HS Chemistry - Introduction to Organic Chemistry

Unit Summary

Organic Compounds Introduction

Organic compounds are compounds found in living organisms that are necessary to their function.
- Hydrocarbons are organic compounds that are made of only Hydrogen and Carbon atoms.
All organic molecules contain functional groups, which are different groups of atoms in an organic compound responsible for its physical and chemical properties. An organic molecule can contain more than one functional group.
- Functional groups are not only determined by their atoms, but also by the bonds (single bonds, double bonds, etc.) between those atoms.
The most basic functional group is an alkane, a hydrocarbon containing only single bonds. It can be thought of as the default functional group - if no other functional group is present, the molecule is an alkane.

The IUPAC system for naming organic molecules is prefix $es$ -parent-suffix, where:
- The prefix $es$ of an organic molecule's name are responsible for noting any chains or other atoms in the molecule.
- The parent part of the name notes the number of Carbon atoms in the main chain of the molecule $"meth-", "eth-", "prop-", etc.$ .
- The suffix is determined by the organic molecule's main functional group. Usually, the last few letters of the functional group's name are used as the suffix.
Organic compounds that have the same functional group $s$ in the same amount $s$ are all part of the same homologous series:
- Members of a homologous series display similar chemical properties, and trends in their physical properties.
- Organic compounds that are part of the same homologous series have the same general formula, which is an algebraic representation of the molecular formula of molecules in that homologous series. The general formula for the homologous series of alkanes is C_nH_2n+2.
Since the empirical and molecular formula of an organic molecule don't give much information about how the atoms are arranged in the molecule, scientists use the structural formula, the displayed formula, the 3D displayed formula, and the skeletal formula as methods of showing that information.

Branched Organic Molecules

Many organic compounds have smaller chains branching off the main chain $aka carbon skeleton$ of the organic molecule. These smaller chains and their positions are noted in the prefix part of the organic molecule's name.

The smaller chain is named using the same rules for naming organic compounds in general. However, the suffix is different. If the side chain is an alkane, then the suffix is "-yl", and it is referred to as an alkyl chain or an alkyl group. Otherwise, if the side chain is another functional group, to form the suffix of the side chain, take the normal suffix of the functional group, removing the ending "e" if necessary, and append "-yl" after it.

When numbering the prefixes in the organic molecule, the numbering starts from the end that gives a smaller number for the first side chain encountered when counting. After that, we keep counting from that end, even if another side chain is encountered from the other end.

Sometimes, we have multiple instances of a certain side chain in an organic molecule. In these cases, we need to append the prefix to make note of this, by adding an affix like "di" $for two instances of the side chain$ or "tri" $for three instances of the side chain$ before the prefix $to form a prefix like "dimethyl" or "trimethyl"$ .

Prefixes are ordered in alphabetical order when naming the organic molecule.

In a skeletal formula, atoms that are not Carbon or Hydrogen are represented as chains of their own, even if there are no other atoms attached to them.

Isomers

Isomers are different organic molecules that have the same chemical formula. There are many different kinds of isomers:
- Structural isomers:
  - Functional group isomers
  - Chain isomers
  - Position isomers
- Stereoisomers $aka geometric isomers$ :
  - Cis-trans isomers
  - Optical isomers $aka enantiomers$
Molecules that contain the same atoms, but which have the atoms bonded to each other in different ways, are structural isomers:
- Functional group isomers are isomers with the same chemical formula but different functional groups
- Chain isomers are isomers with the same chemical formula and functional groups, but different main chains.
- Position isomers are isomers with the same chemical formula, functional group and main chain, but with different arrangements of atoms.
  - Atoms can freely rotate around single bonds, so merely drawing the same molecule in a different orientation does not count as position isomerism.
Alkene functional groups are characterized by two Carbon atoms being double-bonded to one another.

Molecules that have the same atoms bonded to each other, but with different arrangements, are stereoisomers $aka geometric isomers$ :
- Cis-trans isomers:
  - Cis-trans isomerism is due to the fact that double and triple bonds "lock" Carbon atoms into place relative to one another, and don't allow atoms to freely rotate relative to one another they way that single bonds do.
  - When there is one group attached to each Carbon atom in the double-bonded functional group, a cis isomer is an isomer where both functional groups are on the same level, and a trans isomer is an isomer where both functional groups are on different levels. This can be shown through the example of 1,2-dichloroethene:
    
    The molecule shown above is cis-1,2-dichloroethene, and the molecule shown below is trans-1,2-dichloroethene:
- Optical isomers $aka enantiomers$ :
  - Optical isomerism is due to the fact that when a Carbon atom is bonded to 4 other atoms, we can have mirror images of the molecule. These isomers have different effects on polarized light.
  - The Carbon atom that is involved in the optical isomerism is known as the chiral center.

Organic Compound Reactions

Organic compounds often undergo different types of reactions, using different mechanisms.

Electrophiles are atoms/ions/molecules that attract, or sometimes "steal", electrons in reactions. Electrophiles often have a deficit of electrons, and therefore draw electrons in reactions, initiating the reaction.

Nucleophiles are atoms/ions/molecules that donate, or "give away", electrons in reactions. Nucleophiles often have excess electrons that initiate the reaction.

Addition reactions involve two molecules reacting and combining into one larger molecule.

Substitution reactions involve one atom/ion/molecule replacing another atom/ion/molecule's place in a larger organic molecule.

Elimination reactions involve one molecule breaking up into two or more smaller molecules. Sometimes, another molecule will facilitate this process, causing it to occur.

Hydrolysis reactions occur when water $or a dilute acid or base$ breaks down a larger organic molecule into two or more smaller molecules.

Condensation reactions occur when two organic molecules react and combine together, and in the process, a small molecule $such as water$ is removed.

An oxidation reaction, broadly speaking, occurs when there is either a gain in the number of bonds between Carbon and a more electronegative atom $usually Oxygen$ OR a reduction in the number of bonds between Carbon and a less electronegative atom $usually Hydrogen$ .
- This typically occurs when one of the reactants has been acidified, and its ions have been displaced in solution. To show this, Oxygen atoms are often written as [O] in the equation.
- The compound that gives the [O] is referred to as the oxidizing agent.
- Some examples of common oxidizing agents:
  - Acidified K₂Cr₂O₇ solution will oxidize primary alcohols to aldehydes, aldehydes to carboxylic acids, and secondary alcohols to ketones, changing color from orange to green over the course of the oxidation reaction.
  - Acidified KMnO₄ solution will oxidize primary alcohols to aldehydes, aldehydes to carboxylic acids, secondary alcohols to ketones, and alkenes to diols, losing its purple color over the course of the oxidation reaction.
A reduction reaction, broadly speaking, occurs when there is either a reduction in the number of bonds between Carbon and a more electronegative atom $usually Oxygen$ OR a gain in the number of bonds between Carbon and a less electronegative atom $usually Hydrogen$ .
- This typically occurs when one of the reactants has been acidified, and its ions have been displaced in solution. To show this, Hydrogen atoms are often written as [H] in the equation.
- The compound that gives the [H] is referred to as the reducing agent.
- Some examples of common reducing agents:
  - Sodium Borohydride $NaBH~4~$ will reduce carboxylic acids to aldehydes, aldehydes to primary alcohols, and ketones to secondary alcohols.
  - Lithium Aluminum Hydride $LiAlH~4~$ will reduce carboxylic acids to aldehydes, aldehydes to primary alcohols, and ketones to secondary alcohols.
In order for a chemical reaction to occur between organic molecules, existing chemical bonds have to be broken. There are two main reaction mechanisms:
- Homolytic fission:
  - Homolytic fission is when each of the two atoms in the bond that is being broken gets one of the electrons that were shared in the bond.
  - It tends to happen when a non-polar molecule is broken, or when the difference between the electronegativities of the two atoms isn't too large.
  - It can lead to the formation of free radicals, which can carry out their own type of reaction, called a free-radical reaction.
  - Homolytic fission is often shown in a chemical reaction using the following symbol:
    
    Where the half-arrows point towards both atoms between which the bond is being broken.
- Heterolytic fission:
  - Heterolytic fission is when the more electronegative atom in the bond that is being broken takes both of the electrons that were shared in the bond. This leaves the other side as a positively charged ion.
  - Heterolytic fission in an organic molecule will often occur with an alkyl group in the organic molecule, leaving the Carbon atom with a positive charge. This positively charged alkyl group is called a carbocation.
  - There are three types of carbocations:
    - Primary carbocations are formed when the Carbon atom that is left with the positive charge is bonded to two other Hydrogen atoms and one other group. It is the least stable type of carbocation.
    - Secondary carbocations are formed when the Carbon atom that is left with the positive charge is bonded to one other Hydrogen atom and two other groups. Secondary carbocations are more stable than primary carbocations but less stable than tertiary carbocations.
    - Tertiary carbocations are formed when the Carbon atom that is left with the positive charge isn't bonded to any Hydrogen atoms, but is instead bonded to three other groups. It is the most stable type of carbocation.
  - Carbocations are not seen at the end of reactions, as they tend to get rid of their positive charge. However, when a reaction occurs, the most stable carbocation possible for that reaction is the one most likely to form. Thus, carbocations can help us determine the final product of a reaction.
  - Heterolytic fission is often shown in a chemical reaction using the following symbol:
    
    Where the arrow points towards the atom that takes both electrons from the bond that is being broken.