Isomers

Introduction

Before we jump to stereoisomers, let us quickly review what isomers are. Isomers are molecules that have the same molecular formula but differ in the way the atoms are arranged around the central atom. For example, a molecule with the formula AB2C2, has two ways it can be drawn:

 Isomer 1:                                                    Isomer 2:

The above two pictures are examples of isomers, specifically cis-trans isomers which we will discuss later on. One thing to remember whenever talking about stereoisomers is that all other options that may come to mind are just rotations of the existing isomers. For example, a molecule that has both C's on the top right plane and both B's on the bottom left plane is not another isomer. Instead it is just a 180o rotation of isomer 2.

Stereoisomers are isomers that mainly differ in the way the ligands or atoms are placed relative to the central atom. There are two types of stereoisomers:

Geometric Isomers = Isomers that differ in the way the ligand is bound to the metal.

Optical Isomers = Isomers that do not have symmetry and are not superimposable on their mirror images.

In terms of their differences, geometric isomers show much more activity than optical isomers. What this statement means is that optical isomers often display similar properties and do not seem all that different. That is until they react with other optical isomers or when they react with light. As discussed later on, one of the main ways optical isomers are detected is their ability to polarize or change the direction of light. Geometric isomers on the other hand exhibit different properties from one isomer to another.

Review of Molecular Geometry

To really understand stereoisomers, one must understand all the possible molecular geometries. For stereoisomers, only these geometries will be relevant:

Linear Square Planar Tetrahedral Octahedral

It is also important to remember the coordination number associated with these geometries. Coordination numbers refer to the number of ligands or atoms bound to the central atom. Thus, linear has a coordination number of 2 because it consists of 2 atoms bound to the central atom. Square planar and tetrahedral have a coordination number of 4 while octahedral has a coordination number of 6.

These geometries are very important as they dictate whether or not certain isomers exist. 

Linear

An example of linear geometry is provided below of the molecule Xenon Difluoride (XeF2). Recall that linear is the geometry where the molecule looks like a line.

XeF2:

Square Planar

Square planar is the geometry where the molecule looks like it is a square plane. An example of the molecule Xenon Tetrafluoride (XeF4) is provided below.

XeF4:

Tetrahedral

Tetrahedral is the geometry where the molecule looks like a pyramid. An example of the molecule Methane (CH4) is provided below.

CH4:

Octahedral

Octahedral is the geometry where the bases of two pyramids are stuck together. Alternatively, it can also be though as where the center consists of a square plane with a ligand sticking out above it and another ligand sticking out below it. An example of the molecule Sulfur Hexafluoride (SF6) is provided below. A quick note on octahedral geometry: sometimes an octahedral molecule may contain polydentate ligands. Polydentate ligands are ligands that "bite" the central atom in several locations. In other words, polydentate ligands have the ability to form more than one bond with the central metal, unlike other ligands. An example of a polydentate ligand is ethylenediamine, a bidentate ligand, which is abbreviated as en. 

SF6:

Geometric Isomers

Geometric Isomers are isomers that differ in the arrangement of the ligands around the metal or the central atom. In other words, these isomers differ from each other based on where the ligands are placed in the coordinate compound. This will be much easier to understand as examples will be considered.

There are 2 main types of geometric isomers:

Cis-Trans Isomers Mer-Fac Isomers

Cis-Trans Isomers

Cis-Trans Isomers are isomers that differ in the arrangement of 2 ligands in square planar and octahedral geometry. Cis isomers are isomers where the two ligands are 90 degrees apart from one another in relation to the central molecule. This is because Cis isomers have a bond angle of 90o, between two same atoms. Trans isomers, on the other hand, are isomers where the two ligands are on opposite sides in a molecule because trans isomers have a bond angle of 180o, between the two same atoms. When naming cis or trans isomers, the name begins either with cis or trans, whichever applies, followed by a hyphen and then the name of a molecule. For example a cis isomer of CoCl2F2 would be called cis-CoCl2F2. Finally, the last thing to keep in mind when examining cis and trans isomers is that only square planar and octahedralgeometries can have cis or trans isomers. Examples of both isomers are provided below.

Tetrahedral Cis Isomers

CoCl2F2:

(Color scheme: pink=cobalt, blue=fluorine, green=chlorine)

This above is an example of the molecule cis-CoCl2F2 or cis-dichlorodifluorocobalt (IV). The molecule pictured above is a cis isomer because both fluorine and chlorine ligands, respectively, are on the same side of the molecule. Additionally, one can approximate that the bond angle between each of the chlorine atoms and between each of the fluorine atoms is 90o.

Tetrahedral Trans Isomers

CoCl2F2:

(Color scheme: pink=cobalt, blue=fluorine, green=chlorine)

(Note, the differences in the length of the bond between the two pictures are not intentional and have nothing to do with cis-trans isomerism)

This above is an example of the molecule trans-CoCl2F2 or trans-dichlorodifluorocobalt (IV).

We know the above molecule is a trans isomer because the two same chlorine atoms and the two same fluorine atoms are opposite each other. Furthermore, the bond angle between the two chlorine atoms and between the two fluorine atoms is 180o. The above examples were all for square planar geometry but as the examples below illustrate, cis-trans isomerism can also occur in octahedral geometry. Both the molecules below are isomers of the molecule SCl2F4 (color scheme: yellow=sulfur, blue=fluorine, green=chlorine).

Octahedral cis Isomers

SCl2F4:

We know this isomer above is a cis isomer because both the chlorine ligands are on the same side and the bond angle between the chlorine atoms appears to be 90o. 

Octahedral Trans Isomers

SCl2F4:

We know this isomer above is a trans isomer because the chlorine ligands are on opposite sides and the bond angle between the chlorine atoms is 180o. All other isomers are essentially just rotations of these two isomers. Once again when trying to find cis and trans isomers look at the arrangement of the ligands. If two same ligands are on the same side, it is a cis isomer and if the ligands are on opposite sides, it is a trans isomer. Another way to tell the isomers apart is the bond angles: cis isomers have a 90o bond angle whereas trans isomers have a 180o bond angle.

Mer-Fac Isomers

Mer-Fac isomers are easier to notice than cis-trans isomers in the sense that they only exist in octahedral geometry. Just like cis-trans isomers, mer-fac isomers are determined based on whether or not the ligands exist on the same side. Instead of dealing with 2 ligands, mer-fac isomers deal with 3 ligands. If the 3 ligands are all on the same side, the isomer is called a fac-isomer. Another way to identify fac isomers is to look at the bond angle between the ligands because fac isomers have a 90o bond angle between each of the 3 atoms. The mer isomer on the other hand is where only 2 of the 3 ligands are on the same side. In mer isomers, there exists a 90o-90o-180o bond angle between the 3 same ligands. In terms of nomenclature, mer-fac isomers follow the same rule as cis-trans isomers where you put the isomer type, followed by a hyphen, followed by the molecular formula. Examples have been provided below.

Fac Isomers Example

Below is an example of the fac isomer, fac-CoCl3F3:

(note the color scheme: pink=cobalt, green=chlorine, blue=fluorine)

2d version:

Through the 2d version, it is easier to see how the ligands are all on the same side. Nonetheless, in the 3D version, one can observe that the bond angle between the 3 same ligands is 90o, thus making this isomer a fac-isomer.

Mer Isomers Example

Below is an example of the mer isomer, mer-CoCl3F3:

(note the color scheme: pink=cobalt, green=chlorine, blue=fluorine)

2d version:

Its hard to tell in the 3D version but in the 2D version, one can easily tell how the same ligands are not on the same side. Additionally, one can approximate that the bond angle between the three chlorine atoms and between the three fluorine atoms is 90o-90o-180o, thus making the above molecule a mer isomer.

Optical Isomers (Enantiomers)

Optical isomers are isomers in octahedral and tetrahedral geometry that do not exhibit symmetry and do not have identical mirror images. Optical isomers are difficult to understand because one must be able to visualize them in a 3D manner. 

Before we jump into identifying optical isomers, let's learn some of the terminology associated with optical isomers. Optical activity refers to whether or not a coordinate compound has optical isomers. A coordinate compound that is optically active has optical isomers and a coordinate compound that is not optically active does not have optical isomers. 

Let's go through a quick review of symmetry and mirror images. A mirror image of an object is that object flipped or the way the object would look in front of a mirror. For example, the mirror image of your left hand would be your right hand. Symmetry on the other hand refers to when an object looks exactly the same when sliced in a certain direction with a plane. For example imagine the shape of a square. No matter in what direction it is sliced, the two resulting images will be the same. 

As we will discuss later, optical isomers have the unique property of rotating light. When light is shot through a polarimeter, optical isomers can rotate the light so it comes out in a different direction on the other end. A youtube video has been attached below in the outside links section that further explains how to discern optical isomers and their ability to change the direction of li

Armed with the knowledge of symmetry and mirror images, optical isomers should not be very difficult. There are two ways optical isomers can be determined: using mirror images or using planes of symmetry.

Plane of Symmetry Method

The plane of symmetry method uses symmetry, as it's name indicates, to identify optical isomers. In this method, one tries to see if such a plane exists which when cut through the coordinate compound produces two exact images. In other words, one looks for the existence of a plane of symmetry within the coordinate compound. If a plane of symmetry exists, then no optical isomers exist. On the other hand, if there is no plane of symmetry, the coordinate compound has optical isomers. Furthermore, if a plane of symmetry exists around the central atom, then that molecule is called achiral but if a plane of symmetry does not exist around the central molecule, then that molecule has chiral center.

Mirror Images Method

The mirror images method uses a mirror image of the molecule to determined whether optical isomers exist or not. If the mirror image can be rotated in such a way that it looks identical to the original molecule, then the molecule is said to be superimposable and has no optical isomers. On the other hand, if the mirror image cannot be rotated in any way such that it looks identical to the original molecule, then the molecule is said to be non-superimposable and the molecule has optical isomers. Once again, if the mirror image is superimposable, then no optical isomers but if the mirror image is non-superimposable, then optical isomers exist.

Non-superimposable means the structure cannot be rotated in a way that one can be put on top of another. This means that no matter how the structure is rotated, it cannot be put on top of another with all points matching. An example of this is your

hands. Both left and right hands are identical, but they cannot be put on top of each other with all points matching. 

Example  

Consider the tetrahedral molecule, CHBrClF (note the color scheme: grey=carbon, white=hydrogen, green=chlorine, blue=fluorine, red=bromine)

Is this molecule optically active? In other words, does this molecule have optical isomers?

First take the Mirror-image method. The mirror image of the molecule is:

Note that this mirror image is not superimposable. In other words, the mirror image above cannot be rotated in any such way that it looks identical to the original molecule. Remember, if the mirror image is not superimposable, then optical isomers exist. Thus we know that this molecule has optical isomers.

Let's try approaching this problem using the symmetry method. If we take the original molecule and draw an axis or plane of symmetry down the middle, this is what we get:

Since the left side is not identical to the right, this molecule does not have a symmetrical center and thus can be called chiral. Additionally, because it does not have a symmetrical center, we can conclude that this molecule has optical isomers. In general, when dealing with a tetrahedral molecule that has 4 different ligands, optical isomers will exist most of the time.

No matter which method you use, the answer will end up being the same.

Example  

This time we will be analyzing the octahedral compound FeCl3F3 (note the color scheme: orange=iron, blue=fluorine, green=chlorine):

If we try to attempt this problem using the mirror image method, we notice that the mirror image is essentially identical to the original molecule. In other words, the mirror image can be placed on top of the original molecule and is thus superimposable. Since the mirror image is superimposable, this molecule does not have any optical isomers. Let's attempt this same problem using the symmetry method. If we draw an axis or plane of symmetry, this is what we get:

Since the left side is identical to the right side, this molecule has a symmetrical center and is an achiral molecule. Thus, it has no optical isomers. 

What is a polarimeter?

A polarimeter is a cylinder tube which a single ray of light can be shot through. Another way to distinguish whether a molecule is chiral or achiral is to shine light through that molecule. If no light passes that molecule then the molecule is achiral and does not have optical isomers. On the other hand, if light passes through the molecule, it is chiral and has optical isomers. Another interesting fact about optical isomers is that they have the ability to polarize and rotate light passed through them. These type of optical isomers are classified based on how they rotate the light. If the isomer rotates the light in the left direction, then it is called levorotatory. If the isomer rotates the light in the right direction, then it is called dextrorotatory. Often times, certain drugs or proteins also depend on stereoisomers for function because only one correct stereoisomer of the molecule can function effectively as the drug or protein.

Applications

Stereoisomers have a lot of applications in biology as well as our day to day lives. Surprisingly, our own tongue contains chiral molecules that help us discern the taste of some of the foods we eat. For example, we may eat two of the same leaves but one may taste bitter and the other may taste sweet because of chirality. As discussed above, optical isomers also have the ability to rotate light in certain directions. In biological terms, chirality is key to the proper functioning of an enzyme. This is because chirality allows the enzyme to function efficiently by being able to bind to only certain substrates.

Problems

1) Draw all possible geometric isomers for the tetrahedral molecule MnCl2F2.

2) What type of isomer is the molecule pictured below? Are there any other types of isomers possible for this molecule?

3) Draw all possible stereoisomers for the molecule CrF3I3. 

4) What is the difference between a dextrorotatory optical isomer and a levorotatory optical isomer?

5) Draw the molecule Fe(en)3 and state if it is optically active or not.

6) True or False: An octahedral molecule can have cis-trans isomers? 

Answers

1) MnCl2F2 has no geometric isomers because recall that tetrahedral molecules do not have geometric isomers.

2) The molecule, FeBr2I2 pictured in problem 3 is a cis isomer, or cis-FeBr2I2, because both the Br and I ligands are on the same side. There is one more stereoisomer for this molecule: trans-FeBr2I2, pictured below:

3) This molecule has two isomers: mer-CrF3I3 and fac-CrF3I3, both are pictured below. The mer isomer is where the ligands are not on the same plane and there exists a 90-90-180 degree bond angle between the 3 same ligands. The fac isomer is where the ligands are on the same plane and there exists a 90-90-90 degree bond angle between the 3 same ligands.

fac-CrF3I3:

mer-CrF3I3:

4) A dextrorotatory optical isomer is a isomer that can rotate light in the right direction. A levorotatory optical isomer on the other hand is a isomer that can rotate light in the left direction.

5) In the molecule Fe(en)3, recall that the en ligand, ethylenediamine is a bidentate ligand. The 2D structure of this molecule is shown below:

Note, the black lines represent the bonds and the blue lines represent the bonds ethylenediamine binds to. Using either the symmetry method or the mirror image method, one can observe that this molecule has a chiral center and that the mirror image is not superimposable on the original molecule. Thus, this molecule is optically active because it has optical isomers.

6) True. Octahedral geometry as well as square planar geometry can have cis-trans isomers. The only geometry that cannot have cis-trans isomers is tetrahedral.