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.

The Hydrogen Covalent bond

Hydrogen - Hydrogen binding

Hydrogen 74pm

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.

Carbon 109pm
413 Kj/mol
Nitrogen 101pm
391 Kj/mol
Oxygen 96pm
366 Kj/mol

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.

Methane CH4
HCH angle 109.5°
Ammonia NH3
HNH angle 107.8°
Water H2O HOH angle 104.5°

Water H2O
HOH angle 104.5°

Carbon bonding and the Hydrocarbons

C-C Covalent 154pm
348 Kj/mol

C-C Aromatic 144pm
470 Kj/mol

C-C Double 134pm
614 Kj/mol

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 bonding and the Carbohydrates

Oxygen Covalent bonding for alcohols and sugars

C-O Covalent 143pm
360 Kj/mol

Methanol

Ethanol

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.

Glycerol
Glucose

Alpha Glucose is in a ring structure and flattened out. These combine to become starches and cell coatings. Beta Glucose becomes plant cellulose.

AlphaGlucose Ring (front view)
AlphaGlucose Ring (side view)

Oxygen Double Covalent bonding for acids

C-O Double 135pm
498 Kj/mol

Formic Acid

Acetic Acid

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.

Citric Acid

Long hydrocarbon acid chains are called fatty acids. Palmitic and Oleic acids form the basis of lipids, the main building block of biological cell walls.

Lauric Acid
Palmitic Acid
Oleic Acid

Nitrogen bonding for Amino and Nucleic acids

C-N Covalent 147pm
308 Kj/mol

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.

Amino acid Glycine bonding with Alanine
Nucleic acid A-DNA bonded to T-DNA

References

Virtual Textbook of Organic Chemistry Electron Configurations