Accurately Computing the Interacted Volume of Molecules over Their 3D Mesh Models

Area of Science:

• Computational chemistry
• Molecular modeling
• Chemical informatics

Background:

• Accurate calculation of molecular interacted volumes is crucial for predicting catalyst-substrate arrangements.
• Previous methods using 3D point clouds suffered from inaccuracies due to nonuniform density.
• A more robust method is needed for precise volume interaction calculations.

Purpose of the Study:

• To develop a more accurate and stable method for computing molecular interacted volumes.
• To address the limitations of previous methods caused by nonuniform molecular point cloud density.
• To enhance the prediction of rational arrangements of catalysts and substrates.

Main Methods:

• A two-step approach involving prematched mesh slicing of electrostatic potential isosurfaces.
• Layering 3D triangular mesh models to transform volume calculation into area intersection analysis.
• Subdividing polygonal edges for precise identification of intersecting parts within layers and incorporating bounding boxes for efficiency.

Main Results:

• The proposed method achieves high accuracy across different datasets, with an average relative error of 0.07%.
• This represents a significant improvement over the previous algorithm, which had an average relative error of 1.73%.
• The method demonstrates enhanced accuracy and stability in calculating molecular interacted volumes.

Conclusions:

• The novel two-step method significantly improves the accuracy and stability of molecular interacted volume calculations.
• This advancement provides a more reliable tool for predicting catalyst-substrate interactions and molecular arrangements.
• The refined computational approach overcomes previous limitations related to molecular point cloud density variations.