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Quantum Chemical Approaches for Investigating Reaction Mechanisms in Organic Chemistry
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Quantum Chemical Approaches for Investigating Reaction Mechanisms in Organic Chemistry

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Physical Chemistry and Chemical Physics".

Deadline for manuscript submissions: 20 September 2026 | Viewed by 2898

Special Issue Editor

Dr. Robert O'Reilly

E-Mail Website
Guest Editor
School of Science and Technology, University of New England, Armidale, NSW 2351, Australia
Interests: quantum mechanics; density functional theory; coupled cluster theory; biochemistry; organic chemistry; reaction mechanisms; free-radical

Special Issue Information

Dear Colleagues,

As you are aware, since the advent of quantum chemical calculations, it is now possible to study reaction mechanisms using such methods. Previously, this was challenging using experimental techniques, no less given that transition states were not ‘observable’, and only on some occasions were intermediates detectable. This Special Issue is therefore dedicated to how QM methods may be applied to studying the mechanisms of organic reactions. This is an inherently broad topic, and we indeed welcome diverse submissions. In this regard, we welcome submissions that make use of modern DFT functions, as well as higher-level CCSD(T) (or higher-level) methods (i.e., W1-W4), or composite Gn methods (e.g., G3-G4) for the computation of barrier heights of specific processes, or complete reaction mechanisms for reactions related to organic chemistry. I look forward to your submissions in this field.

Dr. Robert O'Reilly
Guest Editor

Manuscript Submission Information

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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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Keywords

  • organic chemistry
  • biochemistry
  • density functional theory
  • coupled cluster theory
  • free radicals
  • reaction mechanisms
  • transition states

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Published Papers (3 papers)

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Research

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29 pages, 8097 KB  
Article
Identification of GPI-Anchored Wall Transfer Protein 1 Modulators for Fungal Infections Through Generative AI and Physics-Based Approaches
by Ibrahim A. Alsarra, Rupesh Chikhale, Abdullah M. Al-Mohizea and Md Ataul Islam
Int. J. Mol. Sci. 2026, 27(11), 4767; https://doi.org/10.3390/ijms27114767 - 25 May 2026
Viewed by 310
Abstract
Glycosylphosphatidylinositol (GPI) anchored wall transfer protein 1 (GWT1), a fungal-specific inositol acyltransferase, catalyzes the palmitoylation of GlcN-PI in GPI-anchor biosynthesis, crucial for mannoprotein trafficking and attachment, which are vital for cell wall integrity, biofilm formation, and virulence. More than 60,000 AI-generated molecules produced [...] Read more.
Glycosylphosphatidylinositol (GPI) anchored wall transfer protein 1 (GWT1), a fungal-specific inositol acyltransferase, catalyzes the palmitoylation of GlcN-PI in GPI-anchor biosynthesis, crucial for mannoprotein trafficking and attachment, which are vital for cell wall integrity, biofilm formation, and virulence. More than 60,000 AI-generated molecules produced using REINVENT4 were screened using ADMET-AI and GNINA. DeepSA and PharmacoNet were used to select synthesizable and pharmacophorically rich molecules. The dynamic behaviour was explored using molecular dynamics (MD). Finally, molecular reactivity was assessed using density functional theory (DFT). After ADMET filtering, 6190 compounds were docked against GWT1, of which 315 showed better predicted binding energies than the co-crystal ligand. DeepSA identified 105 readily synthesizable candidates, and PharmacoNet retained 32 compounds with favourable pharmacophoric features, from which four final candidates (AF_M1, AF_M2, AF_M3, and AF_M4) were prioritized for further analysis. MD simulation suggested stable binding behavior towards GWT1. DFT analysis indicated favourable electronic properties, low HOMO-LUMO energy gaps, and stable optimized geometries. These molecules could serve as promising lead candidates and potential new therapeutic agents for invasive fungal infections, pending validation. Full article
(This article belongs to the Special Issue Quantum Chemical Approaches for Investigating Reaction Mechanisms in Organic Chemistry)
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16 pages, 2244 KB  
Article
Fine Structure Investigation and Laser Cooling Study of the CdBr Molecule
by Ali Mostafa, Israa Zeid, Nariman Abu El Kher, Nayla El-Kork and Mahmoud Korek
Int. J. Mol. Sci. 2026, 27(1), 184; https://doi.org/10.3390/ijms27010184 - 23 Dec 2025
Viewed by 693
Abstract
The ab initio calculations of the electronic structure of the low-lying electronic states of the CdBr molecule are characterized in the 2S+1Λ(+/−) and Ω(+/−) representations using the complete active-space self-consistent field (CASSCF) method, followed by the multireference configuration interaction (MRCI) [...] Read more.
The ab initio calculations of the electronic structure of the low-lying electronic states of the CdBr molecule are characterized in the 2S+1Λ(+/−) and Ω(+/−) representations using the complete active-space self-consistent field (CASSCF) method, followed by the multireference configuration interaction (MRCI) method with Davidson correction (+Q). The potential energy curves are investigated, and spectroscopic parameters (Te, Re, ωe, Be, αe, μe, and De) of the bound states are determined and analyzed. In addition, the rovibrational constants (Ev, Bv, Dv, Rmin, and Rmax) are reported for the investigated states with and without spin–orbit coupling. The electronic transition dipole moment curve (TDMC) is obtained for the C2Π1/2 − X2Σ+1/2 transition. Based on these data, Franck–Condon factors (FCFs), Einstein coefficient of spontaneous emission Aν’ν, radiative lifetime τ, vibrational branching ratios, and the associated slowing distance are evaluated. The results indicated that CdBr is a promising candidate for direct laser cooling, and a feasible cooling scheme employing four pumping and repumping lasers in the ultraviolet region with suitable experimentally accessible parameters is presented. These findings provide practical guidance for experimental spectroscopists exploring ultracold diatomic molecules and their applications. Full article
(This article belongs to the Special Issue Quantum Chemical Approaches for Investigating Reaction Mechanisms in Organic Chemistry)
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Review

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30 pages, 2887 KB  
Review
Simultaneous Multi-Ion Heavy Metal Sensing Using Pulse and Stripping Voltammetry at Functionalized Nanomaterial-Modified Glassy Carbon Electrodes
by Aidyn Abilkas, Nargiz Kazhkenova, Bakhytzhan Baptayev, Robert J. O’Reilly and Mannix P. Balanay
Int. J. Mol. Sci. 2026, 27(6), 2586; https://doi.org/10.3390/ijms27062586 - 11 Mar 2026
Viewed by 1105
Abstract
Glassy carbon electrodes (GCEs) have gained increased attention for the sensitive electrochemical detection of heavy metals due to their excellent chemical stability, wide potential window, and good electrical conductivity. These characteristics make GCEs an effective platform for sensor development. In particular, nanomaterial-modified GCEs [...] Read more.
Glassy carbon electrodes (GCEs) have gained increased attention for the sensitive electrochemical detection of heavy metals due to their excellent chemical stability, wide potential window, and good electrical conductivity. These characteristics make GCEs an effective platform for sensor development. In particular, nanomaterial-modified GCEs have emerged as a promising strategy, offering enhanced sensitivity, selectivity, and faster response compared to conventional analytical techniques. This review summarizes recent advances over the past five years in the use of GCEs modified with chemically synthesized nanoparticles for the simultaneous detection of multiple heavy metal ions, including cadmium, lead, mercury, and chromium. It also includes how quantum chemical methods have aided our understanding of these phenomena. Heavy metals pose significant environmental and public health risks, with well-documented neurological, cardiovascular, reproductive, and carcinogenic effects, highlighting the need for accurate and rapid monitoring methods. Regulatory limits established by organizations such as the World Health Organization and the Environmental Protection Agency further emphasize the demand for highly sensitive detection technologies. This review examines the fundamental properties of GCEs, common nanomaterial modification techniques, and their application in multi-ion detection systems. Key advantages such as cost-effectiveness, portability, and adaptability to diverse sample matrices are highlighted. Current challenges, including electrode fouling, selectivity, and matrix interference, are also addressed, along with future perspectives for improving GCE-based sensors for real-world environmental monitoring. Full article
(This article belongs to the Special Issue Quantum Chemical Approaches for Investigating Reaction Mechanisms in Organic Chemistry)
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