I gotta give a couple of minutes here
just for anybody who's getting between
classes but we've got a great great
place here we've got a great room and by
the way great class I was just so happy
yesterday coming out of here with all
the great questions engagement the the
fact that a I'm hearing that you're
exactly where I'd like you to be in
terms of sort of bringing some of your
knowledge from your chem 51 or chem 52
or other organic chemistry along so
that's great so anyway I'm real excited
to to be here and I'm real excited to be
working with you so Stan and stand in
Sebastian I met yesterday we had a
chance to talk a little bit more about
the homework and our plans for basically
going over things in discussion sections
and how we're going to do this and it's
going to be a lot like the graduate
class I've taught where people will go
to the blackboard and we'll share a lot
of answers and so forth all right we'll
give it give it just just one more
moment here any questions to begin
alright well in that case let's pick up
with our discussion of nomenclature and
this is going to finish it off and as I
for for chapter one and as I said last
time what I want us to be doing is not
to be a hundred percent masters of
organic chemical nomenclature I've got a
book this thick 300 and some pages
called the I you pack blue book that
goes ad nauseam through nomenclature and
the great thing on a lot of that is you
can look it up what I want us to do is
to start to see molecules and see
molecules beyond the functional groups
with a little bit of alkyl group spinach
thrown on that you got in sophomore
organic chemistry and see some of the
beauty of them and some of the
complexity and are going to try to do
that today and of course we will see a
lot of different classes of molecules as
well and a lot of different classes of
nomenclature so last time we were
talking about by cyclic compounds and
bridged by cyclic compounds and so I
think sort of as an archetype I started
with this molecule we talked a little
bit about it by sight glow three two one
octane and we talked about the
nomenclature a little bit and remember I
said the basic ideas we've got
bridgeheads in the molecule the two
junction points and your number around
the biggest bridge and then the next
bridge and then an expert one two three
four five six seven eight and these
numbers here ordered from biggest to
smallest represent the three Adam bridge
the two Adam bridge and the one Adam
bridge so what I want to do at this
point is to juxtapose that nomenclature
with that of Spira cyclic compounds
and also throw in a few other or at
least one other prefix so I'm going to
give us an isomer of this molecule
molecule that also has two rings to it
but now instead of having the Rings
bridged or fused so we call this a
bridge bicyclic compound when I showed I
ASA unde esti and I aiza unde esti NAT
the very end of last class we call that
a fused bicyclic compound this we call a
spira cyclic compound because you've got
sort of a you've got a quaternary
juncture you've got one ring one carbon
one quaternary carbon with four
substituents on it that joins the two
rings and it's sort of funny in spyro
cyclic compounds everything that you do
in by cyclic compounds you do opposite
in spira cyclic compounds so this
compound here is called Spiro 25 octane
and so we go from small number two big
number small and then big and sometimes
you gotta laugh at nomenclature some of
this is arcane some of this is funny but
you see it once and you start to say ok
there's at least a system to it and then
we do everything backwards you don't
start here we started at the bridgehead
and did the big chain here we start on
the small ring and we number around 12
for the small into the spiral carbon 3 4
5 6 7 8 and so if you make a derivative
like so now we're going to name this
compound as a derivative of Spyro octane
and more specifically
as a derivative of Spyro 25 octane we've
got a ketone group so remember you call
like propanone is the ketone the three
carbon ketone with the carbonyl at the
2-position of it so we call this own and
it's going to be spyro 2 dot 5 octan
dash for own now you might look at the
way just number and say what's going on
here while we're still numbering the
smallest ring first and we're going to
try to place the carbonyl the carbonyl
is in the bigger ring so we're going to
place the carbonyl at the lowest number
possible so we just go one two three
four five six seven eight all right the
other thing I think that this is a nice
point to bring out is we talked before
and I said to you there were terms for
replacing atoms and I showed you oxa
aiza and thyA these are terms that are
actually worth worth knowing they roll
off organic chemists tongues and I also
cautioned you when I said oxa that we
have an a in the end and that it it
means an oxygen in the ring oops geez
so for example if we take our Spiro
octane example and I put an oxygen into
the ring now we named that oxygen as oxa
so we're going to call it one oxa Spiro
25 now let's give us our carbonyl just
so we sort of add to our molecule and
add complexity octan for own that sort
of builds on itself in terms of
nomenclature in other words we started
with a parent ring system we identified
the Nate way we named the parent ring
system we started to modify the parent
ring system when we saw the
modifications or tacked on we continue
to modify the parent ring system and we
just tack on the modification yeah yeah
because we could have had the oxygen
over here in which case we would have
had a different number for it or we
could have had it over here or over here
so yeah there is ah because the parent
and we saw this last time when we went
to the deoxy by cyclo 221 hep teen
system it's the parent system which is
that number of atoms 8 atoms and then
it's replace one and these are good
questions and the bigger picture here I
come to you in a second the bigger
picture here is not necessarily
remembering all of the nomenclature
although you'll be surprised how much
you internalize without even trying
the bigger picture is seeing Anatomy
it's that you take somebody in the 51 a
course in the introductory sophomore
course and they're struggling to see a
ketone functional group if you just draw
something that's the level of mastery
and now we're starting to see this
progression of oh yeah we've got this
ring system it's built up of this and
this and so when you start to go to
really profound molecules like morphine
which is one that I use as an example a
lot in teaching well in teaching a
molecular modeling course and teaching
spectral spectroscopy class being able
to see the molecule and its components
and its shape all fit into that real
inside the head understanding of organic
chemistry it's the same I absolutely
absolutely we started with the parent
and then we just keep the parent and
then we just keep modifying and
modifying so that's a that's a great
question so then it would be diox-- so
if we went ahead and did this it would
be one to die oxa spyro 2 5 octa for own
and again see oh
and again seeing that anatomy and being
able to see that Anatomy is really
profound and that's essential to our
thinking so I'm going to draw a really
horrible horrible molecule based on
based on this question I wasn't planning
on drawing this i'm probably going to
get arrested for doing this all right
does anybody know what this really
really horrible molecule is that has
these two oxygens next to it yeah it's
explosive what is this what no yeah it's
acetone and hydrogen peroxide this is
the Tri acetone try peroxide that's
going in the suicide vests which have
been wreaking havoc with terrorists now
come to take this molecule for anatomy
for a second and we start to see a
couple of things first of all as we saw
over here this is a peroxy linkage in
other words you can see now as an
organic chemist and as somebody who's
been steeped in organic chemistry for
one year and or you know three quarters
plus two lectures you can start to see
okay wait a second I can understand this
functionality here is an asset al in
other words you can start to look at
this and say oh wait a second the
anatomy of this molecule is an asset
towel of acetone and it comes here it's
an asset asset towel right if you have
this molecule this is an
as a towel of acetone and methanol right
and you learned you made that you form
that by methanol plus acetone I'll write
it in the same way out right it is meoh
with acid catalyst and so you can start
to say oh wait a second this is an acid
towel of acetone and hydrogen peroxide
and that's what makes this really scary
is basically you can get these
ingredients in a hardware store in a
drugstore and so this is very accessible
but being able to look at this molecule
and assimilate the anatomy being able to
look at this molecule and assimilate the
anatomy is what we're talking about
right now and reagents like this get
used as oxidizing agents in organic
chemistry and when we come to chapter I
think it's sick son functional group
transformation you'll learn about
various reagents I don't know for going
to cover the I think it's just the
acetone it's the mono acetone peroxide
Sebastian do you remember the oxidizing
agent from synthesis think it's this one
anyway basically we'll start to see but
yeah so you we start to understand that
anatomy and then these reagents make
sense so I want to finish up with what I
was juxtaposed ingush up this little
segment so I cautioned that AXA is
oxygen in ring ox 0 is equal to a
carbonyl substituent on a ring or chain
when you've got a higher priority
substituent so remember I said it goes
by oxidation states you've got alkane at
the lowest oxidation state then you've
got the alcohol ether oxidation state
then you've got the ketone aldehyde
sedation state finally the carboxylic
acid oxidation state in dictating names
so just to fill things out here and
perhaps drive you crazy or at least
drive home a point I'm going to go ahead
and this is actually really similar to
an example in your textbook and draw out
this molecule and at this point we're
naming this molecule as the carboxylic
acid and so it becomes an ox 0 Spiro
octane carboxylic acid and all of the
numbering and that we did before
basically putting the lowest number on
the smallest chain and putting the
lowest number on the substituents and
then numbering around as beyond that to
give the functional groups the lowest
possible number applies and so this
molecule becomes for ox 0 notice we're
using ox 0 not AXA Spiro 25 octane one
carboxylic acid
alright so at this point I want to move
on to some polycyclic compounds and
maybe if i have time tell you a story
about cancer so all right we all know
benzene right so polycyclic many rings
and so we'll start with polycyclic I
guess more than compounds I'll say
polycyclic aromatic hydrocarbons so all
the aromatic hydrocarbons were initially
isolated from cult well not all but the
ones that were isolated in there many
were isolated from coal tar basically
taking coal from under the ground
heating the heck out of it without air
and boiling off the volatile compounds
and so as you get beyond so you get
benzene and toluene and bigger and
bigger compounds so we've got one
compound here anyone know the name of
this compound napthalene right you know
where you can find napthalene kind of I
heard somebody say it mothballs so it's
one of the two compounds that's widely
used to pack clothes to prevent moths or
more specifically the caterpillars the
larvae from eating particularly willing
clothes so what I think I want to do
with naphthalene is use this as a
starting point to talk a little bit
about numbering and then take us further
through so okay so you number aromatic
hydrocarbons polycyclic aromatic
hydrocarbons starting in the upper
right-hand ring as drawn and generally
you draw them horizontally to put his
mini rain
horizontal as possible and then beyond
that try to put as many rings in the
upper right-hand corner as possible and
so you start in the upper right and you
go round you skip the ring fusion so you
go one two three four five six seven
eight and then the ring fusions sort of
get a lower priority because there's
nothing happening in other words I could
make two chloro napthalene or one chloro
napthalene but as soon as I put a
chlorine on this carbon which is fully
fully valent in other words i can
replace a hydrogen here but then I break
unsaturation so I can't make a cake or
Oh napthalene at this position it
becomes a hydro nap you know
chlorohydrate a filling so we give a
lower numbering system and we call those
4a and 8a so i'm going to write here and
sort of junk junk number from top right
so you have it in your notes as drawn
and i'll show you as i said its tried to
draw as many rings as possible top right
ring as drawn and skip the junctions
just like we did with naturally i guess
i'll say you know junctions fusions
whatever all right there are three that
probably roll off my tongue very easily
as an organic chemists I pray
embarrassingly have a better name memory
for molecules name than people's names
and my memory for molecules names isn't
that great but there are things as an
organic chemists that you just see so
much again and again that that you know
as I said before they sort of become
part of you if you if you use them or
think about them on occasion and so i'll
show you two more
polycyclic molecules that I don't know I
mean I couldn't couldn't imagine not
being a practicing organic chemists and
knowing their names phenanthrene and
anthracene and so all of these molecules
are fully unsaturated in other words no
carbon has every carbon has you know
just double bonds to it or most one
hydrogen to it anyone recognize the name
anthracene and Thrax to my knowledge no
connection maybe I don't know but
another one anybody recognize you
anthracite coal there's a hard coal that
has the name I think it's called an
anthracite and it basically you know
given that these are all originally
isolated by heating the heck out of coal
without air it's not completely
surprising so keeping keeping the same
principles here I'll just show you here
for the numbering of them this is going
to come back in a moment as I said I
want to give an example that relates to
cancer so here's our numbering here
here's our numbering here so 510
dihydroxy and racine would have a
hydroxy group at this position and a
hydroxy group at this position or 5 510
and through seen dial you could call it
alright the other thing we talked a
little bit and I sort of throw in as an
aside numbering these know
unsubstituted bowl positions so beyond a
you get be so if you really care about
it this junction here becomes for a this
one becomes for B and then you're a day
and so on and so forth not super
important but but something that's sort
of cool and arcane all right at this
point I want to say it is very easy to
get stressed and sort of bent out of
shape because it seems that there's so
many different molecules and as I said
these are done as some of these not
everyone is going to become internal for
you and what I guess I'd also want to
add is a little bit of stress is good I
mean it makes you learn stuff and makes
you say I really have to pay attention
too much too much stress is bad because
it just means you're going crazy here so
I mean you know right now work the
problems you're going to read the book
you're going to internalize a lot of it
it is my plan if we end up with anything
that has names on it in the exam I
probably will pull something basically
to share with you the tables that you
print it out on the exam so you know
here's common names and these are cool
cool compounds all right I want to talk
to you at this point about a carcinogen
and also maybe give us a little bit of
appreciation of some of the nomenclature
of it and some of the arcane arcane
stuff that's involved all right so let's
take as an example benzo a pyrene and
this gets us into one more example of
nomenclature all right benzo a pyrene is
really bad stuff you heat the heck
out of almost any carbonaceous material
and you get polycyclic aromatic
hydrocarbons that's what's happening in
coal it's been under the ground for
hundreds of millions of years with
pressure and heat you're starting with
all sorts of carbon molecules from
plants and I don't know what dinosaurs
heating and pressing on it for hundreds
of millions of years and you get
graphite and pieces of graphite smaller
and smaller like an through seen and
naphthalene okay benzopyrene heat the
heck out of it it's a carcinogen in
tobacco smoke it goes right into your
lungs so I want to talk about the
nomenclature here so okay we've got
pyrene there's a bunch there's about 35
polycyclic molecules that have common
polycyclic aromatic that have common
names so I want to show you what benzo a
pyrene is all right so let's draw a
pyrene you can copy it there or you can
copy it from me i'm going to start and
draw napthalene i'm going to add a ring
to napthalene here's something cool I
can't add just one ring to napthalene
and keep a fully unsaturated compound
you notice I've put in my double bonds
and I've run out of room for double
bonds here but you put in one more ring
and you're up to a point where you can
go ahead and have a fully unsaturated
compound so this is pyrene we're going
to number around as drawn and you see
that you have it here so basically as
drawn we've drawn horizontal rings as
many as possible we'll start in the
upper right one two three four five six
seven eight nine ten it's right there on
you
screen as well now so i'll say number is
drawn from the upper right now the next
piece of arcane business in nomenclature
it's all sort of cool and freaky at the
same time is we're going to letter
starting with 1 to 2 i'll say letter our
edges starting with 122 and doing all so
in other words we'll letter this edge a
that's good because i said we have benzo
a pyrene this edge be this edge see
we're going to continue around right to
position 3 a d e f g h i j k l m n
alright so benzo a pyrene then we're
just going to fuse another benzene on to
the a ring so I'm going to redraw a
pyrene and part of this is an exercise
and us just spending a few moments to
see the anatomy here we're going to add
a benzene ring on to the a-rank or onto
the a edge and so that's benzo a pyrene
okay now now the crazy part and I'm
going to go somewhere with this so okay
so then for numbering now you reorient
and it's this principle of maximum
number of fused rings horizontal and
then we start numbering from the upper
right-hand ring so maximum number of
rings 1 2 3 so just like anthra seen
we're going to do one two three I'm
coming here to a nasty in even nastier
carcinogen and then we're going to take
the remaining two rings and stick them
up in the upper right-hand corner so all
I've done is flip and rotate our
molecule around so that's how we orient
it for numbering and then we number from
the upper right-hand ring and that's how
you number your benzo a pyrene all right
well benzo a pyrene as I said is what
you breathe in when you're one of the
many carcinogens when you breathe in
hamburger smoke I think it also for up
tobacco smoke I think it also forms and
burned burned meats but your lungs are
really vulnerable to cancer now your
body takes big greasy objects big greasy
molecules and it can't process them it
can't carry them it can't excrete them
when they are so greasy so your body
does what it does to process big greasy
molecules it oxidizes them with an
enzyme called cytochrome p450 and so
benzo a pyrene forms in your body the 78
dial nine ten epoxide what's the POC
sides another word for oxy grain my
cytochrome p450 so your body does what
it tries to do to rid itself of big
greasy molecules it oxidizes them with a
heem containing enzyme and so we're
going to draw that molecule now and so
now we know the secret of nomenclature
and I actually until I read this book
never quite knew how one got there and
it's sort of like oh cool now I know
this little arcane piece of knowledge
and so we're just going to number or
as we have done and will come to this
ring which we said seven eight dial I'm
going to draw there a couple of
diastereomers that can form actually 22
enantiomer is I'm just going to draw one
of them i'm specifically not specifying
the stereochemistry in my nomenclature
so i will just say this is one
stereoisomer and this is what gives you
cancer anybody have any idea what this
big flat hydrophobic region greasy
region looks like something related to
cancer we're just cancer start DNA yeah
it intercalation helix big flat greasy
molecules stick themselves in between
the bases who's had a biochem lab or
anyone work with ethidium bromide okay
ethidium bromide is a big fat
fluorescent dye molecule that goes into
your DNA but your body has just put a
warhead on this big flat molecule what
do you think that epoque side ring think
back to all the way to sophomore organic
chemistry to that molecule to oxy rain
you used it for something in sophomore
organic chemistry exactly it's a DNA
alkylating nucleophile like nitrogen
reacts here and a nucleophile like
nitrogen i believe it's reacting right
over right over here and what if i hold
on i have managed i managed
do oh one more double bond there we go
so benzylic position and so it is
particularly reactive you can find x-ray
crystallographic structures people have
studied this obviously we want to
understand how cancer comes about x-ray
crystallographic structures of
benzopyrene basically intercalated in
and covalently alkylated to DNA and so
that stuff is just like one of the worst
carcinogens you can possibly imagine it
we're talking micrograms of this
compound because you get a whole bunch
of junk when you burn tobacco and you
only get a little bit of benzopyrene but
a little bit of benzopyrene is all it
takes to really mess things up with your
DNA and your lungs are so so vulnerable
because you've got basically tissue
exposed right there for all of those
organic compounds to coming anyway as I
said sort of beautiful and horrible at
the same time all right I want to talk
about heterocyclic compounds and I want
to take you through a comp a few common
ones i'm going to talk about
heterocyclic compounds monocyclic and
then i want to show you another table to
make some sense of it and so i'm just
going to write out a bunch that probably
roll off of sebastian and stands tongue
oxy rain aziridine now let me talk about
the numbering for a second you number
from the hetero atom so you number one
two three so if we go ahead and we say
one methyl is your Dean this is one
methyl is your Dean if I go ahead and
say let's say or two methyl 80 Dean
oops then we're going to go ahead and
say okay that means we have a methyl
group on the carbon and we're going to
put that methyl group so that we have
the our stereo chemistry and we'll
remember okay there's a hydrogen here we
site down to the bond to the hydrogen
nitrogen highest priority this carbon
with just two hydrogen's and one carbon
attached to it in a nitrogen higher
priority than the methyl so one two
three so there's our our our group and
there are all sorts of other names if
you have a double bonded I'm going to
show you how to make sense of all this
in a second so don't don't worry too
much oxi reen that makes sense we've got
a double bond ane for saturated eeny for
unsaturated occitane and as I said if
you use these a lot they roll off your
tongue azetidine and then just to have
some fun let's do a few variations here
so if we do a five-membered ring with
two oxygens it's going to be 13 in the
one in three position will be 13 dioxo
lane you might have seen for as a
solvent 14 dioxane and let's say i'll
give you one more example i think we're
going to see this in our chapter on
synthesis where they talk about umpa Lum
and this is this is 13 die sighing yeah
Oh diox-- no dioxo Lane diox-- yep dioxo
Lane doesn't doesn't follow it now let
me show you the the key on all of this
and I want to put all of these into into
context here so remember I told you that
those tables had a lot of good stuff in
them okay tables 1.2 and 1.3 make sense
of all of this craziness let me let me
go ahead I'll make this a little bit
bigger for us all right making sense of
all of this craziness so you choose your
adam saaks for example ox two oxygens if
they're two oxygens you choose whether
you have compounds containing no
nitrogen or nitrogen no nitrogen you
choose whether they're saturated or
unsaturated dioxo Lane if you have so
what about that crazy occitane but
azetidine business here okay compounds
with ox oxygen get ox compounds with
nitrogen get a's compounds containing
nitrogen go under this category here
four membered ring as a team compounds
without nitrogen oxide chain here so
basically it's just run down the table
on naming them yeah
you could you could certain compounds
have special names and I want you when
you're seeing all of this take it in
also have a little bit of a laugh at
this because some of this some of this
is funny some of this is funny these
arcane rules and again realize if I ask
you anything from this i'll give you the
table just have worked through it once
as you're working through the chapter
and the homework problems make sure you
internalize it but it is sort of funny
now things get even funnier here all
right things things get even funnier
because all of this you can say at least
by some way shape or form is systemic in
other words oops okay in other words it
may not make sense that it's azetidine
but occitane but you can walk through a
system on it these are molecules that
got their names when we understood
structure or at least got their names
that really stuck when we understood
structure but all of those names like
phenanthrene and anthro seen came from
organic chemists sort of in the 19th
century and maybe early 20th century
where organic chemistry was isolating
stuff figuring out okay it has this
melting point so it's a pure compound
when I burn it and I calculate how much
co2 and h2o are produced I get an
empirical formula of say c 10 h eight
and so you say okay I don't know the
structure of naphthalene but I know it
is c 10 h eight and then as
understanding came along and we
understood the valances of carbon we
eventually were able to piece out the
structure but a lot of these initially
got the name that they were you know
this was the molecule that I isolated
when I heat distilled anthracite coal so
okay so with that there are certain
monocyclic heterocyclic compounds and
carbon well all the carbocyclic ones of
course I'm talking about have sorted
well at least the 35 that I mentioned
sort of have crazy names special names
so I'll say with special names you can
call them you can call them trivial
names these are the names that came
before people knew their structure and
stuck and they just roll off the tongues
of organic chemists so for example
breaking the rules on the tables one
point to this molecule here is called
parola Dean py RR loi di n E and again
don't I'm going to take us back here and
again I'll sort of take us over to this
table so don't stress too much about
this have a little bit of laughs of
history but these are ones that also
wrote roll off of stands tongue and and
sebastian's tongue this molecule is
called parole we're going to talk a
little bit about aromaticity in the
course but I hope that you remember from
sophomore organic chemistry when you
have six pi electrons in a ring you have
special stability of an aromatic
compound there's a lone pair on this
night
drogen that lone pair is in a p-orbital
and so we get to 46 parole is an
aromatic molecule like benzene although
with about half as much resonance
stabilization it's much more reactive in
electrophilic aromatic substitution but
it still behaves like an aromatic
compound not like an alkene this
molecule here is called few ran this
molecule here is called thiophene and
again most of these molecules would go
back to isolation before people had
systemic understanding of their
structure all right so let's see so I
think I want to conclude with a couple
of comments about unsaturation here
alright so for unsaturation we take a
lot of these names and we know where the
hydrogen is added all right so let's
start with pure an it's okay so here's
for an we number it starting with the
hetero atom 1 2 3 4 5 and so if we add
two hydrogen's to the molecule we come
up with 23 die hydro furin if we've
added them across the two and three
positions if we add them across the one
in five positions we now have one fought
to 5 i'm sorry across the two and five
positions we now have 25 die hydro pure
an and hopefully all of us have seen
this molecule in the course of our
sophomore organic chemistry what's the
name of that molecule tetrahydrofuran
commonly called thf thf is widely used
as a solvent in for example green yard
and organolithium reactions I think we
use it widely if who's had the chem 160
class by the way okay and we've probably
used it I'm pretty sure we use it in the
chem 160 class for certainly the first
first reaction is a nice aldol reaction
and I think we run it in thf all right
last thing i want to say rings that
cannot have full unsaturation get let's
number and age to show the position all
right so take a six membered ring with
oxygen in it I cannot have a neutral
six-membered ring with oxygen with three
double bonds I can have three double
bonds and a positive charge on oxygen
that's called / ilium but the only
neutral molecule I can make oh I mean
any neutral molecule I can make has one
carbon that is unsaturated so we call
this molecule to h pi ran pi ran was one
of those trivial names on your chart and
then if we so our numbering around the
ring so it basically is 123456 so if i
make a substituted variant of it this
would be six methyl to h pi ram by the
way if you print in on your computer you
would print it with the h and italics
and just to juxtapose this i'll show you
one isomer of pi rayon of 2 h pi ran
this molecule is 4 h pi ran
all right with this brief discussion and
the textbook you have a learner's permit
to play with the problems and once you
play with the problems you'll have as
much of a license as you should have
read it carefully play with the problems
and internalize some of this stuff and
we will pick up talking about the
literature for Friday register for
sciFinder there's a link on the website
and feel free to bring your laptop
computers will play around with some
online resources on Friday which should
make some chaos in the class