20.1 - Determination of structure
20.1.1: State that the structure of a compound can be determined using information from a variety of spectroscopic and chemical techniques. Students should realize that information from only one technique is usually insufficient to determine or confirm a structure.
Determination of structure
Determination of structure (finding out what the structure of a molecule is) has been a quest of organic chemists since the very beginning. The problem is that the molecules cannot be 'seen' as such and indirect evidence for the structure must be gleaned by a variety of methods. The final 'proof' may be the synthesis of the molecule from simpler units producing a compound with identical characteristics to the unknown substance.
The first stage to find out is the relative molecular mass of the substance in question. Nowadays, this may be done accurately using a mass spectrometer. In the past it was necessary to find the percentage composition of each component element to find the empirical formula and then to find the molecular mass by one of several physical techniques.
Once the relative molecular mass and chemical formula are known, structural information may be obtained by both electronic and 'wet' chemical means.
Nuclear magnetic resonance
This tells us the number of hydrogen atoms in different environments within the molecule. As hydrogen is present in (almost) all organic compounds this technique is very useful. The pattern produced by the hydrogens is often split into finer structure that also gives information about the number of hydrogen adjacent to the absorbing atoms.
This shows characteristic absorptions due to specific bends and stretches of the bonds associated with certain functional groups such as the carbonyl group, the hydroxyl group etc.
May be useful to show the presence of unsaturation or conjugation in organic systems.
As stated above, a complete analysis is often the result of applying several analytical techniques some of which are described in more detail below.
20.1.2: Describe and explain how information from an infrared spectrum can be used to identify functional groups in a compound. Restrict this to using infrared spectra to show the presence of the functional groups: and to match the fingerprint region to a known spectrum.
Infra-red radiation has ust the correct frequency to interact with the bonds in molecules. These can absorb the radiation at specific wavelengths to change their vibrational states. As with all energy values at atomic and molecular level these are quantised, i.e. energy absorption is not continuous but occurs at frequencies corresponding to the difference in energy between two quantum states.
Each bond type has a different absorption frequency and a scan over a range of frequencies shows absorptions corresponding to the bonds present in the molecule. In reality, the patterns produced by IR spectra are complex and only a few bond types can be identified, such as carbonyl groups C=O, and hydroxyl (alcohol) groups O-H.
The fingerprint region
Use is made of the complexity of the spectrum as no two compounds have exactly the same series of absorptions. This means that a complex region of the spectrum, known as the fingerprint region, can be used to compare an nknown substance wth a database of known substances. If the unknown has a spectrum identical to a known spectrum then a positive identification has been made. The fingerprint region appears at the right hand side of the diagram below.
The lower 'x' axis has units of cm-1. This is known as the wavenumber, it is the reciprocal of the wavelength in cm. This unit of measurement is traditional for IR spectra and is used to produce convenient numbers. In the diagram a strong absorptin can be seen at about 3000 cm-1 corresponding to the bond between the benzene ring and a hydrogen atom
20.1.3: Describe and explain how information from a mass spectrum can be used to determine the structure of a compound. Restrict this to using mass spectra to determine the relative molecular mass of a compound and to identify simple fragments, for example: (Mr - 15)+ loss of CH3; (Mr - 29)+ loss of C2H5 or CHO; (Mr - 31)+ loss of CH3O; (Mr - 45)+ loss of COOH.
20.1.4: Describe and explain how information
from a 1H NMR spectrum can be used to determine the structure of a compound.
Restrict this to using NMR spectra to determine the number of different
environments in which hydrogen is found and the number of hydrogens in
each environment. Splitting patterns are not required