research communications\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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Crystal structure and absolute configuration of (4S,5R,6S)-4,5,6-trihy­dr­oxy-3-methyl­cyclo­hex-2-enone (gabosine H)

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aDepartamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo 11800, Uruguay, bDepartment of Chemistry, Universidad de los Andes, Cra 1 N° 18A-12, 111711 Bogotá, Colombia, and cCryssmat-Lab./DETEMA, Facultad de Química - Universidad de la República, Av. Gral. Flores 2124, Montevideo 11800, Uruguay
*Correspondence e-mail: leopoldo@fq.edu.uy

Edited by C. Rizzoli, Universita degli Studi di Parma, Italy (Received 10 March 2017; accepted 21 March 2017; online 28 March 2017)

The mol­ecule of the title keto carbasugar, C7H10O4, is formed by a cyclo­hexene skeleton with an envelope conformation, substituted by carbonyl, methyl and hydroxyl groups. The crystal structure is controlled mainly by a combination of strong O—H⋯O and weak C—H⋯O hydrogen bonds, forming nearly perpendicular chains running parallel to the [110] and [-110] directions. This perpendicularity is caused by a tetra­gonal pseudosymmetry influenced by the similarity between the a and b axes, the value of 90.9770 (10)° of the β angle and the action of a 21 screw axis, which transform each chain into its corresponding nearly orthogonal one.

1. Chemical context

Gabosines are regarded as secondary metabolites and were first isolated in 1974 from Streptomyces strains (Tsushiya et al., 1974[Tsushiya, T., Mikami, N., Umezawa, S., Umezawa, H. & Naganawa, H. (1974). J. Antibiot. 27, 579-586.]). These compounds are closely related to carbasugars and exhibit DNA binding properties (Tang et al., 2000[Tang, Y. Q., Maul, C., Höfs, R., Sattler, I., Grabley, S., Feng, X. Z., Zeeck, A. & Thiericke, R. (2000). Eur. J. Org. Chem. 2000, 149-153.]). To date, 15 gabosines have been isolated, of which 14 have been synthesized. Gabosine H is one of such kind, whose total synthesis has recently been achieved by our research group (Tibhe et al., 2017[Tibhe, G. D., Macías, M. A., Pandolfi, E., Suescun, L. & Schapiro, V. (2017). Synthesis, 49, 565-570.]), starting from a biotransformation of toluene that introduces chirality. A further sequence of reactions, including Mitsunobu and final removal of the acetyl protective group, led to the title compound.

[Scheme 1]

2. Structural commentary

Fig. 1[link] shows the mol­ecule of the title compound. The absolute configuration of gabosine H with the carbonyl, methyl and hydroxyl groups in equatorial positions, determined as 4S,5R,6S on the basis of synthetic pathway, was confirmed by X-ray diffraction on the basis of anomalous dispersion of light atoms only. The six-membered ring (C1–C6) in the mol­ecule adopts an envelope conformation with atom C5 as the flap [deviating from the plane through the other ring atoms by 0.639 (2) Å] and puckering parameters Q = 0.4653 (19) Å, θ = 129.5 (2)° and φ = 66.7 (3)°.

[Figure 1]
Figure 1
The mol­ecular structure of the title compound, showing the anisotropic displacement ellipsoids drawn at the 50% probability level.

3. Supra­molecular features

In the crystal structure, hydrogen bonds O4—H41⋯O1i [symmetry code: (i) x − 1, y − 1, z] link the mol­ecules into chains that run along the [110] direction (Table 1[link]). These chains are further connected by weaker C6—H6⋯O4ii and C4—H4⋯O6iii [symmetry codes: (ii) x + 1, y, z; (iii) x, y − 1, z] hydrogen bonds along the [[\overline{1}]10] direction, forming (001) sheets (Fig. 2[link]). Considering that the chains run along the diagonal of the ab plane and the fact that ab, it is possible to observe that the 21 screw axis parallel to b transforms each chain into a nearly orthogonal one along [[\overline{1}]10] (Fig. 3[link]). The orthogonal chains are connected by single C6—H6⋯O6iv, O6—H61⋯O5v and bifurcated O5—H51⋯O4vi and O5—H51⋯O5vi hydrogen bonds [symmetry codes: (iv) −x + 1, y − [{1\over 2}], −z + 1; (v) −x + 1, y + [{1\over 2}]; (vi) −x, y + [{1\over 2}], −z + 1] to define a three-dimensional array along the [001] direction. These hydrogen bonds connect the orthogonal chains by pairs along [001]. Between these neighboring [001] sheets, weak dipolar or van der Waals forces stabilize the assembly along the c-axis direction.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
O4—H41⋯O1i 0.94 (4) 1.96 (4) 2.873 (2) 163 (3)
C6—H6⋯O4ii 0.98 2.46 3.195 (2) 131
C4—H4⋯O6iii 0.98 2.36 3.345 (3) 179
C6—H6⋯O6iv 0.98 2.62 3.306 (2) 127
O6—H61⋯O5v 0.87 (4) 1.99 (4) 2.811 (2) 155 (3)
O5—H51⋯O4vi 0.85 (4) 2.45 (3) 3.050 (2) 128 (3)
O5—H51⋯O5vi 0.85 (4) 2.26 (4) 3.0402 (12) 152 (3)
Symmetry codes: (i) x-1, y-1, z; (ii) x+1, y, z; (iii) x, y-1, z; (iv) [-x+1, y-{\script{1\over 2}}, -z+1]; (v) [-x+1, y+{\script{1\over 2}}, -z+1]; (vi) [-x, y+{\script{1\over 2}}, -z+1].
[Figure 2]
Figure 2
Partial crystal packing of the title compound showing the C—H⋯O and O—H⋯O hydrogen bonds (dotted lines) along [110] and [[\overline{1}]10], forming sheets parallel to the (001) plane.
[Figure 3]
Figure 3
Partial crystal packing of the title compound connected into a nearly orthogonal assembly along [001] through C—H⋯O and O—H⋯O hydrogen bonds (dotted lines).

4. Database survey

A search of the Cambridge Structural Database (CSD Version 5.36 with one update; Groom et al., 2016[Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171-179.]) was carried out considering mol­ecular structures similar to gabosine and its derivatives. Among the natural compounds, only the structure of gabosine N, (4R,5R,6R)-4,5,6-trihy­droxy-2-methylcyclo­hex-2-enone (Tang et al. 2000[Tang, Y. Q., Maul, C., Höfs, R., Sattler, I., Grabley, S., Feng, X. Z., Zeeck, A. & Thiericke, R. (2000). Eur. J. Org. Chem. 2000, 149-153.]), has been reported. The remaining hits were mainly derivatives of other gabosines different from H or derivatives such as 5-hy­droxy-4-methyl-7-oxabi­cyclo­[4.1.0]hept-3-en-2-one (White et al., 2010[White, L. V., Dietinger, C. E., Pinkerton, D. M., Willis, A. C. & Banwell, M. G. (2010). Eur. J. Org. Chem., pp. 4365-4367.]), which is an epoxide with different configuration of the asymmetric carbons compared with gabosine H.

5. Synthesis and crystallization

The synthesis of gabosine H was achieved by inversion of the allylic –OH group using Mitsunobu conditions followed by deprotection. (4R,5R,6S)-5-Acet­oxy-4,5-dihy­droxy-3-methyl­cyclo­hex-2-enone (2, Fig. 4[link]; 0.149 mmol, 0.030 g) was dissolved in 1 ml of benzene and TPP (0.283 mmol, 0.078 g) was added along with p-nitro­benzoic acid (0.299 mmol, 0.050 g) and diisopropyl azodi­carboxyl­ate (DIAD; 0.297 mmol, 0.060 g). The reaction mixture was stirred at room temperature for 6 h. The solvent was evaporated and the crude mass was used for the next reaction without further purification. The crude product was dissolved in MeOH (3.4 mL), a catalytic qu­antity of K2CO3 was added and the reaction mixture was stirred at room temperature for 5 min and filtered. Evaporation of the solvent from the filtrate afforded crude gabosine H, which was purified by column chromatography (CH2Cl2/MeOH, 9:1 v/v) to afford pure gabosine H as a white crystalline powder (yield: 7.2 mg, 30%; m.p. 390.6 K. Suitable crystals for X-ray analysis were obtained by dissolving the solid in a minimum amount of methanol and allowing it to evaporate at room temperature. IR (KBr): 3400, 2875, 1660 cm−1. 1H NMR (400 MHz, CD3OD): δ = 2.07 (s, 3 H), 3.56 (dd, J = 10.8, 2.4 Hz, 1 H), 4.01 (d, J = 10.8 Hz, 1 H), 4.23 (d, J = 8.4 Hz, 1 H), 5.92 (s, 1 H).

[Figure 4]
Figure 4
Reaction scheme.

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2[link]. H atoms bonded to C were placed in calculated positions (C—H = 0.93–0.98 Å) and included as riding contributions with isotropic displacement parameters set to 1.2–1.5 times the Ueq of the parent atom. Hy­droxy H atoms were located in difference density maps and were refined with Uiso(H) = 1.5 Ueq(O). The absolute structure parameter y was calculated using PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]). The resulting value of 0.07 (7) indicates that the absolute structure was determined correctly (Hooft et al., 2008[Hooft, R. W. W., Straver, L. H. & Spek, A. L. (2008). J. Appl. Cryst. 41, 96-103.]).

Table 2
Experimental details

Crystal data
Chemical formula C7H10O4
Mr 158.15
Crystal system, space group Monoclinic, P21
Temperature (K) 298
a, b, c (Å) 5.4143 (2), 5.4176 (2), 11.9200 (5)
β (°) 90.977 (1)
V3) 349.59 (2)
Z 2
Radiation type Cu Kα
μ (mm−1) 1.06
Crystal size (mm) 0.37 × 0.34 × 0.10
 
Data collection
Diffractometer Bruker D8 Venture/Photon 100 CMOS
Absorption correction Multi-scan (SADABS; Bruker, 2013[Bruker (2013). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.])
Tmin, Tmax 0.588, 0.754
No. of measured, independent and observed [I > 2σ(I)] reflections 12187, 1492, 1472
Rint 0.046
(sin θ/λ)max−1) 0.637
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.033, 0.088, 1.08
No. of reflections 1492
No. of parameters 111
No. of restraints 1
H-atom treatment H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3) 0.25, −0.18
Absolute structure Flack x determined using 639 quotients [(I+)−(I)]/[(I+)+(I)] (Parsons et al., 2013[Parsons, S., Flack, H. D. & Wagner, T. (2013). Acta Cryst. B69, 249-259.])
Absolute structure parameter 0.09 (11)
Computer programs: SAINT (Bruker, 2013[Bruker (2013). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]), SHELXS2014 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]), SHELXL2014 (Sheldrick, 2015[Sheldrick, G. M. (2015). Acta Cryst. C71, 3-8.]), Mercury (Macrae et al., 2008[Macrae, C. F., Bruno, I. J., Chisholm, J. A., Edgington, P. R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., van de Streek, J. & Wood, P. A. (2008). J. Appl. Cryst. 41, 466-470.]).

Supporting information


Computing details top

Data collection: SAINT (Bruker, 2013); cell refinement: SAINT (Bruker, 2013); data reduction: SAINT (Bruker, 2013); program(s) used to solve structure: SHELXS2014 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: Mercury (Macrae et al., 2008); software used to prepare material for publication: SHELXL2014 (Sheldrick, 2015).

(4S,5R,6S)-4,5,6-Trihydroxy-3-methylcyclohex-2-enone top
Crystal data top
C7H10O4F(000) = 168
Mr = 158.15Dx = 1.502 Mg m3
Monoclinic, P21Cu Kα radiation, λ = 1.54178 Å
a = 5.4143 (2) ÅCell parameters from 9784 reflections
b = 5.4176 (2) Åθ = 3.7–78.8°
c = 11.9200 (5) ŵ = 1.06 mm1
β = 90.977 (1)°T = 298 K
V = 349.59 (2) Å3Parallelepiped, colorless
Z = 20.37 × 0.34 × 0.10 mm
Data collection top
Bruker D8 Venture/Photon 100 CMOS
diffractometer
1492 independent reflections
Radiation source: Cu Incoatec microsource1472 reflections with I > 2σ(I)
Detector resolution: 10.4167 pixels mm-1Rint = 0.046
\j and ω scansθmax = 79.1°, θmin = 3.7°
Absorption correction: multi-scan
(SADABS; Bruker, 2013)
h = 66
Tmin = 0.588, Tmax = 0.754k = 66
12187 measured reflectionsl = 1514
Refinement top
Refinement on F2Hydrogen site location: mixed
Least-squares matrix: fullH atoms treated by a mixture of independent and constrained refinement
R[F2 > 2σ(F2)] = 0.033 w = 1/[σ2(Fo2) + (0.0546P)2 + 0.0518P]
where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.088(Δ/σ)max < 0.001
S = 1.08Δρmax = 0.25 e Å3
1492 reflectionsΔρmin = 0.18 e Å3
111 parametersExtinction correction: SHELXL2014 (Sheldrick, 2015), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
1 restraintExtinction coefficient: 0.161 (15)
Primary atom site location: structure-invariant direct methodsAbsolute structure: Flack x determined using 639 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013)
Secondary atom site location: difference Fourier mapAbsolute structure parameter: 0.09 (11)
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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
C10.4992 (3)0.2954 (4)0.22586 (16)0.0293 (4)
C20.3815 (4)0.1293 (4)0.14457 (16)0.0313 (5)
H20.43040.13730.07020.038*
C30.2068 (3)0.0338 (3)0.17173 (15)0.0262 (4)
C310.0921 (4)0.2029 (5)0.08715 (17)0.0374 (5)
H31A0.17110.18130.01630.056*
H31B0.08070.16560.07900.056*
H31C0.11190.37060.11160.056*
C40.1234 (3)0.0631 (3)0.29155 (15)0.0249 (4)
H40.21900.19650.32690.030*
C50.1658 (3)0.1719 (4)0.35829 (15)0.0237 (4)
H50.05340.30050.33020.028*
C60.4314 (3)0.2607 (3)0.34819 (14)0.0258 (4)
H60.54180.13680.38180.031*
O10.6472 (3)0.4524 (3)0.19769 (14)0.0453 (5)
O40.1316 (3)0.1192 (3)0.29994 (14)0.0398 (4)
H410.172 (6)0.273 (8)0.269 (3)0.060*
O50.1120 (3)0.1206 (3)0.47319 (11)0.0336 (4)
H510.096 (5)0.263 (7)0.502 (3)0.050*
O60.4549 (3)0.4821 (3)0.40965 (13)0.0374 (4)
H610.606 (7)0.485 (7)0.437 (3)0.056*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0252 (8)0.0305 (10)0.0322 (9)0.0046 (8)0.0038 (7)0.0021 (8)
C20.0322 (9)0.0360 (11)0.0257 (8)0.0051 (8)0.0055 (7)0.0002 (8)
C30.0251 (8)0.0263 (9)0.0274 (8)0.0013 (7)0.0018 (6)0.0011 (7)
C310.0429 (11)0.0358 (11)0.0335 (10)0.0084 (10)0.0007 (8)0.0050 (9)
C40.0241 (8)0.0219 (9)0.0289 (9)0.0001 (7)0.0061 (6)0.0011 (7)
C50.0227 (8)0.0242 (9)0.0243 (8)0.0024 (6)0.0037 (6)0.0007 (6)
C60.0240 (8)0.0267 (10)0.0267 (8)0.0011 (7)0.0004 (6)0.0019 (7)
O10.0464 (9)0.0459 (10)0.0440 (8)0.0236 (8)0.0080 (7)0.0002 (7)
O40.0287 (8)0.0363 (9)0.0548 (9)0.0099 (6)0.0152 (6)0.0124 (7)
O50.0363 (7)0.0388 (8)0.0260 (7)0.0005 (6)0.0091 (5)0.0016 (6)
O60.0329 (7)0.0364 (9)0.0429 (8)0.0016 (6)0.0044 (6)0.0125 (7)
Geometric parameters (Å, º) top
C1—O11.220 (3)C4—C51.517 (2)
C1—C21.461 (3)C4—H40.9800
C1—C61.521 (2)C5—O51.432 (2)
C2—C31.338 (3)C5—C61.523 (2)
C2—H20.9300C5—H50.9800
C3—C311.490 (3)C6—O61.410 (2)
C3—C41.514 (2)C6—H60.9800
C31—H31A0.9600O4—H410.94 (4)
C31—H31B0.9600O5—H510.85 (4)
C31—H31C0.9600O6—H610.87 (4)
C4—O41.419 (2)
O1—C1—C2121.89 (18)O4—C4—H4108.6
O1—C1—C6121.36 (18)C3—C4—H4108.6
C2—C1—C6116.75 (16)C5—C4—H4108.6
C3—C2—C1123.26 (17)O5—C5—C4107.89 (15)
C3—C2—H2118.4O5—C5—C6110.15 (14)
C1—C2—H2118.4C4—C5—C6110.99 (14)
C2—C3—C31122.04 (17)O5—C5—H5109.3
C2—C3—C4121.40 (16)C4—C5—H5109.3
C31—C3—C4116.52 (16)C6—C5—H5109.3
C3—C31—H31A109.5O6—C6—C1111.83 (16)
C3—C31—H31B109.5O6—C6—C5107.72 (14)
H31A—C31—H31B109.5C1—C6—C5110.99 (14)
C3—C31—H31C109.5O6—C6—H6108.7
H31A—C31—H31C109.5C1—C6—H6108.7
H31B—C31—H31C109.5C5—C6—H6108.7
O4—C4—C3113.27 (15)C4—O4—H41113 (2)
O4—C4—C5106.33 (14)C5—O5—H51103 (2)
C3—C4—C5111.22 (14)C6—O6—H61106 (2)
O1—C1—C2—C3175.5 (2)O4—C4—C5—C6175.86 (15)
C6—C1—C2—C35.4 (3)C3—C4—C5—C652.12 (19)
C1—C2—C3—C31179.29 (19)O1—C1—C6—O628.4 (3)
C1—C2—C3—C41.9 (3)C2—C1—C6—O6152.56 (18)
C2—C3—C4—O4145.37 (18)O1—C1—C6—C5148.7 (2)
C31—C3—C4—O437.2 (2)C2—C1—C6—C532.2 (2)
C2—C3—C4—C525.7 (2)O5—C5—C6—O662.1 (2)
C31—C3—C4—C5156.85 (17)C4—C5—C6—O6178.49 (14)
O4—C4—C5—O563.37 (19)O5—C5—C6—C1175.17 (16)
C3—C4—C5—O5172.89 (14)C4—C5—C6—C155.8 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O4—H41···O1i0.94 (4)1.96 (4)2.873 (2)163 (3)
C6—H6···O4ii0.982.463.195 (2)131
C4—H4···O6iii0.982.363.345 (3)179
C6—H6···O6iv0.982.623.306 (2)127
O6—H61···O5v0.87 (4)1.99 (4)2.811 (2)155 (3)
O5—H51···O4vi0.85 (4)2.45 (3)3.050 (2)128 (3)
O5—H51···O5vi0.85 (4)2.26 (4)3.0402 (12)152 (3)
Symmetry codes: (i) x1, y1, z; (ii) x+1, y, z; (iii) x, y1, z; (iv) x+1, y1/2, z+1; (v) x+1, y+1/2, z+1; (vi) x, y+1/2, z+1.
 

Footnotes

Joint first author.

Acknowledgements

The authors would like to thank ANII (EQC_2012_07), CSIC and the Facultad de Química for funds to purchase the diffractometer and the financial support of OPCW and PEDECIBA. GT and MM also thank ANII for their respective postdoctoral fellowships (PD_NAC_2014_1_102498 and PD_NAC_2014_1_102409).

Funding information

Funding for this research was provided by: Organisation for the Prohibition of Chemical Weapons; Agencia Nacional de Investigación e Innovación (award Nos. PD_NAC_2014_1_102498, PD_NAC_2014_1_102409, EQC_2012_07).

References

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