Doublet non liant

Un doublet non liant (ou doublet libre) est un doublet d'électrons de valence qui n'est pas impliqué dans une liaison covalente. Un tel doublet est formé d'électrons appariés, ce qui les distingue des électrons célibataires rencontrés dans une orbitale atomique incomplète. L'atome d'azote possède un doublet non liant dans la molécule d'ammoniac , celui d'oxygène en possède deux dans la molécule d'eau , et celui de chlore en possède trois dans la molécule de chlorure d'hydrogène HCl. thumb|200px|Ammoniac : N avec son doublet non liant Les doublets non liants peuvent être mobilisés dans des liaisons covalentes de coordination, comme c'est le cas par exemple de l'ion hydronium (ou oxonium) dans lequel l'atome d'oxygène « cède » un électron d'un de ses deux doublets non liants à un proton pour former un atome d'hydrogène lié à lui par un doublet liant (ce qu'on appelait autrefois une « liaison dative »). De tels doublets agissent sur la géométrie des liaisons atomiques en réduisant les

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Assessing the persistence of chalcogen bonds in solution with neural network potentials

Frédéric Célerse, Veronika Juraskova, Rubén Laplaza Solanas

Non-covalent bonding patterns are commonly harvested as a design principle in the field of catalysis, supramolecular chemistry, and functional materials to name a few. Yet, their computational description generally neglects finite temperature and environment effects, which promote competing interactions and alter their static gas-phase properties. Recently, neural network potentials (NNPs) trained on density functional theory (DFT) data have become increasingly popular to simulate molecular phenomena in condensed phase with an accuracy comparable to ab initio methods. To date, most applications have centered on solid-state materials or fairly simple molecules made of a limited number of elements. Herein, we focus on the persistence and strength of chalcogen bonds involving a benzotelluradiazole in condensed phase. While the tellurium-containing heteroaromatic molecules are known to exhibit pronounced interactions with anions and lone pairs of different atoms, the relevance of competing intermolecular interactions, notably with the solvent, is complicated to monitor experimentally but also challenging to model at an accurate electronic structure level. Here, we train direct and baselined NNPs to reproduce hybrid DFT energies and forces in order to identify what the most prevalent non-covalent interactions occurring in a solute-Cl−–THF mixture are. The simulations in explicit solvent highlight the clear competition with chalcogen bonds formed with the solvent and the short-range directionality of the interaction with direct consequences for the molecular properties in the solution. The comparison with other potentials (e.g., AMOEBA, direct NNP, and continuum solvent model) also demonstrates that baselined NNPs offer a reliable picture of the non-covalent interaction interplay occurring in solution.

2022

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How Important is Self-Consistency for the dDsC Density Dependent Dispersion Correction?

Eric Albert Georges Bremond, Nikolay Golubev

The treatment of dispersion interactions is ubiquitous but computationally demanding for seamless ab initio approaches. A highly popular and simple remedy consists in correcting for the missing interactions a posteriori by adding an attractive energy term summed over all atom pairs to standard density functional approximations.These corrections were originally based on atom pairwise parameters and, hence, had a strong touch of empiricism. To overcome such limitations, we recently proposed a robust system-dependent dispersion correction, dDsC, that is computed from the electron density and that provides a balanced description of both weak inter- and intramolecular interactions. From the theoretical point of view and for the sake of increasing reliability, we here verify if the self-consistent implementation of dDsC impacts ground-state properties such as interaction energies, electron density, dipole moments, geometries and harmonic frequencies. In addition, we investigate the suitability of the a posteriori scheme for molecular dynamics simulations, for which the analysis of the energy conservation constitutes a challenging test.

American Institute of Physics2014

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System-Dependent Density Based Dispersion Correction

Density functional approximations fail to provide a consistent description of weak molecular interactions arising from small electron density overlaps. A simple remedy to correct for the missing interactions is to add a posteriori an attractive energy term summed over all atom pairs in the system. The density-dependent energy correction, presented herein, is applicable to all elements of the periodic table and is easily combined with any electronic structure method, which lacks the accurate treatment of weak interactions. Dispersion coefficients are computed according to Becke and Johnson’s exchange-hole dipole moment (XDM) formalism, thereby depending on the chemical environment of an atom (density, oxidation state). The long- range ∼R-6 potential is supplemented with higher-order correction terms (∼R-8 and ∼R-10) through the universal damping function of Tang and Toennies. A genuine damping factor depending on (iterative) Hirshfeld (overlap) populations, atomic ionization energies, and two adjustable parameters specifically fitted to a given DFT functional is also introduced. The proposed correction, dDXDM, dramatically improves the performance of popular density functionals. The analysis of 30 (dispersion corrected) density functionals on 145 systems reveals that dDXDM largely reduces the errors of the parent functionals for both inter- and intramolecular interactions. With mean absolute deviations (MADs) of 0.74-0.84 kcal mol-1, PBE-dDXDM, PBE0-dDXDM, and B3LYP-dDXDM outperform the computationally more demanding and most recent functionals such as M06-2X and B2PLYP-D (MAD of 1.93 and 1.06 kcal mol-1, respectively).

2010

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CH-160(en): Advanced general chemistry (english)

This course aims to teach essential notions of the structure of matter, chemical equilibria and reactivity. Classes and exercises provide the means to analyze and solve, by reasoning and calculation, novel problems of geeneral chemistry.

CH-112: Organic chemistry

L'objectif de ce cours est de fournir les connaissances et le moyen de comprendre, au niveau moléculaire, le fonctionnement des réactions chimiques organiques. Pendant le cours, l'étudiant réfléchira et résoudra de nouveaux problèmes.

CH-335: Asymmetric synthesis and retrosynthesis

La première partie du cours décrit les méthodes classiques de synthèse asymétrique. La seconde partie du cours traite des stratégies de rétrosynthèse basées sur l'approche par disconnection.

Ammoniac

L'ammoniac est un composé chimique de formule (du groupe générique des nitrures d'hydrogène). Dans les conditions normales de température et de pression, c'est un gaz noté gaz. Il est incolore et

Azote

L'azote est l'élément chimique de numéro atomique 7, de symbole N (du latin nitrogenium). C'est la tête de file du groupe des pnictogènes. Dans le langage courant, l'azote désigne le corps simple N

Géométrie moléculaire

La géométrie moléculaire ou structure moléculaire désigne l'arrangement 3D des atomes dans une molécule. . Détermination La géométrie moléculaire peut être établie à l'aide de différents