Predicting Reduction Potentials of Blue Copper Proteins Using Quantum Mechanical Calculations.

ABSTRACT: We have calculated redox potentials of 12 blue copper protein sites comparing 64 computational methods, systematically varying the quantum mechanics (QM) system size, dielectric constants, density functional, and basis sets. All methods were based on structures optimized with combined QM and molecular mechanics (QM/MM) approaches. The redox potentials were evaluated using 10 quality metrics. The best results for relative potentials were achieved using a QM system of intermediate size (∼70 atoms), the TPSS density functional, and a SV(P) basis set, using QM-cluster calculations in a continuum solvent with a dielectric constant of 20, yielding a mean absolute deviation of 0.09 V and a maximum deviation of 0.26 V. For absolute redox potentials, methods using larger QM systems (∼340 atoms), th

SUBMITTER: Dehabadi MH 

PROVIDER: S-EPMC11881046 | biostudies-literature | 2025 Mar

REPOSITORIES: biostudies-literature