An accurate and practical method for the calculation and use of thermal x-ray absorption fine structure (XAFS) Debye-Waller factors (DWFs) in active sites of metalloproteins is presented. These factors are calculated on model clusters within the local density functional approximation with nonlocal corrections. The DWFs are mapped out and parametrized as a function of the first shell distance and an angle (where applicable), for all significant single and multiple scattering paths, as well as the sample temperature. This approach is applied to the biologically essential but spectroscopically silent Zn+2 active sites composed of histidines, cysteines, and carboxylate ligands in homogeneous and heterogeneous environments. Detailed analysis of the relative scattering paths for Zn metalloproteins using projected vibrational density of states further explain why these paths are not detectable by XAFS for first shell metal-ligand distances above a “cutoff” value.
Dimakis, Nicholas, and Bunker, Grant. XAFS Debye-Waller factors for Zn metalloproteins. United States: N. p., 2004. Web. doi:10.1103/PhysRevB.70.195114.
Physical Review B