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Drawing Enantiomers: Mastering Isomerism and Stereochemistry
Unlock the secrets of molecular structures! Learn how to draw enantiomers and understand isomerism, stereochemistry, and chirality. Boost your organic chemistry skills for better drug design and material creation.

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Now Playing:Drawing structures isomerism stereochemistry and chirality – Example 0a
Intros
  1. Drawing correct chemical structures.
  2. Drawing correct chemical structures.
    How do different chemicals have the same formula?
  3. Drawing correct chemical structures.
    Chain isomers.
Drawing structures in organic chemistry
Jump to:NotesConceptExampleFAQsPrerequisites
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.
    Concept

    Introduction to Isomerism and Stereochemistry

    Isomerism and stereochemistry are fundamental concepts in organic chemistry that deal with the spatial arrangement of atoms in molecules. Isomers are compounds with the same molecular formula but different structural arrangements, while stereochemistry focuses on the three-dimensional orientation of atoms in space. Understanding these concepts is crucial for grasping the behavior and reactivity of organic structures. The ability to visualize and interpret 3D representations of molecules is essential for predicting their reactivity, physical properties of molecules, and biological activity. This article includes an introductory video that explains these concepts in detail, helping students and researchers alike to better comprehend the complexities of molecular structures. By mastering isomerism and stereochemistry, chemists can design more effective drugs, create novel materials, and unravel the mysteries of biochemical processes. Whether you're a beginner or an experienced chemist, this overview will enhance your understanding of these vital aspects of organic chemistry.

    Understanding the reactivity of organic structures is essential for predicting their behavior in different chemical reactions. Additionally, knowing the physical properties of molecules helps in determining their suitability for various applications in pharmaceuticals, materials science, and biochemistry.

    Example

    Drawing correct chemical structures. How do different chemicals have the same formula?

    Step 1: Introduction to Isomerism and Stereochemistry

    This lesson introduces the concepts of isomerism and stereochemistry. These are crucial topics in organic chemistry that help us understand how different chemicals can have the same molecular formula but different structures and properties. When we draw organic structures, we need to think beyond the 2D representation on paper or a screen and consider the 3D nature of these molecules in the real world.

    Step 2: Understanding the Objectives

    The objectives of this lesson include recalling the types of isomerism, learning their definitions, and identifying and drawing organic molecules in a way that distinguishes them. This is important to avoid confusion, especially when dealing with asymmetrical molecules that can be easily mistaken for different compounds if not drawn correctly.

    Step 3: Types of Isomerism

    Isomerism refers to compounds that have the same chemical formula but different arrangements of atoms in 3D space. There are several types of isomerism, including structural isomerism and stereoisomerism. Structural isomers have the same molecular formula but different bonding arrangements among atoms. Stereoisomers have the same bonding arrangements but differ in the spatial orientation of atoms.

    Step 4: Drawing Organic Molecules

    When drawing organic molecules, it is essential to represent them in a way that clearly shows their 3D structure. This helps in distinguishing between different isomers. For example, using skeletal formulas can simplify the representation of carbon chains, focusing on the functional groups that interact with the outside world.

    Step 5: The Concept of Asymmetry

    Asymmetry in organic molecules means that the molecule lacks symmetry, which can lead to different properties and behaviors. Drawing these molecules correctly is crucial to avoid confusing one molecule for another. This is especially important in stereochemistry, where the 3D arrangement of atoms can significantly impact the molecule's properties.

    Step 6: Functional Groups and Their Importance

    In a chemical compound, the carbon chain provides stability, but it is the functional groups that determine the molecule's reactivity and interactions. Drawing structures correctly, including the functional groups, helps prevent confusion with isomers. Functional groups are the parts of the molecule that participate in chemical reactions, and their arrangement can lead to different isomers with distinct properties.

    Step 7: Analogies to Understand Isomerism

    To understand isomerism, consider an analogy of a stick figure. If you rearrange the parts of the stick figure without adding or removing any components, you get a different arrangement that represents an isomer. Similarly, in chemistry, isomers have the same core components but are arranged differently in 3D space, leading to different properties.

    Step 8: Stereochemistry and 3D Arrangement

    Stereochemistry focuses on the 3D arrangement of atoms in a molecule. Different arrangements can result in different properties, even if the molecular formula remains the same. Understanding and drawing the stereochemistry of molecules is essential for accurately representing their structure and predicting their behavior.

    Step 9: Practical Examples of Isomerism

    To solidify your understanding, look at practical examples of isomerism in simple hydrocarbons and more complex organic molecules. Practice drawing these molecules to show their 3D nature and distinguish between different isomers. This will help you develop a strong foundation in organic chemistry and avoid confusion when dealing with more complex compounds.

    FAQs

    Here are some frequently asked questions about drawing enantiomers:

    1. What is the method of drawing enantiomers?

    To draw enantiomers, start by drawing the original molecule using wedge-and-dash notation or Fischer projection. Then, create the mirror image by switching the positions of any two substituents around each chiral center. Alternatively, draw the mirror image of the entire structure and rotate it 180 degrees.

    2. Does it matter how you draw enantiomers?

    Yes, it matters. The spatial arrangement of atoms in enantiomers is crucial. Ensure you accurately represent the 3D structure using proper notation (e.g., wedges and dashes) and maintain the correct stereochemistry at all chiral centers.

    3. How to figure out enantiomers?

    Identify chiral centers in the molecule (usually carbon atoms with four different substituents). Draw the mirror image of the molecule, then check if the mirror image is superimposable on the original. If not superimposable, they are enantiomers.

    4. How to draw enantiomers of cyclic compounds?

    For cyclic compounds, focus on the chiral centers. Draw the ring structure, then create the enantiomer by changing the orientation of substituents at the chiral centers. Remember to maintain the ring's shape and connectivity while altering the stereochemistry.

    5. How do you draw S and R enantiomers?

    To draw S and R enantiomers, first assign priorities to substituents using CIP rules. For the S enantiomer, arrange substituents so that priority decreases clockwise when viewed with the lowest priority group in the back. For the R enantiomer, arrange them counterclockwise. Use wedge-and-dash notation to clearly show the 3D arrangement.

    Prerequisites

    Understanding the fundamental concepts of organic chemistry is crucial before delving into the complex world of "Drawing structures: Isomerism, stereochemistry and chirality." While there are no specific prerequisite topics listed for this subject, it's important to recognize that a strong foundation in basic chemistry principles is essential for grasping these advanced concepts.

    To fully comprehend isomerism, stereochemistry, and chirality, students should have a solid understanding of atomic structure, chemical bonding, and molecular geometry. These foundational topics provide the necessary framework for visualizing and interpreting the three-dimensional arrangements of atoms in molecules.

    Additionally, familiarity with organic compounds and their nomenclature is vital. This knowledge allows students to recognize different functional groups and understand how they contribute to the overall structure and properties of molecules. Being able to identify and name organic compounds is a stepping stone to exploring their isomeric relationships and stereochemical characteristics.

    Basic principles of chemical reactions and mechanisms are also relevant, as they help explain how different isomers can form and interconvert. Understanding reaction kinetics and thermodynamics can provide insights into the stability and reactivity of various stereoisomers.

    Moreover, a grasp of basic mathematical concepts, particularly geometry and spatial reasoning, is beneficial when studying stereochemistry and chirality. These skills aid in visualizing and manipulating molecular structures in three-dimensional space.

    While not explicitly listed as prerequisites, topics such as Lewis structures, VSEPR theory, and hybridization are closely related to drawing structures and understanding molecular geometry. These concepts serve as a bridge between basic atomic theory and the more advanced ideas of isomerism and stereochemistry.

    By building a strong foundation in these underlying principles, students will be better equipped to tackle the complexities of isomerism, stereochemistry, and chirality. They will be able to draw and interpret structural diagrams more effectively, recognize different types of isomers, and understand the significance of chirality in chemical and biological systems.

    As students progress in their study of "Drawing structures: Isomerism, stereochemistry and chirality," they will find that these fundamental concepts continually resurface, reinforcing their importance. The ability to draw accurate structural representations, identify isomeric relationships, and understand the three-dimensional nature of molecules is crucial in many areas of chemistry, including organic synthesis, drug design, and biochemistry.

    In conclusion, while there may not be a specific list of prerequisite topics, a comprehensive understanding of basic chemistry principles is essential for success in this advanced area of study. Students are encouraged to review and strengthen their knowledge of these foundational concepts to ensure a smooth transition into the fascinating world of isomerism, stereochemistry, and chirality.