PFAS Quantum Chemistry Database

This repository contains curated quantum chemistry datasets for per- and polyfluoroalkyl substances (PFAS).
Two complementary datasets are provided:

• PFAS_BM – a benchmarking dataset used to evaluate quantum mechanical methods.
• PFAS_QM – a larger dataset generated using the automated workflow described below.

The datasets include bond dissociation energies (BDEs) and related electronic and thermodynamic properties across multiple PFAS classes, protonation states, and phases.

All energies in this repository are reported in Hartree unless otherwise noted.

---

Database Overview

1. Benchmark Database (PFAS_BM)

The benchmarking dataset contains gas-phase neutral/neutral radical and anion/anion radical PFAS species used in the study:

"A Comprehensive Benchmark Database of Per- and Polyfluoroalkyl Substance Properties from Quantum Mechanical Methods."

These structures were calculated across many quantum methods and used to evaluate accuracy for PFAS thermochemistry and electronic structure predictions.

Files:

Neutral_BM.csv

Anion_BM.csv

---

2. Validated PFAS Database (PFAS_QM)

The validated dataset contains PFAS structures and fragments generated using the automated fragmentation and conformer workflow shown below.

This dataset expands the chemical space beyond the benchmarking set and includes neutral, radical, and anionic species across gas and water A much larger datbase with more PFAS families and solvents (DMSO and 1-OCTANOL) is coming Summer 2026. These datapotins are generated using this pipeline:

Files:

PFAS_QM

Reported Properties

The database contains the following computed properties:

• Dipole moments (Debye)
• HOMO–LUMO energies
• Mulliken and Löwdin charges
• XYZ coordinates (Å)
• Vibrational frequencies
• Electron affinity (vertical and adiabatic) (Hartree)
• Ionization potential (vertical and adiabatic) (Hartree)
• Enthalpy corrections using the quasi-rigid-rotor-harmonic oscillator (quasi-RRHO) approximation
• Entropy (Hartree/K)
• Gibbs Free Energy (Hartree)

---

Notes on Thermodynamic Quantities

Electron Affinity and Ionization Potential

• In Neutral_BM and Anion_BM, adiabatic EA and IP were calculated using:

  • electronic energy
  • zero-point energy (ZPE)

• In all other datasets, adiabatic EA and IP are calculated using the full Gibbs free energy.

---

Entropy and Gibbs Free Energy

• In Neutral_BM and Anion_BM, entropy and Gibbs free energy values are taken directly from ORCA/Gaussian outputs.

• In all other datasets, entropy and Gibbs free energy are calculated using vibrational frequencies and the quasi-RRHO correction.

---

---

Usage

The Neutral_BM and Anion_BM files are designed to be used with the companion analysis script:

https://github.com/mmarciesky/PFAS_BDE_helper

This script provides utilities for:

• BDE analysis
• radical fragment matching
• PFAS property comparisons

---

Disclaimer

This is a research-grade database.

Extensive cleaning and validation steps were applied, including:

• imaginary frequency checks
• spin contamination flags
• conformer filtering

However, users should independently validate specific entries for critical applications.

---

Lab & Project Acknowledgments

This dataset and workflow were developed as part of a PhD project in the Ng Group at the University of Pittsburgh.

We acknowledge support from:

• National Institutes of Health (NIH)
  Grant: 5 R01 ES032717-04

• University of Pittsburgh Center for Research Computing and Data
  RRID: SCR_022735

This work used the H2P cluster, supported by:

NSF Award OAC-2117681

---

Citation

If this database or associated workflow is useful to your research, please cite: