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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--