Structure determination

MASS SPECTROMETRY Mass spectrometry is used to measure relative atomic masses of isotopes and relative molecular masses Vaporisation: sample turned into gas Ionisation: gas particles bombarded with high-energy electrons- electrons knocked off leaving positive ions Acceleration: positive ion accelerated by an electric field Deflection: ions deflected by an magnetic field- deflection depends on mass/charge ratio Detection: ions reach detector and a mass spectrum is produced particles lose an electron- free radical cation formed-[C2H5OH]+

MOLECULAR RELATIVE MOLECULAR MASS Some ions fragment- bonds break/ some remain intact and give a peak corresponding to thr relative molecular mass, Mr, of the compound Ionised molecules- molecular ions- peak furthest to the right corresponds to the molecular ion (highest mass) Mass spectrometry is the most important technique of measuring Mr

FRAGMENTATION Molecular ion breaks up one fragment will carry a positive charge and the other an unpaired electron- only charged fragment detected because uncharged fragment will not be deflected 1 Other peaks come from fragments of the molecule- useful when two compounds have the same relative molecular mass but the spectrum will be different as the fragments of the two molecules will be different Butane, shows the following main peaks: 2 Mr = 58 molecular ion, CH3CH2CH2CH3+ Mr = 43 CH3CH2CH2+, formed when CH3 is lost Mr = 29 CH3CH2+, formed when C2H5 is lost Any unchanged species are removed by the vacuum pump Methylpropanone, shows the following main peaks: 3 Mr = 58 molecular ion, CH3CH(CH3)CH3+ Mr = 43 CH3CHCH3+ formed when CH3 is lost It is not possible to get a peak of Mr = 29 from methylpropanone by breaking just one bond. Fragmentation is more likely to take place at weaker bonds The more stable the fragment that forms, the greater its abundance in the spectrum Stability of carbocations: tertiary > secondary >primary

Fragmentation of carbonyl compounds Typically fragment at the carbonyl group to give an alkyl radical and a stable RCO+ cation (acylium ion)- stable because the RCO+ ion has a positive charge localised on the carbon atom, the carbonyl group is polarised Cdelta+=Odelta- because oxygen is more electronegative than carbon: RCOR+ RCO+ + R

The abundant peak at m/z=43 suggests a CH3CO group in the parent molecule- can be seen in a propanone spectrum Isotope Peaks Some molecules containing isotopes will produce more than one molecular ion Example, butane, C4H10, will give a molecular ion at mass 58 in which all carbon atoms carbon-12, and one at 59 in which one of the carbons is carbon-13. Since 1% of carbon atoms are carbon-13, and there are four carbons, this peak will be 4% of the peak at mass 58. Chlorine has two isotopes (35Cl and 37Cl) in the abundance ratio 3:1. Peaks with intensity ratio 3:1 two m/z values apart in the spectrum suggest the presence of chlorine Bromine has two isotopes (79Br and 81Br), in the abundance ratio 1:1 two m/z values apart in the spectra suggest presence of bromine.

INFRA-RED SPECTROSCOPY Infra-red spectrometer is used to help identify particular groups of atoms- shines a beam of infra-red radiation through the sample and produces a graph of transmission against wavenumber. When we shine a beam of infra-red radiation (heat energy) through a sample absorbs energy and the bonds vibrate more. But any particular molecule can only absorb radiation that has the same frequency as the natural vibrational frequency of a bond. Finger print region: the area of IR spectrum below 1500cm-1 has many peaks, caused by the vibrations of the whole molecule- shape of this region is unique for any substance- used to identify it by matching its IR spectrum with that of a known sample- matching of spectra id done with a computer data base Identifying groups of atoms: functional groups produce peaks in different areas of the spectrum- frequencies of the peaks are called wave numbers (cm-1)

Infra-red spectra of alcohols IR spectra of alcohols show a peak caused by an O-H vibration between 3230cm-1 and 3550cm-1 stretching vibration- large range is caused by hydrogen bonding between alcohol molecules. Each vibrating hydrogen will be hydrogen bonded to a varying number of other alcohol molecules, which

will slow down the vibration. Therefore the O-H has a range of frequencies, depending on the number of other molecules being dragged along. Alcohols also show a narrower peak between 1000 and 1300cm-1 caused by a C-O stretching vibration. INFRA-RED SPECTRA OF COMPOUNDS CONTAINING THE C=O GROUP. Aldehydes, ketones, carboxylic acids, and esters are all carbonyl compounds It has a stretching frequency of 1700 cm-1

Infra-red spectra of ketones and aldehydes Peak produced by ketones and aldehydes is usually strong and sharp - Aldehydes: between 1740 and 1720 cm-1 - Ketones: between 1725 and 1700 cm-1 the IR spectrum of propanone shows a peak at around 1700 cm-1 due to C=O stretching vibration in the ketone

Infra-red spectra of carboxylic acids two peaks in the spectrum of ethanoic acid- one is at 3100 cm-1 due to a O-H stretch and the other is at 1700 cm-1 C=O stretch O-H peak is broadened due to hydrogen bonding

Infra-red spectra of esters Contain a carbonyl group and therefore show a strong C=O stretching vibration at 1750 cm-1 (may alter by 50 cm-1). Two C-O peaks present because there are two C-O bonds- the stretching frequency of each C-O bond is different, because the atoms around them are slightly different.

Identifying impurities IR spectra can be used to spot the presence of impurities- a caffeine sample showed that unwanted water was present, when compared to the IR spectrum of a pure sample of caffeine because an O-H stretching peak was seen which cannot appear with pure caffeine