OrganicPad: A Tablet PC Based Chemistry Tool
Sam Bryfczynski
Clemson University
School of Computing
Clemson SC, 29631
(770) 973-2514
sbryfcz@clemson.edu
ABSTRACT
This paper describes a software tool that provides a natural user
interface through the use of a Tablet PC to provide interactivity
between an instructor and her students in an organic chemistry
course. The teacher and all students are equipped with wireless
internet access and either a Tablet PC or a WACOM [3] slate
device. Our software tool, called OrganicPad, enables an
instructor to engage their students in the classroom by sending
them problems to solve. Students then develop answers to those
problems. The tool may provide students tips and hints to help
them arrive at an answer. All communication is through the web,
using the HTTP communication protocol. At any time, the
instructor can automatically evaluate student submissions and can
quickly understand where students are having difficulty.
Furthermore, the instructor can hide the identities of the students
and anonymously use the submissions pedagogically. Finally, the
instructor can develop tutorial exercises that students can work on
outside of class. We present how we have used OrganicPad and
our plans to extend its functionality in the future.
Categories and Subject Descriptors
J.3 [Software Applications]: Physical Science and Engineering –
Chemistry.
Keywords
Tablet PC, Graph Isomorphism, Organic Chemistry, Lewis
Structures
1. INTRODUCTION
Tablet PCs are becoming more popular in the academic
environment. Proof of this is from increased submission count at
ACM SIGCSE and IEEE FIE and new conferences such as
WIPTE 2007 [1] (Workshop on the Impact of Pen Technology in
Education) and PLT 2007 [2](International Workshop on Pen-
based Learning Technologies). Tablet PCs are largely popular in
academics because of ease of use. Students of all ages use Tablet
PCs in the classroom. From the time children learn to hold a pen,
they are able to utilize a Tablet PC’s functionality.
We have developed an application that uses the Tablet PC’s
unique features for use in organic chemistry. OrganicPad enables
Permission to make digital or hard copies of all or part of this work for
personal or classroom use is granted without fee provided that copies are
not made or distributed for profit or commercial advantage and that
copies bear this notice and the full citation on the first page. To copy
otherwise, or republish, to post on servers or to redistribute to lists,
requires prior specific permission and/or a fee.
ACM-SE ‘08, March 28–29, 2008, Auburn, AL, USA.
Copyright 2008 ACM ISBN 978-1-60558-105-7/08/03…$5.00.
162
students to complete stand alone exercises as well as engage with
the teacher and other students in interactive quiz exercises.
Teachers are then able to get instant feedback and discover
concepts that may need to be reinforced to the class.
The contents of this paper are as follows. Section 2 is used to
describe why a program such as OrganicPad is needed. In section
2, we describe the current status of the project. We describe the
main features and workings of both the stand alone program and
the interactive program. Section 3 describes some of the inner
workings of OrganicPad and how they can be expanded and
applied to other fields of study. Finally, section 4 of this paper
closes with a summary and a discussion of the future of
OrganicPad and its technology.
2. STATEMENT OF NEED
Organic chemistry is a very technical and advanced field of study.
Students who fail to understand the introductory material will
never be able to succeed in later courses. Furthermore, the
majority of introductory chemistry classes contain several
hundred students and teachers cannot take the time to work with
each student individually. Organic chemistry teachers have no
real way of knowing how well students are grasping concepts
until the test results come back and by then it is too late. A
chemistry program is needed that is able to evaluate student’s
understanding of the material quickly.
Students are also taught to create molecules through drawings
using a pen and paper. Together a pen and paper provide
chemists with great flexibility in their drawings. Currently the
majority of organic chemistry programs on the market strip away
this flexibility by utilizing a drag and drop user interface and
restricting the length and angle of the chemical bonds. For
example, Figure 1 demonstrates how a simple freehand drawing
can look quite different in a commercial program.
H H
H C C O
H H H
Figure 1. (a) A free-form Lewis structure on the left. (b) The
same molecule drawn using ChemDraw.
There are numerous tools and programs to study molecules and
their interactions. These tools assume that chemists are very
familiar with the chemical rules. This leaves a gap with students
who are just learning organic chemistry and have yet to master all
the chemical properties. Students need software to help them
learn the common properties of chemical molecules. Current
software is just far too complex for introductory students to use.
3. CURRENT WORK
Our solution to this learning gap in organic chemistry is
OrganicPad. OrganicPad utilizes Tablet PC functionality to
allow students to freely create molecular drawings without
imposing predefined formats like so many other chemistry
programs. Furthermore, OrganicPad allows a chemistry
instructor to interact with their students during lecture, exercise
their student’s understanding of the course material by sending
out word problems, collect student-developed answers to a
problem, evaluate student submissions, and conduct lecture after
the exercise using the students’ own submissions as examples.
The instructor can also develop step-by-step tutorials which
students can follow on their own time. The tutorials are designed
so that the student must provide the correct answer at each step;
otherwise, OrganicPad will not allow the student to continue.
3.1 Drawing Molecules
Because students are taught about molecule construction through
pen and paper, the Tablet PC makes the perfect medium for
students to gain extra interactivity in the drawing process.
OrganicPad has the ability to translate the strokes users draw on
the screen into a fully interactive molecular structure. By
breaking the strokes down into segments, OrganicPad can
recognize a growing number of handwritten atoms such as
Figure 2. (a) An example of some of the molecules that can be
created using OrganicPad (b) A molecule that has been
converted to 3D.
Hydrogen, Carbon, Oxygen, Nitrogen, and the Halogens. For
example, users who write an “H” on the screen will have that
letter converted to an interactive atom which can be further built
upon. Connecting these atoms is as easy as on a piece of paper.
Simply drawing a line between two atoms will transform the
stroke into a bond. By following these simple steps, users can
quickly build a molecule for further analysis.
OrganicPad also provides functionality for more advanced
students. OrganicPad allows for chemists to draw structures in
line notation. This form of drawing molecules removes the need
to draw Carbon and Hydrogen atoms and is easier to use for more
complex molecules.
Some areas of chemistry challenge students to see molecules in
three dimensions. In order to represent the third dimension on
paper, special bonds are drawn to indicate atoms going into the
paper or back out towards the student. OrganicPad has the ability
to recognize these special bonds structures and display the
molecule correctly.
Once a molecule is drawn, further analysis can be made on the
molecule. By clicking the 3D button, OrganicPad will create a
three dimensional model of the molecule and display it on screen.
Users can then manipulate the model and learn about its structural
163
formation. Teachers may find this useful while discussing
stereochemistry which is a field of organic chemistry that focuses
on the three dimensional structure of molecules and how they
interact with one another. Furthermore, OrganicPad provides a
tool to generate the scientific name, elemental composition, and
exact mass of the molecule.
Figure 3. OrganicPad has correctly recognized that the
Carbon highlighted has too many bonds.
3.2 Error Checking
One of the main features of OrganicPad is the ability to analyze
molecules drawn. By clicking the “Check” button, OrganicPad
will check for common errors in drawn molecules that do not
agree with specific chemical properties such as Octet rules.
Figure 3 shows an example of a user create molecule. Once the
“Check” button was clicked a red rectangle has indicated that this
Carbon has too many bonds attached to it. This is one of the most
common errors students make.
3.3 Student-Teacher Evaluation
Teachers and students can also interact in real time inside the
classroom through quiz sessions. OrganicPad allows teachers to
set up a server on their computer so that all the students may
connect to it. At this step, OrganicPad has created an ad hoc
network for the students to connect. OrganicPad will display the
instructor’s IP address for the students to use as way of
connecting to the instructor’s machine. The instructor will then
display this IP address and the students will enter it into an
OrganicPad prompt window along with their name. Next,
OrganicPad will connect to the instructor’s machine so that data
may be sent back and forth between the instructor and students. It
is important to note that all of this is done through HTTP. This
allows for these sessions to be created anywhere there is internet
access. This allows for interaction between students and
instructors that are not physically together. Once students have
connected they are able to receive questions from the instructor as
well as respond with answers. While the students have been
working on their solutions, the instructor would create the correct
answer and add it to the solution bank. Once all of the solutions
have been gathered, OrganicPad will then use graph isomorphism
algorithms to determine if the molecules are equal to that of the
instructor. Following this comparison, OrganicPad will give
feedback to the students indicating to them whether their solution
was found to be correct or incorrect.

Figure 4. Student about to submit an Incorrect answer to the
teacher's request.
Figure 5. Teacher has checked the student’s submission
against the solution given.
One of the key features to note is the ability to have multiple
solutions to the same problem. This idea was first brought to our
attention in a trial we ran on a group of chemistry students. The
instructor asked a question and to her surprise several students
responded with different molecules that met the requirements and
were both equally correct. OrganicPad has the ability to mark
those student submissions that were initially marked incorrect as
correct. The molecules will then be added to the solution list and
OrganicPad will compare all of the incorrect solutions against the
newly added solution(s).
3.4 Tutorials
One of the easiest and versatile ways for interaction is through
tutorial lessons. Teachers are given an authoring tool to create
tutorial lessons which can step students through the process of
creating specific molecules. Teachers then have the ability to
upload these lessons online. Students then may download any of
these lessons and proceed through them at their own pace.
Tutorials are essentially a series of steps that are used to lead the
student to a final molecular creation. Students must complete
each step before proceeding to the next. OrganicPad will
164
automatically determine this through graph comparisons. Once
the student’s current drawing structurally matches the one the
teacher provided as the solution, the tutorial will automatically
proceed on to the next step. Figure 6 shows what a student could
expect from a tutorial.
3.5 Graph Isomorphism
The main driving force behind the interactive features of
OrganicPad is graph comparisons. OrganicPad handles these
comparisons using an algorithm called graph isomorphism. This
algorithm simply detects if two graphs are logically equivalent.
Formally, given two graphs, is there a bijection between the nodes
of the graphs preserving edges? The graph isomorphism problem
is unusual in algorithm complexity theory as it defies
conventional classification: it is known to be NP but is
conjectured not to be NP-complete [5].
In OrganicPad, the molecule that has been drawn can be thought
of as a graph. The number of nodes (atoms) and the degree
(maximum bond) in any one graph (molecule) will rarely exceed
20 and 3, respectively. Hence, although the graph isomorphism
algorithm for a general graph problem is potentially time-
consuming for large graphs, the graphs in OrganicPad are small
and bounded allowing for fast and efficient comparison of each
student’s molecule submission and the instructor’s solution list.
This small size also makes it possible for the graph to contain
many cycles which is common in molecular drawings. Usually
cycles are a time consuming problem in graph comparisons but
because of the small size of the graph all of the comparisons can
be handled without any slow down for the user.
This comparison algorithm is even simpler than the standard
graph isomorphism algorithm because unlike the regular
algorithm, no relabeling of the student’s solution is necessary.
The approach OrganicPad takes is to work with one of the
teacher’s solutions at a time. By holding the solution fixed,
OrganicPad uses a backtracking algorithm to test for equality. If
an atom match is found is found, mark it, and continue matching
the solution key’s subsequent atoms with the student’s remaining
atoms. The student’s node names (atoms) must match those of the
Figure 6. Student completing various steps of a tutorial on
drawing a Benzene molecule.
instructor exactly, so although some backtracking may be
necessary to investigate alternative bijections, no renaming of
student nodes is necessary. Once this backtracking discovers that
a student’s graph matches the solution, the student’s submission is
marked as correct. If no match is found the submission is marked
as incorrect.
Our algorithm is fully compatible with cyclic graphs as well. This
is especially important in organic chemistry where many of the
structures drawn are of a cyclic nature.
3.6 Evaluation
OrganicPad is currently being tested in an organic chemistry class
at Clemson University. Feedback from the students and instructor
are helping strengthen its functionality and improve its usability.
In initial trials with student volunteers using a WACOM drawing
tablet attached to a desktop computer (rather than a tablet PC), all
the students were able to access the software and draw a given
structure within five minutes of the beginning of the trial.
Subsequently all students were able to connect to the instructor’s
PC, receive assignments, and send answers back to the instructor
on each attempt. The instructor could access each student’s
structure – evaluate and store comments for each student.
Students who participated in these trials were asked to complete a
short survey on their experience. In this informal evaluation, all of
the students strongly agreed (average 5.0 on a Likert scale where
5 is strongly agree and 1 is strongly disagree) that the software
would be very useful in learning to draw Lewis structures, they
thought the interface was intuitive and easy to use and get started.
Since the initial trial, we have had another one with updated
software. This trial was a little more challenging than the first
one. Students were generally asked to create more complex
molecular structures than the first trial. In addition, the number of
students increased from 22 students to 36 students. Our software
had no trouble passing information back and forth between the
instructor and students. We again used a Likert scale in a survey
to evaluate the students’ impressions of the software. On average,
students who participated in this trial felt that OrganicPad was
easy to use, OrganicPad would be useful to help students learn to
draw Lewis Structures, and OrganicPad allows you to draw
structures in the same manner that you would draw structures with
a paper and pencil.
3.7 Expansion
Because of the flexibility of the core structures and algorithms,
the principles of OrganicPad can be applied to other academic
fields such as computer science and mathematics. The
relationship to computer science is probably the more obvious
expansion since the structure of a molecule could be stripped
down to just represent a graph. The main features of OrganicPad
would remain in place as well since they are all based on flexible
graph isomorphism algorithms.
We have already started to create a computer science version of
OrganicPad called GraphPad. The GraphPad software was used
frequently last semester during a section of CpSc 212: Advanced
Structures. Students responded very positively to the software.
We are also currently looking into a similar program to be used
with mathematics. Algebraic expressions can be transformed into
a tree structure. Once in this tree form, expressions can be
compared to one another. This could allow teachers to quiz
students in real time and get a better feel of how students are
165
grasping concepts like simplification and expansion. Both of
these fields could use software such as this to help identify
common errors students make.
4. SUMMARY AND FUTURE WORK
OrganicPad has steadily been improving since it was initially
created in the Fall of 2006. Several papers have been submitted
already using OrganicPad as the premise. Notably a paper has
been accepted at PLT 2007 and a poster was accepted at WIPTE
2007. In addition, a proposal for grant funding was submitted to
NSF [6] and was accepted. With this grant, we plan on
purchasing a server to help improve OrganicPad’s features. This
server will enable us to store user information and chemical
drawings into a database. The structure of our database entries
will contain: unique id, timestamp, molecular structure
represented as an adjacency list, and the various steps the user
took in creating the submission. With these drawings, we will try
to find common student errors in the molecule creation process.
Not only will analysis of the final structures be able to help a
teacher identify problems, but since we store each step of the
creation process we will be able to identify at which points the
student got off course. Teachers could then go back and correct
certain repeated errors by reinforcing them in classroom activities.
Most of our future work will surround using OrganicPad in the
classroom. We are planning on using OrganicPad in a lab section
to get a better feel for student ease of use and statistical evidence
that OrganicPad can be used to improve learning. Furthermore
unlike the first trial for the software, we now are equipped with
enough Tablet PC’s for a small class of students. By using a
Tablet PC instead of WACOM slates, we believe students will
respond even better. In subsequent evaluations, we will design
studies to investigate whether the software improves a student’s
ability to draw accurate structures, and ultimately whether they
can use this skill to predict physical and chemical properties.
5. ACKNOWLEDGEMENTS
OrganicPad is funded by Clemson University. A special thanks
goes to Dr. Melanie Cooper and Dr. Roy Pargas. Dr. Melanie
Cooper is a head in the Chemistry department and has helped give
direction and motivation to the project. Dr. Roy Pargas is a
teacher in Computer Science. He teaches a class on Tablet PC
Development. He has helped give guidance throughout this
project. This project has been supported in part by a 2005 Tablet
PC and Computing Curriculum Grant from Microsoft Corporation
(Jane Prey, Program Manager). HP has provided a large number
of Tablet PCs which are currently being used to evaluate the
software on a large scale. NSF is also supporting this project
through a grant which will allow us to continue to work on
OrganicPad for years to come.
6. References
1. WIPTE: http://www.itap.purdue.edu/tlt/conference/wipte/
2. “OrganicPad: A Tablet PC Based Interactivity Tool for
Organic Chemistry”, Pargas, Cooper, Williams, and
Bryfczynski, PLT 2007: http://plt2007.ing.unict.it
3. WACOM: http://www.wacom.com
4. ChemDraw:
http://www.cambridgesoft.com/software/ChemDraw/
5. Toran, J. (2000), “On the Hardness of Graph Isomorphism”,
SIAM J. Comput. 33(5), pp. 1093-1108
6. “OrganicPad: A Tablet PC Based Interactivity Tool for
Organic Chemistry”, co-PIs Cooper, Williams, and Pargas,
NSF Award Number DRL-0735655