Reorganization Free Energy for Azurin Oxidation at Gold Interfaces Evaluated by Perturbed Matrix Method
O. V. Kontkanen1,2, D. Biriukov2, Z. Futera1
1Faculty of Science, University of South Bohemia, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic
2Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 16610 Prague 6, CR.
zfutera@prf.jcu.cz
Charge transfer reactions of various complexities naturally occur in redox proteins and their complexes. On the other hand, these proteins could be incorporated into nanobioelectronic devices as a charge-carrier components, which could beneficiate in new electronic properties. However, the charge transfer reactions have to be fully understood in various enviroments such as in vacuum, which provides the challenge to investigate them accurately. From the theoretical point of view, a lot of computational resources (tools, time) are required to capture the the details of charge transfer, e.g. by computing the reorganization free energy, in a reasonable accuracy. Traditionally, QM/MM is used to invfestigate large systems, namely proteins, but it can grow demanding as the size of the system grows. Alternatively, Perturbed Matrix Method (PMM) [1,2] could be applied, as a faster approach, which can handle large number of molecular-dynamics (MD) samples and provide thus statistically-converged data
We previously investigated azurin and its reorganization free energy in vacuum and adsorbed on the gold surface through QM/MM.[3] Our study suggests that azurin gains structural flexibility near redox center in vacuum, which gives similar reorganization free energies as in solution. Now we apply PMM for the same azurin systems in vacuum and show that a) PMM is applicable outside from the aqueous solution, b) it can re-produce the results within a reasonable accuracy when compared to QM/MM (Δ = 0.1-0.2 eV), and c) to go beyond, we compute the reorganization free energy of azurin junction, 0.73 eV, in vacuum (Figure 1). The reorganization free energy is similar to the azurin in solution, ~0.6 – 0.7 eV, which indicates that the flexibility gained from vacuum is restrained in the junction structure. In conclusion, PMM is able to replicate the reorganization free energies in vacuum and on bio/metal surfaces within the same accuracy as QM/MM with an appropiate description of the the redox center.
Figure 1. Azurin adsorbed through both disulfide bridge and Cu-site on gold in vacuum.
1. Aschi, M., Spezia, R., Di Nola, A. and Amadei, A., 2001. A first-principles method to model perturbed electronic wavefunctions: the effect of an external homogeneous electric field. Chemical physics letters, 344(3-4), 374.
2. Spezia, R., Aschi, M., Di Nola, A. and Amadei, A., 2002. Extension of the perturbed matrix method: application to a water molecule. Chemical physics letters, 365(5-6), 450.
3. Kontkanen, O. V., Biriukov, D., & Futera, Z. (2022). Reorganization free energy of copper proteins in solution, in vacuum, and on metal surfaces. The Journal of Chemical Physics, 156(17), 175101.