Mass Spectrometry

Mass Spectrometry Used to identify organic compounds mainly through molar mass and identification of major fragments. A mass spectrometer is often used as the “detector” for a gas chromatograph (GC-MS) A mixture is separated and a total ion chromatogram (TIC) obtained. A TIC is the GC-MS equivalent of a gas chromatogram. The MS then allows identification of the components without having to rely on a comparison of retention times.

Mass Spectrometers

Mass Spectrometry Analysis time once the GC has been set up (column chosen, gas flow set, oven program finalized) is about 20 minutes. Not too expensive Our benchtop model was $30K. Compounds that can be analyzed are those that can be analyzed on a GC: Low to moderate boiling liquids (and, of course, gases)

Mass Spectrometers analyze particles…cations!, not photons. Impact from a high-energy electron knocks an electron from the organic compound and creates the Molecular ion (aka parent ion) a cation with an unpaired electron M+• It has the m/z of the molecule, so the value of m/z in most cases is the value of the molar mass (provided z, the charge of the cation, is +1)

Mass Spectrometers analyze cations, not photons Impact from a high-energy electron also causes fragmentation. Base peak is the most intense m/z peak is the most stable fragment Other fragments form as well, some from complex rearrangements

Mass Spectrometers The MS detects the m/z of each fragment by directing the ionized particles through a magnetic quadrupole The trajectory of the ions in the magnetic field bends as a function of the mass of the particle and its charge:

Mass Spectrometers The magnetic quadrupole thus acts as a mass filter. For a given magnetic field strength, light particles are bent more and heavier particles less. By changing the magnetic field strength, m/z can be focused on the detector (an electron multiplier) in succession and yield a mass spectrum A plot of signal vs m/z

OCCC’s GC-MS Shimadzu GC GC-17A version 3 Restek Rtx-XLB 30 meter fused silica capillary column with 0.25 mm inner diameter and a 0.25μm coating (the liquid phase is low polarity…and proprietary) for a column volume of 1.5 mL Column operates from 30° - 340°C

OCCC’s GC-MS Shimadzu MS parameters GCMS-QP5000 quadruple mass filter requires an operating pressure of approximately 2 Pa quadruple mass filter electron multiplier detector turns on after 2 min to clear solvent set up for 2 scans of 35-300 m/z per second

Fragmentation Patterns - Benzene Ring Odd m/z suggests N may be present. Peaks at 51 and 77 are very typical of the benzene ring.

Fragmentation Patterns - the benzylic cation, the allylic cation Extraneous peaks happen.

Fragmentation Patterns - Amines

Fragmentation Patterns - alcohols Alcohols can fragment so easily that the M+ peak may be missing altogether.

Fragmentation Patterns - aldehydes and ketones

Fragmentation Patterns - halogens Chlorine has 3:1 ratio of 35Cl : 37Cl Look for peaks at 35 and 37 Look for a gap of 35. Look for M:M+2 ratio of 3:1. Bromine has 1:1 ratio of 79Br : 81Br Look for peaks at 79 and 81 Look for a gap of 79. Look for M:M+2 ratio of 1:1. Iodine Look for peak at 127. Look for a gap of 127.

Rule of Thirteen Once you have the molecular weight (MW)… Divide MW by 13 and express the result as an integer (n) and a remainder (r). If your compound is a hydrocarbon, its formula is approximated as CnHn+r. You may then find elements of unsaturation from the molecular formula.

Rule of Thirteen If you have hetero atoms in your compound, adjust the formula to accommodate: For O, add O and subtract CH4. For N, add N and subtract CH2. For Cl, add Cl and subtract either C2H11 or C3H-1. Again, calculate elements of unsaturation from the formula.

How to Analyze a Mass Spectrum Identify the molecular ion peak, if present. Note if the MW is odd. Mark the base peak and show the fragment which gives rise to it. Mark significant fragment peaks and identify the fragments giving rise to them. Mark peaks or gaps that indicate the halogens, Cl (M : M+2 peaks = 3:1), Br (M : M+2 peaks = 1:1), I (M or gap = 127). The mass of the compound with Br will be M+1.