Glossary

A reversible reaction where a carboxylic acid and alcohol react to produce an ester and water under heated conditions with an acid catalyst. The reverse reaction is known as ester hydrolysis. Le Chatelier's principle is used to drive this forward reaction by using a high concentration of alcohol and a minimal amount of water.

A small molecule (such as water) is added to a multiple bond (a double or a triple bond). This results in one π–bond and one σ–bond being broken and two new σ–bonds being formed.

A unit of length, equal to 0.1 nanometer.

A property of certain molecules that make it extremely stable due to the delocalization of the electrons located in the p orbitals, forming an aromatic π orbital system. There are three criteria for a molecule to be aromatic. It must (1) contain a ring structure, (2) be comprised of either sp2-hybrdized or sp-hybridized atoms, and (3) follow Hückel’s rule.

An experiment used to measure the activity or presence of a molecule.

The result of the overlap of individual atomic orbitals, with the pair of electrons occupying the overlapping orbital space

A scientific field between branching chemistry and biology. The discipline often involves the application of chemical techniques, analysis, and small molecule to the study and manipulation of biological systems

The process of modifying a lead compound with various functional groups at multiple sites to create a large library of compounds.

A library, or large collection, of unique compounds, all with the same core structure derived from a lead compound.

A mechanism in which bonds are broken and formed simultaneously, occurring all in one step. This is typically seen when an anionic nucleophile attacks an electrophile that is not sterically hindered (such as in SN2 reactions).

A permanent geometry of a molecule resulting from spatial arrangements of its bonds, usually seen in alkenes.

Different 3-dimensional spatial arrangements which atoms in a molecule can freely change between

Control wells performed alongside the actual experiment to ensure that the experimental design is sound and that the different components of the assay are working as intended. The controls ensure experimental reliability, and that results are not due to other interfering or unpredictable factors. Control experiments may have combinations of components used in the experiment or expected products from the assay, and contain both a positive and negative control.

A bond where the two atoms share a pair of electrons between the two nuclei.

A mechanism where bonds are broken and formed in multiple steps. This is typically seen when a neutral nucleophile attacks a sterically hindered electrophile, with the first step being the loss of a leaving group followed by a nucleophilic attack (SN1 reaction).

An atom on a lead compound which can have its functional groups modified to other functional groups of choice.

An electron-deficient species, such as an alkyl halide (C–X). It accepts electrons from nucleophiles (electron donors) in a chemical reaction. These often have a positive charge, partially positive charge, or an incomplete octet. The electrophilic center is the specific atom on the electrophile that is electron-deficient and will accept electrons.

Also known as an ELISA, it is a type of assay used to determine if a molecule of interest is present through colourimetric change. The assay works using horseradish peroxidase as a coloured indicator, which is bound to a secondary antibody. This secondary antibody will bind to a primary antibody that is specific for the molecule of interest. ELISAs are used in high throughput-screening as they can be performed in 96-well plates and give a coloured response to quickly determine the presence of a molecule

The charge assigned to atoms in molecules to keep track of electrons.

A group of atoms bonded together in a particular way that impact the molecule’s chemical behaviour. Examples include alkanes, hydroxyls, and amines.

The addition of halogens (Cl2 or Br2) across a double bond, creating two adjacent C–­X bonds, where X is a halogen (Br or Cl).

An atom other than carbon, such as oxygen, nitrogen, and sulfur.

A process used to screen many compounds of their therapeutic potential. Automated and robotic processes are utilized to run multiple assays in parallel, or all at once, to determine this. The two characteristics of this process is that it uses fast assays and that it uses massively parallel assays, where the large number of wells and automated processes enable this to occur.

A compound in an assay which has been determined, through the assay, to have a desired effect.

1 of the 3 requirements of aromaticity which represents the amount of π electrons needed to maintain aromaticity calculated by the formula 4n+2 where n represents a non-negative whole number (0, 1, 2…).

The mixing of two or more standard atomic orbitals (such as s, p, d, f orbitals) to form new hybrid orbitals (such as sp3 orbitals) suitable for bonding.

Also known as an acid-catalyzed hydration, this reaction involves the addition of water (H2O) across a double bond, producing an alcohol. This is commonly performed in a dilute aqueous solution of sulfuric acid, H2SO4.

Also known as a reduction of alkenes, this reaction adds a hydrogen molecule (H2)  to a double bond in a way that each carbon atom bonds with one hydrogen atom. This requires the presence of a metal catalyst.

The addition reaction of a hydrogen halide to an alkene. This produces an alkyl halide as a product.

A reaction which involves using water (hydro) to break a molecule apart (lysis), such as an ester. The products of ester hydrolysis are a carboxylic acid and an alcohol. This is a reversible reaction, in which the reverse reaction is known as acid-catalyzed esterification. Le Chatelier's principle is used to drive this reaction by using a larger amount of water. Heat and an acid catalyst is required for this reaction.

Experiments that are conducted in cells or microorganisms outside of their normal biological context. This includes cells grown in a well plate or flasks.

A compound that already exists and its effects are well characterized. It is used to derive novel compounds to test for a desired therapeutic effect. This is done by changing the lead compound’s functional groups.

Refers to a carbon atom that is bonded to more hydrogen atoms and less substituents. SN2 reactions favour less substituted carbons.

A compound in an assay which has been determined, through the assay, to have a non-desired effect.

Refers to a carbon atom that is bonded to less hydrogen atoms and more substituents, such as other carbon atoms. SN1 reactions favour more substituted carbons.

A control well expected to produce a negative signal. For example, in an ELISA assay, the lack of colour change is considered a negative signal for controls.

A covalent bond where the electron density resides equally between the two atoms, as the electrons aren’t largely attracted to one atom over the other.

An electron-rich species, such as hydroxide (OH-). Nucleophiles seek positively charged or electron-deficient species to form bonds with. Generally, any species, either neutral or anionic, which contains a lone pair of electrons can behave as a nucleophile in an organic reaction.

A reaction type which involves the substitution of a leaving group with a nucleophile. The reactants are a nucleophile and an electrophile bonded to a leaving group. The products are the lone leaving group and an electrophile now bonded to the nucleophile. It can be also viewed as the nucleophile “taking place” of the leaving group.

The tendency of atoms to prefer to have eight electrons in the valence shell to increase its stability. This rule generally holds true for second row elements such as C, N, and O.

In the field of organic chemistry, an oxidation reaction results in either the gain of an electronegative atom (like oxygen, nitrogen or a halide) or the loss of hydrogens atoms. Typically, oxidation of an alcohol or aldehyde increases the number of C–O bonds.

Oxidizing agents are commonly metals with a high oxidation state. Examples of oxidizing agents include potassium permanganate (KMnO4), potassium dichromate, (K2Cr2O7), and pyridinium chlorochromate (PCC).

A cation intermediate that is typically formed when water performs a nucleophilic attack on an electrophilic substrate. The oxygen atom will have a formal charge of +1.

A chemical that is secreted and released outside the body to affect individuals of the same species. These tend to trigger a specific response in the receiving individual, often causing hormonal or behavioural changes.

A covalent in which the electron density is more biased towards one atom over the other. This is because one atom is more electronegative than the other, pulling electrons towards itself.

A control well expected to produce a positive signal. For example, in the ELISA assay, the colourimetric change from blue to green is a positive signal.

In the field of organic chemistry, a reduction reaction is defined as the loss of an oxygen atom or gain of two hydrogen atoms. Reducing a carboxylic acid, an aldehyde, or ketone will decrease the number of C–O bonds

A reaction in which the concentrations of two molecules influence the rate of reaction.

An SN1 reaction is a nucleophilic substitution reaction that occurs in multiple steps. The leaving group first dissociates, breaking a bond, and the nucleophile subsequently attacks, forming a new bond.

An SN2 reaction is a nucleophilic substitution reaction that occurs in a single step with both bond breaking and bond forming happening simultaneously.

The relative spatial arrangement of groups relative to a carbon-carbon double bond.

The effect that substituents have on a reaction due to the spatial arrangement of the groups. This plays a large part in determining the rate of SN2 reaction for primary, secondary, and tertiary alkyl halides. More sterically hindered compounds, such as the tertiary alkyl halides, have a larger steric effect resulting in a very slow rate for SN2 reactions.

The highest energy structure found in a reaction, which shows the partially formed and partially broken bonds. This is found at the maximum of an energy profile diagram.

A geometry where a central carbon is bonded to five substituents. Two groups in the same plane, with two groups pointing downwards, and one pointing upwards.