Infrared Spectroscopy and Mass Spectrometry Organic Chemistry Second Edition David Klein Chapter 15 Infrared Spectroscopy and Mass Spectrometry 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. 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. 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. Klein, Organic Chemistry 2e

15.2 IR Spectroscopy Molecular bonds can vibrate by stretching or by bending in a number of ways 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. Klein, Organic Chemistry 2e

15.2 IR Spectroscopy Some night vision goggles can detect IR light that is emitted IR or thermal imaging is also used to detect breast cancer Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. Klein, Organic Chemistry 2e

15.2 IR Spectroscopy The energy necessary to cause vibration depends on the type of bond Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. Klein, Organic Chemistry 2e

15.2 IR Spectroscopy 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 Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. Klein, Organic Chemistry 2e

15.2 IR Spectroscopy Analyze the units for the wavenumber, ν = frequency and c = the speed of light Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. Klein, Organic Chemistry 2e

15.2 IR Spectroscopy A signal on the IR spectrum has three important characteristics: wavenumber, intensity, and shape Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. Klein, Organic Chemistry 2e

15.3 IR Signal Wavenumber 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? Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. Klein, Organic Chemistry 2e

15.3 IR Signal Wavenumber Rationalize the trends below using the wavenumber formula Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. Klein, Organic Chemistry 2e

15.3 IR Signal Wavenumber The wavenumber formula and empirical observations allow us to designate regions as representing specific types of bonds Explain the regions above Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. Klein, Organic Chemistry 2e

15.3 IR Signal Wavenumber The region above 1500 cm-1 is called the diagnostic region. WHY? The region below 1500 cm-1 is called the fingerprint region. WHY? FINGERPRINT REGION DIAGNOSTIC REGION Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. Klein, Organic Chemistry 2e

15.3 IR Signal Wavenumber Analyze the diagnostic and fingerprint regions below Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. Klein, Organic Chemistry 2e

15.3 IR Signal Wavenumber Analyze the diagnostic and fingerprint regions below Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. Klein, Organic Chemistry 2e

15.3 IR Signal Wavenumber Compare the IR spectra Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. Klein, Organic Chemistry 2e

15.3 IR Signal Wavenumber Greater difference in masses of atoms attached, greater the greater the wavenumber C-H stretch ≈ 3000 cm-1 O-H stretch ≈ 3400 cm-1 Practice with conceptual checkpoint 15.1 Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. Klein, Organic Chemistry 2e

15.3 IR Signal Wavenumber Compare the IR stretching wavenumbers below Are the differences due to mass or bond strength? Which bond is strongest, and WHY? Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. Klein, Organic Chemistry 2e

15.3 IR Signal Wavenumber Note how the region ≈3000 cm-1 in the IR spectrum can give information about the functional groups present Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. Klein, Organic Chemistry 2e

15.3 IR Signal Wavenumber 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 Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. Klein, Organic Chemistry 2e

15.3 IR Signal Wavenumber 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? Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. Klein, Organic Chemistry 2e

15.3 IR Signal Wavenumber Use the given examples to explain HOW and WHY the conjugation and the –OR group affect resonance and thus the IR signal? Practice with conceptual checkpoint 15.3 Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. Klein, Organic Chemistry 2e

15.4 IR Signal Strength The strength of IR signals can vary Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. Klein, Organic Chemistry 2e

15.4 IR Signal Strength 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 Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. Klein, Organic Chemistry 2e

15.4 IR Signal Strength 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 Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. Klein, Organic Chemistry 2e

15.5 IR Signal Shape Some IR signals are broad, while others are very narrow O-H stretching signals are often quite broad Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. Klein, Organic Chemistry 2e

15.5 IR Signal Shape 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 WHY does H-bonding affect the O-H bond strength? Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. Klein, Organic Chemistry 2e

15.5 IR Signal Shape In a sample with an intermediate concentration, both narrow and broad signals are observed. WHY? Explain the cm-1 readings for the two O-H stretching peaks Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. Klein, Organic Chemistry 2e

15.5 IR Signal Shape 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 Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. Klein, Organic Chemistry 2e

15.5 IR Signal Shape H-bonding is often more pronounced in carboxylic acids, because they can forms H-bonding dimers Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. Klein, Organic Chemistry 2e

15.5 IR Signal Shape For the molecule below, predict all of the stretching signals in the diagnostic region Practice with conceptual checkpoint 15.9 Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. Klein, Organic Chemistry 2e

15.5 IR Signal Shape 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 Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. Klein, Organic Chemistry 2e

15.5 IR Signal Shape Klein, Organic Chemistry 2e Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 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. 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. 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 spectra Focus on the diagnostic region (above 1500 cm-1) 1600-1850 cm-1 – check for double bonds 2100-2300 cm-1 – check for triple bonds 2700-4000 cm-1 – check for X-H bonds Analyze wavenumber, intensity, and shape for each signal Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. Klein, Organic Chemistry 2e

15.6 Analyzing an IR Spectrum Often, the molecular structure can be identified from an IR spectra Focus on the 2700-4000 cm-1 (X-H) region Practice with SkillBuilder 15.1 Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 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. Klein, Organic Chemistry 2e

Klein, Organic Chemistry 2e Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 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? Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. Klein, Organic Chemistry 2e

Klein, Organic Chemistry 2e Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. Klein, Organic Chemistry 2e

Klein, Organic Chemistry 2e Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. Klein, Organic Chemistry 2e

15.6 Analyzing an IR Spectrum Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. Klein, Organic Chemistry 2e

Klein, Organic Chemistry 2e Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. Klein, Organic Chemistry 2e

Klein, Organic Chemistry 2e Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. Klein, Organic Chemistry 2e

Klein, Organic Chemistry 2e Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. Klein, Organic Chemistry 2e

Klein, Organic Chemistry 2e Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. Klein, Organic Chemistry 2e

15.8 Into to Mass Spectrometry Mass spectrometry is primarily used to determine the molar mass and formula for a compound A compound is vaporized and then ionized The masses of the ions are detected and graphed Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 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. What is a radical cation? Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 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. Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 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. Neutral fragments are not detected. Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 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. 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. 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. 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 Base peak M+. Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 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. 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. Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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 CnH2n+2 Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. Klein, Organic Chemistry 2e

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. 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. 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. 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? Forget this formula below (you can use if you want) Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. Klein, Organic Chemistry 2e

15.16 Degrees of Unsaturation NOTrogen for Nitrogen Halogen 0xygen (the O is a zero) Copyright © 2015 John Wiley & Sons, Inc. All rights reserved. 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. Klein, Organic Chemistry 2e