Deep Learning-Driven Molecular Generation and Electrochemical Property Prediction for Optimal Electrolyte Additive Design
Abstract
:1. Introduction
2. Materials and Methods
2.1. Electrolyte Additives Dataset
2.2. Model’s Architecture
- Architecture aligned with our requirements and objectives. The dataset described in the following Section 2.1 includes significant candidate molecules used in lithium-ion battery electrolytes. We aim to extract meaningful and valuable information from this high-quality dataset to explore new molecules that could serve as potential electrolyte additives. Additionally, we require accurate predictions of electrochemical parameters such as HOMO/LUMO, which are critical for electrolyte additives. If new materials can be discovered and their HOMO/LUMO values predicted without direct experimentation, lithium-ion battery researchers would be able to anticipate experimental results quickly and efficiently. The VAE-based model with its continuous latent space representation fits these requirements and objectives, enabling us to explore the desired chemical space effectively.
- Performance. Among the VAE-based 3D molecule generation models NPVAE demonstrates the best performance outperforming models such as ChemicalVAE, CG-VAE, JT-VAE, and HierVAE, with a 2D reconstruction accuracy of 0.813 [22,26,27,28]. Based on experimental results from the literature NPVAE was deemed the most suitable model for achieving our performance goals.
- Utilization of structural information. Deep learning models that handle large sets of molecules typically employ various molecular representation methods. While SMILES is a simple and widely used format, it has limitations in capturing full structural information [29]. The NPVAE model overcomes this by converting SMILES inputs into graph-based representations, incorporating structural information through the use of a Tree-LSTM model.
- Chirality handling. Chirality refers to the geometric property of a molecule where its mirror image cannot be superimposed on the original structure, which is crucial in many chemical applications including pharmaceuticals. The NPVAE model by utilizing 3D molecular structures can effectively incorporate chirality enabling more accurate modeling of stereochemical properties. In NPVAE, the model determines whether a molecule is chiral or not by incorporating chirality information from its ECFP.
3. Results
3.1. Dataset Analysis
3.2. Results and Experimental Setup
3.2.1. Reconstruction
3.2.2. Generation
3.2.3. Molecular Property Prediction
4. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
HOMO | Highest occupied molecular orbital |
LUMO | Lowest unoccupied molecular orbital |
DFT | Density Functional Theory |
SEI layer | Solid electrolyte interphase |
GNN | Graph neural network |
VAE | Variational Autoencoder |
Appendix A
Appendix A.1. Preprocessing
- Initial fragmentation: The molecular structure is represented as a graph , where V denotes atoms and E denotes bonds. Bonds that are not part of ring structures but connect ring atoms are identified and removed, breaking the structure into subgraphs .
- Frequency-based filtering: Among the fragmented substructures, those that do not contain ring structures and appear infrequently (below a set frequency threshold, ) are selected. These substructures become unique labels in the vocabulary, denoted as .
- Functional group decomposition: Further decomposition focuses on specific functional groups. For instance:
- -
- Amide groups: Substructures containing amide groups are identified, and bonds involving the amide C(=O)N are broken to create individual labels.
- -
- Carboxyl and ester bonds: Substructures with carboxyl or ester groups are similarly decomposed of separating bonds involving C(=O)O.
- -
- Aldehyde and ketone groups: Bonds within aldehyde or ketone groups C(=O) are also separated to generate labeled substructures.
- -
- Hydroxyl and ether bonds: Finally, bonds between oxygen and carbon in hydroxyl or ether groups are broken, adding further meaningful labels to the vocabulary.
Appendix A.2. NP-VAE Encoder Process
Appendix A.3. NP-VAE Decoder Process
- Root label prediction: Predicts a substructure label for the root node by applying fully connected layers to the latent variable z. This multi-class classification selects a substructure label from those generated during preprocessing. Specifically, transformations are applied to z through fully connected layers, with a softmax operation at the final layer to determine the most likely root label.
- Topological prediction: Determines whether a child node should be generated under the current node. Binary classification is performed to decide on generating a child node. If a child node is created, bond and label prediction steps follow. Otherwise, the process either terminates (at the root) or backtracks to the parent node for further structure generation.
- Bond prediction: Predicts the type of bond (single, double, or triple) between the current node’s substructure and the child node’s substructure. A ternary classification is applied through -layer fully connected transformations to .
- Label prediction: Predicts the substructure label for the newly generated child node. -layer fully connected layers are applied to for multi-class classification. The predicted substructure label is validated for chemical plausibility. If invalid, bond prediction attempts are adjusted until a valid connection is achieved.
- Latent variable update (z): Updates the latent variable to after label prediction or backtracking. is updated using a fully connected layer that integrates the feature vector , derived from Child-Sum Tree-LSTM. Node-specific features propagate to enrich feature representation.
- Conversion to compound structure: Constructs the compound structure from the generated substructure labels. The tree structure is converted to the final compound structure by linking substructure labels, with bonding information uniquely defining the compound.
- Chirality assignment: Assigns stereochemistry to ensure correct 3D structural representation. -layer fully connected transformations produce an ECFP value, and stereoisomers are generated. The final structure is chosen based on the smallest Euclidean distance between predicted and calculated ECFP.
Appendix B
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Dataset | Minimum (Min) | Maximum (Max) | Average (Avg) | Molecules |
---|---|---|---|---|
QM9 | 16 | 152 | 122 | 133,885 |
Polymer | 83 | 1768 | 766 | 17,124 |
Drug-and-Natural-Product | 3 | 8272 | 379 | 10,597 |
Electrolyte | 9 | 705 | 183 | 17,271 |
Metric | Value |
---|---|
PBValid | 0.995 |
Validity | 1.000 |
Novelty | 1.000 |
Frag Similarity | 0.445 |
Scaffold Similarity | 0.239 |
IntDiv | 0.869 |
SA Score | 0.4253 |
Model | Dataset | Test Molecules | Property | MAE (eV) |
---|---|---|---|---|
Unimol | Electrolyte | 1000 | HOMO | 0.22385 |
LUMO | 0.04176 | |||
*Generated | 110 | HOMO | 0.10706 | |
LUMO | 0.16052 | |||
NPVAE | Electrolyte | 1000 | HOMO | 0.02099 |
LUMO | 0.00158 | |||
*Generated | 1060 | HOMO | 0.04996 | |
LUMO | 0.06895 |
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Yoon, D.; Lee, J.; Lee, S. Deep Learning-Driven Molecular Generation and Electrochemical Property Prediction for Optimal Electrolyte Additive Design. Appl. Sci. 2025, 15, 3640. https://doi.org/10.3390/app15073640
Yoon D, Lee J, Lee S. Deep Learning-Driven Molecular Generation and Electrochemical Property Prediction for Optimal Electrolyte Additive Design. Applied Sciences. 2025; 15(7):3640. https://doi.org/10.3390/app15073640
Chicago/Turabian StyleYoon, Dongryun, Jaekyu Lee, and Sangyub Lee. 2025. "Deep Learning-Driven Molecular Generation and Electrochemical Property Prediction for Optimal Electrolyte Additive Design" Applied Sciences 15, no. 7: 3640. https://doi.org/10.3390/app15073640
APA StyleYoon, D., Lee, J., & Lee, S. (2025). Deep Learning-Driven Molecular Generation and Electrochemical Property Prediction for Optimal Electrolyte Additive Design. Applied Sciences, 15(7), 3640. https://doi.org/10.3390/app15073640