Next Article in Journal
Quantum Modeling: A Bridge between the Pumping and Signaling Functions of Na/K-ATPase
Next Article in Special Issue
Cellular Pharmacology of Palladinum(III) Hematoporphyrin IX Complexes: Solution Stability, Antineoplastic and Apoptogenic Activity, DNA Binding, and Processing of DNA-Adducts
Previous Article in Journal
N6-Methyladenosine Role in Acute Myeloid Leukaemia
Previous Article in Special Issue
Binding of Organometallic Ruthenium Anticancer Complexes to DNA: Thermodynamic Base and Sequence Selectivity
Article Menu
Issue 8 (August) cover image

Export Article

Open AccessArticle
Int. J. Mol. Sci. 2018, 19(8), 2346; https://doi.org/10.3390/ijms19082346

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

1
Department of Applied Physics, Aalto University, P.O. Box 11100, 00076 Aalto, Finland
2
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.
Received: 18 June 2018 / Revised: 16 July 2018 / Accepted: 20 July 2018 / Published: 9 August 2018
Full-Text   |   PDF [2590 KB, uploaded 9 August 2018]   |  

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. View Full-Text
Keywords: DNA; silver; ECD; QM/MM; TDDFT DNA; silver; ECD; QM/MM; TDDFT
Figures

Figure 1

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).
SciFeed

Share & Cite This Article

MDPI and ACS Style

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.

Show more citation formats Show less citations formats

Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Related Articles

Article Metrics

Article Access Statistics

1

Comments

[Return to top]
Int. J. Mol. Sci. EISSN 1422-0067 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top