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Three-Dimensional Representation of Organic Molecules Video Lecture - Class 11
FAQs on Three-Dimensional Representation of Organic Molecules Video Lecture - Class 11
| 1. What is a three-dimensional representation of organic molecules? |  |
Ans. A three-dimensional representation of organic molecules is a graphical depiction that shows the spatial arrangement of atoms in a molecule. It provides a visual representation of the molecule's structure in three dimensions, allowing scientists to understand its shape and how it interacts with other molecules.
| 2. Why are three-dimensional representations important in studying organic molecules? | |
Ans. Three-dimensional representations are crucial in studying organic molecules as they help scientists understand the molecule's structure and properties. By visualizing the spatial arrangement of atoms, researchers can analyze how the molecule interacts with other molecules, determine its chemical reactivity, and predict its biological activity.
| 3. What are the different methods used for creating three-dimensional representations of organic molecules? | |
Ans. There are several methods used for creating three-dimensional representations of organic molecules. These include ball-and-stick models, space-filling models, and computer-generated models. Ball-and-stick models represent atoms as balls and bonds as sticks, providing a clear depiction of the molecular geometry. Space-filling models show the relative sizes of atoms and their van der Waals radii. Computer-generated models, often used in computational chemistry, use algorithms to calculate the optimal positions of atoms based on their connectivity and electron density.
| 4. How can three-dimensional representations aid in drug discovery and development? | |
Ans. Three-dimensional representations play a crucial role in drug discovery and development. They help researchers understand the interactions between drugs and their target molecules, such as enzymes or receptors. By studying the three-dimensional shape of both the drug and the target molecule, scientists can design drugs that fit precisely into the target's active site, enhancing their effectiveness. Three-dimensional representations also aid in virtual screening, where millions of compounds are screened computationally to identify potential drug candidates.
| 5. Are there any limitations or challenges in creating three-dimensional representations of organic molecules? | |
Ans. Yes, there are limitations and challenges in creating three-dimensional representations of organic molecules. One limitation is that the accuracy of these representations depends on the quality of experimental data or computational calculations used to generate them. Additionally, representing large and complex molecules accurately can be challenging due to the sheer number of atoms and the intricacies of their arrangement. Finally, three-dimensional representations may not fully capture the dynamic nature of molecules, as they depict a single static conformation while molecules can adopt multiple conformations in reality.
Text Transcript from Video
- [Voiceover] In the video
on bond line structures,
we started with this Lewis dot structure
on the left, and I showed you how
to turn this Lewis dot structure
into a bond line structure.
So here's the bond line
structure that we drew
in that video.
Bond line structures
contain the same information
as a Lewis dot structure,
but it's obviously much easier,
much faster, to draw
the bond line structure
on the right than the
full Lewis dot structure
on the left.
What about three dimensional
bond line structure?
So how could you represent this molecule
in three dimensions, using a flat sheet
of paper?
Well, on the left here, is a picture
where I made a model of this molecule,
and this is going to help us draw
this molecule in three dimensions.
So we have a flat sheet of paper,
how could we represent this picture
on our flat sheet of paper?
Let's start with the carbon in the center,
so that's our carbon in magenta,
so that's this one on
our Lewis dot structure,
this one on our bond line structure.
Well, the carbon in magenta
is SP3 hybridized,
this is SP3 hybridized, so we would expect
tetrahedral geometry around that carbon.
And if you look at that carbon
on the picture here, you can see that
this bond and this bond
are in the same plane.
So if you had a flat sheet of paper,
you could say those bonds are in
the same plane.
So a line represents a bond in the plane
of the paper, let me
go ahead and draw that,
so this is the carbon in magenta,
and then we have these two bonds here,
and those bonds are in
the plane of the paper.
Next, let's look at what else
is connected to the carbon in magenta.
Well, obviously, there is an OH,
so let me go ahead and circle that.
There is an OH we can see
there is an OH here,
and the OH, the OH in our picture,
is coming out at us in space,
so hopefully you can visualize
that this bond in here
is coming towards you
in space, which is why this oxygen,
this red oxygen atom, looks so big.
So this is coming towards you,
we would represent that with a wedge,
so let me go ahead and
draw a wedge in here,
and a wedge means that the bond
is in front of your paper,
so this means the OH is coming out at you
in space, let me draw in the OH like that.
Now let's look at what else is connected
to that carbon in magenta,
we know there's a hydrogen.
We didn't draw it over here,
but we know there's a hydrogen connected
to that carbon, and we can see
that this hydrogen, this
hydrogen right here,
let me go ahead and switch colors,
this hydrogen is going
away from us in space,
so this bond is going away from us
in space, or into the paper,
or the bond is behind the paper.
And we represent that with a dash,
so I'm going to draw a dash here,
showing that this hydrogen
is going away from us.
So we're imagining our flat sheet of paper
and the OH coming out at us,
and that hydrogen going away from us.
All right, next, let's look at the carbon
on the left here, so this carbon
in blue, so that's this carbon,
and I'll say that's this carbon
over here on the left.
So we know that this carbon,
we can see that this bond,
and this bond are in the same plane,
so let's go ahead and draw in the carbon,
so the carbon that I just put in
is the carbon in blue, and this hydrogen
over here on the left, right,
this bond is in the same plane,
so I'm going to draw a line
representing the bond is in the plane
of the paper, and so we
have a hydrogen right here.
What about the other two hydrogens?
Well, let me highlight those,
so this hydrogen, hopefully you can see
that this is coming out at us in space.
So we represent that with a wedge,
so we draw a wedge right here,
and then we draw in a hydrogen,
so the bond is in front of the paper,
the bond is coming towards us in space.
And there's another hydrogen bonded
to the carbon in blue,
and my thumb here is
blocking it a little bit
but hopefully you can see that's going
away from us in space, so this hydrogen
is going away from us in space.
So the carbon in blue,
is also SP3 hybridized.
This carbon is SP3 hybridized,
we expect tetrahedral
geometry around that carbon.
And then finally, let's
look at the last carbon,
so this carbon right here in red,
so that's this one right here,
and this one right here.
This carbon is also SP3 hybridized,
so we expect tetrahedral geometry,
and if we look at this carbon,
let me use yellow again.
This bond, and this bond
are in the same plane,
so let's draw in the carbon in red,
and we can draw in the hydrogen right here
in the same plane, and
then let's visualize
the other two hydrogens.
So this hydrogen is coming out at us
in space, so we represent
that with a wedge
like that, so we have
a hydrogen coming out
at us in space, and
this other hydrogen here
is going away from us in space,
so it looks a little bit smaller,
so that's a dash right here.
So we've drawn everything out,
and notice when you have
a tetrahedral carbon,
an SP3 hybridized carbon,
you have this pattern,
you have this pattern of two bonds
in the plane of the paper,
and one wedge, and one dash,
so that's how we're representing
our tetrahedral geometry
around those carbons,
around those SP3 hybridized carbons.
It's usually --
usually you don't see the hydrogens drawn
in on one of these, so we can simplify
our three dimensional bond line structure
even more, we could just say,
we have an OH coming out at us
in space, so I draw a wedge right here.
And you could draw it like that,
which is implied that there's a hydrogen
going away from you, so if you draw
an OH coming out at you,
that implies that there is a hydrogen
going away from you in space.
So three dimensional bond line structures
are an important skill to be able
to visualize.
For this molecule, it's not so important
that the OH is coming out at us,
that's just how I drew it here,
because that's what it looks like
in the picture, but later,
in organic chemistry, it's very important
to understand what's coming out at you
in space, what's going away from you,
what does the molecule look like
in three dimensions, and
bond line structures,
three dimensional bond line structures,
allow us to visualize that.
Model sets help, so you should definitely
purchase a model set at this point
in your study of organic chemistry,
because it's going to help you
a lot later in the course.
On the left is the Lewis dot structure
for acetone, and we can turn that into
a bond line structure really quickly.
So here is the bond line structure
for acetone.
I could put in lone pairs of electrons
on the oxygen or I could leave them off.
I'll just go ahead and
put those lone pairs
in there like that.
What would be a three dimensional
bond line structure for acetone?
Well, on the left here,
is a model of the acetone molecule,
and hopefully you can see that these atoms
right here, these atoms are all
in the same plane of the page.
And so is oxygen, actually,
so is this oxygen here.
And it's a little bit easier to see
in the picture on the right.
So in the picture on the right,
these are the atoms that
we were just talking
about, so these are all in the same plane,
so hopefully you can visualize,
like a sheet of paper, so let me see
if I can sketch in a sheet of paper
right here like this.
And so all of those atoms,
all of those atoms are in the same plane
of that paper.
So we could draw that in like this,
we could have our carbons over here
like that, our three carbons,
and according to this picture,
these two hydrogens here,
so if we're trying to copy this picture,
those two hydrogens are in the plane
of the page, and so is this oxygen,
so this oxygen right here
is in the plane of the page,
so we'll draw it in there like that.
I'll go ahead and put in lone pairs
of electrons on the oxygen.
Let's focus in on the carbon in the center
for right now, I'm not done
with my three dimensional
bond line structure, I just want
to point something out right here.
So this carbon right here in magenta,
is this carbon, which is this one,
it's hiding back here,
but we know that carbon is SP2 hybridized,
so we would expect
trigonal planar geometry
around that carbon, so trigonal planar,
we would expect everything to be planar
so the atoms connected to the carbon
in magenta, we would expect those
to be in the same plane.
Now it's a little bit easier to see that
on the right here, so these carbons,
and these carbons, and this oxygen,
those are all in the same plane.
We have SP2 hybridization.
Let's now look at the other carbons,
so let's do blue here,
so carbon on the left right here,
I'm saying that's this one.
This carbon is SP3 hybridized,
which means tetrahedral geometry.
We would expect tetrahedral geometry
around that carbon, and
so we have these two bonds
in the plane of the page,
and then this hydrogen's coming out
at us in space, and then
this other hydrogen back here
is going away from us in space.
So on our three dimensional
bond line structure,
we could draw hydrogen
coming out at us in space
so that's a wedge,
and then hydrogen going away from us
in space, so that would be a dash.
And then the carbon on the right,
which I'll make red,
this is also SP3 hybridized,
so we would expect tetrahedral geometry,
and we can see this bond is in the plane
of the page, and this
hydrogen is coming out
at us, and then this one
is going away from us,
so we can complete our three dimensional
bond line structure over here on the right
by showing hydrogen coming out at us,
and a hydrogen going away from us
in space.
All right, if we look at this picture
on the right again,
we've already visualized our flat sheet
of paper, imagine your eye is right here,
imagine your eye is looking down
on your flat sheet of paper,
so your eye would see,
let me use dark blue for this,
these two hydrogens coming
out at you in space,
so that's these two hydrogens coming out
at you, so hopefully that
just helps you visualize it
a little bit better,
and then your eye would
see these two hydrogens,
behind the plane of the paper,
so that's going away from you in space.
So the hydrogens in green would be going
away from you, so we
represent that with a dash.
So hopefully that helps you visualize it
a little bit better here.
Now for acetone, you normally wouldn't
draw out a three dimensional
bond line structure.
There's not much of a point
to drawing the structure on the right.
I just did it to help you visualize things
a little bit better, and to contrast
an SP2 hybridized carbon with an SP3
hybridized carbon, to think about
what it looks like in three dimensions.
So pretty much, for
something like acetone,
you're going to stick with
the bond line structure
right here and not make
it three dimensional.
But I think it is important to think about
these things, and to make these molecules,
build them yourself, visualize it,
and understand this
concept before you move on
to other parts of organic chemistry.
on bond line structures,
we started with this Lewis dot structure
on the left, and I showed you how
to turn this Lewis dot structure
into a bond line structure.
So here's the bond line
structure that we drew
in that video.
Bond line structures
contain the same information
as a Lewis dot structure,
but it's obviously much easier,
much faster, to draw
the bond line structure
on the right than the
full Lewis dot structure
on the left.
What about three dimensional
bond line structure?
So how could you represent this molecule
in three dimensions, using a flat sheet
of paper?
Well, on the left here, is a picture
where I made a model of this molecule,
and this is going to help us draw
this molecule in three dimensions.
So we have a flat sheet of paper,
how could we represent this picture
on our flat sheet of paper?
Let's start with the carbon in the center,
so that's our carbon in magenta,
so that's this one on
our Lewis dot structure,
this one on our bond line structure.
Well, the carbon in magenta
is SP3 hybridized,
this is SP3 hybridized, so we would expect
tetrahedral geometry around that carbon.
And if you look at that carbon
on the picture here, you can see that
this bond and this bond
are in the same plane.
So if you had a flat sheet of paper,
you could say those bonds are in
the same plane.
So a line represents a bond in the plane
of the paper, let me
go ahead and draw that,
so this is the carbon in magenta,
and then we have these two bonds here,
and those bonds are in
the plane of the paper.
Next, let's look at what else
is connected to the carbon in magenta.
Well, obviously, there is an OH,
so let me go ahead and circle that.
There is an OH we can see
there is an OH here,
and the OH, the OH in our picture,
is coming out at us in space,
so hopefully you can visualize
that this bond in here
is coming towards you
in space, which is why this oxygen,
this red oxygen atom, looks so big.
So this is coming towards you,
we would represent that with a wedge,
so let me go ahead and
draw a wedge in here,
and a wedge means that the bond
is in front of your paper,
so this means the OH is coming out at you
in space, let me draw in the OH like that.
Now let's look at what else is connected
to that carbon in magenta,
we know there's a hydrogen.
We didn't draw it over here,
but we know there's a hydrogen connected
to that carbon, and we can see
that this hydrogen, this
hydrogen right here,
let me go ahead and switch colors,
this hydrogen is going
away from us in space,
so this bond is going away from us
in space, or into the paper,
or the bond is behind the paper.
And we represent that with a dash,
so I'm going to draw a dash here,
showing that this hydrogen
is going away from us.
So we're imagining our flat sheet of paper
and the OH coming out at us,
and that hydrogen going away from us.
All right, next, let's look at the carbon
on the left here, so this carbon
in blue, so that's this carbon,
and I'll say that's this carbon
over here on the left.
So we know that this carbon,
we can see that this bond,
and this bond are in the same plane,
so let's go ahead and draw in the carbon,
so the carbon that I just put in
is the carbon in blue, and this hydrogen
over here on the left, right,
this bond is in the same plane,
so I'm going to draw a line
representing the bond is in the plane
of the paper, and so we
have a hydrogen right here.
What about the other two hydrogens?
Well, let me highlight those,
so this hydrogen, hopefully you can see
that this is coming out at us in space.
So we represent that with a wedge,
so we draw a wedge right here,
and then we draw in a hydrogen,
so the bond is in front of the paper,
the bond is coming towards us in space.
And there's another hydrogen bonded
to the carbon in blue,
and my thumb here is
blocking it a little bit
but hopefully you can see that's going
away from us in space, so this hydrogen
is going away from us in space.
So the carbon in blue,
is also SP3 hybridized.
This carbon is SP3 hybridized,
we expect tetrahedral
geometry around that carbon.
And then finally, let's
look at the last carbon,
so this carbon right here in red,
so that's this one right here,
and this one right here.
This carbon is also SP3 hybridized,
so we expect tetrahedral geometry,
and if we look at this carbon,
let me use yellow again.
This bond, and this bond
are in the same plane,
so let's draw in the carbon in red,
and we can draw in the hydrogen right here
in the same plane, and
then let's visualize
the other two hydrogens.
So this hydrogen is coming out at us
in space, so we represent
that with a wedge
like that, so we have
a hydrogen coming out
at us in space, and
this other hydrogen here
is going away from us in space,
so it looks a little bit smaller,
so that's a dash right here.
So we've drawn everything out,
and notice when you have
a tetrahedral carbon,
an SP3 hybridized carbon,
you have this pattern,
you have this pattern of two bonds
in the plane of the paper,
and one wedge, and one dash,
so that's how we're representing
our tetrahedral geometry
around those carbons,
around those SP3 hybridized carbons.
It's usually --
usually you don't see the hydrogens drawn
in on one of these, so we can simplify
our three dimensional bond line structure
even more, we could just say,
we have an OH coming out at us
in space, so I draw a wedge right here.
And you could draw it like that,
which is implied that there's a hydrogen
going away from you, so if you draw
an OH coming out at you,
that implies that there is a hydrogen
going away from you in space.
So three dimensional bond line structures
are an important skill to be able
to visualize.
For this molecule, it's not so important
that the OH is coming out at us,
that's just how I drew it here,
because that's what it looks like
in the picture, but later,
in organic chemistry, it's very important
to understand what's coming out at you
in space, what's going away from you,
what does the molecule look like
in three dimensions, and
bond line structures,
three dimensional bond line structures,
allow us to visualize that.
Model sets help, so you should definitely
purchase a model set at this point
in your study of organic chemistry,
because it's going to help you
a lot later in the course.
On the left is the Lewis dot structure
for acetone, and we can turn that into
a bond line structure really quickly.
So here is the bond line structure
for acetone.
I could put in lone pairs of electrons
on the oxygen or I could leave them off.
I'll just go ahead and
put those lone pairs
in there like that.
What would be a three dimensional
bond line structure for acetone?
Well, on the left here,
is a model of the acetone molecule,
and hopefully you can see that these atoms
right here, these atoms are all
in the same plane of the page.
And so is oxygen, actually,
so is this oxygen here.
And it's a little bit easier to see
in the picture on the right.
So in the picture on the right,
these are the atoms that
we were just talking
about, so these are all in the same plane,
so hopefully you can visualize,
like a sheet of paper, so let me see
if I can sketch in a sheet of paper
right here like this.
And so all of those atoms,
all of those atoms are in the same plane
of that paper.
So we could draw that in like this,
we could have our carbons over here
like that, our three carbons,
and according to this picture,
these two hydrogens here,
so if we're trying to copy this picture,
those two hydrogens are in the plane
of the page, and so is this oxygen,
so this oxygen right here
is in the plane of the page,
so we'll draw it in there like that.
I'll go ahead and put in lone pairs
of electrons on the oxygen.
Let's focus in on the carbon in the center
for right now, I'm not done
with my three dimensional
bond line structure, I just want
to point something out right here.
So this carbon right here in magenta,
is this carbon, which is this one,
it's hiding back here,
but we know that carbon is SP2 hybridized,
so we would expect
trigonal planar geometry
around that carbon, so trigonal planar,
we would expect everything to be planar
so the atoms connected to the carbon
in magenta, we would expect those
to be in the same plane.
Now it's a little bit easier to see that
on the right here, so these carbons,
and these carbons, and this oxygen,
those are all in the same plane.
We have SP2 hybridization.
Let's now look at the other carbons,
so let's do blue here,
so carbon on the left right here,
I'm saying that's this one.
This carbon is SP3 hybridized,
which means tetrahedral geometry.
We would expect tetrahedral geometry
around that carbon, and
so we have these two bonds
in the plane of the page,
and then this hydrogen's coming out
at us in space, and then
this other hydrogen back here
is going away from us in space.
So on our three dimensional
bond line structure,
we could draw hydrogen
coming out at us in space
so that's a wedge,
and then hydrogen going away from us
in space, so that would be a dash.
And then the carbon on the right,
which I'll make red,
this is also SP3 hybridized,
so we would expect tetrahedral geometry,
and we can see this bond is in the plane
of the page, and this
hydrogen is coming out
at us, and then this one
is going away from us,
so we can complete our three dimensional
bond line structure over here on the right
by showing hydrogen coming out at us,
and a hydrogen going away from us
in space.
All right, if we look at this picture
on the right again,
we've already visualized our flat sheet
of paper, imagine your eye is right here,
imagine your eye is looking down
on your flat sheet of paper,
so your eye would see,
let me use dark blue for this,
these two hydrogens coming
out at you in space,
so that's these two hydrogens coming out
at you, so hopefully that
just helps you visualize it
a little bit better,
and then your eye would
see these two hydrogens,
behind the plane of the paper,
so that's going away from you in space.
So the hydrogens in green would be going
away from you, so we
represent that with a dash.
So hopefully that helps you visualize it
a little bit better here.
Now for acetone, you normally wouldn't
draw out a three dimensional
bond line structure.
There's not much of a point
to drawing the structure on the right.
I just did it to help you visualize things
a little bit better, and to contrast
an SP2 hybridized carbon with an SP3
hybridized carbon, to think about
what it looks like in three dimensions.
So pretty much, for
something like acetone,
you're going to stick with
the bond line structure
right here and not make
it three dimensional.
But I think it is important to think about
these things, and to make these molecules,
build them yourself, visualize it,
and understand this
concept before you move on
to other parts of organic chemistry.
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