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Ben-Asher A, Landau A, Moiseyev N. Uniform vs Partial Scaling within Resonances via Padé Based on the Similarities to Other Non-Hermitian Methods: Illustration for the Beryllium 1 s22 p3 s State. J Chem Theory Comput 2021; 17:3435-3444. [PMID: 33945263 DOI: 10.1021/acs.jctc.1c00223] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Resonance via Padé (RVP) is an efficient method for calculating autoionization resonance states. It is based on the stabilization technique in which the basis set is scaled. The scaling can be uniform (i.e., all basis functions are scaled) or partial. Herein, we compare the two RVP scaling schemes for calculating an autoionization eigenvalue; moreover, the effect of freezing the core electrons is intertwined within this comparison. In order to study the different behavior of the RVP schemes, we associate each RVP scaling scheme with a complex contour of integration. Similarities between RVP and other non-Hermitian methods emerge from the generated contours, which suggest that RVP introduces similar outgoing boundary conditions as the complex scaling (CS), complex basis function (CBF), and reflection-free complex absorbing potential (RF-CAP) methods. A uniform-RVP contour, unlike a partial one, immediately penetrates the complex plane and influences the interaction region. Hence, uniform scaling within RVP destroys the description of the core electrons, as well as the description of the reference state, and yields less reliable results than partial scaling. The 1s22p3s 1P autoionization state of Be, at the equation-of-motion coupled-cluster level, is used as our case study model.
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Affiliation(s)
- Anael Ben-Asher
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Arie Landau
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Nimrod Moiseyev
- Schulich Faculty of Chemistry, Department of Physics and Russell-Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, Haifa 32000, Israel
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Lemelin V, Bass AD, Sanche L. Low energy (6-18 eV) electron scattering from condensed thymidine (dT) III: absolute electronic excitation cross sections. Phys Chem Chem Phys 2020; 22:8364-8372. [PMID: 32266899 DOI: 10.1039/d0cp00198h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Absolute cross sections (CSs) for electronic excitation by low-energy electron (LEE) scattering, from condensed thymidine (dT) in the 6-18 eV incident energy range, were measured by high-resolution electron energy loss spectroscopy (HREELS). Various electron energy loss (EEL) spectra were acquired using 1 ML of dT condensed on a multilayer film of Ar held at about 20 K under ultra-high vacuum (∼1 × 10-11 Torr). dT is one of the most complex DNA constituents to be studied by HREELS and these spectra provide the first LEE energy-loss data for electronic excitation of a nucleoside. CSs for transitions to the states 13A', 13A'', 23A', 21A', 33A', 23A'', 43A', 33A'', 53A' and 51A' of dT were extracted from the EEL spectra. These states correlate to those previously measured for the thymine moiety. Two broad resonances are observed in the energy dependence of the CSs at around 8 and 10 eV; these energies are close to those found in earlier gas- and solid-phase studies on the interaction of LEEs with dT, thymine and related molecules. A quantitative comparison between the electronic CSs of dT and those of thymine and tetrahydrofuran indicates that no variation is induced in the electronic CSs of thymine upon chemically binding to a deoxyribose group.
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Affiliation(s)
- V Lemelin
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et Sciences des radiations, Université de Sherbrooke, Québec J1H 5N4, Canada.
| | - A D Bass
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et Sciences des radiations, Université de Sherbrooke, Québec J1H 5N4, Canada.
| | - L Sanche
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et Sciences des radiations, Université de Sherbrooke, Québec J1H 5N4, Canada.
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Lemelin V, Bass AD, Cloutier P, Sanche L. Low energy (1-19 eV) electron scattering from condensed thymidine (dT) II: comparison of vibrational excitation cross sections with those of tetrahydrofuran and the recalibrated values of thymine. Phys Chem Chem Phys 2019; 21:23818-23825. [PMID: 31503272 DOI: 10.1039/c9cp03448j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Recent measurements of absolute vibrational cross sections (CSs) for low-energy electron (LEE) scattering from condensed thymidine (dT) allows comparison with CSs of its constituents; thymine and tetrahydrofuran (THF). To facilitate this comparison, the vibrational CSs of condensed thymine were remeasured at six electron incident energies and a correction was applied to the earlier thymine CS values measured by Lévesque et al. [Nucl. Instrum. Methods Phys. Res., Sect. B, 2003, 208, 225]. The incident energy dependence of the CS of each vibrational mode of dT is compared with the corresponding modes in thymine and/or THF. It is found that the magnitude of the CSs of the thymine breathing mode and the C-C stretch mode of THF are greatly attenuated in dT. Finally, the magnitudes of the total vibrational CSs of each molecule are compared. Below 4 eV, the total vibrational CSs of dT is greater than each of its two constituents. Interestingly, at higher energy (>6 eV), the magnitude of the total vibrational CS of dT is roughly equal to that of THF and is greater than thymine by only 15% at 10 eV, showing that the CSs of dT cannot be approximated by the addition of the CSs of its constituents over the entire energy range. These comparisons are discussed in terms of the basic principles involved in the formation and decay of shape resonances, which are known to be responsible for major enhancements of LEE-induced vibrational excitation at low electron energies.
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Affiliation(s)
- V Lemelin
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et Sciences des radiations, Université de Sherbrooke, Québec J1H 5N4, Canada.
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Lemelin V, Bass AD, Cloutier P, Sanche L. Low energy (1-19 eV) electron scattering from condensed thymidine (dT) I: absolute vibrational excitation cross sections. Phys Chem Chem Phys 2019; 21:23808-23817. [PMID: 31503266 DOI: 10.1039/c9cp03447a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Absolute cross sections (CSs) for vibrational excitation by electrons of energy between 1-19 eV scattering from condensed thymidine (dT) were measured by means of high-resolution electron energy loss spectroscopy (HREELS). The CSs were extracted from electron energy loss spectra of dT condensed on multilayers film of Ar held at about 20 K under ultra-high vacuum (∼1 × 10-11 Torr). dT is one of the most complex molecules to be studied in condensed phase by HREELS. The magnitudes of the vibrational CSs lie within the 10-17 cm2 range. Structures observed in the energy dependence of the vibrational CSs under 3 eV and around 4 eV were compared with previous results of gas- and solid-phase studies on dT and related molecules (e.g., thymine and tetrahydrofuran). These structures were attributed to the formation of shape resonances.
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Affiliation(s)
- V Lemelin
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et Sciences des radiations, Université de Sherbrooke, Québec J1H 5N4, Canada.
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Mette G, Adamkiewicz A, Reutzel M, Koert U, Dürr M, Höfer U. Controlling an S N
2 Reaction by Electronic and Vibrational Excitation: Tip-Induced Ether Cleavage on Si(001). Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201806777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Gerson Mette
- Fachbereich Physik und Zentrum für Materialwissenschaften; Philipps-Universität Marburg; Renthof 5 35032 Marburg Germany
| | - Alexa Adamkiewicz
- Fachbereich Physik und Zentrum für Materialwissenschaften; Philipps-Universität Marburg; Renthof 5 35032 Marburg Germany
| | - Marcel Reutzel
- Fachbereich Physik und Zentrum für Materialwissenschaften; Philipps-Universität Marburg; Renthof 5 35032 Marburg Germany
| | - Ulrich Koert
- Fachbereich Chemie; Philipps-Universität; Hans-Meerwein-Straße 4 35032 Marburg Germany
| | - Michael Dürr
- Institut für Angewandte Physik; Justus-Liebig-Universität Giessen; Heinrich-Buff-Ring 16 35392 Giessen Germany
| | - Ulrich Höfer
- Fachbereich Physik und Zentrum für Materialwissenschaften; Philipps-Universität Marburg; Renthof 5 35032 Marburg Germany
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Mette G, Adamkiewicz A, Reutzel M, Koert U, Dürr M, Höfer U. Controlling an SN
2 Reaction by Electronic and Vibrational Excitation: Tip-Induced Ether Cleavage on Si(001). Angew Chem Int Ed Engl 2019; 58:3417-3420. [DOI: 10.1002/anie.201806777] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 12/08/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Gerson Mette
- Fachbereich Physik und Zentrum für Materialwissenschaften; Philipps-Universität Marburg; Renthof 5 35032 Marburg Germany
| | - Alexa Adamkiewicz
- Fachbereich Physik und Zentrum für Materialwissenschaften; Philipps-Universität Marburg; Renthof 5 35032 Marburg Germany
| | - Marcel Reutzel
- Fachbereich Physik und Zentrum für Materialwissenschaften; Philipps-Universität Marburg; Renthof 5 35032 Marburg Germany
| | - Ulrich Koert
- Fachbereich Chemie; Philipps-Universität; Hans-Meerwein-Straße 4 35032 Marburg Germany
| | - Michael Dürr
- Institut für Angewandte Physik; Justus-Liebig-Universität Giessen; Heinrich-Buff-Ring 16 35392 Giessen Germany
| | - Ulrich Höfer
- Fachbereich Physik und Zentrum für Materialwissenschaften; Philipps-Universität Marburg; Renthof 5 35032 Marburg Germany
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Lemelin V, Bass AD, Sanche L. Note: Absolute electronic excitation cross sections for 8.5-17.5 eV electron scattering from condensed dimethyl phosphate (DMP). J Chem Phys 2018; 149:246101. [DOI: 10.1063/1.5059387] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- V. Lemelin
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et Sciences des Radiations, Université de Sherbrooke, Québec J1H 5N4, Canada
| | - A. D. Bass
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et Sciences des Radiations, Université de Sherbrooke, Québec J1H 5N4, Canada
| | - L. Sanche
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et Sciences des Radiations, Université de Sherbrooke, Québec J1H 5N4, Canada
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Lemelin V, Bass AD, Wagner JR, Sanche L. Absolute vibrational excitation cross sections for 1-18 eV electron scattering from condensed dimethyl phosphate (DMP). J Chem Phys 2017; 147:234305. [DOI: 10.1063/1.5008486] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- V. Lemelin
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et Sciences des Radiations, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
| | - A. D. Bass
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et Sciences des Radiations, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
| | - J. R. Wagner
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et Sciences des Radiations, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
| | - L. Sanche
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et Sciences des Radiations, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
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Lemelin V, Bass AD, Cloutier P, Sanche L. Absolute cross sections for electronic excitation of condensed tetrahydrofuran (THF) by 11-16 eV electrons. J Chem Phys 2017; 145:174703. [PMID: 27825202 DOI: 10.1063/1.4966650] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Absolute cross section (CS) data on the interaction of low energy electrons with DNA and its molecular constituents are required as input parameters in Monte-Carlo type simulations, for several radiobiological applications. Previously [V. Lemelin et al., J. Chem. Phys. 144, 074701 (2016)], we measured absolute vibrational CSs for low-energy electron scattering from condensed tetrahydrofuran, a convenient surrogate for the deoxyribose. Here we report absolute electronic CSs for energy losses of between 6 and 11.5 eV, by electrons with energies between 11 and 16 eV. The variation of these CSs with incident electron energy shows no evidence of transient anion states, consistent with theoretical and other experimental results, indicating that initial electron capture leading to DNA strand breaks occurs primarily on DNA bases or the phosphate group.
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Affiliation(s)
- V Lemelin
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et Sciences des Radiations, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
| | - A D Bass
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et Sciences des Radiations, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
| | - P Cloutier
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et Sciences des Radiations, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
| | - L Sanche
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et Sciences des Radiations, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
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