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

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12. Structure Determination: Mass Spectrometry and Infrared Spectroscopy

Based on

McMurry’sOrganic Chemistry, 7th edition

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 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)

  • 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

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

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

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

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

  • 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

  • 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 (C5H12)

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?

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

  • Amines undergo -cleavage, generating radicals

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 Aldehydes

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

12.5 The Electromagnetic Spectrum

Wavelength and Frequency

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

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

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 Modes

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)

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 Spectrum

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 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

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

12.8 Infrared Spectra of Hydrocarbons





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:


IR: Alcohols



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:


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

  • 1735 cm1 in saturated esters

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

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

  • 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)

  • 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

Prob. 12.32: Cyclohexane or Cyclohexene?

Problem 12.41: Unknown hydrocarbon

Problem 12.42: Unknown hydrocarbon2

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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