Fall Organic Chemistry Experiment #8
Molecular Modeling, Part 2
Introduction
This week you will continue to explore the power of computer-assisted molecular
modeling using Spartan02. In particular, you will be interested in developing a better
understanding of the ability of molecular models illustrate acid-base concepts, conjugation, and
aromaticity.
Prelaboratory Preparation
Part 1: Draw each of the compounds that you'll be asked to model and look up/record the pKa
value for the most acidic hydrogen in each molecule (this may require some investigating on your
part -- plenty of organic chemistry textbooks available in S303 -- I suggest Fox and Whitesell,
pages 305-307 or Bruice, Appendix pages A-8 to A-9).
Part 2: Draw a series resonance structures for each of the compounds that you'll be asked to
model.
Part 3: Read Sections 11.4-11.6 of your Jones text. Define the term conjugation and list some of
the unusual properties exhibited by these systems.
Part 4: Read Sections 11.5 and 12.4 of your Jones text, paying particularly close attention to
Figure 12.14 on page 536. Using this as a model, draw the structures of all of the compounds you
will be modeling and try to predict the DHrxn for the hydrogenation.
Procedure
Part 1: Acidity within a series of compounds
The acidity of a compound is typically measured by its pKa value. As we've seen in class, the
smaller the value of the pKa, the more acidic that particular hydrogen will be. A number of
factors are involved in determining the acidity of the hydrogen atom. However, it should be
obvious that as we increase the positive charge character around a hydrogen atom, the more likely
it is that the hydrogen can be donated (and, therefore, the more acidic that hydrogen is). The
most effective way to view charge distribution is through an electrostatic potential map. That is
exactly what you'll be doing in this part of the experiment.
(1) Build ethane, ethylene, acetylene and minimize using the AM1 (semi-empirical method).
Submit for electron density (surface) with an electrostatic potential (property) mapped on it.
Display all three maps and record the most positive value for potential at each hydrogen.
(2) Build acetic acid, trifluoroacetic acid, and tricholoracetic acid and repeat the procedure as
above.
(3) Build butanoic acid, 2-fluorobutanoic acid, and 3-fluorobutanoic acid and repeat the
procedure as above.
(4) Build benzoic acid, cyclohexanol, and phenol and repeat the procedure as above.
(5) Build the conjugate bases of the compounds in (4) (following loss of the hydrogen atom) and
repeat the procedure as above. This time record the most NEGATIVE value for potential and its
location.
Part 2: Density-LUMO maps as a method for predicting electrophilic sites
We have observed that the carbonyl group consists of a carbon-oxygen double bond in which the
electrons are shared unequally between the two bonding partners. As a result, the carbon carries a
slight positive charge, while the oxygen is slightly negative. From this, we should predict that
electrophilic reagents (+) should be attracted to the carbonyl oxygen and that nucleophilic
reagents (-) should attack the carbonyl carbon. So, if we react 2-butanone with NaCN, we should
expect that the CN anion (NUC) will attack the carbonyl carbon (E). According to frontier
molecular orbital theory, the nucleophile (or Lewis base) must donate its electrons to an empty
orbital of the carbonyl. Your job is to figure out which orbital of the carbonyl will most likely
accept this electron pair from CN and to locate the precise location of attack.
(1) Build 2- butanone and submit for geometry optimization at the AM1 level. Be sure to also
select LUMO (surface) and LUMO (property) mapped onto a density surface. View the LUMO
and record observations.
(2) Build cyclohexenone and repeat the protocol as above.
(3) Build norbornanone and repeat as above.
Part 3: HOMO and LUMO observations in conjugated systems
As our network of pi bonds becomes more extended in conjugated systems, we expect to observe
changes in the shapes and energies of the HOMOs and LUMOs. Molecular modeling is
especially useful in helping us to visualize this important change. Let's check it out.
(1) Build propene, 1,4-hexadiene, 1,3-hexadiene, and 1,3,5-hexatriene and perform geometry
optimizations at the AM1 level. Be sure to also select LUMO (surface), LUMO (property)
mapped onto a density surface, and electrostatic potential (property) mapped onto a density
surface. Measure bond lengths throughout each molecule and compare with "normal" C-C and
C=C derived from propene (model system). View HOMO, LUMO, and electrostatic potential
maps noting any differences among the set of molecules. HOMO-1, LUMO+1, etc.????
Part 4: Conjugation, resonance, and aromaticity
Conjugated systems tend to exhibit different properties than their non-conjugated counterparts -see Sections 11.5, 11.6, 12.3, and 12.4 in your Jones text. For example, conjugated systems are
typically characterized by an unusual energetic stability. In order to observe this effect, it is
customary to consider the change in energy that occurs when unsaturated systems are reacted
with H2 (a process called hydrogenation -- see reaction below).
We would naturally predict that each time we react a C=C double bond, it should release the
same amount of energy (in comparison with ethylene as a standard). Therefore, if ethylene
releases X amount of energy, then a diene (containing 2 C=C) should release 2X amount of
energy. However, this rule does not hold for conjugated systems. Because of their unusual
stability, they actually release a lower amount of energy than expected. This resonance energy
stabilization is especially evident in aromatic systems. Let's collect some data and see the effect.
(1) Build H2, hexane, 1-hexene, 1,2-hexadiene, 1,3-hexadiene, 1,4-hexadiene, and 1,3,5hexatriene and perform Hartree-Fock 3-21g* geometry optimizations starting from the AM1
geometry. This means you'll have to first perform a geometry optimization at the AM1 level.
Record energy values for each molecule.
(2) Build H2, cyclohexane, cyclohexene, 1,3-cyclohexadiene, and benzene. Perform HartreeFock 3-21g* geometry optimizations starting from the AM1 geometry. Record energy values for
each molecule.