CST Physical Chemistry Practical
Molecular Modeling
Introd uction
The need for computer modelling
Traditionally chemists have synthesized molecules and then tested their properties by experiment. In
the pharmaceutical industry, it was in the past common for a company to produce hundreds of
compounds for every one worth pursuing into the clinic. This is naturally very expensive. lf instead a
compound with the desired properties can be designed merely by executing an appropriate computer
program, there are obvious benefits both intellectually and commercially. This hope has become in
large part a reality. All major pharmaceutical and agrochemical companies now employ specialists in
computer-aided molecular design and the synthetic chemists are increasingly using these facilities for
themselves. Long before the advent of computers, chemists used models to aid their understanding of
molecules. Basically these were of two types: wire models such as the Dreiding sort which represent
bonds by fine metal tubes giving an idea of the molecular skeleton, and space-filling models like the
CPK (Corey, Pauling, Kolthun) type which represent each atom by a sphere of the appropriate radius
and give an idea of the electronic "flesh". These types of representation have been carried over into
the computer graphic molecular modelling programs, as you will see during this experiment. There
are, however, major advantages in the computer displays over mechanical models. Molecular
geometries can be drawn from crystallographic databases so that they are realistic rather than
average values of bond lengths and angles; the display is created in moments rather than weeks for
large molecules; the images may be manipulated interactively and parls may be removed or added.
Galculating molecular properties
Two quite distinct approaches are used in the computation of the energy of a molecule as a function of
its shape. The purer of the possibilities is the use of molecular quantum mechanics to solve the
Schrodinger equation in an approximate manner. These computations may be of the so-called ab
initio variety in which all the many millions of integrals implied in the theory are rigorously evaluated.
The alternative is a semi-empirical calculation, in which time is saved by replacing computed values of
integrals by experimentally determined parameters. Quantum mechanical calculations are the favored
approach if, in addition to a value of the energy or stability of a molecule, we also require some other
molecular properties which can be derived from the molecular wave function (such as dipole moment,
electrostatic potential or energies of individual molecular orbital).
Procedure
This experiment is run on a PC in the computer laboratory. No special knowledge of computing is
required. Quantum chemistry package "GaussianO3" along with Gaussview will be used for the
purpose.
The experiment consists of two parts. In the first, you will use the molecular modeling package
GaussianO3 to complete a number of straightfonryard tasks, whose aim is to allow you to become
familiar with the software. In the second, you will carry out two exercises.
Demonstration
Carrying out an electronic structure calculation using GaussianO3 software consists of three steps, 1,
Building the molecule using Gaussview, 2. Startirrg and running the job r.rsing Gaussian and 3.
analyzing the results using Gaussview. We will construct water, methane and vinyl alcohol molecules.
1) Construct water and CH2=CHOH)
icon on your DesktoP. s will aPPear,
view 4.1.2. Select the c your molecule
and then on the required valence structure' Single
same manner ano replace the initial hydrogen atoms present on
the central atom, in the New window'
with the ligand atoms by single clicking on the hydrogen atoms.
To modify bond rength, angle, dih ight crick on New window Builder --- click on the
required option. tto'i ciicr 5n ih" i ln the New window. Respective windows appear'
change required Parameters as You
--' Calculate -+ Gaussian calculation setup -
n.
3) Viewing log file: Results of the calculation are in the .log file,
.log file can also be viewed from the
Gauss view 4.1.2 window --- Files ---+ open/open recent' lt
gets saved in the same directory as your
, you can view the different vibrational moOes ty
animate a vibration, click on its frequency in the
clicking a second time on the frequency You may
Checkthattheformofeachvibrationisconsistent
wn in the vibrations table' Sketch the form of each
thwhichvibration,andidentifythosewhichshou|d
be lnfrared active.
"Help" section in Gaussview to get an
b. you can also view the different molecular orbitals: check the
idea about this.
Exercises:
1. Basis set - Construct water molecule using Ga
and LUMO (orbital no 9) orbitals of the molecules
of ethylene.
at HF level us-lng 3-21G' 6-3'1G' 6-
3. Scan - perform a potential energy curve scan for H2 molecule
comment on the differences'
31G** basis sets. Plot the results on a single Excel sheet and
cis-, trans-, and acetaldehyde at
4. perform optimizations on two different conformers of vinyl alcohol,
B3LYP16-31g*|ev.el.Comparetherespectiveenergiesandcommentontheresu|t.
'1)Construct water and CH2=CHOH)
icon on your DesktoP. s will aPPear,
view 4.'l -2. Select the c your molecule
and then on the required valence structure' Single
same manner and replace the initial hydrogen atoms present on
the central atom, in the New window'
with the ligand atoms by single clicking on the hydrogen atoms.
To modify bond rength, angle, dih ight crick on New window Builder --+ click on the
required option. Novi click 6n the i in the New window. Respective windou"s appear'
change required Parameters as You
--' Calculate -, Gaussian calculation setup ---'
to appear, close it. Another window titled 'Gaussian
this is the output file which contains all the information'
3) Viewing log file: Results of the calculation are in the .log file, .log file can
also be viewed from the
same directory as your
Gauss view 4.1.2 window --+ FileS --+ Open/open rr cent. lt gets saved in the
input file.
modes by
a. lf you have carried out a frequency calculation, you can view the different vibrational in the
on its frequency
selecting Vibrations under the Display menu. To inimate a vibration, click
on the frequency. You may
vibrations dialogue. you can stop the animation by clicking a second time-
adjust the otion. check that the form of each vibration is consistent
with what ry shcwn in the vibrations table. Sketch the form of each
vibration, teO w th which vibration, and identify those which should
be Infrared active.
"Help" section in Gaussview to get an
b. you can also view the different molecular orbitals: check the
idea about this.
Exercises:
ssview and then perform optimizations at HF level
sets. Once the optimizations are over, report the
ent basis sets in a tabular format and compare with
thepredictedvibrationa|frequencieswiththeir
and LUMO (orbital no 9) orbitals of the molecules
of ethylene
HF level us-ing 3-21G,6-31G' 6-
3. Scan - perform a potential energy curve scan for H2 molecule at
on the differences'
31G** basis sets. plot the results on a single Excel sheet and comment
cis-, trans-, and acetaldehyde at
4. per-form optimizations on two different conformers of vinyl alcohol,
on the result'
B3LYP16-3'1g" level. compare the respective energies and comment
