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Drawing Organic Structures: Foundation of Chemistry
Unlock the power of organic chemistry drawings. Learn essential techniques for representing molecules, predicting reactivity, and mastering structural concepts. Perfect for students and aspiring chemists.

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Now Playing:Drawing structures in organic chemistry – Example 0a
Intros
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  1. Communicating in organic chemistry.
  2. Communicating in organic chemistry.
    Why we use skeletal formula.
  3. Communicating in organic chemistry.
    How to draw skeletal formula.
Introduction to organic chemistry
Jump to:NotesConceptFAQsPrerequisites
Notes

In this lesson, we will learn:

  • To understand and apply skeletal formula in communicating structures in organic chemistry.
  • To understand the limitations of using skeletal formula alone.
  • To recognize and draw organic structures using skeletal formula and group abbreviations.

  • Skeletal formula is the major tool chemists use to communicate the structure of a compound in organic chemistry. There are a few reasons why this became convention:
    • All organic compounds contain a carbon 'backbone' of some sort, so carbon-carbon bonds are extremely common.
    • Carbon-hydrogen bonds are also extremely common in organic molecules, and most of them do very little reacting in organic reactions!
    • Most of the properties and reactions of a chemical compound are predicted by its functional groups, not the carbon chain length! Chemists are normally only interested a few atoms in what could be a very large molecule.
  • This means chemists needed a way of communicating chemicals quickly without wasting time on basics that were not of interest. Skeletal formula represents carbon and hydrogen atoms as the background 'skeleton' of organic molecules:
    • Carbon atoms are drawn as a joint in a zig-zag chain. The zig-zag is the carbon chain backbone of the organic compound being shown. The 'ends' of the zig zag chains count as carbon atoms as well. Zig-zags are a reasonable compromise for the bond angles around a tetrahedral carbon atom.
    • Hydrogen atoms bonded to carbon are 'implicit' meaning they are present but not shown in the zig zag structure. This means that wherever a zig-zag joint (a carbon atom) is found, if the number of bonds to it does not add up to four (carbon's valence) then it is implied that the carbon atom is bonded to as many hydrogen atoms to add up to four bonds in total.
    • Multiple bonds are simply shown with the appropriate number of lines between 'joints' in the zig zag. For example a double line shows a C=C bond, a triple line shows a C≡\equivC bond. The zig-zag chain is straight at the atoms with multiple bonds – double and triple bonded carbon have different bond angles to an all single bonded carbon!
  • These are the fundamentals of skeletal formula. In short, skeletal formula allows chemists to be:
    • Practical - we don't waste time measuring and drawing the precise bond angles between atoms on our drawings. The zig-zag chains show approximate angles of a 3d molecule on a 2d surface (e.g. the paper you draw the structure on).
    • Clear – it is easy to see what is important as the unimportant features (e.g. parts that are not reacting) are not given unnecessary attention.
    • Concise – only the most important parts of a chemical structure, the atoms and functional groups where reactions take place, are shown prominently.
    You can think of skeletal formula as a sketch in chemistry, instead of a full portrait painting!
  • There are however, times when skeletal formula is still not enough. Let's recap earlier points - how useful is skeletal formula alone?
    • There are millions of unique organic compounds which have a carbon 'backbone' of some sort.
    • It is the functional groups, not carbon chain length that dictates a substance's chemical properties. In most cases, chain length does not have a lot of impact on chemical properties.
    Add to this some other points:
    • Some organic compounds are very complex but differ from other very different compounds by only one or two atoms/bonds.
    • When writing a complete equation, you normally include the solvent and all other reagents like any bases, acids or catalysts you used. It is very time consuming to draw skeletal formula for all the compounds present in a full experimental method.
  • With that said, skeletal formula can still leave chemists with too many bonds to draw or a lot of pointless communicating to do, especially when describing complex molecules!
    Chemists have abbreviations for alkyl chains and functional groups to simplify a structure, so only the bonding of the important (read: reacting) groups are displayed:
    • Terminal alkyl chains are by far the most 'abbreviated' groups in complex organic structures because when part of complex molecules, alkyl chains are normally not changing. The abbreviations are:
      • Methyl chain (-CH3): -Me
      • Ethyl chain (-CH2CH3): -Et
      • Propyl chain (-CH2CH2CH3): -Pr
      • Butyl chain (-CH2CH2CH2CH3): -Bu
    • With some alkyl chains, there may be specific chain isomers named. This is common with butyl and propyl chains where the isomers are sometimes used (e.g. in organometallics). The most common of these are:
      • Isopropyl, (-CH(CH3)CH3): -iPr
      • N-butyl (-CH2CH2CH2CH3): -nBu
      • Sec-butyl (-CH(CH3)CH2CH2): -sBu
      • Isobutyl (-CH2CH(CH3)2): -iBu
      • Tert-butyl (-C(CH3)3): -tBu
      • Neopentyl (-CH2C(CH3)3): -Np
    • Common cyclic and aromatic rings are also abbreviated a lot in complex molecules:
      • Phenyl (-C6H5): -Ph
      • Benzyl (-CH2C6H5): -Bn
      • Pyridyl (-C5H5N): Py
      • Aryl, a generic word for any substituted aromatic ring: -Ar
    • Many functional groups and compounds that are generally used or otherwise important in chemical reactions (e.g. solvents, bases and leaving groups) will be abbreviated in equations:
      • Ethanoyl groups (-C(O)CH3) are nearly always called acetyl: -Ac
      • Tosyl (-SO2C6H4(CH3)), a common leaving group used in organic synthesis: -Ts
    The abbreviations are used on terminal parts of a molecule only! It is incorrect to use abbreviations in between skeletal formula – the abbreviations are for ends of the molecule that are not playing a part in the chemistry being investigated at that moment. Abbreviations and acronyms combined with skeletal formula allow chemists to communicate only the most important aspects of a reaction or chemical structure conveniently without leaving any information out.
  • The abbreviations are often seen with otherwise simple compounds in chemical equations:
    • Alcohols will be abbreviated in equations such as EtOH for ethanol or MeOH for methanol, especially if they are not a reacting species (e.g. if they are the solvent).
    • The Ac (acetyl/ethanoyl) abbreviation is very common in carbonyl chemistry such as for AcOH (acetic acid AKA ethanoic acid) and EtOAc (the ester ethyl acetate AKA ethyl ethanoate).
    • Reagents or ligands with straightforward but large structures are abbreviated, such as triphenylphosphine which is written PPh3. This can be bound to some metals numerous times, such as [Pd(PPh3)4)] – understandably chemists prefer to abbreviate this compound instead of drawing twelve aromatic rings!
    Concept

    Introduction to Drawing Structures in Organic Chemistry

    Drawing structures is a fundamental skill in organic chemistry drawings, essential for understanding molecular composition and reactivity. This article introduces the importance of structural representation and provides a comprehensive guide for students. The accompanying introduction video serves as a visual aid, demonstrating basic techniques and conventions used in organic chemistry drawings. By mastering these skills, students can effectively communicate complex molecular information and predict chemical behavior. Topics covered include Lewis structures, skeletal formulas, and stereochemistry representations. We'll explore how different drawing methods convey specific details about bonding, geometry, and spatial arrangements of atoms. Understanding these representations is crucial for success in organic chemistry courses and research. The ability to accurately draw and interpret molecular structures forms the foundation for more advanced concepts in the field. This guide aims to equip students with the necessary tools to confidently approach structural drawing in organic chemistry.

    FAQs

    1. What is the importance of skeletal formulas in organic chemistry?

      Skeletal formulas are crucial in organic chemistry as they provide a simplified yet informative representation of molecular structures. They focus on the carbon skeleton, emphasizing carbon-carbon bonds and functional groups while omitting hydrogen atoms for clarity. This method allows chemists to quickly identify and analyze important structural features, especially in complex molecules. Skeletal formulas are particularly useful in reaction schemes, structural analysis, and communication of molecular information in both academic and industrial settings.

    2. How do abbreviations enhance the representation of organic molecules?

      Abbreviations in organic chemistry significantly enhance molecular representation by condensing complex structural elements into manageable symbols. Common abbreviations like "Me" for methyl, "Et" for ethyl, and "Ph" for phenyl groups save space and improve readability, especially in reaction schemes or when comparing multiple compounds. They are particularly valuable when dealing with large molecules, natural products, or pharmaceuticals, allowing chemists to highlight important structural features while simplifying less relevant portions of the molecule.

    3. What are some limitations of skeletal formulas?

      While skeletal formulas are widely used, they have limitations, especially when dealing with complex molecules. They can become cluttered and difficult to interpret for large molecules or those with numerous substituents. Skeletal formulas may not effectively represent certain structural features like stereochemistry or complex ring systems. Additionally, they can be unwieldy when representing repeating units in polymers or large biomolecules. To overcome these limitations, chemists often use additional notations and conventions to supplement skeletal formulas.

    4. How are skeletal formulas and abbreviations used in reaction schemes?

      In reaction schemes, skeletal formulas and abbreviations are combined to represent complex chemical transformations concisely. This approach allows chemists to clearly communicate reaction pathways, especially in multi-step syntheses. For example, in a Diels-Alder reaction, the diene and dienophile can be represented using simple line structures, with double bonds clearly visible. Common reagents are often abbreviated (e.g., LiAlH4 for lithium aluminum hydride). This notation system is particularly valuable in academic publications, patent applications, and industrial process development, where clarity and efficiency in communication are crucial.

    5. Why is mastering structural representation techniques important for students of organic chemistry?

      Mastering structural representation techniques is essential for success in organic chemistry because it forms the foundation for understanding molecular composition, reactivity, and properties. Proficiency in drawing and interpreting structures like Lewis structures, skeletal formulas, and using abbreviations enables students to effectively communicate complex chemical information, predict chemical behavior, and solve problems in organic synthesis. These skills are crucial for advanced coursework, research, and future careers in chemistry-related fields. Regular practice in drawing structures and using abbreviations enhances overall comprehension of organic chemistry principles and improves performance in both academic and professional settings.

    Prerequisites

    Understanding the fundamental concepts that lay the groundwork for drawing structures in organic chemistry is crucial for students aiming to master this essential skill. Two key prerequisite topics that significantly contribute to this understanding are Lewis structures and arrow pushing (curly arrows) in organic chemistry.

    Lewis structures serve as the foundation for visualizing molecular geometry and understanding bonding in organic compounds. These diagrams represent the distribution of valence electrons around atoms, showing how they form covalent bonds. Mastering Lewis structures is essential because they provide insights into the arrangement of atoms within molecules, which directly translates to drawing more complex organic structures.

    When students become proficient in creating Lewis structures, they develop a intuitive understanding of how atoms connect and share electrons. This knowledge is invaluable when progressing to drawing structures in organic chemistry, as it allows for a more natural comprehension of molecular shapes, bond types, and electron distribution. The ability to quickly sketch Lewis structures also aids in predicting reactivity and understanding reaction mechanisms in organic chemistry.

    Building upon the foundation of Lewis structures, arrow pushing (curly arrows) in organic chemistry is another critical prerequisite topic. This concept involves using curved arrows to illustrate the movement of electron pairs during chemical reactions. Understanding arrow pushing is vital for drawing structures in organic chemistry because it allows students to visualize and predict how molecules transform during reactions.

    Arrow pushing techniques enable students to track the flow of electrons, helping them understand how bonds break and form. This skill is particularly important when drawing reaction mechanisms, where multiple steps may be involved in transforming one organic structure into another. By mastering arrow pushing, students can more easily draw and interpret complex organic structures, including those involved in multi-step syntheses and reaction pathways.

    The synergy between Lewis structures and arrow pushing creates a powerful toolkit for drawing structures in organic chemistry. Students who have a solid grasp of these prerequisite topics will find themselves better equipped to tackle more advanced concepts in organic chemistry. They will be able to draw structures with greater accuracy, predict reaction outcomes more reliably, and understand the underlying principles of organic transformations more deeply.

    In conclusion, the importance of mastering these prerequisite topics cannot be overstated. A strong foundation in Lewis structures and arrow pushing will significantly enhance a student's ability to draw and interpret organic structures, setting the stage for success in more advanced organic chemistry courses and research.