Redetermined structure of oxaline: absolute configuration using Cu Kα radiation

In the title compound, C24H25N5O4, the stereogenic C atom bonded to three N atoms and one C atom has an S configuration and its directly bonded neighbour has an R configuration. An intramolecular N—H⋯O hydrogen bond supports the near coplanarity of the two C3N2-five-membered rings [dihedral angle = 5.64 (10)°]. In the crystal, molecules are linked by N—H⋯N hydrogen bonds, forming a C(8) chain propagating in [001]. The chains are connected by C—H⋯O interactions, generating a three-dimensional network. The previous study [Nagel et al. (1974 ▶). Chem. Commun. pp. 1021–1022] did not establish the absolute structure and no atomic coordinates were published or deposited.

In the title compound, C 24 H 25 N 5 O 4 , the stereogenic C atom bonded to three N atoms and one C atom has an S configuration and its directly bonded neighbour has an R configuration. An intramolecular N-HÁ Á ÁO hydrogen bond supports the near coplanarity of the two C 3 N 2 -five-membered rings [dihedral angle = 5.64 (10) ]. In the crystal, molecules are linked by N-HÁ Á ÁN hydrogen bonds, forming a C(8) chain propagating in [001]. The chains are connected by C-HÁ Á ÁO interactions, generating a three-dimensional network. The previous study [Nagel et al. (1974). Chem. Commun. pp. 1021-1022] did not establish the absolute structure and no atomic coordinates were published or deposited.

Comment
Oxaline is a member of a class of biologically active indole alkaloids, characterized by a unique indoline spiroaminal framework and substitution of a 1,1-dimethylallyl ("reverse-prenyl") group at the benzylic ring junction. Oxaline was originally isolated from the culture broth of Penicillium oxalicum HK14-01 containing several unique structural features, including the N-OMe group, the unusual coupling of tryptophan and histidine, a single carbon atom bearing three nitrogen functionalities and a reversed prenyl group (Steyn, 1970). Besides, oxaline was found to inhibit tubulin polymerization in Jarkat cells, resulting in cell cycle arrest at the M phase (Koizumi et al., 2004). The X-ray structure of oxaline on Mo-Kα data was determined without definite absolute configuration (Nagel, et al., 1974). We isolated oxaline as part of our ongoing studies on characterizing bioactive metabolites from marine-derived halotolerant fungi.
And the crystal structure on Cu-Kα and the absolute configuration are reported here.
The title compound I contains a four fused rings structure as illustrated in Fig Table 2) and a non-classical one along the b axis. These two kinds of chains together weave a three-dimensional supramolecular structure (Fig. 3).

Experimental
The halotolerant fugal strain Penicillium chrysogenum HK14-01, was isolated from the sediments collected in the Yellow River Delta, Dongying, Shandong, China. The working strain was cultured under static conditions at 298 K for 35 days in two hundred 1L conical flasks containing the liquid medium (300 ml/flask) composed of glucose (10 g/L), peptone (5 g/L), yeast extract (3 g/L), malt extract (1.5 g/L), marinum salt (100 g/L). The fermented whole broth (60 L) was filtered through cheese cloth to separate into supernatant and mycelia. The mycelia was extracted three times with acetone. The acetone solution was concentrated under reduced pressure to afford an aqueous solution. The acetone solution was extracted three times with ethyl acetate to give an ethyl acetate solution which was concentrated under reduced pressure to give a crude extract (39 g). The crude extract, which was subjected to chromatography over silica gel column using a stepwise gradient elution of CH 2 Cl 2 /petroleum ether(50-100%,V/V) and CH 2 Cl 2 /MeOH (0-100%,V/V),to yield twelve fractions (Fr.1-Fr.12). Fr.9, was fractionated on a C-18 ODS column using a step gradient elution of MeOH/H 2 O (60- 100%,V/V) and was separated into 6 subfractions (Fr.9.1-Fr.9.6). Fr.9.3 was applied on Sephadex LH-20 using CH 2 Cl 2 /MeOH (1:1) to yield the title compound (145.0 mg). Colourless blocks were obtained by slow evaporation of petroleum ether/acetone (1:1) solution at 298 K.

Refinement
H atoms on C23 and C25 were placed in calculated positions, with C-H distances of 0.95 (C23) and 0.98 Å (C25), and were included in the final cycles of refinement in a riding model, with U iso (H) values equal to 1.2U eq (C23) or 1.5U eq (C25). All other H atoms were located in a difference Fourier map and included in structure-factor calculations with free refinement. The highest difference peak is 0.83Å from atom H25C.      A view of a three-dimensional hydrogen-bonding networks assembled by the classical chains above and the nonclassical ones parallel to the b axis. [Symmetry code: (ii) 1/2 -x, -y, z + 1/2; (iii) -x, y + 1/2, 3/2 -z; (iv) -x, y -1/2, 3/2 -z]

Special details
Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'s involving l.s. planes. Refinement. Refinement of F 2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F 2 , conventional R-factors R are based on F, with F set to zero for negative F 2 . The threshold expression of F 2 > 2σ(F 2 ) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F 2 are statistically about twice as large as those based on F, and R-factors based on ALL data will be even larger.