Computational chemistry
● Chemistry in the computer instead of in the laboratory
● Use computer calculations to predict the structures,
reactivites and other properties of molecules
Computational chemistry has become widely used
because of
● Dramatic increase in computer speed
● Design of efficient quantum mechanical algorithms
● Computational chemistry uses result of theoretical
chemistry incorporated in to efficient computer
programmed to calculate structure and properties
of molecules
It calculate properties of molecules such as
● Structure
● Relative energy
● Charge distribution
● Dipole moment
● Vibrational frequency
● Reactivity
● Spectroscopic quantity
● Computational chemistry range from highly
accurate (Ab initio method )to less accurate
(semiemiprical) to very approximate (molecular
mechanics)
Computational methods
● There are two type methods
● 1.classical method
● Method use Newton mechanics to model molecular system
●
● 2.Quantum chemistry method
● Which makes quantum mechanics to model the molecular
system
● This method use different type of approximation to solve
Schrödinger equation
●
Classical mechanics
1. Molecular mechanics
2. Molecular dynamics
Quantum mechanics method
1. Semi empirical method
2. Ab initio method
3. Density functional theory
Molecular mechanics
● Molecular mechanics programs use equations
based on classical physics to calculate force field
● Atoms treated as spheres,bonds as springs
and electrons are ignored
● It assume that total potential energy of molecule
is given by sum of all energies of all attractive and
repulsive forces between atom in structure
Basic principle of molecular
mechanics
● Each atom is simulated as a single particle
● Each particle has a radius( van der waals radius),
polarizability and constant net charge
● Bonded interactions are treated as “springs” with
an equilibrium distance equal to the experimental
or calculated bond
Molecular mechanics equation
E = EB +EA+ED+ENB
EB =The energy involved in the deformation bond
either by stretching or compression
EA=Energy involved in the angle bending
ED= The tortional angle energy
ENB=Energy involved in the interaction between
atoms that are not directly bonded
● Molecular mechanics also called force field
method
● Ignores the electronic motions and calculate the
potential energy of a system as a function of
nuclear position only
● Can be used to study molecules of the system
ranging in size as and complexity from small to
large biological system
Force field
● It is a computational method used to estimate the
forces between atoms within a molecule and
between molecules
● More precisely force field refers to the functional
form and parameter sets used to calculate
potential energy of a system of atoms
● Parameters for a chosen energy function may be
derived from experiments
Classical empirical force
field
1. AMBER (Assisted Model Building and Energy
Refinement )
2. CHRAM (Chemistry at Harvard Macromolecular
Mechanics)
3. CVFF (Consistent Valence Force Field)
Molecular dynamics
● Molecular dynamics is a molecular mechanics
program designed to mimic the movement of
atoms with in a molecule
● Molecular dynamics can be carried out on a
molecule to generate different conformation which
on energy minimization, give a range of stable
conformation. Alternatively bonds can be rotated
in a stepwise process to generate different
conformation
● Also be used to find minimum energy structures
and conformational analysis
Quantum mechanics
● Quantum mechanics is based on finding on
solution to Schrödinger wave equation
● This is based on arrangement of electrons
of molecule and interaction of those electron and
nuclei of other molecule
● It is based on the realization that electron and all
materials exhibit wave like properties
Schrödinger's Equation
The Schrödinger equation is the basis of quantum mechanics
and gives a complete description of the electronic structure of
a molecule. If the equation could be fully solved all information
of a molecule could be determined.
Ηψ = Εψ
Where
H=Hamiltonian operator
Y=wave fuction
E=Energy system
Quantum mechanics method
1. Ab initio method
2. Semi emperical method
3. Density functional theory
Ab Initio method
● Ab initio translated from Latin means “ from first
principle”
● This refers to the fact that no experimentel data
is used and computations are based on quantum
mechanics
● It refers to an approximate quantum mechanical
calculations
● Relatively slow
● High accuracy
● Used for studying small molecules
Different levels of ab initio method
1. Hartree Fock method ( HF method)
2. Density functional theory
Hartree Fock method
● Most common type and simplest ab initio method
● Based on central field approximation
● Electron correlation is not taken in to
consideration
Density functional theory
● Used to investigate electronic structure of many
body system
● Using this theory the properties of many electron
system can be determined by using functionals
● Instead of considering wave function we
considered density functional
● DFT= work in terms of density
● Total energy expressed as total electron cloud
density
● Less computational time than HF and more
accurate
Semi emperical method
● Simplified version of HF theory
● Make many approximation and obtain some
parameters from empirical ( experimental) data
● Treating large molecule
● Use of empirical parameters appears to allow
some inclusion of electron correlation effects in to
the methods
● Accuracy is less compared to Ab Initio method and
more compared to molecular mechanics
● Use experimental data to parameterize equations
● Used to calculate transition state and exited States
Advantage of semi- emperical method
● Calculations are very fast
● Medium sized system
Disadvantages
● Depend on experimental data
● Low accuracy
