1. Understanding mass spectroscopy

2. Mass spectroscopy is a very powerful analytical tool that can provide information on the molecular mass of a compound, the isotopic composition of its atoms, and aspects of its structure from the way it fragments. Extremely small samples (a few nanograms, 10 -9 g) can be analysed using MS, making it about 1000 times more sensitive than IR or NMR analysis. MS is now in very common use in analytical laboratories studying a wide variety of compounds. It is also an important tool for forensic sciences (as seen on CSI, Bones and other popular TV programmes). Mass spectroscopy

3. If an object is moving in a straight line and you apply a continuous sideways force it will move in a curve - deflected out of its original path by the sideways force. For a given sideways force, the amount of deflection depends on the mass of the object. The smaller the deflection, the greater the mass. If you know the size of the force and the speed of the object you can calculate the mass. sideways force How MS works

4. In a mass spectrometer an electron gun knocks electrons off molecules to create positively-charged ions. Powerful electron guns also break the molecule into fragments. The ions are accelerated, and are then deflected by a magnetic field. The amount of deflection is determined by the mass of the particle and its charge. The detector reports the number of particles collected with each charge/mass ratio.

5. 1Vaporisation: it is important that the atoms or the molecules of the substance being investigated are free to move, so if the sample is not a gas it must first be vaporised. 2Ionisation: the vaporised sample is ionised by knocking one or more electrons off to give positive ions. Once an electron is knocked off it is very difficult to knock more off, especially when the molecule is a small as the ones you will be working with. 3Acceleration: the ions are accelerated so that they all have the same kinetic energy. (A vacuum pump evacuates the machine so the ions have a ‘free’ run.) Steps in mass spectroscopy

6. 4Deflection: the ions are then deflected by the magnetic field according to their masses. The lighter they are, the more they are deflected. The more the ion is charged, the more it gets deflected. 5Detection: the beam of ions passing through the machine is detected electrically. The following simple mnemonic may help you remember these stages. VICTOR IS A DAFT DUCK

7. The molecular ion One of the most useful particles detected in MS is called the molecular ion, symbolised M +, or [M] +. It is a molecule of the substance under study, with a single electron knocked off to form a positive ion. The dot in the second symbol indicates the fact that the ion contains an unpaired electron – since its partner was knocked off during the ionisation process. The m/z value for M + gives the M r of the compound. The peak for the molecular ion should be the peak with the greatest m/z value, unless: there is a small peak to its right caused by the inclusion of a heavier isotope in some molecules the molecule fragments so easily that there are very few intact molecules present to give a peak for M +.

8. High resolution mass spectrometers measure m/z to sufficient accuracy to distinguish species with the same approximate mass. Ethanoic acid and 1-propanol both have M r = 60, but MS can distinguish between ethanoic acid (C 2 H 4 O 2 ) at 60.02112, and 1-propanol (C 3 H 8 O) at 60.05751. How does it work? If the computer attached to the MS is given the mass of every isotope to 4 decimal places or more, it can work out the combinations of atoms that could combine to give the M + mass obtained – although when the molar mass is high, the computer may have a small number of suggestions, rather than a single formula. The molecular formula

9. Molecular ion fragments occur due to covalent bonds breaking: [M] + → X + + Y [C 5 H 12 ] + → [CH 3 CH 2 CH 2 CH 2 ] + + CH 3 or[C 5 H 12 ] + → [CH 3 CH 2 CH 2 ] + + CH 2 CH 3 or … Here are the masses of some common fragments: 15 = CH 3 17 = OH 29 = CH 2 CH 3 or CHO 31 = OCH 3 35 = Cl Fragmentation

10. M + = 72 M + – CH 3 = 57 M + – CH 2 CH 3 = 43 [CH 2 CH 3 ] + = 29 This is the MS spectrum for pentane. Using our knowledge of fragmentation, we can identify some of the peaks.

11. You may be given a mass spectrum and asked to draw some conclusions about some of the peaks on it. If the spectrum includes the molecular ion, you will probably be expected to identify it. Fortunately, you will not be expected to identify every peak on the spectrum!

12. Isotopes are atoms of the same element with different atomic masses – such as 12 C and 13 C, 1 H and 2 H or 35 Cl and 37 Cl. If these isotopes were evenly distributed – so that each C atom was as likely to be 13 C as 12 C – then MS would be so confusing that not even a computer could be sure of the identify of the different peaks. Fortunately, most elements have one dominant isotope, with the other(s) so rare we can forget about them – such as the 0.015% of hydrogen atoms that are 2 H, and the 0.20% of oxygen atoms that are 18 O. The way to 'forget' them is to tell the computer not to display any peak that's less than 1% the height of the most abundant peak. MS and isotopic abundance

13. There are, however, a few elements with more than one isotope we can't ignore, including carbon, chlorine and bromine. Most carbon atoms are 12 C, but 1.10% are 13 C. This abundance is greater than our 1% threshold, so many of the MS spectra you encounter are likely to have some small peaks one mass unit above a larger peak, due to 13 C. The ratio 35 Cl : 37 Cl is 75.77 : 24.23 – roughly 3 : 1. Thus, any particle containing a Cl atom creates two peaks, the second 2 mass units higher than the first, and one third its height. The ratio 79 Br : 81 Br is 50.69 : 49.31 – roughly 1 : 1. Any particle containing a Br atom also creates two peaks, of equal height and two mass units apart.

14. 1-heptene 1-heptene's molecular ion is at 98, but we see a small peak at 99 due to 13 C. Peaks at 30, 58 and 71 may also be due to 13 C M + + 1 M+M+

15. 2-chloro-2-butene Mass of molecular ion: 90 Here we see the characteristic 3:1 peaks, 2 units apart that indicate particles containing 35 Cl and 37 Cl. Also notice the small peak at 91 due to 13 C. 35 Cl 37 Cl 13 C

16. 8-bromo-1-octene Mass of molecular ion: 190 This spectrum shows the twin peaks indicative of bromine. The peak for the molecular ion is so small it is below the 1% threshold for inclusion on this spectrum. 79 Br 81 Br