Carbon-containing Compounds

Organic chemistry focuses on the structure, properties, and applications of various carbon-containing molecules that make up important biological molecules such as proteins, enzymes, carbohydrates, lipids, nucleic acids, and vitamins. A number of organic compounds are found in nature such as cotton, wool, and natrual petroleum while others are purely man-made. Industries have been able to synthesize many organic compounds such as plastics, photographic film, synthethic fabrics, and pharmeceutical drugs using applications of organic chemistry.

Organic Foods

Many people think of organic food as the healthier alternative because they associate organic foods with no pesticides, no chemicals and are not genetically modified. That may be true because the United States Departments of Agriculture has specific standards farmers have to follow. The questions are what is the difference between organic and non-organic produce? Are organic foods more nutritional? There have not been any real evidences about whether organic foods are more nutritional than non-organic foods. There are not as many differences between organic and non-organic as one would think, people claim that they can taste the difference between the two, but taste is solely based on personal preferences. The only differences between organic and non-organic foods are the way the food were grown, they do not look as "perfect" as non-organic foods and they spoil faster.

The definition of organic is: "having properties or characteristics of living organisms" (21). It is true that organic foods were from living beings, but the fact that people are associating organic foods as: pesticide free, hormone free, and other natural processes, is not the correct perspective. "Organic" just means things from living organisms, including: organs, hair, fruits, and even seeds.

Why learn Organic Chemistry?

Organic chemistry is everywhere as every living organism contains organic compounds. Organic chemistry has many applications in medicine, biology, technology, industrial production, and business. Other applications of organic chemistry include making plastics, gasoline, detergent and plenty of other industrial products. Organic chemistry is an important aspect of our lives.

Why is Carbon so special? 

Carbon has an atomic number of 6; it is a second row element in the p-block.

Carbon is the sixth most abundant element in the universe (24). Carbon is able to form strong polar and non-polar covalent bonds by sharing its electrons to construct long chains and various structures. Some examples of polar covalent bonds are: C-F, C-O, and C-N. Some examples of non-polar covalent bonds are: C-C and C-H. Carbon can also attach with many metallic and nonmetallic elements. When a carbon shares its electrons with hydrogens, a hydrocarbon is formed which is considered to be the simplest organic compound. A unique property of carbon is that it can form many polymers in different structures like tubes, spheres, rings and chains. Carbon likes to form four bonds, which allows it to interact with a variety of molecules. The 4 bonds are essential for the formation of stable molecules. Carbon can bond in many different ways with many different elements.

Skeletal Structure (Kekulé Structure)

In this form of representation, atoms are placed on a plane and lines are drawn between atoms to represent bonding electrons. Lone pairs are not included in this representation.

Condensed Structure

A simplified version of the bond-line structure that omits the lines. When there are 2 or more of the same kinds of atoms attached to a central atom, a subscript is used to indicate how many of these atoms are attached.

Lewis Structure

In this structure, valence electrons are represented as dots. This structure shows us what atoms are bonded together, which electrons are involved in bonding, lone pairs, and any formal charges.

Perspective Formula

In this formula, bonds that are on the plane are drawn normally. Bonds that protrude out of the plane towards the viewer are drawn as black wedges. Bonds that go into the plane away from the viewer are drawn as dashed wedges.

Alcohols:

consists of a hydrocarbons chain that has a hydroxide in place of hydrogen (anywhere in the compound). The common formula for an alcohol is R-OH, where R is any hydrocarbon (residue group). Naming alcohols is not hard either; for example propanol which comes from the propane hydrocarbon therefore instead of having the –ane suffix you have –anol.  Other examples are ethanol, butanol, Alcohols have the ability of making acids solutions. A common reaction of alcohols is with carboxylic acids to make water and an ester.

Ethers:

consists of two hydrocarbons joined by a oxygen between the them. Naming theses two compounds is as easy as naming the two alkyl groups (in alphabetical order) and ether at the end. An example is ethyl ether propyl, the structural formula is CH₃CH₂OCH₂CH₂CH₃. Another example is ethyl ethyl ether more commonly named as diethyl ether. The common formula for ethers is R-O-R, this means there are two alkyl groups (aka residue groups).

Carboxylic Acids:

consists of an alkyl group missing three hydrogen that were replaced by double bonded oxygen and a hydroxide group. The common formula for carboxylic acids is R-COOH. Naming carboxylic acids is not hard, starting with propane and replaces the suffix –ane with -anoic acid, this compound is propanoic acid and has the structural formula of CH₃CH₂COOH. Some characteristics of this compound are reacting with alcohols to form water and an ester. Carboxylic acids also have a similar property to that of alcohols; both alcohols and carboxylic acids form weak acidic solutions in water.

Ester:

are generally formed through the reaction of carboxylic acids and alcohols. Esters are the reason why certain foods have certain scents; this makes the useful with perfumes. The general formula for an ester is R-COOR; naming esters is a little harder than naming other compounds but basically the alcohol gets the alkyl name ending and the carboxylic acid gets the –anoate i.e. methanol reacting with butanoic acid to make water and methyl butanoate; structural formula being CH₃COOCH₂CH₂CH₂CH₃.

Aldehydes:

have the general formula R-CHO. Naming these compounds should not be confused with alcohols; aldehydes have the –al suffix while alcohols have the –ol suffix. For example methanal (aka formaldehyde) is the simplest aldehyde.

Ketones:

have the general formula R-COR and contain the suffix –one. An example of a ketone is butanone also know as methyl ethyl ketone to distinguish where the oxygen is located. Other was of identifying the location of the oxygen is by naming each carbon numerically and adding the number of the carbon, where the oxygen is found, to the formula, such as 2-butanone.

Halocarbons:

are essentially hydrocarbons where hydrogens have been replaced by halogens. When the halogens are in the compound you change the name, fluorine to fluoro, chlorine to chloro, bromine to bromo, and iodine to iodo. An example of this compound is 2-choloropropane, CH₃CHClCH₃. Like ketones, you should denote where the halogen is located in the compound by numbering the carbons in the compound.

Amines:  

contain a nitrogenous base and have the structural formula R-NH₂. These compounds have the ability of making weak basic solutions by attracting hydrogen to form A R-NH₃⁺. Naming this compounds just requires the addition of the suffix –amine after the alkyl name i.e. methylamine, CH₃NH₂.

Cycloalkanes

Cycloalkanes are alkanes that have ring, or cyclic structures. They have the molecular formula C_nH_2n. Because the atoms are arranged in a ring shape, the bond angles are less than they would be in ideal sp³ carbon. This is referred to as ring strain. As a result of ring strain, the bond energies of cycloalkanes are much less than those of regular alkanes. In order to avoid ring strain, cycloalkanes in nature are often found in different conformations. One example is the chair conformation of cyclohexane.

Cyclohexane

Cyclohexane, C₆H₁₂, is a cycloalkane with 6 carbons.

Cyclohexane is rarely found in its ring structure though because of its ring strain. More often it is found in a chair conformation. The bond angles in the chair conformer are very close to the ideal bond angles of sp³ carbons. About 110.9^o compared to 109.5^o (25) which is why this conformation is more stable than the ring structure.

Benzene

Benzene is a very important organic compound that is commonly used in manufacturing and as an organic solvent in labs. Its molecular formula is C₆H₆. In your organic chemistry textbook, you may see it presented in a ring structure:

It may be confusing as to how these "lines" can be a molecular structure. This notation is a quick method for chemists to draw organic molecules because the molecules can be very complex. In every corner, there is a carbon, bonded to hydrogen because carbon likes to make 4 bonds.

This is what the above structures of benzene actually represent:

Chirality and Enantiomers

In organic chemistry, the concept of chirality is often applied in medicine or compounds because the D-Dopa and the L-Dopa have different functions, one of them does the desired function, while the other one does not. This is because many biological receptor proteins in the body are shaped so that only one enantiomer can bind to the substrate, while the other cannot fit.  An example is sugar in biological systems, sugar is preferred in the D-Dopa form because in biological system, amino acids is preferred in the L-Dopa. The mirror images of the molecules does not have the same function as the other, they are usually called chiral. The two chiral molecules are called enantiomers. Non-chiral molecules are molecules that have a plane of symmetry in them and they are called achiral.

Helpful Links

1. A time line of Organic Chemistry: http://www.google.com/search?q=history+behind+organic+chemistry&hl=en&client=firefox-a&hs=0gO&sa=X&rls=org.mozilla:en-US:official&prmd=b&tbs=tl:1&tbo=u&ei=m4H3S52WFI2KNODNiMwF&oi=timeline_result&ct=title&resnum=11&ved=0CFgQ5wIwCg
2. Here is an introductory lecture explaining what is organic chemistry: http://www.youtube.com/watch?v=ndOwa5zET8Y&playnext_from=TL&videos=ITH6Tlk20rc
3. These songs may also be helpful:http://www.youtube.com/watch?v=DXa2QDQzwzM&playnext_from=TL&videos=Q_Z_n2SHhBk http://www.youtube.com/watch?v=mAjrnZ-znkY&playnext_from=TL&videos=0pKprCP_0Wk

Solutions

1. Carbon is able to form structures such as tubes, spheres, chains, and rings.
2. Organic molecules come from living organisms, such as proteins and carbohydrates.
3. Hydrocarbons are compounds with hydrogen and carbon; they are usually called the simplest organic compound.
4. The differences between alkanes, alkenes, and alkynes are: (Shown in table)
5. Examples: (Shown in table - There are multiple correct answers!)