Bulletin of the American Physical Society
50th Annual Meeting of the APS Division of Atomic, Molecular and Optical Physics APS Meeting
Volume 64, Number 4
Monday–Friday, May 27–31, 2019; Milwaukee, Wisconsin
Session H09: Collisions with Biomolecules |
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Sponsoring Units: GEC Chair: James Colgan, LANL Room: Wisconsin Center 103DE |
Wednesday, May 29, 2019 8:00AM - 8:30AM |
H09.00001: Electron Impact Ionization and Fragmentation of Bio-Relevant Molecules: Hydration Dependence Invited Speaker: Alexander Dorn Ionizing radiation penetrating biological tissue produces large numbers of low-energy secondary electrons which effectively induce damages in molecules. Here we discuss the influence of hydration on electron impact ionization of organic molecules, i.e. how water which is hydrogen bonded to the target molecule affects the reaction. As a model system we use tetrahydrofuran (THF, C$_{\mathrm{4}}$H$_{\mathrm{8}}$O) a five membered ring that is often regarded as the simplest surrogate for the sugar deoxyribose in the DNA backbone. Oxygen in THF is capable of one hydrogen-bonding link to water and forms reasonable simple THF-water dimers for which gas phase experiments and also electronic structure calculations are feasible. In contrast to the naive expectation that a water environment quenches THF fragmentation we find that water even catalyzes THF ring-break reactions. Compared to the THF monomer in the dimer the reaction barrier for the ring-break reaction is reduced by 3 eV and in hydrated THF ionization of the HOMO is sufficient to break the molecular ring. Qualitatively we can reproduce this observation by quantum chemical calculations. Furthermore, we were able to experimentally identify intermolecular Coulombic decay (ICD) in the THF-H$_{\mathrm{2}}$O dimers [1]. In this energy transfer process an inner-valence electron-vacancy in the water molecule decays by ionizing the neighboring THF molecule. Therefore, ICD can produce rather severe damage in a biological system. These experiments were done at an impact energy of E$_{\mathrm{0}}=$ 67 eV using a reaction microscope. For ionization of monomers and clusters produced in a supersonic jet two outgoing electrons were detected in coincidence with one or two ions. [1] X. Ren, E. Wang, A. D. Skitnevskaya, A. B. Trofimov, K. Gokhberg and A. Dorn, Nature Phys. \textbf{14}, 1062 (2018). [Preview Abstract] |
Wednesday, May 29, 2019 8:30AM - 9:00AM |
H09.00002: Resonance formation in biological molecules Invited Speaker: Jimena Gorfinkiel Resonances (temporary anion states) can enhance non-dissociative electron-induced processes and be chemistry initiators by leading to the production of reactive species. They are also important in other processes like photo-detachment. Their theoretical identification and characterization is therefore crucial for the understanding of a number of electron-induced processes in biological systems. Electron-molecule scattering approaches have been successfully applied to resonance identification and characterization: shape resonances can be accurately described by a number of them both for small and larger, biological molecules. Core-excited resonances, that involve the electronic excitation of the target molecule, are harder to model accurately. However, both types of resonances (and vibrational Feshbach resonances) play an important role in biological processes like radiation induced damage and electron transfer reactions. Recent joint theoretical-experimental work [1,2] has confirmed the ability of R-matrix [3] method to accurately describe core-excited resonances in biologically relevant molecules. Biological processes occur in a condensed environment where molecules with a biological function are surrounded by water. Hydrated clusters are being investigated as systems that bridge the gap between the pure gas phase and the actual environment in which these collisions take place. Small clusters can be treated using the same ab initio methodology as isolated molecules. Using the R-matrix approach, simple calculations of electron scattering from pyridine-(H$_2$O)$_n$ and thymine-(H$_2$O)$_n$ with $n$=1,2,3,5 have been performed and the effects of microhydration analyzed. The results have been linked to recent experiments on microsolvated uracil and thymine [4]. [1] Regeta K, Allan M, Ma\v{s}\'{i}n Z and Gorfinkiel J D 2016 {\em J. Chem. Phys.} {\bf 144} , 024302. [2] Loupas A, Regeta K, Allan M and Gorfinkiel J D 2018 {\em J. Phys. Chem.} A {\bf 122},~1146. [3] Tennyson J 2010 {\em Phys. Rep.} {\bf 491},~29. [4] Gorfinkiel J~D and Ptasinska S 2017 {\em J. Phys B.} {\bf 50},~182001. [Preview Abstract] |
Wednesday, May 29, 2019 9:00AM - 9:30AM |
H09.00003: Dissociative Electron Attachment to Biomolecules. Invited Speaker: Sylwia Ptasinska Dissociative electron attachment (DEA) to biomolecules plays an essential role in radiation damage initiated by high-energy radiation. A variety of biomolecular systems, including DNA, RNA, and proteins constituents have been the focus of a lot of the DEA experimental work over last two decades [1]. These studies showed rich fragmentation patterns formed via resonant electron capture into one of the metastable valence states of a molecule. However, resonance characterization still remains challenging in spite of a number of theoretical and experimental attempts. Therefore, our recent work focuses on targets, such as amides, that can be considered models for larger biologically relevant molecules, that are peptides. The choice of these simpler systems, containing amide bonds, was dictated by a possibility of performing high-level electronic structure calculations and a possibility of studying them in the gas phase. In this talk, we present our results of experimental and computational studies of the gas-phase DEA to three prototypical peptide molecules, formamide, N-methylformamide (NMF), and N,N-dimethylformamide (DMF). In addition to careful investigations of all fragments formed via DEA [2], our great focus has been on amide bond rupture. Interestingly, a double-resonant structure was observed at similar energies in the ion yields for all ions resulting from this C-N bond cleavage, such as NH2- for formamide, NHCH3- for NMF, and N(CH3)2- for DMF. Several of possible mechanisms of electron attachment were considered computationally in order to characterize these peaks. Based on our calculations, these resonances can be assigned to core-excited dipole-supported resonances populated upon DEA [3]. Our results suggest that the formation of ``spin-forbidden'' dipole-supported resonances can be of a general implication of DEA to larger biological complexes, containing the amide bond. [1] J.D. Gorfinkiel, S. Ptasinska - Electron scattering from molecules and molecular aggregates of biological relevance. Journal of Physics B: Atomic, Molecular, Optical Physics (2017) 182001 [2] M.M. Dawley, S. Ptasinska - Dissociative electron attachment to gas-phase N-methylformamide, International Journal of Mass Spectrometry 365-366 (2014) 143-151 [3] Z. Li, M. Ryszka, M.M. Dawley, I. Carmichael, K. Bravaya, S. Ptasinska - Dipole-supported electronic resonances mediate electron-induced amide bond cleavage. Physical Review Letters (2019) in press [Preview Abstract] |
Wednesday, May 29, 2019 9:30AM - 10:00AM |
H09.00004: An independent-atom-model-based description of ion collisions with complex biomolecules Invited Speaker: Tom Kirchner Collisions with biomolecules have generated a lot of interest and scientific activity lately, in large parts because of their relevance in a number of applications, specifically in the context of ion-beam cancer therapy. For ion-impact collisions, both experimental and theoretical efforts have largely focused on relatively small systems, such as DNA nucleobases and their precursors. While on the experimental side the technique of electrospray ionization holds the promise to make a systematic investigation of more complex systems feasible [1], it does not look like ab-initio theoretical methods can be pushed to deal with a much larger number of target nuclei and electrons anytime soon. There is therefore a role to be played by (sophisticated) modeling. This talk will report on our recent progress in this area. We have developed an independent-atom-like model that is capable of dealing, in principle, with arbitrarily large target systems. It is based on a geometrical interpretation of a cross section as an effective area composed of overlapping circular disks which represent the cross sections of the atomic constituents of the system under study. The latter are calculated using a well-tested time-dependent density-functional theory framework, and a pixel-counting method is used to carry out the effective-area calculation for any target molecule orientation of interest [2,3]. Orientation-averaged proton-impact net ionization and electron transfer cross sections will be presented for a number of target systems ranging from structural analogues of DNA building blocks, such as pyrimidine and purine, to a select set of amino acids and nucleotides. We will also discuss a recent extension of the model that allows for {\it multiple}-ionization calculations. $^1$D. Egorov {\it et al.}, J. Phys.: Conf. Series {\bf 635}, 112083 (2015). $^2$H. J. L\"udde {\it et al.}, Eur. Phys. J. D {\bf 70}, 82 (2016). $^3$H. J. L\"udde {\it et al.}, Eur. Phys. J. B {\bf 91}, 99 (2018). [Preview Abstract] |
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