Metallic surface dynamics of genomic DNA and its nitrogenous bases: SERS assessment and theoretical considerations

J Mol Model. 2019 May 15;25(6):162. doi: 10.1007/s00894-019-4039-y.

Abstract

The dynamics of genomic DNA and its nucleobases at a silver surface were explored using surface-enhanced Raman spectroscopy (SERS) and ab initio Verlet-type dynamics, respectively. The bands observed had full widths at half-maximum (FWHMs) in the wavenumber range 10-29 cm-1. (Sub)picosecond molecular dynamics with global relaxation times of 0.37-1.06 ps were noted. Furthermore, the on-surface ab initio dynamics of the DNA bases were examined using DFT with a Verlet-type algorithm. The results attained for these ergodic dynamic systems describe real systems quite well and could therefore be correlated with corresponding experimental data.

Keywords: (Sub)picosecond molecular dynamics; Ab initio dynamics; Genomic DNA; Metallic surface; Nitrogenous bases.

MeSH terms

  • Algorithms
  • DNA / chemistry*
  • Models, Theoretical
  • Molecular Dynamics Simulation*
  • Nitrogen / chemistry*
  • Nucleic Acid Conformation
  • Silver / chemistry*
  • Spectrum Analysis, Raman*

Substances

  • Silver
  • DNA
  • Nitrogen