Organic chemistry

From The Book of THoTH (Leaves of Wisdom)

Organic chemistry is a specific discipline within the subject of chemistry. It is the scientific study of the structure, properties, composition, reactions, and preparation (by synthesis or by other means) of chemical compounds of carbon and hydrogen, which may contain any number of other elements, such as nitrogen, oxygen, halogens, and more rarely phosphorus or sulphur (Robert T. Morrison, Robert N. Boyd, and Robert K. Boyd, Organic Chemistry, 6th edition Benjamin Cummings 1992 ISBN 0136436692 - this is "Morrison and Boyd", a classic textbook). [1]

Contents

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Definition and main concepts

The original definition, (see Historic highlights) which came from the perception that these compounds were always related to life processes is no longer valid as over the years a very large number of chemical compounds have been artificially produced which, do not necessarily relate to life processes, but due to their similarity in characteristics to the previously known organic compounds are classed as organic compounds. Those compounds that are related to life processes are dealt with in the branch of organic chemistry which is called Biochemistry.

However: organic compounds are all compounds containing carbon. Inorganic chemistry deals, apart from elemental carbon, only with simple carbon compounds, with molecular structures which do not contain carbon to carbon connections (its oxides, acids, salts, carbides, and minerals) This does not mean that single-carbon organic compunds do not exist (viz. methane and its simple derivatives)

The nexus is thus carbon, which is almost unique among the elements of the periodic table in that its atoms combining directly with one another can form long molecular chains and rings which may also include nitrogen, oxygen, halogens, phosphorus, sulfur, and a variety of other atomic species. The straight chains and rings can again combine with one another to make their structure very complex.

Because of their unique properties, multi-carbon compounds exhibit extremely large variety and the range of application of organic compounds is enormous. They form the basis or are important constituents of many industries (paints, plastics, food, explosives, drugs, petrochemicals, and many others) and of course (apart from a small exception) they form the basis of all life processes.

The different shapes and chemical reactivities of the substituents provide an astonishing variety of functions, like those of enzyme catalysts in biochemical reactions of live systems. The autopropagating nature of these is what life is all about.

Because of the special properties of carbon, it is likely that life on other star systems will be found to be carbon-based, in spite of speculations about the possibility of substituting silicon, which lies just below carbon in the periodic table.

Trends in organic chemistry include chiral synthesis, green chemistry, microwave chemistry and microwave spectroscopy which has identified dozens of organic molecules in interstellar space

Another subject area is the group of substances called fullerenes but one could argue that these should be included with inorganic chemistry, because they are allotrope modifications of pure carbon such as graphite or diamond, though their structures are complex.

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Historic highlights

Towards the beginning of the nineteenth century when modern chemistry really begun the chemists generally thought that the compounds that came from living organisms were too complicated in structure, and could only be made by life itself through a 'vital force' or vitalism. They named these compounds 'organic' and in general ignored them.

Organic chemistry has really started when someone demonstrated that these compounds could be treated in similar ways to inorganic compounds and finally to manufacture them by other means than by a 'life process'. Around 1816 Michel Chevreuil 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, and recognized that these were all individual compounds, thereby demonstrating that it was possible to make a chemical change, producing new compounds without life processes in fats which came from an organic source.

The real event that has completely destroyed the myth of 'vitalism' occurred, however, when in 1828 Friedrich Woehler first manufactured urea (carbamide), a constituent of the liquid waste matter urine and in his report stated that he made it entirely without the assistance of a kidney. He obtained it after trying unsuccessfully to make ammonium cyanate by reacting cyanides with ammonium hydroxide. When he used cyanogen instead of the salts he produced something else, which he analysed and recognized to be urea. Making urea by evaporating an aqueous solution of ammonium cyanate NH4OCN, is now called the Wöhler synthesis.

Progress was slow at the beginning. A great step was when in 1856 William Henry Perkin, whilst trying to manufacture quinine, again accidentally came to manufacture the organic dye now called Perkin's mauve. Another step was the laboratory preparation of DDT by Othmer Zeidler in 1874, but the insecticide properties of this compound were not discovered till much later.

The history of organic chemistry continues with the discovery of petroleum and its separation into fractions according to boiling ranges and dissecting these further by fine fractionation, and by type separation using, for instance, solvent extraction or refrigeration. 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 linked to the manufacture of 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 acetyl-salicilic acid (aspirin) manufacture started in Germany by Bayer.

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 brand new chapter of organic chemistry with enormous scope, which deserves a completely independent treatment.

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Classification of organic substances

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Description and nomenclature

Classification is not possible without having a full description of the individual compounds. In contrast with inorganic chemistry, in which describing a chemical compound could be achieved by simply enumerating the chemical symbols of the elements present in the compound together with the number of these elements in the molecule, in organic chemistry the relative arrangement of the atoms within a molecule has to be added for a full description.

Structural formula: One way of describing the molecule is by drawing its structural formula. Because of the complexity this method has changed, simplified over the years. The latest version is the line formula, which achieves simplicity without introducing ambiguity, whilst representing carbon and hydrogen by implication. The disadvantage which arises from the fact that structural formulae cannot be described by words, and that they are not easily printable does not arise when the structure is described by the organic nomenclature .

Organic nomenclature: Because of the difficulty due to the very large number and variety of organic compounds it was realised early on in its history that the establishment of an internationally accepted sytem of naming organic compounds is of paramount importance. The Geneva Nomenclature was born in 1892 as a result of a number of international meetings raising this subject.

It was also realised that as the family of organic compounds grew the system would have to be expanded and modified to take account of this. Ultimately this task was taken on by the International Union on Pure and Applied Chemistry, IUPAC

Recognising the fact that in the branch of Biochemistry the complexity of organic structures becomes even greater the IUPAC organisation joined forces with IUBMB the International Union of Biochemistry and Molecular Biology to produce a list of joint recommendations on nomenclature.

Phanes: Further on, as number and complexity grew new recommendations were made within IUPAC for simplification. The first such recommendation was presented in 1951 when a cyclic benzene structure was named a cyclophane. Later recommendations extended the method to the simplification of other complex cyclic structures and named such structures Phanes. Thus Phane Nomenclature was born. Because the classical, and Wikipedia meaning of a phane is a mythical creature disambiguation is necessary and it is recommended that for the first instance we call phanes used for naming organic structures organic-phanes. [2] [3]

To be noted: For ordinary communication, to spare a tedious description, the official IUPAC naming recommendations are not always followed in practice except when it is necessary to give a concise definition to a compound, or when the IUPAC name is simpler (viz. ethanol against ethyl alcohol). Otherwise the common or trivial name may be used, often derived from the source of the compound.

In summary: organic substances are classified by their molecular structural arrangement, and by what other atoms are present with the chief (carbon) constituent in their makeup, whilst in their structural formula hydrogen is implicitly assumed to occupy all free valencies of an appropriate carbon atom, unless a double or triple bond is indicated. The ways that O, N, or Cl bond within the organic molecules presenting themselves in functional groups is quite characteristic to the individual element concerned. In chemistry, structure is quite synonymous with function, and so the structural categories double as categories of property or activity.

By chain type broadly two main categories exist: Open Chain aliphatic compounds and Closed Chain cyclic compounds. Those in which both open chain and cyclic parts are present are normally classed with the latter. Those compounds that only contain carbon and hydrogen are called hydrocarbons.

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Aliphatic compounds

The aliphatic hydrocarbons are subdivided into three groups (called homologues) according to their state of saturation: paraffins alkanes without any double or triple bonds, olefins alkenes with double bonds, which can be mono-olefins with a single double bond, di-olefins, or di-enes with two, or poly-olefins with more. The third group with a triple bond is named after the name of the shortest member of the homologue series as the acetylenes alkynes.

Another classification specifies the difference in complexity. According to this the compound can be straight chain or branched chain compound.

Important functional group based categories are listed below

Family name Functional group Example Note No
Alcohol -OH Methanol CH3OH
Aldehyde -(H)O Formaldehyde HCH(O) 1.
Ketone =O Acetone CH3-C(O)-CH3
Ether -O- Dimethylether CH3-O-CH3
Amines =N-,or =NH,or –NH2 Dimethylamine CH3-NH-CH3
Carboxylic acid -C(O)OH Formic acid H-C(O)OH 2.
Amide -C(O)NH2 Acet(ic)amide CH3-C(O)NH2 2.
Ester -C(O)O- Methyl form(i)ate H-C(O)O-CH3

See Notes

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Notes

(1) This sort of representation in a formula means that the oxygen is bonded directly to the C atom with both its valencies (2) In this representation the =O, -OH and NH2 radicals respectively are bonded directly to the C

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Aromatic and alicyclic compounds

Cyclic compounds can, again, be saturated or unsaturated. Because of the bonding angle of carbon, the most stable configuration of the cyclic compounds contain six carbon atoms, but rings with five carbon atoms are also frequent, others are rarer. The cyclic compounds may be homocyclic, containing only carbon in the closed chain itself, or heterocyclic, with atoms of other elements in the chain of the molecule.

Of the alicyclic compounds the cycloalkanes (cycloparaffins) do not contain double bonds, whilst cycloalkenes (cyclo-olefins) do. The simplest member of the cycloalkane family is cyclopropane. Terpenes represent one notable group amongst the alicyclics.

What is different in aromatic hydrocarbons is that they contain conjugated or alternating double bonds. The simplest example of this is benzene. The structure of this was formulated by Kekulé who first proposed the delocalization or resonance principle for explaining its structure.

The heteroatom of the heterocyclic molecules is generally O, S, N, but most often nitrogen. The basic constituents of live systems are compounds with such heterocyclics. Examples of major heterocyclic groups are the aniline dyes, the great majority of the compounds discussed in biochemistry such as alkaloids, many compounds related to vitamins, steroids, nucleic acids and also numerous medicines. Constructionally simple representatives of the group are pyrrole (5-membered) and indole (6-membered).

Many, if not all of the functional groups mentioned with the aliphatics are also represented within the aromatics and hydroaromatics. Unless they are dehydrated, which would lead to nonreacting cooptional groups.

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Polymers

One important property of carbon in organic chemistry is that it can form certain groups, radicals, called monomers which are capable of attaching themselves to one another thereby forming a chain or a network. Such long chains or networks are the polymers. When only two units are combined we talk about dimers, with three of trimers. When the segments are all the same the macromolecule is called a homopolymer. When it was found that physical characteristics such as hardness, density, mechanical strength, abrasion resistance etc could be changed to advantage by the addition of a secondary monomer to the polymerising mixture a new type of polymer was born called a heteropolymer. The secondary, (property-modifying) monomer added in smaller proportions to the first to make the polymer is sometimes called a co-polymer.

Since the discovery of the first such compound, bakelite, the family has quickly grown with the discovery of others. Common synthetic organic polymers are polyethylene or polythene, polypropylene, nylon, teflon or PTFE, polystyrene, polyesters, polymethylmethacrylate (commonly known as perspex or plexiglas) polyvinylchloride or PVC, and polyisobutylene important artificial or synthetic rubber also the polymerised butadiene, a rubber component.

The only other element that can produce polymers is silicon. These are the silicones.

Polymers are grouped roughly into two groups: thermosetting polymers , which harden and stay hard, (like bakelite) and thermoplastic polymers which soften on heating. These form the basis of the plastics industry and the rubber industry.

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Biomolecules

Biomolecular chemistry is a major category within organic chemistry. Many complex multi-functional group molecules are important in living organisms. Some are long-chain biopolymers. The main classes are carbohydrates, amino acids and proteins, polysaccharides, lipids, and nucleic acids.

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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.


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Characteristics of organic substances

Organic compounds are generally covalently bonded. This allows for unique structures such as long carbon chains and rings. The reason carbon is excellent at forming unique structures and that there are so many carbon compounds is that carbon atoms form very stable covalent bonds with one another (catenation). In contrast to inorganic materials, organic compounds typically melt, boil, sublimate, or decompose below 300°C. Neutral organic compounds tend to be less soluble in water compared to many inorganic salts, with the exception of certain compounds such as ionic organic compounds and low molecular weight alcohols and carboxylic acids where hydrogen bonding occurs.

Organic compounds tend rather to dissolve in organic solvents which are either pure substances like ether or ethyl alcohol, or mixtures, such as the parffinic 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. Solutions are studied by the science of Physical Chemistry. Like inorganic salts, organic compounds may also form crystals. Unique property of carbon in organic compounds is that its valency does not always have to be taken up by atoms of other elements, and when it is not a condition termed unsaturation results. In such cases we talk about carbon carbon double bonds or triple bonds. Double bonds alternating with single in a chain are called conjugated double bonds. An aromatic structure is a special case in which the conjugated chain is a closed ring (see Molecular Structure).

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Molecular structure of an organic compound

Organic compounds are generally made from carbon atoms, hydrogen atoms, and functional groups. The valence of carbon is 4, and hydrogen is 1, functional groups are generally 1. Many, but not all structures can be envisioned by the simple valence rule that there will be one bond for each valence number. The knowledge of the chemical formula for an organic compound is not sufficient information because many isomers can exist. Organic compounds often exist as mixtures. Because many organic compound have relatively low boiling points and/or dissolve easily in organic solvents there exist many methods for separating mixtures into pure constituents that are specific to organic chemistry such as distillation, crystallization and chromatography techniques. Currently, there exist several methods for deducing the structure an organic compound. In general usage are (in alphabetical order):

  • Crystallography: This is the most precise method; however, it is very difficult to grow crystals of sufficient size and high quality to get a clear picture, so it remains a secondary form of analysis.
  • Degree of unsaturation: An elementary formula to determine without instrumentation how many rings and double bonds a molecule contains.
  • Elemental Analysis: A destructive method used to determine the elemental composition of a molecule.
  • Infrared spectroscopy: Chiefly used to determine the presence (or absence) of certain functional groups.
  • Mass spectrometry: Used to determine the molecular weight of a compound and the fragmentation pattern.
  • Nuclear magnetic resonance (NMR) spectrometry
  • UV/VIS spectroscopy: Used to determine degree of conjugation in the system

Additional methods are provided by analytical chemistry.

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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, and bond strengths. These issues can determine the relative stability of short-lived reactive intermediates, which usually directly determine the path of the reaction. A common reaction is generically written here as an example:

R-F + X-Y → R-Y + X-F

where F is some functional group such as the hydroxyl or -OH group . It is presumed that functional group F is bonded to one of the carbon atoms in R. R is often one of the hydrocarbon categories mentioned previously. The example above is a substitution reaction, since Y is substituted for F.

There are many important aspects of a specific reaction. Whether it will occur spontaneously or not is determined by the Gibbs free energy change of the reaction. The heat that is either produced or needed by the reaction is found from the total Enthalpy change. Other concerns include whether side reactions occur from the same reaction conditions. Any side reactions which occur typically produce undesired compounds which may be anywhere from very easy or very difficult to separate from the desired compound.

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See also

  • Important publications in organic chemistry


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External links


--Angel 16:11, 4 June 2006 (CDT)

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