Terms and Definitions
Computational Chemistry and Cheminformatics Glossary
Definitions of abbreviations and technical terms used throughout this site, linked to their detailed chapters.
1. A–F
- AFIR
- Artificial Force Induced Reaction method for systematically exploring reaction-path candidates by applying artificial forces. Related chapter
- Basis set
- A set of known functions used to expand molecular orbitals; it controls both accuracy and cost. Related chapter
- Boltzmann weight
- A statistical population derived from conformer relative free energies and temperature. Related chapter
- Canonical SMILES
- A SMILES string canonicalized by a particular implementation; identity across implementations is not guaranteed. Related chapter
- Conformer
- A three-dimensional structure interconvertible mainly by bond rotation without changing connectivity. Related chapter
- Cube
- A file format storing atomic coordinates and scalar values on a regular three-dimensional grid. Related chapter
- DFT
- Density functional theory, which treats many-electron systems using electron density as the basic variable. Related chapter
- Dual descriptor
- A conceptual-DFT descriptor comparing local responses to electron addition and removal. Related chapter
- EDA
- Energy decomposition analysis that partitions an interaction energy into terms defined by a chosen reference scheme. Related chapter
- ESP
- Electrostatic potential generated by nuclei and electrons at a point in space; the evaluation surface must be specified. Related chapter
- ETKDG
- RDKit conformer generation that augments distance geometry with experimentally derived torsional preferences. Related chapter
- Fingerprint
- A bit or count vector encoding molecular substructures or local environments. Related chapter
- Fukui function
- A conceptual-DFT quantity describing the local density response to a change in electron number. Related chapter
2. G–M
- Gasteiger charge
- An empirical partial charge estimated iteratively from atom types and connectivity; it is not a quantum-chemical charge. Related chapter
- GRRM
- A program suite for automated reaction-route mapping, including ADDF and AFIR approaches. Related chapter
- IGM / IGMH
- Interaction-region analyses based on density-gradient cancellation; IGMH uses Hirshfeld partitioning. Related chapter
- InChIKey
- A fixed-length string derived from InChI; useful for lookup but not reversible to the original structure. Related chapter
- IRC
- The intrinsic reaction coordinate followed from a transition state toward reactants and products. Related chapter
- Isovalue
- The scalar value selected to draw an isosurface; surface extent and interpretation depend on it. Related chapter
- LASSO
- Regularized regression using an L1 penalty, capable of shrinking some coefficients exactly to zero. Related chapter
- MC-AFIR
- A multicomponent AFIR approach that explores association and reaction pathways between components. Related chapter
- MMFF
- The Merck Molecular Force Field, commonly used for initial optimization of organic conformers. Related chapter
- Molecular orbital
- An orbital represented as a one-electron function; plot colors normally indicate phase, not charge. Related chapter
3. N–S
- NCI
- Analysis of noncovalent interactions using low-density, low-reduced-gradient regions; it is not an interaction energy. Related chapter
- NCIplot
- A program for generating grids and visualization files for NCI analysis. Related chapter
- PCA
- Principal component analysis projects data onto orthogonal high-variance directions; preprocessing must be fit within validation folds. Related chapter
- RDG
- The dimensionless reduced density gradient derived from electron density and its gradient. Related chapter
- RMSD
- Root-mean-square deviation between two structures after defining atom correspondence and optimal alignment. Related chapter
- SAPT
- A perturbative decomposition of intermolecular interactions into electrostatics, exchange, induction, dispersion, and related terms. Related chapter
- SC-AFIR
- A single-component AFIR approach for exploring intramolecular rearrangement and dissociation pathways. Related chapter
- SCF
- An iterative procedure in which orbitals generated from a density produce a new density until self-consistency is reached. Related chapter
- SHAP
- An explanation method that allocates the difference between a prediction and a baseline among feature contributions; it is not causal evidence. Related chapter
- SMILES
- A line notation for atoms, bonds, branches, and rings; it normally does not encode a three-dimensional conformer. Related chapter
- Steric map
- A map projecting steric congestion in a defined coordinate system onto a two-dimensional plane. Related chapter
- Sterimol
- Substituent length L and minimum/maximum widths B1/B5 relative to a defined primary axis. Related chapter
4. T–Z and symbols
- Transition state
- A first-order saddle point on a potential-energy surface, normally checked by one imaginary frequency and pathway connectivity. Related chapter
- UFF
- The broadly element-covering Universal Force Field; applicability and charge state should be checked. Related chapter
- Voxel
- One volume element of a three-dimensional grid and a basic unit for field-based machine learning. Related chapter
- Wavefunction
- A function representing a quantum state; analysis files may store orbital coefficients, basis information, and related data. Related chapter
- %Vbur
- Percent buried volume within a defined sphere; it depends on the center, radius, and atomic-radius convention. Related chapter
- ΔΔG‡
- The activation-free-energy difference between competing pathways; conversion from ratios requires a fixed temperature and sign convention. Related chapter
Last reviewed: August 4, 2026