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Enumeration Approach to Atom-to-Atom Mapping Accelerated by Ising Computing.

Mohammad Ali1,2, Yuta Mizuno1,3,4, Seiji Akiyama4,5

  • 1Graduate School of Chemical Sciences and Engineering, Hokkaido University, Kita 13, Nishi 8, Kita-ku, Sapporo 060-8628, Hokkaido, Japan.

Journal of Chemical Information and Modeling
|February 2, 2025
PubMed
Summary
This summary is machine-generated.

This study introduces a novel rule-free algorithm for atom-to-atom mapping (AAM) in chemical reactions. By utilizing Ising computing, it efficiently finds all optimal atom correspondences, overcoming limitations of traditional methods.

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Area of Science:

  • Chemoinformatics
  • Computational Chemistry
  • Chemical Informatics

Background:

  • Atom-to-atom mapping (AAM) is crucial for understanding chemical transformations.
  • Current automatic AAM tools struggle with complex reactions due to combinatorial challenges and reliance on reaction rules.
  • Accurate AAM is vital for various chemoinformatics applications.

Purpose of the Study:

  • To develop a rule-free AAM algorithm that accurately identifies atom correspondences.
  • To address the computational challenges of AAM for complex chemical reactions.
  • To improve the efficiency and accuracy of automatic AAM.

Main Methods:

  • Proposed a rule-free AAM algorithm enumerating all atom-to-atom correspondences.
  • Employed Ising computing to optimize the minimization of bond cleavages and formations.
  • Evaluated the algorithm's performance against conventional combinatorial optimization and heuristic-based AAM methods.

Main Results:

  • The Ising computing framework significantly reduced computation times for AAM.
  • The proposed algorithm successfully identified correct AAM solutions for all benchmark problems.
  • Conventional heuristic-based AAM algorithms failed on several problems, highlighting the limitations of rule-based approaches.

Conclusions:

  • Rule-free AAM using Ising computing is a feasible and efficient approach for complex chemical reactions.
  • Enumerating all optimal correspondences that minimize bond changes is critical for accurate AAM.
  • This method offers a significant advancement over existing AAM tools in chemoinformatics.