12 structure determination mass spectrometry and infrared spectroscopy
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12. Structure Determination: Mass Spectrometry and Infrared Spectroscopy. Based on McMurry’s Organic Chemistry , 7 th edition. Determining the Structure of an Organic Compound.

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12 structure determination mass spectrometry and infrared spectroscopy

12. Structure Determination: Mass Spectrometry and Infrared Spectroscopy

Based on

McMurry’sOrganic Chemistry, 7th edition

Determining the structure of an organic compound

Determining the Structure of an Organic Compound

  • The analysis of the outcome of a reaction requires that we know the full structure of the products as well as the reactants

  • In the 19th and early 20th centuries, structures were determined by synthesis and chemical degradation that related compounds to each other

Determining the structure of an organic compound1

Determining the Structure of an Organic Compound

  • Physical methods now permit structures to be determined directly. We will examine:

    • mass spectrometry (MS)—this chapter

    • infrared (IR) spectroscopy—this chapter

    • nuclear magnetic resonance spectroscopy (NMR)—Chapter 13

    • ultraviolet-visible spectroscopy (VIS)—Chapter 14

12 1 mass spectrometry ms

12.1 Mass Spectrometry (MS)

  • Sample vaporized and bombarded by energetic electrons that remove an electron, creating a cation-radical

  • Bonds in cation radicals begin to break (fragment)

Mass spectrometer

Mass Spectrometer

Mass spectrometer1

Mass Spectrometer

The mass spectrum

The Mass Spectrum

  • Plot mass of ions (m/z) (x-axis) versus the intensity of the signal (corresponding to the number of ions) (y-axis)

  • Tallest peak is base peak (100%)

    • Other peaks listed as the % of that peak

  • Peak that corresponds to the unfragmented radical cation is parent peak or molecular ion (M+)

Ms examples methane and propane

MS Examples: Methane and Propane

  • Methane produces a parent peak (m/z = 16) and fragments of 15 and 14

Ms examples methane and propane1

MS Examples: Methane and Propane

  • The Mass Spectrum of propane is more complex (Figure 12-2 ) since the molecule can break down in several ways

Mass spectrum of propane

Mass spectrum of propane

12 2 interpreting mass spectra

12.2 Interpreting Mass Spectra

  • Molecular weight from the mass of the molecular ion

  • Double-focusing instruments provide high-resolution “exact mass”

    • 0.0001 atomic mass units – distinguishing specific atoms

  • Example MW “72” is ambiguous: C5H12 and C4H8O but:

    • C5H12 72.0939 amu exact mass C4H8O 72.0575 amu exact mass

    • Result from fractional mass differences of atoms 16O = 15.99491, 12C = 12.0000, 1H = 1.00783

Other mass spectral features

Other Mass Spectral Features

  • If parent ion not present due to electron bombardment causing breakdown, “softer” methods such as chemical ionization are used

  • Peaks above the molecular weight appear as a result of naturally occurring heavier isotopes in the sample

    • (M+1) from 13C that is randomly present

Interpreting mass spectral fragmentation patterns

Interpreting Mass-Spectral Fragmentation Patterns

  • The way molecular ions break down can produce characteristic fragments that help in identification

    • Serves as a “fingerprint” for comparison with known materials in analysis (used in forensics)

    • Positive charge goes to fragments that best can stabilize it

2 2 dimethylpropane mm 72 c 5 h 12

2,2-Dimethylpropane: MM = 72 (C5H12)

Mass spectral fragmentation of hexane

Mass Spectral Fragmentation of Hexane

Hexane (m/z = 86 for parent) has peaks at m/z = 71, 57, 43, 29



Worked example 12 1 methylcyclohexane or ethylcyclopentane

Worked example 12.1: methylcyclohexane or ethylcyclopentane?

Mass spectral cleavage reactions of alcohols

Mass Spectral Cleavage Reactions of Alcohols

  • Alcohols undergo -cleavage (at the bond next to the C-OH) as well as loss of H-OH to give C=C

Mass spectral cleavage of amines

Mass Spectral Cleavage of Amines

  • Amines undergo -cleavage, generating radicals

Fragmentation of ketones and aldehydes

Fragmentation of Ketones and Aldehydes

  • A C-H that is three atoms away leads to an internal transfer of a proton to the C=O, called the McLafferty rearrangement

  • Carbonyl compounds can also undergo  cleavage

Fragmentation of ketones and aldehydes1

Fragmentation of Ketones and Aldehydes

12 4 mass spec in biochemistry tof

12.4 Mass Spec. in Biochemistry: TOF

  • ESI and MALDI are techniques to produce charged molecules at relatively low energy, to minimize fragmentation.

  • The large biological molecules are separated by Time of Flight analysis (TOF) in a drift tube without a magnetic field imposed.

Maldi tof spectrum of chicken egg white lysozyme

MALDI-TOF spectrum of chicken egg-white lysozyme

12 5 the electromagnetic spectrum

12.5 The Electromagnetic Spectrum

Wavelength and frequency

Wavelength and Frequency

Absorption spectra

Absorption Spectra

  • Organic compounds exposed to electromagnetic radiation can absorb photons of specific energies (wavelengths or frequencies)

  • Changing wavelengths to determine which are absorbed and which are transmitted produces an absorption spectrum

  • Energy absorbed is distributed internally in a distinct and reproducible way (See Figure 12-11)

Infrared absorption spectrum of ethanol

Infrared Absorption Spectrum of Ethanol

12 6 infrared spectroscopy of organic molecules

12.6 Infrared Spectroscopy of Organic Molecules

  • IR region is lower in photon energy than visible light (below red – produces heating as with a heat lamp)

  • 2.5  106 m to 2.5  105 m region used by organic chemists for structural analysis

  • IR energy in a spectrum is usually measured as wavenumber (cm-1), the inverse of wavelength and proportional to frequency:

  • Wavenumber (cm-1) = 1/l(cm)

  • Specific IR absorbed by organic molecule is related to its structure

Ir region and vicinity

IR region and vicinity

Infrared energy modes

Infrared Energy Modes

  • IR energy absorption corresponds to specific modes, corresponding to combinations of atomic movements, such as bending and stretching of bonds between groups of atoms called “normal modes”

  • Energy is characteristic of the atoms in the group and their bonding

  • Corresponds to molecular vibrations

Infrared energy modes1

Infrared Energy Modes

12 7 interpreting infrared spectra

12.7 Interpreting Infrared Spectra

  • Most functional groups absorb at about the same energy and intensity independent of the molecule they are in

  • Characteristic IR absorptions in Table 12.1 can be used to confirm the existence of the presence of a functional group in a molecule

  • IR spectrum has lower energy region characteristic of molecule as a whole (“fingerprint” region)

Regions of the infrared spectrum

4000-2500 cm-1 N-H, C-H, O-H (stretching)

3300-3600 N-H, O-H

3000 C-H

2500-2000 cm-1 CºC and C º N (stretching)

2000-1500 cm-1 double bonds (stretching)

C=O 1680-1750

C=C 1640-1680 cm-1

Below 1500 cm-1 “fingerprint” region

Regions of the Infrared Spectrum

Regions of the infrared spectrum1

Regions of the Infrared Spectrum

Differences in infrared absorptions

Differences in Infrared Absorptions

  • Molecules vibrate and rotate in normal modes, which are combinations of motions (relates to force constants)

  • Bond stretching dominates higher energy (frequency) modes

Differences in infrared absorptions1

Differences in Infrared Absorptions

  • Light objects connected to heavy objects vibrate fastest (at higher frequencies): C-H, N-H, O-H

  • For two heavy atoms, stronger bond requires more energy (higher frequency): C º C, C º N > C=C, C=O, C=N > C-C, C-O, C-N, C-halogen

12 8 infrared spectra of hydrocarbons

C-H, C-C, C=C, C º C have characteristic peaks

12.8 Infrared Spectra of Hydrocarbons





1 hexene




12 8 infrared spectra of some common functional groups

12.8 Infrared Spectra of Some Common Functional Groups

  • Spectroscopic behavior of functional groups is discussed in later chapters

  • Brief summaries presented here

Aromatic compounds

Aromatic compounds:



Ir alcohols

IR: Alcohols




Ir carbonyl compounds

IR: Carbonyl Compounds

  • Strong, sharp C=O peak 1670 to 1780 cm1

  • Exact absorption characteristic of type of carbonyl compound

    • 1730 cm1 in saturated aldehydes

    • 1705 cm1 in aldehydes next to double bond or aromatic ring

Practice problem 12 7

Practice problem 12.7:



C o in ketones

C=O in Ketones

  • 1715 cm1 in six-membered ring and acyclic ketones

  • 1750 cm1 in 5-membered ring ketones

  • 1690 cm1 in ketones next to a double bond or an aromatic ring

C o in esters

C=O in Esters

  • 1735 cm1 in saturated esters

  • 1715 cm1 in esters next to aromatic ring or a double bond

Chromatography purifying organic compounds

Chromatography: Purifying Organic Compounds

  • Chromatography : a process that separates compounds using adsorption and elution

    • Mixture is dissolved in a solvent (mobile phase) and placed into a glass column of adsorbent material (stationary phase)

    • Solvent or mixtures of solvents passed through

    • Compounds adsorb to different extents and desorb differently in response to appropriate solvent (elution)

    • Purified sample in solvent is collected from end of column

    • Can be done in liquid or gas mobile phase

Principles of liquid chromatography

Principles of Liquid Chromatography

  • Stationary phase is alumina (Al2O3) or silica gel (hydrated SiO2)

  • Solvents of increasing polarity are used to elute more and more strongly adsorbed species

  • Polar species adsorb most strongly to stationary phase

    • For examples, alcohols adsorb more strongly than alkenes

High pressure or high performance liquid chromatography hplc

High-Pressure (or High-Performance) Liquid Chromatography (HPLC)

  • More efficient and complete separation than ordinary LC

  • Coated silica microspheres (10-25 µm diameter) in stationary phase

  • High-pressure pumps force solvent through tightly packed HPLC column

  • Detector monitors eluting material

  • Figure 12.18: HPLC analysis of a mixture of ten fat-soluble vitamins, using acetonitrile as the mobile phase

Hplc of fat soluble vitamins

HPLC of Fat Soluble Vitamins

Prob 12 32 cyclohexane or cyclohexene

Prob. 12.32: Cyclohexane or Cyclohexene?

Problem 12 41 unknown hydrocarbon

Problem 12.41: Unknown hydrocarbon

Problem 12 42 unknown hydrocarbon 2

Problem 12.42: Unknown hydrocarbon2

Some useful websites

Some Useful Websites:

  • Interpretation of IR spectra (CSU Stanislaus): http://wwwchem.csustan.edu/Tutorials/INFRARED.HTM

  • IR Spectroscopy Tutorial (CU Boulder): http://orgchem.colorado.edu/hndbksupport/irtutor/tutorial.html

  • NIST Chemistry WebBook: http://webbook.nist.gov/chemistry/

  • SDBS Data Base: http://www.aist.go.jp/RIODB/SDBS/menu-e.html

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