| Literature DB >> 29250403 |
Sergey N Britvin1, Andrey M Rumyantsev2.
Abstract
The cage of 2,5-di-aza-bicyclo-[2.2.1]heptane is frequently employed in synthetic chemistry as a rigid bicyclic counterpart of the piperazine ring. The 2,5-di-azabicyclo-[2.2.1]heptane scaffold is incorporated into a variety of compounds having pharmacological and catalytic applications. The unsubstituted parent ring of the system, 2,5-di-aza-bicyclo-[2.2.1]heptane itself, has not been structurally characterized. We herein report on the mol-ecular structure of the parent ring in (1S,4S)-2,5-diazo-niabi-cyclo-[2.2.1]heptane dibromide, C5H12N22+·2Br-. The asymmetric unit contains two crystallographically independent cages of 2,5-di-aza-bicyclo-[2.2.1]heptane. Each cage is protonated at the two nitro-gen sites. The overall charge balance is maintained by four crystallographically independent bromide ions. In the crystal, the components of the structure are linked via a complex three-dimensional network of N-H⋯Br hydrogen bonds.Entities:
Keywords: 2,5-diazabicyclo[2.2.1]heptane; bicyclic amine; bridged heterocycle; crystal structure; diamine; piperazine
Year: 2017 PMID: 29250403 PMCID: PMC5730240 DOI: 10.1107/S2056989017015870
Source DB: PubMed Journal: Acta Crystallogr E Crystallogr Commun
Figure 1Two views of the diprotonated 2,5-diazabicyclo[2.2.1]heptane parent ring in 1 (in one of the two independent molecules in the asymmetric unit). The atomic numbering scheme is according to IUPAC notation. Displacement ellipsoids are drawn at the 30% probability level. Hydrogen atoms are depicted as fixed-size spheres of arbitrary radius. The bromide counter-ions have been omitted for clarity.
Figure 2(a) The two independent molecules of 2,5-diazabicyclo[2.2.1]heptane in the crystal structure of 1 (this work). (b) The chair conformer of piperazine in piperazine-1,4-diium dibromide monohydrate (Bujak, 2015 ▸). The atomic numbering schemes are given in IUPAC notation. Symmetrically equivalent atoms in the piperazine ring are noted in parentheses. Displacement ellipsoids are drawn at the 30% probability level. Hydrogen atoms, bromide counter-ions and water molecules have been omitted for clarity.
Figure 3Hydrogen bonding in the crystal structure of 1. Protonated molecules of 2,5-diazabicyclo[2.2.1]heptane are linked by N—H⋯Br hydrogen bonds, forming slabs parallel to (100). These slabs are linked by N—H⋯Br hydrogen bonds into a three-dimensional network. Displacement ellipsoids are drawn at the 30% probability level. H atoms not involved in hydrogen bonding have been omitted for clarity.
Hydrogen-bond geometry (Å, °)
|
|
| H⋯ |
|
|
|---|---|---|---|---|
| N2—H2 | 0.93 (3) | 2.49 (3) | 3.358 (2) | 156 (2) |
| N5—H5 | 0.92 (3) | 2.44 (3) | 3.261 (2) | 148 (3) |
| N5—H5 | 0.78 (3) | 2.50 (3) | 3.242 (2) | 161 (3) |
| N2 | 0.89 (3) | 2.53 (4) | 3.344 (2) | 152 (3) |
| N2 | 0.86 (3) | 2.48 (3) | 3.273 (2) | 155 (2) |
| N5 | 0.91 (3) | 2.42 (3) | 3.292 (2) | 160 (3) |
| N5 | 0.77 (3) | 2.77 (3) | 3.399 (2) | 140 (3) |
Symmetry codes: (i) ; (ii) .
Experimental details
| Crystal data | |
| Chemical formula | C5H12N2 2+·2Br− |
|
| 259.99 |
| Crystal system, space group | Orthorhombic, |
| Temperature (K) | 100 |
|
| 9.7298 (6), 11.8643 (5), 14.4933 (7) |
|
| 1673.07 (15) |
|
| 8 |
| Radiation type | Mo |
| μ (mm−1) | 9.61 |
| Crystal size (mm) | 0.2 × 0.08 × 0.05 |
| Data collection | |
| Diffractometer | Bruker APEXII CCD |
| Absorption correction | Multi-scan ( |
| No. of measured, independent and observed [ | 15838, 4031, 3959 |
|
| 0.026 |
| (sin θ/λ)max (Å−1) | 0.661 |
| Refinement | |
|
| 0.014, 0.035, 1.02 |
| No. of reflections | 4031 |
| No. of parameters | 195 |
| H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
| Δρmax, Δρmin (e Å−3) | 0.53, −0.34 |
| Absolute structure | Flack |
| Absolute structure parameter | 0.009 (5) |
Computer programs: APEX2 and SAINT (Bruker, 2015 ▸), SHELXT (Sheldrick, 2015a ▸), SHELXL2014 (Sheldrick, 2015b ▸), Mercury (Macrae et al., 2008 ▸), OLEX2 (Dolomanov et al., 2009 ▸) and publCIF (Westrip, 2010 ▸).
| C5H12N22+·2Br− | |
| Mo | |
| Orthorhombic, | Cell parameters from 9887 reflections |
| θ = 2.5–31.5° | |
| µ = 9.61 mm−1 | |
| Block, colourless | |
| 0.2 × 0.08 × 0.05 mm | |
| Bruker APEXII CCD diffractometer | 4031 independent reflections |
| Radiation source: fine focus sealed tube | 3959 reflections with |
| Graphite monochromator | |
| φ and ω scans | θmax = 28.0°, θmin = 2.2° |
| Absorption correction: multi-scan (SADABS; Bruker, 2015) | |
| 15838 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 = 0.53 e Å−3 | |
| 4031 reflections | Δρmin = −0.34 e Å−3 |
| 195 parameters | Absolute structure: Flack |
| 0 restraints | Absolute structure parameter: 0.009 (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. |
| C1 | 0.5925 (3) | 0.3998 (2) | 0.37609 (18) | 0.0160 (5) | |
| H1 | 0.6722 | 0.4501 | 0.3797 | 0.019* | |
| N2 | 0.4926 (2) | 0.4270 (2) | 0.29906 (15) | 0.0143 (4) | |
| H2A | 0.479 (3) | 0.505 (3) | 0.2960 (18) | 0.011 (7)* | |
| H2B | 0.519 (4) | 0.403 (3) | 0.245 (3) | 0.038 (11)* | |
| C3 | 0.3610 (3) | 0.3669 (2) | 0.32592 (18) | 0.0162 (5) | |
| H3A | 0.3377 | 0.3084 | 0.2818 | 0.019* | |
| H3B | 0.2848 | 0.4192 | 0.3310 | 0.019* | |
| C4 | 0.3987 (3) | 0.3168 (3) | 0.41995 (18) | 0.0183 (6) | |
| H4 | 0.3203 | 0.2983 | 0.4596 | 0.022* | |
| N5 | 0.4954 (2) | 0.2198 (2) | 0.40090 (17) | 0.0167 (5) | |
| H5A | 0.454 (3) | 0.170 (3) | 0.361 (2) | 0.024 (9)* | |
| H5B | 0.504 (3) | 0.186 (3) | 0.446 (2) | 0.013 (8)* | |
| C6 | 0.6277 (3) | 0.2749 (2) | 0.36993 (18) | 0.0158 (5) | |
| H6A | 0.6511 | 0.2534 | 0.3073 | 0.019* | |
| H6B | 0.7033 | 0.2557 | 0.4106 | 0.019* | |
| C7 | 0.4971 (3) | 0.4045 (2) | 0.45944 (18) | 0.0205 (6) | |
| H7A | 0.4546 | 0.4778 | 0.4678 | 0.025* | |
| H7B | 0.5411 | 0.3802 | 0.5161 | 0.025* | |
| C1A | 0.6072 (3) | 0.8241 (2) | 0.59473 (17) | 0.0139 (5) | |
| H1A | 0.6918 | 0.8624 | 0.5758 | 0.017* | |
| N2A | 0.4792 (2) | 0.8628 (2) | 0.54520 (15) | 0.0141 (4) | |
| H2AA | 0.478 (4) | 0.844 (3) | 0.486 (2) | 0.033 (10)* | |
| H2AB | 0.476 (3) | 0.935 (3) | 0.5432 (19) | 0.010 (7)* | |
| C3A | 0.3626 (2) | 0.8184 (2) | 0.60478 (19) | 0.0160 (5) | |
| H3AA | 0.3103 | 0.7610 | 0.5726 | 0.019* | |
| H3AB | 0.3011 | 0.8786 | 0.6233 | 0.019* | |
| C4A | 0.4384 (3) | 0.7687 (2) | 0.68803 (18) | 0.0152 (5) | |
| H4A | 0.3835 | 0.7635 | 0.7446 | 0.018* | |
| N5A | 0.5014 (2) | 0.6592 (2) | 0.65645 (16) | 0.0154 (4) | |
| H5AA | 0.437 (3) | 0.612 (3) | 0.631 (2) | 0.019 (8)* | |
| H5AB | 0.534 (3) | 0.629 (3) | 0.698 (2) | 0.021 (9)* | |
| C6A | 0.6121 (3) | 0.6950 (2) | 0.58809 (17) | 0.0163 (5) | |
| H6AA | 0.5907 | 0.6694 | 0.5262 | 0.020* | |
| H6AB | 0.7015 | 0.6662 | 0.6059 | 0.020* | |
| C7A | 0.5656 (3) | 0.8433 (2) | 0.69531 (17) | 0.0161 (5) | |
| H7AA | 0.6328 | 0.8149 | 0.7389 | 0.019* | |
| H7AB | 0.5439 | 0.9214 | 0.7087 | 0.019* | |
| Br1 | 0.52194 (2) | 0.62674 (2) | 0.88905 (2) | 0.01450 (6) | |
| Br2 | 0.22116 (2) | 0.51516 (2) | 0.60873 (2) | 0.01567 (6) | |
| Br3 | 0.46504 (3) | 0.70005 (2) | 0.35710 (2) | 0.01494 (6) | |
| Br4 | 0.26144 (3) | 0.04454 (2) | 0.32745 (2) | 0.01680 (6) |
| C1 | 0.0142 (12) | 0.0157 (14) | 0.0181 (13) | −0.0018 (10) | −0.0058 (10) | 0.0015 (10) |
| N2 | 0.0145 (10) | 0.0138 (12) | 0.0148 (10) | 0.0003 (9) | 0.0011 (8) | 0.0031 (9) |
| C3 | 0.0109 (11) | 0.0191 (14) | 0.0185 (12) | −0.0006 (10) | 0.0001 (10) | 0.0020 (11) |
| C4 | 0.0136 (12) | 0.0217 (15) | 0.0195 (12) | 0.0003 (10) | 0.0063 (10) | 0.0044 (11) |
| N5 | 0.0191 (11) | 0.0135 (12) | 0.0174 (11) | −0.0037 (9) | −0.0026 (9) | 0.0043 (9) |
| C6 | 0.0125 (11) | 0.0177 (14) | 0.0173 (13) | 0.0002 (10) | −0.0025 (9) | 0.0005 (10) |
| C7 | 0.0285 (15) | 0.0199 (15) | 0.0130 (12) | 0.0033 (11) | −0.0022 (10) | −0.0030 (10) |
| C1A | 0.0107 (11) | 0.0138 (14) | 0.0173 (13) | −0.0008 (9) | −0.0006 (9) | 0.0023 (10) |
| N2A | 0.0172 (11) | 0.0115 (12) | 0.0135 (10) | 0.0008 (9) | −0.0007 (8) | 0.0004 (8) |
| C3A | 0.0108 (11) | 0.0168 (14) | 0.0206 (13) | 0.0024 (9) | −0.0019 (9) | 0.0010 (11) |
| C4A | 0.0143 (12) | 0.0164 (14) | 0.0150 (12) | −0.0014 (10) | 0.0001 (9) | 0.0016 (10) |
| N5A | 0.0148 (10) | 0.0141 (11) | 0.0173 (11) | −0.0008 (9) | −0.0031 (8) | 0.0034 (9) |
| C6A | 0.0147 (12) | 0.0163 (14) | 0.0178 (12) | 0.0029 (10) | 0.0008 (9) | 0.0006 (10) |
| C7A | 0.0173 (12) | 0.0147 (14) | 0.0162 (12) | −0.0020 (10) | −0.0027 (10) | 0.0012 (10) |
| Br1 | 0.01665 (12) | 0.01277 (12) | 0.01407 (12) | −0.00094 (9) | −0.00018 (9) | −0.00022 (9) |
| Br2 | 0.01471 (12) | 0.01456 (13) | 0.01775 (11) | −0.00228 (9) | −0.00073 (10) | 0.00003 (10) |
| Br3 | 0.01588 (12) | 0.01335 (13) | 0.01560 (12) | 0.00039 (9) | 0.00032 (9) | 0.00008 (9) |
| Br4 | 0.01390 (12) | 0.01434 (13) | 0.02214 (12) | −0.00278 (9) | 0.00270 (9) | −0.00030 (10) |
| C1—H1 | 0.9800 | C3A—H3AA | 0.9700 |
| C1—N2 | 1.516 (3) | C3A—H3AB | 0.9700 |
| C1—C6 | 1.523 (4) | C3A—C4A | 1.532 (4) |
| C1—C7 | 1.525 (4) | C4A—H4A | 0.9800 |
| N2—H2A | 0.93 (3) | C4A—N5A | 1.508 (3) |
| N2—H2B | 0.87 (4) | C4A—C7A | 1.525 (4) |
| N2—C3 | 1.516 (3) | N5A—H5AA | 0.91 (3) |
| C3—H3A | 0.9700 | N5A—H5AB | 0.77 (3) |
| C3—H3B | 0.9700 | N5A—C6A | 1.523 (3) |
| C3—C4 | 1.532 (4) | C6A—H6AA | 0.9700 |
| C4—H4 | 0.9800 | C6A—H6AB | 0.9700 |
| C4—N5 | 1.512 (4) | C7A—H7AA | 0.9700 |
| C4—C7 | 1.525 (4) | C7A—H7AB | 0.9700 |
| N5—H5A | 0.92 (3) | N2—N5 | 2.868 (3) |
| N5—H5B | 0.78 (3) | N2A—N5A | 2.912 (3) |
| N5—C6 | 1.512 (3) | C1—C4 | 2.220 (4) |
| C6—H6A | 0.9700 | C1A—C4A | 2.226 (4) |
| C6—H6B | 0.9700 | C3—C6 | 2.887 (4) |
| C7—H7A | 0.9700 | C3A—C6A | 2.845 (4) |
| C7—H7B | 0.9700 | N2—C7 | 2.340 (4) |
| C1A—H1A | 0.9800 | N2A—C7A | 2.344 (3) |
| C1A—N2A | 1.509 (3) | N5—C7 | 2.350 (4) |
| C1A—C6A | 1.535 (4) | N5A—C7A | 2.340 (4) |
| C1A—C7A | 1.530 (3) | C3—C7 | 2.387 (4) |
| N2A—H2AA | 0.89 (3) | C3A—C7A | 2.390 (4) |
| N2A—H2AB | 0.86 (3) | C6—C7 | 2.380 (4) |
| N2A—C3A | 1.521 (3) | C6A—C7A | 2.391 (4) |
| N2—C1—H1 | 114.7 | N2A—C1A—H1A | 114.8 |
| N2—C1—C6 | 107.9 (2) | N2A—C1A—C6A | 107.4 (2) |
| N2—C1—C7 | 100.66 (19) | N2A—C1A—C7A | 101.0 (2) |
| C6—C1—H1 | 114.7 | C6A—C1A—H1A | 114.8 |
| C6—C1—C7 | 102.7 (2) | C7A—C1A—H1A | 114.8 |
| C7—C1—H1 | 114.7 | C7A—C1A—C6A | 102.5 (2) |
| C1—N2—H2A | 109.5 (17) | C1A—N2A—H2AA | 113 (2) |
| C1—N2—H2B | 114 (3) | C1A—N2A—H2AB | 111 (2) |
| C1—N2—C3 | 104.64 (19) | C1A—N2A—C3A | 103.90 (18) |
| H2A—N2—H2B | 109 (3) | H2AA—N2A—H2AB | 102 (3) |
| C3—N2—H2A | 111.1 (18) | C3A—N2A—H2AA | 117 (2) |
| C3—N2—H2B | 109 (3) | C3A—N2A—H2AB | 110 (2) |
| N2—C3—H3A | 111.4 | N2A—C3A—H3AA | 111.2 |
| N2—C3—H3B | 111.4 | N2A—C3A—H3AB | 111.2 |
| N2—C3—C4 | 102.0 (2) | N2A—C3A—C4A | 102.76 (19) |
| H3A—C3—H3B | 109.2 | H3AA—C3A—H3AB | 109.1 |
| C4—C3—H3A | 111.4 | C4A—C3A—H3AA | 111.2 |
| C4—C3—H3B | 111.4 | C4A—C3A—H3AB | 111.2 |
| C3—C4—H4 | 114.9 | C3A—C4A—H4A | 114.9 |
| N5—C4—C3 | 106.4 (2) | N5A—C4A—C3A | 106.7 (2) |
| N5—C4—H4 | 114.9 | N5A—C4A—H4A | 114.9 |
| N5—C4—C7 | 101.4 (2) | N5A—C4A—C7A | 101.0 (2) |
| C7—C4—C3 | 102.7 (2) | C7A—C4A—C3A | 102.9 (2) |
| C7—C4—H4 | 114.9 | C7A—C4A—H4A | 114.9 |
| C4—N5—H5A | 110 (2) | C4A—N5A—H5AA | 112 (2) |
| C4—N5—H5B | 108 (2) | C4A—N5A—H5AB | 109 (3) |
| C4—N5—C6 | 104.7 (2) | C4A—N5A—C6A | 104.2 (2) |
| H5A—N5—H5B | 104 (3) | H5AA—N5A—H5AB | 108 (3) |
| C6—N5—H5A | 118 (2) | C6A—N5A—H5AA | 113.2 (19) |
| C6—N5—H5B | 113 (2) | C6A—N5A—H5AB | 110 (2) |
| C1—C6—H6A | 111.3 | C1A—C6A—H6AA | 111.3 |
| C1—C6—H6B | 111.3 | C1A—C6A—H6AB | 111.3 |
| N5—C6—C1 | 102.2 (2) | N5A—C6A—C1A | 102.4 (2) |
| N5—C6—H6A | 111.3 | N5A—C6A—H6AA | 111.3 |
| N5—C6—H6B | 111.3 | N5A—C6A—H6AB | 111.3 |
| H6A—C6—H6B | 109.2 | H6AA—C6A—H6AB | 109.2 |
| C1—C7—C4 | 93.4 (2) | C1A—C7A—H7AA | 113.0 |
| C1—C7—H7A | 113.0 | C1A—C7A—H7AB | 113.0 |
| C1—C7—H7B | 113.0 | C4A—C7A—C1A | 93.6 (2) |
| C4—C7—H7A | 113.0 | C4A—C7A—H7AA | 113.0 |
| C4—C7—H7B | 113.0 | C4A—C7A—H7AB | 113.0 |
| H7A—C7—H7B | 110.4 | H7AA—C7A—H7AB | 110.4 |
| C1—N2—C3—C4 | 3.2 (3) | C1A—N2A—C3A—C4A | 5.5 (3) |
| N2—C1—C6—N5 | −71.1 (2) | N2A—C1A—C6A—N5A | −74.2 (2) |
| N2—C1—C7—C4 | 56.3 (2) | N2A—C1A—C7A—C4A | 56.7 (2) |
| N2—C3—C4—N5 | −73.1 (2) | N2A—C3A—C4A—N5A | −75.1 (2) |
| N2—C3—C4—C7 | 33.0 (3) | N2A—C3A—C4A—C7A | 30.8 (3) |
| C3—C4—N5—C6 | 71.2 (2) | C3A—C4A—N5A—C6A | 67.9 (2) |
| C3—C4—C7—C1 | −55.1 (2) | C3A—C4A—C7A—C1A | −53.4 (2) |
| C4—N5—C6—C1 | 0.8 (3) | C4A—N5A—C6A—C1A | 4.5 (2) |
| N5—C4—C7—C1 | 54.9 (2) | N5A—C4A—C7A—C1A | 56.8 (2) |
| C6—C1—N2—C3 | 69.0 (2) | C6A—C1A—N2A—C3A | 67.2 (2) |
| C6—C1—C7—C4 | −55.1 (2) | C6A—C1A—C7A—C4A | −54.1 (2) |
| C7—C1—N2—C3 | −38.2 (2) | C7A—C1A—N2A—C3A | −39.8 (2) |
| C7—C1—C6—N5 | 34.7 (2) | C7A—C1A—C6A—N5A | 31.7 (2) |
| C7—C4—N5—C6 | −35.9 (2) | C7A—C4A—N5A—C6A | −39.3 (2) |
| H··· | ||||
| N2—H2 | 0.93 (3) | 2.49 (3) | 3.358 (2) | 156 (2) |
| N5—H5 | 0.92 (3) | 2.44 (3) | 3.261 (2) | 148 (3) |
| N5—H5 | 0.78 (3) | 2.50 (3) | 3.242 (2) | 161 (3) |
| N2 | 0.89 (3) | 2.53 (4) | 3.344 (2) | 152 (3) |
| N2 | 0.86 (3) | 2.48 (3) | 3.273 (2) | 155 (2) |
| N5 | 0.91 (3) | 2.42 (3) | 3.292 (2) | 160 (3) |
| N5 | 0.77 (3) | 2.77 (3) | 3.399 (2) | 140 (3) |