COMPUTATIONAL STUDY OF IODINE CONTAINING REAGENTS AND
INTERMEDIATES OF THE CLOCK REACTION
All Spartan files and recorded data should be attached to an ELN page titled “Computational
Study” in the Clock Reaction Folder.
Part A. I vs. I-, electron density
Spartan can be used to generate images (called surfaces) that represent electron density. Electron
density (|Ψ2|) is the volume of space with a 90% probability of finding an electron. These
electron density surfaces are useful representations of atomic or molecular size.
1. Express the electron configuration for “I” and “I-”. Use [Kr] to signify the inner core
electrons.
2. Build “I” in Spartan. Open Spartan and choose New from the File menu (this should open
the Builder window on the right hand side of the screen. Using the Organic builder (the
builder that is shown by default on the screen), choose –I. Click anywhere within the teal
blue screen, a purple sphere with a yellow stick (called an open valence) should appear. Go
to the Build menu and choose Delete, click on the open valence so that it disappears (the
purple sphere should still be visible).
3. Go to the Setup menu and choose Calculations. Do not change the default settings of
Equilibrium Geometry and Hartree-Fock 3-21G. Enter “1” in the Unpaired Electrons
field. Click Submit. The Save As window will open, enter a descriptive name and click
Save. Click OK for the next two windows that appear. (Depending on your computer, the
second window may appear quickly, requiring you to only click OK once.)
4. Go to the Setup menu and choose Surfaces. Click on Add. Make sure the default values
(below) are all chosen. Click OK.
Surface: density
Property: none
5. Go to the Setup menu and choose Submit. Click OK for the next two windows. Click on
the box next to density in the Surfaces window to observe the gray electron density surface.
Click on the image and the Style box in the lower right corner of the screen appear. Change
the Style from Solid to Mesh. Close this file.
6. Repeat steps 2-5 to build “I-”. Exceptions: Set Charge to Anion for I- and leave the
Unpaired Electrons at 0.
Part B. I-, atomic orbitals
Spartan can also be used to generate atomic and molecular orbital (Ψ) surfaces. In this section
you will look at the orbitals containing the valence and outer core electrons of I-. The surfaces
are labeled HOMO (highest occupied molecular orbital). “Occupied” means that the orbital is
filled with one or two electrons. “Highest” indicates that the orbital is of the highest energy that
contains the outermost electrons. If the HOMO is followed by a set of parentheses with a
minus followed by a number, the number indicates how much lower that orbital is than the
HOMO without a parentheses. The red and blue coloring indicates phase. The concept of phase
will be explained further in future assignments.
Open the “I-“ file created above.
Go to the Setup menu and choose Surfaces.
Click on Add. Choose HOMO. Click OK.
Repeat the above step for HOMO(-1), HOMO(-2), HOMO(-3), HOMO(-4), HOMO(-5),
HOMO(-6), HOMO(-7), and HOMO(-8). Close this file.
5. Create a table in the ELN and paste in each orbital in order of increasing energy. Label each
orbital with the principal quantum number (n = 1, 2, 3, et cetera) and the symbol for the
angular momentum quantum number (l = s, p, d, f). Indicate which orbitals are degenerate
(of the same energy but a different spatial orientation).
1.
2.
3.
4.
Part C. I2, different calculation methods and measuring bond lengths
The Spartan Student Edition is able to solve 5 different tasks: Energy, Equilibrium Geometry,
Equilibrium Conformer, Transition State Geometry, and Energy Profile. In this section you will
be calculating the equilibrium geometry of I2. An Equilibrium Geometry calculation results in
the lowest energy, most stable form of a molecule (the ground state). Therefore, all of the
energies, bond lengths, orbitals, et cetera are ground state quantities. They are values
comparable to those listed in tables in your textbook and other reference material. (Energy and
Energy Profile will be discussed later in this assignment. Equilibrium Conformer and Transition
State Geometry are not used in this course.)
For each task, 6 different calculation models are available in Spartan Student Edition: Molecular
Mechanics, Semi-Empirical, Hartree-Fock, B3LYP, EDF2, and MP2. (We’ll just work with the
first 3 here.) Each model is increasingly more mathematically complex and requires more
computation time. Some models do not work for every chemical system. (If you encounter such
a situation, the calculation may fail. Go to the Display menu and choose Output to find an
explanation.)
Molecular Mechanics is based on classical physics: atoms are treated as point charges and
bonds are treated as springs.
• Semi-Empirical uses a mixture of empirical data (values that have been found by
experiment) and quantum mechanics. For smaller molecules, where data for “like” systems
is known, this method gives results very close to experimental findings.
• Hartree-Fock methods are completely based on quantum mechanics. Approximations are
made so that wave functions can be solved. Basis sets, which indicate the level of
mathematical complexity used in a calculation, are indicated by the “3-21G” and “6-31G*”
suffixes.
In this section you will compare the equilibrium bond lengths for I2 calculated from the 3 models
listed above.
•
1. Build I2 in Spartan. Using the Organic builder (the builder that is shown by default on the
screen), choose –I and click on the screen. Click on the yellow open valence to add the
2.
3.
4.
5.
6.
second I. Click on the minimize button (
). (Minimizing will clean up structures,
providing a good starting guess at bond lengths (or angles for more complex molecules.)
Go to the Setup menu and choose Calculations. Leave the default setting of Equilibrium
Geometry but change Hartree-Fock 3-21G to Molecular Mechanics. Click Submit. The
Save As window will open, enter a descriptive name and click Save. Click OK for the next
two windows that appear.
Go to the Geometry menu and choose Measure Distance. Click on each “I” atom (each
will have a gray covering). Record the bond length in the bottom right corner of the screen.
Close this file.
Repeat steps 1-3 substituting Semi-Empirical for Molecular Mechanics.
Repeat steps 1-3 substituting Hartree-Fock 3-21G for Molecular Mechanics.
Repeat steps 1-3 substituting Hartree-Fock 6-31G* for Molecular Mechanics.
Part D. I3- linear vs. bent, comparing energies
In this section, the Energy task will be used to calculate the energies for different geometries
(linear or bent). The Energy task calculates the energies for the geometry provided instead a
changing bond lengths and angles to find the lowest energy arrangement for the molecule like
the Equilibrium Geometry task does.
In this section you will compare total energy values to determine the most likely structure of I3-.
Molecular stability is indicated by a low (usually negative) total energy. Therefore, the lower
(more negative) the value is, the more stable the molecule.
1. Build bent I-I-I- in Spartan. Using the Organic builder (the builder that is shown by default
on the screen), choose –I, and click on the screen. Switch to the Inorganic builder, select
, choose “I”, and then click on the yellow open valence to add the central iodide atom.
Return to the Organic builder, choose –I, and then click on the yellow open valence. Click
on the minimize button (
).
2. Go to the Setup menu and choose Calculations. Change Equilibrium Geometry to Energy
and Hartree Fock to Semi-Empirical. Change the charge to Anion. Click Submit. The
Save As window will open, enter a descriptive name and click Save. Click OK for the next
two windows that appear.
3. Go to the Display menu and choose Properties. Record the Energy (half way down the left
column). Close window.
IO3-, molecular geometry determination
Multiple Energies are calculated to create an Energy Profile. In this section, the systematic
change of a O-I-O bond angle results in 15 different atomic arrangements for the iodate ion. The
relative energy (rel. E) of each arrangement and the number of ions in each arrangement (the
Boltzmann Distribution) will be plotted as a function of bond angle. (Note: The Energy
calculation giving the highest Boltzmann distribution and the lowest relative energy is closest to
the Equilibrium Geometry of IO3-.)
1. Build IO3- with a pyramidal geometry. In the Inorganic builder, choose “I” and
click on the screen. Choose “O” and
the minimize button (
,
, then click on the three open valences. Click on
).
2. Go to the Geometry menu and choose Measure Angle. Click on any “O”, then the “I”, then
either one of the two other “O”s. Type 105 in the box that appears in the bottom right corner
of the program window and then hit “Enter”. Go to the Geometry menu and choose
Constrain Angle. Click the same 3 atoms in the same order. Click on the open lock in the
bottom right corner of the screen. When you do this, 105.00° will appear in the box just to
the left of the lock and the lock will close. Click the box next to Profile. Enter 120.00 in the
box that appears after to and change the Steps to 15.
3. Go to the Setup menu and choose Calculations. Change Equilibrium Geometry calculation
type to Energy Profile, leave the default method Hartree-Fock 3-21G. Set the Total
Charge to Anion. Click Submit. The Save As window will open, enter a descriptive name
and click Save. Click OK. The calculation will take 5-10 minutes.
4. Once the calculation completes, you will be prompted with “Your job created a new
document. Would you like to open it?” Click Yes. Click OK on the next window.
5. Go to the Display menu and choose Spreadsheet. Go to the Geometry menu and choose
Measure Angle. You must find the three atoms, that when clicked in the correct order,
measure the 105° angle. Once you have done this, click on the P next to the angle value in
the bottom right hand corner of the screen. An angle column with values should show up on
the spreadsheet. Click Add, choose rel. E. (relative energy) in the window that appears, and
then click Apply. Scroll down and click on Boltzmann Distribution. Click OK. Close the
window.
6. Go to the Display menu and choose Plots. Click on
. Choose Angle (O#,I#,O#) for the
x-axis and rel. E. and Boltzmann Distribution for the y-axis. Click Add.
7. Click on
. Enter Title for the plot and change the Range “From” field from 100 to 105.
Under the Y-Axis section choose Smooth next to Curve for both Labels (rel. E (kJ/mol) and
Boltzmann Dist). Use the
buttons in the bottom middle of the screen to change the
ion’s geometry.
8. Along with Spartan file, attach a copy of your curve with the ion in the most stable geometry
to your ELN.