Editorial

2 pages, 193 KiB

Open AccessEditorial

Special Issue on “The Application of Quantum Mechanics in Reactivity of Molecules”

by Sérgio F. Sousa

Appl. Sci. 2021, 11(3), 1132; https://doi.org/10.3390/app11031132 - 26 Jan 2021

Viewed by 1164

Over the last few decades, the increase in computational resources, coupled with the popularity of competitive quantum mechanics alternatives (particularly DFT (Density Functional Theory methods)), has promoted the widespread penetration of quantum mechanics applications into a variety of fields targeting the reactivity of [...] Read more.

Over the last few decades, the increase in computational resources, coupled with the popularity of competitive quantum mechanics alternatives (particularly DFT (Density Functional Theory methods)), has promoted the widespread penetration of quantum mechanics applications into a variety of fields targeting the reactivity of molecules [...] Full article

(This article belongs to the Special Issue The Application of Quantum Mechanics in Reactivity of Molecules)

Research

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31 pages, 779 KiB

Open AccessFeature PaperArticle

Phase Equalization, Charge Transfer, Information Flows and Electron Communications in Donor–Acceptor Systems

by Roman F. Nalewajski

Appl. Sci. 2020, 10(10), 3615; https://doi.org/10.3390/app10103615 - 23 May 2020

Cited by 8 | Viewed by 1797

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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14 pages, 1628 KiB

Open AccessArticle

A General User-Friendly Tool for Kinetic Calculations of Multi-Step Reactions within the Virtual Multifrequency Spectrometer Project

by Surajit Nandi, Bernardo Ballotta, Sergio Rampino and Vincenzo Barone

Appl. Sci. 2020, 10(5), 1872; https://doi.org/10.3390/app10051872 - 09 Mar 2020

Cited by 7 | Viewed by 2981

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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22 pages, 7767 KiB

Open AccessArticle

A Never-Ending Conformational Story of the Quercetin Molecule: Quantum-Mechanical Investigation of the O3′H and O4′H Hydroxyl Groups Rotations

by Ol’ha O. Brovarets’ and Dmytro M. Hovorun

Appl. Sci. 2020, 10(3), 1147; https://doi.org/10.3390/app10031147 - 08 Feb 2020

Cited by 7 | Viewed by 2132

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) TSs^{O3′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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12 pages, 3345 KiB

Open AccessArticle

Probing the Structure of [NiFeSe] Hydrogenase with QM/MM Computations

by Samah Moubarak, N. Elghobashi-Meinhardt, Daria Tombolelli and Maria Andrea Mroginski

Appl. Sci. 2020, 10(3), 781; https://doi.org/10.3390/app10030781 - 22 Jan 2020

Cited by 3 | Viewed by 1948

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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15 pages, 3527 KiB

Open AccessArticle

Major Depressive Disorder and Oxidative Stress: In Silico Investigation of Fluoxetine Activity against ROS

by Cecilia Muraro, Marco Dalla Tiezza, Chiara Pavan, Giovanni Ribaudo, Giuseppe Zagotto and Laura Orian

Appl. Sci. 2019, 9(17), 3631; https://doi.org/10.3390/app9173631 - 03 Sep 2019

Cited by 30 | Viewed by 3529

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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Graphical abstract

16 pages, 2798 KiB

Open AccessArticle

Atomic-Scale Understanding of Structure and Properties of Complex Pyrophosphate Crystals by First-Principles Calculations

by Redouane Khaoulaf, Puja Adhikari, Mohamed Harcharras, Khalid Brouzi, Hamid Ez-Zahraouy and Wai-Yim Ching

Appl. Sci. 2019, 9(5), 840; https://doi.org/10.3390/app9050840 - 27 Feb 2019

Cited by 6 | Viewed by 2817

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

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26 pages, 7189 KiB

Open AccessReview

Structure, Properties, and Reactivity of Porphyrins on Surfaces and Nanostructures with Periodic DFT Calculations

by Bhaskar Chilukuri, Ursula Mazur and K. W. Hipps

Appl. Sci. 2020, 10(3), 740; https://doi.org/10.3390/app10030740 - 21 Jan 2020

Cited by 18 | Viewed by 7782

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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31 pages, 2290 KiB

Open AccessFeature PaperReview

Understanding Electronic Structure and Chemical Reactivity: Quantum-Information Perspective

by Roman F. Nalewajski

Appl. Sci. 2019, 9(6), 1262; https://doi.org/10.3390/app9061262 - 26 Mar 2019

Cited by 19 | Viewed by 3309

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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