> For the complete documentation index, see [llms.txt](https://jamesbrayy.gitbook.io/atar/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://jamesbrayy.gitbook.io/atar/chemistry/organic.md).

# organic

***

## **hydrocarbons**

#### *alkanes*

* contain only single $$\mathrm{C-C}$$ bonds (saturated)
* always demonstrate the formula $$\mathrm{C\_nH\_{2n+2}}$$
* *substitution reactions:*
  * slow
  * require UV light for halogens

#### *alkenes*

* contain at least one double $$\mathrm{C=C}$$ bond (unsaturated)
* demonstrate the formula $$\mathrm{C\_nH\_{2n}}$$
* *addition reactions:*
  * substances such as halogens, hydrogen, hydrogen halides will readily add across the double bond
  * fast
  * once the reaction has completed, substitution can occur if exposed to UV light

#### *aromatic compounds*

* aromatic compounds are composed of a benzene ring with atoms/groups bonded to it
* all the carbon-carbon bonds in benzene are equivalent, meaning they are neither single nor double bonds; they are all te same length somewhere between the length of a single and double carbon-carbon bond

## **functional groups**

#### *alcohols (*$$-\mathrm{OH}$$*):*

* *types of alcohols:*
  * primary alcohols have 1 carbon atom attached to the carbon atom that the $$\mathrm{OH}$$ group is bonded to
  * secondary alcohols have 2, and tertiary alcohols have 3
* *physical properties:*
  * boiling point is higher than that of the parent alcohol
  * solubility in water decreases with increasing chain length
    * this is due to an increased number of electrons, causing an increase in the strength of dispersion forces
* alcohols also combust in excess air to form $$\mathrm{CO\_2}$$ and $$\mathrm{H\_2O}$$

#### *carboxylic acid (*$$-\mathrm{COOH}$$*):*

* *physical properties:*
  * boiling points are higher than similar alcohols as the carbonyl group acts as another location for hydrogen bonding
  * soluble in water
  * weak acids, with strength decreasing as the chain length increases

#### *esters (*$$-\mathrm{COO}-$$*):*

* esters are formed from the esterification reaction of a carboxylic acid with an alcohol in the presence of a concentrated acid catalyst (*e.g.* concentrated $$\mathrm{H\_2SO\_4}$$)
  * ![](/files/7rnfJwTx3rgPtWK5QyPv) ethanoic acid ethanol ethanoate (ethyl)
* *hydrolysis of esters:*
  * hydrolysis is a means of conversion of the ester to the original alcohol and either the carboxylic acid or the salt of the acid
  * either $$\mathrm{H\_3O^+}$$ or $$\mathrm{OH^-}$$ acts as a catalyst
    * *warming with acid ($\mathrm{H\_3O^+}$):*
      * $$\mathrm{R-COO-R' \rightarrow RCOOH + R'OH}$$
      * $$\mathrm{H\_3COCOH + H\_2O \rightarrow HCOOH + CH\_3OH}$$
    * *warming with base ($\mathrm{OH^-}$):*
      * $$\mathrm{R-COO-R' \rightarrow RCOO^- + R'OH}$$
* *physical properties:*
  * fruity odour

#### *amines (*$$-\mathrm{NH}*2$$*):\_

* *physical properties:*
  * boiling point is relatively low as the hydrogen bonding between amines is weaker because the difference in electronegativity between $$-\mathrm{N}$$ and $$-\mathrm{H}$$ is less than that between $$-\mathrm{O}$$ and $$-\mathrm{H}$$
  * soluble in water through hydrogen bonding
  * pungent odour like ammonia
  * weak bases and form basic solutions when hydrolysed

#### *amides (*$$=\mathrm{O}$$*,* $$-\mathrm{NH}*2$$*):\_

* formed similarly to esters with an amine reacting with a carboxylic acid
  * ![](/files/b2kihEniwABqUqiD7620)
  * primary amides are prepared by reaction of $$(\mathrm{NH\_4})\_2\mathrm{CO\_3}$$ with a corresponding carboxylic acid:
    * *e.g.* $$\mathrm{2CH\_3COOH (aq) + (NH\_4)\_2CO\_3 (aq) \rightarrow 2CH\_3COONH\_4 (aq) + CO\_2 (g) + H\_2O (l)}$$
* *types of amides:*
  * ![](/files/ZV4m6rTP8BGsVxsfhWSX) primary secondary tertiary
* *hydrolysis of amides:*
  * $$\mathrm{R-CO-NH\_2 + H\_2O + H^+ \rightarrow R-COOH + NH\_4^+}$$
  * $$\mathrm{R-CO-NH\_2 + NaOH \rightarrow R-COONa + NH\_3}$$
* *physical properties:*
  * boiling points are higher than similar amines as there are two locations for hydrogen bonding

#### *aldehydes (*$$=\mathrm{O}$$ *at terminal):*

* *physical properties:*
  * boiling point is lower than that of the parent alcohol
  * solubility in water decreases with increasing chain length

#### *ketones (*$$=\mathrm{O}$$ *mid-chain):*

* *physical properties:*
  * not able to be easily oxidised

#### *α-amino acids (*$$-\mathrm{COOH}$$*,* $$-\mathrm{NH}*2$$*):\_

* the α indicates that both the amine and carboxyl groups are attached to the same terminal carbon atom
* behave as amphoteric molecules as they can form zwitterions (molecules with both + and - ions)
  * in basic conditions the carboxylic acid group can donate an $$\mathrm{H^+}$$ ion
  * in acidic conditions the amine functional group accepts an $$\mathrm{H^+}$$ ion
* *physical properties:*
  * at room temperature, amino acids are all solids with relatively high melting/boiling points
  * soluble in water
  * typically exist in their ionic forms in the solid and aqueous state

## **redox of organic molecules**

* there are two oxidants that are typically used. these are either:
  * acidified dichromate ($$\mathrm{Cr\_2O\_7^{2-}/H^+}$$)
    * orange
    * reduced to $$\mathrm{Cr^{3+}}$$ (green)
  * acidified permanganate ($$\mathrm{MnO\_4^- / H^+}$$)
    * purple
    * reduced to $$\mathrm{Mn^{2+}}$$ (pale pink, virtually colourless)
* ![](/files/ZNbwMvu8D9ccCcIvb5Bh)

## **polymers:**

* polymers are large molecules formed by the reaction of small molecules called monomers **proteins:**
* proteins are macromolecules consisting of amino acid monomers joined together by peptide linkages
  * ![](/files/HwdQ1j37Ctw3W9x2Jcqt)
* sequences of less than 50 amino acids are typically called peptides

#### *protein structure*

* *primary structure:*
  * the primary structure of a protein is given by the amino acids sequence of the protein
* *secondary structure:*
  * within the long protein chains there are regions in which the chains are organised into regular structures
  * *alpha helix:*
    * ![](/files/vx1K7Ki7VD43xGN6Hp34)
  * *beta pleated sheets:*
    * ![](/files/tAYFhOEvU7HOAYTlzZMW)
* *tertiary structure:*
  * the tertiary structure of a protein is a description of the way the whole chain (including the secondary structures) folds itself into its final 3-dimensional shape
  * this shape determines the function of the protein
  * *forces involved:*
    * ionic interactions
    * H-bonds in side chains
    * dispersion forces
    * disulfide bridges
* *quaternary structure:*
  * the quaternary structure is the arrangement of proteins with more than one amino acid chain and how these fold and arrange themselves in 3D
* ![](/files/jVy7wcdC1YuU4fCuKJHC)

## **soaps and detergents**

#### *fats and oils*

* soaps are derived from natural fats and oils (esters referred to as triglycerides) and are formed from the same alcohol precursor (glycerol / triol)
  * ![](/files/qptGdNorEtM5398EqR1m)
* glycerol requires a carboxylic acid (normally referred to as a fatty acid) to form a triester fat
  * they have long unbranched chains, between $$\mathrm{C\_{10}}$$ and $$\mathrm{C\_{20}}$$ and contain no other functional groups
  * ![](/files/a67eYaI1ramwEPhXugip)
* *properties:*
  * the long hydrocarbon chains of the fat (triglyceride) is non-polar meaning dispersion forces over most molecules are predominant
  * animal fats are usually saturated (*i.e.* single $$\mathrm{C-C}$$ bond) whereas plant oils are often unsaturated (*i.e.* containing at least one $$\mathrm{C=C}$$ bond)

#### *hydrolysis of triglycerides*

* triglycerides may be hydrolysed using a strong base such as $$\mathrm{NaOH}$$ or $$\mathrm{KOH}$$ to produce glycerol and the salt of the long chain fatty acid in a process known as saponification
* the salt of the fatty acid precipitates and is removed by filtration
* ![](/files/1D3LwERfxTOJHJkIiOCF)
* *soaps:*
  * soap is used as a cleaning agent due to its emulsifying properties
    * an emulsifying agent (*i.e.* a surfactant) helps two immiscible substances to remain mixed
  * water with soap is slightly basic
  * *structure:*
    * soap is the salt of a long chain fatty acid
    * ![](/files/TGnwQ1NgY1ZeHbQVVNp7)
    * ![](/files/zyDaDyRmRRKFckrP5IIO)
    * the polar head of the molecule hydrogen bonds to water molecules around it while the non-polar tail dissolves in the oil forming a micelle
* *detergents:*
  * when soap is mixed with water containing $$\mathrm{Ca^{2+}}$$ or $$\mathrm{Mg^{2+}}$$ ions, an insoluble 'scum' is produced (calcium or magnesium stearate)
    * this deposits on clothes and is difficult to remove, so detergents were developed which don't produce scum
  * by replacing the carboxylate, $$\mathrm{COO^-}$$, with a sulfonate group, $$\mathrm{SO\_3^-}$$, an effective surfactant that does not produce scum is made
    * this is achieved as shown below:
    * ![](/files/2S22jojZjLzCmSItneBd)

## **biodiesel**

#### *transesterification*

* a triester (vegetable oil) has its three fatty acids removed
* the fatty acids react with a small alcohol molecule to produce three esters
* ![](/files/cde68yFU9eWAPgPrccO5)
* where $$\mathrm{R^1}$$ represents the hydrocarbon chains for the fatty acid and $$\mathrm{R^2}$$ is an alkyl group (typically methyl or ethyl)
* the low purity glycerol formed is immiscible with the biodiesel so it forms a separate layer
  * if good separation is not achieved then this can lead to poor fuel quality and engine damage