@article{Bonfrate2024,

title = {Analytic Gradients for the Electrostatic Embedding QM/MM Model in Periodic Boundary Conditions Using Particle-Mesh Ewald Sums and Electrostatic Potential Fitted Charge Operators},

author = {Simone Bonfrate and Nicolas Ferré and Miquel Huix-Rotllant},

doi = {10.1021/acs.jctc.4c00201},

issn = {1549-9626},

year  = {2024},

date = {2024-05-28},

journal = {J. Chem. Theory Comput.},

volume = {20},

number = {10},

pages = {4338--4349},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Diao2024,

title = {Light-Induced Reactivity Switch at O_{2}–Activating Bioinspired Copper(I) Complexes},

author = {Donglin Diao and Anna Baidiuk and Leo Chaussy and Iago De Assis Modenez and Xavi Ribas and Marius Réglier and Vlad Martin-Diaconescu and Paola Nava and A. Jalila Simaan and Alexandre Martinez and Cédric Colomban},

doi = {10.1021/jacsau.4c00184},

issn = {2691-3704},

year  = {2024},

date = {2024-05-27},

journal = {JACS Au},

volume = {4},

number = {5},

pages = {1966--1974},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Chaussy2024,

title = {Spectroscopy of End-On Copper(II) Superoxido Complexes: A Wave Function-Based Analysis},

author = {Léo Chaussy and Vijay Gopal Chilkuri and Stéphane Humbel and Paola Nava},

doi = {10.1021/acs.inorgchem.3c04401},

issn = {1520-510X},

year  = {2024},

date = {2024-05-06},

journal = {Inorg. Chem.},

volume = {63},

number = {18},

pages = {8038--8049},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Chou2024,

title = {Atropisomeric N‐Heterocyclic Carbene‐Palladium(II) Complexes: Influence of the Backbone Substitution},

author = {Yajie Chou and Mathilde Vançon and Muriel Albalat and Carla Deschodt and Paola Nava and Stéphane Humbel and Nicolas Vanthuyne and Hervé Clavier},

doi = {10.1002/ejic.202300780},

issn = {1099-0682},

year  = {2024},

date = {2024-04-22},

journal = {Eur J Inorg Chem},

volume = {27},

number = {12},

publisher = {Wiley},

abstract = {AbstractIn order to facilitate the synthesis of NHC precursors as well as to incorporate new moieties, the influence of the NHC backbone substitution was investigated within the concept of atropisomeric NHC‐metal complexes. A series of NHC precursors was prepared from new anilines and used to synthesize the corresponding Pd(allyl)Cl(NHC) complexes, most of the time as a mixture of diastereomers (meso and chiral). Chiral HPLC at preparative scale enabled to obtain enantiopure complexes in low to excellent yields. These complexes displayed good activity in the intramolecular α‐arylation of amides and, as a function of the structure of the chiral catalyst, excellent enantioselectivities were reached (up to 96 % ee).},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Mukherjee2024,

title = {Prediction Challenge: Simulating Rydberg photoexcited cyclobutanone with surface hopping dynamics based on different electronic structure methods},

author = {Saikat Mukherjee and Rafael S. Mattos and Josene M. Toldo and Hans Lischka and Mario Barbatti},

doi = {10.1063/5.0203636},

issn = {1089-7690},

year  = {2024},

date = {2024-04-21},

volume = {160},

number = {15},

publisher = {AIP Publishing},

abstract = {This research examines the nonadiabatic dynamics of cyclobutanone after excitation into the n → 3s Rydberg S2 state. It stems from our contribution to the Special Topic of the Journal of Chemical Physics to test the predictive capability of computational chemistry against unseen experimental data. Decoherence-corrected fewest-switches surface hopping was used to simulate nonadiabatic dynamics with full and approximated nonadiabatic couplings. Several simulation sets were computed with different electronic structure methods, including a multiconfigurational wavefunction [multiconfigurational self-consistent field (MCSCF)] specially built to describe dissociative channels, multireference semiempirical approach, time-dependent density functional theory, algebraic diagrammatic construction, and coupled cluster. MCSCF dynamics predicts a slow deactivation of the S2 state (10 ps), followed by an ultrafast population transfer from S1 to S0 (<100 fs). CO elimination (C3 channel) dominates over C2H4 formation (C2 channel). These findings radically differ from the other methods, which predicted S2 lifetimes 10–250 times shorter and C2 channel predominance. These results suggest that routine electronic structure methods may hold low predictive power for the outcome of nonadiabatic dynamics.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Bizet2024,

title = {Structural insights into the semiquinone form of human Cytochrome P450 reductase by DEER distance measurements between a native flavin and a spin labelled non‐canonical amino acid},

author = {Maxime Bizet and Deborah Byrne and Frédéric Biaso and Guillaume Gerbaud and Emilien Etienne and Giuseppina Briola and Bruno Guigliarelli and Philippe Urban and Pierre Dorlet and Tamas Kalai and Gilles Truan and Marlène Martinho},

doi = {10.1002/chem.202304307},

issn = {1521-3765},

year  = {2024},

date = {2024-04-02},

journal = {Chemistry A European J},

volume = {30},

number = {19},

publisher = {Wiley},

abstract = {AbstractThe flavoprotein Cytochrome P450 reductase (CPR) is the unique electron pathway from NADPH to Cytochrome P450 (CYPs). The conformational dynamics of human CPR in solution, which involves transitions from a “locked/closed” to an “unlocked/open” state, is crucial for electron transfer. To date, however, the factors guiding these changes remain unknown. By Site‐Directed Spin Labelling coupled to Electron Paramagnetic Resonance spectroscopy, we have incorporated a non‐canonical amino acid onto the flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) domains of soluble human CPR, and labelled it with a specific nitroxide spin probe. Taking advantage of the endogenous FMN cofactor, we successfully measured for the first time, the distance distribution by DEER between the semiquinone state FMNH• and the nitroxide. The DEER data revealed a salt concentration‐dependent distance distribution, evidence of an “open” CPR conformation at high salt concentrations exceeding previous reports. We also conducted molecular dynamics simulations which unveiled a diverse ensemble of conformations for the “open” semiquinone state of the CPR at high salt concentration. This study unravels the conformational landscape of the one electron reduced state of CPR, which had never been studied before.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Hodille2024,

title = {Deuterium uptake, desorption and sputtering from W(110) surface covered with oxygen},

author = {E.A. Hodille and B. Pavec and J. Denis and A. Dunand and Y. Ferro and M. Minissale and T. Angot and C. Grisolia and R. Bisson},

doi = {10.1088/1741-4326/ad2a29},

issn = {1741-4326},

year  = {2024},

date = {2024-04-01},

journal = {Nucl. Fusion},

volume = {64},

number = {4},

publisher = {IOP Publishing},

abstract = {Abstract

               Rate equation modelling is performed to simulate 

                     

                     

                        

                           

                              

                                 D

                                 2

                              

                           

                        

                     

                   and 

                     

                     

                        

                           

                              

                                 D

                                 2

                              

                           

                        

                        +

                        

                           

                              

                                 D

                              

                              2

                              +

                           

                        

                     

                   exposure of the 

                     

                     

                        

                           

                              W

                           

                           (

                           110

                           )

                        

                     

                   surface with varying coverage of oxygen atoms (O) from the clean surface up to 0.75 monolayer of O. Density Functional Theory (DFT) calculated energetics are used as inputs for the surface processes and desorption energies are optimized to best reproduce the Thermal Desorption Spectrometry (TDS) experiments obtained for 

                     

                     

                        

                           

                              

                                 D

                                 2

                              

                           

                        

                     

                   exposure. For the clean surface, the optimized desorption energies (1.10 eV–1.40 eV) are below the DFT ones (1.30 eV–1.50 eV). For the O covered surface, the main desorption peak is reproduced with desorption energies of 1.10 eV and 1.00 eV for 0.50 and 0.75 monolayer of O respectively. This is slightly higher than the DFT predicted desorption energies. In order to simulate satisfactorily the total retention obtained experimentally for 

                     

                     

                        

                           

                              

                                 D

                                 2

                              

                           

                        

                        +

                        

                           

                              

                                 D

                              

                              2

                              +

                           

                        

                     

                   exposure, a sputtering process needs to be added to the model, describing the sputtering of adsorbed species (D atoms) by the incident D ions. The impact of the sputtering process on the shape of the TDS spectra, on the total retention and on the recycling of D from the wall is discussed. In order to better characterize the sputtering process, especially its products and yields, atomistic calculations such as molecular dynamics are suggested as a next step for this study.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Lin2024,

title = {Synthesizing impurity clustering in the edge plasma of tokamaks using neural networks},

author = {Zetao Lin and Thibault Maurel-Oujia and Benjamin Kadoch and Philipp Krah and Nathaniel Saura and Sadruddin Benkadda and Kai Schneider},

doi = {10.1063/5.0178085},

issn = {1089-7674},

year  = {2024},

date = {2024-03-01},

volume = {31},

number = {3},

publisher = {AIP Publishing},

abstract = {This work investigates the behavior of impurities in edge plasma of tokamaks using high-resolution numerical simulations based on Hasegawa–Wakatani equations. Specifically, it focuses on the behavior of inertial particles, which has not been extensively studied in the field of plasma physics. Our simulations utilize one-way coupling of a large number of inertial point particles, which model plasma impurities. We observe that with Stokes number (St), which characterizes the inertia of particles being much less than one, such light impurities closely track the fluid flow without pronounced clustering. For intermediate St values, distinct clustering appears, with larger Stokes values, i.e., heavy impurities even generating more substantial clusters. When St is significantly large, very heavy impurities tend to detach from the flow and maintain their trajectory, resulting in fewer observable clusters and corresponding to random motion. A core component of this work involves machine learning techniques. Applying three different neural networks—Autoencoder, U-Net, and Generative Adversarial Network (GAN)—to synthesize preferential concentration fields of impurities, we use vorticity as input and predict impurity number density fields. GAN outperforms the two others by aligning closely with direct numerical simulation data in terms of probability density functions of the particle distribution and energy spectra. This machine learning technique holds the potential to reduce computational costs by eliminating the need to track millions of particles modeling impurities in simulations.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ma2024,

title = {An averaged mass correction scheme for the simulation of high subsonic turbulent internal flows using a lattice Boltzmann method},

author = {Jingtao Ma and Lincheng Xu and Jérôme Jacob and Eric Serre and Pierre Sagaut},

doi = {10.1063/5.0192360},

issn = {1089-7666},

year  = {2024},

date = {2024-03-01},

volume = {36},

number = {3},

publisher = {AIP Publishing},

abstract = {This paper addresses the simulation of internal high-speed turbulent compressible flows using lattice Boltzmann method (LBM) when it is coupled with the immersed boundary method for non-body-fitted meshes. The focus is made here on the mass leakage issue. The recent LBM pressure-based algorithm [Farag et al. Phys. Fluids 32, 066106 (2020)] has shown its superiority on classical density-based algorithm to simulate high-speed compressible flows. Following our previous theoretical work on incompressible flows [Xu et al. Phys. Fluids 34, 065113 (2022)], we propose an averaged mass correction technique to mitigate mass leakage when simulating high-Mach-number compressible flows. It is adapted to deal here with a density, which is decoupled from the zero-moment definition. The simulations focus on two generic but canonical configurations of more complex industrial devices, the straight channel at different angles of inclination at Mach numbers (Ma) ranging from 0.2 to 0.8, and the National Aeronautics and Space Administration Glenn S-duct at Ma = 0.6. The present results show that mass leakage can be a critical issue for the accuracy of the solution and that the proposed correction technique effectively mitigates it and leads to significant improvements in the prediction of the solution.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Lazarotto2024,

title = {Island myriads in periodic potentials},

author = {Matheus J. Lazarotto and Iberê L. Caldas and Yves Elskens},

doi = {10.1063/5.0185891},

issn = {1089-7682},

year  = {2024},

date = {2024-03-01},

volume = {34},

number = {3},

publisher = {AIP Publishing},

abstract = {A phenomenon of emergence of stability islands in phase space is reported for two periodic potentials with tiling symmetries, one square and the other hexagonal, inspired by bidimensional Hamiltonian models of optical lattices. The structures found, here termed as island myriads, resemble web-tori with notable fractality and arise at energy levels reaching that of unstable equilibria. In general, the myriad is an arrangement of concentric island chains with properties relying on the translational and rotational symmetries of the potential functions. In the square system, orbits within the myriad come in isochronous pairs and can have different periodic closure, either returning to their initial position or jumping to identical sites in neighbor cells of the lattice, therefore impacting transport properties. As seen when compared to a more generic case, i.e., the rectangular lattice, the breaking of square symmetry disrupts the myriad even for small deviations from its equilateral configuration. For the hexagonal case, the myriad was found but in attenuated form, mostly due to extra instabilities in the potential surface that prevent the stabilization of orbits forming the chains.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Dral2024,

title = {MLatom 3: A Platform for Machine Learning-Enhanced Computational Chemistry Simulations and Workflows},

author = {Pavlo O. Dral and Fuchun Ge and Yi-Fan Hou and Peikun Zheng and Yuxinxin Chen and Mario Barbatti and Olexandr Isayev and Cheng Wang and Bao-Xin Xue and Max Pinheiro Jr and Yuming Su and Yiheng Dai and Yangtao Chen and Lina Zhang and Shuang Zhang and Arif Ullah and Quanhao Zhang and Yanchi Ou},

doi = {10.1021/acs.jctc.3c01203},

issn = {1549-9626},

year  = {2024},

date = {2024-02-13},

journal = {J. Chem. Theory Comput.},

volume = {20},

number = {3},

pages = {1193--1213},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Sartoretto2024,

title = {Ecological and genomic characterization of a remarkable natural heritage: a mesophotic ‘giant’ Paramuricea clavata forest},

author = {S Sartoretto and JB Ledoux and E Gueret and D Guillemain and C Ravel and L Moirand and D Aurelle},

doi = {10.3354/meps14427},

issn = {1616-1599},

year  = {2024},

date = {2024-02-08},

journal = {Mar. Ecol. Prog. Ser.},

volume = {728},

pages = {85--101},

publisher = {Inter-Research Science Center},

abstract = {Paramuricea clavata is an ecosystem engineer, structuring hard bottom communities in the Mediterranean Sea, from 10 to 200 m depth. For more than 2 decades, shallow populations of P. clavata have been impacted by marine heatwaves, resulting in massive mortality events. Recently, a new dense population characterized by the tallest colonies ever recorded (up to 1.80 m) in the Mediterranean Sea was discovered between 50 and 60 m depth. Here, we analyzed the size and genetic structure of this ‘deep giant population’ and conducted a reciprocal transplant experiment with a shallow population inhabiting the same area to test for local adaptation. The experiment showed no significant difference in the survival rate despite the high temperatures registered in the shallow area. Nevertheless, we observed a significant differentiation by depth in this area, with low estimates of gene flow. The particular local oceanographic conditions could lead to a relative isolation of the population. In conclusion, the reduced connectivity of this newly discovered giant population with shallower ones questions its potential role as a climate refuge. Additionally, this population constitutes a unique natural heritage site that should be effectively protected from physical impacts and other direct consequences of anthropogenic activities.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Miton2023,

title = {A Cyclotriveratrylene Solvent‐Dependent Chiral Switch},

author = {Louise Miton and Élise Antonetti and Diego García‐López and Paola Nava and Vincent Robert and Muriel Albalat and Nicolas Vanthuyne and Alexandre Martinez and Yoann Cotelle},

doi = {10.1002/chem.202303294},

issn = {1521-3765},

year  = {2024},

date = {2024-02-07},

journal = {Chemistry A European J},

volume = {30},

number = {8},

publisher = {Wiley},

abstract = {AbstractChiral molecular switches are attracting attention as they could pave the way to chiral molecular machines. Herein, we report on the design and synthesis of a single molecule chiral switch based on a cyclotriveratrylene scaffold, in which the chirality inversion is controlled by the solvent. Hemicryptophanes are built around a C3 cyclotriveratrylene chiral unit, with either M or P handedness, connected to another tripod and usually displaying an “out” configuration. Here, we demonstrate that solvents are able to control the “in” and “out” configurations of the CTV unit, creating a chiral molecular switch from (M/P)”in” to (P/M)”out” handedness. The full characterization of the “in” and “out” configurations and of the chirality switch were made possible by combining NMR, HPLC, ECD, DFT and molecular dynamics. Interestingly, bulky aromatic solvents such as 2‐t‐butylphenol favor the “in” configuration while polar aprotic solvents such as acetone favor the “out” configuration. This chiral switch was found to be fully reversible allowing the system to oscillate between two different M and P configurations several times upon the action of solvents stimuli.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Toldo2024,

title = {Recommendations for Velocity Adjustment in Surface Hopping},

author = {Josene M. Toldo and Rafael S. Mattos and Max Pinheiro and Saikat Mukherjee and Mario Barbatti},

doi = {10.1021/acs.jctc.3c01159},

issn = {1549-9626},

year  = {2024},

date = {2024-01-23},

journal = {J. Chem. Theory Comput.},

volume = {20},

number = {2},

pages = {614--624},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Pieri2024,

title = {Modeling pH-Dependent Biomolecular Photochemistry},

author = {Elisa Pieri and Oliver Weingart and Miquel Huix-Rotllant and Vincent Ledentu and Marco Garavelli and Nicolas Ferré},

doi = {10.1021/acs.jctc.3c00980},

issn = {1549-9626},

year  = {2024},

date = {2024-01-23},

journal = {J. Chem. Theory Comput.},

volume = {20},

number = {2},

pages = {842--855},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Puthumana2024,

title = {Assessment of coupled bilayer–cytoskeleton modelling strategy for red blood cell dynamics in flow},

author = {V. Puthumana and P.G. Chen and M. Leonetti and R. Lasserre and M. Jaeger},

doi = {10.1017/jfm.2023.1092},

issn = {1469-7645},

year  = {2024},

date = {2024-01-22},

journal = {J. Fluid Mech.},

volume = {979},

publisher = {Cambridge University Press (CUP)},

abstract = {The red blood cell (RBC) membrane is composed of a lipid bilayer and a cytoskeleton interconnected by protein junction complexes, allowing for potential sliding between the lipid bilayer and the cytoskeleton. Despite this biological reality, it is most often modelled as a single-layer model, a hyperelastic capsule or a fluid vesicle. Another approach involves incorporating the membrane's composite structure using double layers, where one layer represents the lipid bilayer and the other represents the cytoskeleton. In this paper, we computationally assess the various modelling strategies by analysing RBC behaviour in extensional flow and four distinct regimes that simulate RBC dynamics in shear flow. The proposed double-layer strategies, such as the vesicle–capsule and capsule–capsule models, account for the fluidity and surface incompressibility of the lipid bilayer in different ways. Our findings demonstrate that introducing sliding between the layers offers the cytoskeleton a considerable degree of freedom to alleviate its elastic stresses, resulting in a significant increase in RBC elongation. Surprisingly, our study reveals that the membrane modelling strategy for RBCs holds greater importance than the choice of the cytoskeleton's reference shape. These results highlight the inadequacy of considering mechanical properties alone and emphasise the need for careful integration of these properties. Furthermore, our findings fortuitously uncover a novel indicator for determining the appropriate stress-free shape of the cytoskeleton.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}