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  • >> 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--

>> Good morning.

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ケム 203有機分光学講義01.赤外分光法序論 (Chem 203. Organic Spectroscopy. Lecture 01. Infrared Spectroscopy: Introduction)

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    Cheng-Hong Liu に公開 2021 年 01 月 14 日
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