2. Course Evaluation Last semester the average response rate for the on-line form was 54% as compared to about 80% for the old paper forms. Let’s do better !
We are going to do the course evaluation
in class on Fri., Dec., 5, 2014
Please bring your laptop.
Thanks !

3. Structure Determination
Chemistry
Organic Chemistry I
Fall, 2014
Day 36
12/1/14
Chapter 12
Structure Determination
Infrared Spectroscopy (IR) Chem Activity L-01
Mass Spectrometry (MS) Chem Activity L-02

4. Great Spectroscopy Sites http://www.chem.ucla.edu/~webspectra/

5. Substitution vs. Elimination
How can you tell which reaction occurs ?

6. The Electromagnetic Spectrum25

7. The Electromagnetic Spectrum

8. Molecular Motions ν ≈ k/m # IR bands = 3n – 6 for n non co-linear atoms Peak Intensity related to Δ in dipole moment

9. The Infrared Spectrum ȳ (cm-1) = 10,000/ λ in μm

10. Functional Groups in the IR

11. Chem Act L-01 The Infrared Spectrum

12. Model 5

13. Model 5

14. Model 5

15. Model 5
1715 cm-1

16. Exercise 1 # 1

17. Exercise 1 # 1
R-NH2
3350 asym
3250 sym

18. Exercise 1 # 2

19. Exercise 1 # 2
3340 broad

20. Exercise 1 # 3

21. Exercise 1 # 3
3300
H-CΞ
stretch
2100
CΞC
630
H-CΞ
bend

22. Exercise 1 # 4

23. Exercise 1 # 4
3050
H-C=C
sp2 C-H
1660
C=C
weak
1690
C=O unsat

24. Exercise 1 # 5

25. Exercise 1 # 5
1125 C-O

26. Alkanes, Alkenes, Alkynes

27. Infrared Spectra - Hydrocarbons

28. Cyclohexane and Cyclohexene which is which?

29. Benzenoid Aromatics
=C-H ca cm-1
C=C ca cm-1

30. Alcohols

31. Carbonyls C=O

32. What functionality ?

33. mono substituted

34. Problems 12. 34, 12. 35 How can you distinguish by IR
Problems 12.34, How can you distinguish by IR ? What distinguishing peaks in the IR ?

35. ChemAct S-16 Exercise Part A

37. Problem page 453

38. Problem page 453

39. What are the possible products?

40. What are the possible products?

41. What is the best way to prepare the ether ?

43. Chemistry 250-02 Organic Chemistry I Fall, 2014 Day 37 12/3/14
Chemistry
Organic Chemistry I
Fall, 2014
Day 37
12/3/14
Chapter 12
Chem Activity L2
Structure Determination
Q: How do we know the structure of an organic molecule ?
A: MS, IR, UV-Vis, NMR !

44. epibatidine ↓

45. A Mass Spectrometer

46. History of Mass Spectrometry
Mass Spectrum of
Neon Showing Major and Minor Natural Isotopes
20Ne
90.48%
rel. int
J.J. Thompson, the discoverer
of the electron in 1912, showed
there are 2 neon isotopes that are deflected differently by a magnet. His student, F. Aston, designed more elaborate instruments.
22Ne
9.25%
21Ne
0.27%
m/z

48. Electron Impact (EI) Mass Spectrometry
≈ MW !

49. base peak parent peak fragment analyte none of these
In mass spectrometry, what is the term used to describe the ion that results from the ejection of one electron from a molecule?
base peak
parent peak
fragment
analyte
none of these

50. What EI Mass Spectra Look Like

51. What quantity is detected in mass spectrometry?
the energy of a molecule
the number of electrons ejected from a molecule
the number of ions of a particular mass to charge (m/z) ratio
the number of electrons needed to ionize a molecule
the number of hydrogen atoms in a molecule

52. Chem Activity L2 Mass Spectrometry
Do Model page

57. Peak at m/z > MW ?!

58. Problem 12.1 Given the EI MS of Testosterone What is the molecular formula ?

59. Problem 12.1 Given the EI MS of Testosterone What is the molecular formula ?
C19H28O2

60. Which of the following reasons explains why some peaks are larger than others in a mass spectrum?
The larger peaks represent fragments that are more stable.
The larger peaks represent fragments that are less stable.
Cations tend to give larger peaks than radical cations.
Radical cations tend to give larger peaks than cations.
None of these

63. Problem page 453

64. Problem page 453

66. High Resolution MS Masses measured to 1 part in 20,000 !
Masses measured to 1 part in 20,000 !
A molecule with nominal mass of 44 could be
C3H8, C2H4O, CO2, or CN2H4.
If a more exact mass is, for example , pick the correct structure from:
C3H C2H4O CO CN2H4

67. Mass Spectra 1-Bromopropane
CH3-CH=CH2 + HBr in air 
CH3-CH2-CH3

68. 1-bromopropane  propene  2-bromopropane 1-bromopropane  propane  2-bromopropane43
CH3CH2CH2-Br
(CH3)2CH+

69. Mass Spectrometry
The presence of Bromine in a compound
The two (2) principal Bromine Isotopes in nature are
Br-79 and Br-81 (2 additional Neutrons in Br-81)
The relative abundance ratio of 79Br to 81Br is : or : or  1 : 1
Molecules containing a single Bromine atom will also show two molecular ion peaks one for Br-79 (M+) and one for Br-81 M+2).
Based on the natural abundance ratio of 100 / 97.1 (about 1:1), the relative intensity of the Br-79 peak will be about the same as the Br-81 peak.
Note: Fluorine exists in nature principally as a single isotope - 19F9
Therefore, single Molecular Ion peak (assuming no other Halogens present.

70. bromotoluene  Methylbenzene  benzylbromide

71. Mass Spectra 1- and 2-Chloropropane43
CH3CH2CH2-Cl

72. Mass Spectrometry
The Presence of Chlorine in a Compound
The two (2) principal Chlorine Isotopes in nature are Cl-35 and Cl-37 (2 additional Neutrons in Cl-37)
The relative abundance ratio of 35Cl to 37Cl is : or : or  3 : 1
Therefore, a Molecule containing a single Chlorine atom will show two Mass Spectrum Molecular Ion peaks, one for Cl-35 (M+) and one for Cl-37 (M+2)
Note: M+2 denotes 2 more neutrons than M+
Based on the natural abundance ratio of 100 / 32.6 (about 3:1), the relative intensity (peak height) of the Cl-35 peak will be 3 times the intensity of the Cl-37 peak.

73. EI MS – Alkanes n-Hexane (C6H14)57
41, 43
27, 29 71

74. Mass Spectra C5H12 pentane 2-methylbutane 2,2-dimethylpropane

75. EI MS 2,2-dimethylpropane
is the parent ion detected ?

76. Problem 12.24 43 29 71 57 86

77. Worked Example 12.1 EI MS methylcyclohexane and ethylcyclopentane

78. Mass Spectra - Alkenes

79. Mass Spectra - Alkenes

80. Problem 12.2 EI MS 2-methylpent-2-ene and hex-2-ene

81. EI Mass Spectra - Alkynes 1-Pentyne

82.  2-bromobutane 
CH3CH2CH=CH2
CH3CH=CHCH3

83. Mass Spectra - Ketones

84. EI MS 2- and 3-Pentanone
CH3-CH2-CH2-CO-CH3
CH3-CH2-CO-CH2-CH3

85. Mass Spectra - Alcohols

86. 1-propanol  propene  2-propanol
CH3-CH2-CH2-OH
CH3-CH(OH)-CH3

87. EI MS 1-Butanol

88. EI MS 2-Hexanol

101. Problem 12.2 (worked)

103. MALDI TOF MS of the Protein Insulin and an Enzyme Lysozyme
MW 14,

104. GC-MS Gas Chromatography - Mass Spectrometry

105. MS in Natural Products

106. MS and C60 !