1
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Holland DMP, Suchan J, Janoš J, Bacellar C, Leroy L, Barillot TR, Longetti L, Coreno M, de Simone M, Grazioli C, Chergui M, Muchová E, Ingle RA. Deconvolution of the X-ray absorption spectrum of trans-1,3-butadiene with resonant Auger spectroscopy. Phys Chem Chem Phys 2024; 26:15130-15142. [PMID: 38525924 DOI: 10.1039/d4cp00053f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
High-resolution carbon K-edge X-ray photoelectron, X-ray absorption, non-resonant and resonant Auger spectra are presented of gas phase trans-1,3-butadiene alongside a detailed theoretical analysis utilising nuclear ensemble approaches and vibronic models to simulate the spectroscopic observables. The resonant Auger spectra recorded across the first pre-edge band reveal a complex evolution of different electronic states which remain relatively well-localised on the edge or central carbon sites. The results demonstrate the sensitivity of the resonant Auger observables to the weighted contributions from multiple electronic states. The gradually evolving spectral features can be accurately and feasibly simulated within nuclear ensemble methods and interpreted with the population analysis.
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Affiliation(s)
- David M P Holland
- STFC, Daresbury Laboratory, Daresbury, Warrington, Cheshire WA4 4AD, UK
| | - Jiří Suchan
- Institute for Advanced Computational Science, Stony Brook University, Stony Brook, New York 11794-5250, USA
| | - Jiří Janoš
- Department of Physical Chemistry, University of Chemistry and Technology, Technická 5, 166 28 Prague, Czech Republic.
| | - Camila Bacellar
- Laboratoire de Spectroscopie Ultrarapide, Ecole Polytechnique Fédérale de Lausanne, ISIC, FSB, CH-1015 Lausanne, Switzerland
| | - Ludmila Leroy
- Laboratoire de Spectroscopie Ultrarapide, Ecole Polytechnique Fédérale de Lausanne, ISIC, FSB, CH-1015 Lausanne, Switzerland
| | - Thomas R Barillot
- Laboratoire de Spectroscopie Ultrarapide, Ecole Polytechnique Fédérale de Lausanne, ISIC, FSB, CH-1015 Lausanne, Switzerland
| | - Luca Longetti
- Laboratoire de Spectroscopie Ultrarapide, Ecole Polytechnique Fédérale de Lausanne, ISIC, FSB, CH-1015 Lausanne, Switzerland
| | - Marcello Coreno
- ISM-CNR, Istituto di Struttura dei Materiali, LD2 Unit, 34149 Trieste, Italy
| | | | - Cesare Grazioli
- IOM-CNR, Istituto Officina dei Materiali, 34149 Trieste, Italy
| | - Majed Chergui
- Laboratoire de Spectroscopie Ultrarapide, Ecole Polytechnique Fédérale de Lausanne, ISIC, FSB, CH-1015 Lausanne, Switzerland
- Elettra-Sincrotrone Trieste S.C.p.A., S.S. 14 km 163,5 in Area Science Park, I-34012 Basovizza, Trieste, Italy
| | - Eva Muchová
- Department of Physical Chemistry, University of Chemistry and Technology, Technická 5, 166 28 Prague, Czech Republic.
| | - Rebecca A Ingle
- Department of Chemistry, 20 Gordon Street, London, WC1H 0AJ, UK.
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2
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Muchova E, Hollas D, Holland DMP, Bacellar C, Leroy L, Barillot TR, Longetti L, Coreno M, de Simone M, Grazioli C, Chergui M, Ingle RA. Jahn-Teller effects in initial and final states: high-resolution X-ray absorption, photoelectron and Auger spectroscopy of allene. Phys Chem Chem Phys 2023; 25:6733-6745. [PMID: 36799466 DOI: 10.1039/d2cp05299g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Carbon K-edge resonant Auger spectra of gas-phase allene following excitation of the pre-edge 1s → π* transitions are presented and analysed with the support of EOM-CCSD/cc-pVTZ calculations. X-Ray absorption (XAS), X-ray photoelectron (XPS), valence band and non-resonant Auger spectra are also reanalysed with a series of computational approaches. The results presented demonstrate the importance of including nuclear ensemble effects for simulating X-ray observables and as an effective strategy for capturing Jahn-Teller effects in spectra.
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Affiliation(s)
- Eva Muchova
- Department of Physical Chemistry, University of Chemistry and Technology, Technická 5, 166 28 Prague, Czech Republic
| | - Daniel Hollas
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | | | - Camila Bacellar
- Laboratoire de Spectroscopie Ultrarapide, Ecole Polytechnique Fédérale de Lausanne, ISIC, FSB, CH-1015 Lausanne, Switzerland
| | - Ludmila Leroy
- Laboratoire de Spectroscopie Ultrarapide, Ecole Polytechnique Fédérale de Lausanne, ISIC, FSB, CH-1015 Lausanne, Switzerland
| | - Thomas R Barillot
- Laboratoire de Spectroscopie Ultrarapide, Ecole Polytechnique Fédérale de Lausanne, ISIC, FSB, CH-1015 Lausanne, Switzerland
| | - Luca Longetti
- Laboratoire de Spectroscopie Ultrarapide, Ecole Polytechnique Fédérale de Lausanne, ISIC, FSB, CH-1015 Lausanne, Switzerland
| | - Marcello Coreno
- ISM-CNR, Istituto di Struttura dei Materiali, LD2 Unit, 34149 Trieste, Italy
| | | | - Cesare Grazioli
- IOM-CNR, Istituto Officina dei Materiali, 34149 Trieste, Italy
| | - Majed Chergui
- Laboratoire de Spectroscopie Ultrarapide, Ecole Polytechnique Fédérale de Lausanne, ISIC, FSB, CH-1015 Lausanne, Switzerland
| | - Rebecca A Ingle
- Department of Chemistry, 20 Gordon Street, London, WC1H 0AJ, UK.
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3
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Zhou J, Belina M, Jia S, Xue X, Hao X, Ren X, Slavíček P. Ultrafast Charge and Proton Transfer in Doubly Ionized Ammonia Dimers. J Phys Chem Lett 2022; 13:10603-10611. [PMID: 36350084 DOI: 10.1021/acs.jpclett.2c02560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
We investigate the ultrafast energy and charge transfer processes between ammonia molecules following ionization reactions initiated by electron impact. Exploring ionization-induced processes in molecular clusters provides us with a detailed insight into the dynamics using experiments in the energy domain. We ionize the ammonia dimer with 200 eV electrons and apply the fragment ions coincident momentum spectroscopy and nonadiabatic molecular dynamics simulations. We identify two mechanisms leading to the doubly charged ammonia dimer. In the first one, a single molecule is ionized. This initiates an ultrafast proton transfer process, leading to the formation of the NH2+ + NH4+ pair. Alternatively, a dimer with a delocalized charge is formed dominantly via the intermolecular Coulombic decay, forming the NH3+·NH3+ dication. This dication further dissociates into two NH3+ cations. The ab initio calculations have reproduced the measured kinetic energy release of the ion pairs and revealed the dynamical processes following the double ionization.
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Affiliation(s)
- Jiaqi Zhou
- School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Michal Belina
- Department of Physical Chemistry, University of Chemistry and Technology,Technická 5, 16628Prague 6, Czech Republic
| | - Shaokui Jia
- School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Xiaorui Xue
- School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Xintai Hao
- School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Xueguang Ren
- School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Petr Slavíček
- Department of Physical Chemistry, University of Chemistry and Technology,Technická 5, 16628Prague 6, Czech Republic
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4
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Different timescales during ultrafast stilbene isomerization in the gas and liquid phases revealed using time-resolved photoelectron spectroscopy. Nat Chem 2022; 14:1126-1132. [PMID: 35953643 PMCID: PMC7613649 DOI: 10.1038/s41557-022-01012-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 06/28/2022] [Indexed: 11/08/2022]
Abstract
Directly contrasting ultrafast excited-state dynamics in the gas and liquid phases is crucial to understanding the influence of complex environments. Previous studies have often relied on different spectroscopic observables, rendering direct comparisons challenging. Here, we apply extreme-ultraviolet time-resolved photoelectron spectroscopy to both gaseous and liquid cis-stilbene, revealing the coupled electronic and nuclear dynamics that underlie its isomerization. Our measurements track the excited-state wave packets from excitation along the complete reaction path to the final products. We observe coherent excited-state vibrational dynamics in both phases of matter that persist to the final products, enabling the characterization of the branching space of the S1-S0 conical intersection. We observe a systematic lengthening of the relaxation timescales in the liquid phase and a red shift of the measured excited-state frequencies that is most pronounced for the complex reaction coordinate. These results characterize in detail the influence of the liquid environment on both electronic and structural dynamics during a complete photochemical transformation.
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5
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Li J, Jin Y, Su NQ, Yang W. Combining Localized Orbital Scaling Correction and Bethe-Salpeter Equation for Accurate Excitation Energies. J Chem Phys 2022; 156:154101. [PMID: 35459294 PMCID: PMC9033305 DOI: 10.1063/5.0087498] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We applied localized orbital scaling correction (LOSC) in Bethe-Salpeter equation (BSE) to predict accurate excitation energies for molecules. LOSC systematically eliminates the delocalization error in the density functional approximation and is capable of approximating quasiparticle (QP) energies with accuracy similar or better than the GW Green's function approach and with much less computational cost. The QP energies from LOSC instead of commonly used G0 W0 and ev GW are directly used in BSE. We show that the BSE/LOSC approach greatly outperforms the commonly used BSE/ G0W0 approach for predicting excitations with different characters. For the calculations for Truhlar-Gagliardi test set containing valence, charge transfer (CT) and Rydberg excitations, BSE/LOSC with the Tamm-Dancoff approximation provides a comparable accuracy to time-dependent density functional theory (TDDFT) and BSE/ev GW. For the calculations of Stein CT test set and Rydberg excitations of atoms, BSE/LOSC considerably outperforms both BSE/ G0W0 and TDDFT approaches with a reduced starting point dependence. BSE/LOSC is thus a promising and efficient approach to calculate excitation energies for molecular systems.
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Affiliation(s)
- Jiachen Li
- Department of Chemistry, Duke University, United States of America
| | - Ye Jin
- Department of Chemistry, United States of America
| | | | - Weitao Yang
- Department of Chemistry, Duke University, United States of America
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6
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Prlj A, Marsili E, Hutton L, Hollas D, Shchepanovska D, Glowacki DR, Slavíček P, Curchod BFE. Calculating Photoabsorption Cross-Sections for Atmospheric Volatile Organic Compounds. ACS EARTH & SPACE CHEMISTRY 2022; 6:207-217. [PMID: 35087992 PMCID: PMC8785186 DOI: 10.1021/acsearthspacechem.1c00355] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/25/2021] [Accepted: 12/03/2021] [Indexed: 05/30/2023]
Abstract
Characterizing the photochemical reactivity of transient volatile organic compounds (VOCs) in our atmosphere begins with a proper understanding of their abilities to absorb sunlight. Unfortunately, the photoabsorption cross-sections for a large number of transient VOCs remain unavailable experimentally due to their short lifetime or high reactivity. While structure-activity relationships (SARs) have been successfully employed to estimate the unknown photoabsorption cross-sections of VOCs, computational photochemistry offers another promising strategy to predict not only the vertical electronic transitions of a given molecule but also the width and shape of the bands forming its absorption spectrum. In this work, we focus on the use of the nuclear ensemble approach (NEA) to determine the photoabsorption cross-section of four exemplary VOCs, namely, acrolein, methylhydroperoxide, 2-hydroperoxy-propanal, and (microsolvated) pyruvic acid. More specifically, we analyze the influence that different strategies for sampling the ground-state nuclear density-Wigner sampling and ab initio molecular dynamics with a quantum thermostat-can have on the simulated absorption spectra. We highlight the potential shortcomings of using uncoupled harmonic modes within Wigner sampling of nuclear density to describe flexible or microsolvated VOCs and some limitations of SARs for multichromophoric VOCs. Our results suggest that the NEA could constitute a powerful tool for the atmospheric community to predict the photoabsorption cross-section for transient VOCs.
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Affiliation(s)
- Antonio Prlj
- Department
of Chemistry, Durham University, Durham DH1 3LE, U.K.
| | - Emanuele Marsili
- Department
of Chemistry, Durham University, Durham DH1 3LE, U.K.
| | - Lewis Hutton
- Department
of Chemistry, Durham University, Durham DH1 3LE, U.K.
| | - Daniel Hollas
- Department
of Chemistry, Durham University, Durham DH1 3LE, U.K.
- Department
of Physical Chemistry, University of Chemistry
and Technology, Prague, Technická 5, Prague 16628, Czech Republic
| | - Darya Shchepanovska
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TH, U.K.
| | - David R. Glowacki
- ArtSci
International Foundation, 5th Floor Mariner House, Bristol BS1 4QD, U.K.
- CiTIUS
Intelligent Technologies Research Centre, Rúa de Jenaro de La Fuente, s/n, Santiago de Compostela 15705, A Coruña, Spain
| | - Petr Slavíček
- Department
of Physical Chemistry, University of Chemistry
and Technology, Prague, Technická 5, Prague 16628, Czech Republic
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7
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On-the-Fly Ring-Polymer Molecular Dynamics Calculations of the Dissociative Photodetachment Process of the Oxalate Anion. Molecules 2021; 26:molecules26237250. [PMID: 34885831 PMCID: PMC8658898 DOI: 10.3390/molecules26237250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 11/22/2021] [Accepted: 11/26/2021] [Indexed: 11/16/2022] Open
Abstract
The dissociative photodetachment dynamics of the oxalate anion, C2O4H- + hν → CO2 + HOCO + e-, were theoretically studied using the on-the-fly path-integral and ring-polymer molecular dynamics methods, which can account for nuclear quantum effects at the density-functional theory level in order to compare with the recent experimental study using photoelectron-photofragment coincidence spectroscopy. To reduce computational time, the force acting on each bead of ring-polymer was approximately calculated from the first and second derivatives of the potential energy at the centroid position of the nuclei beads. We find that the calculated photoelectron spectrum qualitatively reproduces the experimental spectrum and that nuclear quantum effects are playing a role in determining spectral widths. The calculated coincidence spectrum is found to reasonably reproduce the experimental spectrum, indicating that a relatively large energy is partitioned into the relative kinetic energy between the CO2 and HOCO fragments. This is because photodetachment of the parent anion leads to Franck-Condon transition to the repulsive region of the neutral potential energy surface. We also find that the dissociation dynamics are slightly different between the two isomers of the C2O4H- anion with closed- and open-form structures.
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8
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Olivieri G, Kladnik G, Cvetko D, Brown MA. Determination of the valence band edge of Fe oxide nanoparticles dispersed in aqueous solution through resonant photoelectron spectroscopy from a liquid microjet. NANOSCALE ADVANCES 2021; 3:4513-4518. [PMID: 36133461 PMCID: PMC9419094 DOI: 10.1039/d1na00275a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 05/30/2021] [Indexed: 06/01/2023]
Abstract
We use X-ray photoemission and a near ambient pressure with a liquid microjet setup to investigate the electronic structure of FeOOH nanoparticles dispersed in aqueous solution. In particular, we show that by using X-ray resonant photoemission in dilute solutions, we can overcome the limits of conventional photoemission such as low nanoparticle-to-solvent signal ratio, and local nanoparticle charging and measure the valence band structure of FeOOH nanoparticles in aqueous solution with chemical specificity. The resonant photoemission signal across the Fe 2p3/2 absorption edge is measured for 2 wt% aqueous solutions of FeOOH nanoparticles (NPs) and the valence band maximum (VBM) of the hydrated FeOOH nanoparticles is determined. We compare the obtained VBM value in aqueous solution to that of FeOOH NPs in the dry phase. We show that the valence band edge position of NPs in the liquid phase can be accurately predicted from the values obtained in the dry phase provided that a simple potential shift due to solution chemistry is applied. Our results demonstrate the suitability of resonant photoemission in measuring the electronic structure of strongly diluted nanosystems where the conventional non-resonant photoemission technique fails.
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Affiliation(s)
- Giorgia Olivieri
- Laboratory for Surface Science and Technology, Department of Materials ETH Zürich, Vladimir-Prelog-Weg 5 CH-8093 Zürich Switzerland
| | - Gregor Kladnik
- Faculty for Mathematics and Physics, University of Ljubljana Jadranska 19 Ljubljana SI-1000 Slovenia
- IOM-CNR, Laboratorio TASC Basovizza SS-14, km 163.5 Trieste 34149 Italy
| | - Dean Cvetko
- Faculty for Mathematics and Physics, University of Ljubljana Jadranska 19 Ljubljana SI-1000 Slovenia
- IOM-CNR, Laboratorio TASC Basovizza SS-14, km 163.5 Trieste 34149 Italy
- Jožef Stefan Institute Jamova 39 Ljubljana SI-1000 Slovenia
| | - Matthew A Brown
- Laboratory for Surface Science and Technology, Department of Materials ETH Zürich, Vladimir-Prelog-Weg 5 CH-8093 Zürich Switzerland
- Metrology Research Centre, National Research Council of Canada Ottawa Ontario Canada
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9
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de Almeida JM, Nguyen NL, Colonna N, Chen W, Rodrigues Miranda C, Pasquarello A, Marzari N. Electronic Structure of Water from Koopmans-Compliant Functionals. J Chem Theory Comput 2021; 17:3923-3930. [PMID: 34137253 DOI: 10.1021/acs.jctc.1c00063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Obtaining a precise theoretical description of the spectral properties of liquid water poses challenges for both molecular dynamics (MD) and electronic structure methods. The lower computational cost of the Koopmans-compliant functionals with respect to Green's function methods allows the simulations of many MD trajectories, with a description close to the state-of-art quasi-particle self-consistent GW plus vertex corrections method (QSGW + fxc). Thus, we explore water spectral properties when different MD approaches are used, ranging from classical MD to first-principles MD, and including nuclear quantum effects. We have observed that different MD approaches lead to up to 1 eV change in the average band gap; thus, we focused on the band gap dependence with the geometrical properties of a system to explain such spread. We have evaluated the changes in the band gap due to variations in the intramolecular O-H bond distance and HOH angle, as well as the intermolecular hydrogen bond O···O distance and the OHO angles. We have observed that the dominant contribution comes from the O-H bond length; the O···O distance plays a secondary role, and the other geometrical properties do not significantly influence the gap. Furthermore, we analyze the electronic density of states (DOS), where the KIPZ functional shows good agreement with the DOS obtained with state-of-art approaches employing quasi-particle self-consistent GW plus vertex corrections. The O-H bond length also significantly influences the DOS. When nuclear quantum effects are considered, broadening of the peaks driven by the broader distribution of the O-H bond lengths is observed, leading to a closer agreement with the experimental photoemission spectra.
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Affiliation(s)
- James Moraes de Almeida
- Universidade Federal do ABC, Centro de Ciências Naturais e Humanas, Santo André, 09210-580 SP, Brazil.,Theory and Simulation of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (MARVEL), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ngoc Linh Nguyen
- Theory and Simulation of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (MARVEL), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Nicola Colonna
- Laboratory for Neutron Scattering and Imaging, Paul Scherrer Institute, CH-5232 Villigen-PSI, Switzerland.,National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Wei Chen
- Institute of Condensed Matter and Nanoscience, Université Catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium
| | | | - Alfredo Pasquarello
- Chaire de Simulation à l'Echelle Atomique (CSEA), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Nicola Marzari
- Theory and Simulation of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (MARVEL), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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10
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Saito K, Sugiura Y, Miyazaki T, Takahashi Y, Takayanagi T. Quantum calculations of the photoelectron spectra of the OH -·NH 3 anion: implications for OH + NH 3→ H 2O + NH 2 reaction dynamics. Phys Chem Chem Phys 2021; 23:6950-6958. [PMID: 33729225 DOI: 10.1039/d0cp06514e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We present the results of quantum dynamics calculations for analyzing the experimentally measured photoelectron spectra of the OH-·NH3 anion complex. Detachment of an excess electron of OH-·NH3 initially produces a molecular arrangement, which is close to the transition-state structure of the neutral OH + NH3→ H2O + NH2 hydrogen abstraction reaction due to the Franck-Condon principle, and thus finally leads to the OH + NH3 or H2O + NH2 asymptotic channel. We used both the path integral method and the reduced-dimensionality quantum wave packet method to simulate the photoelectron spectra of the OH-·NH3 anion. The calculated spectra were found to be in qualitative agreement with the experimental spectra. It was found that the photodetached complex mainly dissociates into the OH + NH3 channel; however, we found that the hydrogen exchange process also contributes to the photodetachment spectra.
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Affiliation(s)
- Kohei Saito
- Department of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama City, Saitama 338-8570, Japan.
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11
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Med J, Sršeň Š, Slavíček P, Domaracka A, Indrajith S, Rousseau P, Fárník M, Fedor J, Kočišek J. Vibrationally Mediated Stabilization of Electrons in Nonpolar Matter. J Phys Chem Lett 2020; 11:2482-2489. [PMID: 32154726 DOI: 10.1021/acs.jpclett.0c00278] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We explore solvation of electrons in nonpolar matter, here represented by butadiene clusters. Isolated butadiene supports only the existence of transient anions (resonances). Two-dimensional electron energy loss spectroscopy shows that the resonances lead to an efficient vibrational excitation of butadiene, which can result into the almost complete loss of energy of the interacting electron. Cluster-beam experiments show that molecular clusters of butadiene form stable anions, however only at sizes of more than 9 molecular units. We have calculated the distribution of electron affinities of clusters using classical and path integral molecular dynamics simulations. There is almost a continuous transition from the resonant to the bound anions with an increase in cluster size. The comparison of the classical and quantum dynamics reveals that the electron binding is strongly supported by molecular vibrations, brought about by nuclear zero-point motion and thermal agitation. We also inspected the structure of the solvated electron, finding it well localized.
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Affiliation(s)
- Jakub Med
- Department of Physical Chemistry, University of Chemistry and Technology, Technická 5, 16628 Prague 6, Czech Republic
| | - Štěpán Sršeň
- Department of Physical Chemistry, University of Chemistry and Technology, Technická 5, 16628 Prague 6, Czech Republic
| | - Petr Slavíček
- Department of Physical Chemistry, University of Chemistry and Technology, Technická 5, 16628 Prague 6, Czech Republic
- J. Heyrovský Institute of Physical Chemistry v.v.i., The Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech Republic
| | - A Domaracka
- Normandie Univ., ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, 14000 Caen, France
| | - S Indrajith
- Normandie Univ., ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, 14000 Caen, France
| | - P Rousseau
- Normandie Univ., ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, 14000 Caen, France
| | - M Fárník
- J. Heyrovský Institute of Physical Chemistry v.v.i., The Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech Republic
| | - J Fedor
- J. Heyrovský Institute of Physical Chemistry v.v.i., The Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech Republic
| | - J Kočišek
- J. Heyrovský Institute of Physical Chemistry v.v.i., The Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech Republic
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12
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Longetti L, Randulová M, Ojeda J, Mewes L, Miseikis L, Grilj J, Sanchez-Gonzalez A, Witting T, Siegel T, Diveki Z, van Mourik F, Chapman R, Cacho C, Yap S, Tisch JWG, Springate E, Marangos JP, Slavíček P, Arrell CA, Chergui M. Photoemission from non-polar aromatic molecules in the gas and liquid phase. Phys Chem Chem Phys 2020; 22:3965-3974. [PMID: 32022040 DOI: 10.1039/c9cp06799j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The photoelectron spectra of both liquid and gas phase aromatic molecules are reported. The spectra were obtained using a 34.1 eV source produced by high harmonic generation and analysed with the help of high-level ab initio simulations using the reflection principle combined with path integral molecular dynamics simulations accounting for nuclear quantum effects for the gas phase. We demonstrate the suitability of three trimethylbenzenes (1,3,5-trimethylbenzene, 1,2,3-trimethylbenzene and 1,2,4-trimethylbenzene) as a solvent for liquid photoelectron spectroscopy of solute species. We also discuss the electrokinetic charging of a non-polar liquid jet.
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Affiliation(s)
- L Longetti
- Laboratory of Ultrafast Spectroscopy and the Lausanne Centre for Ultrafast Science, ISIC, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
| | - M Randulová
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, Prague 6, 166 28, Czech Republic
| | - J Ojeda
- Laboratory of Ultrafast Spectroscopy and the Lausanne Centre for Ultrafast Science, ISIC, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
| | - L Mewes
- Laboratory of Ultrafast Spectroscopy and the Lausanne Centre for Ultrafast Science, ISIC, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
| | - L Miseikis
- Department of Physics, The Blackett Laboratory, Imperial College, London SW7 2AZ, UK
| | - J Grilj
- Laboratory of Ultrafast Spectroscopy and the Lausanne Centre for Ultrafast Science, ISIC, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
| | - A Sanchez-Gonzalez
- Department of Physics, The Blackett Laboratory, Imperial College, London SW7 2AZ, UK
| | - T Witting
- Department of Physics, The Blackett Laboratory, Imperial College, London SW7 2AZ, UK
| | - T Siegel
- Department of Physics, The Blackett Laboratory, Imperial College, London SW7 2AZ, UK
| | - Z Diveki
- Department of Physics, The Blackett Laboratory, Imperial College, London SW7 2AZ, UK
| | - F van Mourik
- Laboratory of Ultrafast Spectroscopy and the Lausanne Centre for Ultrafast Science, ISIC, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
| | - R Chapman
- Central Laser Facility, STFC Rutherford Appleton Laboratory, Oxon OX11 0QX, UK
| | - C Cacho
- Central Laser Facility, STFC Rutherford Appleton Laboratory, Oxon OX11 0QX, UK
| | - S Yap
- Central Laser Facility, STFC Rutherford Appleton Laboratory, Oxon OX11 0QX, UK
| | - J W G Tisch
- Department of Physics, The Blackett Laboratory, Imperial College, London SW7 2AZ, UK
| | - E Springate
- Central Laser Facility, STFC Rutherford Appleton Laboratory, Oxon OX11 0QX, UK
| | - J P Marangos
- Department of Physics, The Blackett Laboratory, Imperial College, London SW7 2AZ, UK
| | - P Slavíček
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, Prague 6, 166 28, Czech Republic
| | - C A Arrell
- Laboratory of Ultrafast Spectroscopy and the Lausanne Centre for Ultrafast Science, ISIC, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland. and Laboratory for Advanced Photonics, Paul Scherrer Institut, Villigen, 5232, Switzerland.
| | - M Chergui
- Laboratory of Ultrafast Spectroscopy and the Lausanne Centre for Ultrafast Science, ISIC, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
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13
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Affiliation(s)
- Toshinori Suzuki
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502,
Japan
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Muchová E, Slavíček P. Beyond Koopmans' theorem: electron binding energies in disordered materials. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2019; 31:043001. [PMID: 30524069 DOI: 10.1088/1361-648x/aaf130] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The topical review focuses on calculating ionization energies (IE), or electronic polarons in quasi-particle terminology, in large disordered systems, e.g. for a solute dissolved in a molecular solvent. The simplest estimate of the ionization energy is provided by one-electron energies in the Hartree-Fock theory, but the calculated quantities are not accurate. Density functional theory as many-body theory provides a principal opportunity for calculating one-electron energies including correlation and relaxation effects, i.e. the true energies of electronic polarons. We argue that such a principal possibility materializes within the concept of optimally tuned range-separated hybrid functionals (OT-RSH). We describe various schemes for optimal tuning. Importantly, the OT-RSH scheme is investigated for systems capped with dielectric continuum, providing a consistent picture on the QM/dielectric boundary. Finally, some limitations and open issues of the OT-RSH approach are addressed.
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Affiliation(s)
- Eva Muchová
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Czech Republic
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15
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Pohl MN, Muchová E, Seidel R, Ali H, Sršeň Š, Wilkinson I, Winter B, Slavíček P. Do water's electrons care about electrolytes? Chem Sci 2019; 10:848-865. [PMID: 30774880 PMCID: PMC6346409 DOI: 10.1039/c8sc03381a] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 11/01/2018] [Indexed: 01/01/2023] Open
Abstract
Ions have a profound effect on the geometrical structure of liquid water and an aqueous environment is known to change the electronic structure of ions. Here we combine photoelectron spectroscopy measurements from liquid microjets with molecular dynamical and quantum chemical calculations to address the reverse question, to what extent do ions affect the electronic structure of liquid water? We study aqueous solutions of sodium iodide (NaI) over a wide concentration range, from nearly pure water to 8 M solutions, recording spectra in the 5 to 60 eV binding energy range to include all water valence and the solute Na+ 2p, I- 4d, and I- 5p orbital ionization peaks. We observe that the electron binding energies of the solute ions change only slightly as a function of electrolyte concentration, less than 150 ± 60 meV over an ∼8 M range. Furthermore, the photoelectron spectrum of liquid water is surprisingly mildly affected as we transform the sample from a dilute aqueous salt solution to a viscous, crystalline-like phase. The most noticeable spectral changes are a negative binding energy shift of the water 1b2 ionizing transition (up to -370 ± 60 meV) and a narrowing of the flat-top shape water 3a1 ionization feature (up to 450 ± 90 meV). A novel computationally efficient technique is introduced to calculate liquid-state photoemission spectra using small clusters from molecular dynamics (MD) simulations embedded in dielectric continuum. This theoretical treatment captured the characteristic positions and structures of the aqueous photoemission peaks, reproducing the experimentally observed narrowing of the water 3a1 feature and weak sensitivity of the water binding energies to electrolyte concentration. The calculations allowed us to attribute the small binding energy shifts to ion-induced disruptions of intermolecular electronic interactions. Furthermore, they demonstrate the importance of considering concentration-dependent screening lengths for a correct description of the electronic structure of solvated systems. Accounting for electronic screening, the calculations highlight the minimal effect of electrolyte concentration on the 1b1 binding energy reference, in accord with the experiments. This leads us to a key finding that the isolated, lowest-binding-energy, 1b1, photoemission feature of liquid water is a robust energetic reference for aqueous liquid microjet photoemission studies.
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Affiliation(s)
- Marvin N Pohl
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6 , D-14195 Berlin , Germany .
- Fachbereich Physik , Freie Universität Berlin , Arnimallee 14 , D-14195 Berlin , Germany
| | - Eva Muchová
- Department of Physical Chemistry , University of Chemistry and Technology , Technická 5 , 16628 Prague , Czech Republic .
| | - Robert Seidel
- Helmholtz-Zentrum Berlin für Materialien und Energie , Hahn-Meitner-Platz 1 , D-14109 Berlin , Germany .
- Humboldt-Universität zu Berlin , Department of Chemistry , Brook-Taylor-Str. 2 , D-12489 Berlin , Germany
| | - Hebatallah Ali
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6 , D-14195 Berlin , Germany .
- Fachbereich Physik , Freie Universität Berlin , Arnimallee 14 , D-14195 Berlin , Germany
| | - Štěpán Sršeň
- Department of Physical Chemistry , University of Chemistry and Technology , Technická 5 , 16628 Prague , Czech Republic .
| | - Iain Wilkinson
- Helmholtz-Zentrum Berlin für Materialien und Energie , Hahn-Meitner-Platz 1 , D-14109 Berlin , Germany .
| | - Bernd Winter
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6 , D-14195 Berlin , Germany .
| | - Petr Slavíček
- Department of Physical Chemistry , University of Chemistry and Technology , Technická 5 , 16628 Prague , Czech Republic .
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16
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17
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Kronik L, Kümmel S. Dielectric Screening Meets Optimally Tuned Density Functionals. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1706560. [PMID: 29665112 DOI: 10.1002/adma.201706560] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 12/19/2017] [Indexed: 06/08/2023]
Abstract
A short overview of recent attempts at merging two independently developed methods is presented. These are the optimal tuning of a range-separated hybrid (OT-RSH) functional, developed to provide an accurate first-principles description of the electronic structure and optical properties of gas-phase molecules, and the polarizable continuum model (PCM), developed to provide an approximate but computationally tractable description of a solvent in terms of an effective dielectric medium. After a brief overview of the OT-RSH approach, its combination with the PCM as a potentially accurate yet low-cost approach to the study of molecular assemblies and solids, particularly in the context of photocatalysis and photovoltaics, is discussed. First, solvated molecules are considered, with an emphasis on the challenge of balancing eigenvalue and total energy trends. Then, it is shown that the same merging of methods can also be used to study the electronic and optical properties of molecular solids, with a similar discussion of the pros and cons. Tuning of the effective scalar dielectric constant as one recent approach that mitigates some of the difficulties in merging the two approaches is considered.
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Affiliation(s)
- Leeor Kronik
- Department of Materials and Interfaces, Weizmann Institute of Science, Rehovoth, 76100, Israel
| | - Stephan Kümmel
- Theoretical Physics IV, Universität Bayreuth, 95440, Bayreuth, Germany
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18
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Zuehlsdorff TJ, Napoli JA, Milanese JM, Markland TE, Isborn CM. Unraveling electronic absorption spectra using nuclear quantum effects: Photoactive yellow protein and green fluorescent protein chromophores in water. J Chem Phys 2018; 149:024107. [PMID: 30007372 DOI: 10.1063/1.5025517] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Many physical phenomena must be accounted for to accurately model solution-phase optical spectral line shapes, from the sampling of chromophore-solvent configurations to the electronic-vibrational transitions leading to vibronic fine structure. Here we thoroughly explore the role of nuclear quantum effects, direct and indirect solvent effects, and vibronic effects in the computation of the optical spectrum of the aqueously solvated anionic chromophores of green fluorescent protein and photoactive yellow protein. By analyzing the chromophore and solvent configurations, the distributions of vertical excitation energies, the absorption spectra computed within the ensemble approach, and the absorption spectra computed within the ensemble plus zero-temperature Franck-Condon approach, we show how solvent, nuclear quantum effects, and vibronic transitions alter the optical absorption spectra. We find that including nuclear quantum effects in the sampling of chromophore-solvent configurations using ab initio path integral molecular dynamics simulations leads to improved spectral shapes through three mechanisms. The three mechanisms that lead to line shape broadening and a better description of the high-energy tail are softening of heavy atom bonds in the chromophore that couple to the optically bright state, widening the distribution of vertical excitation energies from more diverse solvation environments, and redistributing spectral weight from the 0-0 vibronic transition to higher energy vibronic transitions when computing the Franck-Condon spectrum in a frozen solvent pocket. The absorption spectra computed using the combined ensemble plus zero-temperature Franck-Condon approach yield significant improvements in spectral shape and width compared to the spectra computed with the ensemble approach. Using the combined approach with configurations sampled from path integral molecular dynamics trajectories presents a significant step forward in accurately modeling the absorption spectra of aqueously solvated chromophores.
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Affiliation(s)
- Tim J Zuehlsdorff
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
| | - Joseph A Napoli
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Joel M Milanese
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
| | - Thomas E Markland
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Christine M Isborn
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
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Manna D, Blumberger J, Martin JML, Kronik L. Prediction of electronic couplings for molecular charge transfer using optimally tuned range-separated hybrid functionals. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1489084] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Debashree Manna
- Department of Materials and Interfaces, Weizmann Institute of Science, Rehovoth, Israel
| | - Jochen Blumberger
- Department of Physics and Astronomy, Thomas Young Centre, University College London, London, UK
- Institute for Advanced Study, Technische Universität Munchen, Garching, Germany
| | - Jan M. L. Martin
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovoth, Israel
| | - Leeor Kronik
- Department of Materials and Interfaces, Weizmann Institute of Science, Rehovoth, Israel
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20
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Law YK, Hassanali AA. The importance of nuclear quantum effects in spectral line broadening of optical spectra and electrostatic properties in aromatic chromophores. J Chem Phys 2018; 148:102331. [PMID: 29544302 DOI: 10.1063/1.5005056] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
In this work, we examine the importance of nuclear quantum effects on capturing the line broadening and vibronic structure of optical spectra. We determine the absorption spectra of three aromatic molecules indole, pyridine, and benzene using time dependent density functional theory with several molecular dynamics sampling protocols: force-field based empirical potentials, ab initio simulations, and finally path-integrals for the inclusion of nuclear quantum effects. We show that the absorption spectrum for all these chromophores are similarly broadened in the presence of nuclear quantum effects regardless of the presence of hydrogen bond donor or acceptor groups. We also show that simulations incorporating nuclear quantum effects are able to reproduce the heterogeneous broadening of the absorption spectra even with empirical force fields. The spectral broadening associated with nuclear quantum effects can be accounted for by the broadened distribution of chromophore size as revealed by a particle in the box model. We also highlight the role that nuclear quantum effects have on the underlying electronic structure of aromatic molecules as probed by various electrostatic properties.
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Affiliation(s)
- Y K Law
- School of Natural Sciences and Mathematics, Indiana University East, Richmond, Indiana 47374, USA
| | - A A Hassanali
- Condensed Matter and Statistical Physics Section, The Abdus Salaam International Center for Theoretical Physics, Strada Costiera 11, Trieste 34151, Italy
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21
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Chalabala J, Uhlig F, Slavíček P. Assessment of Real-Time Time-Dependent Density Functional Theory (RT-TDDFT) in Radiation Chemistry: Ionized Water Dimer. J Phys Chem A 2018. [PMID: 29513531 DOI: 10.1021/acs.jpca.8b01259] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ionization in the condensed phase and molecular clusters leads to a complicated chain of processes with coupled electron-nuclear dynamics. It is difficult to describe such dynamics with conventional nonadiabatic molecular dynamics schemes since the number of states swiftly increases as the molecular system grows. It is therefore attractive to use a direct electron and nuclear propagation such as the real-time time-dependent density functional theory (RT-TDDFT). Here we report a RT-TDDFT benchmark study on simulations of singly and doubly ionized states of a water monomer and dimer as a prototype for more complex processes in a condensed phase. We employed the RT-TDDFT based Ehrenfest molecular dynamics with a generalized gradient approximate (GGA) functional and compared it with wave-function-based surface hopping (SH) simulations. We found that the initial dynamics of a singly HOMO ionized water dimer is similar for both the RT-TDDFT/GGA and the SH simulations but leads to completely different reaction channels on a longer time scale. This failure is attributed to the self-interaction error in the GGA functionals and it can be avoided by using hybrid functionals with large fraction of exact exchange (represented here by the BHandHLYP functional). The simulations of doubly ionized states are reasonably described already at the GGA level. This suggests that the RT-TDDFT/GGA method could describe processes following the autoionization processes such as Auger emission, while its applicability to more complex processes such as intermolecular Coulombic decay remains limited.
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Affiliation(s)
- Jan Chalabala
- Department of Physical Chemistry , University of Chemistry and Technology , Technická 5 , 16628 Prague , Czech Republic
| | - Frank Uhlig
- Department of Physical Chemistry , University of Chemistry and Technology , Technická 5 , 16628 Prague , Czech Republic.,Institute for Computational Physics , University of Stuttgart , Allmandring 3 , 70569 Stuttgart , Germany
| | - Petr Slavíček
- Department of Physical Chemistry , University of Chemistry and Technology , Technická 5 , 16628 Prague , Czech Republic.,Jaroslav Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic , Dolejškova 3 , 18200 Prague , Czech Republic
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22
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23
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Suchan J, Hollas D, Curchod BFE, Slavíček P. On the importance of initial conditions for excited-state dynamics. Faraday Discuss 2018; 212:307-330. [DOI: 10.1039/c8fd00088c] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The vast majority of ab initio excited-state simulations are performed within semiclassical, trajectory-based approaches. Apart from the underlying electronic-structure theory, the reliability of the simulations is controlled by a selection of initial conditions for the classical trajectories. We discuss appropriate choices of initial conditions for simulations of different experimental arrangements: dynamics initiated by continuum-wave (CW) laser fields or triggered by ultrashort laser pulses.
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Affiliation(s)
- Jiří Suchan
- Department of Physical Chemistry
- University of Chemistry and Technology, Prague
- 16628 Prague
- Czech Republic
| | - Daniel Hollas
- Department of Physical Chemistry
- University of Chemistry and Technology, Prague
- 16628 Prague
- Czech Republic
| | | | - Petr Slavíček
- Department of Physical Chemistry
- University of Chemistry and Technology, Prague
- 16628 Prague
- Czech Republic
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24
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Pohl R, Socha O, Slavíček P, Šála M, Hodgkinson P, Dračínský M. Proton transfer in guanine-cytosine base pair analogues studied by NMR spectroscopy and PIMD simulations. Faraday Discuss 2018; 212:331-344. [PMID: 30234207 DOI: 10.1039/c8fd00070k] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
It has been hypothesised that proton tunnelling between paired nucleobases significantly enhances the formation of rare tautomeric forms and hence leads to errors in DNA replication. Here, we study nuclear quantum effects (NQEs) using deuterium isotope-induced changes of nitrogen NMR chemical shifts in a model base pair consisting of two tautomers of isocytosine, which form hydrogen-bonded dimers in the same way as the guanine-cytosine base pair. Isotope effects in NMR are consequences of NQEs, because ro-vibrational averaging of different isotopologues gives rise to different magnetic shielding of the nuclei. The experimental deuterium-induced chemical shift changes are compared with those calculated by a combination of path integral molecular dynamics (PIMD) simulations with DFT calculations of nuclear shielding. These calculations can directly link the observable isotope-induced shifts with NQEs. A comparison of the deuterium-induced changes of 15N chemical shifts with those predicted by PIMD simulations shows that inter-base proton transfer reactions do not take place in this system. We demonstrate, however, that NMR isotope shifts provide a unique possibility to study NQEs and to evaluate the accuracy of the computational methods used for modelling quantum effects in molecules. Calculations based on the PBE functional from the general-gradient-approximation family provided significantly worse predictions of deuterium isotope shifts than those with the hybrid B3LYP functional.
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Affiliation(s)
- Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Flemingovo nám. 2, 16610, Prague, Czech Republic.
| | - Ondřej Socha
- Institute of Organic Chemistry and Biochemistry, Flemingovo nám. 2, 16610, Prague, Czech Republic.
| | - Petr Slavíček
- University of Chemistry and Technology Prague, Department of Physical Chemistry, Technická 5, 16628 Prague, Czech Republic
| | - Michal Šála
- Institute of Organic Chemistry and Biochemistry, Flemingovo nám. 2, 16610, Prague, Czech Republic.
| | - Paul Hodgkinson
- Department of Chemistry, Durham University, South Road, DH1 3LE, Durham, UK
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry, Flemingovo nám. 2, 16610, Prague, Czech Republic.
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Rubešová M, Muchová E, Slavíček P. Optimal Tuning of Range-Separated Hybrids for Solvated Molecules with Time-Dependent Density Functional Theory. J Chem Theory Comput 2017; 13:4972-4983. [DOI: 10.1021/acs.jctc.7b00675] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Martina Rubešová
- Department of Physical Chemistry, University of Chemistry and Technology, Technická 5, 16628 Prague, Czech Republic
| | - Eva Muchová
- Department of Physical Chemistry, University of Chemistry and Technology, Technická 5, 16628 Prague, Czech Republic
| | - Petr Slavíček
- Department of Physical Chemistry, University of Chemistry and Technology, Technická 5, 16628 Prague, Czech Republic
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26
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Brumboiu IE, Prokopiou G, Kronik L, Brena B. Valence electronic structure of cobalt phthalocyanine from an optimally tuned range-separated hybrid functional. J Chem Phys 2017; 147:044301. [DOI: 10.1063/1.4993623] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Affiliation(s)
- Iulia Emilia Brumboiu
- Department of Theoretical Chemistry and Biology, School of Biotechnology, Royal Institute of Technology, 10691 Stockholm, Sweden
| | - Georgia Prokopiou
- Department of Materials and Interfaces, Weizmann Institute of Science, Rehovoth 76100, Israel
| | - Leeor Kronik
- Department of Materials and Interfaces, Weizmann Institute of Science, Rehovoth 76100, Israel
| | - Barbara Brena
- Department of Physics and Astronomy, Uppsala University, 75120 Uppsala, Sweden
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Rubešová M, Jurásková V, Slavíček P. Efficient modeling of liquid phase photoemission spectra and reorganization energies: Difficult case of multiply charged anions. J Comput Chem 2017; 38:427-437. [DOI: 10.1002/jcc.24696] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 10/25/2016] [Accepted: 11/23/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Martina Rubešová
- Department of Physical Chemistry; University of Chemistry and Technology; Technická 5 Prague 16628 Czech Republic
| | - Veronika Jurásková
- Department of Physical Chemistry; University of Chemistry and Technology; Technická 5 Prague 16628 Czech Republic
| | - Petr Slavíček
- Department of Physical Chemistry; University of Chemistry and Technology; Technická 5 Prague 16628 Czech Republic
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