Final Report on NSF Grant DUE-9850645 "Incorporation of Computational Chemistry into the Undergraduate Curriculum"

PI: Scott H. Northrup

Co-PI: Jeffrey O. Boles

Department of Chemistry

Tennessee Tech. University

I. Project Activities

In this NSF CCLI project, entitled Incorporation of Computational Chemistry into the Undergraduate Curriculum, the Department of Chemistry at Tennessee Technological University (TTU) sought to address the need for hands-on student use of computer technology in chemical education by incorporating several novel computer exercises into our present undergraduate curriculum in general chemistry, physical chemistry, biochemistry and senior seminar. We received matching funds for the purchase of 19 high performance personal computers and molecular modeling software HyperChem and ChemOffice to establish a student molecular graphics and modeling laboratory. In addition, the university purchased a Proxima projection system and completely renovated a space in the chemistry building to make an attractive PC Lab for this project.

The project successfully provided upper division physical chemistry, biochemistry, and senior seminar students in-depth meaningful training exercises in the use of computer modeling of atomic and molecular structure and dynamics. We also provided general chemistry students an initial taste of the power and insight afforded by the visualization capabilities of modern molecular graphics. Below we provide a more in-depth description of the research and educational activities we engaged in to achieve these objectives. A collection of developed exercises, tutorials and software generated by this project is available on the Web at:

http://gemini.tntech.edu/~snorthrup/nsfccli/index.html,

Subproject One: Molecular Graphics of Macromolecular Structure

The project developed and implemented molecular graphics exercises for our biochemistry students in CHEM462/465 (General Biochemistry lecture and lab) enabling them to more readily grasp the elements of protein and nucleic acid structure. The students were asked to apply the graphics skills they learned to form hypotheses regarding biological function of their own selected target macromolecules. Using the molecular graphics and modeling software package HyperChem, exercises were be developed to teach students how to download, display, manipulate, and examine macromolecular structures. Profs. Boles taught the students: (i) downloading protein and nucleic acids coordinates from the Protein Data Bank; (ii) highlighting objects of interest in the molecular display by selective coloring, labeling, and rotations; (iii) displaying molecular surfaces; (iv) locating and examining secondary structural features of protein (alpha helices, beta sheets); (v) ribbon drawing of protein backbone structures; (vi) computing and displaying electrostatic fields; (vii) manual docking of molecules. After the completion of learning molecular graphics techniques, students were given a practicum to develop an hypothesis for the structural features responsible for molecular recognition in certain protein systems.

Subproject Two: Molecular Modeling Exercises

The HyperChem molecular modeling software purchased by this grant enabled Prof. David Crouse to perform exercises with his undergraduate organic chemistry classes (Chem311, 312) involving 40 students. Specifically these exercises dealt with teaching students how to perform conformational analyses on internal degrees of freedom in small organic molecules ethane, propane and butane. The tutorials developed for these activities entitled Using HyperChem in Organic Chemistry and Conformational Analysis are posted on the TTU Chemistry Web Site at URL:

http://gemini.tntech.edu/~Snorthrup/nsfccli/organic.html

The senior chemistry majors in Chem491 (Senior Seminar) were exposed to an entire four-week unit of teaching on molecular modeling by Dr. Scott Northrup. Students in this class received formal instruction in computational chemistry in the classroom. The lecture notes may be viewed at URL

http://gemini.tntech.edu/~snorthrup/chem491/lecturenotes.html

They then were given assignments in computational chemistry. The Web table of contents of these assignments can be found at URL:

http://gemini.tntech.edu/~snorthrup/chem491/homework.html

The four assignments are described below as follows.

In Assignment One The students gained familiarity with HyperChem molecular modeling software by working through Lesson 5 of the manual entitled HyperChem: Getting Started Tutorial 1. They then picked one of the compounds on a list provided by the instructor, looked up its structure and properties by Web compound database searching, and built the structure using the HyperChem software. They then followed Dr. Northrup's tutorial on making a Web page and displayed their structure in two different renderings on their own Web page, accompanied by a description of the properties and significance of the compound. The student results of this project can be found on the Web at:

http://gemini.tntech.edu/~snorthrup/chem491/assign1.html.

In Assignment Two, the students measured the structural properties, optimized geometries, and performed a quick conformational analysis on several disubstituted ethanes.

In Assignment Three, the students learned how small molecules are studied by quantum methods and what types of information are available through calculations. They performed a semiempirical quantum mechanical calculation of the nitrogen diatomic molecule, generating plots of the filled molecular orbitals. They constructed potential energy curves for bond stretching of a diatomic molecule. Finally they built the chlorobenzene and nitrobenzene molecules and optimized their geometries using the AM1 quantum mechanical method. Based on what they already knew about relative reactivity of ortho and para positions on substituted benzene rings, they used their HOMO plots to learn the underlying reason behind the relative reactivity of these two molecules at different positions?

In Assignment Four, the students a) used HyperChem to build the biphenyl molecule and performed a molecular mechanics conformational study on it, making a plot of energy versus dihedral angle; b) performed a molecular dynamics simulation on a substituted ethane molecule, describing qualitatively how the motions of the substituent atoms compare to motions of the C and H atoms and observing gauche to trans transitions. c) worked through Lesson 11 - Molecular Orbital Calculations in the HyperChem manual showing how small molecules are studied by quantum methods and what types of information are available through calculations; d) optimized the geometry of the water molecule using semiempirical and ab initio quantum methods and determined the bond angle in each structure, discussing which method compares most favorably with the experimental value of the bond angle of water; e) studied the energetics of angle bending in the water molecule predicted by the AM1 method and constructed a "Walsh diagram" for water.

Subproject Three: Kinetic Molecular Theory Simulation

The Trinity Software product BOLTZMANN, purchased by the NSF grant, was used extensively to teach students about molecular motion at the atomic level by computer simulation in both Chem111 (General Chemistry and CHEM253 (Physical Chemistry). The tutorial prepared by Dr. Northrup for use by the hundreds of science and engineering students taking Chem111 can be viewed at URL:

http://gemini.tntech.edu/~snorthrup/nsfccli/boltzmann.html.

First, the students observed the qualitative motional behavior of the molecules and reflected on their properties relative to the basic concepts of the kinetic-molecular theory of gases: In the next set of observations, the students looked at cumulative statistics on the particles, including the instantaneous speed distribution, the kinetic energy distribution, and the free path distribution of the molecules. The final exercise involved the effusion of gas molecules through a small orifice, which is described by Graham’s Law of effusion. They set up a simulation of a mixture of two gases of different mass both effusing through the same opening and observed which gas makes more rapid progress in populating the region on the other side of the orifice.

Subproject Four: Spreadsheet Applications in Chemistry (SPREAD)

Students made extensive use of MicroSoft EXCEL spreadsheet through the NSF project in CHEM111, CHEM112, CHEM211, CHEM212, and CHEM253. Because the reviewers pointed out that spreadsheets should be introduced early, we modified our original plan to include extensive tutorial exercises and application of EXCEL in first semester general chemistry.

On the first day of general chemistry lab the students were taught to use Excel to perform calculations related to Experiment 1 in our newly revised Chem111/112 Lab Manual entitled Principles of Physical Measurement. Dr. Northrup developed a tutorial for this purpose which can be viewed at Web location:

http://gemini.tntech.edu/~snorthrup/nsfccli/excel.html

As a follow-up, the students used Excel in numerous other experiments throughout the year to tabulate and analyze their experimental data.

In addition, Dr. Northrup developed another tutorial on using EXCEL to numerically study the approach to equilibrium in the ammonia synthesis reaction. This can be viewed at URL:

http://gemini.tntech.edu/~snorthrup/nsfccli/equilib.html

In quantitative analysis CHEM211, Dr. Tye Barber had the students do more advanced exercises using EXCEL to study Fourier analysis principles and superposition of sine waves.

Subproject Five: Accessing Chemical Data Bases (CHEMINFO).

Students of organic chemistry were given numerous opportunities within the context of their laboratory synthesis experiments to use the molecular database searching, including structure searching. No formal training was necessary for this purpose, as the graphical user interfaces of ChemInfo and other Web sites are very intuitive.

Subproject Six: Visualization of Atomic and Molecular Orbitals by Electron Dot Density Maps

One of the primary goals of this project was to transform our existing interactive program for student viewing of atomic and molecular orbitals on a Unix workstation and port it to the PC Windows NT platform in order that a large number of students could make use of these powerful visualization tools in comprehending atomic and molecular orbitals. This was to be done by trying to interface our dot density data with HyperChem. After arduous attempts it was determined this was not feasible, and we decided to rewrite the program in Visual C++. This caused a delay and the work is still in progress, though nearing completion. A presentation was given by the PI at the 1999 Southeastern Regional ACS meeting in Knoxville, entitled Interactive Visualization of Orbitals Using Electron Dot Density Maps. This presentation is being posted on the Web at URL

http://gemini.tntech.edu/~snorthrup/nsfccli/avamo.html

and a copy of the accompanying tutorials can be found at

http://gemini.tntech.edu/~snorthrup/nsfccli/avamo_tut.html,

The Fortran 77 program used to generate the electron dot density data can be downloaded at:

http://gemini.tntech.edu/~snorthrup/nsfccli/ao.html,

The Midas script for Unix users who also have UCSF MidasPlus software who wish to use this product at their site is freely available at:

http://gemini.tntech.edu/~snorthrup/nsfccli/midas.html,

Subproject Seven: Miscellaneous Computational Applications in Chemical Education

In addition to the above reported major subprojects, the department integrated computer usage throughout its curriculum in several other activities and coursework. Freshman chemistry students were taught to use plotting routines and linear regression analysis to study the Beer-Lambert law of spectrophotometric absorption and the Rydberg plot of Hydrogen emission, as described in the tutorial which may viewed on the Web at location:

http://gemini.tntech.edu/~snorthrup/nsfccli/graphics.html

Students of freshman chemistry and sophomore organic chemistry were taught and applied the use of CambridgeSoft ChemDraw software to draw molecular structures for reports. The tutorial on this usage can be viewed at URL:

http://gemini.tntech.edu/~snorthrup/nsfccli/ChemDraw.html

Also, students of freshman chemistry were taught to use Chem3D to construct and view simple organic molecules as a part of a VSEPR lab exercise. This activity is described in detail by the tutorial at location:

http://gemini.tntech.edu/~snorthrup/nsfccli/Chem3D.html

II. Project Findings

Assessment Data Collection:

The primary assessment of the effects of the incorporation of these computer exercises into our curriculum has been done at the end of the Chem111/112 sequence in the Spring each year. A survey has been administered to all laboratory students pertaining to their laboratory experience, where all of the NSF-funded subprojects have take place. A copy of this survey, which would be useful to almost all chemistry departments as an instrument to be used for their freshman chem laboratories, can be downloaded at:

http://gemini.tntech.edu/~snorthrup/nsfccli/survey.html,

In a series of statements, the approximately 300 students were asked whether they "strongly agree (SA)", "somewhat agree (A)", "somewhat disagree (D)", or "strongly disagree (SD)" with the statement. This instrument was given in a year prior to the implementation of the project and then in the subsequent year. Their responses to the following statements most pertinent to the NSF project are as follows:

The computing part of the course was beneficial.

Before NSF: SA=20% A=56% D=23% SD=10% SCORE = 2.80

After NSF SA=27% A=53% D=15% SD=4% SCORE=3.06

I learned much in general chem lab this year

Before NSF: SA=13% A=63% D=23% SD=9% SCORE=2.71

After NSF: SA=19% A=56% D=19% SD=6% SCORE=2.87

I enjoyed general chemistry lab this year

Before NSF: SA=25% A=42% D=19% SD=13% SCORE= 2.79

After NSF: SA=31% A=50% D=17% SD=7% SCORE= 3.00

The results are clear. The students perceived that the computing portion of the course was beneficial to them to a significantly greater degree than before. "Before" means after we had installed the PC hardware and made it available but before we had developed and implemented all the software exercises of the funded project. Those who strongly felt that computing was beneficial to their learning jumped from 20% to 27%. The students also perceived that they learned more in general chemistry lab with the new exercises, those strongly agreeing jumping from 13 to 19%. The enjoyment of general chem lab increased dramatically. Those who to some degree felt that they enjoyed general chem lab jumped from 67% to 81%. This means 4 out of 5 students enjoyed general chemistry lab, which is a remarkable story for a course that is typically shunned if possible by college students.

Upper division physical chemistry students who performed kinetic theory of gases simulations with the software BOLTZMANN reported that is was "fun" and a great "aid to understanding." The instructor perceived that the students had a greater comprehension of microscopic dynamical behavior than before.

III. Training Activities

The PI of the project, Dr. Scott Northrup, and the Co-PI, Dr. Jeffrey Boles, coordinated two in-house workshops in the Department of Chemistry at TTU. These were held in August of 1999 and 2000. The target audience included chemistry departmental faculty, graduate teaching assistants of the department, and education faculty and students having a vested interest in chemical education. Both sessions were well-attended.

In the first Department of Chemistry In-House Chemical Education Workshop, Prof. Tom Furtsch served as the discussion facilitator, and four topics were presented and discussed: Dr. Ed Lisic did a presentation on "Incorporation of Calculator-Based Laboratory (CBL) Data Acquisition Devices into the General Chemistry Laboratory," followed by discussion. Prof. Dave Crouse presented "Use of HyperChem Molecular Modeling Software" in the new NSF/CCLI-funded PC Lab, with hands-on training of the attendees in using HyperChem for chemical education. Prof. Furtsch did a presentation of "Use of WWW in Chemical Education", and Prof. Frank Kutzler shoed the faculty the results of his "Incorporation of Java-based On-line Tutorials in Chemistry Classes." In the second workshop, Professor Jeffrey O. Boles was the Presenter and Discussion Leader and gave a talk on "Incorporation of WebCT into Chemistry Courses."

IV. Outreach Activities

The Department of Chemistry sponsored science enrichment events on three different days over a period of two years for the high school students of two Clay County high schools in Tennessee. These students are disadvantaged in not having laboratory facilities in their school. The students were brought into the campus on weekday mornings, treated to a one-hour chemical demonstration by Dr. Dan Swartling of the Chemistry Department, then provided a two-hour laboratory exercise by Drs. Crouse and Northrup. Inthis activity, students acquired spectrometer data in the general chemistry lab, and then were taken to the new NSF-funded PC lab where they learned to plot their data in 2-D and perform linear regression according to Beer's Law. Students also were allowed to interact with 3-D models of macromolecules using Chem3D and perform dynamical simulations of these molecules. The students were very enthusiastic about their day at TTU and several have entered college at TTU majoring in a science field.

The Department of Chemistry at TTU annuals sponsors the Chemistry Olympiad for the Nashville Section of the ACS. Dr. David Crouse in the coordinator of this event for the Nashville Section and runs the event each year at TTU. Up to a dozen area high schools participate in this event. While students are involved in both experimental and conventional testing activities, the high school teachers were taken into the NSF-funded PC Lab and introduced to chemical education software by Dr. Northrup, PI of this grant.

The Department of Chemistry at TTU participated in the university's ACE Camp this year. This was held for the first time, and stands for African American College Enrichment Camp. Fifteen high school students were brought on campus for a week to participate in a whole host of activities by various colleges and departments of the university. The Department of Chemistry hosted the students for an entire day, providing a morning laboratory exercise and an afternoon PC Lab series of exercises. The handouts describing these exercises are posted on the Web at URL

http://gemini.tntech.edu/~Snorthrup/nsfccli/ACECamp.html

These minority students were excited by their hands-on use of molecular modeling software provided by the NSF grant.

V. Publications and Products

The Department of Chemistry has created a Web site to make available to the chemical education community at-large the results of this NSF-funded CCLI project. This is located at:

http://gemini.tntech.edu/~Snorthrup/nsfccli/

At this location chemical educators can download a wide variety of tutorials, exercises and software developed through this project for the purpose of integration of computation in the chemistry curriculum.

VI. Contributions

In the past three decades the use of computers in chemistry has expanded beyond highly specialized applications into an essential tool for every chemist. The adoption of computers in chemical education has unfortunately lagged behind and our project has made great strides to remedy this situation at our institution. Our certifying body, the American Chemical Society, has increasingly emphasized the vital need for computer training and literacy in postsecondary education, and is taking a strong leadership role in encouraging greater use of computers in chemical education. The hands-on student use of computer technology in the chemistry classroom and laboratory is mandatory in preparing undergraduate students for careers in the basic sciences and technology^.

We have responded to this challenge in the Chemistry Department at Tennessee Tech by agressively implementing this NSF/CCLI project. Not only have we changed the face of how we teach chemistry in our department, but we have developed resources and tools that can provide guidance to other departments wishing to do the same.

One unique way this work has been exploited is in our outreach efforts to disadvantaged students of the Upper Cumberland region of Tennessee and to minority students. These students have been provided a first-time ever exposure to computational science through the funding to this program.