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Molecular Orbital Animations for Organic Chemistry W

Steven A. Fleming,* Greg R. Hart, and Paul B. Savage**
Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602-5700
*steve_fleming@byu.edu; **paul_savage@byu.edu

There are several approaches to teaching organic chem-
istry (1), and a current trend is presentation of the various
subjects (alkanes, alkenes, ketones, etc.) with a theme. Students
benefit when they can find a common element that ties the
subject matter together. One such theme for organic chem-
istry is the use of electrophile + nucleophile for the description
of organic reactions. We have also found that students can
understand simple molecular orbital explanations of electrophile
and nucleophile. In this paper we describe our teaching meth-
ods, including an animation package that we have developed,
which build upon a fundamental understanding of molecular
orbital (MO) interactions.
Background
Use of electrophilic and nucleophilic molecular properties
to understand and predict organic reactions is not a new
approach to teaching mechanistic organic chemistry (2). It
is well understood that electrophiles are Lewis acids that are
characterized by a positive or partial positive charge and
nucleophiles are Lewis bases because they have an available
pair of electrons. Chemical reactivity then can usually be
represented as a nucleophile (negative character) attacking an
electrophile (positive character). Most organic chemistry text-
books treat this subject well and there appears to be increasing
attention given to this logical approach to understanding
chemical reactions (3). Typically, the reactions are shown using
an electron-flow formalism, which is sometimes referred to
as “arrow pushing”. This Lewis dot approach effectively
describes some aspects of reaction mechanisms but does not
provide a realistic picture of electron flow between molecular
orbitals.
Few organic texts have taken the next step of analysis
(MO interactions), which allows the students to consider
“why” a molecule is a nucleophile or electrophile (4 ). Use of
molecular orbitals can be very instructive (5). The basic
concept is that an electrophile has an energetically low-lying
empty MO, which is referred to as the lowest unoccupied
molecular orbital (LUMO). It is precisely an empty orbital
that can receive electrons and is the reason an electrophile is
a Lewis acid. It is this molecular orbital that is an electron
pair acceptor. Similarly, a nucleophile has electrons that are
relatively high in energy (i.e., a lone pair of π electrons). These
electrons, which make the molecule a nucleophile and a Lewis
base, can be discussed in terms of the highest occupied
molecular orbital (HOMO). It is from this molecular orbital
that an electron pair is donated. The HOMO of the nucleo-
phile must mix with the LUMO of the electrophile in order
for the new bond to form.
We have found that students can benefit from three-
dimensional computer representations of chemical events (6 ).
Therefore, we have combined our molecular orbital approach
to understanding organic chemistry (a HOMO attacking a
LUMO) with the advantages offered by computer animations,
to produce a series of reaction clips. The goal in preparing our
animations was to facilitate visualization and understanding
of these topics, including electronegativity differences, bond
polarization, delocalization of charges and partial charges through
resonance and hyperconjugation, steric environments, and
electron distribution within molecules (7). By viewing three-
dimensional representations of the molecules involved in a
reaction, students can gain a better mental image of the course
of the reaction. Careful observation of the animated space-
filling molecular models, for example, will help reveal steric

A B

1 2 3 4 5

C D

1 2 3 4 5 1 2 3 4 5
Figure 1. Representations of the SN2 reaction of cyanide with ethyl bromide (for simplicity in each representation the cyanide counterion
is not included). Representations B–D include key structures used in creating animations. A: “Arrow-pushing” description of the reaction.
B: Ball-and-stick representation of the reaction. C: Superimposition of the calculated HOMO for the reaction. D: Superimposition of the
calculated LUMO for the reaction.

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 Information • Textbooks • Media • Resources

effects on reactions such as the E2 reaction. Viewing molecular
orbital interactions will help in understanding how electrons flow
in a reaction and why certain molecules react the way they do.
We hope that these animations will make learning organic
chemistry easier and more enjoyable. Samples can be viewed
on our Web page (http://chemwww.byu.edu/ora/). Any feedback
on how these cartoon aids facilitate learning or suggestions
for improvement would be greatly appreciated.
Results
These animations were produced by performing semi-
empirical (AM1 or PM3) or ab initio (HF/3-21G*) calculations
using Spartan (Wavefunction, Inc.). Between 15 and 45 steps
along the pathway were calculated for each reaction. The
energy-minimized geometries were determined, then HOMO
and LUMO surfaces were calculated. We prepared animations
showing a ball-and-stick perspective, a space-filling represen-
tation, a HOMO surface change, and a LUMO surface flow.
An estimated energy diagram is also sketched for each reaction.
The relative energies for the species along the reaction coor-
dinate were approximated rather than taken from the calculated
structures.1
Melding between the minimized points was accomplished
using the program Alias Wavefront. Usually the minimization
for an individual step had to be constrained. For example, if
a step in the SN2 reaction (see Fig. 1) were minimized with
the nucleophile (cyanide ion) 1.6 Å from the back-side of the
C-1 carbon, the unconstrained minimization would result in
a new distance between the nucleophile and C-1 that matches
the final product. Therefore, to determine the reaction picture
at 1.6 Å, we constrained the distance between the nucleophile
and the carbon bearing the leaving group. The calculations
at each step along the reaction pathway represent the energy-
minimized angles and distances for the two groups at the
specified distances. In Figure 1, we show 5 steps (1–5) from
the animation of this particular reaction in the ball-and-stick
(B), HOMO (C), and LUMO (D) perspectives.
Similarly, the E2 reaction was calculated at several points
along its pathway (see Fig. 2). As the base approaches the
alkyl halide, it may undergo attack at the back side of the
carbon–bromine bond (see the large LUMO density calculated
in that area in Fig. 2D-1) or it may attack the β-hydrogen,
which has LUMO density due to hyperconjugation (hyper-
conjugation is also visible in the LUMO calculation for the
final product as shown in Fig. 2D-4). The space-filling version
of the animated E2 reaction is illustrated in Figure 2E. The
space-filling model is a useful tool for comparing the E2 with
the competing SN2 reaction between methoxide and 2-bromo-
propane, since sterics resulting from the angle of approach by
the methoxy group determines the outcome of the reaction.
This is obvious in the space-filling version of the E2.
The Friedel–Crafts reaction animation is particularly
informative because it shows students a clearer picture of reso-
nance. There is a tendency to think of contributing resonance

A B

1 2 3 4

C D

1 2 3 4 1 2 3 4

1 2 3 4
Figure 2. Representations of the E2 reaction of methoxide with isopropyl bromide (for simplicity in each representation the methoxide
counterion is not included). Representations B–E include key structures used in creating animations. A: “Arrow-pushing” description of the
reaction. B: Ball-and-stick representation of the reaction. C: Superimposition of the calculated HOMO for the reaction. D: Superimposition
of the calculated LUMO for the reaction. E: Space-filling representation of the reaction.

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Figure 3. Representations of the carbocationic intermediate in the Friedel–Crafts acylation of toluene (for simplicity in each representation
a counterion is not included). A: A resonance structure description of the intermediate is shown. B: Two views of a ball-and-stick represen-
tation of the cation. C: Two views of the cation with the LUMO superimposed. These two views show the LUMO density located on
alternating carbons in the ring and the hyperconjugation from the methyl group bonded to the ring.

structures as being “in equilibrium” on the basis of chalkboard
drawings, as shown in Figure 3A. The LUMO density for the
intermediate in Friedel–Crafts acylation of toluene clearly
depicts a simultaneous buildup of positive charge distributed
between the para and two ortho positions illustrated from
two angles in Figure 3C (the ball-and-stick version is shown in
Fig. 3B from two angles for clarity). One can also see the hyper-
conjugation from the methyl group stabilizing the intermediate
cation in the side-on LUMO view of the intermediate.
We have omitted solvent from our calculations. Although
Spartan is capable of giving reasonable data for solvation of
stable compounds, we did not feel comfortable with its ability
to determine solvent interactions of transition states and species
along the reaction pathway. More importantly, we did not want
to tackle the animating nightmare that solvent shells would pose.
As a result, the reactions are closer to those under gas-phase
conditions. 2 The major goal of this project, showing the
reactions in 3-D with electron flow, is still accomplished.
Another shortcut in the animations relates to the issue of
vibrational and translational energy. The molecules appear in
static form with no kinetic energy, and only the productive
collisions are shown. One can easily imagine all the non-
reactive collisions that could potentially occur. Most of the
reactions require considerable heat in order to go on to the
products shown (intermolecular more so than intramolecular).
Once again, we believe the major goal is better accomplished
without this extra layer of detail.
A few of the reactions have HOMO or LUMO densi-
ties that are very difficult to animate. This is particularly true
of carbonyl compounds and proton-transfer reactions with
molecules containing many oxygens. For example, a HOMO
picture for a compound with three oxygens will have 6 MOs
that are essentially equivalent. This is shown in Figure 4 for
the intermediate in Fischer esterification. Owing to the
complexity and to the lack of information transfer to the
student, we have elected not to include some portions of the
HOMO and LUMO movies in these cases.3
Our initial animations included orbital phase information.
The positive lobes were blue and the negative lobes were red.
We found that the node information did not enhance the
mechanistic understanding of most reactions, nor did the dif-
ferent colored orbitals help the students see why one reagent
would interact with another.4 A simple illustration of the
complexity added by a change of color between each node is
shown in Figure 5. We plan to have the two-color orbitals
available for the Diels–Alder reaction and the Cope rearrange-
ment so that students can see both versions.
We have used our animations in several settings. We have
shown them to general chemistry students (a class of 20),
health profession students in a one-semester organic chemistry
course (two classes of 80 each), students in a typical two-
semester organic chemistry course (four classes of 150–250
students each), the students in an undergraduate organic spec-
troscopic identification course (two classes of 20 students
each), and students in the 1st-year graduate-level physical
organic chemistry course (two classes of 10 students each).
In each of these settings we have chosen to spend a limited
time (ca. 5 minutes) of any given class period presenting the
animations (8).
We have found that information can be gained from the
movie clips regardless of the course level. Beginning chemistry
students have expressed appreciation of finally “seeing” the
molecules undergoing reactions in the ball-and-stick movie.
The space-filling models give them additional perspective on
the relative sizes of the atoms. The advanced undergraduates
and beginning graduate students have found more subtle
details. For example, they can observe stereoelectronic effects,
π-complex formation, reaction reversibility, and the role of
orbital symmetry. Many of these issues can be addressed at a
research level based on the animations.
The HOMO/LUMO presentations are a great aid for
undergraduate students who are using a molecular orbital
approach in the classroom. We don’t expect this information
to be immediately obvious to students who are coming from
a traditional, non-molecular-orbital approach to organic
chemistry. In other words, the HOMO/LUMO aspects of this
program are not “stand alone” for the average undergraduate
who has not been taught using molecular orbital concepts.

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 Information • Textbooks • Media • Resources
A B C
Figure 4. Representations of an intermediate formed in the Fisher
esterification of acetic acid. A: Conventional drawing of the inter-
mediate. B: Ball-and-stick representation of the intermediate. C:
Representation of the intermediate showing the complexity of the
superimposed HOMO.
Class surveys from the one-semester and two-semester
organic courses indicate that students feel they benefit from
use of these animations in class. In the one-semester course, 77%
of 157 responses were favorable when students were asked if
they benefited from the animations. In the two-semester
course there were 91% of 965 responding students felt the
animations were helpful in learning organic chemistry. The
major difference between the two levels of instruction is that
the two-semester course uses the molecular orbital reasoning
for electrophilic and nucleophilic properties. Thus, we believe
that the higher appreciation of the animation package in the
two-semester course is a result of the HOMO and LUMO clips.
We asked two separate classes the question “The E2
mechanism requires a β hydrogen that is anti-periplanar to
the halogen. Why is this arrangement necessary for the elimi-
nation?” The class that had been using these animations in
the classroom and in homework (247 students) had an aver-
age score of 7.1 out of a possible 10. The class that did not
use the animations (207 students) averaged 2.8 out of 10. We
are currently attempting to quantify the improvement that
students experience as a result of these animations. It is very
difficult to separate the teaching approach from the benefit
of the visualization.
Conclusion
Although there are many approaches to teaching organic
chemistry, having a central theme for the course is critical.
We have presented our approach, which integrates frontier
molecular orbital concepts into each reaction the students
see. This theme has allowed students to better understand
the “whys” and “hows” of organic chemistry. Our animations
incorporate this molecular orbital approach and they have
been well received by all levels of students.
W
Supplemental Material
This article is available with color figures in this issue of
JCE Online.
Notes
1. Semiempirical methods are not very reliable for their ab-
solute calculated energy values. Since solvent is not included in the
JChemEd.chem.wisc.edu • Vol. 77 No. 6 June 2000 • Journal of Chemical Education
A B
Figure 5. Two drawings of a key structure used in the animation of an
E2 reaction. A: Structure with the LUMO of a single color superim-
posed. B. Structure with the LUMO showing phase differences.
modeling, realistic numbers would not be obtained. The energy lev-
els used are only a guide for the student.
2. Solvent plays a major role in the rate and outcome of most
organic reactions and gas-phase calculations avoid additional com-
plicated situations.
3. We have also opted not to simplify the orbital representa-
tions by using localization methods. Those models are the com-
mon textbook pictures that are presented elsewhere.
4. Student responses to in-class surveys. Of the few students
who were not helped by the animations (ca. 10%), many expressed
that they were uncertain about the meaning of the red and blue
lobes in our initial animations.
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