Molecular Modeling Lab - Explaining Acid Strength
Dr. Greg Zimmerman, Chem. 52-116, Spring 2009
Adapted from “Getting Started with Spartan, 3rd Ed., Wavefunction Inc., 2004.
Introduction
More than one student has asked questions such as: “How did you know that was an
acid?” or “How did you know that acid X was a weak (strong) acid? You probably
received answers that amounted to “memorize this list”, or for so-called organic acids “If
you have a –COOH, the compound is an acid.” While it is good for you have memorized
the names and formulas of the strong acids so that via elimination you can know that a
given acid is strong or weak, there are molecular reasons for acids strength. The purpose
of this exercise is to use electrostatic potential maps calculated with the Spartan software
to determine relative acid strength. After using this tool, you will use the concept of
electronegativity and the fact that electron clouds (charge distributions) are skewed (not
symmetrical) in molecules.
By way of review, here is a description of these electrostatic potential maps. Imagine
taking a point positive charge and placing it at some spot near a molecule. If this positive
charge is attracted, this must be negative region since opposites attract. If the positive
charge is repelled, this must be a positive region of the molecule since like charges repel.
Now imagine that this point charge is systematically moved all around the molecule, and
at each point this attraction or repulsion is recorded. The computer can then assign
different colors to negative regions of the molecule (red) and the positive regions
(blue). Additionally, the computer uses a color scheme according to the colors of the
rainbow (ROY G BIV) to account for the charges in between the extremes. The result is
a color coded map around the molecule.
Experimental
Exercise 1: Spartan tutorial refresher
Note: Each student needs to be responsible to learn how to draw molecules in
Spartan. This may be required on the final exam.
It has been several months since you used Spartan, so a refresher is in order. (Instructors,
if you have students that did not have Chemistry 115 last semester here at BU, please pair
them with a student who did.)
After logging in to the computer assigned to you, click Start, scroll to Specialized
Software, then Spartan Student folder, and finally click on the Spartan Student V3.0.2
icon. The program should start. Click on the file menu and choose New. You should
see a window that looks like this:
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It is usually helpful to maximize the window by clicking the standard Windows button
immediately next to the red box with the white X
.
For practice, build ethane, C2H6 or better written as CH3CH3 because
this gives some structural information. Ethane can be thought of as two CH3
groups joined together, so use the same 4-pronged carbon shown to the right.
(This is commonly referred to as an sp3 carbon atom for those that were introduced to
hybridization last semester.) Choose this carbon from the organic palette and click on the
screen. Then, on one of the yellow valences, click again to put in and connect the second
CH3 group. Remember that any yellow prong that remains will automatically be changed
to a hydrogen atom when doing any calculations. To see this, click on the
across the top.
button
Now, play with your ethane molecule. Click on the
button so that you re-enter the
build mode (a. k. a. the add fragment mode). Play with your ethane molecule on the
screen using each of the commands below:
a. Make the molecule bigger by simultaneously holding down the Shift key, right
clicking and dragging the cursor (arrow) up and down. By moving the mouse away
from you, the molecule will get larger. Moving the mouse towards you makes the
molecule smaller.
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b. To move the molecule to a different part of the screen, right click on the molecule and
drag it to wherever you need to.
c. To rotate a molecule (X/Y rotate) left click on the molecule and drag the mouse.
You will be given some specific instructions in order to build some of these molecules.
While there are often several ways to build these molecules, you may encounter some
“trouble” if you do not follow these specific instructions. The reason for this is too
complicated to explain.
Before moving on to exercise 2, do two things:
1. Click the
button. This is a fast way to optimize the geometry.
2. Save this molecule with the file name ethane and nitric acid.
Exercise 2 – Finding an “Acidic” or “Ionizable” Hydrogen atom on a Molecule
No one ever considers ethane to be an acid. By comparing it to something known to be
an acid will give us a method that will enable you to determine relative acid strength.
In the file ethane and nitric acid you should already have
built ethane. Open this file if needed. Now you need to build
nitric acid, but make sure that
you build it in the same
document. This requires using
the New Molecule command
under the File menu shown at
the left. If you choose New
instead you will encounter
trouble and make life more
difficult for yourself.
There is a fast way to build
nitric acid, which will be
useful when building some
other molecules in this
exercise. With the organic palette showing, click on
“Groups” and choose “Nitro”. These are ready-made
molecule fragments that occur in many molecules (and they
already have included resonance). Click on the building field
and the nitro group appears. Finish the nitric acid molecule
by choosing a “bent” O atom and adding it to the open
nitrogen valence. The H atom will be added automatically to
the only open valence.
The next step is to calculate the electrostatic potential map
for both molecules. Bring up the Calculations dialog box
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which is found uner the Setup drag-down menu. Specify calculation of equilibrium
geometry using the Hartree-Fock/6-31G* model. (Hartree and Fock are the last names of
the scientists who came up with this method.) Click on OK. Bring up the Surfaces
dialog under the Setup draw-down menu. and click on Add… (at the bottom of the
dialog). Select density from the Surface menu and potential for the Property menu in
the Add Surface dialog which appears. Click on OK. Leave the Surfaces dialog on
screen. Save the file and submit the calculation (under the Setup menu).
When the calculation is completed, bring up the spreadsheet (found under the Display
menu) and check the box immediately to the right of the molecule label for both entries.
Both molecules will now be displayed simultaneously on screen. Select (uncheck)
Coupled from the Model menu so that they may be independently manipulated, and
arrange on screen such that the H atom on nitric acid is visible.
Click and “check” the box inside the Surfaces dialog. Electrostatic potential maps for
both molecules will be displayed.
The color scale needs to be made the same for both molecules. (Recall that this surface
mapping ability is similar to a globe of the earth that has colors representing elevation:
green might represent sea level with yellow meaning higher elevations, with brown
representing the high mountains.) To do this, select Properties (Display menu) and click
on one of the colored maps. You should see a dialog box that looks like:
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If you see a different box, click on the molecule again. Click in the red end of the
Property Range, type 0.0 and hit enter. The number should change to 0. Click in the
“blue” end of the Property Range, type 90 and hit enter. This effectively sets both
molecules to the same color code, so valid comparisons can be made.
?1. What is different about the color maps between these two molecules?
?2. What does the color “blue” mean on these maps?
Considering that one simple definition of an acid is “a substance that produces H+ in
water” we could say that nitric acid is “closer” to producing an H+ than ethane is. The
fact of the matter is that ethane is so far from producing H+ that it is not considered an
acid, solubility issues aside. An oft stated phrase to describe this is that substances such
as ethane (and methane, propane ….) do not have ionizable hydrogen atoms.
Does this mean that any blue region in the vicinity of a hydrogen atom indicates an
ionizable hydrogen? NO! In order for a hydrogen to be acidic, it must be “positive
enough” to be pulled away by solvent molecules (for our purposes water). If you were to
include in the calculation ethanol (CH3CH2OH) there would be a very light blue region in
the vicinity of the hydrogen atom on the H atom connected to the oxygen atom. This H
atom however, is not “positive enough” to be an ionizable hydrogen.
We now have at least a “recipe” to determine acid strength, but the real reason why nitric
acid now needs to be deduced.
?3. Considering electronegativity, propose in your notebook, a reason why the H-atom on
nitric acid is ionizable.
The general guidelines for the rest of the procedure all follow the same pattern:
Build the sets of molecules all in the same document using New Molecule. Set up the
calculation that is specified (which may be semi-empirical, Hartree-Fock 3-21 or HartreeFock/6-31G*) and the electrostatic potential map. Save the file and submit the
calculation. Uncouple the molecules and then check the Surfaces box to show the
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electrostatic potential map. Open the Properties dialog box and click on one of the
surfaces. Change the color scale to what is specified. Answer the questions in your
notebook for each set.
Acid Set 1
Build HOF and HOCl in the same document (use New Molecule again) using the Organic
palette. Save the file as hypohalous acids. Calculate the electrostatic potential surface
using the semiempirical method. Once you have set the color scales for both molecule to
0 for red and 50 for blue, answer the questions in your notebook.
?4. Which is has the bluest region in the vicinity of the H-atom?
?5. Which is therefore the strongest acid?
?6. Propose a reason for why one acid is stronger than the other. (Hint: Focus on the
atoms that are different.)
Acid Set 2
Build sulfuric acid as follows. Select Sulfone from the Groups menu on the Organic
palette and click anywhere on the screen. Add “bent” oxygen atoms to both free valences
on the sulfur atom. Select New Molecule (as before) and build sulfurous acid. This is
most easily done by building sulfuric acid as just done. Now, click on the delete button
, and click on one of the double-bonded oxygen atoms and valences to remove it.
Click on the
anything.
button to get back to build mode so you don’t accidentally delete
Save the file as sulfuric and sulfurous acids. Calculate the electrostatic potential surface
using the Hartree-Fock/6-31G* method. Once you have set the color scales for both
molecule to 0 for red and 70 for blue, answer these questions in your notebook:
?7. Which is has the bluest region in the vicinity of the H-atom?
?8. Which is therefore the strongest acid?
?9. Propose a reason for why one acid is stronger than the other. (Hint: Focus on how
these two molecules are different.)
Acid Set 3
Build acetic (CH3COOH) , monochloroacetic (CClH2COOH), dichloroacetic
(CHCl2COOH) and trichloroacetic (CCl3COOH) acids in the same document (use New
Molecule again) using the Organic palette. It is fastest to use the carboxylic acid in the
group menu, add an sp3 carbon , and finally add Cl atoms as needed. Save the file
as chloroacetic acids. Calculate the electrostatic potential surface using the
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Hartree-Fock/6-31G* method. Once you have set the color scales for these molecule to 0
for red and 80 for blue, answer these questions in your notebook:
?10. List these acids in order of most blue to least blue regions in the vicinity of the Hatom.
?11. List these acids in order of strongest to weakest.
?12. Propose a reason for why the acid strength changes. (Hint: Focus on how this set
of molecules gradually becomes different.)
Post-Lab Exercise
1. Check your answers with your instructor. Make sure you understand how to tell
which acid is stronger than another as well as the reasons.
2. Prepare yourself for a quiz to be taken before the end of the lab period without your
notebook. When you believe that you are ready, (or 20 minutes before the period
ends), get the quiz from your instructor and complete it. There will be no report for
you to turn in.
Final-Note
Make sure that you review this material for all exams and quizzes in the lecture portion of
the course.
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