HCN Isomerization Tutorial

Date:

2026-03-14

1 Overview

HCN → HNC isomerization is the simplest NEB example (3 atoms). Use this to validate your installation.

2 Reaction

Linear hydrogen cyanide isomerizes to hydrogen isocyanide:

HCN (reactant) → [TS] → HNC (product)

Expected barrier: ~1.8 eV with PET-MAD-XS v1.5.0

3 Running the Example

cd eon_orchestrator

# Dry-run (validates workflow, no eOn needed)
pixi run validate

# Full calculation (requires eOn)
pixi run -e eon hcn

4 Expected Outputs

4.1 NEB Results

cat results/neb/hcn_isom/results.dat

Should show:

  • 18-20 images

  • Barrier around image 9-10 (climbing image)

  • Energy ~0.07-0.09 eV above reactant

4.2 Plots

  • results/plots/hcn_isom/1D_path.png - Energy profile

  • results/plots/hcn_isom/1D_index.png - Energy vs image index

5 IRA Alignment

For this simple linear isomerization, IRA provides minimal benefit. The real value is shown in more complex examples (SN2, Diels-Alder).

6 Next Steps

After validating with HCN:

  1. Try SN2 reaction (6 atoms, backside attack)

  2. Try Vinyl alcohol (8 atoms, H-transfer)

  3. Try Diels-Alder (16 atoms, ring closure)