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Autodesm

Autodesmotic reactions for strain energy evaluation

DOI

Source codes: Autodesmotic reactions for strain energy evaluation
Last modified: September 25, 2025
License: For academic and non-commercial use only
Author: Yang Wang (ORCID: 0000-0003-2540-2199; Email: yangwang@yzu.edu.cn)


Overview

This repository provides the datasets, MATLAB source codes, and demonstration scripts used in the study:

"Autodesmotic reactions for general strain energy evaluation in polycyclic aromatic nanocarbons."

The package includes:

  • Datasets used for training the models
  • MATLAB scripts for training models and applying them to new systems
  • Trained models for energy and bond length prediction
  • Benchmark test cases for carbon nanobelts (CNBs), carbon nanotubes (CNTs), helicenes, bowl-shaped PAHs, and fullerenes

All molecular geometries of polycyclic aromatic hydrocarbons (PAHs) and test systems were optimized at the B3LYP/6-31G(d) level, and all total energies were obtained from B3LYP/6-311G(d)//B3LYP/6-31G(d) single-point calculations.

All scripts have been tested and verified with MATLAB R2023.


Repository Structure

.
├── Datasets/                     # Molecular datasets
│   ├── Benzenoids_C48H24/        # 1,516 isomers of C48H24
│   │   ├── DATA_complete.dat     # Data for energy model training
│   │   └── AllData_BL_C48H24.mat # Data for bond length model training
│   └── Benzenoids_C6H6_C96H24/   # 2,275 PAHs from C6H6 to C96H24
│       ├── DATA_small.dat        # Data for energy model training
│       ├── DATA_medium.dat       # Data for energy model training
│       ├── DATA_larger.dat       # Data for energy model training
│       ├── DATA_big.dat          # Data for energy model training
│       ├── DATA_big88.dat        # Data for energy model training
│       └── AllData_BL.mat        # Data for bond length model training
│
├── Models_Train/                 # Model training scripts
│   ├── Energy_Models/
│   │   ├── Isomeric_C48H24/
│   │   │   └── model_EDFT_EHMO_CCBond_numHH.m
│   │   └── Heterogeneous/
│   │       └── model_EDFT_EHMO_CCBond_numHH.m
│   └── BondLength_Models/
│       ├── Isomeric_C48H24/
│       │   └── model_BL_fit.m
│       └── Heterogeneous/
│           └── model_BL_fit.m
│
└── Test_Cases/                   # Demonstration test cases
    ├── Fig3_Benchmark_CNBs_C48H24/
    │   ├── CNB_6_6_1.m
    │   ├── ... ... ...
    │   └── CNB_8_4_21.m
    ├── Fig4_Benchmark_Armchair_CNBs/
    │   └── armchair_CNBs.m
    ├── Fig5_CNBs_Helicenes_Bowls/
    │   ├── a_CNB_9_0_3_1.m
    │   ├── b_7circulene.m
    │   ├── ... ... ...
    │   └── d_carboncone.m
    ├── Fig6_CNTs/
    │   ├── a_cnt_5_5_2.m
    │   ├── a_cnt_5_5_21.m
    │   ├── ... ... ...
    │   └── b_cnt_12_6_1.m
    ├── Fig7_Fullerenes/
    │   ├── C60_2.m
    │   ├── ... ... ...
    │   └── C60_1812.m
    └── Vogtle_Belt/
        ├── vogtle_belt.m
        └── mobius_belt.m

Datasets

Isomeric Space of C48H24

  • DATA_complete.dat ASCII file with information for 1,516 planar benzenoid PAHs of C48H24:

    • Encoded name (BEC code)
    • Planarity
    • DFT total energy (in Hartree)
    • Simple HMO energy (in |beta|)
    • Atom counts (C, H)
    • H···H count and distances (in Angstrom)
    • C–C bond count and bond lengths (in Angstrom)
    • C–H bond count and bond lengths (in Angstrom)

    Each line corresponds to each PAH molecule.

  • AllData_BL_C48H24.mat MATLAB binary file containing bond-level variables for 90,960 C–C bonds:

    • bndLen: C–C bond lengths (in Angstrom)
    • bndOrd: Coulson bond orders (distance-dependent HMO)
    • bndTyp: Simple C–C bond types (CH–CH, CH–C, C–C)
    • bndTypExt: Atom-based bond types
    • bndTypRB: Ring-based bond types

Heterogeneous Space (C6H6 to C96H24)

  • Data files (in the same format as Benzenoids_C48H24/DATA_complete.dat):

    • DATA_small.dat (C6H6 – C34H20)
    • DATA_medium.dat (C36H18 – C56H24)
    • DATA_larger.dat (C56H24 – C82H24)
    • DATA_big.dat (C84H24 – C96H24)
    • DATA_big88.dat (C84H24, C88H26)

    A total of 2,275 planar benzenoid PAHs

  • AllData_BL.mat

    MATLAB binary file containing bond-level variables for 205,350 C–C bonds across the heterogeneous dataset. Format is identical to AllData_BL_C48H24.mat.


Model Training

Energy Models

  • Isomeric space of C48H24:

    Run model_EDFT_EHMO_CCBond_numHH.m in Energy_Models/Isomeric_C48H24/ to train the energy prediction model.

  • Heterogeneous space (C6H6–C96H24):

    Run model_EDFT_EHMO_CCBond_numHH.m in Energy_Models/Heterogeneous/.

Bond Length Models

  • Isomeric space of C48H24:

    Run model_BL_fit.m in BondLength_Models/Isomeric_C48H24/ to train the bond length prediction model.

  • Heterogeneous space (C6H6–C96H24):

    Run model_BL_fit.m in BondLength_Models/Heterogeneous/.


Test Cases

Benchmark calculations can be reproduced using the provided MATLAB scripts:

  • C48H24 CNBs (Fig. 3): Test_Cases/Fig3_Benchmark_CNBs_C48H24/

  • Armchair CNBs of varying size (Fig. 4): run armchair_CNBs.m

  • Unconventional CNBs, helicenes, and bowls (Fig. 5): Test_Cases/Fig5_CNBs_Helicenes_Bowls/

  • CNTs (Fig. 6): Test_Cases/Fig6_CNTs/

    Note: Only two representative lengths per CNT type are provided.

  • C60 fullerenes (Fig. 7): Test_Cases/Fig7_Fullerenes/

    Note: Selected representative isomers covering different NAPPs (0–16).

  • Vögtle belt and its Möbius form: Test_Cases/Vogtle_Belt/

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Autodesmotic reactions for strain energy evaluation

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