Concept Definitions: reactions, equations, transformations, substrates, reagents, products, by-products, etc.
Sources of definitions are IUPAC Gold Book and Wikipedia (modified in some cases) Gold book is not
necessarily a definitive source
Refer (or not) to Gold Book
Chemical reactions
A process that results or may result in the interconversion 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 chemical
concentration, and rapid reactions are often described as spontaneous, requiring no input of extra energy
other than thermal energy. Non-spontaneous reactions run so slowly that they are considered to require the
input of some type of additional energy (such as extra heat, light, ultrasound, or electricity) in order to
proceed to completion (chemical equilibrium) at human time scales.
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 protein enzymes. These enzymes increase the rates of biochemical
reactions, 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 directrional arrow(s) 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 formulae 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 hydrochloric acid 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
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 HCl react to form NaCl and H 2. It also indicates that two sodium
molecules are required for every two hydrochloric acid molecules and the reaction will form two sodium
chloride molecules and one diatomic molecule of hydrogen gas molecule 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
The conversion of a substrate into a particular product, irrespective of reagents or mechanisms involved. 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, which
are called endothermic reactions. Understanding chemical changes is a major part of the science of
chemistry.
When chemical reactions occur, the chemical bonds are rearranged and the reaction is accompanied by an
energy change as new products are generated. 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.
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.
Products
Substances that are formed during a chemical reaction. (IUPAC Gold Book)
Product(s) are formed during chemical reactions as reactants are reagents are consumed. Products have
lower energy than the reagents and are produced during the reaction according to the second law of
thermodynamics. The released energy comes from changes in chemical bonds between atoms in reactants
and reagent molecules and may be given off in the form of heat or light. Products are formed as the
chemical reaction progresses toward chemical equilibrium at a certain reaction rate, which depends on the
reagents and environmental conditions.
Depending on the relative amounts of the reagents and the equilibrium of the reaction, the terms "reagent"
and "product" may also overlap.
But in the end, the product is the result of a chemical reaction.
By-products
A by-product is a secondary (usually undesired) product derived from a manufacturing process or chemical
reaction. It is not the primary product or service being produced. A by-product frequently considered waste,
but at times can be useful and marketable in its own right.
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 reactions(s) to obtain a product,
or several products. 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 diminishes the yield of the desired product.
Metabolic pathways
In biochemistry, metabolic pathways are series of chemical reactions occurring within a cell. 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 within a cell. 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
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.
Substrates
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
active site, and an enzyme-substrate complex is formed. The substrate is transformed into one or more
products, which 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 upon adding the enzyme rennin
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.
It is important to note that the substrates that a given amino acid in vitro may not necessarily reflect the
physiological, endogenous substrates of the enzyme in vivo. That is to say that enzymes do not necessarily
perform all the reactions in the body that may be possible in the laboratory. For example, while fatty acid
amide hydrolase (FAAH) can hydrolyze the endocannabinoids 2-arachidonoylglycerol (2-AG) and anandamide
at comparable rates in vitro, genetic or pharmacological disruption of FAAH elevates anandamide but not 2AG, suggesting that 2-AG is not an endogenous, in vivo substrate for FAAH. In another example, the N-acyl
taurines (NATs) are observed to increase dramatically in FAAH-disrupted animals, but are actually poor in
vitro FAAH substrates.
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
nanomaterial-based catalyst is an example of a heterogeneous catalyst. Analogous events associated with
substrate binding and product dissociation apply to homogeneous catalysts.
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 /ˈɛnzaɪmz/ are large biological molecules responsible for the thousands of chemical
interconversions that sustain life. They are highly selective catalysts, greatly accelerating both the rate and
specificity of metabolic reactions, from the digestion of food to the synthesis of DNA. Most enzymes are
proteins, although some catalytic RNA molecules have been identified. Enzymes adopt a specific threedimensional 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, called 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.
Like all catalysts, enzymes work by lowering the activation energy (Ea‡) for a reaction, thus dramatically
increasing the rate of the reaction. As a result, products are formed faster and reactions reach their
equilibrium state more rapidly. Most enzyme reaction rates are millions of times faster than those of
comparable un-catalyzed reactions. As with all catalysts, enzymes are not consumed by the reactions they
catalyze, nor do they alter the equilibrium of these reactions. However, enzymes do differ from most other
catalysts in that they are highly specific for their substrates. Enzymes are known to catalyze about 4,000
biochemical reactions. A few RNA molecules called ribozymes also catalyze reactions, with an important
example being some parts of the ribosome. Synthetic molecules called artificial enzymes also display
enzyme-like catalysis.
Enzyme activity can be affected by other molecules. Inhibitors are molecules that decrease enzyme activity;
activators are molecules that increase activity. Many drugs and poisons are enzyme inhibitors. Activity is also
affected by temperature, pressure, chemical environment (e.g., pH), and the concentration of substrate.
Some enzymes are used commercially, for example, in the synthesis of antibiotics. In addition, some
household products use enzymes to speed up biochemical reactions (e.g., enzymes in biological washing
powders break down protein or fat stains on clothes; enzymes in meat tenderizers break down proteins into
smaller molecules, making the meat easier to chew).