che2202, chapter 12 learn, 1 structure determination: mass spectrometry and infrared spectroscopy...
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CHE2202, Chapter 12Learn, 1
Structure Determination: Mass
Spectrometry and Infrared Spectroscopy
Chapter 12
Suggested Problems – 1-11,14-16,18,23,26,30-34,41-2
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CHE2202, Chapter 12Learn, 2
• 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)
Determining the Structure of an Organic Compound
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CHE2202, Chapter 12Learn, 3
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
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CHE2202, Chapter 12Learn, 4
Electron-Ionization, Magnetic-Sector 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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CHE2202, Chapter 12Learn, 5
Electron-Ionization, Magnetic-Sector 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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CHE2202, Chapter 12Learn, 6
The electron-ionization, magnetic-sector mass spectrometer
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CHE2202, Chapter 12Learn, 7
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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CHE2202, Chapter 12Learn, 8
The Quadrupole Mass Analyzer
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CHE2202, Chapter 12Learn, 9
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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CHE2202, Chapter 12Learn, 10
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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CHE2202, Chapter 12Learn, 11
High Resolution Mass Spectrometry Can DistinguishBetween Compound with the Same Molecular Mass
Exact Masses of Isotopes
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CHE2202, Chapter 12Learn, 12
Natural Abundance of Isotopes
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CHE2202, Chapter 12Learn, 13
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
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CHE2202, Chapter 12Learn, 14
Mass Spectral Fragmentation of Hexane
• Hexane (m/z = 86 for parent) has peaks at m/z = 71, 57, 43, 29
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CHE2202, Chapter 12Learn, 15
Worked Example
• The male sex hormone testosterone contains only C, H, and O and has a mass of 288.2089 amu, as determined by high-resolution mass spectrometry– Determine the possible molecular formula of
testosterone
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CHE2202, Chapter 12Learn, 16
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
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CHE2202, Chapter 12Learn, 17
Worked Example
– The possible formula for testosterone is C19H28O2
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CHE2202, Chapter 12Learn, 18
Mass Spectrometry of Some Common Functional Groups
• Alcohols– Fragment through alpha cleavage and
dehydration
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CHE2202, Chapter 12Learn, 19
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, nitrogen-containing cation
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CHE2202, Chapter 12Learn, 20
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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CHE2202, Chapter 12Learn, 21
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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CHE2202, Chapter 12Learn, 22
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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CHE2202, Chapter 12Learn, 23
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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CHE2202, Chapter 12Learn, 24
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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CHE2202, Chapter 12Learn, 25
MALDI–TOF Mass Spectrum of Chicken Egg-White Lysozyme
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CHE2202, Chapter 12Learn, 26
Spectroscopy and the Electromagnetic Spectrum
• Waves are classified by frequency or wavelength ranges
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CHE2202, Chapter 12Learn, 30
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
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CHE2202, Chapter 12Learn, 33
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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CHE2202, Chapter 12Learn, 34
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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CHE2202, Chapter 12Learn, 35
Characteristic IR Absorptions of Some Functional Groups
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CHE2202, Chapter 12Learn, 36
IR Spectra of Hexane, 1-Hexene, and 1-Hexyne
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CHE2202, Chapter 12Learn, 37
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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CHE2202, Chapter 12Learn, 39
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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CHE2202, Chapter 12Learn, 40
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
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CHE2202, Chapter 12Learn, 41
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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CHE2202, Chapter 12Learn, 42
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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CHE2202, Chapter 12Learn, 43
Some Vibrations are Infrared Inactive
A bond absorbs IR radiation only if its dipole moment changes when it vibrates.
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CHE2202, Chapter 12Learn, 44
Aromatic Compounds
• Weak C–H stretch at 3030 cm1
• Weak absorptions at 1660 to 2000 cm1 range
• Medium-intensity absorptions at 1450 to 1600 cm1
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CHE2202, Chapter 12Learn, 45
Alcohols and Amines
• Alcohols– O–H 3400 to 3650 cm1
• Usually broad and intense
• Amines– N–H 3300 to 3500 cm1
• Sharper and less intense than an O–H
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CHE2202, Chapter 12Learn, 46
The IR Spectrum of an Alcohol
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CHE2202, Chapter 12Learn, 47
The IR Spectrum of an Amine
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CHE2202, Chapter 12Learn, 48
Carbonyl Compounds
• Strong, sharp C=O peak in the range of 1670 to 1780 cm1
• 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
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CHE2202, Chapter 12Learn, 49
Carbonyl Compounds
• Aldehydes– 1730 cm1 in saturated aldehydes– 1705 cm1 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
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CHE2202, Chapter 12Learn, 50
The IR Spectrum of an Aldehyde
The carbon—hydrogen stretch of an aldehyde hydrogen occursat 2820 cm–1 and at 2720 cm–1.
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CHE2202, Chapter 12Learn, 51
Ketones
• Saturated open-chain ketones and six-membered 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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CHE2202, Chapter 12Learn, 52
This C═O Bond Is Essentially a Pure Double Bond
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CHE2202, Chapter 12Learn, 53
This C═O Bond Has Significant Single Bond Character
The less double bond character, the lower the frequency.
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CHE2202, Chapter 12Learn, 54
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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CHE2202, Chapter 12Learn, 55
The IR Spectrum of an Ester
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CHE2202, Chapter 12Learn, 56
The IR Spectrum of a Carboxylic Acid
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CHE2202, Chapter 12Learn, 57
Hydrogen Bonded OH Groups Stretch at a Lower Frequency
It is easier to stretch a hydrogen bonded OH group.
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CHE2202, Chapter 12Learn, 58
The IR Spectrum of an Amide
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CHE2202, Chapter 12Learn, 59
Worked Example
• Identify the possible location of IR absorptions in the compound below
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CHE2202, Chapter 12Learn, 60
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