Electron nuclear dynamics of proton collisions with DNA/RNA bases at ELab=80keV: A contribution to proton cancer therapy research

Privett, Austin J.; Morales, Jorge A.

doi:10.1016/j.cplett.2014.04.018

Cited by 16 publications

(37 citation statements)

References 32 publications

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“…Eq 5). As proven previously [6, 26, 27], classical nuclear dynamics does not impair the accuracy of PCT simulations because they happen at high collision energies. The SLEND electronic wavefunction is a spin-unrestricted, single-determinantal wavefunction in the Thouless representation [31].…”

Section: Methodssupporting

confidence: 60%

“…While the predominant paradigm for cancer research is experimental/clinical, theoretical/computational methods can reveal microscopic details of PCT more exhaustively than experimental/clinical techniques and without putting human subjects at risk. Therefore, time-independent scattering [21–23] and time-dependent dynamics methods [6, 24–27] have been applied to computationally feasible prototypes of PCT reactions (e.g. H + + (H 2 O) 1–4 to model water radiolysis reactions [6, 21–26, 28] and H + + DNA/RNA bases to model DNA proton damage [6, 21, 22, 26, 27]).…”

Section: Introductionmentioning

confidence: 99%

“…Among quantum-mechanics methods for PCT [6, 24–27], the electron nuclear dynamics (END) theory [26, 29] offers distinctive capabilities to study PCT reactions. END is a (1) time-dependent, (2) direct and (3) non-adiabatic method to simulate chemical reactions.…”

Section: Introductionmentioning

confidence: 99%

“…Thus, SLEND possesses a suitable balance between accuracy and computational feasibility to simulate large PCT prototypes (cf. previous SLEND studies of H + + (H 2 O) n , n = 1 [24, 28], 2 [25], and 3–4 [6, 26] and of H + + DNA/RNA bases and DNA base pairs [6, 26, 27]).…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Exploring water radiolysis in proton cancer therapy: Time-dependent, non-adiabatic simulations of H+ + (H2O)1-6

et al. 2017

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To elucidate microscopic details of proton cancer therapy (PCT), we apply the simplest-level electron nuclear dynamics (SLEND) method to H+ + (H2O)1-6 at ELab = 100 keV. These systems are computationally tractable prototypes to simulate water radiolysis reactions—i.e. the PCT processes that generate the DNA-damaging species against cancerous cells. To capture incipient bulk-water effects, ten (H2O)1-6 isomers are considered, ranging from quasi-planar/multiplanar (H2O)1-6 to “smallest-drop” prism and cage (H2O)6 structures. SLEND is a time-dependent, variational, non-adiabatic and direct method that adopts a nuclear classical-mechanics description and an electronic single-determinantal wavefunction in the Thouless representation. Short-time SLEND/6-31G* (n = 1–6) and /6-31G** (n = 1–5) simulations render cluster-to-projectile 1-electron-transfer (1-ET) total integral cross sections (ICSs) and 1-ET probabilities. In absolute quantitative terms, SLEND/6-31G* 1-ET ICS compares satisfactorily with alternative experimental and theoretical results only available for n = 1 and exhibits almost the same accuracy of the best alternative theoretical result. SLEND/6-31G** overestimates 1-ET ICS for n = 1, but a comparable overestimation is also observed with another theoretical method. An investigation on H+ + H indicates that electron direct ionization (DI) becomes significant with the large virtual-space quasi-continuum in large basis sets; thus, SLEND/6-31G** 1-ET ICS is overestimated by DI contributions. The solution to this problem is discussed. In relative quantitative terms, both SLEND/6-31* and /6-31G** 1-ET ICSs precisely fit into physically justified scaling formulae as a function of the cluster size; this indicates SLEND’s suitability for predicting properties of water clusters with varying size. Long-time SLEND/6-31G* (n = 1–4) simulations predict the formation of the DNA-damaging radicals H, OH, O and H3O. While “smallest-drop” isomers are included, no early manifestations of bulk water PCT properties are observed and simulations with larger water clusters will be needed to capture those effects. This study is the largest SLEND investigation on water radiolysis to date.

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Section: Methodssupporting

confidence: 60%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Exploring water radiolysis in proton cancer therapy: Time-dependent, non-adiabatic simulations of H+ + (H2O)1-6

et al. 2017

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“…Other studies have modeled collisions with heavier ions [16,17]. Simulations have also been performed that include the electron dynamics in the collision using various theoretical treatments, but these calculations used atomic orbital (Gaussian based) basis sets on various small molecules [12][13][14][15]. However, localization of the wave function from a limited Gaussian basis will prevent electrons from ionizing into continuum states and studies on such radiation-molecular interactions using real-space grids could better model the ionization process [79,81,82,86,87].…”

Section: Introductionmentioning

confidence: 99%

Time-dependent density-functional-theory investigation of the collisions of protons and α particles with uracil and adenine

et al. 2017

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Time-dependent density functional theory was employed to study the e↵ects of proton and ↵-particle radiation on uracil and adenine. This method has the advantage of treating nuclear motion and electronic motion simultaneously, allowing for the study of electronic excitation, charge transfer, ionization, and nuclear motion. Particle energies were surveyed in the range of 15-500 keV for protons and 100-2000 keV for ↵-particles in conjunction with impact points both on and o↵ carbon bonds in order to investigate the electron and nuclear dynamics of irradiated molecules and the form and quantity of transferred energy. The stopping power, energy transferred, and ionization were found and the relationship between incident particle energy and electron density of to the target molecule was characterized for proton and ↵-particle radiation incident on adenine and uracil.

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Testing standard basis sets for direct ionizations: H⁺ + H at E_Lab = 0.1–100 keV

Kim,

Morales

2023

J Comput Chem

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With the simplest‐level electron nuclear dynamics (SLEND) method, we test standard Slater‐type‐orbital/contracted‐Gaussian‐functions (STO/CGFs) basis sets for the simulation of direct ionizations (DIs), charge transfers (CTs), and target excitations (TEs) in H+ + H at ELab = 0.1–100 keV. SLEND is a time‐dependent, variational, on‐the‐fly, and nonadiabatic method that treats nuclei and electrons with classical dynamics and a Thouless single‐determinantal state, respectively. While previous tests for CTs and TEs exist, this is the first SLEND/STO/CGFs test for challenging DIs. Spin‐orbitals with negative/positive energies are treated as bound/unbound states for bound‐to‐bound (CT and TE) and bound‐to‐unbound (DI) transitions. SLEND/STO/CGFs simulations correctly reproduce all the features of DIs, CTs and TEs over all the considered impact parameters and energies. SLEND/STO/CGFs simulations correctly predict CT integrals cross‐sections (ICSs) over all the considered energies and predict satisfactory DI and TE ICSs within some energy ranges. Strategies to improve SLEND/STO/CGFs for DI predictions are discussed.

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Electron nuclear dynamics of proton collisions with DNA/RNA bases at ELab=80keV: A contribution to proton cancer therapy research

Cited by 16 publications

References 32 publications

Exploring water radiolysis in proton cancer therapy: Time-dependent, non-adiabatic simulations of H+ + (H2O)1-6

Exploring water radiolysis in proton cancer therapy: Time-dependent, non-adiabatic simulations of H+ + (H2O)1-6

Time-dependent density-functional-theory investigation of the collisions of protons and α particles with uracil and adenine

Testing standard basis sets for direct ionizations: H⁺ + H at E_Lab = 0.1–100 keV

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Electron nuclear dynamics of proton collisions with DNA/RNA bases at ELab=80keV: A contribution to proton cancer therapy research

Cited by 16 publications

References 32 publications

Exploring water radiolysis in proton cancer therapy: Time-dependent, non-adiabatic simulations of H+ + (H2O)1-6

Exploring water radiolysis in proton cancer therapy: Time-dependent, non-adiabatic simulations of H+ + (H2O)1-6

Time-dependent density-functional-theory investigation of the collisions of protons and α particles with uracil and adenine

Testing standard basis sets for direct ionizations: H+ + H at ELab = 0.1–100 keV

Contact Info

Product

Resources

About

Testing standard basis sets for direct ionizations: H⁺ + H at E_Lab = 0.1–100 keV