The molecular structure of a substance is described by the combination of nuclei and electrons that comprise its constitute molecules. This includes the molecular geometry (essentially the arrangement, in space, of the equilibrium positions of the constituent atoms—in reality, these are in a state of constant vibration, at temperatures above absolute zero), the electronic properties of the bonds, and further molecular properties.
The determination of molecular structure uses a multitude of experimental methods, that include X-ray diffraction, electron diffraction, many kinds of optical spectroscopy, nuclear magnetic resonance, electron spin resonance, and mass spectrometry. The prediction and explanation of molecular structure uses quantum theory of valency and methods of molecular modeling.
The term "molecular structure" extends to multi-molecular complexes.
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“The syntactic component of a grammar must specify, for each sentence, a deep structure that determines its semantic interpretation and a surface structure that determines its phonetic interpretation.”
—Noam Chomsky (b. 1928)