Experiment 7- Computer Simulation

Experiment
Pre-Report
Group 9: 四化二甲 B11006011 蔡美先 (Writer)
四化二甲 B11006012 Nicholas Wahjudi
四化二乙 B11006111 龐兆恩
四化二乙 B11006112 Elizabeth Loid Urtecho

1. Purpose
(1) Use simulated molecular calculations to understand molecular structure and spectra.
(2) Use simulation calculations to understand the physical and chemical properties of
molecules or chemical reactions.
(3) Guide students to solve molecular orbital domain, molecular vibration, transition state,
reaction heat, and activation energy, and compare the theoretical predicted molecular
infrared spectrum with the experimental value.
2. Instruments
PC and Computing Software Gaussian.
3. Chemicals
No chemicals are needed in this experiment.
4. Principle
Computational chemistry is a branch of chemistry that uses computer simulation to
assist in solving chemical problems. It uses methods of theoretical chemistry, incorporated
into computer programs, to calculate the structures and properties of molecules, groups of
molecules, and solids. It is essential because, apart from relatively recent results concerning
the hydrogen molecular ion (dihydrogen cation, see references therein for more details),
the quantum many-body problem cannot be solved analytically, much less in closed form.
Computational chemistry has two different aspects:
(a) Computational studies, are used to find a starting point for a laboratory synthesis or to
assist in understanding experimental data, such as the position and source of
spectroscopic peaks.
(b) Computational studies, used to predict the possibility of so far entirely unknown
molecules or to explore reaction mechanisms not readily studied via experiments.
Thus, computational chemistry can assist the experimental chemist or it can challenge
the experimental chemist to find entirely new chemical objects [1].
There are some of the important principles used in computational chemistry:
(a) Molecular Modelling
Central to computational chemistry is the art of constructing mathematical models of
molecules and molecular systems. These models include representations of atoms,
bonds, and the elusive electronic structure, which is crucial for understanding a
molecule's properties and behaviour.
(b) Schrödinger Equation
The Schrödinger equation stands as the keystone of computational chemistry. This
equation, rooted in quantum mechanics, provides insights into the behaviour of
electrons in a molecular system. Computational methods either solve this equation
directly or seek approximations to predict molecular properties with astonishing
accuracy.
(c) Ab Initio vs. Empirical Methods
In the realm of computational chemistry, two major approaches coexist: ab initio and
empirical methods. Ab initio methods strive to solve the Schrödinger equation from
first principles, offering unparalleled accuracy. Conversely, empirical methods rely
on experimental data to create parameterized models, sacrificing some accuracy for
computational efficiency.
(d) Basis Sets
Basis sets are a versatile tool in computational chemistry, serving to approximate the
wavefunctions of electrons within a molecule. Researchers can choose from a range
of basis sets, with larger sets providing more accurate results but demanding greater
computational resources.
(e) Density Functional Theory (DFT)
Density Functional Theory, or DFT, is a prevalent computational approach. DFT
simplifies the quantum description of a system by using the electron density rather
than the wave function. This method strikes a balance between accuracy and
computational cost, making it a go-to choice for many researchers.
(f) Molecular Mechanics
 Molecular mechanics offers a classical perspective on molecular behavior. It's a
valuable tool for studying the structural and energetic properties of large molecules,
particularly in fields such as biochemistry.
(g) Geometry Optimization
Computational chemists frequently embark on the journey of optimizing molecular
geometries. This pursuit helps uncover the most stable structures of molecules,
offering insights into their reactivity and stability.
(h) Solvation Models
In the real world, molecules often interact with solvents. Computational chemistry
accommodates this by integrating solvation models, allowing the study of molecular
behavior in solution.
(i) Energy Minimization
Understanding the energy landscape of molecules is vital. Computational chemistry
can identify the lowest-energy conformations and calculate energy differences
between different structures, shedding light on reaction mechanisms and stability.
(j) Thermodynamics and Kinetics
Thermodynamics, encompassing properties like enthalpy, entropy, and free energy,
as well as kinetics, which deals with reaction rates, play a pivotal role in computational
chemistry. These principles help decipher chemical reactions and equilibria [2].
The applications of computational chemistry are as diverse as they are influential.
They extend across a multitude of scientific disciplines, leaving an indelible mark on fields
such as drug discovery, materials science, catalysis, and environmental chemistry, among
others. In drug discovery, computational chemistry aids in the design of novel
pharmaceuticals with enhanced efficacy and reduced side effects. In materials science, it
guides the development of advanced materials with tailored properties. In catalysis, it plays
a pivotal role in optimizing chemical reactions. Furthermore, computational chemistry
contributes to our understanding of environmental processes, facilitating the design of eco-
friendly materials and sustainable chemical processes. The versatility of computational
chemistry makes it an invaluable asset for scientific progress[3].
There are a lot of software that can be used to do computational chemistry. However,
in this experiment, we are going to use the Gaussian software to learn how to do
computational chemistry. Gaussian is a widely used software package for computational
chemistry that specializes in performing electronic structure calculations. It is known for
its accuracy in simulating the behavior of atoms and molecules at the quantum level[4].
5. Procedures
In this experiment, Gaussian calculation software was used to optimize the molecular
structure, followed by IR, NMR and UV-Vis spectroscopy simulations and analysis.
(1) Click the "GaussView" icon to open the GaussView and G1:M1:V1 → New windows.

Plot area

The structure shown

here will appear in the
drawing area if you left-
click on the drawing
area.

(2) Use the toolbar in the GaussView interface to paint the structure in the G1:M1:V1 –
New window.
(3) Click the mouse in the G1:M1:V1-New window and the benzene ring will appear in
this window.
(4) Structural drawing completed. Make the calculations.

(5) Select the calculation type in the Job Type field, and perform Optimization first.

(6) Select the calculation method at Method, where Advanced Shape Structure
Optimization.
(7) When you are done typing, press Submit and archive.

(8) After the file name is set, the following window will appear, asking you if you want to
operate automatically, select Cancel.

(9) Open the calculation program and open the previously saved .gif file.
(10) Click the Run icon in the upper right corner to start the calculation.

(11) After the automatic calculation is completed, the magnifying glass icon in the upper
right corner will turn yellow (as shown in the figure on the right).

(12) Archive the results of the calculations (.out).

(13) Go back to the GaussView interface and open the file (.out) that was saved for the
calculation.

(14) When you open the archive, you will see the optimized molecular structure.
 (15) Right-click Results → View File to see the results of the calculation.

(16) The above is the optimization process, and other calculations only need to change the
parameters according to the calculation spectrum:
Change the Job Type and Base function
(a) IR: Job Type changed frequency (Week 1)
(b) NMR: Job Type changed to NMR (Week 2)
(c) UV-vis: Job Type changed to NMR, Method changed to ZINDO (Week 2)
6. References
[1] Computational Chemistry, Wikipedia, (n.d.).
[2] Young, D., Introduction to Computational Chemistry, Auburn University Division of
Computing, (n.d.).
[3] Basic Introduction of Computational Chemistry, EMSL, (n.d.).
[4] Gaussian (Software), Wikipedia, (n.d.).