Theoretical simulation of the spectroscopy and dynamics of a red copper protein

Abstract

The electronic absorption, circular dichroism and X-ray absorption spectroscopy of the red copper protein nitrosocyanin is simulated with classical molecular dynamics simulations in conjunction with time-dependent density functional theory (TDDFT) and multireference configuration interaction (MRCI) calculations on the active site, with the remainder of the protein and solvent included via point charges. In the molecular dynamics simulations of the oxidised form of the protein an exogenous water coordinates with the copper centre. Both TDDFT and MRCI approaches predict accurate excitation energies and give qualitatively correct absorption spectra. The most significant discrepancy with experiment is an underestimation of the intensity for the Cys_π band. Circular dichroism spectra are more difficult to compute accurately, and the best agreement with experiment is found using the velocity formulation for the rotational strength. However, this predicts the Cys_σ band with an incorrect sign. In the X-ray region, TDDFT in conjunction with a short-range corrected functional provides an accurate description of the pre-edge features at the copper and sulfur K-edges.