How to Draw Skeletal Structure or Bond-Line Notation for Organic Molecules

Do you find it overwhelming to draw every
carbon and hydrogen and bond when drawing organic molecules? In this video, we’re gonna simplify the process
and learn how to draw skeletal structures for organic molecules. Skeletal structures give you a simple way
to quickly represent organic molecules. Organic compounds are molecules that have
carbon and hydrogen, but they can also have other atoms like oxygen, nitrogen, sulfur
and even phosphorous. Why do organic molecules have carbon? Carbon in its hybridized state as an sp3 molecule,
has 4 valence electrons, capable of forming up to 4 different bonds. If an atom can bind 4 different things and
say one of those things is another carbon, and that carbon combine 3 more atoms and that
combine more atoms and more atoms, you go from something really simple to something
big and complex that can ultimately support life. But when you want to draw this molecules,
that’s where it helps to know how to do it simply. Let’s start with something simple. For example, a molecule like butane which
is C4H10. We have many ways to represent it, for example
the condensed structural formula which gives us different groups in that molecule. So we have a CH3 bound to a CH2, another CH2
and CH3. If we want more information about how the
atoms are bound, we can use a Lewis Structure. A Lewis Structure gives us a little more information
because we actually see exactly how the atoms are bound to each other. These are all very helpful except that it
takes a really long time to draw it and we are only looking at a 4-carbon chain. Now imagine if you have to draw the same thing
for a molecule like Octane, which is 8 carbons long, or Decane which is 10 carbons long. Don’t worry about the naming for now because
I cover that in a separate video series If I want to draw these molecules, Octane
is eight, we take twice as long to draw as butane and decane at 10 carbons will take
even longer. Now imagine you’re doing the mechanism and
you have to draw a version of the molecule once and again and again and again! Not only is it gonna take so much time, can
you imagine how messy your paper’s going to be? And you’re under enough pressure as it is
with your exams, so you need a simpler and easier way and that’s why we have Skeletal
Structure so we can quickly and easily represent these molecules and still know exactly what’s
going on. The trick with skeletal structure is that
we want to make this as simple as possible and that means we’re going to assume rather
than show a lot of what is going on. You don’t show any hydrogen atoms that are
on carbon. You only show the bonds between the atoms
again, unless it’s carbon to hydrogen, which we don’t show. The only atoms you show are the non-carbon
and hydrogen atoms: Oxygen, Nitrogen, Sulfur, Phosphorous, and so on. So how does this work? If we have molecule like butane, we’re not
going to show the carbon atoms but we’re going to show the bonds between carbon atoms. That means we have one, two, three, and four. Four carbon atoms and three bonds between
them. We’re not gonna show any hydrogens we’re going
to simply assume that they’re there and so you put pen to paper and draw a line. This line represents the bond between two
carbon atoms unless something else is shown. And then we draw another line, and another
line. The problem is, that a lot of students count
it when they draw a line rather than the first atom you write. So they draw a line and call that carbon 1,
2, and 3. But that is incorrect. When you’re drawing it, remember you have
fewer bonds than you have atoms. Four carbons have three bonds between them
and the trick to recognize is that every corner, every angle, every bend represents another
hidden carbon atom. So with that same structure even though we
only have three lines we have a total of 1,2,3,4 carbon atoms. I’m showing you the dots to help you count
them but I caution you not to get used to it, it is a crutch that wastes time and even
though you think it’s easier now, you’re going to be hurting yourself down the line. Imagine that those dots are there and instead
of drawing them, number it. So we have 1,2,3,and 4, that’s a 4-carbon
chain. What about hydrogen atoms? honestly, we don’t care! They’re there, but we don’t need to show them. If your professor asks you how many hydrogens
you have or you’re trying to figure it out for the molecular formula, use this trick. Knowing that a carbon atom has a total of
four bonds, we take the number 4 and then we subtract the number of visible bonds. Visible bonds means it’s not connected to
hydrogen, and whatever is missing is a hidden hydrogen atom. If we look at carbon number 1, we see one
bond to carbon number 2. 4 minus 1 is 3, that right there would be
our three hydrogen atoms. Carbon number 2 has a bond to 1 and a bond
to 3. That’s two bonds, 4 minus 2 is 2 and we have
2 invisible hydrogen atoms. And again for 3, 4 has three more. I’m showing this to you so you understand
that it’s there but I want you to forget the hydrogens and simply focus on the skeleton
at hand. Let’s try another example, in this case looking
at pentane given a molecular formula. First thing we do is count the number of carbon
atoms: 1,2,3,4,5. Now we need a skeleton to represent these
5 carbons and only the 5 carbons. When you first touch pen to paper that is
your first carbon, so that’ll be 1,2,3,4,5. Always, always number especially when you’re
just starting out to make sure you don’t make a mistake. 1,2,3,4,5 and we are good to go. If by mistake you drew something like this,
1,2,3,4,5 notice you didn’t count when you put your pen down but instead you drew the
first line and then counted to 1, you will catch this mistake when you number it, 1,2,3,4,5,6
then you’ll realize that’s not what I was looking for. That’s why you always wanna double check your
work and put the numbers to see what’s going on. As a beginner orgo student and even when doing
it with advanced mechanisms in organic chemistry 2. What about the hidden hydrogen atoms? we don’t
care! We know they’re there, we’re not asked about
it so we’re not worrying about it. Let’s take a minute to break it down and understand
why we’re drawing it like this. Remember that carbon is our central atom and
when sp3 hybridized carbon will have a bond angle of 109.5 and a shape that is tetrahedral. There are many different ways to draw this
in three dimensions. Here is the format that I prefer: If we have
a carbon atom with 2 bonds in the plane of the page, a line means it’s not coming out
or going into the page but instead it’s flat parallel to the page. The other two will have to be in the opposite
dimensions. One will come straightforward and the other
will go back. Remember that wedge means it’s getting bolder
and bigger and coming out at you. The dashes it’s fading away into the distance
into the page. If we go back to our example of pentane, we
can imagine that this carbon is one of the five in the chain. Here we have another one and again two bonds
in the plane of the page, one coming forward, one going back. We could do this for all 5 carbons. These are the five carbons of the molecule,
that means the missing bonds have to be hydrogen atoms. Hydrogens were typically invisible in line
structure but we’re showing them here to complete the molecule. Notice that when we have the carbons at 109.5,
it’s kinda difficult to show that on paper so we’ve settled for approximately 120 degree
bond angle. The hydrogens are going in and out of the
page but we keep it simple, we specifically chose all the atoms in the plane of the page
to represent the carbon bonds and anything going forward or back to be the hydrogens
because they’re difficult to draw and we don’t wanna draw them anyway. This gives us the zigzag structure that you’re
going to see when drawing skeletal structure. To simplify this, we simply start with the
first carbon and draw a zigzag to represent that same molecule, faster, easier, and so
much less confusing. But don’t forget when you have a sigma bond,
that’s a single bond there’s a free rotation about the bond. This gives me a different way to represent
the molecule. And when that rotates, this group which is
attached to the carbon that’s turning will swing around and ultimately go towards the
top of the molecule. To represent that inline structure I start
with everything that hasn’t moved and then the group that moved upward I simply draw
that upward. If I count this, 1,2,3,4,5, and 1,2,3,4,5
you’ll recognize that it’s the same exact molecule, just drawn in a different way. In fact if you’re not sure, use the highlighter
trick. If you can put your highlighter down and then
keep it down as you trace the path through the entire molecule you know that it’s one
continuous chain and in this structure even though it’s different I can trace that same
path 1 through 5 so I know it’s the same exact thing. Let’s look at an even more complex structure:
Cyclohexane. In watching me draw this, did you get a little
bit of a sense of panic? if so, let me know in the comments below. I find it tedious and I bet you find it tedious
as well. If I had to draw this in the exam, I could
lose my mind. Not to mention it would be messy and waste
of a whole lot of time. So what do we do? We number it, 1,2,3,4,5,6. I have 6 carbons attached to hydrogen. Let’s do the same thing in skeletal structure. Let’s show where the carbons are going to
be. We have 1,2,3,4,5,6. This is a helpful trick to get an idea of
where to draw the atoms when you’re still learning how to do skeletal structure. 1,2,3,4,5,6 but don’t forget because this
molecule is a cyclic compound, a ring, we have to connect 6 back to 1. Isn’t that so much faster and so much easier? Later in the course you’ll gonna learn yet
another way to draw a cyclohexane as chair conformations which is something I cover in
the tutorial link below. If your molecule contains sp2 hybridized carbons,
you’re likely going to see a double bond. For example, let’s take a look at Trans-2-butene. This molecule has 4 carbons but the 2 carbons
in the middle have a second bond between them, that’s a pi-bond or a double bond. Sp2 hybridized carbons have a bond angle of
120 degrees which is much easier to represent in two dimensions. To draw this in skeletal structure we do the
same thing as with sp3 hybridized carbons. Start by figuring out how many carbons you
need in your chain. In this case we have a total of 4 so we draw
a zigzag of 4 carbons 1,2,3,4. If you’re not confident, just add the dots
and count them or number accordingly. And then, to show that double bond, well we
simply show a double bond by drawing a second line or that second bond between carbons 2
and 3. Triple bonds is where it gets tricky. A triple bond has an sp hybridized atom with
a 180 degree bond angle. The geometry for an sp3 hybridized atom is
linear and this can get really confusing. Let’s take a look at 2-butyne. Once again, we have 4 carbon atoms attached
in a row but this time the two central carbons have 3 bounds between them, one sigma and
two pi. One of my pet peeves is to see this drawn
as an sp2 or an sp3 molecule with simply two extra pi-bonds as a triple. This is absolutely incorrect. Remember, 180 degrees gives us linear molecule,
it should be a straight line not a zigzag especially at those sp hybridized carbons. When you do this on line structure, it’s counter
intuitive because the molecule is simply a line. So how would you know where the carbons start
and end? Let’s not forget our triple bond. We have first pi and second pi. This is the proper way to draw a triple in
line or skeletal structure but I understand that it can get confusing. As you’ve just starting out, draw a little
dot to remind you that there is an extra carbon atoms sitting on other side of triple bond
before the start and end of the molecule. That means we have 1,2,3,4 carbons total. For even more examples make sure you try the
skeletal structure practice quiz linked on the description. Let’s look at an example of working backwards
where you’re given a skeletal structure of the molecule and asked to turn it into a molecular
formula, a lewis structure, or any other format where you have to show all the atoms. The first thing you want to do is to understand
what you’re looking at. And my first step, if I need to know what’s
going on is to number it. I see a total of 5 carbons in a row. Since we’re not naming it, it doesn’t matter
how you number it, right to left or left to right. It’s simply about understanding what’s going
on. I see a total of 5 carbons so I will draw
a structure that has 5 carbons and then I’ll number it so I’ll know what’s what when I’m
comparing between the skeletal and the lewis. On carbon 2 and carbon 3, I see a line coming
out with nothing on it so I know that’s a carbon atom with invisible hydrogens so we’ll
draw one coming up on carbon 2, and one coming down on carbon 3. Now we have to fill in the hydrogen atoms. Remember the formula, 4 minus the number of
visible bonds is equal to your hydrogen atoms. Carbon 1 has one visible bond, that means
4 minus 1 equals 3 hydrogen atoms. Carbon 2 has three visible bonds that’s one
hydrogen atom. The purple carbon on top has one visible with
3 hydrogens same with this one. Carbon 3 has three visible, 1 hydrogen. 4 has two visible, 2 hydrogen and 5 has one
visible, therefore 3 more hydrogen. If you want to verify, quickly count the total
number of bonds on each carbon atom 1,2,3,4. 1,2,3,4 and so on to verify that it’s correct. If you’re asked to condense this even more,
just count your groups and then draw them out. But instead writing bonds, take every group
as carbon followed by the attached hydrogen. So for example, we’re starting with the C
bound to 3 hydrogens that’s a CH3. The next carbon is a CH2, the next carbon
is a CH but it also has a CH3 coming off it so that would be CH parenthesis CH3 showing
that the CH3 is a substituent off that carbon. Same thing for the next one, CH bound to CH3. And finally a CH3 at the end of the molecule. Till now we’ve looked at skeletal structures
with just carbon and hydrogen but what happens if you have another atom like oxygen, or nitrogen? For example, how do you draw the skeletal
structure from molecule like Ethanol? Ethanol is CH3CH2OH. If you see the carbon, you start the same
way. What is my carbon chain have? 1,2 so I draw a line that represents one carbon
bound to its second one and it definitely helps if you can number it. The hydrogens when bound to carbon are invisible. Oxygen is not invisible so we have to draw
a bond from the skeleton of carbon to the hetero atom that is attached so meaning non
carbon or hydrogen. In this case I draw an Oxygen. And because Oxygen has a hydrogen that is
not bound to carbon, we have to show that hydrogen atom. So what do we have here? 2 carbon atoms and then a bond going to oxygen
and hydrogen. This is where students tend to make a mistake. They count this and they say Oh, that’s 1
carbon, 2 carbon, 3 carbon. That is not a third carbon atom. If that line terminates in nothing meaning
the line ends that’s a carbon atom. If the line terminates and there’s another
atom visible, it’s not an imaginary carbon, it’s not a self understood carbon, it’s a
very very non imaginary, visible atom in this case oxygen. Let’s look at another one. Say we are given Butanamide which is CH3CH2CH2,
C double bound to O, NH2. We treat this the same exact way. It doesn’t matter what is on that carbon atom,
count your carbon atoms and start there. We have 1,2,3,4. So we draw a skeleton 1,2,3,4. Number it to make sure all your atoms work,
count to 4, forget your hydrogens unless they’re not sitting on carbon and then add in everything
else. We have a double bond between carbon and oxygen
so from that imaginary carbon at the end of the line, we draw double bond and add oxygen
because it’s not imaginary, we have to show that. Same thing for Nitrogen but it’s only a single
bond. Nitrogen has two hydrogen atoms, that means
there are hydrogens not sitting on carbon so we draw them in as 1 and 2. For even more practice going from molecules
in any form to skeletal structure or taking that skeleton and converting it back, be sure
to try the practice quiz on my website or visit the link in the description


Leave a Reply

Your email address will not be published. Required fields are marked *