Molecular forces Flashcards
covalent bond
atoms share electrons
non-covalent bond
different types of interactions lead to bond formation
weakness of non-covalent bond
inheritance - DNA strands separate
compartment - bilayers etc
signalling - proteins and ligands
ionic
for from permanent gain/ lose of e- forming permanent charge
e.g. Na+ and Cl-
Quantitively description of ionic bond
E{coulomb} = q1q2 / kcr
r
distance between q1 and q2 (charges)
dipole interaction
have no net charge - partial charges such as water
quanititive dipole interaction equation
E{dipole, charge} = q (vector) cos* / kcr(2)
interaction energy between dipole and charge
falls with 1/r(2)
dipole dipole equation
E{dip, dip} = (2(vector1 , vector2) / kcr(3)) f(angles)
interaction energy between dipole and dipole
falls with 1/r(3)
dispersion forces
neutral molecules with out partial charges can have temporary charges
how dispersion forces are formed
by short lived uneven electron distribution
induced induced equation
E{ind, ind} = -const / r(6)
energy interaction between induced and induced
1/r(6)
dispersion forces being universal
all molecules being attracted to each other
Pauli exclusion principle
Quantum mechanics dictates no more than 2 electrons than occupy same orbital so can only get as close as electron distribution allows without overlapping
VdW potential
where energy if minimal - specifies optimal distance between 2 atoms
combining energy in VdW potential due to….
VdW radius with dispersion energy
hydrogen bond requirements
2 electronegative atoms (N, O, F)
H donor
H bond to electronegative
H bond accepter
H can only bond with non-bonding pair of electrons on another electronegative atom
examples in DNA
alpha helices - H bond between CO and NH
beta sheet - H bond between CO and NH - antiparallel strands - at angle (weaker)
dipole-dipole attraction
dominating H bond interaction - electrostatic
angular dependence
best of donor and acceptor in straight line - 180 degrees
d{0} on graph
optimal distance
How H bonds vary
dependent on donor and acceptor atoms
Hydrophobic effect
non-polar molecules don’t mix well with polar molecules
perturbation
effect increases as non-polar molecules affects polar solvent
minimize free energy
more favourable when non-polar molecules cluster together
non-polar molecules clustering
minimises perturbation of solvent
driven by maximizing entropy
perturbation of polar solvent example
water - tetrahedron therefore has 6 options of H bond with neighbouring O atoms
When adding hydrophobic group at the corner of tetrahedron
to decrease entropy of system
single C atom halves no. microstates
packing together the hydrophobic group
causes less water perturbation
hydrophobic effect driven
lipid assembly in to vesicles
bilayer sheets, liposome, micelle
protein folding of hydrophobic effect
burying majority of amino acid with hydrophobic side chains in the core of protein
