Spectroscopic Properties of Protein‐Bound Cofactors: Calculation by Combined Quantum Mechanical/Molecular Mechanical ( QM / MM ) Approaches

Abstract

In this article, we discuss some aspects of the combined quantum mechanics/molecular mechanics (QM/MM) method for the calculation of energetics and spectroscopic parameters of protein‐bound cofactors. Following a brief introduction to the theory of the QM/MM approach, some selected examples are discussed that illustrate the use of this methodology in theoretical spectroscopic studies. The examples cover the following: (i) excitation energies for the S 0 → S 1 transition in bacteriorhodopsin; (ii) electron paramagnetic resonance (EPR) and absorption spectra of plastocyanin; and (iii) the spin Hamiltonian parameters of compound I in cytochrome P 450 cam .

The nature of tryptophan radicals involved in the long‐range electron transfer of lignin peroxidase and lignin peroxidase‐like systems: Insights from quantum mechanical/molecular mechanics simulations

“…Hybrid quantum mechanical/molecular mechanics (QM/MM) calculations are the state of the art method for the investigation of spectroscopic properties and chemical processes occurring within biomolecular systems 13–22. In such a method, a confined and electronically important region of the system is treated at a high level of theory (by quantum mechanics, QM) while the environment is taken into account explicitly by a classical force field (MM).…”

Asn47 and Phe114 modulate the inner sphere reorganization energies of type zero copper proteins

“…37 We have previously studied the structures and redox properties of rusticyanin mutants, 25 pseudo-azurin and its congeners 40 using similar QM/MM methods. 41 Because of the presence of long-range electrostatic interactions as well as the steric strain imposed by the protein backbone, the computed inner sphere reorganization energies are small (B0.3-0.4 eV) as compared to the values computed in the gas phase (as large as 1.7 eV). 25 Recent studies that compare cluster models with QM/MM calculations indicate that in many cases a sufficiently large cluster model (100-200 atoms) can yield results that are representative of the active site inside the protein.…”

“…25 Recent studies that compare cluster models with QM/MM calculations indicate that in many cases a sufficiently large cluster model (100-200 atoms) can yield results that are representative of the active site inside the protein. [41][42][43][44][45][46] However, convergence towards the 'whole protein' limit is faster if QM/MM methods are applied.…”