Download Lecture - Ch 12

Chapter 12
Structure
Determination: Mass
Spectrometry and
Infrared Spectroscopy
Suggested Problems – 111,14-16,18,23,26,3034,41-2
CHE2202, Chapter 12
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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 (UV-VIS)
CHE2202, Chapter 12
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Mass Spectrometry of Small Molecules:
Magnetic-Sector Instruments
• Mass spectrometry (MS) determines
molecular weight by measuring the mass of a
molecule
• Components of a mass spectrometer:
– Ionization source - Electrical charge assigned to
sample molecules
– Mass analyzer - Ions are separated based on
their mass-to-charge ratio
– Detector - Separated ions are observed and
counted
CHE2202, Chapter 12
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Electron-Ionization, MagneticSector Mass Spectrometer
• Small amount of sample undergoes
vaporization at the ionization source to form
cation radicals
• Amount of energy transferred causes
fragmentation of most cation radicals into
positive and neutral pieces
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Electron-Ionization, MagneticSector Mass Spectrometer
• Fragments pass through a strong magnetic
field in a curved pipe that segregates them
according to their mass-to-charge ratio
• Positive fragments are sorted into a detector
and are recorded as peaks at the various m/z
ratios
– Mass of the ion is the m/z value
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The electron-ionization, magneticsector mass spectrometer
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Quadrupole Mass Analyzer
• Comprises four iron rods arranged parallel to
the direction of the ion beam
• Specific oscillating electrostatic field is
created in the space between the four rods
– Only the corresponding m/z value is able to pass
through and reach the detector
– Other values are deflected and crash into the
rods or the walls of the instrument
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The Quadrupole Mass Analyzer
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Representing 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 (Intensity of 100%)
• Peak that corresponds to the unfragmented radical
cation is parent peak or molecular ion (M+)
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Interpreting Mass Spectra
• Provides the molecular weight from the mass of
the molecular ion
• Double-focusing mass spectrometers have a
high accuracy rate
• In compounds that do not exhibit molecular ions,
soft ionization methods are used
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High Resolution Mass Spectrometry Can Distinguish
Between Compound with the Same Molecular Mass
Exact Masses of Isotopes
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Natural Abundance of Isotopes
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Other Mass Spectral Features
• Mass spectrum provides the molecular
fingerprint of a compound
– The way molecular ions break down, can produce
characteristic fragments that help in identification
• Interpretation of molecular fragmentation pattern
assists in the derivation of structural information
CHE2202, Chapter 12
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Mass Spectral Fragmentation of
Hexane
• Hexane (m/z = 86 for parent) has peaks at m/z
= 71, 57, 43, 29
CHE2202, Chapter 12
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Worked Example
• The male sex hormone testosterone contains
only C, H, and O and has a mass of
288.2089 amu, as determined by highresolution mass spectrometry
– Determine the possible molecular formula of
testosterone
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Worked Example
• Solution:
– Assume that hydrogen contributes 0.2089 to the
mass of 288.2089
– Dividing 0.2089 by 0.00783 ( difference between
the atomic weight of one H atom and 1) gives
26.67
• Approximate number of H in testosterone
– Determine the maximum number of carbons by
dividing 288 by 12
– List reasonable molecular formulas containing
C,H, and O that contain 20-30 hydrogens and
whose mass is 288
CHE2202, Chapter 12
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Worked Example
– The possible formula for testosterone is
C19H28O2
CHE2202, Chapter 12
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Mass Spectrometry of Some
Common Functional Groups
• Alcohols
– Fragment through alpha cleavage and
dehydration
CHE2202, Chapter 12
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Mass Spectrometry of Some
Common Functional Groups
• Amines
– Nitrogen rule of mass spectrometry
• A compound with an odd number of nitrogen
atoms has an odd-numbered molecular weight
– Amines undergo -cleavage, generating alkyl
radicals and a resonance-stabilized, nitrogencontaining cation
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Mass Spectrometry of Some
Common Functional Groups
• Halides
– Elements comprising
two common isotopes
possess a distinctive
appearance as a mass
spectra
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Fragmentation of Carbonyl
Compounds
• 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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Worked Example
• List the masses of the parent ion and of
several fragments that can be found in the
mass spectrum of the following molecule
2-methyl-2-pentanol
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Worked Example
• Solution:
– The molecule is 2-methyl-2-pentanol
• It produces fragments resulting from dehydration and
alpha cleavage
• Peaks may appear at M+=102(molecular ion), 87, 84,
59
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Mass Spectroscopy in Biological Chemistry:
Time-of-Flight (TOF) Instruments
• Most biochemical analyses by MS use soft
ionization methods that charge molecules with
minimal fragmentation
– Electrospray ionization (ESI)
• High voltage is passed through the solution sample
• Sample molecule gains one or more protons from the
volatile solvent, which evaporates quickly
– Matrix-assisted laser desorption ionization (MALDI)
• Sample is absorbed onto a suitable matrix compound
• Upon brief exposure to laser light, energy is
transferred from the matrix compound to the sample
molecule
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MALDI–TOF Mass Spectrum of
Chicken Egg-White Lysozyme
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Spectroscopy and the
Electromagnetic Spectrum
• Waves are classified by frequency or
wavelength ranges
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Absorption Spectrum
• Organic compounds exposed to electromagnetic
radiation can absorb energy of only certain
wavelengths (unit of energy)
– Transmit energy of other wavelengths
• Changing wavelengths to determine which are
absorbed and which are transmitted produces
an absorption spectrum
• In infrared radiation, absorbed energy causes
bonds to stretch and bend more vigorously
• In ultraviolet radiation, absorbed energy causes
electrons to jump to a higher-energy orbital CHE2202, Chapter 12
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Infrared Energy Modes
• Molecules possess a certain amount of
energy that causes them to vibrate
• Molecule absorbs energy upon
electromagnetic radiation only if the radiation
frequency and the vibration frequency match
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Interpreting Infrared Spectra
• IR spectrum interpretation is difficult as the
arrangement of organic molecules is complex
– Disadvantage - Generally used only in pure
samples of fairly small molecules
– Advantage - Provides a unique identification of
compounds
• Fingerprint region - 1500cm-1 to 400 cm-1 (approx)
• Complete interpretation of the IR spectrum is not
necessary to gain useful structural information
– IR absorption bands are similar among compounds
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Characteristic IR Absorptions of
Some Functional Groups
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IR Spectra of Hexane, 1-Hexene,
and 1-Hexyne
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Regions of the Infrared Spectrum
• Region from 4000 to 2500 cm-1 can be divided
into areas characterized by:
–
–
–
–
Single-bond stretching motions
Triple-bond stretching motions
Absorption by double bonds
Fingerprint portion of the IR spectrum
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Worked Example
• Using IR spectroscopy, distinguish
between the following isomers:
– CH3CH2OH and CH3OCH3
• Solution:
– CH3CH2OH is a strong hydroxyl bond at
3400–3640 cm-1
– CH3OCH3 does not possess a band in the
region 3400–3640 cm-1
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Infrared Spectra of Some Common
Functional Groups
• Alkanes
– No functional groups
– C–H and C–C bonds are responsible for
absorption
– C–H bond absorption ranges from 2850 to 2960
cm-1
– C–C bonds show bands between 800 to 1300
cm-1
CHE2202, Chapter 12
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Infrared Spectra of Some Common
Functional Groups
• Alkenes
– Vinylic =C–H bonds are responsible for
absorption from 3020 to 3011cm-1
– Alkene C=C bonds are responsible for absorption
close to 1650cm-1
– Alkenes possess =C–H out-of-plane bending
absorptions in the 700 to 1000 cm-1 range
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Infrared Spectra of Some Common
Functional Groups
• Alkynes
– C≡C stretching absorption exhibited at 2100 to
2260 cm-1
• Similar bonds in 3-hexyne show no absorption
– Terminal alkynes such as 1-hexyne possess
≡C–H stretching absorption at 3300 cm-1
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Some Vibrations are Infrared Inactive
A bond absorbs IR radiation only if its dipole moment changes when it vibrates.
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Aromatic Compounds
• Weak C–H stretch at 3030 cm1
• Weak absorptions at 1660 to 2000 cm1
range
• Medium-intensity absorptions at 1450 to
1600 cm1
CHE2202, Chapter 12
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Alcohols and Amines
• Alcohols
– O–H 3400 to 3650 cm1
• Usually broad and intense
• Amines
– N–H 3300 to 3500 cm1
• Sharper and less intense than an O–H
CHE2202, Chapter 12
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The IR Spectrum of an Alcohol
CHE2202, Chapter 12
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The IR Spectrum of an Amine
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Carbonyl Compounds
• Strong, sharp C=O peak in the range of 1670
to 1780 cm1
• Exact absorption is characteristic of type of
carbonyl compound
• Principles of resonance, inductive electronic
effects, and hydrogen bonding provides a
better understanding of IR radiation
frequencies
CHE2202, Chapter 12
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Carbonyl Compounds
• Aldehydes
– 1730 cm1 in saturated aldehydes
– 1705 cm1 in aldehydes next to double bond
or aromatic ring
– Low absorbance frequency is due to the
resonance delocalization of electron density
from the C=C into the carbonyl
CHE2202, Chapter 12
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The IR Spectrum of an Aldehyde
The carbon—hydrogen stretch of an aldehyde hydrogen occurs
at 2820 cm–1 and at 2720 cm–1.
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Ketones
• Saturated open-chain ketones and sixmembered cyclic ketones absorb at 1715cm-1
• Five-membered ketones absorb at 1750cm-1
– Stiffening of C=O bond due to ring strain
• Four members absorb at 1780cm-1
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This C═O Bond Is Essentially a
Pure Double Bond
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This C═O Bond Has Significant
Single Bond Character
The less double bond character, the lower the frequency.
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Carbonyl Compounds
• Esters
– Saturated esters absorb at 1735 cm-1
– Esters possess two strong absorbances
within the range of 1300 to 1000 cm-1
– Esters adjacent to an aromatic ring or a
double bond absorb at 1715 cm-1
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The IR Spectrum of an Ester
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The IR Spectrum of a Carboxylic Acid
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Hydrogen Bonded OH Groups
Stretch at a Lower Frequency
It is easier to stretch a hydrogen bonded OH group.
CHE2202, Chapter 12
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The IR Spectrum of an Amide
CHE2202, Chapter 12
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Worked Example
• Identify the possible location of IR
absorptions in the compound below
CHE2202, Chapter 12
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Worked Example
• Solution:
– The compound possesses nitrile and ketone groups
as well as a carbon–carbon double bond
– Nitrile absorption occurs at 2210–2260 cm-1
– Ketone exhibits an absorption bond at 1690 cm-1
– Double bond absorption occurs at 1640–1680 cm-1
CHE2202, Chapter 12
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