Hydrocarbon links in an octet truss

• Published in: Journal of mathematical chemistry 2008-02, Vol.43 (2), p.874-891
• Main Authors: Cox, Mary A., Hughes, Thomas S., Ellis-Monaghan, Joanna A., Mondanaro, Kathleen R.
• Format: Article
• Language: English
• Subjects: Chemistry; Chemistry and Materials Science; Combinatorics. Ordered structures; Exact sciences and technology; General and physical chemistry; Math. Applications in Chemistry; Mathematics; Order, lattices, ordered algebraic structures; Original Paper; Physical Chemistry; Sciences and techniques of general use; Theoretical and Computational Chemistry; Theory of reactions, general kinetics. Catalysis. Nomenclature, chemical documentation, computer chemistry
• ISSN: 0259-9791; 1572-8897
• DOI: 10.1007/s10910-007-9323-x

We use the octet truss of R. Buckminster Fuller to develop a geometric placement method for synthesizing braid representations of knots and links of oligo (phenylene ethynylene)s using the 60° ortho , 120° meta or 180° para phenyl ring substitution angles and respecting the van der Waals repulsion constraints. We show that any knot or link can be realized by a phenylene ethynylene oligomer modeled on the octet truss. Use of this lattice is motivated by the structural constraints of these phenylene ethynylene units. Where in bio-organic chemistry, questions often involve identifying existing knots, for example in DNA strands, organic synthesis is concerned with assembling molecular structures that can be verified to exist in a desired knot topology. This physical realization of a knot as a construction of common organic molecular subunits then facilitates further study of the properties of knotted molecules in general.