@article{Alías-Rodríguez2023,

title = {Solvent Effects and pH Dependence of the X-ray Absorption Spectra of Proline from Electrostatic Embedding Quantum Mechanics/Molecular Mechanics and Mixed-Reference Spin-Flip Time-dependent Density-Functional Theory},

author = {Marc Alías-Rodríguez and Simone Bonfrate and Woojin Park and Nicolas Ferré and Cheol Ho Choi and Miquel Huix-Rotllant},

doi = {10.1021/acs.jpca.3c05070},

issn = {1520-5215},

year  = {2023},

date = {2023-12-14},

journal = {J. Phys. Chem. A},

volume = {127},

number = {49},

pages = {10382--10392},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Cárdenas2023,

title = {Automatic Rhodopsin Modeling with Multiple Protonation Microstates},

author = {Gustavo Cárdenas and Vincent Ledentu and Miquel Huix-Rotllant and Massimo Olivucci and Nicolas Ferré},

doi = {10.1021/acs.jpca.3c05413},

issn = {1520-5215},

year  = {2023},

date = {2023-11-09},

journal = {J. Phys. Chem. A},

volume = {127},

number = {44},

pages = {9365--9380},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Kriaa2023,

title = {Two-way coupling Eulerian numerical simulations of particle clouds settling in a quiescent fluid},

author = {Quentin Kriaa and Benjamin Favier and Michael Le Bars},

doi = {10.1103/physrevfluids.8.074302},

issn = {2469-990X},

year  = {2023},

date = {2023-10-25},

journal = {Phys. Rev. Fluids},

volume = {8},

number = {7},

publisher = {American Physical Society (APS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{LiManni2023,

title = {The OpenMolcas \textit{Web}: A Community-Driven Approach to Advancing Computational Chemistry},

author = {Giovanni Li Manni and Ignacio Fdez. Galván and Ali Alavi and Flavia Aleotti and Francesco Aquilante and Jochen Autschbach and Davide Avagliano and Alberto Baiardi and Jie J. Bao and Stefano Battaglia and Letitia Birnoschi and Alejandro Blanco-González and Sergey I. Bokarev and Ria Broer and Roberto Cacciari and Paul B. Calio and Rebecca K. Carlson and Rafael Carvalho Couto and Luis Cerdán and Liviu F. Chibotaru and Nicholas F. Chilton and Jonathan Richard Church and Irene Conti and Sonia Coriani and Juliana Cuéllar-Zuquin and Razan E. Daoud and Nike Dattani and Piero Decleva and Coen de Graaf and Mickaël G. Delcey and Luca De Vico and Werner Dobrautz and Sijia S. Dong and Rulin Feng and Nicolas Ferré and Michael Filatov(Gulak) and Laura Gagliardi and Marco Garavelli and Leticia González and Yafu Guan and Meiyuan Guo and Matthew R. Hennefarth and Matthew R. Hermes and Chad E. Hoyer and Miquel Huix-Rotllant and Vishal Kumar Jaiswal and Andy Kaiser and Danil S. Kaliakin and Marjan Khamesian and Daniel S. King and Vladislav Kochetov and Marek Krośnicki and Arpit Arun Kumaar and Ernst D. Larsson and Susi Lehtola and Marie-Bernadette Lepetit and Hans Lischka and Pablo López Ríos and Marcus Lundberg and Dongxia Ma and Sebastian Mai and Philipp Marquetand and Isabella C. D. Merritt and Francesco Montorsi and Maximilian Mörchen and Artur Nenov and Vu Ha Anh Nguyen and Yoshio Nishimoto and Meagan S. Oakley and Massimo Olivucci and Markus Oppel and Daniele Padula and Riddhish Pandharkar and Quan Manh Phung and Felix Plasser and Gerardo Raggi and Elisa Rebolini and Markus Reiher and Ivan Rivalta and Daniel Roca-Sanjuán and Thies Romig and Arta Anushirwan Safari and Aitor Sánchez-Mansilla and Andrew M. Sand and Igor Schapiro and Thais R. Scott and Javier Segarra-Martí and Francesco Segatta and Dumitru-Claudiu Sergentu and Prachi Sharma and Ron Shepard and Yinan Shu and Jakob K. Staab and Tjerk P. Straatsma and Lasse Kragh Sørensen and Bruno Nunes Cabral Tenorio and Donald G. Truhlar and Liviu Ungur and Morgane Vacher and Valera Veryazov and Torben Arne Voß and Oskar Weser and Dihua Wu and Xuchun Yang and David Yarkony and Chen Zhou and J. Patrick Zobel and Roland Lindh},

doi = {10.1021/acs.jctc.3c00182},

issn = {1549-9626},

year  = {2023},

date = {2023-10-24},

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

volume = {19},

number = {20},

pages = {6933--6991},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{He2023,

title = {Internal shear layers in librating spherical shells: the case of attractors},

author = {Jiyang He and Benjamin Favier and Michel Rieutord and Stéphane Le Dizès},

doi = {10.1017/jfm.2023.761},

issn = {1469-7645},

year  = {2023},

date = {2023-10-23},

journal = {J. Fluid Mech.},

volume = {974},

publisher = {Cambridge University Press (CUP)},

abstract = {Following our previous work on periodic ray paths (He et al., J. Fluid Mech., vol. 939, 2022, A3), we study asymptotically and numerically the structure of internal shear layers for very small Ekman numbers in a three-dimensional spherical shell and in a two-dimensional cylindrical annulus when the rays converge towards an attractor. We first show that the asymptotic solution obtained by propagating the self-similar solution generated at the critical latitude on the librating inner core describes the main features of the numerical solution. The internal shear layer structure and the scaling for its width and velocity amplitude in 

	      

		

		$E^{1/3}$

	      

	     and 

	      

		

		$E^{1/12}$

	      

	    , respectively, are recovered. The amplitude of the asymptotic solution is shown to decrease to 

	      

		

		$E^{1/6}$

	      

	     when it reaches the attractor, as is also observed numerically. However, some discrepancies are observed close to the particular attractors along which the phase of the wave beam remains constant. Another asymptotic solution close to those attractors is then constructed using the model of Ogilvie (J. Fluid Mech., vol. 543, 2005, pp. 19–44). The solution obtained for the velocity has an 

	      

		

		$O(E^{1/6})$

	      

	     amplitude, but a self-similar structure different from the critical-latitude solution. It also depends on the Ekman pumping at the contact points of the attractor with the boundaries. We demonstrate that it reproduces correctly the numerical solution. Surprisingly, the numerical solution close to an attractor with phase shift (that is, an attractor touching the axis in three or two dimensions with a symmetric forcing) is also found to be 

	      

		

		$O(E^{1/6})$

	      

	    , but its amplitude is much weaker. However, its asymptotic structure remains a mystery.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Mansour2023,

title = {Temperature effects on the internal conversion of excited adenine and adenosine},

author = {Ritam Mansour and Josene M. Toldo and Saikat Mukherjee and Max Pinheiro and Mario Barbatti},

doi = {10.1039/d3cp03234e},

issn = {1463-9084},

year  = {2023},

date = {2023-10-18},

journal = {Phys. Chem. Chem. Phys.},

volume = {25},

number = {40},

pages = {27083--27093},

publisher = {Royal Society of Chemistry (RSC)},

abstract = {Temperature has a strikingly different impact on adenine and adenosine photodynamics. Surface hopping reveals the reason underlying it.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Sun2023,

title = {Asymmetric Allenylation of Alkynes mediated by Chiral Organoselenated Reagents under Oxidative Conditions},

author = {Rongyu Sun and Emilie Viaud and Rajesh Nomula and Jean‐Valère Naubron and Nicolas Daugey and Thierry Buffeteau and Frédéric Castet and Patrick Y. Toullec and Stéphane Quideau and Philippe A. Peixoto},

doi = {10.1002/anie.202310436},

issn = {1521-3773},

year  = {2023},

date = {2023-10-16},

journal = {Angew Chem Int Ed},

volume = {62},

number = {42},

publisher = {Wiley},

abstract = {AbstractThe reactivity of novel chiral lactamide‐substituted diselenide‐based reagents under oxidative conditions was exploited to develop a metal‐free method for the preparation of enantioenriched allenylamides from simple alkynes in good yields, and with enantiomeric excesses up to 99 %. The key of the success in this method is attributed to the hydrogen‐bonded lactamide appendages that ensure configurational stability of chiral vinyl selenoxide intermediates for an optimal enantiotopic β‐syn‐elimination step.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Dalton2023,

title = {Understanding the Impact of Symmetrical Substitution on the Photodynamics of Sinapate Esters Using Gas-Phase Ultrafast Spectroscopy},

author = {Jack Dalton and Josene M. Toldo and Florent Allais and Mario Barbatti and Vasilios G. Stavros},

doi = {10.1021/acs.jpclett.3c02134},

issn = {1948-7185},

year  = {2023},

date = {2023-10-05},

journal = {J. Phys. Chem. Lett.},

volume = {14},

number = {39},

pages = {8771--8779},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Alías-Rodríguez2023b,

title = {Ultrafast Spin Crossover Photochemical Mechanism in [Fe^{II}(2,2′-bipyridine)_{3}]^{2+}] Revealed by Quantum Dynamics},

author = {Marc Alías-Rodríguez and Swarnendu Bhattacharyya and Miquel Huix-Rotllant},

doi = {10.1021/acs.jpclett.3c02201},

issn = {1948-7185},

year  = {2023},

date = {2023-09-28},

journal = {J. Phys. Chem. Lett.},

volume = {14},

number = {38},

pages = {8571--8576},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{doCasal2023,

title = {Classification of doubly excited molecular electronic states},

author = {Mariana T. do Casal and Josene M. Toldo and Mario Barbatti and Felix Plasser},

doi = {10.1039/d2sc06990c},

issn = {2041-6539},

year  = {2023},

date = {2023-04-12},

journal = {Chem. Sci.},

volume = {14},

number = {15},

pages = {4012--4026},

publisher = {Royal Society of Chemistry (RSC)},

abstract = {A rigorous classification scheme for doubly excited states is proposed and the different possible types are exemplified in various molecules.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{PinheiroJr2023,

title = {WS22 database, Wigner Sampling and geometry interpolation for configurationally diverse molecular datasets},

author = {Max Pinheiro Jr and Shuang Zhang and Pavlo O. Dral and Mario Barbatti},

doi = {10.1038/s41597-023-01998-3},

issn = {2052-4463},

year  = {2023},

date = {2023-02-15},

journal = {Sci Data},

volume = {10},

number = {1},

publisher = {Springer Science and Business Media LLC},

abstract = {<jats:title>Abstract</jats:title><jats:p>Multidimensional surfaces of quantum chemical properties, such as potential energies and dipole moments, are common targets for machine learning, requiring the development of robust and diverse databases extensively exploring molecular configurational spaces. Here we composed the WS22 database covering several quantum mechanical (QM) properties (including potential energies, forces, dipole moments, polarizabilities, HOMO, and LUMO energies) for ten flexible organic molecules of increasing complexity and with up to 22 atoms. This database consists of 1.18 million equilibrium and non-equilibrium geometries carefully sampled from Wigner distributions centered at different equilibrium conformations (either at the ground or excited electronic states) and further augmented with interpolated structures. The diversity of our datasets is demonstrated by visualizing the geometries distribution with dimensionality reduction as well as via comparison of statistical features of the QM properties with those available in existing datasets. Our sampling targets broader quantum mechanical distribution of the configurational space than provided by commonly used sampling through classical molecular dynamics, upping the challenge for machine learning models.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Lemasquerier2023,

title = {Zonal jets experiments in the gas giants’ zonostrophic regime},

author = {D. Lemasquerier and B. Favier and M. Le Bars},

doi = {10.1016/j.icarus.2022.115292},

issn = {0019-1035},

year  = {2023},

date = {2023-02-15},

journal = {Icarus},

volume = {390},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Bonfrate2023,

title = {An efficient electrostatic embedding QM/MM method using periodic boundary conditions based on particle-mesh Ewald sums and electrostatic potential fitted charge operators},

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

doi = {10.1063/5.0133646},

issn = {1089-7690},

year  = {2023},

date = {2023-01-14},

volume = {158},

number = {2},

publisher = {AIP Publishing},

abstract = {Hybrid quantum mechanics/molecular mechanics (QM/MM) models are successful at describing the properties and reactivity of biological macromolecules. Combining ab initio QM/MM methods and periodic boundary conditions (PBC) is currently the optimal approach for modeling chemical processes in an infinite environment, but frequently, these models are too time-consuming for general applicability to biological systems in a solution. Here, we define a simple and efficient electrostatic embedding QM/MM model in PBC, combining the benefits of electrostatic potential fitted atomic charges and particle-mesh Ewald sums, which can efficiently treat systems of an arbitrary size at a reasonable computational cost. To illustrate this, we apply our scheme to extract the lowest singlet excitation energies from a model for Arabidopsis thaliana cryptochrome 1 containing circa 93 000 atoms, accurately reproducing the experimental absorption maximum.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{David2022,

title = {Consistent Evaluation of Magnetic Exchange Couplings in Multicenter Compounds in KS-DFT: The Recomposition Method},

author = {Grégoire David and Nicolas Ferré and Boris Le Guennic},

doi = {10.1021/acs.jctc.2c01022},

issn = {1549-9626},

year  = {2023},

date = {2023-01-10},

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

volume = {19},

number = {1},

pages = {157--173},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Huix-Rotllant2022,

title = {Photochemistry of Thymine in Solution and DNA Revealed by an Electrostatic Embedding QM/MM Combined with Mixed-Reference Spin-Flip TDDFT},

author = {Miquel Huix-Rotllant and Karno Schwinn and Vladimir Pomogaev and Maryam Farmani and Nicolas Ferré and Seunghoon Lee and Cheol Ho Choi},

doi = {10.1021/acs.jctc.2c01010},

issn = {1549-9626},

year  = {2023},

date = {2023-01-10},

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

volume = {19},

number = {1},

pages = {147--156},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}