Literature DB >> 22798882

(Z,1S,10aR)-(-)-Menthyl 1-hy-droxy-1,2,3,5,6,7,10,10a-octa-hydro-pyrrolo-[1,2-a]azocine-10a-carboxyl-ate.

Daniele Muroni, Emilio Napolitano, Olivier Perez, Nicola Culeddu, Antonio Saba.   

Abstract

The structure determination confirms the stereochemistry of the title compound, C(21)H(35)NO(3), obtained as an inter-mediate in the enanti-oselective synthesis of de-oxy-nojirimicine analogs. The system contains a pyrrolo-[1,2-a]azocine backbone, which was synthesized by a domino process involving a [2,3]-sigmatropic rearrangement. The incorporation of a chiral auxiliary (-)-menthyl, whose stereocentres are not involved during the synthesis, enables the assignation of absolute configuration. The crystal structure features O-H⋯O hydrogen bonds involving the hy-droxy groups as donors and the carbonyl groups as acceptors, which link the mol-ecules into chains running along [010].

Entities:  

Year:  2012        PMID: 22798882      PMCID: PMC3394017          DOI: 10.1107/S1600536812027900

Source DB:  PubMed          Journal:  Acta Crystallogr Sect E Struct Rep Online        ISSN: 1600-5368


Related literature

For the construction of the pyrrolo­[1,2-a]azocine backbone by the domino sequence, see: Clark et al. (2001 ▶); Muroni et al. (2006 ▶). For domino processes promoted by catalytic decomposition of diazo­compounds, see: Doyle et al. (1997 ▶). For [2,3]-sigmatropic rearrangement, see: Sweeney (2009 ▶); Zhang & Wang (2010 ▶). For manzamine alkaloids and other biologically active compounds containing the pyrrolo­[1,2-a]azocine subunit, see: Rao et al. (2006 ▶); Yap et al. (2011 ▶); Sun et al. (2011 ▶). For de­oxy­nojirimicine and imino­sugars, see: Asano et al. (2000 ▶); Watson et al. (2001 ▶). For chiral auxiliary (−)-menthyl, see: Wang et al. (2006 ▶).

Experimental

Crystal data

C21H35NO3 M = 349.5 Orthorhombic, a = 10.7804 (8) Å b = 7.7938 (7) Å c = 23.8862 (17) Å V = 2006.9 (3) Å3 Z = 4 Mo Kα radiation μ = 0.08 mm−1 T = 120 K 0.36 × 0.13 × 0.13 mm

Data collection

Bruker APEXII CCD diffractometer Absorption correction: multi-scan (SADABS; Sheldrick, 2008 ▶) T min = 0.716, T max = 0.746 21709 measured reflections 3281 independent reflections 2331 reflections with I > 3σ(I) R int = 0.048

Refinement

R[F 2 > 2σ(F 2)] = 0.041 wR(F 2) = 0.047 S = 1.23 3281 reflections 230 parameters H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.23 e Å−3 Δρmin = −0.28 e Å−3 Data collection: APEX2 (Bruker, 2005 ▶); cell refinement: SAINT (Bruker, 2007 ▶); data reduction: SAINT; program(s) used to solve structure: SIR2011 (Burla et al., 2012 ▶); program(s) used to refine structure: JANA2006 (Petricek et al., 2006 ▶); molecular graphics: DIAMOND (Brandenburg & Putz, 2005 ▶) and ORTEP-3 (Farrugia, 1997 ▶); software used to prepare material for publication: publCIF (Westrip, 2010 ▶) and PLATON (Spek, 2009 ▶). Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536812027900/bh2433sup1.cif Supplementary material file. DOI: 10.1107/S1600536812027900/bh2433Isup2.cdx Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536812027900/bh2433Isup3.hkl Supplementary material file. DOI: 10.1107/S1600536812027900/bh2433Isup4.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C21H35NO3Dx = 1.156 Mg m3
Mr = 349.5Melting point: 389 K
Orthorhombic, P212121Mo Kα radiation, λ = 0.71069 Å
Hall symbol: P 2ac 2abCell parameters from 192 reflections
a = 10.7804 (8) Åθ = 3.8–17.2°
b = 7.7938 (7) ŵ = 0.08 mm1
c = 23.8862 (17) ÅT = 120 K
V = 2006.9 (3) Å3Prism, colourless
Z = 40.36 × 0.13 × 0.13 mm
F(000) = 768
Bruker APEXII CCD diffractometer3281 independent reflections
Radiation source: sealed X-ray tube2331 reflections with I > 3σ(I)
Graphite monochromatorRint = 0.048
ω scansθmax = 30.0°, θmin = 1.7°
Absorption correction: multi-scan (SADABS; Sheldrick, 2008)h = −15→14
Tmin = 0.716, Tmax = 0.746k = −10→4
21709 measured reflectionsl = −33→33
Refinement on FH atoms treated by a mixture of independent and constrained refinement
R[F2 > 2σ(F2)] = 0.041Weighting scheme based on measured s.u.'s w = 1/(σ2(F) + 0.0004F2)
wR(F2) = 0.047(Δ/σ)max = 0.016
S = 1.23Δρmax = 0.23 e Å3
3281 reflectionsΔρmin = −0.28 e Å3
230 parametersExtinction correction: B-C type 1 Gaussian isotropic
0 restraintsExtinction coefficient: 16900 (1800)
0 constraints
xyzUiso*/Ueq
N10.67923 (4)0.06933 (14)0.867458 (19)0.0178 (4)
C40.67762 (4)−0.11800 (4)0.865956 (9)0.0220 (5)
C50.80174 (3)−0.19770 (3)0.849823 (11)0.0257 (6)
C60.83930 (2)−0.17312 (6)0.788428 (13)0.0300 (6)
C70.87823 (6)0.0057 (2)0.77279 (3)0.0269 (6)
C80.80364 (17)0.13680 (12)0.76224 (5)0.0248 (6)
C90.66451 (6)0.12758 (8)0.76547 (3)0.0217 (5)
C100.61339 (12)0.16447 (13)0.82487 (7)0.0164 (5)
C10.63656 (4)0.35106 (14)0.84420 (7)0.0191 (5)
O10.54447 (13)0.46881 (18)0.82643 (6)0.0257 (4)
C20.63894 (2)0.34119 (7)0.90814 (3)0.0217 (5)
C30.67015 (2)0.15400 (4)0.92186 (3)0.0210 (5)
C110.47217 (16)0.1302 (2)0.82373 (7)0.0164 (5)
O20.41170 (12)0.10136 (18)0.78189 (5)0.0266 (4)
O30.42289 (10)0.13359 (17)0.87513 (5)0.0182 (4)
C120.28911 (11)0.1047 (2)0.88055 (3)0.0181 (5)
C170.22301 (3)0.27715 (11)0.880303 (16)0.0229 (6)
C160.08230 (4)0.24991 (5)0.88606 (2)0.0268 (6)
C210.01309 (2)0.42102 (2)0.886679 (15)0.0438 (8)
C150.05454 (3)0.14406 (3)0.93799 (2)0.0280 (6)
C140.12697 (3)−0.02306 (5)0.940244 (13)0.0253 (6)
C130.26755 (15)0.00578 (9)0.93465 (2)0.0188 (5)
C180.34514 (5)−0.16029 (4)0.93837 (3)0.0251 (6)
C200.32327 (3)−0.25601 (4)0.993247 (7)0.0414 (8)
C190.32833 (4)−0.27844 (2)0.888694 (8)0.0426 (8)
H4a0.614688−0.1561110.8403840.0264*
H4b0.6521−0.1613510.9017680.0264*
H5a0.800812−0.3179010.8585910.0309*
H5b0.865733−0.1532070.8737030.0309*
H6b0.904465−0.2521270.7791730.036*
H6a0.772558−0.2091880.7645650.036*
H7a0.9657490.0270440.770190.0323*
H8a0.8406560.2442580.751910.0298*
H9a0.6372410.0162920.7534170.0261*
H9b0.6290270.2073040.7393490.0261*
H1a0.7121040.3934890.8280430.023*
H2a0.5582550.3685560.9226150.0261*
H2b0.7032410.4145690.922270.0261*
H3b0.7490010.1488240.9404590.0251*
H3a0.6034360.1040840.942920.0251*
H12a0.2565290.0389410.8499220.0217*
H17b0.240250.3358030.8458290.0275*
H17a0.252350.345550.9109930.0275*
H16a0.0532480.18750.8539870.0322*
H21a0.0327390.484410.8533790.0526*
H21c−0.0746140.4001510.8880790.0526*
H21b0.0376790.4859980.918970.0526*
H15b−0.0326950.119830.9396460.0336*
H15a0.0722450.2107930.9708140.0336*
H14a0.099119−0.0977750.9108670.0303*
H14b0.10981−0.0808070.9748890.0303*
H13a0.2963570.0712570.966110.0225*
H18a0.430002−0.1230460.9375750.0302*
H20a0.33419−0.1785791.0241120.0496*
H20c0.240371−0.3009480.9937760.0496*
H20b0.381516−0.3486970.9963620.0496*
H19a0.34236−0.2155560.8547210.0512*
H19c0.386534−0.3713570.891130.0512*
H19b0.245414−0.323380.888710.0512*
H1o0.556 (2)0.499 (3)0.7944 (9)0.0309*
U11U22U33U12U13U23
N10.0178 (7)0.0180 (8)0.0174 (7)0.0028 (6)−0.0002 (6)0.0006 (6)
C40.0200 (9)0.0191 (10)0.0268 (10)0.0010 (7)−0.0007 (8)0.0041 (8)
C50.0218 (10)0.0180 (10)0.0374 (11)0.0050 (7)−0.0012 (8)−0.0013 (9)
C60.0215 (10)0.0320 (12)0.0364 (11)0.0038 (9)0.0023 (9)−0.0108 (10)
C70.0169 (9)0.0376 (12)0.0263 (10)−0.0026 (8)0.0056 (8)−0.0079 (10)
C80.0239 (9)0.0303 (11)0.0203 (9)−0.0050 (9)0.0069 (8)−0.0030 (9)
C90.0211 (9)0.0252 (10)0.0189 (9)0.0016 (8)0.0046 (7)−0.0009 (8)
C100.0148 (8)0.0183 (9)0.0162 (8)0.0005 (7)0.0025 (7)0.0033 (8)
C10.0180 (8)0.0179 (9)0.0215 (9)0.0000 (7)0.0040 (7)0.0033 (8)
O10.0307 (7)0.0224 (7)0.0241 (7)0.0078 (6)0.0055 (6)0.0083 (6)
C20.0214 (9)0.0205 (10)0.0232 (9)−0.0018 (8)0.0017 (7)−0.0020 (8)
C30.0173 (9)0.0263 (10)0.0193 (9)0.0007 (8)−0.0017 (7)0.0004 (8)
C110.0193 (8)0.0142 (9)0.0159 (8)0.0040 (7)0.0016 (7)0.0014 (8)
O20.0197 (6)0.0408 (9)0.0192 (7)0.0014 (6)−0.0014 (5)−0.0028 (6)
O30.0139 (6)0.0243 (7)0.0164 (6)−0.0016 (5)0.0022 (5)0.0009 (6)
C120.0132 (8)0.0227 (10)0.0184 (9)−0.0017 (7)0.0015 (6)−0.0005 (8)
C170.0226 (9)0.0239 (11)0.0223 (10)0.0032 (8)0.0007 (8)0.0037 (8)
C160.0189 (9)0.0340 (12)0.0276 (11)0.0040 (9)−0.0018 (8)0.0000 (9)
C210.0283 (11)0.0506 (16)0.0527 (15)0.0167 (11)0.0056 (10)0.0170 (13)
C150.0183 (9)0.0321 (12)0.0336 (11)0.0022 (9)0.0067 (8)−0.0013 (10)
C140.0189 (9)0.0251 (11)0.0318 (11)−0.0023 (8)0.0052 (8)0.0000 (9)
C130.0177 (8)0.0202 (10)0.0185 (9)−0.0009 (7)0.0014 (7)−0.0001 (8)
C180.0202 (9)0.0203 (10)0.0348 (11)0.0020 (8)0.0071 (8)0.0055 (9)
C200.0396 (13)0.0359 (13)0.0485 (13)0.0092 (11)0.0061 (11)0.0186 (11)
C190.0566 (16)0.0222 (12)0.0492 (14)0.0067 (11)0.0135 (12)−0.0031 (10)
N1—C41.4605 (11)C11—O31.338 (2)
N1—C101.4450 (16)O3—C121.4654 (16)
N1—C31.4607 (9)C12—C171.5209 (17)
C4—C51.5247 (5)C12—C131.5228 (11)
C4—H4a0.9600C12—H12a0.9600
C4—H4b0.9600C17—C161.5379 (6)
C5—C61.5335 (4)C17—H17b0.9600
C5—H5a0.9600C17—H17a0.9600
C5—H5b0.9600C16—C211.5282 (4)
C6—C71.5029 (18)C16—C151.5195 (7)
C6—H6b0.9600C16—H16a0.9600
C6—H6a0.9600C21—H21a0.9600
C7—C81.324 (2)C21—H21c0.9600
C7—H7a0.9600C21—H21b0.9600
C8—C91.5035 (19)C15—C141.5196 (5)
C8—H8a0.9600C15—H15b0.9600
C9—C101.5492 (17)C15—H15a0.9600
C9—H9a0.9600C14—C131.5379 (16)
C9—H9b0.9600C14—H14a0.9600
C10—C11.5461 (16)C14—H14b0.9600
C10—C111.546 (2)C13—C181.5436 (11)
C1—O11.4169 (17)C13—H13a0.9600
C1—C21.5294 (18)C18—C201.5266 (6)
C1—H1a0.9600C18—C191.5128 (6)
O1—H1o0.81 (2)C18—H18a0.9600
C2—C31.5327 (6)C20—H20a0.9600
C2—H2a0.9600C20—H20c0.9600
C2—H2b0.9600C20—H20b0.9600
C3—H3b0.9600C19—H19a0.9600
C3—H3a0.9600C19—H19c0.9600
C11—O21.214 (2)C19—H19b0.9600
C4—N1—C10119.33 (6)C11—O3—C12117.97 (11)
C4—N1—C3118.20 (5)O3—C12—C17108.98 (11)
C10—N1—C3111.19 (8)O3—C12—C13107.64 (10)
N1—C4—C5113.76 (3)O3—C12—H12a112.00
N1—C4—H4a109.47C17—C12—C13112.28 (7)
N1—C4—H4b109.47C17—C12—H12a107.00
C5—C4—H4a109.47C13—C12—H12a109.00
C5—C4—H4b109.47C12—C17—C16109.87 (7)
H4a—C4—H4b105.00C12—C17—H17b109.47
C4—C5—C6115.00 (2)C12—C17—H17a109.47
C4—C5—H5a109.47C16—C17—H17b109.47
C4—C5—H5b109.47C16—C17—H17a109.47
C6—C5—H5a109.47H17b—C17—H17a109.00
C6—C5—H5b109.47C17—C16—C21111.22 (4)
H5a—C5—H5b103.00C17—C16—C15110.02 (4)
C5—C6—C7115.30 (4)C17—C16—H16a109.00
C5—C6—H6b109.47C21—C16—C15111.69 (4)
C5—C6—H6a109.47C21—C16—H16a107.00
C7—C6—H6b109.47C15—C16—H16a108.00
C7—C6—H6a109.47C16—C21—H21a109.47
H6b—C6—H6a103.00C16—C21—H21c109.47
C6—C7—C8126.38 (9)C16—C21—H21b109.47
C6—C7—H7a117.00H21a—C21—H21c109.00
C8—C7—H7a117.00H21a—C21—H21b109.00
C7—C8—C9124.00 (10)H21c—C21—H21b109.47
C7—C8—H8a118.00C16—C15—C14113.14 (3)
C9—C8—H8a118.00C16—C15—H15b109.00
C8—C9—C10113.14 (8)C16—C15—H15a109.47
C8—C9—H9a109.47C14—C15—H15b109.47
C8—C9—H9b109.47C14—C15—H15a109.47
C10—C9—H9a109.47H15b—C15—H15a106.00
C10—C9—H9b109.47C15—C14—C13112.21 (4)
H9a—C9—H9b105.53C15—C14—H14a109.47
N1—C10—C9112.01 (8)C15—C14—H14b109.47
N1—C10—C1101.14 (11)C13—C14—H14a109.47
N1—C10—C11114.03 (11)C13—C14—H14b109.47
C9—C10—C1112.99 (10)H14a—C14—H14b107.00
C9—C10—C11107.60 (11)C12—C13—C14107.36 (9)
C1—C10—C11109.07 (10)C12—C13—C18113.00 (9)
C10—C1—O1114.00 (10)C12—C13—H13a110.00
C10—C1—C2104.69 (10)C14—C13—C18113.97 (6)
C10—C1—H1a110.00C14—C13—H13a109.00
O1—C1—C2110.07 (10)C18—C13—H13a103.00
O1—C1—H1a105.00C13—C18—C20112.05 (5)
C2—C1—H1a114.00C13—C18—C19113.60 (5)
C1—O1—H1o111.1 (16)C13—C18—H18a105.00
C1—C2—C3105.37 (6)C20—C18—C19110.95 (2)
C1—C2—H2a109.47C20—C18—H18a108.00
C1—C2—H2b109.47C19—C18—H18a106.00
C3—C2—H2a109.47C18—C20—H20a109.47
C3—C2—H2b109.47C18—C20—H20c109.47
H2a—C2—H2b113.00C18—C20—H20b109.47
N1—C3—C2104.74 (6)H20a—C20—H20c109.47
N1—C3—H3b109.47H20a—C20—H20b109.47
N1—C3—H3a109.47H20c—C20—H20b109.47
C2—C3—H3b109.47C18—C19—H19a109.47
C2—C3—H3a109.47C18—C19—H19c109.47
H3b—C3—H3a114.00C18—C19—H19b109.47
C10—C11—O2125.10 (15)H19a—C19—H19c109.47
C10—C11—O3111.82 (14)H19a—C19—H19b109.47
O2—C11—O3123.07 (16)H19c—C19—H19b109.00
D—H···AD—HH···AD···AD—H···A
O1—H1o···O2i0.81 (2)2.02 (2)2.8259 (19)174 (2)
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A D—HH⋯A DA D—H⋯A
O1—H1o⋯O2i 0.81 (2)2.02 (2)2.8259 (19)174 (2)

Symmetry code: (i) .

  6 in total

Review 1.  Polyhydroxylated alkaloids -- natural occurrence and therapeutic applications.

Authors:  A A Watson; G W Fleet; N Asano; R J Molyneux; R J Nash
Journal:  Phytochemistry       Date:  2001-02       Impact factor: 4.072

2.  Manzamine B and E and ircinal A related alkaloids from an Indonesian Acanthostrongylophora sponge and their activity against infectious, tropical parasitic, and Alzheimer's diseases.

Authors:  Karumanchi V Rao; Marwa S Donia; Jiangnan Peng; Esther Garcia-Palomero; Diana Alonso; Ana Martinez; Miguel Medina; Scott G Franzblau; Babu L Tekwani; Shabana I Khan; Subagus Wahyuono; Kristine L Willett; Mark T Hamann
Journal:  J Nat Prod       Date:  2006-07       Impact factor: 4.050

3.  Sigmatropic rearrangements of 'onium' ylids.

Authors:  J B Sweeney
Journal:  Chem Soc Rev       Date:  2009-03-05       Impact factor: 54.564

4.  Grandilodines A-C, biologically active indole alkaloids from Kopsia grandifolia.

Authors:  Wai-Sum Yap; Chew-Yan Gan; Yun-Yee Low; Yeun-Mun Choo; Tadahiro Etoh; Masahiko Hayashi; Kanki Komiyama; Toh-Seok Kam
Journal:  J Nat Prod       Date:  2011-03-23       Impact factor: 4.050

5.  Potent bivalent Smac mimetics: effect of the linker on binding to inhibitor of apoptosis proteins (IAPs) and anticancer activity.

Authors:  Haiying Sun; Liu Liu; Jianfeng Lu; Longchuan Bai; Xiaoqin Li; Zaneta Nikolovska-Coleska; Donna McEachern; Chao-Yie Yang; Su Qiu; Han Yi; Duxin Sun; Shaomeng Wang
Journal:  J Med Chem       Date:  2011-04-13       Impact factor: 7.446

6.  Structure validation in chemical crystallography.

Authors:  Anthony L Spek
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-01-20
  6 in total

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