Chemical transferability of single- and multiple-scattering EXAFS Debye–Waller factors

Abstract

Single- and multiple-scattering EXAFS Debye-Waller factors are amplitude reduction parameters that appear in the EXAFS chi(k) equation accounting for the structural and thermal disorder of a given sample. These parameters must be known accurately in order to obtain quantitative agreement between theory and experiment. Since experimental data can only support a limited number of fitted parameters these factors must be known from another source. Although various approaches have been considered in the past with a variety of results, the self-consistent ab initio Density functional theory stands for the most accurate and reliable method regardless of molecular symmetry or other specific sample requirements. Since DFT scales as N3 where N is the number of atomic basis set, an ab initio calculation on a large structure is not feasible due to enormous CPU demand and in many cases due to hard energy/geometry convergence. In this paper we present two ways of overcoming this problem. Both they use the idea that by reducing the structure, the DWFs are still chemically transferable. In order to test this we use the Zn tetraimidazole. This molecule represents typical metalorganic ring samples that can be seen in active sites of metaloproteins. Results are compared to experimental EXAFS spectra.

Cytochrome c in a Dry Trehalose Matrix: Structural and Dynamical Effects Probed by X-Ray Absorption Spectroscopy

“…As far as values of the DW factors are concerned, five different models were considered. In the first one, all the DWs were set equal to zero, thus without any treatment of disorder; in the second one, DW values were selected on the basis of literature results (26,38,39,(46)(47)(48)(49) to mimic the dynamic behavior expected for a protein embedded in a noninteracting medium at room temperature: DW (N p ) ¼ 2.5 3…”

Group-fittedab initiosingle- and multiple-scattering EXAFS Debye-Waller factors

“…Active sites of metalloproteins typically consist of a central metal atom that is coordinated to amino acid residues from the protein. Previously 14 we have found that a reduced model cluster can be used to calculate DWF's by DFT methods with good accuracy. Our approach is to model those vibrational properties relevant to XAFS by applying such methods to the most common amino acid side groups found in metal sites ͑e.g., imidazole, carboxyl, phenol͒.…”

New methods for EXAFS analysis in structural genomics

“…This is not a very satisfactory procedure, however, and better alternatives are desirable. Dimakis and Bunker (Dimakis et al, 1999;Dimakis & Bunker, 2001) have explored this issue and have recently found that calculating the force constants by density functional theory (DFT) can prove multiple-scattering DWFs that are reliable and accurate. The force`constants' are rather strongly dependent on bond length, being dependent on chemistry, and tabulated force constants were insuf®cient for the purpose.…”

“…Another key point is that it is possible (Dimakis & Bunker, 2002) to model the spectra on a group-by-group basis, i.e. apart from scattering through the central metal atom the intergroup multiple scattering is negligible to a ®rst approximation and only intra-group scattering is included.…”

“…However, with a number of modern inexpensive computers, rapid solution of unknown structures is possible because the approach is inherently parallel and asynchronous and requires only moderate-bandwidth interconnects between the computers. Other parallel Structure of Zn tetraimidazole, test case for ab initio Debye±Waller calculations (Dimakis et al, 1999;Dimakis & Bunker, 2001).…”