University of South Carolina

CHEM 141 Fall 2021

Laboratory 6: Molecular Modeling

PURPOSE

The objectives of this experiment are:

1. To learn how to use molecular modeling software, a commonly used tool in chemical
research and industry.
2. To examine the structures of several simple molecules to search for common factors
affecting molecular structure.

PROCEDURE
There are a variety of software programs available to perform molecular modeling experiments;
we will use a program called Spartan ‘18. First, you will learn how to build molecules, analyze
bond lengths, analyze bond angles, analyze torsion angles and visualize your results. You will
then use these skills to perform analyses on a series of small molecules.

[Adapted in part from “General Chemistry Molecular Modeling using WebMO”. Links to full
program documentation and an in-development SUNY Oneonta computational chemistry wiki
can be found at http://irene.oneonta.edu.]

PART I: INTRODUCTION TO SPARTAN1

Spartan is a molecular modelling and computational chemistry application. It contains code
for molecular mechanics, semi-empirical methods, ab initio models, density functional models,
post-Hartree–Fock models, and thermochemical recipes including G3(MP2) and T1. Quantum
chemistry calculations in Spartan are powered by Q-Chem.
The software’s primary functions are to supply information about structures, relative stabilities
and other properties of isolated molecules. Molecular mechanics calculations on complex
molecules are common in the chemical community. Quantum chemical calculations are more
time consuming in comparison but can supply information to complement existing experimental
data or replace it altogether.
Spartan applies computational chemistry methods (theoretical models) to many standard tasks
that provide calculated data applicable to the determination of molecular
shape conformation, structure (equilibrium and transition state geometry), NMR, IR, Raman,
and UV-visible spectra, molecular (and atomic) properties, reactivity, and selectivity.

PART II: HOW TO BUILD MOLECULES AND MEASURE BOND LENGTHS AND ANGLES

Building a Molecule: You will first build a molecule of water, which you will return to in later parts
of this laboratory exercise. Under the File menu, select “New Build” which will open up a panel on
the right-hand side of the screen. Click on the button that has “O<” and then double click anywhere
on the screen. A red oxygen atom with two open bonds should appear. Next click on the “-H”

1 Adapted from https://en.wikipedia.org/wiki/Spartan_(chemistry_software).

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button and double click on the ends of the two oxygen bonds to create a water molecule.

Correcting the geometry of your molecule quickly: You now have a model of a water molecule,
but the geometry of your model is probably quite different from that of a real water molecule. Every
time you build a molecule you must optimize the geometry.

1. Build water ( ), minimize ( ) and click ( ).

2. Select Calculations from the Setup menu or click on ( ) if it appears at the top
of the screen, and perform the following operations in the Calculations dialog
which appears.
3. Select Equilibrium Geometry from the top menu to the right of Calculate. This
specifies optimization of equilibrium geometry. At Ground state in Gas should appear in
the menus to the right of Equilibrium Geometry.
4. Select Molecular Mechanics, MMFF from the bottom menu to the right of
Calculate.
5. Click on Submit at the bottom of the dialog. A file browser appears.

Figure 1: Molecular Mechanics Options

6. Because the molecule is in SSPD (even though we will not use the data), the name
water will be presented to you in the box to the right of file name. Either use it or
type in whatever name you like and then click on Save. You will be notified that the
calculation has been submitted.
7. Click on OK to remove the message from the screen.

After a molecule has been submitted, and until the

calculation has completed, you are not permitted to modify
any dialogs or other information associated with it.

8. You will be notified when the calculation has completed. Click on OK to remove the
message from the screen. Select Output from the Display menu or click on ( ) if it

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appears at the top of the screen. Displayed initially is a brief summary, describing the
task and providing the molecule name and molecular formula together with the total
charge (if it is not 0) and number of unpaired electrons (if it is not 0), the calculation
model and the total energy.
9. You may examine the total energy and dipole moment among other calculated
properties without having to go through the output. Select Properties from the Display
menu to bring up the Molecule Properties dialog (make certain that the Molecule tab
and not the QSAR, Thermodynamics, 2D Drawing or 13C NMR tab is selected).

Figure 2: How to Visualize a Dipole

10. To see the dipole moment vector (indicating the sign and direction of the dipole
moment), check the box to the left of Display Dipole Vector. Wire, ball-and-wire or tube
models are best for this display.

Measuring bond lengths and angles: To measure a bond length, go to the “Geometry” tab and
click “Measure Distance”. First click on the oxygen atom and then one of the hydrogen atoms.
The distance will appear in the bottom right hand corner of the screen. To measure the bond
angle, go to the “Geometry” tab and click “Measure Angle”. Select all three atoms and the bond
angle will display on the bottom right hand side of the screen.

Measure the bond lengths and angles of your water molecule for the Molecular Mechanics
geometry optimization methods described above and record them in your report sheet.

Correcting the geometry of your molecule with a semi-empirical calculation:

To run a more thorough calculation to correct your model's geometry, select “Calculate” from the
“Setup” tab. Select Equilibrium Geometry from the top menu to the right of Calculate. This

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specifies optimization of equilibrium geometry. At Ground state in Gas should appear in the
menus to the right of Equilibrium Geometry. This time select Semi-Empirical, PM3 from the
bottom menu to the right of Calculate. Click on Submit as before. There are different
theories/methods for calculating molecular properties, each with its own strengths and
weaknesses. Semi-empirical techniques like AM1 and PM3 work well for determining molecular
geometries.

Figure 3: Semi-Empirical Options

Measure the bond lengths and angles of your water molecule for the Semi-Empirical
geometry optimization methods described above and record them in your report sheet.
How do they compare with the measurements made using Molecular Mechanics?

PART III- WHAT CONTROLS BOND LENGTH?

We have learned that the angle between two bonds depends mainly on electron-pair geometry of
the central atom, which in turn depends on the number of structurally important electron pairs on
the central atom. Many factors can influence the length of a chemical bond. In this exercise, you
will examine several of the main determinants of bond length by examining a series of related
compounds.

Draw the Lewis structures for the molecules in Table 1 and use optimized semi-empirical
models to measure bond lengths, as described in Part II. From your results, deduce the
main factors that influence bond length.

Build and optimize the geometry of the molecules needed for the following exercises, including
one of your own choosing, as listed in the table below. Begin optimization of your initial model
using minimize ( ) and then click ( ). Then run a calculation using the Semi-Empirical
method to complete the optimization. Determine the bond lengths and angles for each molecule.

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Table 1: Molecules to Build

H2O PF5 CH3Cl CH3NH2 CH3CN

CO2 SF6 CH3Br CH3CH3 CH2O

BF3 NH3 CH3OH CH2CH2 CH2ClCH2Cl†

CH4 CH3F CF3OH CHCH Your choice

† Draw this molecule with the chlorine atoms one up and the other down (180°).

PART IV- TORSION ANGLES

When a series of atoms are connected together, their relative positions are referred to as a
conformation. A torsion angle (also called a dihedral angle), which is defined by four atoms,
describes the twisting of one part of the molecule with respect to another. The easiest way to
observe this is to examine atoms bonded to adjacent central atoms and see if they line up (they
are eclipsed) or seem to avoid each other (they are staggered).

There are two factors that might control how one fragment of a molecule will twist with respect to
another fragment- steric hindrance and bonding. Steric hindrance comes about when atoms get
in each other's way and take up space. The result is that atoms are arranged in order to avoid
other atoms to which they are not bonded. Bonding control of conformation comes about when
certain types of bonds require a particular orientation of the atoms involved. The most common
and important of these are pi bonds.

View your molecular models of CH3CH3, CH2CH2, and CH2ClCH2Cl. Record the value for the
H-C-C-H and Cl-C-C-Cl torsion angles and describe the relative positions of the atoms.
Perform a coordinate scan for CH2ClCH2Cl as described below and describe how the
molecular energy changes with torsion angle. What does this molecular energy mean?

A coordinate scan is a calculation in which you step through many possible conformations and
calculate properties of the molecule in each conformation (energy, for example). To examine the
Cl-C-C-Cl torsion in CH2ClCH2Cl, open your optimized model.

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Figure 4: Torsion Angle Coordinate Scan

1. If the molecule is not already in an anti conformation, select Measure Dihedral from the
Geometry menu ( ), click on Cl-C-C-Cl atoms in order, click inside the box to the right of
Dihedral... and enter 180 (180°) using the number pad that appears. Do not minimize.
2. Select Constrain Dihedral from the Geometry menu ( ). Select the Cl-C-C-Cl torsion
(click on Cl-C-C-Cl atoms in order), and then click on at the bottom right of the screen.
The icon will change to indicating that a dihedral constraint is to be applied.

3. Check the box to the left of Profile at the bottom right of the screen. This will result in two
additional text boxes.

Leave 180° in the original (leftmost) box alone, but change the value in the box to the right
of to to 0°. Click inside the box and enter 0 using the number pad. Steps should be 10. If it
is not, click inside the box and enter 10 using the number pad. What you have specified is
that the dihedral angle will be constrained first to 180°, then to 160°, etc. and finally to 0°.
Click on .

4. Select Calculations... from the Setup menu ( ) and specify Energy Profile from the
top menu to the right of Calculate, and Semi-Empirical, and PM3 from the bottom
menus. Click on Submit and accept the file name.
5. When the calculations have completed, they will go into a file named 1,2-
dichloroethane.Prof.M0001. A prompt will ask you if you want to open this file. Click
on OK. Align the conformers. Select Align from the Geometry menu ( ), select
Structure from the Align by menu at the bottom right of the screen and, one after the
other, click on both oxygens and on one of the carbons. Then click on the Align by
button at the bottom right of the screen. Select Spreadsheet from the Display menu
( ), and enter both the energies relative to the 180° conformer, and the Cl-C-C-Cl
dihedral angles. First click on the label (M0001) for the top entry in the spreadsheet

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(the 180° conformer), then click on the header cell for the leftmost blank column, and
finally, click on Add... at the bottom of the spreadsheet. Select rel. E (kJ/mol) from the
quantities in the Molecule List tab, and click on the spreadsheet to release the dialog.
To enter the dihedral angle constraints, select Constrain Dihedral from the Geometry
menu ( ), click on the constraint marker attached to dichloroethane and click on
at the bottom of the screen (to the right of the value of the dihedral angle). Click on
.
6. Select Plots from the Display menu ( ). Click on at the top of the (empty)
plot pane and select Constraint(Con1) from the X Axis menu and rel. E(kJ/mol) from
the Y Axes list and then click Create.

To fit the points to a Fourier series, click on at the top of the plot pane, select Fourier to the
right of Curve in the resulting dialog and click on Done.

PART V - MOLECULAR VIBRATIONS

How to calculate the vibrations in a molecule:

1. Build or build your molecule ( ), minimize ( ) and click ( ).
2. Select Calculations from the Setup menu or click on ( ) if it appears at the top
of the screen, and perform the following operations in the Calculations dialog which
appears.
3. Select Equilibrium Geometry from the top menu to the right of Calculate. Select Density
Functional, HF and 6-31G* from three menus immediately below. This specifies
optimization of equilibrium geometry. At Ground state in Gas should appear in the menus to
the right of Equilibrium Geometry.
4. Once completed, select Calculations... from the Setup menu ( ). Select Energy
from the top menu to the right of Calculate. (Density Functional, HF and 6-31G from
three menus immediately below.) You already have the equilibrium structure from SSPD
and only need to obtain the energy and wave function as the basis of an Infrared (IR)
spectrum calculation. Check the box to the left of IR (to the right of Compute). Click on
Submit. Accept the file name.
5. The calculation will take several minutes. When completed, select Spectra from the

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Display menu ( ). Click on ( ) inside the spectra pane, and select ( ). The
calculated Infrared spectrum will appear in the spectra pane.

6. Click on the vibrational band in the spectrum to animate the molecule.

Calculate and examine the vibrations for H2O and CO2. Record the frequency of each
vibration for both molecules. Describe the difference in motion between the two bending
modes for carbon dioxide.

Calculate the vibrations for CH4, C2H2, C2H4, and C2H6. Record the number of vibrational
modes for each on your report form.

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Laboratory 6 Data Sheet

Name: _______________________________________________________________

Section:_____________

Water (using Molecular Mechanics)

Bond length
Bond length
Bond Angle

Water (using Semi-Empirical)

Bond length
Bond length
Bond Angle

How do the two different methods compare?

Molecule Bond Lengths Bond Angles

CO2
BF3
CH4
PF5
SF6
NH3
CH3F
CH3Cl
CH3Br
CH3OH
CF3OH
CH3NH2
CH3CH3
CH2CH2
CHCH
CH3CN
CH2O
CH2ClCH2Cl
Your Choice

Molecule Torsion Angles

CH3CH3
CH2CH2
CH2ClCH2Cl

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CH2ClCH2Cl Coordinate Scan Describe how the molecular energy changes with torsion angle. What
does this molecular energy mean?

Molecule Vibrations Frequency of Vibrations

H2O
CO2

Describe the difference in motion between the two bending modes for carbon dioxide.

Molecule Vibrations Number of Modes

CH4
C2H2
C2H4
C2H6

10