Circular dichroism (CD) spectroscopy is widely used to characterize the structures of DNA G-quadruplexes. CD bands at 200-300 nm have been empirically related to G-quadruplexes having parallel or antiparallel sugar-phosphate backbones. We propose that a more fundamental interpretation of the origin of the CD bands is in the stacking interactions of neighboring G-quartets, which can have the same or opposing polarities of hydrogen bond acceptors and donors. From an empirical summation of CD spectra of the d(G)5 G-quadruplex and of the thrombin binding aptamer that have neighboring G-quartets with the same and opposite polarities, respectively, the spectra of aptamers selected by the Ff gene 5 protein (g5p) appear to arise from a combination of the two types of polarities of neighboring G-quartets. The aptamer CD spectra resemble the spectrum of d(G3T4G3), in which two adjacent quartets have the same and two have opposite polarities. Quantum-chemical spectral calculations were performed using a matrix method, based on guanine chromophores oriented as in d(G3T4G3). The calculations show that the two types of G-quartet stacks have CD spectra with features resembling experimental spectra of the corresponding types of G-quadruplexes.

ABSTRACT:The circular dichroism (CD) of the biaryl alkaloid dioncophylline A (2) was investigated by CD calculations; the structures were generated by molecular dynamics (MD) simulations using the force field CVFF. From these structures the CD spectra were calculated with the semiempirical method CNDO/2S. Summing up the single CD spectra yielded the final spectrum. In contrast to our earlier method based on the Boltzmann weighting, the MD-assisted approach permitted to assign the flexible biaryl axis of dioncophylline A (2), which is found to be P.

Keywords: Natural products / Azo compounds / Chiral sulfoxides / Quantum chemical calculations / Enantioselective synthesisThe orange pigment rubroflavin (1) from the dried fruit bodies of Calvatia rubro-flava (Lycoperdaceae) owes its high optical rotation to a methanesulfinyl group directly attached to a 1,4-benzoquinone semicarbazone chromophore. Rubroflavin is present in fresh fungi in its leuco form 4, which is easily oxidized to 1. Thermal fragmentation of 1 yields (−)-3-methanesulfinyl-5-(methylthio)phenol (6), whose configuration was assigned as (S) by quantum mechanical calculations.

ABSTRACT:The absolute configuration of rubroflavin has been determined by comparison of its measured and calculated CD spectra. For this purpose the structures of 30 plausible isomers of the title compound have been optimized with density functional theory (DFT/BP86) using a triple-zeta valence basis set. The absolute (S) configuration at the OS(AO)CH 3 group has been assumed in these calculations. One quinoid isomer, which is separated from all other structures by an energy gap of about 4 kcal/mol, was found to be the most stable species and to dominate the CD spectrum. The structure of this isomer has been reoptimized under the influence of a solvent using an electrostatic model (COSMO). Based on the geometries of the most stable isomer obtained in the presence and absence of the solvent the excitation energies and oscillator as well as rotational strengths have then been calculated using timedependent DFT (TDDFT/TZVP/BP86). Comparison of the measured CD spectrum with that calculated for the energetically lowest isomer shows that especially the long wavelength parts of the spectra agree fairly well as far as the wavelengths and the signs of the Cotton effects are concerned while the correspondence between calculated and measured intensities is less satisfying. The agreement between the measured and calculated spectrum is better if the geometry optimized under the influence of the solvent is used. A detailed analysis of the spectra led us to the conclusion that the absolute configuration of rubroflavin is (S). These results support earlier assignments based on semiempirical and ab initio studies on a thermal decomposition product of rubroflavin.