Organic Chemistry Online

A

Acid:   any species capable of producing a positively charged hydrogen ion (H+). In an aqueous medium the H+ usually exists in a solvated form (H3O+) called the hydronium or hydroxonium ion.

Achiral:   not chiral. A compound (or object) that is superimposible on its mirror image. Example:

Activation energy:   the miminmum energy which reacting species must possess in order to be able to form an 'activated complex', or 'transition state', before proceeding to the products. Activation energy is influenced by reaction conditions such as temperature, pressure, catalysts etc.

Addition reaction:   a reaction in which an unsaturated system is saturated or part saturated by the addition of a molecule across the multiple bond.[E.g. the addition of bromine to ethene to form 1,2-dibromoethane]

Alkaloid:   One of a varied family of alkaline, nitrogen-containing substances, usually plant-derived, reacting with acids to form salts. Normally intensely bitter, alkaloids form a body of substances widely used in drug and herbal therapy. Examples include caffeine, morphine, codein etc. .

Allyl group:   a group containing 3 carbon atoms and a double bond.



Allylic rearrangement: the migration of a double bond in a 3-carbon system from carbon atoms 1 and 2 to carbon atoms 2 and 3.

Anomers:   the specific term used to describe carbohydrate stereoisomers differing only in configuration at the hemi-acetal carbon atom. Example is the anomeric forms of D-glucose.

Aromaticity:   the special property of planar (or nearly planar) cyclic, conjugated systems having (4n+2) conjugated pi electrons. For benzene, the most common aromatic system (n = 1, therefore 6 pi electrons. The delocalised pi electrons gives aromatic compounds a special stability, hence they tend to undergo substitution rather than addition reactions.

Association:   a term applied to the combination of molecules of a substance with one another to form more complex systems.

Asymmetric: a term applied an object or molecule that does not possess symmetry.

A symmetric induction:   a term applied to the selective synthesis of one diastereomeric form of a compound resulting from the influence of an existing chiral centre adjacent to the developing asymmetric carbon atom. This usually arises because, for steric reasons, the incoming atom or group does not have equal access to both sides of the molecule. See nucleophilic substitution reactions.

Atomic orbital:   the energy levels of electrons in an atom which may be described in terms of the four quantum numbers.

Avogadro's constant:   the total number of particles (atoms or molecules) in one mole of any pure substance i.e.

B

Base:   an organic base is a species that can produce a hydroxide ion (OH-) or combine with a proton to from a salt.

Benzene: a colourless, rather pleasant-smelling, volatile and flammable liquid. It has the chemical formula C6H6 and is used primarily in the production of plastics and other chemical products. Benzene is also a known human carcinogen, causing various types of leukemia, lymphoma, and blood diseases.

Bimolecular reaction:   a chemical reaction in which two species (e.g. molecules, ions or radicals) react to form new species. Most reactions are bimolecular or proceed through a series of bimolecular steps.

Bond energy:   the energy required to break a particular bond by a homolytic process.

Buffer solution:   an equilibrium solution made of a weak acid or base and its conjugate salt, and its pH only alters slightly when small quantities of acids or bases are added.

C

Canonical structures:   any of two or more hypothetical structures of resonance theory which can be written for a molecule simply by rearranging the valence electrons of the molecule. [E.g. the two Kekule structures of benzene. They are sometimes called 'valence bond isomers']

Catalyst:   a substance that, when added to a reaction mixture, changes (speeds up) the rate of attainment of equilibrum in the system without itself undergoing a permanent chemical change.

Catalytic cracking:   the method for producing gasoline from heavy petroleum distillates. [Generally the catalysts are mixtures of silica and alumina or synthetic conjugates such as the zeolites.]

Catalytic reforming:   the process of improving the octane number of straight-run gasoline by increasing the proportion of aromatic and branched chain alkanes. [Catalysts employed are either molybdenum-aluminium oxides or platinum based.]

Chain reaction:   reactions which proceed by means of a set of repeating cyclical steps, e.g. the free radical addition of hydrogen bromide to an alkene.

Chirality:   a term which may be applied to any asymmetric object or molecule. The property of non-identity of an object with its mirror image.

Chromatography:   a series of related techniques for the separation of a mixture of compounds by their distribution between two phases. In gas-liquid chromatography the distribution is between a gaseous and a liquid phase. In column chromatography the distribution is between a liquid and a solid phase.

Compound:   a term used generally to indicate a definite combination of elements into a more complex structure (a molecule) but it is also applied to systems with non-stoichiometric proportions of elements.

Configuration:   the order and relative spatial arrangement of the atoms in a molecule. Absolute configuration is when the relative 3 dimensional arrangement in space of atoms in a chiral molecule have been correlated with an absolute standard.

Configurational isomers:   a series of compounds which have the same constitution and bonding of atoms but which differ in their atomic spatial arrangement. [E.g. glucose and mannose are configurational isomers. Also called stereoisomers. See also positional or structural isomers.]

Conformation:   the spatial arrangement of a molecule in space at any particular moment in time. [Most molecules can adopt an infinite number of conformations because of the possible rotation about single covalent bonds. Of these possibilities most compounds tend to spend most time in only one or a few conformational states, called the preferred conformations.]

Conformer:   a conformation of a molecule; generally these will be at energy minima.

Conjugation:   a sequence of alternating double (or triple) and single bonds. (E.g. C=C-C=C and C=C-C=O). Conjugation can also be relayed by the participation of lone pairs of electrons or vacant orbitals.

Co-ordinate bond:   the linkage of two atoms by a pair of electrons both electrons being provided by one of the atoms (the donor). [Coordinate bonds are covalent bonds.]

Constitution:   the number and type of atoms in a molecule.

Covalent bond:   the linkage of two atoms by the sharing of two electrons.

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D

Delocalization:   electron systems in which bonding electrons are not localised between two atoms as for a single bond but are spread (delocalized) over the whole group. [E.g pi-bond electrons, in particular the delocalised pi-electrons associated with aromatic molecules.]

Dextrorotatory:   the phenomenon in which plane polarised light is turned in a clockwise direction.
diastereomers (or diastereoisomers): stereoisomeric structures which are not enantiomers (mirror images) of one another. [Often applied to systems which differ only in the configuration at one carbon atom, e.g. meso- and d- or l-tartaric acids are diastereoisomeric.]

Dihedral angle:   the angle between groups attached on adjacent carbon atoms when viewed in a Newman projection.

Disproportionation:   a process in which a compound of one oxidation state changes to compounds two or more oxidation states [E.g. 2Cu+ --> Cu + Cu2+]

Dissociation:   the process whereby a molecule is split into simpler fragments which may be smaller molecules, atoms, free radicals or ions.

Dissociation constant:   the measure of the extent of dissociation, measured by the dissociation constant K. For the process:
AB = A + B.     K = ([A][B])/[AB]

Dissymmetric:   chiral

Double bond:   some atoms can share two pairs of electrons to form a double bond (two covalent bonds). Formally the second (double) bond arises from the overlap of p orbitals from two atoms, already united by a sigma bond, to form a pi bond.

Dyestuffs:   intensely coloured compounds applied to a substrate. Colours are due to the absorption of light to give electronic transitions.

E

Eclipsed: a conformation in which substituents on two attached saturated carbon atoms overlap when viewed as a Newman projection.

Electronegativity: the tendency for atoms in a molecule to attract electrons. [Measured in terms of the HOMO and LUMO energy levels.]

Electronic configuration: the particular order in which electrons are arranged in an atom or molecule. [Used in a distinct and different sense from stereochemical configuration.]

Electronic transition: in an atom or molecule the electrons have certain allowed energies only (orbitals). If an electron passes from one orbital to another an electronic transition occurs and there is the emission or absorption of energy corresponding to the difference in energy of the two orbitals.

Electrophile: an atom, molecule or ion able to accept an electron pair.

Electrophilic substitution: an overall reaction in which an electrophile binds to a substrate with the expulsion of another electrophile. [The most common example is the electrophilic substitution of a proton by another electrophile, such as a nitronium ion, on an aromatic substrate such as benzene.

Electrovalent (ionic) bond: bonding by electrostatic attraction.

Element: a substance which cannot be further subdivided by chemical methods.

Enantiomers: a pair of isomers which are related as mirror images of one another. [E.g. isomers differing only in the configuration about the chiral atoms.]

Endothermic: a reaction in which heat is absorbed.

Energy diagram (or reaction energy diagram): a graph of the energy of a reaction against the progress of the reaction.

Enthalpy: a thermodynamic state function, generally measured in kilojoules per mole. In chemical reactions the enthalpy change (deltaH) is related to changes in the free energy (deltaG) and entropy (deltaS) by the equation:
deltaG = deltaH - T.deltaS

Entropy: a thermodynamic quantity which is a measure of the degree of disorder within any system. [The greater the degree of order the higher the entropy; for an increase in entropy S is positive. Entropy has the units of joules per degree K per mole.]

Enzyme: a naturally occurring substance able to catalyse a chemical reaction.

Epimerization: a process in which the configuration about one chiral centre of a compound, containing more than one chiral atom, is inverted to give the opposite configuration. [The term epimers is often used to describe two related compounds which differ only in the configuration about one chiral atom.]

Epoxidation: the addition of an oxygen bridge across a double bond to give an oxirane. [Achieved by use of a peracid or, in a few cases, by use of a catalyst and oxygen.]

Equilibrium constant: according to the law of mass action, for any reversible chemical reaction:
aA + bB = cC + dD, the equilibrium constant (K)is defined as:
K = ([C]c[D]d)/([A]a[B]b)

Excited state: the state of an atom, molecule or group when it has absorbed energy and become excited to a higher energy state as compared to the normal ground state. The excited state may be electronic, vibrational, rotational, etc.

F

Fischer projection: a convention for drawing carbon chains so that the relative 3-dimensional stereochemistry of the carbon atoms is relatively easy portrayed on a 2-dimensional draw

Free energy (deltaG): a thermodynamic state function; the free energy change (deltaG) in any reaction is related to the enthalpy and entropy:
deltaG = deltaH - T.deltaS

Free radicals: molecules or ions with unpaired electrons and hence generally extremely reactive. ['Stable' free radicals include molecular oxygen, NO, and NO2. Organic free radicals range from those of transient existence only to very long-lived species. Alkyl free radicals tend to be very reactive and short lived.]

Frontier orbital symmetry: the theory that the site and rates of reaction depend on the geometries, sign of the wave function and relative energies of the highest occupied molecular orbital (HOMO) of one molecule and the lowest unoccupied molecular orbital (LUMO) of the other.


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G