edited by JAMES
P. BlRK
The Use of the Desktop Molecular Modeller Software in the Teaching of Structural Chemistry S. Aduldecha. P. Akhter, P. Field, P. Nagle, . E. O'Sullivan, K. O'Connor, and B. J. Hathaway University College, Cork, Ireland Molecular graphics are normally associated with very sophisticated programs, such as CHEM-X ( I ) , requiring hoth large processing power and expensive graphics capability. This picture has suddenly changed (2) with the appearance of a new software program, Desktop Molecular Modeller, published by Oxford Electronic Publishing, Oxford University Press, Oxford, a t a cost of f300 sterling, with a 50% academic discount. DTMM is a molecular modeling program that can he used for the computer graphics display of molecules, their construction from smaller molecules or fragments, and for the manipulation of molecular structures. The program is written in Pascal by M. James C. Crabbe, Reader in Microbiology a t the University of Reading, and John R. Appleyard of Polyhedron Software Ltd. The hardware reauirements are an IBM AT microcomputer, 512 RAM, a graphics adapter, and a color EGA or V ~ screen. A The mort imoortant feature of DTMM is that it is one of the most user-friendly pieces of commercial software available. The program is entirely menu driven, Figure l(a), with less than 20 menu options frequently used. I t requires no previous knowledge of microcomputing or of the use of a mouse. Once set up, the DTMM program can be loaded from its own directory or hard disk by typing DTMM and pressing return. A logo and a Software agreement screen, are followed by a Menu Bar with the following options:
Figure 1. Desk-top molecular rnodeller, menu options. (a) Full menu: (b) dropdawn menu.
FILE STYLE VIEW CALC EDIT UTIL.
Each command may be accessed by pressing the first letter of each option or by moving the highlighted box with the horizontd cursor arrow keys,- and -, followed by pressing the return key or by the use of a mouse. This results in the appearance of a drop-down MENU, under the appropriate command option, with 6-10 items, Figure l(b). All menu items have a simple help facility available on the F1 key. The FILE menu allows access to hoth the molecule and the fragment data files, which on the published disk are entirely organic or biochemical in type, but a selection of inorganic data and crystal structure data files are available from the authors. Alternatively, data files may be built from scratch by "saving" a molecule constructed on screen (the SAVE MOLECULE option on the FILE menu). Molecules containing up to 1500 atoms and honds may be viewed, and up to 1800 atoms and bonds may be displayed, if the system has a math coprocessor option. T o get students started, they are asked t o load a given molecule such as cyclohexane, using the CYCLOHEX.MOL file on the load molecule option in the FILE menu, and to display it in the different options in the STYLE menu. The STYLE menu offers six alternative display modes, Figure 2, from stick, (color stick, greenlred stereographic stick), fast fill, to space fill or hall and stick. 576
Journal of Chemical Education
Stick
Space Fill Figure 2. Display styles available In DTMM.
color Fill
Ball and Stick
Conversion between these display options is very fast, except for the space fill option. The color option involves a choice of lfi colors on an EGA or VGA screen. For reasonahlv sized molecules greater than 60 atoms and bonds ( m k . 1500). thesoacefillootion is rather slow. but is acceotable for occasional ;se. The appearance of the stick end the hall and stick disolavs can be enhanced bv line thickeninr rT) and perspectivei~)toale options, andall t he solid displays have simple, but effective, highlighting (H)and depth-cuing iS) toggle options. An atom-laheling option ( I ) , except for the hydrogen atoms, is available for all the display options. While all of these toggle options improve rhe quality of the display, they noticeably slow down the screen refresh timea. Thus while all the display options of the display menu (except SPACE FILL) are virtually instantaneous for molecules with 20-30 atoms. with lareer files. such as LYSOZYME.MOL, even redrawing in stilk modetakes over 10 s. All disolavs, excluding the space fill option, involve a rotate commiid, via theeursorarrow keys a n d t h e Page Up and Page Down keys, a translation option on the 1, r, u, d, b, and f keys, and azoom and pan option on the Home and End keys. All of these options are best carried out in the stick mode of display, to optimize a view, before using a color fill display. The F2 key offers a convenient toggle between the stick and the ball and stick disolav. facility for producing a DTMM also has ~''DTMMS~OW" slide seouence of cantured disolavs: . . . this facilitv should be invaluadle in a teac(ing environment. The DTMM package is accompanied by a 97-page, ring-hound manual that contains five excellent tutorials on getting started with DTMM, with an emphasis on biochemical molecules. In ateaching environment, a 1-hour display tutorial and a 1-h building tutorial is all that is needed to get students started in displaying and building simple inorianic and organic molecules. T o date, the following 1-h tutorial topics have been prepared by the authors at V.C.C.: No. 1 Display styles from files; No. 2 Build a molecule. 2CH -- C,H,; No. 3 Conwrt mdecules, ('H; SiF, ISO;]'; No. 1 Building organic funrtionnl groups: No. 5 Organic isomerism and conformation; No. 6 Organic stereoisomerism; No. 7 Inorganic stereoisomerism; No. 8 Crystal chemistry and interatomic distances; No. 9 Space group model building, P21lc; No. 10 Plotting molecular structures.
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section of the FILE menu, rotating the second fragment by 5O, inserting a bond hetween the two carbon atoms and then subjecting the very irregular molecule to a visually impressive energy minimization process (31, Figure 3(a), using an approximate molecular mechanics calculation. All the atoms of the ethane molecule are successively highlighted, Figure 3(h), and at the end of each cycle the shape of the displayed molecule changes to the improved conformation. At the same time a window opens listing the separate components contributing to the total energy of the displayed molecule, Figure 3(b), which progressively decreases toward a total energy near zero. From a teaching point of view this is one of the most impressive facilities of DTMM, as it visually emphasizes the connection between the shape of a molecule and its energy. T o be able to introduce this at first science level is a major attraction of DTMM. Tutorial No. 3 introduces the Conversion facilities of DTMM, using the Edit optionof theMain Menu. Usingdata
2C2H3fragments
bond formed
1st energy cycle
2nd energy cycle
-
Each tutorial involves an introduction to the topic, with instructions to get the student started on a relevant molecule, some suggestions for the student t o try on their own, and some ouestions to answer. For examole. in the build CzHs tutorial, after energy minimization the student is asked t o convert the displayed conformation t o the alternative staggeredleclipsed form and to recalculate the total energy in order to determine the most stable structure. The student is then asked to measure, using the calculated distances and angles facility of the CALC menu, the long H-H distances in both structures and t o correlate these with the respective total energies. Each tutorial is described in a 1-2page handout and takes approximately 1h to work through, including exercises.
11
new molecule
eclipsed view
lter 1
40.805 75.454
2.582
Tutorials No. 1 and 2 are designed to introduce the user to the Menu System, Figure l i a ) and ib), and to the Display and Build capability of DT.MM, Figures 2 and 3. Tutorial So. 1 introduces the various display styles of DTMM using the expanded library of data files. Tutorial No. 2 introduces the building and energy minimization facilities of DTMM through the EDIT and CALC menu commands. A molecule of ethane is constructed from two CH, fragments. Figure 3, by loading two identical CHI fragments from the fragment
Vdw
3.917
Sum
122.757
kjlmol Figure3. (a)Build andenergy minimization sequence for C2H.(b) Intermediate energy minimlratlon display for &He, wnh display window and highlight atom (0). Volume 68 Number 7 July 1991
577
linear BeH2
bent H20
trigonal planar BC13
trigonal pyramidal NH3
tetrahedral Sic14
A
trigonal bipyramidal PC!,
octahedral SF6
Figure 4. Basic geometries predicted by VSEPR theory, inorganic examples.
Figure 5. Inorganic stereochernistry.
files for the display of simple inorganic molecules, cations and anions, such as HzO, NHs, PC15, SFs, [NH4]+, [BFJ, [BO3I3-, [NOz]-, [NO3]-, [SO4I2-, [SO3I2-, [PO4I3-, and [Coal2- data files. These enable the student to display in various styles, simple structures, the shapes of which will have been determined by the VSEPR theory elsewhere in the lecture course, Figure 4. Data files are also included for the shapes of transition metal oxyanions, Figure 5, such as [MnOa]- and [Cr207]2-,which are associated with the redox reactions of the transition metals. The latter are then extended to files on transition metal hexahydrate complex cations, such as [Fe(OHhI2+, [Mn(OHh,I2+, [Co(OHz)sI2+ and [ C U ( O H ~ ) ~and ] ~ +also , tetrahedral metal anions such as [CoC14]2- and [FeC14]-2.In this way the student relates the formula of a chemical species with its shape, enhanced by a clear visual picture that may he manipulated on screen. Equally, he or she learns that a basic shape, such as octahedral, can be associated with neutral molecules, e.g., SFs, anions, e.g., [PC&, or cations, e.g., [ M ~ ( O H Z ) ~Likewise, ]~+. a tetrahedral geometry is associated with molecules, such as SiC14, cations [NH4]+,or anions [S04]2- and [COCI~]~-. Once this is realized, i t is then only a matter of using a comhination of the EDIT and BUILD facilities of DTMM to carry out the following conversions: Octahedral: SFs
- - -
Tetrahedral: SiFn
[PCI6]- [Mn(OHn)slZi
-
-
[NHd]+ [SOdIZ- [CoC4I2-
[MnOll-
Figure 6. Soma bansition metal complex cations and anions. At the second science level the DISPLAY, BUILD, and EDIT modes in tutorials No. 1, 2, and 3 may involve more complicated structures such as [Cz04]2-, [Sz03]2-, [ S q 0 ~ ] ~ - , which are species involved in the chemistry lecture and prac[SzOn]2-, [Cr2O7I2-,Nz04, and P205, while the transition tical courses at the second science level, Figure 6. metal complexes may involve more complicated ligands as in Tutorials No. 4,5, and 6 are used to illustrate some of the [Ni(N02)6I4- (5). all of [Co(NH3)6Iw+,[ F e ( C ~ 0 4 ) ~(4) ] ~ and -
578
Journal of Chemical Education
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