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Theoretical insights into the dissociation process for dissociative electron attachment to adenine and its tautomer

Published online by Cambridge University Press:  22 December 2020

Ying Zhang
Affiliation:
MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
Xing Wang
Affiliation:
MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
Zhongfeng Xu*
Affiliation:
MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
*
Author for correspondence: Z. Xu, MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China. E-mail: zhfxu@mail.xjtu.edu.cn

Abstract

The ab initio molecular dynamics (MD) simulations using an atom-centered density matrix propagation method are carried out in the first time to investigate the dissociative electron attachment (DEA) processes of adenine and its tautomer in the gas phase. Since the incoming electron are captured on the lowest π∗ anti-bond orbital, which is led to the different N–H bond, the C–H bond and the C–N bond are broken. The dominant anion observed in DEA dissociation process is the closed-shell dehydrogenated anion (Ade − H). The additional anions (Ade − NH2) and (Ade − 2H) are also obtained in ADMP simulation. The results are well consistent with the previous DEA experimental results. Thus, the ADMP method is used to gain a more intuitive and better understanding of the necessary dissociation process in the DEA experiment.

Type
Research Article
Copyright
Copyright © The Author(s) 2020. Published by Cambridge University Press

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References

Abdoul-Carime, H, Gohlke, S and Illenberger, E (2004) Site-specific dissociation of DNA bases by slow electrons at early stages of irradiation. Physical Review Letters 92, 168103.10.1103/PhysRevLett.92.168103CrossRefGoogle ScholarPubMed
Aflatooni, K, Gallup, GA and Burrow, PD (1998) Electron attachment energies of the DNA bases. The Journal of Physical Chemistry A 102, 62056207.CrossRefGoogle Scholar
AlZamil, NO (2020) Synthesis, DFT calculation, DNA-binding, antimicrobial, cytotoxic and molecular docking studies on new complexes VO(II), Fe(III), Co(II), Ni(II) and Cu(II) of pyridine Schiff base ligand. Materials Research Express 7, 6.10.1088/2053-1591/ab95d6CrossRefGoogle Scholar
Dawley, MM, Tanzer, K, Carmichael, I, Denifl, S and Ptasinska, S (2015) Dissociative electron attachment to the gas-phase nucleobase hypoxanthine. Journal of Chemical Physics 142, 215101.10.1063/1.4921388CrossRefGoogle ScholarPubMed
Denifl, S, Sulzer, P, Huber, D, Zappa, F, Probst, M, Mark, TD, Scheier, P, Injan, N, Limtrakul, J, Abouaf, R and Dunet, H (2007) Influence of functional groups on the site-selective dissociation of adenine upon low-energy electron attachment. Angewandte Chemie International Edition in English 46, 52385241.10.1002/anie.200700032CrossRefGoogle ScholarPubMed
d'Errico, F (2005) NCRP Report no. 144—Radiation protection for particle accelerator facilities National Council on Radiation Protection and Measurements Issued 31 December 2003; revised 7 January 2005: NCRP, Bethesda, MD, USA ISBN: 0-929600-77-0, 499 pp. 100(Hardcover), 80. Oxford University Press. Available at http://ncrppublications.orgGoogle Scholar
Deutsch, C and Maynard, GJM (2016) Ion stopping in dense plasmas: a basic physics approach. Matter and Radiation at Extremes 1, 277307.10.1016/j.mre.2016.11.004CrossRefGoogle Scholar
Esmaili, S, Bass, AD, Cloutier, P, Sanche, L and Huels, MA (2017) Synthesis of complex organic molecules in simulated methane rich astrophysical ices. Journal of Chemical Physics 147, 224704.CrossRefGoogle ScholarPubMed
Feng, WL and Tian, SX (2015) Ab initio molecular dynamics simulation study of dissociative electron attachment to dialanine conformers. Journal of Physical Chemistry A 119, 18381845.CrossRefGoogle ScholarPubMed
Frances-Monerris, A, Segarra-Marti, J, Merchan, M and Roca-Sanjuan, D (2015) Complete-active-space second-order perturbation theory (CASPT2//CASSCF) study of the dissociative electron attachment in canonical DNA nucleobases caused by low-energy electrons (0-3 eV). Journal of Chemical Physics 143, 215101.10.1063/1.4936574CrossRefGoogle Scholar
Frisch, MJ, Trucks, GW, Schlegel, HB, Scuseria, GE and Robb, MA (2009) Gaussian 09, Revision D.01. Wallingford, CT: Gaussian, Inc.Google Scholar
Gianturco, FA and Lucchese, RR (2004) Radiation damage of biosystems mediated by secondary electrons: resonant precursors for uracil molecules. Journal of Chemical Physics 120, 74467455.10.1063/1.1688320CrossRefGoogle ScholarPubMed
Gohlke, S, Abdoul-Carime, H and Illenberger, E (2003) Dehydrogenation of adenine induced by slow (<3 eV) electrons. Chemical Physics Letters 380, 595599.10.1016/j.cplett.2003.09.013CrossRefGoogle Scholar
Gürel, HH and Salmankurt, B (2017) Binding mechanisms of DNA/RNA nucleobases adsorbed on graphene under charging: first-principles van der Waals study. Materials Research Express 4, 6.10.1088/2053-1591/aa6e67CrossRefGoogle Scholar
Huber, D, Beikircher, M, Denifl, S, Zappa, F, Matejcik, S, Bacher, A, Grill, V, Mark, TD and Scheier, P (2006) High resolution dissociative electron attachment to gas phase adenine. Journal of Chemical Physics 125, 084304.10.1063/1.2336775CrossRefGoogle ScholarPubMed
Iyengar, SS and Frisch, MJ (2004) Effect of time-dependent basis functions and their superposition error on atom-centered density matrix propagation (ADMP): connections to wavelet theory of multiresolution analysis. Journal of Chemical Physics 121, 50615070.10.1063/1.1780157CrossRefGoogle ScholarPubMed
Iyengar, SS and Jakowski, J (2005) Quantum wave packet ab initio molecular dynamics: an approach to study quantum dynamics in large systems. Journal of Chemical Physics 122, 114105.CrossRefGoogle ScholarPubMed
Iyengar, SS, Schlegel, HB, Millam, JM, Voth, GA, Scuseria, GE and Frisch, MJ (2001) Ab initio molecular dynamics: propagating the density matrix with Gaussian orbitals. II. Generalizations based on mass-weighting, idempotency, energy conservation and choice of initial conditions. Journal of Chemical Physics 115, 10291.10.1063/1.1416876CrossRefGoogle Scholar
Iyengar, SS, Schlegel, HB and Voth, GA (2003) Atom-centered density matrix propagation (ADMP): generalizations using Bohmian mechanics. Journal of Physical Chemistry A 107, 72697277.10.1021/jp034633mCrossRefGoogle Scholar
Katrík, P, Hoffmann, DHH, Mustafin, E and Strašík, I (2019) Experimental study of residual activity induced in aluminum targets irradiated by high-energy heavy-ion beams: a comparison of experimental data and FLUKA simulations. Matter and Radiation at Extremes 4, 5.CrossRefGoogle Scholar
Rega, N, Iyengar, SS, Voth, GA, Schlegel, HB, Vreven, T and Frisch, MJ (2004) Hybrid ab-initio/empirical molecular dynamics: combining the ONIOM scheme with the atom-centered density matrix propagation (ADMP) approach. Journal of Physical Chemistry B 108, 42104220.10.1021/jp0370829CrossRefGoogle Scholar
Roca-Sanjuan, D, Merchan, M, Serrano-Andres, L and Rubio, M (2008) Ab initio determination of the electron affinities of DNA and RNA nucleobases. Journal of Chemical Physics 129, 095104.10.1063/1.2958286CrossRefGoogle ScholarPubMed
Sanche, L (2002) Nanoscopic aspects of radiobiological damage: fragmentation induced by secondary low-energy electrons. Mass Spectrometry Reviews 21, 349369.10.1002/mas.10034CrossRefGoogle ScholarPubMed
Schlegel, HB, Millam, JM, Iyengar, SS, Voth, GA, Daniels, AD, Scuseria, GE and Frisch, MJ (2001) Ab initio molecular dynamics: propagating the density matrix with Gaussian orbitals. Journal of Chemical Physics 114, 97589763.10.1063/1.1372182CrossRefGoogle Scholar
Schlegel, HB, Iyengar, SS, Li, X, Millam, JM, Voth, GA, Scuseria, GE and Frisch, MJ (2002) Ab initio molecular dynamics: propagating the density matrix with Gaussian orbitals. III. Comparison with Born–Oppenheimer dynamics. Journal of Chemical Physics 117, 86948704.10.1063/1.1514582CrossRefGoogle Scholar
Stephansen, AB, King, SB, Yokoi, Y, Minoshima, Y, Li, WL, Kunin, A, Takayanagi, T and Neumark, DM (2015) Dynamics of dipole- and valence bound anions in iodide-adenine binary complexes: a time-resolved photoelectron imaging and quantum mechanical investigation. Journal of Chemical Physics 143, 104308.10.1063/1.4929995CrossRefGoogle ScholarPubMed
Szymanska, E, Prabhudesai, VS, Mason, NJ and Krishnakumar, E (2013) Dissociative electron attachment to acetaldehyde, CH3CHO. A laboratory study using the velocity map imaging technique. Physical Chemistry Chemical Physics: PCCP 15, 9981005.CrossRefGoogle ScholarPubMed
Tonzani, S and Greene, CH (2006) Low-energy electron scattering from DNA and RNA bases: shape resonances and radiation damage. Journal of Chemical Physics 124, 054312.CrossRefGoogle ScholarPubMed
Tripathi, D and Dutta, AK (2019) Electron attachment to DNA base pairs: an interplay of dipole- and valence-bound states. Journal of Physical Chemistry A 123, 1013110138.10.1021/acs.jpca.9b08974CrossRefGoogle ScholarPubMed
Wang, YF and Tian, SX (2011) Shape resonance states of the low-energy electron attachments to DNA base tautomers. Physical Chemistry Chemical Physics: PCCP 13, 61696175.10.1039/c0cp01721cCrossRefGoogle ScholarPubMed
Wang, G, Yi, H, Li, Y, Wang, Y, Liu, D, Gao, F, Liu, W, Ren, J, Wang, X and Zhao, YJM (2018) Review of stopping power and Coulomb explosion for molecular ion in plasmas. Matter and Radiation at Extremes 3, 6777.10.1016/j.mre.2018.01.002CrossRefGoogle Scholar
Zawadzki, M, Rankovic, M, Kocisek, J and Fedor, J (2018) Dissociative electron attachment and anion-induced dimerization in pyruvic acid. Physical Chemistry Chemical Physics: PCCP 20, 68386844.10.1039/C7CP07472GCrossRefGoogle ScholarPubMed
Zhang, Y, Xu, Z, Zhao, Y and Zhang, X (2019) Ab initio molecular dynamics simulation study of dissociation electron attachment to lactic acid and isomer. Scientific Reports 9, 19532.10.1038/s41598-019-56019-4CrossRefGoogle ScholarPubMed