Organic compound

In chemistry, an organic compound is generally any chemical compound that contains carbon. Due to carbon's ability to catenate (form chains with other carbon atoms), millions of organic compounds are known. Study of the properties and synthesis of organic compounds is the discipline known as organic chemistry. For historical reasons, a few classes of carbon-containing compounds (e.g., carbonates and cyanides), along with a handful of other exceptions (e.g., carbon dioxide), are not classified as organic compounds and are considered inorganic. No consensus exists among chemists on precisely which carbon-containing compounds are excluded, making the definition of an organic compound elusive.[1]

Although organic compounds make up only a small percentage of the Earth's crust, they are of central importance because all known life is based on organic compounds. Living things incorporate inorganic carbon into organic compounds through a network of processes (the carbon cycle) that begins with the conversion of carbon dioxide and a hydrogen source like water into simple sugars and other organic molecules by autotrophic organisms using light (photosynthesis) or other sources of energy. Most synthetically produced organic compounds are ultimately derived from petrochemicals consisting mainly of hydrocarbons, which are themselves formed from the high pressure and temperature degradation of organic matter underground over geological timescales.[2] This ultimate derivation notwithstanding, organic compounds are no longer defined as compounds originating in living things, as they were historically.

In chemical nomenclature, an organyl group, frequently represented by the letter R, refers to any monovalent substituent whose open valence is on a carbon atom.[3]

Methane-2D-stereo
Methane, CH4; it is one of the simplest organic compounds.

Definitions of organic vs inorganic

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. Allotropes of carbon, such as diamond, graphite, fullerenes, and carbon nanotubes[4] are also excluded because they are simple substances composed of only a single element and therefore allotropes are not generally considered to be chemical compounds.

History

Vitalism

For many centuries, Western physicians and chemists believed in vitalism. This was the widespread conception that substances found in organic nature are created from the chemical elements by the action of a "vital force" or "life-force" (vis vitalis) that only living organisms possess. Vitalism taught that these "organic" compounds were fundamentally different from the "inorganic" compounds that could be obtained from the elements by chemical manipulations.

Vitalism survived for a while even after the rise of modern ideas about the atomic theory and chemical elements. 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.[5]

Modern classification and ambiguities

L-isoleucine-3D-balls
The L-isoleucine molecule, C6H13NO2, showing features typical of organic compounds. Carbon atoms are in black, hydrogens gray, oxygens red, and nitrogen blue.

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 term carbogenic has been proposed by E. J. Corey as a modern alternative to organic, but this neologism remains relatively obscure.

The organic compound L-isoleucine molecule presents some features typical of organic compounds: carbon–carbon bonds, carbon–hydrogen bonds, as well as covalent bonds from carbon to oxygen and to nitrogen.

As described in detail below, any definition of organic compound that uses simple, broadly applicable criteria turns out to be unsatisfactory, to varying degrees. The modern, commonly accepted definition of organic compound essentially amounts to any carbon containing compound, excluding several classes of substances traditionally considered as 'inorganic'. However, the list of substances so excluded varies from author to author. Still, it is generally agreed upon that there are (at least) a few carbon containing compounds that should not be considered organic. For instance, almost all authorities would require the exclusion of alloys that contain carbon, including steel (which contains cementite, Fe3C), as well as other metal and semimetal carbides (including "ionic" carbides, e.g, Al4C3 and CaC2 and "covalent" carbides, e.g. B4C and SiC, and graphite intercalation compounds, e.g. KC8). Other compounds and materials that are considered 'inorganic' by most authorities include: metal carbonates, simple oxides (CO, CO2, and arguably, C3O2), the allotropes of carbon, cyanide derivatives not containing an organic residue (e.g., KCN, (CN)2, BrCN, CNO, etc.), and heavier analogs thereof (e.g., CP 'cyaphide anion', CSe, COS; although CS2 'carbon disulfide' is often classed as an organic solvent). Halides of carbon without hydrogen (e.g., CF4 and CClF3), phosgene (COCl2), carboranes, metal carbonyls (e.g., nickel carbonyl), mellitic anhydride (C12O9), and other exotic oxocarbons are also considered inorganic by some authorities.

Nickel carbonyl (Ni(CO)4) and other metal carbonyls present an interesting case. They are often volatile liquids, like many organic compounds, yet they contain only carbon bonded to a transition metal and to oxygen and are often prepared directly from metal and carbon monoxide. Nickel carbonyl is frequently considered to be organometallic. Although many organometallic chemists employ a broad definition, in which any compound containing a carbon-metal covalent bond is considered organometallic, it is debatable whether organometallic compounds form a subset of organic compounds.[6]

Metal complexes with organic ligands but no carbon-metal bonds (e.g., Cu(OAc)2) are not considered organometallic; instead they are classed as metalorganic. Likewise, it is also unclear whether metalorganic compounds should automatically be considered organic.

The relatively narrow definition of organic compounds as those containing C-H bonds 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[7] and oxalic acid.[8] 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.[9] Terrestrially, it, and its anhydride, mellitic anhydride, are associated with the mineral mellite (Al2C6(COO)6·16H2O).

A slightly broader definition of organic compound includes all compounds bearing C-H or C-C bonds. This would still exclude urea. Moreover, this definition still leads to somewhat arbitrary divisions in sets of carbon-halogen compounds. For example, CF4 and CCl4 would be considered by this rule to be "inorganic", whereas CF3H, CHCl3, and C2Cl6 would be organic, though these compounds share many physical and chemical properties.

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 on 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 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.

Synthetic compounds

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.

Biotechnology

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.

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.
  • 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.

Structure determination

The main tools are proton and carbon-13 NMR spectroscopy, IR Spectroscopy, Mass spectrometry, UV/Vis Spectroscopy and X-ray crystallography.[10]

See also

References

  1. ^ Spencer L. Seager, Michael R. Slabaugh. Chemistry for Today: general, organic, and biochemistry. Thomson Brooks/Cole, 2004, p. 342. ISBN 0-534-39969-X
  2. ^ Smith, Cory. "Petrochemicals". American Fuel & Petrochemical Manufacturers. American Fuel & Petrochemical Manufacturers. Retrieved 18 December 2016.
  3. ^ IUPAC, Compendium of Chemical Terminology, 2nd ed. (the "Gold Book") (1997). Online corrected version:  (2006–) "organyl groups". doi:10.1351/goldbook.O04329.html
  4. ^ Fullerene derivatives are more frequently considered to be organic, and fullerene chemistry is usually considered a branch of organic chemistry. Moreover, the methods of organic synthesis have been applied to the rational synthesis of fullerenes and carbon nanotubes.
  5. ^ Henry Marshall Leicester; Herbert S. Klickstein (1951). A Source Book in Chemistry, 1400-1900. Harvard University Press. p. 309.
  6. ^ For example, since there is evidence of covalent Fe-C bonding in cementite (https://aip.scitation.org/doi/10.1063/1.2884529), a major component of steel, the broad definition would result in the classification of this compound as organometallic. However, steel and other carbon-containing alloys are seldom regarded as organic compounds. Thus, it is unclear whether the definition of organometallic should be narrowed, and/or whether these considerations imply that organometallic compounds are not necessarily organic.
  7. ^ "IUPAC Blue Book, Urea and Its Derivatives Rule C-971". Retrieved 2009-11-22.
  8. ^ "IUPAC Blue Book, Table 28(a) Carboxylic acids and related groups. Unsubstituted parent structures". Retrieved 2009-11-22.
  9. ^ S. A. Benner; K. G. Devine; L. N. Matveeva; D. H. Powell (2000). "The missing organic molecules on Mars". Proceedings of the National Academy of Sciences. 97 (6): 2425–2430. Bibcode:2000PNAS...97.2425B. doi:10.1073/pnas.040539497. PMC 15945. PMID 10706606.
  10. ^ Ernö Pretsch, Philippe Bühlmann, Martin Badertscher (2009), Structure Determination of Organic Compounds (Fourth, Revised and Enlarged Edition). Springer-Verlag Berlin Heidelberg

External links

4-Caffeoyl-1,5-quinide

4-Caffeoyl-1,5-quinide (4-caffeoylquinic-1,5-lactone or 4-CQL) is found in roasted coffee beans. It is formed by lactonization of 4-O-caffeoylquinic acid during the roasting process.

It is reported to possess opioid antagonist properties in mice.

4-Hydroxy-3-methoxymethamphetamine

4-Hydroxy-3-methoxymethamphetamine (HMMA) is an active metabolite of 3,4-methylenedioxymethamphetamine (MDMA). It is a slightly more potent stimulant than MDMA.

Broxaterol

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Domesticine

Domesticine is an alpha-1D-adrenoceptor antagonist.

Ersentilide

Ersentilide is a beta adrenergic receptor antagonist.

Falintolol

Falintolol is a beta-adrenergic receptor antagonist.

GBR-13119

GBR-13119 is a psychostimulant and dopamine re-uptake inhibitor.

Metazosin

Metazosin is an antihypertensive alpha-adrenergic antagonist.

Methylenedioxy

Methylenedioxy is the term used in the field of chemistry, particularly in organic chemistry, for a functional group with the structural formula R-O-CH2-O-R' which is connected to the rest of a molecule by two chemical bonds. The methylenedioxy group consists of two oxygen atoms connected to a methylene bridge (-CH2- unit). The methylenedioxy group is generally found attached to an aromatic structure such as phenyl where it forms the methylenedioxyphenyl or benzodioxole functional group which is widely found in natural products, including safrole, and drugs and chemicals such as tadalafil, MDMA, paroxetine and piperonyl butoxide.

Enzymes within the cytochrome P450 superfamily are able to form methylenedioxy bridges by closure of an open, adjacent phenol and methoxy group. Examples of products formed by this process are canadine and berberine. Similarly, ortho-demethylenation can be carried out by other members of the superfamily to open a bridge; a process which is applied to, as examples, both MDMA and MDA during their metabolism.

Nifenalol

Nifenalol is a beta-adrenoceptor antagonist.

Niravoline

Niravoline is a chemical compound with the formula C22H25N3O3. It has diuretic and aquaretic effects and has been studied for its potential use for cerebral edema and cirrhosis.It exerts its pharmacological effect as a kappa opioid receptor agonist.

Normetanephrine

Normetanephrine is a metabolite of norepinephrine created by action of catechol-O-methyl transferase on norepinephrine. It is excreted in the urine and found in certain tissues. It is a marker for catecholamine-secreting tumors such as pheochromocytoma.

Pacrinolol

Pacrinolol is a beta adrenergic receptor antagonist.

Photoanethole

Photoanethole is a naturally occurring organic compound that is found in anise and fennel. It has estrogenic activity, and along with anethole and dianethole, may be responsible for the estrogenic effects of anise and fennel. These compounds bear resemblance to the estrogens stilbene and diethylstilbestrol, which may explain their estrogenic activity. In fact, it is said that diethylstilbestrol and related drugs were originally modeled after photoanethole and dianethole.

Pyrazolopyridine

The pyrazolopyridines are a group of drugs investigated as anxiolytics which act as positive allosteric modulators of the GABAA receptor via the barbiturate binding site. They include the following compounds:

Cartazolate (SQ-65,396)

Etazolate (SQ-20,009)

ICI-190,622

Tracazolate (ICI-136,753)

Saturation (chemistry)

In chemistry, saturation (from the Latin word saturare, meaning 'to fill') has diverse meanings, all based on the idea of reaching a maximum capacity.

Tienoxolol

Tienoxolol is a beta adrenergic receptor antagonist.

Vinyl group

In chemistry, vinyl or ethenyl (abbreviated as Vi) is the functional group with the formula −CH=CH2. It is the ethylene (IUPAC ethene) molecule (H2C=CH2) less one hydrogen atom. The name is also used for any compound containing that group, namely R−CH=CH2 where R is any other group of atoms.

An industrially important example is vinyl chloride, precursor to PVC, a plastic commonly known as vinyl.

Vinyl is one of the alkenyl functional groups. On a carbon skeleton, sp2-hybridized carbons or positions are often called vinylic. Allyls, acrylates and styrenics contain vinyl groups. (A styrenic crosslinker with two vinyl groups is called divinyl benzene.)

Volatile organic compound

Volatile organic compounds (VOCs) are organic chemicals that have a high vapor pressure at ordinary room temperature. Their high vapor pressure results from a low boiling point, which causes large numbers of molecules to evaporate or sublimate from the liquid or solid form of the compound and enter the surrounding air, a trait known as volatility. For example, formaldehyde, which evaporates from paint and releases from materials like resin, has a boiling point of only –19 °C (–2 °F).

VOCs are numerous, varied, and ubiquitous. They include both human-made and naturally occurring chemical compounds. Most scents or odors are of VOCs. VOCs play an important role in communication between plants, and messages from plants to animals. Some VOCs are dangerous to human health or cause harm to the environment. Anthropogenic VOCs are regulated by law, especially indoors, where concentrations are the highest. Harmful VOCs typically are not acutely toxic, but have compounding long-term health effects. Because the concentrations are usually low and the symptoms slow to develop, research into VOCs and their effects is difficult.

Concepts in organic chemistry
Molecules
Deuterated
molecules
Unconfirmed
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