MASS SPECTROMETRY

• Mass spectrometry (MS) is an analytical laboratory technique used to separate the

components of a sample by their mass and electrical charge. The instrument used in
MS is called mass spectrometer.
• It produces a mass spectrum that plots the mass-to-charge (m/z) ratio of compounds in
a mixture.
• MS is used for both qualitative and quantitative chemical analysis. It may be used to
identify the elements and isotopes of a sample, to determine the masses of molecules,
and as a tool to help identify chemical structures. It can measure sample purity and
molar mass.
• A big advantage of mass spec over many other techniques is that it is incredibly
sensitive (parts per million). It is an excellent tool for identifying unknown components
in a sample or confirming their presence.
• Disadvantages of mass spec are that it isn't very good at identifying hydrocarbons that
produce similar ions and it's unable to tell optical and geometrical isomers apart. The
disadvantages are compensated for by combining MS with other techniques, such as
gas chromatography (GC-MS).
➢ Electrospray ionization is today the most widely used ionization technique in chemical and biochemical
analysis. Electrospray ionization (ESI) is a technique used in mass spectrometry to produce ions using
an electrospray in which a high voltage is applied to a liquid to create an aerosol. It is especially useful
in producing ions from macromolecules because it overcomes the propensity of these molecules to
fragment when ionized.
➢ The ions observed by mass spectrometry may be quasimolecular ions created by the addition of
a hydrogen cation and denoted [M + H]+, or of another cation such as sodium ion, [M + Na]+, or the
removal of a hydrogen nucleus, [M − H]−
MASS SPECTROMETRY ➢ Analyze each starting material separately by
chromatography (GC or HPLC coupled to a mass
spectrophotometer)
➢ Obtain the MS spectrum of each of the substrates.
➢ Analyze the product using same conditions (method)
as for the substrates.
➢ Obtain the MS spectrum of each peak on the
chromatogram of the products.
➢ Products usually have different m/z to those of
reactants.
In analyzing mass spectrum, knowledge of the fragmentation pattern of the various
functional groups of organic compound is paramount.
Alkanes
Order of stability of carbocations
primary < secondary < tertiary

The base peak is the most abundant ion, assigned a

relative abundance of 100%.
Molecular ion peak represents the unfragmented
molecule (M+) and indicates its molecular weight.
Alkenes

Molecular ion peak is intense in

unsaturated compounds. Molecular
ion represents the most stable cation
formed by the removal of an electron
from the parent molecule.
 Alcohol
An alcohol's molecular ion is small or non-existent. Cleavage of the C-C bond next to the
oxygen usually occurs. A loss of H2O may occur as in the spectrum below.

3-Pentanol (C5H12O) with MW = 88.15

Aldehyde
Ketone
Major fragmentation peaks result from cleavage of the C-C bonds adjacent to the
carbonyl. 4-Heptanone (C7H14O) with MW = 114.19
The McLafferty rearrangement is a fragmentation process in mass spectrometry where
a carbonyl compound containing a gamma-hydrogen undergoes a specific bond shift,
resulting in the loss of a neutral alkene and the formation of an enol radical cation.
 Amine
Molecular ion peak is an odd number. Alpha-cleavage dominates aliphatic amines.
n-Butylamine (C4H11N) with MW = 73.13

Another example is a secondary amine shown

below. Again, the molecular ion peak is an odd
number. The base peak is from the C-C cleavage
adjacent to the C-N bond.
Amide
 Aromatic
Molecular ion peaks are strong due to the stable structure. Naphthalene (C10H8) with MW = 128.17

Carboxylic Acid
In short chain acids, peaks due to the loss of OH (molecular ion less 17) and COOH
(molecular ion less 45) are prominent due to cleavage of bonds next to C=O. 2-Butenoic
acid (C4H6O2) with MW = 86.09
Ester
Fragments appear due to bond cleavage next to C=O (alkoxy group loss, -OR) and
hydrogen rearrangements. Ethyl acetate (C4H8O2) with MW = 88.11

Ether
Halide
The presence of chlorine or bromine atoms is usually recognizable from isotopic peaks.
1-Bromopropane (C3H7Br) with MW = 123.00
 INFRARED SPECTROSCOPY
• Infrared (IR) spectroscopy deals with the interaction of infrared radiation with matter.
• IR spectrum provides important information about its chemical nature and molecular
structure, hence mostly used for qualitative analysis.
• Absorption in the infrared region arise from molecular vibrational transitions
• Thus, IR spectra provides more specific qualitative information
• IR spectra is called “fingerprints”
- because no other chemical species will have identical IR spectrum
• IR applicability:
• Analysis of organic materials
• Polyatomic inorganic molecules
• Organometallic compounds

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 Electromagnetic Spectrum

⚫ Energy of IR photon insufficient to cause electronic

excitation but can cause vibrational
21 excitation
Comparison between transmittance (upper) vs absorbance (lower) plot

The transmittance
spectra provide better
contrast btw
intensities of strong
and weak bands
compared to
absorbance spectra

22
 1. IR absorption only occurs when IR radiation interacts with a molecule
undergoing a change in dipole moment as it vibrates or rotates.
2. Infrared absorption only occurs when the incoming IR photon has sufficient
energy for the transition to the next allowed vibrational state.

Note: If the 2 rules above are not met, no absorption can occur.
The energy absorbed will increase the amplitude of the vibrational motions of the
bonds in the molecule.
NOT ALL bonds in a molecule are capable of absorbing IR energy. Only those bonds
that have change in dipole moment are capable to absorb IR radiation.
The larger the dipole change, the stronger the intensity of the band in an IR spectrum.
In heteronuclear diatomic molecule, because of the difference in electronegativities of
the two atoms, one atom acquires a small positive charge (q+), the other a negative
charge (q-).
 Molecular vibration

divided
into

involves
back & change in
forth stretching bending bond angles
movement

wagging
scissoring

symmetrical asymmetrical rocking twisting

in-plane out of
vibration plane
vibration

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How to Interpret Infrared Spectra?

25
SUMMARY
C-H bond stretching
of all hydrocarbons
occur in the range of
2800-3300 cm-1, and
the exact location can
be used to distinguish
between alkane,
alkene and alkyne.
Specifically:
≡C-H (sp C-H) bond of
terminal alkyne give
absorption at about
3300 cm-1
=C-H (sp2 C-H) bond
of alkene give
absorption at about
3000-3100 cm-1
-C-H (sp3 C-H) bond of
alkane give absorption
at about ~2900 cm-1
 ALKANE
H H H C-H Stretch for sp3 C-H around 3000 – 2840 cm-1.
CH2 Methylene groups have a characteristic bending absorption
H C C C H
at approx 1465 cm-1
CH3 Methyl groups have a characteristic bending absorption at
H H H
n approx 1375 cm-1
CH2 The bending (rocking) motion associated with four or more
CH2 groups in an open chain occurs at about 720
cm-1 29
ALKENE

H H
C C
H H =C-H Stretch for sp2 C-H occurs at values greater than 3000 cm-1.
=C-H out-of-plane (oop) bending occurs in the range 1000 – 650 cm-1
C=C stretch occurs at 1660 – 1600 cm-1;
often conjugation moves C=C stretch to lower frequencies
and increases the intensity 30
 ALKYNE
HC CH

CH Stretch for sp C - H occurs near 3300 cm-1.

C C Stretch occurs near 2150 cm-1; conjugation moves

stretch to lower frequency.

31
 AROMATIC RINGS

C H Stretch for sp2 C-H occurs at values greater than 3000 cm-1.

Ring stretch absorptions occur in pairs at 1600 cm-1 and

C C 1475 cm-1.

C H Bending occurs at 900 - 690cm-1.

32
 ALCOHOL

O-H The hydrogen-bonded O-H band is a broad peak at 3400 – 3300 cm-1.
This band is usually the only one present in an alcohol that has not
been dissolved in a solvent (neat liquid).
C-O-H Bending appears as a broad and weak peak at 1440 – 1220 cm-1 often
obscured by the CH3 bendings.
C-O Stretching vibration usually occurs in the range 1260 – 1000 cm-1.
This band can be used to assign a primary, secondary or tertiary
structure to an alcohol.
33
PHENOL
OH

34
 ETHER

R O R'
C-O The most prominent band is that due to C-O stretch, 1300 – 1000 cm-1.

Absence of C=O and O-H is required to ensure that C-O stretch

is not due to an ester or an alcohol.

Phenyl alkyl ethers give two strong bands at about 1250 – 1040 cm-1,
while aliphatic ethers give one strong band at about 1120 cm-1.

35
 ETHER

C-O The most prominent band is that

due to C-O stretch, 1300 – 1000 cm-1.

Absence of C=O and O-H is required

to ensure that C-O stretch
is not due to an ester or an
alcohol.

Phenyl alkyl ethers give two strong bands

at about 1250 – 1040 cm-1,
while aliphatic ethers give one
strong band at about 1120 cm-1.

36
 CARBONYL COMPOUNDS

cm-1

1810 1800 1760 1735 1725 1715 1710 1690

Anhydride Acid Anhydride Ester Aldehyde Ketone Carboxylic
Amide
(band 1) Chloride (band 2) acid

Normal base values for the C=O stretching vibrations for carbonyl groups

37
 A. ALDEHYDE

R C H
O
R C H C=O stretch appear in range 1740-1725 cm-1 for normal
O aliphatic aldehydes

Ar C H Conjugation of C=O with phenyl; 1700 – 1660 cm-1 for

C=O
O and 1600 – 1450 cm-1 for ring (C=C)

C-H Stretch, aldehyde hydrogen (-CHO), consists of weak

bands, one at 2860 - 2800 cm-1 and
the other at 2760 – 2700 cm-1.
38
39
 B. KETONE

R C R'
O
R C R' C=O stretch appear in range 1720-1708 cm-1 for
O normal aliphatic ketones

Ar C R' Conjugation of C=O with phenyl; 1700 – 1680 cm-1 for C=O
O and 1600 – 1450 cm-1 for ring (C=C)

40
41
C. CARBOXYLIC ACID

R C OH
O

42
43
 D. ESTER

R C O R
O
R C O R C=O stretch appear in range 1750-1735 cm-1 for normal
O aliphatic esters

Ar C O R Conjugation of C=O with phenyl; 1740 – 1715 cm-1 for C=O

O and 1600 – 1450 cm-1 for ring (C=C)

C–O Stretch in two or more bands, one stronger and broader than
the other, occurs in the range 1300 – 1000 cm-1

44
45
 E. AMIDE

O O O
H H R
R C N R C N R C N
H R R
10 20 30

46
AMIDE

47
 F. ACID CHLORIDE

O
R C Cl
Stretch appear in range 1810 -1775 cm-1 in conjugated
C O chlorides. Conjugation lowers the frequency to 1780 – 1760
cm-1

C Cl Stretch occurs in the range 730 -550 cm-1

Acid chloride show a very strong band for the C=O group.

48
 F. ANHYDRIDE

O O
R C O C R

Stretch always has two bands, 1830 -1800 cm-1 and 1775 – 1740 cm-1,
C O with variable relative intensity.
Conjugation moves the absorption to a lower frequency. Ring strain
(cyclic anhydride) moves absorptions to a higher frequency.

C O Stretch (multiple bands) occurs in the range 1300 -900 cm-1

49
➢ In IR spectroscopy, ketones generally exhibit a stronger carbonyl (C=O) absorption band than amides,
due to the ketone's higher dipole moment and the lack of resonance stabilization in the carbonyl group.
➢ In IR spectroscopy, a higher wavenumber (or frequency) does not directly translate to a stronger dipole
moment; rather, a stronger dipole moment change during vibration leads to a stronger IR absorption,
which is observed as a stronger signal in the IR spectrum.
 AMINE

Stretching occurs in the range 3500 – 3300 cm-1.

Primary amines have two bands.
N–H Secondary amines have one band: a vanishingly weak one for
aliphatic compounds and a stronger one for aromatic secondary
amines.
Tertiary amines have no N – H stretch.

N–H Bending in primary amines results in a broad band in the range

1640 – 1560 cm-1.
Secondary amines absorb near 1500 cm-1

N–H Out-of-plane bending absorption can sometimes be observed

near 800 cm-1

C–N Stretch occurs in the range 1350 – 1000 cm-1

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Primary Amine

Secondary Amine

52
Tertiary Amine

Aromatic Amine

53
 Example: Analysis of aspirin

Fingerprint region

Two carbonyl stretches

Resonance structures for an amide are shown
and the final structure is a hybrid of the two
resonance structures. Esters also will have
similar resonance structures, but oxygen being
more electronegative than nitrogen, the lone
pairs on oxygen will participate in resonance to
a lesser extent than the lone pairs present on
nitrogen and hence the contribution of the
second resonance structure is even less than
amides i.e. the resonance structure in which
C=O bond has double bond character has a
greater contribution to the final overall structure
resulting in a stronger C=O bond in ester than in
amides. Stronger bonds have higher stretching
frequency.
➢ Electron-withdrawing groups lead to a C=O stretch at
larger wavenumbers, whereas electron-donating groups
have the opposite effect.
Resonance structures for an amide are shown and the final
structure is a hybrid of the two resonance structures.
➢ Esters also will have similar resonance structures, but
oxygen being more electronegative than nitrogen, the
lone pairs on oxygen will participate in resonance to a
lesser extent than the lone pairs present on nitrogen and
hence the contribution of the second resonance structure
is even less than amides i.e. the resonance structure in
which C=O bond has double bond character has a
greater contribution to the final overall structure resulting
in a stronger C=O bond in ester than in amides. Stronger
bonds have higher stretching frequency.
An IR correlation spectra chart and or IR
spectrum can be used to monitor course of
reaction. Example, synthesis of aspirin from
salicylic acid (Use of spectrum).
Salicylic acid:
▪ Stretching vibration frequencies of C=O at
around 1700cm-1.
▪ The presence of the carboxylic O-H
stretching frequency at around 3000cm-1 –
2500 cm -1.
▪ The O-H stretching vibration at around 3600
-3200cm-1 for phenol.
Acetylsalicylic acid/Aspirin
▪ Two strong peaks in the carbonyl
(C=O) stretching region (1650 – 1800
cm-1), because it has two different
carbonyl groups. — while salicylic acid
has only one.
▪ No O-H stretching vibration at around 3600
-3200cm-1 for phenol.
 Use of IR spectroscopy to identify compounds
Assume there is a mix up in labelling the following three compounds. How would you use the IR
spectroscopy to identify the compounds?

➢ Measure the IR spectra of the three compounds, compounds A, B and paracetamol.

Compound A will have broad absorption peaks at the ranges 300-2500 cm-1 indicating presence of
OH for carboxylic acids.
➢ There will also be an absorption peak in the ranges 1760-1690 cm-1 indicating presence of C=O
for carboxylic acid in Compound A.
➢ For paracetamol, there will be a peak in the ranges 1653 - 1609 cm-1 attributed to C=O of an
amide.
➢ The O-H stretching vibration at around 3600 -3200cm-1 indicating the presence of OH for phenol.
➢ All the above mentioned peaks will be missing in Compound B
IR: Correlation table for characteristic Group Frequencies of Organic Molecules
Frequency, Bond Functional group
cm–1
3640–3610 O–H, free hydroxyl alcohols, phenols
3500–3200 O–H, H–bonded alcohols, phenols
3400–3250 N–H primary, secondary amines, amides
3300–2500 O–H carboxylic acids
3330–3270 –C(triple bond)C–H: C–H alkynes (terminal)
3100–3000 C–H Aromatics
3100–3000 =C–H Alkenes
3000–2850 C–H Alkanes
2830–2695 H–C=O: C–H Aldehydes
2260–2210 C(triple bond)N Nitriles
2260–2100 –C(triple bond)C– Alkynes
1760–1665 C=O carbonyls (general)
1760–1690 C=O carboxylic acids
1750–1735 C=O esters, saturated aliphatic
1740–1720 C=O aldehydes, saturated aliphatic
1730–1715 C=O alpha,beta–unsaturated esters
1715 C=O ketones, saturated aliphatic
1710–1665 C=O alpha, beta–unsaturated aldehydes, ketones
 IR: Correlation table for characteristic Group Frequencies of Organic Molecules
1680–1640 –C=C– Alkenes
1650–1580 N–H primary amines
1600–1585 C–C (in–ring) Aromatics
1550–1475 N–O nitro compounds
1500–1400 C–C (in–ring) Aromatics
1470–1450 C–H Alkanes
1370–1350 C–H Alkanes
1360–1290 N–O nitro compounds
1335–1250 C–N aromatic amines
1320–1000 C–O alcohols, carboxylic acids, esters, ethers
1300–1150 C–H (–CH2X) alkyl halides
1300–1150 C–H (–CH2X) alkyl halides
1250–1020 C–N aliphatic amines
1000–650 =C–H Alkenes
950–910 O–H carboxylic acids
910–665 N–H primary, secondary amines
900–675 C–H Aromatics
850–550 C–Cl alkyl halides
725–720 C–H alkanes
700–610 –C(triple bond)C–H: C–H alkynes