Mathematical Framework to Identify Optimal Molecule Based on Virtual Ligand Strategy

Identifying molecular entities with desired properties from a vast pool of potential candidates is a fundamental challenge in organic chemistry. In particular, ligand engineering─designing optimal ligands for transition metal catalysis─has been extensively studied over the past few decades. To address this challenge, we previously proposed the virtual ligand (VL) approach, a computational method that introduces a mathematical model to approximate ligand molecules within quantum chemical calculations. This model is then optimized to identify the electronic and steric properties most suited for a given reaction. However, the interpretability of the resulting VL parameters remained elusive, limiting predictions to a qualitative level. In this study, we establish a mathematical framework that links real molecules to the VL parameters, thereby enabling rapid and quantitative prediction of optimal ligands. The prediction algorithm was validated across four different reactions, and its accuracy, limitations and potential improvements are discussed.

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Publication Details

Journal
Journal of Chemical Information and Modeling
Published
2025-06-13
DOI
https://doi.org/10.1021/acs.jcim.5c00815
Citations
2
Primary Topic
Computational Drug Discovery Methods
Type
article
Field-Weighted Citation Impact
3.01

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article

Mathematical Framework to Identify Optimal Molecule Based on Virtual Ligand Strategy

Satoshi Maeda, Wataru Matsuoka, Satoru Iwata, Kazuko Hirose et al.
2 citations
Journal of Chemical Information and Modeling
Computational Drug Discovery Methods
3.01
article

Mathematical Framework to Identify Optimal Molecule Based on Virtual Ligand Strategy

Satoshi Maeda, Wataru Matsuoka, Satoru Iwata, Kazuko Hirose, Taihei Oki, Ren Yamada
article en
2 citations

Abstract

Identifying molecular entities with desired properties from a vast pool of potential candidates is a fundamental challenge in organic chemistry. In particular, ligand engineering─designing optimal ligands for transition metal catalysis─has been extensively studied over the past few decades. To address this challenge, we previously proposed the virtual ligand (VL) approach, a computational method that introduces a mathematical model to approximate ligand molecules within quantum chemical calculations. This model is then optimized to identify the electronic and steric properties most suited for a given reaction. However, the interpretability of the resulting VL parameters remained elusive, limiting predictions to a qualitative level. In this study, we establish a mathematical framework that links real molecules to the VL parameters, thereby enabling rapid and quantitative prediction of optimal ligands. The prediction algorithm was validated across four different reactions, and its accuracy, limitations and potential improvements are discussed.

Journal of Chemical Information and ModelingVol. 65(13)
Hokkaido University (JP), The University of Tokyo (JP)
Ministry of Education, Culture, Sports, Science and Technology, Core Research for Evolutional Science and Technology, Exploratory Research for Advanced Technology
Openalex Percentile: Top 8%
Computational Drug Discovery Methods
3.01
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Mathematical Framework to Identify Optimal Molecule Based on Virtual Ligand Strategy — Satoshi Maeda, Wataru Matsuoka, et al. · Journal of Chemical Information and Modeling (2025) | TGRS Research Map | TGRS