The effects of macrocyclic constraints on electron transfer in peptides

Research undertaken in this thesis focuses on electron transfer in peptides constrained into either a 3₁₀-helical or a β-strand conformation in order to progress the field of molecular electronics. Chapter One: Natural proteins have evolved to promote electron transfer in many biological processes. However, their complex conformational nature inhibits a thorough investigation, so in order to study electron transfer in proteins, simple peptide models containing redox active moieties present as ideal candidates. Chapter One introduces the importance of secondary structure characteristic to proteins/peptides, and its relevance to electron transfer. The proposed mechanisms responsible for such electron transfer are discussed, along with the various approaches used to further constrain the peptides into their geometric conformations. The methods used to characterize the conformation of all peptides synthesized throughout this thesis are outlined, as are details of the electrochemical techniques used to investigate their electronic properties. A literature review describing several factors that have been shown to influence electron transfer in peptides, and a brief summary of molecular electronics follows. Chapter Two: Two 3₁₀-helical peptides were synthesized, one constrained via a covalent side-chain staple using Huisgencycloaddition, and the other a linear analogue. Both peptides contain a redox active terminal ferrocene moiety, and were separately attached to a single walled carbon nanotube (SWCNT)/gold electrode array for electrochemical analysis. The effect of backbone rigidity imparted by the side-bridge constraint was revealed, which was shown to restrict the necessary torsional motions that lead to facile intramolecular electron transfer along the peptide backbone. High level calculations were used to support the electrochemical observations. Chapter Three: A series of peptides constrained into either a 3₁₀-helix or β-strand conformation were synthesized, each containing a varied number of electron rich alkene side chains. The ability of the alkene(s) to facilitate electron transfer through the peptides by exploiting a hopping mechanism, and thus act as a “stepping stone” was investigated. Ring closing metathesis was used to further rigidify the backbones of a helical and a β-strand peptide via side chain tethers. The ensuing saturated and unsaturated compounds were electrochemically interrogated in order to explore any possible interplay between the effects of the alkene side-chains and backbone rigidity. High level calculations were conducted to verify the observed electrochemical data. Chapter Four: Two β-strand peptides were synthesized, one constrained via a covalent side-chain staple using Huisgen cycloaddition, and the other a linear analogue. Both peptides contain a redox active terminal ferrocene moiety, and were separately attached to a SWCNT/gold electrode array for electrochemical analysis. The charge transfer pathway was determined to be intramolecular by measuring the electron transfer rate at various concentrations of the constrained peptidebound to the electrode. This pathway is analogous to charge transfer through a molecular junction involving a single peptide. Theoretical conductance simulations were then undertaken using two peptide analogues in order to establish a link between the electrochemical observations and conductance measurements through a molecular junction. Chapter Five: Two macrocyclic peptides were synthesized, one constrained into a 3₁₀-helical conformation by linking its i to i+3 residues to form a lactam bridge, and the other constrained into a β- strand geometry via a lactam-bridge tether, linking its i to i+2 residues. These peptides were chosen in order to define the role of the amide bond in a lactam bridge constraint. Direct linear analogues of each were used to establish the effect on electron transfer from a terminal amide bond located in an untethered side-chain. High level calculations were also conducted in order to elucidate the mechanism(s) responsible for electron transfer in each of the linear and macrocyclic helical peptides.Thesis (Ph.D.) (Research by Publication) -- University of Adelaide, School of Physical Sciences, 2015