For historical reasons discussed below, a few types of carbon-containing compounds, such as carbides, carbonates, simple oxides of carbon (for example, CO and CO2), and cyanides are considered inorganic. The distinction between organic and inorganic carbon compounds, while "useful in organizing the vast subject of chemistry... is somewhat arbitrary".
Organic chemistry is the science concerned with all aspects of organic compounds. Organic synthesis is the methodology of their preparation.
The word organic is historical, dating 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 the action of a "life-force" (vis vitalis) that only organisms possessed. 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 1824, 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 an "organic" compound, as it was known to occur only in the urine of living organisms. Wöhler's experiments were followed by many others, in which increasingly complex "organic" substances were produced from "inorganic" ones without the involvement of any living organism.
Even though vitalism has been discredited, scientific nomenclature retains the distinction between organic and inorganic compounds. The modern meaning of organic compound is any compound that contains a significant amount of carbon—even though many of the organic compounds known today have no connection to any substance found in living organisms.
The organic compound L-isoleucine molecule presents some features typical of organic compounds: carbon–carbon bonds, carbon–hydrogen bonds, as well as covalent bonds between carbon to oxygen and to nitrogen.
Still, even the broadest definition (of "carbon-containing molecules" as organic) requires excluding alloys that contain carbon, including steel. Other 'excluded' materials are: compounds such as carbonates and carbonyls, simple oxides of carbon, simple carbon halides and sulfides, the allotropes of carbon, and cyanides not containing the −C≡N functional group—all which are considered inorganic.
The "C-H" definition excludes compounds that are (historically and practically) considered 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 and oxalic acid. Other compounds lacking C-H bonds but traditionally considered organic include benzenehexol, mesoxalic acid, and carbon tetrachloride. Mellitic acid, which contains no C-H bonds, is considered a possible organic substance in Martian soil.
The "C-H bond-only" rule also leads to somewhat arbitrary divisions in sets of carbon-fluorine compounds. For example, CF4 would be considered by this rule to be "inorganic", whereas CF3H would be organic.
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 on the size of organic compounds, distinguishes between small molecules and polymers.
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 more expensive to produce 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.
Compounds that are prepared by reaction of other compounds are known 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.
Many organic compounds—two examples are ethanol and insulin—are manufactured industrially using organisms such as bacteria and yeast. Typically, the DNA of an organism is altered to express compounds not ordinarily produced by the organism. Many such biotechnology-engineered compounds did not previously exist in nature.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.
PubChem contains 18.4 million entries on compounds and especially covers the field of medicinal chemistry.
A great number of more specialized databases exist for diverse branches of organic chemistry.See Structure determination
The main tools are proton and carbon-13 NMR spectroscopy, IR Spectroscopy, Mass spectrometry, UV/Vis Spectroscopy and X-ray crystallography.