Ch. 15 - Analytical Techniques: IR, NMR, Mass SpectWorksheetSee all chapters
All Chapters
Ch. 1 - A Review of General Chemistry
Ch. 2 - Molecular Representations
Ch. 3 - Acids and Bases
Ch. 4 - Alkanes and Cycloalkanes
Ch. 5 - Chirality
Ch. 6 - Thermodynamics and Kinetics
Ch. 7 - Substitution Reactions
Ch. 8 - Elimination Reactions
Ch. 9 - Alkenes and Alkynes
Ch. 10 - Addition Reactions
Ch. 11 - Radical Reactions
Ch. 12 - Alcohols, Ethers, Epoxides and Thiols
Ch. 13 - Alcohols and Carbonyl Compounds
Ch. 14 - Synthetic Techniques
Ch. 15 - Analytical Techniques: IR, NMR, Mass Spect
Ch. 16 - Conjugated Systems
Ch. 17 - Aromaticity
Ch. 18 - Reactions of Aromatics: EAS and Beyond
Ch. 19 - Aldehydes and Ketones: Nucleophilic Addition
Ch. 20 - Carboxylic Acid Derivatives: NAS
Ch. 21 - Enolate Chemistry: Reactions at the Alpha-Carbon
Ch. 22 - Condensation Chemistry
Ch. 23 - Amines
Ch. 24 - Carbohydrates
Ch. 25 - Phenols
Ch. 26 - Amino Acids, Peptides, and Proteins
Ch. 26 - Transition Metals
Purpose of Analytical Techniques
Infrared Spectroscopy
Infrared Spectroscopy Table
IR Spect: Drawing Spectra
IR Spect: Extra Practice
NMR Spectroscopy
1H NMR: Number of Signals
1H NMR: Q-Test
1H NMR: E/Z Diastereoisomerism
H NMR Table
1H NMR: Spin-Splitting (N + 1) Rule
1H NMR: Spin-Splitting Simple Tree Diagrams
1H NMR: Spin-Splitting Complex Tree Diagrams
1H NMR: Spin-Splitting Patterns
NMR Integration
NMR Practice
Carbon NMR
Structure Determination without Mass Spect
Mass Spectrometry
Mass Spect: Fragmentation
Mass Spect: Isotopes
Additional Practice
IR Spect: Frequencies Considering Solution Effects
IR Spect: Structure Determination
1H NMR: Proton Exchange
1H NMR: Fast Proton Exchange (D2O)
13C NMR: Cumulative Practice
Mass Spect: McLafferty Rearrangement
Structure Determination with Mass Spect

Concept #1: Equipment and Theory


Hey guys in the next few sets of videos I'm going to be breaking down step by step how to understand an analytical technique called mass spectrometry, in this video I'm just going to introduce the general concepts of mass spec including how the equipment works and how to read a mass spectrum, so guys mass spec is an analytical technique that's used to weigh your sample so you place a sample of an unknown molecule through a mass spectrometer strong mass spectrometer and it should tell you the weight of your molecule, OK? Now the way this is accomplished usually is through a process called electron impact ionization or simply EI this is the most common form of mass spec and it has to do with electrons hitting your sample at a very very high speed so guys here have the general scheme of how a mass spectrum works like the actual equipment and what you do is you have your unknown sample so in this case you can tell that my sample is methane, I know it because I happen to draw it but if I was out in the field I might not know what the sample is so I'm processing through my mass spectrometer and what's going to happen is it's going to go through a series of steps whereby at the end I can actually tell what it's molecular weight is so let's go ahead and follow the bullet points I'm going to go over how this machine works so the first thing that happens is that electrons are going to be beamed at these molecules remember that I said that this is called electron impact ionization so you're going to be shooting very high energy electrons at your molecule and what this is going to do is it's going to generate a high energy intermediate called a radical cation so where is this happening? If we're looking at my diagram this will happen right at the ionization phase, OK? So your sample is a first vaporized, it's turned into a gas that's over here so that you're putting a gas through your mass spectrometer and then we're ionizing it, we're shooting these very fast single beams of electrons at the molecules and trying to break them apart essentially, OK? So when you break it apart you're going to get something called the molecular ion, OK? Now what a molecular ion is it's your same exact molecule but it's with one thing missing and what it is that it's your molecule missing one electron let me show you how this works. Imagine that this carbon initially has 8 octet electrons, right? Remember that every second row element most of them want to have 8 electrons to fulfill their octet well after I shoot these high energy electrons at my molecule what's going to happen is that one of them is going to get dislodged that's what I'm counting on I'm counting on one of these electrons is going to go missing it's going to just bounce off and what's going to happen at the end is that we get this thing called the radical cation so what you can see is that the radical cation is the same thing as the before it's the same molecule but instead of having 2 electrons for this bond I only have one, OK? So imagine that basically that electron is now one of them is missing so that is what my radical cation is called that's how it's made and the reason it's called a Radical cation is because first of all it has a radical now it just has 1 electron between those atoms instead of 2 but also the entire molecule has a positive charge because as you can see we're missing an electron So that means one of these one of.... Basically this entire molecule is going to have a net charge now, OK? So the way we symbolize in short, a molecular ion is we write capital M and then we write a positive and we write a radical and this is the same way to say that it's a radical cation because it has both positive character and it has a radical you may also see in your textbook or in your homework that it's abbreviated as M + radical to the side it's the same thing just a different way to draw it but I like to draw them up and down it takes less space, All right? This is also by the way it's also called the parent ion, so if you hear parentsÕ ion if you hear molecular ion if you here radical ion these are all the same exact things you need to know your terminology. Alright guys so now we've ionize my sample, right? That's the ionization phase what happens to the rest? You can see there's other stages it says deflection, detection there's a magnet what's going on? Well guys it turns out that only some of these fragments are going to be magnetically sensitive, OK? And it's the ones that are charged so it turns out that fragment cations, OK? Whenever you get a cation produced by the ionization of this molecule that's going to be deflected by the magnetic field but not all cations are alike it turns out that smaller ones are affected more than bigger ones so that means that this is just due to physics due to inertia imagine a small ion if it's moving through the 2 it's much easier to deflect it because it has very little inertia whereas a large ion if it's very very big it's going to be more difficult to change its path it's going to be more difficult to accelerate it and to deflect it, OK? So what this does is it gives us the ability to detect where these radicals are....I'm sorry where these cations are hitting if it doesn't deflect very much I know it's really big and heavy if it deflects a lot then I know OK this thing small and that's exactly what happens here, it passes through a magnet where it gets deflected and I detect how much did it get deflected and through this I'm able to determine how big the mass is so what we actually get as a reading for a mass spectrometer is not exactly mass but it's close what it's called is the mass to charge ratio where your mass is equal to M....That's an ugly M let's do this again your mass is equal to M and your charge is equal to Z, OK? Now we just stated what kinds of charges are sensitive to the electromagnetic? Positive charges, OK? Cations so what that means is that even though we're detecting the mass to charge ratio MZ really Z is usually going to be equal to 1, right? Because we said that the ones that are sensitive in getting detected are the cations so that means that even though you're detecting mass over charge what this really equal is mass over 1 because the charge is always 1 and any number over 1 is just itself so what that means is that really this is just a fancy way to determine the molecular weight of your catatonic fragments the ones that are positively charged, is that making sense so far? So now we've got the mass of your fragment, OK?

Now we have to learn in terms of finishing this page how are we going to read a mass spectrum were given one? So guys here is the mass spectrum of our molecule, OK? This is what we would actually get in the reading and what we would see is that the radical cation, remember that the radical cation only had an electron missing so the radical cation is going to have the weight of the initial sample, OK? So remember that the formula for this is CH4 and if you were to approximate the weight of this molecule carbon is equal to 1 2 and your 4s..I'm sorry and your Hs H4 is equal to 4 so you should get 16, OK? And that's exactly what the mass spectrum says it says that the largest peak, the largest peak the base peak is my radical cation, now you may be wondering Johnny how can it have the same weight as it did originally if you knocked away an electron? But keep in mind guys that electrons don't really count towards more molecular weight because they're so tiny they have such a little mass that you can afford to knock it off and your molecule is basically going to have the same mass, OK? So really what we're doing is we're just measuring the weight of our radical cation here this is what we would call our molecular biology ions so that would be M+radical, OK? But now we see that there's these other peaks on our mass spectrum as well, there's one at 15 there's a smaller one at 14, what's going on there? Well guys these would be basically fragments, these would be catatonic fragments that formed because this molecule was hit with very high energy electrons so sometimes it's just going to knock off an electron and that's all that happens but sometimes it's going to bust the molecule open so the 15 would be what we call our M-1, OK? Cause it's out molecular ion minus 1 but why is it minus 1? Well that would be losing a hydrogen that would be if I actually knocked off an entire hydrogen instead of just knocking off and electron I would get 15, OK? And what you can see is that is this a common fragment? Absolutely, notice that my M-1 peak is almost as tall as my molecular ion, why is that? Well because it's very easy for methane to knock off one hydrogen, OK? But you can see that the more hydrogen you have to knock off the less probable it is to get these signals and that's exactly what happened so 14 that would be that I'm knocking off 2 hydrogens, right? This would be my M-2 it's much more difficult to get that because you can see that the number is far far lower so it just kind of makes common sense that the more atoms you have to knock off of this fragment the less likely you're going to get it the less you're going to detect it in your mass spectrum, OK?

Now I just want to point out a few other things about how the axes work here, the X axis is easy mass to charge you guys already know that that really just stands for mass, right? But I haven't talked about the Y axis yet which is the relative abundance, we're saying that there's 85 percent of one, a 100 percent of another what does that mean? Well guys it doesn't mean for example it doesn't mean that 85 percent of you are noticed that I have an 85 next to 15 guys that does not mean that 85 percent of the whole is made out of your M-1 well all it means is that compared to your tallest peak which my tallest peak here happens to be my radical cation, right? Happens to be the molecular ion compared to the tallest peak which is the 100 I have 85 percent of my M-1 so essentially all this is saying is that if at the end of the day I run my whole spectrum and I get 100 of these molecules I should expect to find 85 of these, Ok? So it's just 85 percent as likely as the base peak, OK? Now that comes to another term where I keep using this term base peak.

Concept #2: How to Read a Mass Spectrum


So the base peak of the sample is simply going to be the tallest peak out of all of them and we always scale the base peak to be 100, so that means that we make our base peak 100 and then we compare everything else to that, okay? Now, in this case my base peak happened to be my molecular ion, right? The m plus radical, okay? But, this isn't always the case later on when we talk about fragmentation, what we'll see is that sometimes the base peak is actually going to be one of the fragments because sometimes the fragments are more stable than the molecular ion themselves. So, in this case I gave you a simple situation where the base peak is actually equal to the molecular ion but we're going to see later on is that sometimes one of the smaller fragments is actually your base peak and your molecular ion is lower because it's more common that it fragments than that it doesn't, does that making sense? Awesome guys, so this is just an intro. Now, what we're going to do is we're going to go more into fragmentation patterns and we're going to talk about isotopes, okay? By the way, I want to point out one thing, which is that notice that there is a tiny peak at 17 that I didn't talk about, how did that happen? does that mean it has one extra hydrogen, will get there, okay? That's its own kind of phenomenon but for right now just focus on 16 and below because that's what we can understand through the process of ionization. Alright, so let's move on to the next video.