chem-nmr-analysis

Deconvolve 1H NMR mixture spectra against reference spectra using Wasserstein optimal transport.

144|21|Updated Jan 8, 2026
One-click install
npx skills add https://github.com/learningmatter-mit/AtomisticSkills --skill chem-nmr-analysis
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: chem-nmr-analysis
Source: https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-nmr-analysis
Command: npx skills add https://github.com/learningmatter-mit/AtomisticSkills --skill chem-nmr-analysis

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires numpy, scipy, matplotlib, rdkit, requests, nmrsim, scikit-learn, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill helps quantify known components in an 1H NMR mixture by decomposing the mixture spectrum against reference spectra and summarizing both proportions and fit quality.

Core Features & Use Cases

  • Wasserstein deconvolution for mixture quantification: Estimate component proportions using optimal-transport (Wasserstein distance) matching to reference spectra.
  • Reaction product prediction support: Predict likely reaction products from reactant/reagent SMILES via ReactionT5, enabling creation of additional references for deconvolution.
  • Time-series kinetics analysis: Perform supervised deconvolution across multiple crude spectra time points and produce a kinetics table plus plots.
  • Spectral plotting utilities: Generate overlays for visual inspection of mixture vs references before/after deconvolution.

Quick Start

Use the chem-nmr-analysis skill to deconvolve your mixture spectrum file against reference component spectra and output proportions and Wasserstein distance as JSON.

Frequently Asked Questions about chem-nmr-analysis

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I quantify component mole fractions in a 1H NMR mixture spectrum?

Quantify component mole fractions in a 1H NMR mixture spectrum by deconvolving the mixture spectrum against known reference spectra using Wasserstein-distance optimal transport. Supply per-component proton counts to convert the optimal transport weights into accurate mole fractions.

How does Wasserstein distance deconvolution work for NMR spectral analysis?

Wasserstein distance deconvolution works for NMR spectral analysis by treating spectral intensity distributions as probability measures and using optimal transport to find the best mixture weights. This approach matches mixture spectra against reference components to estimate proportions and generate fit-quality metrics.

Can I predict reaction products from SMILES to use as NMR reference spectra?

Predict reaction products from reactant or reagent SMILES via ReactionT5 to generate hypothesized components. These predicted products can supplement your known reference spectra for Wasserstein deconvolution when analyzing crude reaction mixtures.

What is the best way to analyze reaction kinetics from time-series NMR spectra?

Analyze reaction kinetics from time-series NMR spectra by performing supervised deconvolution across multiple crude spectra time points. Apply Wasserstein fitting to each time point to produce a kinetics table and overlay plots for end-to-end reaction monitoring.

Do I need specific data formats for NMR mixture deconvolution?

Provide mixture and reference spectra as two-column ppm and intensity files for NMR mixture deconvolution. Optionally apply baseline correction to the input files and supply per-component proton counts to convert spectral proportions into mole fractions.

What are the limitations of using optimal transport for NMR spectral deconvolution?

Optimal transport for NMR spectral deconvolution requires known or hypothesized component identities and corresponding reference spectra. Fit quality depends on reference accuracy, and the method outputs machine-readable JSON with metrics to help evaluate deconvolution limitations and spectral matching performance.