Review pathway analysis for peptide‐mediated electronic coupling in the super‐exchange mechanism of ET and EET

Abstract

Electron and excitation energy transfers (ET and EET) have an important role in biological energy-exchange processes. Proteins are an inhomogeneous and anisotropic medium for ET and EET. The protein structure influences electronic coupling, an important factor for ET and EET. The structure factor may be predicted by obtaining information about the tunneling pathways. The present paper mainly focuses on tunneling pathway analysis using the tunneling current (flux) of the electron or configuration density. The tunneling pathways for ET and singlet EET through peptides are introduced using tunneling current (flux) analysis. These tunneling pathways differ greatly between ET and singlet EET. This paper also reviews both the theoretical background and other methods for determining electronic tunneling pathways. These pathways are related to the effect of protein coordinates on the electronic coupling between the initial and final states of the ET and EET.

Tuning electronic transport via hepta-alanine peptides junction by tryptophan doping

“…Actually, it has been observed for ET via a protein that "folded polypeptide matrices do not create a uniform barrier to electron tunneling" (17). In the pathway model for tunneling via proteins (14,55,56), the heterogeneous barrier is composed of superexchange-mediated transfer steps via distinct structural elements such as covalent and hydrogen bonds, and free space. A similar idea of "series tunneling" was recently applied to organic molecular junctions (57), where the heterogeneous states of alkyl-and phenyl groups of the molecule in the junction are modeled as series barriers [a Wentzel-KramersBrillouin model-based approximation (20)] or sites with different energies and coupling (superexchange).…”

Progress and challenges in simulating and understanding electron transfer in proteins

“…Common quantum chemistry methods to evaluate the EC have been reviewed on several occasions [43,[125][126][127]. We will briefly recall some of these methods taking a few examples for illustrative purposes, and emphasizing the most recent approaches.…”

Efficient algorithms for semiclassical instanton calculations based on discretized path integrals

“…In Subsection IV B 2, we examine these five quantum chemical methods to combine with our method for calculating the tunneling splittings of the ammonia umbrella flips. 3 We show computational results of the tunneling splittings for the ammonia umbrella flip of NH 3 using five different quantum chemical methods for the force fields of interatomic potential in Table II. Best result compared with the experimental data is given by the RHF-MP2/6-311++G(3d3p) which presents the closest equilibrium structure to the experimental structure among five calculations; the error is found to be less than 1%.…”

“…The tunneling effect often plays an important role to describe molecular processes occurred in chemical and biological systems [1][2][3] as well as fundamental physical processes. 4,5 The experimental observable concerning the effect is the energy difference of nearly degenerate ground and first excited states of the system, which is called the tunneling splitting.…”