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Organic Chemistry

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Introduction to Chemical Formulae
Organic Chemistry | Alkanes | Alkenes | Alkynes | Alkanols
Alkanoic acids | Esters | Alkanals | Alkanones | Further information

Organic chemistry is a branch of science that studies carbon-based molecules and reactions1. As the name would suggest, most of its applications have to do with biological functions and medicinal research. It was first born in 1828 when Friedrich Wöhler accidentally synthesized urea2 while he was trying to synthesize ammonium cyanate, an inorganic molecule. Up until Wöhler's discovery, scientists had assumed that organic chemicals could not be created through inorganic means. Wöhler opened up an entirely new field of study for the scientific world.

Types of Organic Molecules

Some of the many types of molecules that fall under the jurisdiction of organic chemistry are as follows:

  • Alkanes, alkenes, and alkynes are varieties of molecules that have a chain of carbon atoms as their basis.

  • Alkyl halides are a halogen molecule (fluorine, chlorine, bromine, iodine, or astatine) bonded to a carbon atom on a carbon-based molecule.

  • Aromatic hydrocarbons are carbon atoms (usually six) bonded together in a ring formation.

  • Alcohols are carbon-based molecules with a hydroxide group (an oxygen atom and a hydrogen atom bonded together) attached.

  • Ethers are an oxygen molecule with two carbons (or carbon chains) attached.

  • Amines are a nitrogen atom with three carbon or hydrogen molecules/groups attached to it.

  • Aldehydes and Ketones are two varieties of molecules with a carbon atom double-bonded to an oxygen atom.

  • Carboxylic Acids are a carbon atom double-bonded to an oxygen atom with a hydroxide group attached (usually written as -COOH, although this does not represent its actual shape or bonding structure).

Other types of molecules studied in organic chemistry include esters, nitriles, and amides, but they are a bit more complicated and are used less frequently at a basic level than some of the others.

Topics and Concepts of Organic Chemistry

A great deal of time is spent in organic chemistry trying to come up with ways to synthesize different types of molecules. It is therefore necessary to study what chemicals you can use to create what you want, which entails spending countless hours staring at diagrams of reaction mechanisms. Before long, you realise that molecules can be extremely stubborn and annoying little things, refusing to do what you want them to, even if the textbook disagrees with them.

The basic point of synthesis is to put a specific atom (or group of atoms) at a specific point on another molecule. To do this, chemists can use certain chemicals, conditions, and reaction pathways. It is also sometimes necessary to eliminate or create multiple bonds between parts of the molecule.

Since there is so much of an emphasis on synthesizing molecules, it is necessary to spend time looking at each of the above types of molecule and how they react to certain types of situations. Each type of atom affects a molecule differently depending on where it is placed in that molecule, so there can be mind-boggling numbers of variables involved in determining what exactly might happen in a given reaction. However, there are general rules that apply to each basic type of molecule, and there are certain chemicals that usually work well to gain a desired affect.

Other factors involved in synthesis include stereochemistry (a painful subject that looks at the specific 3-D relationship of each atom in relation to the rest of the molecule), thermochemistry (a slightly less painful subject that looks at heat and energy to see how or if the reaction will proceed), and kinetics (which tries to determine how long it will take the reaction to go to completion).

What to Expect in an Organic Chemistry Lab

The most common characteristic of organic labs is that they smell awful. One of the chemicals frequently used in a lab is ether, which was used as an anaesthetic in the past and causes nausea. It is not uncommon for organic labs to create some pretty nasty stuff, so don't stick your nose or hands in anything unless you are absolutely certain what it is. Even then, it's not a bad idea to ask someone who knows what they're doing.

Many of the techniques and procedures in labs are fairly ubiquitous to all of chemistry, but here are some that particularly come in handy for organic chemistry:

  • Synthesis procedures - most techniques for synthesis have to do with fiddling with the reaction temperature, pressure, or atmosphere. Examples might include boiling (also called refluxing) or cooling, increasing/decreasing the atmospheric pressure on the reaction pot, or conducting the reaction in the presence of a certain gas.

  • Separation procedures - once a chemical has been synthesized, it has to be separated out of the rest of the chemicals used in the reaction. Some ways of doing this include crystallization, filtration, and distillation (varieties of which include fractional, steam, and vacuum).

  • Analysis procedures - it does little good to separate out a certain chemical if is not then analyzed to determine its content and purity. The basic method of doing this is to use heat, a solvent, or magnetic fields to pull one chemical out of another, thereby separating a sample into its component chemicals. Each chemical can then be analyzed through whatever type of detector is appropriate. Two common analysis methods are chromatography (gas, thin layer, liquid, and column) and spectroscopy (mass, infrared, ultraviolet, and nuclear magnetic resonance).

College courses offered in organic chemistry are almost universally dreaded. This is not without good reason. They are awful. The labs in particular smell bad (trust us on this one) and only small parts of them make any sense whatsoever. If someone tells you that you should study organic chemistry, hit them over the head and then run away very fast.

1Because silicon behaves in similar ways to carbon, some branches of organic chemistry now include the study of silicon based molecules and reactions.2An organic molecule found in - you guessed it - urine.

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