edited bv

computer series, 1 68 JAMES P. BIRK

Arizona State University Tempe. AZ 85287-1 604

Teaching Practical Computer Skills to Chemistry Majors Boyd L. Earl, David W. ~ m e r s o n , ' Brian J. Johnson, and Richard L. Titus The University of Nevada, Las Vegas, Box 454003,4505 Maryland Parkway, Las Vegas, NV 89154-4003

In a plenary lecture a t the 1988 biennial Chemical Edu- cation Conference, Crosby ( 1 ) suggested that chemistry de- partments should consider reducing requirements in com- puter programming for majors and emphasize instead the use of commercially available, user-friendly software pack- ages. The justification is that, unlike the situation a dec- ade ago, there is now a much wider availability of good software and ever more powerful, reasonably priced desk- top computers. Taking this advice, we instituted a one-se- mester, one-credit course that introduces students to a va- riety of software useful to chemists.

Objectives Our goals are to:

1. acquaint students with various types of software useful tc chemists,

2. insure that they get some rudimentary, hands-on experi- ence with this software using subject material drawn from their maior: " .

3. increase the quality of the written submissions, ealeula- tions, graphs, ete., that the students turnin after complet- ing the course;

4. give students the benefit of some labor-saving tools so that they can do more and better work in a given length of time:

uet oTtjle ex&ience of taking a programming co&&

One of our best graduates of recent years, now a doc- toral student a t a leading research university, reported that after his required programming course, he dreaded using a computer and that this course removed his fear.

The course is rewired of all nnderaaduate chemistrv majors, and completion of organic chemistry is a prereq- uisite. The majors used to have to take two computer pro- gramming courses. Now they must take one programming course and the course described here, but neither the pro- gramming course nor this course is a prerequisite for'the other. For budgetary reasons we spread the teaching load for this course over a number of volunteer faculty each of whom is responsible for teaching the fundamentals of one or two d l w a r c packages and one ol'whom is rt!sponiihl(! for preparing the syilnhu~ find coordineting t h course. Few cumnuters ;Ire awil;ihli~ so rhc course IS orered everv semester. The team-teaching approach is advantageous because several neonle have innut into the content. several of the subdisci$inks of che&istry are represented, and participating faculty members enjoy the advantage of be- coming more proficient themselves in the use of certain software packages that are useful in their teaching and re- search. The library also is involved in the course by having a staff member assist students in conductiup database searches thereby polishing their own skills a s well a s those

of the students. In retrospect, being a member of the team teaching this course has heen more of a boon than a bnr- den. The various parts of the course are described in more detail below.

Discussion

The overall topical outline is as follows.

Week 1 2 & 3 4-5

6-8 9 & 1 0 11 12-1 5

Hardware

Tonic ~Gdware and MS-DOS Basics Word Processing Drawing Chemical Structures and Molecular Modelling Spreadsheet and Statistics Graphing Initiation of Literature Search Computations

We have two 386 machines in a separate room available for student use, which includes this course, assignments for other courses, and other work that students mav wish to do. Demand as yet has been insufficient to requ$e for- mal allocation of time. Initially, students gathered in the . . - computer room for instructional demonstrations. Lately a n LCD panel with a n overhead projector (supplied by our campus audiovisual department) has become available in a lecture room. The library has one terminal in a librar- ian's office dedicated to CAS searches.

Software

The software used in this course (identified specifically below) was chosen because i t is commonly used, reason- ably inexpensive, and the suppliers are willing to license its use on several different machines. We are not wedded to the specific software mentioned, and we frequently up- grade and evaluate new software packages. We make no claim of having the state of the art, absolute best software available anywhere; but what we use works.

Other

Class time is devoted to a discussion-demonstration of the software to be used with special emphasis on the de- tails of getting the program started followed by one or more examoles of the avolication of the software to some . . specific task. The students are expected to do their assign- ments outside of class time. There is wide variation in the time students need for completion of assignments. Those with some comvnter exnerience and t v ~ i n e skills are usu- ally quicker than those naive in both caieg&ies. Part of the class time is used a t the two computers the students use: a student a t the keyboard, othershbserving how i t is done. Each student is provided with a disk on which to store work. Students are encouraged not to store their work on

Volume 71 Number 12 December 1994 1065

t h e hard disks, because th i s increases t he opportunities for cheating, unless t h e files a r e protected.

The Operating System and Word Processing (Weeks 1-3)

The first s e m e n t of t he course deals with t he MS-DOS' operating system and word processing (WordPerfect 5.1L2 The objectives a r e to enable t he s tudents to:

1. start the computer, run a program, and do basic file man- agement,

2. create and run a simple hatch file, and 3. enter a document with several complicated mathematical

expressions in Wordperfect, using the equation editor.

Three handouts a r e provided, one dealing with the op- erat ing system, one with the main WordPerfect program, a n d one with t he WordPerfect equation editor. As with all segments of t he course, careful choices mus t be made a s to what i s to be covered, because t he operating system itself . could occupy a n ent ire semester, if covered thoroughly.

Week One I . Com~onents of a desk to^ cornouter svstem 11. The DOSoprmtmg sysfmm

\ Filcs and filcrunws B. ('<mmon commands C' 1)ircctorirs and the director). tree D. External rnmrnands execurnhle files

1. Batch files E. The DOS editor

Week n u o

I. WardPerfect A. Starting and stopping the program B. Savine and retrievine files C. Menus; mouse and keyboard operation D. Entering and editing text

1. Cursor movement 2. Copying, moving, and deleting text

E. Checking spelling F. Formatting G. Printing H. The file manager I. Timed backup J. Looking a t the editing codes

Week Three I. The WordPerfect Equation Editor

A. Entering and leaving the equation editor B. Creating equations

1. The equation palette and examples of commands

C. Editing existing equations D. Equation options

1. The equation box 2. Location 3. Paint size for praahics minting 4. Equation nu<be;ing .

- E. Equation codes and removing equations

11. Use of alternate character sets

Assignment I. Write a batch file which, run your (the student's) disk from

a disk drive, allows you to set thedateand time, clears the screen, changes to the hard disk, and runs WordPerfect.

11. Transcribe a page of a technical article, assigned by the instructor, containing several mathematical equations. II- lustrate: bold, underline, centering, variable line spacing, italics, full justification, subscripts and superscripts, changing margins, and using a header.

Structures and Minimum Energy Computations (Weeks 4-6)

One module of t he software course is devoted to two re- lated needs of chemists. One is t he need to he able to gen-

e ra te chemical s t ructures a n d equations in a graphics for- ma t t ha t can be incorporated easily into documents gener- a ted by word processor programs; t h e second is to be able t o construct dimensionally accurate chemical structures using a molecular modeling program.

The two software packages currently used a r e Chem- Draft I1 for t he graphics portion,3 a n d Alchemy 114 for t he molecular modeling portion.

Week One I. Introduction to ChemDraft

1. Heteroatoms 2. Multiple bonds 3. An aromatic ring 4. C h i d centers

D. Editing the structure E. Rotating the molecule in space

11. Writing a reaction A. Arrows and reaction conditions

111. Copying a page from an organic text A. Write text B. Draw structures C. Write reactions

C. Edit graphics D. Print

Assignment: ' h rn in printed page of text to instructor

Week liuo

I. Demonstration of molecular modeling program 11. Completion of a tutorial (written instructions,

students work through it a t the computer)

Assignment: Students are given a complex organic structure to create containing chiral centers, heteraatams, and ring systems. They must create it, instruct the program to minimize the energy, and report the distances between certain atoms in the structure. The disks are turned in to the instructor for evaluation.

The capability of these programs to display molecular structures in stereo and as space-filling models conveys a much better understanding of molecular structure than do the hall-and-stick representations that are used so often. Experience shows that students are surprisingly adept a t learning how to use these versatile programs.

Spreadsheets and Statistics (Weeks 6-8)

The focus of the unit is on learning the basic operations inherent to spreadsheets (3) and. for the statistics software. to hrcorne acquainted w t h thc avail:~hle features of the soft: wa re Cunr-nrl\: Quattro Pro' is used ac the, s~ r r adshee t Dro- gram; however, the techniques discussed in'the coursecan generally be transferred to other spreadsheet programs.

Although spreadsheets have some statistical functions, software packages a r e available commercially t h a t offer much more extensive capabilities. We have used a program called N C S S q n t he course, a n d a r e investigating others.

'MS-DOS 5.0 and Windows 3.1; Microsoft Corporation; o n e x crosoft Way, Redmond, WA 98052-6399.

ZWord~erfect 5.1; WordPerfect Corporation; 1555 N. Technology Way, Orem. UT84057.

%hem~raft I I : C Graph Software, Inc.; PO. Box 5641, Austin, TX 78763.

'~lchemy 11; Tripos Associates, Inc.; 1699 South Hanley Road, Suite 303. St. Louis. MO 63144.

orl land International, lnc.. 1800 Green Hills Road, P. 0. Box 660001, Scotts Valley, CA 95067-0001.

6 ~ C S ~ ; Number Cruncher Statistical System; Layton, UT 84041.

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While time limitations do not allow in-depth coverage of statistical principles, students do learn how the program functions and the features the program offers.

Week One I. Introduction to Spreadsheet Principles

A. What is a spreadsheet? 1. Addressing conventions

a. Relative versus absolute 2. Data types

a. Text b. Numbers c. Formulas (prepragrammed and user

defined) 3. Data entry

B. Data operations 1. Creating blocks of data 2. Copying

a. Text and numbers b. Formulas (relative and absolute addressing)

3. Sorting 4. Erasing 5. Graphing

Assignment: Analyze spectraphatometric data; print out and graph the results.

Week l h o

2. Linear regression B. Numerical integration of a function C. Solution of complex equilibrium expressions

Assignment: Determine the exact pH of polypratie acid salu- tions using an algorithm supplied by the instructor. (Note: the algorithm used is similar to a published method (4) but was developed independently here.)

Week Three I. Use of a Statistics Software Packaw

D. Demonstration of program features

Assignment: Analyze and interpret a non-Gaussian data base supplied by the instructor.

Once students appreciate the capabilities of spread- sheets, they often wonder how they ever survived without them! Our students routinely use these programs to ana- lyze data obtained in their upper division lahoratories and in their research projects.

Furthermore, the ease of use and the power of the soft- ware often encourage students to learn more about the advanced features of the software (and even more statis- tics) on their own.

Graphing (Weeks 9 & 10) The purpose of this exercise is to teach the fundamentals

of making publication quality graphs. Sigmaplot 4.07 i s currently being used, hut various spreadsheet software can also he used. In the first week students are introduced to the software in a hands-on tutorial in which they learn how to log on, to enter data, to produce a plot, scale the axes appropriately, label the axes, title the graph, print the graph, save their work on a disk, delete their file from the hard disk, read their files from their disks to the hard disk. In the second week the students are given data from a ki- netics experiment. They are required to enter the data, write a simple formula to compute the specific rate con- stant in terms the software can "understand", plot the re- sults, label the graph appropriately, and print i t and the

worksheet. Grading is based on the accuracy and appear- ance of the graphs.

Week One I. Introduction

A. Terminology. What is a graph, what is a plot? B. Logging on to Sigmaplot

11. Operations A. Entering data B. Producing a rough plat C. Refining the plat

1. Adjusting the axes 2. Selectine tvoes of lines and svmbals .. 3. Labeling the axes, titling the graph 4. Printing the graph

111. Concluding the session A. Saving the file B. Copying the file from the hard disk to a disk C. Copying the file from the disk to the hard disk D. Deleting the file from the hard disk and exiting

Assignment: Turn in hard copy of graph

Week Buo

I. Starting the program and entering the data from a kinetics experiment.

11. Operations A. Convert the formula for comoutine the rate . -

constant into lanrmaee the oromam will moeess u - . -

B. Use the program to compute the required derived quantit~es and enter the results in a column in the spreadsheet

C. Plot the data and massage the plot until it is presentable.

Assignment: Produce hardcopy of the graph and data sheet.

Literature Search ( ~ e e k ' l l ) In this module students select either a specific or general

tovie and emolov either the Chemical Abstracts Service ((%AS) or somk other database such a s government docu- ments to compile a biblioeravhv on the ohiect of the search. In the case of CAS ~ea&6es -~os t -5 PM appointments (cost!) are made with the non-chemist librarian who is fa- miliar with using the system and actually performs the keyboard operations while the student sits with him or her to devise the search strategy from the chemist's viewpoint and judge the appropriateness of the output. Each student i s limited to a maximum of $20 for the search. l b ~ i c s are . ~~ ~

frequently suggested by members of the faculty, or the stu- dents mav sueeest their own. subiect to the a ~ ~ r o v a l of the " -- . " . . course coordinator.

Assignment: ' h rn in a printout of the results of the search.

Computations (Weeks 12-15) This segment of the course deals with the use of an applica-

tions program to perform computations that may be unduly laborious or even impossible by other means. The objective is to familiarize the students with the program sufficiently that thev are able to use it as needed in other courses. The Dro- gram currmtlg in use is Mathcad 3.1.'. ' Windows' ver&,n. Instruct~on becini u.ith a \VN brief introduction to Microsnft Windows, witK the suggestion that those not familiar with this environment eo through the Windows tutorial. At this time, Windows is k e d o n 5 to get in and out of Mathcad. Some instruction is ~rovided in the use and manipulation of document windows-within Mathcad.

'Sigmaplot 4.0; Jandel Scientific; 2591 Kerner Blvd. San Rafael, CA 94901.

'Mathcad 3.1; MathSoft Inc., 201 Broadway, Cambridge, MA 07139

'Maple; Waterloo Maple Software. Inc., 450 Phillips St.. Waterloo, Ontario, Canada N2L532.

Volume 71 Number 12 December 1994 1067

A handout is provided covering the features of the pro- gram to be used. I n addition, five practice exercises are provided, to familiarize the students with these features, which are then used i n the assignment.

Week One I. Entering and exiting the pmgram 11. Entering and editing text and equations

A. Eouation made B. &t mode C. Using the palette

111. Finding the zeroes of a polynomial (the root function)

N. Graphing a function (range variables)

Week !Iluo

I. Evaluating the derivative of a function 11. Multiple graphs (a function and its derivative)

A. Findine relative extrema of a function ushe the roots of the derivative

111. Solving simultaneous equations (solve blocks)

Week Three I. The symbolic processor

A. Symbolic solution of polynomials B. Symbolic integration and comparison to numerical inte-

gration .

C. Symbolic differentiation and evaluation of the resulting function

Assignment I. Solving a polynomial resulting from an equilibrium prob-

lem. The ammonia synthesis reaction is used, which gen- erates a fourth-order polynomial.

11. Solving simultaneous equations using a solve block. The dissoeiatian of adioic acid is used. The results can be com- pared to malonic acid, which was illustrated in the exer- cises, to show the effect of increasing carbon chain length.

III. The mots of a fourth-order polynomial (chosen ta have four real roots) are found. A table of values for the function and its de- rivativeis mated, and both functions are plotted on the same graph. The m t s of the derivative are found and the values of the original fundion at these mots are determined.

Week Four Assignment I. Symbolic calculation

A. The roots of a cubic equation (chosen to have two complex roots)

B. Symhalic integration 1. Indefinite integration 2. Definite integration, including Gaussian

integrals a. Symhalic versus numerical evaluation of

definite integrals C. Finding the derivative of a function (chosen to be

nontrivial).

Grading Students turn i n one or more assignments (hardcopy

andlor disk) for each segment of the course in addition to t h e results of t h e l i terature search. Assignments a re graded on accuracy and completeness. Of the 53 students who have completed the course i n seven offerings, 35 have received A's, 12 B's, 2 C's, and 4 F's (resulting from failure to completework or cheating).

-

Conclusions After several cycles of offering the course we are confi-

dent that the course is meeting i ts objectives. Students are learning useful computer skills and are using these in other courses and projects. The longest stint for a faculty member is four weeks for any one unit. Different software packages have been introduced as they have become avail- able, and different faculty members have been involved. In these respects, we think the course i s dynamic and organ- ized to accommodate change readily.

Literature Cited 1. Crosby,G. A. FlPSE LECTURE I. "TeehnologiealThruat versus lnrfruetional Inertia"

I h h Biennial Conference an Chemical Education, Purdue University, West La- fayet-, IN July 31-August 4.1988.

2. Martins, L. J. A. J Chcm Educ 1988.65,861462. 3. Xeh, R. L.: Coleman. W. F.; Lytle. F E.; Marshall. J. C.: 8mith.A. L.; Henderson. J.;

Met.. C.; Donato, H. Jr; Denick, M. E.; Joshi. B. D.: Nambi. P, Judkins, J. W.: Lagowski. J. J.; Wi1son.A. M.: Rodwe1l.V W:Kuhn,D. N.Spre=dsheetsodEquo- lion Sdvem. Symposium; 10th Biennial Conference on Chemical Education. Fur- due Univereitx West Lsfayetfe. IN. July 31LAugust 4. 1988.

4. Freiser, H. Compts and Colculofions in Anolyliml Chemistry: A Sprmdshp~t Ap- prooeh: CRC Press: Boea Ratan, FL, 1992, pp 13-14.

Acknowledgment We thank Stephen G. Jolley, MD, for support that enabled

this project to get started and Lawrence J. Tini and Thurston Miller for their participation i n the first few cycles of this course. We thank Shelley J. Heaton for the enthusiastic sup- port of the Reference Department of the library.

1068 Journal of Chemical Education