Fragment shape variation index for periodicity deficiency and gradual changes of internal coordinates along linear polymers

Abstract

A special adaptation of the fragment shape variation index approach is applied to a series of rod-like structures obtained by replacing all C-C atom pairs by B-N atom pairs in linear polymers constructed by stacking adamantane units on top of each other. A special feature of these structures is a systematic, monotonic increase of the length of B-N bonds roughly parallel with the axis of the rods when moving from the B-terminus towards the N-terminus of the rods. All other changes in the unit cells of these short polymers are less important and less systematic, consequently, focusing on these B-N bonds of the given structures is especially suitable for the application of the fragment shape variation index approach used for a single type of internal coordinate shape descriptor. The results reveal additional trends which are easy to miss if one is restricted to a simple inspection of the data. The study also confirms that in special cases one may replace the detailed electron density shape descriptors with the far simpler bond length data as formal, but limited shape descriptors, whenever the overall structures and shapes show only minor changes, affecting primarily only one type of the internal coordinates.

Fuzzy Electron Density Fragments in Macromolecular Quantum Chemistry, Combinatorial Quantum Chemistry, Functional Group Analysis, and Shape–Activity Relations

“…Using fuzzy fragments, we can study the correlations between local shape and activity, including biochemical activities, important in pharmaceutical applications. ,,− The molecular electron density shape analysis methods − originally developed for complete molecules are fully applicable to fuzzy fragments, useful in pharmaceutical drug design …”

“…87 A special case involves a systematic deviation from perfect periodicity in some polymers, which can be analyzed in terms of local features. 90…”