1
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Silva MO, Moreira GM, Rosado J, Blanco F, García G, Bettega MHF, da Costa RF. Elastic and electronically inelastic scattering of electrons by the pyrazine molecule. Phys Chem Chem Phys 2024; 26:7276-7286. [PMID: 37987761 DOI: 10.1039/d3cp04619b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
We report on elastic and electronically inelastic integral and differential cross sections as well as ionization and total cross sections for electron collisions with the pyrazine molecule. The Schwinger multichannel method is applied in calculations carried out according to the minimal orbital basis for single configuration interactions strategy from the 1-channel up to 139-channels close-coupling level of approximation. With these calculations we have obtained integral and differential cross sections as well as excitation functions for elastic electron scattering and, also, integral and differential cross sections for electronic excitation from the ground state to the 3B1u, 3B2u, 3B3u, 1B1u, 1B2u and 1B3u excited states of pyrazine by electron impact. By summing the total ionization cross section obtained by means of the binary-encounter-Bethe model to these elastic and electronically inelastic contributions, we provided an estimate for the total cross section describing the electron-pyrazine interaction process. The independent atom model with the screening-corrected additivity rule plus interference terms method was also used in the present study to determine elastic integral and differential as well as ionization and total cross sections for electron collisions from pyrazine. The present results were, whenever possible, critically compared to the experimental and theoretical data available in the literature. In general, the overall agreement between the present results and the experiment is quite encouraging.
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Affiliation(s)
- Murilo O Silva
- Departamento de Física, Universidade Federal do Paraná, Caixa Postal 19044, 81531-980 Curitiba, Paraná, Brazil
| | - Giseli M Moreira
- Departamento de Física, Universidade Estadual do Centro-Oeste, 85040-167 Guarapuava, Paraná, Brazil
| | - Jaime Rosado
- Departamento de Estructura de la Materia, Física Térmica y Electrónica e IPARCOS, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Francisco Blanco
- Departamento de Estructura de la Materia, Física Térmica y Electrónica e IPARCOS, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Gustavo García
- Instituto de Física Fundamental, Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain
| | - Márcio H F Bettega
- Departamento de Física, Universidade Federal do Paraná, Caixa Postal 19044, 81531-980 Curitiba, Paraná, Brazil
| | - Romarly F da Costa
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, 09210-580 Santo André, São Paulo, Brazil.
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2
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Nakata H, Fedorov DG. Analytic Gradient for Time-Dependent Density Functional Theory Combined with the Fragment Molecular Orbital Method. J Chem Theory Comput 2023; 19:1276-1285. [PMID: 36753486 DOI: 10.1021/acs.jctc.2c01177] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The analytic energy gradient of energy with respect to nuclear coordinates is derived for the fragment molecular orbital (FMO) method combined with time-dependent density functional theory (TDDFT). The response terms arising from the use of a polarizable embedding are derived. The obtained analytic FMO-TDDFT gradient is shown to be accurate in comparison to both numerical FMO-TDDFT and unfragmented TDDFT gradients, at the level of two- and three-body expansions. The gradients are used for geometry optimizations, molecular dynamics, vibrational calculations, and simulations of IR and Raman spectra of excited states. The developed method is used to optimize the geometry of the ground and excited electronic states of the photoactive yellow protein (PDB: 2PHY).
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Affiliation(s)
- Hiroya Nakata
- Department of Chemistry, Kyungpook National University, Daegu 41566, South Korea
| | - Dmitri G Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Central 2, Umezono 1-1-1, Tsukuba 305-8568, Japan
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3
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Liu M, Abdelmouleh M, Giuliani A, Nahon L, Poully JC. UV-VUV Photofragmentation Spectroscopy of Isolated Neutral Fragile Macromolecules: A Proof-of-Principle Based on a Deprotonated Vancomycin-Peptide Noncovalent Complex. J Phys Chem A 2022; 126:9042-9050. [PMID: 36442079 DOI: 10.1021/acs.jpca.2c07744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The gas phase offers the possibility to analyze organic molecules by ultraviolet-vacuum ultraviolet (UV-VUV) spectroscopy without any solvent effect or limitation in terms of spectral range due to absorption by the solvent. Up to now, the size and chemical composition of neutral molecular systems under study have been limited by the use of vaporization methods based on thermal heating. Soft sources of gas-phase thermolabile molecular systems such as electrospray or matrix-assisted laser desorption ionization are appealing alternatives to heating-based techniques, but they lead to the production of ions. In such cases, UV-VUV action spectroscopy is then the method of choice to study the electronic structure and corresponding photodynamics of these gas-phase molecular ions. However, previous investigations have shown that the UV-VUV action spectrum of a given molecular ion depends on the charge state, which in many cases might be a caveat. Here, by means of synchrotron radiation coupled to mass spectrometry and through the test case of the glycopeptide antibiotic vancomycin noncovalently bound to a deprotonated small peptide, we show that the UV-VUV photofragmentation spectrum of neutral thermally fragile organic molecules can be obtained via charge-tagging action spectroscopy.
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Affiliation(s)
- Min Liu
- CIMAP, UMR 6252 CEA/CNRS/ENSICAEN/Université de Caen Normandie, Bd Becquerel, 14070Caen, France
| | - Marwa Abdelmouleh
- CIMAP, UMR 6252 CEA/CNRS/ENSICAEN/Université de Caen Normandie, Bd Becquerel, 14070Caen, France
| | - Alexandre Giuliani
- SOLEIL, l'Orme des Merisiers, St. Aubin, BP48, 91192Gif sur Yvette, Cedex, France.,INRAE, UAR1008, Transform Department, Rue de la Géraudière, BP 71627, 44316Nantes, France
| | - Laurent Nahon
- SOLEIL, l'Orme des Merisiers, St. Aubin, BP48, 91192Gif sur Yvette, Cedex, France
| | - Jean-Christophe Poully
- CIMAP, UMR 6252 CEA/CNRS/ENSICAEN/Université de Caen Normandie, Bd Becquerel, 14070Caen, France
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4
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Xu S, Lukes P. Gas-liquid interface influencing electronic structure of phenol based on molecular dynamics simulations and theoretical X-ray absorption spectroscopy. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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5
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O—H and C—H bond dissociations in non-phenyl and phenyl groups: A DFT study with dispersion and long-range corrections. Theor Chem Acc 2021. [DOI: 10.1007/s00214-021-02781-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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6
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Jones DB, Mendes M, Limão-Vieira P, Ferreira da Silva F, Jones NC, Hoffmann SV, Brunger MJ. Electronic structure and VUV photoabsorption measurements of thiophene. J Chem Phys 2019; 150:064303. [PMID: 30769978 DOI: 10.1063/1.5089505] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The absolute photoabsorption cross sections for thiophene in the 5.0-10.7 eV range were measured using synchrotron radiation. New theoretical calculations performed at the time-dependent density functional theory level were used to qualitatively interpret the recorded photoabsorption spectrum. The calculations facilitated a re-analysis of the observed vibronic and Rydberg structures in the photoabsorption spectrum. Here a number of features have been re-assigned, while a number of other features have been assigned for the first time. This represents the most comprehensive and self-consistent assignment of the thiophene high-resolution photoabsorption spectrum to date.
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Affiliation(s)
- D B Jones
- College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
| | - M Mendes
- Atomic and Molecular Collisions Laboratory, CEFITEC, Department of Physics, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - P Limão-Vieira
- Atomic and Molecular Collisions Laboratory, CEFITEC, Department of Physics, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - F Ferreira da Silva
- Atomic and Molecular Collisions Laboratory, CEFITEC, Department of Physics, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - N C Jones
- ISA, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, DK-8000 Aarhus C, Denmark
| | - S V Hoffmann
- ISA, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, DK-8000 Aarhus C, Denmark
| | - M J Brunger
- College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
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7
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Sarkar S, Ramanathan N, Sundararajan K. Experimental Evidence of Synergistic Interactions in Pyrrole–Phenol Complexes at Low Temperatures under Isolated Conditions. J Phys Chem A 2018; 122:9073-9083. [DOI: 10.1021/acs.jpca.8b09076] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shubhra Sarkar
- Materials Chemistry & Metal Fuel Cycle Group, Homi Bhabha National Institute, Indira Gandhi Centre for Atomic Research, Kalpakkam, Tamil Nadu 603 102, India
| | - N. Ramanathan
- Materials Chemistry & Metal Fuel Cycle Group, Homi Bhabha National Institute, Indira Gandhi Centre for Atomic Research, Kalpakkam, Tamil Nadu 603 102, India
| | - K. Sundararajan
- Materials Chemistry & Metal Fuel Cycle Group, Homi Bhabha National Institute, Indira Gandhi Centre for Atomic Research, Kalpakkam, Tamil Nadu 603 102, India
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8
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Sand AM, Hoyer CE, Truhlar DG, Gagliardi L. State-interaction pair-density functional theory. J Chem Phys 2018; 149:024106. [DOI: 10.1063/1.5036727] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Affiliation(s)
- Andrew M. Sand
- Department of Chemistry, Chemical Theory Center, and The Minnesota Supercomputing Institute, The University of Minnesota, Minneapolis, Minnesota 55455-0431, USA
| | - Chad E. Hoyer
- Department of Chemistry, Chemical Theory Center, and The Minnesota Supercomputing Institute, The University of Minnesota, Minneapolis, Minnesota 55455-0431, USA
| | - Donald G. Truhlar
- Department of Chemistry, Chemical Theory Center, and The Minnesota Supercomputing Institute, The University of Minnesota, Minneapolis, Minnesota 55455-0431, USA
| | - Laura Gagliardi
- Department of Chemistry, Chemical Theory Center, and The Minnesota Supercomputing Institute, The University of Minnesota, Minneapolis, Minnesota 55455-0431, USA
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9
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Abstract
We show that the importance sampling technique can effectively augment the range of problems where the nuclear ensemble approach can be applied. A sampling probability distribution function initially determines the collection of initial conditions for which calculations are performed, as usual. Then, results for a distinct target distribution are computed by introducing compensating importance sampling weights for each sampled point. This mapping between the two probability distributions can be performed whenever they are both explicitly constructed. Perhaps most notably, this procedure allows for the computation of temperature dependent observables. As a test case, we investigated the UV absorption spectra of phenol, which has been shown to have a marked temperature dependence. Application of the proposed technique to a range that covers 500 K provides results that converge to those obtained with conventional sampling. We further show that an overall improved rate of convergence is obtained when sampling is performed at intermediate temperatures. The comparison between calculated and the available measured cross sections is very satisfactory, as the main features of the spectra are correctly reproduced. As a second test case, one of Tully's classical models was revisited, and we show that the computation of dynamical observables also profits from the importance sampling technique. In summary, the strategy developed here can be employed to assess the role of temperature for any property calculated within the nuclear ensemble method, with the same computational cost as doing so for a single temperature.
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Affiliation(s)
- Fábris Kossoski
- Instituto de Fı́sica "Gleb Wataghin" , Universidade Estadual de Campinas , 13083-859 Campinas , São Paulo , Brazil.,Aix Marseille Univ , CNRS, ICR , Marseille , France
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10
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Jones DB, da Costa RF, Kossoski F, Varella MTDN, Bettega MHF, Ferreira da Silva F, Limão-Vieira P, García G, Lima MAP, White RD, Brunger MJ. Electron-impact electronic-state excitation of para-benzoquinone. J Chem Phys 2018; 148:124312. [DOI: 10.1063/1.5023494] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- D. B. Jones
- College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
| | - R. F. da Costa
- Instituto de Física “Gleb Wataghin,” Universidade Estadual de Campinas, 13083-859 Campinas, São Paulo, Brazil
- Centro de Ciências Exatas, Departamento de Física, Universidade Federal do Espírito Santo, 29075-910 Vitória, Espírito Santo, Brazil
| | - F. Kossoski
- Instituto de Física “Gleb Wataghin,” Universidade Estadual de Campinas, 13083-859 Campinas, São Paulo, Brazil
| | - M. T. do N. Varella
- Instituto de Física, Universidade de São Paulo, Rua do Matão 1731, 05508-090 São Paulo, São Paulo, Brazil
| | - M. H. F. Bettega
- Departamento de Física, Universidade Federal do Paraná, CP 19044, 81531-990 Curitiba, Paraná, Brazil
| | - F. Ferreira da Silva
- Laboratório de Colisões Atómicas e Moleculares, CEFITEC, Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - P. Limão-Vieira
- Laboratório de Colisões Atómicas e Moleculares, CEFITEC, Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - G. García
- Instituto de Fisica Fundamental, CSIC, Serrano 113-bis, E-28006 Madrid, Spain
| | - M. A. P. Lima
- Instituto de Física “Gleb Wataghin,” Universidade Estadual de Campinas, 13083-859 Campinas, São Paulo, Brazil
| | - R. D. White
- College of Science and Engineering, James Cook University, Townsville, Australia
| | - M. J. Brunger
- College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
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11
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Rajak K, Ghosh A, Mahapatra S. Photophysics of phenol and pentafluorophenol: The role of nonadiabaticity in the optical transition to the lowest bright 1ππ* state. J Chem Phys 2018; 148:054301. [DOI: 10.1063/1.5015986] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Karunamoy Rajak
- School of Chemistry, University of Hyderabad, Hyderabad 500 046, India
| | - Arpita Ghosh
- School of Chemistry, University of Hyderabad, Hyderabad 500 046, India
| | - S. Mahapatra
- School of Chemistry, University of Hyderabad, Hyderabad 500 046, India
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12
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Jones DB, Blanco F, García G, da Costa RF, Kossoski F, Varella MTDN, Bettega MHF, Lima MAP, White RD, Brunger MJ. Elastic scattering and vibrational excitation for electron impact onpara-benzoquinone. J Chem Phys 2017; 147:244304. [DOI: 10.1063/1.5010831] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- D. B. Jones
- College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - F. Blanco
- Departamento de Física Atómica, Molecular y Nuclear, Universidad Complutense de Madrid, Madrid E-28040, Spain
| | - G. García
- Instituto de Física Fundamental, CSIC, Serano 113-bis, E-28006 Madrid, Spain
| | - R. F. da Costa
- Instituto de Física “Gleb Wataghin,” Universidade Estadual de Campinas, Campinas, São Paulo 13083-859, Brazil
- Centro de Ciências Exatas, Departamento de Física, Universidade Federal do Espírito Santo, 29075-901 Vitória, Espírito Santo, Brazil
| | - F. Kossoski
- Instituto de Física “Gleb Wataghin,” Universidade Estadual de Campinas, Campinas, São Paulo 13083-859, Brazil
| | - M. T. do N. Varella
- Instituto de Física, Universidade de São Paulo, Rua do Matão 1731, São Paulo 05508-090, Brazil
| | - M. H. F. Bettega
- Departamento de Física, Universidade Federal do Paraná, CP 19044, Curitiba, Paraná 81531-990, Brazil
| | - M. A. P. Lima
- Instituto de Física “Gleb Wataghin,” Universidade Estadual de Campinas, Campinas, São Paulo 13083-859, Brazil
| | - R. D. White
- College of Science and Engineering, James Cook University, Townsville, Qld 4811, Australia
| | - M. J. Brunger
- College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
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13
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Jones DB, Limão-Vieira P, Mendes M, Jones NC, Hoffmann SV, da Costa RF, Varella MTDN, Bettega MHF, Blanco F, García G, Ingólfsson O, Lima MAP, Brunger MJ. An experimental and theoretical investigation into the electronically excited states of para-benzoquinone. J Chem Phys 2017. [DOI: 10.1063/1.4982940] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- D. B. Jones
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
| | - P. Limão-Vieira
- Laboratório de Colisões Atómicas e Moleculares, CEFITEC, Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - M. Mendes
- Laboratório de Colisões Atómicas e Moleculares, CEFITEC, Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - N. C. Jones
- ISA, Department of Physics and Astronomy, Aarhus University, Ny Munkegade, DK-8000 Aarhus C, Denmark
| | - S. V. Hoffmann
- ISA, Department of Physics and Astronomy, Aarhus University, Ny Munkegade, DK-8000 Aarhus C, Denmark
| | - R. F. da Costa
- Instituto de Física “Gleb Wataghin,” Universidade Estadual de Campinas, 13083-859 Campinas, São Paulo, Brazil
- Centro de Ciências Exatas, Departamento de Física, Universidade Federal do Espírito Santo, 29075-910 Vitória, Espírito Santo, Brazil
| | - M. T. do N. Varella
- Instituto de Física, Universidade de São Paulo, Rua do Matão 1731, 05508-090 São Paulo, São Paulo, Brazil
| | - M. H. F. Bettega
- Departamento de Física, Universidade Federal do Paraná, CP 19044, 81531-990 Curitiba, Paraná, Brazil
| | - F. Blanco
- Departamento de Física Atómica, Molecular y Nuclear, Universidad Complutense de Madrid, Madrid E-28040, Spain
| | - G. García
- Instituto de Fisica Fundamental, CSIC, Serrano 113-Bis, 28006 Madrid, Spain
| | - O. Ingólfsson
- Science Institute and Department of Chemistry, University of Iceland, Dunhagi 3, 107 Reykjavík, Iceland
| | - M. A. P. Lima
- Instituto de Física “Gleb Wataghin,” Universidade Estadual de Campinas, 13083-859 Campinas, São Paulo, Brazil
| | - M. J. Brunger
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
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14
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Brunger MJ. Electron scattering and transport in biofuels, biomolecules and biomass fragments. INT REV PHYS CHEM 2017. [DOI: 10.1080/0144235x.2017.1301030] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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15
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Limão-Vieira P, Duflot D, Ferreira da Silva F, Lange E, Jones NC, Hoffmann SV, Śmiałek MA, Jones DB, Brunger MJ. Valence and lowest Rydberg electronic states of phenol investigated by synchrotron radiation and theoretical methods. J Chem Phys 2017; 145:034302. [PMID: 27448882 DOI: 10.1063/1.4955334] [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
We present the experimental high-resolution vacuum ultraviolet (VUV) photoabsorption spectra of phenol covering for the first time the full 4.3-10.8 eV energy-range, with absolute cross sections determined. Theoretical calculations on the vertical excitation energies and oscillator strengths were performed using time-dependent density functional theory and the equation-of-motion coupled cluster method restricted to single and double excitations level. These have been used in the assignment of valence and Rydberg transitions of the phenol molecule. The VUV spectrum reveals several new features not previously reported in the literature, with particular reference to the 6.401 eV transition, which is here assigned to the 3sσ/σ(∗)(OH)←3π(3a″) transition. The measured absolute photoabsorption cross sections have been used to calculate the photolysis lifetime of phenol in the earth's atmosphere (0-50 km).
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Affiliation(s)
- P Limão-Vieira
- Laboratório de Colisões Atómicas e Moleculares, CEFITEC, Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - D Duflot
- Univ. Lille, UMR 8523-Physique des Lasers Atomes et Molécules, F-59000 Lille, France
| | - F Ferreira da Silva
- Laboratório de Colisões Atómicas e Moleculares, CEFITEC, Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - E Lange
- Laboratório de Colisões Atómicas e Moleculares, CEFITEC, Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - N C Jones
- ISA, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, DK-8000 Aarhus C, Denmark
| | - S V Hoffmann
- ISA, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, DK-8000 Aarhus C, Denmark
| | - M A Śmiałek
- Department of Control and Power Engineering, Faculty of Ocean Engineering and Ship Technology, Gdańsk University of Technology, Gabriela Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - D B Jones
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
| | - M J Brunger
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
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16
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Nenov A, Mukamel S, Garavelli M, Rivalta I. Two-Dimensional Electronic Spectroscopy of Benzene, Phenol, and Their Dimer: An Efficient First-Principles Simulation Protocol. J Chem Theory Comput 2016; 11:3755-71. [PMID: 26574458 DOI: 10.1021/acs.jctc.5b00443] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
First-principles simulations of two-dimensional electronic spectroscopy in the ultraviolet region (2DUV) require computationally demanding multiconfigurational approaches that can resolve doubly excited and charge transfer states, the spectroscopic fingerprints of coupled UV-active chromophores. Here, we propose an efficient approach to reduce the computational cost of accurate simulations of 2DUV spectra of benzene, phenol, and their dimer (i.e., the minimal models for studying electronic coupling of UV-chromophores in proteins). We first establish the multiconfigurational recipe with the highest accuracy by comparison with experimental data, providing reference gas-phase transition energies and dipole moments that can be used to construct exciton Hamiltonians involving high-lying excited states. We show that by reducing the active spaces and the number of configuration state functions within restricted active space schemes, the computational cost can be significantly decreased without loss of accuracy in predicting 2DUV spectra. The proposed recipe has been successfully tested on a realistic model proteic system in water. Accounting for line broadening due to thermal and solvent-induced fluctuations allows for direct comparison with experiments.
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Affiliation(s)
- Artur Nenov
- Dipartimento di Chimica "G. Ciamician", Università di Bologna , Via F. Selmi 2, 40126 Bologna, Italy
| | - Shaul Mukamel
- Department of Chemistry, University of California , Irvine, California 92697-2025, United States
| | - Marco Garavelli
- Dipartimento di Chimica "G. Ciamician", Università di Bologna , Via F. Selmi 2, 40126 Bologna, Italy.,Université de Lyon , CNRS, Laboratoire de Chimie, École Normale Supérieure de Lyon, UMR 5182, 46 Allée d'Italie, 69364 Lyon, Cedex 07, France
| | - Ivan Rivalta
- Université de Lyon , CNRS, Laboratoire de Chimie, École Normale Supérieure de Lyon, UMR 5182, 46 Allée d'Italie, 69364 Lyon, Cedex 07, France
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17
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Jones DB, da Costa RF, Varella MTDN, Bettega MHF, Lima MAP, Blanco F, García G, Brunger MJ. Integral elastic, electronic-state, ionization, and total cross sections for electron scattering with furfural. J Chem Phys 2016; 144:144303. [DOI: 10.1063/1.4945562] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Affiliation(s)
- D. B. Jones
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - R. F. da Costa
- Instituto de Física “Gleb Wataghin,” Universidade Estadual de Campinas, Campinas, 13083-859 São Paulo, Brazil
- Departamento de Física, Universidade Federal do Espírito Santo, 29075-910, Vitória, Espírito Santo, Brazil
| | - M. T. do N. Varella
- Instituto de Física, Universidade de São Paulo, CP 66318, 05315-970 São Paulo, Brazil
| | - M. H. F. Bettega
- Departamento de Física, Universidade Federal do Paraná, CP 19044, 81531-990 Curitiba, Paraná, Brazil
| | - M. A. P. Lima
- Instituto de Física “Gleb Wataghin,” Universidade Estadual de Campinas, Campinas, 13083-859 São Paulo, Brazil
| | - F. Blanco
- Departamento de Física Atómica, Molecular y Nuclear, Universidad Complutense de Madrid, Madrid E-28040, Spain
| | - G. García
- Instituto de Física Fundamental, CSIC, Serrano 113-bis, 28006 Madrid, Spain
| | - M. J. Brunger
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
- Institute of Mathematical Sciences, University of Malaya, 50603 Kuala Lumpur, Malaysia
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18
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da Costa RF, do N Varella MT, Bettega MHF, Neves RFC, Lopes MCA, Blanco F, García G, Jones DB, Brunger MJ, Lima MAP. The electron-furfural scattering dynamics for 63 energetically open electronic states. J Chem Phys 2016; 144:124310. [PMID: 27036451 DOI: 10.1063/1.4944616] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report on integral-, momentum transfer- and differential cross sections for elastic and electronically inelastic electron collisions with furfural (C5H4O2). The calculations were performed with two different theoretical methodologies, the Schwinger multichannel method with pseudopotentials (SMCPP) and the independent atom method with screening corrected additivity rule (IAM-SCAR) that now incorporates a further interference (I) term. The SMCPP with N energetically open electronic states (N(open)) at either the static-exchange (N(open) ch-SE) or the static-exchange-plus-polarisation (N(open) ch-SEP) approximation was employed to calculate the scattering amplitudes at impact energies lying between 5 eV and 50 eV, using a channel coupling scheme that ranges from the 1ch-SEP up to the 63ch-SE level of approximation depending on the energy considered. For elastic scattering, we found very good overall agreement at higher energies among our SMCPP cross sections, our IAM-SCAR+I cross sections and the experimental data for furan (a molecule that differs from furfural only by the substitution of a hydrogen atom in furan with an aldehyde functional group). This is a good indication that our elastic cross sections are converged with respect to the multichannel coupling effect for most of the investigated intermediate energies. However, although the present application represents the most sophisticated calculation performed with the SMCPP method thus far, the inelastic cross sections, even for the low lying energy states, are still not completely converged for intermediate and higher energies. We discuss possible reasons leading to this discrepancy and point out what further steps need to be undertaken in order to improve the agreement between the calculated and measured cross sections.
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Affiliation(s)
- Romarly F da Costa
- Instituto de Física "Gleb Wataghin," Universidade Estadual de Campinas, Campinas, São Paulo 13083-859, Brazil
| | - Márcio T do N Varella
- Instituto de Física, Universidade de São Paulo, CP 66318, São Paulo, São Paulo 05315-970, Brazil
| | - Márcio H F Bettega
- Departamento de Física, Universidade Federal do Paraná, CP 19044, Curitiba, Paraná 81531-990, Brazil
| | - Rafael F C Neves
- Instituto Federal do Sul de Minas Gerais, Campus Poços de Caldas, Minas Gerais, Brazil
| | - Maria Cristina A Lopes
- Departamento de Física, Universidade Federal de Juiz de Fora, Juiz de Fora, MG 36036-900, Brazil
| | - Francisco Blanco
- Departamento de Física Atómica, Molecular y Nuclear, Universidad Complutense de Madrid, Madrid E-28040, Spain
| | - Gustavo García
- Instituto de Física Fundamental, CSIC, Serrano 113-bis, 28006 Madrid, Spain
| | - Darryl B Jones
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - Michael J Brunger
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - Marco A P Lima
- Instituto de Física "Gleb Wataghin," Universidade Estadual de Campinas, Campinas, São Paulo 13083-859, Brazil
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19
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Regeta K, Allan M, Mašín Z, Gorfinkiel JD. Absolute cross sections for electronic excitation of pyrimidine by electron impact. J Chem Phys 2016; 144:024302. [DOI: 10.1063/1.4939077] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Khrystyna Regeta
- Department of Chemistry, University of Fribourg, Chemin du Musée 9, CH-1700 Fribourg, Switzerland
| | - Michael Allan
- Department of Chemistry, University of Fribourg, Chemin du Musée 9, CH-1700 Fribourg, Switzerland
| | - Zdeněk Mašín
- Max-Born Institute for Nonlinear Optics and Short Pulse Spectroscopy, Max-Born-Straße 2A, 12489 Berlin, Germany
| | - Jimena D. Gorfinkiel
- Department of Physical Sciences, The Open University, Walton Hall, Milton Keynes MK7 6AA, United Kingdom
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20
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Barsotti F, Ghigo G, Vione D. Computational assessment of the fluorescence emission of phenol oligomers: A possible insight into the fluorescence properties of humic-like substances (HULIS). J Photochem Photobiol A Chem 2016. [DOI: 10.1016/j.jphotochem.2015.09.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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21
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Ferreira da Silva F, Lange E, Limão-Vieira P, Jones NC, Hoffmann SV, Hubin-Franskin MJ, Delwiche J, Brunger MJ, Neves RFC, Lopes MCA, de Oliveira EM, da Costa RF, Varella MTDN, Bettega MHF, Blanco F, García G, Lima MAP, Jones DB. Electronic excitation of furfural as probed by high-resolution vacuum ultraviolet spectroscopy, electron energy loss spectroscopy, and ab initio calculations. J Chem Phys 2015; 143:144308. [DOI: 10.1063/1.4932603] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- F. Ferreira da Silva
- Laboratório de Colisões Atómicas e Moleculares, CEFITEC, Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - E. Lange
- Laboratório de Colisões Atómicas e Moleculares, CEFITEC, Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - P. Limão-Vieira
- Laboratório de Colisões Atómicas e Moleculares, CEFITEC, Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - N. C. Jones
- ISA, Department of Physics and Astronomy, Aarhus University, Ny Munkegade, DK-8000 Århus C, Denmark
| | - S. V. Hoffmann
- ISA, Department of Physics and Astronomy, Aarhus University, Ny Munkegade, DK-8000 Århus C, Denmark
| | - M.-J. Hubin-Franskin
- Départment de Chimie, Institut de Chimie-Bât. B6C, Université de Liège, B-4000 Liège 1, Belgium
| | - J. Delwiche
- Départment de Chimie, Institut de Chimie-Bât. B6C, Université de Liège, B-4000 Liège 1, Belgium
| | - M. J. Brunger
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
- Institute of Mathematical Sciences, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - R. F. C. Neves
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
- Departamento de Física, Universidade Federal de Juíz de Fora, Juíz de Fora, MG, Brazil
- Instituto Federal do Sul de Minas Gerais, Campus Poços de Caldas, Minas Gerais, Brazil
| | - M. C. A. Lopes
- Departamento de Física, Universidade Federal de Juíz de Fora, Juíz de Fora, MG, Brazil
| | - E. M. de Oliveira
- Instituto de Física “Gleb Wataghin,” Universidade Estadual de Campinas, 13083-859 Campinas, São Paulo, Brazil
| | - R. F. da Costa
- Instituto de Física “Gleb Wataghin,” Universidade Estadual de Campinas, 13083-859 Campinas, São Paulo, Brazil
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, 09210-580 Santo André, São Paulo, Brazil
| | - M. T. do N. Varella
- Instituto de Física, Universidade de São Paulo, CP 66318, 05315-970 São Paulo, Brazil
| | - M. H. F. Bettega
- Departamento de Física, Universidade Federal do Paraná, CP 19044, Curitiba, Paraná 81531-990, Brazil
| | - F. Blanco
- Departamento de Física Atómica, Molecular y Nuclear, Universidad Complutense de Madrid, Madrid E-28040, Spain
| | - G. García
- Instituto de Fisica Fundamental, CSIC, Serrano 113-bis, 28006 Madrid, Spain
| | - M. A. P. Lima
- Instituto de Física “Gleb Wataghin,” Universidade Estadual de Campinas, 13083-859 Campinas, São Paulo, Brazil
| | - D. B. Jones
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
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22
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Thibodeaux CA, Poliakoff E, Kizilkaya O, Patterson MC, DiTusa MF, Kurtz RL, Sprunger P. Probing environmentally significant surface radicals: Crystallographic and temperature dependent adsorption of phenol on ZnO. Chem Phys Lett 2015; 638:56-60. [PMID: 26388650 PMCID: PMC4570833 DOI: 10.1016/j.cplett.2015.08.026] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Environmentally persistent free radicals (EPFRs) are toxic organic/metal oxide composite particles that have been discovered to form from substituted benzenes chemisorbed to metal oxides. Here, we perform photoelectron spectroscopy, electron energy loss spectroscopy, and low energy electron diffraction of phenol chemisorbed to ZnO(1 0 1̱ 0) and (0 0 0 1̱)-Zn to observe electronic structure changes and charge transfer as a function adsorption temperature. We show direct evidence of charge transfer from the ZnO surfaces to the phenol. This evidence can help gain a better understanding of EPFRs and be used to develop possible future remediation strategies.
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Affiliation(s)
- Chad A. Thibodeaux
- Louisiana State University, Department of Chemistry, 232 Choppin Hall, Highland Road, Baton Rouge, LA 70803, United States
| | - E.D. Poliakoff
- Louisiana State University, Department of Chemistry, 232 Choppin Hall, Highland Road, Baton Rouge, LA 70803, United States
| | - Orhan Kizilkaya
- Louisiana State University, Center for Advanced Microstructures and Devices, 6980 Jefferson Hwy., Baton Rouge, LA 70806, United States
| | - Matthew C. Patterson
- Louisiana State University, Department of Physics and Astronomy, 202 Nicholson Hall, Tower Dr., Baton Rouge, LA 70803, United States
| | - Mark F. DiTusa
- Louisiana State University, Department of Physics and Astronomy, 202 Nicholson Hall, Tower Dr., Baton Rouge, LA 70803, United States
| | - Richard L. Kurtz
- Louisiana State University, Center for Advanced Microstructures and Devices, 6980 Jefferson Hwy., Baton Rouge, LA 70806, United States
- Louisiana State University, Department of Physics and Astronomy, 202 Nicholson Hall, Tower Dr., Baton Rouge, LA 70803, United States
| | - P.T. Sprunger
- Louisiana State University, Department of Physics and Astronomy, 202 Nicholson Hall, Tower Dr., Baton Rouge, LA 70803, United States
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23
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Jones DB, Ellis-Gibbings L, García G, Nixon KL, Lopes MCA, Brunger MJ. Intermediate energy cross sections for electron-impact vibrational-excitation of pyrimidine. J Chem Phys 2015; 143:094304. [PMID: 26342367 DOI: 10.1063/1.4929907] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report differential cross sections (DCSs) and integral cross sections (ICSs) for electron-impact vibrational-excitation of pyrimidine, at incident electron energies in the range 15-50 eV. The scattered electron angular range for the DCS measurements was 15°-90°. The measurements at the DCS-level are the first to be reported for vibrational-excitation in pyrimidine via electron impact, while for the ICS we extend the results from the only previous condensed-phase study [P. L. Levesque, M. Michaud, and L. Sanche, J. Chem. Phys. 122, 094701 (2005)], for electron energies ⩽12 eV, to higher energies. Interestingly, the trend in the magnitude of the lower energy condensed-phase ICSs is much smaller when compared to the corresponding gas phase results. As there is no evidence for the existence of any shape-resonances, in the available pyrimidine total cross sections [Baek et al., Phys. Rev. A 88, 032702 (2013); Fuss et al., ibid. 88, 042702 (2013)], between 10 and 20 eV, this mismatch in absolute magnitude between the condensed-phase and gas-phase ICSs might be indicative for collective-behaviour effects in the condensed-phase results.
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Affiliation(s)
- D B Jones
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
| | - L Ellis-Gibbings
- Instituto de Física Fundamental, CSIC, Serrano 113-bis, 28006 Madrid, Spain
| | - G García
- Instituto de Física Fundamental, CSIC, Serrano 113-bis, 28006 Madrid, Spain
| | - K L Nixon
- Departamento de Física, Universidade Federal de Juiz de Fora, 36036-330 Juiz de Fora, Minas Gerais, Brazil
| | - M C A Lopes
- Departamento de Física, Universidade Federal de Juiz de Fora, 36036-330 Juiz de Fora, Minas Gerais, Brazil
| | - M J Brunger
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
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24
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da Silva GB, Neves RFC, Chiari L, Jones DB, Ali E, Madison DH, Ning CG, Nixon KL, Lopes MCA, Brunger MJ. Triply differential (e,2e) studies of phenol. J Chem Phys 2015; 141:124307. [PMID: 25273437 DOI: 10.1063/1.4896072] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
We have measured (e,2e) triple differential cross sections (TDCS) for the electron-impact ionisation of phenol with coplanar asymmetrical kinematics for an incident electron energy of 250 eV. Experimental measurements of the angular distribution of the slow outgoing electrons at 20 eV are obtained when the incident electron scatters through angles of -5°, -10°, and -15°, respectively. The TDCS data are compared with calculations performed within the molecular 3-body distorted wave model. In this case, a mixed level of agreement, that was dependent on the kinematical condition being probed, was observed between the theoretical and experimental results in the binary peak region. The experimental intensity of the recoil features under all kinematical conditions was relatively small, but was still largely underestimated by the theoretical calculations.
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Affiliation(s)
- G B da Silva
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - R F C Neves
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - L Chiari
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - D B Jones
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - E Ali
- Department of Physics, Missouri University of Science and Technology, Rolla, Missouri 65409, USA
| | - D H Madison
- Department of Physics, Missouri University of Science and Technology, Rolla, Missouri 65409, USA
| | - C G Ning
- Department of Physics, State Key Laboratory of Low-Dimensional Quantum Physics, Tsinghua University, Beijing 100084, China
| | - K L Nixon
- Departamento de Física, UFJF, Juiz de Fora, 36036-330, MG, Brazil
| | - M C A Lopes
- Departamento de Física, UFJF, Juiz de Fora, 36036-330, MG, Brazil
| | - M J Brunger
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
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25
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Neves RFC, Jones DB, Lopes MCA, Blanco F, García G, Ratnavelu K, Brunger MJ. Integral cross sections for electron impact excitation of vibrational and electronic states in phenol. J Chem Phys 2015; 142:194305. [PMID: 26001459 DOI: 10.1063/1.4921313] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report on measurements of integral cross sections (ICSs) for electron impact excitation of a series of composite vibrational modes and electronic-states in phenol, where the energy range of those experiments was 15-250 eV. There are currently no other results against which we can directly compare those measured data. We also report results from our independent atom model with screened additivity rule correction computations, namely, for the inelastic ICS (all discrete electronic states and neutral dissociation) and the total ionisation ICS. In addition, for the relevant dipole-allowed excited electronic states, we also report f-scaled Born-level and energy-corrected and f-scaled Born-level (BEf-scaled) ICS. Where possible, our measured and calculated ICSs are compared against one another with the general level of accord between them being satisfactory to within the measurement uncertainties.
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Affiliation(s)
- R F C Neves
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide SA 5001, Australia
| | - D B Jones
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide SA 5001, Australia
| | - M C A Lopes
- Departamento de Física, Universidade Federal de Juiz de Fora, 36036-330 Juiz de Fora, Minas Gerais, Brazil
| | - F Blanco
- Departamento de Física Atómica, Molecular y Nuclear, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - G García
- Instituto de Física Fundamental, CSIC, Serrano 113-bis, 28006 Madrid, Spain
| | - K Ratnavelu
- Institute of Mathematical Sciences, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - M J Brunger
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide SA 5001, Australia
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26
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Neves RFC, Jones DB, Lopes MCA, Nixon KL, de Oliveira EM, da Costa RF, Varella MTDN, Bettega MHF, Lima MAP, da Silva GB, Brunger MJ. Intermediate energy electron impact excitation of composite vibrational modes in phenol. J Chem Phys 2015; 142:194302. [PMID: 26001456 DOI: 10.1063/1.4921038] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We report differential cross section results from an experimental investigation into the electron impact excitation of a number of the low-lying composite (unresolved) vibrational modes in phenol (C6H5OH). The measurements were carried out at incident electron energies in the range 15-40 eV and for scattered-electron angles in the range 10-90°. The energy resolution of those measurements was typically ∼80 meV. Calculations, using the GAMESS code, were also undertaken with a B3LYP/aug-cc-pVDZ level model chemistry, in order to enable us to assign vibrational modes to the features observed in our energy loss spectra. To the best of our knowledge, the present cross sections are the first to be reported for vibrational excitation of the C6H5OH molecule by electron impact.
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Affiliation(s)
- R F C Neves
- School of Chemical and Physical Sciences, Flinders University, G.P.O. Box 2100, Adelaide, SA 5001, Australia
| | - D B Jones
- School of Chemical and Physical Sciences, Flinders University, G.P.O. Box 2100, Adelaide, SA 5001, Australia
| | - M C A Lopes
- Departamento de Física, Universidade Federal de Juiz de Fora, 36036-900, Juiz de Fora, Minas Gerais, Brazil
| | - K L Nixon
- Departamento de Física, Universidade Federal de Juiz de Fora, 36036-900, Juiz de Fora, Minas Gerais, Brazil
| | - E M de Oliveira
- Instituto de Física 'Gleb Wataghin,' Universidade Estadual de Campinas, 13083-859 Campinas, São Paulo, Brazil
| | - R F da Costa
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, 09210-580 Santo André, São Paulo, Brazil
| | - M T do N Varella
- Instituto de Física, Universidade de São Paulo, C.P. 66318, 05315-970 São Paulo, Brazil
| | - M H F Bettega
- Departamento de Física, Universidade Federal do Paraná, C.P. 19044, 81531-990 Curitiba, Paraná, Brazil
| | - M A P Lima
- Instituto de Física 'Gleb Wataghin,' Universidade Estadual de Campinas, 13083-859 Campinas, São Paulo, Brazil
| | - G B da Silva
- Universidade Federal de Mato Grosso, Barra do Garças, Mato Grosso, Brazil
| | - M J Brunger
- School of Chemical and Physical Sciences, Flinders University, G.P.O. Box 2100, Adelaide, SA 5001, Australia
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27
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Karmakar S, Mukhopadhyay DP, Chakraborty T. Electronic spectra and excited state dynamics of pentafluorophenol: Effects of low-lying πσ∗ states. J Chem Phys 2015; 142:184303. [DOI: 10.1063/1.4919950] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Shreetama Karmakar
- Physical Chemistry Department, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Deb Pratim Mukhopadhyay
- Physical Chemistry Department, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Tapas Chakraborty
- Physical Chemistry Department, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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28
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Patterson MC, Thibodeaux CA, Kizilkaya O, Kurtz RL, Poliakoff ED, Sprunger PT. Electronic signatures of a model pollutant-particle system: chemisorbed phenol on TiO₂(110). LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:3869-3875. [PMID: 25774565 PMCID: PMC4407492 DOI: 10.1021/acs.langmuir.5b00030] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Environmentally persistent free radicals (EPFRs) are a class of composite organic/metal oxide pollutants that have recently been discovered to form from a wide variety of substituted benzenes chemisorbed to commonly encountered oxides. Although a qualitative understanding of EPFR formation on particulate metal oxides has been achieved, a detailed understanding of the charge transfer mechanism that must accompany the creation of an unpaired radical electron is lacking. In this study, we perform photoelectron spectroscopy and electron energy loss spectroscopy on a well-defined model system-phenol chemisorbed on TiO2(110) to directly observe changes in the electronic structure of the oxide and chemisorbed phenol as a function of adsorption temperature. We show strong evidence that, upon exposure at high temperature, empty states in the TiO2 are filled and the phenol HOMO is depopulated, as has been proposed in a conceptual model of EPFR formation. This experimental evidence of charge transfer provides a deeper understanding of the EPFR formation mechanism to guide future experimental and computational studies as well as potential environmental remediation strategies.
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Affiliation(s)
- Matthew C. Patterson
- Department of Physics and Astronomy, Louisiana State University, 202 Nicholson Hall, Baton Rouge, LA 70803
- Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, LA 70803
| | - Chad A. Thibodeaux
- Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, LA 70803
| | - Orhan Kizilkaya
- Center for Advanced Microstructures and Devices, Louisiana State University, 6980 Jefferson Highway, Baton Rouge, LA 70806
| | - Richard L. Kurtz
- Department of Physics and Astronomy, Louisiana State University, 202 Nicholson Hall, Baton Rouge, LA 70803
- Center for Advanced Microstructures and Devices, Louisiana State University, 6980 Jefferson Highway, Baton Rouge, LA 70806
| | - E. D. Poliakoff
- Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, LA 70803
| | - Phillip T. Sprunger
- Department of Physics and Astronomy, Louisiana State University, 202 Nicholson Hall, Baton Rouge, LA 70803
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29
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Neves RFC, Jones DB, Lopes MCA, Nixon KL, da Silva GB, Duque HV, de Oliveira EM, da Costa RF, Varella MTDN, Bettega MHF, Lima MAP, Ratnavelu K, García G, Brunger MJ. Differential cross sections for electron impact excitation of the electronic bands of phenol. J Chem Phys 2015; 142:104305. [DOI: 10.1063/1.4913825] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- R. F. C. Neves
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide SA 5001, Australia
- Instituto Federal do Sul de Minas Gerais, Campus Poços de Caldas, Minas Gerais, Brazil
- Departamento de Física, UFJF, Juiz de Fora, Minas Gerais, Brazil
| | - D. B. Jones
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide SA 5001, Australia
| | - M. C. A. Lopes
- Departamento de Física, UFJF, Juiz de Fora, Minas Gerais, Brazil
| | - K. L. Nixon
- Departamento de Física, UFJF, Juiz de Fora, Minas Gerais, Brazil
| | - G. B. da Silva
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide SA 5001, Australia
- Universidade Federal de Mato Grosso, Barra do Garças, Mato Grosso, Brazil
| | - H. V. Duque
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide SA 5001, Australia
- Departamento de Física, UFJF, Juiz de Fora, Minas Gerais, Brazil
| | - E. M. de Oliveira
- Instituto de Física “Gleb Wataghin,” Universidade Estadual de Campinas, 13083-859 Campinas, São Paulo, Brazil
| | - R. F. da Costa
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, 09210-580 Santo André, São Paulo, Brazil
| | - M. T. do N. Varella
- Instituto de Física, Universidade de São Paulo, CP 66318, 05315-970 São Paulo, Brazil
| | - M. H. F. Bettega
- Departamento de Física, Universidade Federal do Paraná, CP 19044, 81531-990 Curitiba, Paraná, Brazil
| | - M. A. P. Lima
- Instituto de Física “Gleb Wataghin,” Universidade Estadual de Campinas, 13083-859 Campinas, São Paulo, Brazil
| | - K. Ratnavelu
- Institute of Mathematical Sciences, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - G. García
- Instituto de Física Fundamental, CSIC, Madrid E-28006, Spain
| | - M. J. Brunger
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide SA 5001, Australia
- Institute of Mathematical Sciences, University of Malaya, 50603 Kuala Lumpur, Malaysia
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da Costa RF, de Oliveira EM, Bettega MHF, Varella MTDN, Jones DB, Brunger MJ, Blanco F, Colmenares R, Limão-Vieira P, García G, Lima MAP. Electron collisions with phenol: Total, integral, differential, and momentum transfer cross sections and the role of multichannel coupling effects on the elastic channel. J Chem Phys 2015; 142:104304. [DOI: 10.1063/1.4913824] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Affiliation(s)
- Romarly F. da Costa
- Instituto de Física “Gleb Wataghin,” Universidade Estadual de Campinas, 13083-859 Campinas, São Paulo, Brazil
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, 09210-580 Santo André, São Paulo, Brazil
| | - Eliane M. de Oliveira
- Instituto de Física “Gleb Wataghin,” Universidade Estadual de Campinas, 13083-859 Campinas, São Paulo, Brazil
| | - Márcio H. F. Bettega
- Departamento de Física, Universidade Federal do Paraná, CP 19044, 81531-990 Curitiba, Paraná, Brazil
| | - Márcio T. do N. Varella
- Instituto de Física, Universidade de São Paulo, CP 66318, 05315-970 São Paulo, São Paulo, Brazil
| | - Darryl B. Jones
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide SA 5001, Australia
| | - Michael J. Brunger
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide SA 5001, Australia
- Institute of Mathematical Sciences, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Francisco Blanco
- Departamento de Fisica Atomica, Molecular y Nuclear, Universidad Complutense de Madrid, Ciudad Universitaria, 2840 Madrid, Spain
| | | | - Paulo Limão-Vieira
- Laboratório de Colisões Atómicas e Moleculares, CEFITEC, Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Gustavo García
- Instituto de Fisica Fundamental, CSIC, Serrano 113-bis, 28006 Madrid, Spain
| | - Marco A. P. Lima
- Instituto de Física “Gleb Wataghin,” Universidade Estadual de Campinas, 13083-859 Campinas, São Paulo, Brazil
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