Conformational Dependence of Isotropic Polarizabilities
Söderhjelm, Pär LU ; Kongsted, Jacob LU and Ryde, Ulf LU
(2011)
In Journal of Chemical Theory and Computation
7(5).
p.1404-1414
- Abstract
- We perform a statistical and energetic analysis of atomic polarizabilities obtained with the LoProp approach for all atoms in the avidin tetramer for 70 snapshots from molecular dynamics simulations with seven different biotin analogues, and from the crystal structure of the photosynthetic reaction center (in total 560 698 individual polarizabilities). Dynamic effects give a variation of the polarizabilities of 0.09 angstrom(3) on average. Atoms at different positions in the sequence show a variation of 0.14 angstrom(3) on average, caused by the conformational dependence of the polarizabilities. This variation gives errors of 2 and 1 kJ/mol for relative conformational and ligand-binding induction energies. Averaged elementwise or atom type... (More)
- We perform a statistical and energetic analysis of atomic polarizabilities obtained with the LoProp approach for all atoms in the avidin tetramer for 70 snapshots from molecular dynamics simulations with seven different biotin analogues, and from the crystal structure of the photosynthetic reaction center (in total 560 698 individual polarizabilities). Dynamic effects give a variation of the polarizabilities of 0.09 angstrom(3) on average. Atoms at different positions in the sequence show a variation of 0.14 angstrom(3) on average, caused by the conformational dependence of the polarizabilities. This variation gives errors of 2 and 1 kJ/mol for relative conformational and ligand-binding induction energies. Averaged elementwise or atom type polarizabilities give larger errors, e.g., 9 and 7 kJ/mol, respectively, for the relative conformational energies. Therefore, we recommend that polarizabilities should be assigned atomwise (i.e., individual polarizabilities for each atom in all residues), in the same way as for charges. We provide such a set of extensively averaged polarizabilities (xAvPol) for all atoms in avidin and the photosynthetic reaction center, applicable at the B3LYP/aug-cc-pVTZ level, which is converged with respect to the basis-set limit. (Less)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/1987816
- author
- Söderhjelm, Pär
LU
; Kongsted, Jacob
LU
and Ryde, Ulf
LU
- organization
- publishing date
- 2011
- type
- Contribution to journal
- publication status
- published
- subject
- in
- Journal of Chemical Theory and Computation
- volume
- 7
- issue
- 5
- pages
- 1404 - 1414
- publisher
- The American Chemical Society (ACS)
- external identifiers
-
- wos:000290293000018
- scopus:79955879780
- pmid:26610132
- ISSN
- 1549-9618
- DOI
- 10.1021/ct100714e
- 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
- 37b39189-bbaa-4a72-ab2c-9037972d533e (old id 1987816)
- date added to LUP
- 2016-04-01 10:14:12
- date last changed
- 2023-01-02 02:29:58
@article{37b39189-bbaa-4a72-ab2c-9037972d533e,
abstract = {{We perform a statistical and energetic analysis of atomic polarizabilities obtained with the LoProp approach for all atoms in the avidin tetramer for 70 snapshots from molecular dynamics simulations with seven different biotin analogues, and from the crystal structure of the photosynthetic reaction center (in total 560 698 individual polarizabilities). Dynamic effects give a variation of the polarizabilities of 0.09 angstrom(3) on average. Atoms at different positions in the sequence show a variation of 0.14 angstrom(3) on average, caused by the conformational dependence of the polarizabilities. This variation gives errors of 2 and 1 kJ/mol for relative conformational and ligand-binding induction energies. Averaged elementwise or atom type polarizabilities give larger errors, e.g., 9 and 7 kJ/mol, respectively, for the relative conformational energies. Therefore, we recommend that polarizabilities should be assigned atomwise (i.e., individual polarizabilities for each atom in all residues), in the same way as for charges. We provide such a set of extensively averaged polarizabilities (xAvPol) for all atoms in avidin and the photosynthetic reaction center, applicable at the B3LYP/aug-cc-pVTZ level, which is converged with respect to the basis-set limit.}},
author = {{Söderhjelm, Pär and Kongsted, Jacob and Ryde, Ulf}},
issn = {{1549-9618}},
language = {{eng}},
number = {{5}},
pages = {{1404--1414}},
publisher = {{The American Chemical Society (ACS)}},
series = {{Journal of Chemical Theory and Computation}},
title = {{Conformational Dependence of Isotropic Polarizabilities}},
url = {{https://lup.lub.lu.se/search/files/1679686/2338981.pdf}},
doi = {{10.1021/ct100714e}},
volume = {{7}},
year = {{2011}},
}