Computational Chemistry and Chemical Data

Compute Molecules, Interpret Data

Two connected tracks cover the calculation of three-dimensional structures and electronic states, and the comparison and modeling of chemical structures as data.

Track A

Structure and Electronic-Structure Calculations

Prepare molecular structures, calculate energies and wavefunctions, explore reaction paths, and analyze three-dimensional fields.

StructurexTBQuantum chemistryPathsCubeReal space

Track B

Cheminformatics and Data Analysis

Standardize chemical structures, construct fingerprints and descriptors, and use statistical models to interpret chemical trends.

IdentitySearchFeaturesRegression / PCASHAP

Find a Topic

Search the chapter list

Filter the chapters below by software, method, or analysis term.

Track A

Structure and Electronic-Structure Calculations

Follow the sequence from molecular preparation to visualization. Shared theory is summarized in Electronic-Structure Theory.

  1. 01RDKit: 3D preparationSMILES, ETKDG, MMFF/UFF, RMSD
  2. 02xTBGFN methods, single points, optimization, Hessians
  3. 03GaussianSCF, optimization, frequencies, TS, IRC
  4. 04GRRMADDF, AFIR, SC-AFIR, MC-AFIR
  5. 05PySCFSCF/DFT, optimization, GPU4PySCF, Colab
  6. 06Psi4SAPT, Fukui functions, dual descriptor
  7. 07ORCAEDA-NOCV, LED, interaction energies
  8. 08Cube filesGrids, density, orbitals, electrostatic potential
  9. 09MultiwfnNCI, IGM, IGMH, IRI
  10. 10NCIplotRDG, promolecular density, cube, VMD
  11. 11py3DmolInteractive structures and isosurfaces

Track B

Cheminformatics and Data Analysis

Treat identity, search, feature matrices, statistical models, and steric descriptors as one reproducible workflow.

  1. B1RDKit: cheminformaticsInChIKey, fingerprints, Gasteiger charges, SMARTS
  2. B2NumPy, scikit-learn, SHAPMatrices, regularized regression, PCA, interpretation
  3. B3Steric descriptors and 3D fieldsSterimol, %Vbur, steric maps, selectivity

Connection

Connecting the Two Tracks

StageStructure and electronic stateData analysis
DefinitionConformer, charge, spin, theory levelStandardization, target, units, split
RepresentationCoordinates, wavefunction, density, cubeDescriptors, fingerprints, fields, matrices
AnalysisEnergy, paths, real-space functionsRegularized regression, PCA, SHAP
InterpretationInteractions and electronic-state changesStatistical relationships with selectivity
Unit of reproducibility

Save not only structures and calculation settings, but also structure-standardization rules, feature definitions, data splits, and preprocessing.

Concepts and Reference

Read across individual methods

These pages connect research design, descriptors, and reproducibility independently of a particular software package.

Reaction selectivityProduct ratios, ΔΔG‡, conformer ensembles, and statistical modelsElectronic and steric descriptorsDensity, ESP, Fukui functions, NCI/IGMH, and SterimolReproducible computationSettings, environments, data splits, and release checksGlossaryComputational chemistry, cheminformatics, and machine learning