A GNN-Based QSPR Model for Surfactant Properties
Abstract
:1. Introduction
2. Materials and Methods
2.1. Dataset Curation
2.2. Architecture of Machine Learning Model
2.3. Additional Features and Descriptors by MD Simulations
2.4. Hyperparameter Setting
3. Results
3.1. Model Evaluation
3.2. Surfactant Parameter Space Exploration
3.2.1. Polyethylene Oxide (PEO) Surfactants
3.2.2. Anionic Surfactants
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Atom Features | Descriptions | Size |
---|---|---|
Atom type | Type of atom (e.g., C, N, O), by atomic number | 100 |
Number of bonds | Number of bonds the atom is involved in | 6 |
Formal charge | Integer electric charge assigned to atom | 5 |
Chirality | Unspecified, tetrahedral CW/CCw, or others | 4 |
Hybridization | sp, sp2, sp3, sp3d, or sp3d2 | 5 |
Number of hydrogens | Number of bonded hydrogen atoms | 5 |
Aromaticity | Whether this atom is part of an aromatic system | 1 |
Atomic mass | Mass of the atom, divided by 100 | 1 |
Partial charge 2 | Non-integer electric charge assigned by the OPLS force field | 1 |
2 | The distance parameter of the Lennard-Jones potential assigned by the OPLS force field | 1 |
2 | The potential well depth parameter of the Lennard-Jones potential assigned by the OPLS force field | 1 |
Bond Features | Descriptions | Size |
---|---|---|
Bond type | Single, double triple, or aromatic | 4 |
Conjugated | Whether the bond is conjugated | 1 |
In-ring | Whether the bond is part of a ring | 1 |
Stereo | None, any, E/Z, or cis/trans | 6 |
Additional Molecular Descriptors | Descriptions | Size |
---|---|---|
Surface area of tailgroups | Surface area of a fitted ellipsoid encapsulating tailgroups | 1 |
Surface area of headgroups | Surface area of a fitted ellipsoid encapsulating headgroups | 1 |
Hyperparameters | Values |
---|---|
Number of message-passing layers | 2, 3, 4 |
200, 300, 400 | |
Number of fully connected layers | 2, 3, 4 |
Dropout rate | 0, 0.1, 0.2 |
Set | Atom Feature Set | Additional Molecular Descriptors |
---|---|---|
1 | Default | None |
2 | None | |
3 | Default | Surface areas of tailgroup and headgroup |
4 | Surface areas of tailgroup and headgroup |
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Ham, S.; Wang, X.; Zhang, H.; Lattimer, B.; Qiao, R. A GNN-Based QSPR Model for Surfactant Properties. Colloids Interfaces 2024, 8, 63. https://doi.org/10.3390/colloids8060063
Ham S, Wang X, Zhang H, Lattimer B, Qiao R. A GNN-Based QSPR Model for Surfactant Properties. Colloids and Interfaces. 2024; 8(6):63. https://doi.org/10.3390/colloids8060063
Chicago/Turabian StyleHam, Seokgyun, Xin Wang, Hongwei Zhang, Brian Lattimer, and Rui Qiao. 2024. "A GNN-Based QSPR Model for Surfactant Properties" Colloids and Interfaces 8, no. 6: 63. https://doi.org/10.3390/colloids8060063
APA StyleHam, S., Wang, X., Zhang, H., Lattimer, B., & Qiao, R. (2024). A GNN-Based QSPR Model for Surfactant Properties. Colloids and Interfaces, 8(6), 63. https://doi.org/10.3390/colloids8060063