Mass Spectrometry

12.1, 12.2, 12.3

Define mass spectrometry (MS)

A technique for measuring the mass/molecular weight of a molecule aka it’s molecularweight

• possible to gain structural information about a molecule by measuring the masses of the fragments produced when molecules are broken apart

What are the three basic parts of a mass spectrometer?

1) Ionization Source - Sample molecules are given an electrical charge by this source

2) Mass Analyzer - Ions in the sample are separated by their mass to charge (m/z) ratio

3) Detector - Separated ions are observed and counted

What’s the most common mass spectrometer used in lab

The magnetic sector instrument

• used for routine purposes in lab

How does a magnetic sector instrument work?

1. A small sample is vaporized into the ionization chamber

2. The sample is then bombarded by a stream of high - energy electrons

3. When the molecule is struck it dislodges a valence electron from the molecule producing a cation radical - cation because the molecule has lost an electron and the molecule now has an odd number of electrons

4. Electron bombardment transfer so much energy that most of the cation radicals fragment after formation in which some retain the positive charge and some are neutral

5. Fragments then flow through a curved pipe in a magnetic field which deflects them into different paths according to their m/z ratios

What happens to neutral fragments in a mass spectrometer?

• They aren’t deflected and are lost on the walls of the pipe

• Only positive charges show on

What is the common type of mass spectrometer?

The quadruple mass analyzer

• Has four solid rods arranged parallel to the direction of the ion beam with an oscilating electrostatic field generated in the space between the rods

• For a given field, only one m/z will make it through the quadrupole region, the others will crash into the rods or walls of the instrument and never reach the detector

What is the format of a mass spectrum?

A bar graph

• Masses (m/z) values on the x axis

• Intensity or relative abundance of ions of a given m/z striking the detector on the y axis

• The tallest peak, assigned an intensity of 100% is called the base peak

• The peak that corresponds to the unfragmented cation radical is called the precursor peak aka the molecular ion

What is the molecular ion?

The cation forms after ionization, but before fragmentation

• Often not the base peak

What information can we get from a mass spectra?

1. Molecular weight

2. Molecular fingerprint

How does a Mass spectrum give you the molecular weight of a compound?

• With high resolution instruments able to distinguih between different isotopes

  • Can tell apart molecules w/ the same nominal weight but slightly different exact masses

• Analyses the molecular ion to determine molecular weight as electron mass is negligable

  • Molecules that fragment too easily don’t show a molecular ion peak

How do we circumvent quick fragmentation

Utilizing soft ionization methods to perserve the molecular ion

For samples that contain a small percentage of isotopes like C - 13 or H - 2, what are their effects on mass spectra?

• They give rise to extra peaks (like M+1) just above the main molecular ion peak

How does mass spectrometry serve as a molecular fingerprint?

Every organic compound fragments in a unique way depending on its structure

• A computer can try and match a mass spectrum fragmentation to one of the 700k+ searchable spectra recorded in an online databse allowing us to match unknown compounds to known spectra

During fragmentation, where the positive charge stay on?

The fragment that is best able to stabalize it

• the most stable carbocation is formed when a high energy electron collides with a bond

What physical characteristics can fragmentation provide to us?

Can help us identify functional groups as different functional groups have characteristic fragmentation patterns

What are the two main pathways alcohol undergoes fragmentation

1. Alpha - Clevage

   • A C - C bond nearest the hydroxyl group is broken

   • Yields a neutral radical + resonance stabailized, oxygen containing cation

2. Dehydration

• Water is eliminated yielding an alkene radical cation with a mass 18 amu less than M+

  • Only a small peak is formed from dehydration

How do Amines fragment?

They follow the nitrogen rule

• says that a compound with an odd number of nitrogen atoms has an odd numbered molecular weight due to the fact that nitrogen is trivalent requiring an odd number of hydrogen atoms

• An even molecular ion weight will have an even amount of nitrogen atoms

What are the characteristics of an odd number amine molecular ion? even?

• Usually means that the unknown compound has 1 or 3 nitrogen atoms

• Means the compound has either zero or two nitrogen atoms

How exactly does fragmentation occur in amines?

They undergo an alpha clevage next to nitrogen resulting in a C - C bond nearest the nitrogen to be broken

• yields an alkyl radical and a resonance - stabilized, nitrogen - containing cation

What is special about the mass spectra of halides?

Their peaks may have distinct patterns due to how common their isotopes are

ex) Cl 35,37 being in a 3:1 raio and Br 79,81 being in a 1:1 ratio

• results in M vs M + 2 for example to be 3:1 for example

What are the fragmentation patterns for carbonyl compounds?

1. McLafferty Rearrangement

2. Alpha cleavage

How does McLafferty Rearrangement work?

• The ketones and aldehydes must have a hydrogen on a carbon three atoms away from the carbonyl group

• The hydrogen atom is transferered to the carbonyl oxygen

• A C - C bond between the alpha and beta carbons is broken to produce a neutral alkene and an oxygen containg catio

How does alpha cleavage in carbonyl compounds work?

• A bond between the carbonyl carbon and neighboring carbon undergo cleavage to yield a neutral radical and a resonance - stabalized acyl cation

How is mass spectrometry different from spectroscopy techniques?

Spectroscopy is reversible, mass spectrometry isn’t reversible

What type of questions will we get about mass spectrometry?

1. Possible fragments that can form given a molecule

2. If you can add up masses of fragments using the PT & come up with a mass number

Do you have to use high energy electrons in mass spectrometry?

No, can utilize a focused beam of small molecules like methane or ammonia

• both can be used to knock out either a bonding or nonbonding (lonepair, valence) electron

In a mass spectrometer will a nonbonding electron always be knocked out?

If they exist, yes, because their relatively easy. If no NBE exist a bonding electron at any arbitary location will be chosen

How do we calculate the mass of M+

Counting the atoms on the species

If a species has a charge of zero, will you see it on a mass spectrum?

No

When fragmentation occurs what bond breaks?

Exactly one covalent single bond, everywhere in the molecule

• In a sameple there are many molecules so every possibility occurs

In an m/z ratio, what is the value

Always numerically equal to the mass of the particle in amu

• z will always be +1

What does the base peak correspond to

The most stable, thus abundant fragment

How do you identify possible fragments?

• Form a radical due to e- loss

• Take e- w/ an atom to fragment it

• When writing the structure of fragments, always write what is include within the molecule for easy points

• Fragments result due to carboncation rearrangement as well

Since mass spectra will contain peaks of M+ and fragments, what are the peaks of alkyl chains usually separated by

• 14 amus (CH2+)

What will the test ask you to do with mass spectra regarding fragmentationtypes

To draw all possible structures at M/Z, any structure will suffice

• Look out for possible rearrangment