Computational Methods in Organic Chemistry

Computational Methods in Organic Chemistry
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Introduction
Traditionally, chemistry is an experimental science: we know what we know about atoms and molecules
because of careful and clever experiments done in the laboratory. As computing power has increased,
however, the ability to model and predict the behavior of atoms in silico has also increased.
Computational chemical methods are now more accessible and can complement our endeavors in the
laboratory by graphically and quantitatively illustrating atomic level phenomena. This point was made
strongly in 1997, when John Pople and Walter Kohn were awarded the Noble Prize in Chemistry for their
contributions to the development of computational methods in chemistry. Used properly,
computational methods can accelerate our understanding of molecular systems.
There are several computational packages available, but for this lab we will use MOPAC. MOPAC stands
for Molecular Orbital PACage that has been developed to model small organic and inorganic molecules
like the ones we will study in this course.
There are two fundamental aspects to all computational packages: using accurate mathematical models
of the hydrogen-like atomic orbitals (e.g., 1s, 2s, 2p, etc.), and making accurate approximations of the
electron-electron repulsions in many electron systems. (Recall that any atom with two or more electrons
is considered a many-electron system.) The models used to approximate atomic orbitals are called basis
sets, and the electron-electron approximations are called computational methods.
Basis sets—mathematical models of atomic orbitals—are needed because electrons are not localized
particles in space, but are waves distributed over a volume of space. While this makes it impossible to
know the exact location and energy of an electron (the Heisenberg Uncertainty Principle), the behavior
of electrons can accurately approximated using the atomic orbital concept. A wave function is a
mathematical approximation of an atomic orbital. In this lab, we will use the basis set in the AM1 theory
package. This provides a good trade off of minimizing computational time and expense, while producing
reasonable accurate predictions of molecular properties.
While basis sets deal with the (approximate) location of electrons in an atom, computational methods
deal with the electrostatic attractions between the nucleus and the electrons, and the repulsions
between electrons. Because the location of an electron cannot be known exactly, it is impossible to
calculate exactly these energies. This, therefore, makes it impossible to exactly calculate the energies of
atoms and molecules. None-the-less, with the increases in computing power over the last decade, these
calculations can be done with enough accuracy to accurately predict the chemical and physical behavior
of moderately complex chemical systems. In this lab, we will use a semi-empirical method in the AM1
theory package. This method (and all semi-empirical methods) makes approximations about the
properties of electrons from laboratory observations. Semi-empirical methods work well for small
molecule and do not demand a lot of computational time and money.
Another method is ab initio, which calculates all atomic parameters without any empirical input. This
method is more time consuming and expensive, but useful for systems with very little empirical
information.
Computational Methods in Organic Chemistry
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Overview of the Lab
In this lab, you will do several types of calculations, with the expectation that you will learn enough in
lab time to continue doing explorations and work outside of class.
Geometry Optimization
This is the first step of any computation, since more complicated calculations rely on accurate
interatomic distances. Geometry optimization gives information about bond lengths, bond order, bond
angles, and molecular geometries. During this lab, you will need to do a geometry optimization on
each molecule you build before you do more complicated calculations. You will practice on ammonia
and borane, two inorganic molecules you should be familiar with.
Rotational Energies
One property of carbon-carbon single bonds is free rotation, which leads to rotational isomers. The
computational package will be used to produce animations of the rotations in the simple systems of
ethane and 1,2-dichloroethane. The relative energies of these rotational isomers will also be calculated
and compared to experimental measurements.
Vibrational Motions
All molecules are constantly vibrating along their chemical bonds. These vibrations can be predicted by
considering the geometry and energy of a molecule, two properties that can be accurately calculated.
The computational package will be used to produce animations of the vibrations in water and
formaldehyde.
Molecular Orbital Calculations
Calculations of the molecular orbitals allow you to view electrostatic potential surface, which is the
distribution of positive and negative charge across the surface of a molecule. Visualizing this is a key
aspect of predicting the reactive site on atoms and in chemical bonds. The first calculation will be done
on water, a very familiar molecule. Calculations on two fundamental organic species, ethene and
benzene, will also be done.
Procedure
These directions assume no prior knowledge of the WebMO interface and begin with detailed, click by
click instructions on building molecules and setting up calculations. As the lab progresses, fewer
directions are given.
NOTE: You must use Internet Explorer, or a browser that allows Java to run. Chrome does not work.
Begin by logging in to the Cabrillo College WebMO:. http://butane.cabrillo.edu/
At the bottom of the page you will see a link to Truman College.
Your username is the same as your CCC email username (do not include @student.ccc.edu)
Your password is initially set to be “orgo”
Computational Methods in Organic Chemistry
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Geometry Optimization of Ammonia and Borane
A. Ammonia (NH3)
 Click “New Job”. A small window opens where you build molecules.
At this point, the browser may “hang” or crash if Java is not working properly. Each time you start the
browser, you will have to “authorize” Java., Look around for a dialog box. You might have to click on the
following icon at the bottom of the screen to find the dialog box
Make sure to check “Do not show this again for apps from the publisher and location above”
 Click on the Periodic Table icon (5th down the left side). Choose “N” by clicking on it.
 Click once in the center of the workspace. A blue nitrogen atom appears.
(If you click too many times and have extra atoms, choose Edit > Undo.)
 From the menu bar, choose Clean-Up > Comprehensive – Mechanics. WebMO will add three
hydrogen atoms and you should now have a molecule of ammonia. (There is a small wrench icon
on the left hand menu. Clicking it will also perform a Comprehensive – Mechanics Clean-Up.
 Experiment with the Rotate, Translate, and Zoom tools (The top 3 icons on left side).
Does the molecule have the shape you expect?
 Click the blue arrow in the bottom right corner of the screen. If you get a question box asking
you to “symmetrize”, answer no.
 In the Job Options window, choose the following parameters:
o Job Name: NH3 AM1 geometry
o Calculation: Geometry Optimization
o Theory: AM1
o Charge: 0
o Multiplicity: Singlet (Singlet means all of the electrons in the molecule are paired—
either in a chemical bond or a lone pair.)
 Click the blue arrow in the bottom right corner of the screen to begin your calculation. After
about 5 seconds, hit the “refresh” button.
Your job should be complete in 10 seconds or less. If it takes longer, something is wrong!
To kill or stop the job, click on the red “X” under Actions on the right side.
To see the results of your calculations:
 Click on the name of your job. This will open the view screen.
 Choose the “select arrow”, which is the 4th icon down on the left.
 Click on the nitrogen atom. The hybridization and charge should be displayed in the bottom left
corner of the screen.
Does the atom have the hybridization you expect?
 Next, shift and click on a hydrogen atom. (The shift is necessary to keep the nitrogen atom
selected.) A bond length will be displayed in the bottom left corner of the screen. (Where the
hybridization was displayed before.) Note the number of the hydrogen atom, and record the
bond length in the table below. Check the other N-H bond lengths and calculate the average.
The experimental bond length is 1.01 A. Calculate the percent error in your calculated value.
Enter these values in the data sheet to be turned in.
 Check the bond angle by shift clicking on a hydrogen atom, the central nitrogen atom, and
another hydrogen atom. (Remember, it takes three atoms to make a bond angle.) A bond angle
Computational Methods in Organic Chemistry
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will be displayed in the bottom left corner of the screen. Note the number of the hydrogen
atoms, and record the bond angle in the table below. Check the other H-N-H bond angles and
calculate the average. The experimental bond angle is 107o
. Calculate the percent error in your
calculated value. (Note that if you do not click the atoms in the proper order, you will get very
weird bond angles.)
 Scroll down and review the information under Calculated Quantities.
 Next to “dipole moment”, click the small magnifying glass to see the molecular dipole.
Does the result match your expectations?
 Look at the “partial charges” table. Which atoms have a negative charge and which have a
positive charge?
Does the result match your expectations?
 Look at the “bond order” matrix. The first column show the bond order between in each of the
N-H bonds
Does the result match your expectations?
You are finished with the ammonia calculations.
B. Borane (BH3)
Build and optimize borane using a similar procedure. To begin a new job, click on the job manager
link on the left hand side of the screen, and select “New Job” from the top menu.
Rotational Energy Calculations of Ethane and Butane
C. Ethane
 Build and optimize the geometry of ethane using the MOPAC package and the AM1 theory.
 After the geometry optimization calculation is complete, open the job and select New Job Using
This Geometry in the build window.
 Open Tools > Edit Z-matrix. Edit it as shown in the graphic on the next page.
Computational Methods in Organic Chemistry
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 Do a second calculation using the parameters below:
o Job Name: C2H6 AM1 scan
o Calculation: Coordinate Scan
o Theory: AM1
o Charge: 0
o Multiplicity: Singlet
 Rotate the ethane molecule to look down the C-C bond axis. The hydrogens should be in a
staggered conformation (gauche).
 Scroll down and review the information under Calculated Quantities. In the Coordinate Scans
table, click the small film strip. The ethane molecule will start to rotate around the C—C bond. In
the lower left corner of the window, the calculated energy will be displayed for each step of the
rotation.
 In the Coordinate Scans table, click the small magnifying glass. The rotational energy plot will be
displayed. Calculate the energy different between the highest and lowest point. The units are
kcal/mol.
 The experimental value for this is 3 kcal/mol. Calculate the percent error.
You are finished with the ethane calculations.
D. 1,2-dichloroethane
 Build and optimize the geometry of 1,2-dichloroethane using the MOPAC package and the AM1
theory.
 After the geometry optimization calculation is complete, open the job and select New Job Using
This Geometry in the build window.
 Open Tools > Edit Z-matrix. In the z-matrix:
Computational Methods in Organic Chemistry
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o Locate the row that connects the Cl-C-C-Cl backbone. (It may help to look at the
numbers of the atoms in the build window.) In the pull-down menu on the far right side,
set this parameter to “S”. (This stands for scan.)
o Use the same Start, Stop, and # Steps as in the prior example.
o Close the Z-matrix
 Do a second calculation using the parameters below:
o Job Name: C2H4Cl2 AM1 scan
o Calculation: Coordinate Scan
o Theory: AM1
o Charge: 0
o Multiplicity: Singlet
 Rotate the 1,2-dichloroethane molecule to look down the C-C bond axis. The chloro groups
should be in a staggered conformation (gauche).
 Scroll down and review the information under Calculated Quantities. In the Coordinate Scans
table, click the small film strip. The ethane molecule will start to rotate around the C—C bond. In
the lower left corner of the window, the calculated energy will be displayed.
 In the Coordinate Scans table, click the small magnifying glass. The rotational energy plot will be
displayed. Calculate the energy different between the highest and lowest point. The units are
kcal/mol. You are finished with the 1,2-dichloroethane calculations.
Computational Methods in Organic Chemistry
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Vibrational Spectroscopy Calculations of Water and Formaldehyde
E. Water
 Build and optimize the geometry of water using the MOPAC package and the AM1 theory.
 After the geometry optimization calculation is complete, open the job and select New Job Using
This Geometry in the build window.
 Do a second calculation using the parameters below:
o Job Name: H2O AM1 vibrations
o Calculation: Vibrational Frequencies
o Theory: AM1
o Charge: 0
o Multiplicity: Singlet
 Scroll down and review the information under Calculated Quantities.
 In the Vibrational Modes table, click the small magnifying glass next to the first entry (mode 1).
Next, click the small film strip. (Just to the right of the magnifying glass.) This opens an animation of
the “scissoring” mode of water.
 Click the small magnifying glass next to the second entry (mode 2). Next, click the small film strip.
(Just to the right of the magnifying glass.) This opens an animation of the “asymmetrical stretching”
mode of water.
 Click the small magnifying glass next to the third entry (mode 3). Next, click the small film strip. (Just
to the right of the magnifying glass.) This opens an animation of the “symmetrical stretching” mode
of water.
Molecular Orbital Calculations of Water and Ethene
A. Water
 Build and optimize the geometry of water using the MOPAC package and the AM1 theory.
 After the geometry optimization calculation is complete, open the job and select New Job Using
This Geometry in the build window.
 Click the blue arrow in the bottom right corner of the screen. If you get a question box asking
you to “symmetrize”, answer no.
 From the list of Computational Engines, chose MOPAC (almost half way down the list).
 In the Job Options window, choose the following parameters:
o Job Name: H2O AM1 orbitals
o Calculation: Molecular Orbitals
o Theory: AM1
o Charge: 0
o Multiplicity: Singlet
Click the blue arrow in the bottom right corner of the screen to begin your calculation. After
about 5 seconds, hit the “refresh” button.
Your job should be complete in 10 seconds or less. If it takes longer, something is wrong!
To kill or stop the job, click on the red “X” under Actions on the right side.
 Scroll down and review the information under Calculated Quantities.
 In the Molecular Orbitals table, click the small magnifying glass next to “electrostatic potential”.
This will open an electron potential map of your molecule. To see the ball and stick structure
under the electrostatic cloud, open the View menu, and select Opacity >Transparent.
Remember:
 Red is negative
Computational Methods in Organic Chemistry
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 Green is neutral
 Blue is positive
 Rotate the molecule to view the full electrostatic potential surface. Where is the primary
concentration of negative charge? Where is the primary concentration of positive charge?
Does the result match your expectations? Does the electrostatic potential surface match the
values in the Partial Charges table?
You are finished with the water calculations.
Computational Methods DATA Sheet NAME _____________________
1
A. Ammonia
Bond Bond Length (A)
N-H2
N-H3
N-H4
Average
Bond Bond Angle
H2-N-H3
H2-N-H4
H3-N-H4
Average
 Dipole moment – Does the result match your expectations?
 Look at the “partial charges” table. Which atoms have a negative charge and which have a
positive charge? Does the result match your expectations?
 Look at the “bond order” matrix. The first column show the bond order between in each of the
N-H bonds. Does the result match your expectations?
B. Borane (BH3)
a. Measure bond lengths and angles, dipole moment, partial charges, and bond order, record
as above for ammonia
Computational Methods DATA Sheet NAME _____________________
2
C. Ethane
 In the Coordinate Scans table, click the small magnifying glass. The rotational energy plot will be
displayed. Calculate the energy difference between the highest and lowest point. The units are
kcal/mol.
High Energy Low Energy Difference
 The experimental value for this is 3 kcal/mol. Calculate the percent error.
D. 1,2-dichloroethane
 In the Coordinate Scans table, click the small magnifying glass. The rotational energy plot will be
displayed. Calculate the energy difference between the highest and lowest point. The units are
kcal/mol.
High Energy Low Energy Difference
E. Water vibrational motions (No data to enter here, just complete the calculation)
Molecular Orbital Calculations of Water
F. Water
 Rotate the molecule to view the full electrostatic potential surface. Where is the primary
concentration of negative charge?
 Where is the primary concentration of positive charge?
 Does the result match your expectations? Does the electrostatic potential surface match the
values in the Partial Charges table?
You are finished with the water calculations.

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