| Literature DB >> 31921456 |
Minakshi Bhardwaj1, Qianxiang Ai1, Sean R Parkin1, Robert B Grossman1.
Abstract
The title compound [systematic name: (1R*, 8S)-2-acetamidoocta-hydro-pyrrol-izin-4-ium chloride-N-[(1R, 8S)-hexa-hydro-1H-pyrrolizin-2-yl)acetamide (1/1)], 2(C9H16N2O)·HCl or C9H17N2O+·Cl-·C9H16N2O, arose as an unexpected product when 1-exo-acetamido-pyrrolizidine (AcAP; C9H16N2O) was dissolved in CHCl3. Within the AcAP pyrrolizidine group, the unsubstituted five-membered ring is disordered over two orientations in a 0.897 (5):0.103 (5) ratio. Two AcAP mol-ecules related by a crystallographic twofold axis link to H+ and Cl- ions lying on the rotation axis, thereby forming N-H⋯N and N-H⋯Cl⋯H-N hydrogen bonds. The first of these has an unusually short N⋯N separation of 2.616 (2) Å: refinement of different models against the present data set could not distinguish between a symmetrical hydrogen bond (H atom lying on the twofold axis and equidistant from the N atoms) or static or dynamic disorder models (i.e. N-H⋯N + N⋯H-N). Computational studies suggest that the disorder model is slightly more stable, but the energy difference is very small. © Bhardwaj et al. 2020.Entities:
Keywords: crystal structure; short N—H⋯N hydrogen bond
Year: 2020 PMID: 31921456 PMCID: PMC6944077 DOI: 10.1107/S2056989019016517
Source DB: PubMed Journal: Acta Crystallogr E Crystallogr Commun
Figure 1Synthesis of AcAP.
Figure 2An ellipsoid plot (50% probability) showing the molecular structure of 2AcAP·HCl. Unlabeled atoms are related to their labeled counterparts by a crystallographic twofold rotation (−x + 1, y, −z + ). The unusually short N—H⋯N hydrogen bond between the pyrrolizidine N atoms is highlighted by open dashed lines. Weaker N—H⋯Cl hydrogen bonds between the acetamide NH group and the Cl− anion are shown as dotted lines.
Figure 3An ellipsoid plot (50% probability) showing disorder of the non-substituted half of the pyrrolizidine ring. The refined major:minor component occupancy factors are 0.897 (5):0.103 (5).
Hydrogen-bond geometry (Å, °)
|
|
| H⋯ |
|
|
|---|---|---|---|---|
| N4—H4 | 1.31 (1) | 1.31 (1) | 2.616 (2) | 178 (3) |
| N2—H2 | 0.94 (2) | 2.29 (2) | 3.2263 (11) | 176.4 (16) |
Symmetry code: (i) .
Figure 4A difference-Fourier map showing elongated electron density for the hydrogen atom involved in the short N—H⋯N hydrogen bond of 2AcAP·HCl.
Figure 5Computed charge-density line profile from nitrogen to nitrogen in the N—H⋯N hydrogen bond.
Figure 6Computed potential-energy surface as a function of N—H⋯N hydrogen-atom displacement from the midpoint of the two nitrogen atoms.
Experimental details
| Crystal data | |
| Chemical formula | C9H17N2O+·Cl−·C9H16N2O |
|
| 372.93 |
| Crystal system, space group | Monoclinic, |
| Temperature (K) | 90 |
|
| 20.2125 (8), 9.6926 (4), 10.1458 (3) |
| β (°) | 100.445 (1) |
|
| 1954.74 (13) |
|
| 4 |
| Radiation type | Mo |
| μ (mm−1) | 0.22 |
| Crystal size (mm) | 0.40 × 0.36 × 0.04 |
| Data collection | |
| Diffractometer | Bruker D8 Venture dual source |
| Absorption correction | Multi-scan ( |
|
| 0.885, 0.988 |
| No. of measured, independent and observed [ | 31903, 2235, 2096 |
|
| 0.032 |
| (sin θ/λ)max (Å−1) | 0.649 |
| Refinement | |
|
| 0.037, 0.096, 1.12 |
| No. of reflections | 2235 |
| No. of parameters | 144 |
| No. of restraints | 82 |
| H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
| Δρmax, Δρmin (e Å−3) | 0.67, −0.22 |
Computer programs: APEX3 (Bruker, 2016 ▸), SHELXT (Sheldrick, 2015a ▸), SHELXL2018/3 (Sheldrick, 2015b ▸), XP in SHELXTL and SHELX (Sheldrick, 2008 ▸), CIFFIX (Parkin, 2013 ▸) and PLATON (Spek, 2009 ▸).
| C9H17N2O+·Cl−·C9H16N2O | |
| Monoclinic, | Mo |
| Cell parameters from 9978 reflections | |
| θ = 2.3–27.5° | |
| µ = 0.22 mm−1 | |
| β = 100.445 (1)° | |
| Plate, colourless | |
| 0.40 × 0.36 × 0.04 mm |
| Bruker D8 Venture dual source diffractometer | 2235 independent reflections |
| Radiation source: microsource | 2096 reflections with |
| Detector resolution: 7.41 pixels mm-1 | |
| φ and ω scans | θmax = 27.5°, θmin = 2.3° |
| Absorption correction: multi-scan ( | |
| 31903 measured reflections |
| Refinement on | Secondary atom site location: difference Fourier map |
| Least-squares matrix: full | Hydrogen site location: mixed |
| H atoms treated by a mixture of independent and constrained refinement | |
| (Δ/σ)max < 0.001 | |
| 2235 reflections | Δρmax = 0.67 e Å−3 |
| 144 parameters | Δρmin = −0.22 e Å−3 |
| 82 restraints | Extinction correction: SHELXL-2018/3 (Sheldrick 2018), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
| Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.005 (1) |
| Experimental. The crystal was mounted using polyisobutene oil on the tip of a fine glass fibre, which was fastened in a copper mounting pin with electrical solder. It was placed directly into the cold gas stream of a liquid-nitrogen based cryostat (Hope, 1994; Parkin & Hope, 1998). Diffraction data were collected with the crystal at 90K, which is standard practice in this laboratory for the majority of flash-cooled crystals. |
| 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. Refinement progress was checked using |
| Occ. (<1) | |||||
| C1 | 0.63783 (6) | 0.58377 (14) | 0.26083 (13) | 0.0182 (3) | |
| H1 | 0.684523 | 0.622089 | 0.275591 | 0.022* | |
| C2 | 0.60256 (7) | 0.61745 (15) | 0.11816 (14) | 0.0229 (3) | |
| H2A | 0.632627 | 0.601397 | 0.052759 | 0.027* | |
| H2B | 0.561093 | 0.562062 | 0.092144 | 0.027* | |
| C3 | 0.58652 (7) | 0.76915 (15) | 0.12835 (14) | 0.0232 (3) | |
| H3A | 0.626574 | 0.826636 | 0.124182 | 0.028* | |
| H3B | 0.549608 | 0.797166 | 0.055229 | 0.028* | |
| N4 | 0.56555 (6) | 0.78256 (11) | 0.26254 (11) | 0.0184 (3) | |
| H4N | 0.500000 | 0.781 (3) | 0.250000 | 0.056 (9)* | |
| C5 | 0.5885 (2) | 0.9121 (2) | 0.3373 (3) | 0.0249 (7) | 0.897 (5) |
| H5A | 0.554374 | 0.945176 | 0.388570 | 0.030* | 0.897 (5) |
| H5B | 0.597261 | 0.985720 | 0.275018 | 0.030* | 0.897 (5) |
| C6 | 0.65299 (9) | 0.87111 (17) | 0.43106 (16) | 0.0237 (4) | 0.897 (5) |
| H6A | 0.663640 | 0.935711 | 0.507555 | 0.028* | 0.897 (5) |
| H6B | 0.691530 | 0.867102 | 0.383296 | 0.028* | 0.897 (5) |
| C7 | 0.63499 (12) | 0.7276 (2) | 0.4771 (2) | 0.0209 (5) | 0.897 (5) |
| H7A | 0.675941 | 0.673734 | 0.512861 | 0.025* | 0.897 (5) |
| H7B | 0.606530 | 0.733983 | 0.546696 | 0.025* | 0.897 (5) |
| C8 | 0.59630 (6) | 0.66296 (13) | 0.34850 (13) | 0.0178 (3) | 0.897 (5) |
| H8 | 0.559801 | 0.602145 | 0.370299 | 0.021* | 0.897 (5) |
| C5' | 0.595 (2) | 0.9165 (19) | 0.322 (2) | 0.0249 (7) | 0.103 (5) |
| H5'A | 0.561158 | 0.991410 | 0.308580 | 0.030* | 0.103 (5) |
| H5'B | 0.634307 | 0.944647 | 0.282171 | 0.030* | 0.103 (5) |
| C6' | 0.6157 (9) | 0.8793 (15) | 0.4690 (15) | 0.032 (3) | 0.103 (5) |
| H6'A | 0.576222 | 0.871718 | 0.513823 | 0.039* | 0.103 (5) |
| H6'B | 0.647840 | 0.947113 | 0.517395 | 0.039* | 0.103 (5) |
| C7' | 0.6489 (11) | 0.739 (2) | 0.458 (2) | 0.030 (4) | 0.103 (5) |
| H7'A | 0.655595 | 0.689122 | 0.544614 | 0.036* | 0.103 (5) |
| H7'B | 0.692818 | 0.749314 | 0.428958 | 0.036* | 0.103 (5) |
| C8' | 0.59630 (6) | 0.66296 (13) | 0.34850 (13) | 0.0178 (3) | 0.103 (5) |
| H8' | 0.563026 | 0.605013 | 0.385455 | 0.021* | 0.103 (5) |
| N2 | 0.64091 (6) | 0.43798 (12) | 0.29157 (11) | 0.0184 (3) | |
| H2N | 0.6002 (10) | 0.390 (2) | 0.2837 (19) | 0.035 (5)* | |
| C9 | 0.69841 (6) | 0.36514 (14) | 0.31606 (12) | 0.0178 (3) | |
| O1 | 0.75448 (5) | 0.41694 (11) | 0.32142 (11) | 0.0260 (2) | |
| C10 | 0.68897 (7) | 0.21311 (14) | 0.33748 (14) | 0.0224 (3) | |
| H10A | 0.715908 | 0.185291 | 0.423611 | 0.034* | |
| H10B | 0.703494 | 0.160954 | 0.265024 | 0.034* | |
| H10C | 0.641361 | 0.194212 | 0.337727 | 0.034* | |
| Cl1 | 0.500000 | 0.27309 (5) | 0.250000 | 0.02141 (15) |
| C1 | 0.0169 (6) | 0.0170 (6) | 0.0210 (6) | −0.0016 (5) | 0.0044 (5) | 0.0007 (5) |
| C2 | 0.0266 (7) | 0.0247 (7) | 0.0185 (6) | −0.0007 (5) | 0.0071 (5) | 0.0009 (5) |
| C3 | 0.0240 (7) | 0.0244 (7) | 0.0214 (7) | −0.0021 (5) | 0.0041 (5) | 0.0056 (5) |
| N4 | 0.0201 (5) | 0.0139 (5) | 0.0201 (6) | −0.0016 (4) | 0.0006 (4) | 0.0003 (4) |
| C5 | 0.0284 (13) | 0.0147 (7) | 0.0291 (10) | −0.0044 (6) | −0.0014 (9) | −0.0013 (6) |
| C6 | 0.0240 (9) | 0.0220 (8) | 0.0234 (8) | −0.0059 (6) | 0.0001 (6) | −0.0025 (6) |
| C7 | 0.0237 (10) | 0.0206 (8) | 0.0174 (9) | 0.0000 (7) | 0.0015 (7) | −0.0004 (7) |
| C8 | 0.0189 (6) | 0.0154 (6) | 0.0187 (6) | 0.0002 (5) | 0.0020 (5) | 0.0012 (5) |
| C5' | 0.0284 (13) | 0.0147 (7) | 0.0291 (10) | −0.0044 (6) | −0.0014 (9) | −0.0013 (6) |
| C6' | 0.033 (7) | 0.028 (5) | 0.033 (5) | −0.003 (5) | −0.001 (5) | −0.008 (4) |
| C7' | 0.034 (8) | 0.034 (6) | 0.017 (7) | 0.002 (6) | −0.003 (6) | −0.006 (5) |
| C8' | 0.0189 (6) | 0.0154 (6) | 0.0187 (6) | 0.0002 (5) | 0.0020 (5) | 0.0012 (5) |
| N2 | 0.0175 (5) | 0.0155 (6) | 0.0228 (6) | −0.0015 (4) | 0.0049 (4) | −0.0005 (4) |
| C9 | 0.0200 (6) | 0.0191 (6) | 0.0142 (6) | −0.0007 (5) | 0.0028 (5) | −0.0010 (5) |
| O1 | 0.0179 (5) | 0.0247 (5) | 0.0349 (6) | −0.0010 (4) | 0.0029 (4) | 0.0037 (4) |
| C10 | 0.0246 (7) | 0.0178 (7) | 0.0239 (7) | 0.0004 (5) | 0.0022 (5) | −0.0015 (5) |
| Cl1 | 0.0099 (2) | 0.0177 (2) | 0.0354 (3) | 0.000 | 0.00096 (16) | 0.000 |
| C1—N2 | 1.4460 (17) | C6—H6B | 0.9900 |
| C1—C2 | 1.5284 (19) | C7—C8 | 1.529 (2) |
| C1—C8 | 1.5347 (18) | C7—H7A | 0.9900 |
| C1—C8' | 1.5347 (18) | C7—H7B | 0.9900 |
| C1—H1 | 1.0000 | C8—H8 | 1.0000 |
| C2—C3 | 1.513 (2) | C5'—C6' | 1.521 (18) |
| C2—H2A | 0.9900 | C5'—H5'A | 0.9900 |
| C2—H2B | 0.9900 | C5'—H5'B | 0.9900 |
| C3—N4 | 1.5032 (18) | C6'—C7' | 1.528 (17) |
| C3—H3A | 0.9900 | C6'—H6'A | 0.9900 |
| C3—H3B | 0.9900 | C6'—H6'B | 0.9900 |
| N4—H4N | 1.3080 (12) | C7'—C8' | 1.576 (16) |
| N4—C5 | 1.497 (2) | C7'—H7'A | 0.9900 |
| N4—C5' | 1.507 (17) | C7'—H7'B | 0.9900 |
| N4—C8 | 1.5146 (16) | C8'—H8' | 1.0000 |
| N4—C8' | 1.5146 (16) | N2—C9 | 1.3439 (17) |
| N4—H4N | 1.3080 (12) | N2—H2N | 0.94 (2) |
| C5—C6 | 1.520 (4) | C9—O1 | 1.2317 (16) |
| C5—H5A | 0.9900 | C9—C10 | 1.5066 (19) |
| C5—H5B | 0.9900 | C10—H10A | 0.9800 |
| C6—C7 | 1.532 (3) | C10—H10B | 0.9800 |
| C6—H6A | 0.9900 | C10—H10C | 0.9800 |
| N2—C1—C2 | 114.05 (11) | C8—C7—C6 | 102.97 (16) |
| N2—C1—C8 | 111.75 (11) | C8—C7—H7A | 111.2 |
| C2—C1—C8 | 103.41 (11) | C6—C7—H7A | 111.2 |
| N2—C1—C8' | 111.75 (11) | C8—C7—H7B | 111.2 |
| C2—C1—C8' | 103.41 (11) | C6—C7—H7B | 111.2 |
| N2—C1—H1 | 109.1 | H7A—C7—H7B | 109.1 |
| C2—C1—H1 | 109.1 | N4—C8—C7 | 105.73 (12) |
| C8—C1—H1 | 109.1 | N4—C8—C1 | 105.05 (10) |
| C3—C2—C1 | 102.22 (11) | C7—C8—C1 | 116.80 (13) |
| C3—C2—H2A | 111.3 | N4—C8—H8 | 109.7 |
| C1—C2—H2A | 111.3 | C7—C8—H8 | 109.7 |
| C3—C2—H2B | 111.3 | C1—C8—H8 | 109.7 |
| C1—C2—H2B | 111.3 | N4—C5'—C6' | 101.8 (12) |
| H2A—C2—H2B | 109.2 | N4—C5'—H5'A | 111.4 |
| N4—C3—C2 | 104.18 (11) | C6'—C5'—H5'A | 111.4 |
| N4—C3—H3A | 110.9 | N4—C5'—H5'B | 111.4 |
| C2—C3—H3A | 110.9 | C6'—C5'—H5'B | 111.4 |
| N4—C3—H3B | 110.9 | H5'A—C5'—H5'B | 109.3 |
| C2—C3—H3B | 110.9 | C5'—C6'—C7' | 100.7 (16) |
| H3A—C3—H3B | 108.9 | C5'—C6'—H6'A | 111.6 |
| H4N—N4—C5 | 106.1 (12) | C7'—C6'—H6'A | 111.6 |
| H4N—N4—C3 | 110.96 (17) | C5'—C6'—H6'B | 111.6 |
| C5—N4—C3 | 114.78 (16) | C7'—C6'—H6'B | 111.6 |
| H4N—N4—C5' | 112 (2) | H6'A—C6'—H6'B | 109.4 |
| C3—N4—C5' | 106.2 (15) | C6'—C7'—C8' | 102.6 (11) |
| H4N—N4—C8 | 110.4 (12) | C6'—C7'—H7'A | 111.2 |
| C5—N4—C8 | 107.04 (14) | C8'—C7'—H7'A | 111.2 |
| C3—N4—C8 | 107.55 (10) | C6'—C7'—H7'B | 111.2 |
| H4N—N4—C8' | 110.4 (12) | C8'—C7'—H7'B | 111.2 |
| C3—N4—C8' | 107.55 (10) | H7'A—C7'—H7'B | 109.2 |
| C5'—N4—C8' | 109.8 (9) | N4—C8'—C1 | 105.05 (10) |
| H4N—N4—H4N | 0 (3) | N4—C8'—C7' | 101.6 (8) |
| C5—N4—H4N | 106.1 (12) | C1—C8'—C7' | 105.9 (9) |
| C3—N4—H4N | 110.96 (17) | N4—C8'—H8' | 114.3 |
| C5'—N4—H4N | 112 (2) | C1—C8'—H8' | 114.3 |
| C8—N4—H4N | 110.4 (12) | C7'—C8'—H8' | 114.3 |
| C8'—N4—H4N | 110.4 (12) | C9—N2—C1 | 123.73 (11) |
| N4—C5—C6 | 104.5 (2) | C9—N2—H2N | 118.0 (12) |
| N4—C5—H5A | 110.9 | C1—N2—H2N | 117.9 (12) |
| C6—C5—H5A | 110.9 | O1—C9—N2 | 123.50 (13) |
| N4—C5—H5B | 110.9 | O1—C9—C10 | 122.14 (13) |
| C6—C5—H5B | 110.9 | N2—C9—C10 | 114.37 (12) |
| H5A—C5—H5B | 108.9 | C9—C10—H10A | 109.5 |
| C5—C6—C7 | 101.78 (16) | C9—C10—H10B | 109.5 |
| C5—C6—H6A | 111.4 | H10A—C10—H10B | 109.5 |
| C7—C6—H6A | 111.4 | C9—C10—H10C | 109.5 |
| C5—C6—H6B | 111.4 | H10A—C10—H10C | 109.5 |
| C7—C6—H6B | 111.4 | H10B—C10—H10C | 109.5 |
| H6A—C6—H6B | 109.3 | ||
| N2—C1—C2—C3 | 162.24 (11) | N2—C1—C8—C7 | 93.71 (16) |
| C8—C1—C2—C3 | 40.67 (13) | C2—C1—C8—C7 | −143.19 (14) |
| C8'—C1—C2—C3 | 40.67 (13) | H4N—N4—C5'—C6' | 97 (2) |
| C1—C2—C3—N4 | −39.46 (13) | C3—N4—C5'—C6' | −142 (2) |
| C2—C3—N4—H4N | −97.5 (15) | C8'—N4—C5'—C6' | −26 (3) |
| C2—C3—N4—C5 | 142.30 (19) | N4—C5'—C6'—C7' | 45 (3) |
| C2—C3—N4—C5' | 140.9 (15) | C5'—C6'—C7'—C8' | −47 (2) |
| C2—C3—N4—C8 | 23.32 (13) | H4N—N4—C8'—C1 | 123.3 (9) |
| C2—C3—N4—C8' | 23.32 (13) | C3—N4—C8'—C1 | 2.12 (13) |
| H4N—N4—C5—C6 | 141.3 (8) | C5'—N4—C8'—C1 | −113 (2) |
| C3—N4—C5—C6 | −95.81 (19) | H4N—N4—C8'—C7' | −126.5 (13) |
| C8—N4—C5—C6 | 23.5 (3) | C3—N4—C8'—C7' | 112.3 (10) |
| N4—C5—C6—C7 | −39.9 (3) | C5'—N4—C8'—C7' | −3 (2) |
| C5—C6—C7—C8 | 40.9 (2) | N2—C1—C8'—N4 | −149.53 (11) |
| H4N—N4—C8—C7 | −112.6 (9) | C2—C1—C8'—N4 | −26.43 (13) |
| C5—N4—C8—C7 | 2.4 (2) | N2—C1—C8'—C7' | 103.4 (9) |
| C3—N4—C8—C7 | 126.23 (14) | C2—C1—C8'—C7' | −133.5 (9) |
| H4N—N4—C8—C1 | 123.3 (9) | C6'—C7'—C8'—N4 | 30.6 (18) |
| C5—N4—C8—C1 | −121.70 (19) | C6'—C7'—C8'—C1 | 140.1 (14) |
| C3—N4—C8—C1 | 2.12 (13) | C2—C1—N2—C9 | 113.29 (14) |
| C6—C7—C8—N4 | −26.97 (19) | C8—C1—N2—C9 | −129.88 (13) |
| C6—C7—C8—C1 | 89.41 (17) | C8'—C1—N2—C9 | −129.88 (13) |
| N2—C1—C8—N4 | −149.53 (11) | C1—N2—C9—O1 | 3.8 (2) |
| C2—C1—C8—N4 | −26.43 (13) | C1—N2—C9—C10 | −176.47 (12) |
| H··· | ||||
| N4—H4 | 1.31 (1) | 1.31 (1) | 2.616 (2) | 178 (3) |
| N2—H2 | 0.94 (2) | 2.29 (2) | 3.2263 (11) | 176.4 (16) |