Unit 1: Fundamental Chemistry of Drugs and Molecules of Life Flashcards
Heteroatom
Any atom that is not hydrogen or carbon
How to identify an alcohol (-OH)
Polar
Hydrogen bonding
Electronegative
Two lone pairs
How to differentiate between carbonyls (aldehydes and ketones C=O)
Aldehyde – if one of the atoms is carbon and the other one hydrogen
Ketone – if both of the atoms are carbons
Where would you find a thiol (-SH)
Found in α-amino acid cysteine
Linking peptides through a disulphide (-S-S-) bridge
Lower electronegativity than O Cannot undergo hydrogen bonding to the same extent
Feature of a carboxylic acid (-COOH)
Show acidic behaviour – can dissociate to lose a hydrogen ion from the hydroxyl group
How to identify esters (-COO-R’)
Formed from carboxylic acids and alcohols by esterification
Note the difference to carboxylic acid group (R’ = alkyl group instead of H)
How to identify amides (–CONR2)
Consists of a carbonyl group directly attached to a nitrogen atom
Highly polar
Form strong intermolecular interactions
α-lactam
3 atom amide ring
β-lactam
4 atom amide ring
γ-lactam
5 atom amide ring
δ-lactam
6 atom amide ring
ε-lactam
7 atom amide ring
Features of an Amines (N’H’3)
Derived from ammonia NH3
Can undergo hydrogen bonding
Solutions of amines in water are basic
Soluble in water
What determines the order of priority of functional groups in the suffix of the name
The most oxidised functional group in the structure takes precedence when we decide on the suffix.
Order of priority of functional groups
Carboxylic acid, ester, acid halide, amide, nitrile, aldehyde, ketone, alcohol, thiol, amine, alkene, alkyne, alkane
amphoteric compound
a compound able to react as both an acid and base
pKa
the pH at which ionisation of an acid or base is at exactly 50%.
measures how weak or strong an acid is
https://www.youtube.com/watch?v=IQ6gHQAg_Nk
what do pKa values mean in terms of acidity
lower pKa value= stronger acid
greater its ability to donate its protons
what do pKa values mean in terms of basicity
higher pKa value= stronger base
greater ability to accept protons
orbital hybridisation
the concept of mixing these atomic orbitals to form new hybrid orbitals suitable for the pairing of electrons to form covalent bonds in molecules.
Acid
H+ donor
Base
H+ acceptor
pH
pH = -log10[H+]
represent the acidity of a solution – it measures hydrogen ion concentration
An unionised compound is…
less soluble in water than in non-polar solvents
more likely to pass through cell membrane than ionized
An ionised compound is…
more soluble in water than in non-polar solvents
What does an effective drug need to be in terms of solubility
Be sufficiently soluble in water to dissolve in blood plasma and be carried around the body (to reach area where needed) while also being sufficiently soluble in non-polar lipids to pass through cell membranes into cells (and carry out function)
Will an acid be ionised at a pH value higher or lower than its pKa value?
pH > pKa
higher pH is more basic, so acid is in its conjugate base form
Will a base be ionised at a pH value higher or lower than its pKa value?
pH < pKa
lower pH is more acidic, so base is in its conjugate acid form
conjugate acid
species that forms when a base gains a proton
conjugate base
species that forms when an acid donates a proton
sigma bond
sharing electrons by overlap of an sp2 orbital from each atom forming a strong single bond
electron density concentrated between nuclei
pi bond
Overlap of the parallel p-orbitals forms an orbital that places a cloud of electrons above and below the sigma (single) bond
What hybridisation and shape is shown with 4 sigma bonds
Hybridisation- sp3
Shape- Tetrahedral
What hybridisation and shape is shown with 3 sigma bonds
Hybridisation- sp2
Shape- Trigonal
What hybridisation and shape is shown with 2 sigma bonds
Hybridisation- sp
Shape- Linear
Why is a detailed understanding of stereochemistry vital in pharmaceutical science?
- The clinical efficacy of a drug is critically dependent on its three-dimensional structure
- The stereochemistry of a drug can impact upon its toxicity and side effects
enantiomer
structures that are nonsuperposable mirror images of one another
analgesic
painkiller
What is the only detectable physical difference between a pair of enantiomeric molecules?
their ability to rotate the plane of polarised light,
they are often referred to as optical isomers
What happens if a drug is chiral?
Usually only one enantiomer will interact fully with the receptor
Drugs should optimally be administered as single enantiomers
If a drug is chiral, and therefore only one enantiomer is active, what effects can its mirror image isomer have?
Inactive
Producing side effects
Countering the effect of the drug
Being metabolised to a toxic product
What do companies do because chiral synthesis or separation can be expensive?
Companies market racemic mixtures of synthetic drugs if they can. This can be risky
R enantiomer
clockwise
S enantiomer
anticlockwise
how to determine whether it is R or S enantiomer
Step 1. Assign “priority” to each atom attached to the chiral centre (according to atomic number).
Step 2. View the molecule with the lowest priority (4th) group (often H) directed away from the observer.
Step 3. Observe the order of priority: join the 1, 2, 3 groups together, if the direction is clockwise, the isomer is rectus (R), if anticlockwise sinister (S) (Figure 15).
Step 4. If two or more atoms attached to a chiral centre are the same, look to second and third atoms until it is possible to distinguish between groups. The highest priority different atom takes precedence; you do not add the atomic numbers together.
Step 5. For multiple bonds, treat as single bonds to duplicate or triplicate atoms of the same type.
diastereoisomers
are stereoisomers of each other but they are not specifically mirror images of each other
Cis-trans diastereoisomers
found in molecules with double bonds and saturated rings
Chiral Diasteroisomers
Chiral isomers which are not enantiomers, i.e. not mirror images of each other.
Racemic mixture
an equal mixture of both enantiomers of a compound, has no measurable optical rotation
Two types of intermolecular interactions
Electrostatic
Hydrophobic
Hydrogen bonding
Forms when electronegative N, O, F approach a hydrogen atom covalently attached to another electronegative atom, e.g. between carbonyl and amino group.
Charge-charge interactions/PDD
Electrostatic like H bonds but distance between interacting groups isn’t fixed and alignment isn’t as important.
Any group/atom in a molecule which carries a charge (electronegativity difference between atoms the presence of an acidic or basic group, or an atom with a lone pair of electrons)
Can be attractive or repulsive.
What is interactions between charged groups likely to be dependent on?
pH-dependent
e.g. with proteins- the carboxyl group loses the proton and the amino group gains the proton
Hydrophobic interactions
Hydrophobic groups are insoluble, do not contain any particularly electronegative atoms, e.g. CH3.
– Neutral groups- which have no way of interacting with water.
– Apolar groups do not interact or repel each other, but rather come together through the action of the water solvent
What does an amino acid contain?
Contains an acidic group (carboxylic group), basic group (amine), R group, H atom
Why are all standard amino acid classed as “α-amino acids” and what is the exception?
They all have an amino group on the first (α) carbon atom adjacent to the carboxylic acid group
They are primary amino acids since they have a primary amine group
Exception is proline- it has a secondary amine group.
Which α-amino acid is not chiral?
Glycine
5 groups that amino acids can be split into
Non polar (straight or branched chains that may or may not be cyclical)
Aromatic
Uncharged polar
Charged (negative/acidic or positive/basic side chains)
Sulphur containing
How is an amino acid ionised in acidic medium?
The carboxylic group is unionised while the amino group is in its ammonium ionised state
Protonated form
<pKa1
How is an amino acid ionised in a basic medium?
The carboxylic acid group in its ionised carboxylate form while the amino group is in its non-ionised state
Deprotonated form
>pKa2