L10n11 Molecular Interaction
L10n11 Molecular Interaction
Lecture # 10 and # 11
■ directionality of covalent bond: bonds are directed or oriented at well-defined angles relative to each
other
■ Covalent bonds are polar when the electronegativity difference is > 0.4 and non-polar when it is ≤ 0.4
■ Rotational freedom: ability to rotate or not has important consequences for flexibility and stability
(crystals, proteins)
■ covalent forces are short range force (order of inter-atomic separations, 0.1-0.2 nm)
■ the covalent interaction dies away more rapidly than its ionic counterpart(single charges on each ions)
PH60206 Lecture# 10 and # 11 2
Coulomb Interactions
■ The interaction between two charged atoms or ions
■ the force between two charge Q1 and Q2 separated by r distance in a dielectric medium ϵ,
Q1 Q2
F (r) = N
4 π ϵ0 ϵr r2
r
z1 z2 e2
Z
Q1 Q2
u(r) = −F (r) dr = =
∞ 4 π ϵ0 ϵr r 4 π ϵ0 ϵr r
For two isolated ions (Na+ and Cl− ) in contact, i.e. r = 0.276 nm
−(1.6 × 10−19 )2
u(r = 0.276 nm) = −9
= −8.5 × 10−19 J = 200 kB T
4 π ϵ0 (0.276 × 10 )
u(r)
The force needed to break the ionic bond would be F = ∼ 3 n N.
r
Ionic Crystals
■ Ionic crystals have at least two atoms in their base which are ionized. Charge neutrality demands that
the total charge in the base must be zero; so we always need ions with opposing charge.
■ The binding between the ions is mostly electrostatic and rather strong (binding energies around 300
kB T ); it has no directionality.
■ Ionic crystals thus can be described as an ensemble of hard spheres which try to occupy a minimum
volume while minimizing electrostatic energy at the same time (i.e. having charge neutrality in small
volumes, too).
■ Ionic crystals come under simple and more complicated lattice types
q2
For NaCl crystal: uij = λ e−rij /ρ ±
rij
1X X q2
U = uij = N (λ e−rij /ρ ± )
2 i,j i,j
rij
■ Sum over j does not depend on whether the reference ion i is +ve or -ve; which gives total number of
atoms
■ Repulsive interaction is non-zero only for the nearest neighbours because it drops down very quickly
with the distance between atoms.
where R is the distance between nearest neighbours, Z is the no. of nearest neighbours
X±Z
α = , is Madelung Constant
ρij
■ Find the equilibrium distance between nearest neighbours for NaCl type crystal? (Given, α =
1.75, R0 = 2.8 Å, ρ = 0.1 × R0 )
dU αρ q 2
= 0 ⇒ R02 e−R0 /ρ = .
dR Zλ
αN q 2
ρ
The cohesive energy, ⇒ U0 = − 1− . Binding energy per pair of atoms is about 8 eV.
R0 R0
PH60206 Lecture# 10 and # 11 4
e2
4 4 6 6
u(r) = − 4 − √ + − √ + √ .. ⇒ α = 1.6155
4πϵ0 r 2 2 5 8
Nearest neighbour of opposite charge..
e2
4 4 8 4
u(r) = − 4 − √ + − √ + √ .. ⇒ α == 1.6155
4πϵ0 r 2 2 5 8
PH60206 Lecture# 10 and # 11 5
Reference state
■ the reference state is r = ∞ and interaction occurs in vacuum
■ if two ions are interacting in condensed liquid medium; the references state is also r = ∞ and
dielectric constant of the medium (you have to take care)
■ at certain finite separation, a quantum mechanical charge exchange or charge transfer interaction takes
place (electron jumps from one atoms to another form +ve and -ve ions), the two atoms turn into
oppositely charged ions and attract each other with a strong Coulomb force : phenomena is called
Harpooning Effect
■ the reverse process may also happen and strong Coulomb interaction is replaced by weak van der Waal
interaction: phenomena occurs for dissimilar surfaces called contact electrification or Triboelectricity
PH60206 Lecture# 10 and # 11 6
■ repulsion when filled orbitals approach sufficiently close (Pauli exclusion principle will prohibit overlap
of the orbitals)
■ the interaction arises from the instantaneous dipoles exist even in the filled orbitals
A
■ Johannes van der Waals potential: U (r) = −
r6
■ Buckingham potential function:
A
U (r) = B e−r/ζ − 6
r
A B
■ Lennard-Jones potential: U (r) = − 6
+ 12
r r
■ Origin of van der Waals forces:
Concept of dipole
■ For a physical dipole ; equal and opposite charges separated by very small distance
■ how small; separation should be very very small compared to the reference point
■ dipole moment is independent of reference point only when net charge is zero otherwise it will depends
on the choice of reference point
PH60206 Lecture# 10 and # 11 7
N
X
■ p⃗ = qi ri = q r+ − q r−
i=1
⃗ field,
Boltzmann average orientation of the rotating dipole in the presence of external E
p2 E p2
< pind >θ = < p cos θ e(p E cos θ/kT )
>= < cos2 θ >= E;
kT 3kT
Z π Z 2π
2 1 2 1
< cos θ >= cos θ sin θ dθ dϕ =
4π 0 0 3
PH60206 Lecture# 10 and # 11 8
Multipole Expansion
For arbitrary charge distribution
s2 = r2 + r′ 2 − 2 r r′ cos(θ′ )
" ′ 2 ′ #
r r
s2 = r 2 1 + − 2 cos(θ′ )
r r
" #
√ ′ 2
′
r r
s = r 1 + ϵ ; where ϵ is − 2 cos(θ′ )
r r
1 1 −1/2 1 1 3 2 5 3
= (1 + ϵ) = 1 − ϵ + ϵ − ϵ + ...
s r r 2 8 16
" ′ ′ 2 #
2 ′
1 1 r r 3 cos (θ ) − 1
= 1 + cos(θ′ ) +
s r r r 2
PH60206 Lecture# 10 and # 11 9
The solubility of polar molecules in different solvent should increase with dielectric
constant ϵ.
the dipole moment is NOT uniquely define, this is product of charges and their
separation distance. so, it may give you different self energy for a dipole.
The dipole moment vary from solvent to solvent.
Since molecules are large in size ions so additional energy arising from non-electrostatic
solute-solvent interaction, van der Waals self-energy.
Ion-Dipole interaction
The electrostatic pair interaction between ion and dipole,
1 (ze)(p) cos θ
U (r) = −
4πϵ0 ϵ r2
Net average dipole-dipole interaction energy is ZERO. But, each configuration occurs with
a probability proportional to Boltzmann factor.
So, if both dipoles are freely rotating the dipole-dipole interaction energy is given by the
weighted average
p21 p22 p1 p2
U (r) = − ⇐ Keesom energy. for kT >
3(4πϵ0 ϵ)2 kT r6 4πϵ0 ϵr3
1
The interaction energy fall faster than 3 which confirms that neither ion-dipole nor dipole-
r
dipole forces can produce long range alignment effects in liquid.
PH60206 Lecture# 10 and # 11 11
⃗ = − α E2 ∼ 1
U (r) = −⃗p . E
r6
2
p 1 p 2 (1 − 3 cos (θ) )
since V varies as 1/r3 for dipole-dipole interaction V =
4 π ϵ0 r 3
water molecule interact with dipole: upon approach of the molecule with a dipole,
electrons in the atom respond and the atom also develop dipole.
p2 α 2
Ud−id = − 1 + 3 cos θ
(4πϵ0 r3 )2
Fluctuating dipole
■ Freely rotating dipole: U = 0 always; since dipole changes sign
■ The interaction energy for two freely rotating dipoles is not zero.
■ However their mutual potential energy depends on their relative orientation, in fact
molecules do not rotate completely free even in gaseous medium.
PH60206 Lecture# 10 and # 11 12
Quantum fluctuations induces instantaneous dipole and instantaneous dipole in turn cre-
ates another dipole in near by molecules.
Hamiltonian for the system is given by:
p21 1 2 p22 1
H = + c x1 + + c x22 + Hi
2m 2 2m 2
Where Hi is initial energy without fluctuation for nearest and farthest position
e(x1 + x2 ) × e (x1 − x2 )
Hi = −K
R3
p21 1 2 e2 2 p22 1 2 e2 2
H = + (c − K 3 ) x1 + + (c + K 3 ) x2
2m 2 R 2m 2 R
Energy eigenvalue values for the above Hamiltonian are:
p
■ ω0 = c/m
v
u 2 e2
tc ± K 3
u
■ ω1,2 = R
m
ℏ
■ ∆E = [ω1 + ω2 − 2 ω0 ] ; for the same state.
2
1
■ ∆E∼ [Prove it?] expand (1+x)^1/2 for three terms for omega 1 and 2
r6
PH60206 Lecture# 10 and # 11 13
Summary
PH60206 Lecture# 10 and # 11 14
Special Interaction
Hydrogen bonding
■ Attractive interaction between two species
■ A—H- - - B; where A, B are highly electronegative elements like F, O, N
■ B should have lone pair of electrons
■ partial +ve charge of H and partial -ve charge of B
■ All A, B, H contribute one atomic orbital to form three molecular orbitals
Ψ = C1 ΨA + C2 ΨH + C3 ΨB
■ these three orbitals need to accommodate 4 electrons (2 from the original A–H and
2 from lone pair of B)
■ One molecular orbital is bonding; second one is non-bonding, and third one is anti-
bonding
■ So if H-bonding is present it may dominate the other intermolecular interactions
■ Hydrogen bond may be symmetric [H-atom lies midway between the two atoms] for
eg. F–H- - - F
■ mostly H-bonding is asymmetric where A–H is shorter than H- - - B
■ For two monovalent ions in water with thermal energy kB T
1 e2
= kB T ; where lB is Bjerrum length; at room temperature lB = 7.2 Å
4 π ϵ0 lB
■ examples of H-bond
PH60206 Lecture# 10 and # 11 16
Electronegativity effects
Cooperativity in H-bonds
PH60206 Lecture# 10 and # 11 17
Water molecule
There are more than 40 models for water molecule. For ‘ TIP5P’ model: q = 0.24 e ,
l = 0.096 nm, θ = 104.50 , and ϕ = 109.50 . This model predict maximum density
at 40 , and high dielectric constant, but fail to explain phase diagram of water.
1. high melting and boiling point, and latent heat of vaporization through it is low
molecular weight (against the properties of ionic crystal)
2. maximum density at 40 C
3. solid (Ice) is less dense than liquid
4. water molecule tetrahedral coordination rather than higher close packing i.e. 12
5. ice has higher dielectric constant than liquid phase
6. proton conductivity and mobility in ice is also higher than in liquid
7. high dipole moment
8. high dielectric constant
PH60206 Lecture# 10 and # 11 18
Hydrophobic interaction
■ When a hydrocarbon molecule is surrounded by water, the water molecule form a
lattice like structure pierced with holes (Clathrate cage), as a result of this struc-
ture, entropy of water decreases. The dispersal of the hydrocarbon into the water is
entropically opposed and its coalescence is entropy favoured. If the change in G is
negative and the hydrophobic interactions will be spontaneous.
■ +ve Gibb’s free energy transfer from a non-polar to a polar solvent are Hydrophobic
substance
According to van der Waals theory oil and water should not separate and surfactant should
not form membranes, but they do.
Virus and disease propagation in the human body are directly linked to hydrophobic
properties on a cellular level.
■ For Hydrophilic surface: contact angle of water droplet, θc < 900 : water spreads
on the surface
■ For Hydrophobic surface: contact angle of water droplets, θc > 900 : water beads-up
on the surface
■ for super hydrophobic surface: contact angle of water droplets, θc > 1500 : water
droplets are highly beaded (repelled)
■ uses: 1. Low water resistance for boats
■ 2. High efficiency wind mills
■ For maximum hydrophobicity:
– free energy transfer ∆G is maximum where ∆S = 0
∆G
– Equilibrium constant for transfer ∼ − is at a maximum where ∆ H = 0
T
PH60206 Lecture# 10 and # 11 20
G |T,p = H − T S = U + P V − T S
F |T,V = U − T S
The strength of hydrophobic interaction is not due to any intrinsic attraction between
non-polar moieties. It results from the system achieving greatest thermodynamic stabil-
ity by minimizing the no. of ordered water molecules required to surround hydrophobic
portion of the solute molecules.
For small molecular group R: the hydrophobic constant ( Π ) as
s
Π = ln( )
s0
where ‘s’ is the ratio of molar solubility of the compound R–A in Octanol (a non-polar
solvent) to that in water.
s0 is ratio of molar solubility of compound H–A in octonol to that in water
As carbon atom increases for longer chain: ∆transf er H become more +ve and
At molecular level, formation of solvent cage around a hydrophobic molecule involves the
formation of new hydrogen bonds among solvent molecules. This is exothermic process so
-ve value of ∆ H
Increase in order with formation of large no. of small solvent cage decreases the ∆ S , so
-ve value for ∆transf er S
Hydrophobic surface strongly attract each other to eject water into the bulk to minimize
the free energy of the system.
PH60206 Lecture# 10 and # 11 21
Ehdrophobic = −γ (a − a0 ) e−d/Dhydrophobic
a is molecular area
−1/2
d
−
a(d) = a0 1 − e Dhydro
Drug target
Lipids: Cell membrane lipids
Most drugs are in equilibrium between being bound and unbound to their target
Functional groups on the drug are involved in binding interactions and are called
binding groups
Specific regions within the binding site that are involved in binding interactions are
called binding regions
Binding interactions usually result in an induced fit where the binding site changes
shape to accommodate the drug
The induced fit may also alter the overall shape of the drug target
Ionic bonds are the most important initial interactions as a drug enters the binding
site
The van der Waals interaction occur between hydrophobic regions of the drug and
the target
PH60206 Lecture# 10 and # 11 24
Question:
The given Lennard-Jones potential has attractive as well as repulsive terms.
−A B
U (r) = +
r6 r12
where A = 10−77 J-m6 , B = 10−134 J-m12 .
Calculate the distance where potential energy is minimum ( r = re ), ratio of re to r0 ,
and ratio of rs to r0 (at r0 the potential energy is zero), and rs is separation between
molecule where adhesive force is maximum.
Consider two neutral atoms or molecules are interacting via this potential. Calculate the
frequency of small oscillation of atoms/molecules of mass (m = 9 mp ) near that minima
for very small r, (∆r). Discuss anharmonic oscillation away from minima.