Subtitles section Play video Print subtitles >> Good morning. >> Good morning. >> I think we'll get started here. This is Organic Spectroscopy and it's a course I've been teaching for a bit, and I'm really looking forward to it. I am not a spectropiscist and that's good. Because when I started to teach this course my thought was, "Oh my God, I'm just somebody who uses spectroscopy and I've been using it for a long time [inaudible]." I'm not a purist. I'm not a [inaudible]. I just use it in organic chemistry. I realize that's [inaudible] what people want in learning this course. So what I'm going to do over the next 10 weeks is share my take on spectroscopy with you and how [inaudible]. We're going to be going over a bunch of different techniques and we're going to try to break it into certain core techniques that I think valuable. I'll tell you a little bit more about that when I tell you about the syllabus. Here's the website for the course. The website has copywriter materials, not my own materials, I don't care about my own materials but I do care about respecting other people's copyrights. And so right now the site is unlaunched, but it will be launched and you can get the materials under what's called "fair use copyright law". Meaning that a professor can give a handout to the class but just can't sort of broadcast it on the internet. The handouts a little piece of a book or a paper or [inaudible]. All right, the website will have your assignments. I've already made a tentative schedule of assignments. It's probably a good idea to check that just in case we change anything. I know for example there will be a few minor changes to this [inaudible]. I got a bunch of class materials here. We'll be pulling on these at various times. For example, our first discussion section will actually focus on molecular modeling and there's an exercise here we'll be pulling on there. There's also some software. Was anyone able to install the software okay? Mac people figured out Mac [inaudible]. Mac people figured out how to rename? >> I think so. >> All right, so we'll be drawing on that one exercise in during our first discussion section. One thing I'm doing -- I always like to try and do things a little differently in the course. It keeps things interesting for me. Also I like to try to get people's feedback on the course and incorporate it into the next years version of the course. So like 2 years ago people said it would be really good to have a practical component of the course. Meaning how to learn how to run these experiments, and so we implemented that last year. Then people said, "Well, it's a lot of work. Can you cut back?" So I've made some trimming to that. So giving feedback as we go along. It is going to be a course with a lot of homework, and the assignments will get [inaudible] at the end. I'm pretty liberal about giving extensions where you need it. I know last year people said, "Oh it's really heavy. Can I get an extension?" It's like okay, can we get these problems done on time for our daily discussion section and then you can get an extension on the other stuff. So let me know if things get really unmanageable and [inaudible] stuff. If you're not comfortable coming to me, come to Bryan whose in the back, who is the teaching assistant for the course and an A student from last year. All right. Let me tell you what I wanted to go to. [Inaudible] version of the syllabus here. All right. So, as I said here, here's the textbook, here's the website. It'll be password protected with [inaudible] trivial name and password. Just something so we're not broadcasting all this to the whole class. Textbooks. The Silver Stein textbook is a really good one. There are a couple out there. There's one I absolutely love and have assigned as a reference, but it's not really readable and not really friendly and that's the Phil Cruse book, which is a little more hardcore. The Silver Stein one I think is more accessible. There's a supplementary book and it's really table reference component of reference boundaries, and it's by [inaudible]. And I hate to make people spend money. Last year, I think in past years people have found this is really handy to have. If you're looking and saying, "Well, Silverstein's already was 120 bucks or something." Or if you're saying it's a lot of money, you want to share the textbook, you can do that by [inaudible]. All right, as I said, I want to incorporate a molecular modeling component to the class. The reason I have done this is so much of our thinking as organic chemists involves stereochemistry and conformational analysis. Organic spectroscopy as most of you are going to use it, is not about what I'll call structure [inaudible]. It's not about you get this wildly random unknown compound and you have to figure out the structure. That's part of it. You get some surprising product from a reaction. But usually you have some idea what's going in there and its more specific questions that you're asking. I got something where I know the basic structure but something's changed or I don't know the stereochemistry and I want [inaudible]. Molecular modeling ties integrally to those types of questions and as we get into topics like coupling constants and the Nuclear Overhauser Effect and NMR spectroscopy, those are going to be very relevant. It's going to be extremely useful to have molecular models. This is also part of the standard toolbox of practicing organic chemistry. To be able to make simple molecular chemists based molecular models that will tie into 201 and 202 when you get conformational analysis. So we should be able to come up to speed on that in a single workshop and exercise, and we'll do that on Monday. My license for the software actually allows me to distribute it to all my students, which is kind of cool because I paid 800 bucks for this whole license and then they said, "But you can give it to all your students." I said, "Well then darn it, I'm going to share it with as many of my students as possible." So the one thing you really, really need for this, and I'm not kidding, because I know you can use option [inaudible]. But you're going to be using those [inaudible]. You should be able -- if you're a Mac person you probably don't have one of these or wouldn't have had one of these. You can get it for like 9 bucks [inaudible] bookstore or [inaudible]. But you need to buy one [inaudible] our workshop on there. The other thing that you need for the class is a real ruler. Not one of these [inaudible] rulers from elementary school. [Inaudible]. I recommend one of these clear ones here. [Inaudible] chem stores or bookstore. Anyway, it's on the website. You'll be using that to measure integrals and so forth. All right, what else do I want to say on here? So we're going to start with a week talking about infrared spectroscopy. We've had this in organic chemistry. I'm going to give you my perspective on what's important. We'll get some answers [inaudible]. We're going to then go for about a week on mass spectrometry, and one of the travesties in the teaching of mass spectrometry is it still is so focused on electron ionization mass spectrometry while people are moving away from that. We'll have one set of problems, one group of problems that asks some questions related to that. We'll have probably one lecture on that. But there are concepts that I want to bring in on exact masses and isotopic abundance that aren't hard. They're not particularly profound, but it will be nice to have a chance to go over. So we'll spend about three lectures on that. We're then going to move on to [inaudible] spectroscopy and we are going to actually spend a solid amount of time on [inaudible], and the reason comes back to the concept of analysis. You get what the NMR spectroscopy [inaudible], and you kind of get the basics but there are a lot of concepts involving coupling and other things that are really, really important, and [inaudible] patterns that give you deep, deep information. And I want us to really master that. We'll be applying that in [inaudible] analysis. Then mid-term exam is actually going to focus up to this point. So we're not going to have [inaudible] the mid-term exam. That will be [inaudible] of the class, and we'll concurrently be [inaudible]. And I'll give you a basic suite of about six [inaudible] experiments that really constitute core knowledge of the material that you can easily get lost in the [inaudible]. All right, I wanted our problem sets to be sort of a capstone to the chapter. The real learning is going to come from working [inaudible] in the course, and what we're going to do is we're going to be together on Mondays and discuss the problems. As I said, first Monday will be next Monday and [inaudible] Monday. We're not going to have a problem set due. We'll get to the other in 108, and have a workshop on molecular [inaudible]. The second one will be [inaudible] exercises and modeling exercises. [Inaudible]. Anyway, come prepared. We'll be discussing stuff, annotate your homework before handing it in. Let's see, what else do I want to say? So the exams, I like the idea of open book exams and I like the idea of [inaudible]. Basically the exam is a problem set where you're going to [inaudible]. There's one closed book prior to mid-term and I want to give you time because it takes time to do problem sets, and so we're going to have them spill onto Saturdays [inaudible]. [Inaudible] dates of them. November 5th and then we got the final exam, the final exam is going to be December 10th. Grades. Graduate school isn't about grades. For the most part everyone is going to get an A, an A minus, a B plus. It's not going to have a huge impact [inaudible] grade [inaudible]. But it's going to have a huge impact for you in terms of how much [inaudible]. Because what you really want to be shifting from as you come into graduate school is getting away from this mindset of being a student where grades actually are for something, to being an independent [inaudible]. What counts is your ability to solve problems and analyze problems, and just about all of you are going to use [inaudible] spectroscopy as part of your toolbox for solving research problems and it just [inaudible]. To put it another way, this is a really scary time to be getting a PhD in science because pharmaceutical industries and others [inaudible] and there isn't a lot of room out there for people who are not as good as they can be. So when you're thinking about stuff motivating you of course an A grade is a pat on the back and it says, "Yeah you're doing a good job. That's nice." But really the bigger picture, you know, the whole pat on the back, I got a 10 on the problem set or I got a 95 on the mid-term exam is the face [inaudible] and that's what you should be [inaudible]. So the mid-term counts, the final counts, discussion, problem sets and classwork participation count. [Inaudible]. All right, office hours. Come by and catch me. Don't be afraid to catch me in my office. I think Ryan is also going to have some office hours before the problem sets are due. So I think he's picking the area outside my office. I'm in 4126 Natural Sciences 1. He's picking the area outside my office, that little interaction space with couches and blackboards right after -- do people have anything on Monday's? Right, is there a discussion on Monday's [inaudible] time? [Inaudible] >> TA meeting. >> All right, Ryan why don't you [inaudible]. Ryan why don't you send out a sign up sheet just [inaudible] email and just find out what works. Let's do a signup sheet and see [inaudible]. How many have Monday lab [inaudible]? [Inaudible]. How many people have a TA meeting on Monday [inaudible]? Okay, so it sounds like maybe [inaudible] 2:00 o'clock or something [inaudible]. So maybe -- it sounds like [inaudible] 2:00 o'clock on Monday? >> I think 4:00 would be better. >> Four? >> [Multiple speakers]. >> Four? Yeah let's do -- I'm sure we could do 4:00 o'clock on Monday. [Inaudible]. All right, as I said, homework counts. All right, academic honesty. At graduate level I don't think anybody is intending to cheat in the course. What I'm asking of you is to not go back to last years problem sets for previous [inaudible]. Not to go back to last years problem sets [inaudible]. I understand people work together. I think that's okay. In fact the whole theme when we come in is going to be [inaudible] a problem set. The first thing I'm going to do in discussion is say, "Do you have any questions?" More specifically, which questions do we want to discuss? And then before [inaudible] and you can annotate your problem set and get credit for it. I do ask you to annotate them in a different color pen. You will get credit. I ask you not to use the discussion section as a chance to basically not do your homework [inaudible] everything. Obviously there's a difference between working together and not doing your own thing, and I'll give you a perfect example. Most of the NMR problems as going to involve some level of analysis in addition to structure solving. In other words you may be solving the structure, but then you're going to be assigned [inaudible]. Honestly, you get a structure and it's not the right structure and then you talk to a classmate and they say, "Oh I got this structure", and you're like, "Oh, that makes sense." You still have the analysis part of the problem to do on your own and to figure out what those [inaudible] are. That's a perfect example of doing your own work after having solved it, after having done it before, and recognizing the fact that it's not simply copying [inaudible] assignment, the residence assignments. If you're copying the residence assignments you're doing it wrong. Similarly in practical component to the course [inaudible] for people to go down to the [inaudible] spectrometer together to have a cooperative learning [inaudible]. But if you're not collecting your own FID and processing your own FID and you're just submitting your classmates spectrum that's not okay. [Inaudible]. >> [Inaudible]. >> I think that's great. I mean it's honestly it's not going to hurt you and I think it's a wonderful way of [inaudible]. You know, in professional science we've started to move more and more to this. Not all journals do this but one of the things a lot of journals are doing now in authorship is asking the authors to submit what each author contributed and they're asking all authors to take responsibility [inaudible] paper. But they want to know what each person contributed. So and so did the laboratory work in the paper. So and so was the professors [inaudible] the students and helped write the paper. That's the sort of thing they want to know. so I think that type of transparency will work at this level, is fantastic. [Inaudible]. All right, other questions [inaudible] or just in general? All right. I guess the last thing; be here for the class and by that I mean be here, not on Facebook, not text messaging. It's probably not necessary in graduate class. Don't be cruising around the internet. Yes I'm going to get up videos of the class but be here for the class. One person already came to me, this was a great example for use of video, and said, "I can't make thanksgiving needing to travel back east." And I was like, "Great, well we'll have it up there on video and just download it and feel free to use them as you want." All right, I'm going to -- I have a list of topics we're going to be going through those later on. But I think that we need to, you know, I'd like to at this point get on with today's talk and start talking about IR unless there are any other questions. >> Will the videos be posted on [inaudible]? >> The videos will be posted on the site yeah. This is an experiment this year being done as part of UCI's open courseware program which is [inaudible] who's doing today's daily, and so the hope is that they're going to end up in addition to on the site on the open courseware site, on iTunes U, on YouTube and a bunch of places which actually brings to mind something. We're not going to film the discussions with the exemption of the molecular modeling one which is kind of the same format as regular class. [Inaudible]. So for the most part the video is catching the back of your head. If you're shy or concerned that you don't want anyone to see you, to see the back of your head on YouTube basically just sit out of the course of the video camera. But no one is going to be filmed at the blackboard here for example [laughter]. Unless you want to be, in which case [inaudible] come on up and I'll [inaudible] [laughter]. All right, I want to talk about IR spectroscopy and I want to give my take on it. I really believe for those of us who are doing [inaudible] that involve any sort of inter-conversion of functional groups with molecules that are not huge in size, you know, basically maybe the exemption of some of the things [inaudible] big molecules. For people who are doing synthetic methods, synthetic methodology or just anything that involves the synthesis of building blocks IR spectroscopy is really the first technique you want to [inaudible] for your reaction. IR spectroscopy is good at identifying functional groups. And for the most part when you are running a reaction you're doing something that involves changes to functional groups. You're adding a nucleophile to a carbon yield compound and it's going from a ketone or an aldehyde to an alcohol. That's a huge change. This is the sort of stuff an IR [inaudible] and telling us about, and to some extent MNR does. I want to give you an example from my own branch of work that's just a revelation. It's basically realize every experiment you're running is testing a hypothesis. You have an idea and the question becomes what actually happened? So [inaudible] reaction expected this to be simple [inaudible]. I had dylophenal acid [inaudible] and I wanted to do an Aldol reaction [inaudible] LDA and then treated that with cycloexinol and then did an [inaudible] workup [inaudible]. And what I expected to get of course was the alcohol product. And what I got instead was a product with a really strong band in the IR. At 1,820 wave numbers. And I knew my data was screaming at me because the reacting -- you should be running your reactants. IR and NMR you should be using your chance to do chemistry to educate yourself. Your -- the reactant to dylophenal acetate has a band, a carbonyl band of 1,610 and so you'd expect the product to have a band of 18 and 1,710 for this and maybe an alcohol band [inaudible]. And this thing was [inaudible]. It was tremendous and 1,820 stands out. [Inaudible] and I knew exactly what it was right away and I though this would be really cool. It turned out this ended up being the basis for the rest of my dissertation [inaudible] on work. It was a discovery and that was cool. What had happened was under the reaction conditions even at low temperature it cyclized and formed a beta [inaudible]. Not surprising in hindsight, but unexpected and actually [inaudible] way more than [inaudible]. And so that was cool. IR can tell you that type of information in an instant. Now, all right, I want to talk a little bit about how IR works today. Then I want to talk a little bit about my recommendations on running IR experiments because I want them to be easy for you to run. Again, my take on things for theory is very, very basic. It is like an organic chemist because that's what I am, and the theory is basically that we're looking at transitions between [inaudible] vibrations [inaudible]. All of your molecules are going to be in the ground vibrational state and you're going to be exciting them to the first vibrational state. The most important vibrations are stretching vibrations. And stretches vibrations are exactly what you'd expect. You have a bond and it stretches. And remember, think back to G-chem, zero point energy even in the ground vibrational state your bond is vibrating. I want to represent it in very simple language or simple diagram I can say here's a CH bond and it's not static. It's getting longer and shorter, and what's happening is when it absorbs a photon you kick it up a notice and it vibrates more quickly when you're looking at that photon getting [inaudible]. All right, one thing, and this is really of practical importance, is that while we can think of a bond as an atom connected by -- as a ball connected by a spring to another ball, right, your basic quantum mechanical [inaudible] isolator what's happening with many vibrations in a molecule is [inaudible]. In they're practical implications this -- and I'll show you one example today and another example when we talk about it [inaudible]. So okay, so CH2 are not very exciting. Not a really hot function. The CH2 group you end up having two vibrations associated with it. One is a symmetric stretch. And 2,850 wave numbers. And by a symmetric stretch I mean if my body is the carbonide and my fists are the hydrogen atoms we're talking about a motion like this where the two are moving in concert. And then another stretch is asymmetric stretch. And about 2,925 wave numbers. And so an asymmetric stretch means one bond is getting longer while the other is getting shorter and you have this kind of concerted motion. So most of what you're going to be looking at, just because it's in what we'll talk about is the functional group region are stretching vibrations. Also of importance are bending vibrations. And by bending vibrations I just mean a scissor motion where the bonds aren't getting longer and shorter. And again you get coupling between these motions. So for example, I'm a CH. I'll just diagram this [inaudible] you can imagine this as sort of a scissoring in and out like so forth. And here you're also going to have two. You're going to have an [inaudible] bending at 1,465 wave numbers and an out of plane bending at 1,380 wave numbers. And this is below the main functional group region so you're not going to be paying a heck of a lot attention to it. All right. There's a really important principle and you'll see the practical implications of this in the second [inaudible]. For regular IR spectroscopy, not [inaudible] spectroscopy which actually is covered in the newest edition of the textbook that I am currently in the process of reviewing, for regular infrared spectroscopy an allowed transition, the transition that you can observe has to involve the change in [inaudible]. So let me give you a really simple example, which you will actually see in advertantly as part of your work in the course of using an FTIR spectrometer. So carbon dioxide; carbon dioxide, just as I said on couple vibrations you're going to have coupled CO stretches. So you have -- here you have a really big couple. The symmetric stretch is at 1,340 wave numbers and the asymmetric stretch is at 2,350 wave numbers. [Inaudible]. So remember the symmetric stretch is like this and the asymmetric stretch is like this. Which one of these stretches actually has a change in [inaudible]? Only the asymmetric stretch. So the 1,340 stretch is inactive and the 2,350 stretch is active, and the practical implications of this is if you're using an FTIR spectrometer and you go ahead and you put your sample in the [inaudible] you're putting carbon dioxide in the cavity and you will actually see [inaudible] bands and with CO2 you'll actually see the rotational fine structure but you'll see this little fuzziness at about 2,350 and that's your breadth, that's the carbon dioxide component of your breadth. So the other practical implication of this becomes four functional groups. So if you take something like an alkyne. And so let's take as our example two [inaudible]. So normally you would see a carbon carbon triple bond stretch. And two [inaudible] isn't exactly symmetrical but it's pretty darn close and so you are not going to see a carbon carbon triple bond stretch. So what is that mean? That means if you're saying, "Oh, I'm looking for an alkyne in the IR." You say well I don't see a band without 2,100 in the IR so I can't have an alkyne. You're going to be wrong because you're just not going to see it because that stretch for all intensive purposes is not active because you don't have change in the [inaudible]. If you go to internal alkyne where now you have some dipole to the fine, right, the CH2 group and alcohol group is an electron donor so this end of the alkyne is going to be a little bit more electron rich than this end, so I can designate this delta minus and delta plus. Now, when that CC triple bond is stretching you're actually changing the dipole moment. Why do you change the dipole moment? Well, you have two partial charges and as you increase the distance between them and decrease the distance between them the dipole changes. So when you excite it to the first vibrational state or the first excited vibrational state you get change in dipole moment. So here you do see the CC stretch and C triple bond stretch. Seen at about 2,120 wave numbers and I'm going to say it's kind of moderate intensity. Carbonyls really stand out at you. That [inaudible] acetone I gave you is an example of the strongest peak in the spectrum because you've got a really big dipole for carbon yield and it's even bigger for [inaudible] acetone because of organization of bond. But here you're going to have a weaker stretch. All right, another example I put on, on my alkyne, if I lets say have an alto alkyne. So let me take methoxypropane. Which way is this triple bond going to be formed? [Inaudible] more negative charge on it. [Inaudible]. >> [Inaudible] process. >> [Inaudible] residence. Think like an [inaudible] because it's just an alkyne version of an [inaudible]. So the oxygen pushing electron density [inaudible] residence structure like this again here so you've got a delta minus delta plus. So here again you're going to see it, and this is actually strongly [inaudible]. This will be strong. So IR spectroscopy really can talk to you about what's going on in a molecule and certainly in the example I gave talked to me. All right, I want to take a moment at the very simplest level to discuss part of the theory and that's simply the effect of bond strength and mass. And I'll show you a couple of practical examples. So if you think back to you P-chem and you think back to your harmonic oscillator, your quantized, quantum mechanical harmonic oscillator you probably saw a diagram that was something like this. You have two masses connected by a string [inaudible] constant K. Everyone seen something like that? Okay. And you probably remember a solution that involved the term reduce mass. Does that strike horror in the back of your mind from P-chem? All right, so if you solve this oscillator you get the nu bar, that's your frequency in wave numbers is one over two times C times root K over mu. Mu is the reduced mass, K is the forced constant and mu is equal to M one, M two over M one plus M two. I'll talk more about nu bar in a second. I'll talk more about wave numbers. But I want to give you a very, very simple practical application. I wanted to tell you the [inaudible] of this. So you take a CO single bond and -- actually let's start with [inaudible]. You take a CO double bond, right, the carbon yield is [inaudible] in balance at 1,700 wave numbers. [Inaudible] little squiggly to indicate [inaudible]. Now off the top of my head I might not know, or for the purposes of this course really [inaudible] where a CO single bond shows up except [inaudible]. And so I'm going to tell you where it typically is at and it varies a little bit. But about 1,100 wave numbers. And you look at this ratio and you say okay, what's he saying? He's saying if you double the forced constant you increase the frequency not by a factor of two but by a factor of the square root of two. And so it makes sense that single bond isn't going to be half of a double bond in its frequency, it's going to be about one over two. If I had 1,200 it would be one over mu. Single bonds vary here. So I'll say almost, I'll say approximately one over mu [inaudible]. Now, why is this important? Well, let's say we talk now instead of about carbon yield, about carbon nitrogen double bond and say well I don't know that much but I know that, you know, I haven't seen any so I haven't worked with any of those. But I know that in reduced mass of nitrogen, you know, once you plug in here, right, because you've to 12, you've got 16 for oxygen, 14. You've got 12, and 16 and 14; the reduced mass isn't going to differ by a heck of a lot. And the bond strength isn't going to differ by a heck of a lot because carbon nitrogen bonds are pretty similar. You should say, okay, now even if I didn't have a table, even if I didn't have a look up I could say, you know, [inaudible] are going to be somewhere in here. And conversely you could say okay, where's my carbon nitrogen single bonds going to show up? Well they're going to be somewhere about here as well. And so you can bootstrap on information with just a little bit of knowledge. And I think that's one of the really, really [inaudible]. I'll show you another example. All right, show you another example. Let's take chloroform. Chloroform's a common solvent for running IR spectrum these days. CL3 CH, and I'll tell you that it's at about 2,030 wave numbers. And so okay, if you want to be lazy, it's not a crime to be lazy. If you want to be lazy, because I said, you should be getting an IR spectrum. Not saying Oh, [inaudible] write the paper, do my thesis, and do my orals and characterizing. This is a question you're asking. So, okay you want to be lazy and throw your NMR sample in an IR cell, and you don't even want to dissolve it out, and you say okay, where did CL3D show effect? Okay, well the force constant is going to be the C. so, it's just the reduced mass that's changing, right? So, mu for CH, and I'm not going to use exact numbers. I'll just say 12, you know, plus one, instead of 1.007 whatever it is, over 12 plus one is the reduced mass for CH bond and for a CD bond the reduced mass is 12 times two right? Deuterium has heavy hydrogen. It has an extra neutron in there, over 12 plus two. So here we have 12/13 and here we have 24/14 as our numbers. The force constant has got to be the same so you can take this equation, you can back out the force constant into one over two pi C term and you get that nu bar CH times root mu CH is equal to nu bar CD times root mu CD, right? That's just from saying all right we're going to go in to back this out over onto this side and [inaudible] put the two halves in. So, we get 32, we get a 30/20 times root 12 over 13 is equal to mu is equal to nu bar CD times root 24 over 14. So, I would predict that the number for our CD stretch, the wave numbers for our CD stretch is at about 2,216 reciprocal centimeters, and that would be a pretty darn good prediction. I mean remember, this idea of treating this as an isolated mass, just the carbon without coupling to the [inaudible] is an approximation. The actual is about 2,250 wave numbers. So, if you end up throwing your sample into your NMR sample, into an IR cell, and taking a solution phase R, IR and you see a peak from the deuteron chloroform. That peak is going to be right at about 2,250. And so don't say "Oh, I have an alkyne, or oh I have a nitrium, which is another thing that shows up [inaudible]. All right so, I glossed over this issue of frequency and I just want to come back to that for a second. All right, so let's come back to our carbon yield as sort of the archetype for IR spectroscopy. So, 1,700 CM to the negative one, the term that we use for this unit, CM to the negative one is wave numbers. And so, what do I mean by wave numbers? So, that's our re bar, nu bar term. So, what do I mean by wave numbers? Well, wave numbers is equal to waves per centimeter. So, in other words, when the light travels one centimeter, you have 1,700 waves. Well, if you had 1,700 waves per centimeter then your wavelength is 1/1,700 of a centimeter. That's your lambda value, and that's equal to 5.9 times 10 to the negative four centimeters, or 5.9 microns, 5.9 micrometers. Now, you typically run a spectrum from say 4,000 to 600 wave numbers. That's sort of where our typical IR spectrometer works. So, looking at the 4,000 end from about 2.5 microns to about 17 microns. If you ever grind a sample to make [inaudible] pellet and you don't grind it fine enough, you don't grind it so your particle size is below about 3 microns, then the light at the shorter wave lengths is going to get scattered and not absorbed by the particles. And, this is actually pretty common. If you don't do a good job of grinding your sample, you're going to lose the CH region of your spectrum, right? Because that's at 300 wave -- no 3,000 wave numbers. So, that's at like 3.3 microns. So, if your particle size is bigger than 3.3 microns, you won't see your CH peaks. And you'll say "My gosh, I made a compound. It's got to have some CH's in it, but I don't see the peaks." All right, let me at this point take one moment to talk about the instrumentation. So, the instrumentation uses an infrared spectrum spectrometer. And I'm going to show you two real flavors of this instrument but first, I want to show you a fake flavor of the instrument to get into your mind. In the simplest concept, so this is only a concept. In the simplest concept what you are doing is generating IR light, meaning heat, wave length light from a glowing coil. It's passing through the sample, it's getting absorbed at different frequencies. You are breaking up the light with a grading or prism, and again this is a schematic, an over simplification, and you are detecting it. At the simplest level you are simply looking at what light of what frequencies is being absorbed. In practice there are many implementations of this idea. The simplest is a double beam instrument. In a double beam instrument you are actually comparing the amount of light going through a sample, and the amount going through reference. So you have a source, the source is going out to a sample, and a reference, it's coming to a mirror that's allowing the two to be compared, the mirror is going to a grading or prism, and that's going to the detector. And there's still some of these instruments in the department. All right, that is still easy to understand conceptually because it is the exact same concept as my gross, gross, gross, gross over simplification here, making up for the reality that your cell may absorb light, that your source doesn't produce the same intensity of light at all wave lengths and so forth. Now, the instruments that have become very popular are FTIR instruments. And, in an FTIR, it's a little bit more complicated, but the ideas are the same. The big idea you need to absorb is the idea of interference, and if you don't completely get it, you're still fine. You'll have a source. Your source produces light. You have a beam splitter, and what the beam splitter is going to do, is it's going to allow half of the light to go one way, half of the light to go another way. So, you'll have half of your light come up to a fixed mirror, and half of the light goes out to a moving mirror, or variable mirror. And the variable mirror rides on a piston, and what's happening as the mirror is moving, is different wave lengths at any given moment are getting interfered. Some constructively, some destructively. So, in other words, as the mirror moves, the mix of light, it's no longer white light coming out of here, it's white light in which certain frequencies have been removed, certain frequencies have been enhanced by the mirror. And so those frequencies are going to vary. Your light goes to a sample, it goes to a detector, and it goes to a computer, which takes the [inaudible] which basically is the position of the mirror, and works it backwards to get out the streams and various frequencies. You'll typically run this with a reference. All right, I want to take one last moment, I apologize for going over, just to talk about sample [inaudible], and I want to give you my personal take. This is a little [inaudible]. All right, IR has changed a lot. Back in the days where NMR barely existed in 1950's and 60's and even into the 70's, JOC, "Journal of Organic Chemistry" wanted people to report everything. In other words you were creating a fingerprint for [inaudible] because we didn't have a lot of other data. Nowadays JOC says, "Look, tell us about the functional groups [inaudible] and report just the important things." And usually, that doesn't even mean CH's in your sample. It usually means carbon yields and double bonds, and alcohol, and nitriles, and triple bonds, and so forth. And that's the question you're typically asking when you're carrying out a functional group inter-conversion. You're probably not looking for aromatic CH's or aliphatic CH's. You're probably looking for alcohols, and carbon yields. So make it easy. All right, one of the techniques -- the reason people don't want to run an IR is it's a pain in the neck to make. Making a solution is easy, you do it for MNR. No one complains about doing NMR. I'm a big fan of solution IR. Again, if you go back to the old days you would use carbon dipole [inaudible] you would get every peak clear [inaudible]. Five percent solution in chloroform in CH carbonate, CL3, you'll lose a couple of bands in there, you'll see some blackout regions, so you'll lose the bands of chloroform at 775. Typically if you're using an FTIR, you'll see very strange patterns associated with interference here which is no light is getting through. But, that's super, super easy in a 1% in a .1-millimeter cell. Now, my other beef about IR, and this comes from being a PI whose fought far too many sodium chloride cells, is you get one person against the cell [inaudible]. I'm a huge fan of calcium fluoride cells. I've used this in my synthesis lab class for undergraduates, we bought two of these cells and I expected them to get broken with a bunch of undergraduates using them, they've been using them for a couple of years now. Calcium fluoride doesn't dissolve water, if you get water in it, it doesn't hurt. The cells cost a couple of hundred bucks a piece. Some of the TA's in the course told their [inaudible] to get one, your advisors to get one. Calcium fluoride cuts out below 1,000 wave numbers. In other words, you don't get like [inaudible] below 1,000 wave numbers. In other words you don't get like [inaudible]. But that's no big deal because as I said, we're going to concentrate on functional groups who make up [inaudible] and they'll inject it into the cell. Everyone knows about -- okay, who hasn't made a KBR column? Whose enjoyed making a KBR column [laughter]? Okay, a couple of you. Great. [Inaudible] sample [inaudible]. If you're making KBR pellets, I'm a big fan of a ball mortar, called a -- which you use in a wiggle bug, which is a dental mill. You shake it up, one big KBR, one big sample per 100 [inaudible] KBR [inaudible] pressure of the cell. This is what I could find. Another one that you probably haven't seen is a Nujol Mull. Mull is just a fancy word for suspension. Nujol is a fancy word for mineral oil, which is a fancy word for hydrocarbon oil, alkane that has those bends I talked about at 2,850 and 2,920 and 1,380 and 1,465. You just take three migs of your sample, grind it up in a mortar and pestle. Or, I am a big fan of frosted microscope slides, grind it together for 10 seconds with a teeny tiny drop of oil, scrape it onto a salt blade and you get a spectrum that has your CH bends and stretches but that's okay just ignore those for [inaudible]. Anyway, that's my take. We will talk about spectra and functional groups next time and I will see you on [inaudible]. ------------------------------b20976e3b077--
B1 inaudible wave bond stretch ch carbon Chem 203. Organic Spectroscopy. Lecture 01. Infrared Spectroscopy: Introduction 97 7 Cheng-Hong Liu posted on 2015/01/23 More Share Save Report Video vocabulary