Welcome to Organic Chemistry II

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1 Welcome to Organic Chemistry II

2 Erika Bryant, Ph.D.

3 Class Syllabus 3

4 CHAPTER 12: STRUCTURE DETERMINATION 4

5 What is this solution Soda Tea Coffee??? 5

6 What is this solution Soda Tea Coffee??? What is its size and formula What functional groups are present What is its carbon-hydrogen framework Are conjugate systems present 6

7 What is this solution Soda Tea Coffee??? What is its size and formula What functional groups are present Are conjugate mass systems present What spectrometry is its chemical structure Determine using 7

8 What is mass spectrometry 8

9 9 Mass Spectrometry Gives sample an electrical charge Separates ions by its mass-tocharge ratio (m/z) Detects and records separated ions

10 Mass Spectrometry Set up for one of the most common mass spectrometers 10

11 Mass Spectrometry 1. Inject sample 2. Sample is vaporized 3. Gaseous sample bombarded by highenergy electrons Energy of electron beam is commonly ~70 ev or 6700 kj/mol 11

12 Mass Spectrometry 4. Cation radical is produced 1. High energy electron strikes molecule 2. A valence electron is dislodge from the molecule 3. A radical cation is produced 1. Radical: molecule with an unpaired electron 2. Cation: a positive ion 12

13 Mass Spectrometry 5. Cation radicals fragments due to energy transfer from electron bombardment Smaller pieces are cations and neutral molecules 13

14 Mass Spectrometry 6. Fragments flow through a curved pipe in a magnetic field 7. Fragments are deflected into different paths according to their m/z Neutral charges are not deflected and collide with pipe walls 14

15 Mass Spectrometry 8. Positively charged fragments are detected 9. Detected results are recorded as peaks at varying m/z ratios 15

16 Mass Spectrometry 10. m/z value is equal to the fragments mass Charge is usually 1 Up to ~2500 amu can be analyzed by this type of instrument 16

17 Mass Spectrometry 17

18 Mass Spectrometry Bars parallel to the ion beam A common type of mass spectrometer Quadrupole mass analyzer 18

19 Mass Spectrometry Bars parallel to the ion beam Oscillating electrostatic field is generated between bars For a given field, only one m/z value will make it through the charge region 19

20 Mass Spectrometry Magnetic-sector mass spectrometer and quadrupole mass analyzer have a similar resolution Mass spectrometry can easily distinguish between molecular weights within ones place High resolution spectrometry can distinguish between molecules within amu (as with specific isotopic compositions) Double-focusing mass spectrometers: has two magnetic sections Example MW 72 is ambiguous: C 5 H 12 and C 4 H 8 O but: C 5 H amu exact mass C 4 H 8 O amu exact mass Result from fractional mass differences of atoms 16 O = , 12 C = , 1 H =

21 Mass spectrometry Mass spectrometry may be used to Measure mass Determine molecular weight Gain structural information Determine the identity of an unknown substance By molecular fingerprinting Each organic compound fragments in a unique way 21

22 Interpreting Mass Spectra 22

23 Mass Spectrometry Results Propane H H H C H C H C H H H Plot mass of ions (m/z) (x-axis) versus the intensity of the signal (roughly corresponding to the number of ions) (yaxis) Tallest peak assigned 100% intensity Called base peak Other peaks listed as percentage of base peak Parent peak is the unfragmented cation radical Also called molecular ion (M + or M) 23

24 Mass Spectrometry Not all compounds shows a molecular ion 2,2-dimethylpropane fragments easily and no molecular ion is observed If parent ion not present due to electron bombardment, softer methods such as chemical ionization are used (M+1) from 13 C that is randomly present 2,2-dimethylpropane 24

25 How do you determine what fragmentation occurs 25

26 Interpreting Mass-Spectral Fragmentation Patterns Fragmentation occurs by spontaneous cleavage of chemical bond One fragment retains the positive charge (charge remains on more stable fragment) Other fragment is its neutral radical 26

27 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 27

28 Interpreting Mass-Spectral Fragmentation Patterns Difficult to assign structures to fragment ions because fragmentation patterns are complex Especially true in hydrocarbons Most hydrocarbons fragment in many ways 28

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

30 Interpreting Mass-Spectral Fragmentation Patterns Difficult to assign structures to fragment ions because fragmentation patterns are complex Especially true in hydrocarbons Most hydrocarbons fragment in many ways Mass spectral fragmentations of functional groups can be interpreted to provide structural information 30

31 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 31

32 Mass Spectral Cleavage of Amines Amines undergo -cleavage, generating radicals Nitrogen rule: compounds with an odd number of nitrogen have an odd numbered molecular weight (Nitrogen is trivalent) 32

33 Mass Spectral Cleavage of Halides Elements with two common isotopes give a distinctive appearance 35 Cl and 37 Cl have a 3:1 ratio Moleclar ion peaks are M:M + 2 (Figure 12-11) 79 Br and 81 Br have a nearly 1:1 ratio Molecular ion peaks are M:M + 2 (Figure

34 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 34

35 Fragmentation of Carbonyl Compounds Most biochemical analyses by MS use: - Soft ionization methods (produce charges with little framentation - Electrospray ionization (ESI) - Matrix-assisted laser desorption ionization (MALDI) - Linked to a time-of-flight mass analyzer - More sensitive than the magnetic sector alternative - Separate fragments to an accuracy of 3 ppm - Biologists use the unit dalton (Da) instead of amu - 1 dalton = 1 amu 35

36 SPECTROSCOPY AND THE ELECTROMAGNETIC SPECTRUM 36

37 Spectroscopy and the Electromagnetic Spectrum Nondestructive spectroscopic techniques Infrared (IR) Ultraviolet (UV) Nuclear magnetic resonance (NMR) 37

38 Spectroscopy and the Electromagnetic Spectrum Nondestructive spectroscopic techniques Infrared (IR) Ultraviolet (UV) Nuclear magnetic resonance (NMR) What wavelength of electromagnetic radiation do these techniques use? 38

39 Spectroscopy and the Electromagnetic Spectrum Electromagnetic spectrum is divided into regions Different types are classified by frequency or wavelength ranges 39

40 Spectroscopy and the Electromagnetic Spectrum Radiant energy is proportional to its frequency (cycles/s = Hz) as a wave (Amplitude is its height) 40

41 Spectroscopy and the Electromagnetic Spectrum Electromagnetic radiation has a dual behavior Properties of a particle (called a photon) Behaves as an energy wave Characterized by a wavelength, frequency and amplitude 41

42 Spectroscopy and the Electromagnetic Spectrum c = speed of light = 3.00 X 10 8 m/s = frequency (s -1 ) = wavelength (m) 42

43 Spectroscopy and the Electromagnetic Spectrum Energy of Avogadro s number of photons of wavelength E= energy N A = Avogadro s number = number of particles/mol h = Planck s constant = 6.62 X J. s; = frequency (s -1 ) c = speed of light = 3.00 X 10 8 m/s; = wavelength (m) 43

44 Absorption Spectra An 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 44

45 Infrared Spectroscopy IR region lower energy than visible light (below red produces heating as with a heat lamp) m to m region used by organic chemists for structural analysis 45

46 Infrared Spectroscopy IR energy in a spectrum is usually measured as wavenumber (cm -1 ), the inverse of wavelength and proportional to frequency Specific IR absorbed by an organic molecule is related to its structure 46

47 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 47

48 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 48

49 Interpreting Infrared Spectra IR spectrum has lower energy region characteristic of molecule as a whole ( fingerprint region) Let s examine Figure

50 Figure

51 Regions of the Infrared Spectrum cm -1 N-H, C-H, O-H (stretching) N-H, O-H 3000 C-H cm -1 C C and C N (stretching) cm -1 double bonds (stretching) C=O C=C cm -1 Below 1500 cm -1 fingerprint region 51

52 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 C, C N > C=C, C=O, C=N > C C, C O, C N, C halogen 52

53 Infrared Spectra of Some Common Functional Groups Alkanes, Alkenes, Alkynes C-H, C-C, C=C, C C have characteristic peaks absence helps rule out C=C or C C 53

54 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

55 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 55

56 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 56

57 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 57

58 Let s Work a Problem Propose structures for a compound that fits the following data: It is an alcohol with M + = 88 and fragments at m/z = 73, m/z = 70, and m/z = 59 58

59 Answer Answer: We must first decide on the the formula of an alcohol that could undergo this type of fragmentation via mass spectrometry. We know that an alcohol possesses an O atom (MW=16), so that leads us to the formula C 5 H 12 O for an alcohol with M + = 88, with a structure of: One fragmentation peak at 70 is due to the loss of water, and alpha cleavage can result in m/z of 73 and

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