1. Chapter 11 Structure Determination: Mass Spectrometry, Infrared Spectroscopy, and Ultraviolet Spectroscopy

2. Introduction
Modern techniques for structure determination of organic compounds include:
Mass spectrometry
What is the size and formula of the compound
Infrared spectroscopy
What functional groups are present in the compound
Ultraviolet spectroscopy
Is a conjugated p electron system present in the compound
Nuclear magnetic resonance spectroscopy
What is the carbon-hydrogen framework of the compound

3. 11.1 Mass Spectrometry of Small Molecules: Magnetic-Sector Instruments
Mass spectrometry (MS) measures the mass and molecular weight (MW) of a molecule
Provides structural information by finding the masses of fragments produced when molecules break apart
Three basic parts of mass spectrometers:

4. Mass Spectrometry of Small Molecules: Magnetic-Sector Instruments
Electron-impact, magnetic-sector instrument
Sample is vaporized into ionization source
Bombarded by electron beam (70 eV) dislodging valence electron of sample producing cation-radical
Most cation-radicals fragment and are separated in magnetic field according to their mass-to-charge ratio (m/z)
Since z = 1 for most ions the value of m/z is mass of ion

5. Mass Spectrometry of Small Molecules: Magnetic-Sector Instruments
Mass spectrum of propane (C3H8; MW = 44)
Base peak
Tallest peak
Assigned intensity of 100%
Base peak at m/z = 29 in propane mass spectrum
Parent peak
Unfragmented cation radical – molecular ion (M+)
Parent peak only 30% of base peak for propane

6. 11.2 Interpreting Mass Spectra
Molecular weight determined from molecular ion peak
High resolution double-focusing mass spectrometers are accurate to about amu
M+1 peak results from presence of 13C and 2H
Fragmentation occurs when high-energy cation radical falls apart
One fragment retains positive charge and is a carbocation
One fragment is a neutral radical fragment

7. Interpreting Mass Spectra
Mass spectrum of 2,2-dimethylpropane (MW = 72)
No M+ peak observed when electron-impact ionization is used
“Soft” ionization methods can prevent fragmentation of molecular ion

8. Interpreting Mass Spectra
Base peak in mass spectrum of 2,2-dimethylpropane is at m/z = 57
m/z = 57 corresponds to t-butyl cation
Molecular ion fragments to give most stable carbocation

9. Interpreting Mass Spectra
Mass spectrum of hexane (C6H14; MW = 86)
All carbon-carbon bonds of hexane are electronically similar and break to a similar extent
Mass spectrum contains mixture of ions

10. Interpreting Mass Spectra
M+ = 86 for hexane
m/z = 71 arises from loss of methyl radical from hexane cation radical
m/z = 57 arises from loss of ethyl radical from hexane cation radical
m/z = 43 arises from loss of propyl radical from hexane cation radical
m/z = 29 arises from loss of butyl radical from hexane cation radical

11. Worked Example 11.1 Using Mass Spectra to Identify Compounds
Assume that you have two unlabeled samples, one of methylcyclohexane and the other of ethylcyclopentane.
How could you use mass spectrometry to identify them?

12. Worked Example 11.1 Using Mass Spectra to Identify Compounds
Strategy
Look at the two possible structures and determine how they differ. Then think about how any of these differences in structure might give rise to differences in mass spectra. Methylcyclohexane, for instance, has a –CH3 group, and ethylcyclopentane has a –CH2CH3 group, which should affect the fragmentation process.

13. Worked Example 11.1 Using Mass Spectra to Identify Compounds
Solution
The mass spectra of both samples show molecular ions at M+ = 98, corresponding to C7H14, but the two spectra differ in their fragmentation patterns. Sample A has its base peak at m/z = 69, corresponding to the loss of a CH2CH3 group (29 mass units), but B has a rather small peak at m/z = 69. Sample B shows a base peak at m/z = 83, corresponding to the loss of a CH3 group (15 mass units), but sample A has only a small peak at m/z = 83. We can therefore be reasonably certain that A is ethylcyclopentane and B is methylcyclohexane.

14. 11.3 Mass Spectrometry of Some Common Functional Groups
Alcohols
Fragment by two pathways
Alpha cleavage
Dehydration

15. Mass Spectrometry of Some Common Functional Groups
Amines
Aliphatic amines undergo characteristic a cleavage

16. Mass Spectrometry of Some Common Functional Groups
Carbonyl compounds
Ketones and aldehydes with C-H three atoms away from carbonyl group undergo McLafferty rearrangement

17. Mass Spectrometry of Some Common Functional Groups
Ketones and aldehydes also undergo a cleavage of bond between carbonyl group and neighboring carbon

18. Worked Example 11.2 Identifying Fragmentation Patterns in a Mass Spectrum
The mass spectrum of 2-methylpentan-3-ol is shown in Figure What fragments can you identify?

19. Worked Example 11.2 Identifying Fragmentation Patterns in a Mass Spectrum
Strategy
Calculate the mass of the molecular ion, and identify the functional groups in the molecule. Then write the fragmentation processes you might expect, and compare the masses of the resultant fragments with the peaks present in the spectrum.

20. Worked Example 11.2 Identifying Fragmentation Patterns in a Mass Spectrum
Solution
2-Methylpentan-3-ol, an open-chain alcohol, has M+ = 102 and might be expected to fragment by a cleavage and by dehydration. These processes would lead to fragment ions of m/z = 84, 73, and 59. Of the three expected fragments, dehydration is not observed (no m/z = 84 peak), but both a cleavages take place (m/z = 73, 59).

21. 11. 4 Mass Spectrometry in Biological Chemistry:
11.4 Mass Spectrometry in Biological Chemistry: Time-of-Flight (TOF) Instruments
Most biological analyses use “soft” ionization methods:
Electrospray ionization (ESI)
Sample dissolved in polar solvent and sprayed through steel capillary tube
As sample exits tube it is subjected to high voltage producing variably protonated sample ions (M + Hnn+)
Matrix-assisted laser desorption ionization (MALDI)
Sample is adsorbed onto a suitable matrix compound, such as 2,5-dihydroxybenzoic acid, which is ionized by laser light
Matrix compound then transfers energy to the sample and protonates it, forming M + Hnn+ ions
Protonated sample ions are focused into small packet and hit with energy from accelerator electrode
Ions begin moving with velocity(v)
Molecules separate based on different times of flight through analyzer drift tube

22. Mass Spectrometry in Biological Chemistry: Time-of-Flight (TOF) Instruments
MALDI-TOF mass spectrum of chicken egg-white lysozyme
Peak at 14, daltons (amu) is due to the mono-protonated protein

23. Spectroscopy and the Electromagnetic Spectrum
Absorption spectrum
Spectrum of compound’s selective absorption of electromagnetic radiation
Infrared absorption spectrum of ethanol

24. 11.6 Infrared Spectroscopy
Infrared (IR) region
Ranges from 7.8 x 10-7 m to 10-4 m
2.5 x 10-6 m to 2.5 x 10-5 m used by organic chemists
Wavelengths given in micrometers (1 mm = 10-6 m)
Frequencies given in wavenumbers
Wavenumber
Reciprocal of wavelength in centimeters
Expressed in units of cm-1

25. Infrared Spectroscopy
Molecules stretch or bend at specific frequencies
Energy is absorbed if the frequency of the radiation matches the frequency of the vibration
IR spectrum What molecular motions? What functional groups?

26. 11.7 Interpreting Infrared Spectra
Most functional groups have characteristic IR absorption bands that don’t change from one compound to another

27. Interpreting Infrared Spectra

28. Interpreting Infrared Spectra

29. Interpreting Infrared Spectra
Hexane
Hex-1-ene
Hex-1-yne

30. Infrared Spectra of Some Common Functional Groups

31. Infrared Spectra of Some Common Functional Groups