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EXAFS structure refinement supplemented by computational chemistry

Hsiao, Ya-Wen LU ; Tao, Ye ; Shokes, Jacob E. ; Scott, Robert A. and Ryde, Ulf LU orcid (2006) In Physical Review B (Condensed Matter and Materials Physics) 74(21).
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... (More)
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. (Less)
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author
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organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Physical Review B (Condensed Matter and Materials Physics)
volume
74
issue
21
article number
214101
publisher
American Physical Society
external identifiers
  • wos:000243195500023
  • scopus:33845249275
ISSN
1098-0121
DOI
10.1103/PhysRevB.74.214101
language
English
LU publication?
yes
additional info
The information about affiliations in this record was updated in December 2015. The record was previously connected to the following departments: Theoretical Chemistry (S) (011001039)
id
c6b5c323-78f3-4f2a-9c57-83241bacc6a5 (old id 679880)
date added to LUP
2016-04-01 16:03:15
date last changed
2021-09-01 01:41:08
@article{c6b5c323-78f3-4f2a-9c57-83241bacc6a5,
  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.},
  author       = {Hsiao, Ya-Wen and Tao, Ye and Shokes, Jacob E. and Scott, Robert A. and Ryde, Ulf},
  issn         = {1098-0121},
  language     = {eng},
  number       = {21},
  publisher    = {American Physical Society},
  series       = {Physical Review B (Condensed Matter and Materials Physics)},
  title        = {EXAFS structure refinement supplemented by computational chemistry},
  url          = {http://dx.doi.org/10.1103/PhysRevB.74.214101},
  doi          = {10.1103/PhysRevB.74.214101},
  volume       = {74},
  year         = {2006},
}