INSTRUMENTAL ANALYSIS

CHEM 4811

CHAPTER 10
DR. AUGUSTINE OFORI AGYEMAN
Assistant professor of chemistry
Department of natural sciences
Clayton state university
CHAPTER 10


MASS SPECTROMETRY II

SPECTRAL INTERPRETATION
AND APPLICATIONS
SPECTRAL INTERPRETATION
- Structural determination of simple molecules will be covered

- The mass spectrum is a plot or a table

- m/z values are on the x-axis of the spectrum

- Relative abundance (relative concentration) on the y-axis

- Base peak is the most abundant peak and is assigned
abundance of 100%

- Others are percentages of the base peak
SPECTRAL INTERPRETATION
Two ways to interpret spectra

- Compare spectrum to those in a searchable engine
(over 400,000 spectra are available)

and

- Use interpretation procedure for evaluating spectra
EVALUATION OF SPECTRA
- Involves a lot of educational guess work

- The structure must be confirmed by analyzing the pure form of
the substance identified

- Identify the molecular ion if present

- Apply the nitrogen rule

- Evaluate for A+2 elements

- Calculate A+1 and A elements
EVALUATION OF SPECTRA
- Look for loss peaks from the molecular ion


- Look for characteristic low mass fragments


- Postulate a possible formula


- Calculate rings plus double bonds


- Postulate a reasonable structure
MOLECULAR ION
- Forms by loss of electron when a molecule is ionized by EI

- The radical cation (M
+
) formed has the same mass as the
neutral molecule

- The m/z value of the molecular ion indicates the molecular
weight of the molecule

- Molecular ion absorbs excess energy which causes it to break
apart into fragments

- Fragments may be ions, neutral molecules, or radicals
FRAGMENTATION PATTERNS
- Is the mass and abundance of fragment ions

- Is used to deduce the structure of the molecule

- Ions in the mass spectrum are called fragment ions

- Fragments may break apart to form smaller fragments

- A given molecule will always produce the same fragments if
ionization conditions remain the same
FRAGMENTATION PATTERNS
- The base peak is usually not the molecular ion in EI

- A molecular ion is always a radical (odd number of electrons
and never an even electron ion)

M + e
-
M
+
+ 2e
-

- Even electron ions result from fragmentation

- Aromatic compounds and conjugated hydrocarbons give more
intense molecular ion peaks
FRAGMENTATION PATTERNS
- Alkanes, aliphatic alcohols and nitrates give less intense
molecular peaks

- Highly branched compounds tend not to give molecular peaks

- Abundant fragment peak typically shows loss of
neutral fragment

Alpha Cleavage
- Cleavage at the bond adjacent to the C to which a functional
group is attached
ISOTOPIC ABUNDANCES
- The most abundant isotope and the unit atomic mass are used to
calculate the molecular weights

-
13
C results in a peak one mass number greater than the mass
of the molecular ion in all organic compounds

- The peak is designated as M+1

CH
4
= 12 + 4(1) = 16 = m/z of molecular ion

- A small peak of m/z = 17 is also seen on spectrum because
of the isotope
13
C which is also stable
ISOTOPIC ABUNDANCES
- Natural abundance of deuterium (
2
H) is usually ignored
(0.016%)


- Nominal mass is the integer mass of the most abundant naturally
occurring isotope


- Nominal mass is used in MS calculations but not the atomic
weight or the exact mass
COUNTING CARBON ATOMS
- For a hydrocarbon with only one C atom
(M+1)/M = 1.1%

- For a hydrocarbon with two C atoms
(M+1)/M = 2.2%

In general
(M+1)/M = 1.1% x # of C atoms in the molecule

If (M+1) << 1% implies no C atom is present
COUNTING OTHER ELEMENTS
- Assume that only C, H, N, O, F, P, and I are present

- The other elements such as N and S contribute to the (M+1)
peak intensity

Generally
(M+1)/M
=
1.1(# C atoms) + 0.016(# H atoms) + 0.3(# N atoms) + 0.78(# S atoms) + .

- Contribution from hydrogen is small and is ignored
COUNTING OXYGEN ATOMS
- Oxygen has two important isotopes:
16
O and
18
O


- Relative abundance
18
O/
16
O = 0.2%


- Number of oxygen atoms in a given molecule is given as

(M+2)/M = 0.20(# O atoms) + [1.1(# C atoms)]
2
/200
HETEROATOMIC COMPOUNDS
Elements are grouped into 3 categories

- A elements are the monoisotopic elements
(F, P, I and somehow H)


- A+1 elements are those with two isotopes whose
difference is 1 Da (C, N)


- A+2 elements are those with an isotope 2 Da heavier than
the most abundant isotope (Cl, Br, O, S, Si)
RINGS AND DOUBLE BONDS
- The number of rings + double bonds in a molecule with
formula C
x
H
y
N
z
O
m
is given as

x 1/2y + 1/2z +1

For n-hexane (C
6
H
14
)
6 (14) + 0 + 1 = 6 7 + 1 = 0

For cyclohexane (C
6
H
12
)
6 (12) + 0 + 1 = 6 6 + 1 = 1

For benzene (C
6
H
6
)
6 (6) + 0 + 1 = 6 3 + 1 = 4
RINGS AND DOUBLE BONDS
- A triple bond is equivalent to two double bonds


For acetylene (C
2
H
2
)
2 (2) + 0 + 1 = 2


- This equation does not distinguish between double bonds,
rings, or triple bonds


- It is thus used together with IR, NMR, etc.
NITROGEN CONTAINING COMPOUNDS
- Amines, amides, nitriles, nitro compounds

- Many N-containing compounds give no detectable molecular ion

- Alpha cleavage is seen in aliphatic amines
(RCH
2
NH
2
gives rise to CH
2
NH
2
+
with m/z = 30, 44, 58, .)

The Nitrogen Rule
- Used to identify a molecular ion peak

- The m/z value of the molecular ion and hence the molecular
weight is an odd number if the molecule contains an
odd number of N atoms
- Amides, cyclic aliphatic amines, aromatic amines, nitriles, and
nitro groups give measurable molecular ions

- Amides have fragmentation patterns similar to their corresponding
carboxylic acids

-,Nitro compounds usually have NO
+
(m/z = 30) and
NO
2
+
(m/z = 46)

- Aromatic nitro compounds have characteristic peaks at
M-30 and M-46 (due to loss of NO

and NO
2

)
NITROGEN CONTAINING COMPOUNDS
- Successive loss of methylene groups (CH
2
, 14 Da)

- CH
3
with m/z = 15 is seen

- m/z = 15, 29, 43, 57 ..

- Branched chain alkanes are less likely to show a molecular
ion peak than n-alkanes

- Cycloalkanes show strong molecular ion peaks and characteristic
peaks separated by 14 Da
ALKANES
- Both show strong molecular ion peaks
(double and triple bonds are able to absorb energy)


- Alkenes with C atoms > 4 often show a strong peak at m/z = 41
(formation of allyl ion)


- Alkynes show strong (M-1) peaks (loss of 1 H atom)


- It is difficult to use MS to locate position of double
or triple bonds
ALKENES AND ALKYNES
- CH
2
OH

- Aliphatic alcohols usually fragment with loss of H
+
or H
2
O

- m/z = 31, 45, 59, .

- Look for M-18 peak corresponding to loss of H
2
O

- Alpha cleavage is seen

- Molecular ion peak is usually weak in primary and secondary
aliphatic alcohols and absent in tertiary alcohols
ALCOHOLS
- Alpha cleavage plus loss of H
2
O in primary aliphatic alcohols


Tertiary alcohols tend to lose OH rather than H
2
O (M-17 peak)


- Alcohols containing more than 4 C atoms often lose both
water and ethylene simultaneously
ALCOHOLS
- Very stable and do not fragment easily

- Very intense molecular ion peak is seen

- Very little fragmentation

- Usually show noninteger m/z values due to doubly
charged ions (M
++
)

- Benzene ring with alkyl groups under rearrangement
of benzyl cation
AROMATIC COMPOUNDS
- Fragment by alpha cleavage

- Aldehydes also fragment by beta cleavage

- For aldehydes m/z = 29, 43, 57, 71, .

- For ketones m/z = 43, 57, 71, ..

- Ketones and aromatic aldehydes have strong molecular ion peak

- Aliphatic aldehydes give a weak but measurable molecular
ion peak
ALDEHYDES AND KETONES
- Aliphatic carboxylic acids and small aliphatic esters (4 or 5 C
atoms) have weak but measurable molecular ion peak


- Larger esters show no molecular ion peak


- Aromatic carboxylic acids give strong molecular ion peak


- Acids typically lose OH and COOH through alpha cleavage
(M-17 and M-45 peaks)
CARBOXYLIC ACIDS AND ESTERS
- Characteristic peak for acids is m/z = 45


- Esters undergo alpha cleavage to form RCO
+
ion


- Characteristic peak for esters is m/z = 74


- Can undergo McLafferty rearrangement (not discussed here)
CARBOXYLIC ACIDS AND ESTERS
- Chlorine has two isotopes:
35
Cl/
37
Cl = 100/33

- M+2 peak is about 33% of M peak

- Bromine has two isotopes:
79
Br/
81
Br = 1/1

- M and M+2 peaks are approximately equal

- Bromine compounds fragment by loss of Br

- Chlorine compounds fragment by loss of HCl
Cl AND Br CONTAINING COMPOUNDS
- Form isotope cluster patterns

- Isotopic clusters are seen when more than one Cl or Br atom is
present in a molecule

- One Cl atom will exhibit masses of R+35 and R+37 with
relative abundances 100:33

- Two Cl atoms will have R+70, R+72, R+74 with
relative abundances 100:66:11
Cl AND Br CONTAINING COMPOUNDS
- Three Cl atoms will have R+105, R+107, R+109, R+111 with
relative abundances 100:98:32:3


- One Br atom will have R+79 and R+81 with
relative abundances 1:1



- Two Br atoms will have R+158, R+160, R+162 with
relative abundances 51:100:49
Cl AND Br CONTAINING COMPOUNDS
- Iodine compounds fragment by loss of I


- Iodine and fluorine do not form clusters since they
are monoisotopic


- Fluorine compounds undergo unique reactions
(will not be discussed here)


- F also fragments resulting in (M-19) peak
F AND I CONTAINING COMPOUNDS
- Thiols (RSH) show stronger molecular ion peaks than their
corresponding alcohols


- M+2 peak is enhanced due to
34
S isotope


- Primary thiols lose H
2
S on fragmentation: (M-34) peak


- Fragmentation patterns are similar to those of alcohols
SULFUR CONTAINING COMPOUNDS
- For molecular weight determination

- Molecular structure determination

- Reaction kinetics

- Dating of minerals, fossils, and artifacts

- Quantitative analysis of elements and compounds

- Protein sequencing (proteomics)
APPLICATIONS OF MOLECULAR MS
- Gas analysis


- Environmental applications
(holomethanes, PCBs, pesticides, dioxins)
APPLICATIONS OF MOLECULAR MS
- Compound must be volatile


- Must be able to be converted into the gas phase
without decomposing


- Carboxylic acids must be converted to the corresponding
volatile methyl esters


- MS cannot distinguish between certain isomers
LIMITATIONS OF MOLECULAR MS
- For determination of atomic weights and isotope
distribution of elements



Ionization Sources

GD
Spark source
ICP
ATOMIC MS
- ICP-MS with quadrupole mass analyzer can be used to determine
most elements on the periodic table in a few seconds

- Sensitivity is very high

- Wide concentration range

- Used to obtain isotope ratios

- Ionization efficiency is almost 100%
INDUCTIVELY COUPLED PLASMA
MASS SPECTROMETRY (ICP-MS)
- Has simple mass spectra (elements easily identified)


- For analyzing inorganic materials in solution
(ash, bones, rocks)


- Indium cannot be identified by ICP-MS


- Petroleum fractions for trace elements
INDUCTIVELY COUPLED PLASMA
MASS SPECTROMETRY (ICP-MS)
- Aqueous solutions are commonly analyzed by ICP-MS

- Extremely high purity water, acids, bases reagents are used

- Solid samples can be analyzed by laser ablation ICP-MS or by
coupling graphite furnace to ICP-MS

- GDMS and spark source MS are also used for solid samples
(for analysis of art works and jewelry)

- Chromatography or CE is coupled to ICP-MS for the determination
of halogen oxyanions (IO
4
-
, IO
3
-
, BrO
3
-
, ClO
3
-
)
APPLICATIONS OF ATOMIC MS
- For rapid multielement analysis of metals and nonmetals at
ppm and even ppt levels

- Analysis of environmental samples

- Analysis of body fluids for toxic elements (lead, arsenic)

- Trace elements in geological samples

- Metals in alloys

- Ceramics and semiconductors
APPLICATIONS OF ATOMIC MS
- Pharmaceutical

- Cosmetics samples

- Food chemistry

GC-ICP-MS or LC-ICP-MS
- For determination of arsenic compounds in shellfish

- For analyzing breakfast cereal, peanut butter, wine, beer

- Whole blood and serum for Al, Cu, Zn, blood lead, etc.
APPLICATIONS OF ATOMIC MS
- Inefficient introduction system


- Matrix effect


- Isobaric interference


- Degree of interference from polyatomic ions
LIMITATIONS OF ATOMIC MS