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It’s time for molecular analysis! On this episode of Crash Course Organic Chemistry, we’re learning about mass spectrometry and infrared spectroscopy through the lens of a forensic investigation. Put on your lab coats, and let’s solve this mystery!

Episode Sources:
Silverstein, R. M., Webster, F. X., Kiemle, D. J., & Bryce, D. L (2007). Spectrometric identification of organic compounds, 8th ed., Hoboken, NJ: John Wiley & Sons, Inc.
Spectra for pseudoephedrine: BioRad/Sadtler Data Collection, Bio-Rad Laboratories, Philadelphia, PA (US), Spectra ID: BR125952
Spectra for methamphetamine: Kunalan, V., Daeid, N. N, Kerr, W. J., Buchanan, H. A. S., McPherson, A. R., “Characterization of Route Specific Impurities Found in Methamphetamine Synthesized by the Leuckart and Reductive Amination Methods,” Anal Chem, 2009, 81, 7342-7348.

Other spectra reproduced with permission from: SDBSWeb : (National Institute of Advanced Industrial Science and Technology, 6/9/2020.

Series Sources:
Brown, W. H., Iverson, B. L., Ansyln, E. V., Foote, C., Organic Chemistry; 8th ed.; Cengage Learning, Boston, 2018.
Bruice, P. Y., Organic Chemistry, 7th ed.; Pearson Education, Inc., United States, 2014.
Clayden, J., Greeves, N., Warren., S., Organic Chemistry, 2nd ed.; Oxford University Press, New York, 2012.
Jones Jr., M.; Fleming, S. A., Organic Chemistry, 5th ed.; W. W. Norton & Company, New York, 2014.
Klein., D., Organic Chemistry; 1st ed.; John Wiley & Sons, United States, 2012.
Louden M., Organic Chemistry; 5th ed.; Roberts and Company Publishers, Colorado, 2009.
McMurry, J., Organic Chemistry, 9th ed.; Cengage Learning, Boston, 2016.
Smith, J. G., Organic chemistry; 6th ed.; McGraw-Hill Education, New York, 2020.
Wade., L. G., Organic Chemistry; 8th ed.; Pearson Education, Inc., United States, 2013.

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Hi! I'm Deboki Chakravarti and welcome back to Crash Course Organic Chemistry!

Movies and TV shows are full of instant science. A TV cop brings back a mysterious white powder from some crime scene and lab techs run it through a machine. Seconds later, the substance is identified with a sciencey-looking graph, and the tech says something like, “I thought so.

It's... powdered sugar.” Reality is not so clean or easy or fast. TV has it right on one level. We can use instruments to learn things about molecules, like their mass, different functional groups, or what geometric isomer they are.

But it's not so easy to know what you're looking at, and it usually takes a couple instruments to get a more conclusive answer. Today, we'll look at two important tools that we can use to examine molecular compounds: infrared spectroscopy, and mass spectrometry. And to make it fun, we'll do it through the lens of a forensic investigation….

Let's set the scene: firefighters and police are called to an explosion in a building. After the fire is contained, evidence is collected. Among lots of samples, investigators find what looks like chemistry lab equipment and some white powder in part of the building not affected by the explosion or the fire-fighting chemicals.

Now, let's step into the shoes of the crime scene techs. A sample of white powder has been delivered to us and it's our job to identify it. Time for molecular analysis. [Theme Music].

Before we get too deep into our mystery, we need to set something straight. Spectroscopy and spectrometry are not interchangeable words. Spectroscopy is the study of how matter interacts with visible light and other electromagnetic radiation, from gamma rays to microwaves and everything in between.

These techniques are usually non-destructive, so the sample of our compound won't be changed after the analysis. Spectrometry is the generation of interpretable data, or spectra, from a lot of different techniques, including spectroscopy. Some of the techniques that generate spectra can be destructive, like mass spectrometry that we're going to talk about today.

Basically, the main difference is that spectroscopy is just observing how electromagnetic radiation interacts with molecules, while spectrometry provides data that we can use to interpret the structure. Both of them can be used for individual substances or mixtures, but mixtures are way more complicated, so we'll stick to one substance at a time for now. Okay.

Now that we've cleared that up, let's dive into the techniques. Using a very small amount of sample, mass spectrometry, or mass spec for short, gives us information about a molecule's molecular mass, which is the added-up weights of all of its atoms. Inside a mass spectrometer, there aren't any air particles whizzing around, so it's a vacuum, like outer space.

A sample molecule goes into a chamber and the ion source, which generates a stream of electrons with a high temperature electrical current. In the ion source, a metal gets zapped, electrons get liberated, and that electron stream hits the sample molecule. This technique is called electron impact.

It's a destructive approach, but also one of the most common in mass spec. When this stream of focused electrons strikes a molecule, an electron splits off from the molecule and it forms a radical cation. It leaves behind an unpaired electron -- a radical.

And it's a cation, with a positive charge, because a neutral molecule loses an electron. This radical cation is called the molecular ion. In an ideal situation, it flies down the tube of the mass spectrometer to the detector as-is.

However, electron impact is sort of like a bullet hitting a glass bottle… so sometimes the sample molecule is broken apart into other ion fragments. Any molecular ions and ion fragments are sent down a tube where a variable magnetic field sorts them by mass. This way, only particles of a specific mass can hit the detector at one time.

Then, a mass spectrum is produced, with mass on the x-axis, and the relative number of ions on the y-axis. Technically, the units of the x-axis are m over z, which is the mass to charge ratio. This is related to how each ion traveled down the tube.

Since most ions created by a mass spectrometer have a positive one charge, that equation simplifies down to m over one, or just m: the mass of the particle. Now, the molecular fragments hitting the detector form a fragmentation pattern that's unique to the molecule. For example, let's look at mass spectra for octane and iso-octane, or 2,2,4-trimethylpentane if you wanna be IUPAC-official.

Both molecules have the same molecular formula and therefore the same molecular mass of 114 mass units. But mass spec can tell the two apart! Starting with octane, we notice that the right-most peak on the mass spectrum shows up at 114 m/z.

Knowing the molecular mass of octane, 114 mass units, that peak is the molecular ion. If we subtract the next highest peak, so 114 minus 85, the difference is 29 mass units. This means that the octane molecule split into two chunks here -- one of 85 mass units and one of 29 mass units.

It's often easier to identify the smaller fragment that split off than the big one that got left behind and made the peak. To figure out what the 29 mass unit piece is, we know that one carbon has a mass of 12 and each hydrogen has a mass of 1. Then we can add more carbons and hydrogens until we get to 29.

In this case, 2 carbons is 24 mass units, plus 5 hydrogens is 29 mass units. This gets us to CH3CH2-, an ethyl group fragment! This means that the 85 m/z peak is whatever's left of the octane when an ethyl group splits off.

So it's a hexyl group. There's always a bit of trial and error, but that's what we chemists do best! All of the peaks in the mass spectrum represent different chunks of octane, and we can calculate them.

But here's one peak that's very important to organic chemists: the base peak. This is the tallest peak at 43 m/z. If we do the same math, we know that corresponds to a pentyl fragment splitting off and a propyl group left over, which is what's causing the peak.

The propyl group having the tallest peak means that it has the highest relative intensity, and it's the most stable ion that forms in the fragmentation. Sometimes the most stable fragment can tell us a lot about the structure of a compound. Switching over to the spectrum for iso-octane, we can see that the pattern is very different.

We know its molecular mass is also 114 mass units, so we can see that the molecular ion isn't there. The highest recorded mass is that small blip at 99 m/z. And 114 minus 99 is 15 mass units, which corresponds to the loss of a CH3, or methyl group.

The base peak is 57 m/z. And using the same math, we can figure out that this is a 4-carbon group with 9 hydrogens. The branching of iso-octane leads to a very different base peak from octane.

Over the years, we've developed databases called spectral libraries, which contain known spectra of different molecules. Most operating programs can search through thousands of libraries to give us the most likely matches. But even with the help of computer programs, we still need to use our human brains to think critically and check whether the fragments make sense for our experiment!

Now that we have one tool, let's go back to the mystery white powder from that exploding building. If we run a mass spec experiment, in about 30 minutes, we'll get a spectrum. Then, we can ask the program to run a comparison with a library of spectra to help us identify our molecule.

But the library spits out around 605 matches, which means there are 605 different spectra that could be the spectra for our mystery powder. To narrow this down and get a better sense of the chemical formula it might have, we can use a slightly modified version of this tool. High resolution mass spectrometry is a more sensitive technique with a more focused electron beam that lets us determine the exact mass, which is the molecular mass to more decimal places and therefore more certainty.

We can use the exact mass along with the molecular mass databases to identify the molecular formula! After doing this high-res mass spec on our substance, we learn that the molecular mass is 165.1154 g/mol, and the published tables of exact mass and molecular formula lead us to C10H15NO. The top match for this fragmentation pattern and formula in the mass spec library is 2-methylamino-1-phenylpropan-1-ol.

And the program gave us the common name too, pseudoephedrine. So we're getting closer…. But this white powder is coming from a crime scene and our crime lab training tells us that pseudoephedrine can be used to make methamphetamine.

And the molecules are pretty similar. So it's better to have more data to support our claim. Mass spectrometry can tell us important things.

But, alone, it might not give us information about molecular structure or what functional groups are present. This is where infrared spectroscopy can help! Infrared, or IR, spectroscopy is the study of how light in the infrared region of the electromagnetic spectrum interacts with stuff.

For us that basically means: molecules don't stand still, so IR spectroscopy can measure these molecular vibrations by recording what wavelengths of IR radiation are absorbed. To think about molecular vibrations, we can think of molecular bonds as springs with atoms attached. Stronger springs take more energy to move around, so molecules with stronger bonds need to absorb light with more energy to keep those vibrations going.

A triple bond will absorb light at a higher energy than a single bond. Bonds within molecules can vibrate in different ways, like a stretch, a wag, and a bend. All these dancey-sounding motions need different wavelengths of IR radiation.

So, basically, IR spectroscopy involves blasting a molecule with IR radiation and seeing what gets absorbed as the molecule's bonds vibrate. Then, an infrared spectrum is produced and we can use it to help figure out what molecule it is. The y-axis is the intensity of the absorption, which is related to the kind of molecular motion.

Some vibrations are more intense than others. And the x-axis uses wave numbers as the units. It's a complicated energy term, so for the sake of this already-tricky concept, we're just going to say higher wave numbers mean higher energy absorption.

So let's compare the IR spectra of octane, oct-1-ene and oct-1-yne. Carbon-hydrogen stretches occur around 3000 wave numbers. Looking at the octane spectrum, we see a nicely defined set of peaks around 3000 wave numbers.

In the oct-1-ene spectrum, the peak slightly to the left of those C-H stretches is the hydrogen next to the double bond. Because the double bond is a stronger bond, its C-H stretch has higher wave numbers. Finally, in the IR spectrum of oct-1-yne, that sharp peak is even further to the left and at higher wave numbers because it marks the C-H stretch of the triple bond.

The region of an IR spectrum that's most complex is called the fingerprint region. Kind of like our fingerprints, this region can give us a clue to more complicated molecules. For example, let's compare our old friends octane and iso-octane.

Look at the region from 1400 to 600 wave numbers. Because iso-octane has more complicated connections between atoms, its fingerprint region is more complicated. But aside from this kind of comparison, it's pretty hard to interpret fingerprint regions.

So we usually look for bigger structural clues around 3000 to 1000 wave numbers, like functional groups. Let's look at IR spectra for the molecules butan-1-ol and butanal. The fingerprint regions are different, but there are other differences that let us quickly identify some functional groups.

Looking at butanal, there's a super sharp and strong peak at 1731 wave numbers, which indicates the carbonyl group. This peak is missing in butan-1-ol because it doesn't have a carbonyl group. But there is a strong broad peak at 3300 wave numbers, which indicates the alcohol group.

To double-check this, we can look at butanoic acid, because it has both a carbonyl group and an alcohol group. So its IR spectrum has two strong peaks, this sharp one for the carbonyl and this broad one for the alcohol. In fact, all the carbonyl-containing functional groups we met in the previous episode have a sharp peak at distinct wave numbers.

So this can be a really useful clue. Like mass spectra, there are libraries of IR spectra to help with identification. But, even though it can be a little tedious, we want to be able to recognize different regions on an IR spectrum to make sure our data makes sense when compared to a library spectrum.

And now that we're ready, we'll go back to our mystery substance. IR spectroscopy will help us really decide between pseudoephedrine and methamphetamine, because the first one has an extra alcohol group. In methamphetamine, the N-H stretch shows up as a characteristic sharp peak around 3300 wave numbers.

But in the spectrum of pseudoephedrine, that peak is completely obscured by the broad alcohol peak at 3500 wave numbers. With this extra information, it's probably safe to identify the white powder as pseudoephedrine, the active ingredient in Sudafed-D. Good job, fictional lab tech.

You may not have solved the case, but you solved this one very small mystery! In this episode, we learned about:. Mass spectrometry.

Infrared spectroscopy. And pattern recognition to help identify different molecular structures and functional groups. Next time, we'll delve more deeply into our couch potato friends the alkanes, from where we get them to how they like to arrange themselves.

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