Crystal Structure of a Cyclopentanone Oxime from the Toxic Fungus Stachybotrys Chartarum

Abstract

We previously observed E-sitosterol, the hydrocarbon undecane, and a compound identified as 5-[(2-methoxyphenoxy)methyl]-1,3-oxazolidin-2-one in metabolic products from the microscopic fungus Stachybotrys chartarum [1].In continuation of research in this area, crystalline compound 1 that was unstable (hygroscopic) and deliquesced on standing was isolated from fractions obtained by chromatographic separation of total extracted substances. Its structure was established by an x-ray crystal structure analysis (XSA).Single crystals of 1 (C 5 H 9 NO) were transparent elongated plates that crystallized in the hexagonal system with a = b = 19.843(3), c = 7.796(2) A° , J = 120°, V = 2658.5(8) A° 3 , U calc = 1.115 g/cm 3 , space group P6 3 , and Z = 18. Unit-cell constants were determined and refined on an Xcalibur Ruby CCD diffractometer (Oxford Diffraction) using Cu KD-radiation (300 K, graphite monochromator). A three-dimensional dataset of reflections was obtained on the same diffractometer. Absorption corrections were applied semi-empirically using the SADABS program [2]. A high-quality XSA could not be performed because of the small amount of isolated compound and the hygroscopicity.The structure was solved by direct methods using the SHELXS-97 program suite. The structure was refined using the SHELXL-97 program [3]. All non-hydrogen atoms were refined by anisotropic full-matrix least-squares methods (over F 2 ). Positions of H atoms were found geometrically and refined with fixed isotropic thermal parameters U iso = nU eq , where n = 1.5 for methyls and 1.2 for others, and U eq is the equivalent isotropic thermal parameter of the corresponding C atoms. Hydroxyl H atoms were located in a difference electron-density synthesis and were refined isotropically. The final agreement factors (R) were 0.094 (wR2 = 0.263) over 895 reflections [I > 2V(I)] and 0.229 (wR2 = 0.321) over all 2023 reflections. The XSA data were deposited in the Cambridge Crystallographic Data Centre (CCDC No. 1042802).The XSA results showed that the isolated compound was the known cyclopentanone oxime (1). The CCDC database contains crystallographic data for its oxygen derivatives [4-6] and metal complexes [7,8] but not for the molecule itself.The asymmetric unit in the crystal included three molecules of 1 that were bound through a sequence of H-bonds between the hydroxyl of one molecule and the N atom of another (Table 1). As a result, the molecules formed a closed planar cluster with a pseudo-axis of three-fold symmetry that was perpendicular to the cluster plane (Fig. 1). The pseudo-axis was directed along the c axis (parallel to the 6 3 symmetry axis). The conformations of the three cyclopentanone rings in these molecules were different, i.e., planar, twist, and 4s D-envelope, but canonical ones that are observed in cyclopentanone oxime derivatives [4][5][6][7][8].Discrete small spherical cavities of radius 1.2 A° that repeated in steps of 0.7 A° and volumes of 12.29 A° 3 (2.7% of the total volume) formed in the crystal packing along the c axi...

Low Molecular Metabolites of Fungi. 13, 3-Dimetoxystachibotrinis Stachybotrys Chartarum

“…When the column was eluted with system I, 40 mg of 13,3dimethoxystachibotrin was isolated. (10), 256 (7,5), 242 (10), 234 (12,5), 223 (30), 221 (20), 189 (15),[189,1649;С14Н21], 149 (12,5), 135 (12,5),129 (12,5),109 (12,5).…”

“…2. The alicyclic part of the molecule consists of 15 carbon atoms and resembles the skeleton of the dryman sesquiterpenoid [14][15][16][17][18][19][20][21][22].…”