Aims & Objectives:

• Give an exposure to quantum chemical and molecular modeling

packages/software
• Build and visualize 3D structures of molecules and determine the
molecular geometry using the molecular mechanics
• To determine physical properties of small molecules applying quantum
mechanics using the GAMESS computational chemistry software
• Visualizing vibrational modes, molecular orbitals and electron density of
small molecules

Software/Packages – GAMESS (US Version), Avogadro, MacMolPlt, Jmol

Introduction:
Chemists have been some of the most active and innovative participants in this
rapid expansion of computational science. Computational chemistry is simply
the application of chemical, mathematical and computing skills to the solution
of interesting chemical problems. It uses computers to generate information
such as properties of molecules or simulated experimental results. Some
common computer software used for computational chemistry includes:

 Gaussian xx, Gaussian 94 currently

 GAMESS
 MOPAC
 Spartan
 Sybyl

Computational chemistry has become a useful way to investigate materials

that are too difficult to find or too expensive to purchase. It also helps chemists
make predictions before running the actual experiments so that they can be
better prepared for making observations. The Schroedinger equation
(explained in another section) is the basis for most of the computational
chemistry scientists use. This is because the Schroedinger equation models the
atoms and molecules with mathematics. For instance, you can calculate:

 electronic structure determinations

 geometry optimizations
  frequency calculations
 transition structures
 protein calculations, i.e. docking
 electron and charge distributions
 potential energy surfaces (PES)
 rate constants for chemical reactions (kinetics)
 thermodynamic calculations- heat of reactions, energy of activation

Currently, there are two ways to approach chemistry problems:

computational Quantum chemistry and non-computational quantum
chemistry Computational quantum chemistry is primarily concerned with the
numerical computation of molecular electronic structures by ab initio and
semi-empirical techniques and non-computational quantum chemistry deals
with the formulation of analytical expressions for the properties of molecules
and their reactions.

We just mentioned ab initio and semi-empirical numerical techniques.

Definitions of these terms are helpful in understanding the use of
computational techniques for chemistry. Scientists mainly use three different
methods to make calculations:

 ab initio, (Latin for "from scratch") a group of methods in which

molecular structures can be calculated using nothing but the
Schroedinger equation, the values of the fundamental constants and the
atomic numbers of the atoms present (Atkins, 1991).
 Semi-empirical techniques use approximations from empirical
(experimental) data to provide the input into the mathematical models.
 Molecular mechanics uses classical physics to explain and interpret the
behavior of atoms and molecules

The table below attempts to capture the specifics of each of these three
methods:
Method Advantages Disadvantages Best for
Type
Molecular  uses  Computationally  particular  large
Mechanics classical least intensive - force systems
physics fast and useful field (thousan
 relies on with limited applicabl ds of
force- computer e only atoms)
field with resources for a  systems
embedde  can be used for limited or
d molecules as class of processe
empirical large as enzymes molecule s with
parameter s no
s  does not breaking
calculate or
electroni forming
c of bonds
propertie
s
 requires
experime
ntal data
(or data
from ab
initio) for
paramete
rs

Semi-  uses
Empirical quantum
physics
 uses
experime
ntally
derived
empirical
parameter
s
 uses
approxim
ation
extensivel
y
Ab Initio  uses  useful for a  computat  small
quantum broad range of ionally systems
physics systems expensiv (tens of
 does not depend e atoms)
on experimental
data

To summarize, computational chemistry is:

 a branch of chemistry that generates data which complements

experimental data on the structures, properties and reactions of
substances. The calculations are based primarily on Schroedinger's
equation and include:
1. calculation of electron and charge distributions
2. molecular geometry in ground and excited states
3. potential energy surfaces
4. rate constants for elementary reactions
5. details of the dynamics of molecular collisions
 particularly useful for:
1. determination of properties that are inaccessible experimentally
2. interpretation of experimental data

In this practical we learn how to use a quantum chemistry package (i.e.

GAMESS) to determine equilibrium geometry, energy, harmonic vibrational
frequencies, etc. To run a quantum chemistry calculation first we need to
select a method and a basis set. The selection of a method and basis set is
based on the tradeoff between the computational cost and accuracy. Some of
the quantum mechanical methods are listed below.
• Restricted Hartree-Fock (RHF) self-consistent field theory
• Moller-Plesset perturbation theory (MP2, MP3, MP4)
• Configuration interation (CI) singles and doubles
• Coupled cluster theory (eg: CCSD, CCSD(T))
• Density functional (DFT)
• B3LYP
 • M06
Basis set is a mathematical representation of atom centered orbitals. Some of
the popular basis sets are listed below in the order of increasing sophistication.
• STO-3G Minimal basis set (Slater type orbital approximate by 3-
Gaussians)
• 3-21G Split valence basis set
• 6-31G(d) Polarized basis set – adding d-type orbitals to main group
atoms
• 6-31G(d,p) Polarized basis set with additional p orbitals added to H
atoms
• 6-311+G(d,p) Diffuse functions are added
• cc-pVTZ Correlation consistent basis sets
There are various software to do quantum mechanical calculations such as
Gaussian, Molpro, Q-Chem and GAMESS. GAMESS is an open source (free)
software. This practical is designed to carry out in windows 8 operating system.
Exercises
• Building Molecules and Molecular Mechanics Optimization
1. The Avogadro program was opened and the structures of, H2O2, C6H6,
Adenine and S4N4 were built.
2. The energy of each molecule was minimized using molecular mechanics field
by clicking auto minimizer option and selecting MMFF94 as the force field.
3. The images were exported and saved.

Geometry – Bent with respect to the

Symmetry point group- D Oxygen on the left.

Symmetry point group– C2

 Geometry – Trigonal planar at each Carbon Symmetry point group – C1

Symmetry point group– D6h

C6H12 (Cyclohexane) Chair and Twisted Boat Conformations were imported

from the fragment library. (Build --> Insert --> Fragments)
• The images were saved and the MMFF94 force field energy of each
molecule was determined.

MMFF94 force field energy = -14.909 kJ/mol MMFF94 force field energy = 9.91757 kJ/mol

• Anti and Gauche conformations of Butane were built. To get the gauche
conformation the C-C-C-C dihedral angle was changed to 60°. ( View -->
Properties --> Torsion Properties --> Select and change the dihedral
angle)
 • The images were saved and the MMFF94 force field energies of the two
conformations were determined.

MMFF94 force field energy = -21.2521 kJ/mol MMFF94 force field energy = -17.9773 kJ/mol

• Quantum Mechanical Geometry Optimization

i. The structures of CHCH and CHCHO molecules were built in Avogadro.
ii. Extensions --> GAMESS --> Input generator
Input Generator Select
Calculate - Equilibrium geometry
Select the method and basis set
a. HF/STO-3G
b. B3LYP/6-31G(d,p)
Advanced Setup --> Data --> Coordinate --> Select Cartesian Coordinates
Click Generate.
The input files were saved to the BP25 G folder by giving appropriate
coordinates name
iii. The .inp files were opened in Notepad and copied/pasted to include in the
report.
iv. Open Command prompt.
To go to the directory named BP25 G; "cd Desktop:/BP25 G".
To run it, "rungms CHCH1a.inp > CHCH1a.out".
Appropriate output file names were chosen.
v. The output files were opened in Notepad and the required information
was extracted to complete the following table.
For CHCH
Method RHF DFT/B3LYP
Basis set STO-3G 6-31G(d,p)
Number of optimization steps 18 14
Properties of the minimum geometry
Total kinetic energy 75.5900843668 76.5693268928

Total potential energy -151.4463320659 -153.8476251223

Nuclear energy 25.2676014514 24.7913858518
Total energy -75.8562476991 -77.2782982295
Dipole moment under Electrostatic
moments 0.000009 D 0.000095 D
Total wall clock time 0.1 s 29.9 s

For CHCHO
Method RHF DFT/B3LYP
Basis set STO-3G 6-31G(d,p)
Number of optimization steps 14 12
Properties of the minimum geometry
Total kinetic energy 149.6230344344 152.4160522725

Total potential energy -300.5690274134 -306.1632954913

Nuclear energy 69.0480627398 69.4906238617
Total energy -150.9459929790 -153.7472432188
Dipole moment under Electrostatic
moments 1.805266 D 2.646589 D
Total wall clock time 0.5 s 97.3 s
MacMolPlt for visualizing GAMESS OUTPUT
1. RHF/STO-3G output files were opened in wxMacMolPlt and the
molecules were visualized.
2. Subwindow --> Energy plot
Energy Plot of CHCH

Energy Plot of CHCHO

3. Subwindow --> Surface --> Visualize HOMO and LUMO molecular orbitals

CHCH

CHCHO
4. Subwindow --> Surface --> "3D electron density surface MEP"
"Colourize using the surface MEP"
"Invert color map"
Change "Max val. to map" to 0.200

CHCH

CHCHO
5. Another .inp file was created to calculate the harmonic vibrational
frequencies.
Subwindow --> Input builder --> Select Hessian under 'run type'
Select RHF under 'method'
Select 6-31G(d,p) under 'basis'
The input files were saved as CHCH1Frequency.inp and
AcetaldehydeFrequency.inp.
Open Command prompt ---> Go to the BP25 G directory --> Run GAMESS
• "rungms CHCH1Frequency.inp > CHCH1Frequency.out"
• "rungms AcetaldehydeFrequency.inp >
AcetaldehydeFrequency.out"

Molecule CHCH CHCHO

Total energy -75.8534235409 -150.9444082768
0.066277
0.031670 Hartree/molecule Hartree/molecule =
= 19.873419 kcal/mol = 41.589706 kcal/mol =
Zero point energy 83.150384 kJ/mol 174.011331 kJ/mol
Moments of Inertia
0.00000 50.84263
along the three 32.46468 177.13391
50.84263
principle axes 198.11557
Atom Pair 1 & 2 :
1.092
Atom Pair 2 & 3 :
1.093
Atom Pair 2 & 4 :
1.092
Atom Pair 2 & 5 :
Atom Pair - 1 & 2 : 1.200 1.498
Atom Pair 5 & 6 :
Atom Pair - 1 & 3 : 1.066 1.103
Atom Pair 5 & 7 :
Atom Pair - 2 & 4 : 1.066
Bond distances 1.227
 Atom Pair 1 & 2 :
0.974
Atom Pair 2 & 3 :
0.980
Atom Pair 2 & 4 :
0.974
Atom Pair 2 & 5 :
0.978
Atom Pair 5 & 6 :
Atom Pair - 1 & 2 : 2.997 0.931
Atom Pair - 1 & 3 : 0.984 Atom Pair 5 & 7 :
Bond orders Atom Pair - 2 & 4 : 0.984 2.001
 Physical Chemistry Laboratory Course Section-B
BP 25
Experiment: - No-15
Title of Experiment: - : Computational Chemistry Calculations on
Small Molecules

Name:- S.F Sanoh Nath-ha

Index Number:-164578
Date:-12 /02/2018