1. 12. Structure Determination: Mass Spectrometry and Infrared Spectroscopy
Based on
McMurry’s Organic Chemistry, 6th edition
©2003 Ronald Kluger
Department of Chemistry
University of Toronto

2. Determining the Structure of an Organic Compound
The analysis of the outcome of a reaction requires that we know the full structure of the products as well as the reactants
In the 19th and early 20th centuries, structures were determined by synthesis and chemical degradation that related compounds to each other
Physical methods now permit structures to be determined directly. We will examine:
mass spectrometry (MS)
infrared (IR) spectroscopy
nuclear magnetic resonance spectroscopy (NMR)
ultraviolet-visible spectroscopy (VIS)
McMurry Organic Chemistry 6th edition Chapter 12 (c) 2003

3. 12.1 Mass Spectrometry (MS)
Measures molecular weight
Sample vaporized and subjected to bombardment by electrons that remove an electron
Creates a cation-radical
Bonds in cation radicals begin to break (fragment)
Charge to mass ratio is measured (see Figure 12-1)
McMurry Organic Chemistry 6th edition Chapter 12 (c) 2003

4. McMurry Organic Chemistry 6th edition Chapter 12 (c) 2003
The Mass Spectrum
Plot mass of ions (m/z) (x-axis) versus the intensity of the signal (roughly corresponding to the number of ions) (y-axis)
Tallest peak is base peak (100%)
Other peaks listed as the % of that peak
Peak that corresponds to the unfragmented radical cation is parent peak or molecular ion (M+)
McMurry Organic Chemistry 6th edition Chapter 12 (c) 2003

5. MS Examples: Methane and Propane
Methane produces a parent peak (m/z = 16) and fragments of 15 and 14 (See Figure 12-2 a)
The MS of propane is more complex (Figure 12-2 b) since the molecule can break down in several ways
McMurry Organic Chemistry 6th edition Chapter 12 (c) 2003

6. 12.2 Interpreting Mass Spectra
Molecular weight from the mass of the molecular ion
Double-focusing instruments provide high-resolution “exact mass”
atomic mass units – distinguishing specific atoms
Example MW “72” is ambiguous: C5H12 and C4H8O but:
C5H amu exact mass C4H8O amu exact mass
Result from fractional mass differences of atoms 16O = , 12C = , 1H =
Instruments include computation of formulas for each peak
McMurry Organic Chemistry 6th edition Chapter 12 (c) 2003

7. Other Mass Spectral Features
If parent ion not present due to electron bombardment causing breakdown, “softer” methods such as chemical ionization are used
Peaks above the molecular weight appear as a result of naturally occurring heavier isotopes in the sample
(M+1) from 13C that is randomly present
McMurry Organic Chemistry 6th edition Chapter 12 (c) 2003

8. 12.3 Interpreting Mass-Spectral Fragmentation Patterns
The way molecular ions break down can produce characteristic fragments that help in identification
Serves as a “fingerprint” for comparison with known materials in analysis (used in forensics)
Positive charge goes to fragments that best can stabilize it
McMurry Organic Chemistry 6th edition Chapter 12 (c) 2003

9. Mass Spectral Fragmentation of Hexane
Hexane (m/z = 86 for parent) has peaks at m/z = 71, 57, 43, 29
McMurry Organic Chemistry 6th edition Chapter 12 (c) 2003

10. 12.4 Mass-Spectral Behavior of Some Common Functional Groups
Functional groups cause common patterns of cleavage in their vicinity
McMurry Organic Chemistry 6th edition Chapter 12 (c) 2003

11. Mass Spectral Cleavage Reactions of Alcohols
Alcohols undergo -cleavage (at the bond next to the C-OH) as well as loss of H-OH to give C=C
McMurry Organic Chemistry 6th edition Chapter 12 (c) 2003

12. Mass Spectral Cleavage of Amines
Amines undergo -cleavage, generating radicals
McMurry Organic Chemistry 6th edition Chapter 12 (c) 2003

13. Fragmentation of Ketones and Aldehydes
A C-H that is three atoms away leads to an internal transfer of a proton to the C=O, called the McLafferty rearrangement
Carbonyl compounds can also undergo  cleavage
McMurry Organic Chemistry 6th edition Chapter 12 (c) 2003

14. 12.5 Spectroscopy of the Electromagnetic Spectrum
Radiant energy is proportional to its frequency (cycles/s = Hz) as a wave (Amplitude is its height)
Different types are classified by frequency or wavelength ranges
McMurry Organic Chemistry 6th edition Chapter 12 (c) 2003

15. McMurry Organic Chemistry 6th edition Chapter 12 (c) 2003
Absorption Spectra
Organic compound exposed to electromagnetic radiation, can absorb energy of only certain wavelengths (unit of energy)
Transmits, energy of other wavelengths.
Changing wavelengths to determine which are absorbed and which are transmitted produces an absorption spectrum
Energy absorbed is distributed internally in a distinct and reproducible way (See Figure 12-11)
McMurry Organic Chemistry 6th edition Chapter 12 (c) 2003

16. 12.6 Infrared Spectroscopy of Organic Molecules
IR region lower energy than visible light (below red – produces heating as with a heat lamp)
2.5  106 m to 2.5  105 m region used by organic chemists for structural analysis
IR energy in a spectrum is usually measured as wavenumber (cm-1), the inverse of wavelength and proportional to frequency
Specific IR absorbed by organic molecule related to its structure
McMurry Organic Chemistry 6th edition Chapter 12 (c) 2003

17. McMurry Organic Chemistry 6th edition Chapter 12 (c) 2003
Infrared Energy Modes
IR energy absorption corresponds to specific modes, corresponding to combinations of atomic movements, such as bending and stretching of bonds between groups of atoms called “normal modes”
Energy is characteristic of the atoms in the group and their bonding
Corresponds to vibrations and rotations
McMurry Organic Chemistry 6th edition Chapter 12 (c) 2003

18. 12.7 Interpreting Infrared Spectra
Most functional groups absorb at about the same energy and intensity independent of the molecule they are in
Characteristic higher energy IR absorptions in Table 12.1 can be used to confirm the existence of the presence of a functional group in a molecule
IR spectrum has lower energy region characteristic of molecule as a whole (“fingerprint” region)
See samples in Figure 12-13
McMurry Organic Chemistry 6th edition Chapter 12 (c) 2003

19. Regions of the Infrared Spectrum
cm-1 N-H, C-H, O-H (stretching)
N-H, O-H
3000 C-H
cm-1 CºC and C º N (stretching)
cm-1 double bonds (stretching)
C=O
C=C cm-1
Below 1500 cm-1 “fingerprint” region
McMurry Organic Chemistry 6th edition Chapter 12 (c) 2003

20. Differences in Infrared Absorptions
Molecules vibrate and rotate in normal modes, which are combinations of motions (relates to force constants)
Bond stretching dominates higher energy modes
Light objects connected to heavy objects vibrate fastest: C-H, N-H, O-H
For two heavy atoms, stronger bond requires more energy: C º C, C º N > C=C, C=O, C=N > C-C, C-O, C-N, C-halogen
McMurry Organic Chemistry 6th edition Chapter 12 (c) 2003

21. 12.8 Infrared Spectra of Hydrocarbons
C-H, C-C, C=C, C º C have characteristic peaks
absence helps rule out C=C or C º C
McMurry Organic Chemistry 6th edition Chapter 12 (c) 2003

22. 12.9 Infrared Spectra of Some Common Functional Groups
Spectroscopic behavior of functional group is discussed in later chapters
Brief summaries presented here
McMurry Organic Chemistry 6th edition Chapter 12 (c) 2003

23. IR: Alcohols and Amines
O–H 3400 to 3650 cm1
Usually broad and intense
N–H 3300 to 3500 cm1
Sharper and less intense than an O–H
McMurry Organic Chemistry 6th edition Chapter 12 (c) 2003

24. IR: Aromatic Compounds
Weak C–H stretch at 3030 cm1
Weak absorptions cm1 range
Medium-intensity absorptions 1450 to 1600 cm1
See spectrum of phenylacetylene, Figure 12.15
McMurry Organic Chemistry 6th edition Chapter 12 (c) 2003

25. IR: Carbonyl Compounds
Strong, sharp C=O peak 1670 to 1780 cm1
Exact absorption characteristic of type of carbonyl compound
1730 cm1 in saturated aldehydes
1705 cm1 in aldehydes next to double bond or aromatic ring
McMurry Organic Chemistry 6th edition Chapter 12 (c) 2003

26. McMurry Organic Chemistry 6th edition Chapter 12 (c) 2003
C=O in Ketones
1715 cm1 in six-membered ring and acyclic ketones
1750 cm1 in 5-membered ring ketones
1690 cm1 in ketones next to a double bond or an aromatic ring
McMurry Organic Chemistry 6th edition Chapter 12 (c) 2003

27. McMurry Organic Chemistry 6th edition Chapter 12 (c) 2003
C=O in Esters
1735 cm1 in saturated esters
1715 cm1 in esters next to aromatic ring or a double bond
McMurry Organic Chemistry 6th edition Chapter 12 (c) 2003

28. Chromatography: Purifying Organic Compounds
Chromatography : a process that separates compounds using adsorption and elution
Mixture is dissolved in a solvent (mobile phase) and placed into a glass column of adsorbent material (stationary phase)
Solvent or mixtures of solvents passed through
Compounds adsorb to different extents and desorb differently in response to appropriate solvent (elution)
Purified sample in solvent is collected from end of column
Can be done in liquid or gas mobile phase
McMurry Organic Chemistry 6th edition Chapter 12 (c) 2003

29. Principles of Liquid Chromatography
Stationary phase is alumina (Al2O3) or silica gel (hydrated SiO2)
Solvents of increasing polarity are used to elute more and more strongly adsorbed species
Polar species adsorb most strongly to stationary phase
For examples, alcohols adsorb more strongly than alkenes
McMurry Organic Chemistry 6th edition Chapter 12 (c) 2003

30. High-Pressure (or High-Performance) Liquid Chromatography (HPLC)
More efficient and complete separation than ordinary LC
Coated silica microspheres (10-25 µm diameter) in stationary phase
High-pressure pumps force solvent through tightly packed HPLC column
Detector monitors eluting material
Figure 12.17: HPLC analysis of a mixture of 14 pesticides, using acetonitrile/water as the mobile phase
McMurry Organic Chemistry 6th edition Chapter 12 (c) 2003