Organic chemistry

Organic Chemistry is a discipline within chemistry that involves the scientific study of the structure, properties, composition, reactions, and preparation (by synthesis or by other means) of hydrocarbons and their derivatives. These compounds may contain any number of other elements, including hydrogen, nitrogen, oxygen, the halogens as well as phosphorus, silicon and sulfur.^[1][2][3].

Organic compounds are structurally diverse, and the range of application of organic compounds is enormous. They form the basis of, or are important constituents of many products (paints, plastics, food, explosives, drugs, petrochemicals, to name but a few) and, with very few exceptions. they form the basis of all earthly life processes.

Organic chemistry, like all areas of science, evolves with particular waves of innovation. These innovations are motivated by practical considerations as well as theoretical innovations. The area is, however, underpinned financially by the very large applications in polymer science, pharmaceutical chemistry, and agrichemicals.

Structure of the methane molecule: the simplest hydrocarbon compound‎

History

Friedrich Wöhler

At the beginning of the nineteenth century, chemists generally thought that compounds obtained from living organisms were too complex to be obtained synthetically. According to the concept of vitalism, organic matter was endowed with a 'vital force'. They named these compounds 'organic' and directed their investigations toward inorganic materials that seemed more easily studied.^{[citation needed]}

Over the course of the first half of the nineteenth century, it was realized that organic compounds could in fact be synthesized in the laboratory. Around 1816 Michel Chevreul started a study of soaps made from various fats and alkali. He separated the different 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 the inorganic ammonium cyanate NH₄OCN, in what is now called the Wöhler synthesis. Although Wöhler was, at this time as well as afterwards, cautious about claiming that he had thereby destroyed the theory of vital force, historians have looked to this event as the turning point.

A great next step was when in 1856 William Henry Perkin, while trying to manufacture quinine, again accidentally came to manufacture the organic dye now called Perkin's mauve, which by generating a huge amount of money greatly increased interest in organic chemistry.

The crucial breakthrough for the organic chemistry was the concept of chemical structure, developed independently and simultaneously by Friedrich August Kekule and Archibald Scott Couper in 1858. Both men 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.

The history of organic chemistry continued with the discovery of petroleum and its separation into fractions according to boiling ranges. The conversion of different compound types or individual compounds by various chemical processes created the petroleum chemistry leading to the birth of the petrochemical industry, which successfully manufactured artificial rubbers, the various organic adhesives, the property-modifying petroleum additives, and plastics.

The pharmaceutical industry began in the last decade of the 19th century when acetylsalicylic acid (more commonly referred to as aspirin) manufacture was started in Germany by Bayer. The first time a drug was systematically improved was with arsphenamine (Salvarsan). Numerous derivatives of the dangerously toxic atoxyl were examined by Paul Ehrlich and his group, and the compound with best effectiveness and toxicity characteristics was selected for production.

Although early examples of organic reactions and applications were often serendipitous, the latter half of the 19th century witnessed highly systematic studies of organic compounds. Beginning in the 20th century, progress of organic chemistry allowed the synthesis of highly complex molecules via multistep procedures. Concurrently, polymers and enzymes were understood to be large organic molecules, and petroleum was shown to be of biological origin. The process of finding new synthesis routes for a given compound is called total synthesis. Total synthesis of complex natural compounds started with urea, increased in complexity to glucose and terpineol, and in 1907, total synthesis was commercialized the first time by Gustaf Komppa with camphor. Pharmaceutical benefits have been substantial, for example cholesterol-related compounds have opened ways to synthesis of complex human hormones and their modified derivatives. Since the start of the 20th century, complexity of total syntheses has been increasing, with examples such as lysergic acid and vitamin B12. Today's targets feature tens of stereogenic centers that must be synthesized correctly with asymmetric synthesis.

Biochemistry, the chemistry of living organisms, their structure and interactions in vitro and inside living systems, has only started in the 20th century, opening up a new chapter of organic chemistry with enormous scope. Biochemistry, like organic chemistry, primarily focuses on compounds containing carbon as well.

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.^[4] Listed in approximate order of utility, the chief analytical methods are:

• Nuclear magnetic resonance (NMR) spectroscopy is the most commonly used technique, often permitting complete assignment of atom connectivity and even stereochemistry using correlation spectroscopy. The principle constituent atoms of organic chemistry - hydrogen and carbon - exist naturally with NMR-responsive isotopes, respectively ¹H and ¹³C.
• Elemental analysis: A destructive method used to determine the elemental composition of a molecule. See also mass spectrometry, below.
• Mass spectrometry indicates the molecular weight of a compound and, from the fragmentation patterns, its structure. High resolution mass spectrometry can usually identify the exact formula of a compound and is used in lieu of elemental analysis. In former times, mass spectrometry was restricted to neutral molecules exhibiting some volatility, but advanced ionization techniques allows one to obtain the "mass spec" of virtually any organic compound.
• Crystallography is an unambiguous method for determining molecular geometry, the proviso being that single crystals of the material must be available and the crystal must be representative of the sample. Highly automated software allowing a structure to be determined within hours of obtaining a suitable crystal.

Traditional spectroscopic methods such as infrared spectroscopy, optical rotation, UV/VIS spectroscopy provide relatively nonspecific structural information but remain in use for specific classes of compounds.

Additional methods are described in the article on analytical chemistry.

Properties

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

Melting and boiling properties

In contrast to many inorganic materials, organic compounds typically melt and many boil. 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 mothballs. Organic compounds are usually not very stable at temperatures above 300 °C, although some exceptions exist.

Color

Organic compounds are typically colorless or white. The situation is quite different for organic compounds that contain several adjacent multiple bonds. These compounds, where the double bonds are "conjugated" can be deeply colored. The biological pigments carotene and heme illustrate the relationship between "conjugation" and color. Impure organic compounds, as well as many biological materials, often are yellow or brownish owing to the presence of trace amounts of intensely colored impurities.

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 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.

Solid state properties

Various specialized properties are of interest depending on applications, e.g. thermo-mechanical and electro-mechanical such as piezoelectricity, electrical conductivity (see organic metals), 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.‎

The names of organic compounds is either systematic, following logically from a set of rules, or nonsystematic, following various traditions. Systematic nomenclature is stipulated by recommendations 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. Nonsystematic names 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. The depiction of organic compounds with drawings is greatly simplified by the fact that carbon in almost all organic compounds has four bonds, oxygen two, hydrogen one, and nitrogen three.

Classification of organic compounds

Functional groups

Main article: Functional group

The family of carboxylic acids contains a carboxyl (-COOH) functional group. Acetic acid 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 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.

Aliphatic compounds

Main article: Aliphatic compound

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

• paraffins, which are alkanes without any double or triple bonds,
• olefins or alkenes which contain one or more single double bonds, i.e di-olefins (dienes) or poly-olefins.
• alkynes, which have one or more triple bonds.

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 aromatics.

Aromatic hydrocarbons contain conjugated double bonds. 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

Main article: Heterocyclic compound

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.

Examples of groups among the heterocyclics are the aniline dyes, the great majority of the compounds discussed in biochemistry such as alkaloids, many compounds related to vitamins, steroids, nucleic acids (e.g. DNA, RNA) and also numerous medicines. Heterocyclics with relatively simple strucures are pyrrole (5-membered) and indole (6-membered carbon ring).

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

Main article: Polymer

This swimming board is made of polystyrene, an example of a polymer

One important property of carbon is that it readily forms chain or even networks linked by carbon-carbon bonds. The linking process is called polymerization, and the chains or networks polymers, while the source compound is a monomer. Two main groups of polymers exist: those artificially manufactured are referred to as industrial polymers ^[5] or synthetic polymers and those naturally occurring as biopolymers.

Since the invention of the first artificial polymer, bakelite, the family has quickly grown with the invention of others. Common synthetic organic polymers are polyethylene (polythene), polypropylene, nylon,teflon (PTFE), polystyrene, polyesters, polymethylmethacrylate (called perspex and plexiglas), and polyvinylchloride (PVC). Both synthetic and natural rubber are polymers.

The examples are generic terms, and many varieties of each of these may exist, with their physical characteristics fine tuned for a specific use. Changing the conditions of polymerisation changes the chemical composition of the product by altering chain length, or branching, or the tacticity. With a single monomer as a start the product is a homopolymer. Further, 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. Physical characteristics, such as hardness, density, mechanical or tensile strength, abrasion resistance, heat resistance, transparency, colour, etc. will depend on the final composition.

Biomolecules

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 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 unique set of hydrocarbons called biopolymer polyisoprenoids present in latex sap, which is the basis for making rubber.

Peptide Syntheis

See also peptide synthesis

Oligonucleotide Synthesis

See also Oligonucleotide synthesis

Carbohydrate Synthesis

See also Carbohydrate synthesis

Small molecules

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.

Molecular models of caffeine

Fullerenes

Fullerenes and carbon nanotubes, carbon compounds with spheroidal and tubual structures, have stimulated much research into the related field of materials science.

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 synthesis

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.

There are several strategies to design a synthesis. The modern method of retrosynthesis, developed by E.J. Corey, 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.

Organic reactions

Organic reactions are chemical reactions involving organic compounds. While pure hydrocarbons undergo certain limited classes of reactions, many more reactions which organic compounds undergo are largely determined by 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 issues 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.