Upload
others
View
6
Download
0
Embed Size (px)
Citation preview
1
Computational Chemistry in Organic Chemistry Lecture using WebMO Brian J. Esselman,* Aubrey J. Ellison,* and Jia Zhou
Department of Chemistry, 1101 University Avenue, Madison, WI 53706
ABSTRACT 5
Advances in computational software and hardware have allowed computational chemistry to
become a more integrated component of undergraduate organic chemistry curriculum. With a few
exceptions, most of this attention has been given to small lecture activities or individual laboratory
exercises. To allow students to fully utilize the insights of computational chemistry, it must become
fully integrated into all aspects of instruction. Here we present out on-going efforts in integrating 10
computational chemistry into the entire lecture curriculum via carefully chosen examples on lecture
slides, problem sets, and assessments. Rather than having students perform these calculations
themselves, as they do in our laboratory course, we have taken advantage of the HTML-export feature
of WebMO to provide students with direct links to computational data. As students work through our
curriculum, their learning is supported by the ability to view relevant molecular geometries, charge 15
distributions, orbitals, vibrational modes, etc. We are confident that use of these tools leads to better
learning outcomes.
INTRODUCTION
Coinciding with the availability of student-friendly software, computational chemistry has been
introduced in many graduate and undergraduate courses over the past few decades.1-7 Many excellent 20
examples of lecture and laboratory exercises have been presented in the literature across college-level
instruction. Given the obvious ability of computational chemistry to help students understand and
visualize the three-dimensional nature of molecules and highlight the connection between structure
and reactivity, it is unsurprising that instructors of general, organic, and inorganic chemistry have
seized upon this capability. Importantly, computational results can provide chemical insights to 25
students without the need to understand the details of how the calculations were performed. Hence,
many published exercises designed for early undergraduate chemistry students are able to avoid
2
delving deeply into the details of quantum mechanics and computational chemistry. This
demonstrates the ability of computational results to provide chemical insights to students without the
need to understand the details of how the results were obtained. While there is definitely substantial 30
value in a proper understanding of quantum mechanics, levels of theory, basis sets, optimization
routines, etc., these topics can be reserved for upper-level physical chemistry and computational
chemistry courses without sacrificing substantial student understanding of structure and bonding in
the introductory courses.
Stand-alone computational chemistry exercises have the inherent drawback of time, cognitive load, 35
and effort required to learn how to perform the calculations. This burden, in cases of infrequent
implementation, can easily overshadow the insights derived from the exercise that would be useful to
the early college student. A few university courses8-10 and department-wide chemistry programs11-13
have embedded computational chemistry throughout the curriculum. These implementations reduce
the cognitive load on students in any particular computational exercise as students become 40
increasingly familiar with the software due to repeated exposure. Additionally, students and
instructors inherently see the benefit of mastering the new software necessary to complete their
calculations, knowing that this skill will serve them well in their future coursework. Undoubtedly,
such repeated utilizations can provide a more meaningful and longer-lasting impact on students’
understanding of three-dimensional structures and chemical bonding. 45
In organic chemistry, there are two very natural avenues for computational chemistry to support
the curriculum: supporting analysis of experimental data and elucidating how the electronic or
molecular structure drives the chemical outcome. In the organic laboratory, many authors have
demonstrated that computational chemistry can help students assign IR or NMR spectra.4, 14-22 This
support can allow students to make assignments and perform analyses that may be beyond their 50
abilities without computational predictions. Further, a number of authors have demonstrated the
utility of calculations to help students predict or rationalize the outcome of an organic reaction in
lecture and laboratory settings,23-26 helping students obtain a deeper understanding of many
important concepts. Student exercises have been used to investigate conformational isomerism,9-10, 27-
31 structure and relative energy of reactive intermediates,19, 21, 25-26, 32-37 the selectivity of an organic 55
3
reaction,19, 25-26, 38-42 assessing relative acidity,43-44 evaluation of a reaction mechanism,45 etc. All of
these examples provide other educators a template for how they can enhance their curricula and lead
to better student learning.
We wish to take this process one step further and integrate computational outputs throughout the
entire organic lecture curriculum. Focusing on interpreting computational results will provide the 60
benefits of a deeper conversation about structure, bonding, and reactivity, without substantially
adding to the cognitive load and time necessary for students to perform the calculations. Based upon
previous work,30, 46-47 we have embedded WebMO7-HTML exports into our course materials: student
handouts, problem sets, lecture slides, discussion activities, and exams. In a manner similar to
Springer,46 we present computationally generated images of molecules alongside more common two-65
dimensional images in lecture. We have extended this use of three-dimensional images from WebMO
to include all course content, allowing students to view structures and orbitals in a virtual model kit.
Alongside these computer-generated structures, we encourage students to use wedge-dash notation
for molecules drawn on paper and traditional model kits to help build their representational
translation. While we have just begun this modernization of our curricular materials, we intend to 70
make virtually all images of molecules presented in course content accessible via student engagement
with HTML links. Even during this early adaptation and implementation, we have observed several
important anecdotal outcomes. Our students seem to have a deeper grasp of three-dimensional
structures, an improved understanding of how atomic and molecular orbitals influence chemical
reactivity, and a greater mechanistic focus on why and how reactions occur. As an intended 75
consequence, students are able to move away from pattern recognition and memorization and toward
utilizing key concepts to rationalize reactivity. We have changed our own teaching frame of mind to be
more focused on how the molecular and electronic structure leads to the function of the molecule.
This article presents some of our initial work and reflections.
CURRICULAR IMPLEMENTATION 80
The representative examples shown here are from 1st and 2nd semester organic chemistry lectures
(CHEM 343 and CHEM 345) at the University of Wisconsin–Madison. This is the main sequence of
4
organic chemistry and has between 200 and 300 students per lecture in a wide range of majors.
Together, these courses cover the topics presented in the 6th edition of Organic Chemistry by Loudon
and Parise.48 The course does not have a laboratory component, and students may take the 85
laboratory course (CHEM 344) concurrently with or subsequent to CHEM 345. Students may have
some exposure to computational chemistry through use of computational outputs in general chemistry
or later in CHEM 344 where they run calculations to support their understanding of molecular
structure and properties.9-10 Regardless of their level of exposure to output files prior to CHEM 343,
virtually none of these students have used any computational chemistry software to perform 90
calculations themselves. These representative examples demonstrate the usage of WebMO-HTML
exports in lecture notes, problem sets, and on course assessments. Each figure, in the following
section, is an authentic image of computational results used in our courses and instruction to support
student learning. These figures include examples of geometry optimizations, vibrational frequencies,
NMR chemical shift predictions, and Natural Bond Orbital (NBO) calculations. The NBO calculation 95
generates and visualizes the molecular orbitals and natural bond orbitals; we use whichever is most
impactful for illustrating a concept to students. In general, MOs are useful for depicting conjugated
systems as MOs inherently show the delocalization of electrons throughout a molecule. NBOs are
useful for depicting lone pairs and bonds using the hybridizations and localized notions of bonding
common in organic and general chemistry. 100
1st semester examples
Starting with the very first lecture, students are introduced to computational depictions of
chemical structures. The early introduction is done in such a way that computational models are
intentionally presented in parallel with Lewis structure drawings. This pairing serves to build student
confidence and understanding in translating two-dimensional representations into accurate chemical 105
geometries, as well as to demonstrate the utility of computational models. Figure 1 shows the WebMO
output of methane embedded directly into the lecture slide. Incorporation of the live output allows its
manipulation by the instructor, demonstrating geometric shape at the same time as providing initial
familiarity with the WebMO interface. Adjacent to the active WebMO window are traditional,
5
instructor-drawn depictions of methane. The juxtaposition of the three-dimensional visualization and 110
two-dimensional drawing can then be used to demonstrate how wedge-dash notation better aligns with
geometric reality than a simple two-dimensional Lewis structure. As the semester progresses,
students will continue to have static images or live outputs of WebMO molecules presented in lecture
in conjunction with two-dimensional hand drawings.
115
Figure 1. The first usage of WebMO to support a review lecture on Lewis structures. The methane WebMO output is embedded directly
into the lecture slide to allow the instructor to manipulate the WebMO image live without the need to switch between applications. The slide
also contains a clickable link to the methane WebMO output for student use after lecture through the pdf export.
While model kits have been used for conveying three-dimensionality of molecular structures for
quite some time, computational molecular depictions add to the depth and breadth of topics that can 120
be presented by including optimized geometries, molecular orbitals, and more accurate charge
distributions. As an example, Figure 2 shows the reactive carbocation intermediate from HBr addition
to 1-methylcyclohexene. Use of WebMO images can quickly highlight the loss of a p bond and
subsequent change of the C-atom hybridizations throughout the reaction, supporting the electron-
pushing mechanism. In the first step, WebMO can be used to display the NBO-depiction of an empty 125
p orbital on the carbocation intermediate, focusing student attention on this (formally) empty orbital.
With the depiction of the empty p orbital of the carbocation, students can more easily visualize the
structural and electronic factors that contribute to regio- and stereochemical outcomes. For molecules
like 1-methylcyclohexene, the regiochemistry of cation formation is largely controlled by the relative
stability of the carbocation. For aliphatic carbocations, hyperconjugation is dominant stabilization 130
6
factor, application of which requires students to visualize the overlap of filled orbitals with the
carbocation p orbital. The computational depiction reinforces this concept because of the plainly
visible alignment of the C–H and C–C bonds with the empty p orbital in the optimized carbocation
structure. Additionally, visualization of the geometry changes, otherwise difficult to convey with hand-
drawn structures, as well as depiction of the NBO of the empty p orbital on C7H13+ showing the orbital 135
shape, helps students to rationalize the possibility of a nucleophilic addition to either face of the
intermediate. Such visualization of computational results promote a better connection between
reactivity and stereochemistry than an electron-pushing mechanism can do alone.
Figure 2. Lecture slide NBO depiction of the formally empty (occupancy = 0.43 e-) p orbital on C7H13+ formed in the electrophilic addition 140
of HBr to 1-methylcyclohexene.
As shown in Figure 3, student understanding of the regiochemistry and stereochemistry of
halohydrin formation can be enhanced by providing computational geometries for each mechanistic
step together with the relevant orbitals. The acceptor orbitals on each electrophile (s*Br–Br on bromine
and s*C–Br on the bromonium ion) are displayed, corresponding to each of the s bonds that break 145
during the course of the reaction. The initial addition of bromine to isobutene is more complex than
depicted here, as the orbitals shown are for only one donor-acceptor interaction. More correctly, this
step involves two simultaneous donor-acceptor interactions in a concerted three-membered ring
formation. Students can rationalize that as the p orbital electrons are transferred to the s*Br–Br orbital,
the bond order of Br2 is lowered to zero and the corresponding s bond is broken. Students can see 150
7
that the p bond on isobutene has a symmetric orbital density above and below the plane of the
molecule, either lobe of which can react with bromine. Two parallel reactions are displayed to show
how the two enantiomeric bromonium intermediates are formed as a result of the orbital symmetry of
isobutene. The two enantiomeric intermediates react via an SN2 reaction with a water nucleophile.
When bromonium ions are depicted in most textbooks, they are shown as having two equivalent sC–Br 155
bonds. In contrast, the WebMO image showcases the lengthening of the sC–Br bond connected to the
more substituted carbon atom. This difference in bond length coincides with an increase in positive
charge at the more substituted carbon atom and allows students to rationalize the regioselectivity of
the SN2 reaction. Additionally, it is apparent from the location and shape of the s*C–Br orbital that the
nucleophilic water must approach the electrophilic carbon from the back side of the sC–Br bond. 160
Finally, there is a subtle feature of this SN2 reaction that becomes more apparent with the
computationally predicted structure: the geometry around the C-atoms of the three-membered ring are
flattened (the C-atoms are more sp2-like) allowing the nucleophile to effectively approach the s*C–Br
orbital by reducing the impact of the steric repulsion of alkyl substituents on the more substituted C-
atom. Once again, the teaching of halohydrin formation by simultaneously using the electron-pushing 165
mechanism and computational outputs helps students rationalize the Markovnikov regiochemistry
and anti stereochemistry far more effectively than a combination of electron-pushing formalism and
model kit usage.
8
Figure 3. Lecture slide depicting electrophilic addition of bromine to isobutene. Occupied orbital on isobutene depicted in red/blue and 170
unoccupied orbitals on bromine and the bromonium ion depicted in yellow/green.
Later in the semester, the course delves into the SN2-ring opening of epoxides, which is closely tied
conceptually to halohydrin formation. With the familiarity of bromonium ions already presented in
lecture and student handouts, we ask students to analyze the structure and derive reactivity from
WebMO images of the protonated and non-protonated epoxide of 2,2-dimethyloxirane (Figure 4). 175
Structurally, there are subtle differences between the protonated and non-protonated epoxide that are
not always well-captured in two-dimensional drawings. To assist in student interpretation, calculated
bond lengths and partial charges are provided for each structure. In 2,2-dimethyloxirane, the C–O
bond lengths are nearly identical. The protonated 2,2-dimethyloxirane, however, bears a strong
similarity to a bromonium cation in the depletion of electron density on the tertiary carbon, resulting 180
in a longer, weaker bond on the more substituted side. This tertiary carbon also shows a flatter
geometry, as it is more sp2-like, reducing steric repulsion for nucleophilic substitution. Using these
structures, students are able to predict that the unprotonated epoxide reacts via a normal SN2
reaction at the least substituted carbon atom, while the protonated epoxide displays a reversal of
regiochemistry. This exercise helps students rationalize the difference in regioselectivity for epoxides 185
reacting under acidic versus basic conditions, drawing from their previous conceptual understanding.
9
Figure 4. Annotated problem set answer key discussing of the geometry changes of 2,2-dimethyloxirane and protonated 2,2-
dimethyloxirane
2nd semester examples 190
Our 2nd semester course begins with spectroscopy and spectrometry (1H-NMR, 13C-NMR, 13C-NMR
APT, HSQC, IR, and EI-MS). As has been previously reported, there are numerous ways of supporting
student analysis and interpretation of the experimental spectra with computational chemistry.4, 14-22
Figure 5A shows a typically-assigned IR spectrum of vinyl propionate.49 Using WebMO’s HTML-export
feature and editing of line of code, it is possible to directly link the assigned stretches (C(sp2)–H, 195
C(sp2)=O, C(sp2)=C(sp2), and C(sp2)–O), giving students a quick visual connection between vibrational
mode and the absorption observed in the IR spectrum. Figure 5B shows the 13C-NMR spectrum of
ethyl acetate with the isotropic NMR chemical shifts provided. While most of our students can assign
C1 and C2 with ease, the computational NMR prediction allows students to confidently assign each of
the methyl group 13C-NMR signals (C3 and C4). For IR and NMR analysis, students are made aware 200
that the predicted relative position of signals is more reliable than the absolute absorption frequency
or chemical shift. For example, students do not seem confused by the vinyl propionate
computationally-predicted IR stretches of the C=O (1840 cm-1) and C=C (1736 cm-1) being too high
compared to experimental values (1762 and 1649 cm-1, respectively). Nor has anyone raised concern
about the over-prediction of the ethyl acetate carbonyl 13C-atom NMR chemical shift by 10 ppm. Our 205
hope is that students are learning to use these tools as guides or to confirm their assignments.
Furthermore, we expect that students are increasing their awareness of the difference between a
predicted or estimated value and its empirical or experimental counterpart. It is critical to emphasize
to students that the experimental value is the real one and should be trusted.
10
210
Figure 5. Annotated problem set answer keys with linked computational predictions of associated spectra. A) The optimization and
vibrational frequency calculation allows students to view each of the vinyl propionate key functional group stretches identified in the
experimental IR spectrum on the answer key. B) An NMR calculation provides estimated chemical shift data for each 1H- (not shown) and
13C- atom nucleus referenced to TMS for support in assigning the experimental 13C NMR spectrum.
Electrophilic aromatic substitution (EAS) reactions are a standard part of second semester organic 215
chemistry, where aromatic p systems react as nucleophiles. While some instructors have explored
EAS activation and directing effects via computational investigations of the aryl substrate, we employ
computational chemistry to help students rationalize the regioselectivity of these reactions using the
arenium cation intermediates. The charge distribution in the aryl substrate or the electron density
distribution of its highest-energy occupied molecular orbital (HOMO) can indicate the more 220
nucleophilic carbon atoms of the ring. While this is correlated to their relative reactivity, it is a missed
opportunity to explore the potential energy surface (PES) of this reaction and connect the relative rates
of product formation to the transition states of their rate-determining steps. Using a more rigorous
approach, our students use Hammond’s Postulate and the energies of the high energy cationic
intermediates (A and B, Figure 6) to rationalize the outcome of these kinetically controlled EAS 225
11
reactions. An example exam question is provided in Figure 6, where students were asked to
rationalize the experimental spectra provided from the reaction of bleach with 4'-
methoxyacetophenone in acidic conditions.50 As part of that analysis, students were instructed to
rationalize the energy difference between the two regioisomeric arenium cations (A and B) using
resonance arguments. Computational data were provided to highlight the combined impact of the p 230
conjugation represented by the associated resonance structures, steric interactions, and dipole-dipole
interactions on the potential energy surface rather than simply asking students to depict the p
conjugation. For exams, where students do not have access directly to a computer, the data is
provided and organized/pre-analyzed for them to allow the students to use the data to make useful
conclusions. (For a graduate course, where academic misconduct was less of a concern, students 235
were given computational data to use directly via HTML exports during the exam.)
Figure 6. Annotated exam answer key with the two regioisomeric chlorination arenium cations of 4'-methoxyacetophenone (A and B).
Resonance structures are provided for the lower-energy arenium cation A.
Arguably the most important reaction of 2nd semester organic chemistry lecture courses is the 240
attachment of a nucleophile to a carbonyl. We have adapted a recently published lab exercise10 into a
problem set question for the lecture course where students use computational outputs depicting the
12
relevant HOMO and LUMO orbitals to rationalize the attachment of cyanide to acetone. Figure 7
shows a small portion of this question in which the trajectory of attachment (Bürgi-Dunitz Angle51)
corresponds to a favorable overlap of the large lobes of the nucleophile’s HOMO and electrophile’s 245
LUMO. This also highlights the nucleophilicity and electrophilicity of the bond-forming carbon atoms
in this reaction. Students can view the motion of the atoms at the transition state and visualize how
the acetone geometry changes as the cyanide approaches. Throughout the course of the question,
students view the optimized structures of cyanide, acetone, the two molecules coming together in the
transition state, and the resulting tetrahedral intermediate. As the question progresses, students view 250
the relevant orbitals (HOMO of cyanide and LUMO of acetone) of this reaction and compare the LUMO
on isobutylene to acetone to rationalize the differences in reactivity of pC–O and pC–C bonds. It is hard
to imagine students making these comparisons in the absence of computational data to support and
assist in their analysis.
255
Figure 7. Annotated problem set answer key displaying the reaction of acetone with a cyanide nucleophile.
With the understanding of the fundamentals of organic reactivity, molecular comparisons become
central to rationalizing reactivity as the course progresses. Computational chemistry can be used to
showcase the differing electrophilicity of the carbonyl and b C-atoms of a,b-unsaturated carbonyl-
containing compounds. Figure 8 presents a lecture slide with NBO charge data and depictions of the 260
LUMO for chalcone and protonated ethyl 2-butenoate. While resonance structures are traditionally
13
drawn to show the electron-withdrawing effect of the O-atom on the carbonyl and b C-atoms in both
molecules, the inclusion of the charge data and LUMO provides additional depth. These data allow
students to clearly see that the carbonyl C-atom will be more electrophilic in a neutral or protonated
system than the b C-atom, which is difficult to ascertain from resonance structures alone. This allows 265
students to rationalize the preference for nucleophiles to attach to the carbonyl C-atom for a,b-
unsaturated carbonyl-containing compounds, which further allows them to rationalize 1,2- versus 1,4-
conjugate additions for these systems without relying almost entirely upon memorization of reaction
rates.
270
Figure 8. LUMO acceptor orbitals and NBO charge data of two a,b-unsaturated carbonyl compounds: chalcone (top) and protonated
ethyl 2-butenoate (bottom)
COMPUTATIONAL METHODS Calculations
All of the calculations here were obtained using Gaussian 0952 or Gaussian 1653 using WebMO 275
installed on the University of Wisconsin–Madison Chemistry Department educational computer cluster
(Sunbird). Nearly all geometry optimization and vibrational frequency calculations were carried out
using B3LYP/6-31G(d). Subsequent NMR or NBO calculations were carried out to obtain NMR
chemical shift data or depictions of relevant orbitals. For most of the molecules presented in
undergraduate organic chemistry textbooks, the optimization will take a few minutes to a few hours, 280
14
and NMR or NBO calculations add only a small fraction of the optimization time to the total time to
generate the desired computational output. A significant advantage of the WebMO-based approach
presented here is that it can be implemented for little to no cost. At institutions with a computer
cluster running any modern computational software, WebMO can be added for a relatively low cost.
For an institution without the necessary infrastructure to maintain a computational cluster, the free 285
version of WebMO can be linked to GAMESS2-3 (also free) to generate computational data from an
individual PC.
The B3LYP/6-31G(d) level of theory and basis set is adequate for calculation of most geometries
and properties of organic molecules for the undergraduate level. B3LYP/6-31G(d) calculations do not
handle all molecules with experimental accuracy and instructors should use all computational data 290
with caution. As needed, both the level of theory and the basis set can be improved for better
modeling of experimental data in a one-time calculation. Additionally, instructors must use care when
translating two-dimensional structures into three dimensions. Many of the images drawn in textbooks
and on websites of organic molecules are not the low-energy conformation or even a stable structure.
HTML export and embedding 295
As shown in Scheme 1, once the desired computational output is obtained, selecting the HTML-
export feature of WebMO creates a .tar file containing the necessary files to open that output in a
modified local HTML WebMO version, similar to what the user sees in WebMO itself. These files can
be given directly to students via a learning management system or via the construction of a simple web
site with links to the hosted HTML files. Alternately, we have found it convenient to place links to the 300
relevant computational outputs directly into the documents we use for lecture presentations,
discussion notes, problem sets, exams, etc. By editing one line of the Javascript code, it is possible to
generate clickable items that direct students to specific content (orbitals, dipoles, vibrational modes,
charge distribution, etc). in the output file, further minimizing student barriers for usage of WebMO.
Students can click on these links at the moment that they are most relevant and be taken directly to 305
the three-dimensional structure, important orbital, or property.
15
Scheme 1. Work flow for generating and posting computational outputs for students.
RESULTS AND DISCUSSION
Initial Reflections on Implementation 310
The representative examples shown here provide students with an easily accessible resource that will
enhance their understanding of organic chemistry. Having the WebMO images embedded in all aspects
of the course materials provides a framework that allows instructors to focus on how reactivity is driven
by physical organic principles. Instruction carried out in this manner forces students to move further
away from memorizing reactions, patterns of reactivity, or oversimplified criteria for predicting reaction 315
outcomes. We have found that exposure to computational chemistry results, even without students
performing the calculations, improves student ability to focus on key concepts: p conjugation,
hyperconjugation, electrophilicity, nucleophilicity, bond strength, etc. Finally, student intuition about
molecular and electronic structure is enhanced by repeated exposure to more realistic depictions of
molecules and orbital geometries 320
CONCLUSION AND FUTURE DIRECTIONS
We believe that the benefits of including computational chemistry in the early undergraduate
curriculum have not been fully explored or understood. Given the relatively recent wide-spread
availability of these tools, instructors have not fully grasped their utility in teaching students to think
about the reactions of organic chemistry and the properties of molecules using computational results. 325
Certainly, organic chemistry instructors have been focusing on the relationship between electronic
16
structure and the reactivity of molecules since before use of computational chemistry in the classroom.
Computational chemistry just makes that focus easier for instructors to engender in their students.
Students can see depictions of s bonds, p bonds, lone pairs, acceptor orbitals, etc. This ability to
visualize the electronic structure directly can reduce the cognitive load of trying to predict the reactivity 330
of a molecule, in a manner more similar to an expert who can fluidly move between two- and three-
dimensional representations. To understand the behavior of an organic molecule, students must view a
two-dimensional image, assign the hybridization of the atoms using a valid method, determine the three-
dimensional geometry of each atom, and then use the hybridization and three-dimensional structure to
understand how the orbitals might lead to a particular reactivity. The value of the computational 335
outputs is to provide the scaffolding necessary for students to translate organic molecules in such a way
that they can predict reactivity. With exposure to these images and their repeated use, students should
become more able to predict the reactivity of analogous molecules without the computational outputs.
It is easy to imagine a future in which computational chemistry is an embedded component of all
chemistry textbooks from the high school level onward. As the migration of textbooks to an online 340
platform continues to accelerate, it would be easy for all depicted molecules to become clickable links
highlighting their structure, properties, or relevant orbitals. This external support for courses would
allow educators to routinely enhance instruction with readily-available data and to easily develop
curricula where computational chemistry is a natural and authentic component.
While we will continue to grow the organic chemistry curriculum described to include more direct 345
application of computational chemistry outputs, it is clear that students would benefit from these types
of implementations at the general chemistry and high school levels. Currently, two related projects are
underway, providing computational outputs to high school teachers and their students via WebMO-
HTML exports.
ASSOCIATED CONTENT 350
Supporting Information
Examples of lecture notes, problem sets, and assessments associated with the chapters of Organic
Chemistry48 are available upon request.
17
AUTHOR INFORMATION Corresponding Authors 355
*E-mail: Brian J. Esselman ([email protected]), Aubrey J. Ellison ([email protected])
ACKNOWLEDGMENTS The authors gratefully acknowledge the input of the many teaching assistants and students that
have helped refine the curricular approach. We also thank the participation of Nicholas Hill, Maria
Zdanovskaia, Asif Habib, Cara Schwarz, and Amy Van Aartsen on this project and related projects that 360
have improved our approach to implementing calculations within the organic curriculum. We thank
Paul McGuire, Alan Silver, and J. R. Schmidt for their assistance with WebMO and computational
resources. Computer resources are partially supported by National Science Foundation Grant CHE-
0840494.
REFERENCES 365 1. Spartan. https://www.wavefun.com/products/spartan.html (accessed Oct 2018). 2. Schmidt, M. W.; Baldridge, K. K.; Boatz, J. A.; Elbert, S. T.; Gordon, M. S.; Jensen, J. H.; Koseki, S.; Matsunaga, N.; Nguyen, K. A.; Su, S.; Windus, T. L.; Dupuis, M.; Montgomery, J. A. General Atomic and Molecular Electronic Structure System. J. Comput. Chem. 1993, 14, 1347-1363. 370 3. Gordon, M. S.; Schmidt, M. W., Advances in electronic structure theory: GAMESS a decade later. In Theory and Applications of Computational Chemistry: the first forty years, Dykstra, C. E.; Frenking, G.; Kim, K. S.; Scuseria, G. E., Eds. Elsevier: Amsterdam, 2005; pp 1167-1189. 375 4. Karatjas, A. G. Use of iSpartan in Teaching Organic Spectroscopy. J. Chem. Educ. 2014, 91 (6), 937-938. 5. Perri, M. J.; Weber, S. H. Web-Based Job Submission Interface for the GAMESS Computational Chemistry Program. J. Chem. Educ. 2014, 91 (12), 2206-2208. 380 6. Parrish, R. M.; Burns, L. A.; Smith, D. G. A.; Simmonett, A. C.; DePrince, A. E.; Hohenstein, E. G.; Bozkaya, U.; Sokolov, A. Y.; Di Remigio, R.; Richard, R. M.; Gonthier, J. F.; James, A. M.; McAlexander, H. R.; Kumar, A.; Saitow, M.; Wang, X.; Pritchard, B. P.; Verma, P.; Schaefer, H. F.; Patkowski, K.; King, R. A.; Valeev, E. F.; Evangelista, F. A.; Turney, J. M.; Crawford, T. D.; Sherrill, 385 C. D. Psi4 1.1: An Open-Source Electronic Structure Program Emphasizing Automation, Advanced Libraries, and Interoperability. Journal of Chemical Theory and Computation 2017, 13 (7), 3185-3197. 7. Schmidt, J. R.; Polik, W. F. WebMO Enterprise, 17.0.012e; WebMO, LLC.: Holland, MI, USA, 2017. 390 8. Clauss, A. D.; Nelsen, S. F. Integrating Computational Molecular Modeling into the Undergraduate Organic Chemistry Curriculum. J. Chem. Educ. 2009, 86 (8), 955-958.
18
9. Esselman, B. J.; Hill, N. J. Integration of Computational Chemistry in the Undergraduate 395 Organic Chemistry Laboratory. J. Chem. Educ. 2016, 93 (5), 932-936. 10. Esselman, B. J.; Hill, N. J. Integrating Computational Chemistry into an Organic Chemistry Laboratory Curriculum using WebMO. ACS Symp. Ser. 2019, Manuscript Accepted. 400 11. Martin, N. H. Integration of Computational Chemistry into the Chemistry Curriculum. J. Chem. Educ. 1998, 75 (2), 241. 12. Gasyna, Z. L.; Rice, S. A. Computational Chemistry in the Undergraduate Chemistry Curriculum: Development of a Comprehensive Course Formula. J. Chem. Educ. 1999, 76 (7), 1023. 405 13. Paselk, R. A.; Zoellner, R. W. Molecular Modeling and Computational Chemistry at Humboldt State University. J. Chem. Educ. 2002, 79 (10), 1192-1195. 14. Lane, C. A.; Green, T. K. Usnic Acid and the Intramolecular Hydrogen Bond. A Computational 410 Experiment for the Organic Laboratory. J. Chem. Educ. 2006, 83 (7), 1046. 15. Stokes-Huby, H.; Vitale, D. E. Coupling Molecular Modeling to the Traditional "IR-ID" Exercise in the Introductory Organic Chemistry Laboratory. J. Chem. Educ. 2007, 84 (9), 1486-1487. 415 16. Csizmar, C. M.; Force, D. A.; Warner, D. L. Examination of Bond Properties through Infrared Spectroscopy and Molecular Modeling in the General Chemistry Laboratory. J. Chem. Educ. 2012, 89 (3), 379-382. 17. Hein, S. M.; Kopitzke, R. W.; Nalli, T. W.; Esselman, B. J.; Hill, N. J. Use of 1H, 13C, and 19F-420 NMR Spectroscopy and Computational Modeling To Explore Chemoselectivity in the Formation of a Grignard Reagent. J. Chem. Educ. 2015, 92 (3), 548-552. 18. Palazzo, T. A.; Truong, T. T.; Wong, S. M. T.; Mack, E. T.; Lodewyk, M. W.; Harrison, J. G.; Gamage, R. A.; Siegel, J. B.; Kurth, M. J.; Tantillo, D. J. Reassigning the Structures of Natural Products 425 Using NMR Chemical Shifts Computed with Quantum Mechanics: A Laboratory Exercise. J. Chem. Educ. 2015, 92 (3), 561-566. 19. Esselman, B. J.; Hill, N. J.; Tucker, W. B.; Zdanovskaia, M. A.; Habib, A. D. Deeper Analysis of the EAS Nitration of Bromobenzene: A Computational and Spectroscopic Study for the Undergraduate 430 Organic Laboratory. Chem. Educ. 2016, 21, 166-172. 20. Adams, W.; Sonntag, M. D. Vibrational Spectroscopy of Hexynes: A Combined Experimental and Computational Laboratory Experiment. J. Chem. Educ. 2018, 95 (7), 1205-1210. 435 21. Esselman, B. J.; Hill, N. J. Revisiting the Bleach Oxidation of 4-tert-Butylcyclohexanol. Chem. Educ. 2018, 23, 23-27. 22. Balija, A. M.; Morsch, L. A. Inquiry-Based IR-Spectroscopy Activity Using iSpartan or Spartan for Introductory-Organic-Chemistry Students. J. Chem. Educ. 2019. 440
19
23. Klassen, J. B.; Graham, K. J.; Muldoon, W. P. Molecular Modeling as an Aid to Understanding Stereoselectivity. J. Chem. Educ. 1999, 76 (7), 985. 24. Ball, D. B. Diastereoselectivity in the Reduction of α-Hydroxyketones. An Experiment for the 445 Chemistry Major Organic Laboratory. J. Chem. Educ. 2006, 83 (1), 101-105. 25. Best, K. T.; Li, D.; Helms, E. D. Molecular Modeling of an Electrophilic Addition Reaction with “Unexpected” Regiochemistry. J. Chem. Educ. 2017, 94 (7), 936-940. 450 26. Schuster, M. L.; Peterson, K. P.; Stoffregen, S. A. Isobutylene Dimerization: A Discovery-Based Exploration of Mechanism and Regioselectivity by NMR Spectroscopy and Molecular Modeling. J. Chem. Educ. 2018, 95 (6), 1040-1044. 27. Erickson, L. E.; Morris, K. F. The Energy Profile for Rotation about the C-C Bond in Substituted 455 Ethanes: A Multi-Part Experimental Computational Project for the Physical Chemistry Laboratory. J. Chem. Educ. 1998, 75 (7), 900. 28. Hill, N. J.; Hoover, J. M.; Stahl, S. S. Aerobic Alcohol Oxidation Using a Copper(I)/TEMPO Catalyst System: A Green, Catalytic Oxidation Reaction for the Undergraduate Organic Chemistry 460 Laboratory. J. Chem. Educ. 2013, 90 (1), 102-105. 29. Hill, N. J.; Bowman, M. D.; Esselman, B. J.; Byron, S. D.; Kreitinger, J.; Leadbeater, N. E. Ligand-Free Suzuki-Miyaura Coupling Reactions Using an Inexpensive Aqueous Palladium Source: A Synthetic and Computational Exercise for the Undergraduate Organic Chemistry Laboratory. J. Chem. 465 Educ. 2014, 91 (7), 1054-1057. 30. Zdanovskaia, M. A.; Schwarz, C. E.; Habib, A. D.; Hill, N. J.; Esselman, B. J. Access to Computational Chemistry for Community Colleges via WebMO. J. Chem. Educ. 2018, 95 (11), 1960-1965. 470 31. Winfield, L. L.; McCormack, K.; Shaw, T. Using iSpartan To Support a Student-Centered Activity on Alkane Conformations. J. Chem. Educ. 2019, 96 (1), 89-92. 32. Macomber, R. S. Exploring the C4H7+ Energy Surface: A Computational Discovery Process for 475 Students. J. Chem. Educ. 1998, 75 (10), 1346. 33. Hessley, R. K. Computational Investigations for Undergraduate Organic Chemistry: Predicting the Mechanism of the Ritter Reaction. J. Chem. Educ. 2000, 77 (2), 202. 480 34. Poon, T.; Mundy, B. P.; Shattuck, T. W. The Michael Reaction. J. Chem. Educ. 2002, 79 (2), 264. 35. Nassabeh, N.; Tran, M.; Fleming, P. E. Dissociation of the Ethyl Radical: An Exercise in Computational Chemistry. J. Chem. Educ. 2014, 91 (8), 1248-1253. 485 36. Esselman, B. J.; Hill, N. J. Proper Resonance Depiction of Acylium Cation: A High-Level and Student Computational Investigation. J. Chem. Educ. 2015, 92 (4), 660-663.
20
37. Montgomery, C. D. Fischer and Schrock Carbene Complexes: A Molecular Modeling Exercise. 490 J. Chem. Educ. 2015, 92 (10), 1653-1660. 38. Graham, K. J.; Skoglund, K.; Schaller, C. P.; Muldoon, W. P.; Klassen, J. B. Molecular Modeling to Predict Regioselectivity of Hydration Reactions. J. Chem. Educ. 2000, 77 (3), 396. 495 39. Hessley, R. K. Computational Investigations for Undergraduate Organic Chemistry: Modeling Markovnikov and anti-Markovnikov Reactions for the Formation of Alkyl Halides and Alcohols. J. Chem. Educ. 2000, 77 (6), 794. 40. Palmer, D. R. J. Integration of Computational and Preparative Techniques To Demonstrate 500 Physical Organic Concepts in Synthetic Organic Chemistry: An Example Using Diels-Alder Reactions. J. Chem. Educ. 2004, 81 (11), 1633. 41. Skonieczny, S.; Staikova, M. G.; Dicks, A. P. Molecular orbital analysis of Diels-Alder reactions: a computational experiment for an advanced organic chemistry course. Chem. Educ. 2010, 15, 505 55-58. 42. Csizmar, C. M.; Daniels, J. P.; Davis, L. E.; Hoovis, T. P.; Hammond, K. A.; McDougal, O. M.; Warner, D. L. Modeling SN2 and E2 Reaction Pathways and Other Computational Exercises in the Undergraduate Organic Chemistry Laboratory. J. Chem. Educ. 2013, 90 (9), 1235-1238. 510 43. Ziegler, B. E. Theoretical Hammett Plot for the Gas-Phase Ionization of Benzoic Acid versus Phenol: A Computational Chemistry Lab Exercise. J. Chem. Educ. 2013, 90 (5), 665-668. 44. D’Ambruoso, G. D.; Cremeens, M. E.; Hendricks, B. R. Web-Based Animated Tutorials Using 515 Screen Capturing Software for Molecular Modeling and Spectroscopic Acquisition and Processing. J. Chem. Educ. 2018, 95 (4), 666-671. 45. Albrecht, B. Computational Chemistry in the Undergraduate Laboratory: A Mechanistic Study of the Wittig Reaction. J. Chem. Educ. 2014, 91 (12), 2182-2185. 520 46. Springer, M. T. Improving Students’ Understanding of Molecular Structure through Broad-Based Use of Computer Models in the Undergraduate Organic Chemistry Lecture. J. Chem. Educ. 2014, 91 (8), 1162-1168. 525 47. Esselman, B. J.; Block, S., B. VSEPR-plus: Correct Molecular and Electronic Structures Can Lead to Better Student Conceptual Models. J. Chem. Educ. 2019, 96 (1), 75-81. 48. Loudon, G. M.; Parise, J., Organic chemistry. 2016. 530 49. SDBSWeb. https://sdbs.db.aist.go.jp (accessed Mar 2019). 50. Ballard, C. E. pH-Controlled Oxidation of an Aromatic Ketone: Structural Elucidation of the Products of Two Green Chemical Reactions. J. Chem. Educ. 2010, 87 (2), 190-193. 535 51. Brügi, H. B.; Dunitz, J. D.; Lehn, J. M.; Wipff, G. Stereochemistry of reaction paths at carbonyl centres. Tetrahedron 1974, 30 (12), 1563-1572.
21
52. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A.; Nakatsuji, H.; Caricato, M.; Li, X.; 540 Hratchian, H. P.; Izmaylov, A. F.; Bloino, J.; Zheng, G.; Sonnenberg, J. L.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Vreven, T.; Montgomery Jr., J. A.; Peralta, J. E.; Ogliaro, F.; Bearpark, M. J.; Heyd, J.; Brothers, E. N.; Kudin, K. N.; Staroverov, V. N.; Kobayashi, R.; Normand, J.; Raghavachari, K.; Rendell, A. P.; Burant, J. C.; Iyengar, S. S.; Tomasi, J.; Cossi, M.; Rega, N.; Millam, N. J.; Klene, M.; Knox, J. E.; Cross, J. B.; 545 Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Martin, R. L.; Morokuma, K.; Zakrzewski, V. G.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Dapprich, S.; Daniels, A. D.; Farkas, Ö.; Foresman, J. B.; Ortiz, J. V.; Cioslowski, J.; Fox, D. J. Gaussian 09, Gaussian, Inc.: Wallingford, CT, USA, 2009. 550 53. Gaussian 16, Revision B.01, Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Petersson, G. A.; Nakatsuji, H.; Li, X.; Caricato, M.; Marenich, A. V.; Bloino, J.; Janesko, B. G.; Gomperts, R.; Mennucci, B.; Hratchian, H. P.; Ortiz, J. V.; Izmaylov, A. F.; Sonnenberg, J. L.; Williams-Young, D.; Ding, F.; Lipparini, F.; Egidi, F.; Goings, J.; Peng, B.; Petrone, A.; Henderson, T.; Ranasinghe, D.; Zakrzewski, V. G.; Gao, J.; Rega, N.; Zheng, 555 G.; Liang, W.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Vreven, T.; Throssell, K.; Montgomery, J. A., Jr.; Peralta, J. E.; Ogliaro, F.; Bearpark, M. J.; Heyd, J. J.; Brothers, E. N.; Kudin, K. N.; Staroverov, V. N.; Keith, T. A.; Kobayashi, R.; Normand, J.; Raghavachari, K.; Rendell, A. P.; Burant, J. C.; Iyengar, S. S.; Tomasi, J.; Cossi, M.; Millam, J. M.; Klene, M.; Adamo, C.; Cammi, R.; Ochterski, J. W.; Martin, R. L.; 560 Morokuma, K.; Farkas, O.; Foresman, J. B.; Fox, D. J. Gaussian, Inc., Wallingford CT, 2016.