Comment on “Applicability of perturbed matrix method for charge transfer studies at bio/metallic interfaces: a case of azurin” by O. Kontkanen, D. Biriukov and Z. Futera, Phys. Chem. Chem. Phys., 2023, 25, 12479

Abstract

Cofactors of biological energy chains are highly polarizable posing the question of the effect of polarizability on enzymatic activity. Hybrid quantum mechanical/molecular mechanical calculations should satisfy restrictions on polarizabilities of quantum sites.

Redox Conduction Through Cytochrome ‘Nanowires’ Can Sustain Cellular Respiration

“…This range falls within the experimental uncertainty on α ୧ୱ୭ for the heme memetic meso-tetraphenyliron(III) porphyrin, 79 and exceeds the prior estimates of 54 and 27 Å 3 in the reduced and oxidized states, respectively, from the Zerner's Intermediate Neglect of Differential Overlap with Singles (ZINDO/S) 80,81 method applied to a His-Met ligated c-type heme. The change in isotropic polarizability between oxidation states ሺΔαሻ is found by DFT methods to be at most 6.5 Å 3 , which is 4-fold smaller than the previous prediction by ZINDO/s, but in good agreement with the lower-estimate obtained from an analysis of the UV-visible absorption spectrum of cytochrome c. 82 Figure 7. Predicted iso-and anisotropic polarizabilities for a His-His ligated c-type heme in the reduced and oxidized states, as well as the difference polarizabilities between oxidation states are similar regardless of the approximate density functional and basis set combination tested, especially in contrast to results previously published with ZINDO/s.…”

“…, no correction for the polarizability of the environment) 55 is sufficient to bring simulations into accord with λ measured electrochemically. Using density functional theory (DFT) techniques that accurately reproduce the (iso/aniso)-tropic polarizabilities of rigid to semi-rigid molecules, 57–59 including a heme memetic, 60 the reduction-induced change in polarizability for His-Met (as in cytochrome c ) and His-His (as in OmcS) ligated hemes is found both in vacuum and the protein-water environment to be much too small 61 (<15 Å 3 for iso- or anisotropic polarizability; see the Assessment of Heme Electronic Polarizability section of the Supplementary information) to substantially change λ. Change in polarizability for the heme group upon reduction appears to be irrelevant for lowering electron transfer reorganization energy for hemoproteins in general.…”

“…Using density functional theory (DFT) techniques that accurately reproduce the (iso/aniso)-tropic polarizabilities of rigid to semi-rigid molecules, 57-59 including a heme memetic, 60 the reductioninduced change in polarizability for His-Met (as in cytochrome c) and His-His (as in OmcS) ligated hemes is found both in vacuum and the protein-water environment to be much too small 61 (<15 Å 3 for iso-or anisotropic polarizability; see the Assessment of Heme Electronic…”