fragments of molecules already on file or by creating new ones. To create a new structure one enters coordinates, hond connections, bond angles and torsional angles. For these new structures an initiated hlank disk is used for stornee and Inter recall There are sir programs in the package. and the written manual isessrntial tooperation of the programs. CONFIG is for configurating the disk to your hardware, as mentioned earlier. HELP defines single letter commands, a duplicate of the manual list. FAST has files of molecules of up to 50 atoms and allows rapid manipulation of these molecules. For example, rotation is nearly instantaneous and by holding down the space bar rotation can almost seem continuous. MODEL, the heart of the system, provides for molecules up to 60 atoms hut operates more slowly; this program also lets you construct and file new molecules and store picture data for later printing. VAST can handle uo t o 600 atoms and onerates much like FACT hut much more sl;lwly. Picture files can aim be created from VAST. Finally, GROW allows you to add or delete hydrogen atoms, normally not shown on the skeletal models. You can add them in an up, down, or five- or six-membered ring.. position. Simple one-letter commands allow one to ooerate within the main oroeram. In MODEL all the letters of thealpkahet are used, an indication of the complexity of the prugram and the porsibilitier for its use. For example, X converts X-ray coordinates to Cartesian coordina1es.a useful tool for those in research. L (LOOK) allows one to look at and change data files. Data entered and filed by this reviewer all worked well, as did the other letter commands. Coordinates, bond sites, hond angles, and torsional angles can all be either displayed on the screen or printed. Printing provides neat hard copy of the molecular data, labeled with the malecule's name. Distances can be asked for hetween any atoms, banded or nonhonded. This proves very useful in docking molecules. Another heloful feature is that if vou request a nmhundeddistance a lineappears on the screen showing you the d~sronreyuu requested. Correction of newly entered data can he done relatively easily. A new feature, J, in the 2.0 version allows fragments of a molecule to he formed by simply entering the hond to be broken. Response time t o J is variable, for example, removing the carboxylic group from benzoic acid took seven seconds. Pictures can he saved from MODEL and VAST and a copy disk can now he modified t o contain the picture dump. Instructions for doing this were confusing, however. The package appears to this reviewer to be worth the cost t o researchers or advanced biochemistry students hut not t o the typical undergraduate student. Students in a nonmajors organic-biochemistry course did not have the time or the patience t o learn to operate the program. The youngest student who did spend time with the program was a high school senior in second-year chemistry. He commented that "It would not help muchwith school work, hut i t does allow one t o view and manipulate molecules and realize how complicated they really are". The same student said the commands were not hard to "get the hang o f ' a t all. Students definitely need to know chemistry well enough t o understand the framework mole~
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cules that appear on the screen. No double or triple bonds are shown and this is confusing t o organic chemistry students. Heteroatoms are also not shown except for files suffixed by .Z, where a W command will box heteroatoms or metal ions and the N command that numbers atoms will also give a readout of the element. If a student calls for CALCITEGCA, six calcium ions in a crystal, nothing visible appears on the screen without more commands. This disturbs students. Both the students and this reviewer had difficulty using the manual in that the changes for the Enhanced Version 2.0 are given in a n Appendix and one has to switch back and forth between the old directions for Version 1.0 and the changes. Examples are also based on the Version 1.0, and for examples like number three, Creating Benzene from BPPPO, the LOOK command has been so changed that it is impossihle to follow the exercise. A new set of instructions for 2.0 is badly needed. The authors do promise a hook hy Academic Press in the future that will give possible applications, and this should he very useful. Except for the major problem of meshing two sets of directions, few problems occurred in operations. Errors are corrected without losing the file hy typing GOT0999 which brings hack the command line. The program itself had some features troubling to students. One student commented that the program lacked an easy exit out of the whole program. Others found the disappearance of the molecule during rotation distracting to follow the molecule's movement, esneciallv in MODEL or VAST where one sumetrmes walls 10 seconds for the new rotatwn to appear Students are also b ~ t h r r e d by the disappearance of some lines as the molecule rotates. Depth perception is also a problem for most of us. Both black and white and color monitors were tried. In black and white the use of solid and dotted lines gave nearly as good depth perception as did the use of colors. However, with longer use the varied color might give hetter depth perception. The use of K (contrast) is definitely superior in color. Here the atoms of an enzyme, for example, can be muted while the color of the ligand is enhanced. There are many features t o explore in this oackaee. I t would he of most use t o those in research or advanced hh~uhemistry.Ilndergraduate student^ find it interesting. bur more as a novelty than as having pedngoglcal value. A junior chemistry major eommented: "I would probably not find much use for this molecular graphics program. I find that drawn structures and ball-andstick models give me a better representation of molecules than does this program. The only use for such a program might be as a visual aid (on the teacher's part) for molecules that are too complex to build, and as a source for obtaining relative hond lengths and angles of molecules. However, I would prefer lookingat an actual3-Dmodel". This reviewer concurs with this student; bond and torsion angles are understood by students well after some model building, and one can turn the model in any desired configuration. The need t o know coordinates limits students'abilities to create new molecules. Nevertheless, Molecular Graphics is an amazing package, and this reviewer ap-
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preciated the exposure toits techniques and capabilities. Justlne Walhout Rockford College Rockford. IL 61 108
Molecular Graphics on t h e IBM PC Microcomputer J. G. Henkel and F. H. Clarke. Academic Press. Inc., Orlando, FL 32887 Hardware: IBM PC Components: One disk and User's Manual Level and Subiect: Colleae - oroanic - chernistry or biochemistry Cost: $129.50 Summary Ratings: Category Ease of Use: Subjecf Maner Content: Pedagogic Value: Student Reaction:
Rallng Good
Excellent Good Good
Features Molecular Graphics an the IBM PC Microcomputer is an advanced BASIC (BASICA) program that draws and manipulates molecules in graphic form using the IBM PC, P C K T , PCIAT, PCjr and eompatihle personal computers. Molecular Graphics requires 256 K RAM under DOS 2.0,Z.l or 3.0, as well as a graphics adapter card and a color monitor. The program can display molecules containing up to 1199 atoms and bonds. Atomic positions must he entered either as standard atomic Cartesian or Xray coordinates. The orimarv market for the oroeram is " not entirely el&, perhaps because there are so many potential applications for a general purpose microcomputer program of this kind. The descriptive material aeeompanying the program refers t o research applications. The program will also have useful applications in the classroom, ~articularlvfor students of organic and biochemistry. Molecular Graohics is exceotianallv fast for a BASI('A pr&am and csnlain,a;anyc of features, some qoirr innmalive fur a mirrcuumpurer eercwn ota n~olrculargraphicprogram. The more innovative features include: The ability to rotate and translate the molecule about any axis or hond. There is alsoareal time dynamicmotion feature that draws a structure in the display window, rotates it three degrees, erases the display window, and immediately redraws t h e structure in its newly oriented position. This feature works well for small molecules hut leaves spurious lines if the rotation causes any part of the molecule t o leave the display windaw. Interatomicdistances, bond angles, and torsional angles can he measured a t any time once a molecule is plotted. This feature is valuable in trying to extract structural information far complex molecules from Cartesian or X-ray coordinates. Knowledge of interatomic distances and angles also fa-
Volume 65
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cilitates the construction of actual three-dimensional models of complex structures. Any structure can he converted to a erauhic reoresentation of a suace-filling h atomic radius and the color mobel. ~ 0 t the in a hich aMma are plutted on thewreen are determined by the typeot atam indicated hy the label given to that atom a t the time the coordinates are entered. Up t o 20 different data files can be drawn on the screen simultaneously, and the most recently added structure can be manipulated independently of the previously added ones. This permits a "docking" function, where, for example, a substrate can be moved into position a t the active site of an enzyme. While manipulating structures, users can simultaneously monitor the interatomic distances between as many as three pairs of atoms. The stereochemistry of a molecule on disolav also can he inverted. When comhinedkith the ability of the program tomanipulatr two structures indeprndently, it hecmws possiblp t,, draw a molecule next to its mirror image and test for superimposahility and therefore chirality. Color can he used t o denote either depth from the viewer or atom type. Although valuable, this feature is fundamentallv,limited bv the choice of onlv three foreground cdc,rs'in HASICA. C& is put to wry nod use by one ieature u hich pluts m e structure (rotated by 5 degrees about the yaxis) on top of a second. If the first is plotted in red, and the second in green, the use of red-green glasses converts the image into a three-dimensional representation of the molecule. In practice, this feature is disappointing with a medium resolution screen. The manual suggests much better images will be obtained with a high resolution (RGB) monitor. Without access to such a monitor, I was unable t o verify this statement. Printer listings of coordinates, connectivities, and interatomic distances are readily available. A screen dump of the graphics image also can be obtained on a graphics printer, provided the user has the necessary utility software (GRAPHICS.COM in DOS 2.10). ~
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Student Reactlon This program was used as an option for several first-year general chemistry students and for aspecific assignment withsecond-year organic chemistry students. It was used both on IBM PC and PCjr microcomputers. I found it necessary to prepare a supplemental sheet giving several examples t o help the organic students perform superimpasability studies on simple chiral molecules. Students generally did not feel a pragram such as this could replace molecular models, but they thought i t would augment their use, and might actually assist them in makine models of comolex structures from X-my crystal darn R'ithuut rxception, btur l ~ n t s~njm.rdthe pnl,gram, and were reasonshly n ~ n v m a n w t t h the main menu options in one to twa hours. They particularly appreciated the dynamic motion and spacefilling model features of the program. SeverA88
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of Chemical Education
al students criticized the organization of material in the manual that accompanies the program. Students also suggested adding several examples of the manipulation of molecules, particularly relating to the inversion, orientation, and superimposability features of the program t o help them become familiar with the available options. Overall Assessment Molecular Grauhics is one of the first versatile entries into the aoolicetion of microcomputer graphics ior purpose, of risualiz. ing three-dimensional structure. The pn,gram is innovative and offers a considerable range of options once the Cartesian coordinates have been generated for a structure. I believe that the program may even have applications to nonchemical systems, allowing data which can he entered in the form of Cartesian coordinates to be readily visualized and manipulated in space. The limitation of three foreground colors will be restrictive for many applications. Furthermore, unless a user has access to a color graphin printer, most vivid three-dimensional images will he left in the mind of the viewer. Molecular Graphics will probably prove most useful t o students in organic and biochemistry courses. Some obvious educational applications are for the visualization of crystal structure data for large molecules, where building a molecular model would be tedious, examination of structnre-reactivity relationshins in biaoreanic chemistrv. .. and carrying o;t superimp&ahility studies. Given the great deal of attention paid t o the development and refinement of the pmgram, i t is disappointing that a similar effort was not paid to the accompanying manual. I t was originally well conceived, but when the program was revised and enhanced, the changes in documentation simply were added to the end of the manual that had already been published. This leads to considerable confusion for first time users who must often go to a t least two places to find information on a single feature. For a t least one feature (three-dimensional representation using redlgreen structures), important information is contained in the original reference and then not repeated in the new section that describes that option. Clarity in documentation is particularly important if the program is t o be used successfully in introductory and lower level courses. Peter G. Mahaffy The King's College 10766-97th Street Edmonton. Alberta, Canada TSH ZM1 ~~~~~
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Molecular Animator, IBM PC Verslon J. Jeffrey Howbert, COMPress, A Division of Wadsworth. Inc. P.O. Box 102, Wentworth, NH 03282 Hardware: IBM PC Components: 1 disk with backup, User's Manual Level and Sublect: Any chemistry course in which molecular structure is discussed. cost: $95.00
Review I The Molecular Animator is s modeline prugram that alloxs thr user to display and umitrurt ball-and-stir< mudels uf organlc and inorganic molecules. Thi, sotruarc package provides a unique opportunity for teacher and student alike to explore graphically a variety of geometric forms associated with molecular structure. Primarily intended for students with some exposure in the fundamentals of chemical hondine. this m o gram raanexcelltnt vehicle i n \\ hich to view the depth in all threp dimensions, ln a convmring fashion,oisurh nvtaolrs as thechair and boat conformations of cyclohexane, the planarity of aromatics like hennent. ur the octahedral arrangcrnrnr of driulfurdccafluoride. 1 found m e o i its attributrs to he the mare than 20 typical molecular structures. ~. includine those listed above. that can be displayd in front of n large lrrture revtion on aaorren thruughaprqection dpwrc. This latter vharacrerisr~cha\ many advantages over the omnipresent overheadprojector with two-dimensional transparencies, or attempts, futile as they are, to build a model of a molecule from a kit large enough to be seen well by all in the class, or worse yet, the practice still common with t h e artists among us t o draw structures on the chalkboard, a practice that baffles our colleagues in business and industry. While one molecule is displayed on the screen, or monitor, the user can manipulate, by a single stroke of the function keys, the structure to rotate about its center of mass in either direction along an x,y, or z axis, a t slow or fast speeds. It can also be made to stop in any position, he enlarged, or reduced in size, and, as a ball-and-stick model, it can be displayed or rotated as just a stick (wire frame) or as just atoms in the full model. Students in my second-semester General Chemistry class used the program individually and found it to be far more helpful in understanding the full picture of molecular geometry thanjust relying on textbook illustrations and one's imagination. Though I did not have such a class a t the time, I believe from past experience that introductory organic chemistry students would benefit greatly not only from the ready display models, hut also from the flexibility to construct their own models from the various editors and menus that are accessed easily, and from the ample instructions given in the User's Manual. Their newly constructed models can then be saved and stored on a second formatted disk. Most of my students seemed to feel a t ease with the utilization of the main menu and the displaying of the stored figures from the files, but they were more tentative about the construction of models. They seemed also to marvel a t their ability to manipulate the rotation, size, and direction in which the structure moved by use of the function keys. Yet I also detected that they tended totire after an hour or so of working with the shapes stored on the main disk, which is why, I believe, their overall evaluation tended toward good rather than excellent. But this is not unusual for any chemistry student today considering that most of them are not chemistry majors and view the subject matter with some amount of reproach and scepticism as to its reievance for their chosen vocations. Because of its ease of use and pedagogical value, the Molecular animator ranks as a significant
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