POTENTIAL ENERGY

SURFACE (PES)

MOLECULAR GRAPHICS

Presentation By S.Prasanth Kumar

POTENTIAL ENERGY
SURFACE (PES)
Wave function

 Describe the physical system

 Deals about a function of the possible states of the system
 Molecule : the possible configurations of all the electrons
and the wave function describes the probabilities of those
configurations.
Born–Oppenheimer approximation

Ψtotal = Ψ electronic x Ψ nuclear

 Computation of the energy and wave function of

a molecule
 Born–Oppenheimer approximation allows the
wave function of a molecule to be broken into its
electronic and nuclear motions

 Ψtotal = product function

Schrödinger equation

Describes how the quantum state of a physical system

changes in time
H ψ= E ψ

For a general quantum system

i imaginary unit
Ψ(r,t) wave function
ħ Planck constant
Hamiltonian operator
Also considers Electronic Energy Of Each Of These Orientations
A potential energy surface must be created to take into
account :

1.Every possible orientation of the reactant molecules

2.Every possible orientation of the product molecules
3.The electronic energy of the reactant molecules
4.The electronic energy of the product molecules
Let us consider a system comprising M nuclei and N
electrons. By including only electrostatic interactions,
the Hamiltonian of the system is given by

M Nucleus
N Electrons

r Electronic coordinates { r1, r2, . . . . . , rN }

R Nuclear coordinates { R1, R2 , . . . .. . ., RM}

σ Electronic Spin Coordinates {σ1 , σ2 , . . . . . . σN }

V(r,R) All electrostatic interactions
Mα Mass of the nucleus α
me Mass of the electron e
 The time-independent Schrödinger equation

In the Born-Oppenheimer approximation the wave function

    is written as a product function

ψE (r, σ,R) ψB.O = ψe (r, σ;R)Φ(R)

 Equation for electronic motion:

Remember:
r Electronic Coordinates
R Nuclear Coordinates

The Potential Energy Surface (PES) depends

parametrically on the position of the nuclei R
The electronic wavefunction    is a solution of the
electronic Schrödinger equation                     

The Schrödinger equation for the nuclear wave function

Transition state
The state corresponding to the highest energy along the
reaction coordinate

Reaction Coordinate
Coordinate of a geometric parameter that changes during the
conversion of one or more molecular entities

bond length, bond angle , bond order, . . . . . . . . . .

 LOCAL MAXIMA

LOCAL MINIMA
Ethane Dihedral Motion
 GLOBAL MINIMUM
CH2Cl-CH2Cl Dihedral Motion
Saddle Points
{Minimum in all variables except one variable, Maximum
in this Excepted variable}

Saddle Point 2 minima & a

Saddle point

This corresponds to a transition state in theories of reaction

mechanisms
Minima, Maxima & Saddle Points
Cyclohexane

COURTESY: Molecular Modeling:Geometry Optimization-

Introduction to Cheminformatics II by Kelsey Forsythe
The Real Picture….
 What these points tell us ?
Global Minimum Energy value corresponds to
the most stable
nuclear configuration

Reaction Coordinate The path along the

potential energy surface
that the atoms "travel"
during the chemical
reaction

Saddle Points or Correspond to transition

Local Maxima states

Local Minima Reactive

Intermediates
It’s the Right time to define the Potential Energy
Surface. . . .

A geometric hyper surface on which the potential energy of a

set of reactants is plotted as a function of the coordinates
representing the molecular geometries of the system
A PES displays the energy of a molecule as a
function of its geometry

Potential Energy
Potential Energy

Geometric Coordinate Geometric Coordinates

e.g. bond length e.g. bond length, bond order

1-D 3-D
KEY FEATURES OF
PES
 Equilibrium molecular structures correspond to the
positions of the minima

 Energetics of reactions can be calculated from the

altitudes of the minima for reactants and products

 A transition structure is the highest point on the lowest

energy path

 Reaction rates can be obtained from the height and

profile of the potential energy surface around the transition
structure

 The shape of the valley around a minimum determines the

vibrational spectrum
APPLICATIONS
ADVANTAGE
S
The structure, energetics, properties, reactivity, spectra
and dynamics of molecules can be readily understood in
terms of potential energy surfaces

LIMITATIONS

Stability and reactivity are not precise concepts

Resonance, nucleophilicity, leaving group ability

not considered
MOLECULAR GRAPHICS
MOLECULAR GRAPHICS: The discipline and
philosophy of studying molecules and their
properties through graphical representations
MILESTONES
Early Cathode ray tube screens or through
plotters drawing on paper
1966 Display of a protein molecule
(Project MAC) - Cyrus Levinthal and
Robert Langridge
Realistic" Rendering Of Macromolecules
Using Reflecting Spheres - Nelson
Max
1982 Molecular Graphics Society (MGS) in UK
1980s Programs for calculating molecular
properties (such as molecular dynamics
and
quantum mechanics)
Vector Graphics
◙ No 3-D renderings
used
◙ Hence, Geometrical
attributes like bond
length, torsional angle
cannot be used
◙ a.k.a 1-D Diagram
3-D Rendered Image
x,y,z coordinates should be known
All geometric transformations (rotation, scaling, etc)
can be done
Reference frames

Drawing molecules requires a transformation between

molecular coordinates and the screen

Molecular transformations requires:

 Scaling of the display (but not the molecule).
 Translations of the molecule and objects on the screen.
 Rotations about points and lines
Ambient occlusion

Local lighting Ambient Occlusion

Ambient occlusion is a global lighting technique

Concept : light each point p with normal vector with its
computed irradiance.
Irradiance : the quantity of light reaching p from any direction…
Ambient occlusion applied to Proteins

WITHOUT AMBIENT OCCLUSION WITH AMBIENT OCCLUSION

DIFFERENT ATTRRIBUTES

TRANSLATION :A translation moves an object into a different position in a scene

SCALING : A scaling changes the size of an object with two scale factors, Sx
and Sy
ROTATION : Using the trigonometric relations, a point rotated by an angle
about the origin

SHEARING : A shearing affects an object in a particular direction (in 2D,

it’s either in the x or in the y direction)
DIFFERENT MODELS USED IN
VISUALIZATION SOFTWARES
 Ligand: Sialic Acid
Ribbon Model

Carbon
Oxygen
Nitrogen
Alpha Helices

Structure of Hemagglutinin
Space-Fill Models

Structure of Formic Acid

Atoms are drawn to suggest the amount of space they occupy

CPK Model = Corey, Pauling, Koltan
The quantum mechanical representation of molecules,
there are only (positively charged) nuclei and a "cloud" of
negative electrons. The electron cloud defines an
approximate size for the molecule
Isosurface

Negative
Positive
Neutral

Zirconocene where part (left) is rendered as ball-and-stick and part

(right) as an isosurface.

Isosurfaces that have been coloured to show quantities such

as electrostatic potential
Stick Model

Space-Fill Model
Cylindrical or
"Licorice" modes

Cylindrical-Med
But Not the least, The Animation
Structure Visualization & Manipulation Softwares

RasMol
Swiss PDB viewer
Molscript
Ribbons
Grasp
VMD
WebMol
Chime
Cn3D
PyMol
QMol
References:
POTENTIAL ENERGY SURFACE (PES)
Molecular Modelling : Principles and Applications by Andrew R Leech
Molecular Modelling for Beginners by Alan Hinchliffe, UMIST, Manchester, UK
Potential energy surfaces and applications for CmHn by Bastiaan J. Braams
Emory University with Joel M. Bowman

MOLECULAR GRAPHICS (MG)

History of Visualization of Biological Macromolecules by Eric Martz and

Eric Francoeur.
Brief History of Molecular Mechanics/Graphics in LSU CHEM7770 lecture notes
Desktop Molecular Modeling by Peter L.Hurray
Ambient Occlusion and Edge Cueing for enhancing Real Time Molecular
Visualization by Marco Tarini, Paolo Cignoni, Claudio Montani
Online Programs: PDB, JMol,
FOR YOUR ATTENTION