ChemPad
Organic Chemistry
 The study of carbon-containing
compounds and their properties.
 A critical and difficult college course
for aspiring chemists and doctors.
Visualizing 3D Molecules
 The ability to understand the 3D
nature of molecule and their 2D
representations is key to mastering
chemistry.
 The 3D form of a molecule determines its
properties.
Visualizing 3D Molecules
Project Goals
 To create a pedagogically-oriented
Tablet PC application which converts
hand drawn molecules into 3D
models.
 For the tool to be stable and usable in
Chem 35 in Spring 2005.
 Partnered with Professor Matthew Zimmt
from Chemistry.
Existing Tools
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Cambridgesoft ChemDraw.
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Doesn’t generate 3D models.
Doesn’t use handwriting.
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Only generates 3D.
Too complicated for beginning chemists.
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Doesn’t use handwriting.
Lousy input method for many basic organic molecules.
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No 2D version.
Very slow work.
Easy to spill.
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Recognizes a large number of handwritten symbols and gestures.
Doesn’t know chemistry at all.
Professional molecule modeling software.
ACD Labs ChemSketch
Physical “Ball and Stick” models.
Fluid Inking.
Using ChemPad
 Demo
Stereochemistry
 Some molecular
formulas can
represent multiple
molecules with
different 3D
structures.
Stereochemistry
 Demo
Stage 1: Proof of Concept Model
and Design Test Bed.
 June-December 2004:
 3D scenes built from spheres and
cylinders in DirectX.
 Inking recognition through XP
recognizers. Unrecognized characters
assumed to be bonds.
 Molecular Interpreting oblivious to
positioning cues in drawing.
 No pedagogical tools.
Stage 2: Preparing for Release.
 January-February 2005:
 Refitting of user interface.
 DirectX replaced with JMol.
 SDK Ink control replaced with Fluid Inking.
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Rethinking of Interpretation algorithm.
Addition of stereochemistry.
IRB protocol approval for user study.
Version 1.0 code freeze.
Stage 3: Release.
 March 2005: Version 1.1 Code
Freeze.
 Used in Organic Chemistry lecture twice.
 Pilot study week.
 12 early adopter students participated.
 Post quiz deployment.
 55 personal invitations.
 16 users yesterday afternoon.
Problems Solved: 2D to 3D
Mapping.
 Overview: Place each atom one at a time in
3-space.
 Find the atom with the highest p-value.
 P-value determined by number of
stereochemistry indicators available to the
atom.
 Position this atom at the origin.
 Use two neighbors to define the XY plane.
 Connect atoms along the main carbon chain in
the XY plane.
 Connect atoms that are off the carbon chain.
 Connect implicit hydrogen atoms.
Problems Solved: 2D to 3D
Mapping.
 For each atom, use its atomic
number, bond orders, and
neighboring bond orders to find the
correct 3D template.
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Tetrahedral
Trigonal-Planar
Linear
Terminal
Problems Solved: 2D to 3D
Mapping.
 Rotate the template so that its
primary connection faces the ‘parent’
atom.
 Rotate the initial atom to match slope
with the drawing.
 Use a cross product to determine an axis
perpendicular to both connections.
 Use a dot product to determine the angle
around that axis.
Problems Solved: 2D to 3D
Mapping.
 Place the atom at a distance based on the
atoms involved and the order of the bond.
 When deciding the parent template
connection to use, take advantage of cues
in the drawing.
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Wedge and dash notation.
Turn directions of the atoms and bonds.
Minimize energy conformation for implicit atoms.
The parent template may need to be rotated.
Problems Solved: CIP
 Chemists describe CIP in vague terms.
 Higher atomic number takes precedence over lower.
 When two atoms directly attached to the stereogenic
center are identical, compare the atoms attached to
these two on the basis of their atomic numbers. Work
outward from the point of attachment and evaluate
substituent atoms one by one. Precedence is
determined at the first point of difference.
 The difference is determined by the substituent of the
highest atomic number and is not additive if there is
more than one substituent.
 Where there is a double or triple bond, both atoms
are considered to be duplicated or triplicated.
Problems Solved: CIP
 Recursively generate a CIP ‘score’
string for each constituent.
 Base case is a terminal atom. Return
the atomic number expressed as a 3
digit string.
 For a non-terminal atom, generate two
lists.
 First is a sorted list of the neighboring
atomic values.
 Second is a sorted list of the nested scores
of the constituents.
Problems Solved: CIP
 Perform an alphabetical string
comparison of the scores.
 Alphabetical ordering finds point of first
difference.
 String lengths may vary greatly in
length.
Problems Solved: R/S
Stereochemistry?
 Given a CIP ordering, rotate the
lowest priority onto the positive Z
axis.
 Project the other constituents onto
the XY plane.
 Note the turn direction from 1 to 2 to
3.
 Right is R
 Left is S
Things We Tried
 “Rotate” 2D image to match 3D
rotation.
 Chemists didn’t like it.
 Multi-stroke symbols using a greedy
algorithm.
 Was prone to errors. Carbon chains look
like letter N.
 Made development more difficult.
User Study
 Demoed in Chem 35.01 last week
 Lab sessions open to students
 4 sessions a week starting last week.
 Students complete a worksheet using
ChemPad.
 28 students so far. Can make up to
29 spaces available per session.
 Personal invites to 55 students.
User Study
 Getting feedback about whether or not
ChemPad is accomplishing its goals.
 Students complete a survey at the end of a
session.
 Gives the development team feedback on
usability.
 Gives us anecdotal evidence of pedagogical
value.
 Comparing quiz scores of students who do and
don’t use ChemPad.
 Comparing only scores on 3D questions.
User Responses
 It's pretty cool.
 It's cool how you can draw a molecule in 2D and have
it represented in 3D.
 I like being able to flip the molecules to see it in the
right orientation.
 Having a 3-D representation of the molecule for
learning purposes is extremely helpful...much better
than on paper
 I like that it shows the C.I.P. numbering so that you
can see if it is clockwise or counter-clockwise very
easily.
 It helped me understand rotation better. It also
helped me visualize which atoms were stereocenters.
Future Work
 General Chemistry Interface.
 Multistroke “normal” input.
 Recognize entire drawing at end of input.
 Expanding Notational Vocabulary.
 More elements.
 More notations such as charges.
 More visualizations for students.
 Allow for larger molecules.
 Combine with other tablet software such as
MathPad.
Acknowledgements
 Special Thanks To:
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Professor Matthew Zimmt
Sascha Becker
Loring Holden
Bob Zeleznik
Professor Andries van Dam
 Funders & Donors:
 Atlantic Philanthropies
 HP