15 Problems in Spectroscopy 2010

Fifteen Problems in
Spectroscopy
1.0
0.9
0.8
0.7
Normalized Intensity
0.6
0.5
0.4
0.3
0.2
0.1
0
0.96 2.10
8.0 7.9 7.8 7.7 7.6 7.5 7.4 7.3 7.2 7.1 7.0 6.9
Chemical Shift (ppm)
Søren Brøgger Christensen

Department of Medicinal Chemistry
Faculty of Pharmaceutical Sciences
University of Copenhagen
2010
1
©2009 The University of Copenhagen. All rights reserved. No part of this material may be reproduced
without prior written permission of the publisher.
Preface
The following fifteen problems are a continuation of Ten Problem in Spectroscopy, which was used
as supplementary exercises for a course in spectroscopy at FARMA. The intention is to offer some
possibilities for students to work with problems in spectroscopy either individually or in groups.
The present edition differs from the first edition by adding five problems (Problem 1-5, Part 1) with
1
compounds, the structures of which can be solved solely by taking advantage of the IR, H NMR and
13
molecular weight as revealed from the mass spectrum. The C NMR spectrum and DEPT135 spectrum are
also given. If the signal in the 13C NMR spectrum is assigned a ”0” the signal will disappear in the DEPT
spectrum, a “+” indicates that the signal will have a positive intensity and a “-“ indicates a negative intensity.
13
The C NMR spectra can be used as a possibility for interpreting such spectra when the students feel
confident with this spectroscopical technique.
In some of the problems two 1H NMR spectra are recorded: one spectrum of the compound
dissolved in a deuterated solvent and one spectrum after addition deuterium oxide (D2O). By comparison of
the spectra you will observe that one or more signals have disappeared from the latter spectrum. In this case
advantage is taken of the possibility of exchanging protons attached to oxygen, nitrogen or sulfur atoms with
deuterium by shaking the solution with deuterium oxide. Consequently it can be concluded that the
disappeared signal originates in a proton attached to either an oxygen, a nitrogen, or a sulfur atom.
In worked Problem 1 an example is given on a strategy for structure elucidation.
The problems 6-15 (Part 2) present molecules with more complex structures. Such problems are
solved using all the information available from MS, 1H NMR, and 13C NMR spectra. Worked Problem 2
presents a strategy for dealing with this kind of problems.
It is always difficult to predict the challenge of problems, especially for someone who knows the
answers. That is why the problems appear at random. I would, however, assume the problems 11, 12, and
13 might appear a minor challenge than other problems in Part 2.
1
In the problems 6 and 7 you will notice that the H NMR spectrum is recorded at 300 MHz as well as
at 600 MHz. These spectra illustrate how a complex NMR pattern simplifies at higher field. In problem 6 a
COSY spectrum helps interpreting the contiguity of the molecule.
The following spectra are spectra recorded of real compound, meaning that you will experience the
false signal that might appear e.g. in an IR spectrum, if the potassium bromide used for preparing the disc is
humid.
Before looking up the solution I suggest that you draw the expected molecule in a drawing program
that enables you to predict the spectra (e.g. ChemBioDraw) and ask the program to predict the 1H and 13C
NMR spectra.
The solutions to the problems are given the last page as the CAS numbers of the compounds.
Finally I wish you fun when solving the problems.
Acknowledgement: Nils T. Nyberg has recorded the 600 MHz spectra, Birgitte Simonsen the IR spectra,
and Dorthe M. Skytte has performed careful prove reading and given creative inputs.
Copenhagen, October 2009
S. Brøgger Christensen
2
Index
Preface ........................................................................................................................................................... 2
Part 1 ............................................................................................................................................................. 4
Worked Problem 14
Elucidation of configuration using molecular weight, IR and 1H NMR spectra ............................................. 6
Problem 1 .................................................................................................................................................. 8
Problem 2 ................................................................................................................................................ 10
Problem 3 ................................................................................................................................................ 12
Problem 4 ................................................................................................................................................ 15
Problem 5 ................................................................................................................................................ 17
Part 2: Problems 6 – 15 ................................................................................................................................... 20
Elucidation of the configuration of organic compounds using EIMS, IR, 1H NMR and 13C NMR spectra 20
Mass spectrometry for Analysis of Elemental Composition of Organic Compounds.............................. 21
Worked Problem 2....................................................................................................................................... 22
Elucidation of configuration: ........................................................................................................................... 24
Problem 6 ................................................................................................................................................ 27
Problem 7 ................................................................................................................................................ 31
Problem 8 ................................................................................................................................................ 35
Problem 9 ................................................................................................................................................ 38
Problem 10 .............................................................................................................................................. 41
Problem 11 .............................................................................................................................................. 45
Problem 12 .............................................................................................................................................. 47
Problem 13 .............................................................................................................................................. 50
Problem 14 .............................................................................................................................................. 53
Problem 15 .............................................................................................................................................. 56
Solutions to the problems (CAS numbers): ............................................................................................. 59
3
Part 1
Worked Problem 1
EIMS (75eV)
43
100
MS+· = 86
O
50
86
27 41 58 71
15 29 39 42 44
26 87
0
10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100
(ma inlib ) 2-Penta none
IR (Liquid sandwich)
4
Worked problem 1
1
H NMR (300 MHz, CDCl3)
1.0
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0
2.00 3.10 1.95 3.07
2.5 2.0 1.5 1.0

13
C NMR (75 MHz, CDCl3)
-
- +
45.65
13.72
+
17.32
1.00
29.87
0.75
0.50
208.91
0.25
200 180 160 140 120 100 80 60 40 20

5
Elucidation of the configuration of an organic compound using molecular
weight, IR and 1H NMR spectra
The structures of the compounds, in which the spectra given in problems 1 to 5 originate, can be
elucidated solely by interpreting the IR and 1H NMR spectra and taking advantage of the molecular
weight as stated on the EIMS spectrum. The EIMS and 13C NMR spectra are also given. The latter
spectra might be interpreted at a later stage.
Molecular weight
The molecular weight is stated to be 86 g/mol.
Functional groups
The IR spectrum reveals a strong absorbance just below 3000 cm-1 indicating the presence of
hydrogen atoms attached to sp3 hybridized carbon atoms. In addition the spectrum reveals a
strong absorbance at 1720 cm-1 indicating the presence of a ketone group. Besides these bands
the spectrum reveals no strong absorbance above 1500 cm-1.
Building blocks
1
H NMR spectrum
The building blocks of the molecule can be interpreted from the 1H NMR spectrum revealing the
presence of two methyl groups (2 × CH3, 2.10 and 0.90 ppm, integral 3H for each) and two
methylene groups (2 × CH2, 2.40 and 1.60 ppm, integral 2H for each). A combination of the atoms
present in the groups affords a weight of 2×15 + 2×14 = 58. Since the molecular weight was 86 the
weight of the remaining building block must be 28, corresponding to a C=O group. This latter group
already was expected from the IR spectrum revealing that the compound was a ketone.
The contiguity of the molecule

The contiguity of the molecule is revealed from the multiplicities (coupling patterns) of the signals in
the 1H NMR spectrum as listed in the below Table 1.
δ Intensity Multiplicity J Interpretation
2.40 2 t 6.9 Hz CH2-CH2-CO
2.10 3 s 6.9 Hz CH3-CO
1.60 2 sextet 6.9 Hz CH3-CH2-CH2
0.90 3 t 6.9 Hz CH3-CH2
Table 1: Systematic representation of the signals in the 1H NMR spectrum.
The coupling constants, J, are measured on the spectrum as illustrated below:
1. The distance between δ 1.0 and 2.0 on the X-axis measured with a ruler is 56 mm.
2. Since the spectrum is recorded at 300 MHz 1 ppm equals 300 Hz. From point 1 it appears
that 56 mm is the distance between 1 and 2 ppm on the X-axis and therefore 56 mm also is
the distance of 300 Hz on the X-axis. Division 300/56 reveals that 1 mm equals 5.3 Hz.
6
3. The distances between the peaks of the triplet at 2.4 ppm measured with a ruler is 1.3 mm
corresponding to 1.3×5.3 = 6.9 Hz.
The signal at δ 2.40 is a triplet (J 6.9 Hz) integrating for two protons. The δ-value indicates that the
signal is next to the C=O group and the multiplicity indicates that the signal is also next to a CH2-
group.
The signal at δ 2.10 is a singlet integrating for three protons. The δ-value indicates that the signal is
next to a C=O group: CH3-(C=O)-.
The signal at δ 1.60 is a sextet (J 6.9 Hz) integrating for two protons, indicating that the signal is
only weakly affected by elctronegative groups and 5 neighboring protons are affecting the signal.
The neighboring groups have to be a methyl and a methylene group.
The signal at δ 0.90 is a triplet (J 6.9 Hz) integrating for three protons, indicating a methyl group
affected by a neighboring methylene group.
All this information is given in the table.
Based on this knowledge the molecule has to be: CH3-(C=O)-CH2-CH2-CH3.
Prediction of spectrum
Figure 1 reveals the spectrum predicted by ChemBioDraw (Draw the compound in the drawing
program, mark the compound, go into structure, and choose predict 1H-NMR shifts):
Figure 1: 1H NMR spectrum predicted by ChemBioDraw. As often is the case with simple molecules the
prediction is very good.
7
Problems 1-5
Problem 1
EIMS (75 eV)
57
100
MS+· = 86
29
O
50
86
27
28 56 58
26 30 39 41 43 87
0
10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100
IR (Liquid sandwich, the peak at 1600 cm-1 is an internal reference)
8
Problem 1
1
1.0
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0
2.06 3.00
3.5 3.0 2.5 2.0 1.5 1.0 0.5

13
+
35.45
7.94
1.0
0.9
0.8
0.7
0.6
0.5 0
0.4
211.95
0.3
0.2
0.1
220 200 180 160 140 120 100 80 60 40 20 0 -20

9
Problem 2
EIMS (75 eV)
45
100
HO
MS+· = 74
50
27 31 59
29
41 43
18
28
30 42 46 55 57 73
0
10 14 18 22 26 30 34 38 42 46 50 54 58 62 66 70 74 78
IR (Liquid sandwich, the peak at 1600 cm-1 is an internal reference)
10
Problem 2
1
1.0
0.9
0.15
0.8
0.7 0.10
0.6
0.05
0.5
0.4
0
1.00
0.3 3.85 3.80 3.75 3.70 3.65 3.60 3.55 3.50 3.45
0.2
0.1
0
1.00 1.20 2.02 3.03 2.93
4.0 3.5 3.0 2.5 2.0 1.5 1.0 0.5

1
H NMR (300 MHz, CDCl3 added D2O)
1.0
1.0
0.9
0.9
0.8
0.8 0.7
0.6
0.7
0.5
0.4
0.6
0.3
0.5 0.2
0.1
0.4
0
2.02 3.03 2.93
1.5 1.4 1.3 1.2 1.1 1.0 0.9 0.8 0.7

0.3 Chemical Shift (ppm)
0.2
0.1
0
1.00 2.08 3.16 2.95
3.5 3.0 2.5 2.0 1.5 1.0

11
Problem 2
13
+
-
22.89
+
32.01
1.0
10.03
+
0.9
0.8
69.42
0.7
0.6
0.5
0.4
0.3
0.2
0.1
85 80 75 70 65 60 55 50 45 40 35 30 25 20 15 10 5
Problem 3
EIMS (75 eV)
43
100
41
42
MS+· = 74
OH
50
31
33
39
27
29 74
55
57
38 40 44 59
15 26 28 30 50 53 73
0
10 14 18 22 26 30 34 38 42 46 50 54 58 62 66 70 74 78
12
Problem 3
1
1.0
0.07
0.9
0.06
0.8
0.05
0.7
0.04
0.6
0.03
0.5
0.02
0.4
0.01
0.3 0
1.00
0.2 2.00 1.95 1.90 1.85 1.80 1.75 1.70 1.65 1.60 1.55
0.1
0
2.15 1.13 1.00 6.18
4.0 3.5 3.0 2.5 2.0 1.5 1.0

13
Problem 3
1
1.0
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0
2.00 0.93 5.95
3.5 3.0 2.5 2.0 1.5 1.0 0.5

13
18.91
1.0
0.9
0.8
-
0.7
+
69.64
0.6
30.81
0.5
0.4
0.3
0.2
0.1
85 80 75 70 65 60 55 50 45 40 35 30 25 20 15 10
14
Problem 4
EIMS (75 eV)
56
100 31
41
MS+· = 74
43
27
OH
50
42
29
55
39
28
26
15 33
38 45 57
14 19
32 73
0
10 14 18 22 26 30 34 38 42 46 50 54 58 62 66 70 74 78
IR spectrum (Liquid sandwich, the peak at 1600 cm-1 is an internal reference)
15
Problem 4
1
1.0
0.20
0.9
0.8
0.15
0.7
0.10
0.6
0.5 0.05
0.4
0
2.06 2.06
0.3
1.60 1.55 1.50 1.45 1.40 1.35 1.30 1.25 1.20 1.15
0.2
0.1
0
2.07 1.08 2.06 2.06 3.00
4.5 4.0 3.5 3.0 2.5 2.0 1.5 1.0

1
1.0
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0
2.03 1.92 2.04 3.00
4.0 3.5 3.0 2.5 2.0 1.5 1.0 0.5

16
Problem 4
13
-
-
- +
62.60
34.82
13.91
18.94
1.0
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
-0.1
85 80 75 70 65 60 55 50 45 40 35 30 25 20 15 10 5
Problem 5
EIMS (75 eV) MS+· = 222
149
100
50
O
177 O
29 65 76 105
93 121
50 222
39 45 132
0
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230
17
Problem 5
1
1.0
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0
0.93 0.99 2.05 3.00
7.5 7.0 6.5 6.0 5.5 5.0 4.5 4.0 3.5 3.0 2.5 2.0 1.5
18
Problem 5
13
+
130.79
-
128.69
+
1.00
61.60
14.17
0.75
0 0
132.07
0.50
167.41
0.25
170 160 150 140 130 120 110 100 90 80 70 60 50 40 30 20 10

19
Part 2: Problems 6 – 15
Elucidation of the configuration of an organic compound using EIMS, IR, 1H
NMR and 13C NMR spectra
On the following pages you will find the EIMS, IR, 1H NMR, and 13CNMR spectra of ten organic
compounds. The challenge is to elucidate the configurations of the compounds. A possible strategy
is firstly to interpret the MS to deduce the molecular weight. Inspection of the pattern at M+·,
(M+1)+·, and (M+2)+· or the similar pattern at dominant peaks in the mass spectrum can be used for
estimating the elemental composition of the molecule (cf. the following paragraph on mass
spectrometry). The functional group(s) in the molecule might be deduced from the IR spectrum
and, if the functional group contains a carbon atom, from the 13C NMR spectrum. The DEPT-135
combined with the 13C NMR spectrum reveals the number of quaternary carbon atoms, the number
of methine, methylene and methyl groups in the molecule. The DEPT-135 spectrum is indicated in
the 13C NMR spectra by annotation of “0” if the signal disappears, “+” if the signal has a positive
intensity, and “-“ if the signal has a negative intensity in the DEPT-135 spectrum. Use the
integration curves in the 1H NMR spectrum to confirm the number of hydrogen atoms in the
molecule. By adding the weight of the revealed groups an estimate of the molecular weight can be
made. If the estimated weight corresponds to the weight as revealed from the MS the building
blocks involved in the molecule are known. Finally the contiguity of the molecule to give the final
configuration can be obtained by interpreting the coupling pattern of the signals in the 1H NMR
spectrum.
In Worked Problem 2 you will find an example of structure elucidation using the mentioned
strategy. In the following paragraph you will find see how the signals in the mass spectra with m/z
values a few units higher than the value of the molecular weight might be used for estimation of the
molecular formula.
20
Mass spectrometry for Analysis of Elemental Composition of Organic
Compounds
Almost all elements are a mixture of more isotopes. In general the major isotope possesses the
smallest atomic mass (an exception is borine). The molecular mass is defined as the mass of the
molecule containing the lightest isotopes. A mass spectrum thus will display a peak for the
molecular ion plus a number of peaks with larger values for m/z. The pattern of these peaks will
depend on the elemental composition of the molecule and might thus be helpful for estimating the
molecular formula. The most common elements in organic molecules are listed in Table 1:
Table 2: Isotopes of common elements in organic compounds:
A A+1 A+2
Element Atomic weight % Atomic weight % Atomic weight % Type of element
H 1 100 2 0.015 A
C 12 100 13 1.1 A+1
N 14 100 15 0.37 A+1
O 16 100 17 0.04 18 0.20 A+2
F 19 100 A
Si 28 100 29 5.1 30 3.4 A+2
P 31 100 A
S 32 100 33 0.79 34 4.4 A+2
Cl 35 100 37 32.0 A+2
Br 79 100 81 97.3 A+2
I 127 100 A
The elements might be grouped into three types of elements: Type A, Type A+1, and Type A+2. If
the intensity of the peak two units higher than the molecular ion is less than three per cent of that
of the molecular ion it may be concluded that none of the elements Si, S, Cl or Br is present. Some
characteristic patterns for molecules containing chlorine and bromine molecules are given in (Table
2).
Table 3: Abundance of isotope peaks in chlorine and bromine containing ions.

A A+2 A+4 A+6
Cl 100 32
Cl2 100 64 10
Br 100 97
Cl3 100 96 31 3
BrCl 77 100 24
BrCl2 62 100 45 6
Br2 51 100 49
Some drawing software like ChemDraw shows the pattern above the molecular peak in the
analysis window (in ChemBioDraw mark the molecule, choose the View drop down menu, choose
Analysis Window).
The number of carbon atoms in the molecule can be calculated according to the below equation:
in which 1.1 is the percentage of naturally occurring 13C, n is the number of carbon atoms in the
molecule, I(M+1) is the intensity of the peak at (M+1), I(M) is the intensity of the molecular peak.
21
Worked Problem 2
EIMS (75 ev)
67
100
40
39
50
53
27
29
41
68
38 51
37 65
26 28 52 63
15 31 43 49 54
0
10 14 18 22 26 30 34 38 42 46 50 54 58 62 66 70 74 78
22
1
H NMR Spectrum (300 MHz, CDCl3)
1.0
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0
2.06 1.00 2.12 3.16
2.3 2.2 2.1 2.0 1.9 1.8 1.7 1.6 1.5 1.4 1.3 1.2 1.1 1.0 0.9
13
C NMR Spectrum (75 MHz, CDCl3)
+
-
68.15
+
-
1.0
13.42
22.00
0.9
20.44
0.8
0.7
0
0.6
84.46
0.5
0.4
0.3
0.2
0.1
85 80 75 70 65 60 55 50 45 40 35 30 25 20 15
23
Elucidation of configuration of worked problem 2:
Molecular weight
EIMS indicates a molecular weight of 68
Building blocks
13
C NMR and DEPT-135 shows
1 quaternary C
2 CH2
1 CH and 1 CH3, or 2 CH, or 2 CH3.
The chemical shifts of the signals indicate 1 CH and 1 CH3. This is confirmed by inspection of the
1
H NMR spectrum in which one signal integrates for 1H and one signal for 3H.
Addition of the weights of these building blocks gives 12 + 2×14 + 13 + 15 = 68. All the building
blocks of the molecule have been found.
Molecular formula: C5H8 → DBE: ½(10+2-8) = 2
Functional groups
IR spectrum:
A strong band at 3311 cm-1 and 2117 cm-1 shows the presence of a terminal triple bond. No
additional functional groups appear to be present.
The presence of a triple bond is confirmed by signals at 84 and 68 ppm in the 13C NMR spectrum.
The contiguity of the molecule

1
H NMR spectrum
The contiguity of the molecule is revealed from the coupling patterns of the signals of the protons
in the molecule (Table 4).
δ Intensity Multiplicity J Interpretation
2.15 2 dt 3 and 7 Hz H- - CH2-CH2
1.93 1 t 3 Hz H- - CH2
1.55 2 sextet 7 Hz CH2-CH2-CH3
0.90 3 t 7 Hz CH3-CH2
Table 4: Systematic representation of the signals in the 1H NMR spectrum.
The small size of the coupling constant (3 Hz) of the signals at 2.15 ppm and 1.93 ppm indicate
that this is a long range coupling (larger than 3-bonds coupling, indicated by using two hyphens
between the H and the C in the Table). All the other coupling constants (7 Hz) are as expected for
vicinal couplings (3-bonds couplings).
24
The coupling constants are measured as described in Worked Problem 1
The splitting pattern of the terminal CH3 (t) reveals that it must be bound to a CH2 group: CH3-CH2-.
The splitting pattern of the CH2 group bound to the CH3 (sextet) reveals that it must be bound to an
additional CH2: CH3-CH2-CH2-.
Remaining building blocks are C and CH. Since the IR and 13C NMR spectrum indicated a terminal
triple bond we can conclude that these two carbons must be a CΞC-H group yielding the molecule:
CH3-CH2-CH2-CΞC-H.
The presence of a coupling constant of 3 Hz in only in the two signals at 2.15 and 1.93 proves that
the protons, in which these signals origin, must couple with each other.
The coupling pattern of the CH2-group next to the triple bond can be explained by the coupling
diagram (Figure 2):
1.0
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0
2.06
2.35 2.30 2.25 2.20 2.15 2.10

Figure 2: Coupling diagram of the CH2 group next to the triple bond.
Prediction of the spectra

If the molecule is drawn in ChemBioDraw and the program is prompted to predict the 1H NMR
spectrum (mark the molecule, choose the drop down menu at Structure and ask for the prediction
of 1H NMR) the below spectrum is predicted (Figure 3):
Figure 3: 1H NMR spectrum predicted by ChemBioDraw for 1-pentyne.
25
Notice that the signal originating in the CΞC-H is predicted to appear at 2.7 ppm but actually
appears at 1.93 ppm. The other signals are reasonably well predicted. Notice also the good
prediction of the coupling patterns.
The predicted 13C NMR spectrum is shown below (Figure 4):
Figure 4: 13C NMR of 1-pentyne predicted by ChemBioDraw.
Interpretation of the spectra (Figure 5):

1 13
H NMR C NMR
Figure 5: Interpretation of the NMR spectra
Interpretation of the MS
In the MS spectrum the peak at m/z 53 must origin form M+·-15, the peak at m/z 67 must origin
form M+·-1, and the peak at m/z 40 equals the loss of an ethylene molecule, which could be caused
by at McLafferty rearrangement (Figure 6):
m/z = 68 m/z = 40
Figure 6: Possible McLafferty fragmentation of 1-pentyne.

26
Problem 6
EIMS (75 ev)
60
100
125
MS+·O= 222
Br
HO
50
73 83
55
143
41
97
163
27 69
87
101 115 135 179 193 205 223
0
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240
(ma inlib ) 8-Bromooc ta noic a c id
IR (KBr)
27
Problem 6
1
1.0
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0
0.68 2.00 2.04 2.03 8.04
12 11 10 9 8 7 6 5 4 3 2 1
1.0
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0
2.00 2.04 2.03 8.04
3.5 3.0 2.5 2.0 1.5

28
Problem 6
13
77.42
77.00
76.58
1.0
32.67
27.92
0.9
28.37
1.0
33.88
28.81
33.99
24.50
0.8
32.67
24.50 27.92
0.9
28.37
0.7
33.88
28.81
33.99
0.6
0.8 0.5
0.4
0.7
0.3
0.6 0.2
0.1
0.5 0
36 34 32 30 28 26 24 22 20
0.4 Chemical Shift (ppm)
0.3
180.30
0.2
0.1
180 170 160 150 140 130 120 110 100 90 80 70 60 50 40 30 20

The signal at δ 180 will disappear in a DEPT-135 experiment and all the other peaks will obtain a
negative intensity.
1
H NMR spectrum (600 MHz, CDCl3)
1.0
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0
0.80 2.00 2.08 2.01 4.02
12 11 10 9 8 7 6 5 4 3 2 1
The signal at 11 ppm disappears after addition of D2O.
29
Problem 6
1
1.0
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0
2.00 2.08
3.7 3.6 3.5 3.4 3.3 3.2 3.1 3.0 2.9 2.8 2.7 2.6 2.5 2.4 2.3 2.2 2.1
1.0
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0
2.01 2.07 2.02 4.02
2.0 1.9 1.8 1.7 1.6 1.5 1.4 1.3 1.2 1.1 1.0 0.9 0.8
30
Problem 7
EIMS (75 ev)
182
100
O OH 107
50
O
149
137
51
65 153
79
122 167
15 39 53 63
68 81 92
29 41 45 96
74
0
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190
IR (KBr)
31
Problem 7
1
1.0
0.9
0.8
0.7
0.6
1.0
0.5 0.9
0.8
After addition of D2O
0.7
0.4
0.6
0.5
0.4
0.3
0.3
0.2
0.2 0.1
11.5 11.0 10.5 10.0 9.5 9.0

0.1
0
0.69 1.00 2.15 3.18
12 11 10 9 8 7 6 5 4
1.0
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0
0.96 2.10
7.9 7.8 7.7 7.6 7.5 7.4 7.3 7.2 7.1 7.0 6.9 6.8 6.7 6.6
32
13
0 +
+ +
123.70
117.33
56.17
124.82
1.00 +
62.19
0.75
0 0
0.50
151.89
121.99
165.33
148.00
0.25
168 160 152 144 136 128 120 112 104 96 88 80 72 64 56 48 40

33
Problem 7
1
H NMR spectrum (600 MHz, CDCl3)
1.0
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0
0.90 2.03 3.27
8.0 7.5 7.0 6.5 6.0 5.5 5.0 4.5 4.0 3.5
1.0
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0
0.90 2.03
7.85 7.80 7.75 7.70 7.65 7.60 7.55 7.50 7.45 7.40 7.35 7.30 7.25 7.20 7.15 7.10 7.05
34
Problem 8
EIMS (75 ev)
166
100
76
O
O O
50
39 107 148
63
65
51
90
104
122 133
29 41
15 55 69 95
31 43
112
0
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180
IR (KBr)
35
Problem 8
1
1.0
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0
0.90 1.06 2.14 6.89
10.5 10.0 9.5 9.0 8.5 8.0 7.5 7.0 6.5 6.0 5.5 5.0 4.5 4.0 3.5
1.0
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0
1.06 2.14
7.7 7.6 7.5 7.4 7.3 7.2 7.1 7.0 6.9 6.8 6.7 6.6 6.5 6.4 6.3 6.2
36
Problem 8
13
+
+
56.04
103.72
1.0
0.9
0.8
+ +
0.7
0
189.17
0.6
77.43
76.58
135.77
77.00
0.5
161.96
0.4 0
0.3
114.14
0.2
0.1
190 180 170 160 150 140 130 120 110 100 90 80 70 60 50 40
37
Problem 9
EIMS (75 ev)
138
100
HO
O
50
OH
109
81
42 51 63
55
66 69
0
40 50 60 70 80 90 100 110 120 130 140 150
IR (KBr)
38
Problem 9
1
H NMR Spectrum (300 MHz, CD3OD)
1.0
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0
1.10 0.98
10.0 9.5 9.0 8.5 8.0 7.5 7.0 6.5 6.0 5.5 5.0 4.5 4.0 3.5 3.0
1.0
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0
2.08 0.98
7.10 7.05 7.00 6.95 6.90 6.85 6.80 6.75 6.70 6.65 6.60 6.55 6.50 6.45 6.40 6.35 6.30 6.25
39
Problem 9
13
C NMR (75 MHz, CD3OD)
+
108.76
1.0
0.9
0.8
0.7 +
0.6
109.82
194.06
0
0.5 0
160.42
0.4
140.03
0.3
0.2
0.1
192 184 176 168 160 152 144 136 128 120 112 104 96 88
40
Problem 10
EIMS (75 ev)
164
100
OH
50
77 103 149
131
91
55
137
121
51
39 65
53 94
41 63
27 81 115
15 75
0
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180
IR (liquid sandwich)
41
Problem 10
1
0.55
0.13
0.50 0.12
0.11
0.10
After addition of D2O
0.45 0.09
0.08
0.40 0.07
0.06
0.05
0.35 0.04
0.03
0.02
0.30 0.01
6.2 6.1 6.0 5.9 5.8 5.7 5.6 5.5 5.4 5.3 5.2 5.1 5.0
0.25
0.20
0.15
0.10
0.05
0
1.02 2.00 0.95 0.90 2.05 3.17 2.18
7.5 7.0 6.5 6.0 5.5 5.0 4.5 4.0 3.5 3.0
1.0
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0
1.02 2.00
7.05 7.00 6.95 6.90 6.85 6.80 6.75 6.70 6.65 6.60 6.55 6.50 6.45 6.40
42
Problem 10
1
0.15
0.10
0.05
0
0.95 0.90 2.05
6.2 6.1 6.0 5.9 5.8 5.7 5.6 5.5 5.4 5.3 5.2 5.1 5.0 4.9 4.8
1.0
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0
3.17 2.18
4.3 4.2 4.1 4.0 3.9 3.8 3.7 3.6 3.5 3.4 3.3 3.2 3.1 3.0 2.9
43
Problem 10
13
+
+
+ -
+
55.83
114.11
39.92
121.02
115.40
110.96
1.0
0.9 0 +
77.00
77.42
76.58
0.8 0
137.66
0.7 0
131.75
0.6
-
143.69
0.5
146.23
0.4
0.3
0.2
0.1
-0.1
152 144 136 128 120 112 104 96 88 80 72 64 56 48 40 32
COSY spectrum (300 MHz, CDCl3)
F1 Chemical Shift (ppm)

4
7
7.0 6.5 6.0 5.5 5.0 4.5 4.0 3.5 3.0
F2 Chemical Shift (ppm)
44
Problem 11
EIMS (75 ev)
75
100
201
155
O O
N
50
50
171
Br
143
30
38 63
28 92 129 185
80 117
0
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210
IR (KBr)
45
Problem 11
1
H NMR (CDCl3, 300 MHz)
1.0
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0
2.01 2.00
8.5 8.0 7.5 7.0 6.5

13
C NMR (CDCl3, 75 MHz)
+ 124.86 +
132.46
1.0
0.9
0.8
0.7
0.6
0.5 0
0.4
0
129.84
0.3
0.2
146.80
0.1
165 160 155 150 145 140 135 130 125 120 115 110 105
46
Problem 12
EIMS (75 ev)
43
100
MS+· = 114
O
50
58
27
15 41
29 71
55 81 99 114
0
10 20 30 40 50 60 70 80 90 100 110 120 130
47
Problem 12
1
1.0
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0
2.07 2.96 3.06 6.00
2.5 2.4 2.3 2.2 2.1 2.0 1.9 1.8 1.7 1.6 1.5 1.4 1.3 1.2 1.1 1.0 0.9
1.0
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0
2.07 2.96 3.06
2.5 2.4 2.3 2.2 2.1 2.0 1.9 1.8 1.7 1.6 1.5 1.4 1.3
1.0
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0
3.06 6.00
1.6 1.5 1.4 1.3 1.2 1.1 1.0 0.9 0.8 0.7 0.6
48
Problem 12
13
- +
22.38
1.00 -
0.75
0
41.85
32.66
27.70
0.50
209.25
0.25
0
220 200 180 160 140 120 100 80 60 40 20 0 -20
49
Problem 13
EIMS (75 ev)
M+· = 99
31
100
54 N
59
50
29
27
45 55 57
41
28 84
15 43
52 70 98
44 56 60
0
10 20 30 40 50 60 70 80 90 100 110
50
Problem 13
1
1.0
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0
4.02 2.00 2.80
3.5 3.0 2.5 2.0 1.5 1.0

1.0
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0
4.02 2.00
3.5 3.0 2.5

51
Problem 13
1
1.0
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0
2.00 2.80
2.5 2.0 1.5

13
- -
65.31
19.30
1.00
67.05
15.36
0.75
0.50 0
118.19
0.25
120 112 104 96 88 80 72 64 56 48 40 32 24 16

52
Problem 14
EIMS (75 ev)
86
100
M+· = 131
44
30 OH
O
50
NH2
74
28
41
39
46 57 70
15
18
0
10 20 30 40 50 60 70 80 90 100 110 120 130 140
IR (KBr)
53
Problem 14
1
H NMR (D2O, 300 MHz)
1.0
0.9
0.8
0.7
0.6
0.5
MeCN
0.4
0.3
0.2
0.1
0
0.98 3.18 6.00
5.0 4.5 4.0 3.5 3.0 2.5 2.0 1.5 1.0 0.5
1.0
0.9
0.8
0.7
0.6
0.5
MeCN
0.4
0.3
0.2
0.1
0
0.98
3.5 3.0 2.5 2.0

54
Problem 14
1
H NMR (D2O, 300 MHz)
1.0
0.9
0.8
0.7
0.6
0.5
M eC N
0.4
0.3
0.2
0.1
0
3.18 6.00
2.0 1.5 1.0 0.5

13
C NMR (D2O, 75 MHz)
-
+
+
40.02
24.40
21.12
22.28
53.59
1.00
+
0
0.75
175.54
0.50
0.25
180 170 160 150 140 130 120 110 100 90 80 70 60 50 40 30 20

55
Problem 15
EIMS (75 ev) M+· = 258
129
100
O
O
O
57
50
185
41
111
29
101
87
143 156
73
18 147
0
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 250 260 270
56
Problem 15
1
1.0
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0
2.07 2.13 0.97 2.17 6.00
4.5 4.0 3.5 3.0 2.5 2.0 1.5 1.0 0.5

1.0
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0
2.07 2.13
4.0 3.5 3.0 2.5

1.0
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0
0.97 2.17 6.00
2.0 1.9 1.8 1.7 1.6 1.5 1.4 1.3 1.2 1.1 1.0 0.9 0.8 0.7 0.6 0.5
57
Problem 15
13
+ +
19.17
1.00
- -
0.75
34.02
70.48
24.55
0
27.76
0.50
173.22
0.25
170 160 150 140 130 120 110 100 90 80 70 60 50 40 30 20 10

58
Solutions to the problems (CAS numbers):
Problem 1 96-22-0
Problem 2 78-92-2
Problem 3 78-83-1
Problem 4 71-36-3
Problem 5 84-66-2
Problem 6 17696-11-6
Problem 7 1521-38-6
Problem 8 3392-97-0
Problem 9 26153-38-8
Problem 10 97-53-0
Problem 11 586-78-7
Problem 12 110-12-3
Problem 13 2141-62-0
Problem 14 61-90-5
Problem 15 141-04-8
59

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Fifteen Problems in

Søren Brøgger Christensen

In worked Problem 1 an example is given on a strategy for structure elucidation.

Finally I wish you fun when solving the problems.

Copenhagen, October 2009

Elucidation of configuration using molecular weight, IR and 1H NMR spectra ............................................. 6

Part 2: Problems 6 – 15 ................................................................................................................................... 20

Mass spectrometry for Analysis of Elemental Composition of Organic Compounds.............................. 21

Worked Problem 2....................................................................................................................................... 22

Elucidation of configuration: ........................................................................................................................... 24

Solutions to the problems (CAS numbers): ............................................................................................. 59

2.5 2.0 1.5 1.0

200 180 160 140 120 100 80 60 40 20

The contiguity of the molecule

δ Intensity Multiplicity J Interpretation

2.40 2 t 6.9 Hz CH2-CH2-CO

2.10 3 s 6.9 Hz CH3-CO

1.60 2 sextet 6.9 Hz CH3-CH2-CH2

0.90 3 t 6.9 Hz CH3-CH2

Table 1: Systematic representation of the signals in the 1H NMR spectrum.

The coupling constants, J, are measured on the spectrum as illustrated below:

All this information is given in the table.

Based on this knowledge the molecule has to be: CH3-(C=O)-CH2-CH2-CH3.

IR (Liquid sandwich, the peak at 1600 cm-1 is an internal reference)

3.5 3.0 2.5 2.0 1.5 1.0 0.5

220 200 180 160 140 120 100 80 60 40 20 0 -20

IR (Liquid sandwich, the peak at 1600 cm-1 is an internal reference)

4.0 3.5 3.0 2.5 2.0 1.5 1.0 0.5

1.5 1.4 1.3 1.2 1.1 1.0 0.9 0.8 0.7

3.5 3.0 2.5 2.0 1.5 1.0

4.0 3.5 3.0 2.5 2.0 1.5 1.0

3.5 3.0 2.5 2.0 1.5 1.0 0.5

IR spectrum (Liquid sandwich, the peak at 1600 cm-1 is an internal reference)

4.5 4.0 3.5 3.0 2.5 2.0 1.5 1.0

4.0 3.5 3.0 2.5 2.0 1.5 1.0 0.5

170 160 150 140 130 120 110 100 90 80 70 60 50 40 30 20 10

Table 2: Isotopes of common elements in organic compounds:

Table 3: Abundance of isotope peaks in chlorine and bromine containing ions.

1 CH and 1 CH3, or 2 CH, or 2 CH3.

Molecular formula: C5H8 → DBE: ½(10+2-8) = 2

The contiguity of the molecule

δ Intensity Multiplicity J Interpretation

2.15 2 dt 3 and 7 Hz H- - CH2-CH2

1.55 2 sextet 7 Hz CH2-CH2-CH3

Table 4: Systematic representation of the signals in the 1H NMR spectrum.

2.35 2.30 2.25 2.20 2.15 2.10

Prediction of the spectra

Figure 3: 1H NMR spectrum predicted by ChemBioDraw for 1-pentyne.

The predicted 13C NMR spectrum is shown below (Figure 4):

Figure 4: 13C NMR of 1-pentyne predicted by ChemBioDraw.

Interpretation of the spectra (Figure 5):

Figure 5: Interpretation of the NMR spectra

Figure 6: Possible McLafferty fragmentation of 1-pentyne.

3.5 3.0 2.5 2.0 1.5

180 170 160 150 140 130 120 110 100 90 80 70 60 50 40 30 20

The signal at 11 ppm disappears after addition of D2O.

11.5 11.0 10.5 10.0 9.5 9.0

168 160 152 144 136 128 120 112 104 96 88 80 72 64 56 48 40

COSY spectrum (300 MHz, CDCl3)

F1 Chemical Shift (ppm)

8.5 8.0 7.5 7.0 6.5

3.5 3.0 2.5 2.0 1.5 1.0