An Approach to the Electronic Textbook of Basic Chemistry Linking

Chemical Experiments

CG Teaching Materials based on Quantum Chemical Calculation

Akira Ikuo,

Yusuke Yoshinaga and Haruo Ogawa

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

Keywords: Chemical Experiment, Teaching Material, Tablet Computer, CG, Visualization, Quantum Chemical

Calculation.

Abstract: We tried to make CG teaching materials toward electronic textbook of basic chemistry linking chemical

experiment for university student. The CG teaching materials could demonstrate the nature of the reaction

such as structural change by ball-and-stick model or space filling model with electrostatic potential, and

potential energy change by the reaction profile. The materials included 1) formation of di-atomic molecule

such as hydrogen iodide, 2) hydroxylation of methyl chloride as a model of Walden’s inversion. These CG

teaching materials enabled to load with desktop, laptop, tablet computer, and smart phone. The CG teaching

material of hydroxylation of methyl chloride was tried to combine with chemical experiments to make

electronic textbook of basic chemistry.

1 INTRODUCTION

Chemistry is the subject that has been studied

through the experiment. Understanding the observed

phenomena, chemists use to imagine and explain

observations in terms of molecules. Observed

phenomena and molecular-level models are then

represented in terms of mathematics and chemical

equation. These three thinking levels of observable

level, symbolic level, and molecular level,

respectively was mentioned (Tasker and Dalton,

2010). Visualization is great help for students to

have images of phenomena, chemical concepts, and

molecular world. It is our aim to produce computer

graphics (CG) teaching material, which provides

realizable images of the nature of chemical reaction

(Ikuo et al., 2006).

The reaction of simple molecule such as

hydrogen halide and related compounds plays a

fundamental role in the development of chemical

kinetics and theoretical chemistry (Allison et al.,

1995; Eyring and Polanyi, 1913; Sullivan, 1962).

The reaction of equation (1) is often used for

explanation of reaction rate and

I + H

→ HI + H

(1)

chemical equilibrium in “Chemistry II” of Japanese

high school (Sanseido, 2004). Generally, reaction

profile is used to represent relationship between

potential energies (PE) and reaction coordinate. The

profile is often used in high school chemistry

textbooks (Daiichigakusyusya, 2004;

Jikkyosyuppan, 2004; Keirinkan, 2003; Sanseido,

2004; Tokyosyoseki, 2004). It is sometimes difficult

for student to realize the meaning of reaction

coordinate in the profile because of the

representation by a diagram of PE surface in two-

dimensions (PE-2D) except the rare case of rough

sketch of analogues in three-dimensions (PE-3D) in

physical chemistry textbook of university (Atkins

and Paula, 2002; Moor, 1982). Also images of

synchronization with successive changes of the

structure of objective molecules and distribution of

electrical character can provide clear images of the

reaction.

We developed CG teaching material based on

quantum chemical calculation of chemical reaction

for university student, which can be used to desktop,

laptop, and tablet computer, as well as smart phone.

This paper introduces our works of CG visualization

of fundamental chemical reactions for realizing

certain images of the reaction mechanism and an

approach to the electronic textbook of basic

chemistry linking chemical experiments, which

integrates the observable level experiment and the

molecular world.

688

Ikuo A., Yoshinaga Y. and Ogawa H..

An Approach to the Electronic Textbook of Basic Chemistry Linking Chemical Experiments - CG Teaching Materials based on Quantum Chemical

Calculation.

DOI: 10.5220/0004387406880691

In Proceedings of the 5th International Conference on Computer Supported Education (CSEDU-2013), pages 688-691

ISBN: 978-989-8565-53-2

 2013 SCITEPRESS (Science and Technology Publications, Lda.)

2 PROCEDURE

2.1 Quantum Chemical Calculation

The semi-empirical molecular orbital calculation

software MOPAC (Stewart, 1989a, b, 1991) with

AM1, PM3, and PM5 Hamiltonians in CAChe Work

System for Windows (ver. 6.01, FUJITSU, Inc.) was

used in all of calculations (Ikuo et al., 2009) for

optimization of geometry, for search of potential

energies of various geometries of intermediates, for

search of transition state, and search of the reaction

path from the reactants to the products via the

transition state. The optimized structure of the

transition state was verified by the observation of a

single absorption peak in the imaginary number by

the use of the program Force in MOPAC (Stewart,

1989a, b, 1991) for vibration analysis. If the peak

was observed, Intrinsic Reaction Coordinate (IRC)

(Fukui, 1970) calculation was done and the reaction

path was confirmed.

2.2 CG Teaching Material

A movie of the reaction path was produced by the

software DIRECTOR (ver. 8.5.1J, Macromedia,

Inc.) or Flash CS4 software (Adobe, Inc.) following

the display of the bond order of the structure of the

reactants in each reaction stage, which was drawn by

the CAChe. It was confirmed that the Cast members

were arranged on the stage and the molecular

models of reactants moves smoothly. The ball was

arranged on the reaction profile and the movement

of the ball and the reactants was confirmed. The

movie file was converted to the Quick Time movie

by the Quick Time PRO (ver. 7.66, Apple, Inc.) and

was saved to iPad (Apple, Inc.) by using the iTunes

(ver. 10.7, Apple, Inc.).

2.3 Practice of Teaching Material

Teaching material was practiced to the first year

students of teacher training course for elementary

school and the second year students of natural

environmental science course, of “Chemistry

laboratory” at Tokyo Gakugei University. Teaching

material used for the trial was the CG movie shown

by the tablet computer.

3 RESULTS AND DISCUSSION

3.1 I + H

→ Hi + H

The CG teaching material of rearrangement by

collision of diatomic molecule and one atom as

shown in equation (1) was developed. PE of 2-D and

3-D is shown in figure 1. The figure clearly shows

these changes of PEs with display on PE surface in

3-D, which offers a bird-eye view of the reaction

profile. Two Valleys of lower energies and hilltop

on the transition state at the saddle point can be

recognized boldly. Possible pathways of the reaction

from the reactants of I and H

to the products of HI

and H via the transition state at saddle point can be

readily traced. The CG teaching material is able to

provide information about change of the PE and

structure of reactants in a certain state

simultaneously.

The electrostatic potential on electron density

(EPED) model and ball-and-stick model of the

intermediate, I-H-H, and the reaction profile were

combined in the left side of figure 1 for easier

recognition of those three. The electrostatic potential

(Kahn et al., 1986) was calculated based on the

coordinates of atoms from the IRC calculation

(Fukui, 1970) and superimposed on to the iso-

surface of the electron density at the value of 0.01 e

-3

as shown in the upper left part of the CG. The

values of electrostatic potentials were represented in

different colour on the model of intermediate. The

model by EPED provides information about

electrostatic distribution of the intermediate with

realistic shape on the way of the reaction. In the

middle of the CG, skeletal structure in the ball-and-

stick model in which diameter of the stick reflects

calculated bond order is shown. The lower left part

of the CG shows the reaction profile, which

demonstrates the degree of the reaction progress by

the ball indicating the PE versus the reaction

coordinate. Student could correlate this reaction

profile with the reaction path in the right side of CG.

The left side of the CG is able to provide

information about characteristics of intermediate of

molecule in a certain state on the progress of

reaction.

From the posteriori survey, number of correct

answers in question about “Energy” increased 28%

compared with the preliminary survey (n=49).

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 reaction and changes of energy.” and “I

could see that reaction mechanism and energy

AnApproachtotheElectronicTextbookofBasicChemistryLinkingChemicalExperiments-CGTeachingMaterials

basedonQuantumChemicalCalculation

689

change is closely related.” These comments suggest

that many students were able to obtain the concept

of energy change in chemical reaction from the CG

teaching material.

Figure 1: CG teaching material of I + H

→ HI + H.

3.2 OH

+ CH

Cl → CH

OH + Cl

Structural change of reactants in the reaction shown

in equation (2) was studied as a model of Walden’s

inversion, which is also shown in scheme 1.

+ CH

Cl → CH

OH + Cl

(2)

Scheme 1: Images of Walden’s inversion.

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.

Therefore, the transition state was searched from the

reactants where the bond angle of O-C-Cl was

adjusted to 180°.

The inter-atomic distances of C-Cl in CH

Cl was

calculated as 1.87 Å (1.87 Å) (Weast, 1982), and C-

O in CH

OH was 1.41 Å (1.43 Å) (Shida, 1981).

These values were in good agreement with the

literature values in the parentheses. Energy between

the initial state of reactants and the final state of

products was 165.01 kJmol

-1

. The value was in fairly

good agreement with literature (Shida, 1981) value

of 162.90 kJ mol

-1

Figure 2: Selected picture of CG movies: from the CG

teaching material; Reaction profile and image of reactants;

in space filling and ball-and-stick model.

Selected picture of CG movies are shown in the

figure 2. The CG shows the reaction profile, which

demonstrates the degree of the reaction progress by

the ball indicating the potential energy versus the

reaction coordinate. Movies were made by using not

only the space filling model which shows realistic

shape but also the ball-and-stick model which shows

change in molecular configuration easily. A student

is expected to obtain the image of an umbrella

reverse like motion in Walden’s inversion. In the

space filling, the existence probability of the

electron is 90 %. In the ball-and-stick, the thickness

of stick changes by bond order.

When the CG is touched by student, the Quick

Time control bar appears and the red ball can move

by student’s choice. This manual control feature

provides “Hands-on” feeling to student. This CG

teaching material could provide not only images of

energy change during reaction but also images of

dynamical structure change during chemical

reaction.

The CG teaching material could demonstrate the

structural change of reactants with both space filling

and ball-and-stick models along with the reaction

profile, which can provide image of energy change

during the reaction.

From the result of the questionnaires (n=103),

the answer judged to be able to acquire the image of

Walden’s inversion (the image to which an umbrella

reverses) was follows; the image obtained from the

reaction formula was 24% and from the CG teaching

material was 51%. The number of CG teaching

material was better than that of the reaction formula.

Students were abele to obtain the image of drastic

change of the structure in Walden’s inversion from

the CG teaching material.

C Cl

‐

＋

CSEDU2013-5thInternationalConferenceonComputerSupportedEducation

690

The CG teaching material can be loaded with note

PC, tablet PC, and smart phone.

We tried to produce electric textbook for

chemical laboratory (Figure 3), which integrates the

observable level experiment and the molecular

world.

Figure 3: Prototype electronic textbook.

4 CONCLUSIONS

We produced CG teaching materials included 1)

formation of di-atomic molecule such as hydrogen

iodide, 2) hydroxylation of methyl chloride as a

model of Walden’s inversion. These teaching

materials could demonstrate the nature of the

reaction such as structural change by ball-and-stick

model or space filling model with electrostatic

potential, and potential energy change by the

reaction profile. The CG teaching materials enabled

to load with note PC, tablet PC, and smart phone.

The CG teaching material of hydroxylation of

methyl chloride was tried to combine with chemical

experiments to make electronic textbook of basic

chemistry.

ACKNOWLEDGEMENTS

This work was supported by JSPS Grant-in-Aid for

Scientific Research (C) (22500803).

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AnApproachtotheElectronicTextbookofBasicChemistryLinkingChemicalExperiments-CGTeachingMaterials

basedonQuantumChemicalCalculation

691