Organic chemistry

Historical highlights

 

See also: History of chemistry

At the beginning of the nineteenth century chemists generally thought that compounds from living organisms were too complicated in structure to be capable of artificial vitalism conferred the characteristics of living beings on this form of matter. They named these compounds 'organic', and preferred to direct their investigations toward inorganic materials that seemed more promising.

Organic chemistry received a boost when it was realized that these compounds could be treated in ways similar to 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, most have looked to this event as the turning point.

A great next step was when in 1856 DDT by Othmer Zeidler in 1874, but the insecticide properties of this compound were not discovered until much later.

The crucial breakthrough for the theory of organic chemistry was the concept of chemical structure, developed independently and simultaneously by 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 continues 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 plastics.

The atoxyl were systematically synthesized and tested by Paul Ehrlich and his group, and the compound with best effectiveness and toxicity characteristics was selected for production.

Early examples of organic reactions and applications were serendipitous, such as Perkin's accidental discovery of Perkin's mauve. However, from the 20th century, the progress of organic chemistry allowed for synthesis of specifically selected compounds or even molecules designed with specific properties, as in 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 brand new chapter of organic chemistry with enormous scope.

Classification of organic substances

Description and nomenclature

Classification is not possible without having a full description of the individual compounds. In contrast with 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 must be added for a full description.

One way of describing the molecule is by drawing its organic nomenclature .

Because of the difficulties arising from the very large number and variety of organic compounds, chemists realized early on that the establishment of an internationally accepted system of naming organic compounds was of paramount importance. The Geneva Nomenclature was born in 1892 as a result of a number of international meetings on the subject.

It was also realized that as the family of organic compounds grew, the system would have to be expanded and modified. This task was ultimately taken on by the International Union on Pure and Applied Chemistry (IUPAC). Recognizing the fact that in the branch of biochemistry the complexity of organic structures increases, the IUPAC organization joined forces with the International Union of Biochemistry and Molecular Biology, IUBMB, to produce a list of joint recommendations on nomenclature.

Later, as the numbers and complexities of organic molecules 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, including heterocyclics, and named such structures phanes.

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 versus 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 along with the chief (carbon) constituent in their makeup, whilst in a structural formula, hydrogen is implicitly assumed to occupy all free valences of an appropriate carbon atom which remain after accounting for branching, other element(s) and/or multiple bonding.

Hydrocarbons and functional groups

  Classification normally starts with the hydrocarbons: compounds which contain only carbon and hydrogen. For sub-classes see below. Other elements present themselves in atomic configurations called polar atomic configurations which pass during chemical reactions from one chemical compound into another without change.

Some of the elements of the functional groups (O, S, N, halogens) may stand alone and the group name is not strictly appropriate, but because of their decisive effect on the way they modify the characteristics of the hydrocarbons in which they are present they are classed with the functional groups, and their specific effect on the properties lends excellent means for characterisation and classification.

Referring to the hydrocarbon types below, many, if not all of the aromatic and alicyclic group of compounds, unless they are dehydrated, which would lead to non-reacting co-optional groups.

Reference is made here again to the trivial names. Putting compounds in sub-classes becomes more difficult when more than one functional group is present.

Two overarching chain type 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.

Aliphatic compounds

The aliphatic hydrocarbons are subdivided into three groups, alkynes. The rest of the group is classed according to the functional groups present.

From another aspect aliphatics can be straight chain or branched chain compounds, and the degree of branching also affects characteristics, like octane number or cetane number in petroleum chemistry.

Aromatic and alicyclic compounds

  Cyclic compounds can, again, be saturated or unsaturated. Because of the bonding angle of carbon, the most stable configurations contain six carbon atoms, but while rings with five carbon atoms are also frequent, others are rarer. The cyclic hydrocarbons divide into alicyclics and arenes).

Of the alicyclic compounds the cyclopropane.

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.

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 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.

Rings can fuse with other rings on an edge to give natural products.

Polymers

  One important property of carbon in organic chemistry is that it can form certain compounds, the individual molecules of which are capable of attaching themselves to one another, thereby forming a chain or a network. The process is called industrial polymers ^[4] 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 butadiene, a rubber component.

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 tensile strength, abrasion resistance, heat resistance, transparency, colour, etc. will depend on the final composition.

Biomolecules

  rubber.

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 organosilicon chemistry.

Characteristics of organic substances

  Organic compounds are generally hydrogen bonding occurs.

Organic compounds tend to dissolve in organic aromatic structure is a special case in which the conjugated chain is a closed ring.

Molecular structure elucidation

  isomers can exist. Organic compounds often exist as chromatography techniques. There exist several methods for deducing the structure an organic compound. In general usage are (in alphabetical order):

• molecular geometry; 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. Crystallography has seen especially extensive use in biochemistry (for protein structure determination) and in the characterization of organometallic catalysts, which often possess significant symmetry.
• Elemental analysis: A destructive method used to determine the elemental composition of a molecule. See also mass spectrometry, below.
• functional groups.
• molecular weight of a compound and from the fragmentation pattern its structure. High resolution mass spectrometry can often identify the precise formula of a compound through knowledge of isotopic masses and abundances; it is thus sometimes used in lieu of elemental analysis.
• correlation spectroscopy).
• HPLC with a chiral column also can supply this information.
• UV/VIS spectroscopy: Used to determine degree of conjugation in the system. While still sometimes used to characterize molecules, UV/VIS is more commonly used to quantitate how much of a known compound is present in a (typically liquid) sample.

Additional methods are provided by analytical chemistry.

Organic reactions

substitution reaction written as:

Nu⁻ + C-X → C-Nu + X⁻

where X is some nucleophile.

There are many important aspects of a specific reaction. Whether it will occur spontaneously or not is determined by the 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.

See also

• Important publications in organic chemistry
• List of organic reactions

References

• MIT OpenCourseWare: Organic Chemistry I
• Organic Chemistry Lectures, Videos and Text
• Journal of Organic Chemistry (Table of Contents)
• Organic Letters (Table of Contents)
• Synlett
• Synthesis
• Organic Chemistry Portal - Recent Abstracts and (Name)Reactions
• Home of a full, online, peer-reviewed organic chemistry text.
• Virtual Textbook of Organic Chemistry
• Organic Chemistry Teaching kit
• Organic World Wide - A collection of Links
• Organic Families and Their Functional Groups
• Roger Frost's Chemistry Teaching Tools - Organic Chemistry
• Organic chemistry help
• Chemical Freeware on http://www.acdlabs.com
• Organic Chemistry - Learning Resources