| Literature DB >> 36250108 |
Gavin Collis1, Alex Bilyk1, Ueno Kazanori1, Craig M Forsyth2.
Abstract
The structure of N-methyl-N'-(pyridin-2-yl)benzene-1,2-di-amine, C12H13N3, at 123 K has ortho-rhom-bic (Pna21) symmetry. The title compound displays an unexpected proton-splitting pattern when studied by 1H NMR spectroscopy. The X-ray crystallography analysis determined this to be caused by strong dual N-H⋯N hydrogen bonding. © Collis et al. 2022.Entities:
Keywords: crystal structure; dimerization; heterocycles.; hydrogen bonding
Year: 2022 PMID: 36250108 PMCID: PMC9535833 DOI: 10.1107/S2056989022009173
Source DB: PubMed Journal: Acta Crystallogr E Crystallogr Commun
Figure 1Two-dimensional COSY spectrum of N-methyl-N-phenyl-1,2-diaminobenzene, IV (d 6-DMSO).
Figure 2Molecular diagram of the title compound, with non-hydrogen atoms represented by 50% displacement ellipsoids and hydrogen atoms as spheres of arbitrary size.
Hydrogen-bond geometry (Å, °)
|
|
| H⋯ |
|
|
|---|---|---|---|---|
| N4—H4⋯N2 | 0.90 (3) | 2.11 (3) | 3.001 (3) | 173 (2) |
| N1—H1⋯N5 | 0.88 (3) | 2.11 (3) | 2.981 (3) | 173 (2) |
| N6—H6⋯N2 | 0.88 (3) | 2.62 (2) | 3.374 (2) | 145 (2) |
| N3—H3⋯N5 | 0.87 (3) | 2.61 (3) | 3.337 (2) | 142 (2) |
Figure 3A view of the unit-cell packing, showing a single 2-D layer of hydrogen-bonded dimer molecules.
Experimental details
| Crystal data | |
| Chemical formula | C12H13N3 |
|
| 199.25 |
| Crystal system, space group | Orthorhombic, |
| Temperature (K) | 123 |
|
| 13.4639 (2), 7.8555 (1), 20.1288 (3) |
|
| 2128.94 (5) |
|
| 8 |
| Radiation type | Cu |
| μ (mm−1) | 0.60 |
| Crystal size (mm) | 0.25 × 0.13 × 0.10 |
| Data collection | |
| Diffractometer | Oxford Diffraction Gemini Ultra CCD |
| Absorption correction | Multi-scan ( |
|
| 0.989, 1.000 |
| No. of measured, independent and observed [ | 11852, 3104, 3018 |
|
| 0.022 |
| (sin θ/λ)max (Å−1) | 0.596 |
| Refinement | |
|
| 0.029, 0.072, 1.06 |
| No. of reflections | 3104 |
| No. of parameters | 290 |
| No. of restraints | 1 |
| H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
| Δρmax, Δρmin (e Å−3) | 0.12, −0.16 |
| Absolute structure | Refined as an inversion twin |
| Absolute structure parameter | 0.3 (5) |
Computer programs: CrysAlis PRO (Rigaku OD, 2015 ▸), SHELXT2018/3 (Sheldrick, 2015a ▸), SHELXL2018/3 (Sheldrick, 2015b ▸), X-SEED (Barbour, 2001 ▸), publCIF (Westrip, 2010 ▸).
| C12H13N3 | |
| Cu | |
| Orthorhombic, | Cell parameters from 6421 reflections |
| θ = 5.5–66.8° | |
| µ = 0.60 mm−1 | |
| Prism, colourless | |
| 0.25 × 0.13 × 0.10 mm | |
| Oxford Diffraction Gemini Ultra CCD diffractometer | 3104 independent reflections |
| Radiation source: fine focus sealed tube | 3018 reflections with |
| Detector resolution: 10.3389 pixels mm-1 | |
| ω scans | θmax = 66.8°, θmin = 6.1° |
| Absorption correction: multi-scan (CrysAlisPro; Rigaku OD, 2015) | |
| 11852 measured reflections |
| Refinement on | Hydrogen site location: mixed |
| Least-squares matrix: full | H atoms treated by a mixture of independent and constrained refinement |
| (Δ/σ)max < 0.001 | |
| Δρmax = 0.12 e Å−3 | |
| 3104 reflections | Δρmin = −0.16 e Å−3 |
| 290 parameters | Absolute structure: Refined as an inversion twin |
| 1 restraint | Absolute structure parameter: 0.3 (5) |
| Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes. |
| Refinement. Refined as a 2-component inversion twin. |
| N1 | 0.05732 (12) | 0.4385 (2) | 0.17463 (9) | 0.0216 (4) | |
| N2 | 0.17895 (11) | 0.6413 (2) | 0.18021 (8) | 0.0197 (3) | |
| N3 | −0.12863 (12) | 0.4264 (2) | 0.23539 (10) | 0.0218 (4) | |
| N4 | 0.20213 (12) | 0.5712 (2) | 0.32597 (9) | 0.0215 (4) | |
| N5 | 0.08245 (12) | 0.3655 (2) | 0.31899 (9) | 0.0191 (3) | |
| N6 | 0.38962 (12) | 0.5723 (2) | 0.26687 (9) | 0.0213 (4) | |
| C1 | 0.10475 (13) | 0.5720 (2) | 0.14465 (10) | 0.0182 (4) | |
| C2 | 0.07758 (14) | 0.6353 (3) | 0.08167 (10) | 0.0220 (4) | |
| H2 | 0.024921 | 0.584736 | 0.057237 | 0.026* | |
| C3 | 0.12892 (16) | 0.7717 (3) | 0.05649 (14) | 0.0276 (5) | |
| H3A | 0.111761 | 0.816520 | 0.014189 | 0.033* | |
| C4 | 0.20612 (16) | 0.8445 (3) | 0.09273 (12) | 0.0286 (5) | |
| H4A | 0.242660 | 0.938570 | 0.075915 | 0.034* | |
| C5 | 0.22743 (15) | 0.7749 (3) | 0.15392 (12) | 0.0229 (5) | |
| H5 | 0.279645 | 0.824378 | 0.179112 | 0.027* | |
| C6 | −0.01999 (14) | 0.3405 (2) | 0.14590 (10) | 0.0200 (4) | |
| C7 | −0.00450 (17) | 0.2503 (3) | 0.08767 (13) | 0.0273 (5) | |
| H7 | 0.058430 | 0.255938 | 0.066431 | 0.033* | |
| C8 | −0.07908 (18) | 0.1521 (3) | 0.05989 (12) | 0.0325 (5) | |
| H8 | −0.068144 | 0.092462 | 0.019500 | 0.039* | |
| C9 | −0.17014 (17) | 0.1423 (3) | 0.09204 (12) | 0.0316 (5) | |
| H9 | −0.221668 | 0.074427 | 0.073659 | 0.038* | |
| C10 | −0.18668 (15) | 0.2303 (3) | 0.15057 (13) | 0.0244 (5) | |
| H10 | −0.249258 | 0.221028 | 0.172068 | 0.029* | |
| C11 | −0.11291 (14) | 0.3325 (2) | 0.17851 (10) | 0.0192 (4) | |
| C12 | −0.21406 (16) | 0.3957 (3) | 0.27773 (12) | 0.0297 (5) | |
| H12A | −0.274707 | 0.430287 | 0.254431 | 0.045* | |
| H12B | −0.207321 | 0.461959 | 0.318748 | 0.045* | |
| H12C | −0.217817 | 0.274311 | 0.288601 | 0.045* | |
| C13 | 0.15406 (13) | 0.4378 (2) | 0.35580 (10) | 0.0179 (4) | |
| C14 | 0.17762 (14) | 0.3787 (3) | 0.41966 (11) | 0.0235 (4) | |
| H14 | 0.228036 | 0.432290 | 0.445205 | 0.028* | |
| C15 | 0.12622 (17) | 0.2417 (3) | 0.44443 (14) | 0.0281 (5) | |
| H15 | 0.141481 | 0.198837 | 0.487358 | 0.034* | |
| C16 | 0.05185 (16) | 0.1657 (3) | 0.40675 (12) | 0.0277 (5) | |
| H16 | 0.015320 | 0.071136 | 0.423112 | 0.033* | |
| C17 | 0.03327 (15) | 0.2328 (3) | 0.34494 (12) | 0.0230 (5) | |
| H17 | −0.017626 | 0.181957 | 0.318960 | 0.028* | |
| C18 | 0.28032 (14) | 0.6664 (2) | 0.35511 (10) | 0.0196 (4) | |
| C19 | 0.26463 (16) | 0.7599 (3) | 0.41236 (13) | 0.0252 (5) | |
| H19 | 0.200977 | 0.758902 | 0.432723 | 0.030* | |
| C20 | 0.34067 (17) | 0.8553 (3) | 0.44053 (11) | 0.0307 (5) | |
| H20 | 0.329472 | 0.918276 | 0.480110 | 0.037* | |
| C21 | 0.43291 (16) | 0.8573 (3) | 0.41021 (12) | 0.0288 (5) | |
| H21 | 0.485315 | 0.922046 | 0.429208 | 0.035* | |
| C22 | 0.44960 (16) | 0.7658 (3) | 0.35234 (13) | 0.0240 (5) | |
| H22 | 0.513234 | 0.769323 | 0.331998 | 0.029* | |
| C23 | 0.37397 (14) | 0.6684 (2) | 0.32350 (10) | 0.0191 (4) | |
| C24 | 0.47575 (16) | 0.6013 (3) | 0.22502 (12) | 0.0289 (5) | |
| H24A | 0.470921 | 0.530363 | 0.185112 | 0.043* | |
| H24B | 0.536175 | 0.571693 | 0.249577 | 0.043* | |
| H24C | 0.478297 | 0.721543 | 0.212130 | 0.043* | |
| H1 | 0.0701 (18) | 0.421 (3) | 0.2170 (14) | 0.027 (7)* | |
| H3 | −0.0774 (19) | 0.465 (3) | 0.2568 (13) | 0.026 (6)* | |
| H4 | 0.1913 (19) | 0.585 (3) | 0.2824 (16) | 0.034 (7)* | |
| H6 | 0.3354 (18) | 0.540 (3) | 0.2465 (12) | 0.022 (6)* |
| N1 | 0.0207 (8) | 0.0279 (9) | 0.0160 (9) | −0.0072 (7) | −0.0018 (7) | 0.0013 (7) |
| N2 | 0.0170 (7) | 0.0225 (7) | 0.0194 (8) | −0.0011 (6) | 0.0000 (6) | −0.0029 (7) |
| N3 | 0.0195 (8) | 0.0224 (9) | 0.0236 (9) | −0.0020 (6) | 0.0016 (7) | −0.0022 (7) |
| N4 | 0.0197 (8) | 0.0283 (9) | 0.0165 (9) | −0.0069 (7) | −0.0027 (7) | 0.0031 (8) |
| N5 | 0.0164 (7) | 0.0216 (8) | 0.0192 (8) | −0.0005 (6) | 0.0009 (6) | −0.0004 (7) |
| N6 | 0.0181 (8) | 0.0222 (8) | 0.0235 (9) | −0.0027 (6) | 0.0016 (7) | −0.0012 (8) |
| C1 | 0.0161 (8) | 0.0197 (9) | 0.0187 (10) | 0.0009 (7) | 0.0028 (7) | −0.0035 (8) |
| C2 | 0.0215 (9) | 0.0246 (10) | 0.0197 (10) | 0.0011 (8) | −0.0004 (8) | −0.0016 (9) |
| C3 | 0.0329 (12) | 0.0271 (11) | 0.0226 (12) | 0.0000 (9) | −0.0001 (9) | 0.0048 (10) |
| C4 | 0.0341 (11) | 0.0241 (10) | 0.0278 (12) | −0.0064 (9) | 0.0034 (9) | 0.0025 (9) |
| C5 | 0.0223 (9) | 0.0237 (9) | 0.0227 (13) | −0.0056 (8) | 0.0021 (8) | −0.0027 (9) |
| C6 | 0.0204 (9) | 0.0208 (9) | 0.0187 (10) | −0.0035 (7) | −0.0011 (8) | 0.0030 (8) |
| C7 | 0.0295 (11) | 0.0301 (12) | 0.0222 (13) | −0.0054 (9) | 0.0028 (9) | −0.0011 (9) |
| C8 | 0.0454 (13) | 0.0309 (12) | 0.0212 (11) | −0.0094 (10) | −0.0003 (10) | −0.0052 (10) |
| C9 | 0.0385 (12) | 0.0300 (11) | 0.0263 (12) | −0.0141 (9) | −0.0099 (10) | 0.0005 (10) |
| C10 | 0.0216 (9) | 0.0251 (10) | 0.0265 (13) | −0.0049 (8) | −0.0026 (9) | 0.0056 (9) |
| C11 | 0.0207 (9) | 0.0169 (9) | 0.0200 (10) | 0.0004 (7) | −0.0033 (8) | 0.0038 (8) |
| C12 | 0.0263 (11) | 0.0295 (11) | 0.0333 (13) | −0.0034 (9) | 0.0102 (9) | −0.0011 (10) |
| C13 | 0.0149 (8) | 0.0203 (9) | 0.0185 (10) | 0.0010 (7) | 0.0029 (7) | −0.0024 (8) |
| C14 | 0.0215 (9) | 0.0266 (10) | 0.0224 (10) | −0.0012 (8) | −0.0046 (8) | 0.0004 (9) |
| C15 | 0.0349 (13) | 0.0280 (11) | 0.0213 (12) | −0.0011 (9) | −0.0042 (9) | 0.0061 (9) |
| C16 | 0.0306 (10) | 0.0227 (10) | 0.0299 (12) | −0.0056 (8) | 0.0000 (9) | 0.0044 (9) |
| C17 | 0.0217 (10) | 0.0204 (9) | 0.0270 (14) | −0.0024 (8) | −0.0013 (8) | −0.0033 (9) |
| C18 | 0.0187 (9) | 0.0220 (9) | 0.0181 (10) | −0.0036 (7) | −0.0030 (8) | 0.0031 (8) |
| C19 | 0.0255 (10) | 0.0289 (12) | 0.0213 (13) | −0.0036 (8) | 0.0035 (9) | 0.0002 (9) |
| C20 | 0.0373 (12) | 0.0349 (11) | 0.0198 (11) | −0.0098 (10) | 0.0007 (9) | −0.0060 (10) |
| C21 | 0.0296 (11) | 0.0317 (11) | 0.0252 (11) | −0.0123 (8) | −0.0050 (9) | 0.0007 (10) |
| C22 | 0.0193 (9) | 0.0264 (10) | 0.0264 (13) | −0.0048 (8) | −0.0028 (8) | 0.0045 (9) |
| C23 | 0.0200 (9) | 0.0176 (9) | 0.0197 (10) | 0.0001 (7) | −0.0014 (8) | 0.0044 (8) |
| C24 | 0.0277 (10) | 0.0276 (11) | 0.0315 (12) | −0.0015 (9) | 0.0111 (9) | −0.0005 (10) |
| N1—C1 | 1.368 (3) | C6—C7 | 1.386 (3) |
| N1—C6 | 1.418 (3) | C6—C11 | 1.414 (3) |
| N2—C5 | 1.344 (3) | C7—C8 | 1.384 (3) |
| N2—C1 | 1.344 (2) | C8—C9 | 1.389 (3) |
| N3—C11 | 1.378 (3) | C9—C10 | 1.384 (4) |
| N3—C12 | 1.452 (3) | C10—C11 | 1.395 (3) |
| N4—C13 | 1.370 (3) | C13—C14 | 1.403 (3) |
| N4—C18 | 1.418 (3) | C14—C15 | 1.373 (3) |
| N5—C17 | 1.341 (3) | C15—C16 | 1.391 (3) |
| N5—C13 | 1.342 (3) | C16—C17 | 1.374 (3) |
| N6—C23 | 1.384 (3) | C18—C19 | 1.383 (3) |
| N6—C24 | 1.451 (3) | C18—C23 | 1.412 (3) |
| C1—C2 | 1.410 (3) | C19—C20 | 1.390 (3) |
| C2—C3 | 1.372 (3) | C20—C21 | 1.384 (3) |
| C3—C4 | 1.393 (3) | C21—C22 | 1.387 (4) |
| C4—C5 | 1.378 (3) | C22—C23 | 1.400 (3) |
| C1—N1—C6 | 125.37 (18) | N3—C11—C10 | 122.23 (18) |
| C5—N2—C1 | 117.88 (18) | N3—C11—C6 | 119.83 (17) |
| C11—N3—C12 | 121.38 (17) | C10—C11—C6 | 117.92 (19) |
| C13—N4—C18 | 124.93 (17) | N5—C13—N4 | 114.92 (17) |
| C17—N5—C13 | 117.96 (18) | N5—C13—C14 | 121.87 (18) |
| C23—N6—C24 | 120.93 (17) | N4—C13—C14 | 123.21 (18) |
| N2—C1—N1 | 115.00 (17) | C15—C14—C13 | 118.6 (2) |
| N2—C1—C2 | 121.89 (18) | C14—C15—C16 | 120.1 (2) |
| N1—C1—C2 | 123.09 (18) | C17—C16—C15 | 117.4 (2) |
| C3—C2—C1 | 118.5 (2) | N5—C17—C16 | 124.1 (2) |
| C2—C3—C4 | 120.2 (2) | C19—C18—C23 | 120.39 (18) |
| C5—C4—C3 | 117.4 (2) | C19—C18—N4 | 120.74 (18) |
| N2—C5—C4 | 124.1 (2) | C23—C18—N4 | 118.84 (17) |
| C7—C6—C11 | 120.20 (18) | C18—C19—C20 | 120.9 (2) |
| C7—C6—N1 | 120.80 (18) | C21—C20—C19 | 119.2 (2) |
| C11—C6—N1 | 118.97 (17) | C20—C21—C22 | 120.64 (19) |
| C8—C7—C6 | 121.2 (2) | C21—C22—C23 | 120.9 (2) |
| C7—C8—C9 | 118.9 (2) | N6—C23—C22 | 121.96 (19) |
| C10—C9—C8 | 120.7 (2) | N6—C23—C18 | 120.07 (17) |
| C9—C10—C11 | 121.1 (2) | C22—C23—C18 | 117.95 (19) |
| H··· | ||||
| N4—H4···N2 | 0.90 (3) | 2.11 (3) | 3.001 (3) | 173 (2) |
| N1—H1···N5 | 0.88 (3) | 2.11 (3) | 2.981 (3) | 173 (2) |
| N6—H6···N2 | 0.88 (3) | 2.62 (2) | 3.374 (2) | 145 (2) |
| N3—H3···N5 | 0.87 (3) | 2.61 (3) | 3.337 (2) | 142 (2) |