School of Biological Sciences

URL: http://www.ntu.edu.sg/sbs

Gaussian Practical (computer)

GAUSSIAN 2:
Software for computational applications to organic reactivity and properties
of biomolecules

BS1002, MU Yuguang, 2020

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INTRODUCTION

This is a continuation of the previous computer practical Spartan 1. In the present practical a few
more advanced applications of the software are performed. Three exercises are performed. In the
first, calculations of LUMO (lowest unoccupied molecular orbital) and HOMO (highest occupied
molecular orbital) are performed to illustrate the relation between molecular orbitals and
reactivity for a certain type of organic reactions These so-called concerted reactions (uncatalyzed
reactions with a single transition state) of the pericyclic type (with a cyclic conjugated transition
state), can be explained by orbital symmetry arguments. Secondly, calculation of the electrostatic
potential map for the vitamin E molecule is performed. This gives insight into the hydrophobic
character of the molecule and why vitamin E may have a protective role in the cells. Third, it is
demonstrated how the Spartan software can be used to investigate the electrostatic character of a
DNA complex. In addition, this shows how you can use a molecular structure in a so-called PDB
(protein data bank) format and load it into a graphical display program like Spartan and look on
the 3D structure of the molecule. Spartan is a commercial software, but other free ware programs
that can be used to display the three dimensional structure of molecules can be found and
downloaded on the web. Examples of such software that you can download to your own
computer are pymol.

The aim of the practical is to demonstrate how computational methods involving quantum
chemical calculations and graphical display of molecules, can aid as a tool to understanding
chemical and biochemical problems at a molecular level.

EXERCISE 1: Relation between symmetry in valence molecular orbitals and reactivity in

pericyclic reactions.

(More information: http://classes.yale.edu/chem220a/studyaids/pericyclic/pericyclic.htm)

It may be noted that addition reactions between two molecules in organic chemistry can
generally often be considered as forming a new bond by combination of the LUMO of the orbital
of one molecule with the HOMO of the other molecule. This is an alternative picture to a Lewis
acid-base reaction where the bond is formed by an acceptor and donor (containing a free electron
pair).

This exercise demonstrates one of the most successful examples of using computational quantum
chemistry to account for reactivity of organic reactions. This relates to the so-called Woodward-
Hoffman rules for pericyclic reactions. In the attachment “4.9.4” to this instruction, some
introduction to this is given. More organic chemistry background for this exercise can be found
in organic chemistry texbooks (e.g. Maitland Jones, pp 500-501, 1063-1065, 1075-1080). The
task is to calculate the HOMO and LUMO orbitals for ethene and cis-1,3-butadiene. This can be
applied to the well-known Diels-Alder reaction between these two molecules, to produce
cyclohexene. It enables the stereospecificity of such pericyclic reactions to be understood in
terms of electronic structure, i.e. on the grounds of the molecular orbitals that are expected to be
involved in reaction.

Two separate molecules should be built and calculations using Density Functional Theory (DFT
6-31G*) made. The molecules are ethene and cis-1,3-butadiene. Note that it is the cis form that
should be used.

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3. To be included in the report:

a) For both molecules make notes of the Energies and make printouts of the HOMO and LUMO.
Remember that the red/blue colours correspond to different phase (sign) of the wave function.
b) Note the colour, indicating the sign of the orbitals.
c) On the basis of your results for HOMO and LUMO, discuss which of the reactions i) and ii)
that are expected to occur with the highest yield:
i) cis-1,3-butadiene + ethene (heat) -----> cyclohexene
ii ) ethene + ethene (heat) -----> cyclobutane
d) In the case of the two reactions above being photochemically (light) induced (instead of heat
induced), the experimental observation of reactivity is interchanged. Try to explain this
observation on the basis of the following: For reaction i), light absorption results in one electron
of butadiene in the HOMO being promoted to the LUMO (thus what was previously a LUMO is
now a HOMO). For reaction ii), the similar occurs for ethane.

EXERCISE 2: Design experiments to make proof of the Hund rule. The Hund rule says
that for a given electron configuration, the term with maximum multiplicity has the lowest
energy. The multiplicity is equal to 2S+1, where S is the total spin angular momentum for
all electrons. The multiplicity is also equal to the number of unpaired electrons plus one.
With Gaussian program at hand, you can calculate the total energies of a molecular system
with different multiplicity, then compare their energies.

REPORT:

Start with an introduction outlining the objective and background.

Account for your results of the exercise 1 and 2.
End with some conclusion.

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