learningmatter-mit/AtomisticSkills

learningmatter-mit/AtomisticSkills

Skill Claude CodeCodex

Calculate homolytic and heterolytic bond dissociation energies (BDEs) for all single bonds in a molecule using MLIPs with RDKit fragmentation.

learningmatter-mit/AtomisticSkills

Skill Claude CodeCodex

Generate molecular conformers with RDKit ETKDG, relax with MLIPs, and rank by energy with Boltzmann weighting.

learningmatter-mit/AtomisticSkills

Skill Claude CodeCodex

Query multiple MOF databases (QMOF via MPContribs; ARC-MOF DB7/Majumdar et al. via Zenodo) and download CIF structures with optional element or identifier filters.

learningmatter-mit/AtomisticSkills

Skill Claude CodeCodex

Query the Quantum MOF (QMOF) database via Materials Project's MPContribs platform for DFT-computed properties (bandgap) and optimized crystal structures of Metal-Organic Frameworks.

learningmatter-mit/AtomisticSkills

Skill Claude CodeCodex

Search and download experimental InfraRed (IR), Mass spectra, and UV-Vis spectra data (JCAMP-DX format) for molecules.

learningmatter-mit/AtomisticSkills

Skill Claude CodeCodex

Write and run custom ORCA input files for advanced electronic structure methods or settings not available through the SCINE wrapper, including multi-reference methods, excited states, relativistic effects, advanced SCF, NMR/EPR, and more.

learningmatter-mit/AtomisticSkills

Skill Claude CodeCodex

Run DFT geometry optimization (minimization or TS search) on a molecular structure using ORCA via SCINE/ReaDuct wrapper.

learningmatter-mit/AtomisticSkills

Skill Claude CodeCodex

Run a DFT or Coupled Cluster single-point energy calculation (with optional gradients/Hessian) on a molecular structure with ORCA through SCINE wrapper.

learningmatter-mit/AtomisticSkills

Skill Claude CodeCodex

Dock small-molecule guests into a porous host material using the VOID library (Voronoi Clustering), generating multiple 3D conformers with RDKit and ranking generated complexes.

learningmatter-mit/AtomisticSkills

Skill Claude CodeCodex

Extract explicit safety warnings, GHS classifications, LD50 toxicity profiles, and acute oral toxicity triage from PubChem PUG VIEW.

learningmatter-mit/AtomisticSkills

Skill Claude CodeCodex

Verify non-periodic molecular TS connectivity with forward/reverse IRC using endpoint connectivity and RMSD checks.

learningmatter-mit/AtomisticSkills

Skill Claude CodeCodex

Predict LC-MS/MS (MS2, tandem mass spectra) from SMILES via ICEBERG, a two-stage deep neural network. Outputs predicted m/z vs intensity spectrum, fragment ion SMILES, and a spectrum plot.

learningmatter-mit/AtomisticSkills

Skill Claude CodeCodex

Calculate activation barrier using Nudged Elastic Band (NEB) method with MLIPs.

learningmatter-mit/AtomisticSkills

Skill Claude CodeCodex

Scripts for Wasserstein deconvolution of 1H NMR mixture spectra against reference spectra, reaction product prediction, time-series kinetics, and spectral plotting.

learningmatter-mit/AtomisticSkills

Skill Claude CodeCodex

Predict 1H NMR spectra from SMILES strings via NMRdb.org SPINUS neural network prediction and nmrsim quantum mechanical spin simulation.

learningmatter-mit/AtomisticSkills

Skill Claude CodeCodex

Generate transition state structures for chemical reactions using React-OT.

learningmatter-mit/AtomisticSkills

Skill Claude CodeCodex

Find structurally similar chemical compounds using PubChem's 2D fast similarity engine via the PUG-REST API.

learningmatter-mit/AtomisticSkills

Skill Claude CodeCodex

Set up and run molecular dynamics simulations of molecules in explicit solvent boxes using Packmol for box construction and MLIPs for dynamics.

learningmatter-mit/AtomisticSkills

Skill Claude CodeCodex

Calculates gas adsorption isotherms via BVT/GCMC Monte Carlo simulations in a porous framework using MLIP.

learningmatter-mit/AtomisticSkills

Skill Claude CodeCodex

Prepares supercells for porous frameworks based on minimum interplanar distance and relaxes them using standard MLIP relaxation tools.

learningmatter-mit/AtomisticSkills

Skill Claude CodeCodex

Calculates Henry coefficient and heat of adsorption for a gas in a porous framework using Widom insertion with any supported MLIP.

learningmatter-mit/AtomisticSkills

Skill Claude CodeCodex

Match an experimental spectrum (1H NMR, 13C NMR, IR) against predicted or database reference spectra for candidate ranking and structure confirmation. Supports local catalog lookup, public database fallback, and pluggable similarity metrics.

learningmatter-mit/AtomisticSkills

Skill Claude CodeCodex

Compute gas-phase thermodynamic quantities (H, S, G) and reaction thermochemistry (ΔH, ΔS, ΔG) using MLIPs with the ideal-gas/rigid-rotor/harmonic-oscillator approximation.

learningmatter-mit/AtomisticSkills

Skill Claude CodeCodex

Optimize non-periodic molecular TS guesses and verify first-order saddle point from vibrational modes.