Mass Spectrometry

Spectroscopy vs. spectrometry

• Spectroscopy traditionally involves the absorption of some type of energy leading to an “excited state” that is subsequently emitted - This returns the molecule to the initial state non-destructively.

• Energy of excitation is just enough to promote a ground state to an excited state ... no more, no less because it is quantized

• Typical spectroscopy examples: UV-vis, fluorescence, IR, NMR

• Versus typically spectrometry destructive techniques (mass spec) or those that involve the scattering of radiation (X-ray crystallography)

Mass Spectrometry (MS)

THE MAIN USE OF MS IN ORG CHEM IS:

• DETERMINE THE MOLECULAR MASS OFORGANIC COMPOUNDS

• DETERMINE THE MOLECULAR FORMULA OF ORGANIC COMPOUNDS

Allows sequencing of proteins to determine their structures on a virtually single-cell scale

Basics of mass spectrometry

• Using a mass spectrometer, we will ionize an analyte and then Detect it (the details of this will not be covered here).

• In one typical example, the molecule is bombarded with high energy Electrons, that cause an electron to be ejected from the analyte. (called “electron impact” mass spec)

• In mass spec, we can only detect charged species

• The energy of this impact renders the ionized molecule subject to Fragmentation chemistries leading to smaller but still charged structures

Electron Impact Ionization

A high-energy electron can dislodge an electron from a bond, creating a radical cation (a positive ion with an unpaired e-).

Separation of Ions

• Only the cations are deflected by the magnetic field.

• Amount of deflection depends on m/z.

• The detector signal is proportional to the number of ions hitting it.

• By varying the magnetic field, ions of all masses are collected and counted.

Mass Spectrometer

measuring the mass-to-charge ratio (m/z) of ions

1. Vaporization

2. Ionization

3. Separation

4. Detection

Mass Spectrometry Ionization Techniques

• Electron ionization mass spectrometry (EI-MS)

• Fast-atom bombardment mass spectrometry (FAB)

• Matrix-assisted laser desorption ionization mass spectrometry (MALDI)

• Chemical ionization mass spectrometry (CI)

• Electrospray ionization mass spectrometry (ESI-MS)

The mass spectrum Masses are graphed or tabulated according to their relative abundance.

• In mass spectrometry, what is the term used to describe the ion that results from the ejection of one electron from a molecule?

1. Base peak2. Parent peak3. Fragment4. Analyte5. None of these

• What quantity is detected in mass spectrometry?

1. The energy of a molecule2. The number of electrons

ejected from a molecule3. The number of ions of a

particular mass-to-charge ratio

4. The number of electrons needed to ionize a molecule

5. The number of hydrogen atoms in a molecule

• Which of the following reasons explains why some peaks are larger than others in a mass spectrum?

1. The larger peaks represent fragments that are more stable

2. The larger peaks represent fragments that are less stable

3. Cations tend to give larger peaks than radical cations

4. Radical cations tend to give larger peaks than cations

5. None of these

The GC-MS

A mixture of compounds is separatedby gas chromatography, then identifiedby mass spectrometry.

LC/MS are also widely used.

High Resolution MS

• Masses measured to 1 part in 20,000.• A molecule with mass of 44 (atomic mass units, AMU)

could be C3H8, C2H4O, CO2, or CN2H4.• If a more exact mass is 44.029, pick the correct

structure from the table:

C3H8 C2H4O CO2 CN2H4

44.06260 44.02620 43.98983 44.03740

Low-resolution mass spectrometry vs High-resolution mass spectrometry

• High-resolution mass spectrometry allows one to determine the molecular formula of a molecule

1. True2. False

• High-resolution mass spectrometry would allow one to distinguish between the following two molecules

1. True2. False

Br Br

Mass Spectrum with Sulfur

Mass Spectrum with Chlorine

Mass Spectrum with Bromine

• Under a given set of ionizing conditions, fragmentation pattern and relative abundances of ions are unique for each compound and are characteristic of that compound

• Fragmentation patterns provide valuable information about molecular structure• The probability of fragmentation to form new carbocations increases in the following

order:

Fragmentation of Molecular Ions

Interpreting a Mass Spectrum

• If no large M + 2 peak is present, the elements 18O, 34S, 37Cl, and 81Br are

absent

• These are the only elements to give significant M + 2 peaks

• Find if the mass of the molecular ion is odd or even using the nitrogen rule

• Nitrogen rule: If a compound has an:

• Even number (including zero) of nitrogen atoms, its molecular ion will appear at an even

m/z value

• Odd number of nitrogen atoms, its molecular ion will appear at an odd m/z value

Mass Spectrum of Octane

Unbranched alkanes fragment to form a series of cations differing by 14 amu (a CH2group), with each fragment formed by a one-bond cleavage having an odd mass number

Mass Spectrum of 2,2,4-Trimethylpentane

• Fragmentation tends to occur toward the middle of unbranched chains rather than at the ends

• Differences in energy among allylic, benzylic, 3°, 2°, 1°, and methyl carbocations in gas phase are much greater than the differences among comparable radicals• Where alternative modes of fragmentation are possible, the more

stable carbocation tends to form in preference to the more stable radical

Mass Spectrum of Methylcyclopentane

The base peak at m/z 56 in the mass spectrum of methylcyclopentanecorresponds to loss of ethylene to give a radical cation with the molecular formula C4H8

+·

Mass Spectrum of 1-Butene

Alkenes show a strong molecular ion peak and cleave readily to form resonance-stabilized allylic cations

[CH2=CHCH2CH2CH3] CH2=CHCH2+ + •CH2CH3

+•

Alkynes

• Alkynes show a strong molecular ion peak• One of the most prominent peaks is from the delocalization-stabilized 3-propynyl

(propargyl) cation (m/z 39) or a substituted propargyl cation

Mass Spectrum of 1-Pentyne

Mass Spectrum of 1-Butanol

• Loss of H2O, M – 18• Loss of an alkyl group

radical from the carbon bearing the —OH

• Oxonium ion is stable because of delocalization of charge

• The peak at m/z 73 (M – 15) corresponds to loss of a methyl radical from the molecular ion

• The peak at m/z 59 (M – 29) corresponds to loss of an ethyl radical• Loss of water as a neutral molecule from the molecular ion gives an alkene at m/z 70 (M –

18) as a radical cation• Loss of methyl from this radical cation gives an allylic carbocation at m/z 55

2-methyl2-Butanol

Fragmentation Patterns of Aldehydes and Ketones

• Characteristic pattern of aliphatic aldehydes and ketones is cleavage of a bond to the carbonyl group (α-cleavage)

• α-Cleavage of the aldehyde proton gives an M - 1 peak, which helps distinguish an aldehyde from a ketone

• McLafferty rearrangement - Fragmentation shown by aldehydes and ketones with a sufficiently long carbon chain

•+

m/z 58

McLaffertyrearrangement

Molecular ionm/z 114

•+OH OH

+

McLafferty Rearrangement of a Ketone• Reaction occurs through a six-membered ring transition state

• Example - McLafferty rearrangement of 2-octanone gives 1-pentene and a radical cation at m/z 58, which is the enol of acetone

2-Octanone

Characteristic Fragmentation Patterns of Carboxylic Acids• α-Cleavage of the carboxyl group to give the ion [COOH]+ at m/z 45

• McLafferty rearrangement • Base peak is often the result of the McLafferty rearrangement product

Butanoic Acid

m/z 88 - Molecular ionm/z 45 - [COOH]+m/z 60 - McLaffertyrearrangement product

Characteristic Fragmentation Patterns of Carboxylic Acidsα-Cleavage McLafferty rearrangement

m/z 102 - Molecular ionm/z 74 - McLaffertyrearrangementm/z 71 and 59 - Result of a-cleavage

Methyl Butanoate

Aromatic Hydrocarbons

• Most of them show an intense molecular ion peak

• Toluene and most alkylbenzenes show a fragment ion at m/z 91

Mass spectrum of toluene

Characteristic Fragmentation Pattern of Amines

• Pattern for 1°, 2°, and 3° amines is β-cleavage

Mass spectrum of 3-methyl-1-butanamine

Applications of Mass Spectrometry

• Routine molecule identification in the organic synthesis laboratory in both industrial and academic settings

• Uses gas chromatography (GC-MS) and liquid chromatography (LC-MS) as the primary methods

• Drug testing of athletes and advanced forensic science• Use GC-MS to identify traces of pharmaceuticals or illicit drugs in blood samples

• Luggage screening devices to identify traces of known explosives

• Which of the following C6H12O isomers would be expected to produce an m/z peak at M+−18?

1. 2.

3. 4.

O O

OHO

NH2O O

OH OH

• Which of the following compounds is most likely to undergo a McLaffertyrearrangement?

1. 2. 3.

4. 5.