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Quantum Chemical Calculations of Molecular Reaction Processes

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

Deadline for manuscript submissions: closed (30 April 2025) | Viewed by 4644

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Dr. Naoki Kishimoto

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Department of Chemistry, Graduate School of Science, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
Interests: computational chemistry; quantum chemical calculations
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Shiro Koseki

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Dear Colleagues,

Theoretical chemical calculations are becoming increasingly important in molecular science and are indispensable for elucidating complex chemical reaction processes and quantitatively predicting observations. The accuracy of quantum chemical calculations has been supported by developments in electronic state theory and the increasing speed of computers. In quantum chemical calculations for reactions, novel algorithms have been developed to reveal reaction pathways, and eventually artificial intelligence will be used to a great extent for molecular design.

In this Special Issue, we feature papers that use quantum chemical calculations to reveal the reaction processes of molecules. We then publish the latest results on using computers to understand the complex world of chemistry as an open access journal, making the potential of quantum chemical calculations widely known to the world.

Dr. Naoki Kishimoto
Prof. Dr. Shiro Koseki
Guest Editors

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Keywords

computational chemistry
electronic structure
MO theory
DFT calculation
potential energy surface
reaction process
ab initio molecular dynamics
molecular design

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Related Special Issue

Quantum Chemical Calculations of Molecular Reaction Processes, 2nd Edition in Molecules

Published Papers (11 papers)

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Research

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37 pages, 3196 KiB

Open AccessArticle

The Mechanism of Boron–Carbon Bond Formation in the DA Reaction of the Pyridine Adduct of Borabenzene with Acetylene: A Topological Analysis of the ELF Function and Catastrophe Theory

by Slawomir Berski

Molecules 2025, 30(11), 2357; https://doi.org/10.3390/molecules30112357 (registering DOI) - 28 May 2025

Abstract

The mechanism of the DA cycloaddition reaction between the pyridine adduct of borabenzene and acetylene has been investigated using topological analysis of the electron localization function (ELF) and catastrophe theory (bonding evolution theory, BET). The study focuses on the differences in the electronic structures of C-C and C-B bonds during their formation. Additionally, the influence of electron density functionals with different constructions (B3LYP, CAM-B3LYP, B2PLYP, M06, M062X, and M052X) on the BET results was examined. The reaction proceeds through ten distinct phases. The B-C bond forms first, followed by the C-C bond. Significant differences were observed in the behavior of the non-bonding basins V(C) and V(B) compared to the V(C), V(C) basins, which precede the formation of the bonding basins V(B,C) and V(C,C). The use of different functionals results in quantitative variations in the lengths and positions of the reaction phases—for example, relative to the transition state structure. A possible qualitative influence on the overall picture of the reaction mechanism is suggested by the results obtained using the CAM-B3LYP and B2PLYP functionals, particularly in phases VI and VII. Full article

(This article belongs to the Special Issue Quantum Chemical Calculations of Molecular Reaction Processes)

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14 pages, 3746 KiB

Open AccessArticle

Theoretical Insights into the Impact of Pyrrole and Imidazole Substituents on the BODIPY Chromophore

by Patrycja Piękoś, Paweł Lipkowski, Wim Dehaen, Robert Wieczorek and Aleksander Filarowski

Molecules 2025, 30(10), 2209; https://doi.org/10.3390/molecules30102209 - 18 May 2025

Viewed by 383

Abstract

This paper concerns the in silico studies of the influence of heterocyclic substituents as well as their protonated and deprotonated forms on the spectral characteristics of BODIPY (4,4-difluoro-4-bora-3a,4a-diaza-s-indacene) dyes. Computational studies were carried out in order to reveal the most effective method of modeling of the spectral features of fluorescent BODIPY dyes. To perform these studies, the pyrrole and imidazole derivatives of BODIPY dyes were selected, and their spectral features were investigated with DFT and TD-DFT calculations. The calculations showed that the deprotonation of the substituents leads to a bathochromic shift of the calculated absorption wavelength, while the protonation (imidazole derivative) brings about a hypsochromic shift with respect to the neutral form of the dye. The calculated spectral characteristics, considering the influence of the solvent polarity (PCM model), were correlated with the

E_{T}^{N}

solvatochromic parameter. These correlations show that the increase in the solvent polarity causes a hypsochromic shift of the calculated absorption and emission wavelengths, whereas the bathochromic shift of the wavelengths is observed for the protonated form. Full article

(This article belongs to the Special Issue Quantum Chemical Calculations of Molecular Reaction Processes)

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19 pages, 1713 KiB

Open AccessFeature PaperArticle

Quantum Chemical Studies on the Prototropic and Acid/Base Equilibria for 2-Aminopyrrole in Vacuo—Role of CH Tautomers in the Design of Strong Brønsted Imino N-Bases

by Ewa Daniela Raczyńska, Pierre-Charles Maria and Jean-François Gal

Molecules 2025, 30(10), 2112; https://doi.org/10.3390/molecules30102112 - 9 May 2025

Viewed by 248

Abstract

In the quest of the pivotal origin of the very strong gas-phase proton basicity for some iminopyrrole derivatives, proposed in the literature on the basis of quantum chemical calculations, the full tautomeric and acid/base equilibria were investigated in vacuo for 2-aminopyrrole exhibiting enamino–imino tautomerism. Thermochemistry of these processes investigated at the Density Functional Theory (DFT) level indicates a lower stability for the imino than for the enamino tautomers. However, the imino N atom in the imino forms displays an exceptionally high basicity, particularly in the minor and rare tautomers containing at least one tautomeric proton at the pyrrole C atom. This explains why derivatives of CH tautomers (being free of prototropy) display exceptionally high gas-phase proton basicity. As predicted by the Maksić group using quantum chemical methods, these derivatives can be considered as good organic imino N-superbase candidates. Unfortunately, some other structures of iminopyrrole derivatives (proposed by the same group) possess labile protons, and, thus, exhibit prototropy, resulting in the transformation into the more stable but less basic aminopyrrole derivatives under synthesis conditions or acid/base equilibria measurements. Full article

(This article belongs to the Special Issue Quantum Chemical Calculations of Molecular Reaction Processes)

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21 pages, 3486 KiB

Open AccessArticle

Intramolecular Versus Intermolecular Diels–Alder Reactions: Insights from Molecular Electron Density Theory

by Luis R. Domingo and Patricia Pérez

Molecules 2025, 30(9), 2052; https://doi.org/10.3390/molecules30092052 - 5 May 2025

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Abstract

The intramolecular Diels–Alder (IMDA) reactions of four substituted deca-1,3,9-trienes and one N-methyleneocta-5,7-dien-1-aminium with different electrophilic/nucleophilic activations have been studied within the Molecular Electron Density Theory (MEDT) and compared to their intermolecular processes. The topological analysis of the electron density and DFT-based reactivity indices reveal that substitution does not modify neither the electronic structure nor the reactivity of the reagents relative to those involved in the intermolecular processes. The analysis of the relative energies establishes that the accelerations found in the polar IMDA reactions follow the same trend as those found in the intermolecular processes. The geometries and the electronic structures of the five transition state structures involved in the IMDA reactions are highly similar to those found in the intermolecular processes. A relative interacting atomic energy (RIAE) analysis of Diels–Alder and IMDA reactions allows for the establishment of the substituent effects on the activation energies. Although the nucleophilic frameworks are destabilized, the electrophilic frameworks are further stabilized, resulting in a reduction in the activation energies. The present MEDT study demonstrates the remarkable electronic and energetic similarity between the intermolecular and intramolecular Diels–Alder reactions. Only the lower, unfavorable activation entropy associated with the latter renders it 10⁴ times faster than the former. Full article

(This article belongs to the Special Issue Quantum Chemical Calculations of Molecular Reaction Processes)

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14 pages, 1969 KiB

Open AccessFeature PaperArticle

Improving the Long-Range Intramolecular Proton Transfer—Further Molecular Design of the Successful Molecular Switch 8-(Benzo[d]thiazol-2-yl)quinolin-7-ol (HQBT)

by Daniela Nedeltcheva-Antonova and Liudmil Antonov

Molecules 2025, 30(9), 1935; https://doi.org/10.3390/molecules30091935 - 26 Apr 2025

Viewed by 312

Abstract

Previously, we have described a successful molecular switch (8-(benzo[d]thiazol-2-yl)quinolin-7-ol), working on the basis of long-range proton transfer. Bearing in mind that its switching efficiency in low-polarity aprotic solvents is not sufficient, in the current communication, we investigate in detail the effect of the substitution in the benzothiazole ring. By using the DFT approach, the ground-state stability of the tautomeric forms, involved in the switching process, is modeled with the aim of finding conditions where clean switching could be possible in variety of aprotic solvents. The results indicate that the substitution with electron-acceptor substituents could increase the switching efficiency, but the overall improvement depends on the positions and electronic effect of the particular substituent. Full article

(This article belongs to the Special Issue Quantum Chemical Calculations of Molecular Reaction Processes)

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22 pages, 4177 KiB

Open AccessArticle

Global Reaction Route Mapping of C₃H₂O: Isomerization Pathways, Dissociation Channels, and Bimolecular Reaction with a Water Molecule

by Dapeng Zhang and Naoki Kishimoto

Molecules 2025, 30(8), 1829; https://doi.org/10.3390/molecules30081829 - 18 Apr 2025

Viewed by 225

Abstract

A comprehensive theoretical investigation of the C₃H₂O potential energy surface (PES) was conducted, revealing 30 equilibrium structures (EQs), 128 transition state structures (TSs), and 35 direct dissociation channels (DCs), establishing a global reaction network comprising 101 isomerization pathways and dissociation channels. Particular focus was placed on the five most stable isomers, H₂CCCO (EQ3), OC(H)CCH (EQ7), H-c-CC(O)C-H (EQ0), HCC(H)CO (EQ1), and HO-c-CCC-H (EQ12), and their reactions with water molecules. Multicomponent artificial force-induced reaction (MC-AFIR) calculations were employed to study bimolecular collisions between H₂O and these stable isomers. The product distributions revealed isomer-specific reactivity patterns: EQ3 and EQ7 predominantly formed neutral species at high collision energies, EQ0 produced both ionic and neutral species, while EQ1 and EQ12 exhibited more accessible reaction pathways at lower collision energies with a propensity for spontaneous isomerization. Born–Oppenheimer Molecular Dynamics (BOMD) simulations complemented these findings, suggesting several viable products emerge from reactions with water molecules, including HCCC(OH)₂H (EQ7 + H₂O), OCCHCH₂OH (EQ1 + H₂O), and HO-c-CC(H)C(OH)-H (EQ12 + H₂O). This investigation elucidates the intrinsic relationships between isomers and their potential products, formed through biomolecular collisions with water molecules, establishing a fundamental framework for future conformational and reactivity studies of the C₃H₂O family. Full article

(This article belongs to the Special Issue Quantum Chemical Calculations of Molecular Reaction Processes)

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9 pages, 3329 KiB

Open AccessArticle

To Transfer or Not to Transfer an Electron: Anionic Metal Centers Reveal Dual Functionality for Polymerization Reactions

by Andrei Evdokimov and Evangelos Miliordos

Molecules 2025, 30(7), 1570; https://doi.org/10.3390/molecules30071570 - 31 Mar 2025

Viewed by 244

Abstract

Catalysts with anionic metal centers have recently been proposed to enhance the performance of various chemical processes. Here, we focus on the reactivity of

{Co (CO)}_{4}^{-}

for the polymerization of aziridine and carbon monoxide to form polypeptoids, motivated by [...] Read more.

Catalysts with anionic metal centers have recently been proposed to enhance the performance of various chemical processes. Here, we focus on the reactivity of

{Co (CO)}_{4}^{-}

for the polymerization of aziridine and carbon monoxide to form polypeptoids, motivated by earlier experimental studies. We used multi-reference and density functional theory methods to investigate possible reaction mechanisms and provide insights into the role of the negatively charged cobalt center. Two different reaction paths were identified. In the first path,

{Co}^{-}

acts as a nucleophile, donating an electron pair to the reaction substrate, while in the second path, it performs a single electron transfer to the substrate, initiating radical polymerization. The difference in the activation barriers for the two key steps is small and falls within the accuracy of our calculations. As suggested in the literature, solvent effects can play a primary role in determining the outcomes of such reactions. Future investigations will involve different metals or ligands and will investigate the effects of these two reaction paths on other chemical transformations. Full article

(This article belongs to the Special Issue Quantum Chemical Calculations of Molecular Reaction Processes)

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24 pages, 5269 KiB

Open AccessArticle

Hydrogenated Planar Aluminum Clusters: A Density Functional Theory Study

by Changhong Yao, Meijiao Wang and Lianzhen Cao

Molecules 2025, 30(6), 1389; https://doi.org/10.3390/molecules30061389 - 20 Mar 2025

Viewed by 322

Abstract

The low-lying energy structures of small planar aluminum clusters Al_n (n = 3–6, 8–10), hydrogenated small planar aluminum clusters Al_nH_m (n = 3–8, m = 1–2) and the lowest-energy structure of Al_nH_m (n = 6–10, m = 0–2) are determined by density functional theory (DFT) calculations. Many stable planar structures have been found; some are consistent with the reported ones, and some are new configurations. The preservation of planar cluster structures has been observed during the dissociative adsorption of H₂.Hydrogen is adsorbed at different positions on planar aluminum clusters. Dissociative adsorption configurations of the planar structure and lowest-energy structure experienced a decrease in hydrogen adsorption energy with an increase in cluster size. Among the clusters we calculated, Al₄H₁ and Al₄H₂ have the highest HOMO-LUMO gap, indicating that they may be more abundant than other clusters. The geometric structure and electronic properties of these clusters are also discussed. Full article

(This article belongs to the Special Issue Quantum Chemical Calculations of Molecular Reaction Processes)

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14 pages, 2768 KiB

Open AccessArticle

The Adsorption of Ru-Based Dyes on the TiO₂ Surface to Enhance the Photovoltaic Efficiency of Dye-Sensitized Solar Cell Devices

by Malgorzata Makowska-Janusik, Katarzyna Filipecka-Szymczyk, Daniel Pelczarski, Waldemar Stampor and Maciej Zalas

Molecules 2025, 30(6), 1312; https://doi.org/10.3390/molecules30061312 - 14 Mar 2025

Viewed by 444

Abstract

Adsorption of mononuclear tris(bipyridine) ruthenium(II) complexes and binuclear tris(bipyridine) ruthenium(II) complexes equipped with carboxyl groups (-COOH) on the (111) surface of TiO₂ crystal in anatase form was modeled using Monte Carlo simulations, applying the Universal force field. It was shown that the adsorption efficiency of the ruthenium-based dyes on the TiO₂ surface depends on the position of the anchoring -COOH group in the molecular structure. The increase in the number of possible anchor groups in the dyes increases their ability to deposit on the surface of semiconductors. The chemisorbed molecules, such as mononuclear tris(bipyridine) ruthenium(II) complexes with the -COOH group in para position (RuLp) and binuclear tris(bipyridine) ruthenium(II) complexes called B3 with two anchoring -COOH groups and phenyl in the spacer, interact with the adsorber and other neighboring dyes, changing their electron and optical properties. The obtained computational results help to explain the behavior of the dyes on the TiO₂ surface, giving impact on their DSSC applications. Full article

(This article belongs to the Special Issue Quantum Chemical Calculations of Molecular Reaction Processes)

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17 pages, 5267 KiB

Open AccessArticle

The Puzzle of the Regioselectivity and Molecular Mechanism of the (3+2) Cycloaddition Reaction Between E-2-(Trimethylsilyl)-1-Nitroethene and Arylonitrile N-Oxides: Molecular Electron Density Theory (MEDT) Quantumchemical Study

by Mikołaj Sadowski, Ewa Dresler and Radomir Jasiński

Molecules 2025, 30(4), 974; https://doi.org/10.3390/molecules30040974 - 19 Feb 2025

Viewed by 496

Abstract

The regioselectivity and molecular mechanism of the (3+2) cycloaddition reaction between E-2-(trimethylsilyl)-1-nitroethene and arylonitrile N-oxides were explored on the basis of the ωB97XD/6-311+G(d) (PCM) quantumchemical calculations. It was found that the earlier postulate regarding the regioselectivity of the cycloaddition stage should be undermined. Within our research, several aspects of the title reaction were also examined: interactions between reagents, electronic structures of alkenes and nitrile oxides, the nature of transition states, the influence of the polarity solvent on the reaction selectivity and mechanism, substituent effects, etc. The obtained results offer a general conclusion for all of the important aspects of some groups of cycloaddition processes. Full article

(This article belongs to the Special Issue Quantum Chemical Calculations of Molecular Reaction Processes)

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Review

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23 pages, 3152 KiB

Open AccessReview

Thermal and Photochemical Reactions of Organosilicon Compounds

by Masae Takahashi

Molecules 2025, 30(5), 1158; https://doi.org/10.3390/molecules30051158 - 4 Mar 2025

Viewed by 697

Abstract

This article provides a comprehensive review of quantum chemical computational studies on the thermal and photochemical reactions of organosilicon compounds, based on fundamental concepts such as initial complex formation, HOMO-LUMO interactions, and subjacent orbital interactions. Despite silicon’s position in group 14 of the periodic table, alongside carbon, its reactivity patterns exhibit significant deviations from those of carbon. This review delves into the reactivity behaviors of organosilicon compounds, particularly focusing on the highly coordinated nature of silicon. It is poised to serve as a valuable resource for chemists, offering insights into cutting-edge research and fostering further innovations in synthetic chemistry and also theoretical chemistry. Full article

(This article belongs to the Special Issue Quantum Chemical Calculations of Molecular Reaction Processes)

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