Organic Analysis Flashcards
What can organic analysis/identifying organic substances be used for ?
Modern instrumental methods
- such as mass spectrometry
- and infrared spectroscopy
have made the identification
of organic substances much simpler.
Mass spectrometry can identify chemical composition of a sample
based on mass:charge ratio.
— Can be used to:
• detecting banned drugs in sport
• monitor and track pollutants in the air or in water supplies
• detect toxins in food
• locate oil deposits by testing rock samples
• determine the extent of damage to human genes due to the environment
• identify the country of origin of diamonds.
What happens in Mass spectrometry of organic compounds
When an element sample of passes through a mass spectrometer,
- the spectrum produced consists of several lines.
- The lines are due to different isotopes of the element
When an organic compound passes through a mass spectrometer
- the spectrum produced also consists of several lines.
- In this case, lines are due to original molecule and fragments of molecule.
> The line with largest m/z ratio is known as the molecular ion.
> This line has been produced by a molecule wch lost one electron.
Eg. A simplified version of mass spectrum of pentan2one diagram 1
- The lines on spectrum are due to molecular ion
- and ions produced by fragments of molecule. The molecular ion is at 86.
What are The mass spectra of compounds containing chlorine like
There are two molecular ion peaks in mass spectra of compounds containing a single chlorine atom.
- because chlorine exists as two isotopes, 35Cl and 37Cl.
-
- The peak at m/z ratio 78 is due to molecular ion (CH3CH35ClCH3)+
- containing atom of 35Cl.
- The peak at m/z ratio 80 is due to molecular ion (CH3CH37CICH3)+
- containing an atom of 37Cl.
> > The ratio of the peaks is 3:1.
-This ratio reflects abundance of the chlorine isotopes; 35Cl:37Cl is 3:1.
diagram 2
..
Are three molecular ion peaks in mass spectrum of 2,2-dichloropropane, two chlorine atoms
- They correspond to
(CH3C35Cl35CICH3)+
(CH3C35Cl37CICH3)+ and
(CH3C37Cl37CICH3)+.
>
> The three peaks are in a ratio 9:6:1.
»_space; The ratio can be understood by working out probability of 35Cl or 37Cl being present in the molecule.
- Remember there is 3/4 chance of a chlorine atom being 35Cl
- and 1/4 chance of a chlorine atom being 37Cl.
- In a molecule containing two chlorine atoms the possible combinations are:
** DIAGRAM 3** - LEARN!
This gives a distinctive pattern in a mass spectrum.
A pattern of 3 molecular ions, M, M+2 and M+4, in a ratio of 9:6:1
is an indication molecule has 2 Cl atoms.
What are The mass spectra of compounds containing bromine like (2)
Bromine exists as two isotopes,
79Br and 81Br,
> an almost 1:1 ratio (50.5:49.5).
The mass spectrum of 2-bromopropane will show two molecular ions
- one at 122; (CH3CH79BrCH3)+
- and at 124; (CH3CH81BrCH3)+.
These molecular ion peaks will be in the ratio 1:1
reflecting the relative abundance of bromine isotopes.
Whats high resolution mass spectrometry (do questions on!)
Consider the three mass spectra (diagram 6)
> which are of three High resolution mass spectrometry
- different organic compounds pentane and structural isomers, butanone and butanal.
- Each spectrum has a molecular ion peak at a mass:charge ratio of 72.
..
High resolution mass spectrometry
> can help distinguish between these three compounds.
- It can measure relative atomic masses to 4 decimal places.
-
- A more accurate value of relative molecular mass of molecular ion can establish wch compound is pentane.
- The Ar of 12C is exactly 12.0000 by definition.
> Relative atomic masses of other atoms are measured relative to 12C isotope.
>
> Using these values (on diagram), relative molecular mass of pentane is 72.0939
- and the relative molecular mass of butanone and butanal is 72.0575.
In diagram 6
Spectrum A is pentane as m/z ratio of molecular ion
on high resolution mass spec is 72.0939.
What is Infrared spectroscopy (do questions!!)
Pairs of atoms joined by a covalent bond continually vibrate.
> The frequency of vibration is unique to atom combo of bond
> differs if bond is single/double/triple.
> A C-C single bond vibrates at a diff frequency to C-C double bond
> or an O-H bond.
These vibrations have a frequency in infrared region of EM spectrum.
— called the natural frequency of vibration of the bond.
..
When a beam of infrared radiation is shone onto an organic compound
- some energy is absorbed and amplitude of vibration of covalent bond increases.
- bond only absorbs radiation that has same freq as natural freq of bond.
-
- Each type of bond has a natural vibration freq
- and same bond surrounded by diff groups of atoms has a diff natural freq of vibration.
»_space; This knowledge enables chemists to identify groups of atoms in a molecule
»_space; and enviro. surrounding this group.
»_space;
Eg. analysis of an IR spectrum of a compound may indicate
A C=O group is present and will also indicate if it is part of a
-CHO group in an aldehyde, or part of a
-COOH group in a carboxylic acid.
All organic compounds absorb infrared radiation.
Bonds in molecules absorb infrared radiation at characteristic wavenumbers.
What are infrared spectra (the graph?)
The spectrum begins at top of graph
and consists of a series of dips,
> wch represent infrared frequency absorbed by particular bonds.
>These dips are called ‘peaks’.
> dips are troughs in other cases.
Another unusual aspect of an infrared spectrum is the scale.
- The x-axis scale of infrared spectrum is diff to right and left of 2000 cm-1.
- begins at 4000 cm-1 and ends at 500.
-
- An infrared spectrometer doesnt contain any glass or quartz
>as these absorb infrared radiation.
>
>All internal reflecting and refracting surfaces
>are from polished sodium chloride crystals.
The samples can easily be prepared.
The mass of sample required is very small; approximately 1 mg is needed.
How would we analyise infrared spectra
The functional group(s) of a molecule can be found by analysing infrared spectra
- in region between 4000 and 1500cm-1.
diagram 6
> shows IR spectra of ethanol, ethanoic acid and propanone.
> All the compounds
have C—H bonds,
two have OH groups,
two have C=O groups in molecule.
..
The C-H bond is in almost all organic compounds.
> A peak just under 3000 cm-1 is probably due to C—H bonds.
>
> Absorption of O-H bond varies slight, depending on compound sort it is in.
- The -OH bond in alcohol absorbs at higher wavenumber than in an acid.
- its easily recognised as produces a broad peak in an alcohol
- and a very broad peak in an acid.
The C=O produces a peak present in spectra for ethanoic acid and propanone.
- an absence of broad OH peak in spectrum of propanone.
- small absorbance at approx 2900 cm- is probably due to C-H bonds.
The fingerprint region in IR spectra
The area of spectrum below 1500 cm-1
> known as fingerprint region of spectra.
>
The absorptions are complex
- caused by varied and complicated vibrations of entire molecule.
- This part of spectrum is unique to the molecule.
..
- IR spectra of many known organic molecules have been recorded and are available in a database.
- To identify a molecule, the IR spectra is produced and compared to this database.
-
- The infrared spectra of ethanoic acid and butanoic acid are in diagram 7
> is an C=O group and a broad peak indicating OH in both
> These peaks indicate that both the compounds are carboxylic acids.
the infrared spectra of ethanoic acid and butanoic acid are compared
- The region between 1500 cm-1 and 4000 cm- 1 are very similar
- but the fingerprint region below 1500 cm-1 is unique to each compound.
Checking purity with IR spectra
Infrared spectra can be used to check the purity of a compound.
- When the infrared spectrum of a known compound is produced extra peaks can indicate that the compound is not pure.
How is greenhouse effect related to absorbing IR radiation
The greenhouse effect shows how the greenhouse gases,
> carbon dioxide, water and methane
absorb infrared radiation, leading to the greenhouse effect and global warming.
The bonds in these gases are very efficient at absorbing infrared radiation.
- Infrared spectra of carbon dioxide, methane and water have deep bands
- indicating their high efficiency in absorption of infrared radiation.
- When infrared radiation hits a molecule of these gases
- its absorbed and causes bonds to vibrate.
Oxygen and nitrogen, the other major gases in the atmosphere do not have this property.
> It is the absorption of infrared radiation by greenhouse gases that contributes to global warming.
diagram 8
Identification of functional groups by test-tube reactions (4)
Some simple chemical tests can be used to identify presence of functional groups
» most organic comidont mix with water
»_space; but short chain alcohols and carboxylic acids do
• Alkenes (C=C)
The reagent is bromine water
> solution goes orange to colourless if positive
• alcohols (OH)
Reagent is acidified potassium dichromate
• primary/secondary
> orange to green solution if positive
• tertiary
> orange solution remains orange
• aldehydes (C=O)
Tollens Reagent
> colourless solution to silver ppt / silver
mirror form on test tube sides if positive
Fehlings solution
> blue solution to orange/red ppt formed
if positive
• carboxylic acids (COOH)
solid sodium carbonate is reagent
> turns from white solid, to producing effervescence (CO2 tested w limewater)
