Combining crystallography with quantum mechanics
Bergmann, Justin LU ; Oksanen, Esko LU and Ryde, Ulf LU
(2022)
In Current Opinion in Structural Biology
72.
p.18-26
- Abstract
In standard crystallographic refinement of biomacromolecules, the crystallographic raw data are supplemented by empirical restraints that ensure that the structure makes chemical sense. These restraints are typically accurate for amino acids and nucleic acids, but less so for cofactors, substrates, inhibitors, ligands and metal sites. In quantum refinement, this potential is replaced by more accurate quantum mechanical (QM) calculations. Several implementations have been presented, differing in the level of QM and whether it is used for the entire structure or only for a site of particular interest. It has been shown that the method can improve and correct errors in crystal structures and that it can be used to determine protonation and... (More)
In standard crystallographic refinement of biomacromolecules, the crystallographic raw data are supplemented by empirical restraints that ensure that the structure makes chemical sense. These restraints are typically accurate for amino acids and nucleic acids, but less so for cofactors, substrates, inhibitors, ligands and metal sites. In quantum refinement, this potential is replaced by more accurate quantum mechanical (QM) calculations. Several implementations have been presented, differing in the level of QM and whether it is used for the entire structure or only for a site of particular interest. It has been shown that the method can improve and correct errors in crystal structures and that it can be used to determine protonation and tautomeric states of various ligands and to decide what is really seen in the structure by refining different interpretations and using standard crystallographic and QM quality measures to decide which fits the structure best.
(Less)
- author
- Bergmann, Justin
LU
; Oksanen, Esko
LU
and Ryde, Ulf
LU
- organization
- publishing date
- 2022-02
- type
- Contribution to journal
- publication status
- published
- subject
- keywords
- ligand strain, protonation state, quantum refinement, tautomeric state, X-ray crystallography
- in
- Current Opinion in Structural Biology
- volume
- 72
- pages
- 9 pages
- publisher
- Elsevier
- external identifiers
-
- scopus:85112410211
- pmid:34392061
- ISSN
- 0959-440X
- DOI
- 10.1016/j.sbi.2021.07.002
- language
- English
- LU publication?
- yes
- id
- 53b79956-18ed-4151-bd20-90af594f98f9
- date added to LUP
- 2021-09-03 11:20:53
- date last changed
- 2024-06-15 15:38:04
@article{53b79956-18ed-4151-bd20-90af594f98f9,
abstract = {{<p>In standard crystallographic refinement of biomacromolecules, the crystallographic raw data are supplemented by empirical restraints that ensure that the structure makes chemical sense. These restraints are typically accurate for amino acids and nucleic acids, but less so for cofactors, substrates, inhibitors, ligands and metal sites. In quantum refinement, this potential is replaced by more accurate quantum mechanical (QM) calculations. Several implementations have been presented, differing in the level of QM and whether it is used for the entire structure or only for a site of particular interest. It has been shown that the method can improve and correct errors in crystal structures and that it can be used to determine protonation and tautomeric states of various ligands and to decide what is really seen in the structure by refining different interpretations and using standard crystallographic and QM quality measures to decide which fits the structure best.</p>}},
author = {{Bergmann, Justin and Oksanen, Esko and Ryde, Ulf}},
issn = {{0959-440X}},
keywords = {{ligand strain; protonation state; quantum refinement; tautomeric state; X-ray crystallography}},
language = {{eng}},
pages = {{18--26}},
publisher = {{Elsevier}},
series = {{Current Opinion in Structural Biology}},
title = {{Combining crystallography with quantum mechanics}},
url = {{http://dx.doi.org/10.1016/j.sbi.2021.07.002}},
doi = {{10.1016/j.sbi.2021.07.002}},
volume = {{72}},
year = {{2022}},
}