scholarly journals Insights into Non-Covalent Interactions with a Machine-Learned Electron Density

2019 ◽  
Author(s):  
Alberto Fabrizio ◽  
Andrea Grisafi ◽  
benjamin meyer ◽  
Michele Certiotti ◽  
Clemence Corminboeuf
Keyword(s):  
Electron Density ◽  
Real Space ◽  
Total Electron Density ◽  
Total Electron ◽  
Chemical Systems ◽  
Machine Learning Model ◽  
Non Covalent Interactions ◽  
Diverse Ensemble ◽  
Covalent Interactions ◽  
Atomic Coordinates

<div>Chemists continuously harvest the power of non-covalent interactions to control phenomena in both the micro- and macroscopic worlds. From the quantum chemical perspective, the strategies essentially rely upon an in-depth understanding of the physical origin of these interactions, the quantification of their magnitude and their visualization in real-space. </div><div>The total electron density rho(r) represents the simplest yet most comprehensive piece of information available for fully characterizing bonding patterns and non-covalent interactions. The charge density of a molecule can be computed by solving the Schrodinger equation, but this approach becomes rapidly demanding if the electron density has to be evaluated for thousands of different molecules or for very large chemical systems, such as peptides and proteins. </div><div>Here we present a transferable and scalable machine-learning model capable of predicting the total electron density directly from the atomic coordinates. The regression model is used to access qualitative and quantitative insights beyond the underlying rho(r) in a diverse ensemble of sidechain-sidechain dimers extracted from the BioFragment database (BFDb). The transferability of the model to more complex chemical systems is demonstrated by predicting and analyzing the electron density of a collection of 8 polypeptides.</div>

Insights into Non-Covalent Interactions with a Machine-Learned Electron Density

2019 ◽  
Author(s):  
Alberto Fabrizio ◽  
Andrea Grisafi ◽  
benjamin meyer ◽  
Michele Certiotti ◽  
Clemence Corminboeuf
Keyword(s):  
Electron Density ◽  
Real Space ◽  
Total Electron Density ◽  
Total Electron ◽  
Chemical Systems ◽  
Machine Learning Model ◽  
Non Covalent Interactions ◽  
Diverse Ensemble ◽  
Covalent Interactions ◽  
Atomic Coordinates

<div>Chemists continuously harvest the power of non-covalent interactions to control phenomena in both the micro- and macroscopic worlds. From the quantum chemical perspective, the strategies essentially rely upon an in-depth understanding of the physical origin of these interactions, the quantification of their magnitude and their visualization in real-space. </div><div>The total electron density rho(r) represents the simplest yet most comprehensive piece of information available for fully characterizing bonding patterns and non-covalent interactions. The charge density of a molecule can be computed by solving the Schrodinger equation, but this approach becomes rapidly demanding if the electron density has to be evaluated for thousands of different molecules or for very large chemical systems, such as peptides and proteins. </div><div>Here we present a transferable and scalable machine-learning model capable of predicting the total electron density directly from the atomic coordinates. The regression model is used to access qualitative and quantitative insights beyond the underlying rho(r) in a diverse ensemble of sidechain-sidechain dimers extracted from the BioFragment database (BFDb). The transferability of the model to more complex chemical systems is demonstrated by predicting and analyzing the electron density of a collection of 8 polypeptides.</div>

Revisiting the charge density analysis of 2,5-dichloro-1,4-benzoquinone at 20 K

2017 ◽  
Vol 73 (4) ◽  
pp. 654-659 ◽  
Author(s):  
Zhijie Chua ◽  
Bartosz Zarychta ◽  
Christopher G. Gianopoulos ◽  
Vladimir V. Zhurov ◽  
A. Alan Pinkerton
Keyword(s):  
Charge Density ◽  
Electron Density ◽  
Topological Analysis ◽  
Diffraction Measurement ◽  
X Ray Diffraction ◽  
Total Electron Density ◽  
Total Electron ◽  
Structure Factors ◽  
Density Analysis ◽  
Experimental Charge Density

A high-resolution X-ray diffraction measurement of 2,5-dichloro-1,4-benzoquinone (DCBQ) at 20 K was carried out. The experimental charge density was modeled using the Hansen–Coppens multipolar expansion and the topology of the electron density was analyzed in terms of the quantum theory of atoms in molecules (QTAIM). Two different multipole models, predominantly differentiated by the treatment of the chlorine atom, were obtained. The experimental results have been compared to theoretical results in the form of a multipolar refinement against theoretical structure factors and through direct topological analysis of the electron density obtained from the optimized periodic wavefunction. The similarity of the properties of the total electron density in all cases demonstrates the robustness of the Hansen–Coppens formalism. All intra- and intermolecular interactions have been characterized.

scholarly journals Understanding the Reactivity of Trimethylsilyldiazoalkanes Participating in [3+2] Cycloaddition Reactions towards Diethylfumarate with a Molecular Electron Density Theory Perspective

Organics ◽  
2020 ◽  
Vol 1 (1) ◽  
pp. 3-18
Author(s):  
Luis R. Domingo ◽  
Nivedita Acharjee ◽  
Haydar A. Mohammad-Salim
Keyword(s):  
Electron Density ◽  
Energy Cost ◽  
Trimethylsilyl Group ◽  
Gibbs Energies ◽  
Molecular Electron ◽  
One Step ◽  
Molecular Electron Density Theory ◽  
Non Covalent Interactions ◽  
Covalent Interactions ◽  
Step Mechanism

A Molecular Electron Density Theory (MEDT) study is presented here for [3+2] cycloaddition (32CA) reactions of three trimethylsilyldiazoalkanes with diethyl fumarate. The presence of silicon bonded to the carbon of these silyldiazoalkanes changes its structure and reactivity from a pseudomonoradical to that of a zwitterionic one. A one-step mechanism is predicted for these polar zw-type 32CA reactions with activation enthalpies in CCl4 between 8.0 and 19.7 kcal·mol−1 at the MPWB1K (PCM)/6-311G(d,p) level of theory. The negative reaction Gibbs energies between −3.1 and −13.2 kcal·mole−1 in CCl4 suggests exergonic character, making the reactions irreversible. Analysis of the sequential changes in the bonding pattern along the reaction paths characterizes these zw-type 32CA reactions. The increase in nucleophilic character of the trimethylsilyldiazoalkanes makes these 32CA reactions more polar. Consequently, the activation enthalpies are decreased and the TSs require less energy cost. Non-covalent interactions at the TSs account for the stereoselectivity found in these 32CA reactions involving the bulky trimethylsilyl group.

Electron densities and the VSEPR model of molecular geometry

1992 ◽  
Vol 70 (3) ◽  
pp. 742-750 ◽  
Author(s):  
R. J. Gillespie
Keyword(s):  
Electron Density ◽  
Present Status ◽  
Electron Pair ◽  
Molecular Geometry ◽  
Physical Basis ◽  
Valence Shell ◽  
Electron Densities ◽  
Total Electron Density ◽  
Total Electron

This paper reviews the present status of the VSEPR model of molecular geometry in relation to electron densities. The discussion is based on the electron pair domain version of this model. The fundamental postulates of the model are summarized and illustrated by a discussion of the structures of some molecules with five and seven electron pair domains in the valence shell, including the recently discovered ions XeF5− and XeOF6−. The total electron density does not provide any obvious support for the model and although electron density deformation maps do provide some support they are not always reliable. The Laplacian of the electron density, however, shows the presence of valence shell charge concentrations that correspond closely in number and properties to the electron pair domains of the VSEPR model. This correspondence between electron pair domains and valence shell charge concentrations provides a physical basis for a better understanding of the VSEPR model. Keywords: VSEPR model, electron densities, molecular geometry, Laplacian of the electron density, electron pair domain.

Total electron density from thes-electron density

1998 ◽  
Vol 57 (5) ◽  
pp. 3458-3461 ◽  
Author(s):  
Á. Nagy ◽  
E. Bene
Keyword(s):  
Electron Density ◽  
Total Electron Density ◽  
Total Electron

scholarly journals Early results from the Whisper instrument on Cluster: an overview

2001 ◽  
Vol 19 (10/12) ◽  
pp. 1241-1258 ◽  
Author(s):  
P. M. E. Décréau ◽  
P. Fergeau ◽  
V. Krasnoselskikh ◽  
E. Le Guirriec ◽  
M. Lévêque ◽  
...  
Keyword(s):  
Electron Density ◽  
Small Scale ◽  
Data Sets ◽  
Total Density ◽  
Total Electron Density ◽  
Data Set ◽  
Total Electron ◽  
Density Data ◽  
Early Results ◽  
Natural Emissions

Abstract. The Whisper instrument yields two data sets: (i) the electron density determined via the relaxation sounder, and (ii) the spectrum of natural plasma emissions in the frequency band 2–80 kHz. Both data sets allow for the three-dimensional exploration of the magnetosphere by the Cluster mission. The total electron density can be derived unambiguously by the sounder in most magnetospheric regions, provided it is in the range of 0.25 to 80 cm-3 . The natural emissions already observed by earlier spacecraft are fairly well measured by the Whisper instrument, thanks to the digital technology which largely overcomes the limited telemetry allocation. The natural emissions are usually related to the plasma frequency, as identified by the sounder, and the combination of an active sounding operation and a passive survey operation provides a time resolution for the total density determination of 2.2 s in normal telemetry mode and 0.3 s in burst mode telemetry, respectively. Recorded on board the four spacecraft, the Whisper density data set forms a reference for other techniques measuring the electron population. We give examples of Whisper density data used to derive the vector gradient, and estimate the drift velocity of density structures. Wave observations are also of crucial interest for studying small-scale structures, as demonstrated in an example in the fore-shock region. Early results from the Whisper instrument are very encouraging, and demonstrate that the four-point Cluster measurements indeed bring a unique and completely novel view of the regions explored.Key words. Space plasma physics (instruments and techniques; discontinuities, general or miscellaneous)

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