Special Issue "The Application of Quantum Mechanics in Reactivity of Molecules II"

A special issue of Applied Sciences (ISSN 2076-3417). This special issue belongs to the section "Quantum Science and Technology".

Deadline for manuscript submissions: 20 June 2022.

Special Issue Editor

Dr. Sérgio F. Sousa
E-Mail Website
Guest Editor
UCIBIO/REQUIMTE, BioSIM - Departamento de BioMedicina, Faculdade de Medicina da Universidade do Porto, 4200-319 Porto, Portugal
Interests: computational enzymatic catalysis; QM/MM; docking; virtual screening; molecular dynamics simulations
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Special Issue Information

Dear Colleagues,

Over the last few decades, the increase in the computational resources, coupled to the popularity of competitive quantum mechanics alternatives (particularly DFT), has promoted a widespread penetration of quantum mechanics calculations in a variety of fields targeting the reactivity of molecules.

The present Special Issue aims to explore this diversity of application of QUANTUM MECHANICS, including ab initio, semi-empirical, DFT, and post-Hartree–Fock methods, in the study of the electronic structure of molecules and their reactivity.

This Special Issue invites researchers to submit original research papers and review articles related to any chemical problem to which quantum mechanics has been applied. The topics of interest include but are not limited to:

  • Development and application of QM methods;
  • QM studies on catalysis;
  • QM studies on magnetic systems;
  • QM studies on excited states;
  • QM studies on transition metal chemistry;
  • QM studies on organic chemistry;
  • QM and QM/MM studies applied biological systems;
  • Quantum dynamics;
  • New or improved quantum mechanical methods;
  • Software programs featuring QM codes.

Dr. Sérgio F. Sousa
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 papers will be 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. Applied Sciences 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 2000 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

  • Density functional theory
  • Ab initio
  • Semi-empirical methods
  • Quantum dynamics
  • QM/MM
  • Quantum dynamics

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Published Papers (3 papers)

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Research

Article
Mechanistic Insight into SARS-CoV-2 Mpro Inhibition by Organoselenides: The Ebselen Case Study
Appl. Sci. 2021, 11(14), 6291; https://doi.org/10.3390/app11146291 - 07 Jul 2021
Cited by 1 | Viewed by 772
Abstract
The main protease (Mpro) of SARS-CoV-2 is a current target for the inhibition of viral replication. Through a combined Docking and Density Functional Theory (DFT) approach, we investigated in-silico the molecular mechanism by which ebselen (IUPAC: 2-phenyl-1,2-benzoselenazol-3-one), the most famous and [...] Read more.
The main protease (Mpro) of SARS-CoV-2 is a current target for the inhibition of viral replication. Through a combined Docking and Density Functional Theory (DFT) approach, we investigated in-silico the molecular mechanism by which ebselen (IUPAC: 2-phenyl-1,2-benzoselenazol-3-one), the most famous and pharmacologically active organoselenide, inhibits Mpro. For the first time, we report on a mechanistic investigation in an enzyme for the formation of the covalent -S-Se- bond between ebselen and a key enzymatic cysteine. The results highlight the strengths and weaknesses of ebselen and provide hints for a rational drug design of bioorganic selenium-based inhibitors. Full article
(This article belongs to the Special Issue The Application of Quantum Mechanics in Reactivity of Molecules II)
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Article
Unveiling the Reaction Mechanism of the Das/Chechik/Marek Synthesis of Stereodefined Quaternary Carbon Centers
Appl. Sci. 2021, 11(11), 5002; https://doi.org/10.3390/app11115002 - 28 May 2021
Viewed by 577
Abstract
The reaction mechanism of the Cu+-catalyzed introduction of two all-carbon-substituted stereocenters in an ynamide system using a Grignard reagent, a zinc carbenoid, and an aldehyde, was investigated using density-functional theory. In contrast to the formation of an organocopper(I) compound and subsequent [...] Read more.
The reaction mechanism of the Cu+-catalyzed introduction of two all-carbon-substituted stereocenters in an ynamide system using a Grignard reagent, a zinc carbenoid, and an aldehyde, was investigated using density-functional theory. In contrast to the formation of an organocopper(I) compound and subsequent carbocupration reaction, previously postulated as the initial step, the reaction proved to instead proceed through an initial complexation of the substrate alkyne bond by the Cu+-catalyst, which primes this bond for reaction with the Grignard reagent. Subsequent addition of the zinc carbenoid then enables the nucleophilic attack on the incoming aldehyde, which is revealed as the rate-limiting step. Our computations have also identified the factors governing the regio- and setereoselectivity of this interesting reaction, and suggest possible paths for its further development. Full article
(This article belongs to the Special Issue The Application of Quantum Mechanics in Reactivity of Molecules II)
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Article
The Oxidative Process of Acarbose, Maysin, and Luteolin with Maltase-Glucoamylase: Molecular Docking and Molecular Dynamics Study
Appl. Sci. 2021, 11(9), 4067; https://doi.org/10.3390/app11094067 - 29 Apr 2021
Viewed by 453
Abstract
Type 2 diabetes mellitus has been classified as the epidemic of the XXI century, making it a global health challenge. Currently, the commonly used treatment for this disease is acarbose, however, the high cost of this medicine has motivated the search for new [...] Read more.
Type 2 diabetes mellitus has been classified as the epidemic of the XXI century, making it a global health challenge. Currently, the commonly used treatment for this disease is acarbose, however, the high cost of this medicine has motivated the search for new alternatives. In this work, the maysin, a characteristic flavonoid from maize inflorescences, and its aglycon version, luteolin, are proposed as acarbose substitutes. For this, a theoretical comparative analysis was conducted on the molecular interactions of acarbose, maysin, and luteolin with human maltase-glucoamylase (NtMGAM), as well as their oxidative process. The binding energies in the active site of NtMGAM with acarbose, maysin, and luteolin molecules were predicted using a molecular docking approach applying the Lamarckian genetic algorithm method. Theoretical chemical reactivity parameters such as chemical hardness (η) and chemical potential (µ) of the acarbose, maysin, and luteolin molecules, as well as of the amino acids involved in the active site, were calculated using the electronic structure method called Density Functional Theory (DFT), employing the M06 meta-GGA functional in combination with the 6-31G(d) basis set. Furthermore, a possible oxidative process has been proposed from quantum-chemical calculations of the electronic charge transfer values (ΔN), between the amino acids of the active site and the acarbose, maysin, and luteolin. Molecular docking predictions were complemented with molecular dynamics simulations. Hence, it was demonstrated that the solvation of the protein affects the affinity order between NtMGAM and ligands. Full article
(This article belongs to the Special Issue The Application of Quantum Mechanics in Reactivity of Molecules II)
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