Drawing structures in organic chemistry - Introduction to Organic Chemistry

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Drawing structures in organic chemistry

Lessons

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?C 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!
    • Intro Lesson
      Communicating in organic chemistry.
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    Drawing structures in organic chemistry

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