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Logo of actae2this articlesearchopen accesssubmitActa Crystallographica Section E: Crystallographic CommunicationsActa Crystallographica Section E: Crystallographic Communications
 
Acta Crystallogr E Crystallogr Commun. 2017 July 1; 73(Pt 8): 1242–1245.
Published online 2017 July 21. doi:  10.1107/S2056989017010015
PMCID: PMC5598857

Structural elucidation of a hy­droxy–cineole product obtained from cytochrome P450 monooxygenase CYP101J2 catalysed transformation of 1,8-cineole

Abstract

1,8-Cineole is an abundant natural product that has the potential to be transformed into other building blocks that could be suitable alternatives to petroleum-based chemicals. Mono­hydroxy­lation of 1,8-cineole can potentially occur at eight different carbon sites around the bicyclic ring system. Using cytochrome P450 monooxygenase CYP101J2 from Sphingobium yanoikuyae B2, the hy­droxy­lation can be regioselectively directed at the C atom adjacent to the methyl-substituted quaternary bridgehead atom of 1,8-cineole. The unambiguous location of the hydroxyl functionality and the stereochemistry at this position was determined by X-ray crystal analysis. The mono­hydroxy­lated compound derived from this microorganism was determined to be (1S)-2a-hy­droxy-1,8-cineole (trivial name) or (1S,4R,6S)-1,3,3-trimethyl-2-oxabi­cyclo­[2.2.2]octan-6-ol (V) (systematic), C10H18O2. In the solid state this compound exhibits an inter­esting O—H(...)O hydrogen-bonding motif.

Keywords: crystal structure

Chemical context  

The terpenoid compound commonly known as 1,8-cineole, or less easily identified using systematic nomenclature as 1,3,3-trimethyl-2-oxabi­cyclo­[2.2.2]octane (I) (Fig. 1  ), is a key component of the leaf oil from eucalypts and is also found in a variety of plant types, such as sage, thyme and fruit extracts, albeit in lower qu­anti­ties (Fig. 1  ). Its natural abundance makes it a suitable bio-derived feedstock from which other useful chemical building blocks could be accessed and used as an alternative to petrochemical based-materials. Although continued research into the chemical and biochemical transformation of 1,8-cineole (I) is being directed towards accessing high quality and commercial qu­anti­ties of these derivatives, the naming of these products by using non-systematic nomenclature, coupled with the chiral nature of these products has created inconsistencies and made it challenging to compare data of these derivatives in the literature. To address this Azerad (2014  ) recently published an extremely useful review article capturing all the oxidation products of 1,8-cineole (I) by providing trivial and systematic names along with characterization data (i.e. melting point, optical rotation and proton and carbon NMR spectroscopic information).

Figure 1
Trivial and systematic naming and atom numbering used for compound (I).

In continuing our research activities on the biocatalytic mono-hy­droxy­lation of 1,8-cineole (I) at the C atom adjacent to the quaternary C1 bridgehead atom (i.e. labelled 6 or 7 following IUPAC rules) four possible stereoisomers [Fig. 2  , compounds (II), (III), (IV) and (V)] could be formed. However, there is no current crystallographic information of these pure materials to support these assignments. Knowing the inconsistencies with the nomenclature of these compounds and to gain a better understanding of how to control the regio- and stereo-chemistry at the different sites around the 1,8-cineole bicyclic ring system, we sought confirmation of the absolute configuration by undertaking X-ray crystallographic studies.

Figure 2
Biotransformation of 1,8-cineole (I) by S. yanoikuyae B2 to produce four possible isomeric mono-hy­droxy­lated products (Unterweger et al., 2016  ).

Structural commentary  

Suitable crystals for X-ray diffraction were prepared by the slow diffusion of petroleum ether into a solution of the compound dissolved in ethyl acetate. The X-ray crystal structure of the purified mono-hy­droxy­lated 1,8-cineole (V) Fig. 3  ) was solved in the P21 space group and revealed the location of the hydroxyl group to be in the 6 position (IUPAC) (Fig. 1  ). The absolute configuration was determined by the method of Parsons et al. (2013  ) and confirmed the proposed stereochemistry (i.e. structure (V) see above, Fig. 2  ).

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Object name is e-73-01242-scheme1.jpg

Figure 3
Mol­ecular structure of (1S,4R,6S)-1,3,3-trimethyl-2-oxabi­cyclo­[2.2.2]octan-6-ol (V) with non-H atoms represented by 50% displacement ellipsoids and H atoms as spheres of arbitrary size.

The presence of the axial hydroxyl substituent in (V) breaks the crystallographic symmetry of the parent 1,8-cineole (I), with P21/m space group (Bond & Davies, 2001  ), resulting in a slight twisting of the mol­ecular framework as shown by the torsion angle C1—O2—C7—C4 of −12.8 (2)° and is presumably steric in origin. For the related 1,8-cineole-5,6-diol, three of the four possible diastereoisomers have been structurally characterized and only the one with the 6α hydroxyl group showed a similar distortion (Farlow et al., 2013  ).

Supra­molecular features  

Individual mol­ecules of (V) are connected by O–H(...)O hydrogen bonds between the hydroxyl and ether moieties (Table 1  ) and form spiral chains parallel to the b axis (Fig. 4  ).

Figure 4
Ball-and-stick representation of a hydrogen-bonded chain of mol­ecules of (V). Only selected H atoms are shown and O—H(...)O contacts are indicated as dashed bonds.
Table 1
Hydrogen-bond geometry (Å, °)

Database survey  

A search of the Cambridge Structural Database (V5.38; Groom et al., 2016  ) for the 1,3,3-trimethyl-2-oxabi­cyclo­[2.2.2]octane (cineole) skeleton gave the parent structure (I) (ref code MOFPAY; Bond & Davies, 2001  ) and the oxidation products, 5,6-di­hydroxy­cineole (three steroisomers: ref codes DIFJAF, DIFJEJ and DIFJIN; Farlow et al., 2013  ), 6-(1,3-dioxolan-2-yl)-5-ketocineole and 5-(1,3-dioxolan-2-yl)-6-ketocineole (ref codes DIFHOR and DIFHUX; Farlow et al., 2013  ).

Synthesis and crystallization  

1,8-Cineole (I) was mono-hy­droxy­lated using a recombinant Escherichia coli whole-cell fed-batch process using CYP101J2 in combination with suitable redox partner proteins from S. yanoikuyae B2 to provide a major product (Unterweger, 2016  ). The isolated material was further purified by recrystallization from diethyl ether/petroleum ether to afford white needles. The melting point (this work m.p. 371.2–371.8 K, lit. m.p. 371–372 K (Carman et al., 1986  ), 370, 370, 369, 368, 371–372, 371–372, 371–372 369–372, 372 and 370 K as cited in Azerad (2014  )) and 1H NMR spectrum are in agreement with cited literature values (Azerad, 2014  ) for either compound (IV) and/or (V). Optical rotation {this work [a]D +32.0 (c 1.3, EtOH), lit [a]D +31.9 (c 1.3, EtOH)}. The experimental data for the current material produced from the biotransformation of cineole is well aligned with one set of literature data (Carman et al., 1986  ).

Refinement  

Crystal data, data collection and structure refinement details are summarized in Table 2  . H atoms potentially involved in hydrogen-bonding inter­actions were located by difference methods and were freely refined. Other H atoms were included in the refinement at calculated positions with C—H = 0.95–0.98 Å and treated as riding with U iso(H) = 1.2U eq(C) or 1.52U eq(O or methyl C).

Table 2
Experimental details

Supplementary Material

Crystal structure: contains datablock(s) I, global. DOI: 10.1107/S2056989017010015/hg5490sup1.cif

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989017010015/hg5490Isup2.hkl

CCDC reference: 1560548

Additional supporting information: crystallographic information; 3D view; checkCIF report

Acknowledgments

The authors are grateful for financial support from Advanced Fibres and Chemical Industries Program at CSIRO Manufacturing and Monash University X-ray facilities.

supplementary crystallographic information

Crystal data

C10H18O2F(000) = 188
Mr = 170.24Dx = 1.146 Mg m3
Monoclinic, P21Cu Kα radiation, λ = 1.54184 Å
a = 6.3121 (1) ÅCell parameters from 4695 reflections
b = 10.5611 (2) Åθ = 7.6–66.8°
c = 7.9925 (2) ŵ = 0.62 mm1
β = 112.126 (3)°T = 123 K
V = 493.57 (2) Å3Plate, colourless
Z = 20.25 × 0.10 × 0.02 mm

Data collection

Oxford Gemini Ultra CCD diffractometer1746 independent reflections
Radiation source: fine focus sealed tube1728 reflections with I > 2σ(I)
Mirror monochromatorRint = 0.027
Detector resolution: 10.3389 pixels mm-1θmax = 66.7°, θmin = 7.6°
ω scansh = −7→7
Absorption correction: multi-scan (CrysAlis PRO; Rigaku OD, 2015)k = −12→12
Tmin = 0.650, Tmax = 1.000l = −9→9
6839 measured reflections

Refinement

Refinement on F2Hydrogen site location: mixed
Least-squares matrix: fullH atoms treated by a mixture of independent and constrained refinement
R[F2 > 2σ(F2)] = 0.029w = 1/[σ2(Fo2) + (0.0408P)2 + 0.077P] where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.076(Δ/σ)max < 0.001
S = 1.05Δρmax = 0.13 e Å3
1746 reflectionsΔρmin = −0.11 e Å3
113 parametersAbsolute structure: Flack x determined using 804 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013)
1 restraintAbsolute structure parameter: 0.07 (9)

Special details

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.

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

xyzUiso*/Ueq
O10.3440 (2)0.06028 (14)0.5824 (2)0.0344 (4)
H10.421 (5)0.000 (3)0.584 (4)0.049 (8)*
C10.3290 (3)0.28323 (16)0.5241 (2)0.0245 (4)
O20.3425 (2)0.37248 (12)0.39090 (15)0.0273 (3)
C20.3671 (3)0.15220 (17)0.4598 (2)0.0268 (4)
H20.5253680.1475970.4597970.032*
C30.1930 (3)0.13171 (17)0.2663 (3)0.0327 (5)
H3A0.2738020.1260320.1817040.039*
H3B0.1095040.0513390.2596980.039*
C40.0233 (3)0.24262 (19)0.2122 (3)0.0311 (4)
H4−0.0952500.2278970.0888370.037*
C5−0.0898 (3)0.2491 (2)0.3515 (3)0.0357 (5)
H5A−0.1526290.1651730.3633260.043*
H5B−0.2170140.3109510.3121080.043*
C60.0917 (3)0.28989 (18)0.5342 (3)0.0299 (4)
H6A0.0605050.3774270.5629090.036*
H6B0.0858330.2332830.6310900.036*
C70.1531 (3)0.36548 (19)0.2146 (2)0.0277 (4)
C80.0064 (4)0.4834 (2)0.1933 (3)0.0394 (5)
H8A−0.1216680.4809750.0761480.059*
H8B−0.0528470.4862200.2902910.059*
H8C0.0992840.5589720.1996650.059*
C90.2605 (3)0.3681 (2)0.0727 (2)0.0360 (4)
H9A0.1398080.363569−0.0480970.054*
H9B0.3471170.4467880.0842610.054*
H9C0.3635680.2955350.0906560.054*
C100.5167 (4)0.3200 (2)0.7013 (3)0.0377 (5)
H10A0.5150330.2621570.7966670.056*
H10B0.6652540.3148620.6891560.056*
H10C0.4911660.4068550.7327370.056*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0373 (8)0.0291 (7)0.0455 (8)0.0094 (6)0.0253 (7)0.0102 (6)
C10.0236 (9)0.0271 (10)0.0230 (8)−0.0020 (7)0.0089 (7)0.0028 (7)
O20.0264 (6)0.0293 (7)0.0244 (6)−0.0054 (5)0.0076 (5)0.0019 (6)
C20.0226 (8)0.0290 (9)0.0315 (9)0.0034 (7)0.0133 (7)0.0045 (8)
C30.0341 (10)0.0280 (11)0.0349 (10)−0.0016 (8)0.0116 (8)−0.0065 (8)
C40.0226 (8)0.0352 (11)0.0303 (9)−0.0013 (7)0.0041 (7)−0.0033 (8)
C50.0217 (9)0.0414 (11)0.0444 (11)0.0002 (8)0.0128 (8)0.0045 (9)
C60.0300 (9)0.0296 (10)0.0357 (9)0.0051 (7)0.0187 (8)0.0028 (8)
C70.0253 (8)0.0329 (9)0.0223 (8)0.0028 (8)0.0061 (6)−0.0001 (8)
C80.0438 (12)0.0399 (12)0.0381 (11)0.0136 (9)0.0194 (10)0.0101 (9)
C90.0347 (9)0.0462 (11)0.0279 (9)0.0039 (10)0.0127 (7)0.0026 (9)
C100.0380 (11)0.0445 (12)0.0266 (9)−0.0091 (9)0.0078 (8)0.0018 (8)

Geometric parameters (Å, º)

O1—C21.425 (2)C5—H5A0.9900
O1—H10.80 (3)C5—H5B0.9900
C1—O21.448 (2)C6—H6A0.9900
C1—C101.515 (2)C6—H6B0.9900
C1—C21.526 (2)C7—C81.523 (3)
C1—C61.532 (2)C7—C91.525 (3)
O2—C71.4665 (18)C8—H8A0.9800
C2—C31.539 (3)C8—H8B0.9800
C2—H21.0000C8—H8C0.9800
C3—C41.535 (3)C9—H9A0.9800
C3—H3A0.9900C9—H9B0.9800
C3—H3B0.9900C9—H9C0.9800
C4—C71.531 (3)C10—H10A0.9800
C4—C51.534 (3)C10—H10B0.9800
C4—H41.0000C10—H10C0.9800
C5—C61.540 (3)
C2—O1—H1109 (2)H5A—C5—H5B108.4
O2—C1—C10106.18 (14)C1—C6—C5109.29 (14)
O2—C1—C2106.40 (13)C1—C6—H6A109.8
C10—C1—C2112.35 (16)C5—C6—H6A109.8
O2—C1—C6109.76 (13)C1—C6—H6B109.8
C10—C1—C6112.00 (15)C5—C6—H6B109.8
C2—C1—C6109.91 (14)H6A—C6—H6B108.3
C1—O2—C7114.93 (12)O2—C7—C8107.90 (15)
O1—C2—C1108.43 (14)O2—C7—C9106.51 (13)
O1—C2—C3112.08 (15)C8—C7—C9108.91 (16)
C1—C2—C3108.81 (14)O2—C7—C4107.07 (14)
O1—C2—H2109.2C8—C7—C4113.06 (15)
C1—C2—H2109.2C9—C7—C4113.05 (16)
C3—C2—H2109.2C7—C8—H8A109.5
C4—C3—C2109.53 (15)C7—C8—H8B109.5
C4—C3—H3A109.8H8A—C8—H8B109.5
C2—C3—H3A109.8C7—C8—H8C109.5
C4—C3—H3B109.8H8A—C8—H8C109.5
C2—C3—H3B109.8H8B—C8—H8C109.5
H3A—C3—H3B108.2C7—C9—H9A109.5
C7—C4—C5110.26 (16)C7—C9—H9B109.5
C7—C4—C3109.25 (15)H9A—C9—H9B109.5
C5—C4—C3107.20 (16)C7—C9—H9C109.5
C7—C4—H4110.0H9A—C9—H9C109.5
C5—C4—H4110.0H9B—C9—H9C109.5
C3—C4—H4110.0C1—C10—H10A109.5
C4—C5—C6108.51 (14)C1—C10—H10B109.5
C4—C5—H5A110.0H10A—C10—H10B109.5
C6—C5—H5A110.0C1—C10—H10C109.5
C4—C5—H5B110.0H10A—C10—H10C109.5
C6—C5—H5B110.0H10B—C10—H10C109.5
C10—C1—O2—C7−171.24 (15)C3—C4—C5—C668.1 (2)
C2—C1—O2—C768.89 (16)O2—C1—C6—C563.37 (18)
C6—C1—O2—C7−50.00 (18)C10—C1—C6—C5−178.95 (17)
O2—C1—C2—O1−177.12 (13)C2—C1—C6—C5−53.32 (19)
C10—C1—C2—O167.09 (18)C4—C5—C6—C1−11.6 (2)
C6—C1—C2—O1−58.34 (18)C1—O2—C7—C8109.18 (16)
O2—C1—C2—C3−54.97 (17)C1—O2—C7—C9−134.02 (16)
C10—C1—C2—C3−170.76 (15)C1—O2—C7—C4−12.81 (18)
C6—C1—C2—C363.81 (17)C5—C4—C7—O265.78 (18)
O1—C2—C3—C4113.35 (17)C3—C4—C7—O2−51.77 (18)
C1—C2—C3—C4−6.56 (19)C5—C4—C7—C8−52.9 (2)
C2—C3—C4—C761.95 (19)C3—C4—C7—C8−170.47 (16)
C2—C3—C4—C5−57.52 (19)C5—C4—C7—C9−177.24 (15)
C7—C4—C5—C6−50.8 (2)C3—C4—C7—C965.2 (2)

Hydrogen-bond geometry (Å, º)

D—H···AD—HH···AD···AD—H···A
O1—H1···O2i0.80 (3)1.97 (3)2.7530 (19)170 (3)

Symmetry code: (i) −x+1, y−1/2, −z+1.

References

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