UNIVERSITY OF CAMBRIDGE

DEPARTMENT OF CHEMISTRY
IA CHEMISTRY 2009/2010
The Shapes and Structures of Molecules
Part One
O
HO

Me
O

OH

OMe

rs'
so
rvi n
pe sio
Su ver

Cl

HO

HO

HO

Me

H
O

Me

Lecturer: Dr Peter Wothers

email pdw12@cam.ac.uk

OH
OMe

Representing Molecules
Chemists need to be able to communicate with other chemists about the work they do. Over
the years, many dierent systems for drawing and naming compounds have evolved. Whilst
chemists have more or less settled on how to draw structures, naming them is more complicated.
As we shall see, the systematic rules are often put to one side in favour of names that are easier
to handle. In any case, we need to learn the language before we can study the chemistry.
Drawing molecules
There are many dierent ways to depict molecules: butane for example could be written C4 H10 ,
CH3 (CH2 )2 CH3 , CH3 CH2 CH2 CH3 or in a pictorial manner. Which way we use depends on what
we are trying to show. The formula C4 H10 only tells us the elemental composition it does not
tell us which isomer we are referring to. The displayed formulae indicate which isomer we are
referring to, but not the shape of the molecule.

This structure shows the

connectivity of all the atoms
but is rather misleading about
the 3D shape of the molecule.

Don't draw structures like this again!

The structure of a tetravalent carbon atom is based on a tetrahedron methane could be drawn:

these bonds
are in the plane
of the paper

this bond goes

back into the paper

H
C
H

this bond comes

out of the plane

H
H

A more informative
drawing of butane
would be:

C
H

C
H

H
H

The drawing shows the tetrahedral structure but is rather cluttered. With larger molecules, it gets
even harder to see what is important and what is not. What we need is a way of representing
structures in an informative yet clear way. Most chemists would draw butane like this:

this represents a CH3 group

this represents a CH2 group

Guidelines for drawing organic structures

1. Draw chains of atoms as zig-zags with 120 angles to show their shape.
2. Miss out the capital Cs representing carbon atoms.
3. Miss out the Hs attached to carbon atoms, along with the CH bonds.
4. Draw in all other atoms, together with their bonds and all the atoms attached to them.
5. If a carbon atom is drawn in, include all the other atoms attached to it.

Examples

propanol
(propan-1-ol)
no carbon in here

propanol
(propan-2-ol)

OH
OH

CO bond
3-hexene

cis

3-hexyne

trans

draw triple bonds linear

cyclohexane

benzene
or

propanoic acid
O

or
OH

glycine
O
COOH

H2N

propylamine
(CH3CH2CH2NH2)

propionitrile
(CH3CH2CN)
N

or

OH

NH2
CN

Common abbreviations
Some frequently used groups have their own abbreviations to save time writing them out fully:

Me = methyl, -CH3

Et = ethyl, -CH2CH3

nPr = normal propyl, -CH2CH2CH3

i Pr = iso-propyl,

nBu = normal butyl -(CH2)3CH3

t Bu = tertiary butyl -C(CH3)3
O

Ac = acetyl

Ph = phenyl

CH3CO-

= any alkyl group

-C6H5

Ar = any aryl group

(a substituted benzene ring)

Inorganic molecules
In organic structures, a line joining two atoms represents a bond but in inorganic structures this
is not necessarily the case. The lines indicate that the atoms are in some way connected, but
in some cases they are often no more than a guide to the eye to indicate the geometry of the
structure.

F
H

F
F

F
F

H
H B

H
H

F
S has 6 bonds

H
B

NaCl
would not say each
Na & Cl has 6 bonds

B
B

?
should the borons be joined?
does H have 2 bonds?

Naming compounds
Often the simplest way of referring to a compound is to draw its structure in scientific papers,
for example, structures are given and referred to by numbers e.g. 16 was obtained in good
overall yield and converted smoothly to the cyclic ether 17 by treatment with N-iodosuccinimide,
followed by tri-n-butylstannane reduction.
O
MeO

O
MeO

MeO
H

MeO
H

1. N-iodosuccinimide
2. nBu3SnH
(71% yield)

HO

16

OMe

OMe

17

Example taken from an issue of one of the chemical journals, Tetrahdron Letters.
Nonetheless, chemists still need to talk about the chemicals they use. There are books of rules
(and even computer programs) which enable any compound to be given a systematic name, but
these names are rarely used in the laboratory or even in scientific papers. In the above example,
N-iodosuccimide was used. This is not a systematic name but a trivial name. Trivial names are
preferred, mainly because they are often considerably shorter. The names of the very common
reagents will simply have to be learnt.
O

O
O
OH

acetone

acetic acid

(diethyl) ether

O
O

acetic anhydride

toluene

CHCl3

OH

chloroform

OH

succinic acid

N-iodosuccinimide

Determination of molecular structure

Chemists have an array of techniques to help them work out what compound they have made
including X-ray diraction, nuclear magnetic resonance, IR spectroscopy, UV-visible spectroscopy, microwave spectroscopy and mass spectrometry. Each technique reveals dierent
information and each has its own particular advantages and disadvantages.
4

X-ray crystallography

The spacing between atoms in most compounds is comparable to the wavelength of X-rays, both
being around 1 (100 pm). As a result, when a beam of X-rays is focused onto a single crystal,
the beam is diracted. By careful analysis of this diraction pattern, the positions of the atoms
within the crystal can be deduced. This is certainly the most powerful technique for determining
the structure of crystalline materials.

atomic displacement
parameters show
uncertainty in position of
atoms
doesn't show
double or triple
bonds but does
give bond lengths

F(2a)
C(8)

N(3)

C
N
F

S(1a)

C(2) C(1)

F(1)

C(4) C(3)

N(1)

S(1)

F
N

N(1a)

F(1a)

C(5)

F(2)

C(4a) C(3a)

S
S

or

C
N

S
S

or just
N

S
S

Not only does the crystal structure give the bond lengths and angles within a single molecule,
but it also shows how all the molecules pack together. The packing influences the behaviour of
unit cell - shows
the solid.

repeating structure

The X-rays are diracted by interactions with the electrons in the molecule rather than with the
nucleons (protons and neutrons). Hence the technique really produces electron density maps.

contours join
regions of equal
electron density

N(12)

O(11)

C(14)
C(15)

C(13)

H
H

C(11)

O(12)

C(12)

N(11)

note oxygens have most electron density

Notice that the hydrogen atoms do not show up in the above electron density map. This is often
found to be the case in X-ray structures hydrogen atoms have little electron density associated
with them and so are often dicult to locate.
Advantages and disadvantages of X-ray crystallography
Advantages
The ultimate method for structural information. Gives locations of all the atoms.
Disadvantages
Need good quality crystals
(Sometimes hard to locate hydrogen atoms)
6

Mass spectrometry

This technique eectively weighs molecules. The sample is introduced into the instrument,
vaporised and ionised. By focusing the ions onto a detector using magnetic and electric fields,
it is possible to determine the masses of the ions present. The results can be very accurate and
measure to one part per ten million.
Dierent techniques are used to ionise the sample: the crudest is to knock electrons out of the
sample by firing high energy electrons at the vapour. This technique yields a positive molecular
ion, M+ .
A much more eective, gentle ionisation technique is electrospray. In this technique, the
sample is introduced into the instrument as charged aerosol droplets. The solvent evaporates in
the vacuum, leaving charged molecules. What is detected is not the M+ molecular ion, but the
molecule with an ion stuck on. The detected ion may be positive (for example with a sodium
ion attached) or negative (for example with a methoxide ion, MeO or acetate ion, CH3 CO2 ,
attached).
When working out the masses of dierent ions in a mass spectrum, it is important to use the
atomic masses for the specific isotopes present and not the usual relative atomic masses which
are the average of these isotopic masses.

E.g. naturally occurring Br is a 50:50 mixture of 79Br and

81Br. Hence relative atomic mass of Br is 80 but in the
mass spectrum of Br+ no peak is seen at 80, instead see
one at 79 and one at 81.

79 81

Naturally occurring carbon, hydrogen, oxygen and nitrogen all consist of largely one isotope:
12
C, 1 H, 16 O and 14 N with accurate masses 12 (exactly, by definition), 1.00782, 15.99491 and
14.00307 g mol1 respectively.
By very accurately measuring the masses of ions, it is possible to determine their molecular
composition. As an example, consider the molecules CO, N2 and C2 H4 all of which have a mass
of 28 g mol1 . Using the accurate masses for the most common isotopes, we may calculate the
accurate masses of these dierent molecular ions:
12

C16 O 27.99491

12

C2 1 H4 28.03130

14

N2 28.00614

Thus a peak at 28.031 could only be due to [12 C2 1 H4 ]+ .

Example Spirastrellolide A
Spirastrellolide A is a natural product obtained from a marine sponge, and has been synthesised
in these laboratories. The structure, as worked out in May 2004 using MS and NMR, is given
on the front of the handout.
Accurate mass spec of [methyl ester + Na+ ion] = 1049.52026
Best sensible formula = C53 H83 O17 Cl Na (calc mass = 1049.52110, error = 0.8 ppm)

Fragmentation in Mass Spectrometry

Once ionised, the sample molecule begins to fall apart and so typical mass spectra contain many
peaks. Clues may be gained about the structure of the molecule by analysing these peaks but
these days there are many better techniques for structural determination.
Example the negative ion mass spectrum of [Rh6 (CO)16 + MeO ]
-CO

100

666.6

intensity %

-CO
694.6

-CO

638.5

50

-CO

Rh4(CO)9 +

1096.6

-CO -CO

MeO-

1012.6

-CO

610.6

1040.6
984.6

0
500

550

600

Rh6(CO)16 + MeO-

650

700

750

800

850

1068.6

950 1000 1050 1100 1150 1200 m/z

900

The complexity of the fragmentation pattern means that each one is very dierent for dierent
compounds in a sense, it is like a fingerprint for that compound. This makes mass spec an
excellent analysis tool for identifying compounds whose spectra have already been recorded,
especially since only a small sample is needed (just a few million molecules!).
It is also possible to isolate certain ions in the instrument and then follow these individual
ions to see how they fragment. This technique is called MS/MS. In the following example of
negative ion MS/MS, the spectrum has been processed to show only the ions which fragmented
to give NO2 ions (called the daughter ion).
Example - analysis of an explosive mixture

relative intensity %

226

(NO3-)

12.5

[TNT-H ]
or
[NG-H+]

[RDX+
HCO2-]

[RDX+AcO-]
281

267

NO2

6.2

daughter ion

272

46

[PETN-H+]
315

221
0

25

50

75

100

125

150

175

200

225

250

275

MS/MS parent-ion scan spectrum of explosive mixture

negative ion MS/MS of mixture + formate ions + acetate ions

300

325

350 m/z

CH3
O2N

NO2

NO2

TNT
(227)

ONO2
O2NO

ONO2

nitroglycerine, NG (227)
all give NO2- ion
on fragmentation

NO2
O2NO

N
ONO2

O2NO

PETN
(316)

ONO2

O2N

RDX
(222)

NO2

make up SEMTEX

Advantages and disadvantages of mass spectrometry

Advantages
Gives molecular formula
Excellent for analysis of mixtures
Tiny sample needed much less than for any other technique
Disadvantages
Often difficult to interpret, especially when working with unknowns

Spectroscopic techniques
You may already be familiar with the idea that if we were to measure the energy of electron
in an atom, we would find that it could only have certain energies. We say the energy levels
are quantised. To promote an electron from one energy level to another requires a certain fixed
amount of energy.
Similarly, whilst molecules are constantly moving around and therefore possess translational, vibrational and rotational energy, the amount of rotational and vibrational energy a
molecule may possess is also restricted. We say that the vibrational and rotational energy levels
are also quantised. It is possible for a molecule to be promoted from one vibrational energy level
to another or from one rotational energy level to another by absorbing light energy. The separation between the two energy levels, E, is proportional to the frequency of the light absorbed,
.
E = h where h is Plancks constant = 6.626 1034 J s.
9

The exact frequencies of light absorbed depends on the particular molecule in question different molecules absorb dierent frequencies of light. This is the basis of all spectroscopic
techniques.
The type of transition caused by the light depends on the frequency (and hence the energy)
of the light; in other words, dierent regions of the electromagnetic spectrum cause dierent
processes in atoms and molecules.
The Electromagnetic Spectrum
(all regions are approximate)

transitions in
alignment of
nuclear spins
(see NMR)

rotational
transitions
Microwave

nuclear
processes

electronic transitions
Infrared

Ultraviolet

Visible

-Rays

X-rays

red
orange
yellow
green
blue
indigo
violet

Radio

vibrational
transitions

wavelength:
(nm)
wavenumber:

(cm1)

109 (1 m)
0.01

frequency:
(Hz) 300 106
energy:
E (kJ mol1) 0.00012

3 105 (0.3 mm) 780

33.3
1012
0.4

380

12 800 26 300
384 1012 789 1012
150

310

10

0.1

0.001

106

108

1010

30 1015 3 1018
1200

1.2 106

300 1018
108

In this course, we shall look at two types of spectroscopy infrared spectroscopy, which looks
at how bonds vibrate, and nuclear magnetic resonance spectroscopy, NMR.

Nuclear Magnetic Resonance, NMR

10

You may already be familiar with the idea that electrons possess a property called spin and
that we denote electrons with opposite spin with up and down arrows, and . Spin becomes
important, when, for example, working out the lowest energy arrangement of electrons in atoms.
In an analogous manner, certain (but not all) nuclei also possess spin and as a result, the
nucleus has a very weak magnetic field associated with it. When placed in a strong magnetic
field there is an interaction between this nuclear spin and the applied field which gives rise to
a set of nuclear spin energy levels. Radiowaves of the appropriate frequency cause transitions
between these energy levels and this gives rise to the NMR signal.
in magnetic field
E2

NMR
signal

"spin down"
gives

radiowaves
h

frequency

"spin up"

E1

The nuclear spin is specified by the nuclear spin quantum number, I. It may take values of 0, 12 ,
1, 32 , . . . , with the particular value depending on the nucleus concerned. A nucleus with spin I
gives rise to (2I + 1) dierent energy levels when placed in a magnetic field.
Nucleus

% Natural abundance

Number of energy levels

H, a single proton

99.985

1
2

H, a deuterium nucleus, D

0.015

1
2

10

20

11

80

3
2

12

98.9

13

1.1

1
2

14

99.6

16

99.8

100

1
2

19

Note that dierent isotopes of the same element can have dierent values of I. The value of I
for a particular nucleus depends on the number of protons and neutrons in the nucleus. It is not
simple to predict the observed value of I but there are some useful guides:
nuclei with odd masses have half-integral spin (e.g.

11

B, 13 C)

nuclei with odd numbers of protons and odd numbers of neutrons have integral spin
(e.g. 2 H, 10 B, 14 N)

nuclei with even numbers of protons and even numbers of neutrons have zero spin
(e.g.

12

C, 16 O)

11

The exact dierence in energy between the dierent spin states depends on the strength of the
magnetic field the nucleus is in and on the nucleus itself. The stronger the external magnetic
field, the larger the energy separation between the dierent spin states.

energies of
H spin states

1H

13

energies of
C spin states

energy separation of
1H spin states in mag
field of strength B

same energy
in absence of
mag field

13

13C

smaller energy
separation of spin
states for 13C

B
strength of magnetic field

B
strength of magnetic field

As a result, the exact frequency a nucleus resonates at depends on the particular nucleus in
question and the strength of the magnetic field it is in:

Resonance frequency in
a 4.7 T magnetic field
/ MHz
200

30.7

122.8

50

200

Nucleus

13

Resonance frequency in
an 18.8 T magnetic field
/ MHz
800

31

81

324

195

Pt

43.3

173.2

(Earths magnetic field is approx 50 T.)

Local magnetic environments

NMR would be of little use if all hydrogen nuclei (simply called protons in NMR) resonated at
the exact same frequency or if all carbon-13 nuclei resonated at the exact same frequency. But
this is not the case. The exact dierence in energy between the dierent spin states depends on
the local magnetic field experienced by each of the nuclei. This in turn varies depending on the
electron density surrounding each nucleus. In a magnetic field, electrons move in such a way as
to set up their own magnetic field which opposes the applied field.
electron 'cloud'
applied field

magnetic field set up

by moving electrons
opposes the applied
magnetic field

12

The nucleus then experiences a weaker magnetic field than it would have done had the electrons
not been there. The weaker the magnetic field, the smaller the dierence in energy between the
nucleus spin states and hence the smaller the frequency of radio waves absorbed. Electrons are
said to shield the nucleus the more electrons, the more shielded the nucleus is and hence the
lower the frequency that it resonates at. Conversely, anything which removes electron density
from around a nucleus, deshields it and shifts the resonance to a higher frequency.
Since electronegative elements withdraw electrons towards themselves, they will deshield
other atoms attached to them.
CH3F

CH3OH

CH3Cl

CH4

increasing frequency of 13C nucleus

As you might expect, the frequency shift caused by the dierent degrees of shielding is quite
small, just hundreds of Hz. This is in contrast to the dierent frequencies that dierent nuclei
resonate at which are typically hundreds of MHz apart.
Equivalent nuclei number of peaks
Since the exact frequency at which a nucleus resonates at depends on the electronic environment
the nucleus is in, each dierent nucleus will resonate at a dierent frequency. Consider the 13 C
NMR spectra for two isomers of butanol: in n-butyl alcohol, each carbon atom is in a slightly
dierent environment and so gives a separate peak.

2
3
4

1
OH

solvent
CDCl3

nBuOH

200

150

100

50

0 ppm

In t-butyl alcohol, the symmetry of the molecule means that three of the carbon atoms are equivalent and so only two peaks are observed.

tBuOH

OH

200

150

100

50

13

0 ppm

This simple example shows how NMR can help to distinguish between two isomers, simply by
looking for some symmetry in the molecule. When predicting what a spectrum would look like
for a given compound, the first step is to look for symmetry in the molecule to see how many
resonance signals we should expect.

Examples

O
3

5
4

3
1

5
4

9 signals - some may be

very close to each other

5 signals
Cl

1
2
3

Cl

Cl

Cl

1
2

(spectra on p483)

4
2
3

Cl

2
1

Cl

3 signals

2 signals

4 signals

The NMR chemical shift scale

Since the exact frequency that a nucleus resonates at depends on the magnetic field it experiences, the same compound would resonate a dierent frequencies in dierent strength magnetic
fields. To avoid the confusion this would create, we quote the resonance frequency of a line
as its shift from an agreed reference compound, expressed as a fraction to compensate for the
magnetic field strength.
peak of interest
peak from
reference
compound

increasing frequency

The chemical shift of a resonance is calculated from

chemical shift, , in ppm = 106

difference just a few Hz

frequency of resonance - frequency of reference

frequency of reference

multiply by 106 to get a reasonably

sized number expressed in ppm

millions of Hz

Any dierences in the external magnetic field strength aects the frequecies of all the signals
equally by the same factor. Because of the way it is defined, the shift scale remains unaected:

chemical shift (in ppm) = 106

K x frequency of resonance - K x frequency of reference

K x frequency of reference

14

The reference compound

What do we want in an ideal reference compound?
Chemically inert, since it is often added to the sample.
Preferably just on signal nothing too complicated.
Preferably want the signal to be out the way of other peaks in the spectrum.

Compound used is TMS - tetramethylsilane

H

CH3

Si
H

Si

H
H3C

silane, SiH4

CH3
CH3

tetramethylsilane, Si(CH3)4

All the methyl groups in TMS are chemically equivalent, that is, they all have the same electron
density around them. This means that the compound shows just one signal in its carbon NMR
spectrum. All the protons are equivalent too so this compound also shows just one signal in
its proton NMR. Silicon, being below carbon in the periodic table, is less electronegative than
carbon which means that rather than withdrawing electrons from the carbon, it is actually slightly
electron donating and so the carbons are more shielded relative to most organic compounds
which have just CC bonds. The net result is that in the 13 C NMR spectra of most organic
compounds, the TMS reference signal is over to the right, out of the way.
Compound

Shift of methyl carbon / ppm

CH3 Li

14

Si(CH3 )4

0 by definition

CH3 CH3

CH3 Cl

26

CH3 NH2

28

CH3 OH

50

CH3 NO2

61

CH3 F

72

CH3 Li is like CH3 Li+ the carbon is heavily shielded

15

Dividing up the scale

Carbon NMR spectra are usually run from 0 to just over 200 ppm since most organic molecules
fall in this region. The scale can be conveniently broken down into dierent regions:

(sp carbons)

large shifts
('downfield')

C
C

200

150

sp2 carbons with

very electron
withdrawing
groups attached

small shifts
('upfield')

100
sp2 carbons

50

0 ppm

sp3 carbons with

very electron
withdrawing
groups attached

sp3 carbons

These divisions act as guide lines only for example, given enough electron withdrawing
groups, an sp3 hybridised carbon will creep into the 100-150 region.

CH3Cl
CH2Cl2
CHCl3
CCl4

OMe

26 ppm
54
77
96

114 ppm

51 ppm

OMe
OMe

an orthoester

The carbonyl region ca. 150-200 ppm

Whilst most carbonyl groups fall in the 150-200 ppm region, it is useful to sub-divide this region
further:

i) around 200 ppm

O

ketones
typically just over 200 ppm

aldehydes
typically just under 200 ppm

ii) around 160 -170 ppm

O

acid derivatives
O

OH

O
OR

O
Cl

NH2

Note that the carbonyl carbons for the acid derivatives resonate at a lower shift than the ketones
and aldehydes, even though they have more electron withdrawing groups attached! This indicates that the carbon atoms in the acid derivatives are more shielded and that the heteroatoms
(i.e. O, N, Cl) must be donating some electron density. This is an idea we shall return to later in
the course.
16

Example spectrum - hallerone

1

solvent, CDCl3 at 77 ppm

3

HO 5

200

8
7

6
1

O
6
2

7
8

150

100

50

0 ppm

Notice that the resonance lines from the quaternary carbon atoms (i.e. ones with no hydrogen
atoms attached) appear much smaller than those of the carbons that do have protons attached.
This eect is a consequence of the way the spectra are recorded and need not concern us further.
With care this feature can be used to help identify quaternary carbons, although weak signals
could also be due to impurities.

Coupling between nuclei

Coupling between nuclei with spin 12
The exact frequency a nucleus resonates at depends on the magnetic field it experiences. We
have already seen that the electron density surrounding a nucleus aects the local magnetic field
it experiences so too does the magnetic field exerted by nearby nuclei. Consider the 13 C NMR
spectra of acetic acid and fluoroacetic acid.
O

note small
quaternary
peak

C
CH3

HO

acetic acid
200

150

100

0 ppm

C
HO

50

the signal from

each carbon is
split into a doublet

H H

x 5 expansion

200

150

100

17

50

0 ppm

Apart from causing the resonance for the sp3 carbon to shift to a higher ppm, the fluorine atom
has another aect on the 13 C spectrum where before there were single lines for each carbon
resonance, now each signal has split into a pair of lines. Each pair is called a doublet. The two
lines which make up the doublet are placed symmetrically about the chemical shift position and
their separation gives the value of the coupling constant, J, which is measured in Hz. The carbon
and the fluorine nuclei are said to couple with each other.

in 13C spectrum

with no coupling

with coupling
same splitting, J
two doublets

in 19F spectrum

To understand the coupling, consider the 13 C nuclei. In addition to the applied magnetic field,
the 13 C nuclei also experience an additional field due to the nuclear spin of the fluorine atoms.
Since for fluorine I = 12 , the fluorine nuclei could be in either of two spin states: up or down.
Those fluorine nuclei that are spin up reinforce the magnetic field experienced by the carbon
nuclei and shift them to a slightly higher frequency than they would otherwise resonate at.
Conversely, those fluorine nuclei that are spin down reduce the magnetic field experienced
by the carbon nuclei and shift them to a slightly lower frequency.

this is where the carbon signal

would have come if unaffected
by the spin of the F

13C

19F

-13C

13C

F spin up
increases field

-19F

F spin down decreases

field felt by 13C and hence
a smaller shift

The eect of coupling between nuclei is often determined using a tree diagram in which we
show a stick spectrum without coupling and then add the coupling in the next row and show how
the lines in the second row are related to those in the first.

original shift position with no coupling

resultant doublet

18

Notice in the spectrum of fluoroacetic acid that the coupling to the sp3 hybridized carbon is much
larger than that to the carbonyl carbon. This is because coupling is a through bond interaction
and gets weaker the more bonds there are between the coupling nuclei. It is vary rare to see any
coupling at all between nuclei more than four bonds apart. In 13 C NMR, it is rare to see any
coupling through more than one or two bonds.
Coupling constants are represented x JYZ where x is the number of bonds through which
nuclei Y and Z are coupling. In the spectrum of fluoroacetic acid, the coupling constants are
denoted 1 JCF and 2 JCF .
Sometimes splittings are not seen
CH coupling
No CH coupling is usually seen because 13 C NMR spectra are usually proton decoupled (see
later).
CC coupling
No CC coupling is usually seen because of the low abundance of 13 C in naturally occurring
carbon. Could see coupling if the sample has been artificially 13 C-enriched.
O
12

HO

O
13
12

CH3

O
12

12

CH3

HO

HO

13

most molecules
are like this and
not NMR active

O
13
13

CH3

1% have a C
another 1% have a
13
here. Gives 1
C here. Gives 1
peak in spectrum peak in spectrum
at 177 ppm
at 22 ppm

HO

13

CH3

only 0.01% have 2

C atoms next to
each other. Each
signal would be a
doublet but is lost
in the noise.

13

Equivalent nuclei
Splittings due to couplings between equivalent nuclei are not seen! Equivalent spins do
interact with each other, but the eects of this coupling are never seen as splittings. To all
intents, it appears that equivalent nuclei do not couple with each other.
O

O
13C

HO

13

C
OH

no splittings would be seen

in 13C enriched oxalic acid
because the 2 carbon atoms
are equivalent

19

Coupling to more than one nuclei

We can use a tree diagram to predict what the 13 C NMR spectrum for 13 C-enriched fluoroacetic
acid would look like.

O
13

HO

13

H H

1J
CC

Coupling to the other

carbon splits this into a
doublet with coupling
constant 1JCC
The longer range 2bond coupling to the F
splits each line into
another doublet with
coupling constant
2J
CF

2J
CF

1J

Coupling to the
other 13C splits
each of these lines
into a doublet with
coupling constant
1J
CC

1J
CC

The order in which we draw the

splittings makes no difference!
We still get the same spectrum.

2J
CF

1J
CC

2J
CF

CF

1J
CC

1J

CF

1J
CC
1J
CC

a doublet of
doublets

1J

CF

a doublet of doublets

20

Coupling to the fluorine

splits this line into a
doublet with coupling
constant 1JCF

Difluoroacetic acid

C
C

HO

JC-F 28 Hz

5 expansion

200

150

JC-F 239 Hz

100

50

0 ppm

Now each carbon appears as a triplet. Each of the carbon nuclei couples to two equivalent
fluorine nuclei. The spins of these can be arranged in four ways:

with both F spins

up, the13C has
the greatest shift

with one F up and

one F down, no
overall effect on
shift of carbon

with both F spins

down, the carbon
resonance is
shifted to a smaller
chemical shift

since the F nuclei are

indistinguishable, these
two arrangements are
magnetically equivalent
Thus we expect to see three lines in the spectrum and because it is twice as likely that the fluorine
spins are one up and one down rather than both up or both down, the net result is a triplet with
ratio 1 : 2 : 1.
The tree diagram shows that a triplet is really just a special case of a doublet of doublets
where because of the equivalence of the two fluorines, the coupling constants are the same and
hence two of the signals overlap to give twice the intensity.

original shift
Since the coupling
constant is the same,
the 2 central signals fall
on top of each other

coupling to one F splits

the signal into a doublet
coupling to the second F
splits each line into a
doublet again

1 : 2 : 1
net result is a triplet

21

In trifluoroacetic acid, each carbon resonance appears as a quartet.

1

JC-F 38 Hz

JC-F 287 Hz

C
HO

200

150

3 spins up,
larger shift

100

net 1 spin up,

small shift

50

0 ppm

net 1 spin down,

small shift

3 ways

CF3

3 spins down,
larger shift

3 ways

We can construct a tree diagram for the quartet:

original shift

coupling to 1st F splits

the signal into a doublet

same coupling
constant each time

coupling to 2nd F splits

each line again

J
J
1

22

coupling to 3rd F splits

each line into 2 to give
rise to the quartet

In general, when a nucleus couples to n equivalent nuclei with spin I , its resonance signal is
split into (2nI + 1) lines. If the nucleus couples to n equivalent nuclei with spin 12 , the formula
simply becomes (n + 1). Notice how for coupling to spin 12 nuclei, the ratio of the intensities
may be predicted by Pascals Triangle.

singlet

1 : 1

doublet

1: 2 : 1

triplet

1 : 3: 3 : 1
1 : 4: 6 :4 :1

quartet
quintet

Examples PF3 and XeF+3

19F

In 31P spectrum, the P 'sees' 3

equivalent Fs and so is split into a
quartet with intensity ratio 1 : 3 : 3 : 1

spin 1/2
P

In the structure of PF3 , all the fluorine atoms are equivalent. This is not the case in the ion XeF+3
which has a T-shape.
The three fluorine atoms are no longer all equivalent; the two marked Fa
are equivalent, but Fb is dierent. This means that in the 19 F spectrum,
+
Fa
there would be two signals due to the fluorine atoms one resonance
due to Fa and one due to Fb (these would then be split further by couXe
Fb
pling to the 129 Xe). The 129 Xe NMR spectrum has been recorded for
this compound (129 Xe, I = 12 ). The xenon couples to the two equivalent
Fa s to give a triplet, ratio 1 : 2 : 1, but then each of these lines is further
Fa
split into doublets through coupling to Fb . The net result is described as
a triplet of doublets. This is best shown using a tree diagram.

JXe-Fa

coupling to 1st Fa gives a doublet

JXe-Fa

coupling to 2nd Fa gives a triplet

JXe-Fb
1

1 :

Net result is a triplet of doublets

Xe NMR spectrum of XeF3+

coupling to Fb splits
each of these lines into
doublets

129

JXe-Fa 2600 Hz
JXe-Fb

2380 Hz
650

600

550

23

ppm

Natural abundance and satellites

The low abundance of 13 C (1.1%) compared to 1 H (almost 100%) means that more sample is
needed to record a 13 C NMR than a proton NMR. We saw earlier how this low natural abundance
of 13 C means that no CC coupling is observed in 13 C NMR spectra. A further consequence is
that no coupling to carbon is observed in proton NMR.
Consider the NMR spectra for chloroform, CHCl3 . When recording a 13 C NMR each 13 C is
attached to a spin 12 proton and so unless we applied broadband proton decoupling (see later),
coupling to the proton would mean the 13 C signal would appear as a doublet. In contrast, when
recording a 1 H NMR spectrum of chloroform, most protons in the sample are attached to spinzero 12 C and so no coupling is observed. However, in 1% of the sample, the proton is attached to
a 13 C which means if we looked very closely at the baseline, we just might see the tiny fraction
that appears as a doublet.
1

H NMR
13

proton
coupled 13C
NMR of
CHCl3

C satellites

100

1J
C-H

1J
C-H
1H

13 C

The 13 C satellites are usually lost in the background noise of the 1 H spectrum, but there are some
isotopes of other elements where satellites are much more prominent because they are present
at higher levels. One such case is with platinum. There are six naturally occurring isotopes of
platinum and all but one have spin I = 0. The exception is 195 Pt which is 34% abundant and has
spin I = 12 .

Cl

Example Cisplatin
Cisplatin was one of the earliest successful drugs used in chemotherapy
under such names as Neoplatin.

15N

NH3
Pt

Cl

NMR spectrum of 15N enriched cisplatin

NH3

most 15N is attached to

Pt with spin I = 0 so
appears as a singlet

This is not a triplet but a doublet

superimposed on a singlet

smaller amounts of 15N is

attached to spin I = 1/2 195Pt

ratio 17 : 66 : 17

JN-Pt
50

60

70

80 ppm

Most of the nitrogen nuclei are attached to spin zero isotopes of platinum and hence resonate as
a singlet. However, one third of the cisplatin molecules contain 195 Pt which splits the nitrogen
resonance into a doublet what is observed is a doublet superimposed on the singlet.
24

Decoupling
13

C spectra are usually recorded in such a way so that coupling to protons does not appear
such spectra are said to be proton decoupled. All the 13 C NMR spectra you will usually meet
are recorded in this way. While the 13 C spectrum is being recorded, the protons are irradiated in
such a way as to cause their nuclear spins to move rapidly between their up and down spin
states. If this happens fast enough the couplings to 13 C average to zero and all of the splittings
disappear. This process is called broadband proton decoupling. The broadband refers to
the fact that we are irradiating over a range of frequencies so that all the protons are rapidly
interconverting between their dierent spin states.
Shown below are the proton-decoupled and the proton-coupled spectra of 3-methyl-4hydroxybutan-2-one.
O

proton decoupled
spectrum

H3C

2
2

OH

5 CH3

200

150

100

proton coupled
spectrum

200

50

150

100

50

0
4

The proton coupled spectrum gives us more information than the decoupled spectrum in that
it is easy to see whether the carbons are CH3 , CH2 , CH or quaternary since these appear as
quartets, triplets, doublets or singlets respectively. However, there are several disadvantages.
The signal strength is now much weaker (compare the relative sizes of the solvent peaks) which
means that some signals could easily become lost in the background noise. In most compounds
the multiplets will overlap and it would be very hard to say which peaks go together as part of
a multiplet and which are due to dierent carbon nuclei. This particular example was chosen
because all the signals are well separated.
There is a way to get the best of both worlds an experiment called the Attached Proton
Test, APT, is run on the NMR spectrometer. How this works need not concern us, but the result
is that the peaks from the carbon atoms with an even number of protons attached, 0 or 2, point
one way (the same way as the deuterated solvent) and the carbon atoms with an odd number of
protons, 1 or 3, point the other way.

APT
CH & CH3
quaternary & CH2s

200

solvent (CDCl3)
no H's

150

100

25

50

Proton NMR
The chemical shift scale in 1 H NMR is much smaller than that in 13 C NMR. The same reference compound, TMS, provides the zero, but the protons in most organic compounds resonate
between 0 and about 14 ppm. Remember that the actual frequencies that carbon and hydrogen
nuclei resonate at are significantly dierent this 0-14 ppm is not the start of the carbon 0-200
ppm scale!
Proton NMR spectra rapidly get very complicated due to the coupling. However, this also
makes 1 H NMR incredibly useful since so much information can be deduced from the spectra.
Proton NMR will be covered in much greater depth next year at this point we will only look
at some very simple examples.
Example: 1 H NMR spectrum of ethyl acetate

H3 C

quartet since
couple to 3
equivalent Hs
on Me

O
C
H2

CH3

no coupling
seen between
equivalent
nuclei

triplet since
couple to CH2
protons

0 ppm

Example: 1 H NMR spectrum of styrene

Ha

each couple to Ha
to give a doublet.
Coupling between
Hb and Hc too
small to show up!

Hc

phenyl protons
too complicated!
Hb
Ha

doublet of
doublets
Jab
Jac

8.0

7.5

7.0

6.5

Hb

Jab

6.0

26

Jac

5.5

Hc

5.0

4.5

ppm

Coupling to spins greater than

1
2

Many nuclei have spins greater than 12 and in principle these should show a coupling to nuclei
such as 13 C. However, in most cases, this is simply not observed. This is because the spin
states rapidly interconvert due to a process called relaxation. Such a process is common to all
nuclei with spin, but it turns out to be very rapid for most nuclei with spins greater than 12 .
The resulting rapid interconversion of the spin states causes all the couplings to that nucleus to
average to zero, just as in the case where we deliberately irradiated the protons in broadband
decoupling (see page 25). However, there are a few examples of nuclei with spin greater than 12
which do relax suciently slowly for coupling to be seen. A common example is deuterium.
In most of the 13 C spectra we have seen so far there have been a set of peaks at 77 ppm due
to the solvent, CDCl3 . The carbon resonance appears as a triplet because of the coupling to the
deuterium. The nuclear spin for deuterium is I = 1, which means that there are 3 dierent spin
states (2I + 1). Hence the carbon resonance is split into a triplet with ratio 1 : 1 : 1. The tree
diagram is now dierent from the spin 12 case since each line splits directly into three.

original shift

J
1

J
1

coupling to spin I = 1
splits the line into 3
with equal intensities

Notice that no coupling is observed to the chlorine nucleus in the spectra, even though both the
naturally occurring isotopes, chlorine-35 and chlorine-37, have spin I = 32 . Chlorine nuclear
spin states relax too quickly for any coupling to be seen.

original shift
split into a triplet by the 1st D
each line is then split into
another triplet by the 2nd D

1 : 2 : 3 : 2 : 1

Deuterated dichloromethane appears as a quintet, ratio 1 : 2 : 3 : 2 : 1; it comes at 54 ppm.

The number of lines into which a signal is split by coupling to n equivalent nuclei of spin I is
given by the formula (2nI + 1). We can no longer use a simple Pascals triangle to work out the
intensities of the lines these are best found by constructing a tree diagram.

27

Infrared spectroscopy

IR spectroscopy looks at transitions between dierent vibrational energy levels in molecules.

Whereas NMR gives us information about the dierent environments of nuclei in a sample, IR
spectroscopy gives us information about the types of bonds present. A typical IR spectrum is
shown below.
100%

transmission

80%
60%
40%
20%
0%
4000

3500

3000

2500

2000
1500
frequency / cm1

1000

500

By long standing tradition, IR spectra are plotted as percentage transmission versus frequency.
When the sample does not absorb at all, the transmission is 100% and so the trace appears at
the top of the plot. When the sample does absorb light of a specific frequency, the amount of
light being transmitted through the sample drops and the trace moves down the plot. Absorption
peaks thus correspond to the downward pointing features. Notice on this spectrum how the scale
for the frequency on the x-axis changes at 2000 cm1 .
The frequency is plotted in wavenumbers (cm1 ). These are the number of whole waves
in one cm, or one over the wavelength expressed in centimeters. Wavenumbers are directly
proportional to frequency and may be treated as a unit of frequency.
1
( in cm)
wavenumber, , =

c
as = , (where c is the speed of light)

(in Hz) = c (in cm s1 ) (in cm1 ) i.e.

28

Since E = h (see page 9), the frequency of the absorption is proportional to the energy for the
vibrational transition. Hence peaks on the left of the spectrum at high wavenumbers correspond
to vibrations which need more energy.
There are obviously many peaks in the IR spectrum and we need to try to make some sense
out of them. There are many dierent ways in which a molecules can vibrate. The most useful
vibrations in an IR spectra are the stretches and these generally require most energy. Almost all
the peaks over 1500 cm1 correspond to bonds stretching.

Modelling a vibration

energy

We may consider a simple diatomic molecule as two masses connected with a spring representing the bond. As the bond is stretched or compressed, the energy of the system rises and there is
a restoring force trying to return the bond to its equilibrium length.

m1

m2

equilibrium bond length

re

com

extension

on

ssi
pre

re

A useful model to describe such a system, at least for small oscillations, is the harmonic oscillator. Such an oscillator is typified in the mechanical world by a weight hanging from a spring.
When the weight is pulled down, i.e. displaced from its equilibrium position, the spring exerts
a force to return it to the original position. The result is that the weight oscillates about the
equilibrium position.

restoring
force

equilibrium
position

restoring
force

The frequency of the oscillations depends on two things, how heavy the weight is and how sti
the spring is: the fastest oscillations occur with a sti spring and a light mass. The relationship
between these parameters is given by Hookes law:
!
kf

m
where is the frequency of oscillation, k f is the force constant (which corresponds to how hard
it is to stretch the spring and is measured in N m1 ) and m is the mass.
We can adapt this model to apply to a vibrating diatomic. It would be reasonable to expect
stronger bonds to be harder to stretch and so have larger force constants. Although how hard it is
to stretch a bond is not the same thing as how hard it is to break a bond, there is a fair correlation
between the bond strength and the force constant, as shown in the table below.
29

force constant
/ N m1
246
575
1177
1902

bond strength
/ kJ mol1
193
436
498
1077

diatomic
BrBr
HH
O=O
CO

The second thing we need to take into account when modifying the model, is that unlike in the
case of a mass hanging from the ceiling, when a diatomic molecule vibrates, both atoms are
moving. We can take both of the masses into account by using the reduced mass for the system,
.
m1 m2
=
(units of mass)
m1 + m2
Note how the expression for the reduced mass simplifies if one mass is much greater than the
other:
when m1 m2
i.e. when m1 m2

m1 m2
m2
m1

m2 (lighter mass)

For a vibrating diatomic, the frequency of vibration, , in cm1 , is given by:

=

1
2c

"

kf

with k f in N m1 , in kg (per molecule) and the speed of light, c, in cm s1 .

Because of the inverse relationship between the reduced mass, , and the frequency, the smaller
becomes, the higher the frequency of oscillation. As we have seen, the reduced mass will be
small when we have a light atom attached to a heavy atom which in practice means when we
have an H atom attached to just about any other atom. This explains the first region in the IR
spectrum: 2500-4000 cm1 ; X-H stretches. The other regions in the spectrum correspond to the
dierent strengths of bonds (which in turn reflect changes in k f ): triple > double > single.
100%

transmission

80%
60%

X-H single bonds

triple
bonds

N-H

40%

C=O
C-H

C=C

C C

'fingerprint region'
X-Y stretches and
other vibrational
modes, e.g. bending

C N

20%
0%
4000

double bonds

3500

3000

2500

2000
1500
frequency / cm1

30

1000

500

Group vibrations
The actual way in which a molecule vibrates may be rather complicated and involve all the atoms
simultaneously moving. However, it is possible to break this complex motion down into certain
so-called normal modes. The normal modes for ethyne are given below:
H

3374 cm-1
'C-H symmetric stretch'

3287 cm-1
'C-H antisymmetric stretch'

1974 cm-1
'C-C stretch'

612 cm-1
'trans bend'

729 cm-1
'cis bend'

As we can see, it is not true to say that there will be one absorption in the IR spectrum for each
bond. Very often a single absorption corresponds to many bonds all vibrating at once. However,
it is often the case that a given vibrational mode largely corresponds to one particular part of
the molecule vibrating. For example, in the example above, the vibrations around 3300 cm1
are mainly due to the CH bonds stretching. It is this that makes IR so useful for identifying
functional groups in organic chemistry all ketone carbonyls typically vibrate at roughly the
same frequency, slightly dierent from the frequency at which ester carbonyls typically vibrate
and so on.

Strength of absorption
Whilst the frequency at which a bond absorbs depends on its strength, exactly how big the peak
is depends on the dipole moment of the bond. Light is an oscillating electromagnetic field and
this can interact with a vibrating dipole the larger the dipole moment in the bond, the stronger
the absorption. If there is no change in the dipole moment when the bond stretches, then it will
not absorb IR at all.
(+)
C

(-)
O

strong dipole
moment, strong
absorption

(+)
C

If completely
symmetrical,
then no dipole
& no C=C
absorption

(-)
N

strong dipole
moment, strong
absorption

31

no dipole
moment, no
absorption
of IR

Just because a molecule like N2 cannot absorb IR, it does not mean it is not vibrating. Frequencies for such symmetrical vibrations with no change in the dipole moment may be determined
using a technique complementary to IR spectroscopy called Raman spectroscopy. Whereas normal IR spectroscopy looks at the frequencies of light absorbed by a sample, Raman spectroscopy
looks at the frequencies of light scattered by a sample.
A given vibrational mode may be IR active only, Raman active only or both IR and Raman active. Deciding which is the case is rather involved and will be studied next year. For
diatomic molecules however, homonuclear diatomics such as O2 and N2 will only be Raman
active whereas heteronuclear diatomics, such as HCl and CO will be both Raman and IR active.
Example spectrum cyanoacetamide
O
N
C
NH2

100%

fingerprint

transmission

80%
60%
40%
20%
0%
4000

C N
N-H
3500

C-H

3000

C=O
2500

amide bend

2000
1500
frequency / cm1

1000

500

We shall now look at each of the main regions of the IR spectrum in a little more detail.
XH region
CH stretches usually 2900 3200 cm1 typically just less than 3000 cm1 .
exception: CCH unusually strong, sharp absorption 3300 cm1 .

CH stretches are not usually mentioned since all organic compounds contain them and the
sample is often prepared as a nujol mull. Nujol is a paran oil whose spectrum only contains
CH (and CC) vibrations.

32

NH sharp absorption at around 3300 cm1 .

100%

transmission

80%
60%

CH3

40%

N-H
20%
0%
4000

3500

3000

Ph

2500

2000
1500
frequency / cm1

1000

500

NH2 group often shows two absorptions due to symmetric and antisymmetric stretches.
100%

transmission

80%

60%

40%

NH2

20%
0%
4000

3500

Ph
3000

2500

2000
1500
1
frequency / cm

symmetric
ca 3300 cm-1

1000

500

antisymmetric
ca 3400 cm-1

The shape of an OH stretch depends on whether or not there is hydrogen bonding in the sample.
With hydrogen bonding, the absorption is very broad:
100%

transmission

80%
60%

OH

40%
20%
0%
4000

3500

3000

2500

2000
1500
frequency / cm1

H bonding means there are

lots of slightly different
strengths of OH bonds

33

1000

500

Here is an unusual example where the OH stretch is very sharp. No H-bonding is possible due
to the bulky CMe3 groups preventing the OH groups from approaching one another.
100%
80%

transmission

OH
60%
40%
20%

non H-bonded
OH sharp
0%
4000

3500

3000

CH3
2500

2000
1500
frequency / cm1

1000

500

1000

500

Carboxylic acids are typically more V shaped

100%

transmission

80%
60%

OH

40%
20%
0%
4000

3500

3000

2500

2000
1500
frequency / cm1

Triple bond region 20002500 cm1

CN, strong absorption 2250 cm1
CC, weak absorption 2100-2250 cm1

Double bond region 15002000 cm1

C=C, 1635-1690 cm1 , generally weak

number of peaks in
range 1625-1450 cm-1
medium or weak intensity

or

34

NO2 group. Two stretches one at 1530 cm1 and one at 1350 cm1 .

N
O

or
O

symmetric 1350

cm-1

antisymmetric 1530 cm-1

Carbonyl groups
IR spectroscopy is particularly useful in identifying carbonyl groups. The C=O stretching mode
shows a strong absorption due to the large dipole moment and the exact frequency of this stretch
gives a good indication of what sort of carbonyl functional group is present. You will cover these
again in the Reactions course where you will see how the IR stretching frequency also gives a
guide to the chemical reactivity of the group.

take as our starting reference a

ketone which typically absorbs
at ~1715 cm-1

ketone , 1715 cm-1

Anything that strengthens the carbonyl bond will give rise to an absorption at higher frequency
Anything that weakens the carbonyl bond will give rise to an absorption at lower frequency
The carbonyl is strengthened by anything that withdraws electrons and weakened by anything
that donates electrons. We will see later on in the course exactly how the electrons are donated
and withdrawn and why this aects the C=O bond strength.

acid chloride
~1750-1820 cm-1

amide
~1640-1690 cm-1

Cl

chlorine withdraws electrons

and strengthens the carbonyl

O
NH2

nitrogen donates electrons

and weakens the carbonyl

Oxygen lies in between nitrogen and chlorine in its ability to donate or withdraw electrons. This
is reflected in the frequency at which the C=O in an ester or a carboxylic acid absorbs it lies
in between the two extremes of an amide and acid chloride.
O

O
OH

ester
~1745 cm-1

carboxylic acid
~1730 cm-1

35

Aldehydes absorb slightly higher than ketones. Since alkyl groups can weakly donate electrons
into the carbonyl system, when the alkyl group is replaced by a hydrogen (for which no electron
donation is possible), the C=O stretching frequency is observed to increase.
O

aldehydes have an H here instead

of the weakly electron donating
alkyl group in the ketone

~1730 cm-1

Acid anhydrides show two stretches due to the symmetric and antisymmetric stretching modes
of the two carbonyl groups.
100%

transmission

80%
60%
O

40%
O
20%
0%
4000

1827
3500
O

3000
O

2500

1755

2000
1500
frequency / cm1

1000

500

~1820 cm-1 symmetric stretch

O
O

~1750 cm-1 antisymmetric stretch

O

As we shall see later in the course, the carbonyl bond is also weakened by conjugation. The
carbonyl is said to be conjugated with a C=C double bond if the two double bonds are separated
by just one single bond. Conjugation lowers the base frequency by 20-30 cm1 .
O

conjugated ketones
~ 1690 cm-1 C=O stretch

non-conjugated ketones
1715 cm-1 C=O stretch

36

2 single bonds
between double

The final factor which influences the stretching frequency of a C=O concerns compounds where
the carbonyl group forms part of a ring. The smaller the size of the ring, the higher the stretching
frequency.
O

~ 1715 cm-1
6

~ 1745 cm-1
5
+30

~ 1780 cm-1
4
+35

~ 1815 cm-1
3
+35

It turns out that the size of the ring does not alter the strength of the C=O significantly. The correct origin of the eect can be understood by considering what happens during a C=O vibration.
Both the oxygen and the carbon atoms move, but the carbon atom feels some resistance due
to the repulsion from the other carbon atoms bonded to it. The smaller the angle in the ring, the
more the CC bonds need to be compressed during a vibration. This requires more energy and
this is reflected in the higher frequency of the absorption.
C

C
C
C

small CCC angle requires

considerable C-C compression
as C=O stretches
harder

larger CCC angle requires

less C-C compression
as C=O stretches
easier

Predicting carbonyl stretching frequencies

The numbers given for the stretching frequencies of carbonyl groups are only approximate, but
nevertheless can be used to predict reasonably well the frequencies that carbonyls absorb at in
dierent molecules.

ester : 1745
in 5 membered ring : +30
predict : 1775 cm-1

ester : 1745
in 5 membered ring : +30
conjugated : -30
predict : 1745 cm-1

37

Example spectrum aspartame

O

1737
carboxylic acid
C=O stretch

H
N

HO

O
NH2

ester
1748

amide
1668
100%

broad O-H

transmission

80%
60%
40%

3319
N-H
1748

20%
0%
4000

C-H
3500

3000

2500

1737 1668 Ph
2000
1500
frequency / cm1

38

1000

500

Problems
1.

(b)

(a) Write framework structures (as on page 2 of the handout) for the following
molecules: propanol, propanoic acid, propanal, propan-2-ol, cyclohexanol, phenol, acetic
anhydride, CH3 CH=CHCOOH (two isomers), CH2 =C(CH3 )COOEt, PhCHO, C(OMe)2 Ph2 ,
CH3 CH2 CCCH2 CH3 .
Draw structures for the following compounds and name each one:
Ac2 O,

AcOH,
2.

Et2O,

tBuOH,

nBuOH,

PhMe,

MeCOMe

Find the molecular formula (i.e. Ca Hb ...) corresponding to the following framework structures:

OH

pyridine
O

anthracene

OMe

Ph

N
nPr

N
OEt

OH

Sildenafil, the active ingredient in Viagra

HO

HN

NO2

H
N

OH O

HO

OH

tetrodotoxin - the deadly poison that

must be removed from Japanese

Flunitrazepam - better
known as Rohypnol

Me

The following nuclei have spin of either 0, 12 , or 1. What is the spin for each nucleus?
6

4.

OH

3.

HN

cocaine

HN

menthol

Li,

14

N,

15

N,

76

Se,

77

Se,

78

Se,

Predict how many lines you would expect to see in the

molecules; explain briefly your reasoning in each case:

13

110

Cd,

111

Cd

C NMR spectra of the following

(a) benzene, anthracene, 1,4-dinitrobenzene, 1-chloro-4-bromobenzene, 1-chloro-2-nitrobenzene,

Et2 O, EtOMe, CH3 (CH2 )4 COEt.
39

(b)

Cl
CN
CN

the active ingredient

in CS gas

5.

Sketch the 13 C NMR spectra that you expect from the following molecules. You should indicate
on you spectrum which carbon is responsible for which resonance. (You cannot give precise
values of the shifts, but you can predict the region of the spectrum in which each carbon will
give a resonance and for similar carbons what order the shifts will come in).
O
Br

OMe

MeO

NH2

mescaline - an hallucinogenic
and intoxicating drug first
isolated from 'magic mushrooms'

MeO
OMe

6.

Describe what you would expect for the 13 C NMR spectrum of ethanol recorded (a) with and
(b) without broadband proton decoupling. Explain the form of any multiplets you predict.
It is possible to synthesise ethanol in which all of the carbon is 13 C. Predict the form of the
broadband proton decoupled 13 C NMR spectrum of a sample of this material.

7.

(a) The 19 F NMR spectrum of IF5 consists of a doublet (that is two lines with intensity ratio 1:1)
and a quintet (that is five lines with intensity ratios 1 : 4 : 6 : 4 : 1). Suggest a structure for IF5
that is consistent with this spectrum, explaining how you arrive at your result.

(b) The following are three possible structures for the molecule SF4 . Predict the form of the 19 F
NMR spectrum for each of these possible structures. Structures 1 and 2 are based on a trigonal
bipyramid; structure 3 is based on a square based pyramid. (I for 32 S = 0; I for 19 F = 12 )
F
F
F

S
F

8.

S
3

F
F

Explain why the broadband proton decoupled 13 C spectrum of CH2 Cl2 consists of a single line,
whereas that of CD2 Cl2 consists of a 1 : 2 : 3 : 2 : 1 quintet. What would the spectrum for
d6 -DMSO (CD3 SOCD3 ) look like?
40

9.

B has spin 32 and relaxes suciently slowly that couplings to it can be seen. Explain what you
would expect to see in the proton NMR spectrum of diborane, B2 H6 , whose structure is shown
below. (You may assume that all the B atoms are 11 B and that any couplings between the protons
can be ignored.)
11

H
H

10.

11.

B
H

H
H

Explain why the 129 Xe NMR spectrum of XeF+ is a doublet with J = 7600 Hz but the 19 F
spectrum appears to be a triplet with J = 3800 Hz.
(19 F has spin 12 and 100% natural abundance; 129 Xe has spin 12 and 26% natural abundance).
Using the force constant given in the table on page 30, calculate the stretching frequencies for
H2 and 79 Br2 . What experimental technique(s) would you use to determine these frequencies?
[speed of light, c = 3.00 1010 cm s1 ; relative atomic masses: 1 H = 1.0078; 79 Br = 78.918;
NA = 6.02 1023 ]

12.

Given that the stretching frequency for HCl (i.e. 1 H35 Cl) is 2991 cm1 , estimate the stretching
frequency for DCl (2 H35 Cl). What assumption have you made for this calculation and is it
reasonable? What experimental technique(s) could be used to measure the stretching frequencies
for HCl and DCl?

13.

How can an APT NMR experiment distinguish between the following hydrocarbons?

14.

How could the following six isomers be distinguished using 13 C NMR?

41

15.

The carboxylate anion, RCOO , shows two absorptions in the C=X region, one around 1575
and one around 1430 cm1 . The C=O vibrational frequency for a typical carboxylic acid,
RCOOH, is 1725 cm1 ; the vibrational frequency of a CO single bond is around 1100 cm1 .
Discuss.

16.

Shown below is a portion of the 1 H NMR spectrum of bromoethane as measured on a 400 MHz
spectrometer where 1 ppm 400 Hz. In order to magnify the baseline, the spectrum has been
vertically expanded and cropped. Explain the appearance of the spectrum as fully as possible
and determine (in Hz) the 1 JCH coupling constants and the 3 JHH coupling constant.

4.0

17.

3.5

3.0

2.5

2.0

1.5

1.0

How would you distinguish spectroscopically between the following pairs of isomers (i) using
C NMR spectroscopy and (ii) using IR spectroscopy?

13

NH2

CN
O

and

and
O

OH

OH

and

and

O
and

18.

CO2H

For organic molecules, reduction involves adding H2 across double bonds. Reduction of the
following molecule gave two products, both with molecular formula C6 H12 O.

From the following spectroscopic data, identify these two products and explain how the data is
consistent with your proposals for the structures of A and B:
Product A: 13 C NMR: 137, 115, 85, 36 and 17 ppm; IR: 3400 and 1650 cm1 .
Product B: 13 C NMR: 213, 38, 31, 17 and 8 ppm; IR: 1710 cm1 .

42

134.1
129.9
128.5
125.0

62.5

Compound A has the formula C7 H7 NO3 and may be reduced to give compound B with the
formula C7 H9 NO. The 13 C NMR and the IR spectra for A and B are given below. The signals
in the aromatic region of the 1 H NMR spectrum of A appear as two triplets and two doublets.
Deduce the structures of A and B and, as far as possible, assign the spectra.

147.6

136.8

Compound A

140

120

146.0

Compound B

210

200

180

160

140

100

80

100

80

60

40

20

0 ppm

40

20

0 ppm

64.3

160

118.2
116.0

180

124.8

200

129.4
129.2

210

120

60

100%

transmission

1612
1574

80%
60%
40%

Compound A

20%
0%
4000

1512

3500

3000

2500

2000
1500
frequency / cm1

2500

2000
1500
frequency / cm1

1334

1000

500

1000

500

100%
80%
60%

1612
1589

transmission

19.

3386

40%
20%
0%
4000

Compound B

3500

3000

43

20.

(i) The relative molecular mass of a compound, X, has been determined by high resolution
mass spectrometry to be 68.0261. Using the accurate relative atomic masses below, determine
the formula of compound X.
1

(ii)

H : 1.0078

12

C : 12.0000

16

O : 15.9949

The IR spectrum for compound X is shown below. What is its structure? (Hint: you will need
to measure carefully the carbonyl frequency to distinguish between dierent possible structures.)
100%

transmission

80%
60%
40%
20%
0%
4000

21.

3500

3000

2500

2000
1500
frequency / cm1

1000

500

Shown below are six derivatives of the steroid cholestane:

CH3COO

CH3COO

CH3COO

OEt

OEt

Shown in the table are data from six IR spectra, each of one of the cholestane derivatives (only
peaks in the C=X region are listed). In as far as you can, match up the chemical structures with
the IR data; explain your reasoning. Strong and weak absorptions are marked s and w.
spectrum

/ cm1

spectrum

/ cm1

1715(s)

1695(s), 1686(s), 1608(w)

1724(s), 1712(s)

1653(s), 1626, 1592

1730(s), 1695(s), 1642(w)

1730(s), 1658(w), 1626

44

41

40

22.
34
33

37

38

39

35

29
28

O 36 O
32
31

22

30

20

21

23

18

24

12

16
15

13

11
6

NanoBalletDancer

27

14

19

10

17

26
25

5
4
3

2
1

In June 2003, a research paper was published announcing the synthesis of the smallest representations of the human form: 2 nm tall anthropomorphic molecules, nicknamed NanoPutians by
their creators. The molecules synthesised included NanoKid, NanoBaker and NanoAthlete.
The compound shown above was called NanoBalletDancer and has the formula C41 H50 O2 .
13

C NMR spectrum of NanoBalletDancer?

(i)

How many signals do you expect to see in the

Indicate which carbon atoms are equivalent.

(ii)

There are 13 dierent environments of hydrogens in NanoBalletDancer; their signals are

labelled A-M in the 1 H NMR spectrum below. The numbers of hydrogen atoms in each unique
environment is given under the label. Using the numbers of hydrogens in a given environment,
the multiplicities of the signals, and to some extent the chemical shifts of the signals, assign (as
far as possible) which signals correspond to which hydrogen atoms in the compound. As a start,
signal B is due to the hydrogens on carbon atoms 19 and 23.
K
18H

The 1H NMR spectrum

of NanoBalletDancer

H
4H
E
2H

B
2H

I
4H

G
2H

M
3H
J
3H

C
2H
D
1H

A
1H

7.5

F
2H

L
6H

7.0

6.5

6.0

solvent

5.5

5.0

4.5

4.0

45

3.5

3.0

2.5

2.0

1.5

1.0 ppm

Suggested answers to problems

1a.

i)

ii)

OH

iii)

OH

or

O
OH

iv)

OH

v)

OH

vi)

vii)

O
vii)

ix)

or

O
OH

OH

x)

xi)

Ph

or

OMe
OMe

Ph

O
O

other variations are possible!

1b.

O
O

OH

acetic acid

acetic anhydride

(diethyl) ether
O

OH

t-butyl alcohol

2.

pyridine C5 H5 N

OH

n-butyl alcohol

toluene

anthracene C14 H10

menthol C10 H20 O

viagra C22 H30 N6 O4 S tetrodotoxin C11 H17 N3 O8

3.

Li I = 1;
111
Cd I = 12

14

N I = 1;

15

N I = 12 ;

76

acetone

Se I = 0;

46

cocaine C17 H21 NO4

rohypnol C16 H12 FN3 O3

77

Se I = 12 ;

78

Se I = 0;

110

Cd I = 0;

NO 2

4a.

1 signal

4 signals

Cl

Cl

NO 2

Br

2 signals

4 signals
O

NO 2
O

2 signals

6 signals

4b.

3 signals

8 signals

1
2

2 signals

4 signals

6 signals

Cl
CN

1
2

CN

7 signals

4 signals

2
1

1
1

7
6

2
2

7 signals

3 signals

10 signals
(all different)

1
1

2 signals
(make a model!)

2 signals

5.
3

OMe
1

1 23

Br

200

150

100

50

0 ppm

200

150

100

5
3
4

5
4

OMe
15

NH2

6
3

1 MeO

8 7

2
3
150

100

50

0 ppm

200

47

0 ppm

50

2 MeO

200

150

4 6
100

50

0 ppm

6.

with broadband 1H decoupling

HO

2
1

100

50

without broadband 1H decoupling

100

0 ppm

coupling
constants are
not the same

50

with broadband 1H decoupling

for 13C enriched ethanol

coupling
constants are
the same

100

50

0 ppm

0 ppm

7a. Two signals, therefore two dierent fluorine environments. From the splitting patterns, there is
one fluorine in one environment and four in the other.
unique Fa couples to 4
equivalent Fbs to give a quintet

Fa
Fb
Fb

7b.

Fb

four fluorines all equivalent,

couple to Fa to give a doublet

Fb

Structure 1 (the observed structure): two fluorine environments (axial and equatorial with
two in each). Two signals each signal will be a triplet.
Structure 2: again two environments so two signals. Now only one axial and three equatorial. The axial fluorine will be split into a 1 : 3 : 3 : 1 quartet by the three equatorial
fluorines; the equatorial fluorines will be split into a 1 : 1 doublet by the axial fluroine.
Structure 3: One environment all equivalent so no coupling observed. One singlet only.

8. CH2 H2 proton decoupled so no coupling to hydrogens. Chlorine (both 35 Cl and 37 Cl) have spin
and relax too quickly for coupling to be seen.
CD2Cl2
spin for D, I = 1

original shift
split into a triplet by the 1st D
each line is then split into
another triplet by the 2nd D

1 : 2 : 3 : 2 : 1

48

3
2

8. (Continued)
d6DMSO

(2nI+1) predicts 7 lines

In practice, often looks more like
a quintet since outer lines are
lost in the noise of the spectrum.

1 : 3 : 6 : 7 : 6 : 3 : 1
9.
H
H

H
B

terminal Hs couple to one B spin 3/2.

Gives (2 x 1 x 3/2) + 1 = 4 peaks
ratio 1:1:1:1.

CD3
CD3

bridging Hs couple to two B spin 3/2.

Gives (2 x 2 x 3/2) + 1 = 7 peaks
ratio 1:2:3:4:3:2:1.

10.

1 type of carbon coupled

to 3 equivalent Ds.

1 : 2 : 3 : 4 : 3 : 2 :1

The coupling constants between the xenon and the fluorine must be the same. Since the
coupling in the doublet in the xenon spectrum is 7600 Hz, this must be the coupling constant
in the 19 F spectrum. Therefore the 19 F spectrum must be of a doublet (with J = 7600 Hz)
superimposed on a singlet. Most of the fluorine is attached to spin zero xenon only 26% is
attached to spin 12 129 Xe to give the satellites. Ratio of observed peaks will be 13 : 74 : 13.

11.

H2 =

H2

kf

1.0078 1.0078 1.0078

=
g mol1
1.0078 + 1.0078
2

1.0078
= 8.37 1028 kg (molecule1 )
2 1000 NA

1
=
2 3.00 1010
Br2 =

Br2

1
2c

"

575 2 1000 6.02 1023

= 4397 cm1
1.0078

78.918
= 6.55 1026 kg (molecule1 )
2 1000 NA

1
=
2 3.00 1010

246 2 1000 6.02 1023

= 325 cm1
78.918

Note that the BrBr stretching frequency (at 325 cm1 ) is much lower than the HH stretching
frequency (at 4397 cm1 ). H2 is so high due to both the small reduced mass and the strong
single bond. These stretching frequencies can be determined using Raman spectroscopy. Neither
absorbs IR since there is no dipole moment during the stretch.
49

12.

HCl = 2991 cm1

DCl

"
"

kf
HCl
kf
DCl

Assuming the force constant is the same for both HCl and DCl:
!
DCl
HCl
=
HCl
DCl
DCl = HCl

DCl = 2991 cm

HCl
DCl

HCL =

1 35 35
=
g mol1
1 + 35 36

DCL =

2 35 70
=
g mol1
2 + 35 37

35 37

= 2144 cm1
36 70

[If we had used the approximations HCL 1 and DCL 2, get the answer 2115 cm1 .]

We assume that the force constants are the same for both HCl and DCl. This is reasonable
since the degree of bonding is related to the electronic arrangement, which is identical for both
the extra neutron in DCl has little eect.
Both normal IR spectroscopy and Raman spectroscopy could be used to determine these
stretching frequencies.
13.

All of the spectra would show five peaks in the 0-50 region in the 13 C NMR spectrum, hence
we should use the APT to distinguish. Even peaks point in the same direction as the solvent;
odd in the opposite direction.

5 peaks
4 even
1 odd

5 peaks
1 even
4 odd

5 peaks
3 even
2 odd

5 peaks
5 even
0 odd

50

5 peaks
2 even
3 odd

5 peaks
0 even
5 odd

14.

The number of signals can be used to a certain extent to distinguish between the isomers
A and D both have 8; B and C have 5; E and F have 4. In order to distinguish between these
pairs, we need to use the APT paying careful attention in which regions the odd / even peaks are
found. Even peaks point in the same direction as the solvent; odd in the opposite direction.
2e

5e

1o

3o

5e

7e

4o
A

6e

2e
8o

1o

1o
2e

5o

4e

5o

1o

7o
2e

1o
2e

4o

8 peaks; 4 odd 4 even

alkene carbons are even

3e
1o

4 peaks; 2 odd 2 even

alkene carbons are odd

15.

2e

1o

1o
2e

4o

8o

1o

5e

3e

4o

3e

6o

4e

5 peaks; 2 odd 3 even

(alkene carbons are even)
3e

1o

3e

5 peaks; 1 odd 4 even

(alkene carbons are even)

4e
3e

3e

8 peaks; 4 odd 4 even

alkene carbons are odd

2e

4e

2e

3e
4o

4 peaks; 2 odd 2 even

alkene carbons are even
O

(-)

better represented as
R

(-)

both C-O bonds the same

strength and in between a
double and single bond

see two stretches:

antisymmetric ~ 1575 cm-1
symmetric ~ 1430 cm-1
both in between stretching frequencies of
C=O 1725 cm-1 and C-O 1100 cm-1

16.

At the slightly larger shift of 3.4 ppm is the signal from the two protons attached to the carbon
with the bromine. This signal is split into a 1 : 3 : 3 : 1 quartet by the three protons on the other
carbon. (The ratio cannot be seen since the spectrum has been cropped.)
The signal at 1.65 ppm is due to the methyl protons, split into a 1 : 2 : 1 triplet by the
CH2 Br protons.
Either side of each of these signals are the 13 C satellites. Note the coupling between the two
sets of protons and the carbons they are attached to are not the same!
~2.1 mm 21 Hz = 3 x 3JH-H
i.e. 3JH-H = ~ 7 Hz
13 mm 130 Hz = 1JC-H

CH2Br-

-CH3

15 mm 150 Hz = 1JC-H
4.0

3.5
1ppm
1 mm

400 Hz
10 Hz

3.0

2.5

2.0

40 mm

51

1.5

1.0

17.

NH2
CN
O

and

and
O

NMR
ketone ~ 200
2 peaks in 50-100
2 peaks in 0-50

NMR
ester (lactone) ~ 175
1 peak in 50-100
3 peaks in 0-50

NMR
3 peaks in 100-150
(-CN ~ 120)
4 peaks in 0-50

IR
ketone + ring
~ 1715 + 30
= 1745 cm-1

IR
ester + ring
~ 1745 + 30
= 1775 cm-1

IR
-CN ~2200 cm-1

OH

IR
2 peaks ~ 3300 cm-1
for the NH2

OH

and

NMR
4 peaks in 100-150
1 peak in 0-50

and

NMR
2 peaks in total

NMR
4 peaks in total

NMR
6 peaks in total

IR
C=O in 6-mem ring
~1715 cm-1

IR
C=O in 4-mem ring
~1775 cm-1

IR
not much use to
distinguish
O

NMR
4 peaks in total

O
and

CO2H

NMR
5 peaks in total

NMR
3 peaks in total

IR
~1715 - 30 = 1685 conjugated ketone C=O
~1725 - 30 = 1695 conjugated acid C=O
+ broad O-H stretch

IR
~1800 & 1760 cm-1
symm & antisymm
C=O stretches

18.

5
2

2
3

OH

A
1 115 ppm; 2 137 ppm
3 85 ppm; 4 36 ppm
5 17 ppm

B
1 8 ppm;
3 213 ppm;
5 17 ppm

3400 cm-1 is the O-H stretch

1650 cm-1 is the C=C stretch

2 31 ppm
4 38 ppm

1710 cm-1 is the ketone

C=O stretch

52

19.

OH

OH

NO2

NH2

Compound A

Compound B

13

13

C NMR - 6 signals between 100-150

indicate benzene ring with at least two
substituents.
Signal at 62.5 ppm suggests sp3 carbon
with O attached.
Substituents must be either ortho or para.

C NMR - significant changes in aromatic

carbons. Suggests the reduced group is
directly attached to the benzene ring.
Signal at 64.3 ppm unchanged sp3 carbon
with O attached.
IR peaks at 1512 and 1334 cm-1 gone.
Broad peak around 3300 cm-1 still present
but now joined by sharp N-H stretch at
3386 cm-1.

cm-1

IR peaks at 1512 and 1334

suggest
NO2 group. Peaks due to benzene ring
around 1600 cm-1. Broad peak around
3300 cm-1 suggests -OH group
1H NMR two doublets and two triplets in
aromatic region tell us there two
substituents which are ortho to each other.

20.

Formula C4H4O (3 double bond equivalents)

2095 cm-1

C
H

3260 cm-1 C-H stretch of terminal alkyne

1685 cm-1 must be a conjugated C=O

21.

B, C & F all esters so look for the highest frequencies

2,

must be
2 absorptions only
1724 ester
1712 ketone
must be B

only ketone (1715)

must be E
A
4

B
2

C
3

D
5

E
1

F
6

1658(w) and 1626

2 x C=C must be F

1695(s) conjugated ketone

1642(w) C=C must be C

must be

left with A, D & E

and

1,

and

1695(s) & 1686(s)

conjugated C=Os
must be A

53

1 conjugated C=O
and 2 C=C must be D

22.

(i) There are 23 signals in total in the 13 C NMR spectrum. If a model is made of this structure,
at at least in one conformation (rotating about the single bonds 18-17 and 17-10) there is a plane
of symmetry making the left and right hand sides of the molecule equivalent.
1 16, 2 15, 3 14, 4 13, 5 12, 6 8, 9 11, 19 23, 20 22, 24 30, 25 31, 26
32, 37 39.
27, 28, 29, 33, 34, and 35 are all equivalent.
7, 10, 17, 18, 21, 36 38, 40, and 41 all lie in the plane of symmetry and are unique.
Most students are caught out by carbons 40 and 41 being dierent. One is on the same side of
the head ring as the body the other is on the opposite side of the head.
(ii)
Peak

description

due to hydrogens on carbon(s)

1H singlet

2H singlet

19 and 23

2H singlet

9 and 11

1H singlet

36

2H singlet

17

2H doublet

37 and 39

2H doublet

37 and 39

4H triplet

3 and 14

4H sextuplet

2 and 15

3H singlet

40 or 41

18H singlet

27, 28, 29, 33, 34, and 35

6H triplet

1 and 16

3H singlet

41 or 40

Notes: Signal (C) appears shorter than B due to the very weak coupling to the proton on carbon
7; this has not split the signal, just broadened it slightly.
The upper hydrogens on carbons 37 and 39 (on the opposite side of the face ring as the
body) are equivalent and give rise to either signal F or G. Similarly, the lower hydrogens on
carbons 37 and 39 (on the same side of the ring as the body) are equivalent. These upper and
lower hydrogens are not the same and couple with each other, thus giving the doublets. Nasty,
but there we are!

54