a mixture of
independent and constrained refinement
wR(F2) = 0.172  w = 1/[σ2(Fo2) + (0.0955P)2]
where P = (Fo2 + 2Fc2)/3
S = 1.06(Δ/σ)max < 0.001
2767 reflectionsΔρmax = 0.27 e Å−3
186 parametersΔρmin = −0.29 e Å−3
Primary atom site location: structure-invariant direct methodsExtinction correction: none
Crystal data top
C12H16N4O3γ = 64.657 (2)º
Mr = 264.29V = 648.97 (11) Å3
Triclinic, P1Z = 2
a = 7.8350 (7) ÅMo Kα
b = 9.1368 (9) ŵ = 0.10 mm−1
c = 10.3272 (10) ÅT = 302 (2) K
α = 79.720 (2)º0.35 × 0.20 × 0.10 mm
β = 77.381 (2)º
Data collection top
Bruker SMART CCD area detector
diffractometer		2767 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2000)		1991 reflections with I > 2σ(I)
Tmin = 0.966, Tmax = 0.990Rint = 0.033
4521 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.058186 parameters
wR(F2) = 0.172H atoms treated by a mixture of
independent and constrained refinement
S = 1.06Δρmax = 0.27 e Å−3
2767 reflectionsΔρmin = −0.29 e Å−3
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 > 2sigma(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
C10.4786 (3)0.2753 (2)0.45970 (17)0.0404 (4)
C20.6483 (2)0.1345 (2)0.43570 (17)0.0372 (4)
C30.7156 (2)0.0230 (2)0.54871 (17)0.0359 (4)
C40.6070 (2)0.0620 (2)0.67547 (17)0.0377 (4)
C50.4355 (2)0.2018 (2)0.68772 (17)0.0362 (4)
C60.3927 (3)0.4091 (3)0.3547 (2)0.0642 (7)
H6A0.35360.36710.29300.096*
H6B0.48610.44980.30800.096*
H6C0.28370.49560.39630.096*
C70.6634 (3)−0.0413 (2)0.79306 (18)0.0416 (5)
C80.7589 (3)0.0936 (2)0.30234 (18)0.0419 (5)
C90.7834 (3)0.1527 (2)0.06883 (18)0.0508 (5)
H9A0.79460.04720.05320.061*
H9B0.91110.14860.06060.061*
C100.6766 (3)0.2811 (3)−0.0303 (2)0.0607 (6)
H10A0.54830.2884−0.01810.091*
H10B0.73950.2536−0.11880.091*
H10C0.67340.3839−0.01760.091*
C110.1222 (3)0.3504 (2)0.8233 (2)0.0510 (5)
H11A0.05910.32190.90960.061*
H11B0.06340.33610.75580.061*
C120.0869 (4)0.5254 (3)0.8139 (2)0.0636 (6)
H12A−0.04310.58530.85610.076*
H12B0.17250.53580.86340.076*
N10.3761 (2)0.30703 (18)0.58156 (14)0.0422 (4)
N20.8725 (2)−0.11440 (19)0.53691 (17)0.0473 (4)
H2B0.928 (3)−0.122 (2)0.4515 (16)0.057*
H2A0.900 (3)−0.174 (2)0.6103 (17)0.057*
N30.7004 (3)−0.1181 (2)0.89125 (17)0.0560 (5)
N40.3234 (2)0.23730 (19)0.80702 (16)0.0461 (4)
H4A0.372 (3)0.164 (3)0.866 (2)0.055*
O10.9108 (2)−0.02184 (18)0.28168 (15)0.0628 (5)
O20.67814 (19)0.19305 (16)0.20107 (12)0.0496 (4)
O30.1129 (3)0.59692 (18)0.68257 (16)0.0728 (5)
H3A0.111 (5)0.532 (3)0.633 (3)0.109*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0431 (10)0.0397 (9)0.0313 (10)−0.0113 (8)−0.0064 (8)0.0004 (7)
C20.0384 (10)0.0388 (9)0.0303 (9)−0.0129 (8)−0.0036 (7)−0.0026 (7)
C30.0368 (9)0.0315 (8)0.0367 (10)−0.0112 (7)−0.0068 (7)−0.0023 (7)
C40.0415 (10)0.0340 (9)0.0330 (10)−0.0117 (8)−0.0089 (8)0.0019 (7)
C50.0379 (9)0.0355 (9)0.0310 (9)−0.0115 (7)−0.0052 (7)−0.0018 (7)
C60.0650 (14)0.0540 (12)0.0347 (11)0.0083 (11)−0.0050 (10)0.0024 (9)
C70.0395 (10)0.0347 (9)0.0383 (10)−0.0056 (8)−0.0027 (8)−0.0018 (8)
C80.0452 (11)0.0421 (10)0.0360 (10)−0.0155 (9)−0.0056 (8)−0.0050 (8)
C90.0582 (13)0.0539 (12)0.0309 (10)−0.0174 (10)0.0040 (9)−0.0084 (9)
C100.0656 (15)0.0747 (15)0.0353 (11)−0.0241 (12)−0.0067 (10)−0.0024 (10)
C110.0446 (11)0.0516 (11)0.0409 (11)−0.0098 (9)0.0026 (8)−0.0024 (9)
C120.0740 (15)0.0466 (11)0.0450 (13)−0.0019 (10)−0.0076 (11)−0.0041 (9)
N10.0429 (9)0.0391 (8)0.0318 (8)−0.0065 (7)−0.0040 (7)−0.0007 (6)
N20.0499 (10)0.0387 (8)0.0378 (9)−0.0058 (7)−0.0049 (8)0.0002 (7)
N30.0602 (11)0.0499 (10)0.0359 (9)−0.0054 (8)−0.0073 (8)0.0056 (8)
N40.0455 (10)0.0412 (9)0.0321 (9)−0.0025 (7)−0.0042 (7)0.0027 (7)
O10.0578 (9)0.0564 (9)0.0436 (8)0.0027 (7)0.0005 (7)−0.0081 (7)
O20.0509 (8)0.0531 (8)0.0286 (7)−0.0074 (6)−0.0020 (6)−0.0051 (6)
O30.0843 (12)0.0443 (8)0.0532 (10)−0.0013 (8)0.0004 (8)0.0061 (7)
Geometric parameters (Å, °) top
C1—N11.342 (2)C9—C101.493 (3)
C1—C21.410 (2)C9—H9A0.9700
C1—C61.504 (2)C9—H9B0.9700
C2—C31.436 (2)C10—H10A0.9600
C2—C81.474 (2)C10—H10B0.9600
C3—N21.330 (2)C10—H10C0.9600
C3—C41.409 (2)C11—N41.461 (2)
C4—C51.403 (2)C11—C121.490 (3)
C4—C71.424 (2)C11—H11A0.9700
C5—N11.344 (2)C11—H11B0.9700
C5—N41.349 (2)C12—O31.409 (3)
C6—H6A0.9600C12—H12A0.9700
C6—H6B0.9600C12—H12B0.9700
C6—H6C0.9600N2—H2B0.895 (15)
C7—N31.142 (2)N2—H2A0.859 (15)
C8—O11.212 (2)N4—H4A0.84 (2)
C8—O21.333 (2)O3—H3A0.861 (17)
C9—O21.452 (2)
N1—C1—C2123.25 (16)C10—C9—H9B110.1
N1—C1—C6111.78 (16)H9A—C9—H9B108.4
C2—C1—C6124.95 (16)C9—C10—H10A109.5
C1—C2—C3117.65 (15)C9—C10—H10B109.5
C1—C2—C8124.27 (16)H10A—C10—H10B109.5
C3—C2—C8118.08 (16)C9—C10—H10C109.5
N2—C3—C4119.91 (16)H10A—C10—H10C109.5
N2—C3—C2122.47 (16)H10B—C10—H10C109.5
C4—C3—C2117.61 (15)N4—C11—C12115.13 (18)
C5—C4—C3120.14 (15)N4—C11—H11A108.5
C5—C4—C7118.39 (15)C12—C11—H11A108.5
C3—C4—C7121.43 (15)N4—C11—H11B108.5
N1—C5—N4117.00 (15)C12—C11—H11B108.5
N1—C5—C4121.62 (15)H11A—C11—H11B107.5
N4—C5—C4121.38 (16)O3—C12—C11114.25 (18)
C1—C6—H6A109.5O3—C12—H12A108.7
C1—C6—H6B109.5C11—C12—H12A108.7
H6A—C6—H6B109.5O3—C12—H12B108.7
C1—C6—H6C109.5C11—C12—H12B108.7
H6A—C6—H6C109.5H12A—C12—H12B107.6
H6B—C6—H6C109.5C1—N1—C5119.62 (15)
N3—C7—C4176.31 (18)C3—N2—H2B110.1 (13)
O1—C8—O2120.50 (17)C3—N2—H2A115.4 (15)
O1—C8—C2124.55 (18)H2B—N2—H2A134 (2)
O2—C8—C2114.94 (16)C5—N4—C11123.93 (15)
O2—C9—C10107.96 (16)C5—N4—H4A109.6 (16)
O2—C9—H9A110.1C11—N4—H4A123.3 (16)
C10—C9—H9A110.1C8—O2—C9115.70 (15)
O2—C9—H9B110.1C12—O3—H3A105 (2)
N1—C1—C2—C3−1.8 (3)C1—C2—C8—O1175.22 (19)
C6—C1—C2—C3176.79 (18)C3—C2—C8—O1−5.7 (3)
N1—C1—C2—C8177.27 (16)C1—C2—C8—O2−5.8 (3)
C6—C1—C2—C8−4.2 (3)C3—C2—C8—O2173.23 (14)
C1—C2—C3—N2179.06 (17)N4—C11—C12—O378.5 (3)
C8—C2—C3—N2−0.1 (3)C2—C1—N1—C50.4 (3)
C1—C2—C3—C40.2 (2)C6—C1—N1—C5−178.30 (17)
C8—C2—C3—C4−178.96 (15)N4—C5—N1—C1−177.88 (16)
N2—C3—C4—C5−176.27 (17)C4—C5—N1—C12.6 (3)
C2—C3—C4—C52.7 (2)N1—C5—N4—C1118.9 (3)
N2—C3—C4—C71.3 (3)C4—C5—N4—C11−161.55 (17)
C2—C3—C4—C7−179.74 (15)C12—C11—N4—C5−83.0 (2)
C3—C4—C5—N1−4.2 (3)O1—C8—O2—C90.1 (3)
C7—C4—C5—N1178.16 (15)C2—C8—O2—C9−178.88 (15)
C3—C4—C5—N4176.30 (16)C10—C9—O2—C8−177.24 (15)
C7—C4—C5—N4−1.4 (3)
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
O3—H3A···N10.861 (17)2.25 (3)2.780 (2)120 (3)
N2—H2B···O10.895 (15)1.832 (17)2.613 (2)144.6 (19)
N4—H4A···N3i0.84 (2)2.45 (2)3.105 (2)136.1 (19)
N2—H2A···O3ii0.859 (15)2.175 (18)2.887 (2)140 (2)
C12—H12A···N3iii0.972.623.442 (3)142
Symmetry codes: (i) −x+1, −y, −z+2; (ii) x+1, y−1, z; (iii) x−1, y+1, z.
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
O3—H3A···N10.861 (17)2.25 (3)2.780 (2)120 (3)
N2—H2B···O10.895 (15)1.832 (17)2.613 (2)144.6 (19)
N4—H4A···N3i0.84 (2)2.45 (2)3.105 (2)136.1 (19)
N2—H2A···O3ii0.859 (15)2.175 (18)2.887 (2)140 (2)
Symmetry codes: (i) −x+1, −y, −z+2; (ii) x+1, y−1, z.
Acknowledgements top

We gratefully acknowledge financial support of this work by the National Basic Research Program of China (grant No. 2003CB114400), the National Natural Science Foundation of China (grant No. 20372023) and Syngenta.

references
References top

Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1–19.

Bruker (2000). SMART (Version 5.625), SAINT (Version 6.01) SHELXTL (Version 6.10) and SADABS (Version 2.03). Bruker AXS Inc., Madison, Wisconsin, USA.

Sheldrick, G. M. (1997). SHELXS97 and SHELXL97. University of Göttingen, Germany.

Yildiz, D. (2004). Toxicon, 43, 619–632.