References of "Tkatchenko, Alexandre 50009596"
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See detailQuantum machine learning corrects classical forcefields: Stretching DNA base pairs in explicit solvent
Berryman, Josh UL; Taghavi, Amirhossein UL; Mazur, Florian UL et al

in Journal of Chemical Physics (2022), 157(6),

In order to improve the accuracy of molecular dynamics simulations, classical forcefields are supplemented with a kernel-based machine learning method trained on quantum-mechanical fragment energies. As ... [more ▼]

In order to improve the accuracy of molecular dynamics simulations, classical forcefields are supplemented with a kernel-based machine learning method trained on quantum-mechanical fragment energies. As an example application, a potential-energy surface is generalized for a small DNA duplex, taking into account explicit solvation and long-range electron exchange–correlation effects. A long-standing problem in molecular science is that experimental studies of the structural and thermodynamic behavior of DNA under tension are not well confirmed by simulation; study of the potential energy vs extension taking into account a novel correction shows that leading classical DNA models have excessive stiffness with respect to stretching. This discrepancy is found to be common across multiple forcefields. The quantum correction is in qualitative agreement with the experimental thermodynamics for larger DNA double helices, providing a candidate explanation for the general and long-standing discrepancy between single molecule stretching experiments and classical calculations of DNA stretching. The new dataset of quantum calculations should facilitate multiple types of nucleic acid simulation, and the associated Kernel Modified Molecular Dynamics method (KMMD) is applicable to biomolecular simulations in general. KMMD is made available as part of the AMBER22 simulation software. [less ▲]

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See detailBIGDML—Towards accurate quantum machine learning force fields for materials
Huziel E. Sauceda; Stefan Chmiela; Tkatchenko, Alexandre UL

in Nature Communications (2022)

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See detailMachine learning of material properties: Predictive and interpretable multilinear models
Tkatchenko, Alexandre UL; Allen, Alice

in Science Advances (2022)

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See detailInterpolating Nonadiabatic Molecular Dynamics Hamiltonian with Artificial Neural Networks
Bipeng Wang; Weibin Chu; Tkatchenko, Alexandre UL et al

in Journal of Physical Chemistry Letters (2022)

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See detailThe three-center two-positron bond
Charry Martinez, Jorge Alfonso UL; Moncada, Felix; Barborini, Matteo UL et al

in Chemical Science (2022)

Computational studies have shown that one or more positrons can stabilize two repelling atomic anions through the formation of two-center positronic bonds. In the present work, we study the energetic ... [more ▼]

Computational studies have shown that one or more positrons can stabilize two repelling atomic anions through the formation of two-center positronic bonds. In the present work, we study the energetic stability of a system containing two positrons and three hydride anions, namely 2e+[H3-3]. To this aim, we performed a preliminary scan of the potential energy surface of the system with both electrons and positron in a spin singlet state, with a multi-component MP2 method, that was further refined with variational and diffusion Monte Carlo calculations, and confirmed an equilibrium geometry with D3h symmetry. The local stability of 2e+[H3-3] is demonstrated by analyzing the vertical detachment and adiabatic energy dissociation channels. Bonding properties of the positronic compound, such as the equilibrium interatomic distances, force constants, dissociation energies, and bonding densities are compared with those of the purely electronic H+3 and Li+3 systems. Through this analysis, we find compelling similarities between the 2e+[H3-3] compound and the trilithium cation. Our results strongly point out the formation of a non-electronic three-center two-positron bond, analogous to the well-known three-center two-electron counterparts, which is fundamentally distinct from the two-center two-positron bond [D. Bressanini, J. Chem. Phys.155, 054306 (2021)], thus extending the concept of positron bonded molecules. [less ▲]

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See detailCorrelated Wave Functions for Electron–Positron Interactions in Atoms and Molecules
Charry Martinez, Jorge Alfonso UL; Barborini, Matteo UL; Tkatchenko, Alexandre UL

in Journal of Chemical Theory and Computation (2022), 18(4), 22672280

The positron, as the antiparticle of the electron, can form metastable states with atoms and molecules before its annihilation with an electron. Such metastable matter–positron complexes are stabilized by ... [more ▼]

The positron, as the antiparticle of the electron, can form metastable states with atoms and molecules before its annihilation with an electron. Such metastable matter–positron complexes are stabilized by a variety of mechanisms, which can have both covalent and noncovalent character. Specifically, electron–positron binding often involves strong many-body correlation effects, posing a substantial challenge for quantum-chemical methods based on atomic orbitals. Here we propose an accurate, efficient, and transferable variational ansatz based on a combination of electron–positron geminal orbitals and a Jastrow factor that explicitly includes the electron–positron correlations in the field of the nuclei, which are optimized at the level of variational Monte Carlo (VMC). We apply this approach in combination with diffusion Monte Carlo (DMC) to calculate binding energies for a positron e+ and a positronium Ps (the pseudoatomic electron–positron pair), bound to a set of atomic systems (H–, Li+, Li, Li–, Be+, Be, B–, C–, O– and F–). For PsB, PsC, PsO, and PsF, our VMC and DMC total energies are lower than that from previous calculations; hence, we redefine the state of the art for these systems. To assess our approach for molecules, we study the potential-energy surfaces (PES) of two hydrogen anions H– mediated by a positron (e+H22–), for which we calculate accurate spectroscopic properties by using a dense interpolation of the PES. We demonstrate the reliability and transferability of our correlated wave functions for electron–positron interactions with respect to state-of-the-art calculations reported in the literature. [less ▲]

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See detailAnisotropic Interlayer Force Field for Transition Metal Dichalcogenides: The Case of Molybdenum Disulfide
Wengen, Ouyang; Reut, Sofer; Xiang, Gao et al

in Journal of Chemical Theory and Computation (2021)

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See detailSoftware for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package
Evgeny Epifanovsky; Andrew T. B Gilbert; Xintian Feng et al

in Journal of Chemical Physics (2021)

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See detailMachine Learning Force Fields: Recent Advances and Remaining Challenges
Poltavskyi, Igor UL; Tkatchenko, Alexandre UL

in Journal of Physical Chemistry Letters (2021)

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See detailInteractions between large molecules pose a puzzle for reference quantum mechanical methods
Yasmine S. Al-Hamdani; Péter R. Nagy; Andrea Zen et al

in Nature Communications (2021)

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See detailMethyl-Induced Polarization Destabilizes the Noncovalent Interactions of N-Methylated Lysines
Sanim Rahman; Vered Wineman-Fisher; Peter Nagy et al

in Chemistry: A European Journal (2021)

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