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Transition State (TS) Finding Tutorial

This tutorial demonstrates how to use ChemRefine to locate and validate transition states (TS) using a stepwise pipeline that combines PES scans, optimizations, frequency analysis, and final single-point energy evaluation.

Overview

Transition states are critical for understanding chemical reactivity and kinetics.
ChemRefine automates TS exploration with the following workflow:

  1. PES Scan: Explore bond distances/angles to identify high-energy regions.
  2. TS Optimization (Top 5): Optimize the five highest-energy structures from the PES scan.
  3. Frequency Analysis: Confirm the presence of one imaginary mode.
  4. Imaginary Mode Displacement: Remove the mode and generate corrected geometries.
  5. Final SP Calculation: Compute high-level single-point energies on the corrected TS structure.

Prerequisites

  • Installed ChemRefine (see Installation Guide)
  • Access to an ORCA executable
  • Example input (ts_input.yaml) from this tutorial folder
  • Initial structure (step1.xyz)

Input Files

We start with an initial structure located in the templates folder:

## Orca Input Files

You can find the ORCA input files here

Interactive 3D Viewer

YAML Configuration

➡️ Examples/Tutorials/Transition-State/ts_input.yaml

Example content (excerpt):

template_dir: ./templates
scratch_dir: /scratch/ts_jobs
output_dir: ./outputs/ts
orca_executable: /mfs/io/groups/sterling/software-tools/orca/orca_6_1_0_avx2/orca

initial_xyz: ./templates/step1.xyz

steps:
  # Step 1: PES scan
  - step: 1
    operation: "PES"
    engine: "DFT"
    sample_type:
      method: "integer"
      parameters:
        num_structures: 20
    constraints:
      bonds: [(82-91), (0-79), (0-80), (0-82)]

  # Step 2: Optimize top 5 high-energy structures
  - step: 2
    operation: "OPT+SP"
    engine: "DFT"
    sample_type:
      method: "energy_window"
      parameters:
        energy: top5

  # Step 3: Frequency calculation
  - step: 3
    operation: "FREQ"
    engine: "DFT"

  # Step 4: Displace along imaginary mode
  - step: 4
    operation: "NORMAL_MODE_SAMPLING"
    engine: "DFT"
    parameters:
      mode: imaginary

  # Step 5: Final SP calculation on corrected TS
  - step: 5
    operation: "SP"
    engine: "DFT"

How to Run

Before running ChemRefine, ensure that:

  • The ChemRefine environment is activated
  • The ORCA executable is in your PATH
  • The template directory (./templates/) is set up
  • The input structure file (e.g., step1.xyz) is prepared

Option 1: Run from the Command Line

chemrefine ts_input.yaml --maxcores <N>

Here <N> is the maximum number of simultaneous jobs.

Option 2: Run with SLURM

On HPC systems with SLURM:

sbatch ./Examples/templates/chemrefine.slurm

➡️ Example ChemRefine SLURM script

Expected Outputs

  • PES scan geometries in outputs/ts/step1/
  • Top 5 optimized candidates in outputs/ts/step2/
  • Frequency analysis files in outputs/ts/step3/
  • Imaginary mode displacement results in outputs/ts/step4/
  • Final single-point energy in outputs/ts/step5/

Each directory contains .out logs, .xyz geometries, and summary files.

Notes & Tips

  • Increase the PES scan resolution for difficult reactions.
  • Ensure only one imaginary frequency is present for a valid TS.
  • Use NORMAL_MODE_SAMPLING to visualize imaginary modes.
  • Always double-check .xyz files to confirm correct TS geometry.

Identifying Good vs Bad Imaginary Modes

ChemRefine helps distinguish spurious imaginary modes (bad TS guesses) from true transition states.

  • ❌ Bad imaginary frequency:
    Bad Imaginary

  • ✅ Corrected good imaginary frequency:
    Good Imaginary