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12. Structure Determination: Mass Spectrometry and Infrared Spectroscopy. Based on McMurry’s Organic Chemistry , 6 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 l.jpg

12. Structure Determination: Mass Spectrometry and Infrared Spectroscopy

Based on

McMurry’s Organic Chemistry, 6th edition


Determining the structure of an organic compound l.jpg

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

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

    • mass spectrometry (MS)

    • infrared (IR) spectroscopy

    • nuclear magnetic resonance spectroscopy (NMR)

    • ultraviolet-visible spectroscopy (VIS)


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12.1 Mass Spectrometry (MS)

  • Measures molecular weight

  • Sample vaporized and subjected to bombardment by electrons that remove an electron

    • Creates a cation-radical

  • Bonds in cation radicals begin to break (fragment)

  • Charge to mass ratio is measured (see Figure 12-1)


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The Mass Spectrum

  • Plot mass of ions (m/z) (x-axis) versus the intensity of the signal (roughly 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+)


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MS Examples: Methane and Propane

  • Methane produces a parent peak (m/z = 16) and fragments of 15 and 14 (See Figure 12-2 a)

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


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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

  • Instruments include computation of formulas for each peak


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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


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12.3 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


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12.5 Spectroscopy of the Electromagnetic Spectrum

  • Radiant energy is proportional to its frequency (cycles/s = Hz) as a wave (Amplitude is its height)

  • Different types are classified by frequency or wavelength ranges


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Absorption Spectra

  • Organic compound exposed to electromagnetic radiation, can absorb energy of only certain wavelengths (unit of energy)

    • Transmits, energy of other wavelengths.

  • 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)


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12.6 Infrared Spectroscopy of Organic Molecules

  • IR region lower 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

  • Specific IR absorbed by organic molecule related to its structure


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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 vibrations and rotations


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12.7 Interpreting Infrared Spectra

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

  • Characteristic higher energy 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)

  • See samples in Figure 12-13


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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


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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 modes

  • Light objects connected to heavy objects vibrate fastest: C-H, N-H, O-H

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


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12.8 Infrared Spectra of Hydrocarbons

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

    • absence helps rule out C=C or C º C


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12.9 Infrared Spectra of Some Common Functional Groups

  • Spectroscopic behavior of functional group is discussed in later chapters

  • Brief summaries presented here


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IR: Alcohols and Amines

  • O–H 3400 to 3650 cm1

    • Usually broad and intense

  • N–H 3300 to 3500 cm1

    • Sharper and less intense than an O–H


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IR: Aromatic Compounds

  • Weak C–H stretch at 3030 cm1

  • Weak absorptions 1660 - 2000 cm1 range

  • Medium-intensity absorptions 1450 to 1600 cm1

  • See spectrum of phenylacetylene, Figure 12.15


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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


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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


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C=O in Esters

  • 1735 cm1 in saturated esters

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


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