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ChemWiki: The Dynamic Chemistry E-textbook > Organic Chemistry > Case Studies > What is Organic?

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What is Organic?

"Organic" is generally associated the word with organic foods and products, but in the sciences, organic chemistry is refered to as the study of carbon compounds.

Introduction

What do people think organic is? A survey was conducted to ask participants about what they thought organic meant. Most of the replies referred to organic foods, while only a few science majors said carbon compounds. Organic chemistry is the study of the structure, properties, and reactions of carbon compounds. Even though organic chemistry focuses on carbon, many organic compounds can contain hydrogen, nitrogen, oxygen, phosphorous or other elements. Carbon molecules have many different functions; they are commonly used in medicine, food, paints, and gasoline.


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.

Periodic table organic.jpg

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.

A Brief History of Organic Chemistry

The word organic comes from the term "organism", thus explaining the focus of organisms in organic chemistry. In 1770, a Swedish chemist named Torbern Bergman made an important distinction between organic and inorganic substances. In 1807, Jöns Jacob Berzelius was the first person to call components from biological sources "Organic Chemistry". Before the modernization of organic chemistry in the early 19th century, scientists had discovered major distinctions between extracts of living and non-living things. A theory called the vital force theory, or vitalism, stated that there was a force in organic molecules that inorganic molecules do not have. In 1828, Friedrich Wöhler converted ammonium cyanate (inorganic compound) into urea.  This event is considered the start of organic chemistry. Wöhler proved the vitalism theory to be incorrect because it was believed that it was not possible to make organic compounds out of inorganic compounds.

Wohler_synthesis.gif

This animation displays how Ammonia and Cyanate combined to form Urea.

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.

Periodic-Table---carbon.jpg

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.

How is Organic Different from Inorganic Chemistry?

Organic chemistry is defined as chemistry of living things. Most compounds discussed in organic chemistry are made up of carbon molecules. Many people think that organic chemistry revolves around carbon. However, that is not the case; there are some carbon molecules that are inorganic, such as carbon dioxide (CO2). Organic chemistry not only focuses on carbon but also on how electrons move in carbon compounds. The most simple answer for how organic is different from inorganic is that organic molecules are from living organisms while inorganic comes from non-living resources.

Introduction to Organic Chemistry

Organic chemistry is the chemistry of carbon; we know that carbon can also bond with many different elements forming various compounds.

Before learning organic chemistry, a review of the following topics may be useful:

Page 1 - 13 in: http://www.unc.edu/depts/mtcgroup/courses/61/61notes.pdf

Molecular Representations

There are a number of ways that a molecule or atom can be drawn. Some are simpler than others, depending on the type of information that the image is trying to convey. These representations are especially important in organic chemistry when considering the connectivity of atoms, electron distribution, formal charge, or bond type.

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. kekule.png

 

 

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.

condensed.png

 

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.

Lewis.png

 

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.

perspective.png

 

 

Naming Hydrocarbons

The simplest organic compounds are hydrocarbons. Hydrocarbons are compounds that consist of hydrogen and carbon atoms.

When naming hydrocarbons, the prefixes vary depending on the number of carbons in a compound, the prefixes are:

Number of Carbon(s):
Prefix:
Number of Carbon(s): Prefix:
1 Met- 6 Hex-
2 Eth- 7 Hept-
3 Prop- 8 Oct-
4 But- 9 Non-
5 Pent- 10 Dec-

See Nomenclature for Organic Chemistry for more information on how to properly name organic molecules.

A trick to remember the prefixes of Met-, Eth-, Prop-, and But- is: Monkeys Eat Pink (or Plenty) Bananas.

The simplest type of hydrocarbons are called alkanes which consist only of single bonded atoms with a molecular formula of CnH2n+2 where n is equal to the number of carbons. They are named using the prefixes above, and by adding the suffix, "-ane."

Alkanes:                                                                           ethane.png

  • CH4 - Methane
  • C2H6 - Ethane
  • C3H8 - Propane
  • C4H10 - Butane

Other kinds of hydrocarbons include: alkenes and alkynes. Alkenes are carbon compounds with at least 1 double bond between 2 carbon atoms, with the molecular formula CnH2n. They are named by adding the suffix, "-ene" to the prefix based on the number of carbons.ethene.png

Alkenes:

  • C2H4 - Ethene
  • C3H6 - Propene
  • C4H8 - Butene

Alkynes are carbon compounds with one triple bond between two carbon atoms and are expressed with the molecular formula, CnH2n-2. They are named by adding the suffix, "-yne" to the prefix based on the number of carbons.ethyne.png

  • C2H2 - Ethyne
  • C3H4 - Propyne                               
  • C4H6 - Butyne

Naming Alkyl Compounds

Alkanes are often present as alkyl substituents (alkyl groups) that attach to other groups in larger organic molecules. Their molecular formulas have one less hydrogen than a normal alkane. They are named by replacing the normal alkane ending "-ane" with "-yl." The letter "R" commonly refers to any alkyl functional group.

Alkyl Substituents:

  • CH3- methyl
  • CH3CH2- ethyl
  • CH3CH2CH2-propyl
  • CH3CH2CH2CH2- butyl
  • R- any alkyl group

Examples of compounds with alkyl groups:

CH3I: methyl iodide   CH3CH2OH: ethyl alcohol   CH3CH2CH2NH2: propylamine   R-O-R: an ether

CH3NH2: methylamine   CH3CH2OCH3: ethyl methyl ether   CH3CH2CH2CH2Cl: butyl chloride   R-NH2: an amine

Note that when there are two or more alkyl groups present, as in an ether, they must be stated in alphabetical order.

Structures of Organic Compounds

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 CnH2n. 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.png

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 110.9o compared to 109.5o (25) which is why this conformation is more stable than the ring structure.

chair conformation.png

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:

Benzene.PNG

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:

Benzene unsimplified.png

Isomers and Stereochemistry

The structures of organic molecules are very important in considering their properties. Most organic molecules display geometric properties such as isomerism. Isomers are compounds with identical molecular formulas, but with different structures. There are 2 kinds of isomers: constitutional isomers and stereoisomers. Constitutional isomers differ in the connectivity of their atoms. Stereoisomers are compounds that maintain the same connectivity, but differ in the way their atoms are spatially arranged. There are 2 kinds of stereoismers: cis-trans isomers and enantiomers. Cis-trans isomers have different orientations of their functional groups. In a cis isomer, the highest priority functional groups are located on the same side of the double bond. In a trans isomer, the highest priority functional groups are located on opposite sides of the double bond. Enantiomers are compounds that have nonsuperimposable mirror images of each. A molecule or object that has a nonsuperimposable mirror image is chiral.

Constitutional Isomers: CH3CH2OH and CH3OCH3

Cis-trans Isomers:

cis trans.png

Enantiomers:

enantiomers.png

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.

Chirality.jpg

References

  1. McMurry, John. Organic Chemistry Fourth Edition. Pacific Grove, CA: Brooks/Cole Publishing Company, 1995.
  2. Bruice, Paula Y. Essential Organic Chemistry. 2nd. Upper Saddle River, NJ: Prentice Hall, 2010.

Outside Links

  1. http://portal.acs.org/portal/acs/corg/content?_nfpb=true&_pageLabel=PP_ARTICLEMAIN&node_id=1188&content_id=CTP_003397&use_sec=true&sec_url_var=region1&__uuid=c3b007ba-1e7f-4f18-b7fa-7cf7a4c191d8
  2. http://en.wikipedia.org/wiki/Organic_chemistry
  3. http://commons.wikimedia.org/wiki/File:C-TableImage.png
  4. http://en.wikibooks.org/wiki/Organic_Chemistry/Foundational_concepts_of_organic_chemistry/History_of_organic_chemistry
  5. http://www.angelfire.com/bc2/OrgChem/intro.html
  6. http://en.wikipedia.org/wiki/W%C3%B6hler_synthesis
  7. http://commons.wikimedia.org/wiki/File:Wohler_synthesis.gif
  8. http://organic-chemistry.suite101.com/article.cfm/what_is_organic_chemistry
  9. http://www.visionlearning.com/library/module_viewer.php?mid=60
  10. http://www.unc.edu/depts/mtcgroup/courses/61/61notes.pdf
  11. http://library.thinkquest.org/3659/orgchem/
  12. http://organic-chemistry.suite101.com/article.cfm/what_are_organic_molecules
  13. http://commons.wikimedia.org/wiki/File:%E6%A7%8B%E9%80%A0%E5%BC%8F_Benzene.PNG
  14. http://commons.wikimedia.org/wiki/File:Benz1.png
  15. http://commons.wikimedia.org/wiki/File:Benzene-resonance-structures.svg
  16. http://chemistry2.csudh.edu/rpendarvis/BenzStr.html
  17. http://en.wikipedia.org/wiki/Organic_food
  18. http://www.mayoclinic.com/health/organic-food/nu00255
  19. http://www.redbookmag.com/recipes-home/truth-about-organic-foods
  20. http://en.wikipedia.org/wiki/Organic
  21. http://dictionary.reference.com/browse/organic
  22. http://commons.wikimedia.org/wiki/File:Chirality_with_hands.jpg
  23. http://commons.wikimedia.org/wiki/File:Periodic_table.svg
  24. http://education.jlab.org/itselemental/ele006.html
  25. newark.rutgers.edu/~frjordan/chapter2.ppt

Problems

  1. Give examples of the different structures carbon can form.
  2. What are organic molecules?
  3. What are Hydrocarbons?
  4. What is the difference between alkanes, alkenes, and alkynes?
  5. Give at least 2 examples of alkanes, alkenes, and alkynes.

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!)
Alkanes Alkenes Alkynes
Single bonded carbon and hydrogen compounds. Double bonded carbon and hydrogen compounds. Triple bonded carbon and hydrogen compounds.
 (Example) Propane, Nonane  (Example) Decene, Hexene (Example) Butyne, Heptyne

Contributors

  • Sharon Wei (UCD)
  • Jason Ip (UCD)

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Last Modified
18:39, 1 Oct 2013

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