Optical Properties of Silver-Mediated DNA from Molecular Dynamics and Time Dependent Density Functional Theory

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...

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Bibliographic Details
Published in:International journal of molecular sciences 2018-08, Vol.19 (8), p.2346
Main Authors: Makkonen, Esko, Rinke, Patrick, Lopez-Acevedo, Olga, Chen, Xi
Format: Article
Language:English
Subjects:
Circular Dichroism
Computer applications
Density functional theory
Deoxyribonucleic acid
Dichroism
DNA
DNA - chemistry
DNA - genetics
Guanine
Molecular dynamics
Molecular Dynamics Simulation
Nanostructures - chemistry
Optical properties
Quantum mechanics
Quantum Theory
Silver
Silver - chemistry
Spectra
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Summary: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 Hartreeā»Fock exchange in the exchange-correlation functional. Our presented approach provides guidance for future computational investigations of other Ag + -mediated DNA species.
ISSN:1422-0067
1661-6596
1422-0067
DOI:10.3390/ijms19082346