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Chemistry & Materials Science Glossary
This glossary provides definitions for common terms used in computational chemistry, materials science, and chemical data management.
Molecular Representation
SMILES
Simplified Molecular-Input Line-Entry System — a compact, ASCII-based notation for encoding molecular structures as text strings. Example: CC(=O)O represents acetic acid.
InChI
International Chemical Identifier — an IUPAC standard for uniquely identifying chemical substances using a layered text string. Unlike SMILES, InChI is canonical (one molecule = one InChI).
InChIKey
A fixed-length (27-character) hash of an InChI string, designed for database searching and indexing.
CAS Number
A unique numerical identifier assigned by the Chemical Abstracts Service to every described chemical substance. Example: 7732-18-5 (water).
Molecular Formula
A notation indicating the types and numbers of atoms in a molecule (e.g., C₆H₁₂O₆ for glucose).
Force Field
A mathematical model describing the potential energy of a molecular system as a function of atomic positions. Used in molecular dynamics and energy minimization.
Computational Chemistry
DFT (Density Functional Theory)
A quantum mechanical method that calculates electronic structure by modeling electron density rather than individual electron wave functions. Widely used for molecules and materials.
Ab Initio
Computational methods based on fundamental quantum mechanics without empirical parameters. More accurate but more expensive than semi-empirical methods.
Molecular Dynamics (MD)
A simulation method that computes the trajectory of atoms over time by numerically solving Newton's equations of motion.
Basis Set
A set of mathematical functions used to represent electron wave functions in quantum chemistry calculations. Larger basis sets are more accurate but more expensive. Examples: 6-31G*, cc-pVTZ.
Functional (DFT)
The mathematical approximation used in DFT to describe electron exchange and correlation. Examples: B3LYP, PBE, M06-2X.
Geometry Optimization
The process of finding the atomic arrangement that minimizes the total energy of a molecule or material.
Transition State
A first-order saddle point on the potential energy surface, representing the highest-energy configuration along a reaction pathway.
Potential Energy Surface (PES)
A mathematical surface describing the energy of a system as a function of its atomic coordinates.
Materials Science
Crystal Structure
The periodic arrangement of atoms in a crystalline solid, described by a unit cell and its symmetry.
Unit Cell
The smallest repeating unit of a crystal that, when translated in all three dimensions, reproduces the entire crystal structure.
Lattice Parameters
The lengths (a, b, c) and angles (α, β, γ) that define the shape and size of a unit cell.
Band Gap
The energy difference between the top of the valence band and the bottom of the conduction band in a material. Determines whether a material is a conductor, semiconductor, or insulator.
Phase Diagram
A graphical representation of the thermodynamic conditions (temperature, pressure, composition) under which different phases of a material exist.
Defect
An irregularity in the crystal lattice, such as a vacancy (missing atom), interstitial (extra atom), or substitutional impurity.
Spectroscopy
NMR (Nuclear Magnetic Resonance)
A spectroscopic technique that exploits the magnetic properties of atomic nuclei to determine molecular structure, dynamics, and environment.
Chemical Shift
The resonance frequency of a nucleus relative to a standard reference in NMR, expressed in parts per million (ppm). Reflects the electronic environment of the atom.
Mass Spectrometry (MS)
An analytical technique that measures the mass-to-charge ratio (m/z) of ions, used for molecular weight determination and structural elucidation.
IR Spectroscopy (Infrared)
A technique measuring the absorption of infrared light by molecular vibrations, used to identify functional groups.
Raman Spectroscopy
A technique based on inelastic scattering of light by molecular vibrations, complementary to IR spectroscopy.
X-ray Diffraction (XRD)
A technique that determines crystal structure by measuring the diffraction pattern produced when X-rays interact with a crystalline sample.
Data and File Formats
CIF (Crystallographic Information File)
The standard file format for crystallographic data, including unit cell parameters, symmetry, and atomic coordinates.
MOL / SDF
MDL Molfile and Structure-Data File — widely used formats for 2D and 3D molecular structures.
JCAMP-DX
A vendor-neutral text format for spectroscopic data exchange.
Trajectory File
A file containing atomic positions (and optionally velocities) at successive time steps of an MD simulation. Common formats: XTC, TRR, DCD.
mzML
An open XML-based format for mass spectrometry data, replacing proprietary vendor formats.
Cheminformatics
Virtual Screening
Computational evaluation of large compound libraries against a target (protein, material property) to identify promising candidates.
QSAR/QSPR
Quantitative Structure-Activity/Property Relationship — statistical models relating molecular structure to biological activity or physical properties.
Molecular Fingerprint
A binary or count vector encoding structural features of a molecule, used for similarity searching and machine learning.
Tanimoto Coefficient
A similarity metric between two molecular fingerprints, ranging from 0 (no overlap) to 1 (identical).
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