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The molecular structure of the title compound, C16H18N4O2, adopts the trans conformation, and has an inversion center at the midpoint of the C-C bond in the oxamidate plane. The two phenyl planes are parallel, while the dihedral angle between the oxamidate plane and the phenyl ring is 2.5 (2)°.
Supporting information
CCDC reference: 198980
Key indicators
- Single-crystal X-ray study
- T = 293 K
- Mean (C-C) = 0.002 Å
- R factor = 0.040
- wR factor = 0.181
- Data-to-parameter ratio = 12.0
checkCIF results
No syntax errors found
ADDSYM reports no extra symmetry
Alert Level C:
PLAT_369 Alert C Long C(sp2)-C(sp2) Bond C(8) - C(8)a = 1.54 Ang.
0 Alert Level A = Potentially serious problem
0 Alert Level B = Potential problem
1 Alert Level C = Please check
N,N'-Bis(2-pyridylethyl)oxamide was prepared according to a procedure similar to that reported by Ojima et al. (1970). An ethanol solution (50 ml) of diethyl oxalate (14.62 g, 0.10 mol) was added dropwise to 100 ml e thanol solution of 2-(2-aminoethyl)pyridine (24.24 g, 0.20 mol) with stirring. The mixture was then stirred and refluxed at 353 K for 1 h. The resulting solution was cooled to room temperature and a white precipitation appeared. The precipitate was filtered off and washed with water and diethyl ether. The yield was approximately 93%. Colourless single crystals were obtained by recrystallization from ethanol.
Data collection: SMART (Bruker, 1998); cell refinement: SMART; data reduction: SAINT (Bruker, 1998); program(s) used to solve structure: SHELXS97 (Sheldrick, 1990); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL (Bruker, 1998); software used to prepare material for publication: SHELXTL.
Crystal data top
C16H18N4O2 | F(000) = 316 |
Mr = 298.34 | Dx = 1.300 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ytc | Cell parameters from 2131 reflections |
a = 9.489 (6) Å | θ = 2.2–26.8° |
b = 6.248 (4) Å | µ = 0.09 mm−1 |
c = 13.062 (8) Å | T = 293 K |
β = 100.28 (1)° | Prism, colourless |
V = 762.0 (8) Å3 | 0.47 × 0.33 × 0.20 mm |
Z = 2 | |
Data collection top
Bruker CCD area-detector diffractometer | 1642 independent reflections |
Radiation source: fine-focus sealed tube | 1274 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.018 |
Detector resolution: 0.781Å pixels mm-1 | θmax = 27.1°, θmin = 3.2° |
ϕ and ω scans | h = −11→12 |
Absorption correction: multi-scan (SADABS; Sheldrick, 1996; Blessing, 1995) | k = −7→7 |
Tmin = 0.959, Tmax = 0.982 | l = −14→16 |
4245 measured reflections | |
Refinement top
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.040 | All H-atom parameters refined |
wR(F2) = 0.181 | w = 1/[σ2(Fo2) + (0.1359P)2] where P = (Fo2 + 2Fc2)/3 |
S = 1.06 | (Δ/σ)max = 0.001 |
1642 reflections | Δρmax = 0.22 e Å−3 |
137 parameters | Δρmin = −0.13 e Å−3 |
0 restraints | Extinction correction: SHELXL97, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.07 (2) |
Crystal data top
C16H18N4O2 | V = 762.0 (8) Å3 |
Mr = 298.34 | Z = 2 |
Monoclinic, P21/c | Mo Kα radiation |
a = 9.489 (6) Å | µ = 0.09 mm−1 |
b = 6.248 (4) Å | T = 293 K |
c = 13.062 (8) Å | 0.47 × 0.33 × 0.20 mm |
β = 100.28 (1)° | |
Data collection top
Bruker CCD area-detector diffractometer | 1642 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 1996; Blessing, 1995) | 1274 reflections with I > 2σ(I) |
Tmin = 0.959, Tmax = 0.982 | Rint = 0.018 |
4245 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.040 | 0 restraints |
wR(F2) = 0.181 | All H-atom parameters refined |
S = 1.06 | Δρmax = 0.22 e Å−3 |
1642 reflections | Δρmin = −0.13 e Å−3 |
137 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 | x | y | z | Uiso*/Ueq | |
N2 | 0.03947 (14) | 0.1630 (2) | 0.89738 (10) | 0.0489 (4) | |
O1 | 0.17259 (11) | 0.0845 (2) | 1.05455 (9) | 0.0678 (5) | |
C8 | 0.06301 (13) | 0.0690 (2) | 0.98966 (11) | 0.0459 (4) | |
C7 | 0.14418 (17) | 0.3021 (2) | 0.86280 (12) | 0.0503 (4) | |
N1 | 0.21408 (14) | 0.7539 (2) | 0.77070 (9) | 0.0546 (4) | |
C5 | 0.24531 (15) | 0.6710 (2) | 0.86563 (10) | 0.0439 (4) | |
C6 | 0.13294 (17) | 0.5315 (3) | 0.89930 (14) | 0.0549 (5) | |
C4 | 0.37601 (18) | 0.7055 (3) | 0.92896 (13) | 0.0579 (5) | |
C3 | 0.3141 (2) | 0.8751 (3) | 0.73874 (15) | 0.0685 (5) | |
C2 | 0.4470 (2) | 0.9117 (3) | 0.79621 (16) | 0.0674 (5) | |
C1 | 0.47833 (19) | 0.8265 (3) | 0.89319 (15) | 0.0661 (6) | |
H7B | 0.1271 (19) | 0.300 (3) | 0.7856 (14) | 0.061 (5)* | |
H6B | 0.151 (2) | 0.531 (3) | 0.9788 (16) | 0.072 (5)* | |
H7A | 0.238 (2) | 0.245 (3) | 0.8888 (13) | 0.059 (5)* | |
H6A | 0.040 (3) | 0.583 (3) | 0.8719 (17) | 0.083 (6)* | |
H2A | −0.045 (2) | 0.149 (3) | 0.8577 (14) | 0.061 (5)* | |
H1 | 0.570 (2) | 0.850 (3) | 0.9324 (16) | 0.079 (6)* | |
H3 | 0.284 (3) | 0.934 (4) | 0.666 (2) | 0.105 (7)* | |
H2 | 0.517 (2) | 0.999 (4) | 0.7675 (19) | 0.098 (7)* | |
H4 | 0.392 (2) | 0.644 (3) | 0.9969 (16) | 0.074 (5)* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
N2 | 0.0393 (7) | 0.0518 (8) | 0.0541 (7) | −0.0071 (5) | 0.0043 (5) | 0.0035 (5) |
O1 | 0.0401 (6) | 0.0871 (9) | 0.0703 (8) | −0.0179 (5) | −0.0067 (5) | 0.0199 (6) |
C8 | 0.0346 (7) | 0.0461 (8) | 0.0558 (8) | −0.0043 (5) | 0.0048 (6) | 0.0012 (6) |
C7 | 0.0451 (9) | 0.0526 (9) | 0.0546 (9) | −0.0052 (6) | 0.0127 (7) | 0.0024 (6) |
N1 | 0.0488 (8) | 0.0641 (9) | 0.0498 (7) | 0.0001 (6) | 0.0058 (6) | 0.0029 (5) |
C5 | 0.0417 (8) | 0.0425 (8) | 0.0478 (8) | −0.0013 (5) | 0.0087 (6) | −0.0039 (5) |
C6 | 0.0471 (9) | 0.0562 (9) | 0.0645 (10) | −0.0056 (6) | 0.0180 (7) | −0.0025 (7) |
C4 | 0.0521 (9) | 0.0694 (10) | 0.0500 (9) | −0.0032 (7) | 0.0031 (7) | −0.0004 (7) |
C3 | 0.0736 (12) | 0.0682 (11) | 0.0670 (11) | 0.0040 (9) | 0.0216 (9) | 0.0166 (8) |
C2 | 0.0667 (11) | 0.0515 (9) | 0.0905 (13) | −0.0125 (8) | 0.0312 (10) | −0.0023 (8) |
C1 | 0.0459 (10) | 0.0697 (12) | 0.0813 (13) | −0.0147 (8) | 0.0072 (8) | −0.0192 (9) |
Geometric parameters (Å, º) top
N2—C8 | 1.324 (2) | C5—C6 | 1.502 (2) |
N2—C7 | 1.451 (2) | C6—H6B | 1.02 (2) |
N2—H2A | 0.88 (2) | C6—H6A | 0.94 (2) |
O1—C8 | 1.2224 (19) | C4—C1 | 1.376 (3) |
C8—C8i | 1.537 (3) | C4—H4 | 0.95 (2) |
C7—C6 | 1.520 (2) | C3—C2 | 1.367 (3) |
C7—H7B | 0.992 (18) | C3—H3 | 1.01 (3) |
C7—H7A | 0.97 (2) | C2—C1 | 1.357 (3) |
N1—C5 | 1.328 (2) | C2—H2 | 0.99 (3) |
N1—C3 | 1.338 (2) | C1—H1 | 0.94 (2) |
C5—C4 | 1.379 (2) | | |
| | | |
C8—N2—C7 | 122.37 (13) | C5—C6—H6B | 107.5 (11) |
C8—N2—H2A | 118.6 (12) | C7—C6—H6B | 107.8 (11) |
C7—N2—H2A | 118.9 (12) | C5—C6—H6A | 110.7 (14) |
O1—C8—N2 | 125.51 (13) | C7—C6—H6A | 108.3 (13) |
O1—C8—C8i | 120.98 (16) | H6B—C6—H6A | 111.3 (18) |
N2—C8—C8i | 113.51 (14) | C1—C4—C5 | 119.71 (16) |
N2—C7—C6 | 112.13 (13) | C1—C4—H4 | 121.9 (13) |
N2—C7—H7B | 108.1 (11) | C5—C4—H4 | 118.4 (13) |
C6—C7—H7B | 108.9 (11) | N1—C3—C2 | 124.02 (16) |
N2—C7—H7A | 108.2 (11) | N1—C3—H3 | 113.6 (15) |
C6—C7—H7A | 110.4 (11) | C2—C3—H3 | 122.3 (15) |
H7B—C7—H7A | 109.0 (15) | C1—C2—C3 | 118.31 (16) |
C5—N1—C3 | 117.38 (14) | C1—C2—H2 | 121.4 (14) |
N1—C5—C4 | 121.74 (14) | C3—C2—H2 | 120.3 (14) |
N1—C5—C6 | 116.62 (13) | C2—C1—C4 | 118.80 (17) |
C4—C5—C6 | 121.62 (14) | C2—C1—H1 | 118.5 (13) |
C5—C6—C7 | 111.21 (13) | C4—C1—H1 | 122.7 (13) |
| | | |
C7—N2—C8—O1 | −1.0 (2) | N2—C7—C6—C5 | 178.15 (12) |
C7—N2—C8—C8i | 179.36 (14) | N1—C5—C4—C1 | −0.9 (3) |
C8—N2—C7—C6 | −85.67 (18) | C6—C5—C4—C1 | 177.05 (15) |
C3—N1—C5—C4 | −0.7 (2) | C5—N1—C3—C2 | 2.4 (3) |
C3—N1—C5—C6 | −178.75 (14) | N1—C3—C2—C1 | −2.5 (3) |
N1—C5—C6—C7 | 85.13 (18) | C3—C2—C1—C4 | 0.7 (3) |
C4—C5—C6—C7 | −92.89 (18) | C5—C4—C1—C2 | 0.9 (3) |
Symmetry code: (i) −x, −y, −z+2. |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2A···N1ii | 0.878 (19) | 2.204 (19) | 3.008 (3) | 152.1 (17) |
C1—H1···O1iii | 0.94 (2) | 2.452 (19) | 3.308 (3) | 151.4 (17) |
Symmetry codes: (ii) −x, y−1/2, −z+3/2; (iii) −x+1, −y+1, −z+2. |
Experimental details
Crystal data |
Chemical formula | C16H18N4O2 |
Mr | 298.34 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 293 |
a, b, c (Å) | 9.489 (6), 6.248 (4), 13.062 (8) |
β (°) | 100.28 (1) |
V (Å3) | 762.0 (8) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.09 |
Crystal size (mm) | 0.47 × 0.33 × 0.20 |
|
Data collection |
Diffractometer | Bruker CCD area-detector diffractometer |
Absorption correction | Multi-scan (SADABS; Sheldrick, 1996; Blessing, 1995) |
Tmin, Tmax | 0.959, 0.982 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 4245, 1642, 1274 |
Rint | 0.018 |
(sin θ/λ)max (Å−1) | 0.640 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.040, 0.181, 1.06 |
No. of reflections | 1642 |
No. of parameters | 137 |
H-atom treatment | All H-atom parameters refined |
Δρmax, Δρmin (e Å−3) | 0.22, −0.13 |
Selected geometric parameters (Å, º) topN2—C8 | 1.324 (2) | C8—C8i | 1.537 (3) |
N2—C7 | 1.451 (2) | C7—C6 | 1.520 (2) |
O1—C8 | 1.2224 (19) | C5—C6 | 1.502 (2) |
| | | |
C8—N2—C7 | 122.37 (13) | C5—C6—C7 | 111.21 (13) |
N2—C7—C6 | 112.13 (13) | | |
Symmetry code: (i) −x, −y, −z+2. |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2A···N1ii | 0.878 (19) | 2.204 (19) | 3.008 (3) | 152.1 (17) |
C1—H1···O1iii | 0.94 (2) | 2.452 (19) | 3.308 (3) | 151.4 (17) |
Symmetry codes: (ii) −x, y−1/2, −z+3/2; (iii) −x+1, −y+1, −z+2. |
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N,N'-Disubstituted oxamidates are versatile ligands in coordination chemistry. They can adopt either the cis-(I) or trans-(II) conformation to form metal complexes, which are excellent building blocks for more complicated structures, such as metallosupramolecular frameworks (Chen at el., 1994). As part of our systematic study on the coordination chemistry of N,N'-disubstituted oxamidate ligands, we recently synthesized the ligand N,N'-bis(2-pyridylethyl)oxamide, (III), and analyzed its crystal structure. The symmetric center of (III) is located at the midpoint of the bond C8—C8A. Atoms C7 and C7A are in the oxamidate plane, which is composed ofatoms C8, C8A, N2, N2A, O1 and O1A. The dihedral angle between the oxamidate plane and the phenyl planes is only 2.5°, and the two phenyl rings are parallel to each other. The two C═O groups lie on opposite sides of the bond C8—C8A and the molecule adopts the trans conformation. The torsion angle N2—C7—C6—C5 is 178.15 (12)°. Though atoms C8 and C8A are sp2 hybridized, the bond C8—C8A is mainly a single bond and the bond length is 1.537 (3) Å, which is longer than that of a C═C double bond. Similar situations were found in the analogue N,N'-bis(2-pyridylmethyl)oxamide, in which the C—C bond lengths are 1.536 (7) and 1.513 (7) Å (Lloret et al., 1989), as well as in other oxamide compounds (Sanada et al., 1998; Ruiz et al., 1997; Chen et al., 1994; Zhang et al., 1996). In the crystal, symmetry-related molecules are linked by two types of intermolecular hydrogen bonds, viz. N—H···N and C—H···O. As indicated in Table 2, the hydrogen bond between N2 and N1i is much stronger than that between C1 and O1ii.