chapter 15 infrared spectroscopy and mass spectrometry organic chemistry second edition david klein...
Post on 25-Dec-2015
227 Views
Preview:
TRANSCRIPT
Chapter 15Infrared Spectroscopy and Mass Spectrometry
Organic ChemistrySecond Edition
David Klein
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. Klein, Organic Chemistry 2e
15.1 Introduction to Spectroscopy• Spectroscopy involves an interaction between matter
and light (electromagnetic radiation)• Light can be thought of as waves of energy or packets
(particles) of energy called photons• Properties of light waves include wavelength and
frequency• Is wavelength directly or inversely proportional to
energy? WHY?• Is frequency directly or inversely proportional to energy?
WHY?
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-2 Klein, Organic Chemistry 2e
15.1 Introduction to Spectroscopy• There are many wavelengths of light that can not be
observed with your eyes
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-3 Klein, Organic Chemistry 2e
15.1 Introduction to Spectroscopy• When light interacts with molecules, the effect depends
on the wavelength of light used
• This chapter focuses on IR spectroscopy
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-4 Klein, Organic Chemistry 2e
15.1 Introduction to Spectroscopy• Matter exhibits particle-like properties• On the macroscopic scale, matter appears to exhibit
continuous behavior rather than quantum behavior– Consider the example of an engine powering the rotation of a
tire. The tire should be able to rotate at nearly any rate
• Matter also exhibits wave-like properties as we learned in section 1.6
• Matter on the molecular scale exhibits quantum behavior– A molecule will only rotate or vibrate at certain rates
(energies)
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-5 Klein, Organic Chemistry 2e
15.1 Introduction to Spectroscopy• For each of the types of molecular motion/energy
below, describe how it is quantized– Rotation
– Vibration
– Energy of electrons
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-6 Klein, Organic Chemistry 2e
15.1 Introduction to Spectroscopy• For each different bond, vibrational energy levels are
separated by gaps (quantized)• If a photon of light strikes the molecule with the exact
amount of energy needed, a molecular vibration will occur
• Energy is eventually released from the molecule generally in the form of heat
• Infrared (IR) Light generally causes molecular vibration• HOW might IR light absorbed give you information
about a molecule’s structure
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-7 Klein, Organic Chemistry 2e
• Molecular bonds can vibrate by stretching or by bending in a number of ways
15.2 IR Spectroscopy
• This chapter will focus mostly on stretching frequencies• WHY do objects emit IR light?• WHY do some objects emit more IR radiation than
others?• WHERE does that light come from?
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-8 Klein, Organic Chemistry 2e
• Some night vision goggles can detect IR light that is emitted
• IR or thermal imaging is also used to detect breast cancer
15.2 IR Spectroscopy
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-9 Klein, Organic Chemistry 2e
• The energy necessary to cause vibration depends on the type of bond
15.2 IR Spectroscopy
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-10 Klein, Organic Chemistry 2e
• An IR spectrophotometer irradiates a sample with all frequencies of IR light
• The frequencies that are absorbed by the sample tell us the types of bonds (functional groups) that are present
• How do we measure the frequencies that are absorbed?
• Most commonly, samples are deposited neat on a salt (NaCl) plate. WHY is salt used?
• Alternatively, the compound may be dissolved in a solvent or embedded in a KBr pellet
15.2 IR Spectroscopy
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-11 Klein, Organic Chemistry 2e
• In the IR spectrum below, WHAT is % transmittance and how does it relate to molecular structure?
15.2 IR Spectroscopy
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-12 Klein, Organic Chemistry 2e
• Analyze the units for the wavenumber,• ν = frequency and c = the speed of light
15.2 IR Spectroscopy
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-13 Klein, Organic Chemistry 2e
• HOW are wavelength and wavenumber different? • HOW are wavenumbers and energy related?
15.2 IR Spectroscopy
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-14 Klein, Organic Chemistry 2e
• A signal on the IR spectrum has three important characteristics: wavenumber, intensity, and shape
15.2 IR Spectroscopy
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-15 Klein, Organic Chemistry 2e
• The wavenumber for a stretching vibration depends on the bond strength and the mass of the atoms bonded together
• Should bonds between heavier atoms require higher or lower wavenumber IR light to stretch?
15.3 IR Signal Wavenumber
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-16 Klein, Organic Chemistry 2e
• Rationalize the trends below using the wavenumber formula
1.
2.
15.3 IR Signal Wavenumber
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-17 Klein, Organic Chemistry 2e
• The wavenumber formula and empirical observations allow us to designate regions as representing specific types of bonds
• Explain the regions above
15.3 IR Signal Wavenumber
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-18 Klein, Organic Chemistry 2e
• The region above 1500 cm-1 is called the diagnostic region. WHY?
• The region below 1500 cm-1 is called the fingerprint region. WHY?
15.3 IR Signal Wavenumber
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-19 Klein, Organic Chemistry 2e
DIAGNOSTIC REGION FINGERPRINT REGION
• Analyze the diagnostic and fingerprint regions below
15.3 IR Signal Wavenumber
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-20 Klein, Organic Chemistry 2e
• Analyze the diagnostic and fingerprint regions below
15.3 IR Signal Wavenumber
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-21 Klein, Organic Chemistry 2e
• Compare the IR spectra
15.3 IR Signal Wavenumber
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-22 Klein, Organic Chemistry 2e
• Given the formula below and the given IR data, predict whether a C-H or O-H bond is stronger
• C-H stretch ≈ 3000 cm-1
• O-H stretch ≈ 3400 cm-1
• Practice with conceptual checkpoint 15.1
15.3 IR Signal Wavenumber
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-23 Klein, Organic Chemistry 2e
• Compare the IR stretching wavenumbers below
• Are the differences due to mass or bond strength?• Which bond is strongest, and WHY?
15.3 IR Signal Wavenumber
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-24 Klein, Organic Chemistry 2e
• Note how the region ≈3000 cm-1 in the IR spectrum can give information about the functional groups present
15.3 IR Signal Wavenumber
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-25 Klein, Organic Chemistry 2e
• Is it possible that an alkene or alkyne could give an IR spectra without any signals above 3000 cm-1?
• Predict the wavenumbers that would result (if any) above 3000 cm-1 for the molecules below
• Practice with conceptual checkpoint 15.2
15.3 IR Signal Wavenumber
HO
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-26 Klein, Organic Chemistry 2e
• Resonance can affect the wavenumber of a stretching signal
• Consider a carbonyl that has two resonance contributors
• If there were more contributors with C-O single bond character than C=O double bond character, how would that affect the wavenumber?
15.3 IR Signal Wavenumber
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-27 Klein, Organic Chemistry 2e
• Use the given examples to explain HOW and WHY the conjugation and the –OR group affect resonance and thus the IR signal?
15.3 IR Signal Wavenumber
• Practice with conceptual checkpoint 15.3
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-28 Klein, Organic Chemistry 2e
• The strength of IR signals can vary
15.4 IR Signal Strength
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-29 Klein, Organic Chemistry 2e
• When a bond undergoes a stretching vibration, its dipole moment also oscillates
• Recall the formula for dipole moment includes the distance between the partial charges,
• The oscillating dipole moment creates an electrical field surrounding the bond
15.4 IR Signal Strength
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-30 Klein, Organic Chemistry 2e
• The more polar the bond, the greater the opportunity for interaction between the waves of the electrical field and the IR radiation
• Greater bond polarity = stronger IR signals
15.4 IR Signal Strength
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-31 Klein, Organic Chemistry 2e
• Note the general strength of the C=O stretching signal vs. the C=C stretching signal
• Imagine a symmetrical molecule with a completely nonpolar C=C bond: 2,3-dimethyl-2-butene
• 2,3-dimethyl-2-butene does not give an IR signal in the 1500-2000 cm-1 region
15.4 IR Signal Strength
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-32 Klein, Organic Chemistry 2e
• Stronger signals are also observed when there are multiple bonds of the same type vibrating
• Although C-H bonds are not very polar, they often give very strong signals, WHY?
• Because sample concentration can affect signal strength, the Intoxilyzer 5000 can be used to determine blood alcohol levels be analyzing the strength of C-H bond stretching in blood samples
• Practice with conceptual checkpoints 15.5 – 15.7
15.4 IR Signal Strength
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-33 Klein, Organic Chemistry 2e
• Some IR signals are broad, while others are very narrow
• O-H stretching signals are often quite broad
15.5 IR Signal Shape
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-34 Klein, Organic Chemistry 2e
• When possible, O-H bonds form H-bonds that weaken the O-H bond strength
• The H-bonds are transient, so the sample will contain molecules with varying O-H bond strengths
• Why does that cause the O-H stretch signal to be broad?• The O-H stretch signal will be narrow if a dilute solution
of an alcohol is prepared in a solvent incapable of H-bonding
15.5 IR Signal Shape
• WHY does H-bonding affect the O-H bond strength?
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-35 Klein, Organic Chemistry 2e
• In a sample with an intermediate concentration, both narrow and broad signals are observed. WHY?
15.5 IR Signal Shape
• Explain the cm-1 readings for the two O-H stretching peaks
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-36 Klein, Organic Chemistry 2e
• Consider how broad the O-H stretch is for a carboxylic acid and how its wavenumber is around 3000 cm-1 rather than 3400 cm-1 for a typical O-H stretch
15.5 IR Signal Shape
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-37 Klein, Organic Chemistry 2e
• H-bonding is often more pronounced in carboxylic acids, because they can forms H-bonding dimers
15.5 IR Signal Shape
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-38 Klein, Organic Chemistry 2e
• For the molecule below, predict all of the stretching signals in the diagnostic region
• Practice with conceptual checkpoint 15.9
15.5 IR Signal Shape
O
OH
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-39 Klein, Organic Chemistry 2e
• Primary and secondary amines exhibit N-H stretching signals. WHY not tertiary amines?
• Because N-H bonds are capable of H-bonding, their stretching signals are often broadened
• Which is generally more polar, an O-H or an N-H bond?
• Do you expect N-H stretches to be strong or weak signals?
• See example spectra on next slide
15.5 IR Signal Shape
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-40 Klein, Organic Chemistry 2e
15.5 IR Signal Shape
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-41 Klein, Organic Chemistry 2e
15.5 IR Signal Shape• The appearance of two N-H signals
for the primary amine is NOT simply the result of each N-H bond giving a different signal
• Instead, the two N-H bonds vibrate together in two different ways
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-42 Klein, Organic Chemistry 2e
15.5 IR Signal Shape• A single molecule can only vibrate symmetrically or
asymmetrically at any given moment, so why do we see both signals at the same time?
• Similarly, CH2 and CH3 groups can also vibrate as a group giving rise to multiple signals
• Practice with conceptual checkpoint 15.10
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-43 Klein, Organic Chemistry 2e
15.6 Analyzing an IR Spectrum• Table 15.2 summarizes some of the key signals that help
us to identify functional groups present in molecules• Often, the molecular structure can be identified from an
IR spectra1. Focus on the diagnostic region (above 1500 cm-1)
a) 1600-1850 cm-1 – check for double bondsb) 2100-2300 cm-1 – check for triple bondsc) 2700-4000 cm-1 – check for X-H bondsd) Analyze wavenumber, intensity, and shape for each signal
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-44 Klein, Organic Chemistry 2e
15.6 Analyzing an IR Spectrum• Often, the molecular
structure can be identified from an IR spectra
2. Focus on the 2700-4000 cm-1 (X-H) region
• Practice with SkillBuilder 15.1
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-45 Klein, Organic Chemistry 2e
15.7 Using IR to Distinguish Between Molecules
• As we have learned in previous chapters, organic chemists often carry out reactions to convert one functional group into another
• IR spectroscopy can often be used to determine the success of such reactions
• For the reaction below, how might IR spectroscopy be used to analyze the reaction?
• Practice with SkillBuilder 15.2
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-46 Klein, Organic Chemistry 2e
15.7 Using IR to Distinguish Between Molecules
• For the reactions below, identify the key functional groups, and describe how IR data could be used to verify the formation of product
• Is IR analysis qualitative or quantitative?
1) H-Br
2) Et-OK
O3
(CH3)2SO
O
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-47 Klein, Organic Chemistry 2e
15.8 Into to Mass Spectrometry• Mass spectrometry is primarily used to determine the
molar mass and formula for a compound1. A compound is vaporized and then ionized2. The masses of the ions are detected and graphed
• Can you think of ways to get an organic molecule to ionize?
• Will the molecule need to absorb energy or release energy?
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-48 Klein, Organic Chemistry 2e
15.8 Into to Mass Spectrometry• The most common method of ionizing molecules is by
electron impact (EI)• The sample is bombarded with a beam of high energy
electrons (1600 kcal or 70 eV)• EI usually causes an electron to be ejected from the
molecule. HOW? WHY?
• What is a radical cation?
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-49 Klein, Organic Chemistry 2e
15.8 Into to Mass Spectrometry• How does the mass of the radical cation compare to the
original molecule?
• If the radical cation remains intact, it is known as the molecular ion (M+•) or parent ion
• Often, the molecular ion undergoes some type of fragmentation. WHY?
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-50 Klein, Organic Chemistry 2e
15.8 Into to Mass Spectrometry• The resulting fragments may undergo even further
fragmentation
• The ions are deflected by a magnetic field • Smaller mass and higher charge fragments are affected
more by the magnetic field. WHY?• Neutral fragments are not detected. WHY?
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-51 Klein, Organic Chemistry 2e
15.8 Into to Mass Spectrometry• Explain the units on the x and
y axes for the mass spectrum for methane
• The base peak is the tallest peak in the spectrum
• For methane the base peak represents the M+•
• Sometimes, the M+• peak is not even observed in the spectrum, WHY?
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-52 Klein, Organic Chemistry 2e
15.8 Into to Mass Spectrometry• Peaks with a mass of less than M+• represent fragments
• Subsequent H radicals can be fragmented to give the ions with a mass/charge = 12, 13 and 14
• The presence of a peak representing (M+1) +• will be explained in section 15.10
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-53 Klein, Organic Chemistry 2e
15.8 Into to Mass Spectrometry• Mass spec is a relatively sensitive analytical method• Many organic compounds can be identified
– Pharmaceutical: drug discovery and drug metabolism, reaction monitoring
– Biotech: amino acid sequencing, analysis of macromolecules– Clinical: neonatal screening, hemoglobin analysis– Environmental: drug testing, water quality, food
contamination testing– Geological: evaluating oil composition– Forensic: Explosive detection– Many More
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-54 Klein, Organic Chemistry 2e
15.9 Analyzing the M+• Peak
• In the mass spec for benzene, the M+• peak is the base peak
• The M+• peak does not easily fragment
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-55 Klein, Organic Chemistry 2e
15.9 Analyzing the M+• Peak
• Like most compounds, the M+• peak for pentane is NOT the base peak
• The M+• peak fragments easily
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-56 Klein, Organic Chemistry 2e
15.9 Analyzing the M+• Peak • The first step in analyzing a mass spec is to identify the
M+• peak– It will tell you the molar mass of the compound– An odd massed M+• peak MAY indicate an odd number of N
atoms in the molecule– An even massed M+• peak MAY indicate an even number of N
atoms or zero N atoms in the molecule
• Give an alternative explanation for a M+• peak with an odd mass
• Practice with conceptual checkpoint 15.19
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-57 Klein, Organic Chemistry 2e
15.10 Analyzing the (M+1)+• Peak • Recall that the (M+1)+• peak in
methane was about 1% as abundant as the M+• peak
• The (M+1)+• peak results from the presence of 13C in the sample. HOW?
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-58 Klein, Organic Chemistry 2e
15.10 Analyzing the (M+1)+• Peak • For every 100 molecules of decane,
what percentage of them are made of exclusively 12C atoms?
• Comparing the heights of the (M+1)+• peak and the M+• peak can allow you to estimate how many carbons are in the molecule. HOW?
• The natural abundance of deuterium is 0.015%. Will that affect the mass spec analysis?
• Practice with SkillBuilder 15.3
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-59 Klein, Organic Chemistry 2e
15.11 Analyzing the (M+2)+• Peak • Chlorine has two abundant isotopes• 35Cl=76% and 37Cl=24%
• Molecules with chlorine often have strong (M+2)+• peaks
• WHY is it sometimes difficult to be absolutely sure which peak is the (M)+• peak?
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-60 Klein, Organic Chemistry 2e
15.11 Analyzing the (M+2)+• Peak • 79Br=51% and 81Br=49%, so molecules with bromine
often have equally strong (M)+• and (M+2)+• peaks
• Practice with conceptual checkpoints 15.23 and 15.24
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-61 Klein, Organic Chemistry 2e
15.12 Analyzing the Fragments• A thorough analysis of the molecular fragments can
often yield structural information• Consider pentane• Remember, MS only
detects charged fragments
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-62 Klein, Organic Chemistry 2e
15.12 Analyzing the Fragments
• WHAT type of fragmenting is responsible for the “groupings” of peaks observed?
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-63 Klein, Organic Chemistry 2e
15.12 Analyzing the Fragments• In general, fragmentation will be more prevalent when
more stable fragments are produced• Correlate the relative
stability of the fragments here with their abundances on the previous slide
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-64 Klein, Organic Chemistry 2e
15.12 Analyzing the Fragments• Consider the fragmentation below
• All possible fragmentations are generally observed under the high energy conditions employed in EI-MS
• If you can predict the most abundant fragments and match them to the spectra, it can help you in your identification
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-65 Klein, Organic Chemistry 2e
15.12 Analyzing the Fragments• Alcohols generally undergo two main types of
fragmentation: alpha cleavage and dehydration
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-66 Klein, Organic Chemistry 2e
15.12 Analyzing the Fragments• Amines generally undergo alpha cleavage
• Carbonyls generally undergo McLafferty rearrangement
• Practice with conceptual checkpoints 15.25 – 15.28
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-67 Klein, Organic Chemistry 2e
15.13 High Resolution Mass Spec• High Resolution Mass Spectrometry allows m/z to be
measured with up to 4 decimal places• Masses are generally not whole number integers
– 1 proton = 1.0073 amu and 1 neutron = 1.0086 amu
• One 12C atom = exactly 12.0000 amu, because the amu scale is based on the mass of 12C
• All atoms other than 12C will have a mass in amu that can be measured to 4 decimal places by a high-resolution mass spec instrument
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-68 Klein, Organic Chemistry 2e
15.13 High Resolution Mass Spec• Note the exact masses and natural abundances below
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-69 Klein, Organic Chemistry 2e
15.13 High Resolution Mass Spec• Why are the values in table 15.5 different from those on
the periodic table?• Imagine you want to use
high-res MS to distinguish between the molecules below
• Why can’t you use low-res?
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-70 Klein, Organic Chemistry 2e
15.13 High Resolution Mass Spec• Using the exact masses and natural abundances for each
element, we can see the difference high-res makes
• The molecular ion results from the molecule composed of the isotopes with the greatest natural abundance
• What if the molecular ion is not observed?• Practice with conceptual checkpoints 15.19 and 15.30
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-71 Klein, Organic Chemistry 2e
15.14 High Resolution Mass Spec• MS is suited for the identification of pure substances• However, MS instruments are often connected to a gas
chromatograph so mixtures can be analyzed
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-72 Klein, Organic Chemistry 2e
15.14 High Resolution Mass Spec• GC-MS gives two main forms of information
• GC-MS is a great technique for detecting compounds such as drugs in solutions such as blood or urine
1. The chromatogram gives the retention time
2. The Mass Spectrogram (low-res or high-res)
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-73 Klein, Organic Chemistry 2e
15.15 MS of Large Biomolecules• To be analyzed by EI mass spec, substances generally
must be vaporized prior to ionization• Until recently (last 30 years), compounds that
decompose before they vaporize could not be analyzed• In Electrospray ionization (ESI), a high-voltage needle
sprays a liquid solution of an analyte into a vacuum causing ionization
• HOW is ESI relevant for analyzing large biomolecules?• ESI is a “softer” ionizing technique. WHAT does that
mean?
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-74 Klein, Organic Chemistry 2e
15.16 Degrees of Unsaturation• Mass spec can often be used to determine the formula
for an organic compound• IR can often determine the functional groups present• Careful analysis of a molecule’s formula can yield a list of
possible structures• Alkanes follow the formula below, because they are
saturated
• Verify the formula by drawing some isomers of pentane
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-75 Klein, Organic Chemistry 2e
CnH2n+2
15.16 Degrees of Unsaturation• Notice that the general formula for the compound,CnH2n+2, changes when a double or triple bond is present
• Adding a degree of unsaturation decreases the number of H atoms by two
• How many degrees of unsaturation are there in cyclopentane?
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-76 Klein, Organic Chemistry 2e
15.16 Degrees of Unsaturation• Consider the isomers of C4H6
• How many degrees of unsaturation are there?• 1 degree of unsaturation = 1 unit on the hydrogen
deficiency index (HDI)
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-77 Klein, Organic Chemistry 2e
15.16 Degrees of Unsaturation• For the HDI scale, a halogen is treated as if it were a
hydrogen atom
• How many degrees of unsaturation are there in C5H9Br?• An oxygen does not affect the HDI. WHY?
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-78 Klein, Organic Chemistry 2e
15.16 Degrees of Unsaturation• For the HDI scale, a nitrogen increases the number of
expected hydrogen atoms by ONE
• How many degrees of unsaturation are there in C5H8BrN?
• You can also use the formula below
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-79 Klein, Organic Chemistry 2e
15.16 Degrees of Unsaturation• Calculating the HDI can be very useful. For example, if
HDI=0, the molecule can NOT have any rings, double bonds, or triple bonds
• Propose a structure for a molecule with the formula C7H12O. The molecule has the following IR peaks – A strong peak at 1687 cm-1
– NO IR peaks above 3000 cm-1
• Practice with SkillBuilder 15.4
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-80 Klein, Organic Chemistry 2e
• Explain why a completely nonpolar bond will not give a stretching signal in the IR spectra. Would you expect to see a signal for C-H stretching for a nonpolar molecule? Why or why not?
Additional Practice Problems
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-81 Klein, Organic Chemistry 2e
• Explain how IR might be used to qualitatively determine the degree of substitution when ammonia is treated with excess bromoethane.
Additional Practice Problems
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-82 Klein, Organic Chemistry 2e
• How might you use EI GCMS to distinguish between constitutional isomers?
Additional Practice Problems
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-83 Klein, Organic Chemistry 2e
• Explain how an experiment involving isotopic labeling might be used to explore the type of fragmentation that occurs in the MS analysis of organic compounds.
Additional Practice Problems
Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 15-84 Klein, Organic Chemistry 2e
top related