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Molecules
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Theoretical Investigations of Organic Reactions: Mechanisms and Kinetics
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Theoretical Investigations of Organic Reactions: Mechanisms and Kinetics

A Special Issue of Molecules (ISSN 1420-3049) belonging to the section "Computational and Theoretical Chemistry".

Deadline for manuscript submissions: 30 September 2026 | Viewed by 1585

Editor

Dr. Svetlana R. Jeremić

E-Mail Website
Guest Editor
Department of Natural and Mathematical Science, State University of Novi Pazar, Novi Pazar, Serbia
Interests: theoretical organic chemistry; antioxidative activity; thermodynamic properties; kinetic properties; molecular modelling; DFT calculations; molecular docking
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The aim of the theoretical investigation of organic reaction mechanisms and kinetics is to achieve a detailed molecular-level understanding of how and at what rate organic reactions proceed. These investigations describe the sequence of elementary steps, from the breaking and formation of chemical bonds to the formation of intermediates, enabling the rationalization the reaction outcomes and prediction reactivity. This includes identifying thermodynamically acceptable and favourable reaction pathways, intermediates, transition states, and energy barriers using modern computational chemistry methods.

The scope of this Special Issue encompasses preferable quantum mechanical and molecular dynamical calculations in analyzing structure–reactivity relationships, predicting reactivity and selectivity, and rationalizing experimental conditions.

The integration of theoretical results and theoretical investigations of organic reaction mechanisms and kinetics with experimental data supports the design of more efficient reactions, catalysts, and sustainable synthetic strategies, as it provides fundamental insights relevant to organic synthesis, materials science, and pharmaceutical chemistry. Therefore, the results published in this Special Issue will make a significant contribution to the scientific community by elucidating the course of chemical reactions involving organic compounds, as well as by modelling optimal reaction conditions and predicting reaction outcomes.

Dr. Svetlana R. Jeremić
Guest Editor

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Keywords

  • organic reaction mechanisms
  • organic reaction kinetics
  • organic reaction thermodynamic
  • quantum mechanics
  • molecular dynamics
  • molecular docking

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Published Papers (3 papers)

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12 pages, 4197 KB  
Article
The Computational Study of the Mechanism of the Acid-Promoted Pyranoside-into-Furanoside Rearrangement
by Alexey G. Gerbst, Dmitry A. Argunov, Vadim B. Krylov and Nikolay E. Nifantiev
Molecules 2026, 31(18), 3145; https://doi.org/10.3390/molecules31183145 - 8 Sep 2026
Viewed by 150
Abstract
The pyranoside-into-furanoside (PIF) rearrangement is an uncommon but important process in carbohydrate chemistry. The quantum chemical investigation of the driving force of the recently discovered TfOH-catalyzed ring contraction revealed that it stemmed from the π–π interactions of the phenyl rings in [...] Read more.
The pyranoside-into-furanoside (PIF) rearrangement is an uncommon but important process in carbohydrate chemistry. The quantum chemical investigation of the driving force of the recently discovered TfOH-catalyzed ring contraction revealed that it stemmed from the π–π interactions of the phenyl rings in benzoyl-protecting groups. In this study, we focused on the kinetic aspects, which included preliminary 2-O-benzoyl group rotation followed by the protonation of the endo-cyclic O5 atom. Using a combination of DFT and DLPNO-CCSDT methods, we found that in some cases, DFT may not produce adequate energies at the rate-limiting stage of the pyranoside ring opening, presumably due to inadequate modeling of Van der Waals interactions. Predicted rate constants for the PIF rearrangement of the β-O-methyl and β-S-ethyl galactosides were in agreement with NMR kinetic experiments, as the latter reacts significantly slower. The estimated constant for the β-O-phenyl galactoside supports its inability to undergo ring contraction and suggests temperatures of over 400 K for such transformation. The proposed mechanism was additionally confirmed by substituting the triflic acid with the much weaker trifluoroacetic one, which led to a drastic decrease of the reaction rate both in computations and in the experiment. Full article
(This article belongs to the Special Issue Theoretical Investigations of Organic Reactions: Mechanisms and Kinetics)
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23 pages, 11179 KB  
Article
Comparative Adsorption of Phenol and p-Chlorophenol on a Chitosan–Cellobiose Dimer in an Aqueous Medium: A DFT Study of Hydrogen Bonding and Noncovalent Interactions
by Jose Alfonso Prieto Palomo, Juan Jose Carrascal and Joaquín Alejandro Hernández Fernández
Molecules 2026, 31(11), 1871; https://doi.org/10.3390/molecules31111871 - 29 May 2026
Viewed by 575
Abstract
A comparative study was carried out using density functional theory of the adsorption of phenol and p-chlorophenol on two molecular models of biopolymers in aqueous medium: a chitosan dimer and cellobiose. Twelve adsorbent–adsorbate complexes with three initial orientations per system were optimized, [...] Read more.
A comparative study was carried out using density functional theory of the adsorption of phenol and p-chlorophenol on two molecular models of biopolymers in aqueous medium: a chitosan dimer and cellobiose. Twelve adsorbent–adsorbate complexes with three initial orientations per system were optimized, and their structural, electronic, and non-covalent properties were analyzed using boundary orbitals, molecular electrostatic potential, NCI/RDG, and QTAIM. In all four systems, the most stable geometry corresponded to the anchoring of the contaminant hydroxyl group to an adsorbent hydroxyl group, identifying O–H···O as the guiding motif of molecular recognition. However, conformational selectivity was strongly dependent on the adsorbent and the aromatic substituent. For phenol, the alternative orientations were 2.7 and 21.2 kcal mol−1 in chitosan and 6.6 and 48.9 kcal mol−1 in cellobiose. For p-chlorophenol, chitosan showed a much more severe discrimination, with penalties of 43.6 and 46.44 kcal mol−1. In contrast, in cellobiose, the alternative orientations remained close to the minimum, with differences of 5.1 and 3.5 kcal mol−1. The effect of Cl was also reflected in the electron topology: PC increased from 3.2 × 10−2 to 6.34 × 10−2 a.u. in chitosan and from 3.2 × 10−2 to 4.2 × 10−2 a.u. in cellobiose, while |V|/G went from 3.6 to 7.5 in chitosan and from 3.00 to 3.1 in cellobiose. Overall, the results show that p-chlorophenol interacts more intensely and selectively with chitosan, whereas cellobiose favors a more flexible, less topologically differentiated adsorption. These results clarify how a para-chloro substituent reorganizes hydrogen-bond-driven adsorption on two biopolymer microenvironments with different functional heterogeneity. Full article
(This article belongs to the Special Issue Theoretical Investigations of Organic Reactions: Mechanisms and Kinetics)
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11 pages, 664 KB  
Brief Report
From Intermediate Epoxy Group to Stable Ether Bridge: Insights from DFT Study on Graphene Quantum Dots
by Dmitry Romanov, Anatoly Lavrentyev and Igor Ershov
Molecules 2026, 31(13), 2269; https://doi.org/10.3390/molecules31132269 - 29 Jun 2026
Cited by 1 | Viewed by 426
Abstract
This study investigates the mechanism of ether bridge formation on the edges of graphene quantum dots (GQDs) and evaluates its impact on their structural, electronic, and optical properties. Using density functional theory (DFT) coupled with Clar’s aromatic sextet rule, we analyzed different edge [...] Read more.
This study investigates the mechanism of ether bridge formation on the edges of graphene quantum dots (GQDs) and evaluates its impact on their structural, electronic, and optical properties. Using density functional theory (DFT) coupled with Clar’s aromatic sextet rule, we analyzed different edge functionalization sites on a model nanographene. The kinetic parameters evaluated via the Eyring–Polanyi equation demonstrate that the stability of functional groups is fundamentally governed by the retention or migration of aromatic sextets. While epoxidation at thermodynamically favorable edge sites that form stable epoxy intermediates exhibits high kinetic stability with substantial activation barriers, alternative configurations directly relax during geometry optimization to minimize aromaticity disruption. Moreover, highly metastable epoxy intermediates convert to ether bridges via nearly barrierless pathways at ambient temperature. Simplified time-dependent DFT (sTD-DFT) calculations show that oxygen functionalization narrows the energy gap, yielding a distinct bathochromic shift into the visible range. Ultimately, Clar’s rule is established as a predictive tool for ether bridge formation, enabling the rational design of GQDs with tailored stability and optical properties for bioimaging and optoelectronic applications. Full article
(This article belongs to the Special Issue Theoretical Investigations of Organic Reactions: Mechanisms and Kinetics)
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