research communications
S,5R,6S)-4,5,6-trihydroxy-3-methylcyclohex-2-enone (gabosine H)
and of (4aDepartamento 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
The molecule of the title keto carbasugar, C7H10O4, is formed by a cyclohexene skeleton with an substituted by carbonyl, methyl and hydroxyl groups. The 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 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.
CCDC reference: 1539327
1. Chemical context
Gabosines are regarded as Streptomyces strains (Tsushiya et al., 1974). These compounds are closely related to carbasugars and exhibit DNA binding properties (Tang et al., 2000). 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), starting from a biotransformation of toluene that introduces A further sequence of reactions, including Mitsunobu and final removal of the acetyl protective group, led to the title compound.
and were first isolated in 1974 from2. Structural commentary
Fig. 1 shows the molecule of the title compound. The 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 of light atoms only. The six-membered ring (C1–C6) in the molecule adopts an 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)°.
3. Supramolecular features
In the i [symmetry code: (i) x − 1, y − 1, z] link the molecules into chains that run along the [110] direction (Table 1). 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 [10] direction, forming (001) sheets (Fig. 2). Considering that the chains run along the diagonal of the ab plane and the fact that a≃b, it is possible to observe that the 21 screw axis parallel to b transforms each chain into a nearly orthogonal one along [10] (Fig. 3). 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 − , −z + 1; (v) −x + 1, y + ; (vi) −x, y + , −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 stabilize the assembly along the c-axis direction.
hydrogen bonds O4—H41⋯O14. Database survey
A search of the Cambridge Structural Database (CSD Version 5.36 with one update; Groom et al., 2016) 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), 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), 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; 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 (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).
6. Refinement
Crystal data, data collection and structure . 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 parameter y was calculated using PLATON (Spek, 2009). The resulting value of 0.07 (7) indicates that the was determined correctly (Hooft et al., 2008).
details are summarized in Table 2
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Supporting information
CCDC reference: 1539327
https://doi.org/10.1107/S2056989017004509/rz5209sup1.cif
contains datablock I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989017004509/rz5209Isup2.hkl
Supporting information file. DOI: https://doi.org/10.1107/S2056989017004509/rz5209Isup3.cml
Data collection: SAINT (Bruker, 2013); cell
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).C7H10O4 | F(000) = 168 |
Mr = 158.15 | Dx = 1.502 Mg m−3 |
Monoclinic, P21 | Cu Kα radiation, λ = 1.54178 Å |
a = 5.4143 (2) Å | Cell parameters from 9784 reflections |
b = 5.4176 (2) Å | θ = 3.7–78.8° |
c = 11.9200 (5) Å | µ = 1.06 mm−1 |
β = 90.977 (1)° | T = 298 K |
V = 349.59 (2) Å3 | Parallelepiped, colorless |
Z = 2 | 0.37 × 0.34 × 0.10 mm |
Bruker D8 Venture/Photon 100 CMOS diffractometer | 1492 independent reflections |
Radiation source: Cu Incoatec microsource | 1472 reflections with I > 2σ(I) |
Detector resolution: 10.4167 pixels mm-1 | Rint = 0.046 |
\j and ω scans | θmax = 79.1°, θmin = 3.7° |
Absorption correction: multi-scan (SADABS; Bruker, 2013) | h = −6→6 |
Tmin = 0.588, Tmax = 0.754 | k = −6→6 |
12187 measured reflections | l = −15→14 |
Refinement on F2 | Hydrogen site location: mixed |
Least-squares matrix: full | H 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 = 1.08 | Δρmax = 0.25 e Å−3 |
1492 reflections | Δρmin = −0.18 e Å−3 |
111 parameters | Extinction correction: SHELXL2014 (Sheldrick, 2015), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
1 restraint | Extinction coefficient: 0.161 (15) |
Primary atom site location: structure-invariant direct methods | Absolute structure: Flack x determined using 639 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013) |
Secondary atom site location: difference Fourier map | Absolute structure parameter: 0.09 (11) |
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. |
x | y | z | Uiso*/Ueq | ||
C1 | 0.4992 (3) | 0.2954 (4) | 0.22586 (16) | 0.0293 (4) | |
C2 | 0.3815 (4) | 0.1293 (4) | 0.14457 (16) | 0.0313 (5) | |
H2 | 0.4304 | 0.1373 | 0.0702 | 0.038* | |
C3 | 0.2068 (3) | −0.0338 (3) | 0.17173 (15) | 0.0262 (4) | |
C31 | 0.0921 (4) | −0.2029 (5) | 0.08715 (17) | 0.0374 (5) | |
H31A | 0.1711 | −0.1813 | 0.0163 | 0.056* | |
H31B | −0.0807 | −0.1656 | 0.0790 | 0.056* | |
H31C | 0.1119 | −0.3706 | 0.1116 | 0.056* | |
C4 | 0.1234 (3) | −0.0631 (3) | 0.29155 (15) | 0.0249 (4) | |
H4 | 0.2190 | −0.1965 | 0.3269 | 0.030* | |
C5 | 0.1658 (3) | 0.1719 (4) | 0.35829 (15) | 0.0237 (4) | |
H5 | 0.0534 | 0.3005 | 0.3302 | 0.028* | |
C6 | 0.4314 (3) | 0.2607 (3) | 0.34819 (14) | 0.0258 (4) | |
H6 | 0.5418 | 0.1368 | 0.3818 | 0.031* | |
O1 | 0.6472 (3) | 0.4524 (3) | 0.19769 (14) | 0.0453 (5) | |
O4 | −0.1316 (3) | −0.1192 (3) | 0.29994 (14) | 0.0398 (4) | |
H41 | −0.172 (6) | −0.273 (8) | 0.269 (3) | 0.060* | |
O5 | 0.1120 (3) | 0.1206 (3) | 0.47319 (11) | 0.0336 (4) | |
H51 | 0.096 (5) | 0.263 (7) | 0.502 (3) | 0.050* | |
O6 | 0.4549 (3) | 0.4821 (3) | 0.40965 (13) | 0.0374 (4) | |
H61 | 0.606 (7) | 0.485 (7) | 0.437 (3) | 0.056* |
U11 | U22 | U33 | U12 | U13 | U23 | |
C1 | 0.0252 (8) | 0.0305 (10) | 0.0322 (9) | −0.0046 (8) | 0.0038 (7) | 0.0021 (8) |
C2 | 0.0322 (9) | 0.0360 (11) | 0.0257 (8) | −0.0051 (8) | 0.0055 (7) | −0.0002 (8) |
C3 | 0.0251 (8) | 0.0263 (9) | 0.0274 (8) | 0.0013 (7) | 0.0018 (6) | −0.0011 (7) |
C31 | 0.0429 (11) | 0.0358 (11) | 0.0335 (10) | −0.0084 (10) | 0.0007 (8) | −0.0050 (9) |
C4 | 0.0241 (8) | 0.0219 (9) | 0.0289 (9) | 0.0001 (7) | 0.0061 (6) | 0.0011 (7) |
C5 | 0.0227 (8) | 0.0242 (9) | 0.0243 (8) | 0.0024 (6) | 0.0037 (6) | 0.0007 (6) |
C6 | 0.0240 (8) | 0.0267 (10) | 0.0267 (8) | 0.0011 (7) | 0.0004 (6) | −0.0019 (7) |
O1 | 0.0464 (9) | 0.0459 (10) | 0.0440 (8) | −0.0236 (8) | 0.0080 (7) | −0.0002 (7) |
O4 | 0.0287 (8) | 0.0363 (9) | 0.0548 (9) | −0.0099 (6) | 0.0152 (6) | −0.0124 (7) |
O5 | 0.0363 (7) | 0.0388 (8) | 0.0260 (7) | −0.0005 (6) | 0.0091 (5) | −0.0016 (6) |
O6 | 0.0329 (7) | 0.0364 (9) | 0.0429 (8) | −0.0016 (6) | −0.0044 (6) | −0.0125 (7) |
C1—O1 | 1.220 (3) | C4—C5 | 1.517 (2) |
C1—C2 | 1.461 (3) | C4—H4 | 0.9800 |
C1—C6 | 1.521 (2) | C5—O5 | 1.432 (2) |
C2—C3 | 1.338 (3) | C5—C6 | 1.523 (2) |
C2—H2 | 0.9300 | C5—H5 | 0.9800 |
C3—C31 | 1.490 (3) | C6—O6 | 1.410 (2) |
C3—C4 | 1.514 (2) | C6—H6 | 0.9800 |
C31—H31A | 0.9600 | O4—H41 | 0.94 (4) |
C31—H31B | 0.9600 | O5—H51 | 0.85 (4) |
C31—H31C | 0.9600 | O6—H61 | 0.87 (4) |
C4—O4 | 1.419 (2) | ||
O1—C1—C2 | 121.89 (18) | O4—C4—H4 | 108.6 |
O1—C1—C6 | 121.36 (18) | C3—C4—H4 | 108.6 |
C2—C1—C6 | 116.75 (16) | C5—C4—H4 | 108.6 |
C3—C2—C1 | 123.26 (17) | O5—C5—C4 | 107.89 (15) |
C3—C2—H2 | 118.4 | O5—C5—C6 | 110.15 (14) |
C1—C2—H2 | 118.4 | C4—C5—C6 | 110.99 (14) |
C2—C3—C31 | 122.04 (17) | O5—C5—H5 | 109.3 |
C2—C3—C4 | 121.40 (16) | C4—C5—H5 | 109.3 |
C31—C3—C4 | 116.52 (16) | C6—C5—H5 | 109.3 |
C3—C31—H31A | 109.5 | O6—C6—C1 | 111.83 (16) |
C3—C31—H31B | 109.5 | O6—C6—C5 | 107.72 (14) |
H31A—C31—H31B | 109.5 | C1—C6—C5 | 110.99 (14) |
C3—C31—H31C | 109.5 | O6—C6—H6 | 108.7 |
H31A—C31—H31C | 109.5 | C1—C6—H6 | 108.7 |
H31B—C31—H31C | 109.5 | C5—C6—H6 | 108.7 |
O4—C4—C3 | 113.27 (15) | C4—O4—H41 | 113 (2) |
O4—C4—C5 | 106.33 (14) | C5—O5—H51 | 103 (2) |
C3—C4—C5 | 111.22 (14) | C6—O6—H61 | 106 (2) |
O1—C1—C2—C3 | −175.5 (2) | O4—C4—C5—C6 | −175.86 (15) |
C6—C1—C2—C3 | 5.4 (3) | C3—C4—C5—C6 | −52.12 (19) |
C1—C2—C3—C31 | −179.29 (19) | O1—C1—C6—O6 | 28.4 (3) |
C1—C2—C3—C4 | −1.9 (3) | C2—C1—C6—O6 | −152.56 (18) |
C2—C3—C4—O4 | 145.37 (18) | O1—C1—C6—C5 | 148.7 (2) |
C31—C3—C4—O4 | −37.2 (2) | C2—C1—C6—C5 | −32.2 (2) |
C2—C3—C4—C5 | 25.7 (2) | O5—C5—C6—O6 | −62.1 (2) |
C31—C3—C4—C5 | −156.85 (17) | C4—C5—C6—O6 | 178.49 (14) |
O4—C4—C5—O5 | 63.37 (19) | O5—C5—C6—C1 | 175.17 (16) |
C3—C4—C5—O5 | −172.89 (14) | C4—C5—C6—C1 | 55.8 (2) |
D—H···A | D—H | H···A | D···A | 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−1/2, −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 Weaponshttps://doi.org/10.13039/501100004766; Agencia Nacional de Investigación e Innovaciónhttps://doi.org/10.13039/100008725 (award Nos. PD_NAC_2014_1_102498, PD_NAC_2014_1_102409, EQC_2012_07).
References
Bruker (2013). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171–179. Web of Science CSD CrossRef IUCr Journals Google Scholar
Hooft, R. W. W., Straver, L. H. & Spek, A. L. (2008). J. Appl. Cryst. 41, 96–103. Web of Science CrossRef CAS IUCr Journals Google Scholar
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. Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
Parsons, S., Flack, H. D. & Wagner, T. (2013). Acta Cryst. B69, 249–259. Web of Science CrossRef CAS IUCr Journals Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Sheldrick, G. M. (2015). Acta Cryst. C71, 3–8. Web of Science CrossRef IUCr Journals Google Scholar
Spek, A. L. (2009). Acta Cryst. D65, 148–155. Web of Science CrossRef CAS IUCr Journals Google Scholar
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. CrossRef Google Scholar
Tsushiya, T., Mikami, N., Umezawa, S., Umezawa, H. & Naganawa, H. (1974). J. Antibiot. 27, 579–586. PubMed Google Scholar
Tibhe, G. D., Macías, M. A., Pandolfi, E., Suescun, L. & Schapiro, V. (2017). Synthesis, 49, 565–570. CAS Google Scholar
White, L. V., Dietinger, C. E., Pinkerton, D. M., Willis, A. C. & Banwell, M. G. (2010). Eur. J. Org. Chem., pp. 4365–4367. Google Scholar
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