In a crystal, an octahedral magnesium(II) complex cation, [Mg(DMF)6]2+ (DMF: N,N-dimethylformamide), was found to exist as a C2 conformer, which was thought to be energetically unfavorable. In order to find the reason for this, structural analysis was conducted on the basis of semi-empirical PM6 method and density functional theory method. The C2 conformer was not found to be stable in a vacuum; however, it was found to be stabilized when surrounded by four tetraphenyl borate anions like the crystal structure.
Peptoids are a class of peptide mimetics whose side chains contain nitrogen atoms rather than α-carbon atoms. This structural feature restricts the intrinsic capacity to form hydrogen bond networks of α-helix, therefore peptoid oligomers are attracting attention due to the ability to design chemical properties such as self-assembling by selecting proper side chains. This paper shows some illustrative peptoid calculations, based on the fragment molecular orbital (FMO) method.
We performed theoretically to reproduce site-selective X-ray emission spectroscopy (XES) spectra of carbonate in the liquid phase at the oxygen K-edge. Structure sampling as a cluster model was performed from a snapshot of the first principles molecular dynamics simulation. Relative intensities of XES with core-hole excited state dynamics simulation were calculated using density functional theory. Theoretical XES spectra for CO32- and HCO3− were well reproduced experimentally and that for H2CO3 was predicted.