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International audience; We illustrate the domain decomposition Conductor-like Screening Model (ddCOSMO) implementation and how to couple it with an existing classical or quantum mechanical (QM) code. We review in detail what input needs to be provided to ddCOSMO and how to assemble it, describe how the ddCOSMO equations are solved and how to process the results in order to assemble the required quantities, such as Fock matrix contributions for the QM case, or forces for the classical one. Throughout the paper, we will make explicit references to the ddCOSMO module, which is an open source, Fortran 90 implementation of ddCOSMO that can be downloaded and distributed under the LGPL license.

International audience; The Trotterized Unitary Coupled Cluster Single and Double (UCCSD) ansatz has recently attracted interest due to its use in Variation Quantum Eigensolver (VQE) molecular simulations on quantum computers. However, when the size of molecules increases, UCCSD becomes less interesting as it cannot achieve sufficient accuracy. Including higher-order excitations is therefore mandatory to recover the UCC's missing correlation effects. In this Letter, we extend the Trotterized UCC approach via the addition of (true) Triple T excitations introducing UCCSDT. We also include both spin and orbital symmetries. Indeed, in practice, these later help to reduce unnecessarily circuit excitations and thus accelerate the optimization process enabling to tackle larger molecules. Our initial numerical tests (12-14 qubits) show that UCCSDT improves the overall accuracy by at least two-orders of magnitudes with respect to standard UCCSD. Overall, the UCCSDT ansatz is shown to reach chemical accuracy and to be competitive with the CCSD(T) gold-standard classical method of quantum chemistry.

International audience; The Human Immunodeficiency Virus-1 integrase is responsible for the covalent insertion of a newly synthesized double-stranded viral DNA into the host cells, and is an emerging target for antivirus drug design. Raltegravir (RAL) and elvitegravir (EVG) are the first two integrase strand transfer inhibitors used in therapy. However, treated patients eventually develop detrimental resistance mutations. By contrast, a recently approved drug, dolutegravir (DTG), presents a high barrier to resistance. This study aims to understand the increased efficiency of DTG upon focusing on its interaction properties with viral DNA. The results showed DTG to be involved in more extended interactions with viral DNA than EVG. Such interactions involve the halobenzene and scaffold of DTG and EVG and bases 5′G-43′, 3′A35'and 3′C45’.

International audience; In the present work, we investigate different possibilities for the nonempirical localization of nonatomic centers within the context of the design of new generation polarizable force fields. To do so, the positions of electron localization function (ELF) and electron pair localization function (EPLF) attractors and of Boys orbital centroids are determined for a set of thirteen saturated and conjugated biologically relevant molecules. We consider the similarities and differences in the representations of localized lone pairs and π delocalized systems by these approaches, as well as the effects of the basis sets and of the level of quantum chemistry (QC). All three methods give consistent results upon dealing with the localized lone pairs. Concerning aromatic systems, whereas ELF and EPLF methods give mutually consistent results, the Boys scheme breaks the symmetry by alternating the electron distributions along the C-C bonds providing a different distribution of off-centered points. We then investigate the influence of lone pair localization in the water model of the Gaussian electrostatic model/sum of interactions between fragments ab initio computed (GEM/SIBFA) polarizable force field, which embodies an explicit representation of the lone pairs. This is done, in a series of mono- and poly-hydrated Zn(II) complexes, by comparing the overlap-dependent repulsion (Erep) and charge-transfer (Ect) contributions to their QC counterparts. We resort to either the current GEM/SIBFA water lone pair internal coordinates or to the ones derived from the previously mentioned localization procedures. The latter enables closer reproductions by Erep and Ect (GEM/SIBFA) of their exchange repulsion (Eexch) and Ect QC counterparts. The present preliminary results show that QC localization procedures can be used to derive accurate, nonempirical positions for off-centered points intervening in the formulation of the overlap-dependent contributions of next-generation polarizable force fields.; Dans la présente étude, nous examinons les différentes localisations non empiriques possibles des centres non atomiques dans le contexte de la conception de champs de forces polarisables de nouvelle génération. À cette fin, nous déterminons les positions des attracteurs ELF (Electron Localization Function, ou fonction de localisation électronique) et des attracteurs EPLF (Electron Pair Localization Function, ou fonction de localisation de paire d'électrons), ainsi que des centroïdes des orbitales de Boys pour un jeu de treize molécules saturées et conjuguées ayant une importance biologique. Nous considérons les similarités et les différences entre les représentations des paires libres et des systèmes délocalisés obtenues par ces approches, ainsi que les effets des bases et du niveau de chimie quantique (QC). Les trois méthodes donnent des résultats cohérents lorsque l'on s'intéresse aux paires libres localisées. En ce qui concerne les systèmes aromatiques, alors que les méthodes ELF et EPLF donnent des résultats mutuellement cohérents, la méthode de Boys rompt la symétrie en alternant la répartition des électrons le long des liaisons CC , ce qui donne une distribution différente des points excentrés. Nous étudions ensuite l'influence de la localisation des paires libres dans le modèle de l'eau dans le champ de forces polarisable GEM/SIBFA, qui figure une représentation explicite des paires libres. Sur une série de complexes de Zn(II) mono et polyhydratés, nous comparons les contributions des énergies de répulsion (E rép) et de transfert de charge (E tc) dépendantes de la superposition à leurs équiva-lents dans les calculs de chimie quantique (QC). Nous utilisons les coordonnées internes des paires libres de l'eau de la méthode GEM/SIBFA courante ou celles dérivées des procédures de localisation susmentionnées. Les secondes permettent que E rép and E tc (GEM/SIBFA) donnent des reproductions plus proches de leurs équivalents QC E éch et E tc. Les résultats préliminaires présentés ici montrent que des procédures de localisation basées sur la chimie quantique peuvent être utilisées pour calculer les positions exactes, non empiriques, pour les points excentrés intervenant dans la formulation des contributions dépendantes du recou-vrement des champs de forces polarisables de nouvelle génération. [Traduit par la Rédaction]

A consensus has progressively developed that the path towards complex organic molecules could be favoured by the icy mantles of interstellar dust particles. However, the question of whether activation energy is required to promote those reactions is open. This work deals with the simplest process thought to increase complexity i.e. successive additions of a single atom (H). Two situations can be considered, the direct additions of H in the gas phase and the atomic hydrogenation processes on water ice surfaces available in the interstellar medium (ISM). The synthesis of methanol, largely discussed in the literature is revisited as a case study. Computational investigations of the reactions leading from CO to CH3OH show that, with [H...(H2O)n] complexes as hydrogenation vectors, all steps of the process are barrier-less, contrary to the gas phase process and this, whatever the level of theory considered. The key parameter is the position of the CO + [H...(H2O)n] initial system on the global energy scale. At the present level of theory, when H is pre-adsorbed on the ice, the system happens to be high enough above the reaction path, namely, above any intermediates and possible transition states. This is true whatever the dimension of the ice support, even for the simplest model of one H2O molecule. Application of such a simplified synthetic approach, here validated for the synthesis of methanol, could be generalized, providing a simple way to get a fair insight into the important class of atomic hydrogenations on ices in the ISM.

We introduce an efficient and robust method to compute alchemical free energy differences, resulting from the application of multiple walker Adaptive Biasing Force (ABF) in conjunction with strongly damped Langevin $\lambda$-dynamics. Unbiased alchemical free energy surfaces are naturally recovered by Thermodynamic Integration (TI). No manual optimization of the $\lambda$ schedule is required as the sampling of the $\lambda$ variable is continuous and converges towards a uniform distribution. Free diffusion of $\lambda$ improves orthogonal relaxation compared to fixed $\lambda$ methods such as standard TI or Free Energy Perturbation (FEP). Furthermore, the multiple walker strategy provides coverage of orthogonal space in a generic way with minimal user input and negligible computational overhead. Of practical importance, no adiabatic decoupling between the alchemical and Cartesian degrees of freedom is assumed, ensuring unbiased estimates for a wide envelope of numerical parameters. We present two high-performance implementations of the method in production molecular dynamics engines, namely NAMD and Tinker-HP, through coupling with the Colvars open source library. These interfaces enable the combination of the rich feature sets of those packages. We demonstrate the correctness and efficiency of the approach on several real-world cases: from solvation free energies up to ligand-receptor binding (using a recently proposed binding restraint scheme) with both fixed-charge and polarizable models. We find that, for a chosen accuracy, the computational cost is strongly reduced compared to state-of-the-art fixed-lambda methods and that results within 1~kcal/mol of experimental value are recovered for the most complex system. The implementation is publicly available and readily usable by practitioners of current alchemical methods.

We derive and implement an alternative formulation of the Stochastic Lanczos algorithm to be employed in connection with the Many-Body Dispersion model (MBD). Indeed, this formulation, which is only possible due to the Stochastic Lanczos' reliance on matrix-vector products, introduces generalized dipoles and fields. These key quantities allow for a state-of-the-art treatment of periodic boundary conditions via the O(Nlog(N)) Smooth Particle Mesh Ewald (SPME) approach which uses efficient fast Fourier transforms. This SPME-Lanczos algorithm drastically outperforms the standard replica method which is affected by a slow and conditionally convergence rate that limits an efficient and reliable inclusion of long-range periodic boundary conditions interactions in many-body dispersion modelling. The proposed algorithm inherits the embarrassingly parallelism of the original Stochastic Lanczos scheme, thus opening up for a fully converged and efficient periodic boundary condition treatment of MBD approaches.

International audience; The basis-set correction method based on density-functional theory consists in correcting the energy calculated by a wave-function method with a given basis set by a density functional. This basis-set correction density functional incorporates the short-range electron correlation effects missing in the basis set. This results in accelerated basis convergences of ground-state energies to the complete-basis-set limit. In this work, we extend the basis-set correction method to a linear-response formalism for calculating excited-state energies. We give the general linear-response equations, as well as the more specific equations for configuration-interaction wave functions. As a proof of concept, we apply this approach to the calculations of excited-state energies in a one-dimensional two-electron model system with harmonic potential and a Dirac-delta electron-electron interaction. The results obtained with full-configuration-interaction wave functions expanded in a basis of Hermite functions and a local-density-approximation basis-set correction functional show that the present approach does not help in accelerating the basis convergence of excitation energies. However, we show that it significantly accelerates basis convergences of excited-state total energies.

International audience; The mechanisms of H 2 dissociation on three stoichiometric anatase TiO 2 terminations, (001), (100) and (101), have been studied by means of density functional theory (PBE+U) calculations. A two-step process was considered: first, H 2 dissociation into H + and H − pair, and second the H − species migrates to a neighboring O site, transferring the electrons to the substrate. On (001), it shows the lowest activation barriers for hydrogen dissociation, 0.37 eV, whereas the highest value was found on (101), 0.98 eV. For hydrogen transfer from Ti to near O, the activation barriers are higher (from 1.10 to 2.37 eV), which indicates the dissociation step is kinetically more favorable than the H transfer process, although the latter is thermodynamically more favorable. Electronic structure, vibrational frequency analysis as well as temperature effects are studied to characterize the reactivity. The relationship between electronic structure, geometry and reactivity is analyzed by means of reactivity descriptors, and the results are compared with ceria and rutile TiO 2 facets.

International audience; Deep-HP is a scalable extension of the Tinker-HP multi-GPUs molecular dynamics (MD) package enabling the use of Pytorch/TensorFlow Deep Neural Networks (DNNs) models. Deep-HP increases DNNs MD capabilities by orders of magnitude offering access to ns simulations for 100k-atom biosystems while offering the possibility of coupling DNNs to any classical (FFs) and many-body polarizable (PFFs) force fields. It allows therefore to introduce the ANI-2X/AMOEBA hybrid polarizable potential designed for ligand binding studies where solvent-solvent and solvent-solute interactions are computed with the AMOEBA PFF while solute-solute ones are computed by the ANI-2x DNN. ANI-2X/AMOEBA explicitly includes AMOEBA's physical long-range interactions via an efficient Particle Mesh Ewald implementation while preserving ANI-2X's solute short-range quantum mechanical accuracy. The DNNs/PFFs partition can be user-defined allowing for hybrid simulations to include biosimulation key ingredients such as polarizable solvents, polarizable counter ions, etc... ANI-2X/AMOEBA is accelerated using a multiple-timestep strategy focusing on the models contributions to low-frequency modes of nuclear forces. It primarily evaluates AMOEBA forces while including ANI-2x ones only via correction-steps resulting in an order of magnitude acceleration over standard Velocity Verlet integration. Simulating more than 10 μs, we compute charged/uncharged ligands solvation free energies in 4 solvents, and absolute binding free energies of host-guest complexes from SAMPL challenges. ANI-2X/AMOEBA average errors are within chemical accuracy opening the path towards large-scale hybrid DNNs simulations, at force-field cost, in biophysics and drug discovery.

We introduce a novel three-body correlation factor that is designed to vanish in the core region around each nucleus and approach a universal two-body correlation factor for valence electrons. The Transcorrelated Hamiltonian is used to optimize the orbitals of a single Slater determinant within a biorthonormal framework. The Slater-Jastrow wave function is optimized on a set of atomic and molecular systems containing both second-row elements and $3d$ transition metal elements. The optimization of the correlation factor and the orbitals, along with increasing the basis set, results in a systematic lowering of the Variational Monte Carlo energy for all systems tested. Importantly, the optimal parameters of the correlation factor obtained for atomic systems are transferable to molecules. Additionally, the present correlation factor is computationally efficient, using a mixed analytical-numerical integration scheme that reduces the costly numerical integration from $\mathbb{R}^6$ to $\mathbb{R}^3$., Comment: 18 pages, 7 figures

International audience; The existence of a network of structured waters in the vicinity of the bimetallic site of Cu/Zn-superoxide dismutase (SOD) has been inferred from high-resolution X-ray crystallography. Long-duration molecular dynamics (MD) simulations could enable to quantify the lifetimes and possible interchanges of these waters between themselves as well as with a ligand diffusing toward the bimetallic site. The presence of several charged or polar ligands makes it necessary to resort to second-generation polarizable potentials. As a first step toward such simulations, we benchmark in this article the accuracy of one such potential, sum of interactions between fragments Ab initio computed (SIBFA), by comparisons with quantum mechanics (QM) computations. We first consider the bimetallic binding site of a Cu/Zn-SOD, in which three histidines and a water molecule are bound to Cu(I) and three histidines and one aspartate are bound to Zn(II). The comparisons are made for different His6 complexes with either one or both cations, and either with or without Asp and water. The total net charges vary from zero to three. We subsequently perform preliminary short-duration MD simulations of 296 waters solvating Cu/Zn-SOD. Six representative geometries are selected and energy-minimized. Single-point SIBFA and QM computations are then performed in parallel on model binding sites extracted from these six structures, each of which totals 301 atoms including the closest 28 waters from the Cu metal site. The ranking of their relative stabilities as given by SIBFA is identical to the QM one, and the relative energy differences by both approaches are fully consistent. In addition, the lowest-energy structure, from SIBFA and QM, has a close overlap with the crystallographic one. The SIBFA calculations enable to quantify the impact of polarization and charge transfer in the ranking of the six structures. Five structural waters, which connect Arg141 and Glu131, are endowed with very high dipole moments (2.7-3.0 Debye), equal and larger than the one computed by SIBFA in ice-like arrangements (2.7 D).

International audience; The reaction of ketene (H2CCO) with hydrogen atoms has been studied under interstellar conditions through two different experimental methods, occurring on the surface and in the bulk of H2CCO ice. We show that ketene interaction with H-atoms at 10 K leads mainly to four reaction products, carbon monoxide (CO), methane (CH4), formaldehyde (H2CO) and acetaldehyde (CH3CHO). A part of these results shows a chemical link between a simple organic molecule such as H2CCO and a complex one such as CH3CHO, through H-addition reactions taking place in dense molecular clouds. The H-addition processes are very often proposed by astrophysical models as mechanisms for the formation of complex organic molecules based on the abundance of species already detected in the interstellar medium. However, the present study shows that the hydrogenation of ketene under non-energetic conditions may also lead efficiently to fragmentation processes and the formation of small species such as CO, CH4 and H2CO, without supplying external energy such as UV photons or high energy particles. Such fragmentation pathways should be included in the astrophysical modeling of H2CCO + H in the molecular clouds of the interstellar medium. To support these results, theoretical calculations have explicitly showed that, under our experimental conditions, H-atom interactions with the C=C bond of ketene lead mainly to CH3CHO, CH4 and CO. By investigating the formation and reactivity of the reaction intermediate H3C-C=O radical, our calculations demonstrate that the H3C-C=O + H reaction evolves through two barrierless pathways to form either CH3CHO or CH4 and CO fragments.

ADAPT-VQE is a robust algorithm for hybrid quantum-classical simulations of quantum chemical systems on near-term quantum computers. While its iterative process systematically reaches the ground state energy, ADAPT-VQE is sensitive to local energy minima, leading to over-parameterized ans\"atze. We introduce the Overlap-ADAPT-VQE to grow wave-functions by maximizing their overlap with any intermediate target wave-function that already captures some electronic correlation. By avoiding building the ansatz in the energy landscape strewn with local minima, the Overlap-ADAPT-VQE produces ultra-compact ans\"atze suitable for high-accuracy initializations of a new ADAPT procedure. Spectacular advantages over ADAPT-VQE are observed for strongly correlated systems including massive savings in circuit depth. Since this compression strategy can also be initialized with accurate Selected-Configuration Interaction (SCI) classical target wave-functions, it paves the way for chemically accurate simulations of larger systems, and strengthens the promise of decisively surpassing classical quantum chemistry through the power of quantum computing.

Hybrid quantum-classical algorithms hold the potential to outperform classical computing methods for simulating quantum many-body systems. Adaptive Variational Quantum Eigensolvers (VQE) in particular have demonstrated an ability to generate highly accurate ansatz wave-functions using compact quantum circuits. However, the practical implementation of these methods on current quantum processing units (QPUs) faces a significant challenge: the need to measure a polynomially scaling number of observables during the operator selection step so as to optimise a high-dimensional, noisy cost function. In this study, we introduce new techniques to overcome these difficulties and execute hybrid adaptive algorithms on a 25-qubit error-mitigated quantum hardware coupled to a high performance GPU-accelerated quantum simulator. As a physics application, we compute the ground state of a 25-body Ising model using a greedy gradient-free adaptive VQE that requires only five circuit measurements for each iteration, regardless of the number of qubits and the size of the operator pool. As a chemistry application, we combine this greedy, gradient-free approach with the Overlap-ADAPT-VQE algorithm to approximate the ground state of a molecular system. The successful implementation of these hybrid QPU/simulator computations enhances the applicability of adaptive VQEs on QPUs and instills further optimism regarding the near-term advantages of quantum computing.

We introduce FENNIX (Force-Field-Enhanced Neural Network InteraXions), a hybrid approach between machine-learning and force-fields. We leverage state-of-the-art equivariant neural networks to predict local energy contributions and multiple atom-in-molecule properties that are then used as geometry-dependent parameters for physically-motivated energy terms which account for long-range electrostatics and dispersion. Using high-accuracy ab initio data (small organic molecules/dimers), we trained a first version of the model. Exhibiting accurate gas-phase energy predictions, FENNIX is transferable to the condensed phase. It is able to produce stable Molecular Dynamics simulations, including nuclear quantum effects, for water predicting accurate liquid properties. The extrapolating power of the hybrid physically-driven machine learning FENNIX approach is exemplified by computing: i) the solvated alanine dipeptide free energy landscape; ii) the reactive dissociation of small molecules.

International audience; In the present letter, we investigate the double proton transfer (DPT) tautomerization process in guanine−cytosine (GC) DNA base pairs. In particular, we study the influence of the biological environment on the mechanism, the kinetics and thermodynamics of such DPT. To this end, we present a molecular dynamics (MD) study in the tight-binding density functional theory framework, and compare the reactivity of the isolated GC dimer with that of the same dimer embedded in a small DNA structure. The impact of nuclear quantum effects (NQEs) is also evaluated using Path Integral based MD. Results show that in the isolated dimer, the DPT occurs via a concerted mechanism, while in the model biological environment, it turns into a stepwise process going through an intermediate structure. One of the water molecules in the vicinity of the proton transfer sites plays an important role as it changes H-bond pattern during the DPT reaction. The inclusion of NQEs has the effect of speeding up the tautomeric-to-canonical reaction, reflecting the destabilization of both the tautomeric and intermediate forms.

The sampling of the configuration space in diffusion Monte Carlo (DMC) is done using walkers moving randomly. In a previous work on the Hubbard model [\href{https://doi.org/10.1103/PhysRevB.60.2299}{Assaraf et al.~Phys.~Rev.~B \textbf{60}, 2299 (1999)}], it was shown that the probability for a walker to stay a certain amount of time in the same state obeys a Poisson law and that the on-state dynamics can be integrated out exactly, leading to an effective dynamics connecting only different states. Here, we extend this idea to the general case of a walker trapped within domains of arbitrary shape and size. The equations of the resulting effective stochastic dynamics are derived. The larger the average (trapping) time spent by the walker within the domains, the greater the reduction in statistical fluctuations. A numerical application to the Hubbard model is presented. Although this work presents the method for finite linear spaces, it can be generalized without fundamental difficulties to continuous configuration spaces., 14 pages, 4 figures

In this work, we develop a mathematical framework for a Selected Configuration Interaction (SCI) algorithm within a bi-orthogonal basis for transcorrelated (TC) calculations. The bi-orthogonal basis used here serves as the equivalent of the standard Hartree Fock (HF) orbitals. However, within the context of TC, it leads to distinct orbitals for the left and right vectors. Our findings indicate that the use of such a bi-orthogonal basis allows for a proper definition of the frozen core approximation. In contrast, the use of HF orbitals results in bad error cancellations for ionization potentials and atomization energies (AE). Compared to HF orbitals, the optimized bi-orthogonal basis significantly reduces the positive part of the second-order energy (PT2), thereby facilitating the use of standard extrapolation techniques of hermitian SCI. While we did not observe a significant improvement in the convergence of the SCI algorithm, this is largely due to the use in the present work of a simple three-body correlation factor introduced in a recent study. This correlation factor, which depends only on atomic parameters, eliminates the need for re-optimization of the correlation factor for molecular systems, making its use straightforward and user-friendly. Despite the simplicity of this correlation factor, we were able to achieve accurate results on the AE of a series of 14 molecules in a triple-zeta basis. We also successfully broke a double bond until the full dissociation limit while maintaining the size consistency property. This work thus demonstrates the potential of the BiO-TC-SCI approach in handling complex molecular systems.

We consider the calculations of photoionization spectra and core resonances of open-shell systems using range-separated time-dependent density-functional theory. Specifically, we use the time-dependent range-separated hybrid (TDRSH) scheme, combining a long-range Hartree-Fock (HF) exchange potential and kernel with a short-range potential and kernel from a local density-functional approximation, and the time-dependent locally range-separated hybrid (TDLRSH) scheme, which uses a local range-separation parameter. To efficiently perform the calculations, we formulate a spin-unrestricted linear-response Sternheimer approach in a non-orthogonal B-spline basis set and using appropriate frequency-dependent boundary conditions. We illustrate this approach on the Li atom, which suggests that TDRSH and TDLRSH are adequate simple methods for estimating single-electron photoionization spectra of open-shell systems., arXiv admin note: substantial text overlap with arXiv:2203.05951

In this paper, the history, present status, and future of density-functional theory (DFT) is informally reviewed and discussed by 70 workers in the field, including molecular scientists, materials scientists, method developers and practitioners. The format of the paper is that of a roundtable discussion, in which the participants express and exchange views on DFT in the form of 300 individual contributions, formulated as responses to a preset list of 26 questions. Supported by a bibliography of 776 entries, the paper represents a broad snapshot of DFT, anno 2022.

Actin undergoes important structural changes to transition from the G-actin to the F-actin form. Furthermore, mammals express different isoforms, with only slight variations at the amino acid level. While theα-skeletal actin isoform was thoroughly studied using molecular dynamics simulations, the dynamics of theβ-actin isoform remains unexplored. Here, we have used the AMOEBA polarizable force field coupled with adaptive sampling to investigate the plasticity of theβ-actin. This highlighted the role of a post translational modification, i.e. the histidine 73 methylation, to enhance the opening of the actin cleft and change allosteric paths linking the two distant subdomains SD2 and SD4. The action of the methylation can be also modulated by the type of nucleotide bound in the actin cavity and the type of ions surrounding the protein. Taken together, these results shed new lights onto the plasticity of theβ-actin isoform and the coordinated role of several environmental factors. These results may help designing new types of molecules, such as allosteric modulators, specifically targeting theβ-actin isoform.

International audience; Computational modelling approaches have been developed in the last decades to account for environment effects that can remarkably affect the spectroscopic features of organic dyes. With modern computing power, complex systems can be handled through hybrid QM/MM (Quantum Mechanics/Molecular Mechanics) simulations, which are nowadays commonly used to assist experiments in many different fields. We present here some of the latest advances made in our laboratory to develop and apply a Polarizable Embedding QM/MM based molecular dynamics methodology, and discussing applications where it is found useful. Then we report on the spectroscopic study of a ligand protein complex system, together with our perspective on the modelling of reactions in extreme conditions, illustrating our recent study on thermal Diels-Alder.

The photochemistry of nucleobases, important for their role as building blocks of DNA, is largely affected by the electrostatic environment in which they are soaked. For example, despite the numerous studies of thymine in solution and DNA, there is still a debate on the photochemical deactivation pathways after UV absorption. Many theoretical models are oversimplified due to the lack of computationally accurate and efficient electronic structure methodologies that capture excited state electron correlation effects when nucleobases are embedded in large electrostatic media. Here, we combine mixed-reference spin-flip time-dependent density-functional theory (MRSF-TDDFT) with electrostatic embedding QM/MM using electrostatic potential fitting (ESPF) atomic charges, as a strategy to accurately and efficiently describe the electronic structure of chromophores polarized by an electrostatic medium. In particular, we develop analytic expressions for the energy and gradient of MRSF/MM based on the ESPF coupling using atom-centered grids and total charge conservation. We apply this methodology to the study of solvation effects on thymine photochemistry in water and thymine dimers in DNA. In the former, the combination of trajectory surface hopping (TSH) non-adiabatic molecular dynamics (NAMD) with MRSF/MM remarkably revealed the accelerated deactivation decay pathways, which is consistent with the experimental decay time of ~ 400 fs. The enhanced hopping rate can be explained by the preferential stabilization of corresponding conical interactions due to their increased dipole moments. Structurally, it is a consequence of characteristic methyl puckered geometries near the conical intersection region. For the thymine dimer in B-DNA, we found new photochemical pathways through conical intersections that could explain the formation of cyclobutadiene dimers and 6-4 photoproducts.

International audience; In this contribution, we focused on the use of polarizable force fields to model the structural, energetic, and thermodynamical properties of lanthanides and actinides in water. In a first part, we chose the particular case of the Th(IV) cation to demonstrate the capabilities of the AMOEBA polarizable force field to reproduce both reference ab initio gas-phase energetics and experimental data including coordination numbers and radial distribution functions. Using such model, we predicted the first polarizable force field estimate of Th(IV) solvation free energy, which accounts for -1,638 kcal/mol. In addition, we proposed in a second part of this work a full extension of the SIBFA (Sum of Interaction Between Fragments Ab initio computed) polarizable potential to lanthanides (La(III) and Lu(III)) and to actinides (Th(IV)) in water. We demonstrate its capabilities to reproduce all ab initio contributions as extracted from energy decomposition analysis computations, including many-body charge transfer and discussed its applicability to extended molecular dynamics and its parametrization on high-level post-Hartree-Fock data. © 2012 Springer-Verlag.

International audience; Second-harmonic generation (SHG), linear electro-optic effect (LEO) and electric-field induced second-harmonic generation (EFISH) are nonlinear optical processes with important applications in optoelectronics and photovoltaics. SHG and LEO are second-order nonlinear optical processes described by second-order susceptibility. Instead, EFISH is a third-order nonlinear optical process described by third-order susceptibility.LEO and EFISH are only observed in the presence of a static electric field. These nonlinear processes are very sensitive to the symmetry of the systems. In particular, LEO is usually observed through a change in the dielectric properties of the material while EFISH can be used to generate a “second harmonic” response in centrosymmetric material. In this work, we present a first-principle formalism to calculate second- and third-order susceptibility for LEO and EFISH. LEO is studied for GaAs semiconductor and compared with the dielectric properties of this material. We also present how it is possible for LEO to include the ionic contribution to the second-order macroscopic susceptibility. Concerning EFISH we present for the first time the theory we developed in the framework of TDDFT to calculate this nonlinear optical process. Our approach permits to obtain an expression for EFISH which does not contain the mathematical divergences in the frequency-dependent second-order susceptibility that caused until now many difficulties for numerical calculations.

International audience; We introduce a new parametrization of the AMOEBA polarizable force field for water denoted Q-AMOEBA, for use in simulations that explicitly account for nuclear quantum effects (NQEs). This study is made possible thanks to the recently introduced adaptive Quantum Thermal Bath (adQTB) simulation technique which computational cost is comparable to classical molecular dynamics. The flexible Q-AMOEBA model conserves the initial AMOEBA functional form, with an intermolecular potential including an atomic multipole description of electrostatic interactions (up to quadrupole), a polarization contribution based on the Thole interaction model and a buffered 14-7 potential to model van der Waals interactions. It has been obtained by using a Force Balance fitting strategy including high-level quantum chemistry reference energies and selected condensed phase properties targets. The final Q-AMOEBA model is shown to accurately reproduce both gas phase and condensed phase properties, notably improving the original AMOEBA water model. This development allows the fine study of NQEs on water liquid phase properties such as the average H-O-H angle compared to its gas phase equilibrium value, isotope effects etc... Q-AMOEBA also provides improved infrared spectroscopy prediction capabilities compared to AMOEBA03. Overall, we show that the impact of NQEs depends on the underlying model functional form and on the associated strength of hydrogen bonds. Since adQTB simulations can be performed at near classical computational cost using the Tinker-HP package, Q-AMOEBA can be extended to organic molecules, proteins and nucleic acids opening the possibility for the large scale study of the importance of NQEs in biophysics.

International audience; We extend our recently proposed Deep Learning-aided many-body dispersion (DNN-MBD) model to quadrupole polarizability (Q) terms using a generalized Random Phase Approximation (RPA) formalism enabling to include van der Waals contributions beyond dipole. The resulting DNN-MBDQ model only relies on ab initio-derived quantities as the introduced quadrupole polarizabilities are recursively retrieved from dipole ones, in turn modelled via the Tkatchenko-Scheffler method. A transferable and efficient deep-neuronal network (DNN) provides atom in molecule volumes, while a single range-separation parameter is used to couple the model to Density Functional Theory (DFT). Since it can be computed at negligible cost, the DNN-MBDQ approach can be coupled with DFT functionals such as PBE/PBE0 or B86bPBE(dispersionless). DNN-MBQ-PBE/PBE0 reaches chemical accuracy exhibiting superior accuracy compared to other dispersion-corrected models, especially at near-equilibrium ranges where errors are lowered by nearly 25% compared to our dipole-only approach while gains reach nearly 50% compared to other corrected schemes.

In this work, we present an extension of popular selected configuration interaction (SCI) algorithms to the Transcorrelated (TC) framework. Although we used in this work the recently introduced one-parameter correlation factor [E. Giner, J. Chem. Phys. 154, 084119 (2021)], the theory presented here is valid for any correlation factor. Thanks to the formalization of the non-Hermitian TC eigenvalue problem as a search of stationary points for a specific functional depending on both left- and right-functions, we obtain a general framework, allowing for different choices for both the selection criterion in SCI and the second order perturbative correction to the energy. After numerical investigations on different second-row atomic and molecular systems in increasingly large basis sets, we found that taking into account the non-Hermitian character of the TC Hamiltonian in the selection criterion is mandatory to obtain a fast convergence of the TC energy. In addition, selection criteria based on either the first order coefficient or the second order energy lead to significantly different convergence rates, which is typically not the case in the usual Hermitian SCI. Regarding the convergence of the total second order perturbation energy, we find that the quality of the left-function used in the equations strongly affects the quality of the results. Within the near-optimal algorithm proposed here, we find that the SCI expansion in the TC framework converges faster than the usual SCI in terms of both the basis set and the number of Slater determinants.

International audience; Following a previous study by de Courcy et al. ((2009) Interdiscip. Sci. Comput. Life Sci. 1, 55-60), we demonstrate in this contribution, using quantum chemistry, that metal cations exhibit a specific topological signature in the electron localization of their density interacting with ligands according to its "soft" or "hard" character. Introducing the concept of metal cation subvalence, we show that a metal cation can split its outer-shell density (the so-called subvalent domains or basins) according to it capability to form a partly covalent bond involving charge transfer. Such behaviour is investigated by means of several quantum chemical interpretative methods encompasing the topological analysis of the Electron Localization Function (ELF) and Bader's Quantum Theory of Atoms in Molecules (QTAIM) and two energy decomposition analyses (EDA), namely the Restricted Variational Space (RVS) and Constrained Space Orbital Variations (CSOV) approaches. Further rationalization is performed by computing ELF and QTAIM local properties such as electrostatic distributed moments and local chemical descriptors such as condensed Fukui Functions and dual descriptors. These reactivity indexes are computed within the ELF topological analysis in addition to QTAIM offering access to non atomic reactivity local index, for example on lone pairs. We apply this "subvalence" concept to study the cation selectivity in enzymes involved in blood coagulation (GLA domains of three coagulation factors). We show that the calcium ions are clearly able to form partially covalent charge transfer networks between the subdomain of the metal ion and the carboxylate oxygen lone pairs whereas magnesium does not have such ability. Our analysis also explains the different role of two groups (high affinity and low affinity cation binding sites) present in GLA domains. If the presence of Ca(II) is mandatory in the central "high affinity" region to conserve a proper folding and a charge transfer network, external sites are better stabilised by Mg(II), rather than Ca(II), in agreement with experiment. The central role of discrete water molecules is also discussed in order to understand the stabilities of the observed X-rays structures of the Gla domain. Indeed, the presence of explicit water molecules generating indirect cation-protein interactions through water networks is shown to be able to reverse the observed electronic selectivity occuring when cations directly interact with the Gla domain without the need of water.

Here, we introduce a hybrid method, named Kick-Fukui, to explore the potential energy surface (PES) of clusters and molecules using the Coulombic integral between the Fukui functions in the first screening of the best individuals. In the process, small stable molecules or clusters whose combination has the stoichiometry of the explored species are used as assembly units. First, a small set of candidates has been selected from a large and stochastically generated (Kick) population according to the maximum value of the Coulombic integral between the Fukui functions of both fragments. Subsequently, these few candidates are optimized using a gradient method and density functional theory (DFT) calculations. The performance of the program has been evaluated to explore the PES of various systems, including atomic and molecular clusters. In most cases studied, the global minimum (GM) has been identified with a low computational cost. The strategy does not allow to identify the GM of some silicon clusters; however, it predicts local minima very close in energy to the GM that could be used as the initial population of evolutionary algorithms.

International audience; These last decades, it has been widely assumed that 18-crown-6-ether (CE) plays a spectator role during the chemical processes occurring in isolated host-guest complexes between peptides or proteins and CE, after activation in mass spectrometers. Our present experimental and theoretical results challenge this hypothesis by showing that CE can abstract a proton or a protonated molecule from protonated peptides after activation by collisions in argon or electron capture/transfer. Furthermore, thanks to comparison between experimental and calculated values of collision cross-sections, we demonstrate that CE can change binding site after electron transfer. We also propose detailed mechanisms for these processes.

International audience; Microbiological reductive sulfidation (RS) has rarely been documented, although it represents an efficient strategy for thiol formation. In this work, we reported on the sulfate-respiring bacterium Desulfovibrio sp.86 that has previously demonstrated RS activity toward the pesticide chlordecone. The purpose of the study was to assess its substrate-versatility using a set of 28 carbonyls, to compare with chemical RS and to rationalize the observed trends using a dual experimental and theoretical approach. The chemical RS generally proceeds in two steps (S-O exchange using a sulfur donor like P4S10, reduction of the thione intermediate). Intriguingly, chlordecone was found to be converted into chlordecthiol following the first step. Hence, we designed a protocol and applied it to the 28 substrates to assess their propensity to be directly converted into thiols with the P4S10 treatment alone. Finally, we performed density functional theory calculations on these carbonyls and their thiocarbonyl derivatives to build a set of structural, electronic and thermodynamic parameters. The results showed that chemical and microbiological RS probably involved two distinct mechanisms. Chemically, we observed that several carbonyls, possessing electron-withdrawing groups and/or aromatic rings, were directly transformed into thiols in the presence of P4S10. The correlation obtained with the electron affinity of the thiones led us conclude that a probable single-electron reductive transfer occurred during the first step. We also found that Desulfovibrio sp.86 transformed a variety of aldehydes and ketones, without ever detecting thiones. No significant correlation was observed with the calculated parameters but a relationship between aldehyde RS biotransformation and bacterial growth was observed. Differences in selectivity with chemical RS open the way for further applications in organic synthesis.

New magnet design of a magnetic bottle electron spectrometer allowing the detection of multiply charged ions in coincidence with n electrons. Electrons spectra obtained without and with filtering by coincidence with Xen+ ions.

International audience; We present a new method for the optimization of large configuration interaction (CI) expansions in the quantum Monte Carlo (QMC) framework. The central idea here is to replace the non-orthogonal variational optimization of CI coefficients performed in usual QMC calculations by an orthogonal non-Hermitian optimization thanks to the so-called transcorrelated (TC) framework, the two methods yielding the same results in the limit of a complete basis set. By rewriting the TC equations as an effective self-consistent Hermitian problem, our approach requires the sampling of a single quantity per Slater determinant, leading to minimal memory requirements in the QMC code. Using analytical quantities obtained from both the TC framework and the usual CI-type calculations, we also propose improved estimators which reduce the statistical fluctuations of the sampled quantities by more than an order of magnitude. We demonstrate the efficiency of this method on wave functions containing $10^5-10^6$ Slater determinants, using effective core potentials or all-electron calculations. In all the cases, a sub-milliHartree convergence is reached within only two or three iterations of optimization.

International audience; This article is devoted to the mathematical and numerical treatments of a shape optimization problem emanating from the desire to reconcile quantum theories of chemistry and classical heuristic models: we aim to identify Maximum Probability Domains (MPDs), that is, domains $\Omega$ of the 3d space where the probability $\mathbb{P}_\nu(\Omega)$ to find exactly $\nu$ among the $n$ constituent electrons of a given molecule is maximum. In the Hartree-Fock framework, the shape functional $\mathbb{P}_\nu(\Omega)$ arises as the integral over $\nu$ copies of $\Omega$ and $(n-\nu)$ copies of the complement $\mathbb{R}^3 \setminus \Omega$ of an analytic function defined over the space $\mathbb{R}^{3n}$ of all the spatial configurations of the $n$ electron system. Our first task is to explore the mathematical well-posedness of the shape optimization problem: under mild hypotheses, we prove that global maximizers of the probability functions $\mathbb{P}_\nu(\Omega)$ do exist as open subsets of $\mathbb{R}^3$; meanwhile, we identify the associated necessary first-order optimality condition. We then turn to the numerical calculation of MPDs, for which we resort to a level set based mesh evolution strategy: the latter allows for the robust tracking of complex evolutions of shapes, while leaving the room for accurate chemical computations, carried out on high-resolution meshes of the optimized shapes. The efficiency of this procedure is enhanced thanks to the addition of a fixed-point strategy inspired from the first-order optimality conditions resulting from our theoretical considerations. Several three-dimensional examples are presented and discussed to appraise the efficiency of our algorithms.

International audience; GC-rich sequences are recurring motifs in oncogenes and retroviruses, and could be targeted by non-covalent major-groove therapeutic ligands. We considered the palindromic sequence d(G1G2C3G4C5C6)2, and designed several oligopeptide derivatives of the anti-cancer intercalator mitoxantrone. The stability of their complexes with a 18-mer oligonucleotide encompassing this sequence in its center was validated using polarizable molecular dynamics. We report the most salient structural features of two novel compounds, having a dialkylammonium group as a side-chain on both arms. The anthraquinone ring is intercalated in the central d(CpG)2 sequence with its long axis perpendicular to that of the two base-pairs. On each strand, this enables each ammonium group to bind in-register to O6/N7 of the two facing G bases upstream. We subsequently designed tris-intercalating derivatives, each dialkylammonium substituted with a connector to an N9-aminoacridine intercalator extending our target range from six- to a ten-base pair palindromic sequence, d(C1G2G3G4C5G6C7C8C9G10)2. The structural features of the complex of the most promising derivative are reported. The present design strategy paves the way for designing intercalator-oligopeptide derivatives with an even higher selectivity, targeting an increased number of DNA bases, going beyond ten.

International audience; Modeling chemical reactions using Quantum Chemistry is a widely used predictive strategy capable to complement experiments in order to understand the intrinsic mechanisms guiding the chemicals towards the most favorable reaction products. However, at this purpose, it is mandatory to use reliable and computationally tractable theoretical methods. In this work, we focus on six Diels-Alder reactions of increasing complexity and perform an extensive benchmark of middle- to low-cost computational approaches to predict the characteristic reactions energy barriers. We found that Density Functional Theory, using the ωB97XD, LC-ωPBE, CAM-B3LYP, M11 and MN12SX functionals, with empirical dispersion corrections coupled to an affordable 6-31G basis set, provides quality results for this class of reactions, at a small computational effort. Such efficient and reliable simulation protocol opens perspectives for hybrid QM/MM molecular dynamics simulations of Diels-Alder reactions including explicit solvation.

The analysis of the organic matter of meteorites made it possible to identify over 70 amino acids (AA), including 8 of those found in living organisms. However, their relative abundances vary drastically with the type of the carbonaceous chondrite, even for isomers of same chemical formula. In this report, we address the question whether this difference may have its origin in the relative stability of these isomers according to the conditions they experienced when they were formed and after. To this end, we rely on the fact that for most of the species observed so far in the interstellar medium (ISM), the most abundant isomer of a given generic chemical formula is the most stable one (minimum energy principle, MEP). Using quantum density functional theory (DFT) simulations, we investigate the relative stability of the lowest energy isomers of alanine (Ala) and amino butyric acid (ABA) in the neutral, protonated, and zwitterionic structures together with corresponding nitrile precursors. It is shown that β-alanine and γ-ABA are the most stable in a protonated form, whereas α-AA are the most stable in the zwitterionic and nitrile structures. The different composition of the carbonaceous chondrites CIs and CMs could be linked to the chemical context of the aqueous alterations of the parent bodies.

International audience; The bonding and antibonding character of individual molecular orbitals has been previously shown to be related to their orbital energy derivatives with respect to nuclear coordinates, known as dynamical orbital forces. Albeit usually derived from Koopmans' theorem, in this work we show a more general derivation from conceptual DFT, which justifies application in a broader context. The consistency of the approach is validated numerically for valence orbitals in Kohn-Sham DFT. Then, we illustrate its usefulness by showcasing applications in aromatic and antiaromatic systems and in excited state chemistry. Overall, dynamical orbital forces can be used to interpret the results of routine ab initio calculations, be it wavefunction or density based, in terms of forces and occupations.

The association of a mycotoxin-ochratoxin A (OTA)-with a high-affinity DNA aptamer (anti-OTA) immobilized on a functionalized surface has been investigated at the molecular level. Anti-OTA aptamers are coupled by aminolysis in several steps on an acid-terminated alkyl monolayer grafted on a silicon substrate, and Fourier transform infrared spectroscopy in attenuated total reflection geometry is used to assess the immobilization of anti-OTA (in its unfolded single-strand form) and determine its areal density (ca. 1.4/nm2). IR spectra further demonstrate that the OTA/anti-OTA association is efficient and selective and that several association/dissociation cycles may be conducted on the same surface. The areal density of OTA measured after association on the surface (IR spectroscopy) and after dissociation from the surface (UV-vis spectroscopy) falls in the range 0.16-0.3/nm2 which is close to the areal density of a closed-packed monolayer of anti-OTA aptamers folded to form their G-quadruplex structure. The interactions between OTA and its aptamer at the surface are discussed with the help of density functional theory calculations-to identify the complex IR vibrational modes of OTA in solution-and UV-vis spectroscopy-to determine the protonation state of the adsorbing species (i.e., OTA dissolved in the buffer solution).

[EN] High pressure X-ray diffraction, Raman scattering, and electrical measurements, together with theoretical calculations, which include the analysis of the topological electron density and electronic localization function, evidence the presence of an isostructural phase transition around 2 GPa, a Fermi resonance around 3.5 GPa, and a pressure-induced decomposition of SnSb2Te4 into the high-pressure phases of its parent binary compounds (alpha-Sb2Te3 and SnTe) above 7 GPa. The internal polyhedral compressibility, the behavior of the Raman-active modes, the electrical behavior, and the nature of its different bonds under compression have been discussed and compared with their parent binary compounds and with related ternary materials. In this context, the Raman spectrum of SnSb2Te4 exhibits vibrational modes that are associated but forbidden in rocksalt-type SnTe; thus showing a novel way to experimentally observe the forbidden vibrational modes of some compounds. Here, some of the bonds are identified with metavalent bonding, which were already observed in their parent binary compounds. The behavior of SnSb2Te4 is framed within the extended orbital radii map of BA(2)Te(4) compounds, so our results pave the way to understand the pressure behavior and stability ranges of other "natural van der Waals" compounds with similar stoichiometry., This work has been performed under financial support from the Spanish MINECO under Project MALTA-CONSOLIDER TEAM network (RED2018-102612-T) and Project FIS2017-83295-P, from Generalitat Valenciana under Project PROMETEO/2018/123. This publication is a product of the "Programa de Valoracion y Recursos Conjuntos de I+D+i VLC/CAMPUS and has been financed by the Spanish Ministerio de Educacion, Cultura y Deporte, as part of "Programa Campus de Excelencia Internacional". Supercomputer time has been provided by the Red Espanola de Supercomputacion (RES) and the MALTA cluster. J.A.S. acknowledges a "Ramon y Cajal" fellowship (RYC-2015-17482) for financial support, and E.L.D.S. acknowledges Marie Sklodowska-Curie Grant No. 785789-COMEX from the European Union's Horizon 2020 research and innovation program. We also thank ALBA synchrotron and DIAMOND light source for funded experiments.

International audience; The influence of the mixer shape on the stereoselectivity was measured for lithium–bromine exchange on a gem-dibromoalkene followed by proton trapping. Sixteen passive mixers with eight different angles (135, 120, and 105° (Y mixers); 90° (T mixer); 75, 60, 45, and 30° (W mixers)) and two internal diameters (500 and 250 μm) associated with a tubular microflow reactor having an internal diameter of 500 μm were used. The 45° W-shaped mixer with a smaller internal diameter gave the best selectivity for the monobrominated E product over a range of flow rates without the usual cryogenic conditions (20 °C). With methyl benzoylformate as the electrophile, the corresponding polyfunctionalized product was obtained in a space-time yield of 81 kg L–1 h–1.

We present the extension of the SIBFA (Sum of Interactions Between Fragments Ab initio Computed many-body polarizable force field to condensed phase Molecular Dynamics (MD) simulations. The Quantum-Inspired SIBFA procedure is grounded on simplified integrals obtained from localized molecular orbital theory and achieves full separability of its intermolecular potential. It embodies long-range multipolar electrostatics (up to quadrupole) coupled to a short-range penetration correction (up to charge-quadrupole), exchange-repulsion, many-body polarization, many-body charge transfer/delocalization, exchange-dispersion and dispersion (up to C10). This enables the reproduction of all energy contributions of ab initio Symmetry-Adapted Perturbation Theory (SAPT(DFT)) gas phase reference computations. The SIBFA approach has been integrated within the Tinker-HP massively parallel MD package. To do so all SIBFA energy gradients have been derived and the approach has been extended to enable periodic boundary conditions simulations using Smooth Particle Mesh Ewald. This novel implementation also notably includes a computationally tractable simplification of the many-body charge transfer/delocalization contribution. As a proof of concept, we perform a first computational experiment defining a water model fitted on a limited set of (SAPT(DFT)) data. SIBFA is shown to enable a satisfactory reproduction of both gas phase energetic contributions and condensed phase properties highlighting the importance of its physically-motivated functional form.

The present work proposes an approach to obtain a basis-set correction based on density-functional theory (DFT) for the computation of molecular properties in wave-function theory (WFT). This approach allows one to accelerate the basis-set convergence of any energy derivative of a non-variational WFT method, generalizing previous works on the DFT-based basis-set correction where either only ground-state energies could be computed with non-variational wave functions [Loos et al., J. Phys. Chem. Lett. 10, 2931 (2019)] or properties could be computed as expectation values over variational wave functions [Giner et al., J. Chem. Phys. 155, 044109 (2021)]. This work focuses on the basis-set correction of dipole moments in coupled-cluster with single, double, and perturbative triple excitations [CCSD(T)], which is numerically tested on a set of 14 molecules with dipole moments covering two orders of magnitude. As the basis-set correction relies only on Hartree–Fock densities, its computational cost is marginal with respect to the one of the CCSD(T) calculations. Statistical analysis of the numerical results shows a clear improvement of the basis convergence of the dipole moment with respect to the usual CCSD(T) calculations.

International audience; In this article, we prove the first quantitative uniform in time propagation of chaos for a class of systems of particles in singular repulsive interaction in dimension one that contains the Dyson Brownian motion. We start by establishing existence and uniqueness for the Riesz gases, before proving propagation of chaos with an original approach to the problem, namely coupling with a Cauchy sequence type argument. We also give a general argument to turn a result of weak propagation of chaos into a strong and uniform in time result using the long time behavior and some bounds on moments, in particular enabling us to get a uniform in time version of the result of C\'epa-L\'epingle.

International audience We explore the merits of linear-response range-separated time-dependent density-functional theory (TDDFT) for the calculation of photoionization spectra. We consider two variants of range-separated TDDFT, namely the timedependent range-separated hybrid (TDRSH) scheme which uses a global range-separation parameter and the timedependent locally range-separated hybrid (TDLRSH) which uses a local range-separation parameter, and compare with standard time-dependent local-density approximation (TDLDA) and time-dependent Hartree-Fock (TDHF). We show how to calculate photoionization spectra with these methods using the Sternheimer approach formulated in a nonorthogonal B-spline basis set with appropriate frequency-dependent boundary conditions. We illustrate these methods on the photoionization spectrum of the Be atom, focusing in particular on the core resonances. Both the TDRSH and TDLRSH photoionization spectra are found to constitute a large improvement over the TDLDA photoionization spectrum and a more modest improvement over the TDHF photoionization spectrum.

We report a fast-track computationally-driven discovery of new SARS-CoV2 Main Protease (Mpro) inhibitors whose potency range from mM for initial non-covalent ligands to high nM for the final covalent compound (IC50=830 +/- 50 nM). The project extensively relied on high-resolution all-atom molecular dynamics simulations and absolute binding free energy calculations performed using the polarizable AMOEBA force field. The study is complemented by extensive adaptive sampling simulations that are used to rationalize the different ligands binding poses through the explicit reconstruction of the ligand-protein conformation spaces. Machine Learning predictions are also performed to predict selected compound properties. Computations were performed on GPU-accelerated supercomputers and high performance cloud infrastructures to exponentially reduce time-to-solution and were systematically coupled to Nuclear Magnetic Resonance experiments to drive synthesis and in vitro characterization of compounds. Such study highlights the power of in silico strategies that rely on structure-based approaches for drug design and allows to address the protein conformational multiplicity problem. The proposed innovative scaffolds open routes for further optimization of Mpro inhibitors towards low nM affinities.

We introduce a novel multilevel enhanced sampling strategy grounded on Gaussian-accelerated Molecular Dynamics (GaMD). First, we propose a GaMD multi-GPUs-accelerated implementation within the Tinker-HP molecular dynamics package. We introduce the new "dual-water" mode and its use with the flexible AMOEBA polarizable force field. By adding harmonic boosts to the water stretching and bonding terms, it accelerates the solvent-solute interactions while enabling speedups, thanks to the use of fast multiple-time step integrators. To further reduce the time-to-solution, we couple GaMD to Umbrella Sampling (US). The GaMD─US/dual-water approach is tested on the 1D Potential of Mean Force (PMF) of the solvated CD2-CD58 system (168 000 atoms), allowing the AMOEBA PMF to converge within 1 kcal/mol of the experimental value. Finally, Adaptive Sampling (AS) is added, enabling AS-GaMD capabilities but also the introduction of the new Adaptive Sampling-US-GaMD (ASUS-GaMD) scheme. The highly parallel ASUS-GaMD setup decreases time to convergence by, respectively, 10 and 20 times, compared to GaMD-US and US. Overall, beside the acceleration of PMF computations, Tinker-HP now allows for the simultaneous use of Adaptive Sampling and GaMD-"dual water" enhanced sampling approaches increasing the applicability of polarizable force fields to large-scale simulations of biological systems.