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SECTION 1. Definitions: reactions, equations, transformations, substrates, reagents, products,
by-products, etc.
Some definitions are derived from IUPAC Gold Book and Wikipedia (modified in some cases)
Chemical Reactions
A process that results in the interconversion by transformation or chemical change of chemical species.
Chemical reactions may be single step reactions or stepwise reactions (It should be noted that this definition
includes experimentally observable interconversions of conformers.) Detectable chemical reactions normally
involve sets of molecular entities as indicated by this definition, but it is often conceptually convenient to use
the term also for changes involving single molecular entities (i.e. 'microscopic chemical events'). (IUPAC Gold
Book)
A chemical reaction is a process that leads to the transformation of one set of chemical substances to
another. Classically, chemical reactions encompass changes that only involve the positions of electrons in the
forming and breaking of chemical bonds between atoms, with no change to the nuclei (no change to the
elements present), and can often be described by a chemical equation.
The substances (or substance) initially involved in a chemical reaction are called reactants or reagents.
Chemical reactions are usually characterized by a transformation or chemical change, and they yield one or
more products, which usually have properties different from the reactants. Reactions often consist of a
sequence of individual sub-steps, the so-called elementary reactions, and the information on the precise
course of action is part of the reaction mechanism. Chemical reactions are described with chemical
equations, which graphically present the starting materials, end products, and sometimes intermediate
products and reaction conditions.
Chemical reactions happen at a characteristic reaction rate at a given temperature and reactant
concentration. Spontaneous reactions are those that release free energy and move to a thermodynamically
stable energy state, although they may need activation by adding energy in the form of heat or light. Nonspontaneous reactions generally do not proceed in the forward direction, but rather in the revers
Different chemical reactions are used in combinations during chemical synthesis in order to form a desired
product. In biochemistry, a similar series of chemical reactions may be described as metabolic pathways.
These reactions are often catalyzed by enzymes. Such enzymes increase the rates of biochemical reactions
by lowering activation energies, so that metabolic syntheses and decompositions impossible under ordinary
conditions may be performed at the temperatures and concentrations present within a cell.
Chemical Equations
Symbolic representation of a chemical reaction where the reactant entities are shown on the left hand side
and the product entities on the right hand side separated by a directional arrow(s) wherein all reactants,
products are fully accounted for stoichiometry. The coefficients next to the symbols and formulae of entities
are the absolute values of the stoichiometric numbers. Different symbols are used to connect the reactants
and products with the following meanings: for a stoichiometric relation; for a net forward reaction; for a
reaction in both directions; for equilibrium. (IUPAC Gold Book)
A chemical equation is the symbolic representation of a chemical reaction where the reactant entities are
given on the left hand side and the product entities on the right hand side of a directional arrow. The
coefficients next to the symbols and formulas of entities are the absolute values of the stoichiometric
numbers. The first chemical equation was diagrammed by Jean Beguin in 1615.
A chemical equation consists of the chemical (or structural) formulas of the reactants (the starting
substances) and the chemical (or structural) formula of the products (substances formed in the chemical
reaction). The two are separated by an arrow symbol (
, usually read as "yields") and each individual
substance's chemical formula (either as starting material or product) is separated from others by a plus sign.
As an example, the equation for the reaction of hydrogen chloride with sodium can be denoted:
2HCl + 2Na
2NaCl + H2
This equation would be read as "two HCl plus two Na yields two NaCl and Htwo." But for equations involving
complex chemicals, rather than reading the letter and its subscript, the chemical formulas are read using
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IUPAC nomenclature. Using IUPAC nomenclature, this equation would be read as "hydrochloric acid plus
sodium yields sodium chloride and hydrogen (gas)."
This equation indicates that sodium and hydrogen chloride react to form sodium chloride and hydrogen. It
also indicates that two sodium atoms are required for every two hydrochloric acid molecules and the
reaction will form two sodium chloride molecules and one diatomic molecule of hydrogen gas for every two
hydrochloric acid and two sodium molecules that react. The stoichiometric coefficients (the numbers in front
of the chemical formulas) result from the law of conservation of mass and the law of conservation of charge
Transformations or Chemical Changes
Chemists more commonly use chemical transformations to show the conversion of a substrate into a
particular product, irrespective of reagents or mechanisms involved rather than chemical reactions. For
example, the transformation of aniline (C 6H5NH2) into N-phenylacetamide (C6H5NHCOCH3) may be
effected by use of acetyl chloride or acetic anhydride or ketene. A transformation is distinct from a reaction,
the full description of which would state or imply all the reactants and all the products. (IUPAC Gold Book)
Chemical changes occur when one substance reacts with another to form a new substance, called synthesis
or, alternatively, decomposes into two or more different substances. These processes are called chemical
reactions and, in general, are not reversible except by other chemical reactions. Some reactions produce
heat and are called exothermic reactions and others may require heat to enable the reaction to occur and
are called endothermic reactions. Understanding chemical changes is a major part of the science of
chemistry.
When chemical reactions occur, http://en.wikipedia.org/wiki/Atom chemical bonds rearrange and the reaction is
accompanied by an energy change as products are formed. An example of a chemical change is the reaction
between sodium and water to produce sodium hydroxide and hydrogen. So much energy is released that the
hydrogen gas released spontaneously burns in the air. This is an example of a chemical change because the
end products are chemically different from the substances before the reaction.
Chemical Schemes
A chemical scheme is most commonly used to represent chemical transformations wherein the reaction
components and products are not balanced (and thus differs from a chemical equation). Use of chemical
schemes simplifies the reaction representation to focus on the transformation of interest.
A chemical scheme is the symbolic representation of a chemical transformation where the reactant entities
are given on the left hand side and the product entities on the right hand side of a directional arrow.
A chemical scheme consists of the chemical (or structural) formulas of the reactants (the starting
substances) and the chemical (or structural) formula of the products (substances formed in the chemical
reaction). The two are separated by an arrow symbol (
, usually read as "yields") and each individual
substance's chemical formula (either as starting material or product) is separated from others by a plus sign.
Reagents and Reactants
Reactant A substance that is consumed in the course of a chemical reaction. It is sometimes known,
especially in the older literature, as a reagent, but this term is better used in a more specialized sense as a
material that is added to a system in order to bring about a reaction on a reactant or to see whether a
reaction occurs (e.g. an analytical reagent). (IUPAC Gold Book)
A reagent is a "substance or compound that is added to a system in order to bring about a chemical
reaction, or added to see if a reaction occurs." Although the terms reactant and reagent are often used
interchangeably, a reactant is more specifically a "substance that is consumed in the course of a chemical
reaction" caused by a reagent. Solvents, although they are involved in the reaction, are usually not referred
to as reactants. Similarly, catalysts are not consumed by the reaction, so are not described as reactants.
In organic chemistry, reagents are compounds or mixtures, usually composed of inorganic or small organic
molecules that are used to effect a transformation on an organic substrate. Examples of organic reagents
include the Collins reagent, Fenton's reagent, Grignard reagent, etc.
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Products
Substances that are formed during a chemical reaction. (IUPAC Gold Book)
Product(s) are formed during chemical reactions as reactants and reagents are consumed. The reactions
may require energy for their promotion or emit energy. The required energy may be in the from of heat,
light, microwave or others to promote changes in chemical bonds between atoms in reactants and reagent
molecules. Energy may be given off in the form of heat or light. Products are formed as the chemical
reaction progresses and reactants and reagents are consumed.
Depending on the relative amounts of the reagents and the equilibrium of the reaction, the terms "reactant"
and "product" may overlap.
But in the end, the product is the result of a chemical reaction.
Reaction Mechanism
A reaction mechanism depicts in detail what is believed to take place at each stage of an overall chemical
reaction (transformation). It depicts reactive intermediates, activated complexes, and transition states, and
which bonds break and which bonds form. “Electron pushing” usually is used as a method to explain a
reaction mechanism. A reaction mechanism should account for the order in which molecules react. Usually,
but not always, the depicted “steps” are not proven but are predicted from known chemical reactions.
Mechanisms show presumed reaction intermediates, often unstable and short-lived, which are not reactants
or products of the overall chemical reaction, but are temporary products or reactants. Reaction
intermediates are often free radicals or ions. Transition states can be unstable intermediate molecular states
even in the elementary reactions. Transition states are commonly molecular entities involving an unstable
number of bonds and/or unstable geometry. They correspond to maxima on the reaction coordinate, and to
saddle points on the potential energy surface for the reaction.
Catalysts lower energy requirements of transition states to promote the reaction.
Side-products
A side product is the product of a side reaction resulting from alternative reaction pathways or by
subsequent degradation of the desired product. At times, side-products can be useful and marketable in
their own right.
By-products
A by-product is a secondary (usually undesired) product derived from a chemical reaction. These are
frequently not shown in a reaction scheme, but are constituted of spent reagents, catalysts, and ligands. A
by-product is usually considered waste, By-product profiles can be used as ‘fingerprints’ to determine the
synthetic route that was used to synthesize the product. By-products, if they are not removed, can also lead
to undesired properties of the product, for example toxicity in a drug formulation.
Chemical Equilibrium
In a chemical reaction, chemical equilibrium is the state in which both reactants and products are present
at concentrations that have no further tendency to change with time. Usually, this state results when the
forward reaction proceeds at the same rate as the reverse reaction. The reaction rates of the forward and
backward reactions are generally not zero, but equal. Thus, there are no net changes in the concentrations
of the reactant(s) and product(s).
Arrows used in Chemical Equations and Schemes
1. Straight Arrows denote a forward chemical reaction or transformation. (
)
CO2H
+
COCl2
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2. Open Arrows denote a retrosynthetic reaction (or analysis). (
O
O2N
catalyst
O2 N
3. Double Arrows denote equilibrium or tautomerism (
)
or
)
preferred
These arrows denote a reversible reaction where, under normal conditions, both the starting material and
product coexist and/or interconvert. The position of an equilibrium may be denoted by one of the arrows
being longer than the other, showing that the equilibrium favors either the starting material or product.
NMe
NHMe
Equilibrium Favoring Products: (
)
Equilibrium Favoring Reactants: (
)
4. Double Headed Arrows denote resonance equivalence wherein no reaction is occurring but rather there is
electronic equivalence (
)
5. Dashed Arrows represent a theoretical reactions that are proposed (
)
or
6. Broken Arrows represent reactions that have failed; no reaction (
)
7. Double Headed Curved Arrows denote:
a. electron-pair transfer to denote a mechanistic step of a chemical reaction
+
O
O
H
b. approach or elimination of reagents, fragments, etc. denoted in a mechanism of reaction
–Cl
H2O
H
Pd
Cl
H2 O
LnPd(0)
O
Cl
R
D
2 CuCl2
O
D
Cl
Pd
2 CuCl
R
O2 + 2 HCl
OH2
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c. assignment of stereogenic descriptors
Cl
Me
H
F
8. Single Headed Curved Arrows denote mechanistic single electron processes, especially useful in describing
free radical chemistry.
H
H• + H•
H
9. Arrows containing closed loops denote rearrangement reactions
+
CH2NMe3 X–
CH3
CH2NMe2
NaNH2
Placement of Reactants, Reagents, and Products in Depictions of Chemical Reactions and
Transformations
Organic Chemistry
An organic chemical reaction in which substrates are treated with reagents, catalysts, and/or additives under
defined conditions to give products is typically represented as a transformation in a chemical scheme. The
substrates are placed on the right side of the arrow, which points left to right. Multiple substrates, or
reactants, are separated by a plus sign. The products are placed at the head end of the arrow. Multiple
products are separated by a plus sign. Typically the yield is placed in parentheses near the product, or under
the arrow.
Chemical Scheme
Br
H2N
CO2H
+
H
N
CuCl (20 mol %), aq TBAH
CO2H
(41%)
MeCN, reflux, 24 h
The example shown includes a catalyst (CuCl), and an additive (TBAH). These are "reagents", and are
written over the arrow. Stoichiometric amounts of the reagents are written either before the reagent, or in
parentheses behind the reagent.
The solvent (MeCN in this example) is not typically a reagent.
The temperature and time are variables that every reaction is subject to. That is to say, there is always a
temperature and a time associated with a given reaction, even if it is instantaneous. Some adopt the
convention of putting the solvent, temperature, and time under the arrow.
Other data that may be included in a reaction are ratios of stereoisomers (geometric, optical), generally
written as er (enantiomer ratio), dr (diastereomer ratio), (R)/(S), (E)/(Z), etc. The placement of this data is
usually under the structure.
Inorganic Chemistry
The conventions for representing an inorganic reaction are similar. More often, the chemical reactions are
balanced and thus depicted as chemical equations.
Chemical Equation
Cu
+
2NO3–
+
4H+
2NO2
+
Cu2+
+
2H2O
In this example, there are no reagents shown and it appears the reaction proceeds spontaneously. Thus
there is no information either above or below the arrow.
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Solvents
A liquid or solid phase containing more than one substance, when for convenience one (or more) substance,
which is called the solvent, is treated differently from the other substances, which are called solutes. When,
as is often but not necessarily the case, the sum of the mole fractions of solutes is small compared with
unity, the solution is called a dilute solution. A superscript attached to the symbol for a property of a solution
denotes the property in the limit of infinite dilution. (IUPAC Gold Book)
A solvent (from the Latin solvō, "I loosen, untie, I solve") is a substance that dissolves a solute (a
chemically different liquid, solid or gas), resulting in a solution. A solvent is usually a liquid but can also be a
solid or a gas. The maximum quantity of solute that can dissolve in a specific volume of solvent varies with
temperature. Common uses for organic solvents are in dry cleaning (e.g., tetrachloroethylene), as paint
thinners (e.g., toluene, turpentine), as nail polish removers and glue solvents (acetone, methyl acetate, ethyl
acetate), in spot removers (e.g., hexane, petrol ether), in detergents (citrus terpenes), in perfumes
(ethanol), nail polish and in chemical synthesis. The use of inorganic solvents (other than water) is typically
limited to research chemistry and some technological processes.
Chemical synthesis
In chemistry, chemical synthesis is a purposeful execution of a chemical reaction(s) to obtain a product,
or several products, usually through several steps. This happens by physical and/or chemical manipulations
usually involving one or more reactions. In modern laboratory usage, this tends to imply that the process is
reproducible, reliable, and established to work in multiple laboratories.
A chemical synthesis begins by selection of compounds that are known as reagents or reactants. Various
reaction types can be applied to these to synthesize the product, or an intermediate product. This requires
mixing the compounds in a reaction vessel such as a chemical reactor or a simple round-bottom flask. Many
reactions require some form of work-up procedure to isolate and purify the product. The amount of product
in a chemical synthesis is the reaction yield. Typically, chemical yields are expressed as a weight in grams or
as a percentage of the total theoretical quantity of product that could be produced. A side reaction is an
unwanted chemical reaction taking place and that produces one or more by-products and diminishes the
yield of the desired product.
Retrosynthesis
Retrosynthetic analysis is a tool used to plan a (expected) multistep sequence of chemical reactions to
product a target chemical. It is a technique used for the planning of organic syntheses with the goal of
simplifying the target molecules in a backward synthetic progression. This is accomplished by breaking a
target molecule into simpler precursor structures using know chemical steps and without assumptions
regarding starting materials. Each precursor material is examined using the same method. This procedure is
repeated until simple or commercially available structures are reached.
Metabolic pathways
In biochemistry, metabolic pathways are series of chemical reactions occurring within a biological system.
In each pathway, a principal chemical is modified by a series of chemical reactions. Enzymes catalyze these
reactions, and often require dietary minerals, vitamins, and other cofactors in order to function properly.
Because of the many chemicals (a.k.a. "metabolites") that may be involved, metabolic pathways can be
quite elaborate. In addition, numerous distinct pathways co-exist. This collection of pathways is called the
metabolic network. Pathways are important to the maintenance of homeostasis within an organism.
Catabolic (break-down) and Anabolic (synthesis) pathways often work interdependently to create new
biomolecules as the final end-products.
A metabolic pathway involves the step-by-step modification of an initial molecule to form another product.
The resulting product can be used in one of three ways:
 To be used immediately,
 To initiate another metabolic pathway, called a flux generating step
 To be stored by the cell
A molecule called a substrate enters a metabolic pathway depending on the needs of the cell and the
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availability of the substrate. An increase in concentration of anabolic and catabolic intermediates and/or endproducts may influence the metabolic rate for that particular pathway.
A chemical species or reactant, the reaction of which with some other chemical reagent or enzyme is under
observation (e.g. a compound that is transformed under the influence of a catalyst). The term should be
used with care. Either the context or a specific statement should always make it clear which chemical
species in a reaction is regarded as the substrate. (IUPAC Gold Book).
In biochemistry, a substrate is a reactant molecule upon which an enzyme acts. Enzymes catalyze chemical
reactions involving the substrate(s). In the case of a single substrate, the substrate binds with the enzyme’s
active site, and an enzyme-substrate complex is formed. The substrate is transformed into one or more
products that are then released from the active site. The active site is now free to accept another substrate
molecule. In the case of more than one substrate, these may bind in a particular order to the active site,
before reacting together to produce products.
For examples, curd formation (rennet coagulation) is a reaction that occurs when the enzyme rennin is
added to milk. In this reaction, the substrate is a milk protein (e.g., casein) and the enzyme is rennin. The
products are two polypeptides that have been formed by the cleavage of the larger peptide substrate.
Another example is the chemical decomposition of hydrogen peroxide carried out by the enzyme catalase. As
enzymes are catalysts, they are not changed by the reactions they carry out. The substrate(s), however,
is/are converted to product(s). Here, hydrogen peroxide is converted to water and oxygen gas.
E+S
ES
EP
E+P
where E = enzyme, S = substrate(s), P = product(s). While the first (binding) and third (unbinding)
steps are, in general, reversible, the middle step may be irreversible (as in the rennin and catalase reactions
just mentioned) or reversible (e.g., many reactions in the glycolysis metabolic pathway).
By increasing the substrate concentration, the rate of reaction will increase due to the likelihood that the
number of enzyme-substrate complexes will increase; this occurs until the enzyme concentration becomes
the limiting factor.
Catalysis and Catalysts
A substance that increases the rate of a reaction without modifying the overall standard Gibbs energy
change in the reaction; the process is called catalysis. The catalyst is both a reactant and product of the
reaction. The words catalyst and catalysis should not be used when the added substance reduces the rate of
reaction (see inhibitor). Catalysis can be classified as homogeneous catalysis, in which only one phase is
involved, and heterogeneous catalysis, in which the reaction occurs at or near an interface between phases.
Catalysis brought about by one of the products of a reaction is called autocatalysis. Catalysis brought about
by a group on a reactant molecule itself is called intramolecular catalysis. The term catalysis is also often
used when the substance is consumed in the reaction (for example: base-catalysed hydrolysis of esters).
Strictly, such a substance should be called an activator. (IUPAC Gold Book)
Catalysis is the increase in rate of a chemical reaction due to the participation of a substance called a
catalyst. Unlike other reagents in the chemical reaction, a catalyst is not consumed. A catalyst may
participate in multiple chemical transformations. The effect of a catalyst may vary due to the presence of
other substances known as inhibitors or poisons (which reduce the catalytic activity) or promoters (which
increase the activity). An enzyme is a type of catalyst.
Catalyzed reactions have a lower activation energy (rate-limiting free energy of activation) than the
corresponding uncatalyzed reaction, resulting in a higher reaction rate at the same temperature. However,
the mechanistic explanation of catalysis is complex. Catalysts may affect the reaction environment favorably,
or bind to the reagents to polarize bonds, e.g. acid catalysts for reactions of carbonyl compounds, or form
specific intermediates that are not produced naturally, such as osmate esters in osmium tetroxide-catalyzed
dihydroxylation of alkenes, or cause dissociation of reagents to reactive forms, such as chemisorbed
hydrogen in catalytic hydrogenation.
Kinetically, catalytic reactions are typical chemical reactions; i.e. the reaction rate depends on the frequency
of contact of the reactants in the rate-determining step. Usually, the catalyst participates in this slowest
step, and rates are limited by amount of catalyst and its activity. In heterogeneous catalysis, the diffusion of
reagents to the surface and diffusion of products from the surface can be rate determining. A nanomaterialbased catalyst is an example of a heterogeneous catalyst. Analogous events associated with substrate
binding and product dissociation apply to homogeneous catalysts.
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Although catalysts are not consumed by the reaction itself, they may be inhibited, deactivated, or destroyed
by secondary processes. In heterogeneous catalysis, typical secondary processes include coking where the
catalyst becomes covered by polymeric side products. Additionally, heterogeneous catalysts can dissolve into
the solution in a solid–liquid system or evaporate in a solid–gas system.
Enzymes
Macromolecules, mostly of protein nature, that function as (bio)catalysts by increasing the reaction rates. In
general, an enzyme catalyses only one reaction type (reaction specificity) and operates on only one type of
substrate (substrate specificity). Substrate molecules are attacked at the same site (regiospecificity) and only
one or preferentially one of the enantiomers of chiral substrates or of racemic mixtures is attacked
(stereospecificity). (IUPAC Gold Book)
Enzymes are catalytic proteins and are large biological molecules responsible for the thousands of chemical
interconversions that sustain life. Each enzyme is highly selective for a specific conversion. They are highly
selective catalysts, greatly accelerating both the rate and specificity of specific metabolic reactions, from the
digestion of food to the synthesis of DNA. Most enzymes are proteins that adopt a specific three-dimensional
structure, and may employ organic (e.g. biotin) and inorganic (e.g. magnesium ion) cofactors to assist in
catalysis.
In enzymatic reactions, the molecules at the beginning of the process (substrates) are converted into
different molecules called products. Almost all chemical reactions in a biological cell need enzymes in order
to occur at rates sufficient for life. Since enzymes are selective for their substrates and speed up only a few
reactions from among many possibilities, the set of enzymes made in a cell determines which metabolic
pathways occur in that cell.
Enzyme activity can be affected by other molecules. Inhibitors are molecules that decrease enzyme activity;
activators are molecules that increase activity.
While enzymes catalyze natural processes, they have been used for a number of laboratory processes such
as kinetic resolutions to produce enantiomerically pure chemicals, among others.
Other Biological Catalysts
Besides the natural catalytic protein enzymes, there are other natural catalysts. Catalytic antibodies
(abzymes) are monoclonal antibodies that have catalytic activity. While some occur naturally, most
abzymes are artificially produced as a unique type of enzyme to effect a specific reaction by stabilizing an
unstable intermediate.
Ribozymes are RNA molecules capable of catalyzing specific biochemical reactions. Their catalytic activity
was identified in the early 1990s. Many natural ribozymes catalyze either the hydrolysis of one of their own
phosphodiester bonds, or the hydrolysis of bonds in other RNAs, as well as to catalyze the aminotransferase
activity of ribosomes. Since their discovery, modifications have been made for a variety of diagnostic and
therapeutic uses.
Deoxyribozymes are DNA molecules that have catalytic activity. In contrast to the RNA ribozymes, which
have many catalytic capabilities, in nature DNA is only associated with gene replication and nothing else. For
the most part, these molecules are limited to use for laboratory reactions.