Spring 2008 CONFCHEM	Chemistry at the National Science Digital Library An on-line conference, April - June 2008
	Abstracts	Papers	Instructions	Discussion Archive

 

P7: CSERD–Another Important NSDL Pathway for Computational Chemistry Education

Abstract

The high school and undergraduate chemistry curriculum has traditionally focused on teaching the experimental and theoretical foundations of modern chemical knowledge. Faculty members are comfortable with this approach because this is how they were taught. In recent years Internet availability, the rapid increase in desktop computer power, the decreasing cost of hardware, and availability of easy-to-use software have made it possible to use computational chemistry as an additional educational tool.

Computational Chemistry Education may be considered in two different ways. The simplest approach–Computational (Chemistry Education)–is the use of technology to teach chemical concepts. Typically, readily available software is used for interactive sessions, simulation of instruments or data, modeling concepts, or for demonstrations. The second approach–(Computational Chemistry) Education–involves teaching computational tools such as spreadsheet or other mathematical software, molecular and mathematical modeling software, and programming to learn chemistry.

One purpose of the National Science Digital Library (NSDL) is to help the educator locate and evaluate materials quickly and effectively. The Computational Science Education Reference Desk (CSERD) serves as the Pathway to NSDL for computational science–including resources for chemistry education. The catalogued items may be searched and often contain peer reviews. The use of CSERD and the reviewing process is discussed.

Introduction

The high school and undergraduate chemistry curriculum has traditionally focused on teaching the experimental and theoretical foundations of modern chemical knowledge. Faculty members are comfortable with this approach because this is how they were taught. In recent years Internet availability, the rapid increase in desktop computer power, the decreasing cost of hardware, and availability of easy-to-use software have made it possible to use computational chemistry as an additional educational tool.

One of the purposes of the National Science Digital Library (NSDL) is to help the educator to locate and evaluate materials quickly and effectively for the Science, Technology, Engineering, and Mathematics (STEM) areas. The NSDL has several access pathways for a given discipline such as chemistry. For example, in addition to the Chemical Education Digital Library (ChemEd DL) pathway, suitable chemistry educational materials might also be found using the biology and physics pathways at BioSciEdNet hosted by the American Association for the Advancement of Science and at ComPADRE hosted by the American Association of Physics Teachers, respectively. One very important resource for chemistry education materials is the Computational Science Education Reference Desk (CSERD) which serves as the pathway to NSDL focusing on computational science education in more than 40 disciplines–including resources for chemistry education.

CSERD is hosted by The Shodor Education Foundation, Inc. and may be accessed at

http://www.shodor.org/refdesk or http://cserd.nsdl.org. The major goal of the reference desk is to help students learn about computational science and to help faculty members incorporate computational science into the classroom by cataloging and collecting quality resources from the Internet and other easily accessible sources, providing a forum for review of these resources by users and other experts, and providing original computational science resources created by users or the CSERD team.

CSERD Website

The users of the CSERD website fall into three classifications–general users, reviewers, and contributors. There is no registration or log in requirements for a general user to use the reference desk for searching by Subject, Keyword, User level (e.g., student or faculty), Educational level, or Resource type. The general user may browse and have access to all resources and reviews.

Users who wish to serve as reviewers have all of the privileges described above for the general users, but are asked to create an account and use a log-in procedure to submit reviews. Reviews are absent for many catalog items and additional reviewers are needed. Information on volunteering as a reviewer can be found at http://shodor.org/refdesk/join. All reviews are evaluated before being posted on the CSERD website.

Two types of reviews may be submitted for a catalog entry: Guided (Structured) and Unguided (Free Form). Extensive help is available to aid in the completion of both types of reviews.

Guided reviews are a set of specific questions, all of which are optional. They are designed to simplify the review process, especially for users who are unfamiliar with the Verification, Validation, and Accreditation (VV&A) process.

Unguided reviews are for freeform input. A minimal set of questions is provided and reviewers can also upload pre-written review documents if they choose. Submission of an unguided review assumes that the reviewer is familiar with the VV&A process, or has studied the full documentation available on how to write reviews.

The three types of reviews are outlined below:

Verification reviews answer the basic question, “Is the simulation correct with respect to its model?” Verification ensures that the software runs properly on different computer operating systems and browsers and that the model uses the correct algorithm to describe the system being studied. There are four tests in which a model can be judged as to whether it is correct:

          •         What is the consistency in the implementation of the model?

          •         What is the theoretical justification for the model?

          •         Are physical laws applied in the model in meaningful ways?

          •         Are the fundamental assumptions in the model reasonable?

Validation reviews are more complicated than verification reviews in that the reviewer is required to have a greater amount of subject area expertise. Validation ensures the results of the model are correct and could reproduce actual experimental data. The basic questions being answered in a validation review are:

          •         Is the science valid and does the model use current methods and techniques?

          •         Is the numerical model adequate to convey the science principles at the level of the question being asked?

Accreditation reviews should be completed by classroom instructors and those responsible for the learning environment for the target audiences. Accreditation ensures that the model achieves the educational purpose and is appropriate for the audience for which it was designed. Other questions being answered in an accreditation review are:

          •         Is the model correlated to other standards in the model content area?

          •         Is the model accessible to all users and is it useful in achieving a desired learning outcome?

Users who wish to serve as contributors have all of the privileges described above for the general and review users, but also may submit URLS or titles of items that they have discovered and feel would enhance the catalog, submit new materials such as simulations or models to be posted at CSERD, or provide explanatory or supplementary materials for existing items such as a lesson plan. All contributions are reviewed before being posted on the CSERD website and the actual files for new materials may reside either with the contributor or at CSERD.

Use of Materials

The decision to incorporate computational materials into the high school or undergraduate chemistry curriculum should be based on several factors such as the overall expense (hardware, software, and effort) and whether or not the materials are beneficial to the educational process. These materials might simply be incorporated into a single course by an instructor, integrated into several courses “across the curriculum,” or serve as the foundation of a separate course. There is a considerable collection of “free” and low-cost software (e.g., J. Chem Ed. Software) that is available in addition to more expensive commercial software.

The incorporation of computational materials in a course should allow the introduction of new topics, the presentation of current topics in a more efficient and clearer way, or the presentation of topics using a different approach that is more effective. These materials would not necessarily need to be used only in a formal classroom situation, but could be used as demonstrations, supplemental study materials, assigned exercises, graded homework, or even as the basis of a guided discovery situation for a group or individual. One important educational aspect of many computational materials is that they can be used in an interactive manner by the student or instructor. Questions can be asked, predictions can be made, and the answers can be discovered via virtual experimentation. This mode of inquiry often results in higher levels of student engagement and allows for more effective learning as the student can discover important relationships on their own.

Incorporating computational materials often results in curriculum revision. For example, molecular modeling could be integrated “across the curriculum” by having general chemistry students study the structures of the simpler compounds that they are learning about and often shown as text figures. Organic students might compare the relative stabilities of various isomers or conformers and determine regions of molecules that might be subject to either an electrophilic or a nucleophilic attack. Physical chemistry students might consider details of various molecular orbitals, predict thermodynamic properties, and predict and analyze UV-VIS and other types of spectra. Students in the inorganic course might look at the structure of more complex inorganic compounds and students in advanced course might consider NMR predictions, spectral assignments, and group theory.

The curriculum could be changed by the addition of a separate computational modeling course. For example, an introductory course entitled “Computational Science and Informatics” involving the Departments of Biology and Chemistry is taught at North Carolina Central University (NCCU). The hands-on course introduces different types of modeling and serves as an introduction to the area of bioinformatics. NCCU also offers both undergraduate and graduate courses in “Computational Chemistry” that include both molecular modeling and kinetics. The College of Charleston has developed an undergraduate courses entitled “Introduction to Modeling in Chemistry” that emphasizes molecular modeling and also has a brief kinetics section.

Examples

Computational Chemistry Education may be considered in two different ways. The simplest approach–Computational (Chemistry Education)–is the use of technology to teach chemical concepts. Typically, readily available software is used for interactive sessions, simulation of instruments or data, modeling concepts, or for demonstrations. The second approach–(Computational Chemistry) Education–involves teaching computational tools such as spreadsheet or other mathematical software, molecular and mathematical modeling software, and programming to learn chemistry.

To illustrate these two approaches, several examples of computational materials from various CSERD searches are briefly described below. Most of the examples are items from the chemistry listings of CSERD; however, because of the breadth of chemistry, there are items of interest listed in some of the other discipline areas as well. For example, the mathematics section will list materials that may be used to teach or review mathematics tools used in chemistry, the biology section will list materials of interest for biochemistry, and the physics section will list materials of interest for general chemistry and physical chemistry. All of these software examples are available at no cost.

The above search started by selecting “Subject” in the “Browse:” drop down menu at the top of the CSERD home page. Selecting “Chemistry” in the “Subject” drop down window on the Browse page created a second drop down menu asking the user to “Select a Category”. Selecting “Keyword” and choosing “molecular modeling” created a third drop down menu in which the “Education Level” was chosen. This, in turn, created another drop down menu in which the “Audience” was chosen. Successful searches usually do not require all of these steps.

Each search result consists of three sections–a link to an information page at the top, a brief descriptor of the result in the center, and a direct link to the respective website at the bottom.

Molecular Model for an Ideal Gas

http://www.phy.ntnu.edu.tw/ntnujava/index.php?topic=25

search keywords: Boyle's Law Animation, Charles's Law, gas laws, ideal gas, ideal gas law, kinetic molecular theory, kinetic theory, kinetic theory of gases, molecular dynamics, molecular dynamics simulation, molecular dynamics software, Properties of Gases, thermal equilibrium

This JAVA applet may be used as a classroom demonstration or for various homework assignments in general chemistry. In a classroom setting, individuals or groups of students could be assigned to collect data that show V is proportional to 1/P under conditions of fixed N and v, V is proportional to N under conditions of fixed P and v, and V is proportional to v² under conditions of fixed P and N. Combining these relationships with the postulates of an ideal gas, a derivation of PV is proportional to nT can be completed.

Molecular Workbench

http://mw.concord.org/modeler

search keywords: animation, atomic interactions, Atoms, biological phenomena, biology, Chemistry, chemistry software, computational chemistry, computational models, free, gas laws, ideal gas, ideal gas law, kinetic molecular theory, kinetic theory of gases, molecular dynamics, molecular dynamics simulation, molecular dynamics software, molecular interactions, molecular viewer, molecular workbench software, molecules, Properties of Gases, thermal equilibrium

This is a collection of simulations can be used in general chemistry and physical chemistry to illustrate various aspects of the kinetic-molecular theory of gases, heat transfer, and spectroscopy. In addition there are simulations in protein folding suitable for biochemistry, nanotechnology, molecular interactions, chemical kinetics, states of matter, quantum and molecular mechanics, and molecular interactions that can be used in several different courses as classroom demonstrations or supplementary study material.

Mol4D: A Web-Based Computational Chemistry Interface for Educational Purposes

http://www.cmbi.kun.nl/mol4d/index.html

search keywords: chemical drawing, chemical reaction, chemical structure drawing, Chime, computational chemistry, conformational searching, free, models, molecular modeling software, organic chemistry, organic reaction mechanisms, reaction, reaction mechanism, semi-empirical computation, semiempirical, structure drawing, tutorials, vrml, web based

This collection of simple molecular mechanics calculations and structures can be used as a classroom demonstration in organic chemistry, for supplementary study material, and for homework. For example, a comparison of the barrier energy for the rotation of various groups around a carbon-carbon single bond could be made.

Symmetry Tutorial

http://symmetry.otterbein.edu

search keywords: molecular symmetry, symmetry, symmetry elements, symmetry operations, symmetry tutorials, visualization

This software brings to life the various symmetry operations and elements in a way that cannot be presented by models or “hand waving” for inorganic and physical chemistry students. Students may use the program repetitively until they are able to visualize this complex subject.

Virtual Lab

http://www.chemcollective.org/vlab/vlab.php

search keywords: instructional materials, interactive, learning activity, simulation

This is a collection of “dry labs” that might be used in a prelaboratory setting, as a classroom demonstration, or for supplementary study. Shown is the equipment and reagents for explaining an acid-base titration procedure for general chemistry.

Infrared Spectroscopy: Identifying Spectral Modes

http://www.umass.edu/microbio/chime/ir-spect/index.htm

search keywords: infrared spectroscopy, IR, IR spectroscopy, IR spectrum, normal modes, spectra, spectral interpretation, spectroscopy, spectroscopy resources, spectrum, vibrational modes, vibrational spectroscopy

This software is useful for organic students to understand the connection between molecular vibrations and the peaks on a spectrum and is suitable for classroom demonstrations, homework, and individual study. There are also NMR and MS spectral studies available.

An Introduction to Chemistry Shockwave Animations

http://preparatorychemistry.com/Bishop_animations.htm

search keywords: Acid Animation, Acid/Base Reaction Animation, Animation of a Precipitation Reaction, Animation of Dissolving NaCl, animations, Boyle's Law Animation, Charles's Law, chemical education, Chemistry, Element Properties, Ethanol, Gay-Lussac's Law Animation, Pressure-Moles Animation, Single-Displacement Reaction, Solubility, Structure of Matter, The Structure of Water, Volume-Moles Animation, Water Mixing

This collection of animations can be used to supplement the static figures in textbooks. The animations for dissolution processes, chemical reactions, stoichiometry, and gas laws may be used as classroom demonstrations and for supplementary study. Shown is the dissolution of NaCl in water.

NetLogo

http://ccl.northwestern.edu/netlogo

search keywords: agent, agent-based, animation, educational software, modeling, simulation, visualization

Although NetLogo is an agent based programing language, the installation of the program includes a large installed library of applications and access to the shared models posted by members of the large user group. The user group is willing to share applications and help others interested in programing for classroom demonstrations or individual study in general chemistry. These applications can be used as classroom demonstrations and for supplementary study. In addition, a web-delivered chemistry unit on the topic of the gas laws for high-school chemistry focusing on learning with models is available as part of the Modeling Across the Curriculum project (information is available at http://ccl.northwestern.edu/mac/).

References: (1) Wilensky, U. (1999) NetLogo. http://ccl.northwestern.edu/netlogo Center for Connected Learning and Computer-Based Modeling, Northwestern University. Evanston, IL. (2) Wilensky, U. (2003) NetLogo B-Z Reaction model. http://ccl.northwestern.edu/netlogo/models/B-ZReaction Center for Connected Learning and Computer-Based Modeling, Northwestern University, Evanston, IL. (3) Wilensky, U. (1997) NetLogo GasLab Maxwells Demon model. http://ccl.northwestern.edu/netlogo/models/GasLabMaxwellsDemon Center for Connected Learning and Computer-Based Modeling, Northwestern University, Evanston, IL.

Vensim PLE

http://www.vensim.com/venple.html

search keywords: free, math, math software, Math Tools, mathematics software, modeling, shareware, software, system dynamics

This software is an example of system dynamics software (or graphical interface differential equation solver software) that may be used to study simple and complex chemical kinetics without emphasizing the solution of the differential equations involved. The screen shot illustrates a model for simulating the kinetics of a system consisting of consecutive reactions in which both reactions are reversible. With appropriate choices on “slider bars” shown in the above model, several different types of complex kinetics systems can be studied by physical chemistry students. This software may be used as a classroom demonstration, as a homework assignment, or for individual study.

WebMO

http://www.webmo.net

search keywords: chemical drawing, chemical structure drawing, Chemistry modeling, chemistry modeling tools, computational chemistry, free, modeling software, molecular, molecular geometries, molecular mechanics, molecular modeling, molecular modeling software, molecular models, molecular orbital, molecular orbital theory, molecular visualization, molecular visualization and modeling, semi-empirical computation, structure drawing

This software serves as a user interface for use with free molecular modeling engines such as MOPAC and GAMESS or with commercial software to create a web-based molecular modeling system for all level of students for classroom demonstrations, homework, laboratory assignments, and supplemental study. Shown are the steps in determining the minimized structure for formaldehyde.

Computational Chemistry for Chemistry Educators (CCCE)

http://www.computationalscience.org/ccce

search keywords: Basis sets, chemical drawing, Chemical education software, chemical kinetics, chemical structure, Chemical structure viewing, Chemistry, chemistry education, computational chemistry, density functional theory, energy minimization, geometry optimization, Hartree-Fock, molecular mechanics, molecular modeling, molecular modeling software, molecular models, molecular orbital, Molecular Orbital Package, molecular orbital theory, molecular structure, molecular structures, molecular visualization, molecular visualization and modeling, semiempirical, transition state

This website contains lecture slides for a complete introductory course in molecular modeling and a set of exercises written for most of the major software packages. Also available is an exercise for modeling chemical kinetics using various software packages.

Function Flyer

http://www.shodor.org/interactivate/activities/flyall/index.html

search keywords (mathematics): algebra, Cartesian coordinate, Coordinate plane, Coordinate system, Cosecant, Cosine, Cotangent, Exponential, Function properties, Functions, Graph, Integers, Intervals, Inverse, Linear equations, Linear functions, Logarithm, Parabola, Positive part of the operand, Range, Secant, Sine, Slope, Tangent, Trigonometry

This JAVA applet can be used to help students review and understand the relationship between a written equation and a graph of that equation. The web-based applet is one in the series collectively known as Project Interactivate (The Shodor Education Foundation, Inc.).

Least-Squares Polynomial Approximation

http://www.chem.uoa.gr/Applets/AppletPoly/Appl_Poly2.html

search keywords (mathematics): applet, Chemistry, interactive applet, least squares regression, mathematics, Physics, polynomial fit

The purpose of this software is to help students review and understand the least-squares determination of an equation to fit experimental data, the importance of out-lying data, and the significance of R².

AutoDock 

http://autodock.scripps.edu

search keywords (biology): computational chemistry, ligands, receptor, receptor binding, substrate, substrate binding

This link is to a suite of automated docking tools designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.

References: (1) AutoDock 3 & 4: Morris, G. M., Goodsell, D. S., Halliday, R.S., Huey, R., Hart, W. E., Belew, R. K. and Olson, A. J. (1998) “Automated Docking Using a Lamarckian Genetic Algorithm and Empirical Binding Free Energy Function”, J. Computational Chemistry, 19: 1639-1662. (2) AutoDock 4 Scoring Function: Huey, R., Morris, G. M., Olson, A. J. and Goodsell, D. S. (2007) “A Semiempirical Free Energy Force Field with Charge-Based Desolvation”, J. Computational Chemistry, 28: 1145-1152. (3) AutoDock 2.4: Morris, G. M., Goodsell, D. S., Huey, R. and Olson, A. J. (1996) “Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4”, J. Computer-Aided Molecular Design, 10: 293-304. (4) AutoDock 1: Goodsell, D. S. and Olson, A. J. (1990) “Automated Docking of Substrates to Proteins by Simulated Annealing”, Proteins: Structure, Function and Genetics, 8: 195-202.

Elemental Absorption and Emission Spectra

http://jersey.uoregon.edu/vlab/elements/Elements.html

search keywords (physics): absorption, emission, general chemistry, line spectra, spectra

This software may be used to study the atomic spectra of a greater number of atoms than are usually presented in textbooks. In addition to general chemistry, atomic spectra are studied in physical chemistry, advanced inorganic chemistry, and in various analytical chemistry courses.

Conclusion

NSDL through its various Pathways has made finding suitable computational chemistry materials to include in the high school or undergraduate curriculum much easier than simply surfing the web and hoping to find something among the millions of “hits” that most search engines return. Many of these materials are reviewed and instructional aids are often available.

Because today’s students are often more comfortable with technology than are their instructors, it can be beneficial to capture students’ interest in technology and use it to help improve the educational environment. Instructors who effectively incorporate computational tools in their courses will find increased student interest and engagement that can lead to improved student learning outcomes.

Acknowledgments

The Computational Science Education Reference Desk is a project of The Shodor Education Foundation, Inc., and is funded by the National Science Foundation through the Division of Undergraduate Education National Dissemination Grants (DUE 0435187).

Copyright Statement

Copyright © 2008 by Shawn C. Sendlinger and Clyde Metz, all rights reserved. Screen shots shown are with the permission of the authors.