Intra- and inter-molecular hydrogen bonding greatly affects both physical and chemical properties for a wide variety of important molecules. This study focuses on intramolecular hydrogen bonding in polyhydroxy-1,4-naphthoquinones. The little known "bond counting rule", dictates that the global minimum will be comprised of a maximum number of highly stabilizing interactions. Hydrogen bonding was chosen for this work as the energy of the bond is typically 20-40 kJ mol^-1, which is larger than computational error, allowing statistically significant energy differences between conformers to be determined.
A series of interactions between neighbouring hydroxyl groups and each other, and between hydroxyl groups and neighbouring carbonyl groups were postulated.
Quantification of the interaction energies was accomplished using a training set of several hundred unique isomers, allowing a quantitative bond counting rule to be developed. Harmonic vibrational spectroscopic and QTAIM analyses were performed for key interactions to aid in their characterisation as baseline, stabilising or destabilising. The effect of molecular conformation upon the wavelength and absorbance of electronic absorption spectra were also probed, highlighting the need to obtain low-energy conformations.
Potential energy hypersurface (PES) for single and pairs of C-0 bond rotation(s) not only indicate the presence of stationary points corresponding to maxima, minima and transition structures, but also any rotational barriers and reaction pathways for rotamer interconversion. To aid PES visualization, a set of custom Python-based tools were designed and constructed allowing creation of both graphic and haptic Web3D virtual models for teaching purposes. Increased topological perception and object manipulation were obtained using 3-D rapid prototyped models.