Introduction to Molecular Modeling in Chemistry Education E-Book

Johannes Pernaa

• Herausgeber: Books on Demand
• Kategorie: Wissenschaft und neue Technologien
• Sprache: Englisch

Seitenzahl: 93

Veröffentlichungsjahr: 2017

Beschreibung

Welcome to learn molecular modeling in chemistry education. Molecular modeling is an essential tool for chemistry teachers. It can be used for anything from student-centred activities to teacher-oriented visualizations and evaluation. This book offers theoretical insights and hands-on modeling activities. The goal is to learn how to implement molecular modeling in chemistry teaching. The exercises are performed using Edumol.fi web application, which is a free JSmol-JSME-based molecular modeling and visualization service.

Leseprobe

CONTENTS

Molecular modeling in chemistry instruction

The potential and challenges of molecular modeling

Technological pedagogical content knowledge (TPCK) in molecular modeling

Streamlined using of molecular modeling

From desktop software to web applications: The historical analysis of molecular modeling tools used in Finnish chemistry education

Theory of blended learning

The use of ICT in the 1990s

The use of ICT in 2000–2010

The use of ICT from 2011 onward

Edumol

The history and central technologies of Edumol

JSmol

JSME

Edumol features designed to support chemistry learning and teaching

Retrieving structures

2D sketching

Molecular mechanics

Geometry optimization

Visualizations

Measurement tools

File tools

Social interaction

Computer-based molecular models

Supporting visualization skills: Model types and rotation tools

Model types

Wire and tube

Ball-and-stick

CPK model

Dot surface

Exercise 1. Model types

Exercise 2. Rotation tools

Molecular visualizations and informal chemistry learning

Informal learning in chemistry

Exercise 3. Organic compound groups in magazines and newspapers

Example student task

Exercise 4. Information retrieval

Teacher tips

Example Student task

Partial charges and electrostatic potential surface

Exercise 5. Partial charges and solubility

Answers

Exercise 6. Visualizing acid strengths

Implementation

Visualizing chemical bonding

Exercise 7. Intermolecular and intramolecular forces

Ionic bonds

Covalent bonds – small molecules

Dipole–dipole forces – intermolecular forces

Dispersion forces – intermolecular forces

Giant covalent structures

Metallic bonding

Exercise 8. Similarities between ionic, covalent and polar covalent bonding

Exercise 9. Bond length

Visualizing hybridization

Exercise 10. Hybridization of carbon atoms

Warming up

sp

3

sp

2

sp

Exercise 11. Hybridization of nitrogen and oxygen

Nitrogen

Oxygen

Exercise 12. Hybridization of benzene

Isomerism

Exercise 13. Visualizing constitutional isomerism

Exercise 14. Geometrical isomerism and energy

Exercise 15. Enantiomers

Alanine

Thalidomide

Extra – Other interesting molecules

Exercise 16. Conformational isomerism

Introduction to cheminformatics: Biomodels and databases

The history of cheminformatics

Success stories of cheminformatics and Edumol

Visualizing biomodels

Retrieving biomodels

Biomodel menu

Exercise 17. Retrieving data in different ways

Exercise 18. Visualizing biomodels

Compare possibilities and limitations

Exercise 19. Molecule of the Month articles

Next step: Design your own visualization exercises

Exercise 20. Other JSmol sites

Exercise 21. JSmol web development

Your first JSmol page

Build your own user interface

Checkboxes

Buttons

Links

Exercise 22. Designing molecular visualization exercises

Authors

Index

FOREWORD

Welcome to learn molecular modeling in the context of chemistry instruction.

The goal of this book is to offer theoretical insights and hands-on activities so that chemistry teachers can implement molecular modeling in teaching.

This book includes 22 hands-on modeling exercises. They can be performed using the edumol.fi web application, which is a JSmol-JSME-based molecular modeling and visualization environment.

Users can do the exercises via any device that has a modern web browser and access to the internet. It is vital that all exercises can be done via minimal resources. Our research group has spent over a decade working with commercial software. Our experience is that schools don’t have the funds to purchase equipment and software, let alone update them every three years. Free open source solutions are the only way to support the integration of molecular modeling into schools.

In this book, the level of the theory and the exercises are designed to support the work of primary, upper-secondary and high school chemistry teachers all over the world. Molecular modeling is a crucial part of chemistry instruction and chemistry educational research.

We wish you a great modeling experience with our book.

Johannes, Maija & Shenelle

Helsinki, March 2017

ACKNOWLEDGEMENTS

Our sincere thanks to Teemu Arppe for his accurate preliminary reading and hundreds of ideas how to improve the book. It was a pleasure to work with you again.

Thanks to all the graphical designers in e-Oppi Ltd. The book layout is awesome.

The book has been supported by The Finnish Association of Non-fiction Writers. Thank you for your important support.

TOPICS

The first three chapters illustrate why molecular modeling is vital in modern chemistry education. In the first chapter, we explain what molecular modeling is and why it is an important tool in chemistry instruction. How can molecular modeling support chemistry learning? The second chapter presents a technical account of molecular modeling software development. Chapter three introduces Edumol, the software used in the exercises. In the third chapter we discuss the technology and pedagogical features of Edumol.

Chapters 4–11 constitute the hands-on part of the book. The focus of the exercises is to produce concrete ideas for teaching. Many of the chapters include information regarding chemistry education: chapter 5, for example, describes informal contextual learning. Other chapters include discussions on how to model or visualize certain chemistry topics, such as isomerism, bonding, hybridization. The book ends with chapter 11, which encourages teachers to start building their own visualization exercises by providing them with the basic technical information.

1. MOLECULAR MODELING IN CHEMISTRY INSTRUCTION

Computer-aided molecular modeling which is used in chemistry research can also be an effective educational tool at different stages from basic education to universities and teacher training (e.g. Aksela & Lahtela-Kakkonen, 2001; Pernaa, 2011; Aksela & Lundell, 2008). From a chemistry teacher’s point of view, computer-aided modeling is one of the most useful uses of information and communications technology (ICT) in chemistry teaching (Helppolainen & Aksela, 2015).

This chapter first examines molecular modeling, its possibilities and challenges in light of research knowledge. After the theoretical background, we will discuss the usage of molecular modeling in the planning and application of chemistry teaching. In order to understand the real world possibilities and challenges, we use a model called technological pedagogical content knowledge (TPCK).

THE POTENTIAL AND CHALLENGES OF MOLECULAR MODELING

Models and modeling are an essential part of chemistry and its teaching (e.g. Gilbert & Justi, 2016). In the research of chemistry, models are exploited at every stage of the process: forming hypotheses, observing the action of a phenomenon, explaining research results or formulating new predictions based on models. The models unite theoretical and experimental chemistry by visualizing connections between the three levels of chemical knowledge. (Justi & Gilbert, 2002). By using different models of chemistry – analogical models and computer graphics – an invisible phenomenon may be made visible, which then makes it easier to understand chemistry (Barnea, 2000). Molecular modeling is a so called metacognitive tool (Tversky, 2005) that helps us to communicate, to present information about chemistry and to process that information.

A chemistry model is used to describe a visualization of a specific phenomenon in chemistry. These visualizations help to represent thinking: they make it easier to remember and to process information, as well as to cooperate with others (Jones et al., 2005). A model in chemistry can be a concrete model like a scale model or a molecular model made of plastic, a verbal figure of speech used in an oral or a written description, a mathematical model like the general gas law, a visual model like a picture or a graph or a gestural model like the movement of a hand (Gilbert, Boulter & Elmer, 2000). Electronic molecular models can take the following forms: wire, tube, ball-and-stick, space-filling and dot surface.

Computer-aided molecular modeling is advanteageous in teaching because:

it

helps

students understand chemistry on three different levels: macroscopic (a visible phenomenon), submicroscopic (e.g. electron density) and symbolic (e.g. a formula or a template) (Barak & Dori, 2005; Frailich, Kesner, & Hofstein, 2008)

it

helps

to understand chemistry as a modern field of science (Aksela & Lundell, 2009)

it

helps

to improve skills in visualization and to understand the concept of a model and three-dimensional molecular structures (Barnea, 2000, Pernaa et al., 2009)

it

supports

the elucidation and learning of many concepts in chemistry (Aksela & Lundell, 2008; Kozma & Russell, 2005; Russell & Kozma, 2005), for example chemical bonds (Barnea, 2000; Pernaa et al., 2009), isomerism (Dori & Barak, 2001), orbitals (Flemming, Hart & Savage, 2000; Pernaa et al., 2009), functional groups (Dori & Barak, 2001), electrochemistry (Yang, Greenbowe & Andre, 2004), the structure of a substance and the proceeding of a chemical reaction (Williamson & Abraham, 1995), infrared spectroscopy (Aksela & Lundell, 2008), electron density (Aksela & Lundell, 2008), chemical equilibrium and solution chemistry (Russell & Kozma, 2005) and phenomena in biochemistry (Pernaa et al., 2009).

it

supports

higher-order thinking skills (Webb, 2005; Aksela & Lundell, 2008; Dori & Kaberman, 2012)

it

improves

the making of questions and the skills in inquiry-based learning and modeling, and it makes it easier to shift from three-dimensional models to structural formulas (Dori & Kaberman, 2012)

it

inspires

towards learning concepts of chemistry (Barnea & Dori, 1996; Webb, 2005; Aksela & Lundell, 2008)

it

supports

the handling of experimentally achieved phenomena and discussions about them (Kozma, 2003; Aksela & Lundell, 2008).

With the help of molecular modeling, it is possible to practice practice spatial skills (visual-spatial ability) that are extremely important skills in the teaching and learning of natural sciences (Uttal, Meadow, Tipton, Hand, Alden & Warren, 2013).

The challenges one might encounter when using computer-aided molecular modeling are the same as for using ICT in chemistry teaching generally: teachers usually have (i) a shortage of time allocated for molecular modeling, (ii) a shortage of technological pedagogical content knowledge (TPCK) and (iii) a deficiency of suitable software or teaching materials, and (iv) teaching large groups of students may also be quite challenging. (Aksela, & Lundell, 2008; Helppolainen & Aksela, 2015; Pernaa & Aksela, 2009)

The barriers for using molecular modeling can be divided into first-order barriers, second-order barriers and third-order barriers (see figure 1.1). For example, the necessary resources can be thought of as first-order barriers (Ertmer et al., 2012). A second-order barrier is for example a teacher’s beliefs about the usefulness of the usage (Ertmer et al., 2012). Third-order barriers are design thinking skills that mean using the application at the right time in the right place in various teaching environments (Tsai & Chai, 2012). It is important to take the above-mentioned challenges into consideration in the planning and teaching of molecular models.

Figure 1.1 The barriers for using ICT.

TECHNOLOGICAL PEDAGOGICAL CONTENT KNOWLEDGE (TPCK) IN MOLECULAR MODELING

In all teaching that involves the use of ICT, including molecular modeling, a teacher needs technological pedagogical content knowledge (see figure 1.2) (Helppolainen & Aksela, 2015; Koehler, & Mishra, 2008; 2009; Chai, Koh, Tsai, & Tan, 2011; Rogers, & Twidle, 2013).

Figure 1.2 In the instruction of molecular modeling, a teacher needs technological pedagogical content knowledge (TPCK; Koehler, & Mishra, 2008; 2009), which consists of pedagogical content knowledge (PCK), technological content knowledge (TCK) and technological pedagogical knowledge (TPK).