Mean Excitation Energies and Their Directional Characteristics for Energy Deposition by Swift Ions on the DNA and RNA Nucleobases † Stephan P. A. Sauer, ‡ Jens Oddershede, § and John R. Sabin* ,§ Department of Chemistry, UniVersity of Copenhagen, Copenhagen, Denmark, Department of Physics and Chemistry, UniVersity of Southern Denmark, Odense, Denmark, and Quantum Theory Project, Department of Physics, UniVersity of Florida, GainesVille, Florida ReceiVed: March 8, 2010; ReVised Manuscript ReceiVed: April 22, 2010 As the mean excitation energy of a molecule is the materials parameter that describes the energy transfer from a swift ion to a molecule, knowledge of it and its properties are necessary to an understanding of ion-molecule interactions. A particularly important case is the interaction of fast ions with biological material. In this contribution we calculate the mean excitation energies of the nucleobases using the polarization propagator formalism. The mean excitation energies and their directional components are calculated, as are the influence of hydrogen bonding and nucleoside formation. We find that the mean excitation energies of the five nucleobases are remarkably similar, but sensitive to the orientation of the target base with respect to the ion beam direction. The mean excitation energies are also very stable with respect to hydrogen bonding and nucleoside formation. 1. Introduction Understanding the basic physics of the interaction of radiation with biological targets becomes ever more important as we seek to protect healthy cells from radiation damage and to target therapeutic radiation (e.g., in the form of proton or C 6+ ion beams 1,2 ) selectively on pathologic cells. The problem extends over many orders of magnitude in complexity, time scale, and size as the effects of the interaction of radiation with matter become more complicated. For example, the time scales for bioradiological processes begin with attoseconds and continue through tens of years (e.g., the Nagasaki studies 3,4 ). The problem of describing and understanding the effects of radiological action on biological systems is thus exceedingly complicated, as one must describe long chains of sequential and parallel chemical and physical events, as well as possible nonlinearities between initial radiogenic molecular changes and final biological effects. 5-7 The chain of events can be viewed in a hierarchical scheme beginning with the initial interaction of the radiation with a molecule in a biological sample. All of the involved processes must be well-understood to deal effectively with problems such as radiation protection and radiation therapy. However, in all cases, the understanding and description of radiological action on biosystems begin with the determination of the energy deposited. The major biological damage resulting from the exposure of cells to radiation comes from either single (SSB) or double (DSB) strand breaks in DNA and, to a lesser extent, from damage to intracellular proteins. Although a minority of damage is produced by direct hits of ions on either DNA or proteins, energy deposition by a fast ion in direct collision with a biomolecule, and the subsequent excitation and fragmentation of the target, must be understood. In our work, we are therefore concerned with the first step in this process, namely, the energy transfer consequences of swift ions impinging on biomolecules. Massive particles, as opposed to photons, deposit energy in a molecule by collision with either the electrons (the dominant mechanism) or the nuclei of the molecule. The collision typically results in electronic excitation of the target molecule, followed by some combination of ionization, decay, emission of second- ary radiation, or fragmentation. The energy deposition depends on the electronic structure of the target system and its propensity to absorb energy from a swift projectile. The material constant of the target that quantifies energy absorption within the simplest version of the Bethe theory 8,9 is the mean excitation energy. The mean excitation energy of a target is thus a parameter that is very helpful to know before making theoretical predictions or planning experiments, regardless of the theory or model used. In previous studies we have investigated the mean excitation energy of the molecule which is ubiquitous in all biological systems, that is, the water molecule, 10,11 as well as of amino acids and small peptides. 12-16 For the latter we have in particular studied the importance of different conformations, 12,16 the orientation of the molecules with respect to the incoming beam, 12,16 and the influence of the surrounding water mol- ecules. 14 In the present study we turn now to DNA or RNA and their constituent nucleobases: adenine, cytosine, guanine, thymine, and uracil. 2. Bethe-Born Theory of Energy Deposition by Swift Ions Energy transfer to a molecule by a fast ion is frequently described in terms of the so-called linear energy transfer (LET), or stopping power -dE/dx, of the target molecule. 9,17,18 To avoid problems when comparing stopping in targets of different densities, one frequently considers the stopping cross section S(V): † Part of the “Mark Ratner Festschrift”. * Corresponding author. ‡ University of Copenhagen. § University of Southern Denmark and University of Florida. J. Phys. Chem. C 2010, 114, 20335–20341 20335 10.1021/jp1021054  2010 American Chemical Society Published on Web 06/02/2010