Profiling charge transport: A new computational approach

To maintain life, charge transfer processes must be efficient to allow electrons to migrate across distances as large as 30-50 Å within a timescale from picoseconds to milliseconds, and the free-energy cost should not exceed one electron volt. By employing local ionization and local affinity energies, we calculated the pathway for electron and electron-hole transport, respectively. The pathway is then used to calculate both the driving force and the activation energy. The electronic coupling is calculated using configuration interaction procedure. When the charge acceptor is not known, as in oxidative stress, the charge transport terminals are found using Monte-Carlo simulation. These parameters were used to calculate the rate described by Marcus theory. Our approach has been elaborately explained using the famous androstane example and then applied to two proteins: electron transport in azurin protein and hole-hopping migration route from the heme center of cytochrome c peroxidase to its surface. This model gives an effective method to calculate the charge transport pathway and the free-energy profile within 0.1 eV from the experimental measurements and electronic coupling within 3 meV.

Natural bond-bond polarizability: a Hückel-like electronic delocalization index

We show how the bond-bond polarizability index, as originally introduced by Coulson and Longuet-Higgins in the Hückel-theoretic context, can be generalized in the natural bond orbital (NBO) framework to ab initio molecular orbital and density functional theory levels. We demonstrate that such a "natural bond-bond polarizability" (NBBP) index provides a flexible and quantitative descriptor for a broad spectrum of delocalization effects ranging from strong π aromaticity to weak intra- and intermolecular hyperconjugative phenomena. Illustrative applications are presented for representative delocalization effects in saturated and unsaturated species, chemical reactions, and hydrogen-bonding interactions.

Bridge-mediated excitation energy transfer pathways through protein media: a Slater determinant-based electronic coupling calculation combined with localized molecular orbitals

A computational method for calculating electronic coupling and pathway of electron transfer (ET) has been extended to that for excitation energy transfer (EET). A molecular orbital (MO)-based description has been generalized to one based on Slater determinants. This approach reduces the approximations used for the Green's function method from the perturbation of chemical-bond interactions to the perturbation of the configuration interactions. It is, therefore, reasonable to apply this method to EET, which involves the transfer of an electron-hole pair. To represent EET donor, acceptor, and bridge states, we adopted recently developed localized molecular orbitals (LMOs) for constructing locally excited determinants. The LMO approach provides a chemically meaningful interpretation of how each local excitation on the bridge contributes to the total electronic coupling of the EET. We applied the method to six model peptides and calculated their electronic couplings as well as the direct and through-peptide terms. Although the through-peptide term is usually negligibly small compared with the direct term, it can dominate the EET reaction in appropriate situations. The direct term dominates in long-range interactions because the indirect term decays in shorter distances.