12. Structure Determination: Mass Spectrometry and Infrared Spectroscopy

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) – mol.wt. and heteroatoms • infrared (IR) spectroscopy – functional groups • nuclear magnetic resonance spectroscopy (NMR) – structural information • ultraviolet-visible spectroscopy (VIS) – conjugation and quantification (most important use)

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 • This is very important in identifying functional groups that are present (or just as important, eliminating functional groups that are absent)

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” • 0.0001 atomic mass units – distinguishing specific atoms • Example MW “72” is ambiguous: C5H12 and C4H8O but: • C5H12 72.0939 amu exact mass C4H8O 72.0575 amu exact mass • Result from fractional mass differences of atoms 16O = 15.99491, 12C = 12.0000, 1H = 1.00783 • High resolution MS instruments include computation of formulas for each peak present

7. Heteroatoms • MS is very useful in the detection of “heteroatoms” present in an unknown sample. • Oxygen (indirectly “suspected”) • Nitrogen – ‘Nitrogen Rule’ • Halogens • F – presence of M-19 fragments • Cl – isotopic abundances of M+2 peaks that are 20-50% intensity of M • Br – isotopic abundances of M+2 peak of near equal intensity of M • I – presence of m/e 127 peak or M-127 peak

8. Nitrogen Rule • An odd means that N is present (1, 3, 5….) 86 58 30 101 44 42

9. Nitrogen Rule • An even with means lots of relatively large even mass M+ ions means that an even number of N are present (2, 4, 6….) 30 42 59 71 88

10. Chlorine M+2 peak and ratio 126 128

11. Chlorine • M+2 peak and ratio

12. Bromine M+2 peak and ratio

13. Bromine M+2 peak and ratio

14. Iodine

15. 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

16. 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

17. 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

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

19. 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 (M-17 and M-18 common)

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

21. 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

22. 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)

23. 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

24. 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)

25. 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

26. 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

27. 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

28. 4000-2500 cm-1 N-H, C-H, O-H (stretching) 3300-3600 N-H, O-H 3000 C-H 2500-2000 cm-1 CºC and C º N (stretching) 2000-1500 cm-1 double bonds (stretching) C=O 1680-1750 C=C 1640-1680 cm-1 1500-1000 cm-1 “fingerprint” region Regions of the Infrared Spectrum

29. 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

30. 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

31. IR: Aromatic Compounds • Weak C–H stretch at 3030 cm1 • Weak absorptions 1660 - 2000 cm1 range • Medium-intensity absorptions 1450 to 1600 cm1 • See spectrum of phenylacetylene, Figure 12.15

32. 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

33. Alcohols

34. Alcohols

35. Amines Primary amine

36. Amines Secondary amine

37. Amine Tertiary amine

38. 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

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

40. Aldehydes

41. Ketone

42. Carboxylic Acid

43. Ester

44. Amide

45. Ether

46. Vanillin