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Experiment # 4. Molecular Modeling: Conformational Analysis and

Molecular Properties
Pre-Lab Reading Assignments
Dipole Moments; Conformations of Alkanes; Conformations of Cyclohexanes (see
211 / 213 textbook)
Compuational Chemistry: pp. 107-124 in Mohrig
Software (Spartan Student Version 6) Download: Students must first download
this software on their laptop systems. This can be done as follows:
Go to the College server: http:// software.geneseo.edu.
On the opening page, scroll down to Spartan software; click on Spartan
download link.
Follow the download / installation instructions.

Introduction
Models are useful in helping us understand the three-dimensional structure of
molecules. However, putting together models for large molecules is tedious and
time-consuming. Many important biomolecules such as proteins have molecular
masses that are in the tens or even hundreds of thousands. Visualization of these
very large, complicated structures gives chemists and biologists insight into the
function of the molecule or even how different bio-molecules fit together. An
important example of this is in the design of pharmaceuticals. The shape of
molecules plays an important role in the function of the molecule. In fact, studying
structure-function relationships is a very active area of research. Molecular
biologists and biochemists systematically vary amino acid sequence to examine the
effect on the chemistry exhibited by the protein. Thus, much effort has gone into
developing computer programs to facilitate the visualization of complicated
molecules.
Purpose
The purpose of this laboratory is to introduce the concept of modeling the
properties of molecules by computer generated algorithms using the PC Spartan
Essential computer software. In addition, we can use the results from these
molecular modeling experiments to gain understanding about steric interactions,
bond lengths, bond angles, dipole moments, and bond rotation.

Background
The nature of the chemical bonding in a molecule determines two important
properties of the molecule: the strength of the bonds and the three-dimensional
shape of the molecule.
Not all bonds are identical. The number of atoms that are bonded to the central
atom may indicate the type of bonding. If more than one atom is bonded to a
central atom, there is an angle formed between the bonds called the bond angle.
The electrons on atoms and in chemical bonds are negatively charged and thus
repel each other. The bonds therefore attempt to move as far apart as possible.
This is the basis of Valence Shell Electron Pair Repulsion (VSEPR) Theory. The
number of bonded atoms determines how far apart the bonds will be (i.e., the bond
angle).
For molecules with more than one central atom, another angle is defined
between the bonds of two atoms bonded to two consecutive atoms. This angle is
referred to as the torsional or dihedral angle. The optimal dihedral angle is that
which minimizes the close approach of bonding or lone electron pairs on adjacent
central atoms. The three geometric parameters associated with the threedimensional structure of a molecule are represented for ethane in Figure 1.
H1
H1-C1-C2
bond angle

H1

C1

H4
H6
C2

H3

C1

H4

C2

rC-C
H2

H6

H1-C1-C2-H4
dihedral angle

H3

H2

H5
H5

Figure 1. Representation of bond distance (r), bond angle, and dihedral

angle.
In this experiment, bond lengths, dipole moments, bond angles and dihedral
angles of some alkyl halides, butane and cyclohexane derivatives will be measured.

The various geometries, which an organic molecule can attain by bond rotations
and bends are, called conformations or conformers. Note that changing
conformations of a molecule does not involve making or breaking chemical bonds.
Any arrangement of atoms in a molecule has an associated energy. Distorting
bond lengths or angles from their equilibrium positions, bringing atoms or
unshared electron pairs into close contact, or eclipsing of bonds will raise the
energy of a conformer (i.e. make it more positive). These deviations from nonideal geometry are referred to as strain. The real molecule will spend most of its
time in a conformation having the least strain, but which one is that? This question
is of vital importance, because the chemical reactivity of organic molecules is
strongly influenced by their conformations.
There are several theoretical models which allow us to estimate the energy of a
molecule as a function of its conformation using a computer, so that we can
determine more or less quantitatively which conformer is preferred for a given
molecule. It is important to realize that these calculations are all based on theories
of how atoms (and electrons) within molecules behave, so if the model is less than
perfect, the results of the calculation will also deviate to some extent from the
experimentally measured values.Naturally, much experimental work has been
devoted to determining the conformations of organic molecules, and
generalizations based on the results of these experiments are summarized in any
organic textbook. We cannot perform these experiments in the Chem-216 labs, but
we can use the Spartan 10 Essential software program on a PC computer to
model the behavior of a few real molecules, and attempt to deduce many of the
generalizations of conformational analysis for ourselves.
Calculating Conformational Energies
a) Molecular Mechanics
A simple way to estimate the strain energy of an organic molecule is to define a
mechanical force field that is used to calculate the energy for a molecule. For
example, we could assume that the strain energy of a molecule can be broken down
into four terms:
(Equation 1)
Estrain = Estretch + Eangle + Etorsion + Esteric
where the components refer to bond stretching energy, bond angle bending energy,
bond torsion energy, and steric strain (Van der Waals interactions and dipole
repulsions). Each of the terms can be expressed as a mathematical function based

upon classical mechanics where force constants describe the energetic cost of
stretching a bond or bending a bond angle away from normal bond angles, etc. The
apparent force constants for each type of bond are deduced by collating
experimental data for a sample set of organic molecules. The equations with these
empirically derived force constants are then applied to the molecule under study,
with the assumption that, for example, a C-C bond in this compound will be
essentially identical to the average C-C bond in the sample set.
Spartan can perform molecular mechanics calculations using one of four possible
ways of breaking down the strain energy. The calculations in molecular mechanics
are simple, and can be carried out quickly even on small computers. This can be a
good method for many applications, when relatively simple conformational
questions are being considered. It is the only feasible method when studying a very
large molecule.
Energy minimization - An important feature of computer calculations of
molecular structure is that the computer can not only find the energy of a
particular structure, but it can also change the structure slightly and determine the
energy of the changed structure. If the new structure has a lower energy, the
computer accepts that structure as the basis structure and tries another variation. In
this manner, the structure is changed toward lower energy structures until an
energy minimum is reached (a change in any bond angle or length leads to a higher
energy structure). It is important to recognize that this structure may be a local
minimum energy structure and not the lowest energy structure possible. For
example starting with a molecule represented by Point A on the following diagram
would result in an energy minimum at a local minimum, while starting with a
molecule with a structure and energy represented by Point B would result in
obtaining the global minimum structure. It is possible to program the computer to
generate a wide variety of starting structures if it is important to find the global
minimum.

E
n
e
r
g
y

A
*

B
*

global
minimum
(lowest
energy)

local minimum

Structure variation (bond angles, length, etc.)

b) Quantum-Mechanical Calculations
An exact solution to the quantum mechanical equations is not possible for a
complex polyatomic system. A particular problem is that the repulsions among the
electrons in molecules cannot be solved exactly, since we cannot know precisely
both the location and energy of an electron. Various ways to address this problem,
which allow an approximate solution to the quantum mechanics equations, have
been devised. These are known as ab initio methods, and they are beyond the
scope of this course.
Another way to simplify the calculation so that it can be readily solved is to
substitute some experimentally measured parameters for parts of the equations,
which are difficult or impossible to calculate exactly. The parameters are
determined for some reference set of molecules, and they are assumed to be valid
for all other molecules as well. This kind of simplification is called a semiempirical method, because it combines a theoretically sound model of bonding
with some empirically determined parameters. With this simplification, equations
can be created that allow the energies and distributions of the electrons of the
molecule under study to be determined.

Procedure / Report
The detailed procedure for this laboratory exercise is separately posted on
MyCourses. Using the Part A format, perform Sections I - IV, placing the required
data in your laboratory notebook before transferring it to the report sheet. For Part
B, also submit the two Excel plots (dipole moment vs. electronegativity AND
dipole moment / bond length vs. electronegativity), along with the plot of bond
energy vs. constraint angle (butane).