Level and Subject: General or organic chemistry, or biochemistry Cost: $90 semester of the lecture. They are given copies of Aldrich file spectra with their unknowns during the Qualitative Analysis section of the lab course. We selected four students who had never seen an NMR and taught them the principles of setting up the machine and producing the spectra using the program. We did use the real EM360 to explain the general function of the instrument and the parameters which needed to he adjusted for a proper spectrum t o he produced. We t h e n switched t o the program. The quickest student caught on in about 20 minutes and after an hour was able t o select a file and produce a spectrum by following the stepwise directions. The slowest student (deliberately chosen for this trait) was only marginally successful a t following the directions after three one-hour sessions. The other two students were ahle to select a file and run a soectrum after an hour or so of oractice. An inctructor war availahle during practice sesaimsand threeofthe four students required only an occasiunal prompt. Significantly. the three successful students appeared pleased t o have bad the opportunity t o work with the program and learn about the instrument. The fourth student never really figured out how the instrument functioned. Recommendations for the improvement of this program are few and minor. This program does exactly what i t ia advertised to do. The only critical comments that I can make about the program are not really valid criticisms of the program, hutof the concept of replacing a working NMR with a computer. First, all spectra are perfect samples: no solid particles, no spinning sidebands, no silicone eresse. ,. . no incorrect soin rate. no improper conrentratrons, etc. Second, spectra printed on a normal dot matrix printer are difficult tu interpret at a later time because the multiplets are not easy to define. Interpretation of the spectra is most easily done while the spectrum is still on the screen. A more sophisticated graphics plotter was not availahle t o us. I am assuming that use of one of these would produce spectra more comparable to the instrument itself. This review may be somewhat biased by the fact that our department uses Varian NMR instruments and our junior andsenior students are familiar with the EM360. We were unable to compare the effects, if any, that would result from shifting from the EM360 simulation to an entirely different make of spectrometer far actual research or course work. Donna L. Ticknor Florida International University North Miami Campus North Miami. FL 33181
Nuclelc Acld Structure a n d Synthesis J. H. Parish. Bioscience Software. IRL Press inc., P.O. Box Q, McLean. VA 22101
Hardware: IBM PC (or compatible) with color graphics adapter Components: 1 dlsk. Instructor's Notes, and Notes for Students
A298
Journal
of Chemical Education
Summary Ratlngs: Category Ease ot Use: Subject Matter h m t : Pedagogic Value:
Excellent Excellent
Student Reaction:
Excellent
This program is designed t o introduce current understanding of DNA and RNA structure and the dynamic processes of replication and transcription. I t is intended for the secondary level in England and the college level in this country. Various sections of the program have differing levels of difficulty, therefore allowing for some differences in student background. However, even the most elementarv. asnects of coveraee reouire previous iamiliariration with fundamental biochemical concepts. Thus, coumrwurk invohing chemical bonding, simple organic reactivity, cell theory, and genetics is a necessary prerequisite. Using the program is exceedingly easy as only the most rudimentary computer literacy is needed t o begin and continue use. Clear instructions are available for those who lack familiarity with microcomputers. Operation has been reduced to minimal keyboarding, and facile access t o help and the menu are available. Interruption of program function via keyboarding error or misunderstanding of computer operation does not occur readily. Specialized add-on equipment is not utilized, and there is complete user choice in selectine" audio mode. The user mav choose subsect~onsin any order, movement aruund t h program ~ 1s effortless. I n r h m , 11 is dlfficult to imagmea plecr ofsoftware that n d d he any easier to use; obviously, i t has been prepared in the most careful and thoughtful manner. Documentation is svailahle for instructor and student alike, and i t closely parallels the program's sequence of events. The documentation is relatively unimportant for advanced students hut essential for novices. Importantly, advice regarding further reading, hoth of the elementary and advanced types, is provided throughout, and other computer packages in the same series, for example, in protein synthesis, are mentioned. Overall, the documentation is somewhat abbreviated hut helpful, and totally sufficient considering plentiful alternate sources. At this point in the evolution of software, failure often occurs in a most unnecessary way. That is, many programs are inaccurate scientifically. Such is not the case here. From structural detail, to mechanistic explanation of processes, to historical backeround..the ~resentatianis correct and uo to " date. Certain topics, such as DNA primary structure, are briefly introduced to prowde perspective, then left for related t o p m , and returned to in a much more sophisticated manner slightly later. While this approach may lead to initial student anxiety, it rapidly becomes clear that most questions of the beginner are soon to be answered in another subsection. A complex topic such as nucleic
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arid structure and function cannot be dealt with in a ttrtally linear fashion. The author's decision to avoid the completely sequential approach pays dividends as the students' overall perspectives are greatly enhanced, Another strength of the program, again providing crucial context, is an emphasis upon inclusion of historically relevant experimental results. Well chosen historical investigations serve the double purpose of helping students develop appreciation of methodological design and technology and in creating a broader understanding of central concepts. While the HersbeyICbase experiments provide insight into the realm of hacteriaphage virology, the MeselsonIStahl experiment not only explains semi-eonservative replication but also excites one's imagination and introduces important ultracentrifugatiun separation techniques. Watson-Crick structural saphist~eationis lacking. This is both a strenmhand a weakness. For the beginning &dent, excessive elaboration of double helical detail often hlurs some of the more fundamental ideas like base pairing. For the more advanced student, lack of detail thwarts some of the more important recent findings relevant to genetic regulation. This should not prove t o he much of a problem if this program is used for beginnersor as a quick review for others. The program's primary instructional aporoach is tutorial with some simulation. drlll, and temng. Student reaction was gen: erally quite favorable, however, there was some call for more questions within sertiont (as opposed t o separate sections devoted t o questioning), greater explanation t o answers, and agreater orientation towardmastery. Both students and instructor felt that some sections moved too slowly and were overly repetitious. For example, while testing for student comprehension of base pairing during replication, the user is asked to provide complementary base pairs for a long segment of template DNA. I t is understandable that a number of trials are needed to assure recognition of the process's geuerality; nevertheless, overdoing this idea leads to tedium and is counterproductive. Shortening some of these drills would enhance the oromam. ~ i o t h edifficulty r is that graphics used in some of the demonstrations are ponderous. It is clever to show injection of mice in Griffith's transformation experiment, hut the way it is accomplished here is costly in terms of user time. Although the graphical tools are universally of high quality, i t is not clear whether they are always beneficial in the momam. A minor glitch in the presentation has to do with numbering of sugar carbons. While there is no inaccuracy, same student confusion may arise relative to the proper designation of l', 2'. 3' etc. on deoxyribose and ribose. At one point in hoth computer and documentation segments, the sugar positions are shown without mimes: whereas. ~~~~~, both before and after this'point/t is made clear that sugar carbuns are numbered with primes. A much surer approach would be to give the prime a t sugar carbons in every instance. This program was tested a t the introductory college level with most students being ahle to comolete the oroeram is about two hours. ~ t u d k n t were s gen&ally receptive to its contents, and, in some cases, were quite
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enthusiastic about the opportunities i t presented. Even though Nueleie Acid Strueture and Synthesis could be used as the maior focal noint of learnine " for students with other resourcesa t hand. it should nrove. ~~, to he most useful as an adjunct. It is effectiveat presenting tr,pics that aredifficult to cover thoroughly in class or in reading because of spatial and temporal complexity. A high recommendation is justified for this piece of software, because it meets or exceeds all necessary requirements. It uses commonly available hardware, is easy t o use, and sufficiently covers all main concepts. Its accuracy and motivational intent are substantial. I t is not perfect, hut compared t o many pieces of software in its area, it is superior. I t should be seriously eonsidered for inclusion in software libraries emphasizing instruction in molecular biology.
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Keith K. Parker Division of Mathematics and Sclence Western Montana College Dillon, MT 59725 Molecular Deslgn Edltor Frank and Craig Weinhold, COMPress P.O. Box 102, Wentworlh, NH 03282 Hardware: Apple II family Components: 1 disk, 1 backup disk. User's
Guide Level and Subject: Elementary and Advanced Organic Chemistry Cost: $75.00
Summary Ratlngs: Category
Ease of Use: sub/ect Marter Content: Pedagogic Vdwc StOdent Reaction:
programs. The program also directly provides Cartesian coordinates for each atom and a variety of useful information about interatomic distances and angles. T h e graphic images may be printed, providing that the user has a graphics dump utility appropriate for the local printer, although the necessity of leaving the program in order to obtain a print-out is one of the major drawbacks of this program. The program is copy protected and, as would be expected, source code is not available, so that insertion of a direct printing capability by the user would raise both practical and legal diffieulties.
Go@ Excellent Good Good
Features and Intent This program is not a molecular mechmics program. It is not intended t o calculate energy minima, but i t does a good job of calculating and presenting as graphic images conformational structures of small to medium-sized organic molecules. It does so starting with either a line structure which is as similar to standard linear notation as an Apple 11+ keyboard will allow, or with a set of atomic coordinates such as might he available from a molecular mechanics or quantum mechanical caleulatim ur from an S.ras crsstal.ographic structure. T h r program's capacity t u accept the description of a molecule in a form that corresponds t o that normally seen in print is one if its outstanding features. Once obtained, the picture of the molecule can he altered by changing bond angles and leneths. atoms mav be substituted. hunds may be introduced to form rings, and. must importantly, dihedral angles may be changed, resulting in the opportunity to examine aseries of conformations. The results of these manipulations may be saved to a datadisk asdamsetsand asgraphicimngcs. The dnca sets are m the torm of standard 110s 3 3 texr filer, which leads to rhe ooisibility of using the information withother
Ease of Use. Documentation: The instruction manual provided with the program is clear a d straightforward. Students, many of whom had very limited experience with computers, reported little difficulty in using the Program. Instructions are available from within the program. Our experience suggests that if students will he expected to Prepare print-outs aspart of an assignment, care will need t o he taken t o integrate the local printing instructions with the instrue. tiom given for saving graphic images to a data disk. Operation: The program is well structured in most respects. Control flows smoothly through a series of menus, with the most common operations listed first. Pressing the "escape" key returns t o a menu screen, making the program easy to control. The program makes extensive use of disk access, slowing its flow significantly. Work files are maintained on the master disk, allowing for resumption of work on a molecule, but choice of the menu option "Display former view of model" results in a blank screen. This may be overcome by using the program's rotation feature with an angle of zero, but i t would be helpful t o make this clear in the manual. The "twist" and "fuse" operations, essential to the program's ahility to display the results of internal rotations and to prepare cyclic molecules, can be done only one a t a time, making their use somewhat tedious. The program keeps work files on the master disk, so that protection of the disk against accidental or deliberate damage by covering the write-protect notch is not possible. Since this a fairly routine procedure in computer labs, this should be noted prominently in the documentation. I t is possible that this could also lead t o a shorter life for the disk than one that is write protected. The publisher responds promptly to requests for assistance, which minimizes the problems associated with disk damage. The particular copy of the disk available for review did not properly retrieve or catalog data files on a data disk, but it seems likely that this is an isolated instance. Input and Error Handling: The screen that prompts for the input needed in making alterations to the molecule is different from the menu screens, and data entry follows different c o n v e n t i d f this difference is not noticed, it is easy to give erroneous input that is not rejected by the program. Other input is well cheeked, although the "illegal?" response gives the user little guidance regarding the nature of the mistake. "Reset" is not trapped, and results in an abnormal exit from the program. Volume 65
Flexibility: Since "Modeler" is a molecular graphics tool, it is very flexible with respect to potential instructional use. Conaidered as a tool, i t would be much more useful if it offered the option of adding atoms to a n existing molecule or joining fragments of molecules. This would permit convenient construction of rather complex molecular images from a small file of common fragments or base structures. Subject Matter Content The three-dimensional perspective images provided hy this program are very good. The accuracy of the interatomic parameters calculated is quite satisfactory, and the Cartesian coordinates obtained would he useful as input to a molecular mechanics program. The program is limited in the atoms that can be input as part of a line formula, but by changing the atomic number of an atom, essentially the whole periodic table may be used. In the section on more advanced topics, t h e manual describes tricks that can be used t o broaden the utility of the program beyond its obvious application t o organic molecules. Pedagogic Value "Modeler" is not per se an instructional program. That is, i t does not set out to teach a particular lesson in chemistry. Rather, it is a tool, which, like its most obvious traditional analog, a set of molecular models, can be used to tackle problems having to do with numerous aspect3 of molecular structure. Its pedagogic value, then, is largely up to the imagination of the instructor in using it, and in capitalizing on the "Hawthorne Effect9'of students' generally positive reaction to us. ing computers. The program's capacity for saving images for printing permits assignments to be treated like homework, credit for which is a powerful motivator. The program can also provide the hasis for lecture demonstrations in appropriately equipped facilities, providing a n alternative t o the often ineffective use of models in large lecture halls. Student Reaction This program was tested with a second semester organic chemistry class of same 60 students, of whom about three fourths used the program as an extra credit assignment. This group had studied conformation earlier, so that it was not possible to examine the question of "Modeler's" effect on learning. They were asked t o examine the conformational properties of 1,2-dichloroethane using the program, specifically generating images corresponding to the gauche and anti conformations as they would be viewed in a Newman projection. They were then asked to generate a screen image of a cyclic molecule and make a print copy of that image. As part of the assignment, they completed a short questionnaire on their reaction to the program. The time each student used the program ranged from one to three hours. In general, student reactions to the pragram were positive. Most said that they would have used the program t o aid in learning about conformations had it been available a t the appropriate point in the course. Most responded that they either preferred i t to molecular models or would use it as a supplement to molecular models. Many (Continued on page A300) Number 11
November 1988
A299
