hey guys I wanted to go through some more stuff on chem doodle today
last time we use this software we were using the feature that would assign the
IUPAC name to a molecule and we were using that to kind of learn some of the
trickier you pack rules for our polycyclic structures and this time I
want to show you another feature chem doodle is able to assign R and S
stereochemistry to any stereocenter so I want to use that feature to do a little
more practice and expand on my previous tutorial on the cahn-ingold-prelog
convention and extend that convention to some slightly trickier molecules that we
didn't get a chance to do previously so we'll do one quickly to review here
we're looking at this molecule and recall that anytime we have a stair if
there's a carbon connected to four different groups that's gonna be a
stereocenter and the first thing we have to do so
first we're acknowledging that this one is a stereocenter and we're saying that
we buy the cahn-ingold-prelog convention we have to assign these groups priority
and we're gonna do so according to atomic mass so we have to look at these
four groups and say okay which one is heaviest well bromine is definitely
heaviest so let's call that number one and then next heaviest is going to be
chlorine so we'll call that number two and then next heaviest after that will
be nitrogen so that will be three and then certainly the lightest is hydrogen
so we'll call that four now notice that we didn't say that this group here was
the heaviest because it's tempting to look at this and see oh there's some
alkyl groups over here this is very heavy it must be the heaviest recall
that for cahn-ingold-prelog we're going one atom at a time so it's just
bromine beats chlorine beats nitrogen we're not worried at all about any
connected to that atom so that's how we assign the priorities of these groups so
the next thing that we have to do according to cahn-ingold-prelog is we
have to orient ourselves so that the lowest priority group is facing away
from us so in this particular case that would be looking this way right we want
to look as though we're in the screen on this edge of the molecule so if that's
hard to visualize we can always draw a Newman projection so if we're looking
this way we're looking as though we're looking down this carbon hydrogen bond
right because that would put the hydrogen away from us
if we do that then we're looking up straight up at that bromine and we're
looking down and left at the chlorine and then we're looking down and right
nitrogen okay so that's that's making it a little easier to see how we how we're
going to assign clockwise or counterclockwise
recall that we now just go for we trace a circle from one to two to three so if
we were to do that on the Newman projection we would go like this and we
would see that that is counterclockwise so we're going to expect s anytime you
go counterclockwise from one to two to three that's gonna be s so now what we
want to do is use the feature on chem doodle and make sure that we are right
so let's go here let's go to stereochemistry and let's assign R and S
and we see that we were right it is indeed S and so that's that that is good
to know that we did that correctly another interesting feature we can
always go to this carbon and we can see what it would look like with the
opposite stereochemistry so we could force R and you see what happened there
it just swapped two of the groups remember that at any time we swap two
groups or inverting the stereochemistry and we can just undo that to get back to
our original molecule so that's what it would look like with the
stereochemistry so this is a very cool feature of chem doodle because now you
don't have to just work through the examples that I go through in my
tutorials you can use this and you can draw any molecule from your homework
your problem sets from your exams anything like that and you can practice
on it and check and check your answers this will tell you whether you were
correct or not so that's kind of a cool feature of this software let's go
through these other ones that was just a warm-up now I want to go to this one
because this is showing a feature that we didn't talk about in my previous
tutorial we didn't really talk about what to do with pi-bonds so that's a
little bit something new that we can check out right here so first we're
gonna notice that this is a stereocenter we've got we've got four different
groups and the reason we have four different groups these are these seem
like the same chain but this has a pi bond on there if that pi bond wasn't
there then those would be the same group and this would not be a stereocenter it
would be a chiral because of the symmetry but because of that pi bond
this is a stereocenter so let's go ahead and assign let's assign the
priority we've got carbon carbon hydrogen oxygen, oxygen is definitely
whoops is definitely the heaviest so let us assign that as number one and
hydrogen is definitely the lightest so let's call that number four but now
between these two carbons we have to decide which one wins and the way we're
gonna do that is this so let's take this carbon here any time we have a carbon
that has a pi bond if it has a let's say a double bond to another carbon we're
going to treat that as two separate bonds to two separate carbons so what is
this carbon connected to these ties so we have to keep going this carbon is
connected to carbon carbon hydrogen right it's as though it's connected to
two other carbons and now this carbon over here this one is connected to this
carbon atom and then to implied hydrogen's so this one is carbon
hydrogen hydrogen so this group clearly wins it says though a carbon cancels and
a hydrogen cancels and then carbon beets hydrogen
so we are gonna call this carbon
priority two so let's call that number two and let's call this guy number three
now we're all set we're already in the correct orientation to assign R and S
because luckily the lowest priority group the hydrogen is away from us so we
can just trace from one to two to three like that and we have done that in
clockwise fashion so we should expect this stereocenter to be our and so now
let's check let's use this feature let's get the whole molecule there and let's
assign R and S and it is indeed our so we were correct and that is the additional
rule there with the pi bonds for that one so let's let's use that rule oh by
the way let's let's go ahead and and see what would happen if we switch that so
instead of our let's say we force s and so we see right there just the the wedge
and the dash have swapped and that's what S would look like we know that if
we invert that stereos if we invert two groups then we will invert the
stereocenter so that's s we can undo and just go right back to our like we had it
and now let's look at this next example so again we're gonna have to use this
new rule we just learned regarding pi bonds and so this is the stereocenter
right here this carbon because we've got hydrogen we've got this group and we've
got this alkenyl group and we've got this alkynyl group so let's go ahead
and assign priorities so the hydrogen is definitely definitely gonna be number
four that is the lightest but we do have three carbons and carbons they all tie
so now we have to see what they are connected to so this car
is connected to two fluorines and an implied hydrogen so fluorine fluorine
hydrogen now this one over here has three bonds to another carbon so we have
to treat that as three separate carbons and we're gonna say carbon carbon carbon
one for the sigma bond and one for each pi bond then we go over here and we say
that this carbon is attached to two carbons because each of these in the
double bond is connected to carbon and one implied hydrogen so we're gonna say
CCH okay so now to assign the priority we got to find the heaviest element so
that's fluorine here that means this group is gonna be the top priority or
not that yeah it will be the top priority because of those fluorines
right there so that's gonna be priority one then over here we have carbon carbon
carbon versus carbon carbon hydrogen it's as though two of the carbons cancel
out and then carbon beats hydrogen so let's call this one priority two and
then that leaves this as priority three so we've got our one our two or three
and our four and luckily the lowest priority group is away from us already
that's the hydrogen so we can just trace one two two two three
and so once again we have gone clockwise to do that and so we would expect this
to be our and let's now go ahead and check our answer whoops
so let's check our answer and we see that we do get are just like expected
and so that one was correct now let's just quickly check see what happens if
we force S and once again we've just swapped that wedge bond and that dash bond
that's what S would look like and let's just go back to R so that's that one
with those pi bonds let's do one more here with this interesting bicyclic
system so we've got a couple of stereocenters actually here 1 2 3 it's
the presence of this hydroxyl right there this hydroxyl weren't there
there'd be some symmetry but because of this hydroxyl the directions around the
ring are now different and especially this carbon right here is definitely a
stereocenter let's just do one of these otherwise it'll get a bit messy so let's
do this carbon right here we've got oxygen we've got hydrogen we've got
carbon and we've got carbon so we know that oxygen is definitely going to be
number one and we know that hydrogen is going to be number four now in terms of
these two carbons right those tie so we have to see what they are connected to
and this carbon this carbon right here is attached to this carbon and then to
implied hydrogen's so that is carbon hydrogen hydrogen and then down here
this carbon is attached to this carbon and this bridgehead carbon and this
hydrogen so that's carbon carbon hydrogen so carbons cancel hydrogens
cancel but this carbon beats this hydrogen so we are going to say that
this carbon here is priority two and this carbon here is priority three so
now we have it's a little bit of a trickier situation because we do
have to put the hydrogen away from us so the best way to do this is to pretend
we're viewing this top-down it says though we're looking directly down on
the molecule there so if we do that if we envision ourselves in the in the
screen right there and we go 1 to 2 to 3 we are going clockwise if we can imagine
ourselves looking downwards and so we would expect this one to be our and now
let's check
and we do get are for the one that we expected and we also have R and S over
here and you can do those ones on your own to make sure that that's gonna work
recall that this way around the ring with the hydroxyl is going to be a
higher priority than the one without so those are just a couple of examples I
wanted to extend my previous tutorial on cahn-ingold-prelog to show you what to
do when pi bonds are present because that's a little bit of a different rule
that we do need to know and I didn't cover it before and then I also just
wanted to show you some of these features on chem doodle where we can
assign R and S we can invert the stereocenter we can assign attributes to
show the priorities around the stereocenter so there's a lot of cool
tools here to practice your R and S assignments so go ahead if you are
interested there's a link in my in the description of this clip and it's super
super affordable so please check it out if you are interested in practicing your
chemistry this way otherwise that's all for now