Simulating the Polarization Effects of Gas-Phase Nucleic Acids

Molecular dynamics (MD) simulations coupled with ion mobility spectrometry (IMS), a gas-phase extension to mass spectrometry that further filters analytes by conformation, allows researchers to perform three dimensional structural elucidation of nucleic acids. As opposed to neutral liquid phase MD simulations where electrostatic interactions are considered to be relatively weak and short ranged, highly charged, gas phase IMS simulations require a stronger description of Coulomb and polarization effects. In the work presented here, we explore the dynamical properties an appropriately tuned electrostatic force field for gas phase nucleic acids should replicate. Based off of density functional theory calculations of small oligonucleotides, we examine how one could adjust the partial charges throughout an MD simulation to more accurately replicate Coulomb interactions for charged and protonated nucleic acids.