EXAFS structure refinement supplemented by computational chemistry

Abstract

We present a method that combines structure determination using extended x-ray absorption fine structure (EXAFS) measurements and computational chemistry (CC) calculations, EXAFS/CC. Using such an approach, it is possible to obtain a full structure of model complexes or protein metal active sites, although the EXAFS data primarily give radial distance information about the metal ion's nearest neighbors. In essence, CC provides a formalism within which chemical knowledge can be introduced to EXAFS modeling. In this sense, the method is analogous to the use of molecular mechanics in standard crystallographic or NMR structure refinement. In addition, the method provides structures that are a compromise between EXAFS data and the CC calculations. Therefore, they can be used directly to obtain energies or study reaction mechanisms. The method is implemented for both density functional theory and molecular mechanics calculations. It is applied to five Ni(II) (both low- and high-spin) and Cu(I/II) complexes with known crystal structures and it is shown to perform well. We also show that the method can be successfully combined with the calculation of ab initio Debye-Waller factors for all paths using the equation-of-motion method and force constants obtained from the CC calculations.