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Electron Density Analysis Tools
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Electron Density Analysis Tools

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Physical Chemistry".

Deadline for manuscript submissions: closed (30 June 2020) | Viewed by 17863

Special Issue Editor

Prof. Dr. Ricardo Mosquera

E-Mail Website
Guest Editor
Department of Physical Chemistry, Universidad de Vigo, Vigo, Spain
Interests: quantum chemistry; electron density analysis; quantum theory of atoms in molecules; electron delocalization; stacking interactions; anomeric effect and related conformational preferences; metal complexation by anthocyanidins

Special Issue Information

Dear Colleagues,

Modern electron density analysis methods are powerful tools for obtaining chemical insight from quantum chemical calculations. At least two kinds of different approaches can be distinguished: (i) Real space methods, sometimes grouped within the term of quantum chemical topology and comprising, among others, Bader’s quantum theory of atoms in molecules (QTAIM) or the topological study of the electron localization function (ELF); and (ii) those methods where orbitals are still considered as significant mathematical entities, natural bonding orbital (NBO) probably being the most widely used. Extensive application of these techniques on several chemical topics has enriched our knowledge on the electronic origin of diverse physical and chemical properties, trends, or concepts. In many cases, electron density analysis has provided conclusions that are fully compatible with firmly rooted ideas within the chemical community. Nevertheless, there are significant examples where the application of some of these methods has led to alternative interpretations, questioning, reforming, and even denying several previous explanations that are generally accepted for common chemical facts. An example of these cases is the shortcomings of the resonance model and hyperconjugative interpretations revealed by QTAIM studies carried out in past decades. 

This Special Issue focuses on recent advances in methods, implementations for analyzing specific properties or systems, extensions of already developed methods, and significant applications of electron density analysis tools. We are particularly interested in applications uncovering the electron origin behind any kind of weak bonding (stacking interactions, halogen bond, beryllium bond, etc.), firmly established conformational preferences (anomeric effect, Z-effect, etc.), or processes of technical interest. Manuscripts combining theoretical and experimental work, or directly related to biosystems or material science, are also welcomed. By contrast, routine computational work on simple systems is outside the scope of this issue. Works devoted to conceptualization of aromaticity, electron delocalization, electronegativity, approximate transferability of group properties, or any other chemical property or topic, from an electronic point of view will be also appreciated for this Issue.

Prof. Ricardo Mosquera
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Methods for electron density analysis
  • Electron density partitioning
  • Quantum chemical topology
  • Quantum theory of atoms in molecules
  • Electron localization function
  • Natural bond orbitals
  • Interacting quantum atoms
  • Electron density analysis of electronically excited states
  • Transferability of group properties
  • Aromaticity descriptors
  • Electronic origin of weak bonds
  • Electronic origin of conformational preferences

Published Papers (4 papers)

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Research

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14 pages, 310 KiB  
Article
Are Multicentre Bond Indices and Related Quantities Reliable Predictors of Excited-State Aromaticity?
by Robert Ponec, David L. Cooper and Peter B. Karadakov
Molecules 2020, 25(20), 4791; https://doi.org/10.3390/molecules25204791 - 19 Oct 2020
Cited by 4 | Viewed by 1748
Abstract
Systematic scrutiny is carried out of the ability of multicentre bond indices and the NOEL-based similarity index dAB to serve as excited-state aromaticity criteria. These indices were calculated using state-optimized complete active-space self-consistent field wavefunctions for several low-lying singlet and triplet states [...] Read more.
Systematic scrutiny is carried out of the ability of multicentre bond indices and the NOEL-based similarity index dAB to serve as excited-state aromaticity criteria. These indices were calculated using state-optimized complete active-space self-consistent field wavefunctions for several low-lying singlet and triplet states of the paradigmatic molecules of benzene and square cyclobutadiene and the inorganic ring S2N2. The comparison of the excited-state indices with aromaticity trends for individual excited states suggested by the values of magnetic aromaticity criteria show that whereas the indices work well for aromaticity reversals between the ground singlet and first triplet electronic states, addressed by Baird’s rule, there are no straightforward parallels between the two sets of data for singlet excited states. The problems experienced while applying multicentre bond indices and dAB to singlet excited states are explained by the loss of the information inherently present in wavefunctions and/or pair densities when calculating the first-order density matrix. Full article
(This article belongs to the Special Issue Electron Density Analysis Tools)
19 pages, 3715 KiB  
Article
Factors Impacting σ- and π-Hole Regions as Revealed by the Electrostatic Potential and Its Source Function Reconstruction: The Case of 4,4′-Bipyridine Derivatives
by Carlo Gatti, Alessandro Dessì, Roberto Dallocchio, Victor Mamane, Sergio Cossu, Robin Weiss, Patrick Pale, Emmanuel Aubert and Paola Peluso
Molecules 2020, 25(19), 4409; https://doi.org/10.3390/molecules25194409 - 25 Sep 2020
Cited by 15 | Viewed by 2418
Abstract
Positive electrostatic potential (V) values are often associated with σ- and π-holes, regions of lower electron density which can interact with electron-rich sites to form noncovalent interactions. Factors impacting σ- and π-holes may thus be monitored in terms of the shape [...] Read more.
Positive electrostatic potential (V) values are often associated with σ- and π-holes, regions of lower electron density which can interact with electron-rich sites to form noncovalent interactions. Factors impacting σ- and π-holes may thus be monitored in terms of the shape and values of the resulting V. Further precious insights into such factors are obtained through a rigorous decomposition of the V values in atomic or atomic group contributions, a task here achieved by extending the Bader–Gatti source function (SF) for the electron density to V. In this article, this general methodology is applied to a series of 4,4′-bipyridine derivatives containing atoms from Groups VI (S, Se) and VII (Cl, Br), and the pentafluorophenyl group acting as a π-hole. As these molecules are characterized by a certain degree of conformational freedom due to the possibility of rotation around the two C–Ch bonds, from two to four conformational motifs could be identified for each structure through conformational search. On this basis, the impact of chemical and conformational features on σ- and π-hole regions could be systematically evaluated by computing the V values on electron density isosurfaces (VS) and by comparing and dissecting in atomic/atomic group contributions the VS maxima (VS,max) values calculated for different molecular patterns. The results of this study confirm that both chemical and conformational features may seriously impact σ- and π-hole regions and provide a clear analysis and a rationale of why and how this influence is realized. Hence, the proposed methodology might offer precious clues for designing changes in the σ- and π-hole regions, aimed at affecting their potential involvement in noncovalent interactions in a desired way. Full article
(This article belongs to the Special Issue Electron Density Analysis Tools)
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23 pages, 391 KiB  
Article
An Overview of Self-Consistent Field Calculations Within Finite Basis Sets
by Susi Lehtola, Frank Blockhuys and Christian Van Alsenoy
Molecules 2020, 25(5), 1218; https://doi.org/10.3390/molecules25051218 - 8 Mar 2020
Cited by 39 | Viewed by 8088
Abstract
A uniform derivation of the self-consistent field equations in a finite basis set is presented. Both restricted and unrestricted Hartree–Fock (HF) theory as well as various density functional approximations are considered. The unitary invariance of the HF and density functional models is discussed, [...] Read more.
A uniform derivation of the self-consistent field equations in a finite basis set is presented. Both restricted and unrestricted Hartree–Fock (HF) theory as well as various density functional approximations are considered. The unitary invariance of the HF and density functional models is discussed, paving the way for the use of localized molecular orbitals. The self-consistent field equations are derived in a non-orthogonal basis set, and their solution is discussed also in the presence of linear dependencies in the basis. It is argued why iterative diagonalization of the Kohn–Sham–Fock matrix leads to the minimization of the total energy. Alternative methods for the solution of the self-consistent field equations via direct minimization as well as stability analysis are briefly discussed. Explicit expressions are given for the contributions to the Kohn–Sham–Fock matrix up to meta-GGA functionals. Range-separated hybrids and non-local correlation functionals are summarily reviewed. Full article
(This article belongs to the Special Issue Electron Density Analysis Tools)

Review

Jump to: Research

35 pages, 3248 KiB  
Review
Interacting Quantum Atoms—A Review
by José Manuel Guevara-Vela, Evelio Francisco, Tomás Rocha-Rinza  and Ángel Martín Pendás
Molecules 2020, 25(17), 4028; https://doi.org/10.3390/molecules25174028 - 3 Sep 2020
Cited by 68 | Viewed by 5071
Abstract
The aim of this review is threefold. On the one hand, we intend it to serve as a gentle introduction to the Interacting Quantum Atoms (IQA) methodology for those unfamiliar with it. Second, we expect it to act as an up-to-date reference of [...] Read more.
The aim of this review is threefold. On the one hand, we intend it to serve as a gentle introduction to the Interacting Quantum Atoms (IQA) methodology for those unfamiliar with it. Second, we expect it to act as an up-to-date reference of recent developments related to IQA. Finally, we want it to highlight a non-exhaustive, yet representative set of showcase examples about how to use IQA to shed light in different chemical problems. To accomplish this, we start by providing a brief context to justify the development of IQA as a real space alternative to other existent energy partition schemes of the non-relativistic energy of molecules. We then introduce a self-contained algebraic derivation of the methodological IQA ecosystem as well as an overview of how these formulations vary with the level of theory employed to obtain the molecular wavefunction upon which the IQA procedure relies. Finally, we review the several applications of IQA as examined by different research groups worldwide to investigate a wide variety of chemical problems. Full article
(This article belongs to the Special Issue Electron Density Analysis Tools)
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