12. Structure Determination: Mass Spectrometry and Infrared Spectroscopy

1. 12. Structure Determination: Mass Spectrometry and Infrared Spectroscopy Based on McMurry’sOrganic 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

3. Determining the Structure of an Organic Compound • Physical methods now permit structures to be determined directly. We will examine: • mass spectrometry (MS)—this chapter • infrared (IR) spectroscopy—this chapter • nuclear magnetic resonance spectroscopy (NMR)—Chapter 13 • ultraviolet-visible spectroscopy (VIS)—Chapter 14

4. 12.1 Mass Spectrometry (MS) • Sample vaporized and bombarded by energetic electrons that remove an electron, creating a cation-radical • Bonds in cation radicals begin to break (fragment)

5. Mass Spectrometer

6. Mass Spectrometer

7. The Mass Spectrum • Plot mass of ions (m/z) (x-axis) versus the intensity of the signal (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+)

8. MS Examples: Methane and Propane • Methane produces a parent peak (m/z = 16) and fragments of 15 and 14

9. MS Examples: Methane and Propane • The Mass Spectrum of propane is more complex (Figure 12-2 ) since the molecule can break down in several ways

10. Mass spectrum of propane

11. 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

12. 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

13. 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

14. 2,2-Dimethylpropane: MM = 72 (C5H12)

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

16. Hexane

17. Worked example 12.1: methylcyclohexane or ethylcyclopentane?

18. 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

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

20. 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

21. Fragmentation of Ketones and Aldehydes

22. 12.4 Mass Spec. in Biochemistry: TOF • ESI and MALDI are techniques to produce charged molecules at relatively low energy, to minimize fragmentation. • The large biological molecules are separated by Time of Flight analysis (TOF) in a drift tube without a magnetic field imposed.

23. MALDI-TOF spectrum of chicken egg-white lysozyme

24. 12.5 The Electromagnetic Spectrum

25. Wavelength and Frequency

26. Absorption Spectra • Organic compounds exposed to electromagnetic radiation can absorb photons of specific energies (wavelengths or frequencies) • 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)

27. Infrared Absorption Spectrum of Ethanol

28. 12.6 Infrared Spectroscopy of Organic Molecules • IR region is lower in photon 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: • Wavenumber (cm-1) = 1/l(cm) • Specific IR absorbed by organic molecule is related to its structure

29. IR region and vicinity

30. 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 molecular vibrations

31. Infrared Energy Modes

32. 12.7 Interpreting Infrared Spectra • Most functional groups absorb at about the same energy and intensity independent of the molecule they are in • Characteristic 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)

36. 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 Below 1500 cm-1 “fingerprint” region Regions of the Infrared Spectrum

37. Regions of the Infrared Spectrum

38. 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 (frequency) modes

39. Differences in Infrared Absorptions • Light objects connected to heavy objects vibrate fastest (at higher frequencies): C-H, N-H, O-H • For two heavy atoms, stronger bond requires more energy (higher frequency): C º C, C º N > C=C, C=O, C=N > C-C, C-O, C-N, C-halogen

40. C-H, C-C, C=C, C º C have characteristic peaks 12.8 Infrared Spectra of Hydrocarbons

41. Hexane

42. Alkenes

43. 1-Hexene

44. Alkynes

45. 12.8 Infrared Spectra of Some Common Functional Groups • Spectroscopic behavior of functional groups is discussed in later chapters • Brief summaries presented here

46. Aromatic compounds:

47. Phenylacetylene

48. IR: Alcohols Cyclohexanol

49. Amines

50. 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