Infrared Spectroscopy

Infrared Spectroscopy
Chapter 15 Infrared Spectroscopy And Mass Spectrometry Suggested Problems –

Introduction to Spectroscopy
Spectroscopy involves an interaction between light (electromagnetic radiation) and matter Light can be thought of as waves of energy n = c/l Light can be thought of as packets (particles) of energy called photons E = hn = hc/l

Much of the electromagnetic spectrum is invisible to the human eye

When light interacts with molecules, the effect depends on the wavelength of light used

Matter exhibits wave-like properties On the macroscopic scale, matter appears to exhibit continuous 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 particle-like properties On the molecular scale, matter exhibits quantum behavior A molecule will only rotate or vibrate at certain rates (energies are quantized)

Molecular motion/energy is quantized Rotational Vibrational Energy of electrons

For each different bond, vibrational energy levels are separated by gaps (quantized) If a photon of light strikes a molecule with the exact amount of energy needed, a molecular vibration will occur Energy is eventually released from the molecule usually 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? Different types of bonds vibrate at different frequencies.

IR Spectroscopy Molecular bonds can vibrate by stretching or by bending in a number of ways This chapter focuses mostly on stretching frequencies WHY do objects emit IR light? Vibrating bonds can be demoted to a lower vibrational state by emitting IR radiation.

IR Spectroscopy Some night vision goggles can detect IR light that is emitted IR or thermal imaging is also used to detect breast cancer

IR Spectroscopy The energy necessary to cause vibration depends on the type of bond

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 Operationally, 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 The sample is irradiated with all frequencies of infrared light and transmitted light is detected

IR Spectroscopy In the IR spectrum below, WHAT is % transmittance and how does it relate to molecular structure? Higher Energy

IR Spectroscopy A signal on the IR spectrum has three important characteristics: wavenumber, intensity, and shape

IR Signal Wavenumber The wavenumber for a stretching vibration depends on the bond strength and the mass of the atoms bonded together Hooke’s Law

IR Signal Wavenumber Rationalize the trends below using the wavenumber formula The heavier the combination of atoms, the lower the absorption frequency. The greater the bond order, the stronger the bond, the greater the absorption frequency.

IR Signal Wavenumber The wavenumber formula and empirical observations allow us to designate regions as representing specific types of bonds

IR Signal Wavenumber The region above 1500 cm-1 is called the diagnostic or functional group region. The region below 1500 cm-1 is called the fingerprint region. FINGERPRINT REGION DIAGNOSTIC REGION Diagnostic region has fewer peaks and provides the clearest information. Fingerprint region contains signals resulting from the vibrational excitations of most single bonds. It contains many signals and is difficult to analyze.

IR Signal Wavenumber Analyze the diagnostic and fingerprint regions below

IR Signal Wavenumber Compare the IR spectra

IR Signal Wavenumber 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 O-H bond is stronger. 0.92 0.94

IR Signal Wavenumber Compare the IR stretching wavenumbers below
Are the differences due to mass or bond strength? Which bond is strongest, and WHY?

IR Signal Wavenumber Note how the region ≈3000 cm-1 in the IR spectrum can give information about the functional groups present

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 There are no C-H bonds in the molecules on the right so there is no C-H absorption above However, the alcohol O-H would absorb around 3500. 3100 cm-1

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? Wavenumber would decrease.

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 and 15.4. The conjugated ketone has three resonance structures whereas the ketone only has two. Two of the conjugated ketone resonance structures have single bonds between C and O. Thus, there is more single bond character to the C=O bond in the conjugated case and it absorbs at lower frequency. The same analysis works for the esters.

IR Signal Strength The strength of IR signals can vary

IR Signal Strength 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

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

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 cm-1 region Symmetrical bonds without dipole moments do not absorb well in the IR.

IR Signal Strength 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? There are lots of them! Practice with conceptual checkpoints 15.5 – 15.7

IR Signal Shape Some IR signals are broad, while others are very narrow O-H stretching signals are often quite broad

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?

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

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

IR Signal Shape H-bonding is often more pronounced in carboxylic acids, because they can forms H-bonding dimers

IR Signal Shape For the molecule below, predict all of the stretching signals in the diagnostic region Practice with conceptual checkpoint 15.9 O-H stretch (broad peak at roughly 3200) C-H stretch (just above 3000) C-H stretch (just below 3000) C=O stretch (around 1700) C=C stretch (weaker signal around )

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?

IR Signal Shape

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

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

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) cm-1 – check for double bonds cm-1 – check for triple bonds cm-1 – check for X-H bonds Analyze wavenumber, intensity, and shape for each signal

Analyzing an IR Spectrum
Often, the molecular structure can be identified from an IR spectra Focus on the cm-1 (X-H) region Practice with SkillBuilder 15.1

Using IR to Distinguish Between Molecules
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

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?

Intro 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 Can you think of ways to get an organic molecule to ionize?

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?

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.

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?

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?

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 shortly

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

Analyzing the M+• Peak In the mass spec for benzene, the M+• peak is the base peak The M+• peak does not easily fragment

Analyzing the M+• Peak Like most compounds, the M+• peak for pentane is NOT the base peak The M+• peak fragments easily

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 A deuterium in a molecule could account for an odd mass in the molecular ion.

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.

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 1.1% of carbon is C-13. Take M+1 height and divide by M+ height and then multiply by 100 to get percentage M+H peak is of M+ peak. Divide this percent by 1.1% to get the number of carbons in the molecule.

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?

79Br=51% and 81Br=49%, so molecules with bromine often have equally strong (M)+• and (M+2)+• peaks Practice with conceptual checkpoints and 15.24

Analyzing the Fragments
A thorough analysis of the molecular fragments can often yield structural information Consider pentane Remember, MS only detects charged fragments If you see repetitive loss of 14 units in the mass spec it is indicative of a series of CH2 groups. Fragmentation can occur at any one of these bonds.

WHAT type of fragmentation is responsible for the “groupings” of peaks observed?

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

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

Alcohols generally undergo two main types of fragmentation: alpha cleavage and dehydration Dehydration

Amines generally undergo alpha cleavage Carbonyls generally undergo McLafferty rrearearrangement Practice with conceptual checkpoints – 15.28

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 = amu and 1 neutron = amu One 12C atom = exactly 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

Note the exact masses and natural abundances below

Why are the values in table 15.5 different from those in the periodic table? Imagine you want to use high-res MS to distinguish between the molecules below Why can’t you use low-res?

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 and 15.30

GC-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

GC-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 The chromatogram gives the retention time The Mass Spectrogram (low-res or high-res)

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?

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 CnH2n+2

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?

Consider the isomers of C4H6 How many degrees of unsaturation are there? 1 degree of unsaturation = 1 unit on the hydrogen deficiency index (HDI)

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?

For the HDI scale, a nitrogen increases the number of expected hydrogen atoms by ONE How many degrees of unsaturation are there in C5H8BrN? Subtract NH from any molecule for each nitrogen it contains prior to calculating the degree 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

For a formula with a halogen in it, replace the halogen with an H and then determine the degree of unsaturation. For a formula with an O in it, ignore the O and write the formula without it to determine the degree of unsaturation. For a formula with an N in it, subtract NH for each N from the formula and then determine the degree of unsaturation.

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 2 degrees of unsaturation and no C-H unsaturated stretching. Peak at 1687 suggests a conjugated C=O double bond

Infrared Spectroscopy

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