# A-level Applied Science/Synthesising Organic Compounds/Spectroscopy

There are three main spectroscopic techniques which can be used to identify organic molecules: infrared (IR), mass spectroscopy (MS) and nuclear magnetic resonance (NMR).
IR and NMR spectroscopy are based on observing the frequencies of electromagnetic radiation absorbed and emitted by molecules. MS is based on measuring the mass of the molecule and any fragments of the molecule which may be produced in the MS instrument.

# Mass Spectroscopy

A mass spectroscope measures the exact mass of ions. An organic sample can be introduced into a mass spectroscope and ionised. This also breaks some molecules into smaller fragments.
The resulting mass spectrum shows:
1) The heaviest ion is simply the ionised molecule itself. We can simply record its mass.
2) Other ions are fragments of the molecule and give information about its structure. Common fragments are:
| species | formula | mass |
| methyl | CH$_3$$^+$ | 15 |
| ethyl | C$_2$H$_5$$^+$ | 29 |
| phenyl | C$_6$H$_5$$^+$ | 77 |

# NMR Spectroscopy

Nuclear Magnetic Resonance (NMR) Spectroscopy is one of the most useful analytical techniques for determining the structure of an organic compound. There are two main types of NMR, $^1$H-NMR (Proton NMR) and $^{13}$C-NMR (Carbon NMR). At A-level we only need to know about $^1$H-NMR.
NMR is based on the fact that the nuclei of atoms have a quantised property called spin. When a magnetic field is applied to a $^1$H nucleus, the nucleus can align either with (spin +1/2) or against (spin -1/2) the applied magnetic field.
These two states have different potential energies and the energy difference depends on the strength of the magnetic field. The strength of the magnetic field about a nucleus, however, depends on the chemical environment around the nucleus. For example, the negatively charged electrons around and near the nucleus can shield the nucleus from the magnetic field, lowering the strength of the effective magnetic field felt by the nucleus. This, in turn, will lower the energy needed to transition between the +1/2 and -1/2 states. Therefore, the transition energy will be lower for nuclei attached to electron donating groups (such as alkyl groups) and higher for nuclei attached to electron withdrawing groups (such as a hydroxyl group).
In an NMR machine, the compound being analysed is placed in a strong magnetic field and irradiated with radio waves to cause all the $^1$H nuclei to occupy the higher energy -1/2 state. As the nuclei relax back to the +1/2 state, they release radio waves corresponding to the energy of the difference between the two spin states. The radio waves are recorded and analysed by computer to give an intensity versus frequency plot of the sample. This information can then be used to determine the structure of the compound.

# Infrared spectroscopy.

Absorbing infrared radiation makes covalent bonds vibrate. Different types of bond absorb different wavelengths of infrared:
Instead of wavelength, infrared spectroscopists record the wavenumber; the number of waves that fit into 1 cm. (This is easily converted to the energy of the wave.)
For some reason the spectra are recorded backwards (from 4000 to 500 cm$^{−1}$ is typical), often with a different scale below 1000 cm$^{−1}$ (to see the fingerprint region more clearly) and upside-down (% radiation transmitted is recorded instead of the absorbance of radiation).
The wavenumbers of the absorbed IR radiation are characteristic of many bonds, so IR spectroscopy can determine which functional groups are contained in the sample. For example, the carbonyl (C=O) bond will absorb at 1650–1760 cm$^{−1}$.

## Summary of absorptions of bonds in organic molecules

w:Infrared Spectroscopy Correlation Table
| Bond | Minimum wavenumber (cm$^{−1}$) | Maximum wavenumber (cm$^{−1}$) | Functional group (and other notes) |
| C-O | 1000 | 1300 | Alcohols and esters |
| N-H | 1580 | 1650 | Amine or amide |
| C=C | 1610 | 1680 | Alkenes |
| C=O | 1650 | 1760 | Aldehydes, ketones, acids, esters, amides |
| O-H | 2500 | 3300 | Carboxylic acids (very broad band) |
| C-H | 2850 | 3000 | Alkane |
| C-H | 3050 | 3150 | Alkene (Compare intensity to alkane for rough idea of relative number of H atoms involved.) |
| O-H | 3230 | 3550 | H-bonded in alcohols |
| N-H | 3300 | 3500 | Amine or amide |
| O-H | 3580 | 3670 | Free –OH in alcohols (only in samples diluted with non-polar solvent) |
Absorptions listed in cm$^{−1}$.

## Typical method

A beam of infra-red light is produced and split into two separate beams. One is passed through the sample, the other passed through a reference which is often the substance the sample is dissolved in. The beams are both reflected back towards a detector, however first they pass through a splitter which quickly alternates which of the two beams enters the detector. The two signals are then compared and a printout is obtained.
A reference is used for two reasons:
* This prevents fluctuations in the output of the source affecting the data
* This allows the effects of the solvent to be cancelled out (the reference is usually a pure form of the solvent the sample is in).

# References & notes

* ↑ Wikipedia article.
SDBS is a free online database of Spectral analysis including many IR, NMR and MS graphs.