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12.1: Organic Chemistry

Last updated

Apr 13, 2023
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- 12: Organic Chemistry
- 12.2: Hydrocarbons

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How many carbon-containing molecules are there? The current estimate is that there are around 20 million different known organic compounds. Why the uncertainty? Every day, scientists are coming up with new compounds. Some of these materials are of interest for a research project, while others are destined to be developed for a commercial market. As soon as we think we know how many organic compounds exist, more are discovered and our number quickly becomes out of date. The molecule gallery in Figure $\PageIndex{1}$ below shows just 12 of the 20,000,000 or so organic compounds. So, what exactly is an organic compound and why are there so many different possibilities?

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Figure

$\PageIndex{1}$ : Row 1 (top row): methane, ethane, octane. Row 2: acetone, acetic acid, ethanol. Row 3: diethyl ether, ethylene, 2-butyne. Row 4: cyclopropane, benzene, cyclobutene. Carbon atoms are shown in gray, hydrogen in white, and oxygen in red.

Organic Chemistry

At one time in history, it was thought that only living things were capable of synthesizing the carbon-containing compounds present in cells. For that reason, the term organic was applied to those compounds. Eventually it was shown that carbon-containing compounds could be synthesized from inorganic substances, but the term "organic" has remained. Currently, organic compounds are defined as covalently bonded compounds containing carbon, excluding carbonates and oxides. By this definition, compounds such as carbon dioxide, CO₂, and sodium carbonate, Na₂CO₃, are considered to be inorganic compounds. Organic chemistry is the study of all organic compounds.

Organic chemistry is a very vast and complex subject. There are millions of known organic compounds – far more than the number of inorganic compounds. The reason lies within the uniqueness of carbon's structure and bonding capabilities. Carbon has four valence electrons, and therefore makes four separate covalent bonds in compounds. Carbon has the ability to bond to itself repeatedly, making long chains of carbon atoms, as well as ringed structures. In addition, the bonds may be single, double, or triple covalent bonds.

Carbon readily makes covalent bonds with other elements. While Figure $\PageIndex{1}$ showed compounds comprised of only carbon, hydrogen, and oxygen, Figure $\PageIndex{2}$ shows organic compounds that include nitrogen, sulfur, and chlorine. Other organic compounds commonly include the remaining halogens or phosphorus.

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callback set for errorCallback myCallback ERROR

errorCallback = "myCallback"

Viewer cachePut cache://localLOAD_https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/241/SDF?record_type=3d

Viewer cachePut https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/241/SDF?record_type=3d

Viewer cachePut cache://localLOAD_https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/3283/SDF?record_type=3d

Viewer cachePut https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/3283/SDF?record_type=3d

Viewer cachePut cache://localLOAD_https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/6338/SDF?record_type=3d

Viewer cachePut https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/6338/SDF?record_type=3d

Viewer cachePut cache://localLOAD_https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/10419/SDF?record_type=3d

Viewer cachePut https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/10419/SDF?record_type=3d

Viewer cachePut cache://localLOAD_https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/6351/SDF?record_type=3d

Viewer cachePut https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/6351/SDF?record_type=3d

Viewer cachePut cache://localLOAD_https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/6325/SDF?record_type=3d

Viewer cachePut https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/6325/SDF?record_type=3d

Viewer cachePut cache://localLOAD_https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/69972/SDF?record_type=3d

Viewer cachePut https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/69972/SDF?record_type=3d

FileManager.getAtomSetCollectionFromFile(https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/241/SDF?record_type=3d)

Time for openFile(:241): 11 ms

File Error:unrecognized file format for file

https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/241/SDF?record_type=3d

error

script ERROR: unrecognized file format for file

https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/241/SDF?record_type=3d

error

----

load async <<<<":241"

Script completed

Jmol script terminated

FileManager.getAtomSetCollectionFromFile(https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/3283/SDF?record_type=3d)

Time for openFile(:3283): 3 ms

File Error:unrecognized file format for file

https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/3283/SDF?record_type=3d

error

script ERROR: unrecognized file format for file

https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/3283/SDF?record_type=3d

error

----

load async <<<<":3283"

Script completed

Jmol script terminated

FileManager.getAtomSetCollectionFromFile(https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/6338/SDF?record_type=3d)

Time for openFile(:6338): 3 ms

File Error:unrecognized file format for file

https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/6338/SDF?record_type=3d

error

script ERROR: unrecognized file format for file

https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/6338/SDF?record_type=3d

error

----

load async <<<<":6338"

Script completed

Jmol script terminated

FileManager.getAtomSetCollectionFromFile(https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/10419/SDF?record_type=3d)

Time for openFile(:10419): 4 ms

File Error:unrecognized file format for file

https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/10419/SDF?record_type=3d

error

script ERROR: unrecognized file format for file

https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/10419/SDF?record_type=3d

error

----

load async <<<<":10419"

Script completed

Jmol script terminated

FileManager.getAtomSetCollectionFromFile(https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/6351/SDF?record_type=3d)

Time for openFile(:6351): 5 ms

File Error:unrecognized file format for file

https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/6351/SDF?record_type=3d

error

script ERROR: unrecognized file format for file

https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/6351/SDF?record_type=3d

error

----

load async <<<<":6351"

Script completed

Jmol script terminated

Viewer cachePut cache://localLOAD_https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/6137/SDF?record_type=3d

Viewer cachePut https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/6137/SDF?record_type=3d

Viewer cachePut cache://localLOAD_https://cactus.nci.nih.gov/chemical/structure/methane/file?format=sdf&get3d=True

Viewer cachePut https://cactus.nci.nih.gov/chemical/structure/methane/file?format=sdf&get3d=True

FileManager.getAtomSetCollectionFromFile(https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/6325/SDF?record_type=3d)

Time for openFile(:6325): 4 ms

File Error:unrecognized file format for file

https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/6325/SDF?record_type=3d

error

script ERROR: unrecognized file format for file

https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/6325/SDF?record_type=3d

error

----

load async <<<<":6325"

Script completed

Jmol script terminated

FileManager.getAtomSetCollectionFromFile(https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/69972/SDF?record_type=3d)

Time for openFile(:69972): 3 ms

File Error:unrecognized file format for file

https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/69972/SDF?record_type=3d

error

script ERROR: unrecognized file format for file

https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/69972/SDF?record_type=3d

error

----

load async <<<<":69972"

Script completed

Jmol script terminated

FileManager.getAtomSetCollectionFromFile(https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/6137/SDF?record_type=3d)

Time for openFile(:6137): 4 ms

File Error:unrecognized file format for file

https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/6137/SDF?record_type=3d

error

script ERROR: unrecognized file format for file

https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/6137/SDF?record_type=3d

error

----

load async <<<<":6137"

Script completed

Jmol script terminated

FileManager.getAtomSetCollectionFromFile(cache://localLOAD_https://cactus.nci.nih.gov/chemical/structure/methane/file?format=sdf&get3d=True)

The Resolver thinks Mol

CH4

APtclcactv03312523243D 0 0.00000 0.00000

CH4

Time for openFile(cache://localLOAD_https://cactus.nci.nih.gov/chemical/structure/methane/file?format=sdf&get3d=True): 7 ms

reading 5 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Babel

5 atoms created

ModelSet: not autobonding; use forceAutobond=true to force automatic bond creation

Time for creating model: 7 ms

CH4

spinY = 10.0

Script completed

Jmol script terminated

spinFPS is set too fast (30) -- can't keep up!

Viewer cachePut cache://localLOAD_https://cactus.nci.nih.gov/chemical/structure/octane/file?format=sdf&get3d=True

Viewer cachePut https://cactus.nci.nih.gov/chemical/structure/octane/file?format=sdf&get3d=True

FileManager.getAtomSetCollectionFromFile(cache://localLOAD_https://cactus.nci.nih.gov/chemical/structure/octane/file?format=sdf&get3d=True)

The Resolver thinks Mol

C8H18

APtclcactv03312519133D 0 0.00000 0.00000

C8H18

Time for openFile(cache://localLOAD_https://cactus.nci.nih.gov/chemical/structure/octane/file?format=sdf&get3d=True): 6 ms

reading 26 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Babel

26 atoms created

ModelSet: not autobonding; use forceAutobond=true to force automatic bond creation

Time for creating model: 3 ms

C8H18

spinY = 10.0

Script completed

Jmol script terminated

Viewer cachePut cache://localLOAD_https://cactus.nci.nih.gov/chemical/structure/propane/file?format=sdf&get3d=True

Viewer cachePut https://cactus.nci.nih.gov/chemical/structure/propane/file?format=sdf&get3d=True

FileManager.getAtomSetCollectionFromFile(cache://localLOAD_https://cactus.nci.nih.gov/chemical/structure/propane/file?format=sdf&get3d=True)

The Resolver thinks Mol

C3H8

APtclcactv04012505543D 0 0.00000 0.00000

C3H8

Time for openFile(cache://localLOAD_https://cactus.nci.nih.gov/chemical/structure/propane/file?format=sdf&get3d=True): 4 ms

reading 11 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Babel

11 atoms created

ModelSet: not autobonding; use forceAutobond=true to force automatic bond creation

Time for creating model: 2 ms

C3H8

spinY = 10.0

Script completed

Jmol script terminated

Viewer cachePut cache://localLOAD_https://cactus.nci.nih.gov/chemical/structure/caffeine/file?format=sdf&get3d=True

Viewer cachePut https://cactus.nci.nih.gov/chemical/structure/caffeine/file?format=sdf&get3d=True

Viewer cachePut cache://localLOAD_https://cactus.nci.nih.gov/chemical/structure/aceticacid/file?format=sdf&get3d=True

Viewer cachePut https://cactus.nci.nih.gov/chemical/structure/aceticacid/file?format=sdf&get3d=True

Viewer cachePut cache://localLOAD_https://cactus.nci.nih.gov/chemical/structure/ethanol/file?format=sdf&get3d=True

Viewer cachePut https://cactus.nci.nih.gov/chemical/structure/ethanol/file?format=sdf&get3d=True

FileManager.getAtomSetCollectionFromFile(cache://localLOAD_https://cactus.nci.nih.gov/chemical/structure/caffeine/file?format=sdf&get3d=True)

The Resolver thinks Mol

C8H10N4O2

APtclcactv04012505293D 0 0.00000 0.00000

C8H10N4O2

Time for openFile(cache://localLOAD_https://cactus.nci.nih.gov/chemical/structure/caffeine/file?format=sdf&get3d=True): 4 ms

reading 24 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Babel

24 atoms created

ModelSet: not autobonding; use forceAutobond=true to force automatic bond creation

Time for creating model: 2 ms

C8H10N4O2

spinY = 10.0

Script completed

Jmol script terminated

FileManager.getAtomSetCollectionFromFile(cache://localLOAD_https://cactus.nci.nih.gov/chemical/structure/aceticacid/file?format=sdf&get3d=True)

The Resolver thinks Mol

C2H4O2

APtclcactv03312514253D 0 0.00000 0.00000

C2H4O2

Time for openFile(cache://localLOAD_https://cactus.nci.nih.gov/chemical/structure/aceticacid/file?format=sdf&get3d=True): 4 ms

reading 8 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Babel

8 atoms created

ModelSet: not autobonding; use forceAutobond=true to force automatic bond creation

Time for creating model: 2 ms

C2H4O2

spinY = 10.0

Script completed

Jmol script terminated

FileManager.getAtomSetCollectionFromFile(cache://localLOAD_https://cactus.nci.nih.gov/chemical/structure/ethanol/file?format=sdf&get3d=True)

The Resolver thinks Mol

C2H6O

APtclcactv04012507283D 0 0.00000 0.00000

C2H6O

Time for openFile(cache://localLOAD_https://cactus.nci.nih.gov/chemical/structure/ethanol/file?format=sdf&get3d=True): 4 ms

reading 9 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Babel

9 atoms created

ModelSet: not autobonding; use forceAutobond=true to force automatic bond creation

Time for creating model: 1 ms

C2H6O

spinY = 10.0

Script completed

Jmol script terminated

spinFPS is set too fast (30) -- can't keep up!

Viewer cachePut cache://localLOAD_https://cactus.nci.nih.gov/chemical/structure/acetone/file?format=sdf&get3d=True

Viewer cachePut https://cactus.nci.nih.gov/chemical/structure/acetone/file?format=sdf&get3d=True

FileManager.getAtomSetCollectionFromFile(cache://localLOAD_https://cactus.nci.nih.gov/chemical/structure/acetone/file?format=sdf&get3d=True)

The Resolver thinks Mol

C3H6O

APtclcactv04012512103D 0 0.00000 0.00000

C3H6O

Time for openFile(cache://localLOAD_https://cactus.nci.nih.gov/chemical/structure/acetone/file?format=sdf&get3d=True): 4 ms

reading 10 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Babel

10 atoms created

ModelSet: not autobonding; use forceAutobond=true to force automatic bond creation

Time for creating model: 1 ms

C3H6O

spinY = 10.0

Script completed

Jmol script terminated

spinFPS is set too fast (30) -- can't keep up!

Figure

$\PageIndex{2}$ : Caffeine (left), methionine (center, an essential amino acid), and vinyl chloride (right, a monomer of PVC plastic). Nitrogen atoms are shown in blue, sulfur in yellow, and chlorine in green.

The related field of biochemistry overlaps to some extent with organic chemistry. Biochemistry is the study of the chemistry of living systems. Many biochemical compounds are considered to be organic chemicals. Caffeine and methionine shown above are biochemical materials in terms of their use in the body, but organic chemicals in terms of their structure and chemical reactivity.

Summary

Organic compounds are defined as covalently bonded compounds containing carbon, excluding carbonates and oxides. (By this definition, compounds such as carbon dioxide, CO₂, and sodium carbonate, Na₂CO₃, are considered to be inorganic.)
Organic chemistry is the study of all organic compounds.
Biochemistry is the study of the chemistry of living systems.

This page is shared under a CK-12 license and was authored, remixed, and/or curated by Lance S. Lund (Anoka-Ramsey Community College). Original source: https://www.ck12.org/c/chemistry/.

LICENSED UNDER

Organic Chemistry

Summary

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