6: Mass Spectrometry

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Introduction to Mass Spectrometry

MS Experiment

Mass spectrometry (MS) is an instrument that measures the mass of charged particles.

In this instrument, the structure is hit with a high energy electron which causes the loss of an electron from the original structure.

Molecular Ion

The mass spectrometer sorts the ions produced based on their mass-to-charge ratio and a peak shows up for any positively charged ion.

What would be the largest m/z peak for this ion?

This first ionization is called the molecular ion. Does this match the molecular weight of the original compound?

Molecular Weights

Most organic compounds have even molecular weights.

However, If a sample has an odd number of nitrogens the molecular ion must be an odd.

What is the MW for these compounds?

Isotopic Abundance in Mass Spectrometry*

Most elements exist as mixtures of different isotopes. Since a mass spectrometer separates and detects ions of slightly different masses, it easily distinguishes different isotopes of a given element.

Isotopes don’t impact the mass spectra of many organic compounds.

The abundance of ¹²C is _________%.
The abundance of ¹H is _________%.
The abundance of ¹⁶O is _________%.

However, compounds containing bromine and chlorine exhibit two molecular ions as they both have two very abundant isotopes.

Chlorine: 75.77% ³⁵Cl and 24.23% ³⁷Cl

Bromine: 50.50% ⁷⁹Br and 49.50% ⁸¹Br

The mass spectrum of C₆H₆Br is shown below.

Explain the two peaks at 156 and 158 m/z.
Predict the MF (molecular formula) for this compound.

* Spectra in this unit are from SDBS (Japan National Institute of Advanced Industrial Science and Technology).

Practice

The compound that gave this mass spectrum probably contains:

nitrogen
bromine
chlorine
sulfur

The compound that gave this mass spectrum probably contains:

nitrogen
bromine
chlorine
sulfur

How many molecular ions (compounds with different weights) would you expect to see in a molecule with 2 bromines? Explain.

Table of Molecular Ions Containing Br or Cl

Using this table, propose a molecular formula for the compound that produced this spectrum.

Fragmentation in Mass Spectrometry

Initial Ionization

The radical cations (molecular ions) quickly decompose via radical reactions into fragments. Sometimes, the molecular ion is not even observed.

To start predicting fragments, you need to know the structure of the molecular ion.

When a compound is ionized in the mass spectrometer, which electrons would be removed first? Explain your reasoning.

Review: Cation Stability

Usually a molecule will fragment to form the most stable cation. This cation will be most abundant and is called the base peak.

Rank the following cations in order of increasing acidity and explain your ranking:

Rank the following cations in order of increasing acidity and explain your ranking:

Fragmentation Mechanisms

Inductive Cleavage

Show loss of an electron from the following molecule. Also add arrow(s) in the second step.

Circle any ions that would be observed.
What is the mass of the product(s) observed?
Why does a bond break easily after this ionization?

Induction cleavage is also possible in the following pathways.

Show the results of the first ionization and show the inductive cleavage that results, with arrows.

In each case, give reasons why the bond broke easily.

Alpha Cleavage

Show loss of an electron from the following molecule.
Also add arrow(s) in the second step.

Circle any ions that would be observed.
What is the mass of the product(s) observed?
Why does a bond break easily after this ionization?

Alpha cleavage is also possible in the following pathways.

Show the results of the first ionization and show the alpha cleavage that results, with arrows.

In each case, give reasons why the bond broke easily.

McLafferty Rearrangement

Show loss of an electron from the following molecule.
Also add arrow(s) in the second step.

Why does the molecule rearrange after this ionization?
What is the mass of the cationic fragment? Is it even or odd?
What is the mass of the cationic fragments from alpha cleavages? Are they even or odd?

McLafferty rearrangement is also possible in the following pathway.

Show the results of the first ionization and show the inductive cleavage that results, with arrows.

What structural requirements are necessary for a McLafferty rearrangement?

Sigma Cleavage

Show loss of an electron from the indicated sigma bond in the following molecule. Why does that bond then break easily?

What is the molecular weight of the ion that results?
Why is loss of an electron from a sigma bond less likely in the first place?
Although impossible in the molecule shown above, what electrons are most likely to be lost in the initial ionization in mass spectrometry?

Summary of Mass Spectrometry

The mass spectrometer can provide a molecular mass for any [ positively / negatively ] charged molecular ion or fragment.
Mass spectrometry bombards a molecule to cause the loss of an electron and forming a molecular ion.
- The molecular ion is a [ radical / cation / anion / radical cation / radical anion ].
- This molecular ion is [ stable / unstable ].
- The molecular ion has the [ same MW / M+1 / M+2 / M-1 ] as the compound being measured.
There are four major types of fragmentation. Show an example of each of these fragmentations.
- Inductive Cleavage:
- Sigma Cleavage:
- Alpha Cleavage:
- McLafferty Rearrangement:

Practice Fragmentation

1. Analyze the following spectrum of 4-heptanone.

Draw the structure of 4-heptanone.
Show a mechanism for an alpha fragmentation and the McLafferty Rearrangement/Fragmentation for each compound.
Use your predicted fragments to match the peaks within the MS.

2. Compounds X and Y are isomers with the formula C₃H₆O. Compound X has a peak at 1730 cm^-1 in the IR and Y has a peak at 1715 cm^-1. The spectra are shown below. Determine the structures of Compounds X and Y.

Compound X