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Pharmaceutical Sciences: Common Definitions and Terms in Organic Chemistry

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Common Definitions

Common Definitions and Terms in Organic Chemistry

© Dr Jeffrey Gosper and Prof. Peter Sammes, Brunel University, 1995. Credit

These definitions are the preferred ones to be used in Organic Chemistry. Note that some terms (such as configuration) have more than one interpretation.

acid: an agent able to produce positively charged hydrogen ions (H+). [Since the hydrogen ion is a bare proton, it usually exists in a solvated form (such as H3O+).]

achiral: not chiral. A compound (or object) that is superimposible on its mirror image. For example CH4.

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. [The activation energy (Ea) may be derived from the temperature dependence of the reaction rate using the Arrhenius equation.]

addition reactions: reactions 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: organic substances occurring naturally, which are basic, forming salts with acids. The basic group is usually an amino function.

allyl group: a group containing 3 carbon atoms and a double bond [C1=C2-C3, where C3 is called the allyliuc position or allylic carbon atom].

allylic rearrangement: the migration of a double bond in a 3-carbon system from carbon atoms one and two to carbon atoms two and three,

e.g. C1=C2-C3-X X-C1-C2=C3

anomers: the specific term used to describe carbohydrate stereoisomers differing only in configuration at the hemi-acetal carbon atom.


aromatic: an aromatic molecule or ion possesses aromaticity. Aromaticity is the special property of planar (or nearly planar) cyclic, conjugated systems having (4n+2) conjugated pi electrons. The delocalisation of the (4n+2) pi electrons gives them special stability. For benzene, the most common aromatic system (n = 1, therefore 6 pi electrons), the aromaticity confers the characteristic reactivity of electrophilic substitution.

association: a term applied to the combination of molecules of a substance with one another to form more complex systems.[ See dissociation and dissociation constant.]

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

asymmetric 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.]

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 number of particles (atoms or molecules) in one mole of any pure substance. [6.022 x 1023]

base: a base is a substance that can combine with a proton.

bimolecular reaction: a chemical reaction in which two species (e.g. molecules, ions or radicals) react together to form new chemical species. [The majority of 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: a solution of definite pH made up in such a way that the pH alters only gradually with the addition of an acid or a base.

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.

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.

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.

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 drawing.

free energy (deltaG): a thermodynamic state function; the free energy change ( G) 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.

gauche: a conformational isomer in which the groups are neither eclipsed nor trans to one another. [Often taken as the conformation where the dihedral angle between the groups is 60o.]

geometrical isomerism: a term describing isomerism owing to the presence of restricted rotation about a bond. [The major example is (Z) and (E) isomers of unsymmetrically substituted alkenes.]

ground state: the lowest energy state of an atom, molecule or ion.

half-life, t1/2: the time taken for the concentration of a substance in a reaction to reduce to half its original value.

[Used in first order reactions and as a measure of the rate of radioactive decay.]

hard and soft acids and bases: a classification of acids and bases depending on their polarizability. [Hard bases include fluoride ions; soft bases include triphenylphosphine. Hard acids include Na+, whilst an example of a soft, polarisable acid is Pt2+; hard-hard and soft-soft interactions are favoured. Hardness and softness can be described in terms of the HOMO and LUMO interactions.]

heat of reaction: the amount of heat absorbed or evolved when specified amounts of compounds react under constant pressure. [Expressed as kilojoules per mole. For exothermic reactions the convention is that the enthalpy change (heat of reaction) is negative.]

heterogeneous reaction: a reaction which occurs between substances which are mainly present in different phases. [For example, between a gas and a liquid.]

heterolytic reaction: a reaction in which a covalent bond is broken with unequal sharing of the electrons from the bond.

HOMO: the highest occupied molecular orbital of a molecule, ion or atom.

homolytic reaction: a reaction in which a covalent bond is broken with equal sharing of the electrons from the bond.

hybridization: the process whereby atomic orbitals of different type but similar energies are combined to form a set of equivalent hybid orbitals. These hybrid orbitals do not exist in the atoms but only in the formation of molecular orbitals by combining atomic orbitals from different atoms.

hydroboration: the cis-addition of B-H bonds across double (or triple) carbon-carbon bonds.

hydrogenolysis: the cleaving of a chemical bond by hydrogen. [Generally carried out in the presence of a hydrogenation catalyst.]

hydrolysis: the addition of the elements of water to a substance, often with the partition of the substance into two parts, such as in the hydrolysis of an ester to an acid and an alcohol.

inductive effect: an electronic effect transmitted through bonds in an organic compound due to the electronegativity of substituents and the permanent polarization thereof. [The substituent either induces charge towards or away from itself with the formation of a dipole.]

infrared spectroscopy: the study of the absorption of infrared light by substances. [Since this corresponds to vibrational (and some rotational) changes, infrared spectroscopy provides valuable information about the structure of a substance. Detailed correlation tables exist relating infrared bands (absorbances) to functional groups.]

inhibitor: a general term for any compound which will inhibit (slow down) a reaction. [Inhibitors vcan be used to slow down or stop free radical chain reactions.]

ion: an atom or group of atoms that has lost or gained one or more electrons to become a charged species.

isomers: compounds having the same atomic composition (constitution) but differing in their chemical structure. [They include: structural isomers (chain or positional), tautomeric isomers, and stereoisomers - including geometrical isomers, optical isomers and conformational isomers.]

kinetics: the study of the rate of reactions.

kinetically controlled product: the product formed as the result of the fastest reaction in a set of competing reaction pathways.

laevorotatory: the phenomenon that turns plane polarised light in an anticlockwise direction.

LCAO: a method for the calculation of molecular orbitals from a linear combination of atomic orbitals.

Lewis acid: an agent capable of accepoting a pair of electrons to form a coordinate bond.

Lewis base: an agent capable of donating a pair of electrons to form a coordinate bond.

lone pair: a pair of electrons in a molecule which is not shared by two of the constituent atoms.

LUMO: the lowest unoccupied molecular orbital in a molecule or ion.

Markownikow's rule: in the ionic addition of hydrogen halides to a carbon-carbon double bond the halogen attaches itself to the carbon atom bearing the least number of hydrogen atoms.

Example [The rule is useful in the prediction of the major product from such reactions. Free radical reactions proceed in the opposite sense, giving rise to anti-Markownikow addition.]

mass spectrometry: a form of spectrometry in which, generally, high energy electrons are bombarded onto a sample and this generates charged fragments of the parent substance; these ions are then focused by electrostatic and magnetic fields to give a spectrum of the charged fragments.

mesomerism: = resonance.

microwave spectroscopy: the interaction of electromagnetic waves with wavelengths in the range 10-2 to 1 metre. [This energy range corresponds to rotational frequencies and hence microwave spectroscopy is useful in studying the structure of materials (generally gases) and in their characterisation.]

molecular orbitals: the electron orbitals belonging to a group of atoms forming a molecule.

molecule: the smallest particle of matter that can exist in a free state. In the case of ionic substances, such as sodium chloride, the molecule is considered as a pair of ions, NaCl.

Newman projection: a projection obtained by viewing along a carbon-carbon single (double) bond.

nuclear magnetic resonance (nmr) spectroscopy: a form of spectroscopy which depends on the absorption and emission of energy arising from changes in the spin states of the nucleus of an atom. [For aggregates of atoms, as in molecules, minor variations in these energy changes are caused by the local chemical environment. The energy changes used are in the radiofrequency range of the electromagnetic spectrum and depend upon the magnitude of an applied magnetic field.]

nucleophile: a substance which donates a pair of electrons in the reaction considered.

nucleophilic substitution: an overall reaction in which a nucleophile reacts with a compound displacing another nucleophile. [Such reactions commonly occur in aliphatic chemistry. If the reaction is unimolecular they are known as SN1 reactions; for reactions which are bimolecular, they are known as SN2 reactions.]

optical activity: the property of certain substances to rotate plane polarized light. [It is associated with asymmetry. Compounds that possess a chiral carbon atom of all the same 'handedness' will rotate plane polarized light. Isomers that rotate light in equal but opposite directions are sometimes called 'optical isomers', although the better term to use is 'enantiomers'.]

oxidation: a chemical process in which the proportion of electronegative substituents in a compound is increased, or the charge is made more positive, or the oxidation number is increased.

photochemical reaction: a chemical reaction brought about by the action of light.

polarimeter: an instrument used to measure the amount of rotation of plane polarized light by a compound, generally prepared in a solution.

protecting group: a group that is used to protect a functional group from unwanted reactions. After application the protecting group can be removed to reveal the original functional group.

racemic mixture, racemate: an equimolar mixture of the two enantiomeric isomers of a compound. [As a consequence of the equal numbers of laevo- and dextro-rotatory molecules present in a racemate, there is no net rotation of plane polarized light.]

radical: a term applied to an atom or molecule having one or more free valencies. [See 'free radicals'.]

reduction: chemical processes in which the proportion of more electronegative substituents is decreased, or the charge is made more negative, or the oxidation number is lowered.

resolution: the separation of a racemate into its two enantiomers by means of some chiral agency.

resonance: the representation of a compound by two or more canonical structures in which the valence electrons are rearranged to give structures of similar probability. [The actual structure is considered to be a hybrid or the resonance forms.]

reversible process: a process in which the forward reaction can

reach an equilibrium with the reverse reaction.

rotamers: isomers formed by restricted rotation. [See also conformational isomers.]

R,S convention: a formal non-ambiguous, nomenclature system for the assignment of absolute configuration of structure to chiral atoms, using the Cahn, Ingold and Prelog priority rules.

saturated: the term given to organic molecules which contain no multiple bonds.

sawhorse projection: the sideways projection of a carbon-carbon single bond and the attached substituents. [It gives a clearer representation of stereochemistry than the Fischer projection. See also Newman projection.]

spectrometer: an instrument that measures the spectrum of a sample. [For example a mass spectrometer]

spectrophotometer: an instrument that measures the degree of absorption (or emission) of electromagnetic radiation by a substance. The measuring system generally includes a photomultiplier. [ U.v., i.r., visible, and microwave regions of the electromagnetic spectrum may be measured in this way.]

stability constant: when a complex is formed between a metal ion and an a ligand in solution, the equilibrium may be expressed by a constant which is related to the free energy change for the process:

For: M + A = MA : - deltaG = RTlnK

stereochemistry: the study of the spatial arrangements of atoms in molecules and complexes.

stereoisomer: another name for configurational isomer.

stereospecific reactions: reactions in which bonds are broken and made at a particular carbon atom and which lead to a single stereoisomer. If the configuration is altered in the process the reaction is said to involve inversion of configuration; if the configuration remains the same the transformation occurs with retention of configuration.

steric hindrance: the phenomenon of physical blockage of a particular site within a molecule by the presence of local atoms or groups of atoms. [As a consequence of steric hindrance, a reaction at a particular site will be impeded.]

structural isomerism: isomers which differ in the order of bonding of the constituent atoms.

substitution reactions: reactions in which one atom or group of atoms is replaced by another atom or group of atoms. [See electrophilic substitutions and nucleophilic substitutions.]

tautomerism: a form of structural isomerism where the two structures are interconvertible by means of the migration of a proton.

tosylation: a reaction which introduces the toluene-4-sulphonyl group into a molecule. [Generally by reaction of an alcohol with tosyl chloride to give the tosylate ester.]

transition state: the point of highest energy on an energy against reaction coordinate curve. [By definition the transition state is the least stable point (peak) on a reaction path; a reaction path may involve more than one transition states.

ultraviolet light: radiation of an energy range than that of visible light but lower than that of ionising radiations such as X-rays. Many substances absorb ultraviolet light, leading to electronic excitation. [This process is useful both as a means for characterising materials and for stimulating chemical reactions (photochemical reactions.)]

unsaturated: the term given to an organic compound containing multiple bonds.

valence isomerisation: the isomerisation of molecules which involve structural changes resulting only from a relocation of single and double bonds. If a dynamic equilibrium is established between the two isomers it is also referred to as valence tautomerism. An example is the valence tautomerism of cyclo-octa-1,3,5-triene.]

valence bond theory: the wave mechanical basis of resonance theory.

vinyl group: the ethenyl group, -CH=CH2.

Walden inversion: a Walden inversion occurs at a tetrahedral carbon atom during an SN2 reaction when the entry of the reagent and the departure of the leaving group are synchronous. The result is an inversion of configuration at the centre under attack.

© Dr Jeffrey Gosper and Prof. Peter Sammes, Brunel University, 1995.
URL: (link no longer active; 01 November 2005)