12. Structure Determination: Mass Spectrometry and Infrared Spectroscopy Based on McMurry’s Organic Chemistry, 6 th edition ©2003 Ronald Kluger Department

12. Structure Determination: Mass Spectrometry and Infrared Spectroscopy

Based onMcMurry’s Organic Chemistry, 6th edition©2003 Ronald KlugerDepartment of ChemistryUniversity of Toronto

McMurry Organic Chemistry 6th edition Chapter 12 (c) 2003

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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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Mass Spectral Fragmentation of Hexane Hexane (m/z = 86 for parent) has peaks at m/z = 71,

57, 43, 29


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12.4 Mass-Spectral Behavior of Some Common Functional Groups

Functional groups cause common patterns of cleavage in their vicinity


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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


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Mass Spectral Cleavage of Amines

Amines undergo -cleavage, generating radicals


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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


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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) 2.5 106 m to 2.5 105 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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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 CC and C 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


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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 C, C 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 C have characteristic peaks absence helps rule out C=C or C 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 cm1 Usually broad and intense

N–H 3300 to 3500 cm1

Sharper and less intense than an O–H


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IR: Aromatic Compounds

Weak C–H stretch at 3030 cm1

Weak absorptions 1660 - 2000 cm1 range Medium-intensity absorptions 1450 to 1600 cm1 See spectrum of phenylacetylene, Figure 12.15


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IR: Carbonyl Compounds

Strong, sharp C=O peak 1670 to 1780 cm1

Exact absorption characteristic of type of carbonyl compound 1730 cm1 in saturated aldehydes 1705 cm1 in aldehydes next to double bond or

aromatic ring


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C=O in Ketones

1715 cm1 in six-membered ring and acyclic ketones 1750 cm1 in 5-membered ring ketones 1690 cm1 in ketones next to a double bond or an

aromatic ring


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C=O in Esters

1735 cm1 in saturated esters 1715 cm1 in esters next to aromatic ring or a

double bond


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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


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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


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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 12.17: HPLC analysis of a mixture of 14

pesticides, using acetonitrile/water as the mobile phase

Documents

12. Structure Determination: Mass Spectrometry and Infrared Spectroscopy Based on McMurry’s Organic Chemistry, 6 th edition ©2003 Ronald Kluger Department