Download Structure Determination

INFRARED SPECTROSCOPY
THEORY
A molecule is not a rigid assemblage of atoms. The atoms, even in the solid state, vibrate about
an equilibrium position. Each atom vibrates with a frequency which depends on its mass and the
length and strength of any bonds which it has formed. There are two kinds of fundamental
vibrations for molecules, stretching and bending (or deformation).
Stretching
In stretching vibrations, the distance between the atoms increases or decreases, but the atoms
remain in the same bond axis.
symmetrical stretching
asymmetrical stretching
Bending
In bending vibrations, the position of the atom changes relative to the original bond axis.
+
+
+
-
scissoring
rocking
wagging
twisting
(in-plane bending vibrations)
(out-of-plane bending vibrations)
+ and – signify vibrations above and below the plane of the paper respectively
Each of the various stretching and bending vibrations of a bond occur at a certain particular
frequency, in the range 1.20 x 1013 to 1.20 x 1014 Hz, which corresponds to a frequency in the
infrared region of the electromagnetic spectrum. Therefore, when infrared radiation of that same
frequency falls on the molecule, energy is absorbed and the amplitude of that vibration
increases. Only those vibrations which cause a change in the dipole moment of the molecule
will result in the absorption of infrared radiation.
So that the numbers involved are more convenient, absorption is usually quoted at a particular
wavenumber (the reciprocal of the wavelength in cm of the absorbed radiation), which has the
unit cm-1.
Bending vibrations generally require less energy and therefore occur at lower wavenumbers
than stretching vibrations. Stretching vibrations occur in the order of bond strengths. Thus, a
triple bond absorbs radiation of a higher wavenumber than the equivalent double bond, which in
turn absorbs radiation of a higher wavenumber than the equivalent single bond.
TOPIC 13.32: STRUCTURE DETERMINATION
1
THE INFRARED SPECTROMETER
An infrared spectrometer has two beams of radiation from the same source, one passing
through the sample, the other passing through a reference cell.
Sample
Chart recorder
Detector
glowing
source
Monochromatic
grating
Reference
A rotating segmented mirror takes information from the sample and reference beams
alternately. If a particular frequency is absorbed by the sample, less radiation is transmitted, and
the detector compares the intensity of radiation of each wavelength passing through the sample
with the intensity passing through the reference cell.
When the spectrum is determined, a calibration line is usually recorded on the paper. For this
purpose, the absorption peak of polystyrene at 1603cm -1 is commonly used.
Preparing Samples
Glass absorbs infrared radiation. Therefore, cells for use in an infrared spectrometer have to be
made from some other material, which is transparent to infrared. Sodium chloride and
potassium bromide are frequently used. Potassium bromide is preferred, because sodium
chloride absorbs radiation below 625cm-1.
Gases
Gases are placed in a special cell, typically 10cm in length.
Liquids
Liquids are examined in the form of a thin film, formed by sandwiching a small drop of liquid
between sodium chloride discs.
Solutions
Solutions, usually in solvents such as CCl4 and CHCl3, are placed in cells with a path length
between 0.01mm and 0.5mm.
Solids
A disc can be made by finely grinding the solid with KBr in a mortar. The powder is then placed
in a circular die and compressed to give a transparent disc which is used to record the
spectrum.
Alternatively, a paste can be made from the solid and a long-chain liquid hydrocarbon called
Nujol. This mull is then placed between sodium chloride discs.
TOPIC 13.32: STRUCTURE DETERMINATION
2
INTERPRETATION OF INFRARED SPECTRA
Infrared spectra are valuable aids in the identification of unknown compounds.
A complex molecule has a large number of vibrational modes. Some of these vibrations (mainly
above 1500cm-1) are associated with individual bonds or functional groups, while others (below
1500cm-1) are considered as vibrations of the whole molecule.
The absorption associated with a particular individual bond or functional group always occurs at
approximately the same wavenumber, irrespective of the molecule involved.
e.g. the carbonyl (C=O) absorption in the following aliphatic ketones:
butanone
1718cm-1
cyclohexanone
1715cm-1
Structural changes close to the vibrating bond can cause small shifts.
e.g. the carbonyl absorption in the following classes of compounds:
aliphatic ketones
1725-1705cm-1
aromatic ketones
1700-1680cm-1
aliphatic aldehydes
1740-1720cm-1
aromatic aldehydes
1715-1695cm-1
esters
1750-1735cm-1
aliphatic carboxylic acids 1725-1700cm-1
acyl chlorides
1795cm-1
The infrared spectrum can conveniently be split into four regions for interpretation.
4000-2500 cm-1
absorption due to stretching vibrations of single bonds to hydrogen
e.g. C-H, O-H, N-H
2500-2000 cm-1
absorption due to stretching vibrations of triple bonds
e.g. C=C, C=N
2000-1500 cm-1
absorption due to stretching vibrations of double bonds
e.g. C=C, C=O
1500-400 cm-1
absorption due to stretching vibrations of some single bonds
e.g. O-H, C-O
absorption due to various bending vibrations
The region 1500-400 cm-1 is not mainly used for recognising individual bond absorptions. This
region contains absorption bands which are characteristic of the compounds under test and no
other compound. This region is therefore called the fingerprint region. The fingerprint region
can be used to confirm the identity of a substance by comparison with the infrared spectrum of
an authentic sample.
TOPIC 13.32: STRUCTURE DETERMINATION
3
Correlation Table for Infrared Spectroscopy
4600
4200
3800
aliphatic C-H stretch
3400
3000
2600
2200
2000
1800
N-H stretch
amines (v)
1600
1400
1200
1000
C-N stretch
C-H bend
aromatic nitro cpds. aliphatic (v)
C-H stretch
C C-H (sh)
C N stretch
aliphatic nitriles
C=O stretch (vs)
C-H stretch
alkenes (sh)
C
C-H stretch
aromatic ring (w-m)
C stretch (v)
C-Br stretch
haloalkanes
2600
C=C stretch
Ar-C=C (w-m)
Abbreviations used:
w = weak
m = medium
s = strong
vs = very strong
v = variable
br = broad
sh = sharp
C-N stretch
aromatic nitro cpds.
N-H bend (v)
2200
2000
1800
1600
1400
Wavenumber / cm-1
TOPIC 13.32: STRUCTURE DETERMINATION
C-Cl stretch
haloalkanes
C=C stretch
aromatic (m)
C-H stretch (2 bands)
aldehydes
3000
C-N bend
amines
C=C stretch
alkenes (v)
C-H stretch
alkanes (v)
3400
C-H bend
C=C-H (m-s)
C-C skeletal vibration (w)
O-H stretch
ROH (sh)
3800
C-H bend
C C-H (s)
N-O stretch
aromatic nitro cpds.
H-bonded O-H stretch (br)
4200
400
C-O stretch
esters, alcohols, carboxylic acids
O-H stretch
COOH (w, br)
4600
600
C-O-C asymmetric stretch (vs)
free O-H stretch (sh)
aromatic C-H stretch (w)
800
4
Fingerprint region
1200
1000
800
600
400
Characteristic Infrared Absorption Ranges
Wavenumber range/ cm-1
Functional Group
Vibration
3750 – 3200
3500 – 3300
3500 – 3140
3300 – 2500
3095 – 3010
3080 – 3030
2962 – 2853
2900 – 2700 (2 bands)
2260 – 2215
2260 – 2140
1850 – 1800
1790 – 1740
1795
1750 – 1735
1740 – 1720
1730 – 1717
1725 – 1705
1725 – 1700
1700 – 1680
1700 – 1630
1669 – 1645
1650 – 1590
1600, 1500 & 1450
1570 – 1500
1550 – 1330
1485 – 1365
1370 – 1300
1310 – 1100
880 – 700
800 – 600
600 – 500
alcohol & phenol
amine
amide
carboxylic acid
alkene
arene
alkane
aldehyde
nitrile
alkyne
carboxylic anhydrides
carboxylic anhydrides
acyl chloride
ester
aldehyde
aryl ester
ketone
carboxylic acid
aryl carboxylic acid
amide
alkene
amide & amine
arene
aromatic nitro compound
aromatic nitro compound
alkane
aromatic nitro compound
ester, alcohol, carboxylic acid
arene
chloroalkane
bromoalkane
O-H stretch
N-H stretch
N-H stretch
O-H stretch
C-H stretch
C-H stretch
C-H stretch
C-H stretch
C=N stretch
C=C stretch
C=O stretch
C=O stretch
C=O stretch
C=O stretch
C=O stretch
C=O stretch
C=O stretch
C=O stretch
C=O stretch
C=O stretch
C=C stretch
N-H bend
C=C stretch
C-N stretch
N-O stretch
C-H bend
C-N stretch
C-O stretch
C-H bend
C-Cl stretch
C-Br stretch
TOPIC 13.32: STRUCTURE DETERMINATION
5
NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY
Nuclear magnetic resonance (NMR) spectroscopy gives information on the environment in
which the nuclei of atoms are found in molecules. In many cases, so much information can be
obtained from a single spectrum that the structure of the molecule can be determined.
THEORY
All nuclei with an odd mass number have a property called spin, e.g. 1H, 13C, 15N, 19F, 31P. Since
the nuclei are positively charged, this spin is associated with a circulation of electric charge and
thus gives rise to a magnetic field. When placed in an external magnetic field, the nuclei tend to
align themselves in the magnetic field. For a nucleus of spin ½ only two orientations are
allowed: with the external field and against it.
nuclear magnetic moments
with field
against field
external magnetic field
These two orientations have different energies and hence there are two energy levels populated
by the nuclei. Transitions between the two energy levels can occur if radiation of the correct
frequency (E = h) is absorbed. This radiation is in the radiofrequency region. The “resonance”
absorption is recorded as an NMR spectrum. 1H NMR is the most widely used.
Energy
against field
E
with field
no field
TOPIC 13.32: STRUCTURE DETERMINATION
field applied
6
OBTAINING A NMR SPECTRUM
1. The sample is dissolved in a proton-free solvent e.g. CDCl3, CCl4
2. The solution is placed in a glass NMR tube which is then spun at 20 revolutions per second
between the poles of a strong electromagnet. Spinning averages out any lack of uniformity in
the sample or the glass tube. The magnetic field must be stable and homogeneous to a few
parts in 108.
3. The sample is irradiated with radio waves of constant frequency and the absorption
measured as the magnetic field is varied. Alternatively, the magnetic field can be kept
constant and the range of radiofrequencies scanned.
SHIELDING AND CHEMICAL SHIFT
When a molecule is placed in a magnetic field, the electrons surrounding the nuclei behave like
perfectly conducting shells, and weak electric currents are induced in them, which flow in such a
way as to produce a magnetic field which opposes the applied field. Therefore, the nuclei at the
centre experience a magnetic field which is fractionally smaller than the applied field. Since the
electron distribution around chemically different hydrogen atoms in a molecule is not the same,
the nuclei are shielded from the applied field to different extents. Each unique proton gives a
unique NMR signal, which gives a map of the C-H framework of a molecule.
The place at which a particular proton absorbs is called its chemical shift. It is measured
relative to the standard TMS (tetramethylsilane) (CH3)4Si. Chemical shift is given the symbol 
and is measured in ppm.
 = signal (Hz) –TMS (Hz)
ppm
machine frequency (MHz)
Defining chemical shift in this way means that it is independent of the applied magnetic field
which is used.
Resonances at high field
Resonances at low field
(shielded)
(deshielded)
2
integral

10
1
Chemical shift for hydrogen /ppm
0
By definition, the  value for TMS is 0. Most organic proton resonances occur on a scale of 0-10
on the higher frequency/lower field side of zero. The greater the value of , the more the proton
is deshielded by adjacent electron-withdrawing atoms or groups.
TOPIC 13.32: STRUCTURE DETERMINATION
7
The area under each peak in the spectrum is measured by electronic integration, and the
heights of the steps on the integration curve indicate the relative number of protons giving rise to
each peak. At A-level, you will not be expected to measure the integral, instead you will be told
the number of protons in each peak.
A high resolution NMR spectrum reveals that many peaks are not singlets (i.e. single lines), but
are multiplets. This arises because of spin-spin coupling.
SPIN-SPIN COUPLING
The magnetic field experienced by a particular proton is influenced by neighbouring NONEQUIVALENT protons. This interaction is known as coupling, and it causes peaks to be split
into a number of lines.
If a proton couples with n neighbouring non-equivalent
protons, the signal of that proton is split into (n+1) lines
The separation between peaks is called the spin-spin coupling constant, J, and is measured in
Hz.
To decide if protons are equivalent, substitute any one by chlorine and count the possible
isomers. If only one isomer is possible, the protons are equivalent.
Examples:
CH3CH3
all protons are equivalent
1 line only
CH3CH2X
CH3 protons signal split by CH2 protons
3 lines (1:2:1 triplet)
CH2 protons signal split by CH3 protons
4 lines (1:3:3:1 quartet)
CH3CHX2
CH3 protons signal split by CH proton
2 lines (1:1 doublet)
CH proton signal split by CH3 protons
4 lines (1:3:3:1 quartet)
In CH3CHX2
CH
CH3
The relative intensities of
the peaks are 1:3
J
J
J
J
TOPIC 13.32: STRUCTURE DETERMINATION
8
The same coupling constant
is seen in both signals
Protons separated by more than two carbon atoms show little or no coupling. In the example
below, Hb and Hc both couple with Ha but do not couple with each other.
Hb
Hc
Ha
Ha appears as a quartet, where Jab>Jac
Jab
Hb and Hc appear as doublets with splitting
Jab and Jac respectively
-C-C-CHa
Jac
Jac
Benzene Derivatives
In benzene derivatives, such as methylbenzene, the five adjacent aromatic protons have similar
chemical shifts and undergo mutual coupling. The overlapping sets of peaks give a multiplet at
around  = 7.3 which is difficult to analyse.
The NMR spectrum of propyl ethanoate below shows the integration curve and how it is used to
obtain information on the number of protons resonating at each frequency. In this case, the ratio
of protons (not necessarily the absolute number of protons) b:a:c:d is 2:3:2:3
H3C.CO.O.CH2.CH2.CH3
a
b
c d
3
2
 ppm
protons
0.9
1.7
2.0
4.0
CH3
CH2
CH3.CO
CH2O
3
2
8
TOPIC 13.32: STRUCTURE DETERMINATION
7
6
9
5
4
 /ppm
3
2
1
0
Table of Proton Chemical Shifts
Methyl
protons

CH3-R
CH3-C=C
CH3-CN
CH3-COOR
CH3-COR
CH3-Ar
CH3-NRCH3-COOAr
CH3-COAr
CH3-NCOR
CH3-NAr
CH3-OR
0.7 – 1.6
1.6 – 1.9
2.0
2.0
2.2
2.3
2.3
2.4
2.6
2.9
3.0
3.3
CH3-OCOR
CH3-OAr
CH3-OCOAr
3.7
3.8
4.0 – 4.2
ppm
Methylene
protons


ppm
Methine
protons
R-CH2-R
1.4
-CH-R
1.5
R-CH2-CN
2.3
-CH-CN
2.7
R-CH2-COR
R-CH2-Ar
R-CH2-N
2.4
2.3 – 2.7
2.5
-CH-COR
-CH-Ar
2.7
3.0
R-CH2-COAr
R-CH2-NCOR
2.9
3.2
-CH-COAr
-CH-NCOR
3.3
4.0
R-CH2-OR
R-CH2-I
R-CH2-Br
R-CH2-Cl
R-CH2-OH
Ar-CH2-COR
R-CH2-OCOR
R-CH2-OAr
3.4
3.2
3.5
3.6
3.6
3.7
4.1
4.3
-CH-OR
-CH-I
-CH-Br
-CH-Cl
-CH-OH
3.7
4.3
4.3
4.2
3.9
-CH-OCOR
-CH-OAr
4.8
4.5
Ar-CH2-OCOR
4.9
H-C C
-CH=C-
2.5–2.7
5.2–5.7
CH2=C-
4.6 - 5.0
ppm
Protons in Other Environments
R-NH2 *
ArNH2 *
R-OH *
1.1 – 1.5
3.4 – 4.0
3.0 – 5.2
R2-NH *
0.4 – 1.6
Ar-OH *
4.5 – 7.7
* The absorption positions of these groups are concentration-dependent and are shifted to
higher  values in more concentrated solutions.
Ar-H
R-CHO
6.6 – 8.0
9.7 – 9.8
-NH-CO-
5.5 – 8.5
Ar-CHO
9.7 – 10.0
TOPIC 13.32: STRUCTURE DETERMINATION
10
Carbon-13 nmr spectroscopy
After hydrogen, the most useful atom providing information is carbon-13. Natural carbon
contains about 1% of this isotope so the instruments for its detection need to be sensitive and
spectra will take longer to record.
Only the chemical shift is important as each spectrum (in proton decoupled 13C nmr) gives only
single lines for each chemically equivalent carbon.
Environment
C - C (alkanes)
C - C=O
C - Cl or C - Br
C - N (amines)
C - OH
C = C (alkenes)
aromatic C’s (benzene rings)
C=O (esters, acids, amides)
C=O (aldehydes, ketones)
Chemical shift / 
10 - 35
10 - 35
30 - 70
35 - 65
50 - 65
115 - 140
125 - 150
160 - 185
190 – 220
Carbon-13 nmr has wide applications in the study of natural products, biological molecules and
polymers.
Let us consider the 13C nmr spectrum of ethanol (CH3CH2OH)
The spectrum in the box shows where the 1H nmr spectrum would appear.
We can see that there are 2 large peaks in this spectrum at  = 19 and  = 58ppm. This tells us
that there are 2 non-equivalent C atoms in the molecule. Using the chemical shift data above we
can see that the peak at 19ppm is due to a C – C whilst the peak at 58ppm is due to a C-OH.
The first peak is due to CH3CH2OH whilst the other is for CH3CH2OH.
TOPIC 13.32: STRUCTURE DETERMINATION
11
Exercise
How many peaks would you expect there to be in the carbon-13 spectrum of…
•
•
•
•
•
•
•
•
•
•
•
•
•
ethylethanoate
•
cyclohexane
butane
……..
CH3CH2CH2CH3
2-methylpropane CH3CH(CH3)CH3
……..
butanal
CH3CH2CH2CHO
……..
butanone
CH3COCH2CH3
……..
pentan-2-one
CH3COCH2CH2CH3
……..
pentan-3-one
CH3CH2COCH2CH3
……..
CH3COOCH2CH3
……..
C6H12
……..
TOPIC 13.32: STRUCTURE DETERMINATION
12
?
MASS SPECTROMETRY
Mass spectrometry is a useful technique for determining the structure of a compound. It is about
1000 times more sensitive than either infrared or NMR spectroscopy and requires only a
microgram or less of the sample.
Basic features
1. The apparatus is kept under vacuum to prevent ions produced from colliding with air
particles.
2. Ionisation: The sample is dissolved in a volatile solvent and a high voltage is applied.
Positively charged droplets are released as a fine spray and the solvent evaporates. This
leaves individual positively charged ions.
3. Acceleration: The ions are accelerated by attraction towards a negatively charged plate
which gives all of the ions the same kinetic energy. Since kinetic energy = ½ mv2, lighter ions
move faster than heavier ones.
4. Ion drift: The ions are passed through a hole in the negatively charged plate forming a
beam. The ions drift down the ‘flight tube’ towards a detector. They are separated based on
their different velocities. The faster (lighter) ions reach the detector first.
5. Detection: The separated streams of ions strike a negatively-charged detector plate,
which is contained in the detector and flight times are recorded. The arriving ions generate a
current which sends a signal to a computer or a chart recorder. A plot of the intensity of the
signal against m/z is drawn out.
TOPIC 13.32: STRUCTURE DETERMINATION
13
e.g. stick diagram of the mass spectrum of ethanol.
Relative abundance %
[CH2OH]+
100
80
60
parent ion
m/e 46
[C2H5O]+
40
[C2H5]+
[C2H3]+
[C2H5OH]+
20
[M+1]+
10
20
30
40
50
m/z
Applications of Mass Spectrometry
1. Mass spectrometry can be used for the determination of the isotopic composition of a
sample of an element and hence for the measurement of relative atomic mass.
2. A mass spectrum can be used to determine relative molecular masses of compounds since
the line with the highest m/z value is usually the molecular ion, M+. There is always a very
small peak at (M+1) for organic compounds which is due to the 13C isotope, present with a
natural abundance of 1.1%.
3. The high resolution of the double focussing mass spectrometer enables very precise
measurements of masses to be made. Since the mass defect varies from element to
element, the masses of ions with the same nominal mass show small differences if precise
measurements are made. E.g. for a nominal m/z of 28:
Ion
Precise mass
CO+
N2+
CH3N+
C2H4+
27.994914
28.006148
28.018724
28.031300
Thus it is possible with a high resolution spectrum to determine not only the molecular mass but
also the molecular formula.
4. The structure of a molecule can be determined from the fragmentation pattern. Once the
molecular ion has been formed, it will usually decompose into smaller fragments. By looking
at the major peaks in the mass spectrum, it is possible to decide which fragments have been
lost and thence to build up a picture of the original molecule. Occasionally a rearrangement
of an ion may take place.
TOPIC 13.32: STRUCTURE DETERMINATION
14
Interpretation of the Mass Spectrum
The mass of the molecular ion gives the Mr of the compound. Double resolution machines can
measure the mass of the molecular ion with precision sufficient to determine the molecular
formula of the compound.
If the likely structure of the compound is known, it can usually be confirmed by considering the
fragmentation pattern. It is not always possible to distinguish between isomers e.g. the different
disubstituted benzenes.
If the structure is unknown, the mass spectrum can be compared with libraries of mass spectra
which are commercially available on computer software. The mass spectra of all compounds
having the same Mr (or molecular formula) as the unknown can be called up and compared.
A compound containing one atom of chlorine will give two molecular ions which are two units
apart. The higher m/z peak will have an intensity one third that of the lower m/z peak. This is
because chlorine contains the isotopes 35Cl and 37Cl in the ratio 3:1.
A compound containing one atom of bromine will give two molecular ions which are two units
apart. Both peaks will be equal in intensity. This is because bromine contains two isotopes 79Br
and 81Br in the ratio 1:1.
TOPIC 13.32: STRUCTURE DETERMINATION
15
Common Losses from Molecular Ions
Ion
M-15
M-16
M-17
M-18
M-27
M-28
M-29
M-30
M-31
M-32
M-36
M-41
M-42
Group being lost
Possible inference
CH3
O
NH2
OH
H2O
HCN
CO
C2H4
-NO2
-CONH2
alcohol
alcohol, aldehyde, ketone
nitrile
quinone
aromatic ethyl ether (ArOC2H5)
ethyl ester (RCOOC2H5)
propyl ketone (RCOC3H7)
aldehyde
ethyl ketone (RCOC2H5)
aromatic methyl ether (ArOCH3)
aromatic nitro compound
methyl ester (RCOOCH3)
methyl ester (RCOOCH3)
primary haloalkane
propyl ester (RCOOC3H7)
methyl ketone (RCOCH3)
aromatic ethanoate (CH3COOAr)
butyl ketone (RCOC4H9)
aromatic propyl ether (ArOC3H7)
carboxylic acid, ester, acid anhydride
carboxylic acid
ethyl ester (RCOOC2H5)
aromatic nitro compound
CHO
C2H5
OCH2
NO
OCH3
CH3OH
HCl
C3H5
CH2CO
C3H6
M-44
M-45
M-46
CO2
COOH
C2H5OH
NO2
Aromatic compounds often produce fragment ions at m/z 77 (C6H5+) and m/z 91 (C6H5CH2+).
TOPIC 13.32: STRUCTURE DETERMINATION
16