Literature DB >> 24860292

A P212121 polymorph of (+)-clusianone.

Sree Vaneesa Nagalingam1, Janet Wong Pik Ching1, Mohammed Khaled Bin Break2, M Ibrahim M Tahir3, Teng-Jin Khoo1.   

Abstract

The title compound, C33H42O4 [systematic name: (1S,5S,7R)-3-benzoyl-4-hy-droxy-8,8-dimethyl-1,5,7-tris-(3-methyl-but-2--enyl)bi-cyclo-[3.3.1]nona-3-ene-2,9-dione], has a central bi-cyclo-[3.3.1]nonane-2,4,9-trione surrounded by tetra-prenyl-ated and benzoyl groups. The compound was recrystallized several times in methanol using both a slow evaporation method and with a crystal-seeding technique. This subsequently produced diffraction-quality crystals which crystallize in the ortho-rhom-bic space group P212121, in contrast to a previous report of a structure determination in the Pna21 space group [McCandlish et al. (1976 ▶). Acta Cryst. B32, 1793-1801]. The title compound has a melting point of 365-366 K, and a specific rotation [α](20) value of +51.94°. A strong intra-molecular O-H⋯O hydrogen bond is noted. In the crystal, mol-ecules are assembled in the ab plane by weak C-H⋯O inter-actions.

Entities:  

Year:  2013        PMID: 24860292      PMCID: PMC4004436          DOI: 10.1107/S1600536813031036

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


Related literature

For related structural studies, see: McCandlish et al. (1976 ▶); Santos et al. (1998 ▶, 2001 ▶). For background to Clusiaceae metabolites, see: Monache et al. (1991 ▶); de Oliveira et al. (1996 ▶). For discussion of polycyclic polyprenylated acyl­phloroglucinols, including their biological properties, see: Piccinelli et al. (2005 ▶); Garnsey et al. (2011 ▶); Simpkins (2013 ▶).

Experimental

Crystal data

C33H42O4 M = 502.69 Orthorhombic, a = 9.2035 (2) Å b = 13.4629 (2) Å c = 22.9607 (5) Å V = 2844.96 (10) Å3 Z = 4 Cu Kα radiation μ = 0.59 mm−1 T = 100 K 0.21 × 0.14 × 0.08 mm

Data collection

Oxford Diffraction Gemini diffractometer Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2002 ▶) T min = 0.86, T max = 0.95 39826 measured reflections 5498 independent reflections 5269 reflections with I > 2.0σ(I) R int = 0.034

Refinement

R[F 2 > 2σ(F 2)] = 0.034 wR(F 2) = 0.084 S = 0.96 5498 reflections 335 parameters H-atom parameters constrained Δρmax = 0.24 e Å−3 Δρmin = −0.18 e Å−3 Absolute structure: Flack (1983 ▶), 2383 Friedel pairs Absolute structure parameter: −0.04 (15) Data collection: CrysAlis PRO (Agilent, 2011 ▶); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SUPERFLIP (Palatinus & Chapuis, 2007 ▶); program(s) used to refine structure: CRYSTALS (Betteridge et al., 2003 ▶; Cooper et al., 2010 ▶); molecular graphics: CAMERON (Watkin et al., 1996 ▶) and Mercury (Macrae et al., 2006 ▶); software used to prepare material for publication: publCIF (Westrip, 2010 ▶). Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536813031036/tk5270sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536813031036/tk5270Isup2.hkl Click here for additional data file. Supplementary material file. DOI: 10.1107/S1600536813031036/tk5270Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C33H42O4Dx = 1.174 Mg m3
Mr = 502.69Melting point: 365 K
Orthorhombic, P212121Cu Kα radiation, λ = 1.54180 Å
Hall symbol: P 2ac 2abCell parameters from 19011 reflections
a = 9.2035 (2) Åθ = 3–71°
b = 13.4629 (2) ŵ = 0.59 mm1
c = 22.9607 (5) ÅT = 100 K
V = 2844.96 (10) Å3Prismatic, colourless
Z = 40.21 × 0.14 × 0.08 mm
F(000) = 1088
Oxford Diffraction Gemini diffractometer5498 independent reflections
Radiation source: Cu Ka5269 reflections with I > 2.0σ(I)
Graphite monochromatorRint = 0.034
ω scansθmax = 71.6°, θmin = 3.8°
Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2002)h = −11→11
Tmin = 0.86, Tmax = 0.95k = −16→16
39826 measured reflectionsl = −28→28
Refinement on F2Hydrogen site location: difference Fourier map
Least-squares matrix: fullH-atom parameters constrained
R[F2 > 2σ(F2)] = 0.034 Method = Modified Sheldrick w = 1/[σ2(F2) + ( 0.04P)2 + 1.02P] , where P = (max(Fo2,0) + 2Fc2)/3
wR(F2) = 0.084(Δ/σ)max = 0.001
S = 0.96Δρmax = 0.24 e Å3
5498 reflectionsΔρmin = −0.18 e Å3
335 parametersAbsolute structure: Flack (1983), 2383 Friedel pairs
0 restraintsAbsolute structure parameter: −0.04 (15)
Primary atom site location: other
Experimental. The crystal was placed in the cold stream of an Oxford Cryosystems open-flow nitrogen cryostat with a nominal stability of 0.1 K.
xyzUiso*/Ueq
O11.01156 (11)0.23087 (8)0.70014 (5)0.0254
H10.99760.33860.71230.0500*
C20.89022 (15)0.21427 (11)0.67631 (6)0.0196
C30.87580 (15)0.11723 (10)0.64619 (6)0.0196
C40.81066 (17)0.10926 (12)0.59161 (7)0.0252
C50.81469 (18)0.01993 (13)0.56225 (7)0.0333
C60.87951 (19)−0.06283 (13)0.58714 (8)0.0364
C70.94348 (19)−0.05514 (12)0.64160 (8)0.0338
C80.94353 (17)0.03472 (11)0.67054 (7)0.0260
C90.78010 (15)0.29113 (10)0.67650 (6)0.0189
C100.82224 (15)0.38637 (11)0.69421 (6)0.0200
O110.95023 (11)0.40387 (7)0.71561 (4)0.0244
C120.72277 (16)0.47533 (10)0.69123 (6)0.0207
C130.60033 (16)0.45383 (10)0.64825 (6)0.0204
O140.56632 (12)0.51181 (7)0.61064 (5)0.0285
C150.51798 (15)0.35827 (10)0.66056 (6)0.0198
C160.62421 (15)0.26982 (10)0.66719 (6)0.0187
O170.57659 (11)0.18581 (7)0.66667 (5)0.0232
C180.43562 (16)0.37607 (10)0.72158 (6)0.0215
C190.55121 (16)0.40042 (10)0.76906 (6)0.0211
C200.64960 (16)0.48756 (11)0.75201 (6)0.0220
C210.48510 (17)0.42104 (11)0.83005 (7)0.0255
C220.59687 (18)0.41885 (11)0.87765 (7)0.0268
C230.61287 (19)0.35035 (12)0.91878 (7)0.0297
C240.7280 (2)0.36145 (15)0.96492 (8)0.0415
C250.5211 (2)0.25871 (14)0.92400 (9)0.0454
C260.32752 (17)0.46277 (12)0.71414 (7)0.0286
C270.35104 (16)0.28311 (12)0.73993 (7)0.0275
C280.41309 (16)0.33433 (10)0.60982 (6)0.0227
C290.48887 (16)0.31514 (11)0.55260 (7)0.0234
C300.48971 (16)0.23037 (11)0.52250 (6)0.0235
C310.41774 (19)0.13577 (11)0.54147 (7)0.0297
C320.56841 (18)0.22262 (12)0.46514 (7)0.0286
C330.80586 (17)0.57064 (11)0.67524 (6)0.0238
C340.90501 (18)0.55841 (11)0.62358 (6)0.0269
C351.03353 (17)0.60074 (10)0.61558 (6)0.0242
C361.10148 (18)0.67277 (11)0.65730 (7)0.0283
C371.1235 (2)0.57708 (12)0.56262 (7)0.0336
H410.76290.16480.57470.0322*
H510.77200.01540.52450.0408*
H610.8767−0.12390.56620.0448*
H710.9882−0.11200.66030.0423*
H810.98880.04100.70730.0323*
H1910.61410.34130.77390.0240*
H2010.72850.49390.78140.0255*
H2020.59480.54920.75150.0250*
H2110.44040.48550.82980.0302*
H2120.40980.37240.83760.0308*
H2210.66500.47240.87830.0333*
H2410.78080.42520.96040.0629*
H2420.68260.35871.00290.0630*
H2430.79680.30640.96240.0633*
H2510.47740.25710.96260.0712*
H2520.44050.25580.89750.0712*
H2530.57830.19960.92030.0711*
H2610.24890.44600.68690.0435*
H2620.37260.52280.70090.0443*
H2630.27930.47600.75160.0424*
H2710.28270.29890.77200.0415*
H2720.41330.23000.75290.0415*
H2730.29350.25880.70650.0413*
H2810.34880.39130.60460.0275*
H2820.35280.27900.62140.0274*
H2910.54150.36990.53690.0295*
H3110.34500.11610.51210.0463*
H3120.36410.14210.57850.0443*
H3130.48820.08120.54620.0471*
H3210.50280.19780.43550.0443*
H3220.65300.17810.46870.0436*
H3230.60610.28780.45170.0438*
H3310.86190.59020.70930.0268*
H3320.73550.62250.66830.0297*
H3410.86820.51500.59370.0329*
H3611.13710.73250.63790.0438*
H3621.18840.64360.67530.0454*
H3631.03910.69260.68770.0428*
H3711.14240.63550.53920.0501*
H3721.07930.52840.53730.0518*
H3731.21860.55200.57390.0518*
U11U22U33U12U13U23
O10.0188 (5)0.0295 (5)0.0279 (5)0.0028 (4)−0.0055 (4)−0.0029 (4)
C20.0186 (7)0.0247 (7)0.0157 (6)−0.0013 (6)0.0009 (5)0.0033 (5)
C30.0143 (6)0.0228 (7)0.0216 (7)0.0013 (6)0.0031 (5)0.0010 (5)
C40.0223 (7)0.0281 (8)0.0250 (7)0.0033 (6)−0.0014 (6)−0.0008 (6)
C50.0277 (8)0.0415 (9)0.0307 (8)0.0014 (7)−0.0041 (7)−0.0124 (7)
C60.0330 (9)0.0281 (8)0.0480 (10)0.0050 (7)0.0038 (8)−0.0156 (7)
C70.0331 (9)0.0251 (7)0.0432 (9)0.0107 (7)0.0017 (7)0.0014 (7)
C80.0231 (7)0.0299 (8)0.0251 (7)0.0045 (6)−0.0002 (6)0.0012 (6)
C90.0199 (7)0.0209 (7)0.0160 (6)0.0006 (5)0.0006 (5)0.0015 (5)
C100.0192 (6)0.0250 (7)0.0157 (6)−0.0026 (6)0.0016 (5)0.0013 (5)
O110.0215 (5)0.0246 (5)0.0270 (5)−0.0021 (4)−0.0028 (4)−0.0040 (4)
C120.0222 (7)0.0186 (7)0.0215 (7)−0.0026 (5)0.0020 (6)−0.0015 (5)
C130.0213 (7)0.0186 (6)0.0214 (7)0.0034 (6)0.0024 (6)−0.0028 (5)
O140.0349 (6)0.0215 (5)0.0291 (6)0.0015 (4)−0.0056 (5)0.0039 (4)
C150.0170 (6)0.0196 (6)0.0227 (7)0.0005 (5)−0.0002 (5)−0.0006 (5)
C160.0194 (6)0.0199 (6)0.0169 (6)0.0011 (5)0.0005 (5)−0.0007 (5)
O170.0195 (5)0.0185 (5)0.0318 (6)−0.0007 (4)0.0004 (4)−0.0005 (4)
C180.0181 (7)0.0214 (7)0.0248 (7)0.0010 (6)0.0026 (6)−0.0010 (5)
C190.0213 (7)0.0179 (6)0.0242 (7)0.0021 (5)0.0028 (6)−0.0005 (5)
C200.0236 (7)0.0200 (7)0.0223 (7)0.0000 (6)0.0018 (6)−0.0023 (5)
C210.0270 (7)0.0222 (7)0.0272 (7)0.0026 (6)0.0057 (6)−0.0009 (6)
C220.0305 (8)0.0241 (7)0.0259 (7)−0.0004 (6)0.0081 (6)−0.0059 (6)
C230.0340 (8)0.0285 (8)0.0267 (8)0.0077 (7)0.0078 (7)−0.0029 (6)
C240.0491 (11)0.0477 (10)0.0278 (9)0.0143 (9)0.0009 (8)−0.0037 (8)
C250.0507 (12)0.0352 (10)0.0503 (11)0.0003 (9)0.0050 (10)0.0126 (8)
C260.0232 (7)0.0291 (8)0.0335 (8)0.0066 (6)0.0013 (7)−0.0016 (7)
C270.0225 (8)0.0293 (8)0.0306 (8)−0.0031 (6)0.0043 (6)−0.0013 (7)
C280.0178 (7)0.0214 (6)0.0290 (8)0.0030 (5)−0.0052 (6)−0.0002 (6)
C290.0196 (7)0.0252 (7)0.0254 (7)−0.0011 (6)−0.0056 (6)0.0039 (6)
C300.0187 (7)0.0283 (7)0.0235 (7)0.0022 (6)−0.0060 (6)0.0012 (6)
C310.0312 (8)0.0258 (7)0.0322 (8)0.0000 (7)0.0025 (7)−0.0028 (6)
C320.0283 (8)0.0328 (8)0.0247 (7)−0.0003 (7)−0.0015 (6)0.0001 (6)
C330.0282 (8)0.0199 (7)0.0232 (7)−0.0041 (6)0.0019 (6)−0.0015 (6)
C340.0381 (9)0.0209 (6)0.0217 (7)−0.0045 (6)0.0022 (7)−0.0021 (6)
C350.0327 (8)0.0173 (6)0.0227 (7)0.0020 (6)0.0033 (6)0.0028 (5)
C360.0280 (8)0.0250 (7)0.0317 (8)−0.0024 (6)0.0034 (6)−0.0012 (6)
C370.0409 (9)0.0267 (8)0.0332 (9)−0.0057 (7)0.0124 (8)−0.0030 (6)
O1—C21.2635 (17)C23—C241.506 (3)
H1—O110.984C23—C251.500 (3)
C2—C31.4842 (19)C24—H2410.992
C2—C91.448 (2)C24—H2420.968
C3—C41.393 (2)C24—H2430.977
C3—C81.391 (2)C25—H2510.974
C4—C51.379 (2)C25—H2520.960
C4—H410.950C25—H2530.958
C5—C61.387 (3)C26—H2610.983
C5—H510.953C26—H2620.958
C6—C71.386 (3)C26—H2630.984
C6—H610.953C27—H2710.992
C7—C81.380 (2)C27—H2720.964
C7—H710.969C27—H2730.988
C8—H810.945C28—C291.510 (2)
C9—C101.400 (2)C28—H2810.975
C9—C161.479 (2)C28—H2820.967
C10—O111.2979 (17)C29—C301.334 (2)
C10—C121.509 (2)C29—H2910.953
C12—C131.526 (2)C30—C311.500 (2)
C12—C201.5582 (19)C30—C321.507 (2)
C12—C331.5381 (19)C31—H3110.987
C13—O141.2054 (18)C31—H3120.987
C13—C151.5198 (19)C31—H3130.986
C15—C161.5482 (19)C32—H3210.969
C15—C181.6110 (19)C32—H3220.986
C15—C281.5469 (19)C32—H3230.993
C16—O171.2131 (17)C33—C341.506 (2)
C18—C191.558 (2)C33—H3310.973
C18—C261.543 (2)C33—H3320.966
C18—C271.533 (2)C34—C351.326 (2)
C19—C201.5328 (19)C34—H3410.964
C19—C211.552 (2)C35—C361.500 (2)
C19—H1910.990C35—C371.505 (2)
C20—H2010.994C36—H3610.977
C20—H2020.971C36—H3620.982
C21—C221.501 (2)C36—H3630.943
C21—H2110.961C37—H3710.969
C21—H2120.969C37—H3720.966
C22—C231.328 (2)C37—H3730.973
C22—H2210.955
O1—C2—C3115.88 (13)C22—C23—C25124.43 (16)
O1—C2—C9119.39 (13)C24—C23—C25114.94 (15)
C3—C2—C9124.59 (12)C23—C24—H241110.9
C2—C3—C4121.69 (13)C23—C24—H242109.1
C2—C3—C8118.39 (13)H241—C24—H242109.8
C4—C3—C8119.53 (14)C23—C24—H243109.8
C3—C4—C5119.68 (15)H241—C24—H243109.4
C3—C4—H41120.4H242—C24—H243107.7
C5—C4—H41119.9C23—C25—H251108.9
C4—C5—C6120.70 (15)C23—C25—H252114.7
C4—C5—H51119.3H251—C25—H252104.9
C6—C5—H51120.0C23—C25—H253111.5
C5—C6—C7119.63 (15)H251—C25—H253106.8
C5—C6—H61118.2H252—C25—H253109.5
C7—C6—H61122.1C18—C26—H261111.8
C6—C7—C8120.00 (15)C18—C26—H262113.2
C6—C7—H71121.4H261—C26—H262108.1
C8—C7—H71118.6C18—C26—H263109.3
C3—C8—C7120.41 (14)H261—C26—H263105.5
C3—C8—H81119.0H262—C26—H263108.7
C7—C8—H81120.6C18—C27—H271110.6
C2—C9—C10117.48 (13)C18—C27—H272112.9
C2—C9—C16122.67 (13)H271—C27—H272107.8
C10—C9—C16119.24 (13)C18—C27—H273109.2
C9—C10—O11121.85 (13)H271—C27—H273108.0
C9—C10—C12123.08 (13)H272—C27—H273108.3
O11—C10—C12115.06 (12)C15—C28—C29113.75 (11)
H1—O11—C10102.2C15—C28—H281107.9
C10—C12—C13109.07 (11)C29—C28—H281107.9
C10—C12—C20107.79 (11)C15—C28—H282108.1
C13—C12—C20106.27 (11)C29—C28—H282111.9
C10—C12—C33111.80 (12)H281—C28—H282107.0
C13—C12—C33111.78 (12)C28—C29—C30126.86 (14)
C20—C12—C33109.91 (11)C28—C29—H291115.6
C12—C13—O14122.17 (13)C30—C29—H291117.5
C12—C13—C15114.12 (11)C29—C30—C31124.98 (14)
O14—C13—C15123.50 (13)C29—C30—C32120.98 (14)
C13—C15—C16110.76 (11)C31—C30—C32114.03 (13)
C13—C15—C18105.69 (11)C30—C31—H311109.2
C16—C15—C18109.03 (11)C30—C31—H312113.4
C13—C15—C28110.33 (11)H311—C31—H312105.8
C16—C15—C28107.93 (11)C30—C31—H313112.0
C18—C15—C28113.10 (11)H311—C31—H313108.7
C15—C16—C9118.54 (12)H312—C31—H313107.4
C15—C16—O17119.21 (13)C30—C32—H321109.7
C9—C16—O17122.20 (13)C30—C32—H322110.4
C15—C18—C19108.57 (11)H321—C32—H322110.0
C15—C18—C26108.64 (12)C30—C32—H323112.3
C19—C18—C26111.01 (12)H321—C32—H323107.7
C15—C18—C27110.89 (12)H322—C32—H323106.7
C19—C18—C27109.04 (12)C12—C33—C34113.47 (12)
C26—C18—C27108.70 (12)C12—C33—H331107.3
C18—C19—C20112.70 (11)C34—C33—H331110.0
C18—C19—C21113.66 (12)C12—C33—H332108.0
C20—C19—C21108.97 (11)C34—C33—H332110.8
C18—C19—H191108.0H331—C33—H332107.0
C20—C19—H191107.4C33—C34—C35127.09 (14)
C21—C19—H191105.7C33—C34—H341114.5
C19—C20—C12113.78 (11)C35—C34—H341118.4
C19—C20—H201108.9C34—C35—C36124.15 (14)
C12—C20—H201107.5C34—C35—C37120.78 (14)
C19—C20—H202110.5C36—C35—C37115.06 (14)
C12—C20—H202107.7C35—C36—H361112.4
H201—C20—H202108.2C35—C36—H362110.5
C19—C21—C22112.63 (12)H361—C36—H362104.3
C19—C21—H211108.9C35—C36—H363113.8
C22—C21—H211108.4H361—C36—H363108.0
C19—C21—H212108.7H362—C36—H363107.3
C22—C21—H212110.3C35—C37—H371112.1
H211—C21—H212107.8C35—C37—H372113.5
C21—C22—C23127.39 (15)H371—C37—H372106.9
C21—C22—H221116.5C35—C37—H373110.7
C23—C22—H221116.1H371—C37—H373105.5
C22—C23—C24120.62 (16)H372—C37—H373107.6
D—H···AD—HH···AD···AD—H···A
O11—H1···O10.981.482.4227 (14)158
C27—H273···O1i0.992.633.330 (2)128
C36—H363···O1ii0.942.673.523 (2)151
C8—H81···O11iii0.952.623.300 (2)129
C21—H211···O17iv0.962.703.610 (2)158
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A D—HH⋯A DA D—H⋯A
O11—H1⋯O10.981.482.4227 (14)158
C27—H273⋯O1i 0.992.633.330 (2)128
C36—H363⋯O1ii 0.942.673.523 (2)151
C8—H81⋯O11iii 0.952.623.300 (2)129
C21—H211⋯O17iv 0.962.703.610 (2)158

Symmetry codes: (i) ; (ii) ; (iii) ; (iv) .

  2 in total

1.  Asymmetric total synthesis of (+)- and (-)-clusianone and (+)- and (-)-clusianone methyl enol ether via ACC alkylation and evaluation of their anti-HIV activity.

Authors:  Michelle R Garnsey; James A Matous; Jesse J Kwiek; Don M Coltart
Journal:  Bioorg Med Chem Lett       Date:  2011-02-23       Impact factor: 2.823

2.  Adventures in bridgehead substitution chemistry: synthesis of polycyclic polyprenylated acylphloroglucinols (PPAPs).

Authors:  Nigel S Simpkins
Journal:  Chem Commun (Camb)       Date:  2013-02-04       Impact factor: 6.222

  2 in total

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