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

Olga had initiated this article in a special issue of the International Journal of Molecular Science. Esko worked hard to make the deadline. Now the first article of his PhD is published.

In this article 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.

  • Published:
  • Updated:
URL copied!

Related news

Vesa Puttonen's book Miten sijoitan rahastoihin (How to invest in mutual funds)
Research & Art Published:

New book from Professor Vesa Puttonen

The book is titled “Miten sijoitan rahastoihin” (How to invest in mutual funds).
Vesa Puttonen's book published in Estonian.
Research & Art Published:

Professor Vesa Puttonen’s book published in Estonian

The book ”Navigating the investment minefield” by H. Kent Baker and Vesa Puttonen has been published now in Estonian by the publisher Äripäev.
Research & Art Published:

During the COVID-19 crisis, nearly half of Finnish SMEs have applied for public financing, while less than one sixth have applied for a bank loan

Researchers from Aalto University, Erasmus University (The Netherlands) and the University of St. Gallen (Switzerland) have studied Finnish SMEs' financing options and prospects in the covid-19 crisis.
Research & Art Published:

Michael Ungeheuer’s paper accepted to be published in the Journal of Banking and Finance

Finance Assistant Professor Michael Ungeheuer’s paper has been accepted for publication in the Journal of Banking and Finance.