Proton-impact-induced electron emission from biologically relevant molecules studied with a screened independent atom model

Lüdde, Hans Jürgen; Horbatsch, Marko; Kirchner, Tom

doi:10.1088/1361-6455/ab3a63

Cited by 19 publications

(23 citation statements)

References 42 publications

(163 reference statements)

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“…While finishing the present work, we became aware of an accepted manuscript by Luedde et al [31] on total ionization of biological molecules by proton impact, using an independent-atom-model pixel counting method. The authors also raised a scaling with ν α = 4 for C, N, and O, but ν α = 6 for P. The agreement with this independent method for proton impact reinforces our multichargedion findings.…”

Section: Cdw-based Scalingmentioning

confidence: 99%

Ionization of biological molecules by multicharged ions using the stoichiometric model

Mendez

Montanari

Miraglia

2020

J. Phys. B: At. Mol. Opt. Phys.

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In the present work, we investigate the ionization of molecules of biological interest by the impact of multicharged ions in the intermediate to high energy range. We performed full non-perturbative distorted-wave calculations (CDW) for thirty-six collisional systems composed by six atomic targets: H, C, N, O, F and S -which are the constituents of most of the DNA and biological molecules-and six charged projectiles (antiprotons, H, He, B, C, and O). On account of the radiation damage caused by secondary electrons, we inspect the energy and angular distributions of the emitted electrons from the atomic targets. We examine seventeen molecules: DNA and RNA bases, DNA backbone, pyrimidines, tetrahydrofuran (THF), and CnHn compounds. We show that the simple stoichiometric model (SSM), which approximates the molecular ionization cross sections as a linear combination of the atomic ones, gives reasonably good results for complex molecules. We also inspect the extensively used Toburen scaling of the total ionization cross sections of molecules with the number of weakly bound electrons. Based on the atomic CDW results, we propose new active electron numbers, which improves significantly scaling for all the targets and ions studied here in the intermediate to the high energy region. The new scaling describes well the available experimental data for proton impact, including small molecules. We perform full molecular calculations for five nucleobases and test a modified stoichiometric formula based on the Mulliken charge of the composite atoms. The difference introduced by the new stoichiometric formula is less than 3%, which indicates the reliability of the SSM to deal with this type of molecules. The results of the extensive ion-target examination included in the present study allow us to assert that the SSM and the CDW-based scaling will be useful tools in this area.

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Section: Cdw-based Scalingmentioning

confidence: 99%

Ionization of biological molecules by multicharged ions using the stoichiometric model

Mendez

Montanari

Miraglia

2020

J. Phys. B: At. Mol. Opt. Phys.

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“…Another approach is to use collision information obtained for the atomic constituents and to combine them into molecular cross sections, most notably independent atom models (IAM), which either follow the simple Bragg additivity rule (labeled IAM-AR), or more sophisticated versions that take the molecular structure of the target into account, and allow for the fact that the effective cross section should be reduced due to overlap effects. The latter, named pixel counting method (labeled IAM-PCM), tested originally for proton impact [7][8][9][10] was used recently to investigate scaling behavior of net ionization as a function of projectile charge [11].…”

Section: Introductionmentioning

confidence: 99%

Net Electron Capture in Collisions of Multiply Charged Projectiles with Biologically Relevant Molecules

Lüdde

Jorge

Horbatsch

et al. 2020

Atoms

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A model for the description of proton collisions from molecules composed of atoms such as hydrogen, carbon, nitrogen, oxygen and phosphorus (H, C, N, O, P) was recently extended to treat collisions with multiply charged ions with a focus on net ionization. Here we complement the work by focusing on net capture. The ion–atom collisions are computed using the two-center basis generator method. The atomic net capture cross sections are then used to assemble two models for ion–molecule collisions: An independent atom model (IAM) based on the Bragg additivity rule (labeled IAM-AR), and also the so-called pixel-counting method (IAM-PCM) which introduces dependence on the orientation of the molecule during impact. The IAM-PCM leads to significantly reduced capture cross sections relative to IAM-AR at low energies, since it takes into account the overlap of effective atomic cross sectional areas. We compare our results with available experimental and other theoretical data focusing on water vapor (H2O), methane (CH4) and uracil (C4H4N2O2). For the water molecule target we also provide results from a classical-trajectory Monte Carlo approach that includes dynamical screening effects on projectile and target. For small molecules dominated by a many-electron atom, such as carbon in methane or oxygen in water, we find a saturation phenomenon for higher projectile charges (q=3) and low energies, where the net capture cross section for the molecule is dominated by the net cross section for the many-electron atom, and the net capture cross section is not proportional to the total number of valence electrons.

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“…Independent-atom models (IAM) were studied extensively for proton impact in our group [9][10][11][12]. On the basis of proton-atom collision calculations performed using the twocenter basis generator method (TC-BGM) [13] one can form simply an estimate for the ion-molecule cross section by the Bragg additivity rule, and this was called the IAM-AR model.…”

Section: Introductionmentioning

confidence: 99%

“…In Ref. [11] a detailed comparison between IAM-AR, IAM-PCM and molecular-orbital energy based models is provided for proton-pyrimidine (C 4 H 4 N 2 ) collisions in Fig. 2a, and it is evident that the shape of the IAM-PCM cross sections begins to deviate at energies below E = 1 MeV/amu from AR and the other models.…”

Section: Introductionmentioning

confidence: 99%

Non-perturbative scaling behavior for net ionization of biologically relevant molecules by multiply-charged heavy-ion impact

Lüdde,

Kalkbrenner,

Horbatsch

et al. 2020

Preprint

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A recently developed model to describe proton collisions from molecules involving basic atoms such as hydrogen, carbon, nitrogen, oxygen and phosphorus (H, C, N, O, P) is extended to treat collisions with multiply charged ions. The ion-atom collisions are computed using the two-center basis generator method (TC-BGM), which has a proven track record of yielding accurate total cross sections for electron capture and ionization. The atomic net ionization cross sections are then used to assemble two models for ion-molecule collisions: an independent atom model (IAM) that follows the Bragg additivity rule (labeled IAM-AR), and also the so-called pixel-counting method (IAM-PCM). The latter yields reduced cross sections relative to IAM-AR near the maximum, since it takes into account the overlapping nature of effective cross sectional areas. The IAM-PCM for higher-charge projectiles leads to strong reductions of net ionization cross sections relative to the IAM-AR method, and is computed directly for projectile charges Q = 1, 2, 3. The scaling behavior of the IAM-PCM is investigated over a wide range of energies E, and at high E it converges towards the IAM-AR. An empirical scaling rule is established which allows to reproduce these results based on proton impact calculations. Detailed comparisons are provided for the uracil target (C 4 H 4 N 2 O 2 ), for which other theoretical as well as experimental results are available. Data are also shown for targets such as water (H 2 O), methane (CH 4 ), adenine (C 5 H 5 N 5 ), L-valine (C 5 H 11 NO 2 ), and the nucleotide dAMP (C 10 H 14 N 5 O 6 P). Based on the scaling model derived from the IAM-PCM data it is shown how the experimental data for uracil and water bombarded by multiply charged ions can be reduced to effective Q = 1 cross sections respectively, and these are compared to proton impact data.

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Proton-impact-induced electron emission from biologically relevant molecules studied with a screened independent atom model

Cited by 19 publications

References 42 publications

Ionization of biological molecules by multicharged ions using the stoichiometric model

Ionization of biological molecules by multicharged ions using the stoichiometric model

Net Electron Capture in Collisions of Multiply Charged Projectiles with Biologically Relevant Molecules

Non-perturbative scaling behavior for net ionization of biologically relevant molecules by multiply-charged heavy-ion impact

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