The 7-aza­norbornane nucleus of epibatidine: 7-aza­bicyclo­[2.2.1]heptan-7-ium chloride

Britvin, S.N.; Rumyantsev, A.M.

doi:10.1107/S2056989017012105

research communications

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Volume 73| Part 9| September 2017| Pages 1385-1388

https://doi.org/10.1107/S2056989017012105

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The 7-azanorbornane nucleus of epibatidine: 7-azabicyclo[2.2.1]heptan-7-ium chloride

Sergey N. Britvin ^a ^* and Andrey M. Rumyantsev ^b

^aDepartment of Crystallography, Saint-Petersburg State University, Universitetskaya Nab. 7/9, 199034 St Petersburg, Russian Federation, and ^bDepartment of Genetics and Biotechnology, Saint-Petersburg State University, Universitetskaya Nab. 7/9, 199034 St Petersburg, Russian Federation
^*Correspondence e-mail: sergei.britvin@spbu.ru

Edited by M. Zeller, Purdue University, USA (Received 18 August 2017; accepted 22 August 2017; online 30 August 2017)

7-Azabicyclo[2.2.1]heptane (7-azanorbornane) is a bridged heterocyclic nucleus found in epibatidine, the alkaloid isolated from the skin of the tropical poison frog Epipedobates tricolor. Since epibatidine is known as one of the most potent acetylcholine nicotinic receptor agonists, a plethora of literature has been devoted to this alkaloid. However, there are no structural data on the unsubstituted 7-azanorbornane, the parent bicyclic ring of epibatidine and its derivatives. We herein present the structural characterization of the 7-azabicyclo[2.2.1]heptane parent ring as its hydrochloride salt, namely 7-azabicyclo[2.2.1]heptan-7-ium chloride, C₆H₁₂N⁺·Cl⁻. The compete cation is generated by a crystallographic mirror plane with the N atom lying on the mirror, as does the chloride anion. In the crystal, the cations are linked to the anions by N—H⋯Cl hydrogen bonds, which generate [001] chains.

Keywords: crystal structure; cage compounds; nitrogen heterocycles; amine; alkaloid; epibatidine.

CCDC reference: 1511233

1. Chemical context

Since the discovery of the quinuclidine and tropane nuclei (Hamama et al., 2006 ; Pollini et al., 2006 ), elegant frameworks of bridged aza-heterocycles have been the focus of chemists exploring biologically active substances. One famous example in this series is epibatidine, (−)-2-(6-chloropyridin-3-yl)-7-azabicyclo[2.2.1]heptane, an active component of the skin poison extracted from the small tropical frog Epipedobates tricolor (Spande et al., 1992 ; Gerzanich et al., 1995 ; Sullivan & Bannon, 1996 ; Dukat & Glennon, 2003 ). Epibatidine comprises the first natural example of a compound incorporating an 7-azabicyclo[2.2.1]heptane (7-azanorbornane) ring system (Fletcher et al., 1994 ). Due to the extreme binding affinity of the exo isomer of epibatidine towards nicotinic acetylcholine receptors, thousands of articles have been devoted to different aspects of its chemistry and biochemistry (see Carroll, 2004 ; Daly et al., 2005 ; Yogeeswari et al., 2006 ; Garraffo et al., 2009 ). We are not aware, however, that an X-ray structure determination of the alkaloid itself has ever been reported, in spite of numerous publications related to its

synthesis. Moreover, the molecular structure of 7-azanorbornane, the functional core of epibatidine, has also not been explored, in spite of the fact that 7-azanorbornane has been known since 1930 (Braun & Schwarz, 1930

; Fraser & Swingle, 1970

). In continuation of our studies related to bridged aza-heterocyclic systems (Britvin et al., 2015

, 2016

, 2017

), we herein report on the structure of the unsubstituted 7-azabicyclo[2.2.1]heptane parent ring as its hydrochloride salt, namely 7-azabicyclo[2.2.1]heptan-7-ium chloride, 1.

2. Structural commentary

The parent ring of 7-azabicyclo[2.2.1]heptane in 1 adopts a boat conformation (Fig. 1) resembling the molecular geometry of its nearest carbocyclic counterpart, bicyclo[2.2.1]heptane (norbornane), 2 (Fitch & Jobic, 1993 ). In order to achieve consistency of atomic labelling between the bicyclic cages of 1 and 2, we herein apply the numbering scheme according to IUPAC nomenclature (Fig. 1) (Doms et al., 1985 ). There are three unique C atoms (C1, C2 and C6) in the cation of 1, with their clones C1ⁱ [= C4 by IUPAC; symmetry code: (i) 1 − x, y, z], C2ⁱ (= C3 by IUPAC) and C6ⁱ (= C5 by IUPAC) generated by the mirror at x = $[1 \over 2]$ . Interatomic distances between the respective framework sites of 1 are shorter compared with the corresponding values of 2. The distances (Å) in 1 and 2 are: C1—C2 = 1.528 (2) and 1.551 (3), C1—C6 = 1.523 (3) and 1.578 (1), and C1—N7(C7) = 1.508 (2) and 1.551 (3). The C2ⁱ—C2—C1—C6 torsion angle determining the boat-like conformation is 109.4 (1)° in 1 and 108.7 (2)° in 2. The s.u. values for 2 were generated using PLATON (Spek, 2009 ). Further details of the interatomic distances and angles of 1 can be found in the supporting information.

Figure 1
The molecular structure and systematic atomic numbering scheme of the 7-azabicyclo[2.2.1]heptane (7-azanorbornane) parent ring in 1. Displacement ellipsoids are drawn at the 50% probability level. H atoms on C atoms in view (a) and the chloride counter-ion have been omitted for clarity. The labelling in the Figures corresponds to IUPAC notation (see text). Atoms C4, C3 and C5 are generated from C1, C2 and C6, respectively, by the symmetry operation (1 − x, y, z).

3. Supramolecular features

The structural integrity of 1 is maintained via intermolecular hydrogen bonding between the protonated secondary site N7 and the chloride counter-ion Cl1 (Table 1). Each chloride ion is linked to the two adjacent amine centres via N—H⋯Cl hydrogen bonds so that the 7-azanorbornane cages are arranged into zigzag chains flattened on (010) and propagating along the c-axis direction (Fig. 2). That type of interleaved zigzag packing is known among chloride salts of secondary amines, both for alkyl- and arylamines (Adams et al., 1997 ; Nancy et al., 2003 ; Muller et al., 2007 ) and heterocyclic systems (Gribkov et al., 2006 ; Wang et al., 2011 ; Fun et al., 2011 ).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N7—H7B⋯Cl1ⁱ	0.88 (3)	2.25 (3)	3.127 (2)	175 (2)
N7—H7A⋯Cl1	0.87 (4)	2.25 (4)	3.122 (2)	178 (3)
Symmetry code: (i) $[-x+1, -y+1, z+{\script{1\over 2}}]$ .

Figure 2
Hydrogen bonding in the crystal structure of 1. Protonated molecules of 7-azanorbornane are linked via N—H⋯Cl hydrogen bonds to form infinite zigzag chains propagated along the c axis. Displacement ellipsoids are drawn at the 50% probability level. H atoms not involved in hydrogen bonding have been omitted for clarity.

4. Database survey

Of more than 120 structures containing the 7-azanorbornane ring system in the Cambridge Structural Database (CSD, Version 5.38, latest update May 2017; Groom et al., 2016 ), 17 entries represent the 7-azabicyclo[2.2.1]heptane parent ring unsubstituted at the carbon sites. All these compounds belong to N-substituted derivatives of 7-azanorbornane (Ohwada et al. 1998 ; Cheng et al. 2002 ; Otani et al. 2003 ; Hori et al. 2008 ; Longobardi et al. 2015 ).

5. Synthesis and crystallization

7-Azabicyclo[2.2.1]heptane hydrochloride, 1, was obtained from Sigma Aldrich. The purity of the substance has been proven by elemental analysis (analysis calculated for C₆H₁₂ClN: C 53.93, H 9.05, N 10.48%; found: C 53.89, H 9.08, N 10.44%). ¹H NMR (400 MHz) spectrum (Bruker Avance 400, SiMe₄ external standard, D₂O solution): δ 4.21–4.19 (m, 2H, 2 × CH at C1 and C4; the atom-numbering scheme is according to IUPAC nomenclature, see Fig. 1), 1.92–1.84 (m, 4H, 4 × endo-HCH at C2, C3, C5, C6), 1.78–1.71 (m, 4H, 4 × exo-HCH at C2, C3, C5, C6). ¹³C{¹H} NMR (101 MHz): δ 58.9 (s, C1 and C4), 26.7 (s, C2, C3, C5, C6). Crystals of 1 suitable for structural studies were obtained by slow evaporation of its aqueous solution.

6. Refinement

H atoms at the protonated N7 atom were refined freely, whereas H atoms on C atoms were refined based on a riding model. Crystal data, data collection and structure refinement details are summarized in Table 2.

Table 2
Experimental details

Crystal data
Chemical formula	C₆H₁₂N⁺·Cl⁻
M_r	133.62
Crystal system, space group	Orthorhombic, Cmc2₁
Temperature (K)	100
a, b, c (Å)	9.1532 (6), 8.7029 (8), 8.7336 (5)
V (Å³)	695.71 (9)
Z	4
Radiation type	Mo Kα
μ (mm⁻¹)	0.45
Crystal size (mm)	0.08 × 0.06 × 0.04

Data collection
Diffractometer	Bruker APEXII CCD
Absorption correction	Multi-scan (SADABS; Sheldrick, 2015 )
No. of measured, independent and observed [I > 2σ(I)] reflections	3239, 777, 769
R_int	0.017
(sin θ/λ)_max (Å⁻¹)	0.638

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.017, 0.048, 1.15
No. of reflections	777
No. of parameters	47
No. of restraints	1
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.21, −0.12
Absolute structure	Refined as an inversion twin
Absolute structure parameter	0.19 (9)
Computer programs: APEX2 (Bruker, 2015 ), SAINT (Bruker, 2015), SHELXT (Sheldrick, 2015a), OLEX2 (Dolomanov et al., 2009 ), SHELXL2014 (Sheldrick, 2015b), Mercury (Macrae et al., 2008 ) and publCIF (Westrip, 2010 ).

Supporting information

CCDC reference: 1511233

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2056989017012105/zl2713sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989017012105/zl2713Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2056989017012105/zl2713Isup3.mol

Supporting information file. DOI: https://doi.org/10.1107/S2056989017012105/zl2713Isup4.cml

checkCIF report

Computing details top

Data collection: APEX2 (Bruker, 2015); cell refinement: SAINT (Bruker, 2015); program(s) used to solve structure: SHELXT (Sheldrick, 2015a) and OLEX2 (Dolomanov et al., 2009); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015b) and OLEX2 (Dolomanov et al., 2009); molecular graphics: Mercury (Macrae et al., 2008); software used to prepare material for publication: publCIF (Westrip, 2010).

7-Azabicyclo[2.2.1]heptan-7-ium chloride top

Crystal data top

C₆H₁₂N⁺·Cl⁻	D_x = 1.276 Mg m⁻³
M_r = 133.62	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, Cmc2₁	Cell parameters from 2988 reflections
a = 9.1532 (6) Å	θ = 3.2–30.7°
b = 8.7029 (8) Å	µ = 0.45 mm⁻¹
c = 8.7336 (5) Å	T = 100 K
V = 695.71 (9) Å³	Block, colourless
Z = 4	0.08 × 0.06 × 0.04 mm
F(000) = 288

Data collection top

Bruker APEX-II CCD diffractometer	777 independent reflections
Radiation source: fine focus sealed tube	769 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.017
φ and ω scans	θ_max = 27.0°, θ_min = 3.2°
Absorption correction: multi-scan (SADABS; Sheldrick, 2015)	h = −11→11
	k = −4→11
3239 measured reflections	l = −11→10

Refinement top

Refinement on F²	Hydrogen site location: mixed
Least-squares matrix: full	H atoms treated by a mixture of independent and constrained refinement
R[F² > 2σ(F²)] = 0.017	w = 1/[σ²(F_o²) + (0.0282P)² + 0.1322P] where P = (F_o² + 2F_c²)/3
wR(F²) = 0.048	(Δ/σ)_max < 0.001
S = 1.15	Δρ_max = 0.21 e Å⁻³
777 reflections	Δρ_min = −0.12 e Å⁻³
47 parameters	Absolute structure: Refined as an inversion twin
1 restraint	Absolute structure parameter: 0.19 (9)

Special details top

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. Single-crystal data collection was performed using a Bruker Kappa APEX II DUO diffractometer equipped with microfocus optics. Refinement of lattice parameters and subsequent data reduction was carried out with the Bruker SAINT software. The crystal structure of 1 was solved and refined using SHELXT and SHELXL-2014 (Sheldrick, 2015) via the OLEX2 v.1.2 graphical user interface (Dolomanov et al., 2009).

Refined as a 2-component inversion twin.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
C1	0.62232 (18)	0.2599 (3)	0.5813 (2)	0.0174 (4)
H1	0.7205	0.2960	0.5547	0.021*
C2	0.5850 (2)	0.2715 (3)	0.75142 (19)	0.0202 (4)
H2B	0.6233	0.3655	0.7956	0.024*
H2A	0.6233	0.1843	0.8078	0.024*
C6	0.5848 (2)	0.10083 (19)	0.5202 (2)	0.0209 (4)
H6A	0.6231	0.0210	0.5864	0.025*
H6B	0.6231	0.0863	0.4176	0.025*
N7	0.5000	0.3539 (2)	0.5134 (2)	0.0139 (4)
H7B	0.5000	0.449 (4)	0.548 (3)	0.014 (7)*
H7A	0.5000	0.347 (4)	0.414 (5)	0.030 (9)*
Cl1	0.5000	0.31735 (5)	0.15788 (7)	0.01568 (15)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0107 (7)	0.0188 (10)	0.0226 (9)	0.0012 (7)	−0.0009 (6)	0.0003 (7)
C2	0.0227 (10)	0.0240 (10)	0.0140 (8)	0.0018 (8)	−0.0063 (7)	0.0029 (7)
C6	0.0239 (9)	0.0157 (9)	0.0232 (9)	0.0046 (6)	−0.0001 (7)	−0.0022 (8)
N7	0.0199 (10)	0.0119 (9)	0.0100 (9)	0.000	0.000	0.0007 (8)
Cl1	0.0213 (2)	0.0142 (2)	0.0116 (2)	0.000	0.000	0.0005 (2)

Geometric parameters (Å, º) top

C1—H1	0.9800	C6—C6ⁱ	1.553 (4)
C1—C2	1.528 (2)	C6—H6A	0.9700
C1—C6	1.523 (3)	C6—H6B	0.9700
C1—N7	1.508 (2)	N7—C1ⁱ	1.508 (2)
C2—C2ⁱ	1.556 (4)	N7—H7B	0.88 (3)
C2—H2B	0.9700	N7—H7A	0.87 (4)
C2—H2A	0.9700

C2—C1—H1	114.5	C1—C6—C6ⁱ	103.03 (9)
C6—C1—H1	114.5	C1—C6—H6A	111.2
C6—C1—C2	110.50 (19)	C1—C6—H6B	111.2
N7—C1—H1	114.5	C6ⁱ—C6—H6A	111.2
N7—C1—C2	100.39 (16)	C6ⁱ—C6—H6B	111.2
N7—C1—C6	100.82 (15)	H6A—C6—H6B	109.1
C1—C2—C2ⁱ	102.93 (9)	C1—N7—C1ⁱ	95.91 (18)
C1—C2—H2B	111.2	C1—N7—H7B	111.8 (11)
C1—C2—H2A	111.2	C1ⁱ—N7—H7B	111.8 (11)
C2ⁱ—C2—H2B	111.2	C1—N7—H7A	110.6 (14)
C2ⁱ—C2—H2A	111.2	C1ⁱ—N7—H7A	110.6 (14)
H2B—C2—H2A	109.1	H7B—N7—H7A	115 (3)

C2—C1—C6—C6ⁱ	70.63 (12)	C6—C1—N7—C1ⁱ	56.31 (19)
C2—C1—N7—C1ⁱ	−57.1 (2)	N7—C1—C2—C2ⁱ	35.24 (15)
C6—C1—C2—C2ⁱ	−70.56 (14)	N7—C1—C6—C6ⁱ	−34.89 (12)

Symmetry code: (i) −x+1, y, z.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N7—H7B···Cl1ⁱⁱ	0.88 (3)	2.25 (3)	3.127 (2)	175 (2)
N7—H7A···Cl1	0.87 (4)	2.25 (4)	3.122 (2)	178 (3)

Symmetry code: (ii) −x+1, −y+1, z+1/2.

Acknowledgements

The authors thank the X-ray Diffraction Center, Center for Magnetic Resonance and Computer Resource Center of Saint-Petersburg State University for instrumental and computational resources.

Funding information

Funding for this research was provided by: Saint-Petersburg State University (grant Nos. 0.37.235.2015 and 3.37.222.2015).

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