Design and Development of a Multimedia Educational Tool for ...

Education and Information Technologies 8:4, 369–379, 2003.  2003 Kluwer Academic Publishers. Manufactured in The Netherlands.

Design and Development of a Multimedia Educational Tool for Interactive Visualization and Three-Dimensional Perception of Vibrational Spectra Data of Molecules NICKOLAS D. CHARISTOS, VASILIOS I. TEBEREKIDIS, CONSTANTINOS A. TSIPIS and MICHAEL P. SIGALAS ∗ Aristotle University of Thessaloniki, Department of Chemistry, Laboratory of Applied Quantum Chemistry, 54124 Thessaloniki, Greece E-mail: [email protected]

Abstract In this paper the design and development of 3DNormalModes, an educational tool for interactive visualization and three dimensional perception of vibrational spectra data of molecules is presented. The details of the architecture of the tool and its functionality are described. Means of application in chemical education at university level are discussed. A pilot study summarizes the strengths, the educational value and the possible extensions of the system. Keywords:

3D molecular models, vibrational spectra, normal modes, interactive learning, chemical education

1. Introduction Chemistry is considered to be the most visual of sciences (Habraken, 1996), whereas one of the ongoing challenges in teaching chemistry is getting students to explore the various molecular structural features. Often it is difficult and requires quite a lot of imagination to visualize the shape of a molecule in a two-dimensional printed page. Use of plastic physical molecular models in the classroom may help, but such models are typically difficult for students to see when demonstrated by an instructor. These difficulties are more pronounced in teaching spectroscopy, an important part of the undergraduate chemistry curriculum. A firm understanding of the interaction of electromagnetic radiation with matter is extremely useful in studying molecular structure. Especially in the case of vibrational spectroscopy the recognition of the relations between specific spectral transitions and the normal modes of vibration of the molecule, as well as its specific structural features, is of crucial interest. ∗ Corresponding author.

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According to Casanova (1993) and others (McCormick et al., 1987; Box, 1991; Sauers, 1991; Weber et al., 1992; Gotwals, 1995) molecular modeling involves the use of graphicsintensive computer that can model and manipulate images in three dimensions. Because computerized molecular models offer an incredibly rich source of visual and quantitative information, they can be used to great effect to enhance traditional lectures and classroom discussions. Students can use models in a number of different ways on their own computers to learn and explore chemistry. Thus, the use of molecular modeling as an educational tool in the undergraduate curriculum has been prevalent within the past ten years (Canales et al., 1992; Jarret and Si, 1990; Lipkowitz, 1984; Rosenfeld, 1991; Sauers, 1991; Simpson, 1989). In order to provide chemistry education with an applicable tool, this paper presents 3DNormalModes, a discovery-driven “point-and-click” system of interactive visualization of vibrational spectral data. The program is based on molecular modeling and it can be used in university education. It provides a convenient way to illustrate how a molecule vibrates and the properties of its normal modes of vibration in a real 3D environment. By using 3D technology it enables more immersive user experience, allows easy interactivity by letting students to examine and manipulate the vibrating molecules as objects in ways not possible in two dimensions.

2. Vibrational Spectroscopy When a beam of electromagnetic radiation is passed through a substance, it can either be absorbed or transmitted, depending upon its frequency, ν, and the structure of the molecule it encounters. Electromagnetic radiation is energy and hence, when a molecule absorbs radiation gains energy as it undergoes a quantum transition from an energy state (Einitial) to another (Efinal ). The frequency of the absorbed radiation is related to the energy of the transition by Planck’s law: Efinal − Einitial = E = hν. Thus, if a transition exists, related to the frequency of the incident radiation by Planck’s constant, then the radiation can be absorbed. Conversely, if the frequency does not satisfy the Planck expression, then the radiation will be transmitted. A plot of the frequency of the incident radiation vs. some measure of the percent radiation absorbed by the sample is the absorption spectrum of the compound. The type of absorption spectroscopy depends upon the type of transition involved and accordingly upon the frequency range of the electromagnetic radiation absorbed (Bernath, 1995). A minimum energy conformation of a molecule will not be still, even at absolute zero of temperature, but will wobble around. These movements can be separated into a series of simple motions, called the normal modes (Wilson et al., 1955). Each of the vibrational motions of a molecule occurs with a certain frequency, which is characteristic of the molecule and of the particular vibration. The energy involved in a particular vibration is characterized by the amplitude of the vibration, so that the higher the vibrational energy, the larger the amplitude of the motion. According to the results of quantum mechanics, only certain vibrational energies are allowed to the molecule, and thus only certain amplitudes are allowed (Harris and Bertolucci, 1989). Associated with each of the normal modes of the

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molecule, there is a series of energy levels (or vibrational energy states). The molecule may be made to go from one energy level to a higher one by absorption of a quantum of electromagnetic radiation, such that Efinal − Einitial = hν. In undergoing such a transition, the molecule gains vibrational energy, and this is manifested in an increase in the amplitude of the vibration. The frequency of light required to cause a transition for a particular vibration is equal to the frequency of that vibration, so that we may measure the vibrational frequencies by measuring the frequencies of light which are absorbed by the molecule. Since most vibrational motions in molecules occur at frequencies of about 1014 s−1 , then light of wavelength λ = c/ν = 3 × 1010 cm/s/1014 s−1 = 3 × 10−4 cm = 3 µm will be required to cause transitions. As it happens, light of this wavelength lies in the so-called infrared (IR) region of the spectrum. IR spectroscopy, then, deals with transitions between vibrational energy levels in molecules, and therefore is also called vibrational spectroscopy. Raman spectroscopy, although differs in technique, give complementary informations to IR spectroscopy. Analysis of the normal modes of a molecule allows us to see which motions have low energy, and which are less accessible. Thus, one of the ongoing challenges in the teaching of vibrational spectroscopy (IR and Raman) is getting students to recognize the relationship between specific spectral transitions and normal modes of the molecule under investigation. 3. Related Work 3.1. Educational aspects of molecular modeling Casanova (1993) has presented a historical overview of computer-based molecular modeling in chemistry. Lipkowitz (1984) recommends that when his organic chemistry lab students compared computer models with physical models of the same structures, understood that physical models are limited in scope and can give misleading structural information. Simpson (1989) and Jarret and Sin (1990) also used molecular modeling with organic chemistry students. All authors suggested that the combination of molecular and physical models presented a more complete approach to the instruction of molecular stereochemistry. Box (1991) described a molecular graphics program that enables the organic chemistry student to construct, modify, examine, and manipulate organic chemical structures on-screen. A number of applications for molecular modeling are presented by Weber et al. (1992) as well as detailed descriptions of various options available for viewing structures. DeKock et al. (1993) presented an excellent chapter on computational chemistry in the undergraduate curriculum. They presented background information on its use, curriculum issues related to computers and quantum chemistry, molecular mechanics, and molecular dynamics. They concluded that students should emerge with the ability to create three-dimensional mental images, something that in Western civilization has not been important for several centuries. They proposed that the use of the computer as a computational tool needs to be presented in the context of a particular chemical problem and pointed out the need of supervision in computational laboratories to prevent student frustration.

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Hanks (1994) utilized a specific molecule and took the reader through different models of that molecule, such as easy to draw pen and paper structures, ball and stick and space-filling computer generated representations. He discussed the importance of helping students develop models of the microscopic universe and that computer-generated models do deliver the message that molecules are three-dimensional. Martin (1997) has introduced molecular modelling into the undergraduate curriculum starting from Organic Chemistry laboratory. Students learn the theory behind molecular modeling, complete exercises in which they learn how to perform various operations, and then combine what they have learned with a laboratory exercise. The success of this integrated approach has been measured through moderate increases in tested competency in selected aspects of three-dimensional chemistry and also rapid increase in enrolment in upper-level chemistry courses and an increase in the number of majors and minors. Ealy (1999), after a three-year study involving an evaluation of molecular modeling by students in first year college chemistry, found that there was a significant difference in achievement on the final exam between the treatment and non-treatment groups on multiple choice questions pertaining to concepts of resonance, dipole moment, and atomic/molecular stoichiometry.

3.2. Educational tools for vibrational spectroscopy A number of interfaces for the teaching of vibrational spectroscopy have been developed. The Chemistry Hypermedia Project (Tissue, 1995) incorporates the interaction of spectroscopy and interpretation into their multimedia presentation. Some Java-Applets and plug-in based applications (Casher et al., 1995; Rzepa et al., 1998; Lathi et al., 2000) allow the interactive display and manipulation of spectra through the Internet and link such spectra to molecular displays. The IR-Tutor tutorial-based software developed at Columbia University (IR-Tutor, 2002) has an interactive point-and-click interface allowing the student to select an IR peak to visualize the associated vibration; the vibrational animation is not, however, interactive. The Organic Chemistry Online Tutorial (Young, 1999) includes a set of Java-driven spectroscopy problems, with interactive menus having static spectral displays. 3DNormalModes is a tool with an immersive virtual environment, which addresses the specific needs for a highly interactive environment and the ability of the student to manipulate freely the vibrating molecule. Furthermore, it is a standalone application with no need of specific plug-ins. This combination cannot be found in previous systems.

4. Implementation The tool has been developed with the Macromedia Director 8.5 Shockwave Studio authoring tool (Macromedia, 2002). It incorporates Intel’s 3D Graphics software of adaptive 3D geometry including a set of dynamic algorithms that simplifies the tedious task of creating


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interactive 3D content. Also, Macromedia Director, as well as the applications based on it, are available for both Windows and Macintosh platforms. 4.1. Compilation of vibrational spectra data 3DNormalModes includes a database with information concerning the experimental fundamental frequencies (NIST, 2001) and the corresponding normal modes of several inorganic and organic molecules. The normal modes have been calculated by ab initio HF/3-21G calculations (Hehre et al., 1986; NIST, 2002). 4.2. User interface During the design and development of the system, attention has been focused on certain usability features that would ensure the system’s compatibility with user’s requirements, expectations and needs. The results of formative evaluations have been proven valuable in this respect. The basis for the design of the user interface for 3DNormalModes is the usual graphical metaphors of current software used for 3D modeling. The layout for 3DNormalModes is shown in Figure 1. The user can perform all the desired tasks and operations using the various buttons and selection panels. The layout is virtually divided vertically to three sections. In the right section the molecule selection panel (bottom), the simplified IR and Raman spectra (center) and the normal mode selection panel (top) are located. The molecular display and the various buttons that control the animation of the normal modes (top), as well as information concerning the molecule itself and the current normal mode (bottom) are found in the center section. Finally, in the left section the buttons controlling the size and orientation of the molecular model (top), as well as the “Help” and “Exit” buttons are located. Large, textured 3D buttons are used with meaningful 3D icons floating above the buttons to allow easy recognition of their functionality. 4.3. Tools and functions With 3DNormalModes the user can animate a normal mode of a selected molecule in a 3D environment. Also, she/he can rotate, translate and zoom in/out the molecule so that the vibration can be observed from any viewpoint, adjust the speed of the animation to see the motion clearly. Upon entering the program the student is prompted to select a molecule from a list of thirty example molecules available. The selection of a molecule is achieved by clicking the appropriate line in the molecule selection panel. The list of molecules can be sorted by name, formula or their symmetry point group, using the appropriate sorting tab. The selected molecule can be cleared from the screen by pressing the “clear” button in the selection panel. When a molecule is selected, informations concerning its name, formula, symmetry point group and number of normal modes are displayed in the information panel.

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Figure 1. A screen shot of the 3DNormalModes interface.

The 3D molecular model is displayed and the user can translate, rotate or zoom the model as described bellow. Also, a list of its normal modes is displayed in the normal mode selection panel sorted by frequency and the simplified IR and Raman spectra of the molecule, containing the frequencies of the IR or Raman active normal modes, are displayed in the spectrum panel. The selection of a normal mode of vibration of a molecule is achieved by clicking the appropriate line in the normal mode selection panel. When a normal mode is selected, informations concerning its type, symmetry, frequency and IR and Raman activity are displayed in the information panel and the molecule starts to vibrate according to the selected normal mode. The list of normal modes can be sorted by frequency or type, using the appropriate sorting tab. The normal mode can be deselected, resulting in the termination of the animation and the deletion of the normal mode information from the information panel, by pressing the “clear” button. An alternative way for selecting a normal mode of a molecule is by clicking on a spectrum line of the simplified IR and Raman spectra. Upon rolling the mouse over a spectrum line, a tooltip appears containing the information of the corresponding normal mode.


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Figure 2. 3D molecular model display and animation control buttons and sliders.

4.4. 3D molecular display controls Once a molecule is selected and displayed, the user has full control on its orientation and position of the 3D molecular model even when it vibrates according to a normal mode. Thus, she/he can freely rotate the molecule by dragging the mouse on it. Also, using the molecular control buttons (Figure 2), she/he can rotate the molecule around x, y or z axis (button a), translate it on x or y axis (button b), or resize it by zooming in/out (button c). The speed of the rotation, translation or zooming movement can be adjusted by the sensitivity slider (d). The “reset view” button (e) restores molecule’s initial size, orientation and position.

4.5. Animation controls A set of buttons (Figure 2) offers a full control over the animation of a normal mode. Thus, the “Stop/Play” button (f) stops or starts the animation. The “Frame rate” slider (g) controls the speed of the animation. The “Show/Hide Mode” button (h) displays or hides the atom displacement vectors of the current normal mode. The displacement of an atom is represented as a pair of a green and a red vectors showing the directions in which the atoms move forward and backward during the vibration. Finally, the “Displacement” slider (i) controls the length of the displacements of the atoms.

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4.6. Help system The “Help” button is available at the leftmost bottom side of the screen. It points at a series of help screens, where detailed information about the functionality of the program is given, organized by the various tasks a user can perform within the program.

5. User Studies 3DNormalModes is still under development. Until now a prototyping approach has been adopted, characterized by a self-consistent process of design, development, informal evaluation and team discussions. Thus, an informal pilot study has been conducted to evaluate the efficiency of the program and its value for chemistry education.

5.1. Subjects Our 15 participants, aged 22–25, are fourth year students of Chemistry at the University of Thessaloniki. They have been taught spectroscopy and they have good computer skills and basic working knowledge of traditional molecular modeling packages.

5.2. Methods The test session consists of two parts. The first part requires each participant to perform a number of tasks concerning the selection of a molecule, identification of its normal modes of vibration, reorientation of a molecule, control of the animation of a normal mode and construction of paper representation of some normal modes. In the second part all subjects complete a brief survey. The survey contains closed (multiple response items) questions concerning the interface and ease of use of 3DNormalModes, as well as its educational value.

5.3. Results All 15 students received a three-minute introduction into 3DNormalModes, consisting of an explanation how to start the application and how to use the menus and buttons. In total, our students took between 9 and 12 minutes to solve the tasks. This reflects the time they spent using the program. While working with the program, a tutor was present to help when problems occurred and to answer any questions. The assistant gave help regarding mostly the interface and not the scientific concepts presented by the program. From the first time it was obvious that students did not need a long introduction to the program but applied their experience with the known user interfaces to the interface of 3DNormalModes. After selecting a molecule and a specific normal mode all students could complete the tasks easily and without further assistance.


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Figure 3. Two of the normal modes of the methanal molecule as presented in 3DNormalModes and sketched by a student.

The students’ interactions with the program were interesting to be watched. They preferred to examine and compare all the normal modes of a molecule rather than change molecule after one or two of its normal modes have been examined. After the investigation of vibrational data for a number of molecules, they successfully answered to tutor’s questions concerning the characterization of the normal modes of vibration of related molecules, the relation of the type of vibration with the magnitude of its frequency, the effect of center of symmetry in a molecule with the IR and Raman activities of its normal modes, etc. The results of the evaluation survey confirmed our observations. Students found the use of the program easy and self-explanatory. All students’ belief was that they could start working with 3DNormalModes without ever having worked with traditional molecular modeling packages. The quotes from the two students bellow represent some characteristic views: “I rarely visited the Help screen. After the introduction on the use of the program by the tutor I started using it without any difficulties.” “The buttons are almost self explanatory. I liked the way of rotating the molecule by simply dragging it in the space.” Some students quoted that the program helped them to easily describe the motions of the atoms of the normal modes with hand drawing sketches, as such often found in standard textbooks. “The program could help me sketch the normal modes of a molecule for my course work.” Such a drawing of a student along with the corresponding screens of the program is shown in Figure 3. Some students reported problems with the use of the buttons for the orientation of the molecule, as each “click” resulted in a high degree of rotation, translation or zoom, particularly on fast computer systems. Thus, a sensitivity control slider has been added to the program. Setting low sensitivity the user can accurately define the orientation of the molecule in space.

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Concerning the educational value of the program, 14 students felt they benefited from having used 3DNormalModes and believe that it helped them to relate specific spectral transitions to the normal modes of vibration of the molecule. 13 of them think that the program is a good learning environment and it should be further involved in the vibrational spectroscopy courses. Finally, 10 of them said that they find the subject of molecular vibrations and spectroscopy more interesting after the use of 3DNormalModes. Finally, we received a number of good suggestions for improvements. Five students suggested us to implement printing facilities to the program, as well as the ability to save the 3D models and/or normal modes as graphic files in order to include them in their paper work, as quoted bellow: “I would like to have the ability to copy a selected normal mode and paste it in a word processing program.” “If we can print or save the screens as image files, we could have nice transparencies of all the normal modes of a molecule.”

6. Future Work The extension of the system described in order to cover all aspects of vibrational spectroscopy like theoretical background and simulation of experimental procedures is in progress. Furthermore, we are working on the adaptation of 3DNormalModes in order to be delivered through the World Wide Web. This can be done using Shockwave plug in at the client side (Macromedia, 2002), which is included as standard in current versions of popular WWW clients. The fact that the 3D molecular models are created at the client side ensures low transfer times even at low bandwidths. Thus, in the 3DNormalModes site the students will have the choice to run the program on line. The database of the program will be continuously enhanced with new example molecules. Also, a simple mechanism for the upgrade of the standalone application with the current version of the database will be available for downloading via file transfer protocol. Another extension of the program will be the ability for the student to extract and visualize the vibrational data (calculated frequencies and normal modes) from the output files of any of several quantum computational chemistry programs. These programs although were once a research tool for industrial and academic scientists have been developed into tools that are accessible and understandable to undergraduate students. Finally, the implement of saving and printing facilities to the program is in progress.

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