The Elementary and Geometric Levels of Description

The description starts at an elementary level (the one-dimensional structure), where molecules are represented by their chemical formula. The structural information contained in the chemical formula is very limited (e.g., no information on two- and three-dimensional structure), and the single structural attribute one can accurately derive from it is the molecular weight.

The description continues with levels of progressively increasing complexity and richness. At the geometric levels of two-dimensional (2D) and three-dimensional (3D) description, molecules are still considered as abstract entities, i.e., geometrical objects

Table 1. A multi-level description of molecular structure and properties [1]

Conceptual levels of structural description

Corresponding structural attributes and

molecular properties

A) The elementary level

• Molecular weight

B) The geometric levels

• 2D Structure

• Atom connectivity; Z/E configuration

• 3D Structure

• Relative configuration; Absolute

configuration

C) The stereoelectronic levels

Attributes and properties of isolated

molecules:

• Bulk

• Molar volume, surface area

• Stereodynamic structure

• Flexibility, conformation; Prototropic

equilibria

• Stereoelectronic structure

• Ionization, electron distribution,

polarizability; Molecular electrostatic field

D) The level of intermolecular interactions

• Medium-influenced properties of level C

• Emergent properties:

melting point, boiling point

solvation and hydration

chromatographic properties

partitioning (lipophilicity)

colligative properties

E) Interactions with a biological environment

• Biological properties

consisting of atoms represented by their symbols and of bonds represented by lines. This is by far the most common way of representation, and it contains explicit information on such structural attributes as the geometry of the molecule and the adjacency or union of atoms, as well as much implicit chemical information which, however, becomes explicit only at higher levels of description. The two-dimensional description considers how atoms are connected, i.e., it defines the connectivity of atoms in the molecule (presence and nature of chemical bonds). It also explicates configuration (cis or trans, Z or E) in case of geometrical isomerism at double bonds. The three-dimensional description views molecules as rigid geometrical objects in space and explicates not only the nature and connectivity of atoms (2D-structure), but also the overall configuration of the molecule in the case of diastereomerism or enantio-merism.

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