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JOHN W . MOORE Eastern Michigan University,
Ypsilanti, Mi 48197
Bits and Pieces, 14 Most authors of Bits and Pieces willmake availahle listings and/or machine-readahle versions of their programs. Please read each description carefully to determine compatihility with your own computing environment before requesting materials from any of the authors. Revised Guidelines for Authors of Bits and Pieces appeared in the December 1982 issue of the JOURNAL.
Documentation contains mathematical background, listing, input description, and sample input. Documentations and copies of the listing are availahle free from the author.
A Computer Program for Representing Molecules as 3-0 Models
Union College Schenectady, NY 12308
K. Kalcher
One of the most difficult concepts for students to grasp in the study of chemistry is the three-dimensional structure of molecules. There are availahle, on large, mainframe computers, programs for the animated display of three-dimensional structures of molecules. The programs illustrate clearly the shapes of molecules, providing insight into their reactivity. There are, however, few such programs for microcomputers, despite their being capable of "high resolution" graphics ( I 1. There are available, however, a cousiderahle numher of very impressive animated graphics routines, in the form of games, for microcomouters. The followine is a descriotion of an auplication of a>-D graphics routine, designed for use in game develoument, to the animation of molecular graphics disulavs . . . on an kpple 11+ (2a). The 3-D games employ driver routines for the manipulation and display of a particular shape (2). These routines define objects as consisting of a series of points, for which it is necessary to provide x, y, and z coordinates, and lines, for which it is necessary to provide the end points. That data is stored in the form of a shape table. The driver routines can then be called to operate on the shape tahle to transform or "move" the shapes. Since line drawings of molecules are just a series of points (the atoms) and lines (the bonds), these driver routines can he easily adapted to the animation of 3-D line drawings of molecules. Chemists usually think in terms of internal, or relative, coordinates such as hond lengths, hond angles, and twist angles, while the shape tables require x,y,z coordinates. While it is a straightforward task to convert from internal coordinates to a Cartesian (x,y,z) system, it is far from trivial for molecules of any complexity. Fortunately, this problem has been solved in the form of programs developed for large computers (3). One such internal-to-Cartesian coordinate program (3a) has been adapted to run on the Apple in an interactive fashion. For most molecules excellent graphical representations can be generated by providing idealized hond and twist angles and average hond lengths. The program, EDIT, has also been adapted to construct shape tables, for the molecules, that can he operated on by the 3-D driver routine. A structure program, MOVIT, allows the user (student) to choose and view a 3-D nicture of a molecule (see Fie. 2). Usine the paddle controls, the molecule can he rotated ;bout the and v axes, and using the z key, rotated about the z axis. to he
Animated 3-D Graphical Display of Line Drawings of Molecules L. A. Hull
lnstitut fur Analyiische Chemie Karl Franzens Universitai A-8010 Graz Austria The program described here was developed to give students an adequate impression of sterical configurations hy drawing molecules where spheres represent the atoms and connection lines between them the honds. The program's output can he copied easily onto overhead transparencies. Three facilities are implemented to heighten the three-dimensional impression a) the plot of shadows that are produced on the spheres when illuminated by light h) the possibility of a perspective viewing point c) the plot of a 3-D model as a stereo pair. An example plot of the structure of haem is shown in Figure 1.
Program PRJMOL-ANSI-FORTRAN on FORTRAN IV level, 699 statements, 150 comments including input description. High speed storage requires 18.6K 36 bit words on a UNIVAC 1100181. Peripherals used: card reader or terminal and Calcomp incremental plotter. Plotting suhroutines must he implemented from standard CALCOMP lihrary.
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Figure 1. Structure of heme as drawn by PRJMOL 96
Journal of Chemical Education
Principles of Fourier-transform Nuclear Magnetic Resonance J. W. Blunt
University of Canterbury Christchurch, New Zealand There are several aspects of the teaching of Fourier-transform NMR theory and practice which call for the illustration of dynamic phenomena. Examples of this are nuclear precession, the response of the nuclear magnetization to the application of an r.f. pulse, and the subsequent behavior of the magnetization during relaxation. These topics may he illustrated very effectively by means of microcomputer-generated animated graphics. A series of such illustrations has been Figure 2. A screen display from MOVIT.
the observation, in an interactive manner, of the way inwhich variations in the molecular and instrumental parameters, such as relaxation times, pulse width and repetition rate, affect the appearance of the free induction decay (f.i.d.) spectrum and the subsequently derived frequency domain spectrum. The range of topics covered is seen in Figure 4, which is the menu displayed to the user. A typical example is shown in Figure 5, where the effect of applyingan exponential weighting
PRINCIPLES of TT NMR F r e c e s s i o n i n l a b o r a t o r y frame klaenrtisation i n r o t a t i n g frame
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about the two other axes using the paddle controls and halt the rotation or chanre the axis of rotation any time. Some of the seventeen mole&les for which shape tables have been constructed are methane, isobutane, n-butane, cyclopentane, cyclohexane, the decalins, norbornane, phosphorus pentachloride, and sulfur hexafluoride. A hond rotation program, ROTATION, allows the user to view any of six conformers (in steps of 60 degrees) about the 2,3 hond in n-butane (see Fig. 3). Again, each of the conformers can he rotated manually about any of the axes. The molecule can also he rotated manually while the internal rotation is proceeding automatically. The internal rotation gives the illusion of the dynamical aspects of hond rotation. This internal rotation is achieved by modifying the shape table by inserting new molecular coordinates for certain atoms, before calling on the 3-D driver routine. There are several ways in which the material can he extended. Usine the EDIT nroeram molecules of narticular interest to the iktrnctor can h i entered for display. Also using the techniaue of s h a ~ table e modification. as in ROTATION. it should de possibie to illustrate the dinarnica1 aspects of chemical reactions in three dimensions. The programs described are written in Applesoft BASIC with machine language subroutines. An Apple 11+ with 48K, a DOS 3.3 disk system, and installed paddle controls are reanired. A disk with all the Droerams and molecular shaoe tables plus documentation aregvailable for $25. A chick or money order made out to L. A. Hull should be sent to the above address.
Figure 5. Example showing improvement in FT NMR spectrum by application of exponential weighting factor.
Volume 60
Number 2
February 1983
97
