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12. Structure Determination:Mass Spectrometry and Infrared

Spectroscopy

Based onMcMurrysOrganic Chemistry, 7thedition

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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 asthe reactants

In the 19thand early 20thcenturies,structures were determined bysynthesis and chemical degradationthat related compounds to each other

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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) spectroscopythis chapter nuclear magnetic resonance spectroscopy

(NMR)Chapter 13 ultraviolet-visible spectroscopy (VIS)Chapter 14

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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)

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Mass Spectrometer

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Mass Spectrometer

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The Mass Spectrum

Plot mass of ions (m/z) (x-axis) versus theintensity 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 unfragmentedradical cation is parent peakor molecularion (M+)

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MS Examples: Methane

and Propane Methane produces a parent peak (m/z = 16)

and fragments of 15 and 14

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MS Examples: Methane

and Propane The Mass Spectrum of propane is

more complex (Figure 12-2 )

since the molecule can breakdown in several ways

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Mass spectrum of propane

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12.2 Interpreting Mass

Spectra Molecular weight from the mass of the molecular

ion Double-focusinginstruments provide high-

resolution exact mass 0.0001 atomic mass unitsdistinguishing specific

atoms

Example MW 72 is ambiguous: C5H12and

C4H8O but: C5H1272.0939 amu exact mass C4H8O 72.0575 amuexact mass

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

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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 areused

Peaks above the molecular weight appear asa result of naturally occurring heavier

isotopes in the sample (M+1) from 13C that is randomly present

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Interpreting Mass-SpectralFragmentation Patterns

The way molecular ions break down can producecharacteristic 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 canstabilize it

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2,2-Dimethylpropane:

MM = 72 (C5H12)

14

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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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Hexane

16

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Worked example 12.1: methylcyclohexane orethylcyclopentane?

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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

AminesAmines undergo -cleavage,

generating radicals

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Fragmentation of

Ketones and Aldehydes

A C-H that is three atoms awayleads to an internal transfer of aproton to the C=O, called theMcLafferty rearrangement

Carbonyl compounds can alsoundergo cleavage

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Fragmentation of

Ketones and Aldehydes

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12.4 Mass Spec. in

Biochemistry: TOF ESI and MALDI are techniques to

produce charged molecules at

relatively low energy, to minimizefragmentation.

The large biological molecules are

separated by Time of Flight analysis(TOF) in a drift tube without amagnetic field imposed.

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MALDI-TOF spectrum ofchicken egg-white lysozyme

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12.5 The ElectromagneticSpectrum

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Wavelength and Frequency

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Absorption Spectra

Organic compounds exposed to electromagneticradiation can absorb photons of specific energies(wavelengths or frequencies)

Changing wavelengths to determine which areabsorbed and which are transmitted produces anabsorption spectrum

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

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Infrared AbsorptionSpectrum of Ethanol

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12.6 Infrared Spectroscopyof Organic Molecules

IR region is lower in photon energy than visiblelight (below redproduces heating as with aheat lamp)

2.5 106m to 2.5 105m region used byorganic chemists for structural analysis

IR energy in a spectrum is usually measured aswavenumber (cm-1), the inverse of wavelengthand proportional to frequency:

Wavenumber (cm-1) = 1/l(cm)

Specific IR absorbed by organic molecule is

related to its structure

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IR region and vicinity

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Infrared Energy Modes

IR energy absorption corresponds tospecific modes, corresponding to

combinations of atomic movements,such as bending and stretching ofbonds between groups of atoms called

normal modes

Energy is characteristic of the atoms inthe group and their bonding

Corresponds to molecular vibrations

http://www.columbia.edu/cu/chemistry/edison/IRTutor.htmlhttp://www.columbia.edu/cu/chemistry/edison/IRTutor.html

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Infrared Energy Modes

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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 IR absorptions in Table

12.1 can be used to confirm theexistence of the presence of a functional

group in a molecule IR spectrum has lower energy region

characteristic of molecule as a whole(fingerprint region)

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Regions of the Infrared

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

3300-3600 N-H, O-H

3000 C-H

2500-2000 cm-1CC and C N (stretching)

2000-1500 cm-1double bonds(stretching)

C=O 1680-1750

C=C 1640-1680 cm-1

Below 1500 cm-1fingerprint region

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Regions of the Infrared

Spectrum

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Differences in Infrared

AbsorptionsMolecules vibrate and rotate in

normal modes, which are

combinations of motions(relates to force constants)

Bond stretching dominateshigher energy (frequency)modes

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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 (higherfrequency): 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 ofHydrocarbons

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C-H, C-C, C=C, C C have characteristicpeaks

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Hexane

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Alkenes

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1-Hexene

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12.8 Infrared Spectra of SomeCommon Functional Groups

Spectroscopic behavior offunctional groups isdiscussed in later chapters

Brief summaries presentedhere

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Phenylacetylene

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Amines

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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 cm1in saturated aldehydes 1705 cm1in aldehydes next to double bond or

aromatic ring

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Practice problem 12.7:

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Phenylacetaldehyde

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C=O in Ketones

1715 cm1in six-membered ring andacyclic ketones

1750 cm1in 5-membered ring ketones 1690 cm1in ketones next to a double

bond or an aromatic ring

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C=O in Esters

1735 cm1

in saturated esters 1715 cm1in esters next to aromatic ring

or a double bond

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Chromatography: PurifyingOrganic Compounds

Chromatography : a process that separatescompounds using adsorption and elution

Mixture is dissolved in a solvent (mobile phase) and placed

into a glass column of adsorbent material (stationaryphase)

Solvent or mixtures of solvents passed through

Compounds adsorb to different extents and desorbdifferently 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 LiquidChromatography

Stationary phase is alumina (Al2O3) or silicagel (hydrated SiO2)

Solvents of increasing polarity are used toelute more and more strongly adsorbedspecies

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 thanordinary LC

Coated silica microspheres (10-25 m

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 often fat-soluble vitamins, using acetonitrileas the mobile phase

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HPLC ofFatSolubleVitamins

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Prob. 12.32: Cyclohexane orCyclohexene?

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Problem 12.41: Unknownhydrocarbon

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Problem 12.42: Unknownhydrocarbon2

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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

http://wwwchem.csustan.edu/Tutorials/INFRARED.HTMhttp://wwwchem.csustan.edu/Tutorials/INFRARED.HTMhttp://orgchem.colorado.edu/hndbksupport/irtutor/tutorial.htmlhttp://orgchem.colorado.edu/hndbksupport/irtutor/tutorial.htmlhttp://webbook.nist.gov/chemistry/http://www.aist.go.jp/RIODB/SDBS/menu-e.htmlhttp://www.aist.go.jp/RIODB/SDBS/menu-e.htmlhttp://www.aist.go.jp/RIODB/SDBS/menu-e.htmlhttp://www.aist.go.jp/RIODB/SDBS/menu-e.htmlhttp://www.aist.go.jp/RIODB/SDBS/menu-e.htmlhttp://webbook.nist.gov/chemistry/http://orgchem.colorado.edu/hndbksupport/irtutor/tutorial.htmlhttp://orgchem.colorado.edu/hndbksupport/irtutor/tutorial.htmlhttp://wwwchem.csustan.edu/Tutorials/INFRARED.HTMhttp://wwwchem.csustan.edu/Tutorials/INFRARED.HTM