In organic chemistry a number of experimental techniques are carried out to verify the chemical structure of a substance.

An empirical formula shows the simplest ratio of the elements in a molecule.

Elemental microanalysis is used to determine the masses of $C$, $H$, $O$, $S$ and $N$ in a sample of an organic compound in order to determine its empirical formula.

Elemental microanalysis can be determined from

• combustion product masses

  

  

• percentage product by mass

  

Mass spectrometry can be used to determine the accurate $GFM$ and structural features of an organic compound.

In mass spectrometry, a small sample of an organic compound is bombarded by high-energy electrons. This removes electrons from the organic molecule* generating positively charged molecular ions known as parent ions. These molecular ions then break into smaller positively charged ion fragments. These ion fragments are then accelerated by an electric field so they all have the same kinetic energy, after which they are separated as they are deflected by a magnetic field and how much they are deflected depends on their mass — once the ions are detected then the degree of deflection can be used to calculate their mass.

A mass spectrum is obtained showing a plot of the relative abundance of the ions detected against the mass-to-charge, $m/z$*, ratio.

→ *It is typical for one electron to be knocked off the organic molecule, so the charge on parent ions and fragments is $+1$ and the mass-to-charge ratio, $m/z=m/1$, represents the true value of the fragment’s mass. However, sometimes two electrons are knocked off, so the charge becomes $+2$ which means the mass-to-charge ratio is $m/2$, which forms a peak half the size of the regular peak. This can often explain a peak half the size of the $M+$ peak.

Molecular and fragment ions are written in the form $[molecular \space ion]^+$ and molecular ion equations are where a larger fragment is broken down into smaller ones or vice versa.

→ $[CH_3CH_2CH_2CH_2CH_3]^+$ → $[CH_3CH_2CH_2]^+$ + $[CH_2CH_3]^+$

The mass-to-charge ratio of the parent ion can be used to determine the $GFM$ of the molecular ion, and so a molecular formula can be determined using the empirical formula.

→ The peak which gives the $GFM$ of the molecular ion is known as the $M+$ peak.

→ At times, there is an $M+1$ in addition to the $M+$, and these peaks usually appear in the ratio $98:2$. This indicates that there is a $^{13}C$ isotope of carbon in the second molecular ion which gives rise to the $M+1$ peak; as the $^{13}C$ isotope exists is far less common than the $^{12}C$ isotope, this peak is far smaller than the $M+$ peak and will only appear when the $M+$ is sufficiently tall.

$M+1$ peak

The fragmentation data can be interpreted to gain structural information.

→ Sometimes there is an $M+$ and an $M+2$, in the ratio $3:1$. This indicates that there is a $Cl$ atom in the compound, as the isotopes $^{35}Cl$ and $^{37}Cl$ exist in nature in this ratio.