Organic chemistry

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Methane, CH4; the line-angle structural formula shows four carbon-hydrogen single bonds (s, in black), and the typical 3D shape of tetrahedral molecules, with ~109deg interior bond angles (in dashed-green). Ch4-structure.png
Methane, CH4; the line-angle structural formula shows four carbon-hydrogen single bonds (σ, in black), and the typical 3D shape of tetrahedral molecules, with ~109° interior bond angles (in dashed-green).

Organic chemistry is a subdiscipline of chemistry that studies the structure, properties and reactions of organic compounds, which contain carbon in covalent bonding. [1] Study of structure determines their chemical composition and formula. Study of properties includes physical and chemical properties, and evaluation of chemical reactivity to understand their behavior. The study of organic reactions includes the chemical synthesis of natural products, drugs, and polymers, and study of individual organic molecules in the laboratory and via theoretical (in silico) study.

Chemistry scientific discipline

Chemistry is the scientific discipline involved with elements and compounds composed of atoms, molecules and ions: their composition, structure, properties, behavior and the changes they undergo during a reaction with other substances.

Organic compound Chemical compound that contains carbon (except for several compounds traditionally classified as inorganic compounds)

In chemistry, organic compounds are generally any chemical compounds that contain carbon. Due to carbon's ability to catenate, millions of organic compounds are known. The study of the properties, reactions, and syntheses of organic compounds comprises the discipline known as organic chemistry. For historical reasons, a few classes of carbon-containing compounds, along with a handful of other exceptions, are not classified as organic compounds and are considered inorganic. Other than those just named, little consensus exists among chemists on precisely which carbon-containing compounds are excluded, making any rigorous definition of an organic compound elusive.

Carbon Chemical element with atomic number 6

Carbon is a chemical element with the symbol C and atomic number 6. It is nonmetallic and tetravalent—making four electrons available to form covalent chemical bonds. It belongs to group 14 of the periodic table. Three isotopes occur naturally, 12C and 13C being stable, while 14C is a radionuclide, decaying with a half-life of about 5,730 years. Carbon is one of the few elements known since antiquity.

Contents

The range of chemicals studied in organic chemistry includes hydrocarbons (compounds containing only carbon and hydrogen) as well as compounds based on carbon, but also containing other elements, [1] [2] [3] especially oxygen, nitrogen, sulfur, phosphorus (included in many biochemicals) and the halogens. Organometallic chemistry is the study of compounds containing carbon–metal bonds.

Hydrocarbon organic compound consisting entirely of hydrogen and carbon

In organic chemistry, a hydrocarbon is an organic compound consisting entirely of hydrogen and carbon. Hydrocarbons are examples of group 14 hydrides. Hydrocarbons from which one hydrogen atom has been removed are functional groups called hydrocarbyls. Because carbon has 4 electrons in its outermost shell carbon has exactly four bonds to make, and is only stable if all 4 of these bonds are used.

Hydrogen Chemical element with atomic number 1

Hydrogen is the chemical element with the symbol H and atomic number 1. With a standard atomic weight of 1.008, hydrogen is the lightest element in the periodic table. Hydrogen is the most abundant chemical substance in the Universe, constituting roughly 75% of all baryonic mass. Non-remnant stars are mainly composed of hydrogen in the plasma state. The most common isotope of hydrogen, termed protium, has one proton and no neutrons.

Oxygen Chemical element with atomic number 8

Oxygen is the chemical element with the symbol O and atomic number 8. It is a member of the chalcogen group in the periodic table, a highly reactive nonmetal, and an oxidizing agent that readily forms oxides with most elements as well as with other compounds. By mass, oxygen is the third-most abundant element in the universe, after hydrogen and helium. At standard temperature and pressure, two atoms of the element bind to form dioxygen, a colorless and odorless diatomic gas with the formula O
2
. Diatomic oxygen gas constitutes 20.8% of the Earth's atmosphere. As compounds including oxides, the element makes up almost half of the Earth's crust.

In addition, contemporary research focuses on organic chemistry involving other organometallics including the lanthanides, but especially the transition metals zinc, copper, palladium, nickel, cobalt, titanium and chromium.

The lanthanide or lanthanoid series of chemical elements comprises the 15 metallic chemical elements with atomic numbers 57–71, from lanthanum through lutetium. These elements, along with the chemically similar elements scandium and yttrium, are often collectively known as the rare earth elements.

In chemistry, the term transition metal has three possible meanings:

5-alpha-dihydroprogesterone.png
Line-angle representation
5alpha-Dihydroprogesterone 3D ball.png
Ball-and-stick representation
5alpha-Dihydroprogesterone 3D spacefill.png
Space-filling representation
Three representations of an organic compound, 5α-Dihydroprogesterone (5α-DHP), a steroid hormone. For molecules showing color, the carbon atoms are in black, hydrogens in gray, and oxygens in red. In the line angle representation, carbon atoms are implied at every terminus of a line and vertex of multiple lines, and hydrogen atoms are implied to fill the remaining needed valences (up to 4).

Organic compounds form the basis of all earthly life and constitute the majority of known chemicals. The bonding patterns of carbon, with its valence of four—formal single, double, and triple bonds, plus structures with delocalized electrons—make the array of organic compounds structurally diverse, and their range of applications enormous. They form the basis of, or are constituents of, many commercial products including pharmaceuticals; petrochemicals and agrichemicals, and products made from them including lubricants, solvents; plastics; fuels and explosives. The study of organic chemistry overlaps organometallic chemistry and biochemistry, but also with medicinal chemistry, polymer chemistry, and materials science. [1]

Carbon is a primary component of all known life on Earth, representing approximately 45–50% of all dry biomass. Carbon compounds occur naturally in great abundance on Earth. Complex biological molecules almost always consist of carbon atoms bonded with other elements, especially oxygen and hydrogen and frequently also nitrogen, phosphorus, and sulfur.

In chemistry, the valence or valency of an element is a measure of its combining power with other atoms when it forms chemical compounds or molecules. The concept of valence was developed in the second half of the 19th century and helped successfully explain the molecular structure of inorganic and organic compounds. The quest for the underlying causes of valence led to the modern theories of chemical bonding, including the cubical atom (1902), Lewis structures (1916), valence bond theory (1927), molecular orbitals (1928), valence shell electron pair repulsion theory (1958), and all of the advanced methods of quantum chemistry.

Drug Substance having an effect on the body

A drug is any substance that causes a change in an organism's physiology or psychology when consumed.

History

Friedrich Wohler Friedrich woehler.jpg
Friedrich Wöhler

Before the nineteenth century, chemists generally believed that compounds obtained from living organisms were endowed with a vital force that distinguished them from inorganic compounds. According to the concept of vitalism (vital force theory), organic matter was endowed with a "vital force". [4] During the first half of the nineteenth century, some of the first systematic studies of organic compounds were reported. Around 1816 Michel Chevreul started a study of soaps made from various fats and alkalis. He separated the acids that, in combination with the alkali, produced the soap. Since these were all individual compounds, he demonstrated that it was possible to make a chemical change in various fats (which traditionally come from organic sources), producing new compounds, without "vital force". In 1828 Friedrich Wöhler produced the organic chemical urea (carbamide), a constituent of urine, from inorganic starting materials (the salts potassium cyanate and ammonium sulfate), in what is now called the Wöhler synthesis. Although Wöhler himself was cautious about claiming he had disproved vitalism, this was the first time a substance thought to be organic was synthesized in the laboratory without biological (organic) starting materials. The event is now generally accepted as indeed disproving the doctrine of vitalism. [5]

An inorganic compound is typically a chemical compound that lacks C-H bonds, that is, a compound that is not an organic compound, but the distinction is not defined or even of particular interest.

Vitalism Discredited scientific hypothesis

Vitalism is the belief that "living organisms are fundamentally different from non-living entities because they contain some non-physical element or are governed by different principles than are inanimate things". Where vitalism explicitly invokes a vital principle, that element is often referred to as the "vital spark", "energy" or "élan vital", which some equate with the soul. In the 18th and 19th centuries vitalism was discussed among biologists, between those who felt that the known mechanics of physics would eventually explain the difference between life and non-life and vitalists who argued that the processes of life could not be reduced to a mechanistic process. Some vitalist biologists proposed testable hypotheses meant to show inadequacies with mechanistic explanations, but these experiments failed to provide support for vitalism. Biologists now consider vitalism in this sense to have been refuted by empirical evidence, and hence regard it as a superseded scientific theory.

Michel Eugène Chevreul French chemist

Michel Eugène Chevreul was a French chemist whose work with fatty acids led to early applications in the fields of art and science. He is credited with the discovery of margaric acid, creatine, and designing an early form of soap made from animal fats and salt. He lived to 102 and was a pioneer in the field of gerontology. He is also one of the 72 people whose names are inscribed on the Eiffel Tower; of those 72 scientists and engineers, Chevreul was one of only two who were still alive when Gustave Eiffel planted the French Tricolor on the top of the tower on 31 March 1889 and was the last living individual born before the French Revolution.

In 1856 William Henry Perkin, while trying to manufacture quinine accidentally produced the organic dye now known as Perkin's mauve. His discovery, made widely known through its financial success, greatly increased interest in organic chemistry. [6]

Quinine medication used to treat malaria and babesiosis

Quinine is a medication used to treat malaria and babesiosis. This includes the treatment of malaria due to Plasmodium falciparum that is resistant to chloroquine when artesunate is not available. While used for restless legs syndrome, it is not recommended for this purpose due to the risk of side effects. It can be taken by mouth or used intravenously. Malaria resistance to quinine occurs in certain areas of the world. Quinine is also the ingredient in tonic water that gives it its bitter taste.

Dye soluble chemical substance or natural material which can impart color to other materials

A dye is a coloured substance that chemically bonds to the substrate to which it is being applied. This distinguishes dyes from pigments which do not chemically bind to the material they colour. The dye is generally applied in an aqueous solution, and may require a mordant to improve the fastness of the dye on the fiber.

A crucial breakthrough for organic chemistry was the concept of chemical structure, developed independently in 1858 by both Friedrich August Kekulé and Archibald Scott Couper. [7] Both researchers suggested that tetravalent carbon atoms could link to each other to form a carbon lattice, and that the detailed patterns of atomic bonding could be discerned by skillful interpretations of appropriate chemical reactions. [8]

The era of the pharmaceutical industry began in the last decade of the 19th century when the manufacturing of acetylsalicylic acidmore commonly referred to as aspirin in Germany was started by Bayer. [9] By 1910 Paul Ehrlich and his laboratory group began developing arsenic-based arsphenamine, (Salvarsan), as the first effective medicinal treatment of syphilis, and thereby initiated the medical practice of chemotherapy. Ehrlich popularized the concepts of "magic bullet" drugs and of systematically improving drug therapies. [10] [11] His laboratory made decisive contributions to developing antiserum for diphtheria and standardizing therapeutic serums. [12]

An example of an organometallic molecule, a catalyst called Grubbs' catalyst. Its formula is often given as RuCl2(PCy3)2(=CHPh), where the ball-and-stick model is based on X-ray crystallography. The single metal atom ruthenium (Ru), (in turquoise), is at the very center of the structure; two chlorines (green), are bonded to the ruthenium atom--carbon atoms are black, hydrogens gray-white, and phosphorus orange. A phosphorus-ligand bond, tricyclohexyl phosphine, PCy, is below center; (another PCy ligand appears at the top of the image where its rings are obscuring one another). The ring group projecting to the right, an alkylidene, contains a metal-carbon double bond to ruthenium. Grubbs-1G-from-xtal-2010-3D-balls.png
An example of an organometallic molecule, a catalyst called Grubbs' catalyst. Its formula is often given as RuCl2(PCy3)2(=CHPh), where the ball-and-stick model is based on X-ray crystallography. The single metal atom ruthenium (Ru), (in turquoise), is at the very center of the structure; two chlorines (green), are bonded to the ruthenium atom—carbon atoms are black, hydrogens gray-white, and phosphorus orange. A phosphorus-ligand bond, tricyclohexyl phosphine, PCy, is below center; (another PCy ligand appears at the top of the image where its rings are obscuring one another). The ring group projecting to the right, an alkylidene, contains a metal-carbon double bond to ruthenium.

Early examples of organic reactions and applications were often found because of a combination of luck and preparation for unexpected observations. The latter half of the 19th century however witnessed systematic studies of organic compounds. The development of synthetic indigo is illustrative. The production of indigo from plant sources dropped from 19,000 tons in 1897 to 1,000 tons by 1914 thanks to the synthetic methods developed by Adolf von Baeyer. In 2002, 17,000 tons of synthetic indigo were produced from petrochemicals. [14]

In the early part of the 20th century, polymers and enzymes were shown to be large organic molecules, and petroleum was shown to be of biological origin.

The multiple-step synthesis of complex organic compounds is called total synthesis. Total synthesis of complex natural compounds increased in complexity to glucose and terpineol. For example, cholesterol-related compounds have opened ways to synthesize complex human hormones and their modified derivatives. Since the start of the 20th century, complexity of total syntheses has been increased to include molecules of high complexity such as lysergic acid and vitamin B12. [15]

The total synthesis of vitamin B12 marked a major achievement in organic chemistry. Cobalamin.png
The total synthesis of vitamin B12 marked a major achievement in organic chemistry.

The discovery of petroleum and the development of the petrochemical industry spurred the development of organic chemistry. Converting individual petroleum compounds into types of compounds by various chemical processes led to organic reactions enabling a broad range of industrial and commercial products including, among (many) others: plastics, synthetic rubber, organic adhesives, and various property-modifying petroleum additives and catalysts.

The majority of chemical compounds occurring in biological organisms are in fact carbon compounds, so the association between organic chemistry and biochemistry is so close that biochemistry might be regarded as in essence a branch of organic chemistry. Although the history of biochemistry might be taken to span some four centuries, fundamental understanding of the field only began to develop in the late 19th century and the actual term biochemistry was coined around the start of 20th century. Research in the field increased throughout the twentieth century, without any indication of slackening in the rate of increase, as may be verified by inspection of abstraction and indexing services such as BIOSIS Previews and Biological Abstracts, which began in the 1920s as a single annual volume, but has grown so drastically that by the end of the 20th century it was only available to the everyday user as an online electronic database. [16]

Characterization

Since organic compounds often exist as mixtures, a variety of techniques have also been developed to assess purity, especially important being chromatography techniques such as HPLC and gas chromatography. Traditional methods of separation include distillation, crystallization, and solvent extraction.

Organic compounds were traditionally characterized by a variety of chemical tests, called "wet methods", but such tests have been largely displaced by spectroscopic or other computer-intensive methods of analysis. [17] Listed in approximate order of utility, the chief analytical methods are:

Traditional spectroscopic methods such as infrared spectroscopy, optical rotation, and UV/VIS spectroscopy provide relatively nonspecific structural information but remain in use for specific classes of compounds. Traditionally refractive index and density were also important for substance identification.

Properties

Physical properties of organic compounds typically of interest include both quantitative and qualitative features. Quantitative information includes melting point, boiling point, and index of refraction. Qualitative properties include odor, consistency, solubility, and color.

Melting and boiling properties

Organic compounds typically melt and many boil. In contrast, while inorganic materials generally can be melted, many do not boil, tending instead to degrade. In earlier times, the melting point (m.p.) and boiling point (b.p.) provided crucial information on the purity and identity of organic compounds. The melting and boiling points correlate with the polarity of the molecules and their molecular weight. Some organic compounds, especially symmetrical ones, sublime, that is they evaporate without melting. A well-known example of a sublimable organic compound is para-dichlorobenzene, the odiferous constituent of modern mothballs. Organic compounds are usually not very stable at temperatures above 300 °C, although some exceptions exist.

Solubility

Neutral organic compounds tend to be hydrophobic; that is, they are less soluble in water than in organic solvents. Exceptions include organic compounds that contain ionizable (which can be converted in ions) groups as well as low molecular weight alcohols, amines, and carboxylic acids where hydrogen bonding occurs. Organic compounds tend to dissolve in organic solvents. Solvents can be either pure substances like ether or ethyl alcohol, or mixtures, such as the paraffinic solvents such as the various petroleum ethers and white spirits, or the range of pure or mixed aromatic solvents obtained from petroleum or tar fractions by physical separation or by chemical conversion. Solubility in the different solvents depends upon the solvent type and on the functional groups if present in the solution.

Solid state properties

Various specialized properties of molecular crystals and organic polymers with conjugated systems are of interest depending on applications, e.g. thermo-mechanical and electro-mechanical such as piezoelectricity, electrical conductivity (see conductive polymers and organic semiconductors), and electro-optical (e.g. non-linear optics) properties. For historical reasons, such properties are mainly the subjects of the areas of polymer science and materials science.

Nomenclature

Various names and depictions for one organic compound. OrgNom.svg
Various names and depictions for one organic compound.

The names of organic compounds are either systematic, following logically from a set of rules, or nonsystematic, following various traditions. Systematic nomenclature is stipulated by specifications from IUPAC. Systematic nomenclature starts with the name for a parent structure within the molecule of interest. This parent name is then modified by prefixes, suffixes, and numbers to unambiguously convey the structure. Given that millions of organic compounds are known, rigorous use of systematic names can be cumbersome. Thus, IUPAC recommendations are more closely followed for simple compounds, but not complex molecules. To use the systematic naming, one must know the structures and names of the parent structures. Parent structures include unsubstituted hydrocarbons, heterocycles, and monofunctionalized derivatives thereof.

Nonsystematic nomenclature is simpler and unambiguous, at least to organic chemists. Nonsystematic names do not indicate the structure of the compound. They are common for complex molecules, which includes most natural products. Thus, the informally named lysergic acid diethylamide is systematically named (6aR,9R)-N,N-diethyl-7-methyl-4,6,6a,7,8,9-hexahydroindolo-[4,3-fg] quinoline-9-carboxamide.

With the increased use of computing, other naming methods have evolved that are intended to be interpreted by machines. Two popular formats are SMILES and InChI.

Structural drawings

Organic molecules are described more commonly by drawings or structural formulas, combinations of drawings and chemical symbols. The line-angle formula is simple and unambiguous. In this system, the endpoints and intersections of each line represent one carbon, and hydrogen atoms can either be notated explicitly or assumed to be present as implied by tetravalent carbon.

This diagram shows 5 different structural representations of the organic compound butane. The left-most structure is a bond-line drawing where the hydrogen atoms are removed. The 2nd structure has the hydrogens added depicted-the dark wedged bonds indicate the hydrogen atoms are coming toward the reader, the hashed bonds indicate the atoms are oriented away from the reader, and the solid (plain) ponds indicate the bonds are in the plane of the screen/paper. The middle structure shows the four carbon atoms. The 4th structure is a representation just showing the atoms and bonds without 3-dimensions. The right-most structure is a condensed structure representation of butane. Stuctural drawings of butane 854px.jpg
This diagram shows 5 different structural representations of the organic compound butane. The left-most structure is a bond-line drawing where the hydrogen atoms are removed. The 2nd structure has the hydrogens added depicted-the dark wedged bonds indicate the hydrogen atoms are coming toward the reader, the hashed bonds indicate the atoms are oriented away from the reader, and the solid (plain) ponds indicate the bonds are in the plane of the screen/paper. The middle structure shows the four carbon atoms. The 4th structure is a representation just showing the atoms and bonds without 3-dimensions. The right-most structure is a condensed structure representation of butane.

History

By 1880 an explosion in the number of chemical compounds being discovered occurred assisted by new synthetic and analytical techniques. Grignard described the situation as "chaos le plus complet" as due to the lack of convention it was possible to have multiple names for the same compound. This led to the creation of the Geneva rules in 1892. [18]

Classification of organic compounds

Functional groups

The family of carboxylic acids contains a carboxyl (-COOH) functional group. Acetic acid, shown here, is an example. Acetic acid atoms.svg
The family of carboxylic acids contains a carboxyl (-COOH) functional group. Acetic acid, shown here, is an example.

The concept of functional groups is central in organic chemistry, both as a means to classify structures and for predicting properties. A functional group is a molecular module, and the reactivity of that functional group is assumed, within limits, to be the same in a variety of molecules. Functional groups can have decisive influence on the chemical and physical properties of organic compounds. Molecules are classified on the basis of their functional groups. Alcohols, for example, all have the subunit C-O-H. All alcohols tend to be somewhat hydrophilic, usually form esters, and usually can be converted to the corresponding halides. Most functional groups feature heteroatoms (atoms other than C and H). Organic compounds are classified according to functional groups, alcohols, carboxylic acids, amines, etc. [19]

Aliphatic compounds

The aliphatic hydrocarbons are subdivided into three groups of homologous series according to their state of saturation:

The rest of the group is classed according to the functional groups present. Such compounds can be "straight-chain", branched-chain or cyclic. The degree of branching affects characteristics, such as the octane number or cetane number in petroleum chemistry.

Both saturated (alicyclic) compounds and unsaturated compounds exist as cyclic derivatives. The most stable rings contain five or six carbon atoms, but large rings (macrocycles) and smaller rings are common. The smallest cycloalkane family is the three-membered cyclopropane ((CH2)3). Saturated cyclic compounds contain single bonds only, whereas aromatic rings have an alternating (or conjugated) double bond. Cycloalkanes do not contain multiple bonds, whereas the cycloalkenes and the cycloalkynes do.

Aromatic compounds

Benzene is one of the best-known aromatic compounds as it is one of the simplest and most stable aromatics. Benzene-resonance-structures.svg
Benzene is one of the best-known aromatic compounds as it is one of the simplest and most stable aromatics.

Aromatic hydrocarbons contain conjugated double bonds. This means that every carbon atom in the ring is sp2 hybridized, allowing for added stability. The most important example is benzene, the structure of which was formulated by Kekulé who first proposed the delocalization or resonance principle for explaining its structure. For "conventional" cyclic compounds, aromaticity is conferred by the presence of 4n + 2 delocalized pi electrons, where n is an integer. Particular instability (antiaromaticity) is conferred by the presence of 4n conjugated pi electrons.

Heterocyclic compounds

The characteristics of the cyclic hydrocarbons are again altered if heteroatoms are present, which can exist as either substituents attached externally to the ring (exocyclic) or as a member of the ring itself (endocyclic). In the case of the latter, the ring is termed a heterocycle. Pyridine and furan are examples of aromatic heterocycles while piperidine and tetrahydrofuran are the corresponding alicyclic heterocycles. The heteroatom of heterocyclic molecules is generally oxygen, sulfur, or nitrogen, with the latter being particularly common in biochemical systems.

Heterocycles are commonly found in a wide range of products including aniline dyes and medicines. Additionally, they are prevalent in a wide range of biochemical compounds such as alkaloids, vitamins, steroids, and nucleic acids (e.g. DNA, RNA).

Rings can fuse with other rings on an edge to give polycyclic compounds. The purine nucleoside bases are notable polycyclic aromatic heterocycles. Rings can also fuse on a "corner" such that one atom (almost always carbon) has two bonds going to one ring and two to another. Such compounds are termed spiro and are important in a number of natural products.

Polymers

This swimming board is made of polystyrene, an example of a polymer. Girl with styrofoam swimming board.jpg
This swimming board is made of polystyrene, an example of a polymer.

One important property of carbon is that it readily forms chains, or networks, that are linked by carbon-carbon (carbon-to-carbon) bonds. The linking process is called polymerization, while the chains, or networks, are called polymers. The source compound is called a monomer.

Two main groups of polymers exist: synthetic polymers and biopolymers. Synthetic polymers are artificially manufactured, and are commonly referred to as industrial polymers. [20] Biopolymers occur within a respectfully natural environment, or without human intervention.

Since the invention of the first synthetic polymer product, bakelite, synthetic polymer products have frequently been invented.[ citation needed ]

Common synthetic organic polymers are polyethylene (polythene), polypropylene, nylon, teflon (PTFE), polystyrene, polyesters, polymethylmethacrylate (called perspex and plexiglas), and polyvinylchloride (PVC). [ citation needed ]

Both synthetic and natural rubber are polymers. [ citation needed ]

Varieties of each synthetic polymer product may exist, for purposes of a specific use. Changing the conditions of polymerization alters the chemical composition of the product and its properties. These alterations include the chain length, or branching, or the tacticity. [ citation needed ]

With a single monomer as a start, the product is a homopolymer. [ citation needed ]

Secondary component(s) may be added to create a heteropolymer (co-polymer) and the degree of clustering of the different components can also be controlled. [ citation needed ]

Physical characteristics, such as hardness, density, mechanical or tensile strength, abrasion resistance, heat resistance, transparency, colour, etc. will depend on the final composition. [ citation needed ]

Biomolecules

Maitotoxin, a complex organic biological toxin. Maitotoxin 2D structure.svg
Maitotoxin, a complex organic biological toxin.

Biomolecular chemistry is a major category within organic chemistry which is frequently studied by biochemists. Many complex multi-functional group molecules are important in living organisms. Some are long-chain biopolymers, and these include peptides, DNA, RNA and the polysaccharides such as starches in animals and celluloses in plants. The other main classes are amino acids (monomer building blocks of peptides and proteins), carbohydrates (which includes the polysaccharides), the nucleic acids (which include DNA and RNA as polymers), and the lipids. In addition, animal biochemistry contains many small molecule intermediates which assist in energy production through the Krebs cycle, and produces isoprene, the most common hydrocarbon in animals. Isoprenes in animals form the important steroid structural (cholesterol) and steroid hormone compounds; and in plants form terpenes, terpenoids, some alkaloids, and a class of hydrocarbons called biopolymer polyisoprenoids present in the latex of various species of plants, which is the basis for making rubber.

Peptide Synthesis
See also Peptide synthesis
Oligonucleotide Synthesis
See also Oligonucleotide synthesis
Carbohydrate Synthesis
See also Carbohydrate synthesis

Small molecules

Molecular models of caffeine. CAFENE~1.svg
Molecular models of caffeine.

In pharmacology, an important group of organic compounds is small molecules, also referred to as 'small organic compounds'. In this context, a small molecule is a small organic compound that is biologically active, but is not a polymer. In practice, small molecules have a molar mass less than approximately 1000 g/mol.

Fullerenes

Fullerenes and carbon nanotubes, carbon compounds with spheroidal and tubular structures, have stimulated much research into the related field of materials science. The first fullerene was discovered in 1985 by Sir Harold W. Kroto of the United Kingdom and by Richard E. Smalley and Robert F. Curl, Jr., of the United States. Using a laser to vaporize graphite rods in an atmosphere of helium gas, these chemists and their assistants obtained cagelike molecules composed of 60 carbon atoms (C60) joined together by single and double bonds to form a hollow sphere with 12 pentagonal and 20 hexagonal faces—a design that resembles a football, or soccer ball. In 1996 the trio was awarded the Nobel Prize for their pioneering efforts. The C60 molecule was named buckminsterfullerene (or, more simply, the buckyball) after the American architect R. Buckminster Fuller, whose geodesic dome is constructed on the same structural principles.

Others

Organic compounds containing bonds of carbon to nitrogen, oxygen and the halogens are not normally grouped separately. Others are sometimes put into major groups within organic chemistry and discussed under titles such as organosulfur chemistry, organometallic chemistry, organophosphorus chemistry and organosilicon chemistry.

Organic reactions

Organic reactions are chemical reactions involving organic compounds. Many of these reactions are associated with functional groups. The general theory of these reactions involves careful analysis of such properties as the electron affinity of key atoms, bond strengths and steric hindrance. These factors can determine the relative stability of short-lived reactive intermediates, which usually directly determine the path of the reaction.

The basic reaction types are: addition reactions, elimination reactions, substitution reactions, pericyclic reactions, rearrangement reactions and redox reactions. An example of a common reaction is a substitution reaction written as:

Nu + C-X → C-Nu + X

where X is some functional group and Nu is a nucleophile.

The number of possible organic reactions is basically infinite. However, certain general patterns are observed that can be used to describe many common or useful reactions. Each reaction has a stepwise reaction mechanism that explains how it happens in sequence—although the detailed description of steps is not always clear from a list of reactants alone.

The stepwise course of any given reaction mechanism can be represented using arrow pushing techniques in which curved arrows are used to track the movement of electrons as starting materials transition through intermediates to final products.

Organic synthesis

A synthesis designed by E.J. Corey for oseltamivir (Tamiflu). This synthesis has 11 distinct reactions. Corey oseltamivir synthesis.png
A synthesis designed by E.J. Corey for oseltamivir (Tamiflu). This synthesis has 11 distinct reactions.

Synthetic organic chemistry is an applied science as it borders engineering, the "design, analysis, and/or construction of works for practical purposes". Organic synthesis of a novel compound is a problem solving task, where a synthesis is designed for a target molecule by selecting optimal reactions from optimal starting materials. Complex compounds can have tens of reaction steps that sequentially build the desired molecule. The synthesis proceeds by utilizing the reactivity of the functional groups in the molecule. For example, a carbonyl compound can be used as a nucleophile by converting it into an enolate, or as an electrophile; the combination of the two is called the aldol reaction. Designing practically useful syntheses always requires conducting the actual synthesis in the laboratory. The scientific practice of creating novel synthetic routes for complex molecules is called total synthesis.

Strategies to design a synthesis include retrosynthesis, popularized by E.J. Corey, which starts with the target molecule and splices it to pieces according to known reactions. The pieces, or the proposed precursors, receive the same treatment, until available and ideally inexpensive starting materials are reached. Then, the retrosynthesis is written in the opposite direction to give the synthesis. A "synthetic tree" can be constructed, because each compound and also each precursor has multiple syntheses.

See also

Related Research Articles

Allene chemical compound

An allene is a compound in which one carbon atom has double bonds with each of its two adjacent carbon centres. Allenes are classified as polyenes with cumulated dienes. The parent compound of this class is propadiene, which is itself also called allene. Compounds with an allene-type structure but with more than three carbon atoms are called cumulenes. Allenes are much more reactive than most other alkenes. For example, their reactivity with gaseous chlorine is more like the reactivity of alkynes than that of alkenes.

Diene a covalent compound that contains two double bonds

In organic chemistry a diene is a covalent compound that contains two double bonds, usually among carbon atoms. They thus contain two alkene units, with the standard prefix di of systematic nomenclature. As a subunit of more complex molecules, dienes occur in naturally occurring and synthetic chemicals and are used in organic synthesis. Conjugated dienes are widely used as monomers in the polymer industry. Polyunsaturated fats are of interest to nutrition.

Ether class of organic compounds

Ethers are a class of organic compounds that contain an ether group—an oxygen atom connected to two alkyl or aryl groups. They have the general formula R–O–R′, where R and R′ represent the alkyl or aryl groups. Ethers can again be classified into two varieties: if the alkyl groups are the same on both sides of the oxygen atom, then it is a simple or symmetrical ether, whereas if they are different, the ethers are called mixed or unsymmetrical ethers. A typical example of the first group is the solvent and anesthetic diethyl ether, commonly referred to simply as "ether" (CH3–CH2–O–CH2–CH3). Ethers are common in organic chemistry and even more prevalent in biochemistry, as they are common linkages in carbohydrates and lignin.

Ester chemical compounds consisting of a carbonyl adjacent to an ether linkage

In chemistry, an ester is a chemical compound derived from an acid in which at least one –OH (hydroxyl) group is replaced by an –O–alkyl (alkoxy) group. Usually, esters are derived from a carboxylic acid and an alcohol. Glycerides, which are fatty acid esters of glycerol, are important esters in biology, being one of the main classes of lipids, and making up the bulk of animal fats and vegetable oils. Esters with low molecular weight are commonly used as fragrances and found in essential oils and pheromones. Phosphoesters form the backbone of DNA molecules. Nitrate esters, such as nitroglycerin, are known for their explosive properties, while polyesters are important plastics, with monomers linked by ester moieties. Esters usually have a sweet smell and are considered high-quality solvents for a broad array of plastics, plasticizers, resins, and lacquers. They are also one of the largest classes of synthetic lubricants on the commercial market.

Functional group moiety that imparts a molecules characteristic chemical reactions; moiety that participates in similar chemical reactions in most molecules that contain it

In organic chemistry, functional groups are specific substituents or moieties within molecules that are responsible for the characteristic chemical reactions of those molecules. The same functional group will undergo the same or similar chemical reaction(s) regardless of the size of the molecule it is a part of. This allows for systematic prediction of chemical reactions and behavior of chemical compounds and design of chemical syntheses. Furthermore, the reactivity of a functional group can be modified by other functional groups nearby. In organic synthesis, functional group interconversion is one of the basic types of transformations.

Inorganic chemistry deals with the synthesis and behavior of inorganic and organometallic compounds. This field covers all chemical compounds except the myriad organic compounds, which are the subjects of organic chemistry. The distinction between the two disciplines is far from absolute, as there is much overlap in the subdiscipline of organometallic chemistry. It has applications in every aspect of the chemical industry, including catalysis, materials science, pigments, surfactants, coatings, medications, fuels, and agriculture.

Haloalkane group of chemical compounds derived from alkanes containing one or more halogens

The haloalkanes are a group of chemical compounds derived from alkanes containing one or more halogens. They are a subset of the general class of halocarbons, although the distinction is not often made. Haloalkanes are widely used commercially and, consequently, are known under many chemical and commercial names. They are used as flame retardants, fire extinguishants, refrigerants, propellants, solvents, and pharmaceuticals. Subsequent to the widespread use in commerce, many halocarbons have also been shown to be serious pollutants and toxins. For example, the chlorofluorocarbons have been shown to lead to ozone depletion. Methyl bromide is a controversial fumigant. Only haloalkanes which contain chlorine, bromine, and iodine are a threat to the ozone layer, but fluorinated volatile haloalkanes in theory may have activity as greenhouse gases. Methyl iodide, a naturally occurring substance, however, does not have ozone-depleting properties and the United States Environmental Protection Agency has designated the compound a non-ozone layer depleter. For more information, see Halomethane. Haloalkane or alkyl halides are the compounds which have the general formula "RX" where R is an alkyl or substituted alkyl group and X is a halogen.

Organic reaction chemical reactions involving organic compounds

Organic reactions are chemical reactions involving organic compounds. The basic organic chemistry reaction types are addition reactions, elimination reactions, substitution reactions, pericyclic reactions, rearrangement reactions, photochemical reactions and redox reactions. In organic synthesis, organic reactions are used in the construction of new organic molecules. The production of many man-made chemicals such as drugs, plastics, food additives, fabrics depend on organic reactions.

Organolithium reagent organometallic compound with a direct bond between a carbon and a lithium atom

Organolithium reagents are organometallic compounds that contain carbon – lithium bonds. They are important reagents in organic synthesis, and are frequently used to transfer the organic group or the lithium atom to the substrates in synthetic steps, through nucleophilic addition or simple deprotonation. Organolithium reagents are used in industry as an initiator for anionic polymerization, which leads to the production of various elastomers. They have also been applied in asymmetric synthesis in the pharmaceutical industry. Due to the large difference in electronegativity between the carbon atom and the lithium atom, the C-Li bond is highly ionic. Owing to the polar nature of the C-Li bond, organolithium reagents are good nucleophiles and strong bases. For laboratory organic synthesis, many organolithium reagents are commercially available in solution form. These reagents are highly reactive, and are sometimes pyrophoric.

Unsaturated hydrocarbon hydrocarbon that has double or triple covalent bonds between adjacent carbon atoms

Unsaturated hydrocarbons are hydrocarbons that have double or triple covalent bonds between adjacent carbon atoms. The term "unsaturated" means more hydrogen atoms may be added to the hydrocarbon to make it saturated. The configuration of an unsaturated carbons include straight chain, such as alkenes and alkynes, as well as branched chains and aromatic compounds.

In organic chemistry and biochemistry, a substituent is an atom or group of atoms which replaces one or more hydrogen atoms on the parent chain of a hydrocarbon, becoming a moiety of the resultant new molecule. The terms substituent and functional group, as well as other ones are used almost interchangeably to describe branches from a parent structure, though certain distinctions are made in the context of polymer chemistry. In polymers, side chains extend from a backbone structure. In proteins, side chains are attached to the alpha carbon atoms of the amino acid backbone.

In chemistry, a carbene is a molecule containing a neutral carbon atom with a valence of two and two unshared valence electrons. The general formula is R-(C:)-R' or R=C: where the R represent substituents or hydrogen atoms.

Metalation is a chemical reaction which involves the bonding of a metal atom to what is typically an organic molecule to form a new compound. This reaction usually involves the replacement of a halogen atom in an organic molecule with a metal atom to form an organometallic compound. In the laboratory, metalation is commonly used to activate organic molecules during the formation of C—X bonds, which are necessary for the synthesis of many organic molecules.

Cyclic compound Molecule with a ring of bonded atoms

A cyclic compound is a term for a compound in the field of chemistry in which one or more series of atoms in the compound is connected to form a ring. Rings may vary in size from three to many atoms, and include examples where all the atoms are carbon, none of the atoms are carbon, or where both carbon and non-carbon atoms are present. Depending on the ring size, the bond order of the individual links between ring atoms, and their arrangements within the rings, carbocyclic and heterocyclic compounds may be aromatic or non-aromatic, in the latter case, they may vary from being fully saturated to having varying numbers of multiple bonds between the ring atoms. Because of the tremendous diversity allowed, in combination, by the valences of common atoms and their ability to form rings, the number of possible cyclic structures, even of small size numbers in the many billions.

Organozinc compound

Organozinc compounds in organic chemistry contain carbon to zinc chemical bonds. Organozinc chemistry is the science of organozinc compounds describing their physical properties, synthesis and reactions.

The Willard Gibbs Award, presented by the Chicago Section of the American Chemical Society, was established in 1910 by William A. Converse (1862–1940), a former Chairman and Secretary of the Chicago Section of the society and named for Professor Josiah Willard Gibbs (1839–1903) of Yale University. Gibbs, whose formulation of the Phase Rule founded a new science, is considered by many to be the only American-born scientist whose discoveries are as fundamental in nature as those of Newton and Galileo.

Physical organic chemistry, a term coined by Louis Hammett in 1940, refers to a discipline of organic chemistry that focuses on the relationship between chemical structures and reactivity, in particular, applying experimental tools of physical chemistry to the study of organic molecules. Specific focal points of study include the rates of organic reactions, the relative chemical stabilities of the starting materials, reactive intermediates, transition states, and products of chemical reactions, and non-covalent aspects of solvation and molecular interactions that influence chemical reactivity. Such studies provide theoretical and practical frameworks to understand how changes in structure in solution or solid-state contexts impact reaction mechanism and rate for each organic reaction of interest.

A spiropyran is a type of organic chemical compound, known for photochromic properties that provide this molecule with the ability of being used in medical and technological areas. Spiropyrans were discovered in the early twentieth century. However, it was in the middle twenties when Fisher and Hirshbergin observed their photochromic characteristics and reversible reaction. In 1952, Fisher and co-workers announced for the first time photochromism in spiropyrans. Since then, there have been many studies on photochromic compounds that have continued up to the present.

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