Drawing structures: Isomerism, stereochemistry and chirality - Introduction to Organic Chemistry

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Drawing structures: Isomerism, stereochemistry and chirality

Lessons

Notes:

In this lesson, we will learn:

  • To recall the different types of isomerism that exist in organic chemistry.
  • How to identify and draw organic molecules in a way that distinguishes possible isomers.
  • How to identify asymmetric organic molecules and draw them in a way that identifies stereocenters.

Notes:

  • In the lesson CO.1.2: Drawing organic structures we learned how to draw structures and simplify the common and usually not important carbon chains. Drawing structures correctly helps to avoid confusion with possible isomers.
    • Isomers are compounds with the same chemical formula as each other but a different arrangement of their atoms in 3d space.
    There are many different types of isomerism because there are many different ways atoms can arrange in a molecule! Some pairs of isomers are similar in properties and reactivity, whilst others are the difference between a toxic substance and an effective medicine. It's important that when studying and drawing chemical structures using a 2d surface (be it a piece of paper, tablet or computer screen) we understand what it means and will look like in our real-life 3d world. We need to be able to draw molecules in a way that communicates their stereochemistry – their 3d nature.
  • The first type of isomers you are likely to see in organic chemistry are chain isomers. Chain isomers are compounds with the same chemical formula but different branching of the main carbon chain.
    • Examples of chain isomerism hydrocarbons would be with compounds with the chemical formula C5H12. There is more than one way you can draw C5H12 as a molecule:
      These are all different chemical compounds with some different properties.
  • Another common type of isomer is positional isomerism. Positional isomers have the same chemical formula but a different carbon chain numbering of their functional groups.
    • For example, the formula C4H9OH could be butanol. If we assume it is a straight 4-carbon chain with the alcohol group (-OH), it could be drawn and named in the following two ways:
    Butan-1-ol is a primary alcohol (the –OH group is attached to a terminal carbon atom) and butan-2-ol is a secondary alcohol (the –OH group is attached to a carbon bonded to two other carbons), which affects their reactivity.
  • In the previous example we showed butanol as C4H9OH – it's common to write the formula of alcohols like this to show the OH group that makes it an alcohol. It could have (also correctly) be written as C4H10O, which is less clear! Can C4H10O be something other than an alcohol?
    • If we look at the formula C4H8O, we could draw a few different molecules with this formula:
    All of these molecules have the formula C4H8O but the atoms arrange to form different functional groups. This is called functional group isomerism. Because they have different functional groups these compounds all have different chemical properties to each other. We'll look at the actual functional groups and their properties later.
  • When carbon atoms double bond to each other to create an alkene group (C=C), the two carbon atoms experience restricted rotation – their attachments are fixed in position relative to one another! This leads to geometric isomerism, which is a different arrangement of groups or atoms in a molecule around a bond of restricted rotation (such as a double bond). Geometric isomerism leads to compounds with different properties:

    The two isomers that a double bond can create are called the cis ('same side') and trans ('across') isomers, that's why geometric isomerism is sometimes called cis/trans isomerism. When getting into more complicated molecules, the signs E (for cis- positions) and Z (for trans- positions) are used. With cis/trans isomerism, you need restricted rotation (e.g. from a double bond) for the cis/trans positions to be fixed, because a single bond can freely rotate).
  • When carbon has four single bonded attachments it makes a tetrahedral (four faces) shape, with equal bond angles of 109.5° (See our lesson on C11.4.5: Molecular Geometry for more on this).
    This is usually drawn as shown below.
    • Two attachments will face left/right in the plane of the paper pointing down, usually the rest of the molecule's carbon chain.
    • The other two are facing toward/away from the viewer pointing up; imagine those two are in their own separate zig-zagging carbon chain going straight through the paper.
    • Atoms pointing towards us are drawn with wedges for their bond and atoms facing away from us are drawn with dashed lines.
    If all four attachments on a carbon atom are different then the carbon atom is chiral. This chiral center makes an asymmetric molecule; if you made a mirror image of it, one mirror image would never be able to rotate into exactly the same 3d arrangement as its partner.
    • Your hands are equivalent but non-identical mirror image objects! You can rotate your hands to arrange your thumbs in the same direction, but your palms will never face the same way when your thumbs are. They are non-superimposable mirror images.
    In chemistry, non-identical mirror image molecules are called enantiomers. Enantiomers are unique chemical compounds with different properties and when drawing compounds that have chiral centers it is important to draw the wedges and dashed lines in the correct way to represent the molecule. Getting them the wrong way around is drawing the wrong chemical!
    Enantiomers are of interest to chemists because the human body (and nature in general) is full of chiral compounds (like enzymes) which will interact with two different enantiomers in two different ways.
  • The different properties of different isomers will be looked at later on, but the stereochemistry of some compounds has had major real world consequences. Below are a few examples of isomers and the differences between them:
    • Cis-platin, [Pt(NH3)2Cl2] is a compound used in many anti-cancer treatments. You should be able to see from the name that cis-platin has a type of geometric isomerism. Here the bonding of platinum makes a flat square planar (see C11.4.5: Molecular geometry) molecule where the two NH3 and Cl attachments don't rotate (just like if there was a double bond) and the two Cl atoms sit next to each other. In contrast, cisplatin's geometric isomer transplatin does not have the anticancer properties that cisplatin does.
    • Thalidomide was a sedative medicine, also used to treat morning sickness during pregnancy in the mid-1950s. Thalidomide's structure has a chiral carbon atom, so the molecule has two enantiomers. It was supplied as a racemic mixture (an equal amount of both enantiomers), but while one enantiomer was the effective medicine, the other caused defects in unborn children that led to thousands of deaths.
      Even if only the effective, medicinal enantiomer was supplied, the enantiomers can convert from one to the other in the body, so the harmful enantiomer would have still become present in the body and caused the disaster.
    • Intro Lesson
      Drawing correct chemical structures.
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    Drawing structures: Isomerism, stereochemistry and chirality

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