(1 RS,2 SR,5 SR)-9-Benzyl-2-[(1 RS)-1-hy­droxy­benz­yl]-9-aza­bicyclo­[3.3.1]nonan-3-one from synchrotron data

Lazny, Ryszard a * Wolosewicz, Karol a Dauter, Zbigniew b Brzezinski, Krzysztof b a [a ] Institute of Chemistry, University of Bialystok, Hurtowa 1, 15-399 Bialystok, Poland [b ] Synchrotron Radiation Research Section, MCL, National Cancer Institute, Argonne National Laboratory, Biosciences Division, Bldg 202, Argonne, IL 60439, USA

Abstract

In the crystal structure of the racemic title compound, C 22H 25NO 2, solved and refined against sychrotron diffraction data, the hy­droxy group and the carbonyl O atom participate in the formation of O—H⋯O hydrogen bonds between pairs of enanti­omers related by a crystallographic centre of symmetry.

Related literature  

For recent background literature on the synthesis, structure and applications of related granatane-derived aldols, see: Lazny et al. (2011 a ) and references cited therein. For the stereoselective syntheses, applications and structures of related tropinone aldols, see: Sienkiewicz et al. (2009 ); Lazny et al. (2011 b ); Brzezinski et al. (2012 ) and for related nortropin­one aldols, see: Lazny et al. (2001 , 2010 ); Lazny & Nodzewska (2003 ). e-68-o1367-scheme1.jpg

Experimental  

Crystal data  

  • C 22H 25NO 2

  • M r = 335.43

  • Monoclinic, e-68-o1367-efi1.jpg

  • a = 14.380 (3) Å

  • b = 9.3100 (19) Å

  • c = 13.270 (3) Å

  • β = 106.21 (3)°

  • V = 1705.9 (6) Å 3

  • Z = 4

  • Synchrotron radiation

  • λ = 0.61992 Å

  • μ = 0.08 mm −1

  • T = 100 K

  • 0.3 × 0.1 × 0.1 mm

Data collection  

  • Mar Research MAR315 CCD diffractometer

  • Absorption correction: multi-scan ( SCALEPACK; Otwinowski & Minor, 2003 ) T min = 0.975, T max = 0.992

  • 64629 measured reflections

  • 8582 independent reflections

  • 7757 reflections with I > 2σ( I)

  • R int = 0.046

Refinement  

  • R[ F 2 > 2σ( F 2)] = 0.040

  • wR( F 2) = 0.119

  • S = 1.03

  • 8582 reflections

  • 227 parameters

  • H-atom parameters constrained

  • Δρ max = 0.58 e Å −3

  • Δρ min = −0.30 e Å −3

Data collection: NECAT APS beamline software; cell refinement: HKL-2000 (Otwinowski & Minor, 1997 ); data reduction: HKL-2000; program(s) used to solve structure: SHELXD (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ); molecular graphics: ORTEP-3 (Farrugia, 1997 ) and pyMOL (DeLano, 2002 ); software used to prepare material for publication: SHELXL97.

Supplementary Material

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536812014754/kp2402sup1.cif

e-68-o1367-sup1.cif

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536812014754/kp2402Isup2.hkl

e-68-o1367-Isup2.hkl

Supplementary material file. DOI: 10.1107/S1600536812014754/kp2402Isup3.cml

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Notes

[1] Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: KP2402).

Acknowledgements

This work was supported in part by the University of Bialystok (BST-125), the National Science Center, Poland (grant No. N N204 546939), by the Intra­mural Research Program of NIH, National Cancer Institute, Center for Cancer Research, and with Federal funds from the National Cancer Institute, National Institutes of Health, under Contract HHSN2612008000001E.

Appendices

supplementary crystallographic information

Comment

Granatane (9-methyl-9-azabicyclo[3.3.1]nonane) and norgranatane (9-azabicyclo[3.3.1]nonane) are known scaffolds of several molecules tested e.g. as antagonists of human serotonin type-3 receptor (5-HT3 R). So far, relatively few synthetic and natural granatane derivatives have been synthesized and studied as potential pharmaceutically useful agents. Related diastereomerically and enantimerically pure aldols of granatanone have been recently described (Lazny et al., 2011 a). Related aldols of tropinone have been used as key intermediates in several stereoselective syntheses of alkaloids e.g., ferrugine (Sienkiewicz et al., 2009 and references cited therein). The N-benzyl derivative is a potentially useful intermediate for synthesis of nor-aldols of granatanone, preparation of which is unknown. Effective, stereoselective syntheses of related nortropinone aldols (Lazny & Nodzewska, 2003; Lazny et al., 2001) is still an unsolved problem. Therefore synthetically equivalent N-benzylnorgranatanone aldols should open a route to preparative accessibility of substituted norgranatanes for biomedical studies. The described N-benzyl derivative was prepared by a procedure analogous to methods known for N-methyl aldols. The synthetic procedure gave a racemic product.

The crystal structure of the title compound contains one molecule in the asymmetric unit (Fig. 1). Two intermolecular hydrogen bonds are formed between a pair of enantiomers in the crystal lattice. hydroxy group and carbonyl oxygen atom of the azabicyclo[3.3.1]nonan-3-one system participate in this interaction (Table 1, Fig. 2).

Experimental

A solution of n-butyllithium in hexane (2.5 M, 0.88 mL, 2.0 mmol) was added dropwise to a cooled (273 K) and stirred solution of diisopropylamine (0.3 ml, 2.2 mmol) in tetrahydrofuran (6 mL). The mixture was stirred for 30 min at 273 K, and cooled down to 195 K. Then a solution of N-benzylnorgranatanone (0.459 g, 2.0 mmol) in tetrahydrofuran (3 mL) was added dropwise. After stirring for 90 min, benzaldehyde (0.22 ml, 2.18 mmol) was added dropwise and the mixture was stirred for another 15 min. The reaction was quenched with saturated aq. NH 4Cl (2 mL), the mixture was diluted with water (10 mL), and extracted with dichloromethane (3 × 20 mL). The combined organic extracts were dried over Na 2SO 4 and concentrated to give the crude product as a white solid (0.663 g, 99%). Crystallization from a mixed solvent system heptane/dichloromethane gave the product (0.243 g, 75%) as white crystals. Analytical sample was recrystallized from ethyl acetate. [m.p. 412–413 K, R f : 0.65 (50% ethyl acetate/hexanes); HR (MS-ESI): MNa+, found 358.1794, C 22H 25NNaO 2 requires 358.1783; 1H NMR (CDCl 3): 7.43–7.41 (m, 4H), 7.40–7.34 (m, 1H), 7.31–7.28 (m, 1H), 7.26–7.20 (m, 3H), 6.67 (s, 1H), 5.16 (d, J= 4.0 Hz, 1H), 4.04 (q, J= 12.8 Hz, 2H), 3.41 (d, J= 3.6 Hz, 1H), 3.68–3.64 (m, 1H), 2.92 (dd, J 1 = 16.2 Hz, J 2 =7.0 Hz, 1H), 2.57 (d, J= 4.0 Hz, 1H), 2.43 (d, J= 16.2 Hz, 1H), 2.19–2.13 (m, 2H), 1.65–1.62 (m, 2H), 1.37–1.32 (m, 2H)].

Refinement

All hydrogen atoms were constrained to idealized positions with C—H distances fixed at 0.95–1.00 Å and O—H distances fixed at 0.84 Å and U iso(H) = 1.5 U eq(C) for hydroxy hydrogen atom and 1.2 U eq(C) for others.

Figures

Fig. 1.

The molecular structure of the title compound. Displacement ellipsoids are drawn at the 50% probability level.

The molecular structure of the title compound. Displacement ellipsoids are drawn at the 50% probability level.
Fig. 2.

Crystal packing viewed along z-axis. Dashed lines represent hydrogen bonds. For clarity, only hydrogen atoms involved in the intermolecular interactions are shown.

Crystal packing viewed along z-axis. Dashed lines represent hydrogen bonds. For clarity, only hydrogen atoms involved in the intermolecular interactions are shown.

Crystal data

C 22H 25NO 2 F(000) = 720
M r = 335.43 D x = 1.306 Mg m 3
Monoclinic, P2 1/ c Synchrotron radiation, λ = 0.61992 Å
Hall symbol: -P 2ybc Cell parameters from 8582 reflections
a = 14.380 (3) Å θ = 2.4–31.7°
b = 9.3100 (19) Å µ = 0.08 mm 1
c = 13.270 (3) Å T = 100 K
β = 106.21 (3)° Needle, colourless
V = 1705.9 (6) Å 3 0.3 × 0.1 × 0.1 mm
Z = 4

Data collection

Mar Research MAR315 CCD diffractometer 8582 independent reflections
Radiation source: NECAT 24ID-C synchrotron beamline APS, USA 7757 reflections with I > 2σ( I)
Si111 double crystal monochromator R int = 0.046
ω scans θ max = 31.7°, θ min = 2.4°
Absorption correction: multi-scan ( SCALEPACK; Otwinowski et al., 2003) h = −24→23
T min = 0.975, T max = 0.992 k = −15→0
64629 measured reflections l = 0→22

Refinement

Refinement on F 2 Primary atom site location: structure-invariant direct methods
Least-squares matrix: full Secondary atom site location: difference Fourier map
R[ F 2 > 2σ( F 2)] = 0.040 Hydrogen site location: inferred from neighbouring sites
wR( F 2) = 0.119 H-atom parameters constrained
S = 1.03 w = 1/[σ 2( F o 2) + (0.076 P) 2 + 0.3 P] where P = ( F o 2 + 2 F c 2)/3
8582 reflections (Δ/σ) max = 0.001
227 parameters Δρ max = 0.58 e Å 3
0 restraints Δρ min = −0.30 e Å 3

Special details

Experimental. The crystal was mounted with vaseline on a pin-attached capillary. Upon mounting, the crystal was quenched to 100 K in a nitrogen-gas stream supplied by an Oxford Cryo-Jet. Diffraction data were measured at the station 24-ID—C of the APS synchrotron by rotation method.
Geometry. All e.s.d.'s 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.
Refinement. Refinement of F 2 against all reflections. The weighted R-factor wR and goodness of fit S are based on F 2, conventional R-factors R are based on F, with F set to zero for negative F 2. The threshold expression of F 2 > 2σ( F 2) is used only for calculating R-factors etc. and is not relevant to the choice of reflections for refinement. R-factors based on F 2 are statistically about twice as large as those based on F.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å 2)

x y z U iso*/ U eq
C1 0.30958 (3) 0.78442 (5) 0.11193 (4) 0.00793 (8)
H1 0.2751 0.7328 0.1570 0.010*
C2 0.36548 (3) 0.67096 (5) 0.06626 (4) 0.00840 (8)
H2 0.4214 0.6355 0.1241 0.010*
C3 0.40394 (4) 0.73073 (6) −0.02043 (4) 0.01010 (8)
O3 0.48222 (3) 0.69336 (5) −0.03110 (4) 0.01510 (8)
C4 0.33793 (4) 0.83261 (6) −0.09524 (4) 0.01142 (9)
H4A 0.2903 0.7762 −0.1489 0.014*
H4B 0.3768 0.8897 −0.1317 0.014*
C5 0.28317 (4) 0.93572 (6) −0.04151 (4) 0.01032 (8)
H5 0.2313 0.9837 −0.0976 0.012*
C6 0.34966 (4) 1.05349 (6) 0.02088 (4) 0.01288 (9)
H6A 0.3832 1.1020 −0.0254 0.015*
H6B 0.3099 1.1261 0.0443 0.015*
C7 0.42514 (4) 0.99255 (6) 0.11677 (4) 0.01233 (9)
H7A 0.4588 1.0726 0.1614 0.015*
H7B 0.4740 0.9370 0.0933 0.015*
C8 0.37747 (4) 0.89508 (6) 0.18111 (4) 0.01071 (8)
H8A 0.3402 0.9548 0.2178 0.013*
H8B 0.4284 0.8442 0.2350 0.013*
N9 0.23546 (3) 0.85037 (5) 0.02376 (3) 0.00863 (7)
C10 0.29832 (3) 0.54154 (6) 0.02123 (4) 0.00928 (8)
H10 0.2345 0.5823 −0.0194 0.011*
O10 0.33364 (3) 0.45861 (5) −0.05034 (3) 0.01360 (8)
H10A 0.3898 0.4294 −0.0203 0.020*
C11 0.27972 (3) 0.45235 (5) 0.10896 (4) 0.00883 (8)
C12 0.18961 (4) 0.45726 (6) 0.12906 (4) 0.01206 (9)
H12 0.1403 0.5180 0.0881 0.014*
C13 0.17105 (4) 0.37413 (7) 0.20856 (5) 0.01465 (10)
H13 0.1093 0.3782 0.2213 0.018*
C14 0.24272 (4) 0.28511 (6) 0.26930 (4) 0.01428 (10)
H14 0.2298 0.2270 0.3227 0.017*
C15 0.33362 (4) 0.28183 (6) 0.25111 (4) 0.01342 (9)
H15 0.3833 0.2228 0.2933 0.016*
C16 0.35203 (4) 0.36467 (6) 0.17144 (4) 0.01158 (9)
H16 0.4141 0.3616 0.1595 0.014*
C17 0.16235 (4) 0.93738 (6) 0.05545 (4) 0.01253 (9)
H17A 0.1176 0.9806 −0.0079 0.015*
H17B 0.1954 1.0166 0.1014 0.015*
C18 0.10470 (4) 0.85031 (6) 0.11268 (4) 0.01131 (9)
C19 0.13134 (4) 0.84836 (6) 0.22226 (4) 0.01282 (9)
H19 0.1831 0.9076 0.2603 0.015*
C20 0.08325 (4) 0.76093 (7) 0.27672 (5) 0.01567 (10)
H20 0.1035 0.7585 0.3512 0.019*
C21 0.00550 (4) 0.67733 (7) 0.22170 (5) 0.01794 (11)
H21 −0.0269 0.6164 0.2584 0.022*
C22 −0.02467 (4) 0.68332 (8) 0.11257 (5) 0.01934 (11)
H22 −0.0794 0.6292 0.0749 0.023*
C23 0.02508 (4) 0.76839 (7) 0.05837 (5) 0.01621 (10)
H23 0.0047 0.7707 −0.0162 0.019*

Atomic displacement parameters (Å 2)

U 11 U 22 U 33 U 12 U 13 U 23
C1 0.00930 (16) 0.00893 (19) 0.00596 (16) 0.00061 (13) 0.00280 (13) −0.00010 (13)
C2 0.00893 (16) 0.00910 (19) 0.00783 (16) −0.00015 (13) 0.00343 (13) −0.00046 (13)
C3 0.01167 (18) 0.0101 (2) 0.01030 (18) −0.00211 (14) 0.00599 (14) −0.00254 (14)
O3 0.01403 (16) 0.01532 (19) 0.01972 (19) 0.00038 (13) 0.01092 (14) −0.00186 (15)
C4 0.01423 (19) 0.0137 (2) 0.00782 (17) −0.00160 (15) 0.00560 (15) 0.00005 (15)
C5 0.01295 (18) 0.0109 (2) 0.00784 (17) −0.00003 (15) 0.00418 (14) 0.00183 (14)
C6 0.0171 (2) 0.0097 (2) 0.0129 (2) −0.00171 (16) 0.00595 (16) 0.00079 (15)
C7 0.01364 (19) 0.0116 (2) 0.01232 (19) −0.00284 (15) 0.00451 (15) −0.00222 (16)
C8 0.01263 (18) 0.0115 (2) 0.00778 (17) −0.00095 (15) 0.00251 (14) −0.00161 (14)
N9 0.00942 (15) 0.01032 (18) 0.00683 (15) 0.00179 (12) 0.00338 (12) 0.00153 (12)
C10 0.01063 (17) 0.0100 (2) 0.00774 (17) −0.00114 (14) 0.00340 (13) −0.00120 (14)
O10 0.01844 (17) 0.01365 (18) 0.01040 (15) −0.00106 (13) 0.00681 (13) −0.00429 (13)
C11 0.00996 (17) 0.00859 (19) 0.00832 (17) −0.00088 (13) 0.00316 (13) −0.00087 (13)
C12 0.01043 (18) 0.0135 (2) 0.0130 (2) −0.00065 (15) 0.00445 (15) 0.00118 (16)
C13 0.0149 (2) 0.0158 (2) 0.0156 (2) −0.00242 (17) 0.00802 (17) 0.00100 (18)
C14 0.0206 (2) 0.0125 (2) 0.01139 (19) −0.00221 (17) 0.00719 (17) 0.00027 (16)
C15 0.0181 (2) 0.0119 (2) 0.01043 (19) 0.00227 (16) 0.00425 (16) 0.00130 (16)
C16 0.01218 (18) 0.0124 (2) 0.01057 (18) 0.00178 (15) 0.00386 (14) 0.00047 (15)
C17 0.01361 (19) 0.0129 (2) 0.0126 (2) 0.00440 (16) 0.00617 (15) 0.00246 (16)
C18 0.01020 (17) 0.0139 (2) 0.01086 (18) 0.00307 (15) 0.00472 (14) 0.00007 (15)
C19 0.01191 (18) 0.0166 (2) 0.01089 (19) 0.00131 (16) 0.00477 (15) −0.00027 (16)
C20 0.0147 (2) 0.0212 (3) 0.0132 (2) 0.00182 (18) 0.00730 (17) 0.00159 (18)
C21 0.0158 (2) 0.0205 (3) 0.0214 (3) −0.00107 (19) 0.01156 (19) −0.0008 (2)
C22 0.0138 (2) 0.0253 (3) 0.0208 (3) −0.00457 (19) 0.00800 (19) −0.0067 (2)
C23 0.01207 (19) 0.0241 (3) 0.0130 (2) −0.00040 (18) 0.00449 (16) −0.00376 (19)

Geometric parameters (Å, º)

C1—N9 1.4784 (8) O10—H10A 0.8400
C1—C8 1.5353 (8) C11—C12 1.3947 (8)
C1—C2 1.5496 (7) C11—C16 1.3977 (8)
C1—H1 1.0000 C12—C13 1.3931 (8)
C2—C3 1.5147 (7) C12—H12 0.9500
C2—C10 1.5554 (8) C13—C14 1.3910 (9)
C2—H2 1.0000 C13—H13 0.9500
C3—O3 1.2236 (7) C14—C15 1.3942 (9)
C3—C4 1.5033 (8) C14—H14 0.9500
C4—C5 1.5374 (8) C15—C16 1.3924 (8)
C4—H4A 0.9900 C15—H15 0.9500
C4—H4B 0.9900 C16—H16 0.9500
C5—N9 1.4778 (7) C17—C18 1.5075 (8)
C5—C6 1.5362 (8) C17—H17A 0.9900
C5—H5 1.0000 C17—H17B 0.9900
C6—C7 1.5324 (9) C18—C23 1.3969 (9)
C6—H6A 0.9900 C18—C19 1.3966 (8)
C6—H6B 0.9900 C19—C20 1.3936 (8)
C7—C8 1.5326 (8) C19—H19 0.9500
C7—H7A 0.9900 C20—C21 1.3903 (10)
C7—H7B 0.9900 C20—H20 0.9500
C8—H8A 0.9900 C21—C22 1.3920 (10)
C8—H8B 0.9900 C21—H21 0.9500
N9—C17 1.4782 (7) C22—C23 1.3941 (9)
C10—O10 1.4232 (7) C22—H22 0.9500
C10—C11 1.5133 (7) C23—H23 0.9500
C10—H10 1.0000
N9—C1—C8 113.09 (5) O10—C10—C2 112.19 (4)
N9—C1—C2 108.16 (4) C11—C10—C2 110.71 (4)
C8—C1—C2 112.25 (4) O10—C10—H10 106.9
N9—C1—H1 107.7 C11—C10—H10 106.9
C8—C1—H1 107.7 C2—C10—H10 106.9
C2—C1—H1 107.7 C10—O10—H10A 109.5
C3—C2—C1 112.69 (4) C12—C11—C16 118.86 (5)
C3—C2—C10 108.18 (4) C12—C11—C10 120.15 (5)
C1—C2—C10 110.12 (4) C16—C11—C10 120.99 (4)
C3—C2—H2 108.6 C13—C12—C11 120.75 (5)
C1—C2—H2 108.6 C13—C12—H12 119.6
C10—C2—H2 108.6 C11—C12—H12 119.6
O3—C3—C4 122.33 (5) C14—C13—C12 120.14 (5)
O3—C3—C2 121.74 (5) C14—C13—H13 119.9
C4—C3—C2 115.87 (4) C12—C13—H13 119.9
C3—C4—C5 113.48 (4) C13—C14—C15 119.45 (5)
C3—C4—H4A 108.9 C13—C14—H14 120.3
C5—C4—H4A 108.9 C15—C14—H14 120.3
C3—C4—H4B 108.9 C16—C15—C14 120.36 (5)
C5—C4—H4B 108.9 C16—C15—H15 119.8
H4A—C4—H4B 107.7 C14—C15—H15 119.8
N9—C5—C6 112.88 (4) C15—C16—C11 120.42 (5)
N9—C5—C4 108.53 (5) C15—C16—H16 119.8
C6—C5—C4 111.92 (4) C11—C16—H16 119.8
N9—C5—H5 107.8 N9—C17—C18 112.54 (5)
C6—C5—H5 107.8 N9—C17—H17A 109.1
C4—C5—H5 107.8 C18—C17—H17A 109.1
C7—C6—C5 111.92 (5) N9—C17—H17B 109.1
C7—C6—H6A 109.2 C18—C17—H17B 109.1
C5—C6—H6A 109.2 H17A—C17—H17B 107.8
C7—C6—H6B 109.2 C23—C18—C19 118.50 (5)
C5—C6—H6B 109.2 C23—C18—C17 121.36 (5)
H6A—C6—H6B 107.9 C19—C18—C17 120.13 (5)
C6—C7—C8 111.01 (4) C20—C19—C18 121.06 (6)
C6—C7—H7A 109.4 C20—C19—H19 119.5
C8—C7—H7A 109.4 C18—C19—H19 119.5
C6—C7—H7B 109.4 C21—C20—C19 119.83 (6)
C8—C7—H7B 109.4 C21—C20—H20 120.1
H7A—C7—H7B 108.0 C19—C20—H20 120.1
C7—C8—C1 111.89 (4) C22—C21—C20 119.68 (6)
C7—C8—H8A 109.2 C22—C21—H21 120.2
C1—C8—H8A 109.2 C20—C21—H21 120.2
C7—C8—H8B 109.2 C21—C22—C23 120.25 (6)
C1—C8—H8B 109.2 C21—C22—H22 119.9
H8A—C8—H8B 107.9 C23—C22—H22 119.9
C5—N9—C1 109.70 (4) C22—C23—C18 120.58 (6)
C5—N9—C17 110.82 (4) C22—C23—H23 119.7
C1—N9—C17 114.54 (4) C18—C23—H23 119.7
O10—C10—C11 112.85 (5)

Hydrogen-bond geometry (Å, º)

D—H··· A D—H H··· A D··· A D—H··· A
O10—H10 A···O3 i 0.84 2.11 2.9298 (9) 165

Symmetry code: (i) − x+1, − y+1, − z.

References

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Figures and Tables

Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯ A D—H H⋯ A DA D—H⋯ A
O10—H10 A⋯O3 i 0.84 2.11 2.9298 (9) 165

Symmetry code: (i) e-68-o1367-efi2.jpg .