Redox Reaction Tutorial

This tutorial demonstrates how to use ChemRefine to study redox processes, including electron transfer reactions, charge-state changes, and energy evaluation with both MLFF and DFT levels of theory.

Overview

Redox chemistry is central to catalysis, batteries, and energy materials.
ChemRefine automates redox workflows by allowing you to:

Prepare input geometries for different charge states.
Run optimizations at MLFF or DFT levels of theory.
Evaluate redox potentials by comparing total energies of oxidized and reduced species.
Apply solvation corrections if required.

Prerequisites

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

Input Files

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

📄 View input.yaml
📄 View Input XYZ

Orca Input Files

You can find the ORCA input files here

Interactive 3D Viewer

YAML Configuration

➡️ Examples/Tutorials/Redox/redox_input.yaml

Example content (excerpt):

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

charge: 0
multiplicity: 1

initial_xyz: ./templates/step1.xyz

steps:
  - step: 1
    operation: "GOAT"
    engine: "DFT"
    sample_type:
      method: "boltzmann"  
      parameters:
       weight: 95 

  - step: 2
    operation: "OPT+SP"
    engine: "DFT"
    sample_type:
      method: "energy_window"
      parameters:
        energy: 10      
        unit: kcal/mol

  - step: 3
    operation: "OPT+SP"
    engine: "MLFF"
    charge: -1 
    multiplicity: 2
    mlff:
      model_name: "uma-s-1"
      task_name: "omol"
      device: "cuda"
    sample_type:
      method: "integer"  
      parameters:
       num_structures: 0  

  - step: 4
    operation: "OPT+SP"
    engine: "MLFF"
    charge: 0
    multiplicity: 1
    mlff:
      model_name: "uma-s-1"
      task_name: "omol"
      device: "cuda"
    sample_type:
      method: "integer"  
      parameters:
       num_structures: 0  

  - step: 5
    operation: "OPT+SP"
    engine: "MLFF"
    charge: 1
    multiplicity: 2
    mlff:
      model_name: "uma-s-1"
      task_name: "omol"
      device: "cuda"
    sample_type:
      method: "integer"  
      parameters:
       num_structures: 0  

  - step: 6
    operation: "OPT+SP"
    engine: "DFT"
    charge: -1
    multiplicity: 2
    sample_type:
      method: "integer"
      parameters:
       num_structures: 0  

  -  step: 7
     operation: "OPT+SP"
     engine: "DFT"
     charge: 0
     multiplicity: 1
     sample_type:
      method: "integer"
      parameters:
       num_structures: 0  

  -  step: 8
     operation: "OPT+SP"
     engine: "DFT"
     charge: 1
     multiplicity: 2
     sample_type:
      method: "integer"
      parameters:
       num_structures: 0

This workflow optimizes the neutral, reduced (–1), and oxidized (+1) charge states.

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 redox_input.yaml --maxcores <N>

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

Option 2: Run with SLURM

On HPC systems with SLURM:

sbatch ./Examples/templates/chemrefine.slurm

➡️ Example ChemRefine SLURM script

Expected Outputs

Neutral optimization in outputs/redox/step1/
Reduced state in outputs/redox/step2/
Oxidized state in outputs/redox/step3/

Each directory contains .out logs, .xyz geometries, and total energy values.
These energies can be compared to compute redox potentials.

Notes & Tips

Modify charge and multiplicity values to match your redox states.
Use MLFF first for speed, then recheck with DFT.
Solvation can be included with an additional SOLVATOR step.
Always verify convergence in .out files.