User:Edguy99/Organic Molecules

Constructing Organic Molecules in 3-D
Elements are represented by their valence shell bonding properties. Carbon, nitrogen and oxygen in their organic form are given a 3-D Lewis style orbital structure. The molecule representations used here are shown on the right with only the valence electrons shown. The red dot shows the most likely chance of finding an electron (usually in the center of an orbital). The white dots show the most attractive spot on the molecule to attract a stray electron based on the location of the electron orbitals on the molecule. The shell is given as a size reference (Bohr radius of 53 picometers) and the molecule is left partially "see through".

The carbon molecules are constructed with the red dots on the end of a tetrahedral. The four white dots are constructed as a second "inverted" tetrahedral. This figure with eight dots is called a stella octangula. Oxygen and nitrogen are constructed in the same manner but nitrogen has only three valence holes and oxygen has two.

Hydrogen - Hydrogen binding


In a covalent or two center bond, one electron from one hydrogen drops into the hole of the other hydrogen and one electron from the second hydrogen drops into the first hydrogen hole. Distance between the two hydrogen protons is 74 picometers and the bond energy is 436 Kj/mol.

Hydrogen binding with Carbon, Nitrogen and Oxygen
Hydrogen covalently binds with other elements. One electron from the hydrogen drops into the hole of the other element and one electron from the element drops into the hydrogen hole. There are a number of different places where the first hydrogen can bind. Distances are in picometers and bond energies in Kj/mol. The bond energies go down from carbon to nitrogen to oxygen due to the higher coulomb force pushing the hydrogen away from the oxygen.

Multiple Hydrogen bonds for Methane, Ammonia and Water
If we fill up all the available holes, the molecules become methane from carbon, ammonia from nitrogen and water from oxygen. The bond angle goes down from carbon to nitrogen to oxygen due to the attraction of the two electrons in the inner layer (not shown) on the two hydrogen protons in oxygen.

Carbon Covalent bonding chains and circles
In a covalent or two center bond, one electron from each carbon drops into the hole of the other. Other forces keep the elements from being pulled furthur together.

Hydrocarbons are made up of hydrogen and carbon molecules bound together in a variety of ways. When you mix hydrogen molecules with carbon molecules, the relative concentrations are very important. Examples of covalent carbon bonds include ethane, the long octane and the round cyclohexane. A ratio of three hydrogen to one carbon will produce a lot of ethane. A ratio closer to two hydrogen to one carbon will produce more of the longer octane.



Carbon Aromatic bonding circles
For the aromatic bond, one electron drops into a hole of the other carbon and the two closest holes par up with two electrons from the other carbon. Benzene below is an example of an aromatic bond. Each carbon only binds with three other atoms.



Carbon Double Covalent strong bond
The double covalent bond involves four centers, with two electrons and two holes from each carbon. Ethylene below is an example of a double covalent bond. Each carbon atom is bound to three different atoms, but the carbon-carbon bond is taking up two of the holes. This is a strong stable bond between carbon atoms. It can be twisted or rotated by 90° but this requires about 132kJ/mol energy.

Oxygen Covalent bonding for alcohols and sugars




A hydrocarbon with a single oxygen-hydrogen bond (a hydroxide, OH for short) on the end is called an alcohol. Two common alcohols methanol and ethanol are examples. Glycerol is a collection of three OH hydroxides stuck to a short carbon chain and can be used to link two or three of the long hydrocarbons to create lipids. The sugar (glucose), acts as a storage facility for the OH bonds.

Oxygen Double Covalent bonding for acids




An organic acid is a hydrocarbon molecule with a with two oxygens and a hydrogen on the end. The hydrogen proton easily comes off forming an acid at that end of the molecule. The simpliest are Formic acid, acetic acid (vinegar). Citric acid acts as a storehouse of this type of bond.

Nitrogen bonding for Amino and Nucleic acids


Nitrogen with its different charge adds enormous diversity to the structures that can be built. The most important are the structure molecules called amino acids. Proteins are large organic structures built from amino acids. The fundamental binding property of amino acids is to have the 'amino' end of one molecule (where the nitrogen is) bind to the 'acetic' end of the next molecule.

Nitrogen also gives molecules the flexibility to build nucleic acids. This allows information to be encoded, stored and passed on to future generations using the DNA binding code.