Optical properties of silver-mediated DNA from molecular dynamics and time dependent density functional theory

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Journal Title
Journal ISSN
Volume Title
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
Date
2018-08-09
Major/Subject
Mcode
Degree programme
Language
en
Pages
1-13
Series
International Journal of Molecular Sciences, Volume 19, issue 8
Abstract
We report a combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics and time-dependent density functional (TDDFT) study of metal-mediated deoxyribonucleic acid (M-DNA) nanostructures. For the Ag+-mediated guanine tetramer, we found the maug-cc-pvdz basis set to be sufficient for calculating electronic circular dichroism (ECD) spectra. Our calculations further show that the B3LYP, CAM-B3LYP, B3LYP*, and PBE exchange-correlation functionals are all able to predict negative peaks in the measured ECD spectra within a 20 nm range. However, a spurious positive peak is present in the CAM-B3LYP ECD spectra. We trace the origins of this spurious peak and find that is likely due to the sensitivity of silver atoms to the amount of Hartree–Fock exchange in the exchange-correlation functional. Our presented approach provides guidance for future computational investigations of other Ag+-mediated DNA species.
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Keywords
DNA, ECD, QM/MM, Silver, TDDFT
Other note
Citation
Makkonen , E , Rinke , P , Lopez-Acevedo , O & Chen , X 2018 , ' Optical properties of silver-mediated DNA from molecular dynamics and time dependent density functional theory ' , International Journal of Molecular Sciences , vol. 19 , no. 8 , 2346 , pp. 1-13 . https://doi.org/10.3390/ijms19082346