V.M. Andrianarijaona

A Survey of the Ionization Energies of the DNA Nitrogenous Bases via DFT-Based Calculations of their Potential Energy Surfaces

The knowledge of the ionization energies (IE) of the four nitrogenous bases of DNA is crucial in understanding the DNA damage processes. So far, both theoretical and experimental results show that guanine has the least IE [J. Phys. Chem. Chem. Phys., 2014,15, 13833-13837]. But even though the measured IEs seemed to be consistent with the calculated ones, they are not in good agreement. The disagreements might be due to the fact that the IE depends on the location of the leaving electron and its electronic environment. Besides, the calculations of the ionization energies of a molecular ion need the consideration of all directions that are indispensable to define the geometry of the molecule. Another factor which was often obscure when investigating these IEs is the effect of the geometry transition from the relaxed neutral to the relaxed cation.In this study, we considered a relaxed neutral nitrogenous base, which is also assumed to be the geometry of the cation right after its formation. Each single atom of the neutral base (as well as each single atom of the cation) is considered as a site of the departing electron and the corresponding potential curves are calculated in all three directions (x, y, z) using the density functional theory and assuming that all other atoms are frozen during the ionization. Thus, this method of calculations of IE is an all-direction survey of the IEs of the DNA nitrogenous bases. It is different from the standard ones that lead to either vertical IE or adiabatic IE. It gives access to the potential energy surfaces and IEs that are in good agreement with some measurements. The results are reported and discussed in this presentation.

Computational Investigation of the Dissociative Recombination of Adenine, Guanine, Thymine, and Cytosine

Dissociative recombination (DR) is a process during which a molecular cation captures an electron and subsequently dissociates into neutral particles. DR is one of the very efficient processes of molecular cation annihilation and of neutral particles production in dilute environment. The DR of small molecules such as H2+ and H3+ were thoroughly investigated during the past three decades. Recently, the cations of interest have been expanded from small inorganic molecules to macromolecules (Phys. Chem. Chem. Phys., 2010,12, 11670-11673).On the other side, DR in dense environment had been neglected, due perhaps to the challenge that its experimental as well as theoretical investigation represent. However, there are so many important applications of DR in non-dilute environment. For example, DNA could lose an electron due to an ionizing radiation, which, at the same time, generated lots of low-energy electrons. The effects of secondary electrons on molecules of biological interests are currently a hot topic. It is now accepted that the attachment of slow electron on a neutral DNA may induce a strand break via dissociative electron attachments (see Radiat. Res.157, 227, 2002). Because these secondary electrons are slow, they could also be easily captured by the DNA+ which dissociative recombination may lead to a single strand and double strand breaks. As a consequence, the DNA chain break would later result in a mutation amongst the nucleotide bases.We studied the DR of temporary DNA+ using the modern electronic structure program ORCA. Given the periodic structure of DNA, we were doing quantum calculations on Guanine, Adenine, Cytosine, and Thymine only. Our results indicate the existence of autoionizing states within the various nucleotide bases and support the possibility of DR to being a channel of DNA strand break.

Exploring Low Energy Molecular Ion Reactions with Merged Beams

Charge transfer (CT) in molecular ion–neutral interactions can proceed through dynamically coupled electronic, vibrational, and rotational degrees of freedom. Using the upgraded Oak Ridge National Laboratory ion–atom merged–beams apparatus, absolute direct charge transfer is explored from keV/u collision energies where the collision is considered “ro–vibrationally frozen” to sub–eV/u collision energies where collision times are long enough to sample vibrational and rotational modes. Our first molecular ion measurement with the merged‐beams apparatus has been performed for D2++H and is used to benchmark high energy sudden approximation theory and vibrational specific adiabatic theory for the (H2–H)+ complex. CT measurements have also been performed for D3++H from 2 eV/u to 2 keV/u and CO++D from 20 eV/u to 2000 eV/u. With straightforward improvements to the apparatus, we plan to extend our measurements to key “destructive” rate coefficients for H2+ and CH+ with H at temperatures relevant to the interstella...

Investigation of charge transfer in low energy D2+ + H collisions using merged beams

The hydrogen – hydrogen (deuterium) molecular ion is the most fundamental ion-molecule two-electron system. Charge transfer proceeds through dynamically coupled electronic, vibrational and rotational degrees of freedom. Using the ion-atom merged-beams apparatus at Oak Ridge National Laboratory absolute charge transfer cross sections for D2+ + H are measured from keV/u collision energies where the collision is considered ro-vibrationally frozen to meV/u energies where collision times are long enough to sample vibrational and rotational modes. The measurements benchmark high energy theory and vibrationally specific adiabatic theory.