And you'll really, even

with a very high field NMR spectrometer,

not going to be able to see a lot of distinction

between these structures.

But the big difference in mass spectrometry is

that fragmentation will occur at points that give you secondary

and tertiary carbocations more.

So if we look, for example, on the next spectrum,

on the spectrum of 4-methyl undecane, and now we look,

we see a break in this usual pattern, in other words the peak

at 71 is enhanced and the peak at 57 is diminished.

And the other thing that's interesting is for all

and intents and purposes, you don't see the molecular ion,

or it's very, very small.

And of course, the reason

for this is now you've got two desirable break points

in the molecule where cleavage

over here will give you a pentyl cation,

a secondary pentyl carbocation.

And that's going to give rise to your enhanced peak at 71.

And conversely, there are fewer ways to break this molecule

to give you a butyl carbocation

because undecane had two positions you could break,

whereas -- I'm sorry, dodecane had two positions you can break,

whereas methyl undecane has one.

So your peak at 57 is diminished.

And if you look hard, you'll see your peak

at 127 is also enhanced.

Right here you have this sort of downward curve.

So a person with a mass spectrometry --

with a mass spectrometer could look at this molecule

and say this is 4-methyl undecane rather than,

say, 5-methyl undecane.

And this becomes important in marine natural products

where often you get lipid type groups with unusual patterns

as well as in identifying lipid structures.

>> So when we talk, like we're [inaudible] fragmentation,

oftentimes we would try and favor to get [inaudible]

at secondary and tertiary positions?

>> Absolutely.

Absolutely.

>> Like they're in radical position, like, does it matter

if it's a primary [inaudible]?

>> Stabilization of the radical is less important

than stabilization of a carbocation.

Radicals are unhappy, carbocations are really unhappy.

Radicals have at least one electron in the vacant,

what's essentially a p orbital,

whereas carbocations have no electrons there.

So they're much more unhappy,

plus you have charge to stabilize it.

Other questions?

>> At the 71 and 127 fragmentations [inaudible]

migrate over to make the tertiary or [inaudible].

>> I would imagine, yeah, I would imagine you probably --

well, would the methyl.

There's no simple migration.

So if you look at a 2-pentenyl cation,

there's no simple migration that will give you rise.

I guess what you'd need is, yeah,

I don't know the answer to that.

I know in cyclohexane,

cyclohexyl carbocation chemistry,

if you can get a 1,2-hydride shift

that gives you a tertiary, yeah, it'll occur.

If you can get a 1,2-alkyl shift,

that'll give you a tertiary.

So yeah, I'd say if you can find a 1,2-methyl shift,

it will probably occur.

But in this case, I don't think there's one occurring.

And then by the time you go to a highly branched compound,

so here's an example where you really do only have --

you do see the tertiary peak predominating.

So here's another isomer, highly branched isomer.

And you'll notice the peak that predominates is absolutely

that tert-butyl carbocation.

And again, you don't see the M plus,

you don't see the molecular ion.

>> So when you're looking at a spectra like that,

how do you know that there's a peak there?

>> Aha. Great question.

So the first thing that people often do is blow up the region

where they suspect the molecular ion is.

Now, the second thing is,

let's say you have a little bit of information.

Remember the nitrogen rule that I mentioned,

the fact that in the EI mass spectrum,

if a compound has an odd number of nitrogens,

if it has 1 nitrogen or 3 nitrogens or 5 nitrogens,

the molecular weight is odd.

And that's just the math of making up molecules.

So, in this spectrum we were seeing peaks at 43,

peaks at 57, et cetera.

So, if you know, oh my molecule has no nitrogen,

and then you see only odd peaks, you say, oh wait a second,

these all have to be fragments.

So if you have some additional information,

for example you say, okay,

I know my compound is a marine natural product

that has no nitrogens it, but I'm only seeing a peak at 171,

in the EI mass spec -- and remember, it's all reversed

in the CI mass spec because you're putting on a proton,

which adds 1 -- then you'd say, okay,

that can't be the molecular ion.

And that's really important

because otherwise you've gotten yourself stuck

in this mindset saying, oh this is the molecular ion.

How do I get this structure?

All right, I want to talk for a moment about alkenes

and then move on to heteroatom compounds.

So alkanes are the most non-intuitive

because alkanes have no obvious place to take

that odd electron out.

We have to be thinking about sigma bonds

or molecular orbitals.

By the time we get to alkenes, we can say okay,

the highest occupied molecular orbital is a pi orbital.

We'll kick an electron out.

We'll get a radical cation.

And we really can remind ourselves that there are going

to be two resonance structures to it.

And the chemistry of alkenes is very similar to the chemistry

of alkanes, but now at least we sort

of have a way of thinking about it.

And we can think about things as a homolytic cleavage mechanism,

often to give an allylic carbocation.

So let me just write sort of a generic compound.

So imagine that we had an alkene over here.

And now I've taken the alkene

and I've generated the radical cation.

I've generated the molecular ion.

One of the very fundamental reactions

of radicals is homolytic cleavage.

Homolytic cleavage means you take this bond

and you break it equally.

Homo lytic.

You take one electron, you send it one way.

You take one electron, you send it the other way.

So I'll draw my little fishhook curved arrows

that you've been using, hopefully,

since sophomore organic chemistry

for this type of reaction.

And I'll take away minus R prime dot, so we don't see

that because that's a radical.

And this gives rise to an allylic cation.

And so the whole series of peaks --

The whole series of peaks that you might see for an alkane

with 43, 57, 61, you will see largely diminished by 2

for an alkene, 41, 55, et cetera, going up the series.

So in the case of alkanes, we were talking

about CNH2N plus 1 plus.

Here we're talking about CNH2N minus 1 plus.

Now, the alkene tends -- I'm not going to write it

out as a mechanism, but you can write a curved arrow mechanism

to walk your radical all over the molecule by a series

of 1,2-hydride shifts.

And so the alkene tends not to stay put.

So you can't -- you might think, oh I could tell

where the alkene is in the molecule,

but this migrates throughout the molecule.

So you can't pinpoint where the alkene is.

So let me just put up for comparison and contrast,

let me put up 1-dodecene.

That's on the flip side of your page.

Thank you.

And so for 1-dodecene, you see a peak at 41 by this new pathway

and ditto for 55, for 69 and so forth.

And of course, you do still see the 43 peak.

So you do also see the other pathway as well

as a 57 peak and so forth.

So the peak at 41, for example,

is simply this cleavage mechanism I talked about.

And I can at least write it as 1, 2, 3, 4, 5,

6, 7, 8, 9, 10, 11, 12.

I can write it, there are two resonance structures,

one with the primary positive charge

and the other the major contributor

with the secondary positive charge.

But I can write a curved arrow mechanism showing the homolytic

cleavage pathway to give rise to the allylic carbocation.

Woops.

Thoughts or questions at this point?

>> What are the peaks with the circles on top of them?

>> Peaks with the circles are other pathways that involve,

for example, loss of a hydrogen atom and so we're not --

we're not talking about --

we're not going to talk

about every absolutely every mechanism.

So for example, this peak at 42, although some of it comes

from the small amount of C13 isotopomer,

also has to correspond to a species that is a radical cation

with a formula of C3H6, but we're not going to talk

about the mechanism for formation.

All right.

I think at this point what I'd like to do is to move

on to heteroatom-containing compounds.

And what I think is neat

about heteroatom-containing compounds is we really can make

sense of their chemistry from just a few mechanisms.

So in addition to the homolytic cleavage, we can also think

of heterolytic cleavage mechanisms

and hydrogen abstraction fragmentation.

[ Writing on Board ]

All right.

So I'll write a generic heteroatom-containing compound

as R-Y showing a lone pair on Y. And I'm going

to be generic enough that I mean that this could be an alcohol,

an ether, a halide, an amine.

But also the OR group of an ester.