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 Integrating Computational Chemistry (Molecular Modeling) into the
General Chemistry Curriculum
Robert R. Gotwals, Jr.
gotwals@ncssm.edu
North Carolina School of Science and Mathematics, Durham, NC

Abstract: Computational science is considered by many scientists to be the fourth

leg of modern science, joining observational, experimental, and theoretical science. 
Computational chemistry (also known as molecular modeling) is one of the most
important application areas in the computational sciences.  In North Carolina, we
have built a statewide resource to provide pre-college students and teachers with
access to research-grade computational chemistry resources.  We have also
developed several complete courses (Intro to Computational Chemistry and Research
in Computational Chemistry), and have written a textbook specifically for high
school teachers and students.  Recently we have partnered with the Global Grid
Exchange to provide computing resources to a national audience.  In this paper we
will describe these efforts and how they can be utilized by other educators.

Key words: computational chemistry, molecular modeling, pre-college, general chemistry

Available for printing at: http://chemistry.ncssm.edu/chemed.pdf

Introduction
An understanding of and ability to use the
"The underlying physical laws necessary for the technologies, techniques, and tools of
mathematical theory of a large part of physics and computational chemistry are as important for
the whole of chemistry are thus completely known, chemistry students as those technologies,
and the difficulty is only that the exact application of techniques and tools found in the traditional
these laws leads to equations much too complicated “wet” laboratory.
to be soluble." -- P.A.M. Dirac, 1929
A casual scanning of the scientific literature supports
Virtually every paper on computational chemistry this premise. Computational articles are easy to find
begins with this famous quote by the British in journals such as the Journal of Computational
theoretical physicist and one of the pioneers of Chemistry (Wiley Publishers) and the Journal of
quantum mechanics, Paul Adrien Maurice Dirac Computer Aided Chemistry (Japan), but also appear
(1902-1984). His 1929 quote that we now “know” regularly in Science, Nature, and the Journal of
chemistry but that the mathematics are not “soluble” Chemical Education. Given that reality, it is
(able to be solved) serves as the foundation for this critically important that chemical educators at all
and every other paper in computational chemistry. In levels, beginning with pre-college students, include
this case, to know chemistry means that we can computation as an essential skill. We as chemical
describe it using detailed mathematics educators would never ignore the teaching of basic
concepts in acid-base chemistry or fail to provide
Computational chemistry, sometimes referred to as opportunities for students to learn how to perform a
molecular modeling or computational quantum titration or other basic laboratory skill. Likewise, we
chemistry, represents the newest method of can no longer ignore the prominence of computation
conducting chemical research, joining its well- as one of the essential tools in the arsenal of the
established colleagues of observational, research chemist. Computational chemistry must be
experimental, and theoretical chemistry. Given the included in our list of what it means to know
increasing prominence of computation in the chemistry. Our students must be as familiar with the
chemical profession, this paper looks to provide Schrödinger equation as they are with the ideal gas
support for this simple premise: law, and must be able to perform a vibrational

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 Integrating Computational Chemistry (Molecular Modeling) into the General Chemistry Curriculum
R. Gotwals

analysis of a compound as readily as they are able to increase the teaching of computational chemistry at
find its experimental melting point. Likewise, the pre-college level.
especially in this day of high-stakes testing at the pre-
college level, we must expect the student to Computational Chemistry Simplified
demonstrate his or her proficiency in computational
chemistry on end-of-course exams, AP exams, and Simply put, computational chemistry is the merging
other evaluation tools. Without that expectation, of chemistry, computing, and mathematics. In
students will not be exposed to these tools and computational chemistry (again, a term synonymous
methods, and, as a result, will not be adequately with molecular modeling), a molecule or reaction
prepared for careers as scientists. mechanism is studied by applying one or more
mathematical theories to determine one or more
One might ask: why are computational methods not a properties or behaviors of a molecule or chemical
more integral part of the modern chemical curricula system.
at the undergraduate or pre-college levels? A simple
(and perhaps simplistic) reason is offered: teachers In teaching my students, I have a number of “sound-
teach the way they were taught. Those of us in our bite” phrases and sayings that help them to remember
40s and 50s are of that generation where computers what they are trying to accomplish, and how they
were not as powerful, nor as ubiquitous, as they are might interpret the results. The first, and most
today. In my own experience as a computational important of these, is a daily mantra, and comes from
chemist, the calculations that I can now perform on a the industrial statistician George Box: “All models
handheld PDA or a low-end laptop were only are wrong, some are useful”. It is important for
possible on big mainframes or supercomputers when students to remember that all descriptions of
I began my career as a computational chemist in the chemical systems are simply models, and all make
late 1980s. assumptions about those systems that are not found in
reality. Today’s students have to be warned about
Regardless of why computation is not more accepting answers simply because the computer says
prominent, the chemical education profession must it’s right.
begin a serious effort to increase the importance of
computing in chemistry. Organizations such as the In teaching computational chemistry as a formal class
National Science Foundation (NSF) have funded a and in my integration of computational chemistry
considerable number of programs at the into core chemistry classes, I also use the “SPA”
undergraduate and pre-college levels to increase an framework on an almost daily basis: Structure-
understanding of computation in all disciplines of Property-Activity. I teach my students that to really
science, including chemistry. Programs such as the know a molecule or molecular system, they must
SuperQuest Supercomputing Challenge (1987), the understand the structure of the molecule(s), the
National Computational Science Leadership Program property of a molecule (defined as those
(1998), and other NSF-funded programs have looked characteristics of the molecule that the molecule has
to explore what students are capable of doing and by itself), and the activity of a molecule (those
how teachers might be prepared to increase the role properties that a molecule exhibits in the presence of
of computing in the science classrooms. NSF’s other molecules).
concern about increasing the number of
computationally savvy science students has even I also use a number of analogies to help students
reached into non-traditional audiences. My own understand both the basics of computational
funding from NSF has included significant funds to chemistry as well as some of the more challenging
determine how to incorporate computational science concepts. I suggest to students that there are five
into classrooms with deaf children by developing the considerations that the computational chemist needs
sign language vocabulary needed to communicate the to make in applying computation to the study of a
concepts of computation to that audience. molecule or a molecular system. By way of analogy
to cooking chicken, I suggest that the chef needs to
The remainder of this paper will provide a short know what s/he is trying to prepare, the form of the
description of computational chemistry, followed by raw chicken, what ingredients s/he has available,
a description of efforts being made to improve and what cooking tools s/he has, and what recipes s/he
knows or can find. Analogously, the computational

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 Integrating Computational Chemistry (Molecular Modeling) into the General Chemistry Curriculum
R. Gotwals

chemist needs to know what s/he is trying to calculated IR spectra of the water molecule. I teach
compute, the geometry of the molecule or molecular them that, depending on the choice of mathematical
system, the mathematics available in a given software theory (known in the community as a model
package, what software is available to that user, and chemistry), the data from the IR spectra is skewed by
what computational theories the user has and knows. about 11% from that of experimental vibrational
The chart below captures these considerations and frequencies (“all models are wrong....”). They learn
their application to both chicken and molecules. how to compare computed results with that of
Over a span of almost 20 years of teaching experimental results by using resources such as the
computational chemistry to pre-college students, I Computational Chemistry Comparison and
have found that this analogy provides a great deal of Benchmark Database from the National Institute of
comfort to students when they become overwhelmed Standards and Technology (NIST,
with the complexities of a particular computational http://srdata.nist.gov/cccbdb/). Lively discussions on
challenge: who is “right” (experimentalists or
“computationalists”) are not uncommon.

By way of illustration, one of the first computations

students perform is a vibrational analysis of water.
All molecules vibrate in the infrared, and the number
of vibrations can be predicted by various laws such as
the “3N-6” rule, where N is the number of atoms
(producing, in this case, three vibrations).

In this study, students begin by building the water

molecule and performing a basic optimization of the
geometry to determine the lowest energy value of the
molecule. Based on this optimization, they are able to
determine the bond lengths and angles of the
molecule. They then perform a vibrational analysis
of the molecule using the semi-empirical software
package MOPAC1 (Molecular Orbital PACkage),
with a PM3 mathematical parameterization set. Once
the calculation (known as a “job” in computational Other data generated by this job includes partial
chemistry parlance) is completed, the results are charges and bond orders. Also available to the
available for analysis. A screen capture of some of students is the raw output of the job, which provides
the results is shown below. We can see one of the a significant amount of data, much of it beyond the
vibrations of water (scissoring), and some of the realm of most pre-college students (and teachers).
properties of the molecule: energy in terms of heat of
formation (kcal/mol), dipole moment (Debyes), and On the North Carolina High School Computational
its molecular symmetry (C2V). It should be noted that Chemistry Server2 (described in more detail later in
the students can see an animation of the vibrations, this paper), students build molecules, submit jobs,
not just the static image shown in this screen capture. and analyze results using an inexpensive Web/Java-
The students can also rotate the molecule, zoom in or based interface known as WebMO3. This interface
out, and otherwise see the molecule from a variety of provides an easy-to-use connection between the user
perspectives. For this particular calculation and the research-grade quantum chemistry software
(vibrational frequency), students can also view packages, such as MOPAC, Gaussian 034 and

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 Integrating Computational Chemistry (Molecular Modeling) into the General Chemistry Curriculum
R. Gotwals

GAMESS5 (General Atomic and Molecular picture of pedagogy is perhaps useful.

Electronic Structure System). Computational science educators call this, with some
degree of tongue in cheek, the “associative law” of
computational chemistry education:

Computational (chemistry education)

(Computational chemistry) education

This “law” suggests the following. There are two

ways we can use computation in chemistry. The first
is as a tool for teaching the same topics that are
taught using more traditional methods: atomic and
molecular structures, acid/base chemistry, kinetics,
thermochemistry, organic chemistry, and the like.
Conversely, we also teach students about the
technologies, techniques and tools of computation.
What is a semi-empirical method? How do ab initio
methods differ, both in their mathematics and in the
quality of the computation? I believe that learning
about computational chemistry methods is as
important as using those methods to learn about
chemistry.

Classroom Integration

Readers are strongly invited to “take a spin” on the My introduction to computational chemistry came as
server by going to http://chemistry.ncssm.edu, a result of teaching chemistry to very advanced
logging on as guest (password: guest), and, in the students at the Blair Magnet Program at Montgomery
vernacular, performing a Hartree-Fock (HF) 3-21G Blair High School (Silver Spring, MD) in the late
vibrational analysis of water. Detailed instructions 1980s. It was clear that these students had no
are provided on the main page in the lab “Case conceptual idea of what was happening at the
Study: Vibrational Frequencies of Water”. The molecular level, especially when addressing topics
guest account allows users to run very small jobs to such as reaction dynamics, activation energies, and
get a sense of what computational chemistry is like, chemical kinetics. Through work with the NSF on a
but not run production (research) level calculations. number of high school computational science
Resources for that are described later in this paper. programs, we were able to see the power of
computing in providing students with a way to see
Assuming that the reader has a basic sense of what and study scientific events that happen too fast, too
computational chemistry is, we now turn to slow, are too large, or are too small. My experiences
pedagogical issues. How does the chemistry with those programs were life changing: I became a
educator use computational chemistry in the full-time computational science educator, working at
classroom? Over the past 20 years, I have taken three a supercomputing center in North Carolina and with
approaches to academic uses of computational various NSF-supported computational science
chemistry, all at the pre-college level: education organizations.
1. Integration into the “traditional” classroom
curricula Now back in the classroom full-time at the North
2. Establishment of a stand-alone course in Carolina School of Science and Mathematics
computational chemistry (NCSSM, http://www.ncssm.edu, a state-supported
3. Establishment of a research program in residential school for high school juniors and seniors
computational chemistry with a strong interest and aptitude for science and
math), I integrate computational opportunities on a
Each of these approaches is described in this paper. regular basis in my AP Chemistry course. The
Prior to that discussion, however, a broad-scope approach I take is described as “just in time”. By this

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R. Gotwals

I mean that when the students are struggling with In the process of integrating computation into the
some concept, I will bring computation in as a tool traditional classroom, we make every effort to use the
for them to better understand that concept. I do not right tool for the right job, and work hard to help our
take time to provide them with a lengthy background students understand why and how we make those
overview of computational chemistry, its varied decisions. Most of my colleagues are traditional
methods and mathematics, or even its experimental chemists, and I am the only
implementation. I introduce enough information for computational chemist on staff. As such, we work
them to use computational chemistry as a problem- collaboratively to help students decide if a problem is
solving tool. For example, this coming week (Sept better solved by running an experiment in the lab, by
10, 2007) in AP Chemistry we are beginning a running a “comp chem job”, or by some combination
discussion of aqueous solutions, and I will use a of the two. The experimental chemists, of course,
computational analysis of water to introduce the want to address every problem in the lab, while I tend
concepts of molecular structure, bonding, and to run to my computer at the drop of a hat. Because,
properties such as dipole moment and heats of however, we care about the best interests of our
formation. As this is their first exposure to students, my colleagues will sometimes advocate
computational chemistry, I will use the chicken computation while I will sometimes advocate a wet
analogy to help them have a sense of what they are lab approach to a chemical problem!
doing and why, but the focus is on using computation
to learn all we can about water. In other words, At NCSSM, all instructors teach core chemistry
computational (chemistry education). courses – honors and AP – but also teach advanced
electives, including organic, analytical, polymer,
During the course of the year, I routinely have the environmental, and industrial chemistry. In addition,
students perform computational labs, in addition to we offer a program of instruction in chemical
the standard wet lab activities advocated (mandated?) research. NCSSM is on a trimester schedule,
by the AP Chemistry curriculum. Many of the AP meaning an elective course meets for 10-12 weeks
topics are difficult ones for students, especially those from three to 5.5 hours per week.
related to atomic and molecular structures. For
example, Lewis dot structures and their significance Introduction to Computational Chemistry
are conceptually very difficult. With computation,
we can mathematically calculate and visualize lone In addition to the electives described above, I
pair orbitals. A lab (currently in development) looks developed a trimester course “Introduction to
to help students understand why some molecules Computational Chemistry”, a 30-hour program of
violate the octet rule. Without computing, students instruction. A partial screenshot of the syllabus is
have to take it on faith that not all molecules follow shown below. The reader should note that I use the
the rules. In looking at bonding, students can same general course description as that of a graduate
perform molecular and natural bond orbital level course at the University of Denver.
calculations and visualize sigma (σ) and pi (π) bonds.
In reaction kinetics and thermochemistry, we can
computationally determine the activation energies
(Ea) of a reaction, and determine the rate constant for
a particular reaction. We use computation with our
organic chemistry students to help them develop a
more intuitive feel for organic structures and
functional groups, and perform computational
experiments to determine the pKa values for
carboxylic acids. We teach a course at NCSSM in
environmental chemistry, and students use
computation to look at the degradation rates of
atmospheric pollutants. In this activity, students
compare their calculations to the experimentally
determined kinetics of a variety of environmentally
relevant compounds.

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 Integrating Computational Chemistry (Molecular Modeling) into the General Chemistry Curriculum
R. Gotwals

2. What is the fundamental mathematical

expression that needs to be solved in doing
computational chemistry? What are the
terms in this equation, what is their
significance, what variations can be used?
3. What are the approximations that can be
used in doing computational chemistry?
What are the pros and cons of the various
approximations? How does choice of
approximation affect the results, computing
time, etc.?
4. There are roughly four different "flavors" to
computational chemistry: ab initio methods,
semi-empirical methods, density functional
theory (DFT) and molecular
mechanics/molecular dynamics. What are
these methods? How do they differ?
5. What are the fundamental units of measure
used by computational chemists? What are
In this course, which routinely generates a waiting some different ways that these fundamental
list of students wishing to participate, the focus is on units might be expressed?
both aspects of the “associative law” pedagogical 6. What are some of the computer codes that
approach. It is my goal in this course to provide one might use to do computational
students with the opportunity to learn how chemistry? What platforms are needed for
computation helps to solve challenging chemical these codes, what are the strengths and
problems. It is also my goal to provide students with limitations of these codes?
the opportunity to learn the jargon, the foundational
mathematics, and the methodology of computational Most if not all of these questions focus more on the
chemistry. While some of our students will move to (computational chemistry) education aspect, rather
the university with the goal of being able to use than the computational (chemistry education) part of
computation as a tool for chemical learning and the pedagogy. However, each student, generally
research – computational (chemistry research) -- all working with a team of one or two other students,
three of our local universities (Duke, University of also completes a research project on a topic of
North Carolina- Chapel Hill, and North Carolina interest to that group. Most of the students pick
State University) have extensive research programs topics in which they are applying some technique of
in the development of new methods for doing computational chemistry to an interesting chemical
computational chemistry. As such, and since many problem, while a few do studies that compare
of our students matriculate to one of those three different computational approaches to some problem.
universities, it is my goal to prepare them to work in Students must present their research in journal form,
that developmental area of (computational chemistry) following the format of the Journal of Computational
research. Chemistry (the same format used in the PDF version
of this paper). A “Journal of Student Computational
In the Introduction to Computational Chemistry Chemistry” from the Spring 2007 semester can be
(Chem 412) course at NCSSM, I ask my students to found on the Web at
be able to provide a meaningful discussion of the http://chemistry.ncssm.edu/JcompChem.pdf.
following questions by the end of the course
(determined, of course, by the final exam!): The students in this class routinely (approximately
once a week) read and discuss an article from the
1. What is the role and purpose of Journal of Computational Chemistry. Students are
computational chemistry? What does expected to learn how to read the primary scientific
computational chemistry allow us to do that literature in this course, and be able to discuss their
cannot be done using traditional (i.e. wet) readings intelligently with me and with their fellow
chemistry? students.

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 Integrating Computational Chemistry (Molecular Modeling) into the General Chemistry Curriculum
R. Gotwals

The bottom part of the syllabus showing how this

class is structured is provided below. NCSSM is
unusual among high schools in that, since we are
residential, we are able to provide evening classes.
My course is held one night a week for three hours,
so I need to structure it such that students are not
subjected to a three-hour lecture! During the course
of the class, they have a lecture, do an in-class lab,
break out into small groups to discuss a journal
article, and get instructions for the out-of-class lab
that they must complete by the next week. We start
with a 20-minute quiz on the previous week’s
discussions and notes. Students are required to keep a
lab notebook, and learn how a computational lab
notebook is similar to but different from an
experimental lab notebook. All NCSSM courses use
the course management tool Moodle
(http://moodle.org), an open-source (i.e., free) Web-
based tool similar to Blackboard and WebCT.
This course has a support team of computational
chemists at both Duke and UNC-Chapel Hill,
consisting of post-doctoral students and research
faculty. These researchers provide “just in time”
support to me in answering questions that are out of
my area of expertise, or work with students directly
as needed. In addition to the use of standard
computational chemistry tools (Gaussian, GAMESS,
MOPAC), I also introduce other tools, such as
AutoDock6, a protein docking software package
developed by the Scripps Institute.

Sample projects for the current class include one

student who working to improve the functionality of
the WebMO interface by writing additional code; a
student looking at the molecular structure of the
compound responsible for the generation of oxygen
Research in Computational Chemistry through the Photosynthesis II process; and a student
who has been working experimentally with the
molecule heparin through a research program at
Students who wish to continue their studies in UNC-Chapel Hill, and is doing an computational
computational chemistry can elect to take Chemistry study of that molecule to augment his experimental
414, Research in Computational Chemistry. In this work.
course, we explore more advanced techniques and
tools, and students again conduct an independent
research project, typically at a higher level than that Medicinal Chemistry seminar
of the project done in the Intro course. For this
course, with its focus on the software program NCSSM also provides students and faculty with the
Gaussian 03 as the main computational engine, the opportunity to offer seminars based on personal
course uses Exploring Chemistry with Electronic interests, usually meeting once a week for 90
Structure Methods by James Foresman and Aeleen minutes. I offer a seminar in Medicinal Chemistry
Frisch as the textbook. based on work I did earlier in my career in the area of
anesthesiology and toxicology. In this seminar,
which is completely computationally driven, students

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 Integrating Computational Chemistry (Molecular Modeling) into the General Chemistry Curriculum
R. Gotwals

learn the basics of pharmacology, spend several

weeks in drug design activities, and then spend
several weeks looking at pharmacogenomics (using a
variety of computational biology tools!). In one of
the weekly computational labs, they do a small case
study to determine the optimal geometry for the
molecule acetylcholine, and conduct a potential
energy scan (PES, also known as a coordinate scan)
of that molecule:

North Carolina’s Experiment

As mentioned earlier in this article, the computing

tools used by my students were once only available
on high performance computers, and thus off-limits
to students, available only to research university and
commercial scientists. As computers became more
powerful and software was “ported” to desktop
computers, the possibilities for students increased.
At the undergraduate level, more chemistry
departments began to establish computer labs with
one or several computational chemistry software
packages.

These tools, however, were simply too expensive or

required computers not available to most high
schools, even specialized schools such as NCSSM.
In my own work, conversations with software
vendors typically solicited the comment that high
school students were simply not able to use their
software. Even for those vendors (and they were
few) who were supportive of pre-college efforts, they
were unwilling or unable to provide the deep
discounts that would be needed for high school
budgets.
The seminar culminates with a large case study in
which students must apply a variety of computational A number of efforts, such as the NSF-supported
methods to the study of a medicinal compound. “ChemViz”7 program at the National Center for
Playing one of several roles, students must work as a Supercomputing Applications (NCSA), developed
team to solve a complicated case study. A screenshot access via the Web to computational chemistry tools
of the case study is shown below: and curricula for pre-college students. This resource,
highly innovative in its time, did not provide students
with powerful enough tools to do research. Nor did it
have sufficient breadth and depth for teachers to be
able to support a program of instruction in
computational chemistry. At NCSSM, we were able
to badger the software vendors enough to get
software donated or at a very low cost. This model,
however, was not sustainable for many high schools.

Over the years, a number of research-grade codes,

such as MOPAC, GAMESS, and others became

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 Integrating Computational Chemistry (Molecular Modeling) into the General Chemistry Curriculum
R. Gotwals

available for desktop computers and were in the situation for most teachers. These problems,
public domain, meaning no cost. These software however, were solved (at least for us in North
programs typically, however, required a significant Carolina) with the advent of the WebMO interface.
understanding of computing systems (typically
Unix/Linux) and also required students to learn a WebMO is a Java-based tool that provides users with
fairly cryptic system to generate input files for a a very easy to use interface to a number of
calculation. For example, the code below is a sample computational packages, including Gaussian 03,
input file for GAMESS: MOPAC, GAMESS, and others, such as Tinker and
NWChem. The interface can be taught in one class
$CONTRL SCFTYP=RHF RUNTYP=HESSIAN session, and provides advanced users with the option
ICHARG=0 MULT=1 COORD=ZMTMPC $END
to customize jobs by hand. Most users, however, use
$BASIS GBASIS=N21 NGAUSS=3 $END
$DATA the pull-down menus that come with the software and
C15H12O6 that can be customized by the system administrator.
C1 1
C 0.0000000 0 0.0000000 0 0.0000000 0 0 0 0
With funding from the Burroughs Wellcome Fund
O 1.4341000 1 0.0000000 0 0.0000000 0 1 0 0
C 1.3718166 1 114.97905 1 0.0000000 0 2 1 0 (http://bwfund.org) and the North Carolina Science,
C 1.4084832 1 123.81387 1 19.441139 1 3 2 1 Mathematics and Technology Center
C 1.3994155 1 118.83432 1 -179.85275 1 4 3 2 (http://www.ncsmt.org/), we purchased a Dell dual-
C 1.3841214 1 120.93122 1 -0.9970528 1 5 4 3
C 1.4067731 1 119.36659 1 -0.0927585 1 6 5 4
processor Linux server, a commercial version of
C 1.3980438 1 121.32708 1 0.8675006 1 7 6 5 WebMO, and a license for Gaussian 03, with a total
H 1.0972631 1 120.91645 1 179.50426 1 8 7 6 cost of about $5,000. In addition to Gaussian 03, we
O 1.3630382 1 115.97457 1 179.85347 1 7 8 3 installed the GAMESS, MOPAC, and Tinker public
H 0.9495488 1 108.20358 1 179.91360 1 10 7 8
domain codes on the server. This resource is now
H 1.0960879 1 120.74505 1 -179.38483 1 6 7 8
H 1.0973780 1 119.79391 1 179.52810 1 5 6 7 available to any pre-college teacher and student
C 1.4733444 1 121.04055 1 176.87024 1 4 5 6 physically resident in the State of North Carolina.
C 1.5473835 1 113.38224 1 -49.011031 1 1 2 3 Teachers can request classroom accounts, where each
O 1.4112240 1 110.11977 1 -64.884104 1 15 1 2
H 0.9480935 1 106.05570 1 -173.39745 1 16 15 1
student receives an amount of computing time,
H 1.1178096 1 108.10917 1 175.52041 1 15 1 2 limited to small jobs (under four minutes) with a total
O 1.2169777 1 120.33281 1 148.30413 1 14 15 1 time limit (30 minutes). Students can request
C 1.5065672 1 107.29939 1 -174.25849 1 1 2 3 research accounts by submitting a research proposal
C 1.3945558 1 118.56470 1 -134.69061 1 20 1 2
to me, following the format used to request
C 1.3896935 1 120.57845 1 -179.66709 1 21 20 1
C 1.3987819 1 120.06596 1 -0.3073078 1 22 21 20 computing time on supercomputers and other high-
C 1.4148287 1 119.48882 1 0.1891373 1 23 22 21 performance (“big iron”) computing systems.
C 1.3950668 1 121.41952 1 45.467224 1 20 1 2
H 1.0984649 1 119.57851 1 0.4094933 1 25 20 1
In the two years since its establishment, the server
O 1.3686471 1 122.63812 1 179.88063 1 24 25 20
H 0.9494814 1 107.38800 1 0.5338152 1 27 24 25 has accommodated hundreds of students for more
O 1.3670389 1 117.63406 1 -179.85748 1 23 24 25 than 16,000 jobs. In addition to courses offered at
H 0.9495209 1 107.47905 1 -179.52436 1 29 23 24 NCSSM (and described earlier), classes in
H 1.0965534 1 120.42401 1 179.99587 1 22 23 24
computational chemistry are offered via NCSSM’s
H 1.0961999 1 120.19317 1 0.4409991 1 21 20 1
H 1.1201156 1 106.49306 1 68.559180 1 1 2 3 extensive distance learning program
$END (http://www.dlt.ncssm.edu/distance_learning/DLWor
kshops/ComputationaChemistry_Fall-07.pdf).
Needless to say, having students create these types of
input files was, and is, an unrealistic expectation, The main advantage of this system is that all of the
even for the most advanced students (although we did installation and maintenance of the system is done by
that for several years, not much fun for all NCSSM scientists and system administrators, and is
concerned). provided to all schools at no cost. In addition,
schools do not have to install any software, often a
So the problems of getting computational chemistry problem in North Carolina’s public schools. Schools
tools into the hands of students were substantial. only need access to Java-enabled Web browsers, a
Software that was too expensive, requiring advanced technology available to the majority of North
computer knowledge to install, and input files that Carolina’s schools.
were very difficult to create added up to an untenable

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 Integrating Computational Chemistry (Molecular Modeling) into the General Chemistry Curriculum
R. Gotwals

In working to get more teachers aware of and able to Due to licensing constraints, Gaussian 03 is not
use the resources, I offered (and continue to offer) available on this machine.
workshops at various conferences such as the North
Carolina Science Teachers Association annual This new and greatly appreciated resource now
conference. In talking with teachers, it was clear that allows NCSSM to provide free classroom and student
there was limited travel time and funding to attend research accounts to any pre-college teacher or
workshops to learn how to do computational student in the United States. Professional staff at
chemistry. To attempt to address that issue, and with NCSSM and Parabon maintain both the North
additional generous funding from BWF and the Carolina and national servers, with additional support
NCSMT Center, a colleague (Dr. Shawn Sendlinger from a team of six computational chemistry high
at North Carolina Central University) and I school interns at NCSSM.
collaborated to write an electronic textbook entitled A
Chemistry Educator’s Guide to Molecular Modeling Even with these resources in place, it is clear that
(http://chemistry.ncssm.edu/book). This book (with many teachers will want and need additional support
some chapters still in writing) looks to provide prior to implementing computational chemistry in
teachers with enough background in both areas of their classrooms. We are hoping to be able to
computational chemistry (methodology and provide significant support, in the form of FAQs
pedagogy) to integrate computation into their own (frequently asked questions) pages, an increasing
classrooms. I use this book in my “Introduction to number of ready-to-go labs, and the sharing of the
Computational Chemistry” course, in spite of the fact curricular materials developed over the past many
that it is written primarily for chemistry educators. years. With these resources, I am hopeful that
teachers will feel empowered to add a few activities a
National Resources: The Global Grid Exchange year to their classes, and perhaps consider offering a
course in computation at their schools. I am also
In addition to doing workshops and distance learning hopeful that newly trained teachers will develop their
programs across the state of North Carolina, I have own computational chemistry classroom and lab
been giving talks and workshops outside of North activities to be shared with the larger community.
Carolina. During these workshops, the main focus
has been on how participants might set up a WebMO- Conclusions
based server for their own schools, region, and/or
state. After several of these workshops, I was able to The main premise of this paper is that it is critically
arrange for seed funding from BWF to help others important that tomorrow’s chemical scientists
who might wish to replicate the North Carolina understand the technologies, techniques and tools of
resources. computational chemistry. With the resources now
available – access to research-grade hardware and
About the same time, Parabon Computation, Inc. software at no cost, an ever-increasing body of labs
(http://www.parabon.com/), a grid computing and curricular materials, and other support
organization based in Reston, VA, contacted me mechanisms – it is the hope of this author that
about providing grid resources for educational computational chemistry will as familiar to
purposes. In grid computing, computing jobs are tomorrow’s chemistry researchers and teachers as the
distributed to idle computers, to be run when those test tube and the beaker are now.
personal computers are not in use by the owner. The
results of the job are then sent back to the host Acknowledgements
computer for analysis by the originator.
Appreciation is extended to the Burroughs Wellcome
With support funding from Cisco Systems, we Fund and the North Carolina Science, Mathematics
established a mirror site and Technology Center for their funding support for
(http://cli.globalgridexchange.com/) of the North the North Carolina High School Computational
Carolina machine. On the grid computer, we have Server. Appreciation is also expressed to the Global
installed the WebMO interface and access to Grid Exchange, Parabon Computation, Inc.
GAMESS, MOPAC, and Tinker, along with a link to (http://www.parabon.com/) and Cisco Systems
the electronic textbook, labs, and other resources. (http://www.cisco.com/) for their support of the
national computational chemistry server.

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 Integrating Computational Chemistry (Molecular Modeling) into the General Chemistry Curriculum
R. Gotwals

References
1. MOPAC Version 7.00, J. J. P. Stewart, Fujitsu Limited,
Tokyo, Japan.
2. The North Carolina High School Computational
Chemistry Server, http://chemistry.ncssm.edu.
3. Schmidt, J.R.; Polik, W.F. WebMO Pro, version 7.0;
WebMO LLC: Holland, MI, USA, 2007; available from
http://www.webmo.net (accessed April 2007).
4. Gaussian 03, Revision C.02, M. J. Frisch, G. W.
Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J.
R. Cheeseman, J. A. Montgomery, Jr., T. Vreven, K. N.
Kudin, J. C. Burant, J. M. Millam, S. S. Iyengar, J.
Tomasi, V. Barone, B. Mennucci, M. Cossi, G.
Scalmani, N. Rega, G. A. Petersson, H. Nakatsuji, M.
Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa,
M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai,
M. Klene, X. Li, J. E. Knox, H. P. Hratchian, J. B.
Cross, V. Bakken, C. Adamo, J. Jaramillo, R.
Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R.
Cammi, C. Pomelli, J. W. Ochterski, P. Y. Ayala, K.
Morokuma, G. A. Voth, P. Salvador, J. J. Dannenberg,
V. G. Zakrzewski, S. Dapprich, A. D. Daniels, M. C.
Strain, O. Farkas, D. K. Malick, A. D. Rabuck, K.
Raghavachari, J. B. Foresman, J. V. Ortiz, Q. Cui, A.
G. Baboul, S. Clifford, J. Cioslowski, B. B. Stefanov,
G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. L.
Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C. Y.
Peng, A. Nanayakkara, M. Challacombe, P. M. W. Gill,
B. Johnson, W. Chen, M. W. Wong, C. Gonzalez, and
J. A. Pople, Gaussian, Inc., Wallingford CT, 2004.
5. "General atomic and molecular electronic structure
system, M.W.Schmidt, K.K.Baldridge, J.A.Boatz,
S.T.Elbert, M.S.Gordon, J.H.Jensen, S.Koseki,
N.Matsunaga, K.A.Nguyen, S.J.Su, T.L.Windus,
M.Dupuis, J.A.Montgomery, Journal of Computational
Chemistry, vol. 14, pages 1347-1363, 1993."
6. Morris, G.M., Goodsell, D.S., Halliday, R.S., Huey, R,
Hart, W.E., Belew, R.K., Olson, A.J. (1998) Automated
docking using Lamarckian genetic algorithm and an
empirical binding free energy function. J. Comp. Chem.
19:1639-1662.
7. ChemViz, National Center for Supercomputing
Applications (NCSA), University of Illinois at Urbana-
Champaign, http://chemviz.ncsa.uiuc.edu/

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