1. © 2006 Thomson Higher Education 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 (C 3 H 8 ; 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 0.0005 amu M+1 peak results from presence of 13 C and 2 H 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 (C 6 H 14 ; 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 –CH 3 group, and ethylcyclopentane has a –CH 2 CH 3 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 C 7 H 14, 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 CH 2 CH 3 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 CH 3 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  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  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 11.8. 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  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  cleavages take place (m/z = 73, 59).

21. 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 + H n n+ ) 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 + H n n+ 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 14,307.7578 daltons (amu) is due to the mono- protonated protein

23. 11.5 Spectroscopy and the Electromagnetic Spectrum The electromagnetic spectrum covers a continuous range of wavelengths and frequencies, from radio waves at the low- frequency end to gamma (  ) rays at the high-frequency end

24. Spectroscopy and the Electromagnetic Spectrum Electromagnetic radiation exhibits dual behavior Particle-like (photon) Wave-like Wavelength ( ) Distance from one wave maximum to the next Frequency ( ) Number of waves that pass by a fixed point per unit time Measured in hertz (Hz) = 1 sec -1 Amplitude Height of a wave measured from midpoint to peak

25. Spectroscopy and the Electromagnetic Spectrum

27. Electromagnetic energy is transmitted in discrete amounts called quanta Amount of energy,, corresponding to 1 quantum of energy (1 photon) of frequency ( ) is expressed by the Planck equation The energy of a photon varies directly with its frequency but inversely with its wavelength

28. Spectroscopy and the Electromagnetic Spectrum

29. Absorption spectrum Spectrum of compound’s selective absorption of electromagnetic radiation Infrared absorption spectrum of ethanol

30. Worked Example 11.3 Correlating Energy and Frequency of Radiation Which is higher in energy, FM radio waves with a frequency of or visible green light with a frequency of

31. Worked Example 11.3 Correlating Energy and Frequency of Radiation Strategy Remember the equations, which say that energy increases as frequency increases and as wavelength decreases

32. Solution Since visible light has a higher frequency than radio waves, it is higher in energy Worked Example 11.3 Correlating Energy and Frequency of Radiation

33. 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  m = 10 -6 m) Frequencies given in wavenumbers Wavenumber Reciprocal of wavelength in centimeters Expressed in units of cm -1

34. 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?

35. 11.7 Interpreting Infrared Spectra Most functional groups have characteristic IR absorption bands that don’t change from one compound to another

36. Interpreting Infrared Spectra

38. Hexane Hex-1-ene Hex-1-yne

39. Worked Example 11.4 Distinguishing Isomeric Compounds by IR Spectroscopy Acetone (CH 3 COCH 3 ) and prop-2-en-1-ol (H 2 C=CHCH 2 OH) are isomers. How could you distinguish them by IR spectroscopy?

40. Worked Example 11.4 Distinguishing Isomeric Compounds by IR Spectroscopy Strategy Identify the functional groups in each molecule, and refer to Table 11.1

41. Worked Example 11.4 Distinguishing Isomeric Compounds by IR Spectroscopy Solution Acetone has a strong C=O absorption at 1715 cm -1, while prop-2-en-1-ol has an –OH absorption at 3500 cm -1 and a C=C absorption at 1660 cm -1.

42. 11.8 Infrared Spectra of Some Common Functional Groups

43. Infrared Spectra of Some Common Functional Groups

50. Worked Example 11.5 Predicting IR Absorptions of Compounds Where might the following compounds have IR absorptions? (a) (b)

51. Worked Example 11.5 Predicting IR Absorptions of Compounds Strategy Identify the functional groups in each molecule, and check Table 11.1 to see where those groups absorb.

52. Worked Example 11.5 Predicting IR Absorptions of Compounds Solution (a) This molecule has an alcohol O-H group and an alkene double bond. Absorptions: 3400 – 3650 cm -1 (O-H) 3020 – 3100 cm -1 (=C-H) 1640 – 1680 cm -1 (C=C) (b) This molecule has a terminal alkyne triple bond and a saturated ester group. Absorptions:3300 cm -1 ( ) 2100 – 2260 cm -1 ( ) 1735 cm -1 ( C=O )

53. Worked Example 11.6 Identifying Functional Groups from an IR Spectrum The IR spectrum of an unknown compound is shown in Figure 11.17. What functional groups does the compound contain?

54. Worked Example 11.6 Identifying Functional Groups from an IR Spectrum Strategy All IR spectra have many absorptions, but those useful for identifying specific functional groups are usually found in the region from 1500 cm -1 to 3300 cm -1. Pay particular attention to the carbonyl region (1670 – 1780 cm -1 ), the aromatic region (1660 – 2000 cm -1 ), the triple-bond region (2000 – 2500 cm -1 ), and the C-H region (2500 – 3500 cm -1 ).

55. Worked Example 11.6 Identifying Functional Groups from an IR Spectrum Solution The spectrum shows an intense absorption at 1725 cm -1 due to a carbonyl group (perhaps an aldehyde, -CHO), a series of weak absorptions from 1800 to 2000 cm -1 characteristic of aromatic compounds, and a C-H absorption near 3030 cm -1, also characteristic of aromatic compounds. In fact, the compound is phenylacetaldehyde.

56. 11.9 Ultraviolet Spectroscopy Ultraviolet (UV) region 4 x 10 -7 m to 10 -8 m Region of greatest interest to organic chemists from 2 x 10 -7 m to 4 x 10 -7 meters

57. Ultraviolet Spectroscopy Absorption usually measured in nanometers (nm), where 1 nm = 10 -9 m Energy absorbed from UV radiation promotes an electron from highest occupied molecular orbital (HOMO) to the lowest unoccupied molecular orbital (LUMO)

58. Ultraviolet Spectroscopy Absorption detected and displayed on a chart plotting wavelength versus absorbance (A)

59. Ultraviolet Spectroscopy Ultraviolet spectrum of buta-1,3-diene

60. Ultraviolet Spectroscopy Amount of UV light absorbed is expressed as the sample’s molar absorptivity ( ), defined by the equation where A = Absorbance c = Concentration in mol/L l = Sample pathlength in cm

61. 11.10 Interpreting Ultraviolet Spectra: The Effect of Conjugation Wavelength necessary to effect   * transition in a conjugated molecule depends on the energy gap between HOMO and LUMO, which in turn depends on the nature of the conjugated system Energy difference between HOMO and LUMO decreases as conjugation increases

62. Interpreting Ultraviolet Spectra: The Effect of Conjugation

63. 11.11Conjugation, Color, and the Chemistry of Vision Colored organic compounds have extended conjugated systems “UV” absorptions extend into the visible region  -Carotene has max = 455 nm When white light strikes  -carotene wavelengths in the blue region are absorbed while the yellow-orange colors are transmitted to our eyes

64. Conjugation, Color, and the Chemistry of Vision Ultraviolet spectrum of  -carotene, a conjugated molecule with 11 double bonds Absorption occurs in the visible region

65. Conjugation, Color, and the Chemistry of Vision  -carotene is converted in the human body to 11-cis- retinal, an essential molecule for vision

66. Conjugation, Color, and the Chemistry of Vision In the rod cells of the eye 11-cis-retinal is converted into rhodopsin, a light-sensitive substance When light strikes rhodopsin, trans-rhodopsin (metarhodopsin II ) is produced, which is accompanied by a change in geometry The change in geometry causes a nerve impulse to be sent through the optic nerve to the brain, where vision is perceived Metarhodopsin II is then recycled back into rhodopsin

67. Conjugation, Color, and the Chemistry of Vision The cis-trans change in bond geometry accompanying vision