Conformation & topology

Conformation describes the spatial arrangement of a molecule’s atoms; topology describes connectivity and spatial entanglement that persist despite continuous deformation.

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Molecular geometry: The three-dimensional arrangement of atoms in a molecule, described by bond lengths, bond angles, and torsion angles. These geometric variables specify molecular conformations.
Conformational change: A change in a molecule’s spatial arrangement that does not require breaking its covalent bonds. It is the basic motion through which one conformation becomes another.
Protein folding: The process by which a protein chain adopts a functional three-dimensional structure. Folding converts a sequence of connected residues into a specific conformation.
Constitutional isomer: One of two or more compounds with the same molecular formula but different atom-to-atom connectivity. Changing connectivity creates a different molecular structure, unlike changing conformation alone.
Chemical bond: An attractive interaction that holds atoms together in a molecule or solid. Bond connectivity supplies the molecular skeleton whose spatial arrangement conformation describes.
Potential energy surface: A function assigning potential energy to each possible arrangement of a system’s atoms. Its minima and barriers determine which conformations are stable or accessible.
DNA supercoiling: The over- or underwinding of DNA relative to its relaxed helical form. Supercoiling is a direct consequence of DNA’s constrained topology.
Stereoisomer: One of two or more compounds with the same connectivity but different spatial arrangements of atoms. Some stereoisomers cannot interconvert through ordinary conformational motion.
Torsion angle: The angle between two planes defined by four sequentially bonded atoms. Rotation around bonds changes torsion angles and thereby alters conformation.
Molecular dynamics: A computational method that simulates atomic motion by numerically integrating equations of motion. Trajectories reveal conformational transitions and the behavior of entangled molecules.