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

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

Deadline for manuscript submissions: 30 June 2020.

Special Issue Editor

Dr. Sérgio F. Sousa
Website
Guest Editor
UCIBIO/REQUIMTE, BioSIM - Departamento de BioMedicina,Faculdade de Medicina da Universidade do Porto, Porto, Portugal
Interests: computational enzymatic catalysis; QM/MM; docking; virtual screening; molecular dynamics simulations
Special Issues and Collections in MDPI journals

Special Issue Information

Over the last decades, the increase in computational resources, coupled with the popularity of competitive quantum mechanics alternatives (particularly DFT), has promoted the widespread penetration of quantum mechanics calculations into 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 inition, semi-empirical, DFT, and pos-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 Filipe 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 1800 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

Published Papers (8 papers)

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Research

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Open AccessFeature PaperArticle
Phase Equalization, Charge Transfer, Information Flows and Electron Communications in Donor–Acceptor Systems
Appl. Sci. 2020, 10(10), 3615; https://doi.org/10.3390/app10103615 - 23 May 2020
Abstract
Subsystem phases and electronic flows involving the acidic and basic sites of the donor (B) and acceptor (A) substrates of chemical reactions are revisited. The emphasis is placed upon the phase–current relations, a coherence of elementary probability flows in the preferred reaction complex, [...] Read more.
Subsystem phases and electronic flows involving the acidic and basic sites of the donor (B) and acceptor (A) substrates of chemical reactions are revisited. The emphasis is placed upon the phase–current relations, a coherence of elementary probability flows in the preferred reaction complex, and on phase-equalization in the equilibrium state of the whole reactive system. The overall and partial charge-transfer (CT) phenomena in alternative coordinations are qualitatively examined and electronic communications in A—B systems are discussed. The internal polarization (P) of reactants is examined, patterns of average electronic flows are explored, and energy changes associated with P/CT displacements are identified using the chemical potential and hardness descriptors of reactants and their active sites. The nonclassical (phase/current) contributions to resultant gradient information are investigated and the preferred current-coherence in such donor–acceptor systems is predicted. It is manifested by the equalization of equilibrium local phases in the entangled subsystems. Full article
(This article belongs to the Special Issue The Application of Quantum Mechanics in Reactivity of Molecules)
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Open AccessArticle
A General User-Friendly Tool for Kinetic Calculations of Multi-Step Reactions within the Virtual Multifrequency Spectrometer Project
Appl. Sci. 2020, 10(5), 1872; https://doi.org/10.3390/app10051872 - 09 Mar 2020
Abstract
We discuss the implementation of a computer program for accurate calculation of the kinetics of chemical reactions integrated in the user-friendly, multi-purpose Virtual Multifrequency Spectrometer tool. The program is based on the ab initio modeling of the involved molecular species, the adoption of [...] Read more.
We discuss the implementation of a computer program for accurate calculation of the kinetics of chemical reactions integrated in the user-friendly, multi-purpose Virtual Multifrequency Spectrometer tool. The program is based on the ab initio modeling of the involved molecular species, the adoption of transition-state theory for each elementary step of the reaction, and the use of a master-equation approach accounting for the complete reaction scheme. Some features of the software are illustrated through examples including the interconversion reaction of hydroxyacetone and 2-hydroxypropanal and the production of HCN and HNC from vinyl cyanide. Full article
(This article belongs to the Special Issue The Application of Quantum Mechanics in Reactivity of Molecules)
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Open AccessArticle
A Never-Ending Conformational Story of the Quercetin Molecule: Quantum-Mechanical Investigation of the O3′H and O4′H Hydroxyl Groups Rotations
Appl. Sci. 2020, 10(3), 1147; https://doi.org/10.3390/app10031147 - 08 Feb 2020
Abstract
The quercetin molecule is known to be an effective pharmaceutical compound of a plant origin. Its chemical structure represents two aromatic A and B rings linked through the C ring containing oxygen and five OH hydroxyl groups attached to the 3, 3′, 4′, [...] Read more.
The quercetin molecule is known to be an effective pharmaceutical compound of a plant origin. Its chemical structure represents two aromatic A and B rings linked through the C ring containing oxygen and five OH hydroxyl groups attached to the 3, 3′, 4′, 5, and 7 positions. In this study, a novel conformational mobility of the quercetin molecule was explored due to the turnings of the O3′H and O4′H hydroxyl groups, belonging to the B ring, around the exocyclic C-O bonds. It was established that the presence of only three degrees of freedom of the conformational mobility of the O3′H and O4′H hydroxyl groups is connected with their concerted behavior, which is controlled by the non-planar (in the case of the interconverting planar conformers) or locally non-planar (in other cases) TSsO3′H/O4′H transition states, in which O3′H and O4′H hydroxyl groups are oriented by the hydrogen atoms towards each other. We also explored the number of the physico-chemical and electron-topological characteristics of all intramolecular-specific contacts—hydrogen bonds and attractive van der Waals contacts at the conformers and also at the transition states. Long-terms perspectives for the investigations of the structural bases of the biological activity of this legendary molecule have been shortly described. Full article
(This article belongs to the Special Issue The Application of Quantum Mechanics in Reactivity of Molecules)
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Open AccessArticle
Probing the Structure of [NiFeSe] Hydrogenase with QM/MM Computations
Appl. Sci. 2020, 10(3), 781; https://doi.org/10.3390/app10030781 - 22 Jan 2020
Cited by 1
Abstract
The geometry and vibrational behavior of selenocysteine [NiFeSe] hydrogenase isolated from Desulfovibrio vulgaris Hildenborough have been investigated using a hybrid quantum mechanical (QM)/ molecular mechanical (MM) approach. Structural models have been built based on the three conformers identified in the recent crystal structure [...] Read more.
The geometry and vibrational behavior of selenocysteine [NiFeSe] hydrogenase isolated from Desulfovibrio vulgaris Hildenborough have been investigated using a hybrid quantum mechanical (QM)/ molecular mechanical (MM) approach. Structural models have been built based on the three conformers identified in the recent crystal structure resolved at 1.3 Å from X-ray crystallography. In the models, a diamagnetic Ni2+ atom was modeled in combination with both Fe2+ and Fe3+ to investigate the effect of iron oxidation on geometry and vibrational frequency of the nonproteic ligands, CO and CN-, coordinated to the Fe atom. Overall, the QM/MM optimized geometries are in good agreement with the experimentally resolved geometries. Analysis of computed vibrational frequencies, in comparison with experimental Fourier-transform infrared (FTIR) frequencies, suggests that a mixture of conformers as well as Fe2+ and Fe3+ oxidation states may be responsible for the acquired vibrational spectra. Full article
(This article belongs to the Special Issue The Application of Quantum Mechanics in Reactivity of Molecules)
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Open AccessArticle
Major Depressive Disorder and Oxidative Stress: In Silico Investigation of Fluoxetine Activity against ROS
Appl. Sci. 2019, 9(17), 3631; https://doi.org/10.3390/app9173631 - 03 Sep 2019
Cited by 3
Abstract
Major depressive disorder is a psychiatric disease having approximately a 20% lifetime prevalence in adults in the United States (U.S.), as reported by Hasin et al. in JAMA Psichiatry 2018 75, 336–346. Symptoms include low mood, anhedonia, decreased energy, alteration in appetite [...] Read more.
Major depressive disorder is a psychiatric disease having approximately a 20% lifetime prevalence in adults in the United States (U.S.), as reported by Hasin et al. in JAMA Psichiatry 2018 75, 336–346. Symptoms include low mood, anhedonia, decreased energy, alteration in appetite and weight, irritability, sleep disturbances, and cognitive deficits. Comorbidity is frequent, and patients show decreased social functioning and a high mortality rate. Environmental and genetic factors favor the development of depression, but the mechanisms by which stress negatively impacts on the brain are still not fully understood. Several recent works, mainly published during the last five years, aim at investigating the correlation between treatment with fluoxetine, a non-tricyclic antidepressant drug, and the amelioration of oxidative stress. In this work, the antioxidant activity of fluoxetine was investigated using a computational protocol based on the density functional theory approach. Particularly, the scavenging of five radicals (HO, HOO, CH3OO, CH2=CHOO, and CH3O) was considered, focusing on hydrogen atom transfer (HAT) and radical adduct formation (RAF) mechanisms. Thermodynamic as well as kinetic aspects are discussed, and, for completeness, two metabolites of fluoxetine and serotonin, whose extracellular concentration is enhanced by fluoxetine, are included in our analysis. Indeed, fluoxetine may act as a radical scavenger, and exhibits selectivity for HO and CH3O, but is inefficient toward peroxyl radicals. In contrast, the radical scavenging efficiency of serotonin, which has been demonstrated in vitro, is significant, and this supports the idea of an indirect antioxidant efficiency of fluoxetine. Full article
(This article belongs to the Special Issue The Application of Quantum Mechanics in Reactivity of Molecules)
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Open AccessArticle
Atomic-Scale Understanding of Structure and Properties of Complex Pyrophosphate Crystals by First-Principles Calculations
Appl. Sci. 2019, 9(5), 840; https://doi.org/10.3390/app9050840 - 27 Feb 2019
Abstract
The electronic structure and mechanical and optical properties of five pyrophosphate crystals with very complex structures are studied by first principles density functional theory calculations. The results show the complex interplay of the minor differences in specific local structures and compositions can result [...] Read more.
The electronic structure and mechanical and optical properties of five pyrophosphate crystals with very complex structures are studied by first principles density functional theory calculations. The results show the complex interplay of the minor differences in specific local structures and compositions can result in large differences in reactivity and interaction that are rare in other classes of inorganic crystals. These are discussed by dividing the pyrophosphate crystals into three structural units. H2P2O7 is the most important and dominating unit in pyrophosphates. The other two are the influential cationic group with metals and water molecules. The strongest P-O bond in P2O5 is the strongest bond for crystal cohesion, but O-H and N-H bonds also play an important part. Different type of bonding between O and H atoms such as O-H, hydrogen bonding, and bridging bonds are present. Metallic cations such as Mg, Zn, and Cu form octahedral bonding with O. The water molecule provides the unique H∙∙∙O bonds, and metallic elements can influence the structure and bonding to a certain extent. The two Cu-containing phosphates show the presence of narrow metallic bands near the valence band edge. All this complex bonding affects their physical properties, indicating that fundamental understanding remains an open question. Full article
(This article belongs to the Special Issue The Application of Quantum Mechanics in Reactivity of Molecules)
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Review

Jump to: Research

Open AccessReview
Structure, Properties, and Reactivity of Porphyrins on Surfaces and Nanostructures with Periodic DFT Calculations
Appl. Sci. 2020, 10(3), 740; https://doi.org/10.3390/app10030740 - 21 Jan 2020
Abstract
Porphyrins are fascinating molecules with applications spanning various scientific fields. In this review we present the use of periodic density functional theory (PDFT) calculations to study the structure, electronic properties, and reactivity of porphyrins on ordered two dimensional surfaces and in the formation [...] Read more.
Porphyrins are fascinating molecules with applications spanning various scientific fields. In this review we present the use of periodic density functional theory (PDFT) calculations to study the structure, electronic properties, and reactivity of porphyrins on ordered two dimensional surfaces and in the formation of nanostructures. The focus of the review is to describe the application of PDFT calculations for bridging the gaps in experimental studies on porphyrin nanostructures and self-assembly on 2D surfaces. A survey of different DFT functionals used to study the porphyrin-based system as well as their advantages and disadvantages in studying these systems is presented. Full article
(This article belongs to the Special Issue The Application of Quantum Mechanics in Reactivity of Molecules)
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Open AccessFeature PaperReview
Understanding Electronic Structure and Chemical Reactivity: Quantum-Information Perspective
Appl. Sci. 2019, 9(6), 1262; https://doi.org/10.3390/app9061262 - 26 Mar 2019
Cited by 4
Abstract
Several applications of quantum mechanics and information theory to chemical reactivity problems are presented with emphasis on equivalence of variational principles for the constrained minima of the system electronic energy and its kinetic energy component, which also determines the overall gradient information. Continuities [...] Read more.
Several applications of quantum mechanics and information theory to chemical reactivity problems are presented with emphasis on equivalence of variational principles for the constrained minima of the system electronic energy and its kinetic energy component, which also determines the overall gradient information. Continuities of molecular probability and current distributions, reflecting the modulus and phase components of molecular wavefunctions, respectively, are summarized. Resultant measures of the entropy/information descriptors of electronic states, combining the classical (probability) and nonclassical (phase/current) contributions, are introduced, and information production in quantum states is shown to be of a nonclassical origin. Importance of resultant information descriptors for distinguishing the bonded (entangled) and nonbonded (disentangled) states of reactants in acid(A)–base(B) systems is stressed and generalized entropy concepts are used to determine the phase equilibria in molecular systems. The grand-canonical principles for the minima of electronic energy and overall gradient information allow one to explore relations between energetic and information criteria of chemical reactivity in open molecules. The populational derivatives of electronic energy and resultant gradient information give identical predictions of electronic flows between reactants. The role of electronic kinetic energy (resultant gradient information) in chemical-bond formation is examined, the virial theorem implications for the Hammond postulate of reactivity theory are explored, and changes of the overall structure information in chemical processes are addressed. The frontier-electron basis of the hard (soft) acids and bases (HSAB) principle is reexamined and covalent/ionic characters of the intra- and inter-reactant communications in donor-acceptor systems are explored. The complementary A–B coordination is compared with its regional HSAB analog, and polarizational/relaxational flows in such reactive systems are explored. Full article
(This article belongs to the Special Issue The Application of Quantum Mechanics in Reactivity of Molecules)
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

1. Topic: QM/MM computations of r[NiFeSe] hydrogenase

2. abstract: The prediction of accurate reaction rate constants is very challenging
for theoretical chemistry, especially at the low temperature typical
of the interstellar medium, because the rates of reactions are
extremely sensitive to factors such as barrier height and quantum
tunnelling effects. Therefore, integrated methodologies based on
state-of-the-art quantum-chemical computations are required. The key
aspects of such methodologies are: (a) accurate sampling of the
reactive potential energy surface to locate stationary points (minima
and transition states); (b) very accurate evaluation of the energy and
other thermochemical properties of the stationary points; (c)
application of the semi-classical transition state theory combined
with second-order vibrational perturbation theory in conjunction with
master equation models. The methodology developed in our laboratories
is presented and its accuracy and reliability discussed in terms of
significant examples.

3.Title:Structure, Electronic Properties and Reactivity of  Porphyrins on Surfaces and Nanostructures Using Periodic DFT Calculations

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