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SLEND simulation of a cytosine nucleotide SSB with an electron capture at LUMO + 2σ*on the phosphate. Simulation time is in a.u. At initial times (first two frames), the P–O bond along the phosphate-sugar backbone monotonically elongates; at later times (last two frames), that bond finally breaks, generating dihydrogen phosphite H2PO3⁻ and the rest of the nucleotide structure.
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Proton cancer therapy (PCT) utilizes high-energy proton projectiles to obliterate cancerous tumors with low damage to healthy tissues and without the side effects of X-ray therapy. The healing action of the protons results from their damage on cancerous cell DNA. Despite established clinical use, the chemical mechanisms of PCT reactions at the mole...
Citations
... [1][2][3][4][5][6][7] This is mainly due to the fact that water molecules are the basic components of biological tissues and it has been found that irradiated water molecules usually produce a large number of secondary lowenergy electrons, ions and radicals, which cause direct and indirect biological damage to DNA molecules through a series of chain reactions. [8][9][10][11] As the hadron therapy has been applied mostly with proton beams, a variety of works dedicated to proton-water collisions experimentally [3,[12][13][14][15][16][17][18][19] and theoretically. [20][21][22][23][24][25][26][27][28][29][30][31][32] These studies are helpful to understand the ionizing radiation of water impacted by protons. ...
To investigate the collision processes of proton with the water dimer (H 2 O) 2 at 50 eV, the time-dependent density functional theory coupled with molecular dynamics nonadiabatically is applied. Six specific collision orientations with various impact parameters are considered. The reaction channels, the mass distribution and the fragmentation mass spectrum are explored. Among all launched samples, the probability of the channel of NCT and CT is about 80%, hinting that the probability of fragmentation is about 20%. The reaction channel of PE2 is taken as an example to exhibit the detailed microscopic dynamics of the collision process by inspecting the positions, the respective distance, the number of loss of electrons and the evolution of the electron density. The study of the mass distribution and the fragmentation mass spectrum shows that among all possible fragments, the fragment with mass 36 has the highest relative abundance of 65%. The relative abundances of fragments with mass 1, 35 and 34 are 20%, 13% and 1.5%, respectively. For the total electron capture cross section, good agreement has been achieved between the present calculations and the available measurements and calculations over the energy range of 50 eV to 12 keV.
... We successfully applied SLEND to simulate various types of ICT reactions in systems involving H 2 O, DNA/RNA bases, and DNA nucleotides. 8,[21][22][23][24][25][26] For instance, we investigated H + + (H 2 O) n for n = 3-4 at E Lab = 1 keV 22,24 and for n = 1-6 at E Lab = 100 keV 23,24 to predict reactive processes and 1-ET ICSs. Herein, we study again H + + H 2 O, but we consider new conditions, properties, and phenomena. ...
... We successfully applied SLEND to simulate various types of ICT reactions in systems involving H 2 O, DNA/RNA bases, and DNA nucleotides. 8,[21][22][23][24][25][26] For instance, we investigated H + + (H 2 O) n for n = 3-4 at E Lab = 1 keV 22,24 and for n = 1-6 at E Lab = 100 keV 23,24 to predict reactive processes and 1-ET ICSs. Herein, we study again H + + H 2 O, but we consider new conditions, properties, and phenomena. ...
Following our preceding research [PCCP, 21, 5006, (2019)], we present an electron nuclear dynamics (END) investigation of H+ + H2O at ELab = 28.5 – 200.0 eV in conjunction with...
... There is no conflict of interest to report . 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 This article presented here has been accepted for publication in CCS Chemistry and is posted at the 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 This article presented here has been accepted for publication in CCS Chemistry and is posted at the 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 This article presented here has been accepted for publication in CCS Chemistry and is posted at the 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 This article presented here has been accepted for publication in CCS Chemistry and is posted at the 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 This article presented here has been accepted for publication in CCS Chemistry and is posted at the 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 This article presented here has been accepted for publication in CCS Chemistry and is posted at the with benzene and H 2 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 This article presented here has been accepted for publication in CCS Chemistry and is posted at the ...
... They are not stable, and in the subsequent anodic reaction, the second electron or a proton can be lost to form a dication or a neutral radical. Cation radicals are also formed as a response to radiolysis [40-43]: photolysis or ion or particle-beam irradiation; external alpha, beta, and gamma radiation; or radiation by the embedded radionuclides, etc. Different types of radiation produce direct proteins, carbohydrates, DNA and RNA damage, or indirectly destroy the biomolecules by generating water radical ions [43][44][45][46][47]. Similar to monosubstituted benzenes, which are archetypal for monosubstituted aromatics, monosubstituted benzene monocation radicals constitute a reference for cation radical aromatics including PAHs, for which there is evidence for the involvement of one-electron oxidation in PAH carcinogenesis [48][49][50][51][52]. ...
In 30 monosubstituted benzene cation radicals, studied at the ωB97XD/aug-cc-pVTZ level, the phenyl rings usually adopt a compressed form, but a differently compressed form-equivalent to an elongated one-may coexist. The computational and literature ionization potentials are well correlated. The geometrical and magnetic aromaticity, estimated using HOMA and NICS indices, show the systems to be structurally aromatic but magnetically antiaromatic or only weakly aromatic. The partial charge is split between the substituent and ring and varies the most at C(ipso). In the ring, the spin is 70%, concentrated equally at the C(ipso) and C(p) atoms. The sEDA(D) and pEDA(D) descriptors of the substituent effect in cation radicals, respectively, were determined. In cation radicals, the substituent effect on the σ-electron system is like that in the ground state. The effect on the π-electron systems is long-range, and its propagation in the radical quinone-like ring is unlike that in the neutral molecules. The pEDA(D) descriptor correlates well with the partial spin at C(ipso) and C(p) and weakly with the HOMA(D) index. The correlation of the spin at the ring π-electron system and the pEDA(D) descriptor shows that the electron charge supplied to the ring π-electron system and the spin flow oppositely.
... Given the amount of water in the human body, the most likely event that occurs is the collision of the ion with a water molecule, which gives rise to different electronic processes such as the ejection of electrons, followed by further ionization or excitation processes [6]. Different mechanisms after the collision can cause DNA damage, due to the creation of secondary electrons and ions, or of free radicals, or the heating of the medium due to target excitation [7]. ...
A recently proposed classical-trajectory dynamical screening model for the description of multiple ionization and capture during ion–water-molecule collisions is extended to incorporate dynamical screening on both the multicenter target potential and the projectile ion. Comparison with available experimental data for He2+ + H2O collisions at intermediate energies (10–150 keV/u) and Li3+ + H2O at higher energies (100–850 keV/u) demonstrates the importance of both screening mechanisms. The question of how to deal with the repartitioning of the capture flux into allowed capture channels is addressed. The model also provides insights for data on highly charged projectile ions (C6+, O8+, Si13+) in the MeV/u range where the question of saturation effects in net ionization was raised in the literature.
... SLEND and END/KSDFT have accurately described a great variety of reactions in the collision energy range, 10 eV ≤ E Lab ≤ 25 keV, that includes ion-molecule [7,9,11,12,[16][17][18][19][20][21][22][23][24][25][26], Diels-Alder [9], S N 2 [9], and intramolecular [27] reactions as well as reactions under applied electromagnetic field [28][29][30]. However, one of the most fruitful areas of research with SLEND and END/KSDFT is the simulation of the high-energy reactions occurring during proton cancer therapy (PCT) [31]. That research line is illustrated by our pioneering studies of water radiolysis reactions [9,[31][32][33], electron capture by protons from DNA/ RNA bases [34], proton-induced damage on DNA bases [9,31,32,34] and nucleotides [31], and electron-induced damage on DNA nucleotides [31]. ...
... However, one of the most fruitful areas of research with SLEND and END/KSDFT is the simulation of the high-energy reactions occurring during proton cancer therapy (PCT) [31]. That research line is illustrated by our pioneering studies of water radiolysis reactions [9,[31][32][33], electron capture by protons from DNA/ RNA bases [34], proton-induced damage on DNA bases [9,31,32,34] and nucleotides [31], and electron-induced damage on DNA nucleotides [31]. In spite of their success, SLEND and END/KSDFT expose difficulties to describe the scattering/capture of electrons to/from the continuum, processes relevant in highenergy reactions [33,35]. ...
... However, one of the most fruitful areas of research with SLEND and END/KSDFT is the simulation of the high-energy reactions occurring during proton cancer therapy (PCT) [31]. That research line is illustrated by our pioneering studies of water radiolysis reactions [9,[31][32][33], electron capture by protons from DNA/ RNA bases [34], proton-induced damage on DNA bases [9,31,32,34] and nucleotides [31], and electron-induced damage on DNA nucleotides [31]. In spite of their success, SLEND and END/KSDFT expose difficulties to describe the scattering/capture of electrons to/from the continuum, processes relevant in highenergy reactions [33,35]. ...
Electron nuclear dynamics (END) is an ab initio quantum dynamics method that adopts a time-dependent, variational, direct, and non-adiabatic approach. The simplest-level (SL) END (SLEND) version employs a classical mechanics description for nuclei and a Thouless single-determinantal wave function for electrons. A higher-level END version, END/Kohn–Sham density functional theory, improves the electron correlation description of SLEND. While both versions can simulate various types of chemical reactions, they have difficulties to simulate scattering/capture of electrons to/from the continuum due to their reliance on localized Slater-type basis functions. To properly describe those processes, we formulate END with plane waves (PWs, END/PW), basis functions able to represent both bound and unbound electrons. As extra benefits, PWs also afford fast algorithms to simulate periodic systems, parametric independence from nuclear positions and momenta, and elimination of basis set linear dependencies and orthogonalization procedures. We obtain the END/PW formalism by extending the Thouless wave function and associated electron density to periodic systems, expressing the energy terms as functionals of the latter entities, and deriving the energy gradients with respect to nuclear and electronic variables. END/PW has a great potential to simulate electron processes in both periodic (crystal) and aperiodic (molecular) systems (the latter in a supercell approach). Following previous END studies, END/PW will be applied to electron scattering processes in proton cancer therapy reactions.
... Collisions involving complex molecules pose a significant challenge to theory owing to their large number of degrees of freedom and their multi-center geometry. While a few first-principles calculations have been reported in recent years [9][10][11][12], most of the available cross-section a e-mail: tomk@yorku.ca information is based on simplified approaches. ...
Net ionization and net capture cross-section calculations are presented for proton collisions with methane molecules and the DNA/RNA nucleobases adenine, cytosine, guanine, thymine, and uracil. We use the recently introduced independent-atom-model pixel counting method to calculate these cross sections in the 10 keV to 10 MeV impact energy range and compare them with results obtained from the simpler additivity rule, a previously used complete-neglect-of-differential-overlap method, and with experimental data and previous calculations where available. It is found that all theoretical results agree reasonably well at high energies, but deviate significantly in the low-to-intermediate energy range. In particular, the pixel counting method which takes the geometrical overlap of atomic cross sections into account is the only calculation that is able to describe the measurements for capture in proton-methane collisions down to 10 keV impact energy. For the nucleobases it also yields a significantly smaller cross section in this region than the other models. New measurements are urgently required to test this prediction.
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... While progress has been made on both experimental (see [2][3][4][5][6][7][8][9] for proton-impact collisions) and theoretical [10][11][12] fronts, the complexity and multitude of molecules of interest suggest that there is a role to be played by simplified models which are easily applicable to a wide range of collision systems. ...
We use the recently introduced independent-atom-model pixel counting method to calculate proton-impact net ionization cross sections for a large class of biologically relevant systems including pyrimidines, purines, amino acids, and nucleotides from 10 keV to 10 MeV impact energy. Overall good agreement with experimental data, where available, is found. A scaling prescription that involves coefficients derived from the independent atom model is shown to represent the cross section results better than scalings based on the number of (bonding) valence electrons of the target molecules. It is shown that the scaled net ionization cross sections of the proton-nucleotide collision systems can be represented in terms of a simple analytical formula with four parameters to within 3% accuracy.
... While progress has been made on both experimental (see [2][3][4][5][6][7][8][9] for proton-impact collisions) and theoretical [10][11][12] fronts, the complexity and multitude of molecules of interest suggest that there is a role to be played by simplified models which are easily applicable to a wide range of collision systems. ...
We use the recently introduced independent-atom-model pixel counting method to calculate proton-impact net ionization cross sections for a large class of biologically relevant systems including pyrimidines, purines, amino acids, and nucleotides from 10 keV to 10 MeV impact energy. Overall good agreement with experimental data, where available, is found. A scaling prescription that involves coefficients derived from the independent atom model is shown to represent the cross section results better than scalings based on the number of (bonding) valence electrons of the target molecules. It is shown that the scaled net ionization cross sections of the proton-nucleotide collision systems can be represented in terms of a simple analytical formula with four parameters to within 3% accuracy.
... For over a decade, we have successfully investigated various types of chemical reactions [4][5][6][7][8][9][10][11][12][13][14][15] with the electron nuclear dynamics (END) method. [15][16][17] END is a time-dependent, variational, nonadiabatic and direct-dynamics method to simulate chemical reactions. ...
... 25 Moreover, aside from expanding the knowledge of symmetry breaking, this reaction is highly relevant for the chemistry of planetary atmospheres and interstellar matter 25 and for the study of proton cancer therapy reactions. [11][12][13][14][15] The symmetry breaking procedure is herein applied to SLEND but can be equally applied to the END method based on KSDFT. 7,15 Moreover, this procedure can be extended to any direct-dynamic method employing HF or KSDFT electronic descriptions. ...
... To illustrate the predicted reactions, Fig. 3-6 show sequential snapshots of SLEND/6-31G** simulations of four representative reactions: (IIIa), eqn (13), (IVa), eqn (14), (Vc), eqn (15), and (VI), eqn (16), respectively. In those figures, colored spheres represent the classical nuclei (black = C, white = H). ...
We present a computational procedure that introduces low degrees of symmetry breaking into a restricted Hartree-Fock (RHF) state in order to induce higher symmetry breaking during the state’s subsequent dynamics....
