Drug discovery 6a Flashcards
what is the atomic mass?
number of protons + number of neutrons
what is the atomic number ?
number of protons in the nucleus
what are the number of protons equal to in an atom?
number of electrons
what do the atomic number and molecular mass enable ?
enable a schematic drawing of an atom to be produced
what are radioactive isotopes used for ?
to label ligands for binding assays
how are electrons organised in an atom ?
they are organised into electron shells
- each level down an additional shell is added
- first shell only contains 2 electrons while 2nd and 3rd can contain 8
- electrons only occupy the next shell once the previous one has become full
atoms prefer to have a full electron shell so what does this mean ?
it means if they dont have a full electron shell they will either donate or share electrons
atoms are more stable when they have a full outer shell of electrons - therefore group 8 elements are notoriously stable, unreactive
when is formed when atoms donate or accept electrons ?
ionic bonding
what is covalent bonding ?
it is the sharing of electrons to form full outer electron shells
what are lone pairs?
electron pairs that remain unshared in a molecules
what do lone pairs cause?
they are important for defining the shape of the molecule and also forming electrostatic interactions
what is the bond angle between the hydrogen atoms in methane and what shape is this molecule?
109.5 degrees
produces a tetrahedral shape around the central atom - this is an ideal shape but it can vary in non-symmetrical molecules like water
what is the bond angle between the hydrogen atoms in water ?
104.5 degrees
what do lone pairs that are next to each other do ?
they repel each other
how many outer electrons does a nitrogen atom have and what does this mean ?
it have 5 outer shell electrons
shares 3 of them to produce 1 lone pair
what shape is a benzene molecule ?
planar
what property does a cyclohexane ring have ?
it is puckered
- forms a chair or boat conformation
what happens in covalent double bonding ?
atoms share 2 electrons
what shape is ethene and what is the bond angle?
flat/planar shape- trigonal planar
120 degree bond angle
what is the difference between a single covalent bond and a double covalent bond ?
double covalent bonds do not spin they are fixed
what is characteristic of the benzene ring ?
there are 3 double covalent bonds in the ring
the electrons in the 3 double bonds are shared across all 6 bonds in the ring = delocalisation
what structures are common in drug structure ?
aromatic rings
what is electronegativity ?
it is the attraction of an atom for electrons
- some atoms have a very high attraction for electrons e.g. F, O, N = high electronegativity
if there is a large difference in electronegativity between 2 atoms what forms ?
ionic bond
if there is a small difference in electronegativity between 2 atoms what is formed ?
a covalent bond
what is formed if there is an intermediate difference in electronegativity ?
polar covalent bond formed
- the electronegative atom pulls the shared electrons closer to itself giving itself a partial negative charge
what is a polar molecule ?
a molecule that has one end more polar than the other
why is carbon dioxide non-polar ?
even though it has 2 polar bonds it doesnt have a dipole because their polarities cancel each other out
what do polar molecules prefer to interact with and what does this cause ?
prefer to interact with polar molecules
- therefore tend to separate leaving the non-polar molecules to interact with each other by weak van der waals interactions
what is a hydrogen bond ?
it is the interaction of the hydrogen on one molecule to O or N or F that is attracted to an O or N or F of a different molecule
what are the different types of isomers ?
structural isomers geometric isomers stereo isomers (enantiomers)
what are isomers ?
different molecules that contain the same atoms but in a different arrangment
what are structural isomers ?
same atoms but different arrangement in space
what are geometric isomers ?
same molecular formula but different arrangement due to a double bond
- cis and trans isomers
- cis= atoms on same side
- trans= atoms on opposite side
what are stereo isomers ?
same molecular formula but mirror images of each other (non-super imposable)
what is a chiral carbon ?
a carbon atom that has 4 different groups attached to it
it is a chiral centre
what are stereo isomers important for ?
important in molecular recognition
