Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807043383/cv2296sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536807043383/cv2296Isup2.hkl |
CCDC reference: 654090
Key indicators
- Single-crystal X-ray study
- T = 302 K
- Mean (C-C) = 0.003 Å
- R factor = 0.058
- wR factor = 0.172
- Data-to-parameter ratio = 14.9
checkCIF/PLATON results
No syntax errors found
Alert level C PLAT066_ALERT_1_C Predicted and Reported Transmissions Identical . ? PLAT154_ALERT_1_C The su's on the Cell Angles are Equal (x 10000) 200 Deg. PLAT230_ALERT_2_C Hirshfeld Test Diff for C4 - C7 .. 5.29 su PLAT250_ALERT_2_C Large U3/U1 Ratio for Average U(i,j) Tensor .... 2.04 PLAT371_ALERT_2_C Long C(sp2)-C(sp1) Bond C4 - C7 ... 1.42 Ang.
0 ALERT level A = In general: serious problem 0 ALERT level B = Potentially serious problem 5 ALERT level C = Check and explain 0 ALERT level G = General alerts; check 2 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 3 ALERT type 2 Indicator that the structure model may be wrong or deficient 0 ALERT type 3 Indicator that the structure quality may be low 0 ALERT type 4 Improvement, methodology, query or suggestion 0 ALERT type 5 Informative message, check
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).
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.
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).
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).
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).
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).
Fig. 1. The molecular structure of (I) showing 50% probability displacement ellipsoids and the atom-numbering scheme. | |
Fig. 2. A portion of the crystal packing showing hydrogen bonds as dashed lines. |
C12H16N4O3 | Z = 2 |
Mr = 264.29 | F(000) = 280 |
Triclinic, P1 | Dx = 1.352 Mg m−3 |
Hall symbol: -p 1 | Mo Kα radiation, λ = 0.71073 Å |
a = 7.8350 (7) Å | Cell parameters from 1450 reflections |
b = 9.1368 (9) Å | θ = 3.2–20.8° |
c = 10.3272 (10) Å | µ = 0.10 mm−1 |
α = 79.720 (2)° | T = 302 K |
β = 77.381 (2)° | Block, colourless |
γ = 64.657 (2)° | 0.35 × 0.20 × 0.10 mm |
V = 648.97 (11) Å3 |
Bruker SMART CCD area detector diffractometer | 2767 independent reflections |
Radiation source: fine-focus sealed tube | 1991 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.033 |
phi and ω scans | θmax = 27.0°, θmin = 2.0° |
Absorption correction: multi-scan (SADABS; Bruker, 2000) | h = −10→10 |
Tmin = 0.966, Tmax = 0.990 | k = −11→11 |
4521 measured reflections | l = −11→13 |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.058 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.172 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.06 | w = 1/[σ2(Fo2) + (0.0955P)2] where P = (Fo2 + 2Fc2)/3 |
2767 reflections | (Δ/σ)max < 0.001 |
186 parameters | Δρmax = 0.27 e Å−3 |
0 restraints | Δρmin = −0.29 e Å−3 |
C12H16N4O3 | γ = 64.657 (2)° |
Mr = 264.29 | V = 648.97 (11) Å3 |
Triclinic, P1 | Z = 2 |
a = 7.8350 (7) Å | Mo Kα radiation |
b = 9.1368 (9) Å | µ = 0.10 mm−1 |
c = 10.3272 (10) Å | T = 302 K |
α = 79.720 (2)° | 0.35 × 0.20 × 0.10 mm |
β = 77.381 (2)° |
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 = 0.990 | Rint = 0.033 |
4521 measured reflections |
R[F2 > 2σ(F2)] = 0.058 | 0 restraints |
wR(F2) = 0.172 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.06 | Δρmax = 0.27 e Å−3 |
2767 reflections | Δρmin = −0.29 e Å−3 |
186 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
C1 | 0.4786 (3) | 0.2753 (2) | 0.45970 (17) | 0.0404 (4) | |
C2 | 0.6483 (2) | 0.1345 (2) | 0.43570 (17) | 0.0372 (4) | |
C3 | 0.7156 (2) | 0.0230 (2) | 0.54871 (17) | 0.0359 (4) | |
C4 | 0.6070 (2) | 0.0620 (2) | 0.67547 (17) | 0.0377 (4) | |
C5 | 0.4355 (2) | 0.2018 (2) | 0.68772 (17) | 0.0362 (4) | |
C6 | 0.3927 (3) | 0.4091 (3) | 0.3547 (2) | 0.0642 (7) | |
H6A | 0.3536 | 0.3671 | 0.2930 | 0.096* | |
H6B | 0.4861 | 0.4498 | 0.3080 | 0.096* | |
H6C | 0.2837 | 0.4956 | 0.3963 | 0.096* | |
C7 | 0.6634 (3) | −0.0413 (2) | 0.79306 (18) | 0.0416 (5) | |
C8 | 0.7589 (3) | 0.0936 (2) | 0.30234 (18) | 0.0419 (5) | |
C9 | 0.7834 (3) | 0.1527 (2) | 0.06883 (18) | 0.0508 (5) | |
H9A | 0.7946 | 0.0472 | 0.0532 | 0.061* | |
H9B | 0.9111 | 0.1486 | 0.0606 | 0.061* | |
C10 | 0.6766 (3) | 0.2811 (3) | −0.0303 (2) | 0.0607 (6) | |
H10A | 0.5483 | 0.2884 | −0.0181 | 0.091* | |
H10B | 0.7395 | 0.2536 | −0.1188 | 0.091* | |
H10C | 0.6734 | 0.3839 | −0.0176 | 0.091* | |
C11 | 0.1222 (3) | 0.3504 (2) | 0.8233 (2) | 0.0510 (5) | |
H11A | 0.0591 | 0.3219 | 0.9096 | 0.061* | |
H11B | 0.0634 | 0.3361 | 0.7558 | 0.061* | |
C12 | 0.0869 (4) | 0.5254 (3) | 0.8139 (2) | 0.0636 (6) | |
H12A | −0.0431 | 0.5853 | 0.8561 | 0.076* | |
H12B | 0.1725 | 0.5358 | 0.8634 | 0.076* | |
N1 | 0.3761 (2) | 0.30703 (18) | 0.58156 (14) | 0.0422 (4) | |
N2 | 0.8725 (2) | −0.11440 (19) | 0.53691 (17) | 0.0473 (4) | |
H2B | 0.928 (3) | −0.122 (2) | 0.4515 (16) | 0.057* | |
H2A | 0.900 (3) | −0.174 (2) | 0.6103 (17) | 0.057* | |
N3 | 0.7004 (3) | −0.1181 (2) | 0.89125 (17) | 0.0560 (5) | |
N4 | 0.3234 (2) | 0.23730 (19) | 0.80702 (16) | 0.0461 (4) | |
H4A | 0.372 (3) | 0.164 (3) | 0.866 (2) | 0.055* | |
O1 | 0.9108 (2) | −0.02184 (18) | 0.28168 (15) | 0.0628 (5) | |
O2 | 0.67814 (19) | 0.19305 (16) | 0.20107 (12) | 0.0496 (4) | |
O3 | 0.1129 (3) | 0.59692 (18) | 0.68257 (16) | 0.0728 (5) | |
H3A | 0.111 (5) | 0.532 (3) | 0.633 (3) | 0.109* |
U11 | U22 | U33 | U12 | U13 | U23 | |
C1 | 0.0431 (10) | 0.0397 (9) | 0.0313 (10) | −0.0113 (8) | −0.0064 (8) | 0.0004 (7) |
C2 | 0.0384 (10) | 0.0388 (9) | 0.0303 (9) | −0.0129 (8) | −0.0036 (7) | −0.0026 (7) |
C3 | 0.0368 (9) | 0.0315 (8) | 0.0367 (10) | −0.0112 (7) | −0.0068 (7) | −0.0023 (7) |
C4 | 0.0415 (10) | 0.0340 (9) | 0.0330 (10) | −0.0117 (8) | −0.0089 (8) | 0.0019 (7) |
C5 | 0.0379 (9) | 0.0355 (9) | 0.0310 (9) | −0.0115 (7) | −0.0052 (7) | −0.0018 (7) |
C6 | 0.0650 (14) | 0.0540 (12) | 0.0347 (11) | 0.0083 (11) | −0.0050 (10) | 0.0024 (9) |
C7 | 0.0395 (10) | 0.0347 (9) | 0.0383 (10) | −0.0056 (8) | −0.0027 (8) | −0.0018 (8) |
C8 | 0.0452 (11) | 0.0421 (10) | 0.0360 (10) | −0.0155 (9) | −0.0056 (8) | −0.0050 (8) |
C9 | 0.0582 (13) | 0.0539 (12) | 0.0309 (10) | −0.0174 (10) | 0.0040 (9) | −0.0084 (9) |
C10 | 0.0656 (15) | 0.0747 (15) | 0.0353 (11) | −0.0241 (12) | −0.0067 (10) | −0.0024 (10) |
C11 | 0.0446 (11) | 0.0516 (11) | 0.0409 (11) | −0.0098 (9) | 0.0026 (8) | −0.0024 (9) |
C12 | 0.0740 (15) | 0.0466 (11) | 0.0450 (13) | −0.0019 (10) | −0.0076 (11) | −0.0041 (9) |
N1 | 0.0429 (9) | 0.0391 (8) | 0.0318 (8) | −0.0065 (7) | −0.0040 (7) | −0.0007 (6) |
N2 | 0.0499 (10) | 0.0387 (8) | 0.0378 (9) | −0.0058 (7) | −0.0049 (8) | 0.0002 (7) |
N3 | 0.0602 (11) | 0.0499 (10) | 0.0359 (9) | −0.0054 (8) | −0.0073 (8) | 0.0056 (8) |
N4 | 0.0455 (10) | 0.0412 (9) | 0.0321 (9) | −0.0025 (7) | −0.0042 (7) | 0.0027 (7) |
O1 | 0.0578 (9) | 0.0564 (9) | 0.0436 (8) | 0.0027 (7) | 0.0005 (7) | −0.0081 (7) |
O2 | 0.0509 (8) | 0.0531 (8) | 0.0286 (7) | −0.0074 (6) | −0.0020 (6) | −0.0051 (6) |
O3 | 0.0843 (12) | 0.0443 (8) | 0.0532 (10) | −0.0013 (8) | 0.0004 (8) | 0.0061 (7) |
C1—N1 | 1.342 (2) | C9—C10 | 1.493 (3) |
C1—C2 | 1.410 (2) | C9—H9A | 0.9700 |
C1—C6 | 1.504 (2) | C9—H9B | 0.9700 |
C2—C3 | 1.436 (2) | C10—H10A | 0.9600 |
C2—C8 | 1.474 (2) | C10—H10B | 0.9600 |
C3—N2 | 1.330 (2) | C10—H10C | 0.9600 |
C3—C4 | 1.409 (2) | C11—N4 | 1.461 (2) |
C4—C5 | 1.403 (2) | C11—C12 | 1.490 (3) |
C4—C7 | 1.424 (2) | C11—H11A | 0.9700 |
C5—N1 | 1.344 (2) | C11—H11B | 0.9700 |
C5—N4 | 1.349 (2) | C12—O3 | 1.409 (3) |
C6—H6A | 0.9600 | C12—H12A | 0.9700 |
C6—H6B | 0.9600 | C12—H12B | 0.9700 |
C6—H6C | 0.9600 | N2—H2B | 0.895 (15) |
C7—N3 | 1.142 (2) | N2—H2A | 0.859 (15) |
C8—O1 | 1.212 (2) | N4—H4A | 0.84 (2) |
C8—O2 | 1.333 (2) | O3—H3A | 0.861 (17) |
C9—O2 | 1.452 (2) | ||
N1—C1—C2 | 123.25 (16) | C10—C9—H9B | 110.1 |
N1—C1—C6 | 111.78 (16) | H9A—C9—H9B | 108.4 |
C2—C1—C6 | 124.95 (16) | C9—C10—H10A | 109.5 |
C1—C2—C3 | 117.65 (15) | C9—C10—H10B | 109.5 |
C1—C2—C8 | 124.27 (16) | H10A—C10—H10B | 109.5 |
C3—C2—C8 | 118.08 (16) | C9—C10—H10C | 109.5 |
N2—C3—C4 | 119.91 (16) | H10A—C10—H10C | 109.5 |
N2—C3—C2 | 122.47 (16) | H10B—C10—H10C | 109.5 |
C4—C3—C2 | 117.61 (15) | N4—C11—C12 | 115.13 (18) |
C5—C4—C3 | 120.14 (15) | N4—C11—H11A | 108.5 |
C5—C4—C7 | 118.39 (15) | C12—C11—H11A | 108.5 |
C3—C4—C7 | 121.43 (15) | N4—C11—H11B | 108.5 |
N1—C5—N4 | 117.00 (15) | C12—C11—H11B | 108.5 |
N1—C5—C4 | 121.62 (15) | H11A—C11—H11B | 107.5 |
N4—C5—C4 | 121.38 (16) | O3—C12—C11 | 114.25 (18) |
C1—C6—H6A | 109.5 | O3—C12—H12A | 108.7 |
C1—C6—H6B | 109.5 | C11—C12—H12A | 108.7 |
H6A—C6—H6B | 109.5 | O3—C12—H12B | 108.7 |
C1—C6—H6C | 109.5 | C11—C12—H12B | 108.7 |
H6A—C6—H6C | 109.5 | H12A—C12—H12B | 107.6 |
H6B—C6—H6C | 109.5 | C1—N1—C5 | 119.62 (15) |
N3—C7—C4 | 176.31 (18) | C3—N2—H2B | 110.1 (13) |
O1—C8—O2 | 120.50 (17) | C3—N2—H2A | 115.4 (15) |
O1—C8—C2 | 124.55 (18) | H2B—N2—H2A | 134 (2) |
O2—C8—C2 | 114.94 (16) | C5—N4—C11 | 123.93 (15) |
O2—C9—C10 | 107.96 (16) | C5—N4—H4A | 109.6 (16) |
O2—C9—H9A | 110.1 | C11—N4—H4A | 123.3 (16) |
C10—C9—H9A | 110.1 | C8—O2—C9 | 115.70 (15) |
O2—C9—H9B | 110.1 | C12—O3—H3A | 105 (2) |
N1—C1—C2—C3 | −1.8 (3) | C1—C2—C8—O1 | 175.22 (19) |
C6—C1—C2—C3 | 176.79 (18) | C3—C2—C8—O1 | −5.7 (3) |
N1—C1—C2—C8 | 177.27 (16) | C1—C2—C8—O2 | −5.8 (3) |
C6—C1—C2—C8 | −4.2 (3) | C3—C2—C8—O2 | 173.23 (14) |
C1—C2—C3—N2 | 179.06 (17) | N4—C11—C12—O3 | 78.5 (3) |
C8—C2—C3—N2 | −0.1 (3) | C2—C1—N1—C5 | 0.4 (3) |
C1—C2—C3—C4 | 0.2 (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—C1 | 2.6 (3) |
C2—C3—C4—C5 | 2.7 (2) | N1—C5—N4—C11 | 18.9 (3) |
N2—C3—C4—C7 | 1.3 (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—C9 | 0.1 (3) |
C7—C4—C5—N1 | 178.16 (15) | C2—C8—O2—C9 | −178.88 (15) |
C3—C4—C5—N4 | 176.30 (16) | C10—C9—O2—C8 | −177.24 (15) |
C7—C4—C5—N4 | −1.4 (3) |
D—H···A | D—H | H···A | D···A | D—H···A |
O3—H3A···N1 | 0.86 (2) | 2.25 (3) | 2.780 (2) | 120 (3) |
N2—H2B···O1 | 0.90 (2) | 1.83 (2) | 2.613 (2) | 145 (2) |
N4—H4A···N3i | 0.84 (2) | 2.45 (2) | 3.105 (2) | 136.1 (19) |
N2—H2A···O3ii | 0.86 (2) | 2.18 (2) | 2.887 (2) | 140 (2) |
C12—H12A···N3iii | 0.97 | 2.62 | 3.442 (3) | 142 |
Symmetry codes: (i) −x+1, −y, −z+2; (ii) x+1, y−1, z; (iii) x−1, y+1, z. |
Experimental details
Crystal data | |
Chemical formula | C12H16N4O3 |
Mr | 264.29 |
Crystal system, space group | Triclinic, P1 |
Temperature (K) | 302 |
a, b, c (Å) | 7.8350 (7), 9.1368 (9), 10.3272 (10) |
α, β, γ (°) | 79.720 (2), 77.381 (2), 64.657 (2) |
V (Å3) | 648.97 (11) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.10 |
Crystal size (mm) | 0.35 × 0.20 × 0.10 |
Data collection | |
Diffractometer | Bruker SMART CCD area detector |
Absorption correction | Multi-scan (SADABS; Bruker, 2000) |
Tmin, Tmax | 0.966, 0.990 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 4521, 2767, 1991 |
Rint | 0.033 |
(sin θ/λ)max (Å−1) | 0.639 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.058, 0.172, 1.06 |
No. of reflections | 2767 |
No. of parameters | 186 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.27, −0.29 |
Computer programs: SMART (Bruker, 2000), SAINT (Bruker, 2000), SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), SHELXTL (Bruker, 2000).
D—H···A | D—H | H···A | D···A | D—H···A |
O3—H3A···N1 | 0.861 (17) | 2.25 (3) | 2.780 (2) | 120 (3) |
N2—H2B···O1 | 0.895 (15) | 1.832 (17) | 2.613 (2) | 144.6 (19) |
N4—H4A···N3i | 0.84 (2) | 2.45 (2) | 3.105 (2) | 136.1 (19) |
N2—H2A···O3ii | 0.859 (15) | 2.175 (18) | 2.887 (2) | 140 (2) |
Symmetry codes: (i) −x+1, −y, −z+2; (ii) x+1, y−1, z. |
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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).