OrgChem-MedChem

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. [Glucose and mannose]. Also called stereoisomers.

Conformation

the spatial arrangement of a molecule in space at any moment in time.

Co-ordinate bond

The linkage of two atoms by a pair of electrons, both electrons being provided by one of the atoms (the donor).

Acid

an agent able to produce positively charged hydrogen ions (H+).

Bronsted acid

Proton donor

Covalency number

refers to the number of unpaired electrons in the orbital of an atom; determines the number of covalent bonds

Covalent bond

the linkage of two atoms by the sharing of two electrons

Dextrorotatory

the phenomenon in which plane polarized light is turned in a clockwise direction.

Optical Activity

capability of organic compounds to rotate polarized light to the left or right

Polarimeter

Instrument used to measure optical activity

Diastereomers

stereoisomeric structures which are not enantiomers (mirror images) of one another.

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]

Electronegativity

the tendency for atoms in a molecule to attract electrons.

Electronic configuration

the order in which electrons are arranged in an atom or molecule

Electrophile

an atom, molecule, or ion able to accept an electron pair. Electron poor specie/s?) [E.g. H3O+, BF3, AlCl3, Br2, Cl2, I2]

EWG

Electron withdrawing Group

Electrophilic substitution

an overall reaction in which an electrophile binds to a substrate with the expulsion of another electrophile

Electrovalent (ionic) bond

bonding by electrostatic attraction. Formed by transfer of electron/s from one atom to another

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.

Endothermic

a reaction in which heat is absorbed.

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 _____; for an increase in ______ S is positive.

Epimerization

a process in which the configuration of one chiral center of a compound, containing more than one chiral atom, is inverted to give the opposite configuration.

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 becomes 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

Functional group

the atom or group of atoms that defines the structure and at the same time determines the properties of a class or family of organic compounds.

Gauche

a conformational isomer in which the groups are neither eclipsed nor trans to one another.

Ground state

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

Heat of reaction

the amount of heat absorbed or evolved when specified amounts of compounds react under constant pressure.

Hybridization

the process whereby atomic orbitals of different types but similar energies are combined to form a set of equivalent hybid orbitals which are more stable in directional manner.

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.

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

Mechanism of reaction

refers to the detailed course of an overall reaction, its sequence of steps and the details of electron movement, bond breaking, bond making and timing

bond cleavage

Homolytic cleavage and Heterolytic cleavage

Homolytic cleavage

characterized by homolytic fission of bonds and the formation of free radicals. creates reactive oxygen species /ROS.

Heterolytic cleavage

characterized by heterolytic fission and the formation of charged species.

Fundamental Classification of Organic Reactions

Substitution reactions, Additional reactions, Elimination reactions, Rearrangement reactions, Oxidation, Reduction

Rearrangement reactions

one or more atoms in a molecule move to other positions within that molecule

Elimination reactions

a molecule or stable ion is lost from a structure leaving behind a double

Additional reactions

a reagent reacts with a double or triple bond in a substrate to form a single product.

Substitution reactions

an atom or group is replaced by a different atom or group

ISOMERS

compounds having the same molecular formula but different structural formulas

CONSTITUTIONAL or STRUCTURAL ISOMERS

isomers with different atom to atom bonding sequence. Chain or skeletal

STEREOISOMERS

isomers with the same atom-to-atom bonding sequence but with the atoms arranged differently in space

CONSTITUTIONAL ISOMERS

Chain or Skeletal Isomers, Positional Isomers, Functional Isomers

Chain or Skeletal Isomers

compounds that differ in the arrangement of carbons Example: CH3CH2CH2CH2CH3

Positional Isomers

differ in the position of a non carbon group Example: CH3CH2CH2CH2Br

Functional Isomers

differ in the functional group

Example: CH3CH2CH2CHO

Entropy

has the units of joules per degree K per mole.]

Conjugation

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