Quantum Mechanical Calculations of Organic Molecules

One of the main goals of chemistry is to understand the details of chemical reactions. Why do some
molecules react one way but not another. Theoretical calculation of electronic distribution within
molecules is one of the tools used to explore reactivity patterns. Calculations can provide
information not only on overall molecular energies but also bond strengths, and charges on atoms.

The computer program used in these exercises, Gaussian 03, requires that you supply the geometry
of the molecule so that the program may calculate the properties of the molecule. You can do this by
entering the x, y, z coordinates of each atom (painful, at best) or by entering the bond lengths, bond
angles and dihedral angles (much easier) or pictorially build your molecule (actually, sort of fun).
More on this later.

You have to become familiar with several quantum mechanical concepts to understand the
functioning of the program and interpret the results of the calculations. Recall that for atoms the
electrons reside in atomic orbitals. For example, an uncharged carbon atom has six electrons which
occupy the 1s, 2s, 2px 2py, and 2pz orbitals. Each orbital can hold at most two electrons. The atomic
orbitals have different shapes and orientation as shown below.
z

s px py pz
The s orbitals are spherical in shape whereas the p orbitals are shaped like a bow tie. There are three
different p orbitals (px, py and pz) aligned parallel to the x, y, and z axes. The orbitals are actually
mathematical functions which assign a numerical value to each point in space relative to the nucleus.

For example, the 1s atomic orbital of hydrogen atom is proportional to

e-r

where e and  are numerical constants and r is the distance from the nucleus to the point at which
the orbital is being evaluated.. The important thing here is that the value of the function depends
only on the distance from the nucleus; hence spherical in shape.

On the other hand, the 2pz atomic orbital is proportional to

 -r
ze

where z is z coordinate of the point where the orbital is being evaluated relative to the nucleus.
Depending on the point where it is evaluated the p orbital may be either positive or negative. We
represent the algebraic sign by shading (here, black or white) for the p orbitals shown above.

The aim of this experiment is to calculate properties of molecules. We need to specify the geometry
for the molecule: where the nuclei are located. Making use of bond lengths, bond angles and
rotational angles you could calculate the x, y, z coordinates of each nucleus and provide them to the
program. For simple molecules such as H2 this is easily done. For even slightly more complex cases
such as methane the calculations would be cumbersome. The GaussView program, part of the
Gaussian suite of programs, provides a graphical, visual way for both an initial specification and
then tools to modify the molecular structure.

The GaussView program will be used to specify the structure of the molecule, initiate the
calculations, and view the calculated results. Only a few features of the program will be used. The
basic steps, described in more detail later, are
1. Specify the structure of the molecule using GaussView. The tools provided include
a. a Molecular Structure Window (MSW) in which you assemble the new structure.
b. a library of molecular fragments which may be added to the molecule you are
building
c. the capability to rotate the entire molecular structures for easy viewing
d. substitution of one atom for another
e. modification of geometric parameters: bond lengths, bond angles and rotational
angles about bonds (dihedral angles)
f. automatic adjustment of a molecular structure after modification, etc.
2. Specification of some technical parameters for the calculation and starting the actual
calculation.
3. Retrieval of the results of the calculation which can include
a. Energy of the molecule
b. Charges on individual atoms
c. An Electrostatic Potential Surface (EPS) map which indicates the stabilization
(destabilization) of putting a charge at different positions around a molecule.
d. Display of the individual molecular orbitals.
1. Structure Specification

If the GaussView program is not running start the program from the Start menu. GaussView starts
and displays a methane molecule. A blank Molecular Structure Window (MSW) with a name such as
G1:M1:V1 is also presented. The MSW is where you will build your molecule.

Molecular structures and fragments, stored in libraries, are displayed in the GaussView window for
your consideration. They may then be added to the molecule you are building in the MSW. The
GaussView window is initialized with the methane molecule.

The following is a description of some of the tools used to build a molecule in the MSW.

Obtain a new Molecular Structure Window (MSW) by clicking the New button in the
GaussView toolbar. A new window with a name such as G1:M1:V1 will appear. This is
where the molecule to be calculated is designed. A structure is copied from the
GaussView window to a blank structure window by clicking on the structure window.

Structures may be rotated in any window by dragging the mouse over the window.

Molecules or atoms are first created in the GaussView window and then brought into the MSW for a
calculation to be done. When a structure is presented in the GaussView window one atom will be
designated as Hot. When an atom in the molecule being built in the MSW is clicked the Hot atom
(and the rest of the structure in the GaussView window) replaces the atom you clicked. If you
choose to have a different atom be Hot in the GaussView window simply click it.
 Clicking on the Element Fragment icon presents a Periodic Table. If the Periodic Table
has been utilized previously an additional click is needed. First select an element. A
choice of the bare atom itself or the atom linked to hydrogens in various hybridizations is
presented below the Periodic Table. Make your selection by clicking the icon. Your selection now
appears in the GaussView window with one atom designated as a Hot Atom. If you click an empty
space in the MSW then the entire structure in the GaussView window is copied to the MSW. If there
is a molecule already under construction in the MSW and you click on an atom in that molecule the
Hot Atom (and accompanying atoms) replaces the clicked atom.

The Ring Fragment icon will present a library of common ring structures from which
you may select a structure. Clicking on a ring will bring it into the GaussView window.
If the ring library has been utilized previously an additional click may be needed.
Clicking on an empty space in the MSW will copy the ring into the MSW. Alternatively,
clicking on an atom in a molecule being built in the MSW will replace that atom using the Hot Atom
of the ring.

Clicking the Group Fragment icon presents an array of common molecular structures
which can be brought into the GaussView window. If the molecular structure panel has
been utilized previously an additional click is needed. Subsequent clicking on an empty
space in the MSW will copy the structure into the MSW. Alternatively, clicking on an atom in a
molecule being built in the MSW will replace that atom with the Hot Atom of the structure.

Deleting an Atom is accomplished by selecting this icon and then clicking the atom in the
MSW.

After selecting the Add Valence icon you may add a H to the atom you click in the
MSW.

In summary, an atom or more complex structure obtained from a library of structures may be
copied from the GaussView Window to a blank Molecular Structure Window (MSW) by clicking in
the MSW. If there is already a molecular structure in the MSW clicking on an atom replaces it with
the structure in the GaussView window. The atom labeled “Hot” in the GaussView window will
take the place of the atom clicked in the MSW.

Structure Improvement.

As described above molecules are built by combining fragments and, if desired, substituting one
atom for another. Your structure may be improved by further modification. The program provides
two methods to improve the structure.
 Rebonding may be accomplished by clicking on this icon. The program will assume
atoms close to each other are bonded and adjust the display accordingly. This will
improve the pictorial representation of your molecule but not affect the calculations.

Cleaning is done by clicking this icon. This generally improves an estimated structure
when, for example, a nitrogen replaces a carbon or a new atom is added to a molecule.

Structure Modification.
Working with bond lengths, angles and dihedral angles is done only to allow you to easily specify
the geometry of the molecule. The bonds you have designated do not affect the calculated properties
of the molecule. Bond lengths, bond angles and dihedral angles (for rotations about bonds) may be
modified as below.

Bond Lengths are modified by clicking the Modify Bond icon, clicking on the two
atoms of the bond in the MSW and then, in the dialog that appears, entering a numerical
value or using the slider to alter the bond length. Keep the Translate Group option
selected for atom 1 and atom 2. You may indicate the bond multiplicity as none (non-
bonded), single, double, etc.

Bond Angles are modified by clicking the Modify Angle icon, clicking on the three
atoms of the bond angle in the MSW, and then, in the dialog that appears, entering a
numerical value for the bond angle or using the slider. You may specify how the atoms
in the bond angle are moved. You may choose that one or two atoms not move as the
bond angle is modified by choosing Fixed. Alternatively they may be moved along with their
substituents as a unit by choosing “rotate group”.

Dihedral Angles are modified by clicking the Modify Dihedral icon, clicking on four
atoms (Atom 1, Atom2, Atom3, and Atom 4) of the molecule in the MSW. Rotation
occurs around the Atom 2 – Atom 3 bond. Enter a numerical value, in the dialog that
appears, or use the slider. Drop down boxes provide options on how the atoms should
be moved in the rotation process. A value of 0 means that A and D eclipse each other while a value
of 180 specifies an anti geometry.
2. Performing the Calculation
After you have satisfactorily specified a molecular structure in the MSW the calculation is done as
follows
In GaussView choose the drop down menu Calculate  Gaussian. The set-up menu appears. The
technical details of the calculation are entered here. You will use the simplest and fastest methods.

Choose the Job Type tab. From the drop down menu you can choose either
1. Energy which will calculate the energy of the exact molecular structure as you have created it
or
2. Optimization which will automatically change the geometry parameters so as to obtain the
geometry which provides the best (most negative) energy
Choose the Method tab. Use the defaults as shown except
1. Basis Set choose STO3G,
2. Charge is set appropriate to the system you are calculating (usually 0, 1 for a +1 cation, -1
for a -1 anion, etc.)
3. Spin is set to Singlet
Choose the Title tab.
1. Enter a title for your calculation. It should consist of your initials and the name of the
molecule.
At the bottom of the window click the Submit button.

A dialog appears asking you to Save the Gaussian Input File before proceeding. Click Save. A
Save File dialog box will appear and you must enter a name for the Gaussian Input File. It should
consist of your initials and the name of the molecule. Click OK.

A dialog appears asking if you want to run the calculation. Choose OK. The calculation initiates.

3. Displaying the Results of the Calculations

 When the Gaussian program is performing calculations the progress of the
calculation is displayed in a newly created window. To display this window you may
have to click the rightmost icon (black letter G) from the Taskbar at the bottom of the
screen.

 When the calculation is finished you will be asked if you want to close the Gaussian
Window, click OK.

 A dialog appears asking if you want to open a Result File, select Yes. An Open File
dialog is presented. Change the “File of Type” to “Gaussian Output Files (*.out,
*.log)”. Select the .log file for the molecule which you calculated. Click Open.

 A new MSW is opened displaying the structure of the molecule you have just
calculated.

 The energy and dipole moment are obtained from the GaussView drop down menu
Results  Summary. The energy, E(RHF), is in Atomic Units, 1AU/molecule =
627.5 kcal/mol = 2625.5 kJ/Mol and the dipole moment is given in Debyes.

 Atomic charges are obtained from the GaussView drop down menu Results 
Charges. Select Show Charge Numbers and deselect other options.

 Geometric parameters may be “measured” from a molecule in a MSW by means of

the Inquire tool. Click on the Inquire button and then click on atoms in the structure
displayed in the MSW. The measured value is presented at the bottom of the MSW.

 Clicking on two atoms measures the distance between the atoms.

 Clicking on three atoms measures the angle formed by the atoms

 Clicking on four atoms measures the dihedral angle formed by the atoms.
 Exercises
A.1. Manual Optimization of the O – H bond length of Water. There are two geometric
parameters that must be specified to define the structure of the water molecule: the O–H bond
lengths and the H–O–H bond angle. In order to become familiar with how the program works you
will perform a series of calculations to see how the energy depends on the O–H bond length. The
H–O– H bond angle will be held fixed for the structures you calculate. You will use a value
assigned by your instructor between 85 degrees and 115 degrees.

You will seek the bond length which gives the lowest energy (most negative) by calculating the
energies of molecular structures with various bond lengths. You will first perform six calculations
with the bond lengths having values of 0.85, 0.90, 0.95, 1.00, 1.05 and 1.10.

A detailed description of how to use the program in this practice exercise follows.
1 If the GaussView program is not running start it via the
Start  All Programs GaussView folder 
GaussView program.
2 If you receive a warning that the Serial Number cannot
be located click OK

3 Once the program opens click on the Element

Fragment icon.
A periodic table will be displayed.

4 Click on the icon for Oxygen. Several bonding patterns

will be displayed at the bottom of the window. Click on
the one with two single bonds. The periodic table
window will close and an oxygen with two hydrogens
attached (water) will be displayed.

5 Click any place in the molecular structure window to

copy the molecule for calculation. You will not use the
default geometry but will have to specify both the bond
length and the bond angle.
6 First specify the bond angle. Click the Modify Angle
icon on the toolbar and then click on an H, then the O,
and then the other H. the selected atoms become
highlighted and a bond angle dialog will appear. Type
in the bond angle assigned by your instructor.
Be sure to use a decimal point. click OK. The
highlighting disappears.
7 You will now adjust the bond lengths. Click the
Modify Bond tool. Click the O and the H of one bond,
the atoms highlight and the dialog box opens. Type in
your chosen bond length (0.85, 0.90, etc.) Click OK.
The highlighting disappears. Repeat for the other O-
H bond.
8 Click the Calculate drop-down menu in GaussView 
Gaussian. The Gaussian Calculation Setup dialog
appears.
Choose the Job Type Tab. In the dropdown list
select Energy.
Choose the Method Tab. Under Basis Set choose
STO-3G.
Verify that the other parameters are
Method: Ground State, Hartree Fock,
Default Spin,
Basis Set: STO-3G and a blank box,
Charge: 0
Spin: Singlet

9 Click Submit at the bottom of the dialog. You will be

asked to save the input file. Assign it an appropriate
name starting with your initials, the name of the
molecule (water), and the O – H bond length you used
without a decimal point (for example, JMHwater0914).
Click OK.
10 The calculation will be done. A dialog box opens (if it
does not after a few seconds click on the rightmost
button on the taskbar at the bottom of the desktop)
asking if the Gaussian window should be closed. Click
OK.

11 A new dialog opens asking if you want to open a result

file. Click OK. An Open File dialog is presented.
Change the File of Type to Gaussian Output Files.
Select the one for the molecule which you calculated.
Click Open. A new MSW window appears showing the
structure used in the calculation. Click the Results drop
down menu in GaussView, click Summary and obtain
the energy of the molecule. Record it to four digits after
the decimal point
12 Change the bond lengths (step 7) as described above
and repeat the process for the next O-H bond length.
Use an Excel spread sheet to record and plot your data. Plotting should be done after the laboratory
exercises are completed.

A.2. Prediction of molecular geometry. Using GaussView perform calculations on one or more of
the following molecules following the directions of your lab instructor. Note the options to use when
changing a geometric parameter. You modify only the geometric parameters indicated keeping all
others as given to you by the program.
1) Staggered Ethane. Vary the C ( translate group)-C(translate group) distance
2) Staggered Ethane. Vary all the H(move atom)-C(fixed)-C(fixed)- angles simultaneously
3) Dimethyl ether. Vary both the C( translate group)–O ( translate group) distances
simultaneously
4) Dimethyl ether. Vary the C(rotate group)–O(fixed)-C(rotate group) angle
5) Formaldehyde, H2CO. Vary the C ( translate group)-O ( translate group) distance
6) Formaldehyde, H2CO. Vary H(rotate group)-C(fixed)-H(rotate group) angle
7) Ethene, H2C=CH2. Vary the C ( translate group)-C ( translate group) distance
8) Ethene, H2C=CH2. Vary both of the H(rotate group)-C(fixed)-H(rotate group) angles
simultaneously
9) Ammonia. Vary all the N (translate group) - H (translate group) distances simultaneously
10) Nitrous Oxide, N-N-O Vary the N (translate group) – N (translate group) distance
11) Nitrous Oxide. N-N-O Vary the N(translate group) - O(translate group) distance
12) Nitrogen tetroxide
13) O2N-NO2 Vary the N(translate group) -N(translate group) distance
14) Nitrogen tetroxide. O2N-NO2 Vary all the N(translate group) -O(translate group)
distances simultaneously
15) Nitrogen tetroxide. O2N-NO2 Vary both the O (rotate group)-N(fixed)-O (rotate group)
angles simultaneously
16) Allene. H2C=C=CH2 Vary both of the C(translate group) -C(translate group) distances
simultaneously
17) Allene. H2C=C=CH2 Vary both of the H(rotate group)-C(fixed)-H (rotate group) angles
simultaneously

By doing a calculation as described above obtain the energy of your molecule. Record the energy to
four positions after the decimal point. Systematically vary the geometric parameters specified for
your molecule (equivalent bond lengths and/or bond angles should all be varied at the
same time). Vary the geometric parameters both above and below those supplied by the
program as an initial guess. The “best” geometry will be the one which produces the
lowest (most negative) energy. You should vary the bond angles in steps of three
degrees and the bond lengths in steps of 0.05 angstrom being sure that you have found a
minimum in the energy for the bond length or bond angle you are changing.
 Sketch your molecule and show all geometic data.
You will have to use the Inquire tool to "measure" the molecule.

Estimate the best energy (most negative) for your

molecule. You will need to plot how your calculated
energies depend on the geometric parameter you
optimized.

Energy ___________________________

A.3 Automated prediction of Molecular Geometry. Again set up the GaussView program to
calculate the molecule(s) you investigated in the previous section. All the parameters you enter
should be the same as earlier except that you should choose “Optimize” in the Job Type panel of the
Gaussian Calculation Setup window. The program will now predict the best geometry for you
without your having to individually vary the bond lengths or bond angles. Compare the automated
results to those which you obtained.

Sketch your optimized molecule and show all geometic data.

You will have to use the Inquire tool to "measure" the molecule.

Report the Energy for the optimized structure.

Energy ___________________________
B. Rotational Barriers.
 In this section you will calculate the rotational energy curve for one or more molecules. As
an example the calculations are now described for butane. The other molecules are done
similarly.
 Butane is constructed in the MSW. First methane is brought into the GaussView window
and then copied by a click into the MSW. Check that the C of the methane as displayed in
the GaussView window is the Hot atom. Click on a hydrogen in the MSW to construct
ethane, click on a methyl hydrogen to build propane and then again to build butane. The
butane in the MSW will be staggered. Verify this by rotating the molecule in the MSW and
examining it carefully. Be sure that the methyl groups are anti to each other. This is the 180
degree conformation. If they are not anti you may make them anti by clicking on
the Modify Dihedral button, clicking carbon atoms C1, C2, C3, and C4 in that
order, and entering 180 in the panel that appears. Be sure that “Rotate Group” is
selected for Atoms 1 and 4.
 Run the calculation being sure that “Energy” is selected in the Job Type panel of the
Gaussian Calculation Setup window. You will obtain the energy for the conformation
displayed in the MSW. Click on the Modify Dihedral button to modify the dihedral angle.
Now click on the atoms C1, C2, C3, and C4 in that order. A panel appears and allows you to
rotate around the C2-C3 bond. Be sure that “Rotate Group” is selected for Atoms 1 and 4.
Change the angle by 30 degrees and calculate and record the energy for each conformation
that you have produced. Repeat the process until the full rotation of 0 to 180 and 0 to -180
degrees is accomplished. For each conformation record the energy to four decimal positions.
After leaving the computational laboratory use Excel to make a plot of energy vs. angle of
rotation. Be sure that the conformations are clearly indicated on your plot. On your plot
indicate the geometry of the zero degree conformation and the direction of rotation

Following the directions of your laboratory instructor select one or more of the following molecules,
define the starting conformation and record it on the Newman projection template below. Indicate
the direction of rotation.

Obtain, as described above, the energy curve for rotation about the indicated bond.
1) butane (C2-C3)
2) 2-fluoro-3-methyl butane (C2-C3)
3) 1-fluoro butane (C2-C3)
4) 2-fluoro butane (C2-C3)
5) hydrogen peroxide (O-O)
6) Methyl hydroperoxide, CH3OOH (O-O)
7) 1,4-difluoro butane (C2-C3)
8) Hydrazine, H2N-NH2 (N-N)
9) 1-fluoro-3-chloro-propane (C1-C2)
10) 2,3-dimethyl butane (C2-C3)
11) 2-methyl butane (C2-C3)
-150 -120 -90 -60 -30 0

30 60 90 120 150 180

C. Charge Distribution.
The Gaussian program is capable of estimating the charge on each atom in a molecule. In this
section you will look at how charges are distributed in molecules and ions. In particular, you will
investigate how introducing a new group such as a halogen, nitro group, or OH group will change
the charge distribution. The approach will be to calculate a reference molecule, make a change in the
molecular structure, perform another calculation and observe the change.

Alkyl Halides.

C.1 1-fluorobutane Calculate the butane molecule in the default geometry. Display and
record the charges on the carbon atoms. Using the Periodic Table tool select a fluorine atom
and replace a hydrogen atom with the fluorine, making 1-fluoro butane. Improve the structure
using the Cleaning tool. Run the calculations and record the charges.
C1 C2 C3 C4
butane

1-fluoro butane

Change caused
by introduction
of F

C.2 2-fluoro butane Repeat the process above for 2-fluorobutane

C1 C2 C3 C4
butane

2-fluoro butane

Change caused
by introduction
of F
 C.3 Multiple halogention. Perform calculations on methane, fluoro methane, difluoro
methane, trifluoromethane, and tetraflurormethane. After introducing each fluorine use the
Cleaning tool. Obtain the dipole moments and record them below. Indicate the charge next to
each atom (two decimal positions). Compare the dipoles of CH3F and CHF3. Are these as
expected on the basis of bond dipole considerations? Explain
H F F F
H

H H H F
F
H H H H F H F F
F F

C.4 Nitro methane. Specify Optimization as the Job Type and perform calculations on CH4,
CH3-, CH3NO2, and CH2NO2-. Be sure to specify the molecular charge as -1 for anions in the
Method tab of the Gaussian Calculation Setup dialog. Record the charges and calculated
energies below. When using the nitro group be sure to initialize your geometry similar to those
below. Which do you expect to be more acidic, methane or nitromethane? Explain.
H H

H H H H
H H H H N H N H
O O
O O

Energy

Energy differences _________ ____________

 C.5 Delocalization of Charge (Phenol). Choose Optimization as the Job Type and obtain the
charge distributions in the following molecules and ions. Record your results on the diagrams
in the spaces provided. Does the presence of the NO2 group increase or decrease the ease of
ionization of the phenol. Explain.

OH O-

overall charge zero overall charge -1

Energies ______________ ______________

Energy Difference _____________

OH O-

N N
O O O O

overall charge zero overall charge -1

Energies ______________ ______________

Energy Difference _____________

 C.6 Delocalization of Charge (Toluene). Choose Optimization as the Job Type and obtain
the charge distributions in the following molecules and ions. Record your results on the
diagrams in the spaces provided. Does the presence of the NH2 group increase or decrease the
ease of ionization of the toluene molecule?
CH3 CH2+

overall charge zero overall charge +1

Energies ______________ ______________

Energy Difference _____________

CH3 CH2+

N N
H H H H

overall charge zero overall charge +1

Energies ______________ ______________

Energy Difference _____________

D Carbocation stability. A number of reactions are thought to involve carbocations, positive ions
derived from alkanes, as intermediates. An example is the addition of HBr to but-2-ene.

+ Br
H3C H H - Br H H
H3C H H3C H
C C
C C C C
H CH3
H CH3 H CH3
Br
but-2-ene carbocation alkyl bromide
In some cases, more than one carbocation may be formed leading to different ultimate products. An
example is the addition of HBr to 2-methylbut-2-ene which can produce two carbocations and two
products as shown.
H
-B
r

We investigate which carbocation and, thus, which product might be preferred simply by calculating
the stabilities of the various carbocations derived from the 2-methylbutane skeleton.

1. Assemble the 2-methylbutane molecule in the MSW.

2. Execute an “Optimization” calculation on the molecule. Be sure the charge is set
to zero and the spin state is “singlet”.
3. Record the energy and the charges on the carbon atoms below.
Energy

Next we generate various carbocations by removing a hydrogen and setting the charge to
+1.
1. Remove a hydrogen atom from a carbon atom in the molecule with the Delete
Atom tool. This is where the positive charge will be located
2. Perform a “Optimization” calculation (set the charge to 1 and spin state to
singlet).
3. Record the energy and charges from the calculation below.
4. Restore the hydrogen to the carbon in the molecule from which you removed it
earlier using the Add Valence tool.
5. Repeat the process above, removing (and restoring) an H atom from a different carbon atom.

a primary carbocation
Energies

a secondary carbocation

The Gaussian calculations are now complete. The rest of this section should be completed away
from the laboratory.

Find the most negative (most stable) of the carbocation energies above; subtract it from each of the
entries above for carbocation energies to obtain the relative energies of the four different
carbocations and record the relative energies of carbocations located at each site below.

Similarly, obtain the changes in atomic charge at each carbon atom when a carbocation is generated
at that carbon atom by comparing the charges on each carbocation center with the corresponding
atom in the neutral 2-methylbutane.
Changes in charge caused by generation of a carbocation at each site.

Correlate relative energy of a carbocation at a carbon atom with the change in charge produced at the
carbon atom. Further, classify with respect to primary, secondary and tertiary sites.

Finally, by considering the energies of the possible intermediate carbocations predict the products
for addition of HBr to each of the alkenes below.