stereo-nmr

Drag-and-drop Gaussian GIAO log files to group conformers by stereoisomer and Boltzmann-average their NMR chemical shifts at a chosen temperature, with linked 2D and 3D atom highlighting.

A frontend-only React + Vite app, deployed to GitHub Pages.

What it does

1. Drop log files. The number at the start of each file name is the stereoisomer; files that share that number are conformers of the same stereoisomer (e.g. 1_elaeocarpine_c1.log, 1_elaeocarpine_c4.log).
2. From each log it extracts the per-atom isotropic shielding σ (the Isotropic = GIAO values), the 3D geometry (last Standard orientation block) and the final SCF energy.
3. Conformers are grouped by stereoisomer. For each stereoisomer the per-atom shieldings are Boltzmann-averaged using the SCF energies at the chosen temperature: wᵢ ∝ exp(−(Eᵢ − E_min) / kT).
4. Each stereoisomer shows a per-atom table (Boltzmann-averaged σ, and δ when you provide a reference), a 2D depiction (react-ocl, with the atom labels as custom labels) and an interactive 3D model (Mol*).
5. Hovering an atom in the table, the 2D depiction or the 3D model highlights that same atom in all three views.

Chemical shift vs shielding

The logs contain the isotropic shielding σ, which is what is shown by default. Enter a reference shielding for carbon and/or hydrogen (e.g. the value computed for TMS at the same level of theory) to convert to a chemical shift δ = σ_ref − σ.

Connectivity and the 2D depiction

Gaussian logs contain coordinates but no bond list. Bonds are perceived from the 3D geometry (covalent-radii distance test); approximate bond orders are assigned from bond lengths, capped by each atom's valence so aromatic rings come out as a clean Kekulé pattern. The resulting molecule is laid out in 2D by OpenChemLib (inventCoordinates) and rendered with custom atom labels. Atom order is preserved end-to-end, so atom i is the same atom in the table, the 2D depiction and the 3D viewer.

Example dataset

Click Load example to load the bundled elaeocarpine dataset (21 Gaussian 16 GIAO logs at HF/STO-3G: 4 candidate stereoisomers, 4–7 conformers each).

Development

npm install
npm run dev        # start the dev server
npm test           # vitest + coverage, type-check, eslint, prettier
npm run build      # production build into dist/
npm run preview    # preview the production build

Deployment

Pushing to main builds the app and publishes dist/ to GitHub Pages (.github/workflows/deploy-pages.yml). The Vite base is relative (./), so the site works under any project path (https://<org>.github.io/<repo>/). Enable Pages with the GitHub Actions source in the repository settings.

Tech stack

• React 19 + Vite + TypeScript
• openchemlib / react-ocl — 2D depiction
• Mol* — 3D model