Drawing 3-D Structures of Organic Molecules – Part 1

Drawing 3-D Structures of Organic Molecules – Part 1


let’s get some practice doing 3-D
sketches of organic molecules I have shown here
number of condensed formulas and so let’s get some
practice drawing Lewis structures and then from there draw 3-D sketches
so the first thing you want to do is take this condensed formula and show its connectivity – show the skeleton of the molecule CH3 you can draw as having three hydrogens attached to the carbon and then a CH2 remember hydrogen only wants one bond so as soon as
we attach it to the molecule it’s done with its bonding. and the third
carbon another CH2 as the fourth carbon, and finally there’s a carbon and a nitrogen Okay? So now we show our basic connectivity
your skeleton now we want to try and fill all the octets
that we can and remember carbon wants to have four bonds it’s going to be neutral and stable and wants to have four bonds and nitrogen wants to have three bonds and a lone pair. So we arranged to be a
triple bond between the carbon and the nitrogen, and a lone pair on the nitrogen, that would satisfy everybody’s octet and
it would make every atom neutral. We can count for carbon 1, 2, 3, 4 carbon has four and wants four. Nitrogen 1,2,3,4,5. Nitrogen has five and wants five so both of those would be neutral. So we have a
complete Lewis structure now in order to do the 3-D sketch we
need to consider the hybridization for each atom. so for every single atom. Hydrogen of course doesn’t undergo hybridization because
all it has an s orbital there’s no atomic orbitals to mix so it always just brings in its s orbital so let’s think about the hybridization. This carbon has one two three four regions around it. Any carbon that has four regions to
accommodate undergoes sp3 hybridization so that’s going to be
true for every one of these carbons that has four single
bonds it’s going to be sp3 hybridized. Okay now I get to this
next carbon and still has four bonds but the four bonds are arranged differently, they’re grouped differently now we have two regions
of electron density single bond and the triple bond. So if you have two regions of electron density it needs sp hybridization and the same for the nitrogen – it has a triple bond a lone pair so it’s sp hybridized. Now the hybridization is
going to dictate the geometry so now we can start to build our molecule. We
know that sp3 means tetrahedral. In order to draw a tetrahedral atom. we draw two of the bonds in the
plane like so – we can draw the hydrogen and the carbon in the plane and its bond angles
about 109.5 so the way we draw that is so we know what ninety looks like we draw it a little wider than ninety and the other two bonds are going to be down in
this area – one’s going to be a wedge coming out towards you and one is going to be a dash pointing
away from you doesn’t matter which is which but we draw one wedge and one dash and those are going to be the other two hydrogens. So there’s the first carbon and it’s tetrahedral. So now we come to the next carton and the next carbon we’ve drawn one bond in the plane already now there’s gonna be a second bond in
the plane and where is it going to go now we will resist the temptation of drawing it out like we did in our skeleton here because straight
out here would be 180 degrees don’t have 180 degrees – it has to be that 109.5 so that means you can either draw it in this area, or in this area – your choice so let’s go down here okay so these are my two bonds in the plane
and the wedge and the dash up in this area doesn’t matter which one is the wedge and which one is the dash there are my two hydrogens okay now we come to our third carbon this bond is in the plane so the second
bond is either up this way or down this way and we’re going to kind of end up
having a a bit of a zig-zag shape to our molecule so I did this one up so I’ll do this one back up. My dash and wedge are down here 123 123 this is my last CH2 so here’s my first bond and here’s where I have to draw my
second bond on the plane so my wedge and dash are up in this direction again so notice when I have a zig-zag up, my wedge and dash are up, When I have a zig-zag down, my dash and wedge are down. 1234 1234 now ready for our sp hybridized carbon, and what is the geometry for sp when you have two groups linear 180 degrees so here’s the first bond and the second bond
continues in that same direction and the nitrogen is also sp hybridized so what you do is you can kind of
draw a line continuing out and put the lone pair at the end of that line or you can kind of draw the sp orbital in
the plane in that direction and put the lone pair there – either one of those would be good we also want to show these pi bonds. We have two pin bonds and we need to show the electron density here so
remember the way we make a pi bond is we have two aligned p orbitals that are overlapping so if this is my x-axis of the p orbital that is used to
be hybridized and Py is going to be perpendicular to that so we can draw the Py on the carbon and on the nitrogen – show them overlapping sometimes people like to put a lone pair here, two electrons here rather, to
represent the two electrons being shared as the pi bond. And then the second pi bond is going to be perpendicular. The p lobe is coming
straight out and then straight back so maybe we can
show that with kind of a wedged lobe and a dashed lobe sticking back. Whatever you do on the
carbon we’ll do the same thing on the nitrogen and then show them overlapping to represent the second pi bond. That’s kind of what our triple bond looks like. A way to confirm that you’ve drawn a proper 3-D sketch is to build a model so here’s a model of this molecule and
notice this has lots of different conformations there are actually a lot of different drawings you may have for it but if you line it up the way we did We kind of had it zig-zagged – we started up here like this – okay – so we started down here we went up to the CH2 then down to a CH2 up to a CH2 then down, and then straight down in that direction
it’s very similar to what we drew and again we’ll note that when we have an alkane chain like this sp3 hybridized carbons a lot of times we draw it as a zig-zag – it’s a little easier because if you don’t keep going up and down can have the molecule kind of crash into
itself so this is really the most stable conformation. And when we have a zigzag up, the dash and wedge are pointing up, and when we have a zig-zag down the dash and wedge are pointing down. so let’s take a look at another molecule

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