Molecular Interactions Flashcards
(36 cards)
What are molecular interaction ?
Mostly non-covalent
Primarily electrostatic (unlike chargesattract;like charges repel)
Biologically important molecular interaction are individually weak but specific -molecular recognition and nanoscale machines
Typical energies of bonds and interaction
Covalent bonds -highest
Ionic bond
Hydrogen bond
Dispersion forces
Dipole-dipole interaction - lowest
Polarised covalent bonds
Pure covalent bonding only when delta x =0
E.g) isolated H2,n2 o2
Most biologically important molecules are heteroatomic
-non identical atoms covalently bound together
-bonds have delta x ≠ 0
-bonding is partially ionic
The ketelaar triangle
Electrostatic interactions ;no overlap of atomic orbitals ;molecules are not formed
By
Polar molecules and dipoles interaction
Some molecules containing polar covalent bonds are polar overall :they have a permanent dipoles
Permanent dipole electrostatically attracts molecules and ions
Are all heteroatomic molecules polar ?
Not all heteroatomic
Depends on the shape of molecules
Highly symmetrical molecules
Dipoles may point in opposite directions and cancel out
What are dispersion forces ?
These polar interaction do not require a permanent dipole
Because ‘non polar species’ are only non-polar on average
Electron densities temporarily polarized :induced dipoles
Bigger atoms and compound experience bigger dispersion forces
Where are induced dipoles ?
Everywhere ??????
What are Van der walls interaction ?
Refers to overwall non-covalent electrostatic interaction
Sum of
Attraction. Repulsion
-dispersion. -electron-electron
-permanent dipole interactions steric effect ^
What is the energetic of vander waals interaction?
What is important interaction between polar molecules ?
Hydrogen bonds
-some of the most widespread interaction in biology
(DNA,proteins)
-between water molecules
What are the strongest kind of molecular interaction ?
The have an energy of approx 20kJ mol-1
Still much weaker than covalent or ionic bonds
Hydrogen bonds are directional
-require some overlap of atomic orbitals (slightly cov
-strongest H-bonds are linear
What are hydrogen bonds ?
Dipole interactions involving O-H,N-H
- O and N are highly electronegative
- H is very small (allow close approach)
Hydrogen bonds vs dipolar interaction ?
Many polar molecules dont form hydrogen bonds
They do interact electrostatically but much weaker than H-bonds
Eg)-hydrocarbons,SH2,chloroform
-non H-bonding compounds tend to be gases/volatile liquids at room temp ,pressure
-low solubility in water
What are the ionic forces between charged molecules ?
Some molecules are charged :IONS
-SO42-,PO43-,NH4+ etc
Many bigger biomolecules are charged
-eg DNA backbone contains negatively charged phosphate linkages
Some AA side chains charged at pH 7
Charges never exist in isolation
What are the ionic forces in biology ?
In DNA - portion of DNA doubles helix with water molecule and Mg2+ions
??????
What are ions permanent dipole dipole interaction ?
Ions r hydrophilic ;ionic species are typically water soluble ,strong electrolytes
What about other bio molecules ?
Other biomolecules are hydrophobic because they interact only slightly with water
-hydrophobic molecules are uncharged and have few hydrogen bonding opportunities
Called =POLAR
What is the hydrophobic effect ?
Hydrophobic species tend to cluster together in water
Oil doesn’t dissolve in water
Hydrophobic amino acid residue cluster in ‘hydrophobic core ‘
Mostly ENTROPIC EFFECT to maximise disorder of water molecules
The link between hydrophobicity and drug design ?
Many drugs have both hydrophobic and hydrophilic parts
-amphipathic
E.g) paracetamol —— Drugs must be sufficiently hydrophobic to cross cell membrane and sufficiently polar to stay there.
What are states of matter ?
Molecules are not chemically altered in different states
Molecular interactions are made and broken
Solid and its interaction ?
Experience many non-covalent interactions :very tightly associated
Shape of solid is defined the composite molecules are held tightly together they are effectively locked in position and can’t move relative to others
Movement virtually one
Low relative energy
Liquid and its interaction ?
Has fewer non-covalent interactions than a solid hence molecules are held together less tightly and are able to move around more freely
Like water not all molecules are held together thus they can move past one another
Variable shape
Medium relative energy
Gas it s interaction s?
No intermolecular interactions there is essentially nothing to hold molecules so can move freely
Unrestricted shape of substance
High relative energy
