2008PHM Pharmaceutical Analysis

Semester 2, 2014

Unknowns Workshop Booklet:

Analysis of unknown organic and pharmaceutical compounds

You are analysing a sample of raw material of a drug and found that it contained some residual solvent
from the synthesis. Use the spectra below to identify this impurity.

Problem 3
1. What is the molecular formula?

Fragment Box

2. What functional group/s are present in the IR?

3. UV/Vis: what is the possible chromophore?

Proposed Structure

4. Mass Spec: What is the parent peak? What are the fragments that give rise to the peaks observed in
the spectrum?

5. 1H NMR: Identify the chemical environment of the 1Hs, the integration and the spin-spin splitting (how
many neighbouring protons) for the peaks at:
Peak
Chemical Environment
Integration
Splitting & n =
(ppm)
1.3
2.0
4.1
6. 13C NMR: Based on the DEPT spectrum and the chemical shift, propose the chemical environment of the
carbons at:
Peak (ppm)
Chemical Environment
14
21
50
172

Unknown organic compound #4

Problem 4
1. What is the molecular formula?

Fragment Box

2. What functional group/s are present in the IR?

3. UV/Vis: what is the possible chromophore?

Proposed Structure

4. Mass Spec: What is the parent peak? What are the fragments that give rise to the peaks observed in
the spectrum?

5. 1H NMR: Identify the chemical environment of the 1Hs, the integration and the spin-spin splitting (how
many neighbouring protons) for the peaks at:
Peak
Chemical Environment
Integration
Splitting & n =
(ppm)
0.8
2.1
3.4
6. 13C NMR: Based on the DEPT spectrum and the chemical shift, propose the chemical environment of the
carbons at:
Peak (ppm)
Chemical Environment
10
28
32
175

Unknown Organic Compound #8

Problem 8
1. What is the molecular formula?

Fragment Box

2. What functional group/s are present in the IR?

3. UV/Vis: what is the possible chromophore?

Proposed Structure

4. Mass Spec: What is the parent peak? What are the fragments that give rise to the peaks observed in
the spectrum?

5. 1H NMR: Identify the chemical environment of the 1Hs, the integration and the spin-spin splitting (how
many neighbouring protons) for the peak at:
Peak
Chemical Environment
Integration
Splitting & n =
(ppm)
0.9

N/A

6. 13C NMR: Based on the DEPT spectrum and the chemical shift, propose the chemical environment of the
carbons at:
Peak (ppm)
Chemical Environment
27
34

Unknown Organic Compound #11

Problem 11
1. What is the molecular formula?

Fragment Box

2. What functional group/s are present in the IR?

3. UV/Vis: what is the possible chromophore?

Proposed Structure

4. Mass Spec: What is the parent peak? What are the fragments that give rise to the peaks observed in
the spectrum?

5. 1H NMR: Identify the chemical environment of the 1Hs, the integration and the spin-spin splitting (how
many neighbouring protons) for the peaks at:
Peak
Chemical Environment
Integration
Splitting & n =
(ppm)
1.9
2.1
6. 13C NMR: Based on the DEPT spectrum and the chemical shift, propose the chemical environment of the
carbons at:
Peak (ppm)
Chemical Environment
21
38
219

Unknown Organic Compound #13

10

Problem 13
1. What is the molecular formula?

Fragment Box

2. What functional group/s are present in the IR?

3. UV/Vis: what is the possible chromophore?

Proposed Structure

4. Mass Spec: What is the parent peak? What are the fragments that give rise to the peaks observed in
the spectrum?

5. 1H NMR: Identify the chemical environment of the 1Hs, the integration and the spin-spin splitting (how
many neighbouring protons) for the peaks at:
Peak
Chemical Environment
Integration
Splitting & n =
(ppm)
2.1
5.9
6. 13C NMR: Based on the DEPT spectrum and the chemical shift, propose the chemical environment of the
carbons at:
Peak (ppm)
Chemical Environment
32
70

11

A medicinal chemist has devised a new synthetic route for a drug that your pharmaceutical company is
developing. They send a sample to you to see if you can detect any impurities that may have arisen
from this new method. What is the impurity that you have identified from the spectra below?

12

Problem 14
1. What is the molecular formula?

Fragment Box

2. What functional group/s are present in the IR?

3. UV/Vis: what is the possible chromophore?

Proposed Structure

4. Mass Spec: What is the parent peak? What are the fragments that give rise to the peaks observed in
the spectrum?

5. 1H NMR: Identify the chemical environment of the 1Hs, the integration and the spin-spin splitting (how
many neighbouring protons) for the peaks at:
Peak
Chemical Environment
Integration
Splitting & n =
(ppm)
1.2
1.8
4.0
6. 13C NMR: Based on the proton coupled spectrum and the chemical shift, propose the chemical
environment of the carbons at:
Peak (ppm)
Chemical Environment
24
63

13

Organic Unknown Compound #17

14

Problem 17
1. What is the molecular formula?

Fragment Box

2. What functional group/s are present in the IR?

3. UV/Vis: what is the possible chromophore?

Proposed Structure

4. Mass Spec: What is the parent peak? What are the fragments that give rise to the peaks observed in
the spectrum?

5. 1H NMR: Identify the chemical environment of the 1Hs, the integration and the spin-spin splitting (how
many neighbouring protons) for the peaks at:
Peak
Chemical Environment
Integration
Splitting & n =
(ppm)
2.3
3.5
6. 13C NMR: Based on the DEPT spectrum and the chemical shift, propose the chemical environment of the
carbons at:
Peak (ppm)
Chemical Environment
31
37

15

You have been analysing a sample of biological fluid. You suspect that your sample contains a
neurotransmitter, which you have isolated. You run the spectra below to confirm your suspicions. What
is the identity of the neurotransmitter?

16

Problem 21
1. What is the molecular formula?

Fragment Box

2. What functional group/s are present in the IR?

3. UV/Vis: what is the possible chromophore?

Proposed Structure

4. Mass Spec: What is the parent peak? What are the fragments that give rise to the peaks observed in
the spectrum?

5. 1H NMR: Identify the chemical environment of the 1Hs, the integration and the spin-spin splitting (how
many neighbouring protons) for the peaks at:
Peak
Chemical Environment
Integration
Splitting & n =
(ppm)
1.9
2.4
3.0
6. 13C NMR: Based on the DEPT spectrum and the chemical shift, propose the chemical environment of the
carbons at:
Peak (ppm)
Chemical Environment
22
34
40

17

Unknown Organic Compound #22

18

Problem 22
1. What is the molecular formula?

Fragment Box

2. What functional group/s are present in the IR?

3. UV/Vis: what is the possible chromophore?

Proposed Structure

4. Mass Spec: What is the parent peak? What are the fragments that give rise to the peaks observed in
the spectrum?

5. 1H NMR: Identify the chemical environment of the 1Hs, the integration and the spin-spin splitting (how
many neighbouring protons) for the peaks at:
Peak
Chemical Environment
Integration
Splitting & n =
(ppm)
3.5
6.7 &
7.2
6. 13C NMR: Based on the DEPT spectrum and the chemical shift, propose the chemical environment of the
carbons at:
Peak (ppm)
Chemical Environment
55
114, 120, 130, 160

19

Organic Unknown Compound #23

20

Problem 23
1. What is the molecular formula?

Fragment Box

2. What functional group/s are present in the IR?

3. UV/Vis: what is the possible chromophore?

Proposed Structure

4. Mass Spec: What is the parent peak? What are the fragments that give rise to the peaks observed in
the spectrum?

5. 1H NMR: Identify the chemical environment of the 1Hs, the integration and the spin-spin splitting (how
many neighbouring protons) for the peaks at:
Peak
Chemical Environment
Integration
Splitting & n =
(ppm)
2.6
4.6
7.4
6. 13C NMR: Based on the DEPT spectrum and the chemical shift, propose the chemical environment of the
carbons at:
Peak (ppm)
Chemical Environment
65
127-142
(4 peaks)

21

Unknown Organic Compound #101

22

Problem 101
1. What is the molecular formula?

Fragment Box

2. What functional group/s are present in the IR?

3. UV/Vis: what is the possible chromophore?

Proposed Structure

4. Mass Spec: What is the parent peak? What are the fragments that give rise to the peaks observed in
the spectrum?

5. 1H NMR: Identify the chemical environment of the 1Hs, the integration and the spin-spin splitting (how
many neighbouring protons) for the peaks at:
Peak
Chemical Environment
Integration
Splitting & n =
(ppm)
2.6
7.5 &
7.9
6. 13C NMR: Based on the chemical shift, propose the nature of the carbons at:
Peak (ppm)
Chemical Environment
25
~120-140 (4)
188

23

Unknown Organic Compound #109

24

Problem 109
1. What is the molecular formula?

Fragment Box

2. What functional group/s are present in the IR?

3. UV/Vis: what is the possible chromophore?

Proposed Structure

4. Mass Spec: What is the parent peak? What are the fragments that give rise to the peaks observed in
the spectrum?

5. 1H NMR: Identify the chemical environment of the 1Hs, the integration and the spin-spin splitting (how
many neighbouring protons) for the peaks at:
Peak
Chemical Environment
Integration
Splitting & n =
(ppm)
3.5
4.5
6.8 &
7.2
7.7
6. 13C NMR: Based on the DEPT spectrum and the chemical shift, propose the chemical environment of the
carbons at:
Peak (ppm)
Chemical Environment
58
77
~115-130 (4)
158

25

Unknown Organic Compound #122

26

Problem 122
1. What is the molecular formula?

Fragment Box

2. What functional group/s are present in the IR?

3. UV/Vis: what is the possible chromophore?

Proposed Structure

4. Mass Spec: What is the parent peak? What are the fragments that give rise to the peaks observed in
the spectrum?

5. 1H NMR: Identify the chemical environment of the 1Hs, the integration and the spin-spin splitting (how
many neighbouring protons) for the peaks at:
Peak
Chemical Environment
Integration
Splitting & n =
(ppm)
1.4
4.0
6.8 &
7.8
6.7 &
D2O exchangeable
7.6
6. 13C NMR: Based on the chemical shift, propose the chemical environment of the carbons at:
Peak (ppm)
Chemical Environment
12
39
62
~112-160 (4)
169

27

An illicit substance was being analysed for purity by a forensics lab, but was found to have significant
quantities of another compound. A pure sample of contaminating compound was given to you for analysis.
Use the spectra below to identify the unknown substance.

28

Problem 125
1. What is the molecular formula?

Fragment Box

2. What functional group/s are present in the IR?

3. UV/Vis: what is the possible chromophore?

Proposed Structure

4. Mass Spec: What is the parent peak? What are the fragments that give rise to the peaks observed in
the spectrum?

5. 1H NMR: Identify the chemical environment of the 1Hs, the integration and the spin-spin splitting (how
many neighbouring protons) for the peaks at:
Peak (ppm)

Chemical Environment

Integration

Splitting & n =

0.9
2.1
4.0
6.8 & 7.4
8.0
6. 13C NMR: Based on the DEPT spectrum and the chemical shift, propose the chemical environment of the
carbons at:
Peak (ppm)
Chemical Environment
15
24
63
~114-155 (4)
170
Address the points below and place your fragments in the fragment box as you go

29

1. Look at the molecular formula

This can tell us a great deal of information before we even start: are there any heteroatoms (O,N,S,
halogens), therefore what kind of functional groups could be present? It can also tell us about the size of
the molecule, and if there are enough carbons for it to be aromatic (> 6 carbons). You can calculate
degrees of unsaturation.
2. IR spectrum: what functional groups are present?
Use a correlation chart (provided at the back of this workshop), in conjunction with the molecular formula, to
identify what functional groups are present. You should easily be able to identify an OH and carbonyl group
on sight.
3. UV/Vis Spectrum: is there a chromophore?
The UV/Vis will identify whether a chromophore is present. Chromophores arise from conjugation eg.
aromatic rings, ketones, aldehydes again, use the molecular formula to identify what is possible. If the
molecular formula is > 6 carbons, then it may be due to an aromatic ring, if its < 6 carbons then it may be
due to an conjugated alkene, ketone or aldehyde. Also, the chromophore can not be due to an aldehyde or
ketone if the formula doesnt contain oxygen.
4. Mass Spectrum: What is the molecular weight/molecular formula and what fragments are
present?
This is a very powerful technique that can identify important components of the molecule which is produced
upon fragmentation. Use a list of common fragments to help identify what may be giving rise to a particular
peak, or use a combination of the masses of atoms (H = 1, C = 12, N = 14, O = 16, F = 19, S = 32, Cl = 35,
Br = 80) to make up your own (reasonable!) fragment. Always keep in mind the molecular formula when
proposing potential fragments to make sure they are possible. Also keep in mind the specific ways that
functional groups fragment (eg. alpha cleavage of carbonyls).
5. Proton (1H) NMR: The different chemical environments of the hydrogens
This technique will identify how many different chemical environment of 1H there are. There are three very
important aspects of 1H NMR:
Chemical shift: each chemically distinct proton or group of protons will have a unique chemical shift (where
it comes on the x-axis in ppm), depending on the environment it is in, which is very heavily influenced by
proximity to electronegative atoms. See Watson Table 8.1 and 8.2 for a useful correlation chart (provided at
the back of this workshop).
Integration: this is the area under the peak/s and is proportional to the number of protons this peak
represents. Keep in mind the molecular formula when calculating the integration, and the number of
hydrogens in the formula should be the same as the number of protons identified in the spectrum, unless
you have D2O exchange (a proton directly attached to O or N in a solvent of D2O or MeOD.
Coupling: This gives information on the number of neighbouring protons (n) using the the n+1 rule. A
peak will be split into n+1 peaks due to n number of neighbouring protons, eg. A proton adjacent to a CH3
will be split into n+1 (3+1) = 4 peaks, or a quartet.
6. 13C NMR: The different chemical environments of the carbons
Uses the same principles as 1H NMR for chemical shift. See table 8.3 in Watson as a correlation chart.
Refer to NMR lecture 3 regarding 1H coupled and decoupled spectra, JMOD and DEPT spectra.

Correlation Charts
Common Mass Spec Fragments

30

IR Correlation Charts

31

32

1H

and 13C NMR Correlation Charts

33

34