Organic chemistry

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Methane, CH4, in line-angle representation, showing four carbon-hydrogen single () bonds in black, and
the 3Dshape of suchtetrahedral molecules, with ~109 interior bond angles, in green. Methane is the simplestorganic
chemical and simplest hydrocarbon, and molecules can be built up conceptually from it by exchanging up to all 4
hydrogens with carbon or other atoms.
Organic chemistry is a chemistry subdiscipline involving the scientific study of the structure,
properties, and reactions of organic compounds and organic materials, i.e., matter in its various
forms that contain carbon atoms.
[1]
Study of structure includes using spectroscopy (e.g., NMR), mass
spectrometry, and other physical and chemical methods to determine the chemical
composition and constitution of organic compounds and materials. Study of properties includes
both physical properties and chemical properties, and uses similar methods as well as methods to
evaluate chemical reactivity, with the aim to understand the behavior of the organic matter in its pure
form (when possible), but also in solutions, mixtures, and fabricated forms. The study of organic
reactions includes probing their scope through use in preparation of target compounds (e.g., natural
products, drugs, polymers, etc.) by chemical synthesis, as well as the focused study of
the reactivities of individual organic molecules, both in the laboratory and via theoretical (in silico)
study.
The range of chemicals studied in organic chemistry include hydrocarbons (compounds containing
only carbon and hydrogen), as well as myriad compositions based always on carbon, but also
containing other elements,
[1][2][3]
especially:
oxygen, nitrogen, sulfur, phosphorus (these, included in many organic chemicals in biology) and
the radiostable of the halogens.
In the modern era, the range extends further into the periodic table, with main group elements,
including:
Group 1 and 2 organometallic compounds, i.e., involving alkali (e.g., lithium, sodium, and
potassium) or alkaline earth metals (e.g., magnesium), or
metalloids (e.g., boron and silicon) or other metals (e.g., aluminum and tin).
In addition, much modern research focuses on organic chemistry involving further organometallics,
including the lanthanides, but especially the:
transition metals (e.g., zinc, copper, palladium, nickel, cobalt, titanium, chromium, etc.).

Line-angle representation

Ball-and-stick representation

Space-filling representation
Three representations of an organic compound, 5-Dihydroprogesterone (5-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).
Finally, organic compounds form the basis of all earthly life and constitute a significant part of human
endeavors in chemistry. The bonding patterns open to carbon, with its valence of fourformal
single, double, and triple bonds, as well as various structures with delocalized electronsmake the
array of organic compounds structurally diverse, and their range of applications enormous. They
either form the basis of, or are important constituents of, many commercial products
including pharmaceuticals; petrochemicals and products made from them
(including lubricants, solvents, etc.); plastics; fuels and explosives; etc. As indicated, the study of
organic chemistry overlaps with organometallic chemistry andbiochemistry, but also with medicinal
chemistry, polymer chemistry, as well as many aspects of materials science.
[1]


Periodic table of elements of interest in organic chemistry. The table illustrates allelements of current interest in
modern organic and organometallic chemistry, indicatingmain group elements in orange, and transition
metals and lanthanides (Lan) in grey.
Contents
[hide]
1 History
2 Characterization
3 Properties
o 3.1 Melting and boiling properties
o 3.2 Solubility
o 3.3 Solid state properties
4 Nomenclature
o 4.1 Structural drawings
5 Classification of organic compounds
o 5.1 Functional groups
o 5.2 Aliphatic compounds
o 5.3 Aromatic compounds
5.3.1 Heterocyclic compounds
o 5.4 Polymers
o 5.5 Biomolecules
o 5.6 Small molecules
o 5.7 Fullerenes
o 5.8 Others
6 Organic synthesis
7 Organic reactions
8 See also
9 References
10 External links
History[edit]
Main article: History of chemistry

Friedrich Whler
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 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 Whler produced the organic
chemical urea (carbamide), a constituent of urine, from the inorganic ammonium cyanate NH4CNO,
in what is now called the Whler synthesis. Although Whler was always cautious about claiming
that he had disproved the theory of vital force, this event has often been thought of as a turning
point.
[4]

In 1856 William Henry Perkin, while trying to manufacture quinine, accidentally manufactured the
organic dye now known as Perkin's mauve. Through its great financial success, this discovery
greatly increased interest in organic chemistry.
[5]

The crucial breakthrough for organic chemistry was the concept of chemical structure, developed
independently and simultaneously by Friedrich August Kekul and Archibald Scott Couper in
1858.
[6]
Both men suggested thattetravalent 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 pharmaceutical industry began in the last decade of the 19th century when the manufacturing of
acetylsalicylic acid (more commonly referred to as aspirin) in Germany was started by Bayer.
[7]
The
first time a drug was systematically improved was with arsphenamine (Salvarsan). Though
numerous derivatives of the dangerous toxic atoxyl were examined by Paul Ehrlich and his group,
the compound with best effectiveness and toxicity characteristics was selected for production.
[citation
needed]


An example of an organometallic molecule, a catalyst called Grubbs' catalyst, as a ball-and-stick model based on
an X-ray crystal structure.
[8]
The formula of the catalyst is often given as RuCl2(PCy3)2(=CHPh), where the ruthenium
metal atom, Ru, is at very center in turquoise, carbons are in black, hydrogens in gray-white, chlorine in green, and
phosphorus in orange. The metal ligand at the bottom is a tricyclohexyl phosphine, abbreviated PCy, and another of
these appears at the top of the image (where its rings are obscuring one another). The group projecting out to the
right has a metal-carbon double bond, as is known as an alkylidene. Robert Grubbs shared the 2005 Nobel prize in
chemistry with Richard R. Schrock and Yves Chauvin for their work on the reactions such catalysts mediate,
called olefin metathesis.
Early examples of organic reactions and applications were often serendipitous. The latter half of the
19th century however witnessed systematic studies of organic compounds, Illustrative is the
development of synthetic indigo. 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.
[9]

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 multistep 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 aslysergic
acid and vitamin B12.
[10]


The total synthesis of vitamin B12 marked a major achievement in organic chemistry.
The development of organic chemistry benefited from the discovery of petroleum and the
development of the petrochemical industry. The conversion of individual compounds obtained from
petroleum into different compound types by various chemical processes led to the birth of
the petrochemical industry, which successfully manufactured artificial rubbers, various
organic adhesives, property-modifying petroleum additives, and plastics.
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.
[11]

Characterization[edit]
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 HPLCand 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.
[12]
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 usingcorrelation
spectroscopy. The principal constituent atoms of organic chemistry - hydrogen and carbon -
exist naturally with NMR-responsive isotopes, respectively
1
H and
13
C.
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
allow 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 allows 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.
Properties[edit]
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[edit]
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[edit]
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 wherehydrogen 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[edit]
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 polymersand 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[edit]
Main article: IUPAC nomenclature of organic chemistry

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 aparent 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[edit]
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, nitrogen three, oxygen two, and hydrogen one.
Classification of organic compounds[edit]
Functional groups[edit]
Main article: Functional group

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.
Aliphatic compounds[edit]
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 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 orcetane 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[edit]

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 Kekul 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[edit]
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 structures 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[edit]
Main article: Polymer

This swimming board is made ofpolystyrene, 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 calledpolymers. 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.
[13]
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, polymeth
ylmethacrylate (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 thechain 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[edit]

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[edit]
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[edit]
Fullerenes and carbon nanotubes, carbon compounds with spheroidal and tubular
structures, have stimulated much research into the related field of materials science.
Others[edit]
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[edit]

A synthesis designed by E.J. Corey foroseltamivir (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, 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[edit]
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 sequencealthough 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.
See also[edit]

Organic chemistry portal
Main article: Outline of organic chemistry
Important publications in organic chemistry
List of organic reactions
Molecular modelling
References[edit]
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a

b

c
J. Clayden, N. Greeves & S. Warren "Organic Chemistry"
(Oxford University Press, 2012), pp. 1-15.
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3. Jump up^ Robert T. Morrison, Robert N. Boyd, and Robert K. Boyd, Organic
Chemistry, 6th edition, Benjamin Cummings, 1992.
4. ^ Jump up to:
a

b
Greenwood, Norman N.; Earnshaw, Alan (1997). Chemistry of
the Elements (2nd ed.). Butterworth-Heinemann. ISBN 0080379419.
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Couper Retrieved 1 december 2012
from http://www.chemheritage.org/discover/online-resources/chemistry-in-
history/themes/molecular-synthesis-structure-and-bonding/kekule-and-
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aspirin.html
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24 June 2014.
9. Jump up^ Elmar Steingruber "Indigo and Indigo Colorants" Ullmann's
Encyclopedia of Industrial Chemistry 2004, Wiley-VCH,
Weinheim. doi: 10.1002/14356007.a14_149.pub2
10. Jump up^ Nicolaou, K. C.; Sorensen, E. J. (1996). Classics in Total Synthesis:
Targets, Strategies, Methods. Wiley. ISBN 978-3-527-29231-8.
11. Jump up^ Allan, Barbara. Livesey, Brian. How to Use Biological Abstracts,
Chemical Abstracts and Index Chemicus. Pub: Gower 1994. ISBN 978-
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C.K.F. Hermann, T.C. Morrill, D.Y. Curtin, and R.C. Fuson John Wiley & Sons,
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