Module 4

Potential Energy Surfaces

 Molecular Forces
• Intermolecular forces are attractive forces between molecules.

• Intramolecular forces hold atoms together in a molecule.

 Chemical Bonding

• A chemical bond is an interaction between atoms, ions or molecules that enables the
formation of chemical compounds.

• It is a mutual attraction between the nuclei and valence electrons of different atoms that
bonds atom together.
Chemical Bonds

•Three basic types of bonds

•Ionic
• Electrostatic attraction between ions.
•Covalent
• Sharing of electrons.
•Metallic
• Metal atoms bonded to several other
atoms.
 Ionic bond
• Electrons are transferred from one atom to another
• Occurs between one metal and one non-metal
• Metals loose electrons to become cations
• Non-metals gain electrons to become anions
• Examples: NaCl, MgSO4
Covalent Bonding

• In covalent bonds, atoms share electrons.

• There are several electrostatic interactions in

these bonds:
Attractions between electrons and nuclei,
Repulsions between electrons,
Repulsions between nuclei.
Covalent bond

• Electrons are shared between atoms

• Occurs between two non-metals
• Can be formed between two same atoms or two different atoms
• Each combining atom must contribute at least one electron to the shared pair
• Combining atoms should attain noble gas configuration after bond formation
• Examples, H2O, CH4

Bond energies range from 150-700

kJ/mol
Polar Covalent Bonds
• Though atoms often form compounds by sharing
electrons, the electrons are not always shared equally.
• Fluorine pulls harder on the electrons it shares with
hydrogen than hydrogen does.
• Therefore, the fluorine end of the molecule has more
electron density than the hydrogen end.
• The greater the difference in electronegativity, the more
polar is the bond.
 Polar Covalent Bonds

• When two atoms share electrons unequally,

a bond dipole results.
• The dipole moment, μ, produced by two
equal but opposite charges separated by a
distance, r, is calculated:
μ = Qr
• It is measured in debyes (D).
• 1 D = 3.33564 × 10-30 C.m, where C is
Coulomb and m denotes a meter.
 Metallic bond
• Metal atoms share many electrons in a ‘sea’ that is free to move throughout the metal.
• Metallic bond results from attractions between the metal cations and the surrounding sea of
electrons
• Vacant p and d orbitals in metal’s outer energy levels overlap, and allow outer electrons to
move freely throughout the metal.
• Valence electrons do not belong to any one atom
• Examples: metals and alloys
 Intermolecular Forces

• The attractions between molecules are not nearly as strong as the intramolecular attractions that
hold compounds together.
• They are, however, strong enough to control physical properties such as boiling and melting
points, vapor pressures, and viscosities.
 Intermolecular Forces
1. Ion-dipole : ion is attracted to polar molecule

2. Dipole-dipole : polar molecules attracted to each other

3. Dipole-induced dipole : polar molecules attracted to non-polar molecules

4. Induced-dipole - induced-dipole/ van der Waal’s forces/ London forces: non-polar molecules
attraction towards each other due to electron cloud distortion
 Ion-Dipole interactions
• An ion-dipole force exists between an ion and the partial charge on the end of a polar molecule/
neutral molecule with a dipole.

• The strength of these forces are what make it possible for ionic substances to dissolve in polar
solvents.

• Ion-dipole attractions become strong as the charge on the ion increases or the magnitude of dipole on
the polar molecule increases.
 Dipole-Dipole interactions
• Molecules that have permanent dipoles are attracted to each other.

• The positive end of one is attracted to the negative end of the other and vice-versa.

• These forces are only important when the molecules are close to each other.
 Dipole-Dipole interactions

The more polar the molecule, the higher is its boiling point.
 Directional forces

• Which forces require molecules to be aligned such that the interactions are
in optimal direction?
Ion-dipole and dipole-dipole forces
directional in nature

• Which forces do not require molecules to be aligned in a particular

direction?
Ion-ion interactions
non-directional in nature
 Dipole-Dipole Interactions: Hydrogen Bonding
• Special type of dipole-dipole attraction between molecules.

• When H bonded to a highly electronegative atom (such as N, O, F), the bonding

electron pair is drawn towards the electronegative atom.

• NOT a covalent bond to a H atom.

• The energies of H bonds range 4 to 25 kJ/mol. Regular covalent bond strength

range between 150 and 1100 kJ/mol.
 Importance of H-bonding
• H bonds are of fundamental importance in biological molecules, they help to stabilize the structure of
proteins, and are responsible for the way DNA carries genetic information.
• Ice floating, fish surviving winter!
 Induced dipole
• When electrically neutral atom where valence electrons are uniformly distributed around the nucleus
is place in an external electric field, Eext.
• Due to attractive force on electron and repulsive force in nucleus by external electric field,
distribution of valence electrons is no longer uniform.

dipole-induced dipole interaction

 London-Dispersion Forces
• While the electrons in the 1s orbital of helium would repel each other, it does happen
that they occasionally wind up on the same side of the atom.

• At that instant, then, the helium atom is polar, with an excess of electrons on the left side
and a shortage on the right side.

• Another helium nearby, then, would have a dipole induced in it, as the electrons on the
left side of helium atom 2 repel the electrons in the cloud on helium atom 1.

London dispersion forces, or

dispersion forces, are attractions
between an instantaneous dipole
and an induced dipole.
 London-Dispersion Forces

• These forces are present in all molecules, whether they are polar or nonpolar, BUT THEY ARE
THE ONLY ONES THAT EXIST IN NON POLAR MOLECULES!!!
• The tendency of an electron cloud to distort in this way is called polarizability.
• The greater the polarizability of the molecule, the more easily its electron cloud can be distorted to
give a momentary dipole.
• Larger molecules tend to have greater polarizabilities. Polarizability and dispersion forces
increases with molecular mass
van der Waals forces

• Umbrella term for

• London dispersion forces
• Dipole-dipole forces
• Dipole-induced-dipole attractions

• Refers to forces between molecules that do not involve

electrostatic interactions between ions or bond
formation
Relative strength of intermolecular forces
Summarizing Intermolecular Forces
Examples – determine the types of forces present in each:

1. H2O
2. CCl4
3. SO2
4. LiF
5. Ca(NO3)2 aqueous solution
6. HF
7. PCl3
Examples – determine the types of forces present in each:

1. H2O LDF, dipole-dipole, H-bonds

2. CCl4 LDF
3. SO2 LDF and dipole-dipole
4. LiF ionic bonds
5. Ca(NO3)2 aqueous solutionion-dipole forces
6. HF LDF, dipole-dipole, H-bonds
7. PCl3 LDF and dipole-dipole

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 Potential Energy Surface
• Atoms in a molecule are held together by chemical bonds. When the atom is distorted, the
bonds are stretched or compressed, in which increases the potential energy of its system.

• As the new geometry is formed, the molecule stays stationary. Therefore, the energy of the
system is not caused by the kinetic energy, but depending on the position of the atoms
(potential).

• Energy of a molecule is a function of the position of the nuclei. When nuclei moves, electron
readjusts quickly. The relationship between this molecular energy and molecular geometry
(position) is mapped out with potential energy surface.
 Potential Energy Surface

A potential energy surface (PES) represents the relationship between the energy of a molecule and its
geometry.

The y-axis is energy of the molecule, which

relates how stable two molecules or two
conformations of the same molecule are in
relation to one another. The more negative a
molecule's energy, or the lower on the y-axis,
the more stable it is.
 Potential Energy Surface

• Does not change if it translated or rotated in space

• Depends on a molecule’s internal coordinates

 Potential Energy Surface

• Fully specifying the location of a diatomic molecule, AB, would require specifying six numbers, the
x, y, and z coordinates of each of its atoms.

• Potential energy (PE) of the molecule as a function of the distance between the two atoms dAB.
 Conformations

Conformations are different arrangements of atoms that are interconverted by rotation about single
bonds. A particular conformation is called a conformer.
 Staggered & Eclipsed Conformations of Ethane

• In the eclipsed conformation, the C—H bonds on one carbon are directly aligned with the C—H bonds
on the adjacent carbon.

• In the staggered conformation, the C—H bonds on one carbon bisect the H—C—H bond angle on the
adjacent carbon.
 Ethane

Eclipsed conformation Staggered conformation

This PES shows the energy differences between the two conformations of ethane. The eclipsed
conformation with the hydrogen atoms overlapping one another is about 2.6 kcal/mol higher in energy than
the staggered conformation.
 12 kJ/mol

0° 60° 120° 180° 240° 300° 360°

 Conformations of Butane

• An energy minimum and maximum occur every 600 as the conformation changes from
staggered to eclipsed. Conformations that are neither staggered nor eclipsed are
intermediate in energy.
 Molecular structure and variable

RAB RAB RAB

R BC
θ2
θ1
θ

R BC
D
RC

RAB RAB RAC

RAC
θ

RCD
RBC RBC
 Variable(s) in PES

3N-6 (Nonlinear molecules)

Freedom degree =
3N-5 (Linear molecules)

N=2, potential energy curve

Potential energy surfaces
N≧3, potential energy hypersurface

U(q1)
U(q1, q2) q1, q2, …∈ {Rn, θn} or {xn, yn, zn}
U(q1, q2, q3)
U(q1, q2, q3, … …qn)
 More ”Realistic” PES

α
0
PES for proteins
 Characterizing Potential Energy Surface
The most interesting points on PES’s are the stationary points, where the gradients with respect to all
internal coordinates are zero.

1. Minima: correspond to stable or quasi-stable species; i.e., reactants, products, intermediates.

2. Transition states: saddle points which are minima in all dimensions but one; a maximum in that
dimension.

3. Higher-order saddle points: a minimum in all dimensions but n, where n > 1; maximum in the
other n dimensions.
 Characterizing Potential Energy Surface

At the minima and saddle point, the slope of the

function is zero

At the minima, the second derivatives are positive

At the saddle point, the second derivatives are negative

 Potential Energy Surface
• The reactant and the product are both minima on the PES. This indicates that they are
conformations that the molecule can exist in.
• The peak in between is the transition state that leads from the reactant to the product.
• As the transition state is NOT a minima, the molecule can never exist in that conformation, it is not a
stable conformation.
Reaction progress
 Reaction dynamics

Local minimum
Ts

Energy
Ts

R
Intermediate I

Reaction coordination

Reactants Global minimum Stationary point

For a minimum
∂2U/∂q2 > 0 ∂U/∂q = 0
For a transition state
∂2U/∂q2 > 0 ∂U/∂q = 0
Saddle point
Transition state
Products
∂2U/∂q2 < 0
 Geometry - Minimization
• In order to move from a starting geometry to a better geometry, we usually do a minimization.

• Start with a minimization algorithm, also called a geometry optimization algorithm.

Geometry - Minimization
 How to Solve the Problem
• Given a function f which depends on one or more independent variables x1, x2, …, xi, find the values of those
variables where f has a minimum value.

• At a minimum point, the first derivative of the function with respect to each of the variables is zero and the
second derivatives are all positive:

• The function f is the potential energy

• The variables xi are the atomic Cartesian coordinates

• Change the position of the coordinates (xi) until we find the position with the smallest potential energy.
 Geometry - Minimization

• Minimizations proceed iteratively.

• After the input energy is calculated, the geometry is changed slightly, and then the energy is
recalculated.

• At each step, the slope of the curve is calculated.

• The process proceeds till 1 of 2 criteria are met:

• When the slope is zero, the algorithm has found a stationary point on the PES.

• However, in order to prevent calculations from wandering off endlessly in the event of a flat
potential well, a maximum number of steps is usually also included.
 Potential Energy Functions

A potential energy surface is a mathematical function that gives the energy of a molecule as a function
of its geometry.

• Quantum Mechanics provides an energy function which can be exact in principle and works for
any molecule.

• Molecular Mechanics provides this energy as a function of stretches, bends, torsions, etc. This is
an approximate model that breaks down in some situations (e.g., breaking bonds).
 Potential Energy Functions

E = Ecovalent + Enoncovalent

can be further expanded to:

Ecovalent = Ebond + Eangle + Edihedral

Enoncovalent = Eelectrostatic + Evdw
 Potential Energy Functions

Ecovalent = Ebond + Eangle + Edihedral

Bond Stretching Potential Harmonic Angle Potential Dihedral Potential

 Potential Energy Functions

Enoncovalent = Eelectrostatic + Evdw

Coulombic Potential Lennard-Jones Potential

Bond Length Potentials
 Bond Length Potentials

• Whenever a bond is compressed or stretched the energy goes up.

• The energy potential for bond stretching and compressing is described by an equation similar to Hooke's law for a
spring.

Sum over all bonds in the structure

lo – expected/natural bond length

kl – force constant
l – actual/observed bond length

This is the approximation to the energy of a bond as a function of displacement from the ideal bond length, b0. The
force constant, Kb, determines the strength of the bond. Both ideal bond lengths b0 and force constants Kb are specific
for each pair of bound atoms, i.e. depend on chemical type of atoms-constituents.
 Bond Angle Potentials

As the bond angle is bent from the norm, the energy goes up.

Sum over all angles in the structure

φo – expected/natural bond angle
kφ – force constant
φ – actual/observed bond angle

It is the alteration of bond angles theta from ideal values q0 , which is also
represented by a harmonic potential. Values of q0 and Kq depend on chemical type
of atoms constituting the angle.

Plot of Potential
Energy Function
for Bond Length
 Dihedral Angle Potentials

• As the dihedral angle is bent from the norm, the energy goes up.
• The torsion potential is a Fourier series that accounts for all 1-4 through-bond relationships

Sum over all

dihedrals in the structure

…
• φο – expected dihedral
• An – force constant for each term
φ – actual/observed dihedral
• n – multiplicity Plot of Potential
Energy Function
for Dihedrals

Multiple minima
 Improper Dihedral Angle Potentials

• As the improper dihedral is bent from the norm, the energy goes up.

Sum over all improper dihedrals in the

structure

• ωo – expected improper dihedral (usually set to 0o)

• kω – force constant
• ω – actual/observed improper dihedral

Plot of Potential
Energy Function
for Improper
Dihedrals (ωo = 0)
 Non-bonding: van der Waals Potential
One of the most widely used functions for the van der Waals potential is the Lennard-Jones. It is a
compromise between accuracy and computability.

The Constants A and C depend on

the atom types, and are derived
from experimental data.
 Non-bonding: Electrostatic Interactions
• electrostatic interaction

• Electrostatic interaction of charged atoms

• Long-range forces

• Coulomb’s Law

Positive interaction that

Negative interaction if inversely increases
of the same charge distance
Example: Potential Energy Function