Organic molecules


An organic compound is any member of a large class of gaseous, liquid, or solid chemical compounds whose molecules contain carbon. For historical reasons discussed below, a few types of carbon-containing compounds such as carbides, carbonates, simple oxides of carbon (such as CO and CO2), and cyanides are considered inorganic.[1] The distinction between "organic" and "inorganic" carbon compounds, while "useful in organizing the vast subject of chemistry... is somewhat arbitrary".[2]

Organic chemistry is the science concerned with all aspects of organic compounds. Organic synthesis is the methodology of their preparation.

History

Vitalism

Main article: Vitalism

The word "organic" is historical, dating back to the 1st century. For many centuries, Western alchemists believed in vitalism. This is the theory that certain compounds could be synthesized only from their classical elements — Earth, Water, Air, and Fire — by action of a "life-force" (vis vitalis) possessed only by organisms. Vitalism taught that these "organic" compounds were fundamentally different from the "inorganic" compounds that could be obtained from the elements by chemical manipulation.

Vitalism survived for a while even after the rise of modern atomic theory and the replacement of the Aristotelian elements by those we know today. It first came under question in 1804, when Friedrich Wöhler synthesized oxalic acid, a compound known to occur only in living organisms, from cyanogen. A more decisive experiment was Wöhler's 1828 synthesis of urea from the inorganic salts potassium cyanate and ammonium sulfate. Urea had long been considered to be an "organic" compound, as it was known to occur only in the urine of living organisms. Wöhler's experiments were followed by many others, where increasingly complex "organic" substances were produced from "inorganic" ones without the involvement of any living organism.

Modern classification

Even though vitalism has been discredited, the distinction between "organic" and "inorganic" compounds has been retained through the present. The modern meaning of "organic compound" is any one of them that contains a significant amount of carbon – even though many of the "organic compounds" known today have no connection whatsoever with any substance found in living organisms.

There is no "official" definition of an organic compound. Some textbooks define an organic compound as one containing one or more C-H bonds; others include C-C bonds in the definition. Others state that if a molecule contains carbon―it is organic.[3]

Even the broader definition of "carbon-containing molecules" requires the exclusion of carbon-containing alloys (including steel), a relatively small number of carbon-containing compounds such as metal carbonates and carbonyls, simple oxides of carbon and cyanides, as well as the allotropes of carbon and simple carbon halides and sulfides, which are usually considered to be inorganic.

The "C-H" definition excludes compounds that are historically and practically considered to be organic. Neither urea nor oxalic acid is organic by this definition, yet they were two key compounds in the vitalism debate. The IUPAC Blue Book on organic nomenclature specifically mentions urea[4] and oxalic acid.[5] Other compounds lacking C-H bonds that are also traditionally considered to be organic include benzenehexol, mesoxalic acid, and carbon tetrachloride. Mellitic acid, which contains no C-H bonds, is considered to be a possible organic substance in Martian soil. All do, however, contain C-C bonds.[6]

The "C-H bond-only" rule also leads to somewhat arbitrary divisions in sets of carbon-fluorine compounds, as, for example, Teflon is considered by this rule "inorganic" but Tefzel organic. Likewise, many Halons are considered inorganic, whereas the rest are considered organic. For these and other reasons, most sources consider C-H compounds to be only a subset of "organic" compounds.

In summary, most carbon-containing compounds are organic, and almost all organic compounds contain at least a C-H bond or a C-C bond. A compound does not need to contain C-H bonds to be considered organic (e.g. urea), but many organic compounds do.

Classification

Organic compounds may be classified in a variety of ways. One major distinction is between natural and synthetic compounds. Organic compounds can also be classified or subdivided by the presence of heteroatoms, e.g., organometallic compounds, which feature bonds between carbon and a metal, and organophosphorus compounds, which feature bonds between carbon and a phosphorus.

Another distinction, based upon the size of organic compounds, distinguishes between small molecules and polymers.

Natural compounds

Natural compounds refer to those that are produced by plants or animals. Many of these are still extracted from natural sources because they would be far too expensive to be produced artificially. Examples include most sugars, some alkaloids and terpenoids, certain nutrients such as vitamin B12, and, in general, those natural products with large or stereoisometrically complicated molecules present in reasonable concentrations in living organisms.

Further compounds of prime importance in biochemistry are antigens, carbohydrates, enzymes, hormones, lipids and fatty acids, neurotransmitters, nucleic acids, proteins, peptides and amino acids, lectins, vitamins, and fats and oils.

Synthetic compounds

Compounds that are prepared by reaction of other compounds are referred to as "synthetic". They may be either compounds that already are found in plants or animals or those that do not occur naturally.

Most polymers (a category that includes all plastics and rubbers), are organic synthetic or semi-synthetic compounds.

Nomenclature

The IUPAC nomenclature of organic compounds slightly differs from the CAS nomenclature.

Databases

  • The CAS database is the most comprehensive repository for data on organic compounds. The search tool SciFinder is offered.
  • The Beilstein database contains information on 9.8 million substances, covers the scientific literature from 1771 to the present, and is today accessible via Reaxys. Structures and a large diversity of physical and chemical properties is available for each substance, with reference to original literature.

There is a great number of more specialized databases for diverse branches of organic chemistry.

Structure determination

See Structure determination

Today, the main tools are proton and carbon-13 NMR spectroscopy and X-ray crystallography.

See also

References

External links

  • Organic Compounds Database
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