An Approach to Developing Electronic Textbook for Chemical

Experiment

Taking Walden’s Inversion as an Example

Akira Ikuo,

Hayato

Nieda, Nozomi Nishitani,

Yusuke Yoshinaga and Haruo Ogawa

Department of Chemistry, Tokyo Gakugei University, Tokyo 184-8501, Japan

Keywords: CG, Visualization, Walden’s Inversion, Structure Change, Electronic Textbook, Chemical Experiment.

Abstract: We are developing electronic textbook for of basic chemistry-experiment for university students in which

reaction mechanisms are shown by computer graphics (CG). The CGs of chemical reactions was made

based on the empirical molecular orbital calculations. The CGs include following reactions as a model of

Walden’s inversion where drastic change in structure takes place, such as, formation of 2-butyl alcohol and

1-butyl bromide. The CGs could simultaneously demonstrates the nature of the reaction such as structural

change by the space-filling model and by the ball-and-stick model in addition to providing image of energy

change by the reaction profile. The electronic textbook also displays picture of apparatus and flow-chart of

small-scale experiment. Result of preliminary study on effectiveness of the CG is included.

1 INTRODUCTION

Understanding the observation of the reaction,

chemists try to explain observations by using

molecular models. Observation and molecular

models are then described by chemical equation.

Student’s difficulties and misconceptions in

chemistry are from inadequate or inaccurate models

at the molecular level (Kleinman, 1987). A

molecular structure visualized by the computer

graphics (CG) provides a deeper understanding of

molecule (Tuvi-Arad, 2006).

It is our aim to produce a CG teaching material

based on quantum chemistry calculations, which

provides realizable images of the nature of reaction

(Ikuo, 2006 and 2009). Molecular level animations

combined with video clips of macroscopic

phenomena enabled students to predict the outcome

better (Velazquez-Marcano, 2004). If the CG is

combined with textbook of chemical experiments of

student’s laboratory, students can observe the

reaction from the three thinking levels (Gilbert, 2009

and Tasker, 2010), namely, phenomena in the

observable level and the CG in the molecular level,

and chemical equation in the symbolic level. Our

ultimate goal is to produce an electronic textbook of

chemical experiment, which integrates these three

thinking levels.

Electronic textbook has several advantages over

paper textbook. For example, realistic image can be

shown by photograph or 3-dimensional CG, and

movie. These images could be, photograph of

experimental apparatus, CG of molecular structure

and CG movie of reaction mechanism. In addition,

programmable capability (for example. Singhose,

2013), hyper-link, and networking features provide

inter-active operation. Many electronic textbooks of

chemistry are found but most of them are very

similar to the paper book, and very few are related to

the chemical experiment (Morvant, 2013).

Moreover, combination of the CG movie of reaction

and experiment are not seen.

Walden’s inversion is one of typical reactions in

organic chemistry, and the reaction is often adopted

in teaching material on the curriculum of the

university, including some appropriate schemes,

which are trying to show drastic change in structure

(McMurry, 2001). The schemes should be developed

for student to acquire more realizable images of the

nature of the reaction. Reaction of hydroxide and

chloromethane is a typical example of the

Nucleophilic Substitution in the 2nd order reaction.

Carbon atom at the centre to which halogen attaches

is attacked by the nucleophile, hydroxide, from a

position 180 degrees from chlorine and then methyl

alcohol forms. We reported CG visualization of the

416

Ikuo, A., Nieda, H., Nishitani, N., Yoshinaga, Y. and Ogawa, H.

An Approach to Developing Electronic Textbook for Chemical Experiment - Taking Walden’s Inversion as an Example.

In Proceedings of the 8th International Conference on Computer Supported Education (CSEDU 2016) - Volume 2, pages 416-420

ISBN: 978-989-758-179-3

reaction as a simple model of Walden’s inversion

and the produced CG in the tablet PC effectively

provide information about the nature of the reaction,

such as drastic structural change (Ikuo, 2012).

This paper introduces our works of CG

visualization of formation of 2-butyl alcohol and 1-

butyl bromide for realizing certain images of the

reaction mechanism of Walden’s inversion, which is

aiming at development of the electronic textbook for

chemical experiment of student’s laboratory at the

university and trying to integrates the observable

level experiment and the molecular world of the

Walden’s inversion.

2 METHOD

2.1 Developing Experimental Program

and Textbook

Flow chart adopting a policy (Ikuo, 2015) of

developing an electronic textbook for chemical

experiment is shown in the Scheme 1. Reaction was

selected based on importance in fundamental

chemistry. To exhibit phenomena (left side),

experimental condition was optimized for college

level small-scale chemistry-experiment.

Scheme 1: Flow chart of developing experimental

program and textbook.

The experimental program is made based on the

above-mentioned policy. The attainment targets and

contents of an experimental program are shown in

the Scheme 2. The reaction to which methyl alcohol

is generated from methyl chloride is studied with

CG teaching material as a typical example of the

nucleophilic substitution in the 2nd order reaction. A

learner is expected to grasp a three-dimensional

image of Walden’s inversion in STEP1. The

experiment that forms 1-butyl bromide from 1-butyl

alcohol with simple experiment apparatus is

conducted and the reactant and the product are

confirmed by the infrared spectroscopy. A learner

studies an actual reaction of Walden's inversion by

this unit in STEP2. In addition, the reaction that

forms 1-butyl bromide done by the experiment is

studied with CG teaching material to obtain

molecular image of the reaction. A learner is

expected to acquire an actual image of the reaction

in STEP3. The reaction to which 2-butyl alcohol is

generated from 2-butyl bromide and the nucleophilic

substitution is studied with CG and a learner is

expected to integrate observation and molecular

world of Walden’s inversion in STEP4.

Scheme 2: The attainment target and contents of an

experimental program.

2.2 Creating CG based on Quantum

Chemistry Calculation

Structures of intermediates on reaction were

calculated as follows: the semi-empirical molecular

orbital calculation software MOPAC (Stewart, 1989)

with PM5 Hamiltonian in the CAChe Work System

for Windows (Former name of SCIGRESS, ver.

6.01, FUJITSU, Inc.) was used in all of calculations

for optimization of geometry by the Eigenvector

following method, for search of transition state by

use of the program with saddle point search, and for

search of the reaction path from the reactants to the

products via the transition state by the intrinsic

reaction coordinate (IRC) calculation (Fukui, 1970).

A single absorption peak in the imaginary region

was confirmed by -134.36 cm

-1

in the reaction of 1-

butyl bromide formation and -327.28 cm

-1

in the

reaction of 2-butyl alcohol formation. Structure

changes of intermediate at the transition state were

confirmed. The structures of the initial state, the

transition state and the final state were obtained by

the IRC calculation as shown in Figure 1 and 2.

The Gibbs energies and the inter-atomic distances

obtained by the calculation were in good agreement

with the literature values. Energy changes during

reactions were confirmed. Therefore, it was

concluded that the reaction path and the molecular

Actual reaction of Walden's inversion

Grasp a thr ee-dimensional image of

Walden’s inversion

I ntegrate observation and molecular

world of Walden’s i n v er si on

Acquire actual image of the reaction

Attainment target

Contents of study

For mati on M et hyl alcohol

(Reaction of methyl chloride and nucleophilic substituent)

Exp

STEP 1

STEP 2

STEP 3

STEP 4

Formation 2-Butyl alcohol

(Reaction of 2-butyl alcohol and nucleophilic substituent)

Formation 1-Butyl bromide

(Reaction of 1-butyl alcohol and nucleophilic substituent)

Formation 1-Butyl bromide and the

product are confir med by I R

(Experiment of form 1- butyl bromide from 1-butyl alcohol)

An Approach to Developing Electronic Textbook for Chemical Experiment - Taking Walden’s Inversion as an Example

417

geometry obtained by the calculation were

appropriate for making the CG teaching material.

Figure 1: Results of formation 1-butyl bromide.

Figure 2: Results of formation 2-butyl alcohol.

2.3 Creating CG Teaching Material

and Electronic Textbook

A movie of the reaction path was produced by the

software DIRECTOR (ver. 8.5.1J, Macromedia,

Inc.) following the display of the bond order of the

structure of the reactants in each reaction stage,

which was drawn by the CAChe. The obtained CG

of the ball-and-stick and space filling models were

combined with reaction profile of the corresponding

reaction stage. It was confirmed that the drawn CGs

of the molecular models of reactants moves

smoothly. The ball, which indicates progress of the

reaction, was arranged on the reaction profile and

simultaneous movements of the ball and the

reactants were confirmed. Rotational models were

made with PyMOL (ver. 1.7, Schrödinger). Created

movie file was converted to the Quick Time movie

for iPad by the Quick Time PRO (ver. 7.66, Apple,

Inc.). Electric textbook was produced with iBooks

Author (ver. 2.4, Apple, Inc.) and was saved to iPad

(Apple, Inc.) by using the iTunes (ver. 12.3, Apple,

Inc.).

3 RESULTS AND DISCUSSION

3.1 Feature of Electronic Textbook

CG teaching materials of the Walden’s inversion

were combined with chemical experiments of

student’s laboratory for the purpose of making

electronic textbook of basic chemistry to provide

experiment at the observable-level, CG visualization

at the molecular-level, and chemical equation at the

symbolic-level.

The electronic textbook was inserted with images

of experimental procedure of the flow chart (Figure

3) and slides of photographs (Figure 4), which can

be enlarged by students touch.

Figure 3: Enlargeable flow chart of experimental

procedure.

CG teaching materials of reaction profiles in

both models, the space filling and the ball-and-stick,

were also inserted (Figure 5). The CG shows the

reaction profile, which demonstrates the degree of

the reaction progress by the ball indicating the

potential energy vs. the reaction coordinate. When

student touches the CG teaching material in the

tablet computer, the teaching material appears to

show image of the structural change during the

reaction. If student touches the material again, the

Quick Time control bar appears and the red ball on

the profile can move by student’s choice. Student

can manipulate the reaction back and forth until they

obtain the image of the reaction. A student is

expected to obtain the image of an umbrella reverse

like motion in Walden’s inversion.

If student wants to watch the model from different

angle, one could rotate the model (Figure 6) by

touching the CG.

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418

Figure 4: Slide Picture of apparatus.

Figure 5: CG teaching materials.

Figure 6: Rotational models.

3.2 Practice of Teaching Material

The CG Teaching material was practiced on 5

students, the second and third year students of

teacher training course at Tokyo Gakugei

University. Teaching material used for the trial was

the CG movie shown by the tablet computer. Pre and

Post survey about image of Walden’s inversion

reaction were conducted.

After watching CG teaching material, student

image of the structure change was improved.

Students described their comments in the free

description section of the questionnaire, such as,

“With image, it was easier for me to understand the

way of inversion,” and “I could see the reaction

mechanism and progress by the movie.” These

comments suggested that the teaching material was

able to provide image of the inversion. Another

student commented “It was good because I could

rotate the molecule.” This comment suggested that

the rotational model helped student to obtain

structure of molecule.

Although more study need to be done on the

effectiveness of the electronic textbook, students

were able to obtain image of the Walden’s inversion.

4 CONCLUSIONS

We developed computer graphics teaching material

for university student, concerning reaction with

drastic change of the structure of reactants in

following reaction as example of Walden’s

inversion; formation of 2-butyl alcohol and 1-butyl

bromide. The CGs could demonstrate the drastic

change of the structure and the reaction profile can

provide image of energy change during the reaction.

The textbook could display picture of apparatus and

flow-chart of experiment in addition to CGs.

Preliminary study on effectiveness of the CG

suggested that students were able to obtain image of

the Walden’s inversion. The developed electronic

textbook in the tablet could be used to integrate the

observable level experiment and the molecular

world.

ACKNOWLEDGEMENTS

This work was supported by JSPS KAKENHI Grant

Numbers 25350188, 26350227.

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