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
The Hydrogen Covalent bond
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.
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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.
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Methane CH4
HCH angle 109.5° -
Ammonia NH3
HNH angle 107.8° -
Water H2O
HOH angle 104.5°
Carbon bonding and the Hydrocarbons
Carbon Covalent bonding chains and circles
In a
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
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.
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Glycerol
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Glucose
Alpha Glucose is in a ring structure and flattened out. These combine to become starches and cell coatings. Beta Glucose becomes plant cellulose.
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AlphaGlucose Ring (front view)
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AlphaGlucose Ring (side view)
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.
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Citric Acid
Long hydrocarbon acid chains are called fatty acids. Palmitic and Oleic acids form the basis of
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Lauric Acid
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Palmitic Acid
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Oleic Acid
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
Nitrogen also gives molecules the flexibility to build
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Nucleic acid A-DNA bonded to T-DNA
See Also
References
- Virtual Textbook of Organic Chemistry Electron Configurations