1. 12. Structure Determination: Mass Spectrometry and Infrared Spectroscopy
Based on McMurry’s Organic Chemistry, 7th edition

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)

3. Why this Chapter?
Finding structures of new molecules synthesized is critical
To get a good idea of the range of structural techniques available and how they should be used

4. 12.1 Mass Spectrometry of Small Molecules:Magnetic-Sector Instruments
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

5. 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+)

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

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

8. 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

9. Mass Spectral Fragmentation of Hexane
Hexane (m/z = 86 for parent) has peaks at m/z = 71, 57, 43, 29

10. 12.3 Mass Spectrometry of Some Common Functional Groups
Alcohols:
Alcohols undergo -cleavage (at the bond next to the C-OH) as well as loss of H-OH to give C=C

11. Mass Spectral Cleavage of Amines
Amines undergo -cleavage, generating radicals

12. Fragmentation of Carbonyl Compounds
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

13. 12.4 Mass Spectrometry in Biological Chemistry: Time-of-Flight (TOF) Instruments
Most biochemical analyses by MS use:
electrospray ionization (ESI)
Matrix-assisted laser desorption ionization (MALDI)
• Linked to a time-of-flight mass analyzer
(See figure 12.9)

14. 12.5 Spectroscopy and 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

15. 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 12-12)

16. 12.6 Infrared Spectroscopy
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

17. 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

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 12-14

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

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

21. 12.8 Infrared Spectra of Some Common Functional Groups
Alkanes, Alkenes, Alkynes
C-H, C-C, C=C, C º C have characteristic peaks
absence helps rule out C=C or C º C

22. 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

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

24. 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

25. C=O in Ketones C=O in Esters 1735 cm1 in saturated esters
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
C=O in Esters
1735 cm1 in saturated esters
1715 cm1 in esters next to aromatic ring or a double bond