The determination of the structure of an organic molecule begins with the analysis of the elements it contains and their proportion, which is usually done by combustion. Molecular mass determination, previously performed by cryoscopic descent, now uses the high-resolution mass spectrometry technique.

Knowledge of the percent composition and molecular mass allow us to establish the molecular formula of an organic compound. However, two fundamental steps are still missing, which are determining connectivity and spatial arrangement.
a) Connectivity refers to indicating the way in which the different atoms that form an organic molecule are joined. This level of description is done in the plane, without taking into account the spatial arrangement of the molecule.
Let's consider the molecular formula C 3 H 6 O 3 , let's see different forms of connectivity, which give rise to the so-called structural isomers.
All these molecules have the formula C 3 H 6 O 3 but the atoms are joined in a different way in each of them.

The different spatial arrangements that a molecule can adopt and that are interconverted at room temperature by rotation are called conformations.

conformational analysis 01

They are two of the infinite conformations that can be drawn from the ac. 2-hydroxypropanoic. At room temperature the molecule is continuously rotating through all possible conformations.

Now let's look at the two most characteristic conformations of ethane, the alternate and eclipsed conformations.

conformational analysis 02

Alternate conformation of ethane

Eclipsed conformation of ethane

A chiral molecule is one that is not superimposable with its mirror image. Symmetry causes molecules to lose their chirality. Thus, the presence of planes of symmetry, inversion centers or alternating axes give rise to achiral molecules.

a) Axis of symmetry (C n )

symmetry 01

Symmetry axis (C 2 )

Symmetry axis (C 3 )

An axis of symmetry of order m leaves the molecule in a configuration indistinguishable from the initial one when rotating 360/m degrees.

b) Plane of reflection ( s ): Divides the molecule into two equal parts. Every atom of the molecule that is on one side of the plane must have its mirror on the other side.

symmetry 02

Chirality is synonymous with asymmetry, chiral objects are characterized by the absence of symmetry, look at the hands.

The elements of asymmetry that lead to chiral molecules are: chiral centers, chirality axes, chirality planes, and helices.
a) Chiral or stereogenic center: it is an atom that unites four different groups, one of these four groups can be a lone pair.
asymmetry 01
Not only carbon can be the stereogenic center, but also nitrogen from amines or ammonium salts, oxygen in oxonium cations, phosphorus in phosphines......

The rules to give absolute configuration to a stereogenic center are the following:

1. Give priority to the groups that start from the stereogenic center by atomic number
2. In the case of isotopes, priority is given by atomic mass.
3. If the rotation, following the three highest priority groups with the fourth at the bottom, is clockwise, the stereogenic center is R.
4. If the rotation is counterclockwise, the stereogenic center is S.
Ammonium salts with four different substituents are chiral compounds, the notation for chiral nitrogen is given the same as for carbon.
stereogenic center 01

In molecules whose chirality element is an axis, we will give the notation R a / S a , (the subscript "a" refers to axial), by means of the Fischer projection method. The tetrahedron method can also be used.

chirality axis 01

1. For the molecule to have a chirality axis, it is necessary that the two groups on each side are different from each other. In this example the groups are different (-H and -COOH) and the molecule has a chirality axis.

2. We choose one side of the allene (I arbitrarily choose the left one) and begin to give priorities by atomic number to the substituents on that side. Then we move to the right side and give the "c,d" priorities to the groups on that side.
chirality axis 02

These are molecules that have a flat area (phenyl), with a bridge that joins their ends either on the top or bottom face.

chirality plane 01

1. We assign names to certain atoms as shown in the image. "z" is the first atom that is out of plane. Two chains start from x, to which we must give priority by atomic number.

chirality plane 02

2. We project the xy link, placing ourselves in the position of the arrow.

chirality plane 03

propellers 01

The repulsion between the rings prevents the molecule from being arranged in the plane. So one of the rings bends towards us and the other at the bottom. In one enantiomer the ring on the right is bent towards us and in the other to the bottom.

propellers 02

To distinguish both enantiomers, a turn is made from the ring that goes to the bottom to the one that comes towards us. If this turn is clockwise, the enantiomer is M, if the turn is in the opposite direction, the enantiomer is P.