Les publications et communications ayant bénéficié des ressources du mésocentre doivent en faire mention par la phrase : « This work was granted access to the HPC resources of Aix-Marseille Université financed by the project Equip@Meso (ANR-10-EQPX-29-01) of the program « Investissements d’Avenir » supervised by the Agence Nationale de la Recherche.»
2018
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Falahati Konstantin; Tamura Hiroyuki; Burghardt Irene; Huix-Rotllant Miquel Ultrafast carbon monoxide photolysis and heme spin-crossover in myoglobin via nonadiabatic quantum dynamics 2018. Résumé | Liens | BibTeX @book{Falahati2018,
title = {Ultrafast carbon monoxide photolysis and heme spin-crossover in myoglobin via nonadiabatic quantum dynamics},
author = {Falahati Konstantin and Tamura Hiroyuki and Burghardt Irene and Huix-Rotllant Miquel},
editor = {Nature Communications},
url = {https://doi.org/10.1038/s41467-018-06615-1},
doi = {10.1038/s41467-018-06615-1},
year = {2018},
date = {2018-10-29},
abstract = {Light absorption of myoglobin triggers diatomic ligand photolysis and a spin crossover transition of iron(II) that initiate protein conformational change. The photolysis and spin crossover reactions happen concurrently on a femtosecond timescale. The microscopic origin of these reactions remains controversial. Here, we apply quantum wavepacket dynamics to elucidate the ultrafast photochemical mechanism for a heme–carbon monoxide (heme–CO) complex. We observe coherent oscillations of the Fe–CO bond distance with a period of 42 fs and an amplitude of ∼1 Å. These nuclear motions induce pronounced geometric reorganization, which makes the CO dissociation irreversible. The reaction is initially dominated by symmetry breaking vibrations inducing an electron transfer from porphyrin to iron. Subsequently, the wavepacket relaxes to the triplet manifold in ∼75 fs and to the quintet manifold in ∼430 fs. Our results highlight the central role of nuclear vibrations at the origin of the ultrafast photodynamics of organometallic complexes.},
keywords = {},
pubstate = {published},
tppubtype = {book}
}
Light absorption of myoglobin triggers diatomic ligand photolysis and a spin crossover transition of iron(II) that initiate protein conformational change. The photolysis and spin crossover reactions happen concurrently on a femtosecond timescale. The microscopic origin of these reactions remains controversial. Here, we apply quantum wavepacket dynamics to elucidate the ultrafast photochemical mechanism for a heme–carbon monoxide (heme–CO) complex. We observe coherent oscillations of the Fe–CO bond distance with a period of 42 fs and an amplitude of ∼1 Å. These nuclear motions induce pronounced geometric reorganization, which makes the CO dissociation irreversible. The reaction is initially dominated by symmetry breaking vibrations inducing an electron transfer from porphyrin to iron. Subsequently, the wavepacket relaxes to the triplet manifold in ∼75 fs and to the quintet manifold in ∼430 fs. Our results highlight the central role of nuclear vibrations at the origin of the ultrafast photodynamics of organometallic complexes. |
Xiaoliang He; Sourabh Apte; Kai Schneider; Benjamin Kadoch Angular multiscale statistics of turbulence in a porous bed Dans: Phys. Rev. Fluids, 3 , p. 084501, 2018. Liens | BibTeX @article{PhysRevFluids.3.084501,
title = {Angular multiscale statistics of turbulence in a porous bed},
author = {Xiaoliang He and Sourabh Apte and Kai Schneider and Benjamin Kadoch},
url = {https://link.aps.org/doi/10.1103/PhysRevFluids.3.084501},
doi = {10.1103/PhysRevFluids.3.084501},
year = {2018},
date = {2018-08-01},
journal = {Phys. Rev. Fluids},
volume = {3},
pages = {084501},
publisher = {American Physical Society},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
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S Cabanes; B Favier; M Le Bars Some statistical properties of three-dimensional zonostrophic turbulence Dans: Geophysical and Astrophysical Fluid Dynamics, 112 (3), p. 207-221, 2018. Liens | BibTeX @article{cabanes:hal-01904597,
title = {Some statistical properties of three-dimensional zonostrophic turbulence},
author = {S Cabanes and B Favier and M Le Bars},
url = {https://hal.archives-ouvertes.fr/hal-01904597},
doi = {10.1080/03091929.2018.1467413},
year = {2018},
date = {2018-01-01},
journal = {Geophysical and Astrophysical Fluid Dynamics},
volume = {112},
number = {3},
pages = {207-221},
publisher = {Taylor & Francis},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
Sandeep K Reddy; Benjamin Favier; Michael Le Bars Turbulent Kinematic Dynamos in Ellipsoids Driven by Mechanical Forcing Dans: Geophysical Research Letters, 45 (4), p. 1741-1750, 2018. Résumé | Liens | BibTeX @article{doi:10.1002/2017GL076542,
title = {Turbulent Kinematic Dynamos in Ellipsoids Driven by Mechanical Forcing},
author = {Sandeep K Reddy and Benjamin Favier and Michael Le Bars},
url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1002/2017GL076542},
doi = {10.1002/2017GL076542},
year = {2018},
date = {2018-01-01},
journal = {Geophysical Research Letters},
volume = {45},
number = {4},
pages = {1741-1750},
abstract = {Abstract Dynamo action in planetary cores has been extensively studied in the context of convectively driven flows. We show in this letter that mechanical forcings, namely, tides, libration, and precession, are also able to kinematically sustain a magnetic field against ohmic diffusion. Previous attempts published in the literature focused on the laminar response or considered idealized spherical configurations. In contrast, we focus here on the developed turbulent regime and we self-consistently solve the magnetohydrodynamic equations in an ellipsoidal container. Our results open new avenues of research in dynamo theory where both convection and mechanical forcing can play a role, independently or simultaneously.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Abstract Dynamo action in planetary cores has been extensively studied in the context of convectively driven flows. We show in this letter that mechanical forcings, namely, tides, libration, and precession, are also able to kinematically sustain a magnetic field against ohmic diffusion. Previous attempts published in the literature focused on the laminar response or considered idealized spherical configurations. In contrast, we focus here on the developed turbulent regime and we self-consistently solve the magnetohydrodynamic equations in an ellipsoidal container. Our results open new avenues of research in dynamo theory where both convection and mechanical forcing can play a role, independently or simultaneously. |
Thomas Le Reun; Benjamin Favier; Michael Le Bars Parametric instability and wave turbulence driven by tidal excitation of internal waves Dans: Journal of Fluid Mechanics, 840 , p. 498–529, 2018. Liens | BibTeX @article{lereun_favier_lebars_2018,
title = {Parametric instability and wave turbulence driven by tidal excitation of internal waves},
author = {Thomas Le Reun and Benjamin Favier and Michael Le Bars},
doi = {10.1017/jfm.2018.18},
year = {2018},
date = {2018-01-01},
journal = {Journal of Fluid Mechanics},
volume = {840},
pages = {498–529},
publisher = {Cambridge University Press},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
Yongliang Feng; Muhammad Tayyab; Pierre Boivin A Lattice-Boltzmann model for low-Mach reactive flows Dans: Combustion and Flame, 196 , p. 249 - 254, 2018, ISSN: 0010-2180. Résumé | Liens | BibTeX @article{FENG2018249,
title = {A Lattice-Boltzmann model for low-Mach reactive flows},
author = {Yongliang Feng and Muhammad Tayyab and Pierre Boivin},
url = {http://www.sciencedirect.com/science/article/pii/S0010218018302803},
doi = {https://doi.org/10.1016/j.combustflame.2018.06.027},
issn = {0010-2180},
year = {2018},
date = {2018-01-01},
journal = {Combustion and Flame},
volume = {196},
pages = {249 - 254},
abstract = {A new Lattice-Boltzmann model for low-Mach reactive flows is presented. Based on standard lattices, the model is easy to implement, and is the first, to the authors’ knowledge, to pass the classical freely propagating flame test case as well as the counterflow diffusion flame, with strains up to extinction. For this presentation, simplified transport properties are considered, each species being assigned a separate Lewis number. In addition, the gas mixture is assumed to be calorically perfect. Comparisons with reference solutions show excellent agreement for mass fraction profiles, flame speed in premixed mixtures, as well as maximum temperature dependence with strain rate in counterflow diffusion flames.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
A new Lattice-Boltzmann model for low-Mach reactive flows is presented. Based on standard lattices, the model is easy to implement, and is the first, to the authors’ knowledge, to pass the classical freely propagating flame test case as well as the counterflow diffusion flame, with strains up to extinction. For this presentation, simplified transport properties are considered, each species being assigned a separate Lewis number. In addition, the gas mixture is assumed to be calorically perfect. Comparisons with reference solutions show excellent agreement for mass fraction profiles, flame speed in premixed mixtures, as well as maximum temperature dependence with strain rate in counterflow diffusion flames. |
Elisa Pieri; Vincent Ledentu; Miquel Huix-Rotllant; Nicolas Ferré Sampling the protonation states: the pH-dependent UV absorption spectrum of a polypeptide dyad Dans: Phys. Chem. Chem. Phys., 20 , p. 23252-23261, 2018. Résumé | Liens | BibTeX @article{C8CP03557A,
title = {Sampling the protonation states: the pH-dependent UV absorption spectrum of a polypeptide dyad},
author = {Elisa Pieri and Vincent Ledentu and Miquel Huix-Rotllant and Nicolas Ferré},
url = {http://dx.doi.org/10.1039/C8CP03557A},
doi = {10.1039/C8CP03557A},
year = {2018},
date = {2018-01-01},
journal = {Phys. Chem. Chem. Phys.},
volume = {20},
pages = {23252-23261},
publisher = {The Royal Society of Chemistry},
abstract = {When a chromophore interacts with several titratable molecular sites, the modeling of its photophysical properties requires to take into account all their possible protonation states. We have developed a multi-scale protocol, based on constant-pH molecular dynamics simulations coupled to QM/MM excitation energy calculations, aimed at sampling both the phase space and protonation state space of a short polypeptide featuring a tyrosine–tryptophan dyad interacting with two aspartic acid residues. We show that such a protocol is accurate enough to help in the interpretation of the experimental tyrosine UV absorption spectrum at both acidic and basic pH. Moreover, it is confirmed that radical tryptophan probably contributes to the peptide spectrum, thanks to a UV-induced electron transfer from tyrosine to tryptophan, ultimately shedding light on the complex pH-dependent behavior of the peptide spectrum.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
When a chromophore interacts with several titratable molecular sites, the modeling of its photophysical properties requires to take into account all their possible protonation states. We have developed a multi-scale protocol, based on constant-pH molecular dynamics simulations coupled to QM/MM excitation energy calculations, aimed at sampling both the phase space and protonation state space of a short polypeptide featuring a tyrosine–tryptophan dyad interacting with two aspartic acid residues. We show that such a protocol is accurate enough to help in the interpretation of the experimental tyrosine UV absorption spectrum at both acidic and basic pH. Moreover, it is confirmed that radical tryptophan probably contributes to the peptide spectrum, thanks to a UV-induced electron transfer from tyrosine to tryptophan, ultimately shedding light on the complex pH-dependent behavior of the peptide spectrum. |
Cristina García-Iriepa; Pauline Gosset; Romain Berraud-Pache; Madjid Zemmouche; Grégory Taupier; Kokou Dodzi Dorkenoo; Pascal Didier; Jérémie Léonard; Nicolas Ferré; Isabelle Navizet Simulation and Analysis of the Spectroscopic Properties of Oxyluciferin and Its Analogues in Water Dans: Journal of Chemical Theory and Computation, 14 (4), p. 2117-2126, 2018, (PMID: 29509419). Résumé | Liens | BibTeX @article{doi:10.1021/acs.jctc.7b01240,
title = {Simulation and Analysis of the Spectroscopic Properties of Oxyluciferin and Its Analogues in Water},
author = {Cristina García-Iriepa and Pauline Gosset and Romain Berraud-Pache and Madjid Zemmouche and Grégory Taupier and Kokou Dodzi Dorkenoo and Pascal Didier and Jérémie Léonard and Nicolas Ferré and Isabelle Navizet},
url = {https://doi.org/10.1021/acs.jctc.7b01240},
doi = {10.1021/acs.jctc.7b01240},
year = {2018},
date = {2018-01-01},
journal = {Journal of Chemical Theory and Computation},
volume = {14},
number = {4},
pages = {2117-2126},
abstract = {Firefly bioluminescence is a quite efficient process largely used for numerous applications. However, some fundamental photochemical properties of the light emitter are still to be analyzed. Indeed, the light emitter, oxyluciferin, can be in six different forms due to interexchange reactions. In this work, we present the simulation of the absorption and emission spectra of the possible natural oxyluciferin forms in water and some of their analogues considering both the solvent/oxyluciferin interactions and the dynamical effects by using MD simulations and QM/MM methods. On the one hand, the absorption band shapes have been rationalized by analyzing the electronic nature of the transitions involved. On the other hand, the simulated and experimental emission spectra have been compared. In this case, an ultrafast excited state proton transfer (ESPT) occurs in oxyluciferin and its analogues, which impairs the detection of the emission from the protonated state by steady-state fluorescence spectroscopy. Transient absorption spectroscopy was used to evidence this ultrafast ESPT and rationalize the comparison between simulated and experimental steady-state emission spectra. Finally, this work shows the suitability of the studied oxyluciferin analogues to mimic the corresponding natural forms in water solution, as an elegant way to block the desired interexchange reactions allowing the study of each oxyluciferin form separately.},
note = {PMID: 29509419},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Firefly bioluminescence is a quite efficient process largely used for numerous applications. However, some fundamental photochemical properties of the light emitter are still to be analyzed. Indeed, the light emitter, oxyluciferin, can be in six different forms due to interexchange reactions. In this work, we present the simulation of the absorption and emission spectra of the possible natural oxyluciferin forms in water and some of their analogues considering both the solvent/oxyluciferin interactions and the dynamical effects by using MD simulations and QM/MM methods. On the one hand, the absorption band shapes have been rationalized by analyzing the electronic nature of the transitions involved. On the other hand, the simulated and experimental emission spectra have been compared. In this case, an ultrafast excited state proton transfer (ESPT) occurs in oxyluciferin and its analogues, which impairs the detection of the emission from the protonated state by steady-state fluorescence spectroscopy. Transient absorption spectroscopy was used to evidence this ultrafast ESPT and rationalize the comparison between simulated and experimental steady-state emission spectra. Finally, this work shows the suitability of the studied oxyluciferin analogues to mimic the corresponding natural forms in water solution, as an elegant way to block the desired interexchange reactions allowing the study of each oxyluciferin form separately. |
Grégoire David; Frank Wennmohs; Frank Neese; Nicolas Ferré Chemical Tuning of Magnetic Exchange Couplings Using Broken-Symmetry Density Functional Theory Dans: Inorganic Chemistry, 57 (20), p. 12769-12776, 2018. Résumé | Liens | BibTeX @article{doi:10.1021/acs.inorgchem.8b01970,
title = {Chemical Tuning of Magnetic Exchange Couplings Using Broken-Symmetry Density Functional Theory},
author = {Grégoire David and Frank Wennmohs and Frank Neese and Nicolas Ferré},
url = {https://doi.org/10.1021/acs.inorgchem.8b01970},
doi = {10.1021/acs.inorgchem.8b01970},
year = {2018},
date = {2018-01-01},
journal = {Inorganic Chemistry},
volume = {57},
number = {20},
pages = {12769-12776},
abstract = {With broken-symmetry Kohn–Sham density functional theory calculations, it is demonstrated that the ferromagnetic or anti-ferromagnetic character of two prototypical binuclear copper complexes can be modified, both in the sign and in magnitude, by means of chemical substitutions operated on the bridges connecting the two magnetic centers. The level of detail provided by the magnetic exchange decomposition in terms of direct exchange, kinetic exchange, and core polarization puts forward the relative importance of the different bridges. At variance with the principal bridge for which chemical substitutions modify both the direct and the kinetic exchange contributions, modifications of the secondary bridge only affect the magnitude of the anti-ferromagnetic kinetic exchange mechanism, ultimately allowing for a direct control of the magnetic character of the modified compound.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
With broken-symmetry Kohn–Sham density functional theory calculations, it is demonstrated that the ferromagnetic or anti-ferromagnetic character of two prototypical binuclear copper complexes can be modified, both in the sign and in magnitude, by means of chemical substitutions operated on the bridges connecting the two magnetic centers. The level of detail provided by the magnetic exchange decomposition in terms of direct exchange, kinetic exchange, and core polarization puts forward the relative importance of the different bridges. At variance with the principal bridge for which chemical substitutions modify both the direct and the kinetic exchange contributions, modifications of the secondary bridge only affect the magnitude of the anti-ferromagnetic kinetic exchange mechanism, ultimately allowing for a direct control of the magnetic character of the modified compound. |
Transport and Mixing Induced by Beating Cilia in Human Airways Dans: Frontiers in Physiology, 9 , p. 161, 2018, ISSN: 1664-042X. Résumé | Liens | BibTeX @article{10.3389/fphys.2018.00161,
title = {Transport and Mixing Induced by Beating Cilia in Human Airways},
url = {https://www.frontiersin.org/article/10.3389/fphys.2018.00161},
doi = {10.3389/fphys.2018.00161},
issn = {1664-042X},
year = {2018},
date = {2018-01-01},
journal = {Frontiers in Physiology},
volume = {9},
pages = {161},
abstract = {The fluid transport and mixing induced by beating cilia, present in the bronchial airways, are studied using a coupled lattice Boltzmann – Immersed Boundary solver. This solver allows the simulation of both single and multi-component fluid flows around moving solid boundaries. The cilia are modeled by a set of Lagrangian points, and Immersed Boundary forces are computed onto these points in order to ensure the no-slip velocity conditions between the cilia and the fluids. The cilia are immersed in a two-layer environment: the periciliary layer (PCL) and the mucus above it. The motion of the cilia is prescribed, as well as the phase lag between two cilia in order to obtain a typical collective motion of cilia, known as metachronal waves. The results obtained from a parametric study show that antiplectic metachronal waves are the most efficient regarding the fluid transport. A specific value of phase lag, which generates the larger mucus transport, is identified. The mixing is studied using several populations of tracers initially seeded into the pericilary liquid, in the mucus just above the PCL-mucus interface, and in the mucus far away from the interface. We observe that each zone exhibits different chaotic mixing properties. The larger mixing is obtained in the PCL layer where only a few beating cycles of the cilia are required to obtain a full mixing, while above the interface, the mixing is weaker and takes more time. Almost no mixing is observed within the mucus, and almost all the tracers do not penetrate the PCL layer. Lyapunov exponents are also computed for specific locations to assess how the mixing is performed locally. Two time scales are introduced to allow a comparison between mixing induced by fluid advection and by molecular diffusion. These results are relevant in the context of respiratory flows to investigate the transport of drugs for patients suffering from chronic respiratory diseases.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The fluid transport and mixing induced by beating cilia, present in the bronchial airways, are studied using a coupled lattice Boltzmann – Immersed Boundary solver. This solver allows the simulation of both single and multi-component fluid flows around moving solid boundaries. The cilia are modeled by a set of Lagrangian points, and Immersed Boundary forces are computed onto these points in order to ensure the no-slip velocity conditions between the cilia and the fluids. The cilia are immersed in a two-layer environment: the periciliary layer (PCL) and the mucus above it. The motion of the cilia is prescribed, as well as the phase lag between two cilia in order to obtain a typical collective motion of cilia, known as metachronal waves. The results obtained from a parametric study show that antiplectic metachronal waves are the most efficient regarding the fluid transport. A specific value of phase lag, which generates the larger mucus transport, is identified. The mixing is studied using several populations of tracers initially seeded into the pericilary liquid, in the mucus just above the PCL-mucus interface, and in the mucus far away from the interface. We observe that each zone exhibits different chaotic mixing properties. The larger mixing is obtained in the PCL layer where only a few beating cycles of the cilia are required to obtain a full mixing, while above the interface, the mixing is weaker and takes more time. Almost no mixing is observed within the mucus, and almost all the tracers do not penetrate the PCL layer. Lyapunov exponents are also computed for specific locations to assess how the mixing is performed locally. Two time scales are introduced to allow a comparison between mixing induced by fluid advection and by molecular diffusion. These results are relevant in the context of respiratory flows to investigate the transport of drugs for patients suffering from chronic respiratory diseases. |
Nicolas Cavassilas; Demetrio Logoteta; Youseung Lee; Fabienne Michelini; Michel Lannoo; Marc Bescond; Mathieu Luisier Dual-Gated WTe2/MoSe2 van der Waals Tandem Solar Cells Dans: The Journal of Physical Chemistry C, 122 (50), p. 28545-28549, 2018. Résumé | Liens | BibTeX @article{doi:10.1021/acs.jpcc.8b09905,
title = {Dual-Gated WTe2/MoSe2 van der Waals Tandem Solar Cells},
author = {Nicolas Cavassilas and Demetrio Logoteta and Youseung Lee and Fabienne Michelini and Michel Lannoo and Marc Bescond and Mathieu Luisier},
url = {https://doi.org/10.1021/acs.jpcc.8b09905},
doi = {10.1021/acs.jpcc.8b09905},
year = {2018},
date = {2018-01-01},
journal = {The Journal of Physical Chemistry C},
volume = {122},
number = {50},
pages = {28545-28549},
abstract = {We propose and numerically investigate, through a multiscale approach, a tandem solar cell based on a van der Waals heterostructure comprising of two monolayers of transition-metal dichalcogenides. The electronic connection between the two subcells is obtained via tunneling through the van der Waals heterojunction, which is electrostatically controlled by means of a dual gate. Furthermore, by adjusting the dual-gate voltages, the photocurrents in the two subcells can be matched and the tandem cell performances can be optimized. Assuming an optimal absorptance, as expected in light-trapping systems, we predict that a power conversion efficiency of 30.7%, largely exceeding that of the single subcells, can be achieved. The proposed design being suitable for other van der Waals heterojunctions shows that it represents a viable option for future high-efficiency photovoltaic systems.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
We propose and numerically investigate, through a multiscale approach, a tandem solar cell based on a van der Waals heterostructure comprising of two monolayers of transition-metal dichalcogenides. The electronic connection between the two subcells is obtained via tunneling through the van der Waals heterojunction, which is electrostatically controlled by means of a dual gate. Furthermore, by adjusting the dual-gate voltages, the photocurrents in the two subcells can be matched and the tandem cell performances can be optimized. Assuming an optimal absorptance, as expected in light-trapping systems, we predict that a power conversion efficiency of 30.7%, largely exceeding that of the single subcells, can be achieved. The proposed design being suitable for other van der Waals heterojunctions shows that it represents a viable option for future high-efficiency photovoltaic systems. |
Alexis Bottero; Paul Cristini; Dimitri Komatitsch; Quentin Brissaud Broadband transmission losses and time dispersion maps from time-domain numerical simulations in ocean acoustics Dans: Journal of the Acoustical Society of America, 144 (3), p. EL222 - EL228, 2018. Liens | BibTeX @article{bottero:hal-01793392,
title = {Broadband transmission losses and time dispersion maps from time-domain numerical simulations in ocean acoustics},
author = {Alexis Bottero and Paul Cristini and Dimitri Komatitsch and Quentin Brissaud},
url = {https://hal.archives-ouvertes.fr/hal-01793392},
doi = {10.1121/1.5055787},
year = {2018},
date = {2018-01-01},
journal = {Journal of the Acoustical Society of America},
volume = {144},
number = {3},
pages = {EL222 - EL228},
publisher = {Acoustical Society of America},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
M L M Rocco; M Häming; C E V de Moura; M Barbatti; A B Rocha; A Schöll; E Umbach High-Resolution Near-Edge X-ray Absorption Fine Structure Study of Condensed Polyacenes Dans: The Journal of Physical Chemistry C, 122 (50), p. 28692-28701, 2018. Résumé | Liens | BibTeX @article{doi:10.1021/acs.jpcc.8b08945,
title = {High-Resolution Near-Edge X-ray Absorption Fine Structure Study of Condensed Polyacenes},
author = {M L M Rocco and M Häming and C E V de Moura and M Barbatti and A B Rocha and A Schöll and E Umbach},
url = {https://doi.org/10.1021/acs.jpcc.8b08945},
doi = {10.1021/acs.jpcc.8b08945},
year = {2018},
date = {2018-01-01},
journal = {The Journal of Physical Chemistry C},
volume = {122},
number = {50},
pages = {28692-28701},
abstract = {We present a systematic study of high-resolution near-edge X-ray absorption fine structure (NEXAFS) spectra of well-ordered films of condensed benzene and polyacenes, namely naphthalene, anthracene, tetracene, and pentacene. Increased spectral complexity with increasing molecular size is observed: NEXAFS features decrease in intensity and move to lower photon energy (red shift) as the size of the aromatic system grows. Moreover, a second group of transitions arises. The dichroism in the C K-edge spectra increases with molecular size. While benzene molecules are randomly oriented, the polyacenes preferentially lie flat with increasing molecular size. Vibrational fine structures coupled to the C 1s π* transitions are apparent for all investigated molecules. The energy position of the onset of the first resonance decreases from 284.86 eV for benzene to 283.26 eV for pentacene. Calculations of absolute band envelopes with time-dependent density functional theory (TDDFT), followed by analysis of the transition densities, were performed for the whole series of molecules, revealing the nature of the spectroscopic features.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
We present a systematic study of high-resolution near-edge X-ray absorption fine structure (NEXAFS) spectra of well-ordered films of condensed benzene and polyacenes, namely naphthalene, anthracene, tetracene, and pentacene. Increased spectral complexity with increasing molecular size is observed: NEXAFS features decrease in intensity and move to lower photon energy (red shift) as the size of the aromatic system grows. Moreover, a second group of transitions arises. The dichroism in the C K-edge spectra increases with molecular size. While benzene molecules are randomly oriented, the polyacenes preferentially lie flat with increasing molecular size. Vibrational fine structures coupled to the C 1s π* transitions are apparent for all investigated molecules. The energy position of the onset of the first resonance decreases from 284.86 eV for benzene to 283.26 eV for pentacene. Calculations of absolute band envelopes with time-dependent density functional theory (TDDFT), followed by analysis of the transition densities, were performed for the whole series of molecules, revealing the nature of the spectroscopic features. |
Deniz Tuna; Lasse Spörkel; Mario Barbatti; Walter Thiel Nonadiabatic dynamics simulations of photoexcited urocanic acid Dans: Chemical Physics, 515 , p. 521 - 534, 2018, ISSN: 0301-0104, (Ultrafast Photoinduced Processes in Polyatomic Molecules:Electronic Structure, Dynamics and Spectroscopy (Dedicated to Wolfgang Domcke on the occasion of his 70th birthday)). Résumé | Liens | BibTeX @article{TUNA2018521,
title = {Nonadiabatic dynamics simulations of photoexcited urocanic acid},
author = {Deniz Tuna and Lasse Spörkel and Mario Barbatti and Walter Thiel},
url = {http://www.sciencedirect.com/science/article/pii/S0301010418306542},
doi = {https://doi.org/10.1016/j.chemphys.2018.09.036},
issn = {0301-0104},
year = {2018},
date = {2018-01-01},
journal = {Chemical Physics},
volume = {515},
pages = {521 - 534},
abstract = {Urocanic acid (UA) is a UV filter found in human skin, which has been linked to photoimmunosuppression and the formation of skin cancer. Its UV-light-induced photoisomerization and radiationless deactivation mechanisms have been addressed previously by static calculations. In this paper, we present nonadiabatic trajectory-surface-hopping dynamics simulations of photoexcited UA using the semiempirical OM2/MRCI methodology and an adaptive-timestep algorithm. We have simulated almost 6000 trajectories, each for a simulation time of 1.6 ps, covering the entire conformational space of the E and Z isomers of both possible tautomers of the isolated neutral form of UA (overall 32 conformers). Initial conditions for the excited-state dynamics were obtained from 1 ns ground-state dynamics simulations. We find that UA has an ultrashort excited-state lifetime, which is due to ultrafast radiationless excited-state deactivation driven by E↔Z photoisomerization and excited-state intramolecular proton-transfer (ESIPT) processes. The computed S1 excited-state lifetimes for the E and Z isomers of the N1H and N3H tautomers range from 271 to 506 fs. The photoisomerization quantum yield is calculated to be 43% (32%) for the combined E (Z) isomers of both tautomers. The shorter lifetime and the lower photoisomerization quantum yield of the Z isomers can be rationalized by the larger number of available excited-state deactivation processes: the Z isomers can undergo ESIPT and photoisomerization, whereas the E isomers can only deactivate via the latter process. The intramolecular hydrogen bond that is present in many Z conformers can prevent successful photoisomerization to an E isomer. We find no evidence for an excitation-energy-dependent quantum yield for photoisomerization (EEDQY-PI) in isolated (E)-UA, which has previously been detected spectroscopically in aqueous solution. However, we do find an EEDQY-PI as well as a complementary excitation-energy-dependent quantum yield for ESIPT (EEDQY-ESIPT) for the N1H-Z isomers, which demonstrates the competition of the photoisomerization and ESIPT processes. The present comprehensive study lays the groundwork for future photodynamics simulations of UA in the aqueous phase.},
note = {Ultrafast Photoinduced Processes in Polyatomic Molecules:Electronic Structure, Dynamics and Spectroscopy (Dedicated to Wolfgang Domcke on the occasion of his 70th birthday)},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Urocanic acid (UA) is a UV filter found in human skin, which has been linked to photoimmunosuppression and the formation of skin cancer. Its UV-light-induced photoisomerization and radiationless deactivation mechanisms have been addressed previously by static calculations. In this paper, we present nonadiabatic trajectory-surface-hopping dynamics simulations of photoexcited UA using the semiempirical OM2/MRCI methodology and an adaptive-timestep algorithm. We have simulated almost 6000 trajectories, each for a simulation time of 1.6 ps, covering the entire conformational space of the E and Z isomers of both possible tautomers of the isolated neutral form of UA (overall 32 conformers). Initial conditions for the excited-state dynamics were obtained from 1 ns ground-state dynamics simulations. We find that UA has an ultrashort excited-state lifetime, which is due to ultrafast radiationless excited-state deactivation driven by E↔Z photoisomerization and excited-state intramolecular proton-transfer (ESIPT) processes. The computed S1 excited-state lifetimes for the E and Z isomers of the N1H and N3H tautomers range from 271 to 506 fs. The photoisomerization quantum yield is calculated to be 43% (32%) for the combined E (Z) isomers of both tautomers. The shorter lifetime and the lower photoisomerization quantum yield of the Z isomers can be rationalized by the larger number of available excited-state deactivation processes: the Z isomers can undergo ESIPT and photoisomerization, whereas the E isomers can only deactivate via the latter process. The intramolecular hydrogen bond that is present in many Z conformers can prevent successful photoisomerization to an E isomer. We find no evidence for an excitation-energy-dependent quantum yield for photoisomerization (EEDQY-PI) in isolated (E)-UA, which has previously been detected spectroscopically in aqueous solution. However, we do find an EEDQY-PI as well as a complementary excitation-energy-dependent quantum yield for ESIPT (EEDQY-ESIPT) for the N1H-Z isomers, which demonstrates the competition of the photoisomerization and ESIPT processes. The present comprehensive study lays the groundwork for future photodynamics simulations of UA in the aqueous phase. |
Pavlo O Dral; Mario Barbatti; Walter Thiel Nonadiabatic Excited-State Dynamics with Machine Learning Dans: The Journal of Physical Chemistry Letters, 9 (19), p. 5660-5663, 2018, (PMID: 30200766). Résumé | Liens | BibTeX @article{doi:10.1021/acs.jpclett.8b02469,
title = {Nonadiabatic Excited-State Dynamics with Machine Learning},
author = {Pavlo O Dral and Mario Barbatti and Walter Thiel},
url = {https://doi.org/10.1021/acs.jpclett.8b02469},
doi = {10.1021/acs.jpclett.8b02469},
year = {2018},
date = {2018-01-01},
journal = {The Journal of Physical Chemistry Letters},
volume = {9},
number = {19},
pages = {5660-5663},
abstract = {We show that machine learning (ML) can be used to accurately reproduce nonadiabatic excited-state dynamics with decoherence-corrected fewest switches surface hopping in a 1-D model system. We propose to use ML to significantly reduce the simulation time of realistic, high-dimensional systems with good reproduction of observables obtained from reference simulations. Our approach is based on creating approximate ML potentials for each adiabatic state using a small number of training points. We investigate the feasibility of this approach by using adiabatic spin-boson Hamiltonian models of various dimensions as reference methods.},
note = {PMID: 30200766},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
We show that machine learning (ML) can be used to accurately reproduce nonadiabatic excited-state dynamics with decoherence-corrected fewest switches surface hopping in a 1-D model system. We propose to use ML to significantly reduce the simulation time of realistic, high-dimensional systems with good reproduction of observables obtained from reference simulations. Our approach is based on creating approximate ML potentials for each adiabatic state using a small number of training points. We investigate the feasibility of this approach by using adiabatic spin-boson Hamiltonian models of various dimensions as reference methods. |
A Mohamadzade; S Bai; M Barbatti; S Ullrich Intersystem crossing dynamics in singly substituted thiouracil studied by time-resolved photoelectron spectroscopy: Micro-environmental effects due to sulfur position Dans: Chemical Physics, 515 , p. 572-579, 2018. Liens | BibTeX @article{2018CP....515..572M,
title = {Intersystem crossing dynamics in singly substituted thiouracil studied by time-resolved photoelectron spectroscopy: Micro-environmental effects due to sulfur position},
author = {A {Mohamadzade} and S {Bai} and M {Barbatti} and S {Ullrich}},
doi = {10.1016/j.chemphys.2018.08.011},
year = {2018},
date = {2018-01-01},
journal = {Chemical Physics},
volume = {515},
pages = {572-579},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
Vanessa C de Medeiros; Railton B de Andrade; Gessenildo P. Rodrigues; Glauco F Bauerfeldt; Elizete Ventura; Mario Barbatti; Silmar A do Monte Photochemistry of CF3Cl: Quenching of Charged Fragments Is Caused by Nonadiabatic Effects Dans: Journal of Chemical Theory and Computation, 14 (9), p. 4844-4855, 2018, (PMID: 30080978). Résumé | Liens | BibTeX @article{doi:10.1021/acs.jctc.8b00457,
title = {Photochemistry of CF3Cl: Quenching of Charged Fragments Is Caused by Nonadiabatic Effects},
author = {Vanessa C de Medeiros and Railton B de Andrade and Gessenildo P. Rodrigues and Glauco F Bauerfeldt and Elizete Ventura and Mario Barbatti and Silmar A do Monte},
url = {https://doi.org/10.1021/acs.jctc.8b00457},
doi = {10.1021/acs.jctc.8b00457},
year = {2018},
date = {2018-01-01},
journal = {Journal of Chemical Theory and Computation},
volume = {14},
number = {9},
pages = {4844-4855},
abstract = {For the first time, high-level multireference electronic structure calculations have been performed to study the photochemistry of CF3Cl, allowing a comprehensive interpretation and assignment of experimental data concerning fluorescence, ion-pair formation, and generation of CF3 fragments in several electronic states. All studied dissociation channels correlate either with Cl or Cl– in the ground state. On the other hand, a CF3 fragment can be generated either in the ground or excited state. A rationalization for the nonadiabatic relaxation of CF3Cl, including the formation of an (n4s) stable state and internal conversion at multiple-state intersections, has been provided. Our results explain the anomalous quenching of a charged fragment after low-energy excitation, a fact experimentally observed by separate groups. We show that the CF3+···Cl– ion pair undergoes an internal conversion to the ground state, producing neutral CF3 and Cl fragments. The results also allow understanding as to why CF3Cl is usually a nonemitting species and how UV emission could be induced.},
note = {PMID: 30080978},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
For the first time, high-level multireference electronic structure calculations have been performed to study the photochemistry of CF3Cl, allowing a comprehensive interpretation and assignment of experimental data concerning fluorescence, ion-pair formation, and generation of CF3 fragments in several electronic states. All studied dissociation channels correlate either with Cl or Cl– in the ground state. On the other hand, a CF3 fragment can be generated either in the ground or excited state. A rationalization for the nonadiabatic relaxation of CF3Cl, including the formation of an (n4s) stable state and internal conversion at multiple-state intersections, has been provided. Our results explain the anomalous quenching of a charged fragment after low-energy excitation, a fact experimentally observed by separate groups. We show that the CF3+···Cl– ion pair undergoes an internal conversion to the ground state, producing neutral CF3 and Cl fragments. The results also allow understanding as to why CF3Cl is usually a nonemitting species and how UV emission could be induced. |
Li-li Jiang; Dan Luo; Xiong Lu; Qin-yong Zhang; Fang-gong Cai; Jun Chen Comparative Study on Chemical Reduction of Free-standing Flexible GO Films and Their Cyclic Voltammetry Performance Dans: Colloids and Surfaces A: Physicochemical and Engineering Aspects, 555 , 2018. Liens | BibTeX @article{articleb,
title = {Comparative Study on Chemical Reduction of Free-standing Flexible GO Films and Their Cyclic Voltammetry Performance},
author = {Li-li Jiang and Dan Luo and Xiong Lu and Qin-yong Zhang and Fang-gong Cai and Jun Chen},
doi = {10.1016/j.colsurfa.2018.07.050},
year = {2018},
date = {2018-01-01},
journal = {Colloids and Surfaces A: Physicochemical and Engineering Aspects},
volume = {555},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
Hans Lischka; Dana Nachtigallová; Adélia J A Aquino; Péter G Szalay; Felix Plasser; Francisco B C Machado; Mario Barbatti Multireference Approaches for Excited States of Molecules Dans: Chemical Reviews, 118 (15), p. 7293-7361, 2018, (PMID: 30040389). Résumé | Liens | BibTeX @article{doi:10.1021/acs.chemrev.8b00244,
title = {Multireference Approaches for Excited States of Molecules},
author = {Hans Lischka and Dana Nachtigallová and Adélia J A Aquino and Péter G Szalay and Felix Plasser and Francisco B C Machado and Mario Barbatti},
url = {https://doi.org/10.1021/acs.chemrev.8b00244},
doi = {10.1021/acs.chemrev.8b00244},
year = {2018},
date = {2018-01-01},
journal = {Chemical Reviews},
volume = {118},
number = {15},
pages = {7293-7361},
abstract = {Understanding the properties of electronically excited states is a challenging task that becomes increasingly important for numerous applications in chemistry, molecular physics, molecular biology, and materials science. A substantial impact is exerted by the fascinating progress in time-resolved spectroscopy, which leads to a strongly growing demand for theoretical methods to describe the characteristic features of excited states accurately. Whereas for electronic ground state problems of stable molecules the quantum chemical methodology is now so well developed that informed nonexperts can use it efficiently, the situation is entirely different concerning the investigation of excited states. This review is devoted to a specific class of approaches, usually denoted as multireference (MR) methods, the generality of which is needed for solving many spectroscopic or photodynamical problems. However, the understanding and proper application of these MR methods is often found to be difficult due to their complexity and their computational cost. The purpose of this review is to provide an overview of the most important facts about the different theoretical approaches available and to present by means of a collection of characteristic examples useful information, which can guide the reader in performing their own applications.},
note = {PMID: 30040389},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Understanding the properties of electronically excited states is a challenging task that becomes increasingly important for numerous applications in chemistry, molecular physics, molecular biology, and materials science. A substantial impact is exerted by the fascinating progress in time-resolved spectroscopy, which leads to a strongly growing demand for theoretical methods to describe the characteristic features of excited states accurately. Whereas for electronic ground state problems of stable molecules the quantum chemical methodology is now so well developed that informed nonexperts can use it efficiently, the situation is entirely different concerning the investigation of excited states. This review is devoted to a specific class of approaches, usually denoted as multireference (MR) methods, the generality of which is needed for solving many spectroscopic or photodynamical problems. However, the understanding and proper application of these MR methods is often found to be difficult due to their complexity and their computational cost. The purpose of this review is to provide an overview of the most important facts about the different theoretical approaches available and to present by means of a collection of characteristic examples useful information, which can guide the reader in performing their own applications. |
Shuming Bai; Mario Barbatti Mechanism of enhanced triplet decay of thionucleobase by glycosylation and rate-modulating strategies Dans: Phys. Chem. Chem. Phys., 20 , p. 16428-16436, 2018. Résumé | Liens | BibTeX @article{C8CP02306A,
title = {Mechanism of enhanced triplet decay of thionucleobase by glycosylation and rate-modulating strategies},
author = {Shuming Bai and Mario Barbatti},
url = {http://dx.doi.org/10.1039/C8CP02306A},
doi = {10.1039/C8CP02306A},
year = {2018},
date = {2018-01-01},
journal = {Phys. Chem. Chem. Phys.},
volume = {20},
pages = {16428-16436},
publisher = {The Royal Society of Chemistry},
abstract = {The decay of the triplet state of photosensitizers is essential to their performance in singlet-oxygen generation. Experiments have shown that in thionucleosides, this decay is enhanced compared to that in the corresponding thionucleobases. In this work, we applied quantum-chemical methods and chemical-kinetic modeling to investigate the effects of the sugar substituent on the triplet decay of thionucleosides. The computed rates for the energetically favored conformers of thiothymidine, thiouridine, and thioguanosine (and the respective thionucleobases) show a remarkable quantitative agreement with the experimental results. We additionally show that the triplet decay enhancement is caused by the repulsion interaction between the sugar group and the sulfur atom, which reduces the activation energy for intersystem crossing by destabilizing the T1 minimum. In some instances, an intramolecular hydrogen bond stabilizes the energy of the T1/S0 crossing point, also reducing the activation energy. This molecular understanding of the mechanism of enhanced triplet decay provides a guideline to control the triplet decay rate, which was tested in new thiothymidine derivatives.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The decay of the triplet state of photosensitizers is essential to their performance in singlet-oxygen generation. Experiments have shown that in thionucleosides, this decay is enhanced compared to that in the corresponding thionucleobases. In this work, we applied quantum-chemical methods and chemical-kinetic modeling to investigate the effects of the sugar substituent on the triplet decay of thionucleosides. The computed rates for the energetically favored conformers of thiothymidine, thiouridine, and thioguanosine (and the respective thionucleobases) show a remarkable quantitative agreement with the experimental results. We additionally show that the triplet decay enhancement is caused by the repulsion interaction between the sugar group and the sulfur atom, which reduces the activation energy for intersystem crossing by destabilizing the T1 minimum. In some instances, an intramolecular hydrogen bond stabilizes the energy of the T1/S0 crossing point, also reducing the activation energy. This molecular understanding of the mechanism of enhanced triplet decay provides a guideline to control the triplet decay rate, which was tested in new thiothymidine derivatives. |
Fábris Kossoski; Mario Barbatti Nuclear Ensemble Approach with Importance Sampling Dans: Journal of Chemical Theory and Computation, 14 (6), p. 3173-3183, 2018, (PMID: 29694040). Résumé | Liens | BibTeX @article{doi:10.1021/acs.jctc.8b00059,
title = {Nuclear Ensemble Approach with Importance Sampling},
author = {Fábris Kossoski and Mario Barbatti},
url = {https://doi.org/10.1021/acs.jctc.8b00059},
doi = {10.1021/acs.jctc.8b00059},
year = {2018},
date = {2018-01-01},
journal = {Journal of Chemical Theory and Computation},
volume = {14},
number = {6},
pages = {3173-3183},
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.},
note = {PMID: 29694040},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
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. |
Rachel Crespo-Otero; Mario Barbatti Recent Advances and Perspectives on Nonadiabatic Mixed Quantum–Classical Dynamics Dans: Chemical Reviews, 118 (15), p. 7026-7068, 2018, (PMID: 29767966). Résumé | Liens | BibTeX @article{doi:10.1021/acs.chemrev.7b00577,
title = {Recent Advances and Perspectives on Nonadiabatic Mixed Quantum–Classical Dynamics},
author = {Rachel Crespo-Otero and Mario Barbatti},
url = {https://doi.org/10.1021/acs.chemrev.7b00577},
doi = {10.1021/acs.chemrev.7b00577},
year = {2018},
date = {2018-01-01},
journal = {Chemical Reviews},
volume = {118},
number = {15},
pages = {7026-7068},
abstract = {Nonadiabatic mixed quantum–classical (NA-MQC) dynamics methods form a class of computational theoretical approaches in quantum chemistry tailored to investigate the time evolution of nonadiabatic phenomena in molecules and supramolecular assemblies. NA-MQC is characterized by a partition of the molecular system into two subsystems: one to be treated quantum mechanically (usually but not restricted to electrons) and another to be dealt with classically (nuclei). The two subsystems are connected through nonadiabatic couplings terms to enforce self-consistency. A local approximation underlies the classical subsystem, implying that direct dynamics can be simulated, without needing precomputed potential energy surfaces. The NA-MQC split allows reducing computational costs, enabling the treatment of realistic molecular systems in diverse fields. Starting from the three most well-established methods—mean-field Ehrenfest, trajectory surface hopping, and multiple spawning—this review focuses on the NA-MQC dynamics methods and programs developed in the last 10 years. It stresses the relations between approaches and their domains of application. The electronic structure methods most commonly used together with NA-MQC dynamics are reviewed as well. The accuracy and precision of NA-MQC simulations are critically discussed, and general guidelines to choose an adequate method for each application are delivered.},
note = {PMID: 29767966},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Nonadiabatic mixed quantum–classical (NA-MQC) dynamics methods form a class of computational theoretical approaches in quantum chemistry tailored to investigate the time evolution of nonadiabatic phenomena in molecules and supramolecular assemblies. NA-MQC is characterized by a partition of the molecular system into two subsystems: one to be treated quantum mechanically (usually but not restricted to electrons) and another to be dealt with classically (nuclei). The two subsystems are connected through nonadiabatic couplings terms to enforce self-consistency. A local approximation underlies the classical subsystem, implying that direct dynamics can be simulated, without needing precomputed potential energy surfaces. The NA-MQC split allows reducing computational costs, enabling the treatment of realistic molecular systems in diverse fields. Starting from the three most well-established methods—mean-field Ehrenfest, trajectory surface hopping, and multiple spawning—this review focuses on the NA-MQC dynamics methods and programs developed in the last 10 years. It stresses the relations between approaches and their domains of application. The electronic structure methods most commonly used together with NA-MQC dynamics are reviewed as well. The accuracy and precision of NA-MQC simulations are critically discussed, and general guidelines to choose an adequate method for each application are delivered. |
M L M Rocco; M Häming; C E V de Moura; M Barbatti; A B Rocha; A Schöll; E Umbach High-Resolution Near-Edge X-ray Absorption Fine Structure Study of Condensed Polyacenes Dans: The Journal of Physical Chemistry C, 122 (50), p. 28692-28701, 2018. Résumé | Liens | BibTeX @article{doi:10.1021/acs.jpcc.8b08945b,
title = {High-Resolution Near-Edge X-ray Absorption Fine Structure Study of Condensed Polyacenes},
author = {M L M Rocco and M Häming and C E V de Moura and M Barbatti and A B Rocha and A Schöll and E Umbach},
url = {https://doi.org/10.1021/acs.jpcc.8b08945},
doi = {10.1021/acs.jpcc.8b08945},
year = {2018},
date = {2018-01-01},
journal = {The Journal of Physical Chemistry C},
volume = {122},
number = {50},
pages = {28692-28701},
abstract = {We present a systematic study of high-resolution near-edge X-ray absorption fine structure (NEXAFS) spectra of well-ordered films of condensed benzene and polyacenes, namely naphthalene, anthracene, tetracene, and pentacene. Increased spectral complexity with increasing molecular size is observed: NEXAFS features decrease in intensity and move to lower photon energy (red shift) as the size of the aromatic system grows. Moreover, a second group of transitions arises. The dichroism in the C K-edge spectra increases with molecular size. While benzene molecules are randomly oriented, the polyacenes preferentially lie flat with increasing molecular size. Vibrational fine structures coupled to the C 1s π* transitions are apparent for all investigated molecules. The energy position of the onset of the first resonance decreases from 284.86 eV for benzene to 283.26 eV for pentacene. Calculations of absolute band envelopes with time-dependent density functional theory (TDDFT), followed by analysis of the transition densities, were performed for the whole series of molecules, revealing the nature of the spectroscopic features.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
We present a systematic study of high-resolution near-edge X-ray absorption fine structure (NEXAFS) spectra of well-ordered films of condensed benzene and polyacenes, namely naphthalene, anthracene, tetracene, and pentacene. Increased spectral complexity with increasing molecular size is observed: NEXAFS features decrease in intensity and move to lower photon energy (red shift) as the size of the aromatic system grows. Moreover, a second group of transitions arises. The dichroism in the C K-edge spectra increases with molecular size. While benzene molecules are randomly oriented, the polyacenes preferentially lie flat with increasing molecular size. Vibrational fine structures coupled to the C 1s π* transitions are apparent for all investigated molecules. The energy position of the onset of the first resonance decreases from 284.86 eV for benzene to 283.26 eV for pentacene. Calculations of absolute band envelopes with time-dependent density functional theory (TDDFT), followed by analysis of the transition densities, were performed for the whole series of molecules, revealing the nature of the spectroscopic features. |
Hans Lischka; Mario Barbatti; Farhan Siddique; Anita Das; Adelia J A Aquino The effect of hydrogen bonding on the nonadiabatic dynamics of a thymine-water cluster Dans: Chemical Physics, 515 , p. 472 - 479, 2018, ISSN: 0301-0104, (Ultrafast Photoinduced Processes in Polyatomic Molecules:Electronic Structure, Dynamics and Spectroscopy (Dedicated to Wolfgang Domcke on the occasion of his 70th birthday)). Résumé | Liens | BibTeX @article{LISCHKA2018472,
title = {The effect of hydrogen bonding on the nonadiabatic dynamics of a thymine-water cluster},
author = {Hans Lischka and Mario Barbatti and Farhan Siddique and Anita Das and Adelia J A Aquino},
url = {http://www.sciencedirect.com/science/article/pii/S0301010418305500},
doi = {https://doi.org/10.1016/j.chemphys.2018.07.050},
issn = {0301-0104},
year = {2018},
date = {2018-01-01},
journal = {Chemical Physics},
volume = {515},
pages = {472 - 479},
abstract = {Surface hopping photodynamics simulations have been performed on a cluster of thymine interacting with six water molecules (T(H2O)6). The second-order algebraic diagrammatic construction method (ADC(2)) has been used for calculating the required electronic energies and excited state gradients. Comparison with the previously performed photodynamics for the isolated thymine (Molecules 21 (2016) 1603) shows a similar global behavior and the central role of the S1(nπ∗) minimum for further long-term dynamics. The main difference comes from the destabilization of the nπ∗ state by hydrogen bonding, which leads to a significantly enhanced conversion rate from the bright S2(ππ∗) state to S1(nπ∗) for the T(H2O)6 cluster. On the other hand, the decay time to S0 and the trapping in S1 is significantly increased. Due to the localized character of the lone pair orbital involved in the nπ∗ transition at one oxygen atom, specific changes in the structure of the hydrogen bonded network are observed. Since the hydrogen bonding of the water molecules connected to that oxygen atom is specifically weakened, they show dissociations from thymine during the photodynamics, starting within 30 fs after electronic excitation of thymine.},
note = {Ultrafast Photoinduced Processes in Polyatomic Molecules:Electronic Structure, Dynamics and Spectroscopy (Dedicated to Wolfgang Domcke on the occasion of his 70th birthday)},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Surface hopping photodynamics simulations have been performed on a cluster of thymine interacting with six water molecules (T(H2O)6). The second-order algebraic diagrammatic construction method (ADC(2)) has been used for calculating the required electronic energies and excited state gradients. Comparison with the previously performed photodynamics for the isolated thymine (Molecules 21 (2016) 1603) shows a similar global behavior and the central role of the S1(nπ∗) minimum for further long-term dynamics. The main difference comes from the destabilization of the nπ∗ state by hydrogen bonding, which leads to a significantly enhanced conversion rate from the bright S2(ππ∗) state to S1(nπ∗) for the T(H2O)6 cluster. On the other hand, the decay time to S0 and the trapping in S1 is significantly increased. Due to the localized character of the lone pair orbital involved in the nπ∗ transition at one oxygen atom, specific changes in the structure of the hydrogen bonded network are observed. Since the hydrogen bonding of the water molecules connected to that oxygen atom is specifically weakened, they show dissociations from thymine during the photodynamics, starting within 30 fs after electronic excitation of thymine. |
Konstantin Falahati; Carsten Hamerla; Miquel Huix-Rotllant; Irene Burghardt Ultrafast photochemistry of free-base porphyrin: a theoretical investigation of B → Q internal conversion mediated by dark states Dans: Phys. Chem. Chem. Phys., 20 , p. 12483-12492, 2018. Résumé | Liens | BibTeX @article{C8CP00657A,
title = {Ultrafast photochemistry of free-base porphyrin: a theoretical investigation of B → Q internal conversion mediated by dark states},
author = {Konstantin Falahati and Carsten Hamerla and Miquel Huix-Rotllant and Irene Burghardt},
url = {http://dx.doi.org/10.1039/C8CP00657A},
doi = {10.1039/C8CP00657A},
year = {2018},
date = {2018-01-01},
journal = {Phys. Chem. Chem. Phys.},
volume = {20},
pages = {12483-12492},
publisher = {The Royal Society of Chemistry},
abstract = {We examine the mechanism of ultrafast internal conversion between the B band (Soret band) and the Q band in porphine (H2P), the prototypical free-base porphyrin, using electronic structure studies and on-the-fly surface-hopping nonadiabatic dynamics. Our study highlights the crucial role of dark states within the N band which are found to mediate B/Q state transfer, necessitating a treatment beyond Gouterman's classic four-orbital model. The sequential B → N → Q pathway dominates largely over the direct B → Q pathway which is found to be energetically unfavorable. Potential energy surface cuts and conical intersections between excited states are determined by TDDFT and validated by CASSCF/CASPT2 and XMCQDPT2 calculations. Both the static analysis and on-the-fly surface-hopping calculations suggest a pathway which involves minor structural deformations via in-plane vibrations. The B → N conversion is a barrierless adiabatic process occurring within ∼20 fs, while the subsequent N → Q conversion occurs via a conical intersection within ∼100 fs, in agreement with time-resolved experiments for porphine and related free base porphyrins. Furthermore, evidence for both sequential and direct transfer to the Qx and Qy states},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
We examine the mechanism of ultrafast internal conversion between the B band (Soret band) and the Q band in porphine (H2P), the prototypical free-base porphyrin, using electronic structure studies and on-the-fly surface-hopping nonadiabatic dynamics. Our study highlights the crucial role of dark states within the N band which are found to mediate B/Q state transfer, necessitating a treatment beyond Gouterman's classic four-orbital model. The sequential B → N → Q pathway dominates largely over the direct B → Q pathway which is found to be energetically unfavorable. Potential energy surface cuts and conical intersections between excited states are determined by TDDFT and validated by CASSCF/CASPT2 and XMCQDPT2 calculations. Both the static analysis and on-the-fly surface-hopping calculations suggest a pathway which involves minor structural deformations via in-plane vibrations. The B → N conversion is a barrierless adiabatic process occurring within ∼20 fs, while the subsequent N → Q conversion occurs via a conical intersection within ∼100 fs, in agreement with time-resolved experiments for porphine and related free base porphyrins. Furthermore, evidence for both sequential and direct transfer to the Qx and Qy states |
Nicolas Frangieh; Dominique Morvan; Sofiane Meradji; G ACCARY; O Bessonov Numerical simulation of grassland fires behavior using an implicit physical multiphase model Dans: Fire Safety Journal, 102 , p. 37-47, 2018. Liens | BibTeX @article{frangieh:hal-01978037,
title = {Numerical simulation of grassland fires behavior using an implicit physical multiphase model},
author = {Nicolas Frangieh and Dominique Morvan and Sofiane Meradji and G ACCARY and O Bessonov},
url = {https://hal.archives-ouvertes.fr/hal-01978037},
year = {2018},
date = {2018-01-01},
journal = {Fire Safety Journal},
volume = {102},
pages = {37-47},
publisher = {Elsevier},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
Dominique Morvan; Gilbert Accary; Sofiane Meradji; Nicolas Frangieh; Oleg BESSONOV A 3D physical model to study the behavior of vegetation fires at laboratory scale Dans: Fire Safety Journal, 101 , p. 39-52, 2018. Liens | BibTeX @article{morvan:hal-01946956,
title = {A 3D physical model to study the behavior of vegetation fires at laboratory scale},
author = {Dominique Morvan and Gilbert Accary and Sofiane Meradji and Nicolas Frangieh and Oleg BESSONOV},
url = {https://hal.archives-ouvertes.fr/hal-01946956},
year = {2018},
date = {2018-01-01},
journal = {Fire Safety Journal},
volume = {101},
pages = {39-52},
publisher = {Elsevier},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
