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Abstract Background Theoretical analyses of the indigo dye molecule and its derivatives with Chlorine (Cl), Sulfur (S), Selenium (Se) and Bromine (Br) substituents, as well as an analysis of the Hemi-Indigo molecule, were performed using the Gaussian 03 software package. Results Calculations were performed based on the framework of density functional theory (DFT) with the Becke 3- parameter-Lee-Yang-Parr (B3LYP) functional, where the 6-31 G(d,p) basis set was employed. The configuration interaction singles (CIS) method with the same basis set was employed for the analysis of excited states and for the acquisition of the emission spectra. Conclusions The presented absorption and emission spectra were affected by the substitution position. When a hydrogen atom of the molecule was substituted by Cl or Br, practically no change in the absorbed and emitted energies relative to those of the indigo molecule were observed; however, when N was substituted by S or Se, the absorbed and emitted energies increased.

The competence between the possible reaction pathways in the reaction of different cycloalkanes and o-benzyne has been computationally explored. Systems able to undergo complete desaturation by consecutive double hydrogen atom transfer reactions are suggested.

The B19(-) anion and other boron species have been dubbed 'Wankel motors' for the almost barrierless rotation of inner and outer concentric rings relative to each other in these compounds. A single substitution in B19(-) is shown to shut down the well-established fluxionality in the anion. A carbon atom substituted in the structure to give a neutral CB18 species is shown computationally to enforce bond localization.