INSTRUMENTAL ANALYSIS CHEM 4811 CHAPTER 10 DR. AUGUSTINE OFORI AGYEMAN Assistant professor of chemistry Department of natural sciences Clayton state university.

INSTRUMENTAL ANALYSIS CHEM 4811

CHAPTER 10

DR. AUGUSTINE OFORI AGYEMANAssistant professor of chemistryDepartment 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

- 13C 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

CH4 = 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 13C which is also stable

ISOTOPIC ABUNDANCES

- Natural abundance of deuterium (2H) 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: 16O and 18O

- Relative abundance 18O/16O = 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 withformula CxHyNzOm is given as

x – 1/2y + 1/2z +1

For n-hexane (C6H14)6 – ½(14) + 0 + 1 = 6 – 7 + 1 = 0

For cyclohexane (C6H12)6 – ½(12) + 0 + 1 = 6 – 6 + 1 = 1

For benzene (C6H6)6 – ½(6) + 0 + 1 = 6 – 3 + 1 = 4

RINGS AND DOUBLE BONDS

- A triple bond is equivalent to two double bonds

For acetylene (C2H2)2 – ½(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 (RCH2NH2 gives rise to CH2NH2

+ 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 NO2

+ (m/z = 46)

- Aromatic nitro compounds have characteristic peaks at M-30 and M-46 (due to loss of NO• and NO2

•)

NITROGEN CONTAINING COMPOUNDS

- Successive loss of methylene groups (CH2, 14 Da)

- CH3 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

- CH2 – OH

- Aliphatic alcohols usually fragment with loss of H+ or H2O

- m/z = 31, 45, 59, ….

- Look for M-18 peak corresponding to loss of H2O

- 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 H2O in primary aliphatic alcohols

Tertiary alcohols tend to lose OH rather than H2O (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: 35Cl/37Cl = 100/33

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

- Bromine has two isotopes: 79Br/81Br = 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 34S isotope

- Primary thiols lose H2S 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

GDSpark 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 (IO4

-, IO3-, BrO3

-, ClO3-)

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