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Open AccessArticle

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

Department of Applied Physics, Aalto University, P.O. Box 11100, 00076 Aalto, Finland
Grupo de Física Atómica y Molecular, Instituto de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia UdeA, Calle 70 No. 52-21, 050010 Medellín, Colombia
Authors to whom correspondence should be addressed.
Int. J. Mol. Sci. 2018, 19(8), 2346;
Received: 18 June 2018 / Revised: 16 July 2018 / Accepted: 20 July 2018 / Published: 9 August 2018
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. View Full-Text
Keywords: DNA; silver; ECD; QM/MM; TDDFT DNA; silver; ECD; QM/MM; TDDFT
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Makkonen, E.; Rinke, P.; Lopez-Acevedo, O.; Chen, X. Optical Properties of Silver-Mediated DNA from Molecular Dynamics and Time Dependent Density Functional Theory. Int. J. Mol. Sci. 2018, 19, 2346.

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